Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008525.1 Hibiscus syriacus cultivar Beakdansim tig00111394_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: 732385
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:269572 original size:45 final size:46
Alignment explanation
Indices: 269504--269608 Score: 158
Period size: 45 Copynumber: 2.3 Consensus size: 46
269494 GATAGCATCA
* * *
269504 TATCTTACTTGATCTAATTACGATGTATCTTAGTCC-AAAACGTCC
1 TATCTTAGTTGATCTAATAACGATGTATCTTAGTCCAAAAACGGCC
*
269549 TATCTTAGTTGATCTAATAACGATGTATCTTAGTCCAAAAATGGCC
1 TATCTTAGTTGATCTAATAACGATGTATCTTAGTCCAAAAACGGCC
*
269595 TATCCTAGTTGATC
1 TATCTTAGTTGATC
269609 AGAAGTATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 34 0.63
46 20 0.37
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (46 bp):
TATCTTAGTTGATCTAATAACGATGTATCTTAGTCCAAAAACGGCC
Found at i:269577 original size:25 final size:25
Alignment explanation
Indices: 269504--269582 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 25
269494 GATAGCATCA
* *
269504 TATCTTACTTGATCTAATTACGATG
1 TATCTTAGTTGATCTAATAACGATG
* *
269529 TATCTTA---G-TCCAA-AACG-TCC
1 TATCTTAGTTGATCTAATAACGAT-G
269549 TATCTTAGTTGATCTAATAACGATG
1 TATCTTAGTTGATCTAATAACGATG
269574 TATCTTAGT
1 TATCTTAGT
269583 CCAAAAATGG
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
19 1 0.02
20 10 0.24
21 4 0.10
22 1 0.02
23 1 0.02
24 4 0.10
25 20 0.48
26 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.41
Consensus pattern (25 bp):
TATCTTAGTTGATCTAATAACGATG
Found at i:275676 original size:23 final size:23
Alignment explanation
Indices: 275650--275697 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
275640 ATAAAGTATA
*
275650 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
275673 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
275696 AT
1 AT
275698 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:276140 original size:23 final size:23
Alignment explanation
Indices: 276113--276186 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
276103 GACACTTTAC
276113 AATATAACCACTACCTATTACAT
1 AATATAACCACTACCTATTACAT
*
276136 AATATAAACGA-TACCTATTACAT
1 AATAT-AACCACTACCTATTACAT
* * *
276159 TATATAAGCGCTACCTATTACAT
1 AATATAACCACTACCTATTACAT
*
276182 CATAT
1 AATAT
276187 TTTTACCTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
22 2 0.05
23 37 0.86
24 4 0.09
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.32
Consensus pattern (23 bp):
AATATAACCACTACCTATTACAT
Found at i:276379 original size:29 final size:29
Alignment explanation
Indices: 276332--276396 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
276322 TCATTTGCAC
* *
276332 AAAA-ATTATTTGATTATTTGATATTTTAT
1 AAAATATTATTTGATAATTTGA-ATTTAAT
*
276361 AAAATATTATTT-ATAATTTTAATTTAAT
1 AAAATATTATTTGATAATTTGAATTTAAT
276389 AATAATAT
1 AA-AATAT
276397 ATATCGTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 8 0.26
29 16 0.52
30 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTGATAATTTGAATTTAAT
Found at i:276563 original size:428 final size:430
Alignment explanation
Indices: 275764--276817 Score: 2022
Period size: 428 Copynumber: 2.5 Consensus size: 430
275754 TATTACATTA
*
275764 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
275829 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
275894 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
275959 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
*
276024 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACATTT
261 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
*
276089 TTATAAAAAAGATAGACACTTTACAATATAACCACTACCTATTACATAATATAAACGATACCTAT
326 TTATAAAAAAGATAGACACTTTACAATATAACCACTACCTATTACATAATATAAACGATACCCAT
276154 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
276194 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
276259 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
276324 ATTTGCAC-AAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTATAA-TTTTAATTTA
131 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
276387 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
276452 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
261 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
* *
276517 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCCAT
326 TTATAAAAAAGATAGACACTTTACAATATAACCACTACCTATTACATAATATAAACGATACCCAT
276582 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
276622 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
276687 TTATGTTTCAATTTTTTTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
276752 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
276817 A
196 A
276818 CAACATTAAC
Statistics
Matches: 613, Mismatches: 9, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
428 378 0.62
429 87 0.14
430 148 0.24
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (430 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
TTATAAAAAAGATAGACACTTTACAATATAACCACTACCTATTACATAATATAAACGATACCCAT
TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:276578 original size:23 final size:23
Alignment explanation
Indices: 276552--276614 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
276542 ATATAACCAC
276552 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
276575 TACCCATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
276598 TACCTATTACATCATAT
1 TACCTATTACATTATAT
276615 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:277086 original size:39 final size:39
Alignment explanation
Indices: 277032--277117 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
277022 CAAGTTGTAG
* *
277032 ATTTTGATTTCCTTTTGCTTGGTATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
277071 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
277110 ATTTTGAT
1 ATTTTGAT
277118 GAGCATCGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.50
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:277398 original size:18 final size:18
Alignment explanation
Indices: 277375--277411 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
277365 TGAAATATAT
277375 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
277393 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
277411 A
1 A
277412 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:277875 original size:23 final size:23
Alignment explanation
Indices: 277849--277911 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
277839 ATATAACCAC
277849 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
277872 TACCCATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
277895 TACCTATTACATCATAT
1 TACCTATTACATTATAT
277912 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:278314 original size:25 final size:25
Alignment explanation
Indices: 278257--278322 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
278247 CACTCAAAAG
*
278257 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
278282 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
278307 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
278323 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:281099 original size:183 final size:182
Alignment explanation
Indices: 280787--281277 Score: 833
Period size: 183 Copynumber: 2.7 Consensus size: 182
280777 TTAAAATTAC
280787 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
280852 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
280917 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCTGATGTATAAATGT
130 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTATAAATGT
* *
280970 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
281035 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACGCATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
281100 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
130 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTATAAATGT
* *
281153 CGACAC-TTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
1 CGACACTTTTTTA-AATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
281217 ATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGTGCATAAAACCGGTATATTTATACCG
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
281278 ATAGCATTGC
Statistics
Matches: 291, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
181 56 0.19
182 54 0.19
183 181 0.62
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (182 bp):
CGACACTTTTTTAAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
TATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTATAAATGT
Found at i:282787 original size:3 final size:3
Alignment explanation
Indices: 282779--282859 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
282769 ACTTGTTTGA
* * * **
282779 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
282827 AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
282860 GTCAGCTTCA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:282796 original size:12 final size:12
Alignment explanation
Indices: 282783--282871 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
282773 GTTTGAATCA
* *
282783 TCATCTTCATCA
1 TCATCGTCATCT
* *
282795 TCATCATCATCA
1 TCATCGTCATCT
* *
282807 TCGTCATCATCT
1 TCATCGTCATCT
* *
282819 TCATCGCCAGCT
1 TCATCGTCATCT
*
282831 TCATCGTCATCA
1 TCATCGTCATCT
282843 TCATCGTCATCT
1 TCATCGTCATCT
*
282855 TCATCGTCAGCT
1 TCATCGTCATCT
282867 TCATC
1 TCATC
282872 TTCTGCGACC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:282802 original size:18 final size:18
Alignment explanation
Indices: 282783--282874 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
282773 GTTTGAATCA
* *
282783 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
282801 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
** * * *
282819 TCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCT
*
282837 TCATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
282855 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
282873 TC
1 TC
282875 TGCGACCGCT
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:282835 original size:36 final size:36
Alignment explanation
Indices: 282795--282871 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
282785 ATCTTCATCA
*
282795 TCATCATCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
282831 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
282867 TCATC
1 TCATC
282872 TTCTGCGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:282874 original size:6 final size:6
Alignment explanation
Indices: 282783--282874 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
282773 GTTTGAATCA
* * * * * * * *
282783 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
282831 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
282875 TGCGACCGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:284581 original size:199 final size:199
Alignment explanation
Indices: 284336--285306 Score: 1772
Period size: 199 Copynumber: 4.9 Consensus size: 199
284326 TTTAAATTAG
284336 TATCGACACAAACTATA--ACGTGTCG--ACATTATTTAGACATATTCTCTCATAAAACCGGTAT
1 TATCGACACAAACTATATTA-GTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
*
284397 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
*
284462 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGGAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
284527 AAAAA
195 AAAAA
284532 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
284597 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
284662 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
284727 AAAA
196 AAAA
* *
284731 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
284796 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTATGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
284861 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG--AA
284926 AAAAAA
194 AAAAAA
*
284932 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
284997 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
285062 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
285126 AAAA
196 AAAA
*
285130 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* * *
285195 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
285260 TTGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
285307 GGTCATATTG
Statistics
Matches: 754, Mismatches: 13, Indels: 12
0.97 0.02 0.02
Matches are distributed among these distances:
196 17 0.02
197 6 0.01
198 118 0.16
199 378 0.50
200 93 0.12
201 142 0.19
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:285268 original size:400 final size:398
Alignment explanation
Indices: 284336--285306 Score: 1781
Period size: 400 Copynumber: 2.4 Consensus size: 398
284326 TTTAAATTAG
284336 TATCGACACAAACTATA--ACGTGTCG--ACATTATTTAGACATATTCTCTCATAAAACCGGTAT
1 TATCGACACAAACTATATTA-GTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
284397 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
*
284462 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGGAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
284527 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
284592 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
284657 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTG
325 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTG
284722 GAAAAAAAA
390 GAAAAAAAA
* *
284731 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
284796 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTATGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
284861 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG--AA
*
284926 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACC
194 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC
284991 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
259 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
285056 TGGGATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT
324 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT
285120 GGAAAAAAAA
389 GGAAAAAAAA
*
285130 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
285195 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
285260 TTGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
285307 GGTCATATTG
Statistics
Matches: 555, Mismatches: 14, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
395 17 0.03
396 6 0.01
397 1 0.00
398 159 0.29
399 170 0.31
400 202 0.36
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (398 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
AAAAAAAA
Found at i:285471 original size:19 final size:19
Alignment explanation
Indices: 285425--285473 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
285415 TTATATTCAC
*
285425 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
285444 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
285463 ATACAAAATTA
1 ATACAAAATTA
285474 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:287312 original size:33 final size:33
Alignment explanation
Indices: 287266--287331 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
287256 CATCTTAATA
* *
287266 TCACCCCTTAACACCCCAACTTTTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
287299 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
287332 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:287390 original size:21 final size:21
Alignment explanation
Indices: 287365--287429 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
287355 CCCCTTATGC
* *
287365 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
287386 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
287407 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
287428 CT
1 CT
287430 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:289676 original size:17 final size:18
Alignment explanation
Indices: 289654--289696 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
289644 ATATATCCGG
289654 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
289671 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
289691 TATCAT
1 TATCAT
289697 ATTTTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:289868 original size:20 final size:20
Alignment explanation
Indices: 289841--289887 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
289831 TCCGGTAACG
289841 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
289860 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
289881 TTTTACC
1 TTTTACC
289888 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:289995 original size:182 final size:181
Alignment explanation
Indices: 289626--290099 Score: 662
Period size: 182 Copynumber: 2.6 Consensus size: 181
289616 CGTACTTACG
* * *
289626 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * ** *
289691 TATCATATTTTTACTTGTTATATCGTTGTGGATCGATATTTTTTTTTTAAAGTATCGACACATTA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATA-CATTTTTTAAAAGTATCGACACATTA
* * * *
289756 TAGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 TAAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATCCTTATAT
* *
289808 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
289873 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
289938 AAGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCAATCCTTATATT
131 AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATCCTTATA-T
* * * * * *
289990 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACTGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
290054 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
290100 AATTTGGATC
Statistics
Matches: 260, Mismatches: 30, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
181 66 0.25
182 193 0.74
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATCCTTATAT
Found at i:290568 original size:229 final size:229
Alignment explanation
Indices: 290166--290654 Score: 863
Period size: 229 Copynumber: 2.1 Consensus size: 229
290156 ACCTACTTTT
*
290166 ATAAGTATGGACATTTTTATAAAAATGATATATACTTTTTTTTAAAGTTATGTAATTTATGTTTC
1 ATAAGTATGGACATTTTTATAAAAATGATATATACTTTTTTTGAAAGTTATGTAATTTATGTTTC
290231 AATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAA
66 AATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAA
*
290296 AATATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
131 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
* *
290361 CCAAATATAATAATAAATATGTTTTCAACAGTGAA
196 CCAAAGATAATAATAAATATATTTTC-ACAGTGAA
* *
290396 ATAAGTATGTACACTTTTATAAAAATGATATATAC-TTTTTTGAAAGTTATGTAATTTATGTTTC
1 ATAAGTATGGACATTTTTATAAAAATGATATATACTTTTTTTGAAAGTTATGTAATTTATGTTTC
* *
290460 AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
66 AATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAA
*
290525 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGATTTTAAATTTAACAATATTAA
131 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
*
290590 CTAAAGATAATAATAAATATATTTTCACAGTGAA
196 CCAAAGATAATAATAAATATATTTTCACAGTGAA
*
290624 ATAAGTATGGACATTTTTATAAAAAGGATAT
1 ATAAGTATGGACATTTTTATAAAAATGATAT
290655 GTAATTTACA
Statistics
Matches: 246, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
228 36 0.15
229 177 0.72
230 33 0.13
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (229 bp):
ATAAGTATGGACATTTTTATAAAAATGATATATACTTTTTTTGAAAGTTATGTAATTTATGTTTC
AATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAA
AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
CCAAAGATAATAATAAATATATTTTCACAGTGAA
Found at i:294581 original size:118 final size:117
Alignment explanation
Indices: 294359--294586 Score: 348
Period size: 118 Copynumber: 1.9 Consensus size: 117
294349 TTAACAACAT
* *
294359 GTCAAATATGAGATTTTACTTTTAGCATGTTCCTTCACTACAAACTCTTAACAGATATCATAGTG
1 GTCAAATATGAGATTTTACTTTTAGCATGTTCCTACACTACAAACTCTTAACAGATACCATAGTG
* * * *
294424 CATTACTAAATTCCATCTTAGAATACAATTTATAGCATTCTAATATGCTCAAC
66 CACTACTAAATTCCATCTTAGAATAAAAGTTACAGCATTC-AATATGCTCAAC
* *
294477 GTCAAATATGAGATTTTACTTTTAGCATGTTCCTACACTCCAAACTCTTAACAGATACCATGGTG
1 GTCAAATATGAGATTTTACTTTTAGCATGTTCCTACACTACAAACTCTTAACAGATACCATAGTG
* * *
294542 CACTACTTAATTCCATCTTAGAATAAAAGTTCCATCATTCAATAT
66 CACTACTAAATTCCATCTTAGAATAAAAGTTACAGCATTCAATAT
294587 ATGCTTGACC
Statistics
Matches: 99, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
117 5 0.05
118 94 0.95
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.36
Consensus pattern (117 bp):
GTCAAATATGAGATTTTACTTTTAGCATGTTCCTACACTACAAACTCTTAACAGATACCATAGTG
CACTACTAAATTCCATCTTAGAATAAAAGTTACAGCATTCAATATGCTCAAC
Found at i:298251 original size:29 final size:27
Alignment explanation
Indices: 298216--298272 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 27
298206 ACCAATGCTC
298216 ATATAATTAAA-AATAATAATATATATAAT
1 ATATAA-TAAATAATAATAAT-TAT-TAAT
*
298245 ATATAATAAATAGTAATAATTATTAAT
1 ATATAATAAATAATAATAATTATTAAT
298272 A
1 A
298273 CTACTACTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 5 0.19
28 7 0.27
29 14 0.54
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATAATAAATAATAATAATTATTAAT
Found at i:298349 original size:3 final size:3
Alignment explanation
Indices: 298337--298384 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
298327 AATGCGTACT
* *
298337 ATA A-A ATA ATA ATA AT- ATA ATA ATG ATA ATA GTA ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
298382 ATA
1 ATA
298385 CTAACAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:298356 original size:11 final size:11
Alignment explanation
Indices: 298337--298384 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
298327 AATGCGTACT
298337 ATAAAATAATA
1 ATAAAATAATA
*
298348 ATAATATAATA
1 ATAAAATAATA
* *
298359 ATGATAATAGTA
1 AT-AAAATAATA
298371 ATAAAATAATA
1 ATAAAATAATA
298382 ATA
1 ATA
298385 CTAACAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:298365 original size:20 final size:20
Alignment explanation
Indices: 298342--298380 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
298332 GTACTATAAA
*
298342 ATAATAATAATATAATAATG
1 ATAATAATAATAAAATAATG
*
298362 ATAATAGTAATAAAATAAT
1 ATAATAATAATAAAATAAT
298381 AATACTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAATAATAATAAAATAATG
Found at i:298432 original size:22 final size:21
Alignment explanation
Indices: 298407--298456 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
298397 GACAAGTACT
*
298407 AATAATTATAAAATGAAATGAA
1 AATAATTATAAAATAAAAT-AA
**
298429 AATAAAAATAAAATAAAATAA
1 AATAATTATAAAATAAAATAA
298450 AA-AATTA
1 AATAATTA
298457 AATTAAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 3 0.13
21 4 0.17
22 16 0.70
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (21 bp):
AATAATTATAAAATAAAATAA
Found at i:298464 original size:17 final size:16
Alignment explanation
Indices: 298416--298452 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
298406 TAATAATTAT
*
298416 AAAATGAAATGAAAATA
1 AAAATAAAAT-AAAATA
298433 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
298449 AAAA
1 AAAA
298453 ATTAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:301806 original size:20 final size:20
Alignment explanation
Indices: 301783--301905 Score: 99
Period size: 20 Copynumber: 6.0 Consensus size: 20
301773 TTCGTGTTGT
301783 ATTTCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATTTTCC
* **
301803 ATTTCGCGTTGCGATAGTTGA
1 ATTTCGCGTTGCGAT-TTTCC
**
301824 AAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATTTTCC
* *
301844 TTTTCGCGTTGCGATTGTCTAC
1 ATTTCGCGTTGCGATT-T-TCC
*
301866 AGTT-GTCGTTGCGATTTTCC
1 ATTTCG-CGTTGCGATTTTCC
*
301886 AAATT--CGTTGCGATTTTCC
1 -ATTTCGCGTTGCGATTTTCC
301905 A
1 A
301906 AATTCGCGCG
Statistics
Matches: 82, Mismatches: 16, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
18 1 0.01
19 14 0.17
20 32 0.39
21 21 0.26
22 14 0.17
ACGTcount: A:0.15, C:0.21, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTCGCGTTGCGATTTTCC
Found at i:301895 original size:19 final size:19
Alignment explanation
Indices: 301871--301911 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
301861 TCTACAGTTG
301871 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
301890 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
301909 TCG
1 TCG
301912 CGCGAATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:302007 original size:19 final size:19
Alignment explanation
Indices: 301983--302070 Score: 104
Period size: 19 Copynumber: 4.5 Consensus size: 19
301973 CAACGAATTT
301983 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
302002 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
*
302024 TCGCAACTAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
302043 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
302062 TCGCAACGA
1 TCGCAACGA
302071 CAACTGTAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 40 0.71
20 2 0.04
21 2 0.04
22 12 0.21
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:302112 original size:20 final size:20
Alignment explanation
Indices: 302087--302155 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
302077 TAGACCATCT
302087 CAACGCGAAATGGAAAATCG
1 CAACGCGAAATGGAAAATCG
** ** *
302107 CAACGCGATTTTCAACTATCG
1 CAACGCGAAATGGAA-AATCG
*
302128 CAACGCAAAATGGAAAATCG
1 CAACGCGAAATGGAAAATCG
302148 CAACGCGA
1 CAACGCGA
302156 TTTTCAACTA
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 22 0.61
21 14 0.39
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (20 bp):
CAACGCGAAATGGAAAATCG
Found at i:302129 original size:21 final size:21
Alignment explanation
Indices: 302103--302176 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
302093 GAAATGGAAA
302103 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
302124 ATCGCAACGCAAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
302144 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
302165 ATCGCAACGCGA
1 ATCGCAACGCGA
302177 AATGCAACGC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:302143 original size:41 final size:41
Alignment explanation
Indices: 302087--302180 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
302077 TAGACCATCT
302087 CAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCG
1 CAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCG
*
302128 CAACGCAAAATGGAAAATCGCAACGCGATTTTCAACTATCG
1 CAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCG
302169 CAACGCGAAATG
1 CAACGCGAAATG
302181 CAACGCGAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (41 bp):
CAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCG
Found at i:302184 original size:21 final size:21
Alignment explanation
Indices: 302087--302184 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 21
302077 TAGACCATCT
*
302087 CAACGCGAAATGGAA-AATCG
1 CAACGCGAAATGCAACAATCG
** * *
302107 CAACGCGATTTTCAACTATCG
1 CAACGCGAAATGCAACAATCG
* *
302128 CAACGCAAAATGGAA-AATCG
1 CAACGCGAAATGCAACAATCG
** * *
302148 CAACGCGATTTTCAACTATCG
1 CAACGCGAAATGCAACAATCG
302169 CAACGCGAAATGCAAC
1 CAACGCGAAATGCAAC
302185 GCGAATTTGC
Statistics
Matches: 56, Mismatches: 20, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
20 25 0.45
21 31 0.55
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.17
Consensus pattern (21 bp):
CAACGCGAAATGCAACAATCG
Found at i:304482 original size:3 final size:3
Alignment explanation
Indices: 304470--304684 Score: 54
Period size: 3 Copynumber: 72.0 Consensus size: 3
304460 CAGCAATAGT
* * * ** * * * **
304470 AAC AAG AAC AAC AAG AAC AAC AAC AAC AAC AAT AGT AGC AGC AAT AGT
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* ** * * * ** *
304518 AAC AAG AAC AAC AAC AAC AAC AAC AGT AGC AGC AAT AGT AAC AAG AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* ** * ** * *
304566 AAC AAC AAC AAC AAT AGT AAC AA- AAT AGT AAC AAG AAC AAC AAC ATC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* ** * * ** * * *
304613 AAC AAC AAT AGT AGC AAC AAT AGT AAC AAG AAC AAC AAC ATC AAT AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * *
304661 AAT AGC ATC AAC AAT AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC
304685 CATACTAACT
Statistics
Matches: 155, Mismatches: 56, Indels: 2
0.73 0.26 0.01
Matches are distributed among these distances:
2 2 0.01
3 153 0.99
ACGTcount: A:0.59, C:0.22, G:0.09, T:0.10
Consensus pattern (3 bp):
AAC
Found at i:304491 original size:39 final size:39
Alignment explanation
Indices: 304433--304652 Score: 280
Period size: 39 Copynumber: 5.3 Consensus size: 39
304423 ATTATAATTT
304433 AAGAGACAACAACAACAACAATAGTAGCAGCAATAGTAACAAGAACAAC
1 AAGA-ACAACAACAACAACAATAGTAGCAGCAATAGT---------AAC
304482 AAGAACAACAACAACAACAATAGTAGCAGCAATAGTAAC
1 AAGAACAACAACAACAACAATAGTAGCAGCAATAGTAAC
*
304521 AAGAACAACAACAACAACAACAGTAGCAGCAATAGTAAC
1 AAGAACAACAACAACAACAATAGTAGCAGCAATAGTAAC
* *
304560 AAGAACAACAACAACAACAATAGTAACA-AAATAGTAAC
1 AAGAACAACAACAACAACAATAGTAGCAGCAATAGTAAC
*
304598 AAGAACAACAACATCAACAACAATAGTAGCAACAATAGTAAC
1 AAGAACAAC-A-A-CAACAACAATAGTAGCAGCAATAGTAAC
304640 AAGAACAACAACA
1 AAGAACAACAACA
304653 TCAATAACAA
Statistics
Matches: 161, Mismatches: 6, Indels: 18
0.87 0.03 0.10
Matches are distributed among these distances:
38 18 0.11
39 70 0.43
40 2 0.01
41 17 0.11
42 18 0.11
48 32 0.20
49 4 0.02
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.09
Consensus pattern (39 bp):
AAGAACAACAACAACAACAATAGTAGCAGCAATAGTAAC
Found at i:304508 original size:48 final size:48
Alignment explanation
Indices: 304433--304579 Score: 213
Period size: 48 Copynumber: 3.2 Consensus size: 48
304423 ATTATAATTT
304433 AAGAGACAACAACAACAACAATAGTAGCAGCAATAGTAACAAGAACAAC
1 AAGA-ACAACAACAACAACAATAGTAGCAGCAATAGTAACAAGAACAAC
304482 AAGAACAACAACAACAACAATAGTAGCAGCAATAGTAACAAG---AAC
1 AAGAACAACAACAACAACAATAGTAGCAGCAATAGTAACAAGAACAAC
304527 ---AACAACAACAACAAC---AGTAGCAGCAATAGTAACAAGAACAAC
1 AAGAACAACAACAACAACAATAGTAGCAGCAATAGTAACAAGAACAAC
*
304569 AACAACAACAA
1 AAGAACAACAA
304580 TAGTAACAAA
Statistics
Matches: 92, Mismatches: 0, Indels: 16
0.85 0.00 0.15
Matches are distributed among these distances:
39 21 0.23
42 18 0.20
45 11 0.12
48 38 0.41
49 4 0.04
ACGTcount: A:0.59, C:0.22, G:0.12, T:0.07
Consensus pattern (48 bp):
AAGAACAACAACAACAACAATAGTAGCAGCAATAGTAACAAGAACAAC
Found at i:304594 original size:11 final size:12
Alignment explanation
Indices: 304446--304641 Score: 66
Period size: 12 Copynumber: 16.4 Consensus size: 12
304436 AGACAACAAC
304446 AACAACAATAGT
1 AACAACAATAGT
* *
304458 AGCAGCAATAGT
1 AACAACAATAGT
* * **
304470 AACAAGAACAAC
1 AACAACAATAGT
* * **
304482 AAGAACAACAAC
1 AACAACAATAGT
304494 AACAACAATAGT
1 AACAACAATAGT
* *
304506 AGCAGCAATAGT
1 AACAACAATAGT
* **
304518 AACAAGAACAACAAC
1 AAC---AACAATAGT
*
304533 AACAACAACAGT
1 AACAACAATAGT
* *
304545 AGCAGCAATAGT
1 AACAACAATAGT
* **
304557 AACAAGAACAACAAC
1 AAC---AACAATAGT
304572 AACAACAATAGT
1 AACAACAATAGT
304584 AACAA-AATAGT
1 AACAACAATAGT
304595 ---AAC-A-AG-
1 AACAACAATAGT
*
304601 AACAACAACA-T
1 AACAACAATAGT
304612 CAACAACAATAGT
1 -AACAACAATAGT
*
304625 AGCAACAATAGT
1 AACAACAATAGT
304637 AACAA
1 AACAA
304642 GAACAACAAC
Statistics
Matches: 132, Mismatches: 37, Indels: 30
0.66 0.19 0.15
Matches are distributed among these distances:
7 2 0.02
8 3 0.02
9 3 0.02
10 1 0.01
11 7 0.05
12 99 0.75
13 1 0.01
15 16 0.12
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.10
Consensus pattern (12 bp):
AACAACAATAGT
Found at i:304672 original size:21 final size:21
Alignment explanation
Indices: 304563--304673 Score: 73
Period size: 21 Copynumber: 5.3 Consensus size: 21
304553 TAGTAACAAG
* * *
304563 AACAACAACAACAACAATAGT
1 AACAACATCAATAACAATAGC
* * * *
304584 AACAAAAT-AGTAACAAGAAC
1 AACAACATCAATAACAATAGC
* *
304604 AACAACATCAACAACAATAGT
1 AACAACATCAATAACAATAGC
* * * *
304625 AGCAACAAT-AGTAACAAGAAC
1 AACAAC-ATCAATAACAATAGC
304646 AACAACATCAATAACAATAGC
1 AACAACATCAATAACAATAGC
*
304667 ATCAACA
1 AACAACA
304674 ATAACAACAA
Statistics
Matches: 63, Mismatches: 24, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
20 16 0.25
21 45 0.71
22 2 0.03
ACGTcount: A:0.59, C:0.22, G:0.07, T:0.12
Consensus pattern (21 bp):
AACAACATCAATAACAATAGC
Found at i:304679 original size:39 final size:39
Alignment explanation
Indices: 304479--304680 Score: 208
Period size: 39 Copynumber: 5.1 Consensus size: 39
304469 TAACAAGAAC
* * * *
304479 AACAAGAACAACAACAACAACAATAGTAGCAGCAATAGT
1 AACAAGAACAACAACAACAACAACAATAGCAGCAACAAT
* * *
304518 AACAAGAACAACAACAACAACAACAGTAGCAGCAATAGT
1 AACAAGAACAACAACAACAACAACAATAGCAGCAACAAT
* * * * * *
304557 AACAAGAACAACAACAACAACAATAGTAACA-AAATAGT
1 AACAAGAACAACAACAACAACAACAATAGCAGCAACAAT
* *
304595 AACAAGAACAACAACATCAACAACAATAGTAGCAACAATAGT
1 AACAAGAACAACAACAACAACAACAATAGCAGCAAC-A-A-T
* * *
304637 AACAAGAACAACAACATCAATAACAATAGCATCAACAAT
1 AACAAGAACAACAACAACAACAACAATAGCAGCAACAAT
304676 AACAA
1 AACAA
304681 CAACCATACT
Statistics
Matches: 144, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
38 32 0.22
39 75 0.52
40 2 0.01
41 1 0.01
42 34 0.24
ACGTcount: A:0.59, C:0.21, G:0.09, T:0.10
Consensus pattern (39 bp):
AACAAGAACAACAACAACAACAACAATAGCAGCAACAAT
Found at i:304973 original size:18 final size:18
Alignment explanation
Indices: 304933--304970 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
304923 AAATATGCCA
*
304933 AATTTAAAATTAATTATT
1 AATTTAAAATTAATTAAT
304951 AATTTAAAATTAAATTAAT
1 AATTTAAAATT-AATTAAT
304970 A
1 A
304971 TTTCTCACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTTAAAATTAATTAAT
Found at i:305032 original size:30 final size:30
Alignment explanation
Indices: 304998--305054 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
304988 AATAAAAAGT
304998 TTAATTAAAAAATAAATATTCAAATTAGAC
1 TTAATTAAAAAATAAATATTCAAATTAGAC
* * *
305028 TTAATTGAAAGATAAATGTTCAAATTA
1 TTAATTAAAAAATAAATATTCAAATTA
305055 TAATTTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (30 bp):
TTAATTAAAAAATAAATATTCAAATTAGAC
Found at i:306310 original size:43 final size:43
Alignment explanation
Indices: 306249--306336 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
306239 TTCAGCTGCA
306249 ATGGGGGCTCACCACTTGGCCCACGGTTCTCATGGTGGCGGCC
1 ATGGGGGCTCACCACTTGGCCCACGGTTCTCATGGTGGCGGCC
306292 ATGGGGGCTCACCACTTGGCCCACGGTTCTCATGGTGGCGGCC
1 ATGGGGGCTCACCACTTGGCCCACGGTTCTCATGGTGGCGGCC
306335 AT
1 AT
306337 TTTGCACATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.12, C:0.32, G:0.34, T:0.22
Consensus pattern (43 bp):
ATGGGGGCTCACCACTTGGCCCACGGTTCTCATGGTGGCGGCC
Found at i:310176 original size:20 final size:19
Alignment explanation
Indices: 310151--310213 Score: 81
Period size: 20 Copynumber: 3.2 Consensus size: 19
310141 AAGGTGCTCA
310151 CTTAGGTTAGCTCCTACGCC
1 CTTAGGTT-GCTCCTACGCC
*
310171 CTTAGGTTGGCTCCTACTCC
1 CTTAGGTT-GCTCCTACGCC
*
310191 CTTAAGTTGACTCCTACGCC
1 CTTAGGTTG-CTCCTACGCC
310211 CTT
1 CTT
310214 TAGGCCTAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.03
20 37 0.97
ACGTcount: A:0.14, C:0.35, G:0.17, T:0.33
Consensus pattern (19 bp):
CTTAGGTTGCTCCTACGCC
Found at i:313007 original size:85 final size:85
Alignment explanation
Indices: 312864--313038 Score: 341
Period size: 85 Copynumber: 2.1 Consensus size: 85
312854 GTGCTGCCAT
312864 GTAAGCCCATAACTAGAAACATGGATACGAAAGGTAACTCTCAGTGTTAAAAGGAGTAATCCCTT
1 GTAAGCCCATAACTAGAAACATGGATACGAAAGGTAACTCTCAGTGTTAAAAGGAGTAATCCCTT
312929 AAAACTTAGGTTAGGATGAG
66 AAAACTTAGGTTAGGATGAG
*
312949 GTAAGCCCATAACTAGAAACATGGATATGAAAGGTAACTCTCAGTGTTAAAAGGAGTAATCCCTT
1 GTAAGCCCATAACTAGAAACATGGATACGAAAGGTAACTCTCAGTGTTAAAAGGAGTAATCCCTT
313014 AAAACTTAGGTTAGGATGAG
66 AAAACTTAGGTTAGGATGAG
313034 GTAAG
1 GTAAG
313039 AACAGTAACC
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 89 1.00
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (85 bp):
GTAAGCCCATAACTAGAAACATGGATACGAAAGGTAACTCTCAGTGTTAAAAGGAGTAATCCCTT
AAAACTTAGGTTAGGATGAG
Found at i:317208 original size:14 final size:15
Alignment explanation
Indices: 317191--317221 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
317181 AATGTCAAAT
317191 AAAATTTAAAA-TAA
1 AAAATTTAAAATTAA
317205 AAAATTTAAAATTAA
1 AAAATTTAAAATTAA
317220 AA
1 AA
317222 TTATTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTTAAAATTAA
Found at i:325623 original size:37 final size:37
Alignment explanation
Indices: 325533--325629 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
325523 CATTTTCGTC
325533 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
* ** *
325570 TTGTTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
** *
325607 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
325630 GATAGGATCC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.34
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
Found at i:326104 original size:2 final size:2
Alignment explanation
Indices: 326091--326121 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
326081 CATTATTATT
*
326091 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
326122 TTTATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:326350 original size:57 final size:58
Alignment explanation
Indices: 326288--326414 Score: 138
Period size: 57 Copynumber: 2.2 Consensus size: 58
326278 TATTACTATG
* * *
326288 ATTATTATTATTTTAGT-TAATATTATATGTAT-ATTTATTTTTCATTTATTTATTTTTT
1 ATTATTATTATTTTAGTATAATATTATAT-TATAATATATTTTT-ATATATATATTTTTT
* **
326346 -TTATTACTA-TTTAGTATTTTATTATATTATACATATATTTTTATATATATATTTTTT
1 ATTATTATTATTTTAGTATAATATTATATTATA-ATATATTTTTATATATATATTTTTT
326403 ATTATT-TTATTT
1 ATTATTATTATTT
326415 ATACTATTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
56 9 0.16
57 32 0.56
58 16 0.28
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (58 bp):
ATTATTATTATTTTAGTATAATATTATATTATAATATATTTTTATATATATATTTTTT
Found at i:326373 original size:23 final size:21
Alignment explanation
Indices: 326334--326425 Score: 59
Period size: 23 Copynumber: 4.3 Consensus size: 21
326324 ATTTTTCATT
326334 TATTTAT-TTTTTT-TATTAC
1 TATTTATATTTTTTATATTAC
326353 TATTTAGTATTTTATTATATTA-
1 TATTTA-TATTTT-TTATATTAC
**
326375 TACATATA-TTTTTATATATA-
1 TATTTATATTTTTTATAT-TAC
* *
326395 TATTTTTTATTATTTTATTTATAC
1 TA-TTTATATT-TTTTATAT-TAC
326419 TATTTAT
1 TATTTAT
326426 TTATTAACAT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
19 12 0.21
20 8 0.14
21 9 0.16
22 7 0.12
23 19 0.33
24 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (21 bp):
TATTTATATTTTTTATATTAC
Found at i:326384 original size:21 final size:21
Alignment explanation
Indices: 326360--326443 Score: 58
Period size: 20 Copynumber: 4.3 Consensus size: 21
326350 TACTATTTAG
326360 TATTTTATTATATTATACATA
1 TATTTTATTATATTATACATA
326381 TA-TTT-TTATA-TAT--ATA
1 TATTTTATTATATTATACATA
* * **
326397 TTTTTTATTATTTTATTTATA
1 TATTTTATTATATTATACATA
326418 CTA-TTTATT-TATTA-ACATTA
1 -TATTTTATTATATTATACA-TA
326438 TATTTT
1 TATTTT
326444 TAGTTTCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
16 4 0.08
17 3 0.06
18 7 0.14
19 11 0.22
20 12 0.24
21 11 0.22
22 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTATTATATTATACATA
Found at i:326395 original size:14 final size:14
Alignment explanation
Indices: 326372--326445 Score: 55
Period size: 14 Copynumber: 5.2 Consensus size: 14
326362 TTTTATTATA
*
326372 TTATACATATATTT
1 TTATATATATATTT
326386 TTATATATATATTT
1 TTATATATATATTT
*
326400 TT-TAT-TATTTTAT
1 TTATATATATATT-T
*
326413 TTATACTATTTATTT
1 TTATA-TATATATTT
*
326428 ATTA-ACATTATATTT
1 -TTATATA-TATATTT
326443 TTA
1 TTA
326446 GTTTCTTTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
12 5 0.10
13 6 0.12
14 21 0.44
15 9 0.19
16 7 0.15
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATATATATATTT
Found at i:326415 original size:57 final size:57
Alignment explanation
Indices: 326323--326445 Score: 146
Period size: 57 Copynumber: 2.1 Consensus size: 57
326313 TATGTATATT
* *
326323 TATTTTTCATTTATTTATTTTTTTTATTACTATTTAGTA-T-TTTATTATATTATACA-TA
1 TATTTTT-ATATATATATTTTTTTTATTACTATTTA-TACTATTTATT-TATTA-ACATTA
*
326381 TATTTTTATATATATATTTTTTATTATT-TTATTTATACTATTTATTTATTAACATTA
1 TATTTTTATATATATATTTTTT-TTATTACTATTTATACTATTTATTTATTAACATTA
326438 TATTTTTA
1 TATTTTTA
326446 GTTTCTTTGC
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
56 5 0.09
57 35 0.60
58 18 0.31
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (57 bp):
TATTTTTATATATATATTTTTTTTATTACTATTTATACTATTTATTTATTAACATTA
Found at i:326441 original size:28 final size:27
Alignment explanation
Indices: 326348--326442 Score: 75
Period size: 28 Copynumber: 3.3 Consensus size: 27
326338 TATTTTTTTT
326348 ATTACTATTTAGTAT-TTTATTATATTATAC
1 ATTA-TATTTA-TATATTTATT-TATTA-AC
* * * **
326378 ATATATTTTTATATATATATTTTTTATT
1 AT-TATATTTATATATTTATTTATTAAC
*
326406 ATTTTATTTATACTATTTATTTATTAAC
1 ATTATATTTATA-TATTTATTTATTAAC
326434 ATTATATTT
1 ATTATATTT
326443 TTAGTTTCTT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
27 8 0.16
28 21 0.42
29 7 0.14
30 12 0.24
31 2 0.04
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (27 bp):
ATTATATTTATATATTTATTTATTAAC
Found at i:326556 original size:20 final size:19
Alignment explanation
Indices: 326529--326584 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
326519 TTTTATCATC
326529 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
326548 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
326568 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
326585 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:327365 original size:106 final size:106
Alignment explanation
Indices: 327220--328228 Score: 1495
Period size: 106 Copynumber: 9.5 Consensus size: 106
327210 TGGTATATGC
* * *
327220 CAACTTCCCAAATTCAGAGCCAATTTCAACTTCAGAGCGAAGGATATTGGACTCAAGACAACGCA
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* * * *
327285 AGTTCAACTTCATGACGAATGGACCACTGGTTGTCAATAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
*
327326 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCCAGACAACGCA
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
327391 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * * *
327432 TAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATAT-GACTCCAGACAACAC
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT-TGGACTCCAGACAACGC
*
327496 AAGCTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
65 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * *
327538 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGATAACGCA
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
327603 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * *
327644 CAATTTCCCAATTTCGGAGCCAATTTCAACTTCAC-GTCGAAAGATATTGGACTCCAGACAACGC
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTCCAGACAACGC
*
327708 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTAAACAAA
65 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * * *
327750 CAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCATACAACGCA
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* *
327815 AGTTCAACTTCACGACGAAGGGACCGTTGGTTATCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * * * *
327856 CAACTTCTCAATTTCACAGCCAATTTCAACTTCACAACGAATGATACTGGACTCCAGACAACGCA
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
327921 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * *
327962 CAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACGCA
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
328027 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * ** * * * *
328068 CAATTTCTCAATTTTGGAGCCAATTTCAACTTCACAAACAAAGGATATTGGACTCGAGACAACAC
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCAC-AGCGAAGGATATTGGACTCCAGACAACGC
*
328133 AAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAA
65 AAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAA
* ** * * * *
328175 CAATTTCCTGATTCCAGAGCTAATTTCAACTTCA-TGACGGAGGATATTGGACTC
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
328229 GGAACACTGC
Statistics
Matches: 825, Mismatches: 71, Indels: 14
0.91 0.08 0.02
Matches are distributed among these distances:
105 2 0.00
106 732 0.89
107 91 0.11
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
Found at i:329031 original size:37 final size:37
Alignment explanation
Indices: 328979--329082 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
328969 ATTTTCGTCA
*
328979 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
* * *
329016 TGCTAGGATTCAAACTCCTAAAAATATGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
** * *
329053 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
329083 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
Found at i:329765 original size:29 final size:27
Alignment explanation
Indices: 329733--329801 Score: 68
Period size: 30 Copynumber: 2.4 Consensus size: 27
329723 ATATATATTC
* *
329733 TTACTTTATTTTATTTTATATTACTATG
1 TTACTTTATTTTAGTTAATATTA-TATG
*
329761 ATTACTATTTTTTTAGTTAATATTATATG
1 -TTACT-TTATTTTAGTTAATATTATATG
329790 TATA-TTTATTTT
1 T-TACTTTATTTT
329802 TCATTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 6 0.18
28 2 0.06
29 11 0.32
30 15 0.44
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (27 bp):
TTACTTTATTTTAGTTAATATTATATG
Found at i:329841 original size:12 final size:11
Alignment explanation
Indices: 329792--329925 Score: 68
Period size: 11 Copynumber: 12.1 Consensus size: 11
329782 ATTATATGTA
329792 TATTTAT-TTT
1 TATTTATATTT
329802 TCATTTAT-TTAT
1 T-ATTTATATT-T
*
329814 TA-TTACTATTAC
1 TATTTA-TATT-T
329826 TATTTAGTATTT
1 TATTTA-TATTT
*
329838 TA-TTATATTA
1 TATTTATATTT
**
329848 TACATATATTT
1 TATTTATATTT
*
329859 T-TATATATTTT
1 TATTTATA-TTT
*
329870 TATATATATTT
1 TATTTATATTT
329881 T-TTTATTATTT
1 TATTTA-TATTT
329892 TATTTATACTATT
1 TATTTATA-T-TT
329905 TATTTAT-TTT
1 TATTTATATTT
*
329915 CA-TTATATTT
1 TATTTATATTT
329925 T
1 T
329926 TAGTTTCTTT
Statistics
Matches: 101, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
9 4 0.04
10 24 0.24
11 37 0.37
12 20 0.20
13 16 0.16
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.66
Consensus pattern (11 bp):
TATTTATATTT
Found at i:329862 original size:22 final size:22
Alignment explanation
Indices: 329835--329894 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
329825 CTATTTAGTA
*
329835 TTTTATTATATTATACATATAT
1 TTTTATTATTTTATACATATAT
* *
329857 TTTTATATATTTTTATATATATTT
1 TTTTAT-TA-TTTTATACATATAT
329881 TTTTATTATTTTAT
1 TTTTATTATTTTAT
329895 TTATACTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.36
23 4 0.12
24 17 0.52
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTATTATTTTATACATATAT
Found at i:329878 original size:24 final size:22
Alignment explanation
Indices: 329835--329927 Score: 84
Period size: 22 Copynumber: 4.2 Consensus size: 22
329825 CTATTTAGTA
* *
329835 TTTTATTATATTATACATATAT
1 TTTTATTATTTTATATATATAT
*
329857 TTTTATATATTTTTATATATATTT
1 TTTTAT-TA-TTTTATATATATAT
*
329881 TTTTATTATTTTATTTATACTAT
1 TTTTATTATTTTATATATA-TAT
* *
329904 TTAT-TTATTTT-CAT-TATAT
1 TTTTATTATTTTATATATATAT
329923 TTTTA
1 TTTTA
329928 GTTTCTTTGC
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
19 6 0.10
20 2 0.03
21 1 0.02
22 23 0.40
23 9 0.16
24 17 0.29
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTATTATTTTATATATATAT
Found at i:333830 original size:29 final size:29
Alignment explanation
Indices: 333727--333814 Score: 167
Period size: 29 Copynumber: 3.0 Consensus size: 29
333717 CATATGAATA
*
333727 TGAAGAGTCAGGTGACTATTTAGTTACTT
1 TGAAGAGTTAGGTGACTATTTAGTTACTT
333756 TGAAGAGTTAGGTGACTATTTAGTTACTT
1 TGAAGAGTTAGGTGACTATTTAGTTACTT
333785 TGAAGAGTTAGGTGACTATTTAGTTACTT
1 TGAAGAGTTAGGTGACTATTTAGTTACTT
333814 T
1 T
333815 TAATAGCTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (29 bp):
TGAAGAGTTAGGTGACTATTTAGTTACTT
Found at i:335904 original size:29 final size:30
Alignment explanation
Indices: 335871--335931 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
335861 TAATTACATG
*
335871 AATTCTGAATTTGTGTCTAAAAA-AAATAA
1 AATTCTAAATTTGTGTCTAAAAATAAATAA
*
335900 AATTCTAAATTTGTGTCTAAAAATTAATAA
1 AATTCTAAATTTGTGTCTAAAAATAAATAA
335930 AA
1 AA
335932 GAGGTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (30 bp):
AATTCTAAATTTGTGTCTAAAAATAAATAA
Found at i:346141 original size:19 final size:19
Alignment explanation
Indices: 346117--346154 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
346107 GTAAAAGTGT
346117 TAATCATTTCCCATACTTA
1 TAATCATTTCCCATACTTA
346136 TAATCATTTCCCATACTTA
1 TAATCATTTCCCATACTTA
346155 ATCAACTCTT
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:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATCATTTCCCATACTTA
Found at i:346158 original size:17 final size:18
Alignment explanation
Indices: 346116--346158 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
346106 TGTAAAAGTG
346116 TTAATCATTTCCCATACT
1 TTAATCATTTCCCATACT
346134 TATAATCATTTCCCATAC-
1 T-TAATCATTTCCCATACT
346152 TTAATCA
1 TTAATCA
346159 ACTCTTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
18 2 0.08
19 16 0.67
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAATCATTTCCCATACT
Found at i:349632 original size:15 final size:15
Alignment explanation
Indices: 349612--349643 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
349602 ATGTAAAATC
*
349612 TAGTAAATTATTAAT
1 TAGTAAATTAATAAT
349627 TAGTAAATTAATAAT
1 TAGTAAATTAATAAT
349642 TA
1 TA
349644 CTCTCTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (15 bp):
TAGTAAATTAATAAT
Found at i:349853 original size:31 final size:31
Alignment explanation
Indices: 349816--349876 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
349806 AAGACTAAAA
349816 AAAAGAAATTTAAATGTTATTATTTGTTAAT
1 AAAAGAAATTTAAATGTTATTATTTGTTAAT
*
349847 AAAAGAAATTTAAATGTTGTTATTTGTTAA
1 AAAAGAAATTTAAATGTTATTATTTGTTAA
349877 CTTTTGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (31 bp):
AAAAGAAATTTAAATGTTATTATTTGTTAAT
Found at i:357278 original size:152 final size:147
Alignment explanation
Indices: 357004--357302 Score: 528
Period size: 152 Copynumber: 2.0 Consensus size: 147
356994 ATGAAATTTG
357004 ATCGAATTCCAAGAACAAGGTCTATTGAGGAGATCGATTACTAACGATCTAGCAGACATTTAAGG
1 ATCGAATTCCAAGAACAAGGTCTATTGAGGAGATCGATTACTAACGATCTAGCAGACATTTAAGG
357069 TTGATACATTAGAATCCCACTATATTTTCGTGTGCATTAGGAAAACGTTCAGGAACCTTTATACA
66 TTGATACATTAGAATCCCACTATATTTTCGTGTGCATTAGGAAAACGTTCAGGAACC-TTATAC-
357134 TAATAATTCTAAATTCAGAT
129 -AATAATTCTAAATTCAGAT
*
357154 ATCGAATTCCAAGAACAAGGTC-CTTGAGGAGAATCGATTACTAACCGATCTAGCCAGACATTTA
1 ATCGAATTCCAAGAACAAGGTCTATTGAGGAG-ATCGATTACTAA-CGATCTAG-CAGACATTTA
357218 AGGTTGATACATTAGAATCCCACTATATTTTCGTGTGCATTAGGAAAACGTTCAGGAACCTTATA
63 AGGTTGATACATTAGAATCCCACTATATTTTCGTGTGCATTAGGAAAACGTTCAGGAACCTTATA
357283 CAATAATTCTAAATTCAGAT
128 CAATAATTCTAAATTCAGAT
357303 TTACTGCAAG
Statistics
Matches: 145, Mismatches: 1, Indels: 7
0.95 0.01 0.05
Matches are distributed among these distances:
149 27 0.19
150 34 0.23
151 14 0.10
152 70 0.48
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (147 bp):
ATCGAATTCCAAGAACAAGGTCTATTGAGGAGATCGATTACTAACGATCTAGCAGACATTTAAGG
TTGATACATTAGAATCCCACTATATTTTCGTGTGCATTAGGAAAACGTTCAGGAACCTTATACAA
TAATTCTAAATTCAGAT
Found at i:361171 original size:2 final size:2
Alignment explanation
Indices: 361164--361203 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
361154 GGAATGGTTT
*
361164 TA TA TA TA TA TA TA TA GA 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
361204 ATTTATTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:362804 original size:111 final size:111
Alignment explanation
Indices: 362666--362887 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
362656 ATTACAAAAA
* * * *
362666 TTAATTCTTAATTTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
362731 AATTAAAACGTTAAAATGTTACCGTATCAGGAAAATGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
362777 TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
362842 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
362888 ATGATTTCCA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
Found at i:363085 original size:21 final size:21
Alignment explanation
Indices: 363059--363108 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
363049 AAAAGTGATT
*
363059 GAGGATGGGGGTATTTATAGG
1 GAGGATAGGGGTATTTATAGG
363080 GAGGATAGGGGTATTTATAGG
1 GAGGATAGGGGTATTTATAGG
363101 GAGGATAG
1 GAGGATAG
363109 AGACGTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.00, G:0.46, T:0.26
Consensus pattern (21 bp):
GAGGATAGGGGTATTTATAGG
Found at i:363246 original size:50 final size:50
Alignment explanation
Indices: 363155--363261 Score: 130
Period size: 50 Copynumber: 2.1 Consensus size: 50
363145 TCCCCTTCAC
* *
363155 CGCGCTATACCTCACGTGGCGTCAGATCATCGTATATCGCGG-GACAGGAGA
1 CGCGCTATACCTCACGTGGCGCCAAATCA-CGTATATCGCGGTG-CAGGAGA
*
363206 CGCGCTATACC-CACGTGGCGCCAAATCA-GTATATAACGCGGTGCAGGAGG
1 CGCGCTATACCTCACGTGGCGCCAAATCACGTATAT--CGCGGTGCAGGAGA
363256 CGCGCT
1 CGCGCT
363262 TTTCTGCTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
48 6 0.12
50 32 0.64
51 12 0.24
ACGTcount: A:0.23, C:0.29, G:0.30, T:0.18
Consensus pattern (50 bp):
CGCGCTATACCTCACGTGGCGCCAAATCACGTATATCGCGGTGCAGGAGA
Found at i:364533 original size:2 final size:2
Alignment explanation
Indices: 364526--364564 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
364516 AACCGAATCT
364526 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
364565 CAGTGAGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:364710 original size:13 final size:14
Alignment explanation
Indices: 364689--364726 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
364679 TTAATGAGTT
*
364689 TGTACTTAA-AATA
1 TGTATTTAATAATA
364702 TGTATTTAATAATA
1 TGTATTTAATAATA
*
364716 TATATTTAATA
1 TGTATTTAATA
364727 TTTTTGGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (14 bp):
TGTATTTAATAATA
Found at i:366767 original size:39 final size:38
Alignment explanation
Indices: 366688--366774 Score: 95
Period size: 39 Copynumber: 2.3 Consensus size: 38
366678 CTTAATTCAC
** * *
366688 AAATTATTTCACCCTAACATTATAAGTTCTTAATTTTT
1 AAATTATTTCACAATAACATTATAAGATATTAATTTTT
* *
366726 AAAATTATTTCACAATAACATTCTAA-ATATTATTTTCTT
1 -AAATTATTTCACAATAACATTATAAGATATTAATTT-TT
366765 AAATTATTTC
1 AAATTATTTC
366775 TTTTAACTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
38 17 0.41
39 24 0.59
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.47
Consensus pattern (38 bp):
AAATTATTTCACAATAACATTATAAGATATTAATTTTT
Found at i:370097 original size:30 final size:31
Alignment explanation
Indices: 370024--370101 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
370014 TGATCATTTT
* * *
370024 GTAATATTCAATAGTCGAAGGACTCAATAAA
1 GTAATATCCTATAGTCGAAGGACTCAACAAA
* *
370055 GTAA-CTCTCTATAGTTG-AGGACTCAACAAA
1 GTAATATC-CTATAGTCGAAGGACTCAACAAA
370085 GTAATATCCTATAGTCG
1 GTAATATCCTATAGTCG
370102 GGGACCATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
30 25 0.66
31 13 0.34
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (31 bp):
GTAATATCCTATAGTCGAAGGACTCAACAAA
Found at i:375843 original size:23 final size:23
Alignment explanation
Indices: 375813--375873 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
375803 TATACATAAT
375813 TGAGCATTGGCAACAGACTTTGG
1 TGAGCATTGGCAACAGACTTTGG
*
375836 TGAGCATTGGGAACAGACTTTGG
1 TGAGCATTGGCAACAGACTTTGG
375859 TGAGCATTGGCAACA
1 TGAGCATTGGCAACA
375874 TAATCGAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (23 bp):
TGAGCATTGGCAACAGACTTTGG
Found at i:377980 original size:23 final size:23
Alignment explanation
Indices: 377954--378029 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
377944 AAATAAAATT
377954 AAAAATTCAATTTTCTCATTTAA
1 AAAAATTCAATTTTCTCATTTAA
* * * *
377977 AAAAA--AAAATCT-TCATATAA
1 AAAAATTCAATTTTCTCATTTAA
377997 TTAAAAATTCAATTTTCTCATTTAA
1 --AAAAATTCAATTTTCTCATTTAA
378022 AAAAATTC
1 AAAAATTC
378030 TTCATATAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
20 7 0.17
21 4 0.10
22 5 0.12
23 13 0.32
24 4 0.10
25 7 0.17
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAAATTCAATTTTCTCATTTAA
Found at i:378024 original size:22 final size:22
Alignment explanation
Indices: 377954--378025 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
377944 AAATAAAATT
377954 AAAAATTCAATTTTCTCATTTA
1 AAAAATTCAATTTTCTCATTTA
*** *
377976 AAAAAAAAAATCTTCAT-ATAATT-
1 AAAAATTCAATTTTC-TCAT--TTA
377999 AAAAATTCAATTTTCTCATTTA
1 AAAAATTCAATTTTCTCATTTA
378021 AAAAA
1 AAAAA
378026 ATTCTTCATA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
21 2 0.05
22 19 0.51
23 14 0.38
24 2 0.05
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAATTCAATTTTCTCATTTA
Found at i:378037 original size:42 final size:43
Alignment explanation
Indices: 377950--378044 Score: 156
Period size: 45 Copynumber: 2.2 Consensus size: 43
377940 TTTAAAATAA
377950 AATTAAAAATTCAATTTTCTCATTTAAAAAAAAAAATCTTCATAT
1 AATTAAAAATTCAATTTTCTCATTT--AAAAAAAAATCTTCATAT
*
377995 AATTAAAAATTCAATTTTCTCATTT-AAAAAAATTCTTCATAT
1 AATTAAAAATTCAATTTTCTCATTTAAAAAAAAATCTTCATAT
378037 AATTAAAA
1 AATTAAAA
378045 TTTAACCCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
42 24 0.49
45 25 0.51
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (43 bp):
AATTAAAAATTCAATTTTCTCATTTAAAAAAAAATCTTCATAT
Found at i:378042 original size:21 final size:21
Alignment explanation
Indices: 377978--378044 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
377968 CTCATTTAAA
*
377978 AAAAAAAATCTTCATATAATT
1 AAAAAAATTCTTCATATAATT
377999 AAAAATTCAATT-TTC-TCAT--TT
1 AAAAA---AATTCTTCAT-ATAATT
378020 AAAAAAATTCTTCATATAATT
1 AAAAAAATTCTTCATATAATT
378041 AAAA
1 AAAA
378045 TTTAACCCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 16
0.69 0.02 0.30
Matches are distributed among these distances:
18 4 0.11
19 5 0.14
20 1 0.03
21 18 0.49
22 1 0.03
23 5 0.14
24 3 0.08
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAAAATTCTTCATATAATT
Found at i:382427 original size:22 final size:22
Alignment explanation
Indices: 382402--382448 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
382392 GTGTGATTCT
*
382402 AAGATAAAACTGT-AAAATGAGA
1 AAGATAAAACAGTAAAAATGA-A
*
382424 AAGATATAACAGTAAAAATGAA
1 AAGATAAAACAGTAAAAATGAA
382446 AAG
1 AAG
382449 CGAAAACGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.62, C:0.04, G:0.17, T:0.17
Consensus pattern (22 bp):
AAGATAAAACAGTAAAAATGAA
Found at i:385165 original size:22 final size:22
Alignment explanation
Indices: 385139--385183 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
385129 TTGAGTAAAC
*
385139 TTATATAAA-ATTTATAAAATTT
1 TTATAGAAAGATTTA-AAAATTT
385161 TTATAGAAAGTATTTAAAAATTT
1 TTATAGAAAG-ATTTAAAAATTT
385184 GCTAGATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTATAGAAAGATTTAAAAATTT
Found at i:385656 original size:60 final size:60
Alignment explanation
Indices: 385560--385734 Score: 196
Period size: 60 Copynumber: 2.9 Consensus size: 60
385550 TCATATGTCC
385560 TCAAACTATGGT-CCCTATT-TAAAATTAGTCCCTAAACTTTTGAATATTCCAATTTCATCA
1 TCAAACTAT-GTACCCTATTCT-AAATTAGTCCCTAAACTTTTGAATATTCCAATTTCATCA
* * * *
385620 TCAAACTATGATACCC-ATTCTAAATTAGTCCTTAAACTTTTGAATTTTCTAATTTCATGA
1 TCAAACTATG-TACCCTATTCTAAATTAGTCCCTAAACTTTTGAATATTCCAATTTCATCA
* * * * * *
385680 TTAAACTATG-ACCCTAATTCTAAATTATTCCCCAAACTTTTAAATCTTTCAATTT
1 TCAAACTATGTACCCT-ATTCTAAATTAGTCCCTAAACTTTTGAATATTCCAATTT
385735 TATCCCTAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
58 4 0.04
59 1 0.01
60 89 0.91
61 4 0.04
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.41
Consensus pattern (60 bp):
TCAAACTATGTACCCTATTCTAAATTAGTCCCTAAACTTTTGAATATTCCAATTTCATCA
Found at i:385990 original size:60 final size:59
Alignment explanation
Indices: 385871--386059 Score: 149
Period size: 60 Copynumber: 3.2 Consensus size: 59
385861 ATACATATAA
* * * **
385871 TTTG-GGAT-AAAATTGAAATGTTTAAAAGTTTGAGGACTAATTTATAATAAAAGAT-ATAG
1 TTTGAGGATGAAAATAGAAATG-TTAAAAGTTTGAGGACAAATTTAGAAT-GGA-ATCATAG
*
385930 TTTGAGGATGAAAATA-AAATGTTCACAAGTTTGAGGACAAATTTAGAATGGTAATCATAG
1 TTTGAGGATGAAAATAGAAATGTT-AAAAGTTTGAGGACAAATTTAGAATGG-AATCATAG
* * * * *
385990 TTT-AGAAATGAAATTAGAACAT-TTAAAAGTTTAAGGACCAATTTAGAAAATGG-ATCATGG
1 TTTGAG-GATGAAAATAGAA-ATGTTAAAAGTTTGAGGACAAATTTAG--AATGGAATCATAG
386050 TTTGAGGATG
1 TTTGAGGATG
386060 CATTATGTAA
Statistics
Matches: 106, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
59 10 0.09
60 78 0.74
61 11 0.10
62 7 0.07
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (59 bp):
TTTGAGGATGAAAATAGAAATGTTAAAAGTTTGAGGACAAATTTAGAATGGAATCATAG
Found at i:388224 original size:19 final size:19
Alignment explanation
Indices: 388202--388243 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
388192 AAACACGATT
*
388202 AAAAATAAAAAATAATATA
1 AAAAATAAAAAATAAAATA
388221 AAAAATAAAAAATAAAATA
1 AAAAATAAAAAATAAAATA
388240 AAAA
1 AAAA
388244 TATTGAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAATAAAAAATAAAATA
Found at i:388243 original size:12 final size:12
Alignment explanation
Indices: 388203--388242 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
388193 AACACGATTA
388203 AAAATAAAAAAT
1 AAAATAAAAAAT
*
388215 AATATAAAAAAT
1 AAAATAAAAAAT
388227 AAAA-AATAAAAT
1 AAAATAA-AAAAT
388239 AAAA
1 AAAA
388243 ATATTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 2 0.08
12 23 0.92
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:389259 original size:28 final size:27
Alignment explanation
Indices: 389176--389262 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 27
389166 AGGCCCCAAC
** *
389176 TTTTATATTTATAATTGGGGTCTCTAA
1 TTTTATATTTATAATTTAGATCTCTAA
* *
389203 CCTTTATATTTATAA-TTAGAATCTTTAA
1 -TTTTATATTTATAATTTAG-ATCTCTAA
*
389231 TTTGTATATTTATAATTTAGCTCTCTAA
1 TTT-TATATTTATAATTTAGATCTCTAA
389259 TTTT
1 TTTT
389263 GTTTTTAGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
27 5 0.10
28 39 0.81
29 4 0.08
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.54
Consensus pattern (27 bp):
TTTTATATTTATAATTTAGATCTCTAA
Found at i:391348 original size:60 final size:60
Alignment explanation
Indices: 391273--391444 Score: 211
Period size: 60 Copynumber: 2.9 Consensus size: 60
391263 AATTATGATT
* * * * * ** *
391273 TTTATTTTAAATTAGTCCTTAAACTTTTAAAAATTCCAATTTCATCCTTAAACTTTGA-C
1 TTTATTCTAAATTAGTCCTCAAACTTTTGAACATTCCAGTTTCATCCCAAAACTATGACC
*
391332 TATTATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAGTTTCATCCCAAAACTATGACC
1 T-TTATTCTAAATTAGTCCTCAAACTTTTGAACATTCCAGTTTCATCCCAAAACTATGACC
* * *
391393 TTCATTCTAAATTGGTCCCCAAACATTTTGAACATTCCAGTTTCATCCCAAA
1 TTTATTCTAAATTAGTCCTCAAAC-TTTTGAACATTCCAGTTTCATCCCAAA
391445 GTATGCGTAT
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
59 1 0.01
60 68 0.70
61 28 0.29
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
TTTATTCTAAATTAGTCCTCAAACTTTTGAACATTCCAGTTTCATCCCAAAACTATGACC
Found at i:393964 original size:9 final size:9
Alignment explanation
Indices: 393921--393968 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
393911 TTCTTCGTAT
393921 TTTTATATA
1 TTTTATATA
*
393930 TTTTA-ATT
1 TTTTATATA
*
393938 TTTTACA-A
1 TTTTATATA
393946 TTTATATATA
1 TTT-TATATA
393956 TTTTATATA
1 TTTTATATA
393965 TTTT
1 TTTT
393969 GAAATTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 10 0.30
9 19 0.58
10 4 0.12
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTATATA
Found at i:396891 original size:2 final size:2
Alignment explanation
Indices: 396886--396926 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
396876 TGATTGTTTA
396886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
396927 TGATAATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:402553 original size:2 final size:2
Alignment explanation
Indices: 402548--402598 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
402538 TGAAAAAAGA
402548 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
402590 AT AT AT AT A
1 AT AT AT AT A
402599 GACCTAGCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:403284 original size:23 final size:23
Alignment explanation
Indices: 403258--403308 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
403248 ACCTACCCAA
403258 GAAACAAATGGTTGACTTGAACC
1 GAAACAAATGGTTGACTTGAACC
403281 GAAACAAATGGTTGACTTGAACC
1 GAAACAAATGGTTGACTTGAACC
*
403304 AAAAC
1 GAAAC
403309 CAATCAGTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.20
Consensus pattern (23 bp):
GAAACAAATGGTTGACTTGAACC
Found at i:426870 original size:15 final size:15
Alignment explanation
Indices: 426850--426879 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
426840 GTTTTGGGAA
*
426850 ATGAAATGTTTGTTT
1 ATGAAATATTTGTTT
426865 ATGAAATATTTGTTT
1 ATGAAATATTTGTTT
426880 GAAAATTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (15 bp):
ATGAAATATTTGTTT
Found at i:434816 original size:31 final size:32
Alignment explanation
Indices: 434771--434865 Score: 140
Period size: 31 Copynumber: 3.0 Consensus size: 32
434761 GACAATTCAG
*
434771 TTCGGGTCGGGTCAATGTCGGATCGGTTGGTT
1 TTCGGGTCGGGTCAATATCGGATCGGTTGGTT
*
434803 TTCGGGT-GGGTCAATATCGGATCGGTTGGCT
1 TTCGGGTCGGGTCAATATCGGATCGGTTGGTT
* *
434834 TT-GAGTCGGGTCAATATCGAATCGGTTGGTT
1 TTCGGGTCGGGTCAATATCGGATCGGTTGGTT
434865 T
1 T
434866 CAATTCGGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
30 3 0.05
31 47 0.82
32 7 0.12
ACGTcount: A:0.14, C:0.15, G:0.37, T:0.35
Consensus pattern (32 bp):
TTCGGGTCGGGTCAATATCGGATCGGTTGGTT
Found at i:434874 original size:31 final size:32
Alignment explanation
Indices: 434771--434878 Score: 132
Period size: 31 Copynumber: 3.5 Consensus size: 32
434761 GACAATTCAG
* * *
434771 TTCGGGTCGGGTCAATGTCGGATCGGTTGGTT
1 TTCGAGTCGGGTCAATATCGGATCGGTTGGCT
*
434803 TTCGGGT-GGGTCAATATCGGATCGGTTGGCT
1 TTCGAGTCGGGTCAATATCGGATCGGTTGGCT
*
434834 TT-GAGTCGGGTCAATATCGAATCGGTTGG-T
1 TTCGAGTCGGGTCAATATCGGATCGGTTGGCT
* *
434864 TTCAATTCGGGTCAA
1 TTCGAGTCGGGTCAA
434879 CCATTAGGTT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
30 6 0.09
31 55 0.81
32 7 0.10
ACGTcount: A:0.16, C:0.16, G:0.35, T:0.33
Consensus pattern (32 bp):
TTCGAGTCGGGTCAATATCGGATCGGTTGGCT
Found at i:436842 original size:41 final size:40
Alignment explanation
Indices: 436760--436842 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 40
436750 ACTATTAAAA
*
436760 AAACATTGCACTCTTTACTCTATTCATCTTATCCTTTCAC
1 AAACATTGCACTCTTTACTCTATTAATCTTATCCTTTCAC
436800 AAACATTGCACTCTTTACGCTCTA-TAATCTTATCCTTTCAC
1 AAACATTGCACTCTTTA--CTCTATTAATCTTATCCTTTCAC
436841 AA
1 AA
436843 TCCATTATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 17 0.43
41 18 0.45
42 5 0.12
ACGTcount: A:0.28, C:0.29, G:0.04, T:0.40
Consensus pattern (40 bp):
AAACATTGCACTCTTTACTCTATTAATCTTATCCTTTCAC
Found at i:437312 original size:181 final size:181
Alignment explanation
Indices: 437008--437370 Score: 726
Period size: 181 Copynumber: 2.0 Consensus size: 181
436998 TGTTAGTTTA
437008 TCTCACCTATTCTTGCAACCTAATCAACTGATTGCCGGTACGTCTACTGGTTTTGTCACAGTTAA
1 TCTCACCTATTCTTGCAACCTAATCAACTGATTGCCGGTACGTCTACTGGTTTTGTCACAGTTAA
437073 CGTTACTTTTCAGTTGTCACATGGGATTCGGTCCCCATACATCCTTTTTTATACAATTTCAGTTC
66 CGTTACTTTTCAGTTGTCACATGGGATTCGGTCCCCATACATCCTTTTTTATACAATTTCAGTTC
437138 ATGAAAATTTCCATAAAAAACAGGCACATTAAGTATTTTTTTTCTAATTAT
131 ATGAAAATTTCCATAAAAAACAGGCACATTAAGTATTTTTTTTCTAATTAT
437189 TCTCACCTATTCTTGCAACCTAATCAACTGATTGCCGGTACGTCTACTGGTTTTGTCACAGTTAA
1 TCTCACCTATTCTTGCAACCTAATCAACTGATTGCCGGTACGTCTACTGGTTTTGTCACAGTTAA
437254 CGTTACTTTTCAGTTGTCACATGGGATTCGGTCCCCATACATCCTTTTTTATACAATTTCAGTTC
66 CGTTACTTTTCAGTTGTCACATGGGATTCGGTCCCCATACATCCTTTTTTATACAATTTCAGTTC
437319 ATGAAAATTTCCATAAAAAACAGGCACATTAAGTATTTTTTTTCTAATTAT
131 ATGAAAATTTCCATAAAAAACAGGCACATTAAGTATTTTTTTTCTAATTAT
437370 T
1 T
437371 GGTATTCGAT
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
181 182 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (181 bp):
TCTCACCTATTCTTGCAACCTAATCAACTGATTGCCGGTACGTCTACTGGTTTTGTCACAGTTAA
CGTTACTTTTCAGTTGTCACATGGGATTCGGTCCCCATACATCCTTTTTTATACAATTTCAGTTC
ATGAAAATTTCCATAAAAAACAGGCACATTAAGTATTTTTTTTCTAATTAT
Found at i:439949 original size:3 final size:3
Alignment explanation
Indices: 439941--440024 Score: 152
Period size: 3 Copynumber: 28.3 Consensus size: 3
439931 ATATTGGTCC
439941 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
439988 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
440025 CATTTGTGGT
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:450944 original size:23 final size:23
Alignment explanation
Indices: 450911--450978 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
450901 ATTATTATAT
450911 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
450934 GGCACTCCGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
* *
450957 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
450979 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:452377 original size:59 final size:59
Alignment explanation
Indices: 452306--452436 Score: 158
Period size: 59 Copynumber: 2.2 Consensus size: 59
452296 ACAGGTGACT
* * * ** *
452306 ATTTTGTAACTTTTAATAGT-AGGGAACTCATCAAAGCAACACTTTATAGTCAGAGGATC
1 ATTTTGTAACTTTTAATAGTCAAGAAACTCAAC-AAGCAACACCCTACAGTCAGAGGATC
* *
452365 ATTTTGTAACTTTTAATAGTCAAGAAACTCAACACGCAACACCCTACAGTCGGAGGATC
1 ATTTTGTAACTTTTAATAGTCAAGAAACTCAACAAGCAACACCCTACAGTCAGAGGATC
452424 ATTTGTGT-ACTTT
1 ATTT-TGTAACTTT
452437 ACCCTAAATT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 50 0.81
60 12 0.19
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTCAAGAAACTCAACAAGCAACACCCTACAGTCAGAGGATC
Found at i:457888 original size:18 final size:17
Alignment explanation
Indices: 457862--457899 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
457852 TTGGACAATT
457862 AAAATATTA-AAGACAGA
1 AAAATATTAGAAGACA-A
457879 AAAATGATTAGAAGACAA
1 AAAAT-ATTAGAAGACAA
457897 AAA
1 AAA
457900 TTAGTAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 8 0.42
19 6 0.32
ACGTcount: A:0.66, C:0.05, G:0.13, T:0.16
Consensus pattern (17 bp):
AAAATATTAGAAGACAA
Found at i:460903 original size:39 final size:39
Alignment explanation
Indices: 460843--461001 Score: 255
Period size: 39 Copynumber: 4.1 Consensus size: 39
460833 CAACAGCAGC
** * *
460843 TTTTGAAGAATAAGTTGCAACATTAACCTCTTCCTCAAA
1 TTTTGAAGAATCGGTTGCAACATTAACCTCTCCCTCAGA
*
460882 TTTTGAAGAATCGGTTACAACATTAACCTCTCCCTCAGA
1 TTTTGAAGAATCGGTTGCAACATTAACCTCTCCCTCAGA
*
460921 TTTTGAAGAATCTGTTGCAACATTAACCTCTCCCTCAGA
1 TTTTGAAGAATCGGTTGCAACATTAACCTCTCCCTCAGA
*
460960 TTTTGAAGAATCGATTGCAACATTAACCTCTCCCTCAGA
1 TTTTGAAGAATCGGTTGCAACATTAACCTCTCCCTCAGA
460999 TTT
1 TTT
461002 AGACACAGAT
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 111 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (39 bp):
TTTTGAAGAATCGGTTGCAACATTAACCTCTCCCTCAGA
Found at i:464003 original size:21 final size:22
Alignment explanation
Indices: 463976--464029 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
463966 ATGAAGACTA
*
463976 TGCTGAATGAAACATC-AACAC
1 TGCTGAATGAAACAACAAACAC
*
463997 TGTTGAATGAAACAACAAAACAC
1 TGCTGAATGAAACAAC-AAACAC
464020 TGCTGAATGA
1 TGCTGAATGA
464030 TTCAGCATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 14 0.50
23 14 0.50
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (22 bp):
TGCTGAATGAAACAACAAACAC
Found at i:469525 original size:68 final size:67
Alignment explanation
Indices: 469448--469579 Score: 237
Period size: 68 Copynumber: 2.0 Consensus size: 67
469438 CTTCAAATAA
*
469448 TTACTATATATTAAAAATAATAAAAGTTTAGCATAATAAAATCAAATCATGATAATAATGAAGTC
1 TTACTATATATTAAAAATAATAAAAGTTTAGCATAAT-AAAGCAAATCATGATAATAATGAAGTC
469513 ATT
65 ATT
*
469516 TTACTATATATTAAAAATAATAAAAGTTTAGCATAATCAAGCAAATCATGATAATAATGAAGTC
1 TTACTATATATTAAAAATAATAAAAGTTTAGCATAATAAAGCAAATCATGATAATAATGAAGTC
469580 GTTTAGCATA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
67 25 0.40
68 37 0.60
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (67 bp):
TTACTATATATTAAAAATAATAAAAGTTTAGCATAATAAAGCAAATCATGATAATAATGAAGTCA
TT
Found at i:470404 original size:28 final size:28
Alignment explanation
Indices: 470359--470415 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
470349 CTCTGTTTAC
* *
470359 ATTATATTGTTGACCTAGTGCTTGAAAG
1 ATTATATCGTCGACCTAGTGCTTGAAAG
*
470387 ATTATATCGTCGAGCTAGTGCTTGAAAG
1 ATTATATCGTCGACCTAGTGCTTGAAAG
470415 A
1 A
470416 ACGACGATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (28 bp):
ATTATATCGTCGACCTAGTGCTTGAAAG
Found at i:472393 original size:18 final size:18
Alignment explanation
Indices: 472370--472407 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
472360 AGAAAGACTT
472370 ATCAAAAAA-TATCTTATA
1 ATCAAAAAATTAT-TTATA
472388 ATCAAAAAATTATTTATA
1 ATCAAAAAATTATTTATA
472406 AT
1 AT
472408 TTACAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (18 bp):
ATCAAAAAATTATTTATA
Found at i:481691 original size:53 final size:52
Alignment explanation
Indices: 481611--481714 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 52
481601 AATCAAACTT
* * *
481611 AAATAAATTGTTGTTTGTCTCATCTAATTTATATCCATAGCCATGATAAGGAC
1 AAATAAATTGTGGTTTGTCTCACCTAATTTACA-CCATAGCCATGATAAGGAC
*
481664 AAATAAATTGTGGTTTGTCTCACCTAATTTACAGCATAGCCATGATAAGGA
1 AAATAAATTGTGGTTTGTCTCACCTAATTTACACCATAGCCATGATAAGGA
481715 TTTTGATGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 17 0.36
53 30 0.64
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (52 bp):
AAATAAATTGTGGTTTGTCTCACCTAATTTACACCATAGCCATGATAAGGAC
Found at i:481853 original size:22 final size:20
Alignment explanation
Indices: 481828--481868 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
481818 GATGTAAAAA
481828 ATAATTTTTTCTTCTGAAAAGT
1 ATAATTTTTT-TT-TGAAAAGT
481850 ATAATTTTTTTTTGAAAAG
1 ATAATTTTTTTTTGAAAAG
481869 GTCCACTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 10 0.53
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (20 bp):
ATAATTTTTTTTTGAAAAGT
Found at i:485333 original size:19 final size:19
Alignment explanation
Indices: 485309--485365 Score: 105
Period size: 19 Copynumber: 3.0 Consensus size: 19
485299 GCGATTTTGA
485309 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
485328 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
485347 AAAATGTGTTGCGAGAGTT
1 AAAATGTGTTGCGATAGTT
485366 TGAAAAACGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:485827 original size:21 final size:21
Alignment explanation
Indices: 485801--485877 Score: 104
Period size: 21 Copynumber: 3.8 Consensus size: 21
485791 GATTTTGGAA
485801 AATTTCGACTATCGCAACGCG
1 AATTTCGACTATCGCAACGCG
485822 AATTTCGACTATCGCAA--CG
1 AATTTCGACTATCGCAACGCG
* **
485841 AATTTGGAAAATCGCAACGCG
1 AATTTCGACTATCGCAACGCG
*
485862 AACTTCGACTATCGCA
1 AATTTCGACTATCGCA
485878 TCGAATTTGG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 16 0.34
21 31 0.66
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (21 bp):
AATTTCGACTATCGCAACGCG
Found at i:485844 original size:19 final size:20
Alignment explanation
Indices: 485801--485891 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
485791 GATTTTGGAA
485801 AATTTCGACTATCGCAACGCG
1 AATTTCGACTATCGCAAC-CG
485822 AATTTCGACTATCGCAA-CG
1 AATTTCGACTATCGCAACCG
* **
485841 AATTTGGAAAATCGCAACGCG
1 AATTTCGACTATCGCAAC-CG
* *
485862 AACTTCGACTATCGC-ATCG
1 AATTTCGACTATCGCAACCG
*
485881 AATTTGGACTA
1 AATTTCGACTA
485892 ACGTAAATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 27 0.47
20 1 0.02
21 30 0.52
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (20 bp):
AATTTCGACTATCGCAACCG
Found at i:485856 original size:40 final size:40
Alignment explanation
Indices: 485811--485888 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
485801 AATTTCGACT
*
485811 ATCGCAACGCGAATTTCGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
*
485851 ATCGCAACGCGAACTTCGACTATCGCATCGAATTTGGA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGA
485889 CTAACGTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (40 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
Found at i:486968 original size:27 final size:27
Alignment explanation
Indices: 486938--487001 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
486928 TTGCAAACAT
* *
486938 TAAAAGAATATGTTCGT-GAACAATAAA
1 TAAAAGAACAAGTT-GTCGAACAATAAA
* *
486965 TAAATGAACAAGTTTTCGAACAATAAA
1 TAAAAGAACAAGTTGTCGAACAATAAA
*
486992 TAAATGAACA
1 TAAAAGAACA
487002 CAAACAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (27 bp):
TAAAAGAACAAGTTGTCGAACAATAAA
Done.