Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168189.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_426, 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: 27238
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Found at i:109 original size:25 final size:29
Alignment explanation
Indices: 75--128 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 29
65 AAGCAATGAT
75 ATTTTAATAAA-A-A-A-TTAATTTTAAA
1 ATTTTAATAAATATATATTTAATTTTAAA
100 ATTTTAATAAATATATATTTAATTTTAAA
1 ATTTTAATAAATATATATTTAATTTTAAA
129 TATATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 11 0.44
26 1 0.04
27 1 0.04
28 1 0.04
29 11 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTTTAATAAATATATATTTAATTTTAAA
Found at i:145 original size:18 final size:18
Alignment explanation
Indices: 107--145 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
97 AAAATTTTAA
**
107 TAAATATATATTTAATTT
1 TAAATATATATTTAAAAT
125 TAAATATATATTTAAAAT
1 TAAATATATATTTAAAAT
143 TAA
1 TAA
146 CTTGTTACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATATATATTTAAAAT
Found at i:8506 original size:186 final size:187
Alignment explanation
Indices: 8286--8695 Score: 513
Period size: 186 Copynumber: 2.2 Consensus size: 187
8276 TTTTCACTGC
* ** * * *
8286 TCAAATTTTAAGACATTTAGTCAAAGCGTTTATTCTAAAAAAATACATTTACTAATTCTTTCTAA
1 TCAAATTTTAAAACGGTTAGTAAAAGCATTTATTCTAAAAAAACACATTTACTAATTCTTTCTAA
* * *
8351 TTTACGTACATAATTATTGTAGATATTTTTTTAGAACAAACGCCTTTAATAATTTTCTCT-TATA
66 TTTACGTACATAATTATTGTAGATATTTTTTCAAAACAAACGCCTTCAAT-ATTTTCTCTCTATA
* * *
8415 ATTTTTGAAATTATTAAAGATGTCTTCCAA-AGAAAAATG-CTTTCAATATTCCACA-A
130 ATTTTTGAAATTATTAAAGACGTCTTCCAATAAAAAAATGCCTAT-AATATTCCACATA
* * * * * * *
8471 CTCAAATTTTAAAATGGTTAGTGAAGGCATTTATTCTAGAACAACACCTTTACTACTTCTTTCTA
1 -TCAAATTTTAAAACGGTTAGTAAAAGCATTTATTCTAAAAAAACACATTTACTAATTCTTTCTA
* * *
8536 ATTTACGTACATAATTATTGTAGGTATTTTTTCAAAACAAACGCCTTCAATATTTTTTTTCTATA
65 ATTTACGTACATAATTATTGTAGATATTTTTTCAAAACAAACGCCTTCAATATTTTCTCTCTATA
** * *
8601 ATTTTTGGGATTATTAAAGGCGTCTTCCAATAAAAAAATGCCTATAATATTTCACATA
130 ATTTTTGAAATTATTAAAGACGTCTTCCAATAAAAAAATGCCTATAATATTCCACATA
* *
8659 TTAAATTTTAAGACGGTTAGTAAAAGCATTTATTCTA
1 TCAAATTTTAAAACGGTTAGTAAAAGCATTTATTCTA
8696 GAATAATGCC
Statistics
Matches: 190, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
185 7 0.04
186 129 0.68
187 50 0.26
188 4 0.02
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (187 bp):
TCAAATTTTAAAACGGTTAGTAAAAGCATTTATTCTAAAAAAACACATTTACTAATTCTTTCTAA
TTTACGTACATAATTATTGTAGATATTTTTTCAAAACAAACGCCTTCAATATTTTCTCTCTATAA
TTTTTGAAATTATTAAAGACGTCTTCCAATAAAAAAATGCCTATAATATTCCACATA
Found at i:8960 original size:187 final size:186
Alignment explanation
Indices: 8700--9212 Score: 632
Period size: 187 Copynumber: 2.8 Consensus size: 186
8690 ATTCTAGAAT
* * * * *
8700 AATGCCTTTAATAATTATTTCTTATAATTTTTGGGATTATTAAATGCGTCTTCTAGTGAAAAACA
1 AATGCCTTCAATAATTTTTTCTTATAATTTTTAGGATTATTAAAGGCATCTTCTAGTGAAAAACA
* * * *
8765 CCTTCAATATTCTGCAGCTCAAACTTTAATATGGTTAGTGAAGGTGTTTATTATAAAACAACGCC
66 CCTTCAATATTCTACAGCTCAAACTTTAAGATGGTTAGTGAAGGCGTTTATTATAGAACAACGCC
* *
8830 TTTACCAATTCCTTATAATTTGCGTACATAATTATTGAAAGCATTGTTTCAAAACA
131 TTCACCAATTCCTTATAATTTACGTACATAATTATTGAAAGCATTGTTTCAAAACA
* *
8886 AATGCCTTCAATAATTTTTTCTTTATAATTTTTAAGATTATTAAAGGCATCTTTTAGTGAAAAAC
1 AATGCCTTCAATAATTTTTTC-TTATAATTTTTAGGATTATTAAAGGCATCTTCTAGTGAAAAAC
* * * *** * * * *
8951 GCTTTCAATATTCAACAGCTCAAACTTTAAGACAATTAATAAAGGCGTTTATTCTAGAATAACGC
65 ACCTTCAATATTCTACAGCTCAAACTTTAAGATGGTTAGTGAAGGCGTTTATTATAGAACAACGC
* * * * * * * *
9016 CTTCACTAATTCCTTATAATTTACGTATATAATTATTGAAGGTATTTTTTTAGAGCA
130 CTTCACCAATTCCTTATAATTTACGTACATAATTATTGAAAGCATTGTTTCAAAACA
* * * * * *
9073 AACGTCTTCAATAAATTTCTCTTATAATTTTTAGGATTATTAAAGGCATCTTCCAGTGAAAAATA
1 AATGCCTTCAATAATTTTTTCTTATAATTTTTAGGATTATTAAAGGCATCTTCTAGTGAAAAACA
* * *
9138 CCTTCAATATT-TCACAGCTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTATAGAACAATGC
66 CCTTCAATATTCT-ACAGCTCAAACTTTAAGATGGTTAGTGAAGGCGTTTATTATAGAACAACGC
*
9202 CTTCACTAATT
130 CTTCACCAATT
9213 TTTTCTTATA
Statistics
Matches: 273, Mismatches: 52, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
186 120 0.44
187 153 0.56
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (186 bp):
AATGCCTTCAATAATTTTTTCTTATAATTTTTAGGATTATTAAAGGCATCTTCTAGTGAAAAACA
CCTTCAATATTCTACAGCTCAAACTTTAAGATGGTTAGTGAAGGCGTTTATTATAGAACAACGCC
TTCACCAATTCCTTATAATTTACGTACATAATTATTGAAAGCATTGTTTCAAAACA
Found at i:8982 original size:311 final size:311
Alignment explanation
Indices: 8389--9018 Score: 732
Period size: 311 Copynumber: 2.0 Consensus size: 311
8379 TTTTAGAACA
* **
8389 AACGCCTTTAATAATTTTCTCTTATAATTTTTGAAATTATTAAAGATGTCTTCCAAAGAAAAATG
1 AACGCCTTTAATAATTTTCTCTTATAATTTTTGAAATTATTAAAGACGTCTTCCAAAGAAAAACA
* * * *
8454 CTTTCAATATTCCACAACTCAAATTTTAAAATGGTTAGTGAAGGCATTTATTCTAGAACAACACC
66 CCTTCAATATTCCACAACTCAAACTTTAAAATGGTTAGTGAAGGCATTTATTATAAAACAACACC
* * * * * * * *
8519 TTTACTACTTCTTTCTAATTTACGTACATAATTATTGTAGGTATTTTTTCAAAACAAACGCCTTC
131 TTTACCAATTCCTTATAATTTACGTACATAATTATTGAAAGCATTGTTTCAAAACAAACGCCTTC
** * *
8584 AATATTTTTTTTCTATAATTTTTGGGATTATTAAAGGCGTCTTCCAATAAAAAAATGCCTATAAT
196 AATATTTTTTTTCTATAATTTTTAAGATTATTAAAGGCATCTTCCAATAAAAAAACGCCTATAAT
* * * ** *
8649 ATTTCACATATTAAATTTTAAGACGGTTAGTAAAAGCATTTATTCTAGAAT
261 ATTTCACAGATCAAACTTTAAGACAATTAATAAAAGCATTTATTCTAGAAT
* ** * **
8700 AATGCCTTTAATAATTATT-TCTTATAATTTTTGGGATTATTAAATG-CGTCTTCTAGTGAAAAA
1 AACGCCTTTAATAATT-TTCTCTTATAATTTTTGAAATTATTAAA-GACGTCTTCCAAAGAAAAA
** * * ** *
8763 CACCTTCAATATTCTGCAGCTCAAACTTTAATATGGTTAGTGAAGGTGTTTATTATAAAACAACG
64 CACCTTCAATATTCCACAACTCAAACTTTAAAATGGTTAGTGAAGGCATTTATTATAAAACAACA
* *
8828 CCTTTACCAATTCCTTATAATTTGCGTACATAATTATTGAAAGCATTGTTTCAAAACAAATGCCT
129 CCTTTACCAATTCCTTATAATTTACGTACATAATTATTGAAAGCATTGTTTCAAAACAAACGCCT
** * * *
8893 TCAATAATTTTTTCTT-TATAATTTTTAAGATTATTAAAGGCATCTTTTAGT-GAAAAACG-CTT
194 TCAAT-ATTTTTT-TTCTATAATTTTTAAGATTATTAAAGGCATCTTCCAATAAAAAAACGCCTA
* * *
8955 TCAATA-TTCAACAGCTCAAACTTTAAGACAATTAATAAAGGCGTTTATTCTAGAAT
257 T-AATATTTC-ACAGATCAAACTTTAAGACAATTAATAAAAGCATTTATTCTAGAAT
9011 AACGCCTT
1 AACGCCTT
9019 CACTAATTCC
Statistics
Matches: 264, Mismatches: 49, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
310 6 0.02
311 217 0.82
312 39 0.15
313 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (311 bp):
AACGCCTTTAATAATTTTCTCTTATAATTTTTGAAATTATTAAAGACGTCTTCCAAAGAAAAACA
CCTTCAATATTCCACAACTCAAACTTTAAAATGGTTAGTGAAGGCATTTATTATAAAACAACACC
TTTACCAATTCCTTATAATTTACGTACATAATTATTGAAAGCATTGTTTCAAAACAAACGCCTTC
AATATTTTTTTTCTATAATTTTTAAGATTATTAAAGGCATCTTCCAATAAAAAAACGCCTATAAT
ATTTCACAGATCAAACTTTAAGACAATTAATAAAAGCATTTATTCTAGAAT
Found at i:9222 original size:124 final size:124
Alignment explanation
Indices: 9078--9336 Score: 369
Period size: 124 Copynumber: 2.1 Consensus size: 124
9068 GAGCAAACGT
* * * *
9078 CTTCAATAAATTTCTCTTATAATTTTT-AGGATTATTAAAGGCATCTTCCAGTGAAAAATACCTT
1 CTTCACTAATTTTCTCTTATAATTTTTGA-GATTATTAAAAGCATCTTCCAGTGAAAAATACATT
* * *
9142 CAATATT-TCACAGCTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTATAGAACAATGC
65 CAATATTCT-ACAACTCAAATCTTAAGATGGTTAGTAAAGGCATTTATTATAGAACAATGC
* * * *
9202 CTTCACTAATTTTTTCTTATAATTTTTGAGATTATTAAAAGCGTCTTTCAGTGAAAAATGCATTC
1 CTTCACTAATTTTCTCTTATAATTTTTGAGATTATTAAAAGCATCTTCCAGTGAAAAATACATTC
*
9267 AATATTCTACAACTCAAATCTTAAGATGGTTAGTAAAGGCATTTATTTTAGAACAATGC
66 AATATTCTACAACTCAAATCTTAAGATGGTTAGTAAAGGCATTTATTATAGAACAATGC
*
9326 CTTTACTAATT
1 CTTCACTAATT
9337 CCTTCTAATT
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
124 118 0.98
125 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (124 bp):
CTTCACTAATTTTCTCTTATAATTTTTGAGATTATTAAAAGCATCTTCCAGTGAAAAATACATTC
AATATTCTACAACTCAAATCTTAAGATGGTTAGTAAAGGCATTTATTATAGAACAATGC
Found at i:9237 original size:497 final size:496
Alignment explanation
Indices: 8201--9398 Score: 1327
Period size: 497 Copynumber: 2.4 Consensus size: 496
8191 TTACTAAAAT
* * * *
8201 TGCCTTCAATAATT-TTTCTTTAAAAATTGTTTGAGATTATTAAAGGCTTCTTTCAGTAAAAAAA
1 TGCCTTCAATAATTATTTC-TT-ATAATT-TTTGAGATTATTAAAAGCGTCTTTCAGT--GAAAA
* * ** * *** * * *
8265 ACACCTTCAAT-TTTTCACTGCTCAAATTTTAAGACATTTAGTCAAA-GCGTTTATTCTAAAAAA
61 ACACATTCAATATTCT-ACAACTCAAATCTTAAGATGGTTAGT-AAAGGCATTTATTATAAAACA
** * * * * * *
8328 ATACATTTACTAATTCTTTCTAATTTACGTACATAATTATTG-TAGATATTTTTTTAGAACAAAC
124 ACGCCTTTACTAATTCCTTCTAATTTACGTACATAATTATTGAAAG-CA-TTTTTCAAAACAAAC
* ** *
8392 GCCTTTAATAATTTTCTCTTATAATTTTTGAAATTATTAAAGATGTCTTCCAAAGAAAAATGCTT
187 GCCTTCAATAATTTTCTCTTATAATTTTTGAAATTATTAAAGACATCTTCCAAAGAAAAACGCTT
* * *** * * *
8457 TCAATATTCCACAACTCAAATTTTAAAATGGTTAGTGAAGGCATTTATTCTAGAACAACACCTTT
252 TCAATATTCAACAACTCAAACTTTAAAACAATTAATAAAGGCATTTATTCTAGAACAACACCTTC
* * * *
8522 ACTACTTCTTTCTAATTTACGTACATAATTATTGTAGGTATTTTTTCAAAACAAACGCCTTCAAT
317 ACTAATTCCTTATAATTTACGTACATAATTATTGAAGGTATTTTTTCAAAACAAACGCCTTCAAT
* * * * * *
8587 ATTTTTTTTCTATAATTTTTGGGATTATTAAAGGCGTCTTCCAATAAAAAAATGCCTATAATATT
382 AATTTCTCTCTATAATTTTTAGGATTATTAAAGGCATCTTCCAATAAAAAAATACCTATAATATT
* * * *
8652 TCACATATTAAATTTTAAGACGGTTAGTAAAAGCATTTATTCTAGAATAA
447 TCACAGATCAAATTTTAAGACGGTTAGTAAAAGCATTTATTATAGAACAA
* * *
8702 TGCCTTTAATAATTATTTCTTATAATTTTTGGGATTATTAAATGCGTC-TTCTAGTGAAAAACAC
1 TGCCTTCAATAATTATTTCTTATAATTTTTGAGATTATTAAAAGCGTCTTTC-AGTGAAAAACAC
* * * * * **
8766 CTTCAATATTCTGCAGCTCAAA-CTTTAATATGGTTAGTGAAGGTGTTTATTATAAAACAACGCC
65 ATTCAATATTCTACAACTCAAATC-TTAAGATGGTTAGTAAAGGCATTTATTATAAAACAACGCC
* * * *
8830 TTTACCAATTCCTTATAATTTGCGTACATAATTATTGAAAGCATTGTTTCAAAACAAATGCCTTC
129 TTTACTAATTCCTTCTAATTTACGTACATAATTATTGAAAGCATT-TTTCAAAACAAACGCCTTC
* * ** **
8895 AATAATTTTTTCTTTATAATTTTT-AAGATTATTAAAGGCATCTTTTAGTGAAAAACGCTTTCAA
193 AATAATTTTCTC-TTATAATTTTTGAA-ATTATTAAAGACATCTTCCAAAGAAAAACGCTTTCAA
* * * * *
8959 TATTCAACAGCTCAAACTTTAAGACAATTAATAAAGGCGTTTATTCTAGAATAACGCCTTCACTA
256 TATTCAACAACTCAAACTTTAAAACAATTAATAAAGGCATTTATTCTAGAACAACACCTTCACTA
* * * * *
9024 ATTCCTTATAATTTACGTATATAATTATTGAAGGTATTTTTTTAGAGCAAACGTCTTCAATAAAT
321 ATTCCTTATAATTTACGTACATAATTATTGAAGGTATTTTTTCAAAACAAACGCCTTCAAT-AAT
* *
9089 TTCTCT-TATAATTTTTAGGATTATTAAAGGCATCTTCCAGT-GAAAAATACCT-TCAATATTTC
385 TTCTCTCTATAATTTTTAGGATTATTAAAGGCATCTTCCAATAAAAAAATACCTAT-AATATTTC
* * * *
9151 ACAGCTCAAATTTTAAGATGGTTAGTGAAGGCATTTATTATAGAACAA
449 ACAGATCAAATTTTAAGACGGTTAGTAAAAGCATTTATTATAGAACAA
* * **
9199 TGCCTTCACTAATTTTTTCTTATAATTTTTGAGATTATTAAAAGCGTCTTTCAGTGAAAAATGCA
1 TGCCTTCAATAATTATTTCTTATAATTTTTGAGATTATTAAAAGCGTCTTTCAGTGAAAAACACA
* * *
9264 TTCAATATTCTACAACTCAAATCTTAAGATGGTTAGTAAAGGCATTTATTTTAGAACAATGCCTT
66 TTCAATATTCTACAACTCAAATCTTAAGATGGTTAGTAAAGGCATTTATTATAAAACAACGCCTT
* * *
9329 TACTAATTCCTTCTAATTTACATACATAATTATTGAAAGCATTTTTCAAAACAAACACTTTCAAT
131 TACTAATTCCTTCTAATTTACGTACATAATTATTGAAAGCATTTTTCAAAACAAACGCCTTCAAT
9394 AATTT
196 AATTT
9399 CCTTTAAAAA
Statistics
Matches: 582, Mismatches: 102, Indels: 31
0.81 0.14 0.04
Matches are distributed among these distances:
496 29 0.05
497 314 0.54
498 188 0.32
499 27 0.05
500 5 0.01
501 15 0.03
502 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (496 bp):
TGCCTTCAATAATTATTTCTTATAATTTTTGAGATTATTAAAAGCGTCTTTCAGTGAAAAACACA
TTCAATATTCTACAACTCAAATCTTAAGATGGTTAGTAAAGGCATTTATTATAAAACAACGCCTT
TACTAATTCCTTCTAATTTACGTACATAATTATTGAAAGCATTTTTCAAAACAAACGCCTTCAAT
AATTTTCTCTTATAATTTTTGAAATTATTAAAGACATCTTCCAAAGAAAAACGCTTTCAATATTC
AACAACTCAAACTTTAAAACAATTAATAAAGGCATTTATTCTAGAACAACACCTTCACTAATTCC
TTATAATTTACGTACATAATTATTGAAGGTATTTTTTCAAAACAAACGCCTTCAATAATTTCTCT
CTATAATTTTTAGGATTATTAAAGGCATCTTCCAATAAAAAAATACCTATAATATTTCACAGATC
AAATTTTAAGACGGTTAGTAAAAGCATTTATTATAGAACAA
Found at i:9392 original size:124 final size:123
Alignment explanation
Indices: 9107--9399 Score: 279
Period size: 124 Copynumber: 2.3 Consensus size: 123
9097 TAATTTTTAG
* * * * * * *
9107 GATTATTAAAGGCATCTTCCAGTGAAAAATACCTTCAATATTTCACAGCTCAAATTTTAAGATGG
1 GATTATTAAAAGCATCTTTCAG-AAAAAACACATTCAATATTTCACAACTCAAATCTTAAGATGG
* ** ***
9172 TTAGTGAAGGCATTTATTATAGAACAATGCCTTCACTAATTTTTTCTTATAATTTTTGA
65 TTAGTAAAGGCATTTATTATAGAACAATGCCTTCACTAATTCCTTCTTATAATACATGA
* * **
9231 GATTATTAAAAGCGTCTTTCAGTGAAAAATGCATTCAATA-TTCTACAACTCAAATCTTAAGATG
1 GATTATTAAAAGCATCTTTCAG-AAAAAACACATTCAATATTTC-ACAACTCAAATCTTAAGATG
* * *
9295 GTTAGTAAAGGCATTTATTTTAGAACAATGCCTTTACTAATTCCTTCTAATTTACATACAT-A
64 GTTAGTAAAGGCATTTATTATAGAACAATGCCTTCACTAATTCCTTCT--TATA-ATACATGA
* * *
9357 -ATTATTGAAAGCATTTTTCA-AAACAAACACTTTCAATAATTTC
1 GATTATTAAAAGCATCTTTCAGAAA-AAACACATTCAAT-ATTTC
9400 CTTTAAAAAT
Statistics
Matches: 139, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
123 5 0.04
124 106 0.76
125 18 0.13
126 7 0.05
127 3 0.02
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (123 bp):
GATTATTAAAAGCATCTTTCAGAAAAAACACATTCAATATTTCACAACTCAAATCTTAAGATGGT
TAGTAAAGGCATTTATTATAGAACAATGCCTTCACTAATTCCTTCTTATAATACATGA
Found at i:9973 original size:13 final size:14
Alignment explanation
Indices: 9955--10014 Score: 60
Period size: 11 Copynumber: 4.7 Consensus size: 14
9945 AATCGTATGT
9955 TGAATGGTGTTTG-
1 TGAATGGTGTTTGC
9968 TGAAT-G-GTTTGC
1 TGAATGGTGTTTGC
*
9980 TGAATGGTGTTTTC
1 TGAATGGTGTTTGC
*
9994 -GAGT-G-GTTTGC
1 TGAATGGTGTTTGC
10005 TGAATGGTGT
1 TGAATGGTGT
10015 GTCTGAGCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
11 10 0.27
12 10 0.27
13 10 0.27
14 7 0.19
ACGTcount: A:0.15, C:0.05, G:0.37, T:0.43
Consensus pattern (14 bp):
TGAATGGTGTTTGC
Found at i:9983 original size:25 final size:25
Alignment explanation
Indices: 9955--10014 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
9945 AATCGTATGT
9955 TGAATGGTGTTTGT-GAATGGTTTGC
1 TGAATGGTGTTT-TCGAATGGTTTGC
*
9980 TGAATGGTGTTTTCGAGTGGTTTGC
1 TGAATGGTGTTTTCGAATGGTTTGC
10005 TGAATGGTGT
1 TGAATGGTGT
10015 GTCTGAGCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.15, C:0.05, G:0.37, T:0.43
Consensus pattern (25 bp):
TGAATGGTGTTTTCGAATGGTTTGC
Found at i:9985 original size:12 final size:12
Alignment explanation
Indices: 9935--10012 Score: 52
Period size: 12 Copynumber: 6.3 Consensus size: 12
9925 TATATGATAT
*
9935 TGGTATGCTGAA
1 TGGTTTGCTGAA
* * *
9947 TCGTATGTTGAA
1 TGGTTTGCTGAA
9959 TGGTGTTTG-TGAA
1 T-G-GTTTGCTGAA
9972 TGGTTTGCTGAA
1 TGGTTTGCTGAA
* *
9984 TGGTGTT-TTCGAG
1 TGGT-TTGCT-GAA
9997 TGGTTTGCTGAA
1 TGGTTTGCTGAA
10009 TGGT
1 TGGT
10013 GTGTCTGAGC
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
11 5 0.10
12 29 0.56
13 14 0.27
14 4 0.08
ACGTcount: A:0.17, C:0.06, G:0.35, T:0.42
Consensus pattern (12 bp):
TGGTTTGCTGAA
Found at i:14784 original size:20 final size:21
Alignment explanation
Indices: 14759--14797 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
14749 TCTATTTTCT
14759 TATAGTGAAAATAT-AAATAA
1 TATAGTGAAAATATCAAATAA
*
14779 TATAGTTAAAATATCAAAT
1 TATAGTGAAAATATCAAAT
14798 CATAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (21 bp):
TATAGTGAAAATATCAAATAA
Found at i:17772 original size:116 final size:116
Alignment explanation
Indices: 17565--17798 Score: 328
Period size: 116 Copynumber: 2.0 Consensus size: 116
17555 GGAAAGCATC
* *
17565 ATCAAACACCTCATTATATACAACATTATTTGTGCACAAATGAATATTATGATCATTATTTTCAA
1 ATCAAACACCTCAATATATACAACATTATTTGTGCACAAATGAATATCATGATCATTATTTTCAA
*
17630 TTAAAAATTTTAACCCTCCTATTGATGTTACTCTAGAAGCAACTACATATA
66 TTAAAAATTTTAACCCTCCTATTGATGTTACTCTAGAAACAACTACATATA
* ** *
17681 ATCAAACACCTCAATGTATACAACATTATTTGTGCATGAATGAATATCATGATCATTGTTTTCAA
1 ATCAAACACCTCAATATATACAACATTATTTGTGCACAAATGAATATCATGATCATTATTTTCAA
* * * * *
17746 TTAAAAATTTTAA-TCT-CTTTGATGATGTTTCTCTGGAAACAGCTACATATA
66 TTAAAAATTTTAACCCTCCTAT--TGATGTTACTCTAGAAACAACTACATATA
17797 AT
1 AT
17799 TGGCCATGAG
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
114 3 0.03
115 2 0.02
116 99 0.95
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (116 bp):
ATCAAACACCTCAATATATACAACATTATTTGTGCACAAATGAATATCATGATCATTATTTTCAA
TTAAAAATTTTAACCCTCCTATTGATGTTACTCTAGAAACAACTACATATA
Found at i:18473 original size:372 final size:372
Alignment explanation
Indices: 17788--18527 Score: 1175
Period size: 372 Copynumber: 2.0 Consensus size: 372
17778 CTGGAAACAG
* * * ** *
17788 CTACATATAATTGGCCATGAGTGAAAATCAGCTTTGGTAAATACATGCTGACATTTTCAAATGTT
1 CTACATACAATTGGCCATAAGTGAAAACCAGCTTTGACAAATACATGCTGACATTTTCAAATATT
*
17853 TATCCTTGACTCTTGTTTATGGTCATTGCAAAACAAACTTTGATTAGGAACTGTCTTCATGTTAG
66 TATCCTTAACTCTTGTTTATGGTCATTGCAAAACAAACTTTGATTAGGAACTGTCTTCATGTTAG
17918 AGTGAATAGCCATCTTGATTTTGAAGAGGACATTTTCACTCAAGGGATGAAAAACCGACTTCCCA
131 AGTGAATAGCCATCTTGATTTTGAAGAGGACATTTTCACTCAAGGGATGAAAAACCGACTTCCCA
* * *
17983 CATTAGTCCTAGTTATTATCTTAGCTTCAATTACCTTAGAGCCTAATTTTGTGACAATCAATCTA
196 CATTAGTCCTAGTTATTATCTCAGCTTCAATTACCTTAGAGCCCAATTTTGTGACAACCAATCTA
* *
18048 GTACCATTGCAAAGACACATACTTTGATTTATGTTGTGCAAAAGGATAATAGGAACCTCAACTTT
261 GTACCATTGCAAAGACACATACTTGGATTTATGTTGTGCAAAAGAATAATAGGAACCTCAACTTT
* *
18113 CACATCAATTTCATGATTAGGTACCTT-GAGAAACTTAAATGAAGCAA
326 CAAATCAATTTCATGATTAGGTACCTTGGA-AAACATAAATGAAGCAA
* *
18160 CTACATACAATTGGCCATAAGTGAAAACCAGCTTTGACAAATACAT-ATCGACATTTTTAAATAT
1 CTACATACAATTGGCCATAAGTGAAAACCAGCTTTGACAAATACATGCT-GACATTTTCAAATAT
* *
18224 TTGTCCTTAACTCTTGTTTATGGTCATTGCAAAACAAACTTTGATTAGGAACTGTCTTCGTGTTA
65 TTATCCTTAACTCTTGTTTATGGTCATTGCAAAACAAACTTTGATTAGGAACTGTCTTCATGTTA
* * * * *
18289 GAGTGAATGGTCATCTTGTTTTTGAAGGGGACATTTTCACTCAAGGGATGAAAAACCGACTTCCT
130 GAGTGAATAGCCATCTTGATTTTGAAGAGGACATTTTCACTCAAGGGATGAAAAACCGACTTCCC
* *
18354 ATATTAGTCCTAGTTATTATCTCAGCTTTAATTACCTTAGAGCCCAATTTTGTGACAACCAATCT
195 ACATTAGTCCTAGTTATTATCTCAGCTTCAATTACCTTAGAGCCCAATTTTGTGACAACCAATCT
18419 AGTACCATTGCAAAGAC-CAATACTTGGATTTAT-TT-TGCATAAAAGAATAATAGGAACCTCAA
260 AGTACCATTGCAAAGACAC-ATACTTGGATTTATGTTGTGC--AAAAGAATAATAGGAACCTCAA
18481 CTTTCAAATCAATTTCATGATTAGGTACCTTGGAAAACATAAATGAA
322 CTTTCAAATCAATTTCATGATTAGGTACCTTGGAAAACATAAATGAA
18528 TTCAAGAATT
Statistics
Matches: 338, Mismatches: 25, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
370 3 0.01
371 4 0.01
372 329 0.97
373 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (372 bp):
CTACATACAATTGGCCATAAGTGAAAACCAGCTTTGACAAATACATGCTGACATTTTCAAATATT
TATCCTTAACTCTTGTTTATGGTCATTGCAAAACAAACTTTGATTAGGAACTGTCTTCATGTTAG
AGTGAATAGCCATCTTGATTTTGAAGAGGACATTTTCACTCAAGGGATGAAAAACCGACTTCCCA
CATTAGTCCTAGTTATTATCTCAGCTTCAATTACCTTAGAGCCCAATTTTGTGACAACCAATCTA
GTACCATTGCAAAGACACATACTTGGATTTATGTTGTGCAAAAGAATAATAGGAACCTCAACTTT
CAAATCAATTTCATGATTAGGTACCTTGGAAAACATAAATGAAGCAA
Found at i:24286 original size:11 final size:12
Alignment explanation
Indices: 24233--24288 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
24223 ATCAAATTCG
*
24233 ATAATTTAAAAT
1 ATAATATAAAAT
24245 ATAATATAATAAT
1 ATAATATAA-AAT
24258 ATAATAT-AAAT
1 ATAATATAAAAT
* *
24269 GTTATATAAAA-
1 ATAATATAAAAT
24280 ATAATATAA
1 ATAATATAA
24289 TTTAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 15 0.41
12 12 0.32
13 10 0.27
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:24329 original size:27 final size:25
Alignment explanation
Indices: 24241--24370 Score: 99
Period size: 27 Copynumber: 5.2 Consensus size: 25
24231 CGATAATTTA
*
24241 AAATATAAT-ATAATAATATAATAT
1 AAATTTAATAATAATAATATAATAT
* *
24265 AAATGTTATATAAAAATAATATAATTT
1 AAAT-TTA-ATAATAATAATATAATAT
*
24292 AAAATTTTAATAATAATTATAT-ATAT
1 -AAA-TTTAATAATAATAATATAATAT
*
24318 AAATTTAATAATATTAA-A-AATAT
1 AAATTTAATAATAATAATATAATAT
* * **
24341 ATATTTTAT-ATTTTAATATTAATAT
1 AAATTTAATAATAATAATA-TAATAT
24366 AAATT
1 AAATT
24371 ATTACGTATA
Statistics
Matches: 85, Mismatches: 12, Indels: 17
0.75 0.11 0.15
Matches are distributed among these distances:
22 6 0.07
23 13 0.15
24 16 0.19
25 14 0.16
26 5 0.06
27 24 0.28
28 6 0.07
29 1 0.01
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.45
Consensus pattern (25 bp):
AAATTTAATAATAATAATATAATAT
Found at i:24340 original size:23 final size:24
Alignment explanation
Indices: 24297--24346 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
24287 AATTTAAAAT
* *
24297 TTTAATAATAATTATATATATAAA
1 TTTAATAATAATTAAAAATATAAA
*
24321 TTTAATAAT-ATTAAAAATATATA
1 TTTAATAATAATTAAAAATATAAA
24344 TTT
1 TTT
24347 TATATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTAATAATAATTAAAAATATAAA
Found at i:24411 original size:20 final size:20
Alignment explanation
Indices: 24386--24433 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
24376 GTATATTTTT
*
24386 TATATAAAATATAATATAAA
1 TATATAAAATATAATACAAA
* * *
24406 TATATAAATTTTAATACGAA
1 TATATAAAATATAATACAAA
24426 TATATAAA
1 TATATAAA
24434 TTATTAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TATATAAAATATAATACAAA
Done.