Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002757.1 Hibiscus syriacus cultivar Beakdansim tig00005685_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: 67747
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Found at i:18286 original size:36 final size:36
Alignment explanation
Indices: 18246--18345 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
18236 ATCCATTATT
*
18246 AGCTTTGATACATTTGTGTATCAATGTTATCATATC
1 AGCTTTGATACATTAGTGTATCAATGTTATCATATC
*
18282 AGCTTTGATACATTAGTGTATAAATGTTATCATATC
1 AGCTTTGATACATTAGTGTATCAATGTTATCATATC
* * *
18318 AGCTTTGGTACATTCGTGTACCAATGTT
1 AGCTTTGATACATTAGTGTATCAATGTT
18346 CAGCACCATT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (36 bp):
AGCTTTGATACATTAGTGTATCAATGTTATCATATC
Found at i:22964 original size:26 final size:26
Alignment explanation
Indices: 22910--22961 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
22900 AAAATTTTTA
22910 TATATGCTTATTATTTTCATAATATT
1 TATATGCTTATTATTTTCATAATATT
*
22936 TATATG-TATATTATTTT-TTAATATT
1 TATATGCT-TATTATTTTCATAATATT
22961 T
1 T
22962 TATTTCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (26 bp):
TATATGCTTATTATTTTCATAATATT
Found at i:24376 original size:6 final size:7
Alignment explanation
Indices: 24322--24362 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
24312 TTTTCATACA
24322 TGCA-TT
1 TGCATTT
24328 TGCATTT
1 TGCATTT
24335 TGCATCTT
1 TGCAT-TT
24343 TGCATTT
1 TGCATTT
24350 T-CATTT
1 TGCATTT
24356 TGCATTT
1 TGCATTT
24363 GTTGTTTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.31
7 15 0.47
8 7 0.22
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:31036 original size:75 final size:75
Alignment explanation
Indices: 30937--31076 Score: 192
Period size: 75 Copynumber: 1.9 Consensus size: 75
30927 ATTCATTCAT
* ** *
30937 AATCAGGAATATTGACGCATTTTGAATGTTTGTATCAGCAAATG-TTGGGACATGCTGAAAGCCC
1 AATCAGGAATATTGACGCATTTTGAACGTTCATATCAGCAAATGCTTGGG-CATACTGAAAGCCC
31001 ATTTCAAACAG
65 ATTTCAAACAG
* * * *
31012 AATCAGGAATATTGATGTATTTTGAACGTTCATATCAGTAAATGCTTGGGCATACTGAAGGCCCA
1 AATCAGGAATATTGACGCATTTTGAACGTTCATATCAGCAAATGCTTGGGCATACTGAAAGCCCA
31077 CATCATCACA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 51 0.91
76 5 0.09
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (75 bp):
AATCAGGAATATTGACGCATTTTGAACGTTCATATCAGCAAATGCTTGGGCATACTGAAAGCCCA
TTTCAAACAG
Found at i:32385 original size:22 final size:22
Alignment explanation
Indices: 32360--32434 Score: 114
Period size: 22 Copynumber: 3.4 Consensus size: 22
32350 ATCTACATAT
*
32360 TTCAAAGATGATATATTCTATC
1 TTCAAAGATGATATATTCTCTC
*
32382 TTCAAAGATGATAGATTCTCTC
1 TTCAAAGATGATATATTCTCTC
* *
32404 TTCAAAAATGATATATTCTCTT
1 TTCAAAGATGATATATTCTCTC
32426 TTCAAAGAT
1 TTCAAAGAT
32435 AAAAACTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATATATTCTCTC
Found at i:33208 original size:43 final size:43
Alignment explanation
Indices: 33160--33245 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
33150 AGATTGTTTT
* * *
33160 TCTTAAAGCAAATTGTTTCTCGCTTA-AGAAAGTTTCAATTGAA
1 TCTTAAAACAAACTATTTCTCGC-TAGAGAAAGTTTCAATTGAA
* *
33203 TCTTAAAACAAACTATTTCTCTCTAGAGAAAGTTTCACTTGAA
1 TCTTAAAACAAACTATTTCTCGCTAGAGAAAGTTTCAATTGAA
33246 ATATCCATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
42 2 0.05
43 35 0.95
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (43 bp):
TCTTAAAACAAACTATTTCTCGCTAGAGAAAGTTTCAATTGAA
Found at i:33322 original size:73 final size:73
Alignment explanation
Indices: 33203--33355 Score: 288
Period size: 73 Copynumber: 2.1 Consensus size: 73
33193 TTCAATTGAA
33203 TCTTAAAACAAACTATTTCTCTCTAGAGAAAGTTTCACTTGAAATATCCATTTATCTCACTTGAG
1 TCTTAAAACAAACTATTTCTCTCTAGAGAAAGTTTCACTTGAAATATCCATTTATCTCACTTGAG
*
33268 ATTGTTTT
66 ATTATTTT
*
33276 TCTTAAAACAAACTATTTCTCTCTAGAGAAAGTTTCACTTGAAATATCCATTTATCTCATTTGAG
1 TCTTAAAACAAACTATTTCTCTCTAGAGAAAGTTTCACTTGAAATATCCATTTATCTCACTTGAG
33341 ATTATTTT
66 ATTATTTT
33349 TCTTAAA
1 TCTTAAA
33356 GCATTACCAG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
73 78 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (73 bp):
TCTTAAAACAAACTATTTCTCTCTAGAGAAAGTTTCACTTGAAATATCCATTTATCTCACTTGAG
ATTATTTT
Found at i:33537 original size:17 final size:17
Alignment explanation
Indices: 33515--33578 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
33505 TCTGAAGAAG
33515 GAGAAGAAGTTCATAAT
1 GAGAAGAAGTTCATAAT
*
33532 GAGAAGAACTCGTCTGCAGAAT
1 GAGAAGAA---GT-T-CATAAT
33554 GAGAAGAAGTTCATAAT
1 GAGAAGAAGTTCATAAT
*
33571 AAGAAGAA
1 GAGAAGAA
33579 CTTGTTCAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 20 0.51
18 1 0.03
19 2 0.05
20 2 0.05
21 1 0.03
22 13 0.33
ACGTcount: A:0.47, C:0.09, G:0.25, T:0.19
Consensus pattern (17 bp):
GAGAAGAAGTTCATAAT
Found at i:33537 original size:39 final size:39
Alignment explanation
Indices: 33483--33580 Score: 169
Period size: 39 Copynumber: 2.5 Consensus size: 39
33473 TGCCAGGTAG
33483 AGTTCATAATGAGAAGAACTCGTCTGAAGAAGGAGAAGA
1 AGTTCATAATGAGAAGAACTCGTCTGAAGAAGGAGAAGA
* *
33522 AGTTCATAATGAGAAGAACTCGTCTGCAGAATGAGAAGA
1 AGTTCATAATGAGAAGAACTCGTCTGAAGAAGGAGAAGA
*
33561 AGTTCATAATAAGAAGAACT
1 AGTTCATAATGAGAAGAACT
33581 TGTTCAACCT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.20
Consensus pattern (39 bp):
AGTTCATAATGAGAAGAACTCGTCTGAAGAAGGAGAAGA
Found at i:33555 original size:22 final size:22
Alignment explanation
Indices: 33490--33561 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
33480 TAGAGTTCAT
*
33490 AATGAGAAGAACTCGTCTGAAG
1 AATGAGAAGAACTCGTCTGCAG
* *
33512 AAGGAGAAGAA---GT-T-CAT
1 AATGAGAAGAACTCGTCTGCAG
33529 AATGAGAAGAACTCGTCTGCAG
1 AATGAGAAGAACTCGTCTGCAG
33551 AATGAGAAGAA
1 AATGAGAAGAA
33562 GTTCATAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 11 0.28
18 1 0.03
19 2 0.05
20 2 0.05
21 1 0.03
22 23 0.57
ACGTcount: A:0.44, C:0.11, G:0.28, T:0.17
Consensus pattern (22 bp):
AATGAGAAGAACTCGTCTGCAG
Found at i:33683 original size:101 final size:100
Alignment explanation
Indices: 33572--33981 Score: 565
Period size: 101 Copynumber: 4.1 Consensus size: 100
33562 GTTCATAATA
33572 AGAAGAACTTGTTCAACCTTTTGC-TCGACGCTATCACATAAGGAGATAGATCAGCATCAACATT
1 AGAAGAACTTGTTCAACCTTTTGCGT-GACGCTATCACA-AAGGAGATAGATCAGCATCAACATT
* * * *
33636 TTCAGAAGTGTTCATAATGAGAAGAACTCTTCTGAAT
64 TCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
33673 AGAAGAACTTGTTCAACTTTTTGC-TAGACGCTATCACACAAGAAGATAGATCAGCATTAACATT
1 AGAAGAACTTGTTCAACCTTTTGCGT-GACGCTATCACA-AAGGAGATAGATCAGCATCAACATT
*
33737 TCCAGAAGAGTTCATAATGAGAAGAACTTATCTGAAG
64 TCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
* **
33774 AGAAGCACTTGTTCAACCTTTTGCGTGATTCTATCAC-AAGGAGATAGATCAGCATCAACATTTC
1 AGAAGAACTTGTTCAACCTTTTGCGTGACGCTATCACAAAGGAGATAGATCAGCATCAACATTTC
* * *
33838 CAAAAGTGTTCATAATGAGAATAACTCATCTGAAG
66 CAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
** * *
33873 AGAAGAACTTGTTCAACCTTTTGCGTGATTCTATCACAGAAAGAGATAGATCATCATCAACATTT
1 AGAAGAACTTGTTCAACCTTTTGCGTGACGCTATCACA-AAGGAGATAGATCAGCATCAACATTT
*
33938 CCAGAAAGAGTTCATAATGAGAAAAACTCATCTGAAG
65 CCAG-AAGAGTTCATAATGAGAAGAACTCATCTGAAG
33975 AGGAAGA
1 A-GAAGA
33982 GGAGGTTCAT
Statistics
Matches: 278, Mismatches: 26, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
99 92 0.33
101 149 0.54
102 32 0.12
103 5 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (100 bp):
AGAAGAACTTGTTCAACCTTTTGCGTGACGCTATCACAAAGGAGATAGATCAGCATCAACATTTC
CAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
Found at i:33923 original size:200 final size:202
Alignment explanation
Indices: 33572--33981 Score: 596
Period size: 200 Copynumber: 2.0 Consensus size: 202
33562 GTTCATAATA
33572 AGAAGAACTTGTTCAACCTTTTGCTCGACGCTATCACATAAGGAGATAGATCAGCATCAACATTT
1 AGAAGAACTTGTTCAACCTTTTGCTCGACGCTATCACA-AAGGAGATAGATCAGCATCAACATTT
* * * * *
33637 TCAGAAGTGTTCATAATGAGAAGAACTCTTCTGAATAGAAGAACTTGTTCAACTTTTTGCTAGAC
65 CCAAAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAACTTGTTCAACCTTTTGCTAGAC
* * * *
33702 GCTATCACACAAGAAGATAGATCAGCATTAACATTTCCAG-AAGAGTTCATAATGAGAAGAACTT
130 GCTATCACAAAAGAAGATAGATCAGCATCAACATTTCCAGAAAGAGTTCATAATGAGAAAAACTC
33766 ATCTGAAG
195 ATCTGAAG
* **
33774 AGAAGCACTTGTTCAACCTTTTGCGT-GATTCTATCAC-AAGGAGATAGATCAGCATCAACATTT
1 AGAAGAACTTGTTCAACCTTTTGC-TCGACGCTATCACAAAGGAGATAGATCAGCATCAACATTT
*
33837 CCAAAAGTGTTCATAATGAGAATAACTCATCTGAAGAGAAGAACTTGTTCAACCTTTTGCGT-GA
65 CCAAAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAACTTGTTCAACCTTTTGC-TAGA
** *
33901 TTCTATCACAGAAAG-AGATAGATCATCATCAACATTTCCAGAAAGAGTTCATAATGAGAAAAAC
129 CGCTATCACA-AAAGAAGATAGATCAGCATCAACATTTCCAGAAAGAGTTCATAATGAGAAAAAC
33965 TCATCTGAAG
193 TCATCTGAAG
33975 AGGAAGA
1 A-GAAGA
33982 GGAGGTTCAT
Statistics
Matches: 186, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
200 114 0.61
201 35 0.19
202 36 0.19
203 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (202 bp):
AGAAGAACTTGTTCAACCTTTTGCTCGACGCTATCACAAAGGAGATAGATCAGCATCAACATTTC
CAAAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAACTTGTTCAACCTTTTGCTAGACG
CTATCACAAAAGAAGATAGATCAGCATCAACATTTCCAGAAAGAGTTCATAATGAGAAAAACTCA
TCTGAAG
Found at i:35159 original size:21 final size:21
Alignment explanation
Indices: 35133--35177 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35123 GATTTCTGGG
* *
35133 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
35154 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
35175 CAA
1 CAA
35178 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:36908 original size:22 final size:22
Alignment explanation
Indices: 36835--36900 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
36825 TATGGACATC
*
36835 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
36857 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
36879 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
36901 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.26
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:39879 original size:21 final size:21
Alignment explanation
Indices: 39853--39897 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
39843 GATTTCTGGG
* *
39853 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
39874 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
39895 CAA
1 CAA
39898 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:41583 original size:13 final size:13
Alignment explanation
Indices: 41565--41627 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
41555 TCTACGGGCA
41565 CTACGGTGCAATT
1 CTACGGTGCAATT
41578 CTACGG-GC-A--
1 CTACGGTGCAATT
*
41587 CTTCGGTGCAATT
1 CTACGGTGCAATT
41600 CTACGG-GC-A--
1 CTACGGTGCAATT
*
41609 CTTCGGTGCAATT
1 CTACGGTGCAATT
41622 CTACGG
1 CTACGG
41628 GCACTTCGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:41648 original size:22 final size:22
Alignment explanation
Indices: 41553--41640 Score: 167
Period size: 22 Copynumber: 4.0 Consensus size: 22
41543 TATGGACATC
*
41553 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
41575 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
41597 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
41619 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
41641 TTTATACGAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.26
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:46908 original size:17 final size:18
Alignment explanation
Indices: 46876--46914 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
46866 AACATGTGTT
46876 TTTAGTTTTATAATATAA
1 TTTAGTTTTATAATATAA
* *
46894 TTTATTTTTAT-ATATTA
1 TTTAGTTTTATAATATAA
46911 TTTA
1 TTTA
46915 AAAGTTAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAGTTTTATAATATAA
Found at i:49974 original size:25 final size:25
Alignment explanation
Indices: 49917--49985 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 25
49907 GTATAAGATT
* **
49917 TTAAAAAATATGAAATGAAATTATTAA
1 TTAAAAAATAT-AAA-GAAAATAACAA
*
49944 TAAAAAAATATAAAGAAAATAACAA
1 TTAAAAAATATAAAGAAAATAACAA
49969 TT--AAAATATAAA-AAAAT
1 TTAAAAAATATAAAGAAAAT
49986 GAAAATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 5 0.14
23 10 0.27
25 9 0.24
26 3 0.08
27 10 0.27
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (25 bp):
TTAAAAAATATAAAGAAAATAACAA
Found at i:50605 original size:13 final size:13
Alignment explanation
Indices: 50587--50620 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
50577 ATCTATTAAA
50587 TTTTTTCTACAAT
1 TTTTTTCTACAAT
*
50600 TTTTTTTTACAAT
1 TTTTTTCTACAAT
50613 TTTTTTCT
1 TTTTTTCT
50621 TTTAATCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTCTACAAT
Found at i:57445 original size:20 final size:20
Alignment explanation
Indices: 57420--57482 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
57410 ATAACAATAT
*
57420 AACATGTTAAAGTTTGACAA
1 AACATGTTTAAGTTTGACAA
*
57440 AACATGTTTCAGTTTGACAA
1 AACATGTTTAAGTTTGACAA
** * *
57460 GTCATGTTTTAGTTTGATAA
1 AACATGTTTAAGTTTGACAA
57480 AAC
1 AAC
57483 CGACAAAGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
AACATGTTTAAGTTTGACAA
Found at i:57800 original size:20 final size:20
Alignment explanation
Indices: 57777--57833 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
57767 AACAGGTTGA
*
57777 AGTTTGACAAAACCGGTTTG
1 AGTTTGACAAAACCGGTTTC
*
57797 AGTTTGACAAAATCGGTTTC
1 AGTTTGACAAAACCGGTTTC
57817 AGTTTGACAAAACCGGT
1 AGTTTGACAAAACCGGT
57834 AGAGATATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.30
Consensus pattern (20 bp):
AGTTTGACAAAACCGGTTTC
Found at i:58042 original size:347 final size:348
Alignment explanation
Indices: 57359--58055 Score: 972
Period size: 347 Copynumber: 2.0 Consensus size: 348
57349 TGACAACCGA
* * * *
57359 TAAACTTAGCTTATCGATAGGTATCGATATCTTGCATAGAAGTATCGATACATAACAATATAACA
1 TAAACTTAGCTTATCGATAGGCATCGATATCTTACACACAAGTATCGATACATAACAATATAACA
* * * * * *
57424 TGTTAAAGTTTGACAAAACATGTTTCAGTTTGACAAGTCATGTTTTAGTTTGATAAAACCGACAA
66 GGTTAAAGTTTGACAAAACAGGTTTCAGTTTGACAAATCAGGTTTCAGTTTGACAAAACCGACAA
* * * *
57489 AGATACTGAAATTATTGAAATTTGTATCGATACTTTTCTAAGTATATACACCAAAGTATCTATAT
131 AGATACTGAAATTATTGAAATTTGTATCGAAACTTATCTAAGTATATACACCAAAGTATCGATAC
* *
57554 TTTAAGAATTTAAAAGAATTGTAATAATAGCACTTAAAAAGTATCGATACCTTAGAAACATTTAT
196 TTTAAGAATTTAAAAGAATTGCAATAATAGCACTTAAAAAGTATCGATACCTTAGAAACATGTAT
* * * *
57619 CGATACATGACAATATAACATGTTAAAATTTGACAAAATCGGTTTCAATATGACAAAACCGGTAA
261 CGATACATGACAATATAAAATGTTAAAATTTGACAAAACCAGTTTCAACATGACAAAACCGGTAA
57684 AGCACTACCGGATATACTGAAGG
326 AGCACTACCGGATATACTGAAGG
* *
57707 TAAACTTAGCTTATCGGTAGGCATCGATA-CTTACACACATGTATCGATACATAACAATATAACA
1 TAAACTTAGCTTATCGATAGGCATCGATATCTTACACACAAGTATCGATACATAACAATATAACA
* * * **
57771 GGTTGAAGTTTGACAAAACCGGTTTGAGTTTGACAAAATC-GGTTTCAGTTTGACAAAACCGGTA
66 GGTTAAAGTTTGACAAAACAGGTTTCAGTTTGAC-AAATCAGGTTTCAGTTTGACAAAACCGACA
* * * *
57835 GAGATA-TCGAAATTGTTGAAATTTGTATCGAAACTTATCTAAGTATATGCACCAAAGTATCGGT
130 AAGATACT-GAAATTATTGAAATTTGTATCGAAACTTATCTAAGTATATACACCAAAGTATCGAT
* * * * **
57899 ACTTTAGGAATTTAAAATAATTGCAATAATAGCGCCTT-GAAAGTATCGATACCTTTTAAACATG
194 ACTTTAAGAATTTAAAAGAATTGCAATAATAGC-ACTTAAAAAGTATCGATACCTTAGAAACATG
57963 TATCGATACATGACAATATAAAATGTTAAAATTTGACAAAACCAGTTTCAACATGACAAAACCGG
258 TATCGATACATGACAATATAAAATGTTAAAATTTGACAAAACCAGTTTCAACATGACAAAACCGG
**
58028 TAAAGCGA-TACCGGATATGTTGAAGG
323 TAAAGC-ACTACCGGATATACTGAAGG
58054 TA
1 TA
58056 TCGATACTTT
Statistics
Matches: 306, Mismatches: 39, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
346 1 0.00
347 270 0.88
348 35 0.11
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (348 bp):
TAAACTTAGCTTATCGATAGGCATCGATATCTTACACACAAGTATCGATACATAACAATATAACA
GGTTAAAGTTTGACAAAACAGGTTTCAGTTTGACAAATCAGGTTTCAGTTTGACAAAACCGACAA
AGATACTGAAATTATTGAAATTTGTATCGAAACTTATCTAAGTATATACACCAAAGTATCGATAC
TTTAAGAATTTAAAAGAATTGCAATAATAGCACTTAAAAAGTATCGATACCTTAGAAACATGTAT
CGATACATGACAATATAAAATGTTAAAATTTGACAAAACCAGTTTCAACATGACAAAACCGGTAA
AGCACTACCGGATATACTGAAGG
Found at i:59209 original size:13 final size:13
Alignment explanation
Indices: 59165--59209 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
59155 TATTTTCTAT
59165 ATTAATTATAATC
1 ATTAATTATAATC
*
59178 TTTATATTATAAATC
1 ATTA-ATTAT-AATC
59193 -TTAATTATAATC
1 ATTAATTATAATC
59205 ATTAA
1 ATTAA
59210 ATTAATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 8 0.29
15 4 0.14
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:59375 original size:2 final size:2
Alignment explanation
Indices: 59368--59411 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
59358 TATTTGAGAT
59368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59410 TA
1 TA
59412 AAGTGAGTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59832 original size:2 final size:2
Alignment explanation
Indices: 59827--59851 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59817 TATATGCTTT
59827 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 T
59852 GATGTATGCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59875 original size:27 final size:27
Alignment explanation
Indices: 59838--59904 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
59828 ATATATATAT
*
59838 ATATATATATATATGATGTATGCACTT
1 ATATATATATATATGATGTATGCACTC
* *
59865 A-AGTATATATATGTGATGTATGTACTC
1 ATA-TATATATATATGATGTATGCACTC
59892 ATATATATATATA
1 ATATATATATATA
59905 GTTTATATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 32 0.94
28 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (27 bp):
ATATATATATATATGATGTATGCACTC
Found at i:60014 original size:2 final size:2
Alignment explanation
Indices: 59952--60001 Score: 77
Period size: 2 Copynumber: 25.5 Consensus size: 2
59942 TTTTACACAT
59952 TA TA TA TA CT- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59993 TA TA TA TA T
1 TA TA TA TA T
60002 TCTTAAATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.04
2 42 0.93
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60145 original size:29 final size:27
Alignment explanation
Indices: 60103--60206 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 27
60093 ATGCATAAGT
*
60103 ATAATGTACATTATAATATATATATATAC
1 ATAAT-TATATTATAATATA-ATATATAC
*
60132 ATGAATTATATTATCATA-ACATTCATCATAC
1 AT-AATTATATTATAATATA-A-T-AT-ATAC
*
60163 AT-ATTATATTATTATATAATATATAC
1 ATAATTATATTATAATATAATATATAC
60189 ATTAATATATATTATAAT
1 A-TAAT-TATATTATAAT
60207 TGTTTCAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
26 5 0.08
27 3 0.05
28 5 0.08
29 37 0.60
30 6 0.10
31 6 0.10
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (27 bp):
ATAATTATATTATAATATAATATATAC
Found at i:62451 original size:45 final size:45
Alignment explanation
Indices: 62395--62491 Score: 167
Period size: 45 Copynumber: 2.2 Consensus size: 45
62385 ATGATGATGG
* *
62395 TGATAAGAAATATTTTATAATTTAAAAAATTATAAATTTTAATGA
1 TGATAATAAATATTTTATAATTTAAAAAATTATAAATTTCAATGA
*
62440 TTATAATAAATATTTTATAATTTAAAAAATTATAAATTTCAATGA
1 TGATAATAAATATTTTATAATTTAAAAAATTATAAATTTCAATGA
62485 TGATAAT
1 TGATAAT
62492 GATTATAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (45 bp):
TGATAATAAATATTTTATAATTTAAAAAATTATAAATTTCAATGA
Found at i:62477 original size:16 final size:16
Alignment explanation
Indices: 62409--62478 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
62399 AAGAAATATT
62409 TTAT-AATTTAAAAAA
1 TTATAAATTTAAAAAA
* **
62424 TTATAAATTTTAATGA
1 TTATAAATTTAAAAAA
*
62440 TTAT-AA--T-AAATA
1 TTATAAATTTAAAAAA
*
62452 TTTTATAATTTAAAAAA
1 TTATA-AATTTAAAAAA
62469 TTATAAATTT
1 TTATAAATTT
62479 CAATGATGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 11
0.68 0.13 0.18
Matches are distributed among these distances:
12 6 0.15
13 1 0.02
14 2 0.05
15 6 0.15
16 18 0.44
17 8 0.20
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (16 bp):
TTATAAATTTAAAAAA
Found at i:64507 original size:30 final size:31
Alignment explanation
Indices: 64458--64521 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
64448 ATATGTATTT
*
64458 AAATTTATAAAGACCAAAATATAAAAAACAA
1 AAATTTATAAAGACCAAAATAGAAAAAACAA
* * *
64489 AAATTT-TAAGGATCAAAATAGCAAAAACAA
1 AAATTTATAAAGACCAAAATAGAAAAAACAA
64519 AAA
1 AAA
64522 CTTAAGTGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (31 bp):
AAATTTATAAAGACCAAAATAGAAAAAACAA
Found at i:64538 original size:30 final size:30
Alignment explanation
Indices: 64472--64527 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
64462 TTATAAAGAC
** *
64472 CAAAATATAAAAAACAAAAATTTTAAGGAT
1 CAAAATAGCAAAAACAAAAATCTTAAGGAT
64502 CAAAATAGCAAAAACAAAAA-CTTAAG
1 CAAAATAGCAAAAACAAAAATCTTAAG
64528 TGACTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.64, C:0.11, G:0.07, T:0.18
Consensus pattern (30 bp):
CAAAATAGCAAAAACAAAAATCTTAAGGAT
Found at i:64648 original size:17 final size:18
Alignment explanation
Indices: 64609--64647 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
64599 GAATAGCCCA
*
64609 AAAATAAAAATAAGAACT
1 AAAATAAAAATAAGAAAT
64627 AAAAT-AAAATAAAGAAAT
1 AAAATAAAAAT-AAGAAAT
64645 AAA
1 AAA
64648 TGGGCCCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAATAAAAATAAGAAAT
Found at i:66845 original size:41 final size:43
Alignment explanation
Indices: 66772--66864 Score: 120
Period size: 41 Copynumber: 2.2 Consensus size: 43
66762 GAACTCAAAC
* *
66772 ATTTTTCGCCTTAACAACTTTTATTTACTTACTCTTGCA-ATT
1 ATTTTTTGCCTTAACAACATTTATTTACTTACTCTTGCATATT
* **
66814 ATTTTTTGCCTTAGCAA-ATTTATTTGTTTACTCTTGCATATT
1 ATTTTTTGCCTTAACAACATTTATTTACTTACTCTTGCATATT
66856 -TTTTTTGCC
1 ATTTTTTGCC
66865 ATGACAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 27 0.60
42 18 0.40
ACGTcount: A:0.20, C:0.18, G:0.08, T:0.54
Consensus pattern (43 bp):
ATTTTTTGCCTTAACAACATTTATTTACTTACTCTTGCATATT
Found at i:66861 original size:42 final size:42
Alignment explanation
Indices: 66772--66861 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
66762 GAACTCAAAC
*
66772 ATTTTTCGCCTTAACAACTTTTATTTACTTACTCTTGCAATT
1 ATTTTTCGCCTTAACAACATTTATTTACTTACTCTTGCAATT
* * **
66814 ATTTTTTGCCTTAGCAA-ATTTATTTGTTTACTCTTGCATATT
1 ATTTTTCGCCTTAACAACATTTATTTACTTACTCTTGCA-ATT
*
66856 TTTTTT
1 ATTTTT
66862 GCCATGACAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 18 0.44
42 23 0.56
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.56
Consensus pattern (42 bp):
ATTTTTCGCCTTAACAACATTTATTTACTTACTCTTGCAATT
Done.