Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003168.1 Hibiscus syriacus cultivar Beakdansim tig00006663_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: 72075
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6190 original size:3 final size:3
Alignment explanation
Indices: 6184--6243 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
6174 TTTACTCATT
* *
6184 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TAA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
6232 TTA TTA TTA TTA
1 TTA TTA TTA TTA
6244 AAAAATAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:11549 original size:15 final size:15
Alignment explanation
Indices: 11529--11560 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11519 ATCAATACCT
11529 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
11544 TTTTGCATACATTCA
1 TTTTGCATACATGCA
11559 TT
1 TT
11561 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:18890 original size:7 final size:7
Alignment explanation
Indices: 18888--18984 Score: 76
Period size: 7 Copynumber: 13.7 Consensus size: 7
18878 GAAAAAGGAA
18888 AAAAAAG
1 AAAAAAG
18895 AAAAAAGG
1 AAAAAA-G
18903 AAAAAAAG
1 -AAAAAAG
**
18911 AATGAAG
1 AAAAAAG
18918 -AAAAA-
1 AAAAAAG
*
18923 AAAAGAG
1 AAAAAAG
18930 AAAAAA-
1 AAAAAAG
18936 AAAGAAAG
1 AAA-AAAG
*
18944 AAAAGA-
1 AAAAAAG
18950 AAAAAAG
1 AAAAAAG
*
18957 AAAAGAAA
1 AAAA-AAG
18965 AAAGAAAG
1 AAA-AAAG
18973 AAAAAAG
1 AAAAAAG
18980 AAAAA
1 AAAAA
18985 GGGGGTCAAG
Statistics
Matches: 71, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
6 15 0.21
7 34 0.48
8 15 0.21
9 7 0.10
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:18901 original size:17 final size:17
Alignment explanation
Indices: 18873--18984 Score: 113
Period size: 17 Copynumber: 6.5 Consensus size: 17
18863 TATTATGCTT
*
18873 AAAGAGAAAAAGGAAAAA
1 AAAGA-AAAAAGAAAAAA
*
18891 AAAGAAAAAAG-GAAAA
1 AAAGAAAAAAGAAAAAA
**
18907 AAAGAATGAAGAAAAAA
1 AAAGAAAAAAGAAAAAA
* *
18924 AAAGAGAAAA-AAAAAG
1 AAAGAAAAAAGAAAAAA
18940 AAAGAAAAGAA-AAAAAGA
1 AAAGAAAA-AAGAAAAA-A
18958 AAAGAAAAAAGAAAGAAA
1 AAAGAAAAAAGAAA-AAA
18976 AAAGAAAAA
1 AAAGAAAAA
18985 GGGGGTCAAG
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
16 25 0.32
17 26 0.33
18 26 0.33
19 2 0.03
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (17 bp):
AAAGAAAAAAGAAAAAA
Found at i:18935 original size:29 final size:27
Alignment explanation
Indices: 18885--18985 Score: 114
Period size: 29 Copynumber: 3.5 Consensus size: 27
18875 AGAGAAAAAG
*
18885 GAAAAAAAAGAAA-AAAGGAAAAAAAGAAT
1 GAAAAAAAA-AAAGAAA--AAAAAAAGAAA
18914 GAAGAAAAAAAAAGAGAAAAAAAAAGAAA
1 GAA-AAAAAAAAAGA-AAAAAAAAAGAAA
18943 GAAAAGAAAAAAAGAAAAGAAAAAAGAAA
1 GAAAA-AAAAAAAGAAAA-AAAAAAGAAA
18972 GAAAAAAGAAAAAG
1 GAAAAAA-AAAAAG
18986 GGGGTCAAGG
Statistics
Matches: 65, Mismatches: 1, Indels: 12
0.83 0.01 0.15
Matches are distributed among these distances:
28 7 0.11
29 49 0.75
30 7 0.11
31 2 0.03
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (27 bp):
GAAAAAAAAAAAGAAAAAAAAAAGAAA
Found at i:18985 original size:17 final size:16
Alignment explanation
Indices: 18877--18984 Score: 101
Period size: 16 Copynumber: 6.4 Consensus size: 16
18867 ATGCTTAAAG
*
18877 AGAAAAAGGAAAAAAA
1 AGAAAAAAGAAAAAAA
*
18893 AGAAAAAAGGAAAAAA
1 AGAAAAAAGAAAAAAA
**
18909 AGAATGAAGAAAAAAAA
1 AGAAAAAAG-AAAAAAA
*
18926 AGAGAAAAA-AAAAGAA
1 AGA-AAAAAGAAAAAAA
*
18942 AGAAAAGAAAAAAAGAAA
1 AGAAAA-AAGAAAA-AAA
18960 AGAAAAAAGAAAGAAAAA
1 AGAAAAAAG-AA-AAAAA
18978 AGAAAAA
1 AGAAAAA
18985 GGGGGTCAAG
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
15 3 0.04
16 32 0.43
17 15 0.20
18 23 0.31
19 2 0.03
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (16 bp):
AGAAAAAAGAAAAAAA
Found at i:20031 original size:95 final size:94
Alignment explanation
Indices: 19828--20184 Score: 594
Period size: 93 Copynumber: 3.8 Consensus size: 94
19818 CGTAAACCCA
* * *
19828 ATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCCCAAAAAACCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTAAAAAACCA
*
19893 ATCATTGAATTTGGAAGATGAATATGCTC
66 ATCATTGAATTTGGAAGATGAATGTGCTC
* *
19922 ATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTATGAACCCTAAAAAAACC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCT-AAAAAACC
19987 AATCATTGAATTTGGAAGATGAATGTGCTC
65 AATCATTGAATTTGGAAGATGAATGTGCTC
20017 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCT-AAAAACCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTAAAAAACCA
20081 ATCATTGAATTTGGAAGATGAATGTGCTC
66 ATCATTGAATTTGGAAGATGAATGTGCTC
* * *
20110 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAA-CC-ACAGAACCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTAAAAAACCA
20173 ATCATTGGAATT
66 ATCATT-GAATT
20185 AAAAGATGAA
Statistics
Matches: 249, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
92 14 0.06
93 93 0.37
94 51 0.20
95 91 0.37
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (94 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTAAAAAACCA
ATCATTGAATTTGGAAGATGAATGTGCTC
Found at i:21083 original size:112 final size:111
Alignment explanation
Indices: 20917--21521 Score: 836
Period size: 112 Copynumber: 5.5 Consensus size: 111
20907 TGTCAGTTAG
*
20917 AGTTCATAATGAGAAGAACTCATCTGAAGAGAGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGA-AGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
20982 AACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
65 AACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
21029 AGTTCATAATGAGAAGAACTCATCTGAAGAGAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGA-AGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
21094 AACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
65 AACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
* * *
21141 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
** * ** * * ****
21206 AACCTTTTGCTAAAATCCATCATTCAATGGATCAGTTTTTCCAGTTCG
65 AA-CTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
21254 AGTTCATAATGAGAAGAACTCATCT---GAAG-A-AA-AAGTTCATAATAAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
21313 ACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
66 ACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
* * *
21359 AGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
* * * * * * *
21424 AACCCTTTG-TTCAAATTCATCACTTAATGGATAAACCTTT-ACAGAGAA
65 AA-CTTTTGCTT-GAATTCATCATTTGATGGAT-CAGCTTTGCCAGAGAA
21472 AGTTCATAATGAGAAGAACTCATCTGAAGAAG-AG-A-AAGTTCATAATAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGA
21522 GCTTATTCAA
Statistics
Matches: 441, Mismatches: 40, Indels: 27
0.87 0.08 0.05
Matches are distributed among these distances:
105 58 0.13
106 26 0.06
107 2 0.00
108 4 0.01
109 16 0.04
110 5 0.01
111 5 0.01
112 202 0.46
113 118 0.27
114 5 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (111 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
ACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
Found at i:21350 original size:218 final size:219
Alignment explanation
Indices: 20917--21521 Score: 894
Period size: 218 Copynumber: 2.7 Consensus size: 219
20907 TGTCAGTTAG
*
20917 AGTTCATAATGAGAAGAACTCATCTGAAG-AGAGAAGAAGAAGTTCATAATAAGAAGAATTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAG-GAAGAAGAAGTTCATAATGAGAAGAATTTGTT
** * *
20981 CAA-CTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAAAGTTCATAATGAGAAG
65 CAACCTTTTGCTAAAATTCATCA-TTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
21045 AACTCATCTGAAGAGAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATT
129 AACTCATCT---GA-AGAAGAA-AAGTTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATT
21110 CATCATTTGATGGATCAGCTTTGCCAGAGAA
189 CATCATTTGATGGATCAGCTTTGCCAGAGAA
*
21141 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * ****
21206 AACCTTTTGCTAAAATCCATCATTCAATGGATCAGTTTTTCCAGTTCGAGTTCATAATGAGAAGA
66 AACCTTTTGCTAAAATTCATCATT-AATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGA
21271 ACTCATCTGAAG-A-AAAAGTTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCAT
130 ACTCATCTGAAGAAGAAAAGTTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCAT
21334 TTGATGGATCAGCTTTGCCAGAGAA
195 TTGATGGATCAGCTTTGCCAGAGAA
* * *
21359 AGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * * *
21424 AACCCTTTGTTCAAATTCATCACTTAATGGATAAACCTTTACAGAGAAAGTTCATAATGAGAAGA
66 AACCTTTTGCTAAAATTCATCA-TTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGA
21489 ACTCATCTGAAGAAGAGAAAGTTCATAATAAGA
130 ACTCATCTGAAGAAGA-AAAGTTCATAATAAGA
21522 GCTTATTCAA
Statistics
Matches: 345, Mismatches: 29, Indels: 17
0.88 0.07 0.04
Matches are distributed among these distances:
218 195 0.57
219 5 0.01
220 2 0.01
221 18 0.05
222 2 0.01
224 64 0.19
225 59 0.17
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (219 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTAAAATTCATCATTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGAAAAGTTCATAATAAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCATT
TGATGGATCAGCTTTGCCAGAGAA
Found at i:21769 original size:3 final size:3
Alignment explanation
Indices: 21763--21825 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
21753 TTTACTCATT
* * *
21763 TTA TTA TTA TTA TTA TTA TTA TAA TAA TTA TTA TTA TAA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21810 TATA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA
21826 AAAATAATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:34965 original size:21 final size:21
Alignment explanation
Indices: 34939--34988 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
34929 TGATTGTTAT
34939 GGTGCTGATCTGGTTATCCAC
1 GGTGCTGATCTGGTTATCCAC
*
34960 GGTGCTGATGTGGTTATCCAC
1 GGTGCTGATCTGGTTATCCAC
*
34981 AGTGCTGA
1 GGTGCTGA
34989 CATGGTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.32
Consensus pattern (21 bp):
GGTGCTGATCTGGTTATCCAC
Found at i:34994 original size:21 final size:20
Alignment explanation
Indices: 34940--34994 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
34930 GATTGTTATG
*
34940 GTGCTGATCTGGTTATCCACG
1 GTGCTGA-CTGGTTATCCACA
*
34961 GTGCTGATGTGGTTATCCACA
1 GTGCTGA-CTGGTTATCCACA
34982 GTGCTGACATGGT
1 GTGCTGAC-TGGT
34995 AATTCATAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (20 bp):
GTGCTGACTGGTTATCCACA
Found at i:35815 original size:24 final size:23
Alignment explanation
Indices: 35787--35872 Score: 77
Period size: 22 Copynumber: 3.7 Consensus size: 23
35777 ATAAAAAAGT
35787 AATAATATATATTTTAAATTTTTG
1 AATAAT-TATATTTTAAATTTTTG
* *
35811 AATAATT-TAATTTAATTTTTTG
1 AATAATTATATTTTAAATTTTTG
* * *
35833 TATTATTATA-TTTAAGTTTTTG
1 AATAATTATATTTTAAATTTTTG
*
35855 AATATTTTTATATTTTAA
1 AATA--ATTATATTTTAA
35873 TTTAAAACAT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
22 31 0.62
23 3 0.06
24 11 0.22
25 5 0.10
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (23 bp):
AATAATTATATTTTAAATTTTTG
Found at i:35901 original size:22 final size:23
Alignment explanation
Indices: 35858--35900 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
35848 GTTTTTGAAT
35858 ATTTTTATATTTTAATTTAAAAC
1 ATTTTTATATTTTAATTTAAAAC
*
35881 ATTTTT-TATTTT-TTTTAAAA
1 ATTTTTATATTTTAATTTAAAA
35901 ATCAAATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 6 0.32
23 6 0.32
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTTTTATATTTTAATTTAAAAC
Found at i:39856 original size:15 final size:15
Alignment explanation
Indices: 39838--39875 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
39828 ATTGTTTTAT
39838 GTGAAAATGTGCTAA
1 GTGAAAATGTGCTAA
* *
39853 GTGAAAATGTTCTAC
1 GTGAAAATGTGCTAA
39868 GTGAAAAT
1 GTGAAAAT
39876 ACCCTATGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (15 bp):
GTGAAAATGTGCTAA
Found at i:40091 original size:24 final size:25
Alignment explanation
Indices: 40006--40104 Score: 137
Period size: 25 Copynumber: 4.0 Consensus size: 25
39996 GAGTCGAGGG
*
40006 TTCTACGTGGTCCTTTAGGACAAAT
1 TTCTACGTGGTCCTTTGGGACAAAT
*
40031 TTATACGTGGTCCTTTGGGACAAAT
1 TTCTACGTGGTCCTTTGGGACAAAT
*
40056 TTCTACGTGGTCATTTGGGACAAA-
1 TTCTACGTGGTCCTTTGGGACAAAT
* * *
40080 TTCTACGCGGTCCTTCGGGATAAAT
1 TTCTACGTGGTCCTTTGGGACAAAT
40105 CTATGTGGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
24 20 0.31
25 45 0.69
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (25 bp):
TTCTACGTGGTCCTTTGGGACAAAT
Found at i:41676 original size:17 final size:17
Alignment explanation
Indices: 41654--41695 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
41644 ATCATGTACT
*
41654 GAAAATCTGATTACCAC
1 GAAAATCCGATTACCAC
*
41671 GAAAATCCGATTATCAC
1 GAAAATCCGATTACCAC
41688 GAAAATCC
1 GAAAATCC
41696 TTATTTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (17 bp):
GAAAATCCGATTACCAC
Found at i:41816 original size:29 final size:29
Alignment explanation
Indices: 41737--41819 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
41727 TAAAATATAT
*
41737 AACTTTTAAAAATTACATTTT-GTCTCTA
1 AACTTTCAAAAATTACATTTTAGTCTCTA
** * *
41765 AACTTTTCAAAGTTTATACTTTAG-CTACTA
1 AAC-TTTCAAAAATTACATTTTAGTCT-CTA
*
41795 AACTTTCAAAACTTACATTTTAGTC
1 AACTTTCAAAAATTACATTTTAGTC
41820 ACTAGCTAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
28 3 0.07
29 31 0.74
30 8 0.19
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (29 bp):
AACTTTCAAAAATTACATTTTAGTCTCTA
Found at i:42136 original size:17 final size:18
Alignment explanation
Indices: 42116--42155 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
42106 TAATAGTGAG
42116 TTATATAA-AATATATTT
1 TTATATAATAATATATTT
*
42133 TTATTATAATTATATATTT
1 TTA-TATAATAATATATTT
42152 TTAT
1 TTAT
42156 TTGTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 6 0.30
19 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATAATAATATATTT
Found at i:42304 original size:21 final size:20
Alignment explanation
Indices: 42265--42312 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
42255 TAAGTGTCAA
* *
42265 TATAATTTATATATTATATT
1 TATAATTTAAATATAATATT
*
42285 TTTAATTTACAATATAATATT
1 TATAATTTA-AATATAATATT
42306 TATAATT
1 TATAATT
42313 GACATTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TATAATTTAAATATAATATT
Found at i:42589 original size:20 final size:21
Alignment explanation
Indices: 42564--42615 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
42554 TTTTCCCAAT
*
42564 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
42584 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
42605 TCGCAATGCGA
1 TCGCAATGCGA
42616 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:42629 original size:20 final size:20
Alignment explanation
Indices: 42604--42717 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
42594 AATTGGGAAA
*
42604 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
42624 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
42644 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
42665 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
42685 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
42705 TTCGCAACGCGAT
1 ATCGCAACGCGAT
42718 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:42648 original size:61 final size:61
Alignment explanation
Indices: 42601--42717 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
42591 GCGAATTGGG
* * * * *
42601 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
42662 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
42718 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:43295 original size:19 final size:19
Alignment explanation
Indices: 43271--43315 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
43261 GCAACGAGAG
*
43271 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
43290 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
43309 AATCGCA
1 AATCGCA
43316 TTACGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:43333 original size:19 final size:19
Alignment explanation
Indices: 43311--43352 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
43301 GAAACCAAAA
43311 TCGCATTACGATTTTCATT
1 TCGCATTACGATTTTCATT
* *
43330 TCGCGTTGCGATTTTCATT
1 TCGCATTACGATTTTCATT
43349 TCGC
1 TCGC
43353 GTTGCGATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTACGATTTTCATT
Found at i:43353 original size:19 final size:19
Alignment explanation
Indices: 43319--43456 Score: 89
Period size: 19 Copynumber: 7.7 Consensus size: 19
43309 AATCGCATTA
43319 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
43338 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
* **
43357 CGA--TTC-TCTC-C-TCA
1 CGATTTTCATTTCGCGTTG
** *
43371 CGATAGTCATTTCGCGTTA
1 CGATTTTCATTTCGCGTTG
*
43390 CGA--TTC---TCTCGTTG
1 CGATTTTCATTTCGCGTTG
**
43404 CGATAGTCATTTTCGCGTTG
1 CGATTTTCA-TTTCGCGTTG
* *
43424 CGATTCTCATTATCTCGTTG
1 CGATTTTCATT-TCGCGTTG
43444 CGATTTTCATTTC
1 CGATTTTCATTTC
43457 AACCAAAAGA
Statistics
Matches: 92, Mismatches: 15, Indels: 24
0.70 0.11 0.18
Matches are distributed among these distances:
14 13 0.14
15 1 0.01
16 7 0.08
17 8 0.09
18 1 0.01
19 31 0.34
20 31 0.34
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTG
Found at i:43386 original size:33 final size:33
Alignment explanation
Indices: 43344--43431 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
43334 GTTGCGATTT
43344 TCATTTCGCGTTGCGATTCTCTCCTCACGATAG
1 TCATTTCGCGTTGCGATTCTCTCCTCACGATAG
* * **
43377 TCATTTCGCGTTACGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCCTCACGATAG
43410 TCATTTTCGCGTTGCGATTCTC
1 TCA-TTTCGCGTTGCGATTCTC
43432 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 32 0.65
34 17 0.35
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCCTCACGATAG
Found at i:43448 original size:20 final size:20
Alignment explanation
Indices: 43396--43454 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
43386 GTTACGATTC
** *
43396 TCTCGTTGCGATAGTCATTT
1 TCTCGTTGCGATTCTCATTA
*
43416 TCGCGTTGCGATTCTCATTA
1 TCTCGTTGCGATTCTCATTA
*
43436 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTCTCATT
43455 TCAACCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (20 bp):
TCTCGTTGCGATTCTCATTA
Found at i:45623 original size:42 final size:42
Alignment explanation
Indices: 45547--45626 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
45537 GACTCGCCTG
* * *
45547 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
45589 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
45627 ACTGTCATAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.21, C:0.39, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:47181 original size:19 final size:19
Alignment explanation
Indices: 47157--47209 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
47147 AAAAAGTACT
*
47157 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
47176 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
47195 ATCGCAACGAGAAAT
1 ATCGCAACGCGAAAT
47210 TAAATTCGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:47236 original size:19 final size:19
Alignment explanation
Indices: 47214--47364 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
47204 AGAAATTAAA
47214 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
47233 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
47248 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
47266 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
47280 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
47299 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
47314 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
47332 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
47351 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
47365 AGACATTAAG
Statistics
Matches: 97, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
14 29 0.30
16 6 0.06
17 6 0.06
19 46 0.47
20 10 0.10
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:47260 original size:33 final size:32
Alignment explanation
Indices: 47218--47344 Score: 202
Period size: 33 Copynumber: 3.9 Consensus size: 32
47208 ATTAAATTCG
47218 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
47251 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
47284 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
47317 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
47345 AGTAATTTCC
Statistics
Matches: 88, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
31 3 0.03
33 82 0.93
35 3 0.03
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:47307 original size:66 final size:66
Alignment explanation
Indices: 47211--47343 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
47201 ACGAGAAATT
47211 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
47276 G
66 G
*
47277 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
47342 G
66 G
47343 A
1 A
47344 TAGTAATTTC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:49653 original size:12 final size:12
Alignment explanation
Indices: 49636--49660 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49626 TCTTCGTGGA
49636 CTTTTTCTTCTT
1 CTTTTTCTTCTT
49648 CTTTTTCTTCTT
1 CTTTTTCTTCTT
49660 C
1 C
49661 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:49869 original size:24 final size:24
Alignment explanation
Indices: 49835--49888 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
49825 CTGAAACATC
*
49835 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
49859 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
49883 ATCAAA
1 ATCAAA
49889 TTTCGAATAC
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:50714 original size:20 final size:20
Alignment explanation
Indices: 50628--50722 Score: 93
Period size: 20 Copynumber: 4.7 Consensus size: 20
50618 GATTCTGTAT
* *
50628 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
50648 AATCGCGTTGTGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
50668 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
50689 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
50709 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
50723 TTTCCCAATT
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.05
20 42 0.69
21 14 0.23
22 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:50736 original size:41 final size:41
Alignment explanation
Indices: 50649--50743 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
50639 GAAAGTCAGA
* * * ** *
50649 ATCGCGTTGTGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
50690 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
50732 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
50744 TTACTTATTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:50833 original size:21 final size:21
Alignment explanation
Indices: 50793--50833 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
50783 ACTGTAGACC
**
50793 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
50814 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
50834 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:51042 original size:25 final size:26
Alignment explanation
Indices: 50987--51045 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
50977 AAATACCTAA
* * *
50987 ATTTTAAAATTTACTTTTTATAATAC
1 ATTTAAAAATTTACTTTTAACAATAC
* *
51013 TTTTAAAAATTTA-TTTTAACAGTAC
1 ATTTAAAAATTTACTTTTAACAATAC
51038 ATTTAAAA
1 ATTTAAAA
51046 GTTGTTTTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (26 bp):
ATTTAAAAATTTACTTTTAACAATAC
Found at i:51438 original size:31 final size:31
Alignment explanation
Indices: 51382--51441 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
51372 ATGTACTTTT
* *
51382 GAATAAATTATATTAGATATTATTAAATTTA
1 GAATAAATTATATGAGATATAATTAAATTTA
51413 GAATAAATTATATGAG-TGATAATTAAATT
1 GAATAAATTATATGAGAT-ATAATTAAATT
51442 ACGGTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (31 bp):
GAATAAATTATATGAGATATAATTAAATTTA
Found at i:57668 original size:23 final size:24
Alignment explanation
Indices: 57638--57687 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
57628 GAAAAGGTAT
57638 AAAAATAA-ATAATT-ATAAATTAA
1 AAAAATAATA-AATTAATAAATTAA
*
57661 AAAAATAATAAATTAATGAATTAA
1 AAAAATAATAAATTAATAAATTAA
57685 AAA
1 AAA
57688 TAGTAATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAAATAATAAATTAATAAATTAA
Found at i:57762 original size:4 final size:4
Alignment explanation
Indices: 57746--57779 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
57736 AGATAAAAAT
*
57746 TAAA TAAA CAAA TAAA TAAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA T
57780 TGGGATAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:57762 original size:17 final size:17
Alignment explanation
Indices: 57742--57780 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
57732 AATGAGATAA
57742 AAATTAAATAAACAAAT
1 AAATTAAATAAACAAAT
* *
57759 AAATAAAATAAATAAAT
1 AAATTAAATAAACAAAT
57776 AAATT
1 AAATT
57781 GGGATAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATTAAATAAACAAAT
Found at i:58933 original size:133 final size:134
Alignment explanation
Indices: 58681--58944 Score: 361
Period size: 133 Copynumber: 2.0 Consensus size: 134
58671 AAATTTGGAG
* * * * *
58681 ATAACACGGTTCCTATGTGATGTGGAAGTCTGTCTATCTAAGGGTGACACGACTCCTACGTGATG
1 ATAACACGGTTCATACGTGATGAGGAAGACTGTCTATCTAAGAGTGACACGACTCCTACGTGATG
* * *
58746 AGGAGATCTGGTCGATGGATGACATGGTTCCTACGTGATGAAAATGACATACCATCTTTAGGGAT
66 AGGAGATCTGGTCGATGGATGACACGATTCCTACGTGATGAAAATGACAAACCATCTTTAGGGAT
58811 GGTA
131 GGTA
*
58815 ATAACACGGTTCATACGTGATGAGGATGACTG-CTTATCT-AGAGTGACACGACTCCTACGTGAT
1 ATAACACGGTTCATACGTGATGAGGAAGACTGTC-TATCTAAGAGTGACACGACTCCTACGTGAT
* * *** * *
58878 GAGGAGGTCTGGTCGGTGGATGACACGATTCCTACGTGATGTGGATGATAAACCATTTTTAGGGA
65 GAGGAGATCTGGTCGATGGATGACACGATTCCTACGTGATGAAAATGACAAACCATCTTTAGGGA
58943 TG
130 TG
58945 ATAACATACC
Statistics
Matches: 113, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
133 81 0.72
134 32 0.28
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (134 bp):
ATAACACGGTTCATACGTGATGAGGAAGACTGTCTATCTAAGAGTGACACGACTCCTACGTGATG
AGGAGATCTGGTCGATGGATGACACGATTCCTACGTGATGAAAATGACAAACCATCTTTAGGGAT
GGTA
Found at i:59189 original size:67 final size:66
Alignment explanation
Indices: 58971--59363 Score: 488
Period size: 67 Copynumber: 5.9 Consensus size: 66
58961 AGGGATAATG
* * *
58971 GTTTCAAGAGAAACCATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-ATACTCAAAGATTG
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGAT-CTCAAAGATTG
*
59035 GT
65 AT
* * *
59037 GTTTCTAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA-GAGAAACGATCTCAAAGA-TG
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGA-AAACGATCTCAAAGATTG
59100 AT
65 AT
* * * *
59102 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACAATCTCAAATATTTT
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGATCTCAAAGA-TTG
59167 AT
65 AT
* * * *
59169 GTTTCGAGAGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAAACAATCTCAAAGA-TG
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAA-GGAAAACGATCTCAAAGATTG
59233 AT
65 AT
* * * * * *
59235 GTTTCAAGAGAAATTGTCTCAAGAGAGACTAAATTTGTTTCAAGGGAAACGATCTCAAAGATTTT
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGATCTCAAAGA-TTG
59300 AT
65 AT
* * * *
59302 GTTTCGAGAGAAACTATCTCAAGGGAGACAAAACTCGTTTCAAGGGAAACGATCTCAAAGAT
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGATCTCAAAGAT
59364 CTTGTCTTAA
Statistics
Matches: 286, Mismatches: 33, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
65 74 0.26
66 94 0.33
67 101 0.35
68 17 0.06
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (66 bp):
GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGATCTCAAAGATTGA
T
Found at i:59255 original size:133 final size:131
Alignment explanation
Indices: 58971--59406 Score: 590
Period size: 133 Copynumber: 3.3 Consensus size: 131
58961 AGGGATAATG
** *
58971 GTTTCAAGAGAAACCATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATACTCAAAGA-TTG
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAT-CTCAAAGATTTT
* * * * * *
59035 GTGTTTCTAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACGATCTCAAAGATG
65 ATGTTTCGAGAGAAACTATCTCAAGAGAGACAAAACTCGTTTCAAGGGAAACGATCTCAAAGATG
59100 AT
130 AT
* * *
59102 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACAATCTCAAATATTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-ATCTCAAAGATTTT
* *
59167 ATGTTTCGAGAGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAAACAATCTCAAAGAT
65 ATGTTTCGAGAGAAACTATCTCAAGAGAGACAAAACTCGTTTCAAGGG-AAACGATCTCAAAGAT
59232 GAT
129 GAT
* *
59235 GTTTCAAGAGAAATTGTCTCAAGAGAGACTAAATTTGTTTCAAGGGAAACGATCTCAAAGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-ATCTCAAAGATTTT
* *
59300 ATGTTTCGAGAGAAACTATCTCAAGGGAGACAAAACTCGTTTCAAGGGAAACGATCTCAAAGATC
65 ATGTTTCGAGAGAAACTATCTCAAGAGAGACAAAACTCGTTTCAAGGGAAACGATCTCAAAGATG
*
59365 TT
130 AT
* * * *
59367 GTCTT-AAG-GAAGATTCTCTCAAGTGAGACAAATTTTGTTT
1 GT-TTCAAGAGAA-ACTGTCTCAAGAGAGACAAAATTTGTTT
59407 TGAGAAAAAT
Statistics
Matches: 271, Mismatches: 29, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
131 56 0.21
132 90 0.33
133 125 0.46
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (131 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATCTCAAAGATTTTA
TGTTTCGAGAGAAACTATCTCAAGAGAGACAAAACTCGTTTCAAGGGAAACGATCTCAAAGATGA
T
Found at i:59291 original size:36 final size:36
Alignment explanation
Indices: 59234--59359 Score: 95
Period size: 36 Copynumber: 3.6 Consensus size: 36
59224 TCAAAGATGA
*
59234 TGTTTCAAGAGAAATTG-TCTCAAGAGAGACTAAATT
1 TGTTTCAAGAGAAA-CGATCTCAAGAGAGACTAAATT
* *
59270 TGTTTCAAGGGAAACGATCTC-A-A-AGA-T--TTT
1 TGTTTCAAGAGAAACGATCTCAAGAGAGACTAAATT
* * * * *
59300 ATGTTTCGAGAGAAACTATCTCAAGGGAGACAAAACT
1 -TGTTTCAAGAGAAACGATCTCAAGAGAGACTAAATT
* *
59337 CGTTTCAAGGGAAACGATCTCAA
1 TGTTTCAAGAGAAACGATCTCAA
59360 AGATCTTGTC
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
30 2 0.03
31 18 0.26
32 2 0.03
33 3 0.04
34 4 0.06
35 2 0.03
36 36 0.53
37 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACGATCTCAAGAGAGACTAAATT
Found at i:59398 original size:198 final size:198
Alignment explanation
Indices: 58971--59363 Score: 565
Period size: 198 Copynumber: 2.0 Consensus size: 198
58961 AGGGATAATG
* * ** *
58971 GTTTCAAGAGAAACCATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATACTCAAAGATTGG
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAACATACTCAAAGATTGA
*
59036 TGTTTCTAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACGATCTCAAAGATGA
66 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACGATCTCAAAGATGA
* * * *
59101 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACAATCTCAAATATTT
131 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTCGTTTCAAGGAAAACAATCTCAAAGATTC
59166 TAT
196 TAT
*
59169 GTTTCGAGAGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAAACA-ATCTCAAAGA-T
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGG-AAACATA-CTCAAAGATT
* * *
59232 GATGTTTCAAGAGAAATTGTCTCAAGAGAGACTAAATTTGTTTCAAGGGAAACGATCTCAAAGAT
64 GATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACGATCTCAAAGA-
* * * * *
59297 TTTATGTTTCGAGAGAAACTATCTCAAGGGAGACAAAACTCGTTTCAAGGGAAACGATCTCAAAG
128 -TGATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTCGTTTCAAGGAAAACAATCTCAAAG
59362 AT
192 AT
59364 CTTGTCTTAA
Statistics
Matches: 173, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
198 102 0.59
199 13 0.08
200 58 0.34
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (198 bp):
GTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAACATACTCAAAGATTGA
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACGATCTCAAAGATGA
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTCGTTTCAAGGAAAACAATCTCAAAGATTC
TAT
Found at i:59527 original size:38 final size:38
Alignment explanation
Indices: 59478--59593 Score: 128
Period size: 38 Copynumber: 3.1 Consensus size: 38
59468 ATCTCAAAGG
*
59478 AAAAA-TGTCTCAAGCGAGACAAAATTTATTTTGAGAA
1 AAAAATTGTCTCAAGCGAGACAAAATTTATTTTAAGAA
* * * *
59515 AAAAATTGTCTCAAGCGAGAAAAAAATTGTTTTTAG-A
1 AAAAATTGTCTCAAGCGAGACAAAATTTATTTTAAGAA
* * * *
59552 GAAAATTGTCTCAAACAAGACAAAATTTCTTTTTAAGAA
1 AAAAATTGTCTCAAGCGAGACAAAATTT-ATTTTAAGAA
59591 AAA
1 AAA
59594 CTATATCTAG
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
37 29 0.45
38 32 0.50
39 3 0.05
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.28
Consensus pattern (38 bp):
AAAAATTGTCTCAAGCGAGACAAAATTTATTTTAAGAA
Found at i:59585 original size:37 final size:37
Alignment explanation
Indices: 59477--59592 Score: 135
Period size: 37 Copynumber: 3.1 Consensus size: 37
59467 CATCTCAAAG
* *
59477 GAAAAATGTCTCAAGCGAGACAAAATTTATTTTGAGAA
1 GAAAATTGTCTCAAGCGAGACAAAATTTATTTTTAG-A
* * * *
59515 AAAAATTGTCTCAAGCGAGAAAAAAATTGTTTTTAGA
1 GAAAATTGTCTCAAGCGAGACAAAATTTATTTTTAGA
* * *
59552 GAAAATTGTCTCAAACAAGACAAAATTTCTTTTTA-A
1 GAAAATTGTCTCAAGCGAGACAAAATTTATTTTTAGA
59588 GAAAA
1 GAAAA
59593 ACTATATCTA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 6 0.09
37 30 0.45
38 30 0.45
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (37 bp):
GAAAATTGTCTCAAGCGAGACAAAATTTATTTTTAGA
Found at i:60819 original size:16 final size:16
Alignment explanation
Indices: 60791--60832 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
60781 CTTCTTATCC
*
60791 TCTTTTTTCTTTTGCT
1 TCTTTTTTTTTTTGCT
60807 T-TGTTTTTTTTTTGCT
1 TCT-TTTTTTTTTTGCT
60823 TCTTTTTTTT
1 TCTTTTTTTT
60833 CTTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 1 0.04
16 21 0.91
17 1 0.04
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (16 bp):
TCTTTTTTTTTTTGCT
Found at i:60842 original size:12 final size:11
Alignment explanation
Indices: 60793--60853 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 11
60783 TCTTATCCTC
60793 TTTTTTCTTTT
1 TTTTTTCTTTT
* *
60804 GCTTTGT-TTTT
1 -TTTTTTCTTTT
*
60815 TTTTTGCTTCTT
1 TTTTTTCTT-TT
60827 TTTTTTCTTTT
1 TTTTTTCTTTT
60838 ATTTTTTCTTTGT
1 -TTTTTTCTTT-T
60851 TTT
1 TTT
60854 GATGTGATCT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 3 0.08
11 8 0.21
12 27 0.69
13 1 0.03
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.82
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:60844 original size:16 final size:16
Alignment explanation
Indices: 60793--60844 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
60783 TCTTATCCTC
60793 TTTTTTCTTTTGCTTTGT
1 TTTTTTCTTTT-CTTT-T
*
60811 TTTTTT-TTTGCTTCTT
1 TTTTTTCTTTTCTT-TT
*
60827 TTTTTTCTTTTATTTT
1 TTTTTTCTTTTCTTTT
60843 TT
1 TT
60845 CTTTGTTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 14 0.48
17 9 0.31
18 6 0.21
ACGTcount: A:0.02, C:0.10, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTTCTTTTCTTTT
Found at i:63200 original size:19 final size:20
Alignment explanation
Indices: 63176--63230 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 20
63166 ATACTCAAGG
63176 TACAGTATCGATACT-TACT
1 TACAGTATCGATACTATACT
*
63195 TACAGTGGCATCGATATTATACT
1 TACAGT---ATCGATACTATACT
63218 T-CAGTATCGATAC
1 TACAGTATCGATAC
63231 CCATTCTCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
19 13 0.43
22 12 0.40
23 5 0.17
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (20 bp):
TACAGTATCGATACTATACT
Found at i:68173 original size:19 final size:18
Alignment explanation
Indices: 68139--68174 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
68129 CTGCAAAATG
68139 TAATAAAATAATTAATAA
1 TAATAAAATAATTAATAA
*
68157 TAATAATAATGATTAATA
1 TAATAA-AATAATTAATA
68175 TTTTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TAATAAAATAATTAATAA
Found at i:68661 original size:16 final size:16
Alignment explanation
Indices: 68607--68661 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
68597 CTAAATTACC
*
68607 ACTTTCCTTGTTTGCT
1 ACTTTCCTTTTTTGCT
68623 ACTTTCC--TTTT--T
1 ACTTTCCTTTTTTGCT
68635 --TTTCCTTTTTTGCT
1 ACTTTCCTTTTTTGCT
68649 ACTTTCCTTTTTT
1 ACTTTCCTTTTTT
68662 TCCTTTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
10 5 0.16
12 5 0.16
14 4 0.12
16 18 0.56
ACGTcount: A:0.05, C:0.24, G:0.05, T:0.65
Consensus pattern (16 bp):
ACTTTCCTTTTTTGCT
Found at i:68665 original size:25 final size:26
Alignment explanation
Indices: 68609--68671 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
68599 AAATTACCAC
*
68609 TTTCCTTGTTTGCTACTTTCCTTTTT
1 TTTCCTTTTTTGCTACTTTCCTTTTT
68635 TTTCCTTTTTTGCTACTTTCC-TTTT
1 TTTCCTTTTTTGCTACTTTCCTTTTT
68660 TTTCCTTTTTTG
1 TTTCCTTTTTTG
68672 ATTCATGATA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 16 0.44
26 20 0.56
ACGTcount: A:0.03, C:0.22, G:0.06, T:0.68
Consensus pattern (26 bp):
TTTCCTTTTTTGCTACTTTCCTTTTT
Done.