Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002146.1 Hibiscus syriacus cultivar Beakdansim tig00004385_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: 60365
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4306 original size:18 final size:18
Alignment explanation
Indices: 4279--4317 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
4269 CTATTTAGTG
4279 AAAAAAATAA-AATTAAA
1 AAAAAAATAACAATTAAA
*
4296 AAAAGAAATAACGATTAAA
1 AAAA-AAATAACAATTAAA
4315 AAA
1 AAA
4318 TTACAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 6 0.32
19 9 0.47
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAAAATAACAATTAAA
Found at i:5329 original size:35 final size:36
Alignment explanation
Indices: 5265--5371 Score: 198
Period size: 36 Copynumber: 3.0 Consensus size: 36
5255 TAATTGAGTT
*
5265 TGACCATGGAGATGAAGACACGATAAGATTAAATGA
1 TGACCATGGAGATGAAGACACGATGAGATTAAATGA
5301 TGACCATGGAGATG-AGACACGATGAGATTAAATGA
1 TGACCATGGAGATGAAGACACGATGAGATTAAATGA
5336 TGACCATGGAGATGAAGACACGATGAGATTAAATGA
1 TGACCATGGAGATGAAGACACGATGAGATTAAATGA
5372 CAAAGCTGTT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
35 34 0.49
36 35 0.51
ACGTcount: A:0.42, C:0.11, G:0.27, T:0.20
Consensus pattern (36 bp):
TGACCATGGAGATGAAGACACGATGAGATTAAATGA
Found at i:5347 original size:20 final size:20
Alignment explanation
Indices: 5290--5348 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
5280 AGACACGATA
5290 AGATTAAATGATGACCATGG
1 AGATTAAATGATGACCATGG
* * *
5310 AGA-T-GA-GA-CACGAT-G
1 AGATTAAATGATGACCATGG
5325 AGATTAAATGATGACCATGG
1 AGATTAAATGATGACCATGG
5345 AGAT
1 AGAT
5349 GAAGACACGA
Statistics
Matches: 28, Mismatches: 6, Indels: 10
0.64 0.14 0.23
Matches are distributed among these distances:
15 4 0.14
16 5 0.18
17 3 0.11
18 3 0.11
19 5 0.18
20 8 0.29
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.22
Consensus pattern (20 bp):
AGATTAAATGATGACCATGG
Found at i:14512 original size:21 final size:21
Alignment explanation
Indices: 14487--14531 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
14477 AAAATTATTA
*
14487 AAAAATATTAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
14508 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
14529 AAA
1 AAA
14532 TTTTTATCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:15497 original size:22 final size:20
Alignment explanation
Indices: 15472--15517 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
15462 CATGATGTTG
15472 TATTCTTAAAATATTGTATTAA
1 TATT-TTAAAATATT-TATTAA
*
15494 TA-TTTAAAATATTTATTAT
1 TATTTTAAAATATTTATTAA
15513 TATTT
1 TATTT
15518 GAGGTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 7 0.32
20 12 0.55
21 1 0.05
22 2 0.09
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTTTAAAATATTTATTAA
Found at i:15516 original size:19 final size:20
Alignment explanation
Indices: 15477--15517 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
15467 TGTTGTATTC
15477 TTAAAATATTGTATTAATAT
1 TTAAAATATTGTATTAATAT
*
15497 TTAAAATATT-TATTATTAT
1 TTAAAATATTGTATTAATAT
15516 TT
1 TT
15518 GAGGTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAAAATATTGTATTAATAT
Found at i:15888 original size:17 final size:17
Alignment explanation
Indices: 15832--15882 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
15822 ACGTTTTCCG
15832 AAAAATAT-TTTTCGTAA
1 AAAAATATATTTTC-TAA
15849 AATAAATTATATTTTCTAA
1 AA-AAA-TATATTTTCTAA
15868 AAAAATATATTTTCT
1 AAAAATATATTTTCT
15883 GGAAAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 12 0.39
18 6 0.19
19 8 0.26
20 5 0.16
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (17 bp):
AAAAATATATTTTCTAA
Found at i:15888 original size:19 final size:18
Alignment explanation
Indices: 15832--15888 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
15822 ACGTTTTCCG
15832 AAAAATAT-TTTTC-GTAA
1 AAAAATATATTTTCTG-AA
15849 AATAAATTATATTTTCT-AA
1 AA-AAA-TATATTTTCTGAA
*
15868 AAAAATATATTTTCTGGA
1 AAAAATATATTTTCTGAA
15886 AAA
1 AAA
15889 TGTTTTACGA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
17 12 0.35
18 10 0.29
19 7 0.21
20 5 0.15
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (18 bp):
AAAAATATATTTTCTGAA
Found at i:16050 original size:17 final size:18
Alignment explanation
Indices: 16030--16067 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
16020 ATTTTTAAAA
16030 TATTAAAATAAT-TTTTT
1 TATTAAAATAATATTTTT
**
16047 TATTATTATAATATTTTT
1 TATTAAAATAATATTTTT
16065 TAT
1 TAT
16068 AATTTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTAAAATAATATTTTT
Found at i:16075 original size:20 final size:21
Alignment explanation
Indices: 16021--16075 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
16011 ATTATTATTA
* * *
16021 TTTTTAAAATATTAAAATAAT
1 TTTTTATAATTTTATAATAAT
16042 TTTTT-T-ATTATTATAAT-AT
1 TTTTTATAATT-TTATAATAAT
16061 TTTTTATAATTTTAT
1 TTTTTATAATTTTAT
16076 TAAAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 9 0.32
20 11 0.39
21 8 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTATAATTTTATAATAAT
Found at i:16390 original size:35 final size:35
Alignment explanation
Indices: 16343--16428 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
16333 AAAACAGTCA
* * *
16343 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
16378 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
16413 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
16429 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:16422 original size:21 final size:21
Alignment explanation
Indices: 16397--16439 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
16387 TTCTAAACCC
16397 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
16418 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
16439 T
1 T
16440 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:16590 original size:16 final size:18
Alignment explanation
Indices: 16558--16591 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
16548 TATTAATGTA
16558 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
16576 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
16592 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:23327 original size:21 final size:22
Alignment explanation
Indices: 23303--23385 Score: 89
Period size: 21 Copynumber: 3.8 Consensus size: 22
23293 TTGGTGCAGA
*
23303 GGGAATCGATTCCCCCCTTGA-
1 GGGAACCGATTCCCCCCTTGAG
*
23324 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTG-AG
**
23347 GGGAACCGATTCCCCCC-ACAG
1 GGGAACCGATTCCCCCCTTGAG
* *
23368 GGGAATCGATACCCCCCT
1 GGGAACCGATTCCCCCCT
23386 GGGGTTCTGC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
21 35 0.67
22 1 0.02
23 16 0.31
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTTGAG
Found at i:23354 original size:23 final size:21
Alignment explanation
Indices: 23301--23363 Score: 90
Period size: 21 Copynumber: 2.9 Consensus size: 21
23291 TTTTGGTGCA
*
23301 GAGGGAATCGATTCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
23322 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
23343 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
23364 ACAGGGGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 20 0.54
22 1 0.03
23 16 0.43
ACGTcount: A:0.21, C:0.35, G:0.25, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:27687 original size:19 final size:18
Alignment explanation
Indices: 27625--27687 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
27615 ACCCTAAAAA
*
27625 TATTATAAAATATATTAAT
1 TATT-TAAAAAATATTAAT
* * * *
27644 TATTTAGTAAACTAATAAA
1 TATTTA-AAAAATATTAAT
27663 TATTTAAAAAATATTAAT
1 TATTTAAAAAATATTAAT
27681 TAGTTTA
1 TA-TTTA
27688 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
18 12 0.36
19 21 0.64
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (18 bp):
TATTTAAAAAATATTAAT
Found at i:27865 original size:23 final size:23
Alignment explanation
Indices: 27835--27917 Score: 82
Period size: 23 Copynumber: 3.6 Consensus size: 23
27825 TTAAAATAAA
*
27835 AATATAATATCTTATATTATTAT
1 AATATAATATATTATATTATTAT
*
27858 AATATAAT-TGATTATTTTATTAT
1 AATATAATAT-ATTATATTATTAT
*
27881 AATATAAAAATATTATATTA-TATT
1 AATAT-AATATATTATATTATTA-T
*
27905 ATTATAA-ATATTA
1 AATATAATATATTA
27918 ATAAATATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
22 7 0.14
23 28 0.55
24 15 0.29
25 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:27902 original size:52 final size:53
Alignment explanation
Indices: 27807--27911 Score: 144
Period size: 52 Copynumber: 2.0 Consensus size: 53
27797 CATTTTATTA
* *
27807 ATAATTTATTATATATTATTAAAATAAAAATATAATATCTTATATTATTATAAT
1 ATAATTGATTATATATTATTAAAATAAAAATAT-ATATATTATATTATTATAAT
27861 ATAATTGATTAT-T-TTATTATAATATAAAAATAT-TATATTATATTATTATAA
1 ATAATTGATTATATATTATTA-AA-ATAAAAATATATATATTATATTATTATAA
27912 ATATTAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
52 23 0.49
53 3 0.06
54 21 0.45
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (53 bp):
ATAATTGATTATATATTATTAAAATAAAAATATATATATTATATTATTATAAT
Found at i:27931 original size:29 final size:29
Alignment explanation
Indices: 27818--27926 Score: 90
Period size: 29 Copynumber: 3.9 Consensus size: 29
27808 TAATTTATTA
*
27818 TATATTATTA-AA-ATAAAAATATAATATCT
1 TATATTATTATAATATAAAAATAT--TATAT
*
27847 TATATTATTATAATAT----A-ATT-GAT
1 TATATTATTATAATATAAAAATATTATAT
*
27870 TATTTTATTATAATATAAAAATATTATAT
1 TATATTATTATAATATAAAAATATTATAT
27899 TATATTATTATAAATATTAATAAATATT
1 TATATTATTAT-AATA-TAA-AAATATT
27927 TTATAAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 19
0.73 0.06 0.22
Matches are distributed among these distances:
23 16 0.25
24 1 0.02
26 2 0.03
27 2 0.03
28 3 0.05
29 22 0.34
30 6 0.09
31 5 0.08
32 7 0.11
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
TATATTATTATAATATAAAAATATTATAT
Found at i:27938 original size:11 final size:11
Alignment explanation
Indices: 27900--27940 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
27890 ATATTATATT
27900 ATATTATTATAA
1 ATATT-TTATAA
*
27912 ATA-TTAATAA
1 ATATTTTATAA
27922 ATATTTTATAA
1 ATATTTTATAA
27933 ATATTTTA
1 ATATTTTA
27941 ATAATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 8 0.31
11 15 0.58
12 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATTTTATAA
Found at i:37694 original size:13 final size:13
Alignment explanation
Indices: 37676--37734 Score: 72
Period size: 13 Copynumber: 4.7 Consensus size: 13
37666 TTTTTTTTGT
37676 GTTTATGTTGTTC
1 GTTTATGTTGTTC
37689 GTTTAT-TGTGTTC
1 GTTTATGT-TGTTC
37702 GTTTATGTTTGTTC
1 GTTTATG-TTGTTC
37716 G-TT-TG-TGTTC
1 GTTTATGTTGTTC
37726 GTTTATGTT
1 GTTTATGTT
37735 CATTCATTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
10 6 0.15
11 2 0.05
12 5 0.12
13 20 0.50
14 6 0.15
15 1 0.03
ACGTcount: A:0.07, C:0.07, G:0.24, T:0.63
Consensus pattern (13 bp):
GTTTATGTTGTTC
Found at i:37726 original size:24 final size:24
Alignment explanation
Indices: 37676--37755 Score: 99
Period size: 24 Copynumber: 3.2 Consensus size: 24
37666 TTTTTTTTGT
37676 GTTTATG-TTGTTCGTTTATTGTGTTC
1 GTTTATGTTTGTTCG--T-TTGTGTTC
37702 GTTTATGTTTGTTCGTTTGTGTTC
1 GTTTATGTTTGTTCGTTTGTGTTC
** *
37726 GTTTATGTTCATTCATTTGTGTTC
1 GTTTATGTTTGTTCGTTTGTGTTC
37750 GTTTAT
1 GTTTAT
37756 TTATTAAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
24 35 0.70
25 1 0.02
26 7 0.14
27 7 0.14
ACGTcount: A:0.09, C:0.09, G:0.21, T:0.61
Consensus pattern (24 bp):
GTTTATGTTTGTTCGTTTGTGTTC
Found at i:37757 original size:14 final size:14
Alignment explanation
Indices: 37684--37757 Score: 51
Period size: 14 Copynumber: 5.9 Consensus size: 14
37674 GTGTTTATGT
37684 TGTTCGTTTA-TTG
1 TGTTCGTTTATTTG
37697 TGTTCGTTTATGTT-
1 TGTTCGTTTAT-TTG
37711 TGTTCG----TTTG
1 TGTTCGTTTATTTG
37721 TGTTCGTTTA----
1 TGTTCGTTTATTTG
* *
37731 TGTTCATTCATTTG
1 TGTTCGTTTATTTG
37745 TGTTCGTTTATTT
1 TGTTCGTTTATTT
37758 ATTAAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 21
0.65 0.06 0.30
Matches are distributed among these distances:
9 2 0.04
10 15 0.33
13 10 0.22
14 17 0.37
15 2 0.04
ACGTcount: A:0.08, C:0.09, G:0.20, T:0.62
Consensus pattern (14 bp):
TGTTCGTTTATTTG
Found at i:38060 original size:33 final size:33
Alignment explanation
Indices: 38023--38288 Score: 217
Period size: 33 Copynumber: 7.8 Consensus size: 33
38013 GAAGAGCCGC
* *
38023 CTTGATTGGCAGAAACATTGCGAGGAGAACCAA
1 CTTGAATGGCAGAAACATTGCGAGGAGAACCTA
* *
38056 CTTGATTGGCAGAAACATTGCGAGGAGAAAAAGGAGAACCTC
1 CTTGAATGGCAGAAACATTGC-----G----AGGAGAACCTA
** * * *
38098 CTCAAATGGAAGAAACATTGCAAGGAGAACCTC
1 CTTGAATGGCAGAAACATTGCGAGGAGAACCTA
* ** *
38131 CTCGAATGGCAGAAACATTGAAAGGAGAACCTC
1 CTTGAATGGCAGAAACATTGCGAGGAGAACCTA
* * * *
38164 CTCGAATGGAAGTAACAATGCGAGGAGAACCTA
1 CTTGAATGGCAGAAACATTGCGAGGAGAACCTA
* * *
38197 CTTGATTGGCAGTAACAATGCGAGGAGAACCTA
1 CTTGAATGGCAGAAACATTGCGAGGAGAACCTA
* *
38230 CTTGAATGACAGAAACATTGCGAGGAGAACCCA
1 CTTGAATGGCAGAAACATTGCGAGGAGAACCTA
* * * *
38263 GTTGAAGGGAAGCAACATTGCGAGGA
1 CTTGAATGGCAGAAACATTGCGAGGA
38289 CGGAGAGGAG
Statistics
Matches: 195, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
33 168 0.86
38 1 0.01
42 26 0.13
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (33 bp):
CTTGAATGGCAGAAACATTGCGAGGAGAACCTA
Found at i:38343 original size:75 final size:75
Alignment explanation
Indices: 38218--38356 Score: 199
Period size: 75 Copynumber: 1.9 Consensus size: 75
38208 GTAACAATGC
* * * * *
38218 GAGGAGAACCTACTTGAATGACAGAAACATTGCGAGGAGAACCCAGTTGAAGGGAAGCAACATTG
1 GAGGAGAACCTACTTGAATGAAAGAAACATTGCAAGAAGAACCCACTTGAAGGGAAGAAACATTG
38283 CGAGGACGGA
66 CGAGGACGGA
* *
38293 GAGGAGAACCTTCTTGAATGAAAGAAACATTGCAAGAAGAACCGC-CTTGAATGGAAGAAACATT
1 GAGGAGAACCTACTTGAATGAAAGAAACATTGCAAGAAGAACC-CACTTGAAGGGAAGAAACATT
38357 ACCAAGGAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 55 0.98
76 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.28, T:0.16
Consensus pattern (75 bp):
GAGGAGAACCTACTTGAATGAAAGAAACATTGCAAGAAGAACCCACTTGAAGGGAAGAAACATTG
CGAGGACGGA
Found at i:51083 original size:23 final size:23
Alignment explanation
Indices: 51057--51113 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
51047 GTGCCCATTT
*
51057 GTTTAGCATTTGTAAACAAATTC
1 GTTTAACATTTGTAAACAAATTC
* * *
51080 GTTTAACGTTCGTAAACATATTC
1 GTTTAACATTTGTAAACAAATTC
*
51103 ATTTAACATTT
1 GTTTAACATTT
51114 ACGTACATGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (23 bp):
GTTTAACATTTGTAAACAAATTC
Found at i:51426 original size:27 final size:28
Alignment explanation
Indices: 51373--51427 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
51363 TTCAACTTTT
* **
51373 TATTCAATTATTATAAATTTTTTAATCA
1 TATTCAATTATTATAAATTATCAAATCA
*
51401 TATTCATTTATT-TAAATTATCAAATCA
1 TATTCAATTATTATAAATTATCAAATCA
51428 ACGTAAACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (28 bp):
TATTCAATTATTATAAATTATCAAATCA
Found at i:59825 original size:14 final size:14
Alignment explanation
Indices: 59790--59828 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
59780 CGATTAATTC
* *
59790 TATGTTCATTCGTT
1 TATGTTCGTTTGTT
59804 TATGTTCGTTTGTT
1 TATGTTCGTTTGTT
59818 TATGTTCGTTT
1 TATGTTCGTTT
59829 ATATTCATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.10, C:0.10, G:0.18, T:0.62
Consensus pattern (14 bp):
TATGTTCGTTTGTT
Found at i:59825 original size:24 final size:24
Alignment explanation
Indices: 59798--59854 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
59788 TCTATGTTCA
* * *
59798 TTCGTTTATGTTCGTTTGTTTATG
1 TTCGTTTATATTCATTCGTTTATG
*
59822 TTCGTTTATATTCATTCGTTTGTG
1 TTCGTTTATATTCATTCGTTTATG
*
59846 CTCGTTTAT
1 TTCGTTTAT
59855 CATTTTAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.11, C:0.12, G:0.18, T:0.60
Consensus pattern (24 bp):
TTCGTTTATATTCATTCGTTTATG
Done.