Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004877.1 Hibiscus syriacus cultivar Beakdansim tig00010991_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: 95190
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4593 original size:18 final size:19
Alignment explanation
Indices: 4552--4590 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4542 ATCCCTTTCT
4552 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTCTTA
4571 TTATTTC-TTTCATTACTTA
1 TTATTTCATTTCATT-CTTA
4590 T
1 T
4591 ATTATTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTCATTTCATTCTTA
Found at i:9295 original size:35 final size:36
Alignment explanation
Indices: 9248--9315 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
9238 ATTTAGAAGT
9248 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
9283 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
9316 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:11658 original size:36 final size:36
Alignment explanation
Indices: 11611--11715 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
11601 GATACAATCT
11611 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
11647 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
11683 TTCCATCATCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
11716 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:16679 original size:33 final size:33
Alignment explanation
Indices: 16617--16684 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
16607 GCAAAAATTA
*
16617 AAGAAAGAAATGATTAAAATAGAATATGAA-AG
1 AAGAAAGAAATGATTAAAAAAGAATATGAATAG
16649 AAGAAAGGAAATGA-TAAGAAAAGGAA-ATGAATAG
1 AAGAAA-GAAATGATTAA-AAAA-GAATATGAATAG
16683 AA
1 AA
16685 ATGTTATCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
32 9 0.29
33 15 0.48
34 7 0.23
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAAAAGAATATGAATAG
Found at i:16873 original size:35 final size:36
Alignment explanation
Indices: 16826--16893 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
16816 ATTTAGAAGT
* *
16826 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAAGCGTGATAATGGCGATGGAATA
*
16861 TGGTGATGATATAAGCGTGATAATGGCGATGGA
1 TGGTGATAATATAAGCGTGATAATGGCGATGGA
16894 CAGATTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.29
Consensus pattern (36 bp):
TGGTGATAATATAAGCGTGATAATGGCGATGGAATA
Found at i:17574 original size:15 final size:15
Alignment explanation
Indices: 17556--17599 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
17546 ATTAAGAAAG
17556 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
17571 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
*
17586 GAAATGGATAGAAT
1 GAAATGGAAAGAAT
17600 AGTTATCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.52, C:0.00, G:0.27, T:0.20
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:17814 original size:36 final size:36
Alignment explanation
Indices: 17741--17841 Score: 168
Period size: 36 Copynumber: 2.8 Consensus size: 36
17731 ATTTATAAGT
* *
17741 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATAGAATA
*
17776 TGGTGATGATATAGGCGTGATAATGGTGATAGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATAGAATA
17812 TGGTGATGATATAGGCGTGATAATGGTGAT
1 TGGTGATGATATAGGCGTGATAATGGTGAT
17842 GGACAGATTC
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
35 20 0.32
36 42 0.68
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATAGAATA
Found at i:18234 original size:19 final size:20
Alignment explanation
Indices: 18187--18237 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
18177 GAAACCCCTT
**
18187 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
18207 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
18226 TGAAGATACATG
1 TGAAAATACATG
18238 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:20996 original size:15 final size:15
Alignment explanation
Indices: 20946--20997 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
20936 AAGATATGGT
* *
20946 AATGAAATAAGAAAA
1 AATGAAATGATAAAA
*
20961 GATGAAA-GAATAAAGA
1 AATGAAATG-ATAAA-A
20977 AATGAAATGATAAAA
1 AATGAAATGATAAAA
20992 AATGAA
1 AATGAA
20998 GATAACTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 17 0.57
16 12 0.40
17 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (15 bp):
AATGAAATGATAAAA
Found at i:21644 original size:13 final size:12
Alignment explanation
Indices: 21625--21710 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
21615 ATATAGGCGT
21625 GATATGGTGATG
1 GATATGGTGATG
21637 GAATATGGTGAT-
1 G-ATATGGTGATG
*
21649 GATATAGGCG-T-
1 GATAT-GGTGATG
21660 GATAATGGTGATG
1 GAT-ATGGTGATG
21673 GACTATGGTGAT-
1 GA-TATGGTGATG
*
21685 GATATAGGCG-T-
1 GATAT-GGTGATG
21696 GATAATGGTGATG
1 GAT-ATGGTGATG
21709 GA
1 GA
21711 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:21680 original size:36 final size:36
Alignment explanation
Indices: 21607--21711 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
21597 ATTTATAAGT
* *
21607 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
21642 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
21678 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
21712 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:23299 original size:12 final size:12
Alignment explanation
Indices: 23282--23310 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
23272 GCGGCATAGG
23282 GGCTTATGGTGT
1 GGCTTATGGTGT
23294 GGCTTATGGTGT
1 GGCTTATGGTGT
23306 GGCTT
1 GGCTT
23311 CTTCTTGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.10, G:0.41, T:0.41
Consensus pattern (12 bp):
GGCTTATGGTGT
Found at i:23873 original size:8 final size:8
Alignment explanation
Indices: 23860--23886 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
23850 TAAGTAATAT
23860 AATGTATA
1 AATGTATA
23868 AATGTATA
1 AATGTATA
23876 AATGTATA
1 AATGTATA
23884 AAT
1 AAT
23887 ATGTGGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (8 bp):
AATGTATA
Found at i:24868 original size:15 final size:16
Alignment explanation
Indices: 24840--24870 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
24830 GGGGATAATA
24840 ATATAAGTAATGAAAT
1 ATATAAGTAATGAAAT
24856 ATATAAG-AATGAAAT
1 ATATAAGTAATGAAAT
24871 GAAATAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (16 bp):
ATATAAGTAATGAAAT
Found at i:24877 original size:16 final size:16
Alignment explanation
Indices: 24836--24877 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
24826 TAAAGGGGAT
24836 AATAATATAAGTAATGA
1 AATAA-ATAAGTAATGA
*
24853 AATATATAAG-AATGA
1 AATAAATAAGTAATGA
24868 AATGAAATAA
1 AAT-AAATAA
24878 AGAAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 8 0.36
16 10 0.45
17 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (16 bp):
AATAAATAAGTAATGA
Found at i:29114 original size:5 final size:5
Alignment explanation
Indices: 29104--29169 Score: 57
Period size: 5 Copynumber: 12.6 Consensus size: 5
29094 GAACTTCTCT
29104 TTTTC TTTTC TTTTC TTTTCC TGATTT- TTTTC TTCTT- TTTGTC TTTTTC
1 TTTTC TTTTC TTTTC TTTT-C T--TTTC TTTTC TT-TTC TTT-TC -TTTTC
29153 TTTTC TTTT- TTTTC TTT
1 TTTTC TTTTC TTTTC TTT
29170 GCACGCCAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
4 8 0.15
5 31 0.60
6 7 0.13
7 3 0.06
8 3 0.06
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:29117 original size:11 final size:11
Alignment explanation
Indices: 29101--29162 Score: 58
Period size: 11 Copynumber: 5.6 Consensus size: 11
29091 TTTGAACTTC
29101 TCTTTTTCTTT
1 TCTTTTTCTTT
29112 TC-TTTTCTTT
1 TCTTTTTCTTT
*
29122 TCCTGATTT-TTT
1 T-CT-TTTTCTTT
*
29134 TCTTCTTT-TTG
1 TCTT-TTTCTTT
29145 TCTTTTTCTTT
1 TCTTTTTCTTT
29156 TCTTTTT
1 TCTTTTT
29163 TTTCTTTGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 12 0.29
11 23 0.55
12 4 0.10
13 3 0.07
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:29137 original size:22 final size:19
Alignment explanation
Indices: 29109--29162 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
29099 TCTCTTTTTC
29109 TTTTCTTTTCTTTTCCTGAT-T
1 TTTTCTTTTCTTTT--TG-TCT
*
29130 TTTT-TCTTCTTTTTGTCT
1 TTTTCTTTTCTTTTTGTCT
29148 TTTTCTTTTCTTTTT
1 TTTTCTTTTCTTTTT
29163 TTTCTTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 1 0.03
18 7 0.24
19 9 0.31
20 8 0.28
21 4 0.14
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTCTTTTCTTTTTGTCT
Found at i:41559 original size:20 final size:18
Alignment explanation
Indices: 41536--41580 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 18
41526 ATCATTCACT
41536 TGCATACTATATGATTTTCA
1 TGCATAC-ATATG-TTTTCA
41556 TGCATAACATATGTTTTCA
1 TGCAT-ACATATGTTTTCA
41575 TGCATA
1 TGCATA
41581 TTATGGTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.04
19 11 0.46
20 10 0.42
21 2 0.08
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (18 bp):
TGCATACATATGTTTTCA
Found at i:42907 original size:18 final size:18
Alignment explanation
Indices: 42883--42921 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
42873 AAAAAAATTC
*
42883 AGAAAATAAGAAAAGAGAA
1 AGAAATTAA-AAAAGAGAA
*
42902 AGAAATTCAAAAAGAGAA
1 AGAAATTAAAAAAGAGAA
42920 AG
1 AG
42922 CAAGCCAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.69, C:0.03, G:0.21, T:0.08
Consensus pattern (18 bp):
AGAAATTAAAAAAGAGAA
Found at i:47282 original size:22 final size:20
Alignment explanation
Indices: 47257--47296 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
47247 ATGTTTGTTT
47257 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
47279 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
47297 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:47529 original size:15 final size:15
Alignment explanation
Indices: 47506--47541 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
47496 ACTAATATTC
* *
47506 TTATCATAATATATA
1 TTATAATAACATATA
47521 TTATAATAACATATA
1 TTATAATAACATATA
47536 TTATAA
1 TTATAA
47542 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:51534 original size:22 final size:20
Alignment explanation
Indices: 51509--51548 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
51499 ATGTTTGTTT
51509 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
51531 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
51549 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:51781 original size:15 final size:15
Alignment explanation
Indices: 51758--51793 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
51748 ACTAATATTC
* *
51758 TTATCATAATATATA
1 TTATAATAACATATA
51773 TTATAATAACATATA
1 TTATAATAACATATA
51788 TTATAA
1 TTATAA
51794 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:52499 original size:22 final size:21
Alignment explanation
Indices: 52460--52501 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
52450 CCATCTCCAT
52460 TTCATCATCAACAACATCATC
1 TTCATCATCAACAACATCATC
* *
52481 TTCATCCATCAAGACCATCAT
1 TTCAT-CATCAACAACATCAT
52502 TTCCGCAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.36, C:0.33, G:0.02, T:0.29
Consensus pattern (21 bp):
TTCATCATCAACAACATCATC
Found at i:55466 original size:13 final size:13
Alignment explanation
Indices: 55444--55473 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
55434 ACTAAACACC
55444 TTTC-ACATACCT
1 TTTCAACATACCT
55456 TTTCAACATACCT
1 TTTCAACATACCT
55469 TTTCA
1 TTTCA
55474 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:73284 original size:25 final size:25
Alignment explanation
Indices: 73254--73337 Score: 168
Period size: 25 Copynumber: 3.4 Consensus size: 25
73244 CCCACTTTGA
73254 TATCATTTCTATCCATTTCAATTCT
1 TATCATTTCTATCCATTTCAATTCT
73279 TATCATTTCTATCCATTTCAATTCT
1 TATCATTTCTATCCATTTCAATTCT
73304 TATCATTTCTATCCATTTCAATTCT
1 TATCATTTCTATCCATTTCAATTCT
73329 TATCATTTC
1 TATCATTTC
73338 CTTTCTTCTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (25 bp):
TATCATTTCTATCCATTTCAATTCT
Found at i:73285 original size:15 final size:15
Alignment explanation
Indices: 73267--73337 Score: 54
Period size: 15 Copynumber: 5.4 Consensus size: 15
73257 CATTTCTATC
73267 CATTTCAATTCTTAT
1 CATTTCAATTCTTAT
*
73282 CATTTCTA-TC----
1 CATTTCAATTCTTAT
73292 CATTTCAATTCTTAT
1 CATTTCAATTCTTAT
*
73307 CATTTCTA-TC----
1 CATTTCAATTCTTAT
73317 CATTTCAATTCTTAT
1 CATTTCAATTCTTAT
73332 CATTTC
1 CATTTC
73338 CTTTCTTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 20
0.64 0.06 0.30
Matches are distributed among these distances:
10 14 0.33
11 4 0.10
14 4 0.10
15 20 0.48
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (15 bp):
CATTTCAATTCTTAT
Found at i:73598 original size:6 final size:6
Alignment explanation
Indices: 73557--73600 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
73547 TACTGCAACA
*
73557 AAAAGAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
73601 CTACAACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:76510 original size:22 final size:22
Alignment explanation
Indices: 76484--76525 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
76474 TATTTATAGT
*
76484 TATGATGATAATATTATGAATG
1 TATGAAGATAATATTATGAATG
* *
76506 TATGAAGTTATTATTATGAA
1 TATGAAGATAATATTATGAA
76526 CCACATAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (22 bp):
TATGAAGATAATATTATGAATG
Found at i:76580 original size:73 final size:73
Alignment explanation
Indices: 76461--76631 Score: 258
Period size: 73 Copynumber: 2.4 Consensus size: 73
76451 GTGATAATAG
* *
76461 CTTACAAACATTATATTTATAGTTATGATGATAATATTATGAATGTATGAAGTTATT-ATTATGA
1 CTTACATACATTATATTTATAGTTATGATGATAATATTATGAATGTATGAAGTTATTAAATATGA
76525 ACCACATAA
66 ACCACAT-A
*
76534 CTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTATGAAGTTATTAAATATGA
1 CTTACATACATTATATTTATAGTTATGATGATAATATTATGAATGTATGAAGTTATTAAATATGA
76599 ACCACATA
66 ACCACATA
* *
76607 TTTACAT-TATTATATCTTATA-TTAT
1 CTTACATACATTATAT-TTATAGTTAT
76632 TTAGCTTATT
Statistics
Matches: 91, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
72 11 0.12
73 67 0.74
74 13 0.14
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (73 bp):
CTTACATACATTATATTTATAGTTATGATGATAATATTATGAATGTATGAAGTTATTAAATATGA
ACCACATA
Found at i:80147 original size:17 final size:17
Alignment explanation
Indices: 80125--80167 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
80115 TATTAAGAGT
80125 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
80142 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
80159 TAGTTTAAT
1 TAGTTTAAT
80168 TAATTAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:81928 original size:23 final size:25
Alignment explanation
Indices: 81902--81956 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
81892 AAATCCAGCA
81902 AAGAAAATCAAAGCACTC-AAAA-G
1 AAGAAAATCAAAGCACTCAAAAAGG
* *
81925 AAGAAATTGAAAGCACTCAAAAAGG
1 AAGAAAATCAAAGCACTCAAAAAGG
81950 AAGAAAA
1 AAGAAAA
81957 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 16 0.59
24 4 0.15
25 7 0.26
ACGTcount: A:0.62, C:0.13, G:0.16, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAAAGG
Found at i:81961 original size:6 final size:6
Alignment explanation
Indices: 81950--81978 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
81940 CTCAAAAAGG
81950 AAGAAA AAG-AA AAGAAA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
81979 GAAAGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:81964 original size:11 final size:11
Alignment explanation
Indices: 81950--81982 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
81940 CTCAAAAAGG
81950 AAGAAAAAGAA
1 AAGAAAAAGAA
81961 AAGAAAAAGAA
1 AAGAAAAAGAA
*
81972 AA-AGAAAGAA
1 AAGAAAAAGAA
81982 A
1 A
81983 GTTGAAGCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:81972 original size:17 final size:16
Alignment explanation
Indices: 81950--81982 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
81940 CTCAAAAAGG
81950 AAGAAAAAGAAAAGAAA
1 AAGAAAAAG-AAAGAAA
81967 AAGAAAAAGAAAGAAA
1 AAGAAAAAGAAAGAAA
81983 GTTGAAGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAAGAAA
Done.