Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002800.1 Hibiscus syriacus cultivar Beakdansim tig00005765_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: 69705
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7958 original size:19 final size:19
Alignment explanation
Indices: 7936--7982 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
7926 ACTGCAAATG
7936 CCATGCTGCACCATGCCGC
1 CCATGCTGCACCATGCCGC
* * *
7955 CCATGCTGGATCATGCTGC
1 CCATGCTGCACCATGCCGC
7974 CC-TGCTGCA
1 CCATGCTGCA
7983 GATTTCAGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.15, C:0.40, G:0.23, T:0.21
Consensus pattern (19 bp):
CCATGCTGCACCATGCCGC
Found at i:21291 original size:15 final size:15
Alignment explanation
Indices: 21271--21317 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
21261 ATATAGCCCC
21271 CCCCGGCCGTATAAT
1 CCCCGGCCGTATAAT
21286 CCCCGGCCGTATAAT
1 CCCCGGCCGTATAAT
21301 CCCCGGCCGTATAAT
1 CCCCGGCCGTATAAT
21316 CC
1 CC
21318 TTCATAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.19, C:0.43, G:0.19, T:0.19
Consensus pattern (15 bp):
CCCCGGCCGTATAAT
Found at i:21806 original size:21 final size:21
Alignment explanation
Indices: 21777--21829 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
21767 ATTCTGACTA
21777 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
21798 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
21819 TCGCAATGCGA
1 TCGCATTGCGA
21830 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:21849 original size:20 final size:20
Alignment explanation
Indices: 21819--21892 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
21809 TTTTCCTAAT
21819 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * ** *
21839 TTGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
21860 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
21880 TCGCAATGCGAAT
1 TCGCAATGCGAAT
21893 CTGACTATCG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:21902 original size:20 final size:20
Alignment explanation
Indices: 21879--21930 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
21869 GATTACGTAA
21879 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
*
21899 ATCGCAATGCCAATCTGACT
1 ATCGCAATGCGAATCTGACT
*
21919 ATCACAATGCGA
1 ATCGCAATGCGA
21931 TTTACATAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATCTGACT
Found at i:22133 original size:22 final size:22
Alignment explanation
Indices: 22108--22169 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 22
22098 GGCGACATCC
22108 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
22130 GTCCCCA----CGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
22148 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
22170 TTCACGATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 16 0.50
22 16 0.50
ACGTcount: A:0.26, C:0.39, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:22582 original size:20 final size:20
Alignment explanation
Indices: 22557--22603 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
22547 TCAAATCGCA
22557 TTGCGATAGTT-ATTTTCGTG
1 TTGCGAT-GTTCATTTTCGTG
*
22577 TTGCGATTTTCATTTTCGTG
1 TTGCGATGTTCATTTTCGTG
22597 TTGCGAT
1 TTGCGAT
22604 TTAAATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.51
Consensus pattern (20 bp):
TTGCGATGTTCATTTTCGTG
Found at i:22604 original size:20 final size:20
Alignment explanation
Indices: 22568--22605 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
22558 TGCGATAGTT
22568 ATTTTCGTGTTGCGATTTTC
1 ATTTTCGTGTTGCGATTTTC
22588 ATTTTCGTGTTGCGATTT
1 ATTTTCGTGTTGCGATTT
22606 AAATTTTCAG
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:0.11, C:0.13, G:0.21, T:0.55
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTC
Found at i:22611 original size:20 final size:20
Alignment explanation
Indices: 22568--22613 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
22558 TGCGATAGTT
**
22568 ATTTTCGTGTTGCGATTTTC
1 ATTTTCGTGTTGCGATTTAA
22588 ATTTTCGTGTTGCGATTTAA
1 ATTTTCGTGTTGCGATTTAA
22608 ATTTTC
1 ATTTTC
22614 AGAAACTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTAA
Found at i:24507 original size:20 final size:20
Alignment explanation
Indices: 24482--24565 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
24472 AGAATAGTTT
24482 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
24502 ACTATCGCAACACGAAAATG
1 ACTATCGCAATGCGAAAATG
*
24522 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
24538 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
24556 ACTATCGCAA
1 ACTATCGCAA
24566 CGAAAGAATC
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.13
16 4 0.07
17 4 0.07
18 4 0.07
20 35 0.65
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:24552 original size:34 final size:34
Alignment explanation
Indices: 24505--24586 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
24495 GAAAATGACT
** *
24505 ATCGCAACACGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
24539 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
24573 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
24587 TGAAAATCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:24596 original size:19 final size:18
Alignment explanation
Indices: 24538--24603 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
24528 GCAACGAGAG
24538 AATCGCAATGCGAAAATGA
1 AATCGCAATGCG-AAATGA
*
24557 CTATCGCAA--CGAAA-G-
1 -AATCGCAATGCGAAATGA
24572 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-A
*
24591 AATCGCATTGCGA
1 AATCGCAATGCGA
24604 TTCTCTCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
14 7 0.18
16 6 0.16
17 4 0.11
18 2 0.05
19 12 0.32
20 7 0.18
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17
Consensus pattern (18 bp):
AATCGCAATGCGAAATGA
Found at i:24641 original size:20 final size:20
Alignment explanation
Indices: 24616--24658 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
24606 CTCTCGTTGT
24616 GATAGTCAAATTCGCATTGC
1 GATAGTCAAATTCGCATTGC
** *
24636 GATAGTCATTTTCGCGTTGC
1 GATAGTCAAATTCGCATTGC
24656 GAT
1 GAT
24659 TTTATTGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (20 bp):
GATAGTCAAATTCGCATTGC
Found at i:24671 original size:87 final size:87
Alignment explanation
Indices: 24580--24749 Score: 250
Period size: 87 Copynumber: 2.0 Consensus size: 87
24570 AGAATCGCAA
*
24580 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGTGATAGTCAAATTCGCATTGCGATAGTCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
24645 TTTCGCGTTGCGATTTTATTGT
66 TTTCGCGTTGCGATTTTATTGT
** ** ** ** *
24667 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
24732 TTTCGCGTTGCGATTTTA
66 TTTCGCGTTGCGATTTTA
24750 AGTTTCAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (87 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
TTTCGCGTTGCGATTTTATTGT
Found at i:24689 original size:33 final size:34
Alignment explanation
Indices: 24632--24725 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
24622 CAAATTCGCA
* *
24632 TTGCGATAGTCATTTTCGCGTTGCGATTTTATTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTATCG
** * *
24666 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTATCG
24699 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCGTTGCGAT
24726 AGTCATTTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 27 0.54
34 23 0.46
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTCTATCG
Found at i:24722 original size:20 final size:20
Alignment explanation
Indices: 24697--24745 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
24687 GCGATTCTCT
24697 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
24717 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
24737 CGTTGCGAT
1 CGTTGCGAT
24746 TTTAAGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:24755 original size:20 final size:20
Alignment explanation
Indices: 24697--24755 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
24687 GCGATTCTCT
* *
24697 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* *
24717 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
24737 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATAGTAAGTTTC
24756 AAATTCTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:25257 original size:21 final size:21
Alignment explanation
Indices: 25231--25287 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
25221 CTCACCTGTC
25231 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGGCCTCCCCT
25252 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGGCCTCCCCT
25273 ATCGTTCAAGAGGCC
1 ATCGTTCAAGAGGCC
25288 CCTATCATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCTCCCCT
Found at i:25341 original size:21 final size:21
Alignment explanation
Indices: 25230--25357 Score: 107
Period size: 21 Copynumber: 6.1 Consensus size: 21
25220 ACTCACCTGT
25230 CATCGTTCAAGAGGCCTCC-CC
1 CATCGTTCAAGAGGCC-CCTCC
*
25251 TATCGTTCAAGAGGCCTCC-CC
1 CATCGTTCAAGAGGCC-CCTCC
* **
25272 TATCGTTCAAGAGGCCCCTAT
1 CATCGTTCAAGAGGCCCCTCC
** *
25293 CATCCCTCAAGAGTCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * **
25314 CACCGTTCAAGAGGCCACTGT
1 CATCGTTCAAGAGGCCCCTCC
* *
25335 CATCGTTGAAGAGGTCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
25356 CA
1 CA
25358 ACATTCTAGA
Statistics
Matches: 84, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
20 2 0.02
21 82 0.98
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:26732 original size:14 final size:14
Alignment explanation
Indices: 26713--26748 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
26703 ATTGTTTAAT
26713 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
26727 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
26741 TGATTTGT
1 TGATTTGT
26749 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:26900 original size:33 final size:33
Alignment explanation
Indices: 26850--26978 Score: 186
Period size: 33 Copynumber: 3.8 Consensus size: 33
26840 AAAACAGACT
* ** *
26850 ATCGCAACGCGGAAATGACTATCGCAAAGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
26884 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
26917 ATCACAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
26950 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
26979 CGAAACTAAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
33 61 0.70
34 26 0.30
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:27009 original size:19 final size:19
Alignment explanation
Indices: 26987--27074 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
26977 CGCGAAACTA
*
26987 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
27006 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
27024 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
27040 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
27059 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
27075 CTCTCATTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
14 6 0.10
16 7 0.12
17 3 0.05
18 4 0.07
19 28 0.47
20 12 0.20
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:27086 original size:52 final size:53
Alignment explanation
Indices: 26987--27096 Score: 168
Period size: 52 Copynumber: 2.1 Consensus size: 53
26977 CGCGAAACTA
* * **
26987 ATTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCATTGCGATAGTC
*
27040 ATTTCGCATTGCGATTTTCA-TTTCGCATTGCGATTCTCTCATTGCGATAGTC
1 ATTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCATTGCGATAGTC
27092 ATTTC
1 ATTTC
27097 CGTGTTACGA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
52 33 0.63
53 19 0.37
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (53 bp):
ATTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCATTGCGATAGTC
Found at i:27109 original size:20 final size:20
Alignment explanation
Indices: 27084--27133 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
27074 TCTCTCATTG
*
27084 CGATAGTCATTTCCGTGTTA
1 CGATAGTCATTTCCGCGTTA
* *
27104 CGATAGTCAATTCCGCGTTG
1 CGATAGTCATTTCCGCGTTA
27124 CGATAGTCAT
1 CGATAGTCAT
27134 ATTCACGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (20 bp):
CGATAGTCATTTCCGCGTTA
Found at i:27142 original size:20 final size:19
Alignment explanation
Indices: 27081--27147 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 19
27071 GATTCTCTCA
27081 TTGCGATAGTCAT-TTCCGTG
1 TTGCGATAGTCATATTCC--G
*
27101 TTACGATAGTCA-ATTCCGCG
1 TTGCGATAGTCATATT-C-CG
27121 TTGCGATAGTCATATTCACG
1 TTGCGATAGTCATATTC-CG
27141 TTGCGAT
1 TTGCGAT
27148 TTCCGCGTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 35 0.88
21 4 0.10
22 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (19 bp):
TTGCGATAGTCATATTCCG
Found at i:29615 original size:24 final size:24
Alignment explanation
Indices: 29581--29634 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
29571 CTGAAAAATC
29581 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
29605 ATCAAAGTCCGGGTATTTACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
29629 ATCAAA
1 ATCAAA
29635 TTTCGAATAC
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:30523 original size:20 final size:20
Alignment explanation
Indices: 30496--30602 Score: 119
Period size: 20 Copynumber: 5.3 Consensus size: 20
30486 CAGAATCTCG
30496 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
*
30516 TTGTGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
30536 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* **
30556 TTGCGATTTTC-TAAATTCGTG
1 TTGCGATTTACGT--ATTCGCA
*
30577 TTGCGATTTACGTATTCGTA
1 TTGCGATTTACGTATTCGCA
30597 TTGCGA
1 TTGCGA
30603 ATTAGGAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
19 2 0.03
20 57 0.77
21 14 0.19
22 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:38116 original size:15 final size:15
Alignment explanation
Indices: 38096--38205 Score: 62
Period size: 15 Copynumber: 7.7 Consensus size: 15
38086 CATATTCACT
38096 TAGTTCACTTACACA
1 TAGTTCACTTACACA
38111 TAGTTCACTT-C-CA
1 TAGTTCACTTACACA
*
38124 TA--TGA-TT-CACA
1 TAGTTCACTTACACA
* *
38135 T-G-TCACATATTCACT
1 TAGTTCAC-T-TACACA
38150 TAGTTCACTTACACA
1 TAGTTCACTTACACA
38165 TAGTTCACTT-C-CA
1 TAGTTCACTTACACA
*
38178 TATGATTCACATATCACA
1 TA-G-TTCACTTA-CACA
38196 TA-TTCACTTA
1 TAGTTCACTTA
38206 TTCATATCAC
Statistics
Matches: 75, Mismatches: 7, Indels: 26
0.69 0.06 0.24
Matches are distributed among these distances:
10 3 0.04
11 7 0.09
13 9 0.12
14 4 0.05
15 41 0.55
16 2 0.03
17 5 0.07
18 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.37
Consensus pattern (15 bp):
TAGTTCACTTACACA
Found at i:38165 original size:54 final size:53
Alignment explanation
Indices: 38079--38209 Score: 237
Period size: 54 Copynumber: 2.5 Consensus size: 53
38069 ATATTATCAT
38079 ACATTCACATATTCACTTAGTTCACTTACACATAGTTCACTTCCATATGATTC
1 ACATTCACATATTCACTTAGTTCACTTACACATAGTTCACTTCCATATGATTC
38132 ACATGTCACATATTCACTTAGTTCACTTACACATAGTTCACTTCCATATGATTC
1 ACAT-TCACATATTCACTTAGTTCACTTACACATAGTTCACTTCCATATGATTC
38186 ACATATCACATATTCACTTA-TTCA
1 ACAT-TCACATATTCACTTAGTTCA
38210 TATCACATAG
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
53 8 0.11
54 68 0.89
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.37
Consensus pattern (53 bp):
ACATTCACATATTCACTTAGTTCACTTACACATAGTTCACTTCCATATGATTC
Found at i:43136 original size:15 final size:14
Alignment explanation
Indices: 43110--43222 Score: 51
Period size: 15 Copynumber: 8.0 Consensus size: 14
43100 ATCATACATT
43110 CACATATTCACTTA
1 CACATATTCACTTA
43124 CACATAGTTCACTT-
1 CACATA-TTCACTTA
*
43138 C-CATA-TGA-TT-
1 CACATATTCACTTA
* * *
43148 TACAT-GTCACATATT
1 CACATATTCAC-T-TA
43163 CACATAGTTCACTTA
1 CACATA-TTCACTTA
*
43178 CACATAGTTCACTTC
1 CACATA-TTCACTTA
*
43193 CATATAATTCACATGT-
1 CACAT-ATTCAC-T-TA
43209 CACATATTCACTTA
1 CACATATTCACTTA
43223 TTCATATCAC
Statistics
Matches: 77, Mismatches: 9, Indels: 26
0.69 0.08 0.23
Matches are distributed among these distances:
10 2 0.03
11 7 0.09
13 6 0.08
14 9 0.12
15 41 0.53
16 7 0.09
17 5 0.06
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (14 bp):
CACATATTCACTTA
Found at i:43178 original size:54 final size:53
Alignment explanation
Indices: 43107--43226 Score: 204
Period size: 54 Copynumber: 2.2 Consensus size: 53
43097 ATTATCATAC
* *
43107 ATTCACATATTCACTTACACATAGTTCACTTCCATATGATTTACATGTCACAT
1 ATTCACATATTCACTTACACATAGTTCACTTCCATATAATTCACATGTCACAT
43160 ATTCACATAGTTCACTTACACATAGTTCACTTCCATATAATTCACATGTCACAT
1 ATTCACATA-TTCACTTACACATAGTTCACTTCCATATAATTCACATGTCACAT
*
43214 ATTCACTTATTCA
1 ATTCACATATTCA
43227 TATCACATAG
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
53 13 0.21
54 50 0.79
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (53 bp):
ATTCACATATTCACTTACACATAGTTCACTTCCATATAATTCACATGTCACAT
Found at i:44060 original size:2 final size:2
Alignment explanation
Indices: 44053--44080 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44043 ACTTATGTAA
44053 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
44081 TACTTATATT
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:53281 original size:24 final size:24
Alignment explanation
Indices: 53254--53302 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
53244 TATATCAAAA
* *
53254 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGATCAAGT
* *
53278 ATCATATCAGAAATCAGATCAAGT
1 ATCAAAACAGAAATCAGATCAAGT
53302 A
1 A
53303 GAATCCAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGATCAAGT
Found at i:53329 original size:24 final size:24
Alignment explanation
Indices: 53302--53378 Score: 104
Period size: 24 Copynumber: 3.2 Consensus size: 24
53292 CAGATCAAGT
*
53302 AGAATCCAAGTCAAGTATCATATC
1 AGAATCCAAGTCAAGTATCAGATC
*
53326 AGAATCCATGTC-AGATATCAGATC
1 AGAATCCAAGTCAAG-TATCAGATC
53350 AGAATCCATA-TCAAGTATCAGATC
1 AGAATCCA-AGTCAAGTATCAGATC
53374 AGAAT
1 AGAAT
53379 TCAAATCGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
23 2 0.04
24 43 0.91
25 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAATCCAAGTCAAGTATCAGATC
Found at i:53393 original size:24 final size:24
Alignment explanation
Indices: 53302--53396 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 24
53292 CAGATCAAGT
* * *
53302 AGAATCCAAGTCAAGTATCATATC
1 AGAATCCAAATCAAGAATCAGATC
**
53326 AGAATCCATGTC-AGATATCAGATC
1 AGAATCCAAATCAAGA-ATCAGATC
* *
53350 AGAATCCATATCAAGTATCAGATC
1 AGAATCCAAATCAAGAATCAGATC
*
53374 AGAATTCAAATCGAA-AATCAGAT
1 AGAATCCAAATC-AAGAATCAGAT
53397 AAAATATTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
23 2 0.03
24 54 0.90
25 4 0.07
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAATCCAAATCAAGAATCAGATC
Found at i:53394 original size:48 final size:48
Alignment explanation
Indices: 53283--53396 Score: 115
Period size: 48 Copynumber: 2.3 Consensus size: 48
53273 CAAGTATCAT
* *
53283 ATCAGAAATCAGATCAAGTAGAATCCAAGTCAAGTATCATATCAGAATCCAT
1 ATCAGAAATCAGATC----AGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* * *
53335 GTCAGATATCAGATCAGAATCCATA-TCAAGTATCAGATCAGAATTCAA
1 ATCAGAAATCAGATCAGAATCCA-AGTCAAGTATCAGATCAGAATCCAA
53383 ATC-GAAAATCAGAT
1 ATCAG-AAATCAGAT
53397 AAAATATTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
47 1 0.02
48 38 0.72
49 1 0.02
52 13 0.25
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (48 bp):
ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
Found at i:54591 original size:18 final size:18
Alignment explanation
Indices: 54570--54604 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54560 TGCCATCCGG
*
54570 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
54588 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
54605 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:63192 original size:31 final size:31
Alignment explanation
Indices: 63116--63192 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 31
63106 TTGGGGCCTG
* * *
63116 AGAGCCTACCCAAGATAATTCTCATGGCCAC
1 AGAGCCTACCCAAGAAAAATCTCAGGGCCAC
* * * *
63147 GGAGACTTACCCAAGAAAAATCTCAGGGTCGC
1 AGAG-CCTACCCAAGAAAAATCTCAGGGCCAC
63179 AGAGCCTACCCAAG
1 AGAGCCTACCCAAG
63193 GGTTGACTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
31 12 0.33
32 24 0.67
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.16
Consensus pattern (31 bp):
AGAGCCTACCCAAGAAAAATCTCAGGGCCAC
Found at i:68851 original size:4 final size:4
Alignment explanation
Indices: 68844--68869 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
68834 ATTCATATCT
68844 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
68870 ATTCCTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Done.