Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006702.1 Hibiscus syriacus cultivar Beakdansim tig00016692_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: 97137
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3310 original size:3 final size:3
Alignment explanation
Indices: 3302--3326 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3292 GTTGGTTTTA
3302 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
3327 TTTTTTCGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:10292 original size:37 final size:37
Alignment explanation
Indices: 10242--10655 Score: 265
Period size: 37 Copynumber: 11.2 Consensus size: 37
10232 AGTCGGACTC
*
10242 AAGATCGATTTGCTTCACTACTCTTCGGTGAAGGCTT
1 AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
* * *
10279 AAGATTGATTTGCTTCACTACTTTTTGGTGAAGGCTT
1 AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
*
10316 AAGAT-GATTTTGCTTCACTACTCTTTGGTGAAGGCTT
1 AAGATGGA-TTTGCTTCACTACTCTTCGGTGAAGGCTT
** *
10353 AAGATCGCCCGA-AGGACTT-AAT-CATCATGCTC-G-GAAGGCTT
1 AAGAT-G---GATTTG-CTTCACTAC-TC-T--TCGGTGAAGGCTT
* *
10394 ATTGATGGATTTGCTTCACTACTCTTC--------CGT
1 A-AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
* * *
10424 --GATGGATTTGCTTCACTACTTTTTGGTGAAGTCTT
1 AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
* *
10459 AAGATGAATTTGCTTCACTACTCTTTGGTGAAGGCTT
1 AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
*** * *
10496 AAGATGGCCCGGATGACTT-AATCAC-CATGCTC-G-GAAGGATT
1 AAGATGG---ATTTG-CTTCACT-ACTC-T--TCGGTGAAGGCTT
* *
10537 ACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTT
1 A-AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
*
10575 ATGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
1 AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
* * * *
10612 TAGATTGATTTGCTTTACTACTCTTTGGTGAAGGCTT
1 AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
10649 AAGATGG
1 AAGATGG
10656 CTCGGAGGAC
Statistics
Matches: 299, Mismatches: 40, Indels: 76
0.72 0.10 0.18
Matches are distributed among these distances:
27 22 0.07
30 2 0.01
35 2 0.01
36 6 0.02
37 183 0.61
38 20 0.07
39 11 0.04
40 11 0.04
41 28 0.09
42 12 0.04
43 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (37 bp):
AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
Found at i:10543 original size:143 final size:145
Alignment explanation
Indices: 10285--10685 Score: 583
Period size: 143 Copynumber: 2.7 Consensus size: 145
10275 GCTTAAGATT
*
10285 GATTTGCTTCACTACTTTTTGGTGAAGGCTTAAGATGATTTTGCTTCACTACTCTTTGGTGAAGG
1 GATTTGCTTCACTACTTTTTGGTGAAGGCTTAAGATGAATTTGCTTCACTACTCTTTGGTGAAGG
* * * *
10350 CTTAAGATCGCCCGAAGGACTTAATCATCATGCTCGGAAGGCTTATTGATGGATTTGCTTCACTA
66 CTTAAGATGGCCCGGAGGACTTAATCATCATGCTCGGAAGGATTACTGATGGATTTGCTTCACTA
10415 CTCTTCC-G-TGATG
131 CTCTTCCGGTTGATG
*
10428 GATTTGCTTCACTACTTTTTGGTGAAGTCTTAAGATGAATTTGCTTCACTACTCTTTGGTGAAGG
1 GATTTGCTTCACTACTTTTTGGTGAAGGCTTAAGATGAATTTGCTTCACTACTCTTTGGTGAAGG
* *
10493 CTTAAGATGGCCCGGATGACTTAATCACCATGCTCGGAAGGATTACTGATGGATTTGCTTCACTA
66 CTTAAGATGGCCCGGAGGACTTAATCATCATGCTCGGAAGGATTACTGATGGATTTGCTTCACTA
10558 CTCTTCCGTGAAGGCTTATGATG
131 CTCTTCC-----GG--T-TGATG
* * * *
10581 GATTTGCTTCACTACTCTTCGGTGAAGGCTTTAGATTG-ATTTGCTTTACTACTCTTTGGTGAAG
1 GATTTGCTTCACTACTTTTTGGTGAAGGCTTAAGA-TGAATTTGCTTCACTACTCTTTGGTGAAG
*
10645 GCTTAAGATGGCTCGGAGGACTTAATCATCATGCTCGGAAG
65 GCTTAAGATGGCCCGGAGGACTTAATCATCATGCTCGGAAG
10686 ACTTACAAAT
Statistics
Matches: 231, Mismatches: 16, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
143 129 0.56
149 1 0.00
153 99 0.43
154 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (145 bp):
GATTTGCTTCACTACTTTTTGGTGAAGGCTTAAGATGAATTTGCTTCACTACTCTTTGGTGAAGG
CTTAAGATGGCCCGGAGGACTTAATCATCATGCTCGGAAGGATTACTGATGGATTTGCTTCACTA
CTCTTCCGGTTGATG
Found at i:10897 original size:21 final size:21
Alignment explanation
Indices: 10864--10905 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10854 ATGTGAAAAA
*
10864 CATCCTGCCCGAATGACTTAT
1 CATCCTGCCCGAAAGACTTAT
* *
10885 CATCTTGCTCGAAAGACTTAT
1 CATCCTGCCCGAAAGACTTAT
10906 AGATGACTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (21 bp):
CATCCTGCCCGAAAGACTTAT
Found at i:11052 original size:214 final size:214
Alignment explanation
Indices: 10661--11098 Score: 675
Period size: 214 Copynumber: 2.0 Consensus size: 214
10651 GATGGCTCGG
* *
10661 AGGACTTAATCATCATGCTCGGAAGACTTACAAATGACCTGAAGGATTTAAGCATTATGCTCGAA
1 AGGACTT-ATCATCATGCTCGAAAGACTTACAAATGACCTGAAGGATTTAAGCATCATGCTCGAA
* *
10726 AGACTTACTGATGGGCCGAAGGACTTATAAATTTTTAAAATAGTTTACTGGATAAGAAACATTTC
65 AGACTTACTGATGGGCCGAAGGACTTATAAATTTTGAAAATAGTTTACTGGATAAGAAACATTTA
*
10791 TTACTTTTCAAAAATTTTAAATTTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGATAGACAT
130 TTACTTTTCAAAAATTTCAAATTTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGATAGACAT
* *
10856 GTGAAAAACATCCTGCCCGA
195 GTGAAAAACATCATGCCCAA
* * * *
10876 ATGACTTATCATCTTGCTCGAAAGACTTATAGATGA-CTCGAAGGATTTAAGCATCATGCTCGAA
1 AGGACTTATCATCATGCTCGAAAGACTTACAAATGACCT-GAAGGATTTAAGCATCATGCTCGAA
* *
10940 AGACTTACTGAT-GGCCTGAAGGACTTATAAATTTTGGAAATAGTTTACTAGG-TAAGAATCATT
65 AGACTTACTGATGGGCC-GAAGGACTTATAAATTTTGAAAATAGTTTACT-GGATAAGAAACATT
* * *
11003 TATTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACCTTTCTCATTTTTTTATAGAC
128 TATTACTTTTCAAAAATTTCAAATTTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGATAGAC
11068 ATGTGAAAAACATCATGCCCAA
193 ATGTGAAAAACATCATGCCCAA
11090 AGGACTTAT
1 AGGACTTAT
11099 GGATAGCCCG
Statistics
Matches: 203, Mismatches: 17, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
213 6 0.03
214 189 0.93
215 8 0.04
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (214 bp):
AGGACTTATCATCATGCTCGAAAGACTTACAAATGACCTGAAGGATTTAAGCATCATGCTCGAAA
GACTTACTGATGGGCCGAAGGACTTATAAATTTTGAAAATAGTTTACTGGATAAGAAACATTTAT
TACTTTTCAAAAATTTCAAATTTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGATAGACATG
TGAAAAACATCATGCCCAA
Found at i:11201 original size:151 final size:151
Alignment explanation
Indices: 10927--11208 Score: 406
Period size: 151 Copynumber: 1.9 Consensus size: 151
10917 AGGATTTAAG
* * * * *
10927 CATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTATAAATTTTGGAAATAGTTTACTAGG
1 CATCATGCTCCAAAGACTTACTGATAGCCCGAAGGACTTATAAATTTTGGAAAAAGTTTACTAGC
* * * * *
10992 TAAGAATCATTTATTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACCTTTCTCATT
66 TAAGAAACATTTATTACTTTTCAAAAATTTAAATTTTCAGATTGAAATGAGAAACCTTTCCCATT
11057 TTTTTATAGACATGTGAAAAA
131 TTTTTATAGACATGTGAAAAA
*
11078 CATCATGC-CCAAAGGACTTA-TGGATAGCCCGAAGGACTTATAAATTTTGGAAAAATTTTACTA
1 CATCATGCTCCAAA-GACTTACT-GATAGCCCGAAGGACTTATAAATTTTGGAAAAAGTTTACTA
* * *
11141 GCTAAGAAACCTTTCTTACTTTTCAAAAATTTAAATTTTCAGATTGGAATGAGAAACCTTTCCCA
64 GCTAAGAAACATTTATTACTTTTCAAAAATTTAAATTTTCAGATTGAAATGAGAAACCTTTCCCA
11206 TTT
129 TTT
11209 CATTTTTACT
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
150 5 0.04
151 110 0.96
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (151 bp):
CATCATGCTCCAAAGACTTACTGATAGCCCGAAGGACTTATAAATTTTGGAAAAAGTTTACTAGC
TAAGAAACATTTATTACTTTTCAAAAATTTAAATTTTCAGATTGAAATGAGAAACCTTTCCCATT
TTTTTATAGACATGTGAAAAA
Found at i:11957 original size:37 final size:37
Alignment explanation
Indices: 11907--12075 Score: 198
Period size: 37 Copynumber: 4.6 Consensus size: 37
11897 TGGTCATGTC
* *
11907 CCAAAGAGTAGTGAACCAAATCAATCTTAAGCCTTAA
1 CCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCA
* * *
11944 CCAAAAAGTAGTGAAG-AAAGTCCATTTTAAGCCTTCA
1 CCAAAGAGTAGTGAAGCAAA-TCAATCTTAAGCCTTCA
* * * **
11981 CGAAAGAGGAGTGAAACAAATC-ATCCCAAGCCTTCA
1 CCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCA
* *
12017 CCGAAGAGTAGTGAAGCAAATCAATCTTAAGTCTTCA
1 CCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCA
*
12054 CCGAAGAGTAGTGAAGCAAATC
1 CCAAAGAGTAGTGAAGCAAATC
12076 CATCAATCTA
Statistics
Matches: 110, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
36 32 0.29
37 75 0.68
38 3 0.03
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (37 bp):
CCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCA
Found at i:12047 original size:73 final size:75
Alignment explanation
Indices: 11909--12075 Score: 198
Period size: 73 Copynumber: 2.3 Consensus size: 75
11899 GTCATGTCCC
* ** * *
11909 AAAGAGTAGTGAACCAAATCAATCTTAAGCCTTAACCAAAAAGTAGTGAAGAAAGTCCATTTTAA
1 AAAGAGTAGTGAAACAAATCAATCCCAAGCCTTAACCAAAAAGTAGTGAAGAAAGTCAATCTTAA
11974 GCCTTCA-CG
66 GCCTTCACCG
* * * *
11983 AAAGAGGAGTGAAACAAATC-ATCCCAAGCCTTCACCGAAGAGTAGTGAAGCAAA-TCAATCTTA
1 AAAGAGTAGTGAAACAAATCAATCCCAAGCCTTAACCAAAAAGTAGTGAAG-AAAGTCAATCTTA
*
12046 AGTCTTCACCG
65 AGCCTTCACCG
*
12057 -AAGAGTAGTGAAGCAAATC
1 AAAGAGTAGTGAAACAAATC
12076 CATCAATCTA
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
73 56 0.71
74 23 0.29
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (75 bp):
AAAGAGTAGTGAAACAAATCAATCCCAAGCCTTAACCAAAAAGTAGTGAAGAAAGTCAATCTTAA
GCCTTCACCG
Found at i:12180 original size:42 final size:41
Alignment explanation
Indices: 12132--12282 Score: 149
Period size: 42 Copynumber: 3.5 Consensus size: 41
12122 TTGCAAGATT
12132 TGATATTCCCTGAGTGACAACGGAACAAGTCTACCCCATATC
1 TGATATTCCCTGAGTGACAACGGAACAAGTCT-CCCCATATC
* * *
12174 TGATATTCCCTGAGTGACAACGAAACAGGTCTCTCTTTTCCAATATT
1 TGATATTCCCTGAGTGACAACGGAACAAGTCTC-C----CC-ATATC
* * * * * * *
12221 TGATATTCCCTAACTGATAGCAGAACAAGTCTGCTCATATC
1 TGATATTCCCTGAGTGACAACGGAACAAGTCTCCCCATATC
12262 TGATATTCCCTGAGTGACAAC
1 TGATATTCCCTGAGTGACAAC
12283 AACAGAATAT
Statistics
Matches: 86, Mismatches: 17, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
41 22 0.26
42 32 0.37
46 3 0.03
47 29 0.34
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (41 bp):
TGATATTCCCTGAGTGACAACGGAACAAGTCTCCCCATATC
Found at i:12334 original size:91 final size:89
Alignment explanation
Indices: 12109--12434 Score: 331
Period size: 91 Copynumber: 3.7 Consensus size: 89
12099 AAGAAGTGAC
* *
12109 ACATGTCACTCTTTT-GCAAGATTTGATATTCCCTGAGTGACAACGGAACAAGTCTACCCCATAT
1 ACATGTCACTCTTTTCG-AAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCCATAT
*
12173 CTGATATTCCCTGAGTGACAACGAA
65 CTGATATTCCCTGAGTGACAACCAA
* * * * * * * * *
12198 ACAGGTCTCTCTTTTCCAATATTTGATATTCCCTAACTGATAGCAGAACAAGTCT-GCTCATATC
1 ACATGTCACTCTTTTCGAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCCATATC
12262 TGATATTCCCTGAGTGACAACAACAGA
66 TGATATTCCCTGAGTGACAAC--CA-A
* * * *
12289 ATATGTCAATCTTTTCGAAGATTTGATATTCCCTGAGTGACAGCAGAACACGTCTACCCCAGATC
1 ACATGTCACTCTTTTCGAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCCATATC
* * * * *
12354 CGATATTCACTTAGTGACAGCGGAA
66 TGATATTCCCTGAGTGACAAC-CAA
* * * *
12379 TATAT-TC-CTC-TTTC-AAGATTTGATATTCCCTTAGTGACAACGGAACAAGTCTACCC
1 -ACATGTCACTCTTTTCGAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCC
12435 GATTCAATGG
Statistics
Matches: 195, Mismatches: 36, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
87 38 0.19
88 32 0.16
89 47 0.24
90 4 0.02
91 51 0.26
92 23 0.12
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (89 bp):
ACATGTCACTCTTTTCGAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCCATATC
TGATATTCCCTGAGTGACAACCAA
Found at i:14692 original size:37 final size:37
Alignment explanation
Indices: 14642--14898 Score: 220
Period size: 37 Copynumber: 6.8 Consensus size: 37
14632 CAAAATTAGA
*
14642 CACTACTTTTCGGTGAAGGCTTAAGATGGATTTTCTT
1 CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGCTT
14679 CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGCTT
1 CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGCTT
*
14716 CACTACTCTTTTGGTGAAGGCTTAAGATAGCCCGGA--TGACTT
1 CACTACT-TTTCGGTGAAGGCTTAAGAT-----GGATTTG-CTT
* ** * *
14758 -AATCATCATAATC-G-GAAGGATTAGTGATGGATTTGCTT
1 CACT-A-C-TTTTCGGTGAAGGCTTA-AGATGGATTTGCTT
* * * * *
14796 CACTGCTCTTCCGTGAAGGCTTATGATGGATTTACTT
1 CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGCTT
* * *
14833 CACTACTCTTCGGTGAAGGCTTTAGATTGATTTGCTT
1 CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGCTT
*
14870 CATTACTCTTT-GGTGAAGGCTTAAGATGG
1 CACTACT-TTTCGGTGAAGGCTTAAGATGG
14899 CCCGGAGGAC
Statistics
Matches: 179, Mismatches: 24, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
36 3 0.02
37 114 0.64
38 32 0.18
39 4 0.02
41 12 0.07
42 8 0.04
43 5 0.03
44 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (37 bp):
CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGCTT
Found at i:14931 original size:22 final size:21
Alignment explanation
Indices: 14901--14975 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 21
14891 TAAGATGGCC
*
14901 CGGAGGACTTAATCATCATGCT
1 CGGAAGACTTAA-CATCATGCT
*
14923 CGGAAGACTT-ACA-GATGAC-
1 CGGAAGACTTAACATCATG-CT
* *
14942 CTGAAGGATTTAAGCATCATGCT
1 CGGAA-GACTTAA-CATCATGCT
14965 CGGAAGACTTA
1 CGGAAGACTTA
14976 CTGATGGTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
19 7 0.17
20 7 0.17
21 2 0.05
22 17 0.43
23 7 0.17
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (21 bp):
CGGAAGACTTAACATCATGCT
Found at i:14961 original size:42 final size:42
Alignment explanation
Indices: 14904--14995 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
14894 GATGGCCCGG
*
14904 AGGACTTAATCATCATGCTCGGAAGACTTACAGATGACCTGA
1 AGGACTTAAGCATCATGCTCGGAAGACTTACAGATGACCTGA
* * **
14946 AGGATTTAAGCATCATGCTCGGAAGACTTACTGATGGTCTGA
1 AGGACTTAAGCATCATGCTCGGAAGACTTACAGATGACCTGA
14988 AGGACTTA
1 AGGACTTA
14996 TAAATTTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (42 bp):
AGGACTTAAGCATCATGCTCGGAAGACTTACAGATGACCTGA
Found at i:15138 original size:21 final size:21
Alignment explanation
Indices: 15105--15145 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15095 ATGTGAAAAA
*
15105 CATCCTGCCCGAAGGACTTAT
1 CATCCTGCCCGAAAGACTTAT
* *
15126 CATCTTGCTCGAAAGACTTA
1 CATCCTGCCCGAAAGACTTA
15146 CAGATGACCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (21 bp):
CATCCTGCCCGAAAGACTTAT
Found at i:17548 original size:12 final size:12
Alignment explanation
Indices: 17525--17565 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
17515 CAATTTCTTT
17525 TTTTCTTCTTTTA
1 TTTTC-TCTTTTA
17538 TTTTCTCTTTTA
1 TTTTCTCTTTTA
* *
17550 TTTTCTTTTTTC
1 TTTTCTCTTTTA
17562 TTTT
1 TTTT
17566 TTTTCTACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTCTCTTTTA
Found at i:17558 original size:17 final size:16
Alignment explanation
Indices: 17533--17571 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
17523 TTTTTTCTTC
*
17533 TTTTATTTTCTCTTTT
1 TTTTCTTTTCTCTTTT
*
17549 ATTTTCTTTTTTCTTTT
1 -TTTTCTTTTCTCTTTT
17566 TTTTCT
1 TTTTCT
17572 ACTTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTCTCTTTT
Found at i:17577 original size:17 final size:17
Alignment explanation
Indices: 17530--17590 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
17520 TCTTTTTTTC
17530 TTCTTTTATTTTCTCTT
1 TTCTTTTATTTTCTCTT
* * *
17547 TTATTTTCTTTTTTCTT
1 TTCTTTTATTTTCTCTT
* *
17564 TTTTTTCTACTTTTTTCTT
1 TTCTTT-TA-TTTTCTCTT
17583 CTTCTTTT
1 -TTCTTTT
17591 TGATGGATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 19 0.54
18 1 0.03
19 10 0.29
20 5 0.14
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (17 bp):
TTCTTTTATTTTCTCTT
Found at i:17578 original size:13 final size:13
Alignment explanation
Indices: 17522--17591 Score: 63
Period size: 13 Copynumber: 5.4 Consensus size: 13
17512 ATTCAATTTC
17522 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
*
17535 TTATTTTC-TCTT
1 TTTTTTTCTTCTT
*
17547 TTATTTTCTT-TT
1 TTTTTTTCTTCTT
* *
17559 TTCTTTTTTTTCTA
1 TT-TTTTTCTTCTT
*
17573 CTTTTTTCTTCTT
1 TTTTTTTCTTCTT
17586 CTTTTT
1 -TTTTT
17592 GATGGATGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
12 16 0.36
13 23 0.51
14 6 0.13
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:17591 original size:32 final size:30
Alignment explanation
Indices: 17519--17590 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
17509 TTGATTCAAT
*
17519 TTCTTTTTTTCTTCTTTTATTTTCTCTTTTA
1 TTCTTCTTTT-TTCTTTTATTTTCTCTTTTA
17550 TT-TTCTTTTTTCTTTT-TTTTCTACTTTT-
1 TTCTTCTTTTTTCTTTTATTTTCT-CTTTTA
17578 TTCTTCTTCTTTT
1 TTCTTCTT-TTTT
17591 TGATGGATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
28 8 0.22
29 17 0.46
30 10 0.27
31 2 0.05
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (30 bp):
TTCTTCTTTTTTCTTTTATTTTCTCTTTTA
Found at i:19488 original size:28 final size:28
Alignment explanation
Indices: 19448--19507 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
19438 GAGGCATTAA
19448 CAACCTTTATATCTTTAATAGCTTCCTT
1 CAACCTTTATATCTTTAATAGCTTCCTT
*
19476 CAACCTTTATATCTTTAATAGTTTCCTT
1 CAACCTTTATATCTTTAATAGCTTCCTT
19504 CAAC
1 CAAC
19508 AACTTGAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.25, G:0.03, T:0.45
Consensus pattern (28 bp):
CAACCTTTATATCTTTAATAGCTTCCTT
Found at i:28935 original size:2 final size:2
Alignment explanation
Indices: 28928--28953 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28918 TTTCCTTAAC
28928 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28954 CTTTTTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31003 original size:73 final size:73
Alignment explanation
Indices: 30919--31067 Score: 280
Period size: 73 Copynumber: 2.0 Consensus size: 73
30909 TATTTGTATA
30919 GGAGAATTATGTTAAATTTTAAATATTTTAGGGTTTTAAGTCTTTTACTTCTGATATTGTGATGT
1 GGAGAATTATGTTAAATTTTAAATATTTTAGGGTTTTAAGTCTTTTACTTCTGATATTGTGATGT
30984 TTACACTC
66 TTACACTC
* *
30992 GGAGAATTATGTTAAATTTTAAATTTTTTAGGGTTTTAAGTCTTTTACTTCTGATATTTTGATGT
1 GGAGAATTATGTTAAATTTTAAATATTTTAGGGTTTTAAGTCTTTTACTTCTGATATTGTGATGT
31057 TTACACTC
66 TTACACTC
31065 GGA
1 GGA
31068 TATTAAATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (73 bp):
GGAGAATTATGTTAAATTTTAAATATTTTAGGGTTTTAAGTCTTTTACTTCTGATATTGTGATGT
TTACACTC
Found at i:31604 original size:19 final size:19
Alignment explanation
Indices: 31564--31605 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
31554 ACGTTTTGCC
**
31564 ATTTTAAGTAAAACAATTA
1 ATTTTAAGTAAAACAACAA
*
31583 ATTTTAATTAAAACAACAA
1 ATTTTAAGTAAAACAACAA
31602 ATTT
1 ATTT
31606 AGGTATGCGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTTTAAGTAAAACAACAA
Found at i:36424 original size:6 final size:6
Alignment explanation
Indices: 36413--36439 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
36403 CACCCTAAAC
36413 AATTAA AATTAA AATTAA AATTAA AAT
1 AATTAA AATTAA AATTAA AATTAA AAT
36440 AATTAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTAA
Found at i:38668 original size:9 final size:9
Alignment explanation
Indices: 38585--38674 Score: 72
Period size: 10 Copynumber: 9.3 Consensus size: 9
38575 AGGGCTGGAA
38585 ACCGGTTTG
1 ACCGGTTTG
* *
38594 ACTGGTTTTCA
1 ACCGG-TTT-G
*
38605 ACCGGTCCTG
1 ACCGGT-TTG
38615 ACCGGTTTCG
1 ACCGGTTT-G
38625 ACCGGTTTCG
1 ACCGGTTT-G
38635 ACCGGTTTG
1 ACCGGTTTG
* *
38644 ACTGGTATG
1 ACCGGTTTG
38653 AACCGGTTTG
1 -ACCGGTTTG
*
38663 ACCGGTCTG
1 ACCGGTTTG
38672 ACC
1 ACC
38675 CGACCCGACT
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
9 24 0.37
10 36 0.55
11 5 0.08
ACGTcount: A:0.14, C:0.27, G:0.29, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:38681 original size:5 final size:5
Alignment explanation
Indices: 38671--38717 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
38661 TGACCGGTCT
* * *
38671 GACCC GACCC GA-CT AACCC GACCC GACCC GA-CT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
38718 GTTGACCATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 5 0.15
5 29 0.85
ACGTcount: A:0.23, C:0.53, G:0.19, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:38695 original size:19 final size:19
Alignment explanation
Indices: 38671--38717 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
38661 TGACCGGTCT
38671 GACCCGACCCGACTAACCC
1 GACCCGACCCGACTAACCC
*
38690 GACCCGACCCGACTGACCC
1 GACCCGACCCGACTAACCC
38709 GACCCGACC
1 GACCCGACC
38718 GTTGACCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.23, C:0.53, G:0.19, T:0.04
Consensus pattern (19 bp):
GACCCGACCCGACTAACCC
Found at i:38707 original size:14 final size:14
Alignment explanation
Indices: 38690--38716 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38680 CGACTAACCC
38690 GACCCGACCCGACT
1 GACCCGACCCGACT
38704 GACCCGACCCGAC
1 GACCCGACCCGAC
38717 CGTTGACCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.52, G:0.22, T:0.04
Consensus pattern (14 bp):
GACCCGACCCGACT
Found at i:45188 original size:9 final size:9
Alignment explanation
Indices: 45174--45213 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
45164 AGGGCTGGAA
45174 ACCGGTTTG
1 ACCGGTTTG
*
45183 ACCGGTTCG
1 ACCGGTTTG
45192 AACCGGTTTG
1 -ACCGGTTTG
*
45202 ACCGGTCTG
1 ACCGGTTTG
45211 ACC
1 ACC
45214 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:45220 original size:5 final size:5
Alignment explanation
Indices: 45210--45242 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
45200 TGACCGGTCT
*
45210 GACCC GACCC GACCC GA-CT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACC
45243 GTTGACCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.21, C:0.55, G:0.21, T:0.03
Consensus pattern (5 bp):
GACCC
Found at i:45223 original size:19 final size:19
Alignment explanation
Indices: 45201--45243 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
45191 GAACCGGTTT
*
45201 GACCGGTCTGACCCGACCC
1 GACCGGACTGACCCGACCC
*
45220 GACCCGACTGACCCGACCC
1 GACCGGACTGACCCGACCC
45239 GACCG
1 GACCG
45244 TTGACCGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.26, T:0.07
Consensus pattern (19 bp):
GACCGGACTGACCCGACCC
Found at i:45232 original size:14 final size:14
Alignment explanation
Indices: 45215--45241 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45205 GGTCTGACCC
45215 GACCCGACCCGACT
1 GACCCGACCCGACT
45229 GACCCGACCCGAC
1 GACCCGACCCGAC
45242 CGTTGACCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.52, G:0.22, T:0.04
Consensus pattern (14 bp):
GACCCGACCCGACT
Found at i:47713 original size:53 final size:53
Alignment explanation
Indices: 47653--47761 Score: 173
Period size: 53 Copynumber: 2.1 Consensus size: 53
47643 AGTAAGGGTC
* * *
47653 AGGGTTAAAGAAAATAAACAGAGATAGAAGATGAAGAGGCTTGGTTTGGGTTT
1 AGGGTTAAAGAAAATAAACAGAGATAGAAGATGAAAAGGCTAGGTTAGGGTTT
* *
47706 AGGGTTAAAGAAGATAAACATAGATAGAAGATGAAAAGGCTAGGTTAGGGTTT
1 AGGGTTAAAGAAAATAAACAGAGATAGAAGATGAAAAGGCTAGGTTAGGGTTT
47759 AGG
1 AGG
47762 ATTAGTGTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.41, C:0.04, G:0.32, T:0.23
Consensus pattern (53 bp):
AGGGTTAAAGAAAATAAACAGAGATAGAAGATGAAAAGGCTAGGTTAGGGTTT
Found at i:49305 original size:14 final size:15
Alignment explanation
Indices: 49286--49314 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
49276 TCAAGCATCT
49286 AACAATCCA-AAACA
1 AACAATCCAGAAACA
49300 AACAATCCAGAAACA
1 AACAATCCAGAAACA
49315 TCAAAACAAT
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:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:51264 original size:23 final size:22
Alignment explanation
Indices: 51234--51313 Score: 92
Period size: 22 Copynumber: 3.6 Consensus size: 22
51224 GCATGACCTT
51234 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
51256 CGTGCATCGGTGCA-ACTTC-ATG
1 -GTGCATCGATGCACA-TTCAAGG
*
51278 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
51300 ATGCATCGATGCAC
1 GTGCATCGATGCAC
51314 TATTAGATGT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
21 14 0.30
22 18 0.38
23 15 0.32
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:51290 original size:21 final size:23
Alignment explanation
Indices: 51235--51312 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
51225 CATGACCTTG
*
51235 TGCATCGATGC-ACATTCAAGGCG
1 TGCATCGATGCAACATTCAAGG-A
* *
51258 TGCATCGGTGCAAC-TTCATGG-
1 TGCATCGATGCAACATTCAAGGA
*
51279 TGTATCGATGC-ACATTCAAGGA
1 TGCATCGATGCAACATTCAAGGA
51301 TGCATCGATGCA
1 TGCATCGATGCA
51313 CTATTAGATG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.04
21 15 0.33
22 10 0.22
23 16 0.36
24 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCAACATTCAAGGA
Found at i:51327 original size:20 final size:21
Alignment explanation
Indices: 51279--51332 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
51269 AACTTCATGG
51279 TGTATCGATGCACATTCAAGGA
1 TGTATCGATGCACATT-AAGGA
*
51301 TGCATCGATGCACTATT-A-GA
1 TGTATCGATGCAC-ATTAAGGA
51321 TGTATCGATGCA
1 TGTATCGATGCA
51333 TTAAGCACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 13 0.45
21 1 0.03
22 12 0.41
23 3 0.10
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (21 bp):
TGTATCGATGCACATTAAGGA
Found at i:56579 original size:45 final size:45
Alignment explanation
Indices: 56486--56616 Score: 144
Period size: 45 Copynumber: 2.9 Consensus size: 45
56476 CATCGAATGC
* *
56486 ATTTTATGCATCGATGCACACA-CCATGCATCGATGCACTCAGTGT
1 ATTTGATGCATCGATGCACA-AGCCATGCATCGATGCACTCTGTGT
56531 ATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCTG-GCT
1 ATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCTGTG-T
** **
56576 ATTTTGAAACATCGAATGCACTTG--ATGCATCGATGCACTCT
1 A-TTTGATGCATCG-ATGCACAAGCCATGCATCGATGCACTCT
56617 TAGTGCACCG
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
44 2 0.03
45 57 0.75
46 10 0.13
47 7 0.09
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (45 bp):
ATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCTGTGT
Found at i:56613 original size:17 final size:19
Alignment explanation
Indices: 56585--56633 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
56575 TATTTTGAAA
56585 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
56603 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
56622 CACCGATGCACT
1 CATCGATGCACT
56634 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:57414 original size:18 final size:18
Alignment explanation
Indices: 57391--57431 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
57381 GTTCAGGTTT
57391 AGGTTCAAGTTTGGATTC
1 AGGTTCAAGTTTGGATTC
*
57409 AGGTTCGAGTTTGGATTC
1 AGGTTCAAGTTTGGATTC
57427 AGGTT
1 AGGTT
57432 TAGGTTTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.10, G:0.32, T:0.39
Consensus pattern (18 bp):
AGGTTCAAGTTTGGATTC
Found at i:57438 original size:18 final size:18
Alignment explanation
Indices: 57398--57440 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
57388 TTTAGGTTCA
*
57398 AGTTTGGATTCAGGTTCG
1 AGTTTGGATTCAGGTTAG
57416 AGTTTGGATTCAGGTTTAG
1 AGTTTGGATTCAGG-TTAG
57435 -GTTTGG
1 AGTTTGG
57441 GATCGTGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.16, C:0.07, G:0.35, T:0.42
Consensus pattern (18 bp):
AGTTTGGATTCAGGTTAG
Found at i:57461 original size:6 final size:6
Alignment explanation
Indices: 57452--57530 Score: 61
Period size: 6 Copynumber: 13.2 Consensus size: 6
57442 ATCGTGATCA
* * * * * **
57452 GGTTTG GGTTTG GTTTTG GTTTTA GGTTCG AGTTCA GGTTTG GGTTTG
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG
* *
57500 AGTTTG GGTTCT- GGTTTG GGTTCG GGTTTG G
1 GGTTTG GGTT-TG GGTTTG GGTTTG GGTTTG G
57531 ATTCCAGTTG
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
5 1 0.02
6 55 0.96
7 1 0.02
ACGTcount: A:0.05, C:0.05, G:0.42, T:0.48
Consensus pattern (6 bp):
GGTTTG
Found at i:57478 original size:24 final size:25
Alignment explanation
Indices: 57451--57530 Score: 85
Period size: 24 Copynumber: 3.3 Consensus size: 25
57441 GATCGTGATC
* *
57451 AGGTTTGGGTT-TGGTTTTGGTTTT
1 AGGTTTGGGTTCTGGTTTGGGTTTG
* * *
57475 AGGTTCGAGTTCAGGTTTGGGTTTG
1 AGGTTTGGGTTCTGGTTTGGGTTTG
*
57500 A-GTTTGGGTTCTGGTTTGGGTTCG
1 AGGTTTGGGTTCTGGTTTGGGTTTG
57524 -GGTTTGG
1 AGGTTTGG
57531 ATTCCAGTTG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
24 34 0.76
25 11 0.24
ACGTcount: A:0.06, C:0.05, G:0.41, T:0.47
Consensus pattern (25 bp):
AGGTTTGGGTTCTGGTTTGGGTTTG
Found at i:57497 original size:18 final size:18
Alignment explanation
Indices: 57433--57503 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
57423 ATTCAGGTTT
* * *
57433 AGGTTTGGGATCGTGATC
1 AGGTTTGGGTTCGAGTTC
* *
57451 AGGTTTGGGTTTG-GTTT
1 AGGTTTGGGTTCGAGTTC
* *
57468 TGGTTTTAGGTTCGAGTTC
1 AGG-TTTGGGTTCGAGTTC
*
57487 AGGTTTGGGTTTGAGTT
1 AGGTTTGGGTTCGAGTT
57504 TGGGTTCTGG
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
17 4 0.10
18 31 0.77
19 5 0.12
ACGTcount: A:0.11, C:0.06, G:0.38, T:0.45
Consensus pattern (18 bp):
AGGTTTGGGTTCGAGTTC
Found at i:57504 original size:12 final size:12
Alignment explanation
Indices: 57452--57530 Score: 72
Period size: 12 Copynumber: 6.6 Consensus size: 12
57442 ATCGTGATCA
57452 GGTTTGGGTT-T
1 GGTTTGGGTTCT
* *
57463 GGTTTTGGTTTT
1 GGTTTGGGTTCT
* * *
57475 AGGTTCGAGTTCA
1 -GGTTTGGGTTCT
57488 GGTTTGGGTT-T
1 GGTTTGGGTTCT
57499 GAGTTTGGGTTCT
1 G-GTTTGGGTTCT
*
57512 GGTTTGGGTTCG
1 GGTTTGGGTTCT
57524 GGTTTGG
1 GGTTTGG
57531 ATTCCAGTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
11 10 0.19
12 35 0.65
13 9 0.17
ACGTcount: A:0.05, C:0.05, G:0.42, T:0.48
Consensus pattern (12 bp):
GGTTTGGGTTCT
Found at i:58187 original size:61 final size:61
Alignment explanation
Indices: 58121--58250 Score: 224
Period size: 61 Copynumber: 2.1 Consensus size: 61
58111 TTTAATTTTT
* *
58121 TTCAATTTAGTCCAAATTTAATGATGCAATGTATTGATTTAAGCTTCATATTTAAAATTTG
1 TTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAGCTTCATATTTAAAACTTG
* *
58182 TTCAATTTAGTCCAAATTTAATGTTGCAATTTATTAATTTAAGCTTCATATTTAAAACTTG
1 TTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAGCTTCATATTTAAAACTTG
58243 TTCAATTT
1 TTCAATTT
58251 GATCATTATA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (61 bp):
TTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAGCTTCATATTTAAAACTTG
Found at i:58382 original size:33 final size:33
Alignment explanation
Indices: 58282--58368 Score: 165
Period size: 33 Copynumber: 2.6 Consensus size: 33
58272 ATTAATAAAT
*
58282 TAATATATAGGTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
58315 TAATATATAGTTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
58348 TAATATATAGTTTATATATAC
1 TAATATATAGTTTATATATAC
58369 CATACACTCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.43
Consensus pattern (33 bp):
TAATATATAGTTTATATATACTAATGAACTATA
Found at i:58547 original size:15 final size:15
Alignment explanation
Indices: 58532--58566 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
58522 TACTTTGAAT
58532 TTATAT-AGTATAAA
1 TTATATAAGTATAAA
58546 TTATATAAGTATAAA
1 TTATATAAGTATAAA
58561 TTATAT
1 TTATAT
58567 TATACAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (15 bp):
TTATATAAGTATAAA
Found at i:58626 original size:27 final size:27
Alignment explanation
Indices: 58535--58633 Score: 108
Period size: 27 Copynumber: 3.7 Consensus size: 27
58525 TTTGAATTTA
* * * * *
58535 TATAGTATAAATTATATAAGTATAAAT
1 TATAGTATATAGTATATAAATATCAAC
* * *
58562 TATATTATACAATATATAAATATCAAC
1 TATAGTATATAGTATATAAATATCAAC
*
58589 TATAGTGTATAGTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATCAAC
*
58616 TATAGTATATAGTTTATA
1 TATAGTATATAGTATATA
58634 TATAAATTAT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (27 bp):
TATAGTATATAGTATATAAATATCAAC
Found at i:58719 original size:11 final size:11
Alignment explanation
Indices: 58703--58760 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
58693 AACTATTTAG
58703 TATATATAGTT
1 TATATATAGTT
58714 TATATAT-G--
1 TATATATAGTT
* *
58722 TAGTATATACTA
1 TA-TATATAGTT
*
58734 TATAAATAGTT
1 TATATATAGTT
58745 TATATATAGTT
1 TATATATAGTT
*
58756 CATAT
1 TATAT
58761 GTAAATTACT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
8 2 0.05
9 5 0.14
10 1 0.03
11 27 0.73
12 2 0.05
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (11 bp):
TATATATAGTT
Found at i:58863 original size:20 final size:20
Alignment explanation
Indices: 58784--58869 Score: 61
Period size: 20 Copynumber: 4.1 Consensus size: 20
58774 CTATATATAT
58784 TATATAGTTTACATAGTTTA-TA
1 TATATAGTTTACATA---TAGTA
58806 TATATAGTTTATACATATAGT-
1 TATATAG-TT-TACATATAGTA
* **
58827 TCATAT-CTAAACTATATAGTA
1 T-ATATAGTTTAC-ATATAGTA
58848 TATATAGTTTACATATAGTA
1 TATATAGTTTACATATAGTA
58868 TA
1 TA
58870 AGTTAATATA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
19 2 0.04
20 22 0.43
21 7 0.14
22 12 0.24
23 2 0.04
24 6 0.12
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (20 bp):
TATATAGTTTACATATAGTA
Found at i:59042 original size:20 final size:19
Alignment explanation
Indices: 59013--59131 Score: 84
Period size: 20 Copynumber: 6.0 Consensus size: 19
59003 ATTAAAAAAT
59013 TATATAATTTATACATAATA
1 TATATAATTTATA-ATAATA
*
59033 TATATTATTTATAAT--TA
1 TATATAATTTATAATAATA
*
59050 TATATAATATATAATTAA-A
1 TATATAATTTATAA-TAATA
* *
59069 GGTGTATAATATATATATAATTCA
1 --TATATAATTTATA-ATAA-T-A
59093 TATATAATTTATATATAA-A
1 TATATAATTTATA-ATAATA
*
59112 CTATATAATTTATATTAATA
1 -TATATAATTTATAATAATA
59132 AACTATATAG
Statistics
Matches: 81, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
17 14 0.17
18 1 0.01
19 7 0.09
20 26 0.32
21 15 0.19
22 17 0.21
24 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
TATATAATTTATAATAATA
Found at i:59053 original size:17 final size:16
Alignment explanation
Indices: 59010--59066 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 16
59000 TATATTAAAA
59010 AATTATATA-ATTTAT
1 AATTATATATATTTAT
59025 ACATAATATATATTATTTAT
1 A-AT--TATATA-TATTTAT
*
59045 AATTATATATAATATAT
1 AATTATATAT-ATTTAT
59062 AATTA
1 AATTA
59067 AAGGTGTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 1 0.03
16 3 0.09
17 16 0.46
18 6 0.17
19 2 0.06
20 7 0.20
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTATATATATTTAT
Found at i:59062 original size:11 final size:11
Alignment explanation
Indices: 58959--59151 Score: 71
Period size: 11 Copynumber: 17.6 Consensus size: 11
58949 ACCTTAAACC
*
58959 ATATATACTAT
1 ATATATAATAT
*
58970 ATATATAA-AC
1 ATATATAATAT
* *
58980 A-ATATAGTTT
1 ATATATAATAT
* *
58990 ATATATAGTTT
1 ATATATAATAT
* *
59001 ATAT-TAAAAA
1 ATATATAATAT
*
59011 ATTATATAATTT
1 A-TATATAATAT
*
59023 ATACATAATAT
1 ATATATAATAT
*
59034 ATATTATTTATAATT
1 ATA-TA-TAAT-A-T
59049 ATATATAATAT
1 ATATATAATAT
*
59060 ATA-ATTAA-AG
1 ATATA-TAATAT
* *
59070 GTGTATAATAT
1 ATATATAATAT
59081 ATATATAAT-T
1 ATATATAATAT
*
59091 CATATATAATTT
1 -ATATATAATAT
59103 ATATATAA-A-
1 ATATATAATAT
* *
59112 CTATATAATTT
1 ATATATAATAT
*
59123 ATAT-TAATAA
1 ATATATAATAT
* *
59133 ACTATATAGTTT
1 A-TATATAATAT
59145 ATATATA
1 ATATATA
59152 GTTCAATAGT
Statistics
Matches: 133, Mismatches: 32, Indels: 34
0.67 0.16 0.17
Matches are distributed among these distances:
9 12 0.09
10 18 0.14
11 79 0.59
12 11 0.08
13 6 0.05
14 3 0.02
15 4 0.03
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (11 bp):
ATATATAATAT
Found at i:59105 original size:9 final size:10
Alignment explanation
Indices: 59013--59126 Score: 62
Period size: 9 Copynumber: 11.5 Consensus size: 10
59003 ATTAAAAAAT
59013 TATATAATT-
1 TATATAATTA
* *
59022 TATA-CATAA
1 TATATAATTA
59031 TATAT-ATTA
1 TATATAATTA
*
59040 TTTATAATTA
1 TATATAATTA
59050 TATATAA-TA
1 TATATAATTA
***
59059 TATAATTAAAGG
1 TAT-A-TAATTA
*
59071 TGTATAATATA
1 TATATAAT-TA
59082 TATATAATTCA
1 TATATAATT-A
59093 TATATAATTTA
1 TATATAA-TTA
59104 TATATAA--A
1 TATATAATTA
59112 CTATATAATT-
1 -TATATAATTA
59122 TATAT
1 TATAT
59127 TAATAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
8 3 0.04
9 32 0.40
10 15 0.19
11 27 0.33
12 4 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (10 bp):
TATATAATTA
Found at i:59105 original size:22 final size:22
Alignment explanation
Indices: 59073--59151 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
59063 ATTAAAGGTG
* *
59073 TATAATATATATATAATTCATA
1 TATAATTTATATATAATACATA
59095 TATAATTTATATATAA-AC-TA
1 TATAATTTATATATAATACATA
*
59115 TATAATTTATAT-TAATAAACTA
1 TATAATTTATATATAATACA-TA
*
59137 TATAGTTTATATATA
1 TATAATTTATATATA
59152 GTTCAATAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
19 3 0.06
20 15 0.31
21 1 0.02
22 28 0.57
23 2 0.04
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (22 bp):
TATAATTTATATATAATACATA
Found at i:62386 original size:16 final size:16
Alignment explanation
Indices: 62362--62400 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
62352 ATAGGCCTAT
*
62362 AAAAGAAATAAAAATA
1 AAAATAAATAAAAATA
*
62378 AAAATAAATAATAATA
1 AAAATAAATAAAAATA
*
62394 ATAATAA
1 AAAATAA
62401 TAATAATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAATAAATAAAAATA
Found at i:62392 original size:3 final size:3
Alignment explanation
Indices: 62368--62438 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
62358 CTATAAAAGA
* * * *
62368 AAT AAA AAT AAA AAT AAAT AAT AAT AAT AAT AAT AAT AAT AGT TA-
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
62413 AAT AAT AAT AATT AAT AGT AAT AAT A
1 AAT AAT AAT AA-T AAT AAT AAT AAT A
62439 TAAACGGTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
2 1 0.02
3 48 0.87
4 6 0.11
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:63396 original size:64 final size:63
Alignment explanation
Indices: 63311--63471 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
63301 TTGTTTAAGG
* * * *
63311 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * *
63375 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
63439 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
63472 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:64540 original size:31 final size:31
Alignment explanation
Indices: 64446--64553 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
64436 AGTCGAGGGT
* *
64446 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
64477 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
64508 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
64539 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
64554 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.21
31 47 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:64551 original size:30 final size:30
Alignment explanation
Indices: 64499--64594 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
64489 CTAAGGAACA
* *
64499 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTGTGACC
* *
64530 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
* * *
64560 TCTGGATAGTTACCG-GGGTCTTTGTGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
*
64589 TCTGGA
1 TATGGA
64595 TATGTCCTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.32
30 29 0.52
31 9 0.16
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTGTGACC
Found at i:68005 original size:64 final size:63
Alignment explanation
Indices: 67920--68080 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 63
67910 TTGTTTAAGG
* * * *
67920 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAAGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAAGATTTA
* * * * *
67984 TGCATCGATGCATAAGGAGTGCATCAATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAAGATTTA
*
68048 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
68081 ACCTTCATTA
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
63 1 0.01
64 60 0.73
65 20 0.24
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAAGATTTA
Found at i:69145 original size:31 final size:31
Alignment explanation
Indices: 69051--69145 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 31
69041 AGTCGAGGGT
*
69051 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTATGTTCTTT-GGGACATATGGACAG
* ** *
69082 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTATGTTCTTTGGGACATATGGACAG
*
69113 TTTACCTATGTTCTTTGGGACCTATGGACAG
1 TTTACCTATGTTCTTTGGGACATATGGACAG
69144 TT
1 TT
69146 GCCGAGGTTC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 50 0.94
32 3 0.06
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (31 bp):
TTTACCTATGTTCTTTGGGACATATGGACAG
Found at i:69165 original size:30 final size:31
Alignment explanation
Indices: 69073--69165 Score: 73
Period size: 31 Copynumber: 3.0 Consensus size: 31
69063 TTTCGAGACA
* * * * *
69073 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGTTTACCGAGGTTCTTTAGG-ACC
* * *
69104 TATGGACAGTTTACCTATGTTCTTTGGGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
* *
69135 TATGGACAG-TTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
69165 T
1 T
69166 CTAGATAGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 17 0.33
31 32 0.62
32 3 0.06
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGTTCTTTAGGACC
Found at i:70726 original size:2 final size:2
Alignment explanation
Indices: 70719--70756 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
70709 TTTTATAGCT
70719 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70757 ATTGTTTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75387 original size:16 final size:16
Alignment explanation
Indices: 75366--75407 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
75356 TTTGAGGATT
75366 AAATTTGAAGTTTTGA
1 AAATTTGAAGTTTTGA
75382 AAATTTGAAGTTTTGA
1 AAATTTGAAGTTTTGA
75398 AAATTTGAAG
1 AAATTTGAAG
75408 ACTATTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (16 bp):
AAATTTGAAGTTTTGA
Found at i:76104 original size:18 final size:18
Alignment explanation
Indices: 76070--76106 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
76060 CGATCCAAAC
* *
76070 CGGTCTGAACTGGGTTGA
1 CGGTCTGAACCGAGTTGA
76088 CGGTCTGAACCGAGTTGA
1 CGGTCTGAACCGAGTTGA
76106 C
1 C
76107 CGATCTGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.35, T:0.24
Consensus pattern (18 bp):
CGGTCTGAACCGAGTTGA
Found at i:76192 original size:29 final size:27
Alignment explanation
Indices: 76147--76283 Score: 123
Period size: 29 Copynumber: 4.7 Consensus size: 27
76137 ACCCAGTGAT
76147 ATTTTGGGAATTATTTTTGAAAACATGAC
1 ATTTT-GGAATTATTTTT-AAAACATGAC
*
76176 ATTTTGAGAATT-TTTTTAAAAAATAGTGAC
1 ATTTTG-GAATTATTTTT--AAAACA-TGAC
76206 ATTTTGGTAATTATTTTTAAAACGATGAC
1 ATTTTGG-AATTATTTTTAAAAC-ATGAC
* ** *
76235 ATTTTAGGAATTATTTGTAAAATGGTGAT
1 ATTTT-GGAATTATTTTTAAAA-CATGAC
76264 ATTTTGGGAATTATTTTTAA
1 ATTTT-GGAATTATTTTTAA
76284 TAAAGATGAT
Statistics
Matches: 91, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
28 6 0.07
29 63 0.69
30 17 0.19
31 5 0.05
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (27 bp):
ATTTTGGAATTATTTTTAAAACATGAC
Found at i:76234 original size:59 final size:58
Alignment explanation
Indices: 76141--76298 Score: 196
Period size: 59 Copynumber: 2.7 Consensus size: 58
76131 GACCCGACCC
*
76141 AGTGATATTTTGGGAATTATTTTTGAAAAC-ATGACATTTT-GAGAATT-TTTTTAAAAAAT
1 AGTGATATTTTGGGAATTATTTTT-AAAACGATGACATTTTAG-GAATTATTTGT--AAAAT
* *
76200 AGTGACATTTTGGTAATTATTTTTAAAACGATGACATTTTAGGAATTATTTGTAAAAT
1 AGTGATATTTTGGGAATTATTTTTAAAACGATGACATTTTAGGAATTATTTGTAAAAT
* * *
76258 GGTGATATTTTGGGAATTATTTTTAATAAAGATGATATTTT
1 AGTGATATTTTGGGAATTATTTTTAA-AACGATGACATTTT
76299 TGTAATTTTC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
58 33 0.38
59 49 0.56
60 5 0.06
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.45
Consensus pattern (58 bp):
AGTGATATTTTGGGAATTATTTTTAAAACGATGACATTTTAGGAATTATTTGTAAAAT
Found at i:83632 original size:29 final size:29
Alignment explanation
Indices: 83569--83709 Score: 176
Period size: 29 Copynumber: 4.9 Consensus size: 29
83559 CCGACCCAGC
* *
83569 GACATTTTGGGAATTATTTT-GAAAAGGT
1 GACATTTTGGGAATTATTTTAAAAAAAGT
83597 GACATTTTGGGAATTATTTTAAAAAAAGT
1 GACATTTTGGGAATTATTTTAAAAAAAGT
* *
83626 AACATTTTGGGAATTATTTTGAAAAAAGT
1 GACATTTTGGGAATTATTTTAAAAAAAGT
* *
83655 GACATTTTGGGAATTTTTTTTAAAAACAGT
1 GACATTTTGGGAA-TTATTTTAAAAAAAGT
* ** *
83685 GACATTCTGTTAATTATTTTTAAAA
1 GACATTTTGGGAATTATTTTAAAAA
83710 CGATGATATC
Statistics
Matches: 98, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 20 0.20
29 55 0.56
30 23 0.23
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (29 bp):
GACATTTTGGGAATTATTTTAAAAAAAGT
Found at i:83680 original size:57 final size:57
Alignment explanation
Indices: 83570--83738 Score: 194
Period size: 59 Copynumber: 2.9 Consensus size: 57
83560 CGACCCAGCG
*
83570 ACATTTTGGGAATTATTTTGAAAAGGTGACATTTTGGGAATTATTTTAAAAAAAGTA
1 ACATTTTGGGAATTATTTTGAAAAAGTGACATTTTGGGAATTATTTTAAAAAAAGTA
* * *
83627 ACATTTTGGGAATTATTTTGAAAAAAGTGACATTTTGGGAATTTTTTTTAAAAACAGTG
1 ACATTTTGGGAATTATTTTG-AAAAAGTGACATTTTGGGAA-TTATTTTAAAAAAAGTA
* ** * * * * *
83686 ACATTCTGTTAATTATTTTTAAAACGATGATATCTTGAGAATTATTTGTAAAA
1 ACATTTTGGGAATTATTTTGAAAAAG-TGACATTTTGGGAATTATTT-TAAAA
83739 CGGTGAAATT
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
57 20 0.21
58 29 0.31
59 46 0.48
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (57 bp):
ACATTTTGGGAATTATTTTGAAAAAGTGACATTTTGGGAATTATTTTAAAAAAAGTA
Found at i:83728 original size:29 final size:29
Alignment explanation
Indices: 83696--83765 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
83686 ACATTCTGTT
*
83696 AATTATTTTTAAAACGATGATATCTTGAG
1 AATTATTTTTAAAACGATGAAATCTTGAG
* * * *
83725 AATTATTTGTAAAACGGTGAAATTTTGAT
1 AATTATTTTTAAAACGATGAAATCTTGAG
83754 AATTATTTTTAA
1 AATTATTTTTAA
83766 TAAAGGTGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (29 bp):
AATTATTTTTAAAACGATGAAATCTTGAG
Found at i:87029 original size:17 final size:17
Alignment explanation
Indices: 87004--87046 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
86994 AACCATTGAA
87004 TAAGG-AAAAATAATTT
1 TAAGGAAAAAATAATTT
87020 TAAGGAAAAAATAATTT
1 TAAGGAAAAAATAATTT
* *
87037 AAAGCAAAAA
1 TAAGGAAAAA
87047 TTAAGAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (17 bp):
TAAGGAAAAAATAATTT
Found at i:87591 original size:17 final size:17
Alignment explanation
Indices: 87554--87591 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
87544 AGCTTGTTTA
*
87554 AAAATAAAACTTAAAAT
1 AAAATAAAACTAAAAAT
87571 AAAATAAAA-TAAAAAT
1 AAAATAAAACTAAAAAT
87587 GAAAA
1 -AAAA
87592 CTTGAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAATAAAACTAAAAAT
Found at i:87608 original size:29 final size:28
Alignment explanation
Indices: 87552--87608 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
87542 TTAGCTTGTT
*
87552 TAAAAATAAAACTTAAAATAAAATAAAA
1 TAAAAATAAAACTTAAAATAAAAGAAAA
87580 TAAAAATGAAAACTTGAAAAT-AAAGAAAA
1 TAAAAAT-AAAACTT-AAAATAAAAGAAAA
87609 GAAGAACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.27
29 14 0.54
30 5 0.19
ACGTcount: A:0.72, C:0.04, G:0.05, T:0.19
Consensus pattern (28 bp):
TAAAAATAAAACTTAAAATAAAAGAAAA
Done.