Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008452.1 Hibiscus syriacus cultivar Beakdansim tig00111260_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: 58654
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1561 original size:20 final size:21
Alignment explanation
Indices: 1507--1569 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1497 GATTCCCCTG
1507 TGGGGGGAATCGGTTCCCATTCAA
1 TGGGGGG-ATCGGTTCCC--TCAA
* *
1531 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1551 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1570 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
23 10 0.29
24 5 0.15
ACGTcount: A:0.17, C:0.24, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:10720 original size:18 final size:19
Alignment explanation
Indices: 10697--10735 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
10687 GAGGAAGAAA
10697 ATTC-AAACGAAACGAAGG
1 ATTCAAAACGAAACGAAGG
*
10715 ATTCAAAAACGAACCGAAGG
1 ATTC-AAAACGAAACGAAGG
10735 A
1 A
10736 GAAGGACCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
20 14 0.78
ACGTcount: A:0.51, C:0.18, G:0.21, T:0.10
Consensus pattern (19 bp):
ATTCAAAACGAAACGAAGG
Found at i:14907 original size:23 final size:22
Alignment explanation
Indices: 14876--14956 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
14866 TACACTAGTT
*
14876 AGTGTATCGATGCATCCCTTGAA
1 AGTGCATCGATGCAT-CCTTGAA
* *
14899 AGTGCATCGATTCA-CCATGAA
1 AGTGCATCGATGCATCCTTGAA
* * *
14920 GGTACACCGATGCAATCCTTGAA
1 AGTGCATCGATGC-ATCCTTGAA
*
14943 TGTGCATCGATGCA
1 AGTGCATCGATGCA
14957 CTCTACTGTG
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 28 0.62
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.26
Consensus pattern (22 bp):
AGTGCATCGATGCATCCTTGAA
Found at i:17574 original size:66 final size:63
Alignment explanation
Indices: 17427--17579 Score: 180
Period size: 66 Copynumber: 2.4 Consensus size: 63
17417 ACCCCATTCG
* * ** *
17427 AATGTATTTTATGCACCGATGCACACCCATGCATCGATGCACTCAGAATTTTATGGAATATCA
1 AATGTATTTTATGCATCGATGCACAACCATGCATCGATGCACTCAGAATTTTATAAAACATCA
** ** *
17490 AATGCCTTTTATGCATCGATGCACATACCATGCATCGATGCACTCCAGGCTGTTTTTAAAACATC
1 AATGTATTTTATGCATCGATGCACA-ACCATGCATCGATGCACT-CAGAAT-TTTATAAAACATC
17555 A
63 A
*
17556 ACTGTATTTTATGCATCGATGCAC
1 AATGTATTTTATGCATCGATGCAC
17580 CCCTAGTGTA
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
63 22 0.30
64 17 0.23
65 4 0.05
66 31 0.42
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (63 bp):
AATGTATTTTATGCATCGATGCACAACCATGCATCGATGCACTCAGAATTTTATAAAACATCA
Found at i:18566 original size:2 final size:2
Alignment explanation
Indices: 18559--18590 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18549 ATGCTTAACT
18559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18591 AGTTTAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21230 original size:15 final size:16
Alignment explanation
Indices: 21198--21230 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21188 AATCTAAGCT
*
21198 TAAATATAAAATTCGA
1 TAAAAATAAAATTCGA
21214 TAAAAATAAAA-TCGA
1 TAAAAATAAAATTCGA
21229 TA
1 TA
21231 CTTAAATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (16 bp):
TAAAAATAAAATTCGA
Found at i:21447 original size:16 final size:16
Alignment explanation
Indices: 21406--21439 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
21396 TTCTATTAAA
*
21406 TTCATAATTATGATCC
1 TTCATCATTATGATCC
21422 TTCATCATTATGATCC
1 TTCATCATTATGATCC
21438 TT
1 TT
21440 GCACATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (16 bp):
TTCATCATTATGATCC
Found at i:24857 original size:13 final size:13
Alignment explanation
Indices: 24839--24868 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
24829 TATTTAATAC
*
24839 TATTTATTATAAA
1 TATTTATTAAAAA
24852 TATTTATTAAAAA
1 TATTTATTAAAAA
24865 TATT
1 TATT
24869 AAAATATTAA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTTATTAAAAA
Found at i:27069 original size:14 final size:14
Alignment explanation
Indices: 27050--27084 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
27040 AATTATAATA
27050 ATAATAATAAAATT
1 ATAATAATAAAATT
* *
27064 ATAATAATATATTT
1 ATAATAATAAAATT
27078 ATAATAA
1 ATAATAA
27085 AATTCGGACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATAATAAAATT
Found at i:29238 original size:4 final size:4
Alignment explanation
Indices: 29229--29253 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
29219 TTAACAATTC
29229 CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT C
29254 AAAATAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:29351 original size:39 final size:40
Alignment explanation
Indices: 29305--29796 Score: 275
Period size: 39 Copynumber: 12.2 Consensus size: 40
29295 CCAATAATTT
*
29305 TTTTACAAATTAGGAAAAT-AATTCCAACGATTTATTTCC
1 TTTTACAAAATAGGAAAATAAATTCCAACGATTTATTTCC
** * * * *
29344 TTTTACAAAGCAAGAAAATAAATT-CTATGATTTATTTCA
1 TTTTACAAAATAGGAAAATAAATTCCAACGATTTATTTCC
* *
29383 TTTTACAAAATCA-AAAAATAAA-TCTAACGATTTATTTCC
1 TTTTACAAAAT-AGGAAAATAAATTCCAACGATTTATTTCC
*
29422 TTCTACAAAATAGGAAAATAAA-TCCAACGATTTATTTCC
1 TTTTACAAAATAGGAAAATAAATTCCAACGATTTATTTCC
* ** * ***
29461 GTTTACAAACCAGGAAAAATAAATT-CTACGA-TTACAAACC
1 TTTTACAAAATAGG-AAAATAAATTCCAACGATTTA-TTTCC
** * * * * * *
29501 AGAATCATATAAGATTCTTAGAAAAATAAATT-AAATGATTTATTTCT
1 ----TTTTACAA-A---ATAGGAAAATAAATTCCAACGATTTATTTCC
* * *
29548 TTTTACAAAATAAGACAATAAATT-CAACGTTTTATTTCC
1 TTTTACAAAATAGGAAAATAAATTCCAACGATTTATTTCC
* *
29587 -TTTACAAAATA-GAATATAAAATCCAACGATTTATTTCC
1 TTTTACAAAATAGGAAAATAAATTCCAACGATTTATTTCC
* * **
29625 TTTTAGAAAATAAGAAAATAAATT-C-ACCCTTTCATTTCC
1 TTTTACAAAATAGGAAAATAAATTCCAACGATTT-ATTTCC
* *
29664 TTTTATAAACTAGGAAAATAAA-TCCAATGATTTGTTTCGATTTATTTCC
1 TTTTACAAAATAGGAAAATAAATTCC-A--A-------CGATTTATTTCC
*
29713 TTTTACAAAATA-GAAAACTAAA-TCCAACAATTTATTTCC
1 TTTTACAAAATAGGAAAA-TAAATTCCAACGATTTATTTCC
* * *
29752 TTTTA-TAAATAAGAAAATAAATTCTC--CGATTTTTTTCC
1 TTTTACAAAATAGGAAAATAAATTC-CAACGATTTATTTCC
29790 TTTTACA
1 TTTTACA
29797 TAACAAGATC
Statistics
Matches: 346, Mismatches: 70, Indels: 74
0.71 0.14 0.15
Matches are distributed among these distances:
37 8 0.02
38 57 0.16
39 185 0.53
40 30 0.09
41 1 0.00
42 1 0.00
43 6 0.02
44 4 0.01
45 1 0.00
46 1 0.00
47 14 0.04
48 11 0.03
49 23 0.07
50 4 0.01
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (40 bp):
TTTTACAAAATAGGAAAATAAATTCCAACGATTTATTTCC
Found at i:29614 original size:38 final size:38
Alignment explanation
Indices: 29537--29646 Score: 125
Period size: 38 Copynumber: 2.8 Consensus size: 38
29527 TAAATTAAAT
* *
29537 GATTTATTTCTTTTTACAAAATAAGACAAT-AAATTCAAC
1 GATTTATTTC-CTTTACAAAATAAGA-AATAAAATCCAAC
*
29576 GTTTTATTTCCTTTACAAAAT-AGAATATAAAATCCAAC
1 GATTTATTTCCTTTACAAAATAAGAA-ATAAAATCCAAC
*
29614 GATTTATTTCCTTTTAGAAAATAAGAAAATAAA
1 GATTTATTTCC-TTTACAAAATAAG-AAATAAA
29647 TTCACCCTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
36 1 0.02
37 5 0.08
38 28 0.46
39 18 0.30
40 7 0.11
41 2 0.03
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (38 bp):
GATTTATTTCCTTTACAAAATAAGAAATAAAATCCAAC
Found at i:29618 original size:77 final size:78
Alignment explanation
Indices: 29523--29796 Score: 216
Period size: 77 Copynumber: 3.4 Consensus size: 78
29513 GATTCTTAGA
** * * * * *
29523 AAAATAAATTAAATGATTTATTTCTTTTTACAAAATAAGACAATAAATTCAACGTTTTATTTCC-
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAAGAAAATAAATTCAACCTTTCATTTCCT
29587 TTTACAAAATA-G
66 TTTACAAAATAGG
* * *
29599 AATATAAAATCCAACGATTTATTTCCTTTTAGAAAATAAGAAAATAAATTCACCCTTTCATTTCC
1 AAAAT-AAATCCAACGATTTATTTCCTTTTACAAAATAAGAAAATAAATTCAACCTTTCATTTCC
* *
29664 TTTTATAAACTAGG
65 TTTTACAAAATAGG
*
29678 AAAATAAATCCAATGATTTGTTTCGATTTATTTCCTTTTACAAAAT-AGAAAACTAAATCCAACA
1 AAAATAAATCC-A--A-------CGATTTATTTCCTTTTACAAAATAAGAAAA-TAAATTCAAC-
* * *
29742 ATTT-ATTTCCTTTTA-TAAATAAG
54 CTTTCATTTCCTTTTACAAAATAGG
* ** *
29765 AAAATAAATTCTCCGATTTTTTTCCTTTTACA
1 AAAATAAATCCAACGATTTATTTCCTTTTACA
29797 TAACAAGATC
Statistics
Matches: 159, Mismatches: 24, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
76 4 0.03
77 68 0.43
78 15 0.09
79 6 0.04
81 1 0.01
87 21 0.13
88 41 0.26
89 3 0.02
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.39
Consensus pattern (78 bp):
AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAAGAAAATAAATTCAACCTTTCATTTCCT
TTTACAAAATAGG
Found at i:29714 original size:88 final size:87
Alignment explanation
Indices: 29613--29773 Score: 236
Period size: 88 Copynumber: 1.8 Consensus size: 87
29603 TAAAATCCAA
* * **
29613 CGATTTATTTCCTTTTAGAAAATAAGAAAA-TAAATTC-ACCCTTTCATTTCCTTTTATAAACTA
1 CGATTTATTTCCTTTTACAAAAT-AGAAAACTAAATCCAACAATTT-ATTTCCTTTTATAAA-TA
*
29676 GGAAAATAAATCCAATGATTTGTTT
63 AGAAAATAAATCCAATGATTTGTTT
29701 CGATTTATTTCCTTTTACAAAATAGAAAACTAAATCCAACAATTTATTTCCTTTTATAAATAAGA
1 CGATTTATTTCCTTTTACAAAATAGAAAACTAAATCCAACAATTTATTTCCTTTTATAAATAAGA
29766 AAATAAAT
66 AAATAAAT
29774 TCTCCGATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
87 18 0.27
88 43 0.65
89 5 0.08
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (87 bp):
CGATTTATTTCCTTTTACAAAATAGAAAACTAAATCCAACAATTTATTTCCTTTTATAAATAAGA
AAATAAATCCAATGATTTGTTT
Found at i:29757 original size:49 final size:49
Alignment explanation
Indices: 29652--29757 Score: 124
Period size: 49 Copynumber: 2.2 Consensus size: 49
29642 ATAAATTCAC
* * * ** *
29652 CCTTTCATTTCCTTTTATAAACTAGGAAAATAAATCCAATGATTTGTTT
1 CCTTTTATTTCCTTTTACAAAATAGGAAAATAAATCCAACAATTTATTT
**
29701 CGATTTATTTCCTTTTACAAAATA-GAAAACTAAATCCAACAATTTATTT
1 CCTTTTATTTCCTTTTACAAAATAGGAAAA-TAAATCCAACAATTTATTT
29750 CCTTTTAT
1 CCTTTTAT
29758 AAATAAGAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
48 5 0.11
49 41 0.89
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (49 bp):
CCTTTTATTTCCTTTTACAAAATAGGAAAATAAATCCAACAATTTATTT
Found at i:29789 original size:38 final size:39
Alignment explanation
Indices: 29701--29796 Score: 115
Period size: 38 Copynumber: 2.5 Consensus size: 39
29691 TGATTTGTTT
29701 CGATTTATTTCCTTTTACAAAATAGAAAACTAAATCCAA
1 CGATTTATTTCCTTTTACAAAATAGAAAACTAAATCCAA
* * * **
29740 CAATTTATTTCCTTTTA-TAAATAAGAAAA-TAAATTCTC
1 CGATTTATTTCCTTTTACAAAAT-AGAAAACTAAATCCAA
*
29778 CGATTTTTTTCCTTTTACA
1 CGATTTATTTCCTTTTACA
29797 TAACAAGATC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
38 25 0.53
39 22 0.47
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (39 bp):
CGATTTATTTCCTTTTACAAAATAGAAAACTAAATCCAA
Found at i:29978 original size:116 final size:117
Alignment explanation
Indices: 29808--30026 Score: 270
Period size: 116 Copynumber: 1.9 Consensus size: 117
29798 AACAAGATCC
*
29808 TTCAAGATTCCTAAGAAAATAAATTAACCAATTTATTTACTTTTACAAAATAGAATC-ATTCAAG
1 TTCAAGATTCCTAAGAAAATAAATTAACCAATTTATTTA-TTTTACAAAATAGAATCAATGCAAG
* *
29872 ATT-T-TCAAACAAATAAATTCAATTATTTATTTTCCTTACAAAATTAGAATCA
65 ATTCTAACAAACAAATAAATTCAATAATTTA-TTTCCTTACAAAATTAGAATCA
* **
29924 TTCAAGATT-CTCAAGGAAATAAATTTAA-CAATTTATTT-TTCTTACCAAGCTAGAATCAATGC
1 TTCAAGATTCCT-AAGAAAATAAA-TTAACCAATTTATTTATT-TTA-CAAAATAGAATCAATGC
**
29986 AAGATTCTAACAATGAAATAAATTCAATAATTTATTTCCTT
62 AAGATTCTAACAAACAAATAAATTCAATAATTTATTTCCTT
30027 GATATTTTGT
Statistics
Matches: 88, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
114 2 0.02
115 5 0.06
116 39 0.44
117 13 0.15
118 8 0.09
119 21 0.24
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (117 bp):
TTCAAGATTCCTAAGAAAATAAATTAACCAATTTATTTATTTTACAAAATAGAATCAATGCAAGA
TTCTAACAAACAAATAAATTCAATAATTTATTTCCTTACAAAATTAGAATCA
Found at i:30020 original size:61 final size:58
Alignment explanation
Indices: 29810--30026 Score: 199
Period size: 58 Copynumber: 3.7 Consensus size: 58
29800 CAAGATCCTT
* * * * *
29810 CAAGATTC-CTAAGAAAATAAATT-AACCAATTTATTTACTTTTACAAAA-TAGAATCATT
1 CAAGATTCTC-AAGGAAATAAATTCAA-TAATTTATTTTC-CTTACAAAACTAGAATCATG
* ** * * *
29868 CAAGATTTTCAAACAAATAAATTCAATTATTTATTTTCCTTACAAAATTAGAATCATT
1 CAAGATTCTCAAGGAAATAAATTCAATAATTTATTTTCCTTACAAAACTAGAATCATG
* * * * *
29926 CAAGATTCTCAAGGAAATAAATTTAACAATTTATTTTTCTTACCAAGCTAGAATCAATG
1 CAAGATTCTCAAGGAAATAAATTCAATAATTTATTTTCCTTACAAAACTAGAATC-ATG
*
29985 CAAGATTCTAACAATGAAATAAATTCAATAATTTA-TTTCCTT
1 CAAGATTCT--CAAGGAAATAAATTCAATAATTTATTTTCCTT
30027 GATATTTTGT
Statistics
Matches: 131, Mismatches: 22, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
57 8 0.06
58 82 0.63
59 14 0.11
60 6 0.05
61 21 0.16
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.36
Consensus pattern (58 bp):
CAAGATTCTCAAGGAAATAAATTCAATAATTTATTTTCCTTACAAAACTAGAATCATG
Found at i:35683 original size:21 final size:20
Alignment explanation
Indices: 35658--35697 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
35648 CGAGGAAGAT
*
35658 TTAGGGATTGAGGAGCGAGGG
1 TTAGGGATTGAAGAG-GAGGG
35679 TTAGGGATTGAAGAGGAGG
1 TTAGGGATTGAAGAGGAGG
35698 AATTGAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.28, C:0.03, G:0.50, T:0.20
Consensus pattern (20 bp):
TTAGGGATTGAAGAGGAGGG
Found at i:53826 original size:54 final size:54
Alignment explanation
Indices: 53745--54174 Score: 566
Period size: 54 Copynumber: 8.1 Consensus size: 54
53735 CTATGTGTAT
*
53745 TATAGGCACTAA--GTGCAACCCACAGAATTCATCATATGTTGATGAACGATCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
*
53797 TATAGGCACTAAGTGTGCAAGCCACAGAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
** *
53851 TATAAACACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAAAGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* *
53905 TATAGGCACTAAGTGTGCAACCCACTGAATTCATCATATATTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * **
53959 TATTGGCACTAAGTGTGCAACCCACATAATTCATCATATATTGATGAACGACTA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* ** *
54013 TATAGGTACTAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAACGACAG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * * * *
54067 TATAGGCACTAAGTGTACAACACACATAATT-TTCATATGTTG-TCAACTACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * * *
54119 TATAGGCACTAAGTGTACAAACCAC-GAAATTCATAATAT-TTTACGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCG
54172 TAT
1 TAT
54175 CGATACTACG
Statistics
Matches: 330, Mismatches: 43, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
52 48 0.15
53 25 0.08
54 257 0.78
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
Found at i:54967 original size:41 final size:40
Alignment explanation
Indices: 54876--54967 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
54866 TGAGCATCTG
*
54876 GTATCGATACTACAACCCTCAATATCAACATAAAAGGTCA
1 GTATCGATACTACAACCCTCAATATCAACACAAAAGGTCA
* * * **
54916 GTATCTATACTACAACCCTTAGTATCGATAC-CAAGGGGTCA
1 GTATCGATACTACAACCCTCAATATC-A-ACACAAAAGGTCA
54957 GTATCGATACT
1 GTATCGATACT
54968 CATTCCTTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 23 0.53
41 18 0.42
42 2 0.05
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (40 bp):
GTATCGATACTACAACCCTCAATATCAACACAAAAGGTCA
Found at i:56854 original size:15 final size:15
Alignment explanation
Indices: 56830--56866 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
56820 TGAAATTTCA
56830 GAAC-TACTACATTG
1 GAACATACTACATTG
56844 GAACATACTACATTG
1 GAACATACTACATTG
56859 GAACATAC
1 GAACATAC
56867 GCCATGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (15 bp):
GAACATACTACATTG
Done.