Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000389.1 Hibiscus syriacus cultivar Beakdansim tig00000715_pilon, 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: 2672246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 15
Found at i:2173363 original size:19 final size:19
Alignment explanation
Indices: 2173339--2173375 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2173329 TGCAATACTG
*
2173339 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
2173358 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
2173376 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:2190330 original size:2 final size:2
Alignment explanation
Indices: 2190285--2190310 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2190275 ATATACCGAT
2190285 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
2190311 AGAACTTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2190605 original size:2 final size:2
Alignment explanation
Indices: 2190598--2190624 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2190588 AGAAAACTGC
2190598 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
2190625 GAGAGAGAGA
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:2208548 original size:29 final size:30
Alignment explanation
Indices: 2208481--2208551 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
2208471 AAAAGTTATT
2208481 TTCTAAAAAAAACTCATTAAATTATTAAAA
1 TTCTAAAAAAAACTCATTAAATTATTAAAA
*
2208511 TTCTCAAAAAATAC-C-TTAAATT-TCATAAAA
1 TTCT-AAAAAAAACTCATTAAATTAT--TAAAA
2208541 -TCTAAAAAAAA
1 TTCTAAAAAAAA
2208552 TTCCTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
28 8 0.22
29 10 0.28
30 10 0.28
31 8 0.22
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (30 bp):
TTCTAAAAAAAACTCATTAAATTATTAAAA
Found at i:2208718 original size:74 final size:74
Alignment explanation
Indices: 2208630--2208877 Score: 255
Period size: 74 Copynumber: 3.2 Consensus size: 74
2208620 CATTTTTAGG
* *
2208630 GAGTTTATGATTTTTTGGTAATCCCTAAATTAATTTTAAAAATGAATCTTATGTTTTTTAGGGAT
1 GAGTTTATGATTTTTTGGTAATCCCTAAATTCATTATAAAAATGAATCTTATGTTTTTTAGGGAT
2208695 TACGATTTA
66 TACGATTTA
* *
2208704 GAGTTTATGATTTTTTGATCATCCCTAAATTCATTATAAAAAGTGAATCTTATGAATCCTATGAT
1 GAGTTTATGATTTTTTGGTAATCCCTAAATTCATTATAAAAA-TGAATCTTATG-------T--T
* *
2208769 TTTTAGGGAGTACGATTGA
56 TTTTAGGGATTACGATTTA
* ** * * * *
2208788 GAGTTTGTGATTTTTT-GTAATCTTTAAATTCATTCTATAAAATGAATCTTATGATTTGTATGGA
1 GAGTTTATGATTTTTTGGTAATCCCTAAATTCATTATA-AAAATGAATCTTATGTTTTTTAGGGA
*
2208852 TTATGATTTA
65 TTACGATTTA
*
2208862 GAATTTATGATTTTTT
1 GAGTTTATGATTTTTT
2208878 AGTATTTTTT
Statistics
Matches: 143, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
74 67 0.47
75 11 0.08
82 1 0.01
83 27 0.19
84 37 0.26
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (74 bp):
GAGTTTATGATTTTTTGGTAATCCCTAAATTCATTATAAAAATGAATCTTATGTTTTTTAGGGAT
TACGATTTA
Found at i:2209962 original size:30 final size:30
Alignment explanation
Indices: 2209926--2209983 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2209916 AGTGAACTGG
*
2209926 CGGTTCAAACCAGTTTTGCCGGTTTTCAAC
1 CGGTTCAAACCAGTTTTACCGGTTTTCAAC
** *
2209956 CGGTTCACCCCGGTTTTACCGGTTTTCA
1 CGGTTCAAACCAGTTTTACCGGTTTTCA
2209984 GTTGGTTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.34
Consensus pattern (30 bp):
CGGTTCAAACCAGTTTTACCGGTTTTCAAC
Found at i:2210010 original size:20 final size:21
Alignment explanation
Indices: 2209965--2210011 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2209955 CCGGTTCACC
2209965 CCGGTT-TTACCGGTTTTCAG
1 CCGGTTCTTACCGGTTTTCAG
**
2209985 TTGGTTCTT-CCGGTTTTCAG
1 CCGGTTCTTACCGGTTTTCAG
2210005 CCGGTTC
1 CCGGTTC
2210012 ATTGCCAGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.06, C:0.26, G:0.26, T:0.43
Consensus pattern (21 bp):
CCGGTTCTTACCGGTTTTCAG
Found at i:2211382 original size:48 final size:48
Alignment explanation
Indices: 2211301--2211415 Score: 171
Period size: 48 Copynumber: 2.4 Consensus size: 48
2211291 TTATCATCAA
* *
2211301 AATAATCAAAAT-TAATC-CTTTAAAAAATTAATCAAAATTAATAAGTC
1 AATAATCAAAATGTAA-CAATTTTAAAAATTAATCAAAATTAATAAGTC
*
2211348 AATAATCAAAATGTAGCAATTTTAAAAATTAATCAAAATTAATAAGTC
1 AATAATCAAAATGTAACAATTTTAAAAATTAATCAAAATTAATAAGTC
*
2211396 AATAATCAGAATGTAACAAT
1 AATAATCAAAATGTAACAAT
2211416 CAATAATATA
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
47 13 0.21
48 48 0.79
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (48 bp):
AATAATCAAAATGTAACAATTTTAAAAATTAATCAAAATTAATAAGTC
Found at i:2211401 original size:21 final size:21
Alignment explanation
Indices: 2211377--2211422 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2211367 TTTTAAAAAT
*
2211377 TAATCAAAAT-TAATAAGTCAA
1 TAATCAAAATGTAACAA-TCAA
*
2211398 TAATCAGAATGTAACAATCAA
1 TAATCAAAATGTAACAATCAA
2211419 TAAT
1 TAAT
2211423 ATAAACAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (21 bp):
TAATCAAAATGTAACAATCAA
Found at i:2226862 original size:21 final size:21
Alignment explanation
Indices: 2226809--2226872 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
2226799 ATATGAAATT
*
2226809 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
* *
2226830 TATGTCCTGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
*
2226852 TTGTCCCGAAGGACTTATGAA
1 TTGTCCCGAAGGACCTATGAA
2226873 ACCCTCGACT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 18 0.50
22 18 0.50
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:2230531 original size:2 final size:2
Alignment explanation
Indices: 2230481--2230517 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2230471 TAAAAACTCA
2230481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2230518 ACTTCTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2232003 original size:2 final size:2
Alignment explanation
Indices: 2231998--2232024 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2231988 TAATAACACT
2231998 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2232025 TACCTTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2242267 original size:2 final size:2
Alignment explanation
Indices: 2242260--2242285 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2242250 TGTATTTATC
2242260 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2242286 TACTTTGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2244275 original size:16 final size:16
Alignment explanation
Indices: 2244216--2244275 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
2244206 ATTAATGAGA
*
2244216 TAAAATTATAAAAT-TA
1 TAAAA-TATAAAATATT
*
2244232 TAAAAGATGAAAATAATT
1 TAAAATAT-AAAAT-ATT
*
2244250 TATTAATATAAAATATT
1 TA-AAATATAAAATATT
2244267 TAAAATATA
1 TAAAATATA
2244276 TAGTAATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
15 2 0.06
16 16 0.46
17 5 0.14
18 8 0.23
19 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
TAAAATATAAAATATT
Found at i:2244654 original size:14 final size:14
Alignment explanation
Indices: 2244617--2244656 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 14
2244607 TTAGATTTTC
*
2244617 TAAAATTACATTA-
1 TAAAAATACATTAT
2244630 TAAAAA-A-ATTAT
1 TAAAAATACATTAT
2244642 TAAAAATACATTAT
1 TAAAAATACATTAT
2244656 T
1 T
2244657 GTTAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
11 4 0.17
12 7 0.30
13 6 0.26
14 6 0.26
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAATACATTAT
Found at i:2244825 original size:7 final size:7
Alignment explanation
Indices: 2244813--2244899 Score: 52
Period size: 7 Copynumber: 12.7 Consensus size: 7
2244803 GTTAGATTAC
2244813 ACCCTAA
1 ACCCTAA
2244820 ACCCTAA
1 ACCCTAA
*
2244827 A-TCTAA
1 ACCCTAA
*
2244833 ACCCTGA
1 ACCCTAA
* *
2244840 ACCTTGA
1 ACCCTAA
**
2244847 ACTATAA
1 ACCCTAA
*
2244854 ATCCTAA
1 ACCCTAA
2244861 ACCCTAA
1 ACCCTAA
*
2244868 ATCC-AA
1 ACCCTAA
**
2244874 ACCCTGG
1 ACCCTAA
*
2244881 ATCCTAA
1 ACCCTAA
*
2244888 ACTCTAA
1 ACCCTAA
2244895 ACCCT
1 ACCCT
2244900 TTATCCGATT
Statistics
Matches: 57, Mismatches: 21, Indels: 4
0.70 0.26 0.05
Matches are distributed among these distances:
6 10 0.18
7 47 0.82
ACGTcount: A:0.39, C:0.34, G:0.05, T:0.22
Consensus pattern (7 bp):
ACCCTAA
Found at i:2244834 original size:13 final size:13
Alignment explanation
Indices: 2244816--2244878 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 13
2244806 AGATTACACC
2244816 CTAAACCCTAAAT
1 CTAAACCCTAAAT
* *
2244829 CTAAACCCTGAAC
1 CTAAACCCTAAAT
* **
2244842 CTTGAACTATAAAT
1 C-TAAACCCTAAAT
2244856 CCTAAACCCTAAAT
1 -CTAAACCCTAAAT
*
2244870 CCAAACCCT
1 CTAAACCCT
2244879 GGATCCTAAA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
13 20 0.54
14 16 0.43
15 1 0.03
ACGTcount: A:0.41, C:0.33, G:0.03, T:0.22
Consensus pattern (13 bp):
CTAAACCCTAAAT
Found at i:2244884 original size:13 final size:14
Alignment explanation
Indices: 2244815--2244895 Score: 69
Period size: 14 Copynumber: 5.9 Consensus size: 14
2244805 TAGATTACAC
2244815 CCTAAACCCTAAAT
1 CCTAAACCCTAAAT
*
2244829 -CTAAACCCTGAA-
1 CCTAAACCCTAAAT
* **
2244841 CCTTGAACTATAAAT
1 CC-TAAACCCTAAAT
2244856 CCTAAACCCTAAAT
1 CCTAAACCCTAAAT
**
2244870 CC-AAACCCTGGAT
1 CCTAAACCCTAAAT
*
2244883 CCTAAACTCTAAA
1 CCTAAACCCTAAA
2244896 CCCTTTATCC
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
13 23 0.46
14 25 0.50
15 2 0.04
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (14 bp):
CCTAAACCCTAAAT
Found at i:2244982 original size:7 final size:7
Alignment explanation
Indices: 2244970--2245055 Score: 84
Period size: 7 Copynumber: 12.3 Consensus size: 7
2244960 GTTAGAATAT
2244970 ACCCTAA
1 ACCCTAA
2244977 ACCCTAA
1 ACCCTAA
2244984 ACCCTAA
1 ACCCTAA
*
2244991 A-TCTCAA
1 ACCCT-AA
* *
2244998 ACCTTGA
1 ACCCTAA
2245005 ACCCTAA
1 ACCCTAA
*
2245012 ACCATAA
1 ACCCTAA
*
2245019 ACCATAA
1 ACCCTAA
2245026 ACCCTAA
1 ACCCTAA
*
2245033 GCCCTAA
1 ACCCTAA
*
2245040 ACCATAA
1 ACCCTAA
*
2245047 ACCATAA
1 ACCCTAA
2245054 AC
1 AC
2245056 ATTTAATCTA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
6 2 0.03
7 63 0.95
8 1 0.02
ACGTcount: A:0.45, C:0.36, G:0.02, T:0.16
Consensus pattern (7 bp):
ACCCTAA
Found at i:2245019 original size:28 final size:27
Alignment explanation
Indices: 2244970--2245055 Score: 102
Period size: 28 Copynumber: 3.1 Consensus size: 27
2244960 GTTAGAATAT
* *
2244970 ACCCTAAACCCTAAACCCTAAATC-TCAA
1 ACCCT-AACCCTAAACCATAAACCAT-AA
*
2244998 ACCTTGAACCCTAAACCATAAACCATAA
1 ACCCT-AACCCTAAACCATAAACCATAA
2245026 ACCCTAAGCCCTAAACCATAAACCATAA
1 ACCCTAA-CCCTAAACCATAAACCATAA
2245054 AC
1 AC
2245056 ATTTAATCTA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
27 2 0.04
28 48 0.94
29 1 0.02
ACGTcount: A:0.45, C:0.36, G:0.02, T:0.16
Consensus pattern (27 bp):
ACCCTAACCCTAAACCATAAACCATAA
Found at i:2246506 original size:11 final size:11
Alignment explanation
Indices: 2246490--2246516 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2246480 TTAACCTTTG
2246490 GAGTTTGAATC
1 GAGTTTGAATC
2246501 GAGTTTGAATC
1 GAGTTTGAATC
2246512 GAGTT
1 GAGTT
2246517 CGAGTCTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (11 bp):
GAGTTTGAATC
Found at i:2255939 original size:24 final size:24
Alignment explanation
Indices: 2255907--2255995 Score: 133
Period size: 24 Copynumber: 3.7 Consensus size: 24
2255897 TATGCTCATG
2255907 GTATCGATACTACTTTGTAAAGTA
1 GTATCGATACTACTTTGTAAAGTA
*
2255931 GTATCGATATTACTTTGTAAAGTA
1 GTATCGATACTACTTTGTAAAGTA
* *
2255955 GTATCGATATTATTTTGTAAAGTA
1 GTATCGATACTACTTTGTAAAGTA
* *
2255979 GTATTGATACTCCTTTG
1 GTATCGATACTACTTTG
2255996 AGTATCGATA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (24 bp):
GTATCGATACTACTTTGTAAAGTA
Found at i:2258905 original size:21 final size:21
Alignment explanation
Indices: 2258879--2258921 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2258869 TTTTCGGGCT
* *
2258879 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
2258900 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
2258921 A
1 A
2258922 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:2258979 original size:66 final size:68
Alignment explanation
Indices: 2258901--2259051 Score: 207
Period size: 67 Copynumber: 2.2 Consensus size: 68
2258891 ACCCATTCAA
* *
2258901 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATTGATACCCCCA
1 GGGGAACCGATACCCCTTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
2258965 -GG
66 GGG
* * * * * *
2258967 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCATAATGCTTGGGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCTTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
2259032 GGG
66 GGG
*
2259035 GGGGAACCGATTCCCCT
1 GGGGAACCGATACCCCT
2259052 ATGAGAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
66 26 0.36
67 30 0.41
68 17 0.23
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.20
Consensus pattern (68 bp):
GGGGAACCGATACCCCTTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:2259391 original size:29 final size:29
Alignment explanation
Indices: 2259357--2259428 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
2259347 CATATTATGA
**
2259357 TACATGACATGAATTTGTATTAAATATAT
1 TACATGACATGAATTCATATTAAATATAT
* *
2259386 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATATAT
2259415 TACATGACATGAAT
1 TACATGACATGAAT
2259429 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATATAT
Found at i:2259752 original size:13 final size:13
Alignment explanation
Indices: 2259734--2259796 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
2259724 TTATATGGCA
2259734 CTACGGTGCAATT
1 CTACGGTGCAATT
2259747 CTACGG-GC-A--
1 CTACGGTGCAATT
*
2259756 CTTCGGTGCAATT
1 CTACGGTGCAATT
2259769 CTACGG-GC-A--
1 CTACGGTGCAATT
*
2259778 CTTCGGTGCAATT
1 CTACGGTGCAATT
2259791 CTACGG
1 CTACGG
2259797 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:2259762 original size:22 final size:22
Alignment explanation
Indices: 2259730--2259810 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
2259720 ATCATTATAT
*
2259730 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
2259752 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
2259774 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
2259797 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
2259811 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:2265883 original size:21 final size:21
Alignment explanation
Indices: 2265857--2265899 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2265847 TTTTCGGGCT
* *
2265857 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
2265878 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
2265899 A
1 A
2265900 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:2265951 original size:65 final size:68
Alignment explanation
Indices: 2265879--2266028 Score: 216
Period size: 65 Copynumber: 2.2 Consensus size: 68
2265869 ACCCATTCAA
* *
2265879 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGC-TAGAGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTTAGAGGGAATCGATACCCCCA
2265942 -GG
66 GGG
* * * *
2265944 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGGGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTTAGAGGGAATCGATACCCCCA
2266009 GGG
66 GGG
*
2266012 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
2266029 ATAAGAAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
65 26 0.35
66 12 0.16
67 19 0.25
68 18 0.24
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTTAGAGGGAATCGATACCCCCA
GGG
Found at i:2266015 original size:21 final size:21
Alignment explanation
Indices: 2265989--2266029 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2265979 CAGAATGCTT
*
2265989 GGGGGGAATCGATACCCCCAG
1 GGGGGGAACCGATACCCCCAG
*
2266010 GGGGGGAACCGATTCCCCCA
1 GGGGGGAACCGATACCCCCA
2266030 TAAGAAAAAA
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:0.22, C:0.32, G:0.37, T:0.10
Consensus pattern (21 bp):
GGGGGGAACCGATACCCCCAG
Found at i:2266368 original size:29 final size:29
Alignment explanation
Indices: 2266334--2266405 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
2266324 CATATTATGA
* **
2266334 TACATGACATTAATTTGTATTAAATATAT
1 TACATGACATGAATTCATATTAAATATAT
* *
2266363 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATATAT
2266392 TACATGACATGAAT
1 TACATGACATGAAT
2266406 ATGCAGAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATATAT
Found at i:2266729 original size:13 final size:13
Alignment explanation
Indices: 2266711--2266773 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
2266701 TTATATGGCA
2266711 CTACGGTGCAATT
1 CTACGGTGCAATT
2266724 CTACGG-GC-A--
1 CTACGGTGCAATT
*
2266733 CTTCGGTGCAATT
1 CTACGGTGCAATT
2266746 CTACGG-GC-A--
1 CTACGGTGCAATT
*
2266755 CTTCGGTGCAATT
1 CTACGGTGCAATT
2266768 CTACGG
1 CTACGG
2266774 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:2266739 original size:22 final size:22
Alignment explanation
Indices: 2266707--2266787 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
2266697 ATCATTATAT
*
2266707 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
2266729 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
2266751 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
2266774 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
2266788 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:2271162 original size:16 final size:16
Alignment explanation
Indices: 2271136--2271169 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
2271126 GCTTTACTTT
2271136 TTTTCTGTTTGATTTTA
1 TTTTCTGTTTG-TTTTA
2271153 TTTT-TGTTTGTTTTA
1 TTTTCTGTTTGTTTTA
2271168 TT
1 TT
2271170 AGTAATGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 6 0.35
17 4 0.24
ACGTcount: A:0.09, C:0.03, G:0.12, T:0.76
Consensus pattern (16 bp):
TTTTCTGTTTGTTTTA
Found at i:2276228 original size:60 final size:61
Alignment explanation
Indices: 2276141--2276265 Score: 164
Period size: 60 Copynumber: 2.1 Consensus size: 61
2276131 TTGAATTTGG
* * * *
2276141 TCCCTAAACTATGATTATCATTTTAAATTAGTCTATAAAC-TTTTGAACATTTCAATTTTA
1 TCCCCAAACTATGACTATCATTCTAAATTAGTCTACAAACTTTTTGAACATTTCAATTTTA
* * *
2276201 TCCCCAAACTATGACCT-TCATTCTAAATTGGTTTCCAAACTTTTTGAACATTTCAATTTTA
1 TCCCCAAACTATGA-CTATCATTCTAAATTAGTCTACAAACTTTTTGAACATTTCAATTTTA
2276262 TCCC
1 TCCC
2276266 AAATTATACA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
60 31 0.55
61 25 0.45
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (61 bp):
TCCCCAAACTATGACTATCATTCTAAATTAGTCTACAAACTTTTTGAACATTTCAATTTTA
Found at i:2276490 original size:28 final size:29
Alignment explanation
Indices: 2276454--2276557 Score: 84
Period size: 31 Copynumber: 3.6 Consensus size: 29
2276444 AGGGTCATAA
*
2276454 TTTATGGATGAAATTAGAAT-GTTCAAAG
1 TTTAAGGATGAAATTAGAATAGTTCAAAG
* * * *
2276482 TTTAAGGATTAATTTAGAATGAGAGTCATAG
1 TTTAAGGATGAAATTAGAAT-AG-TTCAAAG
* * * *
2276513 TTTGAGGATGAAATTATAATATTTAAAAG
1 TTTAAGGATGAAATTAGAATAGTTCAAAG
* *
2276542 TTTAAAGATCAAATTA
1 TTTAAGGATGAAATTA
2276558 AGATGAAGGT
Statistics
Matches: 57, Mismatches: 16, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
28 17 0.30
29 17 0.30
30 2 0.04
31 21 0.37
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (29 bp):
TTTAAGGATGAAATTAGAATAGTTCAAAG
Found at i:2276500 original size:59 final size:60
Alignment explanation
Indices: 2276398--2276546 Score: 149
Period size: 59 Copynumber: 2.5 Consensus size: 60
2276388 ATGAATTAGG
* * * ** * *
2276398 GGATGAAATTGGAATATTTAAAAATTTTGGAGACTAATTTAGAAAAAGGGTCATAATTT-A
1 GGATGAAATTAGAATAGTTAAAAGTTTAAG-GATTAATTTAGAAAAAGAGTCATAATTTGA
* ** *
2276458 TGGATGAAATTAGAAT-GTTCAAAGTTTAAGGATTAATTTAGAATGAGAGTCATAGTTTGA
1 -GGATGAAATTAGAATAGTTAAAAGTTTAAGGATTAATTTAGAAAAAGAGTCATAATTTGA
* *
2276518 GGATGAAATTATAATATTTAAAAGTTTAA
1 GGATGAAATTAGAATAGTTAAAAGTTTAA
2276547 AGATCAAATT
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
59 37 0.51
60 21 0.29
61 14 0.19
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (60 bp):
GGATGAAATTAGAATAGTTAAAAGTTTAAGGATTAATTTAGAAAAAGAGTCATAATTTGA
Found at i:2292781 original size:20 final size:20
Alignment explanation
Indices: 2292756--2292795 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2292746 TGATGATGTC
*
2292756 TAAAATATAATTTAT-TAATA
1 TAAAAT-TAAATTATATAATA
2292776 TAAAATTAAATTATATAATA
1 TAAAATTAAATTATATAATA
2292796 AAGAATAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAATTAAATTATATAATA
Found at i:2294142 original size:26 final size:27
Alignment explanation
Indices: 2294087--2294149 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 27
2294077 AATAACGACC
* * *
2294087 AAAATTATATATAAATTATATAAAGTT
1 AAAATTATATATAAAATATACAAAGCT
2294114 AAAATGTATATATAAAAT-TACAAA-CT
1 AAAAT-TATATATAAAATATACAAAGCT
2294140 -AAATTA-ATAT
1 AAAATTATATAT
2294150 TGATGAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 4 0.12
24 2 0.06
25 4 0.12
26 1 0.03
27 10 0.31
28 11 0.34
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (27 bp):
AAAATTATATATAAAATATACAAAGCT
Found at i:2295196 original size:20 final size:21
Alignment explanation
Indices: 2295171--2295222 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2295161 TTTTCCCAAT
*
2295171 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2295191 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2295212 TCGCAATGCGA
1 TCGCAATGCGA
2295223 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2295235 original size:41 final size:41
Alignment explanation
Indices: 2295208--2295285 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
2295198 GCGAATTGGG
* * *
2295208 AAAATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
*
2295249 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATA
2295286 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
Found at i:2295236 original size:20 final size:20
Alignment explanation
Indices: 2295211--2295304 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
2295201 AATTGGGAAA
*
2295211 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
2295231 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
2295252 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
2295272 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
2295292 TTCGCAACGCGAT
1 ATCGCAACGCGAT
2295305 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:2297056 original size:18 final size:18
Alignment explanation
Indices: 2297035--2297079 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2297025 TCCACTTCGG
* *
2297035 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
2297053 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
2297071 GAGCCATCA
1 GAGCCATCA
2297080 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:2297622 original size:14 final size:14
Alignment explanation
Indices: 2297603--2297660 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2297593 ATGCGAAATG
2297603 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2297617 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2297633 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2297649 AAAATCGCAACG
1 AAAATCGCAACG
2297661 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2297645 original size:32 final size:33
Alignment explanation
Indices: 2297587--2297677 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
2297577 GGAAATGGCT
*
2297587 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2297620 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2297652 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
2297678 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2297671 original size:19 final size:19
Alignment explanation
Indices: 2297549--2297682 Score: 92
Period size: 19 Copynumber: 7.6 Consensus size: 19
2297539 TAGTTTACTT
* **
2297549 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
2297568 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
2297588 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2297607 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2297621 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
2297639 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2297653 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2297672 TCGCAATGCGA
1 TCGCAACGCGA
2297683 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 35 0.38
20 17 0.18
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2297713 original size:14 final size:14
Alignment explanation
Indices: 2297694--2297751 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2297684 TTGTGTTTCG
2297694 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2297708 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2297724 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2297740 CGTTGCGATTTT
1 CGTTGCGATTTT
2297752 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2297728 original size:32 final size:33
Alignment explanation
Indices: 2297689--2297767 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2297679 GCGATTTGTG
2297689 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
2297721 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
2297754 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
2297768 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2297766 original size:19 final size:19
Alignment explanation
Indices: 2297708--2297825 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
2297698 GCGATTTTGT
2297708 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2297726 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
2297740 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
2297759 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
2297779 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2297798 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
2297818 TGTTGCGA
1 CGTTGCGA
2297826 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2299831 original size:19 final size:19
Alignment explanation
Indices: 2299799--2299900 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
2299789 AAAACAGACT
* *
2299799 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAATGAAA
*
2299818 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2299837 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2299856 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2299875 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
2299889 ATCGCAATGCGA
1 ATCGCAATGCGA
2299901 TTTTCATTTC
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
14 11 0.14
15 1 0.01
16 2 0.03
17 2 0.03
19 60 0.79
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2301498 original size:19 final size:19
Alignment explanation
Indices: 2301476--2301534 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
2301466 CTTAATGTCC
2301476 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2301495 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2301509 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2301528 ATCGCAA
1 ATCGCAA
2301535 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2301697 original size:14 final size:15
Alignment explanation
Indices: 2301678--2301714 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
2301668 CATCAATTAA
2301678 ACAAATCAAC-TTTT
1 ACAAATCAACATTTT
2301692 ACAAATC-ACATTTT
1 ACAAATCAACATTTT
2301706 ACAAATCAA
1 ACAAATCAA
2301715 TTAAACAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (15 bp):
ACAAATCAACATTTT
Found at i:2303137 original size:21 final size:21
Alignment explanation
Indices: 2303071--2303137 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2303061 GTGAATCGGG
*
2303071 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2303091 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2303113 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2303134 CTCT
1 CTCT
2303138 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2303156 original size:42 final size:41
Alignment explanation
Indices: 2303071--2303193 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
2303061 GTGAATCGGG
* * * * *
2303071 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
2303113 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
2303155 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
2303194 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:2305238 original size:39 final size:37
Alignment explanation
Indices: 2305195--2305345 Score: 130
Period size: 39 Copynumber: 4.1 Consensus size: 37
2305185 TCTTTTGGTT
*
2305195 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACG-GA-AATGAAAATCGCAACGC
** * * *
2305234 GAAATGACTATCGCGAC---CA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGGAAATGAAAATCGCAACGC
*
2305267 GAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CG-GAAATGAAAATCGCAACGC
* * * *
2305306 GAAATGAAAATCACAACGCAAAATGAAAATCACAATGC
1 GAAATGAAAATCGCAACG-GAAATGAAAATCGCAACGC
2305344 GA
1 GA
2305346 TTTTGGTTTC
Statistics
Matches: 90, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
33 26 0.29
34 2 0.02
38 21 0.23
39 41 0.46
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (37 bp):
GAAATGAAAATCGCAACGGAAATGAAAATCGCAACGC
Found at i:2305340 original size:19 final size:19
Alignment explanation
Indices: 2305195--2305336 Score: 150
Period size: 19 Copynumber: 7.6 Consensus size: 19
2305185 TCTTTTGGTT
*
2305195 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
2305214 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
2305234 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
2305252 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2305267 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
2305287 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2305306 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
2305325 AAAATGAAAATC
1 GAAATGAAAATC
2305337 ACAATGCGAT
Statistics
Matches: 104, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
14 10 0.10
15 2 0.02
18 2 0.02
19 55 0.53
20 35 0.34
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2305368 original size:19 final size:19
Alignment explanation
Indices: 2305341--2305407 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
2305331 AAAATCACAA
*
2305341 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
2305360 TGCGGTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
2305379 TGCGATAGTT-ATTTCCGCGT
1 TGCGAT-TTTGATTT-CGCGT
2305399 TGCGATTTT
1 TGCGATTTT
2305408 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 27 0.68
20 13 0.32
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:2306019 original size:20 final size:20
Alignment explanation
Indices: 2305926--2306019 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
2305916 GATTATGTAA
* *
2305926 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
2305946 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* * *
2305966 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTAAGT
*
2305987 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
2306007 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
2306020 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:2306037 original size:21 final size:21
Alignment explanation
Indices: 2306008--2306100 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
2305998 ATAGTAAGTA
2306008 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
2306029 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
2306049 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
2306070 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
2306090 TCGCATTGCGA
1 TCGCATTGCGA
2306101 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:2306038 original size:41 final size:41
Alignment explanation
Indices: 2305947--2306081 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
2305937 AAAGTCAGTA
* * * ** *
2305947 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
2305987 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
2306029 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
2306070 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2306082 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:2306082 original size:41 final size:41
Alignment explanation
Indices: 2306008--2306100 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
2305998 ATAGTAAGTA
2306008 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
2306049 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
2306090 TCGCATTGCGA
1 TCGCATTGCGA
2306101 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2309936 original size:22 final size:22
Alignment explanation
Indices: 2309911--2309955 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2309901 TGTTGGTCCA
*
2309911 TGTCAATGAAAATACTTAAAAG
1 TGTCAATGAAAATAATTAAAAG
2309933 TGTCAATGAAAATAATTAAAAG
1 TGTCAATGAAAATAATTAAAAG
2309955 T
1 T
2309956 ATACGTCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (22 bp):
TGTCAATGAAAATAATTAAAAG
Found at i:2311943 original size:27 final size:27
Alignment explanation
Indices: 2311912--2311992 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
2311902 ATGGCATTAT
2311912 TTATCATCTAGACAGTAAAAGCATAGA
1 TTATCATCTAGACAGTAAAAGCATAGA
* *** *
2311939 TTATC--C-A-AC-CTTTTAGCATTA-T
1 TTATCATCTAGACAGTAAAAGCA-TAGA
2311961 TTATCATCTAGACAGTAAAAGCATAGA
1 TTATCATCTAGACAGTAAAAGCATAGA
2311988 TTATC
1 TTATC
2311993 CAACCTTTTA
Statistics
Matches: 37, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
22 10 0.27
23 4 0.11
24 2 0.05
25 2 0.05
26 4 0.11
27 15 0.41
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.33
Consensus pattern (27 bp):
TTATCATCTAGACAGTAAAAGCATAGA
Found at i:2311977 original size:49 final size:49
Alignment explanation
Indices: 2311905--2312004 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
2311895 GAAAACAATG
2311905 GCATTATTTATCATCTAGACAGTAAAAGCATAGATTATCCAACCTTTTA
1 GCATTATTTATCATCTAGACAGTAAAAGCATAGATTATCCAACCTTTTA
2311954 GCATTATTTATCATCTAGACAGTAAAAGCATAGATTATCCAACCTTTTA
1 GCATTATTTATCATCTAGACAGTAAAAGCATAGATTATCCAACCTTTTA
2312003 GC
1 GC
2312005 TTTTTGCTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (49 bp):
GCATTATTTATCATCTAGACAGTAAAAGCATAGATTATCCAACCTTTTA
Found at i:2316542 original size:30 final size:29
Alignment explanation
Indices: 2316450--2316566 Score: 92
Period size: 30 Copynumber: 3.9 Consensus size: 29
2316440 TCAAAGGACC
* *
2316450 AAAATAGTACAAATAGGAATTTAAAGGACT
1 AAAATAGTAAAAATAGAAATTTAAAGG-CT
* * * * * *
2316480 AATATGGTCAAAACATAAACTTAAATGGCT
1 AAAATAGTAAAAATAGAAATTTAAA-GGCT
* *
2316510 AAAATAGTAAAAATATAAATTTAAGGGTCT
1 AAAATAGTAAAAATAGAAATTTAAAGG-CT
*
2316540 AAAATA-AATAAAATAGAAATTTAAAGG
1 AAAATAGTA-AAAATAGAAATTTAAAGG
2316567 GCTCGAAGCA
Statistics
Matches: 67, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
29 3 0.04
30 62 0.93
31 2 0.03
ACGTcount: A:0.55, C:0.06, G:0.14, T:0.26
Consensus pattern (29 bp):
AAAATAGTAAAAATAGAAATTTAAAGGCT
Found at i:2318189 original size:3 final size:3
Alignment explanation
Indices: 2318181--2318209 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2318171 TAAATTTTAA
2318181 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2318210 ATTAAATAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2318483 original size:40 final size:40
Alignment explanation
Indices: 2318364--2318486 Score: 108
Period size: 40 Copynumber: 3.0 Consensus size: 40
2318354 AAGGTTTGTT
* *
2318364 GGGGACGACAC-TGCTCATACATGATGAAGAGTTCTGGTCGTTTA
1 GGGGATGACACGT-CTCATACGTGATGAAGAGTTCTGGTC----A
* * * **
2318408 AGGG-TGACACAGT-TCCTACGTGATGAGGAAATCTGGTCA
1 GGGGATGACAC-GTCTCATACGTGATGAAGAGTTCTGGTCA
2318447 GGGGATGACACGTCTCATACGTGATGAAGAGTTCTGGTCA
1 GGGGATGACACGTCTCATACGTGATGAAGAGTTCTGGTCA
2318487 TCTTTAGGAA
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
39 6 0.10
40 28 0.44
43 25 0.40
44 3 0.05
45 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (40 bp):
GGGGATGACACGTCTCATACGTGATGAAGAGTTCTGGTCA
Found at i:2318578 original size:43 final size:43
Alignment explanation
Indices: 2318512--2318712 Score: 126
Period size: 43 Copynumber: 4.5 Consensus size: 43
2318502 ATAACTCGGT
* * *
2318512 TCCTACGAGATGAGGACGGCTGGTTATCTAGGGG-TGACACGGC
1 TCCTACGTGATGAGGA-GTCTGGTTATCTAGGGGATGACACGAC
* *
2318555 TCCTACGCGATGAGGAGATCTGG---TC-GGGGGATGACACGAC
1 TCCTACGTGATGAGGAG-TCTGGTTATCTAGGGGATGACACGAC
* * ** * **
2318595 TCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGT
1 TCCTACGTGATGAGGAG-TCTGGTTATC--T----AGGG-GATGACACGAC
*
2318646 TCCTACATGATGAGGACGTCTGGTTATCTAGGGG-TGACACGAC
1 TCCTACGTGATGAGGA-GTCTGGTTATCTAGGGGATGACACGAC
*
2318689 TCCTACGTGATGAAGAGATCTGGT
1 TCCTACGTGATGAGGAG-TCTGGT
2318713 CAGGAGATGA
Statistics
Matches: 121, Mismatches: 22, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
39 4 0.03
40 29 0.24
42 2 0.02
43 47 0.39
44 1 0.01
45 4 0.03
49 1 0.01
50 3 0.02
51 29 0.24
52 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (43 bp):
TCCTACGTGATGAGGAGTCTGGTTATCTAGGGGATGACACGAC
Found at i:2318607 original size:40 final size:39
Alignment explanation
Indices: 2318542--2318617 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 39
2318532 TGGTTATCTA
* * *
2318542 GGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCG
1 GGGGTGACACGACTCATACGCGATGAAGAGATCTGGTCG
* *
2318581 GGGGATGACACGACTCATACGTGATGAAGAGTTCTGG
1 GGGG-TGACACGACTCATACGCGATGAAGAGATCTGG
2318618 CCATCTTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 4 0.13
40 27 0.87
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.20
Consensus pattern (39 bp):
GGGGTGACACGACTCATACGCGATGAAGAGATCTGGTCG
Found at i:2318626 original size:134 final size:134
Alignment explanation
Indices: 2318409--2318762 Score: 530
Period size: 134 Copynumber: 2.6 Consensus size: 134
2318399 GGTCGTTTAA
* * * *
2318409 GGGTGACACAGTTCCTACGTGATGAGGAAATCTGGTCAGGGGATGACACGTCTCATACGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCATACGTGATGA
* * *
2318474 AGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGA-GATGAGGACGGCTGGTTA
66 AGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTAC-ATGATGAGGACGGCTGGTTA
2318538 TCTAG
130 TCTAG
* *
2318543 GGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCATACGTGATGA
*
2318608 AGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACATGATGAGGACGTCTGGTTAT
66 AGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACATGATGAGGACGGCTGGTTAT
2318673 CTAG
131 CTAG
* * * * * * *
2318677 GGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCAGGAGATGACACAACTCACACATGACGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCATACGTGATGA
*
2318742 AGAGTTCTGACCATCTTTAGG
66 AGAGTTCTGGCCATCTTTAGG
2318763 GATAATGATT
Statistics
Matches: 199, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
133 1 0.01
134 198 0.99
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (134 bp):
GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCATACGTGATGA
AGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACATGATGAGGACGGCTGGTTAT
CTAG
Found at i:2319083 original size:30 final size:29
Alignment explanation
Indices: 2319049--2319237 Score: 101
Period size: 29 Copynumber: 6.4 Consensus size: 29
2319039 ACAAAACTTT
2319049 GTTTCAAAAGAAATAAACTCAAAGATTTTG
1 GTTTCAAAAGAAAT-AACTCAAAGATTTTG
*
2319079 GTTTCAAAAGAAATGACTCAAAGA-TTT-
1 GTTTCAAAAGAAATAACTCAAAGATTTTG
* *
2319106 -TTTCACGAAATTGTCTTAAGAGAA-T-AAA-ACTTTG
1 GTTTCA--AAA--G----AA-ATAACTCAAAGATTTTG
* *
2319140 G-TTCAAAAGAAACAGACTCAAAGAATTT-
1 GTTTCAAAAGAAATA-ACTCAAAGATTTTG
* *
2319168 -TTTCAAAAGAAACAACTCAAAGATTTTT
1 GTTTCAAAAGAAATAACTCAAAGATTTTG
* * *
2319196 ATTTCAAAAGAAACAACTCACAGACTTTT-
1 GTTTCAAAAGAAATAACTCAAAGA-TTTTG
*
2319225 GTTTCAAGAGAAA
1 GTTTCAAAAGAAA
2319238 CAAACTTAAA
Statistics
Matches: 130, Mismatches: 9, Indels: 41
0.72 0.05 0.23
Matches are distributed among these distances:
25 2 0.02
26 8 0.06
27 13 0.10
28 22 0.17
29 46 0.35
30 20 0.15
32 4 0.03
33 6 0.05
34 7 0.05
35 2 0.02
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (29 bp):
GTTTCAAAAGAAATAACTCAAAGATTTTG
Found at i:2319098 original size:29 final size:30
Alignment explanation
Indices: 2319049--2319106 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
2319039 ACAAAACTTT
2319049 GTTTCAAAAGAAATAAACTCAAAGATTTTG
1 GTTTCAAAAGAAATAAACTCAAAGATTTTG
*
2319079 GTTTCAAAAGAAAT-GACTCAAAGATTTT
1 GTTTCAAAAGAAATAAACTCAAAGATTTT
2319107 TTCACGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (30 bp):
GTTTCAAAAGAAATAAACTCAAAGATTTTG
Found at i:2319159 original size:90 final size:90
Alignment explanation
Indices: 2318976--2319195 Score: 261
Period size: 90 Copynumber: 2.4 Consensus size: 90
2318966 AGGCACAATT
2318976 TCAAAG-A-TTTTTCAAAAGGAACAGACTCAAAGATTTTTCTCAAGAAAAACTGTCTCAAGAGAG
1 TCAAAGAATTTTTTCAAAA-GAA-AGACTCAAAGATTTTTCTCAAG-AAAACTGTCTCAAGAGAG
* *
2319039 ACAAAACTTTGTTTCAAAAGAAATAAAC
63 ACAAAACTTTGGTTCAAAAGAAACAAAC
* * * *
2319067 TCAAAGATTTTGGTTTCAAAAGAAATGACTCAAAGATTTTT-TCACG-AAATTGTCTTAAGAGA-
1 TCAAAGAATTT--TTTCAAAAGAAA-GACTCAAAGATTTTTCTCAAGAAAACTGTCTCAAGAGAG
* *
2319129 ATAAAACTTTGGTTCAAAAGAAACAGAC
63 ACAAAACTTTGGTTCAAAAGAAACAAAC
*
2319157 TCAAAGAATTTTTTCAAAAGAAACAACTCAAAGATTTTT
1 TCAAAGAATTTTTTCAAAAGAAA-GACTCAAAGATTTTT
2319196 ATTTCAAAAG
Statistics
Matches: 113, Mismatches: 11, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
88 26 0.23
90 34 0.30
91 20 0.18
93 7 0.06
94 18 0.16
95 8 0.07
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.29
Consensus pattern (90 bp):
TCAAAGAATTTTTTCAAAAGAAAGACTCAAAGATTTTTCTCAAGAAAACTGTCTCAAGAGAGACA
AAACTTTGGTTCAAAAGAAACAAAC
Found at i:2319209 original size:29 final size:28
Alignment explanation
Indices: 2319141--2319250 Score: 132
Period size: 29 Copynumber: 3.8 Consensus size: 28
2319131 AAAACTTTGG
*
2319141 TTCAAAAGAAACAGACTCAAAGA-ATTTT
1 TTCAAAAGAAACA-ACTCAAAGATTTTTT
2319169 TTCAAAAGAAACAACTCAAAGATTTTTAT
1 TTCAAAAGAAACAACTCAAAGATTTTT-T
* *
2319198 TTCAAAAGAAACAACTCACAGACTTTTGT
1 TTCAAAAGAAACAACTCAAAGA-TTTTTT
* *
2319227 TTCAAGAGAAACAAACTTAAAGAT
1 TTCAAAAGAAAC-AACTCAAAGAT
2319251 ACGTTTTGTT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
27 9 0.12
28 16 0.22
29 35 0.49
30 12 0.17
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.26
Consensus pattern (28 bp):
TTCAAAAGAAACAACTCAAAGATTTTTT
Found at i:2319444 original size:64 final size:65
Alignment explanation
Indices: 2319296--2319478 Score: 210
Period size: 64 Copynumber: 2.8 Consensus size: 65
2319286 TTGTTTTAAG
* * * * * *
2319296 AGAAATTGTCTTAAAAGAGACAAACCTTTTTTTTTCATAA-AAACATACTTAAAGATTTTTCTTC
1 AGAAACTGTCTCAAAAGAGACAAA--ATTTTGTTTCA-AAGAAACATACTCAAAGATTTCTCTTC
2319360 AAA
63 AAA
*
2319363 AGGAACTGTCTCAAAAGAGACAAAATTTTGTTTCCAAAGAAACATACTCAAAGA-TTCT-TTCAA
1 AGAAACTGTCTCAAAAGAGACAAAATTTTGTTT-CAAAGAAACATACTCAAAGATTTCTCTTCAA
2319426 A
65 A
* * *
2319427 AGAAACTTTTTCAAAAGAGACAAAATTTTGTTATCAAAGAAATATACTCAAA
1 AGAAACTGTCTCAAAAGAGACAAAATTTTGTT-TCAAAGAAACATACTCAAA
2319479 AAAAATTTCA
Statistics
Matches: 102, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
64 52 0.51
65 13 0.13
66 16 0.16
67 21 0.21
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (65 bp):
AGAAACTGTCTCAAAAGAGACAAAATTTTGTTTCAAAGAAACATACTCAAAGATTTCTCTTCAAA
Found at i:2319876 original size:107 final size:105
Alignment explanation
Indices: 2319721--2320034 Score: 409
Period size: 107 Copynumber: 3.0 Consensus size: 105
2319711 TGTTTTTGAG
*
2319721 AAAACGATCTCAAGTGAGATTAACTTTGTTTAATGTGAAAACAAATTCAAATTTTGTATCTCAAA
1 AAAACAATCTCAAGTGAGATTAACTTTGTTTAATGTG-AAACAAATTCAAATTTTGTATCTCAAA
* *
2319786 GGAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAAAAA
65 GGAAAAATGTCTCAAGCGAGATGAAATTTGTTTTGAAAAAA
* * * *
2319827 AATAACAATCTCAAGTGAGATTAATATTTGTTTCAA-GTGAATCAAATTCAAAATTTGTATATCA
1 AA-AACAATCTCAAGTGAGATTAA-CTTTGTTT-AATGTGAAACAAATTCAAATTTTGTATCTCA
* * * * *
2319891 AAGGAAAAAATGTATCAAGCAAGATGAAGTTTGTTTT--AAGAG
63 AAGG-AAAAATGTCTCAAGCGAGATGAAATTTGTTTTGAAAAAA
* * * *
2319933 AAAGCGATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCAAATTTTGTATCTCAAAG
1 AAAACAATCTCAAGTGAGATTAACTTTGTTTAATGTGAAACAAATTCAAATTTTGTATCTCAAAG
*
2319998 GAAAAATGTCTCAAGTGAGATGAAATTTGTTTTGAAA
66 GAAAAATGTCTCAAGCGAGATGAAATTTGTTTTGAAA
2320035 GAAATTGTCT
Statistics
Matches: 177, Mismatches: 24, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
103 30 0.17
104 36 0.20
105 19 0.11
106 7 0.04
107 46 0.26
108 37 0.21
109 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (105 bp):
AAAACAATCTCAAGTGAGATTAACTTTGTTTAATGTGAAACAAATTCAAATTTTGTATCTCAAAG
GAAAAATGTCTCAAGCGAGATGAAATTTGTTTTGAAAAAA
Found at i:2320450 original size:16 final size:16
Alignment explanation
Indices: 2320429--2320468 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2320419 TGTAATATGT
**
2320429 ATGTATGTATGTGTTG
1 ATGTATGTATGCATTG
*
2320445 ATGTATGCATGCATTG
1 ATGTATGTATGCATTG
2320461 ATGTATGT
1 ATGTATGT
2320469 TTTCTCAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.45
Consensus pattern (16 bp):
ATGTATGTATGCATTG
Found at i:2325230 original size:16 final size:16
Alignment explanation
Indices: 2325209--2325263 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2325199 AACGTCTTTT
2325209 AAAAACAATTTTAAGA
1 AAAAACAATTTTAAGA
*
2325225 AAAAACATTTTTTAAG-
1 AAAAACA-ATTTTAAGA
* *
2325241 ACAATC-ATCTTTAAGA
1 AAAAACAAT-TTTAAGA
2325257 AAAAACA
1 AAAAACA
2325264 TTCGCACAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
14 1 0.03
15 6 0.21
16 15 0.52
17 7 0.24
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.27
Consensus pattern (16 bp):
AAAAACAATTTTAAGA
Found at i:2325237 original size:17 final size:17
Alignment explanation
Indices: 2325217--2325265 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
2325207 TTAAAAACAA
2325217 TTTTAAGAAAAAACATT
1 TTTTAAGAAAAAACATT
* *
2325234 TTTTAAG-ACAATCA-T
1 TTTTAAGAAAAAACATT
*
2325249 CTTTAAGAAAAAACATT
1 TTTTAAGAAAAAACATT
2325266 CGCACAGTAC
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
15 7 0.28
16 10 0.40
17 8 0.32
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (17 bp):
TTTTAAGAAAAAACATT
Found at i:2327802 original size:3 final size:3
Alignment explanation
Indices: 2327794--2327825 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2327784 TAAATTTCAA
2327794 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2327826 ATTAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2329737 original size:18 final size:18
Alignment explanation
Indices: 2329704--2329738 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2329694 AGAAACCTCA
*
2329704 TCAGAATCCTCCTCATCC
1 TCAGAATCCTCATCATCC
*
2329722 TCAGAATCTTCATCATC
1 TCAGAATCCTCATCATC
2329739 ATCCTCGGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.37, G:0.06, T:0.31
Consensus pattern (18 bp):
TCAGAATCCTCATCATCC
Found at i:2338275 original size:65 final size:61
Alignment explanation
Indices: 2338199--2338441 Score: 337
Period size: 65 Copynumber: 3.8 Consensus size: 61
2338189 CTTAAAAAAA
*
2338199 TCTTCTTCTTTTATGAAATGGTAGATTCATAATCTTACCTC-ATATATATTTAAAAAAAATCTTC
1 TCTTCTTCTTTTATGAAATGGTAGATTCATAATCTTACCTCTATATATACTT--AAAAAA---TC
2338263 T
61 T
* *
2338264 TCTTCTTCTTTTATAAAATGGTATATTCATAATCTTACCTCTATATATACTT-AAAAATCT
1 TCTTCTTCTTTTATGAAATGGTAGATTCATAATCTTACCTCTATATATACTTAAAAAATCT
2338324 TCTTCTTCTTTTATGAAATGGTAGATTCATAATCCATAATCTTACCTCTATATATACTTAAAAAA
1 TCTTCTTCTTTTATGAAATGGTAG----AT--T-CATAATCTTACCTCTATATATACTTAAAAAA
2338389 TCT
59 TCT
2338392 TCTTCTTCTTTTATGAAATGGTAGATTCATAATCTTACCTCTATATATAC
1 TCTTCTTCTTTTATGAAATGGTAGATTCATAATCTTACCTCTATATATAC
2338442 CTGCAAAGCC
Statistics
Matches: 164, Mismatches: 5, Indels: 22
0.86 0.03 0.12
Matches are distributed among these distances:
60 25 0.15
61 23 0.14
62 1 0.01
63 5 0.03
64 4 0.02
65 39 0.24
66 10 0.06
67 25 0.15
68 32 0.20
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.45
Consensus pattern (61 bp):
TCTTCTTCTTTTATGAAATGGTAGATTCATAATCTTACCTCTATATATACTTAAAAAATCT
Found at i:2338378 original size:67 final size:68
Alignment explanation
Indices: 2338291--2338425 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
2338281 ATGGTATATT
2338291 CATAATCTTACCTCTATATATACTT-AAAAATCTTCTTCTTCTTTTATGAAATGGTAGATTCATA
1 CATAATCTTACCTCTATATATACTTAAAAAATCTTCTTCTTCTTTTATGAAATGGTAGATTCATA
2338355 ATC
66 ATC
2338358 CATAATCTTACCTCTATATATACTTAAAAAATCTTCTTCTTCTTTTATGAAATGGTAGATTCATA
1 CATAATCTTACCTCTATATATACTTAAAAAATCTTCTTCTTCTTTTATGAAATGGTAGATTCATA
2338423 ATC
66 ATC
2338426 TTACCTCTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 25 0.37
68 42 0.63
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (68 bp):
CATAATCTTACCTCTATATATACTTAAAAAATCTTCTTCTTCTTTTATGAAATGGTAGATTCATA
ATC
Found at i:2338427 original size:128 final size:122
Alignment explanation
Indices: 2338199--2338441 Score: 346
Period size: 128 Copynumber: 1.9 Consensus size: 122
2338189 CTTAAAAAAA
*
2338199 TCTTCTTCTTTTATGAAATGGTAGATTCATAATCTTACCTCATATATATTTAAAAAAAATCTTCT
1 TCTTCTTCTTTTATGAAATGGTAGATTCATAATCTTACCTCATATATACTT-AAAAAAA--TTCT
*
2338264 TCTTCTTCTTTTATAAAATGGTATATTCATAATCTTACCTCTATATATACTTAAAAATCT
63 TCTTCTTCTTTTATAAAATGGTAGATTCATAATCTTACCTCTATATATACTTAAAAATCT
2338324 TCTTCTTCTTTTATGAAATGGTAGATTCATAATCCATAATCTTACCTCTATATATACTT-AAAAA
1 TCTTCTTCTTTTATGAAATGGTAG----AT--T-CATAATCTTACCTC-ATATATACTTAAAAAA
*
2338388 A-TCTTCTTCTTCTTTTATGAAATGGTAGATTCATAATCTTACCTCTATATATAC
58 ATTCTTCTTCTTCTTTTATAAAATGGTAGATTCATAATCTTACCTCTATATATAC
2338442 CTGCAAAGCC
Statistics
Matches: 107, Mismatches: 3, Indels: 13
0.87 0.02 0.11
Matches are distributed among these distances:
125 24 0.22
128 51 0.48
129 2 0.02
131 7 0.07
132 14 0.13
133 9 0.08
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.45
Consensus pattern (122 bp):
TCTTCTTCTTTTATGAAATGGTAGATTCATAATCTTACCTCATATATACTTAAAAAAATTCTTCT
TCTTCTTTTATAAAATGGTAGATTCATAATCTTACCTCTATATATACTTAAAAATCT
Found at i:2342689 original size:9 final size:9
Alignment explanation
Indices: 2342658--2342697 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
2342648 CTAGTTTTTG
*
2342658 TTTTATAAT
1 TTTTAAAAT
*
2342667 TTTTAAAAG
1 TTTTAAAAT
*
2342676 ATTTAAAAT
1 TTTTAAAAT
2342685 TTTTAAAAT
1 TTTTAAAAT
2342694 TTTT
1 TTTT
2342698 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:2344356 original size:28 final size:29
Alignment explanation
Indices: 2344325--2344395 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
2344315 AGCACATTAA
2344325 TGTAATTTGTAAAAAG-ATGA-GTCTTTAT
1 TGTAATTTGTAAAAAGTAT-ATGTCTTTAT
* * *
2344353 TGTAATATT-TAAAATGTATATGTTTTTCT
1 TGTAAT-TTGTAAAAAGTATATGTCTTTAT
2344382 TGTAATTTGTAAAA
1 TGTAATTTGTAAAA
2344396 TATTTGGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
28 15 0.42
29 21 0.58
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (29 bp):
TGTAATTTGTAAAAAGTATATGTCTTTAT
Found at i:2344447 original size:58 final size:58
Alignment explanation
Indices: 2344381--2344619 Score: 211
Period size: 58 Copynumber: 4.1 Consensus size: 58
2344371 TATGTTTTTC
* *
2344381 TTGTAATTTGTAAAA-TATTTGGG-ATATTAATT-TAAATTATAAAAGTTTTGAGCCATTA
1 TTGTAATTTGTAAAAGT-TTTGGGTA-ATT-ATTGTAATTTATAAAAGTTTTGGGCCATTA
** * * * *
2344439 TTGTAATTT-TCAAAAGTTTTATGTCATTGTTGTAATTTAGAAAACTTTTGGGCCATTA
1 TTGTAATTTGT-AAAAGTTTTGGGTAATTATTGTAATTTATAAAAGTTTTGGGCCATTA
* * * *
2344497 TTTTATTTTGTAAAAGTCTTT-GGCAATTATTGTAATTTATAAAAGTTTTGGGCAATTA
1 TTGTAATTTGTAAAAGT-TTTGGGTAATTATTGTAATTTATAAAAGTTTTGGGCCATTA
* * * * * ** *
2344555 TTGTAATTTAT-AAATTTTTGGGTAATTACTATAATTTATAAAAGTTATGGGTAACTA
1 TTGTAATTTGTAAAAGTTTTGGGTAATTATTGTAATTTATAAAAGTTTTGGGCCATTA
2344612 TTGTAATT
1 TTGTAATT
2344620 CATATAAATC
Statistics
Matches: 147, Mismatches: 27, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
56 3 0.02
57 46 0.31
58 93 0.63
59 5 0.03
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (58 bp):
TTGTAATTTGTAAAAGTTTTGGGTAATTATTGTAATTTATAAAAGTTTTGGGCCATTA
Found at i:2344462 original size:87 final size:86
Alignment explanation
Indices: 2344349--2344545 Score: 204
Period size: 87 Copynumber: 2.3 Consensus size: 86
2344339 AGATGAGTCT
* ** *
2344349 TTATTGTAATATTTAAAA-TGTATATGTTTTTCTTGTAATTT-GTAAAA-TATTTGGGATATTAA
1 TTATTGTAAT-TTTAAAAGT-TTTATGTCATTCTTGTAATTTAG-AAAACT-TTTGGGACATTAA
*
2344411 TTTAAATTATAAAAGT-TTTGAGCCA
62 TTTAAATTATAAAAGTCTTTG-GCAA
* * *
2344436 TTATTGTAATTTTCAAAAGTTTTATGTCATTGTTGTAATTTAGAAAACTTTTGGGCCATTATTTT
1 TTATTGTAATTTT-AAAAGTTTTATGTCATTCTTGTAATTTAGAAAACTTTTGGGACATTAATTT
** *
2344501 ATTTTGTAAAAGTCTTTGGCAA
65 AAATTATAAAAGTCTTTGGCAA
2344523 TTATTGTAATTTATAAAAGTTTT
1 TTATTGTAATTT-TAAAAGTTTT
2344546 GGGCAATTAT
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
86 3 0.03
87 82 0.88
88 8 0.09
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.49
Consensus pattern (86 bp):
TTATTGTAATTTTAAAAGTTTTATGTCATTCTTGTAATTTAGAAAACTTTTGGGACATTAATTTA
AATTATAAAAGTCTTTGGCAA
Found at i:2344618 original size:29 final size:29
Alignment explanation
Indices: 2344381--2344619 Score: 184
Period size: 29 Copynumber: 8.3 Consensus size: 29
2344371 TATGTTTTTC
*
2344381 TTGTAATTTGTAAAA-TATTTGGG-ATATTAA
1 TTGTAATTTATAAAAGT-TTTGGGTA-ATT-A
* * **
2344411 TT-TAAATTATAAAAGTTTTGAGCCATTA
1 TTGTAATTTATAAAAGTTTTGGGTAATTA
** * *
2344439 TTGTAATTT-TCAAAAGTTTTATGTCATTG
1 TTGTAATTTAT-AAAAGTTTTGGGTAATTA
* * **
2344468 TTGTAATTTAGAAAACTTTTGGGCCATTA
1 TTGTAATTTATAAAAGTTTTGGGTAATTA
* * * *
2344497 TTTTATTTTGTAAAAGTCTTT-GGCAATTA
1 TTGTAATTTATAAAAGT-TTTGGGTAATTA
*
2344526 TTGTAATTTATAAAAGTTTTGGGCAATTA
1 TTGTAATTTATAAAAGTTTTGGGTAATTA
*
2344555 TTGTAATTTAT-AAATTTTTGGGTAATTA
1 TTGTAATTTATAAAAGTTTTGGGTAATTA
* * * *
2344583 CTATAATTTATAAAAGTTATGGGTAACTA
1 TTGTAATTTATAAAAGTTTTGGGTAATTA
2344612 TTGTAATT
1 TTGTAATT
2344620 CATATAAATC
Statistics
Matches: 168, Mismatches: 33, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
28 31 0.18
29 131 0.78
30 6 0.04
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (29 bp):
TTGTAATTTATAAAAGTTTTGGGTAATTA
Found at i:2345713 original size:30 final size:30
Alignment explanation
Indices: 2345679--2345750 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
2345669 AAATTACCAT
* *
2345679 TTTGGTCCCTAAACTTTTCAAAGT-TTATA
1 TTTGGTCCCTAAACTTTACAAAATCTTATA
2345708 CTTTGGTCACC-AAACTTTACAAAATCTTATA
1 -TTTGGTC-CCTAAACTTTACAAAATCTTATA
*
2345739 TTTGGTCACTAA
1 TTTGGTCCCTAA
2345751 CTAAATCCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 1 0.03
30 28 0.78
31 7 0.19
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (30 bp):
TTTGGTCCCTAAACTTTACAAAATCTTATA
Found at i:2351652 original size:24 final size:24
Alignment explanation
Indices: 2351640--2351699 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
2351630 CACCGAAGTG
2351640 CCACGTAGAATTTGTCCCAAAGGA
1 CCACGTAGAATTTGTCCCAAAGGA
* *
2351664 CCGCGTAGAATTTGTCCCTAAGGA
1 CCACGTAGAATTTGTCCCAAAGGA
2351688 CCACGTAGAATT
1 CCACGTAGAATT
2351700 ATCTCGAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCCAAAGGA
Found at i:2351719 original size:23 final size:23
Alignment explanation
Indices: 2351632--2351742 Score: 73
Period size: 24 Copynumber: 4.8 Consensus size: 23
2351622 ATAATTTGCA
* *
2351632 CCGAAGTG-CCACGTAGAATTTGTC
1 CCGAAG-GACCACATAGAA-TTATC
* * * *
2351656 CCAAAGGACCGCGTAGAATTTGTC
1 CCGAAGGACCACATAGAA-TTATC
* *
2351680 CCTAAGGACCACGTAGAATTATC
1 CCGAAGGACCACATAGAATTATC
* * *
2351703 TCGAAGGATCACATAG-ATTGTC
1 CCGAAGGACCACATAGAATTATC
*
2351725 CCGAAAGACCACATAGAA
1 CCGAAGGACCACATAGAA
2351743 CCCTCGACTC
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
22 18 0.25
23 18 0.25
24 36 0.50
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (23 bp):
CCGAAGGACCACATAGAATTATC
Found at i:2351737 original size:22 final size:22
Alignment explanation
Indices: 2351651--2351741 Score: 74
Period size: 24 Copynumber: 4.0 Consensus size: 22
2351641 CACGTAGAAT
* * *
2351651 TTGTCCCAAAGGACCGCGTAGAA
1 TTGTCCCGAAGGACCACATAG-A
* *
2351674 TTTGTCCCTAAGGACCACGTAGAA
1 -TTGTCCCGAAGGACCACATAG-A
* * *
2351698 TTATCTCGAAGGATCACATAGA
1 TTGTCCCGAAGGACCACATAGA
*
2351720 TTGTCCCGAAAGACCACATAGA
1 TTGTCCCGAAGGACCACATAGA
2351742 ACCCTCGACT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 19 0.34
23 16 0.29
24 21 0.38
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (22 bp):
TTGTCCCGAAGGACCACATAGA
Found at i:2352319 original size:19 final size:19
Alignment explanation
Indices: 2352295--2352334 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2352285 ACCGATATTT
*
2352295 CCCTTCTATGGTATCGATA
1 CCCTTCTATGGTACCGATA
*
2352314 CCCTTCTTTGGTACCGATA
1 CCCTTCTATGGTACCGATA
2352333 CC
1 CC
2352335 ATTTCGACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.33, G:0.15, T:0.35
Consensus pattern (19 bp):
CCCTTCTATGGTACCGATA
Found at i:2352997 original size:28 final size:28
Alignment explanation
Indices: 2352957--2353014 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
2352947 AGAAGGCACG
*
2352957 AACCAAGAGAAGAAGAATGAAATAAGCT
1 AACCAAGAGAAGAAGAAGGAAATAAGCT
*
2352985 AACCAATAGAAGAAGAAGGAAATAAGCT
1 AACCAAGAGAAGAAGAAGGAAATAAGCT
2353013 AA
1 AA
2353015 GTATCTAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.59, C:0.10, G:0.21, T:0.10
Consensus pattern (28 bp):
AACCAAGAGAAGAAGAAGGAAATAAGCT
Found at i:2358086 original size:20 final size:20
Alignment explanation
Indices: 2358041--2358092 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2358031 ATTTCAATTA
*
2358041 CAGTATCGATACCTTCCTCT
1 CAGTATCGATACCTTCCACT
**
2358061 TGGTATCGATACC-TCCACAT
1 CAGTATCGATACCTTCCAC-T
2358081 CAGTATCGATAC
1 CAGTATCGATAC
2358093 TGTTCATCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (20 bp):
CAGTATCGATACCTTCCACT
Found at i:2360906 original size:20 final size:20
Alignment explanation
Indices: 2360881--2360921 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2360871 TCTCTCTGAA
2360881 TCTGTAGATCAGAGACCAGG
1 TCTGTAGATCAGAGACCAGG
2360901 TCTGTAGATCAGAGACCAGG
1 TCTGTAGATCAGAGACCAGG
2360921 T
1 T
2360922 TCATCTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (20 bp):
TCTGTAGATCAGAGACCAGG
Found at i:2363567 original size:23 final size:23
Alignment explanation
Indices: 2363532--2363601 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
2363522 CACCACAACT
2363532 CGTATAAAATGCACCGAAGTGCCA
1 CGTA-AAAATGCACCGAAGTGCCA
* * * *
2363556 CGTAGAATTGCACCGTAGTGCCG
1 CGTAAAAATGCACCGAAGTGCCA
2363579 CGTAAAAATGCACCGAAGTGCCA
1 CGTAAAAATGCACCGAAGTGCCA
2363602 TATAAGATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 34 0.89
24 4 0.11
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (23 bp):
CGTAAAAATGCACCGAAGTGCCA
Found at i:2367022 original size:34 final size:33
Alignment explanation
Indices: 2366984--2367077 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 33
2366974 TAATCACTCG
2366984 AAATGAAAATCACACTTAAACAACTCCCTCGCAA
1 AAATGAAAATCACACTTAAACAACTCCCTCGC-A
* * * * * *
2367018 AAATGAAGAGCA-A-AT-CATAA-TCACTCG--
1 AAATGAAAATCACACTTAAACAACTCCCTCGCA
2367045 AAATGAAAATCACACTTAAACAACTCCCTCGCA
1 AAATGAAAATCACACTTAAACAACTCCCTCGCA
2367078 GAAGATTGAA
Statistics
Matches: 42, Mismatches: 12, Indels: 13
0.63 0.18 0.19
Matches are distributed among these distances:
27 10 0.24
28 1 0.02
29 1 0.02
30 9 0.21
31 9 0.21
32 1 0.02
33 1 0.02
34 10 0.24
ACGTcount: A:0.47, C:0.27, G:0.09, T:0.18
Consensus pattern (33 bp):
AAATGAAAATCACACTTAAACAACTCCCTCGCA
Found at i:2367048 original size:61 final size:61
Alignment explanation
Indices: 2366953--2367077 Score: 250
Period size: 61 Copynumber: 2.0 Consensus size: 61
2366943 TCAGACAACT
2366953 GCAAAAATGAAGAGCAAATCATAATCACTCGAAATGAAAATCACACTTAAACAACTCCCTC
1 GCAAAAATGAAGAGCAAATCATAATCACTCGAAATGAAAATCACACTTAAACAACTCCCTC
2367014 GCAAAAATGAAGAGCAAATCATAATCACTCGAAATGAAAATCACACTTAAACAACTCCCTC
1 GCAAAAATGAAGAGCAAATCATAATCACTCGAAATGAAAATCACACTTAAACAACTCCCTC
2367075 GCA
1 GCA
2367078 GAAGATTGAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.47, C:0.25, G:0.10, T:0.18
Consensus pattern (61 bp):
GCAAAAATGAAGAGCAAATCATAATCACTCGAAATGAAAATCACACTTAAACAACTCCCTC
Found at i:2381205 original size:31 final size:30
Alignment explanation
Indices: 2381167--2381226 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
2381157 CGGCCGATAA
*
2381167 ATTTAAATTAG-ACGGATCAATAATATCATAT
1 ATTTAAA-TAGAACGAATCAATAAT-TCATAT
*
2381198 ATTTAAATCGAACGAATCAATAATTCATA
1 ATTTAAATAGAACGAATCAATAATTCATA
2381227 AGATATAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (30 bp):
ATTTAAATAGAACGAATCAATAATTCATAT
Found at i:2382411 original size:7 final size:7
Alignment explanation
Indices: 2382399--2382459 Score: 68
Period size: 7 Copynumber: 8.7 Consensus size: 7
2382389 ATGTGATAGT
2382399 GTTTAGG
1 GTTTAGG
2382406 GTTTAGG
1 GTTTAGG
2382413 GTTTAGG
1 GTTTAGG
* *
2382420 ATTTATG
1 GTTTAGG
2382427 GTTTAGG
1 GTTTAGG
*
2382434 GTTTAAG
1 GTTTAGG
* **
2382441 TTTTATA
1 GTTTAGG
2382448 GTTTAGG
1 GTTTAGG
2382455 GTTTA
1 GTTTA
2382460 AGTTATACAC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (7 bp):
GTTTAGG
Found at i:2382462 original size:21 final size:21
Alignment explanation
Indices: 2382406--2382463 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
2382396 AGTGTTTAGG
* * *
2382406 GTTTAGGGTTTAGGATTTATG
1 GTTTAGGGTTTAAGTTTTATA
2382427 GTTTAGGGTTTAAGTTTTATA
1 GTTTAGGGTTTAAGTTTTATA
2382448 GTTTAGGGTTTAAGTT
1 GTTTAGGGTTTAAGTT
2382464 ATACACAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (21 bp):
GTTTAGGGTTTAAGTTTTATA
Found at i:2383749 original size:2 final size:2
Alignment explanation
Indices: 2383742--2383775 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2383732 TCTTAATTTA
2383742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2383776 TCTTTTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2385047 original size:31 final size:31
Alignment explanation
Indices: 2384987--2385047 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
2384977 GTTCGAGCAT
* * * *
2384987 TTTCGGGTTCGAGTCGAGTTTCAATATTTTC
1 TTTCGAGTTCGAGTCGAGCTTAAAAATTTTC
2385018 TTTCGAGTTCGAGTCGAGCTTAAAAATTTT
1 TTTCGAGTTCGAGTCGAGCTTAAAAATTTT
2385048 AGGCTCTCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.43
Consensus pattern (31 bp):
TTTCGAGTTCGAGTCGAGCTTAAAAATTTTC
Found at i:2391720 original size:20 final size:20
Alignment explanation
Indices: 2391695--2391732 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2391685 CACCTGTTAA
*
2391695 AGAATGCATCAATGCACTGT
1 AGAATGCACCAATGCACTGT
*
2391715 AGAATGCACCGATGCACT
1 AGAATGCACCAATGCACT
2391733 TCAATGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (20 bp):
AGAATGCACCAATGCACTGT
Found at i:2392696 original size:18 final size:18
Alignment explanation
Indices: 2392645--2392687 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2392635 GGGTCTACGC
*
2392645 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAAT
2392663 GGTCCTTCGGGACATAAT
1 GGTCCTTCGGGACATAAT
2392681 GGTCCTT
1 GGTCCTT
2392688 TGAGACATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.30
Consensus pattern (18 bp):
GGTCCTTCGGGACATAAT
Found at i:2394046 original size:20 final size:20
Alignment explanation
Indices: 2394021--2394067 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2394011 TTTTCCAAAT
2394021 TCGCAACGCGAATCTATAAA
1 TCGCAACGCGAATCTATAAA
* *
2394041 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATCTATAAA
2394061 TCGCAAC
1 TCGCAAC
2394068 ATAGAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATCTATAAA
Found at i:2394084 original size:20 final size:20
Alignment explanation
Indices: 2394061--2394147 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
2394051 AATTTGTAAA
* *
2394061 TCGCAACATAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* *
2394081 TCGCAA-AGCGATAGTCAAAT
1 TCGCAACA-CAAAAGTCAAAT
2394101 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
2394121 TCGTAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
2394141 TCGCAAC
1 TCGCAAC
2394148 GCGAAACACA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
19 1 0.02
20 55 0.96
21 1 0.02
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:2394291 original size:22 final size:22
Alignment explanation
Indices: 2394263--2394313 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2394253 CTACGGCGAC
*
2394263 ATCCGTCCCCATCTTCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
2394285 ATTCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
2394307 ATCCGTC
1 ATCCGTC
2394314 TATCTCCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.24
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:2396391 original size:21 final size:21
Alignment explanation
Indices: 2396367--2396409 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2396357 GAGTTATGTG
* *
2396367 ATGAGGTCGGTGCTTTGCGTA
1 ATGAGGTCGGTACTTTACGTA
*
2396388 ATGAGGTTGGTACTTTACGTA
1 ATGAGGTCGGTACTTTACGTA
2396409 A
1 A
2396410 AGATAATGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.33, T:0.35
Consensus pattern (21 bp):
ATGAGGTCGGTACTTTACGTA
Found at i:2396834 original size:21 final size:21
Alignment explanation
Indices: 2396808--2396912 Score: 72
Period size: 21 Copynumber: 5.0 Consensus size: 21
2396798 GAAACCCGAT
*
2396808 GCACCTATCATCATTCAAGAG
1 GCACCTCTCATCATTCAAGAG
*
2396829 GCACCTC-CTATCGTT-AGAGAG
1 GCACCTCTC-ATCATTCA-AGAG
* * *
2396850 GCCCCTCTCATCATTGAAGAA
1 GCACCTCTCATCATTCAAGAG
* * * *
2396871 GCCCCTCCCACCGTTCAAGAG
1 GCACCTCTCATCATTCAAGAG
*
2396892 GC-CTCTGTCATCATTCAAGAG
1 GCAC-CTCTCATCATTCAAGAG
2396913 TTCCCGCCCG
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
20 3 0.05
21 60 0.92
22 2 0.03
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (21 bp):
GCACCTCTCATCATTCAAGAG
Found at i:2396862 original size:42 final size:42
Alignment explanation
Indices: 2396815--2396912 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
2396805 GATGCACCTA
* *
2396815 TCATCATTCAAGAGGCACCTCCTATCGTT-AGAGAGGCCCCTC
1 TCATCATTCAAGAGGCACCTCCCACCGTTCA-AGAGGCCCCTC
* * * * *
2396857 TCATCATTGAAGAAGCCCCTCCCACCGTTCAAGAGGCCTCTG
1 TCATCATTCAAGAGGCACCTCCCACCGTTCAAGAGGCCCCTC
2396899 TCATCATTCAAGAG
1 TCATCATTCAAGAG
2396913 TTCCCGCCCG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCATTCAAGAGGCACCTCCCACCGTTCAAGAGGCCCCTC
Found at i:2396927 original size:42 final size:42
Alignment explanation
Indices: 2396815--2396933 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
2396805 GATGCACCTA
* * * * *
2396815 TCATCATTCAAGAGGCACCTCCTATCGTT-AGAGAGGCCCCTC
1 TCATCATTCAAGAAGCCCCGCCCACCGTTCA-AGAGGCCCCTC
* * * *
2396857 TCATCATTGAAGAAGCCCCTCCCACCGTTCAAGAGGCCTCTG
1 TCATCATTCAAGAAGCCCCGCCCACCGTTCAAGAGGCCCCTC
* *
2396899 TCATCATTCAAG-AGTTCCCGCCCGCCGTTCAAGAG
1 TCATCATTCAAGAAG-CCCCGCCCACCGTTCAAGAG
2396934 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.03
42 61 0.95
43 1 0.02
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.23
Consensus pattern (42 bp):
TCATCATTCAAGAAGCCCCGCCCACCGTTCAAGAGGCCCCTC
Found at i:2398170 original size:24 final size:24
Alignment explanation
Indices: 2398138--2398189 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
2398128 ATTTGCTGTT
2398138 TGTTGGTTTTAGATGTGTAGAAAG
1 TGTTGGTTTTAGATGTGTAGAAAG
*
2398162 TGTTGGTTTTCGATGTGTAGAAAG
1 TGTTGGTTTTAGATGTGTAGAAAG
2398186 TGTT
1 TGTT
2398190 TTTGAGCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (24 bp):
TGTTGGTTTTAGATGTGTAGAAAG
Found at i:2398388 original size:14 final size:14
Alignment explanation
Indices: 2398366--2398397 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2398356 GCTTGTTTAA
*
2398366 TTGATTTGTAAAAG
1 TTGAATTGTAAAAG
2398380 TTGAATTGTAAAAG
1 TTGAATTGTAAAAG
2398394 TTGA
1 TTGA
2398398 TGTGTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (14 bp):
TTGAATTGTAAAAG
Found at i:2398403 original size:14 final size:13
Alignment explanation
Indices: 2398366--2398405 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 13
2398356 GCTTGTTTAA
2398366 TTGATTTGTAAAAG
1 TTGA-TTGTAAAAG
2398380 TTGAATTGTAAAAG
1 TTG-ATTGTAAAAG
2398394 TTGATGTGTAAA
1 TTGAT-TGTAAA
2398406 TAAGACTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.08
14 21 0.88
15 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.40
Consensus pattern (13 bp):
TTGATTGTAAAAG
Found at i:2399066 original size:35 final size:36
Alignment explanation
Indices: 2399020--2399102 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
2399010 ATTTAAAGCA
* * *
2399020 TCAGAAGCATTTC-GGGCGTATGATTTGGGTGGTAC
1 TCAGAAGCATTTCAAGACGTATGATTTGGGTAGTAC
* *
2399055 TCAGAAGCATTTCAAGACTTCTGATTTGGGTAGTAC
1 TCAGAAGCATTTCAAGACGTATGATTTGGGTAGTAC
*
2399091 TCGGAAGCATTT
1 TCAGAAGCATTT
2399103 TGGACTTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
35 13 0.32
36 28 0.68
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.33
Consensus pattern (36 bp):
TCAGAAGCATTTCAAGACGTATGATTTGGGTAGTAC
Found at i:2399594 original size:12 final size:12
Alignment explanation
Indices: 2399577--2399613 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2399567 GAAATTTATA
2399577 TTAAATTCAAAC
1 TTAAATTCAAAC
* *
2399589 TTAAATTGAAAT
1 TTAAATTCAAAC
2399601 TTAAATTCAAAC
1 TTAAATTCAAAC
2399613 T
1 T
2399614 CCAATTACAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.38
Consensus pattern (12 bp):
TTAAATTCAAAC
Found at i:2399628 original size:24 final size:25
Alignment explanation
Indices: 2399574--2399630 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
2399564 ACCGAAATTT
*
2399574 ATATTAAATTCAAACTTAAATTGAA
1 ATATTAAATTCAAACTCAAATTGAA
* *
2399599 AT-TTAAATTCAAACTCCAATT-AC
1 ATATTAAATTCAAACTCAAATTGAA
2399622 ATATTAAAT
1 ATATTAAAT
2399631 GAATTTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.11
24 23 0.82
25 2 0.07
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (25 bp):
ATATTAAATTCAAACTCAAATTGAA
Done.