Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008772.1 Hibiscus syriacus cultivar Beakdansim tig00111877_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: 3098974
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 16
Found at i:2291002 original size:56 final size:58
Alignment explanation
Indices: 2290942--2291078 Score: 172
Period size: 60 Copynumber: 2.4 Consensus size: 58
2290932 GTCAATTGAT
* *
2290942 TATTAAAAGTTATAAAAT-AGT-T-GACTATAAAGAGTTATTTTGTTGAGTATCTCAAC
1 TATTAAAAGTTATAAAATGA-TATCCACTATAAAGAGTTATTTTGTTGAGTACCTCAAC
* * *
2290998 TATTAAAAGTTACAAAATGATCATCCCACTATAAAGAGTTGTTTTGTTGAGTCCCTCAAC
1 TATTAAAAGTTATAAAATGAT-AT-CCACTATAAAGAGTTATTTTGTTGAGTACCTCAAC
*
2291058 AATTAAAAGTTATAAAATGAT
1 TATTAAAAGTTATAAAATGAT
2291079 CACCTAACTA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
56 18 0.26
57 1 0.01
58 1 0.01
60 49 0.71
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (58 bp):
TATTAAAAGTTATAAAATGATATCCACTATAAAGAGTTATTTTGTTGAGTACCTCAAC
Found at i:2291045 original size:60 final size:60
Alignment explanation
Indices: 2290965--2291080 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
2290955 AAAATAGTTG
* *
2290965 ACTATAAAGAGTTATTTTGTTGAGTATCTCAACTATTAAAAGTTACAAAATGATCATCCC
1 ACTATAAAGAGTTATTTTGTTGAGTACCTCAACAATTAAAAGTTACAAAATGATCATCCC
* * *
2291025 ACTATAAAGAGTTGTTTTGTTGAGTCCCTCAACAATTAAAAGTTATAAAATGATCA
1 ACTATAAAGAGTTATTTTGTTGAGTACCTCAACAATTAAAAGTTACAAAATGATCA
2291081 CCTAACTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (60 bp):
ACTATAAAGAGTTATTTTGTTGAGTACCTCAACAATTAAAAGTTACAAAATGATCATCCC
Found at i:2297607 original size:12 final size:12
Alignment explanation
Indices: 2297590--2297666 Score: 54
Period size: 12 Copynumber: 6.8 Consensus size: 12
2297580 TAACACTAAT
*
2297590 TGTATGTATTCA
1 TGTATGTATGCA
*
2297602 TGTATGCATGCA
1 TGTATGTATGCA
*
2297614 TGAATGTAT--A
1 TGTATGTATGCA
*
2297624 T-TATGCATGCA
1 TGTATGTATGCA
*
2297635 TG-ATGCATGCA
1 TGTATGTATGCA
* **
2297646 TTTATGTATATA
1 TGTATGTATGCA
2297658 TGTATGTAT
1 TGTATGTAT
2297667 ATGGAGAGAT
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
9 5 0.10
10 2 0.04
11 12 0.24
12 31 0.62
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (12 bp):
TGTATGTATGCA
Found at i:2298404 original size:131 final size:131
Alignment explanation
Indices: 2298170--2298421 Score: 495
Period size: 131 Copynumber: 1.9 Consensus size: 131
2298160 CCCGAACACA
2298170 CATTGCAGCCACTGCCAGAGCTTGGTACAGGCCCCTCACCGGATATTGTCCTTGAAGTAATGGGT
1 CATTGCAGCCACTGCCAGAGCTTGGTACAGGCCCCTCACCGGATATTGTCCTTGAAGTAATGGGT
2298235 CGATATGCTTCTTTATTGTTTTACTTTCTTCCTCGGAAATATGGAAATAGACAATATCTTACCCA
66 CGATATGCTTCTTTATTGTTTTACTTTCTTCCTCGGAAATATGGAAATAGACAATATCTTACCCA
2298300 G
131 G
2298301 CATTGCAGCCACTGCCAGAGCTTGGTACAGGCCCCTCACCGGATATTGTCCTTGAAGTAATGGGT
1 CATTGCAGCCACTGCCAGAGCTTGGTACAGGCCCCTCACCGGATATTGTCCTTGAAGTAATGGGT
*
2298366 CGTTATGCTTCTTTATTGTTTTACTTTCTTCCTCGGAAATATGGAAATAGACAATA
66 CGATATGCTTCTTTATTGTTTTACTTTCTTCCTCGGAAATATGGAAATAGACAATA
2298422 GTATCTTACC
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 120 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (131 bp):
CATTGCAGCCACTGCCAGAGCTTGGTACAGGCCCCTCACCGGATATTGTCCTTGAAGTAATGGGT
CGATATGCTTCTTTATTGTTTTACTTTCTTCCTCGGAAATATGGAAATAGACAATATCTTACCCA
G
Found at i:2299779 original size:10 final size:9
Alignment explanation
Indices: 2299760--2299835 Score: 53
Period size: 10 Copynumber: 8.0 Consensus size: 9
2299750 TGGAAAACCT
2299760 GTTTGACCG
1 GTTTGACCG
2299769 GTTTCGACCG
1 GTTT-GACCG
*
2299779 GTTCGAACCG
1 GTTTG-ACCG
*
2299789 GTCTGACCG
1 GTTTGACCG
* **
2299798 GTCTGAAATG
1 GTTTG-ACCG
*
2299808 GTCTGACCG
1 GTTTGACCG
*
2299817 GTCTGAACCG
1 GTTTG-ACCG
2299827 GTTTGACCG
1 GTTTGACCG
2299836 ATCTGACCCG
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
9 25 0.45
10 30 0.55
ACGTcount: A:0.16, C:0.26, G:0.32, T:0.26
Consensus pattern (9 bp):
GTTTGACCG
Found at i:2299798 original size:19 final size:19
Alignment explanation
Indices: 2299774--2299841 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
2299764 GACCGGTTTC
2299774 GACCGGT-TCGAACCGGTCT
1 GACCGGTCT-GAACCGGTCT
**
2299793 GACCGGTCTGAAATGGTCT
1 GACCGGTCTGAACCGGTCT
*
2299812 GACCGGTCTGAACCGGTTT
1 GACCGGTCTGAACCGGTCT
*
2299831 GACCGATCTGA
1 GACCGGTCTGA
2299842 CCCGACCCGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 41 0.98
20 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (19 bp):
GACCGGTCTGAACCGGTCT
Found at i:2299800 original size:9 final size:9
Alignment explanation
Indices: 2299763--2299843 Score: 65
Period size: 9 Copynumber: 8.6 Consensus size: 9
2299753 AAAACCTGTT
*
2299763 TGACCGGTT
1 TGACCGGTC
2299772 TCGACCGGT-
1 T-GACCGGTC
2299781 TCGAACCGGTC
1 T-G-ACCGGTC
2299792 TGACCGGTC
1 TGACCGGTC
**
2299801 TGAAATGGTC
1 TG-ACCGGTC
2299811 TGACCGGTC
1 TGACCGGTC
*
2299820 TGAACCGGTT
1 TG-ACCGGTC
*
2299830 TGACCGATC
1 TGACCGGTC
2299839 TGACC
1 TGACC
2299844 CGACCCGACC
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
9 30 0.50
10 29 0.48
11 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (9 bp):
TGACCGGTC
Found at i:2304475 original size:17 final size:17
Alignment explanation
Indices: 2304453--2304488 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2304443 ATGTTGCTCA
2304453 GACTCTTTATTTCCTCT
1 GACTCTTTATTTCCTCT
2304470 GACTCTTTATTTCCTCT
1 GACTCTTTATTTCCTCT
2304487 GA
1 GA
2304489 GATCAGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.28, G:0.08, T:0.50
Consensus pattern (17 bp):
GACTCTTTATTTCCTCT
Found at i:2306318 original size:14 final size:14
Alignment explanation
Indices: 2306281--2306321 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
2306271 ACCAAAATGT
*
2306281 CAAAATCTATATAA
1 CAAAATATATATAA
2306295 CAAAA-ATATATAA
1 CAAAATATATATAA
*
2306308 CAAAATTTATATAA
1 CAAAATATATATAA
2306322 AGCCTGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (14 bp):
CAAAATATATATAA
Found at i:2309259 original size:11 final size:11
Alignment explanation
Indices: 2309243--2309270 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2309233 TTGACTTGAT
2309243 AAGTTCGTGAG
1 AAGTTCGTGAG
2309254 AAGTTCGTGAG
1 AAGTTCGTGAG
2309265 AAGTTC
1 AAGTTC
2309271 ATTAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.29
Consensus pattern (11 bp):
AAGTTCGTGAG
Found at i:2314570 original size:31 final size:29
Alignment explanation
Indices: 2314514--2314572 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
2314504 GATATGATTT
*
2314514 TAAAATAAATTAAAATTTAGGTACTAAAA
1 TAAAATAAATTAAAATTTAGATACTAAAA
*
2314543 TAAAATAAAATTAATAGTTTAGATACTAAA
1 TAAAAT-AAATTAA-AATTTAGATACTAAA
2314573 CTTATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 7 0.27
31 13 0.50
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (29 bp):
TAAAATAAATTAAAATTTAGATACTAAAA
Found at i:2315089 original size:63 final size:63
Alignment explanation
Indices: 2315011--2315139 Score: 240
Period size: 63 Copynumber: 2.0 Consensus size: 63
2315001 TCTGTATGAA
*
2315011 ATTCTTAATTTTTAATGTATTAAATTATTTTTTAATTGATATAAACAATGTTGGGTCCCTATT
1 ATTCTTAATTTTTAATGTATTAAATTATTTTTTAATTGATATAAACAATGTTGGGTCCCAATT
*
2315074 ATTCTTAATTTTTAATTTATTAAATTATTTTTTAATTGATATAAACAATGTTGGGTCCCAATT
1 ATTCTTAATTTTTAATGTATTAAATTATTTTTTAATTGATATAAACAATGTTGGGTCCCAATT
2315137 ATT
1 ATT
2315140 GAGAAGTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.51
Consensus pattern (63 bp):
ATTCTTAATTTTTAATGTATTAAATTATTTTTTAATTGATATAAACAATGTTGGGTCCCAATT
Found at i:2317335 original size:92 final size:92
Alignment explanation
Indices: 2317178--2317362 Score: 370
Period size: 92 Copynumber: 2.0 Consensus size: 92
2317168 TACTTGTCAT
2317178 TTGACTTGAGGAACTTCCACCCACCTTGGATAAAACCCACGCTTGTACCCCCAGTTGACCCGACA
1 TTGACTTGAGGAACTTCCACCCACCTTGGATAAAACCCACGCTTGTACCCCCAGTTGACCCGACA
2317243 CAAAATTCTTATTTTTATTCAATAAAA
66 CAAAATTCTTATTTTTATTCAATAAAA
2317270 TTGACTTGAGGAACTTCCACCCACCTTGGATAAAACCCACGCTTGTACCCCCAGTTGACCCGACA
1 TTGACTTGAGGAACTTCCACCCACCTTGGATAAAACCCACGCTTGTACCCCCAGTTGACCCGACA
2317335 CAAAATTCTTATTTTTATTCAATAAAA
66 CAAAATTCTTATTTTTATTCAATAAAA
2317362 T
1 T
2317363 AGGGAAATAG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (92 bp):
TTGACTTGAGGAACTTCCACCCACCTTGGATAAAACCCACGCTTGTACCCCCAGTTGACCCGACA
CAAAATTCTTATTTTTATTCAATAAAA
Found at i:2323673 original size:17 final size:19
Alignment explanation
Indices: 2323651--2323685 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2323641 CCCCGGGAAA
2323651 TTTAAAA-AAAA-ACTTTG
1 TTTAAAACAAAATACTTTG
2323668 TTTAAAACAAAATACTTT
1 TTTAAAACAAAATACTTT
2323686 AATTTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (19 bp):
TTTAAAACAAAATACTTTG
Found at i:2324251 original size:15 final size:15
Alignment explanation
Indices: 2324228--2324261 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2324218 CCGTATGACC
*
2324228 ACTACGTCCCGAAGG
1 ACTAAGTCCCGAAGG
2324243 ACTAAGTCCCGAAGG
1 ACTAAGTCCCGAAGG
2324258 ACTA
1 ACTA
2324262 CAATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.15
Consensus pattern (15 bp):
ACTAAGTCCCGAAGG
Found at i:2324565 original size:14 final size:15
Alignment explanation
Indices: 2324538--2324566 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2324528 ATATCATATA
2324538 TCTTATGTTTTATGC
1 TCTTATGTTTTATGC
2324553 TCTTATG-TTTATGC
1 TCTTATGTTTTATGC
2324567 ATATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TCTTATGTTTTATGC
Found at i:2328019 original size:6 final size:6
Alignment explanation
Indices: 2328010--2328216 Score: 50
Period size: 6 Copynumber: 34.7 Consensus size: 6
2328000 ATTATTCTTC
* * * * **
2328010 TTCTCA TTCTCT TTCTCA TTCTAA GTCTCA TGCTTC- TTCTCA TTCTTT
1 TTCTCA TTCTCA TTCTCA TTCTCA TTCTCA TTC-TCA TTCTCA TTCTCA
* * * * * * * *
2328058 TTCTCC TCCTCC TCCTCA TTATTA TTCTTCTTC TTCTCA TTCTCT TTCTCA
1 TTCTCA TTCTCA TTCTCA TTCTCA TTC-TC--A TTCTCA TTCTCA TTCTCA
* * * * * ** *
2328109 TTCTCT TTCTCC TTCTAA GTCTCA TGCTTC- TTCTCA TTCTTT TTCTCC
1 TTCTCA TTCTCA TTCTCA TTCTCA TTC-TCA TTCTCA TTCTCA TTCTCA
* * * **
2328157 TCCTCC TCCTCA TTCTTC- TTCT-- TT-TC- TTCTCA TTCTTT TTCTCA
1 TTCTCA TTCTCA TTC-TCA TTCTCA TTCTCA TTCTCA TTCTCA TTCTCA
* *
2328201 TTCTCT TTCTCC TTCT
1 TTCTCA TTCTCA TTCT
2328217 AAGTCTCATG
Statistics
Matches: 145, Mismatches: 45, Indels: 22
0.68 0.21 0.10
Matches are distributed among these distances:
3 1 0.01
4 4 0.03
5 7 0.05
6 121 0.83
7 7 0.05
8 2 0.01
9 3 0.02
ACGTcount: A:0.09, C:0.34, G:0.02, T:0.55
Consensus pattern (6 bp):
TTCTCA
Found at i:2328025 original size:12 final size:12
Alignment explanation
Indices: 2328010--2328216 Score: 94
Period size: 12 Copynumber: 17.8 Consensus size: 12
2328000 ATTATTCTTC
2328010 TTCTCATTCTCT
1 TTCTCATTCTCT
**
2328022 TTCTCATTCTAA
1 TTCTCATTCTCT
* *
2328034 GTCTCATGCT-T
1 TTCTCATTCTCT
*
2328045 CTTCTCATTCTTT
1 -TTCTCATTCTCT
* * *
2328058 TTCTCCTCCTCC
1 TTCTCATTCTCT
* *
2328070 TCCTCATTAT-T
1 TTCTCATTCTCT
*
2328081 AT-TC-TTCT-T
1 TTCTCATTCTCT
2328090 CTTCTCATTCTCT
1 -TTCTCATTCTCT
2328103 TTCTCATTCTCT
1 TTCTCATTCTCT
* **
2328115 TTCTCCTTCTAA
1 TTCTCATTCTCT
* *
2328127 GTCTCATGCT-T
1 TTCTCATTCTCT
*
2328138 CTTCTCATTCTTT
1 -TTCTCATTCTCT
* * *
2328151 TTCTCCTCCTCC
1 TTCTCATTCTCT
*
2328163 TCCTCATTCT-T
1 TTCTCATTCTCT
2328174 CTTCT--TT-TC-
1 -TTCTCATTCTCT
*
2328183 TTCTCATTCTTT
1 TTCTCATTCTCT
2328195 TTCTCATTCTCT
1 TTCTCATTCTCT
*
2328207 TTCTCCTTCT
1 TTCTCATTCT
2328217 AAGTCTCATG
Statistics
Matches: 140, Mismatches: 41, Indels: 28
0.67 0.20 0.13
Matches are distributed among these distances:
8 4 0.03
9 5 0.04
10 7 0.05
11 3 0.02
12 118 0.84
13 3 0.02
ACGTcount: A:0.09, C:0.34, G:0.02, T:0.55
Consensus pattern (12 bp):
TTCTCATTCTCT
Found at i:2328038 original size:24 final size:24
Alignment explanation
Indices: 2328003--2328225 Score: 117
Period size: 24 Copynumber: 9.6 Consensus size: 24
2327993 CCTTATTATT
*
2328003 ATTCTTCTTCTCATTCTCTTTCTC
1 ATTCTTATTCTCATTCTCTTTCTC
* * *
2328027 ATTCTAAGTCTCATGCT-TCTTCTC
1 ATTCTTATTCTCATTCTCT-TTCTC
* * * * *
2328051 ATTCTTTTTCTCCTCCTCCTCCTC
1 ATTCTTATTCTCATTCTCTTTCTC
*
2328075 ATTATTA-T-TC-TTCT-TCTTCTC
1 ATTCTTATTCTCATTCTCT-TTCTC
2328096 ATTCTCT-TTCTCATTCTCTTTCTC
1 ATTCT-TATTCTCATTCTCTTTCTC
* * * *
2328120 CTTCTAAGTCTCATGCT-TCTTCTC
1 ATTCTTATTCTCATTCTCT-TTCTC
* * * * *
2328144 ATTCTTTTTCTCCTCCTCCTCCTC
1 ATTCTTATTCTCATTCTCTTTCTC
*
2328168 ATTCTTCTTCT--TT-TC-TTCTC
1 ATTCTTATTCTCATTCTCTTTCTC
*
2328188 ATTCTTTTTCTCATTCTCTTTCTC
1 ATTCTTATTCTCATTCTCTTTCTC
* * *
2328212 CTTCTAAGTCTCAT
1 ATTCTTATTCTCAT
2328226 GCATCTTCTC
Statistics
Matches: 147, Mismatches: 37, Indels: 30
0.69 0.17 0.14
Matches are distributed among these distances:
20 14 0.10
21 13 0.09
22 7 0.05
23 7 0.05
24 105 0.71
25 1 0.01
ACGTcount: A:0.10, C:0.34, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTCTTATTCTCATTCTCTTTCTC
Found at i:2328225 original size:56 final size:56
Alignment explanation
Indices: 2328128--2328234 Score: 124
Period size: 56 Copynumber: 1.9 Consensus size: 56
2328118 TCCTTCTAAG
* *** * *
2328128 TCTCATGCTTCTTCTCATTCTTTTTCTCCTCCTCCTCCTCATTCTTCTTCTTTTCT
1 TCTCATGCTTCTTCTCATTCTCTTTCTCCTCCTAAGCCTCATGCATCTTCTTTTCT
* * * *
2328184 TCTCATTCTTTTTCTCATTCTCTTTCTCCTTCTAAGTCTCATGCATCTTCT
1 TCTCATGCTTCTTCTCATTCTCTTTCTCCTCCTAAGCCTCATGCATCTTCT
2328235 CCTTTTTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
56 41 1.00
ACGTcount: A:0.08, C:0.35, G:0.03, T:0.54
Consensus pattern (56 bp):
TCTCATGCTTCTTCTCATTCTCTTTCTCCTCCTAAGCCTCATGCATCTTCTTTTCT
Found at i:2328267 original size:3 final size:3
Alignment explanation
Indices: 2328261--2329077 Score: 795
Period size: 3 Copynumber: 277.3 Consensus size: 3
2328251 CTCCTCCTCC
2328261 TCT TCT TC- TCT TCT TCT TCT TCT TCT TCT TCTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT
* * *
2328306 CCT TCT TCT TC- TCT TC- TCT TCT TCT TCT CCT TCT TCT TCT CCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * *
2328352 TC- TCT TCT CCT TCT CCCT TCCT T-T TCT TCT CCT TCT TCT CCT CCT
1 TCT TCT TCT TCT TCT -TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
2328397 T-T T-T TCT TC- CCT TCCT TCT CCT TCT TCT CCT TCT CCT TCT TCT
1 TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
2328440 CCT TC- TCT TC- TCT TTT TCT TCT TCT TCT TCT TCT TCT T-T TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
2328485 TCT CCT TCT TCT TCT CCT TCT TCT TCT TCT CCT TCT TCT CCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * * * *
2328533 TCT CCT TCT TCT CCT CCT TTT TCT CCT TCT CCT TCT TCT CCT CCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * *
2328581 TCT CCT TCT TCT TCT CCT TCT TCT CCT TCT TCT CCT TCT TCT CCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
2328629 TC- TCC TCT TCT TCT TCT TCT CCT TAT TC- TCAT TCT TCT CCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT
* *
2328672 TCT CTCT TC- TCT TCT TCT TCT TCT CCT TCT CCT TCT TCT TCT TCT
1 TCT -TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
2328717 TCT CCT TCT TCT TC- TCAT TCT TCT CCT TCT TCT CCT TCT TCT CCT
1 TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
2328762 TCT TCT CCT CCT TC- TCC TCAT TCT TCT CCT TCT TCT TCT TCT TCCT
1 TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT T-CT
* * * *
2328808 TCT TCT CCT TCT TCT CCT TCT TCT CCT TCT TC- TCC TCT TCT CTCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT
*
2328853 TCT T-T TCT TCT TCT TCT TCT TCT CCT TCT TC- TCT TCT TCT TCT TC-
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * *
2328898 TCC TCT TC- TCC TCT T-T CCT TCT TCT TC- TCAT TCT TCT TC- TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT
* *
2328940 TCT TCT TCT TCT TCT TCT CCT TCT TCT TC- TCT TCT TCT CCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
2328987 TCT TCT CCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * *
2329035 TCT TCT TCT CCT TCT GCT CCT TCA CCT TCT CCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
2329078 TAACAAAAAT
Statistics
Matches: 668, Mismatches: 110, Indels: 72
0.79 0.13 0.08
Matches are distributed among these distances:
2 50 0.07
3 590 0.88
4 28 0.04
ACGTcount: A:0.01, C:0.40, G:0.00, T:0.59
Consensus pattern (3 bp):
TCT
Found at i:2329993 original size:3 final size:3
Alignment explanation
Indices: 2329985--2330025 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
2329975 TTTTGTATTT
* * *
2329985 GAA GAA GAA GAA GAG GAA GAA GAG GAA GAA GAA AAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
2330026 GGAGTTGACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2330003 original size:9 final size:9
Alignment explanation
Indices: 2329985--2330028 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
2329975 TTTTGTATTT
*
2329985 GAAGAAGAA
1 GAAGAGGAA
2329994 GAAGAGGAA
1 GAAGAGGAA
2330003 GAAGAGGAA
1 GAAGAGGAA
**
2330012 GAAGAAAAA
1 GAAGAGGAA
2330021 GAAGAGGA
1 GAAGAGGA
2330029 GTTGACAGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (9 bp):
GAAGAGGAA
Found at i:2330377 original size:31 final size:31
Alignment explanation
Indices: 2330339--2330405 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
2330329 CTGTAAATTA
2330339 GTTTTTAATTTGTACAATTAATATTTAATCT
1 GTTTTTAATTTGTACAATTAATATTTAATCT
2330370 GTTTTTAATTTGTACAATTAATATTTAATCT
1 GTTTTTAATTTGTACAATTAATATTTAATCT
2330401 GTTTT
1 GTTTT
2330406 GATTTTGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.30, C:0.06, G:0.07, T:0.57
Consensus pattern (31 bp):
GTTTTTAATTTGTACAATTAATATTTAATCT
Found at i:2330413 original size:31 final size:31
Alignment explanation
Indices: 2330339--2330413 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
2330329 CTGTAAATTA
*
2330339 GTTTTTAATTTGTACAATTAATATTTAATCT
1 GTTTTGAATTTGTACAATTAATATTTAATCT
*
2330370 GTTTTTAATTTGTACAATTAATATTTAATCT
1 GTTTTGAATTTGTACAATTAATATTTAATCT
*
2330401 GTTTTGATTTTGT
1 GTTTTGAATTTGT
2330414 TAATCTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.57
Consensus pattern (31 bp):
GTTTTGAATTTGTACAATTAATATTTAATCT
Found at i:2330596 original size:23 final size:23
Alignment explanation
Indices: 2330566--2330631 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
2330556 CTGAATGATT
2330566 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
2330589 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
* *
2330612 CAGTGCTGAATGATTAAGCA
1 CAGTGCTGACTGATTCAGCA
2330632 CACAAGTACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (23 bp):
CAGTGCTGACTGATTCAGCAAAA
Found at i:2330658 original size:27 final size:27
Alignment explanation
Indices: 2330617--2330680 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
2330607 CAAAACAGTG
2330617 CTGAATGATTAAGCACACAAGTACATT
1 CTGAATGATTAAGCACACAAGTACATT
* * *
2330644 TTGAATGATTTAGCACAGAAGTACATT
1 CTGAATGATTAAGCACACAAGTACATT
2330671 CTGAATGATT
1 CTGAATGATT
2330681 CAGAGCCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (27 bp):
CTGAATGATTAAGCACACAAGTACATT
Found at i:2336840 original size:4 final size:4
Alignment explanation
Indices: 2336831--2336889 Score: 82
Period size: 4 Copynumber: 14.8 Consensus size: 4
2336821 TAGTTGAAAC
* * * *
2336831 TATG TATG TATG TATG TATA TATG TATG TATG TATA TATT TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2336879 TATG TATG TAT
1 TATG TATG TAT
2336890 ATTGTCATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:2336848 original size:12 final size:12
Alignment explanation
Indices: 2336831--2336923 Score: 89
Period size: 12 Copynumber: 7.7 Consensus size: 12
2336821 TAGTTGAAAC
*
2336831 TATGTATGTATG
1 TATGTATGTATA
* *
2336843 TATGTATATATG
1 TATGTATGTATA
2336855 TATGTATGTATA
1 TATGTATGTATA
*
2336867 TATTTATGTATA
1 TATGTATGTATA
2336879 TATGTATGTATA
1 TATGTATGTATA
*
2336891 T-TGTCATGTAAA
1 TATGT-ATGTATA
* * *
2336903 CTTTCTATGTATG
1 -TATGTATGTATA
2336916 TATGTATG
1 TATGTATG
2336924 GATCATGGAT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
11 3 0.04
12 56 0.84
13 6 0.09
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.51
Consensus pattern (12 bp):
TATGTATGTATA
Found at i:2344174 original size:31 final size:31
Alignment explanation
Indices: 2344125--2344193 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2344115 ATTGATGATT
2344125 ATCACTTTTTGTTCTTATTTAATTAAGATATG
1 ATCAC-TTTTGTTCTTATTTAATTAAGATATG
* * *
2344157 ATCACTTTTGTTTTTATTTATTTAAGATGTG
1 ATCACTTTTGTTCTTATTTAATTAAGATATG
2344188 ATCACT
1 ATCACT
2344194 ACGGATTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 29 0.85
32 5 0.15
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (31 bp):
ATCACTTTTGTTCTTATTTAATTAAGATATG
Found at i:2344460 original size:5 final size:5
Alignment explanation
Indices: 2344452--2344483 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
2344442 TTTGCTTTGT
2344452 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
2344484 TAGTTAGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:2353387 original size:75 final size:74
Alignment explanation
Indices: 2353301--2353445 Score: 263
Period size: 75 Copynumber: 1.9 Consensus size: 74
2353291 GATGTTGATC
* *
2353301 GTTAGTTAACTAACGATCTTCATAAAAAAATTATTTTGACCAAAAATTGAAACGTTTAGGGCTAA
1 GTTAGTCAACTAACGATCTTCATAAAAAAATTATTTTGACCAAAAATTGAAACGTTT-GGACTAA
2353366 AATGCTCTTT
65 AATGCTCTTT
2353376 GTTAGTCAACTAACGATCTTCATAAAAAAATTATTTTGACCAAAAATTGAAACGTTTGGACTAAA
1 GTTAGTCAACTAACGATCTTCATAAAAAAATTATTTTGACCAAAAATTGAAACGTTTGGACTAAA
2353441 ATGCT
66 ATGCT
2353446 TCAAAGAAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 12 0.18
75 56 0.82
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (74 bp):
GTTAGTCAACTAACGATCTTCATAAAAAAATTATTTTGACCAAAAATTGAAACGTTTGGACTAAA
ATGCTCTTT
Found at i:2364714 original size:4 final size:4
Alignment explanation
Indices: 2364705--2364731 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2364695 TAAGAACATA
2364705 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2364732 GTGAACTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2373231 original size:23 final size:23
Alignment explanation
Indices: 2373190--2373252 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
2373180 AAACATATTT
*
2373190 CAGGTCAAATATCAGATCAGAATC
1 CAGGTC-AATATCATATCAGAATC
*
2373214 CATGTCAATATCATATCAGAATC
1 CAGGTCAATATCATATCAGAATC
*
2373237 CAGGTCAGGTATCATA
1 CAGGTCA-ATATCATA
2373253 ACATAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 22 0.65
24 12 0.35
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (23 bp):
CAGGTCAATATCATATCAGAATC
Found at i:2376761 original size:23 final size:25
Alignment explanation
Indices: 2376679--2376754 Score: 136
Period size: 25 Copynumber: 3.1 Consensus size: 25
2376669 TCTTAATTTA
2376679 TTATGAG-AAAAAATAATCTCTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
2376703 TTATGAGAAAAAAATAATCTCTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
*
2376728 TTATGAGAAAAAAATAATCTTTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
2376753 TT
1 TT
2376755 GGAAAAACAC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 7 0.14
25 43 0.86
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (25 bp):
TTATGAGAAAAAAATAATCTCTAAC
Found at i:2384113 original size:2 final size:2
Alignment explanation
Indices: 2384106--2384139 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2384096 GCACCTAAAT
2384106 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
2384140 AATTATATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2386079 original size:20 final size:20
Alignment explanation
Indices: 2386056--2386112 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
2386046 GTTTACACAG
2386056 TATCGATACTATTCATACAA
1 TATCGATACTATTCATACAA
*
2386076 TATCGGTACTATTCATACAA
1 TATCGATACTATTCATACAA
2386096 TATCGATACTATTCATA
1 TATCGATACTATTCATA
2386113 TAGTACAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (20 bp):
TATCGATACTATTCATACAA
Found at i:2387034 original size:21 final size:21
Alignment explanation
Indices: 2387010--2387050 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2387000 GATTGTTTCA
2387010 AGGGTATCAG-TACCCTGCTAT
1 AGGGTA-CAGATACCCTGCTAT
*
2387031 AGGGTACCGATACCCTGCTA
1 AGGGTACAGATACCCTGCTA
2387051 CAATACTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
AGGGTACAGATACCCTGCTAT
Found at i:2387842 original size:21 final size:21
Alignment explanation
Indices: 2387812--2387874 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
2387802 CATATGAAAT
*
2387812 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTATA
* *
2387833 TTGTCTCGAATGACCACTATA
1 TTGTCCCGAAGGACCACTATA
* *
2387854 TTGTCCCAAAAGACCACTATA
1 TTGTCCCGAAGGACCACTATA
2387875 ACTCTCGACT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTATA
Found at i:2390151 original size:31 final size:31
Alignment explanation
Indices: 2390084--2390151 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
2390074 TATGCTCATC
* * **
2390084 GAGAATAACCTGTTAAAGTTTGGGTGTCGTT
1 GAGAGTAACATGTTAAAGTTTGGGTGTCACT
*
2390115 AAGAGTAACATGTTATAA-TTTGGGTGTCACT
1 GAGAGTAACATGTTA-AAGTTTGGGTGTCACT
2390146 GAGAGT
1 GAGAGT
2390152 CAGGAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.29, C:0.09, G:0.28, T:0.34
Consensus pattern (31 bp):
GAGAGTAACATGTTAAAGTTTGGGTGTCACT
Found at i:2391541 original size:18 final size:18
Alignment explanation
Indices: 2391518--2391560 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
2391508 CATCTTGAAC
2391518 TTAGGTAGGAGCACTAAG
1 TTAGGTAGGAGCACTAAG
2391536 TTAGGTAGGAGCACTAAG
1 TTAGGTAGGAGCACTAAG
2391554 TTAGGTA
1 TTAGGTA
2391561 CCAGACTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.26
Consensus pattern (18 bp):
TTAGGTAGGAGCACTAAG
Found at i:2398345 original size:17 final size:18
Alignment explanation
Indices: 2398323--2398459 Score: 167
Period size: 17 Copynumber: 7.8 Consensus size: 18
2398313 ATTCTAAATG
2398323 TTTACAGTTATCAGAT-A
1 TTTACAGTTATCAGATGA
*
2398340 TTTACAGTTATTAGATGA
1 TTTACAGTTATCAGATGA
*
2398358 TTTTCAGTTATCAGAT-A
1 TTTACAGTTATCAGATGA
* *
2398375 TTTACAATTATTAGATGA
1 TTTACAGTTATCAGATGA
*
2398393 TTCT-CAATTATCAGAT-A
1 TT-TACAGTTATCAGATGA
2398410 TTTACAGTTATCAGATGA
1 TTTACAGTTATCAGATGA
*
2398428 -TTACAGTTATCAGATGT
1 TTTACAGTTATCAGATGA
*
2398445 TTTATAGTTATCAGA
1 TTTACAGTTATCAGA
2398460 CGTAGATTAA
Statistics
Matches: 104, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
16 1 0.01
17 59 0.57
18 43 0.41
19 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (18 bp):
TTTACAGTTATCAGATGA
Found at i:2398373 original size:35 final size:35
Alignment explanation
Indices: 2398327--2398442 Score: 180
Period size: 35 Copynumber: 3.3 Consensus size: 35
2398317 TAAATGTTTA
2398327 CAGTTATCAGATATTTACAGTTATTAGATGATTTT
1 CAGTTATCAGATATTTACAGTTATTAGATGATTTT
* *
2398362 CAGTTATCAGATATTTACAATTATTAGATGATTCT
1 CAGTTATCAGATATTTACAGTTATTAGATGATTTT
* * *
2398397 CAATTATCAGATATTTACAGTTATCAGATGA-TTA
1 CAGTTATCAGATATTTACAGTTATTAGATGATTTT
2398431 CAGTTATCAGAT
1 CAGTTATCAGAT
2398443 GTTTTATAGT
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
34 12 0.16
35 61 0.84
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (35 bp):
CAGTTATCAGATATTTACAGTTATTAGATGATTTT
Found at i:2398380 original size:52 final size:53
Alignment explanation
Indices: 2398323--2398443 Score: 151
Period size: 52 Copynumber: 2.3 Consensus size: 53
2398313 ATTCTAAATG
* * *
2398323 TTTACAGTTATCAGAT-ATT-TACAGTTATTAGATGATTTTCAGTTATCAGAT-A
1 TTTACAGTTATCAGATGATTCT-CAATTATCAGAT-ATTTACAGTTATCAGATGA
* *
2398375 TTTACAATTATTAGATGATTCTCAATTATCAGATATTTACAGTTATCAGATGA
1 TTTACAGTTATCAGATGATTCTCAATTATCAGATATTTACAGTTATCAGATGA
2398428 -TTACAGTTATCAGATG
1 TTTACAGTTATCAGATG
2398444 TTTTATAGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
52 44 0.75
53 14 0.24
54 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (53 bp):
TTTACAGTTATCAGATGATTCTCAATTATCAGATATTTACAGTTATCAGATGA
Found at i:2398454 original size:35 final size:34
Alignment explanation
Indices: 2398324--2398459 Score: 173
Period size: 35 Copynumber: 3.9 Consensus size: 34
2398314 TTCTAAATGT
*
2398324 TTACAGTTATCAGATATTTACAGTTATTAGATGA
1 TTACAGTTATCAGATATTTACAGTTATCAGATGA
* * *
2398358 TTTTCAGTTATCAGATATTTACAATTATTAGATGA
1 -TTACAGTTATCAGATATTTACAGTTATCAGATGA
* *
2398393 TTCTCAATTATCAGATATTTACAGTTATCAGATGA
1 TT-ACAGTTATCAGATATTTACAGTTATCAGATGA
* *
2398428 TTACAGTTATCAGATGTTTTATAGTTATCAGA
1 TTACAGTTATCAGAT-ATTTACAGTTATCAGA
2398460 CGTAGATTAA
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
34 13 0.14
35 77 0.86
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (34 bp):
TTACAGTTATCAGATATTTACAGTTATCAGATGA
Found at i:2398456 original size:52 final size:52
Alignment explanation
Indices: 2398323--2398459 Score: 147
Period size: 52 Copynumber: 2.6 Consensus size: 52
2398313 ATTCTAAATG
* * *
2398323 TTTACAGTTATCAGAT-ATTTACAGTTATTAGATGATTTTCAGTTATCAGATA
1 TTTACAGTTATCAGATGTTTTA-AGTTATCAGATGATTTACAGTTATCAGATA
* * *
2398375 TTTACAATTATTAGATGATTCTCAA-TTATCAGAT-ATTTACAGTTATCAGATGA
1 TTTACAGTTATCAGATG-TT-TTAAGTTATCAGATGATTTACAGTTATCAGAT-A
2398428 -TTACAGTTATCAGATGTTTTATAGTTATCAGA
1 TTTACAGTTATCAGATGTTTTA-AGTTATCAGA
2398460 CGTAGATTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
50 2 0.03
51 3 0.04
52 52 0.74
53 9 0.13
54 2 0.03
55 2 0.03
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (52 bp):
TTTACAGTTATCAGATGTTTTAAGTTATCAGATGATTTACAGTTATCAGATA
Found at i:2398786 original size:17 final size:17
Alignment explanation
Indices: 2398764--2398799 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2398754 AAGTTATAAC
2398764 AATATATGAAA-AAAAGA
1 AATATA-GAAAGAAAAGA
2398781 AATATAGAAAGAAAAGA
1 AATATAGAAAGAAAAGA
2398798 AA
1 AA
2398800 AGAAAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (17 bp):
AATATAGAAAGAAAAGA
Found at i:2400073 original size:14 final size:14
Alignment explanation
Indices: 2400056--2400082 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2400046 TAAAAATGTC
2400056 TTTTAAAAATATTT
1 TTTTAAAAATATTT
2400070 TTTTAAAAATATT
1 TTTTAAAAATATT
2400083 AAATTAGCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAAAATATTT
Found at i:2403267 original size:32 final size:32
Alignment explanation
Indices: 2403231--2403295 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
2403221 CACACACACA
*
2403231 TTACTTTATGGTATGTTAATGTCATTTGTGAT
1 TTACTTTATGGTATGTTAACGTCATTTGTGAT
*
2403263 TTACTTTATGGTATGTTAGCGTCATTTGTGAT
1 TTACTTTATGGTATGTTAACGTCATTTGTGAT
2403295 T
1 T
2403296 CTATGCTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (32 bp):
TTACTTTATGGTATGTTAACGTCATTTGTGAT
Found at i:2404772 original size:65 final size:65
Alignment explanation
Indices: 2404619--2404798 Score: 219
Period size: 65 Copynumber: 2.8 Consensus size: 65
2404609 TTGGACCCTT
* *
2404619 AGTGCATCGGTGCACTAAGA-GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCT
1 AGTGCATCGATGCA-TAATATGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCT
2404682 G
65 G
* * *
2404683 AGTGCATCGATGCAT--TGCTGGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAA-A-C
1 AGTGCATCGATGCATAAT-AT-GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC
2404744 TCTG
63 -CTG
*
2404748 AGTGCATCGATGCATAATATGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAATATGTGCATCGATGCATAAAATGCATTCGATGTT
2404799 CAATTTATTC
Statistics
Matches: 100, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
63 1 0.01
64 41 0.41
65 53 0.53
66 4 0.04
67 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
AGTGCATCGATGCATAATATGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTG
Found at i:2406621 original size:20 final size:20
Alignment explanation
Indices: 2406593--2406639 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2406583 AAAACCCGAC
2406593 CGATGCATGACCTTGTGCAT
1 CGATGCATGACCTTGTGCAT
*
2406613 CGATTCATGACCTTGTGCAT
1 CGATGCATGACCTTGTGCAT
2406633 CGATGCA
1 CGATGCA
2406640 CATTCAAGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (20 bp):
CGATGCATGACCTTGTGCAT
Found at i:2406656 original size:23 final size:22
Alignment explanation
Indices: 2406627--2406706 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
2406617 TCATGACCTT
2406627 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
2406649 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
2406671 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
2406693 ATGCATCCATGCAC
1 GTGCATCGATGCAC
2406707 TGTTAGGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 15 0.33
22 15 0.33
23 16 0.35
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:2406682 original size:44 final size:42
Alignment explanation
Indices: 2406631--2406725 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
2406621 GACCTTGTGC
* **
2406631 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCCATGCA-CTGTCA-GGTGT
*
2406675 ATCGATGCACATTCAAGGATGCATCCATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCCATGCACTGTCAGGTGT
2406717 ATCGATGCA
1 ATCGATGCA
2406726 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 16 0.35
43 12 0.26
44 18 0.39
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.27
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCCATGCACTGTCAGGTGT
Found at i:2406683 original size:21 final size:20
Alignment explanation
Indices: 2406627--2406725 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 20
2406617 TCATGACCTT
2406627 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTC-A-G
* *
2406649 CGTGCATCGGTGCACCTTCATG
1 -GTGCATCGATGCACATTCA-G
*
2406671 GTGTATCGATGCACATTCAAG
1 GTGCATCGATGCACATTC-AG
* *
2406692 GATGCATCCATGCAC-TGTTAG
1 G-TGCATCGATGCACAT-TCAG
*
2406713 GTGTATCGATGCA
1 GTGCATCGATGCA
2406726 TTAAGCACAA
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
20 10 0.16
21 21 0.34
22 15 0.24
23 16 0.26
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.27
Consensus pattern (20 bp):
GTGCATCGATGCACATTCAG
Found at i:2410549 original size:21 final size:20
Alignment explanation
Indices: 2410515--2410567 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
2410505 GAGCTTATTT
*
2410515 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTT-AAAAA
2410536 TCATTTTTATATTTTAAAAA
1 TCATTTTTATATTTTAAAAA
*
2410556 TAATTTCTTATA
1 TCATTT-TTATA
2410568 ATCCGAAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (20 bp):
TCATTTTTATATTTTAAAAA
Found at i:2412515 original size:45 final size:46
Alignment explanation
Indices: 2412444--2412551 Score: 143
Period size: 45 Copynumber: 2.4 Consensus size: 46
2412434 GGTGCACTAA
*
2412444 GAGTGCATCGATGCATAAATTGCATTCGATG-TTTCA-AAATAGC-CT
1 GAGTGCATCGATGCATAAATTACATTCGATGTTTTCATAAA-A-CTCT
2412489 GAGTGCATCGATGCATCAAA-TACATTCGATGTTTTCATAAAACTCT
1 GAGTGCATCGATGCAT-AAATTACATTCGATGTTTTCATAAAACTCT
*
2412535 GAGTGTATCGATGCATA
1 GAGTGCATCGATGCATA
2412552 GTATGTGCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
45 28 0.49
46 26 0.46
47 3 0.05
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (46 bp):
GAGTGCATCGATGCATAAATTACATTCGATGTTTTCATAAAACTCT
Found at i:2416226 original size:18 final size:18
Alignment explanation
Indices: 2416203--2416255 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
2416193 CCGTGTAGAA
*
2416203 ATGTCCCAAAGGACCACT
1 ATGTCCCGAAGGACCACT
2416221 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
2416239 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
2416256 ATATCACATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.15
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:2416397 original size:23 final size:23
Alignment explanation
Indices: 2416364--2416407 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2416354 ATTACATATA
*
2416364 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCAAAGGACCACGTAGAAT
*
2416387 TGTCCCAAAGGACCGCGTAGA
1 TGTCCCAAAGGACCACGTAGA
2416408 CCTTCGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (23 bp):
TGTCCCAAAGGACCACGTAGAAT
Found at i:2421127 original size:3 final size:3
Alignment explanation
Indices: 2421119--2421163 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2421109 AATGGTCAAA
2421119 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2421164 GATGATGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2425089 original size:8 final size:9
Alignment explanation
Indices: 2425065--2425093 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2425055 AAAAATATAT
2425065 TAATTTTTA
1 TAATTTTTA
2425074 TAATTTTTA
1 TAATTTTTA
2425083 TAA-TTTTA
1 TAATTTTTA
2425091 TAA
1 TAA
2425094 ATAAGATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TAATTTTTA
Found at i:2425372 original size:15 final size:16
Alignment explanation
Indices: 2425352--2425384 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2425342 ATTACTTTTG
2425352 TATAAAAGT-AATTTA
1 TATAAAAGTAAATTTA
*
2425367 TATAAAATTAAATTTA
1 TATAAAAGTAAATTTA
2425383 TA
1 TA
2425385 AATAGGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TATAAAAGTAAATTTA
Found at i:2425452 original size:3 final size:3
Alignment explanation
Indices: 2425444--2425470 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2425434 TATATGACTA
2425444 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2425471 TAAACATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2425487 original size:14 final size:14
Alignment explanation
Indices: 2425442--2425494 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
2425432 TTTATATGAC
*
2425442 TAAATAATAATAAT
1 TAAACAATAATAAT
* *
2425456 AATAATAATAATAAT
1 TA-AACAATAATAAT
2425471 TAAACATATAA-AAT
1 TAAACA-ATAATAAT
2425485 TAAACAATAA
1 TAAACAATAA
2425495 CTAAACAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 4 0.12
14 13 0.38
15 17 0.50
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAACAATAATAAT
Found at i:2426912 original size:17 final size:17
Alignment explanation
Indices: 2426892--2426941 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
2426882 TAATTATTAT
2426892 AATAATATAAAAATAAA
1 AATAATATAAAAATAAA
*
2426909 AATAATAGTATAAATAAA
1 AATAATA-TAAAAATAAA
*
2426927 ATAAAATAATAAAAA
1 A-ATAAT-ATAAAAA
2426942 ACAAATGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 7 0.26
18 10 0.37
19 9 0.33
20 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AATAATATAAAAATAAA
Found at i:2427237 original size:16 final size:16
Alignment explanation
Indices: 2427185--2427245 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
2427175 AAGTTGAACA
2427185 AATTCTTCTCATTATG
1 AATTCTTCTCATTATG
**
2427201 AACTTCTTCTTTCTAAGATG
1 AA-TTCTTC--TC-ATTATG
2427221 AATTCTTCTCATTATG
1 AATTCTTCTCATTATG
*
2427237 AACTCTTCT
1 AATTCTTCT
2427246 GGAAATGTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
16 14 0.39
17 8 0.22
19 8 0.22
20 6 0.17
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.48
Consensus pattern (16 bp):
AATTCTTCTCATTATG
Found at i:2427639 original size:112 final size:112
Alignment explanation
Indices: 2427513--2428037 Score: 732
Period size: 112 Copynumber: 4.8 Consensus size: 112
2427503 TGAATAAGTT
*
2427513 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCGACAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCGGCAA
*
2427578 TGCTGATCCATCGAGTGATGCATTCGAGCAAAAGGTTGAACAAATTC
66 TGCTGATCCATCGAGTGATGCATTCGAGCAAAAGATTGAACAAATTC
* *
2427625 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTATCTGGGA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TCCGGCA
* * * *
2427690 ATGTTGATCCAT----TGAT-CA----AGCTAAAG-TTGAATAAGTTC
65 ATGCTGATCCATCGAGTGATGCATTCGAGCAAAAGATTGAACAAATTC
* * *
2427728 TTCTCATTATGAACTTCTTCTT-CTTCTTCAAATGAGTTATTCTCATTATGAACTCTACCTGGCA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCC-GGCA
* *
2427792 ATGCTGATCCATCGAGTGATGAATTCAAGCAAAAGATTGAACAAGA-TC
65 ATGCTGATCCATCGAGTGATGCATTCGAGCAAAAGATTGAACAA-ATTC
* *
2427840 TTCTCATTATGGACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTACGGCAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCGGCAA
*
2427905 TGCTGATCCATCGAGTGATGCATTCGAGCAAAAGATTGAACAAATTT
66 TGCTGATCCATCGAGTGATGCATTCGAGCAAAAGATTGAACAAATTC
* * *
2427952 TTCTCATTATGAACTTCTTCTTCGTTCTTCAGATGAGTTCTTCTCATTATGAACTCTATCTGGGA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TCCGGCA
** *
2428017 ATATTGATCCATCGAATGATG
65 ATGCTGATCCATCGAGTGATG
2428038 GATCTGAATC
Statistics
Matches: 364, Mismatches: 33, Indels: 31
0.85 0.08 0.07
Matches are distributed among these distances:
101 1 0.00
102 46 0.13
103 32 0.09
104 7 0.02
106 4 0.01
107 1 0.00
108 2 0.01
109 4 0.01
111 8 0.02
112 189 0.52
113 70 0.19
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (112 bp):
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCGGCAA
TGCTGATCCATCGAGTGATGCATTCGAGCAAAAGATTGAACAAATTC
Found at i:2427873 original size:327 final size:317
Alignment explanation
Indices: 2427395--2428028 Score: 1000
Period size: 327 Copynumber: 2.0 Consensus size: 317
2427385 GAGTCAAGAA
* *
2427395 AAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTA
1 AAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTATTCTCATTA
* * * *
2427460 TGAACTCTACCTGAAAAAGTTGATCCATTGATCAAGCTAAAGTTGAATAAGTTTTCTCATTATGA
66 TGAACTCTACCTGAAAAAGCTGATCCATTGATCAAGCAAAAGTTGAACAAGTCTTCTCATTATGA
*
2427525 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCGACAATGCTGATCCATC
131 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTACGACAATGCTGATCCATC
*
2427590 GAGTGATGCATTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
196 GAGTGATGCATTCGAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
*
2427655 AGATGAGTTCTTCTCATTATGAACTCTATCTGGGAATGTTGATCCATTGATCAAGCT
261 AGATGAGTTCTTCTCATTATGAACTCTATCTGGGAATATTGATCCATTGATCAAGCT
* *
2427712 AAAG-TTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAAATGAGTTATTCTCATTA
1 AAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTATTCTCATTA
** *
2427776 TGAACTCTACCTGGCAATGCTGATCCATCGAGTGATGAATTCAAGCAAAAGATTGAACAAGATCT
66 TGAACTCTACCTGAAAAAGCTGAT-C--C-A-T--TG-A-TCAAGCAAAAG-TTGAACAAG-TCT
* *
2427841 TCTCATTATGGACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTACGGCAAT
120 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTACGACAAT
*
2427906 GCTGATCCATCGAGTGATGCATTCGAGCAAAAGATTGAACAAATTTTTCTCATTATGAACTTCTT
185 GCTGATCCATCGAGTGATGCATTCGAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTT
*
2427971 CTTCGTTCTTCAGATGAGTTCTTCTCATTATGAACTCTATCTGGGAATATTGATCCAT
250 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTATCTGGGAATATTGATCCAT
2428029 CGAATGATGG
Statistics
Matches: 288, Mismatches: 18, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
316 76 0.26
317 5 0.02
319 1 0.00
320 1 0.00
321 1 0.00
323 2 0.01
324 1 0.00
325 10 0.03
326 8 0.03
327 183 0.64
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (317 bp):
AAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTATTCTCATTA
TGAACTCTACCTGAAAAAGCTGATCCATTGATCAAGCAAAAGTTGAACAAGTCTTCTCATTATGA
ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTACGACAATGCTGATCCATC
GAGTGATGCATTCGAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
AGATGAGTTCTTCTCATTATGAACTCTATCTGGGAATATTGATCCATTGATCAAGCT
Found at i:2427875 original size:215 final size:214
Alignment explanation
Indices: 2427388--2428037 Score: 887
Period size: 215 Copynumber: 3.0 Consensus size: 214
2427378 GGAAATGGAG
* * * *
2427388 TCAAGAAAAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTTT
1 TCAAGCAAAAGATTGAACAAGATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * *
2427452 TCTCATTATGAACTCTACCTGAAAAAGTTGATCCATTGATCAAGCTAAAGTTGAATAAGTTTTCT
66 TCTCATTATGAACTCTATCTGGAAATGTTGATCCATTGATCAAGCTAAAGTTGAATAAGTTTTCT
* *
2427517 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCC-GACAATGC
131 CATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGC
*
2427581 TGATCCATCGAGTGATGCAT
195 TGATCCATCGAGTGATGAAT
* *
2427601 TCGAGCAAAAGGTTGAACAA-ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
1 TCAAGCAAAAGATTGAACAAGA-TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
*
2427665 TTCTCATTATGAACTCTATCTGGGAATGTTGATCCATTGATCAAGCTAAAGTTGAATAAGTTCTT
65 TTCTCATTATGAACTCTATCTGGAAATGTTGATCCATTGATCAAGCTAAAGTTGAATAAGTT-TT
* *
2427730 CTCATTATGAACTTCTTCTTCTTCTTCAAATGAGTTATTCTCATTATGAACTCTACCTGGCAATG
129 CTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATG
2427795 CTGATCCATCGAGTGATGAAT
194 CTGATCCATCGAGTGATGAAT
*
2427816 TCAAGCAAAAGATTGAACAAGATCTTCTCATTATGGACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAGCAAAAGATTGAACAAGATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * *
2427881 TCTCATTATGAACTCT-TAC-GGCAATGCTGATCCATCGAGTGATGCATTCGAGCAAAAGATTGA
66 TCTCATTATGAACTCTAT-CTGGAAATGTTGATCCAT----TGAT-CA----AGCTAAAG-TTGA
* *
2427944 ACAAATTTTTCTCATTATGAACTTCTTCTTCGTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
120 A-TAAGTTTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACTCT
* * ** *
2428009 ATCTGGGAATATTGATCCATCGAATGATG
183 ACCTGGCAATGCTGATCCATCGAGTGATG
2428038 GATCTGAATC
Statistics
Matches: 390, Mismatches: 29, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
213 43 0.11
214 121 0.31
215 125 0.32
216 1 0.00
218 4 0.01
219 2 0.01
223 7 0.02
224 28 0.07
225 59 0.15
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (214 bp):
TCAAGCAAAAGATTGAACAAGATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTCTATCTGGAAATGTTGATCCATTGATCAAGCTAAAGTTGAATAAGTTTTCT
CATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCT
GATCCATCGAGTGATGAAT
Found at i:2428431 original size:22 final size:22
Alignment explanation
Indices: 2428406--2428482 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
2428396 AATAAGGCTT
*
2428406 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2428428 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* * *
2428450 TCATCTTTGAAGAGTGTATCTA
1 TCATCTTTGAAAAGAGAATCTA
2428472 TCATCTTTGAA
1 TCATCTTTGAA
2428483 GAATGTAGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2428483 original size:22 final size:22
Alignment explanation
Indices: 2428423--2428489 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
2428413 TAAAAAGAGA
* * *
2428423 ATCTATCATCTTTGAAAAGAGA
1 ATCTATCATCTTTGAAGAGTGT
2428445 ATCTATCATCTTTGAAGAGTGT
1 ATCTATCATCTTTGAAGAGTGT
*
2428467 ATCTATCATCTTTGAAGAATGT
1 ATCTATCATCTTTGAAGAGTGT
2428489 A
1 A
2428490 GATGTAGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (22 bp):
ATCTATCATCTTTGAAGAGTGT
Found at i:2428962 original size:53 final size:53
Alignment explanation
Indices: 2428846--2428988 Score: 225
Period size: 53 Copynumber: 2.7 Consensus size: 53
2428836 ACCATAACTG
*
2428846 GTTCGTAAAACACTT-GACAACACATTCATCATTTCCTATGGTTTCTGCCCAGAT
1 GTTCGTAAAATA-TTCGACAACACATTCATCATTT-CTATGGTTTCTGCCCAGAT
* * *
2428900 GTTCGTAAAATATTCGACAACACATTCATCCTTTCTGTGGTTTCTGCCCAGTT
1 GTTCGTAAAATATTCGACAACACATTCATCATTTCTATGGTTTCTGCCCAGAT
2428953 GTTCGTAAAATATTCGACAACACATTCATCATTTCT
1 GTTCGTAAAATATTCGACAACACATTCATCATTTCT
2428989 TGTGTCTTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
53 54 0.65
54 29 0.35
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (53 bp):
GTTCGTAAAATATTCGACAACACATTCATCATTTCTATGGTTTCTGCCCAGAT
Found at i:2430486 original size:31 final size:31
Alignment explanation
Indices: 2430451--2430562 Score: 206
Period size: 31 Copynumber: 3.6 Consensus size: 31
2430441 ACCATAGATT
* *
2430451 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
2430482 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
2430513 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
2430544 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
2430563 CCTCGACCCT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:2434933 original size:31 final size:31
Alignment explanation
Indices: 2434894--2435049 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
2434884 CCCGAAGGAC
* * *
2434894 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
2434925 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2434956 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
2434987 CATTCCATATGTCCCGAAAAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2435018 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2435049 C
1 C
2435050 CCTCGACCCT
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2435660 original size:35 final size:35
Alignment explanation
Indices: 2435614--2435681 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
2435604 TTTCATTTAG
*
2435614 GGGGAATCGATACCCCCCA-TGGGGAATCTGTTCTC
1 GGGGAATCGATA-CCCCCAGGGGGGAATCTGTTCTC
2435649 GGGGAATCGATACCCCCAGGGGGGAATCTGTTC
1 GGGGAATCGATACCCCCAGGGGGGAATCTGTTC
2435682 CCCATGCACA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 6 0.19
35 25 0.81
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (35 bp):
GGGGAATCGATACCCCCAGGGGGGAATCTGTTCTC
Found at i:2441630 original size:30 final size:30
Alignment explanation
Indices: 2441596--2441664 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
2441586 TTATATGAGT
*
2441596 TATGTGATAAAGGTATGG-AAATGATATGTC
1 TATGTGATAAAGGTA-GGAAAATAATATGTC
2441626 TATGTGATAAAGGTAGGAAAATAATATGTC
1 TATGTGATAAAGGTAGGAAAATAATATGTC
2441656 TATGTGATA
1 TATGTGATA
2441665 CAAATTATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (30 bp):
TATGTGATAAAGGTAGGAAAATAATATGTC
Found at i:2441908 original size:23 final size:23
Alignment explanation
Indices: 2441874--2441942 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
2441864 CATTATTATA
2441874 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
2441897 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
2441920 TGGCACTTCGATGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
2441943 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:2445673 original size:12 final size:14
Alignment explanation
Indices: 2445646--2445684 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
2445636 ACAAACATAA
2445646 AAATGAAAAGATGC
1 AAATGAAAAGATGC
2445660 AAATG-AAA-ATGC
1 AAATGAAAAGATGC
*
2445672 AAATGCAAAGATG
1 AAATGAAAAGATG
2445685 TGAATGTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.39
13 6 0.26
14 8 0.35
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (14 bp):
AAATGAAAAGATGC
Found at i:2445775 original size:16 final size:15
Alignment explanation
Indices: 2445745--2445783 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2445735 CAACAAATGT
2445745 AAAATG-AAA-ATGC
1 AAAATGCAAAGATGC
2445758 AAAGATGCAAAGATGC
1 AAA-ATGCAAAGATGC
2445774 AAAATGCAAA
1 AAAATGCAAA
2445784 TGCATGTACG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.13
14 3 0.13
15 10 0.43
16 7 0.30
ACGTcount: A:0.59, C:0.10, G:0.18, T:0.13
Consensus pattern (15 bp):
AAAATGCAAAGATGC
Found at i:2445786 original size:6 final size:7
Alignment explanation
Indices: 2445739--2445787 Score: 57
Period size: 8 Copynumber: 7.0 Consensus size: 7
2445729 AGCAAACAAC
*
2445739 AAATGTA
1 AAATGCA
2445746 AAATG-A
1 AAATGCA
2445752 AAATGCA
1 AAATGCA
2445759 AAGATGCA
1 AA-ATGCA
2445767 AAGATGCA
1 AA-ATGCA
2445775 AAATGC-
1 AAATGCA
2445781 AAATGCA
1 AAATGCA
2445788 TGTACGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.31
7 12 0.31
8 15 0.38
ACGTcount: A:0.55, C:0.10, G:0.18, T:0.16
Consensus pattern (7 bp):
AAATGCA
Found at i:2447251 original size:2 final size:2
Alignment explanation
Indices: 2447244--2447288 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
2447234 ATAAAGAAGA
* *
2447244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2447286 AT A
1 AT A
2447289 AAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2448191 original size:3 final size:3
Alignment explanation
Indices: 2448183--2448224 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2448173 TATATGACTA
2448183 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2448225 TAAACATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2448253 original size:25 final size:27
Alignment explanation
Indices: 2448216--2448272 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
2448206 TAATAATAAT
*
2448216 AATAATAATTAAAC-AT-A-TAAAATTA
1 AATAATAACTAAACAATGACTAAAA-TA
2448241 AATAATAACTAAACAATGACTAAAATA
1 AATAATAACTAAACAATGACTAAAATA
2448268 AATAA
1 AATAA
2448273 AATTAAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 13 0.46
26 2 0.07
27 8 0.29
28 5 0.18
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (27 bp):
AATAATAACTAAACAATGACTAAAATA
Found at i:2448264 original size:28 final size:24
Alignment explanation
Indices: 2448184--2448272 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 24
2448174 ATATGACTAA
2448184 ATAATAAT-AATAATAA-TAATA-AT
1 ATAA-AATAAATAATAACTAA-ACAT
*
2448207 AATAATAAT-AATAATAATTAAACAT
1 -ATAA-AATAAATAATAACTAAACAT
2448232 ATAAAATTAAATAATAACTAAACAAT
1 ATAAAA-TAAATAATAACTAAAC-AT
2448258 GACTAAAATAAATAA
1 -A-TAAAATAAATAA
2448273 AATTAAAACT
Statistics
Matches: 57, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
23 2 0.04
24 22 0.39
25 18 0.32
26 2 0.04
27 8 0.14
28 5 0.09
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (24 bp):
ATAAAATAAATAATAACTAAACAT
Found at i:2449670 original size:13 final size:13
Alignment explanation
Indices: 2449652--2449690 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
2449642 GAATAGTATA
2449652 AATAAAATAAAAT-
1 AATAAAA-AAAATG
2449665 AATAAAAACAAATG
1 AATAAAAA-AAATG
2449679 AATAAAAAAAAT
1 AATAAAAAAAAT
2449691 TAGTATCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 15 0.62
14 8 0.33
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (13 bp):
AATAAAAAAAATG
Found at i:2467942 original size:21 final size:22
Alignment explanation
Indices: 2467917--2467957 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2467907 ACATTGGTAC
2467917 AATTTACCC-TAAAAAATTGAT
1 AATTTACCCTTAAAAAATTGAT
2467938 AATTTACCCTTAAAAAATTG
1 AATTTACCCTTAAAAAATTG
2467958 TGGAATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (22 bp):
AATTTACCCTTAAAAAATTGAT
Found at i:2474856 original size:23 final size:23
Alignment explanation
Indices: 2474821--2474876 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
2474811 TCGGATTTTG
2474821 CAGGTACCCGTAATTCTGG-TAAT
1 CAGGTACCCGTAATTC-GGATAAT
* *
2474844 CGGGTACCTGTAATTCGGATAAT
1 CAGGTACCCGTAATTCGGATAAT
2474867 CAGGTACCCG
1 CAGGTACCCG
2474877 GTTTTTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (23 bp):
CAGGTACCCGTAATTCGGATAAT
Found at i:2475022 original size:24 final size:23
Alignment explanation
Indices: 2474994--2475042 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
2474984 TTGATTAGTT
*
2474994 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTA-TAA
* *
2475018 TAATTAAATATGTAATATTATAA
1 TAATTAAATATATAAAATTATAA
2475041 TA
1 TA
2475043 TATAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATTAAATATATAAAATTATAA
Found at i:2475654 original size:16 final size:16
Alignment explanation
Indices: 2475630--2475699 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
2475620 TAATAAATAA
*
2475630 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
*
2475646 ACAAACATAAACGAAC
1 ACGAACATAAACGAAC
*
2475662 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
2475678 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
2475694 ATGAAC
1 ACGAAC
2475700 GTTGGAGGCC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.59, C:0.23, G:0.10, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2475950 original size:23 final size:24
Alignment explanation
Indices: 2475896--2475961 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
2475886 AAAAATTTAA
*
2475896 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTAAAGCTCGAGACTC
**
2475920 GAGCTCGATTAAAGCTCGATTCT-
1 GAGCTCGATTAAAGCTCGAGACTC
*
2475943 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTAAAGCTCGA
2475962 CATTGCTCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
23 18 0.47
24 20 0.53
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (24 bp):
GAGCTCGATTAAAGCTCGAGACTC
Found at i:2478571 original size:22 final size:22
Alignment explanation
Indices: 2478543--2478588 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2478533 AAACATGCTC
*
2478543 TAGGGGACTATTTCAGTCCATA
1 TAGGGGACTACTTCAGTCCATA
*
2478565 TAGGGGACTGCTTCAGTCCATA
1 TAGGGGACTACTTCAGTCCATA
2478587 TA
1 TA
2478589 AAGCCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (22 bp):
TAGGGGACTACTTCAGTCCATA
Found at i:2479602 original size:22 final size:20
Alignment explanation
Indices: 2479567--2479609 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
2479557 TTTTTTAATT
*
2479567 TTAATTTATTTTATTTTTCA
1 TTAATTTATTTTATTATTCA
2479587 TTAATATTATTATTATTATTCA
1 TTAAT-TTATT-TTATTATTCA
2479609 T
1 T
2479610 CTTTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 5 0.25
22 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
TTAATTTATTTTATTATTCA
Found at i:2485638 original size:33 final size:33
Alignment explanation
Indices: 2485601--2485667 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
2485591 GATCAATTAT
*
2485601 TAATCGGATGATAAATTCGATTCAAAATTTTAA
1 TAATCGAATGATAAATTCGATTCAAAATTTTAA
*
2485634 TAATCGAATGATAAATTCGATTCAAACTTTTAA
1 TAATCGAATGATAAATTCGATTCAAAATTTTAA
2485667 T
1 T
2485668 GAAAAGTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (33 bp):
TAATCGAATGATAAATTCGATTCAAAATTTTAA
Found at i:2491236 original size:21 final size:20
Alignment explanation
Indices: 2491198--2491236 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2491188 TAATTTTTTT
* *
2491198 TAATTTTTTCTTTTTAAATA
1 TAATTTTTTATTTATAAATA
2491218 TAATATTTTTATTTATAAA
1 TAAT-TTTTTATTTATAAA
2491237 AAATCAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATTTTTTATTTATAAATA
Found at i:2492141 original size:2 final size:2
Alignment explanation
Indices: 2492134--2492160 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2492124 ATCGATAACG
2492134 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2492161 TGTAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2492952 original size:16 final size:14
Alignment explanation
Indices: 2492930--2492966 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 14
2492920 CTCTACTTTA
2492930 TTTATAATATTTAAT
1 TTTATAATA-TTAAT
2492945 TATTATAATATTAAT
1 T-TTATAATATTAAT
2492960 TTTATAA
1 TTTATAA
2492967 ATATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 7 0.33
16 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATAATATTAAT
Found at i:2495612 original size:20 final size:20
Alignment explanation
Indices: 2495583--2495636 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
2495573 GAGGGTTCAT
2495583 AGGTCCTTCGGGACATACAG
1 AGGTCCTTCGGGACATACAG
* * *
2495603 AGGTCATTCGAGACATACAT
1 AGGTCCTTCGGGACATACAG
2495623 A-GTCCTTCGGGACA
1 AGGTCCTTCGGGACA
2495637 AATTTTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (20 bp):
AGGTCCTTCGGGACATACAG
Found at i:2497287 original size:17 final size:17
Alignment explanation
Indices: 2497260--2497299 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2497250 TGTTGGAATA
2497260 AGTCAAGCAGATACATGC
1 AGTC-AGCAGATACATGC
* *
2497278 AGTCAGCAGATGCATGT
1 AGTCAGCAGATACATGC
2497295 AGTCA
1 AGTCA
2497300 CTGATCGTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (17 bp):
AGTCAGCAGATACATGC
Found at i:2508416 original size:17 final size:18
Alignment explanation
Indices: 2508389--2508424 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2508379 TGTTGGAATA
2508389 AGTCGAGCAGATACATGC
1 AGTCGAGCAGATACATGC
*
2508407 AGTC-AGCAGATGCATGC
1 AGTCGAGCAGATACATGC
2508424 A
1 A
2508425 ATCACTGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (18 bp):
AGTCGAGCAGATACATGC
Found at i:2512217 original size:2 final size:2
Alignment explanation
Indices: 2512212--2512253 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2512202 TTTAAAGTAT
2512212 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
2512254 GAAAGCCTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2512755 original size:23 final size:23
Alignment explanation
Indices: 2512729--2512801 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
2512719 CCAAAAGGAA
* * *
2512729 GAGAAAAACGTGTCACAAAGGTT
1 GAGATAAACGTGCCACAAAGGCT
*
2512752 GAGATAAATGTGCCACAAAGGCT
1 GAGATAAACGTGCCACAAAGGCT
* * *
2512775 GAGATAAACTTGCCATAAAGGCA
1 GAGATAAACGTGCCACAAAGGCT
2512798 GAGA
1 GAGA
2512802 ACTTGTCACA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.42, C:0.15, G:0.26, T:0.16
Consensus pattern (23 bp):
GAGATAAACGTGCCACAAAGGCT
Found at i:2515133 original size:26 final size:26
Alignment explanation
Indices: 2515093--2515171 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
2515083 TTTTAATTGG
* *
2515093 AATAAAAGAGGTAATAAATATCTTTT
1 AATAAAAAAGATAATAAATATCTTTT
* *
2515119 AATAAAAAAGATAATAAATTTATTTT
1 AATAAAAAAGATAATAAATATCTTTT
* *
2515145 AATAAAAGAAGAT-GTAAATCTCTTTT
1 AATAAAA-AAGATAATAAATATCTTTT
2515171 A
1 A
2515172 TCTTTATCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 40 0.89
27 5 0.11
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (26 bp):
AATAAAAAAGATAATAAATATCTTTT
Found at i:2517931 original size:36 final size:35
Alignment explanation
Indices: 2517843--2517949 Score: 162
Period size: 36 Copynumber: 3.0 Consensus size: 35
2517833 TTTGTTGATA
* *
2517843 ATGCTCAAATTAGGTTATCCTACTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAATATT-GAAAT
2517879 ATGCT-AAATTAGGTTATCCCACTAATATTGCAAAT
1 ATGCTCAAATTAGGTTATCCCACTAATATTG-AAAT
2517914 ATGCTCAAATTAGGTTATCCCACTAATATTGGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAATATT-GAAAT
2517950 GACGATTTTG
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
34 1 0.02
35 31 0.47
36 33 0.50
37 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (35 bp):
ATGCTCAAATTAGGTTATCCCACTAATATTGAAAT
Found at i:2519388 original size:19 final size:19
Alignment explanation
Indices: 2519364--2519401 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2519354 ATGCAATAAA
2519364 CACTAAACCATGAAAACTG
1 CACTAAACCATGAAAACTG
2519383 CACTAAACCATGAAAACTG
1 CACTAAACCATGAAAACTG
2519402 TATCAGCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (19 bp):
CACTAAACCATGAAAACTG
Found at i:2524118 original size:11 final size:12
Alignment explanation
Indices: 2524093--2524117 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2524083 TGTTTTATAC
2524093 TTAAACAATTTT
1 TTAAACAATTTT
2524105 TTAAACAATTTT
1 TTAAACAATTTT
2524117 T
1 T
2524118 ACAAAGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAACAATTTT
Found at i:2530069 original size:42 final size:44
Alignment explanation
Indices: 2530022--2530116 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
2530012 TTGTGCTTCA
** *
2530022 TGCATCGATACACC-T-AACAGTGCATGGATGCA-TCCTTGAATG
1 TGCATCGATACACCATGAA-AGTGCACCGATGCACGCCTTGAATG
*
2530064 TGCATCGATACACCATGAAGGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
2530108 TGCATCGAT
1 TGCATCGAT
2530117 GCACAAGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 14 0.30
43 12 0.26
44 20 0.43
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.24
Consensus pattern (44 bp):
TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:2530087 original size:21 final size:21
Alignment explanation
Indices: 2530022--2530116 Score: 77
Period size: 23 Copynumber: 4.4 Consensus size: 21
2530012 TTGTGCTTCA
*
2530022 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-TG
* *
2530042 TGCATGGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* *
2530064 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
* *
2530085 TGCACCGATGCACGCCTTGAATG
1 TGCATCGAT--ACACCTTGAATG
2530108 TGCATCGAT
1 TGCATCGAT
2530117 GCACAAGGCC
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 10 0.17
21 17 0.29
22 12 0.21
23 19 0.33
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:2530110 original size:23 final size:23
Alignment explanation
Indices: 2530041--2530121 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
2530031 ACACCTAACA
* *
2530041 GTGCATGGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
2530063 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
2530084 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
2530107 GTGCATCGATGCACA
1 GTGCATCGATGCACA
2530122 AGGCCATGCA
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.33
22 9 0.20
23 21 0.46
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:2530137 original size:43 final size:42
Alignment explanation
Indices: 2530040--2530139 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 42
2530030 TACACCTAAC
* * * *
2530040 AGTGCATGGATGCATCCTTGAATGTGCATCGATACACCATGA
1 AGTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGA
* * *
2530082 AGGTGCACCGATGCACGCCTTGAATGTGCATCGATGCACAAGGCC
1 A-GTGCATCGATGCA-GCCTTGAATGTGCATCGATACACAAGG-A
2530127 A-TGCATCGATGCA
1 AGTGCATCGATGCA
2530140 TCTGTCAGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
42 1 0.02
43 22 0.47
44 23 0.49
45 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (42 bp):
AGTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGA
Found at i:2532843 original size:45 final size:45
Alignment explanation
Indices: 2532806--2532890 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
2532796 TGCACCAATT
*
2532806 AATTTTTC-AAACATCGAATGCATTTGATGCATCGATGCGCTCAG
1 AATTTTTCAAAACATCGAATGCATTTGATGCATCGATGCACTCAG
** *
2532850 GCTTTTTCAAAACATCGAATGCATTTTATGCATCGATGCAC
1 AATTTTTCAAAACATCGAATGCATTTGATGCATCGATGCAC
2532891 ACTTGGTGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 6 0.17
45 30 0.83
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (45 bp):
AATTTTTCAAAACATCGAATGCATTTGATGCATCGATGCACTCAG
Found at i:2534335 original size:35 final size:36
Alignment explanation
Indices: 2534285--2534386 Score: 142
Period size: 35 Copynumber: 2.9 Consensus size: 36
2534275 TGTTGATAAA
2534285 GCTCAAATTAGGTTATCCCACTAGTATTAGAAATAT
1 GCTCAAATTAGGTTATCCCACTAGTATTAGAAATAT
*
2534321 GCT-AAATTAGGTTATCCCACT--TATTTGCAAATAT
1 GCTCAAATTAGGTTATCCCACTAGTATTAG-AAATAT
*
2534355 GCTCAAA-T-GGTTATCCCACTAGTATTGGAAAT
1 GCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
2534387 GATTTTGCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
33 17 0.28
34 14 0.23
35 26 0.43
36 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (36 bp):
GCTCAAATTAGGTTATCCCACTAGTATTAGAAATAT
Found at i:2536614 original size:24 final size:24
Alignment explanation
Indices: 2536566--2536615 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2536556 ATAGGTTTTT
*
2536566 AAGTATTTATTATATAAATATAAA
1 AAGTATTTATTATATAAAGATAAA
2536590 AAGTATTTAAATTATA-AAAGA-AAA
1 AAGTATTT--ATTATATAAAGATAAA
2536614 AA
1 AA
2536616 TATAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 13 0.57
25 4 0.17
26 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (24 bp):
AAGTATTTATTATATAAAGATAAA
Found at i:2539618 original size:34 final size:35
Alignment explanation
Indices: 2539575--2539647 Score: 123
Period size: 34 Copynumber: 2.1 Consensus size: 35
2539565 TTGAGTTACT
2539575 TCCTATGGAAGTGTTCTTTGC-TTCCAAATAGA-AC
1 TCCTATGGAAGTGTTC-TTGCTTTCCAAATAGAGAC
2539609 TCCTATGGAAGTGTTCTTGCTTTCCAAATAGAGAC
1 TCCTATGGAAGTGTTCTTGCTTTCCAAATAGAGAC
2539644 TCCT
1 TCCT
2539648 TAACAATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
33 4 0.11
34 27 0.73
35 6 0.16
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (35 bp):
TCCTATGGAAGTGTTCTTGCTTTCCAAATAGAGAC
Found at i:2541535 original size:54 final size:54
Alignment explanation
Indices: 2541476--2541580 Score: 183
Period size: 54 Copynumber: 1.9 Consensus size: 54
2541466 CATCATCTAC
*
2541476 AACTAGAGAGCAAGATCATTCTGAAGTAACCATTGGATCTATAGCCATCTGTAG
1 AACTAGAGAGCAAGATCATTCTGAAGTAACCATTGAATCTATAGCCATCTGTAG
**
2541530 AACTAGAGAGCAAGATCATTCTGAAGTAACTGTTGAATCTATAGCCATCTG
1 AACTAGAGAGCAAGATCATTCTGAAGTAACCATTGAATCTATAGCCATCTG
2541581 CATTAGCTAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (54 bp):
AACTAGAGAGCAAGATCATTCTGAAGTAACCATTGAATCTATAGCCATCTGTAG
Found at i:2550776 original size:29 final size:29
Alignment explanation
Indices: 2550687--2550779 Score: 80
Period size: 30 Copynumber: 3.1 Consensus size: 29
2550677 TGAGAGGAAT
* *
2550687 TAAATTTTAATTTGATCA-TAAACTTTAAA
1 TAAATATTAATTT-AACACTAAACTTTAAA
* *
2550716 TATAATATTAATTTAACACTGAATTTTAAAA
1 TA-AATATTAATTTAACACTAAACTTT-AAA
* ***
2550747 TAAATATTATTTTATTTCTAAACTTTAAA
1 TAAATATTAATTTAACACTAAACTTTAAA
2550776 TAAA
1 TAAA
2550780 ATATCAATGA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
29 12 0.24
30 34 0.67
31 5 0.10
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAATATTAATTTAACACTAAACTTTAAA
Found at i:2554156 original size:17 final size:18
Alignment explanation
Indices: 2554126--2554159 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2554116 AAACACAGAC
*
2554126 CAATTTTTGTCTTAAAAA
1 CAATTTTTGCCTTAAAAA
2554144 CAATTTTT-CCTTAAAA
1 CAATTTTTGCCTTAAAA
2554160 TTGTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (18 bp):
CAATTTTTGCCTTAAAAA
Found at i:2554300 original size:16 final size:16
Alignment explanation
Indices: 2554275--2554305 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2554265 AATTAAAGTT
2554275 ATAATAGTTTTTAAAC
1 ATAATAGTTTTTAAAC
*
2554291 ATAATTGTTTTTAAA
1 ATAATAGTTTTTAAA
2554306 AAAAATGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (16 bp):
ATAATAGTTTTTAAAC
Found at i:2555550 original size:26 final size:26
Alignment explanation
Indices: 2555514--2555568 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
2555504 AAGATGCAAA
2555514 TATGTAGGATAAATGAAACTAGTTTG
1 TATGTAGGATAAATGAAACTAGTTTG
*
2555540 TATGTGGGATAAATGAAACTAGTTTG
1 TATGTAGGATAAATGAAACTAGTTTG
2555566 TAT
1 TAT
2555569 ATAGTCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (26 bp):
TATGTAGGATAAATGAAACTAGTTTG
Found at i:2558135 original size:21 final size:21
Alignment explanation
Indices: 2558111--2558264 Score: 75
Period size: 21 Copynumber: 7.2 Consensus size: 21
2558101 TCGATGGTTC
*
2558111 TATGTGGTCTTTCGAGACATA
1 TATGTGGTCTTTAGAGACATA
** *
2558132 TATGTAATCCTTTGGA-ACATA
1 TATGTGGT-CTTTAGAGACATA
* *
2558153 TATGTGGTTTATTAGA-ACACA
1 TATGTGGTCT-TTAGAGACATA
* * * *
2558174 TATTTTGTCCTTTGGA-ATATA
1 TATGTGGT-CTTTAGAGACATA
*
2558195 TATGTGGTCCTTAAAGAGA-AGTA
1 TATGTGGT-CTT-TAGAGACA-TA
* *
2558218 TATGTGGTCCTTAGGGACATA
1 TATGTGGTCTTTAGAGACATA
* *
2558239 TATGTGGTCCTTCAG-GACGTA
1 TATGTGGT-CTTTAGAGACATA
2558260 TATGT
1 TATGT
2558265 AGTCCTTCAG
Statistics
Matches: 101, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
20 1 0.01
21 72 0.71
22 17 0.17
23 11 0.11
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (21 bp):
TATGTGGTCTTTAGAGACATA
Found at i:2558269 original size:21 final size:21
Alignment explanation
Indices: 2558193--2558277 Score: 100
Period size: 21 Copynumber: 4.0 Consensus size: 21
2558183 CTTTGGAATA
* *
2558193 TATATGTGGTCCTTAAAGAGAAG
1 TATATGTGGTCCTT-CAG-GACG
*
2558216 TATATGTGGTCCTT-AGGGACA
1 TATATGTGGTCCTTCA-GGACG
2558237 TATATGTGGTCCTTCAGGACG
1 TATATGTGGTCCTTCAGGACG
*
2558258 TATATGTAGTCCTTCAGGAC
1 TATATGTGGTCCTTCAGGAC
2558278 AAATTCTATG
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
21 40 0.71
22 2 0.04
23 14 0.25
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (21 bp):
TATATGTGGTCCTTCAGGACG
Found at i:2559605 original size:18 final size:18
Alignment explanation
Indices: 2559582--2559619 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2559572 TTTTCAGATG
*
2559582 CCCATGCTGGGCCACTGC
1 CCCATGCTGGACCACTGC
2559600 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
2559618 CC
1 CC
2559620 AATCCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.47, G:0.24, T:0.16
Consensus pattern (18 bp):
CCCATGCTGGACCACTGC
Done.