Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008076.1 Hibiscus syriacus cultivar Beakdansim tig00110578_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: 1136582
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:453748 original size:30 final size:30
Alignment explanation
Indices: 453714--453781 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
453704 TTGAATCTAT
453714 CTCTCATCAAAGCACCAGCCTGCCCTGCGC
1 CTCTCATCAAAGCACCAGCCTGCCCTGCGC
453744 CTCTCATCAAAGCACCAGCCTGCCCTGCGC
1 CTCTCATCAAAGCACCAGCCTGCCCTGCGC
453774 CTCTCATC
1 CTCTCATC
453782 GCTCAATCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.19, C:0.47, G:0.15, T:0.19
Consensus pattern (30 bp):
CTCTCATCAAAGCACCAGCCTGCCCTGCGC
Found at i:456961 original size:22 final size:22
Alignment explanation
Indices: 456936--456980 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
456926 TGCTTTACAT
*
456936 CAATTGACGGTACGTGATTTTA
1 CAATTGACGGCACGTGATTTTA
*
456958 CAATTGATGGCACGTGATTTTA
1 CAATTGACGGCACGTGATTTTA
456980 C
1 C
456981 TTTCACAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (22 bp):
CAATTGACGGCACGTGATTTTA
Found at i:460674 original size:13 final size:13
Alignment explanation
Indices: 460653--460687 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
460643 ATAACTACCG
*
460653 AAAAAATTATATG
1 AAAAAATTATATA
*
460666 AACAAATTATATA
1 AAAAAATTATATA
460679 AAAAAATTA
1 AAAAAATTA
460688 AAGAGTTGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (13 bp):
AAAAAATTATATA
Found at i:460941 original size:2 final size:2
Alignment explanation
Indices: 460934--460985 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
460924 GAAAAGGAGC
460934 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
460976 AT AT AT AT AT
1 AT AT AT AT AT
460986 GACTATTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:472195 original size:16 final size:15
Alignment explanation
Indices: 472174--472251 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
472164 CTCAATTATC
472174 AAAATAAAATGAATTA
1 AAAATAAAAT-AATTA
*
472190 AAAATATAATAATTA
1 AAAATAAAATAATTA
** **
472205 AAAATAATTTTTTTA
1 AAAATAAAATAATTA
* *
472220 AAAAT-CAATGA-TA
1 AAAATAAAATAATTA
472233 AAAATAAAATATATTA
1 AAAATAAAATA-ATTA
472249 AAA
1 AAA
472252 TATTTGGTAT
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
13 7 0.15
14 4 0.09
15 21 0.46
16 14 0.30
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (15 bp):
AAAATAAAATAATTA
Found at i:479219 original size:2 final size:2
Alignment explanation
Indices: 479212--479244 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
479202 CTAGTAAGTG
479212 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
479245 TCAAGACGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:482272 original size:14 final size:14
Alignment explanation
Indices: 482236--482262 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
482226 ATTTATTTTT
482236 TAATTATATTTATA
1 TAATTATATTTATA
482250 TAATTATATTTAT
1 TAATTATATTTAT
482263 TATTTAATAT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:483934 original size:7 final size:7
Alignment explanation
Indices: 483922--483951 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
483912 TGCCGACATG
483922 GTTTGCA
1 GTTTGCA
483929 GTTTGCA
1 GTTTGCA
483936 GTTTGCA
1 GTTTGCA
483943 GTTTGCA
1 GTTTGCA
483950 GT
1 GT
483952 CAACAGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.30, T:0.43
Consensus pattern (7 bp):
GTTTGCA
Found at i:488945 original size:28 final size:28
Alignment explanation
Indices: 488913--488972 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
488903 TGGTGTAAGA
488913 ACCATTAATCACATAGACGGTGTTGTCT
1 ACCATTAATCACATAGACGGTGTTGTCT
488941 ACCATTAATCACATAGACGGTGTTGTCT
1 ACCATTAATCACATAGACGGTGTTGTCT
488969 ACCA
1 ACCA
488973 ACTCATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (28 bp):
ACCATTAATCACATAGACGGTGTTGTCT
Found at i:491555 original size:24 final size:24
Alignment explanation
Indices: 491528--491574 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
491518 GTTCGTGAAT
*
491528 GTTCGGTTATGTTCGTTTATGTTC
1 GTTCGGTTATGTTCCTTTATGTTC
491552 GTTCGGTTATGTTCCTTTATGTT
1 GTTCGGTTATGTTCCTTTATGTT
491575 TATTCATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.09, C:0.13, G:0.23, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCCTTTATGTTC
Found at i:491564 original size:34 final size:34
Alignment explanation
Indices: 491504--491574 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
491494 CATAAGTCTC
*
491504 GTTCGTTTATTTACGTTCGTGAATGTTCGGTTAT
1 GTTCGTTTATTTACGTTCGTGAATGTTCCGTTAT
* *
491538 GTTCGTTTATGTT-CGTTCG-GTTATGTTCCTTTAT
1 GTTCGTTTAT-TTACGTTCGTG-AATGTTCCGTTAT
491572 GTT
1 GTT
491575 TATTCATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 1 0.03
34 29 0.91
35 2 0.06
ACGTcount: A:0.11, C:0.13, G:0.23, T:0.54
Consensus pattern (34 bp):
GTTCGTTTATTTACGTTCGTGAATGTTCCGTTAT
Found at i:491585 original size:24 final size:24
Alignment explanation
Indices: 491533--491588 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
491523 TGAATGTTCG
* * *
491533 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCCTTTATGTTCATTCA
*
491557 GTTATGTTCCTTTATGTTTATTCA
1 GTTATGTTCCTTTATGTTCATTCA
*
491581 TTTATGTT
1 GTTATGTT
491589 TAACTTAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.59
Consensus pattern (24 bp):
GTTATGTTCCTTTATGTTCATTCA
Found at i:491721 original size:22 final size:23
Alignment explanation
Indices: 491687--491736 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
491677 TAAAAATATA
491687 TTAAAAATCCTAAACCCTAAAAC
1 TTAAAAATCCTAAACCCTAAAAC
* *
491710 TTAAAACT-CTAAACCCTAAACC
1 TTAAAAATCCTAAACCCTAAAAC
491732 TTAAA
1 TTAAA
491737 CCCTTATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (23 bp):
TTAAAAATCCTAAACCCTAAAAC
Found at i:491768 original size:7 final size:7
Alignment explanation
Indices: 491756--491806 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
491746 TAATTATTAA
491756 AAATCCT
1 AAATCCT
491763 AAATCCT
1 AAATCCT
491770 AAA-CTCT
1 AAATC-CT
*
491777 AAA-CCC
1 AAATCCT
*
491783 AAATCTT
1 AAATCCT
*
491790 AAACCCT
1 AAATCCT
491797 AAATCCT
1 AAATCCT
491804 AAA
1 AAA
491807 CTATAAAACC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
6 5 0.14
7 31 0.86
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (7 bp):
AAATCCT
Found at i:491787 original size:27 final size:27
Alignment explanation
Indices: 491756--491807 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
491746 TAATTATTAA
*
491756 AAATCCTAAATCCTAAA-CTCTAAACCC
1 AAATCCTAAACCCTAAATC-CTAAACCC
*
491783 AAATCTTAAACCCTAAATCCTAAAC
1 AAATCCTAAACCCTAAATCCTAAAC
491808 TATAAAACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (27 bp):
AAATCCTAAACCCTAAATCCTAAACCC
Found at i:491803 original size:34 final size:35
Alignment explanation
Indices: 491760--491833 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
491750 TATTAAAAAT
*
491760 CCTAAATCCTAAACTCT-AAACCCA-AATCTTAAAC
1 CCTAAATCCTAAACTATAAAACCCAGAA-CTTAAAC
*
491794 CCTAAATCCTAAACTATAAAACCTAGAACTTAAAC
1 CCTAAATCCTAAACTATAAAACCCAGAACTTAAAC
491829 CCTAA
1 CCTAA
491834 CCCCTATACC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 16 0.44
35 18 0.50
36 2 0.06
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (35 bp):
CCTAAATCCTAAACTATAAAACCCAGAACTTAAAC
Found at i:491806 original size:14 final size:14
Alignment explanation
Indices: 491756--491807 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
491746 TAATTATTAA
*
491756 AAATCCTAAATCCT
1 AAATCCTAAACCCT
491770 AAA-CTCTAAACCC-
1 AAATC-CTAAACCCT
*
491783 AAATCTTAAACCCT
1 AAATCCTAAACCCT
491797 AAATCCTAAAC
1 AAATCCTAAAC
491808 TATAAAACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 11 0.34
14 21 0.66
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATCCTAAACCCT
Found at i:492998 original size:11 final size:11
Alignment explanation
Indices: 492982--493026 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
492972 CTGGACTGGG
492982 TCAATCGAGCT
1 TCAATCGAGCT
492993 TCAATCGAGC-
1 TCAATCGAGCT
*
493003 TCAAAATTGAGCT
1 TC--AATCGAGCT
493016 TCAATCGAGCT
1 TCAATCGAGCT
493027 CGAGTCAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 2 0.07
11 18 0.62
12 7 0.24
13 2 0.07
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (11 bp):
TCAATCGAGCT
Found at i:493077 original size:16 final size:16
Alignment explanation
Indices: 493056--493088 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
493046 GCTGATGAAA
*
493056 TTTTTTTGAGTTCGAG
1 TTTTTTCGAGTTCGAG
493072 TTTTTTCGAGTTCGAG
1 TTTTTTCGAGTTCGAG
493088 T
1 T
493089 CGAGTTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.24, T:0.55
Consensus pattern (16 bp):
TTTTTTCGAGTTCGAG
Found at i:493295 original size:16 final size:16
Alignment explanation
Indices: 493274--493346 Score: 105
Period size: 16 Copynumber: 4.7 Consensus size: 16
493264 CCAACATTTA
493274 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
493290 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
493306 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
* *
493322 TGTTCGTTTATATTCG
1 TGTTCATTTATGTTCG
493338 T-TT-ATTTAT
1 TGTTCATTTAT
493347 TAAATGAACG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
14 5 0.09
15 2 0.04
16 47 0.87
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.59
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:493427 original size:16 final size:16
Alignment explanation
Indices: 493406--493436 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
493396 CAAAAAAAAT
493406 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
493422 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
493437 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:493427 original size:100 final size:102
Alignment explanation
Indices: 493306--493568 Score: 485
Period size: 100 Copynumber: 2.6 Consensus size: 102
493296 TTTATGTTCG
*
493306 TGTTCGTTTATGTTCGTGTTCGTTTATATTCGTTTATTTATTAAATGAACGAACATGAACAAGTT
1 TGTTCGTTTATGTTCGTGTTCGTTTATGTTCGTTTATTTATTAAATGAACGAACATGAACAAGTT
493371 ATATTCCTTAATAAACGAACATGAAC-AAAAAAAA-T
66 ATATTCCTTAATAAACGAACATGAACAAAAAAAAATT
*
493406 TGTTCGTTTATGTTCGTGTTCGTTTATGTTCATTTATTTATTAAATGAACGAACATGAACAAGTT
1 TGTTCGTTTATGTTCGTGTTCGTTTATGTTCGTTTATTTATTAAATGAACGAACATGAACAAGTT
*
493471 ATATTCCTTAATAAACGAACATGAGCAAAAAAAAATT
66 ATATTCCTTAATAAACGAACATGAACAAAAAAAAATT
493508 TGTTCGTTTATGTTCGTGTTCGTTTATGTTCGTTTATTTATTAAATGAACGAACATGAACA
1 TGTTCGTTTATGTTCGTGTTCGTTTATGTTCGTTTATTTATTAAATGAACGAACATGAACA
493569 TACCTCCGTT
Statistics
Matches: 157, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
100 88 0.56
101 8 0.05
102 61 0.39
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (102 bp):
TGTTCGTTTATGTTCGTGTTCGTTTATGTTCGTTTATTTATTAAATGAACGAACATGAACAAGTT
ATATTCCTTAATAAACGAACATGAACAAAAAAAAATT
Found at i:493529 original size:16 final size:16
Alignment explanation
Indices: 493508--493540 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
493498 AAAAAAAATT
493508 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
493524 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
493540 T
1 T
493541 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:496050 original size:26 final size:26
Alignment explanation
Indices: 495966--496051 Score: 74
Period size: 26 Copynumber: 3.4 Consensus size: 26
495956 TGGTCCTCTG
495966 AATTTTGCTTTGGGTGTAACTATGTC
1 AATTTTGCTTTGGGTGTAACTATGTC
* * *
495992 AACTTTG-TGT-GGTCGT-ACT-T-TT
1 AATTTTGCTTTGGGT-GTAACTATGTC
*
496014 AAGTTCTTGCTTTGGGTATAACTATGTC
1 AA-TT-TTGCTTTGGGTGTAACTATGTC
496042 AATTTTGCTT
1 AATTTTGCTT
496052 GTTTCAACCT
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
22 3 0.07
23 2 0.04
24 9 0.20
25 7 0.16
26 18 0.40
27 3 0.07
28 3 0.07
ACGTcount: A:0.19, C:0.13, G:0.21, T:0.48
Consensus pattern (26 bp):
AATTTTGCTTTGGGTGTAACTATGTC
Found at i:496099 original size:13 final size:13
Alignment explanation
Indices: 496078--496109 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
496068 GCTCCAAATT
*
496078 GGGTGACTTTATG
1 GGGTAACTTTATG
496091 GGGTAACTTTATG
1 GGGTAACTTTATG
496104 GGGTAA
1 GGGTAA
496110 GTTGCGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.38, T:0.34
Consensus pattern (13 bp):
GGGTAACTTTATG
Found at i:496356 original size:546 final size:533
Alignment explanation
Indices: 495337--496412 Score: 1963
Period size: 546 Copynumber: 2.0 Consensus size: 533
495327 ATTTTTGAAC
495337 CGTTTACAATGTTTGTTTTAACATTTTGGAATTTCAGTTTATGTTTTTCTTTTTCATTTTAGGGT
1 CGTTTACAATGTTTGTTTTAACATTTTGGAATTTCAGTTTATGTTTTTCTTTTTCATTTTAGGGT
495402 TATATTTTACTAGCTATATTTTGGTCCTCTGAATTTTGCTTTGGGTGTAACTATGTCAACTTTGT
66 TATATTTTACTAGCTATATTTTGGTCCTCTGAATTTTGCTTTGGGTGTAACTATGTCAACTTTGT
495467 GTGGTCGTACTTTTAAGTTCTTGCTTTGGGTATAACTATGTCAATTTTACTTGTTTCAACCTATT
131 GTGGTCGTACTTTTAAGTTCTTGCTTTGGGTATAACTATGTCAATTTTACTTGTTTCAACCTATT
* *
495532 TTAGCTTCAAATTGGGTGACTTTATGGGGTAAGTTGCGAGTTCTGTTATGGTGATTGTAAGTCAC
196 TTAGCTCCAAATTGGGTGACTTTATGGGGTAAGTTGCGAGTTATGTTATGGTGATTGTAAGTCAC
*
495597 ATTCTGTTATTTTATATAGGTTCATTGTGGTGGTTTACTGGAAGATGTTTAGGTACATTGTATGA
261 ATTCTGTTATTTTATATAGGTTCATTGTGGTGGTTTACTGGAAGATGTTTAAGTACATTGTATGA
* *
495662 TTCTGCTGAGTTTGCTTGTTCTTTTATCGTTGAGTATGTAGTATTTTTTTCTTGATTCTGGACTT
326 TTCTACTGAGTTTGCTTGTTCTTTTATCGCTGAGTATGTAGTATTTTTTTCTTGATTCTGGACTT
*
495727 CTAGTAGGCTAATGGGGAGTTGGGTCTACTTGGTTTGCGTAATTCTTACAATGTCTTGAGTCCAG
391 CTAGTAGGCTAATGGGGAGTTGGGTCTACTTGGTTTGCGTAATTCTTACAATATCTTGAGTCCAG
495792 TGTGCCATGATATTTTTTCCTCAAATGTGTATGTATTCAATCTTATTATACTTTCATCGTTGGTT
456 TGTGCCATGATATTTTTTCCTCAAATGTGTATGTATTCAATCTTATTATACTTTCATCGTTGGTT
495857 AATTTTTAGTCAA
521 AATTTTTAGTCAA
495870 CGTTTACAATGTTTGTTTTAACATTTTGGAATTTCAGTTTATGTTTTTCTTTTTCATTTTAGGGT
1 CGTTTACAATGTTTGTTTTAACATTTTGGAATTTCAGTTTATGTTTTTCTTTTTCATTTTAGGGT
495935 TATATTTTACTAGCTATATTTTGGTCCTCTGAATTTTGCTTTGGGTGTAACTATGTCAACTTTGT
66 TATATTTTACTAGCTATATTTTGGTCCTCTGAATTTTGCTTTGGGTGTAACTATGTCAACTTTGT
*
496000 GTGGTCGTACTTTTAAGTTCTTGCTTTGGGTATAACTATGTCAATTTTGCTTGTTTCAACCTATT
131 GTGGTCGTACTTTTAAGTTCTTGCTTTGGGTATAACTATGTCAATTTTACTTGTTTCAACCTATT
496065 TTAGCTCCAAATTGGGTGACTTTATGGGGTAACTTTATGGGGTAAGTTGCGAGTTATGTTATGGT
196 TTAGCTCCAAATT-GG-G------T---G--ACTTTATGGGGTAAGTTGCGAGTTATGTTATGGT
496130 GATTGTAAGTCACATTCTGTTATTTTATATAGGTTCATTGTGGTGGTTTACTGGAAGATGTTTAA
248 GATTGTAAGTCACATTCTGTTATTTTATATAGGTTCATTGTGGTGGTTTACTGGAAGATGTTTAA
496195 GTACATTGTATGATTCTACTGAGTTTGCTTGTTCTTTTATCGCTGAGTATGTAGTATTTTTTTCT
313 GTACATTGTATGATTCTACTGAGTTTGCTTGTTCTTTTATCGCTGAGTATGTAGTATTTTTTTCT
496260 TGATTCTGGACTTCTAGTAGGCTAATGGGGAGTTGGGTCTACTTGGTTTGCGTAATTCTTACAAT
378 TGATTCTGGACTTCTAGTAGGCTAATGGGGAGTTGGGTCTACTTGGTTTGCGTAATTCTTACAAT
496325 ATCTTGAGTCCAGTGTGCCATGATATTTTTTCCTCAAATGTGTATGTATTCAATCTTATTATACT
443 ATCTTGAGTCCAGTGTGCCATGATATTTTTTCCTCAAATGTGTATGTATTCAATCTTATTATACT
*
496390 TTCATTGTTGGTTAATTTTTAGT
508 TTCATCGTTGGTTAATTTTTAGT
496413 ATATGACTAT
Statistics
Matches: 522, Mismatches: 8, Indels: 13
0.96 0.01 0.02
Matches are distributed among these distances:
533 206 0.39
534 2 0.00
535 1 0.00
541 1 0.00
544 1 0.00
546 311 0.60
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (533 bp):
CGTTTACAATGTTTGTTTTAACATTTTGGAATTTCAGTTTATGTTTTTCTTTTTCATTTTAGGGT
TATATTTTACTAGCTATATTTTGGTCCTCTGAATTTTGCTTTGGGTGTAACTATGTCAACTTTGT
GTGGTCGTACTTTTAAGTTCTTGCTTTGGGTATAACTATGTCAATTTTACTTGTTTCAACCTATT
TTAGCTCCAAATTGGGTGACTTTATGGGGTAAGTTGCGAGTTATGTTATGGTGATTGTAAGTCAC
ATTCTGTTATTTTATATAGGTTCATTGTGGTGGTTTACTGGAAGATGTTTAAGTACATTGTATGA
TTCTACTGAGTTTGCTTGTTCTTTTATCGCTGAGTATGTAGTATTTTTTTCTTGATTCTGGACTT
CTAGTAGGCTAATGGGGAGTTGGGTCTACTTGGTTTGCGTAATTCTTACAATATCTTGAGTCCAG
TGTGCCATGATATTTTTTCCTCAAATGTGTATGTATTCAATCTTATTATACTTTCATCGTTGGTT
AATTTTTAGTCAA
Found at i:502101 original size:2 final size:2
Alignment explanation
Indices: 502094--502122 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
502084 TGTAGTACCA
502094 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 A
502123 GCTTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:506202 original size:51 final size:51
Alignment explanation
Indices: 506025--506604 Score: 651
Period size: 51 Copynumber: 11.1 Consensus size: 51
506015 AAACTTCATA
* * * * *
506025 AAACGTGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATA
1 AAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGAC-T---CAATCTTCAA-C
* * * * *
506081 AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAAT
1 AAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAAC
*
506136 AAACAG-GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAAC
1 AAAC-GTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
* * * * * * *
506187 AAACGTGTTCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGATCTTCAATA
1 AAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAA-C
* * * * *
506239 AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAAT
1 AAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAAC
506294 AAACAG-GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
1 AAAC-GTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
* * * *
506345 GAACTTGTCCGCTCCCTATTCTTTCAGAGAGTACAGGACTCAATCTTCAAC
1 AAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
* * *
506396 GAACTTGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAAC
1 AAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
* * * *
506447 GAACTTGTCCGCTCCCTATTCATTCAGAGAGTATGGGACTCAAACTTCAAC
1 AAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
* *
506498 GAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
1 AAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
* * *
506549 GAACTTGTCCGCTCCCTATTCATTCAGAGAGTATATGACTCAATCTTCAAC
1 AAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
506600 AAACG
1 AAACG
506605 AATTTGCTTC
Statistics
Matches: 468, Mismatches: 43, Indels: 31
0.86 0.08 0.06
Matches are distributed among these distances:
50 1 0.00
51 306 0.65
52 36 0.08
55 73 0.16
56 52 0.11
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (51 bp):
AAACGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
Found at i:506258 original size:158 final size:157
Alignment explanation
Indices: 506030--506583 Score: 720
Period size: 158 Copynumber: 3.5 Consensus size: 157
506020 TCATAAAACG
* * * *
506030 TGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCCGCTC
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGAC-T---CAATCTTCAA-AAAACGGGTCCGCTC
* *
506095 TCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCCTATTCTTT
61 CCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCCTATTCATT
* *
506160 CAGAGAGTATAGGACTCAATCTTCAACAAACG
126 CAGAGAGTATAGGACTCAATCTTCAACGAACT
* * * * * * *
506192 TGTTCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGATCTTCAATAAAACGGGTCCGCTCTCTA
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAA-AAAACGGGTCCGCTCCCTA
506257 TTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCCTATTCATTCAGA
65 TTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCCTATTCATTCAGA
506322 GAGTATAGGACTCAATCTTCAACGAACT
130 GAGTATAGGACTCAATCTTCAACGAACT
* * ** **
506350 TGTCCGCTCCCTATTCTTTCAGAGAGTACAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTAT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAAAAACGGGTCCGCTCCCTAT
* * ** **
506415 TCTTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAG
66 TCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCCTATTCATTCAGAG
* *
506476 AGTATGGGACTCAAACTTCAACGAACT
131 AGTATAGGACTCAATCTTCAACGAACT
** **
506503 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTAT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAAAAACGGGTCCGCTCCCTAT
*
506568 TCATTCAGAGAGTATA
66 TCCTTCAGAGAGTATA
506584 TGACTCAATC
Statistics
Matches: 356, Mismatches: 36, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
153 138 0.39
157 35 0.10
158 156 0.44
161 1 0.00
162 26 0.07
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (157 bp):
TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAAAAACGGGTCCGCTCCCTAT
TCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCCTATTCATTCAGAG
AGTATAGGACTCAATCTTCAACGAACT
Found at i:507755 original size:16 final size:17
Alignment explanation
Indices: 507734--507776 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
507724 TGAACCCTCC
507734 TTTTATTTCTCTTTTT-
1 TTTTATTTCTCTTTTTA
507750 TTTTATTTTTCTCTTTTTA
1 TTTTA--TTTCTCTTTTTA
507769 TTTT-TTTC
1 TTTTATTTC
507777 CATTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 9 0.38
18 11 0.46
19 4 0.17
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTATTTCTCTTTTTA
Found at i:507772 original size:22 final size:21
Alignment explanation
Indices: 507745--507818 Score: 78
Period size: 25 Copynumber: 3.4 Consensus size: 21
507735 TTTATTTCTC
507745 TTTTTTTTTATTTTTCTCTTT
1 TTTTTTTTTATTTTTCTCTTT
*
507766 TTATTTTTTTCCATTTTTTCTCTTC
1 TT-TTTTTTT--A-TTTTTCTCTTT
* *
507791 TTTTTTTTTCTTTTT-TCATT
1 TTTTTTTTTATTTTTCTCTTT
507811 TTTTTTTT
1 TTTTTTTT
507819 CGTTTTTTCC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
20 11 0.24
21 7 0.16
22 7 0.16
24 8 0.18
25 12 0.27
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTTTTTATTTTTCTCTTT
Found at i:507781 original size:24 final size:24
Alignment explanation
Indices: 507743--507807 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 24
507733 CTTTTATTTC
507743 TCTTTTTTTTT--A-TTTTTCTCT
1 TCTTTTTTTTTCCATTTTTTCTCT
*
507764 TTTTATTTTTTTCCATTTTTTCTCT
1 TCTT-TTTTTTTCCATTTTTTCTCT
507789 TCTTTTTTTTT-C-TTTTTTC
1 TCTTTTTTTTTCCATTTTTTC
507808 ATTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 3 0.08
22 14 0.37
23 1 0.03
24 8 0.21
25 12 0.32
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (24 bp):
TCTTTTTTTTTCCATTTTTTCTCT
Found at i:507783 original size:25 final size:22
Alignment explanation
Indices: 507743--507855 Score: 83
Period size: 21 Copynumber: 5.1 Consensus size: 22
507733 CTTTTATTTC
*
507743 TCTTTTTTTTT-ATTTTTCTCT
1 TCTTTTTTTTTCTTTTTTCTCT
*
507764 TTTTATTTTTTTCCATTTTTTCTCT
1 TCTT-TTTTTTT-C-TTTTTTCTCT
*
507789 TCTTTTTTTTTC-TTTTT-TCA
1 TCTTTTTTTTTCTTTTTTCTCT
*
507809 T-TTTTTTTTTCGTTTTTTC-CA
1 TCTTTTTTTTTC-TTTTTTCTCT
**
507830 TCATCATTTTTTCTTTTTTCTTCT
1 TC-TTTTTTTTTCTTTTTTC-TCT
507854 TC
1 TC
507856 AAGCAAAATA
Statistics
Matches: 74, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
19 10 0.14
20 3 0.04
21 16 0.22
22 14 0.19
23 9 0.12
24 10 0.14
25 12 0.16
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (22 bp):
TCTTTTTTTTTCTTTTTTCTCT
Found at i:507812 original size:8 final size:7
Alignment explanation
Indices: 507748--507851 Score: 54
Period size: 7 Copynumber: 14.3 Consensus size: 7
507738 ATTTCTCTTT
*
507748 TTTTTTA
1 TTTTTTC
507755 TTTTTCTC
1 TTTTT-TC
507763 TTTTTAT-
1 TTTTT-TC
507770 TTTTTTCC
1 TTTTTT-C
507778 ATTTTTTC
1 -TTTTTTC
507786 TCTTCTTT-
1 T-TT-TTTC
507794 TTTTTTC
1 TTTTTTC
507801 TTTTTTC
1 TTTTTTC
*
507808 -ATTTT-
1 TTTTTTC
507813 TTTTTTC
1 TTTTTTC
507820 GTTTTTTC
1 -TTTTTTC
** **
507828 CATCATC
1 TTTTTTC
507835 ATTTTTTC
1 -TTTTTTC
507843 TTTTTTC
1 TTTTTTC
507850 TT
1 TT
507852 CTTCAAGCAA
Statistics
Matches: 74, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
6 12 0.16
7 32 0.43
8 21 0.28
9 9 0.12
ACGTcount: A:0.07, C:0.15, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:507816 original size:42 final size:42
Alignment explanation
Indices: 507769--507849 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
507759 TCTCTTTTTA
* **
507769 TTTTTTTCCATTTTTTCTCTTC-TTTTTTTTTCTTTTTTCATT
1 TTTTTTTCCATTTTTTC-CATCATCATTTTTTCTTTTTTCATT
* *
507811 TTTTTTTTCGTTTTTTCCATCATCATTTTTTCTTTTTTC
1 TTTTTTTCCATTTTTTCCATCATCATTTTTTCTTTTTTC
507850 TTCTTCAAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 3 0.09
42 30 0.91
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.75
Consensus pattern (42 bp):
TTTTTTTCCATTTTTTCCATCATCATTTTTTCTTTTTTCATT
Found at i:507825 original size:30 final size:28
Alignment explanation
Indices: 507749--507826 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 28
507739 TTTCTCTTTT
507749 TTTTTATTTTTCTCTTTTTATTTTTTTCCA
1 TTTTT-TTTTTCT-TTTTTATTTTTTTCCA
* * *
507779 TTTTTTCTCTTCTTTTTTTTTCTTTTTTCA
1 TTTTTT-TTTTCTTTTTTATT-TTTTTCCA
507809 TTTTTTTTTTCGTTTTTT
1 TTTTTTTTTTC-TTTTTT
507827 CCATCATCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 12 0.29
30 29 0.71
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.81
Consensus pattern (28 bp):
TTTTTTTTTTCTTTTTTATTTTTTTCCA
Found at i:524742 original size:18 final size:18
Alignment explanation
Indices: 524719--524757 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
524709 CAAATAGTAC
* *
524719 TAGTGACAGTGGCAGTGA
1 TAGTGACAGTGACAATGA
524737 TAGTGACAGTGACAATGA
1 TAGTGACAGTGACAATGA
524755 TAG
1 TAG
524758 CAGTGACAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.33, T:0.23
Consensus pattern (18 bp):
TAGTGACAGTGACAATGA
Found at i:541835 original size:39 final size:38
Alignment explanation
Indices: 541792--541877 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 38
541782 AACGAGTCCT
*
541792 TTGGGAGTTCGAATGTTTTATTGTGAATTTAAGAGTCTC
1 TTGGGAGTTAGAATGTTTTATTGTGAATTTAAGAGT-TC
* *
541831 TTGGGAGTTAGAGTGTTTTATTGTGACTTTAAGAGTTC
1 TTGGGAGTTAGAATGTTTTATTGTGAATTTAAGAGTTC
*
541869 TTGGAAGTT
1 TTGGGAGTT
541878 GGAGAGTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 10 0.23
39 33 0.77
ACGTcount: A:0.22, C:0.06, G:0.28, T:0.44
Consensus pattern (38 bp):
TTGGGAGTTAGAATGTTTTATTGTGAATTTAAGAGTTC
Found at i:541887 original size:38 final size:39
Alignment explanation
Indices: 541806--541887 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
541796 GAGTTCGAAT
* *
541806 GTTTTATTGTGAATTTAAGAGTCTCTTGGGAGTTAGAGT
1 GTTTTATTGTGAATTTAAGAGTCTCTTGGAAGTTAGAGA
* *
541845 GTTTTATTGTGACTTTAAGAGT-TCTTGGAAGTTGGAGA
1 GTTTTATTGTGAATTTAAGAGTCTCTTGGAAGTTAGAGA
541883 GTTTT
1 GTTTT
541888 TGTTTTTGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 18 0.46
39 21 0.54
ACGTcount: A:0.22, C:0.05, G:0.28, T:0.45
Consensus pattern (39 bp):
GTTTTATTGTGAATTTAAGAGTCTCTTGGAAGTTAGAGA
Found at i:542972 original size:20 final size:20
Alignment explanation
Indices: 542949--542990 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
542939 CGATTGTATA
542949 TACTTGCACAAATTTGTGTT
1 TACTTGCACAAATTTGTGTT
542969 TACTTGCACAAATTTGTGTT
1 TACTTGCACAAATTTGTGTT
542989 TA
1 TA
542991 ATTTATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (20 bp):
TACTTGCACAAATTTGTGTT
Found at i:546725 original size:62 final size:63
Alignment explanation
Indices: 546610--546732 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 63
546600 TCCCGAGGAC
* *
546610 CAGTCCATAGATTCCGAAGAACCTAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAAA
1 CAGTCCATAGATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAAA
546673 CAGTCCATATG-TCCCGAAGAACATAGGT-AACAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
546733 CCCTCGACCC
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
62 32 0.56
63 24 0.42
64 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (63 bp):
CAGTCCATAGATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAAA
Found at i:546733 original size:30 final size:31
Alignment explanation
Indices: 546610--546732 Score: 196
Period size: 32 Copynumber: 4.0 Consensus size: 31
546600 TCCCGAGGAC
* *
546610 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
546641 CAGTCCATATGTCCCGAAGAACATAGGTAAAA
1 CAGTCCATATGTCCCGAAGAACATAGGT-AAA
546673 CAGTCCATATGTCCCGAAGAACATAGGT-AA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
546703 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
546733 CCCTCGACCC
Statistics
Matches: 87, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
30 30 0.34
31 25 0.29
32 32 0.37
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:550769 original size:31 final size:31
Alignment explanation
Indices: 550731--550853 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
550721 CCCGAAGGAC
* *
550731 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
550762 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
550793 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
550824 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
550854 CCCTCGACCC
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:553870 original size:19 final size:19
Alignment explanation
Indices: 553846--553882 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
553836 TTAATTAGCG
*
553846 AAAATAACATTTTCAATAA
1 AAAATAACATTTTAAATAA
*
553865 AAAATAATATTTTAAATA
1 AAAATAACATTTTAAATA
553883 TTACGTCTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATAACATTTTAAATAA
Found at i:558306 original size:13 final size:13
Alignment explanation
Indices: 558288--558314 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
558278 TGATACGTAT
558288 TATATTATTTACG
1 TATATTATTTACG
558301 TATATTATTTACG
1 TATATTATTTACG
558314 T
1 T
558315 GTTGGGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (13 bp):
TATATTATTTACG
Found at i:563724 original size:2 final size:2
Alignment explanation
Indices: 563717--563750 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
563707 AAATAAATAA
563717 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
563751 TAGAAGAGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:567510 original size:15 final size:15
Alignment explanation
Indices: 567490--567521 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
567480 AAAATATTTC
*
567490 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTAGAT
567505 TTTCCCGTTCTAGAT
1 TTTCCCGTTCTAGAT
567520 TT
1 TT
567522 CGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.25, G:0.12, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTAGAT
Found at i:568310 original size:17 final size:17
Alignment explanation
Indices: 568273--568304 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
568263 ATCGCCGACC
568273 AAATATTACTATTCACG
1 AAATATTACTATTCACG
568290 AAAT-TTACTATTCAC
1 AAATATTACTATTCAC
568305 ATAAATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATATTACTATTCACG
Found at i:569445 original size:20 final size:20
Alignment explanation
Indices: 569420--569457 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
569410 TCTTATTCCT
569420 TGGTAATCTTACATTCCCAC
1 TGGTAATCTTACATTCCCAC
569440 TGGTAATCTTACATTCCC
1 TGGTAATCTTACATTCCC
569458 GTAATCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
TGGTAATCTTACATTCCCAC
Found at i:569462 original size:36 final size:36
Alignment explanation
Indices: 569422--569492 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
569412 TTATTCCTTG
**
569422 GTAATCTTACATTCCCACTGGTAATCTTACATTCCC
1 GTAATCTTACATTCCCACTAATAATCTTACATTCCC
* * *
569458 GTAATCTTATATTCCTACTAATAATTTTACATTCC
1 GTAATCTTACATTCCCACTAATAATCTTACATTCC
569493 GTGAACCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.41
Consensus pattern (36 bp):
GTAATCTTACATTCCCACTAATAATCTTACATTCCC
Found at i:569463 original size:16 final size:18
Alignment explanation
Indices: 569421--569472 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 18
569411 CTTATTCCTT
569421 GGTAATCTTACATTCCCAC
1 GGTAATCTTACATT-CCAC
569440 TGGTAATCTTACATTCC-C
1 -GGTAATCTTACATTCCAC
*
569458 -GTAATCTTATATTCC
1 GGTAATCTTACATTCC
569473 TACTAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 14 0.45
18 1 0.03
19 2 0.06
20 14 0.45
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (18 bp):
GGTAATCTTACATTCCAC
Found at i:574792 original size:20 final size:20
Alignment explanation
Indices: 574769--574815 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
574759 GTTTCCAAAT
574769 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
* *
574789 TCGCAACGCGAATTTGTAAT
1 TCGCAACGCGAATATGTAAA
574809 TCGCAAC
1 TCGCAAC
574816 ACAGAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:574829 original size:20 final size:20
Alignment explanation
Indices: 574806--574854 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
574796 GCGAATTTGT
574806 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
*
574826 AATTCGCAACACATAAGTCA
1 AATTCGCAACACAGAAGTCA
574846 AATTCGCAA
1 AATTCGCAA
574855 AGTGCGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.18
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:575034 original size:22 final size:22
Alignment explanation
Indices: 575009--575059 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
574999 CTACGGCGAC
575009 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
575031 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
*
575053 ATTCGTC
1 ATCCGTC
575060 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:577492 original size:21 final size:21
Alignment explanation
Indices: 577466--577569 Score: 104
Period size: 21 Copynumber: 5.0 Consensus size: 21
577456 AGCACCTGTC
*
577466 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
*
577487 ATCGTTCAAGAGGCCCCTATCT
1 ATCGTTCAAGAGGCCCCT-CCT
* * *
577509 -TCCTTCAAGAGGCCCTTCCC
1 ATCGTTCAAGAGGCCCCTCCT
* *
577529 ACCGTTCAAGAGGCCCCT-GT
1 ATCGTTCAAGAGGCCCCTCCT
*
577549 CATCGTTCAAGAGGTCCCTCC
1 -ATCGTTCAAGAGGCCCCTCC
577570 CACCGTTCGA
Statistics
Matches: 65, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.02
21 62 0.95
22 2 0.03
ACGTcount: A:0.19, C:0.37, G:0.19, T:0.25
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:577535 original size:42 final size:42
Alignment explanation
Indices: 577464--577582 Score: 143
Period size: 42 Copynumber: 2.8 Consensus size: 42
577454 GAAGCACCTG
* * *
577464 TCATCGTTCAAGAGG-CCTCTCCTATCGTTCAAGAGGCCCCTA
1 TCATCCTTCAAGAGGCCCT-TCCCACCGTTCAAGAGGCCCCTA
* *
577506 TCTTCCTTCAAGAGGCCCTTCCCACCGTTCAAGAGGCCCCTG
1 TCATCCTTCAAGAGGCCCTTCCCACCGTTCAAGAGGCCCCTA
* *
577548 TCATCGTTCAAGAGGTCCC-TCCCACCGTTCGAGAG
1 TCATCCTTCAAGAGG-CCCTTCCCACCGTTCAAGAG
577583 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 61 0.91
43 6 0.09
ACGTcount: A:0.19, C:0.36, G:0.20, T:0.24
Consensus pattern (42 bp):
TCATCCTTCAAGAGGCCCTTCCCACCGTTCAAGAGGCCCCTA
Found at i:577576 original size:21 final size:20
Alignment explanation
Indices: 577468--577582 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 20
577458 CACCTGTCAT
* *
577468 CGTTCAAGAGGCCTCTCCTAT
1 CGTTCAAGAGGCC-CTCCCAC
* **
577489 CGTTCAAGAGGCCCCTATCTTC
1 CGTTCAAGAGG-CCCT-CCCAC
577511 C-TTCAAGAGGCCCTTCCCAC
1 CGTTCAAGAGGCCC-TCCCAC
** *
577531 CGTTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGG-CCCTCCCAC
577552 CGTTCAAGAGGTCCCTCCCAC
1 CGTTCAAGAGG-CCCTCCCAC
*
577573 CGTTCGAGAG
1 CGTTCAAGAG
577583 CCCGATTCAC
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
20 6 0.08
21 61 0.81
22 8 0.11
ACGTcount: A:0.19, C:0.37, G:0.21, T:0.23
Consensus pattern (20 bp):
CGTTCAAGAGGCCCTCCCAC
Found at i:578957 original size:13 final size:14
Alignment explanation
Indices: 578932--578964 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
578922 AAATTGATGT
578932 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
578946 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
578959 ATTTGT
1 ATTTGT
578965 TTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:579021 original size:64 final size:64
Alignment explanation
Indices: 578943--579094 Score: 216
Period size: 64 Copynumber: 2.4 Consensus size: 64
578933 TTTGTAAAAG
578943 TTGATTTGTAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA-TTTTTTGCTTGTTTAA
1 TTGATTTGTAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAA
* * *** *
579006 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTTTTCTTGTTTA
1 TTGATTTGT-AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA-TTTTTTTGCTTGTTTA
579071 A
64 A
*
579072 TTGCTTTGTAAAGTTGATTTGTT
1 TTGATTTGTAAAGTTGATTTGTT
579095 GTTTTAAATT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
63 9 0.11
64 33 0.42
65 14 0.18
66 23 0.29
ACGTcount: A:0.26, C:0.03, G:0.17, T:0.54
Consensus pattern (64 bp):
TTGATTTGTAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAA
Found at i:579195 original size:20 final size:20
Alignment explanation
Indices: 579153--579256 Score: 102
Period size: 20 Copynumber: 5.2 Consensus size: 20
579143 AAGGTACACT
*
579153 TTCGCAACGCGAAAGTC-AA
1 TTCGCAATGCGAAAGTCAAA
** *
579172 TTCGCGTTGCGATAGTCAAA
1 TTCGCAATGCGAAAGTCAAA
579192 TTCGCAATGCGAAAGTCAAA
1 TTCGCAATGCGAAAGTCAAA
* * ** *
579212 TTTGCAACGTAAAAGCCAAA
1 TTCGCAATGCGAAAGTCAAA
* *
579232 TTCGCAACGCGAAAGTCAAC
1 TTCGCAATGCGAAAGTCAAA
579252 TTCGC
1 TTCGC
579257 GTTTCGAATT
Statistics
Matches: 67, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
19 13 0.19
20 54 0.81
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (20 bp):
TTCGCAATGCGAAAGTCAAA
Found at i:581929 original size:12 final size:12
Alignment explanation
Indices: 581908--581942 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
581898 GGTTGTGGGT
*
581908 TTTGAGATTGTG
1 TTTGATATTGTG
581920 TTTGATATTGTG
1 TTTGATATTGTG
*
581932 TTTGGTATTGT
1 TTTGATATTGT
581943 AAATGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:582755 original size:20 final size:19
Alignment explanation
Indices: 582711--582839 Score: 66
Period size: 20 Copynumber: 6.5 Consensus size: 19
582701 CAAAACATTT
*
582711 GTGTTGCGAAACTAAAA-C
1 GTGTTGCGAAATTAAAATC
*
582729 CTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAA-TC
582749 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATT--AAAATC
* * *
582769 GAGTTGCTACAA-CAAAATTC
1 GTGTTGCGA-AATTAAAA-TC
** *
582789 GCATTGCGAATTTAGAAATC
1 GTGTTGCGAAATTA-AAATC
* * *
582809 GAGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATT-AAAATC
582829 AGTGTTGCGAA
1 -GTGTTGCGAA
582840 TTTGGAAACT
Statistics
Matches: 85, Mismatches: 15, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
18 15 0.18
19 9 0.11
20 42 0.49
21 17 0.20
22 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:582854 original size:41 final size:40
Alignment explanation
Indices: 582735--582883 Score: 122
Period size: 40 Copynumber: 3.7 Consensus size: 40
582725 AAACCTGTTG
* * * * *
582735 CGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAGTTG
1 CGAAATTGAAATTCGCGTTGCGAATTTGGAAATCGAGTTA
* ** * * *
582775 CTACAA-CAAAATTCGCATTGCGAATTTAGAAATCGAGTTG
1 CGA-AATTGAAATTCGCGTTGCGAATTTGGAAATCGAGTTA
* *
582815 CGAATTTGAAATTCAGTGTTGCGAATTTGGAAA-CTGAGTTA
1 CGAAATTGAAATTC-GCGTTGCGAATTTGGAAATC-GAGTTA
* *
582856 CGAAATTGGAGTTCGCGTTGCGAATTTG
1 CGAAATTGAAATTCGCGTTGCGAATTTG
582884 TTGGTCATTT
Statistics
Matches: 86, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
39 1 0.01
40 52 0.60
41 33 0.38
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.31
Consensus pattern (40 bp):
CGAAATTGAAATTCGCGTTGCGAATTTGGAAATCGAGTTA
Found at i:584145 original size:23 final size:24
Alignment explanation
Indices: 584072--584145 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 24
584062 AAATATTTTA
* *
584072 TTTTAATTAAATTA-CATTTAGAT-
1 TTTTAATTAATTTATAATTTAG-TG
584095 TTTTAATTAATTTATAATTATA-TG
1 TTTTAATTAATTTATAATT-TAGTG
*
584119 -TTTAA-TATTTTATAATTTAGTG
1 TTTTAATTAATTTATAATTTAGTG
584141 TTTTA
1 TTTTA
584146 TAAATTAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.05
22 13 0.30
23 23 0.53
24 3 0.07
25 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.58
Consensus pattern (24 bp):
TTTTAATTAATTTATAATTTAGTG
Found at i:591375 original size:2 final size:2
Alignment explanation
Indices: 591368--591393 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
591358 TTCTGTACAA
591368 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
591394 TTAAATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:592189 original size:21 final size:22
Alignment explanation
Indices: 592159--592199 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
592149 TCAAGCGTAG
592159 TAATTATCAA-ATAAATAAACA
1 TAATTATCAATATAAATAAACA
* *
592180 TAATTCTCAATTTAAATAAA
1 TAATTATCAATATAAATAAA
592200 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (22 bp):
TAATTATCAATATAAATAAACA
Found at i:605420 original size:6 final size:6
Alignment explanation
Indices: 605409--605459 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
605399 GGACTGTTCG
* *
605409 AAAGAA AAAGAA AAAGAA AAAGAA AAA-AA GACATGAA AAAGAA ATAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA -A-AAGAA AAAGAA AAAGAA
605458 AA
1 AA
605460 CAAAACAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 2 0.05
6 32 0.84
7 2 0.05
8 2 0.05
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:613025 original size:16 final size:17
Alignment explanation
Indices: 612985--613028 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
612975 CCTTACTTGA
612985 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** *
613002 TTTTATATTT-TTAAAT
1 TTAAATATTTAATAAAT
613018 TTAAATATTTA
1 TTAAATATTTA
613029 TTTTTACATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:613471 original size:2 final size:2
Alignment explanation
Indices: 613464--613513 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
613454 TTCCTCATTA
613464 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
613506 AT AT AT AT
1 AT AT AT AT
613514 GAATAATTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:613817 original size:26 final size:25
Alignment explanation
Indices: 613788--613873 Score: 91
Period size: 26 Copynumber: 3.3 Consensus size: 25
613778 ATAAGTACCT
*
613788 AATAAAATAAAATTTACTAAAATTTA
1 AATAAAATAAAATTTACTAAAA-TAA
** * *
613814 AATAAAATAAAATGAACTTTAAATGA
1 AATAAAATAAAATTTAC-TAAAATAA
*
613840 AATGAAATAAAATTTACTAAAAATAA
1 AATAAAATAAAATTTACT-AAAATAA
613866 AATAAAAT
1 AATAAAAT
613874 GGGTTGCCTC
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
25 1 0.02
26 43 0.90
27 4 0.08
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (25 bp):
AATAAAATAAAATTTACTAAAATAA
Found at i:613855 original size:21 final size:21
Alignment explanation
Indices: 613805--613873 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
613795 TAAAATTTAC
613805 TAAAATTTAAATAAAATAAAA
1 TAAAATTTAAATAAAATAAAA
* * * *
613826 TGAACTTTAAATGAAATGAAA
1 TAAAATTTAAATAAAATAAAA
*
613847 TAAAATTT-ACTAAAAATAAAA
1 TAAAATTTAAAT-AAAATAAAA
613868 TAAAAT
1 TAAAAT
613874 GGGTTGCCTC
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 2 0.05
21 36 0.95
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (21 bp):
TAAAATTTAAATAAAATAAAA
Found at i:614117 original size:77 final size:77
Alignment explanation
Indices: 613990--614148 Score: 282
Period size: 77 Copynumber: 2.1 Consensus size: 77
613980 CCAATTAATA
*
613990 ACTTCTTTATTAGAAACTCTACGACCATATAATTCTTTTATTTTTTTCTTATAGATTTTGACATT
1 ACTTCTTTATTAGAAACTCTACGACCATATAATTCTTTTATATTTTTCTTATAGATTTTGACATT
*
614055 CTCATAGGCGTT
66 CTCATACGCGTT
*
614067 ACTTCTTTATTAGAAACTCTACGACCGTATAATTCTTTTATATTTTTCTTATAGATTTTGACATT
1 ACTTCTTTATTAGAAACTCTACGACCATATAATTCTTTTATATTTTTCTTATAGATTTTGACATT
*
614132 CTCATACGCTTT
66 CTCATACGCGTT
614144 ACTTC
1 ACTTC
614149 GAATCCTCTT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (77 bp):
ACTTCTTTATTAGAAACTCTACGACCATATAATTCTTTTATATTTTTCTTATAGATTTTGACATT
CTCATACGCGTT
Found at i:616782 original size:24 final size:24
Alignment explanation
Indices: 616624--616771 Score: 194
Period size: 24 Copynumber: 6.3 Consensus size: 24
616614 GAGTCGAGGG
* * *
616624 TTCTAAGCAGTCCTTTGGGA-AAA
1 TTCTATGCGGTCCTTCGGGACAAA
* * *
616647 -TCTATGTGGTCATTCGGGAC-AT
1 TTCTATGCGGTCCTTCGGGACAAA
**
616669 TTCTATATGGTCCTTCGGGACAAA
1 TTCTATGCGGTCCTTCGGGACAAA
616693 TTCTATGCGGTCCTTCGGGACAAA
1 TTCTATGCGGTCCTTCGGGACAAA
616717 TTCTATGCGGTCCTTCGGGACAAA
1 TTCTATGCGGTCCTTCGGGACAAA
*
616741 TTCTATGCGGTCTTTCGGGACAAA
1 TTCTATGCGGTCCTTCGGGACAAA
616765 TTCTATG
1 TTCTATG
616772 TGGCACTTCG
Statistics
Matches: 110, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.14
23 18 0.16
24 77 0.70
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (24 bp):
TTCTATGCGGTCCTTCGGGACAAA
Found at i:617613 original size:21 final size:21
Alignment explanation
Indices: 617597--617647 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
617587 TGTCCCGGAT
617597 GACCACATAATTATCCCGAAG
1 GACCACATAATTATCCCGAAG
* *
617618 GGCCATATAATTATCCCGAAG
1 GACCACATAATTATCCCGAAG
617639 GACCACATA
1 GACCACATA
617648 TACCCTCGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.20
Consensus pattern (21 bp):
GACCACATAATTATCCCGAAG
Found at i:617849 original size:13 final size:13
Alignment explanation
Indices: 617831--617855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
617821 GTTCATATTT
617831 TCATAAAACATAA
1 TCATAAAACATAA
617844 TCATAAAACATA
1 TCATAAAACATA
617856 GTTTGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (13 bp):
TCATAAAACATAA
Found at i:618308 original size:54 final size:55
Alignment explanation
Indices: 618238--618357 Score: 154
Period size: 54 Copynumber: 2.2 Consensus size: 55
618228 ACCTCCATAT
* * * *
618238 GTACCGATACCGAAATTACATTCGAAGGTTCAAGTGTATCTATA-CCTCC-TCAAG
1 GTACCGATACCGAAATTACATTCAAAGGTTCAAGGGTATCGATATCATCCTTC-AG
* *
618292 GTACCGATACCTAAATTACATTCAAAGGTTTAAGGGTATCGATATCATCCTTCAG
1 GTACCGATACCGAAATTACATTCAAAGGTTCAAGGGTATCGATATCATCCTTCAG
*
618347 GTATCGATACC
1 GTACCGATACC
618358 ACCCTGATGG
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
54 39 0.68
55 16 0.28
56 2 0.04
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (55 bp):
GTACCGATACCGAAATTACATTCAAAGGTTCAAGGGTATCGATATCATCCTTCAG
Found at i:623364 original size:29 final size:29
Alignment explanation
Indices: 623291--623375 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 29
623281 CGTTGACCGT
* * *
623291 GTGTTATTTTGGTAATTATTTGGGAAATG
1 GTGTTATTTTGGTAATTATTTTGAAAAGG
*
623320 GTGTTATTATGGTAATTATTTTGAAAAGG
1 GTGTTATTTTGGTAATTATTTTGAAAAGG
** *
623349 GTGTTATTTTCATAATT-TTTTTAAAAG
1 GTGTTATTTTGGTAATTATTTTGAAAAG
623376 TGGCAATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 9 0.19
29 39 0.81
ACGTcount: A:0.28, C:0.01, G:0.21, T:0.49
Consensus pattern (29 bp):
GTGTTATTTTGGTAATTATTTTGAAAAGG
Found at i:623447 original size:29 final size:29
Alignment explanation
Indices: 623418--623475 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
623408 ATTAGTTATT
*
623418 ATTTTGAAAATAATGCTATTTTGGTAATTA
1 ATTTT-AAAATAATGCTATTTTCGTAATTA
** *
623448 ATTTTAAAATGGTGTTATTTTCGTAATT
1 ATTTTAAAATAATGCTATTTTCGTAATT
623476 TAAAAAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (29 bp):
ATTTTAAAATAATGCTATTTTCGTAATTA
Found at i:623600 original size:25 final size:25
Alignment explanation
Indices: 623560--623620 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
623550 ACGACCTTTA
* *
623560 ATATTTTTCGAGTATATTTATCCTG
1 ATATTTTTTGAATATATTTATCCTG
623585 ATATTTTTTGAATATATTTATCCTG
1 ATATTTTTTGAATATATTTATCCTG
*
623610 ATAATTTTTGA
1 ATATTTTTTGA
623621 TGTTCTGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (25 bp):
ATATTTTTTGAATATATTTATCCTG
Found at i:630495 original size:13 final size:13
Alignment explanation
Indices: 630473--630515 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
630463 ATCCTAACCC
*
630473 GACCCGACCCATT
1 GACCCGACCCGTT
*
630486 GACCCAACCCGTT
1 GACCCGACCCGTT
*
630499 GACTCGACCCGTT
1 GACCCGACCCGTT
630512 GACC
1 GACC
630516 GTTAACCGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.21, C:0.44, G:0.19, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:630592 original size:29 final size:28
Alignment explanation
Indices: 630523--630592 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
630513 ACCGTTAACC
*
630523 GGGTGCTATTTTAGTAATTATTTGGGAAA
1 GGGTGCTA-TTTAGTAATTATTTGGAAAA
* * *
630552 TGGTGCTCATTTGGTAATTATTTTTGAAAA
1 GGGTGCT-ATTTAGTAATTA-TTTGGAAAA
630582 GGGTGCTATTT
1 GGGTGCTATTT
630593 TTGTATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 20 0.59
30 14 0.41
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (28 bp):
GGGTGCTATTTAGTAATTATTTGGAAAA
Found at i:630604 original size:29 final size:29
Alignment explanation
Indices: 630523--630605 Score: 69
Period size: 30 Copynumber: 2.8 Consensus size: 29
630513 ACCGTTAACC
* * * *
630523 GGGTGCTATTTTAGTAATTATTTGGGAAA
1 GGGTGCTATTTTAGTATTTTTTTTGAAAA
* * *
630552 TGGTGCTCA-TTTGGTAATTATTTTTGAAAA
1 GGGTGCT-ATTTTAGT-ATTTTTTTTGAAAA
*
630582 GGGTGCTATTTTTGTATTTTTTTT
1 GGGTGCTATTTTAGTATTTTTTTT
630606 AAAGAAAATG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
29 20 0.49
30 21 0.51
ACGTcount: A:0.22, C:0.05, G:0.23, T:0.51
Consensus pattern (29 bp):
GGGTGCTATTTTAGTATTTTTTTTGAAAA
Found at i:630679 original size:29 final size:29
Alignment explanation
Indices: 630647--630717 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
630637 AAAAAATTGA
* * *
630647 TATTTTAGTAATTATTTTGAAAATGGTGT
1 TATTTTAGTAATTAATTTCAAAATGGTGC
*
630676 TATTTTGGTAATTAATTTCAAAATGGTGC
1 TATTTTAGTAATTAATTTCAAAATGGTGC
*
630705 TATTTTCGTAATT
1 TATTTTAGTAATT
630718 TAAAAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.51
Consensus pattern (29 bp):
TATTTTAGTAATTAATTTCAAAATGGTGC
Found at i:631445 original size:7 final size:7
Alignment explanation
Indices: 631433--631467 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
631423 TACTGTTATG
631433 ACATGAT
1 ACATGAT
631440 ACATGAT
1 ACATGAT
631447 ACATGAT
1 ACATGAT
631454 ACATGAT
1 ACATGAT
*
631461 ACTTGAT
1 ACATGAT
631468 TTTTGAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (7 bp):
ACATGAT
Found at i:636657 original size:16 final size:16
Alignment explanation
Indices: 636636--636667 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
636626 GTTGACTCCA
636636 TGTAGATGCTGCACTT
1 TGTAGATGCTGCACTT
636652 TGTAGATGCTGCACTT
1 TGTAGATGCTGCACTT
636668 GGAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (16 bp):
TGTAGATGCTGCACTT
Found at i:638522 original size:20 final size:21
Alignment explanation
Indices: 638481--638523 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
638471 ATTTTTTGGT
638481 TGCTGGTATGAATATGTTGTG
1 TGCTGGTATGAATATGTTGTG
* *
638502 TGCTGGTTTGAATGT-TTGTG
1 TGCTGGTATGAATATGTTGTG
638522 TG
1 TG
638524 TTTATCTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.14, C:0.05, G:0.35, T:0.47
Consensus pattern (21 bp):
TGCTGGTATGAATATGTTGTG
Found at i:638854 original size:25 final size:25
Alignment explanation
Indices: 638826--638877 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
638816 TAAAACTAAA
638826 AAAATAAAG-AAAAATATAATATAAG
1 AAAATAAAGAAAAAATA-AATATAAG
*
638851 AAAATAAAGAAAAAATAAATATGAG
1 AAAATAAAGAAAAAATAAATATAAG
638876 AA
1 AA
638878 TAACAATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (25 bp):
AAAATAAAGAAAAAATAAATATAAG
Found at i:639947 original size:24 final size:24
Alignment explanation
Indices: 639920--640015 Score: 91
Period size: 24 Copynumber: 4.2 Consensus size: 24
639910 TTCATTTTAC
*
639920 TTAAATTACT-TAAATTATTATTTT
1 TTAAATTACTAT-AATTATTATTAT
*
639944 TTAAATTACTATTATTATTATTAT
1 TTAAATTACTATAATTATTATTAT
639968 TTAAA-TA-TA-AA-TATTATTA-
1 TTAAATTACTATAATTATTATTAT
*
639987 TTATAATTA-T-TTATTATTATTAT
1 TTA-AATTACTATAATTATTATTAT
640010 TTAAAT
1 TTAAAT
640016 AAATACAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
19 3 0.05
20 10 0.16
21 5 0.08
22 13 0.21
23 5 0.08
24 25 0.40
25 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTAAATTACTATAATTATTATTAT
Found at i:639959 original size:3 final size:3
Alignment explanation
Indices: 639948--640010 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
639938 TATTTTTTAA
* * * * * *
639948 ATT ACT ATT ATT ATT ATT ATT -TA AAT ATA AAT ATT ATT ATT ATA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
639995 ATTT ATT ATT ATT ATT
1 A-TT ATT ATT ATT ATT
640011 TAAATAAATA
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
2 1 0.02
3 42 0.91
4 3 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:640439 original size:21 final size:21
Alignment explanation
Indices: 640415--640469 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
640405 TGAAGATCTA
640415 TGGTGAGTCACCGCCATAACT
1 TGGTGAGTCACCGCCATAACT
640436 TGGTGAGTCACCGCCATAACT
1 TGGTGAGTCACCGCCATAACT
* *
640457 TGTTGACTCACCG
1 TGGTGAGTCACCG
640470 AAGACCGCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (21 bp):
TGGTGAGTCACCGCCATAACT
Found at i:641446 original size:2 final size:2
Alignment explanation
Indices: 641439--641465 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
641429 TAATTTAGTG
641439 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
641466 TTCTTTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:641972 original size:16 final size:17
Alignment explanation
Indices: 641943--641975 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
641933 CTGGTATTTT
*
641943 AAAAATAAATAAATATA
1 AAAAACAAATAAATATA
641960 AAAAACAAA-AAATATA
1 AAAAACAAATAAATATA
641976 TATTTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAACAAATAAATATA
Found at i:642096 original size:144 final size:145
Alignment explanation
Indices: 641831--642102 Score: 474
Period size: 144 Copynumber: 1.9 Consensus size: 145
641821 TTTAATTTTG
641831 TTTTATTTAAATTATTTTCTTAGGAAAAATTATTATTTTTAATATTTATTTATTTTTCAAATATT
1 TTTTATTTAAATTATTTTCTT----AAAATTATTATTTTTAATATTTATTTATTTTTCAAATATT
* * *
641896 AAGAAATGGCAGTCTTAAAGCAACTAGATGTCTTATTCTGGTATTTTAAAAATAAATAAATATAA
62 AAGAAATGACAGTCTTAAAGCAACTAGATGTCTTATTCTGATAGTTTAAAAATAAATAAATATAA
641961 AAAACAAAAAATATATATT
127 AAAACAAAAAATATATATT
641980 TTTTATTTAAATTATTTTCTT-AAATTATTATTTTTAATATTTATTTATTTTTCAAATATTAAGA
1 TTTTATTTAAATTATTTTCTTAAAATTATTATTTTTAATATTTATTTATTTTTCAAATATTAAGA
642044 AATGACAGTCTTAAAGCAACTAGATGTCTTATTCTGATAGTTTAAAAATAAATAAATAT
66 AATGACAGTCTTAAAGCAACTAGATGTCTTATTCTGATAGTTTAAAAATAAATAAATAT
642103 CCTGCTTATA
Statistics
Matches: 120, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
144 99 0.82
149 21 0.17
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (145 bp):
TTTTATTTAAATTATTTTCTTAAAATTATTATTTTTAATATTTATTTATTTTTCAAATATTAAGA
AATGACAGTCTTAAAGCAACTAGATGTCTTATTCTGATAGTTTAAAAATAAATAAATATAAAAAA
CAAAAAATATATATT
Found at i:642161 original size:144 final size:142
Alignment explanation
Indices: 641858--642248 Score: 425
Period size: 144 Copynumber: 2.7 Consensus size: 142
641848 TCTTAGGAAA
* *
641858 AATTATTATTTTTAATATTTATTTATTTTTCAAATATTAAGAAATGGCAGTCTTAAAGCAACTAG
1 AATTATTATTATTAATATTTATTTATTTTTCAAATATTAAGAAATGACAGTCTTAAAGCAACTAG
* *** **
641923 ATGTCTTATTCTGGTATTTTAAAAATAAATAAATATAAAAAACAAAAAATATATATTTTTTATTT
66 ATGTCTTATTCTGATA-TTTAAAAATAAATAAATATCCTAAACAAAAAATATATATTCATTATTT
** ** *
641988 AAATTATTTTCTT
130 AAAGAAAATTATT
*
642001 AAATTATTATTTTTAATATTTATTTATTTTTCAAATATTAAGAAATGACAGTCTTAAAGCAACTA
1 -AATTATTATTATTAATATTTATTTATTTTTCAAATATTAAGAAATGACAGTCTTAAAGCAACTA
****
642066 GATGTCTTATTCTGATAGTTTAAAAATAAATAAATATCCTGCTTATAAAAATATATACTTCATTA
65 GATGTCTTATTCTGATA-TTTAAAAATAAATAAATATCCTAAACA-AAAAATATATA-TTCATTA
* *
642131 TTTTTAGGAAAATTATT
127 -TTTAAAGAAAATTATT
* * *
642148 -A-TATTCTTATTAATATTTATTTATTTATT--AATATTAAAGAAAAGACAGTCTTAAAGAAACT
1 AATTATTATTATTAATATTTATTTATTT-TTCAAATATT-AAGAAATGACAGTCTTAAAGCAACT
* * *
642209 AGATGTTCTT-TTATGATATTT-TAAATAAATAAATGTCCTA
64 AGATG-TCTTATTCTGATATTTAAAAATAAATAAATATCCTA
642249 TTTACAAAAA
Statistics
Matches: 214, Mismatches: 27, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
142 16 0.07
143 9 0.04
144 157 0.73
145 18 0.08
146 5 0.02
147 9 0.04
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (142 bp):
AATTATTATTATTAATATTTATTTATTTTTCAAATATTAAGAAATGACAGTCTTAAAGCAACTAG
ATGTCTTATTCTGATATTTAAAAATAAATAAATATCCTAAACAAAAAATATATATTCATTATTTA
AAGAAAATTATT
Found at i:658034 original size:20 final size:20
Alignment explanation
Indices: 658009--658046 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
657999 AAGTAAGGGA
658009 GAGTAATTTCAAAACTTGGG
1 GAGTAATTTCAAAACTTGGG
658029 GAGTAATTTCAAAACTTG
1 GAGTAATTTCAAAACTTG
658047 ATTTCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
GAGTAATTTCAAAACTTGGG
Found at i:660063 original size:19 final size:20
Alignment explanation
Indices: 660016--660070 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
660006 TACATCTACA
* *
660016 TTCTTAAAAGATAATAGATTT
1 TTCTTCAAAGATGATAGA-TT
660037 TCTCTTCAAAGATGATAGA-T
1 T-TCTTCAAAGATGATAGATT
660057 TTCTTCAAAGATGA
1 TTCTTCAAAGATGA
660071 AAGCCTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 13 0.42
20 2 0.06
21 1 0.03
22 15 0.48
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (20 bp):
TTCTTCAAAGATGATAGATT
Found at i:660841 original size:45 final size:45
Alignment explanation
Indices: 660792--660889 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
660782 TTTTTGATAT
** * * *
660792 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGC
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGC
*
660837 TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGT
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGC
660882 TTTCAAAA
1 TTTCAAAA
660890 AAGCCTTCGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (45 bp):
TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGC
Found at i:660949 original size:122 final size:122
Alignment explanation
Indices: 660731--661114 Score: 597
Period size: 122 Copynumber: 3.1 Consensus size: 122
660721 CTATTTCCAA
* * ** *
660731 CATCCATAAGACCTGCAATGAAGGATGTTTAAAAAAAAAGCCTTCGGGAGCTTTTTGATATTTTC
1 CATCCATAAGACCTGCAGTGCAGGATGTTT-TCAAAAAAGCCTTCGGGAGATTTTTGATATTTTC
660796 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
65 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
660854 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAAGCCTTCGGGAGATTTTTGATATTTTCA
1 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAAGCCTTCGGGAGATTTTTGATATTTTCA
660919 AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
66 AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
* * * *
660976 CATCCATAAGACATGCAGTGCAGTATGTTTTCAAAAAAAAAGCATTCGGGAGGTTTTTGATATTT
1 CATCCATAAGACCTGCAGTGCAGGATGTTTTC---AAAAAAGCCTTCGGGAGATTTTTGATATTT
* * * *
661041 TCAAAACCTACAGGTCATTTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
63 TCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
**
661101 CATCTGTAAGACCT
1 CATCCATAAGACCT
661115 ATAGTGCAAG
Statistics
Matches: 242, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
122 119 0.49
123 28 0.12
125 95 0.39
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (122 bp):
CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAAGCCTTCGGGAGATTTTTGATATTTTCA
AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
Found at i:660995 original size:45 final size:45
Alignment explanation
Indices: 660914--661011 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 45
660904 TTTTTGATAT
** * * *
660914 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA-TGATGC
1 TTTCAAAACCTTCGGGTCATCCATAAGACATGCAGTGCAGT-ATGC
*
660959 TTTCAAAACCTTCGGGTCATCCATAAGACATGCAGTGCAGTATGT
1 TTTCAAAACCTTCGGGTCATCCATAAGACATGCAGTGCAGTATGC
661004 TTTCAAAA
1 TTTCAAAA
661012 AAAAAGCATT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 45 0.98
46 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (45 bp):
TTTCAAAACCTTCGGGTCATCCATAAGACATGCAGTGCAGTATGC
Found at i:661102 original size:45 final size:45
Alignment explanation
Indices: 661033--661127 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 45
661023 GGGAGGTTTT
* * *
661033 TGATATTTTCAAAACCTACAGGTCATTTGTAAGCCCT-TCAGTGCA
1 TGATGTTTTCAAAACCTACAGGTCATCTGTAAGACCTAT-AGTGCA
* *
661078 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTATAGTGCA
1 TGATGTTTTCAAAACCTACAGGTCATCTGTAAGACCTATAGTGCA
*
661123 AGATG
1 TGATG
661128 ATAGGACTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 42 0.98
46 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTACAGGTCATCTGTAAGACCTATAGTGCA
Found at i:662679 original size:2 final size:2
Alignment explanation
Indices: 662672--662785 Score: 174
Period size: 2 Copynumber: 56.5 Consensus size: 2
662662 TTTAATTTAG
* *
662672 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
662714 TT TT TA GTA 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
*
662757 TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
662786 TTTAGGATAA
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 103 0.98
3 2 0.02
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (2 bp):
TA
Found at i:663186 original size:19 final size:20
Alignment explanation
Indices: 663151--663188 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
663141 TCTTAGGAAA
*
663151 ATTTATTATTTTTAATATTT
1 ATTTATTATTTTAAATATTT
663171 ATTTATT-TTTTAAATATT
1 ATTTATTATTTTAAATATT
663189 AAGAAATGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTATTATTTTAAATATTT
Found at i:663335 original size:149 final size:152
Alignment explanation
Indices: 663106--663400 Score: 470
Period size: 149 Copynumber: 1.9 Consensus size: 152
663096 ATGTTATATT
* *
663106 TATATATATTTAATTTTGTTTTATTTAAATTATTTTCTTAGGAAAATTTATTATTTTTAATATTT
1 TATATATATATAATATTGTTTTATTTAAATTATTTTCTT---AAAATTTATTATTTTTAATATTT
* * * *
663171 ATTTATTTTTTAAATATTAAGAAATGGCAGTCTTAAAGCAATTAGATGTCTTCTTCTGGTATTTT
63 ATTTATTTTTCAAATATTAAGAAATGGCAGTCTTAAAGCAACTAGATGTCTTATTCTGATATTTT
663236 AAAAATAAATAAATATAAAAACCAA
128 AAAAATAAATAAATATAAAAACCAA
663261 TATATATATAT-ATATTGTTTTATTTAAATTATTTTCTT-AAA-TTATTATTTTTAATATTTATT
1 TATATATATATAATATTGTTTTATTTAAATTATTTTCTTAAAATTTATTATTTTTAATATTTATT
* *
663323 TATTTTTCAAATATTAAGAAATGTCAGTCTTAAAGCAACTAGATGTTTTATTCTGATATTTTAAA
66 TATTTTTCAAATATTAAGAAATGGCAGTCTTAAAGCAACTAGATGTCTTATTCTGATATTTTAAA
663388 AATAAATAAATAT
131 AATAAATAAATAT
663401 CCTACTTATA
Statistics
Matches: 132, Mismatches: 8, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
149 93 0.70
150 3 0.02
154 26 0.20
155 10 0.08
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (152 bp):
TATATATATATAATATTGTTTTATTTAAATTATTTTCTTAAAATTTATTATTTTTAATATTTATT
TATTTTTCAAATATTAAGAAATGGCAGTCTTAAAGCAACTAGATGTCTTATTCTGATATTTTAAA
AATAAATAAATATAAAAACCAA
Found at i:663521 original size:144 final size:146
Alignment explanation
Indices: 663134--663540 Score: 402
Period size: 149 Copynumber: 2.8 Consensus size: 146
663124 TTTTATTTAA
* *
663134 ATTATT-TTCTTAGGAAAATTTATTAT-TT-TTAATATTTATTTATTT-TTTA--AATATTAAGA
1 ATTATTATTTTTAGGAAAA-TTATTATATTATTATTATTTATTTATTTATTTATTAATATTAAGA
* * * *
663193 AATGGCAGTCTTAAAGCAATTAGATG-TCTTCTTCTGGTATTTTAAAAATAAATAAATATAAAAA
65 AATGACAGTCTTAAAGCAACTAGATGTTCTTATTCTGATATTTTAAAAATAAATAAATATAAAAA
* *
663257 CCAATATATATATATAT
130 CCAATATAAAAATATAT
* * * * *
663274 ATTGTT-TTATTTA--AATTATTTTCTTAAATTATTATTTTTAATATTTATTTATTT-TTCAAAT
1 ATTATTATT-TTTAGGAA--A-ATTATTATATTATTATTATT--TATTTATTTATTTATT--AAT
*
663335 ATTAAGAAATGTCAGTCTTAAAGCAACTAGATGTT-TTATTCTGATATTTTAAAAATAAATAAAT
58 ATTAAGAAATGACAGTCTTAAAGCAACTAGATGTTCTTATTCTGATATTTTAAAAATAAATAAAT
*** *
663399 AT-CCTA-C-TTATAAAAATATAT
123 ATAAAAACCAATATAAAAATATAT
663420 ACTTCATTATTTTTAGGAAAATTATTATATTATTATTATTTATTTATTTATTTATTAATATTAAA
1 A-TT-ATTATTTTTAGGAAAATTATTATATTATTATTATTTATTTATTTATTTATTAATATT-AA
*
663485 GAAA-GACAATCTTAAAGCAACTAGATGTTCTT-TTCTGATATTTT--AAATAAATAAAT
63 GAAATGACAGTCTTAAAGCAACTAGATGTTCTTATTCTGATATTTTAAAAATAAATAAAT
663541 GTCATATTTA
Statistics
Matches: 221, Mismatches: 24, Indels: 42
0.77 0.08 0.15
Matches are distributed among these distances:
139 2 0.01
140 7 0.03
141 9 0.04
142 14 0.06
143 6 0.03
144 41 0.19
145 30 0.14
146 17 0.08
147 19 0.09
148 8 0.04
149 65 0.29
150 3 0.01
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (146 bp):
ATTATTATTTTTAGGAAAATTATTATATTATTATTATTTATTTATTTATTTATTAATATTAAGAA
ATGACAGTCTTAAAGCAACTAGATGTTCTTATTCTGATATTTTAAAAATAAATAAATATAAAAAC
CAATATAAAAATATAT
Found at i:663577 original size:12 final size:12
Alignment explanation
Indices: 663560--663608 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
663550 ACAAAAATCC
*
663560 TAAATATATTTA
1 TAAATATATATA
*
663572 TAAATACATATA
1 TAAATATATATA
663584 T-AA-ATATATA
1 TAAATATATATA
663594 TAAATATATATA
1 TAAATATATATA
663606 TAA
1 TAA
663609 TATTTTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 7 0.22
11 4 0.12
12 21 0.66
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATATATATA
Found at i:663592 original size:10 final size:10
Alignment explanation
Indices: 663560--663611 Score: 59
Period size: 10 Copynumber: 4.7 Consensus size: 10
663550 ACAAAAATCC
663560 TAAATATATTTA
1 TAAATATA--TA
663572 TAAATACATATA
1 TAAAT--ATATA
663584 TAAATATATA
1 TAAATATATA
663594 TAAATATATA
1 TAAATATATA
663604 TATAATAT
1 TA-AATAT
663612 TTTTTTCTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
10 17 0.46
11 5 0.14
12 12 0.32
14 3 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (10 bp):
TAAATATATA
Found at i:670189 original size:21 final size:20
Alignment explanation
Indices: 670149--670190 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
670139 CCAACTTACA
*
670149 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
670169 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
670190 A
1 A
670191 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:670656 original size:20 final size:20
Alignment explanation
Indices: 670552--670662 Score: 75
Period size: 20 Copynumber: 5.6 Consensus size: 20
670542 AAATGACCAA
670552 CAAAATCGCAACGCGAA-AT
1 CAAAATCGCAACGCGAACAT
* * **
670571 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGAACAT
* ** ***
670591 CAGAATCGCAAATC-AGTTT
1 CAAAATCGCAACGCGAACAT
*
670610 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAACAT
*
670631 GAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAACAT
670650 CATAAATCGCAAC
1 CA-AAATCGCAAC
670663 TCGTATCCGT
Statistics
Matches: 68, Mismatches: 20, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
19 17 0.25
20 48 0.71
21 3 0.04
ACGTcount: A:0.43, C:0.28, G:0.15, T:0.14
Consensus pattern (20 bp):
CAAAATCGCAACGCGAACAT
Found at i:670658 original size:60 final size:58
Alignment explanation
Indices: 670552--670683 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 58
670542 AAATGACCAA
* * * *
670552 CAAAATCGCAACGCGAAATAAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
1 CAAAATCGCAACGCGAAATAAAAATCGCAACGCGATACACAAAATCGCAAATC-GTATC
* *
670611 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA-ACACATAAATCGCAACTCGTATC
1 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGATACACA-AAATCGCAAATCGTATC
*
670670 CGTAAATCGCAACG
1 C-AAAATCGCAACG
670684 TGTATCCGTA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 25 0.40
60 38 0.60
ACGTcount: A:0.41, C:0.28, G:0.16, T:0.15
Consensus pattern (58 bp):
CAAAATCGCAACGCGAAATAAAAATCGCAACGCGATACACAAAATCGCAAATCGTATC
Found at i:670675 original size:20 final size:20
Alignment explanation
Indices: 670613--670842 Score: 223
Period size: 20 Copynumber: 11.5 Consensus size: 20
670603 TCAGTTTCCA
* ** *
670613 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
670633 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
670653 AAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
670673 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
670693 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
670713 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
670733 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
670753 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
670773 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
670793 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
670813 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
670833 AAATCACAAC
1 AAATCGCAAC
670843 ACTGAAATTT
Statistics
Matches: 174, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 170 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:671761 original size:12 final size:12
Alignment explanation
Indices: 671744--671768 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
671734 ATATAATCCT
671744 GAAGAAGAAAAA
1 GAAGAAGAAAAA
671756 GAAGAAGAAAAA
1 GAAGAAGAAAAA
671768 G
1 G
671769 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:674073 original size:19 final size:19
Alignment explanation
Indices: 674051--674319 Score: 282
Period size: 19 Copynumber: 15.4 Consensus size: 19
674041 CGAAAATTAC
*
674051 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
674070 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
674084 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
674104 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
674118 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
674137 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
674156 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
674175 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
674189 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
674208 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
674227 AATTGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
674241 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
674260 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
674279 AATCGCAA----AGA-GAG
1 AATCGCAATGCGAAATGAA
674293 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
674312 AATCGCAA
1 AATCGCAA
674320 CGAGAGAATC
Statistics
Matches: 210, Mismatches: 14, Indels: 52
0.76 0.05 0.19
Matches are distributed among these distances:
14 51 0.24
15 5 0.02
16 7 0.03
17 6 0.03
18 6 0.03
19 122 0.58
20 13 0.06
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:674138 original size:33 final size:33
Alignment explanation
Indices: 674051--674341 Score: 313
Period size: 33 Copynumber: 8.5 Consensus size: 33
674041 CGAAAATTAC
* * *
674051 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
674084 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
*
674118 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
674156 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
674189 AATCGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* * *
674221 AAT-GAAAATTGC-AACGA-GAGAATCGCAATGCGAAATGAA
1 AATCG-CAA-TGCGAA--ATGAAAATCGCAA--CG--A-GAG
*
674260 AATCGCAATGCGAAATGAAAATCGCAAAGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
674293 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
674326 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
674342 TATAAACGCA
Statistics
Matches: 222, Mismatches: 16, Indels: 40
0.80 0.06 0.14
Matches are distributed among these distances:
31 1 0.00
32 7 0.03
33 121 0.55
34 32 0.14
35 4 0.02
36 3 0.01
37 2 0.01
38 44 0.20
39 7 0.03
40 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:674193 original size:52 final size:52
Alignment explanation
Indices: 674051--674319 Score: 375
Period size: 52 Copynumber: 5.2 Consensus size: 52
674041 CGAAAATTAC
* * *
674051 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
* * * * *
674104 AATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAATGCGAAATGAA
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
674156 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
674208 AATCGCAATGCGAAATGAAAATTGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
674260 AATCGCAATGCGAAATGAAAATCGCAAAGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
674312 AATCGCAA
1 AATCGCAA
674320 CGAGAGAATC
Statistics
Matches: 196, Mismatches: 13, Indels: 15
0.88 0.06 0.07
Matches are distributed among these distances:
50 7 0.04
51 7 0.04
52 147 0.75
53 23 0.12
54 7 0.04
55 4 0.02
56 1 0.01
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:674418 original size:53 final size:52
Alignment explanation
Indices: 674348--674463 Score: 196
Period size: 53 Copynumber: 2.2 Consensus size: 52
674338 AAATTATAAA
*
674348 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTACGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
*
674401 CGTATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 CGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
*
674453 CGCATTGCGAT
1 CGCATTACGAT
674464 AGTCATTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 28 0.47
53 31 0.53
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
CGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
Found at i:674443 original size:19 final size:19
Alignment explanation
Indices: 674366--674463 Score: 125
Period size: 19 Copynumber: 5.4 Consensus size: 19
674356 GATTCTCTCG
674366 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
674386 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
* *
674405 TTACGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
674419 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
674438 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
674457 TTGCGAT
1 TTGCGAT
674464 AGTCATTTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
14 5 0.07
16 7 0.10
17 7 0.10
19 34 0.50
20 15 0.22
ACGTcount: A:0.15, C:0.21, G:0.16, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:674469 original size:19 final size:19
Alignment explanation
Indices: 674428--674471 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
674418 GTTGCGATTT
**
674428 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
674447 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
674466 TCATTT
1 TCATTT
674472 TTGCCTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:674589 original size:14 final size:14
Alignment explanation
Indices: 674570--674605 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
674560 CTTCAATTAC
674570 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
674584 ACAAATCATCTTTT
1 ACAAATCAACTTTT
674598 AC-AATCAA
1 ACAAATCAA
674606 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:676602 original size:14 final size:14
Alignment explanation
Indices: 676583--676639 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
676573 GCGAAATGAA
*
676583 AATCGCAACGACAG
1 AATCGCAACGAAAG
676597 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
676614 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
676630 AATCGCAACG
1 AATCGCAACG
676640 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:676610 original size:33 final size:33
Alignment explanation
Indices: 676564--676656 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
676554 GCGAAACCAA
*
676564 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
676597 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
676630 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
676657 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Done.