Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006378.1 Hibiscus syriacus cultivar Beakdansim tig00015349_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: 88709
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3163 original size:21 final size:21
Alignment explanation
Indices: 3139--3179 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3129 GAAGTGCCAC
* *
3139 ATAATTGTCCCGAAGGACCAA
1 ATAATTGTCCCAAAAGACCAA
3160 ATAATTGTCCCAAAAGACCA
1 ATAATTGTCCCAAAAGACCA
3180 CATAGAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (21 bp):
ATAATTGTCCCAAAAGACCAA
Found at i:7988 original size:23 final size:23
Alignment explanation
Indices: 7922--8007 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
7912 ACAACTCGTA
*
7922 ATTTGCACAGAAGTGCCACATA-
1 ATTTGCACCGAAGTGCCACATAG
*
7944 ATTAT-C-CCAAAG-GACCACATAG
1 ATT-TGCACCGAAGTG-CCACATAG
*
7966 ATTTGCACTGAAGTGCCACATAG
1 ATTTGCACCGAAGTGCCACATAG
*
7989 GTTTGCACCGAAGTGCCAC
1 ATTTGCACCGAAGTGCCAC
8008 GTAATTATCC
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
20 1 0.02
21 12 0.23
22 8 0.15
23 30 0.58
24 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (23 bp):
ATTTGCACCGAAGTGCCACATAG
Found at i:10863 original size:31 final size:31
Alignment explanation
Indices: 10828--10934 Score: 83
Period size: 31 Copynumber: 3.3 Consensus size: 31
10818 TTAGGTCCAT
10828 AAGGAATTACCAGTCGGTGTTGAACCTATAC
1 AAGGAATTACCAGTCGGTGTTGAACCTATAC
* * * * *
10859 AAGGAATCACCAG--GAGTGACTAAACCTGTCTAAG
1 AAGGAATTACCAGTCG-GTG-TTGAACC--TAT-AC
**
10893 ATAGGAATTACCAGTCGGTGTTGAATATATAC
1 A-AGGAATTACCAGTCGGTGTTGAACCTATAC
10925 AAGGAATTAC
1 AAGGAATTAC
10935 TAGCACCTGA
Statistics
Matches: 56, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
29 1 0.02
30 3 0.05
31 26 0.46
32 2 0.04
33 4 0.07
34 2 0.04
35 14 0.25
36 3 0.05
37 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (31 bp):
AAGGAATTACCAGTCGGTGTTGAACCTATAC
Found at i:12072 original size:11 final size:11
Alignment explanation
Indices: 12058--12098 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
12048 TCAACGACAG
*
12058 TCAACGGTCGA
1 TCAATGGTCGA
12069 TCAATGG-CGA
1 TCAATGGTCGA
12079 TCAATGGTC-A
1 TCAATGGTCGA
12089 GTCAATGGTC
1 -TCAATGGTC
12099 AATGGCTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 11 0.41
11 16 0.59
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (11 bp):
TCAATGGTCGA
Found at i:13976 original size:37 final size:37
Alignment explanation
Indices: 13926--14001 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
13916 CTCGTTAAAC
13926 CTCCCTAAACCTAAATAGAGGAATAGAGTACTCTTAA
1 CTCCCTAAACCTAAATAGAGGAATAGAGTACTCTTAA
13963 CTCCCTAAACCTAAATAGAGGAATAGAGTACTCTTAA
1 CTCCCTAAACCTAAATAGAGGAATAGAGTACTCTTAA
14000 CT
1 CT
14002 AGGAAATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.25
Consensus pattern (37 bp):
CTCCCTAAACCTAAATAGAGGAATAGAGTACTCTTAA
Found at i:15666 original size:22 final size:21
Alignment explanation
Indices: 15632--15672 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
15622 ATAATTATTT
15632 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
15653 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
15673 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:17555 original size:9 final size:8
Alignment explanation
Indices: 17490--17553 Score: 69
Period size: 8 Copynumber: 7.9 Consensus size: 8
17480 CAAATCTAAT
17490 AAAATAAA
1 AAAATAAA
17498 TAAAAT-AA
1 -AAAATAAA
17506 AAAATAAA
1 AAAATAAA
17514 AAAATAAA
1 AAAATAAA
17522 AAAATAGAA
1 AAAATA-AA
* *
17531 ACAA-AAC
1 AAAATAAA
17538 AAAATAATA
1 AAAATAA-A
17547 AAAATAA
1 AAAATAA
17554 TATATATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
7 9 0.19
8 21 0.45
9 17 0.36
ACGTcount: A:0.81, C:0.03, G:0.02, T:0.14
Consensus pattern (8 bp):
AAAATAAA
Found at i:17942 original size:2 final size:2
Alignment explanation
Indices: 17937--17971 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17927 AATAAAACAA
17937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17972 AAATGTTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18401 original size:20 final size:20
Alignment explanation
Indices: 18363--18401 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18353 GTCGCCTCGT
* *
18363 CGGCCACCGTTGATCGGCGC
1 CGGCCACCGGTCATCGGCGC
*
18383 CGGCCACCGGTCATTGGCG
1 CGGCCACCGGTCATCGGCG
18402 GTGAAACTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.10, C:0.38, G:0.36, T:0.15
Consensus pattern (20 bp):
CGGCCACCGGTCATCGGCGC
Found at i:19073 original size:2 final size:2
Alignment explanation
Indices: 19066--19151 Score: 131
Period size: 2 Copynumber: 43.0 Consensus size: 2
19056 AAAAGAGAAA
19066 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
*
19108 AT AT AT AT AT AT AT AT AT AT AT A- AT CAT AT CAT -T AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT AT AT AT
19150 AT
1 AT
19152 GGACAAAATA
Statistics
Matches: 78, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
1 2 0.03
2 72 0.92
3 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19995 original size:124 final size:124
Alignment explanation
Indices: 19775--20008 Score: 387
Period size: 124 Copynumber: 1.9 Consensus size: 124
19765 GTTGATCTAT
* **
19775 TGGGCACGATATCCTTCGTCGTGAAGTTAAAATTGTGGATGGCTCCTTCGTTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTAAAATTATGGATGGCTAATTCGTTGTGAAGTTGAGCT
*
19840 TTGAATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTAGAGATGGATACTGCTGG
66 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGGATACTGCTGG
* * * * *
19899 TGGGCACGATATTCTTTGTCGTGAAGTTGAAATTATGGATGTCTAATTTGTTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTAAAATTATGGATGGCTAATTCGTTGTGAAGTTGAGCT
19964 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAG
66 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAG
20009 TTGTATTGCT
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 101 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.36
Consensus pattern (124 bp):
TGGGCACGATATCCTTCGTCGTGAAGTTAAAATTATGGATGGCTAATTCGTTGTGAAGTTGAGCT
TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGGATACTGCTGG
Found at i:20324 original size:64 final size:64
Alignment explanation
Indices: 20094--20324 Score: 327
Period size: 64 Copynumber: 3.6 Consensus size: 64
20084 GCGTTGTTTC
* * ** **
20094 GAGTCCAATATCCTTCGTTGTGTAGTTGAAATTGATTCTGAATGAAACTCCAAAGTTGTTTACT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * *
20158 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGAATCTGAAGGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
20222 GAGTCCAATATCCTTCGTCGTGAAGTTAAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * * *
20286 GAGTCCAATATTCTTTGCTGTGAAGTTGAAATTTACTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
20325 ACAAGCTGCA
Statistics
Matches: 148, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 148 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (64 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:20875 original size:12 final size:12
Alignment explanation
Indices: 20858--20882 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20848 TTCTGTCATC
20858 TGAAATCTTCTG
1 TGAAATCTTCTG
20870 TGAAATCTTCTG
1 TGAAATCTTCTG
20882 T
1 T
20883 TTGTTCAAGC
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:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TGAAATCTTCTG
Found at i:26738 original size:22 final size:23
Alignment explanation
Indices: 26698--26748 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
26688 AAATGTCCTG
*
26698 AAATAAAAAAGAAAATAAATACA
1 AAATAAAAAAGAAAATAAAAACA
* * *
26721 AAATAAAAAA-AGAGTAAAAACC
1 AAATAAAAAAGAAAATAAAAACA
26743 AAATAA
1 AAATAA
26749 GTTAACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (23 bp):
AAATAAAAAAGAAAATAAAAACA
Found at i:26867 original size:21 final size:21
Alignment explanation
Indices: 26774--26867 Score: 61
Period size: 22 Copynumber: 4.4 Consensus size: 21
26764 AAAACAAATC
26774 AAATAAAAT-AAAATAAGAAA
1 AAATAAAATAAAAATAAGAAA
* **
26794 AAA-AGAAAAAAAAATGGGAAA
1 AAATA-AAATAAAAATAAGAAA
26815 ATAATAATAA-AAAACATAA-ACAA
1 A-AATAA-AATAAAA-ATAAGA-AA
* *
26838 AACAAAAAATAAAAATAATAAA
1 AA-ATAAAATAAAAATAAGAAA
26860 AAATAAAA
1 AAATAAAA
26868 ATAATTTATA
Statistics
Matches: 57, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
19 1 0.02
20 6 0.11
21 15 0.26
22 19 0.33
23 16 0.28
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (21 bp):
AAATAAAATAAAAATAAGAAA
Found at i:26872 original size:16 final size:16
Alignment explanation
Indices: 26812--26872 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
26802 AAAAAATGGG
*
26812 AAAATAATAATAA-AA
1 AAAATAAAAATAATAA
* *
26827 AACATAAACAA-AACAA
1 AAAATAAA-AATAATAA
26843 AAAATAAAAATAATAA
1 AAAATAAAAATAATAA
26859 AAAATAAAAATAAT
1 AAAATAAAAATAAT
26873 TTATATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
15 10 0.26
16 29 0.74
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAATAAAAATAATAA
Found at i:27131 original size:4 final size:4
Alignment explanation
Indices: 27122--27146 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27112 AATAAAATTA
27122 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
27147 GTGAAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:29777 original size:13 final size:13
Alignment explanation
Indices: 29747--29798 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
29737 GAACACAAAC
*
29747 GAACAAACATAAAC
1 GAACAAA-ATAAAT
*
29761 GAACATAATAAAT
1 GAACAAAATAAAT
*
29774 GAACACAATAAAT
1 GAACAAAATAAAT
29787 GAACAAAATAAA
1 GAACAAAATAAA
29799 CACAAAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 28 0.82
14 6 0.18
ACGTcount: A:0.65, C:0.13, G:0.08, T:0.13
Consensus pattern (13 bp):
GAACAAAATAAAT
Found at i:30075 original size:14 final size:14
Alignment explanation
Indices: 30056--30106 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
30046 CATATGTTCA
30056 AACATAAATGAACG
1 AACATAAATGAACG
30070 AACATAAAT----G
1 AACATAAATGAACG
*
30080 AACATAGATGAACG
1 AACATAAATGAACG
*
30094 AACATAAACGAAC
1 AACATAAATGAAC
30107 ATATAATCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
10 9 0.30
14 21 0.70
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.14
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:30090 original size:24 final size:24
Alignment explanation
Indices: 30056--30142 Score: 99
Period size: 24 Copynumber: 3.7 Consensus size: 24
30046 CATATGTTCA
*
30056 AACATAAATGAACGAACATAAATG
1 AACATAAATGAACGAACATAAACG
*
30080 AACATAGATGAACGAACATAAACG
1 AACATAAATGAACGAACATAAACG
* **
30104 AACAT--AT-AATCGAACGTTCACG
1 AACATAAATGAA-CGAACATAAACG
30126 AACATAAATGAACGAAC
1 AACATAAATGAACGAAC
30143 GAGCCCTTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.04
22 16 0.30
24 34 0.63
25 2 0.04
ACGTcount: A:0.53, C:0.17, G:0.14, T:0.16
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:31344 original size:124 final size:124
Alignment explanation
Indices: 31118--31593 Score: 684
Period size: 124 Copynumber: 3.8 Consensus size: 124
31108 GTCTATCCAT
* * * * *
31118 TGGGCACGATATCATTCATCGTGAAGTTGAAATCGTGGATGTCTCCTTCTTTGTGAAGTTGAGAT
1 TGGGCACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGTGAAGTTGAGCT
*
31183 TTGAATTGGATATCCTTCGTTATGAAGTT-AAACTCCAATCTAGAGATGGATGCTGCTTG
66 TTGAATTGGATATCCTTCGTTATGAAGTTGAAA-TCCAATCTAGAGATGGATGTTGCTTG
* * * *
31242 TGGGCATGATATCCTTTATCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGATCT
1 TGGGCACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGTGAAGTTGAGCT
* *
31307 TTTAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTAGAGATGGATGTTGCTTG
66 TTGAATTGGATATCCTTCGTTATGAAGTTGAAATCCAATCTAGAGATGGATGTTGCTTG
* * * * * * *
31366 TGGGCAAGATATCCTTCGTCATGAAGTTAAAATCGAGGATGGCTCCTTCCTTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGTGAAGTTGAGCT
* * *
31431 TTGAATTGGATATTCTTCATTGTGAAGTTGAAATCCAATCTAGAGATGGATGTTGCTTG
66 TTGAATTGGATATCCTTCGTTATGAAGTTGAAATCCAATCTAGAGATGGATGTTGCTTG
* * *
31490 TGGGCACGATATCCTTCGTCTTGAAGTTGAAATCATGGATGGCTCATTCATTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGTGAAGTTGAGCT
* * *
31555 TTGAATTAGATATCCTTCGTTGTGAAGTTGAAAACCAAT
66 TTGAATTGGATATCCTTCGTTATGAAGTTGAAATCCAAT
31594 GGTTGTTTCA
Statistics
Matches: 315, Mismatches: 36, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
124 312 0.99
125 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (124 bp):
TGGGCACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGTGAAGTTGAGCT
TTGAATTGGATATCCTTCGTTATGAAGTTGAAATCCAATCTAGAGATGGATGTTGCTTG
Found at i:31706 original size:125 final size:125
Alignment explanation
Indices: 31552--31783 Score: 358
Period size: 125 Copynumber: 1.9 Consensus size: 125
31542 GTGAAGTTGA
* * *
31552 GCTTTGAATTAGATATCCTTCGTTGTGAAGTTGAAAACCAA-TGGTTGTTTCACCAAATTGGTTT
1 GCTTTGAATTAGATATCCTTCGTTCTGAAGTTGAAAACCAAGT-ATTGTTTCACCAAATTGGCTT
*
31616 TGAGTTGGATATCCTTCGTCCTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
65 TGAGTTGGATATCCTTCGTCCTGAAATTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
* * *
31677 GCTTTGAGTTAGATATCCTTCGTTCTGAAGTTGAAATCCAAGTATTGTTTTACCAAATTGGCTTT
1 GCTTTGAATTAGATATCCTTCGTTCTGAAGTTGAAAACCAAGTATTGTTTCACCAAATTGGCTTT
* **
31742 GATTTGGATATCCTTCGTTGTGAAATTGAAATCCAATCTTGA
66 GAGTTGGATATCCTTCGTCCTGAAATTGAAATCCAATCTTGA
31784 ATATTGTTTG
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
125 95 0.99
126 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (125 bp):
GCTTTGAATTAGATATCCTTCGTTCTGAAGTTGAAAACCAAGTATTGTTTCACCAAATTGGCTTT
GAGTTGGATATCCTTCGTCCTGAAATTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
Found at i:31815 original size:57 final size:59
Alignment explanation
Indices: 31552--31838 Score: 283
Period size: 60 Copynumber: 4.8 Consensus size: 59
31542 GTGAAGTTGA
* * * * *
31552 GCTTTGAATTAGATATCCTTCGTTGTGAAGTTGAAAACCAATGGTTGT-TTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAAT-CTTGTAAT-ACCAAATTG
* **
31612 GTTTTGAGTTGGATATCCTTCGTCCTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTT--GTAA---T-ACCAAATTG
* * * **
31677 GCTTTGAGTTAGATATCCTTCGTTCTGAAGTTGAAATCCAAGTATTGTTTTACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAA-TCTTGTAATACCAAATTG
* * ****
31737 GCTTTGATTTGGATATCCTTCGTTGTGAAATTGAAATCCAATCTTG-AATA-TTGTTTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTAATACCAAATTG
* *
31794 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTAAAATCTAATCTT
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTT
31839 TTGCAAGTTG
Statistics
Matches: 191, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
57 44 0.23
58 2 0.01
59 6 0.03
60 82 0.43
61 3 0.02
64 2 0.01
65 49 0.26
66 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40
Consensus pattern (59 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTAATACCAAATTG
Found at i:32545 original size:32 final size:32
Alignment explanation
Indices: 32504--32571 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
32494 TTCACATCTG
* *
32504 GATGTTGAATCCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCCCCAAAGACGCCCCAACATTC
* *
32536 GATGTTGAATCTCCAAAGACGCCCCAACATTT
1 GATGTTGAATCCCCAAAGACGCCCCAACATTC
32568 GATG
1 GATG
32572 ATTCAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGACGCCCCAACATTC
Found at i:40245 original size:46 final size:46
Alignment explanation
Indices: 40178--40271 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
40168 TTGAAGGGTC
40178 GAATAACAAGAGAAAAGTCGAATAAAAAGCAATGCATTCATTTGTT
1 GAATAACAAGAGAAAAGTCGAATAAAAAGCAATGCATTCATTTGTT
* * * *
40224 GAATAACGAGAGAAAAGTCGAATATAAATCGATGCATTCATTTGTT
1 GAATAACAAGAGAAAAGTCGAATAAAAAGCAATGCATTCATTTGTT
40270 GA
1 GA
40272 TTATCGACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.26
Consensus pattern (46 bp):
GAATAACAAGAGAAAAGTCGAATAAAAAGCAATGCATTCATTTGTT
Found at i:41009 original size:85 final size:85
Alignment explanation
Indices: 40866--41035 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 85
40856 AACATCAGCT
* *
40866 CATACCACTAACATTTTAGTTTAAAGCCTAAAAAATAATGTTAACACCGAGAAACCTACTCGATA
1 CATACCACTAACAATTTAGTTTAAAGCCTAAAAAATAATGTTAACACCGACAAACCTACTCGATA
40931 GTACCTCTAAGGAGCATCTG
66 GTACCTCTAAGGAGCATCTG
*
40951 CATACCACTACCAATTTAGTTTAAAGCCTAAAAAATAATGTTAACACCGACAAACCTACTCGATA
1 CATACCACTAACAATTTAGTTTAAAGCCTAAAAAATAATGTTAACACCGACAAACCTACTCGATA
41016 GTACCTCTAAGGAGCATCTG
66 GTACCTCTAAGGAGCATCTG
41036 ACGTCCTCAA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (85 bp):
CATACCACTAACAATTTAGTTTAAAGCCTAAAAAATAATGTTAACACCGACAAACCTACTCGATA
GTACCTCTAAGGAGCATCTG
Found at i:44829 original size:88 final size:88
Alignment explanation
Indices: 44616--44887 Score: 357
Period size: 88 Copynumber: 3.0 Consensus size: 88
44606 TTAGAACTGC
* * *
44616 ATTCATAGGGCTTACCCTAAGCACATAGCAAAAAGGGAGCCAACCTAAGGATATACCTTGGGGCC
1 ATTCGTAGGG-TTACCCTAAGCACACAGC--AAAGGGAACCAACCTAAGGATATACCTTGGGGCC
*
44681 TATGGGCCTACCCATGGAGGATATACTTAG
63 TATGGGCC-ACCCA---AGGATATCCTTAG
*
44711 ATTCGTAGGGTTACCCTAAGCACACAGCAAAGGGAACCAACCTAAGGATATACCATGGGGCCTAT
1 ATTCGTAGGGTTACCCTAAGCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTAT
44776 GGGCCACCCAAGGATATCCTTAG
66 GGGCCACCCAAGGATATCCTTAG
* * *
44799 A-TCTGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGAGGCCTA
1 ATTC-GTAGGGTTACCCTAAGCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTA
* * *
44863 TGGGCTTACCTAAGGGTATCCTTAG
65 TGGGC-CACCCAAGGATATCCTTAG
44888 GTCCGTAAGG
Statistics
Matches: 163, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
87 2 0.01
88 74 0.45
89 16 0.10
91 5 0.03
92 40 0.25
94 17 0.10
95 9 0.06
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (88 bp):
ATTCGTAGGGTTACCCTAAGCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTAT
GGGCCACCCAAGGATATCCTTAG
Found at i:45279 original size:25 final size:24
Alignment explanation
Indices: 45223--45279 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
45213 ATCATAAAAC
* * **
45223 CATAGTTCATAAATTAGTAACTTT
1 CATATTTCATAAATTAGAAAAATT
45247 CATGATTTCATAAATTAGGAAAAATT
1 CAT-ATTTCATAAATTA-GAAAAATT
45273 CATATTT
1 CATATTT
45280 TCGGTGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 3 0.11
25 16 0.59
26 8 0.30
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (24 bp):
CATATTTCATAAATTAGAAAAATT
Found at i:46389 original size:23 final size:23
Alignment explanation
Indices: 46359--46407 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
46349 CATTTACTAA
46359 GTCTAGGCCATAAGGGTATGTTG
1 GTCTAGGCCATAAGGGTATGTTG
46382 GTCTAGGCCATAAGGGTATGTTG
1 GTCTAGGCCATAAGGGTATGTTG
46405 GTC
1 GTC
46408 ATTTGGTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.35, T:0.31
Consensus pattern (23 bp):
GTCTAGGCCATAAGGGTATGTTG
Found at i:47741 original size:18 final size:17
Alignment explanation
Indices: 47715--47748 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
47705 ACGGTCAACG
*
47715 GGTCGGGTCAACAGGTCA
1 GGTCAGGTCAAC-GGTCA
47733 GGTCAGGTCAACGGTC
1 GGTCAGGTCAACGGTC
47749 CGATCAAACG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.21, C:0.24, G:0.38, T:0.18
Consensus pattern (17 bp):
GGTCAGGTCAACGGTCA
Found at i:47764 original size:21 final size:23
Alignment explanation
Indices: 47738--47792 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
47728 GGTCAGGTCA
47738 GGTCAACGGTCCGA-TCAAA-CG
1 GGTCAACGGTCCGAGTCAAACCG
*
47759 GGTCAACGAT-CGAGTCAAACCG
1 GGTCAACGGTCCGAGTCAAACCG
*
47781 GGTCAACTGTCC
1 GGTCAACGGTCC
47793 CAACTGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.11
21 14 0.50
22 10 0.36
23 1 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.16
Consensus pattern (23 bp):
GGTCAACGGTCCGAGTCAAACCG
Found at i:49874 original size:89 final size:88
Alignment explanation
Indices: 49707--49982 Score: 372
Period size: 89 Copynumber: 3.1 Consensus size: 88
49697 TAGAAATACG
* *
49707 TCCGTAGGGCTTACCCTAAGCACATAGCAAAAAGGGAGCCAACTTAAGGATATACCTTGGGGCCT
1 TCCGTAGGG-TTACCCTAAGCAC--A-CAAAAAGGGAACCAACCTAAGGATATACCTTGGGGCCT
49772 ATGGGCCTACCTAAGGATATCCTTAGA
62 ATGGGCCTACCTAAGGATATCCTTAGA
* * * *
49799 TCTGTAGGGTTACCCTAAGCACACAATAAAGGGAACTAACCTAAGTATATACATTGGGGCCTATG
1 TCCGTAGGGTTACCCTAAGCACACAA-AAAGGGAACCAACCTAAGGATATACCTTGGGGCCTATG
* *
49864 GGCCTGCCTAAGGATATTCTTAGA
65 GGCCTACCTAAGGATATCCTTAGA
* * *
49888 TCCGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTATG
1 TCCGTAGGGTTACCCTAAGCACACA-AAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTATG
* * *
49953 GGCTTACCCAAGGGTATCCTTAGA
65 GGCCTACCTAAGGATATCCTTAGA
49977 TCCGTA
1 TCCGTA
49983 AGGTCTTACC
Statistics
Matches: 162, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
88 3 0.02
89 138 0.85
91 13 0.08
92 8 0.05
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (88 bp):
TCCGTAGGGTTACCCTAAGCACACAAAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTATGG
GCCTACCTAAGGATATCCTTAGA
Found at i:52797 original size:14 final size:15
Alignment explanation
Indices: 52778--52806 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52768 TTTAATGATT
52778 GGGTCAAAC-GGGTC
1 GGGTCAAACTGGGTC
52792 GGGTCAAACTGGGTC
1 GGGTCAAACTGGGTC
52807 AACTTCCCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.21, G:0.41, T:0.17
Consensus pattern (15 bp):
GGGTCAAACTGGGTC
Found at i:54198 original size:89 final size:89
Alignment explanation
Indices: 54045--54319 Score: 363
Period size: 89 Copynumber: 3.1 Consensus size: 89
54035 CAGAACTGCG
* *
54045 TCCGTAGGGCTTACCCTAAGCACATAGCAAAAAGGGAGCCAACCTAAGGATATA-CTTGGGGCCT
1 TCCGTAGGG-TTACCCTAAGCACATAG-AAAAA-GGAACTAACCTAAGGATATACCTTGGGGCCT
54109 ATGGGCCTACCCAAGGATATCCTTAGA
63 ATGGGCCTACCCAAGGATATCCTTAGA
* * * * * * *
54136 TCCGTATGGTTACCCTAAGCACACAGTAAAAGGATCTAACCTAAGCATATACCTTGGAGCCTATT
1 TCCGTAGGGTTACCCTAAGCACATAGAAAAAGGAACTAACCTAAGGATATACCTTGGGGCCTATG
54201 GGCCTACCCAAGGATATCCTTAGA
66 GGCCTACCCAAGGATATCCTTAGA
* * * * * *
54225 TCCGTAGGGTTACCTTAAGCACATAGCAAAGGGAACTAGCCTAAGGATATGCCTTGGGGACTATG
1 TCCGTAGGGTTACCCTAAGCACATAGAAAAAGGAACTAACCTAAGGATATACCTTGGGGCCTATG
* *
54290 GGCCTACCCAAGGGTATCCTTAGG
66 GGCCTACCCAAGGATATCCTTAGA
54314 TCCGTA
1 TCCGTA
54320 AGGTCTTACC
Statistics
Matches: 161, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
88 17 0.11
89 120 0.75
90 16 0.10
91 8 0.05
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (89 bp):
TCCGTAGGGTTACCCTAAGCACATAGAAAAAGGAACTAACCTAAGGATATACCTTGGGGCCTATG
GGCCTACCCAAGGATATCCTTAGA
Found at i:55035 original size:26 final size:26
Alignment explanation
Indices: 54999--55107 Score: 200
Period size: 26 Copynumber: 4.2 Consensus size: 26
54989 CATCAGGAAA
54999 GTGTTCAATAATTCGCGGAGTGATTT
1 GTGTTCAATAATTCGCGGAGTGATTT
55025 GTGTTCAATAATTCGCGGAGTGATTT
1 GTGTTCAATAATTCGCGGAGTGATTT
*
55051 GTGTTCAATAATTCGTGGAGTGATTT
1 GTGTTCAATAATTCGCGGAGTGATTT
*
55077 GTGTTCAATAATTCACGGAGTGATTT
1 GTGTTCAATAATTCGCGGAGTGATTT
55103 GTGTT
1 GTGTT
55108 GTTAAAGAAG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (26 bp):
GTGTTCAATAATTCGCGGAGTGATTT
Found at i:57428 original size:23 final size:22
Alignment explanation
Indices: 57398--57479 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 22
57388 GCATGGCCTT
57398 GTGCATCGATGCACATTTAAGG
1 GTGCATCGATGCACATTTAAGG
* * * *
57420 AGTGCATCGGTGCAC-CTTCATG
1 -GTGCATCGATGCACATTTAAGG
* * *
57442 GTGTATTGATGCACATTCAAGGG
1 GTGCATCGATGCACATTTAA-GG
57465 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
57480 TGTTAGGTGT
Statistics
Matches: 43, Mismatches: 13, Indels: 5
0.70 0.21 0.08
Matches are distributed among these distances:
21 11 0.26
22 6 0.14
23 15 0.35
24 11 0.26
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTTAAGG
Found at i:57489 original size:44 final size:44
Alignment explanation
Indices: 57402--57498 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
57392 GGCCTTGTGC
* *
57402 ATCGATGCACATTTAAGGAGTGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGAGTGCATCGATGCACCTTCATGGTGT
* * *
57446 ATTGATGCACATTCAAGGGGATGCATCGATGCA-CTGTTA-GGTGT
1 ATCGATGCACATTCAAGGAG-TGCATCGATGCACCT-TCATGGTGT
57490 ATCGATGCA
1 ATCGATGCA
57499 TTACGCACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 32 0.71
45 13 0.29
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAGTGCATCGATGCACCTTCATGGTGT
Found at i:61330 original size:22 final size:21
Alignment explanation
Indices: 61288--61327 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61278 GAGTTTATTT
*
61288 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
61309 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
61328 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:67501 original size:65 final size:65
Alignment explanation
Indices: 67377--67536 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
67367 TGCACTAAGA
* *
67377 GTGCATCGATGCATAAAATGCATACGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGGCT-
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGG-TA
67440 G
65 G
* *
67441 GTGCATCGAAGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCCTGAGTGCATCGATGCATGGTA
*
67505 T
65 G
* *
67506 GTACATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
67537 CAATTTATTT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 27 0.32
65 55 0.65
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGTAG
Found at i:67578 original size:65 final size:65
Alignment explanation
Indices: 67377--67578 Score: 216
Period size: 65 Copynumber: 3.1 Consensus size: 65
67367 TGCACTAAGA
* * *
67377 GTGCATCGATGCATAAAATGCATACGATGTTTCAA-AATAGCCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAATAATACCCTGAGTGCATCGATGCATGGTTG
* * *
67441 GTGCATCGAAGCATCAAATGCATTCGATGTTTTC-ATAAAACCCTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAATAATACCCTGAGTGCATCGATGCATGGT-
67505 T-
64 TG
* * * ** * *
67506 GTACATCGATGCATGAAATGCATTCGATG-TTCAATTTATTTCATG-GTGCATCAATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA-TAATACCCTGAGTGCATCGATGCATGG-T
67569 TG
64 TG
67571 GTGCATCG
1 GTGCATCG
67579 GTGTATCACT
Statistics
Matches: 115, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
63 3 0.03
64 44 0.38
65 67 0.58
66 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAATAATACCCTGAGTGCATCGATGCATGGTTG
Found at i:68158 original size:95 final size:95
Alignment explanation
Indices: 67988--68167 Score: 263
Period size: 95 Copynumber: 1.9 Consensus size: 95
67978 ATATTATAAA
* *
67988 CACCTTTATCAGGTTAGCTAAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTGCCTTAGAGA
1 CACCTTTATCAGGCTAGCTAAATCTTATCCATAAAATCGGGGCGTTTAACCAATTGCCTTAGAGA
*
68053 GACAACTCAAGCTTTATTGTATAGTATAGT
66 GACAACTCAAGCTTAATTGTATAGTATAGT
* * *
68083 CACCTTTATCATGCTAGCTGAATCTTATCCATAAAATCGGGGTGTTTAACCAATTG-CTCTAGAG
1 CACCTTTATCAGGCTAGCTAAATCTTATCCATAAAATCGGGGCGTTTAACCAATTGCCT-TAGAG
* **
68147 GGACAGTTCAAGCTTAATTGT
65 AGACAACTCAAGCTTAATTGT
68168 GTATATATAA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
94 2 0.03
95 73 0.97
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (95 bp):
CACCTTTATCAGGCTAGCTAAATCTTATCCATAAAATCGGGGCGTTTAACCAATTGCCTTAGAGA
GACAACTCAAGCTTAATTGTATAGTATAGT
Found at i:71989 original size:15 final size:15
Alignment explanation
Indices: 71945--71991 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
71935 AAAAGAGTAG
*
71945 TAAAAATATATAAAA
1 TAAAAATAAATAAAA
* *
71960 TAAAGA-AAGTAAAAA
1 TAAAAATAAAT-AAAA
71975 TAAAAATAAATAAAA
1 TAAAAATAAATAAAA
71990 TA
1 TA
71992 CATAAAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 2 0.08
15 20 0.80
16 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (15 bp):
TAAAAATAAATAAAA
Found at i:72186 original size:6 final size:6
Alignment explanation
Indices: 72165--72281 Score: 53
Period size: 6 Copynumber: 19.2 Consensus size: 6
72155 AAAATAATGA
* * ** *
72165 AAAAAT TAAAAT -AAAAT AAAAAT AAGATAT ATAAAAT -AAAAT GTATAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT A-AAAAT AAAAAT AAAAAT
* * * * * *
72213 AAATAAT AATAAT AATAAT AAAGACT AAAGAAT AATAA- AATAAT ATAGAA-
1 AAA-AAT AAAAAT AAAAAT AAA-AAT AAA-AAT AAAAAT AAAAAT A-AAAAT
72263 AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT A
72282 GTATAATGTA
Statistics
Matches: 87, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
5 18 0.21
6 44 0.51
7 24 0.28
8 1 0.01
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (6 bp):
AAAAAT
Found at i:72200 original size:15 final size:15
Alignment explanation
Indices: 72165--72234 Score: 54
Period size: 15 Copynumber: 4.6 Consensus size: 15
72155 AAAATAATGA
*
72165 AAAAATTAAAATAAAAT
1 AAAAA-TAAAAT-ATAT
*
72182 AAAAATAAGATATAT
1 AAAAATAAAATATAT
*
72197 -AAAATAAAATGTAT
1 AAAAATAAAATATAT
*
72211 ATAAATAATAATA-AT
1 AAAAATAA-AATATAT
*
72226 AATAATAAA
1 AAAAATAAA
72235 GACTAAAGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
14 13 0.30
15 17 0.40
16 8 0.19
17 5 0.12
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AAAAATAAAATATAT
Found at i:72214 original size:25 final size:23
Alignment explanation
Indices: 72171--72278 Score: 69
Period size: 25 Copynumber: 4.4 Consensus size: 23
72161 ATGAAAAAAT
72171 TAAAATAAAATAAAAATAAGATATA
1 TAAAATAAAATAAAAATAA-ATA-A
** *
72196 TAAAATAAAATGTATATAAATAA
1 TAAAATAAAATAAAAATAAATAA
*
72219 TAATAATAATAATAAAGACTAAAGAATAA
1 TAA-AATAA-AATAAA-A--ATA-AATAA
*
72248 TAAAATAATATAGAAAA-AAAT-A
1 TAAAATAAAATA-AAAATAAATAA
72270 -AAAATAAAA
1 TAAAATAAAA
72279 ATAGTATAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
21 8 0.12
22 1 0.01
23 7 0.10
24 9 0.13
25 21 0.31
27 4 0.06
28 9 0.13
29 8 0.12
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (23 bp):
TAAAATAAAATAAAAATAAATAA
Found at i:72218 original size:20 final size:19
Alignment explanation
Indices: 72173--72230 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 19
72163 GAAAAAATTA
72173 AAATAAAATAAAAATAAGAT
1 AAATAAAAT-AAAATAAGAT
* * *
72193 ATATAAAATAAAATGTATAT
1 AAATAAAATAAAAT-AAGAT
72213 AAATAATAATAATAATAA
1 AAATAA-AATAA-AATAA
72231 TAAAGACTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 5 0.17
20 16 0.53
21 6 0.20
22 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
AAATAAAATAAAATAAGAT
Found at i:72269 original size:23 final size:25
Alignment explanation
Indices: 72217--72281 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
72207 GTATATAAAT
*
72217 AATAATAATAATAATAAAGACTAAAG
1 AATAATAATAATAATAAAGAC-AAAA
*
72243 AATAATAA-AATAATATAGA-AAAA
1 AATAATAATAATAATAAAGACAAAA
* *
72266 AATAAAAATAAAAATA
1 AATAATAATAATAATA
72282 GTATAATGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 10 0.29
24 6 0.18
25 10 0.29
26 8 0.24
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (25 bp):
AATAATAATAATAATAAAGACAAAA
Found at i:72357 original size:2 final size:2
Alignment explanation
Indices: 72350--72401 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
72340 AAATAATCAA
72350 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
*
72392 AT AT AA AT AT
1 AT AT AT AT AT
72402 GATAAAAGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72961 original size:17 final size:17
Alignment explanation
Indices: 72935--72970 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
72925 CAAAAAACGC
*
72935 CTCGTGGGGGTATGGAT
1 CTCGTAGGGGTATGGAT
72952 CTCGTAGGGGTATGGAT
1 CTCGTAGGGGTATGGAT
72969 CT
1 CT
72971 AGAAAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.14, G:0.42, T:0.31
Consensus pattern (17 bp):
CTCGTAGGGGTATGGAT
Found at i:73666 original size:2 final size:2
Alignment explanation
Indices: 73659--73687 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
73649 ATAAACATAA
73659 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73688 GTAATATGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74051 original size:34 final size:35
Alignment explanation
Indices: 74008--74080 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
73998 GTGGCATATG
* *
74008 CACATTGCTCAAACTGT-GTTTATGTAAACAAAAC
1 CACATTGCTCAAACTGTGGTTAATGTAAACAAAAA
* **
74042 CACATTGCTCCATGTGTGGTTAATGTAAACAAAAA
1 CACATTGCTCAAACTGTGGTTAATGTAAACAAAAA
74077 CACA
1 CACA
74081 CTCCTCTGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 14 0.42
35 19 0.58
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (35 bp):
CACATTGCTCAAACTGTGGTTAATGTAAACAAAAA
Found at i:78902 original size:18 final size:21
Alignment explanation
Indices: 78864--78906 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 21
78854 ATTTAATTAT
78864 TTTTTTTATTTGTTTATAATA
1 TTTTTTTATTTGTTTATAATA
78885 TTTTTTTA-TT-TTTA-AATA
1 TTTTTTTATTTGTTTATAATA
78903 TTTT
1 TTTT
78907 AGATGGCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.36
19 4 0.18
20 2 0.09
21 8 0.36
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTTTTATTTGTTTATAATA
Found at i:82263 original size:31 final size:31
Alignment explanation
Indices: 82210--82275 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
82200 AAATTACGTA
* * *
82210 TTTAGTATCTAAACAATCAGTTTTGTTCTGT
1 TTTAATATCTAAACAATCAGTTTTGGTATGT
* * *
82241 TTTAATATCTGAACATTTAGTTTTGGTATGT
1 TTTAATATCTAAACAATCAGTTTTGGTATGT
82272 TTTA
1 TTTA
82276 GCACTTAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.52
Consensus pattern (31 bp):
TTTAATATCTAAACAATCAGTTTTGGTATGT
Found at i:84345 original size:24 final size:24
Alignment explanation
Indices: 84313--84362 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
84303 TGATACAAGT
84313 ATCAATCATCCTAATCAGAATTAA
1 ATCAATCATCCTAATCAGAATTAA
84337 ATCAATCATCCTAATCAGAATTAA
1 ATCAATCATCCTAATCAGAATTAA
84361 AT
1 AT
84363 TTGGGGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (24 bp):
ATCAATCATCCTAATCAGAATTAA
Done.