Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005782.1 Hibiscus syriacus cultivar Beakdansim tig00013542_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: 54899
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:4853 original size:11 final size:13
Alignment explanation
Indices: 4821--4850 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4811 TGGCCAAAGA
4821 TGAAAAGGTATGT
1 TGAAAAGGTATGT
4834 TGAAAAGGTATG-
1 TGAAAAGGTATGT
4846 TGAAA
1 TGAAA
4851 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:6190 original size:15 final size:15
Alignment explanation
Indices: 6155--6183 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6145 CTGCTTCAAC
6155 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
6169 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
6184 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:7074 original size:24 final size:21
Alignment explanation
Indices: 7040--7082 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
7030 TCCACAAGAC
*
7040 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
7062 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
7083 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:12006 original size:4 final size:5
Alignment explanation
Indices: 11978--12003 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11968 ACTCAAAAAG
11978 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
12004 GAAGTTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:13908 original size:27 final size:27
Alignment explanation
Indices: 13870--13938 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
13860 TGCTGCCCCA
13870 TTGATGCCATGTCACCTAGACACATGT
1 TTGATGCCATGTCACCTAGACACATGT
13897 TTGATGCCATGTCACCTAGACACATGT
1 TTGATGCCATGTCACCTAGACACATGT
*
13924 TTGATGCCAAGTCAC
1 TTGATGCCATGTCAC
13939 GCCTAAGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (27 bp):
TTGATGCCATGTCACCTAGACACATGT
Found at i:14573 original size:36 final size:36
Alignment explanation
Indices: 14525--14665 Score: 230
Period size: 36 Copynumber: 3.9 Consensus size: 36
14515 GATACAATCT
14525 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
14561 GTCCATCTCCATTATCACGCCTATATCATCACCATC
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
14597 GTCCATCACCATTATCACGCCTATATCATCACCACA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
14633 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
14666 ACTTATAAAT
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 21 0.21
36 77 0.79
ACGTcount: A:0.29, C:0.38, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:15137 original size:14 final size:15
Alignment explanation
Indices: 15113--15146 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
15103 TTTGGAGTGC
15113 AAAAGATAGAAAAGA
1 AAAAGATAGAAAAGA
*
15128 AAAAGA-AGAAAAGC
1 AAAAGATAGAAAAGA
15142 AAAAG
1 AAAAG
15147 CAAAAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (15 bp):
AAAAGATAGAAAAGA
Found at i:20308 original size:23 final size:24
Alignment explanation
Indices: 20280--20383 Score: 78
Period size: 23 Copynumber: 4.4 Consensus size: 24
20270 ACAATCTGTC
20280 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCGCCTATAT
*
20303 CATCACCA-TAGTCCATCTCC-AT-T
1 CATCACCATTA-T-CATCGCCTATAT
* *
20326 -ATCACGCCTATATCATC-ACTATAGT
1 CATCAC-CAT-TATCATCGCCTATA-T
20351 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCGCCTATAT
20375 CATCACCAT
1 CATCACCAT
20384 ATTCCATCAC
Statistics
Matches: 64, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
22 8 0.12
23 26 0.41
24 7 0.11
25 16 0.25
26 2 0.03
27 5 0.08
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (24 bp):
CATCACCATTATCATCGCCTATAT
Found at i:20325 original size:36 final size:36
Alignment explanation
Indices: 20277--20417 Score: 230
Period size: 36 Copynumber: 3.9 Consensus size: 36
20267 GATACAATCT
20277 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
20313 GTCCATCTCCATTATCACGCCTATATCATCACTATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
20349 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
20385 TTCCATCACCA-TATCACACCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
20418 ACTTATAAAT
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 20 0.20
36 78 0.80
ACGTcount: A:0.30, C:0.35, G:0.04, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:27221 original size:8 final size:8
Alignment explanation
Indices: 27200--27239 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
27190 TTTGAACTTC
27200 TCTTATTCT
1 TCTT-TTCT
*
27209 T-TTTTTT
1 TCTTTTCT
27216 TCTTTTCT
1 TCTTTTCT
27224 TCTTTTCT
1 TCTTTTCT
27232 TCTTTTCT
1 TCTTTTCT
27240 GATTTTTCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 4 0.14
8 23 0.82
9 1 0.04
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (8 bp):
TCTTTTCT
Found at i:27246 original size:17 final size:15
Alignment explanation
Indices: 27200--27257 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 15
27190 TTTGAACTTC
*
27200 TCTTATTCTTTTTTTT
1 TCTT-TTCTTTTTTCT
27216 TCTTTTCTTCTTTTCT
1 TCTTTTCTT-TTTTCT
**
27232 TCTTTTCTGATTT-T
1 TCTTTTCTTTTTTCT
*
27246 TCTCTTCTTTTT
1 TCTTTTCTTTTT
27258 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 10 0.29
15 8 0.23
16 17 0.49
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (15 bp):
TCTTTTCTTTTTTCT
Found at i:28993 original size:509 final size:510
Alignment explanation
Indices: 28036--29061 Score: 2009
Period size: 509 Copynumber: 2.0 Consensus size: 510
28026 ATGGTTCGAC
28036 TAACTCTTCATGAGGGGCCTTAATGATTCGGTCAAAGGATGGAGAGACATCTCCCTTGGCCGAAT
1 TAACTCTTCATGAGGGGCCTTAATGATTCGGTCAAAGGATGGAGAGACATCTCCCTTGGCCGAAT
28101 GGTTCATGCTTGTTCATCTTGGCGCCAATTTCCTCTCCTTGGCCGAATAGTCATGTGCCTTATCA
66 GGTTCATGCTTGTTCATCTTGGCGCCAATTTCCTCTCCTTGGCCGAATAGTCATGTGCCTTATCA
*
28166 TGTTTGGCGCCAAAGGCTCTCATGTGCATGCCATGTGATGTGGCCGAATATGCATGGCATTCTTC
131 TGTTTGGCGCCAAAGGCTCTCATGTGCATGCCATGTGATGTGGCCAAATATGCATGGCATTCTTC
28231 CTCATGATGATTTAAGCTTCCAATGGTTGCAATTTCTTCACCAACGTGCTTCTAGATGAAAAGGC
196 CTCATGATGATTTAAGCTTCCAATGGTTGCAATTTCTTCACCAACGTGCTTCTAGATGAAAAGGC
*
28296 TTCTTATGGGCAGCATCATTCATGGAAGGTCACAATGTTTGAGAAAGGTGTCCCTTCATGTTTGA
261 ATCTTATGGGCAGCATCATTCATGGAAGGTCACAATGTTTGAGAAAGGTGTCCCTTCATGTTTGA
*
28361 GCTATTTATGGTGTGAATGAGCTGGTGGTGTGCTGGCCTTAGATGACTTGTAACATGATGAACGT
326 GCTATTTATGGTGTGAATGAGCTGGTGGTGAGCTGGCCTTAGATGACTTGTAACATGATGAACGT
28426 TTGGGCAGCTCCTTGTGGAAAGGTACCTCTCGAGGTGGCAATTATTCGTGAAAAGGTACGATTTC
391 TTGGGCAGCTCCTTGTGGAAAGGTACCTCTCGAGGTGGCAATTATTCGTGAAAAGGTACGATTTC
28491 ACAAATTTTTACTTAGGACATATTTGAAGTACTCTGTGTGGTGGTGATGATGGT-
456 ACAAATTTTTACTTAGGACATATTTGAAGTACTCTGTGTGGTGGTGATGATGGTG
28545 TAACTCTTCATGAGGGGCCTTAATGATTCGGTCAAAGGATGGAGAGACATCTCCCTTGGCCGAAT
1 TAACTCTTCATGAGGGGCCTTAATGATTCGGTCAAAGGATGGAGAGACATCTCCCTTGGCCGAAT
28610 GGTTCATGCTTGTTCATCTTGGCGCCAATTTCCTCTCCTTGGCCGAATAGTCATGTGCCTTATCA
66 GGTTCATGCTTGTTCATCTTGGCGCCAATTTCCTCTCCTTGGCCGAATAGTCATGTGCCTTATCA
28675 TGTTTGGCGCCAAAGGCTCTCATGTGCATGCCATGTGATGTGGCCAAATATGCATGGCATTCTTC
131 TGTTTGGCGCCAAAGGCTCTCATGTGCATGCCATGTGATGTGGCCAAATATGCATGGCATTCTTC
28740 CTCATGATGATTTAAGCTTCCAATGGTTGCAATTTCTTCACCAACGTGCTTCTAGATGAAAAGGC
196 CTCATGATGATTTAAGCTTCCAATGGTTGCAATTTCTTCACCAACGTGCTTCTAGATGAAAAGGC
28805 ATCTTATGGGCAGCATCATTCATGGAAGGTCACAATGTTTGAGAAAGGTGTCCCTTCATGTTTGA
261 ATCTTATGGGCAGCATCATTCATGGAAGGTCACAATGTTTGAGAAAGGTGTCCCTTCATGTTTGA
28870 GCTATTTATGGTGTGAATGAGCTGGTGGTGAGCTGGCCTTAGATGACTTGTAACATGATGAACGT
326 GCTATTTATGGTGTGAATGAGCTGGTGGTGAGCTGGCCTTAGATGACTTGTAACATGATGAACGT
*
28935 TTGGGCAGCTCCTTGTGGAAAGGTACCTCTCGAGGTGGTAATTATTCGTGAAAAGGTACGATTTC
391 TTGGGCAGCTCCTTGTGGAAAGGTACCTCTCGAGGTGGCAATTATTCGTGAAAAGGTACGATTTC
29000 ACAAATTTTTACTTAGGACATATTTGAAGTACTCTGTGTGGTGGTGATGATGGTG
456 ACAAATTTTTACTTAGGACATATTTGAAGTACTCTGTGTGGTGGTGATGATGGTG
29055 TAACTCT
1 TAACTCT
29062 CCAACTGAAA
Statistics
Matches: 512, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
509 505 0.99
510 7 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (510 bp):
TAACTCTTCATGAGGGGCCTTAATGATTCGGTCAAAGGATGGAGAGACATCTCCCTTGGCCGAAT
GGTTCATGCTTGTTCATCTTGGCGCCAATTTCCTCTCCTTGGCCGAATAGTCATGTGCCTTATCA
TGTTTGGCGCCAAAGGCTCTCATGTGCATGCCATGTGATGTGGCCAAATATGCATGGCATTCTTC
CTCATGATGATTTAAGCTTCCAATGGTTGCAATTTCTTCACCAACGTGCTTCTAGATGAAAAGGC
ATCTTATGGGCAGCATCATTCATGGAAGGTCACAATGTTTGAGAAAGGTGTCCCTTCATGTTTGA
GCTATTTATGGTGTGAATGAGCTGGTGGTGAGCTGGCCTTAGATGACTTGTAACATGATGAACGT
TTGGGCAGCTCCTTGTGGAAAGGTACCTCTCGAGGTGGCAATTATTCGTGAAAAGGTACGATTTC
ACAAATTTTTACTTAGGACATATTTGAAGTACTCTGTGTGGTGGTGATGATGGTG
Found at i:36656 original size:15 final size:15
Alignment explanation
Indices: 36621--36649 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36611 GTGCTTCAAC
36621 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
36635 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
36650 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:36694 original size:24 final size:24
Alignment explanation
Indices: 36642--36694 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
36632 CTTTTCTTTG
*
36642 CTTTTCTTCTTTTTGAGTGCTGGA
1 CTTTTCTTCTTTTGGAGTGCTGGA
* *
36666 TTTTTCTTCTTTTGGAGTGCTTGA
1 CTTTTCTTCTTTTGGAGTGCTGGA
36690 CTTTT
1 CTTTT
36695 ATTTGCTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.15, G:0.19, T:0.58
Consensus pattern (24 bp):
CTTTTCTTCTTTTGGAGTGCTGGA
Found at i:37732 original size:19 final size:21
Alignment explanation
Indices: 37708--37759 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
37698 CGGCCAAGAG
* *
37708 CATGTATCTTCA-TTACAA-T
1 CATGTATTTTCATTTAAAAGT
37727 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
37748 CATGTATTTTCA
1 CATGTATTTTCA
37760 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 5 0.17
21 13 0.45
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:38174 original size:4 final size:4
Alignment explanation
Indices: 38165--38206 Score: 50
Period size: 4 Copynumber: 10.0 Consensus size: 4
38155 CATCTCTATC
38165 ATTT ATTT ATTT ATTT ATTT ATTT CATTCT -TATT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT -ATT-T AT-TT ATTT ATTT
38207 TCATTACTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 28 0.82
5 5 0.15
6 1 0.03
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:38202 original size:18 final size:20
Alignment explanation
Indices: 38179--38217 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
38169 ATTTATTTAT
38179 TTATTTA-TTTCATT-CTTA
1 TTATTTATTTTCATTACTTA
38197 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
38217 T
1 T
38218 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:38220 original size:22 final size:20
Alignment explanation
Indices: 38175--38223 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
38165 ATTTATTTAT
38175 TTAT-TTATTTATTTCATTC
1 TTATATTATTTATTTCATTC
38194 -T-TATTATTTATTTTCATTAC
1 TTATATTATTTA-TTTCATT-C
38214 TTATATTATT
1 TTATATTATT
38224 ATCCCTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 7 0.28
20 1 0.04
21 1 0.04
22 7 0.28
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTATTTATTTCATTC
Found at i:41548 original size:35 final size:37
Alignment explanation
Indices: 41479--41558 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
41469 ATACTATTTC
* *
41479 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCATCCATTATCACACCTATAT
*
41516 CATCACCATAGTCCATCAT-CA-TATCACACCTATAT
1 CATCACCATAATCCATCATCCATTATCACACCTATAT
41551 CATCACCA
1 CATCACCA
41559 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 2 0.05
37 17 0.43
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCATCCATTATCACACCTATAT
Found at i:41552 original size:11 final size:12
Alignment explanation
Indices: 41509--41557 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
41499 CATTATCACG
41509 CCTATATCATCA
1 CCTATATCATCA
41521 CC-ATAGTCCATCA
1 CCTATA-T-CATCA
*
41534 TC-ATATCA-CA
1 CCTATATCATCA
41544 CCTATATCATCA
1 CCTATATCATCA
41556 CC
1 CC
41558 AAATTCTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 3 0.10
11 11 0.35
12 8 0.26
13 9 0.29
ACGTcount: A:0.33, C:0.37, G:0.02, T:0.29
Consensus pattern (12 bp):
CCTATATCATCA
Found at i:46028 original size:35 final size:37
Alignment explanation
Indices: 45959--46038 Score: 112
Period size: 35 Copynumber: 2.2 Consensus size: 37
45949 ATACTATTTC
45959 CATCACCATAATCCATATTCCATTATCACACCTATAT
1 CATCACCATAATCCATATTCCATTATCACACCTATAT
* *
45996 TATCACCATAGTCCATCA-T-CA-TATCACACCTATAT
1 CATCACCATAATCCAT-ATTCCATTATCACACCTATAT
46031 CATCACCA
1 CATCACCA
46039 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 21 0.54
36 2 0.05
37 15 0.38
38 1 0.03
ACGTcount: A:0.35, C:0.34, G:0.01, T:0.30
Consensus pattern (37 bp):
CATCACCATAATCCATATTCCATTATCACACCTATAT
Found at i:47899 original size:19 final size:21
Alignment explanation
Indices: 47875--47926 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
47865 CGTCCAAGAG
*
47875 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
47894 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
47915 CATGTATTTTCA
1 CATGTATTTTCA
47927 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:48361 original size:18 final size:20
Alignment explanation
Indices: 48338--48376 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
48328 TATCATTTAT
48338 TTATTTA-TTTCATT-CTTA
1 TTATTTATTTTCATTACTTA
48356 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
48376 T
1 T
48377 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:48379 original size:22 final size:20
Alignment explanation
Indices: 48334--48382 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
48324 TCTATATCAT
48334 TTAT-TTATTTATTTCATTC
1 TTATATTATTTATTTCATTC
48353 -T-TATTATTTATTTTCATTAC
1 TTATATTATTTA-TTTCATT-C
48373 TTATATTATT
1 TTATATTATT
48383 ATCCCCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 7 0.28
20 1 0.04
21 1 0.04
22 7 0.28
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTATTTATTTCATTC
Found at i:49157 original size:19 final size:19
Alignment explanation
Indices: 49116--49165 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
49106 TGTCCAAGAG
* ** *
49116 CATGTATCTTCATTTAAAT
1 CATGTATTTTCATAAAAAA
49135 CATGTATTTTCATAAAAAA
1 CATGTATTTTCATAAAAAA
49154 CATGTATTTTCA
1 CATGTATTTTCA
49166 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAA
Found at i:49723 original size:32 final size:33
Alignment explanation
Indices: 49682--49748 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
49672 TGATAACATT
49682 TTCTATCCAT-TTCAATTCTT-ATAATTTCCTTTC
1 TTCTATCCATATTCAATT-TTAATAATTT-CTTTC
* *
49715 TTCT-TCCATATTCCATTTTAATCATTTCTTTC
1 TTCTATCCATATTCAATTTTAATAATTTCTTTC
49747 TT
1 TT
49749 TTAATTACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (33 bp):
TTCTATCCATATTCAATTTTAATAATTTCTTTC
Found at i:52913 original size:20 final size:20
Alignment explanation
Indices: 52888--52925 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
52878 ATGAAATTGA
52888 AATGGAAAAAGGAAAGAAAT
1 AATGGAAAAAGGAAAGAAAT
52908 AATGGAAAAAGGAAAGAA
1 AATGGAAAAAGGAAAGAA
52926 TTGAAATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.08
Consensus pattern (20 bp):
AATGGAAAAAGGAAAGAAAT
Found at i:53142 original size:35 final size:36
Alignment explanation
Indices: 53082--53184 Score: 167
Period size: 35 Copynumber: 2.9 Consensus size: 36
53072 AAATGGAATT
*
53082 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
*
53117 T-GTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
53152 TGGTGATGATATAGGCGT-ATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
53185 AGATTGTATC
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 19 0.30
35 28 0.44
36 16 0.25
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
Done.