Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002749.1 Hibiscus syriacus cultivar Beakdansim tig00005665_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: 68020
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:199 original size:15 final size:14
Alignment explanation
Indices: 154--212 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 14
144 TATATCATTA
154 TTATT-TTATATAT
1 TTATTATTATATAT
*
167 TT-TTATTACTATAA
1 TTATTATTA-TATAT
181 TTATATATTATATAT
1 TTAT-TATTATATAT
196 TTATTATTTATATAT
1 TTATTA-TTATATAT
211 TT
1 TT
213 CATTTGTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 2 0.05
13 5 0.13
14 8 0.21
15 19 0.49
16 5 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTATTATATAT
Found at i:1311 original size:16 final size:15
Alignment explanation
Indices: 1292--1331 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1282 CCTTTTGAGT
1292 TTTTTTTATTTCGTCA
1 TTTTTTTATTT-GTCA
* *
1308 TTTTTTTATTTTTTA
1 TTTTTTTATTTGTCA
1323 TTTTTTTAT
1 TTTTTTTAT
1332 CTTTTGCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTTTTATTTGTCA
Found at i:1325 original size:15 final size:15
Alignment explanation
Indices: 1292--1336 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1282 CCTTTTGAGT
*
1292 TTTTTTTATTTCGTCA
1 TTTTTTTATTT-TTCA
*
1308 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTCA
1323 TTTTTTTATCTTTT
1 TTTTTTTAT-TTTT
1337 GCCTTTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTTTATTTTTCA
Found at i:22840 original size:9 final size:9
Alignment explanation
Indices: 22826--22855 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
22816 AGGGCGCCCT
22826 AAATTGAAA
1 AAATTGAAA
22835 AAATTGAAA
1 AAATTGAAA
*
22844 AAAGTGAAA
1 AAATTGAAA
22853 AAA
1 AAA
22856 GAACAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (9 bp):
AAATTGAAA
Found at i:24094 original size:110 final size:110
Alignment explanation
Indices: 23896--24099 Score: 336
Period size: 110 Copynumber: 1.9 Consensus size: 110
23886 TCCCAGTTTT
* * *
23896 AGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAT
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACAG
*
23961 CGAAGGGGCGACTAATTGTCAACAAACAACTTTTCAGTTTCATTC
66 CGAAGGGGCGACTAACTGTCAACAAACAACTTTTCAGTTTCATTC
* *
24006 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACAG
* *
24071 CGAAGGGGCGGCTGACTGTCAACAAACAA
66 CGAAGGGGCGACTAACTGTCAACAAACAA
24100 TTTCCAGAGC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 86 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (110 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACAG
CGAAGGGGCGACTAACTGTCAACAAACAACTTTTCAGTTTCATTC
Found at i:25692 original size:13 final size:13
Alignment explanation
Indices: 25585--25685 Score: 61
Period size: 12 Copynumber: 7.6 Consensus size: 13
25575 TATTCTATCG
25585 TTATATATA-TAT
1 TTATATATATTAT
* *
25597 ATATATATACT-T
1 TTATATATATTAT
*
25609 TTA-AT-TCTT-T
1 TTATATATATTAT
25619 TTCATATATCATTAT
1 TT-ATATAT-ATTAT
25634 TATATATATATT-T
1 T-TATATATATTAT
25647 TTATTACTATAATATAT
1 TTA-TA-TAT-AT-TAT
25664 GTTATATATATTAT
1 -TTATATATATTAT
25678 TTATATAT
1 TTATATAT
25686 TTCATTTTGT
Statistics
Matches: 71, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
10 5 0.07
11 3 0.04
12 15 0.21
13 14 0.20
14 11 0.15
15 12 0.17
16 5 0.07
17 3 0.04
18 3 0.04
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (13 bp):
TTATATATATTAT
Found at i:29932 original size:158 final size:156
Alignment explanation
Indices: 29608--29925 Score: 412
Period size: 158 Copynumber: 2.0 Consensus size: 156
29598 AAAACATATT
* ** *
29608 TTTATTCAAAAACCATATTAATCCCTCCAACCGGACACACCATAATGTGTAGGTTCCCCAGAGCC
1 TTTA-TCAAAAACCATAGTAATCCCTCCAACCAAACACACCATAATGTGTAGGTTCCCCAGAACC
* * *
29673 ATACACCACCAACACACCAAGTAAGGCCCTGAGCACAAAGAAGAGGAGCATGTAGTAACGGTAAC
65 ATACACCACCAACACACCAAGTAAGGCCATGAGCACAAAGAAGAGGAACATGCAGTAA--GTAAC
*
29738 TTCCTCCAACAACACCCTCCCATAAAACA
128 TTCCTCCAACAACACCCTCCAATAAAACA
29767 TTTATCAAAAACCATAGTAATCCCTCCAACCAAACACACCATAATGTGTAGGTTCCCCAGAACCA
1 TTTATCAAAAACCATAGTAATCCCTCCAACCAAACACACCATAATGTGTAGGTTCCCCAGAACCA
* * * * *
29832 TACACCCACCTACACACTAAGTAAGGCCATGAGCATAAAGCCA-AGGAACCTGCA-T-A-TATAC
66 TACA-CCACCAACACACCAAGTAAGGCCATGAGCACAAAG-AAGAGGAACATGCAGTAAGTA-AC
*
29893 TTCCTCCAACAATACCC-CCAAATAAAACA
128 TTCCTCCAACAACACCCTCC-AATAAAACA
29922 TTTA
1 TTTA
29926 CCATCAATAA
Statistics
Matches: 141, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
154 4 0.03
155 30 0.21
157 1 0.01
158 62 0.44
159 43 0.30
160 1 0.01
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (156 bp):
TTTATCAAAAACCATAGTAATCCCTCCAACCAAACACACCATAATGTGTAGGTTCCCCAGAACCA
TACACCACCAACACACCAAGTAAGGCCATGAGCACAAAGAAGAGGAACATGCAGTAAGTAACTTC
CTCCAACAACACCCTCCAATAAAACA
Found at i:31920 original size:21 final size:22
Alignment explanation
Indices: 31894--31934 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
31884 ACCCAGAAAA
*
31894 AGTCAACGGT-CGGTCAACGCC
1 AGTCAAAGGTCCGGTCAACGCC
31915 AGTCAAAGGTCCGGTCAACG
1 AGTCAAAGGTCCGGTCAACG
31935 GTGGTCAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (22 bp):
AGTCAAAGGTCCGGTCAACGCC
Found at i:31955 original size:32 final size:33
Alignment explanation
Indices: 31895--31956 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
31885 CCCAGAAAAA
* *
31895 GTCAACGGTCGGTCAACGCCAGTCAAAGGTCCG
1 GTCAACGGTCGGTCAAAGACAGTCAAAGGTCCG
* *
31928 GTCAACGGT-GGTCAAAGACGGTTAAAGGT
1 GTCAACGGTCGGTCAAAGACAGTCAAAGGT
31957 GGTCAATGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 16 0.64
33 9 0.36
ACGTcount: A:0.27, C:0.23, G:0.32, T:0.18
Consensus pattern (33 bp):
GTCAACGGTCGGTCAAAGACAGTCAAAGGTCCG
Found at i:33849 original size:41 final size:42
Alignment explanation
Indices: 33767--33851 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 42
33757 AACTCTACTT
* * *
33767 TAGTGGCATTTTCTTAGAAAACGCCGCAAGAAGATGAATATA
1 TAGTGGCATTTTCTAAGAAAACGCCACAAGAAGACGAATATA
* * *
33809 TAGTGGCATTTT-TAAGCAAACGCCACAATAAGACGCATATA
1 TAGTGGCATTTTCTAAGAAAACGCCACAAGAAGACGAATATA
33850 TA
1 TA
33852 TAGTCCCCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 25 0.68
42 12 0.32
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (42 bp):
TAGTGGCATTTTCTAAGAAAACGCCACAAGAAGACGAATATA
Found at i:34770 original size:175 final size:174
Alignment explanation
Indices: 34480--34828 Score: 644
Period size: 175 Copynumber: 2.0 Consensus size: 174
34470 TTTTTCATAT
*
34480 TTAGAAAAGAAACATATGTGATTTTTTTTTTTTATTGGAGGAATTAGCGGGACTGGGAGCGAGGG
1 TTAGAAAAGAAACATATGTGATTTTTTATTTTTATTGGAGGAATTAGCGGGACTGGGAGCGAGGG
34545 TACATACATGCTCTCAAACTGAATATGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGTT
66 TACATACATGCTCTCAAACTGAATATGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGTT
34610 TCCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
131 TCCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
* **
34654 TTAGAAAAGAAATATATGTGATTTATTTATTTTTATTGGTTGAATTAGCGGGACTGGGAGCGAGG
1 TTAGAAAAGAAACATATGTGATTT-TTTATTTTTATTGGAGGAATTAGCGGGACTGGGAGCGAGG
*
34719 GTACATACATGCTCTCAAACTGAATCTGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGT
65 GTACATACATGCTCTCAAACTGAATATGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGT
34784 TTCCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
130 TTCCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
34829 AGGGAAAAGC
Statistics
Matches: 169, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
174 23 0.14
175 146 0.86
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (174 bp):
TTAGAAAAGAAACATATGTGATTTTTTATTTTTATTGGAGGAATTAGCGGGACTGGGAGCGAGGG
TACATACATGCTCTCAAACTGAATATGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGTT
TCCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
Found at i:36547 original size:21 final size:22
Alignment explanation
Indices: 36521--36561 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
36511 ACCCAGAAAA
*
36521 AGTCAACGGT-CGGTCAACGCC
1 AGTCAAAGGTCCGGTCAACGCC
36542 AGTCAAAGGTCCGGTCAACG
1 AGTCAAAGGTCCGGTCAACG
36562 GTGGTCAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (22 bp):
AGTCAAAGGTCCGGTCAACGCC
Found at i:38483 original size:41 final size:42
Alignment explanation
Indices: 38401--38485 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 42
38391 AACTCTACTT
* * *
38401 TAGTGGCATTTTCTTAGAAAACGCCGCAAGAAGATGAATATA
1 TAGTGGCATTTTCTAAGAAAACGCCACAAGAAGACGAATATA
* * *
38443 TAGTGGCATTTT-TAAGCAAACGCCACAATAAGACGCATATA
1 TAGTGGCATTTTCTAAGAAAACGCCACAAGAAGACGAATATA
38484 TA
1 TA
38486 TAGTCCCCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 25 0.68
42 12 0.32
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (42 bp):
TAGTGGCATTTTCTAAGAAAACGCCACAAGAAGACGAATATA
Found at i:39405 original size:175 final size:173
Alignment explanation
Indices: 39116--39463 Score: 642
Period size: 175 Copynumber: 2.0 Consensus size: 173
39106 TTTTTCATAT
39116 TTAGAAAAGAAACATATGTGATTTTTTTTTTTATTGGAGGAATTAGCGGGACTGGGAGCGAGGGT
1 TTAGAAAAGAAACATATGTGATTTTTTTTTTTATTGGAGGAATTAGCGGGACTGGGAGCGAGGGT
39181 ACATACATGCTCTCAAACTGAATATGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGTTT
66 ACATACATGCTCTCAAACTGAATATGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGTTT
39246 CCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
131 CCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
* **
39289 TTAGAAAAGAAATATATGTGATTTATTTATTTTTATTGGTTGAATTAGCGGGACTGGGAGCGAGG
1 TTAGAAAAGAAACATATGTGATTT-TTT-TTTTTATTGGAGGAATTAGCGGGACTGGGAGCGAGG
*
39354 GTACATACATGCTCTCAAACTGAATCTGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGT
64 GTACATACATGCTCTCAAACTGAATATGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGT
39419 TTCCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
129 TTCCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
39464 AGGGAAAAGC
Statistics
Matches: 169, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
173 23 0.14
174 3 0.02
175 143 0.85
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (173 bp):
TTAGAAAAGAAACATATGTGATTTTTTTTTTTATTGGAGGAATTAGCGGGACTGGGAGCGAGGGT
ACATACATGCTCTCAAACTGAATATGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGTTT
CCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
Found at i:41182 original size:21 final size:22
Alignment explanation
Indices: 41156--41196 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
41146 ACCCAGAAAA
*
41156 AGTCAACGGT-CGGTCAACGCC
1 AGTCAAAGGTCCGGTCAACGCC
41177 AGTCAAAGGTCCGGTCAACG
1 AGTCAAAGGTCCGGTCAACG
41197 GTGGTCAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (22 bp):
AGTCAAAGGTCCGGTCAACGCC
Found at i:41217 original size:32 final size:33
Alignment explanation
Indices: 41157--41218 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
41147 CCCAGAAAAA
* *
41157 GTCAACGGTCGGTCAACGCCAGTCAAAGGTCCG
1 GTCAACGGTCGGTCAAAGACAGTCAAAGGTCCG
* *
41190 GTCAACGGT-GGTCAAAGACGGTTAAAGGT
1 GTCAACGGTCGGTCAAAGACAGTCAAAGGT
41219 GGTCAATGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 16 0.64
33 9 0.36
ACGTcount: A:0.27, C:0.23, G:0.32, T:0.18
Consensus pattern (33 bp):
GTCAACGGTCGGTCAAAGACAGTCAAAGGTCCG
Found at i:43083 original size:41 final size:41
Alignment explanation
Indices: 43038--43121 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 41
43028 AACTCTACTT
* *
43038 TAGTGGCATTTCTT-AGAAAACGCCGCAAGAAGATGAATATA
1 TAGTGGCATTT-TTAAGAAAACGCCACAAGAAGACGAATATA
* * *
43079 TAGTGGCATTTTTAAGCAAACGCCACAATAAGACGCATATA
1 TAGTGGCATTTTTAAGAAAACGCCACAAGAAGACGAATATA
43120 TA
1 TA
43122 TAGTCCCCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.05
41 35 0.95
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (41 bp):
TAGTGGCATTTTTAAGAAAACGCCACAAGAAGACGAATATA
Found at i:44040 original size:175 final size:173
Alignment explanation
Indices: 43751--44098 Score: 642
Period size: 175 Copynumber: 2.0 Consensus size: 173
43741 TTTTTCATAT
43751 TTAGAAAAGAAACATATGTGATTTTTTTTTTTATTGGAGGAATTAGCGGGACTGGGAGCGAGGGT
1 TTAGAAAAGAAACATATGTGATTTTTTTTTTTATTGGAGGAATTAGCGGGACTGGGAGCGAGGGT
43816 ACATACATGCTCTCAAACTGAATATGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGTTT
66 ACATACATGCTCTCAAACTGAATATGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGTTT
43881 CCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
131 CCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
* **
43924 TTAGAAAAGAAATATATGTGATTTATTTATTTTTATTGGTTGAATTAGCGGGACTGGGAGCGAGG
1 TTAGAAAAGAAACATATGTGATTT-TTT-TTTTTATTGGAGGAATTAGCGGGACTGGGAGCGAGG
*
43989 GTACATACATGCTCTCAAACTGAATCTGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGT
64 GTACATACATGCTCTCAAACTGAATATGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGT
44054 TTCCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
129 TTCCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
44099 AGGGAAAAGC
Statistics
Matches: 169, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
173 23 0.14
174 3 0.02
175 143 0.85
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (173 bp):
TTAGAAAAGAAACATATGTGATTTTTTTTTTTATTGGAGGAATTAGCGGGACTGGGAGCGAGGGT
ACATACATGCTCTCAAACTGAATATGAGCTCAACAATTGCTTGCTCCAATGGAAAGCAAGGGTTT
CCAAGTCACGGCTTCAGCGTGCGATGTTCTGAATCAAGCTCAA
Found at i:46990 original size:43 final size:43
Alignment explanation
Indices: 46898--47076 Score: 198
Period size: 43 Copynumber: 4.2 Consensus size: 43
46888 TAAATTACCT
* * * *
46898 ACCTATTGCGACGTTTATAAGAAAAACGCCACGAAAAGTCTGA
1 ACCTATTGCGGCGTTTATAAGAAAAACGCCGCTAAATGTCTGA
* * * * *
46941 ATCTATTGCAGCGTTTATAAGAAAAAAGCTGCTAAATGTTTGA
1 ACCTATTGCGGCGTTTATAAGAAAAACGCCGCTAAATGTCTGA
* * * ** * *
46984 ACCTATTGCGGCTTTTGTAAGAAAAATGTTGCTAAATATATGA
1 ACCTATTGCGGCGTTTATAAGAAAAACGCCGCTAAATGTCTGA
*
47027 ACCTATTGCGGCGTTTATAAG-AAAACGCCGCTAGATGTCTGA
1 ACCTATTGCGGCGTTTATAAGAAAAACGCCGCTAAATGTCTGA
47069 ACCTATTG
1 ACCTATTG
47077 TGAAGATTTT
Statistics
Matches: 111, Mismatches: 25, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
42 23 0.21
43 88 0.79
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (43 bp):
ACCTATTGCGGCGTTTATAAGAAAAACGCCGCTAAATGTCTGA
Found at i:54477 original size:28 final size:28
Alignment explanation
Indices: 54434--54498 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
54424 AACCAAAGTA
*
54434 AGCATCATGGTGTAGCTCGGGTTCACTT
1 AGCATCATGGTGTAGCTCGGGGTCACTT
*
54462 AGTATCATGGTGTAGCTCGGGGTCACTT
1 AGCATCATGGTGTAGCTCGGGGTCACTT
54490 AGCATCATG
1 AGCATCATG
54499 AAACTCACAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (28 bp):
AGCATCATGGTGTAGCTCGGGGTCACTT
Found at i:62768 original size:20 final size:20
Alignment explanation
Indices: 62745--62782 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
62735 ACCGATATTG
62745 ACCCCTGAGTATCGATACTA
1 ACCCCTGAGTATCGATACTA
62765 ACCCCTGAGTATCGATAC
1 ACCCCTGAGTATCGATAC
62783 CCATATTTTT
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:0.29, C:0.32, G:0.16, T:0.24
Consensus pattern (20 bp):
ACCCCTGAGTATCGATACTA
Found at i:66731 original size:22 final size:23
Alignment explanation
Indices: 66698--66753 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
66688 CTGTATGAAT
66698 AGTATC-AGTACCATAAG-GAAGG
1 AGTATCGA-TACCATAAGTGAAGG
*
66720 AGTATCGATACC-TATGTGAAGG
1 AGTATCGATACCATAAGTGAAGG
66742 -GTATCGATACCA
1 AGTATCGATACCA
66754 AGAAACATCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 14 0.47
22 15 0.50
23 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (23 bp):
AGTATCGATACCATAAGTGAAGG
Done.