Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008497.1 Hibiscus syriacus cultivar Beakdansim tig00111342_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: 1504768
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 6
Found at i:552966 original size:4 final size:4
Alignment explanation
Indices: 552957--552982 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
552947 TGGCTTTAAC
552957 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
552983 TTACATGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:555903 original size:24 final size:24
Alignment explanation
Indices: 555871--555922 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
555861 GAGCTATGCA
*
555871 AGGGCATCCGAGGGCAA-CCGAGCG
1 AGGGAATCCGAGGG-AAGCCGAGCG
555895 AGGGAATCCGAGGGAAGCCGAGCG
1 AGGGAATCCGAGGGAAGCCGAGCG
555919 AGGG
1 AGGG
555923 TAGGTCGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.27, C:0.23, G:0.46, T:0.04
Consensus pattern (24 bp):
AGGGAATCCGAGGGAAGCCGAGCG
Found at i:555974 original size:29 final size:29
Alignment explanation
Indices: 555933--556030 Score: 171
Period size: 29 Copynumber: 3.4 Consensus size: 29
555923 TAGGTCGCCC
555933 CATG-CGACCTACAAGGTCGCCAGGAGGG
1 CATGACGACCTACAAGGTCGCCAGGAGGG
555961 CATGACGACCTACAAGGTCGCCAGGAGGG
1 CATGACGACCTACAAGGTCGCCAGGAGGG
* *
555990 CATGGCGACCTACAAGGTCGCCCGGAGGG
1 CATGACGACCTACAAGGTCGCCAGGAGGG
556019 CATGACGACCTA
1 CATGACGACCTA
556031 TGTGTTGGGA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
28 4 0.06
29 62 0.94
ACGTcount: A:0.26, C:0.30, G:0.34, T:0.11
Consensus pattern (29 bp):
CATGACGACCTACAAGGTCGCCAGGAGGG
Found at i:557331 original size:21 final size:21
Alignment explanation
Indices: 557305--557608 Score: 286
Period size: 21 Copynumber: 14.4 Consensus size: 21
557295 CAGTTTCCAG
*
557305 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* *
557326 ATCGCAA--CGAACTTGAAAT
1 ATCGCAACGCGAACTTGGACT
*
557345 AATCGCAACGCGAACTTCGACT
1 -ATCGCAACGCGAACTTGGACT
*
557367 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
557386 AAATCGCAACTCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
* *
557409 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
557428 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
*
557451 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
557470 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
* *
557493 ATCGCAA--CGAACTTAGAAT
1 ATCGCAACGCGAACTTGGACT
*
557512 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
*
557535 ATCGTAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* *
557556 ATCGCAACGCGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
557577 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
557600 ATCGCAACG
1 ATCGCAACG
557609 AATTTGGAAA
Statistics
Matches: 233, Mismatches: 29, Indels: 42
0.77 0.10 0.14
Matches are distributed among these distances:
19 49 0.21
20 7 0.03
21 109 0.47
22 9 0.04
23 59 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:557409 original size:42 final size:42
Alignment explanation
Indices: 557305--557568 Score: 426
Period size: 42 Copynumber: 6.3 Consensus size: 42
557295 CAGTTTCCAG
*
557305 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGAAAT-A
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
557346 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
* * *
557388 ATCGCAACTCGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
557430 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
*
557472 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTAGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
* *
557514 ATCGCAACGCGAACTTCGACTATCGTAACGCGAACTTGGACT--
1 ATCGCAACGCGAACTTCGACTATCGCAA--CGAACTTGGAATAA
557556 ATCGCAACGCGAA
1 ATCGCAACGCGAA
557569 TTTGGAATAA
Statistics
Matches: 209, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
41 39 0.19
42 160 0.77
44 10 0.05
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (42 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:557588 original size:44 final size:44
Alignment explanation
Indices: 557514--557624 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 44
557504 CTTAGAATAA
* * * *
557514 ATCGCAACGCGAACTTCGACT--ATCGTAACGCGAACTTGGACT
1 ATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTGGACT
557556 ATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTGGACT
557600 ATCGCAA--CGAATTTGG-A-AAATCGCA
1 ATCGCAACGCGAATTTGGAATAAATCGCA
557625 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
40 8 0.13
41 1 0.02
42 27 0.43
44 27 0.43
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (44 bp):
ATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTGGACT
Found at i:558338 original size:2 final size:2
Alignment explanation
Indices: 558333--558370 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
558323 AATTCAAGTT
558333 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
558371 CACTATTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:559358 original size:6 final size:6
Alignment explanation
Indices: 559347--559392 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
559337 AATCCTCGTA
* * *
559347 TATATG TATATG TATATT TATATG CATATG CATATG TATATG TATA
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATA
559393 AAATTTACCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (6 bp):
TATATG
Found at i:561799 original size:23 final size:26
Alignment explanation
Indices: 561773--561822 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 26
561763 AAAAAGGGAA
*
561773 GAGGGACAA-ACC-AAAGC-ATGGTG
1 GAGGCACAATACCTAAAGCAATGGTG
*
561796 GAGGCACAATCCCTAAAGCAATGGTG
1 GAGGCACAATACCTAAAGCAATGGTG
561822 G
1 G
561823 TGAAATCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 8 0.36
24 2 0.09
25 5 0.23
26 7 0.32
ACGTcount: A:0.36, C:0.20, G:0.32, T:0.12
Consensus pattern (26 bp):
GAGGCACAATACCTAAAGCAATGGTG
Found at i:568702 original size:21 final size:21
Alignment explanation
Indices: 568647--568703 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
568637 TTTATGTTAT
* *
568647 AATAATAATATGTCAGTTCAC
1 AATATTAATATGACAGTTCAC
* *
568668 AATATTAATGTGACAGTTCAT
1 AATATTAATATGACAGTTCAC
* *
568689 AATGTTGATATGACA
1 AATATTAATATGACA
568704 ATATATCTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (21 bp):
AATATTAATATGACAGTTCAC
Found at i:573629 original size:14 final size:14
Alignment explanation
Indices: 573610--573636 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
573600 TCTCGAATGA
573610 AGAAAATTATACAT
1 AGAAAATTATACAT
573624 AGAAAATTATACA
1 AGAAAATTATACA
573637 GTTTTGACAA
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:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (14 bp):
AGAAAATTATACAT
Found at i:575938 original size:242 final size:241
Alignment explanation
Indices: 575513--576200 Score: 1065
Period size: 242 Copynumber: 2.9 Consensus size: 241
575503 AAAATTTTGG
* * *
575513 GGCCAATTTGTAATTTTATGAAATTTAGAGGACCTATTTGGAAATTTTAAAAAGTTATGTGGTTG
1 GGCCAATTTGTAATTTTATGAAAGTTAGAGGACCTATTTGGTAA-TTTAAAAAGTTATGAGGTTG
* *
575578 ATGTGTAATTGTTAAATAGTTGGTGCACTATACTATAAATTAATGTTAGATTGTTGAATTTAATG
65 ATGTGTAATTGTTAAATAGTTGTTGTACTATACTATAAATTAATGTTAGATTGTTGAATTTAATG
* *
575643 TTAGAATGTGAAATTAGACTATTTTGGGAAGTCGGCAAAGTTTGAGTACTAAATGGAAAATATTG
130 TTAGAATGTGAAATTGGACTATTTTGGGAAGTTGGCAAAGTTTGAGTACTAAATGGAAAATATTG
*
575708 AGAAAGTTAGTGACTTAAGTGGTAATGGTGGAATTATAAAGGTATTA
195 AGAAAGTTAGTGACTTAAGTGGTAATGGTGGAACTATAAAGGTATTA
* * *
575755 GGCCAATTTGTAATATTATGAAAGTTAGAGAACCTATTTGGTAATTTAAAAAAGTTATGGGGTTG
1 GGCCAATTTGTAATTTTATGAAAGTTAGAGGACCTATTTGGTAATTT-AAAAAGTTATGAGGTTG
* * *
575820 ATGTGTAATTGTTAAATAGTTGTTGTACCATACTGTAAATTAATGTTAGATGGTTGAATTTAATG
65 ATGTGTAATTGTTAAATAGTTGTTGTACTATACTATAAATTAATGTTAGATTGTTGAATTTAATG
*
575885 TTAGAATGTGAAATTGGACTATTTTGGGAAGTTGGCAAAGTTTGAGTACTAAATGGTAAATATTG
130 TTAGAATGTGAAATTGGACTATTTTGGGAAGTTGGCAAAGTTTGAGTACTAAATGGAAAATATTG
** *
575950 AGAAAGTTAGTGACTTAAGTGGTAATGGTGGAACTATTGAGGTATTG
195 AGAAAGTTAGTGACTTAAGTGGTAATGGTGGAACTATAAAGGTATTA
* * * * *
575997 GGCCAATTTTTAATTTTATGAAAGTTGGAGGACCTATTCT-ATAATTT-TAAAGTTATAAGGTTG
1 GGCCAATTTGTAATTTTATGAAAGTTAGAGGACCTATT-TGGTAATTTAAAAAGTTATGAGGTTG
* * *
576060 ATGTGTAATTGTTAAATAGTTATTGTACTATGCTAAAAATTAATGTTAGATTGTTGAATTTAATG
65 ATGTGTAATTGTTAAATAGTTGTTGTACTATACTATAAATTAATGTTAGATTGTTGAATTTAATG
* * *
576125 TTAGAATGTGAAATTGGACTATTTTGGGAAGTTGGCAAAGTTTGAGTACTAAATAGCAAGTATTG
130 TTAGAATGTGAAATTGGACTATTTTGGGAAGTTGGCAAAGTTTGAGTACTAAATGGAAAATATTG
*
576190 ATAAAGTTAGT
195 AGAAAGTTAGT
576201 TAGTTAGTTA
Statistics
Matches: 409, Mismatches: 35, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
240 144 0.35
241 3 0.01
242 261 0.64
243 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (241 bp):
GGCCAATTTGTAATTTTATGAAAGTTAGAGGACCTATTTGGTAATTTAAAAAGTTATGAGGTTGA
TGTGTAATTGTTAAATAGTTGTTGTACTATACTATAAATTAATGTTAGATTGTTGAATTTAATGT
TAGAATGTGAAATTGGACTATTTTGGGAAGTTGGCAAAGTTTGAGTACTAAATGGAAAATATTGA
GAAAGTTAGTGACTTAAGTGGTAATGGTGGAACTATAAAGGTATTA
Found at i:576734 original size:6 final size:6
Alignment explanation
Indices: 576723--576747 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
576713 GTTGATCCAA
576723 ATGTTG ATGTTG ATGTTG ATGTTG A
1 ATGTTG ATGTTG ATGTTG ATGTTG A
576748 AAACCTTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (6 bp):
ATGTTG
Found at i:582869 original size:43 final size:43
Alignment explanation
Indices: 582806--582900 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
582796 CCTCCAACCG
*
582806 AACACACCATAATGTGTAGGTTTCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
*
582849 AACACACCATAATGTTTAGGTTCCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
582892 AACACACCA
1 AACACACCA
582901 AGTAAGGCCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.37, C:0.37, G:0.09, T:0.17
Consensus pattern (43 bp):
AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
Found at i:583029 original size:24 final size:24
Alignment explanation
Indices: 583016--583110 Score: 154
Period size: 24 Copynumber: 4.0 Consensus size: 24
583006 AAACATAATT
*
583016 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
*
583040 CAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
583064 CATGTCAAATATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
583088 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
583111 TCAAATCGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:585604 original size:13 final size:13
Alignment explanation
Indices: 585586--585621 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
585576 GTCAACGGTC
585586 AACGGGTCGGGTA
1 AACGGGTCGGGTA
585599 AACGGGTCGGGTA
1 AACGGGTCGGGTA
585612 AACGGGTCGG
1 AACGGGTCGG
585622 ATTATGATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.47, T:0.14
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:587772 original size:43 final size:43
Alignment explanation
Indices: 587711--587848 Score: 267
Period size: 43 Copynumber: 3.2 Consensus size: 43
587701 CCTCCAACCG
*
587711 AACACACCATAATGTGTAGGTTTCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
587754 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
587797 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
587840 AACACACCA
1 AACACACCA
587849 AGTAAGGCCC
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 94 1.00
ACGTcount: A:0.36, C:0.37, G:0.11, T:0.16
Consensus pattern (43 bp):
AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
Found at i:587977 original size:24 final size:24
Alignment explanation
Indices: 587964--588058 Score: 145
Period size: 24 Copynumber: 4.0 Consensus size: 24
587954 AAACATAATT
*
587964 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
*
587988 CAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
* *
588012 CATGTCAAATATCAGATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
588036 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
588059 TCAAATCGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:588074 original size:48 final size:48
Alignment explanation
Indices: 587968--588081 Score: 133
Period size: 48 Copynumber: 2.4 Consensus size: 48
587958 ATAATTCATG
* * * **
587968 TCAAGTATCATATCAAAATCCAGGTCAAGTATCATATCAGAATCCATG
1 TCAAATATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAA
* * *
588016 TCAAATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAA
1 TCAAATATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAA
588064 TCGAAA-ATCAGAT-AAAAT
1 TC-AAATATCAGATCAAAAT
588082 ATTCATGTGG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
47 4 0.07
48 49 0.88
49 3 0.05
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.25
Consensus pattern (48 bp):
TCAAATATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAA
Found at i:593376 original size:24 final size:24
Alignment explanation
Indices: 593347--593440 Score: 116
Period size: 24 Copynumber: 3.9 Consensus size: 24
593337 AACATAATTC
* *
593347 ATGTCAAGTATCATATCAAAATCT
1 ATGTCAAGTATCAGATCAGAATCT
* * * *
593371 AGGTCAAGTATCAGACCGGAATCC
1 ATGTCAAGTATCAGATCAGAATCT
* *
593395 ATGTCAAATATCATATCAGAATCT
1 ATGTCAAGTATCAGATCAGAATCT
593419 ATGTCAAGTATCAGATCAGAAT
1 ATGTCAAGTATCAGATCAGAAT
593441 TTAAATCGAA
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (24 bp):
ATGTCAAGTATCAGATCAGAATCT
Found at i:595962 original size:13 final size:13
Alignment explanation
Indices: 595944--596001 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 13
595934 AGTTTTGGTC
595944 AACGGGTCGGGTT
1 AACGGGTCGGGTT
595957 AACGGGTCGGGTCGGGT
1 AACGGGTCGGGT----T
* *
595974 CAACAGGTCGGGTA
1 -AACGGGTCGGGTT
595988 AACGGGTCGGGTT
1 AACGGGTCGGGTT
596001 A
1 A
596002 TGACCGGTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
13 24 0.67
17 1 0.03
18 11 0.31
ACGTcount: A:0.19, C:0.17, G:0.45, T:0.19
Consensus pattern (13 bp):
AACGGGTCGGGTT
Found at i:595969 original size:18 final size:18
Alignment explanation
Indices: 595946--595986 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
595936 TTTTGGTCAA
* *
595946 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTCAACAGGT
595964 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
595982 CGGGT
1 CGGGT
595987 AAACGGGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.20, G:0.49, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:595983 original size:31 final size:31
Alignment explanation
Indices: 595940--595999 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
595930 TTAAAGTTTT
* *
595940 GGTCAACGGGTCGGGTTAACGGGTCGGGTCG
1 GGTCAACAGGTCGGGTAAACGGGTCGGGTCG
595971 GGTCAACAGGTCGGGTAAACGGGTCGGGT
1 GGTCAACAGGTCGGGTAAACGGGTCGGGT
596000 TATGACCGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.17, C:0.18, G:0.47, T:0.18
Consensus pattern (31 bp):
GGTCAACAGGTCGGGTAAACGGGTCGGGTCG
Found at i:598546 original size:31 final size:32
Alignment explanation
Indices: 598511--598584 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 32
598501 AATGACCTTC
*
598511 TAGGTTATGTATTTGAGGATAATAAGCC-ATT
1 TAGGTTATGTATTTGAGGATAATAAGCCAAAT
*
598542 TAGG-TA--AATTTGAGGATAATAAGCCAAAT
1 TAGGTTATGTATTTGAGGATAATAAGCCAAAT
*
598571 TAGTTTATGTATTT
1 TAGGTTATGTATTT
598585 TATTAGGAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
28 18 0.51
29 5 0.14
30 4 0.11
31 4 0.11
32 4 0.11
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.39
Consensus pattern (32 bp):
TAGGTTATGTATTTGAGGATAATAAGCCAAAT
Found at i:598871 original size:3 final size:3
Alignment explanation
Indices: 598863--598899 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
598853 TTAATTCACA
598863 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
598900 TTTTTTATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:605087 original size:15 final size:16
Alignment explanation
Indices: 605067--605100 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
605057 TTGCCAATGG
*
605067 AACCAGCGGCA-CCCA
1 AACCAGCAGCACCCCA
605082 AACCAGCAGCACCCCA
1 AACCAGCAGCACCCCA
605098 AAC
1 AAC
605101 AGACATTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.38, C:0.47, G:0.15, T:0.00
Consensus pattern (16 bp):
AACCAGCAGCACCCCA
Found at i:610219 original size:2 final size:2
Alignment explanation
Indices: 610212--610240 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
610202 TCGTTATAGA
610212 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
610241 ATAAAAGTCA
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:611736 original size:3 final size:3
Alignment explanation
Indices: 611728--611767 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
611718 TGTAGCCCTC
611728 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
611768 TCATATCTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:612779 original size:18 final size:17
Alignment explanation
Indices: 612756--612801 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
612746 TATTTATGAG
612756 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
612774 GGAATTTGAATCTGTCA
1 GGAATTGGAATCTGTAA
612791 GGAATTGGAAT
1 GGAATTGGAAT
612802 TCAATTCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:613486 original size:31 final size:33
Alignment explanation
Indices: 613374--613492 Score: 134
Period size: 33 Copynumber: 3.6 Consensus size: 33
613364 TTTTCACCCT
*
613374 AAACCCGAACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGAACATCACACTTAAAA
** *** *
613408 AAAATCGATATGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACCCGAACATCACACTTAAAA
* *
613441 AAACCTGACTCGACCCGAACATCACACTT-AAA
1 AAACCCGACCCGACCCGAACATCACACTTAAAA
613473 AAACCCGA-CCGACCCGAACA
1 AAACCCGACCCGACCCGAACA
613493 AAATAAAGTT
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
31 11 0.15
32 10 0.14
33 45 0.63
34 5 0.07
ACGTcount: A:0.44, C:0.33, G:0.10, T:0.13
Consensus pattern (33 bp):
AAACCCGACCCGACCCGAACATCACACTTAAAA
Found at i:623282 original size:29 final size:29
Alignment explanation
Indices: 623226--623291 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
623216 TCTCAAACAG
* * *
623226 AAACAAGATGGGGACATAATCTCGTGCAA
1 AAACAAGACGGGGACATAATCCCATGCAA
*
623255 AAACAAGACGGGGA-ATTAATCCCATGCAT
1 AAACAAGACGGGGACA-TAATCCCATGCAA
*
623284 AATCAAGA
1 AAACAAGA
623292 ATGCATTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (29 bp):
AAACAAGACGGGGACATAATCCCATGCAA
Found at i:625020 original size:21 final size:20
Alignment explanation
Indices: 624982--625029 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
624972 ATATATGATT
*
624982 ATATAAATCGTTTAAATTAGA
1 ATATAAATCATTTAAATTA-A
625003 ATATAAAT-ATTTACAATTAA
1 ATATAAATCATTTA-AATTAA
*
625023 ATTTAAA
1 ATATAAA
625030 CAGAAACTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (20 bp):
ATATAAATCATTTAAATTAA
Found at i:647248 original size:19 final size:18
Alignment explanation
Indices: 647222--647340 Score: 79
Period size: 19 Copynumber: 6.6 Consensus size: 18
647212 TTACATTTAG
647222 TTTTTATATTAATTATAA
1 TTTTTATATTAATTATAA
**
647240 TTATTTATATTTTTTATAA
1 TT-TTTATATTAATTATAA
*
647259 -TTCT-TA-T-ATTATAA
1 TTTTTATATTAATTATAA
* *
647273 TTTGTATATTATAAATT-TGA
1 TTT-T-TA-TATTAATTATAA
647293 TTTTTATATTAATTCA-AA
1 TTTTTATATTAATT-ATAA
*
647311 TTCTTTATATTATTTATAA
1 TT-TTTATATTAATTATAA
*
647330 TTCTTATATTA
1 TTTTTATATTA
647341 TAAATTTTAT
Statistics
Matches: 78, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
14 6 0.08
15 3 0.04
16 2 0.03
17 10 0.13
18 17 0.22
19 32 0.41
20 5 0.06
21 3 0.04
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTTATATTAATTATAA
Found at i:647291 original size:15 final size:14
Alignment explanation
Indices: 647253--647291 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
647243 TTTATATTTT
647253 TTATAATTCT-TATA
1 TTATAATT-TGTATA
647267 TTATAATTTGTATA
1 TTATAATTTGTATA
647281 TTATAAATTTG
1 TTAT-AATTTG
647292 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 16 0.70
15 6 0.26
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (14 bp):
TTATAATTTGTATA
Found at i:647302 original size:71 final size:70
Alignment explanation
Indices: 647222--647356 Score: 211
Period size: 71 Copynumber: 1.9 Consensus size: 70
647212 TTACATTTAG
*
647222 TTTTTATATTAATT-ATAATTATTTATATTTTTTATAATTCTTATATTAT-AATTTGTATATTAT
1 TTTTTATATTAATTCA-AATTATTTATATTATTTATAATTCTTATATTATAAATTT-TAT-TTAT
647285 AAATTTGA
63 AAATTTGA
*
647293 TTTTTATATTAATTCAAATTCTTTATATTATTTATAATTCTTATATTATAAATTTTATTTATAA
1 TTTTTATATTAATTCAAATTATTTATATTATTTATAATTCTTATATTATAAATTTTATTTATAA
647357 TCACTAAATT
Statistics
Matches: 60, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
70 6 0.10
71 48 0.80
72 6 0.10
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (70 bp):
TTTTTATATTAATTCAAATTATTTATATTATTTATAATTCTTATATTATAAATTTTATTTATAAA
TTTGA
Found at i:647354 original size:13 final size:14
Alignment explanation
Indices: 647320--647356 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
647310 ATTCTTTATA
647320 TTATTTAT-AATTC
1 TTATTTATAAATTC
647333 TTATATTATAAATT-
1 TTAT-TTATAAATTC
647347 TTATTTATAA
1 TTATTTATAA
647357 TCACTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:649668 original size:28 final size:28
Alignment explanation
Indices: 649624--649716 Score: 170
Period size: 28 Copynumber: 3.4 Consensus size: 28
649614 AATTTTATAC
*
649624 GGAAAA-AAGAATGAGAGATAGGGAAAT
1 GGAAAAGAACAATGAGAGATAGGGAAAT
649651 GGAAAAGAACAATGAGAGATAGGGAAAT
1 GGAAAAGAACAATGAGAGATAGGGAAAT
649679 GGAAAAGAACAATGAGAGATAGGGAAAT
1 GGAAAAGAACAATGAGAGATAGGGAAAT
649707 GGAAAAGAAC
1 GGAAAAGAAC
649717 CTGAGGAATC
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
27 6 0.09
28 58 0.91
ACGTcount: A:0.55, C:0.03, G:0.32, T:0.10
Consensus pattern (28 bp):
GGAAAAGAACAATGAGAGATAGGGAAAT
Found at i:650456 original size:28 final size:28
Alignment explanation
Indices: 650401--650459 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
650391 AATAAATCAT
*
650401 TTATAATTAATATTAAAATTATTATATA
1 TTATAATTAATATTAAAATTACTATATA
*
650429 TTATAATTAATATTAATATTAACT-TATA
1 TTATAATTAATATTAAAATT-ACTATATA
650457 TTA
1 TTA
650460 ATATAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TTATAATTAATATTAAAATTACTATATA
Found at i:650459 original size:16 final size:16
Alignment explanation
Indices: 650401--650463 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
650391 AATAAATCAT
650401 TTATAATTAATATTAAA
1 TTAT-ATTAATATTAAA
*
650418 AT-TATTATATATTATAA
1 TTATATTA-ATATTA-AA
*
650435 TTAATATTAATATTAAC
1 TT-ATATTAATATTAAA
650452 TTATATTAATAT
1 TTATATTAATAT
650464 AATATAGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.10
16 17 0.44
17 7 0.18
18 6 0.15
19 5 0.13
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATATTAATATTAAA
Found at i:650520 original size:31 final size:31
Alignment explanation
Indices: 650483--650666 Score: 123
Period size: 31 Copynumber: 5.7 Consensus size: 31
650473 TATAATTTGT
650483 AATTAATATTAATATATAA-TATAGTTTATA
1 AATTAATATTAATATATAACTATAGTTTATA
650513 AAGTTAATATTAATATA-AACTATA-TGTTATA
1 AA-TTAATATTAATATATAACTATAGT-TTATA
* * *
650544 AATTATATAGTATAGTTTATAAACTATAGTTAATA
1 AATTA-ATA-T-TAATATAT-AACTATAGTTTATA
*
650579 TAATTAATATT-A-ATAT-AGTATAGTTTATTA
1 -AATTAATATTAATATATAACTATAGTTTA-TA
* *
650609 ATATTATACTGTATTAATATA-AATTATAGTTAATA
1 A-ATTA-A---TATTAATATATAACTATAGTTTATA
*
650644 TAATTAACATTAATATA-AACTAT
1 -AATTAATATTAATATATAACTAT
650667 CTAGTACATT
Statistics
Matches: 123, Mismatches: 11, Indels: 39
0.71 0.06 0.23
Matches are distributed among these distances:
29 10 0.08
30 14 0.11
31 46 0.37
32 1 0.01
33 6 0.05
34 6 0.05
35 21 0.17
36 19 0.15
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (31 bp):
AATTAATATTAATATATAACTATAGTTTATA
Found at i:650529 original size:65 final size:64
Alignment explanation
Indices: 650441--650661 Score: 204
Period size: 65 Copynumber: 3.4 Consensus size: 64
650431 ATAATTAATA
*
650441 TTAATATTAACTT-ATATTAATATAATATAGTTTATAATTTGTA-ATTAATATTAATATATAA-T
1 TTAATA-TAA-TTAATATTAATATAATATAGTTTATAATTT-TATACT-ATATTAATATA-AACT
650503 ATAG
61 ATAG
* * *
650507 TTTATA-AAGTTAATATTAATATAAACTATA-TGTTATAAATTATATAGTATAGTT--TATAAAC
1 TTAATATAA-TTAATATTAATAT-AA-TATAGT-TTAT-AATTTTATACTATA-TTAATATAAAC
650568 TATAG
60 TATAG
* * * *
650573 TTAATATAATTAATATTAATATAGTATAGTTTATTAATATTATACTGTATTAATATAAATTATAG
1 TTAATATAATTAATATTAATATAATATAGTTTA-TAATTTTATACTATATTAATATAAACTATAG
*
650638 TTAATATAATTAACATTAATATAA
1 TTAATATAATTAATATTAATATAA
650662 ACTATCTAGT
Statistics
Matches: 129, Mismatches: 13, Indels: 27
0.76 0.08 0.16
Matches are distributed among these distances:
63 2 0.02
64 21 0.16
65 48 0.37
66 35 0.27
67 15 0.12
68 8 0.06
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (64 bp):
TTAATATAATTAATATTAATATAATATAGTTTATAATTTTATACTATATTAATATAAACTATAG
Found at i:650593 original size:15 final size:15
Alignment explanation
Indices: 650573--650661 Score: 56
Period size: 15 Copynumber: 5.6 Consensus size: 15
650563 TAAACTATAG
650573 TTAATATAATTAATA
1 TTAATATAATTAATA
* *
650588 TTAATATAGTATAGTTTA
1 TTAATATAAT-TA--ATA
* *
650606 TTAATATTA-TACTGTA
1 TTAATATAATTA--ATA
650622 TTAATATAAATT-ATA
1 TTAATAT-AATTAATA
*
650637 GTTAATATAATTAACA
1 -TTAATATAATTAATA
650653 TTAATATAA
1 TTAATATAA
650662 ACTATCTAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
15 24 0.41
16 23 0.40
17 1 0.02
18 10 0.17
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.46
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:650641 original size:16 final size:16
Alignment explanation
Indices: 650561--650646 Score: 56
Period size: 16 Copynumber: 5.3 Consensus size: 16
650551 TAGTATAGTT
*
650561 TATAAACTATAGTTAA
1 TATAAATTATAGTTAA
650577 TAT-AATTAATA-TTAA
1 TATAAATT-ATAGTTAA
* *
650592 TAT--AGTATAGTTTA
1 TATAAATTATAGTTAA
650606 T-TAATATTATACTGTATTAA
1 TATAA-ATTATA--G--TTAA
650626 TATAAATTATAGTTAA
1 TATAAATTATAGTTAA
650642 TATAA
1 TATAA
650647 TTAACATTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
13 4 0.07
14 6 0.11
15 10 0.18
16 20 0.36
18 2 0.04
20 10 0.18
21 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TATAAATTATAGTTAA
Found at i:650731 original size:21 final size:21
Alignment explanation
Indices: 650677--650731 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
650667 CTAGTACATT
*
650677 AATATAAACTATAGTTTATAA
1 AATATAAACTATAGGTTATAA
* * *
650698 ATTATATATTATAGGTTATAA
1 AATATAAACTATAGGTTATAA
650719 AATATAAACTATA
1 AATATAAACTATA
650732 TAGTACACTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (21 bp):
AATATAAACTATAGGTTATAA
Found at i:650825 original size:24 final size:24
Alignment explanation
Indices: 650784--650835 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
650774 ATATATAGTT
*
650784 TATATAGCATATAAATAGATTGTA
1 TATATAGCATATAAATAGATTATA
* *
650808 TATATA-CATATACTATAGGTTATA
1 TATATAGCATATA-AATAGATTATA
650832 TATA
1 TATA
650836 GTTCATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (24 bp):
TATATAGCATATAAATAGATTATA
Found at i:650970 original size:18 final size:18
Alignment explanation
Indices: 650918--651021 Score: 62
Period size: 18 Copynumber: 6.1 Consensus size: 18
650908 ATTAATAAAT
650918 TAATATATAGTTTATATA
1 TAATATATAGTTTATATA
* *
650936 TACTAT-T-G--AACTATA
1 TAATATATAGTTTA-TATA
*
650951 TAATATTTAGTTTATATA
1 TAATATATAGTTTATATA
* *
650969 TACTATATAGTTTATACA
1 TAATATATAGTTTATATA
* *
650987 TACTA-AT-G--AACTATA
1 TAATATATAGTTTA-TATA
*
651002 TAGTATATAGTTTATATA
1 TAATATATAGTTTATATA
651020 TA
1 TA
651022 CTAACGAACT
Statistics
Matches: 65, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
14 2 0.03
15 16 0.25
16 5 0.08
17 5 0.08
18 35 0.54
19 2 0.03
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (18 bp):
TAATATATAGTTTATATA
Found at i:650977 original size:51 final size:51
Alignment explanation
Indices: 650921--651024 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 51
650911 AATAAATTAA
* * *
650921 TATATAGTTTATATATACTATTGAACTATATAATATTTAGTTTATATATAC
1 TATATAGTTTATACATACTAATGAACTATATAATATATAGTTTATATATAC
*
650972 TATATAGTTTATACATACTAATGAACTATATAGTATATAGTTTATATATAC
1 TATATAGTTTATACATACTAATGAACTATATAATATATAGTTTATATATAC
651023 TA
1 TA
651025 ACGAACTATG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (51 bp):
TATATAGTTTATACATACTAATGAACTATATAATATATAGTTTATATATAC
Found at i:651002 original size:33 final size:33
Alignment explanation
Indices: 650965--651057 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
650955 ATTTAGTTTA
* * *
650965 TATATACTATATAGTTTATACATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAACGAAC
*
650998 TATATAGTATATAGTTTATATATACTAACGAAC
1 TATATAATATATAGTTTATATATACTAACGAAC
*
651031 TATGTATAATGTATAGTTTATATATAC
1 TA--TATAATATATAGTTTATATATAC
651058 CATATAGTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
33 32 0.60
35 21 0.40
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.42
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAACGAAC
Found at i:651218 original size:22 final size:22
Alignment explanation
Indices: 651178--651219 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
651168 ACCATATAAT
* * *
651178 ATATATAGTTTTTATATCTATA
1 ATATATAGTATATAAATCTATA
651200 ATATATAGTATATAAATCTA
1 ATATATAGTATATAAATCTA
651220 AACTATAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (22 bp):
ATATATAGTATATAAATCTATA
Found at i:651225 original size:27 final size:27
Alignment explanation
Indices: 651195--651266 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
651185 GTTTTTATAT
* *
651195 CTATAATATATAGTATATAAATCTAAA
1 CTATAGTATATAGTATATAAATATAAA
*
651222 CTATAGTATGTAGTATATAAATATAAA
1 CTATAGTATATAGTATATAAATATAAA
*
651249 CTATAGTTTATA-TATATA
1 CTATAGTATATAGTATATA
651267 GTATATACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 6 0.15
27 34 0.85
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (27 bp):
CTATAGTATATAGTATATAAATATAAA
Found at i:651226 original size:22 final size:22
Alignment explanation
Indices: 651179--651253 Score: 53
Period size: 27 Copynumber: 3.2 Consensus size: 22
651169 CCATATAATA
* * *
651179 TATATAGTTTTTATATCTATAA-
1 TATATAGTATATAAATCTA-AAC
651201 TATATAGTATATAAATCTAAAC
1 TATATAGTATATAAATCTAAAC
*
651223 TATAGTATGTAGTATATAAATATAAAC
1 --TA-TA--TAGTATATAAATCTAAAC
651250 TATA
1 TATA
651254 GTTTATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 2 0.05
22 16 0.37
24 4 0.09
25 4 0.09
27 17 0.40
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (22 bp):
TATATAGTATATAAATCTAAAC
Found at i:651246 original size:20 final size:20
Alignment explanation
Indices: 651196--651295 Score: 80
Period size: 20 Copynumber: 5.0 Consensus size: 20
651186 TTTTTATATC
*
651196 TATAATATATAGTATATA-AA
1 TATAA-ATATAGTATATAGTA
* *
651216 TCTAAACTATAGTATGTAGTA
1 TATAAA-TATAGTATATAGTA
* *
651237 TATAAATATA-AACTATAGTT
1 TATAAATATAGTA-TATAGTA
* *
651257 TATATATATAGTATATACTA
1 TATAAATATAGTATATAGTA
651277 TATAAATA-ATGTATATAGT
1 TATAAATATA-GTATATAGT
651296 TCATATGTAA
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.05
20 52 0.84
21 7 0.11
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (20 bp):
TATAAATATAGTATATAGTA
Found at i:651294 original size:40 final size:40
Alignment explanation
Indices: 651223--651301 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
651213 AAATCTAAAC
* * *
651223 TATAGTATGTAGTATATAAATATAAACTATAGTTTATATA
1 TATAGTATATACTATATAAATATAAACTATAGTTCATATA
**
651263 TATAGTATATACTATATAAATAATGTA-TATAGTTCATAT
1 TATAGTATATACTATATAAAT-ATAAACTATAGTTCATAT
651302 GTAAACTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 30 0.91
41 3 0.09
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (40 bp):
TATAGTATATACTATATAAATATAAACTATAGTTCATATA
Found at i:651313 original size:18 final size:18
Alignment explanation
Indices: 651290--651324 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
651280 AAATAATGTA
651290 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
651308 TATAGTTCATATGTAAA
1 TATAGTTCATATGTAAA
651325 TATCAACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:651351 original size:38 final size:38
Alignment explanation
Indices: 651303--651380 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
651293 AGTTCATATG
*
651303 TAAACTATAGTTCATATGTAAATATCAACCTTAGTATA
1 TAAACTATAGTTCATATATAAATATCAACCTTAGTATA
*
651341 TAAATTATAGTTCATATATAAATATCAACCTTAGTATA
1 TAAACTATAGTTCATATATAAATATCAACCTTAGTATA
651379 TA
1 TA
651381 TATTTATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (38 bp):
TAAACTATAGTTCATATATAAATATCAACCTTAGTATA
Found at i:651360 original size:18 final size:18
Alignment explanation
Indices: 651290--651363 Score: 62
Period size: 18 Copynumber: 4.0 Consensus size: 18
651280 AAATAATGTA
* *
651290 TATAGTTCATATGTAAAC
1 TATAGTTCATATATAAAT
*
651308 TATAGTTCATATGTAAA-
1 TATAGTTCATATATAAAT
*
651325 TATCAACCTT-AGTATATAAAT
1 TAT--A-GTTCA-TATATAAAT
651346 TATAGTTCATATATAAAT
1 TATAGTTCATATATAAAT
651364 ATCAACCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
17 3 0.06
18 28 0.60
19 4 0.09
20 9 0.19
21 3 0.06
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (18 bp):
TATAGTTCATATATAAAT
Found at i:651378 original size:20 final size:20
Alignment explanation
Indices: 651321--651380 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
651311 AGTTCATATG
651321 TAAATATCAACCTTAGTATA
1 TAAATATCAACCTTAGTATA
*
651341 TAAAT-T-ATA-GTTCA-TATA
1 TAAATATCA-ACCTT-AGTATA
651359 TAAATATCAACCTTAGTATA
1 TAAATATCAACCTTAGTATA
651379 TA
1 TA
651381 TATTTATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 12 0.38
19 6 0.19
20 14 0.44
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAATATCAACCTTAGTATA
Found at i:651452 original size:20 final size:20
Alignment explanation
Indices: 651427--651506 Score: 97
Period size: 20 Copynumber: 3.8 Consensus size: 20
651417 ATATAAATAG
651427 TATAAAATATAGTATATAAA
1 TATAAAATATAGTATATAAA
*
651447 TATAAACTATAGTTTATATAAATA
1 TATAAAATATAG--TATAT-AA-A
651471 GTATAAAATATAGTATATAAA
1 -TATAAAATATAGTATATAAA
*
651492 TATAAATTATAGTAT
1 TATAAAATATAGTAT
651507 GTAGTTTATA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
20 25 0.48
21 1 0.02
22 7 0.13
23 7 0.13
24 1 0.02
25 11 0.21
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (20 bp):
TATAAAATATAGTATATAAA
Found at i:651482 original size:25 final size:23
Alignment explanation
Indices: 651417--651493 Score: 106
Period size: 23 Copynumber: 3.4 Consensus size: 23
651407 ACTACAGTTC
651417 ATATAAATAGTATAAAATATAGT
1 ATATAAATAGTATAAAATATAGT
*
651440 ATAT-AA-A-TATAAACTATAGTTT
1 ATATAAATAGTATAAAATATAG--T
651462 ATATAAATAGTATAAAATATAGT
1 ATATAAATAGTATAAAATATAGT
651485 ATATAAATA
1 ATATAAATA
651494 TAAATTATAG
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
20 11 0.23
21 1 0.02
22 7 0.15
23 16 0.34
24 1 0.02
25 11 0.23
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.36
Consensus pattern (23 bp):
ATATAAATAGTATAAAATATAGT
Found at i:651494 original size:29 final size:29
Alignment explanation
Indices: 651462--651530 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
651452 ACTATAGTTT
651462 ATATAAATAGTATAAAATATAG-TATATAA
1 ATATAAATA-TATAAAATATAGTTATATAA
** *
651491 ATATAAAT-TATAGTATGTAGTTTATATAA
1 ATATAAATATATAAAATATAG-TTATATAA
651520 ATATAAATATA
1 ATATAAATATA
651531 ACCCTAAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.26
29 23 0.68
30 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
ATATAAATATATAAAATATAGTTATATAA
Found at i:651503 original size:45 final size:45
Alignment explanation
Indices: 651404--651504 Score: 175
Period size: 45 Copynumber: 2.2 Consensus size: 45
651394 AGTTCATATG
*
651404 TAAACTACAGTTCATATAAATAGTATAAAATATAGTATATAAATA
1 TAAACTATAGTTCATATAAATAGTATAAAATATAGTATATAAATA
*
651449 TAAACTATAGTTTATATAAATAGTATAAAATATAGTATATAAATA
1 TAAACTATAGTTCATATAAATAGTATAAAATATAGTATATAAATA
*
651494 TAAATTATAGT
1 TAAACTATAGT
651505 ATGTAGTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (45 bp):
TAAACTATAGTTCATATAAATAGTATAAAATATAGTATATAAATA
Found at i:651567 original size:22 final size:22
Alignment explanation
Indices: 651542--651598 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
651532 CCCTAAACCA
*
651542 TATATACTATATATATAA-AAAC
1 TATATAATATATAT-TAATAAAC
*
651564 TATATAATTTATATTAATAAAC
1 TATATAATATATATTAATAAAC
*
651586 TATATAATTTATA
1 TATATAATATATA
651599 CAATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 3 0.09
22 29 0.91
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (22 bp):
TATATAATATATATTAATAAAC
Found at i:651576 original size:24 final size:22
Alignment explanation
Indices: 651549--651598 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
651539 CCATATATAC
651549 TATATATATAAAAACTATATAATT
1 TATAT-TA-AAAAACTATATAATT
*
651573 TATATTAATAAACTATATAATT
1 TATATTAAAAAACTATATAATT
651595 TATA
1 TATA
651599 CAATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 18 0.72
23 2 0.08
24 5 0.20
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
TATATTAAAAAACTATATAATT
Found at i:651757 original size:2 final size:2
Alignment explanation
Indices: 651750--651863 Score: 72
Period size: 2 Copynumber: 55.5 Consensus size: 2
651740 TTACACATGG
* * * *
651750 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA AA CTA TA TA GTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * * * *
651792 TA TA TA TA TA TA -A TA CA CA TA CTT TA TA TA TA AA CTA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA
651836 TA TA T- 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
651864 TAGTTGTTTT
Statistics
Matches: 87, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
1 3 0.03
2 78 0.90
3 6 0.07
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:651759 original size:20 final size:20
Alignment explanation
Indices: 651727--651777 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
651717 TATAAACTAT
651727 ATAGTAT-TATAGTTTACAC
1 ATAGTATATATAGTTTACAC
* *
651746 ATGGTATATATAGTTTATAC
1 ATAGTATATATAGTTTACAC
*
651766 ATAATATATATA
1 ATAGTATATATA
651778 TAAACTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (20 bp):
ATAGTATATATAGTTTACAC
Found at i:651800 original size:44 final size:43
Alignment explanation
Indices: 651750--651863 Score: 151
Period size: 44 Copynumber: 2.7 Consensus size: 43
651740 TTACACATGG
*
651750 TATATATAGTTTATACATAATATATATATAAACTATATAGTTTA
1 TATATATA-TATATACATAATATATATATAAACTATATAGTTTA
* * *
651794 TATATATATAATACACATACTTTATATATAAACTATATAGTTTA
1 TATATATAT-ATATACATAATATATATATAAACTATATAGTTTA
*
651838 TAT-TATATATATATAT-ATATATATAT
1 TATATATATATATACATAATATATATAT
651864 TAGTTGTTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
41 8 0.13
42 6 0.10
43 6 0.10
44 41 0.67
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (43 bp):
TATATATATATATACATAATATATATATAAACTATATAGTTTA
Found at i:652334 original size:216 final size:216
Alignment explanation
Indices: 651887--652726 Score: 1388
Period size: 216 Copynumber: 3.9 Consensus size: 216
651877 TTTTTTCTCA
* * * * *
651887 ACTTATTACTTATTTCTATTTATTAATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACAT
1 ACTTATTACTTAATCCTATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* *
651952 TTTTATATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT--T---T-TGTGTT
66 TTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
* * * * *
652011 GTTTAATATATTTTAATTTTTATTTGTAATTTCATATTTATTCAATTTAGTCCTTCAAATTTTAT
131 GTATAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
* *
652076 TTGCATCTGAAATTGACCCAT
196 TTGCATATGAAATTGATCCAT
* * * *
652097 ACTTATTACTTATTTCTATTTTTAAATTGGTCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTAATCCTATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
*
652162 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
66 TTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
*
652227 GTATAATTTATTTAAAATTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
131 GTATAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
652292 TTGCATATGAAATTGATCCAT
196 TTGCATATGAAATTGATCCAT
*
652313 ACTTATTACTTAATCCTATTTTTTAATTGGCCCATAATTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTAATCCTATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
*
652378 TTTTGTATTAATTTCAACCTGACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
66 TTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
652443 GTATAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
131 GTATAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
652508 TTGCATATGAAATTGATCCAT
196 TTGCATATGAAATTGATCCAT
652529 ACTTATTACTTAATCCTATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTAATCCTATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
652594 TTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
66 TTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
* * *
652659 GTTTAATTTATTTAAATTTTTTATTTGTAATTTCATATTTGTTCAATTTAATTCT-CAAATTTAT
131 GTATAATTTATTTAAA-TTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTT-T
652723 ATTT
194 ATTT
652727 TTCATAAAAT
Statistics
Matches: 593, Mismatches: 29, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
210 108 0.18
212 1 0.00
215 1 0.00
216 442 0.75
217 41 0.07
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (216 bp):
ACTTATTACTTAATCCTATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
TTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
GTATAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
TTGCATATGAAATTGATCCAT
Found at i:653964 original size:21 final size:21
Alignment explanation
Indices: 653921--653979 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
653911 CAACTTAGTT
*
653921 TCCAAATTCGCAACGCG-ATA
1 TCCAGATTCGCAACGCGAATA
653941 TCCAGATTCGCAACGCGAATA
1 TCCAGATTCGCAACGCGAATA
*
653962 TCCAGATTCTCAACGCGA
1 TCCAGATTCGCAACGCGA
653980 TTTTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (21 bp):
TCCAGATTCGCAACGCGAATA
Found at i:654035 original size:22 final size:22
Alignment explanation
Indices: 653981--654037 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 22
653971 TCAACGCGAT
*
653981 TTTGAAAAATGTGTTGCGATAG
1 TTTGAAAAATGTGTTGCGAGAG
654003 -TT--AAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
654022 TTTGAAAAACGTGTTG
1 TTTGAAAAATGTGTTG
654038 TTGCGATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 16 0.53
20 2 0.07
21 2 0.07
22 10 0.33
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:654052 original size:22 final size:19
Alignment explanation
Indices: 653986--654052 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 19
653976 GCGATTTTGA
*
653986 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
*
654005 AAAATGTGTTGCGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
654026 AAAAACGTGTTGTTGCGATAGTG
1 -AAAA--TG-TGTTGCGATAGTG
654049 AAAA
1 AAAA
654053 ATCCAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 16 0.41
21 1 0.03
22 8 0.21
23 2 0.05
24 2 0.05
25 10 0.26
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:660731 original size:2 final size:2
Alignment explanation
Indices: 660720--660771 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
660710 AATCTCGAGT
660720 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
660761 TA TA TA TA TA T
1 TA TA TA TA TA T
660772 GAATACACTA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:662166 original size:18 final size:18
Alignment explanation
Indices: 662143--662187 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
662133 CCATTATTAA
662143 TAAATATATATTATTTTT
1 TAAATATATATTATTTTT
*
662161 T-AA-ATATGTTATTTTT
1 TAAATATATATTATTTTT
*
662177 TATATATATAT
1 TAAATATATAT
662188 ATATATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 13 0.59
17 3 0.14
18 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TAAATATATATTATTTTT
Found at i:662182 original size:2 final size:2
Alignment explanation
Indices: 662177--662203 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
662167 TGTTATTTTT
662177 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
662204 CGTATTTTAT
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:662595 original size:4 final size:4
Alignment explanation
Indices: 662586--662682 Score: 51
Period size: 4 Copynumber: 25.0 Consensus size: 4
662576 TTTCCTCATC
* * * *
662586 TTAT TTAT TTAG TTAT CTAT TTAT TTA- TT-T TTCT TTA- TT-T TTCT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * **
662630 TTAT CT-T TGAT TTAT TTACT CATAT TTGT TTAT TTAT TTAT CCAT TTAT
1 TTAT TTAT TTAT TTAT TTA-T -TTAT TTAT TTAT TTAT TTAT TTAT TTAT
662679 TTAT
1 TTAT
662683 GTATGTTGTC
Statistics
Matches: 68, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
3 9 0.13
4 55 0.81
5 2 0.03
6 2 0.03
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:662624 original size:10 final size:10
Alignment explanation
Indices: 662609--662633 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
662599 TATCTATTTA
662609 TTTATTTTTC
1 TTTATTTTTC
662619 TTTATTTTTC
1 TTTATTTTTC
662629 TTTAT
1 TTTAT
662634 CTTTGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:663101 original size:2 final size:2
Alignment explanation
Indices: 663094--663133 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
663084 GGTTGCGACA
663094 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
663134 TAAAATCGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:663389 original size:29 final size:29
Alignment explanation
Indices: 663344--663401 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
663334 GTGTTGGCCG
*
663344 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
663373 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
663402 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:663465 original size:14 final size:14
Alignment explanation
Indices: 663446--663485 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
663436 ATGGGCATCT
663446 GAGGCCATCCGACC
1 GAGGCCATCCGACC
*
663460 GAGGCCATTCGACC
1 GAGGCCATCCGACC
663474 GAGGCCATCCGA
1 GAGGCCATCCGA
663486 GAGCATCCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.23, C:0.38, G:0.30, T:0.10
Consensus pattern (14 bp):
GAGGCCATCCGACC
Found at i:663492 original size:10 final size:10
Alignment explanation
Indices: 663472--663524 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
663462 GGCCATTCGA
663472 CCGAGGCCAT
1 CCGAGGCCAT
663482 CCGAGAG-CAT
1 CCGAG-GCCAT
663492 CCGAGGCCAT
1 CCGAGGCCAT
663502 CCGAGAG--AT
1 CCGAG-GCCAT
663511 CCGAGGCCAT
1 CCGAGGCCAT
663521 CCGA
1 CCGA
663525 ACGAGCTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
8 1 0.03
9 8 0.21
10 27 0.71
11 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.30, T:0.09
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:663514 original size:19 final size:20
Alignment explanation
Indices: 663472--663524 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
663462 GGCCATTCGA
663472 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
663492 CCGAGGCCATCCGAGAG-AT
1 CCGAGGCCATCCGAGAGCAT
663511 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
663525 ACGAGCTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.25, C:0.36, G:0.30, T:0.09
Consensus pattern (20 bp):
CCGAGGCCATCCGAGAGCAT
Found at i:663551 original size:10 final size:10
Alignment explanation
Indices: 663472--663557 Score: 57
Period size: 10 Copynumber: 8.4 Consensus size: 10
663462 GGCCATTCGA
*
663472 CCGAGGCCAT
1 CCGAGGGCAT
*
663482 CCGAGAGCAT
1 CCGAGGGCAT
*
663492 CCGAGGCCAT
1 CCGAGGGCAT
*
663502 CCGAGAG-AT
1 CCGAGGGCAT
*
663511 CCGAGGCCAT
1 CCGAGGGCAT
*
663521 CCGAACGAGCTAT
1 CCG-A-GGGC-AT
**
663534 GTGAGGGCAT
1 CCGAGGGCAT
*
663544 CCGAGGGCAA
1 CCGAGGGCAT
663554 CCGA
1 CCGA
663558 ACGAGCTATG
Statistics
Matches: 56, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
9 7 0.12
10 39 0.70
11 4 0.07
12 3 0.05
13 3 0.05
ACGTcount: A:0.26, C:0.31, G:0.33, T:0.10
Consensus pattern (10 bp):
CCGAGGGCAT
Found at i:663583 original size:33 final size:33
Alignment explanation
Indices: 663509--663583 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
663499 CATCCGAGAG
* * * *
663509 ATCCGAGGCCATCCGAACGAGCTATGTGAGGGC
1 ATCCGAGGGCAACCGAACGAGCTATGAGAGGGA
663542 ATCCGAGGGCAACCGAACGAGCTATGAGAGGGA
1 ATCCGAGGGCAACCGAACGAGCTATGAGAGGGA
663575 ATCCGAGGG
1 ATCCGAGGG
663584 AAGCCGAGCG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.28, C:0.24, G:0.36, T:0.12
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAACGAGCTATGAGAGGGA
Found at i:663726 original size:29 final size:29
Alignment explanation
Indices: 663684--663769 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 29
663674 GAGCAAGGGT
* *
663684 AGGTCGCCCGGAGTGCATGGCGGCCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
663713 AGGTCGCCAGGAGTGCATGGCGACCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
663742 AGGTCGCCCA-GAGTGCATGGCGACCTAC
1 AGGTCG-CCAGGAGTGCATGGCGACCTAC
663770 GGCCAATACT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
29 51 0.94
30 3 0.06
ACGTcount: A:0.21, C:0.30, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCAGGAGTGCATGGCGACCTACA
Found at i:667154 original size:17 final size:18
Alignment explanation
Indices: 667128--667161 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
667118 CTTTATTTGA
*
667128 AAACCTAAAAG-AGAATC
1 AAACCAAAAAGAAGAATC
667145 AAACCAAAAAGAAGAAT
1 AAACCAAAAAGAAGAAT
667162 ACACCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.15, G:0.12, T:0.09
Consensus pattern (18 bp):
AAACCAAAAAGAAGAATC
Found at i:674958 original size:3 final size:3
Alignment explanation
Indices: 674950--675029 Score: 81
Period size: 3 Copynumber: 26.3 Consensus size: 3
674940 TGTATTTATT
* *
674950 TAA TAA TAA TAA TAAA TAA TAA -AA TAA TAA TGTA TAT TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* ** *
674996 CAA TAA TAA TAA TAA TAA TTT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
675030 TTAAATAATT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
2 2 0.03
3 55 0.89
4 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:684606 original size:460 final size:460
Alignment explanation
Indices: 683746--684662 Score: 1753
Period size: 460 Copynumber: 2.0 Consensus size: 460
683736 CGGATGCCTC
683746 TACTCCAGCAGGAACATCAAAATTATCAAAATGTGCTTGCAACATGGCATACTCGTCAACATCCA
1 TACTCCAGCAGGAACATCAAAATTATCAAAATGTGCTTGCAACATGGCATACTCGTCAACATCCA
683811 TATGATCACCAAGGTAATAGTTCTCAAATAAATCATCATCACAGGCCAAATCACAATCTAGGTTA
66 TATGATCACCAAGGTAATAGTTCTCAAATAAATCATCATCACAGGCCAAATCACAATCTAGGTTA
683876 TATACATTGTGTGATCCTTGGGTAGAATTCTTAGAAGGTTCAACCTTGTTTATTAAACCAGTAGG
131 TATACATTGTGTGATCCTTGGGTAGAATTCTTAGAAGGTTCAACCTTGTTTATTAAACCAGTAGG
*
683941 TTTGGCCACAAAATCCTGTAGAGAAATGGGGAAACAGTAAACAAAACAATAATAGGTACAAATGT
196 TTTGGCCACAAAATCCTGTAGAGAAATGGGGAAACAGTAAACAAAAAAATAATAGGTACAAATGT
*
684006 TATAATTGATTTATGCACAGTCAACAGTAACCATGGCAATAAAAATTCAACCTCTCATATACCTC
261 TATAATTGATTTATGCACAATCAACAGTAACCATGGCAATAAAAATTCAACCTCTCATATACCTC
684071 AGCTTGAATAGCACTATAGACACCGGGGCTAATTTTTACTGCCTTCCCTTTGTTCCTTACATCAA
326 AGCTTGAATAGCACTATAGACACCGGGGCTAATTTTTACTGCCTTCCCTTTGTTCCTTACATCAA
*
684136 CCATCTCATCAAGGATCACTATATCACTTGAATCTTTATCCTTATCGGCGTCAATTATTTCTTGA
391 CCATCTCATCAAGGATCACTATATCACTTGAATCTTTATCCTTATCGGCGTCAATTATTTCATGA
684201 ATCTT
456 ATCTT
* *
684206 TACTCCAGCAGGAATATCAAAATTATCAAAATGTGCTTGCAACATGGCATACTCGTCAACATTCA
1 TACTCCAGCAGGAACATCAAAATTATCAAAATGTGCTTGCAACATGGCATACTCGTCAACATCCA
684271 TATGATCACCAAGGTAATAGTTCTCAAATAAATCATCATCACAGGCCAAATCACAATCTAGGTTA
66 TATGATCACCAAGGTAATAGTTCTCAAATAAATCATCATCACAGGCCAAATCACAATCTAGGTTA
*
684336 TATACATTGTGTGATCCTTGGGTAGAATTCTTAGAAGGTTCAACCTTGTTTATTGAACCAGTAGG
131 TATACATTGTGTGATCCTTGGGTAGAATTCTTAGAAGGTTCAACCTTGTTTATTAAACCAGTAGG
*
684401 TTTGGCCACAAAATCCTGTAGAGAAATGGGGAAACAGTAAACAAAAAAATATTAGGTACAAATGT
196 TTTGGCCACAAAATCCTGTAGAGAAATGGGGAAACAGTAAACAAAAAAATAATAGGTACAAATGT
684466 TATAATTGATTTATGCACAATCAACAGTAACCATGGCAATAAAAATTCAACCTCTCATATACCTC
261 TATAATTGATTTATGCACAATCAACAGTAACCATGGCAATAAAAATTCAACCTCTCATATACCTC
* *
684531 AGCTTGAATAGCACTATAGACACCGTGGCTACTTTTTACTGCCTTCCCTTTGTTCCTTACATCAA
326 AGCTTGAATAGCACTATAGACACCGGGGCTAATTTTTACTGCCTTCCCTTTGTTCCTTACATCAA
684596 CCATCTCATCAAGGATCACTATATCACTTGAATCTTTATCCTTATCGGCGTCAATTATTTCATGA
391 CCATCTCATCAAGGATCACTATATCACTTGAATCTTTATCCTTATCGGCGTCAATTATTTCATGA
684661 AT
456 AT
684663 AACAACCTAG
Statistics
Matches: 448, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
460 448 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (460 bp):
TACTCCAGCAGGAACATCAAAATTATCAAAATGTGCTTGCAACATGGCATACTCGTCAACATCCA
TATGATCACCAAGGTAATAGTTCTCAAATAAATCATCATCACAGGCCAAATCACAATCTAGGTTA
TATACATTGTGTGATCCTTGGGTAGAATTCTTAGAAGGTTCAACCTTGTTTATTAAACCAGTAGG
TTTGGCCACAAAATCCTGTAGAGAAATGGGGAAACAGTAAACAAAAAAATAATAGGTACAAATGT
TATAATTGATTTATGCACAATCAACAGTAACCATGGCAATAAAAATTCAACCTCTCATATACCTC
AGCTTGAATAGCACTATAGACACCGGGGCTAATTTTTACTGCCTTCCCTTTGTTCCTTACATCAA
CCATCTCATCAAGGATCACTATATCACTTGAATCTTTATCCTTATCGGCGTCAATTATTTCATGA
ATCTT
Found at i:687320 original size:20 final size:21
Alignment explanation
Indices: 687295--687346 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
687285 TTTTTCCAAT
*
687295 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
687315 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
687336 TCGCAATGCGA
1 TCGCAATGCGA
687347 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:687341 original size:41 final size:41
Alignment explanation
Indices: 687295--687532 Score: 139
Period size: 41 Copynumber: 5.8 Consensus size: 41
687285 TTTTTCCAAT
687295 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAA
* * * *** *
687336 TCGCAATGCG-AT-ACTGACTATCACAATGC-AATTTTCCTAAT
1 TCGCAATGCGAATAAGT-A-AATCGCAATGCGAA-TTTGGAAAA
* * * * ** ** *
687377 TCGCATTGCGATTTACGT-ATTCGCGTTGCG-ATTTTCATAAT
1 TCGCAATGCGA-ATAAGTAAATCGCAATGCGAATTTGGA-AAA
* ** *
687418 TCGCAATGCGAATACA-TAAATCGCAACGCG-ATTAAGTAAA
1 TCGCAATGCGAATA-AGTAAATCGCAATGCGAATTTGGAAAA
* * *
687458 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TAAGTAAATCGCAATGCGAATTTGGAAAA
* *
687500 TTGCAATGCGAATACGTAAATCGCAATGCGAAT
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAAT
687533 CTTACTATCG
Statistics
Matches: 146, Mismatches: 38, Indels: 26
0.70 0.18 0.12
Matches are distributed among these distances:
39 2 0.01
40 26 0.18
41 97 0.66
42 19 0.13
43 1 0.01
44 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAA
Found at i:687421 original size:21 final size:21
Alignment explanation
Indices: 687366--687428 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
687356 TCACAATGCA
*
687366 ATTTTCCTAATTCGCATTGCG
1 ATTTTCATAATTCGCATTGCG
* * *
687387 ATTTACGT-ATTCGCGTTGCG
1 ATTTTCATAATTCGCATTGCG
*
687407 ATTTTCATAATTCGCAATGCG
1 ATTTTCATAATTCGCATTGCG
687428 A
1 A
687429 ATACATAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTGCG
Found at i:687441 original size:20 final size:20
Alignment explanation
Indices: 687412--687550 Score: 115
Period size: 20 Copynumber: 6.8 Consensus size: 20
687402 TTGCGATTTT
*
687412 CATAATTCGCAATGCGAATA
1 CATAAATCGCAATGCGAATA
* *
687432 CATAAATCGCAACGCGATTA
1 CATAAATCGCAATGCGAATA
687452 -AGTAAATCGCAATGCGAATTA
1 CA-TAAATCGCAATGCGAA-TA
*
687473 GGA-AAATCGCAATGCGAATTA
1 -CATAAATCGCAATGCGAA-TA
* *
687494 GGA-AAATTGCAATGCGAATA
1 -CATAAATCGCAATGCGAATA
*
687514 CGTAAATCGCAATGCGAAT-
1 CATAAATCGCAATGCGAATA
* *
687533 CTTACTATCGCAATGCGA
1 CATA-AATCGCAATGCGA
687551 TTTACATAGC
Statistics
Matches: 102, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
19 4 0.04
20 60 0.59
21 37 0.36
23 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (20 bp):
CATAAATCGCAATGCGAATA
Found at i:687479 original size:21 final size:21
Alignment explanation
Indices: 687418--687532 Score: 130
Period size: 20 Copynumber: 5.6 Consensus size: 21
687408 TTTTCATAAT
*
687418 TCGCAATGCGAA-TA-CATAAA
1 TCGCAATGCGAATTAGGA-AAA
* * *
687438 TCGCAACGCG-ATTAAGTAAA
1 TCGCAATGCGAATTAGGAAAA
687458 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
687479 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
687500 TTGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTAGGAAAA
687520 TCGCAATGCGAAT
1 TCGCAATGCGAAT
687533 CTTACTATCG
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.01
20 40 0.49
21 40 0.49
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:687817 original size:27 final size:27
Alignment explanation
Indices: 687760--687812 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
687750 CATCGCCGAC
* *
687760 GAAATCCCTCACAACCATTCACAGTCA
1 GAAATCCCTCACAACCATTCAAAATCA
*
687787 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAACCATTCA-AAAT
687813 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCAAAATCA
Found at i:688129 original size:19 final size:19
Alignment explanation
Indices: 688105--688148 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
688095 GCAACGAGAG
* **
688105 AATCGCTACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
*
688124 AATCGCAACGTGAAACCAA
1 AATCGCAACGCGAAACCAA
688143 AATCGC
1 AATCGC
688149 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.43, C:0.25, G:0.18, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:688196 original size:33 final size:34
Alignment explanation
Indices: 688148--688213 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
688138 ACCAAAATCG
**
688148 CGTTGCGATTTTCATTT-CGCATTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCATTGCGATTCTCT
*
688181 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCATTGCGATTCTC
688214 ATTATCTCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 15 0.52
34 14 0.48
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.41
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCATTGCGATTCTCT
Found at i:688215 original size:20 final size:19
Alignment explanation
Indices: 688145--688238 Score: 81
Period size: 20 Copynumber: 5.1 Consensus size: 19
688135 GAAACCAAAA
*
688145 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
*
688164 TCGCATTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
688180 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
688197 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* *
688217 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTCTCATT
688237 TC
1 TC
688239 AACCAAAAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
14 10 0.17
16 1 0.02
17 1 0.02
19 16 0.27
20 30 0.51
21 1 0.02
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:689745 original size:16 final size:16
Alignment explanation
Indices: 689724--689756 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
689714 TAAAAAATAA
689724 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
689740 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
689756 A
1 A
689757 AAATTTTTTT
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:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:689848 original size:16 final size:16
Alignment explanation
Indices: 689827--689887 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
689817 TAATAAATAA
689827 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
689843 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
689859 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
689875 ACGAACATAAACG
1 ACGAACATAAACG
689888 TTGGAGACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:690649 original size:14 final size:14
Alignment explanation
Indices: 690632--690687 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
690622 AATGAACATA
*
690632 AACGAACATAATCG
1 AACGAACATAACCG
690646 AACGAACAT-A---
1 AACGAACATAACCG
*
690656 AACGAACATAACCA
1 AACGAACATAACCG
690670 AACGAACATAACCG
1 AACGAACATAACCG
690684 AACG
1 AACG
690688 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:690652 original size:24 final size:24
Alignment explanation
Indices: 690612--690686 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
690602 GATTGTGTTA
*
690612 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
690636 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
690660 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
690684 AAC
1 AAC
690687 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:691285 original size:94 final size:89
Alignment explanation
Indices: 691127--691310 Score: 280
Period size: 92 Copynumber: 2.0 Consensus size: 89
691117 TAGATTGCTT
*
691127 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAATTAGTATTT
691192 GTCTTTTTGTTTTGTCTTTTGGTTGA
66 GTC--TTTGTTTTGTCTTTTGGTTGA
* *
691218 AGTAAATTTATTCGGTTGCTG-CAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAATTAGT
691282 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
62 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
691310 A
1 A
691311 AGTTTGAAAT
Statistics
Matches: 86, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
90 13 0.15
91 21 0.24
92 25 0.29
93 2 0.02
94 25 0.29
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (89 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAATTAGTATTT
GTCTTTGTTTTGTCTTTTGGTTGA
Found at i:691608 original size:42 final size:42
Alignment explanation
Indices: 691532--691650 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
691522 GACTCGCCTG
* * * *
691532 TCATCCCTC-AAGA-GTCCACTCCTATCATTGAAGAGGCCCTTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCATTCAAGAGGCCATTA
* *
691574 TCATTCCTCG-AGA-GTCTCCTCCCACCGTTCAAGAGGCCATTG
1 TCA-TCCTCGAAGAGGTC-CCTCCCACCATTCAAGAGGCCATTA
* *
691616 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
691651 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 54 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.25
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCATTA
Found at i:693025 original size:14 final size:14
Alignment explanation
Indices: 693006--693037 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
692996 GTTTAATTGA
693006 TTGTAAAAGGTGAT
1 TTGTAAAAGGTGAT
*
693020 TTGTAAAAGTTGAT
1 TTGTAAAAGGTGAT
693034 TTGT
1 TTGT
693038 TTAATTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TTGTAAAAGGTGAT
Found at i:693218 original size:19 final size:19
Alignment explanation
Indices: 693196--693346 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
693186 CGAAACTAAA
693196 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
693215 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
693230 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
693248 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
693262 TTCGCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
693281 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
693296 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
693314 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
693333 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
693347 AGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:693242 original size:33 final size:32
Alignment explanation
Indices: 693200--693326 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
693190 ACTAAATTCG
*
693200 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
693233 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
693266 CGTTGCAATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
693299 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
693327 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:693277 original size:66 final size:66
Alignment explanation
Indices: 693193--693325 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
693183 ACGCGAAACT
* *
693193 AAATTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
693258 G
66 G
*
693259 AAATTCGCGTTGCAATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
693324 G
66 G
693325 A
1 A
693326 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTCGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:696696 original size:20 final size:20
Alignment explanation
Indices: 696663--696736 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
696653 AATTTGGAAA
* *
696663 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
696683 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
696704 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
*
696724 TTCGCAACGAGAT
1 ATCGCAACGAGAT
696737 TCTAAAAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 25 0.58
21 14 0.33
22 2 0.05
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:696705 original size:41 final size:40
Alignment explanation
Indices: 696660--696751 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
696650 GCGAATTTGG
*
696660 AAAATCGCAATGCGATACTGACTATCGCAACGAGATAATA
1 AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
* * * **
696700 CAAAATCGCAACGAGATTCTGACTTTCGCAACGAGATTCTA
1 -AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
696741 AAAATCGCAAT
1 AAAATCGCAAT
696752 CATCTTCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 10 0.23
41 34 0.77
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (40 bp):
AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
Found at i:696748 original size:20 final size:20
Alignment explanation
Indices: 696683--696750 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
696673 GATACTGACT
**
696683 ATCGCAACGAGATAATACAAA
1 ATCGCAACGAGATTCTA-AAA
* **
696704 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTAAAA
*
696724 TTCGCAACGAGATTCTAAAA
1 ATCGCAACGAGATTCTAAAA
696744 ATCGCAA
1 ATCGCAA
696751 TCATCTTCAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 23 0.62
21 14 0.38
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGATTCTAAAA
Found at i:697023 original size:20 final size:20
Alignment explanation
Indices: 696948--697025 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
696938 ATTCATTTGA
**
696948 CTATCGCAACGCGAAAATGG
1 CTATCGCAACTAGAAAATGG
* * *
696968 CTATCGCAATTTG-AAATGAA
1 CTATCGCAACTAGAAAATG-G
**
696988 AAATCGCAAC-ACGAAAATGG
1 CTATCGCAACTA-GAAAATGG
697008 CTATCGCAACTAGAAAAT
1 CTATCGCAACTAGAAAAT
697026 CGCAATGCGA
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
19 5 0.12
20 32 0.74
21 6 0.14
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (20 bp):
CTATCGCAACTAGAAAATGG
Found at i:697068 original size:14 final size:14
Alignment explanation
Indices: 697049--697102 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
697039 GAAAATCGCA
697049 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
697063 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
697080 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
697096 TTGCGAT
1 TTGCGAT
697103 AGTCAGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:697068 original size:33 final size:33
Alignment explanation
Indices: 697031--697101 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
697021 AAAATCGCAA
697031 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
697064 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
697097 TGCGA
1 TGCGA
697102 TAGTCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:699138 original size:20 final size:20
Alignment explanation
Indices: 699115--699181 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
699105 AAACTTACTT
*
699115 TCGCAACGCGGAAATGACTC
1 TCGCAACGCGGAAATGACTA
*
699135 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
699155 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
699174 TCGCAACG
1 TCGCAACG
699182 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:699248 original size:14 final size:14
Alignment explanation
Indices: 699229--699286 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
699219 TTTTATTTCG
699229 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
699243 CGTTGCGATTTTCATT
1 CGTTGCGATTTT--GT
*
699259 CGCATTGCGGTTTTGT
1 CG--TTGCGATTTTGT
*
699275 CTTTGCGATTTT
1 CGTTGCGATTTT
699287 CATTTCGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 21 0.60
16 5 0.14
18 9 0.26
ACGTcount: A:0.09, C:0.17, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:699267 original size:32 final size:33
Alignment explanation
Indices: 699212--699302 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 33
699202 ACAAATCGCA
* *
699212 TTGCGATTTTTATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
* *
699245 TTGCGATTTTCA-TTCGCATTGCGGTTTTGTCT
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
699277 TTGCGATTTTCATTTCGTATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
699303 AGCCATTTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
32 29 0.57
33 22 0.43
ACGTcount: A:0.11, C:0.16, G:0.22, T:0.51
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:699319 original size:20 final size:20
Alignment explanation
Indices: 699296--699341 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
699286 TCATTTCGTA
699296 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
* *
699316 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTTCGCG
699336 TTGCGA
1 TTGCGA
699342 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:699881 original size:18 final size:18
Alignment explanation
Indices: 699858--699905 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
699848 CGGGTCAATC
699858 AGGTGATGGCTCTGGGCG
1 AGGTGATGGCTCTGGGCG
* *
699876 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGCG
699894 AGGTGATGGCTC
1 AGGTGATGGCTC
699906 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.46, T:0.25
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGCG
Found at i:700676 original size:20 final size:20
Alignment explanation
Indices: 700651--700717 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
700641 GTATTATCTC
*
700651 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTCAGTATCGA
* *
700671 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTCAGTATCGA
*
700691 GTTGCGAAAGTCAGTATCGC
1 GTTGCGAAAGTCAGTATCGA
700711 GTTGCGA
1 GTTGCGA
700718 TTTTGTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.28
Consensus pattern (20 bp):
GTTGCGAAAGTCAGTATCGA
Found at i:700757 original size:21 final size:20
Alignment explanation
Indices: 700733--700779 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
700723 TATTATTGCG
*
700733 TTGCGATTTTCCAAATTCGCA
1 TTGCGA-TTTACAAATTCGCA
**
700754 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACAAATTCGCA
700774 TTGCGA
1 TTGCGA
700780 ATTGGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:701442 original size:18 final size:16
Alignment explanation
Indices: 701419--701457 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
701409 GATATACTTT
701419 AATAATTATAAATATTAA
1 AATAATT-T-AATATTAA
*
701437 AATAATTTCATATTAA
1 AATAATTTAATATTAA
701453 AATAA
1 AATAA
701458 AATAAACCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 1 0.05
18 7 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAATTTAATATTAA
Found at i:701553 original size:26 final size:26
Alignment explanation
Indices: 701515--701567 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
701505 TTTCTACTTT
*
701515 TGTTTTATGTTTTCA-TTTTTAGAAAA
1 TGTTTTATATTTTCAGTTTTTA-AAAA
* *
701541 TGTTTTTTATTTTTAGTTTTTAAAAA
1 TGTTTTATATTTTCAGTTTTTAAAAA
701567 T
1 T
701568 TTAGAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.62
Consensus pattern (26 bp):
TGTTTTATATTTTCAGTTTTTAAAAA
Done.