Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007920.1 Hibiscus syriacus cultivar Beakdansim tig00110324_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: 328425
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:255267 original size:31 final size:30
Alignment explanation
Indices: 255218--255310 Score: 116
Period size: 31 Copynumber: 3.1 Consensus size: 30
255208 ACCTAAATTA
* *
255218 TTAC-TTTTATTCCGTTTTAATACTTAAAGT
1 TTACTTTTTATTTCATTTTAATACTTAAA-T
* *
255248 TTACTTTTTATTTCATTTTAGTACCTAATAT
1 TTACTTTTTATTTCATTTTAATACTTAA-AT
*
255279 TTATTTTTTATTTCATTTTAATACTTAAAT
1 TTACTTTTTATTTCATTTTAATACTTAAAT
255309 TT
1 TT
255311 TTAACGGCGG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
30 8 0.15
31 45 0.83
32 1 0.02
ACGTcount: A:0.27, C:0.11, G:0.03, T:0.59
Consensus pattern (30 bp):
TTACTTTTTATTTCATTTTAATACTTAAAT
Found at i:255645 original size:28 final size:27
Alignment explanation
Indices: 255606--255659 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
255596 ATTCTTAAAT
255606 TTTTTAAATTTTTA-TATAATTTAATTA
1 TTTTT-AATTTTTATTATAATTTAATTA
255633 TTTTTATATTTTTATTATAATTTAATT
1 TTTTTA-ATTTTTATTATAATTTAATT
255660 CTAATTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 1 0.04
27 12 0.48
28 12 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTTAATTTTTATTATAATTTAATTA
Found at i:255698 original size:21 final size:20
Alignment explanation
Indices: 255645--255698 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
255635 TTTATATTTT
* *
255645 TATTATAATTTAATTCTAAT
1 TATTATAATTTAACTCTAAA
* *
255665 TAATATAATTTTACCTCTAAAA
1 TATTATAA-TTTAACTCT-AAA
255687 TATTATAATTTA
1 TATTATAATTTA
255699 TTTATTAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 7 0.26
21 11 0.41
22 9 0.33
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTATAATTTAACTCTAAA
Found at i:258237 original size:17 final size:17
Alignment explanation
Indices: 258215--258254 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
258205 TATGGAACTA
258215 CAGCGCATAATTCACTC
1 CAGCGCATAATTCACTC
258232 CAGCGCATAATTCACTC
1 CAGCGCATAATTCACTC
258249 CAGCGC
1 CAGCGC
258255 TACTCTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.28, C:0.38, G:0.15, T:0.20
Consensus pattern (17 bp):
CAGCGCATAATTCACTC
Found at i:282546 original size:17 final size:18
Alignment explanation
Indices: 282513--282550 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
282503 TATTTTGCTT
282513 AAAGAAGAGATAAAAGAGA
1 AAAGAAGAGATAAAAGA-A
282532 AAAGAAGA-A-AAAAGAA
1 AAAGAAGAGATAAAAGAA
282548 AAA
1 AAA
282551 ATGATGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.21
17 6 0.32
18 1 0.05
19 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (18 bp):
AAAGAAGAGATAAAAGAA
Found at i:282565 original size:23 final size:19
Alignment explanation
Indices: 282560--282631 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 19
282550 AATGATGATG
*
282560 GAAAAAACGAAAAAAAAAT
1 GAAAAAAAGAAAAAAAAAT
*
282579 GAAAAAAAGAAAAAAAAGAA
1 GAAAAAAAGAAAAAAAA-AT
282599 GAGAAAAAATG-AAAAAAAAT
1 GA-AAAAAA-GAAAAAAAAAT
*
282619 -AAAAAGAGAAAAA
1 GAAAAAAAGAAAAA
282632 TGAAAAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
17 1 0.02
18 9 0.20
19 17 0.38
20 4 0.09
21 13 0.29
22 1 0.02
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.04
Consensus pattern (19 bp):
GAAAAAAAGAAAAAAAAAT
Found at i:282595 original size:9 final size:9
Alignment explanation
Indices: 282561--282652 Score: 55
Period size: 9 Copynumber: 9.9 Consensus size: 9
282551 ATGATGATGG
*
282561 AAAAAACGA
1 AAAAAAAGA
282570 AAAAAAA-A
1 AAAAAAAGA
282578 TGAAAAAAAGA
1 --AAAAAAAGA
282589 AAAAAAAGA
1 AAAAAAAGA
282598 AGAGAAAAA-A
1 A-A-AAAAAGA
*
282608 TGAAAAAA-A
1 -AAAAAAAGA
*
282617 ATAAAAAGA
1 AAAAAAAGA
* *
282626 GAAAAATGA
1 AAAAAAAGA
282635 AAAAAAGAGA
1 AAAAAA-AGA
*
282645 AATAAAAG
1 AAAAAAAG
282653 GAGGGTTCAA
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
8 6 0.09
9 36 0.55
10 17 0.26
11 6 0.09
ACGTcount: A:0.79, C:0.01, G:0.14, T:0.05
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:282615 original size:24 final size:24
Alignment explanation
Indices: 282588--282640 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
282578 TGAAAAAAAG
*
282588 AAAAAA-AAGAAGAGAAAAAATGAA
1 AAAAAATAAAAAGAG-AAAAATGAA
282612 AAAAAATAAAAAGAGAAAAATGAA
1 AAAAAATAAAAAGAGAAAAATGAA
282636 AAAAA
1 AAAAA
282641 GAGAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (24 bp):
AAAAAATAAAAAGAGAAAAATGAA
Found at i:282623 original size:30 final size:30
Alignment explanation
Indices: 282572--282652 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
282562 AAAAACGAAA
282572 AAAAAATGAAAAAAAGAAAAAAAAGAAGAG
1 AAAAAATGAAAAAAAGAAAAAAAAGAAGAG
*
282602 AAAAAATG---AAAA-AAAATAAA-AAGAG
1 AAAAAATGAAAAAAAGAAAAAAAAGAAGAG
282627 -AAAAATGAAAAAAAGAGAAATAAAAG
1 AAAAAATGAAAAAAAGA-AAA-AAAAG
282653 GAGGGTTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
24 7 0.17
25 5 0.12
26 7 0.17
27 8 0.19
28 1 0.02
29 3 0.07
30 11 0.26
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (30 bp):
AAAAAATGAAAAAAAGAAAAAAAAGAAGAG
Found at i:283847 original size:51 final size:51
Alignment explanation
Indices: 283781--284192 Score: 662
Period size: 51 Copynumber: 8.0 Consensus size: 51
283771 TGAAGCAAAT
283781 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
283832 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
283883 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
283934 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
*
283985 AAGTTCGTTGAAGATTGAGTCATATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
*
284036 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
* * * *
284087 TACTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
** ** * * * *
284138 CTGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGAC
1 AAGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
284193 CCGTTTTATT
Statistics
Matches: 340, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
51 308 0.91
54 2 0.01
55 30 0.09
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (51 bp):
AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
Found at i:283913 original size:102 final size:102
Alignment explanation
Indices: 283781--284299 Score: 664
Period size: 102 Copynumber: 5.0 Consensus size: 102
283771 TGAAGCAAAT
283781 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
*
283846 TTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
66 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
283883 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
*
283948 TTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
66 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
*
283985 AAGTTCGTTGAAGATTGAGTCATATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
284050 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
66 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
* * * * ** **
284087 TACTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGA
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
* * *
284152 TTTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGAC
66 ---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
** ** * * * * * *
284193 CCGTTTTATTAAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTT-TTA
1 AAG-TTCGTTGAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT-
*
284257 TGAAGATTGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
60 TGAAGA---TT-GAGTCCTATACTCT-CTGAAGGAATAGGGAGC
284300 AGGCTCGTCA
Statistics
Matches: 373, Mismatches: 33, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
102 258 0.69
105 2 0.01
106 32 0.09
107 11 0.03
110 2 0.01
111 68 0.18
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (102 bp):
AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
Found at i:284225 original size:56 final size:56
Alignment explanation
Indices: 283797--284299 Score: 257
Period size: 51 Copynumber: 9.6 Consensus size: 56
283787 GTTGAAGATT
* * * ** **
283797 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
283848 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
283899 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
283950 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
284001 GAGTCATATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * **
284052 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAC--TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGAC-CCGTTTTATTGAAGATTGTTC
* * * * * *
284103 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTG-TTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* *
284158 GAGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * *
284214 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
*
284269 GAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGC
284300 AGGCTCGTCA
Statistics
Matches: 415, Mismatches: 27, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
51 291 0.70
52 1 0.00
54 3 0.01
55 68 0.16
56 51 0.12
57 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (56 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
Found at i:284293 original size:55 final size:55
Alignment explanation
Indices: 284052--284301 Score: 219
Period size: 55 Copynumber: 4.6 Consensus size: 55
284042 GTTGAAGATT
* * * *** **
284052 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTACTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGTTTTATTGAAGATTGTTC
* * * * * *
284103 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACC-TGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGT-TTTATTGAAGATTGTTC
* * *
284158 GAGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGA-CCGTTTTATTGAAGATTGTTC
* *
284214 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
*
284269 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAG
284302 GCTCGTCATT
Statistics
Matches: 167, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
51 42 0.25
54 3 0.02
55 68 0.41
56 52 0.31
57 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (55 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGTTTTATTGAAGATTGTTC
Found at i:284316 original size:55 final size:55
Alignment explanation
Indices: 284053--284333 Score: 195
Period size: 55 Copynumber: 5.1 Consensus size: 55
284043 TTGAAGATTG
* * * * **
284053 AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTACTTCGT-TGAAGATTG----
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-ACGTATTATGAAGATTGTTCA
* * * * * * *
284104 AGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC-CTGT-TTATTGAAGATTTTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACAC-GTATTA-TGAAGATTGTTCA
* * * * *
284159 AGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTCA
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACGTATTA-TGAAGATTGTTCA
* * *
284215 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTATGAAGATTGTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTGTTCA
* * * *
284270 AGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATT-TGAAGATTTTTTCA
1 AGTCTTATACTCT-CTGAAGGAATAGAGAGCAGACACGT-ATTATGAAGA-TTGTTCA
284326 AGTCTTAT
1 AGTCTTAT
284334 TTATCCTGAC
Statistics
Matches: 190, Mismatches: 26, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
49 2 0.01
50 1 0.01
51 40 0.21
54 1 0.01
55 79 0.42
56 66 0.35
57 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (55 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTGTTCA
Found at i:284326 original size:111 final size:111
Alignment explanation
Indices: 284104--284333 Score: 247
Period size: 111 Copynumber: 2.1 Consensus size: 111
284094 TTGAAGATTG
* * * *
284104 AGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATAC
1 AGTCTTATACTCCCTGAAAGAATAGAGAGCAGACCTGTTTATTGAAGATTGTTCGAGTTCTATAC
**
284169 TCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTCA
66 TCTCTGAAGGAAGAGAGAGCGGACCCGTCATATTAAAGATTGTTCA
* *
284215 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACAC-GTTT-TATGAAGATTGTTCGAG-TCTTA
1 AGTCTTATACTCCCTGAAAGAATAGAGAGCAGAC-CTGTTTAT-TGAAGATTGTTCGAGTTC-TA
* * * * *
284277 TACT-TCCTGAAGGAATAGGGAGCAGG-CTCGTCAT-TTGAAGATTTTTTCA
63 TACTCT-CTGAAGGAAGAGAGAGC-GGACCCGTCATATTAAAGA-TTGTTCA
284326 AGTCTTAT
1 AGTCTTAT
284334 TTATCCTGAC
Statistics
Matches: 100, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
110 10 0.10
111 87 0.87
112 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (111 bp):
AGTCTTATACTCCCTGAAAGAATAGAGAGCAGACCTGTTTATTGAAGATTGTTCGAGTTCTATAC
TCTCTGAAGGAAGAGAGAGCGGACCCGTCATATTAAAGATTGTTCA
Found at i:303724 original size:30 final size:29
Alignment explanation
Indices: 303690--303863 Score: 96
Period size: 30 Copynumber: 5.6 Consensus size: 29
303680 GATGGAGATA
*
303690 TAATCTCATGCAAATGTCAGAACGAGGAAC
1 TAATCTCATGCAGATGTCAGAAC-AGGAAC
** * *
303720 TAATCTCATATAGTTGTCAGAACAAGAAAC
1 TAATCTCATGCAGATGTCAGAAC-AGGAAC
* * * * *
303750 TAATCTCGTTACCCGTACAAAGGTTAGAACAGGGAAT
1 TAATCTC---A----TGCAGATGTCAGAACA-GGAAC
* *
303787 TAATCCCATGCAGATGTTAGAACAGTGAAC
1 TAATCTCATGCAGATGTCAGAACAG-GAAC
* *
303817 TAATCTCATGCAGTTGTCAGAACGGGGAAC
1 TAATCTCATGCAGATGTCAGAAC-AGGAAC
* *
303847 CAATCCCATGCAGATGT
1 TAATCTCATGCAGATGT
303864 TAAAACGGGA
Statistics
Matches: 109, Mismatches: 25, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
29 1 0.01
30 85 0.78
31 1 0.01
33 1 0.01
34 1 0.01
36 1 0.01
37 19 0.17
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (29 bp):
TAATCTCATGCAGATGTCAGAACAGGAAC
Found at i:303871 original size:30 final size:30
Alignment explanation
Indices: 303772--303872 Score: 112
Period size: 30 Copynumber: 3.4 Consensus size: 30
303762 CCGTACAAAG
* **
303772 GTTAGAACAGGGAATTAATCCCATGCAGAT
1 GTTAGAACGGGGAACCAATCCCATGCAGAT
* * * * *
303802 GTTAGAACAGTGAACTAATCTCATGCAGTT
1 GTTAGAACGGGGAACCAATCCCATGCAGAT
*
303832 GTCAGAACGGGGAACCAATCCCATGCAGAT
1 GTTAGAACGGGGAACCAATCCCATGCAGAT
*
303862 GTTAAAACGGG
1 GTTAGAACGGG
303873 AAACTATGCT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.22
Consensus pattern (30 bp):
GTTAGAACGGGGAACCAATCCCATGCAGAT
Found at i:308135 original size:18 final size:18
Alignment explanation
Indices: 308114--308153 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
308104 CGTTATACAC
308114 TTTGACTGCTTTATTGTT
1 TTTGACTGCTTTATTGTT
**
308132 TTTGTTTGCTTTATTGTT
1 TTTGACTGCTTTATTGTT
308150 TTTG
1 TTTG
308154 TTTGCTTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.68
Consensus pattern (18 bp):
TTTGACTGCTTTATTGTT
Found at i:308154 original size:18 final size:18
Alignment explanation
Indices: 308120--308160 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
308110 ACACTTTGAC
308120 TGCTTTATTGTTTTTGTT
1 TGCTTTATTGTTTTTGTT
308138 TGCTTTATTGTTTTTGTT
1 TGCTTTATTGTTTTTGTT
308156 TGCTT
1 TGCTT
308161 GCATTACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.05, C:0.07, G:0.17, T:0.71
Consensus pattern (18 bp):
TGCTTTATTGTTTTTGTT
Found at i:310094 original size:11 final size:11
Alignment explanation
Indices: 310078--310103 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
310068 TGAATCAAAA
310078 CTATACATGAC
1 CTATACATGAC
310089 CTATACATGAC
1 CTATACATGAC
310100 CTAT
1 CTAT
310104 CTAACCCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (11 bp):
CTATACATGAC
Found at i:325782 original size:9 final size:9
Alignment explanation
Indices: 325766--325805 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
325756 GAGCTTTATA
325766 AATA-TAAT
1 AATATTAAT
325774 AATATTAAT
1 AATATTAAT
325783 AATATTAAT
1 AATATTAAT
*
325792 ATTA-TAAT
1 AATATTAAT
325800 -ATATTA
1 AATATTA
325806 TAAAAACGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 2 0.07
8 10 0.36
9 16 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AATATTAAT
Done.