Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005687.1 Hibiscus syriacus cultivar Beakdansim tig00013306_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: 100898
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:13041 original size:19 final size:17
Alignment explanation
Indices: 13007--13043 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
12997 TGTGCATATT
13007 TATAAATGTTATAAAAA
1 TATAAATGTTATAAAAA
13024 TATAACATGTTCATAAAAA
1 TATAA-ATGTT-ATAAAAA
13043 T
1 T
13044 CGTGACAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (17 bp):
TATAAATGTTATAAAAA
Found at i:13179 original size:26 final size:26
Alignment explanation
Indices: 13150--13213 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
13140 ATTATATATA
13150 TAATTATAAATAATAAC-ATTAAAA-TT
1 TAATTATAAATAAT--CTATTAAAACTT
*
13176 TAATTATAGAA-AATCTTTTAAAACTT
1 TAATTATA-AATAATCTATTAAAACTT
13202 TAATTATAAATA
1 TAATTATAAATA
13214 TGATAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
24 1 0.03
25 8 0.24
26 22 0.67
27 2 0.06
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (26 bp):
TAATTATAAATAATCTATTAAAACTT
Found at i:17260 original size:13 final size:14
Alignment explanation
Indices: 17232--17258 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17222 TTTTCTTCCA
17232 AAGTTTTTGTTTTT
1 AAGTTTTTGTTTTT
17246 AAGTTTTTGTTTT
1 AAGTTTTTGTTTT
17259 AATTATTTAT
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:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (14 bp):
AAGTTTTTGTTTTT
Found at i:18515 original size:21 final size:21
Alignment explanation
Indices: 18486--18600 Score: 203
Period size: 21 Copynumber: 5.5 Consensus size: 21
18476 TTCCAGATTT
* *
18486 GCAACGCGAACTTCGACTATC
1 GCAATGCGAACTTGGACTATC
18507 GCAATGCGAACTTGGACTATC
1 GCAATGCGAACTTGGACTATC
*
18528 GCAATGTGAACTTGGACTATC
1 GCAATGCGAACTTGGACTATC
18549 GCAATGCGAACTTGGACTATC
1 GCAATGCGAACTTGGACTATC
18570 GCAATGCGAACTTGGACTATC
1 GCAATGCGAACTTGGACTATC
18591 GCAATGCGAA
1 GCAATGCGAA
18601 TATGTAAATC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 90 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (21 bp):
GCAATGCGAACTTGGACTATC
Found at i:18663 original size:42 final size:42
Alignment explanation
Indices: 18589--18696 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
18579 ACTTGGACTA
*
18589 TCGCAATGCGAATATGT-AAA--TCGCAATGCGATAGTCGAAGT
1 TCGCAATGCG-ATA-GTCAAAGTTCGCAATACGATAGTCGAAGT
*
18630 TCGCAATGCGATAGTCGAAGTTCGCAATACGATAGTCGAAGT
1 TCGCAATGCGATAGTCAAAGTTCGCAATACGATAGTCGAAGT
* *
18672 TCGCATTTCGATAGTCAAAGTTCGC
1 TCGCAATGCGATAGTCAAAGTTCGC
18697 GTTGCGATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
39 2 0.03
40 5 0.08
41 10 0.17
42 42 0.71
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (42 bp):
TCGCAATGCGATAGTCAAAGTTCGCAATACGATAGTCGAAGT
Found at i:18704 original size:21 final size:21
Alignment explanation
Indices: 18609--18696 Score: 140
Period size: 21 Copynumber: 4.2 Consensus size: 21
18599 AATATGTAAA
18609 TCGCAATGCGATAGTCGAAGT
1 TCGCAATGCGATAGTCGAAGT
18630 TCGCAATGCGATAGTCGAAGT
1 TCGCAATGCGATAGTCGAAGT
*
18651 TCGCAATACGATAGTCGAAGT
1 TCGCAATGCGATAGTCGAAGT
* * *
18672 TCGCATTTCGATAGTCAAAGT
1 TCGCAATGCGATAGTCGAAGT
18693 TCGC
1 TCGC
18697 GTTGCGATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGATAGTCGAAGT
Found at i:18789 original size:21 final size:21
Alignment explanation
Indices: 18744--18831 Score: 83
Period size: 21 Copynumber: 4.2 Consensus size: 21
18734 ACTTCGACTA
* * *
18744 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCAAAT
*
18764 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAAT
*
18785 TCGCATTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAAT
*
18808 TCG--TTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAT
18827 TCGCA
1 TCGCA
18832 ATGACTGGTG
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
19 11 0.20
20 12 0.22
21 21 0.38
23 11 0.20
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:18789 original size:41 final size:40
Alignment explanation
Indices: 18744--18824 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 40
18734 ACTTCGACTA
*
18744 TCGCATTGCGATTTA-CATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATTTATCAAATTCG--TTGCGATAGTCCAAGT
18785 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TCGCATTGCGATTTA-T-CAAATTCGTTGCGATAGTCCAA
18825 AATCGCAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
41 15 0.42
42 14 0.39
44 7 0.19
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (40 bp):
TCGCATTGCGATTTATCAAATTCGTTGCGATAGTCCAAGT
Found at i:18831 original size:42 final size:40
Alignment explanation
Indices: 18743--18831 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 40
18733 AACTTCGACT
* *
18743 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
1 ATCGCATTGCGATTTACAAATTCG-ATTGCGATAGTCCAAA
*
18784 TTCGCATTGCGATTTATTCCAAATTCG-TTGCGATAGTCCAAA
1 ATCGCATTGCGATTTA---CAAATTCGATTGCGATAGTCCAAA
18826 ATCGCA
1 ATCGCA
18832 ATGACTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 15 0.37
42 19 0.46
44 7 0.17
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (40 bp):
ATCGCATTGCGATTTACAAATTCGATTGCGATAGTCCAAA
Found at i:19416 original size:6 final size:6
Alignment explanation
Indices: 19407--19438 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
19397 CGCCGCCGCC
19407 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
19439 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:19545 original size:19 final size:19
Alignment explanation
Indices: 19524--19659 Score: 137
Period size: 21 Copynumber: 6.7 Consensus size: 19
19514 CGTTGCGATT
* *
19524 TTGGACTATCGTAACGAAT
1 TTGGACTATCGCAACGAAC
*
19543 TTGGAATAAATCGCAACGAAC
1 TTGGACT--ATCGCAACGAAC
19564 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
* *
19583 TTGGAATAAATCGCAACGAAT
1 TTGGACT--ATCGCAACGAAC
*
19604 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
19627 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
19646 TTGGACTATCGCAA
1 TTGGACTATCGCAA
19660 TGCGATAGTC
Statistics
Matches: 101, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
19 42 0.42
21 50 0.50
23 9 0.09
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:19560 original size:21 final size:21
Alignment explanation
Indices: 19531--19650 Score: 140
Period size: 21 Copynumber: 5.8 Consensus size: 21
19521 ATTTTGGACT
* *
19531 ATCGTAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
19552 ATCGCAACGAACTTGGACT--
1 ATCGCAACGAACTTGGAATAA
19571 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
19592 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
19613 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
19634 ATCGCAACGAACTTGGA
1 ATCGCAACGAACTTGGA
19651 CTATCGCAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
19 27 0.31
21 50 0.58
23 9 0.10
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:19580 original size:40 final size:40
Alignment explanation
Indices: 19524--19659 Score: 168
Period size: 40 Copynumber: 3.4 Consensus size: 40
19514 CGTTGCGATT
* *
19524 TTGGACTATCGTAACGAATTTGGAATAAATCGCAACGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
*
19564 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAT
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
* * *
19604 TTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGAAC
1 TTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGAAC
19646 TTGGACTATCGCAA
1 TTGGACTATCGCAA
19660 TGCGATAGTC
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
40 50 0.60
42 24 0.29
44 10 0.12
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (40 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
Found at i:19606 original size:61 final size:62
Alignment explanation
Indices: 19531--19650 Score: 206
Period size: 63 Copynumber: 1.9 Consensus size: 62
19521 ATTTTGGACT
* *
19531 ATCGTAACGAATTTGGAATAAATCGCAA-CGAACTTGGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGAATTTGGAATAAATCGCAACCGAACTTCGACTATCGCAACGAACTTGGAATAA
19592 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
1 ATCGCAACGAATTTGGAATAAATCGCAAC-CGAACTTCGACTATCGCAACGAACTTGGA
19651 CTATCGCAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
61 27 0.49
63 28 0.51
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (62 bp):
ATCGCAACGAATTTGGAATAAATCGCAACCGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:19992 original size:2 final size:2
Alignment explanation
Indices: 19901--19980 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
19891 TATGTTGTTA
19901 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19943 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
19981 CCTTAAATAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20554 original size:25 final size:26
Alignment explanation
Indices: 20507--20555 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
20497 ATAAATAAGT
**
20507 TAAATATTAAATTTTATTTCATATTA
1 TAAATATTAAATTTTATACCATATTA
*
20533 TAAATATTGAA-TTTATACCATAT
1 TAAATATTAAATTTTATACCATAT
20556 AAATTATTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (26 bp):
TAAATATTAAATTTTATACCATATTA
Found at i:29561 original size:22 final size:21
Alignment explanation
Indices: 29536--29579 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
29526 TTTTAACATA
29536 GGTCATTT-AGGACAAACTATGT
1 GGTC-TTTCAGGACAAA-TATGT
*
29558 GGTCTTTCGGGACAAATATGT
1 GGTCTTTCAGGACAAATATGT
29579 G
1 G
29580 ACACTTCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (21 bp):
GGTCTTTCAGGACAAATATGT
Found at i:32805 original size:31 final size:30
Alignment explanation
Indices: 32770--32838 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 30
32760 GGAGTACCTT
* * *
32770 GGGGCCTGAGAGCCTATCCAAGACAATTCTC
1 GGGGCCTGAG-GCCTACCCAAGAAAAATCTC
*
32801 GGGGCCACTGAGGCTTACCCAAGAAAAATCTC
1 GGGG-C-CTGAGGCCTACCCAAGAAAAATCTC
32833 GGGGCC
1 GGGGCC
32839 ACAAAGCCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
30 1 0.03
31 5 0.16
32 21 0.66
33 5 0.16
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (30 bp):
GGGGCCTGAGGCCTACCCAAGAAAAATCTC
Found at i:32854 original size:31 final size:32
Alignment explanation
Indices: 32780--32854 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
32770 GGGGCCTGAG
* * * *
32780 AGCCTATCCAAGACAATTCTCGGGGCCACTGA
1 AGCCTACCCAAGAAAAATCTCGGGGCCACTAA
* *
32812 GGCTTACCCAAGAAAAATCTCGGGGCCAC-AA
1 AGCCTACCCAAGAAAAATCTCGGGGCCACTAA
32843 AGCCTACCCAAG
1 AGCCTACCCAAG
32855 GGTCGCCTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 11 0.31
32 24 0.69
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (32 bp):
AGCCTACCCAAGAAAAATCTCGGGGCCACTAA
Found at i:33686 original size:19 final size:19
Alignment explanation
Indices: 33662--33706 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
33652 TAACTTTTTG
33662 GGTCAAAGTCAAC-AGGTCA
1 GGTCAAAGTCAACGA-GTCA
*
33681 GGTCAAAGTCAACGAGTCG
1 GGTCAAAGTCAACGAGTCA
33700 GGTCAAA
1 GGTCAAA
33707 CAGTTCAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.36, C:0.20, G:0.29, T:0.16
Consensus pattern (19 bp):
GGTCAAAGTCAACGAGTCA
Found at i:38370 original size:55 final size:58
Alignment explanation
Indices: 38302--38412 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 58
38292 TAAAATAGTG
* *
38302 TTAATTATAAATTGAATAG-T-A-TGATTATGCATACAGTTACATCAATTCACATCCT
1 TTAATTATAAATTGAAGAGATAAGTGATTATGCATACAGTCACATCAATTCACATCCT
*
38357 TTAATTA-AGAATTGAAGAGTATAATGTGATTATGCATATAGTCACATCAATTCACA
1 TTAATTATA-AATTGAAGAG-ATAA-GTGATTATGCATACAGTCACATCAATTCACA
38413 ACTATATAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
54 1 0.02
55 16 0.34
57 1 0.02
58 1 0.02
60 28 0.60
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (58 bp):
TTAATTATAAATTGAAGAGATAAGTGATTATGCATACAGTCACATCAATTCACATCCT
Found at i:42068 original size:34 final size:33
Alignment explanation
Indices: 41984--42071 Score: 99
Period size: 34 Copynumber: 2.6 Consensus size: 33
41974 AAATTCTTAC
*
41984 TTTATTTT-ATTAATTTGGTTGGATTTTTTTAAAA
1 TTTATTTTGA-TAATTTTGTTGGATTTTTTT-AAA
* *
42018 TTTATTTTGTTTATTTTGTTGGACTTTTTGTT-AA
1 TTTATTTTGATAATTTTGTTGGA-TTTTT-TTAAA
42052 TTTATTTTGATAATTTTGTT
1 TTTATTTTGATAATTTTGTT
42072 TATTACCATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
34 39 0.85
35 5 0.11
36 2 0.04
ACGTcount: A:0.20, C:0.01, G:0.12, T:0.66
Consensus pattern (33 bp):
TTTATTTTGATAATTTTGTTGGATTTTTTTAAA
Found at i:42666 original size:21 final size:21
Alignment explanation
Indices: 42615--42666 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
42605 TCTTGATGGG
42615 TATGCGAGCAAGCTGCTATCA
1 TATGCGAGCAAGCTGCTATCA
* * *
42636 CATGCAAGCAAGCTGCTATTA
1 TATGCGAGCAAGCTGCTATCA
*
42657 TATGTGAGCA
1 TATGCGAGCA
42667 TGGATACTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (21 bp):
TATGCGAGCAAGCTGCTATCA
Found at i:46912 original size:16 final size:16
Alignment explanation
Indices: 46888--46967 Score: 133
Period size: 16 Copynumber: 5.0 Consensus size: 16
46878 GGGTTTCAGA
46888 TTCAGATTCCAATTCC
1 TTCAGATTCCAATTCC
* *
46904 TTCAAATTCTAATTCC
1 TTCAGATTCCAATTCC
46920 TTCAGATTCCAATTCC
1 TTCAGATTCCAATTCC
46936 TTCAGATTCCAATTCC
1 TTCAGATTCCAATTCC
*
46952 TTCAGATTCTAATTCC
1 TTCAGATTCCAATTCC
46968 CTCATAAACA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 59 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.40
Consensus pattern (16 bp):
TTCAGATTCCAATTCC
Found at i:48054 original size:15 final size:15
Alignment explanation
Indices: 48034--48084 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
48024 AGATGTTATT
48034 TTTTTACTTTTAGGG
1 TTTTTACTTTTAGGG
* * *
48049 TTTTTAGATGTTAGGT
1 TTTTTA-CTTTTAGGG
48065 TTTTTACTTTTAGGG
1 TTTTTACTTTTAGGG
48080 TTTTT
1 TTTTT
48085 GGGACCTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.14, C:0.04, G:0.20, T:0.63
Consensus pattern (15 bp):
TTTTTACTTTTAGGG
Found at i:48059 original size:30 final size:31
Alignment explanation
Indices: 48024--48084 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
48014 ATTAATGAAA
*
48024 AGATGTTA-TTTTTTTACTTTTAGGGTTTTT
1 AGATGTTAGGTTTTTTACTTTTAGGGTTTTT
48054 AGATGTTAGGTTTTTTACTTTTAGGGTTTTT
1 AGATGTTAGGTTTTTTACTTTTAGGGTTTTT
48085 GGGACCTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.16, C:0.03, G:0.20, T:0.61
Consensus pattern (31 bp):
AGATGTTAGGTTTTTTACTTTTAGGGTTTTT
Found at i:48324 original size:10 final size:10
Alignment explanation
Indices: 48309--48377 Score: 59
Period size: 10 Copynumber: 6.7 Consensus size: 10
48299 CATTTAATAA
48309 ATAAACGAAC
1 ATAAACGAAC
48319 ATAAACGAAC
1 ATAAACGAAC
*
48329 ACAAACGAAC
1 ATAAACGAAC
* *
48339 ACAAACATAAAC
1 ATAAAC--GAAC
*
48351 GA-ACACGAAC
1 -ATAAACGAAC
*
48361 ATGAACGAAC
1 ATAAACGAAC
48371 ATAAACG
1 ATAAACG
48378 TTGGAGACCC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 1 0.02
10 40 0.83
12 6 0.12
13 1 0.02
ACGTcount: A:0.58, C:0.23, G:0.12, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:48350 original size:16 final size:16
Alignment explanation
Indices: 48326--48376 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
48316 AACATAAACG
*
48326 AACACAAACGAACACA
1 AACATAAACGAACACA
*
48342 AACATAAACGAACACG
1 AACATAAACGAACACA
* *
48358 AACATGAACGAACATA
1 AACATAAACGAACACA
48374 AAC
1 AAC
48377 GTTGGAGACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.59, C:0.25, G:0.10, T:0.06
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:48371 original size:26 final size:25
Alignment explanation
Indices: 48311--48377 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
48301 TTTAATAAAT
48311 AAACGAACATAAACGAACACAAACG
1 AAACGAACATAAACGAACACAAACG
* *
48336 AACACAAACATAAACGAACACGAAC-
1 AA-ACGAACATAAACGAACACAAACG
48361 ATGAACGAACATAAACG
1 A--AACGAACATAAACG
48378 TTGGAGACCC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 3 0.08
26 32 0.89
27 1 0.03
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (25 bp):
AAACGAACATAAACGAACACAAACG
Found at i:48413 original size:20 final size:20
Alignment explanation
Indices: 48388--48427 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
48378 TTGGAGACCC
48388 TACCTAGGGGTGTAAACGAG
1 TACCTAGGGGTGTAAACGAG
48408 TACCTAGGGGTGTAAACGAG
1 TACCTAGGGGTGTAAACGAG
48428 CCGAGTCGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.35, T:0.20
Consensus pattern (20 bp):
TACCTAGGGGTGTAAACGAG
Found at i:48582 original size:24 final size:24
Alignment explanation
Indices: 48555--48612 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
48545 TAAAATTTAA
48555 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTAAAACTCGAGACTC
*
48579 GAGCTCGATTAAAACTTGAGACTC
1 GAGCTCGATTAAAACTCGAGACTC
48603 GAGCTCGATT
1 GAGCTCGATT
48613 GAAGCTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (24 bp):
GAGCTCGATTAAAACTCGAGACTC
Found at i:48635 original size:11 final size:11
Alignment explanation
Indices: 48604--48655 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
48594 TTGAGACTCG
*
48604 AGCTCGATTGA
1 AGCTCGATTCA
**
48615 AGCTATATTCA
1 AGCTCGATTCA
* *
48626 AACTCGATTCTG
1 AGCTCGATTC-A
48638 AGCTCGATTCA
1 AGCTCGATTCA
48649 AGCTCGA
1 AGCTCGA
48656 CATTGCCCCA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
11 22 0.71
12 9 0.29
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:49539 original size:24 final size:24
Alignment explanation
Indices: 49504--49553 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
49494 GATTGGGTTA
*
49504 AACATAAATGAATGAACATAAACG
1 AACATAAATGAACGAACATAAACG
* * *
49528 AACATAACTGAACGAATATAACCG
1 AACATAAATGAACGAACATAAACG
49552 AA
1 AA
49554 TGAACATAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:49541 original size:14 final size:14
Alignment explanation
Indices: 49524--49569 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
49514 AATGAACATA
*
49524 AACGAACATAACTG
1 AACGAACATAACCG
*
49538 AACGAATATAACCG
1 AACGAACATAACCG
*
49552 AATGAACATAACCG
1 AACGAACATAACCG
49566 AACG
1 AACG
49570 TTCACGAACG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.50, C:0.22, G:0.15, T:0.13
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:50865 original size:24 final size:22
Alignment explanation
Indices: 50835--50888 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 22
50825 AAAAAAGTGC
50835 AAAATAGAATAATAATAATAATAA
1 AAAATAGAATAAT-ATAAT-ATAA
50859 AAAATAG--TAATATAATATAA
1 AAAATAGAATAATATAATATAA
50879 ATAAATAGAA
1 A-AAATAGAA
50889 CCAAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 5 0.19
21 11 0.41
22 4 0.15
24 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (22 bp):
AAAATAGAATAATATAATATAA
Found at i:50935 original size:2 final size:2
Alignment explanation
Indices: 50928--50960 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
50918 GTAATTAAAC
50928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50961 ATAAGGATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52696 original size:37 final size:36
Alignment explanation
Indices: 52655--52823 Score: 165
Period size: 37 Copynumber: 4.8 Consensus size: 36
52645 GCTTCAAGAA
52655 AAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGG
1 AAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGG
* * * *
52692 AAACTGTCTCAAGGGAGACGAAATTTGTTTTAAGGA
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
* * *
52728 AAACAGAT-TC-A-A-AG----ATTTTGTTTTAAGGG
1 AAACTG-TCTCAAGAGAGACAAAATTTGTTTCAAGGG
*
52757 AAAATGTCTCAAGAGAGACAAAACTTTGTTTCAAGGG
1 AAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGG
* *
52794 AAACTGTCTCAAGGGAGACGAAATTTGTTT
1 AAACTGTCTCAAGAGAGACAAAATTTGTTT
52824 TAAAGATTTT
Statistics
Matches: 107, Mismatches: 15, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
28 1 0.01
29 19 0.18
30 1 0.01
31 1 0.01
32 2 0.02
33 2 0.02
35 1 0.01
36 26 0.24
37 54 0.50
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.28
Consensus pattern (36 bp):
AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
Found at i:52836 original size:50 final size:49
Alignment explanation
Indices: 52781--52875 Score: 154
Period size: 50 Copynumber: 1.9 Consensus size: 49
52771 GAGACAAAAC
* *
52781 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTTAAAGAT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAAAC-AAATTTGTTTTAAAGAT
*
52831 TTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAATTTTTTTTAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAATTTGTTTTAA
52876 GAGAAAATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
49 12 0.29
50 30 0.71
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (49 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAATTTGTTTTAAAGAT
Found at i:52846 original size:87 final size:85
Alignment explanation
Indices: 52738--52912 Score: 251
Period size: 85 Copynumber: 2.0 Consensus size: 85
52728 AAACAGATTC
* * * *
52738 AAAGATTTTGTTTTAAGGGAAAATGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCT
1 AAAGATTTTGTTTCAAGGGAAAATGTCTCAAGAGAAAC-AAA-TTTGTTTCAAGAGAAAATGTCT
* *
52803 CAAGGGAGACGAAATTTGTTTT
64 CAAGAGAGACAAAATTTGTTTT
* * *
52825 AAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAATTTTTTTTAAGAGAAAATGTCTCA
1 AAAGATTTTGTTTCAAGGGAAAATGTCTCAAGAGAAACAAATTTGTTTCAAGAGAAAATGTCTCA
52890 AGAGAGACAAAATTTGTTTT
66 AGAGAGACAAAATTTGTTTT
52910 AAA
1 AAA
52913 AGAAACTGTC
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 41 0.52
86 3 0.04
87 35 0.44
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (85 bp):
AAAGATTTTGTTTCAAGGGAAAATGTCTCAAGAGAAACAAATTTGTTTCAAGAGAAAATGTCTCA
AGAGAGACAAAATTTGTTTT
Found at i:52887 original size:35 final size:36
Alignment explanation
Indices: 52831--52947 Score: 148
Period size: 36 Copynumber: 3.3 Consensus size: 36
52821 TTTTAAAGAT
* *
52831 TTTGTTTCAAGGGAAACTGTCTCAAGAGAAAC-AAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAAACAAAA
* * *
52866 TTTTTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAAACAAAA
* *
52902 TTTGTTTTAAAAGAAACTGTCTCAAG-GAAGACGAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAA-ACAAAA
52938 TTTGTTTTAA
1 TTTGTTTTAA
52948 AGATTTTGTT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
35 29 0.41
36 41 0.59
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (36 bp):
TTTGTTTTAAGAGAAACTGTCTCAAGAGAAACAAAA
Found at i:52891 original size:50 final size:50
Alignment explanation
Indices: 52787--52891 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 50
52777 AAACTTTGTT
* * *** *
52787 TCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTTAAAGATTTTGTT
1 TCAAGGGAAACTGTCTCAAGAGAAACGAAATTTGTTTTAAAGAAAATGTC
*
52837 TCAAGGGAAACTGTCTCAAGAGAAAC-AAATTTTTTTTAAGAGAAAATGTC
1 TCAAGGGAAACTGTCTCAAGAGAAACGAAATTTGTTTTAA-AGAAAATGTC
52887 TCAAG
1 TCAAG
52892 AGAGACAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 12 0.26
50 35 0.74
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.30
Consensus pattern (50 bp):
TCAAGGGAAACTGTCTCAAGAGAAACGAAATTTGTTTTAAAGAAAATGTC
Found at i:52963 original size:121 final size:122
Alignment explanation
Indices: 52737--53030 Score: 484
Period size: 121 Copynumber: 2.4 Consensus size: 122
52727 AAAACAGATT
* * **
52737 CAAAGATTTTGTTTTAAGGGAAAATGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTC
1 CAAA-ATTTT-TTTTAAGAGAAAATGTCTCAAGAGAGACAAAA-TTTGTTTTAAAAGAAACTGTC
*
52802 TCAAGGGAGACGAAATTTGTTTTAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAAA
63 TCAAGGAAGACGAAATTTGTTTTAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAAA
52862 C-AAATTTTTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCA
1 CAAAATTTTTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCA
*
52926 AGGAAGACGAAATTTGTTTTAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
66 AGGAAGACGAAATTTGTTTTAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAAA
*
52983 CAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGAC-AAATTTGTTTT
1 CAAAATTTTTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTT
53031 GAGTAAATTA
Statistics
Matches: 161, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
121 88 0.55
122 65 0.40
123 5 0.03
124 2 0.01
125 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.31
Consensus pattern (122 bp):
CAAAATTTTTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCA
AGGAAGACGAAATTTGTTTTAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAAA
Found at i:52981 original size:86 final size:84
Alignment explanation
Indices: 52865--53030 Score: 253
Period size: 86 Copynumber: 2.0 Consensus size: 84
52855 AGAGAAACAA
* *
52865 ATTTTTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAG-G
1 ATTTTTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAAATGTCTCAAGAG
52929 AAGACGAAATTTGTTTTAAAG
66 -AGAC-AAATTTGTTTTAAAG
* * *
52950 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGA
1 ATTTT-TTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAAATGTCTCAAGA
53015 GAGACAAATTTGTTTT
65 GAGACAAATTTGTTTT
53031 GAGTAAATTA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
85 16 0.22
86 57 0.77
87 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (84 bp):
ATTTTTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAAATGTCTCAAGAG
AGACAAATTTGTTTTAAAG
Found at i:52993 original size:36 final size:35
Alignment explanation
Indices: 52952--53029 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 35
52942 TTTTAAAGAT
* *
52952 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGAC-AAA
*
52988 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAA
1 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAA
53023 TTTGTTT
1 TTTGTTT
53030 TGAGTAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 10 0.26
36 29 0.74
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (35 bp):
TTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAA
Found at i:57376 original size:20 final size:20
Alignment explanation
Indices: 57347--57389 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
57337 AAAAGTTAGT
57347 AAAATAAATAAAT-ATATAAA
1 AAAATAAATAAATGATA-AAA
*
57367 AAAATGAATAAATGATAAAA
1 AAAATAAATAAATGATAAAA
57387 AAA
1 AAA
57390 CGAAAAGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAATAAATAAATGATAAAA
Found at i:58424 original size:17 final size:18
Alignment explanation
Indices: 58402--58460 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
58392 AAAAGTAGAG
*
58402 AATAAAAATAAAAAGA-A
1 AATAAAAATAAAAAAATA
58419 AATAAAAAATACAAATAAATA
1 AAT-AAAAATA-AAA-AAATA
*
58440 AATAAAATATAAAAAAGTA
1 AATAAAA-ATAAAAAAATA
58459 AA
1 AA
58461 AACATATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 3 0.09
18 7 0.20
19 9 0.26
20 9 0.26
21 7 0.20
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (18 bp):
AATAAAAATAAAAAAATA
Found at i:58504 original size:19 final size:20
Alignment explanation
Indices: 58480--58527 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
58470 AAAAAGAGCA
58480 AAATAGAAAAATAATAT-AT
1 AAATAGAAAAATAATATAAT
* *
58499 AAATAGTAATATAATATAAAT
1 AAATAGAAAAATAATAT-AAT
58520 AAATAGAA
1 AAATAGAA
58528 CCAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 15 0.62
21 9 0.38
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (20 bp):
AAATAGAAAAATAATATAAT
Found at i:59664 original size:2 final size:2
Alignment explanation
Indices: 59652--59689 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
59642 AAAAATACTC
*
59652 AT AT A- AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59690 ATGTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:59775 original size:18 final size:18
Alignment explanation
Indices: 59741--59774 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
59731 GTGTCAACAA
59741 ATTTAATTTAATATTTTC
1 ATTTAATTTAATATTTTC
59759 ATTTAATTTAAT-TTTT
1 ATTTAATTTAATATTTT
59775 TACCATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTAATTTAATATTTTC
Found at i:61836 original size:3 final size:3
Alignment explanation
Indices: 61830--61857 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
61820 TTTTCATTTG
61830 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
61858 CTAAACAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:63242 original size:18 final size:20
Alignment explanation
Indices: 63213--63265 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 20
63203 TTTATTATCA
*
63213 ATATATTTAAAATATTAT-T
1 ATATATTAAAAATATTATAT
63232 AT-TATTAAAAA-A-TATAT
1 ATATATTAAAAATATTATAT
63249 ATATATTAAATAATATT
1 ATATATTAAA-AATATT
63266 TATTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
16 3 0.11
17 4 0.14
18 15 0.54
19 4 0.14
20 1 0.04
21 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATATTAAAAATATTATAT
Found at i:63273 original size:18 final size:18
Alignment explanation
Indices: 63233--63273 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
63223 AATATTATTA
63233 TTATTAAAAAATATATAT
1 TTATTAAAAAATATATAT
* * *
63251 ATATTAAATAATATTTAT
1 TTATTAAAAAATATATAT
63269 TTATT
1 TTATT
63274 TTATTTTACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTAAAAAATATATAT
Found at i:67650 original size:18 final size:19
Alignment explanation
Indices: 67615--67653 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
67605 ATTCAAGGGG
67615 GTATCGATACCTAGAAGGGTA
1 GTATCGATACC-A-AAGGGTA
67636 GTATCGATACC-AAGGGTA
1 GTATCGATACCAAAGGGTA
67654 CCGATACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
21 11 0.61
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.23
Consensus pattern (19 bp):
GTATCGATACCAAAGGGTA
Found at i:68894 original size:296 final size:295
Alignment explanation
Indices: 68356--69146 Score: 1343
Period size: 296 Copynumber: 2.7 Consensus size: 295
68346 GATAACAACA
*
68356 GAAATAATATATATGACTACATGTGTAAGCTTATATGGTATTGATAGGACATATAAGATTATATG
1 GAAAAAATATATATGACTACATGTGTAAGCTTATATGGTATTGATAGGACATATAAGATTATATG
** *
68421 TCTGTATGCCGATATGAGAAAGTGAACTAAGTTAAATGATATTGAATT-TGTGAATATAAGAGAT
66 -CTGTATGATGATATGAGAAAGTGAACTAAGTTCAATGATATTGAATTATGTGAATATAAGAGAT
* *
68485 TAAAACATAAACTATATGAAAAGATATAAGCCATATGATATGACATTTGTGAACATATGGGAAGG
130 TAAAACATAAACTATATGAAAAAATATAAGCCATATGATATGACATTTGTGAACATATGAGAAGG
68550 TTATAGGTGTTATATGATTTGAGCAGGAAAATAGACATAAGATATAGTCATG-TGAAATTATTAT
195 TTATAGGTGTTATATGATTTGAGCAGGAAAATAGACATAAGATATAGTCA-GATGAAATTATTAT
68614 GTGATATAAGTATATGACATTACTATATGGATTATAT
259 GTGATATAAGTATATGACATTACTATATGGATTATAT
* *
68651 GAAAGAATATATATGACTACATGTGTAAGCTTATATGGTATTGATAGGATATATAAGATTATATG
1 GAAAAAATATATATGACTACATGTGTAAGCTTATATGGTATTGATAGGACATATAAGATTATATG
*
68716 CATGTATGATGATATGTGAAAGTGAACTAAGTTCAATGATATTGAATTATGTGAATATAAGAGAT
66 C-TGTATGATGATATGAGAAAGTGAACTAAGTTCAATGATATTGAATTATGTGAATATAAGAGAT
68781 TAAAACATAAACTATATGAAAAAATATAAGCCATATGATATGACATTTGTGAACATATGAGAAGG
130 TAAAACATAAACTATATGAAAAAATATAAGCCATATGATATGACATTTGTGAACATATGAGAAGG
* * *
68846 TTATTGGTGTTATATGATTTGAGCAGGGAAATGGACATAAGATATAGTCAGATGAAATTATTATG
195 TTATAGGTGTTATATGATTTGAGCAGGAAAATAGACATAAGATATAGTCAGATGAAATTATTATG
68911 TGATATAAGTATATGACATTACTATATGGATTATAT
260 TGATATAAGTATATGACATTACTATATGGATTATAT
*
68947 GAAAAAATATATATGACTACATGTGTAAGCTTATATGGTATTGATAGGACATTTAAGATTATATG
1 GAAAAAATATATATGACTACATGTGTAAGCTTATATGGTATTGATAGGACATATAAGATTATATG
*
69012 CCCGTATGATGATATGAGAAAGTGAACTAAGTTCAATGATATTGAATTATGTGAATATAAGAGAT
66 -CTGTATGATGATATGAGAAAGTGAACTAAGTTCAATGATATTGAATTATGTGAATATAAGAGAT
* *
69077 TAAAACATAAACTATATGAAAATATATAAGCCATATGATATGATATGATATTTGTGAACATATGA
130 TAAAACATAAACTATATGAAAAAATATAAGCC-----ATATGATATGACATTTGTGAACATATGA
69142 GAAGG
190 GAAGG
69147 ATAAGAGATA
Statistics
Matches: 469, Mismatches: 18, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
294 1 0.00
295 106 0.23
296 329 0.70
297 1 0.00
301 32 0.07
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.33
Consensus pattern (295 bp):
GAAAAAATATATATGACTACATGTGTAAGCTTATATGGTATTGATAGGACATATAAGATTATATG
CTGTATGATGATATGAGAAAGTGAACTAAGTTCAATGATATTGAATTATGTGAATATAAGAGATT
AAAACATAAACTATATGAAAAAATATAAGCCATATGATATGACATTTGTGAACATATGAGAAGGT
TATAGGTGTTATATGATTTGAGCAGGAAAATAGACATAAGATATAGTCAGATGAAATTATTATGT
GATATAAGTATATGACATTACTATATGGATTATAT
Found at i:69186 original size:13 final size:14
Alignment explanation
Indices: 69156--69188 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
69146 GATAAGAGAT
69156 ATATATGTTATATG
1 ATATATGTTATATG
*
69170 ATATATG-TATGTG
1 ATATATGTTATATG
69183 ATATAT
1 ATATAT
69189 AAGAAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
ATATATGTTATATG
Found at i:69437 original size:32 final size:30
Alignment explanation
Indices: 69395--69484 Score: 108
Period size: 32 Copynumber: 2.9 Consensus size: 30
69385 AGAGTCGAGG
*
69395 GTTACCTATGTCCTTCGGGATATATGGACA
1 GTTACCTATGTCCTTCGGGACATATGGACA
* *
69425 TGATTACCTATGTCCTTTGGGACATATAGACA
1 -G-TTACCTATGTCCTTCGGGACATATGGACA
* * *
69457 GGTACCTATGTTCTTCGGAACATATGGA
1 GTTACCTATGTCCTTCGGGACATATGGA
69485 TAGGTCTTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 22 0.44
31 2 0.04
32 26 0.52
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGGGACATATGGACA
Found at i:70701 original size:208 final size:207
Alignment explanation
Indices: 70339--70730 Score: 658
Period size: 208 Copynumber: 1.9 Consensus size: 207
70329 AAATAAAACA
*
70339 AAATGAGTGCTCAAAATAAAAAGATTTGGAGTCTTTTTCAGTGACCGAAATACAAGAATAACAAG
1 AAATGAGTGCTCAAAATAAAAAGATTTGGAGCCTTTTTCAGTGACCGAAATACAAGAATAACAAG
*
70404 ATTTAAAACTCAAAATATAAACTCAAAATTTGCATTAAGTGACTAAAATGAAATATTACAAAACA
66 ATTTAAAACTCAAAATATAAACTCAAAATTTGCATTAAGTGACTAAAATGAAATACTACAAAACA
* *
70469 TTGAGGAACCAACAAGGGTTTACCCAAGCGCTGAATATATATCCACCCTTCCCTAGAATACAACA
131 TTGAGGAACCAACAAGGGTTTACCCAAGCGCTGAATATACATCCACCATTCCCTAGAATACAACA
70534 AAATGGAAATAC
196 AAATGGAAATAC
* *
70546 AAATCGAGTGCTCAAAATAAAAAGATTTGGAGCCTTTTTTAGTGACTGAAATACAAGAATAACAA
1 AAAT-GAGTGCTCAAAATAAAAAGATTTGGAGCCTTTTTCAGTGACCGAAATACAAGAATAACAA
* ** ** *
70611 GATTTGAAACTTGAAATATAAACTTGAAATTTGCATTAAGTGACTAAAATGGAATACTACAAAAC
65 GATTTAAAACTCAAAATATAAACTCAAAATTTGCATTAAGTGACTAAAATGAAATACTACAAAAC
*
70676 CTTGAGGAACCAACAAGGGTTTACCCAAGCGCTGAATATACATCCACCATTCCCT
130 ATTGAGGAACCAACAAGGGTTTACCCAAGCGCTGAATATACATCCACCATTCCCT
70731 TAAACGACGT
Statistics
Matches: 171, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
207 4 0.02
208 167 0.98
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (207 bp):
AAATGAGTGCTCAAAATAAAAAGATTTGGAGCCTTTTTCAGTGACCGAAATACAAGAATAACAAG
ATTTAAAACTCAAAATATAAACTCAAAATTTGCATTAAGTGACTAAAATGAAATACTACAAAACA
TTGAGGAACCAACAAGGGTTTACCCAAGCGCTGAATATACATCCACCATTCCCTAGAATACAACA
AAATGGAAATAC
Found at i:71735 original size:3 final size:3
Alignment explanation
Indices: 71722--71766 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
71712 GGATATTATA
71722 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
71767 TAAAAATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:72414 original size:139 final size:139
Alignment explanation
Indices: 72158--72910 Score: 751
Period size: 139 Copynumber: 5.4 Consensus size: 139
72148 TATTTGGGTT
* * * * *
72158 ATTTGGAGACAACACGGTTCCTTCACATTGAGGAAGTCTAATTGTCTAAGGATAACACTGCTCCT
1 ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCAT
* * * * *
72223 TCACATTGAGGAGATCTGGTCGGTGGATGACATTGTTCCTTCGTGTTGAGGACGTATAGCCGTAT
66 TCGCGTTGAAGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGACGTATAACCGTAT
72288 TTGGAGATA
131 TTGGAGATA
* * * * * * *
72297 ATTTAGAGACAATACAGTTCCTTCGCATTGAGGAATTTTGATTGTCTGAGGATGACATTGCTCCT
1 ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCAT
* * * *
72362 TCGCGTTGAAGAGATCTTGTCGGTAGACGACATTGTTCCTTCGTGTTAAGGACGTATAACCATAT
66 TCGCGTTGAAGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGACGTATAACCGTAT
*
72427 TTAGAGATA
131 TTGGAGATA
* ** * * *
72436 ATTTGGAGACAATACAGTTTATTCACATTAAGGAAGTCTAATTGTCTGATGATGACACTGCTCAT
1 ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCAT
* * * * * * * * *
72501 TCGCGTT-AGTGAGATGTGGTCGATGGACGATATTGTTCATTTGTGATGAGGACGTTTAACCGTC
66 TCGCGTTGA-AGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGACGTATAACCGTA
72565 TTTGG-GATA
130 TTTGGAGATA
* * * * * *
72574 ATTTGGAGATAACA-TGATTCTTTCACGTTGAGGAAGTCTGATTATCTGAGGATGACATTGCTCA
1 ATTTGGAGACAACACAG-TTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCA
* * * * ** * **
72638 TTCGC-TTTAAGGAGATGTGGTCGGTGGATGACATTATTTTTTCGTGTTGAGGACGTCTAGTCGT
65 TTCGCGTTGAA-GAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGACGTATAACCGT
72702 ATTTGGAGATA
129 ATTTGGAGATA
** * *
72713 ATTTGGAGAGC-ACACAGTTCCTTCGTATTGAGGAAGTCTGATTGTATGAGGATGACACTGCTCT
1 ATTTGGAGA-CAACACAGTTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCA
* * * * ** * ** * * *
72777 TTTGCGTTAAAGAGATCCGGTCGGTGGACGACATTATTAATTCGTGATGAGGATATCTAGCCGTC
65 TTCGCGTTGAAGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGACGTATAACCGTA
*
72842 TTTGGGGGATA
130 TTT-GGAGATA
* * * * * *
72853 ATTTGGAGACAACACAATTTCTTCACGTTGGGGAAGTCTGATTTTCCGAGGATGACAC
1 ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACAC
72911 CACTCCTTCA
Statistics
Matches: 503, Mismatches: 101, Indels: 19
0.81 0.16 0.03
Matches are distributed among these distances:
137 3 0.01
138 109 0.22
139 333 0.66
140 58 0.12
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (139 bp):
ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCAT
TCGCGTTGAAGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGACGTATAACCGTAT
TTGGAGATA
Found at i:72718 original size:277 final size:275
Alignment explanation
Indices: 72158--72909 Score: 803
Period size: 277 Copynumber: 2.7 Consensus size: 275
72148 TATTTGGGTT
* * * *
72158 ATTTGGAGACAACACGGTTCCTTCACATTGAGGAAGTCTAATTGTCTAAGGATAACACTGCTCCT
1 ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTAATTGTCTGAGGATGACACTGCTCAT
* * * * * *
72223 TCACATTGAGGAGATCTGGTCGGTGGATGACATTGTTCCTTCGTGTTGAGGACGTATAGCCGTAT
66 TCGCGTT-AGGAGATCTGGTCGGTGGACGACATTGTTCATTCGTGATGAGGACGTATAGCCGTCT
* * * * * * *
72288 TTGGAGATAATTTAGAGACAATACAG-TTCCTTCGCATTGAGGAATTTTGATTGTCTGAGGATGA
130 TTGG-GATAATTTGGAGA-AA-ACAGATTCTTTCACGTTGAGGAAGTCTGATTATCTGAGGATGA
* * *
72352 CATTGCTCCTTCGCGTTGAAGAGATCTTGTCGGTAGACGACATTGTTCCTTCGTGTTAAGGACGT
192 CATTGCTCATTCGCGTTGAAGAGATCTGGTCGGTAGACGACATTATTCCTTCGTGTTAAGGACGT
72417 ATAACCATATTTAGAGATA
257 ATAACCATATTTAGAGATA
* ** * *
72436 ATTTGGAGACAATACAGTTTATTCACATTAAGGAAGTCTAATTGTCTGATGATGACACTGCTCAT
1 ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTAATTGTCTGAGGATGACACTGCTCAT
* * * * * *
72501 TCGCGTTAGTGAGATGTGGTCGATGGACGATATTGTTCATTTGTGATGAGGACGTTTAACCGTCT
66 TCGCGTTAG-GAGATCTGGTCGGTGGACGACATTGTTCATTCGTGATGAGGACGTATAGCCGTCT
*
72566 TTGGGATAATTTGGAGATAACATGATTCTTTCACGTTGAGGAAGTCTGATTATCTGAGGATGACA
130 TTGGGATAATTTGGAGAAAACA-GATTCTTTCACGTTGAGGAAGTCTGATTATCTGAGGATGACA
* * * * ** * *
72631 TTGCTCATTCGC-TTTAAGGAGATGTGGTCGGTGGATGACATTATTTTTTCGTGTTGAGGACGTC
194 TTGCTCATTCGCGTTGAA-GAGATCTGGTCGGTAGACGACATTATTCCTTCGTGTTAAGGACGTA
** * *
72695 TAGTCGTATTTGGAGATA
258 TAACCATATTTAGAGATA
** * * *
72713 ATTTGGAGAGC-ACACAGTTCCTTCGTATTGAGGAAGTCTGATTGTATGAGGATGACACTGCTCT
1 ATTTGGAGA-CAACACAGTTCCTTCACATTGAGGAAGTCTAATTGTCTGAGGATGACACTGCTCA
* * * * * ** *
72777 TTTGCGTTAAAGAGATCCGGTCGGTGGACGACATTATTAATTCGTGATGAGGATATCTAGCCGTC
65 TTCGCGTT-AGGAGATCTGGTCGGTGGACGACATTGTTCATTCGTGATGAGGACGTATAGCCGTC
* * *
72842 TTTGGGGGATAATTTGGAGACAACACA-ATT-TCTTCACGTTGGGGAAGTCTGATTTTCCGAGGA
129 TTT--GGGATAATTTGGAGA-AA-ACAGATTCT-TTCACGTTGAGGAAGTCTGATTATCTGAGGA
72905 TGACA
189 TGACA
72910 CCACTCCTTC
Statistics
Matches: 392, Mismatches: 71, Indels: 21
0.81 0.15 0.04
Matches are distributed among these distances:
275 3 0.01
276 6 0.02
277 215 0.55
278 113 0.29
279 51 0.13
280 1 0.00
281 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.33
Consensus pattern (275 bp):
ATTTGGAGACAACACAGTTCCTTCACATTGAGGAAGTCTAATTGTCTGAGGATGACACTGCTCAT
TCGCGTTAGGAGATCTGGTCGGTGGACGACATTGTTCATTCGTGATGAGGACGTATAGCCGTCTT
TGGGATAATTTGGAGAAAACAGATTCTTTCACGTTGAGGAAGTCTGATTATCTGAGGATGACATT
GCTCATTCGCGTTGAAGAGATCTGGTCGGTAGACGACATTATTCCTTCGTGTTAAGGACGTATAA
CCATATTTAGAGATA
Found at i:73402 original size:67 final size:67
Alignment explanation
Indices: 73325--73468 Score: 218
Period size: 67 Copynumber: 2.1 Consensus size: 67
73315 GAAAACTTTA
* *
73325 TCAAGCGAGATGAAATT-TGTTTTTGAGAGAAATAATCTCAAAGGCTTATGTTTCAAAAGAAAAT
1 TCAAGCGAGATGAAATTAT-ATTTGGAGAGAAATAATCTCAAAGGCTTATGTTTCAAAAGAAAAT
73389 GTC
65 GTC
* * *
73392 TCAAGCGAGATGAAATTATATTTGGAGATAAATAATCTCAAAGGTTTATGTTTCAAGAGAAAATG
1 TCAAGCGAGATGAAATTATATTTGGAGAGAAATAATCTCAAAGGCTTATGTTTCAAAAGAAAATG
73457 TC
66 TC
*
73459 TCAAGGGAGA
1 TCAAGCGAGA
73469 CAATTTTGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
67 69 0.99
68 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (67 bp):
TCAAGCGAGATGAAATTATATTTGGAGAGAAATAATCTCAAAGGCTTATGTTTCAAAAGAAAATG
TC
Found at i:81020 original size:11 final size:11
Alignment explanation
Indices: 80998--81033 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
80988 GTTTGATGCT
80998 TTCTCT-TTGA
1 TTCTCTCTTGA
81008 TTCTCTCTTGA
1 TTCTCTCTTGA
81019 TTCTCTCTTGA
1 TTCTCTCTTGA
81030 TTCT
1 TTCT
81034 AGTTGCTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:81239 original size:18 final size:17
Alignment explanation
Indices: 81185--81233 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
81175 TTGGATCCTT
* *
81185 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
81203 TAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
81221 AGTGCATTCGATG
1 AGTGCA-TCGATG
81234 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:81338 original size:65 final size:64
Alignment explanation
Indices: 81179--81364 Score: 196
Period size: 65 Copynumber: 2.9 Consensus size: 64
81169 TGACCGTTGG
* ** *
81179 ATCCTTAGTGCATCGGTGCACTAATAGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAAT
1 ATCCTCAGTGCATCGGTGCA-TGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
* ** * *
81243 AGCCAGAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
1 ATCCTCAGTGCATCGGTGCATGG-TAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAA
81308 -
64 T
* * ** *
81308 ATCCTCAGTGCATCGGTGCATGGTATGTGCACCGATGTAAGAAATACATTCGATGTT
1 ATCCTCAGTGCATCGGTGCATGGTA-GTGCATCGATGCATCAAATGCATTCGATGTT
81365 CAATTTAATT
Statistics
Matches: 100, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
63 1 0.01
64 46 0.46
65 50 0.50
66 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (64 bp):
ATCCTCAGTGCATCGGTGCATGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
Found at i:89249 original size:23 final size:23
Alignment explanation
Indices: 89223--89282 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
89213 ATGGCACTAC
89223 GGTGCATTTCTACGCAGCACTTA
1 GGTGCATTTCTACGCAGCACTTA
* ** *
89246 GGTGCAATTCTACGTGGCACTTT
1 GGTGCATTTCTACGCAGCACTTA
*
89269 GGTGCATTTATACG
1 GGTGCATTTCTACG
89283 AGCTGTGGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (23 bp):
GGTGCATTTCTACGCAGCACTTA
Found at i:91393 original size:2 final size:2
Alignment explanation
Indices: 91386--91482 Score: 180
Period size: 2 Copynumber: 49.5 Consensus size: 2
91376 CATTGAAAGA
91386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
91427 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
91468 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
91483 AACATACAAC
Statistics
Matches: 93, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 91 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:93283 original size:14 final size:14
Alignment explanation
Indices: 93264--93294 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
93254 TTATATCCAA
93264 GCTTTATAATTTGG
1 GCTTTATAATTTGG
93278 GCTTTATAATTTGG
1 GCTTTATAATTTGG
93292 GCT
1 GCT
93295 CCATTTAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.10, G:0.23, T:0.48
Consensus pattern (14 bp):
GCTTTATAATTTGG
Found at i:93334 original size:3 final size:3
Alignment explanation
Indices: 93326--93357 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
93316 TAATTAGGAT
93326 ATA ATA ATA ATA ATA ATA ATTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA A
93358 ACAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.