Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002458.1 Hibiscus syriacus cultivar Beakdansim tig00005032_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: 43990
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7750 original size:2 final size:2
Alignment explanation
Indices: 7743--7776 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
7733 AAACATGTGA
7743 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
7777 GATAAGACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9251 original size:2 final size:2
Alignment explanation
Indices: 9244--9269 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9234 ATTATTATTA
9244 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
9270 TTTACAAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10685 original size:16 final size:17
Alignment explanation
Indices: 10662--10708 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
10652 GTTCTAATTG
* *
10662 TATTTTTATTGTTTTAA
1 TATTTTTATTATTTAAA
10679 T-TTTTTATATATTTAAA
1 TATTTTTAT-TATTTAAA
10696 TATTTTTATTATT
1 TATTTTTATTATT
10709 ATATAGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 7 0.27
17 12 0.46
18 7 0.27
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTTTTATTATTTAAA
Found at i:10733 original size:13 final size:14
Alignment explanation
Indices: 10708--10736 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
10698 TTTTTATTAT
10708 TATATAGTAATAAA
1 TATATAGTAATAAA
10722 TATATA-TAATAAA
1 TATATAGTAATAAA
10735 TA
1 TA
10737 ATAATTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TATATAGTAATAAA
Found at i:13878 original size:7 final size:7
Alignment explanation
Indices: 13843--13883 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
13833 TTTTCATACA
13843 TGCATTT
1 TGCATTT
13850 T-CATTT
1 TGCATTT
13856 TGCATCTT
1 TGCAT-TT
13864 TGCATTT
1 TGCATTT
*
13871 TTCATTT
1 TGCATTT
13878 TGCATT
1 TGCATT
13884 CATACTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:20854 original size:22 final size:22
Alignment explanation
Indices: 20825--20879 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
20815 ATCTACACTC
20825 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
20847 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
20869 TTCAAAAATGA
1 TTCAAAGATGA
20880 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:21454 original size:76 final size:76
Alignment explanation
Indices: 21326--22880 Score: 2905
Period size: 76 Copynumber: 20.5 Consensus size: 76
21316 CTATTTCCCA
*
21326 CATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
21391 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
21402 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
21467 AGCCTTAGGGT
66 AGCCTTAGGGT
21478 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
21543 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
21554 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
21619 AGCCTTAGGGT
66 AGCCTTAGGGT
21630 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
21695 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
21706 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTTATGATTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
21771 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
21782 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
21847 AGCCTTAGGGT
66 AGCCTTAGGGT
21858 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
21923 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
21934 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
21999 AGCCTTAGGGT
66 AGCCTTAGGGT
22010 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
22075 AGCCTTAGGGT
66 AGCCTTAGGGT
*
22086 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
22151 AGCCTTAGGGT
66 AGCCTTAGGGT
22162 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
22227 AGCCTTAGGGT
66 AGCCTTAGGGT
22238 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
22303 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
22314 CATCTGTAAGCCCTTCAGTGCACGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
22379 AGCCTTAGGGT
66 AGCCTTAGGGT
22390 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
22455 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
22466 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
22531 AGCCTTAGGGT
66 AGCCTTAGGGT
22542 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
22607 AGCCTTAGGGT
66 AGCCTTAGGGT
22618 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
22683 AGCCTTAGGGT
66 AGCCTTAGGGT
22694 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
22759 AGCCTTAGGGT
66 AGCCTTAGGGT
*
22770 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
22835 AGCCTTCA-GGT
66 AGCCTT-AGGGT
* *
22846 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
22881 CATTTCCATC
Statistics
Matches: 1442, Mismatches: 36, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
76 1441 1.00
77 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:23017 original size:3 final size:3
Alignment explanation
Indices: 23011--23068 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
23001 TATTTAAATT
* * *
23011 TTA TTA TTA TTA TTA -AA TTTA TTA TTA CTAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA
23057 TTA TTA TTA TTA
1 TTA TTA TTA TTA
23069 ATATATATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
2 1 0.02
3 42 0.91
4 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:23049 original size:34 final size:32
Alignment explanation
Indices: 22996--23059 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 32
22986 CATCATTTTT
*
22996 TTTATTATTTAAATTTTATTATTATTATTAAA
1 TTTATTATTTAAATATTATTATTATTATTAAA
23028 TTTATTATTACTAAATATTATTATTATTATTA
1 TTTATTATT--TAAATATTATTATTATTATTA
23060 TTATTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 9 0.31
34 20 0.69
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTATTATTTAAATATTATTATTATTATTAAA
Found at i:23064 original size:31 final size:32
Alignment explanation
Indices: 22996--23068 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 32
22986 CATCATTTTT
*
22996 TTTATTATT-TAAATTTTATTATTATTATTAAA
1 TTTATTATTATAAATATTATTATTATTATT-AA
23028 TTTATTATTACTAAATATTATTATTATTATT-A
1 TTTATTATTA-TAAATATTATTATTATTATTAA
23060 -TTATTATTA
1 TTTATTATTA
23069 ATATATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
31 9 0.24
32 10 0.26
34 19 0.50
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (32 bp):
TTTATTATTATAAATATTATTATTATTATTAA
Found at i:29348 original size:20 final size:19
Alignment explanation
Indices: 29297--29353 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
29287 AACCAATAAT
29297 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
29316 GATGAAAAAAAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
29337 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
29354 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 12 0.39
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:29472 original size:19 final size:19
Alignment explanation
Indices: 29440--29478 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
29430 AAGAAACTAA
* * *
29440 AAATATAATGATAATAAAT
1 AAATAAAATAATAAAAAAT
29459 AAATAAAATAATAAAAAAT
1 AAATAAAATAATAAAAAAT
29478 A
1 A
29479 TATATATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (19 bp):
AAATAAAATAATAAAAAAT
Found at i:29516 original size:24 final size:22
Alignment explanation
Indices: 29464--29516 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
29454 TAAATAAATA
29464 AAATAATAAAAAATATATATAT
1 AAATAATAAAAAATATATATAT
* *
29486 AAA-AATATAAAAATGTATGTAT
1 AAATAATA-AAAAATATATATAT
29508 AATATAATA
1 AA-ATAATA
29517 CAATACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 17 0.65
23 1 0.04
24 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (22 bp):
AAATAATAAAAAATATATATAT
Found at i:29782 original size:23 final size:24
Alignment explanation
Indices: 29747--29794 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
29737 ACGCAAAGAA
29747 AAATGAAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAAA-TATAATTAAAT
*
29771 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAAAAAAATATAATTAAAT
29794 A
1 A
29795 TATATATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
AAATGAAAAAAAATATAATTAAAT
Found at i:30307 original size:37 final size:38
Alignment explanation
Indices: 30209--30311 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 38
30199 ATGCTTGTGG
* ** *
30209 ATCCTATCTTTAGGAGTTTAAATAATA-TTAGAACTAT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTGAGAACTAT
* *
30246 ATCCTATTTTTAGGAGTTTGAATCCTAGTGA-AATTAT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTGAGAACTAT
30283 ATCCTATTTTTAGGAGTTTAAATCCTAGT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGT
30312 AGGACGAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 56 0.97
38 2 0.03
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.43
Consensus pattern (38 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTGAGAACTAT
Found at i:31256 original size:106 final size:106
Alignment explanation
Indices: 31064--32340 Score: 1991
Period size: 106 Copynumber: 12.0 Consensus size: 106
31054 GCATTGTTCC
* * * * *
31064 GAGTCCAATAT-CTTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTCTTTGTTGACA
1 GAGTCCAATATCCTT-CGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
31128 ACCAGCTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G
* * *
31171 G-GTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
31235 CCAGTGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
31276 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
31341 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
31382 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAATTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
31447 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
31488 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
31553 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
31594 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTGGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
31659 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
31700 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
31765 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
31806 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
31871 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
31912 GAGTCAAATATCCTTCGCTGTGAAGTTTAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
31977 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
32018 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
32083 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
32124 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCACTGAAATTGAGAAGTTGTTTATTGAAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
32189 CCAACAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
32230 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
32295 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
32336 GAGTC
1 GAGTC
32341 GCACGATATC
Statistics
Matches: 1082, Mismatches: 86, Indels: 5
0.92 0.07 0.00
Matches are distributed among these distances:
105 2 0.00
106 1076 0.99
107 4 0.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:33959 original size:15 final size:14
Alignment explanation
Indices: 33941--33997 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 14
33931 CCCTTTTTCT
33941 TTTTTATTTTTGTTC
1 TTTTT-TTTTTGTTC
33956 -TTTTTTTTTGTT-
1 TTTTTTTTTTGTTC
33968 TTCTTCTTTTTTGCTTC
1 TT-TT-TTTTTTG-TTC
33985 TTTTTTTTTTGTT
1 TTTTTTTTTTGTT
33998 TTTGCCCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
13 9 0.24
14 8 0.22
15 14 0.38
16 4 0.11
17 2 0.05
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTTGTTC
Found at i:34008 original size:29 final size:28
Alignment explanation
Indices: 33948--34014 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 28
33938 TCTTTTTTAT
* **
33948 TTTTGTTCTTTTTTTTTGTTTTCTTCTT
1 TTTTGTTCTTTTTTTTTGTTTTCTGCCC
33976 TTTTGCTTCTTTTTTTTTTGTTTT-TGCCC
1 TTTTG-TTC-TTTTTTTTTGTTTTCTGCCC
34005 TTTTTGTTCT
1 -TTTTGTTCT
34015 GATTGAATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 6 0.18
29 8 0.24
30 19 0.58
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.78
Consensus pattern (28 bp):
TTTTGTTCTTTTTTTTTGTTTTCTGCCC
Found at i:38471 original size:2 final size:2
Alignment explanation
Indices: 38464--38488 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38454 AAATAAAATA
38464 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
38489 AAAATGTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39294 original size:37 final size:37
Alignment explanation
Indices: 39201--39298 Score: 133
Period size: 37 Copynumber: 2.6 Consensus size: 37
39191 ATGCTTGTGG
* * * * *
39201 ATCATATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGCAAAACTCT
*
39238 ATCATATTTTTAGGAGTTTGAATCATAGCAAAATTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGCAAAACTCT
*
39275 ATCATATTTTTAAGAGTTTGAATC
1 ATCATATTTTTAGGAGTTTGAATC
39299 CTAGTAGGAC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCATAGCAAAACTCT
Found at i:41363 original size:42 final size:39
Alignment explanation
Indices: 41317--41394 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
41307 TAAATAAAAT
*
41317 TATTATAAATTATAGTAATTATTTATTGAAATAAGAATAATA
1 TATTATAAA-T-TA-TAATTATTTATTAAAATAAGAATAATA
* *
41359 TATTATTAATTATAATTATTTATTAAAATAATAATA
1 TATTATAAATTATAATTATTTATTAAAATAAGAATA
41395 CTATTTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 22 0.67
40 2 0.06
41 1 0.03
42 8 0.24
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (39 bp):
TATTATAAATTATAATTATTTATTAAAATAAGAATAATA
Found at i:41415 original size:39 final size:39
Alignment explanation
Indices: 41333--41426 Score: 93
Period size: 39 Copynumber: 2.4 Consensus size: 39
41323 AAATTATAGT
* * *
41333 AATTATTTATTGAAATAAGAATAATATATTATTAATTAT
1 AATTATTTATTAAAATAAGAATAATATATTAATAATTAA
* *
41372 AATTATTTATTAAAATAATAATACTAT-TTAA-ATATTGAA
1 AATTATTTATTAAAATAAGAATAATATATTAATA-ATT-AA
*
41411 AATTATAATATTAAAA
1 AATTAT-TTATTAAAA
41427 GAATGTTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
37 1 0.02
38 6 0.13
39 31 0.67
40 8 0.17
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (39 bp):
AATTATTTATTAAAATAAGAATAATATATTAATAATTAA
Found at i:41613 original size:19 final size:18
Alignment explanation
Indices: 41565--41615 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
41555 TTAATATTTT
41565 TAAAATTATACTAAAATA
1 TAAAATTATACTAAAATA
*
41583 -ATATATTAATACTAAACATA
1 TA-AAATT-ATACTAAA-ATA
41603 TAAAATTATACTA
1 TAAAATTATACTA
41616 TTAAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.04
18 4 0.15
19 14 0.52
20 7 0.26
21 1 0.04
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATTATACTAAAATA
Done.