Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009081.1 Hibiscus syriacus cultivar Beakdansim tig00112523_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: 1718667
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:453842 original size:83 final size:83
Alignment explanation
Indices: 453702--453866 Score: 294
Period size: 83 Copynumber: 2.0 Consensus size: 83
453692 TTATGAAAAC
*
453702 ATTAAAAGTTTAAATACTAAAACAGACCAAAATTGATAATTCAAGTATTAAAAATATAATTTACC
1 ATTAAAAGTTTAAATACTAAAACAGACCAAAACTGATAATTCAAGTATTAAAAATATAATTTACC
453767 CAATAATGTTAGTCCAAT
66 CAATAATGTTAGTCCAAT
* * *
453785 ATTAAAAGTTTAAATACTAAAACAGACTAAAACTGATAATTTAAGTATTAAACATATAATTTACC
1 ATTAAAAGTTTAAATACTAAAACAGACCAAAACTGATAATTCAAGTATTAAAAATATAATTTACC
453850 CAATAATGTTAGTCCAA
66 CAATAATGTTAGTCCAA
453867 GAATCTTCGT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (83 bp):
ATTAAAAGTTTAAATACTAAAACAGACCAAAACTGATAATTCAAGTATTAAAAATATAATTTACC
CAATAATGTTAGTCCAAT
Found at i:454598 original size:17 final size:18
Alignment explanation
Indices: 454567--454600 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
454557 TGTACTTAAA
454567 TTTTTTAAATCATAAGTG
1 TTTTTTAAATCATAAGTG
*
454585 TTTTTTTAAT-ATAAGT
1 TTTTTTAAATCATAAGT
454601 AACTATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (18 bp):
TTTTTTAAATCATAAGTG
Found at i:455120 original size:16 final size:17
Alignment explanation
Indices: 455080--455123 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
455070 ATAAATAATT
455080 TTTTAATTA-TAAGATA
1 TTTTAATTATTAAGATA
455096 TTATT--TTATTAAG-TA
1 TT-TTAATTATTAAGATA
455111 TTTTAATTATTAA
1 TTTTAATTATTAA
455124 TTATGTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 2 0.08
15 7 0.29
16 13 0.54
17 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (17 bp):
TTTTAATTATTAAGATA
Found at i:457551 original size:19 final size:19
Alignment explanation
Indices: 457524--457560 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
457514 AGATTCTGAT
*
457524 ATTAGATTATATCATATAG
1 ATTAAATTATATCATATAG
*
457543 ATTAAATTATATCGTATA
1 ATTAAATTATATCATATA
457561 TCAGTTAGTA
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:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (19 bp):
ATTAAATTATATCATATAG
Found at i:459865 original size:25 final size:25
Alignment explanation
Indices: 459832--459901 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
459822 AAATAATTTT
*
459832 AAAATTTAAGTACTTAATTGTAT-A
1 AAAAATTAAGTACTTAATTGTATCA
*
459856 AAAAACTTAAGTACCTAATTGTATCA
1 AAAAA-TTAAGTACTTAATTGTATCA
* *
459882 AAAAATTAGGTACTCAATTG
1 AAAAATTAAGTACTTAATTG
459902 CACCATTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 4 0.10
25 29 0.74
26 6 0.15
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (25 bp):
AAAAATTAAGTACTTAATTGTATCA
Found at i:460415 original size:21 final size:22
Alignment explanation
Indices: 460389--460429 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
460379 TTCGAATTAG
*
460389 TAAAAAATAAAC-TTAAAAAAA
1 TAAAAAAAAAACATTAAAAAAA
460410 TAAAAAAAAAACATTAAAAA
1 TAAAAAAAAAACATTAAAAA
460430 GAAATCAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (22 bp):
TAAAAAAAAAACATTAAAAAAA
Found at i:460533 original size:2 final size:2
Alignment explanation
Indices: 460526--460552 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
460516 TTAAAAATTA
460526 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
460553 AATAAAATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:461097 original size:19 final size:19
Alignment explanation
Indices: 461073--461112 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
461063 CTCAAACATC
461073 AAACCCTAAACCATTAACT
1 AAACCCTAAACCATTAACT
461092 AAACCCTAAACCATTAACT
1 AAACCCTAAACCATTAACT
461111 AA
1 AA
461113 GTAACTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (19 bp):
AAACCCTAAACCATTAACT
Found at i:461961 original size:60 final size:60
Alignment explanation
Indices: 461895--462026 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
461885 TAGTTGGGTG
* * * ** *
461895 ATCATTTTGTAACTTTTAATAGTCGTTAGACTTAACAAAACAACGT-TC-TATAGTCAGAGA
1 ATCATTTTATAACTTATAACAGTCGAGAAACTTAACAAAACAA--TATCTTATAGTCAGAGA
* *
461955 ATCATTTTATAACTTATAACAGTTGAGAAACTTAATAAAACAATATCTTATAGTCAGAGA
1 ATCATTTTATAACTTATAACAGTCGAGAAACTTAACAAAACAATATCTTATAGTCAGAGA
*
462015 ACCATTTGTATA
1 ATCATTT-TATA
462027 TTTAATCTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 1 0.02
59 2 0.03
60 53 0.88
61 4 0.07
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (60 bp):
ATCATTTTATAACTTATAACAGTCGAGAAACTTAACAAAACAATATCTTATAGTCAGAGA
Found at i:462477 original size:2 final size:2
Alignment explanation
Indices: 462470--462497 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
462460 TTGATTTTAA
462470 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
462498 GTCATCGTCG
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):
AT
Found at i:462583 original size:39 final size:39
Alignment explanation
Indices: 462525--462603 Score: 142
Period size: 39 Copynumber: 2.0 Consensus size: 39
462515 AATGTCATCA
462525 TCGAGTGGTTTAACATTTGATATCGCTTAAGTAAAGTTT
1 TCGAGTGGTTTAACATTTGATATCGCTTAAGTAAAGTTT
462564 TCGAGTGG-TTAACATTTTGATATCGCTTAAGTAAAGTTT
1 TCGAGTGGTTTAACA-TTTGATATCGCTTAAGTAAAGTTT
462603 T
1 T
462604 AAGTTTGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 6 0.15
39 33 0.85
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (39 bp):
TCGAGTGGTTTAACATTTGATATCGCTTAAGTAAAGTTT
Found at i:464843 original size:114 final size:112
Alignment explanation
Indices: 464701--464928 Score: 422
Period size: 114 Copynumber: 2.0 Consensus size: 112
464691 CACGGTCAAT
464701 AACATGATCCGAAAAAAATCTGTAAGAAAGATCTTAC-TTACAATAAATTTAATTGAAAAGATAT
1 AACATGATCCGAAAAAAATCTGTAAGAAAGATCTTACTTTACAATAAATTTAATTGAAAAGATAT
464765 TATATCCCATTTGAACTCAATTATGACTTCTAAGTGATTAATGCACGA
66 T-TATCCCATTTGAACTCAATTATGACTTCTAAGTGATTAATGCACGA
464813 AACATGATCCGACAAAAACATCTGTAAGAAAGATCTTACTTTACAATAAATTTAATTGAAAAGAT
1 AACATGATCCGA-AAAAA-ATCTGTAAGAAAGATCTTACTTTACAATAAATTTAATTGAAAAGAT
464878 ATTTATCCCATTTGAACTCAATTATGACTTCTAAGTGATTAATGCACGA
64 ATTTATCCCATTTGAACTCAATTATGACTTCTAAGTGATTAATGCACGA
464927 AA
1 AA
464929 TACAAGGGCT
Statistics
Matches: 113, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
112 12 0.11
113 5 0.04
114 68 0.60
115 28 0.25
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (112 bp):
AACATGATCCGAAAAAAATCTGTAAGAAAGATCTTACTTTACAATAAATTTAATTGAAAAGATAT
TTATCCCATTTGAACTCAATTATGACTTCTAAGTGATTAATGCACGA
Found at i:468202 original size:25 final size:26
Alignment explanation
Indices: 468174--468223 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
468164 GTGTTGGCCG
468174 TAGGT-CGCCATGCCTTCCAGGCGAC
1 TAGGTCCGCCATGCCTTCCAGGCGAC
* *
468199 TAGGTCCGCCATGTCTTCCCGGCGA
1 TAGGTCCGCCATGCCTTCCAGGCGA
468224 GCTACAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (26 bp):
TAGGTCCGCCATGCCTTCCAGGCGAC
Found at i:468303 original size:14 final size:14
Alignment explanation
Indices: 468270--468349 Score: 81
Period size: 14 Copynumber: 5.4 Consensus size: 14
468260 CGCTGGGCAT
*
468270 CCGAGGCCACCCGA
1 CCGAGGCCATCCGA
468284 -CGAGGCCATCCGA
1 CCGAGGCCATCCGA
468297 CCGAGGCCATCCGAGAGCA
1 CCGAGGCCATCC----G-A
468316 TCCGAGGCCATCCGA
1 -CCGAGGCCATCCGA
468331 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
468345 ACGAG
1 CCGAG
468350 CTATGCGAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
13 12 0.21
14 29 0.51
15 1 0.02
16 1 0.02
18 1 0.02
19 1 0.02
20 12 0.21
ACGTcount: A:0.24, C:0.40, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:468319 original size:47 final size:47
Alignment explanation
Indices: 468266--468369 Score: 156
Period size: 47 Copynumber: 2.2 Consensus size: 47
468256 AACACGCTGG
*
468266 GCATCCGAGGCCACCCGA-CGAGGCCATCCGACCGAGGCCATCCGAGA
1 GCATCCGAGGCCACCCGACCGAGGCCATCCGAACGA-GCCATCCGAGA
* * *
468313 GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGAGCTATGCGAGA
1 GCATCCGAGGCCACCCGACCGAGGCCATCCGAACGAGCCATCCGAGA
468360 GCATCCGAGG
1 GCATCCGAGG
468370 GCAACCGAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
47 36 0.69
48 16 0.31
ACGTcount: A:0.24, C:0.37, G:0.31, T:0.09
Consensus pattern (47 bp):
GCATCCGAGGCCACCCGACCGAGGCCATCCGAACGAGCCATCCGAGA
Found at i:468383 original size:33 final size:33
Alignment explanation
Indices: 468331--468415 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
468321 GGCCATCCGA
* * * *
468331 CCGAGGCCATCCGAACGAGCTATGCGAGAGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGAGAAT
*
468364 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGAGAAT
468397 CCGAGGG-AAGCCGAGCGAG
1 CCGAGGGCAA-CCGAGCGAG
468416 GGTAGGTCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.04
33 44 0.96
ACGTcount: A:0.27, C:0.27, G:0.38, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGAGAAT
Found at i:468509 original size:20 final size:21
Alignment explanation
Indices: 468474--468514 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
468464 TGCCATGCAC
468474 ACGTTCATTCTCTCTGTTTGA
1 ACGTTCATTCTCTCTGTTTGA
468495 ACGTTCATT-TCTCTGTTTGA
1 ACGTTCATTCTCTCTGTTTGA
468515 GCAAGGGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.49
Consensus pattern (21 bp):
ACGTTCATTCTCTCTGTTTGA
Found at i:468592 original size:29 final size:29
Alignment explanation
Indices: 468550--468623 Score: 148
Period size: 29 Copynumber: 2.6 Consensus size: 29
468540 TGGCGAGGTC
468550 GTGCATGGCGACCTACAAGGTCGCCCGGA
1 GTGCATGGCGACCTACAAGGTCGCCCGGA
468579 GTGCATGGCGACCTACAAGGTCGCCCGGA
1 GTGCATGGCGACCTACAAGGTCGCCCGGA
468608 GTGCATGGCGACCTAC
1 GTGCATGGCGACCTAC
468624 GGCCAACACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.20, C:0.31, G:0.34, T:0.15
Consensus pattern (29 bp):
GTGCATGGCGACCTACAAGGTCGCCCGGA
Found at i:468970 original size:14 final size:14
Alignment explanation
Indices: 468951--468977 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
468941 CATCCAAAGT
468951 CATCCGACCGAGGG
1 CATCCGACCGAGGG
468965 CATCCGACCGAGG
1 CATCCGACCGAGG
468978 CCATTCGAGC
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:0.22, C:0.37, G:0.33, T:0.07
Consensus pattern (14 bp):
CATCCGACCGAGGG
Found at i:468990 original size:14 final size:14
Alignment explanation
Indices: 468951--468981 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
468941 CATCCAAAGT
*
468951 CATCCGACCGAGGG
1 CATCCGACCGAGGC
468965 CATCCGACCGAGGC
1 CATCCGACCGAGGC
468979 CAT
1 CAT
468982 TCGAGCGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.39, G:0.29, T:0.10
Consensus pattern (14 bp):
CATCCGACCGAGGC
Found at i:469743 original size:2 final size:2
Alignment explanation
Indices: 469691--469735 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
469681 TGTTTCCATT
469691 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
469731 TA TA T
1 TA TA T
469736 GAATATATGG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:470397 original size:88 final size:88
Alignment explanation
Indices: 470270--470446 Score: 313
Period size: 88 Copynumber: 2.0 Consensus size: 88
470260 GGCCATTCTT
470270 TTCATCGTTCCGTCTTATTCCTCATCGGCATCGTCTCTCGGCTTGCTCGGAAA-ATTTTCCTCCG
1 TTCATCGTTCCGTCTTATTCCTCATCGGCATCGTCTCTCGGCTTGCTCGGAAACA-TTTCCTCCG
470334 GGGCCGAGAGGGATG-CGATAATC
65 GGGCCGAGAGGGATGCCGATAATC
470357 TTCATCGTTCCGTTCTTATTCCTCATCGGCATCGTCTCTCGGCTTGCTCGGAAACCATTTCCTCC
1 TTCATCGTTCCG-TCTTATTCCTCATCGGCATCGTCTCTCGGCTTGCTCGGAAA-CATTTCCTCC
470422 GGGGCCGAGAGGGATGCCGATAATC
64 GGGGCCGAGAGGGATGCCGATAATC
470447 GGCAACATGT
Statistics
Matches: 86, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
87 12 0.14
88 41 0.48
89 24 0.28
90 9 0.10
ACGTcount: A:0.16, C:0.30, G:0.24, T:0.31
Consensus pattern (88 bp):
TTCATCGTTCCGTCTTATTCCTCATCGGCATCGTCTCTCGGCTTGCTCGGAAACATTTCCTCCGG
GGCCGAGAGGGATGCCGATAATC
Found at i:500123 original size:35 final size:36
Alignment explanation
Indices: 500057--500159 Score: 116
Period size: 32 Copynumber: 3.1 Consensus size: 36
500047 TTTTTATATT
* *
500057 TTTAATTTTGTAAA-AAATTATA-AAATA-TATG-A
1 TTTAATTTTTTAAAGAAAATATATAAATATTATGAA
500089 TTTAATTTTTTAAAGAAAATATATAAATATTATGAA
1 TTTAATTTTTTAAAGAAAATATATAAATATTATGAA
500125 TTTAA-TTTTT-AAG-AAATATAT-AATATTTAT-AA
1 TTTAATTTTTTAAAGAAAATATATAAATA-TTATGAA
500157 TTT
1 TTT
500160 GTAATATTAT
Statistics
Matches: 64, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
32 22 0.34
33 19 0.30
34 8 0.12
35 9 0.14
36 6 0.09
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (36 bp):
TTTAATTTTTTAAAGAAAATATATAAATATTATGAA
Found at i:500159 original size:32 final size:31
Alignment explanation
Indices: 500057--500159 Score: 100
Period size: 33 Copynumber: 3.1 Consensus size: 31
500047 TTTTTATATT
* * *
500057 TTTAATTTTGTAAAAAAT-TATAAAATATATGA
1 TTTAATTTT-TAAGAAATATAT-AAATTTATAA
500089 TTTAATTTTTTAAAGAAAATATATAAATATTATGAA
1 TTTAA-TTTTT-AAG-AAATATATAAAT-TTAT-AA
500125 TTTAATTTTTAAGAAATATATAATATTTATAA
1 TTTAATTTTTAAGAAATATATAA-ATTTATAA
500157 TTT
1 TTT
500160 GTAATATTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
32 11 0.18
33 20 0.33
34 13 0.21
35 11 0.18
36 6 0.10
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTAATTTTTAAGAAATATATAAATTTATAA
Found at i:500318 original size:18 final size:20
Alignment explanation
Indices: 500295--500334 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
500285 TTCTCAGTAA
500295 TTTTATT-CC-CTGATAATC
1 TTTTATTCCCACTGATAATC
500313 TTTTATTCCCACTGATAATC
1 TTTTATTCCCACTGATAATC
500333 TT
1 TT
500335 ACATTCCGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 2 0.10
20 11 0.55
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTATTCCCACTGATAATC
Found at i:500340 original size:20 final size:20
Alignment explanation
Indices: 500304--500341 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
500294 ATTTTATTCC
**
500304 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
500324 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
500342 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:500434 original size:20 final size:20
Alignment explanation
Indices: 500396--500434 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
500386 TCTTTGGTTA
* * *
500396 TTTTATTTTTCTAATTAAAT
1 TTTTATTTTACCAAATAAAT
500416 TTTTATTTTACCAAATAAA
1 TTTTATTTTACCAAATAAA
500435 AATAAATTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTATTTTACCAAATAAAT
Found at i:504511 original size:14 final size:13
Alignment explanation
Indices: 504483--504509 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
504473 AAAATCCTAA
504483 TCGTTGATTTTTT
1 TCGTTGATTTTTT
504496 TCGTTGATTTTTT
1 TCGTTGATTTTTT
504509 T
1 T
504510 TCTATTGATG
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:0.07, C:0.07, G:0.15, T:0.70
Consensus pattern (13 bp):
TCGTTGATTTTTT
Found at i:510655 original size:20 final size:20
Alignment explanation
Indices: 510597--510658 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
510587 TTTTTAGTGT
* *
510597 TAAAATATGTTATTTAATTA
1 TAAAATATATTATTTTATTA
* * **
510617 TTCAAATATAATAAATTATTA
1 -TAAAATATATTATTTTATTA
510638 TAAAATATATTATTTTATTA
1 TAAAATATATTATTTTATTA
510658 T
1 T
510659 TTTAAATAAT
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TAAAATATATTATTTTATTA
Found at i:510674 original size:23 final size:23
Alignment explanation
Indices: 510631--510674 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
510621 AATATAATAA
*
510631 ATTATTATAAAATATATTATTTT
1 ATTATTATAAAATATAATATTTT
*
510654 ATTATT-TTAAATAATAATATT
1 ATTATTATAAAAT-ATAATATT
510675 CAGGTTGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTATTATAAAATATAATATTTT
Found at i:518050 original size:2 final size:2
Alignment explanation
Indices: 518043--518074 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
518033 TGATCCAGTC
518043 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
518075 CAATTTCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:519508 original size:60 final size:60
Alignment explanation
Indices: 519424--519569 Score: 147
Period size: 60 Copynumber: 2.4 Consensus size: 60
519414 GAGTATTTAG
* * * * * **
519424 AAGTTTAGGGACGAATTTAGAATGAG-AGACATAGTTT-GAGGATGATATTAGAATTTTAAA
1 AAGTTTAAGGACTAATTTAAAATGAGTA-ACATACTTTAG-GGATGAAATTAGAATAATAAA
*
519484 AAGTTTAAGGACTAATTTAAAATGAGTATCATACTTTAGGGATGAAATTAGAATAATAAA
1 AAGTTTAAGGACTAATTTAAAATGAGTAACATACTTTAGGGATGAAATTAGAATAATAAA
*
519544 ATA-TTT-AGAGATTAATTTAAAATGAG
1 A-AGTTTAAG-GACTAATTTAAAATGAG
519570 GGTTATAGTT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
59 2 0.03
60 68 0.93
61 3 0.04
ACGTcount: A:0.44, C:0.03, G:0.20, T:0.33
Consensus pattern (60 bp):
AAGTTTAAGGACTAATTTAAAATGAGTAACATACTTTAGGGATGAAATTAGAATAATAAA
Found at i:529061 original size:15 final size:15
Alignment explanation
Indices: 529041--529085 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
529031 TAAAAAGGTT
529041 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
529056 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
529071 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
529086 TGGATTGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:529126 original size:33 final size:36
Alignment explanation
Indices: 529056--529138 Score: 127
Period size: 33 Copynumber: 2.4 Consensus size: 36
529046 TTTTAAAATA
*
529056 ATTTATTTTAAAATAATTTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTAT-AAATATGAATTG
529093 ATTTATTTTAAAATAATTTA-T-T-AATATGAATTG
1 ATTTATTTTAAAATAATTTATTATAAATATGAATTG
529126 ATTTATTTTAAAA
1 ATTTATTTTAAAA
529139 CATGGATTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
33 23 0.51
35 1 0.02
36 1 0.02
37 20 0.44
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (36 bp):
ATTTATTTTAAAATAATTTATTATAAATATGAATTG
Found at i:529147 original size:22 final size:22
Alignment explanation
Indices: 529122--529242 Score: 215
Period size: 22 Copynumber: 5.5 Consensus size: 22
529112 ATTAATATGA
529122 ATTGATTTATTTTAAAACATGG
1 ATTGATTTATTTTAAAACATGG
529144 ATTGATTTATTTTAAAACATGG
1 ATTGATTTATTTTAAAACATGG
529166 ATTGATTTATTTTAAAACATGG
1 ATTGATTTATTTTAAAACATGG
*
529188 ATTGATTTATTTTAAAATATGG
1 ATTGATTTATTTTAAAACATGG
* *
529210 ATTGATTTATTTTAAAATATTG
1 ATTGATTTATTTTAAAACATGG
529232 ATTGATTTATT
1 ATTGATTTATT
529243 ATTGTAGTTG
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 97 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (22 bp):
ATTGATTTATTTTAAAACATGG
Found at i:529172 original size:44 final size:44
Alignment explanation
Indices: 529115--529349 Score: 254
Period size: 44 Copynumber: 5.0 Consensus size: 44
529105 ATAATTTATT
* *
529115 AATATGAATTGATTTATTTTAAAACATGGATTGATTTATTTTAA
1 AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* *
529159 AACATGGATTGATTTATTTTAAAACATGGATTGATTTATTTTAA
1 AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* *
529203 AATATGGATTGATTTATTTTAAAATATTGATTGATTTATTATTGTAGT
1 AATATGGATTGATTTATTTTAAAATATGGATTGATTTA-T-TT-TA-A
** *
529251 TGTATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGAATTATTTTAA
1 AATATGGATTGATTTATTTT-AA-AA--TA-T-G----GATTGATTTATTTTAA
*
529305 AATATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
529349 A
1 A
529350 TAATTTATTA
Statistics
Matches: 162, Mismatches: 15, Indels: 28
0.79 0.07 0.14
Matches are distributed among these distances:
44 93 0.57
45 1 0.01
46 2 0.01
47 2 0.01
48 19 0.12
49 3 0.02
50 4 0.02
52 4 0.02
53 3 0.02
54 17 0.10
55 2 0.01
56 2 0.01
57 1 0.01
58 9 0.06
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.50
Consensus pattern (44 bp):
AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
Found at i:529200 original size:66 final size:66
Alignment explanation
Indices: 529115--529349 Score: 254
Period size: 66 Copynumber: 3.3 Consensus size: 66
529105 ATAATTTATT
* * * *
529115 AATATGAATTGATTTATTTTAAAACATGGATTGATTTATTTTAAAACATGGATTGATTTATTTTA
1 AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTA
529180 A
66 A
* *
529181 AACATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATTGATTGATTTATTATT
1 AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATAGATTGATTTA-T-TT
*
529246 GTAGT
64 -TA-A
** *
529251 TGTATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGAATTATTTTAAAATATAGATTG
1 AATATGGATTGATTTATTTT-AA-AA--TA-T-G----GATTGATTTATTTTAAAATATAGATTG
529316 ATTTATTTTAA
56 ATTTATTTTAA
529327 AATATGGATTGATTTATTTTAAA
1 AATATGGATTGATTTATTTTAAA
529350 TAATTTATTA
Statistics
Matches: 141, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
66 55 0.39
67 1 0.01
68 2 0.01
69 2 0.01
70 17 0.12
71 2 0.01
72 2 0.01
74 3 0.02
75 3 0.02
76 19 0.13
77 2 0.01
78 2 0.01
79 1 0.01
80 30 0.21
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.50
Consensus pattern (66 bp):
AATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTA
A
Found at i:529314 original size:22 final size:22
Alignment explanation
Indices: 529289--529349 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
529279 TATTAGTATT
*
529289 GATTGAATTATTTTAAAATATA
1 GATTGATTTATTTTAAAATATA
*
529311 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATA
529333 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
529350 TAATTTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATA
Found at i:529348 original size:76 final size:79
Alignment explanation
Indices: 529209--529376 Score: 245
Period size: 76 Copynumber: 2.2 Consensus size: 79
529199 TTAAAATATG
* ***
529209 GATTGATTTATTTTAAAATATTGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAA
1 GATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGAAATATGGATTGATTTATTTTAAA
529274 TAATTTATTAGTATT
66 TAATTTATTAGTA-T
*
529289 GATTGAATTATTTTAAAATATAGATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAA
1 GATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGAAATATGGATTGATTTATTTTAAA
529350 TAATTTATTAGTAT
66 TAATTTATTAGTAT
529364 GAATTGATTTATT
1 G-ATTGATTTATT
529377 ATTGTAGTTG
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
75 2 0.02
76 44 0.54
77 2 0.02
78 2 0.02
79 1 0.01
80 30 0.37
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (79 bp):
GATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGAAATATGGATTGATTTATTTTAAA
TAATTTATTAGTAT
Found at i:529370 original size:54 final size:54
Alignment explanation
Indices: 529312--529456 Score: 227
Period size: 58 Copynumber: 2.6 Consensus size: 54
529302 TAAAATATAG
529312 ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA
1 ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA
***
529366 ATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGA
1 ATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA
529424 ATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTGATTTATTTTAAAATATGGATTGATTTATT
529457 ATTGTAGTTG
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
54 25 0.31
55 3 0.04
56 4 0.05
57 3 0.04
58 46 0.57
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA
Found at i:529372 original size:32 final size:32
Alignment explanation
Indices: 529329--529439 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 32
529319 TATTTTAAAA
*
529329 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGAATTGATTTATTTTAAATAATTTATTAG
*
529361 TATGAATTGATTTA--TT--AT--TGTAGTT-G
1 TATGAATTGATTTATTTTAAATAATTTA-TTAG
*
529387 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGAATTGATTTATTTTAAATAATTTATTAG
529419 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
529440 ATATGGATTG
Statistics
Matches: 66, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
26 17 0.26
27 2 0.03
28 4 0.06
30 4 0.06
31 2 0.03
32 37 0.56
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (32 bp):
TATGAATTGATTTATTTTAAATAATTTATTAG
Found at i:529381 original size:134 final size:138
Alignment explanation
Indices: 529232--529551 Score: 487
Period size: 134 Copynumber: 2.4 Consensus size: 138
529222 TAAAATATTG
529232 ATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATTG-ATTGAA
1 ATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTA-TGAATTGAA
529296 TTATTTTAAAATATAGATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTA
65 TTATTTTAAAATATAGATTGATTTATTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTA
529357 TTAGTATGA
130 TTAGTATGA
*
529366 ATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATT
1 ATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGAAT
* ***
529431 TATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTAT
66 TATTTTAAAATATAGATTGATTTATTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTAT
*
529496 TAGTATGG
131 TAGTATGA
***
529504 ATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTA
1 ATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTA
529552 TTGTATTTGT
Statistics
Matches: 172, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
133 2 0.01
134 115 0.67
135 3 0.02
136 4 0.02
137 3 0.02
138 45 0.26
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (138 bp):
ATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGAAT
TATTTTAAAATATAGATTGATTTATTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTAT
TAGTATGA
Found at i:529389 original size:26 final size:25
Alignment explanation
Indices: 529355--529482 Score: 91
Period size: 26 Copynumber: 4.8 Consensus size: 25
529345 TTAAATAATT
*
529355 TATTAGTATGAATTGATTTATTATTG
1 TATT-GTATGGATTGATTTATTATTG
*
529381 TAGTTGTATGGATTGATTTATTTTAAATAATT
1 TA-TTGTATGGATTGATTTA--TT--AT--TG
*
529413 TATTAGTATGAATTGATTTA-T-TT-
1 TATT-GTATGGATTGATTTATTATTG
***
529436 TAAAATATGGATTGATTTATTATTG
1 TATTGTATGGATTGATTTATTATTG
529461 TAGTTGTATGGATTGATTTATT
1 TA-TTGTATGGATTGATTTATT
529483 TTAAATAATT
Statistics
Matches: 80, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
22 13 0.16
23 3 0.04
24 3 0.04
25 2 0.03
26 33 0.41
27 2 0.03
28 2 0.03
29 1 0.01
30 2 0.03
31 2 0.03
32 17 0.21
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.53
Consensus pattern (25 bp):
TATTGTATGGATTGATTTATTATTG
Found at i:529400 original size:80 final size:79
Alignment explanation
Indices: 529253--529487 Score: 236
Period size: 80 Copynumber: 3.0 Consensus size: 79
529243 ATTGTAGTTG
* *** *
529253 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGA---ATTATTTTA-AAATATAGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTA-TGATTGATTTATTATTGTAGTTGTATGGAT
529314 TGATTTATTTTAAAA
65 TGATTTATTTTAAAA
529329 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTATTGTAGTTGTATGGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTATTGTAGTTGTATGGAT
529394 TGATTTATTTT-AAA
65 TGATTTATTTTAAAA
* * * * * *
529408 TA---ATTTA-TTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTA
1 TATGGATTGATTTA-TTTTAAATAATTTA--TT--AGTAT-GATTGATTTATTATTGTAGTTGTA
529469 TGGATTGATTTATTTTAAA
60 TGGATTGATTTATTTTAAA
529488 TAATTTATTA
Statistics
Matches: 136, Mismatches: 11, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
75 5 0.04
76 53 0.39
78 2 0.01
79 13 0.10
80 60 0.44
81 3 0.02
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (79 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTATTGTAGTTGTATGGATT
GATTTATTTTAAAA
Found at i:529499 original size:80 final size:80
Alignment explanation
Indices: 529361--529536 Score: 334
Period size: 80 Copynumber: 2.2 Consensus size: 80
529351 AATTTATTAG
*
529361 TATGAATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAAT
1 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAAT
529426 TGATTTATTTTAAAA
66 TGATTTATTTTAAAA
*
529441 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
1 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAAT
529506 TGATTTATTTTAAAA
66 TGATTTATTTTAAAA
529521 TATGGATTGATTTATT
1 TATGGATTGATTTATT
529537 TTAAATAATT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 94 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAAT
TGATTTATTTTAAAA
Found at i:529524 original size:22 final size:22
Alignment explanation
Indices: 529499--529541 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
529489 AATTTATTAG
529499 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
529521 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
529542 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:529600 original size:31 final size:31
Alignment explanation
Indices: 529565--529625 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
529555 TATTTGTATG
* *
529565 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
529596 AATTATTTAAATCTCAGTATTGCAAAACTA
1 AATTATTTAAATCTCAGTATTGCAAAACTA
529626 TTTTAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:530366 original size:24 final size:23
Alignment explanation
Indices: 530317--530371 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
530307 AAATCTCTGT
* * *
530317 TCTTGTGACATGTTTTTCTTTCC
1 TCTTGTGGCACGTTTTTCTATCC
*
530340 TCTTGTGGCACGTGTTTTCTATGC
1 TCTTGTGGCACGT-TTTTCTATCC
530364 TCTTGTGG
1 TCTTGTGG
530372 ACGATCCTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.07, C:0.20, G:0.22, T:0.51
Consensus pattern (23 bp):
TCTTGTGGCACGTTTTTCTATCC
Found at i:531206 original size:21 final size:21
Alignment explanation
Indices: 531180--531224 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
531170 GATTTCTGGG
* *
531180 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
531201 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
531222 CAA
1 CAA
531225 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:532094 original size:32 final size:31
Alignment explanation
Indices: 532052--532148 Score: 117
Period size: 31 Copynumber: 3.1 Consensus size: 31
532042 AGAGTCGAGG
*
532052 GTTTACCTATGTTCTACGGAACATATGGACT
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
532083 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
532115 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
532146 GTT
1 GTT
532149 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
31 28 0.51
32 27 0.49
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:532235 original size:29 final size:30
Alignment explanation
Indices: 532140--532232 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
532130 AAGGAACATA
532140 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
532170 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
532200 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
532229 TGGA
1 TGGA
532233 TAGGTCCTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
29 18 0.30
30 42 0.70
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:542866 original size:26 final size:26
Alignment explanation
Indices: 542830--542906 Score: 145
Period size: 26 Copynumber: 3.0 Consensus size: 26
542820 TTCAGCATTG
542830 GTGCATATATTAATTGTGAATCCTTA
1 GTGCATATATTAATTGTGAATCCTTA
542856 GTGCATATATTAATTGTGAATCCTTA
1 GTGCATATATTAATTGTGAATCCTTA
*
542882 GTGCATATATTAGTTGTGAATCCTT
1 GTGCATATATTAATTGTGAATCCTT
542907 CATCATTGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.43
Consensus pattern (26 bp):
GTGCATATATTAATTGTGAATCCTTA
Found at i:542924 original size:33 final size:33
Alignment explanation
Indices: 542882--543038 Score: 224
Period size: 33 Copynumber: 4.8 Consensus size: 33
542872 TGAATCCTTA
*
542882 GTGCATATATTAGTTGTGAATCCTTCATCATTG
1 GTGCATATATTAGTTGTGAATCCTTCAGCATTG
* *
542915 GTGCATATATTAGTTGTGAATCCTTCAACATTA
1 GTGCATATATTAGTTGTGAATCCTTCAGCATTG
* * *
542948 GAGCATGTATTAGTTGTGAATCCTTCAGCATAG
1 GTGCATATATTAGTTGTGAATCCTTCAGCATTG
*
542981 GTGCATACATTAGTTGTGAATCCTTCAGCATTG
1 GTGCATATATTAGTTGTGAATCCTTCAGCATTG
* * *
543014 ATGTATATATTAGTTTTGAATCCTT
1 GTGCATATATTAGTTGTGAATCCTT
543039 TGAAGCTTAA
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 109 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (33 bp):
GTGCATATATTAGTTGTGAATCCTTCAGCATTG
Found at i:547714 original size:29 final size:29
Alignment explanation
Indices: 547672--547729 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
547662 CAGTACCGGG
547672 GGTAGGTCGCCATGCACGCCCAGCGACCT
1 GGTAGGTCGCCATGCACGCCCAGCGACCT
* *
547701 GGTAGGTCGCCATGCATGCCCTGCGACCT
1 GGTAGGTCGCCATGCACGCCCAGCGACCT
547730 ACCTCAACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.36, G:0.31, T:0.17
Consensus pattern (29 bp):
GGTAGGTCGCCATGCACGCCCAGCGACCT
Found at i:547753 original size:10 final size:10
Alignment explanation
Indices: 547740--547822 Score: 57
Period size: 10 Copynumber: 8.3 Consensus size: 10
547730 ACCTCAACCT
547740 CCATGCACGC
1 CCATGCACGC
547750 CCATGCACGC
1 CCATGCACGC
*
547760 CCA-ACGAC-C
1 CCATGC-ACGC
*
547769 TCCATGCATGC
1 -CCATGCACGC
*
547780 CCAGGCACGC
1 CCATGCACGC
*
547790 CCA-ACGAC-C
1 CCATGC-ACGC
*
547799 TCCATGCACGG
1 -CCATGCACGC
547810 CCATGCACGC
1 CCATGCACGC
547820 CCA
1 CCA
547823 ACGACCTCCA
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
9 4 0.07
10 49 0.88
11 3 0.05
ACGTcount: A:0.23, C:0.48, G:0.19, T:0.10
Consensus pattern (10 bp):
CCATGCACGC
Found at i:547770 original size:30 final size:30
Alignment explanation
Indices: 547736--547842 Score: 187
Period size: 30 Copynumber: 3.6 Consensus size: 30
547726 ACCTACCTCA
547736 ACCTCCATGCACGCCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
* *
547766 ACCTCCATGCATGCCCAGGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
*
547796 ACCTCCATGCACGGCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
547826 ACCTCCATGCACGCCCA
1 ACCTCCATGCACGCCCA
547843 GCTCGCCAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.23, C:0.49, G:0.18, T:0.10
Consensus pattern (30 bp):
ACCTCCATGCACGCCCATGCACGCCCAACG
Found at i:552770 original size:32 final size:34
Alignment explanation
Indices: 552695--552776 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
552685 CCAAACCCTT
* *
552695 AAAC-AACTAATAAAATATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
552728 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTTCA-TATAACTA
*
552761 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
552777 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 11 0.25
33 8 0.18
34 20 0.45
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTTTTTCATATAACTA
Found at i:552908 original size:46 final size:49
Alignment explanation
Indices: 552817--552908 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 49
552807 CAACAAACAA
552817 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTTT
*
552866 ATATAAC-TAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTT
1 ATATAACTTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT
552909 AACTATAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
45 12 0.29
46 11 0.27
47 5 0.12
48 6 0.15
49 7 0.17
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (49 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTTT
Found at i:553042 original size:16 final size:18
Alignment explanation
Indices: 553013--553051 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
553003 ACTAATTAAC
*
553013 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
553031 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
553047 ATTTA
1 ATTTA
553052 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:553335 original size:50 final size:50
Alignment explanation
Indices: 553264--553372 Score: 179
Period size: 50 Copynumber: 2.2 Consensus size: 50
553254 TAGGATCACA
*
553264 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAG-TTATCT
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTTAT-T
553313 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTTATT
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTTATT
553363 TGGC-TGCATG
1 TGGCATGCATG
553373 TGCATGCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
49 14 0.25
50 39 0.68
51 4 0.07
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.21
Consensus pattern (50 bp):
TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTTATT
Found at i:553440 original size:29 final size:29
Alignment explanation
Indices: 553407--553501 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
553397 TGGACGCCGG
553407 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
553436 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
553465 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
553494 GGCGACCT
1 GGCGACCT
553502 CTCTATTGGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:553530 original size:32 final size:32
Alignment explanation
Indices: 553488--553559 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
553478 GTCGCCCAGA
*
553488 CTGCATGGCGACCTCTCTATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
* *
553520 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
553552 CTGCATGG
1 CTGCATGG
553560 TGAGTATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:553624 original size:24 final size:19
Alignment explanation
Indices: 553574--553611 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
553564 TATATGGCTT
553574 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
553593 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
553612 TGAGTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.37, T:0.32
Consensus pattern (19 bp):
GTATGGCTCGTCTGCATGG
Found at i:553646 original size:11 final size:11
Alignment explanation
Indices: 553632--553663 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
553622 GCTTGTATGG
553632 CTCGTATGTCA
1 CTCGTATGTCA
*
553643 CTCGTATGTCT
1 CTCGTATGTCA
553654 CTCGTATGTC
1 CTCGTATGTC
553664 GCCTGGATTG
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:0.12, C:0.28, G:0.19, T:0.41
Consensus pattern (11 bp):
CTCGTATGTCA
Found at i:575198 original size:19 final size:20
Alignment explanation
Indices: 575171--575210 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
575161 TTAATATTTT
575171 ATTTATTTAT-TACATATGTA
1 ATTTATTTATGTACA-ATGTA
575191 ATTT-TTTATGTACAATGTA
1 ATTTATTTATGTACAATGTA
575210 A
1 A
575211 CATTTTAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (20 bp):
ATTTATTTATGTACAATGTA
Found at i:575216 original size:19 final size:19
Alignment explanation
Indices: 575176--575217 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
575166 ATTTTATTTA
**
575176 TTTATTACATATGTAATTT
1 TTTATTACATATGTAACAT
575195 TTTATGTACA-ATGTAACAT
1 TTTAT-TACATATGTAACAT
575214 TTTA
1 TTTA
575218 ACCTGAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (19 bp):
TTTATTACATATGTAACAT
Found at i:579170 original size:37 final size:37
Alignment explanation
Indices: 579129--579202 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
579119 ACTATAAAGT
579129 AAGAATAAATTCTGCTAAGCTTAAAGATTATTTTATA
1 AAGAATAAATTCTGCTAAGCTTAAAGATTATTTTATA
*
579166 AAGAATAAATTTTGCTAAGCTTAAAGATTATTTTATA
1 AAGAATAAATTCTGCTAAGCTTAAAGATTATTTTATA
579203 TTAATTAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (37 bp):
AAGAATAAATTCTGCTAAGCTTAAAGATTATTTTATA
Found at i:580071 original size:14 final size:14
Alignment explanation
Indices: 580033--580083 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
580023 CGATTGAATG
580033 ATAAAAAAAATTCA
1 ATAAAAAAAATTCA
* **
580047 ATATATTAAATTCA
1 ATAAAAAAAATTCA
* *
580061 GTAAAAAAAATTTA
1 ATAAAAAAAATTCA
580075 A-AAAAAAAA
1 ATAAAAAAAA
580084 CTTAAATTCG
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
13 8 0.29
14 20 0.71
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (14 bp):
ATAAAAAAAATTCA
Found at i:581014 original size:59 final size:59
Alignment explanation
Indices: 580893--581017 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 59
580883 TCGGGTGACC
* * *
580893 ATTTCGTAACTTTTAATAGTCAAGTGACTTAACAAAATAACATTCTATAGTCGAATGGCT
1 ATTT-GTAACTTTTAATAGTCAAGTGACTTAACAAAATAAAATTCTATAATCGAAGGGCT
* * *
580953 ATTTGTAACTTTTAATAGTCAAAG-GACTTAATAAAGTAATAATT-TATAAT-TAAGGGACT
1 ATTTGTAACTTTTAATAGTC-AAGTGACTTAACAAAATAA-AATTCTATAATCGAAGGG-CT
581012 ATTTGT
1 ATTTGT
581018 GTACTTTACC
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
58 4 0.07
59 42 0.75
60 10 0.18
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (59 bp):
ATTTGTAACTTTTAATAGTCAAGTGACTTAACAAAATAAAATTCTATAATCGAAGGGCT
Found at i:586270 original size:2 final size:2
Alignment explanation
Indices: 586263--586288 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
586253 CATGAGTTCT
586263 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
586289 ATTTAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:586647 original size:22 final size:22
Alignment explanation
Indices: 586621--586669 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
586611 CATCCGTTAA
*
586621 AAACTTAAC-GTGTTTAGTACTT
1 AAACTTAACAGT-TTTAGTACCT
*
586643 AAAC-TATCAGTTTTAGTACCT
1 AAACTTAACAGTTTTAGTACCT
586664 AAACTT
1 AAACTT
586670 TCGAGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
AAACTTAACAGTTTTAGTACCT
Found at i:588610 original size:20 final size:20
Alignment explanation
Indices: 588585--588636 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
588575 TTTTCCGACT
588585 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
588605 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
588625 ATCGCAATGCGA
1 ATCGCAATGCGA
588637 TTCTGACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:588648 original size:20 final size:20
Alignment explanation
Indices: 588523--588671 Score: 79
Period size: 20 Copynumber: 7.3 Consensus size: 20
588513 GTTTCCAGAT
*
588523 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* * * *
588543 TCGCATTGCGATTTTTTA-AA
1 TCGCAATGCGA-TTCTGACTA
** *
588563 TTCGCGTTGCGATTTTCCGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
588586 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* * *
588606 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
588626 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
588646 TCGCAACGCGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
588666 TCGCAA
1 TCGCAA
588672 CACTGAATTT
Statistics
Matches: 102, Mismatches: 21, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
19 1 0.01
20 72 0.71
21 15 0.15
22 13 0.13
23 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:589543 original size:24 final size:24
Alignment explanation
Indices: 589486--589545 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
589476 TAGTCGGTAT
589486 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
589510 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
589534 TCGAATTTTGAT
1 TCGAAATTTGAT
589546 GATGTTTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:590444 original size:17 final size:17
Alignment explanation
Indices: 590422--590460 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
590412 TGAATCAAAT
590422 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
590439 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
590456 -AATTA
1 TAATTA
590461 ATTATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:592398 original size:18 final size:18
Alignment explanation
Indices: 592375--592414 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
592365 AGAAAAAGGT
*
592375 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
*
592393 AATCAAAATCCCAATCAC
1 AATCAAAATCCCAATCAA
592411 AATC
1 AATC
592415 GACTTCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.28, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:592721 original size:140 final size:140
Alignment explanation
Indices: 592469--592738 Score: 531
Period size: 140 Copynumber: 1.9 Consensus size: 140
592459 AAACGTTGTA
592469 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
592534 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
592599 TATGTGTATT
131 TATGTGTATT
592609 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
592674 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
592739 CGCAACTCAA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 129 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:592734 original size:20 final size:20
Alignment explanation
Indices: 592709--592945 Score: 186
Period size: 20 Copynumber: 12.8 Consensus size: 20
592699 TTACACATTC
*
592709 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
592729 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
592748 A----A-AATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
592763 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
592783 ATATGACTATCGCAACAC-A
1 ATTTGACTATCGCAACGCGA
*
592802 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
592817 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
592837 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
*
592857 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
592877 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
592891 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
592911 ATTTGATTATCGCAATGGGT
1 ATTTGACTATCGCAACGCGA
*
592931 ATTTTACTATCGCAA
1 ATTTGACTATCGCAA
592946 TGAGAAAATC
Statistics
Matches: 175, Mismatches: 24, Indels: 36
0.74 0.10 0.15
Matches are distributed among these distances:
14 30 0.17
15 6 0.03
16 1 0.01
18 1 0.01
19 5 0.03
20 132 0.75
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:592791 original size:54 final size:54
Alignment explanation
Indices: 592709--592852 Score: 225
Period size: 54 Copynumber: 2.7 Consensus size: 54
592699 TTACACATTC
* *
592709 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACTCAAAAATCGCAACACGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACACAAAAATCGCAACACGA
* * *
592763 ATTTGACTATCGCAACACGAATATGACTATCGCAACACAAAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACACAAAAATCGCAACACGA
* *
592817 ATTTGTCTATCGCAACGCGAATTTGATTATCGCAAC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAAC
592853 GGGTATTTGA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (54 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACACAAAAATCGCAACACGA
Found at i:592829 original size:74 final size:74
Alignment explanation
Indices: 592751--592985 Score: 283
Period size: 74 Copynumber: 3.2 Consensus size: 74
592741 CAACTCAAAA
* *
592751 ATCGCAACACGAATTTGACTATCGCAACACGAATATGACTATCGCAAC-ACAAAAATCGCAACGC
1 ATCGCAACGCGAATTTGATTATCGCAACACGAATATGACTATCGCAACGA-AAAAATCGCAACGC
*
592815 GAATTTGTCT
65 GAATTTGACT
** * * *
592825 ATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCGCAACGCG
1 ATCGCAACGCGAATTTGATTATCGCAACACGAATATGACTATCGCAACGAAAAAATCGCAACGCG
592890 AATTTGACT
66 AATTTGACT
*** * * * * * *
592899 ATCGCAACGCGAATTTGATTATCGCAATGGGTATTTTACTATCGCAATGAGAAAATCGCAAAGCG
1 ATCGCAACGCGAATTTGATTATCGCAACACGAATATGACTATCGCAACGAAAAAATCGCAACGCG
* *
592964 TATTAGACT
66 AATTTGACT
592973 ATCGCAACGCGAA
1 ATCGCAACGCGAA
592986 CTGACTTTCG
Statistics
Matches: 146, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
74 145 0.99
75 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGATTATCGCAACACGAATATGACTATCGCAACGAAAAAATCGCAACGCG
AATTTGACT
Found at i:592861 original size:40 final size:40
Alignment explanation
Indices: 592709--592945 Score: 186
Period size: 34 Copynumber: 6.4 Consensus size: 40
592699 TTACACATTC
* * *
592709 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCGA
* * * *
592748 A----A-AATCGCAACACGAATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCGA
* * *
592783 ATATGACTATCGCAACAC-AA----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCGA
* * *
592817 ATTTGTCTATCGCAACGCGAATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCGA
*
592857 ATTTGACTATCGCAACGAGAA----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCGA
* * *
592891 ATTTGACTATCGCAACGCGAATTTGATTATCGCAATGGGT
1 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCGA
*
592931 ATTTTACTATCGCAA
1 ATTTGACTATCGCAA
592946 TGAGAAAATC
Statistics
Matches: 159, Mismatches: 21, Indels: 35
0.74 0.10 0.16
Matches are distributed among these distances:
34 84 0.53
35 6 0.04
36 1 0.01
38 1 0.01
39 5 0.03
40 62 0.39
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (40 bp):
ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCGA
Found at i:593182 original size:14 final size:14
Alignment explanation
Indices: 593122--593183 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
593112 CACAAATAAG
*
593122 AATTATTTACACATC
1 AATT-TTTACAAATC
**
593137 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
593152 AACTTTTACAAATC
1 AATTTTTACAAATC
*
593166 AATTTTTATAAATC
1 AATTTTTACAAATC
593180 AATT
1 AATT
593184 AAAAAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:594659 original size:18 final size:19
Alignment explanation
Indices: 594636--594679 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
594626 CTCTTGAGGG
594636 ATGATA-GAGGCCTCTTGA
1 ATGATAGGAGGCCTCTTGA
594654 ATGATAGGGGAGGCCTCTTGA
1 ATGATA--GGAGGCCTCTTGA
594675 ATGAT
1 ATGAT
594680 GACAGGTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
21 17 0.74
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (19 bp):
ATGATAGGAGGCCTCTTGA
Found at i:595215 original size:20 final size:20
Alignment explanation
Indices: 595175--595230 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
595165 CATTCAACTT
*
595175 AAATGACTATCGCAACGCGA
1 AAATGACTATCGCAACACGA
*
595195 AAATGACTATCGCAATACGA
1 AAATGACTATCGCAACACGA
** *
595215 ATTTGACTATCACAAC
1 AAATGACTATCGCAAC
595231 GAGAGAATCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.21
Consensus pattern (20 bp):
AAATGACTATCGCAACACGA
Found at i:595299 original size:20 final size:20
Alignment explanation
Indices: 595270--595328 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
595260 CATTGCGATT
595270 ATTT-CGTTGCGATAGTAAA
1 ATTTGCGTTGCGATAGTAAA
*
595289 ATTTGCGTTGCGATAGT-CA
1 ATTTGCGTTGCGATAGTAAA
* *
595308 TTTTCGCGTTGCGAAAGTAAA
1 ATTT-GCGTTGCGATAGTAAA
595329 CTATTCTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 8 0.24
20 24 0.73
21 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.36
Consensus pattern (20 bp):
ATTTGCGTTGCGATAGTAAA
Found at i:595545 original size:20 final size:20
Alignment explanation
Indices: 595516--595583 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
595506 AGTTTTACTT
595516 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
595536 TCGCACCGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* **
595556 TCGCAATGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
595576 TCGTAACG
1 TCGCAACG
595584 TGAGAATCGC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:595873 original size:20 final size:20
Alignment explanation
Indices: 595844--595911 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
595834 TAGTTTACTT
595844 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
595864 TCGCACCGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* **
595884 TCGCAATGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
595904 TCGTAACG
1 TCGCAACG
595912 TGAGAATCGC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:595998 original size:328 final size:329
Alignment explanation
Indices: 595294--596132 Score: 1572
Period size: 328 Copynumber: 2.5 Consensus size: 329
595284 GTAAAATTTG
595294 CGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTTCTGCAAATTGAAACTT
1 CGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTA---TTCTTCTTCTGCAAATTGAAACTT
* * * *
595359 GAATGGATTGCATTACTTCAACCAAAAGGCAACAAAAAACAAACACTAACTTCACAGTGTTAAAG
63 GAATGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACAGGGTTAAAG
595424 AATAAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCA
128 AATAAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCA
595489 ATTTGCAGAAGAAGATTAGTTTTACTTTCGCAACGCGAAAATGACTATCGCACCGCGAAAATGAC
193 ATTTGCAGAAGAAGATTAGTTTTACTTTCGCAACGCGAAAATGACTATCGCACCGCGAAAATGAC
595554 TATCGCAATGCGAATTTGACTATCGTAACGTGAGAATCGCAATGTGATTTTCATTTCGCATTGCG
258 TATCGCAATGCGAATTTGACTATCGTAACGTGAGAATCGCAATGTGATTTTCATTTCGCATTGCG
595619 ATTCTTT
323 ATTCTTT
595626 CGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAA
1 CGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAA
* *
595691 TGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATATTAACTTCATAGGGTTAAAGAAT
66 TGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACAGGGTTAAAGAAT
*
595756 AAACAATTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATT
131 AAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATT
595821 TGCAGAAGAAGATTAG-TTTACTTTCGCAACGCGAAAATGACTATCGCACCGCGAAAATGACTAT
196 TGCAGAAGAAGATTAGTTTTACTTTCGCAACGCGAAAATGACTATCGCACCGCGAAAATGACTAT
595885 CGCAATGCGAATTTGACTATCGTAACGTGAGAATCGCAATGTGATTTTCATTTCGCATTGCGATT
261 CGCAATGCGAATTTGACTATCGTAACGTGAGAATCGCAATGTGATTTTCATTTCGCATTGCGATT
595950 CTTT
326 CTTT
595954 CGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAA
1 CGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAA
596019 TGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACAGGGTTAAAGAAT
66 TGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACAGGGTTAAAGAAT
*
596084 AAACAGTTTAGCAGTATTGACAGCAACCGAATGAATTTACTAAGCAATC
131 AAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAGCAATC
596133 TAAGTGAAAT
Statistics
Matches: 496, Mismatches: 11, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
328 292 0.59
329 166 0.33
332 38 0.08
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (329 bp):
CGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAA
TGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACAGGGTTAAAGAAT
AAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATT
TGCAGAAGAAGATTAGTTTTACTTTCGCAACGCGAAAATGACTATCGCACCGCGAAAATGACTAT
CGCAATGCGAATTTGACTATCGTAACGTGAGAATCGCAATGTGATTTTCATTTCGCATTGCGATT
CTTT
Found at i:597978 original size:19 final size:20
Alignment explanation
Indices: 597891--598016 Score: 132
Period size: 20 Copynumber: 6.5 Consensus size: 20
597881 TCTGAAACTT
*
597891 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
*
597911 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** * **
597931 ACTATTGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
597951 ACTATCGCAACGC-AAAATG
1 AAAATCGCAACGCGAAAATG
597970 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
* *
597989 AAAATCACAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
598008 AAAATCGCA
1 AAAATCGCA
598017 TTGCGATTAT
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
19 41 0.46
20 49 0.54
ACGTcount: A:0.48, C:0.22, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:598416 original size:20 final size:21
Alignment explanation
Indices: 598391--598437 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
598381 TCTGAGAGAT
598391 GGAGAT-AGACGGATTTCGTC
1 GGAGATGAGACGGATTTCGTC
* *
598411 GGAGATGGGGACTGATTTCGTC
1 GGAGAT-GAGACGGATTTCGTC
598433 GGAGA
1 GGAGA
598438 CGGGGACGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
22 17 0.74
ACGTcount: A:0.23, C:0.13, G:0.40, T:0.23
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGTC
Found at i:598429 original size:22 final size:22
Alignment explanation
Indices: 598402--598444 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
598392 GAGATAGACG
*
598402 GATTTCGTCGGAGATGGGGACT
1 GATTTCGTCGGAGACGGGGACT
598424 GATTTCGTCGGAGACGGGGAC
1 GATTTCGTCGGAGACGGGGAC
598445 GGATATCGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.42, T:0.23
Consensus pattern (22 bp):
GATTTCGTCGGAGACGGGGACT
Found at i:598654 original size:20 final size:20
Alignment explanation
Indices: 598620--598713 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
598610 GTGTTTTAAA
*
598620 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
598640 CATCGCGTTGTGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
598660 AATCTCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
598680 AATCGTGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
*
598700 AATCGCATTGCGAT
1 AATCGCGTTGCGAT
598714 TTACATATTC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:600354 original size:15 final size:15
Alignment explanation
Indices: 600334--600369 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
600324 TTTATAACTT
600334 TTAATAGTTAAA-GAC
1 TTAATAGTTAAATG-C
600349 TTAATAGTTAAATGC
1 TTAATAGTTAAATGC
600364 TTAATA
1 TTAATA
600370 AAAGAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (15 bp):
TTAATAGTTAAATGC
Found at i:600931 original size:521 final size:513
Alignment explanation
Indices: 599902--600932 Score: 1830
Period size: 521 Copynumber: 2.0 Consensus size: 513
599892 GGGGGGGGGG
599902 ATACACTATAGGGTAAAGTATATAAACGATCCGATTATAGTTATAGAATATTAAGTTAATTATTA
1 ATACACTATAGGGTAAAGTATATAAACGATCCGATTATAGTTATAGAATATTAAGTTAATTATTA
599967 AAAGTTACAAAATGATCCTTAGATTATAAAATATTACTTTGTTAAATCTCTCGACTATTAAAAGT
66 AAAGTTACAAAATGATCCTTAGATTATAAAATATTACTTTGTTAAATCTCTCGACTATTAAAAGT
* * *
600032 TACAAAATAGTCACCTGATTATTTATTATATTCTAAACTCGTCATTTTCCGTTAAAAAAATGACG
131 TACAAAATAGTCACCCGACTATTTATTATATTCTAAACTCGTCATTTTCCGTTAAAAAAATGACA
600097 ATATTATGAGCCGAACGTTAACATGTTGACTGTAATATAATAAAATCCGATCTCAAAATTATAAA
196 ATATTATGAGCCGAACGTTAACATGTTGACTGTAATATAATAAAATCCGATCTCAAAATTATAAA
*
600162 TGACTATTATATCTCAGTCATCATGTTAATTTCCATCTTAAACAATAACCAATTTTTTAATAGAA
261 TGACTATTATATCTCAGTCATCATGTTAATTTCCATCTTAAACAATAACCAATATTTTAATAGAA
600227 AATGACGAGTTAAAACATAATGAATAACAAATGATCATTTTGTAACTTCTAATAATTGAAGTACT
326 AATGACGAGTTAAAACATAATGAATAACAAATGATCATTTTGTAACTTCTAATAATTGAAGTACT
*
600292 TAATAAACAATACTCTATAATTAAAGAACCATTTTATAACTTTTAATAGTTAAAGACTTAATAGT
391 TAATAAACAATACTCTATAATTAAAGAACCATTTTATAACTTTTAATAATTAAAGACTTAATAGT
* * *
600357 TAAATGCTTAATAAAAGAATATCTTATGATCGAGATCATTTGTGTAGTTTACCTGGAA
456 TAAATGCTTAATAAAAGAATATATTATGATCGAGATCATTTGTATACTTTACCTGGAA
*
600415 ATACACTATAGGGTAAAGTATATAAACGGTCCGATTATAGTTATAGATTATTGTTATATTAAGTT
1 ATACACTATAGGGTAAAGTATATAAACGATCCGATTATAGTTATAG---A-----ATATTAAGTT
600480 AATTATTAAAAGTTACAAAATGATCCTTAGATTATAAAATATTACTTTGTTAAATCTCTCGACTA
58 AATTATTAAAAGTTACAAAATGATCCTTAGATTATAAAATATTACTTTGTTAAATCTCTCGACTA
600545 TTAAAAGTTACAAAATAGTCACCCGACTATTTATTATATTCTAAACTCGTCATTTTCCGTT-AAA
123 TTAAAAGTTACAAAATAGTCACCCGACTATTTATTATATTCTAAACTCGTCATTTTCCGTTAAAA
*
600609 AAATGACAATATTATGAGCCGAACGTTAACATGTTGATTGTAATATAATAAAATCCGATCTCAAA
188 AAATGACAATATTATGAGCCGAACGTTAACATGTTGACTGTAATATAATAAAATCCGATCTCAAA
*
600674 ATTATAAATGACTATTATATCTCAGTCATCATGTTAATTTTCATCTTAAACAATAACCAATATTT
253 ATTATAAATGACTATTATATCTCAGTCATCATGTTAATTTCCATCTTAAACAATAACCAATATTT
600739 TAATAGAAAATGACGAGTTAAAACATAATGAATAACAAATGATCATTTTGTAACTTCTAATAATT
318 TAATAGAAAATGACGAGTTAAAACATAATGAATAACAAATGATCATTTTGTAACTTCTAATAATT
* *
600804 GAAGTACTTAATAAAACAATATTCTATAATTAAAGAACTATTTTATAACTTTTAATAATTAAAGA
383 GAAGTACTTAAT-AAACAATACTCTATAATTAAAGAACCATTTTATAACTTTTAATAATTAAAGA
* * *
600869 CTTAATAGTTAAATGTTTAGTAAAAGAATATATTATGATCGGGATCATTTGTATACTTTACCTG
447 CTTAATAGTTAAATGCTTAATAAAAGAATATATTATGATCGAGATCATTTGTATACTTTACCTG
600933 CAATATAATA
Statistics
Matches: 493, Mismatches: 16, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
513 45 0.09
516 1 0.00
520 206 0.42
521 241 0.49
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (513 bp):
ATACACTATAGGGTAAAGTATATAAACGATCCGATTATAGTTATAGAATATTAAGTTAATTATTA
AAAGTTACAAAATGATCCTTAGATTATAAAATATTACTTTGTTAAATCTCTCGACTATTAAAAGT
TACAAAATAGTCACCCGACTATTTATTATATTCTAAACTCGTCATTTTCCGTTAAAAAAATGACA
ATATTATGAGCCGAACGTTAACATGTTGACTGTAATATAATAAAATCCGATCTCAAAATTATAAA
TGACTATTATATCTCAGTCATCATGTTAATTTCCATCTTAAACAATAACCAATATTTTAATAGAA
AATGACGAGTTAAAACATAATGAATAACAAATGATCATTTTGTAACTTCTAATAATTGAAGTACT
TAATAAACAATACTCTATAATTAAAGAACCATTTTATAACTTTTAATAATTAAAGACTTAATAGT
TAAATGCTTAATAAAAGAATATATTATGATCGAGATCATTTGTATACTTTACCTGGAA
Found at i:606880 original size:23 final size:23
Alignment explanation
Indices: 606862--606922 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
606852 CTCGTATAAA
606862 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
606885 TGCACCAAAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
606908 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
606923 TATAAAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:608309 original size:64 final size:65
Alignment explanation
Indices: 608155--608313 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 65
608145 AGTTAAATTG
* * * *
608155 AACATCGAATGCATTTCATGCATCAATGCACTTACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTCAGGATTTTATGAA
** * *
608220 AACATCGAATGCATTTGATGCATCGATGCACCAT-CCATGCATTGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCA-CATACCATGCACCGATGCACTCAGGAT-TTTATG
608283 -A
64 AA
*
608284 AACATCGAATGCACTTGATGCATCGATGCA
1 AACATCGAATGCATTTGATGCATCGATGCA
608314 TTCTTAGTAC
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 30 0.36
65 48 0.58
66 5 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTCAGGATTTTATGAA
Found at i:608402 original size:21 final size:21
Alignment explanation
Indices: 608372--608427 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
608362 TTTTACACTG
*
608372 ATGCACCGATGCACCATGGGT
1 ATGCATCGATGCACCATGGGT
608393 ATGCATCGATGCACCATGGGT
1 ATGCATCGATGCACCATGGGT
608414 ATGCATCGATGCAC
1 ATGCATCGATGCAC
608428 TGACGCTCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (21 bp):
ATGCATCGATGCACCATGGGT
Found at i:612082 original size:46 final size:45
Alignment explanation
Indices: 612026--612132 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
612016 TGCACTTACC
* * * *
612026 ATGCACCGATGTACTGAGGAT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTG
* *
612072 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTG
612117 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
612133 TTAGTACACC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 33 0.61
46 18 0.33
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTG
Found at i:615835 original size:2 final size:2
Alignment explanation
Indices: 615828--615853 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
615818 CTAGGACCCT
615828 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
615854 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:615894 original size:2 final size:2
Alignment explanation
Indices: 615853--615882 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
615843 ACACACACAC
615853 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
615883 GAAACATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:617447 original size:57 final size:55
Alignment explanation
Indices: 617310--617447 Score: 145
Period size: 57 Copynumber: 2.4 Consensus size: 55
617300 ATCGGGTGAC
* *
617310 ATTTTGAGAATTAATTTAAAATAGGTGTTATTTTGGGAATTTAATTTGAAAAAGTTCT
1 ATTTTG-GAATTATTTTAAAA-A-GTGTTATTTTGGGAATTTAATTTGAAAAAGTGCT
* * *
617368 ATTTTGGGAATT-TAATTCAAAAGTGTTATTTTTGGGAA-TTAATTTGAAAAGGGTGCT
1 ATTTT-GGAATTAT-TTTAAAAAGTGTTA-TTTTGGGAATTTAATTTGAAAA-AGTGCT
617425 ATTTTGGTAATTATTTTAAAAAG
1 ATTTTGG-AATTATTTTAAAAAG
617448 GGTGCTATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
56 20 0.30
57 30 0.45
58 16 0.24
59 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (55 bp):
ATTTTGGAATTATTTTAAAAAGTGTTATTTTGGGAATTTAATTTGAAAAAGTGCT
Found at i:617448 original size:29 final size:29
Alignment explanation
Indices: 617310--617457 Score: 137
Period size: 29 Copynumber: 5.1 Consensus size: 29
617300 ATCGGGTGAC
* *
617310 ATTTTGAGAATTAATTTAAAATA-GGTGTT
1 ATTTTGGGAATTAATTTAAAA-AGGGTGCT
*
617339 ATTTTGGGAATTTAATTTGAAAAA--GTTCT
1 ATTTTGGGAA-TTAATTT-AAAAAGGGTGCT
* *
617368 ATTTTGGGAATTTAA-TTCAAAA--GTGTT
1 ATTTTGGGAA-TTAATTTAAAAAGGGTGCT
*
617395 ATTTTTGGGAATTAATTTGAAAAGGGTGCT
1 A-TTTTGGGAATTAATTTAAAAAGGGTGCT
* *
617425 ATTTTGGTAATTATTTTAAAAAGGGTGCT
1 ATTTTGGGAATTAATTTAAAAAGGGTGCT
617454 ATTT
1 ATTT
617458 CTGTACAATG
Statistics
Matches: 102, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
27 12 0.12
28 17 0.17
29 56 0.55
30 13 0.13
31 4 0.04
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.45
Consensus pattern (29 bp):
ATTTTGGGAATTAATTTAAAAAGGGTGCT
Found at i:624599 original size:30 final size:29
Alignment explanation
Indices: 624553--624701 Score: 203
Period size: 29 Copynumber: 5.1 Consensus size: 29
624543 ATCAGGTGAC
*
624553 ATTTTGGGAA-TTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTTAATTCGAAA-AGGTGCT
*
624582 ATTTTGGAAATTTAATTCGAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
* *
624611 ATTTTGGGAATTTAATTTGAAAAAGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
* *
624640 ATTTTGGGTATTTAATTCGAAAATGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
*
624669 ATTTTGGGAA-TTAATTCGAAAATGGTGAT
1 ATTTTGGGAATTTAATTCGAAAA-GGTGCT
624698 ATTT
1 ATTT
624702 CTGTAAAATG
Statistics
Matches: 107, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
28 12 0.11
29 84 0.79
30 11 0.10
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCGAAAAGGTGCT
Found at i:635030 original size:24 final size:24
Alignment explanation
Indices: 635003--635054 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
634993 TTAACGGTTC
635003 AGCGATTCCGGCCGGTTCACTAAT
1 AGCGATTCCGGCCGGTTCACTAAT
635027 AGCGATTCCGGCCGGTTCACTAAT
1 AGCGATTCCGGCCGGTTCACTAAT
635051 AGCG
1 AGCG
635055 GTTCAACCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.29, G:0.27, T:0.23
Consensus pattern (24 bp):
AGCGATTCCGGCCGGTTCACTAAT
Found at i:636405 original size:23 final size:24
Alignment explanation
Indices: 636365--636412 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
636355 AAAAACAGTG
636365 ATTTAATTGAAAAAAATAATATAT
1 ATTTAATTGAAAAAAATAATATAT
636389 ATTTAATTG-AAAAAATAATATAT
1 ATTTAATTGAAAAAAATAATATAT
636412 A
1 A
636413 GAGATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
ATTTAATTGAAAAAAATAATATAT
Found at i:650767 original size:33 final size:33
Alignment explanation
Indices: 650725--650822 Score: 178
Period size: 33 Copynumber: 3.0 Consensus size: 33
650715 CTTTTCCAGG
650725 CAGTGTTTTATCACCCTGTATATCAGTGATAGC
1 CAGTGTTTTATCACCCTGTATATCAGTGATAGC
650758 CAGTGTTTTATCACCCTGTATATCAGTGATAGC
1 CAGTGTTTTATCACCCTGTATATCAGTGATAGC
* *
650791 CAGTGTTTTTTCACCCTGTATATCAGTAATAG
1 CAGTGTTTTATCACCCTGTATATCAGTGATAG
650823 GATAGAAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.38
Consensus pattern (33 bp):
CAGTGTTTTATCACCCTGTATATCAGTGATAGC
Found at i:658352 original size:19 final size:19
Alignment explanation
Indices: 658325--658372 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
658315 ACCGGTCCAA
658325 ACCGGTCTGAATCGGTTTG
1 ACCGGTCTGAATCGGTTTG
*
658344 ACTGGTCTGAATCGGTTTG
1 ACCGGTCTGAATCGGTTTG
658363 ACCGGTCTGA
1 ACCGGTCTGA
658373 CCCGACCCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (19 bp):
ACCGGTCTGAATCGGTTTG
Found at i:658435 original size:29 final size:28
Alignment explanation
Indices: 658392--658496 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 28
658382 ACCCGACCCA
*
658392 GTGATATTCTGGGAAATATTTTGAAAAAG
1 GTGACATTCT-GGAAATATTTTGAAAAAG
* * *
658421 GTGACATTCTAGGAAATGTTTTAAAAAAT
1 GTGACATTCT-GGAAATATTTTGAAAAAG
*
658450 GTGACATTCTGAGAATTATTTTGAAAAAAAG
1 GTGACATTCTG-GAAATATTTTG--AAAAAG
* *
658481 GTGATATTTTGGAAAT
1 GTGACATTCTGGAAAT
658497 TTTCGAATGT
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
28 1 0.02
29 42 0.69
30 4 0.07
31 14 0.23
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (28 bp):
GTGACATTCTGGAAATATTTTGAAAAAG
Found at i:659842 original size:21 final size:21
Alignment explanation
Indices: 659817--659866 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
659807 TTCAAGTTGA
659817 CTTTATTTTGGTAGCATGGGC
1 CTTTATTTTGGTAGCATGGGC
*
659838 CTTTATTTTGGTATCATGGGC
1 CTTTATTTTGGTAGCATGGGC
659859 CTTTATTT
1 CTTTATTT
659867 GAAGTATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.50
Consensus pattern (21 bp):
CTTTATTTTGGTAGCATGGGC
Found at i:670518 original size:19 final size:19
Alignment explanation
Indices: 670491--670540 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
670481 ACCGGTCCAA
*
670491 ACCGGTCTGAACCGATTTG
1 ACCGATCTGAACCGATTTG
* *
670510 ACCGATCTGAATCGGTTTG
1 ACCGATCTGAACCGATTTG
*
670529 ACTGATCT-AACC
1 ACCGATCTGAACC
670541 CGACCCGTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (19 bp):
ACCGATCTGAACCGATTTG
Found at i:670659 original size:31 final size:30
Alignment explanation
Indices: 670570--670727 Score: 139
Period size: 29 Copynumber: 5.4 Consensus size: 30
670560 ACCCAATGAT
**
670570 ATTCTGGG-AAT-TTTTGTGAAAAAGATGAC
1 ATTCTGGGAAATATTTTGAAAAAAAG-TGAC
*
670599 ATTCTGGGAAATATTTTG-AAAAATGTGAC
1 ATTCTGGGAAATATTTTGAAAAAAAGTGAC
670628 ATTCTGGGAAATATTTTGAAAAAAAGTTGAC
1 ATTCTGGGAAATATTTTGAAAAAAAG-TGAC
* * * *
670659 ATTATAGGAAATGTTTTG-AAAAAGGTGAC
1 ATTCTGGGAAATATTTTGAAAAAAAGTGAC
* ** * *
670688 ATTATAAGAATTATTTTG-AAAAAGGTGAC
1 ATTCTGGGAAATATTTTGAAAAAAAGTGAC
*
670717 ATT-TTGGAAAT
1 ATTCTGGGAAAT
670728 TTTCGAATGT
Statistics
Matches: 112, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
28 5 0.04
29 63 0.56
30 20 0.18
31 24 0.21
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (30 bp):
ATTCTGGGAAATATTTTGAAAAAAAGTGAC
Found at i:670661 original size:60 final size:60
Alignment explanation
Indices: 670570--670710 Score: 169
Period size: 60 Copynumber: 2.4 Consensus size: 60
670560 ACCCAATGAT
** * * *
670570 ATTCTGGG-AAT-TTTTGTGAAAAAGATGACATTCTGGGAAATATTTTGAAAAATGTGAC
1 ATTCTGGGAAATATTTTGAAAAAAAGATGACATTATAGGAAATATTTTGAAAAAGGTGAC
* *
670628 ATTCTGGGAAATATTTTGAAAAAAAGTTGACATTATAGGAAATGTTTTGAAAAAGGTGAC
1 ATTCTGGGAAATATTTTGAAAAAAAGATGACATTATAGGAAATATTTTGAAAAAGGTGAC
* ** *
670688 ATTATAAGAATTATTTTGAAAAA
1 ATTCTGGGAAATATTTTGAAAAA
670711 GGTGACATTT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
58 8 0.11
59 3 0.04
60 59 0.84
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (60 bp):
ATTCTGGGAAATATTTTGAAAAAAAGATGACATTATAGGAAATATTTTGAAAAAGGTGAC
Found at i:671838 original size:21 final size:21
Alignment explanation
Indices: 671812--671860 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
671802 GAGAAGGGAT
671812 TTAAACTATAAGTTTCAAAAG
1 TTAAACTATAAGTTTCAAAAG
*
671833 TTAAACTATGAGTTTCAAAAG
1 TTAAACTATAAGTTTCAAAAG
671854 TTAAACT
1 TTAAACT
671861 TCATTATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (21 bp):
TTAAACTATAAGTTTCAAAAG
Found at i:674956 original size:19 final size:19
Alignment explanation
Indices: 674932--674974 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
674922 TTTATCTCTA
674932 TTTTTT-TATAGTTTTCGAT
1 TTTTTTCTATAGTTTTC-AT
* *
674951 TTTTTTCTGTTGTTTTCAT
1 TTTTTTCTATAGTTTTCAT
674970 TTTTT
1 TTTTT
674975 CAGGGTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.09, C:0.07, G:0.09, T:0.74
Consensus pattern (19 bp):
TTTTTTCTATAGTTTTCAT
Found at i:675593 original size:19 final size:19
Alignment explanation
Indices: 675554--675593 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
675544 ATATTAAACT
*
675554 TAATAAAATATTTAAATAA
1 TAATAAAATACTTAAATAA
675573 TAATATAAATACTTAAA-AA
1 TAATA-AAATACTTAAATAA
675592 TA
1 TA
675594 TGTTTATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
TAATAAAATACTTAAATAA
Found at i:678161 original size:23 final size:23
Alignment explanation
Indices: 678131--678177 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
678121 TCCATTAATG
678131 ATTTTTGTTCTCTATTCTTTTTT
1 ATTTTTGTTCTCTATTCTTTTTT
678154 ATTTTTGTTCTCTATTCTTTTTT
1 ATTTTTGTTCTCTATTCTTTTTT
678177 A
1 A
678178 ATTTGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.11, C:0.13, G:0.04, T:0.72
Consensus pattern (23 bp):
ATTTTTGTTCTCTATTCTTTTTT
Found at i:678182 original size:22 final size:23
Alignment explanation
Indices: 678134--678182 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
678124 ATTAATGATT
*
678134 TTTGTTCTCTATTCTTTTTTATT
1 TTTGTTCTCTATTCTTTTTTATA
678157 TTTGTTCTCTATTCTTTTTTA-A
1 TTTGTTCTCTATTCTTTTTTATA
678179 TTTG
1 TTTG
678183 AAATTATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.10, C:0.12, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTGTTCTCTATTCTTTTTTATA
Found at i:678599 original size:14 final size:14
Alignment explanation
Indices: 678580--678607 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
678570 CGCTGGGCAT
678580 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
678594 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
678608 GGCCATCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:678622 original size:24 final size:24
Alignment explanation
Indices: 678577--678622 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
678567 ACACGCTGGG
*
678577 CATCCGAGGCCATCCGACCGAGGC
1 CATCCGAGGCCATCCGAACGAGGC
*
678601 CATCCGAGGCCATCTGAACGAG
1 CATCCGAGGCCATCCGAACGAG
678623 CTATGTGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.37, G:0.28, T:0.11
Consensus pattern (24 bp):
CATCCGAGGCCATCCGAACGAGGC
Found at i:678656 original size:33 final size:33
Alignment explanation
Indices: 678595--678688 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 33
678585 GCCATCCGAC
* * * * *
678595 CGAGGCCATCCGAGGCCATCTGAACGAGCTATG
1 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
*
678628 TGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
* *
678661 CGAGAGAATCCGAGGG-AAGCCGAGCGAG
1 CGAGGGCATCCGAGGGCAA-CCGAGCGAG
678689 GGTAGGTCGC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 2 0.04
33 49 0.96
ACGTcount: A:0.27, C:0.26, G:0.37, T:0.11
Consensus pattern (33 bp):
CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
Done.