Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003117.1 Hibiscus syriacus cultivar Beakdansim tig00006524_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: 73048
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:15346 original size:20 final size:20
Alignment explanation
Indices: 15323--15364 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
15313 CAACACGAAC
* *
15323 TCCAATTTCGTAACACAGTT
1 TCCAAATTCGAAACACAGTT
*
15343 TCCAAATTCGAAACTCAGTT
1 TCCAAATTCGAAACACAGTT
15363 TC
1 TC
15365 TGAAATCGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (20 bp):
TCCAAATTCGAAACACAGTT
Found at i:15395 original size:20 final size:21
Alignment explanation
Indices: 15361--15447 Score: 92
Period size: 21 Copynumber: 4.2 Consensus size: 21
15351 CGAAACTCAG
15361 TTTCTGAAA-TCGCAACGCGAA
1 TTTCT-AAATTCGCAACGCGAA
**
15382 TTTCT-TTTTCGCAACGCAGAA
1 TTTCTAAATTCGCAACGC-GAA
*
15403 TTT-TAAATTCGCAACTCG-A
1 TTTCTAAATTCGCAACGCGAA
*
15422 TTTCTGAATTCGCAACGCGAA
1 TTTCTAAATTCGCAACGCGAA
15443 TTTCT
1 TTTCT
15448 TTTCGGAACA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
19 4 0.07
20 24 0.44
21 26 0.48
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (21 bp):
TTTCTAAATTCGCAACGCGAA
Found at i:15496 original size:20 final size:20
Alignment explanation
Indices: 15473--15558 Score: 68
Period size: 20 Copynumber: 4.3 Consensus size: 20
15463 TTCCTTTTCA
15473 CAACAAGATTTTCTAATTCG
1 CAACAAGATTTTCTAATTCG
* * *
15493 CAACACAAATTTTGT-TTTCG
1 CAACA-AGATTTTCTAATTCG
** *
15513 CAACTCGATTTTCAAATTCG
1 CAACAAGATTTTCTAATTCG
* *
15533 CAACACGAATTT-TAATTTCG
1 CAACAAGATTTTCTAA-TTCG
15553 CAACAA
1 CAACAA
15559 CTTTTATTTT
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
19 7 0.14
20 36 0.72
21 7 0.14
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (20 bp):
CAACAAGATTTTCTAATTCG
Found at i:15545 original size:40 final size:40
Alignment explanation
Indices: 15370--15556 Score: 132
Period size: 40 Copynumber: 4.7 Consensus size: 40
15360 GTTTCTGAAA
*
15370 TCGCAACGCGAATTTCT-TTTTCGCAACGCAGAATTTT-AAAT
1 TCGCAACACGAATTT-TGTTTTCGCAACGC-G-ATTTTCAAAT
* ** * **
15411 TCGCAACTCG-ATTTCTGAATTCGCAACGCGAATTTC-TTT
1 TCGCAACACGAATTT-TGTTTTCGCAACGCGATTTTCAAAT
* ** * ** *
15450 TCGGAACAC-AAGTTTCCTTTTCACAACAAGATTTTCTAAT
1 TCGCAACACGAA-TTTTGTTTTCGCAACGCGATTTTCAAAT
* *
15490 TCGCAACACAAATTTTGTTTTCGCAACTCGATTTTCAAAT
1 TCGCAACACGAATTTTGTTTTCGCAACGCGATTTTCAAAT
**
15530 TCGCAACACGAATTTTAATTTCGCAAC
1 TCGCAACACGAATTTTGTTTTCGCAAC
15557 AACTTTTATT
Statistics
Matches: 112, Mismatches: 28, Indels: 13
0.73 0.18 0.08
Matches are distributed among these distances:
39 26 0.23
40 65 0.58
41 21 0.19
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (40 bp):
TCGCAACACGAATTTTGTTTTCGCAACGCGATTTTCAAAT
Found at i:15749 original size:16 final size:15
Alignment explanation
Indices: 15714--15752 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
15704 TCCCCATCTC
*
15714 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
15729 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
15745 TAATTTTT
1 TAATTTTT
15753 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:16523 original size:24 final size:24
Alignment explanation
Indices: 16496--16549 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
16486 GTATTTGAAA
16496 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
16520 TTTGATCTTGGTTAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
16544 TTTGAT
1 TTTGAT
16550 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:16739 original size:9 final size:9
Alignment explanation
Indices: 16725--16760 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
16715 TATAACCCTG
16725 AAGAAGAAA
1 AAGAAGAAA
*
16734 AAGAAGAAG
1 AAGAAGAAA
16743 AA-AAGAAA
1 AAGAAGAAA
16751 AAGAAGAAA
1 AAGAAGAAA
16760 A
1 A
16761 TGCCACGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:18824 original size:6 final size:6
Alignment explanation
Indices: 18802--18865 Score: 76
Period size: 6 Copynumber: 10.7 Consensus size: 6
18792 AAGAAAAAGG
* * * *
18802 AAATCA AAATCG CAATCA AAATCA AAATCG CAATCA AAATCA AAAT-A
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
18849 ACAATCA AAATCA AAAT
1 A-AATCA AAATCA AAAT
18866 AGCAATTACA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
5 2 0.04
6 44 0.92
7 2 0.04
ACGTcount: A:0.61, C:0.19, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:18825 original size:18 final size:18
Alignment explanation
Indices: 18802--18871 Score: 113
Period size: 18 Copynumber: 3.9 Consensus size: 18
18792 AAGAAAAAGG
*
18802 AAATCAAAATCGCAATCA
1 AAATCAAAATAGCAATCA
*
18820 AAATCAAAATCGCAATCA
1 AAATCAAAATAGCAATCA
*
18838 AAATCAAAATAACAATCA
1 AAATCAAAATAGCAATCA
18856 AAATCAAAATAGCAAT
1 AAATCAAAATAGCAAT
18872 TACAACCGGC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.60, C:0.19, G:0.04, T:0.17
Consensus pattern (18 bp):
AAATCAAAATAGCAATCA
Found at i:19220 original size:49 final size:49
Alignment explanation
Indices: 19161--19255 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
19151 TGAAAATAAA
* *
19161 AATCGCAACGCAAATTTGACTTTCGCGTTGCGAATCTGACTTTCGCAAC
1 AATCGCAACGCAAATTTGACTTTCGCATTGCGAATCTGAATTTCGCAAC
* * * *
19210 AATCGTAACGCGAATTTGACTTTCGCATTGTGAATTTGAATTTCGC
1 AATCGCAACGCAAATTTGACTTTCGCATTGCGAATCTGAATTTCGC
19256 GTTACGAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (49 bp):
AATCGCAACGCAAATTTGACTTTCGCATTGCGAATCTGAATTTCGCAAC
Found at i:19264 original size:20 final size:20
Alignment explanation
Indices: 19220--19265 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
19210 AATCGTAACG
* *
19220 CGAATTTGACTTTCGCATTG
1 CGAATTTGAATTTCGCATTA
* *
19240 TGAATTTGAATTTCGCGTTA
1 CGAATTTGAATTTCGCATTA
19260 CGAATT
1 CGAATT
19266 CGATTTTCCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (20 bp):
CGAATTTGAATTTCGCATTA
Found at i:20801 original size:21 final size:21
Alignment explanation
Indices: 20775--20949 Score: 181
Period size: 21 Copynumber: 8.3 Consensus size: 21
20765 AGTATGCCAT
20775 GTGGATCCTGAACGATGGGAG
1 GTGGATCCTGAACGATGGGAG
*
20796 GTGGATCCTGAACGGTGGGAG
1 GTGGATCCTGAACGATGGGAG
*
20817 GTGGATCCTGAACGATGGAAG
1 GTGGATCCTGAACGATGGGAG
* * *
20838 G-GGCCTCTTGAACTATGGGAG
1 GTGG-ATCCTGAACGATGGGAG
** * **
20859 GTGCCTCTTGAACGATGACAG
1 GTGGATCCTGAACGATGGGAG
* * *
20880 ATGAATCCTGAACAATGGGAG
1 GTGGATCCTGAACGATGGGAG
*
20901 GTGGATCCTGAACAATGGGAG
1 GTGGATCCTGAACGATGGGAG
* * *
20922 GTGGATCCTAAACAATGGTAG
1 GTGGATCCTGAACGATGGGAG
20943 GTGGATC
1 GTGGATC
20950 GGGCTTTCTC
Statistics
Matches: 130, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
20 2 0.02
21 127 0.98
22 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.37, T:0.21
Consensus pattern (21 bp):
GTGGATCCTGAACGATGGGAG
Found at i:21319 original size:21 final size:21
Alignment explanation
Indices: 21295--21340 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
21285 CCATTGTCAT
21295 CACGTAAA-ACAGCTACCTCAC
1 CACGTAAAGACAG-TACCTCAC
* *
21316 CACGTAAAGACCGTACCTCAT
1 CACGTAAAGACAGTACCTCAC
21337 CACG
1 CACG
21341 CCATGCACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.35, C:0.37, G:0.13, T:0.15
Consensus pattern (21 bp):
CACGTAAAGACAGTACCTCAC
Found at i:21333 original size:63 final size:64
Alignment explanation
Indices: 21266--21411 Score: 170
Period size: 63 Copynumber: 2.3 Consensus size: 64
21256 GTAACGTAGA
* * * *
21266 TACCTCACCACGTAAAGCACCATTGTCATCACGTAAAACAGCTACCTCACCACGTAAAG-ACCG
1 TACCTCATCACGTAAAGCACCATTGTCATCACGTAAAACACCAACCTCACCACGCAAAGCACCG
** * ** ** *
21329 TACCTCATCACGCCATGCACCATTGTTGTCACGTAAAGTACCAACCTCATCACGCAAAGCACCG
1 TACCTCATCACGTAAAGCACCATTGTCATCACGTAAAACACCAACCTCACCACGCAAAGCACCG
21393 -ACCTCATCACGTAAAGCAC
1 TACCTCATCACGTAAAGCAC
21412 TGACCTCATC
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
63 63 0.94
64 4 0.06
ACGTcount: A:0.33, C:0.36, G:0.13, T:0.18
Consensus pattern (64 bp):
TACCTCATCACGTAAAGCACCATTGTCATCACGTAAAACACCAACCTCACCACGCAAAGCACCG
Found at i:21337 original size:42 final size:42
Alignment explanation
Indices: 21246--21340 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
21236 TAGAGCGGCT
***
21246 TCCTCATCACGTAACGTAGATACCTCACCACGTAAAGCACCA
1 TCCTCATCACGTAAAACAGATACCTCACCACGTAAAGCACCA
** * *
21288 TTGTCATCACGTAAAACAGCTACCTCACCACGTAAAG-ACCG
1 TCCTCATCACGTAAAACAGATACCTCACCACGTAAAGCACCA
21329 TACCTCATCACG
1 T-CCTCATCACG
21341 CCATGCACCA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
41 4 0.09
42 39 0.91
ACGTcount: A:0.33, C:0.35, G:0.13, T:0.20
Consensus pattern (42 bp):
TCCTCATCACGTAAAACAGATACCTCACCACGTAAAGCACCA
Found at i:21381 original size:21 final size:21
Alignment explanation
Indices: 21357--21427 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
21347 ACCATTGTTG
* *
21357 TCACGTAAAGTACCAACCTCA
1 TCACGTAAAGCACCGACCTCA
*
21378 TCACGCAAAGCACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
*
21399 TCACGTAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCTCA
*
21420 TCATGTAA
1 TCACGTAA
21428 CTCCCCTAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.35, C:0.34, G:0.13, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:21601 original size:42 final size:42
Alignment explanation
Indices: 21542--21640 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
21532 ATGATGGAAT
* * *
21542 AGGTGATGGCTCTCGGTGTCTAGGTGTATAATCAGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCTCGATC
*
21584 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCTCGATC
21626 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
21641 AAGTAGGGGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCTCGATC
Found at i:23836 original size:20 final size:19
Alignment explanation
Indices: 23813--23859 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
23803 ACAAATTCGC
23813 GTTGCGATTTCAGAAACTGA
1 GTTGCGATTT-AGAAACTGA
* *
23833 GTTGCGAATTTGGAAACTGT
1 GTTGCG-ATTTAGAAACTGA
23853 GTTGCGA
1 GTTGCGA
23860 AATTGGAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 19 0.79
21 4 0.17
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.32
Consensus pattern (19 bp):
GTTGCGATTTAGAAACTGA
Found at i:23860 original size:20 final size:20
Alignment explanation
Indices: 23825--23866 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
23815 TGCGATTTCA
*
23825 GAAACTGAGTTGCGAATTTG
1 GAAACTGAGTTGCGAAATTG
*
23845 GAAACTGTGTTGCGAAATTG
1 GAAACTGAGTTGCGAAATTG
23865 GA
1 GA
23867 GTTCGCATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (20 bp):
GAAACTGAGTTGCGAAATTG
Found at i:25083 original size:42 final size:41
Alignment explanation
Indices: 25032--25272 Score: 179
Period size: 41 Copynumber: 5.8 Consensus size: 41
25022 AAAATGATAC
* *
25032 TTTAGCGGCGTTTTTTAAACAAACACCGTAATAGAGTGGTAA
1 TTTAGCGGCG-TTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * *
25074 TTTAGCGGCGTTTAT-AGCTAAAACGCCGCAATAGA-TATGT--
1 TTTAGCGGCGTTTTTAAAC--AAACGCCGCAATAGAGT-GGTAA
* * *
25114 TTATAGTGGCGTTTTTTCAACAAACGCCACAATAGAGTGGTAA
1 TT-TAGCGGCG-TTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * * *
25157 TTTAGCGGCGTTTTTACACAAACGCCGCGATAGTGTTGT--
1 TTTAGCGGCGTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * * * **
25196 TTATAGTGGCGTTTGTTCAACAAACGACGCTATAGAGAAGTAA
1 TT-TAGCGGCGTTT-TTAAACAAACGCCGCAATAGAGTGGTAA
* *
25239 TTTCGCGGCGTTTATCAAACAAACGCCGCAATAG
1 TTTAGCGGCGTTT-TTAAACAAACGCCGCAATAG
25273 TATTGTTTAT
Statistics
Matches: 154, Mismatches: 32, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
39 2 0.01
40 14 0.09
41 70 0.45
42 62 0.40
43 6 0.04
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAAACAAACGCCGCAATAGAGTGGTAA
Found at i:25139 original size:41 final size:41
Alignment explanation
Indices: 25094--25311 Score: 146
Period size: 41 Copynumber: 5.3 Consensus size: 41
25084 TTTATAGCTA
25094 AAACGCCGCAATAGATATGTTTATAGTGGCGTTTTTTCAAC
1 AAACGCCGCAATAGATATGTTTATAGTGGCGTTTTTTCAAC
* * * *
25135 AAACGCCACAATAGAGT-GGTAATT-TAGCGGCGTTTTTAC-AC
1 AAACGCCGCAATAGA-TATGT--TTATAGTGGCGTTTTTTCAAC
* * *
25176 AAACGCCGCGATAG-TGTTGTTTATAGTGGCGTTTGTTCAAC
1 AAACGCCGCAATAGAT-ATGTTTATAGTGGCGTTTTTTCAAC
* * * * * * *
25217 AAACGACGCTATAGAGAAGTAATT-TCGCGGCG-TTTATCAAAC
1 AAACGCCGCAATAGATATGT--TTATAGTGGCGTTTTTTC-AAC
* * *
25259 AAACGCCGCAATAG-TATTGTTTATAGTGGCATTTGTGCAA-
1 AAACGCCGCAATAGATA-TGTTTATAGTGGCGTTTTTTCAAC
*
25299 AAAAGCCGCAATA
1 AAACGCCGCAATA
25312 TGTTGTTTAT
Statistics
Matches: 133, Mismatches: 30, Indels: 29
0.69 0.16 0.15
Matches are distributed among these distances:
39 3 0.02
40 26 0.20
41 60 0.45
42 40 0.30
43 4 0.03
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (41 bp):
AAACGCCGCAATAGATATGTTTATAGTGGCGTTTTTTCAAC
Found at i:25208 original size:82 final size:81
Alignment explanation
Indices: 25038--25311 Score: 309
Period size: 83 Copynumber: 3.3 Consensus size: 81
25028 ATACTTTAGC
* * * *
25038 GGCGTTTTTTAAACAAACACCGTAATAGAGTGGTAATTTAGCGGCGTTTATAGCTA-AAACGCCG
1 GGCGTTTTTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTTTA-C-ACAAACGCCG
*
25102 CAATAGATATGTTTATAGT
64 CAATAG-TTTGTTTATAGT
* *
25121 GGCGTTTTTTCAACAAACGCCACAATAGAGTGGTAATTTAGCGGCGTTTTTACACAAACGCCGCG
1 GGCGTTTTTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTTTACACAAACGCCGCA
25186 ATAGTGTTGTTTATAGT
66 ATAGT-TTGTTTATAGT
* * * ** * * *
25203 GGCGTTTGTTCAACAAACGACGCTATAGAGAAGTAATTTCGCGGCGTTTATCAAACAAACGCCGC
1 GGCGTTTTTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTT-TTACACAAACGCCGC
25268 AATAGTATTGTTTATAGT
65 AATAGT-TTGTTTATAGT
* * * *
25286 GGCATTTGTGCAA-AAAAGCCGCAATA
1 GGCGTTTTTTCAACAAACGCCGCAATA
25312 TGTTGTTTAT
Statistics
Matches: 165, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
81 2 0.01
82 76 0.46
83 87 0.53
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (81 bp):
GGCGTTTTTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTTTACACAAACGCCGCA
ATAGTTTGTTTATAGT
Found at i:25294 original size:83 final size:82
Alignment explanation
Indices: 25094--25294 Score: 269
Period size: 82 Copynumber: 2.4 Consensus size: 82
25084 TTTATAGCTA
* * **
25094 AAACGCCGCAATAG-ATATGTTTATAGTGGCGTTTTTTCAACAAACGCCACAATAGAGTGGTAAT
1 AAACGCCGCAATAGTAT-TGTTTATAGTGGCGTTTGTTCAACAAACGACACAATAGAGAAGTAAT
* *
25158 TTAGCGGCGTTTTTACAC
65 TTAGCGGCGTTTTCAAAC
* * * *
25176 AAACGCCGCGATAGTGTTGTTTATAGTGGCGTTTGTTCAACAAACGACGCTATAGAGAAGTAATT
1 AAACGCCGCAATAGTATTGTTTATAGTGGCGTTTGTTCAACAAACGACACAATAGAGAAGTAATT
*
25241 TCGCGGCGTTTATCAAAC
66 TAGCGGCGTTT-TCAAAC
*
25259 AAACGCCGCAATAGTATTGTTTATAGTGGCATTTGT
1 AAACGCCGCAATAGTATTGTTTATAGTGGCGTTTGT
25295 GCAAAAAAGC
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
82 65 0.63
83 38 0.37
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (82 bp):
AAACGCCGCAATAGTATTGTTTATAGTGGCGTTTGTTCAACAAACGACACAATAGAGAAGTAATT
TAGCGGCGTTTTCAAAC
Found at i:28574 original size:11 final size:11
Alignment explanation
Indices: 28547--28575 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
28537 TTATAACACC
28547 CCCAACCCGTA
1 CCCAACCCGTA
28558 -CCAACCCGTA
1 CCCAACCCGTA
28568 CCCAACCC
1 CCCAACCC
28576 AGATACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.28, C:0.59, G:0.07, T:0.07
Consensus pattern (11 bp):
CCCAACCCGTA
Found at i:29199 original size:18 final size:18
Alignment explanation
Indices: 29176--29210 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29166 ACTGAATATT
29176 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
29194 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
29211 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:29862 original size:19 final size:19
Alignment explanation
Indices: 29838--29909 Score: 126
Period size: 19 Copynumber: 3.8 Consensus size: 19
29828 TTTAAGCAGG
29838 TGCATCGATGCACTACTTA
1 TGCATCGATGCACTACTTA
*
29857 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTACTTA
*
29876 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTACTTA
29895 TGCATCGATGCACTA
1 TGCATCGATGCACTA
29910 ATTGCATTCG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTACTTA
Found at i:42963 original size:44 final size:45
Alignment explanation
Indices: 42913--42999 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
42903 CAACTTTTAA
* *
42913 CGGCG-TTTGTATCCTAAAAACT-CCGCTATATACCT-GACCTATAG
1 CGGCGTTTTGTACCCTAAAAA-TGCCGCTAAATA-CTAGACCTATAG
42957 CGGCGTTTTGTACCCTAAAAATGCCGCTAAATACTAGACCTAT
1 CGGCGTTTTGTACCCTAAAAATGCCGCTAAATACTAGACCTAT
43000 TGCGACATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
44 8 0.21
45 30 0.79
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (45 bp):
CGGCGTTTTGTACCCTAAAAATGCCGCTAAATACTAGACCTATAG
Found at i:43033 original size:24 final size:24
Alignment explanation
Indices: 43001--43052 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
42991 TAGACCTATT
43001 GCGACATTTTCATAAAAAAATACC
1 GCGACATTTTCATAAAAAAATACC
43025 GCGACATTTTCATAAAAAAATACC
1 GCGACATTTTCATAAAAAAATACC
43049 GCGA
1 GCGA
43053 AATATCAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23
Consensus pattern (24 bp):
GCGACATTTTCATAAAAAAATACC
Found at i:43152 original size:43 final size:43
Alignment explanation
Indices: 43047--43202 Score: 136
Period size: 43 Copynumber: 3.6 Consensus size: 43
43037 TAAAAAAATA
* * * * * * *
43047 CCGCGAAATATCAACACTTATTGCGACGTTTGTGATAA-AAATG
1 CCGCTAAATATCGATACCTATTGCGGCGTTTGTTA-AACAAACG
* * **
43090 CCGCTAAATATTGAAACCTATTGCGTTGTTT-TTAAGACAAACG
1 CCGCTAAATATCGATACCTATTGCGGCGTTTGTTAA-ACAAACG
* * *
43133 CCGCTAAATATCGGTACCTATTGTGGCGTTTGTTAAACAAGCG
1 CCGCTAAATATCGATACCTATTGCGGCGTTTGTTAAACAAACG
* *
43176 CCGCTATATATCGTTACCTATTGCGGC
1 CCGCTAAATATCGATACCTATTGCGGC
43203 ATTTTTGGTT
Statistics
Matches: 91, Mismatches: 19, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 83 0.91
44 4 0.04
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (43 bp):
CCGCTAAATATCGATACCTATTGCGGCGTTTGTTAAACAAACG
Found at i:43895 original size:94 final size:94
Alignment explanation
Indices: 43733--43992 Score: 385
Period size: 94 Copynumber: 2.7 Consensus size: 94
43723 TCTTACCATC
* *
43733 TGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAAAGGGACAACTTAAGCTTTATT
1 TGAATCTTATCCATAAAGCCGGGGCG-TTAACCAATTGCTCTAGAGGGACAACTTAAGCTTTATT
*
43798 GTATATTATAATCACCTTTATCAGGCTAGA
65 GTATATCATAATCACCTTTATCAGGCTAGA
* *
43828 TGAATCTTATTCATAAAGCCGAGGCGTTAACCAATTGCTCTAGAGGGACAACTTAAGCTTTATTG
1 TGAATCTTATCCATAAAGCCGGGGCGTTAACCAATTGCTCTAGAGGGACAACTTAAGCTTTATTG
* *
43893 TATCTCATAATCACCTTTATCAGGCTAGC
66 TATATCATAATCACCTTTATCAGGCTAGA
* * * * *
43922 TAAATCTTATCCATAAAGTCGGGGCATTTAACCAATTGCTCTAGAGGGACATCTCAAGCTTTATT
1 TGAATCTTATCCATAAAGCCGGGGC-GTTAACCAATTGCTCTAGAGGGACAACTTAAGCTTTATT
*
43987 ATATAT
65 GTATAT
43993 AAATATAATT
Statistics
Matches: 148, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
94 85 0.57
95 63 0.43
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (94 bp):
TGAATCTTATCCATAAAGCCGGGGCGTTAACCAATTGCTCTAGAGGGACAACTTAAGCTTTATTG
TATATCATAATCACCTTTATCAGGCTAGA
Found at i:72538 original size:21 final size:21
Alignment explanation
Indices: 72508--72592 Score: 127
Period size: 21 Copynumber: 4.1 Consensus size: 21
72498 ATATCCAGAA
72508 CCCT-CGGGGGGTATCGATTC
1 CCCTACGGGGGGTATCGATTC
72528 CCCTACGGGGGGTATCGATTC
1 CCCTACGGGGGGTATCGATTC
* *
72549 CCCTACGGGGGGAATCGGTTC
1 CCCTACGGGGGGTATCGATTC
* *
72570 CCCTTCAGGGGGTATCGATTC
1 CCCTACGGGGGGTATCGATTC
72591 CC
1 CC
72593 TCTGCACCAA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 4 0.07
21 54 0.93
ACGTcount: A:0.13, C:0.31, G:0.33, T:0.24
Consensus pattern (21 bp):
CCCTACGGGGGGTATCGATTC
Done.