Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004715.1 Hibiscus syriacus cultivar Beakdansim tig00010630_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: 45910
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:423 original size:3 final size:3
Alignment explanation
Indices: 415--572 Score: 198
Period size: 3 Copynumber: 52.7 Consensus size: 3
405 TTAATATATT
* * * *
415 TAA TAA TAA AAA TAA T-A TAA TAA TTTA TAA TAT TAA TAA TGA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA
*
461 TAA T-A TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
507 TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TTAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
554 T-A TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
573 TATGGATAAA
Statistics
Matches: 135, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
2 8 0.06
3 117 0.87
4 10 0.07
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1465 original size:224 final size:226
Alignment explanation
Indices: 860--2079 Score: 2029
Period size: 224 Copynumber: 5.5 Consensus size: 226
850 GATATCAAAC
*
860 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTTCAGATGAG---TTCTCAT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCAT
* ** * * ** * *** * *
922 TCATGAACTTTCTTTGGCCATG-TGATCCATCAAATGATGATTTAAACAAAAAAGTTGAACAAGT
65 T-ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGGTTCAGGTAAAAGGTTGAACAAAT
986 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
129 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * *
1051 -AAATATGATCCACC-AATGATGGATTCAGGTA
194 AAAAGATGATCCACCAAATGATGGATTCAAGCA
* *
1082 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT--TTTC-TCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
1144 ATGAACTTTTTCTGGAAAAGATAATCCACCAAATGAT-GGTTCAGGTAAAAGGTTGAACAAATTC
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGGTTCAGGTAAAAGGTTGAACAAATTC
1208 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
*
1273 AAGATGATCCACCAAATGATGGATTCAAACA
196 AAGATGATCCACCAAATGATGGATTCAAGCA
1304 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1369 ATG-ACTTTCTCTGG-AAAGATGATCCACCAAATGATGGGTTCAGGTAAAAGGTTGAACAAATTC
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGGTTCAGGTAAAAGGTTGAACAAATTC
1432 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1497 AAGATGATCCACCAAATGATGGATTCAAGCA
196 AAGATGATCCACCAAATGATGGATTCAAGCA
1528 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1592 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGGTTCAGGT-AAAGGTTGAACAAATTC
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGGTTCAGGTAAAAGGTTGAACAAATTC
1656 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
* *
1721 ATGTTGATCCACCAAATGATGGATTCAAGCA
196 AAGATGATCCACCAAATGATGGATTCAAGCA
1752 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1817 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGGTTCAGGTAAAAGGTTGAACAAATTC
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGGTTCAGGTAAAAGGTTGAACAAATTC
1882 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
* * * *
1947 ATG-TGATCCATCAAGTGATGAATTCAAGCA
196 AAGATGATCCACCAAATGATGGATTCAAGCA
*
1977 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
2042 ATGAACTTTCTCTGGTAATGATGATCCATCAAATGATG
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATG
2080 AATTTGAATC
Statistics
Matches: 948, Mismatches: 36, Indels: 25
0.94 0.04 0.02
Matches are distributed among these distances:
220 97 0.10
221 41 0.04
222 106 0.11
223 48 0.05
224 335 0.35
225 236 0.25
226 85 0.09
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (226 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGGTTCAGGTAAAAGGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
AAGATGATCCACCAAATGATGGATTCAAGCA
Found at i:1572 original size:112 final size:113
Alignment explanation
Indices: 860--2079 Score: 1932
Period size: 113 Copynumber: 10.9 Consensus size: 113
850 GATATCAAAC
**
860 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTTCAGATGAG---TTCTCAT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCAT
* ** * * * *
922 TCATGAACTTTCTTTGGCCATG-TGATCCATCAAATGAT-GATTTAAACAA
65 T-ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGC-A
* *
971 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
1036 ATGAACTTTCTCTGG-AAATATGATCCACC-AATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
*
1082 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT--TTTC-TCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
1144 ATGAACTTTTTCTGGAAAAGATAATCCACCAAATGATGG-TTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
1191 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
1256 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAACA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
*
1304 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
1369 ATG-ACTTTCTCTGG-AAAGATGATCCACCAAATGATGGGTTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
1415 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1480 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
*
1528 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* **
1592 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGGTTC-AGGT
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
1639 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
1704 ATGAACTTTCTCTGGAAATGTTGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
*
1752 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
1817 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGGTTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
1865 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
1930 ATGAACTTTCTCTGGAAATG-TGATCCATCAAGTGATGAATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
1977 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
2042 ATGAACTTTCTCTGGTAATGATGATCCATCAAATGATG
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATG
2080 AATTTGAATC
Statistics
Matches: 1035, Mismatches: 58, Indels: 30
0.92 0.05 0.03
Matches are distributed among these distances:
108 21 0.02
109 74 0.07
110 18 0.02
111 237 0.23
112 330 0.32
113 355 0.34
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
Found at i:2715 original size:52 final size:52
Alignment explanation
Indices: 2637--3351 Score: 1313
Period size: 52 Copynumber: 13.7 Consensus size: 52
2627 CACTTCTTCG
* * *
2637 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCCATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
2689 GATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
2741 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
2793 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
* *
2845 GATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
2897 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
2949 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
3001 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
3053 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
3105 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
3157 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
3210 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
3262 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
3314 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
3352 TGAGCACATA
Statistics
Matches: 644, Mismatches: 18, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
52 593 0.92
53 51 0.08
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.24
Consensus pattern (52 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:4299 original size:1 final size:1
Alignment explanation
Indices: 4288--4333 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
4278 CCTTGACCCC
* * * *
4288 TTTTTTCTTTTTCTTCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4334 CAAGCATAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:15724 original size:19 final size:19
Alignment explanation
Indices: 15703--15738 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
15693 AATATATTTA
15703 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
15721 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
15739 GACTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:16316 original size:13 final size:13
Alignment explanation
Indices: 16298--16326 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16288 CCACCGTACT
16298 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
16311 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
16324 CCG
1 CCG
16327 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:17086 original size:3 final size:3
Alignment explanation
Indices: 17078--17220 Score: 250
Period size: 3 Copynumber: 47.7 Consensus size: 3
17068 TTAATATATT
* * * *
17078 TAA TAA TAA AAA TAA TAA TAA TAA TAT TAA TAA TAA TAT TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17126 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17174 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17221 TGGATAAAAA
Statistics
Matches: 132, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 132 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27413 original size:12 final size:12
Alignment explanation
Indices: 27396--27437 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
27386 TCAGAATTGG
27396 ACCGGTTATCGA
1 ACCGGTTATCGA
*
27408 ACCGGTCAT-GCA
1 ACCGGTTATCG-A
*
27420 ATCGGTTATCGA
1 ACCGGTTATCGA
27432 ACCGGT
1 ACCGGT
27438 AATACTATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (12 bp):
ACCGGTTATCGA
Found at i:30098 original size:26 final size:25
Alignment explanation
Indices: 30069--30120 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
30059 TAGTGTATAA
*
30069 ATAT-TTAAATTCATAATATTTTAT
1 ATATATTAAATTAATAATATTTTAT
*
30093 ATATATTAACTTAATAATATTTT-T
1 ATATATTAAATTAATAATATTTTAT
30117 ATAT
1 ATAT
30121 TAACTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
ATATATTAAATTAATAATATTTTAT
Found at i:30109 original size:25 final size:23
Alignment explanation
Indices: 30081--30167 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 23
30071 ATTTAAATTC
30081 ATAATATTTTATATATATTAACTTA
1 ATAATATTTT-T-TATATTAACTTA
30106 ATAATA-TTTTTATATTAACTTA
1 ATAATATTTTTTATATTAACTTA
*
30128 TTAAATATATTTTGT-TATTAACTTA
1 AT-AATAT-TTTT-TATATTAACTTA
30153 ATTTAAT-TTTTTTAT
1 A--TAATATTTTTTAT
30168 TTTTATTTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
22 13 0.25
23 6 0.11
24 8 0.15
25 21 0.40
26 4 0.08
27 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (23 bp):
ATAATATTTTTTATATTAACTTA
Found at i:30122 original size:22 final size:24
Alignment explanation
Indices: 30094--30154 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 24
30084 ATATTTTATA
30094 TATATTAACTTAAT-AATAT-TTT
1 TATATTAACTTAATAAATATATTT
*
30116 TATATTAACTTATTAAATATATTT
1 TATATTAACTTAATAAATATATTT
*
30140 TGTTATTAACTTAAT
1 T-ATATTAACTTAAT
30155 TTAATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.39
23 5 0.15
24 4 0.12
25 11 0.33
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (24 bp):
TATATTAACTTAATAAATATATTT
Found at i:35033 original size:18 final size:17
Alignment explanation
Indices: 35010--35049 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
35000 AGTTTATGAA
35010 TATTATATATATTTTCTT
1 TATTATATATATTTT-TT
35028 TATTATATATATTTTTT
1 TATTATATATATTTTTT
35045 TATTA
1 TATTA
35050 ATTTTGTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTATATATATTTTTT
Found at i:35264 original size:22 final size:23
Alignment explanation
Indices: 35209--35254 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
35199 TTAAGTTATT
*
35209 TATATAGA-AATTTTATTTAAAA
1 TATATAAATAATTTTATTTAAAA
*
35231 TATATAAATAATTTTATTAAAAA
1 TATATAAATAATTTTATTTAAAA
35254 T
1 T
35255 TAAATGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATATAAATAATTTTATTTAAAA
Found at i:40213 original size:16 final size:16
Alignment explanation
Indices: 40192--40250 Score: 109
Period size: 16 Copynumber: 3.7 Consensus size: 16
40182 ACGATGGACT
*
40192 CTTCGATTTCTTCATC
1 CTTCGATCTCTTCATC
40208 CTTCGATCTCTTCATC
1 CTTCGATCTCTTCATC
40224 CTTCGATCTCTTCATC
1 CTTCGATCTCTTCATC
40240 CTTCGATCTCT
1 CTTCGATCTCT
40251 ATGGTCCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.12, C:0.36, G:0.07, T:0.46
Consensus pattern (16 bp):
CTTCGATCTCTTCATC
Found at i:40227 original size:7 final size:7
Alignment explanation
Indices: 40201--40243 Score: 50
Period size: 7 Copynumber: 5.6 Consensus size: 7
40191 TCTTCGATTT
40201 CTTCATC
1 CTTCATC
40208 CTTCGATC
1 CTTC-ATC
40216 TCTTCATC
1 -CTTCATC
40224 CTTCGATC
1 CTTC-ATC
40232 TCTTCATC
1 -CTTCATC
40240 CTTC
1 CTTC
40244 GATCTCTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 12 0.38
8 12 0.38
9 8 0.25
ACGTcount: A:0.12, C:0.40, G:0.05, T:0.44
Consensus pattern (7 bp):
CTTCATC
Done.