Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003615.1 Hibiscus syriacus cultivar Beakdansim tig00007644_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: 68510
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:9433 original size:22 final size:23
Alignment explanation
Indices: 9394--9436 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
9384 TTTATTTGAA
*
9394 AATGGTAATATTTTTTTATGTTT
1 AATGGTAATATTTATTTATGTTT
9417 AATGGTAA-ATTTATTTATGT
1 AATGGTAATATTTATTTATGT
9437 CGATGTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (23 bp):
AATGGTAATATTTATTTATGTTT
Found at i:10347 original size:20 final size:22
Alignment explanation
Indices: 10314--10366 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
10304 CATAATGATA
10314 TATATATATATTTAT-T-TATTTT
1 TATATA-AT-TTTATATGTATTTT
*
10336 TATATAATTTTATATGTTTTTT
1 TATATAATTTTATATGTATTTT
10358 TAT-TAATTT
1 TATATAATTT
10367 AAGGTGATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.18
21 9 0.32
22 14 0.50
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
TATATAATTTTATATGTATTTT
Found at i:10864 original size:11 final size:11
Alignment explanation
Indices: 10838--10880 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
10828 TTCATGAACA
*
10838 TGTTTGTTTAT
1 TGTTCGTTTAT
* *
10849 CGTTCATTTAT
1 TGTTCGTTTAT
10860 TGTTCGTTTAT
1 TGTTCGTTTAT
10871 TGTTCGTTTA
1 TGTTCGTTTA
10881 GTGCTTATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.12, C:0.09, G:0.16, T:0.63
Consensus pattern (11 bp):
TGTTCGTTTAT
Found at i:17238 original size:20 final size:20
Alignment explanation
Indices: 17215--17348 Score: 155
Period size: 20 Copynumber: 6.7 Consensus size: 20
17205 GAATATATAA
*
17215 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTATGACT
17235 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTATGACT
* * *
17255 AGCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTATGACT
*
17275 ATCGCAACACGATTATGAAC-
1 ATCGCAACGCGATTATG-ACT
*
17295 GTCGCAACGCGA-TACTGACT
1 ATCGCAACGCGATTA-TGACT
**
17315 ATCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTATGACT
*
17335 ATCGCAATGCGATT
1 ATCGCAACGCGATT
17349 TTCAAAGCAC
Statistics
Matches: 95, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
19 4 0.04
20 89 0.94
21 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:17348 original size:60 final size:60
Alignment explanation
Indices: 17215--17348 Score: 182
Period size: 60 Copynumber: 2.2 Consensus size: 60
17205 GAATATATAA
*
17215 ATCGCAATGCGATTATGACTATCGCAACGCGATTATGACTAGCGCAACGAGATTCTGACT
1 ATCGCAATGCGATTATGACTATCGCAACGCGATTATGACTAGCGCAACGAGATGCTGACT
** * * *
17275 ATCGCAACACGATTATGAAC-GTCGCAACGCGA-TACTGACTATCGCAACGCGATGCTGACT
1 ATCGCAATGCGATTATG-ACTATCGCAACGCGATTA-TGACTAGCGCAACGAGATGCTGACT
17335 ATCGCAATGCGATT
1 ATCGCAATGCGATT
17349 TTCAAAGCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 2 0.03
60 60 0.94
61 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (60 bp):
ATCGCAATGCGATTATGACTATCGCAACGCGATTATGACTAGCGCAACGAGATGCTGACT
Found at i:17564 original size:22 final size:22
Alignment explanation
Indices: 17523--17565 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17513 GGCGACATCC
*
17523 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACAAAATCA
*
17545 GTCCCCATCTCCGGCAAAATC
1 GTCCCCATCTCCGACAAAATC
17566 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.42, G:0.14, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACAAAATCA
Found at i:17975 original size:19 final size:20
Alignment explanation
Indices: 17953--18005 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
17943 AATCGCAATA
17953 CGATTTT-AGTTTCGCGTTG
1 CGATTTTAAGTTTCGCGTTG
* * *
17972 CGATTTTCATTTTCGTGTTG
1 CGATTTTAAGTTTCGCGTTG
17992 CGATTTTAAGTTTC
1 CGATTTTAAGTTTC
18006 AGAAACTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
CGATTTTAAGTTTCGCGTTG
Found at i:20015 original size:18 final size:19
Alignment explanation
Indices: 19973--20019 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
19963 GCGATTCTCT
19973 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
19993 CGTTGCGATAGTCA-TTCG
1 CGTTGCGATAGTCATTTCG
*
20011 TGTTGCGAT
1 CGTTGCGAT
20020 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:20536 original size:21 final size:21
Alignment explanation
Indices: 20510--20563 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
20500 CTCACCTGTC
20510 ATCGTTCAAGAGGCCTCCCAT
1 ATCGTTCAAGAGGCCTCCCAT
20531 ATCGTTCAAGAGGCCTCCCAT
1 ATCGTTCAAGAGGCCTCCCAT
20552 ATCGTTCAAGAG
1 ATCGTTCAAGAG
20564 ACCCTATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCTCCCAT
Found at i:22078 original size:14 final size:14
Alignment explanation
Indices: 22041--22102 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
22031 TTGCTTGTTT
*
22041 AATTGATTTATAAA
1 AATTGATTTGTAAA
22055 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
22069 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
22084 TATTGATGTGTAAA
1 AATTGATTTGTAAA
22098 TAATT
1 -AATT
22103 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:22254 original size:20 final size:20
Alignment explanation
Indices: 22201--22254 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
22191 AGGTACACTT
* **
22201 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCAAAAGACAAAA
* *
22221 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCAAAAGACAAAA
*
22241 TCTCAACGCAAAAG
1 TCGCAACGCAAAAG
22255 TCAATTCGCG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (20 bp):
TCGCAACGCAAAAGACAAAA
Found at i:22290 original size:20 final size:20
Alignment explanation
Indices: 22253--22533 Score: 335
Period size: 20 Copynumber: 14.4 Consensus size: 20
22243 TCAACGCAAA
22253 AGTC-AATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* * *
22272 AGTCTAATACGCTTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
22292 --T----TTCTCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* *
22306 AGTCAAATACCCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* * *
22326 AATCAAATTCACATTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
22346 ACTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
22366 AGTCAAA-TAGTCGTTGCGAT
1 AGTCAAATTCG-CGTTGCGAT
*
22386 AATCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
22406 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* *
22426 AGACAAATTCGTGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
22446 AGACAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
22466 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* *
22486 AATCAAATTCGCATTGCGAT
1 AGTCAAATTCGCGTTGCGAT
22506 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
22526 ATTCAAAT
1 AGTCAAAT
22534 GAATGTGTAA
Statistics
Matches: 225, Mismatches: 28, Indels: 17
0.83 0.10 0.06
Matches are distributed among these distances:
14 10 0.04
16 1 0.00
18 1 0.00
19 6 0.03
20 205 0.91
21 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTCAAATTCGCGTTGCGAT
Found at i:22756 original size:140 final size:140
Alignment explanation
Indices: 22504--22773 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
22494 TCGCATTGCG
22504 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
* * *
22569 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACTCATAA
66 TAGCAATATTCAAACTCAAATTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
22634 AATACACATA
131 AATACACATA
22644 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
22709 TAGCAATATTCAAACTCAAATTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATATTCAAACTCAAATTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
22774 TACAACGTTT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAGCAATATTCAAACTCAAATTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:24895 original size:14 final size:14
Alignment explanation
Indices: 24876--24912 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
24866 TCCTGTGGCA
24876 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
24890 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
24904 TTCTTCTTC
1 TT-TTCTTC
24913 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:25136 original size:24 final size:24
Alignment explanation
Indices: 25102--25155 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
25092 CTGAAACATC
25102 ATCAAAATCCGAGTATTAACCAAT
1 ATCAAAATCCGAGTATTAACCAAT
* * *
25126 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTAACCAAT
25150 ATCAAA
1 ATCAAA
25156 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAT
Found at i:26002 original size:20 final size:20
Alignment explanation
Indices: 25977--26034 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
25967 GAAATTCAGT
*
25977 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
25997 GTTGCGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
*
26017 ATTGCGATAGTCAGAATC
1 GTTGCGATAGTCAGAATC
26035 ATATTGCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:26040 original size:20 final size:19
Alignment explanation
Indices: 25978--26044 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
25968 AAATTCAGTG
* **
25978 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATC-TA
25998 TTGCGATAGTCAGAATCTCA
1 TTGCGATAGTCAGAATCT-A
26018 TTGCGATAGTCAGAATCATA
1 TTGCGATAGTCAGAATC-TA
26038 TTGCGAT
1 TTGCGAT
26045 TTACATATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 41 0.98
21 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (19 bp):
TTGCGATAGTCAGAATCTA
Found at i:47277 original size:15 final size:15
Alignment explanation
Indices: 47257--47288 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
47247 GACGAAGCGA
47257 TTAAAATTTCCCCCT
1 TTAAAATTTCCCCCT
47272 TTAAAATTTCCCCCT
1 TTAAAATTTCCCCCT
47287 TT
1 TT
47289 TGTACTCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAAATTTCCCCCT
Found at i:47553 original size:41 final size:41
Alignment explanation
Indices: 47497--47780 Score: 318
Period size: 41 Copynumber: 7.0 Consensus size: 41
47487 ATTTATTCAA
*
47497 AAAAACGCCACTAAAGTACGAGTCTTTGGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
* * *
47538 AAAAATGCCATTAAAGTACGGGTCTTTGGCGACGTTTGTAT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
* *
47579 AAAAACACCACTAAAGTACGGGTCTTTGGTGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
* * * *
47620 TAAAACACCACTAAAGTACAGGTCTTTGGCGACGTTTGTAT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
* * **
47661 AAAAA-ACCACTAAAGTACGGGTATTTGGCGTTGTTTGTAT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
* * * *** * *
47701 AGAAACGACACTAAAGTCCGGGTAAGTAGCGGCATTTGTAT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
* * ** *
47742 AGAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGT
1 AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGT
47781 GCTTACAATG
Statistics
Matches: 207, Mismatches: 35, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
40 35 0.17
41 172 0.83
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTAT
Found at i:47778 original size:122 final size:123
Alignment explanation
Indices: 47498--47780 Score: 349
Period size: 122 Copynumber: 2.3 Consensus size: 123
47488 TTTATTCAAA
* * *
47498 AAAACGCCACTAAAGTACGAGTCTTTGGCGGCGTTTGTATAAAAATGCCATTAAAGTACGGGTCT
1 AAAACGCCACTAAAGTACGAGTCTTTGGCGGCGTTTGTATAAAAATACCACTAAAGTACGGGTAT
*** * * *
47563 TTGGCGACGTTTGTATAAAAACACCACTAAAGTACGGGTCTTTGGTGGCGTTTGTATT
66 TTGGCGACGTTTGTATAAAAACACCACTAAAGTACGGGTAAGTAGCGGCATTTGTATT
* *
47621 AAAACACCACTAAAGTAC-AGGTCTTTGGCGACGTTTGTATAAAAA-ACCACTAAAGTACGGGTA
1 AAAACGCCACTAAAGTACGA-GTCTTTGGCGGCGTTTGTATAAAAATACCACTAAAGTACGGGTA
** * *
47684 TTTGGCGTTGTTTGTATAGAAACGA-CACTAAAGTCCGGGTAAGTAGCGGCATTTGTA-T
65 TTTGGCGACGTTTGTATAAAAAC-ACCACTAAAGTACGGGTAAGTAGCGGCATTTGTATT
** *
47742 AGAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGT
1 A-AAACGCCACTAAAGTACGAGTCTTTGGCGGCGTTTGT
47781 GCTTACAATG
Statistics
Matches: 136, Mismatches: 20, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
121 2 0.01
122 91 0.67
123 43 0.32
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (123 bp):
AAAACGCCACTAAAGTACGAGTCTTTGGCGGCGTTTGTATAAAAATACCACTAAAGTACGGGTAT
TTGGCGACGTTTGTATAAAAACACCACTAAAGTACGGGTAAGTAGCGGCATTTGTATT
Found at i:47813 original size:82 final size:82
Alignment explanation
Indices: 47727--47923 Score: 279
Period size: 82 Copynumber: 2.4 Consensus size: 82
47717 TCCGGGTAAG
* * * *
47727 TAGCGGCATTTGTATAGAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTT-ACAATG
1 TAGCGGCATTTATACAAAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTCA-AACG
*
47791 CCACTAAAGTACAATATT
65 ACACTAAAGTACAATATT
* * * * *
47809 TAGCGGCATTTATACACAAACGCCGCTAAAATATGAGCATTTAGCGGCGTTTGTGCTTCAAACGA
1 TAGCGGCATTTATACAAAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTCAAACGA
*
47874 CACTAAAGTACATTATT
66 CACTAAAGTACAATATT
47891 TAGCGGCATTTATACAAAAACGCCACTAAAGTA
1 TAGCGGCATTTATACAAAAACGCCACTAAAGTA
47924 TAGTATTTAT
Statistics
Matches: 101, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 100 0.99
83 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (82 bp):
TAGCGGCATTTATACAAAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTCAAACGA
CACTAAAGTACAATATT
Found at i:47918 original size:40 final size:41
Alignment explanation
Indices: 47482--47961 Score: 222
Period size: 41 Copynumber: 11.7 Consensus size: 41
47472 CTGATAAATT
* * * *
47482 GCGGCATTTATTCAAAAAAACGCCACTAAAGTACGAGTCTTTG
1 GCGGCATTTATAC-TAAAAACGCCACTAAAGTAC-AGTATTTA
* * * * * * *
47525 GCGGCGTTTGTA-TAAAAATGCCATTAAAGTACGGGTCTTTG
1 GCGGCATTTATACTAAAAACGCCACTAAAGTAC-AGTATTTA
* * * * * * *
47566 GCGACGTTTGTA-TAAAAACACCACTAAAGTACGGGTCTTTG
1 GCGGCATTTATACTAAAAACGCCACTAAAGTAC-AGTATTTA
* * * * * * *
47607 GTGGCGTTTGTA-TTAAAACACCACTAAAGTACAGGTCTTTG
1 GCGGCATTTATACTAAAAACGCCACTAAAGTACA-GTATTTA
* * * * * *
47648 GCGACGTTTGTA-TAAAAA-ACCACTAAAGTACGGGTATTTG
1 GCGGCATTTATACTAAAAACGCCACTAAAGTAC-AGTATTTA
*** * * * * * **
47688 GCGTTGTTTGTA-TAGAAACGACACTAAAGTCCGGGTAAGTA
1 GCGGCATTTATACTAAAAACGCCACTAAAGTAC-AGTATTTA
* * *
47729 GCGGCATTTGTA-TAGAAACGCCACTAAAGTACGAGAATTTA
1 GCGGCATTTATACTAAAAACGCCACTAAAGTAC-AGTATTTA
* * * * * * *
47770 GCGGCGTTTGTGCTTACAATGCCACTAAAGTACAATATTTA
1 GCGGCATTTATACTAAAAACGCCACTAAAGTACAGTATTTA
* * * * *
47811 GCGGCATTTATAC-ACAAACGCCGCTAAAATATGAGCATTTA
1 GCGGCATTTATACTAAAAACGCCACTAAAGTA-CAGTATTTA
* * * ** * *
47852 GCGGCGTTTGTGCTTCAAACGACACTAAAGTACATTATTTA
1 GCGGCATTTATACTAAAAACGCCACTAAAGTACAGTATTTA
*
47893 GCGGCATTTATAC-AAAAACGCCACTAAAGTATAGTATTTA
1 GCGGCATTTATACTAAAAACGCCACTAAAGTACAGTATTTA
* *
47933 TCGGCATTTATACAAAAAACGCCACTAAA
1 GCGGCATTTATACTAAAAACGCCACTAAA
47962 TCACAATTAT
Statistics
Matches: 353, Mismatches: 77, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
40 80 0.23
41 234 0.66
42 30 0.08
43 9 0.03
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (41 bp):
GCGGCATTTATACTAAAAACGCCACTAAAGTACAGTATTTA
Found at i:47971 original size:82 final size:82
Alignment explanation
Indices: 47727--47974 Score: 277
Period size: 82 Copynumber: 3.0 Consensus size: 82
47717 TCCGGGTAAG
* * * * * *
47727 TAGCGGCATTTGTATAGAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTACAATGC
1 TAGCGGCATTTATACAAAAACGCCACTAAAGTA-TAGAATTTAGCGGCGTTTGTGCTTAAAACGC
47792 CACTAAAGTACAA-TATT
65 CACTAAAGTACAATTATT
* * * * * *
47809 TAGCGGCATTTATACACAAACGCCGCTAAAATATGAGCATTTAGCGGCGTTTGTGCTTCAAACGA
1 TAGCGGCATTTATACAAAAACGCCACTAAAGTAT-AGAATTTAGCGGCGTTTGTGCTTAAAACGC
47874 CACTAAAGTAC-ATTATT
65 CACTAAAGTACAATTATT
* * * * * **
47891 TAGCGGCATTTATACAAAAACGCCACTAAAGTATAGTATTTATCGGCATTTATACAAAAAACGCC
1 TAGCGGCATTTATACAAAAACGCCACTAAAGTATAGAATTTAGCGGCGTTTGTGCTTAAAACGCC
47956 ACTAAA-TCACAATTATT
66 ACTAAAGT-ACAATTATT
47973 TA
1 TA
47975 TCAGCGTTTA
Statistics
Matches: 139, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
80 1 0.01
81 31 0.22
82 107 0.77
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (82 bp):
TAGCGGCATTTATACAAAAACGCCACTAAAGTATAGAATTTAGCGGCGTTTGTGCTTAAAACGCC
ACTAAAGTACAATTATT
Found at i:53813 original size:14 final size:14
Alignment explanation
Indices: 53796--53829 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
53786 TTTATTTTAA
*
53796 TAAATATAGAAGAG
1 TAAAAATAGAAGAG
*
53810 TAAAAATATAAGAG
1 TAAAAATAGAAGAG
53824 TAAAAA
1 TAAAAA
53830 ATTTAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.21
Consensus pattern (14 bp):
TAAAAATAGAAGAG
Found at i:54698 original size:31 final size:30
Alignment explanation
Indices: 54663--54747 Score: 75
Period size: 32 Copynumber: 2.7 Consensus size: 30
54653 GGAGTACCTT
*
54663 GGGGCCTGAGAGCCTACCCAAG-ACAATTCTC
1 GGGGCC-GAGAGCCTACCCAAGAAAAATT-TC
* *
54694 GGGGCC-ACGGAGGCTTACCTAAGAAAAATTTC
1 GGGGCCGA--GA-GCCTACCCAAGAAAAATTTC
54726 GGGGCCGCAGAGCCTACCCAAG
1 GGGGCCG-AGAGCCTACCCAAG
54748 GGTCGCCTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
29 1 0.02
31 17 0.40
32 19 0.44
33 5 0.12
34 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.14
Consensus pattern (30 bp):
GGGGCCGAGAGCCTACCCAAGAAAAATTTC
Found at i:56312 original size:2 final size:2
Alignment explanation
Indices: 56305--56343 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
56295 ATATAAAACA
56305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56344 TTTGACTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60186 original size:21 final size:21
Alignment explanation
Indices: 60160--60201 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
60150 ATATTTGTAA
60160 AATGAACATTTCTCAGCTAAT
1 AATGAACATTTCTCAGCTAAT
60181 AATGAACATTTCTCAGCTAAT
1 AATGAACATTTCTCAGCTAAT
60202 GTCCGGGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (21 bp):
AATGAACATTTCTCAGCTAAT
Found at i:62154 original size:19 final size:19
Alignment explanation
Indices: 62127--62171 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
62117 GGTAATTTCT
*
62127 TGATTTTTATAATAAACTG
1 TGATATTTATAATAAACTG
* *
62146 TGATATTTATAGTAAATTG
1 TGATATTTATAATAAACTG
62165 TGATATT
1 TGATATT
62172 GATTACTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (19 bp):
TGATATTTATAATAAACTG
Found at i:65582 original size:24 final size:26
Alignment explanation
Indices: 65549--65603 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 26
65539 TTATATAGCC
65549 ATTATATTAAAAA-AAT-TTAAATAA
1 ATTATATTAAAAATAATGTTAAATAA
*
65573 ATTATCTTAAAAATGTAATGTTAAATAA
1 ATTATATTAAAAA--TAATGTTAAATAA
65601 ATT
1 ATT
65604 TACATAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 12 0.46
27 3 0.12
28 11 0.42
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (26 bp):
ATTATATTAAAAATAATGTTAAATAA
Found at i:65757 original size:30 final size:31
Alignment explanation
Indices: 65713--65770 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
65703 TGCTTTTCTT
65713 CGCAACGAAGAAGTTATCTTTGCTCTTTCCA
1 CGCAACGAAGAAGTTATCTTTGCTCTTTCCA
65744 CGCAACG-AGAAGTTATCTTTGCTCTTT
1 CGCAACGAAGAAGTTATCTTTGCTCTTT
65771 GCTCTTCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (31 bp):
CGCAACGAAGAAGTTATCTTTGCTCTTTCCA
Found at i:66148 original size:22 final size:22
Alignment explanation
Indices: 66105--66159 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
66095 TTATTTATAA
* * *
66105 AATTATTTAAA-ATTTAATTAT
1 AATTAATTAAAGAATTAACTAT
66126 AATTAATTAAAGAATTAACTAT
1 AATTAATTAAAGAATTAACTAT
**
66148 AAGAAATTAAAG
1 AATTAATTAAAG
66160 TATAATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (22 bp):
AATTAATTAAAGAATTAACTAT
Found at i:68028 original size:32 final size:34
Alignment explanation
Indices: 67992--68079 Score: 135
Period size: 34 Copynumber: 2.6 Consensus size: 34
67982 TAAGGAAACA
*
67992 TCTTGGGGCTTGAGAGCCTACCA-A-AGAGAGTT
1 TCTTGGGGCCTGAGAGCCTACCATAGAGAGAGTT
*
68024 TCTTGAGGCCTGAGAGCCTACCATAGAGAGAGTT
1 TCTTGGGGCCTGAGAGCCTACCATAGAGAGAGTT
*
68058 TCTTGGGGCCTAAGAGCCTACC
1 TCTTGGGGCCTGAGAGCCTACC
68080 CAAGGGTCAC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 21 0.42
33 1 0.02
34 28 0.56
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.24
Consensus pattern (34 bp):
TCTTGGGGCCTGAGAGCCTACCATAGAGAGAGTT
Done.