Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008591.1 Hibiscus syriacus cultivar Beakdansim tig00111540_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: 1730314
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:879221 original size:29 final size:29
Alignment explanation
Indices: 879179--879237 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
879169 ATTTTCACCT
879179 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
879208 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
879237 A
1 A
879238 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:883932 original size:29 final size:29
Alignment explanation
Indices: 883856--883914 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
883846 ATTTTCACCT
*
883856 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
883885 AACTAAATTGATGTAAACAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
883914 A
1 A
883915 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAACAATGACATCAA
Found at i:884970 original size:19 final size:19
Alignment explanation
Indices: 884937--884980 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
884927 AGGTTTTTTG
*
884937 TTTTTTTAATTATAATATTAA
1 TTTTTTTAA-TATAA-AATAA
884958 TTTTTTTAA-ATAAAATAA
1 TTTTTTTAATATAAAATAA
884976 TTTTT
1 TTTTT
884981 GAAATTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 4 0.18
21 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTTTAATATAAAATAA
Found at i:886248 original size:215 final size:214
Alignment explanation
Indices: 885877--886306 Score: 851
Period size: 215 Copynumber: 2.0 Consensus size: 214
885867 ACCACTTACG
885877 CTACACTTCCTTGCAGCCATCCTTTCTGCAGCGGCGAGCAAAGACACTACAATTGTGTCAACGAC
1 CTACACTTCCTTGCAGCCATCCTTTCTGCAGCGGCGAGCAAAGACACTACAATTGTGTCAACGAC
885942 GTATGTGTCTACGATGTTACATACGGAGGCGGATCGTCTACCCAAGGCGTCGCGTCGTTGGAGAC
66 GTATGTGTCTACGATGTTACATACGGAGGCGGATCGTCTACCCAAGGCGTCGCGTCGTTGGAGAC
886007 GTTCGACTTCTTCGTCAACCAACAAATGCATGCTTTCCCCCAATGTCCTCTTCGGCTGCTCCGAC
131 GTTCGACTTCTTCGTCAACCAACAAATGCATGCTTT-CCCCAATGTCCTCTTCGGCTGCTCCGAC
886072 GCCAGTAGTGACATTAGCTT
195 GCCAGTAGTGACATTAGCTT
886092 CTACACTTCCTTGCAGCCATCCTTTCTGCAGCGGCGAGCAAAGACACTACAATTGTGTCAACGAC
1 CTACACTTCCTTGCAGCCATCCTTTCTGCAGCGGCGAGCAAAGACACTACAATTGTGTCAACGAC
886157 GTATGTGTCTACGATGTTACATACGGAGGCGGATCGTCTACCCAAGGCGTCGCGTCGTTGGAGAC
66 GTATGTGTCTACGATGTTACATACGGAGGCGGATCGTCTACCCAAGGCGTCGCGTCGTTGGAGAC
886222 GTTCGACTTCTTCGTCAACCAACAAATGCATGCTTTCCCCAATGTCCTCTTCGGCTGCTCCGACG
131 GTTCGACTTCTTCGTCAACCAACAAATGCATGCTTTCCCCAATGTCCTCTTCGGCTGCTCCGACG
886287 CCAGTAGTGACATTAGCTT
196 CCAGTAGTGACATTAGCTT
886306 C
1 C
886307 GAGAACAGCG
Statistics
Matches: 215, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
214 49 0.23
215 166 0.77
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (214 bp):
CTACACTTCCTTGCAGCCATCCTTTCTGCAGCGGCGAGCAAAGACACTACAATTGTGTCAACGAC
GTATGTGTCTACGATGTTACATACGGAGGCGGATCGTCTACCCAAGGCGTCGCGTCGTTGGAGAC
GTTCGACTTCTTCGTCAACCAACAAATGCATGCTTTCCCCAATGTCCTCTTCGGCTGCTCCGACG
CCAGTAGTGACATTAGCTT
Found at i:892684 original size:9 final size:9
Alignment explanation
Indices: 892670--892699 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
892660 TTTAAAATTA
892670 TTATATATT
1 TTATATATT
892679 TTATATATTT
1 TTATATA-TT
892689 TTATATATT
1 TTATATATT
892698 TT
1 TT
892700 CTATTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTATATATT
Found at i:893857 original size:20 final size:20
Alignment explanation
Indices: 893821--893860 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
893811 TTGTAATATT
*
893821 TAAAAACTTTAGATTTTTTA
1 TAAAAACTTAAGATTTTTTA
893841 TAAATAACTTAAG-TTTTTTA
1 TAAA-AACTTAAGATTTTTTA
893861 AATCTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
TAAAAACTTAAGATTTTTTA
Found at i:895865 original size:31 final size:31
Alignment explanation
Indices: 895825--895915 Score: 137
Period size: 31 Copynumber: 2.9 Consensus size: 31
895815 AAGAGTCGAG
*
895825 GGTTACCTATGTCTTTCGAGACATATGGACA
1 GGTTACCTATGTCTTTCGGGACATATGGACA
* *
895856 GTTTACCTATGTCTTTCGGGACATATAGACA
1 GGTTACCTATGTCTTTCGGGACATATGGACA
* *
895887 GGTTACCTATGTCATTCGGGACAGATGGA
1 GGTTACCTATGTCTTTCGGGACATATGGA
895916 TAGTGGTCCT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (31 bp):
GGTTACCTATGTCTTTCGGGACATATGGACA
Found at i:896109 original size:5 final size:5
Alignment explanation
Indices: 896101--896144 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
896091 GTTTGTTTGG
* * * *
896101 TGATA TGATA TGACA TGACA TGACA TGACA TGATA TGATA TGAT
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGAT
896145 GTGCATGAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (5 bp):
TGATA
Found at i:896128 original size:15 final size:15
Alignment explanation
Indices: 896105--896143 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
896095 GTTTGGTGAT
896105 ATGATATGACATGAC
1 ATGATATGACATGAC
* *
896120 ATGACATGACATGAT
1 ATGATATGACATGAC
896135 ATGATATGA
1 ATGATATGA
896144 TGTGCATGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (15 bp):
ATGATATGACATGAC
Found at i:898924 original size:3 final size:3
Alignment explanation
Indices: 898916--898988 Score: 87
Period size: 3 Copynumber: 24.7 Consensus size: 3
898906 CTCGAAAACA
* * * *
898916 TAT TAT TAT AAT AAT AAT TAT TAT AAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
898963 TAT TAT TAAT TAT TAT TAT TA- TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TA
898989 ACATATATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
2 4 0.06
3 56 0.89
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:898952 original size:30 final size:30
Alignment explanation
Indices: 898916--898985 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
898906 CTCGAAAACA
898916 TATTATTATAATAATAATTATTA-TAATTAT
1 TATTATTATAAT-ATAATTATTATTAATTAT
* *
898946 TATTATTATTATATTATTATTATTAATTAT
1 TATTATTATAATATAATTATTATTAATTAT
898976 TATTATTATA
1 TATTATTATA
898986 TTAACATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 9 0.25
30 27 0.75
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TATTATTATAATATAATTATTATTAATTAT
Found at i:902315 original size:32 final size:32
Alignment explanation
Indices: 902256--902317 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
902246 TCTTACCTAT
* *
902256 ACTAACTAATTTCTTTTTTTTTCTTTGTGTGC
1 ACTAACTAATTTATTTTCTTTTCTTTGTGTGC
* *
902288 ACTAACTTATTTATTTTCTTTTGTTTGTGT
1 ACTAACTAATTTATTTTCTTTTCTTTGTGT
902318 TTTTTTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.16, C:0.13, G:0.10, T:0.61
Consensus pattern (32 bp):
ACTAACTAATTTATTTTCTTTTCTTTGTGTGC
Found at i:902840 original size:12 final size:13
Alignment explanation
Indices: 902823--902855 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
902813 TCAATATTTC
902823 TGCATTTGCAT-T
1 TGCATTTGCATAT
902835 TGCATTTGCATCAT
1 TGCATTTGCAT-AT
902849 TGCATTT
1 TGCATTT
902856 TGCACAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
14 8 0.42
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (13 bp):
TGCATTTGCATAT
Found at i:906322 original size:104 final size:103
Alignment explanation
Indices: 906067--906389 Score: 413
Period size: 101 Copynumber: 3.2 Consensus size: 103
906057 ACAAATTTCA
* * * *
906067 TCGCTTGAGACA--TTTTTCCTTTGAGATACAAATTTGAATTTGTTTCACTTGAAACAAAATAAT
1 TCGCTTGAGACATTTTTTTCCTTTGAGAAACAATTTTGAATTTGCTTCACTTGAAAC-AAATTAT
* * * *
906130 CTCACTTGAGATTGTTATTTC-TCAAAAAAAACTTCGTC
65 CTCACTTGAGATTGTTGTTTCTTTAAAAACAATTTCGTC
* * *
906168 TCGCTTGAGACA-TTTTTTCCTTTGATACA-AATTTTGAATTTGCTTCACTTGAAATAAATTATT
1 TCGCTTGAGACATTTTTTTCCTTTGAGAAACAATTTTGAATTTGCTTCACTTGAAACAAATTA-T
* * *
906231 CTCATTTGAGATTGTTGTTTCTTTTAAAACAATTTCATC
65 CTCACTTGAGATTGTTGTTTCTTTAAAAACAATTTCGTC
* *
906270 TCGCTTGGGTCATTTTTTTCCTTTGAGAAACAATTTTGAATTTGCTTCACTTGAAACAAATTATC
1 TCGCTTGAGACATTTTTTTCCTTTGAGAAACAATTTTGAATTTGCTTCACTTGAAACAAATTATC
* *
906335 TCACTTGAGATTGTTGTTTATTTCAAAACAAATTTCGTC
66 TCACTTGAGATTGTTGTTTCTTTAAAAAC-AATTTCGTC
*
906374 TCACTTGAGACATTTT
1 TCGCTTGAGACATTTT
906390 CCCTCAGAAT
Statistics
Matches: 191, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
100 5 0.03
101 55 0.29
102 36 0.19
103 43 0.23
104 52 0.27
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (103 bp):
TCGCTTGAGACATTTTTTTCCTTTGAGAAACAATTTTGAATTTGCTTCACTTGAAACAAATTATC
TCACTTGAGATTGTTGTTTCTTTAAAAACAATTTCGTC
Found at i:906363 original size:103 final size:103
Alignment explanation
Indices: 906046--906389 Score: 441
Period size: 103 Copynumber: 3.4 Consensus size: 103
906036 CTTAAGACAA
* *
906046 TTTATTTCAAAACAAATTTCA--TCGCTTGAGACA-TTTTTCCTTTGAGATACAAATTTGAATTT
1 TTTATTTCAAAACAAATTTCATCTCGCTTGAGACATTTTTTCCTTTGAGAAACAATTTTGAATTT
* *
906108 GTTTCACTTGAAACAAAATAATCTCACTTGAGATTGTT-
66 GCTTCACTTGAAAC-AAATTATCTCACTTGAGATTGTTG
* * * * * * *
906146 ATT-TCTCAAAAAAAACTTCGTCTCGCTTGAGACATTTTTTCCTTTGATACA-AATTTTGAATTT
1 TTTATTTCAAAACAAATTTCATCTCGCTTGAGACATTTTTTCCTTTGAGAAACAATTTTGAATTT
* *
906209 GCTTCACTTGAAATAAATTATTCTCATTTGAGATTGTTG
66 GCTTCACTTGAAACAAATTA-TCTCACTTGAGATTGTTG
* * * *
906248 TTTCTTTTAAAAC-AATTTCATCTCGCTTGGGTCATTTTTTTCCTTTGAGAAACAATTTTGAATT
1 TTTATTTCAAAACAAATTTCATCTCGCTTGAGACA-TTTTTTCCTTTGAGAAACAATTTTGAATT
906312 TGCTTCACTTGAAACAAATTATCTCACTTGAGATTGTTG
65 TGCTTCACTTGAAACAAATTATCTCACTTGAGATTGTTG
* *
906351 TTTATTTCAAAACAAATTTCGTCTCACTTGAGACATTTT
1 TTTATTTCAAAACAAATTTCATCTCGCTTGAGACATTTT
906390 CCCTCAGAAT
Statistics
Matches: 205, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
99 13 0.06
100 7 0.03
101 51 0.25
102 33 0.16
103 53 0.26
104 48 0.23
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (103 bp):
TTTATTTCAAAACAAATTTCATCTCGCTTGAGACATTTTTTCCTTTGAGAAACAATTTTGAATTT
GCTTCACTTGAAACAAATTATCTCACTTGAGATTGTTG
Found at i:906934 original size:28 final size:28
Alignment explanation
Indices: 906903--907010 Score: 108
Period size: 28 Copynumber: 3.9 Consensus size: 28
906893 AACACATCAG
*
906903 CTTTGAGTTTGTTTTTCTTGAAACAAAT
1 CTTTGAGTTTGTTTCTCTTGAAACAAAT
* * * *
906931 CTTTGAGTTTATTTTTCCTGAAACCAAT
1 CTTTGAGTTTGTTTCTCTTGAAACAAAT
** **
906959 CTTTGAGTAAGTTTCTCTTGAAACTTAT
1 CTTTGAGTTTGTTTCTCTTGAAACAAAT
* **
906987 CTTTGAATCGGTTTCTCTTGAAAC
1 CTTTGAGTTTGTTTCTCTTGAAAC
907011 CAATATCCCT
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 67 1.00
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (28 bp):
CTTTGAGTTTGTTTCTCTTGAAACAAAT
Found at i:907460 original size:131 final size:132
Alignment explanation
Indices: 907018--907667 Score: 728
Period size: 131 Copynumber: 4.9 Consensus size: 132
907008 AACCAATATC
* * *
907018 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCTCCTGACCAGA-CTCTTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCAC-TATGAGCCGTGTCATCCCCTGACCAGACCTCCTCAT
*
907082 CACG--CGAGCCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGTGTTATCGC
65 CACGTAGGAGCCGTGTCA-CCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGTGTTATCGC
*
907145 CCGT
129 CCTT
** * * *
907149 CCCCAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCTCCTGACCAGAACTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCAC-TATGAGCCGTGTCATCCCCTGACCAGACCTCCTCAT
* * ** * * *
907214 CGCGTAGGAACCACGTCAACCATAGATAACCA-ACCATCCTCATTACGTAGGAACCGTGTTATCG
65 CACGTAGGAGCCGTGTC-ACCCTAGATAACCAGA-CGTCCTCATCACGTAGGAACCGTGTTATCG
907278 CCCTT
128 CCCTT
*
907283 CCTAAAGATGGCCAGAACTCTT-ATCACGTATGAGCCGGGTCATCCCCTGACCAGACCTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCAC-TATGAGCCGTGTCATCCCCTGACCAGACCTCCTCAT
*
907347 CACGTAGGAGCCGTGTCACCCTAGATAACCAGTCGTCCTCATCACGTAGGAA-CGTGTTATCGCC
65 CACGTAGGAGCCGTGTCACCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGTGTTATCGCC
907411 CTT
130 CTT
* * * *
907414 CTTAAAGATGGCAAGAACT-TCTCATCA-TATGAGCCGTGCCATTCCCC-GACCAGACCTTCTCA
1 CCTAAAGATGGCCAGAACTCT-TCATCACTATGAGCCGTGTCA-TCCCCTGACCAGACCTCCTCA
* * * * * *
907476 TTACGTAGGAGTCGTG-CACCCATAGATAACCAGTCGTCCTCATCGCGTAGGAACC-AGTTATCA
64 TCACGTAGGAGCCGTGTCACCC-TAGATAACCAGACGTCCTCATCACGTAGGAACCGTGTTATCG
* *
907539 TCATT
128 CCCTT
* * * *
907544 CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTTAACCAGATCTCCTCA
1 CCTAAAGATGGCC-AGAACTCTTCATCAC-TATGAGCCGTGTCATCCCCTGACCAGACCTCCTCA
** ** * * * *
907609 TCACGTAGGAGTTGTGTCACCCTTAGACGACCAGACCTCTTCATCACGTATGAGCCGTG
64 TCACGTAGGAGCCGTGTCACCC-TAGATAACCAGACGTCCTCATCACGTAGGAACCGTG
907668 GCGTCCCCCA
Statistics
Matches: 443, Mismatches: 58, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
129 5 0.01
130 91 0.21
131 105 0.24
132 49 0.11
133 90 0.20
134 101 0.23
135 2 0.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (132 bp):
CCTAAAGATGGCCAGAACTCTTCATCACTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATC
ACGTAGGAGCCGTGTCACCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGTGTTATCGCCC
TT
Found at i:907655 original size:43 final size:40
Alignment explanation
Indices: 907562--907663 Score: 107
Period size: 40 Copynumber: 2.5 Consensus size: 40
907552 TGGCCAAGAA
* *
907562 CTCTTCATCACGTATGAGCAGTGTCATCCCTTAACCAGAT
1 CTCTTCATCACGTAGGAGCAGTGTCATCCCTTAACCAGAC
* **
907602 CTCCTCATCACGTAGGAGTTGTGTCA-CCCTTAGACGACCAGAC
1 CTCTTCATCACGTAGGAGCAGTGTCATCCCTT--A--ACCAGAC
*
907645 CTCTTCATCACGTATGAGC
1 CTCTTCATCACGTAGGAGC
907664 CGTGGCGTCC
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
39 5 0.10
40 22 0.44
41 1 0.02
43 22 0.44
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (40 bp):
CTCTTCATCACGTAGGAGCAGTGTCATCCCTTAACCAGAC
Found at i:907837 original size:3 final size:3
Alignment explanation
Indices: 907829--907901 Score: 87
Period size: 3 Copynumber: 24.7 Consensus size: 3
907819 CTCGAAAACA
* * * *
907829 TAT TAT TAT AAT AAT TAT TAT TAT AAT AAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
907876 TAT TAT TAAT TAT TAT TAT TA- TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TA
907902 ACATATATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
2 4 0.06
3 56 0.89
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:907885 original size:27 final size:28
Alignment explanation
Indices: 907829--907901 Score: 112
Period size: 27 Copynumber: 2.6 Consensus size: 28
907819 CTCGAAAACA
*
907829 TATTATTATAATAATTATTATTATAATAAT
1 TATTATTATTAT-ATTATTATTAT-ATAAT
907859 TATTATTATTATATTATTATTAT-TAAT
1 TATTATTATTATATTATTATTATATAAT
907886 TATTATTATTATATTA
1 TATTATTATTATATTA
907902 ACATATATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 20 0.48
29 11 0.26
30 11 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TATTATTATTATATTATTATTATATAAT
Found at i:913797 original size:2 final size:2
Alignment explanation
Indices: 913734--913779 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
913724 TGTGTGAGTT
913734 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
913776 TA TA
1 TA TA
913780 GTTTTTTAAT
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):
TA
Found at i:913935 original size:2 final size:2
Alignment explanation
Indices: 913928--913953 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
913918 CCGTTGCTTT
913928 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
913954 AGTTCTTCTA
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:914429 original size:34 final size:34
Alignment explanation
Indices: 914386--914487 Score: 186
Period size: 34 Copynumber: 3.0 Consensus size: 34
914376 ATAAGATCAC
* *
914386 GTTGCATTGTGGTTCCTAGGGTACTTTTGCTGCT
1 GTTGCATTGTGGTTCTTCGGGTACTTTTGCTGCT
914420 GTTGCATTGTGGTTCTTCGGGTACTTTTGCTGCT
1 GTTGCATTGTGGTTCTTCGGGTACTTTTGCTGCT
914454 GTTGCATTGTGGTTCTTCGGGTACTTTTGCTGCT
1 GTTGCATTGTGGTTCTTCGGGTACTTTTGCTGCT
914488 TTTGAGCTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.07, C:0.18, G:0.29, T:0.46
Consensus pattern (34 bp):
GTTGCATTGTGGTTCTTCGGGTACTTTTGCTGCT
Found at i:920220 original size:66 final size:66
Alignment explanation
Indices: 920114--920311 Score: 353
Period size: 66 Copynumber: 3.0 Consensus size: 66
920104 CATAGTCAAT
*
920114 TATCCAGATTAACCTTCCACCCCGAAGAGCCCTCATAGGTCCGAAGAATACCCTTAGAACATTGA
1 TATCCAGATTAACCTTCCACCCCAAAGAGCCCTCATAGGTCCGAAGAATACCCTTAGAACATTGA
920179 G
66 G
*
920180 TATCCAGATTAACCTTCCACCCCAAAGAGCCCTCATAGGTCCGAAGAATACCCTTAGAGCATTGA
1 TATCCAGATTAACCTTCCACCCCAAAGAGCCCTCATAGGTCCGAAGAATACCCTTAGAACATTGA
920245 G
66 G
*
920246 TATCCAGATTAACCTTCCACCCCAAAGAGCCCTCATAGGTCGGAAGAATACCCTT-GAAACATTG
1 TATCCAGATTAACCTTCCACCCCAAAGAGCCCTCATAGGTCCGAAGAATACCCTTAG-AACATTG
920310 AG
65 AG
920312 CTTCGTACGA
Statistics
Matches: 127, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
65 1 0.01
66 126 0.99
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (66 bp):
TATCCAGATTAACCTTCCACCCCAAAGAGCCCTCATAGGTCCGAAGAATACCCTTAGAACATTGA
G
Found at i:924227 original size:24 final size:24
Alignment explanation
Indices: 924181--924228 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
924171 AAACGTTAAT
*
924181 TGAATATATTCATCACAACTAAAA
1 TGAATATATTCATCAAAACTAAAA
* *
924205 TGAATATATTCATGAAAATTAAAA
1 TGAATATATTCATCAAAACTAAAA
924229 AAACAATCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.31
Consensus pattern (24 bp):
TGAATATATTCATCAAAACTAAAA
Found at i:925224 original size:228 final size:225
Alignment explanation
Indices: 924885--925950 Score: 1217
Period size: 228 Copynumber: 4.7 Consensus size: 225
924875 CCAGGGTCCT
* * * * * * * *
924885 CCATCTTCAAGCTGCTTCCCAGCAAAGATCAACCTCTGCTGATCCGGGGGAATTCCTTCCTTATC
1 CCATCCTCAAGTTGCTTACCAGCAAAGATCAACCTCTGTTGGTCTGGGGG-ATACCCTCCTTATC
* * * * * * *
924950 CTGAATCTTGGCCTTGACATTATCAATCGTGTCCGAGCTCTCAACCTCTAGGGTGATAGTTTTCC
65 CTGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGTTTT-C
* *
925015 CAGTGAGGGTCTTCACAAAAATTTGCATCCCACCACGAAGACGAAGCACCAAGTGGAGGGTGGAC
129 CAGTGAGGGTCTTAACAAAAATTTGCATACCACCACGAA-ACGAAGCACCAAGTGGAGGGTGGAC
925080 TCCTTTTGGATGTTATAGTCAGCCAAGGTGCGC
193 TCCTTTTGGATGTTATAGTCAGCCAAGGTGCGC
* * * *
925113 CCATCCTCAAGTTGCTTACCTGCAAAAATCAACCTCTGCTGGTCTGGCGGGATACCCTCCTTGTC
1 CCATCCTCAAGTTGCTTACCAGCAAAGATCAACCTCTGTTGGTCTGG-GGGATACCCTCCTTATC
* * * *
925178 CTGAATCTTGGCCTTGACATTATCTATTGTGTCGGAACTTTCAACCTCCAAGGTGATGGTCTTTC
65 CTGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGT-TTTC
* * * * *
925243 CAGTAAGTGTCTTCACAAAAATCTGCATACCACCACG-AACGGAGCACCAAGTGGAGGGTGGACT
129 CAGTGAGGGTCTTAACAAAAATTTGCATACCACCACGAAACGAAGCACCAAGTGGAGGGTGGACT
*
925307 CCTTTTGGATGTTATAGTCTGCCAAGGTGCGC
194 CCTTTTGGATGTTATAGTCAGCCAAGGTGCGC
* * * * *
925339 CCATCTTCCAGTTGCTTCCCAGCAAAGATCAGCCTCTGTTGGTCTGGGGGGATACCCTCCTTGTC
1 CCATCCTCAAGTTGCTTACCAGCAAAGATCAACCTCTGTTGGTCT-GGGGGATACCCTCCTTATC
* * *
925404 CTGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAGCTTTCAACTTCCAA-GTGATGGTCTTCC
65 CTGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGT-TTTC
* * * * * *
925468 CAGTAAGTGTCTTAACAAATATCTGCATACCACCTCGAAGACGGAGCACCAAGTGGAGGGTGGAC
129 CAGTGAGGGTCTTAACAAAAATTTGCATACCACCACGAA-ACGAAGCACCAAGTGGAGGGTGGAC
*
925533 TCCTTTTGGATGTTATAGTCTGCCAAGGTGCGC
193 TCCTTTTGGATGTTATAGTCAGCCAAGGTGCGC
* *
925566 CCATCCTCCAGTTGCTTACCAGCAAAGATCAGCCTCTGTTGGTCTGGGGGATACCCTCCTTATCC
1 CCATCCTCAAGTTGCTTACCAGCAAAGATCAACCTCTGTTGGTCTGGGGGATACCCTCCTTATCC
* * * * * * *
925631 TGAATCTTGGCCTTGACATTGTCAATGGTATCTGAACTCTCCACCTCCAATGTAATGGTCTTTCC
66 TGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGT-TTTCC
* * * * * * * *
925696 GGTGAGGGTCTTAACAAAGATTTGCATACCACCCCTCAATCGAAGGACCAAGTGGAGTGTGGATT
130 AGTGAGGGTCTTAACAAAAATTTGCATACCACCAC-GAAACGAAGCACCAAGTGGAGGGTGGACT
* * * *
925761 CCTTCTGGATGTTATAATCAG-CAAGGGTCCGG
194 CCTTTTGGATGTTATAGTCAGCCAA-GGTGCGC
* * * *
925793 CCATCCTCCAA-CTGTTTACCAGCAAAGAT-AAGCCTCTGTTGGTCAGGAGGGATTCCCTCCTTA
1 CCATCCT-CAAGTTGCTTACCAGCAAAGATCAA-CCTCTGTTGGTCTGG-GGGATACCCTCCTTA
* * * * * * *
925856 TCTTGGATCTTGGCCTTTACATTGTCGATGGTATCAGAACTTTCCACCT-CAAGGGTGATGGTCT
63 TCCTGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAA-GGTGATGGT-T
* * *
925920 TGCCAGTGAGGGTCTTGACGAAAATTTGCAT
126 TTCCAGTGAGGGTCTTAACAAAAATTTGCAT
925951 CTATTGTGAG
Statistics
Matches: 737, Mismatches: 89, Indels: 24
0.87 0.10 0.03
Matches are distributed among these distances:
225 46 0.06
226 223 0.30
227 229 0.31
228 233 0.32
229 6 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (225 bp):
CCATCCTCAAGTTGCTTACCAGCAAAGATCAACCTCTGTTGGTCTGGGGGATACCCTCCTTATCC
TGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGTTTTCCA
GTGAGGGTCTTAACAAAAATTTGCATACCACCACGAAACGAAGCACCAAGTGGAGGGTGGACTCC
TTTTGGATGTTATAGTCAGCCAAGGTGCGC
Found at i:925569 original size:227 final size:227
Alignment explanation
Indices: 924897--925950 Score: 1254
Period size: 227 Copynumber: 4.6 Consensus size: 227
924887 ATCTTCAAGC
* * * * * * * *
924897 TGCTTCCCAGCAAAGATCAACCTCTGCTGATCCGGGGGAATTCCTTCCTTATCCTGAATCTTGGC
1 TGCTTACCAGCAAAGATCAGCCTCTGTTGGTCTGGGGGGATACCCTCCTTATCCTGAATCTTGGC
* * * * * * * *
924962 CTTGACATTATCAATCGTGTCCGAGCTCTCAACCTCTAGGGTGATAGTTTTCCCAGTGAGGGTCT
66 CTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCT
* * *
925027 TCACAAAAATTTGCATCCCACCACGAAGACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATG
131 TAACAAAAATCTGCATACCACCACGAA-ACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATG
*
925092 TTATAGTCAGCCAAGGTGCGCCCATCCTCAAGT
195 TTATAGTCAGCCAAGGTGCGCCCATCCTCCAGT
* * * * * *
925125 TGCTTACCTGCAAAAATCAACCTCTGCTGGTCTGGCGGGATACCCTCCTTGTCCTGAATCTTGGC
1 TGCTTACCAGCAAAGATCAGCCTCTGTTGGTCTGGGGGGATACCCTCCTTATCCTGAATCTTGGC
* * * * * * *
925190 CTTGACATTATCTATTGTGTCGGAACTTTCAACCTCCAAGGTGATGGTCTTTCCAGTAAGTGTCT
66 CTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCT
* *
925255 TCACAAAAATCTGCATACCACCACG-AACGGAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGT
131 TAACAAAAATCTGCATACCACCACGAAACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGT
* *
925319 TATAGTCTGCCAAGGTGCGCCCATCTTCCAGT
196 TATAGTCAGCCAAGGTGCGCCCATCCTCCAGT
* *
925351 TGCTTCCCAGCAAAGATCAGCCTCTGTTGGTCTGGGGGGATACCCTCCTTGTCCTGAATCTTGGC
1 TGCTTACCAGCAAAGATCAGCCTCTGTTGGTCTGGGGGGATACCCTCCTTATCCTGAATCTTGGC
* * * *
925416 CTTGACATTGTCAATCGTGTCAGAGCTTTCAACTTCCAA-GTGATGGTCTTCCCAGTAAGTGTCT
66 CTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCT
* * *
925480 TAACAAATATCTGCATACCACCTCGAAGACGGAGCACCAAGTGGAGGGTGGACTCCTTTTGGATG
131 TAACAAAAATCTGCATACCACCACGAA-ACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATG
*
925545 TTATAGTCTGCCAAGGTGCGCCCATCCTCCAGT
195 TTATAGTCAGCCAAGGTGCGCCCATCCTCCAGT
925578 TGCTTACCAGCAAAGATCAGCCTCTGTTGGTCT-GGGGGATACCCTCCTTATCCTGAATCTTGGC
1 TGCTTACCAGCAAAGATCAGCCTCTGTTGGTCTGGGGGGATACCCTCCTTATCCTGAATCTTGGC
* * * * * * * * *
925642 CTTGACATTGTCAATGGTATCTGAACTCTCCACCTCCAATGTAATGGTCTTTCCGGTGAGGGTCT
66 CTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCT
* * * * * * * * *
925707 TAACAAAGATTTGCATACCACCCCTCAATCGAAGGACCAAGTGGAGTGTGGATTCCTTCTGGATG
131 TAACAAAAATCTGCATACCACCAC-GAAACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATG
* * * **
925772 TTATAATCAG-CAAGGGTCCGGCCATCCTCCAAC
195 TTATAGTCAGCCAA-GGTGCGCCCATCCTCCAGT
* * * * * * *
925805 TGTTTACCAGCAAAGATAAGCCTCTGTTGGTCAGGAGGGATTCCCTCCTTATCTTGGATCTTGGC
1 TGCTTACCAGCAAAGATCAGCCTCTGTTGGTCTGGGGGGATACCCTCCTTATCCTGAATCTTGGC
* * * * * *
925870 CTTTACATTGTCGATGGTATCAGAACTTTCCACCT-CAAGGGTGATGGTCTTGCCAGTGAGGGTC
66 CTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAA-GGTGATGGTCTTCCCAGTGAGGGTC
* * *
925934 TTGACGAAAATTTGCAT
130 TTAACAAAAATCTGCAT
925951 CTATTGTGAG
Statistics
Matches: 726, Mismatches: 93, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
225 46 0.06
226 224 0.31
227 230 0.32
228 226 0.31
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (227 bp):
TGCTTACCAGCAAAGATCAGCCTCTGTTGGTCTGGGGGGATACCCTCCTTATCCTGAATCTTGGC
CTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCT
TAACAAAAATCTGCATACCACCACGAAACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGT
TATAGTCAGCCAAGGTGCGCCCATCCTCCAGT
Found at i:926949 original size:60 final size:59
Alignment explanation
Indices: 926856--926976 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 59
926846 TTTTCGTTGG
* *
926856 ATAAACTATCAAAATGGTCTCTTCATTTTCATAAACATTCACTTTTAGCCACTTAATTAT
1 ATAAACTATCAAAACGGTCTCTTCAGTTTCATAAACATTCA-TTTTAGCCACTTAATTAT
** * * * *
926916 ATAAACTATCAAAACGGTCTCTTTGGTTTCATAAATATTTATTTTGGTCACTTAATTAT
1 ATAAACTATCAAAACGGTCTCTTCAGTTTCATAAACATTCATTTTAGCCACTTAATTAT
926975 AT
1 AT
926977 TAAATATTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 18 0.34
60 35 0.66
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (59 bp):
ATAAACTATCAAAACGGTCTCTTCAGTTTCATAAACATTCATTTTAGCCACTTAATTAT
Found at i:932743 original size:235 final size:237
Alignment explanation
Indices: 932307--932778 Score: 898
Period size: 234 Copynumber: 2.0 Consensus size: 237
932297 TCATGTTTCT
932307 GGTTTAAGACACAATATGCTATGAAAACAAACATGTGGTAGAATGTATGATACATGAGCTGAATG
1 GGTTTAAGACACAATATGCTATGAAAACAAACATGTGGTAGAATGTATGATACATGAGCTGAATG
932372 GCAATTAAATACAGAAAACAAATCAACACTAACAAATGCCCAAAGCACTAGCAGAGAGTATCATC
66 GCAATTAAATACAGAAAACAAATCAACACTAACAAATGCCCAAAGCACTAGCAGAGAGTATCATC
932437 TTGACAGGTTATATACCATACAAACAAACACTATAGTCTAACAAAAGCACAACTTAAAGATTGAT
131 TTGACAGGTTATATACCATACAAACAAACACTATAGTCTAACAAAAGCACAACTTAAAGATTGAT
932502 TGAAATATAGTGT-CCCTCGTCTACTTCAGATATTAACTCCC
196 TGAAATATAGTGTCCCCTCGTCTACTTCAGATATTAACTCCC
932543 GGTTTAAGACAC-ATATGCTATG-AAACAAACATGTGGTAGAATGTATGATACATGAGCATGAAT
1 GGTTTAAGACACAATATGCTATGAAAACAAACATGTGGTAGAATGTATGATACATGAGC-TGAAT
932606 GGCAATTAAATACAGAAAACAAATCAACACTAAC-AATGCCCAAAGCACTAGCAGAGAGTATCAT
65 GGCAATTAAATACAGAAAACAAATCAACACTAACAAATGCCCAAAGCACTAGCAGAGAGTATCAT
932670 CTTGACAGGTTATATACCATACAAACAAACACTATAGTCTAACAAAAGCACAACTTAAAAGATTG
130 CTTGACAGGTTATATACCATACAAACAAACACTATAGTCTAACAAAAGCACAACTT-AAAGATTG
932735 ATTGAAATATAGTGTCCCCTCGTCTACTTCAGATATTAACTCCC
194 ATTGAAATATAGTGTCCCCTCGTCTACTTCAGATATTAACTCCC
932779 TTTTATCTAA
Statistics
Matches: 233, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
234 121 0.52
235 72 0.31
236 40 0.17
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (237 bp):
GGTTTAAGACACAATATGCTATGAAAACAAACATGTGGTAGAATGTATGATACATGAGCTGAATG
GCAATTAAATACAGAAAACAAATCAACACTAACAAATGCCCAAAGCACTAGCAGAGAGTATCATC
TTGACAGGTTATATACCATACAAACAAACACTATAGTCTAACAAAAGCACAACTTAAAGATTGAT
TGAAATATAGTGTCCCCTCGTCTACTTCAGATATTAACTCCC
Found at i:933520 original size:21 final size:21
Alignment explanation
Indices: 933496--933535 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
933486 AAAAAATTAA
* *
933496 CTAAAATATTATTATTTTTAT
1 CTAAAACATTAATATTTTTAT
933517 CTAAAACATTAATATTTTT
1 CTAAAACATTAATATTTTT
933536 TAATATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
CTAAAACATTAATATTTTTAT
Found at i:933799 original size:17 final size:17
Alignment explanation
Indices: 933779--933813 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
933769 ATTATATCGA
*
933779 TAAATTAAGATTGAATT
1 TAAATTAAGATTAAATT
*
933796 TAAATTAATATTAAATT
1 TAAATTAAGATTAAATT
933813 T
1 T
933814 TAAAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
TAAATTAAGATTAAATT
Found at i:935247 original size:77 final size:75
Alignment explanation
Indices: 935145--935300 Score: 269
Period size: 77 Copynumber: 2.0 Consensus size: 75
935135 ATCAATCTCT
935145 GAATCAATGTTGCATAAAATGAGAGCTCAATACC-ATACTAATAATTGTAAATGTTTTCTGATTT
1 GAATCAATGTTGCATAAAATGAGAGCTCAATACCAATACTAATAATTGTAAA--TTTTCTGATTT
935209 CGTTGGCAGCTC
64 CGTTGGCAGCTC
935221 GAATCAATGTTTGCATAAAATGAGAGCTCAATACCAGATACTAATAATTGTAAATTTTCTGATTT
1 GAATCAATG-TTGCATAAAATGAGAGCTCAATACCA-ATACTAATAATTGTAAATTTTCTGATTT
935286 CGTTGGCAGCTC
64 CGTTGGCAGCTC
935298 GAA
1 GAA
935301 GATGCTGCGA
Statistics
Matches: 77, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
76 9 0.12
77 51 0.66
79 17 0.22
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (75 bp):
GAATCAATGTTGCATAAAATGAGAGCTCAATACCAATACTAATAATTGTAAATTTTCTGATTTCG
TTGGCAGCTC
Found at i:938414 original size:29 final size:29
Alignment explanation
Indices: 938373--938588 Score: 177
Period size: 29 Copynumber: 7.7 Consensus size: 29
938363 ACGGAGAAAC
* *
938373 AGGAGGCGATGGTGCAGCATGA-GATCAG
1 AGGAGGAGGTGGTGCAGCATGAGGATCAG
938401 CAGGAGGAGGTGGTGCAGCATGA-G----G
1 -AGGAGGAGGTGGTGCAGCATGAGGATCAG
*
938426 AGGAGGCGGTGGTGCAGCATGAGGATCAG
1 AGGAGGAGGTGGTGCAGCATGAGGATCAG
* *
938455 CGGAGGCA-GTGGTGCAGCAAGAGGATCAGG
1 AGGAGG-AGGTGGTGCAGCATGAGGATCA-G
* * *
938485 AGGTGGTGGTGGTGCAGCAAGAGGATCAG
1 AGGAGGAGGTGGTGCAGCATGAGGATCAG
* * *
938514 AGGTGGTGGTGGTGCCA-CGTGA-GATCAGG
1 AGGAGGAGGTGGTG-CAGCATGAGGATCA-G
*
938543 AGG-GAACGGTGGTGCAGCATGAGGATC-G
1 AGGAGGA-GGTGGTGCAGCATGAGGATCAG
*
938571 -GGAGAAGGTGGTGCAGCA
1 AGGAGGAGGTGGTGCAGCA
938589 CGAGACTCGG
Statistics
Matches: 159, Mismatches: 14, Indels: 30
0.78 0.07 0.15
Matches are distributed among these distances:
24 21 0.13
25 2 0.01
27 14 0.09
28 12 0.08
29 79 0.50
30 31 0.19
ACGTcount: A:0.25, C:0.13, G:0.48, T:0.14
Consensus pattern (29 bp):
AGGAGGAGGTGGTGCAGCATGAGGATCAG
Found at i:938436 original size:24 final size:24
Alignment explanation
Indices: 938373--938450 Score: 93
Period size: 24 Copynumber: 3.0 Consensus size: 24
938363 ACGGAGAAAC
*
938373 AGGAGGCGATGGTGCAGCATGAGATCAG
1 AGGAGGCGGTGGTGCAGCATGAG----G
*
938401 CAGGAGGAGGTGGTGCAGCATGAGG
1 -AGGAGGCGGTGGTGCAGCATGAGG
938426 AGGAGGCGGTGGTGCAGCATGAGG
1 AGGAGGCGGTGGTGCAGCATGAGG
938450 A
1 A
938451 TCAGCGGAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
24 24 0.52
25 1 0.02
29 21 0.46
ACGTcount: A:0.26, C:0.13, G:0.49, T:0.13
Consensus pattern (24 bp):
AGGAGGCGGTGGTGCAGCATGAGG
Found at i:938441 original size:53 final size:53
Alignment explanation
Indices: 938373--938479 Score: 164
Period size: 53 Copynumber: 2.0 Consensus size: 53
938363 ACGGAGAAAC
*
938373 AGGAGGCGATGGTGCAGCATGA-GATCAGCAGGAGG-AGGTGGTGCAGCATGAGG
1 AGGAGGCGATGGTGCAGCATGAGGATCAGC-GGAGGCA-GTGGTGCAGCAAGAGG
*
938426 AGGAGGCGGTGGTGCAGCATGAGGATCAGCGGAGGCAGTGGTGCAGCAAGAGG
1 AGGAGGCGATGGTGCAGCATGAGGATCAGCGGAGGCAGTGGTGCAGCAAGAGG
938479 A
1 A
938480 TCAGGAGGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
53 42 0.84
54 8 0.16
ACGTcount: A:0.26, C:0.14, G:0.48, T:0.12
Consensus pattern (53 bp):
AGGAGGCGATGGTGCAGCATGAGGATCAGCGGAGGCAGTGGTGCAGCAAGAGG
Found at i:938490 original size:53 final size:53
Alignment explanation
Indices: 938346--938492 Score: 156
Period size: 53 Copynumber: 2.7 Consensus size: 53
938336 GAGGAATAGG
* *
938346 AGGAGGCAGT-GTGCAGCACGGAGAAACAGGAGGCGATGGTGCAGCATGAGATCAGC
1 AGGAGGCAGTGGTGCAGCA-AGAGGAACAGGA-G-G-TGGTGCAGCATGAGATCAGC
* ** *
938402 AGGAGG-AGGTGGTGCAGCATGAGGAGGAGGCGGTGGTGCAGCATGAGGATCAGC
1 AGGAGGCA-GTGGTGCAGCAAGAGGAACAGGAGGTGGTGCAGCATGA-GATCAGC
*
938456 -GGAGGCAGTGGTGCAGCAAGAGGATCAGGAGGTGGTG
1 AGGAGGCAGTGGTGCAGCAAGAGGAACAGGAGGTGGTG
938493 GTGGTGCAGC
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
53 44 0.56
54 9 0.12
55 2 0.03
56 15 0.19
57 8 0.10
ACGTcount: A:0.27, C:0.14, G:0.47, T:0.12
Consensus pattern (53 bp):
AGGAGGCAGTGGTGCAGCAAGAGGAACAGGAGGTGGTGCAGCATGAGATCAGC
Found at i:938491 original size:24 final size:24
Alignment explanation
Indices: 938405--938492 Score: 95
Period size: 24 Copynumber: 3.5 Consensus size: 24
938395 GATCAGCAGG
**
938405 AGGAGGTGGTGCAGCATGAGGAGG
1 AGGAGGTGGTGCAGCATGAGGATC
*
938429 AGGCGGTGGTGCAGCATGAGGATC
1 AGGAGGTGGTGCAGCATGAGGATC
*
938453 AGCGGAGGCAGTGGTGCAGCAAGAGGATC
1 A--GGA-G--GTGGTGCAGCATGAGGATC
938482 AGGAGGTGGTG
1 AGGAGGTGGTG
938493 GTGGTGCAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
24 28 0.52
26 3 0.06
27 4 0.07
29 19 0.35
ACGTcount: A:0.24, C:0.12, G:0.50, T:0.14
Consensus pattern (24 bp):
AGGAGGTGGTGCAGCATGAGGATC
Found at i:940518 original size:30 final size:30
Alignment explanation
Indices: 940484--940570 Score: 138
Period size: 30 Copynumber: 2.9 Consensus size: 30
940474 GGACCACCAT
* *
940484 CAGCTTTCGGAGGAGGTGGCGGAGGAGCAC
1 CAGCTTTTGGAGGAGGTGGAGGAGGAGCAC
940514 CAGCTTTTGGAGGAGGTGGAGGAGGAGCAC
1 CAGCTTTTGGAGGAGGTGGAGGAGGAGCAC
* *
940544 CAGCTTTTGGAGGAGGAGGAGGTGGAG
1 CAGCTTTTGGAGGAGGTGGAGGAGGAG
940571 GACCTGGTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.22, C:0.14, G:0.48, T:0.16
Consensus pattern (30 bp):
CAGCTTTTGGAGGAGGTGGAGGAGGAGCAC
Found at i:944010 original size:22 final size:21
Alignment explanation
Indices: 943985--944038 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
943975 ATATTAGTTC
* *
943985 ATAAAAAACAAAGATGAAGTAA
1 ATAAAAAACAAACAT-AAATAA
*
944007 ATAATAAAATAAACATAAATAA
1 ATAA-AAAACAAACATAAATAA
944029 ATAAATAAAC
1 ATAAA-AAAC
944039 TCAACACAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 16 0.62
23 9 0.35
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.19
Consensus pattern (21 bp):
ATAAAAAACAAACATAAATAA
Found at i:944025 original size:18 final size:18
Alignment explanation
Indices: 944004--944038 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
943994 AAAGATGAAG
944004 TAAAT-AATAAAATAAACA
1 TAAATAAAT-AAATAAACA
944022 TAAATAAATAAATAAAC
1 TAAATAAATAAATAAAC
944039 TCAACACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAATAAATAAATAAACA
Found at i:945901 original size:3 final size:3
Alignment explanation
Indices: 945893--945931 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
945883 TAAAATTCAA
945893 AAT AAT AAT AAT AAT AAT AAT AAT AATT AA- AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT A
945932 GAAAAGACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:946363 original size:135 final size:135
Alignment explanation
Indices: 946116--946819 Score: 1227
Period size: 135 Copynumber: 5.2 Consensus size: 135
946106 AGTTCGGGTC
*
946116 ATCTAAGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
** *
946181 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTATACAATGAGGATGGC
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
946246 TGGTT
131 TGGTT
* *
946251 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTACTCATACG
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
* * *
946316 TGATGAAGAGTTCATGGCCATCTTTAGGAATGGTGATAACTCAGTTCCTACGCGATGAGGATGGC
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
946381 TGGTT
131 TGGTT
946386 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
*
946451 TGATGAAGAGTTCCTGGCCATCTTTAGAAAGGGTGATAACTCGGTTCCTACGCGATGATGG--GG
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGA-GGATGG
*
946514 TTGG-T
130 CTGGTT
*
946519 ATCTAGGGGTGACACGGTTCCTA-GTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACG
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
*
946583 TGATGAAGAGTTCCTGTCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
946648 TGGTT
131 TGGTT
*
946653 ATCTAGGGGTGACACGGTTCTTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
*
946718 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGA
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
946783 TGGTT
131 TGGTT
*
946788 ATCTAGGGGTGACACGGCTCCTACGTGATGAG
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAG
946820 GATGACTGGC
Statistics
Matches: 538, Mismatches: 26, Indels: 10
0.94 0.05 0.02
Matches are distributed among these distances:
131 2 0.00
132 96 0.18
133 29 0.05
134 28 0.05
135 381 0.71
136 2 0.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (135 bp):
ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
TGGTT
Found at i:946656 original size:267 final size:269
Alignment explanation
Indices: 946116--946819 Score: 1234
Period size: 267 Copynumber: 2.6 Consensus size: 269
946106 AGTTCGGGTC
*
946116 ATCTAAGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
** * *
946181 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTATACAATGAGGATGGC
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGA-GGA
946246 TGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTACTC
130 TGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTACTC
*
946311 ATACGTGATGAAGAGTTCATGGCCATCTTTAGGAATGGTGATAACTCAGTTCCTACGCGATGAGG
195 ATACGTGATGAAGAGTTCATGGCCATCTTTAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGG
946376 ATGGCTGGTT
260 ATGGCTGGTT
946386 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
* *
946451 TGATGAAGAGTTCCTGGCCATCTTTAGAAAGGGTGATAACTCGGTTCCTACGCGATGATGG-GGT
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGA-GGAGGA
*
946515 TGG-TATCTAGGGGTGACACGGTTCCTA-GTGATGAGAAAATCTGGTCGAGGGATGACACTGCTC
130 TGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTACTC
* * *
946578 ATACGTGATGAAGAGTTCCTGTCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGG
195 ATACGTGATGAAGAGTTCATGGCCATCTTTAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGG
946643 ATGGCTGGTT
260 ATGGCTGGTT
*
946653 ATCTAGGGGTGACACGGTTCTTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
946718 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGA
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGA-GGA
*
946783 TGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAG
130 TGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAG
946820 GATGACTGGC
Statistics
Matches: 414, Mismatches: 15, Indels: 10
0.94 0.03 0.02
Matches are distributed among these distances:
266 2 0.00
267 227 0.55
268 29 0.07
269 28 0.07
270 126 0.30
271 2 0.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (269 bp):
ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGAGGAT
GGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTACTCA
TACGTGATGAAGAGTTCATGGCCATCTTTAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGA
TGGCTGGTT
Found at i:946952 original size:35 final size:36
Alignment explanation
Indices: 946912--947005 Score: 102
Period size: 36 Copynumber: 2.6 Consensus size: 36
946902 GACAAAATTC
** * **
946912 GTTTCAAGGGAAATGATCTCAAAGAT-ATTTGTTTT
1 GTTTCAAGGGAAACAAACTCAAAGATGATTAATTTT
946947 GTTTCAAGGGAAACAAACTCAAAGATGATTAATTTT
1 GTTTCAAGGGAAACAAACTCAAAGATGATTAATTTT
* *
946983 GTTTCCAA-AGAAACAGACTCAAA
1 GTTT-CAAGGGAAACAAACTCAAA
947006 TATTTTTCTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
35 23 0.46
36 24 0.48
37 3 0.06
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (36 bp):
GTTTCAAGGGAAACAAACTCAAAGATGATTAATTTT
Found at i:947225 original size:27 final size:26
Alignment explanation
Indices: 947195--947264 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
947185 CTCAAAGATT
947195 ATTTTGTTAAGAGAAACAAACTCAAAG
1 ATTTT-TTAAGAGAAACAAACTCAAAG
* * * *
947222 ATTTTTCAAAAGGAACATACTCAAAG
1 ATTTTTTAAGAGAAACAAACTCAAAG
947248 ATTTATTTCAAGAGAAA
1 ATTT-TTT-AAGAGAAA
947265 TTGTCTCAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
26 21 0.62
27 7 0.21
28 6 0.18
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (26 bp):
ATTTTTTAAGAGAAACAAACTCAAAG
Found at i:947339 original size:66 final size:66
Alignment explanation
Indices: 947225--947396 Score: 215
Period size: 66 Copynumber: 2.6 Consensus size: 66
947215 CTCAAAGATT
* * * * * *
947225 TTTCAAAAGGAACATACTCAAAGA-TTTATTTCAAGAGAAATTGTCTCAATAGAGACAAAA-TTC
1 TTTCCAAAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAATTTC
947288 G
66 G
* * *
947289 TTT-TAAGAGAAACAGATTCAAAGATTTTTTTCTCAAAAGAGATTGTCTCAAGAGAGACAAAATT
1 TTTCCAA-AGAAACAGACTCAAAGATTTTTTT-TCAAAAGAAATTGTCTCAAGAGAGACAAAATT
*
947353 TTG
64 TCG
947356 TTTCCAAAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAA
1 TTTCCAAAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAA
947397 CAACTCAAAG
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
63 2 0.02
64 17 0.19
65 5 0.05
66 36 0.40
67 29 0.32
68 2 0.02
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (66 bp):
TTTCCAAAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAATTTC
G
Found at i:947382 original size:29 final size:28
Alignment explanation
Indices: 947346--947411 Score: 98
Period size: 29 Copynumber: 2.4 Consensus size: 28
947336 TCAAGAGAGA
*
947346 CAAA-ATTTTGTTTCCAAAGAAACAGACT
1 CAAAGATTTTGTTTCAAAAGAAACA-ACT
*
947374 CAAAGATTTTTTTTCAAAAGAAACAACT
1 CAAAGATTTTGTTTCAAAAGAAACAACT
947402 CAAAGATTTT
1 CAAAGATTTT
947412 TTCACGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (28 bp):
CAAAGATTTTGTTTCAAAAGAAACAACT
Found at i:947412 original size:29 final size:29
Alignment explanation
Indices: 947346--947413 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
947336 TCAAGAGAGA
* *
947346 CAAA-ATTTTGTTTCCAAAGAAACAGACT
1 CAAAGATTTTTTTTCAAAAGAAACAGACT
947374 CAAAGATTTTTTTTCAAAAGAAACA-ACT
1 CAAAGATTTTTTTTCAAAAGAAACAGACT
947402 CAAAGATTTTTT
1 CAAAGATTTTTT
947414 CACGAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 19 0.51
29 18 0.49
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (29 bp):
CAAAGATTTTTTTTCAAAAGAAACAGACT
Found at i:947485 original size:28 final size:29
Alignment explanation
Indices: 947429--947512 Score: 127
Period size: 29 Copynumber: 2.9 Consensus size: 29
947419 AATTATCTGT
*
947429 TTCAAAAGAAACAGACTCAAAGATTTTTT
1 TTCAAAAGAAACAGACTCAAAGATTTTTA
947458 TCTCAAAAGAAACA-ACTCAAAGATTTTTA
1 T-TCAAAAGAAACAGACTCAAAGATTTTTA
947487 TTCAAAAG-AACAGACTCAATAGATTT
1 TTCAAAAGAAACAGACTCAA-AGATTT
947513 GTTTAAAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
27 4 0.08
28 13 0.25
29 22 0.43
30 12 0.24
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (29 bp):
TTCAAAAGAAACAGACTCAAAGATTTTTA
Found at i:947522 original size:29 final size:28
Alignment explanation
Indices: 947428--947524 Score: 121
Period size: 28 Copynumber: 3.5 Consensus size: 28
947418 AAATTATCTG
947428 TTTCAAAAGAAACAGACTCAAAGATTTTT
1 TTTCAAAAGAAACAGACTCAAAGA-TTTT
947457 TTCTCAAAAGAAACA-ACTCAAAGATTTT
1 TT-TCAAAAGAAACAGACTCAAAGATTTT
*
947485 TATTCAAAAG-AACAGACTCAATAGATTTG
1 T-TTCAAAAGAAACAGACTCAA-AGATTTT
947514 TTT-AAAA-AAAC
1 TTTCAAAAGAAAC
947525 TGTCTCAAGA
Statistics
Matches: 62, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
27 11 0.18
28 20 0.32
29 19 0.31
30 12 0.19
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.29
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTT
Found at i:948380 original size:16 final size:16
Alignment explanation
Indices: 948359--948395 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
948349 ACTCATGTAA
*
948359 TATGTATGTGTTGATG
1 TATGTATGTATTGATG
948375 TATGTATGTATTGATG
1 TATGTATGTATTGATG
948391 TATGT
1 TATGT
948396 TTTTCTCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (16 bp):
TATGTATGTATTGATG
Found at i:949573 original size:11 final size:11
Alignment explanation
Indices: 949559--949606 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
949549 TGCTTTTGTC
949559 TTCTTTTTCTT
1 TTCTTTTTCTT
949570 TTCTTTTTCTT
1 TTCTTTTTCTT
949581 TTGCTATTTTTCTT
1 TT-C--TTTTTCTT
**
949595 TGATTTTTCTT
1 TTCTTTTTCTT
949606 T
1 T
949607 GTACTCTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 22 0.69
12 1 0.03
14 9 0.28
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:950902 original size:14 final size:14
Alignment explanation
Indices: 950883--950929 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
950873 ATGAATAATG
*
950883 AAATGCATATGCAA
1 AAATGCAGATGCAA
950897 AAATGCAAAGATGC--
1 AAATGC--AGATGCAA
950911 AAATGCAGATGCAA
1 AAATGCAGATGCAA
950925 AAATG
1 AAATG
950930 TTGATCCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
12 6 0.21
14 17 0.61
16 5 0.18
ACGTcount: A:0.51, C:0.13, G:0.19, T:0.17
Consensus pattern (14 bp):
AAATGCAGATGCAA
Found at i:960747 original size:23 final size:24
Alignment explanation
Indices: 960703--960747 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
960693 ATAAAGCAGG
*
960703 CAGAACAGCAGAAAATACAAGTGA
1 CAGAACAGAAGAAAATACAAGTGA
*
960727 CAGAACAGAAG-ATATACAAGT
1 CAGAACAGAAGAAAATACAAGT
960748 CTATAATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.53, C:0.16, G:0.20, T:0.11
Consensus pattern (24 bp):
CAGAACAGAAGAAAATACAAGTGA
Found at i:965731 original size:352 final size:351
Alignment explanation
Indices: 965060--965760 Score: 1384
Period size: 352 Copynumber: 2.0 Consensus size: 351
965050 ATACTACTTT
965060 GTATTCTTCTTAGCTTAATAAATAAAATTATGATTTTAAAAAATAATAGTTAGGTGGCTAAAACG
1 GTATTCTTCTTAGCTTAATAAATAAAATTATGATTTTAAAAAATAATAGTTAGGTGGCTAAAACG
965125 GAACAACAAGAATAATTAGGTGATTAAATACATAATTTACCCTATTTATTTTTCTAATTTAATGT
66 GAACAACAAGAATAATTAGGTGATTAAATACATAATTTACCCTATTTATTTTTCTAATTTAATGT
965190 GTTAAAAAATGTTGGGAAGAAGCATATTGAAAAGAGAAAATATTTGGAACAAATCCTTCCACGTT
131 GTTAAAAAATGTTGGGAAGAAGCATATTGAAAAGAGAAAATATTTGGAACAAATCCTTCCACGTT
965255 ACAAACACCAACATAATTGATTAAAGCAAACACATTTGATTATTAAAAAGATTAAAAAAAGGAGA
196 ACAAACACCAACATAATTGATTAAAGCAAACACATTTGATTATTAAAAAGATTAAAAAAAGGAGA
965320 CGGCCAAACGAGCCAACCCAGAACAGAGGAGAGAGATCTTTAAAAGGCTAGCTTTGTTATTGTTG
261 CGGCCAAACGAGCCAACCCAGAACAGAGGAGAGAGATCTTTAAAAGGCTAGCTTTGTTATTGTTG
965385 TAGAAACCCCAAATCTTTTCATTTGG
326 TAGAAACCCCAAATCTTTTCATTTGG
965411 GTATTCTTCTTAGCTTAATAAATAAAAGTTATGATTTTAAAAAATAATAGTTAGGTGGCTAAAAC
1 GTATTCTTCTTAGCTTAATAAATAAAA-TTATGATTTTAAAAAATAATAGTTAGGTGGCTAAAAC
965476 GGAACAACAAGAATAATTAGGTGATTAAATACATAATTTACCCTATTTATTTTTCTAATTTAATG
65 GGAACAACAAGAATAATTAGGTGATTAAATACATAATTTACCCTATTTATTTTTCTAATTTAATG
965541 TGTTAAAAAATGTTGGGAAGAAGCATATTGAAAAGAGAAAATATTTGGAACAAATCCTTCCACGT
130 TGTTAAAAAATGTTGGGAAGAAGCATATTGAAAAGAGAAAATATTTGGAACAAATCCTTCCACGT
*
965606 TACAAACACCAACGTAATTGATTAAAGCAAACACATTTGATTATTAAAAAGATTAAAAAAAGGAG
195 TACAAACACCAACATAATTGATTAAAGCAAACACATTTGATTATTAAAAAGATTAAAAAAAGGAG
965671 ACGGCCAAACGAGCCAACCCAGAACAGAGGAGAGAGATCTTTAAAAGGCTAGCTTTGTTATTGTT
260 ACGGCCAAACGAGCCAACCCAGAACAGAGGAGAGAGATCTTTAAAAGGCTAGCTTTGTTATTGTT
965736 GTAGAAACCCCAAATCTTTTCATTT
325 GTAGAAACCCCAAATCTTTTCATTT
965761 TGGGAAAGGC
Statistics
Matches: 348, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
351 27 0.08
352 321 0.92
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.30
Consensus pattern (351 bp):
GTATTCTTCTTAGCTTAATAAATAAAATTATGATTTTAAAAAATAATAGTTAGGTGGCTAAAACG
GAACAACAAGAATAATTAGGTGATTAAATACATAATTTACCCTATTTATTTTTCTAATTTAATGT
GTTAAAAAATGTTGGGAAGAAGCATATTGAAAAGAGAAAATATTTGGAACAAATCCTTCCACGTT
ACAAACACCAACATAATTGATTAAAGCAAACACATTTGATTATTAAAAAGATTAAAAAAAGGAGA
CGGCCAAACGAGCCAACCCAGAACAGAGGAGAGAGATCTTTAAAAGGCTAGCTTTGTTATTGTTG
TAGAAACCCCAAATCTTTTCATTTGG
Found at i:967693 original size:33 final size:32
Alignment explanation
Indices: 967646--967749 Score: 147
Period size: 33 Copynumber: 3.2 Consensus size: 32
967636 ACAAAGTTTA
* *
967646 CGAT-AATTGAAATACATAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAA-ACTTCCAAGTT
*
967678 CGATAAATTCAAATACTTAAAAACTTCCAAATT
1 CGATAAATTCAAATACTT-AAAACTTCCAAGTT
967711 CGATAAATTCAAATACTTAAAATCTTCCAAGTT
1 CGATAAATTCAAATACTTAAAA-CTTCCAAGTT
967744 CGATAA
1 CGATAA
967750 TTGAAACAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
32 8 0.12
33 54 0.83
34 3 0.05
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (32 bp):
CGATAAATTCAAATACTTAAAACTTCCAAGTT
Found at i:967769 original size:21 final size:21
Alignment explanation
Indices: 967744--967785 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
967734 CTTCCAAGTT
967744 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
967765 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
967786 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:969790 original size:109 final size:109
Alignment explanation
Indices: 969662--969878 Score: 357
Period size: 109 Copynumber: 2.0 Consensus size: 109
969652 AGCATATGCT
969662 TGTTCATAATTATCCATTTAATTTACAGTTTTAAACATTAAATTATCCATTTAAAAACGTGTAAT
1 TGTTCATAATTATCCATTTAATTTACA-TTTTAAACATTAAATTATCCATTTAAAAACGTGTAAT
* *
969727 TAAGACTC-TTTTTCCACCTATAAAG-TTTTTCAATAGATAATTTG
65 TAAGAATCTTTTTTCCACCTAAAAAGCTTTTT-AATAGATAATTTG
* *
969771 TGTTCGTAATTATCCATTTAATTTGCATTTTAAACATTAAATTATCCATTTAAAAACGTGTAATT
1 TGTTCATAATTATCCATTTAATTTACATTTTAAACATTAAATTATCCATTTAAAAACGTGTAATT
*
969836 AAGAATCTTTTTTCGACCTAAAAAGCTTTTTAATAGATAATTT
66 AAGAATCTTTTTTCCACCTAAAAAGCTTTTTAATAGATAATTT
969879 ATGTACTATA
Statistics
Matches: 101, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
108 44 0.44
109 52 0.51
110 5 0.05
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (109 bp):
TGTTCATAATTATCCATTTAATTTACATTTTAAACATTAAATTATCCATTTAAAAACGTGTAATT
AAGAATCTTTTTTCCACCTAAAAAGCTTTTTAATAGATAATTTG
Found at i:970332 original size:14 final size:14
Alignment explanation
Indices: 970310--970348 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
970300 TTTGATAGTA
970310 TGTTCGTTTATATT
1 TGTTCGTTTATATT
*
970324 T-TATCGTTTATGTT
1 TGT-TCGTTTATATT
970338 TGTTCGTTTAT
1 TGTTCGTTTAT
970349 TTATTAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.13, C:0.08, G:0.15, T:0.64
Consensus pattern (14 bp):
TGTTCGTTTATATT
Found at i:970471 original size:10 final size:10
Alignment explanation
Indices: 970456--970493 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
970446 TGTTCGTTAA
970456 TTTATGTTCG
1 TTTATGTTCG
*
970466 TTTATGTTTG
1 TTTATGTTCG
*
970476 TTTATGTTCA
1 TTTATGTTCG
970486 TTTATGTT
1 TTTATGTT
970494 TAGCTCAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.13, C:0.05, G:0.16, T:0.66
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:970481 original size:20 final size:20
Alignment explanation
Indices: 970456--970494 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
970446 TGTTCGTTAA
*
970456 TTTATGTTCGTTTATGTTTG
1 TTTATGTTCATTTATGTTTG
970476 TTTATGTTCATTTATGTTT
1 TTTATGTTCATTTATGTTT
970495 AGCTCAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.05, G:0.15, T:0.67
Consensus pattern (20 bp):
TTTATGTTCATTTATGTTTG
Found at i:970741 original size:24 final size:24
Alignment explanation
Indices: 970658--970747 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
970648 AAAATCTATT
* * *
970658 TTCATTTACGTTCTTTTACGTTCA
1 TTCATTTGCGTTCGTTTATGTTCA
* * * *
970682 TTTA-TTGTGTTCGTTTATGCTCG
1 TTCATTTGCGTTCGTTTATGTTCA
*
970705 TTTATATT-CGTTCGTTTATGTTCA
1 TTCAT-TTGCGTTCGTTTATGTTCA
*
970729 TTCATTTGTGTTCGTTTAT
1 TTCATTTGCGTTCGTTTAT
970748 CATTTAAGTG
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
23 19 0.37
24 30 0.59
25 2 0.04
ACGTcount: A:0.13, C:0.14, G:0.14, T:0.58
Consensus pattern (24 bp):
TTCATTTGCGTTCGTTTATGTTCA
Found at i:971990 original size:20 final size:20
Alignment explanation
Indices: 971960--972000 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
971950 AAATAGGAAT
971960 AATTAAAAAAATTAAAGAGTA
1 AATTAAAAAAATTAAA-AGTA
971981 AATTAAAAAAATTAAAAGTA
1 AATTAAAAAAATTAAAAGTA
972001 CAATGAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
AATTAAAAAAATTAAAAGTA
Found at i:972012 original size:22 final size:21
Alignment explanation
Indices: 971964--972006 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
971954 AGGAATAATT
*
971964 AAAAAAATTAAAGAGTAAATT
1 AAAAAAATTAAAGAGTAAATG
971985 AAAAAAATTAAA-AGTACAATG
1 AAAAAAATTAAAGAGTA-AATG
972006 A
1 A
972007 GTAAAATAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.21
Consensus pattern (21 bp):
AAAAAAATTAAAGAGTAAATG
Found at i:972402 original size:22 final size:21
Alignment explanation
Indices: 972345--972422 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 21
972335 AAAAATATGT
* *
972345 TGCGATAGTTAAAATGTGTTG
1 TGCGATAGTGAAAAAGTGTTG
* *
972366 TGAGAGT-TTGAAAAACGTGTTG
1 TGCGA-TAGTGAAAAA-GTGTTG
972388 TTGCGATAGTGAAAAAGTGTTG
1 -TGCGATAGTGAAAAAGTGTTG
972410 T--GATAGTGAAAAA
1 TGCGATAGTGAAAAA
972423 TCCAAAATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
19 12 0.26
21 10 0.21
22 14 0.30
23 11 0.23
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (21 bp):
TGCGATAGTGAAAAAGTGTTG
Found at i:972422 original size:19 final size:19
Alignment explanation
Indices: 972342--972422 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 19
972332 TTGAAAAATA
* * *
972342 TGTTGCGATAGTTAAAATG
1 TGTTGTGATAGTGAAAAAG
*
972361 TGTTGTGAGAGTTTGAAAAACG
1 TGTTGTGATAG--TGAAAAA-G
972383 TGTTGTTGCGATAGTGAAAAAG
1 TGTTG-T--GATAGTGAAAAAG
972405 TGTTGTGATAGTGAAAAA
1 TGTTGTGATAGTGAAAAA
972423 TCCAAAATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
19 21 0.41
21 6 0.12
22 12 0.24
23 8 0.16
25 4 0.08
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (19 bp):
TGTTGTGATAGTGAAAAAG
Found at i:977193 original size:91 final size:91
Alignment explanation
Indices: 977038--977220 Score: 366
Period size: 91 Copynumber: 2.0 Consensus size: 91
977028 GATGCGGATG
977038 ACTTGATCCGATCTAGAGAGTCACATCGGAGCGACCCACCGTTAAAATCTCAGAAAATTTAAAAC
1 ACTTGATCCGATCTAGAGAGTCACATCGGAGCGACCCACCGTTAAAATCTCAGAAAATTTAAAAC
977103 TTTTATTAAAACATGTAACTCATAAA
66 TTTTATTAAAACATGTAACTCATAAA
977129 ACTTGATCCGATCTAGAGAGTCACATCGGAGCGACCCACCGTTAAAATCTCAGAAAATTTAAAAC
1 ACTTGATCCGATCTAGAGAGTCACATCGGAGCGACCCACCGTTAAAATCTCAGAAAATTTAAAAC
977194 TTTTATTAAAACATGTAACTCATAAA
66 TTTTATTAAAACATGTAACTCATAAA
977220 A
1 A
977221 TGATTTATCA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (91 bp):
ACTTGATCCGATCTAGAGAGTCACATCGGAGCGACCCACCGTTAAAATCTCAGAAAATTTAAAAC
TTTTATTAAAACATGTAACTCATAAA
Found at i:980146 original size:20 final size:20
Alignment explanation
Indices: 980121--980168 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
980111 CCGAAAAAAG
980121 TCAACGGTGGTCAACAACGA
1 TCAACGGTGGTCAACAACGA
980141 TCAACGGTGGTCAACAACGA
1 TCAACGGTGGTCAACAACGA
980161 TCAACGGT
1 TCAACGGT
980169 TAACAACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (20 bp):
TCAACGGTGGTCAACAACGA
Found at i:980175 original size:20 final size:20
Alignment explanation
Indices: 980121--980175 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
980111 CCGAAAAAAG
**
980121 TCAACGGTGGTCAACAACGA
1 TCAACGGTGAACAACAACGA
**
980141 TCAACGGTGGTCAACAACGA
1 TCAACGGTGAACAACAACGA
*
980161 TCAACGGTTAACAAC
1 TCAACGGTGAACAAC
980176 TCAGTGGCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (20 bp):
TCAACGGTGAACAACAACGA
Found at i:985364 original size:18 final size:18
Alignment explanation
Indices: 985341--985381 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
985331 GATAACCAAA
985341 AATTGCCAAGAGGGGTTG
1 AATTGCCAAGAGGGGTTG
985359 AATTGCCAAGAGGGGTTG
1 AATTGCCAAGAGGGGTTG
985377 AATTG
1 AATTG
985382 GTTTTTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.10, G:0.37, T:0.24
Consensus pattern (18 bp):
AATTGCCAAGAGGGGTTG
Found at i:985879 original size:258 final size:256
Alignment explanation
Indices: 985417--985932 Score: 935
Period size: 258 Copynumber: 2.0 Consensus size: 256
985407 ATTAAAAAGA
*
985417 TAGACAAATTGCACAACGATTTATAGTGGTTCGACTTCTCAACCAAGTCTACCTCCACTACCTAA
1 TAGACAAATTGCACAACGATTTATAGTGGTTCGACTTCTCAACCAAGTCTACATCCACTACCTAA
*
985482 GCTCTCACTTAGGATTTTCTAACAAATTCACCAATTTGTTCTTTTTTTCAAGGACAAAGAGATAA
66 GCTCTCACTTAGAATTTTCTAACAAATTCACCAATTTGTTCTTTTTTTCAAGGACAAAGAGATAA
985547 CCATTTACAACTCCCTAACTTTTCAATGGCTAAACTAAAACCAATCTCTATATTTTCACTTGGCT
131 CCATTTACAACTCCCTAACTTTTCAATGGCTAAACTAAAACCAATCTCTATATTTTCACTTGGCT
*
985612 AAAATAGAACCAATCCCCTTTTATAAGGAAAAGAAATGTAAACAAGAAAACCTCTCTAAGG
196 AAAATAGAACCAATCCCCTTTTACAAGGAAAAGAAATGTAAACAAGAAAACCTCTCTAAGG
*
985673 TAGACAAATTGCACATCGATTTATAGTGGTTCGACTTCTCAACCAAGTCTACATCCACTACCTAA
1 TAGACAAATTGCACAACGATTTATAGTGGTTCGACTTCTCAACCAAGTCTACATCCACTACCTAA
985738 GCTCCTCACTTAGAATTTTCTAACAAATTCACCAATTTGTTCTTTCTTTTTCAAGGACAAAGAGA
66 GCT-CTCACTTAGAATTTTCTAACAAATTCACCAATTTGTTC-TT-TTTTTCAAGGACAAAGAGA
* *
985803 TAACC-TTTACAACTCCCTAACTTTTCAATGGCTAAACTAAAACTAATCTCTATCTTTTCACTTG
128 TAACCATTTACAACTCCCTAACTTTTCAATGGCTAAACTAAAACCAATCTCTATATTTTCACTTG
*
985867 GCTAAGATAGAACCAATCCCCTTTTACAAGGAAAAGAAATGTAAACAAGAAAACCTCTCTAAGG
193 GCTAAAATAGAACCAATCCCCTTTTACAAGGAAAAGAAATGTAAACAAGAAAACCTCTCTAAGG
985931 TA
1 TA
985933 TGTGTTTACA
Statistics
Matches: 250, Mismatches: 7, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
256 66 0.26
257 37 0.15
258 123 0.49
259 24 0.10
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.30
Consensus pattern (256 bp):
TAGACAAATTGCACAACGATTTATAGTGGTTCGACTTCTCAACCAAGTCTACATCCACTACCTAA
GCTCTCACTTAGAATTTTCTAACAAATTCACCAATTTGTTCTTTTTTTCAAGGACAAAGAGATAA
CCATTTACAACTCCCTAACTTTTCAATGGCTAAACTAAAACCAATCTCTATATTTTCACTTGGCT
AAAATAGAACCAATCCCCTTTTACAAGGAAAAGAAATGTAAACAAGAAAACCTCTCTAAGG
Found at i:986265 original size:21 final size:21
Alignment explanation
Indices: 986239--986295 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
986229 GGCTTGATAG
986239 TATCGATACTACTGTTCACAA
1 TATCGATACTACTGTTCACAA
* ***
986260 TATCGATACTACTTTTCATGG
1 TATCGATACTACTGTTCACAA
986281 TATCGATACTACTGT
1 TATCGATACTACTGT
986296 AGCAGTATCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (21 bp):
TATCGATACTACTGTTCACAA
Found at i:986320 original size:42 final size:42
Alignment explanation
Indices: 986238--986316 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
986228 GGGCTTGATA
*
986238 GTATCGATACTACTGTTCACAATATCGATACTACTTTTCATG
1 GTATCGATACTACTGTTCACAATATCGATACCACTTTTCATG
* *
986280 GTATCGATACTACTG-T-AGCAGTATCGATACCATTTTT
1 GTATCGATACTACTGTTCA-CAATATCGATACCACTTTT
986317 TCATTCTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 1 0.03
41 17 0.52
42 15 0.45
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (42 bp):
GTATCGATACTACTGTTCACAATATCGATACCACTTTTCATG
Found at i:986391 original size:20 final size:20
Alignment explanation
Indices: 986363--986415 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
986353 GTATCGATAC
* * *
986363 TACTGTTCACACAGTATCGG
1 TACTATTCACACAATATCAG
* *
986383 TACTATTCATACAATATTAG
1 TACTATTCACACAATATCAG
986403 TACTATTCACACA
1 TACTATTCACACA
986416 TAGGTTACTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (20 bp):
TACTATTCACACAATATCAG
Found at i:994740 original size:16 final size:16
Alignment explanation
Indices: 994719--994757 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
994709 TTGACCCAAA
994719 TTTATA-AATAATATAT
1 TTTATATAATAA-ATAT
*
994735 TTTATATATTAAATAT
1 TTTATATAATAAATAT
994751 TTTATAT
1 TTTATAT
994758 TTTCAGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATATAATAAATAT
Found at i:994856 original size:19 final size:19
Alignment explanation
Indices: 994828--994872 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
994818 AATAATATAT
*
994828 ATAATATATTAAATTTTTA
1 ATAATTTATTAAATTTTTA
994847 ATAATTTATTAAATTTTTA
1 ATAATTTATTAAATTTTTA
994866 ATAATTT
1 ATAATTT
994873 TGATAACCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATAATTTATTAAATTTTTA
Found at i:1000349 original size:2 final size:2
Alignment explanation
Indices: 1000342--1000437 Score: 56
Period size: 2 Copynumber: 54.5 Consensus size: 2
1000332 GAAAATATTT
* *
1000342 TA TA TA TA -A T- TA -A TA TA TA -A AA TA TA -A AA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1000378 TA TA TA TA TA TA TA TA -A T- TA -A TA TA -A AA AA TA TA -A AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1000415 TA T- TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1000438 GGGCGGGTCG
Statistics
Matches: 77, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
1 13 0.17
2 64 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1000401 original size:44 final size:44
Alignment explanation
Indices: 1000342--1000433 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
1000332 GAAAATATTT
*
1000342 TATATATAATTAATATATAAAATATAAAATATTATATATATATA
1 TATATATAATTAATATAAAAAATATAAAATATTATATATATATA
1000386 TATATATAATTAATATAAAAAATATAAAATATTATATATATATA
1 TATATATAATTAATATAAAAAATATAAAATATTATATATATATA
1000430 TATA
1 TATA
1000434 ATATGGGCGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (44 bp):
TATATATAATTAATATAAAAAATATAAAATATTATATATATATA
Found at i:1001302 original size:13 final size:13
Alignment explanation
Indices: 1001284--1001308 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1001274 TTGATAACTG
1001284 ATTTGATTAGTTA
1 ATTTGATTAGTTA
1001297 ATTTGATTAGTT
1 ATTTGATTAGTT
1001309 GTTTATATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (13 bp):
ATTTGATTAGTTA
Found at i:1007041 original size:91 final size:93
Alignment explanation
Indices: 1006884--1007067 Score: 354
Period size: 91 Copynumber: 2.0 Consensus size: 93
1006874 GACGAACCAG
1006884 ACGAATGTGTATCATTCGGTCGATTCGGTCCAATTCGGAGGTGATAAATAAGCCCTGAAAACAAA
1 ACGAATGTGTATCATTCGGTCGATTCGGTCCAATTCGGAGGTGATAAATAAGCCCTGAAAACAAA
1006949 GACCAATAACCACAAAAAATTATCAAAA
66 GACCAATAACCACAAAAAATTATCAAAA
1006977 ACGAATGTGTATC-TTCGGTCGATTCGGTCCAATTCGGA-GTGATAAATAAGCCCTGAAAACAAA
1 ACGAATGTGTATCATTCGGTCGATTCGGTCCAATTCGGAGGTGATAAATAAGCCCTGAAAACAAA
1007040 GACCAATAACCACAAAAAATTATCAAAA
66 GACCAATAACCACAAAAAATTATCAAAA
1007068 GATCAGAAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
91 53 0.58
92 25 0.27
93 13 0.14
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.22
Consensus pattern (93 bp):
ACGAATGTGTATCATTCGGTCGATTCGGTCCAATTCGGAGGTGATAAATAAGCCCTGAAAACAAA
GACCAATAACCACAAAAAATTATCAAAA
Found at i:1010219 original size:14 final size:13
Alignment explanation
Indices: 1010202--1010248 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1010192 TCAAAATAAA
*
1010202 AAAATTAAAATTAT
1 AAAATTAAAA-TAC
1010216 AAAATTAAAATAC
1 AAAATTAAAATAC
*
1010229 AAAATTATTAATA-
1 AAAATTA-AAATAC
1010242 AAAATTA
1 AAAATTA
1010249 TCAAACTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 16 0.53
14 14 0.47
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTAAAATAC
Found at i:1011481 original size:3 final size:3
Alignment explanation
Indices: 1011473--1011543 Score: 87
Period size: 3 Copynumber: 24.3 Consensus size: 3
1011463 GGCATGTTTG
*
1011473 TAA TAA TAA TAA TAT TAA TAA TAA -AA TAAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TAA TAA
1011519 TAA TAA -AA -AA TAA -AA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1011544 GAAGATAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 8 0.13
3 47 0.76
4 7 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1011509 original size:31 final size:30
Alignment explanation
Indices: 1011473--1011543 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 30
1011463 GGCATGTTTG
*
1011473 TAATAATAATAATATTAATAATAAAAT-AAA
1 TAATAATAATAATAATAATAA-AAAATAAAA
1011503 TAAATAATAATAATAATAATAAAAAATAAAA
1 T-AATAATAATAATAATAATAAAAAATAAAA
1011534 TAATAATAAT
1 TAATAATAAT
1011544 GAAGATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
30 15 0.39
31 23 0.61
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATAATAATAATAATAATAAAAAATAAAA
Found at i:1011512 original size:19 final size:19
Alignment explanation
Indices: 1011473--1011542 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
1011463 GGCATGTTTG
*
1011473 TAATAATAATAAT-ATTAA
1 TAATAATAATAATAAATAA
1011491 TAATAA-AATAAATAAATAA
1 TAATAATAAT-AATAAATAA
*
1011510 TAATAATAATAATAAAAAA
1 TAATAATAATAATAAATAA
1011529 TAA-AATAATAATAA
1 TAATAATAATAATAA
1011543 TGAAGATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.06
18 20 0.43
19 21 0.45
20 3 0.06
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TAATAATAATAATAAATAA
Found at i:1011561 original size:27 final size:27
Alignment explanation
Indices: 1011477--1011543 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 27
1011467 TGTTTGTAAT
*
1011477 AATAATAATATTAATAATAAAATAA-ATA
1 AATAATAATAATAATAATAAAA-AATA-A
1011505 AATAATAATAATAATAATAAAAAATAA
1 AATAATAATAATAATAATAAAAAATAA
1011532 AATAATAATAAT
1 AATAATAATAAT
1011544 GAAGATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
27 15 0.41
28 22 0.59
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (27 bp):
AATAATAATAATAATAATAAAAAATAA
Found at i:1011629 original size:32 final size:33
Alignment explanation
Indices: 1011572--1011638 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 33
1011562 GAAAAAAAAC
1011572 TAGTGTCTTCAGCTGCCCCTCTTTGCTCATTCT
1 TAGTGTCTTCAGCTGCCCCTCTTTGCTCATTCT
1011605 TAGTGTCTTCAGCTG-CCCTCTTTGCTCATTCT
1 TAGTGTCTTCAGCTGCCCCTCTTTGCTCATTCT
1011637 TA
1 TA
1011639 TGTTAATGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 19 0.56
33 15 0.44
ACGTcount: A:0.10, C:0.31, G:0.15, T:0.43
Consensus pattern (33 bp):
TAGTGTCTTCAGCTGCCCCTCTTTGCTCATTCT
Found at i:1012512 original size:22 final size:22
Alignment explanation
Indices: 1012387--1012510 Score: 185
Period size: 22 Copynumber: 5.6 Consensus size: 22
1012377 AATAAAGCTT
*
1012387 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
1012409 TTATCTTTGAAGAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTA
*
1012431 TCATCTCTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
1012453 CCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
1012475 TCATATTTGAAGAGTGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1012497 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
1012511 TGTAAATGTG
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 90 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:1013962 original size:75 final size:75
Alignment explanation
Indices: 1013831--1014085 Score: 302
Period size: 75 Copynumber: 3.4 Consensus size: 75
1013821 CATGATGATG
* * * * *
1013831 TGGGCCTTCAGCATGCCTCAGCATTTGCTGATATG-AACGTTCAAAATGAGTTAATATTCCAATT
1 TGGGCTTTCAGCATGCCCCAACATTTGCTGATA-GAAACGTTCAAAATGCGTTAATATTCCGATT
1013895 TCTGATTGAAA
65 TCTGATTGAAA
* * * *
1013906 TGGGCTTTTAGCATGCCCCAACATTTGTTGATAGAAACGTTCAAAATGCGTCAATATTCTTGA-T
1 TGGGCTTTCAGCATGCCCCAACATTTGCTGATAGAAACGTTCAAAATGCGTTAATATTC-CGATT
1013970 TCTGATTGAAA
65 TCTGATTGAAA
** * * *
1013981 TGGG-TTTTTGAAATGCTCCAACATTTTGCTGATACAAACGTTCAAAATGCGTTAATATTCCTGA
1 TGGGCTTTCAG-CATGCCCCAACA-TTTGCTGATAGAAACGTTCAAAATGCGTTAATATTCC-GA
1014045 TTT-TGATTGAAA
63 TTTCTGATTGAAA
*
1014057 TGGGCTTTCAACATGCCCCAACATTTGCT
1 TGGGCTTTCAGCATGCCCCAACATTTGCT
1014086 TCTTGCTAAT
Statistics
Matches: 152, Mismatches: 21, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
74 6 0.04
75 82 0.54
76 59 0.39
77 5 0.03
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (75 bp):
TGGGCTTTCAGCATGCCCCAACATTTGCTGATAGAAACGTTCAAAATGCGTTAATATTCCGATTT
CTGATTGAAA
Found at i:1014039 original size:76 final size:73
Alignment explanation
Indices: 1013854--1014082 Score: 262
Period size: 76 Copynumber: 3.0 Consensus size: 73
1013844 TGCCTCAGCA
** * ** *
1013854 TTTGCTGATATGAACGTTCAAAATGAGTTAATATTCCAATTTCTGATTGAAATGGGCTTTTAGCA
1 TTTGCTGATACAAACGTTCAAAATGCGTTAATATTCTGA-TTCTGATTGAAATGGG-TTTTA-AA
1013919 TGCCCCAACA-
63 TGCCCCAACAT
* * *
1013929 TTTGTTGATAGAAACGTTCAAAATGCGTCAATATTCTTGATTCTGATTGAAATGGGTTTTTGAAA
1 TTTGCTGATACAAACGTTCAAAATGCGTTAATATTC-TGATTCTGATTGAAATGGG-TTTT-AAA
*
1013994 TGCTCCAACAT
63 TGCCCCAACAT
* *
1014005 TTTGCTGATACAAACGTTCAAAATGCGTTAATATTCCTGATTTTGATTGAAATGGGCTTTCAACA
1 TTTGCTGATACAAACGTTCAAAATGCGTTAATATT-CTGATTCTGATTGAAATGGG-TTTTAA-A
1014070 TGCCCCAACAT
63 TGCCCCAACAT
1014081 TT
1 TT
1014083 GCTTCTTGCT
Statistics
Matches: 132, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
75 63 0.48
76 68 0.52
77 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (73 bp):
TTTGCTGATACAAACGTTCAAAATGCGTTAATATTCTGATTCTGATTGAAATGGGTTTTAAATGC
CCCAACAT
Found at i:1014724 original size:43 final size:43
Alignment explanation
Indices: 1014658--1014872 Score: 376
Period size: 43 Copynumber: 5.0 Consensus size: 43
1014648 TTGAAAGTAA
* *
1014658 ATGTGCAAGAACTGAATGATGATCTGTTGGAGCAATTGATGAG
1 ATGTGCAAGAACTGAATGGTGATCGGTTGGAGCAATTGATGAG
*
1014701 ATGTGCAAGAACTTAATGGTGATCGGTTGGAGCAATTGATGAG
1 ATGTGCAAGAACTGAATGGTGATCGGTTGGAGCAATTGATGAG
1014744 ATGTGCAAGAACTGAATGGTGATCGGTTGGAGCAATTGATGAG
1 ATGTGCAAGAACTGAATGGTGATCGGTTGGAGCAATTGATGAG
* *
1014787 ATGTGAAAGAACTGAATGGTGATCGGTTGAAGCAATTGATGAG
1 ATGTGCAAGAACTGAATGGTGATCGGTTGGAGCAATTGATGAG
*
1014830 ATGTGCAAGAACTAAATGGTGATCGGTTGGAGCAATTGATGAG
1 ATGTGCAAGAACTGAATGGTGATCGGTTGGAGCAATTGATGAG
1014873 TAGATTTGGC
Statistics
Matches: 163, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 163 1.00
ACGTcount: A:0.32, C:0.09, G:0.33, T:0.27
Consensus pattern (43 bp):
ATGTGCAAGAACTGAATGGTGATCGGTTGGAGCAATTGATGAG
Found at i:1016630 original size:6 final size:7
Alignment explanation
Indices: 1016613--1016638 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1016603 TTGATTCAAT
1016613 TTTTTCC
1 TTTTTCC
1016620 TTTTTCC
1 TTTTTCC
1016627 TTTTTCC
1 TTTTTCC
1016634 TTTTT
1 TTTTT
1016639 TTTTGATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCC
Found at i:1018591 original size:13 final size:13
Alignment explanation
Indices: 1018553--1018594 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1018543 AAAGCAAACA
1018553 TAAAAGTACAAATG
1 TAAAA-TACAAATG
*
1018567 AAAAATGA-AAATG
1 TAAAAT-ACAAATG
1018580 TAAAATACAAATG
1 TAAAATACAAATG
1018593 TA
1 TA
1018595 TGTATGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 1 0.04
13 18 0.75
14 5 0.21
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.21
Consensus pattern (13 bp):
TAAAATACAAATG
Found at i:1020658 original size:2 final size:2
Alignment explanation
Indices: 1020653--1020683 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1020643 TATTAAATAA
1020653 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 A
1020684 CATTTAGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1020837 original size:11 final size:11
Alignment explanation
Indices: 1020823--1020873 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
1020813 TATGACTAAT
1020823 ATAATAATAAA
1 ATAATAATAAA
*
1020834 ATAATAATTTAA
1 ATAATAA-TAAA
1020846 ATATATAA-AAA
1 ATA-ATAATAAA
*
1020857 ATAATAAAAAA
1 ATAATAATAAA
1020868 ATAATA
1 ATAATA
1020874 TTGCAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 4 0.11
11 21 0.60
12 6 0.17
13 4 0.11
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:1020882 original size:34 final size:34
Alignment explanation
Indices: 1020823--1020888 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1020813 TATGACTAAT
* * *
1020823 ATAATAATAAAATAATAATTTAAATATATAAAAA
1 ATAATAAAAAAATAATAATTCAAATAAATAAAAA
1020857 ATAATAAAAAAATAAT-ATTGCAAATAAATAAA
1 ATAATAAAAAAATAATAATT-CAAATAAATAAA
1020889 TATCAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 3 0.11
34 25 0.89
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (34 bp):
ATAATAAAAAAATAATAATTCAAATAAATAAAAA
Found at i:1022163 original size:3 final size:3
Alignment explanation
Indices: 1022155--1022217 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
1022145 GGCCAGTTTG
* *
1022155 TAA TAA TAA TAA TAT TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1022203 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
1022218 AGATAAAAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1026869 original size:2 final size:2
Alignment explanation
Indices: 1026862--1026918 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1026852 AGAATTTTAA
1026862 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
1026904 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1026919 ATTAGAGTTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1027528 original size:21 final size:21
Alignment explanation
Indices: 1027512--1027575 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
1027502 CGATTGTTAG
1027512 ATTTGGCTTGCAAATTGTCAA
1 ATTTGGCTTGCAAATTGTCAA
* *
1027533 ATTT-G---GC-AATTGTTAG
1 ATTTGGCTTGCAAATTGTCAA
* *
1027549 GTTTGACTTGCAAATTGTCAA
1 ATTTGGCTTGCAAATTGTCAA
1027570 ATTTGG
1 ATTTGG
1027576 TAAGTTTACA
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
16 10 0.33
17 2 0.07
20 3 0.10
21 15 0.50
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (21 bp):
ATTTGGCTTGCAAATTGTCAA
Found at i:1027559 original size:37 final size:37
Alignment explanation
Indices: 1027504--1027575 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
1027494 TTCTGTTGCG
*
1027504 ATTGTTAGATTTGGCTTGCAAATTGTCAAATTTGGCA
1 ATTGTTAGATTTGACTTGCAAATTGTCAAATTTGGCA
*
1027541 ATTGTTAGGTTTGACTTGCAAATTGTCAAATTTGG
1 ATTGTTAGATTTGACTTGCAAATTGTCAAATTTGG
1027576 TAAGTTTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42
Consensus pattern (37 bp):
ATTGTTAGATTTGACTTGCAAATTGTCAAATTTGGCA
Found at i:1029854 original size:18 final size:17
Alignment explanation
Indices: 1029800--1029848 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1029790 TTGAACCCTT
* *
1029800 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1029818 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1029836 AGTGCATTCGATG
1 AGTGCA-TCGATG
1029849 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1029917 original size:46 final size:45
Alignment explanation
Indices: 1029819--1029924 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 45
1029809 GTGCACTAAG
* *
1029819 AGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* *
1029864 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
*
1029910 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
1029925 GGTATGTGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 29 0.54
46 22 0.41
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:1039620 original size:45 final size:45
Alignment explanation
Indices: 1039570--1039674 Score: 210
Period size: 45 Copynumber: 2.3 Consensus size: 45
1039560 TGCATAGTAT
1039570 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATG
1 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATG
1039615 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATG
1 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATG
1039660 GTGCATCGATGCATG
1 GTGCATCGATGCATG
1039675 GATTGGTGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (45 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATG
Found at i:1043146 original size:21 final size:21
Alignment explanation
Indices: 1043122--1043185 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
1043112 GATTTGTTAG
1043122 ATTTGGCTTGCAAATTGTCAA
1 ATTTGGCTTGCAAATTGTCAA
* * *
1043143 ATTT-G---ACAAA-TGTTAT
1 ATTTGGCTTGCAAATTGTCAA
*
1043159 GTTTGGCTTGCAAATTGTCAA
1 ATTTGGCTTGCAAATTGTCAA
1043180 ATTTGG
1 ATTTGG
1043186 TAAGTTGACA
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
16 7 0.23
17 5 0.17
20 5 0.17
21 13 0.43
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (21 bp):
ATTTGGCTTGCAAATTGTCAA
Found at i:1046209 original size:18 final size:18
Alignment explanation
Indices: 1046186--1046220 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1046176 AGATTGGGGG
*
1046186 TTATTTTATTAATTTTAA
1 TTATTTAATTAATTTTAA
*
1046204 TTATTTAATTTATTTTA
1 TTATTTAATTAATTTTA
1046221 TTTTCAACTG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTAATTAATTTTAA
Found at i:1046573 original size:20 final size:20
Alignment explanation
Indices: 1046548--1046585 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1046538 ATATATAATC
1046548 ATTAAATTATT-TTTAATATA
1 ATTAAATT-TTATTTAATATA
1046568 ATTAAATTTTATTTAATA
1 ATTAAATTTTATTTAATA
1046586 ATTATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTAAATTTTATTTAATATA
Found at i:1046588 original size:18 final size:18
Alignment explanation
Indices: 1046543--1046589 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
1046533 GTTTTATATA
*
1046543 TAATCATTAAATTATTTT
1 TAATAATTAAATTATTTT
1046561 TAATATAATTAAATT-TTATT
1 T-A-ATAATTAAATTATT-TT
1046581 TAATAATTA
1 TAATAATTA
1046590 TATATAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 8 0.32
19 4 0.16
20 13 0.52
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATAATTAAATTATTTT
Found at i:1046754 original size:21 final size:21
Alignment explanation
Indices: 1046713--1046769 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
1046703 AAATTAATTT
*
1046713 TTAAATTTA-TTTTAAAAATA
1 TTAAATTTATTTTTATAAATA
*
1046733 TTAAATTTATTTTTATACATA
1 TTAAATTTATTTTTATAAATA
*
1046754 TTAAATTTATTATTAT
1 TTAAATTTATTTTTAT
1046770 TTTAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 9 0.27
21 24 0.73
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAATTTATTTTTATAAATA
Found at i:1052464 original size:117 final size:116
Alignment explanation
Indices: 1052254--1052725 Score: 449
Period size: 117 Copynumber: 4.1 Consensus size: 116
1052244 TCTCCTCCAT
* * *
1052254 TTTTTTCATCTTTGCCTCGTACTGTTTTAATTGTTCCCGTAATGTATCATTTTCCTGTTCTTTTT
1 TTTTTGCATTTTTGCCTCGTACTGTTTTAATTGTTCCCGTAATGT-GCATTTTCCTGTTCTTTTT
* * * *
1052319 GCATATGTGCTTCATACTGTTGTAATTGTTCCCGTATGGCATTTTCCAATTC
65 GCATATTTGCCTCGTACTGTTGTAATTGTTCCCGTATGGCATTTTCCTATTC
* *
1052371 TTTTTGCATTTTTGCCTCGTGCTGTTTTAACTGTTCCCGTAATGTGCGATTTTCCTGTTCTTTTT
1 TTTTTGCATTTTTGCCTCGTACTGTTTTAATTGTTCCCGTAATGTGC-ATTTTCCTGTTCTTTTT
* * * *
1052436 GCATATTTGCCTCGTACAGTTGTGATTGTTCCCG--T-GCTTTTTCCTGTTC
65 GCATATTTGCCTCGTACTGTTGTAATTGTTCCCGTATGGCATTTTCCTATTC
* * * * * * * *
1052485 CTTCTGCATTTTTTCTTCATACTGTTGTAATTGTTCCTGT-ATG-GCATTTTCCAGTTCTTTTTG
1 TTTTTGCATTTTTGCCTCGTACTGTTTTAATTGTTCCCGTAATGTGCATTTTCCTGTTCTTTTTG
* *
1052548 CATCTTTGCCTCGTACTGTTGTAATTGTTCCCGTAATGTGTCATTTTCCTCTTC
66 CATATTTGCCTCGTACTGTTGTAATTGTTCCCGT-ATG-G-CATTTTCCTATTC
* * ** * * *
1052602 TTTTCGCATATTTT-CCGCGTACAATTGTAATTGTTCCCCT-AT-AGCATTTTCCTGTTCCTTTT
1 TTTTTGCAT-TTTTGCCTCGTACTGTTTTAATTGTTCCCGTAATGTGCATTTTCCTGTT-CTTTT
* * * * * * * *
1052664 T-CATTTTTTCCTCATATTGTCGTAATTGTTCCCATAATGTGGCATTTTCCTGTTG
64 TGCATATTTGCCTCGTACTGTTGTAATTGTTCCCGT-A--TGGCATTTTCCTATTC
1052719 TTTTTGC
1 TTTTTGC
1052726 CCCAAAGTTG
Statistics
Matches: 295, Mismatches: 48, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
111 47 0.16
112 2 0.01
113 3 0.01
114 43 0.15
115 1 0.00
116 2 0.01
117 184 0.62
118 11 0.04
119 2 0.01
ACGTcount: A:0.13, C:0.22, G:0.15, T:0.50
Consensus pattern (116 bp):
TTTTTGCATTTTTGCCTCGTACTGTTTTAATTGTTCCCGTAATGTGCATTTTCCTGTTCTTTTTG
CATATTTGCCTCGTACTGTTGTAATTGTTCCCGTATGGCATTTTCCTATTC
Found at i:1052558 original size:171 final size:174
Alignment explanation
Indices: 1052301--1052696 Score: 548
Period size: 171 Copynumber: 2.3 Consensus size: 174
1052291 CGTAATGTAT
* * * *
1052301 CATTTTCCTGTTCTTTTTGCATATGTGCTTCATACTGTTGTAATTGTTCCCGTATGGCATTTTCC
1 CATTTTCCTGTTCCTTTTGCATTTTTTCTTCATACTGTTGTAATTGTTCCCGTATGGCATTTTCC
* * * *
1052366 AATTCTTTTTGCATTTTTGCCTCGTGCTGTTTTAACTGTTCCCGTAATGTG-CGATTTTCCTGTT
66 AATTCTTTTTGCATCTTTGCCTCGTACTGTTGTAACTGTTCCCGTAATGTGTC-ATTTTCCTCTT
* * * * *
1052430 CTTTTTGCATATTTGCCTCGTACAGTTGTGATTGTT-CCC-GT-G
130 CTTTTCGCATATTTGCCGCGTACAATTGTAATTGTTCCCCTATAG
* * *
1052472 CTTTTTCCTGTTCCTTCTGCATTTTTTCTTCATACTGTTGTAATTGTTCCTGTATGGCATTTTCC
1 CATTTTCCTGTTCCTTTTGCATTTTTTCTTCATACTGTTGTAATTGTTCCCGTATGGCATTTTCC
* *
1052537 AGTTCTTTTTGCATCTTTGCCTCGTACTGTTGTAATTGTTCCCGTAATGTGTCATTTTCCTCTTC
66 AATTCTTTTTGCATCTTTGCCTCGTACTGTTGTAACTGTTCCCGTAATGTGTCATTTTCCTCTTC
*
1052602 TTTTCGCATATTTTCCGCGTACAATTGTAATTGTTCCCCTATAG
131 TTTTCGCATATTTGCCGCGTACAATTGTAATTGTTCCCCTATAG
* * * *
1052646 CATTTTCCTGTTCCTTTTTCATTTTTTCCTCATATTGTCGTAATTGTTCCC
1 CATTTTCCTGTTCCTTTTGCATTTTTTCTTCATACTGTTGTAATTGTTCCC
1052697 ATAATGTGGC
Statistics
Matches: 195, Mismatches: 26, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
171 145 0.74
172 4 0.02
173 1 0.01
174 45 0.23
ACGTcount: A:0.13, C:0.22, G:0.15, T:0.50
Consensus pattern (174 bp):
CATTTTCCTGTTCCTTTTGCATTTTTTCTTCATACTGTTGTAATTGTTCCCGTATGGCATTTTCC
AATTCTTTTTGCATCTTTGCCTCGTACTGTTGTAACTGTTCCCGTAATGTGTCATTTTCCTCTTC
TTTTCGCATATTTGCCGCGTACAATTGTAATTGTTCCCCTATAG
Found at i:1052963 original size:60 final size:57
Alignment explanation
Indices: 1052793--1053052 Score: 304
Period size: 57 Copynumber: 4.5 Consensus size: 57
1052783 TGCTCATTTG
* * * *
1052793 GTATTGCATTTTCCTGTTCCTTCTGCATTTTTTCCTCGTACTGTTGTAATGGTTCCC
1 GTATGGCATTTTCCTGTTCTTTTTGCATTTTTTCCTCGTACTGTTGTAATTGTTCCC
* * * * *
1052850 ATATGGCATTTTCCAGTTCTTTTTGCATCTTTGCCTCGTACTGTCGTAATTGTTCCC
1 GTATGGCATTTTCCTGTTCTTTTTGCATTTTTTCCTCGTACTGTTGTAATTGTTCCC
* * * ** *
1052907 GTAGTGTGTCATTTTCCTCTTCTTTTTGCATATTTTCCGCGTAAAGTTGTAGTTGTTCCC
1 GTA-TG-G-CATTTTCCTGTTCTTTTTGCATTTTTTCCTCGTACTGTTGTAATTGTTCCC
* * *
1052967 CTATGGCATTTTCCTGTTCCTTCTGCATTTTTTCCTCGTACTGTTGTAATTGTTCCC
1 GTATGGCATTTTCCTGTTCTTTTTGCATTTTTTCCTCGTACTGTTGTAATTGTTCCC
1053024 GTAATGTGGCATTTTCCTGTTCTTTTTGC
1 GT-A--TGGCATTTTCCTGTTCTTTTTGC
1053053 CCCAGAGTTG
Statistics
Matches: 166, Mismatches: 31, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
57 94 0.57
58 4 0.02
59 3 0.02
60 65 0.39
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.48
Consensus pattern (57 bp):
GTATGGCATTTTCCTGTTCTTTTTGCATTTTTTCCTCGTACTGTTGTAATTGTTCCC
Found at i:1052965 original size:117 final size:117
Alignment explanation
Indices: 1052798--1053052 Score: 348
Period size: 117 Copynumber: 2.2 Consensus size: 117
1052788 ATTTGGTATT
* * * * **
1052798 GCATTTTCCTGTTCCTTCTGCATTTTTTCCTCGTACTGTTGTAATGGTTCCCATATGGCATTTTC
1 GCATTTTCCTGTTCTTTTTGCATATTTTCCGCGTAAAGTTGTAATGGTTCCCATATGGCATTTTC
* * *
1052863 CAGTTCTTTTTGCATCTTTGCCTCGTACTGTCGTAATTGTTCCCGTAGTGTG
66 CAGTTCCTTCTGCATCTTTGCCTCGTACTGTCGTAATTGTTCCCGTAATGTG
* * * * *
1052915 TCATTTTCCTCTTCTTTTTGCATATTTTCCGCGTAAAGTTGTAGTTGTTCCCCTATGGCATTTTC
1 GCATTTTCCTGTTCTTTTTGCATATTTTCCGCGTAAAGTTGTAATGGTTCCCATATGGCATTTTC
* * * *
1052980 CTGTTCCTTCTGCATTTTTTCCTCGTACTGTTGTAATTGTTCCCGTAATGTG
66 CAGTTCCTTCTGCATCTTTGCCTCGTACTGTCGTAATTGTTCCCGTAATGTG
1053032 GCATTTTCCTGTTCTTTTTGC
1 GCATTTTCCTGTTCTTTTTGC
1053053 CCCAGAGTTG
Statistics
Matches: 118, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
117 118 1.00
ACGTcount: A:0.12, C:0.24, G:0.16, T:0.48
Consensus pattern (117 bp):
GCATTTTCCTGTTCTTTTTGCATATTTTCCGCGTAAAGTTGTAATGGTTCCCATATGGCATTTTC
CAGTTCCTTCTGCATCTTTGCCTCGTACTGTCGTAATTGTTCCCGTAATGTG
Found at i:1053068 original size:327 final size:327
Alignment explanation
Indices: 1052474--1053123 Score: 1095
Period size: 327 Copynumber: 2.0 Consensus size: 327
1052464 TTCCCGTGCT
* * **
1052474 TTTTCCTGTTCCTTCTGCATTTTTTCTTCATACTGTTGTAATTGTTCCTGTATGGCATTTTCCAG
1 TTTTCCTGTTCCTTCTGCATTTTTTCCTCATACTGTTGTAATGGTTCCCATATGGCATTTTCCAG
*
1052539 TTCTTTTTGCATCTTTGCCTCGTACTGTTGTAATTGTTCCCGTAATGTGTCATTTTCCTCTTCTT
66 TTCTTTTTGCATCTTTGCCTCGTACTGTCGTAATTGTTCCCGTAATGTGTCATTTTCCTCTTCTT
* *
1052604 TTCGCATATTTTCCGCGTACAATTGTAATTGTTCCCCTATAGCATTTTCCTGTTCCTTTTTCATT
131 TTCGCATATTTTCCGCGTACAATTGTAATTGTTCCCCTATAGCATTTTCCTGTTCCTTCTGCATT
* *
1052669 TTTTCCTCATATTGTCGTAATTGTTCCCATAATGTGGCATTTTCCTGTTGTTTTTGCCCCAAAGT
196 TTTTCCTCATACTGTCGTAATTGTTCCCATAATGTGGCATTTTCCTGTTCTTTTTGCCCCAAAGT
* *
1052734 TGCTTCCATGTCGAGAATCCTTCTTTGAAGCTCTGACATTGCTGAAGGCTGCTCATTTGGTATTG
261 TGCTTCCACGTCGAGAATCCTTCTTTGAAGCTCTGACATTGCAGAAGGCTGCTCATTTGGTATTG
1052799 CA
326 CA
*
1052801 TTTTCCTGTTCCTTCTGCATTTTTTCCTCGTACTGTTGTAATGGTTCCCATATGGCATTTTCCAG
1 TTTTCCTGTTCCTTCTGCATTTTTTCCTCATACTGTTGTAATGGTTCCCATATGGCATTTTCCAG
*
1052866 TTCTTTTTGCATCTTTGCCTCGTACTGTCGTAATTGTTCCCGTAGTGTGTCATTTTCCTCTTCTT
66 TTCTTTTTGCATCTTTGCCTCGTACTGTCGTAATTGTTCCCGTAATGTGTCATTTTCCTCTTCTT
* * *
1052931 TTTGCATATTTTCCGCGTA-AAGTTGTAGTTGTTCCCCTATGGCATTTTCCTGTTCCTTCTGCAT
131 TTCGCATATTTTCCGCGTACAA-TTGTAATTGTTCCCCTATAGCATTTTCCTGTTCCTTCTGCAT
* * * *
1052995 TTTTTCCTCGTACTGTTGTAATTGTTCCCGTAATGTGGCATTTTCCTGTTCTTTTTGCCCCAGAG
195 TTTTTCCTCATACTGTCGTAATTGTTCCCATAATGTGGCATTTTCCTGTTCTTTTTGCCCCAAAG
*
1053060 TTGCTTCCACGTCGAGAATCCTTCTTTGAAGCTCTGCCATTGCAGAAGGCTGCTCATTTGGTAT
260 TTGCTTCCACGTCGAGAATCCTTCTTTGAAGCTCTGACATTGCAGAAGGCTGCTCATTTGGTAT
1053124 GTCCTGGTCA
Statistics
Matches: 301, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
326 2 0.01
327 299 0.99
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.46
Consensus pattern (327 bp):
TTTTCCTGTTCCTTCTGCATTTTTTCCTCATACTGTTGTAATGGTTCCCATATGGCATTTTCCAG
TTCTTTTTGCATCTTTGCCTCGTACTGTCGTAATTGTTCCCGTAATGTGTCATTTTCCTCTTCTT
TTCGCATATTTTCCGCGTACAATTGTAATTGTTCCCCTATAGCATTTTCCTGTTCCTTCTGCATT
TTTTCCTCATACTGTCGTAATTGTTCCCATAATGTGGCATTTTCCTGTTCTTTTTGCCCCAAAGT
TGCTTCCACGTCGAGAATCCTTCTTTGAAGCTCTGACATTGCAGAAGGCTGCTCATTTGGTATTG
CA
Found at i:1053613 original size:33 final size:34
Alignment explanation
Indices: 1053576--1053659 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 34
1053566 GTCGATGCTG
* *
1053576 AGTAGCTACTTGCCTCTTCCTTAGTCAACGCT-A
1 AGTAGCTACTTGCCTCCTCCTTAGTCAACACTGA
* * * *
1053609 AGTAGCTACTTTCCACCTCCTTAGTCGACATTGA
1 AGTAGCTACTTGCCTCCTCCTTAGTCAACACTGA
1053643 A-TAGCTACTTGCCTCCT
1 AGTAGCTACTTGCCTCCT
1053660 TATTAGTGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 40 0.95
34 2 0.05
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (34 bp):
AGTAGCTACTTGCCTCCTCCTTAGTCAACACTGA
Found at i:1060756 original size:25 final size:23
Alignment explanation
Indices: 1060703--1060756 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
1060693 AAATCCTCTT
**
1060703 TCAATAAATAGAGTTTTATTTCA
1 TCAATAAATAGAGTTTTATGACA
*
1060726 TGCAATAAATAGATTTATTATGACA
1 T-CAATAAATAGAGTT-TTATGACA
1060751 CTCAAT
1 -TCAAT
1060757 TCTCAACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 13 0.52
25 10 0.40
26 1 0.04
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (23 bp):
TCAATAAATAGAGTTTTATGACA
Found at i:1067137 original size:114 final size:113
Alignment explanation
Indices: 1066934--1067279 Score: 413
Period size: 114 Copynumber: 3.0 Consensus size: 113
1066924 TTGGCCAAGC
* * * * *
1066934 TTGAGTGGGTATACTTGTGCCGGTGGATGGAAGCTGTTGCGTATTTTCAGGAGCAGATTTAGCTG
1 TTGAGTGGGTATGCTTGTGCCGGTGGATGGAGGATG-TGAGTATTTACAGGAGCAGATTTAGCTG
*
1066999 CAGCAGCCATGAGAAGGGACTGTTGATGTGCTAACAAAGCTAGTTGTTG
65 CAGCAGCCATGAGAAGGGACTGTTGATGTGCTAGCAAAGCTAGTTGTTG
** * * **
1067048 TTGAGTGGGTATGCTTGTGGTGGTAGATGGAGGATGCTGAGTATTTCCAGGAGCACCTTTAGCTG
1 TTGAGTGGGTATGCTTGTGCCGGTGGATGGAGGATG-TGAGTATTTACAGGAGCAGATTTAGCTG
* * * * * *
1067113 CAGAAGCCATGAAAAGAGATTGTTGCTGTGCTAGCAAAGCTAGCTGTTG
65 CAGCAGCCATGAGAAGGGACTGTTGATGTGCTAGCAAAGCTAGTTGTTG
* * ** ** * *
1067162 TTGAGAGGGTATGATTGCACCATTGGATGGTGAATGTCGAGTATTTACAGGAGCAGATTTAGCTG
1 TTGAGTGGGTATGCTTGTGCCGGTGGATGGAGGATGT-GAGTATTTACAGGAGCAGATTTAGCTG
* *
1067227 CAGCAGCCATCAGAAGGGACTGTTGATGTGCTAGCAATGCTAGTTGTTG
65 CAGCAGCCATGAGAAGGGACTGTTGATGTGCTAGCAAAGCTAGTTGTTG
1067276 TTGA
1 TTGA
1067280 TGCATTGCAT
Statistics
Matches: 191, Mismatches: 40, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
113 1 0.01
114 190 0.99
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (113 bp):
TTGAGTGGGTATGCTTGTGCCGGTGGATGGAGGATGTGAGTATTTACAGGAGCAGATTTAGCTGC
AGCAGCCATGAGAAGGGACTGTTGATGTGCTAGCAAAGCTAGTTGTTG
Found at i:1068423 original size:114 final size:114
Alignment explanation
Indices: 1068220--1068453 Score: 407
Period size: 114 Copynumber: 2.1 Consensus size: 114
1068210 CACCAGCAAA
*
1068220 AGAACTTAATACCAGATTCAGTCCCTTGGGAGGAACAGTAAGACTAATTCTTGTAGCAGGAAGAT
1 AGAACTTAATACCAGATTCAGTCCCTTGGGAGGAACAGGAAGACTAATTCTTGTAGCAGGAAGAT
*
1068285 TTTCATTTCTGTTAGATGCCTGAATGGTCCTTTCCTCAAAAGAATTATC
66 TTTCATTTCTGCTAGATGCCTGAATGGTCCTTTCCTCAAAAGAATTATC
*
1068334 AGAACTTAATACC-GAATTCAGTCCCTTGGGATGAACAGGAAGACTAATTCTTGTAGCAGGAAGA
1 AGAACTTAATACCAG-ATTCAGTCCCTTGGGAGGAACAGGAAGACTAATTCTTGTAGCAGGAAGA
* *
1068398 TTTTCATTTCTGCTAGATGCTTGAATGGTCCTTTCCTCAAATGAATTATC
65 TTTTCATTTCTGCTAGATGCCTGAATGGTCCTTTCCTCAAAAGAATTATC
1068448 AGAACT
1 AGAACT
1068454 ATGAACACGC
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
113 1 0.01
114 113 0.99
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (114 bp):
AGAACTTAATACCAGATTCAGTCCCTTGGGAGGAACAGGAAGACTAATTCTTGTAGCAGGAAGAT
TTTCATTTCTGCTAGATGCCTGAATGGTCCTTTCCTCAAAAGAATTATC
Found at i:1070451 original size:6 final size:6
Alignment explanation
Indices: 1070440--1070467 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1070430 ATAGAAAGAG
1070440 ACGATT ACGATT ACGATT ACGATT ACGA
1 ACGATT ACGATT ACGATT ACGATT ACGA
1070468 GGGGGTGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (6 bp):
ACGATT
Found at i:1078169 original size:39 final size:40
Alignment explanation
Indices: 1078125--1078216 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
1078115 ATTACTAAAG
* *
1078125 TTTAGTTTTTGTTTCA-TTTAGTA-CCTCGCCGGTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAGTATCAT-GACGGTAAAAAC
* *
1078164 TTTAGTCTTTGTTTCATTTTAGTATCATGACGTTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAGTATCATGACGGTAAAAAC
*
1078204 TTTAGTTGTTGTT
1 TTTAGTTTTTGTT
1078217 CGTACCCCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 15 0.33
40 28 0.62
41 2 0.04
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (40 bp):
TTTAGTTTTTGTTTCATTTTAGTATCATGACGGTAAAAAC
Found at i:1078544 original size:29 final size:31
Alignment explanation
Indices: 1078512--1078571 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1078502 AAATTTGTAA
*
1078512 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1078541 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1078572 CCTTAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1081749 original size:21 final size:21
Alignment explanation
Indices: 1081723--1081764 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1081713 CCAGAATGGG
*
1081723 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1081744 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1081765 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Done.