Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002209.1 Hibiscus syriacus cultivar Beakdansim tig00004501_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: 69035
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:3743 original size:3 final size:3
Alignment explanation
Indices: 3735--3773 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
3725 TAAAATTAGT
3735 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3774 GAATGATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3759 original size:17 final size:17
Alignment explanation
Indices: 3737--3771 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3727 AAATTAGTTA
3737 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
3754 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
3771 A
1 A
3772 ATGAATGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:3760 original size:20 final size:20
Alignment explanation
Indices: 3735--3773 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3725 TAAAATTAGT
3735 TAATAATAATAATAATAATA
1 TAATAATAATAATAATAATA
3755 TAATAATAATAATAATAAT
1 TAATAATAATAATAATAAT
3774 GAATGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATAATAATAATAATAATA
Found at i:5401 original size:35 final size:35
Alignment explanation
Indices: 5357--5424 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
5347 TTGGTCACAT
*
5357 TTGAATGATGTTATTGTTGAAGATGGTCGAAACTC
1 TTGAATGATGTTATTGTTGAAGATGGTCAAAACTC
* *
5392 TTGACTGATGTTGTTGTTGAAGATGGTCAAAAC
1 TTGAATGATGTTATTGTTGAAGATGGTCAAAAC
5425 CCTTATGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (35 bp):
TTGAATGATGTTATTGTTGAAGATGGTCAAAACTC
Found at i:5451 original size:47 final size:48
Alignment explanation
Indices: 5394--5510 Score: 148
Period size: 47 Copynumber: 2.5 Consensus size: 48
5384 CGAAACTCTT
* * **
5394 GACTGATGTTGTTGTTGAAGATGGTCAAAAC-CCTTATGA-TTTTTAAA
1 GACTGATGTTGTTGTTGAAGATGATCAAAACTCC-GATGACTTTCCAAA
* * *
5441 GATTGATGTTGTTGTTGAAGATGATCGAAACTCCGATGACTTTCCCAA
1 GACTGATGTTGTTGTTGAAGATGATCAAAACTCCGATGACTTTCCAAA
5489 GACTGATGTTGTTGTTGAAGAT
1 GACTGATGTTGTTGTTGAAGAT
5511 TATCGGAACT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
47 32 0.53
48 28 0.47
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (48 bp):
GACTGATGTTGTTGTTGAAGATGATCAAAACTCCGATGACTTTCCAAA
Found at i:8931 original size:64 final size:63
Alignment explanation
Indices: 8882--9005 Score: 198
Period size: 64 Copynumber: 2.0 Consensus size: 63
8872 TGCACTAAGG
*
8882 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAGCCTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAACCTGAGTGCATCGATGCATGG--
8945 T
63 T
8946 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCAT
9006 AAAATGCATT
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
64 29 0.51
65 26 0.46
66 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCATGGT
Found at i:11713 original size:23 final size:23
Alignment explanation
Indices: 11683--11728 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
11673 ATGCACTACT
11683 GAGTGCATCGATGCATATTCATG
1 GAGTGCATCGATGCATATTCATG
* *
11706 GAGTGCATCGGTGCATCTTCATG
1 GAGTGCATCGATGCATATTCATG
11729 ATTTATCGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (23 bp):
GAGTGCATCGATGCATATTCATG
Found at i:19353 original size:19 final size:19
Alignment explanation
Indices: 19326--19377 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
19316 ACAAGCATGA
*
19326 GTGCATCGATGCATGGTCT
1 GTGCATCGATGCATGGTAT
*
19345 GTGCCTCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
19364 GTGCATCGATGCAT
1 GTGCATCGATGCAT
19378 AAAATGCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:20341 original size:2 final size:2
Alignment explanation
Indices: 20334--20360 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20324 ATATCATAAA
20334 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
20361 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:20365 original size:2 final size:2
Alignment explanation
Indices: 20360--20385 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20350 ACACACACAC
20360 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
20386 CACATATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20581 original size:31 final size:31
Alignment explanation
Indices: 20543--20607 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
20533 GAACCTCAGC
20543 AACTGTCCATAGGTCTCGAAGAACCCAGGTA
1 AACTGTCCATAGGTCTCGAAGAACCCAGGTA
*
20574 AACTGTCCATAGGTCTCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCTCGAAGAACCCAGGTA
20605 AAC
1 AAC
20608 CCTCGACTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.20
Consensus pattern (31 bp):
AACTGTCCATAGGTCTCGAAGAACCCAGGTA
Found at i:21437 original size:20 final size:23
Alignment explanation
Indices: 21412--21465 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 23
21402 CCTTGAAGTT
21412 CATCGATGCATTC-T-ACA-GTG
1 CATCGATGCATTCTTAACATGTG
*
21432 CATCGATGTATTCTTTAACATGTG
1 CATCGATGCATTC-TTAACATGTG
21456 CATCGATGCA
1 CATCGATGCA
21466 CTACCCATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.43
22 1 0.04
23 3 0.11
24 12 0.43
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (23 bp):
CATCGATGCATTCTTAACATGTG
Found at i:21528 original size:64 final size:63
Alignment explanation
Indices: 21453--21614 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 63
21443 TCTTTAACAT
* * *
21453 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCA-ATTTAAGGGG
1 GTGCATCGATGCACT-CCAATGCATCGATACACCAATCACATTCGATGTTTCCATATTTAA-GGG
* * ** * *
21517 GTGCATCGATGCACTCCTAATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTTAATGG
1 GTGCATCGATGCACTCC-AATGCATCGATACACCAATCACATTCGATGTTTCCA-TATTTAAGGG
**
21582 GTGCATCGATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCAC-TCCAATGCATCGATACAC
21615 ACTGAATAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
63 2 0.02
64 44 0.54
65 28 0.34
66 8 0.10
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTCCAATGCATCGATACACCAATCACATTCGATGTTTCCATATTTAAGGG
Found at i:24924 original size:30 final size:30
Alignment explanation
Indices: 24885--24955 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
24875 GAAGGACCTA
*
24885 TCCAGAGGTCATAAAGAACCT-CGAAAACTG
1 TCCATAGGTCAT-AAGAACCTACGAAAACTG
* * *
24915 TCCATAGGTCCCTAAGAACCTAGGTAAACTG
1 TCCATAGGT-CATAAGAACCTACGAAAACTG
24946 TCCATAGGTC
1 TCCATAGGTC
24956 TCGAAGAACC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
30 17 0.49
31 18 0.51
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (30 bp):
TCCATAGGTCATAAGAACCTACGAAAACTG
Found at i:24947 original size:31 final size:31
Alignment explanation
Indices: 24909--24974 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
24899 AGAACCTCGA
*
24909 AAACTGTCCATAGGTCCCTAAGAACCTAGGT
1 AAACTGTCCATAGGTCCCGAAGAACCTAGGT
*
24940 AAACTGTCCATAGGTCTCGAAGAACCTAGGT
1 AAACTGTCCATAGGTCCCGAAGAACCTAGGT
24971 AAAC
1 AAAC
24975 CCTCGACTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (31 bp):
AAACTGTCCATAGGTCCCGAAGAACCTAGGT
Found at i:25831 original size:24 final size:20
Alignment explanation
Indices: 25777--25814 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
25767 TTTCCCTTGA
25777 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
25797 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
25815 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:25909 original size:64 final size:64
Alignment explanation
Indices: 25822--25983 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 64
25812 TCTTTAACAT
* * * *
25822 GTGCATCGATACACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCA-TTTT-AAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTGAA-GG
25885 G
64 G
* * * *
25886 GTGCATCGATGCACTCCTAATGCATCGATGCACTAATTACATTCGATGTTTCCATTTTTGAATGG
1 GTGCATCGATGCACTCCT-ATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTGAAGGG
* *
25951 GTACATCGATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCAC-TCCTATGCATCGATACAC
25984 ACTGAATAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
63 2 0.02
64 44 0.53
65 31 0.37
66 6 0.07
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTGAAGGG
Found at i:25978 original size:65 final size:64
Alignment explanation
Indices: 25841--25983 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 64
25831 TACACTACCC
* * *
25841 ATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGGGTGCATCGATGCACTCCTA
1 ATGCATCGATACACCAATCACATTCGATGTTTCCATTTTAAGGGGGTACATCGATGCACTCCTA
* * * *
25905 ATGCATCGATGCACTAATTACATTCGATGTTTCCATTTTTGAA-TGGGTACATCGATGCACTTCC
1 ATGCATCGATACACCAATCACATTCGATGTTTCCA-TTTT-AAGGGGGTACATCGATGCAC-TCC
25969 T-
63 TA
*
25970 GTGCATCGATACAC
1 ATGCATCGATACAC
25984 ACTGAATAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
64 30 0.45
65 31 0.46
66 6 0.09
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (64 bp):
ATGCATCGATACACCAATCACATTCGATGTTTCCATTTTAAGGGGGTACATCGATGCACTCCTA
Found at i:28630 original size:21 final size:21
Alignment explanation
Indices: 28604--28653 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
28594 TCCAAACCAT
28604 AAGCAAGATCTGATGTTTCCA
1 AAGCAAGATCTGATGTTTCCA
*
28625 AAGCAAGATCTGTTGTTTCCA
1 AAGCAAGATCTGATGTTTCCA
28646 AAGCAAGA
1 AAGCAAGA
28654 AATTGGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (21 bp):
AAGCAAGATCTGATGTTTCCA
Found at i:31972 original size:31 final size:31
Alignment explanation
Indices: 31920--31980 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
31910 ATTTAAAAGA
* *
31920 ATTTTATTTTTATTTTCATTTAAAAATATGT
1 ATTTTATGTTAATTTTCATTTAAAAATATGT
*
31951 ATTTTATGTTAATATTT-ATTTAAAAGTATG
1 ATTTTATGTTAAT-TTTCATTTAAAAATATG
31981 ACTAAATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (31 bp):
ATTTTATGTTAATTTTCATTTAAAAATATGT
Found at i:31979 original size:27 final size:27
Alignment explanation
Indices: 31902--31979 Score: 68
Period size: 31 Copynumber: 2.7 Consensus size: 27
31892 AAGTTGGGAG
* *
31902 AATACTTTATTTAAAAGAATTTTATTTT
1 AATA-TTTATTTAAAAGTATTTTATGTT
*
31930 TAT-TTTCATTTAAAAATATGTATTTTATGTT
1 AATATTT-ATTT--AAA-A-GTATTTTATGTT
31961 AATATTTATTTAAAAGTAT
1 AATATTTATTTAAAAGTAT
31980 GACTAAATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
26 3 0.08
27 8 0.20
28 3 0.08
29 6 0.15
30 1 0.03
31 16 0.40
32 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (27 bp):
AATATTTATTTAAAAGTATTTTATGTT
Found at i:33294 original size:131 final size:131
Alignment explanation
Indices: 33060--33295 Score: 301
Period size: 131 Copynumber: 1.8 Consensus size: 131
33050 TAATTTCAAG
* * ** * * *
33060 AGTGAAAACGATAATATCAAATTATTTACAATCGAGAATAAATGACATTTCGTGCACTAAAACAA
1 AGTGAAAACGATAATAGCAAATGAAATACAATCGAGAATAAATGACATCTCATACACTAAAACAA
* * * *
33125 TCATTTATTACCCCAATTGAAATAAAGAGATATTACTATTTCGTCTTAAAATTCAATATCGATTC
66 TCATTTATCACCCCAATCGAAACAAAAAGATATTACTATTTCGTCTTAAAATTCAATATCGATTC
33190 A
131 A
* * * * *
33191 AGTGAAAACGATAATAGCTAATGAAATCCAATCGAGAATAAATGACCTCTCATACATTAAAGCAA
1 AGTGAAAACGATAATAGCAAATGAAATACAATCGAGAATAAATGACATCTCATACACTAAAACAA
* **
33256 TCATTTATCACTCGGATCGAAACAAAAAGATATTACTATT
66 TCATTTATCACCCCAATCGAAACAAAAAGATATTACTATT
33296 CTCAGTGTCG
Statistics
Matches: 86, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
131 86 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (131 bp):
AGTGAAAACGATAATAGCAAATGAAATACAATCGAGAATAAATGACATCTCATACACTAAAACAA
TCATTTATCACCCCAATCGAAACAAAAAGATATTACTATTTCGTCTTAAAATTCAATATCGATTC
A
Found at i:35351 original size:3 final size:3
Alignment explanation
Indices: 35343--35391 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
35333 TAAAATTAGT
*
35343 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35391 T
1 T
35392 GATGATGATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:35396 original size:3 final size:3
Alignment explanation
Indices: 35390--35418 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
35380 AATAATAATA
35390 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
35419 AATAGGACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:37039 original size:35 final size:35
Alignment explanation
Indices: 36995--37062 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
36985 TTGGTCACAT
*
36995 TTGAATGATGTTATTGTTGAAGATGGTCGAAACTC
1 TTGAATGATGTTATTGTTGAAGATGGTCAAAACTC
* *
37030 TTGACTGATGTTGTTGTTGAAGATGGTCAAAAC
1 TTGAATGATGTTATTGTTGAAGATGGTCAAAAC
37063 CCTTATGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (35 bp):
TTGAATGATGTTATTGTTGAAGATGGTCAAAACTC
Found at i:37089 original size:47 final size:48
Alignment explanation
Indices: 37032--37148 Score: 148
Period size: 47 Copynumber: 2.5 Consensus size: 48
37022 CGAAACTCTT
* * **
37032 GACTGATGTTGTTGTTGAAGATGGTCAAAAC-CCTTATGA-TTTTTAAA
1 GACTGATGTTGTTGTTGAAGATGATCAAAACTCC-GATGACTTTCCAAA
* * *
37079 GATTGATGTTGTTGTTGAAGATGATCGAAACTCCGATGACTTTCCCAA
1 GACTGATGTTGTTGTTGAAGATGATCAAAACTCCGATGACTTTCCAAA
37127 GACTGATGTTGTTGTTGAAGAT
1 GACTGATGTTGTTGTTGAAGAT
37149 TATCGGAACT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
47 32 0.53
48 28 0.47
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (48 bp):
GACTGATGTTGTTGTTGAAGATGATCAAAACTCCGATGACTTTCCAAA
Found at i:43286 original size:23 final size:22
Alignment explanation
Indices: 43259--43338 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
43249 CACTGCTGAG
43259 TGCATCGATGCACATTCATGGA
1 TGCATCGATGCACATTCATGGA
*
43281 GTGCATCGGTGCATC-TTCAT-GA
1 -TGCATCGATGCA-CATTCATGGA
* * *
43303 TGTATCGATGCAAATTCAAAGGA
1 TGCATCGATGCACATTC-ATGGA
*
43326 TGCATCAATGCAC
1 TGCATCGATGCAC
43339 TAGTGATAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
21 13 0.29
22 3 0.07
23 28 0.62
24 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACATTCATGGA
Found at i:50918 original size:19 final size:19
Alignment explanation
Indices: 50891--50942 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
50881 ACAAGCCTGA
*
50891 GTGCATCGATGCATGGTCT
1 GTGCATCGATGCATGGTAT
*
50910 GTGCCTCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
50929 GTGCATCGATGCAT
1 GTGCATCGATGCAT
50943 AAAATGCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:51032 original size:20 final size:20
Alignment explanation
Indices: 51007--51044 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
50997 TTCGAAATGG
51007 TGAGTGCATCGATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
51027 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
51045 CCTTTACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:51906 original size:2 final size:2
Alignment explanation
Indices: 51899--51947 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
51889 ATATCATAAA
*
51899 AC AC AC AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
51941 AC AC AC A
1 AC AC AC A
51948 TATATATATC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.47, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:52138 original size:30 final size:32
Alignment explanation
Indices: 52102--52178 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
52092 AGAGGTCATA
* *
52102 AAGAACCTCA-G-CAACTGTCCATATGTCTCG
1 AAGAACCTCAGGTAAACTGTCCATAGGTCTCG
52132 AAGAACC-CAGGTAAACTGTCCATAGGTCTCG
1 AAGAACCTCAGGTAAACTGTCCATAGGTCTCG
52163 AAGAACCT-AGGTAAAC
1 AAGAACCTCAGGTAAAC
52179 CCTCGACTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
29 2 0.05
30 8 0.19
31 32 0.76
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (32 bp):
AAGAACCTCAGGTAAACTGTCCATAGGTCTCG
Found at i:52151 original size:31 final size:31
Alignment explanation
Indices: 52114--52178 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
52104 GAACCTCAGC
*
52114 AACTGTCCATATGTCTCGAAGAACCCAGGTA
1 AACTGTCCATAGGTCTCGAAGAACCCAGGTA
*
52145 AACTGTCCATAGGTCTCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCTCGAAGAACCCAGGTA
52176 AAC
1 AAC
52179 CCTCGACTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCTCGAAGAACCCAGGTA
Found at i:53008 original size:20 final size:23
Alignment explanation
Indices: 52983--53036 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 23
52973 CCTTGAAGTT
52983 CATCGATGCATTC-T-ACA-GTG
1 CATCGATGCATTCTTAACATGTG
53003 CATCGATGCATTCTTTAACATGTG
1 CATCGATGCATTC-TTAACATGTG
53027 CATCGATGCA
1 CATCGATGCA
53037 CTACCCCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.43
22 1 0.03
23 3 0.10
24 13 0.43
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (23 bp):
CATCGATGCATTCTTAACATGTG
Found at i:56357 original size:31 final size:31
Alignment explanation
Indices: 56314--56378 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
56304 GAACCTCGAC
*
56314 AACTGTCCATAGGTCCCTAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
* *
56345 AACTGTCTATAGGTCTCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
56376 AAC
1 AAC
56379 CCTCGACTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:57205 original size:20 final size:22
Alignment explanation
Indices: 57180--57237 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
57170 TTTCCCTTGA
57180 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
57200 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
57223 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
57238 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:57381 original size:65 final size:64
Alignment explanation
Indices: 57228--57386 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 64
57218 TTAACATGTG
* * * * *
57228 CATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGGGTG
1 CATCGATGCACTTCCTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTAAGGGGGTA
* * *
57292 CATCGATGCAC-TCCTAATGCATCGATGA-ACTAATTACATTCGATGTTTCCATTTTTGAA-TGG
1 CATCGATGCACTTCCT-ATGCATCGAT-ACACCAATCACATTCGATGTTTCCA-TTTT-AAGGGG
57354 GTA
62 GTA
*
57357 CATCGATGCACTTCCTGTGCATCGATACAC
1 CATCGATGCACTTCCTATGCATCGATACAC
57387 ACTGAATAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
63 2 0.03
64 41 0.51
65 31 0.39
66 6 0.08
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (64 bp):
CATCGATGCACTTCCTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTAAGGGGGTA
Found at i:60033 original size:21 final size:21
Alignment explanation
Indices: 60007--60056 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
59997 TCCAAACCAT
*
60007 AAGCAAGATCTGATGTTTCCA
1 AAGCAAGATATGATGTTTCCA
*
60028 AAGCAAGATATGTTGTTTCCA
1 AAGCAAGATATGATGTTTCCA
*
60049 AAGAAAGA
1 AAGCAAGA
60057 AATTGGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (21 bp):
AAGCAAGATATGATGTTTCCA
Found at i:60768 original size:31 final size:31
Alignment explanation
Indices: 60726--60784 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
60716 AACTTAAAAG
* *
60726 AGTTTTGTAATACTGAAATTTAAATAATTTT
1 AGTTTTATAATAATGAAATTTAAATAATTTT
60757 AGTTTTATAATAATGAAATTTAAATAAT
1 AGTTTTATAATAATGAAATTTAAATAAT
60785 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (31 bp):
AGTTTTATAATAATGAAATTTAAATAATTTT
Found at i:60833 original size:22 final size:22
Alignment explanation
Indices: 60808--61051 Score: 161
Period size: 22 Copynumber: 11.5 Consensus size: 22
60798 ATAATAAATT
60808 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
60830 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
**
60852 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
** **
60874 TTTTAAAATCCAT--AT-TTTA
1 TTTTAAAATAAATCAATCCATA
*** * *
60893 AAAT-AAATCAATCCAT--AT-
1 TTTTAAAATAAATCAATCCATA
* * *
60911 TTTAAAATAAATCAATCCAT--AT-
1 TTT--TA-AAATAAATCAATCCATA
60933 TTTTAA-ATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
60954 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
* *** *
60976 TCTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
* *
60998 TTTAAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
61020 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
61042 TTTTAAAATA
1 TTTTAAAATA
61052 GATTTAAATA
Statistics
Matches: 176, Mismatches: 35, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
18 15 0.09
19 5 0.03
20 6 0.03
21 8 0.05
22 138 0.78
23 4 0.02
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:60859 original size:44 final size:44
Alignment explanation
Indices: 60808--61051 Score: 310
Period size: 44 Copynumber: 5.7 Consensus size: 44
60798 ATAATAAATT
60808 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
**
60852 TTTTAAAATAAAAT-TTTCCATATTTT---A-AAATC---C-ATA
1 TTTTAAAAT-AAATCAATCCATATTTTAAAATAAATCAATCTATA
*
60888 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
*
60932 TTTTTAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
* *** * *
60976 TCTTAAAATAAATTTTTTCATATTTAAAAATAAATCAAT-TCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCT-ATA
61020 TTTTAAAATAAATCAATCCATATTTTAAAATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATA
61052 GATTTAAATA
Statistics
Matches: 170, Mismatches: 19, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
35 4 0.02
36 22 0.13
37 1 0.01
39 1 0.01
40 10 0.06
41 1 0.01
43 2 0.01
44 125 0.74
45 4 0.02
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (44 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
Found at i:60878 original size:66 final size:66
Alignment explanation
Indices: 60808--61051 Score: 326
Period size: 66 Copynumber: 3.8 Consensus size: 66
60798 ATAATAAATT
*
60808 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAAATTTTCCAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAATTTTCCAT
60873 A
66 A
**
60874 -TTT----T-AA--AATCCATATTTTAAAATAAATCAATCCATATTTTAAAAT-AAATCAATCCA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAAT-TTTCCA
60930 TA
65 TA
* * * * *
60932 TTTTTAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATCTTAAAATAAATTTTTTCAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAATTTTCCAT
60997 A
66 A
* *
60998 TTTAAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATA
61052 GATTTAAATA
Statistics
Matches: 154, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
57 4 0.03
58 44 0.29
59 3 0.02
60 2 0.01
61 1 0.01
63 1 0.01
64 2 0.01
65 3 0.02
66 91 0.59
67 3 0.02
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (66 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAATTTTCCAT
A
Found at i:60887 original size:14 final size:14
Alignment explanation
Indices: 60868--60896 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
60858 AATAAAATTT
60868 TCCATATTTTAAAA
1 TCCATATTTTAAAA
60882 TCCATATTTTAAAA
1 TCCATATTTTAAAA
60896 T
1 T
60897 AAATCAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (14 bp):
TCCATATTTTAAAA
Found at i:60988 original size:26 final size:23
Alignment explanation
Indices: 60880--61044 Score: 166
Period size: 22 Copynumber: 7.5 Consensus size: 23
60870 CATATTTTAA
*
60880 AATCCATATTTTA-AAATAAATC
1 AATCCATATTTAATAAATAAATC
*
60902 AATCCATATTTTA-AAATAAATC
1 AATCCATATTTAATAAATAAATC
*
60924 AATCCATATTT-TTAAATAAATC
1 AATCCATATTTAATAAATAAATC
*
60946 AATCCATATTTTA-AAATAAATC
1 AATCCATATTTAATAAATAAATC
* *
60968 AATCTATATCTT-A-AAATAAATT
1 AATCCATAT-TTAATAAATAAATC
** *
60990 TTTTCATATTTAA-AAATAAATC
1 AATCCATATTTAATAAATAAATC
* *
61012 AATTCATATTTTA-AAATAAATC
1 AATCCATATTTAATAAATAAATC
61034 AATCCATATTT
1 AATCCATATTT
61045 TAAAATAGAT
Statistics
Matches: 126, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
21 2 0.02
22 122 0.97
23 2 0.02
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (23 bp):
AATCCATATTTAATAAATAAATC
Found at i:63118 original size:211 final size:207
Alignment explanation
Indices: 62594--63195 Score: 981
Period size: 199 Copynumber: 2.9 Consensus size: 207
62584 ATTTCAGAGT
*
62594 GACTGTTCATTCTCGGACGAACATGGTGTCAATATGTTGTAGAATGGTTAAAGGTCTCCTCTCAA
1 GACTGTTCATTCTCGGACGAACATGGTGTCAATATGTTGTAGAATGGTTAAATGTCTCCTCTCAA
*
62659 ACTTATCATCTTTGATCAGCTTCATTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCG
66 ACTTATCATCTTTGATCAGCTTCACTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCG
* *
62724 CCTGCTTTCCAGTCTGTTCGAAGTCC-CTAGAGTATTTCCCATAATTCTGATTCCAGTGGGGATA
131 CCTGCTTTCCAGGCTGTTCGAAGTCCTC-AGAGTATGTCCCATAATTCTGATTCCAGTGGGGATA
*
62788 AGAAGTTCCTCGT
195 AGAAGTTCCTCGC
*
62801 GACTGTTCATTCTC-G--G-----GGTGTCAATATGTTGTAGAATGGCTAAATGTCTCCTCTCAA
1 GACTGTTCATTCTCGGACGAACATGGTGTCAATATGTTGTAGAATGGTTAAATGTCTCCTCTCAA
62858 ACTTATCATCTTTGATCAGCTTCACTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCG
66 ACTTATCATCTTTGATCAGCTTCACTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCG
*
62923 CCTGCTTTCCAGGCTGTTCGAAGTCCATCGAGTATGTATGTACCATAATTCTGATTCCAGTGGGG
131 CCTGCTTTCCAGGCTGTTCGAAGTCC-TC-AG-A-GTATGTCCCATAATTCTGATTCCAGTGGGG
62988 ATAAGAAGTTCCTCGC
192 ATAAGAAGTTCCTCGC
* *
63004 GACTGTTCATTCTCGGACGAACATGGTGTCAATATATTGTAGAATGTTTAAATGTCTCCTCTCAA
1 GACTGTTCATTCTCGGACGAACATGGTGTCAATATGTTGTAGAATGGTTAAATGTCTCCTCTCAA
*
63069 ACGTATCATCTTTGATCAGCTTCACTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCG
66 ACTTATCATCTTTGATCAGCTTCACTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCG
*
63134 CCTGCTTTCCAGGCTGTTCGAAGTCCCTC-GAGTATGTCCCATAATTCTGATACCAGTGGGGA
131 CCTGCTTTCCAGGCTGTTCGAAGT-CCTCAGAGTATGTCCCATAATTCTGATTCCAGTGGGGA
63196 GCAGTAATAT
Statistics
Matches: 368, Mismatches: 14, Indels: 26
0.90 0.03 0.06
Matches are distributed among these distances:
199 128 0.35
201 3 0.01
202 1 0.00
203 57 0.15
204 2 0.01
206 2 0.01
207 43 0.12
208 1 0.00
209 1 0.00
211 128 0.35
212 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (207 bp):
GACTGTTCATTCTCGGACGAACATGGTGTCAATATGTTGTAGAATGGTTAAATGTCTCCTCTCAA
ACTTATCATCTTTGATCAGCTTCACTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCG
CCTGCTTTCCAGGCTGTTCGAAGTCCTCAGAGTATGTCCCATAATTCTGATTCCAGTGGGGATAA
GAAGTTCCTCGC
Found at i:64164 original size:30 final size:29
Alignment explanation
Indices: 64124--64190 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
64114 GGGTAGAAGC
* *
64124 AAAAAA-AAGGAAAAATTAATGACAAAAGG
1 AAAAAAGAAGGAAAAAGTAA-AACAAAAGG
* *
64153 AAAAAAGAAGGAGAAAGTAAAAGAAAAGG
1 AAAAAAGAAGGAAAAAGTAAAACAAAAGG
64182 AAAAAAGAA
1 AAAAAAGAA
64191 AATTAATGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 22 0.67
30 11 0.33
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.06
Consensus pattern (29 bp):
AAAAAAGAAGGAAAAAGTAAAACAAAAGG
Found at i:64437 original size:2 final size:2
Alignment explanation
Indices: 64430--64454 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
64420 ACCTAACTTG
64430 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 T
64455 TTAAGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:65750 original size:42 final size:42
Alignment explanation
Indices: 65683--65763 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
65673 TTGTGGCATT
* *
65683 TATTACAAAAACGCCACTAAGGTGCATGACTATAGCGGTTTC
1 TATTACAAAAACACCACTAAAGTGCATGACTATAGCGGTTTC
* * * *
65725 TATTACAAAAACATCGCTAAAGTGCATGATTATTGCGGT
1 TATTACAAAAACACCACTAAAGTGCATGACTATAGCGGT
65764 GTTTATCTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (42 bp):
TATTACAAAAACACCACTAAAGTGCATGACTATAGCGGTTTC
Found at i:66053 original size:29 final size:28
Alignment explanation
Indices: 66012--66068 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
66002 ATATTATTAT
66012 AATTAATTTATAT-ATTTTCTTTAAAAAA
1 AATTAATTTATATAATTTT-TTTAAAAAA
*
66040 AATTAAATTTATATAATTTTTTTACAAAA
1 AATT-AATTTATATAATTTTTTTAAAAAA
66069 TTGAAAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 17 0.65
30 5 0.19
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (28 bp):
AATTAATTTATATAATTTTTTTAAAAAA
Found at i:66495 original size:41 final size:39
Alignment explanation
Indices: 66446--66585 Score: 176
Period size: 40 Copynumber: 3.5 Consensus size: 39
66436 CAAACGGGGC
66446 CTAAAGTGCATGACTATTGCGTGTTTATTGCAAAAACGTCA
1 CTAAAGTGCATGACTATTG-GTGTTTATT-CAAAAACGTCA
*
66487 CTAAAGTGCATGACTATGTGGTGTTTATT-ACAAAATGTCA
1 CTAAAGTGCATGACTAT-TGGTGTTTATTCA-AAAACGTCA
* * *
66527 CTAAAGTGCATGACTATTGTGGTGTTTA-TAAAAAACGCCG
1 CTAAAGTGCATGACTA-T-TGGTGTTTATTCAAAAACGTCA
66567 CTAAAGTGCATGACTATTG
1 CTAAAGTGCATGACTATTG
66586 TGGCTTTTAT
Statistics
Matches: 91, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 47 0.52
41 38 0.42
42 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (39 bp):
CTAAAGTGCATGACTATTGGTGTTTATTCAAAAACGTCA
Found at i:66538 original size:40 final size:41
Alignment explanation
Indices: 66446--66725 Score: 239
Period size: 41 Copynumber: 6.9 Consensus size: 41
66436 CAAACGGGGC
* * *
66446 CTAAAGTGCATGACTATTG-CGTGTTTATTGCAAAAACGTCA
1 CTAAAGTGCATGACTATTGTGGTGTTTATT-AAAAAACGCCA
* * *
66487 CTAAAGTGCATGACTA-TGTGGTGTTTATTACAAAATGTCA
1 CTAAAGTGCATGACTATTGTGGTGTTTATTAAAAAACGCCA
*
66527 CTAAAGTGCATGACTATTGTGGTGTTTA-TAAAAAACGCCG
1 CTAAAGTGCATGACTATTGTGGTGTTTATTAAAAAACGCCA
* *
66567 CTAAAGTGCATGACTATTGTGGCT-TTTATCAAAAAATGCCA
1 CTAAAGTGCATGACTATTGTGG-TGTTTATTAAAAAACGCCA
* * * ** *
66608 CTAAATTGTATGATTATTGTGGCATTTA-T-AAAAACGCCG
1 CTAAAGTGCATGACTATTGTGGTGTTTATTAAAAAACGCCA
* * ** * * * *
66647 CTAAAGTGCATGACTACTGCGGCATTTTTGTAATAAACACCG
1 CTAAAGTGCATGACTATTGTGGTGTTTAT-TAAAAAACGCCA
* * * * *
66689 CTAAGGTGAATGACTATTGCGGTATTTATTACAAAAC
1 CTAAAGTGCATGACTATTGTGGTGTTTATTAAAAAAC
66726 ACCGCCTATA
Statistics
Matches: 198, Mismatches: 33, Indels: 16
0.80 0.13 0.06
Matches are distributed among these distances:
39 30 0.15
40 60 0.30
41 76 0.38
42 32 0.16
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (41 bp):
CTAAAGTGCATGACTATTGTGGTGTTTATTAAAAAACGCCA
Found at i:66588 original size:81 final size:79
Alignment explanation
Indices: 66446--66662 Score: 267
Period size: 81 Copynumber: 2.7 Consensus size: 79
66436 CAAACGGGGC
* * *
66446 CTAAAGTGCATGACTATTG-CGTGTTTATTGCAAAAACGTCACTAAAGTGCATGACTATGTGG-T
1 CTAAAGTGCATGACTATTGTGGTGTTTA-T--AAAAACGCCGCTAAAGTGCATGACTATGTGGCT
* * *
66509 GTTTATTACAAAATGTCA
63 -TTTATCAAAAAATGCCA
66527 CTAAAGTGCATGACTATTGTGGTGTTTATAAAAAACGCCGCTAAAGTGCATGACTATTGTGGCTT
1 CTAAAGTGCATGACTATTGTGGTGTTTAT-AAAAACGCCGCTAAAGTGCATGACTA-TGTGGCTT
66592 TTATCAAAAAATGCCA
64 TTATCAAAAAATGCCA
* * * **
66608 CTAAATTGTATGATTATTGTGGCATTTATAAAAACGCCGCTAAAGTGCATGACTA
1 CTAAAGTGCATGACTATTGTGGTGTTTATAAAAACGCCGCTAAAGTGCATGACTA
66663 CTGCGGCATT
Statistics
Matches: 121, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
80 50 0.41
81 63 0.52
82 8 0.07
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Consensus pattern (79 bp):
CTAAAGTGCATGACTATTGTGGTGTTTATAAAAACGCCGCTAAAGTGCATGACTATGTGGCTTTT
ATCAAAAAATGCCA
Done.