Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001377.1 Hibiscus syriacus cultivar Beakdansim tig00002689_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: 78806
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2713 original size:18 final size:18
Alignment explanation
Indices: 2692--2739 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
2682 TCTGAATTTA
*
2692 TTTTTTTATTT-TATTTT
1 TTTTTTTATTTCTATCTT
2709 CTTTTTATATATTTCTATCTT
1 -TTTTT-T-TATTTCTATCTT
2730 TTTTTTTATT
1 TTTTTTTATT
2740 ATTTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 9 0.35
19 2 0.08
20 10 0.38
21 5 0.19
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTTATTTCTATCTT
Found at i:2839 original size:33 final size:32
Alignment explanation
Indices: 2774--2840 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 32
2764 ATTTTTGAAA
* *
2774 ATTTTTAAAACGGTTTTCAAAAAAACATATAT
1 ATTTTTAAAACGATTTTCAAAAAAACAAATAT
* * *
2806 ATTTTTAAAATCGATTTTCGAAAATATAAATAT
1 ATTTTTAAAA-CGATTTTCAAAAAAACAAATAT
2839 AT
1 AT
2841 AGTTTTGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 10 0.34
33 19 0.66
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.40
Consensus pattern (32 bp):
ATTTTTAAAACGATTTTCAAAAAAACAAATAT
Found at i:2868 original size:25 final size:26
Alignment explanation
Indices: 2837--2951 Score: 101
Period size: 25 Copynumber: 4.2 Consensus size: 26
2827 AAATATAAAT
2837 ATATAG-TTTTGAAAACATTTGAAAA
1 ATATAGTTTTTGAAAACATTTGAAAA
*
2862 ATATAGTTTTTGAAAACGGGTTTGGAAATA
1 ATATAGTTTTTGAAAAC--ATTT-GAAA-A
*
2892 TATATAGTTTTTGAAAAACATTT--TAA
1 -ATATAGTTTTTG-AAAACATTTGAAAA
*
2918 ATATAGTTTTTAAAAAGCATTTTGAAAAA
1 ATATAGTTTTTGAAAA-CA-TTTG-AAAA
2947 ATATA
1 ATATA
2952 ATATATAATT
Statistics
Matches: 73, Mismatches: 5, Indels: 20
0.74 0.05 0.20
Matches are distributed among these distances:
24 4 0.05
25 19 0.26
26 14 0.19
27 1 0.01
28 3 0.04
29 11 0.15
30 4 0.05
31 12 0.16
32 5 0.07
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.39
Consensus pattern (26 bp):
ATATAGTTTTTGAAAACATTTGAAAA
Found at i:2951 original size:56 final size:55
Alignment explanation
Indices: 2833--2951 Score: 134
Period size: 56 Copynumber: 2.1 Consensus size: 55
2823 TCGAAAATAT
* * *
2833 AAATATATAGTTTTGAAAACATTTGAAAAATATAGTTTTTGAAAACGGGTTTGGAA
1 AAATATATAGTTTTGAAAACATTT-AAAAATATAGTTTTTAAAAACGAGTTTGAAA
* * *
2889 ATATATATAGTTTTTGAAAAACATTT-TAAATATAGTTTTTAAAAA-GCATTTTGAAA
1 AAATATATAG-TTTTG-AAAACATTTAAAAATATAGTTTTTAAAAACG-AGTTTGAAA
2945 AAATATA
1 AAATATA
2952 ATATATAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
55 1 0.02
56 38 0.72
57 5 0.09
58 9 0.17
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (55 bp):
AAATATATAGTTTTGAAAACATTTAAAAATATAGTTTTTAAAAACGAGTTTGAAA
Found at i:2991 original size:35 final size:35
Alignment explanation
Indices: 2900--3065 Score: 175
Period size: 33 Copynumber: 4.8 Consensus size: 35
2890 TATATATAGT
* *
2900 TTTTGAAAAACAT-TTTAAATATAGTTTTTAAAAAGCA
1 TTTTGAAAAA-ATATATATATATAGTTTTT-AAAA-CA
*
2937 TTTTGAAAAAATATA-ATATATAATTTTTAAAACA
1 TTTTGAAAAAATATATATATATAGTTTTTAAAACA
2971 TTTTG-AAAAA-ATATATATATAGTTTTTAAAACA
1 TTTTGAAAAAATATATATATATAGTTTTTAAAACA
* ** *
3004 TTGTTGAAAATATATAT-TATATAAATTTTAAAATA
1 TT-TTGAAAAAATATATATATATAGTTTTTAAAACA
*
3039 TTTT-TAAAAATATAT-TATATAGTTTTT
1 TTTTGAAAAAATATATATATATAGTTTTT
3066 TAATTTTTAT
Statistics
Matches: 112, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
32 3 0.03
33 44 0.39
34 12 0.11
35 25 0.22
36 17 0.15
37 11 0.10
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (35 bp):
TTTTGAAAAAATATATATATATAGTTTTTAAAACA
Found at i:3012 original size:68 final size:69
Alignment explanation
Indices: 2900--3065 Score: 212
Period size: 68 Copynumber: 2.4 Consensus size: 69
2890 TATATATAGT
* * *
2900 TTTTGAAAAACATTTTAAATATAGTTTTTAAAAAGCATTTTGAAAAAATATAATATATAATTTTT
1 TTTTGAAAAA-A-TATATATATAGTTTTTAAAAAGCATTTTGAAAAAATATAATATATAAATTTT
2965 AAAACA
64 AAAACA
* *
2971 TTTTGAAAAAATATATATATAGTTTTT-AAAA-CATTGTTGAAAATATATATTATATAAATTTTA
1 TTTTGAAAAAATATATATATAGTTTTTAAAAAGCATT-TTGAAAAAATATAATATATAAATTTTA
*
3034 AAATA
65 AAACA
*
3039 TTTT-TAAAAATATATTATATAGTTTTT
1 TTTTGAAAAAATATA-TATATAGTTTTT
3066 TAATTTTTAT
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
67 13 0.15
68 48 0.56
69 14 0.16
70 1 0.01
71 10 0.12
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (69 bp):
TTTTGAAAAAATATATATATAGTTTTTAAAAAGCATTTTGAAAAAATATAATATATAAATTTTAA
AACA
Found at i:9561 original size:169 final size:169
Alignment explanation
Indices: 9282--9996 Score: 986
Period size: 169 Copynumber: 4.2 Consensus size: 169
9272 AAAAACACAT
* * * *
9282 TCAACCAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAA
1 TCAACCAAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTGCAGCATAGCTCAA
9347 GGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
66 GGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
9412 CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
131 CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* * * *
9451 TCAACCAAAACCTTTGAGTTCGATTACACTCAGCTCAAAGGCTCATCAATTGCAGTATAACTCAA
1 TCAACCAAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTGCAGCATAGCTCAA
* *
9516 GGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACGCTCAGCTCAAAGGCACAT
66 GGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
* * * *
9581 CCCATTTACAACATAACTTAAGGTGAGAAGGGTTATCTG
131 CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* *
9620 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
1 TCAACCAAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTGCAGCATAGCTCAA
* * *
9685 GGCGAGAAGGGATATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAATGTACAT
66 GGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
* * * * *
9750 CCAATTTACTGCATAGCTCAAGGTGAGAAAGGCTATCTG
131 CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* * * * *
9789 TCAA-CAAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGCATATCCAATTTACAGTATAGCT
1 TCAACCAAA-ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CAA-TTGCAGCATAGCT
** ** * *
9853 CAAGGCGAGAAGGGTTATCTATCGTC-AAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGCA
63 CAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
** ** *
9917 TGTAAAATTTACAGTATAACTCAAGGCGAGAAGGGTTATCTG
128 CATCCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
* * *
9959 TC-ATCAAAGACCTTTGAGTTCGATTACATTCAGCTCAA
1 TCAACCAAA-ACCTTCGAGTTCGATTACACTCAGCTCAA
9997 GGGAATGCCA
Statistics
Matches: 483, Mismatches: 59, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
168 3 0.01
169 346 0.72
170 102 0.21
171 32 0.07
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (169 bp):
TCAACCAAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTGCAGCATAGCTCAA
GGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
CCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
Found at i:10022 original size:85 final size:85
Alignment explanation
Indices: 9282--9996 Score: 922
Period size: 85 Copynumber: 8.4 Consensus size: 85
9272 AAAAACACAT
* * * * *
9282 TCAACCAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACAT-C-ATTTGCAGCATAGCTT
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACTC
9345 AAGGCGAGAAGGGTTATCTG
66 AAGGCGAGAAGGGTTATCTG
*
9365 CCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACT
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACT
9430 CAAGGCGAGAAGGGTTATCTG
65 CAAGGCGAGAAGGGTTATCTG
* * * *
9451 TCAACCAAA-ACCTTTGAGTTCGATTACACTCAGCTCAAAGGCTCAT-CAA-TTGCAGTATAACT
1 TCAA-CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACT
*
9513 CAAGGCGAGAAGGGCTATCTG
65 CAAGGCGAGAAGGGTTATCTG
* * * *
9534 CCAACAAAAGACCTTCGAGTTCGATTACGCTCAGCTCAAAGGCACATCCCATTTACAACATAACT
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACT
* *
9599 TAAGGTGAGAAGGGTTATCTG
65 CAAGGCGAGAAGGGTTATCTG
* * *
9620 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-C-ATTTGCAGCATAGCTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACTC
*
9683 AAGGCGAGAAGGGATATCTG
66 AAGGCGAGAAGGGTTATCTG
* * * * *
9703 CCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAATGTACATCCAATTTACTGCATAGCT
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACT
* * *
9768 CAAGGTGAGAAAGGCTATCTG
65 CAAGGCGAGAAGGGTTATCTG
* * * * *
9789 TCAACAAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGCATATCCAATTTACAGTATAGCTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACTC
*
9854 AAGGCGAGAAGGGTTATCTA
66 AAGGCGAGAAGGGTTATCTG
** * * ** ** *
9874 TCGTCAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGCATGTAAAATTTACAGTATAACTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACTC
9939 AAGGCGAGAAGGGTTATCTG
66 AAGGCGAGAAGGGTTATCTG
* * *
9959 TCATCAAAGACCTTTGAGTTCGATTACATTCAGCTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAA
9997 GGGAATGCCA
Statistics
Matches: 558, Mismatches: 63, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
82 1 0.00
83 75 0.13
84 115 0.21
85 260 0.47
86 106 0.19
87 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (85 bp):
TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACTC
AAGGCGAGAAGGGTTATCTG
Found at i:10042 original size:85 final size:85
Alignment explanation
Indices: 9288--10079 Score: 505
Period size: 85 Copynumber: 9.4 Consensus size: 85
9278 ACATTCAACC
* * * * * * *
9288 AAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACAT--C--ATTTGCAGCATAGCTTAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTC-AAGGGA-ATGCCAAATTTACAGTATAACTCAAGG
* * ** *
9349 CGAGAAGGGTTATCTGCCAACAA
64 CGAGAAAGGCTATCTATCATC-A
* * *
9372 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CC-AATTTACAGCATAACTCAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTC-AAGGGA-ATGCCAAATTTACAGTATAACTCAAGG
* * * *
9435 CGAGAAGGGTTATCTGTCAACCA
64 CGAGAAAGGCTATCTATC-ATCA
* * * * *
9458 AA-ACCTTTGAGTTCGATTACACTCAGCTCAAAGG-CT--CATCAA-TTGCAGTATAACTCAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGAATGCCA--AATTTACAGTATAACTCAAGG
* ** *
9518 CGAGAAGGGCTATCTGCCAACAA
64 CGAGAAAGGCTATCTATCATC-A
** * * ** *
9541 AAGACCTTCGAGTTCGATTACGCTCAGCTCAAAGGCACAT-CC-CATTTACAACATAACTTAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTC-AAGGGA-ATGCCAAATTTACAGTATAACTCAAGG
* * * * * *
9604 TGAGAAGGGTTATCTGTCAACC
64 CGAGAAAGGCTATCTATCATCA
* * * * *
9626 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT--C--ATTTGCAGCATAGCTCAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTC-AAGGGA-ATGCCAAATTTACAGTATAACTCAAGG
* * ** *
9687 CGAGAAGGGATATCTGCCAACAA
64 CGAGAAAGGCTATCTATCATC-A
* * * * * *
9710 AAGACCTTCGAGTTCGATTACACTCAGCTCAAATGTACAT-CC-AATTTACTGCATAGCTCAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTC-AAGGGA-ATGCCAAATTTACAGTATAACTCAAGG
* * *
9773 TGAGAAAGGCTATCTGTCAACA
64 CGAGAAAGGCTATCTATCATCA
* * *
9795 AAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGCATAT-CC-AATTTACAGTATAGCTCAAGG
1 AAGACCTTCGAGTTCGATTACATTCAGCTC-AAGGGA-ATGCCAAATTTACAGTATAACTCAAGG
* * *
9858 CGAGAAGGGTTATCTATCGTCA
64 CGAGAAAGGCTATCTATCATCA
* * * **
9880 AAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGCATGTAAAATTTACAGTATAACTCAAGGCG
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGAATGCCAAATTTACAGTATAACTCAAGGCG
* * *
9945 AGAAGGGTTATCTGTCATCA
66 AGAAAGGCTATCTATCATCA
* * * * *
9965 AAGACCTTTGAGTTCGATTACATTCAGCTCAAGGGAATGCCAAATTCACAGTATAACTTAAGTCA
1 AAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGAATGCCAAATTTACAGTATAACTCAAGGCG
*
10030 AGAAAAGCTATCTATCAAT-A
66 AGAAAGGCTATCTATC-ATCA
* *
10050 AA-AACTGTCGAGTTCGATTCCATTCAGCTC
1 AAGACCT-TCGAGTTCGATTACATTCAGCTC
10080 GATGATACAT
Statistics
Matches: 604, Mismatches: 84, Indels: 39
0.83 0.12 0.05
Matches are distributed among these distances:
81 1 0.00
82 3 0.00
83 71 0.12
84 114 0.19
85 305 0.50
86 106 0.18
87 3 0.00
88 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (85 bp):
AAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGAATGCCAAATTTACAGTATAACTCAAGGCG
AGAAAGGCTATCTATCATCA
Found at i:10907 original size:35 final size:35
Alignment explanation
Indices: 10868--10965 Score: 112
Period size: 37 Copynumber: 2.8 Consensus size: 35
10858 TTGAAAATAT
10868 TTTTTAAAACGGTTTTCGAAAAACATATA-ATATAC
1 TTTTTAAAACGGTTTTCG-AAAACATATATATATAC
* *
10903 TTTTTAAAAATCGGTTTTCGAAAATATATATATATAG
1 TTTTT-AAAA-CGGTTTTCGAAAACATATATATATAC
* *
10940 TTTTGAAAAC-ATTTT-GAAAACATATA
1 TTTTTAAAACGGTTTTCGAAAACATATA
10966 GTTTTTGAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
33 10 0.18
34 4 0.07
35 6 0.11
36 17 0.31
37 18 0.33
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (35 bp):
TTTTTAAAACGGTTTTCGAAAACATATATATATAC
Found at i:10922 original size:37 final size:36
Alignment explanation
Indices: 10867--10965 Score: 107
Period size: 36 Copynumber: 2.8 Consensus size: 36
10857 TTTGAAAATA
*
10867 TTTTTTAAAACGGTTTTCGAAAAACATATA-ATATAC
1 TTTTTAAAAACGGTTTTCG-AAAACATATATATATAC
*
10903 TTTTTAAAAATCGGTTTTCGAAAATATATATATATA-
1 TTTTTAAAAA-CGGTTTTCGAAAACATATATATATAC
* * *
10939 GTTTTGAAAAC-ATTTT-GAAAACATATA
1 TTTTTAAAAACGGTTTTCGAAAACATATA
10966 GTTTTTGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
33 10 0.18
34 4 0.07
35 1 0.02
36 26 0.47
37 14 0.25
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.40
Consensus pattern (36 bp):
TTTTTAAAAACGGTTTTCGAAAACATATATATATAC
Found at i:10971 original size:64 final size:66
Alignment explanation
Indices: 10897--11031 Score: 195
Period size: 64 Copynumber: 2.1 Consensus size: 66
10887 AAAACATATA
10897 ATATACTTTTTAAAAATCGGTTTTCGAAAATATATA-TATATAG-TTTTG-AAAACATTTTGAAA
1 ATATACTTTTTAAAAA-CGGTTTTCGAAAATATATATTATATAGTTTTTGAAAAACATTTTGAAA
10959 AC
65 AC
* * * *
10961 ATATAGTTTTTGAAAACGGTTTTTGGAAATATATATTATATAGTTTTTGAAAAACATTTTGAAAA
1 ATATACTTTTTAAAAACGGTTTTCGAAAATATATATTATATAGTTTTTGAAAAACATTTTGAAAA
*
11026 T
66 C
11027 ATATA
1 ATATA
11032 TAATATATAG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
63 17 0.27
64 21 0.33
65 5 0.08
66 20 0.32
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.42
Consensus pattern (66 bp):
ATATACTTTTTAAAAACGGTTTTCGAAAATATATATTATATAGTTTTTGAAAAACATTTTGAAAA
C
Found at i:11031 original size:38 final size:36
Alignment explanation
Indices: 10961--11190 Score: 244
Period size: 36 Copynumber: 6.4 Consensus size: 36
10951 TTTTGAAAAC
* * *
10961 ATATAGTTTTTGAAAACGGTTTTTGGAAATATATAT-T
1 ATATAGTTTTTAAAAAC--ATTTTGAAAATATATATAT
10998 ATATAGTTTTTGAAAAACATTTTGAAAATATATATAAT
1 ATATAGTTTTT-AAAAACATTTTGAAAATATATAT-AT
11036 ATATAGTTTTTAAAAAACATTTTGAAAATATATATAAT
1 ATATAGTTTTT-AAAAACATTTTGAAAATATATAT-AT
* * *
11074 ATATA-ATTTTAAAATA-TTTTTGAATATATATATAT
1 ATATAGTTTTTAAAA-ACATTTTGAAAATATATATAT
11109 ATTATAGTTTTT-AAAACATTGTTG-AAA-ATATATAT
1 A-TATAGTTTTTAAAAACATT-TTGAAAATATATATAT
*
11144 ATATA--TTTTAAAGACATTTTTGAAAATATATAT-T
1 ATATAGTTTTTAAAAACA-TTTTGAAAATATATATAT
11178 ATATAGTTTTTAA
1 ATATAGTTTTTAA
11191 TTTTTTTATA
Statistics
Matches: 168, Mismatches: 11, Indels: 29
0.81 0.05 0.14
Matches are distributed among these distances:
32 4 0.02
33 8 0.05
34 15 0.09
35 19 0.11
36 51 0.30
37 23 0.14
38 48 0.29
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (36 bp):
ATATAGTTTTTAAAAACATTTTGAAAATATATATAT
Found at i:11140 original size:31 final size:33
Alignment explanation
Indices: 10922--11187 Score: 147
Period size: 38 Copynumber: 7.6 Consensus size: 33
10912 ATCGGTTTTC
10922 GAAAATATATATATATAGTTTTGAAA-ACATT-TT
1 GAAAATATATATATATA-TTTT-AAAGACATTGTT
* * * * *
10955 GAAAACATATA-GT-T-TTTGAAA-ACGGTTTTT
1 GAAAATATATATATATATTTTAAAGAC-ATTGTT
* *
10985 GGAAATATATATTATATAGTTTTTGAAAAACATT-TT
1 GAAAATATATA-TATATA--TTTT-AAAGACATTGTT
*
11021 GAAAATATATATAATATATAGTTTTTAAAAAACATT-TT
1 G-AAA-ATATAT-ATATATA--TTTT-AAAGACATTGTT
* *
11059 GAAAATATATATAATATATAATTTTAAA-ATATTTTT
1 G-AAA-ATATAT-ATATAT-ATTTTAAAGACATTGTT
11095 GAATATATATATATATTATAGTTTTTAAA-ACATTGTT
1 GAA-A-ATATATATA-TATA--TTTTAAAGACATTGTT
*
11132 GAAAATATATATATATATTTTAAAGACATTTTT
1 GAAAATATATATATATATTTTAAAGACATTGTT
11165 GAAAATATATATTATATAGTTTT
1 GAAAATATATA-TATATA-TTTT
11188 TAATTTTTTT
Statistics
Matches: 196, Mismatches: 15, Indels: 42
0.77 0.06 0.17
Matches are distributed among these distances:
28 5 0.03
29 5 0.03
30 11 0.06
31 1 0.01
32 9 0.05
33 29 0.15
34 10 0.05
35 23 0.12
36 24 0.12
37 27 0.14
38 50 0.26
39 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (33 bp):
GAAAATATATATATATATTTTAAAGACATTGTT
Found at i:11240 original size:14 final size:13
Alignment explanation
Indices: 11220--11269 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
11210 AATATTATTA
11220 TTTTATTTATTTT
1 TTTTATTTATTTT
*
11233 TATTTATTATATGTT
1 T-TTTATT-TATTTT
11248 TTTTA-TTATTTT
1 TTTTATTTATTTT
*
11260 CTTT-TTTATT
1 TTTTATTTATT
11270 AATGCCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 13 0.42
13 2 0.06
14 10 0.32
15 6 0.19
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTATTTATTTT
Found at i:12915 original size:2 final size:2
Alignment explanation
Indices: 12908--12932 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12898 CGACTGCGAC
12908 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12933 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14699 original size:13 final size:14
Alignment explanation
Indices: 14681--14713 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
14671 TTTATATAAC
*
14681 TTAAAA-AAATTAT
1 TTAAAACAAAGTAT
14694 TTAAAACAAAGTAT
1 TTAAAACAAAGTAT
14708 TTAAAA
1 TTAAAA
14714 TTATATTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (14 bp):
TTAAAACAAAGTAT
Found at i:18564 original size:48 final size:48
Alignment explanation
Indices: 18479--18584 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 48
18469 CGGAGATATT
* * * *
18479 AGAAATCAAAACAAAATTCAGATCAGATATCATAACAGAATCCAGATC
1 AGAAATCAGAACAAAATCCAGATCAGATATCAGAACAGAATCCAAATC
* * * *
18527 AGAAATCAGAACAGAATCCAGGTCAGGTATCAGAACAGAATTCAAATC
1 AGAAATCAGAACAAAATCCAGATCAGATATCAGAACAGAATCCAAATC
*
18575 GGAAATCAGA
1 AGAAATCAGA
18585 TAAAACATTC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.17
Consensus pattern (48 bp):
AGAAATCAGAACAAAATCCAGATCAGATATCAGAACAGAATCCAAATC
Found at i:18582 original size:24 final size:24
Alignment explanation
Indices: 18479--18584 Score: 113
Period size: 24 Copynumber: 4.4 Consensus size: 24
18469 CGGAGATATT
* * *
18479 AGAAATCAAAACAAAATTCAGATC
1 AGAAATCAGAACAGAATCCAGATC
* *
18503 AGATATCATAACAGAATCCAGATC
1 AGAAATCAGAACAGAATCCAGATC
*
18527 AGAAATCAGAACAGAATCCAGGTC
1 AGAAATCAGAACAGAATCCAGATC
** * *
18551 AGGTATCAGAACAGAATTCAAATC
1 AGAAATCAGAACAGAATCCAGATC
*
18575 GGAAATCAGA
1 AGAAATCAGA
18585 TAAAACATTC
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.17
Consensus pattern (24 bp):
AGAAATCAGAACAGAATCCAGATC
Found at i:23177 original size:24 final size:24
Alignment explanation
Indices: 23150--23234 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
23140 GATATTAGAA
* *
23150 ATCAAAACAAAATTCAGATCAAAT
1 ATCAGAACAAAATCCAGATCAAAT
* *
23174 ATCATAACAGAATCCAGATCAGAA-
1 ATCAGAACAAAATCCAGATCA-AAT
* * **
23198 ATCAGAACAGAATCCAGGTCAGGT
1 ATCAGAACAAAATCCAGATCAAAT
23222 ATCAGAACAAAAT
1 ATCAGAACAAAAT
23235 TCAAATCGGA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 49 0.96
25 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.18
Consensus pattern (24 bp):
ATCAGAACAAAATCCAGATCAAAT
Found at i:23225 original size:48 final size:48
Alignment explanation
Indices: 23146--23251 Score: 113
Period size: 48 Copynumber: 2.2 Consensus size: 48
23136 CAGAGATATT
* * * * *
23146 AGAAATCAAAACAAAATTCAGATCAAATATCATAACAGAATCCAGATC
1 AGAAATCAGAACAAAATCCAGATCAAATATCAGAACAAAATCCAAATC
* * ** *
23194 AGAAATCAGAACAGAATCCAGGTCAGGTATCAGAACAAAATTCAAATC
1 AGAAATCAGAACAAAATCCAGATCAAATATCAGAACAAAATCCAAATC
*
23242 GGAAATCAGA
1 AGAAATCAGA
23252 TAAAATATTC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.17
Consensus pattern (48 bp):
AGAAATCAGAACAAAATCCAGATCAAATATCAGAACAAAATCCAAATC
Found at i:23249 original size:24 final size:24
Alignment explanation
Indices: 23147--23251 Score: 79
Period size: 24 Copynumber: 4.4 Consensus size: 24
23137 AGAGATATTA
* *
23147 GAAATCAAAACAAAATTCAGATC-
1 GAAATCAGAACAAAATCCAGATCG
* * * *
23170 AAATATCATAACAGAATCCAGATCA
1 GAA-ATCAGAACAAAATCCAGATCG
* *
23195 GAAATCAGAACAGAATCCAGGTCAG
1 GAAATCAGAACAAAATCCAGATC-G
* * *
23220 G-TATCAGAACAAAATTCAAATCG
1 GAAATCAGAACAAAATCCAGATCG
23243 GAAATCAGA
1 GAAATCAGA
23252 TAAAATATTC
Statistics
Matches: 64, Mismatches: 14, Indels: 7
0.75 0.16 0.08
Matches are distributed among these distances:
23 4 0.06
24 57 0.89
25 3 0.05
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.17
Consensus pattern (24 bp):
GAAATCAGAACAAAATCCAGATCG
Found at i:28812 original size:2 final size:2
Alignment explanation
Indices: 28805--28831 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28795 TTTAATAAAT
28805 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28832 GATGCTATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33962 original size:24 final size:24
Alignment explanation
Indices: 33930--33998 Score: 129
Period size: 24 Copynumber: 2.9 Consensus size: 24
33920 ACACCAGGAA
33930 GAAGAAGAAGATGATGATGATGAT
1 GAAGAAGAAGATGATGATGATGAT
33954 GAAGAAGAAGATGATGATGATGAT
1 GAAGAAGAAGATGATGATGATGAT
*
33978 GAAGAAGAAGAAGATGATGAT
1 GAAGAAGAAGATGATGATGAT
33999 CATAAACTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (24 bp):
GAAGAAGAAGATGATGATGATGAT
Found at i:33991 original size:6 final size:6
Alignment explanation
Indices: 33930--33988 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
33920 ACACCAGGAA
* * * * * *
33930 GAAGAA GAAGAT GATGAT GATGAT GAAGAA GAAGAT GATGAT GATGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
33978 GAAGAA GAAGA
1 GAAGAT GAAGA
33989 AGATGATGAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.34, T:0.17
Consensus pattern (6 bp):
GAAGAT
Found at i:33996 original size:3 final size:3
Alignment explanation
Indices: 33939--33998 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
33929 AGAAGAAGAA
* * * * * *
33939 GAT GAT GAT GAT GAT GAA GAA GAA GAT GAT GAT GAT GAT GAA GAA GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
33987 GAA GAT GAT GAT
1 GAT GAT GAT GAT
33999 CATAAACTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.22
Consensus pattern (3 bp):
GAT
Found at i:35667 original size:17 final size:18
Alignment explanation
Indices: 35641--35674 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35631 CCAGTGCTCA
35641 GAATTAATTA-TAAAATG
1 GAATTAATTATTAAAATG
*
35658 GAATTTATTATTAAAAT
1 GAATTAATTATTAAAAT
35675 ATCACGTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
GAATTAATTATTAAAATG
Found at i:42722 original size:29 final size:29
Alignment explanation
Indices: 42689--43128 Score: 238
Period size: 29 Copynumber: 15.2 Consensus size: 29
42679 TGTAAAATAT
*
42689 ATTAATTATTAGAATATCCAGCGATCAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * *** *
42718 ATTAATGATTAGGATATCCAGTTTTTAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * * * *
42747 ATTAATTAGTAAAATATCCA-AGTTTAAA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* *
42775 ATTAATCATTAAAATATCCAGAGATCAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
** * * * *
42804 ATTAACGATTAGACTATCCAGTGTTTAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * * * * * *
42833 AATAATTAGTAAAATATCC-TAGTTTAAA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* *
42861 ATTAATTATTAGCATATCCAAAGATCAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * *** *
42890 ATTAATGATTAGGATATCCAGTTTTTAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * * * ** *
42919 AATAATTAGTAAAATATCCACATTTCAAA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* *
42948 ATTACTTATTAGAATATCCAGAGATCATA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * *** *
42977 ATTAATGATTAGGATATCCAGTTTTTAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * * * ** *
43006 AATAATTAGTAAAATATCCACATTTCAAA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * *
43035 ATTAATTATTAGAATATCCAAAAATCAAA
1 ATTAATTATTAGAATATCCAGAGATCAGA
* * * * ** *
43064 ATCAATTATTAGGATACCCTCG-TTTTAGA
1 ATTAATTATTAGAATATCC-AGAGATCAGA
*
43093 ATTAATTATTAGAATATCCAGAGATAAGA
1 ATTAATTATTAGAATATCCAGAGATCAGA
43122 ATTAATT
1 ATTAATT
43129 GGATATCAGT
Statistics
Matches: 302, Mismatches: 105, Indels: 8
0.73 0.25 0.02
Matches are distributed among these distances:
28 45 0.15
29 257 0.85
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (29 bp):
ATTAATTATTAGAATATCCAGAGATCAGA
Found at i:42839 original size:86 final size:87
Alignment explanation
Indices: 42689--43112 Score: 581
Period size: 87 Copynumber: 4.9 Consensus size: 87
42679 TGTAAAATAT
* *
42689 ATTAATTATTAGAATATCCAGCGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAATTAATT
1 ATTAATTATTAGAATATCCAGAGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
42754 AGTAAAATATCCA-AGTTT-AAA
66 AGTAAAATATCCACA-TTTCAAA
* * * *
42775 ATTAATCATTAAAATATCCAGAGATCAGAATTAACGATTA-GACTATCCAGTGTTTAGAAATAAT
1 ATTAATTATTAGAATATCCAGAGATCAGAATTAATGATTAGGA-TATCCAGTTTTTAGAAATAAT
*
42839 TAGTAAAATATCCTA-GTTT-AAA
65 TAGTAAAATATCC-ACATTTCAAA
* *
42861 ATTAATTATTAGCATATCCAAAGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
1 ATTAATTATTAGAATATCCAGAGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
42926 AGTAAAATATCCACATTTCAAA
66 AGTAAAATATCCACATTTCAAA
* *
42948 ATTACTTATTAGAATATCCAGAGATCATAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
1 ATTAATTATTAGAATATCCAGAGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
43013 AGTAAAATATCCACATTTCAAA
66 AGTAAAATATCCACATTTCAAA
* * * * * * * *
43035 ATTAATTATTAGAATATCCAAAAATCAAAATCAATTATTAGGATACCCTCG-TTTTAGAATTAAT
1 ATTAATTATTAGAATATCCAGAGATCAGAATTAATGATTAGGATATCC-AGTTTTTAGAAATAAT
* *
43099 TATTAGAATATCCA
65 TAGTAAAATATCCA
43113 GAGATAAGAA
Statistics
Matches: 303, Mismatches: 29, Indels: 11
0.88 0.08 0.03
Matches are distributed among these distances:
85 3 0.01
86 145 0.48
87 154 0.51
88 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (87 bp):
ATTAATTATTAGAATATCCAGAGATCAGAATTAATGATTAGGATATCCAGTTTTTAGAAATAATT
AGTAAAATATCCACATTTCAAA
Found at i:44057 original size:70 final size:70
Alignment explanation
Indices: 43938--44094 Score: 219
Period size: 70 Copynumber: 2.2 Consensus size: 70
43928 GGGGTAAAGA
* ** *
43938 TCGAAATTTACGTGAATCGGAACTTAAAGCCCTTAGTCTACCTCGGATCCTCGAGAGGTC-GAGG
1 TCGAAATTTACGTGCATAAGAACTTAAAGCCCTTAGTCTACCTCAGATCCTCGAGAGGTCAG-GG
44002 TGAGGT
65 TGAGGT
* * *
44008 AT-GGAATTTATGTGCATAAGAACTTAAAGCCCTTAGTCTACCTCAGATCCTTGAGAGGTCAGGG
1 -TCGAAATTTACGTGCATAAGAACTTAAAGCCCTTAGTCTACCTCAGATCCTCGAGAGGTCAGGG
44072 TGAGGT
65 TGAGGT
44078 TCGAAATTTACGTGCAT
1 TCGAAATTTACGTGCAT
44095 CAAAAACTCA
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
69 1 0.01
70 72 0.96
71 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (70 bp):
TCGAAATTTACGTGCATAAGAACTTAAAGCCCTTAGTCTACCTCAGATCCTCGAGAGGTCAGGGT
GAGGT
Found at i:44529 original size:20 final size:19
Alignment explanation
Indices: 44500--44555 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 19
44490 TTTTGAAAAA
44500 TACT-TGGGTATCGATACTC
1 TACTCTGGGTATCGATAC-C
44519 TACTCTGGGTATCGATACC
1 TACTCTGGGTATCGATACC
* *
44538 CAC-CTGAGTATCGATACC
1 TACTCTGGGTATCGATACC
44556 AGTTTTCGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 14 0.41
19 7 0.21
20 13 0.38
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (19 bp):
TACTCTGGGTATCGATACC
Found at i:60473 original size:31 final size:30
Alignment explanation
Indices: 60437--60534 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 30
60427 CATACCTAAT
*
60437 ATTTACTTTTTGTTTCATTTTATTACCCGGA
1 ATTTACTTTTTGTTTCATTTTATTACCC-AA
* * *
60468 GTTTACTTTTTATTTAATTTTATTACCCAA
1 ATTTACTTTTTGTTTCATTTTATTACCCAA
* *
60498 ATATTAACTTTTTTGTTTCATTTTAGTACCTAA
1 AT-TT-AC-TTTTTGTTTCATTTTATTACCCAA
60531 ATTT
1 ATTT
60535 TTAACAGAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
30 2 0.04
31 27 0.49
32 4 0.07
33 22 0.40
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.56
Consensus pattern (30 bp):
ATTTACTTTTTGTTTCATTTTATTACCCAA
Found at i:60675 original size:30 final size:30
Alignment explanation
Indices: 60607--60675 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
60597 AAGTTTAGAA
* *
60607 ACTAAACAGAATAAAAGTGATTGTTTAAGT
1 ACTAAACATAATAAAACTGATTGTTTAAGT
*
60637 ACTAAACATAATAAAACTTATTGTTTAAGT
1 ACTAAACATAATAAAACTGATTGTTTAAGT
60667 ACTAAACAT
1 ACTAAACAT
60676 GTAATTTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (30 bp):
ACTAAACATAATAAAACTGATTGTTTAAGT
Found at i:61414 original size:17 final size:17
Alignment explanation
Indices: 61392--61434 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
61382 TATTTAAATA
61392 TTTTTATTTAATCTAAT
1 TTTTTATTTAATCTAAT
*
61409 TTTTTATTT-ATTTAAT
1 TTTTTATTTAATCTAAT
61425 TTTTTATTTA
1 TTTTTATTTA
61435 CCTCGATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTATTTAATCTAAT
Found at i:71107 original size:35 final size:35
Alignment explanation
Indices: 71068--71135 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
71058 TGTATTACCT
*
71068 TGTTTGGTTTGTTTAGCAAGAATGTAAGATTACAG
1 TGTTTGGTTTGTTTAACAAGAATGTAAGATTACAG
*
71103 TGTTTGGTTTGTTTAACAGGAATGTAAGATTAC
1 TGTTTGGTTTGTTTAACAAGAATGTAAGATTAC
71136 TTGGATGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (35 bp):
TGTTTGGTTTGTTTAACAAGAATGTAAGATTACAG
Found at i:71418 original size:16 final size:17
Alignment explanation
Indices: 71399--71435 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
71389 TAAAATATTA
71399 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
71415 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
71432 TTTT
1 TTTT
71436 TTCATCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:73213 original size:20 final size:20
Alignment explanation
Indices: 73188--73225 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
73178 TTTCCTATAA
73188 AGAAAAATATTAAATTTAAT
1 AGAAAAATATTAAATTTAAT
*
73208 AGAAAAATATTTAATTTA
1 AGAAAAATATTAAATTTA
73226 TTTTATTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
AGAAAAATATTAAATTTAAT
Done.