Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002599.1 Hibiscus syriacus cultivar Beakdansim tig00005257_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: 106672
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9584 original size:5 final size:5
Alignment explanation
Indices: 9574--9599 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
9564 TCCATGTATG
9574 TTTGA TTTGA TTTGA TTTGA TTTGA T
1 TTTGA TTTGA TTTGA TTTGA TTTGA T
9600 GGGATAGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (5 bp):
TTTGA
Found at i:10119 original size:30 final size:30
Alignment explanation
Indices: 10083--10156 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
10073 AATGAATAAT
* *
10083 AGCTTAGTAAGGCTATTAGAGAGAGGGTAA
1 AGCTTAGCAAAGCTATTAGAGAGAGGGTAA
*
10113 AGCTTAGCAAAGCTATTAGAGAGAGGGTGA
1 AGCTTAGCAAAGCTATTAGAGAGAGGGTAA
10143 AGCTTAGCAAAGCT
1 AGCTTAGCAAAGCT
10157 TAGAATACTG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.36, C:0.11, G:0.31, T:0.22
Consensus pattern (30 bp):
AGCTTAGCAAAGCTATTAGAGAGAGGGTAA
Found at i:12339 original size:22 final size:22
Alignment explanation
Indices: 12320--12408 Score: 74
Period size: 22 Copynumber: 3.9 Consensus size: 22
12310 AATTAAAGGG
12320 AAAATAAAATAAAATCAAAGAA
1 AAAATAAAATAAAATCAAAGAA
* **
12342 AAAATAAAATAAAATAAAATCA
1 AAAATAAAATAAAATCAAAGAA
* *
12364 TAAATAAAAATAAAAAT-AAAAATA
1 AAAAT-AAAAT-AAAATCAAAGA-A
12388 AAAATATTAAAT-AAATCAAAG
1 AAAATA--AAATAAAATCAAAG
12409 GGGAAATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
22 23 0.43
23 13 0.25
24 13 0.25
25 4 0.08
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.19
Consensus pattern (22 bp):
AAAATAAAATAAAATCAAAGAA
Found at i:12355 original size:12 final size:12
Alignment explanation
Indices: 12320--12402 Score: 59
Period size: 12 Copynumber: 7.1 Consensus size: 12
12310 AATTAAAGGG
12320 AAAATAAAAT--
1 AAAATAAAATAA
* *
12330 AAAATCAAAGAA
1 AAAATAAAATAA
12342 AAAATAAAAT--
1 AAAATAAAATAA
*
12352 AAAATAAAATCA
1 AAAATAAAATAA
*
12364 TAAATAAAA-ATA
1 AAAATAAAATA-A
12376 AAAATAAAAATAA
1 AAAAT-AAAATAA
*
12389 AAATATTAAATAA
1 AAA-ATAAAATAA
12402 A
1 A
12403 TCAAAGGGGA
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
10 18 0.32
12 21 0.37
13 15 0.26
14 3 0.05
ACGTcount: A:0.77, C:0.02, G:0.01, T:0.19
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:12376 original size:6 final size:6
Alignment explanation
Indices: 12320--12393 Score: 70
Period size: 5 Copynumber: 13.0 Consensus size: 6
12310 AATTAAAGGG
*
12320 AAAAT- AAAAT- AAAATCA AAGA-A AAAAT- AAAAT- AAAAT- AAAATCA
1 AAAATA AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAAT-A
*
12364 TAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA
12394 TTAAATAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
5 29 0.48
6 24 0.40
7 7 0.12
ACGTcount: A:0.78, C:0.03, G:0.01, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:13543 original size:19 final size:20
Alignment explanation
Indices: 13519--13561 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
13509 ATATATATAT
*
13519 AACTTC-AAAACGTTTTCAA
1 AACTTCAAAAACATTTTCAA
13538 AACTTCAAAAACATTTTCAA
1 AACTTCAAAAACATTTTCAA
13558 AACT
1 AACT
13562 AAATATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (20 bp):
AACTTCAAAAACATTTTCAA
Found at i:15035 original size:20 final size:20
Alignment explanation
Indices: 15006--15049 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
14996 TGATTAGAAA
15006 TTAA-TTTTTTTTAAAATTG
1 TTAATTTTTTTTTAAAATTG
15025 TTAATTTTTTTTTAAAATTG
1 TTAATTTTTTTTTAAAATTG
*
15045 ATAAT
1 TTAAT
15050 CAAAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTAATTTTTTTTTAAAATTG
Found at i:17574 original size:2 final size:2
Alignment explanation
Indices: 17567--17594 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17557 CCATATTTAA
17567 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
17595 TCAATATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21142 original size:2 final size:2
Alignment explanation
Indices: 21117--21156 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
21107 AAACCCGTGA
* * *
21117 CT CT CT CC CT CT CC CT CT CC CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
21157 ACCCTGATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.42
Consensus pattern (2 bp):
CT
Found at i:21154 original size:12 final size:12
Alignment explanation
Indices: 21117--21156 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
21107 AAACCCGTGA
21117 CTCTCTCCCTCT
1 CTCTCTCCCTCT
*
21129 CCCTCTCCCTCT
1 CTCTCTCCCTCT
*
21141 CTCTCTCTCTCT
1 CTCTCTCCCTCT
21153 CTCT
1 CTCT
21157 ACCCTGATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.42
Consensus pattern (12 bp):
CTCTCTCCCTCT
Found at i:22698 original size:22 final size:22
Alignment explanation
Indices: 22657--22698 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
22647 TTTTAATAAT
* * *
22657 TTTACTTTTATGACATGTTTTC
1 TTTACTTATATGAAACGTTTTC
22679 TTTACTTATATGAAACGTTT
1 TTTACTTATATGAAACGTTT
22699 CTCTATATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (22 bp):
TTTACTTATATGAAACGTTTTC
Found at i:24582 original size:2 final size:2
Alignment explanation
Indices: 24575--24601 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24565 TCAAAACTTT
24575 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
24602 GACTTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26537 original size:12 final size:12
Alignment explanation
Indices: 26522--26554 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
26512 ATGAATGAAG
26522 GAAAATTAATTT
1 GAAAATTAATTT
26534 GAAAATTAATTT
1 GAAAATTAATTT
26546 GAAAATTAA
1 GAAAATTAA
26555 ACGATGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (12 bp):
GAAAATTAATTT
Found at i:30565 original size:13 final size:13
Alignment explanation
Indices: 30547--30616 Score: 63
Period size: 13 Copynumber: 5.4 Consensus size: 13
30537 ATAAATAATA
*
30547 AAAAAATTACAAT
1 AAAAAACTACAAT
*
30560 AAAAAAGT-CTAAT
1 AAAAAACTAC-AAT
*
30573 AAACAACTACAAT
1 AAAAAACTACAAT
*
30586 AAAAAAGT-CTAAT
1 AAAAAACTAC-AAT
*
30599 AAACAACTACAAT
1 AAAAAACTACAAT
30612 AAAAA
1 AAAAA
30617 GTACTAAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
12 2 0.04
13 41 0.91
14 2 0.04
ACGTcount: A:0.66, C:0.13, G:0.03, T:0.19
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:30629 original size:25 final size:26
Alignment explanation
Indices: 30554--30642 Score: 128
Period size: 26 Copynumber: 3.5 Consensus size: 26
30544 ATAAAAAAAT
30554 TACAATAAAAAAGTCTAATAAACAAC
1 TACAATAAAAAAGTCTAATAAACAAC
30580 TACAATAAAAAAGTCTAATAAACAAC
1 TACAATAAAAAAGTCTAATAAACAAC
* *
30606 TACAAT-AAAAAGTACTAA-ATACAAA
1 TACAATAAAAAAGT-CTAATAAACAAC
*
30631 TATAATAAAAAA
1 TACAATAAAAAA
30643 AACAAAATCT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
25 17 0.29
26 41 0.71
ACGTcount: A:0.64, C:0.12, G:0.03, T:0.20
Consensus pattern (26 bp):
TACAATAAAAAAGTCTAATAAACAAC
Found at i:30753 original size:3 final size:3
Alignment explanation
Indices: 30745--30776 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
30735 CTCCTCGCTG
*
30745 TCA TCA TCA TCA CCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
30777 GTCGTGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:32476 original size:9 final size:9
Alignment explanation
Indices: 32462--32495 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
32452 TAAGTAAAAT
32462 ATTAAATAA
1 ATTAAATAA
32471 ATTAAAT-A
1 ATTAAATAA
*
32479 CTTAAATAA
1 ATTAAATAA
32488 ATTAAATA
1 ATTAAATA
32496 TAAAATATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:32476 original size:17 final size:16
Alignment explanation
Indices: 32458--32502 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
32448 TAATTAAGTA
32458 AAATATTAAATAAATT
1 AAATATTAAATAAATT
32474 AAATACTTAAATAAATT
1 AAATA-TTAAATAAATT
*
32491 AAATATAAAATA
1 AAATATTAAATA
32503 TTGAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATTAAATAAATT
Found at i:39471 original size:2 final size:2
Alignment explanation
Indices: 39464--39498 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39454 CACTATATGA
39464 AT 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 AT A
39499 AATTACCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40110 original size:22 final size:22
Alignment explanation
Indices: 40054--40119 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
40044 AATAAAATTA
* *
40054 AAATAAATGAAAAATAAA-GAGT
1 AAATAAAT-AAAAATAAATAAAT
* *
40076 AAAGATAACAAAAATAAATAAAT
1 AAATA-AATAAAAATAAATAAAT
*
40099 AAATAAATAAAAGTAAATAAA
1 AAATAAATAAAAATAAATAAA
40120 GTTGTCAAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
22 27 0.77
23 8 0.23
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.18
Consensus pattern (22 bp):
AAATAAATAAAAATAAATAAAT
Found at i:46723 original size:5 final size:5
Alignment explanation
Indices: 46713--46737 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
46703 TTTCGGAGGA
46713 TTGAG TTGAG TTGAG TTGAG TTGAG
1 TTGAG TTGAG TTGAG TTGAG TTGAG
46738 GTATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
TTGAG
Found at i:55233 original size:15 final size:15
Alignment explanation
Indices: 55213--55243 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55203 CAACAAATAG
55213 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
55228 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
55243 A
1 A
55244 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:55627 original size:7 final size:7
Alignment explanation
Indices: 55615--55643 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
55605 TAAACCATTT
55615 CTTGCAA
1 CTTGCAA
55622 CTTGCAA
1 CTTGCAA
55629 CTTGCAA
1 CTTGCAA
55636 CTTGCAA
1 CTTGCAA
55643 C
1 C
55644 GTAAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.28
Consensus pattern (7 bp):
CTTGCAA
Found at i:65055 original size:85 final size:82
Alignment explanation
Indices: 64917--65100 Score: 235
Period size: 85 Copynumber: 2.2 Consensus size: 82
64907 TAAAATCAAT
* *
64917 TTTAGGATAATATTTTAAACATTATATTTTATATTTGTTTTAAGTATTTTAGTTTAAATAGGTTT
1 TTTAGGATATTATTTTAAACATTATATTTTATATTTGTTTTAAGTATTTTAGTTTAAATA-ATTT
64982 T-AGTATTTCAATTAGAA
65 TAAGTATTTCAATTAGAA
* * *
64999 TTTAGGATATTATTTTAAATATTATTTTATTTTATTTTTGTTTTAGGTATTTTAGTTTAAATAAT
1 TTTAGGATATTATTTTAAACATTA---TATTTTATATTTGTTTTAAGTATTTTAGTTTAAATAAT
* * *
65064 TTTAAGTGTTTTAATTAGGA
63 TTTAAGTATTTCAATTAGAA
* *
65084 TCTAAGATATTATTTTA
1 TTTAGGATATTATTTTA
65101 GGAATTATCT
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
82 22 0.25
84 4 0.05
85 62 0.70
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (82 bp):
TTTAGGATATTATTTTAAACATTATATTTTATATTTGTTTTAAGTATTTTAGTTTAAATAATTTT
AAGTATTTCAATTAGAA
Found at i:67820 original size:13 final size:13
Alignment explanation
Indices: 67802--67831 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
67792 TTGATATTCG
67802 AATAATTATATCA
1 AATAATTATATCA
*
67815 AATAATTATATCG
1 AATAATTATATCA
67828 AATA
1 AATA
67832 TACTTAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (13 bp):
AATAATTATATCA
Found at i:69807 original size:22 final size:23
Alignment explanation
Indices: 69735--69821 Score: 113
Period size: 23 Copynumber: 3.8 Consensus size: 23
69725 CGATTCCCTC
*
69735 AAGGAGGGAATTGGTTCCCATTCA
1 AAGG-GGGAATCGGTTCCCATTCA
69759 AAGGGGGAATCGGTTCCCATTCA
1 AAGGGGGAATCGGTTCCCATTCA
* *
69782 AAGGGGGGATCGGTTCCCCTTC-
1 AAGGGGGAATCGGTTCCCATTCA
* *
69804 AAGGGGGTATCGATTCCC
1 AAGGGGGAATCGGTTCCC
69822 TCTGTACTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 16 0.28
23 38 0.66
24 4 0.07
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (23 bp):
AAGGGGGAATCGGTTCCCATTCA
Found at i:73672 original size:22 final size:21
Alignment explanation
Indices: 73630--73669 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
73620 GAGTTTATTT
*
73630 TCATTTTTAAATTTTGAAACA
1 TCATTTTTAAATTTTAAAACA
*
73651 TCATTTTTATATTTTAAAA
1 TCATTTTTAAATTTTAAAA
73670 ACAATTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTAAATTTTAAAACA
Found at i:76595 original size:2 final size:2
Alignment explanation
Indices: 76526--76580 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
76516 AAATAACATC
76526 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
76568 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
76581 ATAAAATCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:84894 original size:3 final size:3
Alignment explanation
Indices: 84888--84956 Score: 95
Period size: 3 Copynumber: 22.7 Consensus size: 3
84878 CTCCATTTTC
84888 TAT TAT TAT TAT TAT TAT ATAT TAT TAT TAT TAT TAT T-T TATT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* *
84934 TAT TAT TAA AAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
84957 CAAACAGGCC
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 51 0.86
4 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:86572 original size:20 final size:19
Alignment explanation
Indices: 86547--86588 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
86537 CTATTTTATA
86547 AATTATATATTAATTATTTT
1 AATTATATATTAATT-TTTT
* *
86567 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
86586 AAT
1 AAT
86589 ATCGAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:86584 original size:119 final size:119
Alignment explanation
Indices: 86445--86680 Score: 280
Period size: 120 Copynumber: 2.0 Consensus size: 119
86435 TTTAATCTTG
* * * * *
86445 TTTTAATATTTATTTATTTTTCAATAT-TA-AGAAAGGGCAGTCTTAAAACAACTGGATGTCCAT
1 TTTTAATATTTATTTATTTTTCAATATCGAGAAAAAGAGCAGTCTTAAAACAACTAGAAGTCC-T
* *
86508 TTTCTAATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATATATTAATTA
65 TTTCTAATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATAAATTAATTA
* ** ** *
86563 TTTTAATTATTTATTTATTTTTTAATATCGAGAAAAAGAGTTGTCTTAAGGCACCTAGAAGTCCT
1 TTTTAA-TATTTATTTATTTTTCAATATCGAGAAAAAGAGCAGTCTTAAAACAACTAGAAGTCCT
* **
86628 TTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAAT
65 TTTCTAATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAAT
86681 ATATATTTTT
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 6 0.06
119 29 0.30
120 40 0.41
121 23 0.23
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.46
Consensus pattern (119 bp):
TTTTAATATTTATTTATTTTTCAATATCGAGAAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTT
TTCTAATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAATTA
Found at i:94235 original size:44 final size:42
Alignment explanation
Indices: 94143--94225 Score: 125
Period size: 44 Copynumber: 2.0 Consensus size: 42
94133 TAGATAAACT
94143 TGTTTTTATTTAATTATGGACTTTTTATTTATTTTGTTTCTTAA
1 TGTTTTTATTTAATTATGGA--TTTTATTTATTTTGTTTCTTAA
*
94187 TGTTTTTATTTAATTTTGGA-TTT-TTTATTTTGTTTCTTA
1 TGTTTTTATTTAATTATGGATTTTATTTATTTTGTTTCTTA
94226 GGGTCTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
40 16 0.42
41 3 0.08
44 19 0.50
ACGTcount: A:0.18, C:0.04, G:0.10, T:0.69
Consensus pattern (42 bp):
TGTTTTTATTTAATTATGGATTTTATTTATTTTGTTTCTTAA
Found at i:96220 original size:47 final size:45
Alignment explanation
Indices: 96151--96308 Score: 171
Period size: 47 Copynumber: 3.5 Consensus size: 45
96141 CAAACGGACC
*
96151 CTTAATG-TTT-TTATTTAATTATAGACTTTTTATTTATTTTGTTT
1 CTTAATGTTTTATTATTTAATTATAGA-TTTTTATTTATTATGTTT
* *
96195 CATAATGATTTTATTATTTTATTATAGATTTTGTATTTATTATGTTT
1 CTTAATG-TTTTATTATTTAATTATAGATTTT-TATTTATTATGTTT
* * * * *
96242 CTTGATGTTTTATTAGTTAATTA-GGATTTATTATTTATTCTATTT
1 CTTAATGTTTTATTATTTAATTATAGATTT-TTATTTATTATGTTT
96287 CTTAATGTTTTTATTA-TTAATT
1 CTTAATG-TTTTATTATTTAATT
96309 GTGTGAATTG
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
44 6 0.06
45 29 0.30
46 30 0.31
47 32 0.33
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.63
Consensus pattern (45 bp):
CTTAATGTTTTATTATTTAATTATAGATTTTTATTTATTATGTTT
Found at i:96410 original size:16 final size:16
Alignment explanation
Indices: 96389--96420 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
96379 TATTTAATTT
*
96389 TCACTTGAGTAGCACA
1 TCACTTGAGTAACACA
96405 TCACTTGAGTAACACA
1 TCACTTGAGTAACACA
96421 ATAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (16 bp):
TCACTTGAGTAACACA
Done.