Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 6 of 171
Found at i:2358028 original size:59 final size:60
Alignment explanation
Indices: 2357943--2358062 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 60
2357933 GGTAGGCATT
* *
2357943 TGATGTCCATATTTTAGG--CCTTTTTTTAGTCTCTGAAAGTAATTGGTCATGCATTTGCC
1 TGATGTCCATATTTTAGGCCCCTTTTTCTAGTATCTGAAAGTAA-TGGTCATGCATTTGCC
* * *
2358002 TGATGTCCATATTTTAGGCCCCTTTTTCTAGTATCTGAAATTAATGTTTATGCATTTGCC
1 TGATGTCCATATTTTAGGCCCCTTTTTCTAGTATCTGAAAGTAATGGTCATGCATTTGCC
2358062 T
1 T
2358063 TGTGTTTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
59 18 0.33
60 15 0.28
61 21 0.39
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (60 bp):
TGATGTCCATATTTTAGGCCCCTTTTTCTAGTATCTGAAAGTAATGGTCATGCATTTGCC
Found at i:2376015 original size:5 final size:5
Alignment explanation
Indices: 2376005--2376033 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2375995 AACTCAGAGT
2376005 GAGAA GAGAA GAGAA GAGAA GAGAA GAGA
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGA
2376034 GAAACCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:2378087 original size:23 final size:23
Alignment explanation
Indices: 2378059--2378171 Score: 108
Period size: 23 Copynumber: 5.0 Consensus size: 23
2378049 GAAACAATAA
*
2378059 GCACACACAGTGC-AATCCAGTAG
1 GCACACAAAGTGCAAAT-CAGTAG
*
2378082 GCACACATAGTGC-AATCAGTAG
1 GCACACAAAGTGCAAATCAGTAG
* * * *
2378104 GCGCACATAGCGCAAATCAATAG
1 GCACACAAAGTGCAAATCAGTAG
*
2378127 GCACACAAAGTGCGAAA-CAGTAA
1 GCACACAAAGTGC-AAATCAGTAG
2378150 GCACACAAAGTGCGAAA-CAGTA
1 GCACACAAAGTGC-AAATCAGTA
2378172 AGCGCGCTAG
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
22 17 0.22
23 59 0.75
24 3 0.04
ACGTcount: A:0.41, C:0.25, G:0.22, T:0.12
Consensus pattern (23 bp):
GCACACAAAGTGCAAATCAGTAG
Found at i:2385944 original size:23 final size:24
Alignment explanation
Indices: 2385898--2385959 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
2385888 ATTCCTCTAA
2385898 TATACTTAAATTTGAGATATAATT
1 TATACTTAAATTTGAGATATAATT
* *
2385922 TATACTTTAATTTTA-ATATAATT
1 TATACTTAAATTTGAGATATAATT
*
2385945 TGATCCTTACAATTT
1 T-ATACTTA-AATTT
2385960 TATAATATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 9 0.28
24 18 0.56
25 5 0.16
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (24 bp):
TATACTTAAATTTGAGATATAATT
Found at i:2386019 original size:21 final size:22
Alignment explanation
Indices: 2385971--2386019 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2385961 ATAATATTAT
*
2385971 TAATTAATCCAAAGAATTAATA
1 TAATTAATCCAAAGAATTAAAA
*
2385993 TCATTAAT-CAAA-AAGTTAAAA
1 TAATTAATCCAAAGAA-TTAAAA
2386014 TAATTA
1 TAATTA
2386020 TATATAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 14 0.61
22 7 0.30
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (22 bp):
TAATTAATCCAAAGAATTAAAA
Found at i:2388944 original size:23 final size:23
Alignment explanation
Indices: 2388891--2388944 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
2388881 AAGGGGTGTC
* *
2388891 AAAATT-AAATTATAATTTTTAC
1 AAAATTAAAAATATAATTTTTAA
* *
2388913 AATAGTAAAAATATAATTTTTAA
1 AAAATTAAAAATATAATTTTTAA
2388936 AAAATTAAA
1 AAAATTAAA
2388945 TCAAATTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAATTAAAAATATAATTTTTAA
Found at i:2397205 original size:15 final size:16
Alignment explanation
Indices: 2397177--2397209 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2397167 AAAAACAATT
2397177 TAAATTATATTTAAAA
1 TAAATTATATTTAAAA
2397193 TAAATTA-ATTTAAAA
1 TAAATTATATTTAAAA
2397208 TA
1 TA
2397210 CATGAGAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTATATTTAAAA
Found at i:2397705 original size:20 final size:19
Alignment explanation
Indices: 2397680--2397727 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
2397670 TGATAAAGGG
*
2397680 TAAAATTTAAAATATATATT
1 TAAAATTTAAAACAT-TATT
*
2397700 TAAAATGTAAAACATTATT
1 TAAAATTTAAAACATTATT
*
2397719 AAAAATTTA
1 TAAAATTTA
2397728 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAAATTTAAAACATTATT
Found at i:2412837 original size:2 final size:2
Alignment explanation
Indices: 2412830--2412864 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2412820 TTCTCAATGC
2412830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2412865 TATCATGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2428600 original size:17 final size:17
Alignment explanation
Indices: 2428562--2428603 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2428552 AATAATCTAA
2428562 AAAAATAA-TTAATTCC
1 AAAAATAATTTAATTCC
*
2428578 ACAAATAATTCTAA-TCC
1 AAAAATAATT-TAATTCC
2428595 AAAAATAAT
1 AAAAATAAT
2428604 AATCTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 12 0.55
18 3 0.14
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATAATTTAATTCC
Found at i:2429868 original size:24 final size:23
Alignment explanation
Indices: 2429839--2429959 Score: 86
Period size: 24 Copynumber: 5.2 Consensus size: 23
2429829 ACAAACAACC
*
2429839 AAAATAACAACCAAAACAGAAACA
1 AAAATAACAA-AAAAACAGAAACA
* * *
2429863 AAAATAATAGAAAAAATAGCAACA
1 AAAATAACA-AAAAAACAGAAACA
* *
2429887 AAAATAACAATAAAAACA-ACACT
1 AAAATAACAA-AAAAACAGAAACA
** *
2429910 AAAATAGTAAAAAAACA-ATACA
1 AAAATAACAAAAAAACAGAAACA
*
2429932 AAAATAACAATCAAAACAGTAAA-A
1 AAAATAACAA-AAAAACAG-AAACA
2429956 AAAA
1 AAAA
2429960 CTAAAACAGC
Statistics
Matches: 75, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
22 18 0.24
23 17 0.23
24 37 0.49
25 3 0.04
ACGTcount: A:0.72, C:0.13, G:0.04, T:0.11
Consensus pattern (23 bp):
AAAATAACAAAAAAACAGAAACA
Found at i:2429889 original size:12 final size:12
Alignment explanation
Indices: 2429832--2429947 Score: 62
Period size: 12 Copynumber: 9.8 Consensus size: 12
2429822 ATAACATACA
*
2429832 AACAACCAAAAT
1 AACAACAAAAAT
* *
2429844 AACAACCAAAAC
1 AACAACAAAAAT
2429856 AGA-AACAAAAAT
1 A-ACAACAAAAAT
*
2429868 AATAGA-AAAAAT
1 AACA-ACAAAAAT
*
2429880 AGCAACAAAAAT
1 AACAACAAAAAT
* *
2429892 AACAATAAAAAC
1 AACAACAAAAAT
*
2429904 AAC-ACTAAAAT
1 AACAACAAAAAT
** *
2429915 AGTAA-AAAAAC
1 AACAACAAAAAT
*
2429926 AA-TACAAAAAT
1 AACAACAAAAAT
2429937 AACAATCAAAA
1 AACAA-CAAAA
2429948 CAGTAAAAAA
Statistics
Matches: 77, Mismatches: 19, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
10 1 0.01
11 20 0.26
12 49 0.64
13 7 0.09
ACGTcount: A:0.71, C:0.16, G:0.03, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:2447325 original size:21 final size:20
Alignment explanation
Indices: 2447277--2447326 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
2447267 AATCTTGAAA
*
2447277 TTTAGGGTTCATGATTTATG
1 TTTAAGGTTCATGATTTATG
*
2447297 TTTGAGGTTCAATG-TTTAGTG
1 TTTAAGGTTC-ATGATTTA-TG
2447318 TTTAAGGTT
1 TTTAAGGTT
2447327 TAAGGTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.20, C:0.04, G:0.26, T:0.50
Consensus pattern (20 bp):
TTTAAGGTTCATGATTTATG
Found at i:2454839 original size:22 final size:21
Alignment explanation
Indices: 2454786--2454841 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
2454776 GTGTTATAAA
*
2454786 ATTAATTTTAAATATTTTAAG
1 ATTAATTTTAAGTATTTTAAG
* *
2454807 ATTTATGTTTAAGTATTTTATAT
1 ATTAAT-TTTAAGTATTTTA-AG
2454830 ATTAATTTTAAG
1 ATTAATTTTAAG
2454842 ATGAATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 5 0.17
22 18 0.62
23 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTAATTTTAAGTATTTTAAG
Found at i:2456696 original size:22 final size:22
Alignment explanation
Indices: 2456668--2456710 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2456658 TAAAATACTT
2456668 AAATAATAATT-TAATATAATTA
1 AAATAATAATTATAAT-TAATTA
2456690 AAATAATAATTATAATTAATT
1 AAATAATAATTATAATTAATT
2456711 CTTTAAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAATAATTATAATTAATTA
Found at i:2465770 original size:32 final size:32
Alignment explanation
Indices: 2465734--2465833 Score: 91
Period size: 32 Copynumber: 3.2 Consensus size: 32
2465724 TGTTTGTTTA
2465734 TTGTAGTTATTTTGGCTCCTTGCATCCTCGTG
1 TTGTAGTTATTTTGGCTCCTTGCATCCTCGTG
** * ** * *
2465766 TTGTAG--AGATTGG--CCTTGAATGTTTGTTTA
1 TTGTAGTTATTTTGGCTCCTTGCATCCTCG--TG
2465796 TTGTAGTTATTTTGGCTCCTTGCATCCTCGTG
1 TTGTAGTTATTTTGGCTCCTTGCATCCTCGTG
2465828 TTGTAG
1 TTGTAG
2465834 AGATTGGCCC
Statistics
Matches: 48, Mismatches: 14, Indels: 12
0.65 0.19 0.16
Matches are distributed among these distances:
28 9 0.19
30 12 0.25
32 18 0.38
34 9 0.19
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.47
Consensus pattern (32 bp):
TTGTAGTTATTTTGGCTCCTTGCATCCTCGTG
Found at i:2465814 original size:62 final size:62
Alignment explanation
Indices: 2465717--2465842 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
2465707 TTTTCAGATC
2465717 CCTTGAATGTTTGTTTATTGTAGTTATTTTGGCTCCTTGCATCCTCGTGTTGTAGAGATTGG
1 CCTTGAATGTTTGTTTATTGTAGTTATTTTGGCTCCTTGCATCCTCGTGTTGTAGAGATTGG
2465779 CCTTGAATGTTTGTTTATTGTAGTTATTTTGGCTCCTTGCATCCTCGTGTTGTAGAGATTGG
1 CCTTGAATGTTTGTTTATTGTAGTTATTTTGGCTCCTTGCATCCTCGTGTTGTAGAGATTGG
2465841 CC
1 CC
2465843 CTTTTCTAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.46
Consensus pattern (62 bp):
CCTTGAATGTTTGTTTATTGTAGTTATTTTGGCTCCTTGCATCCTCGTGTTGTAGAGATTGG
Found at i:2471983 original size:12 final size:12
Alignment explanation
Indices: 2471966--2471990 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2471956 TCCCATAAAC
2471966 GAGCAGCAATAT
1 GAGCAGCAATAT
2471978 GAGCAGCAATAT
1 GAGCAGCAATAT
2471990 G
1 G
2471991 TCACTGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (12 bp):
GAGCAGCAATAT
Found at i:2476495 original size:15 final size:15
Alignment explanation
Indices: 2476464--2476502 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
2476454 TGTTTGATTG
2476464 AAAATAA-TTTTTGA
1 AAAATAATTTTTTGA
*
2476478 AAAATAATTTTTTTA
1 AAAATAATTTTTTGA
2476493 AAAATAATTT
1 AAAATAATTT
2476503 ATCTTTCTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
AAAATAATTTTTTGA
Found at i:2478099 original size:25 final size:25
Alignment explanation
Indices: 2478071--2478121 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
2478061 TTTACCTTCA
2478071 ATACAATCAATATTAGTAAAGAACC
1 ATACAATCAATATTAGTAAAGAACC
*
2478096 ATACAATCAATATTAGTGAAGAACC
1 ATACAATCAATATTAGTAAAGAACC
2478121 A
1 A
2478122 AACTGCATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.24
Consensus pattern (25 bp):
ATACAATCAATATTAGTAAAGAACC
Found at i:2482831 original size:15 final size:16
Alignment explanation
Indices: 2482811--2482841 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2482801 ATAAATTTAC
2482811 AAAAAATTAAA-TTGA
1 AAAAAATTAAAGTTGA
2482826 AAAAAATTAAAGTTGA
1 AAAAAATTAAAGTTGA
2482842 GAGACCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (16 bp):
AAAAAATTAAAGTTGA
Found at i:2484863 original size:9 final size:10
Alignment explanation
Indices: 2484819--2484862 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
2484809 TGTAATTCCG
2484819 AATTGATTAAA
1 AATT-ATTAAA
2484830 TAATTATTAAA
1 -AATTATTAAA
2484841 AATTA-TAAA
1 AATTATTAAA
*
2484850 AAATATTAAA
1 AATTATTAAA
2484860 AAT
1 AAT
2484863 ACAATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 8 0.28
10 11 0.38
11 6 0.21
12 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
AATTATTAAA
Found at i:2503716 original size:15 final size:17
Alignment explanation
Indices: 2503679--2503719 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
2503669 ATAATAAAAA
*
2503679 TATAATTTTTATTATTT
1 TATAATTTATATTATTT
2503696 TAATAATTTATA-TA-TT
1 T-ATAATTTATATTATTT
2503712 TATAATTT
1 TATAATTT
2503720 TTAAATGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 3 0.14
17 3 0.14
18 9 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATAATTTATATTATTT
Found at i:2507014 original size:3 final size:3
Alignment explanation
Indices: 2507006--2507039 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2506996 GTTAAATACG
*
2507006 TGA TGA TGA TGA TGA CGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
2507040 ACCAGATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:2515806 original size:6 final size:6
Alignment explanation
Indices: 2515797--2515822 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2515787 TACAGCTTGC
2515797 AACCAA AACCAA AACCAA AACCAA AA
1 AACCAA AACCAA AACCAA AACCAA AA
2515823 TAAAAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (6 bp):
AACCAA
Found at i:2521569 original size:15 final size:16
Alignment explanation
Indices: 2521536--2521569 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2521526 TTATTAATTT
*
2521536 AAAATGAAAATTTTAA
1 AAAATGAAAATTGTAA
*
2521552 AAAATGAACATTGTAA
1 AAAATGAAAATTGTAA
2521568 AA
1 AA
2521570 TTCTTGATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (16 bp):
AAAATGAAAATTGTAA
Found at i:2522346 original size:21 final size:19
Alignment explanation
Indices: 2522320--2522361 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 19
2522310 TAATTAATGA
2522320 ATTTATTTTTTATTTAACTCT
1 ATTTA-TTTTTATTT-ACTCT
2522341 ATTTATTTTTATTTACTCT
1 ATTTATTTTTATTTACTCT
2522360 AT
1 AT
2522362 GCTTGATGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 9 0.43
21 5 0.24
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTATTTTTATTTACTCT
Found at i:2522981 original size:26 final size:26
Alignment explanation
Indices: 2522952--2523003 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
2522942 TAAAAAAAAT
*
2522952 GTTTGAGAACTAAGTAAATAAATTAC
1 GTTTGAGAAATAAGTAAATAAATTAC
*
2522978 GTTTGAGAAATAAGTAAATAAGTTAC
1 GTTTGAGAAATAAGTAAATAAATTAC
2523004 AAATTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (26 bp):
GTTTGAGAAATAAGTAAATAAATTAC
Found at i:2529141 original size:3 final size:3
Alignment explanation
Indices: 2529133--2529163 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2529123 AGATATTATC
2529133 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2529164 CTAGTCCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2530729 original size:28 final size:29
Alignment explanation
Indices: 2530684--2530738 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
2530674 GTGATTCTAG
* * *
2530684 AAATTTTTTAGAGTTTAAAATA-AATTAT
1 AAATTTTTGAAAGGTTAAAATATAATTAT
2530712 AAATTTTTGAAAGGTTAAAATATAATT
1 AAATTTTTGAAAGGTTAAAATATAATT
2530739 TGCATCACGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (29 bp):
AAATTTTTGAAAGGTTAAAATATAATTAT
Found at i:2539052 original size:3 final size:3
Alignment explanation
Indices: 2539044--2539091 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
2539034 TACATCCCAA
2539044 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2539091 A
1 A
2539092 GAATAGAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2540152 original size:7 final size:7
Alignment explanation
Indices: 2540140--2540226 Score: 99
Period size: 7 Copynumber: 12.7 Consensus size: 7
2540130 TTTCGAAAAA
2540140 GTCAACG
1 GTCAACG
2540147 GTCAACG
1 GTCAACG
*
2540154 TTCAACG
1 GTCAACG
*
2540161 GTCAACA
1 GTCAACG
2540168 GTCAACG
1 GTCAACG
*
2540175 GTCAACA
1 GTCAACG
*
2540182 GTCAA-A
1 GTCAACG
2540188 GTCAACG
1 GTCAACG
*
2540195 ATCAACG
1 GTCAACG
2540202 GTCAAAC-
1 GTC-AACG
2540209 -TCAACG
1 GTCAACG
2540215 GTCAACG
1 GTCAACG
2540222 GTCAA
1 GTCAA
2540227 TCAACACCGA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
5 3 0.04
6 8 0.12
7 54 0.79
8 3 0.04
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:2540192 original size:20 final size:20
Alignment explanation
Indices: 2540147--2540226 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
2540137 AAAGTCAACG
*
2540147 GTCAACGTTCAACGGTCAACA
1 GTCAACGGTCAACGGTCAA-A
*
2540168 GTCAACGGTCAACAGTCAAA
1 GTCAACGGTCAACGGTCAAA
*
2540188 GTCAACGATCAACGGTCAAA
1 GTCAACGGTCAACGGTCAAA
*
2540208 CTCAACGGTCAACGGTCAA
1 GTCAACGGTCAACGGTCAA
2540227 TCAACACCGA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 36 0.68
21 17 0.32
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.16
Consensus pattern (20 bp):
GTCAACGGTCAACGGTCAAA
Found at i:2540242 original size:21 final size:21
Alignment explanation
Indices: 2540190--2540252 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
2540180 CAGTCAAAGT
* *
2540190 CAACGATCAACGGTCAAAC-T
1 CAACGATCAACGGTCAATCAA
*
2540210 CAACGGTCAACGGTCAATCAA
1 CAACGATCAACGGTCAATCAA
* *
2540231 CACCGATCAACGGTCGATCAA
1 CAACGATCAACGGTCAATCAA
2540252 C
1 C
2540253 GTCGGTCAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.37, C:0.32, G:0.17, T:0.14
Consensus pattern (21 bp):
CAACGATCAACGGTCAATCAA
Found at i:2540261 original size:21 final size:20
Alignment explanation
Indices: 2540213--2540281 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
2540203 TCAAACTCAA
*
2540213 CGGTCAACGGTCAATCAACAC
1 CGGTCAACGGTC-ATCAACAT
* *
2540234 CGATCAACGGTCGATCAACGT
1 CGGTCAACGGTC-ATCAACAT
2540255 CGGTCAAC-GTCAGTCAACAT
1 CGGTCAACGGTCA-TCAACAT
2540275 CGGTCAA
1 CGGTCAA
2540282 TGGTTTGACT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.02
20 16 0.39
21 24 0.59
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.17
Consensus pattern (20 bp):
CGGTCAACGGTCATCAACAT
Found at i:2540280 original size:10 final size:10
Alignment explanation
Indices: 2540237--2540281 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
2540227 TCAACACCGA
*
2540237 TCAACGGTCGA
1 TCAAC-GTCGG
2540248 TCAACGTCGG
1 TCAACGTCGG
*
2540258 TCAACGTCAG
1 TCAACGTCGG
*
2540268 TCAACATCGG
1 TCAACGTCGG
2540278 TCAA
1 TCAA
2540282 TGGTTTGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 25 0.83
11 5 0.17
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAACGTCGG
Found at i:2540338 original size:15 final size:15
Alignment explanation
Indices: 2540318--2540347 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2540308 TGGTTCATTT
2540318 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
2540333 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
2540348 AATTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:2540357 original size:21 final size:21
Alignment explanation
Indices: 2540331--2540398 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
2540321 TTGGTTCAAA
2540331 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
2540352 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
2540373 TGGGTTTGGTTTAAATAGAATT
1 TGGGTTTGGTTTAAAT-GAATT
2540395 TGGG
1 TGGG
2540399 CTTAATGGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 36 0.82
22 8 0.18
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATT
Found at i:2540802 original size:11 final size:11
Alignment explanation
Indices: 2540769--2540837 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
2540759 AAGTGTGATT
*
2540769 AAAAGAGGAAG
1 AAAAGAGAAAG
*
2540780 AAAATAGAAAAG
1 AAAAGAG-AAAG
2540792 AAAAGAGAAAG
1 AAAAGAGAAAG
2540803 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
2540815 AATGAGAAAAAG
1 AA-AAGAGAAAG
2540827 AAAAGAGAAAG
1 AAAAGAGAAAG
2540838 GAAATATGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
11 25 0.54
12 17 0.37
13 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.06
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:2540811 original size:23 final size:23
Alignment explanation
Indices: 2540769--2540841 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
2540759 AAGTGTGATT
*
2540769 AAAAGAGGAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAATAGAAAAG
*
2540792 AAAAGAGAAAG-AAATAAGAAATG
1 AAAAGAGAAAGAAAAT-AGAAAAG
* * * *
2540815 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAATAGAAAAG
2540839 AAA
1 AAA
2540842 TATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 15 0.38
25 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAATAGAAAAG
Found at i:2546212 original size:3 final size:3
Alignment explanation
Indices: 2546204--2546236 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2546194 TACATCCCAA
2546204 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2546237 GAATAGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2547340 original size:20 final size:20
Alignment explanation
Indices: 2547315--2547353 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2547305 AAAGTCAACG
2547315 GTCAACGGTCAACGGTCAAA
1 GTCAACGGTCAACGGTCAAA
2547335 GTCAACGGTCAACGGTCAA
1 GTCAACGGTCAACGGTCAA
2547354 TCAACACCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (20 bp):
GTCAACGGTCAACGGTCAAA
Found at i:2547372 original size:7 final size:7
Alignment explanation
Indices: 2547308--2547353 Score: 76
Period size: 7 Copynumber: 6.7 Consensus size: 7
2547298 TTTCGAAAAA
2547308 GTCAACG
1 GTCAACG
2547315 GTCAACG
1 GTCAACG
2547322 GTCAACG
1 GTCAACG
*
2547329 GTCAA-A
1 GTCAACG
2547335 GTCAACG
1 GTCAACG
2547342 GTCAACG
1 GTCAACG
2547349 GTCAA
1 GTCAA
2547354 TCAACACCGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 5 0.14
7 31 0.86
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:2547383 original size:10 final size:10
Alignment explanation
Indices: 2547361--2547408 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
2547351 CAATCAACAC
2547361 CGGTCAACGGT
1 CGGTCAAC-GT
2547372 CGGTCAACGT
1 CGGTCAACGT
*
2547382 CGGTCAACAT
1 CGGTCAACGT
*
2547392 CAGTCAACGT
1 CGGTCAACGT
2547402 CGGTCAA
1 CGGTCAA
2547409 TGGTTTGACT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
10 25 0.76
11 8 0.24
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (10 bp):
CGGTCAACGT
Found at i:2547385 original size:21 final size:21
Alignment explanation
Indices: 2547320--2547408 Score: 87
Period size: 20 Copynumber: 4.3 Consensus size: 21
2547310 CAACGGTCAA
2547320 CGGTCAACGGTCAAAGTCAA---
1 CGGTCAACGGTC--AGTCAACGT
* **
2547340 CGGTCAACGGTCAATCAACAC
1 CGGTCAACGGTCAGTCAACGT
*
2547361 CGGTCAACGGTCGGTCAACGT
1 CGGTCAACGGTCAGTCAACGT
*
2547382 CGGTCAAC-ATCAGTCAACGT
1 CGGTCAACGGTCAGTCAACGT
2547402 CGGTCAA
1 CGGTCAA
2547409 TGGTTTGACT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
18 5 0.08
20 29 0.49
21 25 0.42
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (21 bp):
CGGTCAACGGTCAGTCAACGT
Found at i:2547482 original size:21 final size:21
Alignment explanation
Indices: 2547458--2547525 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
2547448 TTGGTTCAAA
2547458 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
2547479 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
2547500 TGGGTTTGGTTTAAATAGAATT
1 TGGGTTTGGTTTAAAT-GAATT
2547522 TGGG
1 TGGG
2547526 CTTAATGGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 36 0.82
22 8 0.18
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATT
Found at i:2547929 original size:11 final size:11
Alignment explanation
Indices: 2547896--2547964 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
2547886 AAGTGTGATT
*
2547896 AAAAGAGGAAG
1 AAAAGAGAAAG
* *
2547907 AAAATAAAAAAG
1 AAAA-GAGAAAG
2547919 AAAAGAGAAAG
1 AAAAGAGAAAG
2547930 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
2547942 AATGAGAAAAAG
1 AA-AAGAGAAAG
2547954 AAAAGAGAAAG
1 AAAAGAGAAAG
2547965 GAAATATGAG
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
11 24 0.55
12 16 0.36
13 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:2563371 original size:17 final size:18
Alignment explanation
Indices: 2563330--2563364 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2563320 AATTTACAAC
2563330 AAATTTTTAACTTTATTA
1 AAATTTTTAACTTTATTA
*
2563348 AAATTTTTAATTTTATT
1 AAATTTTTAACTTTATT
2563365 TAATTTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
AAATTTTTAACTTTATTA
Found at i:2563968 original size:24 final size:24
Alignment explanation
Indices: 2563919--2563969 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2563909 ACCCTCCTCT
*
2563919 CACCACTCACCGCTCACCACCCTC
1 CACCACTCACCGCTCACCACCATC
* *
2563943 CACCACTCCATCGC-CATCACCATC
1 CACCACT-CACCGCTCACCACCATC
2563967 CAC
1 CAC
2563970 TCTTTTTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.24, C:0.59, G:0.04, T:0.14
Consensus pattern (24 bp):
CACCACTCACCGCTCACCACCATC
Found at i:2585277 original size:16 final size:17
Alignment explanation
Indices: 2585249--2585285 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2585239 TATAAATATA
2585249 ATTT-TATTGTTTTAAT
1 ATTTATATTGTTTTAAT
2585265 ATTTATATT-TTTTAAT
1 ATTTATATTGTTTTAAT
*
2585281 TTTTA
1 ATTTA
2585286 AATGATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
ATTTATATTGTTTTAAT
Found at i:2589434 original size:22 final size:23
Alignment explanation
Indices: 2589383--2589456 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
2589373 GAAACAATAA
*
2589383 GCACACATAGTACAATCCAGTAG
1 GCACACATAGTACAATCAAGTAG
*
2589406 GCACACATAGTGCAAT-AAGTAG
1 GCACACATAGTACAATCAAGTAG
** * *
2589428 GTGCACATAGCACAAATCAA-TAA
1 GCACACATAGTAC-AATCAAGTAG
2589451 GCACAC
1 GCACAC
2589457 GAGGTGCGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 14 0.35
23 24 0.60
24 2 0.05
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (23 bp):
GCACACATAGTACAATCAAGTAG
Found at i:2589479 original size:23 final size:23
Alignment explanation
Indices: 2589448--2589498 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
2589438 CACAAATCAA
*
2589448 TAAGCACACGAGGTGCGAAACAG
1 TAAGCACACGAAGTGCGAAACAG
*
2589471 TAAGTACACGAAGTGCGAAACAG
1 TAAGCACACGAAGTGCGAAACAG
2589494 TAAGC
1 TAAGC
2589499 GCGCTAACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (23 bp):
TAAGCACACGAAGTGCGAAACAG
Found at i:2590011 original size:11 final size:11
Alignment explanation
Indices: 2589984--2590014 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
2589974 TCAGCCTCTA
2589984 ATGATTTTTCT
1 ATGATTTTTCT
2589995 AT-ATTTTTCT
1 ATGATTTTTCT
2590005 ATGATTTTTC
1 ATGATTTTTC
2590015 AAAGTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (11 bp):
ATGATTTTTCT
Found at i:2595458 original size:30 final size:28
Alignment explanation
Indices: 2595385--2595468 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 28
2595375 TACGATAGTA
2595385 TAAATATAATTTTATTATTTTTAAAAGGT
1 TAAAT-TAATTTTATTATTTTTAAAAGGT
**
2595414 TAAATTAAATTTTTATTATTTTTAAGGGGT
1 TAAATT-AA-TTTTATTATTTTTAAAAGGT
* *
2595444 TAAAGTGTAATTTTATCATTATTAA
1 TAAA-T-TAATTTTATTATTTTTAA
2595469 TTTAAAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
28 1 0.02
29 7 0.15
30 35 0.74
31 3 0.06
32 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.51
Consensus pattern (28 bp):
TAAATTAATTTTATTATTTTTAAAAGGT
Found at i:2606898 original size:20 final size:19
Alignment explanation
Indices: 2606848--2606898 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
2606838 ATAAATAATT
2606848 TTTATATAAAAT-TATGTCA
1 TTTATA-AAAATATATGTCA
*
2606867 TTTA-AAATAATATATGTTA
1 TTTATAAA-AATATATGTCA
2606886 CTTTATAAAAATA
1 -TTTATAAAAATA
2606899 AATAGGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 2 0.07
18 4 0.15
19 10 0.37
20 8 0.30
21 3 0.11
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (19 bp):
TTTATAAAAATATATGTCA
Found at i:2617966 original size:16 final size:17
Alignment explanation
Indices: 2617942--2617981 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2617932 GAACGCTCCC
2617942 AAAGAACAA-AAAAAAA
1 AAAGAACAACAAAAAAA
* *
2617958 AAAGTACAACAAAAAAG
1 AAAGAACAACAAAAAAA
2617975 AAAGAAC
1 AAAGAAC
2617982 CCTAAGTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.78, C:0.10, G:0.10, T:0.03
Consensus pattern (17 bp):
AAAGAACAACAAAAAAA
Found at i:2637585 original size:31 final size:31
Alignment explanation
Indices: 2637547--2637613 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
2637537 GATAAAAAAA
** *
2637547 TTTAGGTCTTAATATGGGAAAAATTATCAAG
1 TTTAGGTCACAATATGAGAAAAATTATCAAG
* * *
2637578 TTTAGGTCACAATGTGAGAACAATTGTCAAG
1 TTTAGGTCACAATATGAGAAAAATTATCAAG
2637609 TTTAG
1 TTTAG
2637614 TACCTAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (31 bp):
TTTAGGTCACAATATGAGAAAAATTATCAAG
Found at i:2641092 original size:2 final size:2
Alignment explanation
Indices: 2641085--2641130 Score: 65
Period size: 2 Copynumber: 22.0 Consensus size: 2
2641075 AAGCCTTTTG
*
2641085 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT CAT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT
2641129 AT
1 AT
2641131 TTATTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 36 0.90
3 4 0.10
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2643277 original size:51 final size:51
Alignment explanation
Indices: 2643201--2643297 Score: 176
Period size: 51 Copynumber: 1.9 Consensus size: 51
2643191 TGGTTTTGGA
* *
2643201 GCTGCAGCTGGTGGTAATGATGCTTTCGGGATTGGAAGTGGAAGCGGAAGC
1 GCTGCAGCTGGTGGAAATGATGCTTTCGGGACTGGAAGTGGAAGCGGAAGC
2643252 GCTGCAGCTGGTGGAAATGATGCTTTCGGGACTGGAAGTGGAAGCG
1 GCTGCAGCTGGTGGAAATGATGCTTTCGGGACTGGAAGTGGAAGCG
2643298 CTGCAGCTGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.22, C:0.14, G:0.41, T:0.23
Consensus pattern (51 bp):
GCTGCAGCTGGTGGAAATGATGCTTTCGGGACTGGAAGTGGAAGCGGAAGC
Found at i:2643303 original size:45 final size:46
Alignment explanation
Indices: 2643201--2643310 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 46
2643191 TGGTTTTGGA
* *
2643201 GCTGCAGCTGGTGGTAATGATGCTTTCGGGATTGGAAGTGGAAGCGGAAGC
1 GCTGCAGCTGGTGGAAATGATGCTTTCGGGACTGGAAGT----G-GGAAGC
2643252 GCTGCAGCTGGTGGAAATGATGCTTTCGGGACTGGAAGT-GGAAGC
1 GCTGCAGCTGGTGGAAATGATGCTTTCGGGACTGGAAGTGGGAAGC
2643297 GCTGCAGCTGGTGG
1 GCTGCAGCTGGTGG
2643311 TTTTGGCGGA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
45 20 0.35
51 37 0.65
ACGTcount: A:0.20, C:0.15, G:0.42, T:0.23
Consensus pattern (46 bp):
GCTGCAGCTGGTGGAAATGATGCTTTCGGGACTGGAAGTGGGAAGC
Found at i:2643349 original size:21 final size:21
Alignment explanation
Indices: 2643324--2643364 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2643314 TGGCGGAGAC
*
2643324 GGTGGGGTCGACGGAGTTGAG
1 GGTGGGGTCGAAGGAGTTGAG
*
2643345 GGTGGGGTTGAAGGAGTTGA
1 GGTGGGGTCGAAGGAGTTGA
2643365 CGGAGGAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.56, T:0.22
Consensus pattern (21 bp):
GGTGGGGTCGAAGGAGTTGAG
Found at i:2648887 original size:2 final size:2
Alignment explanation
Indices: 2648869--2648939 Score: 110
Period size: 2 Copynumber: 36.5 Consensus size: 2
2648859 CATATACTAC
*
2648869 TA TA TA -A TA TT TA -A TA TA TA TA 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
*
2648909 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2648940 TATTGAGATT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
1 2 0.03
2 61 0.97
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2653677 original size:12 final size:12
Alignment explanation
Indices: 2653655--2653685 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
2653645 AATGCAACCG
2653655 ATTTAATTAAATA
1 ATTT-ATTAAATA
2653668 ATTTATTAAATA
1 ATTTATTAAATA
2653680 ATTTAT
1 ATTTAT
2653686 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTATTAAATA
Found at i:2663294 original size:29 final size:29
Alignment explanation
Indices: 2663262--2663353 Score: 66
Period size: 29 Copynumber: 3.1 Consensus size: 29
2663252 TTATTCCCCT
2663262 ATGGTTAAGAGAATCATAATTATTGAGAC
1 ATGGTTAAGAGAATCATAATTATTGAGAC
* ***
2663291 ATGG--AAGA-ATTACAGCTAAGTTATT-CCCC
1 ATGGTTAAGAGAAT-CA--TAA-TTATTGAGAC
*
2663320 TATGGTTAAGAGAATTATAATTATTGAGAC
1 -ATGGTTAAGAGAATCATAATTATTGAGAC
2663350 ATGG
1 ATGG
2663354 ACTGCCCAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 18
0.62 0.12 0.25
Matches are distributed among these distances:
26 2 0.04
27 6 0.13
29 17 0.38
30 13 0.29
32 5 0.11
33 2 0.04
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (29 bp):
ATGGTTAAGAGAATCATAATTATTGAGAC
Found at i:2663328 original size:59 final size:59
Alignment explanation
Indices: 2663236--2663354 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
2663226 AATATACAGA
2663236 AAGAATTACAGCTAAGTTATTCCCCTATGGTTAAGAGAATCATAATTATTGAGACATGG
1 AAGAATTACAGCTAAGTTATTCCCCTATGGTTAAGAGAATCATAATTATTGAGACATGG
*
2663295 AAGAATTACAGCTAAGTTATTCCCCTATGGTTAAGAGAATTATAATTATTGAGACATGG
1 AAGAATTACAGCTAAGTTATTCCCCTATGGTTAAGAGAATCATAATTATTGAGACATGG
2663354 A
1 A
2663355 CTGCCCAGTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (59 bp):
AAGAATTACAGCTAAGTTATTCCCCTATGGTTAAGAGAATCATAATTATTGAGACATGG
Found at i:2675026 original size:15 final size:15
Alignment explanation
Indices: 2674998--2675033 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
2674988 AAAAAAATTG
2674998 ATATTTATTATATTT
1 ATATTTATTATATTT
2675013 ATATATTATT-TATTT
1 ATAT-TTATTATATTT
2675028 ATATTT
1 ATATTT
2675034 TGTTCGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 13 0.65
16 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATTTATTATATTT
Found at i:2679098 original size:12 final size:13
Alignment explanation
Indices: 2679049--2679100 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
2679039 TTGATATTCG
2679049 ATTTT-ATATTTA
1 ATTTTAATATTTA
**
2679061 ATTTTTTTATCTTA
1 ATTTTAATAT-TTA
2679075 A-TTTAATATTTA
1 ATTTTAATATTTA
2679087 ATTTTAAT-TTTA
1 ATTTTAATATTTA
2679099 AT
1 AT
2679101 ATTCAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 15 0.44
13 15 0.44
14 4 0.12
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTAATATTTA
Found at i:2679112 original size:18 final size:19
Alignment explanation
Indices: 2679072--2679109 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2679062 TTTTTTTATC
*
2679072 TTAA-TTTAATATTTAATT
1 TTAATTTTAATATTCAATT
2679090 TTAATTTTAATATTCAATT
1 TTAATTTTAATATTCAATT
2679109 T
1 T
2679110 AATATCGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAATTTTAATATTCAATT
Found at i:2684321 original size:2 final size:2
Alignment explanation
Indices: 2684316--2684346 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2684306 CTCTCTACTC
2684316 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
2684347 CGAGTAATGT
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:2695092 original size:3 final size:3
Alignment explanation
Indices: 2695084--2695108 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2695074 GTAATTATCC
2695084 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
2695109 TTTCATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:2695847 original size:2 final size:2
Alignment explanation
Indices: 2695842--2695868 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2695832 TCTTTCCTTC
2695842 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 A
2695869 AAGGAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2696747 original size:27 final size:26
Alignment explanation
Indices: 2696709--2696761 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
2696699 CAATTCATGA
*
2696709 TTTTTTTTTAAATTTTTATGAAATTT
1 TTTTTTTTTAAATTTTTATAAAATTT
2696735 TTTTGTTTTTAAATTTTTATAAAATTT
1 TTTT-TTTTTAAATTTTTATAAAATTT
2696762 AAATTATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTTTTTTTAAATTTTTATAAAATTT
Found at i:2705479 original size:25 final size:24
Alignment explanation
Indices: 2705444--2705490 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
2705434 ATAATCAAAT
*
2705444 TTAAAATTAATAATATATATATATA
1 TTAAAAGTAATAATATA-ATATATA
*
2705469 TTAAAAGTAATTATATAATATA
1 TTAAAAGTAATAATATAATATA
2705491 AAAAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TTAAAAGTAATAATATAATATATA
Found at i:2705492 original size:19 final size:22
Alignment explanation
Indices: 2705454--2705494 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
2705444 TTAAAATTAA
2705454 TAATATATATATATATTAAAAG
1 TAATATATATATATATTAAAAG
*
2705476 TAAT-TATATA-ATATAAAAA
1 TAATATATATATATATTAAAA
2705495 ATATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TAATATATATATATATTAAAAG
Found at i:2705501 original size:28 final size:29
Alignment explanation
Indices: 2705448--2705503 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
2705438 TCAAATTTAA
* *
2705448 AATTAATAATATATATATATATTAAAAGT
1 AATTAATAATATATAAAAATATTAAAAGT
*
2705477 AATTATATAATATA-AAAAATATAAAAA
1 AATTA-ATAATATATAAAAATATTAAAA
2705504 ACTTGATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.65
30 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
AATTAATAATATATAAAAATATTAAAAGT
Found at i:2716066 original size:12 final size:12
Alignment explanation
Indices: 2716049--2716076 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2716039 ACGAAAAAGC
2716049 AAAAAAATATAA
1 AAAAAAATATAA
2716061 AAAAAAATATAA
1 AAAAAAATATAA
2716073 AAAA
1 AAAA
2716077 GGTGAATTTT
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAATATAA
Found at i:2717604 original size:40 final size:40
Alignment explanation
Indices: 2717542--2717619 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
2717532 AGTAGTCAAT
* *
2717542 TTTAAAACATGTGGTAGCTGTGTAAGTAAATATATATACA
1 TTTAAAACATGTGGAAGATGTGTAAGTAAATATATATACA
*
2717582 TTTATAACATGTGGAAGATGTGTAAGTAAATATATATA
1 TTTAAAACATGTGGAAGATGTGTAAGTAAATATATATA
2717620 TATATATTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (40 bp):
TTTAAAACATGTGGAAGATGTGTAAGTAAATATATATACA
Found at i:2719889 original size:16 final size:16
Alignment explanation
Indices: 2719868--2719901 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2719858 AATAAGATTT
2719868 TTTTTAAT-ATCTTTTA
1 TTTTTAATGAT-TTTTA
2719884 TTTTTAATGATTTTTA
1 TTTTTAATGATTTTTA
2719900 TT
1 TT
2719902 GAACTAGACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTTAATGATTTTTA
Found at i:2720927 original size:118 final size:117
Alignment explanation
Indices: 2720781--2721201 Score: 459
Period size: 118 Copynumber: 3.6 Consensus size: 117
2720771 TTGGCCATGC
* * *
2720781 ATGGCTGACACCCCCTATTTCA-AAAAAAAATTACATTTTTGAGTGTTGGCCATTAAATGACCGA
1 ATGGCCGACACCCCCTATTTCAGAAAAAAAATTA-ATTTTTGAGTGTTGGCCATCAAATGGCCGA
* * *
2720845 CACCCCTTATTTCTCGAGAAAAAAATTTTAAATTTTTTTGGTGTTGGCCATCAA
65 CACCCCCTATTTCTTGAGAAAAAAA-TTCAAATTTTTTTGGTGTTGGCCATCAA
* *
2720899 ATGGCTGACACCCCCTATTTC--AAAAAAAATTGCATTTTTGAGTGTTGGCCATCAAATGGCCGA
1 ATGGCCGACACCCCCTATTTCAGAAAAAAAATT-AATTTTTGAGTGTTGGCCATCAAATGGCCGA
*
2720962 CACCCCCTATTTCTTGA-AAAAAAATTCAAATTTTTTTTGTGTTGGCCACTGC--
65 CACCCCCTATTTCTTGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCA-T-CAA
* * ******
2721014 ATGGCCGACACCCCTTTTTCTCGAGAATTTTTTTTTTAATTTTT--GTGTTGGCCACTGC--ATG
1 ATGGCCGACACCCCCTATT-TC-AGAA--AAAAAATTAATTTTTGAGTGTTGGCCA-T-CAAATG
2721075 GCCGACACCCCCT-TTTCTTGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAA
60 GCCGACACCCCCTATTTCTTGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAA
* ***
2721132 ATGGCCGACACCCCCTATTTTTGAGAAAAAAAATTAATTTTTTTTTGTTGGCCATCAAATGGCCG
1 ATGGCCGACACCCCCTA--TTTCAGAAAAAAAATTAATTTTTGAGTGTTGGCCATCAAATGGCCG
2721197 ACACC
64 ACACC
2721202 AACTTCTTCT
Statistics
Matches: 255, Mismatches: 28, Indels: 40
0.79 0.09 0.12
Matches are distributed among these distances:
115 38 0.15
116 21 0.08
117 64 0.25
118 117 0.46
119 4 0.02
120 9 0.04
121 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (117 bp):
ATGGCCGACACCCCCTATTTCAGAAAAAAAATTAATTTTTGAGTGTTGGCCATCAAATGGCCGAC
ACCCCCTATTTCTTGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAA
Found at i:2720949 original size:55 final size:56
Alignment explanation
Indices: 2720781--2721201 Score: 263
Period size: 60 Copynumber: 7.2 Consensus size: 56
2720771 TTGGCCATGC
* *
2720781 ATGGCTGACACCCCCTATTTCAAAAAAAAATTACATTTTTGAGTGTTGGCCATTAA
1 ATGGCCGACACCCCCTATTTCAAAAAAAAATTACATTTTTGAGTGTTGGCCATCAA
* * * *
2720837 ATGACCGACACCCCTTATTTCTCGAGAAAAAAATTTTAAATTTTTTTG-GTGTTGGCCATCAA
1 ATGGCCGACACCCCCTA-TT-TC-A-AAAAAAA-ATTACA--TTTTTGAGTGTTGGCCATCAA
* *
2720899 ATGGCTGACACCCCCTATTTC-AAAAAAAATTGCATTTTTGAGTGTTGGCCATCAA
1 ATGGCCGACACCCCCTATTTCAAAAAAAAATTACATTTTTGAGTGTTGGCCATCAA
* * **
2720954 ATGGCCGACACCCCCTATTTCTTGAAAAAAAATTCAAATTTTTTTTGTGTTGGCCACTGC--
1 ATGGCCGACACCCCCTATTTC--AAAAAAAAATT-ACA-TTTTTGAGTGTTGGCCA-T-CAA
* * ******
2721014 ATGGCCGACACCCCTTTTTCTCGAGAATTTTTTTTTTA-ATTTTT--GTGTTGGCCACTGC--
1 ATGGCCGACACCCCCTATT-TC-A-AA--AAAAAATTACATTTTTGAGTGTTGGCCA-T-CAA
* *
2721072 ATGGCCGACACCCCCT-TTTCTTGAGAAAAAAATTCAAATTTTTTTG-GTGTTGGCCATCAA
1 ATGGCCGACACCCCCTATTTC---AAAAAAAAATT-ACA--TTTTTGAGTGTTGGCCATCAA
* ***
2721132 ATGGCCGACACCCCCTATTTTTGAGAAAAAAAATTA-ATTTTTTTTTGTTGGCCATCAA
1 ATGGCCGACACCCCCTA--TTTCA-AAAAAAAATTACATTTTTGAGTGTTGGCCATCAA
2721190 ATGGCCGACACC
1 ATGGCCGACACC
2721202 AACTTCTTCT
Statistics
Matches: 293, Mismatches: 39, Indels: 64
0.74 0.10 0.16
Matches are distributed among these distances:
54 6 0.02
55 36 0.12
56 20 0.07
57 18 0.06
58 69 0.24
59 9 0.03
60 74 0.25
61 21 0.07
62 29 0.10
63 11 0.04
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (56 bp):
ATGGCCGACACCCCCTATTTCAAAAAAAAATTACATTTTTGAGTGTTGGCCATCAA
Found at i:2721018 original size:60 final size:59
Alignment explanation
Indices: 2720771--2721201 Score: 339
Period size: 58 Copynumber: 7.4 Consensus size: 59
2720761 TTTGTCAGTA
* * * **
2720771 TTGGCCATGC-ATGGCTGACACCCCCTATTTC--AAAAAAAAATT-ACA-TTTTTGAGTG
1 TTGGCCAT-CAATGGCCGACACCCCCTATTTCTTGAAAAAAAATTCAAATTTTTTTTGTG
* * * * * *
2720826 TTGGCCATTAAATGACCGACACCCCTTATTTCTCGAGAAAAAAATTTTAAATTTTTTTGGTG
1 TTGGCCA-TCAATGGCCGACACCCCCTATTTCTTGA-AAAAAAA-TTCAAATTTTTTTTGTG
* **
2720888 TTGGCCATCAAATGGCTGACACCCCCTATTTC---AAAAAAAATTGC--A-TTTTTGAGTG
1 TTGGCCATC-AATGGCCGACACCCCCTATTTCTTGAAAAAAAATT-CAAATTTTTTTTGTG
2720943 TTGGCCATCAAATGGCCGACACCCCCTATTTCTTGAAAAAAAATTCAAATTTTTTTTGTG
1 TTGGCCATC-AATGGCCGACACCCCCTATTTCTTGAAAAAAAATTCAAATTTTTTTTGTG
* * * * ****
2721003 TTGGCCACTGC-ATGGCCGACA-CCCCTTTTTCTCG---AGAATTTTTTTTTTAATTTTTGTG
1 TTGGCCA-T-CAATGGCCGACACCCCCTATTTCTTGAAAAAAAATTCAAATTT--TTTTTGTG
*
2721061 TTGGCCACTGC-ATGGCCGACACCCCCT-TTTCTTGAGAAAAAAATTCAAATTTTTTTGGTG
1 TTGGCCA-T-CAATGGCCGACACCCCCTATTTCTTGA-AAAAAAATTCAAATTTTTTTTGTG
2721121 TTGGCCATCAAATGGCCGACACCCCCTATTT-TTGAGAAAAAAAATT--AATTTTTTTT-TG
1 TTGGCCATC-AATGGCCGACACCCCCTATTTCTT--GAAAAAAAATTCAAATTTTTTTTGTG
2721179 TTGGCCATCAAATGGCCGACACC
1 TTGGCCATC-AATGGCCGACACC
2721202 AACTTCTTCT
Statistics
Matches: 311, Mismatches: 35, Indels: 57
0.77 0.09 0.14
Matches are distributed among these distances:
55 46 0.15
56 28 0.09
57 3 0.01
58 79 0.25
59 35 0.11
60 59 0.19
61 16 0.05
62 45 0.14
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (59 bp):
TTGGCCATCAATGGCCGACACCCCCTATTTCTTGAAAAAAAATTCAAATTTTTTTTGTG
Found at i:2724944 original size:12 final size:12
Alignment explanation
Indices: 2724902--2724949 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
2724892 ATTTGTGTAA
*
2724902 AAATTAATTTGA
1 AAATTAATTTGG
2724914 AAATTAATTTAAGTTG
1 AAATTAATTT--G--G
2724930 AAATTAATTTGG
1 AAATTAATTTGG
2724942 AAATTAAT
1 AAATTAAT
2724950 GAACATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
AAATTAATTTGG
Found at i:2725168 original size:83 final size:83
Alignment explanation
Indices: 2725080--2725436 Score: 572
Period size: 83 Copynumber: 4.3 Consensus size: 83
2725070 AAAAAGATAG
* * * * * * *
2725080 TTATTATATTACAATTTATATCAAATATTGTATTAATTTAACAATACATTATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
2725145 ATTTTTAAATAAAATTTT
66 ATTTTTAAATAAAATTTT
2725163 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
* *
2725228 ATTTTTAGATAAATTTTT
66 ATTTTTAAATAAAATTTT
* *
2725246 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATATATTATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
*
2725311 ATCTTTAAATAAAATTTT
66 ATTTTTAAATAAAATTTT
* *
2725329 TTATTATATTACAATTTTTATCATATAATATGTTGATTTGACAATATAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
2725394 ATTTTTAAAT-AAATTTT
66 ATTTTTAAATAAAATTTT
*
2725411 TTATTATATTATAATTTTTATCATAT
1 TTATTATATTACAATTTTTATCATAT
2725437 TTTATATTTA
Statistics
Matches: 256, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
82 32 0.12
83 224 0.88
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (83 bp):
TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
ATTTTTAAATAAAATTTT
Found at i:2725308 original size:45 final size:45
Alignment explanation
Indices: 2725258--2725391 Score: 115
Period size: 45 Copynumber: 3.1 Consensus size: 45
2725248 ATTATATTAC
*
2725258 AATTTTTATCATATAATGTGTTGATTTGACAATATATTATTTATT
1 AATTTTTATCATATAATATGTTGATTTGACAATATATTATTTATT
* *** * *
2725303 AATTTTATATC-TTTAA-AT-AAAATTT-----TTTATTATATTA-C
1 AATTTT-TATCATATAATATGTTGATTTGACAATATATTAT-TTATT
*
2725341 AATTTTTATCATATAATATGTTGATTTGACAATATAATATTTATT
1 AATTTTTATCATATAATATGTTGATTTGACAATATATTATTTATT
2725386 AATTTT
1 AATTTT
2725392 ATATTTTTAA
Statistics
Matches: 64, Mismatches: 14, Indels: 22
0.64 0.14 0.22
Matches are distributed among these distances:
37 4 0.06
38 17 0.27
39 5 0.08
40 4 0.06
43 4 0.06
44 4 0.06
45 22 0.34
46 4 0.06
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (45 bp):
AATTTTTATCATATAATATGTTGATTTGACAATATATTATTTATT
Found at i:2725646 original size:20 final size:20
Alignment explanation
Indices: 2725618--2725675 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
2725608 CCACCATTGA
* *
2725618 CCGCAGTTGATCGACTTTTT
1 CCGCCGTTGATCGACTTTGT
* *
2725638 CTGCCGTTGACCGACTTTGT
1 CCGCCGTTGATCGACTTTGT
2725658 CCGCCGTTGATCGACTTT
1 CCGCCGTTGATCGACTTT
2725676 CATCCATCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.29, G:0.22, T:0.36
Consensus pattern (20 bp):
CCGCCGTTGATCGACTTTGT
Found at i:2725667 original size:40 final size:40
Alignment explanation
Indices: 2725598--2725675 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
2725588 CGTCCTGAGA
2725598 CTGCCGTTGACCACCATTGACCGCAGTTGATCGACTTTTT
1 CTGCCGTTGACCACCATTGACCGCAGTTGATCGACTTTTT
* * *
2725638 CTGCCGTTGACCGA-CTTTGTCCGCCGTTGATCGACTTT
1 CTGCCGTTGACC-ACCATTGACCGCAGTTGATCGACTTT
2725676 CATCCATCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.14, C:0.31, G:0.22, T:0.33
Consensus pattern (40 bp):
CTGCCGTTGACCACCATTGACCGCAGTTGATCGACTTTTT
Found at i:2727904 original size:30 final size:30
Alignment explanation
Indices: 2727870--2727961 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
2727860 TCCCTTTACT
*
2727870 TTTTAAATTTAATTT-GTAATTTCGTT-TTTA
1 TTTTAAATTTAATTTCG-AATTTC-TTGTATA
2727900 TTTTAAATTTAATTTCGAATTTCTTGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
* ** * *
2727930 TTTTAATTTTTCTTTCTAATTTCATGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
2727960 TT
1 TT
2727962 CTAATTATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
29 2 0.04
30 51 0.94
31 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTCGAATTTCTTGTATA
Found at i:2728863 original size:60 final size:57
Alignment explanation
Indices: 2728730--2729130 Score: 384
Period size: 60 Copynumber: 6.8 Consensus size: 57
2728720 AGGAGAAGTT
* * *
2728730 GGTGTCGACCATTTGATGGCCAACACAAAAAAAAATTTAAATTTTTTTTCTTGAGAATA-GG
1 GGTGTCGGCCATTTGATGGCCAACAC--CAAAAAATTTAAA--TTTTTT-TTGAAAATAGGG
** * * *
2728791 GGTAACGACCATTTGATTGCCAACACCAAAAAATTTGAATTTTTTTCTCGATAAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTAAATTTTTTT-T-GA-AAATAGGG
2728851 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTTTGAGAAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACC-AAAAAATTTAAA-TTTTTTTTGA-AAATAGGG
* * *
2728911 TGTGTCGGCCATTTGATGGCCAACACCCAAAAA--TACAATTTTTTTTG-AAATAGAG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTA-AATTTTTTTTGAAAATAGGG
* ***
2728966 GGTGTCGGCCATTTGATGGCCAACACTAAAAAAATTTGAAATTTTTTTCTCGAGAAATAAAA
1 GGTGTCGGCCATTTGATGGCCAACAC-CAAAAAATTT-AAATTTTTTT-T-GA-AAATAGGG
* *
2729028 GGTGTCGGCCATTTGATGGCAAACATCC-AAAAATAT-AATTTTTTTTG-AAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACA-CCAAAAAATTTAAATTTTTTTTGAAAATAGGG
* *** *
2729083 GGTGTCGGTCATGCAATGGCCAACACCCAAAAATTTTAAATTTTTTTT
1 GGTGTCGGCCATTTGATGGCCAACA-CCAAAAAATTTAAATTTTTTTT
2729131 CTGTATATCA
Statistics
Matches: 288, Mismatches: 34, Indels: 40
0.80 0.09 0.11
Matches are distributed among these distances:
55 59 0.20
56 12 0.04
57 29 0.10
58 15 0.05
59 31 0.11
60 62 0.22
61 42 0.15
62 37 0.13
63 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (57 bp):
GGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTAAATTTTTTTTGAAAATAGGG
Found at i:2728978 original size:55 final size:55
Alignment explanation
Indices: 2728730--2729130 Score: 326
Period size: 55 Copynumber: 6.8 Consensus size: 55
2728720 AGGAGAAGTT
* * *
2728730 GGTGTCGACCATTTGATGGCCAACACAAAAAAAAATTTAAATTTTTTTTCTTGAGAATAGG
1 GGTGTCGGCCATTTGATGGCCAACAC--CAAAAAA-TTAAA-TTTTTTT-TAGA-AATAGG
** * * * *
2728791 GGTAACGACCATTTGATTGCCAACACCAAAAAATTTGAATTTTTTTCTCGATAAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAA-TTAAATTTTTTT-T--AGAAATA-GG
2728851 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTTTGAGAAATAGG
1 GGTGTCGGCCATTTGATGGCCAACACC-AAAAAA-TTAAA-TTTTTTTT-AGAAATAGG
*
2728910 GTGTGTCGGCCATTTGATGGCCAACACCCAAAAA-TACAATTTTTTTT-GAAATAGAG
1 G-GTGTCGGCCATTTGATGGCCAACACCAAAAAATTA-AATTTTTTTTAGAAATAG-G
* **
2728966 GGTGTCGGCCATTTGATGGCCAACACTAAAAAAATTTGAAATTTTTTTCTCGAGAAATAAAA
1 GGTGTCGGCCATTTGATGGCCAACAC-CAAAAAA-TT-AAATTTTTTT-T--AGAAAT-AGG
*
2729028 GGTGTCGGCCATTTGATGGCAAACATCC-AAAAA-TATAATTTTTTTT-GAAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACA-CCAAAAAATTA-AATTTTTTTTAGAAATA-GG
* *** *
2729083 GGTGTCGGTCATGCAATGGCCAACACCCAAAAATTTTAAATTTTTTTT
1 GGTGTCGGCCATTTGATGGCCAACA-CCAAAAA-ATTAAATTTTTTTT
2729131 CTGTATATCA
Statistics
Matches: 288, Mismatches: 29, Indels: 50
0.78 0.08 0.14
Matches are distributed among these distances:
54 1 0.00
55 59 0.20
56 11 0.04
57 20 0.07
58 25 0.09
59 35 0.12
60 59 0.20
61 40 0.14
62 36 0.12
63 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (55 bp):
GGTGTCGGCCATTTGATGGCCAACACCAAAAAATTAAATTTTTTTTAGAAATAGG
Found at i:2729130 original size:117 final size:115
Alignment explanation
Indices: 2728730--2729133 Score: 469
Period size: 117 Copynumber: 3.5 Consensus size: 115
2728720 AGGAGAAGTT
*
2728730 GGTGTCGACCATTTGATGGCCAACACAAAAAAAAATTTAAATTTTTTTTCTTGAG-AATAGGGGT
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAAATTTAAATTTTTTTTC-TGAGAAATAGGGGT
** * * *
2728794 AACGACCATTTGATTGCCAACACCAAAAAATTTGAATTTTTTTCTCGATAAATAGGG
65 GTCGGCCATTTGATGGCCAACACC-AAAAATAT-AATTTTTTT-T-G--AAATAGGG
*
2728851 GGTGTCGGCCATTTGATGGCCAACAC-CAAAAAAATTTAAATTTTTTTT-TGAGAAATAGGGTGT
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAAATTTAAATTTTTTTTCTGAGAAATAGGG-GT
* *
2728914 GTCGGCCATTTGATGGCCAACACCCAAAAATACAATTTTTTTTGAAATAGAG
65 GTCGGCCATTTGATGGCCAACA-CCAAAAATATAATTTTTTTTGAAATAGGG
* **
2728966 GGTGTCGGCCATTTGATGGCCAACAC-TAAAAAAATTTGAAA-TTTTTTTCTCGAGAAATAAAAG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAAATTT-AAATTTTTTTTCT-GAGAAAT-AGGG
*
2729029 GTGTCGGCCATTTGATGGCAAACATCCAAAAATATAATTTTTTTTGAAATAGGG
63 GTGTCGGCCATTTGATGGCCAACA-CCAAAAATATAATTTTTTTTGAAATAGGG
* *** ** *
2729083 GGTGTCGGTCATGCAATGGCCAACAC-CCAAAAATTTTAAATTTTTTTTCTG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAAATTTAAATTTTTTTTCTG
2729134 TATATCAAGA
Statistics
Matches: 252, Mismatches: 23, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
115 50 0.20
116 8 0.03
117 97 0.38
118 7 0.03
119 16 0.06
120 47 0.19
121 27 0.11
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (115 bp):
GGTGTCGGCCATTTGATGGCCAACACAAAAAAAAATTTAAATTTTTTTTCTGAGAAATAGGGGTG
TCGGCCATTTGATGGCCAACACCAAAAATATAATTTTTTTTGAAATAGGG
Found at i:2733050 original size:3 final size:3
Alignment explanation
Indices: 2733042--2733077 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2733032 TGGGCGCTGT
2733042 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2733078 CAAAACAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2735723 original size:29 final size:27
Alignment explanation
Indices: 2735671--2735744 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 27
2735661 TTTTTATAAA
2735671 ATTTTAA-ATTAAAAATAATAAAATTAT
1 ATTTTAATATTAAAAATAATAAAATT-T
*
2735698 ATTTTAATATTCAAAATAATAAAAATTT
1 ATTTTAATATTAAAAATAAT-AAAATTT
*
2735726 AATTTAATCATTTAAAAAT
1 ATTTTAAT-A-TTAAAAAT
2735745 TTAAATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 7 0.17
28 19 0.47
29 7 0.17
30 7 0.17
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (27 bp):
ATTTTAATATTAAAAATAATAAAATTT
Found at i:2760923 original size:17 final size:17
Alignment explanation
Indices: 2760901--2760956 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
2760891 AAGAAAAATA
2760901 AAAAGTTGATCCATTCT
1 AAAAGTTGATCCATTCT
* *
2760918 AAAAG-TAAT-C-TGCT
1 AAAAGTTGATCCATTCT
2760932 ATAAAGTTCGATCCATTCT
1 A-AAAGTT-GATCCATTCT
2760951 AAAAGT
1 AAAAGT
2760957 AATCTGCTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
14 4 0.13
15 5 0.17
16 4 0.13
17 7 0.23
18 6 0.20
19 4 0.13
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (17 bp):
AAAAGTTGATCCATTCT
Found at i:2760946 original size:33 final size:32
Alignment explanation
Indices: 2760902--2760966 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 32
2760892 AGAAAAATAA
2760902 AAAGTTGATCCATTCTAAAAGTAATCTGCTAT
1 AAAGTTGATCCATTCTAAAAGTAATCTGCTAT
2760934 AAAGTTCGATCCATTCTAAAAGTAATCTGCTAT
1 AAAGTT-GATCCATTCTAAAAGTAATCTGCTAT
2760967 CAACCTAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (32 bp):
AAAGTTGATCCATTCTAAAAGTAATCTGCTAT
Found at i:2762356 original size:62 final size:62
Alignment explanation
Indices: 2762283--2762407 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
2762273 ATATCCAACG
2762283 TGGCGGTTCAGACGTCAGCACAAATTCACCATCAAATTTAAGTAACAAACCAAACATATTGA
1 TGGCGGTTCAGACGTCAGCACAAATTCACCATCAAATTTAAGTAACAAACCAAACATATTGA
*
2762345 TGGCGGTTCAGACGTCAGCACAAATTCATCATCAAATTTAAGTAACAAACCAAACATATTGA
1 TGGCGGTTCAGACGTCAGCACAAATTCACCATCAAATTTAAGTAACAAACCAAACATATTGA
2762407 T
1 T
2762408 AATATGCGCG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (62 bp):
TGGCGGTTCAGACGTCAGCACAAATTCACCATCAAATTTAAGTAACAAACCAAACATATTGA
Found at i:2776120 original size:22 final size:21
Alignment explanation
Indices: 2776095--2776136 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2776085 AACTCGTTCA
*
2776095 AAAAATATTAAATATAT-TAAT
1 AAAAAT-TAAAATATATATAAT
2776116 AAAAATTAAAATATATATAAT
1 AAAAATTAAAATATATATAAT
2776137 TAAGAACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAATTAAAATATATATAAT
Found at i:2776264 original size:20 final size:19
Alignment explanation
Indices: 2776239--2776291 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 19
2776229 GTATTTTTTA
2776239 AAATATAATAATAAAATATT
1 AAATATAATAATAAAAT-TT
*
2776259 AAATATACTAATAAAATTT
1 AAATATAATAATAAAATTT
2776278 AACATATATATAAT
1 AA-ATATA-ATAAT
2776292 TAAGAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 21 0.72
21 4 0.14
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATATAATAATAAAATTT
Found at i:2776377 original size:154 final size:155
Alignment explanation
Indices: 2776096--2776499 Score: 756
Period size: 154 Copynumber: 2.6 Consensus size: 155
2776086 ACTCGTTCAA
* * * *
2776096 AAAATATTAAATATATTAATAAAAATTAAAATATATATAATTAAGAACTTATTTTTTAAATAAAA
1 AAAATATTAAATATACTAATAAAATTTAACATATATATAATTAAGAACTTATTTTTTAAATAAAC
2776161 ATTATTTAATTAAATAATATTTTATTATTATATTTAAAAAATTAAAAGAAGTTTTTTCTAGAAAT
66 ATTATTTAATTAAATAATATTTTATTATTATATTTAAAAAATTAAAAGAAGTTTTTTCTAGAAAT
2776226 GGTGTATTTTTTAAAATATAATAAT
131 GGTGTATTTTTTAAAATATAATAAT
2776251 AAAATATTAAATATACTAATAAAATTTAACATATATATAATTAAGAACTTA-TTTTTAAATAAAC
1 AAAATATTAAATATACTAATAAAATTTAACATATATATAATTAAGAACTTATTTTTTAAATAAAC
2776315 ATTATTTAATTAAATAATATTTTATTATTATATTTAAAAAATTAAAAGAAGTTTTTTCTAGAAAT
66 ATTATTTAATTAAATAATATTTTATTATTATATTTAAAAAATTAAAAGAAGTTTTTTCTAGAAAT
2776380 GGTGTATTTTTTAAAATATAATAAT
131 GGTGTATTTTTTAAAATATAATAAT
2776405 AAAATATTAAATATACTAATAAAATTTAACATATATATAATTAAGAACTTATTTTTTAAATAAAC
1 AAAATATTAAATATACTAATAAAATTTAACATATATATAATTAAGAACTTATTTTTTAAATAAAC
*
2776470 ATTATTTAATTAAATAATATATTATTATTA
66 ATTATTTAATTAAATAATATTTTATTATTA
2776500 AATATATCAA
Statistics
Matches: 243, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
154 153 0.63
155 90 0.37
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (155 bp):
AAAATATTAAATATACTAATAAAATTTAACATATATATAATTAAGAACTTATTTTTTAAATAAAC
ATTATTTAATTAAATAATATTTTATTATTATATTTAAAAAATTAAAAGAAGTTTTTTCTAGAAAT
GGTGTATTTTTTAAAATATAATAAT
Found at i:2776418 original size:20 final size:19
Alignment explanation
Indices: 2776393--2776445 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 19
2776383 GTATTTTTTA
2776393 AAATATAATAATAAAATATT
1 AAATATAATAATAAAAT-TT
*
2776413 AAATATACTAATAAAATTT
1 AAATATAATAATAAAATTT
2776432 AACATATATATAAT
1 AA-ATATA-ATAAT
2776446 TAAGAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 21 0.72
21 4 0.14
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATATAATAATAAAATTT
Found at i:2776484 original size:19 final size:18
Alignment explanation
Indices: 2776460--2776503 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2776450 AACTTATTTT
2776460 TTAAATAA-ACATTATTTAA
1 TTAAATAATACATTA-TT-A
*
2776479 TTAAATAATATATTATTA
1 TTAAATAATACATTATTA
2776497 TTAAATA
1 TTAAATA
2776504 TATCAAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 10 0.43
20 5 0.22
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAAATAATACATTATTA
Found at i:2776725 original size:15 final size:15
Alignment explanation
Indices: 2776705--2776757 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
2776695 TACTACAAAT
2776705 TATTTATTATTAATA
1 TATTTATTATTAATA
*
2776720 TATTTATAATTGTAATAAA
1 TATTTATTA-T-TAAT--A
2776739 TATTTATTATTAATA
1 TATTTATTATTAATA
2776754 TATT
1 TATT
2776758 AATATTGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 13 0.41
16 1 0.03
17 8 0.25
18 1 0.03
19 9 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TATTTATTATTAATA
Found at i:2776816 original size:15 final size:16
Alignment explanation
Indices: 2776796--2776825 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2776786 AGAATATTAT
2776796 TTAAAA-TTATTATTC
1 TTAAAATTTATTATTC
2776811 TTAAAATTTATTATT
1 TTAAAATTTATTATT
2776826 AAAATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAAATTTATTATTC
Found at i:2776878 original size:16 final size:16
Alignment explanation
Indices: 2776859--2776889 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2776849 AATTTATTAA
2776859 AATAATTAATTATATT
1 AATAATTAATTATATT
*
2776875 AATAATTTATTATAT
1 AATAATTAATTATAT
2776890 GAAAAGATAT
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:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATAATTAATTATATT
Found at i:2776982 original size:10 final size:9
Alignment explanation
Indices: 2776953--2776978 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2776943 ATTTTATATT
2776953 AATATTTTA
1 AATATTTTA
2776962 AATATTTTA
1 AATATTTTA
2776971 AATATTTT
1 AATATTTT
2776979 TAAAAAGAAA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTA
Found at i:2780656 original size:17 final size:17
Alignment explanation
Indices: 2780634--2780668 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2780624 GTGGATTTAG
2780634 TTTTTATATTTTAATTT
1 TTTTTATATTTTAATTT
*
2780651 TTTTTATTTTTTAATTT
1 TTTTTATATTTTAATTT
2780668 T
1 T
2780669 AAAATTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTATATTTTAATTT
Found at i:2785471 original size:27 final size:26
Alignment explanation
Indices: 2785439--2785507 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 26
2785429 ATTGGTCATC
2785439 AAAAAATTTAAGATAATT-TGATAAAA
1 AAAAAATTTAA-ATAATTATGATAAAA
2785465 AATAAAA-TTAAATAATTGAATGATAAAA
1 AA-AAAATTTAAATAATT--ATGATAAAA
*
2785493 AAGAAATTT-AATAAT
1 AAAAAATTTAAATAAT
2785508 AGTTAAGTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
25 6 0.16
26 6 0.16
27 13 0.35
28 12 0.32
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (26 bp):
AAAAAATTTAAATAATTATGATAAAA
Found at i:2804226 original size:15 final size:16
Alignment explanation
Indices: 2804206--2804235 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2804196 GGAGATGTAC
2804206 TCTTTTTT-TTTTTTT
1 TCTTTTTTCTTTTTTT
2804221 TCTTTTTTCTTTTTT
1 TCTTTTTTCTTTTTT
2804236 CACAGTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
TCTTTTTTCTTTTTTT
Found at i:2806707 original size:6 final size:6
Alignment explanation
Indices: 2806696--2806729 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2806686 TGGTTCTTCT
2806696 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAA
1 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAA
2806730 TGGAGAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (6 bp):
TGAAGA
Found at i:2808906 original size:15 final size:15
Alignment explanation
Indices: 2808886--2808918 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2808876 AGTAAAGTTC
2808886 TTTCAACAATATCGA
1 TTTCAACAATATCGA
2808901 TTTCAACAATATCGA
1 TTTCAACAATATCGA
2808916 TTT
1 TTT
2808919 TAAGTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (15 bp):
TTTCAACAATATCGA
Found at i:2809266 original size:403 final size:403
Alignment explanation
Indices: 2808681--2809492 Score: 1624
Period size: 403 Copynumber: 2.0 Consensus size: 403
2808671 ATTTTTAATT
2808681 TAATAAAAATATTTAAAATGAAGGAGAGTTGATACTCGGTGTCTTTTATGATTATCATTAAAGAT
1 TAATAAAAATATTTAAAATGAAGGAGAGTTGATACTCGGTGTCTTTTATGATTATCATTAAAGAT
2808746 TATCGATGAGAACTTTGCGATGAGATTTAATAATAACATTGCATCATTTATAAGTGTGAATTTAG
66 TATCGATGAGAACTTTGCGATGAGATTTAATAATAACATTGCATCATTTATAAGTGTGAATTTAG
2808811 CTACAAATATTTTCACCCGTTTTATAATTTGAGTCTACTTTTATTCAGGCCAAAAGTGAAATTTA
131 CTACAAATATTTTCACCCGTTTTATAATTTGAGTCTACTTTTATTCAGGCCAAAAGTGAAATTTA
2808876 AGTAAAGTTCTTTCAACAATATCGATTTCAACAATATCGATTTTAAGTTTTAAATTTAATCCAAA
196 AGTAAAGTTCTTTCAACAATATCGATTTCAACAATATCGATTTTAAGTTTTAAATTTAATCCAAA
2808941 TAATTTAAGAAAGAAATTAATTTCCGCTTCTTTTAACCATTGCACCATTTACAAGCGTGAATCAA
261 TAATTTAAGAAAGAAATTAATTTCCGCTTCTTTTAACCATTGCACCATTTACAAGCGTGAATCAA
2809006 ATGCATATATTTTCATCCGTTTTATAATCTAAGTCTAATTTTATTTGAGTCGATAGTGATATTTA
326 ATGCATATATTTTCATCCGTTTTATAATCTAAGTCTAATTTTATTTGAGTCGATAGTGATATTTA
2809071 AATAAAGTTATTC
391 AATAAAGTTATTC
2809084 TAATAAAAATATTTAAAATGAAGGAGAGTTGATACTCGGTGTCTTTTATGATTATCATTAAAGAT
1 TAATAAAAATATTTAAAATGAAGGAGAGTTGATACTCGGTGTCTTTTATGATTATCATTAAAGAT
2809149 TATCGATGAGAACTTTGCGATGAGATTTAATAATAACATTGCATCATTTATAAGTGTGAATTTAG
66 TATCGATGAGAACTTTGCGATGAGATTTAATAATAACATTGCATCATTTATAAGTGTGAATTTAG
2809214 CTACAAATATTTTCACCCGTTTTATAATTTGAGTCTACTTTTATTCAGGCCAAAAGTGAAATTTA
131 CTACAAATATTTTCACCCGTTTTATAATTTGAGTCTACTTTTATTCAGGCCAAAAGTGAAATTTA
2809279 AGTAAAGTTCTTTCAACAATATCGATTTCAACAATATCGATTTTAAGTTTTAAATTTAATCCAAA
196 AGTAAAGTTCTTTCAACAATATCGATTTCAACAATATCGATTTTAAGTTTTAAATTTAATCCAAA
2809344 TAATTTAAGAAAGAAATTAATTTCCGCTTCTTTTAACCATTGCACCATTTACAAGCGTGAATCAA
261 TAATTTAAGAAAGAAATTAATTTCCGCTTCTTTTAACCATTGCACCATTTACAAGCGTGAATCAA
2809409 ATGCATATATTTTCATCCGTTTTATAATCTAAGTCTAATTTTATTTGAGTCGATAGTGATATTTA
326 ATGCATATATTTTCATCCGTTTTATAATCTAAGTCTAATTTTATTTGAGTCGATAGTGATATTTA
2809474 AATAAAGTTATTC
391 AATAAAGTTATTC
2809487 TAATAA
1 TAATAA
2809493 TATCAATTTT
Statistics
Matches: 409, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
403 409 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (403 bp):
TAATAAAAATATTTAAAATGAAGGAGAGTTGATACTCGGTGTCTTTTATGATTATCATTAAAGAT
TATCGATGAGAACTTTGCGATGAGATTTAATAATAACATTGCATCATTTATAAGTGTGAATTTAG
CTACAAATATTTTCACCCGTTTTATAATTTGAGTCTACTTTTATTCAGGCCAAAAGTGAAATTTA
AGTAAAGTTCTTTCAACAATATCGATTTCAACAATATCGATTTTAAGTTTTAAATTTAATCCAAA
TAATTTAAGAAAGAAATTAATTTCCGCTTCTTTTAACCATTGCACCATTTACAAGCGTGAATCAA
ATGCATATATTTTCATCCGTTTTATAATCTAAGTCTAATTTTATTTGAGTCGATAGTGATATTTA
AATAAAGTTATTC
Found at i:2809309 original size:15 final size:15
Alignment explanation
Indices: 2809289--2809321 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2809279 AGTAAAGTTC
2809289 TTTCAACAATATCGA
1 TTTCAACAATATCGA
2809304 TTTCAACAATATCGA
1 TTTCAACAATATCGA
2809319 TTT
1 TTT
2809322 TAAGTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (15 bp):
TTTCAACAATATCGA
Found at i:2836270 original size:18 final size:17
Alignment explanation
Indices: 2836230--2836292 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 17
2836220 TATTTTATAA
*
2836230 TATTTAAATATATAATTT
1 TATTTAAAT-TATATTTT
*
2836248 AATTTAAATGTATATTTT
1 TATTTAAAT-TATATTTT
*
2836266 TATTTTAATTAATATATTT
1 TATTTAAATT-ATAT-TTT
2836285 TACTTTAA
1 TA-TTTAA
2836293 TTTTTAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 1 0.03
18 26 0.72
19 5 0.14
20 4 0.11
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TATTTAAATTATATTTT
Found at i:2837124 original size:30 final size:28
Alignment explanation
Indices: 2837078--2837144 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 28
2837068 GAGAAAAGAA
* *
2837078 AGTTTGAAATTAATATAAAAATAGGTATT
1 AGTTTGAAACTAATATAAAAAGA-GTATT
2837107 AGTTTGATAACTAATATAAAAAGAGTATT
1 AGTTTGA-AACTAATATAAAAAGAGTATT
*
2837136 TGTTTGAAA
1 AGTTTGAAA
2837145 TTTTTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 2 0.06
29 18 0.53
30 14 0.41
ACGTcount: A:0.46, C:0.01, G:0.15, T:0.37
Consensus pattern (28 bp):
AGTTTGAAACTAATATAAAAAGAGTATT
Found at i:2837771 original size:27 final size:27
Alignment explanation
Indices: 2837741--2837795 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2837731 TTCGGACAAG
* ** *
2837741 TGGTGCCTTTGGGGTAGGTGACACCAA
1 TGGTGCCTTTCGAATAGGCGACACCAA
2837768 TGGTGCCTTTCGAATAGGCGACACCAA
1 TGGTGCCTTTCGAATAGGCGACACCAA
2837795 T
1 T
2837796 TATGCCTACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (27 bp):
TGGTGCCTTTCGAATAGGCGACACCAA
Found at i:2837958 original size:25 final size:25
Alignment explanation
Indices: 2837902--2837968 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
2837892 AAATTTTAAT
*
2837902 AGCAAATTTTT-AAGAATGAAATGA
1 AGCAAATTTTTGAAGAATGAAAGGA
2837926 AGCAAAATTTTTGAAGAATGAAAGGA
1 AGC-AAATTTTTGAAGAATGAAAGGA
2837952 AGCAAATTTTTGAAGAA
1 AGCAAATTTTTGAAGAA
2837969 GAGTTCAGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
24 3 0.08
25 22 0.55
26 15 0.38
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.27
Consensus pattern (25 bp):
AGCAAATTTTTGAAGAATGAAAGGA
Found at i:2844180 original size:25 final size:23
Alignment explanation
Indices: 2844142--2844241 Score: 148
Period size: 23 Copynumber: 4.3 Consensus size: 23
2844132 GAACACTAGC
2844142 GTGCTCTCTGATTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTGTGT
2844165 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTG--ATTAGCACTGTGT
*
2844190 GTGCTCTCCGATTAGCACT-TCGT
1 GTGCTCTCTGATTAGCACTGT-GT
*
2844213 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
2844236 GTGCTC
1 GTGCTC
2844242 AGTACTTTGT
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
22 1 0.01
23 47 0.66
24 1 0.01
25 22 0.31
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTGTGT
Found at i:2844215 original size:48 final size:46
Alignment explanation
Indices: 2844142--2844241 Score: 148
Period size: 48 Copynumber: 2.1 Consensus size: 46
2844132 GAACACTAGC
*
2844142 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCCGATTAGCACTGTGTGTGCTCTCTG--ATTAGCACTGTGT
*
2844190 GTGCTCTCCGATTAGCACT-TCGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCCGATTAGCACTGT-GTGTGCTCTCTGATTAGCACTGTGT
2844236 GTGCTC
1 GTGCTC
2844242 AGTACTTTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
46 18 0.37
47 1 0.02
48 30 0.61
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (46 bp):
GTGCTCTCCGATTAGCACTGTGTGTGCTCTCTGATTAGCACTGTGT
Found at i:2844270 original size:39 final size:39
Alignment explanation
Indices: 2844206--2844280 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
2844196 TCCGATTAGC
*
2844206 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
2844245 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
2844281 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:2854791 original size:2 final size:2
Alignment explanation
Indices: 2854786--2854819 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2854776 AAGAAAGACT
2854786 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2854820 GGAGGGAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2856982 original size:71 final size:70
Alignment explanation
Indices: 2856840--2856983 Score: 157
Period size: 71 Copynumber: 2.0 Consensus size: 70
2856830 AGAGCTATAT
* *
2856840 TTTGAACTTTTACTTATGTTTTTTTATAATCTTATTGTGTTATTATTGTTACTTGAGCTTATGTT
1 TTTGAACTTTTACTTATGTTTTTTTATAATCTTATTGTGTTATCATTGTTACTTGAGATTATGTT
**
2856905 GTTTA
66 ACTTA
* * * * * *
2856910 TTTGAACTTTTGCTTTTTTTTTTATTATAATCTTGTTGTGTTGTCATTGTTTACTTG-GATT-TT
1 TTTGAACTTTTACTTATGTTTTT-TTATAATCTTATTGTGTTATCATTG-TTACTTGAGATTATG
2856973 TTCACTTA
64 TT-ACTTA
2856981 TTT
1 TTT
2856984 ATTTCAATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
70 23 0.38
71 31 0.51
72 7 0.11
ACGTcount: A:0.17, C:0.08, G:0.12, T:0.62
Consensus pattern (70 bp):
TTTGAACTTTTACTTATGTTTTTTTATAATCTTATTGTGTTATCATTGTTACTTGAGATTATGTT
ACTTA
Done.