Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168393.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_61, 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: 142147
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
File 5 of 5
Found at i:131939 original size:17 final size:16
Alignment explanation
Indices: 131917--131956 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
131907 AGTAAAACAA
*
131917 AAATAAAAATAAAATT
1 AAATAAAAAGAAAATT
*
131933 AAGATAAAAAGAATATT
1 AA-ATAAAAAGAAAATT
131950 AAATAAA
1 AAATAAA
131957 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATAAAAAGAAAATT
Found at i:133001 original size:3 final size:3
Alignment explanation
Indices: 132995--133116 Score: 51
Period size: 3 Copynumber: 39.3 Consensus size: 3
132985 AACAAAAAAA
132995 AAT AAT AAT -AT AAT AAT AAT AAAT ATAT AACT ATAT ACAT -AT AA-
1 AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AA-T A-AT A-AT AAT AAT
* * * * *
133039 ATCT AAT -CT AAT AAT AAA AAA AAT AA- ATAT ATAT ATT AAT ACAT AAT
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT A-AT AAT
133086 AAT AAT AAT AAAT AAT AA- AAT ACAT AA- AAT A
1 AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT A
133117 CAAAAGAAAC
Statistics
Matches: 94, Mismatches: 9, Indels: 32
0.70 0.07 0.24
Matches are distributed among these distances:
2 11 0.12
3 55 0.59
4 27 0.29
5 1 0.01
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:133079 original size:16 final size:16
Alignment explanation
Indices: 133048--133113 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
133038 AATCTAATCT
* *
133048 AATAATAAAAAAAATA
1 AATAATAATAATAATA
*
133064 AAT-ATATATATTAATA
1 AATAATA-ATAATAATA
*
133080 CATAATAATAATAATA
1 AATAATAATAATAATA
133096 AATAATAA-AATACATA
1 AATAATAATAATA-ATA
133112 AA
1 AA
133114 ATACAAAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
15 7 0.17
16 31 0.76
17 3 0.07
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:133113 original size:48 final size:44
Alignment explanation
Indices: 132993--133113 Score: 111
Period size: 48 Copynumber: 2.6 Consensus size: 44
132983 AAAACAAAAA
132993 AAAATAATAAT-ATAATAATAATAAATATATAACTATATACATAT
1 AAAATAATAATAATAA-AATAATAAATATATAACTATATACATAT
* * *
133037 AAATCTAATCTAATAATAAAAAAAATAAATATATATATTA-ATACATAAT
1 AAA-ATAA--TAATAAT-AAAATAATAAATATATA-ACTATATACAT-AT
133086 AATAATAATAAATAATAAAATACATAAA
1 AA-AATAAT-AATAATAAAATA-ATAAA
133114 ATACAAAAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
44 3 0.05
45 3 0.05
47 10 0.16
48 33 0.53
49 12 0.19
50 1 0.02
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (44 bp):
AAAATAATAATAATAAAATAATAAATATATAACTATATACATAT
Found at i:133324 original size:9 final size:8
Alignment explanation
Indices: 133306--133335 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
133296 ACGTTGTCAC
133306 TTTTTGTT
1 TTTTTGTT
133314 TTTTTGTT
1 TTTTTGTT
*
133322 TTTTTATT
1 TTTTTGTT
133330 TTTTTG
1 TTTTTG
133336 ACCAAAGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (8 bp):
TTTTTGTT
Found at i:133399 original size:41 final size:41
Alignment explanation
Indices: 133342--133815 Score: 740
Period size: 41 Copynumber: 11.5 Consensus size: 41
133332 TTTGACCAAA
* * *
133342 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
133383 GCTCCTCTAAACAGAGGCACCACAACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
* *
133425 GCTCCTCTAAATAGAGGCACCACGACTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
133466 GCTCCTCTAAACAGAGGCACCACGATTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
133507 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTG-AAAAGTAAATT
133549 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
133591 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
133632 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
133673 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
133714 GCTCCTCTAAACAGAGGCA--ACGAAACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG--ACTTTGAAAAGTAAATT
133755 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
133797 GCTCCTCTAAACAGAGGCA
1 GCTCCTCTAAACAGAGGCA
133816 ACGAACTTGG
Statistics
Matches: 403, Mismatches: 19, Indels: 21
0.91 0.04 0.05
Matches are distributed among these distances:
39 5 0.01
40 1 0.00
41 249 0.62
42 142 0.35
43 4 0.01
44 2 0.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:133481 original size:83 final size:84
Alignment explanation
Indices: 133342--133835 Score: 717
Period size: 83 Copynumber: 6.0 Consensus size: 84
133332 TTTGACCAAA
* * *
133342 GCTCCTCTAAACAGAGGCTCAACGACTTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
133406 AACTTTGGAAAAGTAAATT
66 AACTTTGGAAAAGTAAATT
*
133425 GCTCCTCTAAATAGAGGCACCACGAC-TTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
* *
133489 GA-TTTTGAAAAGTAAATT
66 AACTTTGGAAAAGTAAATT
* *
133507 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACC
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACC
* *
133570 ACGACTTTGAAAAAGTAAATT
64 ACAACTTTGGAAAAGTAAATT
*
133591 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGTACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
* *
133655 GACTTT-GAAAAATAAATT
66 AACTTTGGAAAAGTAAATT
*
133673 GCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGC-ACCA
133737 -AACTTTGG-AAAGTAAATT
65 CAACTTTGGAAAAGTAAATT
*
133755 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCA--AC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
133818 GAAC-TTGGAAAGGTAAAT
66 -AACTTTGGAAAAGTAAAT
133836 ACTCCTAGAC
Statistics
Matches: 375, Mismatches: 22, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
80 3 0.01
81 5 0.01
82 159 0.42
83 167 0.45
84 38 0.10
85 1 0.00
86 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (84 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
AACTTTGGAAAAGTAAATT
Found at i:133565 original size:124 final size:123
Alignment explanation
Indices: 133342--133835 Score: 716
Period size: 124 Copynumber: 4.0 Consensus size: 123
133332 TTTGACCAAA
* * * *
133342 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
* * *
133407 ACTTTGGAAAAGTAAATTGCTCCTCTAAATAGAGGCACCACGAC-TTGGAAAAGTAAATT
64 ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
133466 GCTCCTCTAAACAGAGGCACCACGATTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAAC-G-
*
133531 ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
64 ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
133591 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG--CAACG
133656 ACTTTG-AAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATT
64 ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
133714 GCTCCTCTAAACAGAGGCA--ACGAAACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGGCACCACG--ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--A
* *
133777 CGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGAAC-TTGGAAAGGTAAAT
62 CGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAAT
133836 ACTCCTAGAC
Statistics
Matches: 342, Mismatches: 16, Indels: 25
0.89 0.04 0.07
Matches are distributed among these distances:
121 4 0.01
122 9 0.03
123 81 0.24
124 167 0.49
125 77 0.23
126 1 0.00
127 3 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (123 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
TTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
Found at i:135088 original size:17 final size:16
Alignment explanation
Indices: 135057--135100 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
135047 TGAATCTCCC
*
135057 TTTTTCATTTTCTTAG
1 TTTTTCTTTTTCTTAG
*
135073 TTTTTCTTTTTCCTTAT
1 TTTTTCTTTTT-CTTAG
*
135090 TTTTTGTTTTT
1 TTTTTCTTTTT
135101 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.07, C:0.11, G:0.05, T:0.77
Consensus pattern (16 bp):
TTTTTCTTTTTCTTAG
Found at i:139126 original size:60 final size:60
Alignment explanation
Indices: 138998--139234 Score: 293
Period size: 60 Copynumber: 4.0 Consensus size: 60
138988 TCTTGTGTAG
* * * *
138998 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTGGAAA-TTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTGAAATTTTGATTTTCAA
*
139055 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTGAAATTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTGAAATTTTGATTTTCAA
* * *** *
139115 GGAAAATTGATACTTCCAACTTTTCC-CTAAAAATATTTTTTCAAAAATTTTGGTTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAATTTTTTTTTTGAAATTTTGATTTTCAA
* *
139175 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAAATTTGATTTT
1 GGAAAATTGATACTTTCAACTTTT-CCTCAAAA-ATTTTTTTTTT-GAAATTTTGATTTT
139235 TATTTGAAGA
Statistics
Matches: 152, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
57 32 0.21
58 11 0.07
59 4 0.03
60 80 0.53
61 6 0.04
62 8 0.05
63 11 0.07
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTGAAATTTTGATTTTCAA
Found at i:139264 original size:15 final size:13
Alignment explanation
Indices: 139244--139306 Score: 58
Period size: 13 Copynumber: 4.7 Consensus size: 13
139234 TTATTTGAAG
139244 AAAATAGAATAATAA
1 AAAATA-AA-AATAA
*
139259 AAAATATAAATAA
1 AAAATAAAAATAA
139272 AAAATAAAAA-AA
1 AAAATAAAAATAA
*
139284 GTAAAACAAAAAT-A
1 --AAAATAAAAATAA
139298 AAAATAAAA
1 AAAATAAAA
139307 TTAAGATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
12 10 0.24
13 14 0.34
14 11 0.27
15 6 0.15
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.16
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:139273 original size:12 final size:12
Alignment explanation
Indices: 139258--139318 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 12
139248 TAGAATAATA
139258 AAAAATATAAAT
1 AAAAATATAAAT
139270 AAAAA-ATAAA-
1 AAAAATATAAAT
* *
139280 AAAAGTA-AAAC
1 AAAAATATAAAT
*
139291 AAAAATAAAAAT
1 AAAAATATAAAT
139303 -AAAAT-TAAGAT
1 AAAAATATAA-AT
139314 AAAAA
1 AAAAA
139319 GAATATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
10 9 0.22
11 19 0.47
12 12 0.30
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.16
Consensus pattern (12 bp):
AAAAATATAAAT
Found at i:139278 original size:11 final size:10
Alignment explanation
Indices: 139251--139307 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 10
139241 AAGAAAATAG
139251 AATAATAAAAA
1 AATAA-AAAAA
139262 ATATAAATAAAA
1 A-ATAAA-AAAA
139274 AAT-AAAAAA
1 AATAAAAAAA
*
139283 AGTAAAACAAA
1 AATAAAA-AAA
139294 AATAAAAATAA
1 AATAAAAA-AA
139305 AAT
1 AAT
139308 TAAGATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 6 0.15
10 6 0.15
11 18 0.46
12 9 0.23
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:139279 original size:20 final size:20
Alignment explanation
Indices: 139254--139301 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
139244 AAAATAGAAT
139254 AATAAAAAATA-TAAATA-AAA
1 AATAAAAAA-AGTAAA-ACAAA
139274 AATAAAAAAAGTAAAACAAA
1 AATAAAAAAAGTAAAACAAA
139294 AATAAAAA
1 AATAAAAA
139302 TAAAATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (20 bp):
AATAAAAAAAGTAAAACAAA
Found at i:139315 original size:17 final size:16
Alignment explanation
Indices: 139293--139332 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
139283 AGTAAAACAA
*
139293 AAATAAAAATAAAATT
1 AAATAAAAAGAAAATT
*
139309 AAGATAAAAAGAATATT
1 AA-ATAAAAAGAAAATT
139326 AAATAAA
1 AAATAAA
139333 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATAAAAAGAAAATT
Found at i:139920 original size:25 final size:25
Alignment explanation
Indices: 139874--139927 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
139864 AATCTGGAAA
*
139874 TTTCCCAGAAATTTCTAGAAAAATT
1 TTTCCCAAAAATTTCTAGAAAAATT
*
139899 TTTCGCCAAAAATTTCTA-AAAATTT
1 TTTC-CCAAAAATTTCTAGAAAAATT
139924 TTTC
1 TTTC
139928 TCACTCCCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.41
Consensus pattern (25 bp):
TTTCCCAAAAATTTCTAGAAAAATT
Found at i:140369 original size:3 final size:3
Alignment explanation
Indices: 140363--140487 Score: 57
Period size: 3 Copynumber: 40.3 Consensus size: 3
140353 AAAACAAAAA
140363 AAT AAT AAT AAT -AT AAT AAT AAT AAAT ATAT AACT ATAT ACAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AA-T A-AT A-AT AAT
* * * * *
140408 AA- ATCT AAT -CT AAT AAT AAA AAA AAT AA- ATAT ATAT ATT AAT ACAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT A-AT
140454 AAT AAT AAT AAT AAAT AAT AA- AAT ACAT AA- AAT A
1 AAT AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT A
140488 CAGGATAAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
2 11 0.11
3 58 0.60
4 27 0.28
5 1 0.01
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:140450 original size:16 final size:16
Alignment explanation
Indices: 140419--140484 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
140409 AATCTAATCT
* *
140419 AATAATAAAAAAAATA
1 AATAATAATAATAATA
*
140435 AAT-ATATATATTAATA
1 AATAATA-ATAATAATA
*
140451 CATAATAATAATAATA
1 AATAATAATAATAATA
140467 AATAATAA-AATACATA
1 AATAATAATAATA-ATA
140483 AA
1 AA
140485 ATACAGGATA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
15 7 0.17
16 31 0.76
17 3 0.07
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:140484 original size:48 final size:45
Alignment explanation
Indices: 140363--140484 Score: 117
Period size: 48 Copynumber: 2.6 Consensus size: 45
140353 AAAACAAAAA
140363 AATAATAATAAT-ATAATAATAATAAATATATAACTATATACATAT
1 AATAATAATAATAATAA-AATAATAAATATATAACTATATACATAT
*
140408 AAATCTAATCTAATAATAA-AAAA-AATAAATATATATATTA-ATACATAAT
1 -AA--TAA--TAATAATAATAAAATAATAAATATATA-ACTATATACAT-AT
140457 AATAATAATAAATAATAAAATACATAAA
1 AATAATAAT-AATAATAAAATA-ATAAA
140485 ATACAGGATA
Statistics
Matches: 64, Mismatches: 1, Indels: 20
0.75 0.01 0.24
Matches are distributed among these distances:
44 4 0.06
45 5 0.08
46 9 0.14
47 1 0.02
48 28 0.44
49 7 0.11
50 9 0.14
51 1 0.02
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (45 bp):
AATAATAATAATAATAAAATAATAAATATATAACTATATACATAT
Found at i:141854 original size:11 final size:10
Alignment explanation
Indices: 141805--141874 Score: 54
Period size: 10 Copynumber: 6.8 Consensus size: 10
141795 AATAACCTCT
141805 TAAATTATAATA
1 TAAATTAT--TA
* *
141817 TATATTAATA
1 TAAATTATTA
141827 TAAATTATT-
1 TAAATTATTA
141836 T-AATTATTA
1 TAAATTATTA
*
141845 TAACTATATTAA
1 TAAAT-TATT-A
141857 TAAATTATTA
1 TAAATTATTA
*
141867 TAATTTAT
1 TAAATTAT
141875 CAATTTAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
8 7 0.15
9 2 0.04
10 19 0.40
11 8 0.17
12 11 0.23
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (10 bp):
TAAATTATTA
Found at i:141860 original size:30 final size:34
Alignment explanation
Indices: 141808--141871 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 34
141798 AACCTCTTAA
141808 ATTATAATATATATTAATATAAATTATT-TAATT
1 ATTATAATATATATTAATATAAATTATTATAATT
*
141841 ATTATAA-CTATATT-A-ATAAATTATTATAATT
1 ATTATAATATATATTAATATAAATTATTATAATT
141872 TATCAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 10 0.34
31 6 0.21
32 6 0.21
33 7 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (34 bp):
ATTATAATATATATTAATATAAATTATTATAATT
Found at i:141933 original size:34 final size:33
Alignment explanation
Indices: 141850--141937 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 33
141840 TATTATAACT
141850 ATATTAA-TAAATT-ATTATAATTTATCAATTTA
1 ATATTAACT-AATTAATTATAATTTATCAATTTA
141882 ATATTAAAC-AATATAATTATAATTTAAT-AATTTA
1 ATATT-AACTAAT-TAATTATAATTT-ATCAATTTA
*
141916 TTATTAACTTAATTAATTATAA
1 ATATTAAC-TAATTAATTATAA
141938 AATTAGTATA
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
32 8 0.17
33 6 0.12
34 29 0.60
35 5 0.10
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (33 bp):
ATATTAACTAATTAATTATAATTTATCAATTTA
Done.