Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 145 of 210
Found at i:48118516 original size:180 final size:180
Alignment explanation
Indices: 48118210--48118564 Score: 593
Period size: 180 Copynumber: 2.0 Consensus size: 180
48118200 GGAGATTCTA
* * *
48118210 TATTCTCAAAGATTGACTTAAGGTCAGGTTATTATCAGTTGAAGGTAAAAGAAAGTGATGTATCG
1 TATTCTCAAAGACTGACTTAAGGTCAGGTTATTATCAGTTGAAGGTAAAAGAAAGTGATGTACCA
* * * * *
48118275 AAGCCAGCTTTCCGTACGAGGTAAAGCCGCTATGAGTTCTTAGTAATGCCATTTGGGTTGACAAA
66 AAGACAACTTTCCATACGAGGTAAAGCCACTATGAGTTCTTAGTAATGCCATTTAGGTTGACAAA
48118340 TGCCCCAAACACTTTTATGGATCTTATGAATCGTATTTTTCAGCCATATG
131 TGCCCCAAACACTTTTATGGATCTTATGAATCGTATTTTTCAGCCATATG
*
48118390 TATTCTCGAAGACTGACTTAAGGTCAGGTTATTATCAGTTGAAGGTAAAAGAAAGTGATGTACCA
1 TATTCTCAAAGACTGACTTAAGGTCAGGTTATTATCAGTTGAAGGTAAAAGAAAGTGATGTACCA
**
48118455 AAGACAACTTTCCATACGAGGTATGGCCACTATGAGTTCTTAGTAATGCCATTTAGGTTGACAAA
66 AAGACAACTTTCCATACGAGGTAAAGCCACTATGAGTTCTTAGTAATGCCATTTAGGTTGACAAA
**
48118520 TGCCCCAGCCACTTTTATGGATCTTATGAATCGTATTTTTCAGCC
131 TGCCCCAAACACTTTTATGGATCTTATGAATCGTATTTTTCAGCC
48118565 GTATTTAGAC
Statistics
Matches: 162, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
180 162 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (180 bp):
TATTCTCAAAGACTGACTTAAGGTCAGGTTATTATCAGTTGAAGGTAAAAGAAAGTGATGTACCA
AAGACAACTTTCCATACGAGGTAAAGCCACTATGAGTTCTTAGTAATGCCATTTAGGTTGACAAA
TGCCCCAAACACTTTTATGGATCTTATGAATCGTATTTTTCAGCCATATG
Found at i:48125870 original size:20 final size:21
Alignment explanation
Indices: 48125833--48125872 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
48125823 TCTAACCTTA
**
48125833 AAAAAAACATAATTAGAAAAC
1 AAAAAAACATAAAAAGAAAAC
48125854 AAAAAAA-ATAAAAAGAAAA
1 AAAAAAACATAAAAAGAAAA
48125873 TGGAGAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.10
Consensus pattern (21 bp):
AAAAAAACATAAAAAGAAAAC
Found at i:48130380 original size:24 final size:24
Alignment explanation
Indices: 48130353--48130426 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
48130343 ATCTTGTTTA
48130353 CCATGATGCCATGGCATCTATCAC
1 CCATGATGCCATGGCATCTATCAC
* *
48130377 CCATGCT-CTTACT--CAT-TATCA-
1 CCATGATGC-CA-TGGCATCTATCAC
*
48130398 TCATGATGCCATGGCATCTATCAC
1 CCATGATGCCATGGCATCTATCAC
48130422 CCATG
1 CCATG
48130427 CTCTTACTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
20 1 0.03
21 6 0.16
22 9 0.24
23 9 0.24
24 11 0.30
25 1 0.03
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.30
Consensus pattern (24 bp):
CCATGATGCCATGGCATCTATCAC
Found at i:48130404 original size:45 final size:45
Alignment explanation
Indices: 48130354--48130461 Score: 198
Period size: 45 Copynumber: 2.4 Consensus size: 45
48130344 TCTTGTTTAC
48130354 CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTATCAT
1 CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTATCAT
*
48130399 CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTGTCAT
1 CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTATCAT
*
48130444 CATGATGCCATAGCATCT
1 CATGATGCCATGGCATCT
48130462 TTCAACTATG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.32
Consensus pattern (45 bp):
CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTATCAT
Found at i:48130479 original size:45 final size:45
Alignment explanation
Indices: 48130354--48130483 Score: 179
Period size: 45 Copynumber: 2.9 Consensus size: 45
48130344 TCTTGTTTAC
* * *
48130354 CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTATCAT
1 CATGATGCCATAGCATCTATCAACCATGCTCTTACTCATTGTCAT
* *
48130399 CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTGTCAT
1 CATGATGCCATAGCATCTATCAACCATGCTCTTACTCATTGTCAT
* * * *
48130444 CATGATGCCATAGCATCTTTCAACTATGGTTTTACTCATT
1 CATGATGCCATAGCATCTATCAACCATGCTCTTACTCATT
48130484 TTAGGCGTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.35
Consensus pattern (45 bp):
CATGATGCCATAGCATCTATCAACCATGCTCTTACTCATTGTCAT
Found at i:48132685 original size:30 final size:30
Alignment explanation
Indices: 48132651--48132785 Score: 146
Period size: 30 Copynumber: 4.5 Consensus size: 30
48132641 AACCAAGGCT
48132651 ATCCCTTTTCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
** *
48132681 ATCCCTTTTCATTGTTTGATGGTCGCCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
* * * * *
48132711 ATCCTTTTTCGTAATTTGATAGACG-AAGCC
1 ATCCCTTTTCATAATTTGATGGTCGTCA-CC
* **
48132741 ATCCCTTTTCATAGTTCAATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
*
48132771 ATCCCGTTTCATAAT
1 ATCCCTTTTCATAAT
48132786 CGATAGCAGA
Statistics
Matches: 83, Mismatches: 20, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
29 1 0.01
30 81 0.98
31 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATGGTCGTCACC
Found at i:48132726 original size:60 final size:60
Alignment explanation
Indices: 48132651--48132814 Score: 181
Period size: 60 Copynumber: 2.8 Consensus size: 60
48132641 AACCAAGGCT
* * * * **
48132651 ATCCCTTTTCATAATTTGATGGTCGTCA-CCATCCCTTTTCATTGTTTGATGGTCGCCACC
1 ATCCCTTTTCATAATTTGATAGACG-AAGCCATCCCTTTTCATAGTTCAATGGTCGCCACC
* * *
48132711 ATCCTTTTTCGTAATTTGATAGACGAAGCCATCCCTTTTCATAGTTCAATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATAGACGAAGCCATCCCTTTTCATAGTTCAATGGTCGCCACC
* * *
48132771 ATCCCGTTTCATAA-TCGATAG-CAGAAGCTATCCCTTTTCATAGT
1 ATCCCTTTTCATAATTTGATAGAC-GAAGCCATCCCTTTTCATAGT
48132815 CGATATCTGA
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
58 1 0.01
59 27 0.31
60 60 0.68
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (60 bp):
ATCCCTTTTCATAATTTGATAGACGAAGCCATCCCTTTTCATAGTTCAATGGTCGCCACC
Found at i:48132809 original size:29 final size:29
Alignment explanation
Indices: 48132771--48132838 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
48132761 GGTCGTCACC
*
48132771 ATCCCGTTTCATAATCGATAGCAGAAGCT
1 ATCCCTTTTCATAATCGATAGCAGAAGCT
* * *
48132800 ATCCCTTTTCATAGTCGATATCTGAAGCT
1 ATCCCTTTTCATAATCGATAGCAGAAGCT
48132829 ATCCCATTTT
1 ATCCC-TTTT
48132839 ACCCATCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.35
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCAGAAGCT
Found at i:48139912 original size:16 final size:16
Alignment explanation
Indices: 48139891--48139924 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
48139881 AGCTTCCGAT
48139891 AACTACAAAACACAGA
1 AACTACAAAACACAGA
48139907 AACTACAAAACACAGA
1 AACTACAAAACACAGA
48139923 AA
1 AA
48139925 AGTAAACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.65, C:0.24, G:0.06, T:0.06
Consensus pattern (16 bp):
AACTACAAAACACAGA
Found at i:48140280 original size:30 final size:30
Alignment explanation
Indices: 48140246--48140405 Score: 137
Period size: 30 Copynumber: 5.4 Consensus size: 30
48140236 GAAGCTATCT
48140246 CTTTTCATAATTTGATGGTCGTCACCATCC
1 CTTTTCATAATTTGATGGTCGTCACCATCC
** * **
48140276 CTTTTCATTGTTCGACAGTCGTCACCATCC
1 CTTTTCATAATTTGATGGTCGTCACCATCC
* ** ***
48140306 CTTTTTATAATTTGAT-AACCAAAGCCATCC
1 CTTTTCATAATTTGATGGTCGTCA-CCATCC
* *
48140336 CTTTTCATAGTTTGATGATCGTCACCATCC
1 CTTTTCATAATTTGATGGTCGTCACCATCC
* * *
48140366 ATTTCCATAA-TTGATGGTCATCACCA-CTC
1 CTTTTCATAATTTGATGGTCGTCACCATC-C
48140395 CTTTTCATAAT
1 CTTTTCATAAT
48140406 CGGTAGCCAA
Statistics
Matches: 98, Mismatches: 28, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
28 1 0.01
29 25 0.26
30 69 0.70
31 3 0.03
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.39
Consensus pattern (30 bp):
CTTTTCATAATTTGATGGTCGTCACCATCC
Found at i:48140294 original size:90 final size:90
Alignment explanation
Indices: 48140181--48140365 Score: 244
Period size: 90 Copynumber: 2.1 Consensus size: 90
48140171 ATGGTTGACA
* * ** * * * *
48140181 CATCCCTTTTCTTTATTCGACAGTGGAGGCTATCCCTTTTCATAATTTAATAACCGAAGCTATCT
1 CATCCCTTTTCATTATTCGACAGTCGACACCATCCCTTTTCATAATTTAATAACCAAAGCCATCC
*
48140246 CTTTTCATAATTTGATGGTCGTCAC
66 CTTTTCATAATTTGATGATCGTCAC
* * * *
48140271 CATCCCTTTTCATTGTTCGACAGTCGTCACCATCCCTTTTTATAATTTGATAACCAAAGCCATCC
1 CATCCCTTTTCATTATTCGACAGTCGACACCATCCCTTTTCATAATTTAATAACCAAAGCCATCC
*
48140336 CTTTTCATAGTTTGATGATCGTCAC
66 CTTTTCATAATTTGATGATCGTCAC
48140361 CATCC
1 CATCC
48140366 ATTTCCATAA
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.38
Consensus pattern (90 bp):
CATCCCTTTTCATTATTCGACAGTCGACACCATCCCTTTTCATAATTTAATAACCAAAGCCATCC
CTTTTCATAATTTGATGATCGTCAC
Found at i:48140310 original size:60 final size:60
Alignment explanation
Indices: 48140246--48140403 Score: 162
Period size: 60 Copynumber: 2.6 Consensus size: 60
48140236 GAAGCTATCT
* *
48140246 CTTTTCATAATTTGATGGTCGTCACCATCCCTTTTCATTGTTCGACAG-TCGTCACCATCC
1 CTTTTCATAATTTGATGGTCATCACCATCCCTTTTCATAGTTCGA-AGATCGTCACCATCC
* *** * * *
48140306 CTTTTTATAATTTGATAACCA-AAGCCATCCCTTTTCATAGTTTGATGATCGTCACCATCC
1 CTTTTCATAATTTGATGGTCATCA-CCATCCCTTTTCATAGTTCGAAGATCGTCACCATCC
* *
48140366 ATTTCCATAA-TTGATGGTCATCACCA-CTCCTTTTCATA
1 CTTTTCATAATTTGATGGTCATCACCATC-CCTTTTCATA
48140404 ATCGGTAGCC
Statistics
Matches: 78, Mismatches: 16, Indels: 9
0.76 0.16 0.09
Matches are distributed among these distances:
58 1 0.01
59 22 0.28
60 55 0.71
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (60 bp):
CTTTTCATAATTTGATGGTCATCACCATCCCTTTTCATAGTTCGAAGATCGTCACCATCC
Found at i:48140380 original size:29 final size:29
Alignment explanation
Indices: 48140347--48140405 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
48140337 TTTTCATAGT
*
48140347 TTGATGATCGTCACCA-TCCATTTCCATAA
1 TTGATGATCATCACCACTCC-TTTCCATAA
* *
48140376 TTGATGGTCATCACCACTCCTTTTCATAA
1 TTGATGATCATCACCACTCCTTTCCATAA
48140405 T
1 T
48140406 CGGTAGCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.37
Consensus pattern (29 bp):
TTGATGATCATCACCACTCCTTTCCATAA
Found at i:48140428 original size:29 final size:29
Alignment explanation
Indices: 48140396--48140452 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
48140386 TCACCACTCC
*
48140396 TTTTCATAATCGGTAGCCAAAGCTATCCT
1 TTTTCATAATCGATAGCCAAAGCTATCCT
* * * *
48140425 TTTTCGTAGTCGATAGGCGAAGCTATCC
1 TTTTCATAATCGATAGCCAAAGCTATCC
48140453 CATTTCACCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (29 bp):
TTTTCATAATCGATAGCCAAAGCTATCCT
Found at i:48141626 original size:19 final size:20
Alignment explanation
Indices: 48141582--48141629 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
48141572 GGCTGTTACA
48141582 TTTGTGAACTTGATCAAACTC
1 TTTGTGAACTTGATCAAAC-C
48141603 TTTGTGAACTTGATCAAA-C
1 TTTGTGAACTTGATCAAACC
48141622 TTTGTGAA
1 TTTGTGAA
48141630 GATTCAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 9 0.33
21 18 0.67
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTGTGAACTTGATCAAACC
Found at i:48142659 original size:20 final size:20
Alignment explanation
Indices: 48142634--48142674 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
48142624 CAATTCCTGT
*
48142634 AAAGGAATTGAAGAAAGAAG
1 AAAGGAATGGAAGAAAGAAG
48142654 AAAGGAATGGAAGAAAGAAG
1 AAAGGAATGGAAGAAAGAAG
48142674 A
1 A
48142675 TTTGGGGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.07
Consensus pattern (20 bp):
AAAGGAATGGAAGAAAGAAG
Found at i:48145835 original size:29 final size:29
Alignment explanation
Indices: 48145802--48145869 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
48145792 AATTTGTGAG
*
48145802 AATTTG-ACTAAATCAAAATTTCATATATA
1 AATTTGCACAAAATCAAAATTT-ATATATA
*
48145831 AATTTGCACAAAATCAAAGTTTATATATA
1 AATTTGCACAAAATCAAAATTTATATATA
*
48145860 AAGTTGCACA
1 AATTTGCACA
48145870 TTGAATCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (29 bp):
AATTTGCACAAAATCAAAATTTATATATA
Found at i:48154749 original size:7 final size:7
Alignment explanation
Indices: 48154737--48154761 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
48154727 GTCCTTAAAC
48154737 ATTTTAA
1 ATTTTAA
48154744 ATTTTAA
1 ATTTTAA
48154751 ATTTTAA
1 ATTTTAA
48154758 ATTT
1 ATTT
48154762 CAACCCTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTTAA
Found at i:48155197 original size:3 final size:3
Alignment explanation
Indices: 48155189--48155218 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
48155179 TGAAGAATTA
48155189 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
48155219 AATATAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:48162208 original size:9 final size:9
Alignment explanation
Indices: 48162194--48162224 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
48162184 GTTAAACGAA
48162194 TCGAGTTAT
1 TCGAGTTAT
*
48162203 TCGAGTTAA
1 TCGAGTTAT
48162212 TCGAGTTAT
1 TCGAGTTAT
48162221 TCGA
1 TCGA
48162225 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:48162295 original size:9 final size:9
Alignment explanation
Indices: 48162278--48162314 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
48162268 TGAGTTTTCG
48162278 AATTCGAAT
1 AATTCGAAT
*
48162287 AACTCGAAT
1 AATTCGAAT
48162296 AATTCGAAT
1 AATTCGAAT
48162305 AATTCGAAT
1 AATTCGAAT
48162314 A
1 A
48162315 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:48164451 original size:24 final size:24
Alignment explanation
Indices: 48164424--48164475 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
48164414 AGGAAGACAA
48164424 TGGAGACAAAGATGAAG-CCGAAGG
1 TGGAGACAAAGATGAAGACC-AAGG
** *
48164448 TGGAGATGAATATGAAGACCAAGG
1 TGGAGACAAAGATGAAGACCAAGG
48164472 TGGA
1 TGGA
48164476 AATGAAGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.40, C:0.10, G:0.37, T:0.13
Consensus pattern (24 bp):
TGGAGACAAAGATGAAGACCAAGG
Found at i:48164480 original size:24 final size:24
Alignment explanation
Indices: 48164432--48164486 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
48164422 AATGGAGACA
*
48164432 AAGATGAAGCCGAAGGTGGAGATG
1 AAGATGAAGCCGAAGGTGGAAATG
*
48164456 AATATGAAGACC-AAGGTGGAAATG
1 AAGATGAAG-CCGAAGGTGGAAATG
48164480 AAGATGA
1 AAGATGA
48164487 GTACGAGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.44, C:0.07, G:0.35, T:0.15
Consensus pattern (24 bp):
AAGATGAAGCCGAAGGTGGAAATG
Found at i:48165580 original size:279 final size:280
Alignment explanation
Indices: 48165057--48165609 Score: 660
Period size: 279 Copynumber: 2.0 Consensus size: 280
48165047 GGCCTTAATG
* ** * ** * *
48165057 ATCCCTTAATACGGAACATGTTGCTTTTGTATGCCCTGGGTTTCTACAGTACCCGCATAACCTCT
1 ATCCCTCAATACAAAACATGTTGCCTTCATATGCCCTAGGTTTCTACAGTACCCACATAACCTCT
* * * * * *
48165122 GTTTATTGCCTCTCTCCCGAATATCAATATTAGTACTTATCCGAGTAAAATTCGGATGACCTTTT
66 GTTGATTG-CTCTCTCCCGAACATCAATATTAGTACGTATCCGAGTAAAATTCAGACGACCTTTC
* ** * * * * *
48165187 GGGACGCAACACAAGTTCATGTTCGGGTCCAACTCGAATAGAGCTCTGGACACTGGCAAACACAT
130 GGGACACAACACAAGTAAATATTCGGGGCCAACTCAAACAGAGCACTGGACACTGGCAAACACAT
* * * *
48165252 ACTCCCATCTGAGATAGGTGGGAATTTAGATATTCATACATTGTGCATGCCTTCCAATTTGTACA
195 ACTCCCATCTGAGATAGGTGAGAATTCAGATATCCATACATTATGCATGCCTTCCAATTTGTACA
48165317 CATCGTTAATATAATATGTGT
260 CATCGTTAATATAATATGTGT
*
48165338 ATCCCTCAATACAAAACATGTTGCCTTCATATGCTCTAGGTTTCTACAGTACCCACATAACCTCT
1 ATCCCTCAATACAAAACATGTTGCCTTCATATGCCCTAGGTTTCTACAGTACCCACATAACCTCT
* * * * * * * *
48165403 GTTGATTG-TCTCTCCTGAACATCCATATTGGTGCGTATTCGAGTGAAATTTAGACGACGTTTCG
66 GTTGATTGCTCTCTCCCGAACATCAATATTAGTACGTATCCGAGTAAAATTCAGACGACCTTTCG
* * ** **
48165467 GGATACGATGCAAGTAAATATTCGGGGCCAACTCAAACATGA-CACTGGACACTGGCAGCCACAT
131 GGACACAACACAAGTAAATATTCGGGGCCAACTCAAACA-GAGCACTGGACACTGGCAAACACAT
** * * *
48165531 ACTCTTATCTGGGATAGGTGAGAATTCAGATATCCATACATTATGCATGCCTTTCAGTTTGTACA
195 ACTCCCATCTGAGATAGGTGAGAATTCAGATATCCATACATTATGCATGCCTTCCAATTTGTACA
48165596 CATCGTTAATATAA
260 CATCGTTAATATAA
48165610 GGTGTGTACT
Statistics
Matches: 225, Mismatches: 46, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
279 160 0.71
280 2 0.01
281 63 0.28
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (280 bp):
ATCCCTCAATACAAAACATGTTGCCTTCATATGCCCTAGGTTTCTACAGTACCCACATAACCTCT
GTTGATTGCTCTCTCCCGAACATCAATATTAGTACGTATCCGAGTAAAATTCAGACGACCTTTCG
GGACACAACACAAGTAAATATTCGGGGCCAACTCAAACAGAGCACTGGACACTGGCAAACACATA
CTCCCATCTGAGATAGGTGAGAATTCAGATATCCATACATTATGCATGCCTTCCAATTTGTACAC
ATCGTTAATATAATATGTGT
Found at i:48165975 original size:26 final size:26
Alignment explanation
Indices: 48165939--48165989 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
48165929 AAAAGTATGC
*
48165939 TTCTTTGACAATCGAGGTTATTGGTT
1 TTCTTTGACAACCGAGGTTATTGGTT
48165965 TTCTTTGACAACCGAGGTTATTGGT
1 TTCTTTGACAACCGAGGTTATTGGT
48165990 AAATGACGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.43
Consensus pattern (26 bp):
TTCTTTGACAACCGAGGTTATTGGTT
Found at i:48168863 original size:95 final size:95
Alignment explanation
Indices: 48168689--48168863 Score: 242
Period size: 95 Copynumber: 1.8 Consensus size: 95
48168679 TTATTTATTC
* * *
48168689 GAGTTAGCTGAGTTAAGCTCGCAACTCCGAGACAGCTCGCTGACCTACACTCCCAGCTGATAAAC
1 GAGTTAGCTGAGTTAAACTCGCAACTACGAGACAGCTCGCGGACCTACACTCCCAGCTGATAAAC
*
48168754 TCCAACATAACTCGTAACTACGAGATAGCT
66 TCCAACACAACTCGTAACTACGAGATAGCT
* * * * ** *
48168784 GAGTTAGTTGAGTTAAACTTGCAACTACGAGATAGCTTGCGGACCTACGTTCCTAGCTGATAAAC
1 GAGTTAGCTGAGTTAAACTCGCAACTACGAGACAGCTCGCGGACCTACACTCCCAGCTGATAAAC
*
48168849 TCCAACACAGCTCGT
66 TCCAACACAACTCGT
48168864 GGACCTACTT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 68 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (95 bp):
GAGTTAGCTGAGTTAAACTCGCAACTACGAGACAGCTCGCGGACCTACACTCCCAGCTGATAAAC
TCCAACACAACTCGTAACTACGAGATAGCT
Found at i:48169130 original size:102 final size:102
Alignment explanation
Indices: 48168952--48169223 Score: 348
Period size: 102 Copynumber: 2.6 Consensus size: 102
48168942 CTAGTTGATT
* *
48168952 TTTAAAGGTTAGCTAAGTTAAGCTCTCAACCTAACTTTTTTTGAGTTAGCTGAGTCAAGCTCGCA
1 TTTAAAGGTTAGCTAAGTTAAGCTCT-AACCTAA-ATTTTTTGAGTTAGCTGAGTTAAGCTCGCA
* *
48169017 ACTCTGAAACAGCCTGCGGACTTATGTTCCCAACTAATG
64 ACTCTGAAACAGCCTGCGAACCTATGTTCCCAACTAATG
* * * *
48169056 TTTAAAGGTCAGCTAAGTTAAACTCGTAACCTAAATTTTTT-AGTTAGTTGAGTTAAGCTTGCAA
1 TTTAAAGGTTAGCTAAGTTAAGCTC-TAACCTAAATTTTTTGAGTTAGCTGAGTTAAGCTCGCAA
* * *
48169120 CTCTGAAACAGCTTGCGAACCTATGTTCCCAGCTTATG
65 CTCTGAAACAGCCTGCGAACCTATGTTCCCAACTAATG
* * * * * *
48169158 CTTAAAGGTTAGTTGAGTTAAGCTCATAACTTAAATTTTTTGAGTTAACTGAGTTAAGCTCACAA
1 TTTAAAGGTTAGCTAAGTTAAGCTC-TAACCTAAATTTTTTGAGTTAGCTGAGTTAAGCTCGCAA
48169223 C
65 C
48169224 CCTAGCTATT
Statistics
Matches: 144, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
102 87 0.60
103 26 0.18
104 30 0.21
105 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (102 bp):
TTTAAAGGTTAGCTAAGTTAAGCTCTAACCTAAATTTTTTGAGTTAGCTGAGTTAAGCTCGCAAC
TCTGAAACAGCCTGCGAACCTATGTTCCCAACTAATG
Found at i:48175798 original size:2 final size:2
Alignment explanation
Indices: 48175791--48175825 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48175781 NNNNNNNNNN
48175791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48175826 AAATAGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48183415 original size:15 final size:15
Alignment explanation
Indices: 48183395--48183442 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
48183385 ATTTTACATC
* *
48183395 AATAAATAATTTAAA
1 AATAAAAAAATTAAA
48183410 AATAAAAAAATTAAA
1 AATAAAAAAATTAAA
* *
48183425 ATTCAAAAAATATAAA
1 AATAAAAAAAT-TAAA
48183441 AA
1 AA
48183443 AAAGTTCATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (15 bp):
AATAAAAAAATTAAA
Found at i:48190223 original size:24 final size:25
Alignment explanation
Indices: 48190196--48190247 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
48190186 CGATCAGGAT
* *
48190196 GCTCAGAAGAGCCAT-TAAAGGGAA
1 GCTCACAAGAACCATATAAAGGGAA
* *
48190220 GCTCACAAGAACGATATAACGGGAA
1 GCTCACAAGAACCATATAAAGGGAA
48190245 GCT
1 GCT
48190248 TGAGAGGGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.13
Consensus pattern (25 bp):
GCTCACAAGAACCATATAAAGGGAA
Found at i:48190613 original size:21 final size:21
Alignment explanation
Indices: 48190589--48190630 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48190579 TAAATTTAAC
*
48190589 TCAATTTAATACAATTCACAT
1 TCAATTCAATACAATTCACAT
* *
48190610 TCAATTCCATTCAATTCACAT
1 TCAATTCAATACAATTCACAT
48190631 CTTAGGCAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (21 bp):
TCAATTCAATACAATTCACAT
Found at i:48190620 original size:10 final size:11
Alignment explanation
Indices: 48190600--48190630 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
48190590 CAATTTAATA
48190600 CAATTCACATT
1 CAATTCACATT
48190611 CAATTC-CATT
1 CAATTCACATT
48190621 CAATTCACAT
1 CAATTCACAT
48190631 CTTAGGCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (11 bp):
CAATTCACATT
Found at i:48190802 original size:33 final size:34
Alignment explanation
Indices: 48190751--48190822 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 34
48190741 CCAAGAGGTG
48190751 ACACTCAAGGGGTTGTTTTTCCTTGTGGTCCAAT
1 ACACTCAAGGGGTTGTTTTTCCTTGTGGTCCAAT
48190785 ACACTCAA-GGGTTGTTTTTCCTTGTGGTCCAAT
1 ACACTCAAGGGGTTGTTTTTCCTTGTGGTCCAAT
48190818 -CACTC
1 ACACTC
48190823 GAAGCAAGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 5 0.13
33 25 0.66
34 8 0.21
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.38
Consensus pattern (34 bp):
ACACTCAAGGGGTTGTTTTTCCTTGTGGTCCAAT
Found at i:48198043 original size:3 final size:3
Alignment explanation
Indices: 48198035--48198075 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
48198025 NNNNATCCTT
48198035 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
48198076 TAACTAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:48204384 original size:25 final size:26
Alignment explanation
Indices: 48204349--48204404 Score: 96
Period size: 25 Copynumber: 2.2 Consensus size: 26
48204339 TAGCTATTTT
48204349 TCGATAGGCTACGAGCTCGTCCAACA
1 TCGATAGGCTACGAGCTCGTCCAACA
*
48204375 TCGAT-GGCTATGAGCTCGTCCAACA
1 TCGATAGGCTACGAGCTCGTCCAACA
48204400 TCGAT
1 TCGAT
48204405 TCTATCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (26 bp):
TCGATAGGCTACGAGCTCGTCCAACA
Found at i:48206083 original size:46 final size:46
Alignment explanation
Indices: 48206011--48206196 Score: 336
Period size: 46 Copynumber: 4.0 Consensus size: 46
48206001 ACAATGCTAT
* * *
48206011 AACTCAGTATGGTTTCCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
*
48206057 AACTCTGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
48206103 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
48206149 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
48206195 AA
1 AA
48206197 TTTGTCATGG
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 135 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
Found at i:48214337 original size:24 final size:24
Alignment explanation
Indices: 48214310--48214355 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
48214300 TGAACTTCGT
*
48214310 TTTATTCTGTTTTGATAGCTAATG
1 TTTATTATGTTTTGATAGCTAATG
48214334 TTTATTATGTTTTGATAGCTAA
1 TTTATTATGTTTTGATAGCTAA
48214356 CGTGACAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (24 bp):
TTTATTATGTTTTGATAGCTAATG
Found at i:48214370 original size:23 final size:24
Alignment explanation
Indices: 48214317--48214372 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
48214307 CGTTTTATTC
* * **
48214317 TGTTTTGATAGCTAATGTTTATTA
1 TGTTTTGATAGCTAACGTTGACAA
48214341 TGTTTTGATAGCTAACG-TGACAA
1 TGTTTTGATAGCTAACGTTGACAA
48214364 TGTTTTGAT
1 TGTTTTGAT
48214373 CACTGGGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.48
Consensus pattern (24 bp):
TGTTTTGATAGCTAACGTTGACAA
Found at i:48221823 original size:36 final size:37
Alignment explanation
Indices: 48221753--48221825 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
48221743 TATTTAAGTG
*
48221753 TTTTAGTTTTTATTTATCTACTTTTTATTTGTGTATA
1 TTTTAGTTTTTATTTATCTACTCTTTATTTGTGTATA
48221790 TTTTAGTTTTTATTTATCTAC-CTTTATTTGTGTATA
1 TTTTAGTTTTTATTTATCTACTCTTTATTTGTGTATA
48221826 CATTATTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 14 0.40
37 21 0.60
ACGTcount: A:0.19, C:0.07, G:0.08, T:0.66
Consensus pattern (37 bp):
TTTTAGTTTTTATTTATCTACTCTTTATTTGTGTATA
Found at i:48235686 original size:36 final size:37
Alignment explanation
Indices: 48235616--48235688 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
48235606 ATTTAAGTGT
* *
48235616 TTTAGTTTTTATTTATCTACTTTTTATTTATGTATAC
1 TTTAGTTTTTACTTATCTACTCTTTATTTATGTATAC
*
48235653 TTTAGTTTTTACTTATCTAC-CTTTATTTGTGTATAC
1 TTTAGTTTTTACTTATCTACTCTTTATTTATGTATAC
48235689 ATTATTGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 14 0.42
37 19 0.58
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.62
Consensus pattern (37 bp):
TTTAGTTTTTACTTATCTACTCTTTATTTATGTATAC
Found at i:48240470 original size:5 final size:5
Alignment explanation
Indices: 48240460--48240496 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
48240450 TTCGTTCACT
48240460 CAAGC CAAGC CAAGC CAAGC CAAGC CAAGC CAAGC CA
1 CAAGC CAAGC CAAGC CAAGC CAAGC CAAGC CAAGC CA
48240497 GCCCATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.41, C:0.41, G:0.19, T:0.00
Consensus pattern (5 bp):
CAAGC
Found at i:48241305 original size:6 final size:6
Alignment explanation
Indices: 48241296--48241320 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48241286 TTTATTTTAT
48241296 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
48241321 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:48255614 original size:130 final size:130
Alignment explanation
Indices: 48255381--48255640 Score: 520
Period size: 130 Copynumber: 2.0 Consensus size: 130
48255371 AAATGGAAAG
48255381 TGAAATCGTGGCCATGACTGCAGTAGTGACAGACAGCCTCCGATTTTTGCTCTCCTCGGTCGCGT
1 TGAAATCGTGGCCATGACTGCAGTAGTGACAGACAGCCTCCGATTTTTGCTCTCCTCGGTCGCGT
48255446 CGCCCCGTACATCTCCCGATATAATATGGCCAAGACGGCAGAGCCCCAACTCAATTCACCGGCTA
66 CGCCCCGTACATCTCCCGATATAATATGGCCAAGACGGCAGAGCCCCAACTCAATTCACCGGCTA
48255511 TGAAATCGTGGCCATGACTGCAGTAGTGACAGACAGCCTCCGATTTTTGCTCTCCTCGGTCGCGT
1 TGAAATCGTGGCCATGACTGCAGTAGTGACAGACAGCCTCCGATTTTTGCTCTCCTCGGTCGCGT
48255576 CGCCCCGTACATCTCCCGATATAATATGGCCAAGACGGCAGAGCCCCAACTCAATTCACCGGCTA
66 CGCCCCGTACATCTCCCGATATAATATGGCCAAGACGGCAGAGCCCCAACTCAATTCACCGGCTA
48255641 CTCTAAAATC
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 130 1.00
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.22
Consensus pattern (130 bp):
TGAAATCGTGGCCATGACTGCAGTAGTGACAGACAGCCTCCGATTTTTGCTCTCCTCGGTCGCGT
CGCCCCGTACATCTCCCGATATAATATGGCCAAGACGGCAGAGCCCCAACTCAATTCACCGGCTA
Found at i:48256318 original size:51 final size:50
Alignment explanation
Indices: 48256274--48256369 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 50
48256264 AATTATTTAA
* *
48256274 AAATAGGGATTTAAGAGAAATTTAAGAA-GAACTTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTT-AGAAGGAAATTGAGAGAAAATT-AAATT
* * *
48256325 AAATATGGATTTGAGAGAAATTTTGAAGGAAATTGAGAGAAAATT
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGAAAATT
48256370 TGAGAGAGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 3 0.08
51 36 0.92
ACGTcount: A:0.48, C:0.02, G:0.23, T:0.27
Consensus pattern (50 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGAAAATTAAATT
Found at i:48256372 original size:12 final size:12
Alignment explanation
Indices: 48256333--48256376 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
48256323 TTAAATATGG
48256333 ATTTGAGAGAAA
1 ATTTGAGAGAAA
* *
48256345 TTTTGA-AGGAA
1 ATTTGAGAGAAA
48256356 A-TTGAGAGAAA
1 ATTTGAGAGAAA
48256367 ATTTGAGAGA
1 ATTTGAGAGA
48256377 GGATTAGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 4 0.15
11 9 0.35
12 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.27
Consensus pattern (12 bp):
ATTTGAGAGAAA
Found at i:48259988 original size:26 final size:26
Alignment explanation
Indices: 48259850--48259986 Score: 132
Period size: 26 Copynumber: 5.3 Consensus size: 26
48259840 TAAAAAACGA
* *
48259850 AAGCCTTTGTGGTGTATCTAAAATGG
1 AAGCCTTTGTGGCGTATCTGAAATGG
* * *
48259876 AAGCCTTTTTGGCATATCTGAATTGG
1 AAGCCTTTGTGGCGTATCTGAAATGG
*
48259902 AAGCCTTTGTAGCGTATCT-AAATTGG
1 AAGCCTTTGTGGCGTATCTGAAA-TGG
** * * **
48259928 AAGTGTTTGTGGAGTATTTGAAATTA
1 AAGCCTTTGTGGCGTATCTGAAATGG
*
48259954 AAGCCTTCGTGGCGTATCTGAAATGG
1 AAGCCTTTGTGGCGTATCTGAAATGG
*
48259980 GAGCCTT
1 AAGCCTT
48259987 CGATTTTTTG
Statistics
Matches: 85, Mismatches: 24, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
25 2 0.02
26 80 0.94
27 3 0.04
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (26 bp):
AAGCCTTTGTGGCGTATCTGAAATGG
Found at i:48262019 original size:19 final size:19
Alignment explanation
Indices: 48261995--48262047 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
48261985 TATATATACT
*
48261995 AAATAAATTAATAATAATA
1 AAATAAATTAATAATAAAA
* *
48262014 AAATAAAATAAT-TTAAAA
1 AAATAAATTAATAATAAAA
48262032 AAATCAAATTAA-AATA
1 AAAT-AAATTAATAATA
48262048 TTAATAAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAAATTAATAATAAAA
Found at i:48262029 original size:24 final size:24
Alignment explanation
Indices: 48261995--48262055 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
48261985 TATATATACT
*
48261995 AAATAAATTAATAATAAT-AAAATA
1 AAAT-AATTAATAAAAATCAAAATA
*
48262019 AAATAATTTAA-AAAAATCAAATTA
1 AAATAA-TTAATAAAAATCAAAATA
48262043 AAAT-ATTAATAAA
1 AAATAATTAATAAA
48262056 CTAATATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 11 0.34
24 17 0.53
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATAATTAATAAAAATCAAAATA
Found at i:48267584 original size:50 final size:50
Alignment explanation
Indices: 48267507--48267699 Score: 251
Period size: 50 Copynumber: 3.8 Consensus size: 50
48267497 ATTTGGGTAA
* *
48267507 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTCGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
48267557 AGAGGTCCCATATAAGACCATGCCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * *
48267607 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGACATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
48267657 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
48267700 TGTTATTGTT
Statistics
Matches: 121, Mismatches: 21, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
50 88 0.73
51 33 0.27
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:48269821 original size:26 final size:26
Alignment explanation
Indices: 48269792--48270001 Score: 240
Period size: 26 Copynumber: 8.1 Consensus size: 26
48269782 AAACGCTAGA
* *
48269792 AAATGAAAGCCTTTGTGGCGTACCTG
1 AAATGGAAGCCTTTGTGGCGTATCTG
* ** * *
48269818 AAATGGAAGCATTTGCAGTGTATCTA
1 AAATGGAAGCCTTTGTGGCGTATCTG
* *
48269844 AAATGGAAGCCTTTGTAGCGTATTTG
1 AAATGGAAGCCTTTGTGGCGTATCTG
* * *
48269870 AATTGGAAGCTTTTGTGGCATATCTG
1 AAATGGAAGCCTTTGTGGCGTATCTG
*
48269896 AAATGGAAGCCTTTGTGGTGTATCTG
1 AAATGGAAGCCTTTGTGGCGTATCTG
*
48269922 AAATGGAAGCCTTTGTGGTGTATCTG
1 AAATGGAAGCCTTTGTGGCGTATCTG
* ** *
48269948 AAATTGAAGTATTTGTGGTGTATCTG
1 AAATGGAAGCCTTTGTGGCGTATCTG
* *
48269974 AAATGGAAGCTTTTGTGGCATATCTG
1 AAATGGAAGCCTTTGTGGCGTATCTG
48270000 AA
1 AA
48270002 GAAATGGCCC
Statistics
Matches: 155, Mismatches: 29, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 155 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.34
Consensus pattern (26 bp):
AAATGGAAGCCTTTGTGGCGTATCTG
Found at i:48276509 original size:27 final size:27
Alignment explanation
Indices: 48276479--48276545 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
48276469 ATCATGAAGG
* * *
48276479 GATAACCTTTGTGGTGAACCCTGTAAT
1 GATAGCCTTTGTGGCGAACCCTGCAAT
*
48276506 GATAGGCTTTGTGGCGAACCCTGCAAT
1 GATAGCCTTTGTGGCGAACCCTGCAAT
48276533 GATAGCCTTTGTG
1 GATAGCCTTTGTG
48276546 CCGTAATATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (27 bp):
GATAGCCTTTGTGGCGAACCCTGCAAT
Found at i:48276582 original size:26 final size:26
Alignment explanation
Indices: 48276553--48276604 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
48276543 GTGCCGTAAT
48276553 ATGAAA-GAAAGCCCTTGTGGCAAAAC
1 ATGAAAGGAAAGCCCTTGTGG-AAAAC
* *
48276579 ATGAAAGGAATGCCTTTGTGGAAAAC
1 ATGAAAGGAAAGCCCTTGTGGAAAAC
48276605 TCCATAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.19
Consensus pattern (26 bp):
ATGAAAGGAAAGCCCTTGTGGAAAAC
Found at i:48278279 original size:51 final size:51
Alignment explanation
Indices: 48278100--48278443 Score: 278
Period size: 51 Copynumber: 6.8 Consensus size: 51
48278090 ATTTTTATCA
* *
48278100 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC--AG-TT
1 TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * *
48278148 TTAC-AGTTCACGTAGTAGCCTTCACATGGTACTACACACGTGATC-AAG-TT
1 TT-CGA-TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * *
48278198 TTAAGGCT-CACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTT
1 TT--CGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * * * * * *
48278250 TTCGGTACCCATTGTAGCCTTCACTTAGTACAACACATGTAACCATAG-TT
1 TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * *
48278300 TACCGATACACGTAGTAGCATTCACACAGTACTACACACGTG-CTCAAAGCTT
1 T-TCGATACACATAGTAGCCTTCACATAGTACTACACACGTGAC-CAAAGCTT
* * *
48278352 TTCGATACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTA--TT
1 TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGCTT
* * * *
48278402 TATCGATACACGTAGTAGCCTCCACACAGTATTACACACGTG
1 T-TCGATACACATAGTAGCCTTCACATAGTACTACACACGTG
48278444 TTCATCGACA
Statistics
Matches: 239, Mismatches: 43, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
48 3 0.01
49 38 0.16
50 49 0.21
51 140 0.59
52 9 0.04
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (51 bp):
TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
Found at i:48278341 original size:102 final size:102
Alignment explanation
Indices: 48278102--48278443 Score: 392
Period size: 102 Copynumber: 3.4 Consensus size: 102
48278092 TTTTATCATT
* * * * *
48278102 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC--AG-TTTTACAGTTCACGTAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAGT
* * * *
48278164 AGCCTTCACATGGTACTACACACGTGATCA-AGTTTTAA
65 AGCCTTCACTTAGTACTACACATGTGACCATAG-TTTAA
* * * * * *
48278202 GGCT-CACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTTCGGTACCCATTGTA
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTA
* * *
48278266 GCCTTCACTTAGTACAACACATGTAACCATAGTTTAC
66 GCCTTCACTTAGTACTACACATGTGACCATAGTTTAA
* *
48278303 CGATACACGTAGTAGCATTCACACAGTACTACACACGTG-CTCAAAGCTTTTCGATACACATAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGAC-CAAAGCTTTTCGGTACACATAGT
*
48278367 AGCCTTCACTTAGTACTACACATGTGACCATTA-TTTAT
65 AGCCTTCACTTAGTACTACACATGTGACCA-TAGTTTAA
* *
48278405 CGATACACGTAGTAGCCTCCACACAGTATTACACACGTG
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
48278444 TTCATCGACA
Statistics
Matches: 205, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
99 35 0.17
100 2 0.01
101 41 0.20
102 125 0.61
103 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (102 bp):
CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTA
GCCTTCACTTAGTACTACACATGTGACCATAGTTTAA
Found at i:48278421 original size:153 final size:148
Alignment explanation
Indices: 48278100--48278442 Score: 341
Period size: 153 Copynumber: 2.3 Consensus size: 148
48278090 ATTTTTATCA
* * * *
48278100 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTTCACGTAGTA
1 TTCGATACACGTAGTAGCCTTCACATAGTACAACACACGTAACCAGTTTTACAGTACACGTAGTA
* ** * * *
48278165 GCCTTCACATGGTACTACACACGTGATCAAGTTTTAAGGCTCACGTAGTAGCCTTCACATAGTAC
66 GCATTCACACAGTACTACACACGTGATCAAGTTTT-ACGATCACATAGTAGCCTTCACATAGTAC
*
48278230 TACATACGTGACCAAAGCTT
130 TACACACGTGACCAAA-CTT
* * * * * * *
48278250 TTCGGTACCCATTGTAGCCTTCACTTAGTACAACACATGTAACCA-TAGTTTACCGATACACGTA
1 TTCGATACACGTAGTAGCCTTCACATAGTACAACACACGTAACCAGT--TTTACAG-TACACGTA
* *
48278314 GTAGCATTCACACAGTACTACACACGTGCTCAAAGCTTTT-CGATACACATAGTAGCCTTCACTT
63 GTAGCATTCACACAGTACTACACACGTGATC-AAG-TTTTACGAT-CACATAGTAGCCTTCACAT
* *
48278378 AGTACTACACATGTGACCATTA-TT
125 AGTACTACACACGTGACCA-AACTT
* * **
48278402 TATCGATACACGTAGTAGCCTCCACACAGTATTACACACGT
1 T-TCGATACACGTAGTAGCCTTCACATAGTACAACACACGT
48278443 GTTCATCGAC
Statistics
Matches: 153, Mismatches: 32, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
149 1 0.01
150 36 0.24
151 6 0.04
152 39 0.25
153 66 0.43
154 5 0.03
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (148 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACAACACACGTAACCAGTTTTACAGTACACGTAGTA
GCATTCACACAGTACTACACACGTGATCAAGTTTTACGATCACATAGTAGCCTTCACATAGTACT
ACACACGTGACCAAACTT
Found at i:48278759 original size:30 final size:30
Alignment explanation
Indices: 48278725--48278788 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
48278715 GCTTCGACTC
* *
48278725 AACTTTTATAAAATTACAAT-TTTGTCCCTA
1 AACTTTTACAAAATTAC-ATCTTTGTCCCCA
* *
48278755 AACTTTTGCATAATTACATCTTTGTCCCCA
1 AACTTTTACAAAATTACATCTTTGTCCCCA
48278785 AACT
1 AACT
48278789 CGAAAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACATCTTTGTCCCCA
Found at i:48285605 original size:50 final size:49
Alignment explanation
Indices: 48285491--48285827 Score: 243
Period size: 51 Copynumber: 6.7 Consensus size: 49
48285481 TCATTCGATA
*
48285491 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAA-TTTTACAGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTAC-GGT
* *
48285540 CACGTAGTAGCCTTCACATGGTACTACACACATGATCAAGTTTTACGGCT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGG-T
* * *
48285590 CACGTTGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTT-CGGT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTTACGGT
* * * * * * * *
48285640 ACCCATTGTAGCCTTCACTTAGTACTACACATGTAACCATAG-TTTACCGAT
1 -CACGTAGTAGCCTTCACATAGTACTACACACGTGATCA-AGTTTTA-CGGT
* * * * *
48285691 ACACGTAGTAGCATTCACACAGTATTACACACGTGCTCAAAGCTTTT-TGGT
1 -CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTTACGGT
* * * * * * * *
48285742 ACACATAGTAGCCTTCACTTTGTACCACACATGTGA-CCATTATTTATCGAT
1 -CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTA-CGGT
* * *
48285793 ACACGTAGTAGCCTCCACACAGTACTACGCACGTG
1 -CACGTAGTAGCCTTCACATAGTACTACACACGTG
48285828 TTCATCGACA
Statistics
Matches: 225, Mismatches: 49, Indels: 26
0.75 0.16 0.09
Matches are distributed among these distances:
48 1 0.00
49 45 0.20
50 42 0.19
51 129 0.57
52 5 0.02
53 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (49 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGT
Found at i:48285725 original size:102 final size:102
Alignment explanation
Indices: 48285486--48285827 Score: 365
Period size: 102 Copynumber: 3.4 Consensus size: 102
48285476 TTTTATCATT
* * * * *
48285486 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AA--TTTTACAGTTCACGTAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAGT
* * ** *
48285548 AGCCTTCACATGGTACTACACACATGATCA-AGTTTTAC
65 AGCCTTCACTTAGTACTACACATGTGACCATAG-TTTAC
* * * * * * *
48285586 GGCT-CACGTTGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTTCGGTACCCATTGTA
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTA
*
48285650 GCCTTCACTTAGTACTACACATGTAACCATAGTTTAC
66 GCCTTCACTTAGTACTACACATGTGACCATAGTTTAC
* * *
48285687 CGATACACGTAGTAGCATTCACACAGTATTACACACGTG-CTCAAAGCTTTTTGGTACACATAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGAC-CAAAGCTTTTCGGTACACATAGT
* * *
48285751 AGCCTTCACTTTGTACCACACATGTGACCATTA-TTTAT
65 AGCCTTCACTTAGTACTACACATGTGACCA-TAGTTTAC
* *
48285789 CGATACACGTAGTAGCCTCCACACAGTACTACGCACGTG
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
48285828 TTCATCGACA
Statistics
Matches: 201, Mismatches: 34, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
99 34 0.17
100 4 0.02
101 40 0.20
102 121 0.60
103 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (102 bp):
CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTA
GCCTTCACTTAGTACTACACATGTGACCATAGTTTAC
Found at i:48285941 original size:15 final size:17
Alignment explanation
Indices: 48285921--48285953 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
48285911 GTTACGAAAC
48285921 ATAACAA-A-AATAATT
1 ATAACAATATAATAATT
48285936 ATAACAATATAATAATT
1 ATAACAATATAATAATT
48285953 A
1 A
48285954 CATACAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAACAATATAATAATT
Found at i:48292961 original size:38 final size:39
Alignment explanation
Indices: 48292919--48293004 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 39
48292909 GTATGAAACA
* *
48292919 CATCTTGGCGCAA-AAAGTGCTTA-CTGGCACACGAAGTG
1 CATCTTGGCGCAAGAAA-CGCATATCTGGCACACGAAGTG
* **
48292957 CATCTTGGTGCAAGAAACGCATATCTGGCACACGTGGTG
1 CATCTTGGCGCAAGAAACGCATATCTGGCACACGAAGTG
*
48292996 CATCCTGGC
1 CATCTTGGC
48293005 ACATTAGTGC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
38 16 0.41
39 23 0.59
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.22
Consensus pattern (39 bp):
CATCTTGGCGCAAGAAACGCATATCTGGCACACGAAGTG
Found at i:48297171 original size:25 final size:25
Alignment explanation
Indices: 48297143--48297190 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
48297133 AGTTTTTATG
*
48297143 ATTTTACCCTTATAAAATTTTGACA
1 ATTTTACCCTTAGAAAATTTTGACA
* *
48297168 ATTTTGCCCTTGGAAAATTTTGA
1 ATTTTACCCTTAGAAAATTTTGA
48297191 GAAAATATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (25 bp):
ATTTTACCCTTAGAAAATTTTGACA
Found at i:48309772 original size:30 final size:30
Alignment explanation
Indices: 48309738--48309795 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
48309728 AAAAATAATA
*
48309738 ATTTCAACATTTT-ACATTTTAGCCCCTAAC
1 ATTTC-ACATTTTCACAATTTAGCCCCTAAC
*
48309768 ATTTCACATTTTCACAATTTAGTCCCTA
1 ATTTCACATTTTCACAATTTAGCCCCTA
48309796 TTTCAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.41
Consensus pattern (30 bp):
ATTTCACATTTTCACAATTTAGCCCCTAAC
Found at i:48311679 original size:95 final size:95
Alignment explanation
Indices: 48311511--48311695 Score: 325
Period size: 95 Copynumber: 1.9 Consensus size: 95
48311501 TAATAGTGTT
* *
48311511 TGTAGTAAAGTCTGTTTGTGAATGGTATTCGCCAACAAGCGAATTGTATGACTTGCTAAGTTGGA
1 TGTAATAAAGTCTGTTTGTGAATGGTATTCGCCAACAAGCGAATTGTATGACTTACTAAGTTGGA
48311576 AAGGTTTATCAGTATTATATATATAATGTC
66 AAGGTTTATCAGTATTATATATATAATGTC
* *
48311606 TGTAATAAAGTCTGTTTGTGAATGGTATTCGCCAACGAGTGAATTGTATGACTTACTAAGTTGGA
1 TGTAATAAAGTCTGTTTGTGAATGGTATTCGCCAACAAGCGAATTGTATGACTTACTAAGTTGGA
*
48311671 AAGGTTTATCGGTATTATATATATA
66 AAGGTTTATCAGTATTATATATATA
48311696 GCAATTGAGA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 85 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (95 bp):
TGTAATAAAGTCTGTTTGTGAATGGTATTCGCCAACAAGCGAATTGTATGACTTACTAAGTTGGA
AAGGTTTATCAGTATTATATATATAATGTC
Found at i:48312795 original size:26 final size:26
Alignment explanation
Indices: 48312766--48312818 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
48312756 GAAAATGACT
48312766 ATATGTCAAGCTACAAGCTAAAAAAA
1 ATATGTCAAGCTACAAGCTAAAAAAA
48312792 ATATGTCAAGCTACAAGCTAAAAAAA
1 ATATGTCAAGCTACAAGCTAAAAAAA
48312818 A
1 A
48312819 AATTAAGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.11, T:0.19
Consensus pattern (26 bp):
ATATGTCAAGCTACAAGCTAAAAAAA
Found at i:48312990 original size:5 final size:5
Alignment explanation
Indices: 48312980--48313004 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
48312970 TTATCTTGCA
48312980 TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT
48313005 ACTTTGATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:48313924 original size:474 final size:475
Alignment explanation
Indices: 48313026--48313975 Score: 1893
Period size: 474 Copynumber: 2.0 Consensus size: 475
48313016 ACAAATAAAA
48313026 ATATATTCCCTTTGTTCAAATAAATCTTTCGACGAAGTGATTCTAAATAAATATATATATTAAAA
1 ATATATTCCCTTTGTTCAAATAAATCTTTCGACGAAGTGATTCTAAATAAATATATATATTAAAA
48313091 ATTAAATTAATTAAATACTTAAAATAACATATGTCAGAGTTTTAAAAAAAATACAAAAAATCCAA
66 ATTAAATTAATTAAATACTTAAAATAACATATGTCAGAGTTTTAAAAAAAATACAAAAAATCCAA
48313156 CTCTTACATTTTAATTGAGATAAATGAAGTACTAAGTTTCTAGATGACAAATGTTAAAAGAAATC
131 CTCTTACATTTTAATTGAGATAAATGAAGTACTAAGTTTCTAGATGACAAATGTTAAAAGAAATC
48313221 AAAATTCTTAACTTGGTATGATGAAAATAAGTTAGAAGGATTTTCCTACACTATTTATTTGATGA
196 AAAATTCTTAACTTGGTATGATGAAAATAAGTTAGAAGGATTTTCCTACACTATTTATTTGATGA
48313286 GTGGTTGATTCAGATTAATTGTGAGAATTAAAATAAAAGTGTAAATGTTCAAATTACGAATAATA
261 GTGGTTGATTCAGATTAATTGTGAGAATTAAAATAAAAGTGTAAATGTTCAAATTACGAATAATA
48313351 AGTCTAAAACATCATAAATTAAAGAATTCTAAATTTTGATTTATTAATTGAGTATTCATTTATCT
326 AGTCTAAAACATCATAAATTAAAGAATTCTAAATTTTGATTTATTAATTGAGTATTCATTTATCT
48313416 TAAAAATAATTTAAATTTGAATCATAGTTCCATAAAAAATCATCTTAAATTTAAACTTCTGTTTT
391 TAAAAATAATTTAAATTTGAATCATAGTTCCATAAAAAATCATCTTAAATTTAAACTTCTGTTTT
48313481 AAAAAATTGTACTATATAGC
456 AAAAAATTGTACTATATAGC
48313501 ATATATTCCC-TTGTTCAAATAAATCTTTCGACGAAGTGATTCTAAATAAATATATATATTAAAA
1 ATATATTCCCTTTGTTCAAATAAATCTTTCGACGAAGTGATTCTAAATAAATATATATATTAAAA
48313565 ATTAAATTAATTAAATACTTAAAATAACATATGTCAGAGTTTTAAAAAAAATACAAAAAATCCAA
66 ATTAAATTAATTAAATACTTAAAATAACATATGTCAGAGTTTTAAAAAAAATACAAAAAATCCAA
48313630 CTCTTACATTTTAATTGAGATAAATGAAGTACTAAGTTTCTAGATGACAAATGTTAAAAGAAATC
131 CTCTTACATTTTAATTGAGATAAATGAAGTACTAAGTTTCTAGATGACAAATGTTAAAAGAAATC
48313695 AAAATTCTTAACTTGGTATGATGAAAATAAGTTAGAAGGATTTTCCTACACTATTTATTTGATGA
196 AAAATTCTTAACTTGGTATGATGAAAATAAGTTAGAAGGATTTTCCTACACTATTTATTTGATGA
48313760 GTGGTTGATTCAGATTAATTGTGAGAATTAAAATAAAAGTGTAAATGTTCAAATTACGAATAATA
261 GTGGTTGATTCAGATTAATTGTGAGAATTAAAATAAAAGTGTAAATGTTCAAATTACGAATAATA
48313825 AGTCTAAAACATCATAAATTAAAGAATTCTAAATTTTGATTTATTAATTGAGTATTCATTTATCT
326 AGTCTAAAACATCATAAATTAAAGAATTCTAAATTTTGATTTATTAATTGAGTATTCATTTATCT
48313890 TAAAAATAATTTAAATTTGAATCATAGTTCCATAAAAAATCATCTTAAATTTAAACTTCTGTTTT
391 TAAAAATAATTTAAATTTGAATCATAGTTCCATAAAAAATCATCTTAAATTTAAACTTCTGTTTT
48313955 AAAAAATTGTACTATATAGC
456 AAAAAATTGTACTATATAGC
48313975 A
1 A
48313976 AAATATTATA
Statistics
Matches: 475, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
474 465 0.98
475 10 0.02
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (475 bp):
ATATATTCCCTTTGTTCAAATAAATCTTTCGACGAAGTGATTCTAAATAAATATATATATTAAAA
ATTAAATTAATTAAATACTTAAAATAACATATGTCAGAGTTTTAAAAAAAATACAAAAAATCCAA
CTCTTACATTTTAATTGAGATAAATGAAGTACTAAGTTTCTAGATGACAAATGTTAAAAGAAATC
AAAATTCTTAACTTGGTATGATGAAAATAAGTTAGAAGGATTTTCCTACACTATTTATTTGATGA
GTGGTTGATTCAGATTAATTGTGAGAATTAAAATAAAAGTGTAAATGTTCAAATTACGAATAATA
AGTCTAAAACATCATAAATTAAAGAATTCTAAATTTTGATTTATTAATTGAGTATTCATTTATCT
TAAAAATAATTTAAATTTGAATCATAGTTCCATAAAAAATCATCTTAAATTTAAACTTCTGTTTT
AAAAAATTGTACTATATAGC
Found at i:48319572 original size:43 final size:43
Alignment explanation
Indices: 48319524--48319634 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
48319514 GTGATTTCGC
* *
48319524 GTAAGACCACATCTGGGACGTTGGCATCGA-CTTGTGTTTTCAT
1 GTAAGACCACATCTGGGACGTTGGCATCGATC-TGTGATTACAT
*
48319567 GTAAGACC-CTATCTGGGACAG-CGGCATCGATCTGTGATTACAT
1 GTAAGACCAC-ATCTGGGAC-GTTGGCATCGATCTGTGATTACAT
*
48319610 GTAAGACCACGTCTGGGACGTTGGC
1 GTAAGACCACATCTGGGACGTTGGC
48319635 GTTGTACGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.03
43 53 0.91
44 3 0.05
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (43 bp):
GTAAGACCACATCTGGGACGTTGGCATCGATCTGTGATTACAT
Found at i:48320774 original size:19 final size:20
Alignment explanation
Indices: 48320736--48320775 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
48320726 TTTTGAGTGA
48320736 ATTATGGTTTAGGCATATTTTG
1 ATTATGGTTTA-G-ATATTTTG
48320758 ATTATGGTTTA-ATATTTT
1 ATTATGGTTTAGATATTTT
48320776 ATGGATAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
22 11 0.61
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.55
Consensus pattern (20 bp):
ATTATGGTTTAGATATTTTG
Found at i:48321164 original size:2 final size:2
Alignment explanation
Indices: 48321157--48321181 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48321147 TTATAAGGTA
48321157 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
48321182 GATGCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48326525 original size:23 final size:23
Alignment explanation
Indices: 48326468--48326526 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
48326458 TCTTTGTGAG
* *
48326468 CTTCCTGATTAATGGCTCTCTAGAG
1 CTTCCTGA-T-ATGGCTCGCTAGAA
*
48326493 CTT-CTCGATATGGCTCGCTTGAA
1 CTTCCT-GATATGGCTCGCTAGAA
48326516 CTTCCTGATAT
1 CTTCCTGATAT
48326527 ATGGCTATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
23 19 0.66
24 5 0.17
25 5 0.17
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (23 bp):
CTTCCTGATATGGCTCGCTAGAA
Found at i:48326544 original size:25 final size:25
Alignment explanation
Indices: 48326516--48326567 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
48326506 CTCGCTTGAA
*
48326516 CTTCCTGA-TATATGGCTATTCGGAG
1 CTTCCTGATTA-ATGGCTATTCAGAG
48326541 CTTCCTGATTAATGGCTATTCAGAG
1 CTTCCTGATTAATGGCTATTCAGAG
48326566 CT
1 CT
48326568 ACCCGTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (25 bp):
CTTCCTGATTAATGGCTATTCAGAG
Found at i:48326615 original size:73 final size:73
Alignment explanation
Indices: 48326464--48326618 Score: 197
Period size: 73 Copynumber: 2.1 Consensus size: 73
48326454 AGACTCTTTG
* * *
48326464 TGAGCTTCCTGATTAATGGCTCTCTAGAGCTTCTCGATATGGCTCGCTTGAACTTCCTGATATAT
1 TGAGCTTCCTGATTAATGGCTCTCTAGAGCTACCCGATATGGCTCGCATGAACTTCCTGATATAT
*
48326529 GGCTATTC
66 GGCTATTA
* * * *
48326537 GGAGCTTCCTGATTAATGGCTAT-TCAGAGCTACCCGTTATTGGCTCGCATGAGCTTCCTGA-AT
1 TGAGCTTCCTGATTAATGGCTCTCT-AGAGCTACCCGATA-TGGCTCGCATGAACTTCCTGATAT
*
48326600 ATGGCTCTTA
64 ATGGCTATTA
48326610 TGAGCTTCC
1 TGAGCTTCC
48326619 CGTTGTGCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
72 1 0.01
73 50 0.71
74 19 0.27
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (73 bp):
TGAGCTTCCTGATTAATGGCTCTCTAGAGCTACCCGATATGGCTCGCATGAACTTCCTGATATAT
GGCTATTA
Found at i:48327718 original size:42 final size:42
Alignment explanation
Indices: 48327645--48327725 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 42
48327635 TCCACAAGGG
48327645 CAGAGACACAGGCGTGTGTCTCAGCCATGTGTGACACACAGC
1 CAGAGACACAGGCGTGTGTCTCAGCCATGTGTGACACACAGC
* *
48327687 CAGAGACAC-GG-GTGTGTTCCTTAGCCGTGTGTGACACAC
1 CAGAGACACAGGCGTGTG-T-CTCAGCCATGTGTGACACAC
48327726 GGCCTAGCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 5 0.14
41 3 0.09
42 27 0.77
ACGTcount: A:0.23, C:0.27, G:0.30, T:0.20
Consensus pattern (42 bp):
CAGAGACACAGGCGTGTGTCTCAGCCATGTGTGACACACAGC
Found at i:48329448 original size:9 final size:9
Alignment explanation
Indices: 48329416--48329467 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
48329406 TTATCACTAT
48329416 TATTATTAC
1 TATTATTAC
*
48329425 TACTT-TTAT
1 TA-TTATTAC
*
48329434 TATTATTAA
1 TATTATTAC
48329443 TATTATTAC
1 TATTATTAC
* *
48329452 TATTGTTGC
1 TATTATTAC
48329461 TATTATT
1 TATTATT
48329468 GATAATATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
8 2 0.06
9 31 0.89
10 2 0.06
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.60
Consensus pattern (9 bp):
TATTATTAC
Found at i:48329448 original size:15 final size:15
Alignment explanation
Indices: 48329413--48329455 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
48329403 GTATTATCAC
* *
48329413 TATTATTATTACTAC
1 TATTATTATTATTAA
*
48329428 TTTTATTATTATTAA
1 TATTATTATTATTAA
*
48329443 TATTATTACTATT
1 TATTATTATTATT
48329456 GTTGCTATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTATTATTATTAA
Found at i:48329464 original size:27 final size:27
Alignment explanation
Indices: 48329416--48329477 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
48329406 TTATCACTAT
*
48329416 TATTATTACTACTTTTATTATTATTAA
1 TATTATTACTACTTTTACTATTATTAA
* *
48329443 TATTATTACTA-TTGTTGCTATTATTGA
1 TATTATTACTACTT-TTACTATTATTAA
*
48329470 TAATATTA
1 TATTATTA
48329478 TTCGCTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.56
Consensus pattern (27 bp):
TATTATTACTACTTTTACTATTATTAA
Found at i:48332278 original size:22 final size:22
Alignment explanation
Indices: 48332253--48332299 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
48332243 CTTTATATGC
*
48332253 ATTTTT-TAAGAGTGAGGATCAA
1 ATTTTTGT-AGAGTAAGGATCAA
48332275 ATTTTTGTAGAGTAAGGATCAA
1 ATTTTTGTAGAGTAAGGATCAA
48332297 ATT
1 ATT
48332300 AACAAAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.38
Consensus pattern (22 bp):
ATTTTTGTAGAGTAAGGATCAA
Found at i:48338888 original size:16 final size:16
Alignment explanation
Indices: 48338863--48338896 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48338853 TGGGTTTTGC
* *
48338863 TTTGATTGCATGGCAT
1 TTTGACTGCATAGCAT
48338879 TTTGACTGCATAGCAT
1 TTTGACTGCATAGCAT
48338895 TT
1 TT
48338897 CATCCTAAAA
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:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (16 bp):
TTTGACTGCATAGCAT
Found at i:48345027 original size:6 final size:6
Alignment explanation
Indices: 48345016--48345040 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48345006 AGGAAGTTTC
48345016 AGCTCA AGCTCA AGCTCA AGCTCA A
1 AGCTCA AGCTCA AGCTCA AGCTCA A
48345041 TCCCGCAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
AGCTCA
Found at i:48348851 original size:45 final size:45
Alignment explanation
Indices: 48348796--48348898 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
48348786 CCTATCTCCT
* * *
48348796 TGAAGTTGCAGTAGAGTAGATTGAAGATAGC-AGGTCTTATCCCCC
1 TGAAGTTGCAGTAGAGCAGACTGAAGATAGCGA-ATCTTATCCCCC
* * * * *
48348841 TGAATTTGCAGTGGGGCAGACTGAAGATGGCGAATCTTATCTCCC
1 TGAAGTTGCAGTAGAGCAGACTGAAGATAGCGAATCTTATCCCCC
48348886 TGAAGTTGCAGTA
1 TGAAGTTGCAGTA
48348899 CAACAGATTA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
45 46 0.98
46 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (45 bp):
TGAAGTTGCAGTAGAGCAGACTGAAGATAGCGAATCTTATCCCCC
Found at i:48356836 original size:21 final size:21
Alignment explanation
Indices: 48356812--48356862 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
48356802 TTCTTTTGAA
*
48356812 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
48356833 CCTCTGCTTCCCTCGCTGCTG
1 CCTCTGCTTCCCTCGCTGCAG
48356854 CCTCTGCTT
1 CCTCTGCTT
48356863 TTAGTTGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.02, C:0.45, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:48356915 original size:87 final size:87
Alignment explanation
Indices: 48356747--48356906 Score: 230
Period size: 87 Copynumber: 1.8 Consensus size: 87
48356737 TTTTGCTCTG
* * *
48356747 CTCTGCTTCTCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAA
1 CTCTGCTTCCCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTCAA
** *
48356812 CCTCTGCTTCTCTCGCTGCAGC
66 CCTCAACTTCGCTCGCTGCAGC
* * * *
48356834 CTCTGCTTCCCTCGCTGCTGCCTCTGCTTTTAGTTGTAGCTGGAGTTCTTCATATTTCCTTTCAA
1 CTCTGCTTCCCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTCAA
48356899 CCTCAACT
66 CCTCAACT
48356907 GTGGTCGCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 64 1.00
ACGTcount: A:0.12, C:0.30, G:0.17, T:0.41
Consensus pattern (87 bp):
CTCTGCTTCCCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTCAA
CCTCAACTTCGCTCGCTGCAGC
Found at i:48358589 original size:17 final size:17
Alignment explanation
Indices: 48358567--48358626 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
48358557 ATATATTTTA
48358567 AAATTATTAAGTTATGT
1 AAATTATTAAGTTATGT
** *
48358584 AAATTATGCGAGTTGT-T
1 AAATTAT-TAAGTTATGT
*
48358601 AAGTTATTAAGTTATGT
1 AAATTATTAAGTTATGT
*
48358618 AAGTTATTA
1 AAATTATTA
48358627 TGTGAATTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
16 5 0.15
17 24 0.71
18 5 0.15
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.45
Consensus pattern (17 bp):
AAATTATTAAGTTATGT
Found at i:48358612 original size:34 final size:36
Alignment explanation
Indices: 48358570--48358653 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 36
48358560 TATTTTAAAA
* *
48358570 TTATTAAGTTATGTAA-ATTATGCGAGTTGT-TAAG
1 TTATTAAGTTATGTAATATTATGCGAATTATATAAG
*
48358604 TTATTAAGTTATGTAAGTTATTATGTGAATTATATAAG
1 TTATTAAGTTATGTAA--TATTATGCGAATTATATAAG
48358642 TTATTAAGTTAT
1 TTATTAAGTTAT
48358654 ATGGTATGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 16 0.37
37 11 0.26
38 16 0.37
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.48
Consensus pattern (36 bp):
TTATTAAGTTATGTAATATTATGCGAATTATATAAG
Found at i:48358653 original size:8 final size:8
Alignment explanation
Indices: 48358570--48358626 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 8
48358560 TATTTTAAAA
48358570 TTATTAAG
1 TTATTAAG
*
48358578 TTATGTAAA
1 TTAT-TAAG
**
48358587 TTATGCGAG
1 TTAT-TAAG
*
48358596 TTGTTAAG
1 TTATTAAG
48358604 TTATTAAG
1 TTATTAAG
48358612 TTATGTAAG
1 TTAT-TAAG
48358621 TTATTA
1 TTATTA
48358627 TGTGAATTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
8 19 0.49
9 20 0.51
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (8 bp):
TTATTAAG
Found at i:48358655 original size:17 final size:17
Alignment explanation
Indices: 48358600--48358655 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
48358590 TGCGAGTTGT
*
48358600 TAAGTTATTAAGTTATG
1 TAAGTTATTAAGTTATA
*
48358617 TAAGTTATTATGTGAATTATA
1 TAAGTTATTA----AGTTATA
48358638 TAAGTTATTAAGTTATA
1 TAAGTTATTAAGTTATA
48358655 T
1 T
48358656 GGTATGACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 17 0.53
21 15 0.47
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (17 bp):
TAAGTTATTAAGTTATA
Found at i:48362113 original size:9 final size:9
Alignment explanation
Indices: 48362099--48362391 Score: 234
Period size: 9 Copynumber: 34.4 Consensus size: 9
48362089 TTTTTATGTA
48362099 TTATGTAAG
1 TTATGTAAG
48362108 TTATGTACTAAG
1 TTATG---TAAG
48362120 TTATGT-A-
1 TTATGTAAG
48362127 TTATGTAAG
1 TTATGTAAG
48362136 TTATGTAAG
1 TTATGTAAG
*
48362145 TTGTGT-A-
1 TTATGTAAG
*
48362152 TTATGTGAG
1 TTATGTAAG
*
48362161 TTATGTAGG
1 TTATGTAAG
*
48362170 TTGTGT-A-
1 TTATGTAAG
48362177 TTATGTAAG
1 TTATGTAAG
48362186 TTATGT-A-
1 TTATGTAAG
48362193 TTATGT-A-
1 TTATGTAAG
48362200 TTATGTAAG
1 TTATGTAAG
48362209 TTATGTAAG
1 TTATGTAAG
*
48362218 TAATGT-A-
1 TTATGTAAG
48362225 TTATGTAAG
1 TTATGTAAG
*
48362234 TTGTGT-A-
1 TTATGTAAG
*
48362241 TAATGTAAG
1 TTATGTAAG
* *
48362250 CTAAG-AAGG
1 TTATGTAA-G
48362259 TTATGT-A-
1 TTATGTAAG
48362266 TTATGTAAG
1 TTATGTAAG
*
48362275 TTATTTAAG
1 TTATGTAAG
48362284 TTATGTAAG
1 TTATGTAAG
48362293 TTATGTAAG
1 TTATGTAAG
* *
48362302 TTATTTAAT
1 TTATGTAAG
48362311 TTATGTAAG
1 TTATGTAAG
48362320 TTATGTAAG
1 TTATGTAAG
*
48362329 TTATGTAGG
1 TTATGTAAG
*
48362338 CTATGT-A-
1 TTATGTAAG
*
48362345 TTATGTAAA
1 TTATGTAAG
*
48362354 TAATGTAAG
1 TTATGTAAG
*
48362363 TTA-GGAAGG
1 TTATGTAA-G
48362372 TTATGT-A-
1 TTATGTAAG
48362379 TTATGTAAG
1 TTATGTAAG
48362388 TTAT
1 TTAT
48362392 NNNNNNNNNN
Statistics
Matches: 227, Mismatches: 32, Indels: 50
0.73 0.10 0.16
Matches are distributed among these distances:
7 55 0.24
8 19 0.08
9 143 0.63
10 1 0.00
12 9 0.04
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:48362113 original size:16 final size:17
Alignment explanation
Indices: 48362099--48362391 Score: 209
Period size: 16 Copynumber: 17.2 Consensus size: 17
48362089 TTTTTATGTA
48362099 TTATGTAAGTTATGTACTAAG
1 TTATGT-AGTTATGTA---AG
48362120 TTATGTA-TTATGTAAG
1 TTATGTAGTTATGTAAG
*
48362136 TTATGTAAGTTGTGT-A-
1 TTATGT-AGTTATGTAAG
*
48362152 TTATGTGAGTTATGTAGG
1 TTATGT-AGTTATGTAAG
*
48362170 TTGTGTA-TTATGTAAG
1 TTATGTAGTTATGTAAG
48362186 TTATGTA-TTATGT-A-
1 TTATGTAGTTATGTAAG
48362200 TTATGTAAGTTATGTAAG
1 TTATGT-AGTTATGTAAG
*
48362218 TAATGTA-TTATGTAAG
1 TTATGTAGTTATGTAAG
* *
48362234 TTGTGTA-TAATGTAAG
1 TTATGTAGTTATGTAAG
* * *
48362250 CTAAGAAGGTTATGT-A-
1 TTATGTA-GTTATGTAAG
*
48362266 TTATGTAAGTTATTTAAG
1 TTATGT-AGTTATGTAAG
48362284 TTATGTAAGTTATGTAAG
1 TTATGT-AGTTATGTAAG
* *
48362302 TTATTTAATTTATGTAAG
1 TTATGT-AGTTATGTAAG
*
48362320 TTATGTAAGTTATGTAGG
1 TTATGT-AGTTATGTAAG
* *
48362338 CTATGTA-TTATGTAAA
1 TTATGTAGTTATGTAAG
* *
48362354 TAATGTAAGTTA-GGAAGG
1 TTATGT-AGTTATGTAA-G
48362372 TTATGTA-TTATGTAAG
1 TTATGTAGTTATGTAAG
48362388 TTAT
1 TTAT
48362392 NNNNNNNNNN
Statistics
Matches: 220, Mismatches: 35, Indels: 39
0.75 0.12 0.13
Matches are distributed among these distances:
14 6 0.03
15 2 0.01
16 100 0.45
17 17 0.08
18 81 0.37
19 7 0.03
20 1 0.00
21 6 0.03
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.46
Consensus pattern (17 bp):
TTATGTAGTTATGTAAG
Found at i:48362151 original size:25 final size:25
Alignment explanation
Indices: 48362092--48362391 Score: 251
Period size: 25 Copynumber: 11.8 Consensus size: 25
48362082 TGATATATTT
48362092 TTATGTATTATGTAAGTTATGTACTAAG
1 TTATGTATTATGTAAGTTATG---TAAG
48362120 TTATGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
* * *
48362145 TTGTGTATTATGTGAGTTATGTAGG
1 TTATGTATTATGTAAGTTATGTAAG
*
48362170 TTGTGTATTATGTAAGTTATGT-A-
1 TTATGTATTATGTAAGTTATGTAAG
48362193 TTATGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
* *
48362218 TAATGTATTATGTAAGTTGTGT-A-
1 TTATGTATTATGTAAGTTATGTAAG
* * *
48362241 TAATGTAAGCTAAG-AAGGTTATGT-A-
1 TTATGT-A-TTATGTAA-GTTATGTAAG
*
48362266 TTATGTAAGTTATTTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
* *
48362293 TTATGTAAGTTATTTAATTTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
* *
48362320 TTATGTAAGTTATGTAGGCTATGT-A-
1 TTATGT-A-TTATGTAAGTTATGTAAG
* *
48362345 TTATGTAAATAATGTAAGTTA-GGAAGG
1 TTATGT--ATTATGTAAGTTATGTAA-G
48362372 TTATGTATTATGTAAGTTAT
1 TTATGTATTATGTAAGTTAT
48362392 NNNNNNNNNN
Statistics
Matches: 234, Mismatches: 25, Indels: 28
0.82 0.09 0.10
Matches are distributed among these distances:
23 27 0.12
24 6 0.03
25 122 0.52
26 6 0.03
27 52 0.22
28 21 0.09
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:48362181 original size:41 final size:41
Alignment explanation
Indices: 48362116--48362351 Score: 176
Period size: 41 Copynumber: 5.5 Consensus size: 41
48362106 AGTTATGTAC
48362116 TAAGTTATGT-A-TTATGTAAGTTATGTAAGTTGTGTATTATG
1 TAAGTTATGTAAGTTATGT-A-TTATGTAAGTTGTGTATTATG
* * *
48362157 TGAGTTATGTAGGTTGTGTATTATGTAAGTTATGTATTATGTATTATG
1 TAAGTTATGTAAGTTATGTATTATGTAAG-T-TG-----TGTATTATG
* *
48362205 TAAGTTATGTAAGTAATGTATTATGTAAGTTGTGTATAATG
1 TAAGTTATGTAAGTTATGTATTATGTAAGTTGTGTATTATG
* * * *
48362246 TAAGCTAAG-AAGGTTATGTATTATGTAAGTTATTTAAGTTATG
1 TAAGTTATGTAA-GTTATGTATTATGTAAGTTGTGT-A-TTATG
* *
48362289 TAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATG
1 TAAGTTATGTAAGTTATGT-A-TTATGTAAGTTGTGT-A-TTATG
* *
48362334 TAGGCTATGT-A-TTATGTA
1 TAAGTTATGTAAGTTATGTA
48362352 AATAATGTAA
Statistics
Matches: 159, Mismatches: 21, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
40 2 0.01
41 53 0.33
42 4 0.03
43 29 0.18
44 4 0.03
45 30 0.19
46 2 0.01
47 1 0.01
48 34 0.21
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.47
Consensus pattern (41 bp):
TAAGTTATGTAAGTTATGTATTATGTAAGTTGTGTATTATG
Found at i:48364777 original size:13 final size:13
Alignment explanation
Indices: 48364759--48364783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48364749 CTGAAAGGAG
48364759 TTAGGGATTTCAC
1 TTAGGGATTTCAC
48364772 TTAGGGATTTCA
1 TTAGGGATTTCA
48364784 GATCAGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (13 bp):
TTAGGGATTTCAC
Found at i:48365653 original size:7 final size:7
Alignment explanation
Indices: 48365641--48365683 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
48365631 TATTCATTAG
48365641 ACCTTAA
1 ACCTTAA
48365648 ACCTTAA
1 ACCTTAA
48365655 ACCCTTAA
1 A-CCTTAA
*
48365663 CCCTTAA
1 ACCTTAA
*
48365670 CCCTT-A
1 ACCTTAA
48365676 ACCTTAA
1 ACCTTAA
48365683 A
1 A
48365684 TTGACTTGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 5 0.16
7 21 0.66
8 6 0.19
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.28
Consensus pattern (7 bp):
ACCTTAA
Found at i:48365662 original size:15 final size:15
Alignment explanation
Indices: 48365642--48365683 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
48365632 ATTCATTAGA
48365642 CCTTAAACCTTAAAC
1 CCTTAAACCTTAAAC
*
48365657 CCTTAACCCTT-AAC
1 CCTTAAACCTTAAAC
48365671 CCTT-AACCTTAAA
1 CCTTAAACCTTAAA
48365684 TTGACTTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.21
14 9 0.38
15 10 0.42
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (15 bp):
CCTTAAACCTTAAAC
Found at i:48366039 original size:38 final size:40
Alignment explanation
Indices: 48365954--48366040 Score: 99
Period size: 38 Copynumber: 2.2 Consensus size: 40
48365944 TCAGCCATAT
* * *
48365954 TCCTTAAACCATAAATCATAAAATATATATAAACCCTAAA
1 TCCTTAAACCATAAATCATAAAACATACATAAACCATAAA
* * *
48365994 TCC-TAAACCCTAAATCA-ATAACATACATAAACTATAAA
1 TCCTTAAACCATAAATCATAAAACATACATAAACCATAAA
48366032 -CCTTAAACC
1 TCCTTAAACC
48366041 TCAACCCTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 2 0.05
38 22 0.55
39 13 0.32
40 3 0.08
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (40 bp):
TCCTTAAACCATAAATCATAAAACATACATAAACCATAAA
Found at i:48366168 original size:34 final size:34
Alignment explanation
Indices: 48366125--48366192 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
48366115 TCAACAAAAA
*
48366125 AAATATTGTTTTGCTTAATGATTTGCGGCGCTTT
1 AAATATTGTTTTGCTTAACGATTTGCGGCGCTTT
48366159 AAATATTGTTTTGCTTAACGATTTGCGGCGCTTT
1 AAATATTGTTTTGCTTAACGATTTGCGGCGCTTT
48366193 TAAAAAAGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.46
Consensus pattern (34 bp):
AAATATTGTTTTGCTTAACGATTTGCGGCGCTTT
Found at i:48366373 original size:115 final size:112
Alignment explanation
Indices: 48366180--48366420 Score: 245
Period size: 115 Copynumber: 2.1 Consensus size: 112
48366170 TGCTTAACGA
** * *
48366180 TTTGCGGCGCTTTTAAAAAAGCGCCGCTAATTCTTGAATTTTGCGGCGTTTTTTTAAAAGCACCA
1 TTTGCGGCGC--TTAAAAAAGCGCCGCTAAGGCTTGAATTCTGCGGCG-ATTTTTAAAAGCACCA
* ** **
48366245 CTAATGTCTCTAAACATCT-ACAAGAAAACGACGCTGTTTGCTTAAATCTT
63 CTAATGTCTCTAAACAT-TAACAACAAAACGACGCCATTTGCTTAAAAATT
* *
48366295 TTTGCGGCGCTTAACATAAAGCGCCGCTAAGGCTTGACTTCTGCGGC-ATTTTTAAAGTTGCACC
1 TTTGCGGCGCTTAA-A-AAAGCGCCGCTAAGGCTTGAATTCTGCGGCGATTTTTAAA--AGCACC
* * **
48366359 GCTAATGTAC-CTAAACCTTAACAACAAAACGTTGCCATTTGCTTAAAAATT
62 ACTAATGT-CTCTAAACATTAACAACAAAACGACGCCATTTGCTTAAAAATT
48366410 TTTGCGGCGCT
1 TTTGCGGCGCT
48366421 ACCGTAAAAG
Statistics
Matches: 105, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
113 12 0.11
114 2 0.02
115 90 0.86
116 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (112 bp):
TTTGCGGCGCTTAAAAAAGCGCCGCTAAGGCTTGAATTCTGCGGCGATTTTTAAAAGCACCACTA
ATGTCTCTAAACATTAACAACAAAACGACGCCATTTGCTTAAAAATT
Found at i:48388391 original size:25 final size:25
Alignment explanation
Indices: 48388357--48388416 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
48388347 TCTATGGCGC
*
48388357 CCCAAACCCGGTCGGGGCGGTCCGA
1 CCCAAACCCGGTCGGGGCAGTCCGA
* *
48388382 CCCAAACCCGGTCGTGGTAGTCCGA
1 CCCAAACCCGGTCGGGGCAGTCCGA
*
48388407 CCGAAACCCG
1 CCCAAACCCG
48388417 AAACGACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.20, C:0.40, G:0.30, T:0.10
Consensus pattern (25 bp):
CCCAAACCCGGTCGGGGCAGTCCGA
Found at i:48392188 original size:32 final size:32
Alignment explanation
Indices: 48392148--48392216 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
48392138 ATCTCTAACC
*
48392148 AACACAAATGAGTCATGTATCTCCTACCATAT
1 AACACAAATGAGTCATGCATCTCCTACCATAT
48392180 AACACAAATGAGTCATGCATCTCCTACCATAT
1 AACACAAATGAGTCATGCATCTCCTACCATAT
48392212 AACAC
1 AACAC
48392217 CTACCATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.39, C:0.28, G:0.09, T:0.25
Consensus pattern (32 bp):
AACACAAATGAGTCATGCATCTCCTACCATAT
Found at i:48392221 original size:14 final size:14
Alignment explanation
Indices: 48392202--48392233 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
48392192 TCATGCATCT
48392202 CCTACCATATAACA
1 CCTACCATATAACA
48392216 CCTACCATATAACA
1 CCTACCATATAACA
48392230 CCTA
1 CCTA
48392234 ACCAACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.22
Consensus pattern (14 bp):
CCTACCATATAACA
Found at i:48396111 original size:9 final size:9
Alignment explanation
Indices: 48396099--48396365 Score: 77
Period size: 10 Copynumber: 28.4 Consensus size: 9
48396089 TTTTATGATT
48396099 TTTTTATAA
1 TTTTTATAA
48396108 TTTTTATAA
1 TTTTTATAA
48396117 TTTTATATCAA
1 TTTT-TAT-AA
*
48396128 TTTTAAT-A
1 TTTTTATAA
*
48396136 TTTTTAATAC
1 TTTTT-ATAA
*
48396146 TTTTTAAAGA
1 TTTTTATA-A
* * *
48396156 ATTCTAAAA
1 TTTTTATAA
48396165 CGTTTTT-TAA
1 --TTTTTATAA
*
48396175 -CTTTA-AA
1 TTTTTATAA
48396182 TATTTTCAATAA
1 T-TTTT--ATAA
*
48396194 GTTTTATTAA
1 TTTTTA-TAA
*
48396204 TTTTATAAAAA
1 TTTT-T-ATAA
**
48396215 AATTTATAA
1 TTTTTATAA
*
48396224 TTTATTA-GA
1 TTT-TTATAA
*
48396233 TTTCTAT-A
1 TTTTTATAA
48396241 TTTTTATAA
1 TTTTTATAA
*
48396250 TATTTATAA
1 TTTTTATAA
48396259 GTTTTTAT-A
1 -TTTTTATAA
48396268 TTTTTATAA
1 TTTTTATAA
*
48396277 TTTTAATAA
1 TTTTTATAA
*
48396286 GTTTATATCAA
1 -TTTTTAT-AA
*
48396297 TTTTAAT-A
1 TTTTTATAA
* *
48396305 TTTTAAATATT
1 TTTT-TATA-A
48396316 TTTTTATAA
1 TTTTTATAA
*
48396325 CTTTTTCT-A
1 -TTTTTATAA
* *
48396334 TTTTTTTGAT
1 TTTTTAT-AA
48396344 TTTTTAATAA
1 TTTTT-ATAA
48396354 TTTTTAT-A
1 TTTTTATAA
48396362 TTTT
1 TTTT
48396366 AGTTAACGTC
Statistics
Matches: 190, Mismatches: 38, Indels: 61
0.66 0.13 0.21
Matches are distributed among these distances:
7 5 0.03
8 37 0.19
9 55 0.29
10 64 0.34
11 26 0.14
12 3 0.02
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:48396129 original size:20 final size:20
Alignment explanation
Indices: 48396083--48396141 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
48396073 CTAGTCTAGT
*
48396083 TCAAGTTTTTATGATTTTTTTA
1 TCAA-TTTTTAT-ATTTTTATA
*
48396105 T-AATTTTTATAATTTTATA
1 TCAATTTTTATATTTTTATA
*
48396124 TCAATTTTAATATTTTTA
1 TCAATTTTTATATTTTTA
48396142 ATACTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 8 0.25
20 21 0.66
21 2 0.06
22 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TCAATTTTTATATTTTTATA
Found at i:48396273 original size:18 final size:18
Alignment explanation
Indices: 48396240--48396285 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
48396230 AGATTTCTAT
48396240 ATTTTTATAATATTTATA
1 ATTTTTATAATATTTATA
*
48396258 AGTTTTTAT-ATTTTTATA
1 A-TTTTTATAATATTTATA
*
48396276 ATTTTAATAA
1 ATTTTTATAA
48396286 GTTTATATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 6 0.25
18 11 0.46
19 7 0.29
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTTTATAATATTTATA
Found at i:48396275 original size:27 final size:27
Alignment explanation
Indices: 48396223--48396289 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
48396213 AAAATTTATA
*
48396223 ATTTATTAGATTTCTATATTTTTATAAT
1 ATTTATAAG-TTTCTATATTTTTATAAT
*
48396251 ATTTATAAGTTTTTATATTTTTATAAT
1 ATTTATAAGTTTCTATATTTTTATAAT
48396278 -TTTAATAAGTTT
1 ATTT-ATAAGTTT
48396290 ATATCAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 3 0.08
27 25 0.69
28 8 0.22
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (27 bp):
ATTTATAAGTTTCTATATTTTTATAAT
Found at i:48396292 original size:35 final size:35
Alignment explanation
Indices: 48396216--48396285 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
48396206 TTATAAAAAA
*
48396216 ATTTATAATTTATTAGATTTCTATATTTTTATAAT
1 ATTTATAATTTATTAGATTTCTATATTTTAATAAT
* *
48396251 ATTTATAAGTTT-TTATATTTTTATAATTTTAATAA
1 ATTTATAA-TTTATTAGATTTCTAT-ATTTTAATAA
48396286 GTTTATATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 18 0.60
36 12 0.40
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (35 bp):
ATTTATAATTTATTAGATTTCTATATTTTAATAAT
Found at i:48398190 original size:14 final size:14
Alignment explanation
Indices: 48398171--48398210 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
48398161 TTGATTGCCA
48398171 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
48398185 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
48398199 GGAAAATGTTTT
1 GTAAAATGTTTT
48398211 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:48398219 original size:20 final size:20
Alignment explanation
Indices: 48398194--48398233 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
48398184 CGTAAAATGA
*
48398194 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
48398214 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
48398234 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:48398223 original size:34 final size:35
Alignment explanation
Indices: 48398179--48398245 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
48398169 CAGTAAAATG
*
48398179 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
48398213 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
48398246 CTAGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:48398423 original size:13 final size:13
Alignment explanation
Indices: 48398405--48398432 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
48398395 ATTCTTTCTC
48398405 TATTTATGAAGTT
1 TATTTATGAAGTT
48398418 TATTTATGAAGTT
1 TATTTATGAAGTT
48398431 TA
1 TA
48398433 CTTGTACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (13 bp):
TATTTATGAAGTT
Found at i:48399842 original size:12 final size:12
Alignment explanation
Indices: 48399825--48399852 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
48399815 TTTTCCAGAA
48399825 AACATTATATCG
1 AACATTATATCG
48399837 AACATTATATCG
1 AACATTATATCG
48399849 AACA
1 AACA
48399853 CACAAACGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (12 bp):
AACATTATATCG
Found at i:48407566 original size:16 final size:16
Alignment explanation
Indices: 48407547--48407615 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
48407537 TTTGGTTCGC
48407547 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
48407563 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
48407579 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
48407596 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
48407612 TGTA
1 TGTA
48407616 ATAGCAAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:48407593 original size:33 final size:32
Alignment explanation
Indices: 48407547--48407615 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
48407537 TTTGGTTCGC
48407547 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
48407579 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
48407612 TGTA
1 TGTA
48407616 ATAGCAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:48407872 original size:18 final size:17
Alignment explanation
Indices: 48407851--48407885 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48407841 TTATTATTAA
*
48407851 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
48407869 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
48407886 TCTNNNNNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:48410147 original size:121 final size:121
Alignment explanation
Indices: 48409365--48410131 Score: 1498
Period size: 121 Copynumber: 6.3 Consensus size: 121
48409355 GCTTTCGCTT
48409365 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
1 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
48409430 ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAGTCTCCTCCAAACCTTTAA
66 ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAGTCTCCTCCAAACCTTTAA
48409486 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
1 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
48409551 ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAGTCTCCTCCAAACCTTTAA
66 ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAGTCTCCTCCAAACCTTTAA
48409607 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
1 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
48409672 ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAGTCTCCTCCAAACCTTTAA
66 ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAGTCTCCTCCAAACCTTTAA
48409728 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
1 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
48409793 ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAGTCTCCTCCAAACCTTTAA
66 ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAGTCTCCTCCAAACCTTTAA
48409849 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
1 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
48409914 ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAGTCTCCTCCAAACCTTTAA
66 ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAGTCTCCTCCAAACCTTTAA
48409970 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
1 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
* *
48410035 ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAATCTCATCCAAACCTTTAA
66 ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAGTCTCCTCCAAACCTTTAA
* *
48410091 AATATTACTTTACGAATTTAGTTGATTGTATCAATCATACA
1 AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACA
48410132 ATGTGGTCAG
Statistics
Matches: 642, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 642 1.00
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (121 bp):
AATAGTACTTTACGAAATTAGTTGATTGTATCAATCATACATATTTATTTATATTTTATATTTTT
ATTTAAAAATAATTTATTAGTTTATTTTGCAATTTCAGTCTCCTCCAAACCTTTAA
Found at i:48417583 original size:40 final size:40
Alignment explanation
Indices: 48417539--48417627 Score: 160
Period size: 40 Copynumber: 2.2 Consensus size: 40
48417529 TGGAAAAAGC
*
48417539 AGTAAATGGAAGAGCCAAGATGGTATTGAATGAGGATTGG
1 AGTAAATGGAAGAGCCAAGATGGTATTGAATGAGGATTGA
48417579 AGTAAATGGAAGAGCCAAGATGGTATTGAATGAGGATTGA
1 AGTAAATGGAAGAGCCAAGATGGTATTGAATGAGGATTGA
*
48417619 AGTCAATGG
1 AGTAAATGG
48417628 TGAAGTTTAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.38, C:0.06, G:0.34, T:0.22
Consensus pattern (40 bp):
AGTAAATGGAAGAGCCAAGATGGTATTGAATGAGGATTGA
Found at i:48430744 original size:25 final size:25
Alignment explanation
Indices: 48430693--48430784 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 25
48430683 TCTTGTACAT
* * *
48430693 GTATGCTCACACGAGCTATGAATTG
1 GTATGCTCACACGAGCTGTAAACTG
* *
48430718 GTGTGCTCAGACGAGCTGTAAACTG
1 GTATGCTCACACGAGCTGTAAACTG
* *
48430743 GTATGCTCACATGAGCTGTGAAAATGG
1 GTATGCTCACACGAGCTGT-AAACT-G
**
48430770 GCCTGCTCACACGAG
1 GTATGCTCACACGAG
48430785 TTGTGGGTCA
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
25 36 0.68
26 4 0.08
27 13 0.25
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAACTG
Found at i:48432384 original size:54 final size:54
Alignment explanation
Indices: 48432243--48432393 Score: 144
Period size: 54 Copynumber: 2.8 Consensus size: 54
48432233 TCAAGTTAGT
* * * * * *
48432243 GAGTTACATGGCCTAGCACATGGCTTGGCATACGAGCGTGTGTGGCAACTCAGA
1 GAGTTACACGACCTAGCACACGGCTTGGAACACGAGCGTGTGGGGCAACTCAGA
* * * *
48432297 GAGTTACACGACCTAGCACACGGCCTGGAACACGGGCGTGTGGGGCTACTCAGT
1 GAGTTACACGACCTAGCACACGGCTTGGAACACGAGCGTGTGGGGCAACTCAGA
* * * *
48432351 GAGTTACATGA-GTGAGGACACGGGCTTGG-ACACGACCGTGTGG
1 GAGTTACACGACCT-AGCACAC-GGCTTGGAACACGAGCGTGTGG
48432394 CTCTTGTTCT
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
53 1 0.01
54 72 0.91
55 6 0.08
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.19
Consensus pattern (54 bp):
GAGTTACACGACCTAGCACACGGCTTGGAACACGAGCGTGTGGGGCAACTCAGA
Found at i:48450346 original size:27 final size:27
Alignment explanation
Indices: 48450312--48450556 Score: 241
Period size: 27 Copynumber: 9.1 Consensus size: 27
48450302 CAAAATGCCT
48450312 CTATAGGGTAAAATGACTGAAATACCC
1 CTATAGGGTAAAATGACTGAAATACCC
* *
48450339 CTAAAGGGTAGAATGA-TCGAAATACCAC
1 CTATAGGGTAAAATGACT-GAAATACC-C
* * *
48450367 C-ATAAGGTAAAATGGCCGAAATACCC
1 CTATAGGGTAAAATGACTGAAATACCC
* **
48450393 C-ATAGGGTAAAATAACCAAAATA-CC
1 CTATAGGGTAAAATGACTGAAATACCC
*
48450418 CTCATAGGATAAAATGA-TCGAAATACCC
1 CT-ATAGGGTAAAATGACT-GAAATACCC
*
48450446 CTATAGAGTAAAATGACTGAAATACCC
1 CTATAGGGTAAAATGACTGAAATACCC
* * **
48450473 CCATAGGGTAGAATGACCAAAATACCC
1 CTATAGGGTAAAATGACTGAAATACCC
* *
48450500 CCATTGGGTAAAATGA-TCGAAATACCC
1 CTATAGGGTAAAATGACT-GAAATACCC
**
48450527 CTATAGGGTAAAATGACTGTTATACCC
1 CTATAGGGTAAAATGACTGAAATACCC
48450554 CTA
1 CTA
48450557 GGAGATGAAA
Statistics
Matches: 178, Mismatches: 30, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
25 3 0.02
26 21 0.12
27 146 0.82
28 8 0.04
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (27 bp):
CTATAGGGTAAAATGACTGAAATACCC
Found at i:48450478 original size:54 final size:54
Alignment explanation
Indices: 48450314--48450543 Score: 275
Period size: 54 Copynumber: 4.3 Consensus size: 54
48450304 AAATGCCTCT
* * * *
48450314 ATAGGGTAAAATGACTGAAATACCCCTAAAGGGTAGAATGATCGAAATACCACC
1 ATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCC
* * * * * *
48450368 ATAAGGTAAAATGGCCGAAATACCCC-ATAGGGTAAAATAACCAAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCC
* * *
48450421 ATAGGATAAAATGATCGAAATACCCCTATAGAGTAAAATGA-CTGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATC-GAAATACCCCC
* * * * *
48450475 ATAGGGTAGAATGACCAAAATACCCCCATTGGGTAAAATGATCGAAATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCC
48450529 ATAGGGTAAAATGAC
1 ATAGGGTAAAATGAC
48450544 TGTTATACCC
Statistics
Matches: 146, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
53 43 0.29
54 102 0.70
55 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (54 bp):
ATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCC
Found at i:48450516 original size:81 final size:81
Alignment explanation
Indices: 48450314--48450554 Score: 308
Period size: 81 Copynumber: 3.0 Consensus size: 81
48450304 AAATGCCTCT
** * * *
48450314 ATAGGGTAAAATGACTGAAATACCCCTAAAGGGTAGAATGATCGAAATACCACC-ATA-AGGTAA
1 ATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGATCGAAATACC-CCTATAGA-GTAA
* *
48450377 AATGGCCGAAATA-CCCC
64 AATGACTGAAATACCCCC
* * *
48450394 ATAGGGTAAAATAACCAAAATACCCTCATAGGATAAAATGATCGAAATACCCCTATAGAGTAAAA
1 ATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTATAGAGTAAAA
48450459 TGACTGAAATACCCCC
66 TGACTGAAATACCCCC
* * *
48450475 ATAGGGTAGAATGACCAAAATACCCCCATTGGGTAAAATGATCGAAATACCCCTATAGGGTAAAA
1 ATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTATAGAGTAAAA
**
48450540 TGACTGTTATACCCC
66 TGACTGAAATACCCC
48450555 TAGGAGATGA
Statistics
Matches: 140, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
79 2 0.01
80 61 0.44
81 77 0.55
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (81 bp):
ATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTATAGAGTAAAA
TGACTGAAATACCCCC
Found at i:48452729 original size:33 final size:33
Alignment explanation
Indices: 48452687--48452754 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
48452677 ATATCATCTT
*
48452687 AAAACATACCATAATTATGAGCATAAGCAATTC
1 AAAACATACCATAATTATGAGCAAAAGCAATTC
48452720 AAAACATACCATAATTATGAGCAAAAGCAATTC
1 AAAACATACCATAATTATGAGCAAAAGCAATTC
48452753 AA
1 AA
48452755 CATATACATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.51, C:0.18, G:0.09, T:0.22
Consensus pattern (33 bp):
AAAACATACCATAATTATGAGCAAAAGCAATTC
Done.