Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000309.1 Hibiscus syriacus cultivar Beakdansim tig00000581_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: 62302
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:591 original size:2 final size:2
Alignment explanation
Indices: 574--680 Score: 177
Period size: 2 Copynumber: 55.5 Consensus size: 2
564 TAATAATTTT
574 TA TA T- TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
655 TA TA TA TA TA TA TA -A TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
681 GCTCGACCTC
Statistics
Matches: 99, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
1 4 0.04
2 95 0.96
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7120 original size:2 final size:2
Alignment explanation
Indices: 7110--7184 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
7100 AAACACACAC
*
7110 AT AT GT 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
7152 AT 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 AT A
7185 AATGAATTAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9899 original size:13 final size:13
Alignment explanation
Indices: 9881--9924 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
9871 TAATAAATAT
9881 ATAATATTAATTA
1 ATAATATTAATTA
9894 ATAATATTAATTA
1 ATAATATTAATTA
* *
9907 TTAA-ATATAATAA
1 ATAATAT-TAATTA
9920 ATAAT
1 ATAAT
9925 TAAAATGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 2 0.08
13 24 0.92
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATAATATTAATTA
Found at i:9910 original size:147 final size:151
Alignment explanation
Indices: 9714--10146 Score: 482
Period size: 147 Copynumber: 2.7 Consensus size: 151
9704 ATAAATAAAT
* * *
9714 TTATATTATAATAAATATATATAACAATAATTAATAATATTAAACATTAAATATAATAAATAATT
1 TTATATTATAAT-AA-ATATATAATATTAATTAATAATATTAAATATTAAATATAATAAATAATT
*
9779 AAAATATAATAATATAGTAATTAATATAGAAATTTTAT-AAAAAATAATTACAATATATTTTGTA
64 AAAATATAATAATATAGTAATTAAAATAGAAATTTTATAAAAAAATAATTACAATATATTTTGTA
9843 AATTTTGAAATAATG-AA-AAA-
129 AATTTTGAAATAATGAAAGAAAC
*
9863 TTATATTATAATAAATATATAATATTAATTAATAATATTAATTATTAAATATAATAAATAATTAA
1 TTATATTATAATAAATATATAATATTAATTAATAATATTAAATATTAAATATAATAAATAATTAA
* *
9928 AATGTAATAATAACATATAAAATAGTAATTAAAATAGATATTTTATAAAAAAATAATTATAATAT
66 AA--T-ATAAT---A-AT---ATAGTAATTAAAATAGAAATTTTATAAAAAAATAATTACAATAT
9993 ATTTTGTAAATTTTGAAATAATGAAATAATGAAAC
121 ATTTTGTAAATTTTGAAATAATG--A-AA-GAAAC
* *
10028 TTATATTATAATAAATAAATATAATAATAATAACTAAAAATATTAAATATT-AATATAATAAATA
1 TTATATTATAATAAAT--ATATAAT-AT--TAATTAATAATATTAAATATTAAATATAATAAATA
*
10092 ATTAAAAATAATAATATATAAATATAGTAATTAAAATAGACATTTTA-AAAAAAAT
61 ATT---AA-AAT-ATA-AT-AATATAGTAATTAAAATAGAAATTTTATAAAAAAAT
10147 TATAATATAT
Statistics
Matches: 244, Mismatches: 12, Indels: 40
0.82 0.04 0.14
Matches are distributed among these distances:
147 49 0.20
148 2 0.01
149 13 0.05
150 5 0.02
153 1 0.00
154 2 0.01
157 23 0.09
158 40 0.16
162 2 0.01
164 3 0.01
165 24 0.10
166 23 0.09
167 7 0.03
168 2 0.01
169 18 0.07
170 19 0.08
171 5 0.02
172 4 0.02
173 2 0.01
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (151 bp):
TTATATTATAATAAATATATAATATTAATTAATAATATTAAATATTAAATATAATAAATAATTAA
AATATAATAATATAGTAATTAAAATAGAAATTTTATAAAAAAATAATTACAATATATTTTGTAAA
TTTTGAAATAATGAAAGAAAC
Found at i:9939 original size:17 final size:18
Alignment explanation
Indices: 9894--9940 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
9884 ATATTAATTA
*
9894 ATAATATTAATTATTAAAT
1 ATAATAATAATTA-TAAAT
9913 ATAATAAATAATTA-AAAT
1 ATAAT-AATAATTATAAAT
*
9931 GTAATAATAA
1 ATAATAATAA
9941 CATATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 5 0.20
18 8 0.32
19 5 0.20
20 7 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
ATAATAATAATTATAAAT
Found at i:10004 original size:158 final size:158
Alignment explanation
Indices: 9714--10167 Score: 521
Period size: 158 Copynumber: 2.9 Consensus size: 158
9704 ATAAATAAAT
* * * *
9714 TTATATTATAATAAAT-ATAT-ATAACAATAATTAATAATATTAAACATTAAATATAATAAATAA
1 TTATATTATAATAAATAATATAATAA-TATAACTAAAAATATTAAATATT-AATATAATAAATAA
* * *
9777 TT-AAAAT-AT---A-ATAATATAGTAATTAATATAGAAATTTTATAAAAAATAATTACAATATA
64 TTAAAAATAATAACATATAAAATAGTAATTAAAATAGAAATTTTATAAAAAATAATTATAATATA
9836 TTTTGTAAATTTTGAAATAATG-AA-AAA-
129 TTTTGTAAATTTTGAAATAATGAAAGAAAC
* * *
9863 TTATATTATAATAAAT-ATATAAT-AT-TAATTAATAATATTAATTATTAAATATAATAAATAAT
1 TTATATTATAATAAATAATATAATAATATAACTAAAAATATTAAATATT-AATATAATAAATAAT
*
9925 TAAAATGTAATAATAACATATAAAATAGTAATTAAAATAGATATTTTATAAAAAAATAATTATAA
65 T-AAA---AATAATAACATATAAAATAGTAATTAAAATAGAAATTTTAT-AAAAAATAATTATAA
9990 TATATTTTGTAAATTTTGAAATAATGAAATAATGAAAC
125 TATATTTTGTAAATTTTGAAATAATG--A-AA-GAAAC
10028 TTATATTATAATAAATAAATATAATAATAATAACTAAAAATATTAAATATTAATATAATAAATAA
1 TTATATTATAATAAAT-AATATAATAAT-ATAACTAAAAATATTAAATATTAATATAATAAATAA
* *
10093 TTAAAAATAATAATATATAAATATAGTAATTAAAATAGACA-TTT-TAAAAAA-AATTATAATAT
64 TTAAAAATAATAACATATAAA-ATAGTAATTAAAATAGAAATTTTATAAAAAATAATTATAATAT
*
10155 ATTTT-CAAATTTT
128 ATTTTGTAAATTTT
10168 TTAAATTTGA
Statistics
Matches: 267, Mismatches: 13, Indels: 38
0.84 0.04 0.12
Matches are distributed among these distances:
147 36 0.13
149 23 0.09
150 2 0.01
152 3 0.01
153 2 0.01
156 1 0.00
157 27 0.10
158 40 0.15
161 7 0.03
162 18 0.07
163 6 0.02
164 4 0.01
165 34 0.13
166 18 0.07
167 7 0.03
168 5 0.02
169 16 0.06
170 18 0.07
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (158 bp):
TTATATTATAATAAATAATATAATAATATAACTAAAAATATTAAATATTAATATAATAAATAATT
AAAAATAATAACATATAAAATAGTAATTAAAATAGAAATTTTATAAAAAATAATTATAATATATT
TTGTAAATTTTGAAATAATGAAAGAAAC
Found at i:10054 original size:16 final size:16
Alignment explanation
Indices: 10030--10122 Score: 71
Period size: 16 Copynumber: 5.6 Consensus size: 16
10020 AATGAAACTT
*
10030 ATATTATAATAAATAA
1 ATATAATAATAAATAA
10046 ATATAATAAT-AATAA
1 ATATAATAATAAATAA
* * *
10061 CTAAAAATATTAAATATTA
1 AT-ATAATAATAAATA--A
*
10080 ATATAATAAATAATTAA
1 ATATAAT-AATAAATAA
* *
10097 AAATAATAATATATAA
1 ATATAATAATAAATAA
*
10113 ATATAGTAAT
1 ATATAATAAT
10123 TAAAATAGAC
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
15 6 0.10
16 30 0.51
17 11 0.19
18 4 0.07
19 8 0.14
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (16 bp):
ATATAATAATAAATAA
Found at i:10074 original size:28 final size:26
Alignment explanation
Indices: 10035--10112 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 26
10025 AACTTATATT
*
10035 ATAATAAA-TAAATATAATAATAATA
1 ATAAAAAATTAAATATAATAATAATA
10060 ACTAAAAATATTAAATAT--TAAT-ATA
1 A-TAAAAA-ATTAAATATAATAATAATA
* *
10085 ATAAATAATTAAAAATAATAATATATA
1 ATAAAAAATTAAATATAATAATA-ATA
10112 A
1 A
10113 ATATAGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
23 8 0.19
24 5 0.12
25 9 0.21
26 9 0.21
27 5 0.12
28 7 0.16
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (26 bp):
ATAAAAAATTAAATATAATAATAATA
Found at i:10075 original size:32 final size:31
Alignment explanation
Indices: 10039--10117 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 31
10029 TATATTATAA
10039 TAAATA-AATATAATAATAATAACTAAAAATAT
1 TAAATATAATATAAT-A-AATAACTAAAAATAT
* *
10071 TAAATATTAATATAATAAATAATTAAAAATAA
1 TAAATA-TAATATAATAAATAACTAAAAATAT
10103 TAATATATAAATATA
1 TAA-ATAT-AATATA
10118 GTAATTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 23 0.56
33 10 0.24
34 8 0.20
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (31 bp):
TAAATATAATATAATAAATAACTAAAAATAT
Found at i:10128 original size:14 final size:14
Alignment explanation
Indices: 10084--10129 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
10074 ATATTAATAT
10084 AATA-AATAATTAA
1 AATATAATAATTAA
10097 AA-ATAATAATATATA
1 AATATAATAAT-TA-A
*
10112 AATATAGTAATTAA
1 AATATAATAATTAA
10126 AATA
1 AATA
10130 GACATTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 1 0.04
13 8 0.29
14 7 0.25
15 5 0.18
16 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
AATATAATAATTAA
Found at i:15463 original size:260 final size:257
Alignment explanation
Indices: 14997--15508 Score: 742
Period size: 260 Copynumber: 2.0 Consensus size: 257
14987 GTTACAAAAA
* * *
14997 ATATTTCAAATTAATTGTTCCACTTTTTATTGATAGATTACATACAGTTCGTACGTGAGTTTGAG
1 ATATTTCAAATTAATTGTTCCACTTTTTATTGATAGATTACACACACTCCGTACGTGAGTTTGAG
* * *
15062 GACCTGATGTAAGAACTTCAACACATGAATTCTGAGGGCTTCAACTACCTTATTAGAATTCCAAA
66 GACCTGATGCAAGAACTTCAACACATGAATTCTGAGGGCTTCAACTACCTTACTAGAATCCCAAA
* * * *
15127 AGATAAATGGCTTCGATCATTTGATTGGGGTAGACGTTATGGTCACATGACAACGAACTTGGTTG
131 AGAGAAATGGCTTCGACCATTTGATTGGGGTAGACGTTATGATCACATGAAAACGAACTTGGTTG
15192 AGGCAATAAATTCATCACTAAAGGGAATACGCCATTTGTCTATCACGTCCATTGTCAAAGTGGC
196 AGGCAATAAATTCATCACTAAAGGGAAT--GCCATTTGTCTATCACGTCCATTGTCAAAGTGGC
*
15256 ATATTATCAAATTAATTGTTCCA-TTTATTATTGATAGGTTACACACACTCCGTACGTGAGTTTG
1 ATATT-TCAAATTAATTGTTCCACTTT-TTATTGATAGATTACACACACTCCGTACGTGAGTTTG
* * * * * * *
15320 AGGACTTGATGCAGGAACTTCGACACATGAATTCTGAGTGTTTC-ACTATCTTCCTAGAATCCCA
64 AGGACCTGATGCAAGAACTTCAACACATGAATTCTGAGGGCTTCAACTACCTTACTAGAATCCCA
* *
15384 AAGGAGAAATGGCTTTTGACCATTTGATTGGGGTAGACAG-TATGATCACATGAAAACGAACTTG
129 AAAGAGAAATGGC-TTCGACCATTTGATTGGGGTAGAC-GTTATGATCACATGAAAACGAACTTG
* * *
15448 GTTGAGGCAATAAATTCATCACTAAAGGGAGTGTCATTTGTCTATCATGTCCATTGTCAAA
192 GTTGAGGCAATAAATTCATCACTAAAGGGAATGCCATTTGTCTATCACGTCCATTGTCAAA
15509 CTGACAACCC
Statistics
Matches: 226, Mismatches: 23, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
258 27 0.12
259 35 0.15
260 163 0.72
261 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (257 bp):
ATATTTCAAATTAATTGTTCCACTTTTTATTGATAGATTACACACACTCCGTACGTGAGTTTGAG
GACCTGATGCAAGAACTTCAACACATGAATTCTGAGGGCTTCAACTACCTTACTAGAATCCCAAA
AGAGAAATGGCTTCGACCATTTGATTGGGGTAGACGTTATGATCACATGAAAACGAACTTGGTTG
AGGCAATAAATTCATCACTAAAGGGAATGCCATTTGTCTATCACGTCCATTGTCAAAGTGGC
Found at i:17278 original size:21 final size:22
Alignment explanation
Indices: 17254--17309 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
17244 CTGAAATATT
** *
17254 CATTTTAGGTAG-GGAAATTAA
1 CATTTTAGGTAGAAAAAAATAA
*
17275 CATTTTCGGTAGAAAAAAAATAA
1 CATTTTAGGTAG-AAAAAAATAA
17298 CATTTTAGGTAG
1 CATTTTAGGTAG
17310 TGTTCCTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 11 0.39
23 17 0.61
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (22 bp):
CATTTTAGGTAGAAAAAAATAA
Found at i:20848 original size:35 final size:35
Alignment explanation
Indices: 20802--20913 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
20792 AAAACATTCC
*
20802 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
20837 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
20872 TCAATTACATTCTAAAACCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
20907 TCAATTT
1 TCAATTT
20914 AAGGAAGAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:22019 original size:35 final size:34
Alignment explanation
Indices: 21971--22082 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 34
21961 AAAAAGACAA
* *
21971 AAATTGAAGTATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
* *
22006 TAATTGAATTATTTTGGAATTTAGGGTTTAAAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
22041 AAATTGAATTACTTTGGAATTTGTGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTG-GGTTTAGAATG
22076 AAATTGA
1 AAATTGA
22083 GGATTGTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 64 0.94
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:22559 original size:20 final size:20
Alignment explanation
Indices: 22534--22687 Score: 281
Period size: 20 Copynumber: 7.7 Consensus size: 20
22524 TTTTCCTAAT
*
22534 TCGCAATGCGAAAACGTAAA
1 TCGCAATGCGAATACGTAAA
22554 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
22574 TCGCAAATGCGAATACGTAAA
1 TCGC-AATGCGAATACGTAAA
22595 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
22615 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
22635 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
22655 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
22675 TCGCAATGTGAAT
1 TCGCAATGCGAAT
22688 CTGACTATCG
Statistics
Matches: 131, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
20 111 0.85
21 20 0.15
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:22738 original size:60 final size:60
Alignment explanation
Indices: 22674--22801 Score: 175
Period size: 60 Copynumber: 2.1 Consensus size: 60
22664 GAATACGTAA
* *
22674 ATCGCAATGTGAATCTGACTATCGCAACGCGATTATGACTATCGCAACGAGATTCTAACT
1 ATCGCAATGAGAATCTAACTATCGCAACGCGATTATGACTATCGCAACGAGATTCTAACT
* * * * * *
22734 ATCGCAACGAGATTCTAACTATCGCAACGCGATTCTGACTATCGCAATGCGATTCTGACT
1 ATCGCAATGAGAATCTAACTATCGCAACGCGATTATGACTATCGCAACGAGATTCTAACT
*
22794 ATCACAAT
1 ATCGCAAT
22802 ACTGAATTTC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (60 bp):
ATCGCAATGAGAATCTAACTATCGCAACGCGATTATGACTATCGCAACGAGATTCTAACT
Found at i:22801 original size:20 final size:20
Alignment explanation
Indices: 22687--22796 Score: 166
Period size: 20 Copynumber: 5.5 Consensus size: 20
22677 GCAATGTGAA
22687 TCTGACTATCGCAACGCGAT
1 TCTGACTATCGCAACGCGAT
* *
22707 TATGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGCGAT
* *
22727 TCTAACTATCGCAACGAGAT
1 TCTGACTATCGCAACGCGAT
*
22747 TCTAACTATCGCAACGCGAT
1 TCTGACTATCGCAACGCGAT
*
22767 TCTGACTATCGCAATGCGAT
1 TCTGACTATCGCAACGCGAT
22787 TCTGACTATC
1 TCTGACTATC
22797 ACAATACTGA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (20 bp):
TCTGACTATCGCAACGCGAT
Found at i:27810 original size:20 final size:19
Alignment explanation
Indices: 27785--27854 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 19
27775 TTCATTTGAT
27785 TATCGCAACGCGAATATGAC
1 TATCGCAACGCGAA-ATGAC
*
27805 TATCGCAACACAGAAATGAC
1 TATCGCAACGC-GAAATGAC
*
27825 TATCGCAACGCCTAAATGAC
1 TATCGCAACG-CGAAATGAC
27845 TATCGCAACG
1 TATCGCAACG
27855 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
20 41 0.91
21 4 0.09
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (19 bp):
TATCGCAACGCGAAATGAC
Found at i:27865 original size:14 final size:14
Alignment explanation
Indices: 27846--27899 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
27836 CTAAATGACT
27846 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
27860 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
27879 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
27893 ATCGCAA
1 ATCGCAA
27900 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:27883 original size:33 final size:34
Alignment explanation
Indices: 27846--27921 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 34
27836 CTAAATGACT
27846 ATCGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
27879 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
27913 ATCGCAACG
1 ATCGCAACG
27922 CGAATTTAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 25 0.60
34 17 0.40
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:27917 original size:20 final size:19
Alignment explanation
Indices: 27859--27925 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
27849 GCAACGAGAG
27859 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
27878 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
27892 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
27912 AATCGCAACGCGAA
1 AATCGCAATGCGAA
27926 TTTAGTTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
19 11 0.28
20 13 0.33
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:27998 original size:33 final size:33
Alignment explanation
Indices: 27936--28098 Score: 254
Period size: 33 Copynumber: 4.8 Consensus size: 33
27926 TTTAGTTTCG
* *
27936 CGTTGTGATTTTCATTTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
27970 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
28003 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
28037 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
28070 CGTTGCGATAGTCATTTCGGCGTTGCGAT
1 CGTTGCGATTTTCATTTC-GCATTGCGAT
28099 AGTCTGTTTT
Statistics
Matches: 122, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
33 67 0.55
34 55 0.45
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:28044 original size:67 final size:67
Alignment explanation
Indices: 27936--28078 Score: 268
Period size: 67 Copynumber: 2.1 Consensus size: 67
27926 TTTAGTTTCG
*
27936 CGTTGTGATTTTCATTTTCGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCT
1 CGTTGCGATTTTCATTTTCGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCT
28001 CT
66 CT
*
28003 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCT
1 CGTTGCGATTTTCATTTTCGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCT
28068 CT
66 CT
28070 CGTTGCGAT
1 CGTTGCGAT
28079 AGTCATTTCG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 74 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (67 bp):
CGTTGCGATTTTCATTTTCGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCT
CT
Found at i:28223 original size:14 final size:14
Alignment explanation
Indices: 28204--28240 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28194 CATCAATTAA
28204 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
28218 ACAAATCATCTTTT
1 ACAAATCAACATTT
28232 ACAAATCAA
1 ACAAATCAA
28241 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:29728 original size:42 final size:42
Alignment explanation
Indices: 29621--29730 Score: 100
Period size: 42 Copynumber: 2.6 Consensus size: 42
29611 TCTAGAATGT
* *
29621 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACAG
1 TGGGAGAGG-CCTCTTAAACGATGACAGGGGCCTCTTGAACAG
* * * ** *
29663 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAAC-G
1 TGGGAGAGGCCTCTTAAACGATGACAGGGGCCTCTTGAACAG
29704 ATAGGG-GAGGCCTCTTAAACGATGACA
1 -T-GGGAGAGGCCTCTTAAACGATGACA
29731 TGTGAGTCGG
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
41 1 0.02
42 47 0.89
43 5 0.09
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTAAACGATGACAGGGGCCTCTTGAACAG
Found at i:30235 original size:20 final size:20
Alignment explanation
Indices: 30212--30260 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
30202 GAAACTTAAA
*
30212 ATCGCAACGGGAAAATGACT
1 ATCGCAACGCGAAAATGACT
30232 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
30252 ATCGCAACG
1 ATCGCAACG
30261 AGAGAATCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:30334 original size:20 final size:20
Alignment explanation
Indices: 30309--30351 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
30299 CTCTCGTTGT
*
30309 GATAGTCATTTTTGCATTGC
1 GATAGTCATTTTCGCATTGC
*
30329 GATAGTCATTTTCGCGTTGC
1 GATAGTCATTTTCGCATTGC
30349 GAT
1 GAT
30352 TTTGTTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (20 bp):
GATAGTCATTTTCGCATTGC
Found at i:30417 original size:20 final size:20
Alignment explanation
Indices: 30390--30443 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
30380 GCGATTCTCT
30390 CATTGCGATAGTAATTTTCG
1 CATTGCGATAGTAATTTTCG
* *
30410 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTAATTTTCG
30430 CATTGCGATAGTAA
1 CATTGCGATAGTAA
30444 ACTATTATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (20 bp):
CATTGCGATAGTAATTTTCG
Found at i:30421 original size:87 final size:87
Alignment explanation
Indices: 30275--30438 Score: 265
Period size: 87 Copynumber: 1.9 Consensus size: 87
30265 AATCGCAATG
* * * * *
30275 CGATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATAGTCATTTTTGCATTGCGATAGTCATTT
1 CGATTTTCATTTCACATTGCGATTCTCTCATTGCGATAGTAATTTTCGCATTGCGATAGTCATTT
*
30340 TCGCGTTGCGATTTTGTTGTTT
66 TCGCATTGCGATTTTGTTGTTT
*
30362 CGATTTTCATTTCACATTGCGATTCTCTCATTGCGATAGTAATTTTCGCGTTGCGATAGTCATTT
1 CGATTTTCATTTCACATTGCGATTCTCTCATTGCGATAGTAATTTTCGCATTGCGATAGTCATTT
30427 TCGCATTGCGAT
66 TCGCATTGCGAT
30439 AGTAAACTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.16, C:0.19, G:0.20, T:0.45
Consensus pattern (87 bp):
CGATTTTCATTTCACATTGCGATTCTCTCATTGCGATAGTAATTTTCGCATTGCGATAGTCATTT
TCGCATTGCGATTTTGTTGTTT
Found at i:32348 original size:20 final size:20
Alignment explanation
Indices: 32325--32378 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
32315 GAAACTTAAA
*
32325 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
32345 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
32365 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
32379 TAAAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:32751 original size:22 final size:23
Alignment explanation
Indices: 32726--32778 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
32716 TGACCGTGAA
32726 TGATTTCGCT-GGAGATGGGGAC
1 TGATTTCGCTCGGAGATGGGGAC
*
32748 TGATTTCG-TCGGAGATGTGGAC
1 TGATTTCGCTCGGAGATGGGGAC
* *
32770 GGATGTCGC
1 TGATTTCGC
32779 CTTAGAGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.17, C:0.15, G:0.40, T:0.28
Consensus pattern (23 bp):
TGATTTCGCTCGGAGATGGGGAC
Found at i:32990 original size:20 final size:20
Alignment explanation
Indices: 32967--33039 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
32957 TGATAGTCAG
*
32967 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACAT
*
32987 ATTCCCATTGCGATTTACGA-
1 ATTCGCATTGCGATTTAC-AT
*
33007 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACAT
33027 ATTCGCATTGCGA
1 ATTCGCATTGCGA
33040 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 46 0.98
21 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACAT
Found at i:50359 original size:18 final size:18
Alignment explanation
Indices: 50336--50383 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
50326 AAATTGTCCT
*
50336 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
50354 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
50371 TATTTATATATTT
1 TA-TTATATATTT
50384 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Done.