Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005995.1 Hibiscus syriacus cultivar Beakdansim tig00014110_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: 33297
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:359 original size:205 final size:209
Alignment explanation
Indices: 1--478 Score: 896
Period size: 205 Copynumber: 2.3 Consensus size: 209
1 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG-TGAA
1 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
65 ATTGACTCTGAATCTGAGAAATGTTTGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
66 ATTGACTCTGAATCTGAGAAATGTTTGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
130 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG-AATTGAGAAATG-TT
131 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAATGTTT
193 GTTGACAACCAGCG
196 GTTGACAACCAGCG
207 GTCCC-TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC-TCGTTGTGAAGTTGAA
1 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
270 ATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
66 ATTGACTCTGAATCTGAGAAATGTTTG-TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
*
335 GC-TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTT
130 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAATGTT
399 TGTTGACAACCAGCG
195 TGTTGACAACCAGCG
414 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
1 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
479 TTGGCTATGG
Statistics
Matches: 265, Mismatches: 1, Indels: 9
0.96 0.00 0.03
Matches are distributed among these distances:
204 11 0.04
205 119 0.45
206 56 0.21
207 21 0.08
208 42 0.16
209 16 0.06
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (209 bp):
GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
ATTGACTCTGAATCTGAGAAATGTTTGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAATGTTT
GTTGACAACCAGCG
Found at i:484 original size:104 final size:105
Alignment explanation
Indices: 1--478 Score: 882
Period size: 103 Copynumber: 4.6 Consensus size: 105
1 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG-TGAA
1 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
65 ATTGACTCTGAATCTGAGAAATGTTTG-TGACAACCAGCG
66 ATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGCG
104 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
1 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
169 ATTGACTCTGAAT-TGAGAAATG-TTGTTGACAACCAGCG
66 ATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGCG
207 GTCCC-TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC-TCGTTGTGAAGTTGAA
1 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
270 ATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGCG
66 ATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGCG
310 GTCCCTTCGTCGTGAAGTTGAACTTGC-TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
1 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
*
374 ATTGGCTCTGAAAT-TGAGAAATGTTTGTTGACAACCAGCG
66 ATTGACTCTG-AATCTGAGAAATGTTTGTTGACAACCAGCG
414 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
1 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
479 TTGGCTATGG
Statistics
Matches: 366, Mismatches: 1, Indels: 14
0.96 0.00 0.04
Matches are distributed among these distances:
101 29 0.08
102 54 0.15
103 127 0.35
104 116 0.32
105 40 0.11
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
ATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGCG
Found at i:1272 original size:13 final size:14
Alignment explanation
Indices: 1254--1292 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1244 AAACGTTTTC
1254 TTTTGTTTTTT-GT
1 TTTTGTTTTTTCGT
1267 TTTTGTTTTTTTCGT
1 TTTTG-TTTTTTCGT
1282 TTTT-TTTTTTC
1 TTTTGTTTTTTC
1293 AACTTAGGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 6 0.25
15 6 0.25
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (14 bp):
TTTTGTTTTTTCGT
Found at i:11770 original size:10 final size:10
Alignment explanation
Indices: 11755--11779 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11745 TAAATCAAAG
11755 ATAAAGAAAA
1 ATAAAGAAAA
11765 ATAAAGAAAA
1 ATAAAGAAAA
11775 ATAAA
1 ATAAA
11780 TAAATAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (10 bp):
ATAAAGAAAA
Found at i:13542 original size:13 final size:13
Alignment explanation
Indices: 13526--13587 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
13516 ATAAACAAGG
*
13526 TAAATAAAACAAA
1 TAAATAAAATAAA
*
13539 TAAAGTAAAAGAGAA
1 TAAA-TAAAATA-AA
13554 -AAATAAAATAAA
1 TAAATAAAATAAA
13566 TAAA-ATAAATAAA
1 TAAATA-AAATAAA
13579 TAAGATAAA
1 TAA-ATAAA
13588 GGAAAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
12 3 0.07
13 23 0.56
14 12 0.29
15 3 0.07
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:13586 original size:9 final size:9
Alignment explanation
Indices: 13526--13587 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
13516 ATAAACAAGG
13526 TAAATAAAA
1 TAAATAAAA
* *
13535 CAAATAAAG
1 TAAATAAAA
13544 TAAA-AGAGAA
1 TAAATA-A-AA
13554 -AAATAAAA
1 TAAATAAAA
13562 TAAATAAAA
1 TAAATAAAA
13571 TAAAT-AAA
1 TAAATAAAA
13579 TAAGATAAA
1 TAA-ATAAA
13588 GGAAAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
8 9 0.21
9 30 0.70
10 4 0.09
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (9 bp):
TAAATAAAA
Found at i:13887 original size:2 final size:2
Alignment explanation
Indices: 13845--13871 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13835 AAAAAACGAA
13845 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 A
13872 AAGTTATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14151 original size:18 final size:17
Alignment explanation
Indices: 14128--14170 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
14118 ATATATATAT
14128 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
14146 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
14163 ATAA-AATA
1 ATAATAATA
14171 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:14595 original size:37 final size:36
Alignment explanation
Indices: 14552--14653 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
14542 ATAGTAGAAC
14552 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
14589 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
14623 TCTATCCTATTTTTAGGAGTTTCAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
14654 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:15389 original size:100 final size:102
Alignment explanation
Indices: 15201--16155 Score: 1230
Period size: 105 Copynumber: 9.3 Consensus size: 102
15191 CATTGTTCCA
* * ** * *
15201 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA--TTGAAAGT-TTTGTTGACAAG
** * * *
15266 CAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
62 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
15307 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGAA-TGAAA-TTTTGTTGACAAGCAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGC
15370 GGTCCCTTCGTCGTGAAGTTGAA-------------G
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
15394 AGTCCAATAT-CTTCCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAA
1 AGTCCAATATCCTT-CGTTGTGAAGTTGAAATTGGCTCT-GAATT-GAAAGTT-TTGTTGACAAG
* *
15458 CAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGG
62 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
15499 AGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAA-TGAAA-TTTTGTTGACAAGCAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGC
*
15562 GGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
15599 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATT-GAAAGTT-TTGTTGACAAGC
*
15664 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
63 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
15704 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-TGAAA-TTTTGTTGACAAGCAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGC
15767 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
15804 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATT-GAAAGTT-TTGTTGACAAGC
*
15869 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
63 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
15909 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATT--G-AAAGT-TTTGTTGACAA
*
15974 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
61 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
16016 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGA-AAGTT-TT-GTTGACAAG
* * * *
16081 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
62 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
16122 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
16156 CGTGGATGGC
Statistics
Matches: 767, Mismatches: 42, Indels: 77
0.87 0.05 0.09
Matches are distributed among these distances:
86 3 0.00
87 33 0.04
88 2 0.00
89 1 0.00
90 3 0.00
91 2 0.00
92 36 0.05
100 212 0.28
101 7 0.01
102 13 0.02
103 10 0.01
104 9 0.01
105 225 0.29
106 88 0.11
107 100 0.13
108 1 0.00
109 22 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (102 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:15479 original size:92 final size:87
Alignment explanation
Indices: 15306--15484 Score: 243
Period size: 92 Copynumber: 2.0 Consensus size: 87
15296 GTGTTGTCTC
*
15306 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGAATGAAATTTTGTTGACAAACAGCG
*
15371 GTCCCTTCGTCGTGAAGTTGAA
66 GTCCCTTCGTCATGAAGTTGAA
** * *
15393 GAGTCCAATAT-CTTCCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAA
1 GAGTCCAATATCCTT-CGTTGTGAAGTTGAAATTGAATCT--GAAT--GAAATT-TTGTTGACAA
15457 ACAGCGGTCCCTTCGTCATGAAGTTGAA
60 ACAGCGGTCCCTTCGTCATGAAGTTGAA
15485 CTTGCATTGT
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
86 3 0.04
87 33 0.41
89 3 0.04
91 5 0.06
92 36 0.45
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (87 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGAATGAAATTTTGTTGACAAACAGCG
GTCCCTTCGTCATGAAGTTGAA
Found at i:15745 original size:205 final size:204
Alignment explanation
Indices: 15393--16155 Score: 1215
Period size: 205 Copynumber: 3.7 Consensus size: 204
15383 TGAAGTTGAA
* *
15393 GAGTCCAATAT-CTTCCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAA
1 GAGTCCAATATCCTT-CGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAA
* *
15457 ACAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGATGTGAA
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCG-TGTGAA
*
15522 GTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCATTCGTCGTGAAGTTGAACT
129 GTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
15587 TGCGTTGTCTG
194 TGCGTTGTCTG
15598 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAG
15663 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCG-TGTGAAG
15728 TTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
130 TTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
15793 GCGTTGTCTG
195 GCGTTGTCTG
15803 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAG
15868 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCG-TGTGAAG
* *
15933 TTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
130 TTGAAATTGGCTCTG-AA-T--G-AAA-T-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
15998 TGAACTTGCGTTGTCTG
188 TGAACTTGCGTTGTCTG
*
16015 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAGTTGTTGGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGA-AAGTTGTT-GTTGACA
* * * ** * *
16079 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCG
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGT-CCA--ATATCCTTCGT-G
*
16144 TGGAGTTGAAAT
125 TGAAGTTGAAAT
16156 CGTGGATGGC
Statistics
Matches: 526, Mismatches: 18, Indels: 17
0.94 0.03 0.03
Matches are distributed among these distances:
205 339 0.64
206 5 0.01
207 1 0.00
209 1 0.00
210 3 0.01
211 3 0.01
212 102 0.19
213 47 0.09
214 3 0.01
215 1 0.00
216 21 0.04
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (204 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTGTGAAGT
TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTG
Found at i:16850 original size:68 final size:65
Alignment explanation
Indices: 16759--16916 Score: 208
Period size: 68 Copynumber: 2.4 Consensus size: 65
16749 AAGATATCTG
* * ** *
16759 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAG-G
16824 TT
64 TT
* * *
16826 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGT
16891 T
65 T
*
16892 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
16917 ATAGACGAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 32 0.40
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGTT
Found at i:16932 original size:65 final size:67
Alignment explanation
Indices: 16760--16942 Score: 201
Period size: 65 Copynumber: 2.7 Consensus size: 67
16750 AGATATCTGT
* * * * ** *
16760 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAGT
16825 TTG
65 TTG
* * *
16828 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
16892 T-
66 TG
* * * *
16893 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTGTTTTAAGGGAAA
16943 CTGTCTCAAG
Statistics
Matches: 99, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
65 38 0.38
66 7 0.07
67 22 0.22
68 32 0.32
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:16943 original size:36 final size:36
Alignment explanation
Indices: 16892--17014 Score: 151
Period size: 36 Copynumber: 3.4 Consensus size: 36
16882 TTCAAAGGTT
* *
16892 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAAA
16928 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAAA
* * * * *
16963 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGACGAAAA
17001 TTGTTTCAA-AGAAA
1 TTGTTTCAAGAGAAA
17015 ACATATTCAA
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
35 9 0.12
36 37 0.49
37 28 0.37
38 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAAA
Found at i:16988 original size:37 final size:36
Alignment explanation
Indices: 16903--17014 Score: 129
Period size: 37 Copynumber: 3.1 Consensus size: 36
16893 TGTTTCAAGG
* * *
16903 GAAACTGTCTCAAGATAGACGAAAATTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACGAAAATTGTTCCAAAA
16939 GAAACTGTCTCAAGAGAGAC-AAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACGAAAA-TT-GTTCCAAAA
* * * *
16976 GAAACTGTCTCAAGGGAGACGGAATTTGTTTC-AAA
1 GAAACTGTCTCAAGAGAGACGAAAATTGTTCCAAAA
17011 GAAA
1 GAAA
17015 ACATATTCAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
35 11 0.17
36 25 0.38
37 28 0.42
38 2 0.03
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACGAAAATTGTTCCAAAA
Found at i:18035 original size:28 final size:29
Alignment explanation
Indices: 17995--18056 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 29
17985 TTGGCATTTG
17995 ATGCTCAAAGGATTGAT-GGGTAGCTTGC
1 ATGCTCAAAGGATTGATGGGGTAGCTTGC
18023 ATGCTCAAAGGATTGATGGGGTAGCTTGC
1 ATGCTCAAAGGATTGATGGGGTAGCTTGC
18052 ATGCT
1 ATGCT
18057 TCTCTACTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (29 bp):
ATGCTCAAAGGATTGATGGGGTAGCTTGC
Found at i:18702 original size:7 final size:7
Alignment explanation
Indices: 18672--18761 Score: 63
Period size: 7 Copynumber: 11.7 Consensus size: 7
18662 TTTTTGTCCC
18672 TTTTTCT
1 TTTTTCT
**
18679 TTTTGAT
1 TTTTTCT
18686 TTTTGCTCT
1 TTTT--TCT
18695 TTTTTCT
1 TTTTTCT
18702 TTTGTTCT
1 TTT-TTCT
*
18710 TGTTTCT
1 TTTTTCT
*
18717 CTTTTCTT
1 TTTTTC-T
*
18725 TGTTTTTT
1 T-TTTTCT
18733 TTTTTGCT
1 TTTTT-CT
18741 TTTTTGCT
1 TTTTT-CT
18749 TCTTTTCT
1 T-TTTTCT
18757 TTTTT
1 TTTTT
18762 GTTCTTGATT
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
7 31 0.47
8 22 0.33
9 13 0.20
ACGTcount: A:0.01, C:0.13, G:0.08, T:0.78
Consensus pattern (7 bp):
TTTTTCT
Found at i:18704 original size:15 final size:17
Alignment explanation
Indices: 18686--18729 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
18676 TCTTTTTGAT
18686 TTTTGCTCTT-TTT-TC
1 TTTTGCTCTTGTTTCTC
*
18701 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
18718 TTTT-CT-TTGTTT
1 TTTTGCTCTTGTTT
18730 TTTTTTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 15 0.60
16 4 0.16
17 6 0.24
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:18731 original size:33 final size:32
Alignment explanation
Indices: 18694--18767 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
18684 ATTTTTGCTC
*
18694 TTTTTTCTTTTG-TTCTTGTTTC-TCTTTTCTTT
1 TTTTTTCTTTTGCTT-TT-TTGCTTCTTTTCTTT
*
18726 GTTTTTTTTTTTGCTTTTTTGCTTCTTTTCTTT
1 -TTTTTTCTTTTGCTTTTTTGCTTCTTTTCTTT
*
18759 TTTGTTCTT
1 TTTTTTCTT
18768 GATTGGATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 10 0.29
33 23 0.66
34 2 0.06
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (32 bp):
TTTTTTCTTTTGCTTTTTTGCTTCTTTTCTTT
Found at i:21855 original size:37 final size:36
Alignment explanation
Indices: 21812--21913 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 36
21802 ATAGTAGAAC
21812 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
21849 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
* *
21883 TCTATCATATTTTTAGGAGTTTAAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
21914 TAGGACAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
34 31 0.53
37 28 0.47
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:23259 original size:31 final size:31
Alignment explanation
Indices: 23217--23290 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
23207 TTAGGGAAAA
*
23217 AAGTTTTGGTCACTTACGTTATTGTTTTATT
1 AAGTTTTGGTCACTTACGTTATCGTTTTATT
*
23248 AAGTTTCGGTCACTTACGTTATCGTTTTATT
1 AAGTTTTGGTCACTTACGTTATCGTTTTATT
23279 AAGTTTTGGTCA
1 AAGTTTTGGTCA
23291 TTTGGGCATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.50
Consensus pattern (31 bp):
AAGTTTTGGTCACTTACGTTATCGTTTTATT
Found at i:24652 original size:31 final size:31
Alignment explanation
Indices: 24581--24655 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
24571 AACGTCCAAG
**
24581 TGACCAAAACTTAATAAAACGATAATGTAAA
1 TGACCAAAACTTAATAAAACGATAACATAAA
*
24612 TGACCAAAACTTAATAAAACGATAACATAAG
1 TGACCAAAACTTAATAAAACGATAACATAAA
**
24643 TGATTAAAACTTA
1 TGACCAAAACTTA
24656 TGTTTTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.24
Consensus pattern (31 bp):
TGACCAAAACTTAATAAAACGATAACATAAA
Found at i:26057 original size:2 final size:2
Alignment explanation
Indices: 26052--26136 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
26042 AAGACTAAAT
*
26052 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA 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
26094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
26136 T
1 T
26137 CGTGTATGAT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28909 original size:117 final size:117
Alignment explanation
Indices: 28697--28923 Score: 282
Period size: 117 Copynumber: 1.9 Consensus size: 117
28687 TAGCGTGATC
* * *
28697 AAATTTAATTCAAAATTGAATGAAAATTAAGAGAAATGGAAAAAGAGGGTCAAAAACAAAATTTT
1 AAATTTAATTCAAAATTGAATGAAAAATAAGAGAAATGGAAAAAGAGGATCAAAAACAAAAATTT
* **
28762 TATGGAATCATAAAAATTAGGGACCTTAATTATAAATATAAAAAAATTAGTT
66 AATAAAATCATAAAAATTAGGGACCTTAATTATAAATATAAAAAAATTAGTT
* **
28814 AAATTTAATTCAAAATTTAAT-AAATTAATAAGAGAAATGGAAAAAGAGGAT-AAAAGTTAAAAA
1 AAATTTAATTCAAAATTGAATGAAA--AATAAGAGAAATGGAAAAAGAGGATCAAAA-ACAAAAA
* * *
28877 TTTAATAAAAT-TTTAAAATTATGGGTCC-TAATTATAAATATAAAAAA
63 TTTAATAAAATCATAAAAATTA-GGGACCTTAATTATAAATATAAAAAA
28924 TTGGAGGCCC
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
116 3 0.03
117 51 0.54
118 40 0.43
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.30
Consensus pattern (117 bp):
AAATTTAATTCAAAATTGAATGAAAAATAAGAGAAATGGAAAAAGAGGATCAAAAACAAAAATTT
AATAAAATCATAAAAATTAGGGACCTTAATTATAAATATAAAAAAATTAGTT
Found at i:28962 original size:29 final size:29
Alignment explanation
Indices: 28903--28963 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
28893 AATTATGGGT
* *
28903 CCTAATTATAAATATAAAAAATTGGAGGC
1 CCTAATTATAAATAAAAAAAATGGGAGGC
28932 CCTAATTATAAATAAAAAAAACTGGGA-GC
1 CCTAATTATAAATAAAAAAAA-TGGGAGGC
28961 CCT
1 CCT
28964 GAGCGGTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.25
Consensus pattern (29 bp):
CCTAATTATAAATAAAAAAAATGGGAGGC
Done.