Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005426.1 Hibiscus syriacus cultivar Beakdansim tig00012442_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: 63889
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:6908 original size:20 final size:20
Alignment explanation
Indices: 6883--6924 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
6873 TAGTTTAAAA
6883 ATTAATTTGATTCTTTGAAC
1 ATTAATTTGATTCTTTGAAC
*
6903 ATTAATTTGATTGTTTGAAC
1 ATTAATTTGATTCTTTGAAC
6923 AT
1 AT
6925 GATTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
ATTAATTTGATTCTTTGAAC
Found at i:26608 original size:20 final size:20
Alignment explanation
Indices: 26571--26624 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
26561 TAAGATCAAA
*
26571 ATAATAAAATAATTAAAGCC
1 ATAATAAAATAATAAAAGCC
**
26591 ATAATTAAAAT-ATAAAAGTA
1 ATAA-TAAAATAATAAAAGCC
*
26611 ATAACAAAATAATA
1 ATAATAAAATAATA
26625 TTGTAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.18
20 17 0.61
21 6 0.21
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.26
Consensus pattern (20 bp):
ATAATAAAATAATAAAAGCC
Found at i:27721 original size:3 final size:3
Alignment explanation
Indices: 27715--27786 Score: 101
Period size: 3 Copynumber: 24.0 Consensus size: 3
27705 TTATTTTTTT
*
27715 TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* *
27760 TTA TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
27787 ATAAATTAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.92
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:28343 original size:113 final size:113
Alignment explanation
Indices: 28045--28650 Score: 1054
Period size: 113 Copynumber: 5.3 Consensus size: 113
28035 TCATTGTGAA
*
28045 CTTCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCACTGGAAAAGTTGATCCATCG
1 CTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTC--TCTCTGGAAAAGTTGATCCATCG
* *
28109 AGTGATGAATTTGAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
64 AGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
*
28159 CTTCTT-TTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTGGAAAAGTTGATCCATCGAG
1 CTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAG
28223 TGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
66 TGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
*
28271 CTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAATTGATCCATCGAG
1 CTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAG
28336 TGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
66 TGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
*
28384 CTTCTTCTTTTTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAG
1 CTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAG
28449 TGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
66 TGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
* *
28497 CTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCACTGGAAAAATTGATCCATCG
1 CTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTC--TCTCTGGAAAAGTTGATCCATCG
* * * *
28562 AATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTACGAACTT
64 AGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
28612 CTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 CTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
28651 TCTTCTTCTT
Statistics
Matches: 473, Mismatches: 15, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
112 76 0.16
113 254 0.54
114 37 0.08
115 106 0.22
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (113 bp):
CTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAG
TGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
Found at i:28614 original size:341 final size:335
Alignment explanation
Indices: 28019--28650 Score: 1059
Period size: 341 Copynumber: 1.9 Consensus size: 335
28009 TCTAGCAAAG
* *
28019 GTTGCACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
*
28084 TTTCACTGGAAAAGTTGATCCATCGAGTGATGAATTTGAGCGAAAAGTTGAACAAGTTCTTCTCA
66 -TTCACTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTCA
* *
28149 TTATGAACTTCTTCTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTGGAAAAGTTGA
130 TTATGAACTTCTTCTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTATCACTGGAAAAATTGA
* * * *
28214 TCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCT
195 TCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTTCT
28279 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAATTGATCCATCGAGTGATGAAT
260 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAATTGATCCATCGAGTGATGAAT
28344 TCGAGCGAAAA
325 TCGAGCGAAAA
* *
28355 GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTTTTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTC----TTCAGATGAGTTCTTCTCATTATGA
*
28420 ACTC-TCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTC
62 ACTCTTCACTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTC
* *
28484 TTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCACTGGAAA
127 TCATTATGAACTTCTTCTT-TTTCTTCAGATGAGTTCTTCTCATTATGAA--CTATCACTGGAAA
28549 AATTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTACGAACTTCT
189 AATTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTACGAACTTCT
28614 TCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
254 TCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
28651 TCTTCTTCTT
Statistics
Matches: 275, Mismatches: 14, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
336 32 0.12
338 76 0.28
339 30 0.11
340 29 0.11
341 108 0.39
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (335 bp):
GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
TTCACTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTCAT
TATGAACTTCTTCTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTATCACTGGAAAAATTGAT
CCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTTCTT
TCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAATTGATCCATCGAGTGATGAATT
CGAGCGAAAA
Found at i:28650 original size:40 final size:40
Alignment explanation
Indices: 28591--28690 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
28581 AAGTTGAACA
* *
28591 AGTTCTTCTCATTACGAACTTCTTCTTCTTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAAATG
*
28631 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTTAAATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAAATG
* *
28671 AGTTCTTTTTATTATGAACT
1 AGTTCTTCTCATTATGAACT
28691 CTACCTGGCA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.51
Consensus pattern (40 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAAATG
Found at i:28769 original size:153 final size:155
Alignment explanation
Indices: 28476--28809 Score: 494
Period size: 153 Copynumber: 2.2 Consensus size: 155
28466 AAGTTGAACA
* * *
28476 AGTTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAAATGAGTTCTTCTCATTATGAACTCTTAC
* * * *
28541 ACTGGAAAAATTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTAC
66 ACTGGAAAAACTGATCCATCAAATGATGAATTCAAACGAAAAGTTGAACAAATTCTTCTCATTAC
*
28606 GAACTTCTTCTTCTTTCTTCAGATG
131 GAACTTCTTCTTCCTTCTTCAGATG
* * *
28631 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTTAAATGAGTTCTTTTTATTATGAACTC-TAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAAATGAGTTCTTCTCATTATGAACTCTTAC
* **
28695 -CTGGCAATGCTGATCCATCAAATGATGAATTCAAAC-AAAAGGTTGAACAAATTCTTCTCATTA
66 ACTGGAAAAACTGATCCATCAAATGATGAATTCAAACGAAAA-GTTGAACAAATTCTTCTCATTA
*
28758 TGAACTTCTTCTTCCTTCTTCAGATG
130 CGAACTTCTTCTTCCTTCTTCAGATG
*
28784 AGTTCTTCTCATTATGAACTTTTTCT
1 AGTTCTTCTCATTATGAACTTCTTCT
28810 GGAAAAGCTG
Statistics
Matches: 162, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
152 4 0.02
153 100 0.62
154 2 0.01
155 56 0.35
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (155 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAAATGAGTTCTTCTCATTATGAACTCTTAC
ACTGGAAAAACTGATCCATCAAATGATGAATTCAAACGAAAAGTTGAACAAATTCTTCTCATTAC
GAACTTCTTCTTCCTTCTTCAGATG
Found at i:28834 original size:113 final size:113
Alignment explanation
Indices: 28633--29172 Score: 755
Period size: 113 Copynumber: 4.8 Consensus size: 113
28623 TTCAGATGAG
* * * * * *
28633 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTTAAATGAGTTCTTTTTATTATGAACTCTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
*
28698 GCAATGCTGATCCATCAAATGATGAATTCAAAC-AAAAGGTTGAACAAA
66 GCAATGCTGATCCATCAAATGATGAATTCAAGCGAAAA-GTTGAACAAA
****
28746 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
* * * * * *
28811 GAAAAGCTGATTCATCAAGTGATGGAATT-GAGC-AAAAGGTTGAATAAA
66 GCAATGCTGATCCATCAAATGAT-GAATTCAAGCGAAAA-GTTGAACAAA
* * *
28859 TTCTTCTCATTATGAACGTATTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTTGACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
* *
28923 GTAATGCTGATCCATCAAATGATGAATTCAAGCGAAAAGTTGAACAAG
66 GCAATGCTGATCCATCAAATGATGAATTCAAGCGAAAAGTTGAACAAA
28971 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
* * *
29036 GCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAG
66 GCAATGCTGATCCATCAAATGATGAATTCAAGCGAAAAGTTGAACAAA
* * * *
29084 TTCTTCTCATTACGAACTTCTTCTTCTTTGTTCAGATGAGTTCTTCTTATTATGAACTCGACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
*
29149 GCAATGTTGATCCATCAAATGATG
66 GCAATGCTGATCCATCAAATGATG
29173 GATTTGAATC
Statistics
Matches: 385, Mismatches: 38, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
111 5 0.01
112 89 0.23
113 286 0.74
114 5 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
GCAATGCTGATCCATCAAATGATGAATTCAAGCGAAAAGTTGAACAAA
Found at i:29601 original size:22 final size:22
Alignment explanation
Indices: 29576--29630 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
29566 GATAAAGCTT
*
29576 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
29598 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
29620 TCATCTTTGAA
1 TCATCTTTGAA
29631 GAAGTAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:31029 original size:76 final size:76
Alignment explanation
Indices: 30904--31074 Score: 209
Period size: 76 Copynumber: 2.3 Consensus size: 76
30894 GATGTGGGCC
* * * * *
30904 TTCAGCATGCCCCAACA-ATTACTGATACGAACGTTCAAAATACATCAACATTCTTCATTCTGAT
1 TTCAGCATGCCCCAACATTTTACTGATACAAACATTCAAAATACATCAACATTCCTCATTCAGAT
30968 TGAAAAAGGCT
66 TGAAAAAGGCT
* * ** *
30979 TTCAGCATGCCCCAACATTTTGCTGATATAAACATTCAGGATACATCAACATTCCTGATTCAGAT
1 TTCAGCATGCCCCAACATTTTACTGATACAAACATTCAAAATACATCAACATTCCTCATTCAGAT
* *
31044 TGAAAAGGGTT
66 TGAAAAAGGCT
* *
31055 TTCAGCATTCCCTAACATTT
1 TTCAGCATGCCCCAACATTT
31075 GCTTCTTGTT
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
75 17 0.21
76 64 0.79
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (76 bp):
TTCAGCATGCCCCAACATTTTACTGATACAAACATTCAAAATACATCAACATTCCTCATTCAGAT
TGAAAAAGGCT
Found at i:35738 original size:14 final size:14
Alignment explanation
Indices: 35719--35757 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
35709 GCAGAGATGC
35719 CAAATGTAAATATG
1 CAAATGTAAATATG
*
35733 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
35747 TAAATGTAAAT
1 CAAATGTAAAT
35758 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.28
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:39234 original size:15 final size:15
Alignment explanation
Indices: 39214--39243 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39204 ATAGCTATGG
39214 TGGTGACTCACCATA
1 TGGTGACTCACCATA
39229 TGGTGACTCACCATA
1 TGGTGACTCACCATA
39244 GGGCTTCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (15 bp):
TGGTGACTCACCATA
Found at i:39396 original size:3 final size:3
Alignment explanation
Indices: 39390--39458 Score: 104
Period size: 3 Copynumber: 23.0 Consensus size: 3
39380 TTATTTTTTT
*
39390 TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
39435 TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
39459 ATAAATAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:39470 original size:15 final size:14
Alignment explanation
Indices: 39394--39466 Score: 66
Period size: 12 Copynumber: 5.4 Consensus size: 14
39384 TTTTTTTAAT
39394 AATAATAATAATATA
1 AATAATAATAA-ATA
*
39409 TATAATAAT-AAT-
1 AATAATAATAAATA
39421 AATAATAATTATAAT-
1 AATAATAA-TA-AATA
*
39436 TATAATAAT-AAT-
1 AATAATAATAAATA
39448 AATAATAATAAATA
1 AATAATAATAAATA
39462 AATAA
1 AATAA
39467 ATAAAATGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
12 18 0.37
13 6 0.12
14 7 0.14
15 18 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAATAATAAATA
Found at i:39473 original size:9 final size:10
Alignment explanation
Indices: 39391--39470 Score: 75
Period size: 9 Copynumber: 8.5 Consensus size: 10
39381 TATTTTTTTT
39391 AATAATAAT-
1 AATAATAATA
39400 AATAAT-ATA
1 AATAATAATA
*
39409 TATAATAAT-
1 AATAATAATA
39418 AATAATAAT-
1 AATAATAATA
*
39427 AATTATAATTA
1 AATAATAA-TA
39438 TAATAATAAT-
1 -AATAATAATA
39448 AATAATAATA
1 AATAATAATA
39458 AAT-A-AATA
1 AATAATAATA
39466 AATAA
1 AATAA
39471 AATGGGTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
8 9 0.15
9 37 0.62
10 6 0.10
11 1 0.02
12 7 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AATAATAATA
Found at i:42642 original size:113 final size:113
Alignment explanation
Indices: 42443--42664 Score: 320
Period size: 113 Copynumber: 2.0 Consensus size: 113
42433 TGGCACGCTC
** * * *
42443 AAGTTTTTTGTAACTGTAAATGTAACATTTTCCTTTAACTTTGAGATTAACTTCAAATACAATAA
1 AAGTTTTAAGTAACTGCAAATGAAACATTTTCCTTTAACTTTGAGATTAACTGCAAATACAATAA
* *
42508 GCCTTAATATAAACATCAAAAGTAACACACTTCAAATGCAATAATCTG
66 ACCTTAATATAAACATCAAAAGTAACACACTGCAAATGCAATAATCTG
* *
42556 AAGTTTTAAGTAACTGCAATTGAAACATTTTTCCTTTAAC-TTGAGATTAACTGCAAATATAATA
1 AAGTTTTAAGTAACTGCAAATGAAACA-TTTTCCTTTAACTTTGAGATTAACTGCAAATACAATA
* * *
42620 AACCTTAATTTAAACATGAAAAGTAATACACTGCAAATGCAATAA
65 AACCTTAATATAAACATCAAAAGTAACACACTGCAAATGCAATAA
42665 GCCATAATCC
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
113 84 0.88
114 12 0.12
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (113 bp):
AAGTTTTAAGTAACTGCAAATGAAACATTTTCCTTTAACTTTGAGATTAACTGCAAATACAATAA
ACCTTAATATAAACATCAAAAGTAACACACTGCAAATGCAATAATCTG
Found at i:60132 original size:31 final size:30
Alignment explanation
Indices: 60090--60253 Score: 148
Period size: 31 Copynumber: 5.3 Consensus size: 30
60080 CTAATGTGAC
* *
60090 TCTTGGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTGGGTAGGC-CTGTGGCCCTGAGATCTT
* *
60121 TCTTGGATAGGCCTTGTGGCCCTGAGATTTT
1 TCTTGGGTAGGCC-TGTGGCCCTGAGATCTT
* ** * * *
60152 TCTTGGGCAGGCCCCATGGACTTGAGATCAT
1 TCTTGGGTAGG-CCTGTGGCCCTGAGATCTT
* * ** *
60183 TCTTAGATAGGCCCTACGACCCTGAGATCTT
1 TCTTGGGTAGG-CCTGTGGCCCTGAGATCTT
*
60214 TCTTGGGTAGGCCTGTGGCCCTGAGAACTT
1 TCTTGGGTAGGCCTGTGGCCCTGAGATCTT
60244 TCTTGGGTAG
1 TCTTGGGTAG
60254 TCTCTCAAGC
Statistics
Matches: 104, Mismatches: 27, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
30 26 0.25
31 76 0.73
32 2 0.02
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (30 bp):
TCTTGGGTAGGCCTGTGGCCCTGAGATCTT
Done.