Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003838.1 Hibiscus syriacus cultivar Beakdansim tig00008226_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: 68118
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:13814 original size:17 final size:18
Alignment explanation
Indices: 13787--13820 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13777 CCTATTTAAC
*
13787 CAAATTTAATATATTTTT
1 CAAATTTAATAGATTTTT
13805 CAAA-TTAATAGATTTT
1 CAAATTTAATAGATTTT
13821 CAGTTGAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (18 bp):
CAAATTTAATAGATTTTT
Found at i:27201 original size:233 final size:234
Alignment explanation
Indices: 26793--27258 Score: 907
Period size: 233 Copynumber: 2.0 Consensus size: 234
26783 AGAGTTGTTT
26793 TCTCCTTTTTATTAAGAGAGAATTGTCATTGTTTCTCCTTGTTAGATCGAGAGAAGTTGTAATTC
1 TCTCCTTTTTATTAAGAGAGAATTGTCATTGTTTCTCCTTGTTAGATCGAGAGAAGTTGTAATTC
26858 ATATTTTCTCATAGTGAATTTTTTCTACATTTGCCCGTGGTTTTTTACCCTATATTATTTAGGGG
66 ATATTTTCTCATAGTGAATTTTTTCTACATTTGCCCGTGGTTTTTTACCCTATATTATTTAGGGG
26923 TTTTCCACGTAAAATTTGTGTATTCTTTATCTTCATTTTTATTTTCTCAAATTATCAGTTGCGAT
131 TTTTCCACGTAAAATTTGTGTATTCTTTATCTTCATTTTTATTTTCTCAAATTATCAGTTGCGAT
26988 TTTGCTCTATCCGATAGTCGTATTCCACAACAATTGGTG
196 TTTGCTCTATCCGATAGTCGTATTCCACAACAATTGGTG
27027 TCTCCTTTTTATTAAGAGAGAATTGTCATTGTTTCTCCTTGTTAGATCGAGA-AAGTTGTAATTC
1 TCTCCTTTTTATTAAGAGAGAATTGTCATTGTTTCTCCTTGTTAGATCGAGAGAAGTTGTAATTC
27091 ATATTTTCTCATAGTGAATTTTTTCTACATTTGCCCGTGGTTTTTTACCCTATATTATTTAGGGG
66 ATATTTTCTCATAGTGAATTTTTTCTACATTTGCCCGTGGTTTTTTACCCTATATTATTTAGGGG
*
27156 TTTTCCACGTAAAATTTGTGTCTTCTTTATCTTCATTTTTATTTTCTCAAATTATCAGTTGCGAT
131 TTTTCCACGTAAAATTTGTGTATTCTTTATCTTCATTTTTATTTTCTCAAATTATCAGTTGCGAT
*
27221 TTTGCTCTATCCGATAGTCGTATTCCGCAACAATTGGT
196 TTTGCTCTATCCGATAGTCGTATTCCACAACAATTGGT
27259 ATCAGAGCCA
Statistics
Matches: 230, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
233 178 0.77
234 52 0.23
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (234 bp):
TCTCCTTTTTATTAAGAGAGAATTGTCATTGTTTCTCCTTGTTAGATCGAGAGAAGTTGTAATTC
ATATTTTCTCATAGTGAATTTTTTCTACATTTGCCCGTGGTTTTTTACCCTATATTATTTAGGGG
TTTTCCACGTAAAATTTGTGTATTCTTTATCTTCATTTTTATTTTCTCAAATTATCAGTTGCGAT
TTTGCTCTATCCGATAGTCGTATTCCACAACAATTGGTG
Found at i:50593 original size:21 final size:22
Alignment explanation
Indices: 50556--50603 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
50546 GTAACTTATA
*
50556 TTTCAATGAAGTGACTTAACCT
1 TTTCAATGAAATGACTTAACCT
*
50578 TTTCAA-GAAATGACTTAATCT
1 TTTCAATGAAATGACTTAACCT
50599 TTTCA
1 TTTCA
50604 TGTATAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (22 bp):
TTTCAATGAAATGACTTAACCT
Found at i:51747 original size:15 final size:17
Alignment explanation
Indices: 51722--51760 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
51712 TATATATATA
51722 TATATTAAA-TTATT-TG
1 TATA-TAAATTTATTATG
51738 TATATAAATTTATTATG
1 TATATAAATTTATTATG
51755 TATATA
1 TATATA
51761 TATATTGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 9 0.43
17 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TATATAAATTTATTATG
Found at i:57287 original size:23 final size:22
Alignment explanation
Indices: 57253--57295 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
57243 TAATATTTTT
57253 ATTTTAAATAATTTACAATTAG
1 ATTTTAAATAATTTACAATTAG
* *
57275 ATTTGTAATTAATTTATAATT
1 ATTT-TAAATAATTTACAATT
57296 TTACGTTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (22 bp):
ATTTTAAATAATTTACAATTAG
Found at i:58945 original size:21 final size:20
Alignment explanation
Indices: 58906--58948 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
58896 GTTGCATATC
58906 TTGCTTTTTGGTGTCGTGGT
1 TTGCTTTTTGGTGTCGTGGT
* *
58926 TTGCTTCTTTTGTGTTGTGGT
1 TTGCTT-TTTGGTGTCGTGGT
58947 TT
1 TT
58949 TTTCGTTCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.00, C:0.09, G:0.30, T:0.60
Consensus pattern (20 bp):
TTGCTTTTTGGTGTCGTGGT
Found at i:59582 original size:40 final size:39
Alignment explanation
Indices: 59502--59678 Score: 117
Period size: 36 Copynumber: 4.7 Consensus size: 39
59492 AAAAAAATGA
*
59502 TTTT-AAATTATATATTATATAA-TTTTTCAAAAATGTGTTT
1 TTTTAAAACTATATATTATATAATTTTTTC-AAAA-G-GTTT
*
59542 TTTTAAAACTATATTTTATATAAGTTTTTTCAAAAGG-TT
1 TTTTAAAACTATATATTATATAA-TTTTTTCAAAAGGTTT
** **
59581 TTAAAGAAACTATATATTATAT--TTTTTTCAAAA--TGA
1 TTTTA-AAACTATATATTATATAATTTTTTCAAAAGGTTT
* * * *
59617 TTTCAAAACCATATATTATATAA-GTTTTCAAAA---TG
1 TTTTAAAACTATATATTATATAATTTTTTCAAAAGGTTT
*
59652 TTTTAAAAATCATATATTATAT-ATTTT
1 TTTTAAAACT-ATATATTATATAATTTT
59679 CAATTTTTTT
Statistics
Matches: 111, Mismatches: 17, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
35 23 0.21
36 25 0.23
37 11 0.10
39 5 0.05
40 20 0.18
41 17 0.15
42 4 0.04
43 6 0.05
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (39 bp):
TTTTAAAACTATATATTATATAATTTTTTCAAAAGGTTT
Found at i:59651 original size:36 final size:35
Alignment explanation
Indices: 59541--59681 Score: 131
Period size: 36 Copynumber: 3.9 Consensus size: 35
59531 AAAATGTGTT
* * * *
59541 TTTTTAAAACTATATTTTATATAAGTTTTTTCAAAAGG
1 TTTTAAAAACCATATATTATAT-AG--TTTTCAAAATG
* **
59579 TTTTAAAGAAACTATATATTATATTTTTTTCAAAATG
1 TTTT-AA-AAACCATATATTATATAGTTTTCAAAATG
* *
59616 ATTTCAAAACCATATATTATATAAGTTTTCAAAATG
1 TTTTAAAAACCATATATTATAT-AGTTTTCAAAATG
*
59652 TTTTAAAAATCATATATTATATA-TTTTCAA
1 TTTTAAAAACCATATATTATATAGTTTTCAA
59682 TTTTTTTTAA
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
34 7 0.08
35 16 0.18
36 31 0.36
37 13 0.15
38 4 0.05
39 1 0.01
40 15 0.17
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (35 bp):
TTTTAAAAACCATATATTATATAGTTTTCAAAATG
Found at i:59690 original size:34 final size:33
Alignment explanation
Indices: 59568--59717 Score: 129
Period size: 36 Copynumber: 4.3 Consensus size: 33
59558 TATATAAGTT
* * *
59568 TTTTCAAAAGGTTTTAAAGAAACTATATATTATATTT
1 TTTTCAAAATGTTTT-AA-AATC-ATATATTATA-TA
* *
59605 TTTTCAAAATGATTTCAAAACCATATATTATATAA
1 TTTTCAAAATG-TTTTAAAATCATATATTATAT-A
59640 GTTTTCAAAATGTTTTAAAAATCATATATTATATA
1 -TTTTCAAAATGTTTT-AAAATCATATATTATATA
** * * *
59675 TTTTCAATTTTTTTTAAAATTATATACTATATA
1 TTTTCAAAATGTTTTAAAATCATATATTATATA
59708 TATTTCAAAA
1 T-TTTCAAAA
59718 AACCGTTTTC
Statistics
Matches: 95, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
33 17 0.18
34 19 0.20
35 14 0.15
36 30 0.32
37 12 0.13
38 3 0.03
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (33 bp):
TTTTCAAAATGTTTTAAAATCATATATTATATA
Found at i:60452 original size:164 final size:165
Alignment explanation
Indices: 60243--60772 Score: 593
Period size: 164 Copynumber: 3.2 Consensus size: 165
60233 ATATTTGGTT
* * * * *
60243 TGCCCT-G-AGCTGAATGTAATCGAACTCGAAGGTTTTCGGTTGGCAGATAGCCCTCCTCGACTT
1 TGCCCTCGAAGCTGAGTGTAATCGAACTCG-AGG--GTCGCTTGGCAGATAGCCCTTCTAGACTT
*
60306 AAGCTTTGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATTGAACTCGAAGGTCTTTGGTGACA
63 AAGCTTTGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGACA
60371 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
128 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
*
60409 TGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGGTC-CTTGGCAGATAGCCCTTCTAGACTTAAG
1 TGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCGCTTGGCAGATAGCCCTTCTAGACTTAAG
* * * * ** * *
60473 CTATGCTGCAAATGATGTACCTTGGAGCTGAGCGTAGTCAAACTCCCAGGTCTTTGTTTACAGAT
66 CTTTGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGACAGAT
60538 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
131 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
* ** * ** * *
60573 TGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTCACATATAATCTTTCTAGCCTT
1 TGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCGCTTGG---CAGATAGCCCTTCTAGACTT
* * * * * * *
60638 GAG-TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTCGGTTG
63 AAGCTT-TGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGG-TG
* * * * *
60702 GCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATG
125 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
* * * *
60743 TG-CCTTGGAGCTGAGCGTAGTCGAACTCGA
1 TGCCCTCGAAGCTGAGTGTAATCGAACTCGA
60773 AGGCCTTTGG
Statistics
Matches: 308, Mismatches: 47, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
164 150 0.49
165 6 0.02
166 6 0.02
167 4 0.01
168 51 0.17
169 52 0.17
170 39 0.13
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
TGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCGCTTGGCAGATAGCCCTTCTAGACTTAAG
CTTTGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGACAGAT
AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
Found at i:60643 original size:85 final size:84
Alignment explanation
Indices: 60258--60784 Score: 548
Period size: 85 Copynumber: 6.3 Consensus size: 84
60248 TGAGCTGAAT
* * * * * *
60258 GTAATCGAACTCGAAGGT-TTTCGGTTGGCAGATAGCCCTCCTCGACTTAAGCTT-TGCTGCAAA
1 GTAATCGAACTCGAAGGTCTTT-GG-TGACAGATAACCCTTCTAGCCTTGAG-TTATGCTGCAAA
* *
60321 TGATGTG-CCTTGGAGCTGAGC
63 TGATGTGCCCTCGAAGCTGAGC
* *
60342 GTAATTGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
1 GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
* *
60407 TGTGCCCTCAAAGCTGAGT
66 TGTGCCCTCGAAGCTGAGC
* * * * * *
60426 GTAATCGAACTCGAGGGTCCTT-G-G-CAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGA
1 GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
* * *
60488 TGT-ACCTTGGAGCTGAGC
66 TGTGCCCTCGAAGCTGAGC
* * ** * * *
60506 GTAGTCAAACTCCCAGGTCTTTGTTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
1 GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
*
60571 TGTGCCCTCGAAGCTGAGT
66 TGTGCCCTCGAAGCTGAGC
* * * * *
60590 GTAATCGAACTCGAAGGTCTTTTGGTCACATATAATCTTTCTAGCCTTGAGTTATGCTGTAAATG
1 GTAATCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
*
60655 ATGTGCCCTCGAAGCTGAGT
65 ATGTGCCCTCGAAGCTGAGC
* * * * * *
60675 GTAATCGAACTCGAGGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATG
1 GTAATCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* *
60740 ATGTG-CCTTGGAGCTGAGC
65 ATGTGCCCTCGAAGCTGAGC
* *
60759 GTAGTCGAACTCGAAGGCCTTTGGTG
1 GTAATCGAACTCGAAGGTCTTTGGTG
60785 GGAACGATTC
Statistics
Matches: 365, Mismatches: 69, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
80 26 0.07
81 36 0.10
82 3 0.01
83 74 0.20
84 109 0.30
85 117 0.32
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
TGTGCCCTCGAAGCTGAGC
Found at i:60657 original size:249 final size:249
Alignment explanation
Indices: 60312--60770 Score: 733
Period size: 249 Copynumber: 1.8 Consensus size: 249
60302 ACTTAAGCTT
* * * *
60312 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATTGAACTCGAAGGTCTTTGGTGACAGATAAC
1 TGCTGCAAATGATGTGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTCACAGATAAC
60377 CCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGG
66 CCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGG
*
60442 GTC-C-TTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTACCTTGGAGCTGAG
131 GTCTCGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTACCTTGGAGCTGAG
60505 CGTAGTCAAACTCCCAGGTCTTTGTTTACAGATAACCCTTCTAGCCTTGAGTTA
196 CGTAGTCAAACTCCCAGGTCTTTGTTTACAGATAACCCTTCTAGCCTTGAGTTA
* * *
60559 TGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTCACATATA
1 TGCTGCAAATGATGTG-CCTCGAAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGTCACAGATA
* * *
60624 ATCTTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGA
64 ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGA
* * *
60689 GGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGC
129 GGGTC-TC-GTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTACCTTGGAGC
*
60754 TGAGCGTAGTCGAACTC
192 TGAGCGTAGTCAAACTC
60771 GAAGGCCTTT
Statistics
Matches: 191, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
247 15 0.08
248 29 0.15
249 79 0.41
251 1 0.01
253 67 0.35
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (249 bp):
TGCTGCAAATGATGTGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTCACAGATAAC
CCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGG
GTCTCGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTACCTTGGAGCTGAG
CGTAGTCAAACTCCCAGGTCTTTGTTTACAGATAACCCTTCTAGCCTTGAGTTA
Found at i:61101 original size:110 final size:110
Alignment explanation
Indices: 60908--61439 Score: 875
Period size: 110 Copynumber: 4.8 Consensus size: 110
60898 TTTTGAGGCT
* *
60908 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTATTTGTTGACAGTC
1 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTC
* *
60973 AATCGCCTCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCC
66 AGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCC
* *
61018 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGTATGAAATTGAAAAGTTGTTTGTTGACAGTC
1 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTC
*
61083 AGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCC
66 AGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCC
* * * * *
61128 AATATCTTTTGATGTGAAATTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAGTC
1 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTC
*
61193 AATCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCC
66 AGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCC
* *
61238 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTGTTTTTTGACAGTC
1 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTC
* * *
61303 AGTCGCCCCTTCACTGTGAAGTTGAGCTTATGATGTCTCGAGTCC
66 AGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCC
*
61348 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACCGTC
1 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTC
* *
61413 AGTCGCCCTTTCGCTGTAAAGTTGAGC
66 AGTCGCCCCTTCGCTGTGAAGTTGAGC
61440 AACCACCATC
Statistics
Matches: 391, Mismatches: 31, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 391 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (110 bp):
AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTC
AGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCC
Found at i:65034 original size:12 final size:12
Alignment explanation
Indices: 65017--65046 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
65007 TTAATTGCAA
*
65017 AAATTAGAATTT
1 AAATTAAAATTT
65029 AAATTAAAATTT
1 AAATTAAAATTT
65041 AAATTA
1 AAATTA
65047 TTCTATTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (12 bp):
AAATTAAAATTT
Found at i:65948 original size:21 final size:20
Alignment explanation
Indices: 65912--65954 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
65902 GTTGTATATC
65912 TTGCTTTTTGGTGTTGTGGT
1 TTGCTTTTTGGTGTTGTGGT
*
65932 TTGCTTCTTTTGTGTTGTGGT
1 TTGCTT-TTTGGTGTTGTGGT
65953 TT
1 TT
65955 TTTCGTTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.00, C:0.07, G:0.30, T:0.63
Consensus pattern (20 bp):
TTGCTTTTTGGTGTTGTGGT
Found at i:66492 original size:13 final size:12
Alignment explanation
Indices: 66468--66529 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
66458 AGACCGAGAA
66468 AAAAAGAA-AAT
1 AAAAAGAATAAT
66479 AAAAAGAATTAAT
1 AAAAAGAA-TAAT
*
66492 AAAACGAATAACT
1 AAAAAGAATAA-T
*
66505 -AAAATAATAAT
1 AAAAAGAATAAT
* *
66516 AATAATAATAAT
1 AAAAAGAATAAT
66528 AA
1 AA
66530 TATACTAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.21
12 23 0.53
13 11 0.26
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (12 bp):
AAAAAGAATAAT
Found at i:66515 original size:3 final size:3
Alignment explanation
Indices: 66498--66540 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
66488 TAATAAAACG
*
66498 AAT AACT AA- AAT AAT AAT AAT AAT AAT AAT AAT -AT ACT AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
66541 ACTATATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:66556 original size:9 final size:10
Alignment explanation
Indices: 66507--66555 Score: 52
Period size: 9 Copynumber: 5.1 Consensus size: 10
66497 GAATAACTAA
66507 AATAATA-AT
1 AATAATATAT
66516 AATAATA-AT
1 AATAATATAT
66525 AATAATATACT
1 AATAATATA-T
66536 AATAA-ACTAT
1 AATAATA-TAT
66546 -ATAATATAT
1 AATAATATAT
66555 A
1 A
66556 TTTCAAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 23 0.66
10 4 0.11
11 8 0.23
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (10 bp):
AATAATATAT
Found at i:66830 original size:26 final size:26
Alignment explanation
Indices: 66791--66841 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
66781 TTCAAACTAT
66791 ATATTATAAGTTTTCAAAATGTTTTA
1 ATATTATAAGTTTTCAAAATGTTTTA
66817 ATATTATATA-TTTTCAAAATGTTTT
1 ATATTATA-AGTTTTCAAAATGTTTT
66842 TTTAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (26 bp):
ATATTATAAGTTTTCAAAATGTTTTA
Done.