Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003839.1 Hibiscus syriacus cultivar Beakdansim tig00008228_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: 139013
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:12396 original size:16 final size:16
Alignment explanation
Indices: 12377--12431 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
12367 AAACAAAAGC
12377 AACCTGAACCAAATTT
1 AACCTGAACCAAATTT
* * ***
12393 AACCCGATCCAAAAGC
1 AACCTGAACCAAATTT
*
12409 AACCTGAACCGAATTT
1 AACCTGAACCAAATTT
12425 AACCTGA
1 AACCTGA
12432 CCCGAAAGTA
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.42, C:0.29, G:0.11, T:0.18
Consensus pattern (16 bp):
AACCTGAACCAAATTT
Found at i:13584 original size:39 final size:39
Alignment explanation
Indices: 13494--13585 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 39
13484 TACTAGTATT
* ***
13494 TTAGTGGCATTTTTGAACAAACGCCGCTAAAGACTTGTGTT
1 TTAGTGG--TTTTTAAACAAACGCCGCTAAAGACTTGTACA
*
13535 TTAG-GCGTTTTTAAACAAATGCCGCTAAAGACTTGTACA
1 TTAGTG-GTTTTTAAACAAACGCCGCTAAAGACTTGTACA
13574 TTAGTGGTTTTT
1 TTAGTGGTTTTT
13586 TTATAAACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
39 37 0.84
40 2 0.05
41 5 0.11
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (39 bp):
TTAGTGGTTTTTAAACAAACGCCGCTAAAGACTTGTACA
Found at i:15536 original size:25 final size:25
Alignment explanation
Indices: 15507--15559 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
15497 AGCTCAATTT
*
15507 CATAACTGAATTTCATAGAGTTAAA
1 CATAACTCAATTTCATAGAGTTAAA
15532 CATAACTCAATTTCATAGAGTTAAA
1 CATAACTCAATTTCATAGAGTTAAA
15557 CAT
1 CAT
15560 TACCATCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.32
Consensus pattern (25 bp):
CATAACTCAATTTCATAGAGTTAAA
Found at i:16410 original size:40 final size:40
Alignment explanation
Indices: 16360--16451 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 40
16350 AATAGACAAA
* * * * * *
16360 TAGCAACGTTTTAGAAAATGTCACTAAAGATCATAACCTT
1 TAGCGACGTTTGAAAAAATGACACTAAAAAGCATAACCTT
* *
16400 TAGTGACGTTTGAAAAAATGACACTAAAAAGCGTAACCTT
1 TAGCGACGTTTGAAAAAATGACACTAAAAAGCATAACCTT
16440 TAGCGACGTTTG
1 TAGCGACGTTTG
16452 TTTCAAAGGT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (40 bp):
TAGCGACGTTTGAAAAAATGACACTAAAAAGCATAACCTT
Found at i:21748 original size:12 final size:13
Alignment explanation
Indices: 21731--21765 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
21721 TTTTTGCATC
21731 ATTATTATTTAT-
1 ATTATTATTTATA
21743 ATTATTATTTATA
1 ATTATTATTTATA
21756 ATTATATATT
1 ATTAT-TATT
21766 ATTTTACAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 5 0.24
14 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTATTATTTATA
Found at i:22003 original size:26 final size:26
Alignment explanation
Indices: 21963--22075 Score: 138
Period size: 26 Copynumber: 4.3 Consensus size: 26
21953 TTCCAGAACA
* *
21963 AGCCACCACCACTTGGACCACTCAAT
1 AGCCACCACCGCTTGGACCACTCAAC
*
21989 AGCCACTACCGCTTGGACCACTCAAC
1 AGCCACCACCGCTTGGACCACTCAAC
*
22015 AGCCACCACCGCTTTGACCACTCAAC
1 AGCCACCACCGCTTGGACCACTCAAC
* * *
22041 AACCACCGCCGGC-TAGACCACTCAAC
1 AGCCACCACC-GCTTGGACCACTCAAC
*
22067 AACCACCAC
1 AGCCACCAC
22076 TGCTGCCAAC
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 75 0.97
27 2 0.03
ACGTcount: A:0.30, C:0.45, G:0.12, T:0.12
Consensus pattern (26 bp):
AGCCACCACCGCTTGGACCACTCAAC
Found at i:26790 original size:31 final size:32
Alignment explanation
Indices: 26741--26890 Score: 146
Period size: 32 Copynumber: 4.8 Consensus size: 32
26731 AGTTGACCTA
*
26741 AACCAAAAATCAACCGATCCGATATTGATCCG
1 AACCGAAAATCAACCGATCCGATATTGATCCG
* * * *
26773 -ACC-AAAATCTAATCGATCCTATATTAACCCG
1 AACCGAAAATC-AACCGATCCGATATTGATCCG
* * *
26804 -ACCCAAAATCACCCGACCCGATATTGA-CCTG
1 AACCGAAAATCAACCGATCCGATATTGATCC-G
** *
26835 AACCGAAAATCAATTGATCCGATATTGATTCG
1 AACCGAAAATCAACCGATCCGATATTGATCCG
*
26867 AACCGAGAATCAACCGATCCGATA
1 AACCGAAAATCAACCGATCCGATA
26891 ATCATTCGAC
Statistics
Matches: 95, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
30 8 0.08
31 36 0.38
32 50 0.53
33 1 0.01
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.21
Consensus pattern (32 bp):
AACCGAAAATCAACCGATCCGATATTGATCCG
Found at i:26898 original size:32 final size:32
Alignment explanation
Indices: 26834--26923 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 32
26824 ATATTGACCT
** * *
26834 GAACCGAAAATCAATTGATCCGATATTGATTC
1 GAACCGAAAATCAACCGATCCGATAATCATTC
*
26866 GAACCGAGAATCAACCGATCCGATAATCATTC
1 GAACCGAAAATCAACCGATCCGATAATCATTC
* *
26898 G-ACCTGAAAATTAACCTGACCCGATA
1 GAACC-GAAAATCAACC-GATCCGATA
26924 CCCGATCAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 3 0.06
32 37 0.77
33 8 0.17
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (32 bp):
GAACCGAAAATCAACCGATCCGATAATCATTC
Found at i:36437 original size:19 final size:21
Alignment explanation
Indices: 36399--36437 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
36389 AGAGGGTAAG
36399 ATAAGAAGGCGTGAGAGAGAA
1 ATAAGAAGGCGTGAGAGAGAA
*
36420 ATAA-AAGG-GTGAGGGAGA
1 ATAAGAAGGCGTGAGAGAGA
36438 GAAAGAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.46, C:0.03, G:0.41, T:0.10
Consensus pattern (21 bp):
ATAAGAAGGCGTGAGAGAGAA
Found at i:37637 original size:32 final size:31
Alignment explanation
Indices: 37611--37672 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
37601 ATATTTCAAT
37611 TTCATCCCCCAAACTATGACCTATATTCTAAC
1 TTCAT-CCCCAAACTATGACCTATATTCTAAC
* *
37643 TTGATCCTCAAACTATGACCT-TCATTCTAA
1 TTCATCCCCAAACTATGACCTAT-ATTCTAA
37673 ATTTGTCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 1 0.04
31 22 0.81
32 4 0.15
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.34
Consensus pattern (31 bp):
TTCATCCCCAAACTATGACCTATATTCTAAC
Found at i:38253 original size:112 final size:112
Alignment explanation
Indices: 38056--38272 Score: 371
Period size: 112 Copynumber: 1.9 Consensus size: 112
38046 CGGAGACGAA
38056 CTTAAACTTAGGAGGAGGGGCAAACTAAAATTCCAGGAGGGACAAAAACATATTTTCAATAGGAA
1 CTTAAACTTAGGAGGAGGGGCAAACTAAAATTCCAGGAGGGACAAAAACATATTTTCAATAGGAA
* * *
38121 ATATATAAAAGAATCTAAAATATATGACAATTTTAAATTTGTCCCCC
66 ATATATAAAAAAATCTAAAATATATAAAAATTTTAAATTTGTCCCCC
* * * *
38168 CTTAAACTTAGGAGGAGGGGCGAACTAGAATTCCAGGAGGGACAAAAACATGTTTTTAATAGGAA
1 CTTAAACTTAGGAGGAGGGGCAAACTAAAATTCCAGGAGGGACAAAAACATATTTTCAATAGGAA
38233 ATATATAAAAAAATCTAAAATATATAAAAATTTTAAATTT
66 ATATATAAAAAAATCTAAAATATATAAAAATTTTAAATTT
38273 TTAGGGGAGC
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 98 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.27
Consensus pattern (112 bp):
CTTAAACTTAGGAGGAGGGGCAAACTAAAATTCCAGGAGGGACAAAAACATATTTTCAATAGGAA
ATATATAAAAAAATCTAAAATATATAAAAATTTTAAATTTGTCCCCC
Found at i:44573 original size:23 final size:23
Alignment explanation
Indices: 44537--44605 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
44527 CACCACAGCT
* *
44537 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* *
44560 CGTAGAATTACACC-ATAGTGCCG
1 CGTAGAAATACACCGA-AGTGCCA
44583 CGTAGAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
44606 TATAAGGTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:46277 original size:20 final size:22
Alignment explanation
Indices: 46252--46311 Score: 88
Period size: 20 Copynumber: 2.7 Consensus size: 22
46242 TTCCCCTTGA
46252 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
46272 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
46295 ATGTGCATCGATGCATT
1 A-GTGCATCGATGCATT
46312 ACCCATGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.47
22 1 0.03
23 3 0.08
24 15 0.42
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:56052 original size:20 final size:21
Alignment explanation
Indices: 56008--56065 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
55998 TGCATGGTAG
56008 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T-AAGAA
56032 TGCATCGATGCACTG-AAGAA
1 TGCATCGATGCACTGTAAGAA
*
56052 TGCACCGATGCACT
1 TGCATCGATGCACT
56066 TCAATGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 18 0.55
23 2 0.06
24 13 0.39
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (21 bp):
TGCATCGATGCACTGTAAGAA
Found at i:56985 original size:45 final size:46
Alignment explanation
Indices: 56878--56985 Score: 173
Period size: 46 Copynumber: 2.4 Consensus size: 46
56868 GAGGGTCTAC
* *
56878 GTGGTCTTTCGGGATATAGTGGTCCTTCGGGACATATATGTTATAT
1 GTGGTCCTTCGGGACATAGTGGTCCTTCGGGACATATATGTTATAT
*
56924 GTGGTCCTTCGGGACATAGTGGTCCTTCGGGAC-TATGTGTTATAT
1 GTGGTCCTTCGGGACATAGTGGTCCTTCGGGACATATATGTTATAT
*
56969 GTGGTCCTTCGAGACAT
1 GTGGTCCTTCGGGACAT
56986 TTACGTTGTC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 27 0.47
46 31 0.53
ACGTcount: A:0.18, C:0.17, G:0.30, T:0.36
Consensus pattern (46 bp):
GTGGTCCTTCGGGACATAGTGGTCCTTCGGGACATATATGTTATAT
Found at i:60195 original size:20 final size:20
Alignment explanation
Indices: 60170--60208 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
60160 ACACATGTTA
*
60170 AAGAATACATCGATGCACTG
1 AAGAATACACCGATGCACTG
*
60190 AAGAATGCACCGATGCACT
1 AAGAATACACCGATGCACT
60209 TCAATGGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
AAGAATACACCGATGCACTG
Found at i:61082 original size:28 final size:28
Alignment explanation
Indices: 61039--61111 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
61029 TCGGGACATA
*
61039 GTGGTCCTTCGTGACATATGTGTTATAT
1 GTGGTCCTTCGGGACATATGTGTTATAT
61067 GTGGTCCTTCGGGACATATGTGTTATAT
1 GTGGTCCTTCGGGACATATGTGTTATAT
61095 GTGGTCCTTCGGGACAT
1 GTGGTCCTTCGGGACAT
61112 CTACGTGGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.16, C:0.16, G:0.29, T:0.38
Consensus pattern (28 bp):
GTGGTCCTTCGGGACATATGTGTTATAT
Found at i:63951 original size:22 final size:21
Alignment explanation
Indices: 63897--63960 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
63887 AGTCGAGGGT
63897 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
63918 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
63940 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
63961 ATTTCATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:65385 original size:21 final size:21
Alignment explanation
Indices: 65359--65455 Score: 135
Period size: 21 Copynumber: 4.6 Consensus size: 21
65349 CCCTACCAAG
65359 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
* *
65380 GACGAGAAGACTACTCATAAA
1 GACGAGAAGACCATTCATAAA
65401 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
*
65422 GAC-ATGAAGACCCTTCATAAA
1 GACGA-GAAGACCATTCATAAA
65443 GAC-ATGAAGACCA
1 GACGA-GAAGACCA
65456 CTTCGCATTG
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
20 1 0.01
21 68 0.99
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (21 bp):
GACGAGAAGACCATTCATAAA
Found at i:65713 original size:6 final size:6
Alignment explanation
Indices: 65702--65731 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
65692 TAACACTTCA
*
65702 TGCATT TGCATT TGCTTT TGCATT TGCATT
1 TGCATT TGCATT TGCATT TGCATT TGCATT
65732 ATTATTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.13, C:0.17, G:0.17, T:0.53
Consensus pattern (6 bp):
TGCATT
Found at i:65758 original size:20 final size:20
Alignment explanation
Indices: 65717--65754 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
65707 TTGCATTTGC
*
65717 TTTTGCATTTGCATTATTAT
1 TTTTGCATTAGCATTATTAT
65737 TTTTGCATTAGC-TTATTA
1 TTTTGCATTAGCATTATTA
65755 ATTTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.58
Consensus pattern (20 bp):
TTTTGCATTAGCATTATTAT
Found at i:71780 original size:37 final size:37
Alignment explanation
Indices: 71729--71881 Score: 211
Period size: 37 Copynumber: 4.1 Consensus size: 37
71719 ATGAGATTGG
71729 AGCAAAGTCAATCTTAAGCCTTCACCGAAAAGGAGTGA
1 AGCAAA-TCAATCTTAAGCCTTCACCGAAAAGGAGTGA
71767 AGCAAATCAATCTTAAGCCTTCACC-AAAGAGGAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAA-AGGAGTGA
* * *
71804 AGCAAA-CCATCTTAAGCCTTCACCAAAAAGGAGAGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAAAGGAGTGA
* * *
71840 AGCAAATCAATTTGTAAGCCTTCACCGAAGAGTAGTGA
1 AGCAAATCAATCT-TAAGCCTTCACCGAAAAGGAGTGA
71878 AGCA
1 AGCA
71882 CCACCTTGAG
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
36 33 0.32
37 40 0.39
38 30 0.29
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.18
Consensus pattern (37 bp):
AGCAAATCAATCTTAAGCCTTCACCGAAAAGGAGTGA
Found at i:71823 original size:36 final size:36
Alignment explanation
Indices: 71739--71919 Score: 190
Period size: 36 Copynumber: 5.0 Consensus size: 36
71729 AGCAAAGTCA
*
71739 ATCTTAAGCCTTCACCGAAA-AGGAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACC-AAAGAGGAGTGAAGCAAA-CC
71776 ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
* * *
71812 ATCTTAAGCCTTCACCAAAAAGGAGAGAAGCAAATCA
1 ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAA-CC
* * *
71849 ATTTGTAAGCCTTCACCGAAGAGTAGTGAAGC--ACC
1 ATCT-TAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
* * **
71884 ACCTTGAGCCTTCA-CAGAAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCA-AAGAGGAGTGAAGCAAACC
71920 CATCAGTAAG
Statistics
Matches: 123, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
33 1 0.01
34 22 0.18
35 3 0.02
36 40 0.33
37 34 0.28
38 23 0.19
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.18
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
Found at i:71825 original size:73 final size:72
Alignment explanation
Indices: 71739--71917 Score: 236
Period size: 73 Copynumber: 2.5 Consensus size: 72
71729 AGCAAAGTCA
71739 ATCTTAAGCCTTCACCGAAAAGGAGTGAAGCAAATCAATCT-TAAGCCTTCACCAAAGAGGAGTG
1 ATCTTAAGCCTTCACCGAAAAGGAGTGAAGCAAATCAATCTGTAAGCCTTCACCAAAGAGGAGTG
71803 AAGCAAACC
66 AAGC--ACC
* * * * *
71812 ATCTTAAGCCTTCACCAAAAAGGAGAGAAGCAAATCAATTTGTAAGCCTTCACCGAAGAGTAGTG
1 ATCTTAAGCCTTCACCGAAAAGGAGTGAAGCAAATCAATCTGTAAGCCTTCACCAAAGAGGAGTG
71877 AAGCACC
66 AAGCACC
* * * *
71884 ACCTTGAGCCTTCACAGAAGAA-TAGTGAAGCAAA
1 ATCTTAAGCCTTCACCGAA-AAGGAGTGAAGCAAA
71918 CCCATCAGTA
Statistics
Matches: 93, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
72 28 0.30
73 40 0.43
74 25 0.27
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (72 bp):
ATCTTAAGCCTTCACCGAAAAGGAGTGAAGCAAATCAATCTGTAAGCCTTCACCAAAGAGGAGTG
AAGCACC
Found at i:72377 original size:215 final size:214
Alignment explanation
Indices: 71919--72661 Score: 1129
Period size: 215 Copynumber: 3.5 Consensus size: 214
71909 TGAAGCAAAC
71919 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * *
71984 GATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGAGAAGGATGTTTTCACATGAATTTGGAAA
66 GATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* * *
72049 TAAAAAATGATGTTTTAAGAAGATGTAATTTTTGAAAA-TGAAGAATGCGATTTTTAAAATTTCA
131 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACT-AAGAATGCGATTTTCAAAATTTCA
72113 CAATTTATAAGTCCTTCGGG
195 CAATTTATAAGTCCTTCGGG
72133 CCATCAGTAAGTCTTTCGAGCATGATGCTTACAA-CCTTCGGGTCATCTGTAAGCCTTTAGAGCA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTA-AATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
*
72197 AGATGATAAGT-CTTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAA
65 AGATGATAAGTCCTTT-GGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAA
*
72261 AATGAAAAATTGATGTTTTAAGAGGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTT
129 AATGAAAAA-TGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTT
72326 CACAATTTATAAGTCCTTCGGG
193 CACAATTTATAAGTCCTTCGGG
* *
72348 CTATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
*
72413 GATGATAAGTCCTTTGGACCATCCATAAGACC-TCTGGGTAGGATGTTTTCACATGAATTTGAAA
66 GATGATAAGTCCTTTGGGCCATCCATAAGACCTTC-GGGTAGGATGTTTTCACATGAATTTGAAA
* * * *
72477 ATG-AAAATGATGTTTGAAGATGATGAAATTTTTGGAAACTAAGAATGCGATTTCCAAAATTTCA
130 ATGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCA
*
72541 C-ACTTAGTAAGTCCTTCGGG
195 CAATTTA-TAAGTCCTTCGGG
* ** * * * ** *
72561 CCATCAATAAGTCTTTCGAGCATGATATTTAAATCCTTCGGGTCATTTGTGAGTCACTCGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * * *
72626 GATGATAAATCCTTTGGGTCATTCATAAGATCTTCG
66 GATGATAAGTCCTTTGGGCCATCCATAAGACCTTCG
72662 AGCAAGATGT
Statistics
Matches: 487, Mismatches: 33, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
212 4 0.01
213 153 0.31
214 134 0.28
215 191 0.39
216 5 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (214 bp):
CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
GATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCAC
AATTTATAAGTCCTTCGGG
Found at i:76247 original size:81 final size:81
Alignment explanation
Indices: 76153--76315 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
76143 CTTTTCTTTC
*
76153 TTTCAGTAAAAAACAACTCTCTACTTCAATTATTATCAAATAAACAGCTTTAAGTTTTTTATATA
1 TTTCAGCAAAAAACAACTCTCTACTTCAATTATTATCAAATAAACAGCTTTAAGTTTTTTATATA
76218 TAAACTATACTGTAGT
66 TAAACTATACTGTAGT
76234 TTTCAGCAAAAAACAACTCTCTACTTCAATTATTATCAAATAAACAGCTTTAAGTTTTTTATATA
1 TTTCAGCAAAAAACAACTCTCTACTTCAATTATTATCAAATAAACAGCTTTAAGTTTTTTATATA
76299 TAAACTATACTGTAGT
66 TAAACTATACTGTAGT
76315 T
1 T
76316 AATAGCAGAG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.39
Consensus pattern (81 bp):
TTTCAGCAAAAAACAACTCTCTACTTCAATTATTATCAAATAAACAGCTTTAAGTTTTTTATATA
TAAACTATACTGTAGT
Found at i:76579 original size:20 final size:20
Alignment explanation
Indices: 76556--76741 Score: 113
Period size: 20 Copynumber: 9.3 Consensus size: 20
76546 GTTTCCAAAT
76556 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
76576 TCGCAACAC-AGA-A-GTCAAA
1 TCGCAACGCGA-ATATGT-AAA
76595 TTCGCAACGCG-ATA-GTCAAA
1 -TCGCAACGCGAATATGT-AAA
*
76615 TTTGCAACGCG-ATA-GTCAAA
1 -TCGCAACGCGAATATGT-AAA
*
76635 TTCGCAACACTG-A-A-GTCAAA
1 -TCGCAACGC-GAATATGT-AAA
* * *
76655 TTTGCAACGCGAATCTATAAA
1 -TCGCAACGCGAATATGTAAA
* *
76676 TCACAACGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
* *
76696 TCACAACGCGAATTTGTAAA
1 TCGCAACGCGAATATGTAAA
*
76716 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATATGTAAA
76736 TCGCAA
1 TCGCAA
76742 AACAGAAGTC
Statistics
Matches: 143, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
18 2 0.01
19 7 0.05
20 128 0.90
21 5 0.03
22 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:76622 original size:40 final size:40
Alignment explanation
Indices: 76551--76882 Score: 136
Period size: 40 Copynumber: 8.3 Consensus size: 40
76541 ACCCAGTTTC
*
76551 CAAATTCGCAACGCGAATATGT-AAA-TCGCAACACAGA-AGT
1 CAAATTCGCAACGCG-ATA-GTCAAATTTGCAACAC-GATAGT
*
76591 CAAATTCGCAACGCGATAGTCAAATTTGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGTCAAATTTGCAACACGATAGT
* *
76631 CAAATTCGCAACACTGA-AGTCAAATTTGCAACGCGA-A-T
1 CAAATTCGCAACGC-GATAGTCAAATTTGCAACACGATAGT
* * * ** * *
76669 CTATAAATCACAACGCGAATCTGT-AAA-TCACAACGCGAATTTGT
1 C-A-AATTCGCAACGCG-AT-AGTCAAATTTGCAACACG-A-TAGT
* * *
76713 -AAA-TCGCAACGCGAATTTGT-AAA-TCGCAAAACAGA-AGT
1 CAAATTCGCAACGCG-A-TAGTCAAATTTGCAACAC-GATAGT
* * * * *
76751 CAAATTCGTAACACAGA-AATCAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGC-GATAGTCAAATTTGCAACACGATAGT
* * * ** * *
76791 CAAATTCGCAACACTGA-ATTTCAAATTCGCAACATAAAACT
1 CAAATTCGCAACGC-GATA-GTCAAATTTGCAACACGATAGT
* ** * *
76832 CAAATTCGCAACGCGATAATCAAATTCACAATACGAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTTGCAACACGATAGT
76872 CAAATTCGCAA
1 CAAATTCGCAA
76883 AGCGCGTTTA
Statistics
Matches: 233, Mismatches: 36, Indels: 46
0.74 0.11 0.15
Matches are distributed among these distances:
38 7 0.03
39 19 0.08
40 162 0.70
41 41 0.18
42 3 0.01
44 1 0.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.21
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTTGCAACACGATAGT
Found at i:76640 original size:60 final size:60
Alignment explanation
Indices: 76551--76882 Score: 240
Period size: 60 Copynumber: 5.5 Consensus size: 60
76541 ACCCAGTTTC
*
76551 CAAATTCGCAACGCGAATATGT-AAA-TCGCAACACAGAAGTCAAATTCGCAACGCGATAGT
1 CAAATTCGCAACACG-ATA-GTCAAATTCGCAACACAGAAGTCAAATTCGCAACGCGATAGT
* * * *
76611 CAAATTTGCAACGCGATAGTCAAATTCGCAACACTGAAGTCAAATTTGCAACGCGA-A-T
1 CAAATTCGCAACACGATAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACGCGATAGT
* * * * * *
76669 CTATAAATCACAACGCGAATCTGT-AAA-TCACAACGC-GAATTTGT-AAA-TCGCAACGCGAAT
1 C-A-AATTCGCAACACG-AT-AGTCAAATTCGCAACACAGAA---GTCAAATTCGCAACGCG-A-
*
76729 TTGT
57 TAGT
* * *
76733 -AAA-TCGCAAAACAGA-AGTCAAATTCGTAACACAGAAATCAAATTCGCAACGCGATAGT
1 CAAATTCGCAACAC-GATAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACGCGATAGT
* * * * *
76791 CAAATTCGCAACACTGA-ATTTCAAATTCGCAACATAAAACTCAAATTCGCAACGCGATAAT
1 CAAATTCGCAACAC-GATA-GTCAAATTCGCAACACAGAAGTCAAATTCGCAACGCGATAGT
* * *
76852 CAAATTCACAATACGAAAGTCAAATTCGCAA
1 CAAATTCGCAACACGATAGTCAAATTCGCAA
76883 AGCGCGTTTA
Statistics
Matches: 218, Mismatches: 31, Indels: 46
0.74 0.11 0.16
Matches are distributed among these distances:
58 10 0.05
59 21 0.10
60 117 0.54
61 64 0.29
62 5 0.02
64 1 0.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.21
Consensus pattern (60 bp):
CAAATTCGCAACACGATAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACGCGATAGT
Found at i:76768 original size:20 final size:20
Alignment explanation
Indices: 76736--76882 Score: 120
Period size: 20 Copynumber: 7.3 Consensus size: 20
76726 AATTTGTAAA
*
76736 TCGCAAAACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
76756 TCGTAACACAGAAATCAAAT
1 TCGCAACACAGAAGTCAAAT
*
76776 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
76796 TCGCAACACTGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
* * *
76817 TCGCAACATAAAACTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
76837 TCGCAACGC-GATAATCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
76857 TCACAATAC-GAAAGTCAAAT
1 TCGCAACACAG-AAGTCAAAT
76877 TCGCAA
1 TCGCAA
76883 AGCGCGTTTA
Statistics
Matches: 101, Mismatches: 21, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
19 3 0.03
20 79 0.78
21 19 0.19
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.20
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:77067 original size:22 final size:22
Alignment explanation
Indices: 77042--77092 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
77032 CTACGGCGAC
*
77042 ATCCGTCCCCATATCTGACAAA
1 ATCCGTCCCCATATCCGACAAA
*
77064 ATCCGTCCCCATCTCCGACAAA
1 ATCCGTCCCCATATCCGACAAA
77086 ATCCGTC
1 ATCCGTC
77093 TATCTTCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.41, G:0.10, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATATCCGACAAA
Found at i:79459 original size:42 final size:42
Alignment explanation
Indices: 79412--79530 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
79402 GATTCACCTG
* * * * *
79412 TCATCGTTCAAGAGGCACCTCCTATCGTTCAGGAGGCTCCTC
1 TCATCGTTCAAGAGACACCTCCCACCGTTCAAGAGGCTCCTA
* * *
79454 TCATCGTTTAAGAGACCCCTCCCACCGTTCAAGAGGCTTCTA
1 TCATCGTTCAAGAGACACCTCCCACCGTTCAAGAGGCTCCTA
* *
79496 TCATCGTTCAATGGGTC-CCTCCCACCGTTCAAGAG
1 TCATCGTTCAA-GAGACACCTCCCACCGTTCAAGAG
79531 CCCGATTCAT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 62 0.95
43 3 0.05
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (42 bp):
TCATCGTTCAAGAGACACCTCCCACCGTTCAAGAGGCTCCTA
Found at i:79503 original size:21 final size:21
Alignment explanation
Indices: 79412--79506 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
79402 GATTCACCTG
*
79412 TCATCGTTCAAGAGGCACCTC
1 TCATCGTTCAAGAGGCTCCTC
*
79433 -CTATCGTTCAGGAGGCTCCTC
1 TC-ATCGTTCAAGAGGCTCCTC
* * *
79454 TCATCGTTTAAGAGACCCCTC
1 TCATCGTTCAAGAGGCTCCTC
* * * *
79475 CCACCGTTCAAGAGGCTTCTA
1 TCATCGTTCAAGAGGCTCCTC
79496 TCATCGTTCAA
1 TCATCGTTCAA
79507 TGGGTCCCTC
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 1 0.02
21 55 0.96
22 1 0.02
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCTCCTC
Found at i:80940 original size:14 final size:14
Alignment explanation
Indices: 80921--80957 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
80911 GCTTGTTTAA
80921 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
80935 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
80949 TTGATTTGT
1 TTGATTTGT
80958 TTAATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:81009 original size:81 final size:79
Alignment explanation
Indices: 80866--81024 Score: 273
Period size: 81 Copynumber: 2.0 Consensus size: 79
80856 TTTTACATTG
80866 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTA
80931 AAAGTTGATTTGTA
66 AAAGTTGATTTGTA
* * *
80945 AAAGTTGATTTGTTTAATTTTATGTGTAAATAAGAATTATTTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA-TTTTTTTGCTTGTTTAATTGATTTG
81010 TAAAAGTTGATTTGT
64 TAAAAGTTGATTTGT
81025 TGTTTTAAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
79 17 0.23
80 18 0.24
81 40 0.53
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (79 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTA
AAAGTTGATTTGTA
Found at i:81105 original size:20 final size:20
Alignment explanation
Indices: 81080--81127 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
81070 TTGAAGGTAC
*
81080 AAATTCTCAACGCAAAAGGT
1 AAATTCGCAACGCAAAAGGT
*
81100 AAATTCGCAACGCGAAA-GT
1 AAATTCGCAACGCAAAAGGT
81119 CAAATTCGC
1 -AAATTCGC
81128 GTTGCGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATTCGCAACGCAAAAGGT
Found at i:81159 original size:13 final size:14
Alignment explanation
Indices: 81123--81161 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
81113 GAAAGTCAAA
81123 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
81137 TTCG-GTTTGCGA-T
1 TTCGCG-TTGCGATT
81150 TTCGCGTTGCGA
1 TTCGCGTTGCGA
81162 ATTTGACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.08, C:0.21, G:0.31, T:0.41
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:81165 original size:14 final size:14
Alignment explanation
Indices: 81123--81165 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
81113 GAAAGTCAAA
*
81123 TTCGCGTTGCGATT
1 TTCGCGTTGCGAAT
81137 TTCG-GTTTGCG-AT
1 TTCGCG-TTGCGAAT
81150 TTCGCGTTGCGAAT
1 TTCGCGTTGCGAAT
81164 TT
1 TT
81166 GACTTTCGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (14 bp):
TTCGCGTTGCGAAT
Found at i:83701 original size:24 final size:24
Alignment explanation
Indices: 83667--83720 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
83657 CTGAAACATC
83667 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
83691 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
83715 ATCAAA
1 ATCAAA
83721 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:84511 original size:14 final size:15
Alignment explanation
Indices: 84475--84512 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
84465 GAAATCATTG
84475 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
84490 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
84505 AAAAATTA
1 AAAAATTA
84513 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:84694 original size:19 final size:20
Alignment explanation
Indices: 84670--84760 Score: 89
Period size: 19 Copynumber: 4.6 Consensus size: 20
84660 CTAAAACCTA
*
84670 TTGCGAAATT-AAATTCGTG
1 TTGCGAAATTGAAATTCGAG
*
84689 TTGCG-AATTCGAAAATCGAG
1 TTGCGAAATT-GAAATTCGAG
*
84709 TTGCGAATTTGAAATTC-AG
1 TTGCGAAATTGAAATTCGAG
* *
84728 TTGCGAATTTGAAATTCAGTG
1 TTGCGAAATTGAAATTC-GAG
*
84749 TTGCGAATTTGA
1 TTGCGAAATTGA
84761 CTATTGCGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
18 4 0.06
19 24 0.39
20 18 0.29
21 16 0.26
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (20 bp):
TTGCGAAATTGAAATTCGAG
Found at i:84713 original size:20 final size:20
Alignment explanation
Indices: 84670--84860 Score: 154
Period size: 20 Copynumber: 9.6 Consensus size: 20
84660 CTAAAACCTA
* * *
84670 TTGCGAAATT-AAATTCGTG
1 TTGCGAATTTGAAAATCGCG
* *
84689 TTGCGAATTCGAAAATCGAG
1 TTGCGAATTTGAAAATCGCG
* *
84709 TTGCGAATTTGAAATTC-AG
1 TTGCGAATTTGAAAATCGCG
* *
84728 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAAATC-GCG
** *
84749 TTGCGAATTTGACTATTGCG
1 TTGCGAATTTGAAAATCGCG
**
84769 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGAAAATCGCG
**
84789 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGAAAATCGCG
** *
84809 TTGCGAATTTG-ACTTCAGTG
1 TTGCGAATTTGAAAATC-GCG
**
84829 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGAAAATCGCG
84849 TTGCGAATTTGA
1 TTGCGAATTTGA
84861 CTTATGTGTT
Statistics
Matches: 146, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
19 29 0.20
20 101 0.69
21 16 0.11
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCGCG
Found at i:84861 original size:20 final size:20
Alignment explanation
Indices: 84748--84862 Score: 196
Period size: 20 Copynumber: 5.8 Consensus size: 20
84738 GAAATTCAGT
*
84748 GTTGCGAATTTGACTATTGC
1 GTTGCGAATTTGACTATCGC
84768 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
84788 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
84808 GTTGCGAATTTGACT-TCAGT
1 GTTGCGAATTTGACTATC-GC
84828 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
84848 GTTGCGAATTTGACT
1 GTTGCGAATTTGACT
84863 TATGTGTTTG
Statistics
Matches: 90, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
19 2 0.02
20 86 0.96
21 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:84870 original size:40 final size:40
Alignment explanation
Indices: 84727--84863 Score: 222
Period size: 40 Copynumber: 3.4 Consensus size: 40
84717 TTGAAATTCA
* *
84727 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATTGC
1 GTTGCGAATTTG-ACTTCAGTGTTGCGAATTTGACTATCGC
*
84768 GTTGCGAATTTGACTATC-GCGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCAGTGTTGCGAATTTGACTATCGC
84808 GTTGCGAATTTGACTTCAGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTCAGTGTTGCGAATTTGACTATCGC
84848 GTTGCGAATTTGACTT
1 GTTGCGAATTTGACTT
84864 ATGTGTTTGA
Statistics
Matches: 90, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
39 2 0.02
40 74 0.82
41 14 0.16
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (40 bp):
GTTGCGAATTTGACTTCAGTGTTGCGAATTTGACTATCGC
Found at i:92186 original size:8 final size:8
Alignment explanation
Indices: 92173--92213 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
92163 CTCATTTTCA
92173 GAGAATTT
1 GAGAATTT
92181 GAGAATTT
1 GAGAATTT
*
92189 -AGAGTTT
1 GAGAATTT
*
92196 GGGAATTT
1 GAGAATTT
92204 GAGAATTT
1 GAGAATTT
92212 GA
1 GA
92214 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:92512 original size:128 final size:128
Alignment explanation
Indices: 92284--93424 Score: 2122
Period size: 128 Copynumber: 8.9 Consensus size: 128
92274 TAATCGGAGT
*
92284 ACTATTCACATGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
92349 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
92412 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
92477 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
92540 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
92605 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
92668 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
92733 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
92796 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTTAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
92861 TATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
92924 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTTAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
92989 TATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* ***
93052 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
*
93116 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTATCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
93180 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
* *
93245 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTATATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
93308 ACTATTCACATGAAGGTGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
93373 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
93425 AATCAGGTAA
Statistics
Matches: 988, Mismatches: 23, Indels: 4
0.97 0.02 0.00
Matches are distributed among these distances:
127 1 0.00
128 986 1.00
129 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:93885 original size:33 final size:34
Alignment explanation
Indices: 93824--93923 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
93814 AAATTTAATG
*
93824 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* * * *
93858 TTAAA-TTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
*
93891 TTAAATTTTGAATAATATAATTTGTATTTTAAA
1 TTAAATTTTGAATAATATAATTTATATTTTAAA
93924 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (34 bp):
TTAAATTTTGAATAATATAATTTATATTTTAAAT
Found at i:94531 original size:21 final size:21
Alignment explanation
Indices: 94443--94536 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
94433 TATGGTATAA
*
94443 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
94464 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
94485 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
94506 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
94527 AACCCTGCGG
1 AACCCTGCGG
94537 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:94566 original size:21 final size:21
Alignment explanation
Indices: 94540--94587 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
94530 CCTGCGGAGA
*
94540 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
94561 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
94582 GGGCAT
1 TGGCAT
94588 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:96334 original size:15 final size:16
Alignment explanation
Indices: 96314--96388 Score: 57
Period size: 17 Copynumber: 4.8 Consensus size: 16
96304 ATAATTCTAA
96314 ATAAATAATAATT-AT
1 ATAAATAATAATTAAT
* *
96329 ATAAATATTATTTTAAT
1 ATAAATAATA-ATTAAT
*
96346 AAAAATAATAA-T-AT
1 ATAAATAATAATTAAT
* *
96360 TTACATAATATATTAAT
1 ATAAATAATA-ATTAAT
*
96377 ATAAAAAATAAT
1 ATAAATAATAAT
96389 AACTATTTAA
Statistics
Matches: 44, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
14 9 0.20
15 11 0.25
16 5 0.11
17 19 0.43
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAATAATAATTAAT
Found at i:96387 original size:31 final size:31
Alignment explanation
Indices: 96314--96389 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
96304 ATAATTCTAA
* * *
96314 ATAAATAATAATTATATAAATATTATTTTAAT
1 ATAAAAAATAA-TATATAAATAATATATTAAT
* *
96346 A-AAAATAATAATATTTACATAATATATTAAT
1 ATAAAA-AATAATATATAAATAATATATTAAT
96377 ATAAAAAATAATA
1 ATAAAAAATAATA
96390 ACTATTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
31 27 0.73
32 10 0.27
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (31 bp):
ATAAAAAATAATATATAAATAATATATTAAT
Found at i:96414 original size:33 final size:34
Alignment explanation
Indices: 96346--96416 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 34
96336 TTATTTTAAT
* * *
96346 AAAAATAATAATATTTACATAATATATTAATATA
1 AAAAATAATAATATTTACATAAAATACTAACATA
96380 AAAAATAATAACTATTTA-A-AAAATACTAACATA
1 AAAAATAATAA-TATTTACATAAAATACTAACATA
96413 AAAA
1 AAAA
96417 TAAATTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 15 0.45
34 12 0.36
35 6 0.18
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (34 bp):
AAAAATAATAATATTTACATAAAATACTAACATA
Found at i:105373 original size:49 final size:50
Alignment explanation
Indices: 105272--105374 Score: 127
Period size: 49 Copynumber: 2.1 Consensus size: 50
105262 AGTCTGAACT
* * * *
105272 ACATCATCGATTTAAGTGATATATCACGTGTCACATCATCATTTCGAATG
1 ACATCATCAATTTAAGTGATATATCACATGTCACATCATCACTTCCAATG
* * * *
105322 ACAT-ATCAATTTAATTGATATGTTACATGTCACATCATCACTTCCAGTG
1 ACATCATCAATTTAAGTGATATATCACATGTCACATCATCACTTCCAATG
105371 ACAT
1 ACAT
105375 TATATGTTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
49 41 0.91
50 4 0.09
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (50 bp):
ACATCATCAATTTAAGTGATATATCACATGTCACATCATCACTTCCAATG
Found at i:113734 original size:24 final size:22
Alignment explanation
Indices: 113707--113771 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
113697 CTAAGTGTCG
* *
113707 CATAGAAAATACATCGAAGTACCA
1 CATAGAAAAT-C-CCGAAGGACCA
*
113731 CATAGAATATCCCGAAGGACCA
1 CATAGAAAATCCCGAAGGACCA
**
113753 CATAG-ATGTCCCGAAGGAC
1 CATAGAAAATCCCGAAGGAC
113772 TGCGTAGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 13 0.35
22 14 0.38
23 1 0.03
24 9 0.24
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.15
Consensus pattern (22 bp):
CATAGAAAATCCCGAAGGACCA
Found at i:113766 original size:21 final size:22
Alignment explanation
Indices: 113721--113771 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
113711 GAAAATACAT
*
113721 CGAAGTACCACATAGAATATCC
1 CGAAGGACCACATAGAATATCC
*
113743 CGAAGGACCACATAG-ATGTCC
1 CGAAGGACCACATAGAATATCC
113764 CGAAGGAC
1 CGAAGGAC
113772 TGCGTAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (22 bp):
CGAAGGACCACATAGAATATCC
Found at i:113779 original size:21 final size:23
Alignment explanation
Indices: 113721--113797 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 23
113711 GAAAATACAT
* *
113721 CGAAGTACCACATAGAA-TATCC
1 CGAAGGACCACATAGAATTGTCC
113743 CGAAGGACCACATAG-A-TGTCC
1 CGAAGGACCACATAGAATTGTCC
** * *
113764 CGAAGGACTGCGTAGAATTGTCT
1 CGAAGGACCACATAGAATTGTCC
113787 CGAAGGACCAC
1 CGAAGGACCAC
113798 GTATAACCCT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
21 17 0.38
22 15 0.33
23 13 0.29
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (23 bp):
CGAAGGACCACATAGAATTGTCC
Found at i:113998 original size:44 final size:44
Alignment explanation
Indices: 113909--114008 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
113899 AGACCAGTAA
* * * *
113909 TCACGTAGGTTATGTCACATAGCTTATATCCTATGTTCATGTAT
1 TCACGTAGATCATGTCACATAGCTAATATCCTATGTTCATATAT
113953 TCACGTAGATCATGTCACATAGCTAATAT-CT-TGTTCTCATATAT
1 TCACGTAGATCATGTCACATAGCTAATATCCTATG-T-TCATATAT
*
113997 TCACATAGATCA
1 TCACGTAGATCA
114009 CATAGCACAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 2 0.04
43 3 0.06
44 44 0.90
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (44 bp):
TCACGTAGATCATGTCACATAGCTAATATCCTATGTTCATATAT
Found at i:124884 original size:6 final size:6
Alignment explanation
Indices: 124868--124908 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
124858 ATAATATATT
* *
124868 TATAAA GTATAAA TATAAA TATAAA TATATA TATATA TATA
1 TATAAA -TATAAA TATAAA TATAAA TATAAA TATAAA TATA
124909 GAATTATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (6 bp):
TATAAA
Found at i:125051 original size:30 final size:31
Alignment explanation
Indices: 124979--125053 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
124969 GCTAAATATG
124979 AACAAATATGTATAGTTTTGAAATGAACGTT
1 AACAAATATGTATAGTTTTGAAATGAACGTT
125010 AACAAATATGTATAGTTTTGAAATGAACGTT
1 AACAAATATGTATAGTTTTGAAATGAACGTT
*
125041 AA-ATATATGTATA
1 AACAAATATGTATA
125054 TGTATATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 10 0.23
31 33 0.77
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (31 bp):
AACAAATATGTATAGTTTTGAAATGAACGTT
Found at i:129478 original size:20 final size:20
Alignment explanation
Indices: 129448--129488 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
129438 AGATCATTTT
129448 TATTTTTTTATT-TTTGAAA
1 TATTTTTTTATTCTTTGAAA
129467 TATTTTTCTTATTCTTTGAAA
1 TATTTTT-TTATTCTTTGAAA
129488 T
1 T
129489 CATGATCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 5 0.25
21 8 0.40
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTTTTTTATTCTTTGAAA
Found at i:133003 original size:2 final size:2
Alignment explanation
Indices: 132996--133036 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
132986 AAATTATTAT
132996 TA TA TA TA T- TA T- TA -A TA TA T- 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 TA TA
133034 TA T
1 TA T
133037 TATTTATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.11
2 31 0.89
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:133006 original size:15 final size:15
Alignment explanation
Indices: 132975--133050 Score: 70
Period size: 15 Copynumber: 5.1 Consensus size: 15
132965 AATTCATTTT
132975 TATTATTATTA-A-A
1 TATTATTATTATATA
132988 -ATTATTATTATATA
1 TATTATTATTATATA
*
133002 TATTATTAATATAT-
1 TATTATTATTATATA
133016 TATATATATATATATATA
1 TAT-TAT-TAT-TATATA
*
133034 TATTATTTATTAAATA
1 TATTA-TTATTATATA
133050 T
1 T
133051 TAAAAAGCCC
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
12 10 0.19
13 1 0.02
14 4 0.08
15 15 0.29
16 8 0.15
17 10 0.19
18 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTATTATTATATA
Found at i:134342 original size:20 final size:20
Alignment explanation
Indices: 134295--134361 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
134285 GATTCTGACT
* **
134295 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTACGTAA
134315 ATTCGCATTGCGATTACGTAA
1 A-TCGCATTGCGATTACGTAA
134336 ATCGCATTGCGATTACGTAA
1 ATCGCATTGCGATTACGTAA
134356 ATCGCA
1 ATCGCA
134362 ATGCAAATCT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 26 0.60
21 17 0.40
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (20 bp):
ATCGCATTGCGATTACGTAA
Found at i:135296 original size:24 final size:24
Alignment explanation
Indices: 135245--135298 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
135235 GTATTCGAAA
*
135245 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
135269 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
135293 TTTGAT
1 TTTGAT
135299 GATTTTTCAG
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:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:137838 original size:20 final size:20
Alignment explanation
Indices: 137730--137836 Score: 144
Period size: 20 Copynumber: 5.3 Consensus size: 20
137720 GCAACACGAA
*
137730 ATCGCAACGC-GAATATGACT
1 ATCGCAACACGGAA-ATGACT
*
137750 ATCGCAACACGGAAATTACT
1 ATCGCAACACGGAAATGACT
137770 ATCGCAACACGGAAATGACT
1 ATCGCAACACGGAAATGACT
137790 ATCGCAACACGGAAATGACT
1 ATCGCAACACGGAAATGACT
* **
137810 ATCACAATGCGGAAATGACT
1 ATCGCAACACGGAAATGACT
*
137830 ATTGCAA
1 ATCGCAA
137837 TGAGAGAATC
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 75 0.96
21 3 0.04
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACACGGAAATGACT
Found at i:137879 original size:52 final size:53
Alignment explanation
Indices: 137814--137930 Score: 137
Period size: 52 Copynumber: 2.2 Consensus size: 53
137804 ATGACTATCA
** * * * *
137814 CAATGCGGAAATGACTATTGCAATGAGAGAATCGTAATGCG-AAATAAAAATTG
1 CAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATAAAAATCG
* *
137867 CAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATAAAAATCG
*
137920 CAACGCGAAAT
1 CAATGCGAAAT
137931 TAGTTTCGAG
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
52 28 0.52
53 26 0.48
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.18
Consensus pattern (53 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATAAAAATCG
Found at i:137920 original size:20 final size:19
Alignment explanation
Indices: 137843--137930 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
137833 GCAATGAGAG
* *
137843 AATCGTAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
*
137862 AATTGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
137881 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
137895 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
137915 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
137931 TAGTTTCGAG
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
14 8 0.14
16 5 0.09
17 2 0.04
18 3 0.05
19 27 0.48
20 11 0.20
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:137996 original size:33 final size:33
Alignment explanation
Indices: 137940--138023 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
137930 TTAGTTTCGA
*
137940 GTTGCGAATTTCATTTTCGCATTGCGATTCACTC
1 GTTGCGATTTTCA-TTTCGCATTGCGATTCACTC
*
137974 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCACTC
**
138007 GTTGCGATAGTCATTTC
1 GTTGCGATTTTCATTTC
138024 CGCGTTGCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 34 0.74
34 12 0.26
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCACTC
Done.