Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001332.1 Hibiscus syriacus cultivar Beakdansim tig00002601_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: 61391
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:10638 original size:17 final size:17
Alignment explanation
Indices: 10605--10638 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
10595 TTATATATGT
10605 CATATGAAATATACATG
1 CATATGAAATATACATG
10622 CATATTGAAATAT-CATG
1 CATA-TGAAATATACATG
10639 ATCAAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (17 bp):
CATATGAAATATACATG
Found at i:16912 original size:15 final size:15
Alignment explanation
Indices: 16885--16929 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
16875 CTTACATGTA
*
16885 CATGAATACATAATATG
1 CATGAA-ACATAAGA-G
16902 CAT-AAACATAAGAG
1 CATGAAACATAAGAG
16916 CATGAAACATAAGA
1 CATGAAACATAAGA
16930 TATATGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 4 0.15
15 17 0.65
16 2 0.08
17 3 0.12
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (15 bp):
CATGAAACATAAGAG
Found at i:22146 original size:13 final size:13
Alignment explanation
Indices: 22128--22155 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
22118 AATCAAACTA
22128 TTGACCATTGACT
1 TTGACCATTGACT
22141 TTGACCATTGACT
1 TTGACCATTGACT
22154 TT
1 TT
22156 TTCTGTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGACCATTGACT
Found at i:22759 original size:40 final size:40
Alignment explanation
Indices: 22710--22788 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
22700 CATGGGATCC
22710 TCTACGGAGGGCATAATCCCTATCCTAATTCTACATGAGA
1 TCTACGGAGGGCATAATCCCTATCCTAATTCTACATGAGA
* *
22750 TCTATGGAGGGCATAATCCCTATCCTAATTCTATATGAG
1 TCTACGGAGGGCATAATCCCTATCCTAATTCTACATGAG
22789 TTCCTCTACG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (40 bp):
TCTACGGAGGGCATAATCCCTATCCTAATTCTACATGAGA
Found at i:22822 original size:43 final size:44
Alignment explanation
Indices: 22694--22852 Score: 165
Period size: 43 Copynumber: 3.8 Consensus size: 44
22684 CATTTCTGTC
* *
22694 ATTCTGCATGGGATCCTCTAC-GGAGGGCATAAT-CCCTATCCTA
1 ATTCTACATGAGATCCTCTACGGGA-GGCATAATCCCCTATCCTA
*
22737 ATTCTACATGAGA---TCTA-TGGAGGGCATAAT-CCCTATCCTA
1 ATTCTACATGAGATCCTCTACGGGA-GGCATAATCCCCTATCCTA
* * *
22777 ATTCTATATGAGTTCCTCTACGGGAGGCATAATCCCCT-TCTTA
1 ATTCTACATGAGATCCTCTACGGGAGGCATAATCCCCTATCCTA
* *
22820 ATTCTGCATGTGATCCTCTACGGGA-GCATAATC
1 ATTCTACATGAGATCCTCTACGGGAGGCATAATC
22853 TCCATCCCGA
Statistics
Matches: 100, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
40 37 0.37
42 8 0.08
43 48 0.48
44 7 0.07
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (44 bp):
ATTCTACATGAGATCCTCTACGGGAGGCATAATCCCCTATCCTA
Found at i:30776 original size:17 final size:18
Alignment explanation
Indices: 30730--30776 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
30720 ATACTAAAAG
30730 GGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
* *
30748 GGAATTAAAATCTGT-CA
1 GGAATTAGAATCTGTGAA
*
30765 GGAATTGGAATC
1 GGAATTAGAATC
30777 CAATTTCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:30805 original size:38 final size:38
Alignment explanation
Indices: 30763--30847 Score: 98
Period size: 44 Copynumber: 2.1 Consensus size: 38
30753 TAAAATCTGT
*
30763 CAGGAATTGGAATCCAATTTCATATTCTGTTTGGTTGGCAGG
1 CAGGAATTGGAATCCAATTCCATATTCTGTTTGGTT--C--G
*
30805 AAATGGAATTGGAATCCAATTCCATATTCTGTTTGGTTCG
1 -CA-GGAATTGGAATCCAATTCCATATTCTGTTTGGTTCG
30845 CAG
1 CAG
30848 ACATGTCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
38 1 0.03
39 1 0.03
40 1 0.03
42 1 0.03
43 1 0.03
44 33 0.87
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (38 bp):
CAGGAATTGGAATCCAATTCCATATTCTGTTTGGTTCG
Found at i:31605 original size:224 final size:226
Alignment explanation
Indices: 31167--31680 Score: 770
Period size: 229 Copynumber: 2.2 Consensus size: 226
31157 ATTTTTATTT
*
31167 AATATATGAATTAGAAACCCGACCCGACACGAAATAATAAAAAATTATTTTTATTCAATAAAAAC
1 AATATATGAATTAGAAACCCGA--C--C-CGAAATAATAAAAAAATATTTTTATTCAATAAAAAC
*
31232 ATTGACTTAATTGAAAAAATTATATATAAAGGGGTATTATTGTAATTATTCCTAAATATATAAGG
61 AGTGACTTAATTGAAAAAATTATATATAAAGGGGTATTATTGTAATTATTCCTAAATATATAAGG
* *
31297 TAAAATTATATATTTTTTCGGGTCGGGTCCGGTTTTTTTCACCCTAAACCCAAACCCGACCCGAC
126 TAAAATTATATATATTTTCGGGTC-GG--CGGTATTTTTCACCCTAAACCCAAACCCGACCCGAC
31362 CCGAATATCACACTT-AAAAA-A-A-CCGACCCGACCCG
188 CCGAATATCACACTTAAAAAATAGACCCGACCCGACCCG
*
31397 AATATATGAATTAGAAATCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGA
1 AATATATGAATTAGAAACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGA
*
31462 CTTAATTGAAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATATAAGGT
66 CTTAATTG--AAAAAATTATATATAAAGGGGTATTATTGTAATTATTCCT-AA-ATATATAAGGT
* * *
31527 AAAATTGTATATATTTTCGGGTC-G-GGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGA
127 AAAATTATATATATTTTCGGGTCGGCGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCCGA
31590 ATATCACACTTAAAAAAATAGACCCGACCCGACCCG
192 ATATCACACTT-AAAAAATAGACCCGACCCGACCCG
* *
31626 AATATATGAATTAGAAACCCGACCTGAAATAATAATAAAATATTTTTATTCAATA
1 AATATATGAATTAGAAACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATA
31681 TATGAATAGG
Statistics
Matches: 263, Mismatches: 12, Indels: 19
0.89 0.04 0.06
Matches are distributed among these distances:
224 47 0.18
225 47 0.18
226 6 0.02
227 41 0.16
228 4 0.02
229 97 0.37
230 21 0.08
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (226 bp):
AATATATGAATTAGAAACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGA
CTTAATTGAAAAAATTATATATAAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAA
TTATATATATTTTCGGGTCGGCGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCCGAATAT
CACACTTAAAAAATAGACCCGACCCGACCCG
Found at i:33547 original size:52 final size:52
Alignment explanation
Indices: 33481--33761 Score: 172
Period size: 43 Copynumber: 5.9 Consensus size: 52
33471 ACTTGTTAAC
* *
33481 TTTATAATTAAGGCCCTTAAGTCTTTTAATCTCACTTTCTACCTTTTCTACA
1 TTTATAATTGAGGCCCTTAAGTTTTTTAATCTCACTTTCTACCTTTTCTACA
* *
33533 TTTATAATTGAGGCCCCTAATTTTTTTAA--T--C---CTA-CTTTT-TA-A
1 TTTATAATTGAGGCCCTTAAGTTTTTTAATCTCACTTTCTACCTTTTCTACA
* * * *
33575 CTTTATAATTGAGGCTCTTAAGTTTTTTCAATATCGCTTTCTACCTTTTCTACC
1 -TTTATAATTGAGGCCCTTAAGTTTTTT-AATCTCACTTTCTACCTTTTCTACA
* *
33629 TTT-CAATTGAGG-CCTCTAAGTTTTTTTAATCTCA------A--TTTT-TACC
1 TTTATAATTGAGGCCCT-TAAG-TTTTTTAATCTCACTTTCTACCTTTTCTACA
* * * * *
33672 TTTATAATTGAAGCCCCTAA-CTTTTTAATCCCAC--T-T---TTTT-AAC-
1 TTTATAATTGAGGCCCTTAAGTTTTTTAATCTCACTTTCTACCTTTTCTACA
33715 TTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTACCTTT
1 TTTATAATTGAGGCCCTTAAG-TTTTTTAATCTCACTTTCTACCTTT
33762 ATAATTGAGG
Statistics
Matches: 180, Mismatches: 22, Indels: 55
0.70 0.09 0.21
Matches are distributed among these distances:
42 12 0.07
43 51 0.28
44 27 0.15
45 17 0.09
46 2 0.01
47 1 0.01
48 3 0.02
50 1 0.01
51 8 0.04
52 47 0.26
53 11 0.06
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (52 bp):
TTTATAATTGAGGCCCTTAAGTTTTTTAATCTCACTTTCTACCTTTTCTACA
Found at i:33585 original size:43 final size:45
Alignment explanation
Indices: 33384--33914 Score: 320
Period size: 44 Copynumber: 11.8 Consensus size: 45
33374 TTTATACAAT
* * *
33384 CTCACTTTTTATA-TTTATAATTGAAGTCTCTAA-TTTTTTTCAATC
1 CTCACTTTTTA-ACTTTATAATTGAGGCCCCTAAGTTTTTTT-AATC
* * **
33429 CT---TTTTTACCTTTATAATTAAGGCTAC-AA-TTTTTTTAAT-
1 CTCACTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTTAATC
* * * *
33468 CTCACTTGTTAACTTTATAATTAAGGCCCTTAAG-TCTTTTAATCTC
1 CTCACTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTTAA--TC
33514 ACTTTCTACCTTTTCT-ACATTTATAATTGAGGCCCCTAA-TTTTTTTAATC
1 -C--TC-A-CTTTT-TAAC-TTTATAATTGAGGCCCCTAAGTTTTTTTAATC
* * *
33564 CT-ACTTTTTAACTTTATAATTGAGGCTCTTAAGTTTTTTCAATATC
1 CTCACTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTT-TA-ATC
* * *
33610 GCTTTCTACCTTTTCTACCTTT-CAATTGAGGCCTCTAAGTTTTTTTAAT-
1 -C--TC-A-CTTTT-TAACTTTATAATTGAGGCCCCTAAGTTTTTTTAATC
* * * *
33659 CTCAATTTTTACCTTTATAATTGAAGCCCCTAA--CTTTTTAATC
1 CTCACTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTTAATC
*
33702 C-CACTTTTTTAACTTTATAATTGAGGCCCTTAAGTTTTTTTAAT-
1 CTCAC-TTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTTAATC
* * *
33746 CTCACTTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAAT-
1 CTCACTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTTAATC
* * * *
33790 CTCAATTTCT-ACATTTATAATTGAGGTCCCTAAGTTTTTTCAAT-
1 CTCACTTTTTAAC-TTTATAATTGAGGCCCCTAAGTTTTTTTAATC
* * * ** *
33834 CTCGA--TTATACCTTTATAATTGAGACATCT-ATTTTTTTTCAAT-
1 CTC-ACTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTT-AATC
* ** * *
33877 CTCAATTTCCAACTTTATAATTAAGGCCTCTAAGTTTT
1 CTCACTTTTTAACTTTATAATTGAGGCCCCTAAGTTTT
33915 CAATTTTATA
Statistics
Matches: 388, Mismatches: 57, Indels: 82
0.74 0.11 0.16
Matches are distributed among these distances:
39 2 0.01
40 3 0.01
41 9 0.02
42 56 0.14
43 85 0.22
44 128 0.33
45 23 0.06
46 5 0.01
47 3 0.01
48 1 0.00
49 4 0.01
50 5 0.01
51 8 0.02
52 50 0.13
53 6 0.02
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.48
Consensus pattern (45 bp):
CTCACTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTTAATC
Found at i:33729 original size:87 final size:87
Alignment explanation
Indices: 33633--33914 Score: 288
Period size: 87 Copynumber: 3.2 Consensus size: 87
33623 TCTACCTTTC
*
33633 AATTGAGGCCTCTAAGTTTTTTTAATCTCAATTTTTACCTTTATAATTGAAGCCCCTAA-CTTTT
1 AATTGAGGCC-CTAAGTTTTTTTAATCTCAATTTATACCTTTATAATTGAAGCCCCTAAGCTTTT
* *
33697 T-AATCCCACTTTTTTA-ACTTTAT
65 TCAATCCCA-ATTTCTACA-TTTAT
* * * *
33720 AATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTACCTTTATAATTGAGGCCCCTAAGTTTTT
1 AATTGAGGCCC-TAAGTTTTTTTAATCTCAATTTATACCTTTATAATTGAAGCCCCTAAGCTTTT
*
33785 TCAATCTCAATTTCTACATTTAT
65 TCAATCCCAATTTCTACATTTAT
* * ** ***
33808 AATTGAGGTCCCTAAGTTTTTTCAATCTCGA-TTATACCTTTATAATTG-AGACATCTATTTTTT
1 AATTGAGG-CCCTAAGTTTTTTTAATCTCAATTTATACCTTTATAATTGAAG-CCCCTAAGCTTT
* *
33871 TTCAATCTCAATTTCCA-ACTTTAT
64 TTCAATCCCAATTTCTACA-TTTAT
*
33895 AATTAAGGCCTCTAAGTTTT
1 AATTGAGGCC-CTAAGTTTT
33915 CAATTTTATA
Statistics
Matches: 169, Mismatches: 18, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
86 5 0.03
87 115 0.68
88 39 0.23
89 10 0.06
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.46
Consensus pattern (87 bp):
AATTGAGGCCCTAAGTTTTTTTAATCTCAATTTATACCTTTATAATTGAAGCCCCTAAGCTTTTT
CAATCCCAATTTCTACATTTAT
Found at i:35420 original size:23 final size:22
Alignment explanation
Indices: 35367--35421 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
35357 ATAAAAAATA
*
35367 TTATATTATATTTTAAAATTAT
1 TTATAATATATTTTAAAATTAT
*
35389 TAATAAATATATTTTAAAGACTT-T
1 TTAT-AATATATTTTAAA-A-TTAT
35413 TTATAATAT
1 TTATAATAT
35422 TATTAAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 3 0.11
23 17 0.63
24 5 0.19
25 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATAATATATTTTAAAATTAT
Found at i:35497 original size:26 final size:27
Alignment explanation
Indices: 35468--35518 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
35458 AAAGTATCAC
35468 TATTAATAATTCAATA-ATATTATTTT
1 TATTAATAATTCAATATATATTATTTT
* *
35494 TATTAATAATTTATTATATATTATT
1 TATTAATAATTCAATATATATTATT
35519 AAAATAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TATTAATAATTCAATATATATTATTTT
Found at i:35610 original size:25 final size:25
Alignment explanation
Indices: 35542--35648 Score: 69
Period size: 25 Copynumber: 4.2 Consensus size: 25
35532 AATAGTATCA
* *
35542 TATATTATTATAATATAATTGAGTATAT
1 TATATTATTA-AAAAT-ATT-AATATAT
* * *
35570 TAT-TGTAATAATAATATTATTATAT
1 TATAT-TATTAAAAATATTAATATAT
*
35595 TATATTATTAAAAATATTAATA-AA
1 TATATTATTAAAAATATTAATATAT
* *
35619 TATATT-TTAAATATTTTAATA-AT
1 TATATTATTAAAAATATTAATATAT
35642 TAATATT
1 T-ATATT
35649 TTTATTAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
23 15 0.23
24 12 0.18
25 23 0.35
26 4 0.06
27 4 0.06
28 7 0.11
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
TATATTATTAAAAATATTAATATAT
Found at i:35637 original size:23 final size:23
Alignment explanation
Indices: 35595--35650 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
35585 ATTATTATAT
35595 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* * *
35619 TATATTTTAAATATTTTAATAAT
1 TATATTTTAAAAATATTAATAAA
35642 TAATATTTT
1 T-ATATTTT
35651 TATTAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:36372 original size:20 final size:22
Alignment explanation
Indices: 36347--36396 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
36337 GTTTTTCAAT
36347 GAACCGGCTGGGAACCGG-TA-
1 GAACCGGCTGGGAACCGGCTAG
* * *
36367 GAACCGGGTGTGAACTGGCTAG
1 GAACCGGCTGGGAACCGGCTAG
36389 GAACCGGC
1 GAACCGGC
36397 AAAATCGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 15 0.62
21 2 0.08
22 7 0.29
ACGTcount: A:0.24, C:0.24, G:0.40, T:0.12
Consensus pattern (22 bp):
GAACCGGCTGGGAACCGGCTAG
Found at i:41471 original size:183 final size:185
Alignment explanation
Indices: 41113--41500 Score: 615
Period size: 183 Copynumber: 2.1 Consensus size: 185
41103 ATTAAATTTT
* * * * *
41113 AAATTTTAAATATATTATATATAACATATGGGCTCAGTCCAAATCATTTAAAACACAATTAATAA
1 AAATATTAAATATATTATATATAACATATAGGCTAAGCCCAAACCATTTAAAACACAATTAATAA
*
41178 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTATATAAAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTATATAAAAATTTT
*
41243 ATTTTATAATTATATATTATTTAAATTAATTGTAAAC-TGTTTTTTT-AATTAAA
131 ATTTTATAATTATATATTATTTAAATTAATTGAAAACTTGTTTTTTTGAATTAAA
*
41296 AAATATTAAATATATTATATATAACATATAGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATAGGCTAAGCCCAAACCATTTAAAACACAATTAATAA
* *
41361 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATT-AAAAA-TTATATAAAAATT
41426 TTATTTTATAATTATATATTATTTAAATTAATT-AAAACTT-TTTTTTTGAATTAAA
129 TTATTTTATAATTATATATTATTTAAATTAATTGAAAACTTGTTTTTTTGAATTAAA
* *
41481 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
41501 AATTATAAAA
Statistics
Matches: 189, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
183 103 0.54
184 24 0.13
185 62 0.33
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATAGGCTAAGCCCAAACCATTTAAAACACAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTATATAAAAATTTT
ATTTTATAATTATATATTATTTAAATTAATTGAAAACTTGTTTTTTTGAATTAAA
Found at i:41645 original size:15 final size:14
Alignment explanation
Indices: 41622--41660 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
41612 AAAGAAAAAA
41622 AGGTTTGGTTAATT
1 AGGTTTGGTTAATT
41636 AGGTTATGGTTAATT
1 AGGTT-TGGTTAATT
* *
41651 CGGTTCGGTT
1 AGGTTTGGTT
41661 CGATTTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.18, C:0.05, G:0.31, T:0.46
Consensus pattern (14 bp):
AGGTTTGGTTAATT
Found at i:42593 original size:24 final size:25
Alignment explanation
Indices: 42566--42624 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
42556 TTATAATAAT
*
42566 TATGTCTTTTGTGATACGTTT-ATC
1 TATGTCTTTTGTGACACGTTTCATC
* *
42590 TATGTC-TTCGTGACACGTTTCTTC
1 TATGTCTTTTGTGACACGTTTCATC
*
42614 TATGCCTTTTG
1 TATGTCTTTTG
42625 GTAGTTTTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 12 0.43
24 13 0.46
25 3 0.11
ACGTcount: A:0.14, C:0.19, G:0.17, T:0.51
Consensus pattern (25 bp):
TATGTCTTTTGTGACACGTTTCATC
Found at i:43766 original size:2 final size:2
Alignment explanation
Indices: 43754--43814 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
43744 GCATCATAGG
43754 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43795 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
43815 GATTAATTTG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46486 original size:15 final size:16
Alignment explanation
Indices: 46461--46494 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
46451 AGTAAAGACA
*
46461 CATACATCTTCTTTTT
1 CATACATCTTCTATTT
46477 CATA-ATCTTCTATTT
1 CATACATCTTCTATTT
46492 CAT
1 CAT
46495 CTTCTACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (16 bp):
CATACATCTTCTATTT
Found at i:49366 original size:21 final size:21
Alignment explanation
Indices: 49317--49366 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
49307 GGAATTTGCT
* *
49317 ATAATGAATGGTCAATTCGAA
1 ATAATAAAAGGTCAATTCGAA
49338 A-AATTAAAAGGTCAA-TCTGAA
1 ATAA-TAAAAGGTCAATTC-GAA
49359 ATAATAAA
1 ATAATAAA
49367 TGACCAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
20 4 0.17
21 18 0.75
22 2 0.08
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.26
Consensus pattern (21 bp):
ATAATAAAAGGTCAATTCGAA
Found at i:53295 original size:2 final size:2
Alignment explanation
Indices: 53290--53320 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53280 TCATATATTC
53290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53321 ATCCACGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60881 original size:17 final size:17
Alignment explanation
Indices: 60855--60888 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
60845 CAAAAAACAT
60855 AAAATATGACTTTTTGG
1 AAAATATGACTTTTTGG
*
60872 AAAATTTGACTTTTTGG
1 AAAATATGACTTTTTGG
60889 TCAAAGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (17 bp):
AAAATATGACTTTTTGG
Found at i:60916 original size:23 final size:23
Alignment explanation
Indices: 60886--60940 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
60876 TTTGACTTTT
60886 TGGTCAAAGTTAACAGTCAACTC
1 TGGTCAAAGTTAACAGTCAACTC
* * *
60909 TGGTCAAAGGTAACATTCAACTT
1 TGGTCAAAGTTAACAGTCAACTC
60932 TGG-CAAAGT
1 TGGTCAAAGT
60941 CAACGGGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (23 bp):
TGGTCAAAGTTAACAGTCAACTC
Found at i:60963 original size:18 final size:18
Alignment explanation
Indices: 60940--60974 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
60930 TTTGGCAAAG
*
60940 TCAACGGGTTGGGTCAAT
1 TCAACGGGTCGGGTCAAT
*
60958 TCAACGTGTCGGGTCAA
1 TCAACGGGTCGGGTCAA
60975 AGTCAATTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (18 bp):
TCAACGGGTCGGGTCAAT
Done.