Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3186
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: 46239
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Found at i:5254 original size:39 final size:40
Alignment explanation
Indices: 5109--5331 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
5099 TTGAATGATG
* * * *
5109 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
5149 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
5189 TCC-GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5227 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
5266 TCCGGGTTAAGTCCCGAAGGCATTTTTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
5307 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
5332 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
38 28 0.17
39 51 0.32
40 72 0.45
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:5353 original size:79 final size:77
Alignment explanation
Indices: 5116--5364 Score: 263
Period size: 79 Copynumber: 3.2 Consensus size: 77
5106 ATGTCCGGGC
* * * * *
5116 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGA
1 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCGAAGGCATTTGTGCGA
*
5180 GATACTAATTCCGGC
64 GATACTAA-TCCGGT
* *
5195 TAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGA
5259 TACTAAATCCGGGT
66 TACT-AATCC-GGT
* * **
5273 TAAGTCCCGAAGGCATTTTTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGA
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATTTGTGCGA
5337 G-TAGCTATATCCGGT
64 GATA-CTA-ATCCGGT
* *
5352 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
5365 TACGTGATTT
Statistics
Matches: 147, Mismatches: 15, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
77 27 0.18
78 33 0.22
79 62 0.42
80 25 0.17
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (77 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGA
TACTAATCCGGT
Found at i:12271 original size:27 final size:27
Alignment explanation
Indices: 12240--12417 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
12230 TAAATTGTAC
12240 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
12267 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12293 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
12321 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
12349 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12376 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
12403 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12418 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:12354 original size:82 final size:81
Alignment explanation
Indices: 12241--12396 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
12231 AAATTGTACA
* *
12241 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
12305 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
12322 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
12387 TGCGAGTTGA
65 TGCGAATTGA
12397 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:12408 original size:82 final size:81
Alignment explanation
Indices: 12237--12417 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
12227 GATTAAATTG
* *
12237 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
12302 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
12318 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
12382 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
12400 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
12418 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:20320 original size:27 final size:27
Alignment explanation
Indices: 20289--20466 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
20279 TAAATTGTAC
20289 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
20316 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
20342 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
20370 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
20398 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
20425 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
20452 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
20467 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:20403 original size:82 final size:81
Alignment explanation
Indices: 20290--20445 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
20280 AAATTGTACA
* *
20290 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
20354 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
20371 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
20436 TGCGAGTTGA
65 TGCGAATTGA
20446 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:20457 original size:82 final size:81
Alignment explanation
Indices: 20286--20466 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
20276 GATTAAATTG
* *
20286 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
20351 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
20367 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
20431 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
20449 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
20467 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:22739 original size:45 final size:45
Alignment explanation
Indices: 22652--22764 Score: 126
Period size: 45 Copynumber: 2.6 Consensus size: 45
22642 TGGCATTTCA
*
22652 CCTGTTAGGCTCG-AGGCCCG-ATATCAGTCCACCAGCATTATAG
1 CCTGCTAGGCTCGAAGGCCCGAATATCAGTCCACCAGCATTATAG
*
22695 CCTGCTAGGCTCGAAGGCCCGAATAGT-A-TCTCACCGGCATTATAG
1 CCTGCTAGGCTCGAAGGCCCGAATA-TCAGTC-CACCAGCATTATAG
** * *
22740 TTTGCTAAGCTCAAAGGCCCGAATA
1 CCTGCTAGGCTCGAAGGCCCGAATA
22765 ATCAAGTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
43 12 0.20
44 9 0.15
45 38 0.63
46 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (45 bp):
CCTGCTAGGCTCGAAGGCCCGAATATCAGTCCACCAGCATTATAG
Found at i:23129 original size:43 final size:43
Alignment explanation
Indices: 23081--23205 Score: 198
Period size: 43 Copynumber: 2.9 Consensus size: 43
23071 ACATATCATT
23081 TCACCGGCATTACA-CCTGCTAGGCACGAAGGCCCAAATACACA
1 TCACCGGCATTA-AGCCTGCTAGGCACGAAGGCCCAAATACACA
* *
23124 TCACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCATTAAGCCTGCTAGGCACGAAGGCCCAAATACACA
* *
23167 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCTAAATA
1 TCACCGGCATTAAGCCTGCTAGGCACGAAGGCCCAAATA
23206 TAATACTAGC
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
42 1 0.01
43 74 0.99
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.14
Consensus pattern (43 bp):
TCACCGGCATTAAGCCTGCTAGGCACGAAGGCCCAAATACACA
Found at i:25091 original size:27 final size:27
Alignment explanation
Indices: 25061--25685 Score: 670
Period size: 27 Copynumber: 23.2 Consensus size: 27
25051 TAATTTGTAA
* * *
25061 AATTACCGAAATACCCCTATAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
25088 AATTACTGAAATA-CCCTCGTAGAGTAG
1 AATTACTGAAATACCCCT-GTAGGGTAG
* * *
25115 AATTACTAAAATACCCCTATAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
25142 AATTACTGAAATA-CCCTGTATGGTAC
1 AATTACTGAAATACCCCTGTAGGGTAG
*
25168 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
** *
25195 AATTACCAAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
25222 AATTGCTAAAATACCCTTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
25249 AATTACCG-AATACCCCTATAGTGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
25275 AATTACTAAAATACCCCTATAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
25302 AATTACCGAAATACCCTTGTAGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * * *
25329 AATGACTAAAATACCCTTGTAAGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
25356 AATGACTAAAATACCCCTGTAAGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
25383 AATTACTGAAATACCCCTATATGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
25410 AATTACTGAAATACCTCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
25437 AATTA-TCGAAATATCCCTGTAAGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
**
25464 AATTA-TCGAAATACCCCTACAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* *
25491 AATAACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
25518 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
25545 AATTATTGAAATACCTCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
25572 AATTA-TCGAAATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* *
25599 AATTACTGGAATACCCCTGTAGGGTAT
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
25626 AATTACCGAAATACCCTTGTAGGGTAGG
1 AATTACTGAAATACCCCTGTAGGGTA-G
*
25654 AA-TAATGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
25680 CATTAC
1 AATTAC
25686 GAAGAAACTC
Statistics
Matches: 508, Mismatches: 80, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
26 51 0.10
27 450 0.89
28 7 0.01
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:26145 original size:6 final size:6
Alignment explanation
Indices: 26134--26236 Score: 86
Period size: 6 Copynumber: 16.8 Consensus size: 6
26124 TTACCTAATA
* *
26134 CTGATT CTGATT TTGATT CT-ATT ACCTGATA CTGATT CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT CTGATT
* * * *
26183 TTG-TCA CTTAATT TTGATT CTGATT CTGATT CTGATT CTGATT CT-AGTT
1 CTGAT-T C-TGATT CTGATT CTGATT CTGATT CTGATT CTGATT CTGA-TT
26232 CTGAT
1 CTGAT
26237 AATGTTTCTT
Statistics
Matches: 77, Mismatches: 12, Indels: 16
0.73 0.11 0.15
Matches are distributed among these distances:
5 5 0.06
6 65 0.84
7 4 0.05
8 3 0.04
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.50
Consensus pattern (6 bp):
CTGATT
Found at i:26149 original size:31 final size:31
Alignment explanation
Indices: 26106--26215 Score: 130
Period size: 31 Copynumber: 3.5 Consensus size: 31
26096 TTGCATTCAC
* *
26106 ATTCAGATTTTGATTCTATTACCTAATACTG
1 ATTCTGATTCTGATTCTATTACCTAATACTG
* *
26137 ATTCTGATTTTGATTCTATTACCTGATACTG
1 ATTCTGATTCTGATTCTATTACCTAATACTG
* * * * **
26168 ATTCTGATTCTGATTTTGTCACTTAATTTTG
1 ATTCTGATTCTGATTCTATTACCTAATACTG
26199 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
26216 GATTCTGATT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTATTACCTAATACTG
Found at i:26184 original size:37 final size:37
Alignment explanation
Indices: 26106--26228 Score: 111
Period size: 37 Copynumber: 3.5 Consensus size: 37
26096 TTGCATTCAC
*
26106 ATTCAGATTTTGATTCTATTACCT-A-A-T-A--CTG
1 ATTCTGATTTTGATTCTATTACCTGATACTGATTCTG
26137 ATTCTGATTTTGATTCTATTACCTGATACTGATTCTG
1 ATTCTGATTTTGATTCTATTACCTGATACTGATTCTG
** *
26174 ATTCTGATTTTG--TC-ACTTAATTTTGATTCTGATTCTG
1 ATTCTGATTTTGATTCTA-TT-A-CCTGATACTGATTCTG
*
26211 ATTCTGATTCTGATTCTA
1 ATTCTGATTTTGATTCTA
26229 GTTCTGATAA
Statistics
Matches: 75, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
31 23 0.31
32 1 0.01
33 1 0.01
34 2 0.03
35 5 0.07
36 1 0.01
37 39 0.52
39 2 0.03
40 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (37 bp):
ATTCTGATTTTGATTCTATTACCTGATACTGATTCTG
Found at i:27701 original size:41 final size:41
Alignment explanation
Indices: 27656--27774 Score: 161
Period size: 41 Copynumber: 2.9 Consensus size: 41
27646 CTTGTATAAA
* * *
27656 ACACCGGCAC-AGGACCTGCTAGGTAATAAACCTGAT-TCAAT
1 ACACCGGCACAAAG-CCTGCTAGGCAATAAGCCTGATGTC-AT
*
27697 ACACCGGCATAAAGCCTGCTAGGCAATAAGCCTGATGTCAT
1 ACACCGGCACAAAGCCTGCTAGGCAATAAGCCTGATGTCAT
27738 ACACCGGCATCAAAGCCTGCTAGGCAATAAGCCTGAT
1 ACACCGGCA-CAAAGCCTGCTAGGCAATAAGCCTGAT
27775 ATATCACTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
41 40 0.57
42 30 0.43
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (41 bp):
ACACCGGCACAAAGCCTGCTAGGCAATAAGCCTGATGTCAT
Found at i:27766 original size:42 final size:41
Alignment explanation
Indices: 27670--27774 Score: 167
Period size: 41 Copynumber: 2.5 Consensus size: 41
27660 CGGCACAGGA
* *
27670 CCTGCTAGGTAATAAACCTGATTCAATACACCGGCATAAAG
1 CCTGCTAGGCAATAAGCCTGATTCAATACACCGGCATAAAG
27711 CCTGCTAGGCAATAAGCCTGATGTC-ATACACCGGCATCAAAG
1 CCTGCTAGGCAATAAGCCTGAT-TCAATACACCGGCAT-AAAG
27753 CCTGCTAGGCAATAAGCCTGAT
1 CCTGCTAGGCAATAAGCCTGAT
27775 ATATCACTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
41 32 0.53
42 28 0.47
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (41 bp):
CCTGCTAGGCAATAAGCCTGATTCAATACACCGGCATAAAG
Found at i:28718 original size:20 final size:21
Alignment explanation
Indices: 28679--28732 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
28669 TTTGTAATAC
28679 ATTTATTTAATTACTAAAAGAT
1 ATTTA-TTAATTACTAAAAGAT
*
28701 ATTTATTATTTA-TAAAAGAT
1 ATTTATTAATTACTAAAAGAT
28721 ATTTATTAATTA
1 ATTTATTAATTA
28733 AATAATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 19 0.63
21 6 0.20
22 5 0.17
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (21 bp):
ATTTATTAATTACTAAAAGAT
Found at i:28830 original size:19 final size:19
Alignment explanation
Indices: 28802--28840 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28792 TGATCCATGG
*
28802 ATACATATGTA-ATAATAAT
1 ATACACATGTATA-AATAAT
28821 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
28840 A
1 A
28841 AATAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:28967 original size:13 final size:14
Alignment explanation
Indices: 28935--28976 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
28925 TGAAACAGGG
28935 GAAGAAAG-AAGGA
1 GAAGAAAGAAAGGA
28948 GAA-AAAGAAAGGA
1 GAAGAAAGAAAGGA
*
28961 -AAGAAAGAAAAGA
1 GAAGAAAGAAAGGA
28974 GAA
1 GAA
28977 ATTTAAAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 6 0.24
13 17 0.68
14 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
GAAGAAAGAAAGGA
Found at i:29839 original size:15 final size:14
Alignment explanation
Indices: 29819--29860 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
29809 CGATGAATTT
29819 ATTGAATTTATATTG
1 ATTGAA-TTATATTG
*
29834 ATTGAAATTATTTTG
1 ATTG-AATTATATTG
29849 ATTGAATTATAT
1 ATTGAATTATAT
29861 AATATATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 15 0.62
16 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (14 bp):
ATTGAATTATATTG
Found at i:30300 original size:21 final size:22
Alignment explanation
Indices: 30242--30302 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
30232 AGGCATTTTA
30242 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCG-ATTTCAGGCACCTCG
*
30265 TGTGTCGA-ATCAGGCACCTCG
1 TGTGTCGATTTCAGGCACCTCG
*
30286 TGTGTC-ATTTTAGGCAC
1 TGTGTCGATTTCAGGCAC
30303 TTTATGTGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.03
21 25 0.74
22 1 0.03
23 7 0.21
ACGTcount: A:0.16, C:0.25, G:0.26, T:0.33
Consensus pattern (22 bp):
TGTGTCGATTTCAGGCACCTCG
Found at i:35064 original size:23 final size:24
Alignment explanation
Indices: 35020--35071 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
35010 ATTTATATTT
* * *
35020 ATTAATGTTATTATTATTAAATGA
1 ATTAATATTATTATTATGAAATAA
35044 ATTAATATTA-TATTATGAAATAA
1 ATTAATATTATTATTATGAAATAA
35067 ATTAA
1 ATTAA
35072 ATAAAGACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (24 bp):
ATTAATATTATTATTATGAAATAA
Found at i:35290 original size:19 final size:19
Alignment explanation
Indices: 35262--35300 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
35252 TGATCTATGG
*
35262 ATACATATGTA-ATAATAAT
1 ATACACATGTATA-AATAAT
35281 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
35300 A
1 A
35301 AATAAGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:35425 original size:13 final size:13
Alignment explanation
Indices: 35396--35430 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
35386 GAAACAGGGG
35396 AAGAAAG-AAGGA
1 AAGAAAGAAAGGA
*
35408 GAGAAAGAAAGGA
1 AAGAAAGAAAGGA
35421 AAGAAAGAAA
1 AAGAAAGAAA
35431 AGAGAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAAGAAAGGA
Found at i:36296 original size:15 final size:15
Alignment explanation
Indices: 36276--36317 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
36266 CAATGAATTT
36276 ATTGAATTTATATT-G
1 ATTGAA-TTATATTGG
36291 ATTGAAATTAT-TTGG
1 ATTG-AATTATATTGG
36306 ATTGAATTATAT
1 ATTGAATTATAT
36318 AATATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 8 0.33
15 14 0.58
16 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (15 bp):
ATTGAATTATATTGG
Found at i:36724 original size:23 final size:22
Alignment explanation
Indices: 36698--36758 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
36688 AGGCATTTTA
*
36698 TGTGTCGTATTTTAGGCATCTCG
1 TGTGTCG-ATTTTAGGCACCTCG
* *
36721 TGTGTCGA-ATCAGGCACCTCG
1 TGTGTCGATTTTAGGCACCTCG
36742 TGTGTCG-TTTTAGGCAC
1 TGTGTCGATTTTAGGCAC
36759 TTTATGTGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 24 0.75
22 1 0.03
23 7 0.22
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.36
Consensus pattern (22 bp):
TGTGTCGATTTTAGGCACCTCG
Found at i:37030 original size:10 final size:10
Alignment explanation
Indices: 37015--37039 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
37005 GAGTTCAAAT
37015 TGATGATATA
1 TGATGATATA
37025 TGATGATATA
1 TGATGATATA
37035 TGATG
1 TGATG
37040 CCATTTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (10 bp):
TGATGATATA
Found at i:41113 original size:55 final size:56
Alignment explanation
Indices: 40943--41116 Score: 325
Period size: 56 Copynumber: 3.1 Consensus size: 56
40933 ACAAGGGATG
40943 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
40999 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAG-
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
41054 ATGGGCAAAACATGTCATGAAACATG-TGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
41109 ATGGGCAA
1 ATGGGCAA
41117 TAAACTAATA
Statistics
Matches: 116, Mismatches: 1, Indels: 3
0.97 0.01 0.03
Matches are distributed among these distances:
54 27 0.23
55 34 0.29
56 55 0.47
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.22
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:41157 original size:110 final size:111
Alignment explanation
Indices: 40942--41157 Score: 253
Period size: 110 Copynumber: 2.0 Consensus size: 111
40932 GACAAGGGAT
40942 GATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAA
1 GATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAA
* * ** ** *** *
41007 AACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAA
66 AACATATCAAGAAACATGAAGTGAAAAAACAAAAAAAAAATAAGAA
*
41053 GATGGGCAAAACATGTCATGAAACATG-TGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAA
1 GATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAA
*
41117 TAA-ACTAAT-AAGAAA-TTGAAG-GAAAAAACAAAGAAAAAAAT
66 -AACA-T-ATCAAGAAACATGAAGTGAAAAAACAAA-AAAAAAAT
41158 GTGTTCATCA
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
109 6 0.07
110 47 0.53
111 35 0.39
112 1 0.01
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.21
Consensus pattern (111 bp):
GATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAA
AACATATCAAGAAACATGAAGTGAAAAAACAAAAAAAAAATAAGAA
Found at i:45254 original size:57 final size:56
Alignment explanation
Indices: 45183--45353 Score: 235
Period size: 57 Copynumber: 3.1 Consensus size: 56
45173 GACAAGGATG
45183 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAAAAAAATTAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAAAAAAA-TAAGAAGC
* *
45240 ATGGGCAAACCATGTCATGAAACAATGTTGTGTTAATGG-AAAAAAAAATAAGAAGA
1 ATGGGCAAAACATGTCATGAAAC-ATGTTGTGTTAATGGAAAAAAAAAATAAGAAGC
* *
45296 ATGGGGCAAAAACATGTCATGAAACA---TGTG-TAATGGAAGAATAAAATAAGAAGC
1 AT-GGGC-AAAACATGTCATGAAACATGTTGTGTTAATGGAAAAAAAAAATAAGAAGC
45350 ATGG
1 ATGG
45354 CAATAAACTA
Statistics
Matches: 104, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
53 8 0.08
54 20 0.19
56 9 0.09
57 36 0.35
58 31 0.30
ACGTcount: A:0.47, C:0.09, G:0.23, T:0.21
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAAAAAAATAAGAAGC
Done.