Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168120.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_364, 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: 31173
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Found at i:4291 original size:52 final size:52
Alignment explanation
Indices: 4203--4359 Score: 185
Period size: 52 Copynumber: 3.0 Consensus size: 52
4193 TGGATAAGAA
* *
4203 GACTTGCAAAAGAAGAATTCTAAGAGAAAAAAGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGAAAAAAGATTCTTAATAGGCAAGTTT
*
4255 GACTTGCAAGAGAAGAATTCTAA-A-AAGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGAA-AAA-AGATTCTTAATAGGCAAGTTT
** * * * *
4307 GACTTATAGGAGAAGAATTCTAAGAGGAGAAAA-ATTTTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGA-GAAAAAAGATTCTTAATAGGCAAGTTT
4359 G
1 G
4360 TATGATTATA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 79 0.88
53 1 0.01
54 3 0.03
55 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.23, T:0.27
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGAAAAAAGATTCTTAATAGGCAAGTTT
Found at i:4941 original size:25 final size:25
Alignment explanation
Indices: 4920--5009 Score: 92
Period size: 25 Copynumber: 3.6 Consensus size: 25
4910 AAGAAGAGTT
**
4920 AAAGATTCAAGATGTGGAAAGAGCCG
1 AAAG-TTCAAGATGTGGAAAGAGCTA
* * * *
4946 AAGGTTCGAGACGT-GAAAGAGTTA
1 AAAGTTCAAGATGTGGAAAGAGCTA
*
4970 AAAGTTCAAGATGTGGGAAGAGCTA
1 AAAGTTCAAGATGTGGAAAGAGCTA
*
4995 AAAGTTTAAGATGTG
1 AAAGTTCAAGATGTG
5010 AGAAGTGCAT
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
24 18 0.35
25 30 0.59
26 3 0.06
ACGTcount: A:0.40, C:0.08, G:0.31, T:0.21
Consensus pattern (25 bp):
AAAGTTCAAGATGTGGAAAGAGCTA
Found at i:4978 original size:49 final size:50
Alignment explanation
Indices: 4889--4992 Score: 140
Period size: 49 Copynumber: 2.1 Consensus size: 50
4879 AAGTGGTATT
*
4889 AGAGCTGAAGGTTCGAAACATAAGAAGAGTTAAAGATTCAAGATGTGGAA
1 AGAGCCGAAGGTTCGAAACATAAGAAGAGTTAAAGATTCAAGATGTGGAA
* * * *
4939 AGAGCCGAAGGTTCGAGACGTGA-AAGAGTTAAA-AGTTCAAGATGTGGGA
1 AGAGCCGAAGGTTCGAAACATAAGAAGAGTTAAAGA-TTCAAGATGTGGAA
4988 AGAGC
1 AGAGC
4993 TAAAAGTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
48 1 0.02
49 28 0.58
50 19 0.40
ACGTcount: A:0.40, C:0.10, G:0.32, T:0.18
Consensus pattern (50 bp):
AGAGCCGAAGGTTCGAAACATAAGAAGAGTTAAAGATTCAAGATGTGGAA
Found at i:5014 original size:25 final size:25
Alignment explanation
Indices: 4911--5014 Score: 88
Period size: 25 Copynumber: 4.2 Consensus size: 25
4901 TCGAAACATA
*
4911 AGAAGAG-TTAAAGATTCAAGATGTG
1 AGAAGAGCTAAAAG-TTCAAGATGTG
** * * *
4936 -GAAAGAGCCGAAGGTTCGAGACGTG
1 AG-AAGAGCTAAAAGTTCAAGATGTG
*
4961 A-AAGAGTTAAAAGTTCAAGATGTG
1 AGAAGAGCTAAAAGTTCAAGATGTG
* *
4985 GGAAGAGCTAAAAGTTTAAGATGTG
1 AGAAGAGCTAAAAGTTCAAGATGTG
5010 AGAAG
1 AGAAG
5015 TGCATGGTTT
Statistics
Matches: 60, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
24 18 0.30
25 39 0.65
26 3 0.05
ACGTcount: A:0.41, C:0.07, G:0.32, T:0.20
Consensus pattern (25 bp):
AGAAGAGCTAAAAGTTCAAGATGTG
Found at i:5408 original size:52 final size:52
Alignment explanation
Indices: 5325--5427 Score: 154
Period size: 52 Copynumber: 2.0 Consensus size: 52
5315 CAAGAAGACT
* *
5325 TGCAAAAGAAGAATTATAAGAGAAAGAAGATTCTTAATAGGTAAGTTTGACA
1 TGCAAAAGAAGAATTATAAAAGAAAGAAGATTCTTAATAGGCAAGTTTGACA
* *
5377 TGCAAGAGAAGAATTCTAAAAGGAAAG-AGATTCTTAATAGGCAAGTTTGAC
1 TGCAAAAGAAGAATTATAAAA-GAAAGAAGATTCTTAATAGGCAAGTTTGAC
5428 TTACAGAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 41 0.89
53 5 0.11
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.24
Consensus pattern (52 bp):
TGCAAAAGAAGAATTATAAAAGAAAGAAGATTCTTAATAGGCAAGTTTGACA
Found at i:5445 original size:52 final size:52
Alignment explanation
Indices: 5331--5476 Score: 145
Period size: 52 Copynumber: 2.8 Consensus size: 52
5321 GACTTGCAAA
* * * *
5331 AGAAGAATTATAAGA-GAAAGAAGATTCTTAATAGGTAAGTTTGACATGCAAG
1 AGAAGAATTCTAAAAGGAAAG-AGATTCTTAATAGGCAAGTTTGACATACAAG
*
5383 AGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTTGACTTAC-AG
1 AGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTTGACATACAAG
* * * * * *
5434 A-ATAGGGATTCTAAGAGTAGAGGGATTCTTAATGGGCAAGTTT
1 AGA-A-GAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
5477 ATATGGTTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
50 1 0.01
51 4 0.05
52 70 0.88
53 5 0.06
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.27
Consensus pattern (52 bp):
AGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTTGACATACAAG
Found at i:6873 original size:22 final size:25
Alignment explanation
Indices: 6844--6914 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 25
6834 TTAATTCACA
6844 TATATATAAAAATTAAAAATAAAAGTT
1 TATATAT-AAAATTAAAAATAAAAG-T
6871 ATATATATATAAATTAAAAATAAAA-T
1 -TATATATA-AAATTAAAAATAAAAGT
*
6897 T-TATATAAAAATAAAAAT
1 TATATATAAAATTAAAAAT
6915 TTAGTTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
23 10 0.24
24 6 0.15
25 1 0.02
26 1 0.02
27 1 0.02
28 22 0.54
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (25 bp):
TATATATAAAATTAAAAATAAAAGT
Found at i:6874 original size:28 final size:28
Alignment explanation
Indices: 6843--6903 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
6833 TTTAATTCAC
6843 ATATATATAAAAATTAAAAATAAAAGTT
1 ATATATATAAAAATTAAAAATAAAAGTT
* *
6871 ATATATATATAAATTAAAAATAAAATTT
1 ATATATATAAAAATTAAAAATAAAAGTT
6899 ATATA
1 ATATA
6904 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (28 bp):
ATATATATAAAAATTAAAAATAAAAGTT
Found at i:6910 original size:28 final size:28
Alignment explanation
Indices: 6853--6911 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
6843 ATATATATAA
* *
6853 AAATTAAAAATAAAAGTTATATATATAT
1 AAATTAAAAATAAAAGTTATATAAAAAT
*
6881 AAATTAAAAATAAAATTTATATAAAAAT
1 AAATTAAAAATAAAAGTTATATAAAAAT
6909 AAA
1 AAA
6912 AATTTAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (28 bp):
AAATTAAAAATAAAAGTTATATAAAAAT
Found at i:7956 original size:3 final size:3
Alignment explanation
Indices: 7948--7996 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
7938 TAGAACAAAA
7948 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
7994 ATT
1 ATT
7997 GAGCTATTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:10314 original size:20 final size:20
Alignment explanation
Indices: 10295--10361 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
10285 TCTTATTTAT
**
10295 TTATTTATTGTTAT-TATTA
1 TTATTTATTAATATATATTA
*
10314 TTATTTATTAATATATATTT
1 TTATTTATTAATATATATTA
*
10334 TTATCTATTAATATATATTA
1 TTATTTATTAATATATATTA
10354 TTATTTAT
1 TTATTTAT
10362 CTATTAATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 12 0.29
20 29 0.71
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (20 bp):
TTATTTATTAATATATATTA
Found at i:10385 original size:28 final size:24
Alignment explanation
Indices: 10306--10455 Score: 113
Period size: 24 Copynumber: 6.5 Consensus size: 24
10296 TATTTATTGT
*
10306 TATTATTA-TTATTTATT-A-ATA
1 TATTATTATTTATCTATTAATATA
10327 TA-TATT-TTTATCTATTAATATA
1 TATTATTATTTATCTATTAATATA
*
10349 TATTATTATTTATCTATTAATGTA
1 TATTATTATTTATCTATTAATATA
* *
10373 TATAAATT-GTTAT-TATTAACTAT-
1 TAT-TATTATTTATCTATTAA-TATA
*
10396 TATCTATTATTTATCTATTAGTATA
1 TAT-TATTATTTATCTATTAATATA
* *
10421 TA-TATTTATTTAT-TATTTATCTA
1 TATTA-TTATTTATCTATTAATATA
*
10444 TTTTTATTATTT
1 -TATTATTATTT
10456 TTTTTTGGCT
Statistics
Matches: 103, Mismatches: 13, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
20 12 0.12
21 3 0.03
22 5 0.05
23 25 0.24
24 46 0.45
25 12 0.12
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
TATTATTATTTATCTATTAATATA
Found at i:10411 original size:11 final size:11
Alignment explanation
Indices: 10395--10454 Score: 65
Period size: 11 Copynumber: 5.8 Consensus size: 11
10385 TTATTAACTA
10395 TTATCTATTAT
1 TTATCTATTAT
10406 TTATCTATTA-
1 TTATCTATTAT
* *
10416 GTATATA-TAT
1 TTATCTATTAT
*
10426 TTATTTATTAT
1 TTATCTATTAT
10437 TTATCTATT-T
1 TTATCTATTAT
10447 TTAT-TATT
1 TTATCTATT
10455 TTTTTTTGGC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
9 6 0.14
10 15 0.36
11 21 0.50
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (11 bp):
TTATCTATTAT
Found at i:10434 original size:48 final size:45
Alignment explanation
Indices: 10305--10455 Score: 157
Period size: 48 Copynumber: 3.3 Consensus size: 45
10295 TTATTTATTG
*
10305 TTATTATTA-TTATTTATTA--ATATATATTTTTATCTATTAA-TA
1 TTATTATTATTTATCTATTAGTATATATATTTTTAT-TATTAACTA
* *
10347 TATATTATTATTTATCTATTAATGTATATAAATTGTTATTATTAACTA
1 T-TATTATTATTTATCTATT-A-GTATATATATTTTTATTATTAACTA
*
10395 TTATCTATTATTTATCTATTAGTATATATATTTATTTATTATTTATCTA
1 TTAT-TATTATTTATCTATTAGTATATATA-TT-TTTATTA-TTAACTA
*
10444 TTTTTATTATTT
1 TTATTATTATTT
10456 TTTTTTGGCT
Statistics
Matches: 91, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
42 1 0.01
43 8 0.09
44 8 0.09
45 1 0.01
46 8 0.09
47 12 0.13
48 44 0.48
49 9 0.10
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (45 bp):
TTATTATTATTTATCTATTAGTATATATATTTTTATTATTAACTA
Found at i:10451 original size:17 final size:17
Alignment explanation
Indices: 10382--10455 Score: 57
Period size: 17 Copynumber: 4.5 Consensus size: 17
10372 ATATAAATTG
*
10382 TTATTA-TTAACTATTAT
1 TTATTATTTATCTATT-T
* *
10399 CTATTATTTATCTATTA
1 TTATTATTTATCTATTT
* * *
10416 GTA-TATATAT-T-TAT
1 TTATTATTTATCTATTT
10430 TTATTATTTATCTATTT
1 TTATTATTTATCTATTT
10447 TTATTATTT
1 TTATTATTT
10456 TTTTTTGGCT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
14 3 0.07
15 7 0.16
16 7 0.16
17 18 0.42
18 8 0.19
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (17 bp):
TTATTATTTATCTATTT
Found at i:11727 original size:3 final size:3
Alignment explanation
Indices: 11721--11755 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
11711 TTTTTCTTAT
*
11721 TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11756 TATTGATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:11797 original size:5 final size:5
Alignment explanation
Indices: 11787--11849 Score: 67
Period size: 5 Copynumber: 12.4 Consensus size: 5
11777 TTAGTATTCC
* *
11787 TTATT TTATT TTATT TTATTT TTATTT TTACCT TTATT TTATT TT-TA
1 TTATT TTATT TTATT TTA-TT TTA-TT TTA-TT TTATT TTATT TTATT
11834 TT-TT TTATT TTATT TT
1 TTATT TTATT TTATT TT
11850 TTGATTTTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
4 6 0.12
5 30 0.59
6 15 0.29
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:11811 original size:6 final size:6
Alignment explanation
Indices: 11790--11850 Score: 67
Period size: 6 Copynumber: 10.7 Consensus size: 6
11780 GTATTCCTTA
* *
11790 TTTTA- TTTTA- TTTTAT TTTTAT TTTTAC CTTTA- TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
11835 TTTT-T ATTTTAT TTTT
1 TTTTAT -TTTTAT TTTT
11851 TGATTTTGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
5 15 0.31
6 33 0.67
7 1 0.02
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:11845 original size:23 final size:22
Alignment explanation
Indices: 11790--11849 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 22
11780 GTATTCCTTA
11790 TTTTATTTTATTTTATTTTTAT
1 TTTTATTTTATTTTATTTTTAT
*
11812 TTTTACCTTTATTTTATTTTTATT
1 TTTTA-TTTTATTTTATTTTTA-T
11836 TTTTATTTTATTTT
1 TTTTATTTTATTTT
11850 TTGATTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 5 0.15
23 23 0.68
24 6 0.18
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTATTTTATTTTATTTTTAT
Found at i:14619 original size:43 final size:43
Alignment explanation
Indices: 14554--14749 Score: 216
Period size: 43 Copynumber: 4.6 Consensus size: 43
14544 ATTGTCGAGC
* *
14554 AGCCTTATTTACTTTTCAAAGTTGTTAAGCCTTTGTTTAAAGG
1 AGCCTTATTTATTTTTCAAAGTTGTTAAGCCTTTATTTAAAGG
* * * *
14597 AGCTTTATTTATTTTTCAAAGTTAGTTGAGCATTTATTTAGAGG
1 AGCCTTATTTATTTTTCAAAGTT-GTTAAGCCTTTATTTAAAGG
* * ** * *
14641 A-CCTTATTTACTTTTCAAATTTAATGAGCCTTTATTTAGAGG
1 AGCCTTATTTATTTTTCAAAGTTGTTAAGCCTTTATTTAAAGG
* * * * *
14683 AGCCTTATTTATTTTTCAAAGTCG-TAATCCTTTCTTTGAATG
1 AGCCTTATTTATTTTTCAAAGTTGTTAAGCCTTTATTTAAAGG
14725 AGCCTTATTTATTTTTCAAAGTTGT
1 AGCCTTATTTATTTTTCAAAGTTGT
14750 AAATAGAGGC
Statistics
Matches: 127, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
42 53 0.42
43 57 0.45
44 17 0.13
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (43 bp):
AGCCTTATTTATTTTTCAAAGTTGTTAAGCCTTTATTTAAAGG
Found at i:14817 original size:75 final size:74
Alignment explanation
Indices: 14684--14822 Score: 185
Period size: 75 Copynumber: 1.9 Consensus size: 74
14674 ATTTAGAGGA
* *
14684 GCCTTATTTATTTTTCAAAGTCGTAATCCTTTCTTTGAATGAGCCTTATTTATTTTTCA-AAGTT
1 GCCTTATTTATTTTTCAAAGTCGTAATCCTTTATTTGAA-GAGCCTTATTTATGTTTCAGAAGTT
14748 GTAAATAGAG
65 GTAAATAGAG
*
14758 GCCTTATTTATTTTTCAAAGTTGTTGAA-CCTTTATTT-AGAGAAGCCTTATTTATGTTTCAGAA
1 GCCTTATTTATTTTTCAAAGTCG-T-AATCCTTTATTTGA-AG-AGCCTTATTTATGTTTCAGAA
14821 GT
62 GT
14823 GGTTGAGCCT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
74 24 0.42
75 27 0.47
76 6 0.11
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (74 bp):
GCCTTATTTATTTTTCAAAGTCGTAATCCTTTATTTGAAGAGCCTTATTTATGTTTCAGAAGTTG
TAAATAGAG
Found at i:16735 original size:15 final size:14
Alignment explanation
Indices: 16701--16739 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
16691 TATTTTCAAC
*
16701 AATAATAATAAATAA
1 AATAA-AATAAAAAA
16716 AATAAAATAAAAAA
1 AATAAAATAAAAAA
16730 AGATAAAATA
1 A-ATAAAATA
16740 TTTTTGTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AATAAAATAAAAAA
Found at i:18532 original size:27 final size:27
Alignment explanation
Indices: 18502--18560 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
18492 TTCAATTCAC
18502 ATATATATAAAATTAAAAATAAAAATT
1 ATATATATAAAATTAAAAATAAAAATT
* *
18529 ATATGTATAAAATTAAAAATAAAATTT
1 ATATATATAAAATTAAAAATAAAAATT
18556 ATATA
1 ATATA
18561 AAAGTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
ATATATATAAAATTAAAAATAAAAATT
Found at i:18558 original size:21 final size:20
Alignment explanation
Indices: 18508--18558 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 20
18498 TCACATATAT
18508 ATAAAA-TTA-AAAATAAAA
1 ATAAAATTTATAAAATAAAA
* * *
18526 ATTATATGTATAAAATTAAAA
1 ATAAAATTTATAAAA-TAAAA
18547 ATAAAATTTATA
1 ATAAAATTTATA
18559 TAAAAGTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
18 4 0.17
19 2 0.08
20 4 0.17
21 14 0.58
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAATTTATAAAATAAAA
Found at i:23586 original size:52 final size:53
Alignment explanation
Indices: 23493--23649 Score: 214
Period size: 52 Copynumber: 3.0 Consensus size: 53
23483 TGGATAAGAA
* * *
23493 GACTTGCAAAAGAAGAATTCTAAGAGAA-AAAAGATTTTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGAAGAAAAGATTCTTAATAGGCAAGTTT
*
23545 GACTTGCAAGAGAAGAATTCTAA-A-AAGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGAAGAAA-AGATTCTTAATAGGCAAGTTT
* * *
23597 GACTTACAAGAGAAGAATTCTAAGAGAAGAAAA-ATTTTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGAAGAAAAGATTCTTAATAGGCAAGTTT
23649 G
1 G
23650 TATGGTTATA
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 80 0.86
53 1 0.01
54 6 0.06
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.27
Consensus pattern (53 bp):
GACTTGCAAGAGAAGAATTCTAAGAGAAGAAAAGATTCTTAATAGGCAAGTTT
Found at i:24253 original size:24 final size:24
Alignment explanation
Indices: 24185--24254 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
24175 TATCAGAGCT
* * **
24185 GAAGGTTCGAAACATGAGAAAAGTT
1 GAAGGTTCGAGACGTGA-AAAAGCC
* * *
24210 GAAGATTCAAGATGTGGAAAAAGCC
1 GAAGGTTCGAGACGT-GAAAAAGCC
24235 GAAGGTTCGAGACGTGAAAA
1 GAAGGTTCGAGACGTGAAAA
24255 GAGTTAAAAG
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
24 5 0.15
25 27 0.79
26 2 0.06
ACGTcount: A:0.43, C:0.10, G:0.30, T:0.17
Consensus pattern (24 bp):
GAAGGTTCGAGACGTGAAAAAGCC
Found at i:24268 original size:25 final size:25
Alignment explanation
Indices: 24239--24291 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
24229 AAAGCCGAAG
*
24239 GTTCGAGACGTGAAAAGAGTTAAAA
1 GTTCGAGACGTGAAAAGAGCTAAAA
* **
24264 GTTCGAGATGTGGGAAGAGCTAAAA
1 GTTCGAGACGTGAAAAGAGCTAAAA
24289 GTT
1 GTT
24292 TAAGATGTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.32, T:0.23
Consensus pattern (25 bp):
GTTCGAGACGTGAAAAGAGCTAAAA
Found at i:24297 original size:25 final size:25
Alignment explanation
Indices: 24253--24305 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
24243 GAGACGTGAA
* *
24253 AAGAGTTAAAAGTTCGAGATGTGGG
1 AAGAGCTAAAAGTTCAAGATGTGGG
*
24278 AAGAGCTAAAAGTTTAAGATGTGGG
1 AAGAGCTAAAAGTTCAAGATGTGGG
24303 AAG
1 AAG
24306 TGCATGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.34, T:0.23
Consensus pattern (25 bp):
AAGAGCTAAAAGTTCAAGATGTGGG
Found at i:24575 original size:22 final size:22
Alignment explanation
Indices: 24547--24589 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
24537 AAATCTCATA
*
24547 AGAGATTTGTTTAGGATTTGTT
1 AGAGATTTATTTAGGATTTGTT
*
24569 AGAGATTTATTTGGGATTTGT
1 AGAGATTTATTTAGGATTTGT
24590 CAGATATTGC
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:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (22 bp):
AGAGATTTATTTAGGATTTGTT
Found at i:24701 original size:52 final size:52
Alignment explanation
Indices: 24614--24722 Score: 141
Period size: 52 Copynumber: 2.1 Consensus size: 52
24604 TGGATAAGAA
* *
24614 GACTTGCAAATGAAGAATTATAAGAGAAAGAAGATTCTTAATAGGTAAGTTT
1 GACTTGCAAATGAAGAATTATAAAAGAAAGAAGATTCTTAATAGGCAAGTTT
* * *
24666 GACTTGCAAGA-GAAGAATTCTAAAAAGAAAG-AGATTTTTATTAGGCAAGTTT
1 GACTTGCAA-ATGAAGAATTAT-AAAAGAAAGAAGATTCTTAATAGGCAAGTTT
24718 GACTT
1 GACTT
24723 ACAGAATAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
52 41 0.82
53 9 0.18
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.29
Consensus pattern (52 bp):
GACTTGCAAATGAAGAATTATAAAAGAAAGAAGATTCTTAATAGGCAAGTTT
Found at i:24738 original size:52 final size:52
Alignment explanation
Indices: 24625--24769 Score: 143
Period size: 52 Copynumber: 2.8 Consensus size: 52
24615 ACTTGCAAAT
* * * *
24625 GAAGAATTAT-AAGAGAAAGAAGATTCTTAATAGGTAAGTTTGACTTGCAAGA
1 GAAGAATTCTAAAAAGAAAG-AGATTCTTAATAGGCAAGTTTGACTTACAAGA
* *
24677 GAAGAATTCTAAAAAGAAAGAGATTTTTATTAGGCAAGTTTGACTTAC-AGA
1 GAAGAATTCTAAAAAGAAAGAGATTCTTAATAGGCAAGTTTGACTTACAAGA
* * * * *
24728 -ATAGGGATTCTAAGAAGAGAGGGATTCTTAATGGGCAAGTTT
1 GA-A-GAATTCTAAAAAGAAAGAGATTCTTAATAGGCAAGTTT
24770 ATATGGTTAT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
50 1 0.01
51 4 0.05
52 64 0.83
53 8 0.10
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (52 bp):
GAAGAATTCTAAAAAGAAAGAGATTCTTAATAGGCAAGTTTGACTTACAAGA
Found at i:26215 original size:22 final size:23
Alignment explanation
Indices: 26138--26217 Score: 90
Period size: 25 Copynumber: 3.4 Consensus size: 23
26128 TATTCACATA
*
26138 TATATAAAATTAAAAATAAAAGTT
1 TATATAAAAATAAAAAT-AAAGTT
* *
26162 ATATATATAAATCAAAAATAAAATT
1 -TATATAAAAAT-AAAAATAAAGTT
*
26187 TATATAAAAATAAAAATTAAGTT
1 TATATAAAAATAAAAATAAAGTT
26210 TA-ATAAAA
1 TATATAAAA
26218 TATATATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
22 6 0.12
23 12 0.25
24 10 0.21
25 14 0.29
26 6 0.12
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.33
Consensus pattern (23 bp):
TATATAAAAATAAAAATAAAGTT
Found at i:27240 original size:3 final size:3
Alignment explanation
Indices: 27232--27265 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
27222 TAGAACAAAA
27232 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
27266 GAGCTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:30954 original size:33 final size:33
Alignment explanation
Indices: 30894--30964 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
30884 AATTGACATT
** * *
30894 TGCATAGCATGCATTGCATTTCTAAATGTTTAG
1 TGCATAGCATGCATTGCATTTAAAAATGTCTAA
30927 TGCATAGCATGCATTGCATTTAAAAATGTCTAA
1 TGCATAGCATGCATTGCATTTAAAAATGTCTAA
30960 TGCAT
1 TGCAT
30965 GAAGTAGGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (33 bp):
TGCATAGCATGCATTGCATTTAAAAATGTCTAA
Done.