Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003359.1 Hibiscus syriacus cultivar Beakdansim tig00007068_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: 75259
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:4054 original size:40 final size:40
Alignment explanation
Indices: 4008--4116 Score: 191
Period size: 40 Copynumber: 2.7 Consensus size: 40
3998 GACACTAAAG
*
4008 TGTATATGGTGGGCACGACCTTATGTGTAATACATTTTGA
1 TGTATATGGTGGGCACGACCTTATGTGTAATACACTTTGA
* *
4048 TGTATATGGTGGGCACGACCTTATGTGTAATATACTTTGG
1 TGTATATGGTGGGCACGACCTTATGTGTAATACACTTTGA
4088 TGTATATGGTGGGCACGACCTTATGTGTA
1 TGTATATGGTGGGCACGACCTTATGTGTA
4117 GCACTACGGT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.37
Consensus pattern (40 bp):
TGTATATGGTGGGCACGACCTTATGTGTAATACACTTTGA
Found at i:8287 original size:21 final size:21
Alignment explanation
Indices: 8263--8313 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
8253 TTGCCATTTA
8263 TTTTTTTTATTT-TGATTTATT
1 TTTTTTTTATTTCTG-TTTATT
*
8284 TTTTATTTATTTCTGTTTATT
1 TTTTTTTTATTTCTGTTTATT
*
8305 TTTATTTTA
1 TTTTTTTTA
8314 CTAACTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (21 bp):
TTTTTTTTATTTCTGTTTATT
Found at i:8306 original size:20 final size:20
Alignment explanation
Indices: 8258--8311 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
8248 TTTTCTTGCC
8258 ATTTATTTTT-TTTATTTTG
1 ATTTATTTTTATTTATTTTG
8277 ATTTATTTTTTATTTATTTCTG
1 ATTTA-TTTTTATTTATTT-TG
8299 -TTTATTTTTATTT
1 ATTTATTTTTATTT
8312 TACTAACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.16
20 14 0.44
21 11 0.34
22 2 0.06
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.78
Consensus pattern (20 bp):
ATTTATTTTTATTTATTTTG
Found at i:11815 original size:11 final size:11
Alignment explanation
Indices: 11772--11818 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
11762 AATCAAGAAC
*
11772 AAAAAGAAAAG
1 AAAAAAAAAAG
**
11783 AAGTAAAAAAG
1 AAAAAAAAAAG
*
11794 -AAAAAACAAG
1 AAAAAAAAAAG
11804 AAAAAAAAAAG
1 AAAAAAAAAAG
11815 AAAA
1 AAAA
11819 GAAGCAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
10 7 0.25
11 21 0.75
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:11834 original size:22 final size:22
Alignment explanation
Indices: 11773--11821 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
11763 ATCAAGAACA
**
11773 AAAAGAA-AAGAAGTAAAAAAG
1 AAAAGAACAAGAAAAAAAAAAG
11794 AAAA-AACAAGAAAAAAAAAAG
1 AAAAGAACAAGAAAAAAAAAAG
11815 AAAAGAA
1 AAAAGAA
11822 GCAAAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAGAACAAGAAAAAAAAAAG
Found at i:11835 original size:21 final size:18
Alignment explanation
Indices: 11772--11828 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
11762 AATCAAGAAC
11772 AAAAAGAAAAGAAGTAAAA
1 AAAAAGAAAAGAAG-AAAA
* *
11791 AAGAA-AAAACAAGAAAAA
1 AAAAAGAAAAGAAG-AAAA
11809 AAAAAGAAAAGAAGCAAAA
1 AAAAAGAAAAGAAG-AAAA
11828 A
1 A
11829 TCAAAAGGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAGAAGAAAA
Found at i:12915 original size:18 final size:18
Alignment explanation
Indices: 12892--12927 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12882 TCAACATCAA
*
12892 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
12910 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
12928 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:13461 original size:36 final size:37
Alignment explanation
Indices: 13414--13489 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 37
13404 GTGCTCACCA
* *
13414 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-CT
1 TTGTCTCTCTTGAGACAGTTTCCCTTAAAAAAAACCT
13450 TTGTCTCTCTTGAGACAGTTTCCCTTAAAAAAAACCT
1 TTGTCTCTCTTGAGACAGTTTCCCTTAAAAAAAACCT
13487 TTG
1 TTG
13490 AAATTGTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
36 32 0.86
37 5 0.14
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTAAAAAAAACCT
Found at i:13499 original size:28 final size:31
Alignment explanation
Indices: 13467--13524 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
13457 TCTTGAGACA
13467 GTTTCCCTT-AA-A-AAAAACCTTTGAAATT
1 GTTTCCCTTAAACACAAAAACCTTTGAAATT
*
13495 GTTTCTCTTGAAACACAAAAACCTTTGAAA
1 GTTTCCCTT-AAACACAAAAACCTTTGAAA
13525 CATAAACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 8 0.32
30 2 0.08
31 1 0.04
32 14 0.56
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (31 bp):
GTTTCCCTTAAACACAAAAACCTTTGAAATT
Found at i:14654 original size:106 final size:106
Alignment explanation
Indices: 14351--14881 Score: 760
Period size: 106 Copynumber: 5.0 Consensus size: 106
14341 TCGCGCCACC
* * *
14351 CGAGACAACACAAGTTCAACTTCACAACGAAGGGAAGGCTGGTTGTCAACAAAGAACTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* ** * * *
14416 TTCAGAGCCAATTTTAACTTCACAAAGAAAGATATTGGACC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACT
* *
14457 CAAGACAACACAAGTTCAACTTCACAACGAAGGGAC-GCTGGTTGTCAACAAATAATATT-CCAA
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT-TTCCCAA
*
14520 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGGCATTGGACT
65 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACT
14562 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* *
14627 TTCAGAGCCAATTTCAACTTCATAGCGAAGGGCATTGGACT
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACT
* * *
14668 CGAGACAGCACAAGTTCAACTTCACAACGAATGGACGACTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* * * *
14733 TTCAAAACCAATTTCAACTTCACAGCGAAGTATATTGGACT
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACT
* * *
14774 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGATGTCAACAAACAATTTCCCAGT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* * * * * * *
14839 TCCAGAACTAATTTCAACTTCACGGCGGAGAATATTGGACT
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACT
14880 CG
1 CG
14882 GAACAATACA
Statistics
Matches: 387, Mismatches: 35, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
105 94 0.24
106 293 0.76
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (106 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
TTCAGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACT
Found at i:21837 original size:34 final size:34
Alignment explanation
Indices: 21822--21950 Score: 170
Period size: 34 Copynumber: 3.8 Consensus size: 34
21812 CGCGTTCGTT
* * * * *
21822 TATCATTCGCTAACATATTCATTTCA-CGTTCGTT
1 TATCATTCGCGAACATGTTCGTTT-AGCATTAGTT
* *
21856 TTATCATTCGCTAACATGTTCGCTTAGCATTAGTT
1 T-ATCATTCGCGAACATGTTCGTTTAGCATTAGTT
21891 TATCATTCGCGAACATGTTCGTTTAGCATTAGTT
1 TATCATTCGCGAACATGTTCGTTTAGCATTAGTT
21925 TATCATTCGCGAACATGTTCGTTTAG
1 TATCATTCGCGAACATGTTCGTTTAG
21951 AATAAAAAGG
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
34 59 0.69
35 27 0.31
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (34 bp):
TATCATTCGCGAACATGTTCGTTTAGCATTAGTT
Found at i:21866 original size:35 final size:34
Alignment explanation
Indices: 21799--21940 Score: 117
Period size: 34 Copynumber: 4.1 Consensus size: 34
21789 ATTGTTCACG
* * *
21799 AACATGTTCGTTTCGCGTTCGTTTATCATTCGCT
1 AACATATTCATTTCACGTTCGTTTATCATTCGCT
21833 AACATATTCATTTCACGTTCGTTTTATCATTCGCT
1 AACATATTCATTTCACGTTCG-TTTATCATTCGCT
* ** * * *
21868 AACATGTTCGCTT-AGCATTAGTTTATCATTCGCG
1 AACATATTCATTTCA-CGTTCGTTTATCATTCGCT
* * * * *
21902 AACATGTTCGTTT-AGCATTAGTTTATCATTCGCG
1 AACATATTCATTTCA-CGTTCGTTTATCATTCGCT
21936 AACAT
1 AACAT
21941 GTTCGTTTAG
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
34 69 0.72
35 27 0.28
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.42
Consensus pattern (34 bp):
AACATATTCATTTCACGTTCGTTTATCATTCGCT
Found at i:21874 original size:69 final size:68
Alignment explanation
Indices: 21797--21950 Score: 193
Period size: 69 Copynumber: 2.2 Consensus size: 68
21787 TTATTGTTCA
* * * * * *
21797 CGAACATGTTCGTTTCGCGTTCGTTTATCATTCGCTAACATATTCATTTCA-CGTTCGTTTTATC
1 CGAACATGTTCGTTTAGCATTAGTTTATCATTCGCGAACATATTCATTT-AGCATTAG-TTTATC
21861 ATTCG
64 ATTCG
* * * *
21866 CTAACATGTTCGCTTAGCATTAGTTTATCATTCGCGAACATGTTCGTTTAGCATTAGTTTATCAT
1 CGAACATGTTCGTTTAGCATTAGTTTATCATTCGCGAACATATTCATTTAGCATTAGTTTATCAT
21931 TCG
66 TCG
21934 CGAACATGTTCGTTTAG
1 CGAACATGTTCGTTTAG
21951 AATAAAAAGG
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
68 27 0.38
69 45 0.62
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (68 bp):
CGAACATGTTCGTTTAGCATTAGTTTATCATTCGCGAACATATTCATTTAGCATTAGTTTATCAT
TCG
Found at i:28022 original size:5 final size:5
Alignment explanation
Indices: 27986--28013 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
27976 ATATTATTAA
27986 TAATT TAATT TAATT TAATT TAATT TAA
1 TAATT TAATT TAATT TAATT TAATT TAA
28014 AATTAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TAATT
Found at i:32383 original size:37 final size:36
Alignment explanation
Indices: 32275--32372 Score: 144
Period size: 35 Copynumber: 2.7 Consensus size: 36
32265 TGGTAATCAA
32275 CTTTGAAAAAATAATTTTCAAAGTTTGATAAATGTTT
1 CTTT-AAAAAATAATTTTCAAAGTTTGATAAATGTTT
* **
32312 CTTT-GAAAATGGTTTTCAAAGTTTGATAAATGTTT
1 CTTTAAAAAATAATTTTCAAAGTTTGATAAATGTTT
32347 CTTTAAAAAATAATTTTTCAAAGTTT
1 CTTTAAAAAATAA-TTTTCAAAGTTT
32373 AGTACATGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
35 32 0.60
36 5 0.09
37 16 0.30
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (36 bp):
CTTTAAAAAATAATTTTCAAAGTTTGATAAATGTTT
Found at i:32392 original size:37 final size:36
Alignment explanation
Indices: 32277--32392 Score: 139
Period size: 37 Copynumber: 3.2 Consensus size: 36
32267 GTAATCAACT
32277 TTGAAAAAATAATTTTCAAAGTTTGATAAATGTTTC
1 TTGAAAAAATAATTTTCAAAGTTTGATAAATGTTTC
**
32313 TTTG--AAAATGGTTTTCAAAGTTTGATAAATGTTTC
1 -TTGAAAAAATAATTTTCAAAGTTTGATAAATGTTTC
* * *
32348 TTTAAAAAATAATTTTTCAAAGTTT-AGTACATGTTTG
1 TTGAAAAAATAA-TTTTCAAAGTTTGA-TAAATGTTTC
32385 TTGAAAAA
1 TTGAAAAA
32393 TGATAATGAG
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
34 2 0.03
35 29 0.43
36 6 0.09
37 30 0.45
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.43
Consensus pattern (36 bp):
TTGAAAAAATAATTTTCAAAGTTTGATAAATGTTTC
Found at i:36465 original size:27 final size:27
Alignment explanation
Indices: 36427--36488 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
36417 AGATGAGAAT
36427 TGGGAACCTATGTATTCACGTTAACAA
1 TGGGAACCTATGTATTCACGTTAACAA
36454 TGGGAACCTATGTATTCACGTTAACAA
1 TGGGAACCTATGTATTCACGTTAACAA
*
36481 GGGGAACC
1 TGGGAACC
36489 GATATGTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (27 bp):
TGGGAACCTATGTATTCACGTTAACAA
Found at i:39474 original size:29 final size:29
Alignment explanation
Indices: 39442--39509 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
39432 TAATAGAATT
** *
39442 ATTCAGCGTTAAATGTTGAATCGTTCAGC
1 ATTCAGCGCGAAATGTTGAACCGTTCAGC
39471 ATTCAGCGCGAAATGTTGAACCGTTCAGC
1 ATTCAGCGCGAAATGTTGAACCGTTCAGC
*
39500 ATTCAACGCG
1 ATTCAGCGCG
39510 TTTGTTTCGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (29 bp):
ATTCAGCGCGAAATGTTGAACCGTTCAGC
Found at i:40678 original size:2 final size:2
Alignment explanation
Indices: 40671--40761 Score: 52
Period size: 2 Copynumber: 49.0 Consensus size: 2
40661 AAATAATTAT
* * * *
40671 TA TA TA TA TA TA TA TA TA -A T- TA -A TA AA TT TA AA T- TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
40709 T- TA AA TA TA TA TA TA TA TA TA TA -A TA TT TA TA TA TT TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
40748 TT TA AA TA TA TA TA
1 TA TA TA TA TA TA TA
40762 CCCGGCCCGA
Statistics
Matches: 64, Mismatches: 18, Indels: 14
0.67 0.19 0.15
Matches are distributed among these distances:
1 7 0.11
2 57 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:51698 original size:12 final size:12
Alignment explanation
Indices: 51681--51720 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
51671 ACAGCAGCCC
51681 CCCCCTTAGCAG
1 CCCCCTTAGCAG
51693 CCCCCTTAGCAG
1 CCCCCTTAGCAG
51705 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
51718 CCC
1 CCC
51721 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:51709 original size:13 final size:13
Alignment explanation
Indices: 51680--51720 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
51670 TACAGCAGCC
51680 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
51693 -CCCCCTTAGCAG
1 CCCCCCTTAGCAG
51705 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
51718 CCC
1 CCC
51721 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCCCCTTAGCAG
Found at i:55008 original size:15 final size:16
Alignment explanation
Indices: 54980--55011 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
54970 AAAATCTTTC
54980 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
54996 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
55011 T
1 T
55012 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:55784 original size:16 final size:16
Alignment explanation
Indices: 55760--55791 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55750 TATCGCCGAC
*
55760 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
55776 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
55792 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:56214 original size:12 final size:12
Alignment explanation
Indices: 56197--56236 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
56187 CAGCAGCCCC
56197 CCCCCTTAGCAG
1 CCCCCTTAGCAG
56209 CCCCCTTAGCAG
1 CCCCCTTAGCAG
56221 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
56234 CCC
1 CCC
56237 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:56225 original size:13 final size:13
Alignment explanation
Indices: 56196--56236 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
56186 ACAGCAGCCC
56196 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
56209 -CCCCCTTAGCAG
1 CCCCCCTTAGCAG
56221 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
56234 CCC
1 CCC
56237 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCCCCTTAGCAG
Found at i:57784 original size:26 final size:26
Alignment explanation
Indices: 57755--57804 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
57745 TTCCAGTAAT
57755 TAATTTGACAAACTGATTTGATTAGC
1 TAATTTGACAAACTGATTTGATTAGC
*
57781 TAATTTGAGAAACTGATTTGATTA
1 TAATTTGACAAACTGATTTGATTA
57805 ACTGTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (26 bp):
TAATTTGACAAACTGATTTGATTAGC
Found at i:57807 original size:13 final size:13
Alignment explanation
Indices: 57765--57808 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
57755 TAATTTGACA
57765 AACTGATTTGATT
1 AACTGATTTGATT
* * **
57778 AGCTAATTTGAGA
1 AACTGATTTGATT
57791 AACTGATTTGATT
1 AACTGATTTGATT
57804 AACTG
1 AACTG
57809 TTTATAGAAG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (13 bp):
AACTGATTTGATT
Found at i:58463 original size:6 final size:6
Alignment explanation
Indices: 58454--58480 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
58444 TGGTGAAGAT
58454 GAAGCA GAAGCA GAAGCA GAAGCA GAA
1 GAAGCA GAAGCA GAAGCA GAAGCA GAA
58481 TCCAAGTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.33, T:0.00
Consensus pattern (6 bp):
GAAGCA
Found at i:64999 original size:14 final size:14
Alignment explanation
Indices: 64982--65014 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
64972 AAATGCCCTT
64982 AAAAAAATTCTTTC
1 AAAAAAATTCTTTC
64996 AAAAAAATTCTTTC
1 AAAAAAATTCTTTC
65010 AAAAA
1 AAAAA
65015 TATCCTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAAAATTCTTTC
Found at i:65206 original size:36 final size:36
Alignment explanation
Indices: 65165--65236 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
65155 TCATTAAACC
* *
65165 TTTTTAT-ATTTTCAATTTTGTAAAAAAAATTATATA
1 TTTTTATGAATTTAAATTTTGTAAAAAAAA-TATATA
* *
65201 TTTTTATGAATTTAAATTTTTTAAAGAAAATATATA
1 TTTTTATGAATTTAAATTTTGTAAAAAAAATATATA
65237 AATAATTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 13 0.42
37 18 0.58
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (36 bp):
TTTTTATGAATTTAAATTTTGTAAAAAAAATATATA
Found at i:71945 original size:29 final size:29
Alignment explanation
Indices: 71913--72028 Score: 94
Period size: 29 Copynumber: 3.9 Consensus size: 29
71903 ATCCTCGACA
*
71913 ACTGTCCA-AGGTCCCGAAGAACCTAGTAT
1 ACTGTCCATA-GTCCCGAAGAACATAGTAT
* **
71942 ACTGTCCATAGTTCCTTAGAACATAGTAT
1 ACTGTCCATAGTCCCGAAGAACATAGTAT
*
71971 ACTATCCATATGTCCCGAAG-ACATAGGTAATT
1 ACTGTCCATA-GTCCCGAAGAACATA-GT-A-T
* *
72003 A-TGTCCATATGTTCCGTAGAACATAG
1 ACTGTCCATA-GTCCCGAAGAACATAG
72029 GTAAACCCTC
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
29 37 0.53
30 9 0.13
31 17 0.24
32 7 0.10
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (29 bp):
ACTGTCCATAGTCCCGAAGAACATAGTAT
Found at i:73082 original size:21 final size:21
Alignment explanation
Indices: 73058--73102 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
73048 CCATGTTCGT
* *
73058 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
73079 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
73100 TTG
1 TTG
73103 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Done.