Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167913.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_178, 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: 57339
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:2298 original size:14 final size:13
Alignment explanation
Indices: 2262--2296 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2252 AATGATAAAA
2262 ATTATTTTTATTT
1 ATTATTTTTATTT
2275 ATTATTTTTA-TT
1 ATTATTTTTATTT
2287 ATATATTTTT
1 AT-TATTTTT
2297 TAAAAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTATTTTTATTT
Found at i:3402 original size:3 final size:3
Alignment explanation
Indices: 3396--3527 Score: 78
Period size: 3 Copynumber: 45.0 Consensus size: 3
3386 CAACAACAAC
* * * * * *
3396 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAA AAC AAT AAC AAC AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
3444 AGT -AT AAG ATT AAT AAT AAC ACT -AT AAT -AT GCAT -AT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
3486 AAT AAT AAT AAT AAT AAT AAT ATAT AAT -AT ATAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT
3528 GTACTATATT
Statistics
Matches: 102, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
2 10 0.10
3 84 0.82
4 8 0.08
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4245 original size:114 final size:114
Alignment explanation
Indices: 3926--4552 Score: 368
Period size: 114 Copynumber: 5.5 Consensus size: 114
3916 GACTAAGTTG
* * * * * * *
3926 AGGTCATAGATTTATGATCAAAACAATGCTGTGAGTCTAAAAGTAATCT-AACCTAAGTCGAGAT
1 AGGTCATAGATTAATGATCGAGACGATGTTGTGAGTCTAAAAATAATCTGAA-CTGAGTCGAGAT
* ** * **** * ** * * *
3990 CGAATGACTGGGACGATGTTGCAAGTTTGAAAGCAAACAAAATTGAGTCA
65 CGGATGACTAAGATGATACCACGAGTTTGAAAGTGACCAAGATCGAGTCA
* * * * * * * * ** *
4040 AGGCCATAGATTAATGATTGAGATGATGTCGTAAGTGTAAAAATGATCTGACCT-AAACAAAGAT
1 AGGTCATAGATTAATGATCGAGACGATGTTGTGAGTCTAAAAATAATCTGAACTGAGTC-GAGAT
** * * ** * ** *
4104 CAAATGATTGAGACAATGCCATAAGTTTGAAAGTCACCAAGATCGAGTCA
65 CGGATGACTAAGATGATACCACGAGTTTGAAAGTGACCAAGATCGAGTCA
** * * *
4154 AGGTCATAGATTAATGATCGAGACGATGTTGCAAGTCTAAAAACAATCTGATCTGAGTCGAGATT
1 AGGTCATAGATTAATGATCGAGACGATGTTGTGAGTCTAAAAATAATCTGAACTGAGTCGAGATC
* *
4219 GGATGACTAA-AGTGATACCACGAGTTTGAAATTGACCAAGATGGAGTCA
66 GGATGACTAAGA-TGATACCACGAGTTTGAAAGTGACCAAGATCGAGTCA
* * * * *
4268 AGGTCATAGATTAATGACCGAGACGATGCTGTGAGTCTAAAAATGATCTGACCTGA-ACTGAGAT
1 AGGTCATAGATTAATGATCGAGACGATGTTGTGAGTCTAAAAATAATCTGAACTGAGTC-GAGAT
* ** * * * * *
4332 CGGATGACTAGGATGATGTCACGAGTCT-AAAGGTGACTAAGATCAAATCG
65 CGGATGACTAAGATGATACCACGAGTTTGAAA-GTGACCAAGATCGAGTCA
* * *
4382 AGGTCATAGATGAATGATC-AGGATGATGTTGTGAGTTTAAAAATAATCT-AACTTGAGTCGAGA
1 AGGTCATAGATTAATGATCGA-GACGATGTTGTGAGTCTAAAAATAATCTGAAC-TGAGTCGAGA
* ** * * * * * * * * **
4445 TCGGATGACTGAGATGATGTCACTAGTCTAAAAATAACCAAAATCAAATTG
64 TCGGATGACTAAGATGATACCACGAGTTTGAAAGTGACCAAGATCGAGTCA
* * * * ** * *
4496 AGGTCATAAATTAATGATCGGGATGATATTACGAGTCTAAAAATGATATGAACTGAG
1 AGGTCATAGATTAATGATCGAGACGATGTTGTGAGTCTAAAAATAATCTGAACTGAG
4553 CTAAAATTGG
Statistics
Matches: 401, Mismatches: 99, Indels: 26
0.76 0.19 0.05
Matches are distributed among these distances:
113 10 0.02
114 380 0.95
115 11 0.03
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (114 bp):
AGGTCATAGATTAATGATCGAGACGATGTTGTGAGTCTAAAAATAATCTGAACTGAGTCGAGATC
GGATGACTAAGATGATACCACGAGTTTGAAAGTGACCAAGATCGAGTCA
Found at i:4920 original size:114 final size:114
Alignment explanation
Indices: 4598--4939 Score: 353
Period size: 114 Copynumber: 3.0 Consensus size: 114
4588 GAAGATAACT
* * * * * *
4598 AAAATTGAGTCAAGGTTGTAGATGAATAATCAAAACGATGTTATGAGTTTAAAAATAATTTGA-T
1 AAAACTGAGTCAAGGTTGTAGATGAATAATTAAGATGATGCTATGAGTTTAAAAATGATTTGACT
* * * * *
4662 GTGAGCCAAGATCGGATGACTGAAATGATATCGTGAGTTTAAAAGTGATC
66 -TGAGCCGAGATCGAATGACTGAAATGATGTCGTAAGTCTAAAAGTGATC
* * * * * * ** * * *
4712 AAAATTAAGTCAAGTTTGTAAATTAATGATTGGGATGATGCCATAAGTTTAAAAATGATTTGACC
1 AAAACTGAGTCAAGGTTGTAGATGAATAATTAAGATGATGCTATGAGTTTAAAAATGATTTGACT
* * *
4777 TGAGCCGAGATCGAATGACTGAGACGATGTCGCAAGTCTAAAAGTGATC
66 TGAGCCGAGATCGAATGACTGAAATGATGTCGTAAGTCTAAAAGTGATC
** * * *
4826 AGGACTGAGTCAAGGTAGTAGATGAATAATTAAGATGATGCTATGAGTCTAAAAATGATCTGACT
1 AAAACTGAGTCAAGGTTGTAGATGAATAATTAAGATGATGCTATGAGTTTAAAAATGATTTGACT
* * ** *
4891 TGAGCCGAGATTGAATGACTAAAATGATGTTATAAGTCTAAAAATGATC
66 TGAGCCGAGATCGAATGACTGAAATGATGTCGTAAGTCTAAAAGTGATC
4940 TGATTTGAGC
Statistics
Matches: 180, Mismatches: 47, Indels: 2
0.79 0.21 0.01
Matches are distributed among these distances:
114 180 1.00
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.29
Consensus pattern (114 bp):
AAAACTGAGTCAAGGTTGTAGATGAATAATTAAGATGATGCTATGAGTTTAAAAATGATTTGACT
TGAGCCGAGATCGAATGACTGAAATGATGTCGTAAGTCTAAAAGTGATC
Found at i:4930 original size:54 final size:54
Alignment explanation
Indices: 4860--4974 Score: 158
Period size: 54 Copynumber: 2.1 Consensus size: 54
4850 AATAATTAAG
* * * *
4860 ATGATGCTATGAGTCTAAAAATGATCTGACTTGAGCCGAGATTGAATGACTAAA
1 ATGATGTTATAAGTCTAAAAATGATCTGACTTGAGCCAAGATCGAATGACTAAA
* * * *
4914 ATGATGTTATAAGTCTAAAAATGATCTGATTTGAGCTAAGATCGGATGACTAGA
1 ATGATGTTATAAGTCTAAAAATGATCTGACTTGAGCCAAGATCGAATGACTAAA
4968 ATGATGT
1 ATGATGT
4975 CGTGAGTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (54 bp):
ATGATGTTATAAGTCTAAAAATGATCTGACTTGAGCCAAGATCGAATGACTAAA
Found at i:5861 original size:37 final size:37
Alignment explanation
Indices: 5811--5881 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
5801 AGTTGTTCTC
**
5811 ATTTGATTCAAGCTGTTCTTTTGGGTTTTTAACTCGA
1 ATTTGATTCAAGCTGCCCTTTTGGGTTTTTAACTCGA
*
5848 ATTTGGTTCAAGCTGCCCTTTTGGGTTTTTAACT
1 ATTTGATTCAAGCTGCCCTTTTGGGTTTTTAACT
5882 TGAACTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.48
Consensus pattern (37 bp):
ATTTGATTCAAGCTGCCCTTTTGGGTTTTTAACTCGA
Found at i:17513 original size:3 final size:3
Alignment explanation
Indices: 17505--17556 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
17495 TAATATGTAT
* *
17505 ATA ATA ATA ATA CTA ATGT ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
17551 ATA ATA
1 ATA ATA
17557 TACAATATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 42 0.95
4 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:27723 original size:19 final size:20
Alignment explanation
Indices: 27690--27734 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
27680 TATTAGGCAC
27690 GTGGGGAGAGATTGGATGGG
1 GTGGGGAGAGATTGGATGGG
* *
27710 GTGGGGAG-GATTGGGTGTG
1 GTGGGGAGAGATTGGATGGG
27729 GTGGGG
1 GTGGGG
27735 CATTGGGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.13, C:0.00, G:0.64, T:0.22
Consensus pattern (20 bp):
GTGGGGAGAGATTGGATGGG
Found at i:27760 original size:39 final size:39
Alignment explanation
Indices: 27710--27800 Score: 130
Period size: 39 Copynumber: 2.4 Consensus size: 39
27700 ATTGGATGGG
*
27710 GTGGGGA-GGATTGGGTGTGGTGGGGCATTGGGGGGAAA
1 GTGGGGAGGGATTGGGTGTGGTGGGACATTGGGGGGAAA
** *
27748 GTGGGGAGGGATTGGGTGTGGTGGGATGTTGGGGGGAAG
1 GTGGGGAGGGATTGGGTGTGGTGGGACATTGGGGGGAAA
*
27787 GTGGAGAGGGATTG
1 GTGGGGAGGGATTG
27801 ATGGGGGTGG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 7 0.15
39 40 0.85
ACGTcount: A:0.15, C:0.01, G:0.62, T:0.22
Consensus pattern (39 bp):
GTGGGGAGGGATTGGGTGTGGTGGGACATTGGGGGGAAA
Found at i:28350 original size:26 final size:26
Alignment explanation
Indices: 28322--28370 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
28312 TAAAAAATAA
*
28322 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
28347 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
28371 ATTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:28620 original size:20 final size:21
Alignment explanation
Indices: 28583--28621 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
28573 GTATATGAAA
* *
28583 TTTAATAATTTTTTTTGTTGT
1 TTTAATAATTTATATTGTTGT
28604 TTTAAT-ATTTATATTGTT
1 TTTAATAATTTATATTGTT
28622 ATCAATTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (21 bp):
TTTAATAATTTATATTGTTGT
Found at i:31790 original size:27 final size:27
Alignment explanation
Indices: 31751--31802 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
31741 GTCCAACACC
*
31751 AAGTCAGAGTGATGATGGTGGTGGTTT
1 AAGTCAGAGTGATGATGGTGATGGTTT
31778 AAGTCCAGA-TGATGATGGTGATGGT
1 AAGT-CAGAGTGATGATGGTGATGGT
31803 GACGGTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.25, C:0.06, G:0.38, T:0.31
Consensus pattern (27 bp):
AAGTCAGAGTGATGATGGTGATGGTTT
Found at i:32184 original size:21 final size:21
Alignment explanation
Indices: 32159--32198 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
32149 ATTATCCACC
* *
32159 TCAAATGTATCCTCTACCTCT
1 TCAAATATATCCTCCACCTCT
32180 TCAAATATATCCTCCACCT
1 TCAAATATATCCTCCACCT
32199 TAAATGGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.35, G:0.03, T:0.35
Consensus pattern (21 bp):
TCAAATATATCCTCCACCTCT
Found at i:42027 original size:203 final size:203
Alignment explanation
Indices: 41625--42028 Score: 457
Period size: 203 Copynumber: 2.0 Consensus size: 203
41615 AAGAAAAATG
* *
41625 AAAATTTCATTATATTGAAGATTTTCTATAAATATTCCAATACACTGGTAATATTTTACAAAAAA
1 AAAATTTCATTATATTGAAAATTTTCTATAAATACTCCAATACACTGGTAATATTTTA-AAAAAA
* * * *
41690 ATCTTCTCACCTAGAGATTTCTTAAAGCATCTCTACTCGGAATACTTTTAGAATCCCATCATTGG
65 ATCTTCTCACCTAGAGATTTCGTAAAGCATCACTACTCGGAATACCTTTAGAATCCCATCATCGG
* * * *
41755 ATAAAATTTCTTTTCTTCTCATTTTTATTACTCATATTTTTAATATATTCATCAATTTTTATTTA
130 ATAAAATTTCCTTTC-TCTCATTTTTATTACTAATATTATTAATAAATT-AT-AATTTTTATTTA
41820 TTATTTAAAAAA
192 TTATTTAAAAAA
* * *
41832 AAAATTT-ATTGTATTGAAAATTTT-TTTATAATACTCCAATACACTGGTAGTA-TTT-AAAAAA
1 AAAATTTCATTATATTGAAAATTTTCTATA-AATACTCCAATACACTGGTAATATTTTAAAAAAA
* * * *
41893 ATCTTCTCACCTAGATATTTCGT-AGGCATCACTACTCGGAATACCTTT-GAATCTCATCGTCGG
65 ATCTTCTCACCTAGAGATTTCGTAAAGCATCACTACTCGGAATACCTTTAGAATCCCATCATCGG
* *
41956 ATAAAAATTTCCCTTTC-CTACATTTTTTATTAGTTTAATATTATTATTAAATT-T-ATTTTTAT
130 AT-AAAATTT-CCTTTCTCT-CA-TTTTTATTA--CTAATATTATTAATAAATTATAATTTTTAT
42018 ATATATTATTT
189 -T-TATTATTT
42029 TGTTTTTAAA
Statistics
Matches: 169, Mismatches: 19, Indels: 22
0.80 0.09 0.10
Matches are distributed among these distances:
201 24 0.14
202 32 0.19
203 50 0.30
205 20 0.12
206 36 0.21
207 7 0.04
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (203 bp):
AAAATTTCATTATATTGAAAATTTTCTATAAATACTCCAATACACTGGTAATATTTTAAAAAAAA
TCTTCTCACCTAGAGATTTCGTAAAGCATCACTACTCGGAATACCTTTAGAATCCCATCATCGGA
TAAAATTTCCTTTCTCTCATTTTTATTACTAATATTATTAATAAATTATAATTTTTATTTATTAT
TTAAAAAA
Found at i:43252 original size:21 final size:20
Alignment explanation
Indices: 43200--43253 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
43190 ATTTTTCTGT
*
43200 TTTGTTTTATTTTTTTTATA
1 TTTGTATTATTTTTTTTATA
* *
43220 TTT-CATTCATTTTTTTTGTA
1 TTTGTATT-ATTTTTTTTATA
43240 CTTTGTATTATTTT
1 -TTTGTATTATTTT
43254 GGTATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.07
20 14 0.52
21 8 0.30
22 3 0.11
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (20 bp):
TTTGTATTATTTTTTTTATA
Found at i:43789 original size:22 final size:22
Alignment explanation
Indices: 43740--43788 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
43730 TAACATGTCA
*
43740 ATTTTAAAAATAAAAATTAAAC
1 ATTTTAAAAATAAAAAATAAAC
*
43762 ATTTTAAAAATAAAAGAATAAAT
1 ATTTTAAAAATAAAA-AATAAAC
43785 ATTT
1 ATTT
43789 ATATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
ATTTTAAAAATAAAAAATAAAC
Found at i:44543 original size:231 final size:231
Alignment explanation
Indices: 44139--44599 Score: 832
Period size: 231 Copynumber: 2.0 Consensus size: 231
44129 CTTCTCTTCT
44139 AAGTTTAAAATAGAAAACACACCAAAAAAATCTACTTCTAAATAACATACATCGAGTTTCACTAG
1 AAGTTTAAAATAGAAAACACACCAAAAAAATCTACTTCTAAATAACATACATCGAGTTTCACTAG
*
44204 TCAAAGCATGAAATATCTTGCAGCAATCATTAAATGTCATTCTTAATATCAATTAGAAATTTAAT
66 TCAAAGCATGAAATATCTTGCAACAATCATTAAATGTCATTCTTAATATCAATTAGAAATTTAAT
* *
44269 CTTATCCATATACAATAAAAAATATGATTTCTTATCTGAATAGAGATAGAGATGATGATGAATAT
131 CTTATCCATATACAATAAAAAATATGATTTCTTATCCGAATAGAGATAGAGATGAGGATGAATAT
44334 AATTTTAAATTTTTATAGAGTATGAGGATGGGGATG
196 AATTTTAAATTTTTATAGAGTATGAGGATGGGGATG
* *
44370 AAGTTTAAAATAGAAAACACACCAAAAAAATCTTCTTCTAAATAACATACATTGAGTTTCACTAG
1 AAGTTTAAAATAGAAAACACACCAAAAAAATCTACTTCTAAATAACATACATCGAGTTTCACTAG
* * *
44435 TCAAATCATGAAATATCTTGCAACAATTATTAAATGTCATTCTTAATATCAATTAGAAATTTGAT
66 TCAAAGCATGAAATATCTTGCAACAATCATTAAATGTCATTCTTAATATCAATTAGAAATTTAAT
* *
44500 CTTGTCCATATCCAATAAAAAATATGATTTCTTATCCGAATAGAGATAGAGATGAGGATGAATAT
131 CTTATCCATATACAATAAAAAATATGATTTCTTATCCGAATAGAGATAGAGATGAGGATGAATAT
44565 AATTTTAAATTTTTATAGAGTATGAGGATGGGGAT
196 AATTTTAAATTTTTATAGAGTATGAGGATGGGGAT
44600 AGATAGTATA
Statistics
Matches: 220, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
231 220 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (231 bp):
AAGTTTAAAATAGAAAACACACCAAAAAAATCTACTTCTAAATAACATACATCGAGTTTCACTAG
TCAAAGCATGAAATATCTTGCAACAATCATTAAATGTCATTCTTAATATCAATTAGAAATTTAAT
CTTATCCATATACAATAAAAAATATGATTTCTTATCCGAATAGAGATAGAGATGAGGATGAATAT
AATTTTAAATTTTTATAGAGTATGAGGATGGGGATG
Found at i:44643 original size:2 final size:2
Alignment explanation
Indices: 44636--44675 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
44626 CATATCTTAC
* *
44636 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT CT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44676 GATTTTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45149 original size:2 final size:2
Alignment explanation
Indices: 45142--45174 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
45132 CCCTTGTGAG
*
45142 TA TA TA TA TA TA TA TA TA TA TA TA -A TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45175 AATTGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:47478 original size:29 final size:29
Alignment explanation
Indices: 47446--47523 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
47436 TACTTTTTGA
* * *
47446 ATTTTTAAAAATTTAATCTTTTTAGTAAT
1 ATTTTTAAAAATTTAATCATTGTAATAAT
** *
47475 ATTTAAAAAAATTTAATCATTGTAATATT
1 ATTTTTAAAAATTTAATCATTGTAATAAT
47504 ATTTTTTAAAAATTTTAATC
1 A-TTTTTAAAAA-TTTAATC
47524 CATTCATTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 24 0.62
30 8 0.21
31 7 0.18
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (29 bp):
ATTTTTAAAAATTTAATCATTGTAATAAT
Found at i:49883 original size:20 final size:20
Alignment explanation
Indices: 49851--49889 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
49841 GTGAAAAAAC
*
49851 CCAGATTCTGGCGTAAATTT
1 CCAGATTCTGGCGAAAATTT
49871 CCAGAATTC-GGCGAAAATT
1 CCAG-ATTCTGGCGAAAATT
49890 CCACCGGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (20 bp):
CCAGATTCTGGCGAAAATTT
Found at i:50246 original size:15 final size:14
Alignment explanation
Indices: 50214--50265 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
50204 CCGCTCCAGG
50214 TTTTTTTTTTTTGAA
1 TTTTTTTTTTTT-AA
*
50229 TTTTTTTTATTTTCA
1 TTTTTTTT-TTTTAA
*
50244 TTTATTTGTTTTTTTA
1 TTT-TTT-TTTTTTAA
50260 TTTTTT
1 TTTTTT
50266 ATTTATTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 15 0.47
16 15 0.47
17 2 0.06
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTTTTAA
Found at i:50255 original size:23 final size:23
Alignment explanation
Indices: 50230--50272 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
50220 TTTTTTGAAT
50230 TTTTTTTA-TTTTCATTTATTTG
1 TTTTTTTATTTTTCATTTATTTG
*
50252 TTTTTTTATTTTTTATTTATT
1 TTTTTTTATTTTTCATTTATT
50273 AGATTAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (23 bp):
TTTTTTTATTTTTCATTTATTTG
Found at i:50478 original size:58 final size:58
Alignment explanation
Indices: 50398--50856 Score: 534
Period size: 58 Copynumber: 7.7 Consensus size: 58
50388 AAATTTCCAA
* * * *
50398 AAAAAAATATTTTT-AGGAAAAAGTCGAAAGTATCAGTTTTCCTTAAAAATAAATTTTC
1 AAAAAAGTATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
* *
50456 AAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCC
1 AAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AAATTTTC
*
50516 AAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTC
1 AAAAAAG-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAATTTTC
* * *
50576 AAAAAAAAGATTTATTTTTGAGGAAGAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
1 --AAAAAAG---TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
* * *
50639 AAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATTAAAGTTTC
1 AAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATAAATTTTC
* *
50698 AAAAAA-TATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTT-AATA-AAATTTTT
1 AAAAAAGTATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
* * * *
50753 AAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAATTTC
1 AAAAAAGT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAATTTTC
* *
50814 AAAAAA-AATATTTTCAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAGTAT-TTTTGA-GGAAAAGTTGAAAGTATCAATTTTCC
50857 CTGCACAAGA
Statistics
Matches: 349, Mismatches: 33, Indels: 36
0.83 0.08 0.09
Matches are distributed among these distances:
55 12 0.03
56 3 0.01
57 2 0.01
58 143 0.41
59 28 0.08
60 46 0.13
61 61 0.17
62 7 0.02
63 6 0.02
64 41 0.12
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (58 bp):
AAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
Found at i:54754 original size:11 final size:11
Alignment explanation
Indices: 54740--54806 Score: 68
Period size: 11 Copynumber: 6.2 Consensus size: 11
54730 ACAATGGATG
54740 AAAAATGAGAA
1 AAAAATGAGAA
*
54751 AAAAATGAAAAA
1 AAAAATG-AGAA
*
54763 AAAAATGAAAA
1 AAAAATGAGAA
54774 AAAAATGA-AA
1 AAAAATGAGAA
*
54784 AGAAAA--AGGA
1 A-AAAATGAGAA
54794 AAAAATGAGAA
1 AAAAATGAGAA
54805 AA
1 AA
54807 TGAAAAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
9 5 0.10
10 5 0.10
11 28 0.58
12 10 0.21
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (11 bp):
AAAAATGAGAA
Found at i:54764 original size:12 final size:12
Alignment explanation
Indices: 54740--54798 Score: 77
Period size: 12 Copynumber: 5.1 Consensus size: 12
54730 ACAATGGATG
*
54740 AAAAATG-AGAA
1 AAAAATGAAAAA
54751 AAAAATGAAAAA
1 AAAAATGAAAAA
54763 AAAAATG-AAAA
1 AAAAATGAAAAA
*
54774 AAAAATGAAAAG
1 AAAAATGAAAAA
*
54786 AAAAAGGAAAAA
1 AAAAATGAAAAA
54798 A
1 A
54799 TGAGAAAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
11 18 0.43
12 24 0.57
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAAATGAAAAA
Found at i:54770 original size:23 final size:23
Alignment explanation
Indices: 54740--54806 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
54730 ACAATGGATG
54740 AAAAATGAGAAAAAAATGAAAAA
1 AAAAATGAGAAAAAAATGAAAAA
* *
54763 AAAAATGAAAAAAAAATGAAAAG
1 AAAAATGAGAAAAAAATGAAAAA
*
54786 AAAAA-G-G-AAAAAATGAGAAA
1 AAAAATGAGAAAAAAATGAAAAA
54806 A
1 A
54807 TGAAAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 12 0.31
22 1 0.03
23 26 0.67
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (23 bp):
AAAAATGAGAAAAAAATGAAAAA
Found at i:54804 original size:17 final size:17
Alignment explanation
Indices: 54751--54820 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
54741 AAAATGAGAA
*
54751 AAAAATGAAAAAAAAAATG
1 AAAAA-GAAAAAAAAGA-G
*
54770 AAAAA-AAAATGAAA-AG
1 AAAAAGAAAA-AAAAGAG
* *
54786 AAAAAGGAAAAAATGAG
1 AAAAAGAAAAAAAAGAG
*
54803 AAAATGAAAAAAAAGAG
1 AAAAAGAAAAAAAAGAG
54820 A
1 A
54821 TTCAAATTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
16 8 0.20
17 25 0.61
18 3 0.07
19 5 0.12
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (17 bp):
AAAAAGAAAAAAAAGAG
Found at i:54811 original size:23 final size:22
Alignment explanation
Indices: 54750--54813 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
54740 AAAAATGAGA
*
54750 AAAAAATGA-AAAA-AAAAATG
1 AAAAAATGAGAAAAGAAAAAGG
**
54770 AAAAAAAAATGAAAAGAAAAAGG
1 AAAAAATGA-GAAAAGAAAAAGG
54793 AAAAAATGAGAAAATGAAAAA
1 AAAAAATGAGAAAA-GAAAAA
54814 AAAGAGATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 7 0.20
22 9 0.26
23 19 0.54
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (22 bp):
AAAAAATGAGAAAAGAAAAAGG
Found at i:56109 original size:42 final size:41
Alignment explanation
Indices: 56042--56288 Score: 365
Period size: 42 Copynumber: 6.0 Consensus size: 41
56032 GCCAAGGAGT
56042 ATTTACTTTCCAAAGTTCCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAG-T-CGTGGTGCCTCTGTTTAGAGGAGCA
*
56083 ATTTACTTTTCCGAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
56125 ATTTACTTTTCAAAGTCTTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
56166 ATTTACTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
56206 ATTTAATTTCCAAAGGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAA-GTCGTGGTGCCTCTGTTTAGAGGAGCA
* * *
56248 ATTTACTTTCTCAAAGTCGTTGAGCCTCTATTTAGAGGAGC
1 ATTTACTTTC-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
56289 TTTGGTAAAA
Statistics
Matches: 190, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
40 41 0.22
41 52 0.27
42 93 0.49
43 4 0.02
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:56193 original size:123 final size:125
Alignment explanation
Indices: 56042--56288 Score: 380
Period size: 123 Copynumber: 2.0 Consensus size: 125
56032 GCCAAGGAGT
* *
56042 ATTTACTTTCCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCGAA-GTCGTGGT
1 ATTTACTTTCCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTA-ATTTCCAAAGGTCGTGGT
* *
56106 GCCTCTGTTTAGAGGAGCAATTTACTTT-TCAAAGTC-TTGGTGCCTCTGTTTAGAGGAGCA
65 GCCTCTGTTTAGAGGAGCAATTTACTTTCTCAAAGTCGTT-GAGCCTCTATTTAGAGGAGCA
56166 ATTTACTTT-CAAAG-T-CGTGGTGCCTCTGTTTAGAGGAGCAATTTAATTTCCAAAGGTCGTGG
1 ATTTACTTTCCAAAGTTCCGT--TGCCTCTGTTTAGAGGAGCAATTTAATTTCCAAAGGTCGTGG
56228 TGCCTCTGTTTAGAGGAGCAATTTACTTTCTCAAAGTCGTTGAGCCTCTATTTAGAGGAGC
64 TGCCTCTGTTTAGAGGAGCAATTTACTTTCTCAAAGTCGTTGAGCCTCTATTTAGAGGAGC
56289 TTTGGTAAAA
Statistics
Matches: 114, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
121 3 0.03
122 8 0.07
123 66 0.58
124 35 0.31
125 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (125 bp):
ATTTACTTTCCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTAATTTCCAAAGGTCGTGGTG
CCTCTGTTTAGAGGAGCAATTTACTTTCTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCA
Found at i:56301 original size:1 final size:1
Alignment explanation
Indices: 56295--56389 Score: 64
Period size: 1 Copynumber: 95.0 Consensus size: 1
56285 GAGCTTTGGT
* * * * * ** * *
56295 AAAAAAAAACAAAAAAAACAAAACAAAAAAAAAACAAAACAATGAAAAAAATAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
56360 AAAAACACAAAAAATATAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
56390 TGACAATGTT
Statistics
Matches: 67, Mismatches: 27, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.85, C:0.09, G:0.01, T:0.04
Consensus pattern (1 bp):
A
Found at i:56310 original size:9 final size:9
Alignment explanation
Indices: 56296--56389 Score: 79
Period size: 9 Copynumber: 10.7 Consensus size: 9
56286 AGCTTTGGTA
56296 AAAAAAAAC
1 AAAAAAAAC
56305 AAAAAAAAC
1 AAAAAAAAC
*
56314 -AAAACAA-
1 AAAAAAAAC
56321 AAAAAAAAC
1 AAAAAAAAC
* **
56330 AAAACAATG
1 AAAAAAAAC
56339 AAAAAAATA-
1 AAAAAAA-AC
56348 AAAAAACAA-
1 AAAAAA-AAC
56357 AAAAAAAAC
1 AAAAAAAAC
* *
56366 ACAAAAAAT
1 AAAAAAAAC
*
56375 ATAAAAAAC
1 AAAAAAAAC
56384 AAAAAA
1 AAAAAA
56390 TGACAATGTT
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
8 14 0.21
9 53 0.78
10 1 0.01
ACGTcount: A:0.85, C:0.10, G:0.01, T:0.04
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:56324 original size:16 final size:16
Alignment explanation
Indices: 56305--56387 Score: 87
Period size: 16 Copynumber: 4.8 Consensus size: 16
56295 AAAAAAAAAC
56305 AAAAAAAACAAAACAA
1 AAAAAAAACAAAACAA
56321 AAAAAAAACAAAACAATGA
1 AAAAAAAACAAAAC-A--A
*
56340 AAAAAATAAAAAAACAA
1 AAAAAA-AACAAAACAA
56357 AAAAAAAACACAAA-AA
1 AAAAAAAACA-AAACAA
56373 ATATAAAAAACAAAA
1 A-A-AAAAAACAAAA
56388 AATGACAATG
Statistics
Matches: 58, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
16 20 0.34
17 15 0.26
18 8 0.14
19 8 0.14
20 7 0.12
ACGTcount: A:0.84, C:0.10, G:0.01, T:0.05
Consensus pattern (16 bp):
AAAAAAAACAAAACAA
Found at i:56354 original size:36 final size:36
Alignment explanation
Indices: 56296--56389 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
56286 AGCTTTGGTA
* * *
56296 AAAAAAAACAAAAAAAACAAAACAAAAAAAAAACA-
1 AAAAAATATAAAAAAAAAAAAACAAAAAAAAAACAC
*
56331 AAACAATGA-AAAAAATAAAAAAACAAAAAAAAAACAC
1 AAAAAAT-ATAAAAAA-AAAAAAACAAAAAAAAAACAC
*
56368 AAAAAATATAAAAAACAAAAAA
1 AAAAAATATAAAAAAAAAAAAA
56390 TGACAATGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
35 11 0.22
36 27 0.54
37 12 0.24
ACGTcount: A:0.85, C:0.10, G:0.01, T:0.04
Consensus pattern (36 bp):
AAAAAATATAAAAAAAAAAAAACAAAAAAAAAACAC
Found at i:56637 original size:14 final size:14
Alignment explanation
Indices: 56620--56656 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
56610 ATGTATATAG
56620 TTATATATTTATTA
1 TTATATATTTATTA
56634 TTATAT-TATTATTA
1 TTATATAT-TTATTA
56648 TTAT-TATTT
1 TTATATATTT
56657 TTTTGTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATATATTTATTA
Done.