Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold342
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: 288538
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:213353 original size:13 final size:13
Alignment explanation
Indices: 213335--213359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
213325 CATAAAATGT
213335 TGTATCGATACAA
1 TGTATCGATACAA
213348 TGTATCGATACA
1 TGTATCGATACA
213360 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:213357 original size:33 final size:33
Alignment explanation
Indices: 213315--213384 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
213305 TTCAACGATT
213315 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
213348 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
213381 TGTA
1 TGTA
213385 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:213442 original size:13 final size:13
Alignment explanation
Indices: 213424--213448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
213414 ATTACTCACA
213424 TGTATCGATACAT
1 TGTATCGATACAT
213437 TGTATCGATACA
1 TGTATCGATACA
213449 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:213513 original size:52 final size:52
Alignment explanation
Indices: 213457--213581 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 52
213447 CACTGATCTT
* * *
213457 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATATATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
213509 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
213561 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
213582 CTTTTCATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:220500 original size:1 final size:1
Alignment explanation
Indices: 220496--220578 Score: 67
Period size: 1 Copynumber: 83.0 Consensus size: 1
220486 AAAGGTGATG
* * * * * * * * *
220496 AAAAAAAAAAAAAAAAACAAACAAACAAACAAAAAAAACACACAAAAAAAAAACAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
220561 AAAAAAACACAAAAAAAA
1 AAAAAAAAAAAAAAAAAA
220579 GTGCAAAGTC
Statistics
Matches: 60, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:220529 original size:21 final size:21
Alignment explanation
Indices: 220497--220578 Score: 92
Period size: 22 Copynumber: 3.8 Consensus size: 21
220487 AAGGTGATGA
*
220497 AAAAAAAAAAAAAAAACAAAC
1 AAAAAAACAAAAAAAACAAAC
* *
220518 AAACAAACAAAAAAAACACAC
1 AAAAAAACAAAAAAAACAAAC
* *
220539 AAAAAAAAAACAAAAAAACAAAA
1 -AAAAAAACA-AAAAAAACAAAC
220562 AAAAAACACAAAAAAAA
1 AAAAAA-ACAAAAAAAA
220579 GTGCAAAGTC
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 18 0.36
22 20 0.40
23 12 0.24
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (21 bp):
AAAAAAACAAAAAAAACAAAC
Found at i:220543 original size:32 final size:32
Alignment explanation
Indices: 220496--220578 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 32
220486 AAAGGTGATG
* *
220496 AAAAAAAAAA-A-AAAAAACAAACAAACAAAC
1 AAAAAAAAAACACAAAAAAAAAACAAAAAAAC
*
220526 AAAAAAAACACACAAAAAAAAAACAAAAAAAC
1 AAAAAAAAAACACAAAAAAAAAACAAAAAAAC
220558 AAAAAAAAAACACAAAAAAAA
1 AAAAAAAAAACACAAAAAAAA
220579 GTGCAAAGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
30 9 0.19
31 1 0.02
32 37 0.79
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (32 bp):
AAAAAAAAAACACAAAAAAAAAACAAAAAAAC
Found at i:220838 original size:16 final size:15
Alignment explanation
Indices: 220816--220870 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
220806 GTTCTTTTCC
220816 AAAAAAAGAAACAAA
1 AAAAAAAGAAACAAA
220831 ACAAAAAAG--ACAAA
1 A-AAAAAAGAAACAAA
220845 AAAAAAAGAAGA-AAA
1 AAAAAAAGAA-ACAAA
*
220860 AAAAAACGAAA
1 AAAAAAAGAAA
220871 AACCCCTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 7 0.20
14 7 0.20
15 13 0.37
16 8 0.23
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAACAAA
Found at i:220851 original size:13 final size:13
Alignment explanation
Indices: 220815--220864 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
220805 TGTTCTTTTC
*
220815 CAAAAAAAGAA-A
1 CAAAAAAAAAAGA
220827 CAAAACAAAAAAGA
1 CAAAA-AAAAAAGA
220841 CAAAAAAAAAAGA
1 CAAAAAAAAAAGA
220854 -AGAAAAAAAAA
1 CA-AAAAAAAAA
220865 ACGAAAAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
12 6 0.18
13 22 0.65
14 6 0.18
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAGA
Found at i:220859 original size:11 final size:12
Alignment explanation
Indices: 220816--220872 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 12
220806 GTTCTTTTCC
*
220816 AAAAAAAGAAACA
1 AAAAAAA-AAACG
*
220829 AAACAAAAAAGACA
1 AAA-AAAAAA-ACG
*
220843 AAAAAAAAAGAAG
1 AAAAAAAAA-ACG
220856 AAAAAAAAAACG
1 AAAAAAAAAACG
220868 AAAAA
1 AAAAA
220873 CCCCTTTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
12 7 0.18
13 22 0.56
14 10 0.26
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACG
Found at i:220865 original size:14 final size:14
Alignment explanation
Indices: 220816--220865 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
220806 GTTCTTTTCC
220816 AAAAAAAGAAACAAA
1 AAAAAAAG-AACAAA
220831 ACAAAAAAG-ACAAA
1 A-AAAAAAGAACAAA
*
220845 AAAAAAAGAAGAAA
1 AAAAAAAGAACAAA
220859 AAAAAAA
1 AAAAAAA
220866 CGAAAAACCC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 7 0.22
14 17 0.53
15 1 0.03
16 7 0.22
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAACAAA
Found at i:224296 original size:13 final size:13
Alignment explanation
Indices: 224278--224307 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
224268 ACATTTTGCT
224278 ATGTATCGAAACA
1 ATGTATCGAAACA
*
224291 ATGTATCGATACA
1 ATGTATCGAAACA
224304 ATGT
1 ATGT
224308 CCCATGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
ATGTATCGAAACA
Found at i:224376 original size:20 final size:20
Alignment explanation
Indices: 224351--224388 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
224341 TACTGCCAGT
224351 TTCATGTATCGATACAATTC
1 TTCATGTATCGATACAATTC
224371 TTCATGTATCGATACAAT
1 TTCATGTATCGATACAAT
224389 GAACATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
TTCATGTATCGATACAATTC
Found at i:224418 original size:20 final size:19
Alignment explanation
Indices: 224373--224423 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
224363 TACAATTCTT
* *
224373 CATGTATCGATACAATGAA
1 CATGTATCGATAAAAAGAA
224392 CATGTATCGATAAAAAGCAA
1 CATGTATCGATAAAAAG-AA
*
224412 TATGTATCGATA
1 CATGTATCGATA
224424 CTTCTAGGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (19 bp):
CATGTATCGATAAAAAGAA
Found at i:224437 original size:20 final size:21
Alignment explanation
Indices: 224414--224452 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
224404 AAAAGCAATA
*
224414 TGTATCGATAC-TTCTAGGCT
1 TGTATCAATACTTTCTAGGCT
224434 TGTATCAATACTTTCTAGG
1 TGTATCAATACTTTCTAGG
224453 GTTTTGACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (21 bp):
TGTATCAATACTTTCTAGGCT
Found at i:225227 original size:20 final size:21
Alignment explanation
Indices: 225181--225234 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
225171 AAAACCTAGA
*
225181 ATGTATCGATACATTACCAGC
1 ATGTATCGATACATTACAAGC
**
225202 ATGTATCGATACATT-CAATT
1 ATGTATCGATACATTACAAGC
*
225222 ATGTATTGATACA
1 ATGTATCGATACA
225235 ATTTTTTACC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACATTACAAGC
Found at i:225341 original size:21 final size:20
Alignment explanation
Indices: 225294--225347 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
225284 TATTACAAGC
225294 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
225314 ATGTATCGATACA-TCAACTT
1 ATGTATCGATACATTC-ACTT
*
225334 ATTGTATCAATACA
1 A-TGTATCGATACA
225348 AATTGTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 2 0.06
20 18 0.58
21 11 0.35
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:229320 original size:19 final size:21
Alignment explanation
Indices: 229275--229326 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
229265 GTGCCAATTT
**
229275 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
229296 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
229315 CATGTATCGATA
1 CATGTATCGATA
229327 TAATGTATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 15 0.52
20 1 0.03
21 13 0.45
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:229338 original size:32 final size:33
Alignment explanation
Indices: 229297--229359 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
229287 CAATTTGTCC
**
229297 ATGTATCGATACATTG-AACATGTATCGATATA
1 ATGTATCGATACAAAGCAACATGTATCGATATA
*
229329 ATGTATCGATACAAAGCAGCATGTATCGATA
1 ATGTATCGATACAAAGCAACATGTATCGATA
229360 CATCTGGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAACATGTATCGATATA
Found at i:232085 original size:13 final size:13
Alignment explanation
Indices: 232067--232099 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
232057 ACATTTCACC
232067 ATGTATCGATACA
1 ATGTATCGATACA
232080 ATGTATCGATACA
1 ATGTATCGATACA
*
232093 CTGTATC
1 ATGTATC
232100 AAAACTGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:232175 original size:33 final size:33
Alignment explanation
Indices: 232133--232196 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
232123 TGCAAGTTTT
* *
232133 ATGTATCGATAC-AATTCAATGTGTATCGATATA
1 ATGTATCGATACTAA-GCAATATGTATCGATATA
232166 ATGTATCGATACTAAGCAATATGTATCGATA
1 ATGTATCGATACTAAGCAATATGTATCGATA
232197 CATCTGGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (33 bp):
ATGTATCGATACTAAGCAATATGTATCGATATA
Found at i:234810 original size:13 final size:13
Alignment explanation
Indices: 234792--234836 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
234782 ATAGTGCCCT
*
234792 TGTATCGATATAG
1 TGTATCAATATAG
*
234805 TGTATCAATATAA
1 TGTATCAATATAG
*
234818 TGTATCAATACAG
1 TGTATCAATATAG
234831 TGTATC
1 TGTATC
234837 GATACAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (13 bp):
TGTATCAATATAG
Found at i:234841 original size:13 final size:13
Alignment explanation
Indices: 234792--234842 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
234782 ATAGTGCCCT
* *
234792 TGTATCGATATAG
1 TGTATCAATACAG
* *
234805 TGTATCAATATAA
1 TGTATCAATACAG
234818 TGTATCAATACAG
1 TGTATCAATACAG
*
234831 TGTATCGATACA
1 TGTATCAATACA
234843 ATATATTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCAATACAG
Found at i:234854 original size:26 final size:26
Alignment explanation
Indices: 234794--234854 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
234784 AGTGCCCTTG
* * *
234794 TATCGATATAGTGTATCAATATAATG
1 TATCGATACAGTGTATCAATACAATA
* *
234820 TATCAATACAGTGTATCGATACAATA
1 TATCGATACAGTGTATCAATACAATA
*
234846 TATTGATAC
1 TATCGATAC
234855 TAAGAACACA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (26 bp):
TATCGATACAGTGTATCAATACAATA
Found at i:239014 original size:13 final size:13
Alignment explanation
Indices: 238996--239020 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
238986 CAATTCATCA
238996 TGTATCGATACAT
1 TGTATCGATACAT
239009 TGTATCGATACA
1 TGTATCGATACA
239021 ATGTGCCATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:239089 original size:13 final size:13
Alignment explanation
Indices: 239071--239129 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
239061 TGCCTGTTTC
239071 ATGTATCGATACA
1 ATGTATCGATACA
239084 ATGTATCGATAC-
1 ATGTATCGATACA
239096 A-G--T-GA-AC-
1 ATGTATCGATACA
239103 ATGTATCGATACA
1 ATGTATCGATACA
239116 ATGTATCGATACA
1 ATGTATCGATACA
239129 A
1 A
239130 AGCATAATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
9 1 0.03
10 1 0.03
11 3 0.08
12 3 0.08
13 26 0.65
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:240717 original size:13 final size:13
Alignment explanation
Indices: 240699--240738 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
240689 ATAGTAACCC
*
240699 ATGTATCGATATA
1 ATGTATCGATACA
240712 ATGTATCGATACA
1 ATGTATCGATACA
240725 ATGTATCGATACA
1 ATGTATCGATACA
240738 A
1 A
240739 AGAATATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:240831 original size:48 final size:48
Alignment explanation
Indices: 240770--240862 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
240760 TAGGTTTTCC
240770 AGATGTATCGATACATCCTTCAATGTATCCATACATTCTGGAAAACCT
1 AGATGTATCGATACATCCTTCAATGTATCCATACATTCTGGAAAACCT
*
240818 AGATGTATCGATACATCCTTCAATGTATCGATACATTCTGGAAAA
1 AGATGTATCGATACATCCTTCAATGTATCCATACATTCTGGAAAA
240863 TTTTCAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (48 bp):
AGATGTATCGATACATCCTTCAATGTATCCATACATTCTGGAAAACCT
Found at i:243097 original size:79 final size:79
Alignment explanation
Indices: 242966--243126 Score: 304
Period size: 79 Copynumber: 2.0 Consensus size: 79
242956 TTCGGAGGAG
*
242966 TTAGAATCATTAAAAACAATATGGATTGATTCTTCAACAACTAAAGTTCTTTTATTAAACACTCA
1 TTAGAATCATTAAAAACAACATGGATTGATTCTTCAACAACTAAAGTTCTTTTATTAAACACTCA
243031 ATAAGCTTTAAAAT
66 ATAAGCTTTAAAAT
*
243045 TTAGAATCATTAAAAACAACATGGATTGATTCTTCAACAACTAAAGTTCTTTTATTAAACACTCG
1 TTAGAATCATTAAAAACAACATGGATTGATTCTTCAACAACTAAAGTTCTTTTATTAAACACTCA
243110 ATAAGCTTTAAAAT
66 ATAAGCTTTAAAAT
243124 TTA
1 TTA
243127 TTAAATAACG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.35
Consensus pattern (79 bp):
TTAGAATCATTAAAAACAACATGGATTGATTCTTCAACAACTAAAGTTCTTTTATTAAACACTCA
ATAAGCTTTAAAAT
Found at i:245249 original size:13 final size:13
Alignment explanation
Indices: 245231--245256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
245221 TACAGCAAGT
245231 ATGTATCGATACA
1 ATGTATCGATACA
245244 ATGTATCGATACA
1 ATGTATCGATACA
245257 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:250464 original size:13 final size:13
Alignment explanation
Indices: 250446--250471 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
250436 TACAGCAAGT
250446 ATGTATCGATACA
1 ATGTATCGATACA
250459 ATGTATCGATACA
1 ATGTATCGATACA
250472 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:251372 original size:20 final size:21
Alignment explanation
Indices: 251347--251399 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
251337 ATTGATACAT
*
251347 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
251367 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
251388 TGTATCGATACA
1 TGTATCGATACA
251400 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:251477 original size:13 final size:13
Alignment explanation
Indices: 251459--251484 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
251449 TACACAACAG
251459 ATGTATCGATACA
1 ATGTATCGATACA
251472 ATGTATCGATACA
1 ATGTATCGATACA
251485 TCCTAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:258206 original size:20 final size:22
Alignment explanation
Indices: 258181--258225 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
258171 GCAGCACTCA
*
258181 CCAGGTCGCGACC-GGTA-CCC
1 CCAGGTCGCAACCGGGTAGCCC
258201 CCAGGTCGCAACCGGGTAGCCC
1 CCAGGTCGCAACCGGGTAGCCC
258223 CCA
1 CCA
258226 CACTCACAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.55
21 4 0.18
22 6 0.27
ACGTcount: A:0.18, C:0.44, G:0.29, T:0.09
Consensus pattern (22 bp):
CCAGGTCGCAACCGGGTAGCCC
Found at i:267521 original size:23 final size:23
Alignment explanation
Indices: 267495--267541 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
267485 GAAAGCTCGA
267495 GGAAATCTTCCGTTAGAACTTTT
1 GGAAATCTTCCGTTAGAACTTTT
267518 GGAAATCTTCCGTTAGAACTTTT
1 GGAAATCTTCCGTTAGAACTTTT
267541 G
1 G
267542 TGTAGGGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (23 bp):
GGAAATCTTCCGTTAGAACTTTT
Found at i:267689 original size:61 final size:61
Alignment explanation
Indices: 267594--267719 Score: 243
Period size: 61 Copynumber: 2.1 Consensus size: 61
267584 TGTGGTTACC
267594 TCTTTCACATGATTGAAAATTTTAATTGGCTATCTAACCATATGTAAGTTTCAAACTAAGA
1 TCTTTCACATGATTGAAAATTTTAATTGGCTATCTAACCATATGTAAGTTTCAAACTAAGA
*
267655 TCTTTCACATGATTGAAATTTTTAATTGGCTATCTAACCATATGTAAGTTTCAAACTAAGA
1 TCTTTCACATGATTGAAAATTTTAATTGGCTATCTAACCATATGTAAGTTTCAAACTAAGA
267716 TCTT
1 TCTT
267720 GATAGAGTCC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (61 bp):
TCTTTCACATGATTGAAAATTTTAATTGGCTATCTAACCATATGTAAGTTTCAAACTAAGA
Found at i:270620 original size:5 final size:5
Alignment explanation
Indices: 270606--270643 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
270596 TTACAACCCA
*
270606 AAAAG AAAAAG AAAAG AAAAG AATAG AAAAG AAAAG AA
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
270644 GAGGAAAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:270651 original size:15 final size:15
Alignment explanation
Indices: 270615--270652 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
270605 AAAAAGAAAA
*
270615 AGAAAAGAAAAGAAT
1 AGAAAAGAAAAGAAG
270630 AGAAAAGAAAAGAAG
1 AGAAAAGAAAAGAAG
*
270645 AGGAAAGA
1 AGAAAAGA
270653 GGACCAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (15 bp):
AGAAAAGAAAAGAAG
Found at i:271642 original size:7 final size:7
Alignment explanation
Indices: 271630--271655 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
271620 ATTTAAAATT
271630 ATTTTAA
1 ATTTTAA
271637 ATTTTAA
1 ATTTTAA
271644 ATTTTAA
1 ATTTTAA
271651 ATTTT
1 ATTTT
271656 GTGTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTAA
Found at i:273627 original size:28 final size:26
Alignment explanation
Indices: 273576--273627 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
273566 TTTTGATACA
*
273576 TTTATTTATTTGTATTATATTTATAT
1 TTTATTTATTTGTATTATAATTATAT
*
273602 TTTATGTTATGTTGTATTTTAATTAT
1 TTTAT-TTAT-TTGTATTATAATTAT
273628 TTATTTGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 4 0.18
28 13 0.59
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (26 bp):
TTTATTTATTTGTATTATAATTATAT
Found at i:274104 original size:6 final size:7
Alignment explanation
Indices: 274082--274106 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
274072 TAAGATTATA
274082 TTTAGTT
1 TTTAGTT
274089 TTTAGTT
1 TTTAGTT
274096 TTTAGTT
1 TTTAGTT
274103 TTTA
1 TTTA
274107 TATTATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (7 bp):
TTTAGTT
Found at i:275941 original size:22 final size:22
Alignment explanation
Indices: 275916--275957 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
275906 AGATAAACAT
275916 ATTTCTCCCCCTTTATCAAAAC
1 ATTTCTCCCCCTTTATCAAAAC
* *
275938 ATTTCTCCTCCTTTGTCAAA
1 ATTTCTCCCCCTTTATCAAA
275958 TCTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.33, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTTCTCCCCCTTTATCAAAAC
Found at i:276037 original size:92 final size:92
Alignment explanation
Indices: 275880--276066 Score: 320
Period size: 92 Copynumber: 2.0 Consensus size: 92
275870 CTCCCCCTTA
*
275880 ATTGGTTAATGAGATTTTCTCATCCTAGATAAACATATTTCTCCCCCTTTATCAAAACATTTCTC
1 ATTGGTTAACGAGATTTTCTCATCCTAGATAAACATATTTCTCCCCCTTTATCAAAACATTTCTC
* *
275945 CTCCTTTGTCAAATCTTAAAAAAATTT
66 CCCCTTTGTCAAATCTTAAAAAAAATT
* * *
275972 ATTGGTTAACGAGATTTTCTCATCCTAGATAAACATTTTTCTCCCTCTTTATCAAAGCATTTCTC
1 ATTGGTTAACGAGATTTTCTCATCCTAGATAAACATATTTCTCCCCCTTTATCAAAACATTTCTC
276037 CCCCTTTGTCAAATCTTAAAAAAAATT
66 CCCCTTTGTCAAATCTTAAAAAAAATT
276064 ATT
1 ATT
276067 TTCAATAAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (92 bp):
ATTGGTTAACGAGATTTTCTCATCCTAGATAAACATATTTCTCCCCCTTTATCAAAACATTTCTC
CCCCTTTGTCAAATCTTAAAAAAAATT
Found at i:277937 original size:13 final size:13
Alignment explanation
Indices: 277919--277943 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277909 AGTAACCCAC
277919 GTATCGATACAAT
1 GTATCGATACAAT
277932 GTATCGATACAA
1 GTATCGATACAA
277944 GGAATGTTTT
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:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:284146 original size:69 final size:70
Alignment explanation
Indices: 284047--284202 Score: 260
Period size: 69 Copynumber: 2.2 Consensus size: 70
284037 TCCCGTAGCC
* *
284047 ATGTATCGATACAATTCATAATGTATCGATACATTGATTTGAAATTATAGCTGTTTATAGCCATT
1 ATGTATCGATACAA-T-ATAATGTATCGATAAATTGATTTGAAATTATAGCCGTTTATAGCCATT
284112 ATAAGCA
64 ATAAGCA
*
284119 ATGTATCGATACAA-ATAATGTATCGATAAATTGATTTGAAATTATAGCCGTTTATAGCCGTTAT
1 ATGTATCGATACAATATAATGTATCGATAAATTGATTTGAAATTATAGCCGTTTATAGCCATTAT
284183 AAGCA
66 AAGCA
284188 ATGTATCGATACAAT
1 ATGTATCGATACAAT
284203 TCATCATATA
Statistics
Matches: 80, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
69 66 0.82
72 14 0.17
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (70 bp):
ATGTATCGATACAATATAATGTATCGATAAATTGATTTGAAATTATAGCCGTTTATAGCCATTAT
AAGCA
Found at i:284223 original size:33 final size:33
Alignment explanation
Indices: 284186--284254 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
284176 CCGTTATAAG
284186 CAATGTATCGATACAAT-TCATCATATATCGATA
1 CAATGTATCGATACAATGTCAT-ATATATCGATA
*
284219 CAATGTATCGATACAATGTCCTATATATCGATA
1 CAATGTATCGATACAATGTCATATATATCGATA
284252 CAA
1 CAA
284255 ACAGTGGTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 31 0.91
34 3 0.09
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTCATATATATCGATA
Found at i:284229 original size:13 final size:13
Alignment explanation
Indices: 284211--284237 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
284201 ATTCATCATA
284211 TATCGATACAATG
1 TATCGATACAATG
284224 TATCGATACAATG
1 TATCGATACAATG
284237 T
1 T
284238 CCTATATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:284309 original size:20 final size:20
Alignment explanation
Indices: 284283--284337 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
284273 CTGCAAGTTT
*
284283 CATGTATCGATACAATTG-T
1 CATGTATCGATACAATTGAA
*
284302 CAATGTATCGATACGA-TGAA
1 C-ATGTATCGATACAATTGAA
284322 CATGTATCGATACAAT
1 CATGTATCGATACAAT
284338 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:284341 original size:13 final size:13
Alignment explanation
Indices: 284323--284349 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
284313 TACGATGAAC
284323 ATGTATCGATACA
1 ATGTATCGATACA
284336 ATGTATCGATACA
1 ATGTATCGATACA
284349 A
1 A
284350 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:286870 original size:22 final size:22
Alignment explanation
Indices: 286843--286884 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
286833 TTTATTTGCA
286843 AAAAGTTAAAAAAAAATTGAAC
1 AAAAGTTAAAAAAAAATTGAAC
*
286865 AAAAGTTCAAAAAAAATTGA
1 AAAAGTTAAAAAAAAATTGA
286885 CCTTTTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (22 bp):
AAAAGTTAAAAAAAAATTGAAC
Done.