Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001259.1 Hibiscus syriacus cultivar Beakdansim tig00002477_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: 174165
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4628 original size:23 final size:24
Alignment explanation
Indices: 4600--4657 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 24
4590 AAAATCAGCA
4600 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
4623 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
4647 AAGAAAATAAA
1 AAGAAAATAAA
4658 GAAAGAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.64, C:0.10, G:0.16, T:0.10
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:10490 original size:90 final size:91
Alignment explanation
Indices: 10347--10517 Score: 281
Period size: 90 Copynumber: 1.9 Consensus size: 91
10337 CATGTGCCTT
* *
10347 GCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGTTCTCT
1 GCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCTCT
10412 CCCTATTCGGCCAAGCCATGTGTTTA
66 CCCTATTCGGCCAAGCCATGTGTTTA
* * * *
10438 GCATATGAACAG-CCCCATGTGCCTTGTATGTGGTTTATTTAGGCGCCAAGATGAAGAGCTCTCT
1 GCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCTCT
10502 CCCTATTCGGCCAAGC
66 CCCTATTCGGCCAAGC
10518 ATCATTTCCC
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
90 63 0.85
91 11 0.15
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (91 bp):
GCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCTCT
CCCTATTCGGCCAAGCCATGTGTTTA
Found at i:15306 original size:13 final size:14
Alignment explanation
Indices: 15288--15332 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 14
15278 TTAAATGTAG
15288 AAGAAATG-AATGA
1 AAGAAATGAAATGA
15301 AAGAAATGAAATGAA
1 AAGAAATGAAATG-A
15316 AATGAAAATGAAATGA
1 AA-G-AAATGAAATGA
15332 A
1 A
15333 GGATTAGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.29
14 4 0.14
15 3 0.11
16 3 0.11
17 10 0.36
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (14 bp):
AAGAAATGAAATGA
Found at i:15313 original size:5 final size:5
Alignment explanation
Indices: 15290--15332 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
15280 AAATGTAGAA
15290 GAAAT G-AAT GAAA- GAAAT GAAAT GAAAAT GAAAAT GAAAT GAA
1 GAAAT GAAAT GAAAT GAAAT GAAAT G-AAAT G-AAAT GAAAT GAA
15333 GGATTAGTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 8 0.23
5 16 0.46
6 11 0.31
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (5 bp):
GAAAT
Found at i:15320 original size:11 final size:10
Alignment explanation
Indices: 15290--15332 Score: 54
Period size: 9 Copynumber: 4.3 Consensus size: 10
15280 AAATGTAGAA
15290 GAAATG-AAT
1 GAAATGAAAT
15299 GAAA-GAAAT
1 GAAATGAAAT
15308 GAAATGAAAAT
1 GAAATG-AAAT
15319 GAAAATGAAAT
1 G-AAATGAAAT
15330 GAA
1 GAA
15333 GGATTAGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.03
9 11 0.37
10 3 0.10
11 10 0.33
12 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (10 bp):
GAAATGAAAT
Found at i:28943 original size:22 final size:22
Alignment explanation
Indices: 28911--28952 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28901 TCCATTTCAA
28911 CATCAACACCATCAACATCCTC
1 CATCAACACCATCAACATCCTC
* *
28933 CATCAAGACCATCATCATCC
1 CATCAACACCATCAACATCC
28953 ACTTAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.43, G:0.02, T:0.19
Consensus pattern (22 bp):
CATCAACACCATCAACATCCTC
Found at i:34685 original size:35 final size:35
Alignment explanation
Indices: 34602--34713 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 35
34592 TACTATATGT
*
34602 TCATCA-ACATCTTCCATCACCATTTTCATGTCTATA
1 TCATCACA-ATCTTCCATCACCA-TTTCATGCCTATA
* * *
34638 TAATCACTATCTTCCATCACCATTGCATGCCTATA
1 TCATCACAATCTTCCATCACCATTTCATGCCTATA
* * * **
34673 TCATCGCAATCTTCTATCACCGTTTCACACCTATA
1 TCATCACAATCTTCCATCACCATTTCATGCCTATA
34708 TCATCA
1 TCATCA
34714 TCATTCCCTT
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
35 43 0.69
36 19 0.31
ACGTcount: A:0.28, C:0.32, G:0.04, T:0.36
Consensus pattern (35 bp):
TCATCACAATCTTCCATCACCATTTCATGCCTATA
Found at i:36025 original size:22 final size:22
Alignment explanation
Indices: 36000--36041 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
35990 CAATTTATTT
36000 ATCTT-TTATTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
36022 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
36042 CCAACACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:36402 original size:19 final size:20
Alignment explanation
Indices: 36359--36403 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
36349 GCTTTTTTTT
* *
36359 CAAAAAAAACACAAAAAAGG
1 CAAAAAAAAAACAAAAAAGA
36379 C-AAAAAAAAACAAAAAA-A
1 CAAAAAAAAAACAAAAAAGA
36397 CAAAAAA
1 CAAAAAA
36404 GCCAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 20 0.91
20 1 0.05
ACGTcount: A:0.82, C:0.13, G:0.04, T:0.00
Consensus pattern (20 bp):
CAAAAAAAAAACAAAAAAGA
Found at i:40403 original size:403 final size:403
Alignment explanation
Indices: 39656--40769 Score: 2104
Period size: 403 Copynumber: 2.8 Consensus size: 403
39646 CAAAATACAT
*
39656 GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAACA
1 GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAGCA
39721 TATCTATTCGGTAAGTATAATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
66 TATCTATTCGGTAAGTATAATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
*
39786 TTCAGATTCGAGGTCGAATCTTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
131 TTCAGATTCGAGGTCGAATATTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
* *
39851 CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAAGATCAGA
196 CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAATATCATA
* * *
39916 ACAGAAGAAGACTTACGACGACTTTTTAAATGGGATCCTGATCTTATTTAGTCAAGATGTCTTCT
261 ACAGAAGCAGACTAACGACGACTTTTTGAATGGGATCCTGATCTTATTTAGTCAAGATGTCTTCT
* *
39981 GAAGATACGACCTTCTGTCTCTTATCTTTCTAACGGTTCTTGAATCGCATCAATCTGATATCAGG
326 GAAGATACGACCTTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGCATCAATCCGATATCAGG
40046 AACTCAAGATATG
391 AACTCAAGATATG
40059 GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAGCA
1 GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAGCA
40124 TATCTATTCGGTAAGTATAATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
66 TATCTATTCGGTAAGTATAATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
40189 TTCAGATTCGAGGTCGAATATTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
131 TTCAGATTCGAGGTCGAATATTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
40254 CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAATATCATA
196 CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAATATCATA
* *
40319 ACAGAAGCAGACTGACAACGACTTTTTGAATGGGATCCTGATCTTATTTAGTCAAGATGTCTTCT
261 ACAGAAGCAGACTAACGACGACTTTTTGAATGGGATCCTGATCTTATTTAGTCAAGATGTCTTCT
40384 GAAGATACGACCTTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGCATCAATCCGATATCAGG
326 GAAGATACGACCTTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGCATCAATCCGATATCAGG
40449 AACTCAAGATATG
391 AACTCAAGATATG
*
40462 GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAGAA
1 GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAGCA
*
40527 TATCTATTCGGTAAGTATATTGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
66 TATCTATTCGGTAAGTATAATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
40592 TTCAGATTCGAGGTCGAATATTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
131 TTCAGATTCGAGGTCGAATATTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
40657 CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAATATCATA
196 CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAATATCATA
40722 ACAG-AGCAGACTAACGACGACTTTTTGAATGGGATCCTGATCTTATTT
261 ACAGAAGCAGACTAACGACGACTTTTTGAATGGGATCCTGATCTTATTT
40770 TACTGAAGAC
Statistics
Matches: 697, Mismatches: 14, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
402 42 0.06
403 655 0.94
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (403 bp):
GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAGCA
TATCTATTCGGTAAGTATAATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
TTCAGATTCGAGGTCGAATATTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAATATCATA
ACAGAAGCAGACTAACGACGACTTTTTGAATGGGATCCTGATCTTATTTAGTCAAGATGTCTTCT
GAAGATACGACCTTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGCATCAATCCGATATCAGG
AACTCAAGATATG
Found at i:41424 original size:11 final size:11
Alignment explanation
Indices: 41410--41450 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
41400 TTGCAATTCA
41410 TTTATCTT-TT
1 TTTATCTTATT
41420 CTTTATCTTATT
1 -TTTATCTTATT
*
41432 TTAATCTTATT
1 TTTATCTTATT
41443 TTTATCTT
1 TTTATCTT
41451 GTTTCCAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 25 0.93
12 2 0.07
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:45138 original size:24 final size:25
Alignment explanation
Indices: 45111--45157 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
45101 TGATGTAATG
*
45111 TATG-TATATATATATG-AATATATC
1 TATGTTATA-ATAAATGAAATATATC
45135 TATGTTATAATAAATGAAATATA
1 TATGTTATAATAAATGAAATATA
45158 AATCATTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (25 bp):
TATGTTATAATAAATGAAATATATC
Found at i:50981 original size:11 final size:12
Alignment explanation
Indices: 50954--50978 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50944 TGCTGGAAAC
50954 AAGATTAAAAAT
1 AAGATTAAAAAT
50966 AAGATTAAAAAT
1 AAGATTAAAAAT
50978 A
1 A
50979 GATAAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AAGATTAAAAAT
Found at i:77059 original size:8 final size:8
Alignment explanation
Indices: 77048--77072 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
77038 GAGAAAAATC
77048 AGAAAAGA
1 AGAAAAGA
77056 AGAAAAGA
1 AGAAAAGA
77064 AGAAAAGA
1 AGAAAAGA
77072 A
1 A
77073 AAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:77082 original size:16 final size:16
Alignment explanation
Indices: 77031--77082 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
77021 TTGGAGTGCA
77031 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAAA--AG
*
77050 AAAAGAAGAAAAGAAG
1 AAAAGAAGAAAAAAAG
77066 AAAAGAA-AAGAAAAAG
1 AAAAGAAGAA-AAAAAG
77082 A
1 A
77083 GAAGTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.07
16 15 0.50
18 4 0.13
19 9 0.30
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAAAAAAG
Found at i:82801 original size:23 final size:24
Alignment explanation
Indices: 82773--82830 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 24
82763 AAAATCAGCA
82773 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
82796 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
82820 AAGAAAATAAA
1 AAGAAAATAAA
82831 GAAAGAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.64, C:0.10, G:0.16, T:0.10
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:87610 original size:90 final size:91
Alignment explanation
Indices: 87467--87637 Score: 272
Period size: 90 Copynumber: 1.9 Consensus size: 91
87457 CATGTGCCTT
* *
87467 GCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAAGCGCCAAGATGAAGAGTTCTCT
1 GCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAAGCGCCAAGATGAAGAGCTCTCT
87532 CCCTATTCGGCCAAGCCATGTGTTTA
66 CCCTATTCGGCCAAGCCATGTGTTTA
* * * * *
87558 GCATATGAACAG-CCCCATGTGCCTTGTATGTGGTTTATTTAGGCGCCAAGATGAAGAGCTCTCT
1 GCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAAGCGCCAAGATGAAGAGCTCTCT
87622 CCCTATTCGGCCAAGC
66 CCCTATTCGGCCAAGC
87638 ATCATTTCCC
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 62 0.85
91 11 0.15
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (91 bp):
GCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAAGCGCCAAGATGAAGAGCTCTCT
CCCTATTCGGCCAAGCCATGTGTTTA
Found at i:92202 original size:6 final size:6
Alignment explanation
Indices: 92191--92233 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
92181 GATGTAGGAG
*
92191 TCTTTT TC-TTT TCTCTT TCTTTT TCTTTT TCTTCTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT T
92234 GTTGCATCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:92228 original size:19 final size:17
Alignment explanation
Indices: 92191--92233 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 17
92181 GATGTAGGAG
92191 TCTTTTTCTTTTCTCTT
1 TCTTTTTCTTTTCTCTT
92208 TCTTTTTCTTTTTCTTCTT
1 TCTTTTTC-TTTTC-TCTT
92227 TCTTTTT
1 TCTTTTT
92234 GTTGCATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.33
18 5 0.21
19 11 0.46
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TCTTTTTCTTTTCTCTT
Found at i:92436 original size:13 final size:14
Alignment explanation
Indices: 92418--92462 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 14
92408 TTAAATGTAG
92418 AAGAAATG-AATGA
1 AAGAAATGAAATGA
92431 AAGAAATGAAATGAA
1 AAGAAATGAAATG-A
92446 AATGAAAATGAAATGA
1 AA-G-AAATGAAATGA
92462 A
1 A
92463 GGATTAGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.29
14 4 0.14
15 3 0.11
16 3 0.11
17 10 0.36
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (14 bp):
AAGAAATGAAATGA
Found at i:92443 original size:5 final size:5
Alignment explanation
Indices: 92420--92462 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
92410 AAATGTAGAA
92420 GAAAT G-AAT GAAA- GAAAT GAAAT GAAAAT GAAAAT GAAAT GAA
1 GAAAT GAAAT GAAAT GAAAT GAAAT G-AAAT G-AAAT GAAAT GAA
92463 GGATTAGTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 8 0.23
5 16 0.46
6 11 0.31
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (5 bp):
GAAAT
Found at i:92450 original size:11 final size:10
Alignment explanation
Indices: 92420--92462 Score: 54
Period size: 9 Copynumber: 4.3 Consensus size: 10
92410 AAATGTAGAA
92420 GAAATG-AAT
1 GAAATGAAAT
92429 GAAA-GAAAT
1 GAAATGAAAT
92438 GAAATGAAAAT
1 GAAATG-AAAT
92449 GAAAATGAAAT
1 G-AAATGAAAT
92460 GAA
1 GAA
92463 GGATTAGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.03
9 11 0.37
10 3 0.10
11 10 0.33
12 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (10 bp):
GAAATGAAAT
Found at i:109204 original size:23 final size:22
Alignment explanation
Indices: 109151--109204 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
109141 CTTTCTATCT
109151 TATACATAATGATGTTTATTCA
1 TATACATAATGATGTTTATTCA
*
109173 TATGCCATAAT-ATAGTTATATTCA
1 TAT-ACATAATGAT-GTT-TATTCA
109197 TATACATA
1 TATACATA
109205 TTACATATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 13 0.48
24 9 0.33
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (22 bp):
TATACATAATGATGTTTATTCA
Found at i:114312 original size:24 final size:25
Alignment explanation
Indices: 114285--114331 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
114275 TGATGTAATG
*
114285 TATG-TATATATATATG-AATATATC
1 TATGTTATA-ATAAATGAAATATATC
114309 TATGTTATAATAAATGAAATATA
1 TATGTTATAATAAATGAAATATA
114332 AATCATTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (25 bp):
TATGTTATAATAAATGAAATATATC
Found at i:130011 original size:16 final size:16
Alignment explanation
Indices: 129992--130025 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
129982 TTTCTTACTA
129992 TTTCATTTCTTTATTC
1 TTTCATTTCTTTATTC
* *
130008 TTTCATTTTTTTCTTC
1 TTTCATTTCTTTATTC
130024 TT
1 TT
130026 GTTTCATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCATTTCTTTATTC
Found at i:139941 original size:24 final size:24
Alignment explanation
Indices: 139901--139947 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
139891 AAAGTGCTAC
139901 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
139926 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
139948 CTCCTACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:145539 original size:26 final size:27
Alignment explanation
Indices: 145495--145545 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
145485 CAAAAAAAGC
145495 AACAAAAAGAGAAAAAGAAAGAAGAAA
1 AACAAAAAGAGAAAAAGAAAGAAGAAA
145522 AACAAAAA-A-AAAAGAGAAAGAAGA
1 AACAAAAAGAGAAAA-AGAAAGAAGA
145546 GACTCCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.17
26 11 0.48
27 8 0.35
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (27 bp):
AACAAAAAGAGAAAAAGAAAGAAGAAA
Found at i:149664 original size:16 final size:16
Alignment explanation
Indices: 149645--149678 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
149635 TTTCTTACTA
149645 TTTCATTTCTTTATTC
1 TTTCATTTCTTTATTC
* *
149661 TTTCATTTTTTTCTTC
1 TTTCATTTCTTTATTC
149677 TT
1 TT
149679 GTTTCATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCATTTCTTTATTC
Found at i:159302 original size:26 final size:24
Alignment explanation
Indices: 159261--159328 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
159251 TTTTGCTTCA
159261 CTTTTTCTTTGCTTTTTGATTCTT
1 CTTTTTCTTTGCTTTTTGATTCTT
* *
159285 CTTTTTCTTTTCTTTTT-TTTCTT
1 CTTTTTCTTTGCTTTTTGATTCTT
159308 CTTCTTTCTTGTTGCTTTTTG
1 CTT-TTTC-T-TTGCTTTTTG
159329 TTGTAGCACT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.22
24 20 0.54
25 1 0.03
26 8 0.22
ACGTcount: A:0.01, C:0.18, G:0.07, T:0.74
Consensus pattern (24 bp):
CTTTTTCTTTGCTTTTTGATTCTT
Found at i:161256 original size:24 final size:24
Alignment explanation
Indices: 161229--161274 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
161219 AATGTCAACA
*
161229 GACACAACTCTTGGCACTTCAAGT
1 GACACAACTCTTGGAACTTCAAGT
***
161253 GACATTTCTCTTGGAACTTCAA
1 GACACAACTCTTGGAACTTCAA
161275 ACGACATTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (24 bp):
GACACAACTCTTGGAACTTCAAGT
Found at i:161280 original size:24 final size:24
Alignment explanation
Indices: 161236--161282 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
161226 ACAGACACAA
* **
161236 CTCTTGGCACTTCAAGTGACATTT
1 CTCTTGGAACTTCAAACGACATTT
161260 CTCTTGGAACTTCAAACGACATT
1 CTCTTGGAACTTCAAACGACATT
161283 ATCTTTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (24 bp):
CTCTTGGAACTTCAAACGACATTT
Found at i:161298 original size:24 final size:24
Alignment explanation
Indices: 161253--161298 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
161243 CACTTCAAGT
* *
161253 GACATTTCTCTTGGAACTTCAAAC
1 GACATTTCTCTTGAAACATCAAAC
161277 GACATTATCT-TTGAAACATCAA
1 GACATT-TCTCTTGAAACATCAA
161299 GAGATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (24 bp):
GACATTTCTCTTGAAACATCAAAC
Found at i:165774 original size:24 final size:24
Alignment explanation
Indices: 165724--165775 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
165714 TTTGCTTTTC
* *
165724 TTCTTTTGAGTGCTGGATTTTTCT
1 TTCTTTTGAGTGCTGCATTTGTCT
*
165748 TTCTTTTGAGTGCTTCACTTTGT-T
1 TTCTTTTGAGTGCTGCA-TTTGTCT
165772 TTCT
1 TTCT
165776 GATTTTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.08, C:0.15, G:0.17, T:0.60
Consensus pattern (24 bp):
TTCTTTTGAGTGCTGCATTTGTCT
Found at i:168123 original size:18 final size:18
Alignment explanation
Indices: 168096--168142 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
168086 TTGCTTTTGA
168096 TTCTTT-TTTTTTTCTTTC
1 TTCTTTCTTTTTTTC-TTC
*
168114 TT-TTTGTTTTTTTCTTC
1 TTCTTTCTTTTTTTCTTC
168131 TTCTTTCTTTTT
1 TTCTTTCTTTTT
168143 GCTTTGGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (18 bp):
TTCTTTCTTTTTTTCTTC
Found at i:168142 original size:24 final size:22
Alignment explanation
Indices: 168099--168143 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
168089 CTTTTGATTC
168099 TTTTTTTTTTCTTTCTTTTTGT
1 TTTTTTTTTTCTTTCTTTTTGT
168121 TTTTTTCTTCTTCTTTCTTTTTG
1 TTTTTT-TT-TTCTTTCTTTTTG
168144 CTTTGGTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.29
23 2 0.10
24 13 0.62
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.82
Consensus pattern (22 bp):
TTTTTTTTTTCTTTCTTTTTGT
Found at i:171883 original size:7 final size:6
Alignment explanation
Indices: 171832--171883 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
171822 CTTTTCTTCA
* * * *
171832 CTTTTT CTTTTG CTTTTG ATTTTT CTTTTT CTTTTT -TCTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
171879 GCTTT
1 -CTTT
171884 GGATGCAGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
5 4 0.11
6 30 0.79
7 4 0.11
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (6 bp):
CTTTTT
Done.