Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, 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: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 22 of 74
Found at i:5366693 original size:14 final size:15
Alignment explanation
Indices: 5366665--5366696 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5366655 TTTAATTAAT
5366665 TTTTTTATTACAAAA
1 TTTTTTATTACAAAA
*
5366680 TTTTTTATTAAAAAA
1 TTTTTTATTACAAAA
5366695 TT
1 TT
5366697 AAAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTTTATTACAAAA
Found at i:5366980 original size:13 final size:13
Alignment explanation
Indices: 5366960--5367013 Score: 58
Period size: 13 Copynumber: 4.1 Consensus size: 13
5366950 AAAATTTATT
5366960 TAATAAAAATAAAA
1 TAAT-AAAATAAAA
5366974 TTAA-AAAACT-AAA
1 -TAATAAAA-TAAAA
*
5366987 TAATAAATTAAAA
1 TAATAAAATAAAA
5367000 TAATAAAATAAAA
1 TAATAAAATAAAA
5367013 T
1 T
5367014 TTAGATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 4 0.12
13 26 0.76
14 1 0.03
15 3 0.09
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (13 bp):
TAATAAAATAAAA
Found at i:5367039 original size:21 final size:21
Alignment explanation
Indices: 5367000--5367039 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5366990 TAAATTAAAA
* **
5367000 TAATAAAATAAAATTTAGATT
1 TAATAAAAAAAAAAATAGATT
5367021 TAATAAAAAAAAAAATAGA
1 TAATAAAAAAAAAAATAGA
5367040 GTTTTGGAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
TAATAAAAAAAAAAATAGATT
Found at i:5375178 original size:14 final size:14
Alignment explanation
Indices: 5375139--5375181 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
5375129 GATTTATTGT
* *
5375139 TATATATATATATA
1 TATATATGTATTTA
5375153 TATATATGTATTTA
1 TATATATGTATTTA
* *
5375167 TATTTATTTATTTA
1 TATATATGTATTTA
5375181 T
1 T
5375182 TTATTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TATATATGTATTTA
Found at i:5375182 original size:18 final size:18
Alignment explanation
Indices: 5375147--5375193 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
5375137 GTTATATATA
*
5375147 TATATATATATATGTATT
1 TATATTTATATATGTATT
* *
5375165 TATATTTATTTATTTATT
1 TATATTTATATATGTATT
5375183 TAT-TTTATATA
1 TATATTTATATA
5375194 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TATATTTATATATGTATT
Found at i:5375673 original size:9 final size:9
Alignment explanation
Indices: 5375659--5375683 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5375649 ACCTTTAATT
5375659 TTTTTTTTG
1 TTTTTTTTG
5375668 TTTTTTTTG
1 TTTTTTTTG
5375677 TTTTTTT
1 TTTTTTT
5375684 AAATTCTCAA
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:5380485 original size:24 final size:24
Alignment explanation
Indices: 5380453--5380515 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
5380443 AAGCTGGTTT
5380453 CTGGTGTTGTTGGGTTGGA-CGGCA
1 CTGGTGTTGTTGGGTTGGATCGG-A
* *
5380477 CTGGTGTTGTTAGGTTGGATTGGA
1 CTGGTGTTGTTGGGTTGGATCGGA
*
5380501 TTGGTGTTGTTGGGT
1 CTGGTGTTGTTGGGT
5380516 GGTCTGTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 32 0.94
25 2 0.06
ACGTcount: A:0.08, C:0.06, G:0.44, T:0.41
Consensus pattern (24 bp):
CTGGTGTTGTTGGGTTGGATCGGA
Found at i:5381055 original size:19 final size:19
Alignment explanation
Indices: 5381029--5381066 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
5381019 ATTTTTGCTG
5381029 TTTTCTTTTTTTT-TTTTT
1 TTTTCTTTTTTTTGTTTTT
5381047 TTTTACTTTTTTTTGTTTTT
1 TTTT-CTTTTTTTTGTTTTT
5381067 ATAATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 9 0.50
20 5 0.28
ACGTcount: A:0.03, C:0.05, G:0.03, T:0.89
Consensus pattern (19 bp):
TTTTCTTTTTTTTGTTTTT
Found at i:5381067 original size:16 final size:16
Alignment explanation
Indices: 5381037--5381067 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5381027 TGTTTTCTTT
*
5381037 TTTTTTTTTTTTTTAC
1 TTTTTTTTGTTTTTAC
5381053 TTTTTTTTGTTTTTA
1 TTTTTTTTGTTTTTA
5381068 TAATTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.03, G:0.03, T:0.87
Consensus pattern (16 bp):
TTTTTTTTGTTTTTAC
Found at i:5381837 original size:22 final size:22
Alignment explanation
Indices: 5381801--5381862 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
5381791 TTTTGCTTGA
5381801 AAGTCTTGAAA-ATTATGTTTGG
1 AAGTCTT-AAAGATTATGTTTGG
5381823 -AGATCTTAAAGATTATGTTTGG
1 AAG-TCTTAAAGATTATGTTTGG
* *
5381845 AAGTTTTAGAGATTATGT
1 AAGTCTTAAAGATTATGT
5381863 CTGAAGGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 5 0.14
22 28 0.80
23 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.23, T:0.42
Consensus pattern (22 bp):
AAGTCTTAAAGATTATGTTTGG
Found at i:5381893 original size:149 final size:146
Alignment explanation
Indices: 5381570--5381942 Score: 378
Period size: 149 Copynumber: 2.5 Consensus size: 146
5381560 GTTTTTCTTG
* * * *
5381570 GAGGTTTTACAAATCTCAACATTTTTAAATGTTTTTCATATTAGAAGCATTGAAAA-TTTGAAAA
1 GAGGTTTTACAAATCTCAAAATTTTTGAATGTTTCTCATATTAGATGCATT-AAAACTTTGAAAA
* * *
5381634 TTTAAAATGTTTTGTTTAAATATTTATAGATTATACTTGAAAGTCTTAAAGATTATGTTCAAAAG
65 TTTAAAATGTTTTGTTGAAATATTGATAAATTATACTTGAAAGTCTTAAAGATTATGTTCAAAAG
5381699 TTTTAGAAATTATATTC
130 TTTTAGAAATTATATTC
* * * *
5381716 GGGGTTTTACAAATATTAAAAATCTTTGAATGTTTCTCATATTAGATGCATTAAAACTTTGAAAA
1 GAGGTTTTACAAAT-CTCAAAATTTTTGAATGTTTCTCATATTAGATGCATTAAAACTTTGAAAA
* * ** * **
5381781 TTTAAAATATTTTTGCTTGAAAGTCTTGA-AAATTATGTTTG-GAGATCTTAAAGATTATGTTTG
65 TTTAAAAT-GTTTTG-TTGAAA-TATTGATAAATTATACTTGAAAG-TCTTAAAGATTATGTTCA
* * *
5381844 GAAGTTTTAGAGATTAT-GTC
126 AAAGTTTTAGAAATTATATTC
* * * * * * *
5381864 TGAAGGTATTATAAATCTCAATATTTTTGAATGCTTCTCGTATCAGATGCATTGAAACTTTGAAA
1 -G-AGGTTTTACAAATCTCAAAATTTTTGAATGTTTCTCATATTAGATGCATTAAAACTTTGAAA
*
5381929 ATTT-AGATGTTTTG
64 ATTTAAAATGTTTTG
5381943 CTTGGAGCTC
Statistics
Matches: 185, Mismatches: 34, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
146 17 0.09
147 51 0.28
148 12 0.06
149 91 0.49
150 14 0.08
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (146 bp):
GAGGTTTTACAAATCTCAAAATTTTTGAATGTTTCTCATATTAGATGCATTAAAACTTTGAAAAT
TTAAAATGTTTTGTTGAAATATTGATAAATTATACTTGAAAGTCTTAAAGATTATGTTCAAAAGT
TTTAGAAATTATATTC
Found at i:5382228 original size:22 final size:23
Alignment explanation
Indices: 5382188--5382235 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
5382178 GATGTCAGAG
5382188 AAACTAGGTTTAAAATGTCAACT
1 AAACTAGGTTTAAAATGTCAACT
* *
5382211 AAACTGGGTTT-AAATGTCAGCT
1 AAACTAGGTTTAAAATGTCAACT
5382233 AAA
1 AAA
5382236 TTAGACTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (23 bp):
AAACTAGGTTTAAAATGTCAACT
Found at i:5384233 original size:1 final size:1
Alignment explanation
Indices: 5384227--5384296 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
5384217 TTTCTTTGCC
** ** * * * * * *
5384227 TTTTTTTTTTTTTTTACTTTTGCTTTTTCTTTCTTTTTTTCTTTTATTTATTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5384292 TTTTT
1 TTTTT
5384297 GAAACAATTG
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.04, C:0.09, G:0.01, T:0.86
Consensus pattern (1 bp):
T
Found at i:5384254 original size:24 final size:23
Alignment explanation
Indices: 5384217--5384297 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 23
5384207 CATATCTTTC
5384217 TTTC-TTTGCCTTTTTTTTTTTTT
1 TTTCTTTTG-CTTTTTTTTTTTTT
* *
5384240 TTACTTTTGCTTTTTCTTTCTTTT
1 TTTCTTTTGCTTTTT-TTTTTTTT
**
5384264 TTTCTTTTATTTATTTTTTTTCTTT
1 TTTCTTTTGCTT-TTTTTTTT-TTT
*
5384289 TTTTTTTTG
1 TTTCTTTTG
5384298 AAACAATTGA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
23 9 0.20
24 24 0.52
25 13 0.28
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.81
Consensus pattern (23 bp):
TTTCTTTTGCTTTTTTTTTTTTT
Found at i:5384266 original size:30 final size:27
Alignment explanation
Indices: 5384226--5384296 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 27
5384216 CTTTCTTTGC
*
5384226 CTTT-TTTTTTTTTTTTACTTTTGCTTTTT
1 CTTTCTTTTTTTTTTTTA--TTT-ATTTTT
*
5384255 CTTTCTTTTTTTCTTTTATTTATTTTT
1 CTTTCTTTTTTTTTTTTATTTATTTTT
5384282 -TTTCTTTTTTTTTTT
1 CTTTCTTTTTTTTTTT
5384297 GAAACAATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 14 0.37
27 5 0.13
28 3 0.08
29 4 0.11
30 12 0.32
ACGTcount: A:0.04, C:0.10, G:0.01, T:0.85
Consensus pattern (27 bp):
CTTTCTTTTTTTTTTTTATTTATTTTT
Found at i:5384271 original size:17 final size:18
Alignment explanation
Indices: 5384213--5384289 Score: 63
Period size: 18 Copynumber: 4.4 Consensus size: 18
5384203 AGTGCATATC
*
5384213 TTTC-TTTCTTTGCCTTTT
1 TTTCTTTTCTTT-ACTTTT
*
5384231 TTT-TTTTTTTTACTTTT
1 TTTCTTTTCTTTACTTTT
**
5384248 GCT-TTTTCTTT-CTTTT
1 TTTCTTTTCTTTACTTTT
* *
5384264 TTTCTTTTATTTATTTTT
1 TTTCTTTTCTTTACTTTT
5384282 TTTCTTTT
1 TTTCTTTT
5384290 TTTTTTTGAA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
16 6 0.13
17 20 0.43
18 21 0.45
ACGTcount: A:0.04, C:0.13, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTCTTTTCTTTACTTTT
Found at i:5393877 original size:6 final size:6
Alignment explanation
Indices: 5393866--5393890 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5393856 CAAACCAATT
5393866 TCTCTA TCTCTA TCTCTA TCTCTA T
1 TCTCTA TCTCTA TCTCTA TCTCTA T
5393891 GGAAGAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTCTA
Found at i:5395581 original size:17 final size:17
Alignment explanation
Indices: 5395555--5395593 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5395545 AAGAATTCCA
* *
5395555 ATTCATAAGTATTGAAG
1 ATTCACAAGTATTAAAG
5395572 ATTCACAAGTATTAAAG
1 ATTCACAAGTATTAAAG
5395589 ATTCA
1 ATTCA
5395594 TAAGAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (17 bp):
ATTCACAAGTATTAAAG
Found at i:5395766 original size:22 final size:21
Alignment explanation
Indices: 5395691--5395766 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 21
5395681 TCAACTTAGG
* *
5395691 GATTCACATCAAA-ATTTCAA
1 GATTCACACCAAACATTTAAA
**
5395711 GGCTCACACC-AACATTTAAA
1 GATTCACACCAAACATTTAAA
*
5395731 GATTCACATTCAAACATTCTAGAA
1 GATTCACA-CCAAACATT-TA-AA
5395755 G-TTCACACCAAA
1 GATTCACACCAAA
5395767 GGTTAAGATT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 2 0.05
20 19 0.44
21 1 0.02
22 10 0.23
23 8 0.19
24 3 0.07
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (21 bp):
GATTCACACCAAACATTTAAA
Found at i:5395941 original size:23 final size:22
Alignment explanation
Indices: 5395902--5395951 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 22
5395892 CACTTCCAAA
*
5395902 ATTCACATTAAAAATTTTAGAG
1 ATTCAAATTAAAAATTTTAGAG
5395924 ATTCAAATTCAAAAATTTTAGAG
1 ATTCAAATT-AAAAATTTTAGAG
5395947 ATTCA
1 ATTCA
5395952 CACTCAAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (22 bp):
ATTCAAATTAAAAATTTTAGAG
Found at i:5395958 original size:23 final size:22
Alignment explanation
Indices: 5395902--5395959 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 22
5395892 CACTTCCAAA
*
5395902 ATTCACATTAAAAATTTTAGAG
1 ATTCACATCAAAAATTTTAGAG
*
5395924 ATTCAAATTCAAAAATTTTAGAG
1 ATTCACA-TCAAAAATTTTAGAG
5395947 ATTCACACTCAAA
1 ATTCACA-TCAAA
5395960 GGTTAAAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 6 0.19
23 25 0.81
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.33
Consensus pattern (22 bp):
ATTCACATCAAAAATTTTAGAG
Found at i:5397256 original size:20 final size:20
Alignment explanation
Indices: 5397231--5397273 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5397221 AAGTTGAGTA
*
5397231 TTCTTTTTCTCTTTTTTT-AT
1 TTCTTTTTAT-TTTTTTTCAT
5397251 TTCTTTTTATTTTTTTTCAT
1 TTCTTTTTATTTTTTTTCAT
5397271 TTC
1 TTC
5397274 ATCCATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (20 bp):
TTCTTTTTATTTTTTTTCAT
Found at i:5402066 original size:11 final size:11
Alignment explanation
Indices: 5402050--5402082 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5402040 TAAATCCTCA
5402050 CATTTTTTCTT
1 CATTTTTTCTT
5402061 CATTTTTTCCTT
1 CATTTTTT-CTT
5402073 C-TTTTTTCTT
1 CATTTTTTCTT
5402083 TCTTTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 14 0.67
12 4 0.19
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (11 bp):
CATTTTTTCTT
Found at i:5405446 original size:32 final size:32
Alignment explanation
Indices: 5405410--5405470 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
5405400 TACATAAGAT
5405410 TATGATAAAATAAAATAAAATGATATTATAAA
1 TATGATAAAATAAAATAAAATGATATTATAAA
* * * *
5405442 TATGATTAAATTAAATAATATGATCTTAT
1 TATGATAAAATAAAATAAAATGATATTAT
5405471 TTTATATTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (32 bp):
TATGATAAAATAAAATAAAATGATATTATAAA
Found at i:5406547 original size:23 final size:23
Alignment explanation
Indices: 5406484--5406538 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
5406474 AGCATATTCA
5406484 GACGCAATGGTAAAAATTGCTGT
1 GACGCAATGGTAAAAATTGCTGT
5406507 GACGCAATGGTAAAAATTGCTGT
1 GACGCAATGGTAAAAATTGCTGT
*
5406530 GATGCAATG
1 GACGCAATG
5406539 AGTTCAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (23 bp):
GACGCAATGGTAAAAATTGCTGT
Found at i:5407672 original size:25 final size:26
Alignment explanation
Indices: 5407616--5407682 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
5407606 AATTTTAAAA
* * **
5407616 AAATTAATATATTTTAATATATTTATT
1 AAATAAATAT-TTTTAATAAAAATATT
5407643 AAATAAATATTTTTAATAAAAATATT
1 AAATAAATATTTTTAATAAAAATATT
5407669 -AATAAAT-TTTTTAA
1 AAATAAATATTTTTAA
5407683 CGTTGAACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 7 0.19
25 7 0.19
26 13 0.36
27 9 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AAATAAATATTTTTAATAAAAATATT
Found at i:5407786 original size:23 final size:23
Alignment explanation
Indices: 5407723--5407786 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
5407713 AATAATTTTT
*
5407723 TTAATAATTTTTT-TTACATATTA
1 TTAA-AATTTTTTATTAAATATTA
*
5407746 TT--AATTTTCATATTAAATATTA
1 TTAAAATTTT-TTATTAAATATTA
5407768 TTAAAATTTTTTATTAAAT
1 TTAAAATTTTTTATTAAAT
5407787 TATTTATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
20 6 0.18
21 1 0.03
22 11 0.32
23 10 0.29
24 6 0.18
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAAAATTTTTTATTAAATATTA
Found at i:5408864 original size:19 final size:16
Alignment explanation
Indices: 5408829--5408885 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
5408819 TAAATTAGTA
5408829 TATTAAATAATATATT
1 TATTAAATAATATATT
* *
5408845 TATTAATATAATACATA
1 TATTAA-ATAATATATT
*
5408862 T-TTAAAT-ATAAATT
1 TATTAAATAATATATT
*
5408876 TAATAAATAA
1 TATTAAATAA
5408886 CAAAATACAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
14 6 0.18
15 7 0.21
16 11 0.33
17 9 0.27
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TATTAAATAATATATT
Found at i:5413691 original size:21 final size:21
Alignment explanation
Indices: 5413666--5413705 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5413656 CTGAAAAAAC
*
5413666 ATCAAATAAGGTGTTTCAATT
1 ATCAAATAAGGCGTTTCAATT
*
5413687 ATCAATTAAGGCGTTTCAA
1 ATCAAATAAGGCGTTTCAA
5413706 GGCATCTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (21 bp):
ATCAAATAAGGCGTTTCAATT
Found at i:5417991 original size:2 final size:2
Alignment explanation
Indices: 5417984--5418019 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5417974 ATGCTTTCCT
5417984 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5418020 CCCTATCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5421315 original size:19 final size:18
Alignment explanation
Indices: 5421249--5421315 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 18
5421239 AGAAAGTAAC
*
5421249 TTTTATTTTTTTTATATCT
1 TTTTATTTTTATTATAT-T
* *
5421268 TTTTATATTTATAATAATT
1 TTTTATTTTTATTAT-ATT
*
5421287 ATTATATTTTTATTATATT
1 -TTTTATTTTTATTATATT
5421306 GTTTTATTTT
1 -TTTTATTTT
5421316 AATATAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 24 0.63
20 14 0.37
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (18 bp):
TTTTATTTTTATTATATT
Found at i:5421552 original size:48 final size:48
Alignment explanation
Indices: 5421493--5421587 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
5421483 AATCCAATAA
* *
5421493 CTTAGTAAATTTTTTTATCAATCTATAACTATTTGACAAATAAAAAGG
1 CTTAGCAAATTTTTTTATCAATCAATAACTATTTGACAAATAAAAAGG
*
5421541 CTTAGCAAATTTTTTTATCAATCAATAATTATTTGACAAATAAAAAG
1 CTTAGCAAATTTTTTTATCAATCAATAACTATTTGACAAATAAAAAG
5421588 TAATGAGCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (48 bp):
CTTAGCAAATTTTTTTATCAATCAATAACTATTTGACAAATAAAAAGG
Found at i:5422296 original size:4 final size:4
Alignment explanation
Indices: 5422279--5422337 Score: 52
Period size: 4 Copynumber: 15.0 Consensus size: 4
5422269 TTTATATATG
* * *
5422279 TAAA TAAA TGAA TAAA TAAA TAAA CAAA T-AA -AAA TAAA TTAA -AAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
5422324 TAAAA TAAAA TAAA
1 T-AAA T-AAA TAAA
5422338 AATACCAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
3 6 0.13
4 30 0.67
5 9 0.20
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (4 bp):
TAAA
Found at i:5422315 original size:6 final size:6
Alignment explanation
Indices: 5422304--5422354 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
5422294 ATAAATAAAC
*
5422304 AAATAA AAAT-A AATTAA AAAT-A AAAT-A AAATAA AAATACCA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATA--A AAATAA
5422351 AAAT
1 AAAT
5422355 TTGTTTGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 14 0.36
6 19 0.49
8 6 0.15
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:5422338 original size:16 final size:16
Alignment explanation
Indices: 5422304--5422341 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
5422294 ATAAATAAAC
*
5422304 AAATAAAAATAAATTAA
1 AAAT-AAAATAAAATAA
5422321 AAATAAAATAAAATAA
1 AAATAAAATAAAATAA
5422337 AAATA
1 AAATA
5422342 CCAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATAAAATAAAATAA
Found at i:5422339 original size:11 final size:11
Alignment explanation
Indices: 5422304--5422352 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
5422294 ATAAATAAAC
5422304 AAATAAAAATA
1 AAATAAAAATA
*
5422315 AATTAAAAATA
1 AAATAAAAATA
5422326 AAAT-AAAATAA
1 AAATAAAAAT-A
5422337 AAATACCAAAATA
1 AAATA--AAAATA
5422350 AAA
1 AAA
5422353 ATTTGTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 5 0.16
11 18 0.56
13 4 0.12
14 5 0.16
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:5426026 original size:27 final size:26
Alignment explanation
Indices: 5425977--5426036 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
5425967 ATATAAAATG
*
5425977 ATATTATTTAATTTAATTTTATTTATA
1 ATATTATTTAATTTAATTCTA-TTATA
*
5426004 ATATTATTTTATCTT-ATTCTATTATA
1 ATATTATTTAAT-TTAATTCTATTATA
*
5426030 ATTTTAT
1 ATATTAT
5426037 ATATCAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 11 0.38
27 16 0.55
28 2 0.07
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (26 bp):
ATATTATTTAATTTAATTCTATTATA
Found at i:5427802 original size:6 final size:7
Alignment explanation
Indices: 5427785--5427809 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5427775 AAATAACAAA
5427785 AAAAAGT
1 AAAAAGT
5427792 AAAAAGT
1 AAAAAGT
5427799 AAAAAGT
1 AAAAAGT
5427806 AAAA
1 AAAA
5427810 TTAAAAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAAGT
Found at i:5435817 original size:26 final size:25
Alignment explanation
Indices: 5435788--5435836 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5435778 TTTAATATTT
*
5435788 ATATATGAATTCATTTAATATTTATA
1 ATATATAAATTCATTTAA-ATTTATA
* *
5435814 ATATTTAAATTTATTTAAATTTA
1 ATATATAAATTCATTTAAATTTA
5435837 GTATTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
ATATATAAATTCATTTAAATTTATA
Found at i:5435844 original size:26 final size:26
Alignment explanation
Indices: 5435778--5435836 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 26
5435768 TAATTATTTT
*
5435778 TTTAATATTTAT-ATA--TGAATTCA
1 TTTAATATTTATAATATTTAAATTCA
*
5435801 TTTAATATTTATAATATTTAAATTTA
1 TTTAATATTTATAATATTTAAATTCA
5435827 TTTAA-ATTTA
1 TTTAATATTTA
5435837 GTATTATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 12 0.39
24 3 0.10
25 5 0.16
26 11 0.35
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTAATATTTATAATATTTAAATTCA
Found at i:5443698 original size:10 final size:10
Alignment explanation
Indices: 5443683--5443711 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5443673 TTCAGACCTC
5443683 CAATATCATA
1 CAATATCATA
5443693 CAATATCATA
1 CAATATCATA
5443703 CAATATCAT
1 CAATATCAT
5443712 TCTGTAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (10 bp):
CAATATCATA
Found at i:5444853 original size:332 final size:333
Alignment explanation
Indices: 5444352--5445627 Score: 1745
Period size: 332 Copynumber: 3.9 Consensus size: 333
5444342 ACAAATTATT
* * *
5444352 GAAGGCAACTTATAATAAAAGAGGCCTTTAATAATCC-GAAAAAATTTTATTGAA-AAAA-TATT
1 GAAGGCGACTTATAATAAAAGACGCCTTTAATAATCCTG-AAAACTTTTATT-AAGAAAATTATT
* * * *
5444414 GAAGGCATTGTTATCTGAAATCGCCTTCAGTAATTATATACAAACTATTATA-AGAATTATTAAA
64 GAAGGCGTTGTTATCTGAAACCGCCTTCAGTAATTATATACAAACTGTGATAGA-AATTATTAAA
*
5444478 GGCATTTATCTTAAATATACGCCTTCAATAACAATGTTACAATATGTGTAGCAGTATATAG-TGG
128 GGCATTTATCTTAAATATACGCCTTCAATAACAATGTTACAATATGTGTAGCAGTATATAGAAGG
* * * * * * *
5444542 CATTTTACAGTAAAAGACGCCTTTAATAATTTTTAAAATATTTAGTGAAAAAATTATGAAGGCAT
193 CATTTTACAGTAGAAGATGCCTTTAATAATTCTCAAAATATTTAATGAAAAAATTTTGAAGGCGT
* * **
5444607 CTGTTATTAAAAAATGCCTTCAGTAATTAAAGGCACATTTTCTAATAAACGCCTTCGATTA-CAT
258 CTGTTATTAACAAATGCCTTCAGTAATTAAAGGCACCTTTTCTAATACTCGCCTTCGATTACCA-
*
5444671 TCGTGGTATATT
322 TCGTGGTATATC
*
5444683 GAAGGCGACTTATAATAAAAGACGCATTTAATAATCCTGAAAACTTTTATTAAGAAAATTATTGA
1 GAAGGCGACTTATAATAAAAGACGCCTTTAATAATCCTGAAAACTTTTATTAAGAAAATTATTGA
* * *
5444748 AGGTGTTGTTATCTGAAACCGCCTTCAGTAATTATATACAAACTGTGATAGGAATTATTAGAGGC
66 AGGCGTTGTTATCTGAAACCGCCTTCAGTAATTATATACAAACTGTGATAGAAATTATTAAAGGC
* * * *
5444813 ATTTATCTTAAATATACGCCTTCAATAATAGTGGTACAATATGTGTAGCAGTATATAGAAGGTAT
131 ATTTATCTTAAATATACGCCTTCAATAACAATGTTACAATATGTGTAGCAGTATATAGAAGGCAT
* *
5444878 TTTACAGTAGAAGATGCCTTTAATAATTCTCAAAATATTTAATGAAAAAATTTTAAAAGCGTCTG
196 TTTACAGTAGAAGATGCCTTTAATAATTCTCAAAATATTTAATGAAAAAATTTTGAAGGCGTCTG
* * * * *
5444943 TTA-TAACAAATGCCTTTAGTAATTAACGACGCCTTTTCTAATACTCGCATTCGATTACCATCGT
261 TTATTAACAAATGCCTTCAGTAATTAAAGGCACCTTTTCTAATACTCGCCTTCGATTACCATCGT
5445007 GGTATATC
326 GGTATATC
* * *
5445015 GAAGGTGGCTTATAATAAAAGACACCTTTAATAATCCTGAAAACTTTTATTAAGAAAATTATTGA
1 GAAGGCGACTTATAATAAAAGACGCCTTTAATAATCCTGAAAACTTTTATTAAGAAAATTATTGA
* * * *
5445080 AGACGTTGTTATCTAAAACCGCTTTCAGTAATTATATACAAACTGTTATAGAAATTATTAAA-G-
66 AGGCGTTGTTATCTGAAACCGCCTTCAGTAATTATATACAAACTGTGATAGAAATTATTAAAGGC
** ** *
5445143 A--CGTCTTAAATATATACCTTCAATAACAATGTTACAATATGTGTAG-AGGTCTATAGAAGGCA
131 ATTTATCTTAAATATACGCCTTCAATAACAATGTTACAATATGTGTAGCA-GTATATAGAAGGCA
* * *
5445205 TTTTACAATAGAAGATGCCTTTAATAATTCTCAAAATATTTAGTGAAAAAATTTTGAAGGTGTCT
195 TTTTACAGTAGAAGATGCCTTTAATAATTCTCAAAATATTTAATGAAAAAATTTTGAAGGCGTCT
* * * *
5445270 GTTATTAACAAACGCCTTCAGTAATTGAAGGCACCTTTTCAAATACTCGCCTTCAATTACCATCG
260 GTTATTAACAAATGCCTTCAGTAATTAAAGGCACCTTTTCTAATACTCGCCTTCGATTACCATCG
5445335 TGGTATATC
325 TGGTATATC
* *
5445344 GAAGGCGGCTTATAATAAAAGACGCCTTTAATAATCCTAAAAACTTTTATT-AGAAAAATTATTG
1 GAAGGCGACTTATAATAAAAGACGCCTTTAATAATCCTGAAAACTTTTATTAAG-AAAATTATTG
* * * *
5445408 AATGTGTTGTTATCTGAAACCGCTTTTAGTAATTATATACAAACTGTGATAGAAATTATTAAAGG
65 AAGGCGTTGTTATCTGAAACCGCCTTCAGTAATTATATACAAACTGTGATAGAAATTATTAAAGG
** * * * *
5445473 TGTCTATCTTAAATATACGCCTTCAATAACAATGTTACAATATGTATAGC-GATATATAAAAGGT
130 CATTTATCTTAAATATACGCCTTCAATAACAATGTTACAATATGTGTAGCAG-TATATAGAAGGC
* * *
5445537 ATTTTATAGTAGAAGATGTCTTTAATAATTCTCAAAATATTTAATGAAAAAATTTTGAAGCCGTC
194 ATTTTACAGTAGAAGATGCCTTTAATAATTCTCAAAATATTTAATGAAAAAATTTTGAAGGCGTC
*
5445602 TGTT-TCTAACAAATGCCTTCTGTAAT
259 TGTTAT-TAACAAATGCCTTCAGTAAT
5445628 GGATTACTAA
Statistics
Matches: 834, Mismatches: 95, Indels: 30
0.87 0.10 0.03
Matches are distributed among these distances:
327 1 0.00
328 116 0.14
329 175 0.21
330 4 0.00
331 50 0.06
332 293 0.35
333 195 0.23
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (333 bp):
GAAGGCGACTTATAATAAAAGACGCCTTTAATAATCCTGAAAACTTTTATTAAGAAAATTATTGA
AGGCGTTGTTATCTGAAACCGCCTTCAGTAATTATATACAAACTGTGATAGAAATTATTAAAGGC
ATTTATCTTAAATATACGCCTTCAATAACAATGTTACAATATGTGTAGCAGTATATAGAAGGCAT
TTTACAGTAGAAGATGCCTTTAATAATTCTCAAAATATTTAATGAAAAAATTTTGAAGGCGTCTG
TTATTAACAAATGCCTTCAGTAATTAAAGGCACCTTTTCTAATACTCGCCTTCGATTACCATCGT
GGTATATC
Found at i:5449500 original size:19 final size:19
Alignment explanation
Indices: 5449441--5449501 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
5449431 AATAATTTAT
5449441 TAAAACCATTATAAAAA-ACA
1 TAAAA-CATTA-AAAAATACA
* ** *
5449461 -AAAAGATTAAATTATATA
1 TAAAACATTAAAAAATACA
5449479 TAAAACATTAAAAAATACA
1 TAAAACATTAAAAAATACA
5449498 TAAA
1 TAAA
5449502 TTATTTTTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
17 3 0.10
18 6 0.19
19 22 0.71
ACGTcount: A:0.66, C:0.08, G:0.02, T:0.25
Consensus pattern (19 bp):
TAAAACATTAAAAAATACA
Found at i:5449733 original size:16 final size:16
Alignment explanation
Indices: 5449708--5449738 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5449698 ATCACTCTCA
*
5449708 ATTATCTAAAATTATT
1 ATTATATAAAATTATT
5449724 ATTATATAAAATTAT
1 ATTATATAAAATTAT
5449739 CAAATATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATATAAAATTATT
Found at i:5450080 original size:2 final size:2
Alignment explanation
Indices: 5450073--5450146 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
5450063 TAAGAAAAAC
5450073 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5450115 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5450147 ATATATATAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5455080 original size:3 final size:3
Alignment explanation
Indices: 5455072--5455108 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5455062 CCCCACTACC
5455072 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5455109 AATTAATGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5455468 original size:29 final size:27
Alignment explanation
Indices: 5455436--5455509 Score: 67
Period size: 29 Copynumber: 2.6 Consensus size: 27
5455426 TTTAAAAGTC
*
5455436 AATAAAATTTTATATTTATTCATTATTTA
1 AATAAAATTTTATATTTATT-AATA-TTA
** *
5455465 AATATCATTATATAATTTATTAATATTA
1 AATAAAATTTTAT-ATTTATTAATATTA
*
5455493 TATAAAATTTATATATT
1 AATAAAATTT-TATATT
5455510 GATAATACAT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
28 12 0.34
29 16 0.46
30 7 0.20
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (27 bp):
AATAAAATTTTATATTTATTAATATTA
Found at i:5457178 original size:32 final size:32
Alignment explanation
Indices: 5457141--5457208 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 32
5457131 AGATAAAATG
5457141 ATATTATAAAT-A-AAATTAGATTAA-ATAATGTA
1 ATATTATAAATGAGAAA--AGA-TAAGATAATGTA
5457173 ATATTATAAATGAGAAAAGATAAGATAATGTA
1 ATATTATAAATGAGAAAAGATAAGATAATGTA
5457205 ATAT
1 ATAT
5457209 CTTATATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
31 3 0.09
32 26 0.79
33 1 0.03
34 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (32 bp):
ATATTATAAATGAGAAAAGATAAGATAATGTA
Found at i:5457294 original size:16 final size:18
Alignment explanation
Indices: 5457273--5457309 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5457263 AGTATCTTTC
5457273 TTTAAAGT-TT-ATATAA
1 TTTAAAGTATTAATATAA
*
5457289 TTTAAATTATTAATATAA
1 TTTAAAGTATTAATATAA
5457307 TTT
1 TTT
5457310 TTAAAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTAAAGTATTAATATAA
Found at i:5457624 original size:22 final size:24
Alignment explanation
Indices: 5457599--5457642 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
5457589 TTTTTTGTTA
5457599 AAAAAAATTAT-AATA-TAAAAAT
1 AAAAAAATTATAAATACTAAAAAT
5457621 AAAAAAATTATAAATACTAAAA
1 AAAAAAATTATAAATACTAAAA
5457643 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
23 4 0.20
24 5 0.25
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAAAATTATAAATACTAAAAAT
Found at i:5458584 original size:30 final size:29
Alignment explanation
Indices: 5458515--5458586 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
5458505 TTATAATTCA
* *
5458515 ATAATTATTTAAATCTTTAATATTTTATT
1 ATAATTAATTAAAGCTTTAATATTTTATT
*
5458544 ATAATTAATTAAAGCTTTAATCTTTTATT
1 ATAATTAATTAAAGCTTTAATATTTTATT
* *
5458573 TTGATTTAATTAAA
1 AT-AATTAATTAAA
5458587 TTCTTAAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 27 0.73
30 10 0.27
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (29 bp):
ATAATTAATTAAAGCTTTAATATTTTATT
Found at i:5458695 original size:11 final size:11
Alignment explanation
Indices: 5458681--5458715 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5458671 TGAGAGAGAG
*
5458681 AAGAAATAGAA
1 AAGAAAAAGAA
*
5458692 AAGAAAAAAAA
1 AAGAAAAAGAA
5458703 AAGAAAAAGAA
1 AAGAAAAAGAA
5458714 AA
1 AA
5458716 TATATTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:5459596 original size:2 final size:2
Alignment explanation
Indices: 5459589--5459644 Score: 82
Period size: 2 Copynumber: 29.5 Consensus size: 2
5459579 AACTCCAATC
5459589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5459630 AT -T AC A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
5459645 GTTACCAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5460084 original size:16 final size:16
Alignment explanation
Indices: 5460065--5460095 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5460055 ATATATAAAT
*
5460065 ACCAAAATAACTTAAG
1 ACCAAAACAACTTAAG
5460081 ACCAAAACAACTTAA
1 ACCAAAACAACTTAA
5460096 AGAAAGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.23, G:0.03, T:0.16
Consensus pattern (16 bp):
ACCAAAACAACTTAAG
Found at i:5461522 original size:36 final size:36
Alignment explanation
Indices: 5461469--5461541 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 36
5461459 GGGTGCCACA
5461469 TGGCACCCAATGAGTTTTC-TTTTTTTTTAATTTTT
1 TGGCACCCAATGAGTTTTCTTTTTTTTTTAATTTTT
5461504 TGGCACCCAAATGAGTTTTCTTTTTTTTTTAATTTTT
1 TGGCACCC-AATGAGTTTTCTTTTTTTTTTAATTTTT
5461541 T
1 T
5461542 TAACTTCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 8 0.22
36 11 0.31
37 17 0.47
ACGTcount: A:0.18, C:0.14, G:0.11, T:0.58
Consensus pattern (36 bp):
TGGCACCCAATGAGTTTTCTTTTTTTTTTAATTTTT
Found at i:5461589 original size:19 final size:21
Alignment explanation
Indices: 5461536--5461589 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 21
5461526 TTTTTTTTAA
*
5461536 TTTTTTTAA-CTTCTTTATCT
1 TTTTTTTAATTTTCTTTATCT
*
5461556 TCTTTTTTATCTTTTCTTT-TC-
1 T-TTTTTTA-ATTTTCTTTATCT
5461577 TTTTTTTAATTTT
1 TTTTTTTAATTTT
5461590 TATATTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 4 0.14
20 8 0.29
21 8 0.29
22 2 0.07
23 6 0.21
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTTAATTTTCTTTATCT
Found at i:5462686 original size:23 final size:25
Alignment explanation
Indices: 5462660--5462713 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
5462650 TAGATTAATT
*
5462660 AAAATTAATATATT-TTTATTTA-A
1 AAAATTAATATATTATATATTTATA
5462683 AAAA-T-ATATATTAATATATTTATA
1 AAAATTAATATATT-ATATATTTATA
5462707 AAAATTA
1 AAAATTA
5462714 CATAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 7 0.28
22 1 0.04
23 11 0.44
24 5 0.20
25 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAATTAATATATTATATATTTATA
Found at i:5462721 original size:23 final size:23
Alignment explanation
Indices: 5462676--5462723 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5462666 AATATATTTT
* *
5462676 TATTTAAAAAATATATATTAATA
1 TATTTAAAAAATATACATAAATA
5462699 TATTTATAAAAAT-TACATAAATA
1 TATTTA-AAAAATATACATAAATA
5462722 TA
1 TA
5462724 CAAGACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TATTTAAAAAATATACATAAATA
Found at i:5463013 original size:23 final size:22
Alignment explanation
Indices: 5462987--5463029 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
5462977 TGCTTAGACT
*
5462987 TTTTTCTTTTCTTTTTATTTTTG
1 TTTTGCTTTTCTTTTT-TTTTTG
*
5463010 TTTTGGTTTTCTTTTTTTTT
1 TTTTGCTTTTCTTTTTTTTT
5463030 AATTGTCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.84
Consensus pattern (22 bp):
TTTTGCTTTTCTTTTTTTTTTG
Found at i:5463146 original size:17 final size:17
Alignment explanation
Indices: 5463121--5463153 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5463111 TGACTTTCTA
5463121 TTTTGGCTTTTTTTTTG
1 TTTTGGCTTTTTTTTTG
*
5463138 TTTTTGCTTTTTTTTT
1 TTTTGGCTTTTTTTTT
5463154 TCTTTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (17 bp):
TTTTGGCTTTTTTTTTG
Found at i:5463413 original size:16 final size:17
Alignment explanation
Indices: 5463394--5463449 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 17
5463384 TTTATTTAAG
*
5463394 TTTACATTTATATT-TA
1 TTTACATATATATTATA
*
5463410 TTTATATATATATTATA
1 TTTACATATATATTATA
5463427 -TTA-ATATA-ATTATTA
1 TTTACATATATATTA-TA
5463442 TTTA-ATAT
1 TTTACATAT
5463450 CTTAATTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 4 0.11
15 7 0.20
16 22 0.63
17 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTACATATATATTATA
Found at i:5463504 original size:17 final size:17
Alignment explanation
Indices: 5463475--5463510 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
5463465 TACTATATTT
5463475 ATTTATAATTAAAATGTA
1 ATTTATAATTAAAAT-TA
5463493 ATTTAT-ATTAAAATTA
1 ATTTATAATTAAAATTA
5463509 AT
1 AT
5463511 ATTTTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 8 0.44
18 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATTTATAATTAAAATTA
Found at i:5463514 original size:18 final size:19
Alignment explanation
Indices: 5463474--5463519 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
5463464 ATACTATATT
5463474 TATTTATAATTAAAATGTA
1 TATTTATAATTAAAATGTA
5463493 -ATTTAT-ATTAAAAT-TAA
1 TATTTATAATTAAAATGT-A
5463510 TATTTTATAA
1 TA-TTTATAA
5463520 ATATTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.04
17 9 0.39
18 7 0.30
19 5 0.22
20 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TATTTATAATTAAAATGTA
Found at i:5464709 original size:18 final size:18
Alignment explanation
Indices: 5464671--5464709 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5464661 AAATAAATAT
**
5464671 AAATATATGAAAATTTTA
1 AAATATATGAAAATTAAA
5464689 AAATATATGAAAATTAAA
1 AAATATATGAAAATTAAA
5464707 AAA
1 AAA
5464710 ATAAAAATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (18 bp):
AAATATATGAAAATTAAA
Found at i:5465157 original size:19 final size:19
Alignment explanation
Indices: 5465104--5465152 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
5465094 TGGAAAAAAA
5465104 AAAATA-AAGAACATGAA-AC
1 AAAATACAA-AACAT-AAGAC
5465123 AAAATACAAAACATAAGAC
1 AAAATACAAAACATAAGAC
5465142 AACAATACAAA
1 AA-AATACAAA
5465153 GATAAATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.07
19 15 0.56
20 10 0.37
ACGTcount: A:0.69, C:0.14, G:0.06, T:0.10
Consensus pattern (19 bp):
AAAATACAAAACATAAGAC
Found at i:5466260 original size:7 final size:7
Alignment explanation
Indices: 5466248--5466273 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5466238 AATGAGATAA
5466248 AAATATT
1 AAATATT
5466255 AAATATT
1 AAATATT
5466262 AAATATT
1 AAATATT
5466269 AAATA
1 AAATA
5466274 AATACAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATATT
Found at i:5481442 original size:15 final size:12
Alignment explanation
Indices: 5481405--5481432 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5481395 TTAATTTAAT
5481405 TAATTTATAAAA
1 TAATTTATAAAA
5481417 TAATTTATAAAA
1 TAATTTATAAAA
5481429 TAAT
1 TAAT
5481433 ATTTAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATTTATAAAA
Found at i:5481897 original size:4 final size:4
Alignment explanation
Indices: 5481888--5481914 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5481878 AACTTGTATT
5481888 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
5481915 CTTTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:5483697 original size:22 final size:21
Alignment explanation
Indices: 5483672--5483721 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
5483662 CTAATTTTTT
*
5483672 AATAAATAAAAAGTGAAGAAAA
1 AATAAATAAAAA-TCAAGAAAA
*
5483694 AATATAAGAAAAATCAAGAAAA
1 AATA-AATAAAAATCAAGAAAA
5483716 AA-AAAT
1 AATAAAT
5483722 TCTTGTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.08
21 1 0.04
22 14 0.58
23 7 0.29
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.14
Consensus pattern (21 bp):
AATAAATAAAAATCAAGAAAA
Found at i:5485510 original size:8 final size:9
Alignment explanation
Indices: 5485482--5485507 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5485472 ATTAATATAA
5485482 AATATTTTT
1 AATATTTTT
5485491 AATATTTTT
1 AATATTTTT
5485500 AATATTTT
1 AATATTTT
5485508 AATTTTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
AATATTTTT
Found at i:5485602 original size:25 final size:26
Alignment explanation
Indices: 5485551--5485605 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
5485541 AATTTTAAAA
* *
5485551 TTTTTATTATATTGATACTTCAAAATT
1 TTTTTATCACATTGATACTT-AAAATT
*
5485578 TTTTTATCACATTGATACTT-GAATT
1 TTTTTATCACATTGATACTTAAAATT
5485603 TTT
1 TTT
5485606 AATTTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
27 18 0.72
ACGTcount: A:0.29, C:0.09, G:0.05, T:0.56
Consensus pattern (26 bp):
TTTTTATCACATTGATACTTAAAATT
Found at i:5485774 original size:9 final size:10
Alignment explanation
Indices: 5485751--5485799 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
5485741 TTATAAAAAA
5485751 AAAAAATTCT
1 AAAAAATTCT
5485761 AAAAAATTCT
1 AAAAAATTCT
** *
5485771 AAAACTTTTTT
1 AAAA-AATTCT
*
5485782 AAAAAATTTT
1 AAAAAATTCT
5485792 AAAAAATT
1 AAAAAATT
5485800 AAATAATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
10 26 0.79
11 7 0.21
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAAAATTCT
Found at i:5485821 original size:19 final size:18
Alignment explanation
Indices: 5485780--5485825 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5485770 TAAAACTTTT
5485780 TTAAAAAATTTTAAAAAA
1 TTAAAAAATTTTAAAAAA
* * *
5485798 TTAAATAATTTTTAAAAG
1 TTAAAAAATTTTAAAAAA
5485816 TCTAAAAAAT
1 T-TAAAAAAT
5485826 AAAAAAAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
TTAAAAAATTTTAAAAAA
Found at i:5485894 original size:20 final size:19
Alignment explanation
Indices: 5485869--5485942 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
5485859 TTCAAATAAA
5485869 AAAAATTCTAAAAAATCTTT
1 AAAAATTCTAAAAAAT-TTT
*
5485889 AAAAATTCAAAAAAATTTT
1 AAAAATTCTAAAAAATTTT
** *
5485908 AGAAAATTCTAACTATTTTT
1 A-AAAATTCTAAAAAATTTT
5485928 CAAAAATTCTAAAAA
1 -AAAAATTCTAAAAA
5485943 TTCTAAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 4 0.09
20 40 0.89
21 1 0.02
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.34
Consensus pattern (19 bp):
AAAAATTCTAAAAAATTTT
Found at i:5485898 original size:35 final size:34
Alignment explanation
Indices: 5485826--5485903 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
5485816 TCTAAAAAAT
* *
5485826 AAAAAAAATGAAATTCTATAAAATTTCAAAATTTTC
1 AAAAAAAA--AAATTCTAAAAAATTTCAAAATATTC
*
5485862 AAATAAAAAAAATTCTAAAAAATCTTTAAAA-ATTC
1 AAA-AAAAAAAATTCTAAAAAAT-TTCAAAATATTC
5485897 AAAAAAA
1 AAAAAAA
5485904 TTTTAGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
34 4 0.11
35 19 0.51
36 9 0.24
37 5 0.14
ACGTcount: A:0.63, C:0.08, G:0.01, T:0.28
Consensus pattern (34 bp):
AAAAAAAAAAATTCTAAAAAATTTCAAAATATTC
Found at i:5485951 original size:8 final size:9
Alignment explanation
Indices: 5485869--5485950 Score: 56
Period size: 10 Copynumber: 8.4 Consensus size: 9
5485859 TTCAAATAAA
5485869 AAAAATTCT
1 AAAAATTCT
*
5485878 AAAAAATCTTT
1 -AAAAAT-TCT
*
5485889 AAAAATTCAA
1 AAAAATTC-T
*
5485899 AAAAATTTT
1 AAAAATTCT
5485908 AGAAAATTCT
1 A-AAAATTCT
* * *
5485918 AACTATTTTT
1 AA-AAATTCT
5485928 CAAAAATTCT
1 -AAAAATTCT
5485938 AAAAATTCT
1 AAAAATTCT
5485947 AAAA
1 AAAA
5485951 TAATTAAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
9 16 0.29
10 35 0.64
11 4 0.07
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (9 bp):
AAAAATTCT
Found at i:5486169 original size:111 final size:116
Alignment explanation
Indices: 5485964--5486304 Score: 390
Period size: 118 Copynumber: 3.0 Consensus size: 116
5485954 TTAAAAAAAA
* * * * *
5485964 TTATCTCGATCACCTGATCTTAGCTCAGTCTAGATTATTTCTTATGACTCGTGGTTTCGT-TTCG
1 TTATCTCGATCACCTGATCTTGGCTCAGTCCAGATAATTTCATATGACTCGTGATTTCGTCTT-G
* *
5486028 ATCATTTATTTTTGACCTCGACTCGATCTTGGTCGCTTCATTTTGA-TT-TG
65 AACATTTATTTTTAACCTCGACTCGATCTTGGTCGCTTCATTTTGACTTGTG
* * *
5486078 -T-TC-CGATCACCTGATCTTGGCTCAGTCCAGATAATTTCATACGATTTGTGATTTCGTCTTGA
1 TTATCTCGATCACCTGATCTTGGCTCAGTCCAGATAATTTCATATGACTCGTGATTTCGTCTTGA
* * * **
5486140 ACATTTATTTTTAACCTTGACTTGGTCTTGGTTACTTCATTTTGACTTGTG
66 ACATTTATTTTTAACCTCGACTCGATCTTGGTCGCTTCATTTTGACTTGTG
* * ** *
5486191 ATTTATCTCGATCACTTGATCTTGGCTCAGTCCAGATCATTTCATATGACTCGTGATTTTATCCT
1 --TTATCTCGATCACCTGATCTTGGCTCAGTCCAGATAATTTCATATGACTCGTGATTTCGTCTT
* * *
5486256 -AATCATTTATTTTTAACCTCAACTCGATCTTAGTCGTTTCATTTTGACT
64 GAA-CATTTATTTTTAACCTCGACTCGATCTTGGTCGCTTCATTTTGACT
5486305 CGTGGTTTCA
Statistics
Matches: 187, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
111 86 0.46
112 6 0.03
113 3 0.02
116 1 0.01
117 4 0.02
118 87 0.47
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.45
Consensus pattern (116 bp):
TTATCTCGATCACCTGATCTTGGCTCAGTCCAGATAATTTCATATGACTCGTGATTTCGTCTTGA
ACATTTATTTTTAACCTCGACTCGATCTTGGTCGCTTCATTTTGACTTGTG
Found at i:5486233 original size:118 final size:114
Alignment explanation
Indices: 5485964--5486302 Score: 373
Period size: 111 Copynumber: 3.0 Consensus size: 114
5485954 TTAAAAAAAA
* * * * *
5485964 TTATCTCGATCACCTGATCTTAGCTCAGTCTAGATTATTTCTTATGACTCGTGGTTTCGT-TTCG
1 TTATCTCGATCACCTGATCTTGGCTCAGTCCAGATAATTTCATATGACTCGTGATTTCGTCTT-G
* * *
5486028 ATCATTTATTTTTGACCTCGACTCGATCTTGGTCGCTTCATTTTGATTTG
65 AACATTTATTTTTAACCTCGACTCGATCTTGGTCACTTCATTTTGATTTG
* * *
5486078 -T-TC-CGATCACCTGATCTTGGCTCAGTCCAGATAATTTCATACGATTTGTGATTTCGTCTTGA
1 TTATCTCGATCACCTGATCTTGGCTCAGTCCAGATAATTTCATATGACTCGTGATTTCGTCTTGA
* * * *
5486140 ACATTTATTTTTAACCTTGACTTGGTCTTGGTTACTTCATTTTGACTTGTG
66 ACATTTATTTTTAACCTCGACTCGATCTTGGTCACTTCATTTTGA-TT-TG
* * ** *
5486191 ATTTATCTCGATCACTTGATCTTGGCTCAGTCCAGATCATTTCATATGACTCGTGATTTTATCCT
1 --TTATCTCGATCACCTGATCTTGGCTCAGTCCAGATAATTTCATATGACTCGTGATTTCGTCTT
* * **
5486256 -AATCATTTATTTTTAACCTCAACTCGATCTTAGTCGTTTCATTTTGA
64 GAA-CATTTATTTTTAACCTCGACTCGATCTTGGTCACTTCATTTTGA
5486303 CTCGTGGTTT
Statistics
Matches: 185, Mismatches: 31, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
111 86 0.46
112 6 0.03
113 3 0.02
116 1 0.01
117 4 0.02
118 85 0.46
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.45
Consensus pattern (114 bp):
TTATCTCGATCACCTGATCTTGGCTCAGTCCAGATAATTTCATATGACTCGTGATTTCGTCTTGA
ACATTTATTTTTAACCTCGACTCGATCTTGGTCACTTCATTTTGATTTG
Found at i:5486303 original size:118 final size:116
Alignment explanation
Indices: 5485964--5486387 Score: 360
Period size: 118 Copynumber: 3.6 Consensus size: 116
5485954 TTAAAAAAAA
* * * * *
5485964 TTATCTCGATCACCTGATCTTAGCTCAGTCTAGATTATTTCTTATGACTCGTGGTTTCGT-TTC-
1 TTATC-CGATCACCTGATCTTAGCTCAGTCCAGATCATTTCATATGACTCGTGATTT--TATCCT
* *
5486027 GATCATTTATTTTTGACCTCGACTCGATCTTGGTCGCTTCATTTTGA-TT-TG-
63 AATCATTTATTTTTAACCTCGACTCGATCTTGGTCGCTTCATTTTGACTTGTGT
* * * * * ** *
5486078 -T-TCCGATCACCTGATCTTGGCTCAGTCCAGATAATTTCATACGATTTGTGATTTCGTCTTGAA
1 TTATCCGATCACCTGATCTTAGCTCAGTCCAGATCATTTCATATGACTCGTGATTTTATCCT-AA
* * * **
5486141 -CATTTATTTTTAACCTTGACTTGGTCTTGGTTACTTCATTTTGACTTGTGAT
65 TCATTTATTTTTAACCTCGACTCGATCTTGGTCGCTTCATTTTGACTTGTG-T
* *
5486193 TTATCTCGATCACTTGATCTTGGCTCAGTCCAGATCATTTCATATGACTCGTGATTTTATCCTAA
1 TTATC-CGATCACCTGATCTTAGCTCAGTCCAGATCATTTCATATGACTCGTGATTTTATCCTAA
* * * *
5486258 TCATTTATTTTTAACCTCAACTCGATCTTAGTCGTTTCATTTTGACTCGTGGT
65 TCATTTATTTTTAACCTCGACTCGATCTTGGTCGCTTCATTTTGACTTGT-GT
* ** * * * * ** * * *
5486311 TTCATCCTGATTATTTGATTTTAGCTCAGTTCAAATCCTTTTTTATGACTCATAATTTTATCCTG
1 TT-ATCC-GATCACCTGATCTTAGCTCAGTCCAGATCATTTCATATGACTCGTGATTTTATCCTA
*
5486376 GTCATTTATTTT
64 ATCATTTATTTT
5486388 CGACCTTGAC
Statistics
Matches: 248, Mismatches: 48, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
110 1 0.00
111 81 0.33
112 5 0.02
113 3 0.01
116 1 0.00
117 4 0.02
118 93 0.38
119 60 0.24
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (116 bp):
TTATCCGATCACCTGATCTTAGCTCAGTCCAGATCATTTCATATGACTCGTGATTTTATCCTAAT
CATTTATTTTTAACCTCGACTCGATCTTGGTCGCTTCATTTTGACTTGTGT
Found at i:5486417 original size:119 final size:120
Alignment explanation
Indices: 5486141--5486436 Score: 303
Period size: 119 Copynumber: 2.5 Consensus size: 120
5486131 TCGTCTTGAA
* * * *
5486141 CATTTATTTTTAACCTTGACTTGGTCTTGGTTACTTCATTTTGACTTGTGATTT-AT-CTCGATC
1 CATTTATTTTTAACCTTGACTTAGTCTTAGTTGCTTCATTTTGACTCGTGATTTCATCCTCGATC
* * * *
5486204 ACTTGATCTTGGCTCAGTCCAGATCATTTCATATGACTCGTGATTTTATCCTAAT
66 ACTTGATCTTAGCTCAGTCCAAATCATTTCATATGACTCATAATTTTATCCTAAT
** * * * *
5486259 CATTTATTTTTAACCTCAAC-TCGATCTTAGTCGTTTCATTTTGACTCGTGGTTTCATCCT-GAT
1 CATTTATTTTTAACCTTGACTTAG-TCTTAGTTGCTTCATTTTGACTCGTGATTTCATCCTCGAT
* * * * * ** **
5486322 TATTTGATTTTAGCTCAGTTCAAATCCTTTTTTATGACTCATAATTTTATCCTGGT
65 CACTTGATCTTAGCTCAGTCCAAATCATTTCATATGACTCATAATTTTATCCTAAT
** * *
5486378 CATTTATTTTCGACCTTGACTTAGTCCTAGTTGCTTCATTTTTGACTCATGATTTCATC
1 CATTTATTTTTAACCTTGACTTAGTCTTAGTTGCTTCA-TTTTGACTCGTGATTTCATC
5486437 TCAGTCACCT
Statistics
Matches: 141, Mismatches: 32, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
117 2 0.01
118 42 0.30
119 75 0.53
120 22 0.16
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (120 bp):
CATTTATTTTTAACCTTGACTTAGTCTTAGTTGCTTCATTTTGACTCGTGATTTCATCCTCGATC
ACTTGATCTTAGCTCAGTCCAAATCATTTCATATGACTCATAATTTTATCCTAAT
Found at i:5486915 original size:3 final size:3
Alignment explanation
Indices: 5486895--5486981 Score: 72
Period size: 3 Copynumber: 29.7 Consensus size: 3
5486885 GGACTATTTT
* * * * * *
5486895 TTA TTA -TA GTA TTA -TA TTA TTA TTT TTA CTC TTA TTG TTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5486941 -TA ATA TATA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TT
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5486982 TTTTATTTTT
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
2 6 0.09
3 58 0.87
4 3 0.04
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:5487794 original size:19 final size:18
Alignment explanation
Indices: 5487766--5487805 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
5487756 CGATCGTAAG
5487766 TTTTTTTTTTTCATTTTA
1 TTTTTTTTTTTCATTTTA
*
5487784 TTTTTTATTTTTTATTTTA
1 TTTTTT-TTTTTCATTTTA
5487803 TTT
1 TTT
5487806 GATTTTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTTTTTTCATTTTA
Found at i:5487805 original size:24 final size:24
Alignment explanation
Indices: 5487766--5487838 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
5487756 CGATCGTAAG
*
5487766 TTTTTTTTTTTCATTTTATTTTTTA
1 TTTTTTATTTT-ATTTTATTTTTTA
* *
5487791 TTTTTTATTTTATTTGATTTTACT-
1 TTTTTTATTTTATTTTATTTT-TTA
** *
5487815 TTTTTTAACTCATTTTATTTTTTA
1 TTTTTTATTTTATTTTATTTTTTA
5487839 AAAATTTTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
23 1 0.03
24 26 0.68
25 11 0.29
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.77
Consensus pattern (24 bp):
TTTTTTATTTTATTTTATTTTTTA
Found at i:5487956 original size:19 final size:19
Alignment explanation
Indices: 5487934--5487970 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5487924 AAATTCTATA
*
5487934 AAAAAAACCTTTTCAAATG
1 AAAAAAACCTTATCAAATG
*
5487953 AAAAAAATCTTATCAAAT
1 AAAAAAACCTTATCAAAT
5487971 AAAGTTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.27
Consensus pattern (19 bp):
AAAAAAACCTTATCAAATG
Found at i:5488066 original size:25 final size:27
Alignment explanation
Indices: 5488038--5488089 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
5488028 AAATATATTT
5488038 ATAAAAAAAATC-CTTTC-AATAAAAA
1 ATAAAAAAAATCTCTTTCAAATAAAAA
*
5488063 ATAAAAAAAATCTTTTTCAAATAAAAA
1 ATAAAAAAAATCTCTTTCAAATAAAAA
5488090 TCCTTACAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 12 0.50
26 4 0.17
27 8 0.33
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (27 bp):
ATAAAAAAAATCTCTTTCAAATAAAAA
Found at i:5489285 original size:2 final size:2
Alignment explanation
Indices: 5489278--5489306 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5489268 ATAACCATCA
5489278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5489307 CTTTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5490250 original size:27 final size:27
Alignment explanation
Indices: 5490194--5490251 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
5490184 TCATAAATAT
* *
5490194 TAAACAAATATGCTTATAAAACATATA
1 TAAACAAATATACTTATAAAACATAAA
* *
5490221 TAAACAAATATATTTATGAATA-ATAAA
1 TAAACAAATATACTTAT-AAAACATAAA
5490248 TAAA
1 TAAA
5490252 TTATAACCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (27 bp):
TAAACAAATATACTTATAAAACATAAA
Found at i:5491842 original size:2 final size:2
Alignment explanation
Indices: 5491837--5491861 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5491827 TATATACGTG
5491837 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5491862 CACTTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5495118 original size:13 final size:13
Alignment explanation
Indices: 5495100--5495124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5495090 AAAATAAAAT
5495100 AAATTTTATTTTA
1 AAATTTTATTTTA
5495113 AAATTTTATTTT
1 AAATTTTATTTT
5495125 TTTCATATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AAATTTTATTTTA
Found at i:5511770 original size:30 final size:30
Alignment explanation
Indices: 5511705--5511770 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
5511695 ATGCAAGTAT
*
5511705 AAATTAAAAGTTGAAAGTTTATTTTAATAC
1 AAATTAAAAGTTGAAAGTTTATTTAAATAC
* * *
5511735 CAATTAAAAGTT-AATGATTTATTTAAATGC
1 AAATTAAAAGTTGAAAG-TTTATTTAAATAC
5511765 AAATTA
1 AAATTA
5511771 GAATTCAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (30 bp):
AAATTAAAAGTTGAAAGTTTATTTAAATAC
Found at i:5517588 original size:3 final size:3
Alignment explanation
Indices: 5517580--5517608 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5517570 TTGACCATAA
5517580 TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
5517609 AAGTGGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
TGT
Found at i:5518177 original size:2 final size:2
Alignment explanation
Indices: 5518172--5518202 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5518162 TATATATCTA
5518172 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5518203 ATCCGAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5522028 original size:31 final size:31
Alignment explanation
Indices: 5521932--5522031 Score: 80
Period size: 31 Copynumber: 3.3 Consensus size: 31
5521922 TAGTAAAATT
* * * *
5521932 ATATATAAATTTAATA-AAAATAAAAAATAA
1 ATATATAATTTTTATATAAAATATAATATAA
* * * * *
5521962 AAAAATTATTTTTTTAT-AAATATGAAT-TATG
1 ATATATAATTTTTATATAAAATAT-AATATA-A
5521993 ATATATAATTTTTATATAAAATATAATATAA
1 ATATATAATTTTTATATAAAATATAATATAA
5522024 ATATATAA
1 ATATATAA
5522032 ATTATTAATA
Statistics
Matches: 51, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
30 17 0.33
31 26 0.51
32 8 0.16
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (31 bp):
ATATATAATTTTTATATAAAATATAATATAA
Found at i:5522259 original size:2 final size:2
Alignment explanation
Indices: 5522254--5522296 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
5522244 TTTATGTGTG
*
5522254 TA TA TA TA TA TA TA TA TA TA -A TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5522295 TA
1 TA
5522297 ATCAACTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5522282 original size:23 final size:23
Alignment explanation
Indices: 5522252--5522298 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5522242 CTTTTATGTG
5522252 TGTATATATATATATATATATAA
1 TGTATATATATATATATATATAA
5522275 TGTATATATATATATATATATAA
1 TGTATATATATATATATATATAA
5522298 T
1 T
5522299 CAACTCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TGTATATATATATATATATATAA
Found at i:5522437 original size:2 final size:2
Alignment explanation
Indices: 5522430--5522482 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
5522420 AATAGATAAC
* * * *
5522430 AT AT AT AT AT AT AT AT AG GT AT AT AT AT GT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5522472 AT AT TT AT AT A
1 AT AT AT AT AT A
5522483 AGAAGAGATC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5524770 original size:18 final size:19
Alignment explanation
Indices: 5524723--5524770 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
5524713 AATTTATTAA
*
5524723 AAAAATAATTTTAAAGTTT
1 AAAAATAAGTTTAAAGTTT
*
5524742 ACAAAAT-AGTTT-GAGTTT
1 A-AAAATAAGTTTAAAGTTT
5524760 AAAAATAAGTT
1 AAAAATAAGTT
5524771 ATGCATAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 5 0.20
18 10 0.40
19 5 0.20
20 5 0.20
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (19 bp):
AAAAATAAGTTTAAAGTTT
Found at i:5525208 original size:3 final size:3
Alignment explanation
Indices: 5525200--5525227 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5525190 TTAGTTTTAT
5525200 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5525228 TATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5525232 original size:3 final size:3
Alignment explanation
Indices: 5525226--5525260 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5525216 AATAATAATA
5525226 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5525261 CTGTTTAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5525757 original size:21 final size:20
Alignment explanation
Indices: 5525728--5525787 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 20
5525718 TTATTATTGG
*
5525728 TATTATTATTTTTTAATTATTT
1 TATT-TTATTTTTTAA-TAGTT
5525750 TATTTTATTATTTATAA-AGTT
1 TATTTTATT-TTT-TAATAGTT
5525771 TATTTTAGTTTTTTAAT
1 TATTTTA-TTTTTTAAT
5525788 GGAATTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
20 3 0.09
21 18 0.55
22 9 0.27
23 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
TATTTTATTTTTTAATAGTT
Found at i:5526646 original size:14 final size:14
Alignment explanation
Indices: 5526624--5526654 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5526614 TTCTGGTTGC
5526624 TTTTCTTTTTTTTG
1 TTTTCTTTTTTTTG
*
5526638 TTTTTTTTTTTTTG
1 TTTTCTTTTTTTTG
5526652 TTT
1 TTT
5526655 GGTAGAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.90
Consensus pattern (14 bp):
TTTTCTTTTTTTTG
Found at i:5527357 original size:43 final size:43
Alignment explanation
Indices: 5527305--5527455 Score: 142
Period size: 44 Copynumber: 3.5 Consensus size: 43
5527295 CATAGGCTCA
* *
5527305 ACAACTTTTGAAAATTTAAAAAACTCCTCTAAGTAAAGGCTTG
1 ACAACTTTTGAAAATTTAAAAAGCTCCTCTAAGTAAAGACTTG
* ** * * *
5527348 ACAATTTTTGAAAATTCTAAATGGCTCTTCTAAGTAGAGATTTG
1 ACAACTTTTGAAAATT-TAAAAAGCTCCTCTAAGTAAAGACTTG
** * * *
5527392 ATGACTTTTGAAAATTTAAAAAGTTCCTCTAAGCAAAAGCCTT-
1 ACAACTTTTGAAAATTTAAAAAGCTCCTCTAAG-TAAAGACTTG
*
5527435 ACAACTTTTTAAAAATTTAAA
1 ACAAC-TTTTGAAAATTTAAA
5527456 TTGCTCATTT
Statistics
Matches: 83, Mismatches: 22, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
43 31 0.37
44 52 0.63
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (43 bp):
ACAACTTTTGAAAATTTAAAAAGCTCCTCTAAGTAAAGACTTG
Found at i:5532433 original size:19 final size:19
Alignment explanation
Indices: 5532409--5532462 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
5532399 GTGGAATGGC
5532409 AAGAAATGAAAATGAGTGA
1 AAGAAATGAAAATGAGTGA
* *
5532428 AAGAAAAGAGAAATGGATTGA
1 AAGAAATGA-AAAT-GAGTGA
*
5532449 ATG-AATGAAAATGA
1 AAGAAATGAAAATGA
5532463 AAGCAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 2 0.07
19 12 0.41
20 8 0.28
21 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.17
Consensus pattern (19 bp):
AAGAAATGAAAATGAGTGA
Found at i:5540005 original size:3 final size:3
Alignment explanation
Indices: 5539999--5540040 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
5539989 AGTTTTTTTA
5539999 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5540041 TGTTTGGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5542968 original size:3 final size:3
Alignment explanation
Indices: 5542956--5543011 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
5542946 GCTATCTTCT
* * *
5542956 TTA TTT TTA TTA TTA TTA TT- TGA TT- TGA TTA TT- TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
5542999 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
5543012 ATTTAATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5543281 original size:20 final size:19
Alignment explanation
Indices: 5543226--5543281 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
5543216 TTTAGGAAAA
*
5543226 TATATTGGTTAC-TTTATAT
1 TATATT-GTTACATTAATAT
*
5543245 TAATATTGCTA-ATTAATAT
1 T-ATATTGTTACATTAATAT
5543264 TATATTAGTTACATTAAT
1 TATATT-GTTACATTAAT
5543282 GTTACTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.17
19 14 0.47
20 11 0.37
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (19 bp):
TATATTGTTACATTAATAT
Found at i:5544524 original size:16 final size:16
Alignment explanation
Indices: 5544503--5544570 Score: 66
Period size: 16 Copynumber: 4.1 Consensus size: 16
5544493 GTCCAATTCA
5544503 ATTTTTATTTTGTATT
1 ATTTTTATTTTGTATT
*
5544519 ATTTTTATTTTTTATT
1 ATTTTTATTTTGTATT
*
5544535 -TTTTGTATTTTATTATTT
1 ATTTT-TATTTT-GTA-TT
*
5544553 ATTTATTATTATGTATT
1 ATTT-TTATTTTGTATT
5544570 A
1 A
5544571 ATATATGTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
15 4 0.09
16 21 0.48
17 6 0.14
18 4 0.09
19 8 0.18
20 1 0.02
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (16 bp):
ATTTTTATTTTGTATT
Found at i:5544530 original size:7 final size:7
Alignment explanation
Indices: 5544504--5544562 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
5544494 TCCAATTCAA
5544504 TTTTTAT
1 TTTTTAT
*
5544511 TTTGTATT
1 TTTTTA-T
5544519 ATTTTTAT
1 -TTTTTAT
5544527 TTTTTAT
1 TTTTTAT
*
5544534 TTTTTGT
1 TTTTTAT
*
5544541 ATTTTAT
1 TTTTTAT
*
5544548 TATTTAT
1 TTTTTAT
*
5544555 TTATTAT
1 TTTTTAT
5544562 T
1 T
5544563 ATGTATTAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
7 34 0.83
8 2 0.05
9 5 0.12
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (7 bp):
TTTTTAT
Found at i:5544545 original size:21 final size:23
Alignment explanation
Indices: 5544504--5544570 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 23
5544494 TCCAATTCAA
5544504 TTTTTATTTTGTATTATTTTTAT
1 TTTTTATTTTGTATTATTTTTAT
5544527 TTTTTATTTTTTGTATTTTATTATTTAT
1 TTTTTA--TTTTGTA--TTATT-TTTAT
* *
5544555 TTATTATTATGTATTA
1 TTTTTATTTTGTATTA
5544571 ATATATGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
23 6 0.16
24 3 0.08
25 7 0.19
26 6 0.16
27 5 0.14
28 10 0.27
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (23 bp):
TTTTTATTTTGTATTATTTTTAT
Found at i:5544557 original size:25 final size:26
Alignment explanation
Indices: 5544507--5544671 Score: 87
Period size: 26 Copynumber: 6.3 Consensus size: 26
5544497 AATTCAATTT
*
5544507 TTATTTTGTATTATTTTTATTTTTTA
1 TTATTTTGTATTATTATTATTTTTTA
5544533 TT-TTTTGTATT-TTATTATTTATTTA
1 TTATTTTGTATTATTATTATTT-TTTA
* *
5544558 TTATTATGTATTAATATATGTATATCTTTA
1 TTATTTTGTATT-AT-TAT-TAT-TTTTTA
* *
5544588 TT-TATT-TA-T-TTATT-TTTTTTG
1 TTATTTTGTATTATTATTATTTTTTA
* *
5544609 TTAATATTTATATGTATT-TTATTTATATA
1 TT-AT-TTTGTAT-TATTATTATTT-TTTA
* *
5544638 GTTATATT-TATTATTATTATATTATTA
1 -TTATTTTGTATTATTATTAT-TTTTTA
5544665 TTATTTT
1 TTATTTT
5544672 TTTTTACCTT
Statistics
Matches: 106, Mismatches: 14, Indels: 38
0.67 0.09 0.24
Matches are distributed among these distances:
21 6 0.06
22 1 0.01
23 2 0.02
24 13 0.12
25 18 0.17
26 20 0.19
27 13 0.12
28 12 0.11
29 9 0.08
30 11 0.10
31 1 0.01
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.69
Consensus pattern (26 bp):
TTATTTTGTATTATTATTATTTTTTA
Found at i:5544561 original size:14 final size:14
Alignment explanation
Indices: 5544515--5544669 Score: 75
Period size: 14 Copynumber: 11.5 Consensus size: 14
5544505 TTTTATTTTG
5544515 TATTATT-TTTATT
1 TATTATTATTTATT
* * *
5544528 TTTTATTTTTTGTAT
1 TATTATTATTTAT-T
5544543 T-TTATTATTTATT
1 TATTATTATTTATT
*
5544556 TATTATTATGTA-T
1 TATTATTATTTATT
* *
5544569 TAATA-TATGTA--
1 TATTATTATTTATT
5544580 TATCT-TTATTTATT
1 TAT-TATTATTTATT
5544594 TATTTATT-TTT-TT
1 TA-TTATTATTTATT
* *
5544607 TGTTAATATTTATAT
1 TATTATTATTTAT-T
*
5544622 GTATT-TTATTTATA
1 -TATTATTATTTATT
5544636 TAGTTA-TATTTA-T
1 TA-TTATTATTTATT
5544649 TATTATTATATTA-T
1 TATTATTAT-TTATT
5544663 TATTATT
1 TATTATT
5544670 TTTTTTTACC
Statistics
Matches: 111, Mismatches: 14, Indels: 33
0.70 0.09 0.21
Matches are distributed among these distances:
11 2 0.02
12 19 0.17
13 26 0.23
14 48 0.43
15 13 0.12
16 3 0.03
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (14 bp):
TATTATTATTTATT
Found at i:5544630 original size:38 final size:44
Alignment explanation
Indices: 5544538--5544634 Score: 109
Period size: 46 Copynumber: 2.3 Consensus size: 44
5544528 TTTTATTTTT
5544538 TGTATTTTA-TTATTTATTTATTATTATGTATTAATATATGTATA
1 TGTATTTTATTTATTTATTTATTATTATG-ATTAATATATGTATA
* *
5544582 TCTTTATTTATTTATTTATTT-TT-TT-TG-TTAATAT-T-TATA
1 TGTAT-TTTATTTATTTATTTATTATTATGATTAATATATGTATA
5544621 TGTATTTTATTTAT
1 TGTATTTTATTTAT
5544635 ATAGTTATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
38 9 0.19
39 7 0.15
40 1 0.02
41 7 0.15
43 2 0.04
44 5 0.11
45 6 0.13
46 10 0.21
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.67
Consensus pattern (44 bp):
TGTATTTTATTTATTTATTTATTATTATGATTAATATATGTATA
Found at i:5544630 original size:42 final size:41
Alignment explanation
Indices: 5544538--5544677 Score: 109
Period size: 42 Copynumber: 3.5 Consensus size: 41
5544528 TTTTATTTTT
*
5544538 TGTATTTTA-TTATTTATTTATTATTATGTATTAATATATG
1 TGTATTTTATTTATTTATTTATTATTATGTATTAATATATA
* * * *
5544578 TATATCTTTATTTATTTATTTATT-TTTTTTGTTAATATTTATA
1 TGTAT-TTTATTTATTTATTTATTATTATGTATTAATA--TATA
* *
5544621 TGTATTTTATTTATATAGTTA-TATTTAT-TATT-AT-TATA
1 TGTATTTTATTTATTTATTTATTA-TTATGTATTAATATATA
5544659 T-TATTATTATTT-TTT-TTTA
1 TGTATT-TTATTTATTTATTTA
5544678 CCTTGTAATA
Statistics
Matches: 81, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
36 3 0.04
37 6 0.07
38 11 0.14
40 4 0.05
41 17 0.21
42 30 0.37
43 10 0.12
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (41 bp):
TGTATTTTATTTATTTATTTATTATTATGTATTAATATATA
Found at i:5544642 original size:23 final size:23
Alignment explanation
Indices: 5544616--5544659 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5544606 TTGTTAATAT
5544616 TTATATGTATT-TTATTTATATAG
1 TTATATGTATTATTA-TTATATAG
*
5544639 TTATATTTATTATTATTATAT
1 TTATATGTATTATTATTATAT
5544660 TATTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (23 bp):
TTATATGTATTATTATTATATAG
Found at i:5544649 original size:4 final size:4
Alignment explanation
Indices: 5544522--5544602 Score: 53
Period size: 4 Copynumber: 20.8 Consensus size: 4
5544512 TTGTATTATT
* *
5544522 TTTA TTT- TTTA TTTT TTGTA TTT- TATTA TTTA TTTA -TTA -TTA TGTA
1 TTTA TTTA TTTA TTTA TT-TA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA
* * * * *
5544568 TTAA TATA TGTA TATC TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
5544603 TTTTTGTTAA
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
3 10 0.17
4 46 0.77
5 4 0.07
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:5545647 original size:21 final size:21
Alignment explanation
Indices: 5545619--5545664 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
5545609 TTTTTTTGGA
5545619 ATTTTTTTATTTATTTG-TTT
1 ATTTTTTTATTTATTTGTTTT
5545639 ATTTGTTTTATTTATTTGTTTT
1 ATTT-TTTTATTTATTTGTTTT
5545661 ATTT
1 ATTT
5545665 ATTAGATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.17
21 13 0.54
22 7 0.29
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (21 bp):
ATTTTTTTATTTATTTGTTTT
Found at i:5545654 original size:13 final size:13
Alignment explanation
Indices: 5545636--5545667 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
5545626 TATTTATTTG
5545636 TTTATTTGTTTTA
1 TTTATTTGTTTTA
5545649 TTTATTTGTTTTA
1 TTTATTTGTTTTA
5545662 TTTATT
1 TTTATT
5545668 AGATTAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (13 bp):
TTTATTTGTTTTA
Found at i:5545706 original size:5 final size:5
Alignment explanation
Indices: 5545689--5545776 Score: 65
Period size: 5 Copynumber: 16.8 Consensus size: 5
5545679 ATTTAAAATT
* *
5545689 TTTTA TCTTTA TTTTA TTTTTA TTTTTG TTTTA CTTTT- CTTTA TTTT-
1 TTTTA T-TTTA TTTTA -TTTTA -TTTTA TTTTA -TTTTA TTTTA TTTTA
*
5545736 TTTTA TCTTTA -TTTA TTTTCA CTTTTA TTTTG TTTTA TTTT
1 TTTTA T-TTTA TTTTA TTTT-A -TTTTA TTTTA TTTTA TTTT
5545777 CTTTAAATAA
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
4 11 0.16
5 28 0.41
6 25 0.37
7 4 0.06
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:5545776 original size:15 final size:14
Alignment explanation
Indices: 5545687--5545776 Score: 58
Period size: 16 Copynumber: 5.8 Consensus size: 14
5545677 TTATTTAAAA
5545687 TTTTTTATCTTTATTT
1 TTTTTTAT-TTTA-TT
5545703 TATTTTTATTTT-TGT
1 T-TTTTTATTTTAT-T
5545718 TTTACTTT-TCTTTATT
1 TTT--TTTAT-TTTATT
5545734 TTTTTTATCTTTATT
1 TTTTTTAT-TTTATT
*
5545749 TATTTTCACTTTTATT
1 T-TTTTTA-TTTTATT
5545765 TTGTTTTATTTT
1 TT-TTTTATTTT
5545777 CTTTAAATAA
Statistics
Matches: 62, Mismatches: 2, Indels: 21
0.73 0.02 0.25
Matches are distributed among these distances:
14 6 0.10
15 17 0.27
16 30 0.48
17 9 0.15
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTTTATTTTATT
Found at i:5545915 original size:59 final size:58
Alignment explanation
Indices: 5545802--5546098 Score: 291
Period size: 58 Copynumber: 5.0 Consensus size: 58
5545792 AAAAAAAATA
* *
5545802 TTTTTGGGAAAACGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAA-TTTCAAAAAAAGG
1 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTTC-AAAAAA-G
* *
5545860 GTTTTGAGAAAAAGTTGAAAATATCAATTTTCCTTAAAAATCAAAATTTTCAAAAAA-
1 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTTCAAAAAAG
* * * *
5545917 TATTTTTAGGAAAAAGTTGAAAGTATCAATATTT-TTTGAAAATCAAAGTTTTTTCAAAAAGAAT
1 T-TTTTGA-GAAAAAGTTGAAAGTATCAAT-TTTCCTTAAAAATCAAA--ATTTTC-AAAA-AA-
*
5545981 A
58 G
* *
5545982 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAATTTCTAAAAAAAAAAG
1 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTT-T---CAAAAAAG
* * * *
5546042 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTTCAAAAAA
1 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTTCAAAAAA
5546099 AAAAAATATT
Statistics
Matches: 200, Mismatches: 21, Indels: 36
0.78 0.08 0.14
Matches are distributed among these distances:
58 48 0.24
59 44 0.22
60 47 0.23
61 10 0.05
62 16 0.08
63 29 0.14
64 5 0.03
65 1 0.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (58 bp):
TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTTCAAAAAAG
Done.