Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008983.1 Hibiscus syriacus cultivar Beakdansim tig00112347_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: 1350231
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:421497 original size:2 final size:2
Alignment explanation
Indices: 421484--421563 Score: 151
Period size: 2 Copynumber: 40.0 Consensus size: 2
421474 TTTTGTAACC
*
421484 AT AT AC 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
421526 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
421564 TTCGTACTTT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:435792 original size:18 final size:18
Alignment explanation
Indices: 435747--435821 Score: 96
Period size: 18 Copynumber: 4.0 Consensus size: 18
435737 GAGGGATTAT
435747 TAGTGGTCCTTCGGGACATA
1 TAGTGGTCCTTCGGGAC--A
*
435767 TCAGTGGTCCTTCGGGGCA
1 T-AGTGGTCCTTCGGGACA
*
435786 TAGTGGTCCTTCGGGATA
1 TAGTGGTCCTTCGGGACA
*
435804 TAGTGGTCATTCGGGACA
1 TAGTGGTCCTTCGGGACA
435822 AATATTCAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 31 0.63
19 2 0.04
20 1 0.02
21 15 0.31
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.29
Consensus pattern (18 bp):
TAGTGGTCCTTCGGGACA
Found at i:435801 original size:39 final size:36
Alignment explanation
Indices: 435747--435818 Score: 108
Period size: 39 Copynumber: 1.9 Consensus size: 36
435737 GAGGGATTAT
*
435747 TAGTGGTCCTTCGGGACATATCAGTGGTCCTTCGGGGCA
1 TAGTGGTCCTTCGGG--ATAT-AGTGGTCATTCGGGGCA
435786 TAGTGGTCCTTCGGGATATAGTGGTCATTCGGG
1 TAGTGGTCCTTCGGGATATAGTGGTCATTCGGG
435819 ACAAATATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 13 0.41
37 4 0.12
39 15 0.47
ACGTcount: A:0.15, C:0.19, G:0.35, T:0.31
Consensus pattern (36 bp):
TAGTGGTCCTTCGGGATATAGTGGTCATTCGGGGCA
Found at i:440963 original size:18 final size:18
Alignment explanation
Indices: 440919--440992 Score: 94
Period size: 18 Copynumber: 3.9 Consensus size: 18
440909 AGGGATTATC
440919 AGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCGGGAC--AT
*
440939 CAGTGGTCCTTCGGGGCAT
1 -AGTGGTCCTTCGGGACAT
*
440958 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
*
440976 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
440993 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
18 31 0.65
19 2 0.04
21 15 0.31
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:443384 original size:18 final size:18
Alignment explanation
Indices: 443340--443413 Score: 94
Period size: 18 Copynumber: 3.9 Consensus size: 18
443330 AGGGATTATC
443340 AGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCGGGAC--AT
*
443360 CAGTGGTCCTTCGGGGCAT
1 -AGTGGTCCTTCGGGACAT
*
443379 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
*
443397 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
443414 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
18 31 0.65
19 2 0.04
21 15 0.31
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:445774 original size:21 final size:22
Alignment explanation
Indices: 445750--445794 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
445740 GTCGAGGGAT
445750 TATCAGTGGT-CTT-TCGGGACA
1 TATCAGTGGTCCTTAT-GGGACA
445771 TATCAGTGGTCCTTATGGGACA
1 TATCAGTGGTCCTTATGGGACA
445793 TA
1 TA
445795 GTGGTCCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 11 0.50
23 1 0.05
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (22 bp):
TATCAGTGGTCCTTATGGGACA
Found at i:446707 original size:13 final size:13
Alignment explanation
Indices: 446675--446708 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
446665 TTTTAAATTT
446675 TTAATATTAAAAAA
1 TTAAT-TTAAAAAA
446689 TT-ATTTAAAAAA
1 TTAATTTAAAAAA
446701 TTAATTTA
1 TTAATTTA
446709 TTTATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.53
13 7 0.37
14 2 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAATTTAAAAAA
Found at i:447801 original size:30 final size:31
Alignment explanation
Indices: 447760--447820 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
447750 CTCTATTAGT
447760 TTTGAACGTTTATGAATGCAAT-TTTGAACC
1 TTTGAACGTTTATGAATGCAATGTTTGAACC
*
447790 TTTGAATGTTTATGAATGCAATGTTTGAACC
1 TTTGAACGTTTATGAATGCAATGTTTGAACC
447821 AAGTGTTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (31 bp):
TTTGAACGTTTATGAATGCAATGTTTGAACC
Found at i:448137 original size:7 final size:7
Alignment explanation
Indices: 448125--448154 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
448115 AGTGGAGTAT
448125 AACCACA
1 AACCACA
448132 AACCACA
1 AACCACA
448139 AACCACA
1 AACCACA
*
448146 ACCCACA
1 AACCACA
448153 AA
1 AA
448155 ATATCATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.43, G:0.00, T:0.00
Consensus pattern (7 bp):
AACCACA
Found at i:455473 original size:20 final size:20
Alignment explanation
Indices: 455448--455485 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
455438 CACATGTTAA
455448 AGAATGCATCGATGCACTAT
1 AGAATGCATCGATGCACTAT
*
455468 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
455486 TTAAAGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTAT
Found at i:456212 original size:2 final size:2
Alignment explanation
Indices: 456205--456273 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
456195 TGGAGTTATG
456205 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
456247 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
456274 GACTTTATGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:456679 original size:23 final size:24
Alignment explanation
Indices: 456649--456701 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
456639 TCCTTCGGGA
456649 CATAGTGGTCCTCCGGGAC-ATTT
1 CATAGTGGTCCTCCGGGACAATTT
*
456672 CATAGTGGTCCTTCGGGACAAATTT
1 CATAGTGGTCCTCCGGGAC-AATTT
456697 CATAG
1 CATAG
456702 CCCCTAGTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 18 0.67
25 9 0.33
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (24 bp):
CATAGTGGTCCTCCGGGACAATTT
Found at i:461982 original size:21 final size:22
Alignment explanation
Indices: 461958--462013 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
461948 ACCCTTGCTA
461958 TGTATCGATACAT-CTTGAATG
1 TGTATCGATACATCCTTGAATG
* *
461979 TGTACCGATACGTTCCTTGAATG
1 TGTATCGATAC-ATCCTTGAATG
*
462002 TGTATTGATACA
1 TGTATCGATACA
462014 CCTCACAGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 10 0.36
22 1 0.04
23 17 0.61
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (22 bp):
TGTATCGATACATCCTTGAATG
Found at i:462462 original size:19 final size:20
Alignment explanation
Indices: 462434--462471 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
462424 AAAATGTGTG
*
462434 TTTTGTTTTAATT-TGTTGT
1 TTTTGATTTAATTATGTTGT
462453 TTTTGATTTAATTATGTTG
1 TTTTGATTTAATTATGTTG
462472 GTTTCATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (20 bp):
TTTTGATTTAATTATGTTGT
Found at i:466553 original size:131 final size:131
Alignment explanation
Indices: 466328--466662 Score: 435
Period size: 131 Copynumber: 2.6 Consensus size: 131
466318 TCAGTTGGAG
* *
466328 TAATAAATGACTGCTTTAAGGCACGAGATGTCATTTATTCTCAATTGGAAATAATTAGATATTAT
1 TAATAAATGACTGCTTTAAGGCATGAGATGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
* * * *
466393 -TGTTTTCTTTCGAAGTAATATTGATTTTTAAGTCGGAATAGTGATATCTCTTCATTTCGAATGA
66 CT-TTTTCTTTCGAAGTAATATTGAATTTTAAGACGAAATAATGATATCTCTTCATTTCGAATGA
466457 AA
130 AA
* *
466459 TAATAAATGACTGCTTTAAAGCATGAGATGTCATTTATTCTCGATTGGAAATCATTAGATATTAT
1 TAATAAATGACTGCTTTAAGGCATGAGATGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
* * * **
466524 CATTTTTAC-TT-GAA-TCAATGTTGAATTTTAAGACGAAATAATGATGTCTCTTCGTTTCGGTT
66 C-TTTTT-CTTTCGAAGT-AATATTGAATTTTAAGACGAAATAATGATATCTCTTCATTTCGAAT
* *
466586 GGAG
128 GAAA
* * *
466590 TAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGAAAATAATTAGATACTAT
1 TAATAAATGACTGCTTTAAGGCATGAGATGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
*
466655 CGTTTTCT
66 CTTTTTCT
466663 CTCCTAGAAT
Statistics
Matches: 178, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
129 1 0.01
130 5 0.03
131 164 0.92
132 6 0.03
133 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (131 bp):
TAATAAATGACTGCTTTAAGGCATGAGATGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
CTTTTTCTTTCGAAGTAATATTGAATTTTAAGACGAAATAATGATATCTCTTCATTTCGAATGAA
A
Found at i:467674 original size:2 final size:2
Alignment explanation
Indices: 467667--467708 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
467657 CTGTTTAAAT
467667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
467707 TA
1 TA
467709 AAAAAACATC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:467997 original size:357 final size:357
Alignment explanation
Indices: 467335--468044 Score: 1359
Period size: 357 Copynumber: 2.0 Consensus size: 357
467325 GCGTAATAAA
*
467335 ATATATGATATAATATAAAAAAACATCACCTTAATTTCGATTAATATTAAATCCCAAATTTGATA
1 ATATATAATATAATATAAAAAAACATCACCTTAATTTCGATTAATATTAAATCCCAAATTTGATA
* *
467400 CGAACAATTCTCTATCCTTGCAAATAAAATAAAATTGGATAAATTACACGGGTGATTCCTTATGT
66 CGAACAATTCTCCATCCTTGAAAATAAAATAAAATTGGATAAATTACACGGGTGATTCCTTATGT
467465 TTTTCATCTATTTTATTTTGATCACTAATTTTTTAAAAATAATTTTAACCTCTTACTTTATAGGT
131 TTTTCATCTATTTTATTTTGATCACTAATTTTTTAAAAATAATTTTAACCTCTTACTTTATAGGT
*
467530 TTATTCTATTTTAGTCCCTCGAATGTTACCTCCAATTAACCCATAACGAAAGTCTGACTGAACAA
196 TTATTCTATTTTAGTCCCTCGAATGTTACCTCCAATTAACCCAGAACGAAAGTCTGACTGAACAA
467595 TTAAAAAATAAAACAAAAGTTACCTAAGTGAGTCAACTGTAATACAAGTGATATTTAACAAACTG
261 TTAAAAAATAAAACAAAAGTTACCTAAGTGAGTCAACTGTAATACAAGTGATATTTAACAAACTG
467660 TTTAAATTATATATATATATATATATATATAT
326 TTTAAATTATATATATATATATATATATATAT
467692 ATATATAATATAATATAAAAAAACATCACCTTAATTTCGATTAATATTAAATCCCAAATTTGATA
1 ATATATAATATAATATAAAAAAACATCACCTTAATTTCGATTAATATTAAATCCCAAATTTGATA
467757 CGAACAATTCTCCATCCTTGAAAATAAAATAAAATTGGATAAATTACACGGGTGATTCCTTATGT
66 CGAACAATTCTCCATCCTTGAAAATAAAATAAAATTGGATAAATTACACGGGTGATTCCTTATGT
*
467822 TTTTCATCTATTTTATTTTGATCACTAATTTTTTAAAAATAATTTTAATCTCTTACTTTATAGGT
131 TTTTCATCTATTTTATTTTGATCACTAATTTTTTAAAAATAATTTTAACCTCTTACTTTATAGGT
467887 TTATT-TGATTTTAGTCCCTCGAATGTTACCTCCAATTAACCCAGAACGAAAGTCTGACTGAACA
196 TTATTCT-ATTTTAGTCCCTCGAATGTTACCTCCAATTAACCCAGAACGAAAGTCTGACTGAACA
467951 ATTAAAAAATAAAACAAAAGTTACCTAAGTGAGTCAACTGTAATACAAGTGATATTTAACAAACT
260 ATTAAAAAATAAAACAAAAGTTACCTAAGTGAGTCAACTGTAATACAAGTGATATTTAACAAACT
468016 GTTTAAATTATATATATATATATATATAT
325 GTTTAAATTATATATATATATATATATAT
468045 TAAAAATCCT
Statistics
Matches: 347, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
356 1 0.00
357 346 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (357 bp):
ATATATAATATAATATAAAAAAACATCACCTTAATTTCGATTAATATTAAATCCCAAATTTGATA
CGAACAATTCTCCATCCTTGAAAATAAAATAAAATTGGATAAATTACACGGGTGATTCCTTATGT
TTTTCATCTATTTTATTTTGATCACTAATTTTTTAAAAATAATTTTAACCTCTTACTTTATAGGT
TTATTCTATTTTAGTCCCTCGAATGTTACCTCCAATTAACCCAGAACGAAAGTCTGACTGAACAA
TTAAAAAATAAAACAAAAGTTACCTAAGTGAGTCAACTGTAATACAAGTGATATTTAACAAACTG
TTTAAATTATATATATATATATATATATATAT
Found at i:470127 original size:9 final size:9
Alignment explanation
Indices: 470113--470140 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
470103 AGACGCGCAT
470113 ATGATATTA
1 ATGATATTA
470122 ATGATATTA
1 ATGATATTA
470131 ATGATATTA
1 ATGATATTA
470140 A
1 A
470141 CGACTGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (9 bp):
ATGATATTA
Found at i:470616 original size:48 final size:49
Alignment explanation
Indices: 470560--470656 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
470550 TAAGCATCTC
* * *
470560 CAATGTAATTTTTCCTATGC-AAAATGGTTTTGGAAATCTTGGTGTCTT
1 CAATGTAATTTTTCCTATGCAAAAATGATTTTGAAAATCTTGGCGTCTT
470608 CAATGTAATTTTTCCTATGCAAAAATGATTTTGAAAATCTTGGCGTCTT
1 CAATGTAATTTTTCCTATGCAAAAATGATTTTGAAAATCTTGGCGTCTT
470657 TAGGTTTAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 20 0.44
49 25 0.56
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.42
Consensus pattern (49 bp):
CAATGTAATTTTTCCTATGCAAAAATGATTTTGAAAATCTTGGCGTCTT
Found at i:470852 original size:11 final size:10
Alignment explanation
Indices: 470814--470899 Score: 57
Period size: 10 Copynumber: 8.0 Consensus size: 10
470804 AAAATCTTTA
470814 ATTTAAT-AT
1 ATTTAATAAT
*
470823 TTTTAATAAT
1 ATTTAATAAT
470833 ATTTAATAAT
1 ATTTAATAAT
470843 GATTTGATAATAAT
1 -A-TT--TAATAAT
* *
470857 GATTTGATATT
1 -ATTTAATAAT
*
470868 ATTTAATGAT
1 ATTTAATAAT
*
470878 ATGATAATAAT
1 AT-TTAATAAT
470889 GATTTAATAAT
1 -ATTTAATAAT
470900 GATAATAATG
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
9 6 0.10
10 20 0.33
11 19 0.32
12 4 0.07
13 2 0.03
14 9 0.15
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (10 bp):
ATTTAATAAT
Found at i:470855 original size:14 final size:14
Alignment explanation
Indices: 470836--470899 Score: 74
Period size: 14 Copynumber: 4.3 Consensus size: 14
470826 TAATAATATT
470836 TAATAATGATTTGA
1 TAATAATGATTTGA
470850 TAATAATGATTTGA
1 TAATAATGATTTGA
*
470864 TATTATTTAATGATATGA
1 TA--A--TAATGATTTGA
*
470882 TAATAATGATTTAA
1 TAATAATGATTTGA
470896 TAAT
1 TAAT
470900 GATAATAATG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
14 29 0.67
16 2 0.05
18 12 0.28
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (14 bp):
TAATAATGATTTGA
Found at i:470867 original size:32 final size:32
Alignment explanation
Indices: 470829--470915 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
470819 ATATTTTTAA
470829 TAATATTTAATAATGATTTGATAATAATGATT
1 TAATATTTAATAATGATTTGATAATAATGATT
* * *
470861 TGATA-TTATTTAATGATATGATAATAATGATT
1 TAATATTTA-ATAATGATTTGATAATAATGATT
*
470893 TAATAATGATAATAATGATTTGA
1 TAAT-AT-TTAATAATGATTTGA
470916 AAACATTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
31 3 0.07
32 28 0.64
33 1 0.02
34 10 0.23
35 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (32 bp):
TAATATTTAATAATGATTTGATAATAATGATT
Found at i:470903 original size:20 final size:22
Alignment explanation
Indices: 470868--470913 Score: 78
Period size: 20 Copynumber: 2.2 Consensus size: 22
470858 ATTTGATATT
470868 ATTTAATGATATGATAATAATG
1 ATTTAATGATATGATAATAATG
470890 ATTTAAT-A-ATGATAATAATG
1 ATTTAATGATATGATAATAATG
470910 ATTT
1 ATTT
470914 GAAAACATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 16 0.67
21 1 0.04
22 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (22 bp):
ATTTAATGATATGATAATAATG
Found at i:470905 original size:9 final size:9
Alignment explanation
Indices: 470878--470911 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
470868 ATTTAATGAT
470878 ATGATAATA
1 ATGATAATA
470887 ATGATTTAATA
1 ATGA--TAATA
470898 ATGATAATA
1 ATGATAATA
470907 ATGAT
1 ATGAT
470912 TTGAAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 14 0.61
11 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (9 bp):
ATGATAATA
Found at i:471176 original size:11 final size:11
Alignment explanation
Indices: 471146--471198 Score: 61
Period size: 11 Copynumber: 4.4 Consensus size: 11
471136 TAAAAAAATT
471146 TAATGATTTCAAA
1 TAATGATTT--AA
471159 CTAATGATTTAA
1 -TAATGATTTAA
471171 TAATGATTACTAA
1 TAATGATT--TAA
471184 TAATGATTTAA
1 TAATGATTTAA
471195 TAAT
1 TAAT
471199 TATTATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 15 0.41
12 2 0.05
13 11 0.30
14 9 0.24
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.42
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:471191 original size:24 final size:24
Alignment explanation
Indices: 471146--471266 Score: 86
Period size: 24 Copynumber: 4.9 Consensus size: 24
471136 TAAAAAAATT
* *
471146 TAATGATTTCAAACTAATGATTTAA
1 TAATGATTACTAA-TAATGATTTAA
471171 TAATGATTACTAATAATGATTTAA
1 TAATGATTACTAATAATGATTTAA
* * **
471195 TAATTATTATTAATTTAA--AAATAA
1 TAATGATTACTAA--TAATGATTTAA
* * *
471219 GAAATGATTTGA-TACTAATGATTTAG
1 -TAATGA-TT-ACTAATAATGATTTAA
471245 TAATGATTACTAATAATGATTT
1 TAATGATTACTAATAATGATTT
471267 CATTGTGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
23 1 0.01
24 42 0.57
25 20 0.27
26 10 0.14
27 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (24 bp):
TAATGATTACTAATAATGATTTAA
Found at i:471877 original size:14 final size:14
Alignment explanation
Indices: 471858--471884 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
471848 TTTATATATA
471858 TCTAAACCCTAAAC
1 TCTAAACCCTAAAC
471872 TCTAAACCCTAAA
1 TCTAAACCCTAAA
471885 TAATAACTAT
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:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
TCTAAACCCTAAAC
Found at i:473785 original size:24 final size:24
Alignment explanation
Indices: 473753--473801 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
473743 TTATTTTTAA
473753 ATTAATAATAATTATTAAATCATT
1 ATTAATAATAATTATTAAATCATT
* * *
473777 ATTAGTAATCATTATTAAATTATT
1 ATTAATAATAATTATTAAATCATT
473801 A
1 A
473802 GTTTGAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTAATAATAATTATTAAATCATT
Found at i:474062 original size:14 final size:14
Alignment explanation
Indices: 474062--474122 Score: 77
Period size: 14 Copynumber: 4.1 Consensus size: 14
474052 CATTATTATC
*
474062 ATTATTAAATCATT
1 ATTATCAAATCATT
474076 ATTATCAAATCATTAAAT
1 ATTATCAAATCA-T---T
474094 ATTATCAAATCATT
1 ATTATCAAATCATT
474108 ATTATCAAATCATT
1 ATTATCAAATCATT
474122 A
1 A
474123 CTAAATATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 27 0.64
15 1 0.02
17 1 0.02
18 13 0.31
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTATCAAATCATT
Found at i:474071 original size:20 final size:20
Alignment explanation
Indices: 474043--474082 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
474033 ATAAAAAATG
474043 TTATCAAATCATTATTATCA
1 TTATCAAATCATTATTATCA
*
474063 TTATTAAATCATTATTATCA
1 TTATCAAATCATTATTATCA
474083 AATCATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATCAAATCATTATTATCA
Found at i:474073 original size:11 final size:11
Alignment explanation
Indices: 474043--474143 Score: 70
Period size: 11 Copynumber: 9.3 Consensus size: 11
474033 ATAAAAAATG
*
474043 TTATCAAATCA
1 TTATTAAATCA
474054 TTATT--ATCA
1 TTATTAAATCA
474063 TTATTAAATCA
1 TTATTAAATCA
474074 TTATT--ATCAAA
1 TTATTAAATC--A
*
474085 TCATTAAAT-A
1 TTATTAAATCA
*
474095 TTATCAAATCA
1 TTATTAAATCA
474106 TTATTATCAAATCA
1 TTA-T-T-AAATCA
*
474120 TTACTAAAT-A
1 TTATTAAATCA
*
474130 TTATTAAAACA
1 TTATTAAATCA
474141 TTA
1 TTA
474144 AATTAAAGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
9 12 0.17
10 16 0.23
11 30 0.42
12 2 0.03
13 2 0.03
14 9 0.13
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.43
Consensus pattern (11 bp):
TTATTAAATCA
Found at i:474104 original size:32 final size:34
Alignment explanation
Indices: 474043--474122 Score: 128
Period size: 32 Copynumber: 2.4 Consensus size: 34
474033 ATAAAAAATG
* *
474043 TTATCAAATCATTATTATCATTATTAAATCATTA
1 TTATCAAATCATTATAATCATTATCAAATCATTA
474077 TTATCAAATCATTA-AAT-ATTATCAAATCATTA
1 TTATCAAATCATTATAATCATTATCAAATCATTA
474109 TTATCAAATCATTA
1 TTATCAAATCATTA
474123 CTAAATATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 28 0.64
33 2 0.05
34 14 0.32
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (34 bp):
TTATCAAATCATTATAATCATTATCAAATCATTA
Found at i:476418 original size:12 final size:12
Alignment explanation
Indices: 476386--476425 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
476376 TGCGAGAAAA
476386 TTAAAATC-A-T
1 TTAAAATCTATT
476396 TT-AAATCTATT
1 TTAAAATCTATT
*
476407 TTAAAATTTATT
1 TTAAAATCTATT
476419 TTAAAAT
1 TTAAAAT
476426 ATAGATTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 3 0.12
12 15 0.58
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAAAATCTATT
Found at i:476437 original size:22 final size:22
Alignment explanation
Indices: 476412--476799 Score: 530
Period size: 22 Copynumber: 17.6 Consensus size: 22
476402 CTATTTTAAA
*
476412 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
476434 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
***
476456 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
476478 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
476500 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
476522 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
***
476544 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
476566 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
476588 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
476610 ATTAATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
476632 ATTTATTTTAAAATAT-AAAAA
1 ATTTATTTTAAAATATGGATTG
476653 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
*
476676 ATTTATTATAAAATATGGAAAATT-
1 ATTTATTTTAAAATATGG---ATTG
*
476700 -TTTATTTTAAAATATGGATTA
1 ATTTATTTTAAAATATGGATTG
476721 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
476743 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
476765 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
476787 ATTTATTTTAAAA
1 ATTTATTTTAAAA
476800 AATTTATTAT
Statistics
Matches: 324, Mismatches: 35, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
20 3 0.01
21 2 0.01
22 298 0.92
23 18 0.06
25 3 0.01
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:476880 original size:31 final size:31
Alignment explanation
Indices: 476823--476881 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
476813 AGTTGTATGG
*
476823 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
476854 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
476882 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:483535 original size:21 final size:21
Alignment explanation
Indices: 483511--483571 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
483501 AAACATCTAC
483511 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
*
483532 CAAA----G--AAACATTTAT
1 CAAACTTTGAAAAACATTTTT
483547 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
483568 CAAA
1 CAAA
483572 GTTGGTTGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 13 0.41
17 1 0.03
19 1 0.03
21 17 0.53
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:483551 original size:36 final size:36
Alignment explanation
Indices: 483493--483572 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
483483 CCCATTCCTA
*
483493 TTTTC-AACAAACATCTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
* *
483528 TTTTCAAAGAAACATTTATCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
483564 TTTTCAAAG
1 TTTTCAAAG
483573 TTGGTTGCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 5 0.12
36 36 0.88
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (36 bp):
TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
Found at i:489119 original size:75 final size:75
Alignment explanation
Indices: 488996--489217 Score: 381
Period size: 75 Copynumber: 3.0 Consensus size: 75
488986 CCTGTCTGTC
* *
488996 TGCAGGCTGCCAAGGAAACTGGTGCACTCCAAGAAGCCAAGGAAAAGCTGGAACAGGAAGTTAAA
1 TGCAGGCTGCCAAGGAAACTGGTGCATTCCAAGAAGCCAAGGAAAAGCTGGAACAGCAAGTTAAA
*
489061 CAACTTAAGA
66 GAACTTAAGA
*
489071 TGCAGGCTGCCAAGGACACTGGTGCATTCCAAGAAGCCAAGGAAAAGCTGGAACAGCAAGTTAAA
1 TGCAGGCTGCCAAGGAAACTGGTGCATTCCAAGAAGCCAAGGAAAAGCTGGAACAGCAAGTTAAA
489136 GAACTTAAGA
66 GAACTTAAGA
* * *
489146 TGCAGGCTGCCAAGGAAACTGGGGAATTCCAAGAAGCTAAGGAAAAGCTGGAACAGCAAGTTAAA
1 TGCAGGCTGCCAAGGAAACTGGTGCATTCCAAGAAGCCAAGGAAAAGCTGGAACAGCAAGTTAAA
489211 GAACTTA
66 GAACTTA
489218 CAAGCAGCTT
Statistics
Matches: 139, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 139 1.00
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (75 bp):
TGCAGGCTGCCAAGGAAACTGGTGCATTCCAAGAAGCCAAGGAAAAGCTGGAACAGCAAGTTAAA
GAACTTAAGA
Found at i:490608 original size:18 final size:17
Alignment explanation
Indices: 490585--490630 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
490575 TTCCTTGAAT
490585 TTTTTTTTCTGGTTCTGA
1 TTTTTTTTCTGGTTCT-A
* *
490603 TTTTTTTTCATGTTTCTT
1 TTTTTTTTC-TGGTTCTA
490621 TTTTTTTTCT
1 TTTTTTTTCT
490631 TGATGTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 18 0.72
19 6 0.24
ACGTcount: A:0.04, C:0.11, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTTTTTTCTGGTTCTA
Found at i:496197 original size:4 final size:4
Alignment explanation
Indices: 496188--496222 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
496178 TCTGTTTTAT
496188 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
496223 TATTATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:498907 original size:17 final size:17
Alignment explanation
Indices: 498885--498935 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
498875 GTTATTCTAT
*
498885 TTTAAAAAATTTC-CTCC
1 TTTAAAAAA-ATCACTCC
498902 TTTAAAAAAATCAACTCC
1 TTTAAAAAAATC-ACTCC
498920 TTTAAAAAAATTCACT
1 TTTAAAAAAA-TCACT
498936 GCGATATCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.07
17 9 0.30
18 17 0.57
19 2 0.07
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (17 bp):
TTTAAAAAAATCACTCC
Found at i:498911 original size:18 final size:18
Alignment explanation
Indices: 498888--498931 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
498878 ATTCTATTTT
**
498888 AAAAAATTTCCTCCTTTA
1 AAAAAATTAACTCCTTTA
*
498906 AAAAAATCAACTCCTTTA
1 AAAAAATTAACTCCTTTA
498924 AAAAAATT
1 AAAAAATT
498932 CACTGCGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAAATTAACTCCTTTA
Found at i:499180 original size:37 final size:37
Alignment explanation
Indices: 499130--499247 Score: 209
Period size: 37 Copynumber: 3.2 Consensus size: 37
499120 TGAGGAGGGA
*
499130 TGAAGCAGCTGCTGCATTTAAATTAGGAGAATCCCAT
1 TGAAGGAGCTGCTGCATTTAAATTAGGAGAATCCCAT
*
499167 TGAAGGAGCTGCTGCATTTAAATTAGGAGAATCCCGT
1 TGAAGGAGCTGCTGCATTTAAATTAGGAGAATCCCAT
*
499204 TGAAGGAGCTGCTGCATTTAAATTTGGAGAATCCCAT
1 TGAAGGAGCTGCTGCATTTAAATTAGGAGAATCCCAT
499241 TGAAGGA
1 TGAAGGA
499248 CATTGGTGAG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 77 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (37 bp):
TGAAGGAGCTGCTGCATTTAAATTAGGAGAATCCCAT
Found at i:500786 original size:69 final size:67
Alignment explanation
Indices: 500691--500818 Score: 168
Period size: 69 Copynumber: 1.9 Consensus size: 67
500681 ACAAATAATA
* *
500691 TCTTAAAAAGTAATTAAACTATAAAATTAAGAAATTAAGGGTTCAATTTCACTAATTTTAAATTT
1 TCTTAAAAAGTAATTAAACTAGAAAATTAAG-AATT-AGGCTT-AATTTCACTAATTTTAAATTT
500756 AAAGG
63 AAAGG
* * * *
500761 TCTTAAAAA-TGATTAAACTAGAAAATTTAGAGTTAGGCTTAATTTCATTAATTTTAAA
1 TCTTAAAAAGTAATTAAACTAGAAAATTAAGAATTAGGCTTAATTTCACTAATTTTAAA
500819 ACTGAAATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 17 0.33
67 5 0.10
68 3 0.06
69 18 0.35
70 9 0.17
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (67 bp):
TCTTAAAAAGTAATTAAACTAGAAAATTAAGAATTAGGCTTAATTTCACTAATTTTAAATTTAAA
GG
Found at i:511461 original size:2 final size:2
Alignment explanation
Indices: 511454--511488 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
511444 AAGGAAGGCA
511454 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
511489 GTAGGATGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:513921 original size:8 final size:8
Alignment explanation
Indices: 513893--513949 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
513883 GTAATTTAAT
513893 CCTCTCTCC
1 CCTCTCT-C
513902 CCTCTCTTTC
1 CCTCTC--TC
513912 CCTCTCTC
1 CCTCTCTC
513920 CCTC-C-C
1 CCTCTCTC
*
513926 CCCCTCTC
1 CCTCTCTC
513934 CCTCTCTC
1 CCTCTCTC
*
513942 TCTCTCTC
1 CCTCTCTC
513950 TATATATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
6 4 0.10
7 2 0.05
8 21 0.51
9 6 0.15
10 7 0.17
11 1 0.02
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (8 bp):
CCTCTCTC
Found at i:513955 original size:2 final size:2
Alignment explanation
Indices: 513950--513977 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
513940 TCTCTCTCTC
513950 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
513978 ATGTATGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:514505 original size:21 final size:21
Alignment explanation
Indices: 514475--514514 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
514465 ATATTGATGC
*
514475 GTCCAGCCGAGGTTTTGGTGT
1 GTCCAACCGAGGTTTTGGTGT
514496 GTCCAACCGAGGTTTTGGT
1 GTCCAACCGAGGTTTTGGT
514515 TCGTCGGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.20, G:0.35, T:0.33
Consensus pattern (21 bp):
GTCCAACCGAGGTTTTGGTGT
Found at i:527947 original size:8 final size:8
Alignment explanation
Indices: 527934--527961 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
527924 TTTTAGTTTA
527934 TAAATTTT
1 TAAATTTT
527942 TAAATTTT
1 TAAATTTT
527950 TAAATTTT
1 TAAATTTT
527958 TAAA
1 TAAA
527962 ATCATACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TAAATTTT
Found at i:530403 original size:257 final size:257
Alignment explanation
Indices: 529947--530717 Score: 1443
Period size: 257 Copynumber: 3.0 Consensus size: 257
529937 AGTTTTAAAG
* * *
529947 GTATAAAAGAAGGTAAAAGTAGGGGATTAGTTCAGTTTTGGTTAAAATTCGAAATGGAATGGTGA
1 GTATAAAAGAAGGTAAAAGTAGGAGATTAGTTAAGTTTTGGTTAAAATTCGAAATGGAATGGTAA
530012 ATTCTGGGCAAGGGTATCGGTACTGTAAGAACAGTACCGATACTTCAAGGCTAAATCAATTAGAA
66 ATTCTGGGCAAGGGTATCGGTACTGTAAGAACAGTACCGATACTTCAAGGCTAAATCAATTAGAA
530077 TTCAAGGATCAGTATCGGTACTGCTTGAGGGAGGTATTGATACTGAAAGGGGAGTATCGATACCA
131 TTCAAGGATCAGTATCGGTACTGCTTGAGGGAGGTATTGATACTGAAAGGGGAGTATCGATACCA
530142 AGAGTAAGGTATCGATACCAATTTCAAGTTGAAATTCCAGTATGTCGAAATGATATCGATAC
196 AGAGTAAGGTATCGATACCAATTTCAAGTTGAAATTCCAGTATGTCGAAATGATATCGATAC
530204 GTATAAAAGAAGGTAAAAGTAGGAGATTAGTTAAGTTTTGGTTAAAATTCGAAATGGAATGGTAA
1 GTATAAAAGAAGGTAAAAGTAGGAGATTAGTTAAGTTTTGGTTAAAATTCGAAATGGAATGGTAA
530269 ATTCTGGGCAAGGGTATCGGTACTGTAAGAACAGTACCGATACTTCAAGGCTAAATCAATTAGAA
66 ATTCTGGGCAAGGGTATCGGTACTGTAAGAACAGTACCGATACTTCAAGGCTAAATCAATTAGAA
*
530334 TTCAAGGATCAGTATCGGTACTGCTTGAGGGAGGTATTGATACTGAAAGAGGAGTATCGATACCA
131 TTCAAGGATCAGTATCGGTACTGCTTGAGGGAGGTATTGATACTGAAAGGGGAGTATCGATACCA
*
530399 AGAGTAAGGTATCGATACCAATTTCAAGTTGAAATTCCAGTATGTCAAAATGATATCGATAC
196 AGAGTAAGGTATCGATACCAATTTCAAGTTGAAATTCCAGTATGTCGAAATGATATCGATAC
530461 GTATAAAAGAAGGTAAAAGTAGGAGATTAGTTAAGTTTTGGTTAAAATTCGAAATGGAATGGTAA
1 GTATAAAAGAAGGTAAAAGTAGGAGATTAGTTAAGTTTTGGTTAAAATTCGAAATGGAATGGTAA
*
530526 ATTTTGGGCAAGGGTATCGGTACTGTAAGAACAGTACCGATACTTCAAGGCTAAATCAATTAGAA
66 ATTCTGGGCAAGGGTATCGGTACTGTAAGAACAGTACCGATACTTCAAGGCTAAATCAATTAGAA
** **
530591 TTCAAGGATCAGTATTTGTACTGCTTGAGGGAGGTATCAATACTGAAAGGGGAGTATCGATACCA
131 TTCAAGGATCAGTATCGGTACTGCTTGAGGGAGGTATTGATACTGAAAGGGGAGTATCGATACCA
*
530656 AGAGTAAGGTATTGATACCAATTTCAAGTTGAAATTCCAGTATGTCGAAATGATATCGATAC
196 AGAGTAAGGTATCGATACCAATTTCAAGTTGAAATTCCAGTATGTCGAAATGATATCGATAC
530718 CGAAAGGGGG
Statistics
Matches: 501, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
257 501 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.28
Consensus pattern (257 bp):
GTATAAAAGAAGGTAAAAGTAGGAGATTAGTTAAGTTTTGGTTAAAATTCGAAATGGAATGGTAA
ATTCTGGGCAAGGGTATCGGTACTGTAAGAACAGTACCGATACTTCAAGGCTAAATCAATTAGAA
TTCAAGGATCAGTATCGGTACTGCTTGAGGGAGGTATTGATACTGAAAGGGGAGTATCGATACCA
AGAGTAAGGTATCGATACCAATTTCAAGTTGAAATTCCAGTATGTCGAAATGATATCGATAC
Found at i:532413 original size:24 final size:24
Alignment explanation
Indices: 532353--532491 Score: 165
Period size: 24 Copynumber: 5.9 Consensus size: 24
532343 GTCGAGGGTT
* *
532353 CTATGTGGTCATTCGGGATAAAA-
1 CTATGTGGTCCTTCGGGACAAAAC
* * * *
532376 TTATATGGTCCTTCGAGATAAAAC
1 CTATGTGGTCCTTCGGGACAAAAC
532400 CTATGTGGTCCTTCGGGACAAAAC
1 CTATGTGGTCCTTCGGGACAAAAC
* *
532424 ATGTGTGGTCCTTCGGGACAAAAC
1 CTATGTGGTCCTTCGGGACAAAAC
* *
532448 CTGTGTGGTCCTTCAGGAC-AAAC
1 CTATGTGGTCCTTCGGGACAAAAC
*
532471 CTATGTGGTCCTACGGGACAA
1 CTATGTGGTCCTTCGGGACAA
532492 TTATATGGCA
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
23 39 0.39
24 60 0.61
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (24 bp):
CTATGTGGTCCTTCGGGACAAAAC
Found at i:532415 original size:47 final size:48
Alignment explanation
Indices: 532353--532491 Score: 147
Period size: 47 Copynumber: 2.9 Consensus size: 48
532343 GTCGAGGGTT
* * * *
532353 CTATGTGGTCATTCGGGATAAAA-TTATATGGTCCTTCGAGATAAAAC
1 CTATGTGGTCCTTCGGGACAAAACATATATGGTCCTTCGAGACAAAAC
* * *
532400 CTATGTGGTCCTTCGGGACAAAACATGTGTGGTCCTTCGGGACAAAAC
1 CTATGTGGTCCTTCGGGACAAAACATATATGGTCCTTCGAGACAAAAC
* * * * * *
532448 CTGTGTGGTCCTTCAGGAC-AAACCTATGTGGTCCTACGGGACAA
1 CTATGTGGTCCTTCGGGACAAAACATATATGGTCCTTCGAGACAA
532492 TTATATGGCA
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
47 43 0.54
48 36 0.46
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (48 bp):
CTATGTGGTCCTTCGGGACAAAACATATATGGTCCTTCGAGACAAAAC
Found at i:532440 original size:71 final size:71
Alignment explanation
Indices: 532356--532491 Score: 177
Period size: 71 Copynumber: 1.9 Consensus size: 71
532346 GAGGGTTCTA
* * *
532356 TGTGGTCATTCGGGATAAAA-TTATATGGTCCTTC-GAGATAAAACCTATGTGGTCCTTCGGGAC
1 TGTGGTCATTCGGGACAAAACCTATATGGTCCTTCAG-GA-AAAACCTATGTGGTCCTACGGGAC
532419 AAAACATG
64 AAAACATG
* * * *
532427 TGTGGTCCTTCGGGACAAAACCTGTGTGGTCCTTCAGGACAAACCTATGTGGTCCTACGGGACAA
1 TGTGGTCATTCGGGACAAAACCTATATGGTCCTTCAGGAAAAACCTATGTGGTCCTACGGGACAA
532492 TTATATGGCA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
71 42 0.75
72 13 0.23
73 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (71 bp):
TGTGGTCATTCGGGACAAAACCTATATGGTCCTTCAGGAAAAACCTATGTGGTCCTACGGGACAA
AACATG
Found at i:537529 original size:290 final size:290
Alignment explanation
Indices: 537003--537589 Score: 1048
Period size: 290 Copynumber: 2.0 Consensus size: 290
536993 TGCAAAATTT
* *
537003 GCATATAATAACAGTTACCAATCAAGCATTAAAATGGCACCGTATGAAGTATTGTATGGAAGGAA
1 GCATAAAATAACAGTTACCAATCAAGCATTAAAATGGCACCGTATGAAGTATTGTATGGAAAGAA
* * *
537068 GTGCATGACGCCGCTTAATTGGTATGAATTAAAAGACCGGGAAGTTTATGGCCCATATTTGATTA
66 GTGCAGGACACCGCTTAATTGGTATGAATTAAAAGACCGAGAAGTTTATGGCCCATATTTGATTA
*
537133 AAGAAGTTGAAGAAAAAGTTTAGGTAATCCAGTATAATCTTAAAGTGGCATCAGACAGATAAAAG
131 AAGAAGTTGAAGAAAAAGTTCAGGTAATCCAGTATAATCTTAAAGTGGCATCAGACAGATAAAAG
* **
537198 TCATACGCGGATTTGAAGAGGAAAGAAATTGAATTTTAAGTAGGTGACAAAATGTTCATAAAAGT
196 CCATACGCAAATTTGAAGAGGAAAGAAATTGAATTTTAAGTAGGTGACAAAATGTTCATAAAAGT
537263 ATCACCTTGAAAGAAAGTACTTCGTTTTGG
261 ATCACCTTGAAAGAAAGTACTTCGTTTTGG
537293 GCATAAAATAACAGTTACCAATCAAGCATTAAAATGGCACCGTATGAAGTATTGTATGGAAAGAA
1 GCATAAAATAACAGTTACCAATCAAGCATTAAAATGGCACCGTATGAAGTATTGTATGGAAAGAA
*
537358 GTGCAGGACACCGCTTAATTGGTATGAATTAAAAGATCGAGAAGTTTATGGCCCATATTTGATTA
66 GTGCAGGACACCGCTTAATTGGTATGAATTAAAAGACCGAGAAGTTTATGGCCCATATTTGATTA
537423 AAGAAGTTGAAGAAAAAGTTCAGGTAATCCAGTATAATCTTAAAGTGGCATCAGACAGATAAAAG
131 AAGAAGTTGAAGAAAAAGTTCAGGTAATCCAGTATAATCTTAAAGTGGCATCAGACAGATAAAAG
* *
537488 CCATATGCAAATTTGAAGAGGAAAGAAATTGAATTTTAAGTAGGTGACAAAGTGTTCATAAAAGT
196 CCATACGCAAATTTGAAGAGGAAAGAAATTGAATTTTAAGTAGGTGACAAAATGTTCATAAAAGT
*
537553 ATCACCTTGAAAGAAATTACTTCGTTTTGG
261 ATCACCTTGAAAGAAAGTACTTCGTTTTGG
*
537583 GCGTAAA
1 GCATAAA
537590 GGAAAACTCG
Statistics
Matches: 283, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
290 283 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (290 bp):
GCATAAAATAACAGTTACCAATCAAGCATTAAAATGGCACCGTATGAAGTATTGTATGGAAAGAA
GTGCAGGACACCGCTTAATTGGTATGAATTAAAAGACCGAGAAGTTTATGGCCCATATTTGATTA
AAGAAGTTGAAGAAAAAGTTCAGGTAATCCAGTATAATCTTAAAGTGGCATCAGACAGATAAAAG
CCATACGCAAATTTGAAGAGGAAAGAAATTGAATTTTAAGTAGGTGACAAAATGTTCATAAAAGT
ATCACCTTGAAAGAAAGTACTTCGTTTTGG
Found at i:539278 original size:13 final size:14
Alignment explanation
Indices: 539260--539290 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
539250 TTATTTAAGC
539260 TATGTGTG-ATGAT
1 TATGTGTGCATGAT
539273 TATGTGTGCATGAT
1 TATGTGTGCATGAT
539287 TATG
1 TATG
539291 AAATGTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.23, C:0.03, G:0.29, T:0.45
Consensus pattern (14 bp):
TATGTGTGCATGAT
Found at i:539470 original size:24 final size:24
Alignment explanation
Indices: 539438--539505 Score: 102
Period size: 23 Copynumber: 2.9 Consensus size: 24
539428 GTCGCGGGTT
*
539438 CTATCTGGTCCTTCGGGACAAAAC
1 CTATGTGGTCCTTCGGGACAAAAC
* *
539462 CTATGTGGTCCTTTGAGAC-AAAC
1 CTATGTGGTCCTTCGGGACAAAAC
539485 CTATGTGGTCCTTCGGGACAA
1 CTATGTGGTCCTTCGGGACAA
539506 TTATGTGGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
23 21 0.55
24 17 0.45
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (24 bp):
CTATGTGGTCCTTCGGGACAAAAC
Found at i:539528 original size:21 final size:21
Alignment explanation
Indices: 539443--539521 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 21
539433 GGGTTCTATC
*
539443 TGGTCCTTCGGGACAAAACCTATG
1 TGGTCCTTCGGGAC--AA-TTATG
* * *
539467 TGGTCCTTTGAGACAAACCTATG
1 TGGTCCTTCGGGAC-AA-TTATG
539490 TGGTCCTTCGGGACAATTATG
1 TGGTCCTTCGGGACAATTATG
539511 TGG-CACTTCGG
1 TGGTC-CTTCGG
539522 TGCAATTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.02
21 13 0.27
22 2 0.04
23 21 0.43
24 12 0.24
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.29
Consensus pattern (21 bp):
TGGTCCTTCGGGACAATTATG
Found at i:541096 original size:49 final size:49
Alignment explanation
Indices: 541043--541151 Score: 137
Period size: 49 Copynumber: 2.2 Consensus size: 49
541033 CTTGAAAAAT
* * *
541043 GATCGATCCCTTGGATTTTAATAGCCAAGGATCGATCCCTCCAGCAAGG
1 GATCGATCCCTTGGATTTCAATAGCCAAGGATCGATCCCTCCACCAAAG
* ** * *
541092 GATCGATCCGTTGGATTTCAATAGCCATTGATTGATCCCTTCACCAAAG
1 GATCGATCCCTTGGATTTCAATAGCCAAGGATCGATCCCTCCACCAAAG
*
541141 GATTGATCCCT
1 GATCGATCCCT
541152 CGAGGAAACT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (49 bp):
GATCGATCCCTTGGATTTCAATAGCCAAGGATCGATCCCTCCACCAAAG
Found at i:543708 original size:11 final size:11
Alignment explanation
Indices: 543670--543701 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
543660 ATACTTTATA
*
543670 AAATTGTTTTG
1 AAATTATTTTG
543681 AAATTATTTTG
1 AAATTATTTTG
543692 AAATTATTTT
1 AAATTATTTT
543702 AAGATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (11 bp):
AAATTATTTTG
Found at i:545073 original size:19 final size:20
Alignment explanation
Indices: 545030--545077 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
545020 TCTAAATCCT
*
545030 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
545050 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
545069 TTTTCAAAA
1 TTTTCAAAA
545078 GAAAATCGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:548427 original size:31 final size:30
Alignment explanation
Indices: 548353--548455 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 30
548343 GGCCCCAGAT
* *
548353 CCTACCCAAGAAAGTTAT-TCGGGGCCACGGAG
1 CCTACCCAAGAAAG--ATCTCAGGGCCTC-GAG
* * * *
548385 CCTTCCTAAGAATGATCTCAGGG-CTGCAGGG
1 CCTACCCAAGAAAGATCTCAGGGCCT-C-GAG
*
548416 CCTACCCAAGAAAGATCTCGGGGCCTCGAG
1 CCTACCCAAGAAAGATCTCAGGGCCTCGAG
548446 CCTACCCAAG
1 CCTACCCAAG
548456 GTTCTTCTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
30 15 0.27
31 28 0.50
32 13 0.23
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.17
Consensus pattern (30 bp):
CCTACCCAAGAAAGATCTCAGGGCCTCGAG
Found at i:557794 original size:12 final size:12
Alignment explanation
Indices: 557774--557819 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
557764 TCACAAACAG
*
557774 GCTCATTTATGA
1 GCTCGTTTATGA
557786 GCTCGTTTATGA
1 GCTCGTTTATGA
*
557798 GCTCGTTTACCGA
1 GCTCGTTTA-TGA
557811 -CTCGTTTAT
1 GCTCGTTTAT
557820 TTATGTTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 28 0.93
13 2 0.07
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (12 bp):
GCTCGTTTATGA
Found at i:558050 original size:11 final size:11
Alignment explanation
Indices: 558025--558074 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
558015 ATTGAATTTA
**
558025 TAAATGAACAA
1 TAAATGAACGC
*
558036 TAAACGAACGC
1 TAAATGAACGC
**
558047 TAAATGAATAC
1 TAAATGAACGC
558058 TAAATGAACGC
1 TAAATGAACGC
558069 TAAATG
1 TAAATG
558075 GACTTTAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.20
Consensus pattern (11 bp):
TAAATGAACGC
Found at i:558053 original size:22 final size:22
Alignment explanation
Indices: 558025--558074 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
558015 ATTGAATTTA
558025 TAAATGAACAATAAACGAACGC
1 TAAATGAACAATAAACGAACGC
* * *
558047 TAAATGAATACTAAATGAACGC
1 TAAATGAACAATAAACGAACGC
558069 TAAATG
1 TAAATG
558075 GACTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.20
Consensus pattern (22 bp):
TAAATGAACAATAAACGAACGC
Found at i:558106 original size:23 final size:23
Alignment explanation
Indices: 558080--558142 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
558070 AAATGGACTT
* *
558080 TAAAAGAACATGTTTGTGAACGC
1 TAAAAGAACACGTTCGTGAACGC
* *
558103 TAAATGAACACGTTCGTGAAC-A
1 TAAAAGAACACGTTCGTGAACGC
558125 TATAAATGAACACGTTCG
1 TA-AAA-GAACACGTTCG
558143 CAAACATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 2 0.06
23 20 0.61
24 11 0.33
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (23 bp):
TAAAAGAACACGTTCGTGAACGC
Found at i:558148 original size:24 final size:23
Alignment explanation
Indices: 558103--558153 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
558093 TTGTGAACGC
**
558103 TAAATGAACACGTTCGTGAACAT
1 TAAATGAACACGTTCGCAAACAT
558126 ATAAATGAACACGTTCGCAAACAT
1 -TAAATGAACACGTTCGCAAACAT
558150 TAAA
1 TAAA
558154 CAAACATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.24
Consensus pattern (23 bp):
TAAATGAACACGTTCGCAAACAT
Found at i:558159 original size:23 final size:23
Alignment explanation
Indices: 558109--558182 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
558099 ACGCTAAATG
* **
558109 AACACGTTCGTGAACATATAAATG
1 AACACGTTCGCGAACAT-TAAACA
*
558133 AACACGTTCGCAAACATTAAACA
1 AACACGTTCGCGAACATTAAACA
* * *
558156 AACATGTTCGCGAATAATAAACA
1 AACACGTTCGCGAACATTAAACA
558179 AACA
1 AACA
558183 AAAACAAACA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 27 0.64
24 15 0.36
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.20
Consensus pattern (23 bp):
AACACGTTCGCGAACATTAAACA
Found at i:558418 original size:32 final size:32
Alignment explanation
Indices: 558377--558460 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 32
558367 CAACGGAGTT
*
558377 TGAA-GGATTAAATTGATGAAACTTATAAATG
1 TGAAGGGATTAAATTGATGAAACTTATAAACG
* *
558408 TGAAGGGATTAAATTGGTGAAACTTATACACG
1 TGAAGGGATTAAATTGATGAAACTTATAAACG
*
558440 TGAAGGGATTAAATTGTTGAA
1 TGAAGGGATTAAATTGATGAA
558461 TCGTTTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
31 4 0.08
32 44 0.92
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (32 bp):
TGAAGGGATTAAATTGATGAAACTTATAAACG
Found at i:558726 original size:20 final size:20
Alignment explanation
Indices: 558701--558738 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
558691 AGTATAACCA
*
558701 TCAAAAGTATCTATTCATCG
1 TCAAAAGTATATATTCATCG
558721 TCAAAAGTATATATTCAT
1 TCAAAAGTATATATTCAT
558739 TAACTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (20 bp):
TCAAAAGTATATATTCATCG
Found at i:559055 original size:14 final size:14
Alignment explanation
Indices: 559033--559065 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
559023 GACTCTGAAC
*
559033 AAATACTACTTTGT
1 AAATCCTACTTTGT
559047 AAATCCTACTTTGT
1 AAATCCTACTTTGT
559061 AAATC
1 AAATC
559066 GTTAGACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (14 bp):
AAATCCTACTTTGT
Found at i:559258 original size:10 final size:10
Alignment explanation
Indices: 559243--559267 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
559233 ATTTAATAAC
559243 TAAACGAACA
1 TAAACGAACA
559253 TAAACGAACA
1 TAAACGAACA
559263 TAAAC
1 TAAAC
559268 TTTGGAGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.08, T:0.12
Consensus pattern (10 bp):
TAAACGAACA
Found at i:560370 original size:14 final size:14
Alignment explanation
Indices: 560353--560384 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
560343 AATGAACATA
560353 AACGAACATAACCG
1 AACGAACATAACCG
560367 AACGAACATAACCG
1 AACGAACATAACCG
560381 AACG
1 AACG
560385 TTCACGAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:562623 original size:3 final size:3
Alignment explanation
Indices: 562590--562675 Score: 100
Period size: 3 Copynumber: 27.7 Consensus size: 3
562580 CCGGGTTTTG
* * * *
562590 TAA TAT TAA TAAA TAAA TAA TATA TAT TAA TAA TAA TAA TTA TTA TAA
1 TAA TAA TAA T-AA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
562638 TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
562676 TAAATAAAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
3 63 0.86
4 10 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:563139 original size:113 final size:112
Alignment explanation
Indices: 562904--565261 Score: 3722
Period size: 113 Copynumber: 21.0 Consensus size: 112
562894 TAGAGTCATT
** * *
562904 CAAAAGGTTGAACAAGCTCTTTTCA-TAGTGAACTTCTTC-T--TT-TTCAGATTAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTA-TGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* * * *
562964 ATTATGAACTTC-TCTGGGAAAA-CTGACCCATCAAGTGATGGATTTGAG
65 ATTATGAAC-TCATCT-GGAAAAGATAATCCATCAAGTGATAGATTTGAG
563012 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*
563077 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
563125 CAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* *
563190 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAA
66 TTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
563238 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
563303 TTATGAACTTC-TCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAAC-TCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
563350 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
563415 TTATGAACTTC-TCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAAC-TCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
563462 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* *
563527 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAA
66 TTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
563575 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
563640 TTATGAACTC-TCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
563686 CAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* * *
563751 TTATGAACTCGAACTGGAAAAGCTAATCTATCAAGTGATAGATTTGAG
66 TTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
563799 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*
563864 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
563912 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
563977 TTATGAACTTC-TCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAAC-TCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
564024 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAG-TTCTTCTC
* *
564089 ATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAA
65 ATTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
564138 C-AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
564202 TTATGAACTTC-TCTGG-AAA-ATAATCCATCAAGTGATAGATTTGAG
66 TTATGAAC-TCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
* *
564247 CAAAAGGTTGAACAAA-T-TTCTCGTTATGAACTTCTTCATCCTTCTTTAAGTAATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAG--ATGAGTTCTTC
* ***
564310 TCATTATGAACTCTACCTGGAAATTTTAATCCATCAAGTGATAGATTTGAG
63 TCATTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
564361 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* * *
564426 TTATGAACTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAAC-TCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
564474 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 C-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
*
564539 ATTATGAACTCGAACTGG-AAAGATAATCCATCAAGTGAGTAGA-TTGA-
65 ATTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGA-TAGATTTGAG
564586 C-AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
564650 TTATGAACTTC-TCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAAC-TCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
* *
564697 CAAAAGGTTGAACAAATTCTTCTCGTTATGAACTTCTTCATCCTTCTTTAAGTAATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAG--ATGAGTTCTTC
* ***
564762 TCATTATGAACTCTACCTGGAAATTTTAATCCATCAAGTGATAGATTTGAG
63 TCATTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
564813 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-TTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* * *
564877 TTATGAACTTCTTCTGG-AAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAAC-TCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
* *
564924 CAAAAGGTTGAAC-AATTCTTCTCATTATGAAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATG-AACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* * *
564988 ATTATGAACTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
65 ATTATGAAC-TCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
* *
565037 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
1 C-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* * *
565102 ATTATGAACTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
65 ATTATGAAC-TCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
* *
565151 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
1 C-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* *
565216 ATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTT
65 ATTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTT
565262 AAATCTTTGC
Statistics
Matches: 2133, Mismatches: 68, Indels: 92
0.93 0.03 0.04
Matches are distributed among these distances:
108 59 0.03
109 42 0.02
110 129 0.06
111 207 0.10
112 456 0.21
113 729 0.34
114 363 0.17
115 47 0.02
116 101 0.05
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (112 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
Found at i:563535 original size:224 final size:225
Alignment explanation
Indices: 562904--565261 Score: 3764
Period size: 224 Copynumber: 10.5 Consensus size: 225
562894 TAGAGTCATT
** * *
562904 CAAAAGGTTGAACAAGCTCTTTTCA-TAGTGAACTTCTTC-T--TT-TTCAGATTAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTA-TGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* * * *
562964 ATTATGAACTTC-TCTGGGAAAA-CTGACCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAA
65 ATTATGAAC-TCATCT-GGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAA
*
563027 ATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCGAAC
128 ATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC-ATC
563091 TGGAAAAGATAATCCATCAAGTGATAGATTTGAG
192 TGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
563125 CAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* *
563190 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAACAAAAGGTTGAACAAAT
66 TTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAAT
563255 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC-TCTGG
130 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCATCTGG
563319 AAAAGATAATCCATCAAGTGATAGATTTGAG
195 AAAAGATAATCCATCAAGTGATAGATTTGAG
563350 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
563415 TTATGAACTTC-TCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAAC-TCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAAT
*
563479 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCGAACTG
130 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC-ATCTG
*
563543 GAAAAGATAATCCATCAAGTGATAGATTTGAA
194 GAAAAGATAATCCATCAAGTGATAGATTTGAG
563575 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*
563640 TTATGAACTC-TCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTAAACAAATT
66 TTATGAACTCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
*
563704 CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCGAACTGG
131 CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC-ATCTGG
* *
563768 AAAAGCTAATCTATCAAGTGATAGATTTGAG
195 AAAAGATAATCCATCAAGTGATAGATTTGAG
563799 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*
563864 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAAT
563929 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC-TCTGG
130 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCATCTGG
563993 AAAAGATAATCCATCAAGTGATAGATTTGAG
195 AAAAGATAATCCATCAAGTGATAGATTTGAG
564024 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAG-TTCTTCTC
* *
564089 ATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAAC-AAAGGTTGAACAAA
65 ATTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
564153 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC-TCTG
129 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCATCTG
564217 G-AAA-ATAATCCATCAAGTGATAGATTTGAG
194 GAAAAGATAATCCATCAAGTGATAGATTTGAG
* *
564247 CAAAAGGTTGAACAAA-T-TTCTCGTTATGAACTTCTTCATCCTTCTTTAAGTAATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAG--ATGAGTTCTTC
* ***
564310 TCATTATGAACTCTACCTGGAAATTTTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACA
63 TCATTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACA
* *
564375 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTC
127 AATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCATC
* *
564440 TGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
192 TGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
564474 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 C-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
*
564539 ATTATGAACTCGAACTGG-AAAGATAATCCATCAAGTGAGTAGA-TTGA-C-AAAGGTTGAACAA
65 ATTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGA-TAGATTTGAGCAAAAGGTTGAACAA
564600 ATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC-TCT
128 ATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCATCT
564664 GGAAAAGATAATCCATCAAGTGATAGATTTGAG
193 GGAAAAGATAATCCATCAAGTGATAGATTTGAG
* *
564697 CAAAAGGTTGAACAAATTCTTCTCGTTATGAACTTCTTCATCCTTCTTTAAGTAATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAG--ATGAGTTCTTC
* ***
564762 TCATTATGAACTCTACCTGGAAATTTTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACA
63 TCATTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACA
* *
564827 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-TTCTTCTCATTATGAACTTCTTC
127 AATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCATC
* *
564891 TGG-AAAGCTAATCCATCAAGTGATGGATTTGAG
192 TGGAAAAGATAATCCATCAAGTGATAGATTTGAG
* *
564924 CAAAAGGTTGAAC-AATTCTTCTCATTATGAAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATG-AACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* * *
564988 ATTATGAACTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGGTTGAACAA
65 ATTATGAAC-TCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGC-AAAAGGTTGAACAA
* * *
565053 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTTCTTCT
128 ATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCATCT
* *
565118 GGAAAAGCTAATCCATCAAGTGATGGATTTGAG
193 GGAAAAGATAATCCATCAAGTGATAGATTTGAG
* *
565151 CAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
1 C-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* *
565216 ATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTT
65 ATTATGAACTC-ATCTGGAAAAGATAATCCATCAAGTGATAGATTT
565262 AAATCTTTGC
Statistics
Matches: 2021, Mismatches: 73, Indels: 79
0.93 0.03 0.04
Matches are distributed among these distances:
221 58 0.03
222 51 0.03
223 135 0.07
224 540 0.27
225 509 0.25
226 352 0.17
227 172 0.09
228 158 0.08
229 21 0.01
230 25 0.01
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (225 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCATCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCATCTGGA
AAAGATAATCCATCAAGTGATAGATTTGAG
Found at i:563562 original size:337 final size:337
Alignment explanation
Indices: 562904--565261 Score: 3837
Period size: 337 Copynumber: 7.0 Consensus size: 337
562894 TAGAGTCATT
** * *
562904 CAAAAGGTTGAACAAGCTCTTTTCA-TAGTGAACTTCTTC-T--TT-TTCAGATTAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTA-TGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* * * *
562964 ATTATGAACTTCTCTGGGAAAA-CTGACCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
65 ATTATGAACTTCTCT-GGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
*
563028 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
129 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC-ATCTG
*
563093 GAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTAAACAAATTCTTCTCATTATGAAC
193 GAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
563158 TTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCA
258 TTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCA
563223 AGTGATAGATTTGAA
323 AGTGATAGATTTGAA
563238 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
563303 TTATGAACTTCTCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
563368 CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC-TCTGGA
131 CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCATCTGGA
563432 AAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
195 AAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
563497 CTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAG
260 CTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAG
563562 TGATAGATTTGAA
325 TGATAGATTTGAA
563575 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*
563640 TTATGAAC-TCTCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTAAACAAATT
66 TTATGAACTTCTCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
*
563704 CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
131 CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC-ATCTGGA
* *
563769 AAAGCTAATCTATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
195 AAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
563834 CTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAG
260 CTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAG
*
563899 TGATAGATTTGAG
325 TGATAGATTTGAA
563912 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
563977 TTATGAACTTCTCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
*
564042 CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTTCTTCTCATTATGAACTCGAACTGG
131 CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAG-TTCTTCTCATTATGAACTC-ATCTGG
*
564107 AAAAGATAATCCATCAAGTGATAGATTTGAAC-AAAGGTTGAACAAATTCTTCTCATTATGAACT
194 AAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
*
564171 TCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC--TCTGG-AAA-ATAATCCATCA
259 TCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCGAACTGGAAAAGATAATCCATCA
*
564232 AGTGATAGATTTGAG
323 AGTGATAGATTTGAA
* *
564247 CAAAAGGTTGAACAAA-T-TTCTCGTTATGAACTTCTTCATCCTTCTTTAAGTAATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAG--ATGAGTTCTTC
***
564310 TCATTATGAAC-TCTACCTGGAAATTTTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAAC
63 TCATTATGAACTTCT--CTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAAC
* *
564374 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTT
126 AAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCAT
* *
564439 CTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGGTTGAACAAATTCTTCTCATTAT
190 CTGGAAAAGATAATCCATCAAGTGATAGATTTGAGC-AAAAGGTTGAACAAATTCTTCTCATTAT
*
564504 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG-AAAGATAATCC
254 GAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCC
564568 ATCAAGTGAGTAGA-TTG-A
319 ATCAAGTGA-TAGATTTGAA
564586 C-AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
564650 TTATGAACTTCTCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
* * *
564715 CTTCTCGTTATGAACTTCTTCATCCTTCTTTAAGTAATGAGTTCTTCTCATTATGAACTCTACCT
131 CTTCTCATTATGAACTTCTTCATCCTTC-TTCAG--ATGAGTTCTTCTCATTATGAACTC-ATCT
***
564780 GGAAATTTTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
192 GGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
* ** *
564845 CTTCTTCTTCCTTCTTCAGATGA-TTCTTCTCATTATGAACTTC-TTCTGG-AAAGCTAATCCAT
257 CTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCGAACTGGAAAAGATAATCCAT
* *
564907 CAAGTGATGGATTTGAG
321 CAAGTGATAGATTTGAA
* *
564924 CAAAAGGTTGAAC-AATTCTTCTCATTATGAAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATG-AACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* *
564988 ATTATGAACTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGGTTGAACAA
65 ATTATGAACTTC-TCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGC-AAAAGGTTGAACAA
* * *
565053 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTTCTTCT
128 ATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCATCT
* *
565118 GGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGGTTGAACAAATTCTTCTCATTATGA
192 GGAAAAGATAATCCATCAAGTGATAGATTTGAGC-AAAAGGTTGAACAAATTCTTCTCATTATGA
* *
565183 ACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCAT
256 ACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCAT
*
565248 CAAGTGATGGATTT
321 CAAGTGATAGATTT
565262 AAATCTTTGC
Statistics
Matches: 1911, Mismatches: 70, Indels: 79
0.93 0.03 0.04
Matches are distributed among these distances:
333 26 0.01
334 38 0.02
335 50 0.03
336 264 0.14
337 610 0.32
338 506 0.26
339 239 0.13
340 105 0.05
341 73 0.04
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (337 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCTCTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCATCTGGAA
AAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
TTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGT
GATAGATTTGAA
Found at i:565988 original size:63 final size:63
Alignment explanation
Indices: 565889--566011 Score: 237
Period size: 63 Copynumber: 2.0 Consensus size: 63
565879 GGAAAAGGAA
565889 GAAGCAGAGGAAACTTGAAAAGAAGCTTATTAATGAAGATGATCATGCAGTTCATCTTTCGTT
1 GAAGCAGAGGAAACTTGAAAAGAAGCTTATTAATGAAGATGATCATGCAGTTCATCTTTCGTT
*
565952 GAAGCAGAGGAAACTTGAAAAGAAGTTTATTAATGAAGATGATCATGCAGTTCATCTTTC
1 GAAGCAGAGGAAACTTGAAAAGAAGCTTATTAATGAAGATGATCATGCAGTTCATCTTTC
566012 AATTCCAACG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.28
Consensus pattern (63 bp):
GAAGCAGAGGAAACTTGAAAAGAAGCTTATTAATGAAGATGATCATGCAGTTCATCTTTCGTT
Found at i:566774 original size:83 final size:83
Alignment explanation
Indices: 566153--566740 Score: 1054
Period size: 83 Copynumber: 7.1 Consensus size: 83
566143 TTGGGGTTCA
*
566153 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGGGCACT-TT-CATCT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTA-TGAGCA-TATTAC-TC-
* * *
566216 TTCCAAATTCAATAACTAGTTT
62 TTCCAAATTCAATGATTGGTTT
*
566238 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTACTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCC
566303 AAATTCAATGATTGGTTT
66 AAATTCAATGATTGGTTT
* *
566321 TGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTACTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCC
566386 AAATTCAATGATTGGTTT
66 AAATTCAATGATTGGTTT
*
566404 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTACTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCC
566469 AAATTCAATGATTGGTTT
66 AAATTCAATGATTGGTTT
566487 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCC
566552 AAATTCAATGATTGGTTT
66 AAATTCAATGATTGGTTT
566570 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCC
566635 AAATTCAATGATTGGTTT
66 AAATTCAATGATTGGTTT
566653 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCC
566718 AAATTCAATGATTGGTTT
66 AAATTCAATGATTGGTTT
566736 TACCA
1 TACCA
566741 TATACTTCCA
Statistics
Matches: 493, Mismatches: 8, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
83 437 0.89
84 9 0.02
85 47 0.10
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (83 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCC
AAATTCAATGATTGGTTT
Found at i:566774 original size:115 final size:116
Alignment explanation
Indices: 566630--566856 Score: 438
Period size: 115 Copynumber: 2.0 Consensus size: 116
566620 GCATATTACT
566630 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
1 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
566695 TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGG-TTTTACCATATA
66 TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTTACCATATA
*
566745 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAACGAACACTTCCAAAAGA
1 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
566810 TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTTACCA
66 TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTTACCA
566857 ACCAGATCAG
Statistics
Matches: 110, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
115 102 0.93
116 8 0.07
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (116 bp):
CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTTACCATATA
Found at i:566839 original size:83 final size:83
Alignment explanation
Indices: 566745--566986 Score: 450
Period size: 83 Copynumber: 2.9 Consensus size: 83
566735 TTACCATATA
*
566745 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAACGAACACTTCCAAAAGA
1 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
566810 TGCTATGAGCATATTACT
66 TGCTATGAGCATATTACT
*
566828 CTTCCAAATTCAATGATTGGTTTTTACC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 CTTCCAAATTCAATGATTGG-TTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAG
566892 ATGCTATGAGCATATTACT
65 ATGCTATGAGCATATTACT
566911 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
1 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
566976 TGCTATGAGCA
66 TGCTATGAGCA
566987 CATTCATCTG
Statistics
Matches: 154, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
82 7 0.05
83 140 0.91
84 7 0.05
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (83 bp):
CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
TGCTATGAGCATATTACT
Found at i:566885 original size:198 final size:198
Alignment explanation
Indices: 566547--566938 Score: 750
Period size: 198 Copynumber: 2.0 Consensus size: 198
566537 GCATATTACT
566547 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
1 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
566612 TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCA
66 TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCA
566677 AAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCAT
131 AAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCAT
566742 ATA
196 ATA
*
566745 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAACGAACACTTCCAAAAGA
1 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
566810 TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTTACC-AACCAGATCAGATAACTC
66 TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGG-TTTTACCAAACCAGATCAGATAACTC
*
566874 AAAGAACACTTCCAGAAGATGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCA
130 AAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCA
566939 AACCAGATCA
Statistics
Matches: 191, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
198 184 0.96
199 7 0.04
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (198 bp):
CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCA
AAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCAT
ATA
Found at i:566967 original size:281 final size:281
Alignment explanation
Indices: 566464--566986 Score: 1012
Period size: 281 Copynumber: 1.9 Consensus size: 281
566454 GCATATTACT
566464 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
1 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
566529 TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCA
66 TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCA
566594 AAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCAA
131 AAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCAA
566659 ACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCCAAATTC
196 ACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCCAAATTC
566724 AATGATTGGTTTTACCATATA
261 AATGATTGGTTTTACCATATA
*
566745 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAACGAACACTTCCAAAAGA
1 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
566810 TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTTACC-AACCAGATCAGATAACTC
66 TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGG-TTTTACCAAACCAGATCAGATAACTC
*
566874 AAAGAACACTTCCAGAAGATGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCA
130 AAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCA
566939 AACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCA
195 AACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCA
566987 CATTCATCTG
Statistics
Matches: 239, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
281 232 0.97
282 7 0.03
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (281 bp):
CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGA
TGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCA
AAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCCAAATTCAATGATTGGTTTTACCAA
ACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCATATTACTCTTCCAAATTC
AATGATTGGTTTTACCATATA
Found at i:569037 original size:11 final size:11
Alignment explanation
Indices: 569020--569073 Score: 76
Period size: 11 Copynumber: 5.0 Consensus size: 11
569010 CAATTTCTCC
*
569020 CTTTTTT-TTC
1 CTTTTTTCTTT
569030 CTTTTTT-TTT
1 CTTTTTTCTTT
569040 CTTTCTTTCTTT
1 CTTT-TTTCTTT
569052 CTTTTTTCTTT
1 CTTTTTTCTTT
569063 CTTTTTTCTTT
1 CTTTTTTCTTT
569074 TTGTTGTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
10 13 0.32
11 21 0.51
12 7 0.17
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:569044 original size:15 final size:14
Alignment explanation
Indices: 569020--569089 Score: 70
Period size: 15 Copynumber: 4.8 Consensus size: 14
569010 CAATTTCTCC
*
569020 CTTTTTTTTCCTTT
1 CTTTTTTTTTCTTT
569034 -TTTTTTCTTTCTTT
1 CTTTTTT-TTTCTTT
569048 CTTTCTTTTTTCTTT
1 CTTT-TTTTTTCTTT
*
569063 CTTTTTTCTTTTTGTT
1 CTTTTTT-TTTCT-TT
*
569079 GTTTTTTTTTC
1 CTTTTTTTTTC
569090 AAATATAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
13 6 0.13
14 9 0.19
15 21 0.45
16 11 0.23
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (14 bp):
CTTTTTTTTTCTTT
Found at i:569056 original size:19 final size:19
Alignment explanation
Indices: 569030--569075 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
569020 CTTTTTTTTC
569030 CTTT-TTTTTTCTTTCTTT
1 CTTTCTTTTTTCTTTCTTT
569048 CTTTCTTTTTTCTTTCTTT
1 CTTTCTTTTTTCTTTCTTT
569067 -TTTCTTTTT
1 CTTTCTTTTT
569076 GTTGTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
CTTTCTTTTTTCTTTCTTT
Found at i:572596 original size:14 final size:14
Alignment explanation
Indices: 572563--572616 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
572553 TATGACATAA
* *
572563 AAATGCAAAGATGCC
1 AAATGTAAATATG-C
572578 AAATGTAAATATGC
1 AAATGTAAATATGC
* *
572592 AAATGTAAAAATGT
1 AAATGTAAATATGC
572606 AAATGTAAATA
1 AAATGTAAATA
572617 CAAACGTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 23 0.68
15 11 0.32
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (14 bp):
AAATGTAAATATGC
Found at i:576241 original size:3 final size:3
Alignment explanation
Indices: 576208--576287 Score: 79
Period size: 3 Copynumber: 25.7 Consensus size: 3
576198 CCGAGTTTTG
* * * *
576208 TAA TAT TAA TAAA TAAA TAA TATA TAT TAA TAA TAA TAA TTA TTA TAA
1 TAA TAA TAA T-AA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* *
576256 TTA TAA TAA TTA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
576288 TAAATAAAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
3 55 0.85
4 10 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:584096 original size:12 final size:12
Alignment explanation
Indices: 584079--584183 Score: 111
Period size: 12 Copynumber: 8.8 Consensus size: 12
584069 GGAGATATTC
584079 GAAATCAGAACA
1 GAAATCAGAACA
*
584091 GAAATCAGAGCA
1 GAAATCAGAACA
*
584103 GAAATCATAACA
1 GAAATCAGAACA
* *
584115 GAATTCAGAGCA
1 GAAATCAGAACA
* *
584127 TAAATTAGAACA
1 GAAATCAGAACA
* * *
584139 GAATTCAGAGCG
1 GAAATCAGAACA
*
584151 GAAATCATAACA
1 GAAATCAGAACA
*
584163 GAATTCAGAACA
1 GAAATCAGAACA
584175 GAAATCAGA
1 GAAATCAGA
584184 TAAAATATTC
Statistics
Matches: 71, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 71 1.00
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.15
Consensus pattern (12 bp):
GAAATCAGAACA
Found at i:584106 original size:24 final size:24
Alignment explanation
Indices: 584079--584183 Score: 147
Period size: 24 Copynumber: 4.4 Consensus size: 24
584069 GGAGATATTC
*
584079 GAAATCAGAACAGAAATCAGAGCA
1 GAAATCAGAACAGAATTCAGAGCA
*
584103 GAAATCATAACAGAATTCAGAGCA
1 GAAATCAGAACAGAATTCAGAGCA
* * *
584127 TAAATTAGAACAGAATTCAGAGCG
1 GAAATCAGAACAGAATTCAGAGCA
* *
584151 GAAATCATAACAGAATTCAGAACA
1 GAAATCAGAACAGAATTCAGAGCA
584175 GAAATCAGA
1 GAAATCAGA
584184 TAAAATATTC
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.15
Consensus pattern (24 bp):
GAAATCAGAACAGAATTCAGAGCA
Found at i:584156 original size:48 final size:48
Alignment explanation
Indices: 584080--584183 Score: 163
Period size: 48 Copynumber: 2.2 Consensus size: 48
584070 GAGATATTCG
584080 AAATCAGAACAGAAATCAGAGCAGAAATCATAACAGAATTCAGAGCAT
1 AAATCAGAACAGAAATCAGAGCAGAAATCATAACAGAATTCAGAGCAT
* * * * *
584128 AAATTAGAACAGAATTCAGAGCGGAAATCATAACAGAATTCAGAACAG
1 AAATCAGAACAGAAATCAGAGCAGAAATCATAACAGAATTCAGAGCAT
584176 AAATCAGA
1 AAATCAGA
584184 TAAAATATTC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.52, C:0.15, G:0.17, T:0.15
Consensus pattern (48 bp):
AAATCAGAACAGAAATCAGAGCAGAAATCATAACAGAATTCAGAGCAT
Found at i:585760 original size:18 final size:18
Alignment explanation
Indices: 585737--585780 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
585727 CAAAGTCAAC
585737 GGTCAACGGGTCGAGTCG
1 GGTCAACGGGTCGAGTCG
585755 GGTCAACGGGTCGAGTCG
1 GGTCAACGGGTCGAGTCG
585773 GGTCAACG
1 GGTCAACG
585781 AGTCAGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.23, G:0.43, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGAGTCG
Found at i:589636 original size:20 final size:21
Alignment explanation
Indices: 589603--589642 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
589593 ACTAAATGAT
589603 ATTACTAATAAAATT-AAAAG
1 ATTACTAATAAAATTGAAAAG
* *
589623 ATTACTAGTTAAATTGAAAA
1 ATTACTAATAAAATTGAAAA
589643 CTCTCAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
ATTACTAATAAAATTGAAAAG
Found at i:594519 original size:225 final size:225
Alignment explanation
Indices: 594244--594667 Score: 679
Period size: 225 Copynumber: 1.9 Consensus size: 225
594234 ACTGTATATA
* ** *
594244 ATGTAACTTTGTACGTATAAATATGTATGTAACTTAGTGTGCACGTCTTTGGATGTCCTATGTGT
1 ATGTAACTATGTACGTATAAATATGTATACAACTTAGTGTGCACGTCTTTGGATGTCCTATGCGT
* *
594309 ATGCAAGGACTAGTTAGATTGTCTTTCTCGATTATTCAATCCGATTTACGGTTTTCA-TATTTAT
66 ATGCAAGGACTAGTTAGATTGTCTTTCTCGATTATTCAATCCGATTTAAGGCTTT-AGTATTTAT
* * *
594373 ATCTGCTCATGTAGCTGTATGGTACCTTGTGTTTGAAGAAATTCCATATTGAAGATAGTTAACTC
130 ATCTGCTCATGTAGCTGTATGGTACCTTGTGTTTGAACAAATTCCATAGTGAAGATAGTTAACTA
594438 TGTGATGTATTCTTTATAGATATGTGTGTGT
195 TGTGATGTATTCTTTATAGATATGTGTGTGT
* *
594469 ATGTAACTATGTATGTATAAATATGTATACAACTTAGTGTGCATGTCTTTGGATGTCCTATGCGT
1 ATGTAACTATGTACGTATAAATATGTATACAACTTAGTGTGCACGTCTTTGGATGTCCTATGCGT
** *
594534 ATGTGAGGACTAGTTAGATTGTCTTTCTCGATTATTCAGTCCGATTTAAGGCTTTAGTATTTATA
66 ATGCAAGGACTAGTTAGATTGTCTTTCTCGATTATTCAATCCGATTTAAGGCTTTAGTATTTATA
* * *
594599 TTTGCTCATGTGGCTGTATGGTACCTTGTGTTTGAACAAATTCCTTAGTGAAGATAGTTAACTAT
131 TCTGCTCATGTAGCTGTATGGTACCTTGTGTTTGAACAAATTCCATAGTGAAGATAGTTAACTAT
594664 GTGA
196 GTGA
594668 ATGGACAATT
Statistics
Matches: 181, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
224 1 0.01
225 180 0.99
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.42
Consensus pattern (225 bp):
ATGTAACTATGTACGTATAAATATGTATACAACTTAGTGTGCACGTCTTTGGATGTCCTATGCGT
ATGCAAGGACTAGTTAGATTGTCTTTCTCGATTATTCAATCCGATTTAAGGCTTTAGTATTTATA
TCTGCTCATGTAGCTGTATGGTACCTTGTGTTTGAACAAATTCCATAGTGAAGATAGTTAACTAT
GTGATGTATTCTTTATAGATATGTGTGTGT
Found at i:600034 original size:20 final size:20
Alignment explanation
Indices: 600011--600142 Score: 113
Period size: 20 Copynumber: 6.5 Consensus size: 20
600001 CTCAGTTTCC
*
600011 AAAATCGCAGCGTGAATAGT
1 AAAATCGCAACGTGAATAGT
*
600031 AAAATCGCAACGTAAATAGT
1 AAAATCGCAACGTGAATAGT
* * * *
600051 AAAATCACAACGCGAATTGA
1 AAAATCGCAACGTGAATAGT
* *
600071 AAAATCGCAACGTGAATTTGG
1 AAAATCGCAACGTGAA-TAGT
* * *
600092 AAAATCGCAACGCGAATTGG
1 AAAATCGCAACGTGAATAGT
* *
600112 AAAATCGTAACGCGAATTTAG-
1 AAAATCGCAACGTGAA--TAGT
600133 AAAATCGCAA
1 AAAATCGCAA
600143 AATCGCGTTG
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
20 66 0.69
21 27 0.28
22 2 0.02
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGTGAATAGT
Found at i:600105 original size:41 final size:41
Alignment explanation
Indices: 600011--600142 Score: 149
Period size: 41 Copynumber: 3.2 Consensus size: 41
600001 CTCAGTTTCC
* * * * * * *
600011 AAAATCGCAGCGTGAATAGTAAAATCGCAACGT-AAATAGT
1 AAAATCGCAACGCGAATTGAAAAATCGCAACGTGAATTTGG
*
600051 AAAATCACAACGCGAATTGAAAAATCGCAACGTGAATTTGG
1 AAAATCGCAACGCGAATTGAAAAATCGCAACGTGAATTTGG
* * * *
600092 AAAATCGCAACGCGAATTGGAAAATCGTAACGCGAATTTAG
1 AAAATCGCAACGCGAATTGAAAAATCGCAACGTGAATTTGG
600133 AAAATCGCAA
1 AAAATCGCAA
600143 AATCGCGTTG
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 28 0.36
41 50 0.64
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGAATTGAAAAATCGCAACGTGAATTTGG
Found at i:600116 original size:61 final size:61
Alignment explanation
Indices: 600011--600142 Score: 158
Period size: 61 Copynumber: 2.2 Consensus size: 61
600001 CTCAGTTTCC
* * * *
600011 AAAATCGCAGCGTGAATAGTAAAATCGCAACGTAAATAGTAAAATCACAACGCGAATTGA-
1 AAAATCGCAACGTGAATAGGAAAATCGCAACGCAAATAGGAAAATCACAACGCGAATTGAG
* * * ** *
600071 AAAATCGCAACGTGAATTTGGAAAATCGCAACGCGAATTGGAAAATCGTAACGCGAATTTAG
1 AAAATCGCAACGTGAA-TAGGAAAATCGCAACGCAAATAGGAAAATCACAACGCGAATTGAG
600133 AAAATCGCAA
1 AAAATCGCAA
600143 AATCGCGTTG
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 15 0.25
61 35 0.58
62 10 0.17
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.19
Consensus pattern (61 bp):
AAAATCGCAACGTGAATAGGAAAATCGCAACGCAAATAGGAAAATCACAACGCGAATTGAG
Found at i:600526 original size:21 final size:20
Alignment explanation
Indices: 600492--600560 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
600482 CATATAGATT
600492 CGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
600512 CGTTGCGATTTTTACTATTCA
1 CGTTGCGA-TTTTACTATTCA
* * *
600533 CATTGCGAATTTGACTA-TCG
1 CGTTGCG-ATTTTACTATTCA
600553 CGTTGCGA
1 CGTTGCGA
600561 ATTTGACTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
19 1 0.02
20 16 0.37
21 25 0.58
22 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTTTACTATTCA
Found at i:600561 original size:20 final size:21
Alignment explanation
Indices: 600492--600665 Score: 143
Period size: 20 Copynumber: 8.6 Consensus size: 21
600482 CATATAGATT
* *
600492 CGTTGCG-ATTTTACTATTCA
1 CGTTGCGAATTTGACTATTCG
* * *
600512 CGTTGCGATTTTTACTATTCA
1 CGTTGCGAATTTGACTATTCG
*
600533 CATTGCGAATTTGACTA-TCG
1 CGTTGCGAATTTGACTATTCG
*
600553 CGTTGCGAATTTGACT-TTTG
1 CGTTGCGAATTTGACTATTCG
* *
600573 TGTTGCGAGTTTGACTA-TCG
1 CGTTGCGAATTTGACTATTCG
600593 CGTTGCGAATTTGACT-TAT-G
1 CGTTGCGAATTTGACTAT-TCG
* *
600613 TGTTGC-AATTT-ACAAATTCG
1 CGTTGCGAATTTGAC-TATTCG
*
600633 CGTTGCG-ATTT-ACAGATTCG
1 CGTTGCGAATTTGAC-TATTCG
600653 CGTTGCGAATTTG
1 CGTTGCGAATTTG
600666 GAAAATCGCA
Statistics
Matches: 127, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
18 2 0.02
19 6 0.05
20 88 0.69
21 31 0.24
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (21 bp):
CGTTGCGAATTTGACTATTCG
Found at i:600674 original size:21 final size:21
Alignment explanation
Indices: 600650--600767 Score: 71
Period size: 20 Copynumber: 5.8 Consensus size: 21
600640 ATTTACAGAT
600650 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
***
600671 TCGCAACGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
** * ** * *
600692 TCGCAATGTG-ATTTACATAT
1 TCGCGTTGCGAATTTGGAAAA
* *
600712 TCGCGTTGCGAAATTGGAAAC
1 TCGCGTTGCGAATTTGGAAAA
* * **
600733 T-GGGTTGCGAAATTGG-AGT
1 TCGCGTTGCGAATTTGGAAAA
600752 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
600768 ACTTTCGCGT
Statistics
Matches: 73, Mismatches: 22, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
19 2 0.03
20 39 0.53
21 32 0.44
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAAAA
Found at i:604787 original size:20 final size:20
Alignment explanation
Indices: 604764--604841 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 20
604754 AAAACCCCAG
*
604764 GGGGGTATCGATTCCCCT-A
1 GGGGGAATCGATTCCCCTCA
*
604783 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TC--A
*
604806 GGGGGAATCG-GTCCCCTCA
1 GGGGGAATCGATTCCCCTCA
*
604825 TGGGGGTATCGATTCCC
1 -GGGGGAATCGATTCCC
604842 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
19 16 0.33
20 10 0.21
21 6 0.12
22 5 0.10
23 11 0.23
ACGTcount: A:0.17, C:0.27, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTCA
Found at i:604842 original size:20 final size:20
Alignment explanation
Indices: 604764--604843 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 20
604754 AAAACCCCAG
*
604764 GGGGGTATCGATTCCC-C-T
1 GGGGGAATCGATTCCCTCAT
* *
604782 AGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCC-TC-AT
* *
604806 GGGGGAATCGGTCCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
604826 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
604844 TGCACCAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
19 11 0.23
20 19 0.40
21 2 0.04
22 4 0.08
23 12 0.25
ACGTcount: A:0.16, C:0.28, G:0.33, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:612167 original size:17 final size:18
Alignment explanation
Indices: 612140--612180 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
612130 AACACTTATT
612140 TTTATATTAAACCT-AAAA
1 TTTA-ATTAAACCTAAAAA
*
612158 TTTAATTAAACTTAAAAA
1 TTTAATTAAACCTAAAAA
612176 TTTAA
1 TTTAA
612181 ATATATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTAATTAAACCTAAAAA
Found at i:613443 original size:2 final size:2
Alignment explanation
Indices: 613438--613462 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
613428 TATATATATA
613438 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
613463 AATTTGTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:614592 original size:21 final size:21
Alignment explanation
Indices: 614568--614615 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
614558 ATCCAGCATC
614568 AGGCCGTGGACGAGGATTCAG
1 AGGCCGTGGACGAGGATTCAG
614589 AGGCCGTGGACGAGGATTCAG
1 AGGCCGTGGACGAGGATTCAG
614610 AGGCCG
1 AGGCCG
614616 AGGTAGAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.44, T:0.12
Consensus pattern (21 bp):
AGGCCGTGGACGAGGATTCAG
Found at i:618100 original size:2 final size:2
Alignment explanation
Indices: 618093--618157 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
618083 GGCGGTTTAT
618093 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
618135 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
618158 GTGTGTGTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:622887 original size:60 final size:62
Alignment explanation
Indices: 622814--622937 Score: 171
Period size: 66 Copynumber: 2.0 Consensus size: 62
622804 TTTTCTTTTG
*
622814 TAGGTTATGGATC-TTG-TATGTACCCATCTTCTCAAAGGTATTCATGTTTTTCCCTCCATT
1 TAGGTTATGGATCTTTGATATGTACCCATCTTCTCAAAGGTATGCATGTTTTTCCCTCCATT
* *
622874 TAGGTTATGGATCTTGTTTGTATATGTACCCATCTTCTCAATGGTATGCATGTTTTTTCCTCCA
1 TAGGTTATGGATC---TTTG-ATATGTACCCATCTTCTCAAAGGTATGCATGTTTTTCCCTCCA
622938 CCTCTACTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
60 13 0.24
64 3 0.05
66 39 0.71
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.44
Consensus pattern (62 bp):
TAGGTTATGGATCTTTGATATGTACCCATCTTCTCAAAGGTATGCATGTTTTTCCCTCCATT
Found at i:623142 original size:20 final size:20
Alignment explanation
Indices: 623117--623173 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
623107 GTCTCGCAAT
*
623117 GAACCGGCTGAAAATCGCTA
1 GAACCGACTGAAAATCGCTA
623137 GAACCGACTGAAAATCGCTA
1 GAACCGACTGAAAATCGCTA
623157 GAACCGACTGAAAATCG
1 GAACCGACTGAAAATCG
623174 GTAAAACTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.14
Consensus pattern (20 bp):
GAACCGACTGAAAATCGCTA
Found at i:624216 original size:21 final size:19
Alignment explanation
Indices: 624170--624216 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
624160 TAATCATTTT
* *
624170 AAATTTTATTTTTTAATTA
1 AAATATTATTTTTTAAATA
624189 AAA-ATTATTTTTTACTAATA
1 AAATATTATTTTTTA--AATA
624209 AAATATTA
1 AAATATTA
624217 ATACCTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 10 0.43
19 3 0.13
20 6 0.26
21 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATATTATTTTTTAAATA
Found at i:624492 original size:21 final size:22
Alignment explanation
Indices: 624468--624508 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
624458 TTTTAAATAT
*
624468 TGATAAAATATTATT-TTATAA
1 TGATAAAATAATATTATTATAA
*
624489 TGATACAATAATATTATTAT
1 TGATAAAATAATATTATTAT
624509 TAATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (22 bp):
TGATAAAATAATATTATTATAA
Found at i:627621 original size:46 final size:45
Alignment explanation
Indices: 627523--627629 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
627513 GTGCACTAAG
* * *
627523 AGTGCACCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTG
1 AGTGCATCGATACATAAAATGCATTCGATGTTTCAAAATAGCCTA
*
627568 AGTGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-A-CTCTA
1 AGTGCATCGATACATAAAATGCATTCGATG-TTTCA-AAATAGC-CTA
*
627614 AGTGCATCGATGCATA
1 AGTGCATCGATACATA
627630 GTATGTGCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
45 28 0.53
46 22 0.42
47 3 0.06
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (45 bp):
AGTGCATCGATACATAAAATGCATTCGATGTTTCAAAATAGCCTA
Found at i:630406 original size:23 final size:23
Alignment explanation
Indices: 630378--630489 Score: 131
Period size: 23 Copynumber: 5.0 Consensus size: 23
630368 ATGCATGGCC
630378 TTGTGCATCGATGCACATTCAAG
1 TTGTGCATCGATGCACATTCAAG
*
630401 TTGTGCATCGGTGCACATTCAAG
1 TTGTGCATCGATGCACATTCAAG
* *
630424 GTGTGCATCGGTGCACATTCAAG
1 TTGTGCATCGATGCACATTCAAG
* *
630447 GTGTGCATC-AGTGCACTTTC-A-
1 TTGTGCATCGA-TGCACATTCAAG
* *
630468 TGGTGTATCGATGCACATTCAA
1 TTGTGCATCGATGCACATTCAA
630490 AGGGATTCAT
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
21 14 0.18
22 3 0.04
23 61 0.78
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
TTGTGCATCGATGCACATTCAAG
Found at i:630432 original size:46 final size:46
Alignment explanation
Indices: 630379--630489 Score: 163
Period size: 46 Copynumber: 2.5 Consensus size: 46
630369 TGCATGGCCT
* *
630379 TGTGCATCGATGCACATTCAAGTTGTGCATCGGTGCACATTCAAGG
1 TGTGCATCGATGCACATTCAAGGTGTGCATCAGTGCACATTCAAGG
* * *
630425 TGTGCATCGGTGCACATTCAAGGTGTGCATCAGTGCACTTTCATGG
1 TGTGCATCGATGCACATTCAAGGTGTGCATCAGTGCACATTCAAGG
630471 TGT--ATCGATGCACATTCAA
1 TGTGCATCGATGCACATTCAA
630490 AGGGATTCAT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 15 0.25
46 44 0.75
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (46 bp):
TGTGCATCGATGCACATTCAAGGTGTGCATCAGTGCACATTCAAGG
Found at i:635639 original size:18 final size:18
Alignment explanation
Indices: 635616--635658 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
635606 AATTGTGTTC
635616 TTGAAAGCAAAATGAATA
1 TTGAAAGCAAAATGAATA
635634 TTGAAAGCAAAATGAATA
1 TTGAAAGCAAAATGAATA
635652 TTGAAAG
1 TTGAAAG
635659 GAAATTTGGC
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:0.53, C:0.05, G:0.19, T:0.23
Consensus pattern (18 bp):
TTGAAAGCAAAATGAATA
Found at i:636029 original size:64 final size:62
Alignment explanation
Indices: 635953--636160 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 62
635943 TGCACTAAGA
* * *
635953 GTGCATCGATGCATAAAATGCATTCAATGTTTCAAAATAGCCTGAGTGAATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATA-CCTGAGTGCATCGATGCATGG-TG
*
636017 GTGCATCGATGCATGAAATGCATTCGATGTTTTCATAAA-ACTCTGAGTGCATCGATGCATAGTA
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCA-AAATAC-CTGAGTGCATCGATGCATGGT-
*
636081 T
62 G
* * * *
636082 GTGCATCGGTCCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA--AATACC-TGAGTGCATCGATGCATGG--
636145 TG
61 TG
*
636147 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
636161 CACTTTGAAA
Statistics
Matches: 122, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 46 0.38
65 67 0.55
66 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATACCTGAGTGCATCGATGCATGGTG
Found at i:638560 original size:3 final size:3
Alignment explanation
Indices: 638552--638651 Score: 110
Period size: 3 Copynumber: 33.3 Consensus size: 3
638542 TTCCTCACTT
* * * * *
638552 TCA TCA TCA TCA CCA TCA TCA TCA TCA TCC TCG TCG TCA TTA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
* * * * *
638600 TCA TCC TCA TCG TCA TCA TCA TCA TCA TCC TCG TCG TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
638648 TCA T
1 TCA T
638652 TGTAGTCAGG
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:638596 original size:24 final size:24
Alignment explanation
Indices: 638565--638651 Score: 156
Period size: 24 Copynumber: 3.6 Consensus size: 24
638555 TCATCATCAC
638565 CATCATCATCATCATCCTCGTCGT
1 CATCATCATCATCATCCTCGTCGT
* *
638589 CATTATCATCATCATCCTCATCGT
1 CATCATCATCATCATCCTCGTCGT
638613 CATCATCATCATCATCCTCGTCGT
1 CATCATCATCATCATCCTCGTCGT
638637 CATCATCATCATCAT
1 CATCATCATCATCAT
638652 TGTAGTCAGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.24, C:0.36, G:0.06, T:0.34
Consensus pattern (24 bp):
CATCATCATCATCATCCTCGTCGT
Found at i:646725 original size:20 final size:20
Alignment explanation
Indices: 646700--646745 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
646690 ACCTTACTCG
646700 CCCCACCCCGCATCCACCCA
1 CCCCACCCCGCATCCACCCA
* *
646720 CCCCACCCTGCATCCACCCG
1 CCCCACCCCGCATCCACCCA
646740 CCCCAC
1 CCCCAC
646746 TAAATACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.70, G:0.07, T:0.07
Consensus pattern (20 bp):
CCCCACCCCGCATCCACCCA
Found at i:648322 original size:2 final size:2
Alignment explanation
Indices: 648317--648347 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
648307 TTTCTTTCAG
648317 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
648348 AGAAATCGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:651554 original size:23 final size:22
Alignment explanation
Indices: 651500--651568 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
651490 CTTGATTTTA
*
651500 TAATAATTTATTTATTTTTAA-T
1 TAATAATTTATATA-TTTTAACT
651522 ATAATAATTTATATATTTTAACT
1 -TAATAATTTATATATTTTAACT
*
651545 TAATATATTT-TAT-TTTTATCT
1 TAATA-ATTTATATATTTTAACT
651566 TAA
1 TAA
651569 CTTATTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.24
22 14 0.33
23 18 0.43
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (22 bp):
TAATAATTTATATATTTTAACT
Found at i:651642 original size:29 final size:29
Alignment explanation
Indices: 651555--651655 Score: 89
Period size: 29 Copynumber: 3.3 Consensus size: 29
651545 TAATATATTT
651555 TATTTTTA-TCTTAACTTATTAAATATTAAAATA
1 TATTTTTATTCTT-A-TTA-TAAATA--AAAATA
* * *
651588 TATATTTTATTCTTATTTTTATTAAAAATA
1 TAT-TTTTATTCTTATTATAAATAAAAATA
651618 TATTTTTATTCTTA-TATAACATAAAAATA
1 TATTTTTATTCTTATTATAA-ATAAAAATA
*
651647 TATATTTAT
1 TATTTTTAT
651656 CTCATCTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
28 3 0.05
29 27 0.47
30 9 0.16
32 4 0.07
33 5 0.09
34 6 0.10
35 4 0.07
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (29 bp):
TATTTTTATTCTTATTATAAATAAAAATA
Done.