Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000621.1 Hibiscus syriacus cultivar Beakdansim tig00001199_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: 60530
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:889 original size:13 final size:13
Alignment explanation
Indices: 871--896 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
861 AAAGTTACAC
871 TTTTACTCTTACT
1 TTTTACTCTTACT
884 TTTTACTCTTACT
1 TTTTACTCTTACT
897 GTGATGTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTACTCTTACT
Found at i:1582 original size:21 final size:21
Alignment explanation
Indices: 1558--1603 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1548 AATCAATTTT
*
1558 TCAAAAGCATGCACCGATGCA
1 TCAAAACCATGCACCGATGCA
* *
1579 TCAATACCATGCATCGATGCA
1 TCAAAACCATGCACCGATGCA
1600 TCAA
1 TCAA
1604 TGAATAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (21 bp):
TCAAAACCATGCACCGATGCA
Found at i:1604 original size:21 final size:21
Alignment explanation
Indices: 1565--1604 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1555 TTTTCAAAAG
1565 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
1586 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
1605 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:1649 original size:18 final size:19
Alignment explanation
Indices: 1626--1663 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1616 AACAATGCAT
1626 TTCATGCA-CGATGCACTC
1 TTCATGCATCGATGCACTC
1644 TTCATGCATCGATGCACTC
1 TTCATGCATCGATGCACTC
1663 T
1 T
1664 GATTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.21, C:0.32, G:0.16, T:0.32
Consensus pattern (19 bp):
TTCATGCATCGATGCACTC
Found at i:1769 original size:17 final size:19
Alignment explanation
Indices: 1741--1789 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1731 ATTTTTCAAA
1741 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
1759 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
1778 CACCGATGCACT
1 CATCGATGCACT
1790 AGGTGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:1785 original size:64 final size:63
Alignment explanation
Indices: 1619--1788 Score: 179
Period size: 64 Copynumber: 2.7 Consensus size: 63
1609 AAATTGAAAC
*
1619 AATGCATTTCATGCA-CGATGCACTCTTCATGCATCGATGCA-CTCTGATTTAATTAAAACATCG
1 AATGCATTTCATGCATCGATGCACTCTT-ATGCATCGATGCACCGCTGATTT-ATTAAAACATCG
* * * *
1682 AATGCATTTGATGCATCGATGCACAAGC-CATGCATCGATGCACCAGGCT-ATTT-TTCAAACAT
1 AATGCATTTCATGCATCGATGCAC--TCTTATGCATCGATGCACC--GCTGATTTATTAAAACAT
1744 CG
62 CG
* *
1746 AATGCACTTCATGCATCGATGCACTCTTAGTGCACCGATGCAC
1 AATGCATTTCATGCATCGATGCACTCTTA-TGCATCGATGCAC
1789 TAGGTGTCCA
Statistics
Matches: 89, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
62 1 0.01
63 15 0.17
64 65 0.73
65 1 0.01
66 5 0.06
67 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (63 bp):
AATGCATTTCATGCATCGATGCACTCTTATGCATCGATGCACCGCTGATTTATTAAAACATCG
Found at i:3731 original size:20 final size:21
Alignment explanation
Indices: 3706--3752 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3696 GGATTATGAG
*
3706 AAATGAT-TTTTAAAATAT-AA
1 AAATGATGTTTCAAAAT-TGAA
3726 AAATGATGTTTCAAAATTGAA
1 AAATGATGTTTCAAAATTGAA
3747 AAATGA
1 AAATGA
3753 AAACAAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.34
Consensus pattern (21 bp):
AAATGATGTTTCAAAATTGAA
Found at i:10180 original size:21 final size:21
Alignment explanation
Indices: 10156--10201 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
10146 AATCAATTTT
*
10156 TCAAAAGCATGCACCGATGCA
1 TCAAAACCATGCACCGATGCA
* *
10177 TCAATACCATGCATCGATGCA
1 TCAAAACCATGCACCGATGCA
10198 TCAA
1 TCAA
10202 TGAATAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (21 bp):
TCAAAACCATGCACCGATGCA
Found at i:10202 original size:21 final size:21
Alignment explanation
Indices: 10163--10202 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
10153 TTTTCAAAAG
10163 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
10184 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
10203 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:10252 original size:19 final size:19
Alignment explanation
Indices: 10228--10266 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
10218 TTGAATGCAT
10228 TTCATGCACCGATGCACTC
1 TTCATGCACCGATGCACTC
*
10247 TTCATGCATCGATGCACTC
1 TTCATGCACCGATGCACTC
10266 T
1 T
10267 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (19 bp):
TTCATGCACCGATGCACTC
Found at i:10291 original size:64 final size:64
Alignment explanation
Indices: 10184--10392 Score: 212
Period size: 64 Copynumber: 3.2 Consensus size: 64
10174 GCATCAATAC
* * * * *
10184 CATGCATCGATGCA-TCAATGAATAAATTGAAACATTGAATGCATTTCATGCACCGATGCACTCT
1 CATGCATCGATGCACTC--TGATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCT
10248 T
64 T
* ****
10249 CATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGCATTTGATGCATCGATGCACAAGC
1 CATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTT
* *
10313 CATGCATCGATGCACTAGGCT-ATTT--TTCAAACATCGAATGCACTTCATGCATCGATGCACTC
1 CATGCATCGATGCACT---CTGATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTC
10375 TT
63 TT
*
10377 -AGTGCACCGATGCACT
1 CA-TGCATCGATGCACT
10393 AGGAGTCCAA
Statistics
Matches: 121, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
63 1 0.01
64 98 0.81
65 14 0.12
66 6 0.05
67 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (64 bp):
CATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTT
Found at i:10372 original size:17 final size:19
Alignment explanation
Indices: 10344--10392 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
10334 ATTTTTCAAA
10344 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
10362 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
10381 CACCGATGCACT
1 CATCGATGCACT
10393 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:11523 original size:21 final size:21
Alignment explanation
Indices: 11497--11555 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
11487 GATTGCTCGA
11497 AGGGTACCGATACCCCCCAAG
1 AGGGTACCGATACCCCCCAAG
11518 AGGGTACCGATACCCCCCAAG
1 AGGGTACCGATACCCCCCAAG
*
11539 AGGGTAACGATACCCCC
1 AGGGTACCGATACCCCC
11556 ATGTAAGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.29, C:0.37, G:0.24, T:0.10
Consensus pattern (21 bp):
AGGGTACCGATACCCCCCAAG
Found at i:11651 original size:73 final size:74
Alignment explanation
Indices: 11517--11704 Score: 220
Period size: 73 Copynumber: 2.5 Consensus size: 74
11507 TACCCCCCAA
* *
11517 GAGGGTACCGATACCCCCCAAGAGGGTAACGATACCCCCATGTAAGATTTGACTCCAAGAAATTA
1 GAGGGTACCG--ACACCCCAAGAGGGTAACGATACCCCCATGTAAGATTTGACTCCAAGAAATAA
*
11582 CAGATTGCTCG
64 CAGATTACTCG
* * * * *
11593 GAGGGTACTGACACCCCAATAGGGTACCGATA-CCCCATGTAAGATTTGGCTCCGAGAAATAACA
1 GAGGGTACCGACACCCCAAGAGGGTAACGATACCCCCATGTAAGATTTGACTCCAAGAAATAACA
*
11657 TATTACTCG
66 GATTACTCG
* *
11666 GAGGGTACCGATACCCCCAG-GAGGT-ACTGATACCCCCAT
1 GAGGGTACCGACACCCCAAGAG-GGTAAC-GATACCCCCAT
11705 CTTATAACGG
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
72 2 0.02
73 59 0.62
74 25 0.26
76 9 0.09
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (74 bp):
GAGGGTACCGACACCCCAAGAGGGTAACGATACCCCCATGTAAGATTTGACTCCAAGAAATAACA
GATTACTCG
Found at i:17461 original size:23 final size:22
Alignment explanation
Indices: 17420--17499 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
17410 GGGTGCAGGA
*
17420 GGTATCGATACCCCCTTGAATG
1 GGTACCGATACCCCCTTGAATG
* *
17442 GGTACCGATCACCCCTTTGAGTG
1 GGTACCGAT-ACCCCCTTGAATG
** ** *
17465 GGTTTCGATACCTCCCCAGGA-G
1 GGTACCGATACC-CCCTTGAATG
17487 GGTACCGATACCC
1 GGTACCGATACCC
17500 TCCACGAGGT
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
21 1 0.02
22 22 0.50
23 21 0.48
ACGTcount: A:0.20, C:0.31, G:0.25, T:0.24
Consensus pattern (22 bp):
GGTACCGATACCCCCTTGAATG
Found at i:17878 original size:10 final size:10
Alignment explanation
Indices: 17859--17888 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
17849 ATCAAAAACA
17859 CAAGATTTTT
1 CAAGATTTTT
*
17869 CAATATTTTT
1 CAAGATTTTT
17879 CAAGATTTTT
1 CAAGATTTTT
17889 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (10 bp):
CAAGATTTTT
Found at i:19804 original size:22 final size:23
Alignment explanation
Indices: 19779--19823 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19769 TTTAACAAAA
19779 AGGGGGAG-AAGTGTTAAGAGTT
1 AGGGGGAGTAAGTGTTAAGAGTT
* *
19801 AGGGGGAGTAATTTTTAAGAGTT
1 AGGGGGAGTAAGTGTTAAGAGTT
19824 TTAAGAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.40, T:0.29
Consensus pattern (23 bp):
AGGGGGAGTAAGTGTTAAGAGTT
Found at i:20262 original size:55 final size:55
Alignment explanation
Indices: 20178--20336 Score: 264
Period size: 55 Copynumber: 2.9 Consensus size: 55
20168 GAAATAACAT
*
20178 ATTTGGCTCTAAGAAATTACAGATTGCTCGGAAGGTACCGATACCCCCATGTAAG
1 ATTTGGCTCTAAGAAATTACAGATTGCTCGGAGGGTACCGATACCCCCATGTAAG
* *
20233 ATTTGGCTCTAAGAAATTATAGACTGCTCGGAGGGTACCGATACCCCCATGTAAG
1 ATTTGGCTCTAAGAAATTACAGATTGCTCGGAGGGTACCGATACCCCCATGTAAG
** *
20288 ATTTGGCTCCGAGAAATAACAGATTGCTCGGAGGGTACCGATACCCCCA
1 ATTTGGCTCTAAGAAATTACAGATTGCTCGGAGGGTACCGATACCCCCA
20337 GGAGGTACCG
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 96 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (55 bp):
ATTTGGCTCTAAGAAATTACAGATTGCTCGGAGGGTACCGATACCCCCATGTAAG
Found at i:21129 original size:44 final size:44
Alignment explanation
Indices: 21068--21332 Score: 359
Period size: 44 Copynumber: 6.0 Consensus size: 44
21058 ATACCATGAG
* * *
21068 TGGCACCTTTTTGCCAATAATACACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
21112 TGGTACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * ** *
21156 TGGCATCTTTCTGCCAATAATGCACTGTTATTAATTATCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
21200 TGGCACTTTTCTGCCAATAATGAACCGTTAAGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
21244 TGGCACCTTTGTGCCAATAATGCACCATTATGTATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
21288 TGACACCTTTCTGCCAATATTGCACCGTTATGCATTTTCAATTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
21332 T
1 T
21333 TACAGTAACA
Statistics
Matches: 189, Mismatches: 32, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 189 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:21871 original size:61 final size:61
Alignment explanation
Indices: 21776--21890 Score: 221
Period size: 61 Copynumber: 1.9 Consensus size: 61
21766 CAGGCTCAAT
21776 AGTATCGGTACCCCTACCATGGTATTGATACTTCTATACTATGGTATCAATACTCTCTTTC
1 AGTATCGGTACCCCTACCATGGTATTGATACTTCTATACTATGGTATCAATACTCTCTTTC
*
21837 AGTATCGGTACCCCTACCATGGTATTGATACTTCTATACTATGGTATCGATACT
1 AGTATCGGTACCCCTACCATGGTATTGATACTTCTATACTATGGTATCAATACT
21891 GGTATTGATA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (61 bp):
AGTATCGGTACCCCTACCATGGTATTGATACTTCTATACTATGGTATCAATACTCTCTTTC
Found at i:27711 original size:18 final size:18
Alignment explanation
Indices: 27688--27722 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
27678 AATACCACCT
27688 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
27706 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
27723 AAACTTGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.23, G:0.49, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:27715 original size:13 final size:13
Alignment explanation
Indices: 27699--27724 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27689 GTCAACGGGT
27699 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
27712 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
27725 ACTTGTCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:34238 original size:13 final size:13
Alignment explanation
Indices: 34206--34246 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
34196 AATACCACTT
34206 GGTCAACGGGTCG
1 GGTCAACGGGTCG
34219 GGT---CGGGTCG
1 GGTCAACGGGTCG
34229 GGTCAACGGGTCG
1 GGTCAACGGGTCG
34242 GGTCA
1 GGTCA
34247 GACTGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.40
13 15 0.60
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:34264 original size:21 final size:22
Alignment explanation
Indices: 34229--34272 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
34219 GGTCGGGTCG
* *
34229 GGTCAACGGGTCGGGTCAGACT
1 GGTCAACGAGTCGGGTCAAACT
34251 GGTCAAC-AGTCGGGTCAAACT
1 GGTCAACGAGTCGGGTCAAACT
34272 G
1 G
34273 ATTCAACCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.23, C:0.23, G:0.36, T:0.18
Consensus pattern (22 bp):
GGTCAACGAGTCGGGTCAAACT
Found at i:34311 original size:30 final size:31
Alignment explanation
Indices: 34251--34314 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
34241 GGGTCAGACT
*
34251 GGTCAACAGTCGGGTCAAACTGATTCAACCC
1 GGTCAACAGTCGGGTCAAACCGATTCAACCC
34282 GGTCAACAGTCGGGTCAAACCGA-TCAACCC
1 GGTCAACAGTCGGGTCAAACCGATTCAACCC
34312 GGT
1 GGT
34315 TCAAACCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 10 0.31
31 22 0.69
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (31 bp):
GGTCAACAGTCGGGTCAAACCGATTCAACCC
Found at i:34338 original size:20 final size:19
Alignment explanation
Indices: 34296--34334 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
34286 AACAGTCGGG
*
34296 TCAAACCGATCAACCCGGT
1 TCAAACCGATCAAACCGGT
34315 TCAAACCGATCAAACCGGT
1 TCAAACCGATCAAACCGGT
34334 T
1 T
34335 TCAAGATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.18
Consensus pattern (19 bp):
TCAAACCGATCAAACCGGT
Found at i:37126 original size:44 final size:44
Alignment explanation
Indices: 37071--37380 Score: 458
Period size: 44 Copynumber: 7.0 Consensus size: 44
37061 ATACCATGAG
* * * *
37071 TGGCACTTTTCTTCCAATAGTGCATCATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
*
37115 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
37159 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
* * *
37203 TGGAACCTTTATGCCAATAATGCATCATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
* * * *
37247 CGGCACCTTTCTTCCAATAATGCATCGTTATGCATTTTTATTTTT
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCA-TTTA
*
37292 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
* * * *
37336 TGGCACCTATCTGCCAATAATGCACCATTATGCATTTTTATTTA
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
37380 T
1 T
37381 TTCAGTAACA
Statistics
Matches: 241, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
44 202 0.84
45 39 0.16
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
Found at i:42080 original size:60 final size:60
Alignment explanation
Indices: 41975--42087 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
41965 TATTTGGATG
* * * * * *
41975 AATTTGGGGATGAAACTGGAATGTTCAAAAGTTTAAGAACTAATTTAGAATGAGAGTCAT
1 AATTTGGGGATGAAACTAGAATATTAAAAAATATAAGAACTAATTTAAAATGAGAGTCAT
*
42035 AATTTGGGGATGAAATTAGAATATTAAAAAATATAAGGAAC-AATTTAAAATGA
1 AATTTGGGGATGAAACTAGAATATTAAAAAATATAA-GAACTAATTTAAAATGA
42088 AGGTTATAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 41 0.91
61 4 0.09
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.29
Consensus pattern (60 bp):
AATTTGGGGATGAAACTAGAATATTAAAAAATATAAGAACTAATTTAAAATGAGAGTCAT
Found at i:42517 original size:13 final size:13
Alignment explanation
Indices: 42495--42530 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
42485 TGTTTAAAGC
42495 TTTT-TTTCTTCT
1 TTTTGTTTCTTCT
42507 TTTTGTTTCTTCT
1 TTTTGTTTCTTCT
42520 TTTTGTTTCTT
1 TTTTGTTTCTT
42531 ATAGAGCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.81
Consensus pattern (13 bp):
TTTTGTTTCTTCT
Found at i:45753 original size:60 final size:59
Alignment explanation
Indices: 45678--45824 Score: 183
Period size: 60 Copynumber: 2.4 Consensus size: 59
45668 AATATAATGA
* *
45678 ATAGTCGAGTGATCATTTTGTAACTTTTAATAGTC-GAGGGACTCAATAAAGCAACT-TCCT
1 ATAGTCGAG-GATCATTTTGTAACTTTTAATAGCCTGA-GGACTCAACAAAGC-ACTATCCT
* *
45738 ATAGTCGATGGATCATTTTGTAACTTTTAATAGCCTTAGGACTCAACAAAGCAGTATCCT
1 ATAGTCGA-GGATCATTTTGTAACTTTTAATAGCCTGAGGACTCAACAAAGCACTATCCT
45798 ATAGTCGAGGGATCATTTGTGT-ACTTT
1 ATAGTCGA-GGATCATTT-TGTAACTTT
45825 GCCCTAATTC
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
59 2 0.03
60 71 0.91
61 5 0.06
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (59 bp):
ATAGTCGAGGATCATTTTGTAACTTTTAATAGCCTGAGGACTCAACAAAGCACTATCCT
Found at i:45770 original size:29 final size:28
Alignment explanation
Indices: 45677--45770 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
45667 GAATATAATG
45677 AATAGTCGAGTGATCATTTTGTAACTTTT
1 AATAGTCGAG-GATCATTTTGTAACTTTT
*** * *
45706 AATAGTCGAGGGACTCAATAAAGCAACTTCCT
1 AATAGTCGA-GGA-TC-ATTTTGTAACTT-TT
45738 -ATAGTCGATGGATCATTTTGTAACTTTT
1 AATAGTCGA-GGATCATTTTGTAACTTTT
45766 AATAG
1 AATAG
45771 CCTTAGGACT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
28 1 0.02
29 23 0.47
30 5 0.10
31 19 0.39
32 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (28 bp):
AATAGTCGAGGATCATTTTGTAACTTTT
Found at i:46041 original size:2 final size:2
Alignment explanation
Indices: 46034--46069 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
46024 ATTAAACTTA
46034 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
46070 TCACTTTAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46273 original size:15 final size:15
Alignment explanation
Indices: 46253--46282 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
46243 AACATTCATT
46253 CCCTCTCTCTATCTA
1 CCCTCTCTCTATCTA
46268 CCCTCTCTCTATCTA
1 CCCTCTCTCTATCTA
46283 TCTCGCTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (15 bp):
CCCTCTCTCTATCTA
Found at i:49183 original size:23 final size:23
Alignment explanation
Indices: 49157--49201 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
49147 CACTACAGCT
* *
49157 CGTATAAATGCATCGAAGTGCCA
1 CGTAGAAATACATCGAAGTGCCA
*
49180 CGTAGAATTACATCGAAGTGCC
1 CGTAGAAATACATCGAAGTGCC
49202 GAATAGAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (23 bp):
CGTAGAAATACATCGAAGTGCCA
Found at i:49208 original size:23 final size:23
Alignment explanation
Indices: 49167--49219 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
49157 CGTATAAATG
*
49167 CATCGAAGTGCCACGTAGAATTA
1 CATCGAAGTGCCACATAGAATTA
*
49190 CATCGAAGTGCCGA-ATAGAATTG
1 CATCGAAGTGCC-ACATAGAATTA
49213 CATCGAA
1 CATCGAA
49220 ATGTCAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (23 bp):
CATCGAAGTGCCACATAGAATTA
Found at i:49229 original size:23 final size:23
Alignment explanation
Indices: 49167--49229 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
49157 CGTATAAATG
* **
49167 CATCGAAGTGCCACGTAGAATTA
1 CATCGAAATGCCAAATAGAATTA
* * *
49190 CATCGAAGTGCCGAATAGAATTG
1 CATCGAAATGCCAAATAGAATTA
*
49213 CATCGAAATGTCAAATA
1 CATCGAAATGCCAAATA
49230 AAATGTCCCT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (23 bp):
CATCGAAATGCCAAATAGAATTA
Found at i:50678 original size:20 final size:22
Alignment explanation
Indices: 50653--50710 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
50643 TTCCCCTTGA
50653 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
50673 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
50696 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
50711 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:50849 original size:19 final size:19
Alignment explanation
Indices: 50825--50872 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
50815 ATTTTAAAGG
50825 GTGCATCGATGCACTTCCT
1 GTGCATCGATGCACTTCCT
*
50844 GTGCATCTATGCACTTCCT
1 GTGCATCGATGCACTTCCT
50863 GTGCATCGAT
1 GTGCATCGAT
50873 ACACACTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (19 bp):
GTGCATCGATGCACTTCCT
Found at i:50872 original size:64 final size:64
Alignment explanation
Indices: 50699--50857 Score: 209
Period size: 64 Copynumber: 2.5 Consensus size: 64
50689 CTTTAACAGG
* * * *
50699 TGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTCTCATTTTAAGGGGA
1 TGCATCGATGCACT-CCTTATGCATCGATGCACAAATTACATTCGATGTTCTCATTTTAAAGGGA
50763 TGCATCGATGCACTCCTTATGCATCGATGCACAAATTACATTCGATGTT-TCCATTTTAAAGGG-
1 TGCATCGATGCACTCCTTATGCATCGATGCACAAATTACATTCGATGTTCT-CATTTTAAAGGGA
* *
50826 TGCATCGATGCACTTCC-TGTGCATCTATGCAC
1 TGCATCGATGCAC-TCCTTATGCATCGATGCAC
50858 TTCCTGTGCA
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
63 29 0.34
64 57 0.66
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (64 bp):
TGCATCGATGCACTCCTTATGCATCGATGCACAAATTACATTCGATGTTCTCATTTTAAAGGGA
Found at i:54227 original size:23 final size:22
Alignment explanation
Indices: 54189--54251 Score: 99
Period size: 23 Copynumber: 2.8 Consensus size: 22
54179 AACTCGTATA
54189 AATGCACCGAAGTGCCACGTAG
1 AATGCACCGAAGTGCCACGTAG
*
54211 AATGCACCGAAGTTGCCGCGTAG
1 AATGCACCGAAG-TGCCACGTAG
54234 AATTGCACCGAAGTGCCA
1 AA-TGCACCGAAGTGCCA
54252 TATAAAATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 12 0.32
23 15 0.41
24 10 0.27
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (22 bp):
AATGCACCGAAGTGCCACGTAG
Found at i:55746 original size:63 final size:60
Alignment explanation
Indices: 55668--55824 Score: 190
Period size: 62 Copynumber: 2.5 Consensus size: 60
55658 TTCTTTAACA
*
55668 GGTGCATCGATGCACTACCCCATGCATCGATACAAATTACCTTCGATGTTTTCATTTTAAGG
1 GGTGCATCGATGCACT-CCCCATGCATCGATACAAATTACATTCGATGTTTTCA-TTTAAGG
* ** * *
55730 GGATGCATTGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTCATTTAAGG
1 GG-TGCATCGATGCACTCCCCATGCATCGAT--ACAAATTACATTCGATGTTTTCATTTAAGG
* *
55793 GGTGCATCGATGCACT-TCCGTGCATCGATACA
1 GGTGCATCGATGCACTCCCCATGCATCGATACA
55825 CACTGAACAA
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
59 2 0.03
61 9 0.11
62 27 0.34
63 22 0.28
64 20 0.25
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (60 bp):
GGTGCATCGATGCACTCCCCATGCATCGATACAAATTACATTCGATGTTTTCATTTAAGG
Found at i:55758 original size:62 final size:58
Alignment explanation
Indices: 55668--55824 Score: 179
Period size: 63 Copynumber: 2.5 Consensus size: 58
55658 TTCTTTAACA
*
55668 GGTGCATCGATGCACTACCCCATGCATCGATACAAATTACCTTCGATGTTTTCATTTTAAGG
1 GGTGCATCGATGCACT---CCATGCATCGATACAAATTACATTCGATGTTTTCA-TTTAAGG
* * *
55730 GGATGCATTGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTCATTTAAGG
1 GG-TGCATCGATGCACTCC--ATGCATCGAT--ACAAATTACATTCGATGTTTTCATTTAAGG
*
55793 GGTGCATCGATGCACTTCCGTGCATCGATACA
1 GGTGCATCGATGCAC-TCCATGCATCGATACA
55825 CACTGAACAA
Statistics
Matches: 82, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
59 2 0.02
60 2 0.02
61 9 0.11
62 24 0.29
63 25 0.30
64 20 0.24
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (58 bp):
GGTGCATCGATGCACTCCATGCATCGATACAAATTACATTCGATGTTTTCATTTAAGG
Found at i:59244 original size:58 final size:57
Alignment explanation
Indices: 59121--59299 Score: 186
Period size: 58 Copynumber: 3.1 Consensus size: 57
59111 ACACTATATG
* * *
59121 TCCCTAAACTA-GACTCTCATT-TCAAATTAATCCTTAAACTTTAAATATT-TCAATTTCA
1 TCCCTAAACTATGACTCTCATTCT-AAA-TGATCCTTAAACTTTGAACATTCT-AA-TTCA
* *
59179 TCTCTAAACTATGACTCTCATTCTAAATGAGTCCTTAAACATTGAACATTCTAATTCA
1 TCCCTAAACTATGACTCTCATTCTAAATGA-TCCTTAAACTTTGAACATTCTAATTCA
* *
59237 TCCCTAAACCATGACTCTCATTCTAAATTGATCCTCAAACGTTTGAATC-TTCTAATTCCA
1 TCCCTAAACTATGACTCTCATTCTAAA-TGATCCTTAAAC-TTTGAA-CATTCTAATT-CA
59297 TCC
1 TCC
59300 TCAAATTCAT
Statistics
Matches: 104, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
58 49 0.47
59 47 0.45
60 8 0.08
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (57 bp):
TCCCTAAACTATGACTCTCATTCTAAATGATCCTTAAACTTTGAACATTCTAATTCA
Done.