Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000937.1 Hibiscus syriacus cultivar Beakdansim tig00001872_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: 312687
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:3131 original size:16 final size:18
Alignment explanation
Indices: 3100--3133 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
3090 TTATTATCAT
3100 GATTATAGTATAAAGAAA
1 GATTATAGTATAAAGAAA
3118 GATTA-AGT-TAAAGAAA
1 GATTATAGTATAAAGAAA
3134 TTTTCCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (18 bp):
GATTATAGTATAAAGAAA
Found at i:11568 original size:8 final size:8
Alignment explanation
Indices: 11555--11582 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
11545 GTATTTCTTC
11555 TTTCTTAT
1 TTTCTTAT
11563 TTTCTTAT
1 TTTCTTAT
11571 TTTCTTAT
1 TTTCTTAT
11579 TTTC
1 TTTC
11583 CTTCTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTCTTAT
Found at i:11590 original size:16 final size:15
Alignment explanation
Indices: 11548--11592 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
11538 TCTTTTTGTA
11548 TTTCTTCTTTCTTAT
1 TTTCTTCTTTCTTAT
*
11563 TTTCTTATTTTCTTAT
1 TTTCTT-CTTTCTTAT
11579 TTTCCTTCTTTCTT
1 TTT-CTTCTTTCTT
11593 GTTGCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 6 0.23
16 17 0.65
17 3 0.12
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCTTCTTTCTTAT
Found at i:15083 original size:72 final size:71
Alignment explanation
Indices: 14981--15119 Score: 174
Period size: 72 Copynumber: 1.9 Consensus size: 71
14971 TAAATTCATC
* * * * * *
14981 CATTCATGCATATTCATGCAAGAAGCCAAAT-AGTCATGTTCACACAAGG-GGGAAGAATTTCAG
1 CATTCATGAACATTCATCCAAGAAGACAAATCA-ACAAGTTCACACAAGGTGGGAAGAA-TTCAG
15044 CCAAGATA
64 CCAAGATA
*
15052 CATTCATGAACATTCATCCATAGAAGACAAATCAACAAGTTCACACAAGGTGGGATGAATTCAGC
1 CATTCATGAACATTCATCCA-AGAAGACAAATCAACAAGTTCACACAAGGTGGGAAGAATTCAGC
15117 CAA
65 CAA
15120 AGGATGTATT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
71 17 0.29
72 33 0.57
73 8 0.14
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.22
Consensus pattern (71 bp):
CATTCATGAACATTCATCCAAGAAGACAAATCAACAAGTTCACACAAGGTGGGAAGAATTCAGCC
AAGATA
Found at i:19897 original size:22 final size:23
Alignment explanation
Indices: 19854--19897 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
19844 TTTTTCCTCT
19854 TTTTGAGTGCTTTCAATTTCTTC
1 TTTTGAGTGCTTTCAATTTCTTC
* *
19877 TTTTGATTGC-TTCGATTTCTT
1 TTTTGAGTGCTTTCAATTTCTT
19898 TGCTGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.11, C:0.16, G:0.14, T:0.59
Consensus pattern (23 bp):
TTTTGAGTGCTTTCAATTTCTTC
Found at i:33301 original size:59 final size:58
Alignment explanation
Indices: 33238--33357 Score: 161
Period size: 58 Copynumber: 2.1 Consensus size: 58
33228 GGAGGGTTTG
* * * *
33238 TTAGAGCCATATTATCT-TGTTTTCCTTTTCATTATGACTAGGAGGATTCGATAGGACAC
1 TTAGAGCCATATTAT-TGAGTTTTACTTTTC-TTACGACTAGAAGGATTCGATAGGACAC
* *
33297 TTAGAGCCATATTATTGAGTTTTACTTTTCTTGCGACTAGAAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATTGAGTTTTACTTTTCTTACGACTAGAAGGATTCGATAGGACAC
33355 TTA
1 TTA
33358 TCCATCTCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
58 28 0.52
59 26 0.48
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (58 bp):
TTAGAGCCATATTATTGAGTTTTACTTTTCTTACGACTAGAAGGATTCGATAGGACAC
Found at i:40042 original size:24 final size:24
Alignment explanation
Indices: 39988--40042 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
39978 GAAAAATCAG
*
39988 AAAAG-AAGCACTCAAAAAGAAGA
1 AAAAGAAAACACTCAAAAAGAAGA
**
40011 AATTGAAAACACTC-AAAAGAAGAA
1 AAAAGAAAACACTCAAAAAGAAG-A
40035 AAAAGAAA
1 AAAAGAAA
40043 GAAAAGTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.67, C:0.11, G:0.15, T:0.07
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAAAGAAGA
Found at i:46965 original size:15 final size:15
Alignment explanation
Indices: 46945--46974 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46935 TCAATGAAAT
46945 GAAGGGATATTTAAC
1 GAAGGGATATTTAAC
*
46960 GAAGGGATGTTTAAC
1 GAAGGGATATTTAAC
46975 AAATGCACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.27
Consensus pattern (15 bp):
GAAGGGATATTTAAC
Found at i:49064 original size:13 final size:13
Alignment explanation
Indices: 49046--49085 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
49036 CATAGATGGA
49046 TTGAGCTAAAGAT
1 TTGAGCTAAAGAT
49059 TTGAGCTAAAGAT
1 TTGAGCTAAAGAT
49072 TTGAGCTACAAGAT
1 TTGAGCTA-AAGAT
49086 GACTTCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (13 bp):
TTGAGCTAAAGAT
Found at i:50329 original size:24 final size:24
Alignment explanation
Indices: 50295--50342 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
50285 TCATTGTACT
*
50295 TCAATCCTTGCTTTCCAAAACTCA
1 TCAATCATTGCTTTCCAAAACTCA
50319 TCAATCATTGCTTTCCAAAACTCA
1 TCAATCATTGCTTTCCAAAACTCA
50343 CGAACTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.33
Consensus pattern (24 bp):
TCAATCATTGCTTTCCAAAACTCA
Found at i:52221 original size:196 final size:196
Alignment explanation
Indices: 51887--52270 Score: 678
Period size: 196 Copynumber: 2.0 Consensus size: 196
51877 AGAACCATTA
* *
51887 GAAAGATAAGAAACATACGGTCGTATCTTCAGAATACATCTTGACTAAATAAGATCAGTATCCCA
1 GAAAGATAAGAAACATACGGTCGTATCTCCAGAATACATCTTGACTAAATAAGATCAGGATCCCA
* *
51952 TTCAAAAAGTCATCGTAAGTCTGCTTCTATTCTGATCTTCATTTCCAATGCTAGGACGAGTGGAT
66 TTCAAAAAGTCATCGTAAGTCTGATTCTATTCTAATCTTCATTTCCAATGCTAGGACGAGTGGAT
*
52017 CATTTGGAAGAGTTATTACTTCTTCCTTTGATGTGAGCCTTGTGGTGCATGTATCATCAACCGTT
131 CATTTGGAAGAGTTATTACTTCTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATCAACCGTT
52082 G
196 G
* *
52083 GAAAGATAAGAGACATACGGTCGTATCTCCATAATACATCTTGACTAAATAAGATCAGGATCCCA
1 GAAAGATAAGAAACATACGGTCGTATCTCCAGAATACATCTTGACTAAATAAGATCAGGATCCCA
* * *
52148 TTCAAAAAGTCATCGTAAGTCTGATTCTGTTCTAATCTTCTTTTCCAATGCTTGGACGAGTGGAT
66 TTCAAAAAGTCATCGTAAGTCTGATTCTATTCTAATCTTCATTTCCAATGCTAGGACGAGTGGAT
52213 CATTTGGAAGAGTTATTACTTCTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATC
131 CATTTGGAAGAGTTATTACTTCTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATC
52271 CCCCCTTTCT
Statistics
Matches: 178, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
196 178 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (196 bp):
GAAAGATAAGAAACATACGGTCGTATCTCCAGAATACATCTTGACTAAATAAGATCAGGATCCCA
TTCAAAAAGTCATCGTAAGTCTGATTCTATTCTAATCTTCATTTCCAATGCTAGGACGAGTGGAT
CATTTGGAAGAGTTATTACTTCTTCCTTTGATGTGAGCCTTGTGATGCATGTATCATCAACCGTT
G
Found at i:53740 original size:9 final size:9
Alignment explanation
Indices: 53718--53756 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
53708 TTAACGGAAT
*
53718 AATGAAATT
1 AATGAAATA
*
53727 TATGAAATA
1 AATGAAATA
53736 AATGAAATA
1 AATGAAATA
53745 AATGAAATA
1 AATGAAATA
53754 AAT
1 AAT
53757 ATAAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (9 bp):
AATGAAATA
Found at i:58628 original size:19 final size:20
Alignment explanation
Indices: 58578--58628 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
58568 GAAACCCCTT
*
58578 TGAAAATTCATGATTTTTAA
1 TGAAAATTCATGATTTTAAA
*
58598 TAAAAATTCATGA-TTTAAA
1 TGAAAATTCATGATTTTAAA
*
58617 TGAAAATACATG
1 TGAAAATTCATG
58629 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (20 bp):
TGAAAATTCATGATTTTAAA
Found at i:64589 original size:8 final size:8
Alignment explanation
Indices: 64578--64602 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
64568 TCTTTTTCTT
64578 TTCTTTTC
1 TTCTTTTC
64586 TTCTTTTC
1 TTCTTTTC
64594 TTCTTTTC
1 TTCTTTTC
64602 T
1 T
64603 GATTGTTCTC
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:64912 original size:22 final size:19
Alignment explanation
Indices: 64884--64929 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 19
64874 TAAAGGGGAT
64884 AATAATATAAGTAATGAAAATA
1 AATAA-ATAAG-AATG-AAATA
64906 AAT-AATAAGAATGAAATA
1 AATAAATAAGAATGAAATA
64924 AATAAA
1 AATAAA
64930 GGATAGAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.35
19 6 0.26
20 5 0.22
21 1 0.04
22 3 0.13
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (19 bp):
AATAAATAAGAATGAAATA
Found at i:64922 original size:18 final size:20
Alignment explanation
Indices: 64890--64928 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
64880 GGATAATAAT
64890 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
64910 ATAAG-AATG-AAATAAATA
1 ATAAGTAATGAAAATAAATA
64928 A
1 A
64929 AGGATAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:68789 original size:15 final size:16
Alignment explanation
Indices: 68769--68800 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
68759 GTTCTTCAAC
68769 TTTCTTTC-TTTTTCT
1 TTTCTTTCATTTTTCT
68784 TTTCTTTCATTTTTCT
1 TTTCTTTCATTTTTCT
68800 T
1 T
68801 CCTTTTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTCATTTTTCT
Found at i:68833 original size:23 final size:25
Alignment explanation
Indices: 68795--68848 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
68785 TTCTTTCATT
68795 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
68820 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
68843 TTTCTT
1 TTTCTT
68849 TGTTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:86829 original size:59 final size:59
Alignment explanation
Indices: 86757--87175 Score: 561
Period size: 59 Copynumber: 7.1 Consensus size: 59
86747 ATACACTATT
* * *
86757 TTTCATCTAACTTGCATTAGTGGCACCTTTTTGCCAAATGCACAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
* * * *
86816 TTTCATCTAACTTGAATTACTGTCACCTTTCTGCCAAATGCACAGTTAGTCATTTAACC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
*
86875 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGTATTTAACC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
* * * * *
86934 TTTTATCCAACTTGTATTATTGACACCTTTCTACCTAATTG-ACAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCC-AAATGCACAGTTAGGCATTTAACC
* * * * ** **
86993 TTTCATCCAACTTACATTATTGGCAACTTTCTGCCAAATGCTTAGTTAGATATTTAACC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
* * * ** * *
87052 TTTCATCTAGCTTGCATTATTGGCACATTTCTTTCAAATGCAGAGTTAGGCATTTATCC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
*
87111 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTATGCATTTAACC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
87170 TTTCAT
1 TTTCAT
87176 TTTAGAGAAA
Statistics
Matches: 311, Mismatches: 47, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
58 4 0.01
59 303 0.97
60 4 0.01
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (59 bp):
TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
Found at i:104742 original size:59 final size:59
Alignment explanation
Indices: 104665--105142 Score: 740
Period size: 59 Copynumber: 8.1 Consensus size: 59
104655 AGACATTGTT
* * * *
104665 TTTCATCTAACATACATTAGTGGCACCTTTCTGCCAAATGCACAGTTAGGTATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
* *
104724 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTACGCATTTAACT
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
* * * *
104783 TTTCATCTAACTTCCATTATTGGCACCTTTCTACCAAATGCACAGTTAGACGTTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
* *
104842 TTTCATCTAACTTGCATTATTAGCACCTTTCGGCCAAATGCACAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
* * * *
104901 TTTCATCTAACTTGCATTATTGGCACATTTATGCCAAATGCACAGTTAGGCAATTAACA
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
*
104960 TTTCATCTAACTTGCATTATTGGCACCTTTTTGCCAAATGCACAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
**
105019 TTTCATCTAACTTGCATTATTGGCACCTTTCTATCAAATGCACAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
* * ** *
105078 TTTCATGTAACTTGCATTATTGGCACATTTCTATCAAATGCACATTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
105137 TTTCAT
1 TTTCAT
105143 TTTAAAGAAA
Statistics
Matches: 385, Mismatches: 34, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 385 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (59 bp):
TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
Found at i:107445 original size:22 final size:21
Alignment explanation
Indices: 107411--107451 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
107401 TAAGAAGATA
107411 TTGATGGTCTTGATGGATGATG
1 TTGATGGTCTTGAT-GATGATG
* *
107433 TTGATTGTGTTGATGATGA
1 TTGATGGTCTTGATGATGA
107452 AATAGAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.20, C:0.02, G:0.34, T:0.44
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGATG
Found at i:130907 original size:13 final size:13
Alignment explanation
Indices: 130889--130913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
130879 AAGAAAAGCT
130889 AAAGAAAGGAAAC
1 AAAGAAAGGAAAC
130902 AAAGAAAGGAAA
1 AAAGAAAGGAAA
130914 ATGCAAAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGAAAGGAAAC
Found at i:147421 original size:22 final size:24
Alignment explanation
Indices: 147370--147421 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
147360 TTCTTTTATT
*
147370 TTTCTTCTTTTTGAGTGATTTCAA
1 TTTCTTCTTTTTGAGTGACTTCAA
*
147394 TTTCTTC-TTTTGAGTG-CTTCGA
1 TTTCTTCTTTTTGAGTGACTTCAA
147416 TTTCTT
1 TTTCTT
147422 TGTTAGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 10 0.38
23 9 0.35
24 7 0.27
ACGTcount: A:0.12, C:0.15, G:0.13, T:0.60
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTGACTTCAA
Found at i:150702 original size:15 final size:17
Alignment explanation
Indices: 150677--150709 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
150667 CTTTCTTCTT
150677 TCATATTCTAT-TTTAA
1 TCATATTCTATCTTTAA
150693 TCAT-TTCTATCTTTAA
1 TCATATTCTATCTTTAA
150709 T
1 T
150710 TTTTGCAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (17 bp):
TCATATTCTATCTTTAA
Found at i:185792 original size:15 final size:16
Alignment explanation
Indices: 185767--185796 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
185757 CTTTGATAAC
185767 ATTCATTTCCATTTCA
1 ATTCATTTCCATTTCA
185783 ATTC-TTTCCATTTC
1 ATTCATTTCCATTTC
185797 CATTTACTTT
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:0.20, C:0.27, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTCATTTCCATTTCA
Found at i:198325 original size:17 final size:18
Alignment explanation
Indices: 198300--198333 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
198290 AGATGAAAGA
*
198300 AAAGGAAATG-AGATAAT
1 AAAGAAAATGAAGATAAT
198317 AAAGAAAATGAAGATAA
1 AAAGAAAATGAAGATAA
198334 CTTACAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (18 bp):
AAAGAAAATGAAGATAAT
Found at i:199005 original size:35 final size:36
Alignment explanation
Indices: 198957--199040 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 36
198947 ATTTATAAGC
* * *
198957 TGGTGATAATATAGGCGTG-ATATGGTAATGGAATA
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
* * *
198992 TGGTGATGTTATAGGCGTGAAAATGGTGATGGAAGG
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
199028 TGGTGATGA-ATAG
1 TGGTGATGATATAG
199041 ATAGTATCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 21 0.51
36 20 0.49
ACGTcount: A:0.31, C:0.02, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
Found at i:217792 original size:13 final size:12
Alignment explanation
Indices: 217773--217858 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
217763 ATATAGGCGT
217773 GATATGGTGATG
1 GATATGGTGATG
217785 GAATATGGTGAT-
1 G-ATATGGTGATG
*
217797 GATATAGGCG-T-
1 GATAT-GGTGATG
217808 GATAATGGTGATG
1 GAT-ATGGTGATG
217821 GACTATGGTGAT-
1 GA-TATGGTGATG
*
217833 GATATAGGCG-T-
1 GATAT-GGTGATG
217844 GATAATGGTGATG
1 GAT-ATGGTGATG
217857 GA
1 GA
217859 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:217828 original size:36 final size:36
Alignment explanation
Indices: 217755--217859 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
217745 ATTTATAAGT
* *
217755 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
217790 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
217826 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
217860 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:221079 original size:18 final size:18
Alignment explanation
Indices: 221015--221082 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
221005 AAAGGTTTAG
*
221015 AAAAAAAATATGGTAATGAA
1 AAAAAAAATAT-GAAATG-A
221035 AAAAAAAATATGAAA-GA
1 AAAAAAAATATGAAATGA
* *
221052 ATAAAGAA-ATGAAATGA
1 AAAAAAAATATGAAATGA
221069 TAAAAAAAA-ATGAA
1 -AAAAAAAATATGAA
221083 GATAACTTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
16 6 0.15
17 9 0.22
18 12 0.29
19 3 0.07
20 11 0.27
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (18 bp):
AAAAAAAATATGAAATGA
Found at i:221086 original size:16 final size:17
Alignment explanation
Indices: 221035--221087 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
221025 TGGTAATGAA
221035 AAAAAAAATATGAAAGA-
1 AAAAAAAA-ATGAAAGAT
* *
221052 ATAAAGAAATGAAATGAT
1 AAAAAAAAATGAAA-GAT
221070 AAAAAAAAATG-AAGAT
1 AAAAAAAAATGAAAGAT
221086 AA
1 AA
221088 CTTACAACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 11 0.37
17 10 0.33
18 9 0.30
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
AAAAAAAAATGAAAGAT
Found at i:221638 original size:13 final size:12
Alignment explanation
Indices: 221619--221704 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
221609 ATATAGGCGT
221619 GATATGGTGATG
1 GATATGGTGATG
221631 GAATATGGTGAT-
1 G-ATATGGTGATG
*
221643 GATATAGGCG-T-
1 GATAT-GGTGATG
221654 GATAATGGTGATG
1 GAT-ATGGTGATG
221667 GACTATGGTGAT-
1 GA-TATGGTGATG
*
221679 GATATAGGCG-T-
1 GATAT-GGTGATG
221690 GATAATGGTGATG
1 GAT-ATGGTGATG
221703 GA
1 GA
221705 CAGTTTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:221674 original size:36 final size:36
Alignment explanation
Indices: 221601--221705 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
221591 ATTTATAAGT
* *
221601 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
221636 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
221672 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
221706 AGTTTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:238130 original size:19 final size:20
Alignment explanation
Indices: 238106--238145 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
238096 TATCCCATCC
238106 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
**
238125 TTATTTTTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
238145 T
1 T
238146 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:238156 original size:19 final size:19
Alignment explanation
Indices: 238115--238156 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
238105 CTTATTTCAT
* *
238115 TTCATTCTTATTATTTTTT
1 TTCATTCTTATTATTATTA
238134 TTCATTACTTA-TATTATTA
1 TTCATT-CTTATTATTATTA
238153 TTCA
1 TTCA
238157 CTTTATTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (19 bp):
TTCATTCTTATTATTATTA
Found at i:250193 original size:2 final size:2
Alignment explanation
Indices: 250186--250255 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
250176 TATCACCATC
250186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250256 TCCGCTGCCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:251989 original size:19 final size:19
Alignment explanation
Indices: 251965--252014 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
251955 GAAACCCCTT
**
251965 TGAAAATACATGATTTTTA
1 TGAAAATACATGATTTAAA
251984 TGAAAATACATGATTTAAA
1 TGAAAATACATGATTTAAA
*
252003 TGAATATACATG
1 TGAAAATACATG
252015 CTCTTGGTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:252715 original size:24 final size:25
Alignment explanation
Indices: 252683--252732 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
252673 ACCGTTTGTT
*
252683 CTTCATGAT-CTCCCGTGATGTAAGG
1 CTTCATGATGC-CACGTGATGTAAGG
*
252708 CTTC-TGATGCCACTTGATGTAAGG
1 CTTCATGATGCCACGTGATGTAAGG
252732 C
1 C
252733 ATTTATACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (25 bp):
CTTCATGATGCCACGTGATGTAAGG
Found at i:253202 original size:13 final size:12
Alignment explanation
Indices: 253183--253268 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
253173 ATATAGGCGT
253183 GATATGGTGATG
1 GATATGGTGATG
253195 GAATATGGTGAT-
1 G-ATATGGTGATG
*
253207 GATATAGGCG-T-
1 GATAT-GGTGATG
253218 GATAATGGTGATG
1 GAT-ATGGTGATG
253231 GACTATGGTGAT-
1 GA-TATGGTGATG
*
253243 GATATAGGCG-T-
1 GATAT-GGTGATG
253254 GATAATGGTGATG
1 GAT-ATGGTGATG
253267 GA
1 GA
253269 CATATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:253238 original size:36 final size:36
Alignment explanation
Indices: 253165--253269 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
253155 ATTTATAAGT
* *
253165 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
253200 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
253236 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
253270 ATATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:253658 original size:19 final size:20
Alignment explanation
Indices: 253611--253661 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
253601 GAAACCCATT
**
253611 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
253631 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
253650 TGAAGATACATG
1 TGAAAATACATG
253662 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:266066 original size:9 final size:9
Alignment explanation
Indices: 266011--266068 Score: 71
Period size: 9 Copynumber: 6.0 Consensus size: 9
266001 AAATTTTGGT
266011 TTTTTTTTG
1 TTTTTTTTG
266020 TTTTTTTTG
1 TTTTTTTTG
266029 CCTTTTTTTTG
1 --TTTTTTTTG
266040 TTTTTTTTG
1 TTTTTTTTG
*
266049 TTTTGTTTTT
1 TTTT-TTTTG
266059 TGTTTTTTTG
1 T-TTTTTTTG
266069 GAAAAAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
9 22 0.51
10 9 0.21
11 12 0.28
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.84
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:266068 original size:20 final size:20
Alignment explanation
Indices: 266004--266067 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
265994 TTTTTTGAAA
*
266004 TTTTGGTTTTTTTTTGTTTT
1 TTTTGCTTTTTTTTTGTTTT
*
266024 TTTTGCCTTTTTTTTGTTTT
1 TTTTGCTTTTTTTTTGTTTT
*
266044 TTTTGTTTTGTTTTTTGTTTT
1 TTTTGCTTT-TTTTTTGTTTT
266065 TTT
1 TTT
266068 GGAAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.84
Consensus pattern (20 bp):
TTTTGCTTTTTTTTTGTTTT
Found at i:268324 original size:18 final size:18
Alignment explanation
Indices: 268309--268346 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
268299 CCTTACACAC
268309 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
*
268327 TTTGCCACAACAACGCCA
1 TTTGCCACAACAACACCA
268345 TT
1 TT
268347 CTTTACCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.37, G:0.08, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:270677 original size:2 final size:2
Alignment explanation
Indices: 270670--270700 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
270660 TTAGATTACA
*
270670 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
270701 GCTCTACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:275199 original size:33 final size:33
Alignment explanation
Indices: 275147--275315 Score: 241
Period size: 33 Copynumber: 5.1 Consensus size: 33
275137 TTTTATCCTC
*
275147 CTCAACTTTACGTTTTTCTTCCACTTTGGGGTT
1 CTCAACTTTCCGTTTTTCTTCCACTTTGGGGTT
* * *
275180 CTCAGCTTTTCGTTTTTCTTCCACCTTGGGGTT
1 CTCAACTTTCCGTTTTTCTTCCACTTTGGGGTT
* *
275213 CTCAACTCTCCGTTTTTCTTCCACCTTGGGGTT
1 CTCAACTTTCCGTTTTTCTTCCACTTTGGGGTT
* *
275246 CTCAACTCTCCGTTTTTCTTCCACTTTGGAGTT
1 CTCAACTTTCCGTTTTTCTTCCACTTTGGGGTT
*
275279 CTCAACTTTCC-TTTTATCTTCCACTTTGGAGTT
1 CTCAACTTTCCGTTTT-TCTTCCACTTTGGGGTT
275312 CTCA
1 CTCA
275316 GTCTGTAACA
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
32 4 0.03
33 122 0.97
ACGTcount: A:0.11, C:0.29, G:0.14, T:0.46
Consensus pattern (33 bp):
CTCAACTTTCCGTTTTTCTTCCACTTTGGGGTT
Found at i:278162 original size:22 final size:22
Alignment explanation
Indices: 278137--278184 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
278127 CAAACGACCA
278137 AAAATATGTCATAAA-ATTAGAG
1 AAAATATGTCATAAAGA-TAGAG
*
278159 AAAATGTGTCATAAAGATAGAG
1 AAAATATGTCATAAAGATAGAG
278181 AAAA
1 AAAA
278185 ACATAACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.56, C:0.04, G:0.17, T:0.23
Consensus pattern (22 bp):
AAAATATGTCATAAAGATAGAG
Found at i:283069 original size:29 final size:28
Alignment explanation
Indices: 283037--283106 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
283027 TAATGTTCAA
283037 TAAAATTTAATAACTA-ATTCAAAATCATT
1 TAAAATTTAATAACTATATT-AAAA-CATT
* *
283066 TAAAATTTTAATAATTATATTATAACATT
1 TAAAA-TTTAATAACTATATTAAAACATT
283095 TATAAATTTAAT
1 TA-AAATTTAAT
283107 GATCAAAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
29 17 0.47
30 16 0.44
31 3 0.08
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (28 bp):
TAAAATTTAATAACTATATTAAAACATT
Found at i:283102 original size:30 final size:31
Alignment explanation
Indices: 283036--283103 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
283026 GTAATGTTCA
*
283036 ATAAAATTTAATAACTAATTCAAAATCATTT
1 ATAAATTTTAATAACTAATTCAAAATCATTT
* *
283067 A-AAATTTTAATAATTATATT-ATAA-CATTT
1 ATAAATTTTAATAACTA-ATTCAAAATCATTT
283096 ATAAATTT
1 ATAAATTT
283104 AATGATCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 6 0.19
30 22 0.69
31 4 0.12
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAAATTTTAATAACTAATTCAAAATCATTT
Found at i:285459 original size:31 final size:32
Alignment explanation
Indices: 285374--285459 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 32
285364 ATAAATTAGG
*
285374 CTTTTATTTTTTGGATAATATT--TTATTTTTAT
1 CTTTTA-TTTTT-GATAAAATTAATTATTTTTAT
*
285406 -TTTTATTTTTGATAAAAATAATTA-TTTTAT
1 CTTTTATTTTTGATAAAATTAATTATTTTTAT
*
285436 CTTTTATTTTTGATAACATTAATT
1 CTTTTATTTTTGATAAAATTAATT
285460 TGAATGGAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 7 0.15
30 11 0.23
31 29 0.62
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (32 bp):
CTTTTATTTTTGATAAAATTAATTATTTTTAT
Found at i:288841 original size:51 final size:51
Alignment explanation
Indices: 288795--288893 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
288785 TCCCTGCCCT
* **
288795 ACGCTATATGCTGATTTGGCGT-CACGTGGGGTATAGCGCGCCCCCTGTACC
1 ACGCTATACGCTGACATGGCGTACACGT-GGGTATAGCGCGCCCCCTGTACC
* * *
288846 GCGCTATACGCTGACATGGCTTACACGTGGGTATAGCGCGCGCCCTGT
1 ACGCTATACGCTGACATGGCGTACACGTGGGTATAGCGCGCCCCCTGT
288894 TACGCGCTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 36 0.88
52 5 0.12
ACGTcount: A:0.16, C:0.29, G:0.30, T:0.24
Consensus pattern (51 bp):
ACGCTATACGCTGACATGGCGTACACGTGGGTATAGCGCGCCCCCTGTACC
Found at i:288994 original size:22 final size:22
Alignment explanation
Indices: 288963--289012 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
288953 TACCTTTAAT
288963 TACCCCCAACCTTCCCTATAAA
1 TACCCCCAACCTTCCCTATAAA
*
288985 TACCCTCAACCTTCCCTATAAA
1 TACCCCCAACCTTCCCTATAAA
289007 TACCCC
1 TACCCC
289013 TCGTCCATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.30, C:0.46, G:0.00, T:0.24
Consensus pattern (22 bp):
TACCCCCAACCTTCCCTATAAA
Found at i:298462 original size:19 final size:20
Alignment explanation
Indices: 298418--298529 Score: 99
Period size: 19 Copynumber: 5.8 Consensus size: 20
298408 ACTGCTGGAA
* * *
298418 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGGTTCTGA
298438 ACCGGTTCTGACCGGTT-TG-
1 ACCGGTT-TGACCGGTTCTGA
*
298457 ACCGGTTTCAACCGGTTC-GA
1 ACCGGTTT-GACCGGTTCTGA
* *
298477 ATCGGTTTGACC-GATCTGA
1 ACCGGTTTGACCGGTTCTGA
*
298496 AACGGTTTGACCGG-TCTGA
1 ACCGGTTTGACCGGTTCTGA
*
298515 AACGGTTTGACCGGT
1 ACCGGTTTGACCGGT
298530 CTAACCCGAC
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.05
19 50 0.64
20 16 0.21
21 8 0.10
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (20 bp):
ACCGGTTTGACCGGTTCTGA
Found at i:298482 original size:29 final size:30
Alignment explanation
Indices: 298418--298489 Score: 103
Period size: 29 Copynumber: 2.4 Consensus size: 30
298408 ACTGCTGGAA
*
298418 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGGTTTTCAACCGGTTCTG
298448 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
1 ACCGGTTTGACCGGTTTTCAACCGGTTCTG
*
298476 AATCGGTTTGACCG
1 -ACCGGTTTGACCG
298490 ATCTGAAACG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
28 1 0.03
29 25 0.64
30 13 0.33
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (30 bp):
ACCGGTTTGACCGGTTTTCAACCGGTTCTG
Found at i:298529 original size:9 final size:9
Alignment explanation
Indices: 298418--298529 Score: 71
Period size: 10 Copynumber: 11.7 Consensus size: 9
298408 ACTGCTGGAA
*
298418 ACCGGTTTA
1 ACCGGTTTG
*
298427 ACCGGTTTTCA
1 ACCGG-TTT-G
298438 ACCGGTTCTG
1 ACCGGTT-TG
298448 ACCGGTTTG
1 ACCGGTTTG
*
298457 ACCGGTTTCA
1 ACCGGTTT-G
*
298467 ACCGGTTCG
1 ACCGGTTTG
*
298476 AATCGGTTTG
1 -ACCGGTTTG
* *
298486 ACCGATCTG
1 ACCGGTTTG
*
298495 AAACGGTTTG
1 -ACCGGTTTG
*
298505 ACCGGTCTG
1 ACCGGTTTG
*
298514 AAACGGTTTG
1 -ACCGGTTTG
298524 ACCGGT
1 ACCGGT
298530 CTAACCCGAC
Statistics
Matches: 79, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
9 33 0.42
10 39 0.49
11 7 0.09
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:298561 original size:22 final size:22
Alignment explanation
Indices: 298533--298598 Score: 96
Period size: 22 Copynumber: 2.9 Consensus size: 22
298523 GACCGGTCTA
*
298533 ACCCGACCCGACTGTTGACCCG
1 ACCCGACCCGACCGTTGACCCG
298555 ACCCGACCCGACCGTTGACCCG
1 ACCCGACCCGACCGTTGACCCG
*
298577 ACCCGACCGTTGACCGTTGACC
1 ACCCGACC--CGACCGTTGACC
298599 GTTGACTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
22 29 0.73
24 11 0.28
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (22 bp):
ACCCGACCCGACCGTTGACCCG
Found at i:298574 original size:17 final size:17
Alignment explanation
Indices: 298554--298591 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
298544 CTGTTGACCC
298554 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
298571 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
298588 GACC
1 GACC
298592 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:305705 original size:9 final size:9
Alignment explanation
Indices: 305691--305775 Score: 80
Period size: 10 Copynumber: 8.8 Consensus size: 9
305681 GGCTGCTGGA
305691 AACCGGTTT
1 AACCGGTTT
305700 AACCGGTTTT
1 AACCGG-TTT
305710 CAACCGGTTCT
1 -AACCGGTT-T
*
305721 GACCGGTTT
1 AACCGGTTT
*
305730 GACCGGTTT
1 AACCGGTTT
305739 CAACCGGTTT
1 -AACCGGTTT
*
305749 CAACCGGTTCG
1 -AACCGGTT-T
305760 AACCGGTTT
1 AACCGGTTT
*
305769 GACCGGT
1 AACCGGT
305776 CTGACCCGAC
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
9 22 0.33
10 37 0.56
11 7 0.11
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:305716 original size:20 final size:20
Alignment explanation
Indices: 305691--305768 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
305681 GGCTGCTGGA
305691 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGG-TTTC
*
305711 AACCGGTTCTGACCGGTTT-
1 AACCGGTTCTAACCGGTTTC
*
305730 GACCGGTT-TCAACCGGTTTC
1 AACCGGTTCT-AACCGGTTTC
*
305750 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
305769 GACCGGTCTG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.02
19 15 0.31
20 27 0.55
21 6 0.12
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.31
Consensus pattern (20 bp):
AACCGGTTCTAACCGGTTTC
Found at i:305728 original size:30 final size:29
Alignment explanation
Indices: 305692--305781 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
305682 GCTGCTGGAA
305692 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTAACCGG-TTTCAACCGGTTCTG
* *
305722 ACCGGTTTGACCGGTTTCAACCGGTT-TCA
1 ACCGGTTTAACCGGTTTCAACCGGTTCT-G
* *
305751 ACCGGTTCGAACCGGTTT-GACCGG-TCTG
1 ACCGGTT-TAACCGGTTTCAACCGGTTCTG
305779 ACC
1 ACC
305782 CGACCCGACC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
28 5 0.10
29 25 0.49
30 21 0.41
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.29
Consensus pattern (29 bp):
ACCGGTTTAACCGGTTTCAACCGGTTCTG
Found at i:305736 original size:19 final size:19
Alignment explanation
Indices: 305712--305781 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
305702 CCGGTTTTCA
305712 ACCGGTTCTGACCGGTTTG
1 ACCGGTTCTGACCGGTTTG
* *
305731 ACCGGTT-TCAACCGGTTTCA
1 ACCGGTTCT-GACCGGTTT-G
305751 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTG-ACCGGTTTG
305770 ACCGG-TCTGACC
1 ACCGGTTCTGACC
305782 CGACCCGACC
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
18 6 0.14
19 21 0.50
20 15 0.36
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (19 bp):
ACCGGTTCTGACCGGTTTG
Found at i:305750 original size:39 final size:39
Alignment explanation
Indices: 305692--305775 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
305682 GCTGCTGGAA
305692 ACCGGTTTAACCGGTTTTCAACCGGTTCTG-ACCGGTTTG
1 ACCGGTTTAACCGGTTTTCAACCGGTTC-GAACCGGTTTG
305731 ACCGGTTTCAACCGG-TTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTT-AACCGGTTTTCAACCGGTTCGAACCGGTTTG
305770 ACCGGT
1 ACCGGT
305776 CTGACCCGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
38 1 0.02
39 36 0.84
40 6 0.14
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.30
Consensus pattern (39 bp):
ACCGGTTTAACCGGTTTTCAACCGGTTCGAACCGGTTTG
Found at i:305788 original size:5 final size:5
Alignment explanation
Indices: 305778--305835 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
305768 TGACCGGTCT
* * *
305778 GACCC GACCC GACCGTT GACCC GACCC GATCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
305827 GACCC GACC
1 GACCC GACC
305836 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 35 0.81
7 8 0.19
ACGTcount: A:0.19, C:0.50, G:0.22, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:305804 original size:22 final size:22
Alignment explanation
Indices: 305778--305842 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
305768 TGACCGGTCT
305778 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
305800 GACCCGATCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
305822 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
305843 GTTGACTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:308769 original size:31 final size:33
Alignment explanation
Indices: 308719--308807 Score: 137
Period size: 31 Copynumber: 2.7 Consensus size: 33
308709 TAAAAGTATT
*
308719 AAAATGGTTTTCAAGTTTGGTAACCAACTTTGA
1 AAAAAGGTTTTCAAGTTTGGTAACCAACTTTGA
308752 AAAAA-GTTTTC-AGTTTGGTAACCAACTTTGA
1 AAAAAGGTTTTCAAGTTTGGTAACCAACTTTGA
308783 AAAAATGGTTTTCAAAGTTTGGTAA
1 AAAAA-GGTTTTC-AAGTTTGGTAA
308808 ATGTTTTTGA
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
31 25 0.49
32 6 0.12
33 10 0.20
35 10 0.20
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (33 bp):
AAAAAGGTTTTCAAGTTTGGTAACCAACTTTGA
Found at i:308871 original size:36 final size:35
Alignment explanation
Indices: 308831--308918 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 35
308821 TGATTTTTTA
* *
308831 TTTCTATGAAAATGATTTTTTAAAGTTTGGTAAATG
1 TTTCT-TGAAAATGATTTTTCAAAGTTTGATAAATG
*
308867 TTTCTTTGAAAAT-AGTTTTTCAAAGTTTGATAGATG
1 TTTC-TTGAAAATGA-TTTTTCAAAGTTTGATAAATG
*
308903 TTTGTTGAAAAATGAT
1 TTTCTTG-AAAATGAT
308919 AATGAGATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
35 4 0.09
36 38 0.86
37 2 0.05
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (35 bp):
TTTCTTGAAAATGATTTTTCAAAGTTTGATAAATG
Done.