Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, 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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 38 of 91
Found at i:6506836 original size:15 final size:14
Alignment explanation
Indices: 6506818--6506861 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
6506808 GTTTTTTTAT
6506818 TTTTTTGTTTTTCGA
1 TTTTTT-TTTTTCGA
6506833 TTTTTCATTTTTTCGA
1 TTTTT--TTTTTTCGA
6506849 TGTTTTTTTTTTC
1 T-TTTTTTTTTTC
6506862 TTAAGATGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.46
16 9 0.35
17 5 0.19
ACGTcount: A:0.07, C:0.09, G:0.09, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTTTCGA
Found at i:6507010 original size:22 final size:23
Alignment explanation
Indices: 6506985--6507057 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
6506975 TTTGGGTTTG
*
6506985 CATGCCAATTAA-TCTAGGCTTT
1 CATGCCAACTAATTCTAGGCTTT
*
6507007 CATGCCAGCTAATTCTAGGCTTT
1 CATGCCAACTAATTCTAGGCTTT
** *
6507030 TGTGCCAACTAATTCTAGGCTTG
1 CATGCCAACTAATTCTAGGCTTT
6507053 CATGC
1 CATGC
6507058 TAGCTAAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 10 0.24
23 32 0.76
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (23 bp):
CATGCCAACTAATTCTAGGCTTT
Found at i:6507027 original size:23 final size:23
Alignment explanation
Indices: 6506997--6507064 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
6506987 TGCCAATTAA
6506997 TCTAGGCTTTCATGCCAGCTAAT
1 TCTAGGCTTTCATGCCAGCTAAT
** *
6507020 TCTAGGCTTTTGTGCCAACTAAT
1 TCTAGGCTTTCATGCCAGCTAAT
* *
6507043 TCTAGGCTTGCATGCTAGCTAA
1 TCTAGGCTTTCATGCCAGCTAA
6507065 ATACTGGGCT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (23 bp):
TCTAGGCTTTCATGCCAGCTAAT
Found at i:6507263 original size:32 final size:32
Alignment explanation
Indices: 6507201--6507729 Score: 221
Period size: 32 Copynumber: 16.2 Consensus size: 32
6507191 GTTAAGCTAA
* * *
6507201 GCTTAAATTTTTCATTGGGTACCAGCTAAACTAG
1 GCTTAAATCTTT-ATT-GGTGCCAACTAAACTAG
*
6507235 GCTTAACTCTTTATTGGTGCCAACTAAACTAG
1 GCTTAAATCTTTATTGGTGCCAACTAAACTAG
6507267 GCTTAAATCTTT-TCATGAGTGCCAA-TAAACTA-
1 GCTTAAATCTTTAT--TG-GTGCCAACTAAACTAG
* ** * * *
6507299 GCTTAAAAT-TTCATTAGGTGATAGCTAAATTGG
1 GCTT-AAATCTTTATT-GGTGCCAACTAAACTAG
* ** *
6507332 GCTTAAATTTTTTATTGGGTGCCAGTTGAACTAG
1 GCTTAAA-TCTTTATT-GGTGCCAACTAAACTAG
* * * *
6507366 GCTTAAAACTTCA-TGAGTGCCAAATAAATTAG
1 GCTTAAATCTTTATTG-GTGCCAACTAAACTAG
* * **
6507398 GCTTAAATCTTGATTGGTGCTAGA-TAATTTAG
1 GCTTAAATCTTTATTGGTGCCA-ACTAAACTAG
6507430 GCTTAAATCTTT-TCATGAGTGCCAA-TAAACTA-
1 GCTTAAATCTTTAT--TG-GTGCCAACTAAACTAG
* * ** * * *
6507462 GCTTAAAACTTCATTAGGTGATAGCTAAATTGG
1 GCTTAAATCTTTATT-GGTGCCAACTAAACTAG
* **
6507495 GCTTAAATTTTTCATTGGGTGCCAGTTAAACTAG
1 GCTTAAATCTTT-ATT-GGTGCCAACTAAACTAG
* ** * * *
6507529 GCTTAAAAC-TTCGTGAGTGCCAAATAAATTAA
1 GCTTAAATCTTTATTG-GTGCCAACTAAACTAG
* * **
6507561 GCTTAAATCTTGATTGGTGCTAGA-TAATTTAG
1 GCTTAAATCTTTATTGGTGCCA-ACTAAACTAG
*
6507593 GCTTAAATCTTT-TCATGAGTGCCAAATAAACT-G
1 GCTTAAATCTTTAT--TG-GTGCCAACTAAACTAG
* * *
6507626 AGCTTAAATCTTTTACTAGGTGCCAACTAATCTGG
1 -GCTTAAATC-TTTA-TTGGTGCCAACTAAACTAG
* *
6507661 GCTTAAGA-CTTTATTGGTGCCAGA-TAATCTTG
1 GCTTAA-ATCTTTATTGGTGCCA-ACTAAACTAG
* * * *
6507693 GCTTAAAAC-TTA--GGTGCCAGCTAAATTGG
1 GCTTAAATCTTTATTGGTGCCAACTAAACTAG
6507722 GCTTAAAT
1 GCTTAAAT
6507730 TCTCTGAAAT
Statistics
Matches: 379, Mismatches: 79, Indels: 79
0.71 0.15 0.15
Matches are distributed among these distances:
29 19 0.05
31 19 0.05
32 169 0.45
33 61 0.16
34 104 0.27
35 6 0.02
37 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (32 bp):
GCTTAAATCTTTATTGGTGCCAACTAAACTAG
Found at i:6507417 original size:163 final size:163
Alignment explanation
Indices: 6507227--6507633 Score: 681
Period size: 163 Copynumber: 2.5 Consensus size: 163
6507217 GGGTACCAGC
* * * * **
6507227 TAAACTAGGCTTAACTCTTTATTGGTGCCA-ACTAAACTAGGCTTAAATCTTTTCATGAGTGCCA
1 TAAATTAGGCTTAAATCTTGATTGGTGCTAGA-TAATTTAGGCTTAAATCTTTTCATGAGTGCCA
* *
6507291 ATAAACTAGCTTAAAATTTCATTAGGTGATAGCTAAATTGGGCTTAAATTTTTTATTGGGTGCCA
65 ATAAACTAGCTTAAAACTTCATTAGGTGATAGCTAAATTGGGCTTAAATTTTTCATTGGGTGCCA
*
6507356 GTTGAACTAGGCTTAAAACTTCATGAGTGCCAAA
130 GTTAAACTAGGCTTAAAACTTCATGAGTGCCAAA
6507390 TAAATTAGGCTTAAATCTTGATTGGTGCTAGATAATTTAGGCTTAAATCTTTTCATGAGTGCCAA
1 TAAATTAGGCTTAAATCTTGATTGGTGCTAGATAATTTAGGCTTAAATCTTTTCATGAGTGCCAA
6507455 TAAACTAGCTTAAAACTTCATTAGGTGATAGCTAAATTGGGCTTAAATTTTTCATTGGGTGCCAG
66 TAAACTAGCTTAAAACTTCATTAGGTGATAGCTAAATTGGGCTTAAATTTTTCATTGGGTGCCAG
*
6507520 TTAAACTAGGCTTAAAACTTCGTGAGTGCCAAA
131 TTAAACTAGGCTTAAAACTTCATGAGTGCCAAA
*
6507553 TAAATTAAGCTTAAATCTTGATTGGTGCTAGATAATTTAGGCTTAAATCTTTTCATGAGTGCCAA
1 TAAATTAGGCTTAAATCTTGATTGGTGCTAGATAATTTAGGCTTAAATCTTTTCATGAGTGCC-A
6507618 ATAAACTGAGCTTAAA
65 ATAAACT-AGCTTAAA
6507634 TCTTTTACTA
Statistics
Matches: 230, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
163 213 0.93
164 9 0.04
165 8 0.03
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (163 bp):
TAAATTAGGCTTAAATCTTGATTGGTGCTAGATAATTTAGGCTTAAATCTTTTCATGAGTGCCAA
TAAACTAGCTTAAAACTTCATTAGGTGATAGCTAAATTGGGCTTAAATTTTTCATTGGGTGCCAG
TTAAACTAGGCTTAAAACTTCATGAGTGCCAAA
Found at i:6507501 original size:65 final size:64
Alignment explanation
Indices: 6507375--6507540 Score: 199
Period size: 65 Copynumber: 2.5 Consensus size: 64
6507365 GGCTTAAAAC
* * * * *
6507375 TTCATGAGTGCCAAATAAATTAGGCTTAAATCTTGATTGGTGCTAGATAATTTAGGCTTAAATCT
1 TTCATGAGTGCC-AATAAACTAGGCTTAAAACTTCATTGGTGATAGATAAATTAGGCTTAAAT-T
6507440 T
64 T
* *
6507441 TTCATGAGTGCCAATAAACTA-GCTTAAAACTTCATTAGGTGATAGCTAAATTGGGCTTAAATTT
1 TTCATGAGTGCCAATAAACTAGGCTTAAAACTTCATT-GGTGATAGATAAATTAGGCTTAAATTT
* *
6507505 TTCATTGGGTGCCAGTTAAACTAGGCTTAAAACTTC
1 TTCA-TGAGTGCCA-ATAAACTAGGCTTAAAACTTC
6507541 GTGAGTGCCA
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 19 0.22
65 37 0.43
66 19 0.22
67 12 0.14
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (64 bp):
TTCATGAGTGCCAATAAACTAGGCTTAAAACTTCATTGGTGATAGATAAATTAGGCTTAAATTT
Found at i:6507565 original size:66 final size:67
Alignment explanation
Indices: 6507382--6507639 Score: 199
Period size: 66 Copynumber: 3.9 Consensus size: 67
6507372 AACTTCATGA
* * * * * * * *
6507382 GTGCCAAATAAATTAGGCTTAAATCTTGATTG-GTGCTAGATAATTTAGGCTTAAATCTTTTCA-
1 GTGCCAGATAAACTAGGCTTAAAACTTCA-TGAGTGCCAAATAAATTAAGCTTAAATCTTTTCAT
*
6507445 TGA
65 TGG
* ** ** **
6507448 GTGCCA-ATAAACTA-GCTTAAAACTTCATTAGGTGATAGCTAAATTGGGCTTAAAT-TTTTCAT
1 GTGCCAGATAAACTAGGCTTAAAACTTCATGA-GTGCCAAATAAATTAAGCTTAAATCTTTTCAT
6507510 TGG
65 TGG
* * *
6507513 GTGCCAGTTAAACTAGGCTTAAAACTTCGTGAGTGCCAAATAAATTAAGCTTAAATC--TTGATT
1 GTGCCAGATAAACTAGGCTTAAAACTTCATGAGTGCCAAATAAATTAAGCTTAAATCTTTTCATT
6507576 -G
66 GG
* ** * * *
6507577 GTGCTAGATAATTTAGGCTTAAATCTTTTCATGAGTGCCAAATAAACTGAGCTTAAATCTTTT
1 GTGCCAGATAAACTAGGCTTAAAAC--TTCATGAGTGCCAAATAAATTAAGCTTAAATCTTTT
6507640 ACTAGGTGCC
Statistics
Matches: 155, Mismatches: 27, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
63 1 0.01
64 38 0.25
65 40 0.26
66 60 0.39
67 14 0.09
68 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36
Consensus pattern (67 bp):
GTGCCAGATAAACTAGGCTTAAAACTTCATGAGTGCCAAATAAATTAAGCTTAAATCTTTTCATT
GG
Found at i:6507623 original size:98 final size:98
Alignment explanation
Indices: 6507360--6507638 Score: 248
Period size: 98 Copynumber: 2.9 Consensus size: 98
6507350 GTGCCAGTTG
* ** * * * * *
6507360 AACTAGGCTTAAAACTTCATGA-GTGCCAAATAAATTAGGCTTAAA-TCTTGATTG-GTGCTAGA
1 AACTA-GCTTAAAACTTCATTAGGTGATAGATAAATTAGGCTTAAATTTTTCATTGAGTGCCAAA
** *
6507422 TAATTTAGGCTTAAATCTTTTCATGAGTGCCAATA
65 TAAACTAGGCTTAAAAC-TTTCATGAGTGCCAATA
* * * **
6507457 AACTAGCTTAAAACTTCATTAGGTGATAGCTAAATTGGGCTTAAATTTTTCATTGGGTGCCAGTT
1 AACTAGCTTAAAACTTCATTAGGTGATAGATAAATTAGGCTTAAATTTTTCATTGAGTGCCAAAT
*
6507522 AAACTAGGCTTAAAAC-TTCGTGAGTGCCAAATA
66 AAACTAGGCTTAAAACTTTCATGAGTGCC-AATA
* * * * *
6507555 AATTAAGCTTAAATCTTGATT-GGTGCTAGATAATTTAGGCTTAAATCTTTTCA-TGAGTGCCAA
1 AACT-AGCTTAAAACTTCATTAGGTGATAGATAAATTAGGCTTAAAT-TTTTCATTGAGTGCCAA
*
6507618 ATAAACT-GAGCTTAAATCTTT
64 ATAAACTAG-GCTTAAAACTTT
6507639 TACTAGGTGC
Statistics
Matches: 149, Mismatches: 25, Indels: 14
0.79 0.13 0.07
Matches are distributed among these distances:
96 15 0.10
97 35 0.23
98 57 0.38
99 42 0.28
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (98 bp):
AACTAGCTTAAAACTTCATTAGGTGATAGATAAATTAGGCTTAAATTTTTCATTGAGTGCCAAAT
AAACTAGGCTTAAAACTTTCATGAGTGCCAATA
Found at i:6507665 original size:34 final size:33
Alignment explanation
Indices: 6507592--6507699 Score: 91
Period size: 34 Copynumber: 3.2 Consensus size: 33
6507582 AGATAATTTA
*
6507592 GGCTTAAATCTTTT-C-ATGAGTGCCAAATAAACTG
1 GGCTTAAATCTTTTACTA-G-GTGCC-AATAATCTG
*
6507626 AGCTTAAATCTTTTACTAGGTGCCAACTAATCTG
1 GGCTTAAATCTTTTACTAGGTGCCAA-TAATCTG
* *
6507660 GGCTTAAGA-C-TTTA-TTGGTGCCAGATAATCTT
1 GGCTTAA-ATCTTTTACTAGGTGCCA-ATAATCTG
6507692 GGCTTAAA
1 GGCTTAAA
6507700 ACTTAGGTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
31 1 0.02
32 21 0.33
33 7 0.11
34 31 0.48
35 3 0.05
36 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (33 bp):
GGCTTAAATCTTTTACTAGGTGCCAATAATCTG
Found at i:6508234 original size:14 final size:15
Alignment explanation
Indices: 6508215--6508247 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
6508205 CACATTTATT
6508215 TTTTA-TTTTTTTTC
1 TTTTATTTTTTTTTC
6508229 TTTTATTTTTTTTTC
1 TTTTATTTTTTTTTC
6508244 TTTT
1 TTTT
6508248 TCTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTATTTTTTTTTC
Found at i:6508247 original size:20 final size:20
Alignment explanation
Indices: 6508209--6508260 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
6508199 TAGAGCCACA
6508209 TTTATTTTTTATTT-TTTTTC
1 TTTATTTTTT-TTTCTTTTTC
6508229 TTTTATTTTTTTTTCTTTTTC
1 -TTTATTTTTTTTTCTTTTTC
6508250 TTTATTTTTTT
1 TTTATTTTTTT
6508261 GTCATTATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.08, C:0.06, G:0.00, T:0.87
Consensus pattern (20 bp):
TTTATTTTTTTTTCTTTTTC
Found at i:6508257 original size:15 final size:14
Alignment explanation
Indices: 6508214--6508258 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 14
6508204 CCACATTTAT
6508214 TTTTTATTTTTTTTC
1 TTTTT-TTTTTTTTC
6508229 TTTTATTTTTTTTTC
1 TTTT-TTTTTTTTTC
6508244 TTTTTCTTTATTTTT
1 TTTTT-TTT-TTTTT
6508259 TTGTCATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.04
15 20 0.74
16 6 0.22
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTTTTTTTTTC
Found at i:6509194 original size:14 final size:15
Alignment explanation
Indices: 6509175--6509203 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6509165 ATCATTTTTC
6509175 TTTTCTTTTT-TCTT
1 TTTTCTTTTTCTCTT
6509189 TTTTCTTTTTCTCTT
1 TTTTCTTTTTCTCTT
6509204 ATGCCCCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTTCTCTT
Found at i:6509941 original size:28 final size:26
Alignment explanation
Indices: 6509894--6509949 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 26
6509884 AAACTTTCTC
6509894 TTTTTTCCTCTTTTGTTTTTCTTTTT
1 TTTTTTCCTCTTTTGTTTTTCTTTTT
* *
6509920 TTTTTTTCTCTTGTTTTCTTTTCTTTTT
1 TTTTTTCCTCTT-TTGT-TTTTCTTTTT
6509948 TT
1 TT
6509950 AAGGCATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 11 0.42
27 3 0.12
28 12 0.46
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (26 bp):
TTTTTTCCTCTTTTGTTTTTCTTTTT
Found at i:6511637 original size:4 final size:4
Alignment explanation
Indices: 6511618--6511661 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
6511608 TGGATATATA
* * *
6511618 AATG AATG GATT AATG AATG AATG TATG AATG AATG AATG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
6511662 CACCAATGTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (4 bp):
AATG
Found at i:6513702 original size:17 final size:18
Alignment explanation
Indices: 6513680--6513714 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
6513670 AAATCCCATT
6513680 TTTATTTTTATT-TTTTA
1 TTTATTTTTATTATTTTA
6513697 TTTATTTTTATTATTTTA
1 TTTATTTTTATTATTTTA
6513715 GGATTAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTATTTTTATTATTTTA
Found at i:6513761 original size:53 final size:53
Alignment explanation
Indices: 6513704--6513812 Score: 132
Period size: 53 Copynumber: 2.1 Consensus size: 53
6513694 TTATTTATTT
** * *
6513704 TTATTATTTTAGGATTAGGGAATTATATGAA-AAT-TTTAATGAAATAAAACTTC
1 TTATTATTTTA--ATTACAGAATCATATGAAGAATCTATAATGAAATAAAACTTC
* *
6513757 TTATTCTTTTAATTACAGAATCATATGAAGAATCTATAATGAAATAAAATTTC
1 TTATTATTTTAATTACAGAATCATATGAAGAATCTATAATGAAATAAAACTTC
6513810 TTA
1 TTA
6513813 AAAACTCCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
51 15 0.31
52 3 0.06
53 30 0.62
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.41
Consensus pattern (53 bp):
TTATTATTTTAATTACAGAATCATATGAAGAATCTATAATGAAATAAAACTTC
Found at i:6513992 original size:13 final size:13
Alignment explanation
Indices: 6513976--6514014 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
6513966 TTAGAATTTC
6513976 AATTTAAGGTTTT
1 AATTTAAGGTTTT
*
6513989 AATTTTAAAGTTTT
1 AA-TTTAAGGTTTT
*
6514003 AGTTTAAGGTTT
1 AATTTAAGGTTT
6514015 CAAAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
AATTTAAGGTTTT
Found at i:6513995 original size:27 final size:26
Alignment explanation
Indices: 6513957--6514017 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
6513947 TTTATATTAT
6513957 GGTTTCAATTTAGAA-TTTCAATTTAA
1 GGTTTCAATTTA-AAGTTTCAATTTAA
* * *
6513983 GGTTTTAATTTTAAAGTTTTAGTTTAA
1 GGTTTCAA-TTTAAAGTTTCAATTTAA
6514010 GGTTTCAA
1 GGTTTCAA
6514018 AAATTTATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 9 0.31
27 20 0.69
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (26 bp):
GGTTTCAATTTAAAGTTTCAATTTAA
Found at i:6516132 original size:15 final size:15
Alignment explanation
Indices: 6516108--6516204 Score: 75
Period size: 15 Copynumber: 6.8 Consensus size: 15
6516098 TTTTTATTTT
6516108 TATT-TATTTATATA
1 TATTATATTTATATA
6516122 TATTATATTTA-ATA
1 TATTATATTTATATA
6516136 -ATTA-ATTTA-ATAA
1 TATTATATTTATAT-A
*
6516149 TAATT-TTTTTATATA
1 T-ATTATATTTATATA
*
6516164 TATGTAT-TTTATATC
1 TAT-TATATTTATATA
*
6516179 TTTTATATTT-TATA
1 TATTATATTTATATA
*
6516193 TATTTTATTTAT
1 TATTATATTTAT
6516205 TTAGATTTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
12 7 0.10
13 5 0.07
14 23 0.34
15 29 0.43
16 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (15 bp):
TATTATATTTATATA
Found at i:6516145 original size:12 final size:12
Alignment explanation
Indices: 6516113--6516154 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
6516103 ATTTTTATTT
6516113 ATTTATATATATTA
1 ATTTA-ATA-ATTA
6516127 TATTTAATAATTA
1 -ATTTAATAATTA
6516140 ATTTAATAA-TA
1 ATTTAATAATTA
6516151 ATTT
1 ATTT
6516155 TTTTATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.22
12 9 0.33
13 4 0.15
14 3 0.11
15 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTAATAATTA
Found at i:6516187 original size:16 final size:16
Alignment explanation
Indices: 6516155--6516200 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
6516145 ATAATAATTT
* *
6516155 TTTTATATA-TATGTA
1 TTTTATATATTTTATA
*
6516170 TTTTATATCTTTTATA
1 TTTTATATATTTTATA
6516186 TTTTATATATTTTAT
1 TTTTATATATTTTAT
6516201 TTATTTAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTATATATTTTATA
Found at i:6524546 original size:3 final size:3
Alignment explanation
Indices: 6524538--6524580 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
6524528 AATTTAAGAT
*
6524538 ATA ATA ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6524581 GAAAAATAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6524615 original size:21 final size:22
Alignment explanation
Indices: 6524573--6524615 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
6524563 TAATAATAAT
*
6524573 AATAATAAGAAAAATAAGAAAA
1 AATAATAAGAAAAATAACAAAA
6524595 AATAA-AAGAAAAA-AATCAAAA
1 AATAATAAGAAAAATAA-CAAAA
6524616 CAAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.11
21 12 0.63
22 5 0.26
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (22 bp):
AATAATAAGAAAAATAACAAAA
Found at i:6526323 original size:19 final size:18
Alignment explanation
Indices: 6526299--6526334 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6526289 ATGTCTACAT
6526299 TTTTTAAAATTTTTATTTG
1 TTTTT-AAATTTTTATTTG
*
6526318 TTTTTATATTTTTATTT
1 TTTTTAAATTTTTATTT
6526335 TTCATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTTAAATTTTTATTTG
Found at i:6526354 original size:15 final size:15
Alignment explanation
Indices: 6526318--6526351 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6526308 TTTTTATTTG
6526318 TTTTT-ATATTTTTA
1 TTTTTCATATTTTTA
6526332 TTTTTCATATTTTTCA
1 TTTTTCATATTTTT-A
6526348 TTTT
1 TTTT
6526352 CATTTAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 8 0.44
16 5 0.28
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCATATTTTTA
Found at i:6528645 original size:21 final size:21
Alignment explanation
Indices: 6528621--6528684 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
6528611 GTCTAAATAG
*
6528621 GGATCCTTAAAGATCAATTTA
1 GGATCGTTAAAGATCAATTTA
* *
6528642 GGATTGTTATAGAGT-AGA-TTA
1 GGATCGTTAAAGA-TCA-ATTTA
*
6528663 GGATCGTTAGAGATCAATTTA
1 GGATCGTTAAAGATCAATTTA
6528684 G
1 G
6528685 AATTTATATG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 2 0.06
21 30 0.88
22 2 0.06
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.34
Consensus pattern (21 bp):
GGATCGTTAAAGATCAATTTA
Found at i:6532917 original size:17 final size:16
Alignment explanation
Indices: 6532886--6532920 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
6532876 TTAAGCCTTA
*
6532886 TATTTTTATAAAATTT
1 TATTTTTACAAAATTT
6532902 TATTTATTACAAAATTT
1 TATTT-TTACAAAATTT
6532919 TA
1 TA
6532921 ACTAGAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTTTACAAAATTT
Found at i:6537159 original size:3 final size:3
Alignment explanation
Indices: 6537153--6537214 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
6537143 AAAAGAAAAA
* *
6537153 AAT AAT AAC AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6537201 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
6537215 CCAAAGTTGA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6537409 original size:32 final size:33
Alignment explanation
Indices: 6537336--6537409 Score: 78
Period size: 33 Copynumber: 2.3 Consensus size: 33
6537326 AATCGAAATT
* * *
6537336 GAAAGTTAAAATGATTCAAATGAAGTCAAATTA
1 GAAAGTGAAAATGACTCAAATGAAGTCAAAGTA
* * * *
6537369 GAATGTGAAAATGACTGAATTGAA-TCAAAGTC
1 GAAAGTGAAAATGACTCAAATGAAGTCAAAGTA
6537401 GAAAGTGAA
1 GAAAGTGAA
6537410 TGAGTTGTGC
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (33 bp):
GAAAGTGAAAATGACTCAAATGAAGTCAAAGTA
Found at i:6537756 original size:65 final size:63
Alignment explanation
Indices: 6537457--6538014 Score: 218
Period size: 65 Copynumber: 8.6 Consensus size: 63
6537447 ACGGGTTAGA
* * * * * *
6537457 AAAAATAAAAGGATTTGGACTGAGCCAAGATCAAAAT-AGGTGACTAGGATCGAATCATGAA-TC
1 AAAAATAAAATGATCTGGATTGAGTCAAGATCAAAATGA-GTGACCAGGATCGAAT-GT-AAGT-
*
6537520 CG
62 CT
* * * * * * *
6537522 AAAAATAAAATGATCTAGAATGAGTCTAGGTTGAAAA-CAGGTGACCGGGATCGAATCGTAAGTC
1 AAAAATAAAATGATCTGGATTGAGTC-AAGATCAAAATGA-GTGACCAGGATCGAAT-GTAAGTC
*
6537586 AG
63 -T
* * ** * * * *
6537588 AAAAATAAAATGATCTGGAATAAGTTGAGATCAAAAT-AGGTGACCAGAATTGAATTGCAAGACT
1 AAAAATAAAATGATCTGGATTGAGTCAAGATCAAAATGA-GTGACCAGGATCGAA-TGTAAGTCT
* * **
6537652 AAAAATAAAATGATATGAATTGAACCAAGATCAAAATGAGTGACCAGGATCGAACTGTAAGTCT
1 AAAAATAAAATGATCTGGATTGAGTCAAGATCAAAATGAGTGACCAGGATCGAA-TGTAAGTCT
* * * * **
6537716 AAAAGATAAAATAATCTGGATTGAGTCAAGATCAAGATGAGTGATCGGGA-CTGAA-CCACGAGT
1 AAAA-ATAAAATGATCTGGATTGAGTCAAGATCAAAATGAGTGACCAGGATC-GAATGTA--AGT
*
6537779 CAA
62 C-T
* * * * * *** * * ** *
6537782 AAAAATAAAAATAATCTGGATTAAGCCGAGATCGAACCAAGTGACTAGGATTGAACCTCAAGTTT
1 AAAAAT-AAAATGATCTGGATTGAGTCAAGATCAAAATGAGTGACCAGGATCGAATGT-AAGTCT
* * * * * * * * ** *
6537847 GAAAATAAAATGATCTAGACTAAGAT-GAGATCGAAATGAGTGATC-GAGATTGAACCATAAAT-
1 AAAAATAAAATGATCTGGATTGAG-TCAAGATCAAAATGAGTGACCAG-GATCGAA-TGTAAGTC
6537909 T
63 T
* ** * * *
6537910 AGAAAAATAAAACGATCTGGATCAAGTCAAGATCAAAATAAGTGATC-GAGATTGAACTGTAAGT
1 --AAAAATAAAATGATCTGGATTGAGTCAAGATCAAAATGAGTGACCAG-GATCGAA-TGTAAGT
6537974 CT
62 CT
* **
6537976 AAAAATAAAATGATCTGGACTGAGTTGAGATCAAAATGA
1 AAAAATAAAATGATCTGGATTGAGTCAAGATCAAAATGA
6538015 TTGATCGAAA
Statistics
Matches: 377, Mismatches: 93, Indels: 47
0.73 0.18 0.09
Matches are distributed among these distances:
63 3 0.01
64 126 0.33
65 152 0.40
66 94 0.25
67 1 0.00
68 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (63 bp):
AAAAATAAAATGATCTGGATTGAGTCAAGATCAAAATGAGTGACCAGGATCGAATGTAAGTCT
Found at i:6538044 original size:64 final size:64
Alignment explanation
Indices: 6537579--6538051 Score: 224
Period size: 64 Copynumber: 7.3 Consensus size: 64
6537569 GGATCGAATC
* * *
6537579 GTAAGTCAGAAAAATAAAATGATCTGGAATAAGTTGAGATCAAAAT-AGGTGA-CCAGAATTGAA
1 GTAAGTC-CAAAAATAAAATGATCTGGACTAAGTTGAGATCAAAATGA-GTGATCGAG-ATTGAA
*
6537642 TT
63 CT
* * * * * * *** * *
6537644 GCAAGACTAAAAATAAAATGATATGAATTGAA-CCAAGATCAAAATGAGTGA-CCAGGATCGAAC
1 GTAAGTCCAAAAATAAAATGATCTGGACT-AAGTTGAGATCAAAATGAGTGATCGA-GATTGAAC
6537707 T
64 T
* * * * ** * * * *
6537708 GTAAGTCTAAAAGATAAAATAATCTGGATTGAGTCAAGATCAAGATGAGTGATCGGGACTGAACC
1 GTAAGTCCAAAA-ATAAAATGATCTGGACTAAGTTGAGATCAAAATGAGTGATCGAGATTGAACT
*** * * * ** * *** *
6537773 ACGAGTCAAAAAAATAAAAATAATCTGGATTAAGCCGAGATCGAACCAAGTGA-CTAGGATTGAA
1 GTAAGTC-CAAAAAT-AAAATGATCTGGACTAAGTTGAGATCAAAATGAGTGATCGA-GATTGAA
6537837 CCT
63 -CT
* *** * * * *
6537840 -CAAGTTTGAAAATAAAATGATCTAGACTAAGATGAGATCGAAATGAGTGATCGAGATTGAACC
1 GTAAGTCCAAAAATAAAATGATCTGGACTAAGTTGAGATCAAAATGAGTGATCGAGATTGAACT
* * ** * ** *
6537903 ATAAATTAGAAAAATAAAACGATCTGGA-TCAAGTCAAGATCAAAATAAGTGATCGAGATTGAAC
1 GT-AAGTCCAAAAATAAAATGATCTGGACT-AAGTTGAGATCAAAATGAGTGATCGAGATTGAAC
6537967 T
64 T
* * * * *
6537968 GTAAGTCTAAAAATAAAATGATCTGGACTGAGTTGAGATCAAAATGATTGATCGAAATTGAATT
1 GTAAGTCCAAAAATAAAATGATCTGGACTAAGTTGAGATCAAAATGAGTGATCGAGATTGAACT
*
6538032 G-CAGATCCAAAAAATAAAAT
1 GTAAG-TCC-AAAAATAAAAT
6538052 TCAAAATTTT
Statistics
Matches: 310, Mismatches: 81, Indels: 34
0.73 0.19 0.08
Matches are distributed among these distances:
63 3 0.01
64 141 0.45
65 121 0.39
66 44 0.14
67 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (64 bp):
GTAAGTCCAAAAATAAAATGATCTGGACTAAGTTGAGATCAAAATGAGTGATCGAGATTGAACT
Found at i:6538045 original size:129 final size:128
Alignment explanation
Indices: 6537562--6538051 Score: 368
Period size: 129 Copynumber: 3.8 Consensus size: 128
6537552 TTGAAAACAG
* * * *
6537562 GTGACCGGGATCGAA-TCGTAAGTCAGAAAAATAAAATGATCTGGAATAAGTTGAGATCAAAAT-
1 GTGACCAGGATTGAACT-GTAAGTC-TAAAAATAAAATGATCTGGACTAAGTTGAGATCAAAATG
* * * * *
6537625 AGGTGA-CCAGAATTGAATTGCAAGA-CTAAAAATAAAATGATATGAATTGAA-CCAAGATCAAA
64 A-GTGATCGA-AATTGAATTGC-AGATCAAAAAATAAAATGATCTGGA-TCAAGCCAAGATCAAA
*
6537687 ATGA
125 ATAA
* * * * ** *
6537691 GTGACCAGGATCGAACTGTAAGTCTAAAAGATAAAATAATCTGGATTGAGTCAAGATCAAGATGA
1 GTGACCAGGATTGAACTGTAAGTCTAAAA-ATAAAATGATCTGGACTAAGTTGAGATCAAAATGA
** * * * * * * *
6537756 GTGATCGGGACTGAA--CCACGAGTCAAAAAAATAAAAATAATCTGGATTAAGCCGAGATCGAAC
65 GTGATCGAAATTGAATTGCA-GA-TC-AAAAAAT-AAAATGATCTGGATCAAGCCAAGATCAAAA
*
6537819 CAA
126 TAA
* * * * * * *
6537822 GTGACTAGGATTGAACCT-CAAGTTTGAAAATAAAATGATCTAGACTAAGATGAGATCGAAATGA
1 GTGACCAGGATTGAA-CTGTAAGTCTAAAAATAAAATGATCTGGACTAAGTTGAGATCAAAATGA
* **** * * * *
6537886 GTGATCGAGATTGAACCATAAATTAGAAAAATAAAACGATCTGGATCAAGTCAAGATCAAAATAA
65 GTGATCGAAATTGAATTGCAGATCA-AAAAATAAAATGATCTGGATCAAGCCAAGATCAAAATAA
* *
6537951 GTGATC-GAGATTGAACTGTAAGTCTAAAAATAAAATGATCTGGACTGAGTTGAGATCAAAATGA
1 GTGACCAG-GATTGAACTGTAAGTCTAAAAATAAAATGATCTGGACTAAGTTGAGATCAAAATGA
*
6538015 TTGATCGAAATTGAATTGCAGATCCAAAAAATAAAAT
65 GTGATCGAAATTGAATTGCAGAT-CAAAAAATAAAAT
6538052 TCAAAATTTT
Statistics
Matches: 275, Mismatches: 69, Indels: 34
0.73 0.18 0.09
Matches are distributed among these distances:
126 1 0.00
127 3 0.01
128 7 0.03
129 160 0.58
130 59 0.21
131 42 0.15
132 3 0.01
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.23
Consensus pattern (128 bp):
GTGACCAGGATTGAACTGTAAGTCTAAAAATAAAATGATCTGGACTAAGTTGAGATCAAAATGAG
TGATCGAAATTGAATTGCAGATCAAAAAATAAAATGATCTGGATCAAGCCAAGATCAAAATAA
Found at i:6538186 original size:9 final size:10
Alignment explanation
Indices: 6538156--6538192 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
6538146 AAGTTTCATA
6538156 AAAAATTCAC
1 AAAAATTCAC
*
6538166 AAAAATT-TC
1 AAAAATTCAC
6538175 -AAAATTCAC
1 AAAAATTCAC
6538184 AAAAATTCA
1 AAAAATTCA
6538193 AGATTCATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
10 15 0.65
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATTCAC
Found at i:6538192 original size:17 final size:18
Alignment explanation
Indices: 6538157--6538199 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
6538147 AGTTTCATAA
6538157 AAAATTCACAAAAATTTC
1 AAAATTCACAAAAATTTC
6538175 AAAATTCACAAAAA-TTC
1 AAAATTCACAAAAATTTC
*
6538192 AAGATTCA
1 AAAATTCA
6538200 TAAAGGTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAATTCACAAAAATTTC
Found at i:6538229 original size:18 final size:17
Alignment explanation
Indices: 6538206--6538261 Score: 76
Period size: 18 Copynumber: 3.2 Consensus size: 17
6538196 TTCATAAAGG
6538206 TTTGCAAGAATTTCAAGT
1 TTTGCAAGAATTTCAA-T
*
6538224 TTTGCAAGAATTTCTAT
1 TTTGCAAGAATTTCAAT
*
6538241 TTCGCAAGAATTTTCAAT
1 TTTGCAAGAA-TTTCAAT
6538259 TTT
1 TTT
6538262 ATAAGGATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 10 0.30
18 23 0.70
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
TTTGCAAGAATTTCAAT
Found at i:6538249 original size:17 final size:18
Alignment explanation
Indices: 6538205--6538253 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
6538195 ATTCATAAAG
6538205 GTTT-GCAAGAATTTCAA
1 GTTTCGCAAGAATTTCAA
* *
6538222 GTTTTGCAAGAATTTCTA
1 GTTTCGCAAGAATTTCAA
6538240 -TTTCGCAAGAATTT
1 GTTTCGCAAGAATTT
6538254 TCAATTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (18 bp):
GTTTCGCAAGAATTTCAA
Found at i:6543748 original size:15 final size:15
Alignment explanation
Indices: 6543717--6543757 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
6543707 ATGAAATAGA
*
6543717 AAATAAATAAGAAAAT
1 AAATAAA-AATAAAAT
*
6543733 ACATAAAAATAAAAT
1 AAATAAAAATAAAAT
6543748 AAATAAAAAT
1 AAATAAAAAT
6543758 GCAATTGGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATAAAAATAAAAT
Found at i:6544069 original size:18 final size:20
Alignment explanation
Indices: 6544034--6544075 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
6544024 AAAAACCTAG
*
6544034 TTAAAATTTGTCTGAAAC-T
1 TTAAAATTTGTCTAAAACAT
*
6544053 TTAAATTTTGTC-AAAACAT
1 TTAAAATTTGTCTAAAACAT
6544072 TTAA
1 TTAA
6544076 CAAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (20 bp):
TTAAAATTTGTCTAAAACAT
Found at i:6544552 original size:3 final size:3
Alignment explanation
Indices: 6544546--6544610 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
6544536 AAAAAAAGAA
* *
6544546 AAT AAT AAT AAT GAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6544594 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
6544611 CAACAACAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6545442 original size:15 final size:16
Alignment explanation
Indices: 6545419--6545456 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
6545409 AAATATTAAT
*
6545419 AAAGGAAAAGAAAGG-
1 AAAGAAAAAGAAAGGA
6545434 AAAGAAAAAGAAAGGA
1 AAAGAAAAAGAAAGGA
6545450 AAAGAAA
1 AAAGAAA
6545457 GTTTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGAAAGGA
Found at i:6546185 original size:64 final size:62
Alignment explanation
Indices: 6546045--6546203 Score: 175
Period size: 64 Copynumber: 2.6 Consensus size: 62
6546035 TGTTTTTGTA
* * **
6546045 CAAGAAAAATTGATACTTTCAACTTTTCC-C--AAAAAATATTTTTTTGGAATTTTTAATTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAAAATTTTTTTGGAAAATTTAATTT
*
6546104 CGAGGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAAGAACCTTTTTTT-GAAAATTT-ATTC
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAA-AA--TTTTTTTGGAAAATTTAATT-
6546167 T
62 T
* * *
6546168 TAAGGAAAATTGATACTTACAACTTTTCTTCAAAAA
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAA
6546204 TGTTTTTTTG
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
59 27 0.32
60 1 0.01
62 6 0.07
63 4 0.05
64 39 0.46
65 7 0.08
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (62 bp):
CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAAAATTTTTTTGGAAAATTTAATTT
Found at i:6546251 original size:4 final size:4
Alignment explanation
Indices: 6546239--6546320 Score: 53
Period size: 4 Copynumber: 19.2 Consensus size: 4
6546229 TATTTAAAGA
*
6546239 AAAT GAAAT AAAT AAAAT AAAT AAGAAT AAA- ATAA- AAAT CAAT AAAT
1 AAAT -AAAT AAAT -AAAT AAAT -A-AAT AAAT A-AAT AAAT AAAT AAAT
*
6546286 CAAT AAAT AAAT AAAAT GAAAAT AAAT AAA- AAAT A
1 AAAT AAAT AAAT -AAAT --AAAT AAAT AAAT AAAT A
6546321 GAAAAAAATA
Statistics
Matches: 65, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
3 6 0.09
4 37 0.57
5 14 0.22
6 8 0.12
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:6546282 original size:15 final size:15
Alignment explanation
Indices: 6546244--6546316 Score: 78
Period size: 15 Copynumber: 4.8 Consensus size: 15
6546234 AAAGAAAATG
6546244 AAATAAATAAAATAA
1 AAATAAATAAAATAA
*
6546259 ATAA-GAATAAAATAA
1 A-AATAAATAAAATAA
*
6546274 AAATCAAT-AAATCAA
1 AAATAAATAAAAT-AA
*
6546289 TAAATAAATAAAATGA
1 -AAATAAATAAAATAA
6546305 AAATAAATAAAA
1 AAATAAATAAAA
6546317 AATAGAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 6 0.12
15 29 0.59
16 10 0.20
17 4 0.08
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATAAATAAAATAA
Found at i:6547280 original size:21 final size:22
Alignment explanation
Indices: 6547240--6547280 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
6547230 AAAATTAACA
6547240 GATAAATTATAGCATAAAATTT
1 GATAAATTATAGCATAAAATTT
6547262 GATAAA-TATA-CATATAAAT
1 GATAAATTATAGCATA-AAAT
6547281 ATTAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (22 bp):
GATAAATTATAGCATAAAATTT
Found at i:6547301 original size:3 final size:3
Alignment explanation
Indices: 6547293--6547415 Score: 65
Period size: 3 Copynumber: 39.7 Consensus size: 3
6547283 TAAAAGAAAA
* * * * *
6547293 AAT AAT AAT AAT AAT AAC AAG GAT -AT ATAT ATT AAT AAAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT -AAT AAT AAT
* *
6547339 AAT AAT AAAT AAAT AAT AAAT ACAT AA- GAT AAA AAT AA- AA- AAT ATAT
1 AAT AAT -AAT -AAT AAT -AAT A-AT AAT AAT AAT AAT AAT AAT AAT A-AT
* *
6547386 ATAT AAA AAT AAT AAT AAT AAT AAA AAT AA
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
6547416 AAAGAAAATA
Statistics
Matches: 95, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
2 7 0.07
3 62 0.65
4 26 0.27
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:6547351 original size:20 final size:20
Alignment explanation
Indices: 6547290--6547452 Score: 78
Period size: 21 Copynumber: 8.3 Consensus size: 20
6547280 TATTAAAAGA
6547290 AAAAATAATAATA-AT-AAT
1 AAAAATAATAATACATAAAT
* ** * *
6547308 AACAAGGATATATATATTAAT
1 AAAAATAATA-ATACATAAAT
*
6547329 AAATAATAGTAATA-ATAAAT
1 AAA-AATAATAATACATAAAT
6547349 --AAATAATAAATACATAAGAT
1 AAAAATAAT-AATACATAA-AT
* * *
6547369 AAAAATAAAAAATATATATAT
1 AAAAAT-AATAATACATAAAT
6547390 AAAAATAATAATA-AT-AAT
1 AAAAATAATAATACATAAAT
*
6547408 AAAAATAA-AA-AGA-AAAT
1 AAAAATAATAATACATAAAT
* *
6547425 AAAAATGTAA-AATACAAAAAA
1 AAAAA--TAATAATACATAAAT
6547446 AAAAATA
1 AAAAATA
6547453 GACTTACTTA
Statistics
Matches: 113, Mismatches: 16, Indels: 31
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.01
17 16 0.14
18 22 0.19
19 16 0.14
20 17 0.15
21 24 0.21
22 15 0.13
23 2 0.02
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAAATAATAATACATAAAT
Found at i:6547353 original size:24 final size:22
Alignment explanation
Indices: 6547330--6547418 Score: 69
Period size: 22 Copynumber: 4.0 Consensus size: 22
6547320 TATATTAATA
6547330 AATAATAGTAATAATA-AATAAAT
1 AATAATA-TAATAATATAA-AAAT
*
6547353 AATAA-ATACATAAGATAAAAAT
1 AATAATATA-ATAATATAAAAAT
*
6547375 AA-AAAAT-ATATATATAAAAAT
1 AATAATATAATA-ATATAAAAAT
*
6547396 AATAATAATAATAAAAATAAAAA
1 AATAAT-ATAAT-AATATAAAAA
6547419 GAAAATAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
20 3 0.06
21 15 0.28
22 16 0.30
23 9 0.17
24 10 0.19
25 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (22 bp):
AATAATATAATAATATAAAAAT
Found at i:6547382 original size:26 final size:27
Alignment explanation
Indices: 6547340--6547400 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
6547330 AATAATAGTA
*
6547340 ATAATAAATAAATAATAAATACATAAG
1 ATAATAAATAAAAAATAAATACATAAG
* * *
6547367 ATAA-AAATAAAAAATATATATATAAAA
1 ATAATAAATAAAAAATAAATACAT-AAG
6547394 ATAATAA
1 ATAATAA
6547401 TAATAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 16 0.57
27 10 0.36
28 2 0.07
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (27 bp):
ATAATAAATAAAAAATAAATACATAAG
Found at i:6547443 original size:7 final size:6
Alignment explanation
Indices: 6547339--6547448 Score: 64
Period size: 6 Copynumber: 17.3 Consensus size: 6
6547329 AAATAATAGT
*
6547339 AATAATA AATAAA TAATAAA TACAT-AA GATAAA AATAAAA AATATATA
1 AATAA-A AATAAA -AATAAA -A-ATAAA AATAAA AAT-AAA AATA-A-A
* * * * *
6547387 TATAAA AATAAT AATAAT AATAAA AATAAA AA-GAA AATAAA AATGTAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AAT-AAA
6547435 AATACAA AA-AAA AA
1 AATA-AA AATAAA AA
6547449 AATAGACTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 20
0.74 0.09 0.18
Matches are distributed among these distances:
5 10 0.12
6 36 0.43
7 32 0.38
8 6 0.07
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.22
Consensus pattern (6 bp):
AATAAA
Found at i:6547785 original size:88 final size:88
Alignment explanation
Indices: 6547678--6547853 Score: 255
Period size: 88 Copynumber: 2.0 Consensus size: 88
6547668 CAGAGGCTCG
* * *
6547678 ATGACTTTGAAAAAATAAATGGCT-CTTCTAATCAGAGGCTCAACGAATTTGAAAAGTAAATTGC
1 ATGACTTTGAAAAAATAAATGGCTCCTT-TAAACAGAGGCACAACGAATTTGAAAAGTAAATTAC
6547742 TCCTCTAAACAAAGGCACCACGAC
65 TCCTCTAAACAAAGGCACCACGAC
* * * * *
6547766 ATGACTTTTAAAAAGTAAATTGCTCCTTTAAACAGAGGCACCACGACTTTGAAAAGTAAATTACT
1 ATGACTTTGAAAAAATAAATGGCTCCTTTAAACAGAGGCACAACGAATTTGAAAAGTAAATTACT
*
6547831 CCTCTAAACAGAGGCACCACGAC
66 CCTCTAAACAAAGGCACCACGAC
6547854 TTTGAAAAGT
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 75 0.96
89 3 0.04
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (88 bp):
ATGACTTTGAAAAAATAAATGGCTCCTTTAAACAGAGGCACAACGAATTTGAAAAGTAAATTACT
CCTCTAAACAAAGGCACCACGAC
Found at i:6547826 original size:41 final size:41
Alignment explanation
Indices: 6547636--6547875 Score: 223
Period size: 41 Copynumber: 5.7 Consensus size: 41
6547626 CAGAGATTCA
* * * * *
6547636 ACGACTTTGGAAAAATAAATGGCT-CTTCTAATCAGAGGCTCG
1 ACGACTTT-GAAAAGTAAATTGCTCCTT-TAAACAGAGGCACC
* * * * * *
6547678 ATGACTTTGAAAAAATAAATGGCT-CTTCTAATCAGAGGCTCA
1 ACGACTTTG-AAAAGTAAATTGCTCCTT-TAAACAGAGGCACC
* * *
6547720 ACGAATTTGAAAAGTAAATTGCTCCTCTAAACAAAGGCACCAC
1 ACGACTTTGAAAAGTAAATTGCTCCTTTAAACAGAGGCA-C-C
*
6547763 GACATGACTTTTAAAAAGTAAATTGCTCCTTTAAACAGAGGCACC
1 -AC--GAC-TTTGAAAAGTAAATTGCTCCTTTAAACAGAGGCACC
* *
6547808 ACGACTTTGAAAAGTAAATTACTCCTCTAAACAGAGGCACC
1 ACGACTTTGAAAAGTAAATTGCTCCTTTAAACAGAGGCACC
6547849 ACGACTTTGAAAAGTAAATTGCTCCTT
1 ACGACTTTGAAAAGTAAATTGCTCCTT
6547876 GACAATCATG
Statistics
Matches: 170, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
41 80 0.47
42 51 0.30
44 4 0.02
45 1 0.01
46 3 0.02
47 31 0.18
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (41 bp):
ACGACTTTGAAAAGTAAATTGCTCCTTTAAACAGAGGCACC
Found at i:6548885 original size:8 final size:8
Alignment explanation
Indices: 6548872--6548924 Score: 74
Period size: 8 Copynumber: 6.8 Consensus size: 8
6548862 CATTCACTTT
*
6548872 TTTTTTAA
1 TTTTTTCA
6548880 TTTTTT-A
1 TTTTTTCA
6548887 TTTTTTCA
1 TTTTTTCA
6548895 TTTTTTTCA
1 -TTTTTTCA
6548904 -TTTTTCA
1 TTTTTTCA
6548911 TTTTTTCA
1 TTTTTTCA
6548919 TTTTTT
1 TTTTTT
6548925 TTCAAGCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
7 14 0.33
8 20 0.48
9 8 0.19
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCA
Found at i:6548885 original size:9 final size:9
Alignment explanation
Indices: 6548870--6548925 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
6548860 TTCATTCACT
*
6548870 TTTTTTTTA
1 TTTTTTTCA
*
6548879 ATTTTTT-A
1 TTTTTTTCA
6548887 -TTTTTTCA
1 TTTTTTTCA
6548895 TTTTTTTCA
1 TTTTTTTCA
6548904 --TTTTTCA
1 TTTTTTTCA
6548911 -TTTTTTCA
1 TTTTTTTCA
6548919 TTTTTTT
1 TTTTTTT
6548926 TCAAGCATAG
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
7 13 0.31
8 9 0.21
9 20 0.48
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:6548890 original size:16 final size:16
Alignment explanation
Indices: 6548872--6548924 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 16
6548862 CATTCACTTT
*
6548872 TTTTTTAATTTTTT-A
1 TTTTTTATTTTTTTCA
6548887 TTTTTTCATTTTTTTCA
1 TTTTTT-ATTTTTTTCA
*
6548904 TTTTTCA-TTTTTTCA
1 TTTTTTATTTTTTTCA
6548919 TTTTTT
1 TTTTTT
6548925 TTCAAGCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 19 0.58
16 8 0.24
17 6 0.18
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTATTTTTTTCA
Found at i:6548898 original size:24 final size:24
Alignment explanation
Indices: 6548871--6548925 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
6548861 TCATTCACTT
*
6548871 TTTTTTTAATTTTTTATTTTTTCA
1 TTTTTTTAATTTTTCATTTTTTCA
*
6548895 TTTTTTTCATTTTTCATTTTTTCA
1 TTTTTTTAATTTTTCATTTTTTCA
6548919 TTTTTTT
1 TTTTTTT
6548926 TCAAGCATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTTTAATTTTTCATTTTTTCA
Found at i:6552394 original size:14 final size:14
Alignment explanation
Indices: 6552375--6552402 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6552365 TTGAATTCTC
6552375 AAAGCTAACCTCTT
1 AAAGCTAACCTCTT
6552389 AAAGCTAACCTCTT
1 AAAGCTAACCTCTT
6552403 GATTGTCAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
AAAGCTAACCTCTT
Found at i:6555930 original size:59 final size:59
Alignment explanation
Indices: 6555867--6556029 Score: 186
Period size: 59 Copynumber: 2.7 Consensus size: 59
6555857 TTTTGTGCAG
* * * **
6555867 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTG-AAATTTTTTATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATT-CTTAAA
* *
6555926 GAAAAATTGATACTTTCAAATTTTCCTCAAAAAAAATATTTTTTTGAAAATTTATTCTTAAA
1 GAAAAATTGATACTTTCAACTTTTCC-C--CAAAAATATTTTTTTGAAAATTTATTCTTAAA
* * *
6555988 G-AAAATTGATATTTTCAACTTTTCCTCAAAAATGTTTTTTTG
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTG
6556030 TTTTTTTTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
58 14 0.16
59 25 0.28
60 1 0.01
61 22 0.25
62 18 0.20
63 8 0.09
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (59 bp):
GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTCTTAAA
Found at i:6556004 original size:61 final size:62
Alignment explanation
Indices: 6555867--6556019 Score: 190
Period size: 61 Copynumber: 2.5 Consensus size: 62
6555857 TTTTGTGCAG
* * * **
6555867 GAAAAATTGATACTTTCAACTTTTCC-C--CAAAAATATTCTTTTGAAATTTTTTATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAATATTCTTTTGAAATTTATTACTTAAA
* *
6555926 GAAAAATTGATACTTTCAAATTTTCCTCAAAAAAAATATTTTTTTGAAAATTTATT-CTTAAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAATATTCTTTTG-AAATTTATTACTTAAA
*
6555988 G-AAAATTGATATTTTCAACTTTTCCTCAAAAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA
6556020 TGTTTTTTTG
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
59 25 0.31
60 1 0.01
61 29 0.36
62 18 0.22
63 8 0.10
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (62 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAATATTCTTTTGAAATTTATTACTTAAA
Found at i:6556108 original size:15 final size:14
Alignment explanation
Indices: 6556054--6556112 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 14
6556044 TTATTTAAAG
6556054 AAAATGAAATAAA-T
1 AAAAT-AAATAAATT
*
6556068 AAAATAAATAAGAAT
1 AAAATAAATAA-ATT
6556083 AAAAT-AA-AAATT
1 AAAATAAATAAATT
6556095 AAAAATAAATAAA-T
1 -AAAATAAATAAATT
6556109 AAAA
1 AAAA
6556113 AATAGAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.05
13 17 0.44
14 11 0.28
15 9 0.23
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.20
Consensus pattern (14 bp):
AAAATAAATAAATT
Found at i:6556108 original size:21 final size:19
Alignment explanation
Indices: 6556060--6556126 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 19
6556050 AAAGAAAATG
6556060 AAATAAAT-AAAATAAATAA
1 AAATAAATAAAAATAAA-AA
*
6556079 GAATAAAATAAAAATTAAAAA
1 AAAT-AAATAAAAA-TAAAAA
6556100 TAAATAAATAAAAAATAGAAAA
1 -AAATAAAT-AAAAATA-AAAA
6556122 AAATA
1 AAATA
6556127 TTAAACAACC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.08
20 4 0.10
21 17 0.43
22 16 0.40
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (19 bp):
AAATAAATAAAAATAAAAA
Found at i:6556113 original size:15 final size:15
Alignment explanation
Indices: 6556054--6556116 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
6556044 TTATTTAAAG
6556054 AAAATGAAATAAAT--
1 AAAAT-AAATAAATAA
*
6556068 AAAATAAATAAGA-AT
1 AAAATAAATAA-ATAA
*
6556083 AAAAT-AA-AAATTA
1 AAAATAAATAAATAA
6556096 AAAATAAATAAATAA
1 AAAATAAATAAATAA
6556111 AAAATA
1 AAAATA
6556117 GAAAAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
12 1 0.03
13 13 0.32
14 10 0.25
15 16 0.40
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAATAAATAAATAA
Found at i:6556124 original size:32 final size:33
Alignment explanation
Indices: 6556064--6556131 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 33
6556054 AAAATGAAAT
*
6556064 AAATAAAATAAATAAGAATAAAATAAAAATTAA
1 AAATAAAATAAATAAAAATAAAATAAAAATTAA
6556097 AAAT-AAATAAATAAAAAATAGAAA-AAAATATTAA
1 AAATAAAATAAAT-AAAAATA-AAATAAAA-ATTAA
6556131 A
1 A
6556132 CAACCTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 8 0.26
33 14 0.45
34 9 0.29
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (33 bp):
AAATAAAATAAATAAAAATAAAATAAAAATTAA
Found at i:6557200 original size:6 final size:6
Alignment explanation
Indices: 6557189--6557270 Score: 60
Period size: 6 Copynumber: 13.0 Consensus size: 6
6557179 AATACATAAG
* *
6557189 ATAAAA ATAAAAA ATATATAA ATAAAA ACAATA ATAAAA ATAAAA AT-AAA
1 ATAAAA AT-AAAA ATA-A-AA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
* *
6557239 ATACAAA TGTAAAA TACAAAA ATAAAA A-AAAA
1 ATA-AAA -ATAAAA -ATAAAA ATAAAA ATAAAA
6557271 GACTTAGCTA
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
5 9 0.15
6 27 0.44
7 19 0.31
8 7 0.11
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:6557211 original size:15 final size:15
Alignment explanation
Indices: 6557155--6557216 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
6557145 ATAAGGATAT
* *
6557155 ATATATTAATAAATA
1 ATATATAAATAAAAA
* *
6557170 ATAGTAATAAATACATA
1 ATA-T-ATAAATAAAAA
* *
6557187 AGATAAAAATAAAAA
1 ATATATAAATAAAAA
6557202 ATATATAAATAAAAA
1 ATATATAAATAAAAA
6557217 CAATAATAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 24 0.65
16 2 0.05
17 11 0.30
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (15 bp):
ATATATAAATAAAAA
Found at i:6557226 original size:12 final size:12
Alignment explanation
Indices: 6557208--6557270 Score: 65
Period size: 13 Copynumber: 5.2 Consensus size: 12
6557198 AAAAATATAT
6557208 AAATAAAAACAA
1 AAATAAAAACAA
* *
6557220 TAATAAAAATAA
1 AAATAAAAACAA
6557232 AAATAAAATACAA
1 AAATAAAA-ACAA
**
6557245 ATGTAAAATACAA
1 AAATAAAA-ACAA
6557258 AAATAAAAA-AA
1 AAATAAAAACAA
6557269 AA
1 AA
6557271 GACTTAGCTA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
11 4 0.10
12 18 0.43
13 20 0.48
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.16
Consensus pattern (12 bp):
AAATAAAAACAA
Found at i:6558071 original size:15 final size:17
Alignment explanation
Indices: 6558040--6558071 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6558030 CTTTTCCTCC
6558040 AAATTGACATATTAAAA
1 AAATTGACATATTAAAA
6558057 AAATTGA-AT-TTAAAA
1 AAATTGACATATTAAAA
6558072 GGGAAACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (17 bp):
AAATTGACATATTAAAA
Found at i:6558188 original size:15 final size:15
Alignment explanation
Indices: 6558151--6558188 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
6558141 GTAAATTTTG
*
6558151 TTTCCTTTACTTTCT
1 TTTCCTTTACTTTCC
*
6558166 TTTACTTTACTTTCC
1 TTTCCTTTACTTTCC
6558181 TTTCCTTT
1 TTTCCTTT
6558189 CTCTCCTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTCCTTTACTTTCC
Found at i:6561498 original size:14 final size:16
Alignment explanation
Indices: 6561473--6561505 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
6561463 ATAAATAGAC
6561473 AAAAAACAAAT-ATAT
1 AAAAAACAAATAATAT
6561488 AAAAAAC-AATAATAT
1 AAAAAACAAATAATAT
6561503 AAA
1 AAA
6561506 TCTTAAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAAACAAATAATAT
Found at i:6562760 original size:44 final size:44
Alignment explanation
Indices: 6562712--6562801 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
6562702 TTAAAAAATT
* * ** *
6562712 TAAAAAGGCTCTTCTAAATAGAGGCTCAATGATTTTTGAAAACA
1 TAAAAAGGCTCCTCTAAATAAAGGCTCAATGACCTCTGAAAACA
* *
6562756 TAAAAGGGTTCCTCTAAATAAAGGCTCAATGACCTCTGAAAACA
1 TAAAAAGGCTCCTCTAAATAAAGGCTCAATGACCTCTGAAAACA
6562800 TA
1 TA
6562802 GCAAGCTTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (44 bp):
TAAAAAGGCTCCTCTAAATAAAGGCTCAATGACCTCTGAAAACA
Found at i:6562977 original size:23 final size:23
Alignment explanation
Indices: 6562941--6562993 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
6562931 GCAAAGACAT
6562941 AAATAAT-AAAATCAATAACAAA-A
1 AAATAATAAAAATC-ATAA-AAATA
6562964 AAA-AATAAAAATCATAAAAATA
1 AAATAATAAAAATCATAAAAATA
6562986 AAATAATA
1 AAATAATA
6562994 TTACTAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 3 0.11
22 11 0.41
23 13 0.48
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (23 bp):
AAATAATAAAAATCATAAAAATA
Found at i:6564708 original size:19 final size:19
Alignment explanation
Indices: 6564680--6564751 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 19
6564670 CTTCTTGAAT
*
6564680 TAAACTAAAAGAATTTAAA
1 TAAACAAAAAGAATTTAAA
*
6564699 TAAACAAAAACTTTG-TTCTTAAA
1 TAAACAAAAA----GAAT-TTAAA
*
6564722 TTAAACTAAAAGAATTTAAA
1 -TAAACAAAAAGAATTTAAA
6564742 TAAACAAAAA
1 TAAACAAAAA
6564752 CTTTGTAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
19 18 0.44
20 6 0.15
21 1 0.02
22 1 0.02
23 6 0.15
24 9 0.22
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.28
Consensus pattern (19 bp):
TAAACAAAAAGAATTTAAA
Found at i:6564726 original size:43 final size:43
Alignment explanation
Indices: 6564671--6564757 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
6564661 GGAAAAATAC
*
6564671 TTCTTGAATTAAACTAAAAGAATTTAAATAAACAAAAACTTTG
1 TTCTTAAATTAAACTAAAAGAATTTAAATAAACAAAAACTTTG
6564714 TTCTTAAATTAAACTAAAAGAATTTAAATAAACAAAAACTTTG
1 TTCTTAAATTAAACTAAAAGAATTTAAATAAACAAAAACTTTG
6564757 T
1 T
6564758 AGTTATTGGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (43 bp):
TTCTTAAATTAAACTAAAAGAATTTAAATAAACAAAAACTTTG
Found at i:6566056 original size:18 final size:18
Alignment explanation
Indices: 6566035--6566069 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6566025 ATTTTCCCTA
6566035 TTTTT-TCATTTTTCATT
1 TTTTTATCATTTTTCATT
6566052 TTTTTATCATTTTTCATT
1 TTTTTATCATTTTTCATT
6566070 CATTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTATCATTTTTCATT
Found at i:6566386 original size:13 final size:14
Alignment explanation
Indices: 6566358--6566407 Score: 66
Period size: 15 Copynumber: 3.5 Consensus size: 14
6566348 GCATTTTGCC
6566358 TCATGTTTCAATTTT
1 TCAT-TTTCAATTTT
6566373 TCATTTTC-ATTTT
1 TCATTTTCAATTTT
*
6566386 TCATTCTCAATTTTT
1 TCATTTTCAA-TTTT
6566401 TCATTTT
1 TCATTTT
6566408 TCAAGAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 12 0.39
14 5 0.16
15 14 0.45
ACGTcount: A:0.18, C:0.16, G:0.02, T:0.64
Consensus pattern (14 bp):
TCATTTTCAATTTT
Found at i:6568127 original size:3 final size:3
Alignment explanation
Indices: 6568119--6568278 Score: 113
Period size: 3 Copynumber: 54.7 Consensus size: 3
6568109 ATTTTCGTTG
*
6568119 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TGCTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T--TA TTA TTA TTA
* * * ** * *
6568165 TCA TTA TTA TTA -TA GTA -TA GT- TTA CAA TGTA GTG TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* * *
6568207 -TA TTA -TA TTA TTA TTA TTA CGT- TTA GTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
6568250 TTA TTA TTA TTTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT
6568279 TTCTTTCTTC
Statistics
Matches: 124, Mismatches: 19, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
2 16 0.13
3 101 0.81
4 5 0.04
5 2 0.02
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:6573785 original size:20 final size:21
Alignment explanation
Indices: 6573732--6573785 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
6573722 AATGATGGAT
*
6573732 AAAAA-AAAGAAAAAACAAAA
1 AAAAATAAAGAGAAAACAAAA
6573752 AAAAATAAAG-GAAAAC-AAA
1 AAAAATAAAGAGAAAACAAAA
* *
6573771 AACAATGAAGAGAAA
1 AAAAATAAAGAGAAA
6573786 TTGTTGGGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 11 0.38
20 14 0.48
21 4 0.14
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.04
Consensus pattern (21 bp):
AAAAATAAAGAGAAAACAAAA
Found at i:6574115 original size:11 final size:11
Alignment explanation
Indices: 6574089--6574131 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
6574079 AAAATTTGAA
6574089 AAAAAAAAGAAGC
1 AAAAAAAA-AA-C
*
6574102 AAAAACAAAAC
1 AAAAAAAAAAC
6574113 AAAAAAAAAAC
1 AAAAAAAAAAC
6574124 ACAAAAAA
1 A-AAAAAA
6574132 GCAAGAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 12 0.44
12 8 0.30
13 7 0.26
ACGTcount: A:0.84, C:0.12, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:6574119 original size:29 final size:29
Alignment explanation
Indices: 6574056--6574122 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
6574046 AAGGCATGCT
* **
6574056 AAAAAAAAAAAAGAAGAAACTACAAAATT
1 AAAAAAAAAAAAGAAGAAACAACAAAACA
**
6574085 TGAAAAAAAAAAGAAGCAAA-AACAAAACA
1 AAAAAAAAAAAAGAAG-AAACAACAAAACA
6574114 AAAAAAAAA
1 AAAAAAAAA
6574123 CACAAAAAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 27 0.90
30 3 0.10
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.06
Consensus pattern (29 bp):
AAAAAAAAAAAAGAAGAAACAACAAAACA
Found at i:6575132 original size:120 final size:120
Alignment explanation
Indices: 6574945--6575314 Score: 286
Period size: 120 Copynumber: 3.1 Consensus size: 120
6574935 TTCGTCTCAG
* * * **
6574945 TCATTCATCTTGGACCTCGACTCAGTCTTGGTTGCTTTATCTCT-GAACTCACAATTTCATCCTG
1 TCATTCATCTTCGACCTCAACTTAGTCTTGGTCACTTTATCTCTAG-ACTCACAATTTCATCCTG
* *
6575009 GTCATTCCATCTCAACTCAATCTAAATCATTTTTTTGACTCGCAATTTCATCCCA-T
65 GTCATTCAATCTCAACTCAATCTAAATCA-TTTTCTGACTCGCAATTTCATCCCAGT
** * *
6575065 TCATTCATCTTCGACCTCAACTTAGTCTTGGTCACTTTATCTCTAGACTCGTAGTTTGA-CCTCG
1 TCATTCATCTTCGACCTCAACTTAGTCTTGGTCACTTTATCTCTAGACTCACAATTTCATCCT-G
* ** * *** * *
6575129 GTCATTCAATCTCGACTCTGTCTAGATCATTTTCTGACTCGTGGTTTCCTCCTAGT
65 GTCATTCAATCTCAACTCAATCTAAATCATTTTCTGACTCGCAATTTCATCCCAGT
* * * * * ** * *
6575185 T-ATTAATCTTTGACCTCAAC-TCGATATTGGTCACTTTATCTTTAGACTCATGATTTTATCCCG
1 TCATTCATCTTCGACCTCAACTTAG-TCTTGGTCACTTTATCTCTAGACTCACAATTTCATCCTG
* ** * * * * * *
6575248 ATCA-TCTAATCTTGACCCAATCTAGATTATTTTTTTGACTCACGATTTCATCCCAGT
65 GTCATTC-AATCTCAACTCAATCTAAATCA-TTTTCTGACTCGCAATTTCATCCCAGT
*
6575305 T-ATTTATCTT
1 TCATTCATCTT
6575315 TTGACCTTGA
Statistics
Matches: 200, Mismatches: 43, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
118 4 0.02
119 88 0.44
120 107 0.54
121 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (120 bp):
TCATTCATCTTCGACCTCAACTTAGTCTTGGTCACTTTATCTCTAGACTCACAATTTCATCCTGG
TCATTCAATCTCAACTCAATCTAAATCATTTTCTGACTCGCAATTTCATCCCAGT
Found at i:6575259 original size:119 final size:121
Alignment explanation
Indices: 6575017--6575416 Score: 339
Period size: 119 Copynumber: 3.3 Consensus size: 121
6575007 TGGTCATTCC
* * * * * * *
6575017 ATCTCAACTCAATCTAAATCATTTTTTTGACTCGCAATTTCATCCCA-TTCATTCATC-TTCGAC
1 ATCTCGACTCAATCTAGATCATTTTTCTGACTCACGATTTCATCCCAGTT-ATTAATCTTTTGAC
* * * * * *
6575080 CTCAACT-TAGTCTTGGTCACTTTATCTCTAGACTCGTAGTTTGA-CCTCGGTCAT-TCA
65 CTCAACTCGA-TATTGGTCACTTTATCTTTAGACTCATAGTTTCATCC-CGATCATCT-A
** ** * * *
6575137 ATCTCGACTCTGTCTAGATCA-TTTTCTGACTCGTGGTTTCCTCCTAGTTATTAATC-TTTGACC
1 ATCTCGACTCAATCTAGATCATTTTTCTGACTCACGATTTCATCCCAGTTATTAATCTTTTGACC
*
6575200 TCAACTCGATATTGGTCACTTTATCTTTAGACTCAT-GATTTTATCCCGATCATCTA
66 TCAACTCGATATTGGTCACTTTATCTTTAGACTCATAG-TTTCATCCCGATCATCTA
* * * * *
6575256 ATCTTGACCCAATCTAGATTATTTTTTTGACTCACGATTTCATCCCAGTTATTTATCTTTTGACC
1 ATCTCGACTCAATCTAGATCATTTTTCTGACTCACGATTTCATCCCAGTTATTAATCTTTTGACC
** * * ** * ** *
6575321 TTGACTCGATCTTAGTTGCTTTATCTTTAAACTCATAGTTTCATCTTGATCATCTG
66 TCAACTCGATATTGGTCACTTTATCTTTAGACTCATAGTTTCATCCCGATCATCTA
* * * *
6575377 ATCTCGACTCAATCCAAATCATTTTTCTAACTCACAATTT
1 ATCTCGACTCAATCTAGATCATTTTTCTGACTCACGATTT
6575417 TGTCTTAGTC
Statistics
Matches: 223, Mismatches: 49, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
118 1 0.00
119 88 0.39
120 51 0.23
121 82 0.37
122 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (121 bp):
ATCTCGACTCAATCTAGATCATTTTTCTGACTCACGATTTCATCCCAGTTATTAATCTTTTGACC
TCAACTCGATATTGGTCACTTTATCTTTAGACTCATAGTTTCATCCCGATCATCTA
Found at i:6575372 original size:121 final size:120
Alignment explanation
Indices: 6575173--6575474 Score: 300
Period size: 121 Copynumber: 2.5 Consensus size: 120
6575163 TGACTCGTGG
* ** * * * *
6575173 TTTCCTCCTAGTTATTAATCTTTGACCTCAACTCGATATTGGTCACTTTATCTTTAGACTCATGA
1 TTTCATCCTAGTTATTAATCTTTGACCTTGACTCGATCTTAGTCGCTTTATCTTTAAACTCATGA
* * * * * * * *
6575238 TTTTATCCCGATCATCTAATCTTGACCCAATCTAGATTATTTTTTTGACTCACGA
66 TTTCATCCCGATCATCTAATCTCGACCCAATCCAAATCATTTTTCTAACTCACAA
* * *
6575293 TTTCATCCCAGTTATTTATCTTTTGACCTTGACTCGATCTTAGTTGCTTTATCTTTAAACTCAT-
1 TTTCATCCTAGTTATTAATC-TTTGACCTTGACTCGATCTTAGTCGCTTTATCTTTAAACTCATG
** * *
6575357 AGTTTCATCTTGATCATCTGATCTCGACTCAATCCAAATCATTTTTCTAACTCACAA
65 A-TTTCATCCCGATCATCTAATCTCGACCCAATCCAAATCATTTTTCTAACTCACAA
** * * * * * * *
6575414 TTTTGTCTTAGTCATTCATCTTTGACCTTGACTCAATCCTAGCCGTTTTATCTTTAAACTC
1 TTTCATCCTAGTTATTAATCTTTGACCTTGACTCGATCTTAGTCGCTTTATCTTTAAACTC
6575475 GTGGTTTCGT
Statistics
Matches: 147, Mismatches: 33, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
120 54 0.37
121 93 0.63
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.43
Consensus pattern (120 bp):
TTTCATCCTAGTTATTAATCTTTGACCTTGACTCGATCTTAGTCGCTTTATCTTTAAACTCATGA
TTTCATCCCGATCATCTAATCTCGACCCAATCCAAATCATTTTTCTAACTCACAA
Found at i:6575809 original size:3 final size:3
Alignment explanation
Indices: 6575803--6575832 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6575793 GTTGTTGTTG
6575803 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6575833 CTACTACTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6575931 original size:3 final size:3
Alignment explanation
Indices: 6575914--6575955 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
6575904 TATAGTCTTA
6575914 TAT TA- TAT T-T TAT TAT TAT TAT TAT TAT TAT T-T TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6575956 TCTTCTTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 8 0.23
3 27 0.77
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:6575934 original size:6 final size:6
Alignment explanation
Indices: 6575914--6575955 Score: 56
Period size: 5 Copynumber: 7.7 Consensus size: 6
6575904 TATAGTCTTA
6575914 TATTA- TATT-T TATTAT TATTAT TATTAT TATT-T TATT-T TATT
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATT
6575956 TCTTCTTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TATTAT
Found at i:6576459 original size:11 final size:10
Alignment explanation
Indices: 6576431--6576470 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
6576421 CTGAAAAATT
*
6576431 TAGGGTTTTC
1 TAGGTTTTTC
*
6576441 TGGGTTTTTC
1 TAGGTTTTTC
6576451 TAAGGTTTTTC
1 T-AGGTTTTTC
6576462 TAGGTTTTT
1 TAGGTTTTT
6576471 GGGGTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.10, C:0.07, G:0.25, T:0.57
Consensus pattern (10 bp):
TAGGTTTTTC
Found at i:6579105 original size:7 final size:7
Alignment explanation
Indices: 6579089--6579144 Score: 58
Period size: 7 Copynumber: 7.6 Consensus size: 7
6579079 TAATAATTTA
6579089 ATGATGC
1 ATGATGC
*
6579096 ATGATTC
1 ATGATGC
6579103 ATGATGC
1 ATGATGC
*
6579110 ATGAATGA
1 ATG-ATGC
6579118 ATGTATGC
1 ATG-ATGC
*
6579126 ATGCATTC
1 ATG-ATGC
6579134 ATGATGC
1 ATGATGC
6579141 ATGA
1 ATGA
6579145 GAGGCAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 22 0.55
8 18 0.45
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.32
Consensus pattern (7 bp):
ATGATGC
Found at i:6580821 original size:19 final size:19
Alignment explanation
Indices: 6580799--6580855 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
6580789 TAAATTAATT
6580799 AATTAAATCAAAATAAA-CA
1 AATTAAATC-AAATAAATCA
*
6580818 AATTAGATCAAATAAATCA
1 AATTAAATCAAATAAATCA
6580837 AA-TAAA--AAATTAAATCA
1 AATTAAATCAAA-TAAATCA
6580854 AA
1 AA
6580856 CACATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 3 0.09
17 9 0.26
18 10 0.29
19 12 0.35
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.23
Consensus pattern (19 bp):
AATTAAATCAAATAAATCA
Found at i:6580829 original size:10 final size:10
Alignment explanation
Indices: 6580799--6580855 Score: 61
Period size: 9 Copynumber: 6.2 Consensus size: 10
6580789 TAAATTAATT
6580799 AATTAAATCA
1 AATTAAATCA
*
6580809 AAATAAA-CA
1 AATTAAATCA
*
6580818 AATTAGATCA
1 AATTAAATCA
6580828 AA-TAAATCA
1 AATTAAATCA
6580837 AA-TAAA--A
1 AATTAAATCA
6580844 AATTAAATCA
1 AATTAAATCA
6580854 AA
1 AA
6580856 CACATTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 19 0.49
10 13 0.33
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.23
Consensus pattern (10 bp):
AATTAAATCA
Found at i:6585953 original size:186 final size:187
Alignment explanation
Indices: 6585667--6586505 Score: 972
Period size: 186 Copynumber: 4.5 Consensus size: 187
6585657 ACTGAAGGTG
* * *
6585667 TCTTGTAGTGAAAAATACCTTCAATATTCCACTACACAAATTTTAAGATGGTTAGTGAAGGCGTT
1 TCTTCTAGTGAAAAATACCTTCAATATTTCACTACTCAAATTTTAAGATGGTTAGTGAAGGCGTT
* * * * *
6585732 TATTCTAGAAAAACGCATTTACTAATTCTTTTTAATTTTTGTACAAAATTATTGAATGCATTTTT
66 TATTCTAGAAAAATGCCTTCACTAATTCTTTTTAATTTTTGTAAAAAATTATTGAAGGCATTTTT
* *** *
6585797 TTAGAACAAACACCTTCAATAATTT-TTTTTTTTAATTTTTGGGATTATTAAAGGCA
131 TTAGAACAAACACCTTCAATAATTTCCTTTTAAAAATTTTTGAGATTATTAAAGGCA
* * * * * *
6585853 TCTTGTAATGAAAAATACCTTTAATATTTCAGTACTCAAATTTTAAAATGGTTAGTGAATGCGTT
1 TCTTCTAGTGAAAAATACCTTCAATATTTCACTACTCAAATTTTAAGATGGTTAGTGAAGGCGTT
* * * *
6585918 TATTCTAGAAAAATGCCTTCACCAATTCCTTTTAATTTTTGTACAAAATTATTGAAGGCGTTTGT
66 TATTCTAGAAAAATGCCTTCACTAATTCTTTTTAATTTTTGTAAAAAATTATTGAAGGCATTT-T
* * * * * * * *
6585983 TCTCA-AA-AAACGCCTTTAATAATTTTCTTGTAAAAATTTTTAAGATTATTAAAAGCG
130 T-TTAGAACAAACACCTTCAATAATTTCCTTTTAAAAATTTTTGAGATTATTAAAGGCA
* * * * *
6586040 TCTTCTAGT-AAAAATGCCTTCAATA-TTCTACTACTCGAATTTTAAGACGGTTAGTCAAGGCAT
1 TCTTCTAGTGAAAAATACCTTCAATATTTC-ACTACTCAAATTTTAAGATGGTTAGTGAAGGCGT
* ****
6586103 TTATTCTAGAAAAATGCCTTCACTAATTCTTTTTCATTTAAAAAAAAAATTATTGAAGGCATTTT
65 TTATTCTAGAAAAATGCCTTCACTAATTCTTTTTAATTTTTGTAAAAAATTATTGAAGGCATTTT
* * ** *
6586168 CTGAGAACAAATGCCTTCAATAATTTCCTTTTAAAAATTTTTGGGATTATTAAAGGCA
130 TTTAGAACAAACACCTTCAATAATTTCCTTTTAAAAATTTTTGAGATTATTAAAGGCA
* * * *
6586226 TATTCTAGTGAAAAATACCTTCAATATTTCATTACTCAAATTTTAAGATGGTTAGTCAAGGTGTT
1 TCTTCTAGTGAAAAATACCTTCAATATTTCACTACTCAAATTTTAAGATGGTTAGTGAAGGCGTT
**** * * **
6586291 TATTCTAGAAAAAAAATTTCACTAATTTTTTTTTTAATTTTTG-AAAAAATTATTAAAGGTGTTT
66 TATTCTAGAAAAATGCCTTCACTAA--TTCTTTTTAATTTTTGTAAAAAATTATTGAAGGCATTT
* *
6586355 TTTTAGAACAAACACCTTCAATAATTTCCTTTTAAAAATTTTTTAGATTATTAAAGGCT
129 TTTTAGAACAAACACCTTCAATAATTTCCTTTTAAAAATTTTTGAGATTATTAAAGGCA
* * * *
6586414 TCTTCTAGTGAAAAACACCTTCAATA-TTCTACTACTCAAATTTTAAGACGGTTAGTGAAAGCAT
1 TCTTCTAGTGAAAAATACCTTCAATATTTC-ACTACTCAAATTTTAAGATGGTTAGTGAAGGCGT
* * *
6586478 TTATTTTAAAAAAATGCCTTCAGTAATT
65 TTATTCTAGAAAAATGCCTTCACTAATT
6586506 TGCTATAATT
Statistics
Matches: 545, Mismatches: 97, Indels: 22
0.82 0.15 0.03
Matches are distributed among these distances:
184 2 0.00
185 6 0.01
186 278 0.51
187 102 0.19
188 146 0.27
189 11 0.02
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (187 bp):
TCTTCTAGTGAAAAATACCTTCAATATTTCACTACTCAAATTTTAAGATGGTTAGTGAAGGCGTT
TATTCTAGAAAAATGCCTTCACTAATTCTTTTTAATTTTTGTAAAAAATTATTGAAGGCATTTTT
TTAGAACAAACACCTTCAATAATTTCCTTTTAAAAATTTTTGAGATTATTAAAGGCA
Found at i:6587231 original size:25 final size:25
Alignment explanation
Indices: 6587184--6587232 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
6587174 AATATTGCGG
* *
6587184 TTTGCTTAATGGTATTATGTGATAC
1 TTTGCTGAATGGTATTATATGATAC
*
6587209 TTTGCTGAATGGTATTGTATGATA
1 TTTGCTGAATGGTATTATATGATA
6587233 TTGGTATGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.06, G:0.22, T:0.47
Consensus pattern (25 bp):
TTTGCTGAATGGTATTATATGATAC
Found at i:6588929 original size:21 final size:21
Alignment explanation
Indices: 6588885--6588929 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6588875 ATAAGTTTAA
* *
6588885 TATTAATTTGTTTATTATATT
1 TATTAATTTGTTTATAATACT
6588906 TATTAATTTGGTTT-TAATACT
1 TATTAATTT-GTTTATAATACT
6588927 TAT
1 TAT
6588930 ATTTCATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (21 bp):
TATTAATTTGTTTATAATACT
Found at i:6591272 original size:305 final size:306
Alignment explanation
Indices: 6590563--6591348 Score: 829
Period size: 305 Copynumber: 2.6 Consensus size: 306
6590553 ATTAATAAAG
* * * * *** * * *
6590563 GCATTTTTAGTAAGAAAAAGCTTTGAATCATTTATAACAAAATGTTATTGAAGGCGTTTTTAAC-
1 GCATATTTAGTAAGAAAATGCCTTGAATAATCCCTAACAAAATATTATTGAAGGCATTTTTTACA
* * * ** ** *
6590627 CAAACCTGCCTTCAATAATC-CAATTTAAAAACATATTGTGTGGAATATTAAAGGCATTTTGGGA
66 AAAATC-ACCTTCAATAATCTC-ACCTAAAAATTTATTGTGTGGAATATTAAAGGCATTTTGGGC
* * * * * * * *
6590691 CAAAAACGCCTTCAAGAATTCTTTCCAAATATTTTGTATGGATTA--CTAAATGCATTTTTGACA
129 CAAAAACGCCTTCAAGAATCCGTTCTAACT-TTTTGTATGGATTATTCAAAATG-ATTTCTAAAA
* * * * * *
6590754 AAAACCGTCTTCAATAATCTCTATTAAAAATTTATTGATTGGATTATTGAAGGTACTTTCACCTA
192 AAAACCGACTTCAATAATCTCAACTAAAAATTAATTGAATGGATTATTGAAGGCACTTTCACCTA
* * * * *
6590819 AAAACGCCTTCAAGAATCCATTTCATATTTTTTTCTATGGATTATTAAGG
257 AAAACACCTTCAAGAATCCATTCCATATTTTTCTCTATAGATTATTAAGA
* *
6590869 GCATATTTAGTAAGAAAATGCCTTGAATAATCCTTAACAAAATATTATTGAAGGCATTTTTTACC
1 GCATATTTAGTAAGAAAATGCCTTGAATAATCCCTAACAAAATATTATTGAAGGCATTTTTTACA
*
6590934 AAAATCACCTTCAATAATCTCACCTAAAAATTTATTGTGTGGAATAGTAAAGGCATTTTGGGCCA
66 AAAATCACCTTCAATAATCTCACCTAAAAATTTATTGTGTGGAATATTAAAGGCATTTTGGGCCA
*
6590999 AAAATGCCTTCAAGAATCCGTTCTAACTTTTTGTATGGATTATTCAAAATG-TTTCTAAAAAAAA
131 AAAACGCCTTCAAGAATCCGTTCTAACTTTTTGTATGGATTATTCAAAATGATTTCTAAAAAAAA
* * *
6591063 CTGACTTCAATAATAC-CAACTAAAAATTAATTGAATGGATTGTTGAAGGCATTTTCAGCC-AAA
196 CCGACTTCAATAAT-CTCAACTAAAAATTAATTGAATGGATTATTGAAGGCACTTTCA-CCTAAA
**
6591126 AACACCTTCAAGAATTGATTCCATATTTTTCT-TATAGATTATTAAGA
259 AACACCTTCAAGAATCCATTCCATATTTTTCTCTATAGATTATTAAGA
* * ** **
6591173 GCGTTTTTCTTTCGAAAATGCCTTGAATAATCCCTAACAAAATATTATTGAAGGC-TTTTTTGAC
1 GCATATTTAGTAAGAAAATGCCTTGAATAATCCCTAACAAAATATTATTGAAGGCATTTTTT-AC
* * ** * ** *
6591237 AAAAATCGCTTTCAATAATC-CGACCATTCAAATTTATCGTGTGGAATATTAAAGGTGTTTTGAG
65 AAAAATCACCTTCAATAATCTC-ACC-TAAAAATTTATTGTGTGGAATATTAAAGGCATTTTGGG
* * *
6591301 CTAAAAACGCTTTCAAGAATCCGTT-TCAACTTTTGTGTATAGATTATT
128 CCAAAAACGCCTTCAAGAATCCGTTCT-AACTTTT-TGTATGGATTATT
6591349 GAAGGCGTTT
Statistics
Matches: 404, Mismatches: 65, Indels: 22
0.82 0.13 0.04
Matches are distributed among these distances:
303 7 0.02
304 84 0.21
305 160 0.40
306 142 0.35
307 11 0.03
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (306 bp):
GCATATTTAGTAAGAAAATGCCTTGAATAATCCCTAACAAAATATTATTGAAGGCATTTTTTACA
AAAATCACCTTCAATAATCTCACCTAAAAATTTATTGTGTGGAATATTAAAGGCATTTTGGGCCA
AAAACGCCTTCAAGAATCCGTTCTAACTTTTTGTATGGATTATTCAAAATGATTTCTAAAAAAAA
CCGACTTCAATAATCTCAACTAAAAATTAATTGAATGGATTATTGAAGGCACTTTCACCTAAAAA
CACCTTCAAGAATCCATTCCATATTTTTCTCTATAGATTATTAAGA
Found at i:6592173 original size:22 final size:22
Alignment explanation
Indices: 6592147--6592188 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
6592137 GTGAAACCTA
6592147 TTTCATTACTTTATCCGTAACT
1 TTTCATTACTTTATCCGTAACT
*
6592169 TTTCATTACTTTATCTGTAA
1 TTTCATTACTTTATCCGTAA
6592189 GTGAGTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTCATTACTTTATCCGTAACT
Found at i:6595588 original size:2 final size:2
Alignment explanation
Indices: 6595581--6595605 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6595571 ATCTATCTAT
6595581 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
6595606 TAATCAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6600595 original size:15 final size:15
Alignment explanation
Indices: 6600575--6600606 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6600565 CGAGAGCGAG
*
6600575 AGGAGAATGAGAAGA
1 AGGAGAAGGAGAAGA
6600590 AGGAGAAGGAGAAGA
1 AGGAGAAGGAGAAGA
6600605 AG
1 AG
6600607 CGCCATGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (15 bp):
AGGAGAAGGAGAAGA
Found at i:6602710 original size:27 final size:28
Alignment explanation
Indices: 6602645--6602717 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
6602635 GTATATAAAG
* *
6602645 AAATTTATAATATATATTTAATATTTGTA
1 AAATTTATAA-ATATATTTAAAATTTCTA
*
6602674 AAATTAATAAATA-A-TTAAAATTTACTA
1 AAATTTATAAATATATTTAAAATTT-CTA
6602701 AAATTTATAAAATATAT
1 AAATTTAT-AAATATAT
6602718 ATCATTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
26 8 0.22
27 10 0.28
28 8 0.22
29 10 0.28
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (28 bp):
AAATTTATAAATATATTTAAAATTTCTA
Found at i:6602789 original size:18 final size:19
Alignment explanation
Indices: 6602760--6602799 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
6602750 ATGTTGTAAC
6602760 TATTTATTATAT-ATATAAT
1 TATTTATTATATAAT-TAAT
6602779 TATTT-TTATATAATTAAT
1 TATTTATTATATAATTAAT
6602797 TAT
1 TAT
6602800 ATGTATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTATTATATAATTAAT
Found at i:6602790 original size:14 final size:14
Alignment explanation
Indices: 6602771--6602826 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
6602761 ATTTATTATA
6602771 TATATAATTATTTT
1 TATATAATTATTTT
*
6602785 TATATAATTAATTATA
1 TATATAATT-ATT-TT
* * *
6602801 TGTATAAATATATT
1 TATATAATTATTTT
6602815 TATATAATTATT
1 TATATAATTATT
6602827 CAAAATTTTG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
14 19 0.59
15 5 0.16
16 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
TATATAATTATTTT
Found at i:6602801 original size:30 final size:30
Alignment explanation
Indices: 6602765--6602824 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
6602755 GTAACTATTT
* *
6602765 ATTATATATATAATTATTTTTATATAATTA
1 ATTATATATATAAATATATTTATATAATTA
*
6602795 ATTATATGTATAAATATATTTATATAATTA
1 ATTATATATATAAATATATTTATATAATTA
6602825 TTCAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATTATATATATAAATATATTTATATAATTA
Found at i:6602806 original size:18 final size:18
Alignment explanation
Indices: 6602767--6602819 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
6602757 AACTATTTAT
* * *
6602767 TATATATATAATTATTTT
1 TATAAATATAATTATATG
6602785 TATATAAT-TAATTATATG
1 TATA-AATATAATTATATG
*
6602803 TATAAATATATTTATAT
1 TATAAATATAATTATAT
6602820 AATTATTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 3 0.10
18 24 0.83
19 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TATAAATATAATTATATG
Found at i:6603849 original size:15 final size:16
Alignment explanation
Indices: 6603829--6603860 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
6603819 CCAATTTATG
6603829 ATTGGATAGG-TTGTA
1 ATTGGATAGGTTTGTA
6603844 ATTGGATAGGTTTGTA
1 ATTGGATAGGTTTGTA
6603860 A
1 A
6603861 AAATGATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (16 bp):
ATTGGATAGGTTTGTA
Found at i:6607486 original size:20 final size:21
Alignment explanation
Indices: 6607463--6607503 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6607453 ACTCTTTCTC
*
6607463 TCTTGATT-TTTCTAATTGAT
1 TCTTGATTGTTTCCAATTGAT
6607483 TCTTGATTGTTTCCAATTGAT
1 TCTTGATTGTTTCCAATTGAT
6607504 CCTAATAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.56
Consensus pattern (21 bp):
TCTTGATTGTTTCCAATTGAT
Found at i:6612184 original size:81 final size:82
Alignment explanation
Indices: 6612092--6612256 Score: 269
Period size: 81 Copynumber: 2.0 Consensus size: 82
6612082 AAAGGTGAAG
** * *
6612092 AGAGAAGAGGAGGTTAAGAAAATTGGAAAGGGGGCAAATGATAAATTCAA-AGAGAAGAGGGGGC
1 AGAGAAGAGGAGGCCAAGAAAATTGAAAAGGGGGCAAATGATAAATTCAAGAGAGAAGAGGGGAC
*
6612156 AAGGTATAATATCTGGT
66 AAGGTACAATATCTGGT
*
6612173 AGAGAAGAGGAGGCCAGGAAAATTGAAAAGGGGGCAAATGATAAATTCAAGAGAGAAGAGGGGAC
1 AGAGAAGAGGAGGCCAAGAAAATTGAAAAGGGGGCAAATGATAAATTCAAGAGAGAAGAGGGGAC
6612238 AAGGTACAATATCTGGT
66 AAGGTACAATATCTGGT
6612255 AG
1 AG
6612257 GATTAGTAAC
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
81 46 0.60
82 31 0.40
ACGTcount: A:0.44, C:0.07, G:0.35, T:0.15
Consensus pattern (82 bp):
AGAGAAGAGGAGGCCAAGAAAATTGAAAAGGGGGCAAATGATAAATTCAAGAGAGAAGAGGGGAC
AAGGTACAATATCTGGT
Found at i:6612814 original size:12 final size:12
Alignment explanation
Indices: 6612797--6612830 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
6612787 AGTACAATAA
6612797 AATTTTATTTTT
1 AATTTTATTTTT
6612809 AATTTT-TTATTT
1 AATTTTATT-TTT
6612821 AATTTTATTT
1 AATTTTATTT
6612831 AATTAGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.10
12 16 0.80
13 2 0.10
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
AATTTTATTTTT
Found at i:6613771 original size:16 final size:15
Alignment explanation
Indices: 6613729--6613790 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
6613719 TTATTCCGAT
* *
6613729 TTCAAGTTTTTTGGA
1 TTCAAATTTTTTTGA
*
6613744 GTTTAAATTTTTTTTGAA
1 -TTCAAA-TTTTTTTG-A
* *
6613762 TTCAACTTTTTTAGA
1 TTCAAATTTTTTTGA
6613777 TTCAAATTTTTTTG
1 TTCAAATTTTTTTG
6613791 GAACGAATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
15 13 0.36
16 11 0.31
17 11 0.31
18 1 0.03
ACGTcount: A:0.24, C:0.06, G:0.11, T:0.58
Consensus pattern (15 bp):
TTCAAATTTTTTTGA
Found at i:6616605 original size:10 final size:10
Alignment explanation
Indices: 6616569--6616652 Score: 52
Period size: 10 Copynumber: 8.7 Consensus size: 10
6616559 TATCTATTTG
6616569 TGTATA-TCAA
1 TGTATATTC-A
*
6616579 TGT-TATTTA
1 TGTATATTCA
*
6616588 TGTTTATTCA
1 TGTATATTCA
* *
6616598 TATATATTAA
1 TGTATATTCA
6616608 TGT-TATTCA
1 TGTATATTCA
6616617 TGTATA-TCA
1 TGTATATTCA
*
6616626 T-TGCTATTCA
1 TGT-ATATTCA
*
6616636 TGTTTATTCA
1 TGTATATTCA
*
6616646 TATATAT
1 TGTATAT
6616653 CAGTATTGTC
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
8 1 0.02
9 20 0.35
10 35 0.61
11 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (10 bp):
TGTATATTCA
Found at i:6616633 original size:19 final size:19
Alignment explanation
Indices: 6616592--6616638 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
6616582 TATTTATGTT
* * *
6616592 TATTCATATATATTAATGT
1 TATTCATGTATATCAATGC
*
6616611 TATTCATGTATATCATTGC
1 TATTCATGTATATCAATGC
6616630 TATTCATGT
1 TATTCATGT
6616639 TTATTCATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (19 bp):
TATTCATGTATATCAATGC
Found at i:6617370 original size:22 final size:21
Alignment explanation
Indices: 6617331--6617376 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
6617321 GGTTTAGAAT
*
6617331 TTTAATAAAAATGTATATAAA
1 TTTAATAAAAATGAATATAAA
*
6617352 TTTAATAAAAATAGAATATATA
1 TTTAATAAAAAT-GAATATAAA
6617374 TTT
1 TTT
6617377 TATATTATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
TTTAATAAAAATGAATATAAA
Found at i:6621251 original size:147 final size:151
Alignment explanation
Indices: 6621063--6621422 Score: 521
Period size: 147 Copynumber: 2.3 Consensus size: 151
6621053 TCTTTGCTTG
*
6621063 CTTTTGGAAGGAGGAGAAAAGGGAATGGCAAGGCTAGTAAATTTGGAGCAATGTTACAAGTTTTC
1 CTTTTGGAAGGAGGAGAAAAGGGAATGGCAAGGCTGGTAAATTTGGAGCAATGTTACAAGTTTTC
6621128 AATAAAAGC-AAAAAAGAAAAAAAGAAGCAATCACTGTCACAGTGTCAATAAATATTTGGGAGGA
66 AATAAAAGCAAAAAAAGAAAAAAAGAAGCAATCACTGTCACAGTGTCAATAAATATTTGGGAGGA
*
6621192 TCGTACATGTCCTGG-C-ATT
131 TCGCACATGTCCTGGTCTATT
6621211 -TTTTGGAAGGAGGAGAAAAGGGAATGGCAAGGCTGGTAAATTTGGAGCAATGTTACAAGTTTTC
1 CTTTTGGAAGGAGGAGAAAAGGGAATGGCAAGGCTGGTAAATTTGGAGCAATGTTACAAGTTTTC
*
6621275 AATAAAAGCGAAAAAGAAAAAAGAATAAAAGAAGCAATCACTGTCACAGTGTCAATAAATATTTG
66 AATAAAAGC-----A-AAAAAAGAAAAAAAGAAGCAATCACTGTCACAGTGTCAATAAATATTTG
*
6621340 GGAGGATCGCACATGTCCTGGCCTTTTCTTTGCTT
125 GGAGGATCGCACATGTCCTGG-----TC--T-ATT
6621375 GCTTTTGGAAGGAGGAGAAAAGGGAATGGCAAGGCTGGTAAATTTGGA
1 -CTTTTGGAAGGAGGAGAAAAGGGAATGGCAAGGCTGGTAAATTTGGA
6621423 AGAAAAAAGA
Statistics
Matches: 189, Mismatches: 4, Indels: 20
0.89 0.02 0.09
Matches are distributed among these distances:
147 72 0.38
154 68 0.36
160 1 0.01
164 2 0.01
166 46 0.24
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (151 bp):
CTTTTGGAAGGAGGAGAAAAGGGAATGGCAAGGCTGGTAAATTTGGAGCAATGTTACAAGTTTTC
AATAAAAGCAAAAAAAGAAAAAAAGAAGCAATCACTGTCACAGTGTCAATAAATATTTGGGAGGA
TCGCACATGTCCTGGTCTATT
Found at i:6621539 original size:143 final size:143
Alignment explanation
Indices: 6621382--6621670 Score: 551
Period size: 143 Copynumber: 2.0 Consensus size: 143
6621372 CTTGCTTTTG
*
6621382 GAAGGAGGAGAAAAGGGAATGGCAAGGCTGGTAAATTTGGAAGAAAAAAGAATAAAAGAAGCAAT
1 GAAGGAGGAGAAAAGGGAATGGCAAGGCTGGTAAATTTGGAAGAAAAAAGAAAAAAAGAAGCAAT
*
6621447 CACTGTCACAGTGTCAATAAATATTTGGGAGGATCGTAAATGTCCTGGCCTTTTCTTTGCTTGCT
66 CACTGTCACAGTGTCAATAAATATTTGGGAGGATCGCAAATGTCCTGGCCTTTTCTTTGCTTGCT
6621512 TTTGGAAGGAGGA
131 TTTGGAAGGAGGA
6621525 GAAGGAGGAGAAAAGGGAATGGCAAGGCTGGTAAATTTGGAAGAAAAAAGAAAAAAAGAAGCAAT
1 GAAGGAGGAGAAAAGGGAATGGCAAGGCTGGTAAATTTGGAAGAAAAAAGAAAAAAAGAAGCAAT
*
6621590 CACTGTCACAGTGTCAATAAATATTTGGGAGGATCGCACATGTCCTGGCCTTTTCTTTGCTTGCT
66 CACTGTCACAGTGTCAATAAATATTTGGGAGGATCGCAAATGTCCTGGCCTTTTCTTTGCTTGCT
6621655 TTTGGAAGGAGGA
131 TTTGGAAGGAGGA
6621668 GAA
1 GAA
6621671 AAGGGAATGG
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
143 143 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.24
Consensus pattern (143 bp):
GAAGGAGGAGAAAAGGGAATGGCAAGGCTGGTAAATTTGGAAGAAAAAAGAAAAAAAGAAGCAAT
CACTGTCACAGTGTCAATAAATATTTGGGAGGATCGCAAATGTCCTGGCCTTTTCTTTGCTTGCT
TTTGGAAGGAGGA
Found at i:6623265 original size:15 final size:15
Alignment explanation
Indices: 6623242--6623288 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
6623232 TTTGTGAAGC
*
6623242 TTAAAAAAAATTAAA
1 TTAATAAAAATTAAA
6623257 TTAATAAAAA-T--A
1 TTAATAAAAATTAAA
*
6623269 TTAATAAAATTTAAA
1 TTAATAAAAATTAAA
6623284 TTAAT
1 TTAAT
6623289 GGATTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 10 0.37
13 1 0.04
14 1 0.04
15 15 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATAAAAATTAAA
Found at i:6624649 original size:18 final size:18
Alignment explanation
Indices: 6624619--6624665 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
6624609 CTATCTAACA
*
6624619 TAAAATGATTAATATGAC
1 TAAAATAATTAATATGAC
6624637 -AAACATAATTAATATGAC
1 TAAA-ATAATTAATATGAC
6624655 TAAAATAATTA
1 TAAAATAATTA
6624666 TTATCTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (18 bp):
TAAAATAATTAATATGAC
Found at i:6625807 original size:20 final size:21
Alignment explanation
Indices: 6625766--6625807 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6625756 AAATATTAAT
*
6625766 AATAAAATTTAAAATAACAAA
1 AATAAAATTAAAAATAACAAA
*
6625787 AATAATATTAAAAATAA-AAA
1 AATAAAATTAAAAATAACAAA
6625807 A
1 A
6625808 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AATAAAATTAAAAATAACAAA
Found at i:6627959 original size:31 final size:30
Alignment explanation
Indices: 6627922--6628033 Score: 84
Period size: 30 Copynumber: 3.6 Consensus size: 30
6627912 AACCCTATGA
* *
6627922 AAAAATTTCT-TATCCTTTGAAAAAATTAATT
1 AAAAATTTCTATATCATTT--AAAAATTAAAT
*
6627953 AAAAATTTCTATATTATTTAAAAATTAAAT
1 AAAAATTTCTATATCATTTAAAAATTAAAT
** * * * *
6627983 AAAAAACTCCATAACATTTTAAAATATCAAGT
1 AAAAATTTCTATATCA-TTTAAAA-ATTAAAT
6628015 AAAAACTTTC-ATATCATTT
1 AAAAA-TTTCTATATCATTT
6628034 TGAAAATTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
30 21 0.33
31 20 0.31
32 21 0.33
33 2 0.03
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAAATTTCTATATCATTTAAAAATTAAAT
Found at i:6631172 original size:20 final size:21
Alignment explanation
Indices: 6631143--6631191 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
6631133 TAATATTTAT
*
6631143 TTTTAATTAT-ATTTAATAT-A
1 TTTTATTTATAATTT-ATATCA
*
6631163 TTTTATTTATAATTTTTATCA
1 TTTTATTTATAATTTATATCA
6631184 TTTTATTT
1 TTTTATTT
6631192 TAGGTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATTTATAATTTATATCA
Found at i:6633146 original size:2 final size:2
Alignment explanation
Indices: 6633139--6633175 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
6633129 ACCAGGACCA
6633139 AT AT AT AT AT AT AT A- 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
6633176 TTCTCTATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6634265 original size:18 final size:17
Alignment explanation
Indices: 6634242--6634275 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6634232 TTTTTCTTTT
*
6634242 TTTATCATATATTTTAAA
1 TTTATCAAAT-TTTTAAA
6634260 TTTATCAAATTTTTAA
1 TTTATCAAATTTTTAA
6634276 TTAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATCAAATTTTTAAA
Found at i:6634304 original size:29 final size:27
Alignment explanation
Indices: 6634272--6634326 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
6634262 TATCAAATTT
*
6634272 TTAATTAATTTTTTTTATGATTTGATATC
1 TTAATT-ATTTTATTTAT-ATTTGATATC
*
6634301 TTAATTATTTTATTTATATTTTATAT
1 TTAATTATTTTATTTATATTTGATAT
6634327 ATTTTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
28 10 0.42
29 6 0.25
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
TTAATTATTTTATTTATATTTGATATC
Found at i:6637345 original size:115 final size:116
Alignment explanation
Indices: 6637141--6637355 Score: 272
Period size: 115 Copynumber: 1.9 Consensus size: 116
6637131 GAGGCCCGAT
** * * ***
6637141 TTAAATATAAGACTATCAAAAATTAATTATTTACTAGATGTAGGATAGCACCATTTTAATGGACC
1 TTAAATATAAGACTAAAAAAAATTAATCATTTACTAGATGTAGGATAGCACCACTTTAACAAACC
* * **
6637206 CCCATCACGTGTAGTTAGAAGTGGAAAAA-CTTATTTTGTGACATCCTAAC
66 CCCATCACATATAGGCAGAAGTGGAAAAAGCTTATTTTGTGACATCCTAAC
* * *
6637256 TTAAATATAAGACTAAAAAAAATT-ATACATTTATTAGATGTGGGATAGCACCACTTTAACAAAG
1 TTAAATATAAGACTAAAAAAAATTAAT-CATTTACTAGATGTAGGATAGCACCACTTTAACAAAC
*
6637320 CCCCATCACATATAGGCAGATGTGGAAAAAGCTTAT
65 CCCCATCACATATAGGCAGAAGTGGAAAAAGCTTAT
6637356 CACATAATAG
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
114 2 0.02
115 76 0.92
116 5 0.06
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (116 bp):
TTAAATATAAGACTAAAAAAAATTAATCATTTACTAGATGTAGGATAGCACCACTTTAACAAACC
CCCATCACATATAGGCAGAAGTGGAAAAAGCTTATTTTGTGACATCCTAAC
Done.