Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004098.1 Hibiscus syriacus cultivar Beakdansim tig00008963_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: 102862
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:10247 original size:12 final size:12
Alignment explanation
Indices: 10230--10254 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10220 CACCTGATAC
10230 TTTGATACTAAT
1 TTTGATACTAAT
10242 TTTGATACTAAT
1 TTTGATACTAAT
10254 T
1 T
10255 ATCGTAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTGATACTAAT
Found at i:19330 original size:29 final size:29
Alignment explanation
Indices: 19288--19358 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
19278 TAAATTGATT
19288 TCATTGCTTACATCATTTAAGTAAAGATG
1 TCATTGCTTACATCATTTAAGTAAAGATG
*
19317 TCATTGCTTACATCATTTAAGTAATGATG
1 TCATTGCTTACATCATTTAAGTAAAGATG
19346 TCATTGCTTACAT
1 TCATTGCTTACAT
19359 AAATTTAGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (29 bp):
TCATTGCTTACATCATTTAAGTAAAGATG
Found at i:24084 original size:29 final size:29
Alignment explanation
Indices: 24042--24123 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
24032 AAACTAAATT
24042 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
24071 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
24100 GATTTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
24124 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:37583 original size:18 final size:20
Alignment explanation
Indices: 37542--37584 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
37532 AAATTTAATT
* *
37542 ATTTTTTATTTGTTTATAAT
1 ATTTTTTATTTGTTTAAAAA
37562 ATTTTTTA-TT-TTTAAAAA
1 ATTTTTTATTTGTTTAAAAA
37580 ATTTT
1 ATTTT
37585 AGATGGCGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.52
19 2 0.10
20 8 0.38
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTTTTATTTGTTTAAAAA
Found at i:41973 original size:2 final size:2
Alignment explanation
Indices: 41968--42031 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
41958 CTCTCTCTCG
41968 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
42010 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
42032 GGAAAAATAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48308 original size:21 final size:21
Alignment explanation
Indices: 48292--48419 Score: 152
Period size: 21 Copynumber: 6.2 Consensus size: 21
48282 GCGTTGCATT
48292 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
48313 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
48333 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
48354 TCGCGTTGCGAT-TTTTCATT
1 TCGCGTTGCGATAGTTGAAAA
48374 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
48395 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
48416 TCGC
1 TCGC
48420 AACATTTCGC
Statistics
Matches: 85, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 30 0.35
21 55 0.65
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:48333 original size:41 final size:41
Alignment explanation
Indices: 48288--48565 Score: 238
Period size: 41 Copynumber: 6.7 Consensus size: 41
48278 ATTCGCGTTG
48288 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
48329 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
48370 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT--TT-----T--C
* * * *
48420 AACATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATAGTTG
1 --CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGAT-TTTC
* ** *
48464 AAAATCGCGTTGCGATAGTTGAAAAT--C---GC-A----A
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
48495 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
*
48536 CATTTCGCGTTGCGATAGTTGAAATTCGCG
1 CATTTCGCGTTGCGATAGTTGAAAATCGCG
48566 CGGATACTAT
Statistics
Matches: 191, Mismatches: 21, Indels: 50
0.73 0.08 0.19
Matches are distributed among these distances:
31 19 0.10
32 1 0.01
33 1 0.01
36 3 0.02
37 3 0.02
40 2 0.01
41 104 0.54
42 19 0.10
43 2 0.01
46 1 0.01
48 1 0.01
51 1 0.01
52 33 0.17
53 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:48338 original size:20 final size:20
Alignment explanation
Indices: 48313--48385 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
48303 TAGTTGAAAA
48313 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
48333 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
48354 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
48374 TCGCGTTGCGAT
1 TCGCGTTGCGAT
48386 AGTTGAAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:48360 original size:62 final size:62
Alignment explanation
Indices: 48292--48492 Score: 165
Period size: 52 Copynumber: 3.4 Consensus size: 62
48282 GCGTTGCATT
* * **
48292 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-GTTGAAAATCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAA
* ** ** *
48354 TCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATGTTGAAAATCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAA
** * *
48416 TCGC--AAC-A--TT-----TCGCGTTGCGATAG-TCTACAGTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATGTTGAAAATCGCGTTGCGATAGTTC-AAAATCGCGTTGCGATAGTTGAAAA
48468 TCGCGTTGCGATAGTTGAAAATCGC
1 TCGCGTTGCGAT-GTTGAAAATCGC
48493 AACATTTCGC
Statistics
Matches: 109, Mismatches: 17, Indels: 25
0.72 0.11 0.17
Matches are distributed among these distances:
51 1 0.01
52 41 0.38
54 1 0.01
55 1 0.01
57 2 0.02
58 2 0.02
59 1 0.01
60 1 0.01
61 15 0.14
62 40 0.37
63 4 0.04
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (62 bp):
TCGCGTTGCGATGTTGAAAATCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAA
Found at i:48450 original size:21 final size:21
Alignment explanation
Indices: 48426--48492 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
48416 TCGCAACATT
* *
48426 TCGCGTTGCGATAGTCT-ACAG
1 TCGCGTTGCGATAGT-TGAAAA
48447 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
48468 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
48489 TCGC
1 TCGC
48493 AACATTTCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 1 0.02
21 42 0.98
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:48451 original size:52 final size:52
Alignment explanation
Indices: 48370--48471 Score: 170
Period size: 52 Copynumber: 2.0 Consensus size: 52
48360 TGCGATTTTT
48370 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCAA
* *
48422 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATAGTTGAAAATCGC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATAGTTGAAAATCGC
48472 GTTGCGATAG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 46 0.98
53 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (52 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCAA
Found at i:48472 original size:73 final size:73
Alignment explanation
Indices: 48374--48564 Score: 321
Period size: 73 Copynumber: 2.6 Consensus size: 73
48364 ATTTTTCATT
48374 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCAACATTTCGCGTTGCGATA
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCAACATTTCGCGTTGCGATA
48439 GTCTACAG
66 GTCTACAG
48447 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCAACATTTCGCGTTGCGATA
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCAACATTTCGCGTTGCGATA
48512 GTCTACAG
66 GTCTACAG
* ** ** *
48520 TCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTGAAATTCGC
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGC
48565 GCGGATACTA
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
72 27 0.24
73 85 0.76
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (73 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCAACATTTCGCGTTGCGATA
GTCTACAG
Found at i:48565 original size:21 final size:20
Alignment explanation
Indices: 48498--48565 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
48488 ATCGCAACAT
*
48498 TTCGCGTTGCGATAGTCTACA
1 TTCGCGTTGCGATAGT-TAAA
* * * *
48519 GTCGCGTTGCGAT-TTTCCAT
1 TTCGCGTTGCGATAGTT-AAA
48539 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTT-AAA
48560 TTCGCG
1 TTCGCG
48566 CGGATACTAT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
19 1 0.03
20 13 0.37
21 21 0.60
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.35
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTTAAA
Found at i:48689 original size:20 final size:20
Alignment explanation
Indices: 48662--48775 Score: 111
Period size: 20 Copynumber: 5.6 Consensus size: 20
48652 ACTGTAGACT
48662 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * ** *
48682 ACCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAAATGGAA-A
48703 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
48723 ATCGCAACGCGATCTCCAACT
1 ATCGCAACGCGAAATGGAA-A
48744 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
48764 AACGCAACGCGA
1 ATCGCAACGCGA
48776 TTTTCAACTA
Statistics
Matches: 71, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 41 0.58
21 30 0.42
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:48704 original size:41 final size:41
Alignment explanation
Indices: 48659--48800 Score: 223
Period size: 41 Copynumber: 3.5 Consensus size: 41
48649 ACAACTGTAG
*
48659 ACTATCGCAACGCGAAATGGAAAACCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAAATGGAAAAACGCAACGCGAATTTCA
* *
48700 ACTATCGCAACGCGAAATGGAAAATCGCAACGCG-ATCTCCA
1 ACTATCGCAACGCGAAATGGAAAAACGCAACGCGAAT-TTCA
*
48741 ACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAAACGCAACGCGAATTTCA
*
48782 ACTATCGCAATGCGAAATG
1 ACTATCGCAACGCGAAATG
48801 CAACGTGAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
40 2 0.02
41 90 0.97
42 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAAACGCAACGCGAATTTCA
Found at i:48710 original size:21 final size:21
Alignment explanation
Indices: 48659--48804 Score: 102
Period size: 21 Copynumber: 7.1 Consensus size: 21
48649 ACAACTGTAG
* *
48659 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTGCA
* * *
48680 A-AACCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAATTGCA
* *
48700 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTGCA
* *
48721 A-AATCGCAACGCG-ATCTCCA
1 ACTATCGCAACGCGAAT-TGCA
* *
48741 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTGCA
* * * *
48762 A-AAACGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTGCA
* *
48782 ACTATCGCAATGCGAAATGCA
1 ACTATCGCAACGCGAATTGCA
48803 AC
1 AC
48805 GTGAATTTGC
Statistics
Matches: 90, Mismatches: 30, Indels: 10
0.69 0.23 0.08
Matches are distributed among these distances:
19 1 0.01
20 43 0.48
21 45 0.50
22 1 0.01
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (21 bp):
ACTATCGCAACGCGAATTGCA
Found at i:53082 original size:3 final size:3
Alignment explanation
Indices: 53076--53141 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
53066 TTTACCCATT
* * * *
53076 TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTT TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53124 -TA TATA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA
53142 AAAATAATAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:58583 original size:15 final size:15
Alignment explanation
Indices: 58565--58596 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
58555 GATCAATACC
58565 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
58580 TTTTGCATACATTCA
1 TTTTGCATACATGCA
58595 TT
1 TT
58597 ATTCAATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:60645 original size:12 final size:12
Alignment explanation
Indices: 60628--60653 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
60618 GTGAAATCAT
60628 CTACGGTGATTC
1 CTACGGTGATTC
60640 CTACGGTGATTC
1 CTACGGTGATTC
60652 CT
1 CT
60654 GCACCAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.35
Consensus pattern (12 bp):
CTACGGTGATTC
Found at i:65948 original size:1 final size:1
Alignment explanation
Indices: 65942--66039 Score: 61
Period size: 1 Copynumber: 98.0 Consensus size: 1
65932 ATGCTTGAAG
* * * * * * * * *
65942 AAAAAAAACAAAAAAGAAAAAAGAAAGAAAAGAAAAAAGAAAAAAGAAAAAGAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
66007 AGAAAGAAAAAAAGAGAAAAGAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
66040 GGGGGTCAAG
Statistics
Matches: 67, Mismatches: 30, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.85, C:0.01, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:65956 original size:7 final size:7
Alignment explanation
Indices: 65944--66039 Score: 117
Period size: 7 Copynumber: 13.7 Consensus size: 7
65934 GCTTGAAGAA
*
65944 AAAAAAC
1 AAAAAAG
65951 AAAAAAG
1 AAAAAAG
65958 AAAAAAG
1 AAAAAAG
65965 AAAGAAAAG
1 -AA-AAAAG
65974 AAAAAAG
1 AAAAAAG
65981 AAAAAAG
1 AAAAAAG
65988 -AAAAAG
1 AAAAAAG
65994 -AAAAAG
1 AAAAAAG
66000 AAAAAA-
1 AAAAAAG
*
66006 AAGAAAG
1 AAAAAAG
66013 AAAAAAAG
1 -AAAAAAG
*
66021 AGAAAAG
1 AAAAAAG
66028 AAAAAAG
1 AAAAAAG
66035 AAAAA
1 AAAAA
66040 GGGGGTCAAG
Statistics
Matches: 79, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
6 17 0.22
7 47 0.59
8 10 0.13
9 5 0.06
ACGTcount: A:0.84, C:0.01, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:66412 original size:19 final size:17
Alignment explanation
Indices: 66371--66415 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
66361 AAATTCCAAG
66371 TTCAATTTA-TTTGAGA
1 TTCAATTTATTTTGAGA
*
66387 TTTAATTTATTTTCGAAGA
1 TTCAATTTATTTT-G-AGA
66406 TTCAATTTAT
1 TTCAATTTAT
66416 AATTTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.33
17 3 0.12
18 1 0.04
19 12 0.50
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (17 bp):
TTCAATTTATTTTGAGA
Found at i:67309 original size:35 final size:35
Alignment explanation
Indices: 67263--67334 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
67253 TCTCAATTGG
67263 CAGATTATGAATATAGCCTATTTTCAGTATAACAA
1 CAGATTATGAATATAGCCTATTTTCAGTATAACAA
67298 CAGATTATGAATATAGCCTATTTTCAGTATAACAA
1 CAGATTATGAATATAGCCTATTTTCAGTATAACAA
67333 CA
1 CA
67335 TGAAAATGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (35 bp):
CAGATTATGAATATAGCCTATTTTCAGTATAACAA
Found at i:67625 original size:92 final size:93
Alignment explanation
Indices: 67452--67629 Score: 297
Period size: 92 Copynumber: 1.9 Consensus size: 93
67442 AGGAGCCCCA
*
67452 ATAGCATTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACCACAGAACCAA
1 ATAGCATTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAAACCACAGAACCAA
*
67517 TCATTGAATTTGAAAGATGAATGTGCTC
66 TCATTGAATTTAAAAGATGAATGTGCTC
* *
67545 ATAGCA-TCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCCCAGAACCAA
1 ATAGCATTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAAACCACAGAACCAA
67609 TCATTGGAA-TTAAAAGATGAA
66 TCATT-GAATTTAAAAGATGAA
67630 CTGCATGATC
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
92 71 0.89
93 9 0.11
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (93 bp):
ATAGCATTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAAACCACAGAACCAA
TCATTGAATTTAAAAGATGAATGTGCTC
Found at i:68555 original size:113 final size:113
Alignment explanation
Indices: 68314--69066 Score: 842
Period size: 113 Copynumber: 6.8 Consensus size: 113
68304 GATTCAAATC
* * *
68314 CATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATAAGAAGAACTCATCTGAAG-A--A
1 CATCACTCGATGGATCAACATTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
68376 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCGAATT
* * * *
68424 CATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGAATAACTCATCTGAAGAAAGA
1 CATCACTCGATGGATCAACATTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
68489 AGAAGAAGCTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCGAATT
* *
68537 CATCACTCGATGGATCAACTTTTCCAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCACTCGATGGATCAACATTTCCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * *
68601 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCGAATT
* * * * *
68650 CATCATTCAATGGATCATCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
68715 AGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTT-GCTCAAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTCGCTCGAATT
* * * * ** *
68763 CATCACTTGATGGATTAGCTTTTCCAATTTGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
68828 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCGAATT
* *** *
68876 CATCACTTGATGGATCAGTTTTTCCAGAG--AAGTTCATAATGAGAAGAACTCATCTGAAGAA-G
1 CATCACTCGATGGATCAACATTTCCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* ** * *
68938 -A-AA-AAGTTCACAATGAGAAGAGCTTATTCAACCTTTTTGCAT--AATTT
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTCGC-TCGAA-TT
* * * ** *
68985 TATCA--C-A-GCATCAACCTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCT-AAAATAG
1 CATCACTCGATGGATCAACATTTCCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGA-AG
*
69044 AAAGAAGAAGTTCATAATGAGAA
64 GAAGAAGAAGTTCATAATGAGAA
69067 TAGCTTATCC
Statistics
Matches: 568, Mismatches: 58, Indels: 34
0.86 0.09 0.05
Matches are distributed among these distances:
105 17 0.03
106 28 0.05
108 27 0.05
109 17 0.03
110 75 0.13
111 2 0.00
112 36 0.06
113 360 0.63
114 6 0.01
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (113 bp):
CATCACTCGATGGATCAACATTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCGAATT
Found at i:69322 original size:3 final size:3
Alignment explanation
Indices: 69314--69379 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
69304 TTTACCCATT
* * *
69314 TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
69362 -TA TATA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA
69380 AAAAAATAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.04
3 50 0.91
4 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:70797 original size:23 final size:24
Alignment explanation
Indices: 70761--70808 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
70751 AATATATATA
*
70761 ATAAATAATATTTAATATTTTTTT
1 ATAAATAATATTTAATATTTATTT
*
70785 ATAAATTAT-TTTAATATTTATTT
1 ATAAATAATATTTAATATTTATTT
70808 A
1 A
70809 CTTATTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATAAATAATATTTAATATTTATTT
Found at i:76514 original size:64 final size:63
Alignment explanation
Indices: 76438--76558 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 63
76428 ATTGTTCAAG
* * * *
76438 GTGTATCGATGCACATG-AAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGTAA-TGCATCGATGCACCCCCTT-AAATAAAAACATCGAATGCCATCA
*
76502 GTGTATCGATGCACAAGTAATGCATCGATGCACCCCCTTAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGTAATGCATCGATGCACCCCCTTAAATAAAAACATCGAATG
76559 GAATTTATGC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
63 17 0.33
64 32 0.63
65 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (63 bp):
GTGTATCGATGCACAAGTAATGCATCGATGCACCCCCTTAAATAAAAACATCGAATGCCATCA
Found at i:77265 original size:2 final size:2
Alignment explanation
Indices: 77258--77300 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
77248 TAGCGTAAAC
77258 TA TA 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 TA TA
77300 T
1 T
77301 GTAAATTAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77789 original size:23 final size:21
Alignment explanation
Indices: 77762--77810 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
77752 GATATGCGAT
77762 TATGAGTATTGAATATGT-ATATA
1 TATGA-TA-TGAATATGTGAT-TA
*
77785 TATGATATGACTATGTGATTA
1 TATGATATGAATATGTGATTA
77806 TATGA
1 TATGA
77811 AAAGAATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 15 0.62
22 4 0.17
23 5 0.21
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (21 bp):
TATGATATGAATATGTGATTA
Found at i:78215 original size:23 final size:23
Alignment explanation
Indices: 78183--78249 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
78173 AACTTATATG
*
78183 GCACTTCGGTGCATTTCTACGCG
1 GCACTTCGGTGCATTTCTACGCA
* *
78206 GCA-TTACGGTGCAATTCTACGTA
1 GCACTT-CGGTGCATTTCTACGCA
*
78229 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCATTTCTACG
78250 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 2 0.05
23 33 0.89
24 2 0.05
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.31
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCA
Found at i:83195 original size:23 final size:23
Alignment explanation
Indices: 83127--83195 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
83117 CAAACTTATA
*
83127 TGGCACTTCGGTGTATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * *
83150 CGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
83173 TGGCACTTCAGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
83196 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:84877 original size:22 final size:19
Alignment explanation
Indices: 84834--84878 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
84824 CATGTGAAAA
*
84834 ATATCCCAATGACCTATGC
1 ATATCCCAATGACCTATCC
84853 ATATCCCGAATGACCACTATCC
1 ATATCCC-AATGA-C-CTATCC
84875 ATAT
1 ATAT
84879 GTTCCGAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 5 0.23
21 1 0.05
22 9 0.41
ACGTcount: A:0.33, C:0.31, G:0.09, T:0.27
Consensus pattern (19 bp):
ATATCCCAATGACCTATCC
Found at i:84906 original size:30 final size:30
Alignment explanation
Indices: 84872--84961 Score: 126
Period size: 32 Copynumber: 2.9 Consensus size: 30
84862 ATGACCACTA
*
84872 TCCATATGTTCCGAAGAACATAGGTAGCTG
1 TCCATATGTCCCGAAGAACATAGGTAGCTG
* *
84902 TCCATATGTCCCGAAGGACATAGGTAATCCTG
1 TCCATATGTCCCGAAGAACATAGGT-A-GCTG
*
84934 TCCATATGTCCCGAAGTACATAGGTAGC
1 TCCATATGTCCCGAAGAACATAGGTAGC
84962 CTCGACTCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
30 24 0.45
31 2 0.04
32 27 0.51
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (30 bp):
TCCATATGTCCCGAAGAACATAGGTAGCTG
Found at i:93604 original size:3 final size:3
Alignment explanation
Indices: 93596--93623 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
93586 CATGCAAAGT
93596 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
93624 AACCCAATTC
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:96004 original size:2 final size:2
Alignment explanation
Indices: 95999--96031 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
95989 TACAAATTAT
*
95999 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
96032 TTTCTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.