Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006322.1 Hibiscus syriacus cultivar Beakdansim tig00015106_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: 61340
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5182 original size:3 final size:3
Alignment explanation
Indices: 5174--5199 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5164 ATTCCCTCTA
5174 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
5200 GCTCTTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:5381 original size:36 final size:36
Alignment explanation
Indices: 5334--5403 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
5324 GTGCGCTACA
*
5334 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTAGATGCT
5370 TCCTTCCGTTCGACTTGAATCGGAAGTGTAGATG
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTAGATG
5404 AAATCATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.33
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGTAGATGCT
Found at i:9422 original size:88 final size:85
Alignment explanation
Indices: 9284--9555 Score: 284
Period size: 86 Copynumber: 3.2 Consensus size: 85
9274 TATATTTAAC
* * * *
9284 TTGTTTAAAAATAGTTGTTTTACAATTATTTTTAAATGATAAATGAATAACAAATATTGTAAAAA
1 TTGTTTTAAAATAATTATTTTA-AA--ATTTTTAAATGATAAATGAATAACAAATATTGTAAGAA
9349 AGAAATATAATATATAATATAAAT
63 AGAAA-ATAATATATAATATAAAT
* **
9373 TTGTTTTAAAATAATTATTTTATAAATTTCTTAAATGATAAATGTATAACAAACGTTGTAAGAAA
1 TTGTTTTAAAATAATTATTTTA-AAATTT-TTAAATGATAAATGAATAACAAATATTGTAAGAAA
* *
9438 -AAAATAATATATAATTTAATT
64 GAAAATAATATATAATATAAAT
* * *
9459 TTTTTTTAAAATAATTATTCTAAAA---TTAAATGATAAATCAATAA-AAATATTGTAAGAAAGA
1 TTGTTTTAAAATAATTATTTTAAAATTTTTAAATGATAAATGAATAACAAATATTGTAAGAAAGA
* * * * *
9520 AAAAACATGTCTAATTTAAAC
66 AAATA-ATATATAATATAAAT
*
9541 TTGTTTAAAAATAAT
1 TTGTTTTAAAATAAT
9556 CATATAAAAA
Statistics
Matches: 157, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
80 13 0.08
81 22 0.14
82 24 0.15
85 3 0.02
86 36 0.23
87 7 0.04
88 31 0.20
89 21 0.13
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (85 bp):
TTGTTTTAAAATAATTATTTTAAAATTTTTAAATGATAAATGAATAACAAATATTGTAAGAAAGA
AAATAATATATAATATAAAT
Found at i:9572 original size:25 final size:25
Alignment explanation
Indices: 9543--9647 Score: 63
Period size: 25 Copynumber: 4.2 Consensus size: 25
9533 ATTTAAACTT
9543 GTTTAAAAATAATCATATAAAAATA
1 GTTTAAAAATAATCATATAAAAATA
*** *
9568 GTTTAATTTTAA-AATATAAAAAT-
1 GTTTAAAAATAATCATATAAAAATA
* ** * * * * *
9591 -TTTAAACTCATTTTTATTTTAAACTT
1 GTTTAAA--AATAATCATATAAAAATA
9617 GTTTAAAAATAATCATATAAAAATA
1 GTTTAAAAATAATCATATAAAAATA
9642 GTTTAA
1 GTTTAA
9648 TTTTAAAATA
Statistics
Matches: 54, Mismatches: 21, Indels: 10
0.64 0.25 0.12
Matches are distributed among these distances:
22 5 0.09
24 11 0.20
25 32 0.59
27 6 0.11
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (25 bp):
GTTTAAAAATAATCATATAAAAATA
Found at i:9624 original size:74 final size:75
Alignment explanation
Indices: 9534--9689 Score: 305
Period size: 74 Copynumber: 2.1 Consensus size: 75
9524 ACATGTCTAA
9534 TTTAAACTTGTTTAAAAATAATCATATAAAAATAGTTTAATTTTAAAATATAAAAATTTTAAACT
1 TTTAAACTTGTTTAAAAATAATCATATAAAAATAGTTTAATTTTAAAATATAAAAATTTTAAACT
9599 CATTTTTA-T
66 CATTTTTATT
9608 TTTAAACTTGTTTAAAAATAATCATATAAAAATAGTTTAATTTTAAAATATAAAAATTTTAAACT
1 TTTAAACTTGTTTAAAAATAATCATATAAAAATAGTTTAATTTTAAAATATAAAAATTTTAAACT
9673 CATTTTTATT
66 CATTTTTATT
9683 TTTAAAC
1 TTTAAAC
9690 CTTGCATTAA
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 73 0.90
75 8 0.10
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.45
Consensus pattern (75 bp):
TTTAAACTTGTTTAAAAATAATCATATAAAAATAGTTTAATTTTAAAATATAAAAATTTTAAACT
CATTTTTATT
Found at i:15666 original size:23 final size:23
Alignment explanation
Indices: 15634--15679 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
15624 ATCTGTTTTG
*
15634 CCTCCCTAAAATTGTATAAGTTC
1 CCTCCATAAAATTGTATAAGTTC
*
15657 CCTCCATAAAATTTTATAAGTTC
1 CCTCCATAAAATTGTATAAGTTC
15680 ATTCCTAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.37
Consensus pattern (23 bp):
CCTCCATAAAATTGTATAAGTTC
Found at i:17607 original size:29 final size:28
Alignment explanation
Indices: 17575--17632 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
17565 TTAGGAGTTA
* * *
17575 TATCATTTATACTATTAAACTTTTAATTT
1 TATCAATTATAATACTAAAC-TTTAATTT
17604 TATCAATTATAATACTAAACTTTAATTT
1 TATCAATTATAATACTAAACTTTAATTT
17632 T
1 T
17633 CTTTTCAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (28 bp):
TATCAATTATAATACTAAACTTTAATTT
Found at i:18695 original size:40 final size:39
Alignment explanation
Indices: 18607--18695 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 39
18597 TTTATAAATT
*
18607 TAATATTAATAAAATATTTTAATATCATTTTAATCAAAA
1 TAATATTATTAAAATATTTTAATATCATTTTAATCAAAA
* * *
18646 TATTAATTATTAAAATATATTTATTAAT-ATTTCTAAT-AATA
1 TAAT-ATTATTAAAATAT-TTTAAT-ATCATTT-TAATCAAAA
18687 TAATATTAT
1 TAATATTAT
18696 ATATTATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
39 3 0.07
40 17 0.41
41 15 0.37
42 6 0.15
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (39 bp):
TAATATTATTAAAATATTTTAATATCATTTTAATCAAAA
Found at i:18807 original size:19 final size:18
Alignment explanation
Indices: 18783--18851 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
18773 ATATTATTAA
18783 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
18802 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
18820 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
18842 ATT-TTAATAA
1 ATTATTAATAA
18852 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:18872 original size:23 final size:23
Alignment explanation
Indices: 18846--18890 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
18836 AATAATATTT
18846 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
18869 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
18891 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:19017 original size:19 final size:20
Alignment explanation
Indices: 18985--19023 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
18975 TAATAAAATT
18985 ATAAAAAAAATA-TTTAATA
1 ATAAAAAAAATATTTTAATA
* *
19004 ATAAATAAATTATTTTAATA
1 ATAAAAAAAATATTTTAATA
19024 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAAAAAAATATTTTAATA
Found at i:19239 original size:15 final size:14
Alignment explanation
Indices: 19199--19239 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
19189 AAATGTAATT
*
19199 CATTTTACGAAAAA
1 CATTTTCCGAAAAA
19213 CATTTTCCGAAAAA
1 CATTTTCCGAAAAA
*
19227 CGTTTTCCAGAAA
1 CATTTTCC-GAAA
19240 TATAATTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (14 bp):
CATTTTCCGAAAAA
Found at i:19262 original size:14 final size:14
Alignment explanation
Indices: 19243--19272 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19233 CCAGAAATAT
*
19243 AATTCATTTTCCAG
1 AATTCAATTTCCAG
19257 AATTCAATTTCCAG
1 AATTCAATTTCCAG
19271 AA
1 AA
19273 AACCAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:23731 original size:25 final size:25
Alignment explanation
Indices: 23710--23766 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
23700 ATAATATTTT
23710 ATATTTTATATTAATTATATATATA
1 ATATTTTATATTAATTATATATATA
*
23735 ATATTTTATATTAATTATATATAAA
1 ATATTTTATATTAATTATATATATA
23760 ATATTTT
1 ATATTTT
23767 CGGGTTCGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATATTTTATATTAATTATATATATA
Found at i:24357 original size:6 final size:6
Alignment explanation
Indices: 24346--24383 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
24336 CAATCATGTA
*
24346 ATTAAT ATTAAT ATTAAT ATTATT ATT-AT ATTAAT ATT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATT
24384 TGGGGTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
ATTAAT
Found at i:28846 original size:30 final size:31
Alignment explanation
Indices: 28812--28887 Score: 136
Period size: 30 Copynumber: 2.5 Consensus size: 31
28802 AGTAAAATTA
*
28812 AAAGTTTAGTAGTATAAACGATAT-ATACCT
1 AAAGTTCAGTAGTATAAACGATATAATACCT
28842 AAAGTTCAGTAGTATAAACGATATAATACCT
1 AAAGTTCAGTAGTATAAACGATATAATACCT
28873 AAAGTTCAGTAGTAT
1 AAAGTTCAGTAGTAT
28888 CTGACGCAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 23 0.52
31 21 0.48
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (31 bp):
AAAGTTCAGTAGTATAAACGATATAATACCT
Found at i:33873 original size:16 final size:16
Alignment explanation
Indices: 33852--33893 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
33842 CACTGCACTG
33852 AGAACCGCATGAGACT
1 AGAACCGCATGAGACT
33868 AGAACCGCATGAGACT
1 AGAACCGCATGAGACT
33884 AGAACCGCAT
1 AGAACCGCAT
33894 ACAGTTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (16 bp):
AGAACCGCATGAGACT
Found at i:37968 original size:30 final size:29
Alignment explanation
Indices: 37932--38014 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
37922 TGATATATAT
* * *
37932 AACTTTTCAAAATTATATTTTTGGTCCTTA
1 AACTTTTCAAAATTATATTTTAGCTAC-TA
* *
37962 AACTTTTCAAAGTTTATACTTTAGCTACTA
1 AACTTTTCAAA-ATTATATTTTAGCTACTA
37992 AAC-TTTCAAAACTTATATTTTAG
1 AACTTTTCAAAA-TTATATTTTAG
38015 TCACTAGCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 17 0.39
30 16 0.36
31 11 0.25
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (29 bp):
AACTTTTCAAAATTATATTTTAGCTACTA
Found at i:48710 original size:16 final size:16
Alignment explanation
Indices: 48689--48721 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48679 TTTTATTATT
48689 ATTTAA-TATAATAATA
1 ATTTAATTATAA-AATA
48705 ATTTAATTATAAAATA
1 ATTTAATTATAAAATA
48721 A
1 A
48722 AAATAGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAATTATAAAATA
Found at i:53136 original size:11 final size:13
Alignment explanation
Indices: 53104--53133 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
53094 TTATTATATG
*
53104 TAAACGTATATAA
1 TAAACATATATAA
53117 TAAACATATATAA
1 TAAACATATATAA
53130 TAAA
1 TAAA
53134 TATCACTCAG
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:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (13 bp):
TAAACATATATAA
Found at i:53787 original size:83 final size:82
Alignment explanation
Indices: 53480--53828 Score: 281
Period size: 83 Copynumber: 4.0 Consensus size: 82
53470 CTCGAACTTG
* *
53480 TTTTAC-TCTACTACTCTTCCGTGAAGTTCTCATACTTTGCTGAAAAATCTATTCCACTACTCTT
1 TTTTACTTC-ACTACTCTTCCGTGAAGTT-TGATAATTTGCTGAAAAATCTATTCCACTACTCTT
* *
53544 TCGTGGAGTTCAGATTTGC
64 TCATGGAGTTCAAATTTGC
* * * * * *
53563 TTTTACTTCATTACTTTTTCATGAAGTTTGAAAATGATTAACTTGACAAGAATCTAAGGTT-CAC
1 TTTTACTTCACTACTCTTCCGTGAAGTTTGATAAT--TT-GC-TGA-AA-AATCT-A--TTCCAC
* ** * *
53627 TACTCTTCTGTGAATATTAGATTCAAAATTGA
57 TACTC-T-T-T-CAT-GGAG-TTCAAATTTGC
* * * *
53659 ATTTGCTTCCATTACTCTTCCGTGGAA-TTTGATACTTTGCTGAAAAATCTATTCCACTACTCTT
1 TTTTACTT-CACTACTCTTCCGT-GAAGTTTGATAATTTGCTGAAAAATCTATTCCACTACTCTT
*
53723 TTATGGAGTTCAAATTTGC
64 TCATGGAGTTCAAATTTGC
* *
53742 TTTTACTTCACTACTCTTCCGTGAAGATTTTATAATTTGCTGAAAAATCTGTTCCACTACTCTTT
1 TTTTACTTCACTACTCTTCCGTGAAG-TTTGATAATTTGCTGAAAAATCTATTCCACTACTCTTT
* *
53807 CGTGGAGTTCAGATTTGC
65 CATGGAGTTCAAATTTGC
53825 TTTT
1 TTTT
53829 GTGTTTGCTT
Statistics
Matches: 208, Mismatches: 37, Indels: 42
0.72 0.13 0.15
Matches are distributed among these distances:
81 3 0.01
82 17 0.08
83 90 0.43
84 6 0.03
85 3 0.01
86 4 0.02
87 3 0.01
88 8 0.04
89 9 0.04
90 9 0.04
91 8 0.04
92 3 0.01
93 4 0.02
94 2 0.01
95 4 0.02
96 14 0.07
97 18 0.09
98 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (82 bp):
TTTTACTTCACTACTCTTCCGTGAAGTTTGATAATTTGCTGAAAAATCTATTCCACTACTCTTTC
ATGGAGTTCAAATTTGC
Found at i:54395 original size:22 final size:22
Alignment explanation
Indices: 54370--54415 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
54360 AAAGCTTTCG
* *
54370 TCTTTGAAAAGAGAATCTATCA
1 TCTTTAAAAAGAGAATCCATCA
*
54392 TCTTTAAAAATAGAATCCATCA
1 TCTTTAAAAAGAGAATCCATCA
54414 TC
1 TC
54416 CTTGCAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (22 bp):
TCTTTAAAAAGAGAATCCATCA
Found at i:55962 original size:17 final size:17
Alignment explanation
Indices: 55940--55975 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
55930 CTCCATTTCA
55940 ATTCTCTAAAATCTTTG
1 ATTCTCTAAAATCTTTG
55957 ATTCTCTAAAATCTTTG
1 ATTCTCTAAAATCTTTG
55974 AT
1 AT
55976 CCTATTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (17 bp):
ATTCTCTAAAATCTTTG
Found at i:58848 original size:24 final size:24
Alignment explanation
Indices: 58821--58871 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
58811 TGGTGGTTGA
*
58821 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
58845 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
58869 TTT
1 TTT
58872 GTTCTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.61
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:59358 original size:11 final size:11
Alignment explanation
Indices: 59342--59381 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
59332 AGGATTATTT
59342 TATTTTCATTC
1 TATTTTCATTC
* *
59353 TATTTTCTTTT
1 TATTTTCATTC
*
59364 TATTTACATTC
1 TATTTTCATTC
59375 TATTTTC
1 TATTTTC
59382 TTTTATTTAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTTTCATTC
Found at i:59387 original size:21 final size:22
Alignment explanation
Indices: 59339--59391 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
59329 GTGAGGATTA
*
59339 TTTTATTTTCATTCTATTTTCT
1 TTTTATTTACATTCTATTTTCT
59361 TTTTATTTACATTCTATTTTC-
1 TTTTATTTACATTCTATTTTCT
59382 TTTTATTTAC
1 TTTTATTTAC
59392 TGTTTTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTATTTACATTCTATTTTCT
Found at i:59862 original size:16 final size:16
Alignment explanation
Indices: 59841--59871 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59831 AAAAACAGTA
59841 AATAAAAAGAAAATAG
1 AATAAAAAGAAAATAG
*
59857 AATAAAAATAAAATA
1 AATAAAAAGAAAATA
59872 ATCCTACGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (16 bp):
AATAAAAAGAAAATAG
Found at i:60360 original size:23 final size:23
Alignment explanation
Indices: 60334--60382 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
60324 ATAAAGAACC
*
60334 AAAATAAACTT-AAATATACCATT
1 AAAATAAACTTCAAACA-ACCATT
*
60357 AAAATAAAGTTCAAACAACCATT
1 AAAATAAACTTCAAACAACCATT
60380 AAA
1 AAA
60383 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.24
Consensus pattern (23 bp):
AAAATAAACTTCAAACAACCATT
Done.