Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 145 of 145
Found at i:47942513 original size:15 final size:14
Alignment explanation
Indices: 47942492--47942527 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
47942482 ATAATCCTTA
*
47942492 ATAATTATCTTAAT
1 ATAATTATCCTAAT
47942506 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
47942521 ATAATTA
1 ATAATTA
47942528 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:47943264 original size:45 final size:45
Alignment explanation
Indices: 47943148--47943759 Score: 501
Period size: 45 Copynumber: 13.6 Consensus size: 45
47943138 CATCATGGCG
* * **
47943148 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCA
* * * *
47943192 AATCTTATCTTCCTGAAGTTACGGTGGAGCAAATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCA
* * *
47943237 AATCTTATCTCCTTGAATTTGCAGTGGAGCAAATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCA
** * ** * * *
47943282 AATCTTATCTCTTTGAAGTTGTAGTATAACATATT-AA-A-ACCATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC--A
* * *
47943326 AATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATT--AGA-ACCATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC--A
* * *
47943370 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATT-AAAACTA-TA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TAGCA
* * * ***
47943414 AATCTTATATCTCTGAAGTTACAGTGGAGCAGATTGAAGATAATG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCA
* *
47943459 AATCTTATCTCCCTGAAATTGCAGTGGAGCATATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCA
* * * * * *
47943504 AATCTTATTTCCCTGGAGTTGTAGTGGAACAGATTAAAGCTGCAAGTCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT---AG---CA
* * **
47943555 AATCTTATCTCCCTGAAGTTGCATTGGAGTAGATTGAAGATAATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCA
* *
47943600 AATCTTATCTCCCTCAAGTTGCAGTGGAGCAGATTGAAGATAGTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCA
* * *
47943645 AATCTTATCTCCTTGAAGTTGCAGCGGAGCAGATTAAAGATA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCA
* * * * ** **
47943689 AATCTCATCTTCCTGAGGTTGTA-TCGGAATAGATTGAACTTA-CA
1 AATCTTATCTCCCTGAAGTTGCAGT-GGAGCAGATTGAAGATAGCA
* * *
47943733 ATTCTTATATTCCTGAAGTTGCAGTGG
1 AATCTTATCTCCCTGAAGTTGCAGTGG
47943760 GTTAGAATGA
Statistics
Matches: 461, Mismatches: 90, Indels: 34
0.79 0.15 0.06
Matches are distributed among these distances:
42 2 0.00
43 2 0.00
44 191 0.41
45 227 0.49
47 1 0.00
48 3 0.01
51 35 0.08
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (45 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCA
Found at i:47943489 original size:222 final size:226
Alignment explanation
Indices: 47943148--47943704 Score: 675
Period size: 222 Copynumber: 2.5 Consensus size: 226
47943138 CATCATGGCG
* * *
47943148 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCTTATCT-TCCTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACTATAAATCTTATCTCT-CTGAAGTT
* * * * *
47943212 ACGGTGGAGCAAATTGAAGATAGCAAATCTTATCTCCTTGAATTTGCAGTGGAGCAAATTGAAGA
65 ACAGTGGAGCAGATTGAAGATAACAAATCTTATCTCCCTGAAATTGCAGTGGAGCAAATTGAAGA
** * *
47943277 TAGCAAATCTTATCTCTTTGAAGTTGTAGTATAACATATTAAAAC-C-A-T-AAATCTTATCTCC
130 TAGCAAATCTTATCTCCCTGAAGTTGTAGTAGAACAGATTAAAACGCAAGTCAAATCTTATCTCC
*
47943338 TTGAAGTTGCAGTGGAGTAGATT-AGA-ACCATA
195 CTGAAGTTGCAGTGGAGTAGATTAAGATA--ATA
* * *
47943370 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACTATAAATCTTATATCTCTGAAGTTA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACTATAAATCTTATCTCTCTGAAGTTA
** *
47943435 CAGTGGAGCAGATTGAAGATAATGAATCTTATCTCCCTGAAATTGCAGTGGAGCATATTGAAGAT
66 CAGTGGAGCAGATTGAAGATAACAAATCTTATCTCCCTGAAATTGCAGTGGAGCAAATTGAAGAT
* * * *
47943500 AGCAAATCTTATTTCCCTGGAGTTGTAGTGGAACAGATTAAAGCTGCAAGTCACAAATCTTATCT
131 AGCAAATCTTATCTCCCTGAAGTTGTAGTAGAACAGATTAAAAC-GCAAGT--CAAATCTTATCT
*
47943565 CCCTGAAGTTGCATTGGAGTAGATTGAAGATAATA
193 CCCTGAAGTTGCAGTGGAGTAGATT-AAGATAATA
* *
47943600 AATCTTATCTCCCTCAAGTTGCAGTGGAGCAGATTGAAGA-TAGTAAATCTTATCTC-CTTGAAG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATT-AAAACTA-TAAATCTTATCTCTC-TGAAG
* * * * *
47943663 TTGCAGCGGAGCAGATTAAAGAT-ACAAATCTCATCTTCCTGA
63 TTACAGTGGAGCAGATTGAAGATAACAAATCTTATCTCCCTGA
47943705 GGTTGTATCG
Statistics
Matches: 286, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
222 150 0.52
223 1 0.00
224 1 0.00
225 1 0.00
226 1 0.00
229 34 0.12
230 54 0.19
231 43 0.15
232 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (226 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACTATAAATCTTATCTCTCTGAAGTTA
CAGTGGAGCAGATTGAAGATAACAAATCTTATCTCCCTGAAATTGCAGTGGAGCAAATTGAAGAT
AGCAAATCTTATCTCCCTGAAGTTGTAGTAGAACAGATTAAAACGCAAGTCAAATCTTATCTCCC
TGAAGTTGCAGTGGAGTAGATTAAGATAATA
Found at i:47943577 original size:96 final size:89
Alignment explanation
Indices: 47943148--47943698 Score: 428
Period size: 89 Copynumber: 6.1 Consensus size: 89
47943138 CATCATGGCG
* * ** * *
47943148 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCA-CAAATCTTATCTTCCTGAAGTT
1 AATCTTATCTCCCTCAAGTTGCAGTGGAACAGATTAAAGATAGTAAATCTTATCTCCCTGAAGTT
* * *
47943212 ACGGTGGAGCAAATTGAAGATAGCA
66 GCAGTGGAGCAGATTGAAGATA-CA
* * * * * * * **
47943237 AATCTTATCTCCTTGAATTTGCAGTGGAGCAAATTGAAGATAGCAAATCTTATCTCTTTGAAGTT
1 AATCTTATCTCCCTCAAGTTGCAGTGGAACAGATTAAAGATAGTAAATCTTATCTCCCTGAAGTT
* ** * * * * *
47943302 GTAGTATAACATATT-AAAACCATA
66 GCAGTGGAGCAGATTGAAGA-TACA
* * ** **
47943326 AATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAGAA-CCA-TAAATCTTATCTCCCTGAAGT
1 AATCTTATCTCCCTCAAGTTGCAGTGGAACAGATTA-AAGATAGTAAATCTTATCTCCCTGAAGT
* * *
47943389 TGTAGTGGAGCAGATT-AAAACTATA
65 TGCAGTGGAGCAGATTGAAGA-TACA
* * * * * * * * *
47943414 AATCTTATATCTCTGAAGTTACAGTGGAGCAGATTGAAGATAATGAATCTTATCTCCCTGAAATT
1 AATCTTATCTCCCTCAAGTTGCAGTGGAACAGATTAAAGATAGTAAATCTTATCTCCCTGAAGTT
*
47943479 GCAGTGGAGCATATTGAAGATAGCA
66 GCAGTGGAGCAGATTGAAGATA-CA
* ** * *
47943504 AATCTTATTTCCCTGGAGTTGTAGTGGAACAGATTAAAGCTGCAAGTCACAAATCTTATCTCCCT
1 AATCTTATCTCCCTCAAGTTGCAGTGGAACAGATTAAAGAT---AGT---AAATCTTATCTCCCT
* * *
47943569 GAAGTTGCATTGGAGTAGATTGAAGATAATA
60 GAAGTTGCAGTGGAGCAGATTGAAGAT-ACA
* * *
47943600 AATCTTATCTCCCTCAAGTTGCAGTGGAGCAGATTGAAGATAGTAAATCTTATCTCCTTGAAGTT
1 AATCTTATCTCCCTCAAGTTGCAGTGGAACAGATTAAAGATAGTAAATCTTATCTCCCTGAAGTT
* *
47943665 GCAGCGGAGCAGATTAAAGATACA
66 GCAGTGGAGCAGATTGAAGATACA
*
47943689 AATCTCATCT
1 AATCTTATCT
47943699 TCCTGAGGTT
Statistics
Matches: 371, Mismatches: 77, Indels: 28
0.78 0.16 0.06
Matches are distributed among these distances:
87 2 0.01
88 69 0.19
89 118 0.32
90 104 0.28
93 5 0.01
96 72 0.19
97 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (89 bp):
AATCTTATCTCCCTCAAGTTGCAGTGGAACAGATTAAAGATAGTAAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAGATTGAAGATACA
Found at i:47943598 original size:141 final size:134
Alignment explanation
Indices: 47943148--47943693 Score: 499
Period size: 141 Copynumber: 4.0 Consensus size: 134
47943138 CATCATGGCG
* * * * ** * *
47943148 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAG-CCACAAATCTTATCTTCCTGAAGTT
1 AATCTTATATCCCTGAAGTTACAGTGGAGCAGATTGAAGATAATAAATCTTATCTCCCTGAAGTT
* * * * * * * * *
47943212 ACGGTGGAGCAAATTGAAGATAGCAAATCTTATCTCCTTGAATTTGCAGTGGAGCAAATTGAAGA
66 GCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGC
*
47943277 TAGCA
131 TA-TA
* ** ** ** * * * ** *
47943282 AATCTTATCTCTTTGAAGTTGTAGTATAACATATT-AAAACCATAAATCTTATCTCCTTGAAGTT
1 AATCTTATATCCCTGAAGTTACAGTGGAGCAGATTGAAGATAATAAATCTTATCTCCCTGAAGTT
* *
47943346 GCAGTGGAGTAGATT--AGA-ACCATAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA
66 GCAGTGGAGCAGATTGAAGATAGC--AAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA
*
47943408 ACTATA
129 GCTATA
* * *
47943414 AATCTTATATCTCTGAAGTTACAGTGGAGCAGATTGAAGATAATGAATCTTATCTCCCTGAAATT
1 AATCTTATATCCCTGAAGTTACAGTGGAGCAGATTGAAGATAATAAATCTTATCTCCCTGAAGTT
* * * *
47943479 GCAGTGGAGCATATTGAAGATAGCAAATCTTATTTCCCTGGAGTTGTAGTGGAACAGATTAAAGC
66 GCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGC
47943544 TGCAAGTCACA
131 T---A-T---A
* * * * *
47943555 AATCTTATCTCCCTGAAGTTGCATTGGAGTAGATTGAAGATAATAAATCTTATCTCCCTCAAGTT
1 AATCTTATATCCCTGAAGTTACAGTGGAGCAGATTGAAGATAATAAATCTTATCTCCCTGAAGTT
* * * * *
47943620 GCAGTGGAGCAGATTGAAGATAGTAAATCTTATCTCCTTGAAGTTGCAGCGGAGCAGATTAAAGA
66 GCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGC
*
47943685 TACA
131 TATA
47943689 AATCT
1 AATCT
47943694 CATCTTCCTG
Statistics
Matches: 334, Mismatches: 64, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
131 2 0.01
132 31 0.09
133 74 0.22
134 104 0.31
135 3 0.01
136 2 0.01
137 1 0.00
138 2 0.01
141 115 0.34
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (134 bp):
AATCTTATATCCCTGAAGTTACAGTGGAGCAGATTGAAGATAATAAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGC
TATA
Found at i:47945505 original size:76 final size:77
Alignment explanation
Indices: 47945425--47945578 Score: 301
Period size: 76 Copynumber: 2.0 Consensus size: 77
47945415 TTATTATTAT
47945425 TCTTCATTATATTATTAAATAAAATATTAATCATGTTATAATCATTATCGTTATTATTATAATCA
1 TCTTCATTATATTATTAAATAAAATATTAATCATGTTATAATCATTATCGTTATTATTATAATCA
47945490 A-TTGTGTTGCA
66 ATTTGTGTTGCA
47945501 TCTTCATTATATTATTAAATAAAATATTAATCATGTTATAATCATTATCGTTATTATTATAATCA
1 TCTTCATTATATTATTAAATAAAATATTAATCATGTTATAATCATTATCGTTATTATTATAATCA
47945566 ATTTGTGTTGCA
66 ATTTGTGTTGCA
47945578 T
1 T
47945579 TATTACTTTT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 66 0.86
77 11 0.14
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (77 bp):
TCTTCATTATATTATTAAATAAAATATTAATCATGTTATAATCATTATCGTTATTATTATAATCA
ATTTGTGTTGCA
Found at i:47946308 original size:28 final size:28
Alignment explanation
Indices: 47946277--47946336 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
47946267 AAAAGCCTTT
47946277 TTTTTTTA-AATTTACCGAAATGGGCCGA
1 TTTTTTTATAATTTACCGAAATGGGCC-A
* *
47946305 TTTTTTTATTATTTACCGGAATGGGCCA
1 TTTTTTTATAATTTACCGAAATGGGCCA
47946333 TTTT
1 TTTT
47946337 CCGCGAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (28 bp):
TTTTTTTATAATTTACCGAAATGGGCCA
Found at i:47948264 original size:15 final size:15
Alignment explanation
Indices: 47948244--47948277 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
47948234 NNNNNNATTA
47948244 TATATATATATATTT
1 TATATATATATATTT
47948259 TATATATATATATTT
1 TATATATATATATTT
47948274 TATA
1 TATA
47948278 ATTCACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATATATATATTT
Found at i:47950257 original size:79 final size:80
Alignment explanation
Indices: 47950126--47950284 Score: 311
Period size: 79 Copynumber: 2.0 Consensus size: 80
47950116 GGTATCTTGG
47950126 ATATTTAAACAATAACTTAAGATTTTCGTAATTGAATGTTGAAAAAGAATATATATATATATATA
1 ATATTTAAACAATAACTTAAGATTTTCGTAATTGAATGTTGAAAAAGAATATATATATATATATA
47950191 TATA-ATATGCATGT
66 TATATATATGCATGT
47950205 ATATTTAAACAATAACTTAAGATTTTCGTAATTGAATGTTGAAAAAGAATATATATATATATATA
1 ATATTTAAACAATAACTTAAGATTTTCGTAATTGAATGTTGAAAAAGAATATATATATATATATA
47950270 TATATATATGCATGT
66 TATATATATGCATGT
47950285 TGGTGTTACA
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 69 0.87
80 10 0.13
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (80 bp):
ATATTTAAACAATAACTTAAGATTTTCGTAATTGAATGTTGAAAAAGAATATATATATATATATA
TATATATATGCATGT
Found at i:47950260 original size:2 final size:2
Alignment explanation
Indices: 47950253--47950278 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47950243 TTGAAAAAGA
47950253 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
47950279 GCATGTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47952135 original size:12 final size:13
Alignment explanation
Indices: 47952118--47952149 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
47952108 GCCTAATTTG
47952118 ATTAAATAAAT-T
1 ATTAAATAAATCT
47952130 ATTAAA-AAATCT
1 ATTAAATAAATCT
47952142 ATTAAATA
1 ATTAAATA
47952150 GAAAAATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 13 0.72
13 1 0.06
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTAAATAAATCT
Found at i:47952999 original size:37 final size:35
Alignment explanation
Indices: 47952949--47953025 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 35
47952939 AATTGGAAAA
** * *
47952949 AGAATATTTTTAAATGGTTACGGTTTAACAAAATC
1 AGAATATTTTTAAACAGTTACGATTTAACAAAACC
*
47952984 AGAATATACTTTTAAACAGTTATGATTTAACAAAACC
1 AGAATAT--TTTTAAACAGTTACGATTTAACAAAACC
47953021 AGAAT
1 AGAAT
47953026 CTATCTATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 7 0.20
37 28 0.80
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (35 bp):
AGAATATTTTTAAACAGTTACGATTTAACAAAACC
Found at i:47954439 original size:23 final size:23
Alignment explanation
Indices: 47954407--47954450 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
47954397 TTATTTTAAA
47954407 TTTAA-ATTTTAATAATTTTATTT
1 TTTAATATTTTAA-AATTTTATTT
*
47954430 TTTAATTTTTTAAAATTTTAT
1 TTTAATATTTTAAAATTTTAT
47954451 ATATAACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTAATATTTTAAAATTTTATTT
Found at i:47958065 original size:9 final size:9
Alignment explanation
Indices: 47958053--47958090 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
47958043 ATTCGGTCGG
47958053 TTAACCGAA
1 TTAACCGAA
47958062 TTAACCGAA
1 TTAACCGAA
*
47958071 TTACCCGAA
1 TTAACCGAA
*
47958080 TTACCCGAA
1 TTAACCGAA
47958089 TT
1 TT
47958091 GAATCACTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (9 bp):
TTAACCGAA
Found at i:47958256 original size:18 final size:18
Alignment explanation
Indices: 47958233--47958276 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
47958223 AATTTTTATG
*
47958233 ATTGGGTTCGGTTGGGTA
1 ATTGGGTTCGGTTGGATA
*
47958251 ATTGGGTTGGGTTGGATA
1 ATTGGGTTCGGTTGGATA
*
47958269 CTTGGGTT
1 ATTGGGTT
47958277 TGGATTTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.05, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTCGGTTGGATA
Found at i:47958722 original size:14 final size:14
Alignment explanation
Indices: 47958703--47958729 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47958693 ACACTCGGGG
47958703 ACCAAAACCCAAAT
1 ACCAAAACCCAAAT
47958717 ACCAAAACCCAAA
1 ACCAAAACCCAAA
47958730 CCAACCCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.37, G:0.00, T:0.04
Consensus pattern (14 bp):
ACCAAAACCCAAAT
Found at i:47959963 original size:3 final size:3
Alignment explanation
Indices: 47959957--47959992 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
47959947 ATTAGTATTA
47959957 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
47959993 ACTCATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:47960045 original size:8 final size:8
Alignment explanation
Indices: 47960032--47960059 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
47960022 TTTGTTATGC
47960032 ACATATAT
1 ACATATAT
47960040 ACATATAT
1 ACATATAT
47960048 ACATATAT
1 ACATATAT
47960056 ACAT
1 ACAT
47960060 TTTTATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (8 bp):
ACATATAT
Found at i:47960127 original size:4 final size:4
Alignment explanation
Indices: 47960118--47960154 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
47960108 TTGCTTGATG
*
47960118 TTTA TTTA TTTA TGTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
47960155 ATGTCAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:47963645 original size:18 final size:19
Alignment explanation
Indices: 47963618--47963653 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
47963608 TATTTGTATA
47963618 TTTAATAGATATTTATTAT
1 TTTAATAGATATTTATTAT
47963637 TTTAA-AGATATTTATTA
1 TTTAATAGATATTTATTA
47963654 GATAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTAATAGATATTTATTAT
Found at i:47963819 original size:9 final size:10
Alignment explanation
Indices: 47963797--47963838 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
47963787 AAAGTAAAAT
47963797 AAAAGAAACA
1 AAAAGAAACA
47963807 AAAAGAAAC-
1 AAAAGAAACA
47963816 AAAAGAAGAACA
1 AAAAG-A-AACA
47963828 GAAAAGAAACA
1 -AAAAGAAACA
47963839 GAGAAAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 5 0.18
10 10 0.36
11 7 0.25
12 1 0.04
13 5 0.18
ACGTcount: A:0.76, C:0.10, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAGAAACA
Found at i:47963838 original size:11 final size:11
Alignment explanation
Indices: 47963797--47963846 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
47963787 AAAGTAAAAT
47963797 AAAAGAAACA-
1 AAAAGAAACAG
*
47963807 AAAAGAAACAA
1 AAAAGAAACAG
47963818 AAGAAG-AACAG
1 AA-AAGAAACAG
47963829 AAAAGAAACAG
1 AAAAGAAACAG
47963840 AGAAAGA
1 A-AAAGA
47963847 GACGAAACAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
10 13 0.37
11 14 0.40
12 8 0.23
ACGTcount: A:0.74, C:0.08, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAACAG
Found at i:47963853 original size:22 final size:20
Alignment explanation
Indices: 47963797--47963853 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 20
47963787 AAAGTAAAAT
*
47963797 AAAAGAAACAAAAAGAAACAA
1 AAAAG-AACGAAAAGAAACAA
47963818 AAGAAGAACAGAAAAGAAACAGA
1 AA-AAGAAC-GAAAAGAAACA-A
*
47963841 GAAAGAGACGAAA
1 AAAAGA-ACGAAA
47963854 CAGGGGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 5 0.17
22 21 0.70
23 4 0.13
ACGTcount: A:0.72, C:0.09, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAAGAACGAAAAGAAACAA
Found at i:47963866 original size:11 final size:11
Alignment explanation
Indices: 47963850--47963875 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47963840 AGAAAGAGAC
47963850 GAAACAGGGGA
1 GAAACAGGGGA
47963861 GAAACAGGGGA
1 GAAACAGGGGA
47963872 GAAA
1 GAAA
47963876 GAAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:47967785 original size:17 final size:18
Alignment explanation
Indices: 47967741--47967786 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
47967731 TTAATTATTT
47967741 TGAAAGTTTTAATTTAGA
1 TGAAAGTTTTAATTTAGA
*
47967759 TGAAATTTTTAATTTAGA
1 TGAAAGTTTTAATTTAGA
47967777 TGAAA-TTTTA
1 TGAAAGTTTTA
47967787 TAACTCGGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (18 bp):
TGAAAGTTTTAATTTAGA
Found at i:47969159 original size:341 final size:340
Alignment explanation
Indices: 47968513--47969221 Score: 1211
Period size: 341 Copynumber: 2.1 Consensus size: 340
47968503 AAGATCCCGT
* * * * *
47968513 AATAGCGGCGCTTCTAGGAAAATGCCGCAAAAGAGCATCTTTAGTGGCGATTTTAAACAAAAACG
1 AATAGTGGCGCTTCT-GTAAAACGCCGCAAAAGAGCATCATTAGTGGCGATTTTAAACAAAAAAG
* *
47968578 CCGTAATAAATCTGACAAAACGCATCGTTTAATATTCAGGAATAGTGGCAGTAGCGGCGCATTCT
65 CCGTAATAAATCTGACAAAACGCATCGTTTAATATTCAAGAATACTGGCAGTAGCGGCGCATTCT
* *
47968643 AAAAACGCCACTATAGAGCAGAATTAGCGGCGTTTTTTTGTAAGCGCTACAAAAAATGTTAAACA
130 AAAAACGCCACTATAGAGCAGAATTAGCGGCGTTTGTTTGTAAGCGCCACAAAAAATGTTAAACA
**
47968708 ATACGCAGCGTACAATATTGAGCTATAGTACAATTAGTGGCGCTTCCCTAGAAACGCCGCTGAAG
195 ATACGCAGCGTACAATATTGAGCTATAGTACAATTAGTGGCGCTTCCAAAGAAACGCCGCTGAAG
* * **
47968773 CATAACATTAGTGGCGCTAAAGTACAAGCGCCACAAAATATGTGAATAAAAAACGCAGCGTTTGG
260 CACAACATTAGCGGCGCTAAAGTACAAGCGCCACAAAATATGTGAAT-AAAAACGCAGCGTTTAA
47968838 AAATGAGGCATAGATCC
324 AAATGAGGCATAGATCC
47968855 AATAGTGGCGCTTCTGTAAAACGCCGCAAAAGAGCATCATTAGTGGCGATTTTAAACAAAAAAGC
1 AATAGTGGCGCTTCTGTAAAACGCCGCAAAAGAGCATCATTAGTGGCGATTTTAAACAAAAAAGC
47968920 CGTAATAAATCTGACAAAACGCATCGTTTAATATTCAAGAATACTGGCAGTAGCGGCGCATTCTA
66 CGTAATAAATCTGACAAAACGCATCGTTTAATATTCAAGAATACTGGCAGTAGCGGCGCATTCTA
*
47968985 AAAACGCCACTATAGAGCAGAATTAGCGGCGTTTGTTTGTAAGCGCCACAAAAAATGTTAAACTA
131 AAAACGCCACTATAGAGCAGAATTAGCGGCGTTTGTTTGTAAGCGCCACAAAAAATGTTAAACAA
*
47969050 TACGCAGCGTACAATATTGAGCTATAGTACAATTAGTGGCGCTTCCAAAGAAACGCCGCTGAATC
196 TACGCAGCGTACAATATTGAGCTATAGTACAATTAGTGGCGCTTCCAAAGAAACGCCGCTGAAGC
* *
47969115 ACAGCATTAGCGGCGCTAAAGTACAAGCGCCACAAAATATGTGAATCAAAACGCAGCGTTTAAAA
261 ACAACATTAGCGGCGCTAAAGTACAAGCGCCACAAAATATGTGAATAAAAACGCAGCGTTTAAAA
47969180 ATGAGGCATAGATCC
326 ATGAGGCATAGATCC
* *
47969195 AATAGTGGCGCTTCAGTAAAACACCGC
1 AATAGTGGCGCTTCTGTAAAACGCCGC
47969222 TATAGGCTGC
Statistics
Matches: 346, Mismatches: 21, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
340 56 0.16
341 276 0.80
342 14 0.04
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (340 bp):
AATAGTGGCGCTTCTGTAAAACGCCGCAAAAGAGCATCATTAGTGGCGATTTTAAACAAAAAAGC
CGTAATAAATCTGACAAAACGCATCGTTTAATATTCAAGAATACTGGCAGTAGCGGCGCATTCTA
AAAACGCCACTATAGAGCAGAATTAGCGGCGTTTGTTTGTAAGCGCCACAAAAAATGTTAAACAA
TACGCAGCGTACAATATTGAGCTATAGTACAATTAGTGGCGCTTCCAAAGAAACGCCGCTGAAGC
ACAACATTAGCGGCGCTAAAGTACAAGCGCCACAAAATATGTGAATAAAAACGCAGCGTTTAAAA
ATGAGGCATAGATCC
Found at i:47970196 original size:25 final size:26
Alignment explanation
Indices: 47970164--47970213 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
47970154 ACGATATAAT
47970164 GTGGTTTGGA-TTTTATGG-TAATTTG
1 GTGGTTT-GACTTTTATGGTTAATTTG
47970189 GTGGTTTGACGTTTTATGGTTAATT
1 GTGGTTTGAC-TTTTATGGTTAATT
47970214 GACAAGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 2 0.09
25 7 0.32
26 8 0.36
27 5 0.23
ACGTcount: A:0.16, C:0.02, G:0.30, T:0.52
Consensus pattern (26 bp):
GTGGTTTGACTTTTATGGTTAATTTG
Found at i:47970737 original size:16 final size:16
Alignment explanation
Indices: 47970716--47970747 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
47970706 CAAAAGTAAT
47970716 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
47970732 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
47970748 GAAATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.25
Consensus pattern (16 bp):
TAAAAGATACAATTAA
Found at i:47971037 original size:24 final size:25
Alignment explanation
Indices: 47971009--47971068 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
47970999 CACTTAGCCG
47971009 AAATTCTCCCCAAATTTCT-CCCCA
1 AAATTCTCCCCAAATTTCTCCCCCA
** *
47971033 AAATT-TCCCCCGATTTTTCCCCCA
1 AAATTCTCCCCAAATTTCTCCCCCA
*
47971057 AAA-TCCCCCCAA
1 AAATTCTCCCCAA
47971069 TTCTAGAACC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.28, C:0.43, G:0.02, T:0.27
Consensus pattern (25 bp):
AAATTCTCCCCAAATTTCTCCCCCA
Found at i:47971041 original size:11 final size:12
Alignment explanation
Indices: 47971009--47971042 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
47970999 CACTTAGCCG
47971009 AAATTCTCCCCA
1 AAATTCTCCCCA
*
47971021 AATTTCTCCCCA
1 AAATTCTCCCCA
47971033 AAATT-TCCCC
1 AAATTCTCCCC
47971043 CGATTTTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.29, C:0.41, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATTCTCCCCA
Done.