Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006033.1 Hibiscus syriacus cultivar Beakdansim tig00014241_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: 63585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:9663 original size:178 final size:177
Alignment explanation
Indices: 9365--9719 Score: 674
Period size: 178 Copynumber: 2.0 Consensus size: 177
9355 TAATTTTAAG
*
9365 AGTGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATAATTTTCATGCATTAAAATAGT
1 AGTGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATAATTTTCATGCATTAAAACAGT
*
9430 CATTTGTTACCCCAATCGAAATAAAAATGTATTACTGTTTCGTCTTAAAAATCGGTATTAATTCG
66 CATTTGTTACCCCAATCGAAATAAAAATGTATTACTATTTCGTCTTAAAAATCGGTATTAATTCG
9495 AGAGAAAACGACAATATCAAATTATTTCTAATCGATAATAAATGACC
131 AGAGAAAACGACAATATCAAATTATTTCTAATCGATAATAAATGACC
*
9542 AGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATAATCTTTCATGCATTAAAACAG
1 AGTGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATAAT-TTTCATGCATTAAAACAG
9607 TCATTTGTTACCCCAATCGAAATAAAAATGTATTACTATTTCGTCTTAAAAATCGGTATTAATTC
65 TCATTTGTTACCCCAATCGAAATAAAAATGTATTACTATTTCGTCTTAAAAATCGGTATTAATTC
9672 GAGAGAAAACGACAATATCAAATTATTTCTAATCGATAATAAATGACC
130 GAGAGAAAACGACAATATCAAATTATTTCTAATCGATAATAAATGACC
9720 TCTCATGCCT
Statistics
Matches: 174, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
177 45 0.26
178 129 0.74
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (177 bp):
AGTGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATAATTTTCATGCATTAAAACAGT
CATTTGTTACCCCAATCGAAATAAAAATGTATTACTATTTCGTCTTAAAAATCGGTATTAATTCG
AGAGAAAACGACAATATCAAATTATTTCTAATCGATAATAAATGACC
Found at i:11152 original size:21 final size:20
Alignment explanation
Indices: 11127--11229 Score: 138
Period size: 21 Copynumber: 5.1 Consensus size: 20
11117 CCGTTAGATA
*
11127 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
*
11147 AGGGGGAATCTGTTCCCCCTG
1 -GGGGGAATCTGTACCCCCTG
*
11168 GGGGGGATC-GATACCCCCTGG
1 GGGGGAATCTG-TACCCCCT-G
11189 GGGGGAATCTGTA-CCCCTG
1 GGGGGAATCTGTACCCCCTG
11208 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
11228 GG
1 GG
11230 CAATATGATT
Statistics
Matches: 73, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
19 15 0.21
20 28 0.38
21 29 0.40
22 1 0.01
ACGTcount: A:0.15, C:0.28, G:0.39, T:0.18
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:11183 original size:41 final size:39
Alignment explanation
Indices: 11127--11227 Score: 139
Period size: 41 Copynumber: 2.5 Consensus size: 39
11117 CCGTTAGATA
*
11127 GGGGGAATCGGTACCCCCTGAGGGGGAATCTGTTCCCCCTG
1 GGGGGAATC-GTACCCCCTGAGGGGGAATCTG-TACCCCTG
* *
11168 GGGGGGATCGATACCCCCTGGGGGGGAATCTGTACCCCTG
1 GGGGGAATCG-TACCCCCTGAGGGGGAATCTGTACCCCTG
11208 GGGGGAATCTGTACCCCCTG
1 GGGGGAATC-GTACCCCCTG
11228 GGCAATATGA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
40 25 0.46
41 29 0.54
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.19
Consensus pattern (39 bp):
GGGGGAATCGTACCCCCTGAGGGGGAATCTGTACCCCTG
Found at i:14493 original size:18 final size:19
Alignment explanation
Indices: 14429--14508 Score: 108
Period size: 18 Copynumber: 4.1 Consensus size: 19
14419 CCGTTAGACA
*
14429 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTGTA-CCCCTG
*
14449 GGGGGAAATCTGTTTCCCCTG
1 GGGGG-AATCTG-TACCCCTG
14470 GGGGGAATCTGTACCCCT-
1 GGGGGAATCTGTACCCCTG
14488 GGGGGAATCTGTACCCCTG
1 GGGGGAATCTGTACCCCTG
14507 GG
1 GG
14509 CAATCTGATT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
18 18 0.33
19 8 0.15
20 11 0.20
21 16 0.30
22 1 0.02
ACGTcount: A:0.15, C:0.26, G:0.38, T:0.21
Consensus pattern (19 bp):
GGGGGAATCTGTACCCCTG
Found at i:14515 original size:17 final size:18
Alignment explanation
Indices: 14450--14515 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
14440 TACCCCCTGG
* *
14450 GGGGAAATCTGTTTCCCCT
1 GGGGCAATCTG-TACCCCT
*
14469 GGGGGGAATCTGTACCCCT
1 -GGGGCAATCTGTACCCCT
*
14488 GGGGGAATCTGTACCCCT
1 GGGGCAATCTGTACCCCT
14506 -GGGCAATCTG
1 GGGGCAATCTG
14516 ATTTTTCTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.21
18 18 0.42
19 6 0.14
20 10 0.23
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (18 bp):
GGGGCAATCTGTACCCCT
Found at i:15932 original size:3 final size:3
Alignment explanation
Indices: 15924--15983 Score: 77
Period size: 3 Copynumber: 20.3 Consensus size: 3
15914 TATACTTATG
* * *
15924 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT ATT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
15972 AAT -CT AAT AAT A
1 AAT AAT AAT AAT A
15984 TTATTTAACT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
2 1 0.02
3 47 0.98
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16279 original size:134 final size:133
Alignment explanation
Indices: 16128--16599 Score: 572
Period size: 134 Copynumber: 3.5 Consensus size: 133
16118 ATCTGTTCCC
* *
16128 CTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCAACTGTCT-CTTAGGGAAGAT
1 CTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGT-TACTCAGGGAAGAT
* *
16192 TGAATCGAGGCAGACTTGTTCCACTGTAACTCAGGGAATATCAAATCATGAAATAGAGTGATTTG
65 TGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAATAGAG-GATTTG
16257 TTTCT
129 TTTCT
* * * * *
16262 CTTCTTCTTGAGGGAAAATTAGATCTAGGGACGTTGATTCATTCGACTGTTACTCAGGGATGATT
1 CTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTTACTCAGGGAAGATT
* * * * * * *
16327 GAATCGAGGCAAACTTATTCCACTGTTACTTAGGGAACATCAAATCTTGGAAGAGAGGGTTCTGT
66 GAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAATAGAGGATT-TGT
16392 TTCAT
130 TTC-T
* * *
16397 TTTC-TCTTGAGGGAAAATCAAATATGGGGACGTTGATTCATTCCACTGTTACTCAGAGAAGATT
1 CTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTTACTCAGGGAAGATT
* * * * * * *
16461 GAATCGAGGAAGACTTGTTCCACTGTTACTCAAGGAATATCAAATCTTAGAAGTGGGGGATCTAT
66 GAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTT-GAAATAGAGGATTTGT
*
16526 TTCA
130 TTCT
* * * * * *
16530 CTTCTTCTTGAGGGAGAATCAGATCTGGGGACGTCGATTAACTCCACAGTT-CTTCAGGGAAGAT
1 CTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTTAC-TCAGGGAAGAT
16594 TGAATC
65 TGAATC
16600 AAGTTGATTC
Statistics
Matches: 285, Mismatches: 47, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
133 8 0.03
134 267 0.94
135 10 0.04
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (133 bp):
CTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTTACTCAGGGAAGATT
GAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAATAGAGGATTTGTT
TCT
Found at i:17843 original size:9 final size:9
Alignment explanation
Indices: 17829--17875 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
17819 GTTTTTTCTT
17829 TTTCTTTTC
1 TTTCTTTTC
17838 TTTCTTTTC
1 TTTCTTTTC
17847 TTTCTTTAT-
1 TTTCTTT-TC
17856 TTTCATTTTTC
1 TTTC--TTTTC
17867 TTTCCTTTT
1 TTT-CTTTT
17876 TTCATTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 20 0.61
10 6 0.18
11 6 0.18
12 1 0.03
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:17865 original size:20 final size:19
Alignment explanation
Indices: 17829--17904 Score: 86
Period size: 20 Copynumber: 4.0 Consensus size: 19
17819 GTTTTTTCTT
17829 TTTCTTTTCTTTC--TTTTC
1 TTTCTTTT-TTTCATTTTTC
17847 TTTCTTTATTTTCATTTTTC
1 TTTCTTT-TTTTCATTTTTC
*
17867 TTTCCTTTTTTCATTCTTTC
1 TTTCTTTTTTTCATT-TTTC
*
17887 ATTCTTTTTTT-ATTTTTC
1 TTTCTTTTTTTCATTTTTC
17905 CCTTTTTTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
18 15 0.29
19 12 0.24
20 24 0.47
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTCTTTTTTTCATTTTTC
Found at i:17865 original size:40 final size:37
Alignment explanation
Indices: 17813--17904 Score: 98
Period size: 40 Copynumber: 2.4 Consensus size: 37
17803 TTGAACCCTC
* * *
17813 CTTTTTGT-TTTTTCTTT-TTCTTTTCTTTCTTTTCTTT
1 CTTTTTTTATTTTTCTTTCTT-TTTTCATTC-TTTCATT
17850 CTTTATTTTCATTTTTCTTTCCTTTTTTCATTCTTTCATT
1 CTTT-TTTT-ATTTTTCTTT-CTTTTTTCATTCTTTCATT
17890 CTTTTTTTATTTTTC
1 CTTTTTTTATTTTTC
17905 CCTTTTTTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
37 4 0.09
38 10 0.21
39 4 0.09
40 19 0.40
41 8 0.17
42 2 0.04
ACGTcount: A:0.05, C:0.17, G:0.01, T:0.76
Consensus pattern (37 bp):
CTTTTTTTATTTTTCTTTCTTTTTTCATTCTTTCATT
Found at i:17883 original size:16 final size:16
Alignment explanation
Indices: 17864--17914 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
17854 ATTTTCATTT
17864 TTCTTTCCTTTTTTCA
1 TTCTTTCCTTTTTTCA
*
17880 TTCTTTCATTCTTTTTTTA
1 TTCTTTC---CTTTTTTCA
17899 TT-TTTCCCTTTTTTCA
1 TTCTTT-CCTTTTTTCA
17915 ATTTTTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 15 0.52
18 3 0.10
19 11 0.38
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.71
Consensus pattern (16 bp):
TTCTTTCCTTTTTTCA
Found at i:26770 original size:11 final size:11
Alignment explanation
Indices: 26750--26783 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
26740 TGCGAAAAAA
26750 GTAAATGCAAT
1 GTAAATGCAAT
**
26761 GTGGATGCAAT
1 GTAAATGCAAT
26772 GTAAATGCAAT
1 GTAAATGCAAT
26783 G
1 G
26784 CAAGCTGTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.26
Consensus pattern (11 bp):
GTAAATGCAAT
Found at i:27775 original size:131 final size:131
Alignment explanation
Indices: 27614--27979 Score: 398
Period size: 131 Copynumber: 2.8 Consensus size: 131
27604 AATTTTAAGA
* * *
27614 GTGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCAGT-CGTTAAAATAG
1 GTGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTC-GTGCATTAAAACAA
27678 TCATTTATTAACCCAATCGAAATAAAGAA-ATATTACTATTTCGTCTTAAAATTCAATATTGATT
65 TCATTTATTAACCCAATCGAAATAAA-AAGATATTACTATTTCGTCTTAAAATTCAATATTGATT
27742 CAT
129 CAT
*
27745 GTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACAAT
1 GTGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACAAT
* * * * * *** *
27810 CATTTGTTACCCCAATTGAAATAAAAAGATATTACTATTTCGTCTTAAAAATCGATAAAAATTTG
66 CATTTATTAACCCAATCGAAATAAAAAGATATTACTATTTCGTCTTAAAATTCAATATTGA-TTC
*
27875 AA
130 AT
* *** * * * * * * * *
27877 AT-AAAACGGCAATATCAAATTATTTCCAATCGAGAATACATGACATCTCATGCCTTAAAGCAGT
1 GTGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACAAT
* * * *
27941 CATTTATT-ACTCCGACCAAAATGAAAAGATATTACTATT
66 CATTTATTAAC-CCAATCGAAATAAAAAGATATTACTATT
27980 CTCAAAATCG
Statistics
Matches: 199, Mismatches: 32, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
130 5 0.03
131 190 0.95
132 4 0.02
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.33
Consensus pattern (131 bp):
GTGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACAAT
CATTTATTAACCCAATCGAAATAAAAAGATATTACTATTTCGTCTTAAAATTCAATATTGATTCA
T
Found at i:29419 original size:2 final size:2
Alignment explanation
Indices: 29414--29463 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
29404 TGTTTCGAAC
29414 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
29456 TA TA TA TA
1 TA TA TA TA
29464 ATACCTTTCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30051 original size:3 final size:3
Alignment explanation
Indices: 30033--30091 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
30023 ATGTACTTAT
* * * *
30033 TAA TAA TAT TAT TAA TAA TAA TAA TGA TAT TAA TAA -AA CTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
30078 T-A TAA T-A TAA TAA T
1 TAA TAA TAA TAA TAA T
30092 TTTATTTAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 6 0.13
3 38 0.83
4 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:30054 original size:18 final size:18
Alignment explanation
Indices: 30033--30097 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
30023 ATGTACTTAT
30033 TAATAATATTATTAATAA
1 TAATAATATTATTAATAA
30051 TAATAATGA-TATTAATAA
1 TAATAAT-ATTATTAATAA
*
30069 -AACTAATAATA-TAAT-A
1 TAA-TAATATTATTAATAA
*
30085 TAATAATTTTATT
1 TAATAATATTATT
30098 TAACGGGATG
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 7 0.17
17 10 0.25
18 22 0.55
19 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATAATATTATTAATAA
Found at i:31202 original size:1 final size:1
Alignment explanation
Indices: 31196--31355 Score: 59
Period size: 1 Copynumber: 160.0 Consensus size: 1
31186 ACTACAGTTG
* * * * * * * * * * * *
31196 AAAAAAAAAGAAAAAAGAAGAAAAATATAAAAAAAAATATAAAAAAGAAAAAAGAAGAAAGAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * * * * *
31261 AAAAATAAAAAATATAAAATATAAAAAAATAAAAAAAATAAAAAAATATAAAATATAAAAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * *
31326 AAAAAGGAAAAATATAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31356 GGAGGTTCAA
Statistics
Matches: 103, Mismatches: 56, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
1 103 1.00
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (1 bp):
A
Found at i:31227 original size:17 final size:16
Alignment explanation
Indices: 31198--31352 Score: 81
Period size: 14 Copynumber: 10.4 Consensus size: 16
31188 TACAGTTGAA
*
31198 AAAAAAAGA-AAAAAG
1 AAAAAAATATAAAAAG
31213 AAGAAAAATAT-AAAA-
1 AA-AAAAATATAAAAAG
*
31228 AAAAATATA-AAAAAG
1 AAAAAAATATAAAAAG
*
31243 AAAAAAGA-AGAAAGAAG
1 AAAAAA-ATATAAA-AAG
31260 -AAAAAATA-AAAAA-
1 AAAAAAATATAAAAAG
* *
31273 TATAAAATAT--AAA-
1 AAAAAAATATAAAAAG
* *
31286 AAAATAA-A-AAAAAT
1 AAAAAAATATAAAAAG
*
31300 AAAAAAATATAAAATAT
1 AAAAAAATATAAAA-AG
31317 AAAAAAA-ATAAAAAG
1 AAAAAAATATAAAAAG
*
31332 -GAAAAATAT-AAAAG
1 AAAAAAATATAAAAAG
31346 AAAAAAA
1 AAAAAAA
31353 AAAGGAGGTT
Statistics
Matches: 111, Mismatches: 11, Indels: 36
0.70 0.07 0.23
Matches are distributed among these distances:
12 1 0.01
13 10 0.09
14 35 0.32
15 23 0.21
16 30 0.27
17 12 0.11
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (16 bp):
AAAAAAATATAAAAAG
Found at i:31227 original size:24 final size:22
Alignment explanation
Indices: 31200--31354 Score: 109
Period size: 24 Copynumber: 6.6 Consensus size: 22
31190 CAGTTGAAAA
31200 AAAAAGAAAAAAGAAGAAAAATAT
1 AAAAA-AAAAAA-AAGAAAAATAT
* * *
31224 AAAAAAAAATATA-AAAAAGA-
1 AAAAAAAAAAAAAGAAAAATAT
*
31244 AAAAAGAAGAAAGAAGAAAAA-AT
1 AAAAA-AA-AAAAAAGAAAAATAT
* *
31267 AAAAAATATAAAATATAAAAAAATAA
1 AAAAAA-A-AAAA-A-AGAAAAATAT
*
31293 AAAAAATAAAAAAATATAAAATAT
1 AAAAAA-AAAAAAAGA-AAAATAT
31317 AAAAAAAATAAAAAGGAAAAATAT
1 AAAAAAAA-AAAAA-GAAAAATAT
31341 AAAAGAAAAAAAAA
1 AAAA-AAAAAAAAA
31355 AGGAGGTTCA
Statistics
Matches: 106, Mismatches: 13, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
20 5 0.05
21 8 0.08
22 6 0.06
23 23 0.22
24 40 0.38
25 15 0.14
26 9 0.08
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAAAAAAAAAAAGAAAAATAT
Found at i:31306 original size:34 final size:34
Alignment explanation
Indices: 31260--31330 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
31250 AAGAAAGAAG
31260 AAAAAATAAAAAATATAAAATAT-AAAAAAATAA
1 AAAAAATAAAAAATATAAAATATAAAAAAAATAA
31293 AAAAAATAAAAAAATATAAAATATAAAAAAAATAA
1 AAAAAAT-AAAAAATATAAAATATAAAAAAAATAA
31328 AAA
1 AAA
31331 GGAAAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 7 0.19
34 16 0.44
35 13 0.36
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (34 bp):
AAAAAATAAAAAATATAAAATATAAAAAAAATAA
Found at i:31313 original size:9 final size:8
Alignment explanation
Indices: 31260--31330 Score: 81
Period size: 9 Copynumber: 8.5 Consensus size: 8
31250 AAGAAAGAAG
31260 AAAAAAT-
1 AAAAAATA
31267 AAAAAATA
1 AAAAAATA
*
31275 TAAAATATA
1 -AAAAAATA
31284 AAAAAATAA
1 AAAAAAT-A
31293 AAAAAATA
1 AAAAAATA
31301 AAAAAATA
1 AAAAAATA
*
31309 TAAAATATAA
1 -AAAAAAT-A
31319 AAAAAATA
1 AAAAAATA
31327 AAAA
1 AAAA
31331 GGAAAAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
7 7 0.13
8 20 0.36
9 27 0.49
10 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAAATA
Found at i:31353 original size:17 final size:17
Alignment explanation
Indices: 31195--31354 Score: 86
Period size: 17 Copynumber: 9.6 Consensus size: 17
31185 TACTACAGTT
* *
31195 GAAAAAAAAAGAAAAAA
1 GAAAAAAAAATATAAAA
*
31212 G-AAGAAAAATAT--AA
1 GAAAAAAAAATATAAAA
* *
31226 -AAAAAAATATAAAAAA
1 GAAAAAAAAATATAAAA
* *
31242 GAAAAAAGAAGAAAGAAGAA
1 GAAAAAA-AA-ATATAA-AA
*
31262 AAAATAAAAAATATAAAA
1 GAAA-AAAAAATATAAAA
* *
31280 TATAAAAAAATA-AAAA
1 GAAAAAAAAATATAAAA
*
31296 AAATAAAAAAATATAAAA
1 GAA-AAAAAAATATAAAA
*
31314 TATAAAAAAAATA-AAAA
1 GA-AAAAAAAATATAAAA
*
31331 G---GAAAAATATAAAA
1 GAAAAAAAAATATAAAA
31345 GAAAAAAAAA
1 GAAAAAAAAA
31355 AGGAGGTTCA
Statistics
Matches: 108, Mismatches: 20, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
13 7 0.06
14 15 0.14
16 15 0.14
17 33 0.31
18 19 0.18
19 9 0.08
20 7 0.06
21 3 0.03
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.11
Consensus pattern (17 bp):
GAAAAAAAAATATAAAA
Found at i:33181 original size:36 final size:36
Alignment explanation
Indices: 33141--33209 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
33131 TTAGGAAATA
33141 TATGATATATAGTTACATAATATAAATATATATACG
1 TATGATATATAGTTACATAATATAAATATATATACG
* *
33177 TATGATATATAGTTACGTAATATATATATATAT
1 TATGATATATAGTTACATAATATAAATATATAT
33210 TAAAAAGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (36 bp):
TATGATATATAGTTACATAATATAAATATATATACG
Found at i:33193 original size:17 final size:17
Alignment explanation
Indices: 33145--33204 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
33135 GAAATATATG
*
33145 ATATATAGTTACATAAT
1 ATATATAGTTACGTAAT
33162 ATAAATATA-TATACGT-AT
1 AT--ATATAGT-TACGTAAT
33180 GATATATAGTTACGTAAT
1 -ATATATAGTTACGTAAT
33198 ATATATA
1 ATATATA
33205 TATATTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
17 19 0.53
18 6 0.17
19 11 0.31
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (17 bp):
ATATATAGTTACGTAAT
Found at i:35112 original size:55 final size:54
Alignment explanation
Indices: 35053--35173 Score: 127
Period size: 54 Copynumber: 2.2 Consensus size: 54
35043 CCAATACAAT
* * **
35053 AATTCACCACCTCATTAAGAATTACGTGGGGATGCACAC-CTAATGCCAATACGGA
1 AATTCACAAACTCATTAAGAATTAC-TGCAGATGCACACAC-AATGCCAATACGGA
* * * * *
35108 AATTCATAAACTCATTATGAATTTCTTCAGTTGCACACACAATGCCAATACGGA
1 AATTCACAAACTCATTAAGAATTACTGCAGATGCACACACAATGCCAATACGGA
*
35162 AATTCATAAACT
1 AATTCACAAACT
35174 TATCATGAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
54 35 0.62
55 21 0.38
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (54 bp):
AATTCACAAACTCATTAAGAATTACTGCAGATGCACACACAATGCCAATACGGA
Found at i:35159 original size:54 final size:55
Alignment explanation
Indices: 35085--35200 Score: 184
Period size: 54 Copynumber: 2.1 Consensus size: 55
35075 TACGTGGGGA
*
35085 TGCACAC-CTAATGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTCA-GT
1 TGCACACACTAATGCCAATACGGAAATTCATAAACTCATCATGAATTTCTT-AGGT
*
35139 TGCACACAC-AATGCCAATACGGAAATTCATAAACTTATCATGAATTTCTTAGGT
1 TGCACACACTAATGCCAATACGGAAATTCATAAACTCATCATGAATTTCTTAGGT
35193 TGCACACA
1 TGCACACA
35201 TAGTGCCCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
53 1 0.02
54 56 0.97
55 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.29
Consensus pattern (55 bp):
TGCACACACTAATGCCAATACGGAAATTCATAAACTCATCATGAATTTCTTAGGT
Found at i:39108 original size:89 final size:89
Alignment explanation
Indices: 38957--39134 Score: 347
Period size: 89 Copynumber: 2.0 Consensus size: 89
38947 TCTCGAGCAG
*
38957 TTGAAACATTTTCTATCTCAACTATGAAAGTCTAATTATCTAAATCATTTAATAAGAAGACTTGA
1 TTGAAACATTTTCTATCTCAACTATGAAAGTCTAATTATCAAAATCATTTAATAAGAAGACTTGA
39022 CAACTTTGTAGCAATATCCTCATA
66 CAACTTTGTAGCAATATCCTCATA
39046 TTGAAACATTTTCTATCTCAACTATGAAAGTCTAATTATCAAAATCATTTAATAAGAAGACTTGA
1 TTGAAACATTTTCTATCTCAACTATGAAAGTCTAATTATCAAAATCATTTAATAAGAAGACTTGA
39111 CAACTTTGTAGCAATATCCTCATA
66 CAACTTTGTAGCAATATCCTCATA
39135 GCACTTATTG
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (89 bp):
TTGAAACATTTTCTATCTCAACTATGAAAGTCTAATTATCAAAATCATTTAATAAGAAGACTTGA
CAACTTTGTAGCAATATCCTCATA
Found at i:40456 original size:45 final size:45
Alignment explanation
Indices: 40403--40515 Score: 172
Period size: 45 Copynumber: 2.5 Consensus size: 45
40393 TCATTTATGG
* *
40403 CATCCTTTCATGCCGATAATGCACCGTTATGCATTTTATTTATAA
1 CATCCTTTCATGCCGGTAATGCACCGCTATGCATTTTATTTATAA
* **
40448 CATCCTTTCATGCCGGTAATGGACCGCTATGCATTTTATTTATGG
1 CATCCTTTCATGCCGGTAATGCACCGCTATGCATTTTATTTATAA
*
40493 CATCCTTTCATGCAGGTAATGCA
1 CATCCTTTCATGCCGGTAATGCA
40516 TTCTTATTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (45 bp):
CATCCTTTCATGCCGGTAATGCACCGCTATGCATTTTATTTATAA
Found at i:40921 original size:54 final size:55
Alignment explanation
Indices: 40847--40962 Score: 173
Period size: 54 Copynumber: 2.1 Consensus size: 55
40837 TACGTGGGGA
* * *
40847 TGCACAC-CTAATGCCAATACGGAAATTCATAAACTCGTTATGAATTTCTTCGGT
1 TGCACACACTAATGCCAATACGGAAATTCATAAACTCATCATGAATTTCTTAGGT
* *
40901 TGCACACAC-AATGCTAATACGGAAATTCATAAACTTATCATGAATTTCTTAGGT
1 TGCACACACTAATGCCAATACGGAAATTCATAAACTCATCATGAATTTCTTAGGT
40955 TGCACACA
1 TGCACACA
40963 TAGTGCCCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 55 0.98
55 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (55 bp):
TGCACACACTAATGCCAATACGGAAATTCATAAACTCATCATGAATTTCTTAGGT
Found at i:45131 original size:20 final size:20
Alignment explanation
Indices: 45108--45145 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
45098 AATATAAGTT
45108 TTATATACTAAATATATTGA
1 TTATATACTAAATATATTGA
* *
45128 TTATATATTACATATATT
1 TTATATACTAAATATATT
45146 TTTCTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (20 bp):
TTATATACTAAATATATTGA
Found at i:50418 original size:19 final size:21
Alignment explanation
Indices: 50375--50426 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
50365 ACAAGTAACG
50375 AATTTGACAAAACCGATTGGA
1 AATTTGACAAAACCGATTGGA
*
50396 AA-TTGACAAAACCGGTT-GA
1 AATTTGACAAAACCGATTGGA
50415 AATTTGACAAAA
1 AATTTGACAAAA
50427 TCAGTAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 23 0.79
21 2 0.07
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.23
Consensus pattern (21 bp):
AATTTGACAAAACCGATTGGA
Found at i:55804 original size:21 final size:21
Alignment explanation
Indices: 55778--55897 Score: 111
Period size: 21 Copynumber: 5.6 Consensus size: 21
55768 TTCTACGCGG
*
55778 TCCTTCGTGACATATATATGA
1 TCCTTCGGGACATATATATGA
*
55799 TCCTTCGGGACA-ATTGTATGA
1 TCCTTCGGGACATA-TATATGA
55820 GGTCCTTCGGG--ATATATATGA
1 --TCCTTCGGGACATATATATGA
* *
55841 GGTCCTTCGGGACATATATGTGG
1 --TCCTTCGGGACATATATATGA
* *
55864 TCCTTCGGGACATATATGTGG
1 TCCTTCGGGACATATATATGA
*
55885 TCCTTCGAGACAT
1 TCCTTCGGGACAT
55898 TCTATATGGC
Statistics
Matches: 87, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.01
21 68 0.78
22 1 0.01
23 17 0.20
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (21 bp):
TCCTTCGGGACATATATATGA
Found at i:55866 original size:42 final size:42
Alignment explanation
Indices: 55789--55897 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
55779 CCTTCGTGAC
*
55789 ATATATATGA--TCCTTCGGGACAATTGTATGAGGTCCTTCGGG
1 ATATATATGAGGTCCTTCGGGAC-A-TATATGAGGTCCTTCGGG
*
55831 ATATATATGAGGTCCTTCGGGACATATATGTGGTCCTTCGGG
1 ATATATATGAGGTCCTTCGGGACATATATGAGGTCCTTCGGG
* * *
55873 ACATATATGTGGTCCTTCGAGACAT
1 ATATATATGAGGTCCTTCGGGACAT
55898 TCTATATGGC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
42 48 0.80
43 1 0.02
44 11 0.18
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (42 bp):
ATATATATGAGGTCCTTCGGGACATATATGAGGTCCTTCGGG
Found at i:57656 original size:422 final size:422
Alignment explanation
Indices: 56872--57702 Score: 1635
Period size: 422 Copynumber: 2.0 Consensus size: 422
56862 TCCCTGGCCC
*
56872 GGCAGGATGAAAAGCGGACACTTCTGGGAGTGCCTTTATAAAATTAAGGATTATTTTTAGGTGAT
1 GGCAGGATGAAAAGCGGACACCTCTGGGAGTGCCTTTATAAAATTAAGGATTATTTTTAGGTGAT
*
56937 TGAAATCCCGTTCGAATAATGTTAGAGGGTCTCCATTCCTATGAAGTGGAATAGTTTCTTTGCTA
66 TGAAATCCCGTTCGAATAATGTTAGAGGGTCTCCATTCCTATAAAGTGGAATAGTTTCTTTGCTA
57002 AGTGGGTAAGCTAAAGTATAGTGGATAAATGTTATCATGATAATGTTAAAACATCAAGGGATGAG
131 AGTGGGTAAGCTAAAGTATAGTGGATAAATGTTATCATGATAATGTTAAAACATCAAGGGATGAG
*
57067 GTTATTGTTTTTAGAATAGTTGAAGAATAAGTACATCAGTGATGAGTTTATAAGACAAATGAAGT
196 GTTATTGTTTTTAGAATAGTTGAAGAATAAGTACATCAGTGATAAGTTTATAAGACAAATGAAGT
57132 TAGTATTTTTGAGTTTGAACCAAGGGAATTGTACTGTGTATGAGTAAGAGTATGGAATTGATAAG
261 TAGTATTTTTGAGTTTGAACCAAGGGAATTGTACTGTGTATGAGTAAGAGTATGGAATTGATAAG
57197 TTGAGTAAATTACCACTGAGTTAATTTTGATTGAAAAGGATGTATATGATTGGTTTGAGGAAGGT
326 TTGAGTAAATTACCACTGAGTTAATTTTGATTGAAAAGGATGTATATGATTGGTTTGAGGAAGGT
57262 TTGTTCCCTATATTGAAAGGATGTATATGATT
391 TTGTTCCCTATATTGAAAGGATGTATATGATT
57294 GGCAGGATGAAAAGCGGACACCTCTGGGAGTGCCTTTATAAAATTAAGGATTATTTTTAGGTGAT
1 GGCAGGATGAAAAGCGGACACCTCTGGGAGTGCCTTTATAAAATTAAGGATTATTTTTAGGTGAT
57359 TGAAATCCCGTTCGAATAATGTTAGAGGGTCTCCATTCCTATAAAGTGGAATAGTTTCTTTGCTA
66 TGAAATCCCGTTCGAATAATGTTAGAGGGTCTCCATTCCTATAAAGTGGAATAGTTTCTTTGCTA
57424 AGTGGGTAAGCTAAAGTATAGTGGATAAATGTTATCATGATAATGTTAAAACATCAAGGGATGAG
131 AGTGGGTAAGCTAAAGTATAGTGGATAAATGTTATCATGATAATGTTAAAACATCAAGGGATGAG
57489 GTTATTGTTTTTAGAATAGTTGAAGAATAAGTACATCAGTGATAAGTTTATAAGACAAATGAAGT
196 GTTATTGTTTTTAGAATAGTTGAAGAATAAGTACATCAGTGATAAGTTTATAAGACAAATGAAGT
57554 TAGTATTTTTGAGTTTGAACCAAGGGAATTGTACTGTGTATGAGTAAGAGTATGGAATTGATAAG
261 TAGTATTTTTGAGTTTGAACCAAGGGAATTGTACTGTGTATGAGTAAGAGTATGGAATTGATAAG
57619 TTGAGTAAATTACCACTGAGTTAATTTTGATTGAAAAGGATGTATATGATTGGTTTGAGGAAGGT
326 TTGAGTAAATTACCACTGAGTTAATTTTGATTGAAAAGGATGTATATGATTGGTTTGAGGAAGGT
57684 TTGTTCCCTATATTGAAAG
391 TTGTTCCCTATATTGAAAG
57703 AATTGTACTG
Statistics
Matches: 406, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
422 406 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.34
Consensus pattern (422 bp):
GGCAGGATGAAAAGCGGACACCTCTGGGAGTGCCTTTATAAAATTAAGGATTATTTTTAGGTGAT
TGAAATCCCGTTCGAATAATGTTAGAGGGTCTCCATTCCTATAAAGTGGAATAGTTTCTTTGCTA
AGTGGGTAAGCTAAAGTATAGTGGATAAATGTTATCATGATAATGTTAAAACATCAAGGGATGAG
GTTATTGTTTTTAGAATAGTTGAAGAATAAGTACATCAGTGATAAGTTTATAAGACAAATGAAGT
TAGTATTTTTGAGTTTGAACCAAGGGAATTGTACTGTGTATGAGTAAGAGTATGGAATTGATAAG
TTGAGTAAATTACCACTGAGTTAATTTTGATTGAAAAGGATGTATATGATTGGTTTGAGGAAGGT
TTGTTCCCTATATTGAAAGGATGTATATGATT
Found at i:60446 original size:21 final size:21
Alignment explanation
Indices: 60417--60493 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
60407 GGTTCTACGC
*
60417 GGTCATTTGGGATATATATGT
1 GGTCCTTTGGGATATATATGT
* *
60438 GGTCCTTTGGGATAATTCTACGAT
1 GGTCCTTTGGGAT-A-TATATG-T
* *
60462 -GTCCTTTGGGACATATATAT
1 GGTCCTTTGGGATATATATGT
60482 GGTCCTTTGGGA
1 GGTCCTTTGGGA
60494 CATTCTATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
20 1 0.02
21 26 0.58
22 2 0.04
23 15 0.33
24 1 0.02
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.39
Consensus pattern (21 bp):
GGTCCTTTGGGATATATATGT
Done.