Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167948.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_209, 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: 50768
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:7021 original size:11 final size:11
Alignment explanation
Indices: 6997--7031 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6987 TGGTGATATG
* *
6997 ATATATAAATA
1 ATATAAAAAAA
7008 ATATAAAAAAA
1 ATATAAAAAAA
7019 ATATAAAAAAA
1 ATATAAAAAAA
7030 AT
1 AT
7032 GTTTTGTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
ATATAAAAAAA
Found at i:8515 original size:13 final size:13
Alignment explanation
Indices: 8497--8521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8487 GTATGTACAT
8497 AGATTTGACTTAC
1 AGATTTGACTTAC
8510 AGATTTGACTTA
1 AGATTTGACTTA
8522 TTAGTTATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (13 bp):
AGATTTGACTTAC
Found at i:9787 original size:545 final size:546
Alignment explanation
Indices: 8754--10389 Score: 2888
Period size: 545 Copynumber: 3.0 Consensus size: 546
8744 AATCCAAATT
* * *
8754 AAGTATGACTACAACA-ATAATATACAATTTTCTTCTCTCCTGGTTTTAACTATCTGAAAGTAAT
1 AAGTATGACTACAA-ATATAATACACAATTTTCTTCTCTGCTGGTTTTAACTATCTGAAAGTCAT
* *
8818 CGTAACGGTAACAACATCACC-TTTTCTTACACAACTACCATTCTA--TTTTTATAGTATTTCTG
65 TGTAACGGTAACAATATCACCTTTTTCTTACACAACTACCATTCTACTTTTTTATAGTATTTCTG
* *
8880 TCAACTTGATTCCCATATATTTATACATTAAAATGGTCAATCAACTTTGTATAAAGTTCTTTTGC
130 TCAACTTGATTCCCATATATTTATACATTAAAACGGTCAATCAACTTTGTACAAAGTTCTTTTGC
8945 AACGGACAAACGAGTAAAACCAAAGGGGCTTGTGTTAGCTGGCAGGTCATATGTAGACCCAAGTT
195 AACGGACAAACGAGTAAAACCAAAGGGGCTTGTGTTAGCTGGCAGGTCATATGTAGACCCAAGTT
9010 GGAATATATTAGCGTCTGGAATCAAGCCTGTATACTTAGATTCTTATGGTCTATTTTCACGCAAG
260 GGAATATATTAGCGTCTGGAATCAAGCCTGTATACTTAGATTCTTATGGTCTATTTTCACGCAAG
*
9075 CAGGGTTTTTGTGGATTGCATAGGTGAATAGGTATATACTAAAAGGTAGAAGTATATGGGAAATA
325 CAGGGTTTTTGTGGATTGCATAGGTGAATAGGTATATGCTAAAAGGTAGAAGTATATGGGAAATA
*
9140 CCCGTTACTCCA-AGCCACAGCTAGGGAATTAAAAAGCTACTTCAAATGAGAAGATTAGCATCTA
390 CCCGTTACT-CAGAGCCACAGCTAGGGAATTAAAAAGCTACTTCAAATGAGAAGATTAGCTTCTA
9204 AATTCTTAACGTAGACAAAGAATGAAGTGATTTGGCACAATAAGGAACCGAGCAACTCTATTGCA
454 AATTCTTAACGTAGACAAAGAATGAAGTGATTTGGCACAATAAGGAACCGAGCAACTCTATTGCA
9269 AGTGTCTATGATGAATTAAGGGTAAGAC
519 AGTGTCTATGATGAATTAAGGGTAAGAC
*
9297 AAGTATGACTACAAATATAATACACAATTTTTTTCTCTGCTGGTTTTAACTATCTGAAAGTCATT
1 AAGTATGACTACAAATATAATACACAATTTTCTTCTCTGCTGGTTTTAACTATCTGAAAGTCATT
*
9362 GTAACGGTAACAATATCACCTTTTTCTTACACAACTCCCATTCTACTTTTTTATAGTATTTCTGT
66 GTAACGGTAACAATATCACCTTTTTCTTACACAACTACCATTCTACTTTTTTATAGTATTTCTGT
* *
9427 CAACTTGATTCCCATATATTTATACATTAAAAGGGTCAATCAACTGTGTACAAAGTTCTTTTGCA
131 CAACTTGATTCCCATATATTTATACATTAAAACGGTCAATCAACTTTGTACAAAGTTCTTTTGCA
*
9492 ACGGACAAACGAGTAAAACCAAAGGGGCTTGCGTTAGCTGGCAGGTCATATGTAGACCCAAGTTG
196 ACGGACAAACGAGTAAAACCAAAGGGGCTTGTGTTAGCTGGCAGGTCATATGTAGACCCAAGTTG
* * *
9557 GAATATATTAGCATCTGGAATCAAGCCTGTATACTT-GATTCTTATGTTCTATATTCACGCAAGC
261 GAATATATTAGCGTCTGGAATCAAGCCTGTATACTTAGATTCTTATGGTCTATTTTCACGCAAGC
*
9621 AGGGTTTTTGTGGATTGCATAGTTGAATAGGTATATGCTAAAAGGTAGAAGTATATGGGAAATAC
326 AGGGTTTTTGTGGATTGCATAGGTGAATAGGTATATGCTAAAAGGTAGAAGTATATGGGAAATAC
* *
9686 CCGTTACTCAGAGCCACGGCTAGGGAATTAAAAAGCTACTTCAAATGAGGAGATTAGCTTCTAAA
391 CCGTTACTCAGAGCCACAGCTAGGGAATTAAAAAGCTACTTCAAATGAGAAGATTAGCTTCTAAA
9751 TTCTTAACGTAGACAAAGAATGAAGTGATTTGGCACAATAAGGAACCGAGCAACTCTATTGCAAG
456 TTCTTAACGTAGACAAAGAATGAAGTGATTTGGCACAATAAGGAACCGAGCAACTCTATTGCAAG
9816 TGTCTATGATGAATTAAGGGTAAGAC
521 TGTCTATGATGAATTAAGGGTAAGAC
* *
9842 AAGTATGAGTACAACTATAATACACAATTTTCTTCTCTGCTGGTTTTAACTATCTGAAAGTCATT
1 AAGTATGACTACAAATATAATACACAATTTTCTTCTCTGCTGGTTTTAACTATCTGAAAGTCATT
9907 GTAACGGTAACAATATCACCTTTTTCTTACACAACTACCATTCTACTTTTTTATAGTATTTCTGT
66 GTAACGGTAACAATATCACCTTTTTCTTACACAACTACCATTCTACTTTTTTATAGTATTTCTGT
9972 CAACTTGATTCCCATATATTTATACATTAAAACGGTCAATCAACTTTGTACAAAGTTCTTTTGCA
131 CAACTTGATTCCCATATATTTATACATTAAAACGGTCAATCAACTTTGTACAAAGTTCTTTTGCA
* *
10037 ACGGAAAAACGAGTAAAACCAAAGTGGCTTGTGTTAGCTGGCAGGTCATATGTAGACCCAAGTTG
196 ACGGACAAACGAGTAAAACCAAAGGGGCTTGTGTTAGCTGGCAGGTCATATGTAGACCCAAGTTG
* * **
10102 GAATATATTAGCGTCTGGAATCAAGCCTGTATACTTAGATTCTTGTGGTCTATTTTCCCGCAAAA
261 GAATATATTAGCGTCTGGAATCAAGCCTGTATACTTAGATTCTTATGGTCTATTTTCACGCAAGC
* * * *
10167 AGGGTTTTTGTAGATTGCATAGGTGAAAAGGTATATGCTAAAAGGTAGAAGCATATGGGAAATAT
326 AGGGTTTTTGTGGATTGCATAGGTGAATAGGTATATGCTAAAAGGTAGAAGTATATGGGAAATAC
*
10232 CCGTTACTCCGAGCCACAGCTAGGGAATTAAAAAGCTACTTCAAATGAGAAGATTAGCTTCTAAA
391 CCGTTACTCAGAGCCACAGCTAGGGAATTAAAAAGCTACTTCAAATGAGAAGATTAGCTTCTAAA
* * *
10297 TTCTTAAAGTAGACAAAGAATGAAGTGATTTGGCACAATAAGGAACCGAACTACTCTATTGCAAG
456 TTCTTAACGTAGACAAAGAATGAAGTGATTTGGCACAATAAGGAACCGAGCAACTCTATTGCAAG
10362 TGTCTATGATGAATTAAGGGTAAGAC
521 TGTCTATGATGAATTAAGGGTAAGAC
10388 AA
1 AA
10390 TGTAACGTCT
Statistics
Matches: 1041, Mismatches: 46, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
542 1 0.00
543 77 0.07
544 25 0.02
545 525 0.50
546 413 0.40
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (546 bp):
AAGTATGACTACAAATATAATACACAATTTTCTTCTCTGCTGGTTTTAACTATCTGAAAGTCATT
GTAACGGTAACAATATCACCTTTTTCTTACACAACTACCATTCTACTTTTTTATAGTATTTCTGT
CAACTTGATTCCCATATATTTATACATTAAAACGGTCAATCAACTTTGTACAAAGTTCTTTTGCA
ACGGACAAACGAGTAAAACCAAAGGGGCTTGTGTTAGCTGGCAGGTCATATGTAGACCCAAGTTG
GAATATATTAGCGTCTGGAATCAAGCCTGTATACTTAGATTCTTATGGTCTATTTTCACGCAAGC
AGGGTTTTTGTGGATTGCATAGGTGAATAGGTATATGCTAAAAGGTAGAAGTATATGGGAAATAC
CCGTTACTCAGAGCCACAGCTAGGGAATTAAAAAGCTACTTCAAATGAGAAGATTAGCTTCTAAA
TTCTTAACGTAGACAAAGAATGAAGTGATTTGGCACAATAAGGAACCGAGCAACTCTATTGCAAG
TGTCTATGATGAATTAAGGGTAAGAC
Found at i:11193 original size:10 final size:9
Alignment explanation
Indices: 11172--11204 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
11162 ATCCCCTACC
11172 AAAAA-AAA
1 AAAAACAAA
11180 AAAAACAGAA
1 AAAAACA-AA
11190 AAAAACAAA
1 AAAAACAAA
11199 AAAAAC
1 AAAAAC
11205 CCAGAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 5 0.22
9 9 0.39
10 9 0.39
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAACAAA
Found at i:12731 original size:34 final size:34
Alignment explanation
Indices: 12687--12761 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
12677 ATAAATTATG
* * *
12687 ATATATAATTTTCATATAAAACATGATACAAAAT
1 ATATAAAATTTTAATATAAAACATGATAAAAAAT
*** *
12721 ATATAAAATTTTAATATTTTACATTATAAAAAAT
1 ATATAAAATTTTAATATAAAACATGATAAAAAAT
12755 ATATAAA
1 ATATAAA
12762 TGATCAAATC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (34 bp):
ATATAAAATTTTAATATAAAACATGATAAAAAAT
Found at i:17979 original size:19 final size:19
Alignment explanation
Indices: 17907--17977 Score: 69
Period size: 18 Copynumber: 3.8 Consensus size: 19
17897 GCGTTTCGTC
*
17907 TAAGGTTTAAGGTTTCAAT
1 TAAGGTTTAAGGTTTCACT
17926 TAAGG-TT-AGGTTCTCAC-
1 TAAGGTTTAAGGTT-TCACT
*
17943 TAAGGGTTTTAGGGTTT-ACT
1 TAA-GG-TTTAAGGTTTCACT
17963 TAAGGTTTAAGGTTT
1 TAAGGTTTAAGGTTT
17978 TATCTAGGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
17 8 0.19
18 16 0.37
19 9 0.21
20 6 0.14
21 4 0.09
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (19 bp):
TAAGGTTTAAGGTTTCACT
Found at i:18119 original size:13 final size:13
Alignment explanation
Indices: 18101--18142 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
18091 GTTTTGTTTA
18101 AAGGTTTCCTTTT
1 AAGGTTTCCTTTT
*
18114 AGGGTTTCAC-TTT
1 AAGGTTTC-CTTTT
*
18127 AAGGTTTCATTTT
1 AAGGTTTCCTTTT
18140 AAG
1 AAG
18143 ATTTGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 23 0.96
14 1 0.04
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (13 bp):
AAGGTTTCCTTTT
Found at i:18153 original size:26 final size:26
Alignment explanation
Indices: 18093--18153 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 26
18083 CTTTAAGGGT
* * * *
18093 TTTG-TTTAAAGGTTTCCTTTTAGGG
1 TTTGATTTTAAGGTTTCATTTTAAGA
* *
18118 TTTCACTTTAAGGTTTCATTTTAAGA
1 TTTGATTTTAAGGTTTCATTTTAAGA
18144 TTTGATTTTA
1 TTTGATTTTA
18154 GGATTCTACA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.21, C:0.08, G:0.16, T:0.54
Consensus pattern (26 bp):
TTTGATTTTAAGGTTTCATTTTAAGA
Found at i:19093 original size:37 final size:38
Alignment explanation
Indices: 19041--19114 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 38
19031 CTTTAACCTT
* * *
19041 TGCAAACAACATGAAGAAAAAGGAAACTAATCTATCAA
1 TGCAAACAAAATGAAGAAAAAGGAAACCAAACTATCAA
*
19079 TGCAAA-AAAATGAAGAATAAGGAAACCAAACTATCA
1 TGCAAACAAAATGAAGAAAAAGGAAACCAAACTATCA
19115 GTACCAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 26 0.81
38 6 0.19
ACGTcount: A:0.57, C:0.15, G:0.14, T:0.15
Consensus pattern (38 bp):
TGCAAACAAAATGAAGAAAAAGGAAACCAAACTATCAA
Found at i:19124 original size:37 final size:37
Alignment explanation
Indices: 19051--19124 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
19041 TGCAAACAAC
* * *
19051 ATGAAGAAAAAGGAAACTAATCTATCAATGCAAAAAA
1 ATGAAGAAAAAGGAAACCAAACTATCAATACAAAAAA
* * *
19088 ATGAAGAATAAGGAAACCAAACTATCAGTACCAAAAA
1 ATGAAGAAAAAGGAAACCAAACTATCAATACAAAAAA
19125 TCATGGATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.15
Consensus pattern (37 bp):
ATGAAGAAAAAGGAAACCAAACTATCAATACAAAAAA
Found at i:19286 original size:13 final size:13
Alignment explanation
Indices: 19268--19302 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
19258 TGGACTTGTC
*
19268 TTTTTTTTTTTTG
1 TTTTTTTTTTTAG
*
19281 TTTTTTCTTTTAG
1 TTTTTTTTTTTAG
19294 TTTTTTTTT
1 TTTTTTTTT
19303 GTCTTACGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.03, C:0.03, G:0.06, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTTAG
Found at i:20123 original size:18 final size:17
Alignment explanation
Indices: 20102--20165 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
20092 CAAACTTTTT
*
20102 TTTTACTTAATTTTTATA
1 TTTTA-TTATTTTTTATA
20120 TTTTATATTATTTTGTTATA
1 -TTT-TATTATTTT-TTATA
*
20140 -TTTAATATTTTTTATA
1 TTTTATTATTTTTTATA
20156 TTTT-TTATTT
1 TTTTATTATTT
20166 GTTTTTTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 10 0.26
17 11 0.28
18 2 0.05
19 9 0.23
20 7 0.18
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTATTATTTTTTATA
Found at i:20138 original size:20 final size:19
Alignment explanation
Indices: 20112--20178 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 19
20102 TTTTACTTAA
20112 TTTTTATATTTTATATTAT
1 TTTTTATATTTTATATTAT
20131 TTTGTTATA-TTTA-A-TAT
1 TTT-TTATATTTTATATTAT
* *
20148 TTTTTATATTTTTTATTTGT
1 TTTTTATATTTTATA-TTAT
20168 TTTTTATATTT
1 TTTTTATATTT
20179 AATAATCAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
16 5 0.12
17 9 0.22
18 2 0.05
19 7 0.17
20 18 0.44
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTTATATTTTATATTAT
Found at i:20152 original size:36 final size:36
Alignment explanation
Indices: 20112--20182 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
20102 TTTTACTTAA
20112 TTTTTATATTTTATATTAT-TTTGTTATATTTAATAT
1 TTTTTATATTTTATATT-TGTTTGTTATATTTAATAT
* *
20148 TTTTTATATTTTTTATTTGTTTTTTATATTTAATA
1 TTTTTATATTTTATATTTGTTTGTTATATTTAATA
20183 ATCAACAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 1 0.03
36 31 0.97
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (36 bp):
TTTTTATATTTTATATTTGTTTGTTATATTTAATAT
Found at i:20158 original size:9 final size:9
Alignment explanation
Indices: 20112--20178 Score: 57
Period size: 9 Copynumber: 7.2 Consensus size: 9
20102 TTTTACTTAA
20112 TTTTTATAT
1 TTTTTATAT
*
20121 TTTATATTAT
1 TTTTTA-TAT
20131 TTTGTTATA-
1 TTT-TTATAT
*
20140 -TTTAATAT
1 TTTTTATAT
20148 TTTTTATAT
1 TTTTTATAT
*
20157 TTTTTATTTGT
1 TTTTTA--TAT
20168 TTTTTATAT
1 TTTTTATAT
20177 TT
1 TT
20179 AATAATCAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
7 4 0.09
8 2 0.04
9 22 0.48
10 8 0.17
11 10 0.22
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (9 bp):
TTTTTATAT
Found at i:21485 original size:19 final size:19
Alignment explanation
Indices: 21433--21493 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
21423 CTCGAAATTA
*
21433 ATAAAATA--ATTTATAAT
1 ATAAAATATTATTTTTAAT
*
21450 ATAAAAATATTACTTTTAAT
1 AT-AAAATATTATTTTTAAT
*
21470 ATAAAGTATTATTTTTAAT
1 ATAAAATATTATTTTTAAT
21489 ATAAA
1 ATAAA
21494 TTTAAGATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 2 0.05
18 6 0.16
19 20 0.54
20 9 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
ATAAAATATTATTTTTAAT
Found at i:21536 original size:28 final size:27
Alignment explanation
Indices: 21468--21536 Score: 63
Period size: 28 Copynumber: 2.5 Consensus size: 27
21458 ATTACTTTTA
21468 ATATAAAGTAT-TATTTTTAATATAAAT
1 ATATAAA-TATATATTTTTAATATAAAT
* *
21495 -T-TAAGATAAAATATTTTTAAATGTAAAT
1 ATATAA-AT-ATATATTTTT-AATATAAAT
21523 ATATAAATATATAT
1 ATATAAATATATAT
21537 AATATTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
25 4 0.12
26 3 0.09
27 7 0.21
28 13 0.39
29 3 0.09
30 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (27 bp):
ATATAAATATATATTTTTAATATAAAT
Found at i:27251 original size:18 final size:17
Alignment explanation
Indices: 27225--27258 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
27215 AGAAAAAGCC
*
27225 AAAAAAAAATAGAGAGA
1 AAAAAAAAAAAGAGAGA
27242 AAAAAGAAAAAAGAGAG
1 AAAAA-AAAAAAGAGAG
27259 TTGGTTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAAAGAGAGA
Found at i:31669 original size:54 final size:54
Alignment explanation
Indices: 31603--31933 Score: 257
Period size: 55 Copynumber: 6.1 Consensus size: 54
31593 TAATTTTAAA
* *
31603 AAAAATTAATATTTCAACTTTTTTCTCAAAATATTGAAATCATTTTCTTTTAAGG
1 AAAAATTAATATTTCAACTTTTTTCTCAAAATTTTGAAATTATTTT-TTTTAAGG
* * * *
31658 AAAGATT-ATATTTCAACTATTTTT-TC-TACTCTTTG-AATTATTTTTTTTTTTAGG
1 AAAAATTAATATTTCAACT-TTTTTCTCAAAAT-TTTGAAATTA--TTTTTTTTAAGG
* * * * * * * *
31712 AAAGATTGATACTTAAACTTTTTCCTCAAAAATATGAAATTATTTTTATTTAAGA
1 AAAAATTAATATTTCAACTTTTTTCTCAAAATTTTGAAATTATTTTT-TTTAAGG
* ** ** *
31767 AAAAATTAATATTTTAAC-TTTTTCTTTATTTTTTGAAATTATTTTGTTTAAGG
1 AAAAATTAATATTTCAACTTTTTTCTCAAAATTTTGAAATTATTTTTTTTAAGG
* * *
31820 AAAAAAATTAACATATCAACTTTTTTCTC-AAATTTTGAAATTATTTTTTATTTAAGA
1 --AAAAATTAATATTTCAACTTTTTTCTCAAAATTTTGAAATTA-TTTTT-TTTAAGG
** * *
31877 AAAAATTGGTATTT-AACTTTTTCCTCAAAA-TTTGAGATTA-TTTTTTTAAGG
1 AAAAATTAATATTTCAACTTTTTTCTCAAAATTTTGAAATTATTTTTTTTAAGG
31928 TAAAAA
1 -AAAAA
31934 AACTCACTAA
Statistics
Matches: 217, Mismatches: 43, Indels: 35
0.74 0.15 0.12
Matches are distributed among these distances:
51 6 0.03
52 9 0.04
53 12 0.06
54 79 0.36
55 88 0.41
56 17 0.08
57 6 0.03
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.48
Consensus pattern (54 bp):
AAAAATTAATATTTCAACTTTTTTCTCAAAATTTTGAAATTATTTTTTTTAAGG
Found at i:31933 original size:109 final size:110
Alignment explanation
Indices: 31727--31935 Score: 280
Period size: 109 Copynumber: 1.9 Consensus size: 110
31717 TTGATACTTA
*
31727 AACTTTTTCCTCAAAAATATGAAATTATTTTTATTTAAGAAAAAATTAATATTTTAACTTTTTCT
1 AACTTTTTCCTCAAAAATATGAAATTATTTTTATTTAAGAAAAAATTAATATTTTAACTTTTTCC
* ***
31792 TTATTTTTTGAAATTATTTTGTTTAAGGAAAAAAATTAACATATC
66 TCAAAATTTGAAATTATTTTGTTTAAGGAAAAAAATTAACATATC
* * * **
31837 AACTTTTTTCTC-AAATTTTGAAATTATTTTTTATTTAAGAAAAAATTGGTA-TTTAACTTTTTC
1 AACTTTTTCCTCAAAAATATGAAATTA-TTTTTATTTAAGAAAAAATTAATATTTTAACTTTTTC
*
31900 CTCAAAATTTGAGATTATTTT-TTTAAGGTAAAAAAA
65 CTCAAAATTTGAAATTATTTTGTTTAAGG-AAAAAAA
31936 CTCACTAAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
108 7 0.08
109 46 0.53
110 33 0.38
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (110 bp):
AACTTTTTCCTCAAAAATATGAAATTATTTTTATTTAAGAAAAAATTAATATTTTAACTTTTTCC
TCAAAATTTGAAATTATTTTGTTTAAGGAAAAAAATTAACATATC
Found at i:32477 original size:21 final size:20
Alignment explanation
Indices: 32453--32647 Score: 76
Period size: 21 Copynumber: 9.3 Consensus size: 20
32443 AATTTAGTAA
32453 AATTTTAGTAACCTTTAATAT
1 AATTTT-GTAACCTTTAATAT
*
32474 AATTTTGGTAACCTTTACTACT
1 AATTTT-GTAACCTTTAATA-T
* * *
32496 -ATTTTGATAA-CTCATGACAT
1 AATTTTG-TAACCT-TTAATAT
*
32516 AATTTGAGTAACCATTT-ATAT
1 AATTT-TGTAACC-TTTAATAT
* * * *
32537 AACTTTGGTAATCTTTGATAA
1 AA-TTTTGTAACCTTTAATAT
* *
32558 AATTTTAATAA--GTTAGATAT
1 AATTTT-GTAACCTTTA-ATAT
* * *
32578 AATTTTGATAGCTTTTAATAC
1 AATTTTG-TAACCTTTAATAT
**
32599 AATTTTGGTAAGTTTTAATAT
1 AATTTT-GTAACCTTTAATAT
* *
32620 AATTTTGACAACCTTTGATAT
1 AATTTTG-TAACCTTTAATAT
32641 AATTTTG
1 AATTTTG
32648 ATTTTGATAA
Statistics
Matches: 130, Mismatches: 28, Indels: 32
0.68 0.15 0.17
Matches are distributed among these distances:
19 2 0.02
20 22 0.17
21 94 0.72
22 11 0.08
23 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (20 bp):
AATTTTGTAACCTTTAATAT
Found at i:32585 original size:63 final size:64
Alignment explanation
Indices: 32453--32609 Score: 146
Period size: 63 Copynumber: 2.5 Consensus size: 64
32443 AATTTAGTAA
* ** *
32453 AATTTT-AGTAACCTTTAATATAATTTTGGTAACCTTTACTACTATTTTGATAACTCATGACAT
1 AATTTTGAGTAACCTTTAATATAACTTTGGTAACCTTTACTAAAATTTTAATAACTCATGACAT
* * * *
32516 AA-TTTGAGTAACCATTT-ATATAACTTTGGTAATCTTTGA-TAAAATTTTAATAAGTTA-GATA
1 AATTTTGAGTAACC-TTTAATATAACTTTGGTAACCTTT-ACTAAAATTTTAATAACTCATGACA
32577 T
64 T
* * * *
32578 AATTTTGA-TAGCTTTTAATACAATTTTGGTAA
1 AATTTTGAGTAACCTTTAATATAACTTTGGTAA
32610 GTTTTAATAT
Statistics
Matches: 77, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
61 3 0.04
62 25 0.32
63 45 0.58
64 4 0.05
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (64 bp):
AATTTTGAGTAACCTTTAATATAACTTTGGTAACCTTTACTAAAATTTTAATAACTCATGACAT
Found at i:32645 original size:42 final size:41
Alignment explanation
Indices: 32549--32649 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 41
32539 CTTTGGTAAT
* * *
32549 CTTTGATAAAATTTTAATAAGTTAGATATAATTTTGATAGC
1 CTTTGATAAAATTTTGATAAGTTAGATATAATTTTGACAAC
* * * *
32590 TTTTAATACAATTTTGGTAAGTTTTA-ATATAATTTTGACAAC
1 CTTTGATAAAATTTTGATAAG--TTAGATATAATTTTGACAAC
*
32632 CTTTGATATAATTTTGAT
1 CTTTGATAAAATTTTGAT
32650 TTTGATAACC
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 16 0.34
42 28 0.60
43 3 0.06
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.48
Consensus pattern (41 bp):
CTTTGATAAAATTTTGATAAGTTAGATATAATTTTGACAAC
Found at i:32871 original size:21 final size:20
Alignment explanation
Indices: 32823--32898 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
32813 CTTATTGATG
* *
32823 TAATTTTGATAATCTTTCATA
1 TAATTTTGATAA-CATTAATA
*
32844 CAATTTTGATAACATATAATA
1 TAATTTTGATAACAT-TAATA
* * *
32865 TATTTTTTATAATCATTTATA
1 TAATTTTGATAA-CATTAATA
32886 TAATTTTGATAAC
1 TAATTTTGATAAC
32899 TTTTGACAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (20 bp):
TAATTTTGATAACATTAATA
Found at i:32945 original size:10 final size:10
Alignment explanation
Indices: 32887--32960 Score: 51
Period size: 10 Copynumber: 7.1 Consensus size: 10
32877 TCATTTATAT
32887 AATTTTGATA
1 AATTTTGATA
* *
32897 ACTTTTGACAA
1 AATTTTGA-TA
32908 AATTTT-AGTA
1 AATTTTGA-TA
* *
32918 ATTTATTGGTA
1 AATT-TTGATA
*
32929 TAATTTTGTTA
1 -AATTTTGATA
*
32940 AATTTTAATA
1 AATTTTGATA
32950 AATTTTGATA
1 AATTTTGATA
32960 A
1 A
32961 CTTATGATAT
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
10 30 0.62
11 15 0.31
12 3 0.06
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (10 bp):
AATTTTGATA
Found at i:32974 original size:32 final size:32
Alignment explanation
Indices: 32887--32974 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 32
32877 TCATTTATAT
* *
32887 AATTTTGATAACTTTTGACA-AAATTTTAGTA
1 AATTTTGATAACTTTTGATATAAATTTTAATA
*
32918 ATTTATTGGTATAA-TTTTG-T-TAAATTTTAATA
1 AATT-TT-G-ATAACTTTTGATATAAATTTTAATA
*
32950 AATTTTGATAACTTATGATATAAAT
1 AATTTTGATAACTTTTGATATAAAT
32975 AATTAGTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
29 4 0.09
30 5 0.11
31 6 0.13
32 20 0.44
33 6 0.13
34 4 0.09
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.49
Consensus pattern (32 bp):
AATTTTGATAACTTTTGATATAAATTTTAATA
Found at i:33701 original size:22 final size:22
Alignment explanation
Indices: 33601--33701 Score: 64
Period size: 22 Copynumber: 4.6 Consensus size: 22
33591 ATGACAACAA
*
33601 AAATTAATAATAACTTAATAAT
1 AAATTAATTATAACTTAATAAT
* * *
33623 AAA-TCATCGT-TAATTTAATAGT
1 AAATTAAT--TATAACTTAATAAT
* * * *
33645 AAATTAGTGATACCTTAATAGT
1 AAATTAATTATAACTTAATAAT
* *
33667 -AAGTCATTCATAACTTAATAAT
1 AAATTAATT-ATAACTTAATAAT
33689 AAATTAATTATAA
1 AAATTAATTATAA
33702 GTATTAACTT
Statistics
Matches: 56, Mismatches: 17, Indels: 12
0.66 0.20 0.14
Matches are distributed among these distances:
21 7 0.12
22 41 0.73
23 8 0.14
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.38
Consensus pattern (22 bp):
AAATTAATTATAACTTAATAAT
Found at i:33805 original size:22 final size:21
Alignment explanation
Indices: 33778--33915 Score: 77
Period size: 22 Copynumber: 6.4 Consensus size: 21
33768 ATTAGTTATA
33778 ATAGTAAATCAATGATAACTT
1 ATAGTAAATCAATGATAACTT
*
33799 AGTAGTAAATCAAT-ATTAATTT
1 A-TAGTAAATCAATGA-TAACTT
* *
33821 AATAGTAAAT-TATCAATAACTTT
1 -ATAGTAAATCAAT-GATAAC-TT
** *
33844 ATAGTAAATCTTTTATAA-TT
1 ATAGTAAATCAATGATAACTT
* * *
33864 -TAGTAAATCATTGACAATTT
1 ATAGTAAATCAATGATAACTT
* *
33884 AATAATAAATCAATATATAACTT
1 -ATAGTAAATCAAT-GATAACTT
33907 AGTAGTAAA
1 A-TAGTAAA
33916 ATGTTATCTA
Statistics
Matches: 91, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
19 14 0.15
20 4 0.04
21 4 0.04
22 52 0.57
23 17 0.19
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (21 bp):
ATAGTAAATCAATGATAACTT
Found at i:33852 original size:83 final size:85
Alignment explanation
Indices: 33733--33915 Score: 194
Period size: 83 Copynumber: 2.2 Consensus size: 85
33723 ATAGTTTCTG
* * * *
33733 AACTTAGTGGTAAATCATCAATAACATTGTGCTAAAT-TAGTTATAA-TAGTAAATCAATGATAA
1 AACTTAATAGTAAATCATCAATAACATTATGCTAAATCT-GTTATAATTAGTAAATCAATGACAA
* *
33796 CTTAGTAGTAAATCAATAT-T
65 CTTAATAATAAATCAATATAT
* * * * *
33816 AATTTAATAGTAAATTATCAATAACTTTATAG-TAAATCTTTTATAATTTAGTAAATCATTGACA
1 AACTTAATAGTAAATCATCAATAACATTAT-GCTAAATCTGTTATAA-TTAGTAAATCAATGACA
*
33880 ATTTAATAATAAATCAATATAT
64 ACTTAATAATAAATCAATATAT
*
33902 AACTTAGTAGTAAA
1 AACTTAATAGTAAA
33916 ATGTTATCTA
Statistics
Matches: 81, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
83 35 0.43
84 2 0.02
85 31 0.38
86 13 0.16
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (85 bp):
AACTTAATAGTAAATCATCAATAACATTATGCTAAATCTGTTATAATTAGTAAATCAATGACAAC
TTAATAATAAATCAATATAT
Found at i:33882 original size:19 final size:19
Alignment explanation
Indices: 33845--33884 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33835 AATAACTTTA
* * *
33845 TAGTAAATCTTTTATAATT
1 TAGTAAATCATTGACAATT
33864 TAGTAAATCATTGACAATT
1 TAGTAAATCATTGACAATT
33883 TA
1 TA
33885 ATAATAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (19 bp):
TAGTAAATCATTGACAATT
Found at i:34145 original size:3 final size:3
Alignment explanation
Indices: 34137--34194 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
34127 AAATCAAAAT
34137 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
34185 ATA ATA ATA A
1 ATA ATA ATA A
34195 GTTAGGGATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39484 original size:33 final size:33
Alignment explanation
Indices: 39441--39508 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
39431 CAAGTTCTTT
*
39441 TACTTGTAAAGATCACACCGACACATTAAATAC
1 TACTTGTAAAGATCACACAGACACATTAAATAC
*
39474 TACTTTTAAAGATCACACAGACACATTAAATAC
1 TACTTGTAAAGATCACACAGACACATTAAATAC
39507 TA
1 TA
39509 AACTAACTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.26
Consensus pattern (33 bp):
TACTTGTAAAGATCACACAGACACATTAAATAC
Found at i:41206 original size:18 final size:18
Alignment explanation
Indices: 41183--41221 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41173 CTATCAGTTA
41183 TTTTT-AAATTACTATACT
1 TTTTTAAAATTACTA-ACT
*
41201 TTTTTAAAATTATTAACT
1 TTTTTAAAATTACTAACT
41219 TTT
1 TTT
41222 AATTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTAAAATTACTAACT
Found at i:44828 original size:59 final size:59
Alignment explanation
Indices: 44743--44858 Score: 214
Period size: 59 Copynumber: 2.0 Consensus size: 59
44733 CTTAAAAGAC
*
44743 GAGAAGTTAAGAAAAGGAAGTCAAGAGTAACTGCAATATCATACTCTGGTTAATCTTAT
1 GAGAAGTTAAGAAAAGGAAGTCAAGAGTAACTGCAATATCATACTCTAGTTAATCTTAT
*
44802 GAGAAGTTAAGAAAAGGAAGTCAAGAGTAACTGCAATATCATAGTCTAGTTAATCTT
1 GAGAAGTTAAGAAAAGGAAGTCAAGAGTAACTGCAATATCATACTCTAGTTAATCTT
44859 TTAGTTAAGC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (59 bp):
GAGAAGTTAAGAAAAGGAAGTCAAGAGTAACTGCAATATCATACTCTAGTTAATCTTAT
Found at i:46397 original size:2 final size:2
Alignment explanation
Indices: 46392--46416 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46382 GTTAAAAAAA
46392 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
46417 GTAATTTCAC
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:49410 original size:60 final size:59
Alignment explanation
Indices: 49323--49440 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 59
49313 AGTGAGGAAC
* *
49323 CCTTGAAACCTAATTGTTTTCTCACTACCTTAAACAAGTTGCAATTTTAAAAATTTCAAT
1 CCTTAAAACCTAATTGTTTTCTCACTACCTTAAACAAGTAGCAATTTT-AAAATTTCAAT
* * * *
49383 CCTTAAAACCTAATT-TTTGTCTGACTACTTTAAATAAGTAGCAATTTTGAAATTTCAA
1 CCTTAAAACCTAATTGTTT-TCTCACTACCTTAAACAAGTAGCAATTTTAAAATTTCAA
49441 ACTGACAGGC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 12 0.24
60 39 0.76
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.39
Consensus pattern (59 bp):
CCTTAAAACCTAATTGTTTTCTCACTACCTTAAACAAGTAGCAATTTTAAAATTTCAAT
Done.