Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008211.1 Hibiscus syriacus cultivar Beakdansim tig00110833_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: 2208279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 10
Found at i:842883 original size:18 final size:18
Alignment explanation
Indices: 842860--842900 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
842850 AGAGAACATA
842860 AACGAACA-AAAGGAAACG
1 AACGAACATAAAGG-AACG
*
842878 AACGAACATAAATGAACG
1 AACGAACATAAAGGAACG
842896 AACGA
1 AACGA
842901 GCCTTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.59, C:0.17, G:0.20, T:0.05
Consensus pattern (18 bp):
AACGAACATAAAGGAACG
Found at i:846085 original size:5 final size:6
Alignment explanation
Indices: 846053--846090 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
846043 GACACATATT
846053 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACCA
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCA
846091 GAGACGAGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:846772 original size:21 final size:21
Alignment explanation
Indices: 846748--846801 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
846738 GATTTACATA
846748 TTCGCATTGCGATAATCCAAG
1 TTCGCATTGCGATAATCCAAG
*
846769 TTCGCATTGCGATAATCGAAG
1 TTCGCATTGCGATAATCCAAG
*
846790 TTCGCGTTGCGA
1 TTCGCATTGCGA
846802 ACTTGGAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAATCCAAG
Found at i:853209 original size:21 final size:21
Alignment explanation
Indices: 853183--853255 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
853173 TATGCCATCT
* *
853183 CCGCAGGGTTACATTACGAGC
1 CCGCAGGGTTACATTCCTAGC
853204 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
853225 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
853246 CCGCAGGGTT
1 CCGCAGGGTT
853256 TTATACCATA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
20 2 0.04
21 43 0.91
22 2 0.04
ACGTcount: A:0.19, C:0.33, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:853826 original size:34 final size:34
Alignment explanation
Indices: 853776--853873 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
853766 AAATGTTTTT
*
853776 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
853810 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
853844 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
853874 CATTAAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:854501 original size:128 final size:128
Alignment explanation
Indices: 854273--854770 Score: 824
Period size: 128 Copynumber: 3.9 Consensus size: 128
854263 TTACCTGATT
*
854273 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* * *** * *
854338 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCAAGTCCCTTGAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
854401 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
* *
854465 ATGACAAAATAATGGAAGGCGCGCCCCCAGTAACGCGCCTTCATGTGAATAGTGAAATAATAGG
65 ATGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
854529 TACTGATATATCTAGTGTTCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
854594 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
854657 TACTGATATATCTAGTATCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
854722 TG---AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
854771 ACTCCGATTA
Statistics
Matches: 347, Mismatches: 21, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
125 47 0.14
127 1 0.00
128 298 0.86
129 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:854852 original size:8 final size:8
Alignment explanation
Indices: 854841--854881 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
854831 TCACAAACTT
854841 TCAAATTC
1 TCAAATTC
854849 TCAAATTC
1 TCAAATTC
* *
854857 CCAAACTC
1 TCAAATTC
854865 T-AAATTC
1 TCAAATTC
854872 TCAAATTC
1 TCAAATTC
854880 TC
1 TC
854882 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:860865 original size:21 final size:21
Alignment explanation
Indices: 860841--860924 Score: 109
Period size: 21 Copynumber: 4.1 Consensus size: 21
860831 TTATTAATGC
860841 ATGCATGTATGTATAATATGT
1 ATGCATGTATGTATAATATGT
860862 ATGCATGTATGTATAATATGT
1 ATGCATGTATGTATAATATGT
*
860883 ATGCATATATGTATAAT-T-T
1 ATGCATGTATGTATAATATGT
** * *
860902 ATTAATGCATGTATGATATGT
1 ATGCATGTATGTATAATATGT
860923 AT
1 AT
860925 ATTAATGTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.24
20 2 0.04
21 40 0.73
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.44
Consensus pattern (21 bp):
ATGCATGTATGTATAATATGT
Found at i:861044 original size:40 final size:41
Alignment explanation
Indices: 860950--861037 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 41
860940 ATAGTGTTTC
* * *
860950 TATAAACTATAT-AAGTAATTTACTTTATATAGTTTATATA
1 TATATACTATATAAAGTAAATTACTTTATATAGTTTATAGA
*
860990 TATATATTATATAAAGTAAATTAC-TTATATAGTTTATAGA
1 TATATACTATATAAAGTAAATTACTTTATATAGTTTATAGA
861030 -A-ATACTAT
1 TATATACTAT
861038 GCATAAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 6 0.14
39 1 0.02
40 25 0.60
41 10 0.24
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (41 bp):
TATATACTATATAAAGTAAATTACTTTATATAGTTTATAGA
Found at i:861264 original size:15 final size:15
Alignment explanation
Indices: 861246--861290 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
861236 TTAATCATGT
*
861246 TTTATATAATTTATA
1 TTTAAATAATTTATA
861261 TTTAAATAATTT-TA
1 TTTAAATAATTTATA
861275 -TTAAATAATTTTATA
1 TTTAAATAA-TTTATA
861290 T
1 T
861291 AATATGTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 8 0.31
14 5 0.19
15 13 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAATAATTTATA
Found at i:861294 original size:13 final size:13
Alignment explanation
Indices: 861251--861288 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
861241 CATGTTTTAT
861251 ATAATTTATATTTAA
1 ATAATTT-TA-TTAA
861266 ATAATTTTATTAA
1 ATAATTTTATTAA
861279 ATAATTTTAT
1 ATAATTTTAT
861289 ATAATATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.61
14 2 0.09
15 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATAATTTTATTAA
Found at i:861399 original size:48 final size:50
Alignment explanation
Indices: 861322--861419 Score: 128
Period size: 48 Copynumber: 2.0 Consensus size: 50
861312 TATATATATA
* ** * *
861322 TATATAAAGTAAATTACTTATATAGTTTATAGAAACACTATA-CATAAAC
1 TATATAAAGTAAATAAAATATATAGTTTATAAAAACACTAAATCATAAAC
*
861371 TATATAAAGT-AATAAAATATATAGTTTATAAAAACCCTAAATCATAAAC
1 TATATAAAGTAAATAAAATATATAGTTTATAAAAACACTAAATCATAAAC
861420 CATAAACTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 25 0.60
49 17 0.40
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (50 bp):
TATATAAAGTAAATAAAATATATAGTTTATAAAAACACTAAATCATAAAC
Found at i:861432 original size:21 final size:22
Alignment explanation
Indices: 861408--861466 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
861398 ATAAAAACCC
*
861408 TAAATCATAAACCA-TAAACTT
1 TAAATCATAAACCACTAAACAT
*
861429 TAAATCACAAA-CACTAAACAT
1 TAAATCATAAACCACTAAACAT
861450 TAAATCATAAACC-CTAA
1 TAAATCATAAACCACTAA
861467 TATAAATGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 2 0.06
21 30 0.91
22 1 0.03
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAATCATAAACCACTAAACAT
Found at i:861948 original size:48 final size:49
Alignment explanation
Indices: 861855--861949 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 49
861845 AAACTATACA
* * *
861855 TATATATAAACTATATAAAGTAAATTAATTATATAGTTTATAGAAACAC
1 TATACATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACAC
*
861904 TATACATAAACTATATAAAGT-AGTAAAATATATAGTTTATAGAAAC
1 TATACATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAAC
861950 CTTAAATCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 22 0.52
49 20 0.48
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.35
Consensus pattern (49 bp):
TATACATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACAC
Found at i:861961 original size:49 final size:49
Alignment explanation
Indices: 861860--861963 Score: 140
Period size: 48 Copynumber: 2.1 Consensus size: 49
861850 ATACATATAT
* * *
861860 ATAAACTATATAAAGTAAATTAATTATATAGTTTATAGAAACACTATAC
1 ATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACACTAAAC
*
861909 ATAAACTATATAAAGT-AGTAAAATATATAGTTTATAGAAAC-CTTAAATC
1 ATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACAC-TAAA-C
861958 ATAAAC
1 ATAAAC
861964 CATAAACCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
47 1 0.02
48 25 0.51
49 23 0.47
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (49 bp):
ATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACACTAAAC
Found at i:861976 original size:14 final size:14
Alignment explanation
Indices: 861959--862017 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
861949 CCTTAAATCA
*
861959 TAAACCATAAACCC
1 TAAATCATAAACCC
**
861973 TAAATTTTAAACCAC
1 TAAATCATAAACC-C
*
861988 -AAA-CACTAAACAC
1 TAAATCA-TAAACCC
862001 TAAATCATAAACCC
1 TAAATCATAAACCC
862015 TAA
1 TAA
862018 TGTAAATGGA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
13 1 0.03
14 30 0.88
15 3 0.09
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAATCATAAACCC
Found at i:862017 original size:21 final size:20
Alignment explanation
Indices: 861946--862017 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
861936 TAGTTTATAG
*
861946 AAACCTTAAATCATAAACCAT
1 AAACCCTAAA-CATAAACCAT
** *
861967 AAACCCTAAATTTTAAACCAC
1 AAACCCTAAA-CATAAACCAT
* *
861988 AAACACTAAACACTAAATCAT
1 AAACCCTAAACA-TAAACCAT
862009 AAACCCTAA
1 AAACCCTAA
862018 TGTAAATGGA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (20 bp):
AAACCCTAAACATAAACCAT
Found at i:862322 original size:15 final size:15
Alignment explanation
Indices: 862297--862333 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
862287 ATAAACCATG
862297 TATAGTATATATAAAC
1 TATA-TATATATAAAC
862313 TATATATATATAAAC
1 TATATATATATAAAC
862328 TATATA
1 TATATA
862334 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:862436 original size:14 final size:14
Alignment explanation
Indices: 862408--862478 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
862398 TAGTTTATAG
* *
862408 AAACCTTAAATCCT
1 AAACCATAAACCCT
*
862422 AAATCATAAACCCT
1 AAACCATAAACCCT
** **
862436 AATTC-TAAACTTT
1 AAACCATAAACCCT
*
862449 AAACCATAAACACT
1 AAACCATAAACCCT
862463 AAACCATAAACCCT
1 AAACCATAAACCCT
862477 AA
1 AA
862479 TTTAAATAGA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
13 9 0.20
14 36 0.80
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCATAAACCCT
Found at i:862662 original size:14 final size:14
Alignment explanation
Indices: 862643--862689 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
862633 ATTTTGTCTT
862643 TATATAAATTAAAC
1 TATATAAATTAAAC
862657 TATAT-AATT----
1 TATATAAATTAAAC
862666 TATATAAATTAAAC
1 TATATAAATTAAAC
*
862680 TATATTAATT
1 TATATAAATT
862690 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:862668 original size:23 final size:24
Alignment explanation
Indices: 862641--862690 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
862631 TTATTTTGTC
862641 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
862664 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
862688 TTT
1 TTT
862691 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:863041 original size:16 final size:16
Alignment explanation
Indices: 862962--863044 Score: 116
Period size: 16 Copynumber: 5.2 Consensus size: 16
862952 TCATTTACAG
*
862962 GTCAGGTTAAAAAC-A
1 GTCAGGTTGAAAACAA
862977 GATCAGGTTGAAAAC-A
1 G-TCAGGTTGAAAACAA
*
862993 GATCAGGTTAAAAACAA
1 G-TCAGGTTGAAAACAA
863010 GTCAGGTTGAAAACAA
1 GTCAGGTTGAAAACAA
863026 GTCAGGTTGAAAACAA
1 GTCAGGTTGAAAACAA
863042 GTC
1 GTC
863045 GGGTAATACC
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
15 1 0.02
16 60 0.95
17 2 0.03
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (16 bp):
GTCAGGTTGAAAACAA
Found at i:868904 original size:64 final size:65
Alignment explanation
Indices: 868836--868976 Score: 185
Period size: 64 Copynumber: 2.2 Consensus size: 65
868826 GAACACTTGA
* * *
868836 TGCATCGGTGCACCAAGTGTGCATCAATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGAG
1 TGCATCGATGCACCAAGTGTGCATCAATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAG
*** * * **
868900 TGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG
1 TGCATCGATGCACCAAGTGTGCATCAATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAG
868965 TGCATCGATGCA
1 TGCATCGATGCA
868977 TGGAGAATGC
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 40 0.61
65 26 0.39
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (65 bp):
TGCATCGATGCACCAAGTGTGCATCAATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAG
Found at i:868988 original size:65 final size:65
Alignment explanation
Indices: 868855--869014 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 65
868845 GCACCAAGTG
* * ***
868855 TGCATCAATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGAGTGCATCGATGCATGGATTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* **
868919 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAA
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* * *
868984 TGCATCGGTGCATGGAATGCATTTGATGTTT
1 TGCATCGATGCATGAAATGCATTCGATGTTT
869015 CAATTAATTC
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
64 26 0.31
65 57 0.69
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
Found at i:875415 original size:22 final size:21
Alignment explanation
Indices: 875373--875412 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
875363 GAGTTTGTTT
*
875373 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
875394 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
875413 ACAGTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:877392 original size:64 final size:64
Alignment explanation
Indices: 877339--877502 Score: 238
Period size: 65 Copynumber: 2.5 Consensus size: 64
877329 CGGTGCACCA
*
877339 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * **
877403 ATTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
877468 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
877503 CAATTAATTC
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 33 0.38
65 55 0.62
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:877491 original size:17 final size:19
Alignment explanation
Indices: 877453--877499 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
877443 ATATTCAGAG
877453 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
877472 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
877489 TGCATTCGATG
1 TGCA-TCGATG
877500 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:877522 original size:65 final size:62
Alignment explanation
Indices: 877343--877549 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 62
877333 GCACCAAGTG
*
877343 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAA-TAGCCTGAGTGCATCGATGCATGGATTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCG-CT-AGTGCATCGATGCATGGA--G
877407 -
62 A
*
877407 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAG--AGTGCATCGATGCATGGAG
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTC-GCTAGTGCATCGATGCATGGAG
877470 AA
62 -A
* * * * *
877472 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCGCTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCGCTAGTGCATCGATGCATGG-AGA
*
877537 TGCATCGGTGCAT
1 TGCATCGATGCAT
877550 CACCTCAAAT
Statistics
Matches: 123, Mismatches: 8, Indels: 23
0.80 0.05 0.15
Matches are distributed among these distances:
63 4 0.03
64 34 0.28
65 78 0.63
66 4 0.03
67 1 0.01
68 1 0.01
69 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCGCTAGTGCATCGATGCATGGAGA
Found at i:877741 original size:20 final size:21
Alignment explanation
Indices: 877718--877757 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
877708 GAATCGAATA
877718 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
877738 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
877758 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:877842 original size:31 final size:30
Alignment explanation
Indices: 877807--877929 Score: 106
Period size: 31 Copynumber: 4.0 Consensus size: 30
877797 ACATAAACTC
877807 TAGATGAAATATCAATTTGACCCTTAAATTT
1 TAGAT-AAATATCAATTTGACCCTTAAATTT
* * *
877838 TAGATAGAATA-CAAATTTGA-TCTCTGAACTT
1 TAGATA-AATATC-AATTTGACCCT-TAAATTT
* * *
877869 TAGATAAAATATCATTTTGACCCCTAAAATT
1 TAGAT-AAATATCAATTTGACCCTTAAATTT
* *
877900 TAGATAAATTATGAATTTGACCTTTAAATT
1 TAGATAAA-TATCAATTTGACCCTTAAATT
877930 CAACCAAAGT
Statistics
Matches: 72, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
30 7 0.10
31 62 0.86
32 3 0.04
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (30 bp):
TAGATAAATATCAATTTGACCCTTAAATTT
Found at i:878264 original size:2 final size:2
Alignment explanation
Indices: 878257--878295 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
878247 TTCGAACGTC
878257 AT 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 AT A
878296 AAGTTATCAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:879129 original size:25 final size:25
Alignment explanation
Indices: 879092--879159 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
879082 TGGTCCCCTA
879092 GTCTCCATC-TAAAAAATCTGTACCC
1 GTCTCC-TCTTAAAAAATCTGTACCC
* *
879117 GTCTCCTCTTAAAAAATTTGTACCT
1 GTCTCCTCTTAAAAAATCTGTACCC
*
879142 GTC-CACGCTTAAAAAATC
1 GTCTC-CTCTTAAAAAATC
879160 ACGGGGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.08
25 34 0.92
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (25 bp):
GTCTCCTCTTAAAAAATCTGTACCC
Found at i:879265 original size:12 final size:12
Alignment explanation
Indices: 879248--879307 Score: 93
Period size: 12 Copynumber: 5.0 Consensus size: 12
879238 GTTATTTATA
879248 TGGGTATCGGGC
1 TGGGTATCGGGC
879260 TGGGTATCGGGC
1 TGGGTATCGGGC
*
879272 CGGGTATCGGGC
1 TGGGTATCGGGC
* *
879284 CGGGTATCGGAC
1 TGGGTATCGGGC
879296 TGGGTATCGGGC
1 TGGGTATCGGGC
879308 CAAGTATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.10, C:0.20, G:0.48, T:0.22
Consensus pattern (12 bp):
TGGGTATCGGGC
Found at i:879362 original size:37 final size:37
Alignment explanation
Indices: 879319--879389 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
879309 AAGTATATAT
879319 ATTTAAATTAAATATATAAATAGTATATATATATTTA
1 ATTTAAATTAAATATATAAATAGTATATATATATTTA
* * * *
879356 ATTTAAATTACATTTATTAATATTATATATATAT
1 ATTTAAATTAAATATATAAATAGTATATATATAT
879390 AATTATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (37 bp):
ATTTAAATTAAATATATAAATAGTATATATATATTTA
Found at i:879512 original size:35 final size:36
Alignment explanation
Indices: 879449--879530 Score: 112
Period size: 35 Copynumber: 2.3 Consensus size: 36
879439 AATTACTAAA
* * *
879449 CCCGTCCCCGTCCCCGTTTAACATAAACGGTTTTTC
1 CCCGTCACCGTCCCCGTTTAACATAAACGATTTTCC
*
879485 CCCGTCACTGTCCCCG-TTAACATAAACGATTTTCC
1 CCCGTCACCGTCCCCGTTTAACATAAACGATTTTCC
*
879520 CCCGTCCCCGT
1 CCCGTCACCGT
879531 TTAATTCGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 26 0.65
36 14 0.35
ACGTcount: A:0.17, C:0.41, G:0.13, T:0.28
Consensus pattern (36 bp):
CCCGTCACCGTCCCCGTTTAACATAAACGATTTTCC
Found at i:880677 original size:60 final size:60
Alignment explanation
Indices: 880600--880757 Score: 196
Period size: 60 Copynumber: 2.6 Consensus size: 60
880590 ATTGGTTTTT
* * * * * *
880600 AAACTTTTAAATATTTTAACTTCATCCCTAAACTATGA-CTATTATTCTAAATTAGTCCTCA
1 AAACTTTTGAACATTTTAATTTCATCCCCAAACTATAATCT-TCATTCTAAATTAGTCC-CA
*
880661 AAA-TTTTGAACATTTTAGTTTCATCCCCAAACTATAATCTTCATTCTAAATTAGTCCCA
1 AAACTTTTGAACATTTTAATTTCATCCCCAAACTATAATCTTCATTCTAAATTAGTCCCA
*
880720 AAACTTTTTGAACATTTTAATTTCAT-CCCAAATTATAA
1 AAAC-TTTTGAACATTTTAATTTCATCCCCAAACTATAA
880758 GTATATACTA
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
59 5 0.06
60 55 0.65
61 25 0.29
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.41
Consensus pattern (60 bp):
AAACTTTTGAACATTTTAATTTCATCCCCAAACTATAATCTTCATTCTAAATTAGTCCCA
Found at i:880979 original size:60 final size:59
Alignment explanation
Indices: 880884--881000 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 59
880874 GAATATGGAG
* **
880884 ATGAAATTGGAAGATTCAAAAGTTTGGGGATTAATTT-AGAATGAGAGTCATAGTTTGGTT
1 ATGAAATTGAAAGATTCAAAAGTTTAAGGATTAATTTGA-AATGAGA-TCATAGTTTGGTT
*
880944 ATGAAATTGAAATATTCAAAAGTTTAAGG-TCTAATTTGAAATGAGATCATAGTTTGG
1 ATGAAATTGAAAGATTCAAAAGTTTAAGGAT-TAATTTGAAATGAGATCATAGTTTGG
881001 AAACATATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
59 12 0.24
60 38 0.75
61 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (59 bp):
ATGAAATTGAAAGATTCAAAAGTTTAAGGATTAATTTGAAATGAGATCATAGTTTGGTT
Found at i:882660 original size:21 final size:22
Alignment explanation
Indices: 882627--882671 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
882617 ATAGAATTTT
* *
882627 TATTTTTTTATTATT-AAAATA
1 TATTATTTAATTATTAAAAATA
882648 TATTATTTAATTATTAAAAATA
1 TATTATTTAATTATTAAAAATA
882670 TA
1 TA
882672 AAAATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTATTTAATTATTAAAAATA
Found at i:882676 original size:30 final size:29
Alignment explanation
Indices: 882641--882707 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
882631 TTTTTATTAT
*
882641 TAAAATATATT-ATTTAAT-TATTAAAAATA
1 TAAAA-ATATTAATTTAATCAATT-AAAATA
882670 TAAAAATATTAATTTAATCAATTAAAATA
1 TAAAAATATTAATTTAATCAATTAAAATA
882699 TAATAAATA
1 TAA-AAATA
882708 ATTTTAGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 5 0.15
29 21 0.62
30 8 0.24
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAAATATTAATTTAATCAATTAAAATA
Found at i:886480 original size:26 final size:26
Alignment explanation
Indices: 886451--886500 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
886441 TTATTAGTTC
886451 TATATATTTATGTAATTTTATAATTA
1 TATATATTTATGTAATTTTATAATTA
* * * *
886477 TATATGTTTTTTTAATTTTTTAAT
1 TATATATTTATGTAATTTTATAAT
886501 AATTATCATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (26 bp):
TATATATTTATGTAATTTTATAATTA
Found at i:887497 original size:2 final size:2
Alignment explanation
Indices: 887486--887529 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
887476 TTAACCAGCT
887486 TA TA -A TA TA TA TA TA 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
887527 TA T
1 TA T
887530 TATGTTGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:888132 original size:30 final size:30
Alignment explanation
Indices: 888097--888201 Score: 201
Period size: 30 Copynumber: 3.5 Consensus size: 30
888087 AAGTATTGTC
*
888097 TCAATTAAGCCATTATTTAAAAACTTATGA
1 TCAATTAAGCCATTACTTAAAAACTTATGA
888127 TCAATTAAGCCATTACTTAAAAACTTATGA
1 TCAATTAAGCCATTACTTAAAAACTTATGA
888157 TCAATTAAGCCATTACTTAAAAACTTATGA
1 TCAATTAAGCCATTACTTAAAAACTTATGA
888187 TCAATTAAGCCATTA
1 TCAATTAAGCCATTA
888202 TATAATCAGT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 74 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (30 bp):
TCAATTAAGCCATTACTTAAAAACTTATGA
Found at i:889335 original size:19 final size:20
Alignment explanation
Indices: 889301--889345 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
889291 TTAAATCTCT
889301 ATATTTATTGAATAAAAATA
1 ATATTTATTGAATAAAAATA
* *
889321 ATATTT-TTTAATAAATATA
1 ATATTTATTGAATAAAAATA
*
889340 TTATTT
1 ATATTT
889346 CAGATTGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATATTTATTGAATAAAAATA
Found at i:898250 original size:20 final size:20
Alignment explanation
Indices: 898227--898293 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
898217 AATCTGTAAA
898227 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
898247 TCGCAACGCGAT-AGTCAAATT
1 TCGCAACAC-ATAAGTCAAA-T
* *
898268 TC-TAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
898287 TCGCAAC
1 TCGCAAC
898294 GTGAATAGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
19 4 0.11
20 29 0.76
21 5 0.13
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.21
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:898250 original size:40 final size:41
Alignment explanation
Indices: 898206--898311 Score: 119
Period size: 40 Copynumber: 2.6 Consensus size: 41
898196 AGTTTCCAAT
* *
898206 TTCGCAACGCGAATCTGT-AAATCGC-AACACATAAGTCAAA
1 TTCGCAACGCGAAT-AGTCAAATCGCTAACACAAAAGTCAAA
**
898246 TTCGCAACGCG-ATAGTCAAATTTCTAACACAAAAGTCAAA
1 TTCGCAACGCGAATAGTCAAATCGCTAACACAAAAGTCAAA
* *
898286 TTCGCAACGTGAATAGTAAAAATCGC
1 TTCGCAACGCGAATAGT-CAAATCGC
898312 AATGTGAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
38 2 0.04
39 7 0.13
40 35 0.65
41 5 0.09
42 5 0.09
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.22
Consensus pattern (41 bp):
TTCGCAACGCGAATAGTCAAATCGCTAACACAAAAGTCAAA
Found at i:898311 original size:21 final size:21
Alignment explanation
Indices: 898287--898327 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
898277 AAAGTCAAAT
898287 TCGCAACGTGAATAGTAAAAA
1 TCGCAACGTGAATAGTAAAAA
*
898308 TCGCAATGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
898328 TTGGAACGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (21 bp):
TCGCAACGTGAATAGTAAAAA
Found at i:898728 original size:20 final size:20
Alignment explanation
Indices: 898685--898816 Score: 194
Period size: 20 Copynumber: 6.5 Consensus size: 20
898675 CAACGCGATT
*
898685 TTGCGATTTT-CTAAATTCGCG
1 TTGCGATTTTACT--ATTCACG
*
898706 TTGCGATTTTACTATTCATG
1 TTGCGATTTTACTATTCACG
898726 TTGCGATTTTACTATTCACG
1 TTGCGATTTTACTATTCACG
898746 TTGCGATTTTACTATTCACG
1 TTGCGATTTTACTATTCACG
*
898766 TTGCGATTTTACTATTCACA
1 TTGCGATTTTACTATTCACG
898786 TTGCGATTTTTACTATTCACG
1 TTGCGA-TTTTACTATTCACG
*
898807 CTGCGATTTT
1 TTGCGATTTT
898817 GAAAACTGAG
Statistics
Matches: 103, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
20 73 0.71
21 28 0.27
22 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTACTATTCACG
Found at i:898779 original size:60 final size:61
Alignment explanation
Indices: 898685--898816 Score: 196
Period size: 61 Copynumber: 2.2 Consensus size: 61
898675 CAACGCGATT
* **
898685 TTGCGATTTTCTAAATTCGCGTTGCGATTTTACTATTCATGTTGCGA-TTTTACTATTCACG
1 TTGCGATTTTCT-AATTCACGTTGCGATTTTACTATTCACATTGCGATTTTTACTATTCACG
898746 TTGCGATTTTACT-ATTCACGTTGCGATTTTACTATTCACATTGCGATTTTTACTATTCACG
1 TTGCGATTTT-CTAATTCACGTTGCGATTTTACTATTCACATTGCGATTTTTACTATTCACG
*
898807 CTGCGATTTT
1 TTGCGATTTT
898817 GAAAACTGAG
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
60 30 0.46
61 33 0.51
62 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.46
Consensus pattern (61 bp):
TTGCGATTTTCTAATTCACGTTGCGATTTTACTATTCACATTGCGATTTTTACTATTCACG
Found at i:898830 original size:61 final size:60
Alignment explanation
Indices: 898686--898832 Score: 170
Period size: 61 Copynumber: 2.4 Consensus size: 60
898676 AACGCGATTT
* * * ** *
898686 TGCGATTTTCTAAATTCGCGTTGCGATTTTACTATTCATGTTGCGATTTTACTATTCACGT
1 TGCGATTTT-AAAACTCACGTTGCGATTTTACTATTCACATTGCGATTTTACTATTCACGC
** *
898747 TGCGATTTTACTATTCACGTTGCGATTTTACTATTCACATTGCGATTTTTACTATTCACGC
1 TGCGATTTTAAAACTCACGTTGCGATTTTACTATTCACATTGCGA-TTTTACTATTCACGC
*
898808 TGCGATTTTGAAAACTGA-GTTGCGA
1 TGCGATTTT-AAAACTCACGTTGCGA
898833 AATTGGAGTT
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 30 0.41
61 39 0.53
62 4 0.05
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (60 bp):
TGCGATTTTAAAACTCACGTTGCGATTTTACTATTCACATTGCGATTTTACTATTCACGC
Found at i:902882 original size:7 final size:7
Alignment explanation
Indices: 902867--902901 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
902857 AATATATATT
902867 ATATATTA
1 ATAT-TTA
*
902875 AAATTTA
1 ATATTTA
902882 ATATTTA
1 ATATTTA
902889 ATATTTA
1 ATATTTA
902896 ATATTT
1 ATATTT
902902 TCGTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 22 0.88
8 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
ATATTTA
Found at i:903310 original size:11 final size:12
Alignment explanation
Indices: 903294--903324 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
903284 TCCTATTAGC
903294 TAAATAATATA-
1 TAAATAATATAT
903305 TAAATAATATAT
1 TAAATAATATAT
903317 TAAATAAT
1 TAAATAAT
903325 TAATAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAATAATATAT
Found at i:906283 original size:109 final size:109
Alignment explanation
Indices: 906057--906265 Score: 253
Period size: 107 Copynumber: 1.9 Consensus size: 109
906047 ATAACGGTGG
* * * * * *
906057 GGTACTAAAATGAAATAAAAATTAAACGTTATGTATGATTTTGGATATTTTTTGAAAATTTAGGT
1 GGTACTAAAATAAAAAAAAAACTAAACGTTAGGTATGATTTTGAATATTTTTTGAAAATTTAAGT
* * * * * **
906122 ACTAAAACGGACTAAGACTGATAGTTTATGTACTAAACGTGAGG
66 ACTAAAACGGACAAAAACTGATAATTTAGGCACTAAACGTGAAA
* *
906166 GGTACTAAAATAAAACAAAAACTAAACGTTAGGTATGATTTT-AAT-TTTTTTGGAAATTTAAGT
1 GGTACTAAAATAAAAAAAAAACTAAACGTTAGGTATGATTTTGAATATTTTTTGAAAATTTAAGT
906229 ACTAAAGA-GGACAAAAACTGATAATTTAGGCACTAAA
66 ACTAAA-ACGGACAAAAACTGATAATTTAGGCACTAAA
906266 TGTATAATTT
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
107 46 0.53
108 3 0.03
109 38 0.44
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (109 bp):
GGTACTAAAATAAAAAAAAAACTAAACGTTAGGTATGATTTTGAATATTTTTTGAAAATTTAAGT
ACTAAAACGGACAAAAACTGATAATTTAGGCACTAAACGTGAAA
Found at i:906847 original size:25 final size:27
Alignment explanation
Indices: 906791--906848 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
906781 ATTGAATTAA
*
906791 TAAATATAAGTATAAAATATATATTTT
1 TAAATATAAATATAAAATATATATTTT
*
906818 TAAATATAAATATCAAA-ATAT-TTTT
1 TAAATATAAATATAAAATATATATTTT
906843 TAAATA
1 TAAATA
906849 GTTTTATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 10 0.34
26 4 0.14
27 15 0.52
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (27 bp):
TAAATATAAATATAAAATATATATTTT
Found at i:910540 original size:34 final size:34
Alignment explanation
Indices: 910476--910540 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
910466 TATTAATTTA
* *
910476 TATATTTTCTTTAAAAATTTAAATTCATAAAAGT
1 TATATTTTCTTTAAAAATCTAAAATCATAAAAGT
* *
910510 TATATTTTTTTTACAAAA-CTAAAATGATAAA
1 TATATTTTCTTTA-AAAATCTAAAATCATAAA
910541 TAGGTTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
34 22 0.85
35 4 0.15
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (34 bp):
TATATTTTCTTTAAAAATCTAAAATCATAAAAGT
Found at i:911445 original size:36 final size:38
Alignment explanation
Indices: 911400--911488 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 38
911390 TTTGTATAAT
*
911400 ATTACAAATTATAAAATATTTAT-TTATTTTCTTTA-AAA
1 ATTA-AAATTATAAAATATTTATATAATTTT-TTTACAAA
911438 ATT-AAATTCAT--AATATTTATATAATTTTTTTACAAA
1 ATTAAAATT-ATAAAATATTTATATAATTTTTTTACAAA
*
911474 ATTAAAAATATAAAA
1 ATTAAAATTATAAAA
911489 AAAGTTTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
35 13 0.30
36 19 0.44
37 6 0.14
38 5 0.12
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (38 bp):
ATTAAAATTATAAAATATTTATATAATTTTTTTACAAA
Found at i:911484 original size:31 final size:31
Alignment explanation
Indices: 911401--911484 Score: 75
Period size: 35 Copynumber: 2.6 Consensus size: 31
911391 TTGTATAATA
*
911401 TTAC-AAATTATAAAATATTTATTTATTTTCT
1 TTACAAAATTA-AAAATATTTATTAATTTTCT
911432 TTA-AAAATTAAATTCATAATATTTATATAATTTT-T
1 TTACAAAATT-AA---A-AATATTTAT-TAATTTTCT
911467 TTACAAAATTAAAAATAT
1 TTACAAAATTAAAAATAT
911485 AAAAAAAGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
31 14 0.32
32 2 0.05
34 1 0.02
35 15 0.34
36 12 0.27
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (31 bp):
TTACAAAATTAAAAATATTTATTAATTTTCT
Found at i:913310 original size:14 final size:15
Alignment explanation
Indices: 913282--913320 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
913272 ATTTGTTATA
913282 TAAAATATATCTTTT
1 TAAAATATATCTTTT
913297 TAAAA-ATAT-TTTT
1 TAAAATATATCTTTT
913310 TAATAATATAT
1 TAA-AATATAT
913321 AAGTAGTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
14 6 0.27
15 9 0.41
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
TAAAATATATCTTTT
Found at i:913429 original size:21 final size:21
Alignment explanation
Indices: 913372--913431 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
913362 AAAAAATAAT
*
913372 ATTTATATTCAATTTTTTAGTA
1 ATTTATATTTAA-TTTTTAGTA
*
913394 ATTTA-ATTTTTATTTTTAGTA
1 ATTTATA-TTTAATTTTTAGTA
*
913415 TTTTATATTTAATTTTT
1 ATTTATATTTAATTTTT
913432 TAAATATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 23 0.72
22 9 0.28
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (21 bp):
ATTTATATTTAATTTTTAGTA
Found at i:913438 original size:16 final size:14
Alignment explanation
Indices: 913373--913461 Score: 72
Period size: 14 Copynumber: 6.0 Consensus size: 14
913363 AAAAATAATA
*
913373 TTTATATTCAATTT
1 TTTATATTTAATTT
913387 TTTAGTAATTTAA-TT
1 TTTA-T-ATTTAATTT
* * *
913402 TTTATTTTTAGTAT
1 TTTATATTTAATTT
913416 TTTATATTTAATTT
1 TTTATATTTAATTT
*
913430 TTTAAATATTTGAATAAT
1 TTT--ATATTT-AAT-TT
913448 TTTATATTTAATTT
1 TTTATATTTAATTT
913462 AAAATGTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
13 4 0.07
14 21 0.36
15 10 0.17
16 17 0.29
17 3 0.05
18 4 0.07
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (14 bp):
TTTATATTTAATTT
Found at i:914896 original size:15 final size:14
Alignment explanation
Indices: 914856--914925 Score: 65
Period size: 15 Copynumber: 5.0 Consensus size: 14
914846 ATTTCTAAAA
* *
914856 ATTATTTAATATGT
1 ATTATTTAATTTTT
*
914870 A-TATTCAATTTTT
1 ATTATTTAATTTTT
914883 ATTAATTTAATTTTT
1 ATT-ATTTAATTTTT
914898 ATT-TTTAGTATTTTT
1 ATTATTTA--ATTTTT
914913 A-TATTTAATTTTT
1 ATTATTTAATTTTT
914926 TAAATATTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
13 20 0.43
14 3 0.06
15 24 0.51
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (14 bp):
ATTATTTAATTTTT
Found at i:914919 original size:21 final size:22
Alignment explanation
Indices: 914870--914925 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
914860 TTTAATATGT
* *
914870 ATATTCAATTTTTATTAATTTA
1 ATATTTAATTTTTAGTAATTTA
* * *
914892 AT-TTTTATTTTTAGTATTTTT
1 ATATTTAATTTTTAGTAATTTA
914913 ATATTTAATTTTT
1 ATATTTAATTTTT
914926 TAAATATTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (22 bp):
ATATTTAATTTTTAGTAATTTA
Found at i:916700 original size:21 final size:21
Alignment explanation
Indices: 916662--916701 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
916652 GGTCACTAGT
**
916662 ATAGTTTACCTTTTATTTTAA
1 ATAGTTTACCTTAAATTTTAA
*
916683 ATAGTTTATCTTAAATTTT
1 ATAGTTTACCTTAAATTTT
916702 TTAACTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
ATAGTTTACCTTAAATTTTAA
Found at i:917920 original size:3 final size:3
Alignment explanation
Indices: 917904--917941 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
917894 TATCTGCCTT
*
917904 TTA TTA TT- TT- TTA TTA TTA TTA TTA TCA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
917942 CAAACTAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:917999 original size:24 final size:24
Alignment explanation
Indices: 917972--918019 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
917962 GATCTTGCAG
*
917972 TAATTTTTATCAACTAATTATACC
1 TAATTTTTATCAACAAATTATACC
917996 TAATTTTTATCAACAAATTATACC
1 TAATTTTTATCAACAAATTATACC
918020 ATATTAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATTTTTATCAACAAATTATACC
Found at i:920523 original size:13 final size:13
Alignment explanation
Indices: 920497--920541 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
920487 ATATTCAATT
920497 TTTTTATTAATTTAA
1 TTTTTATT--TTTAA
*
920512 TTTTTATTTTTAG
1 TTTTTATTTTTAA
*
920525 TTTTTATATTTAA
1 TTTTTATTTTTAA
920538 TTTT
1 TTTT
920542 AAATATTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 19 0.70
15 8 0.30
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTTATTTTTAA
Found at i:923498 original size:3 final size:3
Alignment explanation
Indices: 923482--923519 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
923472 TTTATCTGCC
* *
923482 TAT TAT T-T TTT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
923520 CAAACTAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:923577 original size:24 final size:24
Alignment explanation
Indices: 923550--923597 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
923540 GATCTTGCAG
*
923550 TAATTTTTATCAACTAATTATACC
1 TAATTTTTATCAACAAATTATACC
923574 TAATTTTTATCAACAAATTATACC
1 TAATTTTTATCAACAAATTATACC
923598 ATATTAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATTTTTATCAACAAATTATACC
Found at i:929024 original size:214 final size:211
Alignment explanation
Indices: 928638--929065 Score: 804
Period size: 214 Copynumber: 2.0 Consensus size: 211
928628 ATCAGGTGTT
928638 GCCTCGACAACTCAGTGGACTTTAGGCCCAATAGGGTTTAAGGTGTTACTTTTAGTGATATCAGA
1 GCCTCGACAACTCAGTGGACTTTAGGCCCAATAGGGTTTAAGGTGTTACTTTTAGTGATATCAGA
928703 GCATTAGGTTGAGTCGGTCCTTGGACTAATGGTCATTTTTAGTAAAGTGTTAGTGAATACATGTC
66 GCATTAGGTTGAGTCGGTCCTTGGACTAATGGTCATTTTTAGTAAAGTGTTAGTGAATACATGTC
928768 GCTAGGTGCTCAATGTACTTGTATAAGTCTGGAATCCTGACCGTTCGATTACTTCGAATCTGACG
131 GCTAGGTGCTCAATGTACTTGTATAAGTCTGGAATCCTGACCGTTCGATTACTTCGAATCTGACG
928833 CG-TGACGTATGCAAG
196 CGATGACGTATGCAAG
928848 GCCTCGACAACTCAGTGGGACACTTTAGGCCCAATAGGGTTTAAGGTGTTACTTTTAGTGATATC
1 GCCTCGACAACTCAGT-GG--ACTTTAGGCCCAATAGGGTTTAAGGTGTTACTTTTAGTGATATC
928913 AGAGCATTAGGTTGAGTCGGTCCTTGGACCTAATGGTCATTTTTAGTAAAGTGTTAGTGAATACA
63 AGAGCATTAGGTTGAGTCGGTCCTTGGA-CTAATGGTCATTTTTAGTAAAGTGTTAGTGAATACA
928978 TGTCGCTAGGTGCTCAATGTACTTGTATAAGTCTGGAATCCTGACCGTTCGATTACTTCGAATCT
127 TGTCGCTAGGTGCTCAATGTACTTGTATAAGTCTGGAATCCTGACCGTTCGATTACTTCGAATCT
929043 GACGCGTATGACGTATGCAAG
192 GACGCG-ATGACGTATGCAAG
929064 GC
1 GC
929066 TACCCACGTT
Statistics
Matches: 212, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
210 16 0.08
211 2 0.01
213 72 0.34
214 107 0.50
216 15 0.07
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (211 bp):
GCCTCGACAACTCAGTGGACTTTAGGCCCAATAGGGTTTAAGGTGTTACTTTTAGTGATATCAGA
GCATTAGGTTGAGTCGGTCCTTGGACTAATGGTCATTTTTAGTAAAGTGTTAGTGAATACATGTC
GCTAGGTGCTCAATGTACTTGTATAAGTCTGGAATCCTGACCGTTCGATTACTTCGAATCTGACG
CGATGACGTATGCAAG
Found at i:933366 original size:2 final size:2
Alignment explanation
Indices: 933359--933392 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
933349 AGATCGCTTG
933359 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
933393 TAAAATACTC
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:934619 original size:25 final size:25
Alignment explanation
Indices: 934586--934633 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
934576 TTTATGTTGT
934586 GTTTATACATTTCTTAATAATTTGC
1 GTTTATACATTTCTTAATAATTTGC
*
934611 GTTTGTACATTTCTTAATAATTT
1 GTTTATACATTTCTTAATAATTT
934634 CATATTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.54
Consensus pattern (25 bp):
GTTTATACATTTCTTAATAATTTGC
Found at i:936456 original size:21 final size:23
Alignment explanation
Indices: 936430--936473 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
936420 AAATAAATAG
936430 AACTCATAAT-AAATAAT-TTTT
1 AACTCATAATAAAATAATATTTT
*
936451 AACTCATAGTAAAATAATATTTT
1 AACTCATAATAAAATAATATTTT
936474 TTTCTTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (23 bp):
AACTCATAATAAAATAATATTTT
Found at i:936509 original size:14 final size:14
Alignment explanation
Indices: 936490--936551 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
936480 TTAGGGTTAG
936490 GATTTAGGCTTTAA
1 GATTTAGGCTTTAA
* *
936504 GATTTAAGCTTTAG
1 GATTTAGGCTTTAA
936518 GATTTAAGG-TTTATA
1 GATTT-AGGCTTTA-A
* *
936533 -ATTTAGGTTTTGA
1 GATTTAGGCTTTAA
936546 GATTTA
1 GATTTA
936552 AGGTTTTGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
13 4 0.10
14 33 0.85
15 2 0.05
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (14 bp):
GATTTAGGCTTTAA
Found at i:936516 original size:21 final size:21
Alignment explanation
Indices: 936490--936572 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
936480 TTAGGGTTAG
*
936490 GATTTAGGCTTTAAGATTTAA
1 GATTTAGGATTTAAGATTTAA
* *
936511 GCTTTAGGATTTAAGGTTTATA
1 GATTTAGGATTTAAGATTTA-A
* *
936533 -ATTTAGGTTTTGAGATTTAA
1 GATTTAGGATTTAAGATTTAA
* * * *
936553 GGTTTTGGGTTTAAGTTTTA
1 GATTTAGGATTTAAGATTTA
936573 GGATAAGGTT
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.02
21 46 0.96
22 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.48
Consensus pattern (21 bp):
GATTTAGGATTTAAGATTTAA
Found at i:936530 original size:28 final size:28
Alignment explanation
Indices: 936486--936583 Score: 80
Period size: 28 Copynumber: 3.6 Consensus size: 28
936476 TCTTTTAGGG
936486 TTAGGATTT-AGGCTTTAAGATTTAAGCT
1 TTAGGATTTAAGG-TTTAAGATTTAAGCT
*
936514 TTAGGATTTAAGGTTTATA-ATTT-AGGT
1 TTAGGATTTAAGGTTTA-AGATTTAAGCT
* ** * *
936541 TTTGAGATTTAAGGTTTTGGGTTTAAGTT
1 TTAG-GATTTAAGGTTTAAGATTTAAGCT
936570 TTAGGA--TAAGGTTT
1 TTAGGATTTAAGGTTT
936584 TACGTTTGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
26 8 0.14
27 6 0.10
28 34 0.59
29 10 0.17
ACGTcount: A:0.27, C:0.02, G:0.24, T:0.47
Consensus pattern (28 bp):
TTAGGATTTAAGGTTTAAGATTTAAGCT
Found at i:936753 original size:2 final size:2
Alignment explanation
Indices: 936746--936786 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
936736 ATCCTACCCC
936746 AT AT 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 AT AT A
936787 GTTAGATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:938294 original size:29 final size:29
Alignment explanation
Indices: 938215--938294 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
938205 TACCTAACTA
* *
938215 AATTGATGTAAGAAATGACATATTCATCT
1 AATTGATGTAAGCAATGACATCTTCATCT
938244 AATTGATGTAAGCAATGACATCTTCATCT
1 AATTGATGTAAGCAATGACATCTTCATCT
938273 AATTGATGTAAGCAATGACATC
1 AATTGATGTAAGCAATGACATC
938295 AATTTAGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (29 bp):
AATTGATGTAAGCAATGACATCTTCATCT
Found at i:945633 original size:18 final size:19
Alignment explanation
Indices: 945598--945634 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
945588 CACGGAATGT
945598 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
945618 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
945635 TGATTACTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:945858 original size:37 final size:37
Alignment explanation
Indices: 945785--945859 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
945775 GTTGGAAAAT
* *
945785 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
945822 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAA
945859 A
1 A
945860 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:949383 original size:46 final size:41
Alignment explanation
Indices: 949292--949374 Score: 103
Period size: 41 Copynumber: 1.9 Consensus size: 41
949282 AGAGGAATGT
* *
949292 AATAAAAATAAAATTATTAGAAACTCAAAAAATGAAGGAAA
1 AATAAAAATAAAATTATTAGAAACTAAAAAAATGAAAGAAA
949333 AATAAAAATAAAATGTGATATAAGAAACTAAAAAAAATGAAA
1 AATAAAAATAAAAT-T-AT-T-AGAAACT-AAAAAAATGAAA
949375 TATCAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 14 0.40
42 1 0.03
43 2 0.06
44 1 0.03
45 7 0.20
46 10 0.29
ACGTcount: A:0.67, C:0.04, G:0.10, T:0.19
Consensus pattern (41 bp):
AATAAAAATAAAATTATTAGAAACTAAAAAAATGAAAGAAA
Found at i:949861 original size:32 final size:32
Alignment explanation
Indices: 949790--949864 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
949780 TTGAAATTTT
*
949790 AAATCCCCAAATTCCATTTCCCAATCAGAGCC
1 AAATCCCTAAATTCCATTTCCCAATCAGAGCC
949822 AAATCCCTAAATTCCATTTCCCAATCAGAGCC
1 AAATCCCTAAATTCCATTTCCCAATCAGAGCC
949854 AAATCCCTAAA
1 AAATCCCTAAA
949865 AACATCCCTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.37, C:0.35, G:0.05, T:0.23
Consensus pattern (32 bp):
AAATCCCTAAATTCCATTTCCCAATCAGAGCC
Found at i:951258 original size:28 final size:28
Alignment explanation
Indices: 951218--951272 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
951208 TACTCCCTTA
951218 GGTAAGCTCTAAGGCCCCAAGGTACTTG
1 GGTAAGCTCTAAGGCCCCAAGGTACTTG
* *
951246 GGTAGGCTCTAAGGCCTCAAGGTACTT
1 GGTAAGCTCTAAGGCCCCAAGGTACTT
951273 CCTTAGGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (28 bp):
GGTAAGCTCTAAGGCCCCAAGGTACTTG
Found at i:951279 original size:28 final size:28
Alignment explanation
Indices: 951223--951279 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
951213 CCTTAGGTAA
**
951223 GCTCTAAGGCCCCAAGGTACTTGGGTAG
1 GCTCTAAGGCCCCAAGGTACTTCCGTAG
* *
951251 GCTCTAAGGCCTCAAGGTACTTCCTTAG
1 GCTCTAAGGCCCCAAGGTACTTCCGTAG
951279 G
1 G
951280 TGGCCCCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (28 bp):
GCTCTAAGGCCCCAAGGTACTTCCGTAG
Found at i:951825 original size:3 final size:3
Alignment explanation
Indices: 951764--951807 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
951754 TATTTGGGTT
951764 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
951808 TTAAAAGATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:954461 original size:6 final size:6
Alignment explanation
Indices: 954450--954510 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
954440 GACACGTATT
* * *
954450 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
954498 ACCACG ACCACG A
1 ACCACG ACCACG A
954511 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:954518 original size:5 final size:5
Alignment explanation
Indices: 954508--954556 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
954498 ACCACGACCA
* * * *
954508 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
954557 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:960395 original size:6 final size:6
Alignment explanation
Indices: 960384--960486 Score: 197
Period size: 6 Copynumber: 17.2 Consensus size: 6
960374 GACACGTATT
960384 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
960432 ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
960480 ACCACG A
1 ACCACG A
960487 GCCGAGCCGA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 95 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.01
Consensus pattern (6 bp):
ACCACG
Found at i:960494 original size:5 final size:5
Alignment explanation
Indices: 960484--960552 Score: 102
Period size: 5 Copynumber: 13.8 Consensus size: 5
960474 ACCACGACCA
* *
960484 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
* *
960534 CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAG
960553 ACGGACGGAC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 61 1.00
ACGTcount: A:0.17, C:0.38, G:0.41, T:0.04
Consensus pattern (5 bp):
CGAGC
Found at i:975798 original size:2 final size:2
Alignment explanation
Indices: 975793--975845 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
975783 TACGTGTGTG
975793 TA TA TA TA TA TA TA TA 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
975835 TA TA TA TA TA T
1 TA TA TA TA TA T
975846 GTTCGTTTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:977571 original size:30 final size:31
Alignment explanation
Indices: 977524--977582 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
977514 TAAGAAAAAG
*
977524 TCTAAATTTTAAAGATTAAA-TAGATATTTGA
1 TCTAAAATTTAAAGATTAAACTA-ATATTTGA
977555 TCTAAAATTT-AAGATTAAACTAATATTT
1 TCTAAAATTTAAAGATTAAACTAATATTT
977583 TACATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (31 bp):
TCTAAAATTTAAAGATTAAACTAATATTTGA
Found at i:977831 original size:13 final size:13
Alignment explanation
Indices: 977813--977838 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
977803 TAATTTGTTT
977813 ATTAATGTCATTG
1 ATTAATGTCATTG
977826 ATTAATGTCATTG
1 ATTAATGTCATTG
977839 TTTTATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTAATGTCATTG
Found at i:979229 original size:2 final size:2
Alignment explanation
Indices: 979222--979260 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
979212 AAGCACCATC
979222 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
979261 GGTTCATGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:985274 original size:20 final size:20
Alignment explanation
Indices: 985249--985296 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 20
985239 TATCTAAAAC
985249 ATTAAAAATCATT-ATTATAA
1 ATTAAAAATCATTCA-TATAA
985269 ATT-AAAATCATTCATATAA
1 ATTAAAAATCATTCATATAA
985288 ATATAAAAA
1 AT-TAAAAA
985297 AATTCTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 16 0.64
20 5 0.20
21 4 0.16
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTAAAAATCATTCATATAA
Found at i:991418 original size:111 final size:104
Alignment explanation
Indices: 991268--991579 Score: 314
Period size: 111 Copynumber: 2.9 Consensus size: 104
991258 TGACGAGGTT
*
991268 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAA-AATCTTCATAAAATGTGTCCGCTC-CTA
991331 TTCATTCAGAGAGTATAAAACTTGAACAATCTTCAATAAAACGGGTCC
62 TTCATTCAGAGAGTATAAAAC-T---CAATCTTCAA-AAAACGGGTCC
* *
991379 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAAAATCTTCAATAAACA--AGTCCGCTCCCTA
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC-GAAAATCTTC-ATAAA-ATGTGTCCGCT-CCTA
* ** * * *
991442 TTCTTTCAGAGAGTATAGGACTCAATCTTTAACAAACGTGTCC
62 TTCATTCAGAGAGTATAAAACTCAATCTTCAAAAAACGGGTCC
*
991485 GCTCCCTATTCCTTCAGAGAGTATAGGACTCG---ATCTTCATAAAATGTGTCCGCTCCGTATTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAAATCTTCATAAAATGTGTCCGCTCC-TATTC
* ** * *
991547 CTTCAGAGAGTATAGGACTCGATCTTCATAAAA
65 ATTCAGAGAGTATAAAACTCAATCTTCAAAAAA
991580 TGAGTTTGCT
Statistics
Matches: 175, Mismatches: 17, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
100 1 0.01
101 7 0.04
102 46 0.26
105 1 0.01
106 38 0.22
107 9 0.05
110 1 0.01
111 60 0.34
112 11 0.06
113 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (104 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAAATCTTCATAAAATGTGTCCGCTCCTATTCA
TTCAGAGAGTATAAAACTCAATCTTCAAAAAACGGGTCC
Found at i:991580 original size:51 final size:51
Alignment explanation
Indices: 991268--991581 Score: 294
Period size: 51 Copynumber: 5.9 Consensus size: 51
991258 TGACGAGGTT
* *
991268 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAATGTGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAGGACTCG----ATCTTCATAAAATGTGTCC
* * ** * * *
991323 GCTCTCTATTCATTCAGAGAGTATAAAACTTGAACAATCTTCAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGAC-T---CGATCTTC-ATAAAATGTGTCC
* * *
991379 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAAAATCTTCAATAAACA--AGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTC-G---ATCTTC-ATAAA-ATGTGTCC
* * * *
991434 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTTA-ACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCATA-AAATGTGTCC
991485 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCATAAAATGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCATAAAATGTGTCC
*
991536 GCTCCGTATTCCTTCAGAGAGTATAGGACTCGATCTTCATAAAATG
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCATAAAATG
991582 AGTTTGCTTC
Statistics
Matches: 222, Mismatches: 22, Indels: 34
0.80 0.08 0.12
Matches are distributed among these distances:
49 2 0.01
50 3 0.01
51 99 0.45
52 2 0.01
55 63 0.28
56 51 0.23
57 1 0.00
59 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCATAAAATGTGTCC
Found at i:991624 original size:37 final size:36
Alignment explanation
Indices: 991583--991654 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
991573 CATAAAATGA
991583 GTTTGCTTCACTAATCTTCCGTGAAGGCTTACAGATG
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTA-AGATG
* *
991620 GTTTGCTTCACTACTCTTCCGTGAAGGTTTAAGAT
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGAT
991655 TGACTTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (36 bp):
GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGATG
Found at i:992936 original size:10 final size:9
Alignment explanation
Indices: 992913--993007 Score: 55
Period size: 9 Copynumber: 11.3 Consensus size: 9
992903 TTGAACCCTC
992913 CTTTTTCTT
1 CTTTTTCTT
*
992922 CTTTTTTTT
1 CTTTTTCTT
992931 CATTTTTC-T
1 C-TTTTTCTT
992940 CTTTTT-TT
1 CTTTTTCTT
992948 C-TTTTCGTT
1 CTTTTTC-TT
* *
992957 -TTTTCCAT
1 CTTTTTCTT
*
992965 C-ATTT-TT
1 CTTTTTCTT
*
992972 CTTTTTCCT
1 CTTTTTCTT
*
992981 C-ATTT-TT
1 CTTTTTCTT
992988 C-TTTTCTT
1 CTTTTTCTT
992996 CTTTTTCTT
1 CTTTTTCTT
993005 CTT
1 CTT
993008 CTCATTTTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
7 11 0.17
8 19 0.30
9 29 0.45
10 5 0.08
ACGTcount: A:0.04, C:0.21, G:0.01, T:0.74
Consensus pattern (9 bp):
CTTTTTCTT
Found at i:992992 original size:15 final size:15
Alignment explanation
Indices: 992957--993016 Score: 70
Period size: 15 Copynumber: 3.9 Consensus size: 15
992947 TCTTTTCGTT
992957 TTTTCCATCATTTTTC
1 TTTTCC-TCATTTTTC
992973 TTTTTCCTCATTTTTC
1 -TTTTCCTCATTTTTC
*
992989 TTTTCTTC-TTTTTC
1 TTTTCCTCATTTTTC
993003 TTCTT-CTCATTTTT
1 TT-TTCCTCATTTTT
993017 ATTATTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.26
15 14 0.36
16 9 0.23
17 6 0.15
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCCTCATTTTTC
Found at i:993001 original size:30 final size:29
Alignment explanation
Indices: 992967--993060 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 29
992957 TTTTCCATCA
992967 TTTTTCTTTTTCCTCATTTTTCTTTTCTTC
1 TTTTTCTTTTT-CTCATTTTTCTTTTCTTC
* * *
992997 TTTTTCTTCTTCTCATTTTTATTATTATT-
1 TTTTTCTTTTTCTCATTTTTCTT-TTCTTC
*
993026 TTTTTCATTTTTTTCATTTTTTCATTTTC-TC
1 TTTTTC-TTTTTCTCA-TTTTTC-TTTTCTTC
993057 TTTT
1 TTTT
993061 ATTTCTTCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
29 17 0.33
30 22 0.42
31 11 0.21
32 2 0.04
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (29 bp):
TTTTTCTTTTTCTCATTTTTCTTTTCTTC
Found at i:993037 original size:9 final size:9
Alignment explanation
Indices: 993023--993053 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
993013 TTTTATTATT
993023 ATTTTTTTC
1 ATTTTTTTC
993032 ATTTTTTTC
1 ATTTTTTTC
993041 A-TTTTTTC
1 ATTTTTTTC
993049 ATTTT
1 ATTTT
993054 CTCTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (9 bp):
ATTTTTTTC
Found at i:993053 original size:15 final size:14
Alignment explanation
Indices: 992964--993046 Score: 55
Period size: 16 Copynumber: 5.6 Consensus size: 14
992954 GTTTTTTCCA
992964 TCATTTTTCTTTTT
1 TCATTTTTCTTTTT
992978 CCTCATTTTTCTTTTCT
1 --TCATTTTTCTTTT-T
*
992995 TC-TTTTTCTTCTTC
1 TCATTTTTCTT-TTT
*
993009 TCATTTTTATTATTAT
1 TCATTTTTCTT-TT-T
993025 T--TTTTTCATTTTTT
1 TCATTTTTC--TTTTT
993039 TCATTTTT
1 TCATTTTT
993047 TCATTTTCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
14 17 0.31
15 15 0.28
16 21 0.39
17 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (14 bp):
TCATTTTTCTTTTT
Found at i:993060 original size:15 final size:15
Alignment explanation
Indices: 992967--993060 Score: 54
Period size: 15 Copynumber: 6.2 Consensus size: 15
992957 TTTTCCATCA
* *
992967 TTTTTCTTTTTCCTCA
1 TTTTTCATTTT-CTCT
992983 TTTTTC-TTTTCT-T
1 TTTTTCATTTTCTCT
*
992996 CTTTTTC-TTCTTCTCA
1 -TTTTTCATT-TTCTCT
*
993012 TTTTT-ATTATTAT-T
1 TTTTTCATT-TTCTCT
*
993026 TTTTTCATTTTTTTCAT
1 TTTTTCA-TTTTCTC-T
993043 TTTTTCATTTTCTCT
1 TTTTTCATTTTCTCT
993058 TTT
1 TTT
993061 ATTTCTTCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
14 15 0.24
15 26 0.41
16 14 0.22
17 8 0.13
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTCATTTTCTCT
Found at i:999562 original size:45 final size:46
Alignment explanation
Indices: 999502--999592 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
999492 CACAAAAAGA
* *
999502 AAACCTAACCGCATGATATCTAATTCGCATGC-TTGTTCGAAAAAT
1 AAACCTAACCACATGATATCTAATTCGCATGCATTATTCGAAAAAT
*
999547 AAACCTAACCACATGATATCTAGTTCGCATGCATTTATTCGAAAAA
1 AAACCTAACCACATGATATCTAATTCGCATGCA-TTATTCGAAAAA
999593 AACGAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 30 0.73
47 11 0.27
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (46 bp):
AAACCTAACCACATGATATCTAATTCGCATGCATTATTCGAAAAAT
Found at i:1001242 original size:2 final size:2
Alignment explanation
Indices: 1001235--1001280 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1001225 AAACTTTAAA
1001235 AT AT AT AT 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 AT AT AT AT
1001277 AT AT
1 AT AT
1001281 TAAAGTAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1022293 original size:20 final size:21
Alignment explanation
Indices: 1022249--1022302 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1022239 TTTTAAGGGT
* *
1022249 AGTATCGATACTCAATCATAG
1 AGTATCGATACTCAAGCAAAG
*
1022270 AGTATCGATAC-CAAGGAAAG
1 AGTATCGATACTCAAGCAAAG
1022290 AGTATCGATACTC
1 AGTATCGATACTC
1022303 CCCATAGGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTATCGATACTCAAGCAAAG
Found at i:1024349 original size:10 final size:11
Alignment explanation
Indices: 1024324--1024352 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1024314 AATTCTTTAA
1024324 AAATAAAAGAG
1 AAATAAAAGAG
1024335 AAATAAAAG-G
1 AAATAAAAGAG
1024345 AAATAAAA
1 AAATAAAA
1024353 TACTCTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (11 bp):
AAATAAAAGAG
Found at i:1026167 original size:26 final size:27
Alignment explanation
Indices: 1026138--1026192 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1026128 ACCGAATCAA
* * *
1026138 AAAAATGAAGCATTT-AAATCGAACCG
1 AAAAACGAACCATTTAAAACCGAACCG
*
1026164 AAAACCGAACCATTTAAAACCGAACCG
1 AAAAACGAACCATTTAAAACCGAACCG
1026191 AA
1 AA
1026193 CGAACCGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.51, C:0.22, G:0.13, T:0.15
Consensus pattern (27 bp):
AAAAACGAACCATTTAAAACCGAACCG
Found at i:1029200 original size:20 final size:20
Alignment explanation
Indices: 1029175--1029214 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1029165 TCGTTCACTC
1029175 TGATATACTAGGGAAGGTAT
1 TGATATACTAGGGAAGGTAT
1029195 TGATATACTAGGGAAGGTAT
1 TGATATACTAGGGAAGGTAT
1029215 AAGGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.30
Consensus pattern (20 bp):
TGATATACTAGGGAAGGTAT
Found at i:1035027 original size:39 final size:38
Alignment explanation
Indices: 1034954--1035027 Score: 94
Period size: 39 Copynumber: 1.9 Consensus size: 38
1034944 ACCTAATGTT
* *
1034954 AAATTTTGAACAGGGGCATTAAAATGAAACAAAAATTG
1 AAATTTTGAACAGGGGCACTAAAATAAAACAAAAATTG
* * *
1034992 AAATTTTTAACAGTGGGTACTAAAATAAAATAAAAA
1 AAATTTTGAACAG-GGGCACTAAAATAAAACAAAAA
1035028 CTAAACTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 12 0.40
39 18 0.60
ACGTcount: A:0.53, C:0.07, G:0.15, T:0.26
Consensus pattern (38 bp):
AAATTTTGAACAGGGGCACTAAAATAAAACAAAAATTG
Found at i:1040185 original size:42 final size:42
Alignment explanation
Indices: 1040094--1040364 Score: 302
Period size: 42 Copynumber: 6.6 Consensus size: 42
1040084 TCCTTCTTCT
* * * *
1040094 CGCCTCCTTCCTTTTTTTCACCGCCGCCTTCCTTCTTCT---
1 CGCCTCCTTCCTTCTTCTCGCCGCCGCCTTCCTTTTTCTCAC
* * * * * * *
1040133 CGCCTCCTTCCTTTTTATCACCTCCGGCTTCCTTCTTCTCGC
1 CGCCTCCTTCCTTCTTCTCGCCGCCGCCTTCCTTTTTCTCAC
* * *
1040175 CGCCGCCTTCCTTCTTCT---CGCCTCCTTCCTTTTTATCAC
1 CGCCTCCTTCCTTCTTCTCGCCGCCGCCTTCCTTTTTCTCAC
* ** *
1040214 CTCCGGCTTCCTTCTTCTCGCCGCCGCCTTCCTTTTTCTCGC
1 CGCCTCCTTCCTTCTTCTCGCCGCCGCCTTCCTTTTTCTCAC
* *
1040256 CGCCTCCTTCCTTTTTCTCGCCGCCTCCTTCCTTTTTCTCAC
1 CGCCTCCTTCCTTCTTCTCGCCGCCGCCTTCCTTTTTCTCAC
* *
1040298 CGCCGCCTTCCTTCTTCTCGCCGCCGCCTTCCTTTTTTTCAC
1 CGCCTCCTTCCTTCTTCTCGCCGCCGCCTTCCTTTTTCTCAC
1040340 CGCCTCCTTCCTTCTTCTCGCCGCC
1 CGCCTCCTTCCTTCTTCTCGCCGCC
1040365 TGCAGCAACT
Statistics
Matches: 198, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
39 67 0.34
42 131 0.66
ACGTcount: A:0.03, C:0.48, G:0.10, T:0.40
Consensus pattern (42 bp):
CGCCTCCTTCCTTCTTCTCGCCGCCGCCTTCCTTTTTCTCAC
Found at i:1040185 original size:60 final size:61
Alignment explanation
Indices: 1040094--1040364 Score: 339
Period size: 63 Copynumber: 4.4 Consensus size: 61
1040084 TCCTTCTTCT
* * * *
1040094 CGCCTCCTTCCTTTTTTTCACCGCCGCCTTCCTTCTTCT-CGCCTCCTTCCTTTTTATCAC
1 CGCCGCCTTCCTTCTTCTCGCCGCCGCCTTCCTTCTTCTCCGCCTCCTTCCTTTTTATCAC
* *
1040154 CTCCGGCTTCCTTCTTCTCGCCGCCGCCTTCCTTCTTCT-CGCCTCCTTCCTTTTTATCAC
1 CGCCGCCTTCCTTCTTCTCGCCGCCGCCTTCCTTCTTCTCCGCCTCCTTCCTTTTTATCAC
* * * * *
1040214 CTCCGGCTTCCTTCTTCTCGCCGCCGCCTTCCTTTTTCTCGCCGCCTCCTTCCTTTTTCTCGC
1 CGCCGCCTTCCTTCTTCTCGCCGCCGCCTTCCTTCTTCT--CCGCCTCCTTCCTTTTTATCAC
* * * * *
1040277 CGCCTCCTTCCTTTTTCTCACCGCCGCCTTCCTTCTTCTCGCCGCCGCCTTCCTTTTTTTCAC
1 CGCCGCCTTCCTTCTTCTCGCCGCCGCCTTCCTTCTTCT--CCGCCTCCTTCCTTTTTATCAC
*
1040340 CGCCTCCTTCCTTCTTCTCGCCGCC
1 CGCCGCCTTCCTTCTTCTCGCCGCC
1040365 TGCAGCAACT
Statistics
Matches: 188, Mismatches: 20, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
60 92 0.49
63 96 0.51
ACGTcount: A:0.03, C:0.48, G:0.10, T:0.40
Consensus pattern (61 bp):
CGCCGCCTTCCTTCTTCTCGCCGCCGCCTTCCTTCTTCTCCGCCTCCTTCCTTTTTATCAC
Found at i:1040365 original size:21 final size:21
Alignment explanation
Indices: 1040082--1040364 Score: 269
Period size: 21 Copynumber: 13.9 Consensus size: 21
1040072 CGTCCGTCGT
*
1040082 CTTCCTTCTTCT---CGCCTC
1 CTTCCTTCTTCTCGCCGCCGC
* * *
1040100 CTTCCTTTTTTTCACCGCCGC
1 CTTCCTTCTTCTCGCCGCCGC
*
1040121 CTTCCTTCTTCT---CGCCTC
1 CTTCCTTCTTCTCGCCGCCGC
* * * * *
1040139 CTTCCTTTTTATCACCTCCGG
1 CTTCCTTCTTCTCGCCGCCGC
1040160 CTTCCTTCTTCTCGCCGCCGC
1 CTTCCTTCTTCTCGCCGCCGC
*
1040181 CTTCCTTCTTCT---CGCCTC
1 CTTCCTTCTTCTCGCCGCCGC
* * * * *
1040199 CTTCCTTTTTATCACCTCCGG
1 CTTCCTTCTTCTCGCCGCCGC
1040220 CTTCCTTCTTCTCGCCGCCGC
1 CTTCCTTCTTCTCGCCGCCGC
* *
1040241 CTTCCTTTTTCTCGCCGCCTC
1 CTTCCTTCTTCTCGCCGCCGC
* *
1040262 CTTCCTTTTTCTCGCCGCCTC
1 CTTCCTTCTTCTCGCCGCCGC
* *
1040283 CTTCCTTTTTCTCACCGCCGC
1 CTTCCTTCTTCTCGCCGCCGC
1040304 CTTCCTTCTTCTCGCCGCCGC
1 CTTCCTTCTTCTCGCCGCCGC
* * * *
1040325 CTTCCTTTTTTTCACCGCCTC
1 CTTCCTTCTTCTCGCCGCCGC
1040346 CTTCCTTCTTCTCGCCGCC
1 CTTCCTTCTTCTCGCCGCC
1040365 TGCAGCAACT
Statistics
Matches: 216, Mismatches: 40, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
18 40 0.19
21 176 0.81
ACGTcount: A:0.02, C:0.47, G:0.10, T:0.41
Consensus pattern (21 bp):
CTTCCTTCTTCTCGCCGCCGC
Found at i:1040420 original size:21 final size:21
Alignment explanation
Indices: 1040387--1040436 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1040377 TTTCACCTCC
* *
1040387 TCTTTTTTGTCACCGCCGGCG
1 TCTTTCTTCTCACCGCCGGCG
* *
1040408 TCTTTCTTCTCACCGGCGTCG
1 TCTTTCTTCTCACCGCCGGCG
1040429 TCTTTCTT
1 TCTTTCTT
1040437 AGGAGGGACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.04, C:0.34, G:0.18, T:0.44
Consensus pattern (21 bp):
TCTTTCTTCTCACCGCCGGCG
Found at i:1041786 original size:16 final size:16
Alignment explanation
Indices: 1041765--1041795 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1041755 GAGGCGGTTT
1041765 ATGTATGTACGTATGC
1 ATGTATGTACGTATGC
*
1041781 ATGTATGTATGTATG
1 ATGTATGTACGTATG
1041796 ATGGTGATGA
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:0.26, C:0.06, G:0.26, T:0.42
Consensus pattern (16 bp):
ATGTATGTACGTATGC
Found at i:1046416 original size:21 final size:21
Alignment explanation
Indices: 1046392--1046450 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1046382 CAAAACAGAG
1046392 AAGGGATCGATCTTTT-TCTCC
1 AAGGGATCGATCTTTTCTC-CC
*
1046413 AAGGGATCGATCCTTTCTCCC
1 AAGGGATCGATCTTTTCTCCC
*
1046434 GAGGGATCGATCCTTTT
1 AAGGGATCGAT-CTTTT
1046451 AAAAAGTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 27 0.82
22 6 0.18
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (21 bp):
AAGGGATCGATCTTTTCTCCC
Found at i:1048658 original size:16 final size:16
Alignment explanation
Indices: 1048634--1048672 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1048624 CACAACATAT
*
1048634 GACACCAGTGACACAC
1 GACATCAGTGACACAC
1048650 GACATCAGTGACACAC
1 GACATCAGTGACACAC
*
1048666 AACATCA
1 GACATCA
1048673 TTCGATTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.33, G:0.15, T:0.10
Consensus pattern (16 bp):
GACATCAGTGACACAC
Found at i:1050284 original size:15 final size:16
Alignment explanation
Indices: 1050264--1050297 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1050254 ATTTATCATT
1050264 ATTATTT-AATATAAA
1 ATTATTTAAATATAAA
1050279 ATTATTTAAAATATAAA
1 ATTATTT-AAATATAAA
1050296 AT
1 AT
1050298 AAAAATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTATTTAAATATAAA
Found at i:1055290 original size:2 final size:2
Alignment explanation
Indices: 1055283--1055314 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1055273 TCAAATACAA
1055283 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
1055315 TCAGAACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1063044 original size:39 final size:39
Alignment explanation
Indices: 1063000--1063102 Score: 131
Period size: 39 Copynumber: 2.6 Consensus size: 39
1062990 TTTAAAAAAA
1063000 TTAGAATGTTAATGTGAAATAATTTAAGAAATTAAGAAT
1 TTAGAATGTTAATGTGAAATAATTTAAGAAATTAAGAAT
* *
1063039 TTAGAATGTT-ATGGTGGTAA-AATTTAAGAAATTAGGAAT
1 TTAGAATGTTAAT-GT-GAAATAATTTAAGAAATTAAGAAT
*
1063078 TTAGAATGTTAGA-GCGAAATAATTT
1 TTAGAATGTTA-ATGTGAAATAATTT
1063103 GAGATTTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
38 5 0.09
39 46 0.84
40 3 0.05
41 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.19, T:0.36
Consensus pattern (39 bp):
TTAGAATGTTAATGTGAAATAATTTAAGAAATTAAGAAT
Found at i:1064461 original size:2 final size:2
Alignment explanation
Indices: 1064454--1064482 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1064444 AATACCCCTC
1064454 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 T
1064483 TTCAATTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1064954 original size:2 final size:2
Alignment explanation
Indices: 1064949--1064975 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1064939 AAAAAAAAAA
1064949 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
1064976 ATCAAGGTAA
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
Done.