Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 80 of 100
Found at i:14296690 original size:32 final size:31
Alignment explanation
Indices: 14296652--14296734 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
14296642 TATCATTTAA
*
14296652 AAAAATTAAGTAAAAATTTTTATATCGGTTT
1 AAAAATTAAGTAAAAATTTTTATATCGGGTT
* * *
14296683 AAGAAATTAAATTAAAA-CTTTATATCGGGTT
1 AA-AAATTAAGTAAAAATTTTTATATCGGGTT
*
14296714 AAAATATTATGTAAAAATTTT
1 AAAA-ATTAAGTAAAAATTTT
14296735 CAAATCATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
30 2 0.05
31 25 0.61
32 14 0.34
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.40
Consensus pattern (31 bp):
AAAAATTAAGTAAAAATTTTTATATCGGGTT
Found at i:14298349 original size:35 final size:35
Alignment explanation
Indices: 14298298--14298374 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
14298288 GTTTAATTAT
* * ** *
14298298 ACATGTGAAGTCAGTTGTAGTTTTATGCTTAGAAA
1 ACATTTGAAGTCAGTTGTAGGTTTATGCCCAAAAA
14298333 ACATTTGAAGTCAGTTGTAGGTTTATGCCCAAAAA
1 ACATTTGAAGTCAGTTGTAGGTTTATGCCCAAAAA
14298368 ACATTTG
1 ACATTTG
14298375 GTTTATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (35 bp):
ACATTTGAAGTCAGTTGTAGGTTTATGCCCAAAAA
Found at i:14301450 original size:12 final size:12
Alignment explanation
Indices: 14301433--14301520 Score: 52
Period size: 12 Copynumber: 7.2 Consensus size: 12
14301423 CTATAGAAAC
14301433 ACCATTCAGCAA
1 ACCATTCAGCAA
14301445 ACCATTCAGCAA
1 ACCATTCAGCAA
*** *
14301457 TGTGA-TCAGAAA
1 -ACCATTCAGCAA
*
14301469 CACCATCCAGCAA
1 -ACCATTCAGCAA
* **
14301482 ACAATTCAAAAA
1 ACCATTCAGCAA
* *
14301494 TATCATTCAGTAA
1 -ACCATTCAGCAA
14301507 ACCATTCAGCAA
1 ACCATTCAGCAA
14301519 AC
1 AC
14301521 TAATATCATA
Statistics
Matches: 53, Mismatches: 20, Indels: 6
0.67 0.25 0.08
Matches are distributed among these distances:
12 39 0.74
13 14 0.26
ACGTcount: A:0.44, C:0.27, G:0.09, T:0.19
Consensus pattern (12 bp):
ACCATTCAGCAA
Found at i:14301468 original size:37 final size:38
Alignment explanation
Indices: 14301427--14301520 Score: 111
Period size: 37 Copynumber: 2.5 Consensus size: 38
14301417 ATCATACTAT
* ** * *
14301427 AGAAACACCATTCAGCAAACCATTCAGCAATGTGA-TC
1 AGAAACACCATTCAGCAAACAATTCAAAAATATCATTC
*
14301464 AGAAACACCATCCAGCAAACAATTCAAAAATATCATTC
1 AGAAACACCATTCAGCAAACAATTCAAAAATATCATTC
*
14301502 AGTAA-ACCATTCAGCAAAC
1 AGAAACACCATTCAGCAAAC
14301521 TAATATCATA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
37 42 0.88
38 6 0.12
ACGTcount: A:0.46, C:0.27, G:0.10, T:0.18
Consensus pattern (38 bp):
AGAAACACCATTCAGCAAACAATTCAAAAATATCATTC
Found at i:14308673 original size:19 final size:19
Alignment explanation
Indices: 14308651--14308688 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
14308641 AAAATACAAA
14308651 TTAA-ACTTGTGGATGGCTT
1 TTAACACTT-TGGATGGCTT
*
14308670 TTAACAGTTTGGATGGCTT
1 TTAACACTTTGGATGGCTT
14308689 CAATACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (19 bp):
TTAACACTTTGGATGGCTT
Found at i:14311756 original size:21 final size:21
Alignment explanation
Indices: 14311730--14311772 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
14311720 CTCTCCAGAG
14311730 CTGTGCTTGACTATTATAATA
1 CTGTGCTTGACTATTATAATA
14311751 CTGTGCTTGACTATTATAATA
1 CTGTGCTTGACTATTATAATA
14311772 C
1 C
14311773 AATTTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (21 bp):
CTGTGCTTGACTATTATAATA
Found at i:14313141 original size:32 final size:32
Alignment explanation
Indices: 14313104--14313178 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
14313094 ATTATCTCTT
*
14313104 AATTTTAAAGAAATATTGAATATTGATGTTTA
1 AATTTTAAAAAAATATTGAATATTGATGTTTA
* *
14313136 GATTTTAAAAAAATATTGAATATTGCTGTTTA
1 AATTTTAAAAAAATATTGAATATTGATGTTTA
14313168 AATTTTAAAAA
1 AATTTTAAAAA
14313179 TTTTTAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.43
Consensus pattern (32 bp):
AATTTTAAAAAAATATTGAATATTGATGTTTA
Found at i:14318123 original size:26 final size:25
Alignment explanation
Indices: 14318083--14318139 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
14318073 TTGTTCGTGA
* *
14318083 ATATTAAATAAACATGTTCACGAAT
1 ATATTAAACAAACATGTTCACGAAC
*
14318108 ATATGTAAACAAACATGTTCATGAAC
1 ATAT-TAAACAAACATGTTCACGAAC
14318134 ATATTA
1 ATATTA
14318140 TAAATTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (25 bp):
ATATTAAACAAACATGTTCACGAAC
Found at i:14318254 original size:26 final size:26
Alignment explanation
Indices: 14318206--14318255 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
14318196 GATTAATTAT
* * *
14318206 AAATTATAAAATCCTATATAAAAATG
1 AAATTAAAAAATCCTAAAAAAAAATG
*
14318232 AAATTAAAAAATCTTAAAAAAAAA
1 AAATTAAAAAATCCTAAAAAAAAA
14318256 CCTAAAACCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (26 bp):
AAATTAAAAAATCCTAAAAAAAAATG
Found at i:14318349 original size:19 final size:18
Alignment explanation
Indices: 14318295--14318350 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
14318285 AACAACTTTT
14318295 AAAAATTAAGTGATCTTA
1 AAAAATTAAGTGATCTTA
* * * *
14318313 ATCAAA-GAACTTATCTTA
1 A-AAAATTAAGTGATCTTA
14318331 CAAAAATTAAGTGATCTTA
1 -AAAAATTAAGTGATCTTA
14318350 A
1 A
14318351 CCATACAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 6
0.66 0.20 0.15
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (18 bp):
AAAAATTAAGTGATCTTA
Found at i:14322611 original size:23 final size:23
Alignment explanation
Indices: 14322585--14322632 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
14322575 CATAGTATTA
*
14322585 TTATAAGCCTATACTCGGTGAAT
1 TTATAAACCTATACTCGGTGAAT
*
14322608 TTATAAACCTATACTCTGTGAAT
1 TTATAAACCTATACTCGGTGAAT
14322631 TT
1 TT
14322633 TCTTCTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATAAACCTATACTCGGTGAAT
Found at i:14327171 original size:114 final size:115
Alignment explanation
Indices: 14326962--14327193 Score: 367
Period size: 114 Copynumber: 2.0 Consensus size: 115
14326952 TCAATTACAA
* *
14326962 ACTAATAAGGCACACTAATCCTTATCCATTATAGGCTACAAACAAAAAATGTTCAATCTGAGTGG
1 ACTAATAAGGCACACTAATCCTTACCCATTATAGGCTACAAACAAAAAATGTTCAATCTAAGTGG
* *
14327027 AAGTGTTTCACTAGCAAATACAGAAGTTATCACATCACAAAAATGTAGCT
66 AAGTGTTTCACTAGCAAATACAAAAGTTATCACATCACAAAAATGTAACT
* * **
14327077 ACTAATAA-GCACACTAATCCTTACCCATTATGGGCTACAAATAAAAAATGTTTGATCTAAGTGG
1 ACTAATAAGGCACACTAATCCTTACCCATTATAGGCTACAAACAAAAAATGTTCAATCTAAGTGG
* *
14327141 AAGTGTTTCACTAGCAAATGCAAAAGTTATCACATCACGAAAATGTAACT
66 AAGTGTTTCACTAGCAAATACAAAAGTTATCACATCACAAAAATGTAACT
14327191 ACT
1 ACT
14327194 TCACTTCTTC
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
114 99 0.93
115 8 0.07
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (115 bp):
ACTAATAAGGCACACTAATCCTTACCCATTATAGGCTACAAACAAAAAATGTTCAATCTAAGTGG
AAGTGTTTCACTAGCAAATACAAAAGTTATCACATCACAAAAATGTAACT
Found at i:14328045 original size:11 final size:11
Alignment explanation
Indices: 14328024--14328062 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
14328014 ATTTTTCTTG
14328024 AAATATTATTTT
1 AAAT-TTATTTT
14328036 AAATTTATTTT
1 AAATTTATTTT
*
14328047 AAATTAATTTTT
1 AAATTTA-TTTT
14328059 AAAT
1 AAAT
14328063 AATATTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 13 0.52
12 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AAATTTATTTT
Found at i:14328065 original size:11 final size:13
Alignment explanation
Indices: 14328030--14328070 Score: 54
Period size: 11 Copynumber: 3.5 Consensus size: 13
14328020 CTTGAAATAT
14328030 TATTTTAAATT--
1 TATTTTAAATTAA
14328041 TATTTTAAATTAA
1 TATTTTAAATTAA
14328054 T-TTTTAAA-TAA
1 TATTTTAAATTAA
14328065 TATTTT
1 TATTTT
14328071 TCATAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 15 0.56
12 11 0.41
13 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTTAAATTAA
Found at i:14328070 original size:12 final size:12
Alignment explanation
Indices: 14328024--14328070 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
14328014 ATTTTTCTTG
*
14328024 AAATATTATTTT
1 AAATAATATTTT
*
14328036 AAAT-TTATTTT
1 AAATAATATTTT
14328047 AAATTAAT-TTTT
1 AAA-TAATATTTT
14328059 AAATAATATTTT
1 AAATAATATTTT
14328071 TCATAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 14 0.45
12 16 0.52
13 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:14328460 original size:19 final size:19
Alignment explanation
Indices: 14328433--14328494 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
14328423 AGGTTTTTCA
*
14328433 TTTAGGGTTTCACCTAGGG
1 TTTAAGGTTTCACCTAGGG
* *
14328452 TTTAAGGTTTTACTTAGGG
1 TTTAAGGTTTCACCTAGGG
* * *
14328471 CTTTCAGGTTTCGCCTAAGG
1 -TTTAAGGTTTCACCTAGGG
14328491 TTTA
1 TTTA
14328495 GAATTTCACT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.42
Consensus pattern (19 bp):
TTTAAGGTTTCACCTAGGG
Found at i:14328796 original size:26 final size:25
Alignment explanation
Indices: 14328763--14328811 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
14328753 TCATTAGAAT
14328763 TTTATTATTCTTATTATTTATTTAGC
1 TTTATTATTCTTATTA-TTATTTAGC
* *
14328789 TTTATTATTTTTTTTATTATTTA
1 TTTATTATTCTTATTATTATTTA
14328812 ATAATTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTATTATTCTTATTATTATTTAGC
Found at i:14328914 original size:3 final size:3
Alignment explanation
Indices: 14328908--14328941 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
14328898 TTTTTTAACG
14328908 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
14328942 AATATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:14329028 original size:3 final size:3
Alignment explanation
Indices: 14329022--14329053 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
14329012 AAAACAACAA
*
14329022 AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
14329054 ATCCAACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:14337114 original size:20 final size:21
Alignment explanation
Indices: 14337073--14337120 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
14337063 AACTATTAAA
14337073 ATTTTTTTTAAACATTTATTT
1 ATTTTTTTTAAACATTTATTT
*
14337094 ATTTATTTTT-AA-ATTTCTTT
1 ATTT-TTTTTAAACATTTATTT
14337114 ATTTTTT
1 ATTTTTT
14337121 GAATTTGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 3 0.12
20 11 0.44
21 6 0.24
22 5 0.20
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTTTTTAAACATTTATTT
Found at i:14343244 original size:135 final size:135
Alignment explanation
Indices: 14343002--14343256 Score: 420
Period size: 135 Copynumber: 1.9 Consensus size: 135
14342992 TTAGCAGTTT
* * * * *
14343002 TATTTAGTTAAAACAAATAATATCTCGTAAGTTAGTTTTAGTTGCCTACTTACCTAGAATTTTTC
1 TATTTAGTTAAAACAAACAATATCTCATAAGTTAGTTTCACTTGCCTACTCACCTAGAATTTTTC
*
14343067 TTATCCTCAGAATTAGAAGGATATTTGTTTAGTCCTCTAAACATGTATCAAAACAACTTGTGTTT
66 TTATCCTCAGAATTAGAAGGATATTTGTTTAGTCCTCTAAACATGTATAAAAACAACTTGTGTTT
14343132 GCATC
131 GCATC
* *
14343137 TATTTAGTTAAAACAAACAATATCTCATAAGTTGGTTTCACTTGCTTACTCACCTAGAATTTTTC
1 TATTTAGTTAAAACAAACAATATCTCATAAGTTAGTTTCACTTGCCTACTCACCTAGAATTTTTC
* *
14343202 TTATCCTTAGAATTAGAAGTATATTTGTTTAGTCCTCTAAACATGTATAAAAACA
66 TTATCCTCAGAATTAGAAGGATATTTGTTTAGTCCTCTAAACATGTATAAAAACA
14343257 CCTTATATTT
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
135 110 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (135 bp):
TATTTAGTTAAAACAAACAATATCTCATAAGTTAGTTTCACTTGCCTACTCACCTAGAATTTTTC
TTATCCTCAGAATTAGAAGGATATTTGTTTAGTCCTCTAAACATGTATAAAAACAACTTGTGTTT
GCATC
Found at i:14348924 original size:26 final size:26
Alignment explanation
Indices: 14348876--14349027 Score: 117
Period size: 26 Copynumber: 5.8 Consensus size: 26
14348866 ACTGTAGACA
**
14348876 CCCATTAGTGTCTGGGCTTAATTAGG
1 CCCATTAGTGTCTGGGCCCAATTAGG
14348902 CCCATTAGTGTCTGGGCCCAATTAGAG
1 CCCATTAGTGTCTGGGCCCAATTAG-G
** * * *
14348929 TTCATTTGTGTTTGGGCCCAATTAAG
1 CCCATTAGTGTCTGGGCCCAATTAGG
* *
14348955 CCCATTGGTGT-TCGAGCCCAATTAGG
1 CCCATTAGTGTCT-GGGCCCAATTAGG
** * *** *
14348981 CTTATTGGTGTCCAAGCCTAATTAGG
1 CCCATTAGTGTCTGGGCCCAATTAGG
* *
14349007 CCCATTAATGTCTAGGCCCAA
1 CCCATTAGTGTCTGGGCCCAA
14349028 CAAAGCCCAT
Statistics
Matches: 99, Mismatches: 24, Indels: 6
0.77 0.19 0.05
Matches are distributed among these distances:
25 1 0.01
26 77 0.78
27 21 0.21
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.32
Consensus pattern (26 bp):
CCCATTAGTGTCTGGGCCCAATTAGG
Found at i:14349026 original size:52 final size:53
Alignment explanation
Indices: 14348894--14349027 Score: 130
Period size: 52 Copynumber: 2.5 Consensus size: 53
14348884 TGTCTGGGCT
* * ****
14348894 TAATTAGGCCCATTAGTGTCTGGGCCCAATTAGAGTTCATTTGTGTTTGGGCC
1 TAATTAGGCCCATTAGTGTCTAGGCCCAATTAGAGTTCATTGGTGTCCAAGCC
* * * *
14348947 CAATTAAGCCCATTGGTGT-TCGAGCCCAATTAG-GCTT-ATTGGTGTCCAAGCC
1 TAATTAGGCCCATTAGTGTCTAG-GCCCAATTAGAG-TTCATTGGTGTCCAAGCC
*
14348999 TAATTAGGCCCATTAATGTCTAGGCCCAA
1 TAATTAGGCCCATTAGTGTCTAGGCCCAA
14349028 CAAAGCCCAT
Statistics
Matches: 64, Mismatches: 14, Indels: 7
0.75 0.16 0.08
Matches are distributed among these distances:
52 34 0.53
53 30 0.47
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (53 bp):
TAATTAGGCCCATTAGTGTCTAGGCCCAATTAGAGTTCATTGGTGTCCAAGCC
Found at i:14349089 original size:3 final size:3
Alignment explanation
Indices: 14349083--14349184 Score: 63
Period size: 3 Copynumber: 34.3 Consensus size: 3
14349073 TTAATGTTAC
14349083 TAT TAT T-T TAT TAT TAT TAT TAAT TAT TAT TA- TACT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TA-T TAT TAT TAT
* * * * * *
14349127 TTT TAT T-T TCTT TAG TAT TTT TGT GGAT ATAT TAT TAT TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TAT TAT
14349174 T-T TAT T-T TAT T
1 TAT TAT TAT TAT T
14349185 TTCATTTTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
2 12 0.15
3 57 0.73
4 9 0.12
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:14349111 original size:16 final size:16
Alignment explanation
Indices: 14349070--14349115 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 16
14349060 TAACTTTTTT
* *
14349070 TTATTAA-TGTTACTA
1 TTATTAATTATTATTA
14349085 TTATT--TTATTATTA
1 TTATTAATTATTATTA
14349099 TTATTAATTATTATTA
1 TTATTAATTATTATTA
14349115 T
1 T
14349116 ACTTTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 11 0.42
15 5 0.19
16 10 0.38
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
TTATTAATTATTATTA
Found at i:14349221 original size:13 final size:13
Alignment explanation
Indices: 14349203--14349229 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14349193 TTCTCTCCTC
14349203 TTCTTTTCTTTTT
1 TTCTTTTCTTTTT
14349216 TTCTTTTCTTTTT
1 TTCTTTTCTTTTT
14349229 T
1 T
14349230 GTTCAATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTCTTTTCTTTTT
Found at i:14361346 original size:119 final size:119
Alignment explanation
Indices: 14361132--14361637 Score: 429
Period size: 119 Copynumber: 4.3 Consensus size: 119
14361122 CATTATCCAC
* * * * *
14361132 TCACTTGATCCTGGCTT-AGTCCAGATCATCTCTTATGATTCGTGGTTTTATCCCGATTATTTAT
1 TCACTTGATCTTGG-TTCAGTCCACATCATTTCTTATGATTCGTGGTTTCATCCCGATCATTTAT
* * **
14361196 TTTCGACCTCAACTT-GATCCTTGTCACTTTATTTTGACTCGTGGTTTTGTCCTGG
65 TTTAGACCTCAACTTAG-TCCTGGTCACTTTATTTTGACTCGTGGTTTCATCCTGG
* * * *
14361251 TCACTTGATCTTGGTTCAGTCTACATCATTTCTTATGATACATGGTTTCATCTCGATCATTTATT
1 TCACTTGATCTTGGTTCAGTCCACATCATTTCTTATGATTCGTGGTTTCATCCCGATCATTTATT
* * * * * * * * *
14361316 TTAGACCTCGACTTGGTCTTGGTCATTTTATTCTAACTCATGGTTTCATCCCGA
66 TTAGACCTCAACTTAGTCCTGGTCACTTTATTTTGACTCGTGGTTTCATCCTGG
* * * * *
14361370 TCACTTGA-CTTGGTTTAGTCCAAATCATTTGTTGTGATTC-TTGTTGTCATCCCGATCATTTAT
1 TCACTTGATCTTGGTTCAGTCCACATCATTTCTTATGATTCGTGGTT-TCATCCCGATCATTTAT
** * * * * * *
14361433 TTTTTACCTTAACTCAGTCCTGTTCACCTTATTTTGACTTGTGGTTTCATCTTGG
65 TTTAGACCTCAACTTAGTCCTGGTCACTTTATTTTGACTCGTGGTTTCATCCTGG
* * * * * *
14361488 TCACTTGATCTTGGCTCAATCTAGC-TCATCTT-TTATGATTTGTGATTTCATCCTGATCATTTA
1 TCACTTGATCTTGGTTCAGTCCA-CATCAT-TTCTTATGATTCGTGGTTTCATCCCGATCATTTA
* ** ** *
14361551 CTTTCA-ACCTGGACTTAGTCCTGGTCGTTTTATTTTGACTTGTGGTTTCAT-CTCGG
64 -TTTTAGACCTCAACTTAGTCCTGGTCACTTTATTTTGACTCGTGGTTTCATCCT-GG
*
14361607 TTACTTGATCTTGGCTT-AGTCCA-AGTCATTT
1 TCACTTGATCTTGG-TTCAGTCCACA-TCATTT
14361638 TTCAGATTTA
Statistics
Matches: 305, Mismatches: 70, Indels: 25
0.76 0.17 0.06
Matches are distributed among these distances:
117 4 0.01
118 93 0.30
119 198 0.65
120 10 0.03
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (119 bp):
TCACTTGATCTTGGTTCAGTCCACATCATTTCTTATGATTCGTGGTTTCATCCCGATCATTTATT
TTAGACCTCAACTTAGTCCTGGTCACTTTATTTTGACTCGTGGTTTCATCCTGG
Found at i:14361584 original size:237 final size:238
Alignment explanation
Indices: 14361132--14361637 Score: 560
Period size: 237 Copynumber: 2.1 Consensus size: 238
14361122 CATTATCCAC
* * * * *
14361132 TCACTTGATCCTGGCTTAGTCCAGATCATCTCTTATGATTCGTGGTTTTATCCCGATTATTTATT
1 TCACTTGATCTTGGCTTAGTCCAAATCATTTCTTATGATTCGTGGTTTCATCCCGATCATTTATT
* * **
14361197 TTCGACCTCAACTTGATCCTTGTCACTTTATTTTGACTCGTGGTTTTGTCCTGGTCACTTGATCT
66 TTCGACCTCAACTAGATCCTTGTCACCTTATTTTGACTCGTGGTTTCATCCTGGTCACTTGATCT
* * * *
14361262 TGGTTCAGTCTACATCATTTCTTATGATACATGGTTTCATCTCGATCATTTATTTTAGACCTCGA
131 TGGCTCAATCTACATCATTTCTTATGATACATGATTTCATCTCGATCATTTATTTCAGACCTCGA
* *
14361327 CTTGGTCTTGGTCATTTTATTCTAACTCATGGTTTCATCCCGA
196 CTTAGTCCTGGTCATTTTATTCTAACTCATGGTTTCATCCCGA
* * * *
14361370 TCACTTGA-CTTGGTTTAGTCCAAATCATTTGTTGTGATTC-TTGTTGTCATCCCGATCATTTAT
1 TCACTTGATCTTGGCTTAGTCCAAATCATTTCTTATGATTCGTGGTT-TCATCCCGATCATTTAT
** * * *
14361433 TTTTTACCTTAACTCAG-TCC-TGTTCACCTTATTTTGACTTGTGGTTTCATCTTGGTCACTTGA
65 TTTCGACCTCAACT-AGATCCTTG-TCACCTTATTTTGACTCGTGGTTTCATCCTGGTCACTTGA
***
14361496 TCTTGGCTCAATCTAGC-TCATCTT-TTATGATTTGTGATTTCATC-CTGATCATTTACTTTCA-
128 TCTTGGCTCAATCTA-CATCAT-TTCTTATGATACATGATTTCATCTC-GATCATTTA-TTTCAG
* * * * ** * *
14361557 ACCTGGACTTAGTCCTGGTCGTTTTATTTTGACTTGTGGTTTCATCTCGG
189 ACCTCGACTTAGTCCTGGTCATTTTATTCTAACTCATGGTTTCATCCCGA
* *
14361607 TTACTTGATCTTGGCTTAGTCCAAGTCATTT
1 TCACTTGATCTTGGCTTAGTCCAAATCATTT
14361638 TTCAGATTTA
Statistics
Matches: 222, Mismatches: 38, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
236 7 0.03
237 179 0.81
238 36 0.16
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (238 bp):
TCACTTGATCTTGGCTTAGTCCAAATCATTTCTTATGATTCGTGGTTTCATCCCGATCATTTATT
TTCGACCTCAACTAGATCCTTGTCACCTTATTTTGACTCGTGGTTTCATCCTGGTCACTTGATCT
TGGCTCAATCTACATCATTTCTTATGATACATGATTTCATCTCGATCATTTATTTCAGACCTCGA
CTTAGTCCTGGTCATTTTATTCTAACTCATGGTTTCATCCCGA
Found at i:14361810 original size:26 final size:26
Alignment explanation
Indices: 14361781--14361866 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 26
14361771 TTCATTTGTA
14361781 TCTGGGCCTAATTAAGCCCATTGATG
1 TCTGGGCCTAATTAAGCCCATTGATG
* * **
14361807 TCTGAGTCTAATTAAGCTTATT-AGTG
1 TCTGGGCCTAATTAAGCCCATTGA-TG
* * *
14361833 TTTGGGCCCAATTAGGCCCATTGATG
1 TCTGGGCCTAATTAAGCCCATTGATG
*
14361859 TCTAGGCC
1 TCTGGGCC
14361867 CAACTAGGTC
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
25 1 0.02
26 43 0.96
27 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (26 bp):
TCTGGGCCTAATTAAGCCCATTGATG
Found at i:14361916 original size:3 final size:3
Alignment explanation
Indices: 14361908--14362001 Score: 54
Period size: 3 Copynumber: 30.7 Consensus size: 3
14361898 AGGCTAACTC
* *
14361908 TTA TTA TTA TTA TTA TTA TTA TTTA TT- TTC TT- TGGTA TT- TCTG TGTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T--TA TTA T-TA T-TA
* *
14361955 TATA TT- TATA TTA TTA TTA TTA TTA CTA TTA TTA GTA TTA TT- TTA
1 T-TA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14362000 TT
1 TT
14362002 TTCGTTTCTT
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
2 7 0.09
3 55 0.74
4 11 0.15
5 1 0.01
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:14362027 original size:23 final size:24
Alignment explanation
Indices: 14361995--14362045 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
14361985 ATTAGTATTA
14361995 TTTTATTTTCGTTTCTTTCTTTCC
1 TTTTATTTTCGTTTCTTTCTTTCC
* *
14362019 TTTT-TTTTCTTTTTTTTCTTTCC
1 TTTTATTTTCGTTTCTTTCTTTCC
14362042 TTTT
1 TTTT
14362046 CTGTTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (24 bp):
TTTTATTTTCGTTTCTTTCTTTCC
Found at i:14362866 original size:5 final size:5
Alignment explanation
Indices: 14362851--14362881 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
14362841 TCTCTTTTCC
14362851 ATTTT ATTTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT A-TTTT ATTTT ATTTT ATTTT ATTTT
14362882 TAACCTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
ATTTT
Found at i:14362890 original size:21 final size:21
Alignment explanation
Indices: 14362851--14362903 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
14362841 TCTCTTTTCC
***
14362851 ATTTTATTTTTATTTTATTTT
1 ATTTTATTTTTAACCTATTTT
14362872 ATTTTATTTTTAACCTATTTT
1 ATTTTATTTTTAACCTATTTT
14362893 -TTATTATTTTT
1 ATT-TTATTTTT
14362904 TGGTTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (21 bp):
ATTTTATTTTTAACCTATTTT
Found at i:14365882 original size:18 final size:17
Alignment explanation
Indices: 14365861--14365937 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 17
14365851 TTGGTTCAGA
14365861 GTTTAAGTTTAGTTTAGG
1 GTTTAAGTTT-GTTTAGG
*
14365879 GTTTAGGTTTTGTTTAGG
1 GTTTAAG-TTTGTTTAGG
* *
14365897 GTTTAGGGTTTGTTTAAG
1 GTTTA-AGTTTGTTTAGG
* *
14365915 ATTTAAGGTTTCTTTTAGG
1 GTTTAA-GTTT-GTTTAGG
14365934 GTTT
1 GTTT
14365938 GGGGTTAGGG
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
18 35 0.73
19 13 0.27
ACGTcount: A:0.17, C:0.01, G:0.29, T:0.53
Consensus pattern (17 bp):
GTTTAAGTTTGTTTAGG
Found at i:14365907 original size:25 final size:25
Alignment explanation
Indices: 14365817--14365907 Score: 73
Period size: 25 Copynumber: 3.7 Consensus size: 25
14365807 GGTTCGAGTT
* * * *
14365817 TTTAAGGTTTGGGGTCTAGGTTAATG
1 TTTAGGGTTTAGGGTTTAGGTT-TTG
* *
14365843 TTTAGGGTTT--GGTTCAGAGTTTAAG
1 TTTAGGGTTTAGGGTTTAG-GTTT-TG
14365868 TTTA--GTTTAGGGTTTAGGTTTTG
1 TTTAGGGTTTAGGGTTTAGGTTTTG
14365891 TTTAGGGTTTAGGGTTT
1 TTTAGGGTTTAGGGTTT
14365908 GTTTAAGATT
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
23 9 0.17
24 9 0.17
25 25 0.48
26 9 0.17
ACGTcount: A:0.16, C:0.02, G:0.33, T:0.48
Consensus pattern (25 bp):
TTTAGGGTTTAGGGTTTAGGTTTTG
Found at i:14366170 original size:49 final size:49
Alignment explanation
Indices: 14366094--14366189 Score: 111
Period size: 49 Copynumber: 2.0 Consensus size: 49
14366084 TGTGATAAAA
* ** * *
14366094 ACAAATAACAAAAATGCCATTGGTAAAATTATAACTATTGATGCATGTG
1 ACAAATAACAAAAATGCCATTGATAAAAGAATAAATATAGATGCATGTG
** * *
14366143 ACAAATAATGAAAATGGCTTTGATAAAAGAATAAATATAGATGCATG
1 ACAAATAACAAAAATGCCATTGATAAAAGAATAAATATAGATGCATG
14366190 AAAAATGCAC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (49 bp):
ACAAATAACAAAAATGCCATTGATAAAAGAATAAATATAGATGCATGTG
Found at i:14369003 original size:49 final size:48
Alignment explanation
Indices: 14368852--14369026 Score: 131
Period size: 49 Copynumber: 3.6 Consensus size: 48
14368842 AAATAAGGGT
** * *
14368852 TCCTATAAACATAGGTTAGGAAACTTTAAAAATCAATTT-GAAAAAGG-T
1 TCCTATAAACATAGG-TAGG-AACTTTAAAAATCTCTTTGGGAAAAGGAC
* *** * **
14368900 TCCCAT-TTGATAAGTAGGGAACTTTAAAAATCTCTTTGGGAAAAGGGT
1 TCCTATAAACATAGGTA-GGAACTTTAAAAATCTCTTTGGGAAAAGGAC
* ** * *
14368948 TTCTATAAATGTAGGTAGAGAACTTTAAAAATCTCTTTTGGAAAATGAC
1 TCCTATAAACATAGGTAG-GAACTTTAAAAATCTCTTTGGGAAAAGGAC
*
14368997 TCCTATAGACATAGGTAGGAAACTTTAAAA
1 TCCTATAAACATAGGTAGG-AACTTTAAAA
14369027 CCTCAATTTG
Statistics
Matches: 98, Mismatches: 23, Indels: 11
0.74 0.17 0.08
Matches are distributed among these distances:
46 18 0.18
47 13 0.13
48 12 0.12
49 55 0.56
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (48 bp):
TCCTATAAACATAGGTAGGAACTTTAAAAATCTCTTTGGGAAAAGGAC
Found at i:14369151 original size:50 final size:50
Alignment explanation
Indices: 14368969--14369339 Score: 375
Period size: 49 Copynumber: 7.5 Consensus size: 50
14368959 TAGGTAGAGA
* * * * **
14368969 ACTTT-AAAAATCTC-TTTTGGAAAA-TGACTCCTATAGACATAGGTAGGAA
1 ACTTTAAAAAATCTCAATTT-GAAAAGTG-CTCTTATAGACATAGGCAAGTG
*
14369018 ACTTT--AAAACCTCAATTTGAAAAGTGCTCTTATA-AGCATAGGCAAGTG
1 ACTTTAAAAAATCTCAATTTGAAAAGTGCTCTTATAGA-CATAGGCAAGTG
* * * *
14369066 AC-TTCAAAAATCTTAATTTGAAAAGTGCTCTTATAGACATAGGTATGTG
1 ACTTTAAAAAATCTCAATTTGAAAAGTGCTCTTATAGACATAGGCAAGTG
* * * * *
14369115 ACTTTAAAAAATCTCAAATTGAAAACTGATCCTATAGACATAGGTAAGTG
1 ACTTTAAAAAATCTCAATTTGAAAAGTGCTCTTATAGACATAGGCAAGTG
* * *
14369165 ACTTTAAAAAAATCTCAATTTGAAAAGTGCTCTTATAGGCTTAGGCAAGTA
1 ACTTT-AAAAAATCTCAATTTGAAAAGTGCTCTTATAGACATAGGCAAGTG
* **
14369216 ACTTT--AAAATCTCAATTTGAAAAGTGCTC-TATAGACACATACAAGTG
1 ACTTTAAAAAATCTCAATTTGAAAAGTGCTCTTATAGACATAGGCAAGTG
* * * * *
14369263 ACTTTAAAAAAACTCAATTTGAAAAGTGCTCTTATAAACATAGACAGGTA
1 ACTTTAAAAAATCTCAATTTGAAAAGTGCTCTTATAGACATAGGCAAGTG
*
14369313 ACTTTAAAAGAATTTCAATTTGAAAAG
1 ACTTTAAAA-AATCTCAATTTGAAAAG
14369340 CTTTTAAAGT
Statistics
Matches: 270, Mismatches: 40, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
47 20 0.07
48 53 0.20
49 72 0.27
50 68 0.25
51 57 0.21
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (50 bp):
ACTTTAAAAAATCTCAATTTGAAAAGTGCTCTTATAGACATAGGCAAGTG
Found at i:14369317 original size:148 final size:150
Alignment explanation
Indices: 14369023--14369339 Score: 413
Period size: 148 Copynumber: 2.1 Consensus size: 150
14369013 AGGAAACTTT
* * *
14369023 AAAACCTCAATTTGAAAAGTGCTCTTATAAGCATAGGCAAGTGACTTCAAAAATCTTAATTTGAA
1 AAAATCTCAATTTGAAAAGTGCTCTTATAAGCATAGGCAAGTAACTTCAAAAATCTCAATTTGAA
* ** * * *
14369088 AAGTGCTCTTATAGACATAGGTATGTGACTTTAAAAAATCTCAAATTGAAAACTGATCCTATAGA
66 AAGTGCTCTTATAGACACAGACAAGTGACTTTAAAAAAACTCAAATTGAAAACTGATCCTATAAA
** *
14369153 CATAGGTAAGTGACTTTAAA
131 CATAGACAAGTAACTTTAAA
* * *
14369173 AAAATCTCAATTTGAAAAGTGCTCTTATAGGCTTAGGCAAGTAACTT-TAAAATCTCAATTTGAA
1 AAAATCTCAATTTGAAAAGTGCTCTTATAAGCATAGGCAAGTAACTTCAAAAATCTCAATTTGAA
* * * * *
14369237 AAGTGCTC-TATAGACACATACAAGTGACTTTAAAAAAACTCAATTTGAAAAGTGCTCTTATAAA
66 AAGTGCTCTTATAGACACAGACAAGTGACTTTAAAAAAACTCAAATTGAAAACTGATCCTATAAA
*
14369301 CATAGACAGGTAACTTTAAA
131 CATAGACAAGTAACTTTAAA
* *
14369321 AGAATTTCAATTTGAAAAG
1 AAAATCTCAATTTGAAAAG
14369340 CTTTTAAAGT
Statistics
Matches: 144, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
148 78 0.54
149 23 0.16
150 43 0.30
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.30
Consensus pattern (150 bp):
AAAATCTCAATTTGAAAAGTGCTCTTATAAGCATAGGCAAGTAACTTCAAAAATCTCAATTTGAA
AAGTGCTCTTATAGACACAGACAAGTGACTTTAAAAAAACTCAAATTGAAAACTGATCCTATAAA
CATAGACAAGTAACTTTAAA
Found at i:14369373 original size:24 final size:24
Alignment explanation
Indices: 14369331--14369390 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
14369321 AGAATTTCAA
14369331 TTTGAAAAGCTTTTAAAGTCTTATG
1 TTTGAAAAG-TTTTAAAGTCTTATG
14369356 TTTGAAAAGTTTTAAAGTCTTATG
1 TTTGAAAAGTTTTAAAGTCTTATG
14369380 TTTGAAAAGTT
1 TTTGAAAAGTT
14369391 AGGTTGCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 26 0.74
25 9 0.26
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (24 bp):
TTTGAAAAGTTTTAAAGTCTTATG
Found at i:14369761 original size:17 final size:17
Alignment explanation
Indices: 14369720--14369773 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
14369710 TTCCCATTTT
14369720 TTCATTCA-TCATTTCA
1 TTCATTCATTCATTTCA
* *
14369736 TTCTCATTCTTTCGTTTCA
1 -T-TCATTCATTCATTTCA
14369755 TTCATTCATTCATTTCA
1 TTCATTCATTCATTTCA
14369772 TT
1 TT
14369774 TGTTTCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 17 0.55
18 7 0.23
19 7 0.23
ACGTcount: A:0.19, C:0.24, G:0.02, T:0.56
Consensus pattern (17 bp):
TTCATTCATTCATTTCA
Found at i:14369967 original size:31 final size:32
Alignment explanation
Indices: 14369905--14369987 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 32
14369895 AACTAGGCCG
* * * *
14369905 AAATCTTCTTAGTGCCA-TTTAGACTGTGCTT
1 AAATCTTTTTAGTGCTAGCTTAGACTGGGCTT
14369936 AAATCTTTTTAGTGCTAGCTTA-ACTGGGCTT
1 AAATCTTTTTAGTGCTAGCTTAGACTGGGCTT
* *
14369967 AAATATTTATAGGTGCTAGCT
1 AAATCTTTTTA-GTGCTAGCT
14369988 AGAATTTGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 32 0.73
32 12 0.27
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (32 bp):
AAATCTTTTTAGTGCTAGCTTAGACTGGGCTT
Found at i:14370903 original size:205 final size:202
Alignment explanation
Indices: 14370645--14371367 Score: 572
Period size: 202 Copynumber: 3.5 Consensus size: 202
14370635 GAATCCACTG
* * * * *
14370645 TGACAATAAAATAAAATGTCACTTTATGTTTTTTATTTTTTGTGACGTTAGTTTTTGTCAACTAT
1 TGACAATAAAATCAAACGTCACCTTATG--CTTTA-TTTTTGTGACGTTAGTTTTCGTCAACTAT
14370710 TTATGAAAAAAAACAAAGTCATTGAAA-GCTATAATCATCACAAAA-AAATGAGAAAATTCA-AA
63 TTATGAAAAAAAAC--A-TCATT-AAAGGCTATAATCATCACAAAATAAATGAGAAAATT-AGAA
* ** * ** *
14370772 ATAGTAGTGATGAAAGGTAAATCGTCACAATATTAGTGACAAAATTATTGGT-ACT-AATGATTG
123 ATAGTAGAGATGAAAGAAAAATCATCACAATATTAGTGACAAAATTA-TCATCA-TGAATGATTA
* * *
14370835 TAAGATAATGTCTACCA
186 TAAGAAAATGTCAAACA
* *
14370852 TGACAATAAAATCAAACGTCACCTTATGCTTTACTTTTTGTAACGTTAGTTTTGGTCAACTATTT
1 TGACAATAAAATCAAACGTCACCTTATGCTTTA-TTTTTGTGACGTTAGTTTTCGTCAACTATTT
* * * * * *
14370917 ATGAACAAAAACATCATTAAAGGCTATAATCGTCACAAAATAAATTATAAAATTAGATATATTAG
65 ATGAAAAAAAACATCATTAAAGGCTATAATCATCACAAAATAAATGAGAAAATTAGAAATAGTAG
*
14370982 AGATGAAAGAAAAATCATCACAATATTAGTGACACAATTATCATCATGAATGATTATAAGAAAAT
130 AGATGAAAGAAAAATCATCACAATATTAGTGACAAAATTATCATCATGAATGATTATAAGAAAAT
**
14371047 GTCAAATG
195 GTCAAACA
* * *
14371055 TGACAATAAAATCAAACGTCACCTTATGCTTT-TTTTTGTGATGTTAGTTTTCCTCAATTATTTA
1 TGACAATAAAATCAAACGTCACCTTATGCTTTATTTTTGTGACGTTAGTTTTCGTCAACTATTTA
* * * * ** * * * * *
14371119 T-AAGAAAGAACGTCATTGAAGGTTATAATTGTCA-TAAATAAATGATAAAATCATATATATATT
66 TGAA-AAAAAACATCATTAAAGGCTATAATCATCACAAAATAAATGAGAAAAT--TAGAAATAGT
* * * * * * * * * ** * *
14371182 AAAGACGAAATG-TAAATCGTCATAGTATTTGTAACACAATTATTGTCA-CAATTGATTGTAAGA
128 AGAGATGAAA-GAAAAATCATCACAATATTAGTGACAAAATTATCATCATGAA-TGATTATAAGA
**
14371245 TAACAT-T-AAATG
191 -AA-ATGTCAAACA
* ** * * * *
14371257 TGACAATAATATCAAATATCACATTATGCTTTATTTTTTTTGTGACGTTAGTTTTCATTAGCTAT
1 TGACAATAAAATCAAACGTCACCTTATGCTTTA---TTTTTGTGACGTTAGTTTTCGTCAACTAT
** * *
14371322 TTATG-AAAAAAATGTCATTAAAGGCTATAATCATCATAGAATAAAT
63 TTATGAAAAAAAACATCATTAAAGGCTATAATCATCACAAAATAAAT
14371368 TATAAATATA
Statistics
Matches: 429, Mismatches: 69, Indels: 37
0.80 0.13 0.07
Matches are distributed among these distances:
200 17 0.04
201 57 0.13
202 114 0.27
203 110 0.26
204 2 0.00
205 68 0.16
206 36 0.08
207 25 0.06
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (202 bp):
TGACAATAAAATCAAACGTCACCTTATGCTTTATTTTTGTGACGTTAGTTTTCGTCAACTATTTA
TGAAAAAAAACATCATTAAAGGCTATAATCATCACAAAATAAATGAGAAAATTAGAAATAGTAGA
GATGAAAGAAAAATCATCACAATATTAGTGACAAAATTATCATCATGAATGATTATAAGAAAATG
TCAAACA
Found at i:14371063 original size:203 final size:201
Alignment explanation
Indices: 14370643--14371408 Score: 696
Period size: 203 Copynumber: 3.8 Consensus size: 201
14370633 ATGAATCCAC
* * * * *
14370643 TGTGACAATAAAATAAAATGTCACTTTATGTTTTTTATTTTTTGTGACGTTAGTTTTTGTCAACT
1 TGTGACAATAAAATCAAACGTCACCTTATG--CTTTATTTTTTGTGACGTTAGTTTTCGTCAACT
*
14370708 ATTTATGAAAAAAAACAAAGTCATTGAAA-GCTATAATCATCACAAAA-AAATGAGAAAAT-TCA
64 ATTTATG-AAAAAAAC--A-TCATT-AAAGGCTATAATCATCACAAAATAAATGATAAAATAT-A
* * * ** * *
14370770 AAATAGTAGTGATGAAAGGTAAATCGTCACAATATTAGTGACAAAATTATTGGT-ACTAATGATT
123 ATATATTAGAGATGAAAGAAAAATCGTCACAATATTAGTGACACAATTA-TCGTCA-TAATGATT
* * *
14370834 GTAAGATAATGTCTAC
186 GTAAGAAAATGTCAAA
** * * *
14370850 CATGACAATAAAATCAAACGTCACCTTATGCTTTACTTTTTGTAACGTTAGTTTTGGTCAACTAT
1 TGTGACAATAAAATCAAACGTCACCTTATGCTTTATTTTTTGTGACGTTAGTTTTCGTCAACTAT
* *
14370915 TTATGAACAAAAACATCATTAAAGGCTATAATCGTCACAAAATAAATTATAAAAT-TAGATATAT
66 TTATGAA-AAAAACATCATTAAAGGCTATAATCATCACAAAATAAATGATAAAATATA-ATATAT
* * *
14370979 TAGAGATGAAAGAAAAATCATCACAATATTAGTGACACAATTATCATCATGAATGATTATAAGAA
129 TAGAGATGAAAGAAAAATCGTCACAATATTAGTGACACAATTATCGTCAT-AATGATTGTAAGAA
14371044 AATGTCAAA
193 AATGTCAAA
* * *
14371053 TGTGACAATAAAATCAAACGTCACCTTATGC-TT-TTTTTTGTGATGTTAGTTTTCCTCAATTAT
1 TGTGACAATAAAATCAAACGTCACCTTATGCTTTATTTTTTGTGACGTTAGTTTTCGTCAACTAT
* * * ** *
14371116 TTAT-AAGAAAGAACGTCATTGAAGGTTATAATTGTCA-TAAATAAATGATAAAATCATATATAT
66 TTATGAA-AAA-AACATCATTAAAGGCTATAATCATCACAAAATAAATGATAAAAT-ATA-ATAT
* * * * * * * * *
14371179 ATTAAAGACGAAATG-TAAATCGTCATAGTATTTGTAACACAATTATTGTCACAATTGATTGTAA
127 ATTAGAGATGAAA-GAAAAATCGTCACAATATTAGTGACACAATTATCGTCATAA-TGATTGTAA
14371243 GATAACAT-T-AAA
190 GA-AA-ATGTCAAA
* ** * * * *
14371255 TGTGACAATAATATCAAATATCACATTATGCTTTATTTTTTTTGTGACGTTAGTTTTCATTAGCT
1 TGTGACAATAAAATCAAACGTCACCTTATGCTTTA--TTTTTTGTGACGTTAGTTTTCGTCAACT
** * * *
14371320 ATTTATGAAAAAAATGTCATTAAAGGCTATAATCATCATAGAATAAATTAT-AAATATAATATAT
64 ATTTATGAAAAAAACATCATTAAAGGCTATAATCATCACAAAATAAATGATAAAATATAATATAT
* *
14371384 TAGTGAT-AAAAAATAAATCGTCACA
129 TAGAGATGAAAGAA-AAATCGTCACA
14371409 GTAGTGGTGA
Statistics
Matches: 462, Mismatches: 76, Indels: 46
0.79 0.13 0.08
Matches are distributed among these distances:
200 20 0.04
201 55 0.12
202 116 0.25
203 129 0.28
204 7 0.02
205 67 0.15
206 41 0.09
207 27 0.06
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (201 bp):
TGTGACAATAAAATCAAACGTCACCTTATGCTTTATTTTTTGTGACGTTAGTTTTCGTCAACTAT
TTATGAAAAAAACATCATTAAAGGCTATAATCATCACAAAATAAATGATAAAATATAATATATTA
GAGATGAAAGAAAAATCGTCACAATATTAGTGACACAATTATCGTCATAATGATTGTAAGAAAAT
GTCAAA
Found at i:14375461 original size:18 final size:16
Alignment explanation
Indices: 14375429--14375468 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
14375419 TAGCATGTAG
*
14375429 TTAAAATTATTTTTAT
1 TTAAAATTATTTTTAC
14375445 TTAAAATTTATTTTTTAC
1 TTAAAA-TTA-TTTTTAC
14375463 TTAAAA
1 TTAAAA
14375469 AAATTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 3 0.14
18 12 0.57
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAAATTATTTTTAC
Found at i:14376661 original size:183 final size:184
Alignment explanation
Indices: 14376334--14376666 Score: 445
Period size: 183 Copynumber: 1.8 Consensus size: 184
14376324 ATACATCAAT
* * * *
14376334 GTGATGAAATTGCAATGTCATTAATAGTTAACTAAATTATTCAATTTGCGACAAAAATTCATAAC
1 GTGACGAAATTGCAACGTCATTAATAGTTAACTAAAGTATTCAATTTGCGACAAAAATTAATAAC
* * ** *
14376399 GTCACCTTAAATCTATTAGAAAAAATTCATCATGGTTAAAATTTTAAATTACTGATAAAATTATA
66 GTCACCTTAAATATATTAAAAAAAATTCATCAAAGATAAAATTTTAAATTACTGATAAAATTATA
* *
14376464 ATGTCACTTAAAATAAAAAATGTCATAAAAAATTTTTTCACATTATACATTGAC
131 AAGTCACATAAAATAAAAAATGTCATAAAAAATTTTTTCACATTATACATTGAC
* * * * * *
14376518 GTGACGAAATTGCAACGTCATTAATAGTTAACTAAAGTGTTTAATTTGTGGCAAATATTAATAAT
1 GTGACGAAATTGCAACGTCATTAATAGTTAACTAAAGTATTCAATTTGCGACAAAAATTAATAAC
* * ** *
14376583 GTCA-CTTAAA-ATATATAAAAAAAATTCGTCAAAGATAAAATTTTATATTGGTGATGAAATTAT
66 GTCACCTTAAATATAT-TAAAAAAAATTCATCAAAGATAAAATTTTAAATTACTGATAAAATTAT
14376646 AAAGTCACATAAAATAAAAAA
130 AAAGTCACATAAAATAAAAAA
14376667 AAATCACAAA
Statistics
Matches: 126, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
182 3 0.02
183 64 0.51
184 59 0.47
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (184 bp):
GTGACGAAATTGCAACGTCATTAATAGTTAACTAAAGTATTCAATTTGCGACAAAAATTAATAAC
GTCACCTTAAATATATTAAAAAAAATTCATCAAAGATAAAATTTTAAATTACTGATAAAATTATA
AAGTCACATAAAATAAAAAATGTCATAAAAAATTTTTTCACATTATACATTGAC
Found at i:14376927 original size:236 final size:236
Alignment explanation
Indices: 14376508--14376935 Score: 612
Period size: 236 Copynumber: 1.8 Consensus size: 236
14376498 TTTTCACATT
* * * *
14376508 ATACATTGACGTGACGAAATTGCAACGTCATTAATAGTTAACTAAAGTGTTTAATTTGTGGCAAA
1 ATACATTAACGTGACAAAATTGCAACGTCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAA
* * * *
14376573 TATTAATAATGTCACTTAAAATATATAAAAAAAATTCGTCAAAGATAAAATTTTATATTGGTGAT
66 AATTAACAATGTCACCTAAAATATATAAAAAAAATTCGTCAAAGATAAAATTTTATATTGGTGAC
* *
14376638 GAAATTATAAAGTCACATAAAATAAAAAAAAATCACAAATAAATTTTTCACCAAATAAATTTAGC
131 AAAATTATAAAGTCACATAAAATAAAAAAAAATCACAAATAAATTTCTCACCAAATAAATTTAGC
14376703 GGCAAAAATTTGTGACATTTATGTTATCATCATATAACACC
196 GGCAAAAATTTGTGACATTTATGTTATCATCATATAACACC
* * * *
14376744 ATACATTAATGTGACAAAATTGTAATGTCATTGATAGTTAACTAAAGTGTTCAATTTGTGACAAA
1 ATACATTAACGTGACAAAATTGCAACGTCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAA
* * *
14376809 AATTAACAATGTCACCTAAAATCTATCAGAAAAAATTCGTCATAGATAAAATTTTA-AGTTGGTG
66 AATTAACAATGTCACCTAAAATATAT-AAAAAAAATTCGTCAAAGATAAAATTTTATA-TTGGTG
* **
14376873 ACAAAATTATAACA-TCACCTAAAAT-AAAAAATGTCACAAA-AGAATTTCTCACCAAATAAATT
129 ACAAAATTATAA-AGTCACATAAAATAAAAAAAAATCACAAATA-AATTTCTCACCAAATAAATT
14376935 T
192 T
14376936 GGTGGTAAAA
Statistics
Matches: 168, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
235 1 0.01
236 113 0.67
237 53 0.32
238 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.32
Consensus pattern (236 bp):
ATACATTAACGTGACAAAATTGCAACGTCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAA
AATTAACAATGTCACCTAAAATATATAAAAAAAATTCGTCAAAGATAAAATTTTATATTGGTGAC
AAAATTATAAAGTCACATAAAATAAAAAAAAATCACAAATAAATTTCTCACCAAATAAATTTAGC
GGCAAAAATTTGTGACATTTATGTTATCATCATATAACACC
Found at i:14377757 original size:7 final size:7
Alignment explanation
Indices: 14377714--14377759 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
14377704 GAATGATTAC
14377714 TTTTT-T
1 TTTTTGT
14377720 TTTTTGT
1 TTTTTGT
*
14377727 TTATTGT
1 TTTTTGT
*
14377734 TTATTGT
1 TTTTTGT
14377741 TTTTTGT
1 TTTTTGT
14377748 TTTTTGT
1 TTTTTGT
14377755 TTTTT
1 TTTTT
14377760 TAGAAGGCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.04, C:0.00, G:0.11, T:0.85
Consensus pattern (7 bp):
TTTTTGT
Found at i:14377830 original size:51 final size:50
Alignment explanation
Indices: 14377763--14377862 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 50
14377753 GTTTTTTTAG
* *
14377763 AAGGCTTCTATTAACATAAGCTAGGGAACTCTAAAAAGTCATTTT-GAAAA
1 AAGGCTTCTATAAACATAAGCTAAGGAACTCTAAAAA-TCATTTTAGAAAA
* * * *
14377813 AAGGACTTCTATAAACATAGGTTAAGGAAGTTTAAAAATCATTTTAGAAA
1 AAGG-CTTCTATAAACATAAGCTAAGGAACTCTAAAAATCATTTTAGAAA
14377863 GGTTCCTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 11 0.26
51 31 0.74
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (50 bp):
AAGGCTTCTATAAACATAAGCTAAGGAACTCTAAAAATCATTTTAGAAAA
Found at i:14377936 original size:48 final size:45
Alignment explanation
Indices: 14377875--14377990 Score: 117
Period size: 47 Copynumber: 2.4 Consensus size: 45
14377865 TTCCTATTAT
* * * *
14377875 CATAACCAGGGAACTTTAAAAATCTTTTTGGGAAAGGGTTTTTATA-A
1 CATAAGCA-GGAACTTTAAAAAT-TATTT-CGAAAGGGCTTTTATACA
14377922 CCATAAGCTAGGAACTTATAAAAATTATTTCGAAAGGGCTTTTATACA
1 -CATAAGC-AGGAACTT-TAAAAATTATTTCGAAAGGGCTTTTATACA
*
14377970 CATAGGCAGAGAACTTTAAAA
1 CATAAGCAG-GAACTTTAAAA
14377991 TCTCAATTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
46 7 0.12
47 26 0.44
48 18 0.31
49 8 0.14
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (45 bp):
CATAAGCAGGAACTTTAAAAATTATTTCGAAAGGGCTTTTATACA
Found at i:14378019 original size:50 final size:48
Alignment explanation
Indices: 14377954--14378269 Score: 171
Period size: 50 Copynumber: 6.4 Consensus size: 48
14377944 AATTATTTCG
*
14377954 AAAGGGCT-TTTATACACATAGGCAGAGAACTTT-AAAATCTCAATTTGA
1 AAAGTGCTCTTTATA-ACATAGGCAGAG-ACTTTAAAAATCTCAATTTGA
* ** * * *
14378002 AAAGTGTTCTTGTAT-ACATAAACAAGTGACTTTAAAAATTTTAATTTGA
1 AAAGTGCTCTT-TATAACATAGGC-AGAGACTTTAAAAATCTCAATTTGA
* * *
14378051 AAAGTGCTCTTTATAAATATAGGTAGATGACTTTAAAAAATCTCAATTCGA
1 AAAGTGCTCTTTAT-AACATAGGCAGA-GACTTT-AAAAATCTCAATTTGA
* ** * * * * *
14378102 AAACTTTTC-CTACAGACATAGACAAGTGACTTT-AAAATCTCAATTTAA
1 AAAGTGCTCTTTATA-ACATAGGC-AGAGACTTTAAAAATCTCAATTTGA
* * * * *
14378150 AAAGTCCTC-ATATAGACAAAGACAAGTGACTTTAACAAATCTCAATTTGA
1 AAAGTGCTCTTTATA-ACATAGGC-AGAGACTTTAA-AAATCTCAATTTGA
* * * *
14378200 AAAGTGCT-TTTATAGACATAGGTAAGTGATTTTAAAAAAATCTTAATTTGA
1 AAAGTGCTCTTTATA-ACATAGG-CAGAGACTTT--AAAAATCTCAATTTGA
*
14378251 TAAGTGCTC-TTATAGACAT
1 AAAGTGCTCTTTATA-ACAT
14378270 CGATAGGTAA
Statistics
Matches: 209, Mismatches: 42, Indels: 31
0.74 0.15 0.11
Matches are distributed among these distances:
48 60 0.29
49 32 0.15
50 64 0.31
51 51 0.24
52 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (48 bp):
AAAGTGCTCTTTATAACATAGGCAGAGACTTTAAAAATCTCAATTTGA
Found at i:14378034 original size:48 final size:49
Alignment explanation
Indices: 14377982--14378306 Score: 246
Period size: 51 Copynumber: 6.5 Consensus size: 49
14377972 TAGGCAGAGA
* * *
14377982 ACTTT-AAAATCTCAATTTGAAAAGTGTTCTTGTATACATAAACAAGTG
1 ACTTTAAAAATCTCAATTTGAAAAGTGCTCTTATAGACATAAACAAGTG
* * ***
14378030 ACTTTAAAAATTTTAATTTGAAAAGTGCTCTTTATA-A-ATATAGGTAGATG
1 ACTTTAAAAATCTCAATTTGAAAAGTGCTC-TTATAGACATA-AACAAG-TG
* * ** * * *
14378080 ACTTTAAAAAATCTCAATTCGAAAACTTTTCCTACAGACATAGACAAGTG
1 ACTTT-AAAAATCTCAATTTGAAAAGTGCTCTTATAGACATAAACAAGTG
* * *
14378130 ACTTT-AAAATCTCAATTTAAAAAGTCCTCATATAGACA-AAGACAAGTG
1 ACTTTAAAAATCTCAATTTGAAAAGTGCTCTTATAGACATAA-ACAAGTG
* ***
14378178 ACTTTAACAAATCTCAATTTGAAAAGTGCTTTTATAGACATAGGTAAGTG
1 ACTTTAA-AAATCTCAATTTGAAAAGTGCTCTTATAGACATAAACAAGTG
* * * ** * * *
14378228 ATTTTAAAAAAATCTTAATTTGATAAGTGCTCTTATAGACATCGATAGGTA
1 ACTTT--AAAAATCTCAATTTGAAAAGTGCTCTTATAGACATAAACAAGTG
14378279 ACTTTAAAAAAAATCTCAATTTGAAAAG
1 ACTTT---AAAAATCTCAATTTGAAAAG
14378307 CATTTAAAGT
Statistics
Matches: 218, Mismatches: 45, Indels: 24
0.76 0.16 0.08
Matches are distributed among these distances:
47 1 0.00
48 46 0.21
49 26 0.12
50 58 0.27
51 62 0.28
52 25 0.11
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (49 bp):
ACTTTAAAAATCTCAATTTGAAAAGTGCTCTTATAGACATAAACAAGTG
Found at i:14378084 original size:98 final size:99
Alignment explanation
Indices: 14377982--14378306 Score: 275
Period size: 98 Copynumber: 3.3 Consensus size: 99
14377972 TAGGCAGAGA
* * * *
14377982 ACTTT-AAAATCTCAATTTGAAAAGTGTTCTTGTATACATAAACAAGTGACTTTAAAAATTTTAA
1 ACTTTAAAAATCTCAATTTGAAAAGTGTTCTTATAGACATAGACAAGTGACTTTAAAAATCTTAA
* * **
14378046 TTTGAAAAGTGCTCTTTATAAATATAG-GTAGATG
66 TTTGAAAAGTGCTCTTTATAAACAAAGACAAG-TG
* * * * * *
14378080 ACTTTAAAAAATCTCAATTCGAAAACTTTTCCTACAGACATAGACAAGTGACTTT-AAAATCTCA
1 ACTTT-AAAAATCTCAATTTGAAAAGTGTTCTTATAGACATAGACAAGTGACTTTAAAAATCTTA
* * * *
14378144 ATTTAAAAAGTCCTC-ATATAGACAAAGACAAGTG
65 ATTTGAAAAGTGCTCTTTATAAACAAAGACAAGTG
** *
14378178 ACTTTAACAAATCTCAATTTGAAAAGTGCTT-TTATAGACATAGGTAAGTGATTTTAAAAAAATC
1 ACTTTAA-AAATCTCAATTTGAAAAGTG-TTCTTATAGACATAGACAAGTGACTTT--AAAAATC
* * ** * * *
14378242 TTAATTTGATAAGTGCTC-TTATAGACATCGATAGGTA
62 TTAATTTGAAAAGTGCTCTTTATAAACAAAGACAAGTG
14378279 ACTTTAAAAAAAATCTCAATTTGAAAAG
1 ACTTT---AAAAATCTCAATTTGAAAAG
14378307 CATTTAAAGT
Statistics
Matches: 180, Mismatches: 36, Indels: 17
0.77 0.15 0.07
Matches are distributed among these distances:
97 2 0.01
98 56 0.31
99 24 0.13
100 40 0.22
101 38 0.21
103 18 0.10
104 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (99 bp):
ACTTTAAAAATCTCAATTTGAAAAGTGTTCTTATAGACATAGACAAGTGACTTTAAAAATCTTAA
TTTGAAAAGTGCTCTTTATAAACAAAGACAAGTG
Found at i:14378257 original size:51 final size:51
Alignment explanation
Indices: 14377987--14378306 Score: 242
Period size: 50 Copynumber: 6.4 Consensus size: 51
14377977 AGAGAACTTT
* * * * * *
14377987 AAAATCTCAATTTGAAAAGTGTTCTTGTATACATAAACAAGTGACTTT--A
1 AAAATCTCAATTTGAAAAGTGCTCTTATAGACATAGATAAGTGATTTTAAA
* * * * * *
14378036 AAAATTTTAATTTGAAAAGTGCTCTTTATAAATATAGGT-AGATGACTTT-AA
1 AAAATCTCAATTTGAAAAGTGCTC-TTATAGACATAGATAAG-TGATTTTAAA
* * ** * * * *
14378087 AAAATCTCAATTCGAAAACTTTTCCTACAGACATAGACAAGTGACTTT---
1 AAAATCTCAATTTGAAAAGTGCTCTTATAGACATAGATAAGTGATTTTAAA
* * * * * *
14378135 AAAATCTCAATTTAAAAAGTCCTCATATAGACAAAGACAAGTGACTTT-AA
1 AAAATCTCAATTTGAAAAGTGCTCTTATAGACATAGATAAGTGATTTTAAA
* * *
14378185 CAAATCTCAATTTGAAAAGTGCTTTTATAGACATAGGTAAGTGATTTTAAA
1 AAAATCTCAATTTGAAAAGTGCTCTTATAGACATAGATAAGTGATTTTAAA
* * * * * *
14378236 AAAATCTTAATTTGATAAGTGCTCTTATAGACATCGATAGGTAACTTTAAAA
1 AAAATCTCAATTTGAAAAGTGCTCTTATAGACATAGATAAGTGA-TTTTAAA
14378288 AAAATCTCAATTTGAAAAG
1 AAAATCTCAATTTGAAAAG
14378307 CATTTAAAGT
Statistics
Matches: 214, Mismatches: 49, Indels: 13
0.78 0.18 0.05
Matches are distributed among these distances:
48 40 0.19
49 23 0.11
50 69 0.32
51 59 0.28
52 23 0.11
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (51 bp):
AAAATCTCAATTTGAAAAGTGCTCTTATAGACATAGATAAGTGATTTTAAA
Found at i:14378891 original size:31 final size:31
Alignment explanation
Indices: 14378856--14378934 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
14378846 TCTTGATACC
* *
14378856 AGCTAGACTGGGCTTAAATTGT-CTTGGTGTT
1 AGCTAGACTAGGCTT-AATTGTCCTTGGTGAT
* *
14378887 AGCTAGATTAGGCTTAATTTTCCTTGGTGAT
1 AGCTAGACTAGGCTTAATTGTCCTTGGTGAT
* *
14378918 AGCTAGAATAAGCTTAA
1 AGCTAGACTAGGCTTAA
14378935 ATCTTCATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 5 0.12
31 36 0.88
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (31 bp):
AGCTAGACTAGGCTTAATTGTCCTTGGTGAT
Found at i:14379030 original size:31 final size:32
Alignment explanation
Indices: 14378995--14379069 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 32
14378985 GACTCAGTTT
*
14378995 AATTTTTCTTGATACTAGTTAAATTGGG-TTG
1 AATTTTTCTTGATACTAGCTAAATTGGGCTTG
* * **
14379026 AATTTTTCTCGGTTTTAGCTAAATTGGGCTTG
1 AATTTTTCTTGATACTAGCTAAATTGGGCTTG
*
14379058 -ATTTTCCTTGAT
1 AATTTTTCTTGAT
14379070 GACAACAACA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 32 0.91
32 3 0.09
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.49
Consensus pattern (32 bp):
AATTTTTCTTGATACTAGCTAAATTGGGCTTG
Found at i:14382231 original size:17 final size:15
Alignment explanation
Indices: 14382211--14382247 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
14382201 CACTTTCTTG
14382211 TTTTTTCTTTTCTTTT
1 TTTTTTCTTTT-TTTT
14382227 ATTTTTTCTTTTTTTT
1 -TTTTTTCTTTTTTTT
14382243 TTTTT
1 TTTTT
14382248 GCAAGCTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 4 0.20
17 11 0.55
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTCTTTTTTTT
Found at i:14382245 original size:12 final size:12
Alignment explanation
Indices: 14382211--14382245 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
14382201 CACTTTCTTG
*
14382211 TTTTTTCTTTTC
1 TTTTTTTTTTTC
*
14382223 TTTTATTTTTTC
1 TTTTTTTTTTTC
14382235 TTTTTTTTTTT
1 TTTTTTTTTTT
14382246 TTGCAAGCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:14382894 original size:9 final size:9
Alignment explanation
Indices: 14382880--14382904 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14382870 AAACTTAAGG
14382880 AAAATTTTC
1 AAAATTTTC
14382889 AAAATTTTC
1 AAAATTTTC
14382898 AAAATTT
1 AAAATTT
14382905 GATTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATTTTC
Found at i:14388780 original size:31 final size:30
Alignment explanation
Indices: 14388738--14388829 Score: 114
Period size: 31 Copynumber: 3.0 Consensus size: 30
14388728 TTTTCCTCGA
* *
14388738 TGCTAGTTAAATTAGGCTTAATTTTTCTTAG
1 TGCTAGGTAAATT-GGCTTAATTCTTCTTAG
14388769 TAGC-AGGTAAATTGAGCTTAATTCTTCTTAG
1 T-GCTAGGTAAATTG-GCTTAATTCTTCTTAG
*
14388800 TGCTAGGTAAATTGGGCTTAATTCTCCTTA
1 TGCTAGGTAAATT-GGCTTAATTCTTCTTA
14388830 ACGCCAGCTA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
30 3 0.06
31 48 0.89
32 3 0.06
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (30 bp):
TGCTAGGTAAATTGGCTTAATTCTTCTTAG
Found at i:14390441 original size:15 final size:15
Alignment explanation
Indices: 14390423--14390455 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
14390413 TCTTTCTTTC
14390423 TTTTTT-TTTTCTCTT
1 TTTTTTATTTTC-CTT
14390438 TTTTTTATTTTCCTT
1 TTTTTTATTTTCCTT
14390453 TTT
1 TTT
14390456 AATTATTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTATTTTCCTT
Found at i:14390834 original size:19 final size:19
Alignment explanation
Indices: 14390810--14390847 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
14390800 GTTTCTCCCC
14390810 CTTTTT-TTTTTCCCTTTTT
1 CTTTTTATTTTT-CCTTTTT
14390829 CTTTTTATTTTTCCTTTTT
1 CTTTTTATTTTTCCTTTTT
14390848 TTTCTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (19 bp):
CTTTTTATTTTTCCTTTTT
Found at i:14390848 original size:21 final size:20
Alignment explanation
Indices: 14390810--14390875 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 20
14390800 GTTTCTCCCC
*
14390810 CTTTTTTTTTTCC-CTTTTT
1 CTTTTTTTTTTCCTTTTTTT
14390829 CTTTTTATTTTTCCTTTTTTTT
1 CTTTTT-TTTTTCC-TTTTTTT
* *
14390851 CTTTTCTTCTTTCCTTTATTT
1 CTTTT-TTTTTTCCTTTTTTT
14390872 CTTT
1 CTTT
14390876 CACTTTTCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 6 0.15
20 7 0.17
21 10 0.25
22 16 0.40
23 1 0.03
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (20 bp):
CTTTTTTTTTTCCTTTTTTT
Found at i:14397045 original size:19 final size:18
Alignment explanation
Indices: 14397023--14397255 Score: 82
Period size: 19 Copynumber: 12.4 Consensus size: 18
14397013 TCTAAGTTAT
14397023 GGTTTAGGGTTAGGTTTA
1 GGTTTAGGGTTAGGTTTA
** *
14397041 CGGTTTAAAGTCTA-GATTA
1 -GGTTTAGGGT-TAGGTTTA
* *
14397060 GGGTTTAAGGTT-TGTTTA
1 -GGTTTAGGGTTAGGTTTA
***
14397078 GGATTTAATATTTAGGTTTA
1 GG-TTT-AGGGTTAGGTTTA
*
14397098 GGTTTAGGGTTTGGATTTAA
1 GGTTTAGGGTTAGG-TTT-A
** * *
14397118 GGCATAAGGTTAGGGTTTTT
1 GGTTTAGGGTTA-GG-TTTA
*
14397138 TGTTTAGGGTTTAGGTTTAA
1 GGTTTAGGG-TTAGGTTT-A
14397158 GGTTTAAGGGTTA-GTTTA
1 GGTTT-AGGGTTAGGTTTA
* **
14397176 GGTTTAAGGTTTAGGGATA
1 GGTTT-AGGGTTAGGTTTA
*
14397195 -GTTTAGGGTTTGGTTTAA
1 GGTTTAGGGTTAGGTTT-A
**
14397213 GGTTTAAAGTTA-GTTTA
1 GGTTTAGGGTTAGGTTTA
*
14397230 TGGTTT-GGTTTAAGGTTTA
1 -GGTTTAGGGTT-AGGTTTA
*
14397249 GGGTTAG
1 GGTTTAG
14397256 TTTAGGATTT
Statistics
Matches: 156, Mismatches: 40, Indels: 36
0.67 0.17 0.16
Matches are distributed among these distances:
17 13 0.08
18 45 0.29
19 54 0.35
20 32 0.21
21 12 0.08
ACGTcount: A:0.22, C:0.01, G:0.32, T:0.45
Consensus pattern (18 bp):
GGTTTAGGGTTAGGTTTA
Found at i:14397108 original size:13 final size:13
Alignment explanation
Indices: 14397088--14397190 Score: 63
Period size: 13 Copynumber: 8.0 Consensus size: 13
14397078 GGATTTAATA
14397088 TTTA-GGTTTAGG
1 TTTAGGGTTTAGG
14397100 TTTAGGGTTT-GG
1 TTTAGGGTTTAGG
** *
14397112 ATTTAAGGCATAAGG
1 -TTT-AGGGTTTAGG
**
14397127 -TTAGGGTTTTTTG
1 TTTAGGG-TTTAGG
14397140 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
*
14397153 TTTAAGGTTTAAGG
1 TTTAGGGTTT-AGG
*
14397167 GTTA--GTTTAGG
1 TTTAGGGTTTAGG
*
14397178 TTTAAGGTTTAGG
1 TTTAGGGTTTAGG
14397191 GATAGTTTAG
Statistics
Matches: 69, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
11 6 0.09
12 13 0.19
13 32 0.46
14 16 0.23
15 2 0.03
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (13 bp):
TTTAGGGTTTAGG
Found at i:14397149 original size:7 final size:6
Alignment explanation
Indices: 14397139--14397261 Score: 71
Period size: 7 Copynumber: 20.2 Consensus size: 6
14397129 AGGGTTTTTT
*
14397139 GTTTAGG GTTTAG GTTTAAG GTTTAAG GGTTA- GTTTAG GTTTAAG GTTTAG
1 GTTTA-G GTTTAG GTTT-AG GTTT-AG GTTTAG GTTTAG GTTT-AG GTTTAG
** *
14397190 GGATA- GTTTAGG GTTT-G GTTTAAG GTTTAAA G-TTA- GTTTATG GTTT-G
1 GTTTAG GTTTA-G GTTTAG GTTT-AG GTTT-AG GTTTAG GTTTA-G GTTTAG
*
14397237 GTTTAAG GTTTAG GGTTA- GTTTAG G
1 GTTT-AG GTTTAG GTTTAG GTTTAG G
14397262 ATTTGAATGA
Statistics
Matches: 94, Mismatches: 9, Indels: 27
0.72 0.07 0.21
Matches are distributed among these distances:
4 1 0.01
5 25 0.27
6 24 0.26
7 44 0.47
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (6 bp):
GTTTAG
Found at i:14397179 original size:25 final size:25
Alignment explanation
Indices: 14397146--14397214 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 25
14397136 TTTGTTTAGG
*
14397146 GTTTAGGTTTAAGGTTTAAGGGTTA
1 GTTTAGGTTTAAGGTTTAAGGGATA
14397171 GTTTAGGTTTAAGGTTT-AGGGATA
1 GTTTAGGTTTAAGGTTTAAGGGATA
14397195 GTTTAGGGTTT--GGTTTAAGG
1 GTTTA-GGTTTAAGGTTTAAGG
14397215 TTTAAAGTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
23 5 0.12
24 14 0.34
25 22 0.54
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (25 bp):
GTTTAGGTTTAAGGTTTAAGGGATA
Found at i:14397212 original size:30 final size:30
Alignment explanation
Indices: 14397139--14397266 Score: 142
Period size: 30 Copynumber: 4.4 Consensus size: 30
14397129 AGGGTTTTTT
14397139 GTTTAGGGTTTAGGTTTAAGGTTTAAGG---
1 GTTTAGGGTTT-GGTTTAAGGTTTAAGGTTA
* *
14397167 G-TTA--GTTTAGGTTTAAGGTTTAGGGATA
1 GTTTAGGGTTT-GGTTTAAGGTTTAAGGTTA
*
14397195 GTTTAGGGTTTGGTTTAAGGTTTAAAGTTA
1 GTTTAGGGTTTGGTTTAAGGTTTAAGGTTA
* *
14397225 GTTTATGGTTTGGTTTAAGGTTTAGGGTTA
1 GTTTAGGGTTTGGTTTAAGGTTTAAGGTTA
*
14397255 GTTTAGGATTTG
1 GTTTAGGGTTTG
14397267 AATGATGGTT
Statistics
Matches: 85, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
25 20 0.24
27 3 0.04
28 2 0.02
29 3 0.04
30 53 0.62
31 4 0.05
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (30 bp):
GTTTAGGGTTTGGTTTAAGGTTTAAGGTTA
Found at i:14397294 original size:18 final size:18
Alignment explanation
Indices: 14397268--14397305 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
14397258 TAGGATTTGA
* *
14397268 ATGATGGTTTAGGGTTTC
1 ATGAAGGTTTAAGGTTTC
14397286 ATGAAGGTTTAAGGTTTC
1 ATGAAGGTTTAAGGTTTC
14397304 AT
1 AT
14397306 CGGAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.42
Consensus pattern (18 bp):
ATGAAGGTTTAAGGTTTC
Found at i:14397621 original size:21 final size:20
Alignment explanation
Indices: 14397586--14397626 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
14397576 GAAATTCATG
14397586 CAAATAAACACTAAAATAAC
1 CAAATAAACACTAAAATAAC
* *
14397606 CAAATAACCTACTAAACTAAC
1 CAAATAAAC-ACTAAAATAAC
14397627 ATTTTATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.17
Consensus pattern (20 bp):
CAAATAAACACTAAAATAAC
Found at i:14399731 original size:20 final size:20
Alignment explanation
Indices: 14399708--14399762 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
14399698 TTTGGTCAAT
*
14399708 TTTGACCAAGTTTGATTA-A
1 TTTGACCAAGTTTGATCATA
***
14399727 GTTTGACTTTGTTTGATCATA
1 -TTTGACCAAGTTTGATCATA
14399748 TTTGACCAAGTTTGA
1 TTTGACCAAGTTTGA
14399763 CATTAGGGCA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.45
Consensus pattern (20 bp):
TTTGACCAAGTTTGATCATA
Found at i:14410566 original size:19 final size:17
Alignment explanation
Indices: 14410519--14410576 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 17
14410509 TGAAAAAGGA
14410519 AAATTTTATCTTTAAAAT
1 AAATTTTAT-TTTAAAAT
* *
14410537 AAAATTCATTTTATTAAAT
1 AAATTTTATTTTA--AAAT
*
14410556 AAATTTTATTTTCAAA-
1 AAATTTTATTTTAAAAT
14410572 AAATT
1 AAATT
14410577 AAAAAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 5 0.15
17 7 0.21
18 7 0.21
19 14 0.42
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATTTTATTTTAAAAT
Found at i:14415913 original size:50 final size:50
Alignment explanation
Indices: 14415856--14415989 Score: 189
Period size: 50 Copynumber: 2.7 Consensus size: 50
14415846 CCTCATGTAC
* * *
14415856 CAAAGTTTGCATTTTTTTCGATGGCATTTCGATAATTTTGTTACATGCAT
1 CAAAGTTTGCATTTTTATCAATGGCATTTCGATAACTTTGTTACATGCAT
** * *
14415906 CAAAGTTTGCATTTTTATCAATGTTATTTTGGTAACTTTGTTACATGCAT
1 CAAAGTTTGCATTTTTATCAATGGCATTTCGATAACTTTGTTACATGCAT
*
14415956 CAAAGTTTGCA-TTTTCTCAATGGCATTTCGATAA
1 CAAAGTTTGCATTTTTATCAATGGCATTTCGATAA
14415990 ATTATCATAT
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
49 18 0.25
50 54 0.75
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (50 bp):
CAAAGTTTGCATTTTTATCAATGGCATTTCGATAACTTTGTTACATGCAT
Found at i:14416079 original size:19 final size:19
Alignment explanation
Indices: 14416043--14416081 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
14416033 AATTCGAAAC
*
14416043 CCTAAATCCAAATCCAAAT
1 CCTAAATCCAAAACCAAAT
14416062 CCTAAA-CCAAAACTCAAAT
1 CCTAAATCCAAAAC-CAAAT
14416081 C
1 C
14416082 TAGACCCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (19 bp):
CCTAAATCCAAAACCAAAT
Found at i:14416079 original size:25 final size:26
Alignment explanation
Indices: 14416051--14416100 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
14416041 ACCCTAAATC
*
14416051 CAAATCCAAATCCTAAACCA-AAACT
1 CAAATCCAAACCCTAAACCATAAACT
* *
14416076 CAAATCTAGACCCTAAACCATAAAC
1 CAAATCCAAACCCTAAACCATAAAC
14416101 CTTAACCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.50, C:0.32, G:0.02, T:0.16
Consensus pattern (26 bp):
CAAATCCAAACCCTAAACCATAAACT
Found at i:14416174 original size:7 final size:7
Alignment explanation
Indices: 14416085--14416334 Score: 125
Period size: 7 Copynumber: 37.3 Consensus size: 7
14416075 TCAAATCTAG
14416085 ACCCTAA
1 ACCCTAA
*
14416092 ACCATAA
1 ACCCTAA
*
14416099 A-CCTTA
1 ACCCTAA
*
14416105 ACCCCAA
1 ACCCTAA
*
14416112 A-CTTAAA
1 ACCCT-AA
14416119 ACCCTAA
1 ACCCTAA
*
14416126 A-TCTCAA
1 ACCCT-AA
14416133 ACCCTAA
1 ACCCTAA
*
14416140 AACC-AA
1 ACCCTAA
14416146 ACCC-AA
1 ACCCTAA
*
14416152 ATCCTAA
1 ACCCTAA
****
14416159 ATTGAAA
1 ACCCTAA
14416166 ACCCTAA
1 ACCCTAA
14416173 ACCCTAA
1 ACCCTAA
*
14416180 GCCCTAA
1 ACCCTAA
14416187 A-CCTAA
1 ACCCTAA
14416193 ACCCT-A
1 ACCCTAA
* *
14416199 ACGCT-T
1 ACCCTAA
*
14416205 ACACCTTA
1 AC-CCTAA
14416213 ACCCTAA
1 ACCCTAA
*
14416220 ACCTTAGA
1 ACCCTA-A
14416228 A--CTAA
1 ACCCTAA
**
14416233 ACTATAA
1 ACCCTAA
14416240 ACCCTAA
1 ACCCTAA
14416247 A-CC-AA
1 ACCCTAA
*
14416252 AACCTAA
1 ACCCTAA
*
14416259 ACCTTAA
1 ACCCTAA
*
14416266 AGCCTAA
1 ACCCTAA
14416273 ACCCT-A
1 ACCCTAA
14416279 ACCCTAA
1 ACCCTAA
*
14416286 ACCTTAA
1 ACCCTAA
* *
14416293 A-ACAAA
1 ACCCTAA
14416299 ACCCT-A
1 ACCCTAA
14416305 ACCCTAA
1 ACCCTAA
14416312 ACCCTAA
1 ACCCTAA
* *
14416319 AACCAAA
1 ACCCTAA
14416326 ACCCTAA
1 ACCCTAA
14416333 AC
1 AC
14416335 TAACCTCAAA
Statistics
Matches: 179, Mismatches: 47, Indels: 34
0.69 0.18 0.13
Matches are distributed among these distances:
5 5 0.03
6 51 0.28
7 115 0.64
8 8 0.04
ACGTcount: A:0.46, C:0.35, G:0.02, T:0.17
Consensus pattern (7 bp):
ACCCTAA
Found at i:14416193 original size:20 final size:20
Alignment explanation
Indices: 14416117--14416334 Score: 133
Period size: 20 Copynumber: 10.8 Consensus size: 20
14416107 CCCAAACTTA
*
14416117 AAACCCTAAATCTCAAACCCT
1 AAACCCTAAACCT-AAACCCT
* * *
14416138 AAAACC-AAACCCAAATCCT
1 AAACCCTAAACCTAAACCCT
****
14416157 AAATTGAAAACCCTAAACCCT
1 AAACCCTAAA-CCTAAACCCT
*
14416178 AAGCCCTAAACCTAAACCCT
1 AAACCCTAAACCTAAACCCT
* * *
14416198 -AACGCTTACACCTTAACCCT
1 AAAC-CCTAAACCTAAACCCT
* **
14416218 AAACCTTAGAA-CTAAACTAT
1 AAACCCTA-AACCTAAACCCT
*
14416238 AAACCCTAAACC-AAAACCT
1 AAACCCTAAACCTAAACCCT
*
14416257 AAACCTTAAAGCCTAAACCCT
1 AAACCCTAAA-CCTAAACCCT
* *
14416278 -AACCCTAAACCTTAAA-ACA
1 AAACCCTAAACC-TAAACCCT
*
14416297 AAACCCTAACCCTAAACCCT
1 AAACCCTAAACCTAAACCCT
* *
14416317 AAAACCAAAACCCTAAAC
1 AAACCCTAAA-CCTAAAC
14416335 TAACCTCAAA
Statistics
Matches: 148, Mismatches: 37, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
19 33 0.22
20 80 0.54
21 35 0.24
ACGTcount: A:0.46, C:0.35, G:0.02, T:0.17
Consensus pattern (20 bp):
AAACCCTAAACCTAAACCCT
Found at i:14416194 original size:27 final size:27
Alignment explanation
Indices: 14416085--14416334 Score: 139
Period size: 27 Copynumber: 9.3 Consensus size: 27
14416075 TCAAATCTAG
* * *
14416085 ACCCTAAACCATAAACCTTAACCCCAA
1 ACCCTAAACCCTAAACCTTAAACCTAA
* * *
14416112 A-CTTAAAACCCTAAATCTCAAACCCTAA
1 ACCCT-AAACCCTAAACCTTAAA-CCTAA
* *
14416140 AACC-AAACCC-AAATCC-TAAA-TTGAAA
1 ACCCTAAACCCTAAA-CCTTAAACCT--AA
* *
14416166 ACCCTAAACCCTAAGCCCTAAACCTAA
1 ACCCTAAACCCTAAACCTTAAACCTAA
* * *
14416193 ACCCT-AACGCTTACACCTTAACCCTAA
1 ACCCTAAAC-CCTAAACCTTAAACCTAA
*
14416220 ACCTTAGAA--CTAAA-CTATAAACCCTAA
1 ACCCTA-AACCCTAAACCT-TAAA-CCTAA
*
14416247 A-CC-AAAACCTAAACCTTAAAGCCTAA
1 ACCCTAAACCCTAAACCTTAAA-CCTAA
* *
14416273 ACCCT-AACCCTAAACCTTAAAACAAA
1 ACCCTAAACCCTAAACCTTAAACCTAA
* *
14416299 ACCCT-AACCCTAAACCCTAAAACCAAA
1 ACCCTAAACCCTAAA-CCTTAAACCTAA
14416326 ACCCTAAAC
1 ACCCTAAAC
14416335 TAACCTCAAA
Statistics
Matches: 172, Mismatches: 29, Indels: 43
0.70 0.12 0.18
Matches are distributed among these distances:
24 3 0.02
25 3 0.02
26 55 0.32
27 93 0.54
28 14 0.08
29 4 0.02
ACGTcount: A:0.46, C:0.35, G:0.02, T:0.17
Consensus pattern (27 bp):
ACCCTAAACCCTAAACCTTAAACCTAA
Found at i:14416337 original size:26 final size:27
Alignment explanation
Indices: 14416254--14416332 Score: 124
Period size: 26 Copynumber: 3.0 Consensus size: 27
14416244 TAAACCAAAA
* *
14416254 CCTAAACCTTAAAGCCTAAACCCTAAC
1 CCTAAACCTTAAAACCAAAACCCTAAC
14416281 CCTAAACCTTAAAA-CAAAACCCTAAC
1 CCTAAACCTTAAAACCAAAACCCTAAC
*
14416307 CCTAAACCCTAAAACCAAAACCCTAA
1 CCTAAACCTTAAAACCAAAACCCTAA
14416333 ACTAACCTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
26 24 0.50
27 24 0.50
ACGTcount: A:0.47, C:0.37, G:0.01, T:0.15
Consensus pattern (27 bp):
CCTAAACCTTAAAACCAAAACCCTAAC
Found at i:14417335 original size:21 final size:21
Alignment explanation
Indices: 14417306--14417356 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
14417296 TCTTAAAAGG
*
14417306 TGAAAAAATT-GAAAAGAAATT
1 TGAAAAAATTGGAAAA-AAAAT
*
14417327 TGAAGAAATTGGAAAAAAAAT
1 TGAAAAAATTGGAAAAAAAAT
14417348 TGAAAAAAT
1 TGAAAAAAT
14417357 GTTTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.16, T:0.22
Consensus pattern (21 bp):
TGAAAAAATTGGAAAAAAAAT
Found at i:14427705 original size:84 final size:84
Alignment explanation
Indices: 14427583--14427747 Score: 226
Period size: 84 Copynumber: 2.0 Consensus size: 84
14427573 TCAAAGCCGC
* * * *
14427583 TAATGAGACAAGATTTTTGAAAAAAGATCAATCGTAAACAACCCAAATTCACTTTGATGTTTAGT
1 TAATGAGACAAGATTTTTGAAAAAAAATCAATCATAAACAACCCAAATTCACCTTAATGTTTAGT
14427648 ATTT-AAAAATTTGAAACAT
66 ATTTGAAAAA-TTGAAACAT
* * * *
14427667 TAATGAGACAAGATTTTTGAAAAAAAATTAGGT-ATAAACGACCCAGATTCACCTTAATGTTTAG
1 TAATGAGACAAGATTTTTGAAAAAAAATCA-ATCATAAACAACCCAAATTCACCTTAATGTTTAG
14427731 TATTTGAAAAATTGAAA
65 TATTTGAAAAATTGAAA
14427748 ACGGATACTC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
84 65 0.92
85 6 0.08
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (84 bp):
TAATGAGACAAGATTTTTGAAAAAAAATCAATCATAAACAACCCAAATTCACCTTAATGTTTAGT
ATTTGAAAAATTGAAACAT
Found at i:14428053 original size:9 final size:9
Alignment explanation
Indices: 14428039--14428086 Score: 55
Period size: 8 Copynumber: 5.4 Consensus size: 9
14428029 GTCACAAAGA
14428039 AAAAAAATT
1 AAAAAAATT
14428048 -AAAAAATT
1 AAAAAAATT
14428056 -AAAAAATT
1 AAAAAAATT
*
14428064 GAAAAAAATG
1 -AAAAAAATT
*
14428074 AAAAAAATG
1 AAAAAAATT
14428083 AAAA
1 AAAA
14428087 TGAAAATGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 16 0.44
9 13 0.36
10 7 0.19
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (9 bp):
AAAAAAATT
Found at i:14428069 original size:18 final size:18
Alignment explanation
Indices: 14428039--14428086 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
14428029 GTCACAAAGA
*
14428039 AAAAAAATTAAAAAATT-
1 AAAAAAATGAAAAAATTG
* *
14428056 AAAAAATTGAAAAAAATG
1 AAAAAAATGAAAAAATTG
14428074 AAAAAAATGAAAA
1 AAAAAAATGAAAA
14428087 TGAAAATGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (18 bp):
AAAAAAATGAAAAAATTG
Found at i:14428780 original size:50 final size:49
Alignment explanation
Indices: 14428641--14429075 Score: 158
Period size: 50 Copynumber: 8.8 Consensus size: 49
14428631 ATAAATTTTT
* * *
14428641 CAAAATGAAATTTTTAAAAGTTTCCTAGCCT-TTGTT-TAGAAGAGCTATTC
1 CAAAATGAAATTTTTTAAAGTTTCCTAGCCTATT-TTATAGGA-ACCT-TTC
* * * ***
14428691 CAAAATTAAACTTTTTAAAGTTTCTTAATGTATCTTTATAGGAACCTTTC
1 CAAAATGAAATTTTTTAAAGTTTCCTAGCCTAT-TTTATAGGAACCTTTC
* * * * *
14428741 CAAAATGAGATTTTTTAAAGTTTCCTAGCCTATTATTATATGAGCATTTT
1 CAAAATGAAATTTTTTAAAGTTTCCTAGCCTATT-TTATAGGAACCTTTC
* * * * * *
14428791 CAAAAT-AAGA-TTTTTAATGTTTCTTAGCCTTTGTTTAGAGGAGA-TTTTT
1 CAAAATGAA-ATTTTTTAAAGTTTCCTAGCCTAT-TTTATAGGA-ACCTTTC
* ** * * *
14428840 CAAAATTGAAA-ATTTTAAAGTTTTTTAGCTTCTGTTTAGAGGAA-CTTTC
1 CAAAA-TGAAATTTTTTAAAGTTTCCTAGCCTAT-TTTATAGGAACCTTTC
* * * * * * **
14428889 CAAAATTGAAA-ATTTTAAAGCTTACTAGCCTCTGTTTAAATG-AGTTTTC
1 CAAAA-TGAAATTTTTTAAAGTTTCCTAGCCTAT-TTTATAGGAACCTTTC
* * * * * ** *
14428938 CAAAATTGAAATTTTTTAAAGTTTTCTAATCTCCA-TTTAAATG-AGTTTTT
1 CAAAA-TGAAATTTTTTAAAGTTTCCT-AGC-CTATTTTATAGGAACCTTTC
* * * * ** *
14428988 CAAAATTAGA-TTTTTAAAATTTCTTAGCCTATCTTTATAGGAGTCTTTT
1 CAAAATGAAATTTTTTAAAGTTTCCTAGCCTAT-TTTATAGGAACCTTTC
* * *
14429037 CAAAATGAAA-ATTTTAAAGTTTCTTAGCCTCTATTTATA
1 CAAAATGAAATTTTTTAAAGTTTCCTAGCCTAT-TTTATA
14429076 AGAGTTTTCC
Statistics
Matches: 302, Mismatches: 67, Indels: 33
0.75 0.17 0.08
Matches are distributed among these distances:
46 2 0.01
47 2 0.01
48 19 0.06
49 131 0.43
50 132 0.44
51 10 0.03
52 6 0.02
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.43
Consensus pattern (49 bp):
CAAAATGAAATTTTTTAAAGTTTCCTAGCCTATTTTATAGGAACCTTTC
Found at i:14428840 original size:49 final size:47
Alignment explanation
Indices: 14428636--14429182 Score: 267
Period size: 49 Copynumber: 11.1 Consensus size: 47
14428626 TACATATAAA
* * *
14428636 TTTTTCAAAATGAAATTTTTAAAAGTTTCCTAGCCTTTGTTTAGAAGAG
1 TTTTTCAAAAT-AAATTTTT-AAAGTTTCTTAGCCTTTGTTTATAGGAG
* * *** * * *
14428685 CTATTCCAAAATTAAACTTTTTAAAGTTTCTTAATGTATCTTTATAGGAAC
1 -TTTTTCAAAA-TAAA-TTTTTAAAGTTTCTTAGCCTTTGTTTATAGG-AG
* * * * * *
14428736 CTTTCCAAAATGAGATTTTTTAAAGTTTCCTAGCCTATT-ATTATATGAG
1 TTTTTCAAAAT-A-AATTTTTAAAGTTTCTTAGCCT-TTGTTTATAGGAG
* * *
14428785 CATTTTCAAAATAAGATTTTTAATGTTTCTTAGCCTTTGTTTAGAGGAG
1 -TTTTTCAAAATAA-ATTTTTAAAGTTTCTTAGCCTTTGTTTATAGGAG
* * * *
14428834 ATTTTTCAAAATTGAAAATTTTAAAGTTTTTTAG-CTTCTGTTTAGAGGAA
1 -TTTTTCAAAA-T-AAATTTTTAAAGTTTCTTAGCCTT-TGTTTATAGGAG
* * * * * * *
14428884 CTTTCCAAAATTGAAAATTTTAAAGCTTAC-TAGCCTCTGTTTAAATGAG
1 TTTTTCAAAA-T-AAATTTTTAAAG-TTTCTTAGCCTTTGTTTATAGGAG
* ** *** * *
14428933 TTTTCCAAAATTGAAATTTTTTAAAGTTT-TCTAATCTCCATTTAAATGAG
1 TTTTTCAAAA-T-AAA-TTTTTAAAGTTTCT-TAGCCTTTGTTTATAGGAG
* * * *
14428983 TTTTTCAAAATTAGATTTTTAAAATTTCTTAGCCTATCTTTATAGGAG
1 TTTTTCAAAA-TAAATTTTTAAAGTTTCTTAGCCTTTGTTTATAGGAG
* * * *
14429031 TCTTTTCAAAATGAAAATTTTAAAGTTTCTTAGCCTCTATTTATAAGAG
1 T-TTTTCAAAAT-AAATTTTTAAAGTTTCTTAGCCTTTGTTTATAGGAG
* * * * * * *
14429080 TTTTCCAAAATTGAGATTTTAAAAGCTTCATAGCCTTTTATTTATAGAAG
1 TTTTTCAAAA-T-AAATTTTTAAAGTTTCTTAGCC-TTTGTTTATAGGAG
* * * *
14429130 TTTTTCCAAATTAAGA-TTTTAAAGTTTCATAGCCTTTGTTTAGATGAG
1 TTTTT-CAAAATAA-ATTTTTAAAGTTTCTTAGCCTTTGTTTATAGGAG
14429178 TTTTT
1 TTTTT
14429183 GAAAGTTTAC
Statistics
Matches: 388, Mismatches: 85, Indels: 50
0.74 0.16 0.10
Matches are distributed among these distances:
48 51 0.13
49 171 0.44
50 151 0.39
51 15 0.04
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (47 bp):
TTTTTCAAAATAAATTTTTAAAGTTTCTTAGCCTTTGTTTATAGGAG
Found at i:14429179 original size:98 final size:97
Alignment explanation
Indices: 14428637--14429181 Score: 268
Period size: 99 Copynumber: 5.5 Consensus size: 97
14428627 ACATATAAAT
* * * * * *
14428637 TTTTCAAAATGAAATTTTTAAAAGTTTCCTAGCCTTTGTTTAGAA-GAGCTATTCCAAAATTAAA
1 TTTTCAAAATGAAAATTTT-AAAGTTTCATAGCCTCTATTTA-AATGAG-TTTTCCAAAATTAGA
** * *** * *
14428701 CTTTTTAAAGTTTCTTAATGTATCTTTATAGGAA-CC
63 -TTTTTAAAACTTCATAGCCTATATTTATA-GAAGTC
* ** * * * *
14428737 TTTCCAAAATGAGATTTTTTAAAGTTTCCTAGCCTAT-TATTATATGAGCATTTT-CAAAATAAG
1 TTTTCAAAATGA-AAATTTTAAAGTTTCATAGCCTCTAT-TTAAATGAG--TTTTCCAAAATTAG
*** * * * * *
14428800 ATTTTTAATGTTTCTTAGCCTTTGTTTAGAGGAGAT-
62 ATTTTTAAAACTTCATAGCCTATATTTATAGAAG-TC
** * * * * ** * *
14428836 TTTTCAAAATTGAAAATTTTAAAGTTTTTTAGCTTCTGTTTAGAGGAACTTTCCAAAATTGAAAA
1 TTTTCAAAA-TGAAAATTTTAAAGTTTCATAGCCTCTATTTAAATGAGTTTTCCAAAATT-AGAT
* * * *
14428901 TTTTAAAGCTT-ACTAGCCTCTGTTTAAATG-AGT-
64 TTTTAAAACTTCA-TAGCCTATATTTATA-GAAGTC
* * ** * *
14428934 TTTCCAAAATTGAAATTTTTTAAAGTTTTC-TAATCTCCATTTAAATGAGTTTTTCAAAATTAGA
1 TTTTCAAAA-TGAAA-ATTTTAAAG-TTTCATAGCCTCTATTTAAATGAGTTTTCCAAAATTAGA
* * * *
14428998 TTTTTAAAATTTCTTAGCCTATCTTTATAGGAGTC
63 TTTTTAAAACTTCATAGCCTATATTTATAGAAGTC
*
14429033 TTTTCAAAATGAAAATTTTAAAGTTTCTTAGCCTCTATTTATAA-GAGTTTTCCAAAATTGAGA-
1 TTTTCAAAATGAAAATTTTAAAGTTTCATAGCCTCTATTTA-AATGAGTTTTCCAAAATT-AGAT
*
14429096 TTTTAAAAGCTTCATAGCCTTTTATTTATAGAAGT-
64 TTTTAAAA-CTTCATAGCC-TATATTTATAGAAGTC
* * * * * *
14429131 TTTTCCAAATTAAGATTTTAAAGTTTCATAGCCTTTGTTTAGATGAGTTTT
1 TTTTCAAAATGAAAATTTTAAAGTTTCATAGCCTCTATTTAAATGAGTTTT
14429182 TGAAAGTTTA
Statistics
Matches: 347, Mismatches: 75, Indels: 48
0.74 0.16 0.10
Matches are distributed among these distances:
96 4 0.01
97 45 0.13
98 109 0.31
99 131 0.38
100 49 0.14
101 9 0.03
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (97 bp):
TTTTCAAAATGAAAATTTTAAAGTTTCATAGCCTCTATTTAAATGAGTTTTCCAAAATTAGATTT
TTAAAACTTCATAGCCTATATTTATAGAAGTC
Found at i:14429302 original size:31 final size:31
Alignment explanation
Indices: 14429267--14429332 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 31
14429257 ATCTCTAATG
14429267 AAAAAAA-AAAA-AACAATGAAAAAACCAAA-AT
1 AAAAAAAGAAAACAA-AAT-AAAAAA-CAAAGAT
14429298 AAAAAAAGAAAACAAAATAAAAAACAAAGAT
1 AAAAAAAGAAAACAAAATAAAAAACAAAGAT
14429329 AAAA
1 AAAA
14429333 GGGCAATGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
30 4 0.12
31 19 0.59
32 7 0.22
33 2 0.06
ACGTcount: A:0.82, C:0.08, G:0.05, T:0.06
Consensus pattern (31 bp):
AAAAAAAGAAAACAAAATAAAAAACAAAGAT
Found at i:14429320 original size:30 final size:31
Alignment explanation
Indices: 14429268--14429332 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
14429258 TCTCTAATGA
* *
14429268 AAAAAAAAAAAACAATGAAAAAACCAAA-AT
1 AAAAAAAAAAAACAATAAAAAAAACAAAGAT
*
14429298 AAAAAAAGAAAACAA-AATAAAAAACAAAGAT
1 AAAAAAAAAAAACAATAA-AAAAAACAAAGAT
14429329 AAAA
1 AAAA
14429333 GGGCAATGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 23 0.77
31 6 0.20
ACGTcount: A:0.82, C:0.08, G:0.05, T:0.06
Consensus pattern (31 bp):
AAAAAAAAAAAACAATAAAAAAAACAAAGAT
Found at i:14437490 original size:84 final size:84
Alignment explanation
Indices: 14437349--14437517 Score: 302
Period size: 84 Copynumber: 2.0 Consensus size: 84
14437339 AATTGCTTAT
* * *
14437349 ATTGAGGCATCACTATTCTAAATAGCCATCCCTATACACCTTTATCTTGTTATTGGCCAGCATCT
1 ATTGAAGCATCACTATTCTAAATAGCCATCCCTATACACCTTCATCTTGTTACTGGCCAGCATCT
14437414 GTAATTTATAGCTTATCCA
66 GTAATTTATAGCTTATCCA
*
14437433 ATTGAAGCATCACTATTCTAAATAGCCATCCCTATACACCTTCATCTTGTTACTGGCCATCATCT
1 ATTGAAGCATCACTATTCTAAATAGCCATCCCTATACACCTTCATCTTGTTACTGGCCAGCATCT
14437498 GTAATTTATAGCTTATCCA
66 GTAATTTATAGCTTATCCA
14437517 A
1 A
14437518 ATAAATGCTA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (84 bp):
ATTGAAGCATCACTATTCTAAATAGCCATCCCTATACACCTTCATCTTGTTACTGGCCAGCATCT
GTAATTTATAGCTTATCCA
Found at i:14438266 original size:115 final size:115
Alignment explanation
Indices: 14438147--14438678 Score: 396
Period size: 115 Copynumber: 4.6 Consensus size: 115
14438137 TATTGTCCCA
* * *
14438147 ATCATTCATCTTTGACCTCAACTCGATCTTGGTCA-TATTTAGACTTGCAGCATCATCCCAGTCA
1 ATCATTCATCTTTGACCTCGACTCGATCTTGGTCACT-TTTAGACTTACAGCATCATCCCAATCA
*
14438211 TCTAATCTCGACTCAATCCAGAACATTTTCCTAACTCATGGCATCATCCTG
65 TCTAATCTCGACTCAATCCAGAACATTTTCCTAACTCATAGCATCATCCTG
* ** * * * *
14438262 ATCATTCA-CTTTTGACCTCGATTTAATTTTGGTCACTTTCAAAC-T-CATGACATCATCCCAGT
1 ATCATTCATC-TTTGACCTCGACTCGATCTTGGTCACTTTTAGACTTACA-G-CATCATCCCAAT
* * * *
14438324 CATCTAATCT-TAGCTCAATCCA-AATCATTTTCTTAACTCATAGCATCGTCTTG
63 CATCTAATCTCGA-CTCAATCCAGAA-CATTTTCCTAACTCATAGCATCATCCTG
** * * * * * * *
14438377 -TCATTCATCTTCAACCTTGACTCGGTCTTGGTCACTTTCATACTTGCAACATCATCCTAATCAT
1 ATCATTCATCTTTGACCTCGACTCGATCTTGGTCACTTTTAGACTTACAGCATCATCCCAATCAT
** *** * ** * **
14438441 CCGATCTCGACTTGGTCTAGTTCATTTTCCTAACTCGTAGCATCATTTTG
66 CTAATCTCGACTCAATCCAGAACATTTTCCTAACTCATAGCATCATCCTG
* * * * * * * **
14438491 GTCATTCACCTTTGACCTCGACTTGGTCTTAGTCACTTTTAGACTCACGGCATGGTCCCAATCAT
1 ATCATTCATCTTTGACCTCGACTCGATCTTGGTCACTTTTAGACTTACAGCATCATCCCAATCAT
* * * * ** * * *
14438556 CTGATCTTGACTCAATTCAGATCATTTTTTTAACTCACAGTATCGT-CTCG
66 CTAATCTCGACTCAATCCAGAACATTTTCCTAACTCATAGCATCATCCT-G
* ** * * ** *
14438606 ATCATTCATCTATGACCTTAACTCGATCTTAGTCGCTTTTAGACTTACAGCATTGTCCCAACCAT
1 ATCATTCATCTTTGACCTCGACTCGATCTTGGTCACTTTTAGACTTACAGCATCATCCCAATCAT
14438671 CTAATCTC
66 CTAATCTC
14438679 AACTTAGTCT
Statistics
Matches: 323, Mismatches: 81, Indels: 26
0.75 0.19 0.06
Matches are distributed among these distances:
113 2 0.01
114 86 0.27
115 232 0.72
116 3 0.01
ACGTcount: A:0.24, C:0.28, G:0.11, T:0.36
Consensus pattern (115 bp):
ATCATTCATCTTTGACCTCGACTCGATCTTGGTCACTTTTAGACTTACAGCATCATCCCAATCAT
CTAATCTCGACTCAATCCAGAACATTTTCCTAACTCATAGCATCATCCTG
Found at i:14438698 original size:115 final size:115
Alignment explanation
Indices: 14438517--14438759 Score: 267
Period size: 115 Copynumber: 2.1 Consensus size: 115
14438507 CTCGACTTGG
* * * **
14438517 TCTTAGTCACTTTTAGACTCACGGCATGGTCCCAATCATCTGATCTTGACTCAATTCAGATCATT
1 TCTTAGTCACTTTTAGACTCACAGCATGGTCCCAACCATCTAATCTCAACTCAATTCAGATCATT
* *
14438582 TTTTTAACTCACAGTATCGTCTC-GATCATTCATCTAT-GACCTTAACTCGA
66 TTTTTAACTCACAGTATCATCCCTG-TCATTCATCT-TCGACCTTAACTCGA
* * * * * *
14438632 TCTTAGTCGCTTTTAGACTTACAGCATTGTCCCAACCATCTAATCTCAACT-TAGTCTAGATTAT
1 TCTTAGTCACTTTTAGACTCACAGCATGGTCCCAACCATCTAATCTCAACTCAATTC-AGATCAT
* * * *
14438696 TTTTTTGACTCACGGTATCATCCCTGTTATTCATCTTCGACCTTAGCTCGA
65 TTTTTTAACTCACAGTATCATCCCTGTCATTCATCTTCGACCTTAACTCGA
* *
14438747 TCCTGGTCACTTT
1 TCTTAGTCACTTT
14438760 CAAACTCGTG
Statistics
Matches: 105, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
114 4 0.04
115 100 0.95
116 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.38
Consensus pattern (115 bp):
TCTTAGTCACTTTTAGACTCACAGCATGGTCCCAACCATCTAATCTCAACTCAATTCAGATCATT
TTTTTAACTCACAGTATCATCCCTGTCATTCATCTTCGACCTTAACTCGA
Found at i:14439066 original size:12 final size:12
Alignment explanation
Indices: 14439049--14439212 Score: 53
Period size: 12 Copynumber: 13.9 Consensus size: 12
14439039 TATAGTATAC
14439049 TATTATTATTAG
1 TATTATTATTAG
*
14439061 TATTATTA-CAG
1 TATTATTATTAG
14439072 TA--ATTATATAG
1 TATTATTAT-TAG
*
14439083 TACATTATTATTTAT
1 T--ATTATTA-TTAG
*
14439098 TA-TATTATTAA
1 TATTATTATTAG
*
14439109 TATTATAATCT-G
1 TATTATTAT-TAG
14439121 ATATTATTATTCA-
1 -TATTATTATT-AG
* *
14439134 TATTATTATCAT
1 TATTATTATTAG
*
14439146 TA-TACTA-TA-
1 TATTATTATTAG
*
14439155 T-TTATTA-TAC
1 TATTATTATTAG
* * *
14439165 TATAATATATCAA
1 TATTAT-TATTAG
* *
14439178 TACTATTATTAT
1 TATTATTATTAG
*
14439190 TATTATTATTAT
1 TATTATTATTAG
14439202 TATTATTATTA
1 TATTATTATTA
14439213 TTTTTATTCT
Statistics
Matches: 115, Mismatches: 19, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
9 11 0.10
10 2 0.02
11 20 0.17
12 58 0.50
13 16 0.14
15 7 0.06
16 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.54
Consensus pattern (12 bp):
TATTATTATTAG
Found at i:14439094 original size:3 final size:3
Alignment explanation
Indices: 14439086--14439220 Score: 84
Period size: 3 Copynumber: 45.0 Consensus size: 3
14439076 TATATAGTAC
* *
14439086 ATT ATT ATTT ATT A-T ATT ATT AAT ATT ATA ATCT GA-T ATT ATT ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT AT-T -ATT ATT ATT ATT
* * * * *
14439132 CA-T ATT ATT ATC ATT A-T ACT A-T ATTT ATT A-T ACT ATA ATAT ATC
1 -ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT AT-T ATT
* * *
14439176 AAT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
14439221 CTCCCTTCCT
Statistics
Matches: 104, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
2 10 0.10
3 85 0.82
4 8 0.08
5 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:14439168 original size:19 final size:20
Alignment explanation
Indices: 14439136--14439174 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
14439126 ATTATTCATA
* *
14439136 TTATTATCATTATACTATAT
1 TTATTATCACTATAATATAT
14439156 TTATTAT-ACTATAATATAT
1 TTATTATCACTATAATATAT
14439175 CAATACTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATTATCACTATAATATAT
Found at i:14440024 original size:18 final size:17
Alignment explanation
Indices: 14440001--14440080 Score: 65
Period size: 18 Copynumber: 4.5 Consensus size: 17
14439991 TTTTTTCCTT
*
14440001 TTTATTTTATTTTTTTA
1 TTTATTTTATTTATTTA
*
14440018 TTCTATTTTCTTTATTTA
1 TT-TATTTTATTTATTTA
*
14440036 TTTA-TTCATTTATTT-
1 TTTATTTTATTTATTTA
*
14440051 TTTAATTTAATTTAATTTAA
1 TTT-ATTTTATTT-ATTT-A
14440071 TTTAATTTTA
1 TTT-ATTTTA
14440081 CTTTGCTAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
15 3 0.06
16 10 0.20
17 10 0.20
18 19 0.37
20 9 0.18
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTTATTTATTTA
Found at i:14440031 original size:22 final size:21
Alignment explanation
Indices: 14440006--14440046 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
14439996 TCCTTTTTAT
*
14440006 TTTATTTTTTTATTCTATTTTC
1 TTTATTTATTTATTC-ATTTTC
14440028 TTTATTTATTTATTCATTT
1 TTTATTTATTTATTCATTT
14440047 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTATTTATTTATTCATTTTC
Found at i:14440061 original size:5 final size:5
Alignment explanation
Indices: 14440051--14440078 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
14440041 TCATTTATTT
14440051 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
14440079 TACTTTGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:14450769 original size:26 final size:26
Alignment explanation
Indices: 14450740--14450797 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
14450730 TGCATGATTT
* * *
14450740 GTTTAGAATGTGGTTTAGGGTTTAGG
1 GTTTAGAAGGTGATTTAAGGTTTAGG
*
14450766 GTTTGGAAGGTGATTTAAGGTTTAGG
1 GTTTAGAAGGTGATTTAAGGTTTAGG
*
14450792 TTTTAG
1 GTTTAG
14450798 GGATTTGGGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (26 bp):
GTTTAGAAGGTGATTTAAGGTTTAGG
Found at i:14451594 original size:14 final size:14
Alignment explanation
Indices: 14451577--14451611 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
14451567 TCTTTAACTT
*
14451577 TCTTTTTTTTTCTC
1 TCTTTTTTTTGCTC
14451591 TCTTTTTTTTGCTC
1 TCTTTTTTTTGCTC
14451605 T-TTTTTT
1 TCTTTTTT
14451612 CACTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (14 bp):
TCTTTTTTTTGCTC
Found at i:14451598 original size:12 final size:13
Alignment explanation
Indices: 14451581--14451612 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
14451571 TAACTTTCTT
14451581 TTTTTTTCT-CTC
1 TTTTTTTCTGCTC
14451593 TTTTTTT-TGCTC
1 TTTTTTTCTGCTC
14451605 TTTTTTTC
1 TTTTTTTC
14451613 ACTATTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.06
12 17 0.94
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTTTTTCTGCTC
Found at i:14451627 original size:26 final size:23
Alignment explanation
Indices: 14451580--14451647 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 23
14451570 TTAACTTTCT
*
14451580 TTTTTTTTCTCTCTTTTTTTTGC
1 TTTTTTTTCTCTATTTTTTTTGC
*
14451603 TCTTTTTTTCACTATTTTTCCTTTGC
1 T-TTTTTTTCTCTATTTTT--TTTGC
*
14451629 TTTTCTTTGCTCTATTTTT
1 TTTT-TTTTCTCTATTTTT
14451648 GCATTCCTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 1 0.03
24 15 0.41
25 3 0.08
26 18 0.49
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTTTTTTCTCTATTTTTTTTGC
Found at i:14452950 original size:13 final size:12
Alignment explanation
Indices: 14452928--14452963 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
14452918 TACTTGTTGG
14452928 TTTTTTTTTTCT
1 TTTTTTTTTTCT
14452940 TTTTTTGTTTTCT
1 TTTTTT-TTTTCT
14452953 TTTTATTTTTT
1 TTTT-TTTTTT
14452964 TGTCAAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 14 0.64
14 2 0.09
ACGTcount: A:0.03, C:0.06, G:0.03, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTCT
Found at i:14452955 original size:19 final size:19
Alignment explanation
Indices: 14452927--14452966 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
14452917 TTACTTGTTG
* *
14452927 GTTTTTTTTTTCTTTTTTT
1 GTTTTCTTTTTATTTTTTT
14452946 GTTTTCTTTTTATTTTTTT
1 GTTTTCTTTTTATTTTTTT
14452965 GT
1 GT
14452967 CAAGATTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.03, C:0.05, G:0.07, T:0.85
Consensus pattern (19 bp):
GTTTTCTTTTTATTTTTTT
Found at i:14453308 original size:51 final size:50
Alignment explanation
Indices: 14453058--14453310 Score: 185
Period size: 51 Copynumber: 5.0 Consensus size: 50
14453048 TACATAGAAT
* * * * * *
14453058 GGTTGAGACTCACACCAAGATTTTTCAAAAGGTTTAAGATTCATACTG-AAA
1 GGTTGGGATTCACACCAAGATTCTTC-AAAGGTTCATGATTCACAC-GAAAA
* *
14453109 GGTTGGAATTCACACCAAGATTCATT--AAGGTTCGA-GATTCACACCAAAAA
1 GGTTGGGATTCACACCAAGATTC-TTCAAAGGTTC-ATGATTCACA-CGAAAA
* * * **
14453159 GCTTGGGATTCGCACC-AGAATTCTTCACAGGTTTGTGATTCACACTGAGAAA
1 GGTTGGGATTCACACCAAG-ATTCTTCAAAGGTTCATGATTCACAC-GA-AAA
* * * * * ** *
14453211 -GCTAGGATTAACACCAAAATTCTTTAAAGGTTCGGGATTCATATCGAAAA
1 GGTTGGGATTCACACCAAGATTCTTCAAAGGTTCATGATTCACA-CGAAAA
14453261 GGTTGGGATTCACACCAAGATTCTTCAAAGGTTCATGATTCACATCGAAA
1 GGTTGGGATTCACACCAAGATTCTTCAAAGGTTCATGATTCACA-CGAAA
14453311 GGCTCTGAAT
Statistics
Matches: 156, Mismatches: 33, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
49 17 0.11
50 26 0.17
51 106 0.68
52 7 0.04
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (50 bp):
GGTTGGGATTCACACCAAGATTCTTCAAAGGTTCATGATTCACACGAAAA
Found at i:14453328 original size:102 final size:100
Alignment explanation
Indices: 14453035--14453328 Score: 272
Period size: 102 Copynumber: 2.9 Consensus size: 100
14453025 TTCTCATCAA
* * * * * * * *
14453035 AAGGTTCGAGATTTACA-TAGAATGGTTGAGACTCACACCAAGATTTTTCAAAAGGTTTAAGATT
1 AAGGTTCGAGATTCACACCAAAAAGGTTGGGATTCACACCAAGATTCTTC-AAAGGTTTATGATT
* *
14453099 CATACTGAAAGG-TTGGAATTCACACCAAGATTCATT
65 CACACTGAAAGGCTT-GAATTCACACCAAAATTCATT
* * * *
14453135 AAGGTTCGAGATTCACACCAAAAAGCTTGGGATTCGCACC-AGAATTCTTCACAGGTTTGTGATT
1 AAGGTTCGAGATTCACACCAAAAAGGTTGGGATTCACACCAAG-ATTCTTCAAAGGTTTATGATT
* * * * *
14453199 CACACTGAGAAAGCTAGGATTAACACCAAAATTCTTT
65 CACACTGA-AAGGCTTGAATTCACACCAAAATTCATT
* * * * *
14453236 AAAGGTTCGGGATTCATATCGAAAAGGTTGGGATTCACACCAAGATTCTTCAAAGGTTCATGATT
1 -AAGGTTCGAGATTCACACCAAAAAGGTTGGGATTCACACCAAGATTCTTCAAAGGTTTATGATT
*
14453301 CACA-TCGAAAGGCTCTGAATTCGCACCA
65 CACACT-GAAAGGCT-TGAATTCACACCA
14453329 GGATTTTCTA
Statistics
Matches: 153, Mismatches: 33, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
100 36 0.24
101 47 0.31
102 68 0.44
103 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (100 bp):
AAGGTTCGAGATTCACACCAAAAAGGTTGGGATTCACACCAAGATTCTTCAAAGGTTTATGATTC
ACACTGAAAGGCTTGAATTCACACCAAAATTCATT
Found at i:14453404 original size:51 final size:50
Alignment explanation
Indices: 14453347--14453655 Score: 222
Period size: 51 Copynumber: 6.1 Consensus size: 50
14453337 TAATAGTTTG
* * *
14453347 GGATTCACACTAGGAGTTTTCAAGGGTTCGAAATTCACACCAAAAAGGCTA
1 GGATTCACACCAGGA-TTTTCAAAGGTTCGAAATTCACACTAAAAAGGCTA
* * * * * *
14453398 GGATTCACATCAGGATTCTTCAAAGGTACGAGACTAACACTAGAAAGGCTA
1 GGATTCACACCAGGATT-TTCAAAGGTTCGAAATTCACACTAAAAAGGCTA
* * *
14453449 GGATTCACACCAAGA---TCAAAGGTTC-AAGATTCACATTGAAATA-GCTA
1 GGATTCACACCAGGATTTTCAAAGGTTCGAA-ATTCACACT-AAAAAGGCTA
* ** *
14453496 GGATTCACACCAGGATTCTTCAAAGGTTC-AAGATTTACA-TTGAAAGGCTTT
1 GGATTCACACCAGGATT-TTCAAAGGTTCGAA-ATTCACACTAAAAAGGC-TA
* * * *
14453547 GGATTCACACTAAGATTTTTCAAAGGTTTGAGATTCACA-TCAAAAAGGC-A
1 GGATTCACACCAGGA-TTTTCAAAGGTTCGAAATTCACACT-AAAAAGGCTA
* * * * *
14453597 GGGATTCACACCAAGATTTTTCTAAGCTTTGAGATTCACACTAAAAAGGCTA
1 -GGATTCACACCAGGA-TTTTCAAAGGTTCGAAATTCACACTAAAAAGGCTA
*
14453649 GGGTTCA
1 GGATTCA
14453656 AGATTCATAA
Statistics
Matches: 207, Mismatches: 36, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
46 1 0.00
47 33 0.16
48 3 0.01
49 2 0.01
50 5 0.02
51 152 0.73
52 11 0.05
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (50 bp):
GGATTCACACCAGGATTTTCAAAGGTTCGAAATTCACACTAAAAAGGCTA
Found at i:14453798 original size:41 final size:41
Alignment explanation
Indices: 14453753--14454026 Score: 183
Period size: 42 Copynumber: 6.5 Consensus size: 41
14453743 ACTTCCAAAA
* * * *
14453753 TCACAATAGAAAAATGATTCATAATTCGAAGGATTTTGGAT
1 TCACAATAGAAAAATGATTCACAATTTGGAGGACTTTGGAT
* * * *
14453794 TCACAATAAACAAAATGATTCATAGTTTGGATGACTTTGGAT
1 TCACAATAGA-AAAATGATTCACAATTTGGAGGACTTTGGAT
* * ** * *** * *
14453836 TCACAACAGAGTAAACAATTCACAGTTTGGCTAACTCTGAAT
1 TCACAATAGA-AAAATGATTCACAATTTGGAGGACTTTGGAT
* * * * * *
14453878 TCATAACAGAAAAATGATTCATAATTCGAAGGATTTTGGAT
1 TCACAATAGAAAAATGATTCACAATTTGGAGGACTTTGGAT
* * * * *
14453919 TCATAACAAAAAAAAAAATGATTCACAATTTGGATGACTCTGAAT
1 TC---AC-AATAGAAAAATGATTCACAATTTGGAGGACTTTGGAT
* *
14453964 TCACAATAGAGAAATGATTCACAGTTTGGAGGACTTAT--AT
1 TCACAATAGAAAAATGATTCACAATTTGGAGGACTT-TGGAT
14454004 TCACAATAGAAAAAATGATTCAC
1 TCACAATAG-AAAAATGATTCAC
14454027 GGTTTGGATG
Statistics
Matches: 178, Mismatches: 48, Indels: 14
0.74 0.20 0.06
Matches are distributed among these distances:
40 11 0.06
41 67 0.38
42 69 0.39
44 1 0.01
45 30 0.17
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (41 bp):
TCACAATAGAAAAATGATTCACAATTTGGAGGACTTTGGAT
Found at i:14453965 original size:86 final size:82
Alignment explanation
Indices: 14453853--14454055 Score: 219
Period size: 86 Copynumber: 2.4 Consensus size: 82
14453843 AGAGTAAACA
* * * *
14453853 ATTCACAGTTTGGCTAACTCTGAATTCATAACAGAAAAATGATTCATAATTCGAAGGA-TTTTGG
1 ATTCACAGTTTGGATGACTCTGAATTCATAACAGAAAAATGATTCACAATTCGAAGGACTTAT--
14453917 ATTCATAACAAAAAAAAAAATG
64 ATTC---ACAAAAAAAAAAATG
* * * * * * *
14453939 ATTCACAATTTGGATGACTCTGAATTCACAATAGAGAAATGATTCACAGTTTGGAGGACTTATAT
1 ATTCACAGTTTGGATGACTCTGAATTCATAACAGAAAAATGATTCACAATTCGAAGGACTTATAT
* *
14454004 TCACAATAGAAAAAATG
66 TCACAAAAAAAAAAATG
* *
14454021 ATTCACGGTTTGGATGACTCTTAATTCATAACAGA
1 ATTCACAGTTTGGATGACTCTGAATTCATAACAGA
14454056 GAACGATACA
Statistics
Matches: 98, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
82 43 0.44
85 4 0.04
86 48 0.49
87 3 0.03
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (82 bp):
ATTCACAGTTTGGATGACTCTGAATTCATAACAGAAAAATGATTCACAATTCGAAGGACTTATAT
TCACAAAAAAAAAAATG
Found at i:14454032 original size:41 final size:42
Alignment explanation
Indices: 14453708--14454048 Score: 192
Period size: 41 Copynumber: 8.1 Consensus size: 42
14453698 AAAGGCTTTA
** * * * **
14453708 AATTCACAATAGAGTAAATGGTTCATAGTTTGGCT-ACTTCCA
1 AATTCACAATAGAAAAAATGATTCACAGTTTGGATGAC-TCTG
* * * * * * * *
14453750 AAATCACAATAG-AAAAATGATTCATAATTCGAAGGATTTTG
1 AATTCACAATAGAAAAAATGATTCACAGTTTGGATGACTCTG
* * *
14453791 GATTCACAATA-AACAAAATGATTCATAGTTTGGATGACTTTG
1 AATTCACAATAGAA-AAAATGATTCACAGTTTGGATGACTCTG
* * ** ** * *
14453833 GATTCACAACAGAGTAAACAATTCACAGTTTGGCTAACTCTG
1 AATTCACAATAGAAAAAATGATTCACAGTTTGGATGACTCTG
* * * * * * * * *
14453875 AATTCATAACAG-AAAAATGATTCATAATTCGAAGGATTTTG
1 AATTCACAATAGAAAAAATGATTCACAGTTTGGATGACTCTG
* * * *
14453916 GATTCATAACAAAAAAAAAAATGATTCACAATTTGGATGACTCTG
1 AATTC---ACAATAGAAAAAATGATTCACAGTTTGGATGACTCTG
* *
14453961 AATTCACAATAG-AGAAATGATTCACAGTTTGGAGGACT-T-
1 AATTCACAATAGAAAAAATGATTCACAGTTTGGATGACTCTG
* *
14454000 ATATTCACAATAGAAAAAATGATTCACGGTTTGGATGACTCTT
1 A-ATTCACAATAGAAAAAATGATTCACAGTTTGGATGACTCTG
14454043 AATTCA
1 AATTCA
14454049 TAACAGAGAA
Statistics
Matches: 224, Mismatches: 63, Indels: 24
0.72 0.20 0.08
Matches are distributed among these distances:
39 1 0.00
40 12 0.05
41 91 0.41
42 87 0.39
43 2 0.01
44 4 0.02
45 27 0.12
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (42 bp):
AATTCACAATAGAAAAAATGATTCACAGTTTGGATGACTCTG
Found at i:14454047 original size:82 final size:82
Alignment explanation
Indices: 14453931--14454091 Score: 225
Period size: 82 Copynumber: 2.0 Consensus size: 82
14453921 ATAACAAAAA
* * *
14453931 AAAAAATGATTCACAATTTGGATGACTCTGAATTCACAATAGAGAAATGATTCACAGTTTGGAGG
1 AAAAAATGATTCACAATTTGGATGACTCTGAATTCACAACAGAG-AACGATACACAGTTTGGAGG
*
14453996 AC-TTATATTCACAATAG
65 ACATTAGATTCACAATAG
** * * *
14454013 AAAAAATGATTCACGGTTTGGATGACTCTTAATTCATAACAGAGAACGATACATAGTTTGGAGGA
1 AAAAAATGATTCACAATTTGGATGACTCTGAATTCACAACAGAGAACGATACACAGTTTGGAGGA
14454078 CATTAGATTCACAA
66 CATTAGATTCACAA
14454092 CAGAGTAAAC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
81 19 0.28
82 50 0.72
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (82 bp):
AAAAAATGATTCACAATTTGGATGACTCTGAATTCACAACAGAGAACGATACACAGTTTGGAGGA
CATTAGATTCACAATAG
Found at i:14454382 original size:20 final size:20
Alignment explanation
Indices: 14454357--14454394 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
14454347 TATTATGATT
14454357 CAAATGCAAGTGTCCCTAGG
1 CAAATGCAAGTGTCCCTAGG
*
14454377 CAAATGCAAGTGTTCCTA
1 CAAATGCAAGTGTCCCTA
14454395 AGATTTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (20 bp):
CAAATGCAAGTGTCCCTAGG
Found at i:14455688 original size:25 final size:26
Alignment explanation
Indices: 14455635--14455686 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
14455625 TTTCAACATC
14455635 AAGATTTTATAATCAATACAAAAATA
1 AAGATTTTATAATCAATACAAAAATA
14455661 AAGA-TTTATAATCAATA-AAAAATA
1 AAGATTTTATAATCAATACAAAAATA
14455685 AA
1 AA
14455687 AGTTTTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 9 0.35
25 13 0.50
26 4 0.15
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.29
Consensus pattern (26 bp):
AAGATTTTATAATCAATACAAAAATA
Found at i:14456689 original size:13 final size:14
Alignment explanation
Indices: 14456671--14456709 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
14456661 AAAAAAAAAT
14456671 TTTTTTTTCTTTC-
1 TTTTTTTTCTTTCA
14456684 TTTTTTTTAC-TTCA
1 TTTTTTTT-CTTTCA
14456698 TTTTTTTTCTTT
1 TTTTTTTTCTTT
14456710 TTTATTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTTTCTTTCA
Found at i:14456809 original size:5 final size:5
Alignment explanation
Indices: 14456799--14456839 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
14456789 AAATAGGCTA
14456799 AAAAT AAAAT AAAAT CAAAAT -AAA- AAAAT AAAAAT AAAAT A
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT -AAAAT AAAAT A
14456840 GAAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 6 0.19
5 16 0.50
6 10 0.31
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:14456811 original size:11 final size:11
Alignment explanation
Indices: 14456797--14456848 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
14456787 AAAAATAGGC
14456797 TAAAAATAAAA
1 TAAAAATAAAA
14456808 T-AAAATCAAAA
1 TAAAAAT-AAAA
14456819 T--AAA-AAAA
1 TAAAAATAAAA
14456827 TAAAAATAAAA
1 TAAAAATAAAA
14456838 TAGAAAA-AAAA
1 TA-AAAATAAAA
14456849 ACCTATGATC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 5 0.14
10 11 0.31
11 16 0.44
12 4 0.11
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:14456828 original size:19 final size:20
Alignment explanation
Indices: 14456804--14456846 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
14456794 GGCTAAAAAT
14456804 AAAAT-AAAATCAAAATA-AA
1 AAAATAAAAAT-AAAATAGAA
14456823 AAAATAAAAATAAAATAGAA
1 AAAATAAAAATAAAATAGAA
14456843 AAAA
1 AAAA
14456847 AAACCTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAATAAAAATAAAATAGAA
Found at i:14456848 original size:25 final size:24
Alignment explanation
Indices: 14456798--14456849 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
14456788 AAAATAGGCT
*
14456798 AAAAATAAAATAAAATCAAAATAA
1 AAAAATAAAATAAAATCAAAAAAA
*
14456822 AAAAATAAAAATAAAAT-AGAAAAA
1 AAAAAT-AAAATAAAATCAAAAAAA
14456846 AAAA
1 AAAA
14456850 CCTATGATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (24 bp):
AAAAATAAAATAAAATCAAAAAAA
Found at i:14457353 original size:21 final size:20
Alignment explanation
Indices: 14457332--14457370 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
14457322 CTTTTGCAAC
*
14457332 CCTAAATTCAC-CTCTAGAAA
1 CCTAAAATCACAC-CTAGAAA
14457352 CCTAAAATCACACCTAGAA
1 CCTAAAATCACACCTAGAA
14457371 CTACGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.44, C:0.31, G:0.05, T:0.21
Consensus pattern (20 bp):
CCTAAAATCACACCTAGAAA
Found at i:14457734 original size:14 final size:13
Alignment explanation
Indices: 14457715--14457746 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
14457705 AATAAGAGAA
14457715 AAAAACAAAAAAT
1 AAAAACAAAAAAT
14457728 GAAAAACAAAAAAT
1 -AAAAACAAAAAAT
14457742 AAAAA
1 AAAAA
14457747 TAAATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (13 bp):
AAAAACAAAAAAT
Found at i:14457770 original size:3 final size:3
Alignment explanation
Indices: 14457739--14457807 Score: 77
Period size: 3 Copynumber: 23.3 Consensus size: 3
14457729 AAAAACAAAA
* * * * *
14457739 AAT AAA AAT AA- ATT AAT AAT ACT AGT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
14457786 AAC AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
14457808 TGATAAGATA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
2 1 0.02
3 53 0.98
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Done.