Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004620.1 Hibiscus syriacus cultivar Beakdansim tig00010339_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: 78376
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:592 original size:48 final size:48
Alignment explanation
Indices: 509--706 Score: 192
Period size: 48 Copynumber: 4.2 Consensus size: 48
499 CTGTCACTCA
* * ** *
509 GGAATATCAAATCTTGAATG-AGAGGGATATATTCTG-TTTTTGTTGAAG
1 GGAATATCAAATCTTGAA-GAAGAGAGATATGTTCTGCTTACT-CTGAAG
* *
557 GGAATATCAAATCTTGAAGAAGAAAGACT-TGTTCTGCTTACTCCGAAG
1 GGAATATCAAATCTTGAAGAAGAGAGA-TATGTTCTGCTTACTCTGAAG
* * *
605 GGAATATCAAA--TTGGAGAAGAGAGATCTGTTCCGCTTACTCTGAAG
1 GGAATATCAAATCTTGAAGAAGAGAGATATGTTCTGCTTACTCTGAAG
** ** *
651 GGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAA-
1 GGAATATCAAATCTTGAAGAAGAGAGATATGTTCTGCTTACTCTGAAG
698 GGAATATCA
1 GGAATATCA
707 GATATGGGGG
Statistics
Matches: 129, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
45 1 0.01
46 40 0.31
47 10 0.08
48 74 0.57
49 4 0.03
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (48 bp):
GGAATATCAAATCTTGAAGAAGAGAGATATGTTCTGCTTACTCTGAAG
Found at i:642 original size:46 final size:46
Alignment explanation
Indices: 553--706 Score: 204
Period size: 48 Copynumber: 3.3 Consensus size: 46
543 TGTTTTTGTT
* *
553 GAAGGGAATATCAAATCTTGAAGAAGAAAGACTTGTTCTGCTTACTCC
1 GAAGGGAATATCAAA-CTTGAAGAAGAGAGAC-TGTTCCGCTTACTCC
* *
601 GAAGGGAATATCAAA-TTGGAGAAGAGAGATCTGTTCCGCTTACTCT
1 GAAGGGAATATCAAACTTGAAGAAGAGAGA-CTGTTCCGCTTACTCC
*
647 GAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCC
1 GAAGGGAATATCAAA-CTTGAAGAAGAGAGA-CTGTTCCGCTTACTCC
695 GAA-GGAATATCA
1 GAAGGGAATATCA
707 GATATGGGGG
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
46 40 0.42
47 10 0.11
48 45 0.47
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (46 bp):
GAAGGGAATATCAAACTTGAAGAAGAGAGACTGTTCCGCTTACTCC
Found at i:800 original size:45 final size:45
Alignment explanation
Indices: 734--863 Score: 172
Period size: 45 Copynumber: 2.8 Consensus size: 45
724 CCATTGAATC
*
734 GAAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAATCTTGGA
1 GAAG-AGACTTGTTCCACTTACTCTGAAGGGAATATCAATCTTGAA
* *
780 GAAGAGACTTGTTCCGCTTACT-TGAAGGGAATATCAAATTTTGAA
1 GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATC-AATCTTGAA
* *
825 GAAGAGAGACCTGTTCCACTTACTCCGAAGGGAATATCA
1 G-A-AGAGACTTGTTCCACTTACTCTGAAGGGAATATCA
864 GTCTGGGGGA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
44 13 0.18
45 25 0.34
46 5 0.07
47 19 0.26
48 12 0.16
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (45 bp):
GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAATCTTGAA
Found at i:855 original size:156 final size:159
Alignment explanation
Indices: 575--1136 Score: 872
Period size: 156 Copynumber: 3.6 Consensus size: 159
565 AAATCTTGAA
** * *
575 GAAGAAAGACTTGTTCTGCTTACTCCGAAGGGAATATCAAA--TTGGAGAAGAGAGATCTGTTCC
1 GAAG-AAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGA-CT-TGTTCC
638 GCTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAA-GGAA
63 GCTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAAGGGAA
*
702 TATCAGATATGGGGGAGTTAATCCATTGAATC
128 TATCAGATATGGGGGAGTTGATCCATTGAATC
734 GAAGAAGACTTGTTCCACTTACTCTGAAGGGAATATC-AATCTTGGAGAAGAGACTTGTTCCGCT
1 GAAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCGCT
*
798 TACT-TGAAGGGAATATCAAATTTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAAGGGAATAT
66 TACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAAGGGAATAT
*
862 CAG-TCTGGGGGAGTTGATCCATTGAATC
131 CAGATATGGGGGAGTTGATCCATTGAATC
*
890 GTAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCGCT
1 GAAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCGCT
* *
955 TACTCTGAAGGGAATATCAAATCTTGAAGAA-AGATACATGTTCCACTTACT-CGAAGGGAATAT
66 TACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAAGGGAATAT
*
1018 CAGATAT-GGGGAATTGATCCATTGAATC
131 CAGATATGGGGGAGTTGATCCATTGAATC
* * * *
1046 GAAGAAGACTTGTTCTACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCA
1 GAAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAG-A-AGAGACTTGTTCCG
*
1111 CTTACTCTGAAGGGAATATCAGATCT
64 CTTACTCTGAAGGGAATATCAAATCT
1137 GGGGGAGTTG
Statistics
Matches: 376, Mismatches: 19, Indels: 17
0.91 0.05 0.04
Matches are distributed among these distances:
156 190 0.51
157 77 0.20
158 93 0.25
159 16 0.04
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (159 bp):
GAAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCGCT
TACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAAGGGAATAT
CAGATATGGGGGAGTTGATCCATTGAATC
Found at i:957 original size:46 final size:47
Alignment explanation
Indices: 895--1019 Score: 200
Period size: 46 Copynumber: 2.7 Consensus size: 47
885 GAATCGTAGA
*
895 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAG-AAG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAAG
*
941 AGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGAAGAAAG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAAG
* *
988 ATACATGTTCCACTTACTC-GAAGGGAATATCA
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCA
1020 GATATGGGGA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
46 54 0.74
47 19 0.26
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (47 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAAG
Found at i:1055 original size:110 final size:112
Alignment explanation
Indices: 937--1157 Score: 358
Period size: 110 Copynumber: 2.0 Consensus size: 112
927 AAATCTTGGA
* *
937 GAAGAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGAAGAA-AGATACATGTTCCAC
1 GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACATGTTCCAC
1001 TTACTC-GAAGGGAATATCAGATAT-GGGGAATTGATCCATTGAATC
66 TTACTCTGAAGGGAATATCAGATATGGGGGAATTGATCCATTGAATC
* *
1046 GAAGAAGACTTGTTCTACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCA
1 GAAG-AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACATGTTCCA
* *
1111 CTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAAT
65 CTTACTCTGAAGGGAATATCAGATATGGGGGAATTGATCCATTGAAT
1158 TGGGATCAAA
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
109 4 0.04
110 43 0.42
111 19 0.19
112 17 0.17
113 19 0.19
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (112 bp):
GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACATGTTCCAC
TTACTCTGAAGGGAATATCAGATATGGGGGAATTGATCCATTGAATC
Found at i:1108 original size:48 final size:47
Alignment explanation
Indices: 1046--1136 Score: 146
Period size: 48 Copynumber: 1.9 Consensus size: 47
1036 CCATTGAATC
* *
1046 GAAGAAGACTTGTTCTACTTACTCTGAAGGGAATATCAAATCTTGAA
1 GAAGAAGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
*
1093 GAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGATCT
1 GAAGA-AGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCT
1137 GGGGGAGTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 5 0.12
48 35 0.88
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (47 bp):
GAAGAAGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
Found at i:2269 original size:15 final size:16
Alignment explanation
Indices: 2251--2289 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2241 TATTTTTTCC
**
2251 TCATTTTTTTTTC-TT
1 TCATTTTTTAGTCTTT
2266 TCATTTTTTAGTCTTT
1 TCATTTTTTAGTCTTT
2282 TCATTTTT
1 TCATTTTT
2290 ATTCAGGCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (16 bp):
TCATTTTTTAGTCTTT
Found at i:9306 original size:11 final size:11
Alignment explanation
Indices: 9292--9321 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
9282 TGCAATGTAG
9292 ATGCAATATGA
1 ATGCAATATGA
*
9303 ATGCAAAATGA
1 ATGCAATATGA
9314 ATGCAATA
1 ATGCAATA
9322 CAAGGTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (11 bp):
ATGCAATATGA
Found at i:14499 original size:34 final size:34
Alignment explanation
Indices: 14456--14523 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
14446 TCCACACGTT
* *
14456 TTAGTGGAGCAGTAACTGGAGATGAATTATCTAC
1 TTAGTGGAGCAATAACTGGAAATGAATTATCTAC
* *
14490 TTAGTGGAGCAATAACTGGAAATGAGTTGTCTAC
1 TTAGTGGAGCAATAACTGGAAATGAATTATCTAC
14524 ACCCCGAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (34 bp):
TTAGTGGAGCAATAACTGGAAATGAATTATCTAC
Found at i:16457 original size:119 final size:121
Alignment explanation
Indices: 16244--16566 Score: 449
Period size: 119 Copynumber: 2.7 Consensus size: 121
16234 ATATCCTTCG
* *
16244 TGAAG-TTAAATCGTAGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTGGGTATCCTTCGTT
1 TGAAGTTTAAATCGTGGATGGCTCATTCGTTGTGAA--TGAGCTTTGAATTGGATATCCTTCGTT
* *
16308 GTGAAGTTGAAATCTAATCTAGAGACGGATGCTGCTTGTGGGCAC-AGTATCCTTCGTCA
64 GTGAAGTTGAAATCCAATCTAGAGACGGATGCTGCATGTGGGCACGA-TAT-CTTCGTCA
* *
16367 TGAAGTTTAAATCGTGGATGACTCATTCATTGTGAA-G-GCTTTGAATTGGATATCCTT-GTTGT
1 TGAAGTTTAAATCGTGGATGGCTCATTCGTTGTGAATGAGCTTTGAATTGGATATCCTTCGTTGT
* * *
16429 GAAGTTGAAATCCAATCTAGAGATGGATGTTGCATGTGGGCACGATATCTTCGTCG
66 GAAGTTGAAATCCAATCTAGAGACGGATGCTGCATGTGGGCACGATATCTTCGTCA
* *
16485 TGAAGTTGAAATCGTGGATGGCTCTTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTT
1 TGAAGTTTAAATCGTGGATGGCTCATTCGTTGTGAA--TGAGCTTTGAATTGGATATCCTTCGTT
*
16550 GTGAAGTTAAAATCCAA
64 GTGAAGTTGAAATCCAA
16567 GGGTTGTTTC
Statistics
Matches: 179, Mismatches: 14, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
118 39 0.22
119 47 0.26
120 20 0.11
121 2 0.01
122 20 0.11
123 24 0.13
124 27 0.15
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (121 bp):
TGAAGTTTAAATCGTGGATGGCTCATTCGTTGTGAATGAGCTTTGAATTGGATATCCTTCGTTGT
GAAGTTGAAATCCAATCTAGAGACGGATGCTGCATGTGGGCACGATATCTTCGTCA
Found at i:16764 original size:64 final size:64
Alignment explanation
Indices: 16647--16941 Score: 452
Period size: 64 Copynumber: 4.6 Consensus size: 64
16637 TTACATTGTT
*
16647 TTGAGTCCAATATC-TTTGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
1 TTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
* * *
16710 TTGAGTCCAATATCATTTGTTGT-AAGTTGAAATTGATTTTGAAATGAAACTGGAAAGTTGTTTG
1 TTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTG-AATGAAACTGGAAAGTTGTTTG
* * * *
16774 TTGAGTCCAATATCCTTCGTTGTGAAATTGAAATTGACTCTAAATGAAACTGG-AAGTTATTTG
1 TTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
* * *
16837 TTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTTTGAATGAATCTGGAAAGTTGTTTG
1 TTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
*
16901 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
1 TTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCT
16942 AAAAGCTGCA
Statistics
Matches: 209, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
63 86 0.41
64 109 0.52
65 14 0.07
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (64 bp):
TTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
Found at i:16891 original size:127 final size:128
Alignment explanation
Indices: 16647--16944 Score: 494
Period size: 127 Copynumber: 2.3 Consensus size: 128
16637 TTACATTGTT
* * *
16647 TTGAGTCCAATAT-CTTTGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGT
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAGTTATTTGT
* * *
16711 TGAGTCCAATATCATTTGTTGTAAGTTGAAATTGATTTTGAAATGAAACTGGAAAGTTGTTTG
66 TGAGTCCAATATCATTCGCTGTAAGTTGAAATTGACTTTGAAATGAAACTGGAAAGTTGTTTG
*
16774 TTGAGTCCAATATCCTTCGTTGTGAAATTGAAATTGACTCTAAATGAAACTGG-AAGTTATTTGT
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAGTTATTTGT
*
16838 TGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTTTG-AATGAATCTGGAAAGTTGTTTG
66 TGAGTCCAATATCATTCGCTGT-AAGTTGAAATTGACTTTGAAATGAAACTGGAAAGTTGTTTG
16901 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAA
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAA
16945 AGCTGCAAAA
Statistics
Matches: 160, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
127 107 0.67
128 53 0.33
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (128 bp):
TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAGTTATTTGT
TGAGTCCAATATCATTCGCTGTAAGTTGAAATTGACTTTGAAATGAAACTGGAAAGTTGTTTG
Found at i:18063 original size:99 final size:99
Alignment explanation
Indices: 17896--18084 Score: 299
Period size: 99 Copynumber: 1.9 Consensus size: 99
17886 ATATAAACAT
* * **
17896 CTTTATCAGGTTAGTTGAATCTTATCCATAAAGCCAGGGTGTTTAACCAATTGCCTTAGAGGGGC
1 CTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGTGTTTAACCAATTGCCTTAGAGGAAC
17961 AACTCAAGCTTTATTGTATAGATATTATAATCGC
66 AACTCAAGCTTTATTGTATAGATATTATAATCGC
* *
17995 CTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGTGTTTAACCAATTG-CTCTAGATGAA
1 CTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGTGTTTAACCAATTGCCT-TAGAGGAA
*
18059 CAACTCAAGCTTTATTGTATATATAT
65 CAACTCAAGCTTTATTGTATAGATAT
18085 AATATTATAA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 2 0.02
99 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (99 bp):
CTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGTGTTTAACCAATTGCCTTAGAGGAAC
AACTCAAGCTTTATTGTATAGATATTATAATCGC
Found at i:23215 original size:20 final size:20
Alignment explanation
Indices: 23186--23226 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
23176 GTTGTGGTTG
*
23186 TTGCCGAGGAAACCGACGGT
1 TTGCCAAGGAAACCGACGGT
23206 TTGCCAAGGAAACCGACGGT
1 TTGCCAAGGAAACCGACGGT
23226 T
1 T
23227 GACCGAGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.32, T:0.17
Consensus pattern (20 bp):
TTGCCAAGGAAACCGACGGT
Found at i:23425 original size:2 final size:2
Alignment explanation
Indices: 23420--23444 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23410 TGTGTAAATA
23420 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
23445 AACAAGGACG
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:27384 original size:31 final size:32
Alignment explanation
Indices: 27347--27421 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
27337 TTAATCTGAA
**
27347 TTTTTAAAATTTTTGAGGGATC-AAATTA-AAT
1 TTTTTAAAATTTTT-AAAGATCTAAATTATAAT
* *
27378 TTTTTAAAAATTGTAAAGATCTAAATTATAAT
1 TTTTTAAAATTTTTAAAGATCTAAATTATAAT
27410 TTTTT-AAATTTT
1 TTTTTAAAATTTT
27422 AGAAGGACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 5 0.14
31 23 0.64
32 8 0.22
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (32 bp):
TTTTTAAAATTTTTAAAGATCTAAATTATAAT
Found at i:28656 original size:16 final size:16
Alignment explanation
Indices: 28631--28674 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
28621 TAAAAACGTC
28631 TTTTAA-AAAAAACAA
1 TTTTAAGAAAAAACAA
* *
28646 TTTTAAGAAAAATCAT
1 TTTTAAGAAAAAACAA
28662 TTTTAAGACAAAA
1 TTTTAAGA-AAAA
28675 TTGATATGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.32
Consensus pattern (16 bp):
TTTTAAGAAAAAACAA
Found at i:30674 original size:15 final size:16
Alignment explanation
Indices: 30654--30690 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
30644 CAAACATATG
*
30654 TAATAAAAT-TATTAA
1 TAATAAAATATAATAA
30669 TAATAAAATATAATAA
1 TAATAAAATATAATAA
30685 TAATAA
1 TAATAA
30691 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAAAATATAATAA
Found at i:31347 original size:136 final size:136
Alignment explanation
Indices: 31108--31716 Score: 831
Period size: 136 Copynumber: 4.4 Consensus size: 136
31098 AACAAGTTAA
* *
31108 TTCTCATTATGAAC-T-TTCT--C-CTTTAGGACGAGTTCTTCTCATTATGAACTCT---TCTGG
1 TTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTCAAT-TGG
* *
31165 AAATGTCAATCCCTCATGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGGTCGAA
65 AAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAA
* *
31230 TAAGCTA
130 CAAGCTC
* *
31237 TTCTCATTATGAACTTCTTCTCCCAT-TGTCGGATGAGTTCTTCTCATTATGAACTCTCAATTGT
1 TTCTCATTATGAACTTCTTCTCCC-TCTTTCGGATGAGTTCTTCTCATTATGAACTCTCAATTGG
31301 AAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAA
65 AAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAA
*
31366 CAAGATC
130 CAAGCTC
* *
31373 TTCTTATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGA
1 TTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTCAATTGGA
* *
31438 AATGTCAATCCCTCAAGCGAGGTGCCACTGATTCGAAATGCCCTGAATCGAGTGATAGGTCGAAC
66 AATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAAC
31503 AAGCTC
131 AAGCTC
* *
31509 TTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTATTCTCATTATGAACTCTCAATTAGA
1 TTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTCAATTGGA
*
31574 AATGTCAATCCCTCAAACGAGGTGTCACTGATTCGAAATGCCCTGATTTGAAATGACGTGAATCG
66 AATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATG--C-------------CGTGAATCG
*
31639 AGTGATAGGGCGAACAAGCTC
116 AGTGATAGGTCGAACAAGCTC
* *
31660 TTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTTTCATTATGAACTCT
1 TTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCT
31717 GTACTGGAAA
Statistics
Matches: 428, Mismatches: 27, Indels: 28
0.89 0.06 0.06
Matches are distributed among these distances:
129 14 0.03
130 1 0.00
131 4 0.01
133 1 0.00
134 28 0.07
135 1 0.00
136 295 0.69
137 1 0.00
138 1 0.00
151 82 0.19
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (136 bp):
TTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTCAATTGGA
AATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCGAAC
AAGCTC
Found at i:31920 original size:90 final size:88
Alignment explanation
Indices: 31767--31995 Score: 368
Period size: 90 Copynumber: 2.5 Consensus size: 88
31757 TTTCAGACAA
* * *
31767 ATGACCCGAAGGATTTAAAAATCAAGAAACCCCCGAAAGCTCAGTTTCTTAAATCTTATTTGAAA
1 ATGA-CCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTC-TAAATCTCATTTGAAA
31832 ACATCCTGCACTGAAGGTCTTATGG
64 ACATCCTGCACTGAAGGTCTTATGG
*
31857 ATGACTCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAGATCTCATTTGAAA
1 ATGAC-CGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTAA-ATCTCATTTGAAA
31922 ACATCCTGCACTGAAGGTCTTATGG
64 ACATCCTGCACTGAAGGTCTTATGG
*
31947 ATGGCCTGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCT
1 ATGACC-GAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCT
31996 TAATTATCAC
Statistics
Matches: 130, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
89 5 0.04
90 125 0.96
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (88 bp):
ATGACCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTAAATCTCATTTGAAAAC
ATCCTGCACTGAAGGTCTTATGG
Found at i:32112 original size:43 final size:43
Alignment explanation
Indices: 32047--32350 Score: 293
Period size: 43 Copynumber: 7.1 Consensus size: 43
32037 TAAGTGTTCA
* *
32047 TCAAGTTTGTAATC-AAGAAACCCCTACATATCACGATGATCTC
1 TCAAGCTTGTCATCAAAG-AACCCCTACATATCACGATGATCTC
* * *
32090 TCAAGCATATCATCAAAGAACCCCTACATATCACGATGCTC-C
1 TCAAGCTTGTCATCAAAGAACCCCTACATATCACGATGATCTC
* * *
32132 TTTAAGCTTGTTATCAAGGAACCCCTACATATCACGATGATC-C
1 -TCAAGCTTGTCATCAAAGAACCCCTACATATCACGATGATCTC
* *
32175 TTCAAGCTTATCATC-AAGAAACCCCTACATATCACGAT-AACTTC
1 -TCAAGCTTGTCATCAAAG-AACCCCTACATATCACGATGATC-TC
*
32219 TCAAGCTTGTCATCAAAGAACCCCTA-ATATCACGATGGACCT-
1 TCAAGCTTGTCATCAAAGAACCCCTACATATCACGAT-GATCTC
* * * *
32261 TTAAGCTTGTCATCAAGGAACCTCTACATATCACGATGGTC-C
1 TCAAGCTTGTCATCAAAGAACCCCTACATATCACGATGATCTC
* * * * *
32303 TTCAAGCTTTTCATC-AAGAAACCCTTGCATATCACGATGGTTTC
1 -TCAAGCTTGTCATCAAAG-AACCCCTACATATCACGATGATCTC
32347 TCAA
1 TCAA
32351 AATATTGTGT
Statistics
Matches: 218, Mismatches: 30, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
42 42 0.19
43 166 0.76
44 10 0.05
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (43 bp):
TCAAGCTTGTCATCAAAGAACCCCTACATATCACGATGATCTC
Found at i:32203 original size:86 final size:86
Alignment explanation
Indices: 32047--32341 Score: 352
Period size: 86 Copynumber: 3.4 Consensus size: 86
32037 TAAGTGTTCA
* * *
32047 TCAAGTTTGTAATCAAGAAACCCCTACATATCACGATGAT-CTCTCAAGCATATCATCAA-AGAA
1 TCAAGCTTGTTATCAAGAAACCCCTACATATCACGATGATCCT-TCAAGCTTATCATCAAGA-AA
32110 CCCCTACATATCACGATGCTCCT
64 CCCCTACATATCACGATGCTCCT
* *
32133 TTAAGCTTGTTATCAAGGAACCCCTACATATCACGATGATCCTTCAAGCTTATCATCAAGAAACC
1 TCAAGCTTGTTATCAAGAAACCCCTACATATCACGATGATCCTTCAAGCTTATCATCAAGAAACC
* *
32198 CCTACATATCACGATAACTTC-
66 CCTACATATCACGAT-GCTCCT
* * * *
32219 TCAAGCTTGTCATCAA-AGAACCCCTA-ATATCACGATGGA-CCTTTAAGCTTGTCATCAAGGAA
1 TCAAGCTTGTTATCAAGA-AACCCCTACATATCACGAT-GATCCTTCAAGCTTATCATCAAGAAA
* *
32281 CCTCTACATATCACGATGGTCCT
64 CCCCTACATATCACGATGCTCCT
* *
32304 TCAAGCTT-TTCATCAAGAAACCCTTGCATATCACGATG
1 TCAAGCTTGTT-ATCAAGAAACCCCTACATATCACGATG
32342 GTTTCTCAAA
Statistics
Matches: 180, Mismatches: 20, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
84 3 0.02
85 66 0.37
86 105 0.58
87 6 0.03
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (86 bp):
TCAAGCTTGTTATCAAGAAACCCCTACATATCACGATGATCCTTCAAGCTTATCATCAAGAAACC
CCTACATATCACGATGCTCCT
Found at i:32348 original size:128 final size:129
Alignment explanation
Indices: 32058--32350 Score: 453
Period size: 128 Copynumber: 2.3 Consensus size: 129
32048 CAAGTTTGTA
*
32058 ATCAAGAAACCCCTACATATCACGATGATCTCTCAAGCATATCATCAAAGAACCCCTACATATCA
1 ATCAAGAAACCCCTACATATCACGATGATTTCTCAAGCATATCATCAAAGAACCCCTACATATCA
* *
32123 CGATGCTCCTTTAAGCTTGTTATCAAGGAACCCCTACATATCACGATGATCCTTCAAGCTTATC
66 CGATGCACCTTTAAGCTTGTCATCAAGGAACCCCTACATATCACGATGATCCTTCAAGCTTATC
* * * *
32187 ATCAAGAAACCCCTACATATCACGATAACTTCTCAAGCTTGTCATCAAAGAACCCCTA-ATATCA
1 ATCAAGAAACCCCTACATATCACGATGATTTCTCAAGCATATCATCAAAGAACCCCTACATATCA
* * * *
32251 CGATGGACCTTTAAGCTTGTCATCAAGGAACCTCTACATATCACGATGGTCCTTCAAGCTTTTC
66 CGATGCACCTTTAAGCTTGTCATCAAGGAACCCCTACATATCACGATGATCCTTCAAGCTTATC
* * *
32315 ATCAAGAAACCCTTGCATATCACGATGGTTTCTCAA
1 ATCAAGAAACCCCTACATATCACGATGATTTCTCAA
32351 AATATTGTGT
Statistics
Matches: 148, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
128 95 0.64
129 53 0.36
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (129 bp):
ATCAAGAAACCCCTACATATCACGATGATTTCTCAAGCATATCATCAAAGAACCCCTACATATCA
CGATGCACCTTTAAGCTTGTCATCAAGGAACCCCTACATATCACGATGATCCTTCAAGCTTATC
Found at i:32452 original size:36 final size:36
Alignment explanation
Indices: 32358--32658 Score: 265
Period size: 36 Copynumber: 8.3 Consensus size: 36
32348 CAAAATATTG
* * *
32358 TGTTTCGAGTGAAACTATCTCAA-ACGAGATAAAAGCTT
1 TGTTTCAAGGGAAACTGTCTCAAGA-GAGATAAAA--TT
* *
32396 CTGTTTCAAGTGAAATTGTCTCAAGAGAGATAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATT
* *
32433 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATT
* * *
32469 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAACATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATT
* * * *
32505 TGTTTCAAGTGAAATTGTCTC-A-AG-G-T-AGA-C
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATT
* * *
32535 TGTCTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATT
* * *
32571 CGTTTCTAGGGAAACTGTCTCAAGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA---TT
* *
32610 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA---TT
32649 TGTTTCAAGG
1 TGTTTCAAGG
32659 AAAAACAATC
Statistics
Matches: 223, Mismatches: 29, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
30 18 0.08
31 3 0.01
32 2 0.01
33 2 0.01
34 1 0.00
35 3 0.01
36 115 0.52
37 2 0.01
39 76 0.34
40 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATT
Found at i:32493 original size:15 final size:15
Alignment explanation
Indices: 32473--32558 Score: 73
Period size: 15 Copynumber: 5.3 Consensus size: 15
32463 AAAATTTGTT
32473 TCAAGGGAAACTGTC
1 TCAAGGGAAACTGTC
*
32488 TCAAGGGAGACAACATTTGTT
1 TCAA-GG-GA-AAC---TGTC
* *
32509 TCAAGTGAAATTGTC
1 TCAAGGGAAACTGTC
* *
32524 TCAAGGTAGACTGTC
1 TCAAGGGAAACTGTC
32539 TCAAGGGAAACTGTC
1 TCAAGGGAAACTGTC
32554 TCAAG
1 TCAAG
32559 AGAGACAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
15 36 0.65
16 2 0.04
17 2 0.04
18 5 0.09
19 2 0.04
20 1 0.02
21 7 0.13
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (15 bp):
TCAAGGGAAACTGTC
Found at i:32687 original size:40 final size:40
Alignment explanation
Indices: 32593--32725 Score: 187
Period size: 40 Copynumber: 3.4 Consensus size: 40
32583 AACTGTCTCA
* * **
32593 AGCGAGATAAAATCTTTTGTTTCAAGG-GAAACTATCTCA
1 AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
32632 AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
1 AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
* *
32672 AGCGAGATAAAATCTTCTGTTTCAAGAAAAAACAATCTTG
1 AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
**
32712 AATGAGATAAAATC
1 AGCGAGATAAAATC
32726 CAAGTGAGAC
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 27 0.32
40 58 0.68
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (40 bp):
AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
Found at i:37433 original size:28 final size:30
Alignment explanation
Indices: 37397--37483 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 30
37387 CATAATTATG
37397 CAAAGATGAAAATGCAAATGCAAAAAAAAA
1 CAAAGATGAAAATGCAAATGCAAAAAAAAA
* *
37427 -AAA-ATGAAAATGTAAATACAAACGTAAAAAA
1 CAAAGATGAAAATGCAAATGCAAA---AAAAAA
*
37458 GCAAAGATGCAAATGCAAATGCAAAA
1 -CAAAGATGAAAATGCAAATGCAAAA
37484 GGTATCGATT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
28 17 0.37
29 3 0.07
31 7 0.15
33 3 0.07
34 16 0.35
ACGTcount: A:0.63, C:0.10, G:0.14, T:0.13
Consensus pattern (30 bp):
CAAAGATGAAAATGCAAATGCAAAAAAAAA
Found at i:48668 original size:26 final size:25
Alignment explanation
Indices: 48629--48678 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
48619 AGAGGTCTAC
* * *
48629 TATATAATTTATTTTTTTAATATTG
1 TATATAATTCATTTTATCAATATTG
48654 TATATTAATTCATTTTATCAATATT
1 TATA-TAATTCATTTTATCAATATT
48679 TTAACATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (25 bp):
TATATAATTCATTTTATCAATATTG
Found at i:49884 original size:60 final size:60
Alignment explanation
Indices: 49791--49943 Score: 191
Period size: 60 Copynumber: 2.6 Consensus size: 60
49781 GATTTTTTTA
* * * * * * *
49791 AGAAATAAACACATACTTGAACTGGTGTAAGTATGCACATTTCTCAATATCTTAATACCT
1 AGAAAAAAACATATACTTGCACTGGTATAAGTATACACATCTCCCAATATCTTAATACCT
* * *
49851 AGAAAAAAACATATACTTGCACTGGTTTAAGTATATATATCTCCCAATATCTTAATACCT
1 AGAAAAAAACATATACTTGCACTGGTATAAGTATACACATCTCCCAATATCTTAATACCT
* *
49911 AG-AAAAAACATATACTTACACTAGTATAAGTAT
1 AGAAAAAAACATATACTTGCACTGGTATAAGTAT
49944 TTTTCTATAT
Statistics
Matches: 81, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 28 0.35
60 53 0.65
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (60 bp):
AGAAAAAAACATATACTTGCACTGGTATAAGTATACACATCTCCCAATATCTTAATACCT
Found at i:51191 original size:17 final size:17
Alignment explanation
Indices: 51169--51216 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
51159 TTTCTATTTG
51169 AACAAAAATGTTGTTAT
1 AACAAAAATGTTGTTAT
51186 AACAAAAATGTTGTTAT
1 AACAAAAATGTTGTTAT
*
51203 AACACAAATGTTGT
1 AACAAAAATGTTGT
51217 ATATGAATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (17 bp):
AACAAAAATGTTGTTAT
Found at i:59952 original size:28 final size:26
Alignment explanation
Indices: 59895--59952 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 26
59885 TGACATGTGA
* * * *
59895 ATACGAAATGCCTATGTGTAAATGAT
1 ATACGAAATGCCTATATGCAAATAAG
59921 ATACGAGAATGCTCTATATGCAAATAAG
1 ATACGA-AATGC-CTATATGCAAATAAG
59949 ATAC
1 ATAC
59953 ACTTTAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 6 0.23
27 5 0.19
28 15 0.58
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (26 bp):
ATACGAAATGCCTATATGCAAATAAG
Found at i:60106 original size:23 final size:23
Alignment explanation
Indices: 60080--60149 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
60070 TATATGTGAC
*
60080 CCTTTGGGATATTTCTACGTGGT
1 CCTTTGGGATAATTCTACGTGGT
** * *
60103 CCTTCAGGATAAATGCTACGCGGT
1 CCTTTGGGAT-AATTCTACGTGGT
*
60127 CCTTTGGGACAAATTCTACGTGG
1 CCTTTGGGA-TAATTCTACGTGG
60150 CACTTCGGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
23 8 0.23
24 27 0.77
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (23 bp):
CCTTTGGGATAATTCTACGTGGT
Found at i:62085 original size:185 final size:189
Alignment explanation
Indices: 61796--62181 Score: 541
Period size: 185 Copynumber: 2.1 Consensus size: 189
61786 CATAACATGC
* *
61796 GTAAAAATAAAAATACAATTAATATATATACATAAAATATTATTTATTAAATTATATTATACATA
1 GTAAAAATAATAATACAATTAATATATATACATAAAATATTATTTATTAAATTATATCATACATA
* **
61861 TAAAGAAAAGATTAATAATATAGCGCATATGTATGAATTTAAAATTCCTAAGAA-GTTATACAT-
66 GAAAGAAAAGATTAATAATATAGAACATATGTATGAATTTAAAATTCCTAA-AATGTTATACATA
* * * * * * *
61924 CAACAAAATAAAATTTCTAAGATTT-AATATCTATTTACATATATATAT-TTTTAACTTAG
130 AAAAAAAATAAAATTTCAAAGATTTCAA-ATCTATTTACACACACATATATATTAACTTAG
* * *
61983 GTAAAAATAATAATACAATT-A-ATATATGCATAAAATATTATTTATTAATTTATATCATACTTA
1 GTAAAAATAATAATACAATTAATATATATACATAAAATATTATTTATTAAATTATATCATACATA
*
62046 GAAAGCAAAGATTAATAATATAGAACATATGTATGAATTTAAAATTCCTAAAATGTTATACATAA
66 GAAAGAAAAGATTAATAATATAGAACATATGTATGAATTTAAAATTCCTAAAATGTTATACATAA
*
62111 AAAAAAATAAAATTTCAAAGTTTTCAAATCTATTTACACACACATATATATTAACTTAG
131 AAAAAAATAAAATTTCAAAGATTTCAAATCTATTTACACACACATATATATTAACTTAG
*
62170 GATAGAAATAAT
1 G-TAAAAATAAT
62182 TATATTATAT
Statistics
Matches: 176, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
184 2 0.01
185 94 0.53
186 39 0.22
187 32 0.18
188 9 0.05
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (189 bp):
GTAAAAATAATAATACAATTAATATATATACATAAAATATTATTTATTAAATTATATCATACATA
GAAAGAAAAGATTAATAATATAGAACATATGTATGAATTTAAAATTCCTAAAATGTTATACATAA
AAAAAAATAAAATTTCAAAGATTTCAAATCTATTTACACACACATATATATTAACTTAG
Found at i:63092 original size:1 final size:1
Alignment explanation
Indices: 63086--63143 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
63076 GTAAGGTCTC
* * * * * **
63086 TTTTTTTCTTTCTTTTTTTTTTCTTTCTGTTTTTCCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
63144 CGAAAACCAC
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (1 bp):
T
Found at i:63526 original size:52 final size:52
Alignment explanation
Indices: 63448--63552 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
63438 GATGGCGACG
63448 GATACTGTTGATGGCTAGGATTTTAGAAAACTCTAAAATCAATTGGCCTAGA
1 GATACTGTTGATGGCTAGGATTTTAGAAAACTCTAAAATCAATTGGCCTAGA
63500 GATACTGTTGATGGCTAGGATTTTAGAAAACTCTAAAATCAATTGGCCTAGA
1 GATACTGTTGATGGCTAGGATTTTAGAAAACTCTAAAATCAATTGGCCTAGA
63552 G
1 G
63553 TTTCACATTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.30
Consensus pattern (52 bp):
GATACTGTTGATGGCTAGGATTTTAGAAAACTCTAAAATCAATTGGCCTAGA
Found at i:63659 original size:3 final size:3
Alignment explanation
Indices: 63653--63678 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
63643 TAATAATAAA
63653 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
63679 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:64308 original size:259 final size:258
Alignment explanation
Indices: 63846--64411 Score: 909
Period size: 259 Copynumber: 2.2 Consensus size: 258
63836 TGTCCCGAAG
* * *
63846 GATTTAATCATCATGCTTGAAAGACTTACTGATGACCCAAAGGACTTACTAATTTGGAAATAGTT
1 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTGGAAATAGTT
* *
63911 TACTAGGTAAGAAACTTTGGAAATTAATTTCTTACTTTTCAATAATTTCATTTTATGAAAATACT
66 TACTAAGTAAGAAACTTTGGAAATTAATTTCTTACTTTTCAAAAATTTCATTTTATGAAAATACT
*
63976 AAATGAGAAACTTTGAAAATTGCTTTATCATTTTTCAAATTATCTTATGAAAGCATCTTTCCCAA
131 AAATGAAAAACTTTGAAAATTGCTTTATCATTTTTCAAATTATCTTATGAAAGCATCTTTCCCAA
*
64041 AGGTCTTATAGATGGCCCGAAGGACTTATCATATCGCTCGAAAGACTGGCAGATGACCTGAAA
196 AGGTCTTATAGATGGCCCGAAGGACTTATCATATCACTCGAAAGACTGGCAGATGACCTGAAA
*
64104 GATTTAATTATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGT
1 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAA-TTTGGAAATAGT
* *
64169 TTACTAAGTAAGAAACTTTGGAAATTACTTTCTTACTTTTCAAAAATTTCATTTTTTGAAAATAC
65 TTACTAAGTAAGAAACTTTGGAAATTAATTTCTTACTTTTCAAAAATTTCATTTTATGAAAATAC
*
64234 TAAATGAAAAACTTTGAAAATTGCTTTCTCATTTTTCAAATTAT-TATATGAAAGCATCTTTCCC
130 TAAATGAAAAACTTTGAAAATTGCTTTATCATTTTTCAAATTATCT-TATGAAAGCATCTTTCCC
* * * * * * *
64298 AAATGTCTTATAGATGGCCTGAAGGACTTATCATCTTACTCGACAGACTGTCAGATGACCTGAAG
194 AAAGGTCTTATAGATGGCCCGAAGGACTTATCATATCACTCGAAAGACTGGCAGATGACCTGAAA
** * *
64363 GATTTTGTCATCATGCTCGAAAGACTTATTGATGGACCAAAGGACTTAC
1 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTAC
64412 TAAATAAGAA
Statistics
Matches: 283, Mismatches: 23, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
258 49 0.17
259 234 0.83
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (258 bp):
GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTGGAAATAGTT
TACTAAGTAAGAAACTTTGGAAATTAATTTCTTACTTTTCAAAAATTTCATTTTATGAAAATACT
AAATGAAAAACTTTGAAAATTGCTTTATCATTTTTCAAATTATCTTATGAAAGCATCTTTCCCAA
AGGTCTTATAGATGGCCCGAAGGACTTATCATATCACTCGAAAGACTGGCAGATGACCTGAAA
Found at i:64388 original size:42 final size:41
Alignment explanation
Indices: 64309--64388 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
64299 AATGTCTTAT
* * *
64309 AGATGGCCTGAAGGACTTATCATCTTACTCGACAGACTGTC
1 AGATGACCTGAAGGACTTATCATCATACTCGAAAGACTGTC
* * *
64350 AGATGACCTGAAGGATTTTGTCATCATGCTCGAAAGACT
1 AGATGACCTGAAGGA-CTTATCATCATACTCGAAAGACT
64389 TATTGATGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 14 0.44
42 18 0.56
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (41 bp):
AGATGACCTGAAGGACTTATCATCATACTCGAAAGACTGTC
Found at i:66851 original size:11 final size:11
Alignment explanation
Indices: 66835--66861 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
66825 GTTCTCATTC
66835 TTTTTCTTCTT
1 TTTTTCTTCTT
66846 TTTTTCTTCTT
1 TTTTTCTTCTT
66857 TTTTT
1 TTTTT
66862 TTGTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:74027 original size:2 final size:2
Alignment explanation
Indices: 74020--74044 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
74010 CTATTAACAA
74020 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
74045 ACTTAGGATA
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:74725 original size:11 final size:10
Alignment explanation
Indices: 74705--74729 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
74695 TCAAACTCTC
74705 TTTTTCTTTT
1 TTTTTCTTTT
74715 TTTTTCTTTT
1 TTTTTCTTTT
74725 TTTTT
1 TTTTT
74730 GTTCAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:76950 original size:4 final size:4
Alignment explanation
Indices: 76943--77063 Score: 68
Period size: 4 Copynumber: 30.8 Consensus size: 4
76933 TTCATTCTTT
* * *
76943 CATC CATC CATC CATC CATC CATC CA-C CATT CAT- CACC CATT CA-C
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
* * * * * * * * *
76988 TCATG CATT CATT CATC CATC CACC CATT AATG CATT CATC CATC CATT
1 -CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
* * * *
77037 CATT CATT CATC CATC TATC CACC CAT
1 CATC CATC CATC CATC CATC CATC CAT
77064 TTATTCATCC
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
3 5 0.05
4 86 0.95
ACGTcount: A:0.26, C:0.41, G:0.02, T:0.31
Consensus pattern (4 bp):
CATC
Found at i:77069 original size:24 final size:24
Alignment explanation
Indices: 76951--77075 Score: 92
Period size: 24 Copynumber: 5.3 Consensus size: 24
76941 TTCATCCATC
* **
76951 CATCCATCCATCCATCCA-CCATT
1 CATCCATCCATCCACCCATTAATT
* * * **
76974 CAT-CACCCATTCACTCATGCATT
1 CATCCATCCATCCACCCATTAATT
* *
76997 CATTCATCCATCCACCCATTAATG
1 CATCCATCCATCCACCCATTAATT
* ** *
77021 CATTCATCCATCCATTCATTCATT
1 CATCCATCCATCCACCCATTAATT
* *
77045 CATCCATCTATCCACCCATTTATT
1 CATCCATCCATCCACCCATTAATT
77069 CATCCAT
1 CATCCAT
77076 TCATTCATTT
Statistics
Matches: 80, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
22 10 0.12
23 10 0.12
24 60 0.75
ACGTcount: A:0.26, C:0.39, G:0.02, T:0.33
Consensus pattern (24 bp):
CATCCATCCATCCACCCATTAATT
Found at i:77075 original size:12 final size:12
Alignment explanation
Indices: 76935--77083 Score: 78
Period size: 12 Copynumber: 12.9 Consensus size: 12
76925 GCTTTTAATT
*
76935 CATTCTTTCATC
1 CATTCATTCATC
* *
76947 CATCCATCCATC
1 CATTCATTCATC
* *
76959 CATCCATCCA-C
1 CATTCATTCATC
*
76970 CATTCA-TCACC
1 CATTCATTCATC
* *
76981 CATTCACTCATG
1 CATTCATTCATC
76993 CATTCATTCATC
1 CATTCATTCATC
*
77005 CA-TC---CACC
1 CATTCATTCATC
* * *
77013 CATTAATGCATT
1 CATTCATTCATC
* * *
77025 CATCCATCCATT
1 CATTCATTCATC
77037 CATTCATTCATC
1 CATTCATTCATC
* *
77049 CA-TCTATCCACC
1 CATTC-ATTCATC
*
77061 CATTTATTCATC
1 CATTCATTCATC
77073 CATTCATTCAT
1 CATTCATTCAT
77084 TTCATGGCGG
Statistics
Matches: 104, Mismatches: 25, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
8 5 0.05
9 1 0.01
10 2 0.02
11 17 0.16
12 78 0.75
13 1 0.01
ACGTcount: A:0.26, C:0.38, G:0.01, T:0.35
Consensus pattern (12 bp):
CATTCATTCATC
Found at i:77077 original size:8 final size:8
Alignment explanation
Indices: 76941--77084 Score: 59
Period size: 8 Copynumber: 18.2 Consensus size: 8
76931 AATTCATTCT
76941 TTCATCCA
1 TTCATCCA
*
76949 TCCATCCA
1 TTCATCCA
*
76957 TCCATCCA
1 TTCATCCA
*
76965 TCCA-CCA
1 TTCATCCA
76972 TTCATCACCCA
1 TTCAT---CCA
76983 TTCA-CTCA
1 TTCATC-CA
* *
76991 TGCATTCA
1 TTCATCCA
76999 TTCATCCA
1 TTCATCCA
* *
77007 TCCACCCA
1 TTCATCCA
* *
77015 TTAATGCA
1 TTCATCCA
77023 TTCAT-C-
1 TTCATCCA
77029 --CATCCA
1 TTCATCCA
*
77035 TTCATTCA
1 TTCATCCA
77043 TTCATCCA
1 TTCATCCA
77051 -TCTATCCA
1 TTC-ATCCA
** **
77059 CCCATTTA
1 TTCATCCA
77067 TTCATCCA
1 TTCATCCA
*
77075 TTCATTCA
1 TTCATCCA
77083 TT
1 TT
77085 TCATGGCGGA
Statistics
Matches: 101, Mismatches: 23, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
4 3 0.03
5 1 0.01
7 10 0.10
8 79 0.78
9 1 0.01
11 7 0.07
ACGTcount: A:0.26, C:0.38, G:0.01, T:0.35
Consensus pattern (8 bp):
TTCATCCA
Found at i:77085 original size:20 final size:20
Alignment explanation
Indices: 76932--77084 Score: 112
Period size: 20 Copynumber: 7.5 Consensus size: 20
76922 TTTGCTTTTA
*
76932 ATTCATTCTTTCATCCATCC
1 ATTCATTCATTCATCCATCC
* * *
76952 ATCCATCCATCCATCCA-CC
1 ATTCATTCATTCATCCATCC
* *
76971 ATTCATCACCCATTCA-CTCATGC
1 ATTCAT---TCATTCATC-CATCC
* *
76994 ATTCATTCATCCATCCACCC
1 ATTCATTCATTCATCCATCC
* *
77014 ATTAATGCATTCATCCATCC
1 ATTCATTCATTCATCCATCC
*
77034 ATTCATTCATTCATCCATCT
1 ATTCATTCATTCATCCATCC
* ** * *
77054 ATCCACCCATTTATTCATCC
1 ATTCATTCATTCATCCATCC
77074 ATTCATTCATT
1 ATTCATTCATT
77085 TCATGGCGGA
Statistics
Matches: 100, Mismatches: 27, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
19 7 0.07
20 76 0.76
21 2 0.02
22 8 0.08
23 7 0.07
ACGTcount: A:0.25, C:0.37, G:0.01, T:0.36
Consensus pattern (20 bp):
ATTCATTCATTCATCCATCC
Done.