Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005603.1 Hibiscus syriacus cultivar Beakdansim tig00013031_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: 112564
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:6878 original size:23 final size:23
Alignment explanation
Indices: 6852--6924 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
6842 ATGAGTAGGG
*
6852 TAAAAAGAATAAAATAAAGGAAA
1 TAAAAAGAATAAAATAAAGCAAA
*
6875 TAAAAATGAA-AATAA-AAAACAAA
1 TAAAAA-GAATAA-AATAAAGCAAA
* *
6898 TAACAAAAAATAAAAT-AAGTAAA
1 TAA-AAAGAATAAAATAAAGCAAA
6921 TAAA
1 TAAA
6925 TGAAACAAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
22 1 0.03
23 29 0.73
24 10 0.25
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (23 bp):
TAAAAAGAATAAAATAAAGCAAA
Found at i:7349 original size:27 final size:26
Alignment explanation
Indices: 7300--7354 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
7290 AAAATATAAT
*
7300 TAAATAATAATAATGATAGATATAGTA
1 TAAAAAATAATAATGATAGATATA-TA
*
7327 TAAAAAATAATAAAT-ATATATATATA
1 TAAAAAATAAT-AATGATAGATATATA
7353 TA
1 TA
7355 TATATATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.16
27 18 0.72
28 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (26 bp):
TAAAAAATAATAATGATAGATATATA
Found at i:8525 original size:2 final size:2
Alignment explanation
Indices: 8513--8551 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
8503 ATAAACATAA
8513 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8552 AAAAATGTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10089 original size:2 final size:2
Alignment explanation
Indices: 10082--10116 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10072 TTTTCGGTAG
10082 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
10117 GGTTAATCGT
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:15473 original size:20 final size:21
Alignment explanation
Indices: 15448--15499 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
15438 TTTTCCCAAT
15448 TCGCAATGCGAATAAGT-AAA
1 TCGCAATGCGAATAAGTAAAA
* **
15468 TCGCAACGCGAATTGGTAAAA
1 TCGCAATGCGAATAAGTAAAA
15489 TCGCAATGCGA
1 TCGCAATGCGA
15500 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATAAGTAAAA
Found at i:15516 original size:41 final size:41
Alignment explanation
Indices: 15485--15562 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
15475 GCGAATTGGT
*
15485 AAAATCGCAATGCGATACTGACTATCACAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCACAACGCGATAATAC
* *
15526 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCACAACGCGATA
15563 CTGACTATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCACAACGCGATAATAC
Found at i:15521 original size:20 final size:20
Alignment explanation
Indices: 15488--15582 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
15478 AATTGGTAAA
*
15488 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
15508 ATCACAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
15529 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
15549 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
15569 ATCGCAACGAGATA
1 ATCGCAACGCGATA
15583 ATACAGAATC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.03
20 44 0.71
21 14 0.23
22 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:16339 original size:24 final size:24
Alignment explanation
Indices: 16312--16365 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
16302 GTATTCGAAA
*
16312 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
16336 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
16360 TTTGAT
1 TTTGAT
16366 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:18899 original size:33 final size:33
Alignment explanation
Indices: 18857--18977 Score: 181
Period size: 33 Copynumber: 3.7 Consensus size: 33
18847 GGAAATTACT
18857 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* *
18890 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* * *
18922 TTTCACAATGCGAAATGAAAATCACAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCACAACGAGAGA
18956 ATCGCAATGCGAAATGAAAATC
1 ATCGCAATGCGAAATGAAAATC
18978 GGTCGCATTG
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 75 0.97
34 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGA
Found at i:18913 original size:19 final size:19
Alignment explanation
Indices: 18857--18921 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
18847 GGAAATTACT
18857 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
18876 ATCACAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
18890 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
18909 ATCGCAACGCGAA
1 ATCGCAATGCGAA
18922 TTTCACAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:18948 original size:19 final size:19
Alignment explanation
Indices: 18861--18948 Score: 61
Period size: 19 Copynumber: 5.2 Consensus size: 19
18851 ATTACTATCG
18861 CAATGCGAAATGAAAATCA
1 CAATGCGAAATGAAAATCA
* *
18880 CAA--CG--A-GAGAATCG
1 CAATGCGAAATGAAAATCA
*
18894 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCA
* *
18913 CAACGCG-AAT----TTCA
1 CAATGCGAAATGAAAATCA
18927 CAATGCGAAATGAAAATCA
1 CAATGCGAAATGAAAATCA
18946 CAA
1 CAA
18949 CGAGGGAATC
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
14 17 0.33
15 4 0.08
16 2 0.04
17 2 0.04
18 4 0.08
19 22 0.43
ACGTcount: A:0.48, C:0.19, G:0.18, T:0.15
Consensus pattern (19 bp):
CAATGCGAAATGAAAATCA
Found at i:19025 original size:19 final size:19
Alignment explanation
Indices: 18997--19057 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 19
18987 GCGATTCCCT
*
18997 CGTTGGGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
19016 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
19030 CGTTACGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
19049 CATTGCGAT
1 CGTTGCGAT
19058 AGTACTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
14 9 0.29
16 3 0.10
17 3 0.10
19 16 0.52
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:19032 original size:33 final size:33
Alignment explanation
Indices: 18980--19057 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
18970 TGAAAATCGG
**
18980 TCGCATTGCGATTCCCTCGTTGGGATTTTCATT
1 TCGCATTGCGATTCCCTCGTTACGATTTTCATT
* *
19013 TCGCGTTGCGATTCTCTCGTTACGATTTTCATT
1 TCGCATTGCGATTCCCTCGTTACGATTTTCATT
19046 TCGCATTGCGAT
1 TCGCATTGCGAT
19058 AGTACTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTCCCTCGTTACGATTTTCATT
Found at i:19183 original size:14 final size:14
Alignment explanation
Indices: 19164--19200 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
19154 CATCGATTAA
19164 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
19178 ACAAATCACCTTTT
1 ACAAATCAACTTTT
19192 ACAAATCAA
1 ACAAATCAA
19201 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:22552 original size:18 final size:18
Alignment explanation
Indices: 22526--22561 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22516 TCGAAAGGAC
*
22526 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
22544 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
22562 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:23783 original size:24 final size:24
Alignment explanation
Indices: 23706--23795 Score: 103
Period size: 23 Copynumber: 3.8 Consensus size: 24
23696 TCCGACTTGA
* *
23706 ATTCTGTTATGAT-CCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
23729 ATTCTGATATGATA-TTGGCATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
23752 ATTATGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
23776 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
23796 TTGAATTATG
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
23 30 0.57
24 23 0.43
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:25664 original size:42 final size:42
Alignment explanation
Indices: 25618--25697 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
25608 TGATGACAGT
* * *
25618 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
25660 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
25698 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:26094 original size:91 final size:90
Alignment explanation
Indices: 25919--26103 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
25909 ATTTCAAACT
*
25919 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
25984 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
26012 TTCAACCAAAAGATAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
26076 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
26103 T
1 T
26104 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 18 0.21
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:27854 original size:19 final size:19
Alignment explanation
Indices: 27790--27926 Score: 193
Period size: 19 Copynumber: 7.1 Consensus size: 19
27780 TCTTTTGGTT
*
27790 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
27809 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
27829 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
27849 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
27868 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
27887 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
*
27906 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
27925 GA
1 GA
27927 TTTTGGTTTC
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
19 75 0.70
20 30 0.28
21 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:27938 original size:19 final size:18
Alignment explanation
Indices: 27916--27966 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
27906 GAAATGAAAA
* *
27916 TCGCAATGCGATTTTGGTT
1 TCGCATTGCGATTTT-ATT
*
27935 TCGCGTTGCGAATTTTATT
1 TCGCATTGCG-ATTTTATT
27954 TCGCATTGCGATT
1 TCGCATTGCGATT
27967 CTCTCGTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.11
19 19 0.70
20 5 0.19
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:28544 original size:20 final size:20
Alignment explanation
Indices: 28519--28571 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
28509 GCGCTATGTA
28519 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
28539 AATCGCGTTGCGAAAGTTAG
1 AATCGCGTTGCGAAAGTCAG
* *
28559 TATCTCGTTGCGA
1 AATCGCGTTGCGA
28572 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:28632 original size:41 final size:41
Alignment explanation
Indices: 28540--28634 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
28530 GAAAGTCAGA
* * * * ** *
28540 ATCGCGTTGCGAAAGTTAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
28581 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
28623 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
28635 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:28724 original size:21 final size:21
Alignment explanation
Indices: 28684--28724 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28674 ACTGTAGACC
** *
28684 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
28705 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
28725 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:36918 original size:21 final size:21
Alignment explanation
Indices: 36889--36941 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
36879 ATAATAGCTA
* *
36889 ACATGATATCTTACTTTAATT
1 ACATAATATCTTACATTAATT
36910 ACATAATATCTTACATTAATT
1 ACATAATATCTTACATTAATT
36931 ACTATATATAT
1 AC-ATA-ATAT
36942 ATCAACCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 21 0.75
22 3 0.11
23 4 0.14
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (21 bp):
ACATAATATCTTACATTAATT
Found at i:37167 original size:30 final size:30
Alignment explanation
Indices: 37121--37196 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
37111 ATTATGTTTG
* *
37121 TGTTTGTTTGTTTATTTTTGAAAG-TGTTCA
1 TGTTCGTTTATTTATTTTTG-AAGTTGTTCA
*
37151 TGTTCGTTTATTTATTTTTGAAGTTGTTCG
1 TGTTCGTTTATTTATTTTTGAAGTTGTTCA
* *
37181 TGTTCATTTTTTTATT
1 TGTTCGTTTATTTATT
37197 GTTCGCGAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 3 0.08
30 37 0.93
ACGTcount: A:0.14, C:0.05, G:0.17, T:0.63
Consensus pattern (30 bp):
TGTTCGTTTATTTATTTTTGAAGTTGTTCA
Found at i:46356 original size:30 final size:31
Alignment explanation
Indices: 46288--46439 Score: 136
Period size: 30 Copynumber: 5.4 Consensus size: 31
46278 CAATCCATAT
46288 TTTAAATAAATCAATCTATACTAATAAATTA
1 TTTAAATAAATCAATCTATACTAATAAATTA
*
46319 TTTAAATAAATCAAT-TCTACTAA-AAATTA
1 TTTAAATAAATCAATCTATACTAATAAATTA
46348 TTTAAAATAAATCAATC----C--AT--ATT-
1 TTT-AAATAAATCAATCTATACTAATAAATTA
* *
46371 TTAAAAT-AATCAATCCATACTAAT-AATTA
1 TTTAAATAAATCAATCTATACTAATAAATTA
* * *
46400 TTAAAATAAATCAATCCATATTAATAAATTA
1 TTTAAATAAATCAATCTATACTAATAAATTA
46431 -TTAAA-AAAT
1 TTTAAATAAAT
46440 TATTTTAAAA
Statistics
Matches: 104, Mismatches: 4, Indels: 28
0.76 0.03 0.21
Matches are distributed among these distances:
21 8 0.08
22 4 0.04
23 2 0.02
24 3 0.03
25 2 0.02
27 3 0.03
28 3 0.03
29 20 0.19
30 39 0.38
31 20 0.19
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (31 bp):
TTTAAATAAATCAATCTATACTAATAAATTA
Found at i:46381 original size:21 final size:22
Alignment explanation
Indices: 46348--46389 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
46338 CTAAAAATTA
46348 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
46370 TTTAAAAT-AATCAATCCATA
1 TTTAAAATAAATCAATCCATA
46390 CTAATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:46404 original size:51 final size:52
Alignment explanation
Indices: 46322--46421 Score: 159
Period size: 51 Copynumber: 1.9 Consensus size: 52
46312 TAAATTATTT
*
46322 AAATAAATCAATTCTACTAAAAATTATTTAAAATAAATCAATCCATATTTTA
1 AAATAAATCAATCCTACTAAAAATTATTTAAAATAAATCAATCCATATTTTA
*
46374 AAAT-AATCAATCCATACTAATAATTA-TTAAAATAAATCAATCCATATT
1 AAATAAATCAATCC-TACTAAAAATTATTTAAAATAAATCAATCCATATT
46422 AATAAATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
51 30 0.67
52 15 0.33
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (52 bp):
AAATAAATCAATCCTACTAAAAATTATTTAAAATAAATCAATCCATATTTTA
Found at i:46435 original size:82 final size:82
Alignment explanation
Indices: 46271--46437 Score: 248
Period size: 82 Copynumber: 2.0 Consensus size: 82
46261 ATACAACTAC
* * *
46271 AATAAATCAATCCATATTTTAAATAAATCAATCTATACTAATAAATTATTTAAATAAATCAATTC
1 AATAAATCAATCCATATTTTAAATAAATCAATCCATACTAATAAATTATTAAAATAAATCAATCC
46336 TACTAAAAATTATTTAA
66 TACTAAAAATTATTTAA
46353 AATAAATCAATCCATATTTTAAA-ATAATCAATCCATACTAAT-AATTATTAAAATAAATCAATC
1 AATAAATCAATCCATATTTTAAATA-AATCAATCCATACTAATAAATTATTAAAATAAATCAATC
* *
46416 CATATTAATAAATTATTAAA
65 C-TACTAA-AAATTATTTAA
46436 AA
1 AA
46438 ATTATTTTAA
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
81 21 0.27
82 44 0.57
83 12 0.16
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (82 bp):
AATAAATCAATCCATATTTTAAATAAATCAATCCATACTAATAAATTATTAAAATAAATCAATCC
TACTAAAAATTATTTAA
Found at i:47927 original size:21 final size:21
Alignment explanation
Indices: 47901--47944 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
47891 AAGAGACATA
47901 AGGTAAGATAGATGACTATCC
1 AGGTAAGATAGATGACTATCC
47922 AGGTAAGATAGATGACTATCC
1 AGGTAAGATAGATGACTATCC
47943 AG
1 AG
47945 CTCAGTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (21 bp):
AGGTAAGATAGATGACTATCC
Found at i:50139 original size:22 final size:21
Alignment explanation
Indices: 50081--50140 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 21
50071 TTAAATGATG
50081 ACTGTAGACTATCGCAACGAA
1 ACTGTAGACTATCGCAACGAA
** ** *
50102 TTTG-A-AAAATCACAACGACA
1 ACTGTAGACTATCGCAACGA-A
50122 ACTGTAGACTATCGCAACG
1 ACTGTAGACTATCGCAACG
50141 CGAACTGGAA
Statistics
Matches: 26, Mismatches: 10, Indels: 5
0.63 0.24 0.12
Matches are distributed among these distances:
19 10 0.38
20 4 0.15
21 3 0.12
22 9 0.35
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (21 bp):
ACTGTAGACTATCGCAACGAA
Found at i:50178 original size:21 final size:21
Alignment explanation
Indices: 50152--50192 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
50142 GAACTGGAAA
50152 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
50173 ATCGCAACGCGATTTTCAAC
1 ATCGCAACGCGATTTTCAAC
50193 GCGGATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:78124 original size:34 final size:34
Alignment explanation
Indices: 78086--78153 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
78076 TCACAACCAC
*
78086 TTAAATACTAATGTGGT-ATATATTA-TATTAACAA
1 TTAAATAC--ATGTGGTAATATATTACTAATAACAA
78120 TTAAATACATGTGGTAATATATTACTAATAACAA
1 TTAAATACATGTGGTAATATATTACTAATAACAA
78154 AATATTGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 7 0.23
33 8 0.26
34 16 0.52
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (34 bp):
TTAAATACATGTGGTAATATATTACTAATAACAA
Found at i:79703 original size:22 final size:22
Alignment explanation
Indices: 79666--79708 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
79656 CTAAACCAAT
79666 TAATTATTAATAAAAT-TTAAA
1 TAATTATTAATAAAATATTAAA
*
79687 TAATTACTTAATCAAATATTAA
1 TAATTA-TTAATAAAATATTAA
79709 TAACATTCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATTATTAATAAAATATTAAA
Found at i:87446 original size:151 final size:148
Alignment explanation
Indices: 87136--87446 Score: 568
Period size: 151 Copynumber: 2.1 Consensus size: 148
87126 TATGACATCT
*
87136 TATGGAGAATACGGGAAGGTCAATAGGAATCAGTTGAAAATATCTAGGAATCCATCCTCTTTGGT
1 TATGGA-AAAACGGGAAGGTCAATAGGAATCAGTTGAAAATATCTAGGAATCCATCCTCTTTGGT
87201 AATGTGTTTGGCCATGTAATCCGCCGCATGATCTGCAAAAACTCAACATACAACGCTTTTTGCCA
65 AATGTGTTTGGCCATGTAATCCGCCGCATGATCTGCAAAAACTCAACATACAACGCTTTTTGCCA
87266 TAGGCCGCAATGGCTCTCA
130 TAGGCCGCAATGGCTCTCA
87285 TATGGAAAAAACGGTGAAGGTCAATAGGAATCAAGTTGAAAATATCTAGGAATCCATCCTCTTTG
1 TATGG-AAAAACGG-GAAGGTCAATAGGAATC-AGTTGAAAATATCTAGGAATCCATCCTCTTTG
87350 GTAATGTGTTTGGCCATGTAATCCGCCGCATGATCTGCAAAAACTCAACATACAACGCTTTTTGC
63 GTAATGTGTTTGGCCATGTAATCCGCCGCATGATCTGCAAAAACTCAACATACAACGCTTTTTGC
87415 CATAGGCCAGCAATGGCTCTCA
128 CATAGGCC-GCAATGGCTCTCA
87437 TATGGAAAAA
1 TATGGAAAAA
87447 AGGACTATTT
Statistics
Matches: 157, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
149 11 0.07
150 18 0.11
151 110 0.70
152 18 0.11
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (148 bp):
TATGGAAAAACGGGAAGGTCAATAGGAATCAGTTGAAAATATCTAGGAATCCATCCTCTTTGGTA
ATGTGTTTGGCCATGTAATCCGCCGCATGATCTGCAAAAACTCAACATACAACGCTTTTTGCCAT
AGGCCGCAATGGCTCTCA
Found at i:89744 original size:15 final size:16
Alignment explanation
Indices: 89719--89751 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
89709 AAGTTTATGA
89719 AAGTACGAGTTCAGTC
1 AAGTACGAGTTCAGTC
*
89735 AAGT-CGAGTTGAGTC
1 AAGTACGAGTTCAGTC
89750 AA
1 AA
89752 AAAACTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.24
Consensus pattern (16 bp):
AAGTACGAGTTCAGTC
Found at i:104008 original size:39 final size:39
Alignment explanation
Indices: 103952--104035 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
103942 GCCAGCAAAT
103952 GGTTACGATAGGAACCTTACTACAAACGATTAAAAGTTG
1 GGTTACGATAGGAACCTTACTACAAACGATTAAAAGTTG
*
103991 GGTTACGATAGGGACCTTACTACAAACGATTAAAAGTTG
1 GGTTACGATAGGAACCTTACTACAAACGATTAAAAGTTG
104030 GGTTAC
1 GGTTAC
104036 AAAAATGATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (39 bp):
GGTTACGATAGGAACCTTACTACAAACGATTAAAAGTTG
Found at i:104288 original size:19 final size:18
Alignment explanation
Indices: 104261--104296 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
104251 AAAAGTAACG
104261 ATAAAAATAAGAGAAAAAA
1 ATAAAAATAAGA-AAAAAA
*
104280 ATAAGAATAAGAAAAAA
1 ATAAAAATAAGAAAAAA
104297 TATGTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
ATAAAAATAAGAAAAAAA
Done.