Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000252.1 Hibiscus syriacus cultivar Beakdansim tig00000460_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: 76461
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:1063 original size:14 final size:15
Alignment explanation
Indices: 1044--1078 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1034 ACCTCCAATC
1044 AAATTATACA-AATA
1 AAATTATACATAATA
*
1058 AAATTATACATAATG
1 AAATTATACATAATA
1073 AAATTA
1 AAATTA
1079 ATGGCAGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (15 bp):
AAATTATACATAATA
Found at i:5278 original size:20 final size:20
Alignment explanation
Indices: 5246--5295 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5236 GGCTGATGGA
5246 AACCGGTTTTCAACCGGTTCTG
1 AACCGG-TTTCAACCGGTTC-G
*
5268 -ACCGGTTTCAACTGGTTCG
1 AACCGGTTTCAACCGGTTCG
5287 AACCGGTTT
1 AACCGGTTT
5296 GACCAGTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 1 0.04
20 20 0.77
21 5 0.19
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (20 bp):
AACCGGTTTCAACCGGTTCG
Found at i:12545 original size:20 final size:21
Alignment explanation
Indices: 12520--12558 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12510 GGCTGCTGGA
12520 AACCGGTT-TAACCGGTTTAC
1 AACCGGTTCTAACCGGTTTAC
*
12540 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
12559 GACCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTAC
Found at i:12581 original size:17 final size:17
Alignment explanation
Indices: 12559--12597 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
12549 TGACCGGTTT
12559 GACCGTTGACCCGACCC
1 GACCGTTGACCCGACCC
12576 GACCGTTGACCCGACCC
1 GACCGTTGACCCGACCC
12593 GACCG
1 GACCG
12598 GTCCGTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.26, T:0.10
Consensus pattern (17 bp):
GACCGTTGACCCGACCC
Found at i:12593 original size:22 final size:22
Alignment explanation
Indices: 12566--12608 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12556 TTTGACCGTT
12566 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
* *
12588 GACCCGACCGGTCCGTTGACC
1 GACCCGACCCGACCGTTGACC
12609 GTTGACTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.47, G:0.26, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:14832 original size:19 final size:19
Alignment explanation
Indices: 14810--14850 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
14800 ATGACGACTT
*
14810 AAAA-ATAAATTAATTAAAA
1 AAAAGATAAA-TAAATAAAA
14829 AAAAGATAAATAAATAAAA
1 AAAAGATAAATAAATAAAA
14848 AAA
1 AAA
14851 CGTAATGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (19 bp):
AAAAGATAAATAAATAAAA
Found at i:15207 original size:21 final size:21
Alignment explanation
Indices: 15183--15229 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
15173 GTCGCTGAAG
15183 TTTCATGAATTATGCCATTCT
1 TTTCATGAATTATGCCATTCT
15204 TTTCATGAATTATGCCATTCT
1 TTTCATGAATTATGCCATTCT
15225 TTTCA
1 TTTCA
15230 CAAATATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (21 bp):
TTTCATGAATTATGCCATTCT
Found at i:25519 original size:22 final size:22
Alignment explanation
Indices: 25492--25549 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
25482 TTTATGTGAC
* *
25492 TAATATAAAAATAAAAATAATA
1 TAATATAAAAATAAAAACAAAA
* *
25514 TAATATAAAAGTAATAACAAAA
1 TAATATAAAAATAAAAACAAAA
25536 TAATA-AATAAATAA
1 TAATATAA-AAATAA
25550 TGATTAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
TAATATAAAAATAAAAACAAAA
Found at i:25560 original size:36 final size:33
Alignment explanation
Indices: 25499--25566 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
25489 GACTAATATA
*
25499 AAAATAAAAATAATATAATATAAAAGTAATAAC
1 AAAATAAAAATAATATAATATAAAAGCAATAAC
25532 AAAATAATAAATAA-ATAATGATTAAAAAGCAATAA
1 AAAATAA-AAATAATATAAT-A-T-AAAAGCAATAA
25567 TATTAATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 12 0.40
34 7 0.23
35 1 0.03
36 10 0.33
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (33 bp):
AAAATAAAAATAATATAATATAAAAGCAATAAC
Found at i:28374 original size:76 final size:76
Alignment explanation
Indices: 27025--28347 Score: 2434
Period size: 76 Copynumber: 17.4 Consensus size: 76
27015 GAGGTCCTAA
* *
27025 AAACATCATGCACTGAAGGGA-TTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGTA-GGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
27089 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
27101 AAACATCATGCACTGCAGGACTTAC-GAATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGTAGGACTTACAG-ATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
*
27165 AAGGCTTTTTAG
65 AAGGCTTTTTGG
* *
27177 AAAAATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAACCATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
27242 AGGCTTTTTGG
66 AGGCTTTTTGG
*
27253 AAACATCATGCACTGTAGGACTTACAGATGATCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
27318 AGGCGTTTTGG
66 AGGCTTTTTGG
*
27329 AAACATCATGAACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
27394 AGGCTTTTTGG
66 AGGCTTTTTGG
27405 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
27470 AGGCGTTTTGG
66 AGGCTTTTTGG
27481 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
27546 AGGCTTTTTGG
66 AGGCTTTTTGG
*
27557 AAACATCATGCACTGTAGGACTTACAGATAACCCTAAGGCTTTGAAAACATCAAAAAAGCTCCCG
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAAGCTCCCG
27622 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
27634 AAACATAATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
27699 AGGCTTTTTGG
66 AGGCTTTTTGG
*
27710 AAACATCATGCACTGTAGGACTTACAAATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
27775 AGGCTTTTTGG
66 AGGCTTTTTGG
27786 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
27851 AGGCTTTTTGG
66 AGGCTTTTTGG
27862 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
27927 AGGCTTTTTGG
66 AGGCTTTTTGG
*
27938 AAACATCATGCACTATAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
28003 AGGCTTTTTGG
66 AGGCTTTTTGG
28014 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
28079 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
28090 TAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
28155 AGACTTTTTGG
66 AGGCTTTTTGG
28166 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
28231 AGGCTTTTTGG
66 AGGCTTTTTGG
28242 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
28307 AGGCTTTTTGG
66 AGGCTTTTTGG
*
28318 TAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
28348 TGGGAAATAG
Statistics
Matches: 1209, Mismatches: 34, Indels: 8
0.97 0.03 0.01
Matches are distributed among these distances:
75 3 0.00
76 1131 0.94
77 75 0.06
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:29049 original size:22 final size:22
Alignment explanation
Indices: 29024--29075 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
29014 CATAAAGCTT
*
29024 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAACCTA
29046 TCATCTTTAAAAAGAGAACCTA
1 TCATCTTTAAAAAGAGAACCTA
29068 TCATCTTT
1 TCATCTTT
29076 GAAGAGTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAACCTA
Found at i:33830 original size:26 final size:26
Alignment explanation
Indices: 33801--33888 Score: 99
Period size: 26 Copynumber: 3.4 Consensus size: 26
33791 TTCTCCCCTT
*
33801 TTTCTTTTTCCTTTTTTTCTCTTTTC
1 TTTCTTTTTCCTTTTTTTTTCTTTTC
*
33827 TTTCTCTTTT-CTTTTTTTTTCTTTTTT
1 TTTCT-TTTTCCTTTTTTTTTC-TTTTC
** *
33854 TTTCTTTTTTTTTTTTTTTTTTTTTC
1 TTTCTTTTTCCTTTTTTTTTCTTTTC
33880 TTT-TTTTTC
1 TTTCTTTTTC
33889 AAGCATAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
25 5 0.09
26 26 0.49
27 22 0.42
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (26 bp):
TTTCTTTTTCCTTTTTTTTTCTTTTC
Found at i:33843 original size:7 final size:7
Alignment explanation
Indices: 33799--33885 Score: 76
Period size: 7 Copynumber: 12.7 Consensus size: 7
33789 ATTTCTCCCC
33799 TTTTTCT
1 TTTTTCT
*
33806 TTTTCCTT
1 TTTTTC-T
33814 TTTTTCT
1 TTTTTCT
*
33821 CTTTTC-
1 TTTTTCT
*
33827 TTTCTCT
1 TTTTTCT
*
33834 TTTCTTTT
1 TTT-TTCT
33842 TTTTTCT
1 TTTTTCT
33849 TTTTT-T
1 TTTTTCT
33855 TTCTTT-T
1 TT-TTTCT
33862 TTTTT-T
1 TTTTTCT
33868 TTTTT-T
1 TTTTTCT
33874 TTTTTCT
1 TTTTTCT
33881 TTTTT
1 TTTTT
33886 TTCAAGCATA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
6 22 0.33
7 34 0.51
8 11 0.16
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:33844 original size:1 final size:1
Alignment explanation
Indices: 33833--33887 Score: 74
Period size: 1 Copynumber: 55.0 Consensus size: 1
33823 TTTCTTTCTC
* * * *
33833 TTTTCTTTTTTTTTCTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33888 CAAGCATAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:33887 original size:10 final size:10
Alignment explanation
Indices: 33799--33888 Score: 92
Period size: 10 Copynumber: 8.6 Consensus size: 10
33789 ATTTCTCCCC
33799 TTTTTCTTTT
1 TTTTTCTTTT
33809 TCCTTTT-TTTCT
1 T--TTTTCTTT-T
*
33821 CTTTTCTTTCT
1 TTTTTCTTT-T
*
33832 CTTTTCTTTT
1 TTTTTCTTTT
33842 TTTTTCTTTT
1 TTTTTCTTTT
33852 TTTTTCTTTT
1 TTTTTCTTTT
*
33862 TTTTTTTTTT
1 TTTTTCTTTT
*
33872 TTTTTTTCTTT
1 TTTTTCT-TTT
33883 TTTTTC
1 TTTTTC
33889 AAGCATAATA
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
10 41 0.58
11 25 0.35
12 5 0.07
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:36726 original size:13 final size:14
Alignment explanation
Indices: 36699--36727 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
36689 TAAAAATAAG
36699 AATGCAAACTATGT
1 AATGCAAACTATGT
36713 AATGCAAA-TATGT
1 AATGCAAACTATGT
36726 AA
1 AA
36728 AAAGTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (14 bp):
AATGCAAACTATGT
Found at i:39083 original size:16 final size:17
Alignment explanation
Indices: 39062--39098 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
39052 TGAATAAAAT
39062 AAATAA-AA-TAATATAA
1 AAATAATAAGTAATA-AA
39078 AAATAATAAGTAATAAA
1 AAATAATAAGTAATAAA
39095 AAAT
1 AAAT
39099 TTGAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 8 0.42
18 5 0.26
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAATAAGTAATAAA
Found at i:39973 original size:11 final size:10
Alignment explanation
Indices: 39959--40017 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
39949 TTTATGTGAC
39959 TAATATGAAAA
1 TAATAT-AAAA
39970 TAATAATAAAA
1 TAAT-ATAAAA
39981 TAATATAAAA
1 TAATATAAAA
*
39991 GTAATAACAAAA
1 -TAAT-ATAAAA
*
40003 TAATAAATAAA
1 TAATATA-AAA
40014 TAAT
1 TAAT
40018 GATTAAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.19
11 27 0.64
12 7 0.17
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (10 bp):
TAATATAAAA
Found at i:40017 original size:22 final size:22
Alignment explanation
Indices: 39959--40017 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
39949 TTTATGTGAC
* *
39959 TAATATGAAAATAATAATAAAA
1 TAATATAAAAATAATAACAAAA
*
39981 TAATATAAAAGTAATAACAAAA
1 TAATATAAAAATAATAACAAAA
40003 TAATA-AATAAATAAT
1 TAATATAA-AAATAAT
40018 GATTAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (22 bp):
TAATATAAAAATAATAACAAAA
Found at i:41197 original size:3 final size:3
Alignment explanation
Indices: 41191--41248 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
41181 AATAATTATT
* **
41191 TAA TAA TAA T-A TAA T-T TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
41237 TAA TAA AAA TAA
1 TAA TAA TAA TAA
41249 AATGAAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 3 0.07
3 42 0.93
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:41209 original size:16 final size:16
Alignment explanation
Indices: 41180--41222 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
41170 TCTAGGCTTG
41180 TAATAAT-T-ATTTAA
1 TAATAATATAATTTAA
41194 TAATAATATAATTTAA
1 TAATAATATAATTTAA
41210 TAATAATAATAAT
1 TAATAAT-ATAAT
41223 AATTTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.27
15 1 0.04
16 13 0.50
17 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAATATAATTTAA
Found at i:68253 original size:59 final size:59
Alignment explanation
Indices: 68146--68271 Score: 137
Period size: 59 Copynumber: 2.1 Consensus size: 59
68136 TAAAGTACAC
* * * * * * **
68146 AAATGATCCCTCAATTATAGGGTGTTGCTTTGTTGAGTCTCTTGACTATCAAAAGTTAAA
1 AAATGATCCCTCAACTATAAGATATTGATTTGTTGAGTCCCTCAACTATCAAAA-TTAAA
* * *
68206 AAATGATCCCT-AACTATAAGATATTGATTTGTTGAGTCCCTCAACTATTACAATTACA
1 AAATGATCCCTCAACTATAAGATATTGATTTGTTGAGTCCCTCAACTATCAAAATTAAA
68264 AAATGATC
1 AAATGATC
68272 ACCCGACTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 12 0.22
59 32 0.58
60 11 0.20
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (59 bp):
AAATGATCCCTCAACTATAAGATATTGATTTGTTGAGTCCCTCAACTATCAAAATTAAA
Found at i:70887 original size:13 final size:13
Alignment explanation
Indices: 70869--70898 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
70859 TGACTTGTTT
*
70869 TTTGCTACTTAAA
1 TTTGCTACTCAAA
70882 TTTGCTACTCAAA
1 TTTGCTACTCAAA
70895 TTTG
1 TTTG
70899 GAAACAGAAA
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:0.27, C:0.17, G:0.10, T:0.47
Consensus pattern (13 bp):
TTTGCTACTCAAA
Found at i:71185 original size:37 final size:37
Alignment explanation
Indices: 71143--71251 Score: 163
Period size: 37 Copynumber: 3.0 Consensus size: 37
71133 TATAAAAAGT
71143 AAGAATCTAATTGTAAGATTGAAACAATAATAAATAA
1 AAGAATCTAATTGTAAGATTGAAACAATAATAAATAA
*
71180 AAGAATCTAATTGTAAGATT-AAA-AACAATAAA-AA
1 AAGAATCTAATTGTAAGATTGAAACAATAATAAATAA
*
71214 AA-AATATAATTGTAAGATTGAAAACAATAATAAATAA
1 AAGAATCTAATTGTAAGATTG-AAACAATAATAAATAA
71251 A
1 A
71252 TGTTACTTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
33 16 0.25
34 4 0.06
35 11 0.17
36 11 0.17
37 23 0.35
ACGTcount: A:0.61, C:0.05, G:0.09, T:0.26
Consensus pattern (37 bp):
AAGAATCTAATTGTAAGATTGAAACAATAATAAATAA
Found at i:71229 original size:33 final size:33
Alignment explanation
Indices: 71150--71252 Score: 125
Period size: 33 Copynumber: 3.0 Consensus size: 33
71140 AGTAAGAATC
* *
71150 TAATTGTAAGATTGAAACAATAATAAATAAAAGAATC
1 TAATTGTAAGATT-AAA-AACAATAAA-AAAA-AATA
71187 TAATTGTAAGATTAAAAACAATAAAAAAAAATA
1 TAATTGTAAGATTAAAAACAATAAAAAAAAATA
* *
71220 TAATTGTAAGATTGAAAACAATAATAAATAAAT
1 TAATTGTAAGATTAAAAACAATAA-AAAAAAAT
71253 GTTACTTATC
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
33 26 0.43
34 11 0.18
35 8 0.13
36 3 0.05
37 13 0.21
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (33 bp):
TAATTGTAAGATTAAAAACAATAAAAAAAAATA
Done.