Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168319.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_543, 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: 23575
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Found at i:395 original size:30 final size:30
Alignment explanation
Indices: 361--424 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
351 TCTTTTGGTG
361 AATATTACAAAGTTTGATGGACACAACTGT
1 AATATTACAAAGTTTGATGGACACAACTGT
391 AATATTACAAAGTTTGATGGACACAACTGT
1 AATATTACAAAGTTTGATGGACACAACTGT
421 AATA
1 AATA
425 GAATTTTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (30 bp):
AATATTACAAAGTTTGATGGACACAACTGT
Found at i:15160 original size:49 final size:49
Alignment explanation
Indices: 15086--15417 Score: 293
Period size: 49 Copynumber: 6.9 Consensus size: 49
15076 GTTTCGAGAT
* *
15086 AAGATGAAACTTTTT-AAGTTGTTGAGCCTTTGCTTAGAGGAGCTTTTTC
1 AAGATGAAA-TTTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTTC
* * * * *
15135 AAGATGAAATTTTTAATGTTTTTGAGCCACTGCTTAAAGGAGC-TTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTTC
* * * * *
15183 TAAGATGAAA-TCTTAAA--AGTTGATCTTCTACTTAGATGAGCTTTTTC
1 -AAGATGAAATTTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTTC
* * * * ** *
15230 AAGATGAATTTTTTTAAGTTATTGAGCCTCTATTTAGAAAAGCTTTTCC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTTC
* * * *
15279 AAGATGAAA--TTTAAAGTTGTTAAGCCTCTGCTTAGAGTAGGTTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTTC
* * * * *
15326 AAGATGAAATTTTTAAAGTTGTTAAGCCTTTACTTAAAGGAAC-TTGTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTTC
* * * *
15374 TACGATGAAATCTTTAAAATTGTTGAGCCTCTACTTGGAGGAGC
1 -AAGATGAAATTTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGC
15418 ATTCATTATC
Statistics
Matches: 223, Mismatches: 51, Indels: 18
0.76 0.17 0.06
Matches are distributed among these distances:
46 24 0.11
47 48 0.22
48 19 0.09
49 132 0.59
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (49 bp):
AAGATGAAATTTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTTC
Found at i:15229 original size:95 final size:94
Alignment explanation
Indices: 15118--15409 Score: 288
Period size: 96 Copynumber: 3.0 Consensus size: 94
15108 TGAGCCTTTG
* * *
15118 CTTAGAGGAGCTTTTTCAAGATGAAATTTTTAATGTTTTTGAGCCACTGCTTAAAGGAGCTTTTC
1 CTTAGA-GAGCTTTTTCAAGATGAAATTTTTAA-GTTATTGAGCCTCTACTTAAAGGAGCTTTTC
* *
15183 TAAGATGAAATCTTAAAAGTTG-ATCTTCTA
64 TAAGATGAAATCTTAAAAGTTGTAGCCTCTA
* * *
15213 CTTAGATGAGCTTTTTCAAGATGAATTTTTTTAAGTTATTGAGCCTCTATTTAGAA-AAGCTTTT
1 CTTAGA-GAGCTTTTTCAAGATGAA-ATTTTTAAGTTATTGAGCCTCTACTTA-AAGGAGCTTTT
* *
15277 CCAAGATGAAAT-TT-AAAGTTGTTAAGCCTCTG
63 CTAAGATGAAATCTTAAAAGTTG-T-AGCCTCTA
* * * * * *
15309 CTTAGAGTAGGTTTTTCAAGATGAAATTTTTAAAGTTGTTAAGCCTTTACTTAAAGGAACTTGTC
1 CTTAGAG-AGCTTTTTCAAGATGAAATTTTT-AAGTTATTGAGCCTCTACTTAAAGGAGCTTTTC
*
15374 TACGATGAAATCTTTAAAA-TTGTTGAGCCTCTA
64 TAAGATGAAATC-TTAAAAGTTG-T-AGCCTCTA
15407 CTT
1 CTT
15410 GGAGGAGCAT
Statistics
Matches: 162, Mismatches: 24, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
93 7 0.04
94 2 0.01
95 65 0.40
96 68 0.42
98 17 0.10
99 3 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (94 bp):
CTTAGAGAGCTTTTTCAAGATGAAATTTTTAAGTTATTGAGCCTCTACTTAAAGGAGCTTTTCTA
AGATGAAATCTTAAAAGTTGTAGCCTCTA
Found at i:15670 original size:172 final size:172
Alignment explanation
Indices: 15456--15914 Score: 440
Period size: 172 Copynumber: 2.7 Consensus size: 172
15446 GAGCAAAATA
* * * * *
15456 TTTTAAAATTTCAAAACTCATCGAGCCTCTATTTAGAGGAGCCATTTATGTTTTCAAAAGTCATC
1 TTTTAAAATTTAAAAAATCATCGAGCCTCTACTTAAAGGAGCCATTTATATTTTCAAAAGTCATC
** * * * ** * * *
15521 GAACCTCTATTTAAAGGAG-TTTTTTTTTTATTCAAAGGTTGTTGAGCCTCTATTTAGAGAAG-C
66 GAACCTCTATTTAAAGGAGCCATTTATGTT-TTCAAAAGTCATCGAACCTCTATTTAAAGAAGTC
*
15584 TTTTTTATATTCAAAAGTCGTTAAGCCTCTATTTAGAGGAATCC
130 TTTTTT-TATTCAAAAGTCGTTAAGCCTCGATTTAGAGGAATCC
* * *
15628 TTTTAAATTTTAAAAAATCATCGAGCCTCTGCTTAAAGGAGCCATTTATATTTTCAAAAGTTATC
1 TTTTAAAATTTAAAAAATCATCGAGCCTCTACTTAAAGGAGCCATTTATATTTTCAAAAGTCATC
* * *
15693 GAGCCTCTATTTAGAGGAGCCATTTATGTTTTCAAAAGTCATCGAACCTCTATTTAAAGGAGTCT
66 GAACCTCTATTTAAAGGAGCCATTTATGTTTTCAAAAGTCATCGAACCTCTATTTAAAGAAGTCT
* * * * *
15758 TTTTTTATTCAAAGGTTGTTGAGCCTCGATTTAGAGG-AGCT
131 TTTTTTATTCAAAAGTCGTTAAGCCTCGATTTAGAGGAATCC
* * * * * ** * * * * * * *
15799 TTTTTATA-TTCAAAAGTCGTTAAGCCTCTATTTAGAGGAATCCTTTTAAATTTTAAAAAATCAT
1 TTTTAAAATTTAAAAAATCATCGAGCCTCTACTTAAAGG-AGCCATTTATATTTTCAAAAGTCAT
* ** * * *
15863 CGAGCCTCTGCTTAAAGGAGCCATTTATATTTTCAAAAGTTATCGAGCCTCT
65 CGAACCTCTATTTAAAGGAGCCATTTATGTTTTCAAAAGTCATCGAACCTCT
15915 GCTAAAATTA
Statistics
Matches: 234, Mismatches: 50, Indels: 7
0.80 0.17 0.02
Matches are distributed among these distances:
170 22 0.09
171 72 0.31
172 127 0.54
173 13 0.06
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (172 bp):
TTTTAAAATTTAAAAAATCATCGAGCCTCTACTTAAAGGAGCCATTTATATTTTCAAAAGTCATC
GAACCTCTATTTAAAGGAGCCATTTATGTTTTCAAAAGTCATCGAACCTCTATTTAAAGAAGTCT
TTTTTTATTCAAAAGTCGTTAAGCCTCGATTTAGAGGAATCC
Found at i:15839 original size:214 final size:215
Alignment explanation
Indices: 15464--15914 Score: 850
Period size: 214 Copynumber: 2.1 Consensus size: 215
15454 TATTTTAAAA
* *
15464 TTTCAAAACTCATCGAGCCTCTATTTAGAGGAGCCATTTATGTTTTCAAAAGTCATCGAACCTCT
1 TTTCAAAAGTTATCGAGCCTCTATTTAGAGGAGCCATTTATGTTTTCAAAAGTCATCGAACCTCT
* *
15529 ATTTAAAGGAGTTTTTTTTTTATTCAAAGGTTGTTGAGCCTCTATTTAGAGAAGCTTTTTTATAT
66 ATTTAAAGGAGTTCTTTTTTTATTCAAAGGTTGTTGAGCCTCGATTTAGAGAAGCTTTTTTATAT
15594 TCAAAAGTCGTTAAGCCTCTATTTAGAGGAATCCTTTTAAATTTTAAAAAATCATCGAGCCTCTG
131 TCAAAAGTCGTTAAGCCTCTATTTAGAGGAATCCTTTTAAATTTTAAAAAATCATCGAGCCTCTG
15659 CTTAAAGGAGCCATTTATAT
196 CTTAAAGGAGCCATTTATAT
15679 TTTCAAAAGTTATCGAGCCTCTATTTAGAGGAGCCATTTATGTTTTCAAAAGTCATCGAACCTCT
1 TTTCAAAAGTTATCGAGCCTCTATTTAGAGGAGCCATTTATGTTTTCAAAAGTCATCGAACCTCT
*
15744 ATTTAAAGGAG-TCTTTTTTTATTCAAAGGTTGTTGAGCCTCGATTTAGAGGAGCTTTTTTATAT
66 ATTTAAAGGAGTTCTTTTTTTATTCAAAGGTTGTTGAGCCTCGATTTAGAGAAGCTTTTTTATAT
15808 TCAAAAGTCGTTAAGCCTCTATTTAGAGGAATCCTTTTAAATTTTAAAAAATCATCGAGCCTCTG
131 TCAAAAGTCGTTAAGCCTCTATTTAGAGGAATCCTTTTAAATTTTAAAAAATCATCGAGCCTCTG
15873 CTTAAAGGAGCCATTTATAT
196 CTTAAAGGAGCCATTTATAT
15893 TTTCAAAAGTTATCGAGCCTCT
1 TTTCAAAAGTTATCGAGCCTCT
15915 GCTAAAATTA
Statistics
Matches: 231, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
214 157 0.68
215 74 0.32
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (215 bp):
TTTCAAAAGTTATCGAGCCTCTATTTAGAGGAGCCATTTATGTTTTCAAAAGTCATCGAACCTCT
ATTTAAAGGAGTTCTTTTTTTATTCAAAGGTTGTTGAGCCTCGATTTAGAGAAGCTTTTTTATAT
TCAAAAGTCGTTAAGCCTCTATTTAGAGGAATCCTTTTAAATTTTAAAAAATCATCGAGCCTCTG
CTTAAAGGAGCCATTTATAT
Found at i:15917 original size:43 final size:43
Alignment explanation
Indices: 15464--15914 Score: 372
Period size: 43 Copynumber: 10.5 Consensus size: 43
15454 TATTTTAAAA
* * *
15464 TTTCAAAACTCATCGAGCCTCTATTTAGAGGAGCCATTTATGT
1 TTTCAAAAGTCATCGAGCCTCTATTTAGAGGAGCCTTTTATAT
* * * * *
15507 TTTCAAAAGTCATCGAACCTCTATTTAAAGGAG-TTTTTTTTT
1 TTTCAAAAGTCATCGAGCCTCTATTTAGAGGAGCCTTTTATAT
* ** * * *
15549 TATTCAAAGGTTGTTGAGCCTCTATTTAGAGAAG-CTTTTTTAT
1 T-TTCAAAAGTCATCGAGCCTCTATTTAGAGGAGCCTTTTATAT
* * ** * *
15592 ATTCAAAAGTCGTTAAGCCTCTATTTAGAGGAATCCTTTTAAAT
1 TTTCAAAAGTCATCGAGCCTCTATTTAGAGG-AGCCTTTTATAT
* * ** * *
15636 TTTAAAAAATCATCGAGCCTCTGCTTAAAGGAGCCATTTATAT
1 TTTCAAAAGTCATCGAGCCTCTATTTAGAGGAGCCTTTTATAT
* * *
15679 TTTCAAAAGTTATCGAGCCTCTATTTAGAGGAGCCATTTATGT
1 TTTCAAAAGTCATCGAGCCTCTATTTAGAGGAGCCTTTTATAT
* * *
15722 TTTCAAAAGTCATCGAACCTCTATTTAAAGGAGTCTTTT-T-T
1 TTTCAAAAGTCATCGAGCCTCTATTTAGAGGAGCCTTTTATAT
* ** * * *
15763 TATTCAAAGGTTGTTGAGCCTCGATTTAGAGGAG-CTTTTTTAT
1 T-TTCAAAAGTCATCGAGCCTCTATTTAGAGGAGCCTTTTATAT
* * ** * *
15806 ATTCAAAAGTCGTTAAGCCTCTATTTAGAGGAATCCTTTTAAAT
1 TTTCAAAAGTCATCGAGCCTCTATTTAGAGG-AGCCTTTTATAT
* * ** * *
15850 TTTAAAAAATCATCGAGCCTCTGCTTAAAGGAGCCATTTATAT
1 TTTCAAAAGTCATCGAGCCTCTATTTAGAGGAGCCTTTTATAT
*
15893 TTTCAAAAGTTATCGAGCCTCT
1 TTTCAAAAGTCATCGAGCCTCT
15915 GCTAAAATTA
Statistics
Matches: 322, Mismatches: 78, Indels: 16
0.77 0.19 0.04
Matches are distributed among these distances:
41 7 0.02
42 85 0.26
43 172 0.53
44 58 0.18
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (43 bp):
TTTCAAAAGTCATCGAGCCTCTATTTAGAGGAGCCTTTTATAT
Found at i:16133 original size:3 final size:3
Alignment explanation
Indices: 16125--16160 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
16115 CATTTTATAT
16125 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16161 ATTTTTTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17079 original size:17 final size:17
Alignment explanation
Indices: 17050--17084 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17040 TATAGAACTT
17050 AAAATAATGAATGAATA
1 AAAATAATGAATGAATA
17067 AAAATTAAT-AATGAATA
1 AAAA-TAATGAATGAATA
17084 A
1 A
17085 TGAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAATAATGAATGAATA
Found at i:18017 original size:58 final size:59
Alignment explanation
Indices: 17953--18407 Score: 445
Period size: 58 Copynumber: 7.7 Consensus size: 59
17943 TTGTGCAGGA
* *
17953 AAAATTGATACTTTCAACTTTTCCCTGAAAA-TATTTTTTGAAAATTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATTATTTTTTGAAAATTTTAATTTCAAGG
*
18011 AAAATTGATACTTTCAACTTTT-CCTCAAAAATTTATTTTTTGAAAA-TTT-A-TT-AGGG
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAA-TTATTTTTTGAAAATTTTAATTTCAAGG
* * * *
18067 AAAATTTATACTTTCAACTTTTCCCCAAAAACCTTTTTTTTTG-AAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAA--TTATTTTTTGAAAATTTT-AATTTCAAGG
* * * * *
18128 AAAATTGATACTTTCAACTTTT-CCTCAAAATTTTTTTTTGAAATTTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATTATTTTTTGAAAATTTTAATTTCAAGG
18186 AAAATTGATACTTTCAACTTTT-CCTCAAAAATTTATTTTTT-ATGAAA-TTT-ATTTCTAAGG
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAA-TTATTTTTTGA--AAATTTTAATTTC-AAGG
*****
18246 AAAATTGATACTTTCAACTTTTCCCTAAAAA-TATTTTTTTTTTTTTTTGGAAATTT-ATTAGGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATTATTTTTTGAAAATTTT---AATTTCA--A-GG
* ** * *
18309 AAAATTGATACTTTCAACTTTTCCCCAAAAATCCTTTTTTG-AAATTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATTATTTTTTGAAAATTTTAATTTCAAGG
*
18367 AAAATTGATACTTTCAACTTTTCCCTAAAAATGTTTTTTTT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAAT-TATTTTTT
18408 TTTTTGGAAA
Statistics
Matches: 334, Mismatches: 34, Indels: 57
0.79 0.08 0.13
Matches are distributed among these distances:
56 31 0.09
57 19 0.06
58 115 0.34
59 24 0.07
60 68 0.20
61 30 0.09
62 5 0.01
63 36 0.11
64 6 0.02
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.47
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATTATTTTTTGAAAATTTTAATTTCAAGG
Found at i:18361 original size:181 final size:173
Alignment explanation
Indices: 17953--18409 Score: 580
Period size: 175 Copynumber: 2.6 Consensus size: 173
17943 TTGTGCAGGA
* * **
17953 AAAATTGATACTTTCAACTTTTCCCTGAAAATATTTTTTGAAAATTTTAATTTCGAGGAAAATTG
1 AAAATTGATACTTTCAACTTTTCCC-CAAAATATTTTTTG-AAATTTTATTTTTAAGGAAAATTG
* *
18018 ATACTTTCAACTTTTCCTCAAAAATTTA-TTTTTTGAAAATTTATTAGGGAAAATTTATACTTTC
64 ATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTGAAAATTTATTAAGGAAAATTGATACTTTC
*
18082 AACTTTTCCCCAAAAACCTTTTTTTTTGAAATTTTGATTTTCAAGG
129 AACTTTTCCCCAAAAACATTTTTTTTT-AAATTTTGATTTTCAAGG
* *
18128 AAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTTTTGAAATTTTTATTTTTAAGGAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCCAAAA-TATTTTTTGAAA-TTTTATTTTTAAGGAAAATTG
18193 ATACTTTCAACTTTTCCTCAAAAATTTATTTTTTATG-AAATTTATTTCTAAGGAAAATTGATAC
64 ATACTTTCAACTTTTCCTCAAAAATTTATTTTTT-TGAAAATTTA--T-TAAGGAAAATTGATAC
* * ** * *
18257 TTTCAACTTTTCCCTAAAAATATTTTTTTTT-TTTTTTGGAAATTTATTAGGG
125 TTTCAACTTTTCCCCAAAAACATTTTTTTTTAAATTTT-G--ATTT-TCAAGG
*
18309 AAAATTGATACTTTCAACTTTTCCCCAAAAATCCTTTTTTGAAATTTTATTTTTAAGGAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCC-AAAAT-ATTTTTTGAAATTTTATTTTTAAGGAAAATTG
*
18374 ATACTTTCAACTTTTCC-CTAAAAATGTTTTTTTTTT
64 ATACTTTCAACTTTTCCTC-AAAAAT-TTATTTTTTT
18410 TTTGGAAATT
Statistics
Matches: 249, Mismatches: 18, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
174 7 0.03
175 78 0.31
176 12 0.05
177 6 0.02
178 2 0.01
179 42 0.17
180 5 0.02
181 75 0.30
182 22 0.09
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (173 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTTGAAATTTTATTTTTAAGGAAAATTGAT
ACTTTCAACTTTTCCTCAAAAATTTATTTTTTTGAAAATTTATTAAGGAAAATTGATACTTTCAA
CTTTTCCCCAAAAACATTTTTTTTTAAATTTTGATTTTCAAGG
Found at i:18462 original size:9 final size:9
Alignment explanation
Indices: 18448--18587 Score: 70
Period size: 9 Copynumber: 14.2 Consensus size: 9
18438 AAAATAGAAT
18448 AATAAAAAA
1 AATAAAAAA
18457 AATAAAAAA
1 AATAAAAAA
18466 AGA-AAAGTAAA
1 A-ATAAA--AAA
18477 AA-AAATAAA
1 AATAAA-AAA
18486 AATAAAATAA
1 AATAAAA-AA
18496 AGATAAAAAGA
1 A-ATAAAAA-A
18507 ATATTAAATAAA
1 A-A-TAAA-AAA
** *
18519 CCTAATCTAATA
1 ---AATAAAAAA
*
18531 AATAAAAAT
1 AATAAAAAA
18540 AATAATAAATA
1 AATAA-AAA-A
*
18551 AATAAAATA
1 AATAAAAAA
*
18560 AATAAATAA
1 AATAAAAAA
18569 AATAAAAAA
1 AATAAAAAA
18578 AA-AAAAAA
1 AATAAAAAA
18586 AA
1 AA
18588 ACCTGGAGCG
Statistics
Matches: 104, Mismatches: 13, Indels: 29
0.71 0.09 0.20
Matches are distributed among these distances:
8 8 0.08
9 48 0.46
10 17 0.16
11 18 0.17
12 7 0.07
13 4 0.04
14 1 0.01
15 1 0.01
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (9 bp):
AATAAAAAA
Found at i:18464 original size:23 final size:24
Alignment explanation
Indices: 18438--18509 Score: 85
Period size: 23 Copynumber: 3.0 Consensus size: 24
18428 TTATTTAAAG
18438 AAAATAGAATAA-TAAAAAAAATA
1 AAAATAGAATAAGTAAAAAAAATA
*
18461 AAAAAAGAA-AAGTAAAAAAAATA
1 AAAATAGAATAAGTAAAAAAAATA
* *
18484 AAAATAAAATAAAGATAAAAAGAATA
1 AAAATAGAAT-AAG-TAAAAAAAATA
18510 TTAAATAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 2 0.05
23 26 0.63
25 3 0.07
26 10 0.24
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (24 bp):
AAAATAGAATAAGTAAAAAAAATA
Found at i:18471 original size:15 final size:16
Alignment explanation
Indices: 18454--18504 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 16
18444 GAATAATAAA
18454 AAAAATAAAAAAAG--
1 AAAAATAAAAAAAGAT
*
18468 AAAAGTAAAAAAA-AT
1 AAAAATAAAAAAAGAT
18483 AAAAATAAAATAAAGAT
1 AAAAATAAAA-AAAGAT
18500 AAAAA
1 AAAAA
18505 GAATATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 12 0.39
15 9 0.29
16 3 0.10
17 7 0.23
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAAATAAAAAAAGAT
Found at i:18501 original size:6 final size:5
Alignment explanation
Indices: 18448--18587 Score: 63
Period size: 5 Copynumber: 28.4 Consensus size: 5
18438 AAAATAGAAT
*
18448 AATAA AA-AA AATAA AA-AA AGA-AA AGTAA AA-AA AATAAA AATAA AATAA
1 AATAA AATAA AATAA AATAA A-ATAA AATAA AATAA AAT-AA AATAA AATAA
* *
18496 AGATAA AA-AGA ATATTA AATAA ACCTAA TCTAAT-A AATAAA AATAA TAAT-A
1 A-ATAA AATA-A A-ATAA AATAA A-ATAA ---AATAA AAT-AA AATAA -AATAA
18547 AAT-A AATAA AAT-A AAT-A AATAA AATAA AA-AA AA-AA AA-AA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA
18588 ACCTGGAGCG
Statistics
Matches: 111, Mismatches: 6, Indels: 37
0.72 0.04 0.24
Matches are distributed among these distances:
4 42 0.38
5 43 0.39
6 23 0.21
7 1 0.01
8 1 0.01
9 1 0.01
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:18534 original size:4 final size:4
Alignment explanation
Indices: 18527--18574 Score: 53
Period size: 4 Copynumber: 11.5 Consensus size: 4
18517 AACCTAATCT
*
18527 AATA AATA AAAA TAAT- AATA AATA AATAA AATA AATA AATAA AATA AA
1 AATA AATA AATA -AATA AATA AATA AAT-A AATA AATA AAT-A AATA AA
18575 AAAAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 3 0.08
4 25 0.66
5 10 0.26
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:18572 original size:38 final size:36
Alignment explanation
Indices: 18439--18585 Score: 120
Period size: 38 Copynumber: 4.0 Consensus size: 36
18429 TATTTAAAGA
* * * *
18439 AAATAGAATAATAAAAAAAATAAAAA-AAGAAAAGT
1 AAATAAAATAATAAATAAAATAAAAATAAAAAAAAT
* *
18474 AAAAAAAATAA-AAATAAAATAAAGATAAAAAGAATATT
1 AAATAAAATAATAAATAAAATAAAAATAAAAA-AA-A-T
* * *
18512 AAATAAACCTAATCTAAT-AAATAAAAATAATAATAAAT
1 AAATAAA-ATAAT-AAATAAAATAAAAATAA-AAAAAAT
*
18550 AAATAAAATAAATAAATAAAATAAAAAAAAAAAAAA
1 AAATAAAAT-AATAAATAAAATAAAAATAAAAAAAA
18586 AAACCTGGAG
Statistics
Matches: 87, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
34 12 0.14
35 13 0.15
36 2 0.02
37 9 0.10
38 29 0.33
39 4 0.05
40 13 0.15
41 5 0.06
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.18
Consensus pattern (36 bp):
AAATAAAATAATAAATAAAATAAAAATAAAAAAAAT
Found at i:19124 original size:15 final size:14
Alignment explanation
Indices: 19100--19143 Score: 63
Period size: 13 Copynumber: 3.1 Consensus size: 14
19090 GGATTTTTCC
*
19100 AAAAATTCCCAGAAA
1 AAAAAATCCCA-AAA
19115 AAAAAATCCC-AAA
1 AAAAAATCCCAAAA
19128 AAAAAATCCCAAAA
1 AAAAAATCCCAAAA
19142 AA
1 AA
19144 TTTCTTCTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 13 0.48
14 5 0.19
15 9 0.33
ACGTcount: A:0.68, C:0.20, G:0.02, T:0.09
Consensus pattern (14 bp):
AAAAAATCCCAAAA
Found at i:19128 original size:13 final size:13
Alignment explanation
Indices: 19112--19143 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
19102 AAATTCCCAG
19112 AAAAAAAAATCCC
1 AAAAAAAAATCCC
19125 AAAAAAAAATCCC
1 AAAAAAAAATCCC
19138 AAAAAA
1 AAAAAA
19144 TTTCTTCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.75, C:0.19, G:0.00, T:0.06
Consensus pattern (13 bp):
AAAAAAAAATCCC
Found at i:19508 original size:22 final size:23
Alignment explanation
Indices: 19458--19510 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
19448 ATATTATAGT
*
19458 ATAAAAATAAAAAATAACATCAG
1 ATAAAATTAAAAAATAACATCAG
19481 AT--AATTCAAAAAA-AA-ATCAG
1 ATAAAATT-AAAAAATAACATCAG
19501 ATAAAATTAA
1 ATAAAATTAA
19511 CAGATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
20 7 0.27
21 7 0.27
22 10 0.38
23 2 0.08
ACGTcount: A:0.68, C:0.08, G:0.04, T:0.21
Consensus pattern (23 bp):
ATAAAATTAAAAAATAACATCAG
Found at i:19572 original size:3 final size:3
Alignment explanation
Indices: 19566--19702 Score: 55
Period size: 3 Copynumber: 42.0 Consensus size: 3
19556 ACAAAAAAAG
19566 ATA ATA ATA AT- ATA ATA ATA ATA ATA ATAA ATA TATA ACTA TATA CAT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA -ATA A-TA -ATA -ATA
* * * * * *
19614 ATA ATA CATA AAA ATA TTA ACA GAGA AAA AAA GATAA ATAA ATA TATA
1 ATA ATA -ATA ATA ATA ATA ATA -ATA ATA ATA -AT-A AT-A ATA -ATA
* *
19662 CAT- ATA TTA ATAA ATA ATA ATA ATA ATAA ATA ATA AAA ATA
1 -ATA ATA ATA AT-A ATA ATA ATA ATA AT-A ATA ATA ATA ATA
19703 CAAAAGAAGA
Statistics
Matches: 106, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
2 6 0.06
3 63 0.59
4 35 0.33
5 2 0.02
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:19688 original size:16 final size:16
Alignment explanation
Indices: 19566--19702 Score: 76
Period size: 16 Copynumber: 7.6 Consensus size: 16
19556 ACAAAAAAAG
19566 ATAATAATAATATAATA
1 ATAATAATAATA-AATA
19583 ATAATAATAATAAATA
1 ATAATAATAATAAATA
19599 TATAACTATATACATATAATA
1 -ATAA-TA-ATA-ATA-AATA
* * *
19620 CATAAAAATATTAACAGAGA
1 -ATAATAATAAT-A-A-ATA
* *
19640 AAAAAAGATAAATAAATA
1 ATAATA-AT-AATAAATA
19658 TATACATATATTAATAAATA
1 -ATA-ATA-A-TAATAAATA
19678 ATAATAATAATAAATA
1 ATAATAATAATAAATA
*
19694 ATAAAAATA
1 ATAATAATA
19703 CAAAAGAAGA
Statistics
Matches: 96, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
16 21 0.22
17 17 0.18
18 8 0.08
19 19 0.20
20 20 0.21
21 11 0.11
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (16 bp):
ATAATAATAATAAATA
Found at i:19809 original size:20 final size:21
Alignment explanation
Indices: 19786--19824 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
19776 CCTTACCCAT
19786 TTGGGCCAGG-CCCAATTGAC
1 TTGGGCCAGGACCCAATTGAC
*
19806 TTGGGCCTGGACCCAATTG
1 TTGGGCCAGGACCCAATTG
19825 GGTGTCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.18, C:0.28, G:0.31, T:0.23
Consensus pattern (21 bp):
TTGGGCCAGGACCCAATTGAC
Found at i:19930 original size:1 final size:1
Alignment explanation
Indices: 19919--20042 Score: 104
Period size: 1 Copynumber: 124.0 Consensus size: 1
19909 AACATTTTCA
* * * * ** * * * * *
19919 TTTTTTGTTTTTTTTGTTGTTTGTTTTTGATTTTTTTCTCTTTTTTTTTTATTTTTTTTGTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
19984 TTTTTTTTGTTTTGTTTTTTTTGTTTTTTGTTTTTTTTGTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20043 GTCGAAGTTC
Statistics
Matches: 92, Mismatches: 31, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 92 1.00
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (1 bp):
T
Found at i:19945 original size:14 final size:13
Alignment explanation
Indices: 19919--20044 Score: 118
Period size: 12 Copynumber: 9.6 Consensus size: 13
19909 AACATTTTCA
19919 TTTTTTGTTT-TT
1 TTTTTTGTTTGTT
*
19931 TTTGTTGTTTGTT
1 TTTTTTGTTTGTT
* *
19944 TTTGATTTTTTTCTCT
1 TTT--TTTGTTTGT-T
*
19960 TTTTTT-TTTATT
1 TTTTTTGTTTGTT
19972 TTTTTTGTTTTGTT
1 TTTTTTG-TTTGTT
19986 TTTTTTGTTTTGTT
1 TTTTTTG-TTTGTT
20000 TTTTTTGTTT-TT
1 TTTTTTGTTTGTT
20012 TGTTTTT-TTTGTT
1 T-TTTTTGTTTGTT
*
20025 TTTTTT-TTTTTT
1 TTTTTTGTTTGTT
20037 TTTTTTGT
1 TTTTTTGT
20045 CGAAGTTCCT
Statistics
Matches: 98, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
12 38 0.39
13 21 0.21
14 29 0.30
15 6 0.06
16 4 0.04
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (13 bp):
TTTTTTGTTTGTT
Found at i:19954 original size:30 final size:29
Alignment explanation
Indices: 19913--20033 Score: 124
Period size: 28 Copynumber: 4.1 Consensus size: 29
19903 CAACTCAACA
*
19913 TTTTCATTTTTTGTTTTTTTTGTTGTTTGT
1 TTTTGATTTTTTGTTTTTTTTGTTGTTT-T
* * *
19943 TTTTGATTTTTTTCTCTTTTTTTTTTATTTT
1 TTTTGA-TTTTTTGT-TTTTTTTGTTGTTTT
19974 TTTTG---TTTTGTTTTTTTTGTTTTGTTTT
1 TTTTGATTTTTTGTTTTTTTTG--TTGTTTT
*
20002 TTTTG-TTTTTTGTTTTTTTTGTTTTTTT
1 TTTTGATTTTTTGTTTTTTTTGTTGTTTT
20030 TTTT
1 TTTT
20034 TTTTTTTTTG
Statistics
Matches: 77, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
26 7 0.09
27 5 0.06
28 21 0.27
30 19 0.25
31 13 0.17
32 12 0.16
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.85
Consensus pattern (29 bp):
TTTTGATTTTTTGTTTTTTTTGTTGTTTT
Found at i:19978 original size:44 final size:41
Alignment explanation
Indices: 19919--20042 Score: 155
Period size: 44 Copynumber: 2.9 Consensus size: 41
19909 AACATTTTCA
19919 TTTTTTGTTTTTTTTGTTGTTTGTTTTTGATTTTTTTCTCTTTT-
1 TTTTTTGTTTTTTTTGTTGTTT-TTTTTG-TTTTTTT-T-TTTTG
*
19963 TTTTTTATTTTTTTTGTTTTGTTTTTTTTGTTTTGTTTTTTTTG
1 TTTTTTGTTTTTTTTG--TTGTTTTTTTTGTTTT-TTTTTTTTG
20007 TTTTTTGTTTTTTTTGTT-TTTTTTTT-TTTTTTTTTT
1 TTTTTTGTTTTTTTTGTTGTTTTTTTTGTTTTTTTTTT
20043 GTCGAAGTTC
Statistics
Matches: 74, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
39 6 0.08
40 4 0.05
41 8 0.11
42 2 0.03
43 4 0.05
44 35 0.47
45 9 0.12
46 6 0.08
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (41 bp):
TTTTTTGTTTTTTTTGTTGTTTTTTTTGTTTTTTTTTTTTG
Found at i:20028 original size:65 final size:67
Alignment explanation
Indices: 19919--20044 Score: 186
Period size: 65 Copynumber: 1.9 Consensus size: 67
19909 AACATTTTCA
*
19919 TTTTTTGTTTTTTTTGTTGTTTGTTTTTGATTTTTTTCTCTTTTTTTTTTATTTTTTTTGTTTTG
1 TTTTTTGTTTTGTTTGTTGTTTGTTTTTGATTTTTTTCTCTTTTTTTTTTATTTTTTTTGTTTTG
19984 TT
66 TT
* * *
19986 TTTTTTGTTTTGTTT-TT-TTTGTTTTTTGTTTTTTTTGT-TTTTTTTTTTTTTTTTTTTGT
1 TTTTTTGTTTTGTTTGTTGTTTG-TTTTTGATTTTTTTCTCTTTTTTTTTTATTTTTTTTGT
20045 CGAAGTTCCT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
65 24 0.44
66 16 0.30
67 14 0.26
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (67 bp):
TTTTTTGTTTTGTTTGTTGTTTGTTTTTGATTTTTTTCTCTTTTTTTTTTATTTTTTTTGTTTTG
TT
Found at i:20142 original size:41 final size:41
Alignment explanation
Indices: 20051--20261 Score: 336
Period size: 41 Copynumber: 5.1 Consensus size: 41
20041 TTGTCGAAGT
*
20051 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATTGC
*
20093 TCCTCTCAACAGAGGCACCACGACTTTGGAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGC
*
20134 TCCTCTCAACAGAGGCACCACGACTTTGGAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGC
*
20175 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGC
20216 TCCTCTAAACAGAGGCA--ACGGAACTTTGAGAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCAC-G-ACTTTG-GAAAGTAAATTGC
20258 TCCT
1 TCCT
20262 TGACAATCAT
Statistics
Matches: 161, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
39 2 0.01
40 1 0.01
41 114 0.71
42 44 0.27
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (41 bp):
TCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGC
Found at i:21462 original size:10 final size:10
Alignment explanation
Indices: 21447--21520 Score: 69
Period size: 10 Copynumber: 7.3 Consensus size: 10
21437 ATTTTGAATA
21447 TTTTCTCATT
1 TTTTCTCATT
*
21457 TTTTCT-TTT
1 TTTTCTCATT
* *
21466 TTTTTTCTTTT
1 TTTTCTC-ATT
21477 TTTTCTCATT
1 TTTTCTCATT
**
21487 TTTTCTTTTT
1 TTTTCTCATT
21497 TTTTCATCATT
1 TTTTC-TCATT
*
21508 TTTTTTCATT
1 TTTTCTCATT
21518 TTT
1 TTT
21521 CATCCATTGT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
9 7 0.13
10 29 0.56
11 16 0.31
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTCTCATT
Found at i:21471 original size:11 final size:11
Alignment explanation
Indices: 21455--21500 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
21445 TATTTTCTCA
21455 TTTTTTCTTTT
1 TTTTTTCTTTT
21466 TTTTTTCTTTT
1 TTTTTTCTTTT
*
21477 TTTTCTCATTTT
1 TTTTTTC-TTTT
21489 TTCTTTT-TTTT
1 TT-TTTTCTTTT
21500 T
1 T
21501 CATCATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 22 0.71
12 6 0.19
13 3 0.10
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:21483 original size:30 final size:31
Alignment explanation
Indices: 21447--21520 Score: 116
Period size: 30 Copynumber: 2.4 Consensus size: 31
21437 ATTTTGAATA
*
21447 TTTTCTCATTTTTTCTTTTTTTTT-TCTTTT
1 TTTTCTCATTTTTTCTTTTTTTTTATCATTT
21477 TTTTCTCATTTTTTCTTTTTTTTTCATCATTT
1 TTTTCTCATTTTTTCTTTTTTTTT-ATCATTT
21509 TTTT-TCATTTTT
1 TTTTCTCATTTTT
21521 CATCCATTGT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 24 0.59
31 8 0.20
32 9 0.22
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (31 bp):
TTTTCTCATTTTTTCTTTTTTTTTATCATTT
Found at i:21528 original size:21 final size:20
Alignment explanation
Indices: 21464--21528 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
21454 ATTTTTTCTT
**
21464 TTTTTTTTCTTTTTTTTCTCA
1 TTTTTTTTCTTTTTCATC-CA
*
21485 TTTTTTCTTTTTTTTTCAT-CA
1 -TTTTT-TTTCTTTTTCATCCA
21506 TTTTTTTTCATTTTTCATCCA
1 TTTTTTTTC-TTTTTCATCCA
21527 TT
1 TT
21529 GTTGATATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
19 3 0.08
20 13 0.36
21 6 0.17
22 5 0.14
23 9 0.25
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTTTCTTTTTCATCCA
Done.