Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005585.1 Hibiscus syriacus cultivar Beakdansim tig00012966_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: 59207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5587 original size:2 final size:2
Alignment explanation
Indices: 5580--5613 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5570 TTTCCCAGAT
*
5580 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5614 CACATATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8486 original size:26 final size:28
Alignment explanation
Indices: 8457--8510 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
8447 CTATTTACTC
* *
8457 TAAAATT-T-TATTTATATTATTTTAAA
1 TAAAATTATATATGTATATTATCTTAAA
8483 TAAAATTATATATGTATATTATCTTAAA
1 TAAAATTATATATGTATATTATCTTAAA
8511 AATATTTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
27 1 0.04
28 16 0.67
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
TAAAATTATATATGTATATTATCTTAAA
Found at i:14815 original size:29 final size:31
Alignment explanation
Indices: 14783--14840 Score: 102
Period size: 29 Copynumber: 1.9 Consensus size: 31
14773 TTTTTACTTT
14783 TACCACCTATCT-TTTAATT-TTGTCAATTA
1 TACCACCTATCTATTTAATTGTTGTCAATTA
14812 TACCACCTATCTATTTAATTGTTGTCAAT
1 TACCACCTATCTATTTAATTGTTGTCAAT
14841 CATGCCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 12 0.44
30 7 0.26
31 8 0.30
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.47
Consensus pattern (31 bp):
TACCACCTATCTATTTAATTGTTGTCAATTA
Found at i:19183 original size:21 final size:21
Alignment explanation
Indices: 19157--19201 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
19147 TTAAAAATAT
*
19157 TAAAAA-AATTAATATTTTAAA
1 TAAAAATAA-TAATAATTTAAA
19178 TAAAAATAATAATAATTTAAA
1 TAAAAATAATAATAATTTAAA
19199 TAA
1 TAA
19202 TTTTTTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAAATAATAATAATTTAAA
Found at i:23183 original size:51 final size:52
Alignment explanation
Indices: 23085--23183 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
23075 ATTTTCAGTT
* *
23085 AAATGTTATGAAAAATATAATATTTTCGATTGTCAACTAAAAATATTATGAA
1 AAATGTTATAAAAAATATAACATTTTCGATTGTCAACTAAAAATATTATGAA
* *
23137 AAATGTTATAAAAAATTGTAACATTTTCGATT-T-AACTAAAAGTATTA
1 AAATGTTATAAAAAA-TATAACATTTTCGATTGTCAACTAAAAATATTA
23184 AAAATTTGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 13 0.31
52 15 0.36
53 14 0.33
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.37
Consensus pattern (52 bp):
AAATGTTATAAAAAATATAACATTTTCGATTGTCAACTAAAAATATTATGAA
Found at i:25531 original size:29 final size:29
Alignment explanation
Indices: 25484--25540 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
25474 TACCAATGTA
**
25484 TGAGGAGAAAGTTGACATCAGAAACCCTC
1 TGAGGAGAAAACTGACATCAGAAACCCTC
*
25513 TGAGGAGAAAACTGGCATCAGAAACCCT
1 TGAGGAGAAAACTGACATCAGAAACCCT
25541 TTACACGCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (29 bp):
TGAGGAGAAAACTGACATCAGAAACCCTC
Found at i:26404 original size:114 final size:115
Alignment explanation
Indices: 26185--26404 Score: 280
Period size: 114 Copynumber: 1.9 Consensus size: 115
26175 CACTTTGCCA
* **
26185 GTGCTTCTGTCTTGGTGAATGAGGATCAGGAAAAGGATGTCTCATCATTGGATCAATGTGATGAT
1 GTGCTTCTGTCTTGGTGAATGAGCATCAGGAAAAGGATGTCTCATCACAGGATCAATGTGATGAT
* * *
26250 GCTTTTCAGTCAGAAAAACAGCTAAACTGCCATCTGAAATGTGATTGGTT
66 GCTTTCCAGTCAGAAAAACAGCTAAACTGCCAACTAAAATGTGATTGGTT
* ** * *
26300 GTGCTTTTGTCTT-GTGAATGAGCATCAGGATCAGGATGTTTCATCACAGGATCATTGTGATGAT
1 GTGCTTCTGTCTTGGTGAATGAGCATCAGGAAAAGGATGTCTCATCACAGGATCAATGTGATGAT
* * ** * *
26364 GCTTTCCAGTCCGAAAGACATTTACATTGCCAACTAAAATG
66 GCTTTCCAGTCAGAAAAACAGCTAAACTGCCAACTAAAATG
26405 AAGTGTGAAC
Statistics
Matches: 88, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
114 76 0.86
115 12 0.14
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (115 bp):
GTGCTTCTGTCTTGGTGAATGAGCATCAGGAAAAGGATGTCTCATCACAGGATCAATGTGATGAT
GCTTTCCAGTCAGAAAAACAGCTAAACTGCCAACTAAAATGTGATTGGTT
Found at i:27482 original size:33 final size:33
Alignment explanation
Indices: 27445--27722 Score: 360
Period size: 33 Copynumber: 8.2 Consensus size: 33
27435 ATATCGCTGA
27445 CCTCCCATCTGTGGAGAGCCGGAATATTGTTGT
1 CCTCCCATCTGTGGAGAGCCGGAATATTGTTGT
27478 CCTCCCATCTGTGGAGAGCCGGAATATTGTTGT
1 CCTCCCATCTGTGGAGAGCCGGAATATTGTTGT
27511 CCTCCCATCTGTGGAGAGCCGGAATATTGTTGT
1 CCTCCCATCTGTGGAGAGCCGGAATATTGTTGT
27544 CCTCCCATCTGTGGAGAGCCGGAATATTGTTGT
1 CCTCCCATCTGTGGAGAGCCGGAATATTGTTGT
* *
27577 CCTCCCATCTGTGGAGAGCCAGAATATTGCTGTCCT
1 CCTCCCATCTGTGGAGAGCCGGAATATTG-T-T-GT
* *
27613 CCTCCCATCTGTGGAGAACCAGG-ATATTGCTGTCCT
1 CCTCCCATCTGTGGAGAGCC-GGAATATTG-T-T-GT
* * *
27649 CCTCCCATCTGTGGAGAACCAGAATATTGCTGTCCT
1 CCTCCCATCTGTGGAGAGCCGGAATATTG-T-T-GT
* * * *
27685 CCTCCCATCTGTGGAGAACCAGAATATCGCTGT
1 CCTCCCATCTGTGGAGAGCCGGAATATTGTTGT
27718 CCTCC
1 CCTCC
27723 TCCCATCAGT
Statistics
Matches: 232, Mismatches: 8, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
33 133 0.57
34 2 0.01
35 2 0.01
36 94 0.41
37 1 0.00
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.28
Consensus pattern (33 bp):
CCTCCCATCTGTGGAGAGCCGGAATATTGTTGT
Found at i:27738 original size:36 final size:35
Alignment explanation
Indices: 27445--27741 Score: 331
Period size: 36 Copynumber: 8.6 Consensus size: 35
27435 ATATCGCTGA
* * **
27445 CCTCCCATCTGTGGAGAGCCGGAATAT--TGTTGT
1 CCTCCCATCTGTGGAGAACCAGAATATGCTGTCCT
* * **
27478 CCTCCCATCTGTGGAGAGCCGGAATAT--TGTTGT
1 CCTCCCATCTGTGGAGAACCAGAATATGCTGTCCT
* * **
27511 CCTCCCATCTGTGGAGAGCCGGAATAT--TGTTGT
1 CCTCCCATCTGTGGAGAACCAGAATATGCTGTCCT
* * **
27544 CCTCCCATCTGTGGAGAGCCGGAATAT--TGTTGT
1 CCTCCCATCTGTGGAGAACCAGAATATGCTGTCCT
*
27577 CCTCCCATCTGTGGAGAGCCAGAATATTGCTGTCCT
1 CCTCCCATCTGTGGAGAACCAGAATA-TGCTGTCCT
*
27613 CCTCCCATCTGTGGAGAACCAGGATATTGCTGTCCT
1 CCTCCCATCTGTGGAGAACCAGAATA-TGCTGTCCT
27649 CCTCCCATCTGTGGAGAACCAGAATATTGCTGTCCT
1 CCTCCCATCTGTGGAGAACCAGAATA-TGCTGTCCT
27685 CCTCCCATCTGTGGAGAACCAGAATATCGCTGTCCT
1 CCTCCCATCTGTGGAGAACCAGAATAT-GCTGTCCT
*
27721 CCTCCCATCAGTGGAGAACCA
1 CCTCCCATCTGTGGAGAACCA
27742 TATGACTGCC
Statistics
Matches: 253, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
33 124 0.49
34 1 0.00
35 1 0.00
36 127 0.50
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.28
Consensus pattern (35 bp):
CCTCCCATCTGTGGAGAACCAGAATATGCTGTCCT
Found at i:29709 original size:14 final size:14
Alignment explanation
Indices: 29690--29718 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29680 CGCAAATCTT
29690 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
29704 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
29718 A
1 A
29719 GTTAATTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:29835 original size:60 final size:60
Alignment explanation
Indices: 29754--29899 Score: 163
Period size: 60 Copynumber: 2.4 Consensus size: 60
29744 TATAACCTTT
* * *
29754 ATTTTAAATTGGTTCCT-AAACTTTTAAAAATTCTAATTTT-ATCCTTAAACTATGACTATC
1 ATTTTAAATTAG-TCCTCAAACTTTTAAAAATTC-AATTTTCATCCTCAAACTATGAATATC
* * * * *
29814 ATTTTAAATTAGTCCTCAAACTTTTGAACATTCCATTTTCATCCTCAAATTATGAATCTC
1 ATTTTAAATTAGTCCTCAAACTTTTAAAAATTCAATTTTCATCCTCAAACTATGAATATC
*
29874 ATTCTAAATTAGTCC-CTAAACTTTTA
1 ATTTTAAATTAGTCCTC-AAACTTTTA
29900 GATCTTCCAA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 10 0.14
60 63 0.86
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (60 bp):
ATTTTAAATTAGTCCTCAAACTTTTAAAAATTCAATTTTCATCCTCAAACTATGAATATC
Found at i:29908 original size:60 final size:60
Alignment explanation
Indices: 29758--29924 Score: 162
Period size: 60 Copynumber: 2.8 Consensus size: 60
29748 ACCTTTATTT
* * * * * * * *
29758 TAAATTGGTTCCT-AAACTTTTAAAAATTCTAATTTT-ATCCTTAAACTATGACTATCATTT
1 TAAATTAG-TCCTCAAACTTTTGAACATTC-CATTTTCATCCTCAAATTATGAATATCATTC
*
29818 TAAATTAGTCCTCAAACTTTTGAACATTCCATTTTCATCCTCAAATTATGAATCTCATTC
1 TAAATTAGTCCTCAAACTTTTGAACATTCCATTTTCATCCTCAAATTATGAATATCATTC
* * *
29878 TAAATTAGTCC-CTAAACTTTTAGATC-TTCCAATTTCATCCCCAAATT
1 TAAATTAGTCCTC-AAACTTTT-GAACATTCCATTTTCATCCTCAAATT
29925 CATTCAAATA
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
59 10 0.11
60 78 0.86
61 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (60 bp):
TAAATTAGTCCTCAAACTTTTGAACATTCCATTTTCATCCTCAAATTATGAATATCATTC
Found at i:30245 original size:22 final size:22
Alignment explanation
Indices: 30203--30245 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
30193 ACTTGAATTG
*
30203 ATTTAATTTAAAAAATGATTTA
1 ATTTAATTTAAAAAATAATTTA
* *
30225 ATTTAATTTAATATATAATTT
1 ATTTAATTTAAAAAATAATTT
30246 TATGATCTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTAATTTAAAAAATAATTTA
Found at i:32324 original size:17 final size:17
Alignment explanation
Indices: 32270--32324 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
32260 TGGTTGCTAT
*
32270 TGTAATTGAAGTATTAA
1 TGTAATTGAAGTATGAA
* *
32287 TGT-ATATGAAGATTTG-T
1 TGTAAT-TGAAG-TATGAA
32304 TGTAATTGAAGTATGAA
1 TGTAATTGAAGTATGAA
32321 TGTA
1 TGTA
32325 GAGATGATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
16 5 0.17
17 20 0.69
18 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (17 bp):
TGTAATTGAAGTATGAA
Found at i:32979 original size:17 final size:17
Alignment explanation
Indices: 32957--33008 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
32947 ACAACGAAAA
32957 CAATAATGGCAGCAAAC
1 CAATAATGGCAGCAAAC
* *
32974 CAATAAT--CAATCTAA-
1 CAATAATGGC-AGCAAAC
32989 CAATAATGGCAGCAAAC
1 CAATAATGGCAGCAAAC
33006 CAA
1 CAA
33009 AAAAACAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
15 8 0.30
16 8 0.30
17 11 0.41
ACGTcount: A:0.50, C:0.23, G:0.12, T:0.15
Consensus pattern (17 bp):
CAATAATGGCAGCAAAC
Found at i:39000 original size:39 final size:39
Alignment explanation
Indices: 38917--39002 Score: 99
Period size: 37 Copynumber: 2.3 Consensus size: 39
38907 TTTTTTATAT
*
38917 TTTTAAT-TTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTTAATATTTGTAAAAAAAATTATATAAATATTATCAA
* *
38955 -TTTAATATTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTTAATATTTGTAAAAAAAATTATATAAATATTAT-CAA
38992 TTTATAATATT
1 TTT-TAATATT
39003 ATACAAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
36 13 0.32
37 16 0.39
38 5 0.12
39 7 0.17
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (39 bp):
TTTTAATATTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:39015 original size:18 final size:18
Alignment explanation
Indices: 38971--39018 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
38961 ATTTTAAAGA
*
38971 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
*
38990 -AATTTATAATATTATAC
1 AAATATATAATATTATAC
39007 AAATATATAATA
1 AAATATATAATA
39019 AGGACAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:39695 original size:17 final size:17
Alignment explanation
Indices: 39673--39706 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39663 TAAATTTTTT
* *
39673 ATATAATATTCAAAATA
1 ATATAAAATTAAAAATA
39690 ATATAAAATTAAAAATA
1 ATATAAAATTAAAAATA
39707 TCAAAATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATAAAATTAAAAATA
Found at i:46578 original size:18 final size:19
Alignment explanation
Indices: 46555--46590 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
46545 AAACAGGTGG
46555 CTTTATGGTAAGT-TTTTT
1 CTTTATGGTAAGTATTTTT
*
46573 CTTTATGTTAAGTATTTT
1 CTTTATGGTAAGTATTTT
46591 GGTAGCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.19, C:0.06, G:0.14, T:0.61
Consensus pattern (19 bp):
CTTTATGGTAAGTATTTTT
Found at i:52421 original size:23 final size:23
Alignment explanation
Indices: 52395--52455 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
52385 CTCATATAAA
*
52395 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
52418 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
52441 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
52456 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:52816 original size:103 final size:103
Alignment explanation
Indices: 52471--52792 Score: 617
Period size: 103 Copynumber: 3.1 Consensus size: 103
52461 TAATGTCCAT
52471 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
52536 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
52574 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
52639 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
52677 AAAGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
52742 GACTTCACACATGTTTCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
52780 AAGGACCACATAT
1 AAGGACCACATAT
52793 GACCCCTAGC
Statistics
Matches: 214, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 214 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:53852 original size:20 final size:20
Alignment explanation
Indices: 53829--53874 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
53819 TCTTTTATAT
*
53829 TCATATAATTTATTATCATA
1 TCATATAATTTATCATCATA
**
53849 TCATATGGTTTATCATCATA
1 TCATATAATTTATCATCATA
*
53869 ACATAT
1 TCATAT
53875 CACATATTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (20 bp):
TCATATAATTTATCATCATA
Found at i:54265 original size:20 final size:20
Alignment explanation
Indices: 54236--54276 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54226 TTTTCCTTTA
*
54236 GGGGGAATCGGTTCCCTCTT
1 GGGGGAATCGGTTCCCCCTT
*
54256 GGGGGTATCGGTTCCCCCTT
1 GGGGGAATCGGTTCCCCCTT
54276 G
1 G
54277 ACATTCTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.27, G:0.37, T:0.29
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCCCTT
Found at i:58231 original size:16 final size:16
Alignment explanation
Indices: 58210--58242 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
58200 TAATAAATAA
58210 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
58226 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
58242 A
1 A
58243 AATTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:58345 original size:16 final size:16
Alignment explanation
Indices: 58307--58354 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
58297 TTAATAAATA
58307 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
58323 A-GAACATAAATGAAC
1 ACGAACATAAACGAAC
58338 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
58354 A
1 A
58355 TAAACATTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 14 0.48
16 15 0.52
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:58361 original size:16 final size:15
Alignment explanation
Indices: 58309--58354 Score: 74
Period size: 15 Copynumber: 3.0 Consensus size: 15
58299 AATAAATAAC
58309 GAACATAAACGAACA
1 GAACATAAACGAACA
*
58324 GAACATAAATGAACA
1 GAACATAAACGAACA
58339 CGAACATAAACGAACA
1 -GAACATAAACGAACA
58355 TAAACATTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.59, C:0.20, G:0.13, T:0.09
Consensus pattern (15 bp):
GAACATAAACGAACA
Found at i:58734 original size:14 final size:14
Alignment explanation
Indices: 58717--58772 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
58707 AACGAACATA
58717 AACGAACATAACCG
1 AACGAACATAACCG
58731 AACGAACAT-A---
1 AACGAACATAACCG
*
58741 AACAAACATAACCG
1 AACGAACATAACCG
58755 AACGAACATAACCG
1 AACGAACATAACCG
58769 AACG
1 AACG
58773 TAAATGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
13 1 0.03
14 26 0.72
ACGTcount: A:0.54, C:0.27, G:0.12, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:58734 original size:24 final size:24
Alignment explanation
Indices: 58707--58785 Score: 113
Period size: 24 Copynumber: 3.3 Consensus size: 24
58697 AACATAAATA
58707 AACGAACATAAACGAACATAACCG
1 AACGAACATAAACGAACATAACCG
*
58731 AACGAACATAAACAAACATAACCG
1 AACGAACATAAACGAACATAACCG
* * **
58755 AACGAACATAACCGAACGTAAATG
1 AACGAACATAAACGAACATAACCG
58779 AACGAAC
1 AACGAAC
58786 GAGACCTATG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.54, C:0.24, G:0.13, T:0.09
Consensus pattern (24 bp):
AACGAACATAAACGAACATAACCG
Found at i:58770 original size:10 final size:10
Alignment explanation
Indices: 58704--58757 Score: 54
Period size: 10 Copynumber: 5.0 Consensus size: 10
58694 TTAAACATAA
58704 ATAAACGAAC
1 ATAAACGAAC
58714 ATAAACGAAC
1 ATAAACGAAC
58724 ATAACCGAACGAAC
1 AT-A---AACGAAC
*
58738 ATAAACAAAC
1 ATAAACGAAC
*
58748 ATAACCGAAC
1 ATAAACGAAC
58758 GAACATAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 26 0.70
11 1 0.03
13 1 0.03
14 9 0.24
ACGTcount: A:0.57, C:0.24, G:0.09, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Done.