Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006654.1 Hibiscus syriacus cultivar Beakdansim tig00016426_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: 60734
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:1864 original size:3 final size:3
Alignment explanation
Indices: 1856--1939 Score: 129
Period size: 3 Copynumber: 28.7 Consensus size: 3
1846 TTTTTACCCA
1856 TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
*
1901 TAT TAT TA- TAT TAT TAT TAT TAT CAT TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1940 AATATATTAA
Statistics
Matches: 75, Mismatches: 2, Indels: 8
0.88 0.02 0.09
Matches are distributed among these distances:
2 6 0.08
3 66 0.88
4 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2712 original size:43 final size:43
Alignment explanation
Indices: 2651--2735 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
2641 CGTCATTAGG
2651 ACGGTCCGATCTACGTTTAGATAAAAGAAAAATTTTTCCGGCC
1 ACGGTCCGATCTACGTTTAGATAAAAGAAAAATTTTTCCGGCC
2694 ACGGTCCGATCTACGTTTAGATAAAAGAAAAATTTTTCCGGC
1 ACGGTCCGATCTACGTTTAGATAAAAGAAAAATTTTTCCGGC
2736 AACCGAGACG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (43 bp):
ACGGTCCGATCTACGTTTAGATAAAAGAAAAATTTTTCCGGCC
Found at i:4189 original size:15 final size:13
Alignment explanation
Indices: 4169--4206 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
4159 TTTATATGTT
4169 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
4184 TTATTTTATTTCA
1 TTATTTTATTTCA
4197 TTA-TTTATTT
1 TTATTTTATTT
4207 TTCTGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:14827 original size:16 final size:16
Alignment explanation
Indices: 14806--14864 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 16
14796 GCTTGAAGAA
14806 AAAAGAAAAAAGAAAG
1 AAAAGAAAAAAGAAAG
*
14822 AAAAGAAAAAA-ATAG
1 AAAAGAAAAAAGAAAG
14837 AAAATGAAAAAAAGAGAAG
1 AAAA-G-AAAAAAGA-AAG
14856 AAAAAGAAA
1 -AAAAGAAA
14865 GGGGGTCAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 7 0.19
16 12 0.33
17 6 0.17
18 4 0.11
19 3 0.08
20 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAG
Found at i:14865 original size:15 final size:14
Alignment explanation
Indices: 14806--14865 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 14
14796 GCTTGAAGAA
14806 AAAAGAAAAAAGAAAG
1 AAAAG-AAAAA-AAAG
14822 AAAAGAAAAAAATAG
1 AAAAGAAAAAAA-AG
14837 AAAATG-AAAAAAAG
1 AAAA-GAAAAAAAAG
*
14851 AGAAGAAAAAGAAAG
1 AAAAGAAAAA-AAAG
14866 GGGGTCAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
13 1 0.03
14 11 0.28
15 21 0.54
16 6 0.15
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:15229 original size:19 final size:18
Alignment explanation
Indices: 15190--15235 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
15180 CTATTTCAAG
15190 TTCAATTTA--TTTGAAA
1 TTCAATTTATTTTTGAAA
*
15206 GTCAATTTATTTTTGGAAA
1 TTCAATTTATTTTT-GAAA
15225 TTCAATTTATT
1 TTCAATTTATT
15236 CTTTTCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (18 bp):
TTCAATTTATTTTTGAAA
Found at i:16026 original size:83 final size:84
Alignment explanation
Indices: 15887--16437 Score: 881
Period size: 83 Copynumber: 6.7 Consensus size: 84
15877 AATTAAATGA
*
15887 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAG
* *
15951 AACCAATCAGTGAATTTAG
66 AACCAATCATTGAGTTTAG
*
15970 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAG
16034 AA-CAATCATTGAGTTTAG
66 AACCAATCATTGAGTTTAG
16052 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAG
16116 AACCAATCATTGAGTTTAG
66 AACCAATCATTGAGTTTAG
*
16135 AAGATGAATTTGTTC-ATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACA
16198 GAA-CAATCATTGAGTTTAG
65 GAACCAATCATTGAGTTTAG
16217 AAGATGAATTTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
1 AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACA
16280 GAACCAATCATTGAGTTTAG
65 GAACCAATCATTGAGTTTAG
* *
16300 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GATTGGACAG
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAG
* * * *
16364 AATCAAGCATTGAATTTGG
66 AACCAATCATTGAGTTTAG
* *
16383 AACATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
16438 ATTCAGTAGG
Statistics
Matches: 443, Mismatches: 14, Indels: 21
0.93 0.03 0.04
Matches are distributed among these distances:
82 164 0.37
83 276 0.62
84 3 0.01
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (84 bp):
AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAG
AACCAATCATTGAGTTTAG
Found at i:16161 original size:165 final size:165
Alignment explanation
Indices: 15887--16437 Score: 946
Period size: 165 Copynumber: 3.3 Consensus size: 165
15877 AATTAAATGA
*
15887 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAGATGAATTTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
* *
15951 AACCAATCAGTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
65 AACCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
16016 TCTGATCTGGTTGGACAGAACAATCATTGAGTTTAG
130 TCTGATCTGGTTGGACAGAACAATCATTGAGTTTAG
16052 AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAGATGAATTTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
* *
16116 AACCAATCATTGAGTTTAGAAGATGAATTTGTTC-ATAGAATCTTCTGGAAGTGTTCTTTGAGTT
65 AACCAATCATTGAGTTTAGAAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
16180 ATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAG
129 ATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAG
16217 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
16282 ACCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 ACCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* * * *
16347 CTGATCTGATTGGACAGAATCAAGCATTGAATTTGG
131 CTGATCTGGTTGGACAGAA-CAATCATTGAGTTTAG
* *
16383 AACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
16438 ATTCAGTAGG
Statistics
Matches: 369, Mismatches: 13, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
164 1 0.00
165 299 0.81
166 69 0.19
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (165 bp):
AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTGGACAGAACAATCATTGAGTTTAG
Found at i:16325 original size:248 final size:248
Alignment explanation
Indices: 15887--16437 Score: 889
Period size: 248 Copynumber: 2.2 Consensus size: 248
15877 AATTAAATGA
*
15887 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAGATGAATTTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
15951 AACCAATCAGTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
65 AACCAATCAGTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
16016 TCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGG
130 TCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGG
* * *
16081 AAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAGTTTAG
195 AAGTGTTCTTTGAGTTATCTGATCT-GATTGGACAGAACCAAGCATTGAATTTAG
*
16135 AAGATGAATTTGTTCATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
* * *
16199 AA-CAATCATTGAGTTTAGAAGATGAATTTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTT
65 AACCAATCAGTGAATTTAGAAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
16262 ATCTGATCTGGTTTGG-CAGAACCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTC
129 ATCTGATCTGG-TTGGACAGAA-CAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTC
* *
16326 TGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTGG
192 TGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACCAAGCATTGAATTTAG
* *
16383 AACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
16438 ATTCAGTAGG
Statistics
Matches: 283, Mismatches: 14, Indels: 12
0.92 0.05 0.04
Matches are distributed among these distances:
247 81 0.29
248 201 0.71
249 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (248 bp):
AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCAGTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGA
AGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACCAAGCATTGAATTTAG
Found at i:17479 original size:116 final size:116
Alignment explanation
Indices: 17100--17831 Score: 1121
Period size: 116 Copynumber: 6.4 Consensus size: 116
17090 TCCAGAGAAG
*
17100 GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * * * * * *
17162 TCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAG-
66 TCAATCTTTTGCTTGAATTCATC-ATTTGATGGATCAACATTGCCAG-GTAGA
*
17214 GTTCATAATGAGAAGAACT--T-ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * *
17276 TCAACCTTTT-TTCTGAATTCATCAAATTGATGGATTATCATTGCCAGGTAGA
66 TCAATCTTTTGCT-TGAATTCATC-ATTTGATGGATCAACATTGCCAGGTAGA
*
17328 GTTCATAATGAGAAGAACTCGTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
17393 TCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
66 TCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
17444 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
17509 TCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
66 TCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
17560 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
17625 TCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
66 TCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
17676 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* ** *
17741 TCAATCTTTTGCTTGAATTCATCATTTGATGGATCATCATCCCCAGCAG-AAA
66 TCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAG--GTAGA
*
17793 GTTCATAATGAGAAGAA--C-TCATCTGAAGAAAG-AGAAGAA
1 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAA
17832 TTTATTCAAT
Statistics
Matches: 590, Mismatches: 18, Indels: 21
0.94 0.03 0.03
Matches are distributed among these distances:
113 10 0.02
114 133 0.23
115 2 0.00
116 365 0.62
117 78 0.13
118 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (116 bp):
GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
Found at i:17975 original size:3 final size:3
Alignment explanation
Indices: 17967--18040 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
17957 TTTTTACCCA
17967 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
18015 TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
18041 AATATATATT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:18526 original size:7 final size:7
Alignment explanation
Indices: 18514--18539 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18504 GACAGAGACA
18514 GAGAACG
1 GAGAACG
18521 GAGAACG
1 GAGAACG
18528 GAGAACG
1 GAGAACG
18535 GAGAA
1 GAGAA
18540 GGAAGACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.42, T:0.00
Consensus pattern (7 bp):
GAGAACG
Found at i:18826 original size:45 final size:45
Alignment explanation
Indices: 18776--18867 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
18766 GTCATTAGGA
18776 CGGTCCGATCTACGTTTAGATAAAAGAAAAAATTTTTCCGGCCAC
1 CGGTCCGATCTACGTTTAGATAAAAGAAAAAATTTTTCCGGCCAC
18821 CGGTCCGATCTACGTTTAGATAAAAGAAAAAATTTTTCCGGCCAC
1 CGGTCCGATCTACGTTTAGATAAAAGAAAAAATTTTTCCGGCCAC
18866 CG
1 CG
18868 AAGACGGTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (45 bp):
CGGTCCGATCTACGTTTAGATAAAAGAAAAAATTTTTCCGGCCAC
Found at i:19523 original size:14 final size:15
Alignment explanation
Indices: 19506--19544 Score: 62
Period size: 14 Copynumber: 2.6 Consensus size: 15
19496 GTTTTAGTGG
19506 TATTTTTATTGTTT-
1 TATTTTTATTGTTTA
19520 TATTTTTATTTGTTTA
1 TATTTTTA-TTGTTTA
19536 TATTTTTAT
1 TATTTTTAT
19545 GTATTCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 7 0.30
16 8 0.35
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (15 bp):
TATTTTTATTGTTTA
Found at i:21919 original size:3 final size:3
Alignment explanation
Indices: 21911--21993 Score: 85
Period size: 3 Copynumber: 27.7 Consensus size: 3
21901 ATATTATAAA
* * * * * *
21911 TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAC TAT AAT AAT AAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
21959 AAT TAT TAT TAT TAT CAT TAT CAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
21994 AATATATTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:22001 original size:9 final size:10
Alignment explanation
Indices: 21989--22027 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
21979 TCATTATTAT
21989 TATTAAAT-A
1 TATTAAATAA
21998 TATTAAATACA
1 TATTAAATA-A
22009 TATATAAATAA
1 TAT-TAAATAA
22020 TATTAAAT
1 TATTAAAT
22028 TACAAGCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.30
10 5 0.19
11 8 0.30
12 6 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:24110 original size:15 final size:13
Alignment explanation
Indices: 24092--24130 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
24082 TTCATATGTT
24092 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
24107 TTATTTTATTTCA
1 TTATTTTATTTCA
24120 TTA-TTTATTTC
1 TTATTTTATTTC
24131 TCTGTCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 8 0.33
13 4 0.17
14 1 0.04
15 11 0.46
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:34744 original size:7 final size:7
Alignment explanation
Indices: 34732--34810 Score: 79
Period size: 7 Copynumber: 10.4 Consensus size: 7
34722 ATTATGCTTG
34732 AAGAAAA
1 AAGAAAA
34739 AAGAAAAA
1 AAG-AAAA
34747 AAGAAAGAA
1 AAG-AA-AA
34756 AAGAAGAA
1 AAGAA-AA
34764 AA-AAAA
1 AAGAAAA
*
34770 AAAAAAA
1 AAGAAAA
34777 AAGAAAA
1 AAGAAAA
34784 AAGAAAAAA
1 AAG--AAAA
34793 AGAGAAAA
1 A-AGAAAA
34801 AAGAAAA
1 AAGAAAA
34808 AAG
1 AAG
34811 GGGGGTCAAG
Statistics
Matches: 65, Mismatches: 1, Indels: 12
0.83 0.01 0.15
Matches are distributed among these distances:
6 4 0.06
7 27 0.42
8 22 0.34
9 10 0.15
10 2 0.03
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:34746 original size:1 final size:1
Alignment explanation
Indices: 34735--34809 Score: 60
Period size: 1 Copynumber: 75.0 Consensus size: 1
34725 ATGCTTGAAG
* * * * * * * * *
34735 AAAAAAGAAAAAAAGAAAGAAAAGAAGAAAAAAAAAAAAAAAAAGAAAAAAGAAAAAAAGAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
34800 AAAGAAAAAA
1 AAAAAAAAAA
34810 GGGGGGTCAA
Statistics
Matches: 54, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:34748 original size:8 final size:8
Alignment explanation
Indices: 34735--34809 Score: 95
Period size: 8 Copynumber: 9.6 Consensus size: 8
34725 ATGCTTGAAG
34735 AAAAAAGA
1 AAAAAAGA
34743 AAAAAAGA
1 AAAAAAGA
34751 AAGAAAAG-
1 AA-AAAAGA
*
34759 AAGAAA-A
1 AAAAAAGA
34766 AAAAAA-A
1 AAAAAAGA
34773 AAAAAAG-
1 AAAAAAGA
34780 AAAAAAGA
1 AAAAAAGA
34788 AAAAAAGA
1 AAAAAAGA
34796 GAAAAAAGA
1 -AAAAAAGA
34805 AAAAA
1 AAAAA
34810 GGGGGGTCAA
Statistics
Matches: 60, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
7 22 0.37
8 25 0.42
9 13 0.22
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:34759 original size:17 final size:16
Alignment explanation
Indices: 34735--34809 Score: 95
Period size: 17 Copynumber: 4.8 Consensus size: 16
34725 ATGCTTGAAG
34735 AAAAAAGAAAAAAAGA
1 AAAAAAGAAAAAAAGA
*
34751 AAGAAAAG-AAGAAA-A
1 AA-AAAAGAAAAAAAGA
34766 AAAAAA-AAAAAAAG-
1 AAAAAAGAAAAAAAGA
34780 AAAAAAGAAAAAAAGA
1 AAAAAAGAAAAAAAGA
34796 GAAAAAAGAAAAAA
1 -AAAAAAGAAAAAA
34810 GGGGGGTCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 15 0.29
15 11 0.22
16 7 0.14
17 18 0.35
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAGA
Found at i:36086 original size:83 final size:83
Alignment explanation
Indices: 35947--36463 Score: 903
Period size: 83 Copynumber: 6.2 Consensus size: 83
35937 CATTAACTGA
35947 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
36012 ACAAATCATTGAATTTAG
66 ACAAATCATTGAATTTAG
36030 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
36095 ACAAATCATTGAATTTAG
66 ACAAATCATTGAATTTAG
36113 -AGAATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAG-ATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
*
36177 AATAAATCATTGAATTTAG
65 AACAAATCATTGAATTTAG
36196 -AGAATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAG-ATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
*
36260 AACAAACCATTGAATTTAG
65 AACAAATCATTGAATTTAG
36279 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
**
36344 ACAAGCCATTGAATTTAG
66 ACAAATCATTGAATTTAG
* **
36362 AAGATGAATGTGTTTATAGCATAATCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
* *
36427 ACCAATCATTGAATTTGG
66 ACAAATCATTGAATTTAG
* *
36445 AAGATGAATTTGCTCATAG
1 AAGATGAATGTGTTCATAG
36464 TAAAAATAAG
Statistics
Matches: 418, Mismatches: 14, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
82 2 0.00
83 414 0.99
84 2 0.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (83 bp):
AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACAAATCATTGAATTTAG
Found at i:37462 original size:114 final size:113
Alignment explanation
Indices: 37257--37815 Score: 825
Period size: 114 Copynumber: 4.9 Consensus size: 113
37247 TTCAAATCTA
* *
37257 TCATTAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 TCATCAATTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
37322 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTAAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
*
37370 TCATCAAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 TCATC-AATTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
37435 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
65 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* *
37484 TCATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 TCATC-AATTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
37549 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
65 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* * * * *
37598 TCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAG
1 TCATCAATTGATGGATTAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAG
* * *
37662 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAAT
62 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* * * * *
37714 TCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAG
1 TCATCAATTGATGGATTAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAG
* *
37778 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
62 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
37816 TAATTCTATC
Statistics
Matches: 426, Mismatches: 15, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
112 1 0.00
113 40 0.09
114 224 0.53
115 1 0.00
116 160 0.38
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (113 bp):
TCATCAATTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
Found at i:38145 original size:3 final size:3
Alignment explanation
Indices: 38137--38191 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
38127 ATATTAATTA
* * * *
38137 ATT ATT ATT ATT ATA ATA ATA ATA ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
38185 ATG ATT A
1 ATT ATT A
38192 AATATATTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:43099 original size:21 final size:22
Alignment explanation
Indices: 43059--43101 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
43049 ACATAGCTTA
43059 AATAAAACATAAATATTTATTT
1 AATAAAACATAAATATTTATTT
43081 AATAAAA-AT-AATATGTTATTT
1 AATAAAACATAAATAT-TTATTT
43102 TTTTATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 8 0.40
22 7 0.35
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AATAAAACATAAATATTTATTT
Found at i:44125 original size:15 final size:14
Alignment explanation
Indices: 44107--44141 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
44097 AGGGTATAAC
44107 TGAAAGTGGTAGTTG
1 TGAAAGTGGT-GTTG
44122 TGAAAGTGGTGTTG
1 TGAAAGTGGTGTTG
44136 TAGAAA
1 T-GAAA
44142 TGGATAATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.31, C:0.00, G:0.37, T:0.31
Consensus pattern (14 bp):
TGAAAGTGGTGTTG
Found at i:44158 original size:30 final size:30
Alignment explanation
Indices: 44122--44186 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
44112 GTGGTAGTTG
* *
44122 TGAAAGTGGTGTTGTAGAAATGGATAATGC
1 TGAAAGTGGTGGTGTAGAAATGAATAATGC
*
44152 TGAAAGTGGTGGTGTAGAAATGAATAATGT
1 TGAAAGTGGTGGTGTAGAAATGAATAATGC
44182 TGAAA
1 TGAAA
44187 TGGGTAGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.02, G:0.32, T:0.29
Consensus pattern (30 bp):
TGAAAGTGGTGGTGTAGAAATGAATAATGC
Found at i:45768 original size:2 final size:2
Alignment explanation
Indices: 45761--45789 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45751 TAATAGTGTT
45761 TA 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 TA T
45790 TATTTTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48998 original size:21 final size:21
Alignment explanation
Indices: 48973--49014 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
48963 TATCTCCACT
* *
48973 GACCTATGCGGCCAGGTAACG
1 GACCTATACGACCAGGTAACG
48994 GACCTATACGACCAGGTAACG
1 GACCTATACGACCAGGTAACG
49015 TTTTTCAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (21 bp):
GACCTATACGACCAGGTAACG
Found at i:49071 original size:42 final size:42
Alignment explanation
Indices: 48996--49125 Score: 181
Period size: 42 Copynumber: 3.1 Consensus size: 42
48986 AGGTAACGGA
* * *
48996 CCTATACGACCAGGTAACGTTTTTCAATGTCACCGCAATAAC
1 CCTATACGGCCAAGTAACTTTTTTCAATGTCACCGCAATAAC
* *
49038 CCTCTACGGCCAAGTAACTTTTTTCAATTTCACCGCAATAA-
1 CCTATACGGCCAAGTAACTTTTTTCAATGTCACCGCAATAAC
* *
49079 CCTATAAGGCCAAGTAACATTTTTTCAATGTCACTGCAATAAC
1 CCTATACGGCCAAGTAAC-TTTTTTCAATGTCACCGCAATAAC
49122 CCTA
1 CCTA
49126 ATGTTACTTG
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
41 16 0.21
42 57 0.74
43 4 0.05
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.29
Consensus pattern (42 bp):
CCTATACGGCCAAGTAACTTTTTTCAATGTCACCGCAATAAC
Found at i:51190 original size:14 final size:15
Alignment explanation
Indices: 51151--51194 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
51141 TGAACTTTAT
*
51151 AAATTT-AAATTATA
1 AAATTTAAAAATATA
*
51165 AAATTTAGAAATA-A
1 AAATTTAAAAATATA
51179 AAATTTAAAAATATA
1 AAATTTAAAAATATA
51194 A
1 A
51195 CCAATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
AAATTTAAAAATATA
Found at i:51241 original size:20 final size:20
Alignment explanation
Indices: 51197--51242 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
51187 AAATATAACC
51197 AATA-AAATAAATTTATAAA
1 AATATAAATAAATTTATAAA
*
51216 ATTATAAATAAATTTA-AAA
1 AATATAAATAAATTTATAAA
51235 TAATATAA
1 -AATATAA
51243 GAAATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AATATAAATAAATTTATAAA
Found at i:51919 original size:6 final size:6
Alignment explanation
Indices: 51910--51935 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
51900 AGCCACAGTT
51910 AAAACG AAAACG AAAACG AAAACG AA
1 AAAACG AAAACG AAAACG AAAACG AA
51936 TGAAAGTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAACG
Found at i:53739 original size:2 final size:2
Alignment explanation
Indices: 53734--53786 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
53724 ATACACACAC
53734 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53776 AT AT AT AT AT A
1 AT AT AT AT AT A
53787 ATTTAAAATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55034 original size:2 final size:2
Alignment explanation
Indices: 55029--55057 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55019 TAGCTTGAAT
55029 TA 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 TA T
55058 GAAGACCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55957 original size:60 final size:60
Alignment explanation
Indices: 55840--55967 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
55830 AAGTTACCAT
* * * * * *
55840 TTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACTCTATAGTTAGAGGATCC
1 TTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACACCCTATAATCAGAGGATCA
* * * *
55900 TTTTGTAACTTTTAATAGTCAAGAGACTTAATAAA-CTAATACCCTATAATCATAGGATCA
1 TTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGC-AACACCCTATAATCAGAGGATCA
55960 TTTGTGTA
1 TTT-TGTA
55968 TTTTACTCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
59 1 0.02
60 51 0.91
61 4 0.07
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (60 bp):
TTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACACCCTATAATCAGAGGATCA
Found at i:56574 original size:5 final size:5
Alignment explanation
Indices: 56564--57026 Score: 504
Period size: 5 Copynumber: 93.6 Consensus size: 5
56554 ATGGTTTCCC
56564 TATTA TATTA TA-T- TATTA TATT- TATATA TATTA T-TATA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TAT-TA TATTA TAT-TA TATTA TATTA
56612 TATTA TATTA TATTA TATTA TATTA TATTA TATTATA TATTA TATATA
1 TATTA TATTA TATTA TATTA TATTA TATTA TA-T-TA TATTA TAT-TA
56660 TATTA T-TTA TATTA TATTA TATTA TATTTA TATTTA TATTA TA-T- TATTA
1 TATTA TATTA TATTA TATTA TATTA TA-TTA TA-TTA TATTA TATTA TATTA
56709 TATTA TA-TA TATTA TATT- TATTA TA-TA TTATATA TATATA TATATA
1 TATTA TATTA TATTA TATTA TATTA TATTA -TAT-TA TAT-TA TAT-TA
*
56755 TATTA TATTA TATTA TATTA TA-T- TATTA TATTA -ATTA TA-TA TATGA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
* * * * * * * *
56801 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TA-TA TATGA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
56850 TATCTA TATTA -A-TA TATTA TATTA TATTA TATTA TATT- TA-TA TATT-
1 TAT-TA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
56896 TATATA TTATTA TATTA TATTA TATTA TATTA TTATTA TATT- TATTA
1 TAT-TA -TATTA TATTA TATTA TATTA TATTA -TATTA TATTA TATTA
56943 TATTA TA-T- TATTA TATTA TATTA TATTA TATTA TATTA TATTATA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA-T-TA TATTA
* *
56993 TATTA TATTA TATAA TTAATA TATTA TATTA TAT
1 TATTA TATTA TATTA -TATTA TATTA TATTA TAT
57027 AGTAGAGTAT
Statistics
Matches: 412, Mismatches: 8, Indels: 76
0.83 0.02 0.15
Matches are distributed among these distances:
3 11 0.03
4 50 0.12
5 284 0.69
6 54 0.13
7 13 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:58015 original size:12 final size:12
Alignment explanation
Indices: 57990--58059 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
57980 ACGGAGATAT
* *
57990 CAGAAATCAAAA
1 CAGAATTCAGAA
58002 CAGAATTCAGAA
1 CAGAATTCAGAA
58014 CA-AATATCAGAA
1 CAGAAT-TCAGAA
* *
58026 CAGAATCCAGAT
1 CAGAATTCAGAA
*
58038 CAGAAATCAGAA
1 CAGAATTCAGAA
58050 CAGAATTCAG
1 CAGAATTCAG
58060 GTCATGTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 3 0.06
12 42 0.88
13 3 0.06
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:58022 original size:24 final size:24
Alignment explanation
Indices: 57990--58059 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
57980 ACGGAGATAT
*
57990 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* *
58014 CA-AATATCAGAACAGAATCCAGAT
1 CAGAA-ATCAGAACAGAATTCAGAA
58038 CAGAAATCAGAACAGAATTCAG
1 CAGAAATCAGAACAGAATTCAG
58060 GTCATGTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.05
24 36 0.90
25 2 0.05
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:58070 original size:24 final size:23
Alignment explanation
Indices: 57995--58082 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 23
57985 GATATCAGAA
* * *
57995 ATCAAAACAGAATTCAGAACAAAT
1 ATCAGAACAGAATTCAGATC-AGT
* *
58019 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATTCAGATCAG-T
*
58043 ATCAGAACAGAATTCAGGTCATGT
1 ATCAGAACAGAATTCAGATCA-GT
*
58067 ATCAGAACAAAATTCA
1 ATCAGAACAGAATTCA
58083 AGTCGGAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 1 0.02
24 51 0.96
25 1 0.02
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (23 bp):
ATCAGAACAGAATTCAGATCAGT
Found at i:58092 original size:48 final size:48
Alignment explanation
Indices: 57988--58096 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
57978 AAACGGAGAT
* * *
57988 ATCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGAACAAATATCAGAACAAAATCAAG
** **
58036 ATCAGAAATCAGAACAGAATTCAGGTCATGTATCAGAACAAAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGAACAAATATCAGAACAAAA-TCAAG
*
58085 -TCGGAAATCAGA
1 ATCAGAAATCAGA
58097 TAAAATATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 48 0.92
49 4 0.08
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.17
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGAACAAATATCAGAACAAAATCAAG
Found at i:58094 original size:24 final size:25
Alignment explanation
Indices: 58019--58096 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 25
58009 CAGAACAAAT
* *
58019 ATCAGAACAGAA-TCCAGATCA-GAA
1 ATCAGAACAAAATTCAAG-TCAGGAA
* * * *
58043 ATCAGAACAGAATTCAGGTCATG-T
1 ATCAGAACAAAATTCAAGTCAGGAA
58067 ATCAGAACAAAATTCAAGTC-GGAA
1 ATCAGAACAAAATTCAAGTCAGGAA
58091 ATCAGA
1 ATCAGA
58097 TAAAATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 1 0.02
24 39 0.89
25 4 0.09
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (25 bp):
ATCAGAACAAAATTCAAGTCAGGAA
Found at i:60170 original size:17 final size:17
Alignment explanation
Indices: 60148--60180 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
60138 GTCAACAGTG
*
60148 GTCAACGCTGGTCAACA
1 GTCAACGCAGGTCAACA
60165 GTCAACGCAGGTCAAC
1 GTCAACGCAGGTCAAC
60181 GATTGACCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.15
Consensus pattern (17 bp):
GTCAACGCAGGTCAACA
Found at i:60268 original size:22 final size:22
Alignment explanation
Indices: 60242--60284 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
60232 TCTGTAAGTA
* *
60242 TTTACATAACTAATACCCAAAT
1 TTTACACAAATAATACCCAAAT
*
60264 TTTACACAAATAGTACCCAAA
1 TTTACACAAATAATACCCAAA
60285 CAATAATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (22 bp):
TTTACACAAATAATACCCAAAT
Done.