Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 17 of 186
Found at i:5238301 original size:18 final size:17
Alignment explanation
Indices: 5238258--5238302 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
5238248 CAAAAATAAG
5238258 AGAAAAA-GAAAAAAAA
1 AGAAAAAGGAAAAAAAA
5238274 AGAGAAAAGGAAAAAGAAA
1 AGA-AAAAGGAAAAA-AAA
5238293 AGAAAAAGGA
1 AGAAAAAGGA
5238303 GAGGTCAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.12
17 4 0.15
18 13 0.50
19 6 0.23
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAAAAGGAAAAAAAA
Found at i:5240599 original size:50 final size:50
Alignment explanation
Indices: 5240392--5241620 Score: 655
Period size: 50 Copynumber: 24.7 Consensus size: 50
5240382 ATTGCAATTC
* * * * **
5240392 AAAGATTGAAGCCACAACGGTGAATTTTAC-TCCCAGGA-AATGCAGCGGA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCC-CGACATTGCAGTTGA
** * * * * * *
5240441 GCAGATTGAAGCTACAACAGCGAATCTCACTTCCCTGACATTGCAATT-C
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* * * **
5240490 AAAGATTGAAGCCACAACGGTGAATCTTAC-TCCCAGGCGA-TGCAGCGGA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGAC-ATTGCAGTTGA
** * * * * * *
5240539 GCAGATTGAAGCTACAGCGGCGAATCTCACTTCCCCGACATTACAATTTA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* * * ** **
5240589 AAAGATTGAAGCTACAACAGTGAATCTCACCT-CCTTAGCGA-TGCAGCGGA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGA-C-ATTGCAGTTGA
* * * * ** *
5240639 ACAGATCGAAGCTACGACGGTGAATCTCT-CTTCCCTGACATCACAGTTTA
1 AAAGATTGAAGCTACAACGGTGAATCT-TACTTCCCCGACATTGCAGTTGA
* * ** * **
5240689 AAAGATCGAAGCCACAACGGTGAATCTTACTT-CTAGGCGA-TGCAGCGGA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGAC-ATTGCAGTTGA
* ** * * * *
5240738 ACAGATTGAAGCTACAATAGCGAATCTTGCTTCCCCGACATTGCAATTCA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* * * ** ** * **
5240788 AAAGATCGAAGCCACAACGGTGAATCTTGCTT-CCAAACGGTGTAGCGGA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* * * * *
5240837 ACAGATTGAAGCTACGACGGTGAATCTCACTTCCCCGACATTGCAATTCA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* * * * * * * *
5240887 AAAGATCGAAGCCACAACGGCGAATCTTATTTCCCAGGCAGTGTAGTTGA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* * * * * * * *
5240937 ATAGATTGAAGCTACAACAGTGGATCTTGCTTCCTCGACATTACAATTCA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* * ** * **
5240987 AAAGATTGAAGCTACAACAGTGAATCTTACCTCCTTGGCGA-TGCAGCGGA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGAC-ATTGCAGTTGA
* * * *
5241037 ACAGATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTGCAATTCA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* * * * *
5241087 AATGATTGAAGCCACAACAGTGAATCTTACTT-CCCAAGCGA-TGCAGTGGA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGA-C-ATTGCAGTTGA
* * * ** * *
5241137 GAAGATTAAAGTTACAACGACGAATCTCACTTCCCCGACATTGCAGTTCA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* * * * **
5241187 AAAGATTG-AGGTCACAATGGCGAATCTTAC-TCCCAGACGA-TGCAGCAGA
1 AAAGATTGAAGCT-ACAACGGTGAATCTTACTTCCCCGAC-ATTGCAGTTGA
** * * * * * *
5241236 GCAGATTGAAACTACAACGGCGAATCTCACTTCCCCAACATTGCAATTCA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* ** * ** **
5241286 AAAGATTGAAGCCACAACAATGAATCTTACTTCCCAAGTGA-TGCAGCGGA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCC-CGACATTGCAGTTGA
** * * * * *
5241336 GCAGACTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTCA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* * ** **
5241386 AAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGTGA-TGCAGCAGA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCC-CGACATTGCAGTTGA
* * * * * *
5241436 GCAA-ACTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTCA
1 -AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* * * ** **
5241486 AAAGATTGAAGCCACAATGGTGAATCTTACTTCCCAAGTGA-TGCAGCGGA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCC-CGACATTGCAGTTGA
** * * * * * *
5241536 GCAGACTGAAGCTACAACGGCGAATCTCACTTCCCTGACATTGCAATTCA
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
* * * *
5241586 AAATAGTGAAGCCACAAGGGTGAATCTTACTTCCC
1 AAAGATTGAAGCTACAACGGTGAATCTTACTTCCC
5241621 GAACATCATA
Statistics
Matches: 842, Mismatches: 303, Indels: 69
0.69 0.25 0.06
Matches are distributed among these distances:
48 10 0.01
49 199 0.24
50 615 0.73
51 18 0.02
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (50 bp):
AAAGATTGAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTGA
Found at i:5241350 original size:399 final size:398
Alignment explanation
Indices: 5240382--5241616 Score: 1604
Period size: 399 Copynumber: 3.1 Consensus size: 398
5240372 GAAACCATAG
* *
5240382 ATTGCAATTC-AAAGATTGAAGCCACAACGGTGAATTTTACTCCCAGGA-AATGCAGCGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTCCCA-GACGATGCAGCGGAGCAG
* *
5240445 ATTGAAGCTACAACAGCGAATCTCACTTCCCTGACATTGCAATTC-AAAGATTGAAGCCACAACG
65 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCCACAACG
* *
5240509 GTGAATCTTAC-TCCCAGGCGATGCAGCGGAGCAGATTGAAGCTACAGCGGCGAATCTCACTTCC
130 GTGAATCTTACTTCCCAAG-GATGCAGCGGAGCAGATTGAAGCTACAACGGCGAATCTCACTTCC
* *
5240573 CCGACATTACAATTTAAAAGATTGAAGCTACAACAGTGAATCTCACCTCCTTAGCGATGCAGCGG
194 CCGACATTACAATTCAAAAGATTGAAGCTACAACAGTGAATCTTACCTCCTTAGCGATGCAGCGG
* * * * ** * * *
5240638 AACAGATCGAAGCTACGACGGTGAATCTCTCTTCCCTGACATCACAGTTTAAAAGATCGAAGCCA
259 AACAGATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCCA
* * *
5240703 CAACGGTGAATCTTACTT-CTAGGCGATGCAGCGGA-ACAGATTGAAGCTACAA-TAGCGAATCT
324 CAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGA-AGATTGAAGCTACAACGA-CGAATCT
**
5240765 TGCTTCCCCGAC
387 CACTTCCCCGAC
* * * * * * *
5240777 ATTGCAATTCAAAAGATCGAAGCCACAACGGTGAATCTTGCTTCCAAACGGTGTAGCGGAACAGA
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTCCCAGACGATGCAGCGGAGCAGA
* * *
5240842 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACATTGCAATTCAAAAGATCGAAGCCACAACGG
66 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCCACAACGG
* * * ** ** * * * **
5240907 CGAATCTTATTTCCC-AGGCAGTGTAGTTGAATAGATTGAAGCTACAACAGTGGATCTTGCTTCC
131 TGAATCTTACTTCCCAAGG-A-TGCAGCGGAGCAGATTGAAGCTACAACGGCGAATCTCACTTCC
* *
5240971 TCGACATTACAATTCAAAAGATTGAAGCTACAACAGTGAATCTTACCTCCTTGGCGATGCAGCGG
194 CCGACATTACAATTCAAAAGATTGAAGCTACAACAGTGAATCTTACCTCCTTAGCGATGCAGCGG
*
5241036 AACAGATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTGCAATTCAAATGATTGAAGCCA
259 AACAGATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCCA
* * * *
5241101 CAACAGTGAATCTTACTTCCCAAGCGATGCAGTGGAGAAGATTAAAGTTACAACGACGAATCTCA
324 CAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGAAGATTGAAGCTACAACGACGAATCTCA
5241166 CTTCCCCGAC
389 CTTCCCCGAC
* * * * * *
5241176 ATTGCAGTTCAAAAGATTGAGGTCACAATGGCGAATCTTACTCCCAGACGATGCAGCAGAGCAGA
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTCCCAGACGATGCAGCGGAGCAGA
* * **
5241241 TTGAAACTACAACGGCGAATCTCACTTCCCCAACATTGCAATTCAAAAGATTGAAGCCACAACAA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCCACAACGG
*
5241306 TGAATCTTACTTCCCAAGTGATGCAGCGGAGCAGACTGAAGCTACAACGGCGAATCTCACTTCCC
131 TGAATCTTACTTCCCAAG-GATGCAGCGGAGCAGATTGAAGCTACAACGGCGAATCTCACTTCCC
* * * * ** * *
5241371 CGACATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGTGATGCAGCAGA
195 CGACATTACAATTCAAAAGATTGAAGCTACAACAGTGAATCTTACCTCCTTAGCGATGCAGCGGA
* * * *
5241436 GCAAACTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCCAC
260 ACAGATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCCAC
* * * * *
5241501 AATGGTGAATCTTACTTCCCAAGTGATGCAGCGGAGCAGACTGAAGCTACAACGGCGAATCTCAC
325 AACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGAAGATTGAAGCTACAACGACGAATCTCAC
*
5241566 TTCCCTGAC
390 TTCCCCGAC
* * *
5241575 ATTGCAATTCAAAATAGTGAAGCCACAAGGGTGAATCTTACT
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACT
5241617 TCCCGAACAT
Statistics
Matches: 713, Mismatches: 116, Indels: 18
0.84 0.14 0.02
Matches are distributed among these distances:
395 11 0.02
396 84 0.12
397 29 0.04
398 169 0.24
399 414 0.58
400 5 0.01
401 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (398 bp):
ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTCCCAGACGATGCAGCGGAGCAGA
TTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCCACAACGG
TGAATCTTACTTCCCAAGGATGCAGCGGAGCAGATTGAAGCTACAACGGCGAATCTCACTTCCCC
GACATTACAATTCAAAAGATTGAAGCTACAACAGTGAATCTTACCTCCTTAGCGATGCAGCGGAA
CAGATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCCACA
ACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGAAGATTGAAGCTACAACGACGAATCTCACT
TCCCCGAC
Found at i:5241620 original size:100 final size:100
Alignment explanation
Indices: 5240382--5241620 Score: 1533
Period size: 100 Copynumber: 12.5 Consensus size: 100
5240372 GAAACCATAG
* * **
5240382 ATTGCAATTC-AAAGATTGAAGCCACAACGGTGAATTTTAC-TCCCAGGAAATGCAGCGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGCAG
* *
5240445 ATTGAAGCTACAACAGCGAATCTCACTTCCCTGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
*
5240480 ATTGCAATTC-AAAGATTGAAGCCACAACGGTGAATCTTAC-TCCCAGGCGATGCAGCGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGCAG
*
5240543 ATTGAAGCTACAGCGGCGAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* * * * * * ** *
5240578 ATTACAATTTAAAAGATTGAAGCTACAACAGTGAATCTCACCTCCTTAGCGATGCAGCGGAACAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGCAG
* * * * *
5240643 ATCGAAGCTACGACGGTGAATCTCTCTTCCCTGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
** * * * * * *
5240678 ATCACAGTTTAAAAGATCGAAGCCACAACGGTGAATCTTACTT-CTAGGCGATGCAGCGGAACAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGCAG
** **
5240742 ATTGAAGCTACAATAGCGAATCTTGCTTCCCCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* * * * * *
5240777 ATTGCAATTCAAAAGATCGAAGCCACAACGGTGAATCTTGCTT-CCAAACGGTGTAGCGGAACAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGCAG
* *
5240841 ATTGAAGCTACGACGGTGAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* * * * * ** **
5240876 ATTGCAATTCAAAAGATCGAAGCCACAACGGCGAATCTTATTTCCCAGGC-AGTGTAGTTGAATA
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGA-TGCAGCGGAGCA
* * * ** *
5240940 GATTGAAGCTACAACAGTGGATCTTGCTTCCTCGAC
65 GATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* * * * *** *
5240976 ATTACAATTCAAAAGATTGAAGCTACAACAGTGAATCTTACCTCCTTGGCGATGCAGCGGAACAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGCAG
*
5241041 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* * * *
5241076 ATTGCAATTCAAATGATTGAAGCCACAACAGTGAATCTTACTTCCCAAGCGATGCAGTGGAGAAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGCAG
* * *
5241141 ATTAAAGTTACAACGACGAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* * * * * *
5241176 ATTGCAGTTCAAAAGATTGAGGTCACAATGGCGAATCTTAC-TCCC-AGACGATGCAGCAGAGCA
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAG-CGATGCAGCGGAGCA
* *
5241239 GATTGAAACTACAACGGCGAATCTCACTTCCCCAAC
65 GATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
** *
5241275 ATTGCAATTCAAAAGATTGAAGCCACAACAATGAATCTTACTTCCCAAGTGATGCAGCGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGCAG
*
5241340 ACTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* * *
5241375 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGTGATGCAGCAGAGCAA
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGCAG
*
5241440 ACTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* *
5241475 ATTGCAATTCAAAAGATTGAAGCCACAATGGTGAATCTTACTTCCCAAGTGATGCAGCGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGCAG
* *
5241540 ACTGAAGCTACAACGGCGAATCTCACTTCCCTGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* * *
5241575 ATTGCAATTCAAAATAGTGAAGCCACAAGGGTGAATCTTACTTCCC
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCC
5241621 GAACATCATA
Statistics
Matches: 994, Mismatches: 139, Indels: 14
0.87 0.12 0.01
Matches are distributed among these distances:
98 102 0.10
99 277 0.28
100 612 0.62
101 3 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (100 bp):
ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGCAG
ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
Found at i:5243279 original size:3 final size:3
Alignment explanation
Indices: 5243271--5243342 Score: 74
Period size: 3 Copynumber: 23.3 Consensus size: 3
5243261 TTTAGCAATT
* *
5243271 TTA TTA TTA TTA TCA TCTT TTA TTA TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* *
5243318 TTA TTG TTA CTTA TCA -TA TTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA T
5243343 ATAATAGCTT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
2 1 0.02
3 49 0.86
4 7 0.12
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:5243295 original size:16 final size:16
Alignment explanation
Indices: 5243274--5243342 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
5243264 AGCAATTTTA
5243274 TTATTATTATCATCT-T
1 TTATTATTATCAT-TAT
*
5243290 TTATTATTATTATTAT
1 TTATTATTATCATTAT
*
5243306 TTATTATTATTATTA-
1 TTATTATTATCATTAT
*
5243321 TTGTTACTTATCA-TA-
1 TTATTA-TTATCATTAT
5243336 TTATTAT
1 TTATTAT
5243343 ATAATAGCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
14 1 0.02
15 13 0.28
16 33 0.70
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (16 bp):
TTATTATTATCATTAT
Found at i:5243322 original size:19 final size:19
Alignment explanation
Indices: 5243269--5243322 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
5243259 TTTTTAGCAA
*
5243269 TTTTATTATTATTATCATC
1 TTTTATTATTATTATTATC
5243288 TTTTATTATTATTATTAT-
1 TTTTATTATTATTATTATC
5243306 TTATTATTATTATTATT
1 TT-TTATTATTATTATT
5243323 GTTACTTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 2 0.06
19 31 0.94
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTATTATTATTATTATC
Found at i:5243331 original size:19 final size:17
Alignment explanation
Indices: 5243268--5243342 Score: 80
Period size: 19 Copynumber: 4.1 Consensus size: 17
5243258 TTTTTTAGCA
5243268 ATTTTATTATTATTATCAT
1 ATTTTATTATTATTAT--T
*
5243287 CTTTTATTATTATTATT
1 ATTTTATTATTATTATT
5243304 A-TTTATTATTATTATT
1 ATTTTATTATTATTATT
5243320 ATTGTTACTTATCATATTATT
1 ATT-TTA-TTAT--TATTATT
5243341 AT
1 AT
5243343 ATAATAGCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
16 16 0.33
17 2 0.04
18 3 0.06
19 19 0.39
21 9 0.18
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.64
Consensus pattern (17 bp):
ATTTTATTATTATTATT
Found at i:5244504 original size:4 final size:4
Alignment explanation
Indices: 5244497--5244522 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5244487 TTTTTGTCGA
5244497 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
5244523 TAAATTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:5246070 original size:16 final size:16
Alignment explanation
Indices: 5246051--5246096 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5246041 ATAGATGTGC
*
5246051 AAATATATGTGTATAA
1 AAATATATGTATATAA
*
5246067 AAAT-TATAGAATATAA
1 AAATATAT-GTATATAA
5246083 AAA-ATATGTATATA
1 AAATATATGTATATA
5246097 TATGTTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 9 0.36
16 16 0.64
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.35
Consensus pattern (16 bp):
AAATATATGTATATAA
Found at i:5246294 original size:3 final size:3
Alignment explanation
Indices: 5246253--5246280 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5246243 AAAATAAAAC
5246253 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5246281 TGCAGTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5253745 original size:30 final size:29
Alignment explanation
Indices: 5253685--5253761 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
5253675 TTTCATGACC
* *
5253685 ACACGGGTGG-CCACACAAGCCTGTGTTGT
1 ACACGGGTGGTCCACAC-GGCCTGTGCTGT
*
5253714 ACACGGGTGGTCCACACGGTCGTGTGCTGT
1 ACACGGGTGGTCCACACGG-CCTGTGCTGT
* * *
5253744 ACACAGGCGGTTCACACG
1 ACACGGGTGGTCCACACG
5253762 ACCATGTGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 11 0.28
30 29 0.73
ACGTcount: A:0.19, C:0.29, G:0.32, T:0.19
Consensus pattern (29 bp):
ACACGGGTGGTCCACACGGCCTGTGCTGT
Found at i:5255441 original size:18 final size:19
Alignment explanation
Indices: 5255420--5255455 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5255410 GTGCTTTTAT
5255420 TCAA-AAAAAAACTTTGAA
1 TCAAGAAAAAAACTTTGAA
*
5255438 TCAAGAAAATAACTTTGA
1 TCAAGAAAAAAACTTTGA
5255456 TGTATGGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (19 bp):
TCAAGAAAAAAACTTTGAA
Found at i:5256054 original size:3 final size:3
Alignment explanation
Indices: 5256046--5256104 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
5256036 GTGTAAATGA
* * * * *
5256046 AAT AAT AAT AGT CAT AAT AAT ATT AAT AAT AAC AAT AAAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
5256092 AA- AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT
5256105 GTAGCATAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5257669 original size:44 final size:44
Alignment explanation
Indices: 5257576--5257682 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 44
5257566 AGAGAAATGG
* * * *
5257576 GATCTGCTGTACTTGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGCTCTACTTGATCTACTTCACACCAATACAGGAAAACAA
* * **
5257620 AATCTGCTCT-CTTCGATCTACTTCACACCAGTATGGGAAAACAA
1 GATCTGCTCTACTT-GATCTACTTCACACCAATACAGGAAAACAA
* *
5257664 GATCTGCTGTATTTGATCT
1 GATCTGCTCTACTTGATCT
5257683 GCTCTCTTCG
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
43 3 0.06
44 45 0.90
45 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (44 bp):
GATCTGCTCTACTTGATCTACTTCACACCAATACAGGAAAACAA
Found at i:5257686 original size:58 final size:59
Alignment explanation
Indices: 5257621--5257744 Score: 214
Period size: 59 Copynumber: 2.1 Consensus size: 59
5257611 TGAAGACAAA
*
5257621 ATCTGCTCTCTTCGATCTACTTC-ACACCAGTATGGGAAAACAAGATCTGCTGTATTTG
1 ATCTGCTCTCTTCGATCTACTTCGACACCAATATGGGAAAACAAGATCTGCTGTATTTG
* *
5257679 ATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAATACAAGATCTGCTGTATTTG
1 ATCTGCTCTCTTCGATCTACTTCGACACCAATATGGGAAAACAAGATCTGCTGTATTTG
5257738 ATCTGCT
1 ATCTGCT
5257745 TCACGCCAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 23 0.37
59 39 0.63
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (59 bp):
ATCTGCTCTCTTCGATCTACTTCGACACCAATATGGGAAAACAAGATCTGCTGTATTTG
Found at i:5257769 original size:44 final size:44
Alignment explanation
Indices: 5257678--5257858 Score: 146
Period size: 45 Copynumber: 4.1 Consensus size: 44
5257668 TGCTGTATTT
* * * * *** *
5257678 GATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAATACAA
1 GATCTGCTGTCTTTGATCTACTTC-ACGCCAATACATGAAGACAA
* *
5257723 GATCTGCTGTATTTGATCTGCTTCACGCCAATACATGAAGACAA
1 GATCTGCTGTCTTTGATCTACTTCACGCCAATACATGAAGACAA
** * * * * * *** *
5257767 GATCAACTCTCTTCGATCTACTTCGCCACCAGTATGGGGAGACAA
1 GATCTGCTGTCTTTGATCTACTTC-ACGCCAATACATGAAGACAA
*
5257812 GATCTGTTGTCTTTGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGCTGTCTTTGATCTACTTCACGCCAATACATGAAGACAA
5257856 GAT
1 GAT
5257859 TTGTTATCTT
Statistics
Matches: 100, Mismatches: 35, Indels: 3
0.72 0.25 0.02
Matches are distributed among these distances:
44 48 0.48
45 52 0.52
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
GATCTGCTGTCTTTGATCTACTTCACGCCAATACATGAAGACAA
Found at i:5257803 original size:89 final size:89
Alignment explanation
Indices: 5257684--5257858 Score: 296
Period size: 89 Copynumber: 2.0 Consensus size: 89
5257674 ATTTGATCTG
* *
5257684 CTCTCTTCGATCTACTTCGCCACCAATATGGGAATACAAGATCTGCTGTATTTGATCTGCTTCAC
1 CTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCTGTATTTGATCTACTTCAC
5257749 GCCAATACATGAAGACAAGATCAA
66 GCCAATACATGAAGACAAGATCAA
* * * *
5257773 CTCTCTTCGATCTACTTCGCCACCAGTATGGGGAGACAAGATCTGTTGTCTTTGATCTACTTCAC
1 CTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCTGTATTTGATCTACTTCAC
5257838 GCCAATACATGAAGACAAGAT
66 GCCAATACATGAAGACAAGAT
5257859 TTGTTATCTT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (89 bp):
CTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCTGTATTTGATCTACTTCAC
GCCAATACATGAAGACAAGATCAA
Found at i:5257814 original size:45 final size:45
Alignment explanation
Indices: 5257684--5257815 Score: 131
Period size: 44 Copynumber: 3.0 Consensus size: 45
5257674 ATTTGATCTG
* **
5257684 CTCTCTTCGATCTACTTCGCCACCAATATGGGAATACAAGATCTG
1 CTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCAA
* * * * * * ***
5257729 CTGTATTTGATCTGCTTC-ACGCCAATACATGAAGACAAGATCAA
1 CTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCAA
* *
5257773 CTCTCTTCGATCTACTTCGCCACCAGTATGGGGAGACAAGATC
1 CTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATC
5257816 TGTTGTCTTT
Statistics
Matches: 63, Mismatches: 23, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
44 32 0.51
45 31 0.49
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (45 bp):
CTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCAA
Found at i:5257830 original size:45 final size:45
Alignment explanation
Indices: 5257678--5257835 Score: 156
Period size: 45 Copynumber: 3.5 Consensus size: 45
5257668 TGCTGTATTT
*
5257678 GATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAATACAA
1 GATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAA
* * * * * * ***
5257723 GATCTGCTGTATTTGATCTGCTTC-ACGCCAATACATGAAGACAA
1 GATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAA
** * *
5257767 GATCAACTCTCTTCGATCTACTTCGCCACCAGTATGGGGAGACAA
1 GATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAA
* * *
5257812 GATCTGTTGTCTTTGATCTACTTC
1 GATCTGCTCTCTTCGATCTACTTC
5257836 ACGCCAATAC
Statistics
Matches: 84, Mismatches: 28, Indels: 2
0.74 0.25 0.02
Matches are distributed among these distances:
44 32 0.38
45 52 0.62
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (45 bp):
GATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAA
Found at i:5257869 original size:44 final size:44
Alignment explanation
Indices: 5257719--5257869 Score: 131
Period size: 44 Copynumber: 3.4 Consensus size: 44
5257709 ATATGGGAAT
* * * *
5257719 ACAAGATCTGCTGTATTTGATCTGCTTCACGCCAATACATGAAG
1 ACAAGATCTGTTATCTTTGATCTACTTCACGCCAATACATGAAG
*** * * * * * *** *
5257763 ACAAGATCAACTCTCTTCGATCTACTTCGCCACCAGTATGGGGAG
1 ACAAGATCTGTTATCTTTGATCTACTTC-ACGCCAATACATGAAG
*
5257808 ACAAGATCTGTTGTCTTTGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGTTATCTTTGATCTACTTCACGCCAATACATGAAG
*
5257852 ACAAGATTTGTTATCTTT
1 ACAAGATCTGTTATCTTT
5257870 CAACCTGCTC
Statistics
Matches: 79, Mismatches: 27, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
44 47 0.59
45 32 0.41
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (44 bp):
ACAAGATCTGTTATCTTTGATCTACTTCACGCCAATACATGAAG
Found at i:5262108 original size:9 final size:9
Alignment explanation
Indices: 5262090--5262174 Score: 100
Period size: 9 Copynumber: 9.4 Consensus size: 9
5262080 TTTGGTTAAA
5262090 AATTAACCG
1 AATTAACCG
*
5262099 AATTACCCG
1 AATTAACCG
*
5262108 AATTAACCT
1 AATTAACCG
*
5262117 AATTACCCG
1 AATTAACCG
*
5262126 AATTAACAG
1 AATTAACCG
*
5262135 AATTACCCG
1 AATTAACCG
5262144 AATT-ACTCG
1 AATTAAC-CG
5262153 AATTAACCG
1 AATTAACCG
*
5262162 AATTAACCT
1 AATTAACCG
5262171 AATT
1 AATT
5262175 GAATCATACA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
8 1 0.02
9 60 0.95
10 2 0.03
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:5262113 original size:18 final size:18
Alignment explanation
Indices: 5262090--5262174 Score: 118
Period size: 18 Copynumber: 4.7 Consensus size: 18
5262080 TTTGGTTAAA
5262090 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
5262108 AATTAACCTAATTACCCG
1 AATTAACCGAATTACCCG
*
5262126 AATTAACAGAATTACCCG
1 AATTAACCGAATTACCCG
*
5262144 AATT-ACTCGAATTAACCG
1 AATTAAC-CGAATTACCCG
*
5262162 AATTAACCTAATT
1 AATTAACCGAATT
5262175 GAATCATACA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
17 2 0.03
18 55 0.93
19 2 0.03
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:5262126 original size:27 final size:27
Alignment explanation
Indices: 5262090--5262174 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
5262080 TTTGGTTAAA
* *
5262090 AATTAACCGAATTACCCGAATTAACCT
1 AATTACCCGAATTAACCGAATTAACCT
* * *
5262117 AATTACCCGAATTAACAGAATTACCCG
1 AATTACCCGAATTAACCGAATTAACCT
*
5262144 AATTACTCGAATTAACCGAATTAACCT
1 AATTACCCGAATTAACCGAATTAACCT
5262171 AATT
1 AATT
5262175 GAATCATACA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (27 bp):
AATTACCCGAATTAACCGAATTAACCT
Found at i:5262299 original size:18 final size:18
Alignment explanation
Indices: 5262276--5262342 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
5262266 AATTTTTATG
5262276 ATTGGGTTGGATTGGGTA
1 ATTGGGTTGGATTGGGTA
5262294 ATT--G--GG-TTGGGTA
1 ATTGGGTTGGATTGGGTA
**
5262307 ATTGGGTTGGATTGAATA
1 ATTGGGTTGGATTGGGTA
*
5262325 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGATTGGGT
5262343 TTTGGTGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
13 10 0.26
14 2 0.05
15 1 0.03
16 1 0.03
17 2 0.05
18 13 0.34
19 9 0.24
ACGTcount: A:0.16, C:0.01, G:0.42, T:0.40
Consensus pattern (18 bp):
ATTGGGTTGGATTGGGTA
Found at i:5262303 original size:13 final size:13
Alignment explanation
Indices: 5262282--5262316 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
5262272 TATGATTGGG
*
5262282 TTGGATTGGGTAA
1 TTGGGTTGGGTAA
5262295 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
5262308 TTGGGTTGG
1 TTGGGTTGG
5262317 ATTGAATACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.46, T:0.40
Consensus pattern (13 bp):
TTGGGTTGGGTAA
Found at i:5263850 original size:14 final size:14
Alignment explanation
Indices: 5263831--5263858 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5263821 TGTAACGATC
5263831 ACGGTACCGCTCCT
1 ACGGTACCGCTCCT
5263845 ACGGTACCGCTCCT
1 ACGGTACCGCTCCT
5263859 GCTGAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.43, G:0.21, T:0.21
Consensus pattern (14 bp):
ACGGTACCGCTCCT
Found at i:5268640 original size:20 final size:20
Alignment explanation
Indices: 5268615--5268654 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5268605 TAAAGGTCTT
5268615 TAATGCATATAATGCGATGC
1 TAATGCATATAATGCGATGC
*
5268635 TAATGCATATGATGCGATGC
1 TAATGCATATAATGCGATGC
5268655 ATGAGGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (20 bp):
TAATGCATATAATGCGATGC
Found at i:5272061 original size:19 final size:19
Alignment explanation
Indices: 5272039--5272075 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5272029 GTGCTTTTAT
5272039 TCAAAAAAAAAACTTTGAA
1 TCAAAAAAAAAACTTTGAA
* *
5272058 TCAAGAAAATAACTTTGA
1 TCAAAAAAAAAACTTTGA
5272076 TGTATGGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.11, G:0.08, T:0.24
Consensus pattern (19 bp):
TCAAAAAAAAAACTTTGAA
Found at i:5272674 original size:3 final size:3
Alignment explanation
Indices: 5272666--5272724 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
5272656 GTGTAAATGA
* * * * *
5272666 AAT AAT AAT AGT CAT AAT AAT ATT AAT AAT AAC AAT AAAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
5272712 AA- AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT
5272725 GTAGCATAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5276427 original size:103 final size:104
Alignment explanation
Indices: 5276183--5276448 Score: 426
Period size: 103 Copynumber: 2.6 Consensus size: 104
5276173 GTTGTACATA
** *
5276183 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
5276248 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* *
5276287 GAGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
5276352 CTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
5276390 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
5276449 AATAACGGTT
Statistics
Matches: 149, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:5283919 original size:103 final size:104
Alignment explanation
Indices: 5283675--5283940 Score: 419
Period size: 103 Copynumber: 2.6 Consensus size: 104
5283665 GTTGTACATA
** *
5283675 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
5283740 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
5283779 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
5283843 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
5283882 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
5283941 AATAACGGTT
Statistics
Matches: 149, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:5285290 original size:13 final size:14
Alignment explanation
Indices: 5285272--5285301 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5285262 TGTTTAATGT
5285272 TTAATTAAG-TTAA
1 TTAATTAAGTTTAA
5285285 TTAATTAAGTTTAA
1 TTAATTAAGTTTAA
5285299 TTA
1 TTA
5285302 TATTTTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TTAATTAAGTTTAA
Found at i:5285960 original size:17 final size:17
Alignment explanation
Indices: 5285938--5285973 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5285928 AAATCTCTGA
5285938 TTCTGATACCCATATCT
1 TTCTGATACCCATATCT
*
5285955 TTCTGATACTCATATCT
1 TTCTGATACCCATATCT
5285972 TT
1 TT
5285974 GACTTTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.25, G:0.06, T:0.47
Consensus pattern (17 bp):
TTCTGATACCCATATCT
Found at i:5287625 original size:20 final size:21
Alignment explanation
Indices: 5287600--5287645 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5287590 ATAATTTTAT
* *
5287600 AAATTTGT-AAAACATTATTA
1 AAATTTATAAAAACATTAATA
*
5287620 AAATTTATAAAAATATTAATA
1 AAATTTATAAAAACATTAATA
5287641 AAATT
1 AAATT
5287646 CAAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATTTATAAAAACATTAATA
Found at i:5287637 original size:21 final size:21
Alignment explanation
Indices: 5287608--5287655 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5287598 ATAAATTTGT
* * * *
5287608 AAAACATTATTAAAATTTATA
1 AAAATATTAATAAAATTCAAA
5287629 AAAATATTAATAAAATTCAAA
1 AAAATATTAATAAAATTCAAA
5287650 AAAATA
1 AAAATA
5287656 AAATCGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATATTAATAAAATTCAAA
Found at i:5287781 original size:21 final size:21
Alignment explanation
Indices: 5287738--5287782 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5287728 AATTTTATTT
* *
5287738 AATATTTTGATAAATTTTAAA
1 AATATTTTGACAAATTTAAAA
5287759 AATATTTT-ACAAATTTAATAA
1 AATATTTTGACAAATTTAA-AA
5287780 AAT
1 AAT
5287783 TAAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
AATATTTTGACAAATTTAAAA
Found at i:5291560 original size:19 final size:19
Alignment explanation
Indices: 5291533--5291571 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5291523 TAAGTAATGG
*
5291533 ATTATTATCTAATTTTCAT
1 ATTAATATCTAATTTTCAT
5291552 ATTAATATCTAATTTTCAT
1 ATTAATATCTAATTTTCAT
5291571 A
1 A
5291572 ATTTTTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTAATATCTAATTTTCAT
Found at i:5300727 original size:6 final size:6
Alignment explanation
Indices: 5300716--5300742 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5300706 GAAGAAGGGT
5300716 GGAAGA GGAAGA GGAAGA GGAAGA GGA
1 GGAAGA GGAAGA GGAAGA GGAAGA GGA
5300743 GAGTGGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
GGAAGA
Found at i:5301657 original size:23 final size:23
Alignment explanation
Indices: 5301631--5301678 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5301621 AATAAATAAT
5301631 GTTTGCCTAAATCAAAGCTCGAA
1 GTTTGCCTAAATCAAAGCTCGAA
5301654 GTTTGCCTAAATCAAAGCTCGAA
1 GTTTGCCTAAATCAAAGCTCGAA
5301677 GT
1 GT
5301679 CTTCTAGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (23 bp):
GTTTGCCTAAATCAAAGCTCGAA
Found at i:5314142 original size:21 final size:20
Alignment explanation
Indices: 5314113--5314152 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5314103 TTTCCAATCG
*
5314113 AGTCGAGTGAAATTAAATTTA
1 AGTCAAGTGAAA-TAAATTTA
*
5314134 AGTCAAGTGGAATAAATTT
1 AGTCAAGTGAAATAAATTT
5314153 GTTTGAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (20 bp):
AGTCAAGTGAAATAAATTTA
Found at i:5315738 original size:24 final size:24
Alignment explanation
Indices: 5315711--5315772 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
5315701 TGGTTCTTCG
*
5315711 GAGCTACCCGTTATTGGCTCGCAT
1 GAGCTTCCCGTTATTGGCTCGCAT
**
5315735 GAGCTTCCCGGTTA-TGGCTCTTAT
1 GAGCTTCCC-GTTATTGGCTCGCAT
5315759 GAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
5315773 ACAGCCCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 4 0.12
24 25 0.76
25 4 0.12
ACGTcount: A:0.15, C:0.27, G:0.24, T:0.34
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCGCAT
Found at i:5320363 original size:33 final size:31
Alignment explanation
Indices: 5320290--5320366 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 31
5320280 GCATGCGTGC
* * *
5320290 ATTTTTTATATTATACGTACATATTTTTATA
1 ATTTTTTATATTATACATACATACTTATATA
* *
5320321 ATTTATTTATTTATATATATACATACTTATATA
1 ATTT-TTTATAT-TATACATACATACTTATATA
5320354 TATTTTTTATATT
1 -ATTTTTTATATT
5320367 TTATAATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
31 4 0.11
32 7 0.19
33 22 0.59
34 4 0.11
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (31 bp):
ATTTTTTATATTATACATACATACTTATATA
Found at i:5320379 original size:29 final size:29
Alignment explanation
Indices: 5320312--5320400 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
5320302 ATACGTACAT
*
5320312 ATTTTTATAATTTATTTATTTATATATATAC
1 ATTTTTAT-ATATATTT-TTTATATATATAC
** *
5320343 ATACTTATATATATTTTTTATATTTTATA-
1 ATTTTTATATATATTTTTTATA-TATATAC
* * *
5320372 ATTTTTATATACATTTTGTATACATATAC
1 ATTTTTATATATATTTTTTATATATATAC
5320401 GTGCATATAC
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
28 4 0.09
29 24 0.52
30 12 0.26
31 6 0.13
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (29 bp):
ATTTTTATATATATTTTTTATATATATAC
Found at i:5320703 original size:4 final size:4
Alignment explanation
Indices: 5320689--5320732 Score: 79
Period size: 4 Copynumber: 10.8 Consensus size: 4
5320679 ATTTTTATGT
5320689 TTTA GTTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
5320733 GTTATGGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
4 35 0.90
5 4 0.10
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:5320806 original size:14 final size:15
Alignment explanation
Indices: 5320773--5320806 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5320763 TTTTTATTCG
* *
5320773 TTTTTGTTCATATTA
1 TTTTTGTTCACATCA
5320788 TTTTTGTTCACATCA
1 TTTTTGTTCACATCA
5320803 TTTT
1 TTTT
5320807 ATTTATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTTTGTTCACATCA
Found at i:5329179 original size:21 final size:21
Alignment explanation
Indices: 5329153--5329196 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5329143 GTGCCAAAGA
5329153 ATGGATGAATCTGTAGAAGCC
1 ATGGATGAATCTGTAGAAGCC
5329174 ATGGATGAATCTGTAGAAGCC
1 ATGGATGAATCTGTAGAAGCC
5329195 AT
1 AT
5329197 TGTAACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (21 bp):
ATGGATGAATCTGTAGAAGCC
Found at i:5331086 original size:20 final size:19
Alignment explanation
Indices: 5331063--5331116 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
5331053 TTCATGCCAA
5331063 TTTTTTTAATTTTTATAATT
1 TTTTTTTAATTTTTAT-ATT
* **
5331083 TTTTTTAAATTTAAATATT
1 TTTTTTTAATTTTTATATT
*
5331102 TTTATTTTTATTTTT
1 TTT-TTTTAATTTTT
5331117 TCAAAATTAT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTTAATTTTTATATT
Found at i:5335352 original size:51 final size:53
Alignment explanation
Indices: 5335248--5335455 Score: 361
Period size: 51 Copynumber: 4.0 Consensus size: 53
5335238 CTGAAATTAA
*
5335248 GACATAGTTTTGCCATTGTGTAAGGAACACACAGCCTTTCAGGGCCCCTAATT
1 GACATAGTTTTGCCATTGTGTAAGGAACACACAGCCTTTCAGGACCCCTAATT
*
5335301 GACATAGTTTTGCCATTGTGTAAAG-A-ACACAGCCTTTCAGGACCCCTAATT
1 GACATAGTTTTGCCATTGTGTAAGGAACACACAGCCTTTCAGGACCCCTAATT
*
5335352 GACATAGTTTTGCCATTGTGTAAGG-A-ACACAGCCTTTCAGGAACCCTAATT
1 GACATAGTTTTGCCATTGTGTAAGGAACACACAGCCTTTCAGGACCCCTAATT
5335403 GACATAGTTTTGCCATTGTGTAAGGAACACACAGCCTTTCAGGACCCCTAATT
1 GACATAGTTTTGCCATTGTGTAAGGAACACACAGCCTTTCAGGACCCCTAATT
5335456 TTCCCATGGA
Statistics
Matches: 148, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
51 98 0.66
52 2 0.01
53 48 0.32
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (53 bp):
GACATAGTTTTGCCATTGTGTAAGGAACACACAGCCTTTCAGGACCCCTAATT
Found at i:5335440 original size:104 final size:104
Alignment explanation
Indices: 5335248--5335455 Score: 357
Period size: 104 Copynumber: 2.0 Consensus size: 104
5335238 CTGAAATTAA
**
5335248 GACATAGTTTTGCCATTGTGTAAGGAACACACAGCCTTTCAGGGCCCCTAATTGACATAGTTTTG
1 GACATAGTTTTGCCATTGTGTAAGGAACACACAGCCTTTCAGGAACCCTAATTGACATAGTTTTG
5335313 CCATTGTGTAAAGAACACAGCCTTTCAGGACCCCTAATT
66 CCATTGTGTAAAGAACACAGCCTTTCAGGACCCCTAATT
5335352 GACATAGTTTTGCCATTGTGTAAGG-A-ACACAGCCTTTCAGGAACCCTAATTGACATAGTTTTG
1 GACATAGTTTTGCCATTGTGTAAGGAACACACAGCCTTTCAGGAACCCTAATTGACATAGTTTTG
*
5335415 CCATTGTGTAAGGAACACACAGCCTTTCAGGACCCCTAATT
66 CCATTGTGTAAAG-A-ACACAGCCTTTCAGGACCCCTAATT
5335456 TTCCCATGGA
Statistics
Matches: 99, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
102 47 0.47
103 2 0.02
104 50 0.51
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (104 bp):
GACATAGTTTTGCCATTGTGTAAGGAACACACAGCCTTTCAGGAACCCTAATTGACATAGTTTTG
CCATTGTGTAAAGAACACAGCCTTTCAGGACCCCTAATT
Found at i:5338004 original size:127 final size:126
Alignment explanation
Indices: 5337778--5338028 Score: 394
Period size: 127 Copynumber: 2.0 Consensus size: 126
5337768 CAGAAGTTTC
* *
5337778 CTATATGACAGTAAAACTACAAATTGAGCCACACAAGGCTACAAGGTCTTCAACAAATAATACAT
1 CTATATGACAGTAAAACTACAAATTAAGCCACACAACGCTACAAGGTCTTCAACAAATAATACAT
* * * * *
5337843 TTACTAAAAAATTTAATTCAAAACAAGCTTAGAGATCTTTCTCATGCTTGATTGGTGATTTT
66 TTACTAAAAAACTTAATTCAAAACAAACTTAGAGAT-ATTCTCATACTCGATTGGTGATTTT
* *
5337905 CTATATGACTGTAAAACTACAAATTAAGCCACACAACGCTACGAGGTCTTCAACAAATAATACAT
1 CTATATGACAGTAAAACTACAAATTAAGCCACACAACGCTACAAGGTCTTCAACAAATAATACAT
* *
5337970 TTTCTTAAAAACTTAATTCAAAACAAACTTAGAGATATTCTCATACTCGATTGGTGATT
66 TTACTAAAAAACTTAATTCAAAACAAACTTAGAGATATTCTCATACTCGATTGGTGATT
5338029 CTTCGGGCCC
Statistics
Matches: 113, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
126 20 0.18
127 93 0.82
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (126 bp):
CTATATGACAGTAAAACTACAAATTAAGCCACACAACGCTACAAGGTCTTCAACAAATAATACAT
TTACTAAAAAACTTAATTCAAAACAAACTTAGAGATATTCTCATACTCGATTGGTGATTTT
Found at i:5340017 original size:14 final size:14
Alignment explanation
Indices: 5339998--5340025 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5339988 CATATTTCTA
5339998 AGAAATATATACTT
1 AGAAATATATACTT
5340012 AGAAATATATACTT
1 AGAAATATATACTT
5340026 TGAGAGAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
AGAAATATATACTT
Found at i:5340667 original size:3 final size:3
Alignment explanation
Indices: 5340659--5340691 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5340649 TAAATGCAAA
5340659 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
5340692 CAGCAGCAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TAG
Found at i:5340696 original size:3 final size:3
Alignment explanation
Indices: 5340690--5340727 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5340680 TAGTAGTAGT
5340690 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
5340728 TACTAGTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.34, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:5340743 original size:3 final size:3
Alignment explanation
Indices: 5340737--5340765 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5340727 GTACTAGTAC
5340737 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5340766 GAAACTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5347818 original size:87 final size:87
Alignment explanation
Indices: 5347665--5348353 Score: 1035
Period size: 87 Copynumber: 7.9 Consensus size: 87
5347655 ACAGTGTTTT
* * * *
5347665 GGGCTTGGGCTCGTTCGTAAATTTATAAACATGATGTAAATAATGCACGCCACGAAGATAATCAT
1 GGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAATCAT
5347730 TTCAAAAATGGAAATCCCTTTC
66 TTCAAAAATGGAAATCCCTTTC
*
5347752 GGGCATT-GGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCACAAAGAAAATCA
1 GGGC-TTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAATCA
*
5347816 TTTCAAAAATGGATATCCCTTTC
65 TTTCAAAAATGGAAATCCCTTTC
*
5347839 GGGCTTGGGCTCATTCGTAAATTTATAGACATGATGTAATTAACGCACGCCACGAAGAAAATCAT
1 GGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAATCAT
5347904 TTCAAAAATGGAAATCCCTTTC
66 TTCAAAAATGGAAATCCCTTTC
* *
5347926 GGGCATT-GGCTCGTTCGTAAATTTATAAACATGATGTAACTAACGCACGCCACGAAGAAAATCA
1 GGGC-TTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAATCA
*
5347990 TTTCAAAAATGGATATCCCTTTC
65 TTTCAAAAATGGAAATCCCTTTC
* * *
5348013 AGGCTTGGGCTCGTTCGTAAATTTATAAACATGATGTAATTAACGCACACCACGAAG-AAATCAT
1 GGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAATCAT
5348077 TTCAAAAATGGAAATCCCTTTC
66 TTCAAAAATGGAAATCCCTTTC
* * * * * *
5348099 GGGCTTGGG-TTATTCGTAAACTTATAAACATGATGTAATTAAAGCACACGACAAAGAAAATCAT
1 GGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAATCAT
* *
5348163 TTCAAAAATGGAAATCCTTTTT
66 TTCAAAAATGGAAATCCCTTTC
* * * * * *
5348185 GAGCTTGGGCTCGTTCGTAAACTTATAAACATGATGTAATCAACACACGCCACGAAGAAAACCAT
1 GGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAATCAT
5348250 TTCAAAAATGGAAATCCCTTTC
66 TTCAAAAATGGAAATCCCTTTC
* ** * * *
5348272 GGGCTTGGGCTCATTCGTAAATTTATAAGCACAATGTAATCAACACACGCCACAAAGAAAATCAT
1 GGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAATCAT
5348337 TTCAAAAATGGAAATCC
66 TTCAAAAATGGAAATCC
5348354 GGTTAATAGG
Statistics
Matches: 550, Mismatches: 46, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
85 41 0.07
86 75 0.14
87 430 0.78
88 4 0.01
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (87 bp):
GGGCTTGGGCTCATTCGTAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAATCAT
TTCAAAAATGGAAATCCCTTTC
Found at i:5348323 original size:346 final size:348
Alignment explanation
Indices: 5347666--5348353 Score: 1096
Period size: 346 Copynumber: 2.0 Consensus size: 348
5347656 CAGTGTTTTG
* *
5347666 GGCTTGGGCTCGTTCGTAAATTTATAAACATGATGTAAATAATGCACGCCACGAAGATAATCATT
1 GGCTTGGGCTCGTTCGTAAATTTATAAACATGATGTAAATAACGCACACCACGAAGATAATCATT
* *
5347731 TCAAAAATGGAAATCCCTTTCGGGCATTGGCTCATTCGTAAATTTATAAACATGATGTAATTAAC
66 TCAAAAATGGAAATCCCTTTCGGGCATTGGCTCATTCGTAAACTTATAAACATGATGTAATTAAA
* * * *
5347796 GCACGCCACAAAGAAAATCATTTCAAAAATGGATATCCCTTTCGGGCTTGGGCTCATTCGTAAAT
131 GCACACCACAAAGAAAATCATTTCAAAAATGGAAATCCCTTTCGAGCTTGGGCTCATTCGTAAAC
* * * *
5347861 TTATAGACATGATGTAATTAACGCACGCCACGAAGAAAATCATTTCAAAAATGGAAATCCCTTTC
196 TTATAAACATGATGTAATCAACACACGCCACGAAGAAAACCATTTCAAAAATGGAAATCCCTTTC
* ** * *
5347926 GGGCATTGGCTCGTTCGTAAATTTATAAACATGATGTAACTAACGCACGCCACGAAGAAAATCAT
261 GGGCATTGGCTCATTCGTAAATTTATAAACACAATGTAACTAACACACGCCACAAAGAAAATCAT
*
5347991 TTCAAAAATGGATATCCCTTTCA
326 TTCAAAAATGGAAATCCCTTTCA
*
5348014 GGCTTGGGCTCGTTCGTAAATTTATAAACATGATGTAATTAACGCACACCACGAAGA-AATCATT
1 GGCTTGGGCTCGTTCGTAAATTTATAAACATGATGTAAATAACGCACACCACGAAGATAATCATT
* *
5348078 TCAAAAATGGAAATCCCTTTCGGGC-TTGGGTTATTCGTAAACTTATAAACATGATGTAATTAAA
66 TCAAAAATGGAAATCCCTTTCGGGCATTGGCTCATTCGTAAACTTATAAACATGATGTAATTAAA
* * * *
5348142 GCACACGACAAAGAAAATCATTTCAAAAATGGAAATCCTTTTTGAGCTTGGGCTCGTTCGTAAAC
131 GCACACCACAAAGAAAATCATTTCAAAAATGGAAATCCCTTTCGAGCTTGGGCTCATTCGTAAAC
5348207 TTATAAACATGATGTAATCAACACACGCCACGAAGAAAACCATTTCAAAAATGGAAATCCCTTTC
196 TTATAAACATGATGTAATCAACACACGCCACGAAGAAAACCATTTCAAAAATGGAAATCCCTTTC
*
5348272 GGGC-TTGGGCTCATTCGTAAATTTATAAGCACAATGTAA-TCAACACACGCCACAAAGAAAATC
261 GGGCATT-GGCTCATTCGTAAATTTATAAACACAATGTAACT-AACACACGCCACAAAGAAAATC
5348335 ATTTCAAAAATGGAAATCC
324 ATTTCAAAAATGGAAATCC
5348354 GGTTAATAGG
Statistics
Matches: 312, Mismatches: 26, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
345 3 0.01
346 223 0.71
347 32 0.10
348 54 0.17
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (348 bp):
GGCTTGGGCTCGTTCGTAAATTTATAAACATGATGTAAATAACGCACACCACGAAGATAATCATT
TCAAAAATGGAAATCCCTTTCGGGCATTGGCTCATTCGTAAACTTATAAACATGATGTAATTAAA
GCACACCACAAAGAAAATCATTTCAAAAATGGAAATCCCTTTCGAGCTTGGGCTCATTCGTAAAC
TTATAAACATGATGTAATCAACACACGCCACGAAGAAAACCATTTCAAAAATGGAAATCCCTTTC
GGGCATTGGCTCATTCGTAAATTTATAAACACAATGTAACTAACACACGCCACAAAGAAAATCAT
TTCAAAAATGGAAATCCCTTTCA
Found at i:5349741 original size:16 final size:16
Alignment explanation
Indices: 5349716--5349769 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
5349706 TGGTTCAGTA
*
5349716 TAATGGAATAGAGCTG
1 TAATAGAATAGAGCTG
* *
5349732 TAATATAATAGAGTTG
1 TAATAGAATAGAGCTG
* *
5349748 TAATAGAATAAAACTG
1 TAATAGAATAGAGCTG
5349764 TAATAG
1 TAATAG
5349770 CAATTCAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (16 bp):
TAATAGAATAGAGCTG
Found at i:5350235 original size:12 final size:12
Alignment explanation
Indices: 5350205--5350239 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
5350195 TATATGTGAC
5350205 TTAAAGAATAAT
1 TTAAAGAATAAT
*
5350217 TTAAAAGAGTAAT
1 TT-AAAGAATAAT
5350230 TTAAAGAATA
1 TTAAAGAATA
5350240 TCTTGTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (12 bp):
TTAAAGAATAAT
Found at i:5352235 original size:28 final size:30
Alignment explanation
Indices: 5352204--5352268 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
5352194 AGTGATATGG
*
5352204 AAGAGAAATT-GAATAGAGAA-AAGAGAGA
1 AAGAGAAATTAGAAAAGAGAACAAGAGAGA
*
5352232 AAGAG--GTTAGAAAAGAGAACAAGAGAGA
1 AAGAGAAATTAGAAAAGAGAACAAGAGAGA
5352260 AAGAGAAAT
1 AAGAGAAAT
5352269 CTGTTGAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 2 0.07
27 9 0.30
28 18 0.60
30 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.29, T:0.09
Consensus pattern (30 bp):
AAGAGAAATTAGAAAAGAGAACAAGAGAGA
Found at i:5355988 original size:18 final size:18
Alignment explanation
Indices: 5355967--5356039 Score: 83
Period size: 18 Copynumber: 4.1 Consensus size: 18
5355957 CGTTTACGGC
*
5355967 ACTATTCACATTTACAGT
1 ACTATTCACATATACAGT
* * *
5355985 ACTATTCACGTATACGGC
1 ACTATTCACATATACAGT
*
5356003 ACTATTCACATATACGGT
1 ACTATTCACATATACAGT
* *
5356021 ACTGTTCACGTATACAGT
1 ACTATTCACATATACAGT
5356039 A
1 A
5356040 GTTGGGATTG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (18 bp):
ACTATTCACATATACAGT
Found at i:5356008 original size:36 final size:36
Alignment explanation
Indices: 5355961--5356035 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
5355951 TACGACCGTT
*
5355961 TACGGCACTATTCACATTTACAGTACTATTCACGTA
1 TACGGCACTATTCACATATACAGTACTATTCACGTA
* *
5355997 TACGGCACTATTCACATATACGGTACTGTTCACGTA
1 TACGGCACTATTCACATATACAGTACTATTCACGTA
5356033 TAC
1 TAC
5356036 AGTAGTTGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (36 bp):
TACGGCACTATTCACATATACAGTACTATTCACGTA
Found at i:5362016 original size:34 final size:34
Alignment explanation
Indices: 5361978--5362048 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
5361968 GGTGGTCCAA
*
5361978 AATACTGACTCAACAAAGCTTGAAGATCACCCTT
1 AATACTAACTCAACAAAGCTTGAAGATCACCCTT
**
5362012 AATACTAACTCAGTAAAGCTTGAAGATCACCCTT
1 AATACTAACTCAACAAAGCTTGAAGATCACCCTT
5362046 AAT
1 AAT
5362049 CTCGATTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.25
Consensus pattern (34 bp):
AATACTAACTCAACAAAGCTTGAAGATCACCCTT
Found at i:5363572 original size:24 final size:24
Alignment explanation
Indices: 5363545--5363590 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
5363535 CTATTAACAT
*
5363545 TGTTCGTGAACATATTCAATTATA
1 TGTTCATGAACATATTCAATTATA
* * *
5363569 TGTTTATGAACATGTTCGATTA
1 TGTTCATGAACATATTCAATTA
5363591 AGTTAAATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (24 bp):
TGTTCATGAACATATTCAATTATA
Found at i:5366023 original size:28 final size:28
Alignment explanation
Indices: 5365971--5366040 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
5365961 AAATAAAAAA
*
5365971 TTACCAAAATGT-TATAACTTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
*
5365998 TTACCAAAATATATATAATTTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
5366026 TTACCAAAATATATA
1 TTACCAAAATATATA
5366041 AAAAAAAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 11 0.28
28 29 0.73
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:5366435 original size:3 final size:3
Alignment explanation
Indices: 5366427--5366461 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5366417 AAATTTATAG
5366427 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5366462 AGATGTTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5367219 original size:18 final size:18
Alignment explanation
Indices: 5367191--5367235 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
5367181 TTGATATGGT
* *
5367191 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
*
5367209 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
5367227 TGGTGGCGA
1 TGGTGGCGA
5367236 TCATTGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:5369575 original size:15 final size:15
Alignment explanation
Indices: 5369551--5369589 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5369541 CAATAACCAC
*
5369551 AATAACTAAAACTAG
1 AATAATTAAAACTAG
*
5369566 AATAATT-AAATTAG
1 AATAATTAAAACTAG
5369580 AATAATTAAA
1 AATAATTAAA
5369590 TTGATACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (15 bp):
AATAATTAAAACTAG
Found at i:5369582 original size:14 final size:14
Alignment explanation
Indices: 5369563--5369591 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5369553 TAACTAAAAC
5369563 TAGAATAATTAAAT
1 TAGAATAATTAAAT
5369577 TAGAATAATTAAAT
1 TAGAATAATTAAAT
5369591 T
1 T
5369592 GATACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAGAATAATTAAAT
Found at i:5371886 original size:11 final size:11
Alignment explanation
Indices: 5371870--5371897 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5371860 ATTTAGTGTG
5371870 TTTTTTTCTAT
1 TTTTTTTCTAT
5371881 TTTTTTTCTAT
1 TTTTTTTCTAT
5371892 TTTTTT
1 TTTTTT
5371898 GGTTTTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTCTAT
Found at i:5371946 original size:27 final size:28
Alignment explanation
Indices: 5371916--5371983 Score: 122
Period size: 27 Copynumber: 2.5 Consensus size: 28
5371906 ACTTTTTTTG
5371916 ATATATTTTGGTAAATAAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAGTTAT
5371943 ATATATTTTGGTAAATAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAGTTAT
5371971 A-ATATTTTGGTAA
1 ATATATTTTGGTAA
5371984 TTTTTATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAGTTAT
Found at i:5372005 original size:13 final size:13
Alignment explanation
Indices: 5371987--5372012 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5371977 TTGGTAATTT
5371987 TTATTTTTTTATA
1 TTATTTTTTTATA
5372000 TTATTTTTTTATA
1 TTATTTTTTTATA
5372013 AAACTCATAA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTTTTTTATA
Found at i:5372045 original size:19 final size:18
Alignment explanation
Indices: 5372021--5372056 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5372011 TAAAACTCAT
5372021 AATAAAACATTACAAAAAG
1 AATAAAACATTA-AAAAAG
*
5372040 AATAAAATATTAAAAAA
1 AATAAAACATTAAAAAA
5372057 TATCAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (18 bp):
AATAAAACATTAAAAAAG
Found at i:5372786 original size:10 final size:10
Alignment explanation
Indices: 5372773--5372928 Score: 57
Period size: 10 Copynumber: 16.0 Consensus size: 10
5372763 CTTCCTTCCC
5372773 TCTTCTTCTT
1 TCTTCTTCTT
5372783 TCTT-TT-TT
1 TCTTCTTCTT
*
5372791 TTTTC-TCTT
1 TCTTCTTCTT
*
5372800 CTCTTCTCCTT
1 -TCTTCTTCTT
5372811 TCCTT-TTCTT
1 T-CTTCTTCTT
*
5372821 TC--CTTATT
1 TCTTCTTCTT
5372829 T-TTCTTTCTT
1 TCTTC-TTCTT
* **
5372839 TCCTCCCCTT
1 TCTTCTTCTT
5372849 TCCTT-TTCTT
1 T-CTTCTTCTT
5372859 TC--CTTCTT
1 TCTTCTTCTT
5372867 T-TTCTTTCTT
1 TCTTC-TTCTT
* *
5372877 TCCTCTCCTT
1 TCTTCTTCTT
*
5372887 TCCTT-TTCCT
1 T-CTTCTTCTT
*
5372897 TCTTTTTCTT
1 TCTTCTTCTT
*
5372907 GCTTCCTTTCTT
1 TCTT-C-TTCTT
5372919 TCTTCTTCTT
1 TCTTCTTCTT
5372929 CCCCTCTCCT
Statistics
Matches: 105, Mismatches: 21, Indels: 40
0.63 0.13 0.24
Matches are distributed among these distances:
8 17 0.16
9 11 0.10
10 54 0.51
11 15 0.14
12 8 0.08
ACGTcount: A:0.01, C:0.32, G:0.01, T:0.67
Consensus pattern (10 bp):
TCTTCTTCTT
Found at i:5372836 original size:18 final size:18
Alignment explanation
Indices: 5372815--5372925 Score: 86
Period size: 18 Copynumber: 6.1 Consensus size: 18
5372805 CTCCTTTCCT
*
5372815 TTTCTTTCCTTATTTTTC
1 TTTCTTTCCTTCTTTTTC
* * *
5372833 TTTCTTTCCTCCCCTTTCC
1 TTTCTTTCCT-TCTTTTTC
5372852 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCCTTCTTTTTC
*
5372871 TTTCTTTCC-TCTCCTTTC
1 TTTCTTTCCTTCT-TTTTC
*
5372889 -CT-TTTCCTTCTTTTTC
1 TTTCTTTCCTTCTTTTTC
*
5372905 TTGC-TTCCTTTCTTTCTTC
1 TTTCTTTCC-TTCTTT-TTC
5372924 TT
1 TT
5372926 CTTCCCCTCT
Statistics
Matches: 73, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
16 9 0.12
17 11 0.15
18 29 0.40
19 14 0.19
20 10 0.14
ACGTcount: A:0.01, C:0.32, G:0.01, T:0.66
Consensus pattern (18 bp):
TTTCTTTCCTTCTTTTTC
Found at i:5372877 original size:28 final size:28
Alignment explanation
Indices: 5372846--5372925 Score: 76
Period size: 34 Copynumber: 2.8 Consensus size: 28
5372836 CTTTCCTCCC
*
5372846 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
1 CTTTCCTTTTCTTTCCTTCTTTTTCTTG
5372874 CTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCTTG
1 CTTT-C-CT--TTT-C-TTTCCTTCTTTTTCTTG
5372908 C-TTCC-TTTCTTT-CTTCTT
1 CTTTCCTTTTCTTTCCTTCTT
5372926 CTTCCCCTCT
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
25 6 0.13
26 3 0.07
27 1 0.02
28 7 0.16
29 1 0.02
30 2 0.04
31 1 0.02
32 4 0.09
33 3 0.07
34 17 0.38
ACGTcount: A:0.00, C:0.33, G:0.01, T:0.66
Consensus pattern (28 bp):
CTTTCCTTTTCTTTCCTTCTTTTTCTTG
Found at i:5372916 original size:38 final size:38
Alignment explanation
Indices: 5372778--5372894 Score: 168
Period size: 38 Copynumber: 3.1 Consensus size: 38
5372768 TTCCCTCTTC
5372778 TTCTTT-CTT-TTTTT-TTTCTCTTCTCTTCTCCTTTCCTT
1 TTCTTTCCTTATTTTTCTTTCT-TTC-C-TCTCCTTTCCTT
*
5372816 TTCTTTCCTTATTTTTCTTTCTTTCCTCCCCTTTCCTT
1 TTCTTTCCTTATTTTTCTTTCTTTCCTCTCCTTTCCTT
*
5372854 TTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTT
1 TTCTTTCCTTATTTTTCTTTCTTTCCTCTCCTTTCCTT
5372892 TTC
1 TTC
5372895 CTTCTTTTTC
Statistics
Matches: 73, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
38 56 0.77
39 4 0.05
40 8 0.11
41 5 0.07
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (38 bp):
TTCTTTCCTTATTTTTCTTTCTTTCCTCTCCTTTCCTT
Found at i:5372921 original size:22 final size:23
Alignment explanation
Indices: 5372886--5372928 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5372876 TTCCTCTCCT
*
5372886 TTCCTTTTCCTTCTTTTTCTTGC
1 TTCCTTTTCCTTCTTCTTCTTGC
*
5372909 TTCC-TTTCTTTCTTCTTCTT
1 TTCCTTTTCCTTCTTCTTCTT
5372929 CCCCTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.67
Consensus pattern (23 bp):
TTCCTTTTCCTTCTTCTTCTTGC
Found at i:5372926 original size:28 final size:30
Alignment explanation
Indices: 5372747--5372929 Score: 84
Period size: 28 Copynumber: 6.2 Consensus size: 30
5372737 TTACCTTATT
* * *
5372747 TTCTT-TTT-TTTCCTTCCTTCCTTCCCTC
1 TTCTTCTTTCTTTCCTTCCTTTCTTTCTTC
5372775 TTCTTCTTTCTTT--TT--TTT-TTCTCTTC
1 TTCTTCTTTCTTTCCTTCCTTTCTT-TCTTC
* * * * *
5372801 -TCTTC-TCCTTTCCTTTTCTTTCCTTATTT
1 TTCTTCTTTCTTTCC-TTCCTTTCTTTCTTC
**
5372830 TTCTTTCTTTCCTCCCCTTTCCTTTTCTTTCCTTC
1 TTC-TTCTTT-CTTTCC-TTCC-TTTCTTT-CTTC
* *
5372865 TTTTTCTTTCTTTCCTCTCCTTTCCTTT-TCC
1 TTCTTCTTTCTTTCCT-TCCTTT-CTTTCTTC
*
5372896 TTCTT-TTTC-TTGCTTCCTTTCTTTCTTC
1 TTCTTCTTTCTTTCCTTCCTTTCTTTCTTC
5372924 TTCTTC
1 TTCTTC
5372930 CCCTCTCCTT
Statistics
Matches: 115, Mismatches: 21, Indels: 37
0.66 0.12 0.21
Matches are distributed among these distances:
24 5 0.04
25 7 0.06
26 5 0.04
27 6 0.05
28 20 0.17
29 13 0.11
30 10 0.09
31 9 0.08
32 5 0.04
33 19 0.17
34 12 0.10
35 4 0.03
ACGTcount: A:0.01, C:0.33, G:0.01, T:0.66
Consensus pattern (30 bp):
TTCTTCTTTCTTTCCTTCCTTTCTTTCTTC
Found at i:5373045 original size:27 final size:27
Alignment explanation
Indices: 5372977--5373053 Score: 109
Period size: 27 Copynumber: 2.9 Consensus size: 27
5372967 AATTTAAGGG
* **
5372977 TGGTGCCGCCAACAAGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
*
5373004 TGGTACCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
*
5373031 TGGTGCCGCCAACAGTGTTCCCT
1 TGGTGCCGCCAACAGGGTTCCCT
5373054 CCACCAGGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.17, C:0.31, G:0.26, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Found at i:5373132 original size:29 final size:28
Alignment explanation
Indices: 5373083--5373153 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 28
5373073 TGTTTTTTTT
5373083 TATATATTTTGGTAAATAAAAAAA-TTA
1 TATATATTTTGGTAAATAAAAAAAGTTA
5373110 TATATATTTTGGTAAATAAAAAAAAAGTTA
1 TATATATTTTGGTAAAT--AAAAAAAGTTA
*
5373140 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
5373154 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 17 0.43
29 18 0.45
30 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAAGTTA
Found at i:5374687 original size:7 final size:7
Alignment explanation
Indices: 5374671--5374705 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
5374661 ATTCAATTCG
5374671 ATTC-AA
1 ATTCAAA
5374677 ATTCAAA
1 ATTCAAA
5374684 ATTCAAA
1 ATTCAAA
5374691 ATTCAAA
1 ATTCAAA
5374698 ATTCAAA
1 ATTCAAA
5374705 A
1 A
5374706 AAGAAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.14
7 24 0.86
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (7 bp):
ATTCAAA
Found at i:5374712 original size:21 final size:20
Alignment explanation
Indices: 5374671--5374713 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
5374661 ATTCAATTCG
**
5374671 ATTCAAATTCAAAATTCAAA
1 ATTCAAATTCAAAAAACAAA
*
5374691 ATTCAAAATTCAAAAAAGAAA
1 ATTC-AAATTCAAAAAACAAA
5374712 AT
1 AT
5374714 CAAGTTGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (20 bp):
ATTCAAATTCAAAAAACAAA
Found at i:5374853 original size:16 final size:16
Alignment explanation
Indices: 5374832--5374862 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5374822 TTCTCCCTCG
*
5374832 GAATTTTAGTGGCATA
1 GAATTTTAGTCGCATA
5374848 GAATTTTAGTCGCAT
1 GAATTTTAGTCGCAT
5374863 TGACATCGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (16 bp):
GAATTTTAGTCGCATA
Found at i:5376457 original size:87 final size:87
Alignment explanation
Indices: 5376339--5376683 Score: 485
Period size: 87 Copynumber: 4.0 Consensus size: 87
5376329 GGCAACAGTG
* * * * *
5376339 TTTCGGGCTTGGGCTCATTTGTAAATTTATAAACATGATGTAATTAACGCATGCCACAAAGAAAA
1 TTTCGGGCTTGGCCTCGTTCGTAAATTTATAAACATGATGTAATTAACACATGCCACGAAGAAAA
5376404 TCATTTCAAAAATGGAAATACC
66 TCATTTCAAAAATGGAAATACC
* * *
5376426 TTTTGGGCTTGGCCCCGTTCGTAAACTTATAAACATGATGTAATTAACACATGCCACGAAGAAAA
1 TTTCGGGCTTGGCCTCGTTCGTAAATTTATAAACATGATGTAATTAACACATGCCACGAAGAAAA
*
5376491 TCATTTCAAAAATGGAAATCCC
66 TCATTTCAAAAATGGAAATACC
* * * ** *
5376513 TTTCAGGCTTGGGCTTGTTCAAAAATTTATAAACATGATGTAATTATCACATGCCACGAAGAAAA
1 TTTCGGGCTTGGCCTCGTTCGTAAATTTATAAACATGATGTAATTAACACATGCCACGAAGAAAA
*
5376578 TCATTTCAAAAATGGAAATTCC
66 TCATTTCAAAAATGGAAATACC
* * * * *
5376600 TTTCGGGCTTGGCCTCATTTGTAAATTTATAAACATGATGTAAGTT-ACGCACGCCATGAAGAAA
1 TTTCGGGCTTGGCCTCGTTCGTAAATTTATAAACATGATGTAA-TTAACACATGCCACGAAGAAA
5376664 ATCATTTCAAAAATGGAAAT
65 ATCATTTCAAAAATGGAAAT
5376684 CAGATTAACA
Statistics
Matches: 227, Mismatches: 30, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
87 225 0.99
88 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (87 bp):
TTTCGGGCTTGGCCTCGTTCGTAAATTTATAAACATGATGTAATTAACACATGCCACGAAGAAAA
TCATTTCAAAAATGGAAATACC
Found at i:5380598 original size:21 final size:21
Alignment explanation
Indices: 5380573--5380616 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5380563 ATTGGGCTGT
* *
5380573 TACACTCCACCTGTTTTGGAG
1 TACACTCCACCTGCTGTGGAG
5380594 TACACTCCACCTGCTGTGGAG
1 TACACTCCACCTGCTGTGGAG
5380615 TA
1 TA
5380617 TTGCTCGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
TACACTCCACCTGCTGTGGAG
Found at i:5387739 original size:16 final size:15
Alignment explanation
Indices: 5387707--5387737 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5387697 CAAAAAAATT
5387707 ATTTTTTATTAATAA
1 ATTTTTTATTAATAA
*
5387722 ATTTTTTATTTATAA
1 ATTTTTTATTAATAA
5387737 A
1 A
5387738 ATCAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTTTATTAATAA
Found at i:5389291 original size:169 final size:170
Alignment explanation
Indices: 5388821--5389476 Score: 897
Period size: 170 Copynumber: 3.9 Consensus size: 170
5388811 AAATCGAACC
* * *
5388821 ATTTCCTTAAATATCACAAAATTCAACCCAAAACCCTAATTTTTTAAAACTGGCATGTATTTAAA
1 ATTTCCCTAAATATCACAAAATTCAACCCAAAACCCTAATTTTTTAAAACTGGCATATATCTAAA
* **
5388886 ATTTAACCGATGTTATTATTCATTGATAATGCATGAAACTTATATACCGACGATGCATCAAATAT
66 ATTTAACTGATGTTATTATTCATTGATAATGCATGAAACTTATGCACCGACGATGCATCAAATAT
* *
5388951 TATTTTATTTTCTTTCTATTTCTCTTCCCAAAATCAGTCT
131 TATTTTATTTTCTTTCTATTTCTCTTCCCAAGATCGGTCT
** * * *
5388991 ATTTATCAAAATATCGCAAAATTCAGCCCAAAACCCTAATTTTTTAAAACTGGCATATATCTAAA
1 ATTTCCCTAAATATCACAAAATTCAACCCAAAACCCTAATTTTTTAAAACTGGCATATATCTAAA
* * *
5389056 ATTTAATTGATGTTATTATTCACTAATAATGCATGAAACTTATGC-CCGGACGATGCATCAAATA
66 ATTTAACTGATGTTATTATTCATTGATAATGCATGAAACTTATGCACC-GACGATGCATCAAATA
* *
5389120 TTATTTTATTTTCTTTCTATTTATCTTCCCAAGATTGGTCT
130 TTATTTTATTTTCTTTCTATTTCTCTTCCCAAGATCGGTCT
*
5389161 ATTTCCCTAAATATCACAAAATTCAACTCAAAACCCTAA-TTTTTAAAACTGGCATATATCTAAA
1 ATTTCCCTAAATATCACAAAATTCAACCCAAAACCCTAATTTTTTAAAACTGGCATATATCTAAA
* * *
5389225 ATTTAATTGATGTTATTATTCATTGATAATGCATGAAACTTATGCCCCAACGATGCATCAAATAT
66 ATTTAACTGATGTTATTATTCATTGATAATGCATGAAACTTATGCACCGACGATGCATCAAATAT
* * * *
5389290 TATTTTATTTTATTTCTATTTCTCTTTCC-AGAACCGATCT
131 TATTTTATTTTCTTTCTATTTCTCTTCCCAAG-ATCGGTCT
* ** * **
5389330 ATTTCTCTAAATATTGCAAAATTCAACCCAAAACCCTAATTTTTTTAAATCTAACATATATCTAA
1 ATTTCCCTAAATATCACAAAATTCAACCCAAAACCCTAA-TTTTTTAAAACTGGCATATATCTAA
* * * * *
5389395 AATTTAACTGATGTTATTATTCACTTG-TAATGCATGAAGCTTATGTACCGACAATACATAAAAT
65 AATTTAACTGATGTTATTATTCA-TTGATAATGCATGAAACTTATGCACCGACGATGCATCAAAT
* *
5389459 ATTAGTTAATTTTCTTTC
129 ATTATTTTATTTTCTTTC
5389477 CTTGAAATAT
Statistics
Matches: 429, Mismatches: 51, Indels: 11
0.87 0.10 0.02
Matches are distributed among these distances:
168 2 0.00
169 152 0.35
170 184 0.43
171 88 0.21
172 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (170 bp):
ATTTCCCTAAATATCACAAAATTCAACCCAAAACCCTAATTTTTTAAAACTGGCATATATCTAAA
ATTTAACTGATGTTATTATTCATTGATAATGCATGAAACTTATGCACCGACGATGCATCAAATAT
TATTTTATTTTCTTTCTATTTCTCTTCCCAAGATCGGTCT
Found at i:5390045 original size:30 final size:30
Alignment explanation
Indices: 5390011--5390074 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
5390001 ACTTAACAAG
* *
5390011 CAAATGCTTTTAAGAA-ATTAACAAAATTAA
1 CAAATGCCTTTAA-AATAATAACAAAATTAA
5390041 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
5390071 -AAAT
1 CAAAT
5390075 AAAATAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.28
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAACAAAATTAA
Found at i:5391260 original size:16 final size:16
Alignment explanation
Indices: 5391227--5391260 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5391217 GACGTAGGTA
*
5391227 AAAAATATTTTATGTT
1 AAAAATATTATATGTT
*
5391243 AAAAATATTATATTTT
1 AAAAATATTATATGTT
5391259 AA
1 AA
5391261 GGTTTTCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AAAAATATTATATGTT
Found at i:5391422 original size:23 final size:24
Alignment explanation
Indices: 5391391--5391437 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5391381 TATGAAAAAG
*
5391391 AAAAAAAATATTA-ATTATAATTT
1 AAAAAAAATAATATATTATAATTT
* *
5391414 AAAATAAATAATATTTTATAATTT
1 AAAAAAAATAATATATTATAATTT
5391438 TATAACTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAAAAATAATATATTATAATTT
Found at i:5409035 original size:6 final size:6
Alignment explanation
Indices: 5409024--5409058 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
5409014 GCCGCTAGAA
5409024 CCTCTG CCTCTG CCTCTG CCTCTG CCTCTG CCTCT
1 CCTCTG CCTCTG CCTCTG CCTCTG CCTCTG CCTCT
5409059 ACCCCTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.51, G:0.14, T:0.34
Consensus pattern (6 bp):
CCTCTG
Found at i:5409069 original size:18 final size:18
Alignment explanation
Indices: 5409027--5409070 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5409017 GCTAGAACCT
* *
5409027 CTGCCTCTGCCTCTGCCT
1 CTGCCTCTGCCTCTACCC
5409045 CTGCCTCTGCCTCTACCC
1 CTGCCTCTGCCTCTACCC
*
5409063 CTTCCTCT
1 CTGCCTCT
5409071 AGTAGAAGTT
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:0.02, C:0.52, G:0.11, T:0.34
Consensus pattern (18 bp):
CTGCCTCTGCCTCTACCC
Found at i:5412814 original size:15 final size:15
Alignment explanation
Indices: 5412773--5412821 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
5412763 AAGAAAATAA
5412773 ATAAAAGATAT-AAAT
1 ATAAAA-ATATAAAAT
* *
5412788 ATAAGGATTATAAAAT
1 ATAA-AAATATAAAAT
5412804 ATAAAAATATAAAAT
1 ATAAAAATATAAAAT
5412819 ATA
1 ATA
5412822 GGTACGTACG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
ATAAAAATATAAAAT
Found at i:5413257 original size:3 final size:3
Alignment explanation
Indices: 5413222--5413305 Score: 55
Period size: 3 Copynumber: 27.3 Consensus size: 3
5413212 ATAAGAAAAC
* * * * * *
5413222 ATA ATA CTA ACA ATA GTA TTA ATA A-A TATA ATA ATA AAA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
*
5413267 A-A GATA ATA ATG ATA ATA ATA ATA ACTAA ATA ATA ATA A
1 ATA -ATA ATA ATA ATA ATA ATA ATA A-T-A ATA ATA ATA A
5413306 AAAAAATGCT
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
2 2 0.03
3 54 0.87
4 4 0.06
5 2 0.03
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:5414178 original size:20 final size:20
Alignment explanation
Indices: 5414153--5414191 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5414143 GACGGCGCAA
**
5414153 GTGGTGGTGGTGACGTGACC
1 GTGGTGGTGACGACGTGACC
5414173 GTGGTGGTGACGACGTGAC
1 GTGGTGGTGACGACGTGAC
5414192 GTTGGCGGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.15, G:0.49, T:0.23
Consensus pattern (20 bp):
GTGGTGGTGACGACGTGACC
Found at i:5432387 original size:52 final size:48
Alignment explanation
Indices: 5432368--5432570 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
5432358 TGACAAGTGG
* *
5432368 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
5432414 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
5432466 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
5432512 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
5432558 AAAGTGATAAGTG
1 AAAGTGATAAGTG
5432571 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:5432422 original size:98 final size:98
Alignment explanation
Indices: 5432302--5432570 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
5432292 TTTGAGTACT
*
5432302 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
5432367 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
5432400 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
5432465 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
5432498 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
5432563 GATAAGTG
65 GAAAAGTG
5432571 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:5432578 original size:37 final size:37
Alignment explanation
Indices: 5432534--5432679 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
5432524 GATAGCTTTA
*
5432534 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
5432571 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
5432608 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
5432645 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
5432680 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:5438022 original size:83 final size:83
Alignment explanation
Indices: 5437883--5438105 Score: 326
Period size: 83 Copynumber: 2.7 Consensus size: 83
5437873 CAACTTTTCC
* * * *
5437883 TTTAATT-AGTCAATGAAATAGCGCCGTTTTGTTAGATTTTTAATGTATTTTTTGCGGCGTTTTT
1 TTTAATTCAGTCAATGAAATGGCGCCGTTTTGTTA-AATTTTAATATATTTTTTGCGGCGTTTGT
*
5437947 ATATAAAACGCCACTAATA
65 ATACAAAACGCCACTAATA
* *
5437966 TTTAATTCAG-CAATGAAACGGCACCGTTTTGTTAAATTCTTAATATATTTTTTGCGGCGTTTGT
1 TTTAATTCAGTCAATGAAATGGCGCCGTTTTGTTAAATT-TTAATATATTTTTTGCGGCGTTTGT
5438030 ATACAAAACGCCACTAATA
65 ATACAAAACGCCACTAATA
*
5438049 TTTAATTC-GTCAATGAAATGGCGCCGTTTGGTTAAATTTTAAATATATTTTTTGCGG
1 TTTAATTCAGTCAATGAAATGGCGCCGTTTTGTTAAATTTT-AATATATTTTTTGCGG
5438106 TTTTTGACCA
Statistics
Matches: 126, Mismatches: 10, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
82 6 0.05
83 118 0.94
84 2 0.02
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (83 bp):
TTTAATTCAGTCAATGAAATGGCGCCGTTTTGTTAAATTTTAATATATTTTTTGCGGCGTTTGTA
TACAAAACGCCACTAATA
Found at i:5438272 original size:14 final size:14
Alignment explanation
Indices: 5438253--5438280 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5438243 ACATCATTAT
5438253 TAATATTATTTAAA
1 TAATATTATTTAAA
5438267 TAATATTATTTAAA
1 TAATATTATTTAAA
5438281 ATTTTGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTATTTAAA
Found at i:5438820 original size:15 final size:15
Alignment explanation
Indices: 5438785--5438822 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
5438775 TCCCAACACT
5438785 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
5438799 T-AATCCATAATCCC
1 TAAATCCATAATCCC
5438813 TAAATCCATA
1 TAAATCCATA
5438823 TGTAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 12 0.55
15 8 0.36
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:5439162 original size:22 final size:21
Alignment explanation
Indices: 5439115--5439162 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
5439105 ACCCCAGCCT
*
5439115 TTAAACCATAAACCATAACCC
1 TTAAACCATAAACCATAAACC
* *
5439136 CTAAACTCATAATCCATAAACC
1 TTAAAC-CATAAACCATAAACC
5439158 TTAAA
1 TTAAA
5439163 ATGGTAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (21 bp):
TTAAACCATAAACCATAAACC
Found at i:5439510 original size:41 final size:41
Alignment explanation
Indices: 5439395--5439852 Score: 447
Period size: 41 Copynumber: 11.2 Consensus size: 41
5439385 TAAATTATTT
* * *
5439395 TAAATCCCTGAGTATTAGCGGCGC-TTCTCAGAAAATGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCA-AAAACGCCGC
**** ** *
5439436 TAAA-AAAAGAG-AGTTAGCGGCGCTTAATCAAAAACGCCGT
1 TAAAGCCCTGAGCA-TTAGCGGCGCTTTCTCAAAAACGCCGC
* * *
5439476 TAAAGCCCTGATCATTAGCGGTGCTTTCTTAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* ** * *
5439517 TAAATCCCTGAGCATTAGCGGCAATTTCTTAAAAACGCCGT
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
5439558 TAAAACCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* * * * *
5439599 TAAAGCCCTGACCATCAGCGGTGCTTTATCAAAAACACCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* * * * **
5439640 TAAAGCCTTGAGCGTTAGCGGCGCTTTATCAAAATCGTTGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* ** * * *
5439681 TAAATCTTTGACCATTAGCGGCGCTTCCTTAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
5439722 TAAAGCCCTGAGCATTAGGGGCGCTTTATCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* * * *
5439763 TAAAGGCCTCAGCATTAGTGGCGCTTTATCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* * *
5439804 TAAAAG-CCTCAGTATTAGCGGTGCTTTCTCAAAAACGCCGC
1 T-AAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
5439845 TAAAGCCC
1 TAAAGCCC
5439853 CCGAAAACTC
Statistics
Matches: 340, Mismatches: 71, Indels: 12
0.80 0.17 0.03
Matches are distributed among these distances:
39 1 0.00
40 29 0.09
41 305 0.90
42 5 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (41 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
Found at i:5440272 original size:14 final size:14
Alignment explanation
Indices: 5440210--5440278 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
5440200 TATTAATTTA
*
5440210 ATTTTATATAAAAT
1 ATTTTATTTAAAAT
5440224 ATTTTATTTCAAAAT
1 ATTTTATTT-AAAAT
* *
5440239 A--TAATTTAAAAC
1 ATTTTATTTAAAAT
***
5440251 AAAATATTTAAAAT
1 ATTTTATTTAAAAT
*
5440265 ATTTTATTTTAAAT
1 ATTTTATTTAAAAT
5440279 TATATTAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
12 5 0.12
13 5 0.12
14 26 0.62
15 6 0.14
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTTATTTAAAAT
Found at i:5440319 original size:23 final size:22
Alignment explanation
Indices: 5440273--5440319 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
5440263 ATATTTTATT
5440273 TTAAATTATATTAAAATATATA
1 TTAAATTATATTAAAATATATA
* *
5440295 TTAAATTATGATTAAATTATTTA
1 TTAAATTAT-ATTAAAATATATA
5440318 TT
1 TT
5440320 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAATTATATTAAAATATATA
Found at i:5440335 original size:10 final size:10
Alignment explanation
Indices: 5440268--5440335 Score: 68
Period size: 11 Copynumber: 6.7 Consensus size: 10
5440258 TTAAAATATT
*
5440268 TTATTTTAAA
1 TTATATTAAA
5440278 TTATATTAAAA
1 TTATATT-AAA
5440289 TATATATTAAA
1 T-TATATTAAA
5440300 TTATGATTAAA
1 TTAT-ATTAAA
*
5440311 TTAT-TT-AT
1 TTATATTAAA
*
5440319 TTTTATTAAA
1 TTATATTAAA
5440329 TTATATT
1 TTATATT
5440336 TAATAATAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
8 4 0.08
9 4 0.08
10 16 0.33
11 18 0.38
12 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (10 bp):
TTATATTAAA
Found at i:5445375 original size:18 final size:21
Alignment explanation
Indices: 5445333--5445375 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
5445323 TTATTTTTAA
5445333 AAATAAAATGTATTAAAAAGT
1 AAATAAAATGTATTAAAAAGT
5445354 --ATAAAAT-TA-TAAAAA-T
1 AAATAAAATGTATTAAAAAGT
5445370 AAATAA
1 AAATAA
5445376 TATTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 7
0.74 0.00 0.26
Matches are distributed among these distances:
16 1 0.05
17 6 0.30
18 6 0.30
19 7 0.35
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
AAATAAAATGTATTAAAAAGT
Found at i:5447170 original size:3 final size:3
Alignment explanation
Indices: 5447162--5447204 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
5447152 CCAGATCAGA
5447162 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5447205 ATTCCAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5470298 original size:15 final size:15
Alignment explanation
Indices: 5470280--5470311 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5470270 TTTTAAAATT
*
5470280 AAAAAAATATTTTTA
1 AAAAAAATATTTCTA
5470295 AAAAAAATATTTCTA
1 AAAAAAATATTTCTA
5470310 AA
1 AA
5470312 TTTTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAAAATATTTCTA
Found at i:5471797 original size:20 final size:20
Alignment explanation
Indices: 5471774--5471814 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5471764 CCGCACCCAT
*
5471774 CACCTACCCTCTGCCACCGC
1 CACCAACCCTCTGCCACCGC
*
5471794 CACCAACTCTCTGCCACCGC
1 CACCAACCCTCTGCCACCGC
5471814 C
1 C
5471815 GCAACCACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.59, G:0.10, T:0.15
Consensus pattern (20 bp):
CACCAACCCTCTGCCACCGC
Found at i:5487225 original size:27 final size:25
Alignment explanation
Indices: 5487190--5487254 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
5487180 AATAGAGCAC
5487190 ATAATCGGGAAGCACACTCTCGAGCCAT
1 ATAA-CGGGAAGCACA-TCT-GAGCCAT
* *
5487218 ATAACGGGAAGCTCATGTGAGCCAT
1 ATAACGGGAAGCACATCTGAGCCAT
* *
5487243 GTAACAGGAAGC
1 ATAACGGGAAGC
5487255 TTATCCGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 17 0.52
26 2 0.06
27 10 0.30
28 4 0.12
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (25 bp):
ATAACGGGAAGCACATCTGAGCCAT
Found at i:5488812 original size:12 final size:12
Alignment explanation
Indices: 5488795--5488825 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5488785 TAATTCATCC
5488795 ATATATAAATAT
1 ATATATAAATAT
*
5488807 ATATATACATAT
1 ATATATAAATAT
5488819 ATATATA
1 ATATATA
5488826 TAAGCCTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATAAATAT
Found at i:5489156 original size:40 final size:40
Alignment explanation
Indices: 5489102--5489202 Score: 166
Period size: 40 Copynumber: 2.5 Consensus size: 40
5489092 TGATTCCGTA
* * *
5489102 CACCGGCATGAAGCCTGCTAGATGTATAGTCTAAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAATCTAAATATTT
*
5489142 CACCGGCATTAAGCCTGCTAGACGTATAATCTGAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAATCTAAATATTT
5489182 CACCGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
5489203 GCACAAGCCT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACGTATAATCTAAATATTT
Found at i:5493670 original size:18 final size:18
Alignment explanation
Indices: 5493649--5493695 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 18
5493639 TAAATACCAT
5493649 AATTTTAAGGATATTA-AA
1 AATTTTAAGGA-ATTACAA
5493667 AATTTTAAGGAATTACCAA
1 AATTTTAAGGAATTA-CAA
5493686 AATTTCTAAG
1 AATTT-TAAG
5493696 CATGAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.15
18 11 0.42
19 7 0.27
20 4 0.15
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
AATTTTAAGGAATTACAA
Found at i:5494508 original size:15 final size:16
Alignment explanation
Indices: 5494488--5494524 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5494478 ACAAAATCAA
5494488 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
5494503 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
5494519 ATAAAA
1 ATAAAA
5494525 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:5494716 original size:60 final size:60
Alignment explanation
Indices: 5494642--5494763 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
5494632 ATACTAAACT
* * * * *
5494642 AAACACAACAATTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
5494702 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
5494762 AA
1 AA
5494764 TATTCATACA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 4 0.07
60 52 0.93
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:5494785 original size:23 final size:23
Alignment explanation
Indices: 5494757--5494898 Score: 185
Period size: 23 Copynumber: 5.8 Consensus size: 23
5494747 TTATAAAATA
5494757 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
*
5494780 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATAC--AA--ACAAT
* *
5494807 ATTACAATATTCATATAAAATTACAAA
1 ATTACAATATTC--ATACAA--ACAAT
5494834 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
5494857 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
5494880 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
5494899 ATTACAAAAT
Statistics
Matches: 109, Mismatches: 4, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
23 62 0.57
25 7 0.06
27 37 0.34
29 3 0.03
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (23 bp):
ATTACAATATTCATACAAACAAT
Found at i:5494788 original size:8 final size:8
Alignment explanation
Indices: 5494775--5494925 Score: 68
Period size: 8 Copynumber: 19.0 Consensus size: 8
5494765 ATTCATACAA
5494775 ACAATATT
1 ACAATATT
5494783 ACAATATTCAT
1 ACAATA-T--T
*
5494794 ACAAAATT
1 ACAATATT
*
5494802 ACAAAATT
1 ACAATATT
5494810 ACAATATT
1 ACAATATT
5494818 -C-ATA-T
1 ACAATATT
5494823 A-AA-ATT
1 ACAATATT
*
5494829 ACAAAATT
1 ACAATATT
5494837 ACAATATT
1 ACAATATT
**
5494845 -C-ATACAA
1 ACAATA-TT
5494852 ACAATATT
1 ACAATATT
5494860 ACAATATT
1 ACAATATT
**
5494868 -C-ATACAA
1 ACAATA-TT
5494875 ACAATATT
1 ACAATATT
5494883 ACAATATTCAT
1 ACAATA-T--T
*
5494894 ACAAAATT
1 ACAATATT
*
5494902 ACAAAATT
1 ACAATATT
*
5494910 ACAAAATT
1 ACAATATT
*
5494918 AAAATATT
1 ACAATATT
5494926 CATACAAAAT
Statistics
Matches: 112, Mismatches: 14, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
5 2 0.02
6 12 0.11
7 5 0.04
8 71 0.63
9 8 0.07
10 2 0.02
11 12 0.11
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (8 bp):
ACAATATT
Found at i:5494802 original size:19 final size:19
Alignment explanation
Indices: 5494756--5495306 Score: 135
Period size: 19 Copynumber: 27.3 Consensus size: 19
5494746 ATTATAAAAT
5494756 AATTACAATATTCATACAAACA
1 AATTACAATATTCATAC--A-A
5494778 ATATTACAATATTCATACAA
1 A-ATTACAATATTCATACAA
*
5494798 AATTACAA-AAT--TACAA
1 AATTACAATATTCATACAA
* **
5494814 TATT-C-ATATAAAATTACAA
1 AATTACAATAT-TCA-TACAA
5494833 AATTACAATATTCATACAAACA
1 AATTACAATATTCATAC--A-A
5494855 ATATTACAATATTCATACAAACA
1 A-ATTACAATATTCATAC--A-A
5494878 ATATTACAATATTCATACAA
1 A-ATTACAATATTCATACAA
*
5494898 AATTACAA-AAT--TACAA
1 AATTACAATATTCATACAA
*
5494914 AATTAAAATATTCATACAA
1 AATTACAATATTCATACAA
* * *
5494933 AA-TACTA-ATCCAGAACTATA
1 AATTACAATATTCA-TAC-A-A
*
5494953 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
5494974 TAATTACAATATTCATA-AA
1 -AATTACAATATTCATACAA
* *
5494993 CATTATAATATTCATACAA
1 AATTACAATATTCATACAA
* *
5495012 AA-TACTAATCA--AAAACTATA
1 AATTAC-AAT-ATTCATAC-A-A
*
5495032 AA-TACAAAATCAATT-ATAAAA
1 AATTAC--AAT--ATTCATACAA
5495053 TAATTACAATATTCATACAAAATTACAA
1 -AATTACAATA-T--T-C---A-TACAA
5495081 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* *
5495100 AA-TACTAATCA--AAAACAA
1 AATTAC-AAT-ATTCATACAA
* * * *
5495118 TAAATACAAAATTAATTATAA
1 -AATTACAATATTCA-TACAA
* *
5495139 AATAATACATTATTCATAAAA
1 AAT--TACAATATTCATACAA
*
5495160 AATTAAAATATTCATACAAAA
1 AATTACAATATTCATAC--AA
*
5495181 AATTACACTATTCATACAA
1 AATTACAATATTCATACAA
* * *
5495200 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-A-A
*
5495220 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
5495241 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
*
5495261 AATTATAATATTCATACAAA
1 AATTACAATATTCATAC-AA
*
5495281 AAGTTACAATATACATACAA
1 AA-TTACAATATTCATACAA
5495301 AATTAC
1 AATTAC
5495307 CCATTGACGC
Statistics
Matches: 403, Mismatches: 56, Indels: 143
0.67 0.09 0.24
Matches are distributed among these distances:
14 1 0.00
15 2 0.00
16 20 0.05
17 9 0.02
18 43 0.11
19 99 0.25
20 53 0.13
21 60 0.15
22 24 0.06
23 70 0.17
24 2 0.00
25 4 0.01
26 1 0.00
27 11 0.03
28 4 0.01
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Done.