Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003520.1 Hibiscus syriacus cultivar Beakdansim tig00007440_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: 155600
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:32399 original size:21 final size:20
Alignment explanation
Indices: 32375--32414 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
32365 ATTTTCCTTT
32375 TTTTTAAAAAAATTATGAGTG
1 TTTTTAAAAAAA-TATGAGTG
**
32396 TTTTTATTAAAATATGAGT
1 TTTTTAAAAAAATATGAGT
32415 TAATTGCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTTTAAAAAAATATGAGTG
Found at i:39691 original size:15 final size:16
Alignment explanation
Indices: 39668--39697 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39658 AAAAAGGTCA
39668 AAAATTAAAAAATTAT
1 AAAATTAAAAAATTAT
39684 AAAA-TAAAAAATTA
1 AAAATTAAAAAATTA
39698 AGATTTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATTAAAAAATTAT
Found at i:39720 original size:26 final size:25
Alignment explanation
Indices: 39678--39771 Score: 73
Period size: 26 Copynumber: 3.6 Consensus size: 25
39668 AAAATTAAAA
*
39678 AATTATAAAATAAAAAATTAAGATTTC
1 AATTAT-AAATATAAAATTAAGA-TTC
* *
39705 AATTATAAATATAAAATCAAGGGACTC
1 AATTATAAATATAAAATTAA--GATTC
* * *
39732 ATTTAT-AATATAGAAATTAGGCCTTC
1 AATTATAAATATA-AAATTAAG-ATTC
39758 AATTATAAATATAA
1 AATTATAAATATAA
39772 TTGTAAATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
25 1 0.02
26 26 0.49
27 24 0.45
28 2 0.04
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (25 bp):
AATTATAAATATAAAATTAAGATTC
Found at i:39768 original size:27 final size:28
Alignment explanation
Indices: 39702--39771 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
39692 AAATTAAGAT
39702 TTCAATTATAAATATAAAATCAAGGGAC
1 TTCAATTATAAATATAAAATCAAGGGAC
* * *
39730 -TCATTTAT-AATATAGAAAT-TA-GGCC
1 TTCAATTATAAATATA-AAATCAAGGGAC
39755 TTCAATTATAAATATAA
1 TTCAATTATAAATATAA
39772 TTGTAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
25 3 0.09
26 15 0.43
27 17 0.49
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (28 bp):
TTCAATTATAAATATAAAATCAAGGGAC
Found at i:40951 original size:19 final size:20
Alignment explanation
Indices: 40929--40966 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
40919 TAATGTTTTG
*
40929 ATCACTTTTTAA-TTATATT
1 ATCACTTTATAAGTTATATT
*
40948 ATCAGTTTATAAGTTATAT
1 ATCACTTTATAAGTTATAT
40967 CGATTTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (20 bp):
ATCACTTTATAAGTTATATT
Found at i:41060 original size:33 final size:33
Alignment explanation
Indices: 41023--41089 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
41013 AATATATAAA
41023 TAGTTAAATAATTTGATTGATAAATTTAAAGAT
1 TAGTTAAATAATTTGATTGATAAATTTAAAGAT
41056 TAGTTAAATAATTTGATTGATAAATTTAAAGAT
1 TAGTTAAATAATTTGATTGATAAATTTAAAGAT
41089 T
1 T
41090 GGTGATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (33 bp):
TAGTTAAATAATTTGATTGATAAATTTAAAGAT
Found at i:41330 original size:31 final size:31
Alignment explanation
Indices: 41295--41395 Score: 157
Period size: 31 Copynumber: 3.3 Consensus size: 31
41285 AAAATTAATA
* ** *
41295 AAATTAATCATTAACGTTATTAATTTAGAAG
1 AAATTAATTATTAATATTATTAATTTAGAAT
41326 AAATTAATTATTAATATTATTAATTTAGAAT
1 AAATTAATTATTAATATTATTAATTTAGAAT
*
41357 AAATTAATTATTAATATTATTAATTTATAAT
1 AAATTAATTATTAATATTATTAATTTAGAAT
41388 AAATTAAT
1 AAATTAAT
41396 GTTAATAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (31 bp):
AAATTAATTATTAATATTATTAATTTAGAAT
Found at i:41333 original size:15 final size:15
Alignment explanation
Indices: 41313--41410 Score: 69
Period size: 15 Copynumber: 6.5 Consensus size: 15
41303 CATTAACGTT
*
41313 ATTAATTTAGAAGAA
1 ATTAATTTAGAATAA
* *
41328 ATTAA-TTATTAATATT
1 ATTAATTTA-GAATA-A
41344 ATTAATTTAGAATAA
1 ATTAATTTAGAATAA
* *
41359 ATTAA-TTATTAATATT
1 ATTAATTTA-GAATA-A
*
41375 ATTAATTTATAATAA
1 ATTAATTTAGAATAA
41390 ATTAATGTT--AATAA
1 ATTAAT-TTAGAATAA
41404 ATTAATT
1 ATTAATT
41411 ATTCATTATT
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
13 1 0.01
14 17 0.25
15 23 0.34
16 21 0.31
17 6 0.09
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (15 bp):
ATTAATTTAGAATAA
Found at i:49750 original size:21 final size:20
Alignment explanation
Indices: 49683--49751 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
49673 AATTTTATAT
49683 TATATAATTAGATTATAACCC
1 TATATAATTAGATT-TAACCC
* * *
49704 AATATATATCATCA-ATTTTACAC
1 --TATATA--ATTAGATTTAACCC
49727 TATATAATTAGATTCTAACCC
1 TATATAATTAGATT-TAACCC
49748 TATA
1 TATA
49752 CACAAATAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 14 0.39
23 10 0.28
24 3 0.08
25 3 0.08
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (20 bp):
TATATAATTAGATTTAACCC
Found at i:50300 original size:23 final size:23
Alignment explanation
Indices: 50274--50321 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
50264 ATAAAGTACA
* *
50274 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGATTAT
**
50297 ATAATGTAATAGGTAGCGATTAT
1 ATAACATAATAGGTAGCGATTAT
50320 AT
1 AT
50322 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGATTAT
Found at i:50825 original size:23 final size:23
Alignment explanation
Indices: 50798--50865 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
50788 ATACTTTACA
*
50798 ATATAAGCACTACCTATTATATT
1 ATATAAGCACTACCTATTACATT
*
50821 ATATAAACGA-TACCTATTACATT
1 ATATAAGC-ACTACCTATTACATT
*
50844 ATATAAGCGCTACCTATTACAT
1 ATATAAGCACTACCTATTACAT
50866 CATAAATCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:52376 original size:3 final size:3
Alignment explanation
Indices: 52368--52439 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
52358 ACTTGTTTGG
* * * * *
52368 ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GTC AGC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
52416 GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC
52440 GTCAGCTTCA
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:52422 original size:36 final size:36
Alignment explanation
Indices: 52375--52456 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
52365 TGGATCATCA
*
52375 TCATCATCATCATCGTCATCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
* *
52411 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
*
52447 TCATCTTCAT
1 TCATCATCAT
52457 TGACCGCTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.38
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGTCAGCT
Found at i:52440 original size:12 final size:12
Alignment explanation
Indices: 52369--52456 Score: 95
Period size: 12 Copynumber: 7.3 Consensus size: 12
52359 CTTGTTTGGA
* *
52369 TCATCATCATCA
1 TCATCTTCATCG
* * *
52381 TCATCATCGTCA
1 TCATCTTCATCG
52393 TCATCTTCATCG
1 TCATCTTCATCG
*
52405 TCAGCTTCATCG
1 TCATCTTCATCG
*
52417 TCATCATCATCG
1 TCATCTTCATCG
52429 TCATCTTCATCG
1 TCATCTTCATCG
* *
52441 TCAGCTTCATCT
1 TCATCTTCATCG
52453 TCAT
1 TCAT
52457 TGACCGCTTG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.38
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:52465 original size:18 final size:18
Alignment explanation
Indices: 52393--52456 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
52383 ATCATCGTCA
*
52393 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
* * *
52411 TCATCGTCATC-ATCATCG
1 TCATCTTCATCGA-CAGCT
*
52429 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
52447 TCATCTTCAT
1 TCATCTTCAT
52457 TGACCGCTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCGACAGCT
Found at i:54267 original size:200 final size:200
Alignment explanation
Indices: 53920--54496 Score: 1034
Period size: 200 Copynumber: 2.9 Consensus size: 200
53910 TTTAAATTAG
* * * *
53920 TATCGACA-AAACATTAAACAGTGTCGATACA-TATTATATACCA-ATTCTCTCATAAAACCGGT
1 TATCGACACAAAC-TAAAAAAGTGTCGACACATTATT-TAGA-CATATTCTCTCATAAAACCGGT
*
53982 ATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTTTG
63 ATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTG
*
54047 GGATCGACACTTTCTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGG
128 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGG
54112 ACCAAAAA
193 ACCAAAAA
54120 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
54185 CTTGTACCGATTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
54250 TCGACACTTTTTATATATGTATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
54315 AAAAA
196 AAAAA
54320 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
54385 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
54450 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
54497 GGCCATATTG
Statistics
Matches: 364, Mismatches: 10, Indels: 6
0.96 0.03 0.02
Matches are distributed among these distances:
199 2 0.01
200 354 0.97
201 8 0.02
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
AAAAA
Found at i:54643 original size:19 final size:19
Alignment explanation
Indices: 54619--54663 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
54609 ATTCACATAT
54619 AAAATTATAAATCTTATAC
1 AAAATTATAAATCTTATAC
54638 AAAATTATAAATCTTATAC
1 AAAATTATAAATCTTATAC
54657 AAAATTA
1 AAAATTA
54664 ACCCTACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTATAAATCTTATAC
Found at i:56490 original size:33 final size:33
Alignment explanation
Indices: 56453--56518 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
56443 CATCTTAATA
*
56453 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
56486 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
56519 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:56577 original size:21 final size:21
Alignment explanation
Indices: 56552--56616 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
56542 CCCCATATGC
* *
56552 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
56573 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
56594 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
56615 CT
1 CT
56617 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:58867 original size:20 final size:19
Alignment explanation
Indices: 58817--58872 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
58807 TCCAGTATTA
*
58817 TTTTACCGGTTTTATCATT
1 TTTTACCTGTTTTATCATT
* *
58836 TTGATACATGTTTTATCATAT
1 TT-TTACCTGTTTTATCAT-T
*
58857 TTTTACCTGTTATATC
1 TTTTACCTGTTTTATC
58873 GTTGTGGATC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.83
21 3 0.10
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCTGTTTTATCATT
Found at i:59025 original size:20 final size:20
Alignment explanation
Indices: 58998--59044 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
58988 TCCGGTAACG
58998 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
59017 TTCTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
59038 TTTTACC
1 TTTTACC
59045 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.19, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:59097 original size:181 final size:181
Alignment explanation
Indices: 58788--59258 Score: 642
Period size: 181 Copynumber: 2.6 Consensus size: 181
58778 CTTACGAAAG
* *** * *
58788 TATCGACACTTTCAATATATCCAGTATTATTTTACCGGTTTTATCATTTTGATACATGTTTTATC
1 TATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTCATACAGGTTTTATC
* *
58853 ATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTAAAAGTATCGACACATTATAGG-
66 ATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTAAAAGTATCGACACATTATAGGA
* *
58917 CGCTATAACTGCTTCTCTTTTAAATTCACAAAGTATCGATCCTTATA-TAAAT
130 C-CTAAAACTGCTTCTCTTTTAAATTCACAAAGTATCGATCCTTATATTAAAA
* *
58969 TATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTCTTACCGGTTTTATC
1 TATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTCATACAGGTTTTATC
* *
59034 ATATTTTTACCTGGTATATCGTTTTGGATCGATACACTTTTTAAAAGTATCGACACTTTATAGGA
66 ATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTAAAAGTATCGACACATTATAGGA
* * *
59099 CTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTAAAA
130 CCTAAAACTGCTTCTCTTTTAAATTCACAAAGTATCGATCCTTATATTAAAA
* * * * * * * *
59151 TACCGACACTTTAAATGTATCTGGTAGCGCTTTACCGGTTTTATCA-TTTCAATACTGGTTTTGT
1 TATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTC-ATACAGGTTTTAT
* *
59215 CATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTTAA
65 CATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAA
59259 TTTGGATCGA
Statistics
Matches: 257, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
181 168 0.65
182 89 0.35
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (181 bp):
TATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTCATACAGGTTTTATC
ATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATAGGAC
CTAAAACTGCTTCTCTTTTAAATTCACAAAGTATCGATCCTTATATTAAAA
Found at i:66823 original size:17 final size:17
Alignment explanation
Indices: 66801--66834 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
66791 TGAACACTAG
66801 ATAGTCTAAACTTAATT
1 ATAGTCTAAACTTAATT
66818 ATAGTCTAAACTTAATT
1 ATAGTCTAAACTTAATT
66835 TGATGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
ATAGTCTAAACTTAATT
Found at i:82684 original size:21 final size:21
Alignment explanation
Indices: 82660--82754 Score: 115
Period size: 21 Copynumber: 4.6 Consensus size: 21
82650 TTTGAAATAA
82660 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
82681 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
82700 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
82721 ATCGCAACGCGAACTT-GAACT
1 ATCGCAACGCGAACTTCG-ACT
*
82742 ATCGCAATGCGAA
1 ATCGCAACGCGAA
82755 TATGTAAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 15 0.24
20 1 0.02
21 46 0.74
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:82703 original size:19 final size:19
Alignment explanation
Indices: 82639--82708 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
82629 ATTTTGGACT
*
82639 ATCGCAACGAATTTGAAATAA
1 ATCGCAACGAATTTG-GA-AA
* * **
82660 ATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAATTTGGAAA
82681 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
82700 ATCGCAACG
1 ATCGCAACG
82709 CGAACTTCGA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 17 0.45
21 14 0.37
22 1 0.03
23 6 0.16
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.20
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:82713 original size:40 final size:42
Alignment explanation
Indices: 82635--82729 Score: 167
Period size: 40 Copynumber: 2.3 Consensus size: 42
82625 TGCGATTTTG
82635 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTC
*
82677 GACTATCGCAACGAATTTG-GA-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTC
82717 GACTATCGCAACG
1 GACTATCGCAACG
82730 CGAACTTGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
40 32 0.62
41 1 0.02
42 19 0.37
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTC
Found at i:82767 original size:20 final size:20
Alignment explanation
Indices: 82742--82793 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
82732 AACTTGAACT
82742 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
82762 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
82782 ATCGCAATGCGA
1 ATCGCAATGCGA
82794 TAGTCGAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:82786 original size:61 final size:61
Alignment explanation
Indices: 82657--82793 Score: 149
Period size: 61 Copynumber: 2.2 Consensus size: 61
82647 GAATTTGAAA
*
82657 TAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCG
1 TAAATCGCAACGCGAACTTCGACTATCGCAACGAATATGGAAAATCGCAACGCGAACTTCG
* * *
82718 -ACTATCGCAACGCGAACTT-GAACTATCGCAATGCGAATAT-GTAAATCGCAATGCGAA-TAT-
1 TA-AATCGCAACGCGAACTTCG-ACTATCGCAA--CGAATATGGAAAATCGCAACGCGAACT-TC
82778 G
61 G
*
82779 TAAATCGCAATGCGA
1 TAAATCGCAACGCGA
82794 TAGTCGAAGT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
60 2 0.03
61 39 0.61
62 17 0.27
63 6 0.09
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (61 bp):
TAAATCGCAACGCGAACTTCGACTATCGCAACGAATATGGAAAATCGCAACGCGAACTTCG
Found at i:83737 original size:48 final size:47
Alignment explanation
Indices: 83666--83759 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 47
83656 CGTATTCTTC
* * * *
83666 TTTATCATTTTTCTCTGAAAACCTTCATCTTTGATCCCTGTCATTGT
1 TTTATCATTTTCCTATGAAAACCTTCATCTTCGATCCCTATCATTGT
*
83713 TTTATCATTCTTCCTATGAAAACCTTCATCTTCGATCTCTATCATTG
1 TTTATCATT-TTCCTATGAAAACCTTCATCTTCGATCCCTATCATTG
83760 GAATACGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 9 0.22
48 32 0.78
ACGTcount: A:0.21, C:0.24, G:0.07, T:0.47
Consensus pattern (47 bp):
TTTATCATTTTCCTATGAAAACCTTCATCTTCGATCCCTATCATTGT
Found at i:93119 original size:29 final size:31
Alignment explanation
Indices: 93051--93116 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
93041 TGTTCAAAGT
* *
93051 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
1 TTGGTCACCAACCAAGATGAAATTTCC-A-AAC
93084 TTGGTCACCAACCAAGATGAAATTTCC-AAC
1 TTGGTCACCAACCAAGATGAAATTTCCAAAC
93114 TTG
1 TTG
93117 TCAACTTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.16
33 26 0.84
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (31 bp):
TTGGTCACCAACCAAGATGAAATTTCCAAAC
Found at i:101368 original size:2 final size:2
Alignment explanation
Indices: 101361--101385 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
101351 ACTTGTTAAA
101361 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 A
101386 ATAAAGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:103055 original size:27 final size:27
Alignment explanation
Indices: 103025--103078 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
103015 TGGTTAAGTT
103025 GTAAATACAATTTACATTATTATTATA
1 GTAAATACAATTTACATTATTATTATA
*
103052 GTAAATACAATTTACTTTATTATTATA
1 GTAAATACAATTTACATTATTATTATA
103079 CTTTTAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (27 bp):
GTAAATACAATTTACATTATTATTATA
Found at i:103247 original size:24 final size:21
Alignment explanation
Indices: 103174--103235 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
103164 AAATCAGTAG
*
103174 CTAGTTTAACGTAATAGATTT
1 CTAGTTTAACGTAATAGGTTT
* *
103195 TTAATTTAACGTAATAGGTTT
1 CTAGTTTAACGTAATAGGTTT
103216 CTAGTTTAACGTAATAGGTT
1 CTAGTTTAACGTAATAGGTT
103236 GAGTCTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (21 bp):
CTAGTTTAACGTAATAGGTTT
Found at i:103325 original size:76 final size:75
Alignment explanation
Indices: 103216--103404 Score: 245
Period size: 76 Copynumber: 2.5 Consensus size: 75
103206 TAATAGGTTT
* *
103216 CTAGTTTAACGTAATAGGTTG-AGTCTATTTTATTTTATCGTCTACATTATTATTATACCTTTAA
1 CTAGTTTAACGTAATATGTTGCA--CTATTTTATTTTACCGTCTACATTATTATTATACCTTTAA
* *
103280 ATAAACCGGTAG
64 ACAAACCGATAG
* * * *
103292 CTAGTTTAACATAATATGTTGCACATATTTTATTTTACCTTTTACATTATTATTATACTTTTAAA
1 CTAGTTTAACGTAATATGTTGCAC-TATTTTATTTTACCGTCTACATTATTATTATACCTTTAAA
103357 CAAACCGATAG
65 CAAACCGATAG
* *
103368 CTAGTTTAATGTAATATGTTGCGCCTATTTTATTTTA
1 CTAGTTTAACGTAATATGTTGC-ACTATTTTATTTTA
103405 ATTGGTTAAG
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
75 1 0.01
76 96 0.97
77 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (75 bp):
CTAGTTTAACGTAATATGTTGCACTATTTTATTTTACCGTCTACATTATTATTATACCTTTAAAC
AAACCGATAG
Found at i:103438 original size:100 final size:100
Alignment explanation
Indices: 103322--103520 Score: 283
Period size: 100 Copynumber: 2.0 Consensus size: 100
103312 GCACATATTT
* * * * *
103322 TATTTTACCTTTTACATTATTATTATACTTTTAAACAAACC-GATAGCTAGTTTAATGTAATATG
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCAG-TAGCTAGCTTAACGTAATAGG
* **
103386 TTGCGCCTATTTTATTTTAATTGGTTAAGTTGTAAA
65 TTGCACCTATTTTATTTTAACCGGTTAAGTTGTAAA
* * *
103422 TATTTTATCGTTTACATTATTATTATACCTTTAAACGAACCAGTAGCTGGCTTAACGTAATAGGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCAGTAGCTAGCTTAACGTAATAGGT
103487 TGCACCTATTTTATTTTAACCGGTTAAGTTGTAA
66 TGCACCTATTTTATTTTAACCGGTTAAGTTGTAA
103521 TTGTTATTAC
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 86 0.99
101 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (100 bp):
TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCAGTAGCTAGCTTAACGTAATAGGT
TGCACCTATTTTATTTTAACCGGTTAAGTTGTAAA
Found at i:104016 original size:71 final size:70
Alignment explanation
Indices: 103762--104122 Score: 374
Period size: 70 Copynumber: 5.1 Consensus size: 70
103752 TTATTTTAAA
* * * *
103762 AAAAGT-TTGATACTTTGCAACCTTCTCATTTTCTATATATTTTTTAAAATTCGAAAGTATTGAT
1 AAAAGTATTGAAACTTTGCAA-CTTTTCATTTT-T-TATTTTTTTTAAAATTAGAAAGTATTGAT
*
103826 ATTTGTGA
63 ATTTGTGG
* * * * *
103834 AAAAATATTGAAACTTTACAGCTTTCTCATTTTTCATTTTTTTT-AAATTTGAAAGTATTGATAT
1 AAAAGTATTGAAACTTTGCAACTTT-TCATTTTTTATTTTTTTTAAAATTAGAAAGTATTGATAT
103898 TTGTGG
65 TTGTGG
* * ** ** ** *
103904 AAAAGTATCGTAACTTACCGCCTTTTCATTTTACATGTTTTTTAAAATTAGAAAGTATTGATATT
1 AAAAGTATTGAAACTTTGCAACTTTTCATTTTTTATTTTTTTTAAAATTAGAAAGTATTGATATT
*
103969 TTTGGG
66 TGT-GG
* *
103975 AAAA-TATTGAAACTTTGCAACATTTTCATTTTTTATTTTTTTTAAAATTTGAAAGTATCGATAT
1 AAAAGTATTGAAACTTTGCAAC-TTTTCATTTTTTATTTTTTTTAAAATTAGAAAGTATTGATAT
104039 TTGTGG
65 TTGTGG
*
104045 AAAAGTATT-AATACTTTGCAACTTTCTCATTTTCTA-TTTTTTTAAAATTAGAAAGTATCT-AT
1 AAAAGTATTGAA-ACTTTGCAACTTT-TCATTTTTTATTTTTTTTAAAATTAGAAAGTAT-TGAT
* *
104107 ACTTGTGA
63 ATTTGTGG
104115 AAAAGTAT
1 AAAAGTAT
104123 CGATACTTAC
Statistics
Matches: 243, Mismatches: 37, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
69 16 0.07
70 123 0.51
71 77 0.32
72 9 0.04
73 18 0.07
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (70 bp):
AAAAGTATTGAAACTTTGCAACTTTTCATTTTTTATTTTTTTTAAAATTAGAAAGTATTGATATT
TGTGG
Found at i:104094 original size:141 final size:140
Alignment explanation
Indices: 103762--104118 Score: 440
Period size: 141 Copynumber: 2.5 Consensus size: 140
103752 TTATTTTAAA
* *
103762 AAAAGT-TTGATACTTTGCAACCTTCTCATTTTCTATATATTTTTTAAAATTCGAAAGTATTGAT
1 AAAAGTATT-ATACTTTGCAACTTTCTCATTTTC--TATATTTTTTAAAATTAGAAAGTATTGAT
*
103826 ATTTGTGAAAAAATATTGAAACTTTACAGCTTTCTCATTTTTCATTTTTTTTAAATTTGAAAGTA
63 ATTTGTGAAAAAATATTGAAACTTTACAACTTTCTCATTTTTCATTTTTTTTAAATTTGAAAGTA
*
103891 TTGATATTTGTGG
128 TCGATATTTGTGG
** ** *
103904 AAAAGTATCGTA-ACTTACCGCCTTT-TCATTTTAC-ATGTTTTTTAAAATTAGAAAGTATTGAT
1 AAAAGTAT--TATACTTTGCAACTTTCTCATTTT-CTATATTTTTTAAAATTAGAAAGTATTGAT
* ** * *
103966 ATTTTTGGGAAAATATTGAAACTTTGCAACATTT-TCATTTTTTATTTTTTTTAAAATTTGAAAG
63 ATTTGTGAAAAAATATTGAAACTTTACAAC-TTTCTCATTTTTCATTTTTTTT-AAATTTGAAAG
104030 TATCGATATTTGTGG
126 TATCGATATTTGTGG
104045 AAAAGTATTAATACTTTGCAACTTTCTCATTTTCTAT-TTTTTTAAAATTAGAAAGTATCT-ATA
1 AAAAGTATT-ATACTTTGCAACTTTCTCATTTTCTATATTTTTTAAAATTAGAAAGTAT-TGATA
*
104108 CTTGTGAAAAA
64 TTTGTGAAAAA
104119 GTATCGATAC
Statistics
Matches: 182, Mismatches: 22, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
139 1 0.01
140 69 0.38
141 77 0.42
142 23 0.13
143 10 0.05
144 1 0.01
145 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (140 bp):
AAAAGTATTATACTTTGCAACTTTCTCATTTTCTATATTTTTTAAAATTAGAAAGTATTGATATT
TGTGAAAAAATATTGAAACTTTACAACTTTCTCATTTTTCATTTTTTTTAAATTTGAAAGTATCG
ATATTTGTGG
Found at i:108845 original size:20 final size:21
Alignment explanation
Indices: 108798--108859 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
108788 ATTCCCCTGT
108798 GGGGGAAATCGGTTCCCCTTCAAA
1 GGGGG-AATCGGTT-CCC-TCAAA
108822 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
108842 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
108860 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 8 0.22
24 5 0.14
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:122469 original size:23 final size:24
Alignment explanation
Indices: 122443--122493 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
122433 AATTATTTTA
*
122443 TTTTCAAAATCTTACTC-AAACAT
1 TTTTCAAAATATTACTCAAAACAT
122466 TTTTCAAAATATTACTCAAAACAT
1 TTTTCAAAATATTACTCAAAACAT
122490 TTTT
1 TTTT
122494 GGCATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTTCAAAATATTACTCAAAACAT
Found at i:123326 original size:17 final size:17
Alignment explanation
Indices: 123304--123337 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
123294 AGGTAGCTAC
123304 AATAGTGTTTACACTTT
1 AATAGTGTTTACACTTT
123321 AATAGTGTTTACACTTT
1 AATAGTGTTTACACTTT
123338 CACACTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
AATAGTGTTTACACTTT
Found at i:141797 original size:100 final size:101
Alignment explanation
Indices: 141673--141882 Score: 350
Period size: 100 Copynumber: 2.1 Consensus size: 101
141663 AACAAAATCG
** *
141673 CAACGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCACAACGCGATTTT-GACTATCGCATT
1 CAACGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCACAACGCGATTTTGGAAAATCGCAAT
* *
141737 GCGAATATGTAAATCGCAACGCGATTCTGACTATCA
66 ACGAACATGTAAATCGCAACGCGATTCTGACTATCA
*
141773 CAACGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGGAAAATCGCAAT
1 CAACGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCACAACGCGATTTTGGAAAATCGCAAT
*
141838 ACGAACATGTAAATCGCAACGCGATTCTGACTATCG
66 ACGAACATGTAAATCGCAACGCGATTCTGACTATCA
141874 CAACGCGAT
1 CAACGCGAT
141883 AATACAAAAT
Statistics
Matches: 102, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
100 51 0.50
101 51 0.50
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (101 bp):
CAACGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCACAACGCGATTTTGGAAAATCGCAAT
ACGAACATGTAAATCGCAACGCGATTCTGACTATCA
Found at i:141873 original size:20 final size:20
Alignment explanation
Indices: 141850--141984 Score: 130
Period size: 20 Copynumber: 6.7 Consensus size: 20
141840 GAACATGTAA
141850 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
** *
141870 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATTCTGAC--T
*
141891 ATCACAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
141911 ATTGCAACGCAATTCTGACT
1 ATCGCAACGCGATTCTGACT
** *
141931 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATTCTGAC--T
141952 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
141972 ATCACAACGCGAT
1 ATCGCAACGCGAT
141985 AATACAGAAT
Statistics
Matches: 90, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
19 4 0.04
20 55 0.61
21 27 0.30
22 4 0.04
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:141892 original size:61 final size:61
Alignment explanation
Indices: 141827--142110 Score: 211
Period size: 61 Copynumber: 4.6 Consensus size: 61
141817 GCGATTTTGG
* *
141827 AAAATCGCAATACGA-ACATGTA-AATCGCAACGCGATTCTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACACGATAC-TG-ACAATCACAACGCGATTCTGACTATCGCAACGCGATAATAC
* * * * ** *
141888 AAAATCACAACGCGATTCTGACTATTGCAACGCAATTCTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACACGATACTGACAATCACAACGCGATTCTGACTATCGCAACGCGATAATAC
* * * * *** * **
141949 AAAATCGCAACGCGATTCTGACTATCACAACGCGATAATACAGA--ATCGCGTTGTTGCAATTTT
1 AAAATCGCAACACGATACTGACAATCACAACGCGAT--T-CTGACTATCGC---AACGCGATAAT
*
142012 AG
60 AC
*
142014 AAAATCGCAATACGAATA-TGTA-AATCACAACGCGATTCTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACACG-ATACTG-ACAATCACAACGCGATTCTGACTATCGCAACGCGATAATAC
* * * *
142075 AAAATTGCAACGCGATTCTGACTATCACAACGCGAT
1 AAAATCGCAACACGATACTGACAATCACAACGCGAT
142111 AATACATAAT
Statistics
Matches: 173, Mismatches: 36, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
60 4 0.02
61 114 0.66
62 9 0.05
63 2 0.01
64 8 0.05
65 33 0.19
66 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACACGATACTGACAATCACAACGCGATTCTGACTATCGCAACGCGATAATAC
Found at i:141959 original size:41 final size:41
Alignment explanation
Indices: 141914--142166 Score: 267
Period size: 41 Copynumber: 6.1 Consensus size: 41
141904 TCTGACTATT
*
141914 GCAACGCAATTCTGACTATCGCAACGCGATAATACAAAATC
1 GCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATC
* *
141955 GCAACGCGATTCTGACTATCACAACGCGATAATACAGAATC
1 GCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATC
*** * * ** ** **
141996 GCGTTGTTGCAATTTTAGAAAATCGCAATACG--AATATGTAAATC
1 GC---AACGCGATTCT-GACTATCGCAACGCGATAATA-CAAAATC
* *
142040 ACAACGCGATTCTGACTATCGCAACGCGATAATACAAAATT
1 GCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATC
* *
142081 GCAACGCGATTCTGACTATCACAACGCGATAATACATAATC
1 GCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATC
* *
142122 GCAACGCGATTCTGACTATCGCAATGTGATAATACAAAATC
1 GCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATC
142163 GCAA
1 GCAA
142167 TGCAATTTTC
Statistics
Matches: 168, Mismatches: 37, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
40 11 0.07
41 128 0.76
42 4 0.02
43 4 0.02
44 11 0.07
45 10 0.06
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (41 bp):
GCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATC
Found at i:142066 original size:20 final size:20
Alignment explanation
Indices: 142041--142145 Score: 97
Period size: 20 Copynumber: 5.2 Consensus size: 20
142031 ATGTAAATCA
142041 CAACGCGATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
** * *
142061 CAACGCGATAAT-ACAAAATTG
1 CAACGCGATTCTGAC--TATCG
*
142082 CAACGCGATTCTGACTATCA
1 CAACGCGATTCTGACTATCG
**
142102 CAACGCGATAAT-ACATAATCG
1 CAACGCGATTCTGAC-T-ATCG
142123 CAACGCGATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
142143 CAA
1 CAA
142146 TGTGATAATA
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
19 4 0.06
20 30 0.46
21 27 0.42
22 4 0.06
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (20 bp):
CAACGCGATTCTGACTATCG
Found at i:142128 original size:21 final size:21
Alignment explanation
Indices: 142057--142166 Score: 84
Period size: 21 Copynumber: 5.3 Consensus size: 21
142047 GATTCTGACT
*
142057 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACATA
* **
142078 ATTGCAACGCGATTCTGAC-T-
1 ATCGCAACGCGATAAT-ACATA
*
142098 ATCACAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
**
142119 ATCGCAACGCGATTCTGAC-T-
1 ATCGCAACGCGATAAT-ACATA
* * *
142139 ATCGCAATGTGATAATACAAA
1 ATCGCAACGCGATAATACATA
142160 ATCGCAA
1 ATCGCAA
142167 TGCAATTTTC
Statistics
Matches: 67, Mismatches: 16, Indels: 12
0.71 0.17 0.13
Matches are distributed among these distances:
19 4 0.06
20 25 0.37
21 34 0.51
22 4 0.06
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATAATACATA
Found at i:142630 original size:19 final size:19
Alignment explanation
Indices: 142603--142659 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
142593 ACGTTTTTCA
*
142603 AACTCTCGCAACACATTTT
1 AACTATCGCAACACATTTT
142622 AACTATCGCAACACATTTT
1 AACTATCGCAACACATTTT
*
142641 AACTATCACAACACATTTT
1 AACTATCGCAACACATTTT
142660 TTAAAATCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.32
Consensus pattern (19 bp):
AACTATCGCAACACATTTT
Found at i:145622 original size:83 final size:83
Alignment explanation
Indices: 145532--145700 Score: 338
Period size: 83 Copynumber: 2.0 Consensus size: 83
145522 CACTAGACTC
145532 TATATATTAGGGTTAATTACACCCAACCTCCTAGAATTATGGTTTAAATTGTAAATTACTCTATA
1 TATATATTAGGGTTAATTACACCCAACCTCCTAGAATTATGGTTTAAATTGTAAATTACTCTATA
145597 AAGTATATCCAACACGTA
66 AAGTATATCCAACACGTA
145615 TATATATTAGGGTTAATTACACCCAACCTCCTAGAATTATGGTTTAAATTGTAAATTACTCTATA
1 TATATATTAGGGTTAATTACACCCAACCTCCTAGAATTATGGTTTAAATTGTAAATTACTCTATA
145680 AAGTATATCCAACACGTA
66 AAGTATATCCAACACGTA
145698 TAT
1 TAT
145701 CAAATTTAAA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (83 bp):
TATATATTAGGGTTAATTACACCCAACCTCCTAGAATTATGGTTTAAATTGTAAATTACTCTATA
AAGTATATCCAACACGTA
Found at i:148841 original size:5 final size:5
Alignment explanation
Indices: 148828--148857 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
148818 ATAAAAGTTT
*
148828 ACTTC ACTTT ACTTC ACTTC ACTTC ACTTC
1 ACTTC ACTTC ACTTC ACTTC ACTTC ACTTC
148858 TATAAAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (5 bp):
ACTTC
Done.