Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 161 of 204
Found at i:48346961 original size:33 final size:30
Alignment explanation
Indices: 48346919--48346978 Score: 75
Period size: 33 Copynumber: 1.9 Consensus size: 30
48346909 TTAGAACTCC
*
48346919 TAAATAATTTAAAATACTTAAAAATAATAATTA
1 TAAAAAATTTAAAATA---AAAAATAATAATTA
*
48346952 TAAAAAATTTAGAATAAAAAATAATAA
1 TAAAAAATTTAAAATAAAAAATAATAA
48346979 AATAATAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.44
33 14 0.56
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (30 bp):
TAAAAAATTTAAAATAAAAAATAATAATTA
Found at i:48359876 original size:23 final size:24
Alignment explanation
Indices: 48359850--48359903 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
48359840 AGAACAAAAG
48359850 AATAAAAATAAAAAAATAATG-AC-
1 AATAAAAATAAAAAAAT-ATGTACA
* *
48359873 AATAATAATAAATAAATATGTACA
1 AATAAAAATAAAAAAATATGTACA
48359897 AATAAAA
1 AATAAAA
48359904 GAATGTATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.12
23 17 0.65
24 6 0.23
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (24 bp):
AATAAAAATAAAAAAATATGTACA
Found at i:48363045 original size:18 final size:17
Alignment explanation
Indices: 48363024--48363057 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
48363014 ACAAGCCAAT
48363024 ATAAAAAATAATGATAAA
1 ATAAAAAATAAT-ATAAA
*
48363042 ATAAAAACTAATATAA
1 ATAAAAAATAATATAA
48363058 GATGGATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAAAAAATAATATAAA
Found at i:48363105 original size:12 final size:12
Alignment explanation
Indices: 48363090--48363134 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
48363080 AGTAAATAAG
48363090 TAAATAAAATAT
1 TAAATAAAATAT
*
48363102 TAAATGAAATAT
1 TAAATAAAATAT
*
48363114 TAAATAAAATAG
1 TAAATAAAATAT
48363126 TAAA-AAAAT
1 TAAATAAAAT
48363135 GATGAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 5 0.17
12 25 0.83
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
TAAATAAAATAT
Found at i:48364753 original size:44 final size:44
Alignment explanation
Indices: 48364533--48364924 Score: 132
Period size: 44 Copynumber: 9.1 Consensus size: 44
48364523 CTTCGATCCA
* * * * ** *
48364533 CTCCACTGCAACATCAAGGATATAAGATTTGTTGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAATCTG
* * * * * *
48364577 CTCCATTGCGACCTC-GAGAAGATACGATTGGTTTATTCAGTCTG
1 CTCCACTGCAACTTCAG-GGAGATAAGATTGGTTTATTCAATCTG
* * * ** * * *
48364621 CTCCGCTGCAACTTTAGAGAGATAAGA---CCTAATGCAATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAATCTG
* * ** ***
48364662 CTCTACTGCAACTTTAAAGAGATAAGATCCATCATT-TT-AA-CTGG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGT--TTATTCAATCT-G
* *
48364706 CTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAATCTG
* * * * * *
48364750 CTCCTCTACAACCTC-GTGAAGATACGATTGG-TTATT-AGTCTG
1 CTCCACTGCAACTTCAG-GGAGATAAGATTGGTTTATTCAATCTG
* * * * * *
48364792 CTCCGCTACAACTTCATGGAGATAAGACCT-G---ATGCGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-TTGGTTTATTCAATCTG
* * * *** *
48364833 TTCTACTGCAACTTCAGAGAGATAAGATCCATCATT-TT-AACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGT--TTATTCAATCTG
* * *
48364877 CTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAATCTG
48364921 CTCC
1 CTCC
48364925 TCTACAACCT
Statistics
Matches: 248, Mismatches: 77, Indels: 46
0.67 0.21 0.12
Matches are distributed among these distances:
40 2 0.01
41 57 0.23
42 31 0.12
43 11 0.04
44 141 0.57
45 5 0.02
46 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAATCTG
Found at i:48364815 original size:42 final size:44
Alignment explanation
Indices: 48364705--48364815 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 44
48364695 ATTTTAACTG
* * * *
48364705 GCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCAATCT
1 GCTCCACTACAACTTCATGGAGATACGATTGGTTTATTCAATCT
* * * * *
48364749 GCTCCTCTACAACCTCGTGAAGATACGATTGG-TTATT-AGTCT
1 GCTCCACTACAACTTCATGGAGATACGATTGGTTTATTCAATCT
*
48364791 GCTCCGCTACAACTTCATGGAGATA
1 GCTCCACTACAACTTCATGGAGATA
48364816 AGACCTGATG
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 25 0.46
43 4 0.07
44 25 0.46
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (44 bp):
GCTCCACTACAACTTCATGGAGATACGATTGGTTTATTCAATCT
Found at i:48364846 original size:171 final size:173
Alignment explanation
Indices: 48364533--48364936 Score: 575
Period size: 171 Copynumber: 2.3 Consensus size: 173
48364523 CTTCGATCCA
* * * * * * * * *
48364533 CTCCACTGCAACATCAAGGATATAAGATTTGTTGCTTTAATCTGCTCCAT-TGCGACCTCGAGAA
1 CTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCAATCTGCTCC-TCTACAACCTCGAGAA
* * *
48364597 GATACGATTGGTTTATTCAGTCTGCTCCGCTGCAACTTTAGAGAGATAAGACCTAATGCAATTTG
65 GATACGATTGGTTTATTCAGTCTGCTCCGCTACAACTTCAGAGAGATAAGACCTAATGCAATCTG
*
48364662 CTCTACTGCAACTTTAAAGAGATAAGATCCATCATTTTAA-CTGG
130 CTCTACTGCAACTTCAAAGAGATAAGATCCATCATTTTAACCT-G
*
48364706 CTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCAATCTGCTCCTCTACAACCTCGTGAAG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCAATCTGCTCCTCTACAACCTCGAGAAG
* *
48364771 ATACGATTGG-TTATT-AGTCTGCTCCGCTACAACTTCATG-GAGATAAGACCTGATGCGATCTG
66 ATACGATTGGTTTATTCAGTCTGCTCCGCTACAACTTCA-GAGAGATAAGACCTAATGCAATCTG
* *
48364833 TTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAACCTG
130 CTCTACTGCAACTTCAAAGAGATAAGATCCATCATTTTAACCTG
*
48364877 CTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCAATCTGCTCCTCTACAACCTCG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCAATCTGCTCCTCTACAACCTCG
48364937 GGGAGGTAAA
Statistics
Matches: 209, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
171 137 0.66
172 9 0.04
173 63 0.30
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (173 bp):
CTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCAATCTGCTCCTCTACAACCTCGAGAAG
ATACGATTGGTTTATTCAGTCTGCTCCGCTACAACTTCAGAGAGATAAGACCTAATGCAATCTGC
TCTACTGCAACTTCAAAGAGATAAGATCCATCATTTTAACCTG
Found at i:48365054 original size:45 final size:46
Alignment explanation
Indices: 48364973--48365248 Score: 333
Period size: 45 Copynumber: 6.0 Consensus size: 46
48364963 TTTAGTCTGT
* *
48364973 TGCAATGCCAGGGAAATAAGATTCGATGCCTTCAGCTTTAATCTAC
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTAC
* * * *
48365019 TGTAATGCCAGGGAAA-AAGATTTGCTGCCTTCAGCTTTTATCTAC
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTAC
* * * * *
48365064 TACAACACCAGGTAAA-AAGATTTGTTGCCTTCAGCTTTAATCTAC
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTAC
*
48365109 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGC
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTAC
* * * *
48365155 T-CTACTGCCACGCTAGGAAAAAAGATTTGCTGCCTTTAGCTTTAATCTAC
1 TGCAAC-GCCA-G---GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTAC
*
48365205 TGCAACGCCAGAGAAATAAGATTCGCTGCCTTCAGCTTTAATCT
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCT
48365249 GCTCCACTGC
Statistics
Matches: 196, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
45 80 0.41
46 75 0.38
47 1 0.01
49 1 0.01
50 36 0.18
51 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (46 bp):
TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTAC
Found at i:48365200 original size:96 final size:95
Alignment explanation
Indices: 48364984--48365263 Score: 381
Period size: 96 Copynumber: 3.0 Consensus size: 95
48364974 GCAATGCCAG
* * * * *
48364984 GGAAATAAGATTCGATGCCTTCAGCTTTAATCTACTGTAATGCCAGGGAAA-AAGATTTGCTGCC
1 GGAAAAAAGATTTGATGCCTTCAGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTGCC
* * **
48365048 TTCAGCTTTTATCT--ACTAC-AACAC-CA
66 TTCAGCTTTAATCTGCTCTACTGCCACGCA
* *
48365074 GGTAAAAAGATTTGTTGCCTTCAGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTGCC
1 GGAAAAAAGATTTGATGCCTTCAGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTGCC
48365139 TTCAGCTTTAATCTGCTCTACTGCCACGCTA
66 TTCAGCTTTAATCTGCTCTACTGCCACGC-A
* * *
48365170 GGAAAAAAGATTTGCTGCCTTTAGCTTTAATCTACTGCAACGCCAGAGAAATAAGATTCGCTGCC
1 GGAAAAAAGATTTGATGCCTTCAGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTGCC
*
48365235 TTCAGCTTTAATCTGCTCCACTGCCACGC
66 TTCAGCTTTAATCTGCTCTACTGCCACGC
48365264 CAGGGGTATA
Statistics
Matches: 168, Mismatches: 16, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
90 45 0.27
91 25 0.15
93 4 0.02
94 3 0.02
95 1 0.01
96 90 0.54
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (95 bp):
GGAAAAAAGATTTGATGCCTTCAGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTGCC
TTCAGCTTTAATCTGCTCTACTGCCACGCA
Found at i:48369842 original size:30 final size:30
Alignment explanation
Indices: 48369802--48369860 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
48369792 CTGTTCTACC
48369802 ATCCTCAACAAG-TCTGAAGATAAAACACAA
1 ATCCTCAACAAGTTC-GAAGATAAAACACAA
* *
48369832 ATCCTTAACAAGTTCGAAGATAAACCACA
1 ATCCTCAACAAGTTCGAAGATAAAACACA
48369861 GTCTATGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.47, C:0.24, G:0.10, T:0.19
Consensus pattern (30 bp):
ATCCTCAACAAGTTCGAAGATAAAACACAA
Found at i:48375920 original size:16 final size:16
Alignment explanation
Indices: 48375899--48375932 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48375889 TTTTATGATG
* *
48375899 AAATGCTATGCAGTCA
1 AAATGCCATGCAATCA
48375915 AAATGCCATGCAATCA
1 AAATGCCATGCAATCA
48375931 AA
1 AA
48375933 GCAAAACACA
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:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (16 bp):
AAATGCCATGCAATCA
Found at i:48376319 original size:27 final size:27
Alignment explanation
Indices: 48376289--48376348 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
48376279 TCTCACTCCC
48376289 ACTTAAAGGGGTAAAATTGACCAACTT
1 ACTTAAAGGGGTAAAATTGACCAACTT
*
48376316 ACTTAAAGGGGTAAAATTGACTAACTT
1 ACTTAAAGGGGTAAAATTGACCAACTT
48376343 ACTTAA
1 ACTTAA
48376349 TGCAAAATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (27 bp):
ACTTAAAGGGGTAAAATTGACCAACTT
Found at i:48377495 original size:17 final size:18
Alignment explanation
Indices: 48377462--48377495 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48377452 ACAAGCCAAT
48377462 ATAAAAAATAATGATAAA
1 ATAAAAAATAATGATAAA
*
48377480 ATAAAAACTAAT-ATAA
1 ATAAAAAATAATGATAA
48377496 GATGGATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (18 bp):
ATAAAAAATAATGATAAA
Found at i:48377543 original size:12 final size:12
Alignment explanation
Indices: 48377528--48377560 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
48377518 AGTAAATAAG
48377528 TAAATAAAATAT
1 TAAATAAAATAT
*
48377540 TAAATGAAATAT
1 TAAATAAAATAT
48377552 TAAATAAAA
1 TAAATAAAA
48377561 CAGTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (12 bp):
TAAATAAAATAT
Found at i:48377567 original size:12 final size:12
Alignment explanation
Indices: 48377521--48377572 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
48377511 GAGAGTAAGT
48377521 AAATAAGTAAATA
1 AAAT-AGTAAATA
* *
48377534 AAATATTAAATG
1 AAATAGTAAATA
*
48377546 AAATATTAAATA
1 AAATAGTAAATA
*
48377558 AAACAGTAAA-A
1 AAATAGTAAATA
48377569 AAAT
1 AAAT
48377573 GATGAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 4 0.12
12 25 0.76
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (12 bp):
AAATAGTAAATA
Found at i:48377750 original size:17 final size:16
Alignment explanation
Indices: 48377702--48377738 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
48377692 TTAAGATTTA
*
48377702 AATATACATAAAAAAT
1 AATATATATAAAAAAT
48377718 AATATATATAAAAAAT
1 AATATATATAAAAAAT
48377734 AATAT
1 AATAT
48377739 TAACTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AATATATATAAAAAAT
Found at i:48381244 original size:30 final size:30
Alignment explanation
Indices: 48381147--48381318 Score: 275
Period size: 29 Copynumber: 5.9 Consensus size: 30
48381137 TATATGTATA
* *
48381147 ATATACAAATCAATTCGACAA--TATATAC
1 ATATACAAATCAATTCGGCAATGTATATCC
*
48381175 GTATACAAATCAATTCGGCAATGTATATCC
1 ATATACAAATCAATTCGGCAATGTATATCC
48381205 ATA-ACAAATCAATTCGGCAATGTATATCC
1 ATATACAAATCAATTCGGCAATGTATATCC
48381234 ATATACAAATCAATTCGGCAATGTATATCC
1 ATATACAAATCAATTCGGCAATGTATATCC
48381264 ATA-ACAAATCAATTCGGCAATGTATATCC
1 ATATACAAATCAATTCGGCAATGTATATCC
48381293 ATATACAAATCAATTCGG-AA-GTATAT
1 ATATACAAATCAATTCGGCAATGTATAT
48381319 AAAACATATA
Statistics
Matches: 136, Mismatches: 4, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
28 25 0.18
29 60 0.44
30 51 0.38
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (30 bp):
ATATACAAATCAATTCGGCAATGTATATCC
Found at i:48381248 original size:59 final size:59
Alignment explanation
Indices: 48381151--48381318 Score: 281
Period size: 59 Copynumber: 2.9 Consensus size: 59
48381141 TGTATAATAT
* * *
48381151 ACAAATCAATTCGACAA--TATATACGTATACAAATCAATTCGGCAATGTATATCCATA
1 ACAAATCAATTCGGCAATGTATATCCATATACAAATCAATTCGGCAATGTATATCCATA
48381208 ACAAATCAATTCGGCAATGTATATCCATATACAAATCAATTCGGCAATGTATATCCATA
1 ACAAATCAATTCGGCAATGTATATCCATATACAAATCAATTCGGCAATGTATATCCATA
48381267 ACAAATCAATTCGGCAATGTATATCCATATACAAATCAATTCGG-AA-GTATAT
1 ACAAATCAATTCGGCAATGTATATCCATATACAAATCAATTCGGCAATGTATAT
48381319 AAAACATATA
Statistics
Matches: 106, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
57 22 0.21
58 2 0.02
59 82 0.77
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (59 bp):
ACAAATCAATTCGGCAATGTATATCCATATACAAATCAATTCGGCAATGTATATCCATA
Found at i:48382899 original size:30 final size:30
Alignment explanation
Indices: 48382842--48382897 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
48382832 TTATATATAT
* *
48382842 ATATGCATACTTACATTGTTTTATTTTACG
1 ATATACATACTTACATTCTTTTATTTTACG
*
48382872 ATATACATACTTATA-TCTTTTATTTT
1 ATATACATACTTACATTCTTTTATTTT
48382898 TATGTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.54
Consensus pattern (30 bp):
ATATACATACTTACATTCTTTTATTTTACG
Found at i:48384961 original size:20 final size:20
Alignment explanation
Indices: 48384936--48384973 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
48384926 ACGGTATCGA
48384936 AACAAAGGTTAGAAAAATGG
1 AACAAAGGTTAGAAAAATGG
*
48384956 AACAAAGGTTGGAAAAAT
1 AACAAAGGTTAGAAAAAT
48384974 TAGAGCGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.24, T:0.16
Consensus pattern (20 bp):
AACAAAGGTTAGAAAAATGG
Found at i:48387512 original size:21 final size:21
Alignment explanation
Indices: 48387488--48387527 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
48387478 AAGAGAGATG
48387488 AAAAATGAAAA-TGAAAATGAA
1 AAAAATGAAAAGT-AAAATGAA
48387509 AAAAATGAAAAGTAAAATG
1 AAAAATGAAAAGTAAAATG
48387528 GAGAGGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAAATGAAAAGTAAAATGAA
Found at i:48388974 original size:86 final size:86
Alignment explanation
Indices: 48388742--48389935 Score: 1792
Period size: 86 Copynumber: 13.9 Consensus size: 86
48388732 AGATCAGTGA
* *
48388742 AGATCGAAAATAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAA-AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
** *
48388807 CTTCCTGCGTTAACAGTAAAGT
65 CTTCCTGCGTTAACAGCGAAGC
* * *
48388829 AGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAACAGATCTTGC
1 AGATCGAAAA-AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
*
48388894 CTTCCTGCGTTAACAACGAAGC
65 CTTCCTGCGTTAACAGCGAAGC
* *
48388916 AGATCGAAAAAAAACCTTGCCTCCATCAGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
1 AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
48388981 TTCCTGCGTTAACAGCGAAGC
66 TTCCTGCGTTAACAGCGAAGC
48389002 AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
1 AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
**
48389067 TTCCTGCGTTAACAATGAAGC
66 TTCCTGCGTTAACAGCGAAGC
48389088 AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
1 AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
*
48389153 TTCCTGCGTTAACAGTGAAGC
66 TTCCTGCGTTAACAGCGAAGC
*
48389174 AGATCG-AAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCC
1 AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
48389237 TTCCTGCGTTAACAGCGAAGC
66 TTCCTGCGTTAACAGCGAAGC
48389258 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
1 AGATCGAAAA-AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
*
48389323 CTTCCTGCATTAACAGCGAAGC
65 CTTCCTGCGTTAACAGCGAAGC
* * *
48389345 AAATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGTAGATCTTGCA
1 AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
*
48389410 TTCCTACGTTAACAGCGAAGC
66 TTCCTGCGTTAACAGCGAAGC
* * *
48389431 AGCTCGAGAAAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
1 AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
*
48389496 TTCCTGCGTTAACAGCAAAGC
66 TTCCTGCGTTAACAGCGAAGC
* * *
48389517 AGATC-AGAAAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTTAAAGA-AGCAGATCTTGCC
1 AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
**
48389580 TTCCTATGTTAACAGCGAAGC
66 TTCCTGCGTTAACAGCGAAGC
* * *
48389601 AGATCGAAAACAAAGTCTTGCCTCCATCGGTTGCAGTGGAGCTAGTTAAAGA-AGCAGATCTTGC
1 AGATCGAAAA-AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
*
48389665 CTTCCTGCGTTAACAACGAAGC
65 CTTCCTGCGTTAACAGCGAAGC
* *
48389687 AGATCGAAAAGAAAGCTTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGC
1 AGATCGAAAA-AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
48389751 CTTCCTGCGTTAACAGCGAAGC
65 CTTCCTGCGTTAACAGCGAAGC
* * * * *
48389773 AGATCAAAAACAAAACCTTGCCTCCATCGGTTGCAGTGGAGCTAGTTGAAGACAACAGATCTTGC
1 AGATCGAAAA-AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
* * *
48389838 CTTTCTGCCTTGACAGCGAAGC
65 CTTCCTGCGTTAACAGCGAAGC
* * ** * *
48389860 AGATCGAAGACACAAA-CCTTACCTCTC-TCGGTTGTAGCAGAGCTGGTTGAAGACAACAGATCT
1 AGATCGAA-A-A-AAAGCCTTGCCTC-CATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCT
*
48389923 TGCCTTTCTGCGT
62 TGCCTTCCTGCGT
48389936 CGACAGTGAA
Statistics
Matches: 1027, Mismatches: 71, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
84 75 0.07
85 91 0.09
86 633 0.62
87 169 0.16
88 53 0.05
89 6 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (86 bp):
AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
TTCCTGCGTTAACAGCGAAGC
Found at i:48389381 original size:343 final size:346
Alignment explanation
Indices: 48388742--48389935 Score: 1807
Period size: 343 Copynumber: 3.5 Consensus size: 346
48388732 AGATCAGTGA
* * *
48388742 AGATCGAAAATAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
* * * * *
48388807 CTTCCTGCGTTAACAGTAAAGTAGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAATGGAGCT
66 CTTCCTGCGTTAACAGCAAAGCAGATCG-AAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCT
* * *
48388872 GGTTAAAGATAACAGATCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAA-AAAACCTTGC
130 GGTTAAAGACAACAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGC
*
48388936 CTCCATCAGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAG
195 CTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAG
48389001 CAGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
260 CAGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
**
48389066 CTTCCTGCGTTAACAATGAAGC
325 CTTCCTGCGTTAACAGCGAAGC
48389088 AGATCGAAAA-AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
** *
48389152 CTTCCTGCGTTAACAGTGAAGCAGATCGAAA-AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTG
66 CTTCCTGCGTTAACAGCAAAGCAGATCGAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTG
*
48389216 GTTAAAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCC
131 GTTAAAGACAACAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCC
*
48389280 TCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGC
196 TCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGC
* * *
48389345 AAATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGTAGATCTTGCA
261 AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
*
48389410 TTCCTACGTTAACAGCGAAGC
326 TTCCTGCGTTAACAGCGAAGC
* * *
48389431 AGCTCGAGAA-AAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
48389495 CTTCCTGCGTTAACAGCAAAGCAGATC-AGAA-AAAGCCTTGCCTCCATCGGTTGCAGTAGAGCT
66 CTTCCTGCGTTAACAGCAAAGCAGATCGA-AACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCT
* ** *
48389558 GGTTAAAGA-AGCAGATCTTGCCTTCCTATGTTAACAGCGAAGCAGATCGAAAACAAAGTCTTGC
130 GGTTAAAGACAACAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGC
* * *
48389622 CTCCATCGGTTGCAGTGGAGCTAGTTAAAGA-AGCAGATCTTGCCTTCCTGCGTTAACAACGAAG
195 CTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAG
* *
48389686 CAGATCGAAAAGAAAGCTTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTG
260 CAGATCGAAAA-AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTG
48389750 CCTTCCTGCGTTAACAGCGAAGC
324 CCTTCCTGCGTTAACAGCGAAGC
* * * * *
48389773 AGATCAAAAACAAAACCTTGCCTCCATCGGTTGCAGTGGAGCTAGTTGAAGACAACAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
* * * * * * * *
48389838 CTTTCTGCCTTGACAGCGAAGCAGATCGAAGACACAAACCTTACCTCTC-TCGGTTGTAGCAGAG
66 CTTCCTGCGTTAACAGCAAAGCAGATCGAA-ACA-AAGCCTTGCCTC-CATCGGTTGCAGTAGAG
* *
48389902 CTGGTTGAAGACAACAGATCTTGCCTTTCTGCGT
128 CTGGTTAAAGACAACAGATCTTGCCTTCCTGCGT
48389936 CGACAGTGAA
Statistics
Matches: 782, Mismatches: 56, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
342 122 0.16
343 514 0.66
344 5 0.01
345 79 0.10
346 43 0.05
347 19 0.02
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (346 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCAAAGCAGATCGAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTG
GTTAAAGACAACAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCC
TCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGC
AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
TTCCTGCGTTAACAGCGAAGC
Found at i:48389623 original size:429 final size:430
Alignment explanation
Indices: 48388742--48389935 Score: 1858
Period size: 429 Copynumber: 2.8 Consensus size: 430
48388732 AGATCAGTGA
*
48388742 AGATCGAAAATAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAA-AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGC
** * * *
48388807 CTTCCTGCGTTAACAGTAAAGTAGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAATGGAGCT
64 CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
* *
48388872 GGTTAAAGATAACAGATCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAAAAAACCTTGCC
129 GGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAAAAACCTTGCC
*
48388937 TCCATCAGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGC
194 TCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGC
* *
48389002 AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
259 AGATCGAGAAAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
** *
48389067 TTCCTGCGTTAACAATGAAGCAGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
324 TTCCTGCGTTAACAACAAAGCAGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGG
* * *
48389132 TTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGTGAAGC
389 TTAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGC
48389174 AGATCG-AAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCT
1 AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCT
48389238 TCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
66 TCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
* * * *
48389303 TTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAAATCGAAAAAAAGCCTTGCCTC
131 TTAAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAAAAACCTTGCCTC
* * *
48389368 CATCGGTTGCAGTGGAGCTGGTTGAAGATAGTAGATCTTGCATTCCTACGTTAACAGCGAAGCAG
196 CATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAG
*
48389433 CTCGAGAAAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTT
261 ATCGAGAAAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTT
* *
48389498 CCTGCGTTAACAGCAAAGCAGATC-AGAAAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTT
326 CCTGCGTTAACAACAAAGCAGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTT
*
48389562 AAAGA-AGCAGATCTTGCCTTCCTATGTTAACAGCGAAGC
391 AAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGC
* *
48389601 AGATCGAAAACAAAGTCTTGCCTCCATCGGTTGCAGTGGAGCTAGTTAAAGAAGCAGATCTTGCC
1 AGATCGAAAA-AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCC
* * *
48389666 TTCCTGCGTTAACAACGAAGCAGATCGAAAAGAAAGCTTTGCCTCCATCGGTTGCAGTGGAGCTG
65 TTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTG
*
48389731 GTTAAAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCAAAAACAAAACCTTGCC
130 GTTAAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAA-AAAACCTTGCC
* * * * * *
48389795 TCCATCGGTTGCAGTGGAGCTAGTTGAAGACAACAGATCTTGCCTTTCTGCCTTGACAGCGAAGC
194 TCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGC
* * * ** * *
48389860 AGATCGAAGACACAAA-CCTTACCTCTCTCGGTTGTAGCAGAGCTGGTTGAAGACAACAGATCTT
259 AGATCG-AGA-A-AAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTT
*
48389924 GCCTTTCTGCGT
321 GCCTTCCTGCGT
48389936 CGACAGTGAA
Statistics
Matches: 700, Mismatches: 56, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
427 37 0.05
428 86 0.12
429 469 0.67
430 43 0.06
431 56 0.08
432 9 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (430 bp):
AGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCT
TCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
TTAAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAAAAACCTTGCCTC
CATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAG
ATCGAGAAAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTT
CCTGCGTTAACAACAAAGCAGATCGAAAAAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTT
AAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGC
Found at i:48389871 original size:45 final size:45
Alignment explanation
Indices: 48389741--48389958 Score: 132
Period size: 44 Copynumber: 5.0 Consensus size: 45
48389731 GTTAAAGAAG
* * ** *
48389741 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCAAAAACAA
1 CAGATCTTGCCTTTCTGCGTTGACAGCGAAGCAGATTGAAGACAA
* * * *
48389786 -A-ACCTTGCC-TCCAT-CGGTTG-CAGTGGAGCTAG-TTGAAGACAA
1 CAGATCTTGCCTTTC-TGC-GTTGACAGCGAAGC-AGATTGAAGACAA
* *
48389828 CAGATCTTGCCTTTCTGCCTTGACAGCGAAGCAGATCGAAGAC-A
1 CAGATCTTGCCTTTCTGCGTTGACAGCGAAGCAGATTGAAGACAA
* * * * * * *
48389872 CAAACCTTACCTCTCT-CGGTTG-TAGC-AGAGCTGGTTGAAGACAA
1 CAGATCTTGCCTTTCTGC-GTTGACAGCGA-AGCAGATTGAAGACAA
* * *
48389916 CAGATCTTGCCTTTCTGCGTCGACAGTGAAGTAGATTGAAGAC
1 CAGATCTTGCCTTTCTGCGTTGACAGCGAAGCAGATTGAAGAC
48389959 GATAAATCCC
Statistics
Matches: 126, Mismatches: 32, Indels: 30
0.67 0.17 0.16
Matches are distributed among these distances:
42 19 0.15
43 29 0.23
44 46 0.37
45 31 0.25
46 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (45 bp):
CAGATCTTGCCTTTCTGCGTTGACAGCGAAGCAGATTGAAGACAA
Found at i:48391704 original size:30 final size:30
Alignment explanation
Indices: 48391647--48391702 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
48391637 ATATATATAT
* *
48391647 ATATGCATACTTACATTGTTTTATTTTACG
1 ATATACATACTTACATTATTTTATTTTACG
*
48391677 ATATACATACTTATA-TATTTTATTTT
1 ATATACATACTTACATTATTTTATTTT
48391703 TATGTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (30 bp):
ATATACATACTTACATTATTTTATTTTACG
Found at i:48397084 original size:13 final size:13
Alignment explanation
Indices: 48397066--48397091 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48397056 AAGGTTAATT
48397066 TTATGTCATTGTA
1 TTATGTCATTGTA
48397079 TTATGTCATTGTA
1 TTATGTCATTGTA
48397092 ATTGTGATAT
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:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
TTATGTCATTGTA
Found at i:48403856 original size:25 final size:25
Alignment explanation
Indices: 48403807--48403878 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
48403797 GAGGGTAAAG
*
48403807 AAATGAAAT-GATGACATAAATAAAT
1 AAAT-AAATAGATGACATAAAAAAAT
48403832 AAATAAATAGATGA-ATAAAGAAAAT
1 AAATAAATAGATGACATAAA-AAAAT
* * *
48403857 AAATAAAAAGATAAAATAAAAA
1 AAATAAATAGATGACATAAAAA
48403879 TGTCATACTC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 9 0.22
25 27 0.66
26 5 0.12
ACGTcount: A:0.69, C:0.01, G:0.10, T:0.19
Consensus pattern (25 bp):
AAATAAATAGATGACATAAAAAAAT
Found at i:48404018 original size:2 final size:2
Alignment explanation
Indices: 48404011--48404049 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
48404001 ATAAGGGCAA
48404011 AT AT 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 AT AT A
48404050 AATGCTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48404121 original size:15 final size:15
Alignment explanation
Indices: 48404103--48404184 Score: 51
Period size: 15 Copynumber: 5.3 Consensus size: 15
48404093 ATTTAAAAAG
48404103 TAAAAGAATAATAAA
1 TAAAAGAATAATAAA
48404118 TAAATAG-ATAA-AAA
1 TAAA-AGAATAATAAA
* *
48404132 TATAAAAAATATTAAA
1 TA-AAAGAATAATAAA
** * *
48404148 TTTAAGTATTTTAAAAAA
1 TAAAAG-A--ATAATAAA
48404166 TAAAAGAATAATAAA
1 TAAAAGAATAATAAA
48404181 TAAA
1 TAAA
48404185 TTGATAAAAC
Statistics
Matches: 48, Mismatches: 12, Indels: 14
0.65 0.16 0.19
Matches are distributed among these distances:
14 6 0.12
15 25 0.52
16 7 0.15
17 1 0.02
18 9 0.19
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
TAAAAGAATAATAAA
Found at i:48404183 original size:63 final size:63
Alignment explanation
Indices: 48404067--48404448 Score: 383
Period size: 69 Copynumber: 6.0 Consensus size: 63
48404057 AATGAAAAGG
* *
48404067 AAATATAAGTAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGAT-AA
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAATAAAAGAATAATAAATAAATAGATAAA
* * * *
48404129 AAATATAAAAAATATTAAATTTAAGTATTTTAAAAAATAAAAGAATAATAAATAAATTGATAAAA
1 AAATATAAATAATATCAAATTTAAATA-TTTAAAAAATAAAAGAATAATAAATAAATAGAT-AAA
* *
48404194 CAAATATAAATAATATCAAATTTAAATGTTTAAAAAAGTAGAAGAATAACAAATAAATAAATAGA
1 -AAATATAAATAATATCAAATTTAAATATTTAAAAAA-TAAAAGAAT----AATAAATAAATAGA
48404259 TAAA
60 TAAA
*
48404263 ACGAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAG-----
1 A--AATATAAATAATATCAAATTTAAATATTTAAAAAATAAAAGAATAATAAATAAATAGATAAA
* *
48404323 ------AAATAATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAATAAATAGATA
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAATAAAAGAAT----AATAAATAAATAGAT-
48404382 AAA
61 AAA
* * * * * *
48404385 CAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAACAAATAAATAAATAAA
1 -AAATATAAATAATATCAAATTTAAATATTTAAAAAATAAAAGAATAATAAATAAATAGATAAA
48404449 TAGATAAAAC
Statistics
Matches: 271, Mismatches: 21, Indels: 54
0.78 0.06 0.16
Matches are distributed among these distances:
52 38 0.14
56 13 0.05
62 23 0.08
63 31 0.11
64 3 0.01
65 37 0.14
66 31 0.11
68 1 0.00
69 47 0.17
70 47 0.17
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.28
Consensus pattern (63 bp):
AAATATAAATAATATCAAATTTAAATATTTAAAAAATAAAAGAATAATAAATAAATAGATAAA
Found at i:48404183 original size:70 final size:68
Alignment explanation
Indices: 48404067--48404315 Score: 231
Period size: 66 Copynumber: 3.8 Consensus size: 68
48404057 AATGAAAAGG
* *
48404067 AAATATAAGTAATATCAAATTTAA-ATATTTAAAAAGTAAAAG---AAT---AATAAATAAATAG
1 AAATATAAATAATATCAAATTTAATAT-TTTAAAAAATAAAAGAATAATAAAAATAAATAAATAG
48404125 ATAA
65 ATAA
* * **
48404129 AAATATAAAAAATATTAAATTTAAGTATTTTAAAAAATAAAAGAATAAT--AAATAAATTGATA-
1 AAATATAAATAATATCAAATTTAA-TATTTTAAAAAATAAAAGAATAATAAAAATAAATAAATAG
48404191 A-AA
65 ATAA
* *
48404194 CAAATATAAATAATATCAAATTTAA-ATGTTTAAAAAAGTAGAAGAAT-A-ACAAATAAATAAAT
1 -AAATATAAATAATATCAAATTTAATAT-TTTAAAAAA-TAAAAGAATAATAAAAATAAATAAAT
48404256 AGATAAA
63 AGAT-AA
*
48404263 ACGAATATAAATAATATCAAATTTAA-ATATTTAAAAAGTAAAAGAATAATAAA
1 A--AATATAAATAATATCAAATTTAATAT-TTTAAAAAATAAAAGAATAATAAA
48404316 TAAATAGAAA
Statistics
Matches: 154, Mismatches: 15, Indels: 27
0.79 0.08 0.14
Matches are distributed among these distances:
62 21 0.14
63 14 0.09
64 4 0.03
65 12 0.08
66 45 0.29
67 11 0.07
68 1 0.01
69 10 0.06
70 34 0.22
71 2 0.01
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (68 bp):
AAATATAAATAATATCAAATTTAATATTTTAAAAAATAAAAGAATAATAAAAATAAATAAATAGA
TAA
Found at i:48404215 original size:66 final size:65
Alignment explanation
Indices: 48404067--48404448 Score: 382
Period size: 70 Copynumber: 6.0 Consensus size: 65
48404057 AATGAAAAGG
* *
48404067 AAATATAAGTAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGAT--AA-
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAATAAAAGAATAATAAATAAATAGATAAAAC
* * * *
48404129 AAATATAAAAAATATTAAATTTAAGTATTTTAAAAAATAAAAGAATAATAAATAAATTGATAAAA
1 AAATATAAATAATATCAAATTTAAATA-TTTAAAAAATAAAAGAATAATAAATAAATAGATAAAA
48404194 C
65 C
* *
48404195 AAATATAAATAATATCAAATTTAAATGTTTAAAAAAGTAGAAGAATAACAAATAAATAAATAGAT
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAA-TAAAAGAAT----AATAAATAAATAGAT
48404260 AAAAC
61 AAAAC
* *
48404265 GAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAG---AAA-
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAATAAAAGAATAATAAATAAATAGATAAAAC
* ** *
48404326 TAATATCAAAT--T-T-AAATGTTTAAA-AAGTAAAAGAAT--AA-CA-AATAAATAAATAGATA
1 AAATAT-AAATAATATCAAA--TTTAAATATTTAAAA-AATAAAAGAATAATAAATAAATAGATA
48404382 AAAC
62 AAAC
* * * * * *
48404386 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAACAAATAAATAAATAAA
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAATAAAAGAATAATAAATAAATAGATAAA
48404449 TAGATAAAAC
Statistics
Matches: 264, Mismatches: 30, Indels: 49
0.77 0.09 0.14
Matches are distributed among these distances:
56 13 0.05
57 1 0.00
58 5 0.02
59 14 0.05
60 13 0.05
61 14 0.05
62 37 0.14
63 35 0.13
64 1 0.00
65 40 0.15
66 31 0.12
69 8 0.03
70 52 0.20
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.28
Consensus pattern (65 bp):
AAATATAAATAATATCAAATTTAAATATTTAAAAAATAAAAGAATAATAAATAAATAGATAAAAC
Found at i:48404315 original size:26 final size:26
Alignment explanation
Indices: 48404286--48404369 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
48404276 ATATCAAATT
48404286 TAAATATTTAAAAAGTAAAAGAATAA
1 TAAATATTTAAAAAGTAAAAGAATAA
** * *
48404312 TAAATAAATAGAAA-TAATATCA-AAT-T
1 TAAATATTTAAAAAGTAA-A--AGAATAA
*
48404338 TAAATGTTTAAAAAGTAAAAGAATAA
1 TAAATATTTAAAAAGTAAAAGAATAA
*
48404364 CAAATA
1 TAAATA
48404370 AATAAATAGA
Statistics
Matches: 41, Mismatches: 11, Indels: 12
0.64 0.17 0.19
Matches are distributed among these distances:
24 1 0.02
25 6 0.15
26 27 0.66
27 6 0.15
28 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.27
Consensus pattern (26 bp):
TAAATATTTAAAAAGTAAAAGAATAA
Found at i:48404337 original size:52 final size:52
Alignment explanation
Indices: 48404266--48404396 Score: 192
Period size: 52 Copynumber: 2.5 Consensus size: 52
48404256 AGATAAAACG
* *
48404266 AATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATA
1 AATAAAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATA
* *
48404318 AATAGAAATAATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAACAAATA
1 AATAAAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATA
*
48404370 AATAAATAGATAA-AACAAATTTAAATA
1 AATAAA-A-ATAATATCAAATTTAAATA
48404397 ATATCAAATT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
52 54 0.76
53 13 0.18
54 4 0.06
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.28
Consensus pattern (52 bp):
AATAAAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATA
Found at i:48404381 original size:121 final size:122
Alignment explanation
Indices: 48404195--48404442 Score: 426
Period size: 121 Copynumber: 2.0 Consensus size: 122
48404185 TTGATAAAAC
* *
48404195 AAATATAAATAATATCAAATTTAAATGTTTAAAAAAGTAGAAGAATAACAAATAAATAAATAGAT
1 AAATAGAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAGAT
* *
48404260 AAAACGAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAAT
66 AAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAAT
48404317 AAATAGAAATAATATCAAATTTAAATGTTT-AAAAAGTAAAAGAATAACAAATAAATAAATAGAT
1 AAATAGAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAGAT
* * *
48404381 AAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAACAAAT
66 AAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAAT
48404438 AAATA
1 AAATA
48404443 AATAAATAGA
Statistics
Matches: 119, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
121 90 0.76
122 29 0.24
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (122 bp):
AAATAGAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAGAT
AAAACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAAT
Found at i:48406013 original size:44 final size:44
Alignment explanation
Indices: 48405965--48406436 Score: 452
Period size: 44 Copynumber: 10.9 Consensus size: 44
48405955 GATTTGTCTT
* *
48405965 TTCAATTTGCTCCACTGCAACTTCAGGGAGATAAGACTCACTAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTAC
*
48406009 TTCAATCTTGCTCCACT---A---CAGGGAGATAAGACTCACTAC
1 TTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTCACTAC
* *
48406048 TTCAATCTTGCTCCACTACAACTTCAGGGAGATAAGATTTA-TAGC
1 TTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTCACTA-C
* * * *
48406093 TTCAACCTGCTCCACTGCAACTTCAGGGAGACAAAATTC-GTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTA-C
* * *
48406137 TTTAATCTGCTCCACTGCGACTTCAGGGAGATAAGGTTCACT--
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTAC
* *
48406179 TT-AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTC-GTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACT-AC
* * * * * * *
48406222 CTCAATCTGCTCCGCTACAACTTCAAGGATATTAGATTC-GTGAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACT-AC
* * * * *
48406266 TTTAATCTACTCCACTGCAACTTCAAGGAGATAAGACTCACTAT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTAC
**
48406310 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTA-C
* * * **
48406354 TTC-ATCTTGCTCCACTGCATCTTTAGGAAGATAAGATTTGCTATC
1 TTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTCACTA-C
*
48406399 TTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
48406437 TGTGGCTTCA
Statistics
Matches: 355, Mismatches: 54, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
39 38 0.11
40 1 0.00
41 33 0.09
42 4 0.01
43 6 0.02
44 204 0.57
45 66 0.19
46 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (44 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTAC
Found at i:48406042 original size:39 final size:39
Alignment explanation
Indices: 48405988--48406067 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
48405978 ACTGCAACTT
48405988 CAGGGAGATAAGACTCACTACTTCAATCTTGCTCCACTA
1 CAGGGAGATAAGACTCACTACTTCAATCTTGCTCCACTA
48406027 CAGGGAGATAAGACTCACTACTTCAATCTTGCTCCACTA
1 CAGGGAGATAAGACTCACTACTTCAATCTTGCTCCACTA
48406066 CA
1 CA
48406068 ACTTCAGGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (39 bp):
CAGGGAGATAAGACTCACTACTTCAATCTTGCTCCACTA
Found at i:48409572 original size:16 final size:16
Alignment explanation
Indices: 48409551--48409583 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
48409541 TTGCTTGAAC
48409551 TATTATATCGATCAAT
1 TATTATATCGATCAAT
48409567 TATTATATCGATCAAT
1 TATTATATCGATCAAT
48409583 T
1 T
48409584 TTTAAACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (16 bp):
TATTATATCGATCAAT
Found at i:48413312 original size:22 final size:21
Alignment explanation
Indices: 48413294--48413367 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
48413284 TTTATAAATT
*
48413294 TAATTTTTATAATTAATAAAAA
1 TAATTATTAT-ATTAATAAAAA
*
48413316 TAATTATTATATTAATATATTAA
1 TAATTATTATATTAATA-A-AAA
*
48413339 T-ATTAATACTATTAA-ATAAAA
1 TAATTATTA-TATTAATA-AAAA
48413360 TAATTATT
1 TAATTATT
48413368 TAATTTAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 10 0.23
22 24 0.56
23 9 0.21
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATTATTATATTAATAAAAA
Found at i:48418871 original size:24 final size:24
Alignment explanation
Indices: 48418844--48418895 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
48418834 TTAGTAAGTC
*
48418844 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* * *
48418868 AAATATATTATACTAATAAGTACT
1 AAATAAACTATACTAATAAATACT
48418892 AAAT
1 AAAT
48418896 CTTCTAGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:48420475 original size:8 final size:8
Alignment explanation
Indices: 48420423--48420499 Score: 50
Period size: 8 Copynumber: 9.1 Consensus size: 8
48420413 ATAATTTTTT
48420423 TTATAATA
1 TTATAATA
*
48420431 TTATTATA
1 TTATAATA
*
48420439 ATATAATTAA
1 TTATAA-T-A
* *
48420449 TTTTTATA
1 TTATAATA
48420457 TT-T-ATA
1 TTATAATA
48420463 TTTATAATA
1 -TTATAATA
48420472 TTATAATA
1 TTATAATA
48420480 TTATATAATA
1 -T-TATAATA
48420490 TTAATAATA
1 TT-ATAATA
48420499 T
1 T
48420500 ATTATGTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
6 3 0.05
7 3 0.05
8 24 0.44
9 14 0.25
10 11 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
TTATAATA
Found at i:48440988 original size:30 final size:30
Alignment explanation
Indices: 48440945--48441005 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
48440935 TATAACTTGC
* *
48440945 ATAATTTACATAACTTATAAATTTTTAATAT
1 ATAACTTACATAACTTATAAATATTT-ATAT
*
48440976 ATAACTTA-ATAACTTATTAATATTTATAT
1 ATAACTTACATAACTTATAAATATTTATAT
48441005 A
1 A
48441006 CATTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 15 0.56
31 7 0.26
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (30 bp):
ATAACTTACATAACTTATAAATATTTATAT
Found at i:48440995 original size:23 final size:22
Alignment explanation
Indices: 48440954--48440998 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
48440944 CATAATTTAC
*
48440954 ATAACTTATAAATTTTTAATAT
1 ATAACTTATAAATTATTAATAT
*
48440976 ATAACTTAATAACTTATTAATAT
1 ATAACTT-ATAAATTATTAATAT
48440999 TTATATACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAACTTATAAATTATTAATAT
Found at i:48441036 original size:19 final size:19
Alignment explanation
Indices: 48441014--48441057 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
48441004 TACATTTTTA
*
48441014 ATATATTTATTAAAAATTT
1 ATATATTTATTAAAAACTT
* *
48441033 ATATATTTTTTAATAACTT
1 ATATATTTATTAAAAACTT
48441052 ATATAT
1 ATATAT
48441058 AACTTTCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATATTTATTAAAAACTT
Found at i:48441038 original size:21 final size:20
Alignment explanation
Indices: 48441010--48441058 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
48441000 TATATACATT
48441010 TTTA-ATATATTTATTAAAAA
1 TTTATATATATTT-TTAAAAA
*
48441030 TTTATATAT-TTTTTAATAA
1 TTTATATATATTTTTAAAAA
*
48441049 CTTATATATA
1 TTTATATATA
48441059 ACTTTCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 14 0.56
20 7 0.28
21 4 0.16
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATATATATTTTTAAAAA
Found at i:48441070 original size:9 final size:9
Alignment explanation
Indices: 48441056--48441521 Score: 115
Period size: 9 Copynumber: 53.9 Consensus size: 9
48441046 TAACTTATAT
*
48441056 ATAACTTTC
1 ATAACTTAC
48441065 ATAACTTAC
1 ATAACTTAC
48441074 ATAA--TAC
1 ATAACTTAC
* *
48441081 ATAGCCTAC
1 ATAACTTAC
* *
48441090 ATGACTTGC
1 ATAACTTAC
48441099 ATAA--TAC
1 ATAACTTAC
*
48441106 ACAACTTAC
1 ATAACTTAC
*
48441115 ATAAATTAC
1 ATAACTTAC
48441124 ATAA--TAC
1 ATAACTTAC
*
48441131 ATAACTTTC
1 ATAACTTAC
48441140 ATAACTTAC
1 ATAACTTAC
*
48441149 ATTA--TAC
1 ATAACTTAC
*
48441156 ATAACTTAT
1 ATAACTTAC
*
48441165 A-AATCATATC
1 ATAA-CTTA-C
48441175 ATAACTTAC
1 ATAACTTAC
48441184 ATAAC-T-C
1 ATAACTTAC
*
48441191 A-AATTTATC
1 ATAACTTA-C
* *
48441200 A-ATCATATC
1 ATAACTTA-C
*
48441209 ATAACTTATAT
1 ATAAC-T-TAC
48441220 ATACACTTAC
1 ATA-ACTTAC
48441230 ATAA--TAC
1 ATAACTTAC
* *
48441237 ATAA-ATAA
1 ATAACTTAC
*** *
48441245 ATTTTTTAT
1 ATAACTTAC
* *
48441254 TTATTCTTAC
1 ATA-ACTTAC
48441264 ATAA--TAC
1 ATAACTTAC
*
48441271 ATAACTTAAATA
1 ATAACTT--A-C
*
48441283 ATAACCTAC
1 ATAACTTAC
48441292 ATAACTTAC
1 ATAACTTAC
*
48441301 ATAGAAACTTAT
1 AT---AACTTAC
*
48441313 ATAGGAACTTGC
1 AT---AACTTAC
*
48441325 ATAACTTAT
1 ATAACTTAC
48441334 ATAACTTA-
1 ATAACTTAC
* *
48441342 AAAACTTAG
1 ATAACTTAC
48441351 ATAA--TAC
1 ATAACTTAC
* *
48441358 ATAGCCTAC
1 ATAACTTAC
*
48441367 ATAACTTAT
1 ATAACTTAC
48441376 ATAACTTAC
1 ATAACTTAC
48441385 ATAA--TAC
1 ATAACTTAC
**
48441392 ACCACTTAC
1 ATAACTTAC
48441401 AT-A---A-
1 ATAACTTAC
*
48441405 ATAACTTGC
1 ATAACTTAC
48441414 ATAA--TAC
1 ATAACTTAC
* *
48441421 ATAGCCTAC
1 ATAACTTAC
48441430 ATAACTTAC
1 ATAACTTAC
*
48441439 TTAACTTAC
1 ATAACTTAC
48441448 ATAA--TAC
1 ATAACTTAC
**
48441455 ACCACTTAC
1 ATAACTTAC
*
48441464 ATAACTTAA
1 ATAACTTAC
48441473 ATAACTTAC
1 ATAACTTAC
48441482 ATAA--TAC
1 ATAACTTAC
*
48441489 TTAACTTTA-
1 ATAAC-TTAC
48441498 ATAA--TAC
1 ATAACTTAC
*
48441505 ACAACTTAC
1 ATAACTTAC
48441514 ATAACTTA
1 ATAACTTA
48441522 ATTACATTAT
Statistics
Matches: 332, Mismatches: 76, Indels: 98
0.66 0.15 0.19
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
6 4 0.01
7 70 0.21
8 15 0.05
9 185 0.56
10 20 0.06
11 7 0.02
12 27 0.08
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:48441161 original size:25 final size:25
Alignment explanation
Indices: 48441056--48441189 Score: 136
Period size: 25 Copynumber: 5.6 Consensus size: 25
48441046 TAACTTATAT
*
48441056 ATAACTTTCATAACTTACATAATAC
1 ATAACTTACATAACTTACATAATAC
* * * *
48441081 ATAGCCTACATGACTTGCATAATAC
1 ATAACTTACATAACTTACATAATAC
* *
48441106 ACAACTTACATAAATTACATAATAC
1 ATAACTTACATAACTTACATAATAC
* *
48441131 ATAACTTTCATAACTTACATTATAC
1 ATAACTTACATAACTTACATAATAC
*
48441156 ATAACTT--ATAA-AT-CAT-AT-C
1 ATAACTTACATAACTTACATAATAC
48441175 ATAACTTACATAACT
1 ATAACTTACATAACT
48441190 CAAATTTATC
Statistics
Matches: 89, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
19 8 0.09
20 2 0.02
21 7 0.08
22 1 0.01
23 4 0.04
25 67 0.75
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (25 bp):
ATAACTTACATAACTTACATAATAC
Found at i:48441389 original size:34 final size:33
Alignment explanation
Indices: 48441334--48441488 Score: 167
Period size: 34 Copynumber: 4.8 Consensus size: 33
48441324 CATAACTTAT
*
48441334 ATAACTTAAA-AACTTAGATAATACATAGCCTAC
1 ATAACTTAAATAACTTACATAATACATA-CCTAC
*
48441367 ATAACTTATATAACTTACATAATAC--ACC-AC
1 ATAACTTAAATAACTTACATAATACATACCTAC
* * *
48441397 -TTACATAAATAACTTGCATAATACATAGCCTAC
1 ATAACTTAAATAACTTACATAATACATA-CCTAC
** * *
48441430 ATAACTTACTTAACTTACATAATACACCACTTAC
1 ATAACTTAAATAACTTACATAATACA-TACCTAC
48441464 ATAACTTAAATAACTTACATAATAC
1 ATAACTTAAATAACTTACATAATAC
48441489 TTAACTTTAA
Statistics
Matches: 100, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
29 20 0.20
30 2 0.02
31 3 0.03
32 3 0.03
33 11 0.11
34 60 0.60
35 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.30
Consensus pattern (33 bp):
ATAACTTAAATAACTTACATAATACATACCTAC
Found at i:48441400 original size:16 final size:16
Alignment explanation
Indices: 48441378--48441517 Score: 90
Period size: 16 Copynumber: 8.7 Consensus size: 16
48441368 TAACTTATAT
48441378 AACTTACATAATACAC
1 AACTTACATAATACAC
* *
48441394 CACTTACAT-A-A-AT
1 AACTTACATAATACAC
* *
48441407 AACTTGCATAATACAT
1 AACTTACATAATACAC
* * **
48441423 AGCCTACATAACTTACTT
1 AACTTACATAA--TACAC
48441441 AACTTACATAATACAC
1 AACTTACATAATACAC
* * *
48441457 CACTTACATAACTTAAAT
1 AACTTACATAA--TACAC
**
48441475 AACTTACATAATACTT
1 AACTTACATAATACAC
48441491 AACTTTA-ATAATACAC
1 AAC-TTACATAATACAC
48441507 AACTTACATAA
1 AACTTACATAA
48441518 CTTAATTACA
Statistics
Matches: 95, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
13 8 0.08
14 2 0.02
15 5 0.05
16 51 0.54
17 3 0.03
18 26 0.27
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (16 bp):
AACTTACATAATACAC
Found at i:48441411 original size:63 final size:62
Alignment explanation
Indices: 48441340--48441467 Score: 215
Period size: 63 Copynumber: 2.0 Consensus size: 62
48441330 TTATATAACT
48441340 TAAAAACTTAG-ATAATACATAGCCTACATAACTTA-TATAACTTACATAATACACCACTTACA
1 TAAAAACTT-GCATAATACATAGCCTACATAACTTACT-TAACTTACATAATACACCACTTACA
48441402 TAAATAACTTGCATAATACATAGCCTACATAACTTACTTAACTTACATAATACACCACTTACA
1 TAAA-AACTTGCATAATACATAGCCTACATAACTTACTTAACTTACATAATACACCACTTACA
48441465 TAA
1 TAA
48441468 CTTAAATAAC
Statistics
Matches: 63, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
62 5 0.08
63 57 0.90
64 1 0.02
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (62 bp):
TAAAAACTTGCATAATACATAGCCTACATAACTTACTTAACTTACATAATACACCACTTACA
Found at i:48441455 original size:25 final size:24
Alignment explanation
Indices: 48441427--48441523 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 24
48441417 ATACATAGCC
* *
48441427 TACATAACTTACTTAACTTACATAA
1 TACACAACTTACATAACTTA-ATAA
*
48441452 TACACCACTTACATAACTTAAATAA
1 TACACAACTTACATAACTT-AATAA
* *
48441477 CTTACATAA--TACTTAACTTTAATAA
1 --TACACAACTTACATAAC-TTAATAA
48441502 TACACAACTTACATAACTTAAT
1 TACACAACTTACATAACTTAAT
48441524 TACATTATAC
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
23 6 0.10
24 5 0.09
25 39 0.67
26 3 0.05
27 5 0.09
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (24 bp):
TACACAACTTACATAACTTAATAA
Found at i:48443727 original size:44 final size:43
Alignment explanation
Indices: 48443672--48443901 Score: 241
Period size: 43 Copynumber: 5.3 Consensus size: 43
48443662 AGGTCATGGT
* *
48443672 CTTTAGCGGCGTATGTGGGAAAAGCACCGCTAAAAGAACATGAC
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT-AAAGAACATGAC
* * *
48443716 CTTTAGTGGCGTTTGT-GGAGAAAGCGCCGCCAAAGAACATGAT
1 CTTTAGCGGCGTTTGTGGGA-AAAGCGCCGCTAAAGAACATGAC
* *
48443759 CTTTAGCGGCGTTTG-AGGAATAAGCGCCGCTAAAGTACATGAC
1 CTTTAGCGGCGTTTGTGGGAA-AAGCGCCGCTAAAGAACATGAC
* * * *
48443802 CTTTAGCGGCGTTTGTAGGG-AATGCGCCACTAAAGACCCTGAC
1 CTTTAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGAACATGAC
* ******
48443845 CTTTAGCGGCGTTTTTTTTTGTAGCGCCGCTAAAGAACATGAC
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGAC
48443888 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
48443902 ATAAAAATAA
Statistics
Matches: 155, Mismatches: 25, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
42 1 0.01
43 128 0.83
44 24 0.15
45 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGAC
Found at i:48444191 original size:97 final size:94
Alignment explanation
Indices: 48444026--48444210 Score: 289
Period size: 97 Copynumber: 1.9 Consensus size: 94
48444016 TGTAGTTTCT
* * *
48444026 TAATATGTTGCTAATATGTCACCCCAAAGGTTATCTTTTTGTCTGTTTTATTAAAAACATTGATA
1 TAATATGTTCCTAATATGTCACCCCAAAGGTCATCTTTTTGTCTGTTTTATTAAAAACATTGACA
48444091 TTTATGTTGCAAGAATTTATAAACTTTGA
66 TTTATGTTGCAAGAATTTATAAACTTTGA
* * *
48444120 TAATATGTTCCTAATATGTCATCCCATAGGTCATCTTTTTTTTTTCTGTTTTATTAAAAACATTG
1 TAATATGTTCCTAATATGTCACCCCAAAGGTCATC---TTTTTGTCTGTTTTATTAAAAACATTG
48444185 ACATTTATGTTGCAAGAATTTATAAA
63 ACATTTATGTTGCAAGAATTTATAAA
48444211 TATTTAGGGG
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
94 31 0.38
97 51 0.62
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.45
Consensus pattern (94 bp):
TAATATGTTCCTAATATGTCACCCCAAAGGTCATCTTTTTGTCTGTTTTATTAAAAACATTGACA
TTTATGTTGCAAGAATTTATAAACTTTGA
Found at i:48445538 original size:13 final size:13
Alignment explanation
Indices: 48445520--48445545 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48445510 AAGGTTAATT
48445520 TTATGTCATTGTA
1 TTATGTCATTGTA
48445533 TTATGTCATTGTA
1 TTATGTCATTGTA
48445546 ATTGTGATAT
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:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
TTATGTCATTGTA
Found at i:48457915 original size:24 final size:24
Alignment explanation
Indices: 48457888--48457939 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
48457878 TTAGTAAGTC
*
48457888 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
48457912 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
48457936 AAAT
1 AAAT
48457940 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:48459788 original size:16 final size:16
Alignment explanation
Indices: 48459748--48459795 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
48459738 ATTAATTTTT
*
48459748 ATATTTATATT-TATA
1 ATATTAATATTATATA
48459763 ATATTATAATATTATATA
1 ATA-T-TAATATTATATA
*
48459781 ATATTAATAATATAT
1 ATATTAATATTATAT
48459796 TATGTTATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 3 0.11
16 11 0.39
17 7 0.25
18 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTAATATTATATA
Found at i:48462501 original size:73 final size:73
Alignment explanation
Indices: 48462406--48462576 Score: 227
Period size: 73 Copynumber: 2.3 Consensus size: 73
48462396 GCTCAGGGCT
* * *
48462406 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAGGA-CATAAGCCCAACGGCGCCGTTTTCTGAGC
1 TTTAGCGGCGCTTTTGAGAAAGCGCCGCAAAAGAATC-TAAGCCCAACGACGCCGTTTTCTGAGC
*
48462470 TTTCGGGGA
65 TTTCGCGGA
* * *
48462479 TTTAGCGGTGCTTTTGATAAAGCGCCGCAAAATAATCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGCTTTTGAGAAAGCGCCGCAAAAGAATCTAAGCCCAACGACGCCGTTTTCTGAGCT
48462544 TTCGCGGA
66 TTCGCGGA
* * * *
48462552 TTTAGAGGCGTTTTTTAGGAAGCGC
1 TTTAGCGGCGCTTTTGAGAAAGCGC
48462577 TGCTAATGCT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
73 83 0.99
74 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (73 bp):
TTTAGCGGCGCTTTTGAGAAAGCGCCGCAAAAGAATCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGCGGA
Found at i:48462502 original size:115 final size:113
Alignment explanation
Indices: 48462294--48462506 Score: 266
Period size: 115 Copynumber: 1.9 Consensus size: 113
48462284 AAAATAAGCA
* * *
48462294 TTAGCGACGTTTTTTAAAAAGCGCCGCAAAAAACTAAGCCAAACGACGTCGTTTTCTGCGCTTTC
1 TTAGCGACGTTTTTGAAAAAGCGCCGCAAAAAACTAAGCCAAACGACGCCGTTTTCTGAGCTTTC
* * *
48462359 GCAGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAGGGCTT
66 GCAGATTTAGCGGCGCTTTTGAGTAAGCGCCGCTAATGCTCAGGGCTT
* * * * *
48462407 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAGGACATAAGCCCAACGGCGCCGTTTTCTGAGCTT
1 TTAGCGACGTTTTTGAAAAAGCGCCGCAAAA-AAC-TAAGCCAAACGACGCCGTTTTCTGAGCTT
** *
48462472 TCGGGGATTTAGCGGTGCTTTTGA-TAAAGCGCCGC
64 TCGCAGATTTAGCGGCGCTTTTGAGT-AAGCGCCGC
48462507 AAAATAATCT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
113 28 0.34
114 3 0.04
115 52 0.63
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (113 bp):
TTAGCGACGTTTTTGAAAAAGCGCCGCAAAAAACTAAGCCAAACGACGCCGTTTTCTGAGCTTTC
GCAGATTTAGCGGCGCTTTTGAGTAAGCGCCGCTAATGCTCAGGGCTT
Found at i:48462689 original size:188 final size:186
Alignment explanation
Indices: 48462304--48462694 Score: 554
Period size: 188 Copynumber: 2.1 Consensus size: 186
48462294 TTAGCGACGT
* *
48462304 TTTTTAA-AAAGCGCCGCAAAAAACTAAGCCAAACGACGTCGTTTTCTGCGCTTTCGCAGATTTA
1 TTTTTAATAAAGCGCCGCAAAAAACTAAGCCAAACGACGCCGTTTTCTGAGCTTTCGCAGATTTA
* * *
48462368 GTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAGGGCTTTTAGCGGCGTTTTTGAGAAAGCGCCG
66 GAGGCGTTTTTTAGGAAGCGCCGCTAATGCTCAGGGCTTTTAGCGGCATTTTTGAGAAAGCGCCG
** * * * * *
48462433 CAAAAGGACATAAGCCCAACGGCGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGTG
131 CAAAAAAACATAAGCCCAACGACGCCGCTTTCTGAGCTTTCGCGGATTTAGCAGCG
* * * *
48462489 CTTTTGATAAAGCGCCGCAAAATAATCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGCGGATT
1 TTTTTAATAAAGCGCCGCAAAA-AA-CTAAGCCAAACGACGCCGTTTTCTGAGCTTTCGCAGATT
* *
48462554 TAGAGGCGTTTTTTAGGAAGCGCTGCTAATGCTCAGGGCTTTT-GCGGCATTTTTGATAAAGCGC
64 TAGAGGCGTTTTTTAGGAAGCGCCGCTAATGCTCAGGGCTTTTAGCGGCATTTTTGAGAAAGCGC
*
48462618 CGCAAAATAAAC-TAAGCCCAACGACGCCGCTTTCTGAGCTTTCGCGGATTTAGTAGCG
129 CGCAAAA-AAACATAAGCCCAACGACGCCGCTTTCTGAGCTTTCGCGGATTTAGCAGCG
48462676 TTTCTTAATAAAGCGCCGC
1 TTT-TTAATAAAGCGCCGC
48462695 TAATGCTGAG
Statistics
Matches: 180, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
185 5 0.03
186 14 0.08
187 70 0.39
188 91 0.51
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (186 bp):
TTTTTAATAAAGCGCCGCAAAAAACTAAGCCAAACGACGCCGTTTTCTGAGCTTTCGCAGATTTA
GAGGCGTTTTTTAGGAAGCGCCGCTAATGCTCAGGGCTTTTAGCGGCATTTTTGAGAAAGCGCCG
CAAAAAAACATAAGCCCAACGACGCCGCTTTCTGAGCTTTCGCGGATTTAGCAGCG
Found at i:48462876 original size:114 final size:112
Alignment explanation
Indices: 48462479--48462916 Score: 545
Period size: 114 Copynumber: 3.8 Consensus size: 112
48462469 CTTTCGGGGA
* * * *
48462479 TTTAGCGGTGCTTTTGATAAAGCGCCGCAAAATAATCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCT
*
48462544 TTCGCGGATTTAGAGGCGTTTTTTAGGAAGCGCTGCTAATGCTCAGGGC
66 TTCGCGGATTTAGTGGCGTTTTTTAGGAAGC-C-GCTAATGCTCAGGGC
* * * *
48462593 TTTTGCGGCATTTTTGATAAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGCTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCT
* * ** *
48462658 TTCGCGGATTTAGTAGCGTTTCTTAATAAAGCGCCGCTAATGCTGAGGGC
66 TTCGCGGATTTAGTGGCGTTT-TTTAGGAA--GCCGCTAATGCTCAGGGC
* * *
48462708 TTTAGCGCCGTTTTTGAGGAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTTAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCT
* * * * *
48462773 TTTGTGAATTTAGTGTCGTTTTTTAGGATATGCCGCTAATGCTCAGTGC
66 TTCGCGGATTTAGTGGCGTTTTTTAGGA-A-GCCGCTAATGCTCAGGGC
* *
48462822 TTTAGCGGCGTTTGTGAGAAAGCGCCGCAAAA-AGACATAAGCCCAACGACGCCGTTTTCTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAAC-TAAGCCCAACGACGCCGTTTTCTGAGC
* * *
48462886 TTTTGGGGGATTTAGCGGCGTTTTTTAGGAA
65 -TTTCGCGGATTTAGTGGCGTTTTTTAGGAA
48462917 AGCGCCGTAA
Statistics
Matches: 278, Mismatches: 40, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
113 3 0.01
114 154 0.55
115 118 0.42
116 1 0.00
117 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (112 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGCGGATTTAGTGGCGTTTTTTAGGAAGCCGCTAATGCTCAGGGC
Found at i:48463039 original size:14 final size:14
Alignment explanation
Indices: 48463020--48463046 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48463010 GAGTATGGGT
48463020 TTAGGGATTATGGA
1 TTAGGGATTATGGA
48463034 TTAGGGATTATGG
1 TTAGGGATTATGG
48463047 TTTAAGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:48463084 original size:8 final size:7
Alignment explanation
Indices: 48463069--48463125 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
48463059 GATTTAAGGT
48463069 TTAGGGG
1 TTAGGGG
48463076 TTAGAGGG
1 TTAG-GGG
48463084 TTAGGGG
1 TTAGGGG
48463091 TTTAGGGG
1 -TTAGGGG
**
48463099 TTAGACG
1 TTAGGGG
*
48463106 TTTGGGG
1 TTAGGGG
* *
48463113 TTAAGAG
1 TTAGGGG
48463120 TTAGGG
1 TTAGGG
48463126 ATTTAAGGTT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
7 24 0.63
8 14 0.37
ACGTcount: A:0.19, C:0.02, G:0.47, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:48463089 original size:15 final size:15
Alignment explanation
Indices: 48463069--48463115 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
48463059 GATTTAAGGT
48463069 TTAGGGG-TTAGAGGG
1 TTAGGGGTTTAG-GGG
48463084 TTAGGGGTTTAGGGG
1 TTAGGGGTTTAGGGG
**
48463099 TTAGACGTTT-GGGG
1 TTAGGGGTTTAGGGG
48463113 TTA
1 TTA
48463116 AGAGTTAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 7 0.24
15 18 0.62
16 4 0.14
ACGTcount: A:0.17, C:0.02, G:0.47, T:0.34
Consensus pattern (15 bp):
TTAGGGGTTTAGGGG
Found at i:48463336 original size:15 final size:14
Alignment explanation
Indices: 48463316--48463364 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
48463306 CATATTTTAA
*
48463316 GGTTTAGGGAGTAT
1 GGTTTAGGGACTAT
*
48463330 GGGTTTAGGGATTAT
1 -GGTTTAGGGACTAT
*
48463345 GGATTAGGGACTAT
1 GGTTTAGGGACTAT
48463359 GGTTTA
1 GGTTTA
48463365 AGGGTTAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.22, C:0.02, G:0.39, T:0.37
Consensus pattern (14 bp):
GGTTTAGGGACTAT
Found at i:48463391 original size:29 final size:28
Alignment explanation
Indices: 48463362--48463454 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
48463352 GGACTATGGT
48463362 TTAAGGGTTAGGACTTAAGGTTTAGGGG
1 TTAAGGGTTAGGACTTAAGGTTTAGGGG
* ** *
48463390 TTAGGGGTTTAGGGGTTAGACG-TTAGGGG
1 TTAAGGG-TTAGGACTTA-AGGTTTAGGGG
* *
48463419 TTAAGAGTTAGGGATTTAAGGTTTAGGGG
1 TTAAGGGTTA-GGACTTAAGGTTTAGGGG
*
48463448 TTCAGGG
1 TTAAGGG
48463455 GTCGAGTTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
28 11 0.22
29 37 0.74
30 2 0.04
ACGTcount: A:0.23, C:0.03, G:0.42, T:0.32
Consensus pattern (28 bp):
TTAAGGGTTAGGACTTAAGGTTTAGGGG
Found at i:48463395 original size:7 final size:7
Alignment explanation
Indices: 48463383--48463456 Score: 58
Period size: 7 Copynumber: 10.1 Consensus size: 7
48463373 GACTTAAGGT
48463383 TTAGGGG
1 TTAGGGG
48463390 TTAGGGG
1 TTAGGGG
48463397 TTTAGGGG
1 -TTAGGGG
**
48463405 TTAGACG
1 TTAGGGG
48463412 TTAGGGG
1 TTAGGGG
* *
48463419 TTAAGAG
1 TTAGGGG
*
48463426 TTAGGGAT
1 TTAGGG-G
* *
48463434 TTAAGGT
1 TTAGGGG
48463441 TTAGGGG
1 TTAGGGG
48463448 TTCAGGGG
1 TT-AGGGG
48463456 T
1 T
48463457 CGAGTTAAGG
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
7 34 0.65
8 18 0.35
ACGTcount: A:0.20, C:0.03, G:0.45, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:48463399 original size:36 final size:37
Alignment explanation
Indices: 48463359--48463445 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 37
48463349 TAGGGACTAT
* * *
48463359 GGTTTAAGGGTTAGGAC-TTAAGGTTTAGGGGTTAGG
1 GGTTTAAGGGTTAGGACGTTAAGGGTTAAGAGTTAGG
* *
48463395 GGTTTAGGGGTTA-GACGTTAGGGGTTAAGAGTTAGG
1 GGTTTAAGGGTTAGGACGTTAAGGGTTAAGAGTTAGG
* *
48463431 GATTTAAGGTTTAGG
1 GGTTTAAGGGTTAGG
48463446 GGTTCAGGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
35 3 0.07
36 37 0.90
37 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.41, T:0.33
Consensus pattern (37 bp):
GGTTTAAGGGTTAGGACGTTAAGGGTTAAGAGTTAGG
Found at i:48463400 original size:15 final size:15
Alignment explanation
Indices: 48463380--48463456 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
48463370 TAGGACTTAA
48463380 GGTTTAGGGGTTAGG
1 GGTTTAGGGGTTAGG
*
48463395 GGTTTAGGGGTTAGA
1 GGTTTAGGGGTTAGG
* *
48463410 CG-TTAGGGGTTAAG
1 GGTTTAGGGGTTAGG
* * *
48463424 AG-TTAGGGATTTA-A
1 GGTTTAGGG-GTTAGG
48463438 GGTTTAGGGGTTCAGG
1 GGTTTAGGGGTT-AGG
48463454 GGT
1 GGT
48463457 CGAGTTAAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
14 20 0.42
15 25 0.52
16 3 0.06
ACGTcount: A:0.19, C:0.03, G:0.45, T:0.32
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:48463907 original size:136 final size:138
Alignment explanation
Indices: 48463744--48464000 Score: 364
Period size: 136 Copynumber: 1.9 Consensus size: 138
48463734 TTTAGCATAA
* *
48463744 CAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTT-ATGC-AAAATGCCG
1 CAAAACAGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTCA--CAAAAACGCCG
*
48463807 CAAAAGATAA-CAAATAGCGGCGTTTCTATA-AAAACGCCGCA-A-AAAATAAATCAATTTATAG
64 CAAAAGATAAGC-AATAGCGGC-TTTCTATATAAAACGCCGCAGAGAAAATAAATAAATTTATAG
48463868 AAAACAAAATAG
127 AAAACAAAATAG
*
48463880 CAAAACAGTGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTCACAAAAACGCCGCA
1 CAAAACAGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTCACAAAAACGCCGCA
* * * *
48463945 AAATATAAGCAATAGCGGCTTTTTTTATAAAACGTCGCAGAGAAAATAAATAAATT
66 AAAGATAAGCAATAGCGGCTTTCTATATAAAACGCCGCAGAGAAAATAAATAAATT
48464001 AAAAAAATTA
Statistics
Matches: 107, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
135 7 0.07
136 84 0.79
137 3 0.03
138 13 0.12
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (138 bp):
CAAAACAGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTCACAAAAACGCCGCA
AAAGATAAGCAATAGCGGCTTTCTATATAAAACGCCGCAGAGAAAATAAATAAATTTATAGAAAA
CAAAATAG
Found at i:48464220 original size:106 final size:107
Alignment explanation
Indices: 48464002--48464438 Score: 384
Period size: 105 Copynumber: 4.1 Consensus size: 107
48463992 AAATAAATTA
* * * * **
48464002 AAAAAATTATT-TGTATAGCAAAACGGCGCCGTTTTTCTTCAAAATT-AAATAGCGGCGTTTTTG
1 AAAAAATT-TTGTGCATAGCAAAACGGCGTC-ATTTTGTTC-AAATTGAAATAGCGGCGTTTTCC
* *
48464065 TTAAAAATGCCGCAAAAAAGTAAATCAATTTATAAAAAACAAAAT
63 CTAAAAACGCCGCAAAAAAGTAAATCAATTTATAAAAAACAAAAT
* * *
48464110 AAAAAATTTTGTGCATAGCAAAACGGCGTCATTTTGTTCAAATTGAAGTTGTGGCGTTTTCCCTA
1 AAAAAATTTTGTGCATAGCAAAACGGCGTCATTTTGTTCAAATTGAAATAGCGGCGTTTTCCCTA
48464175 AAAACGCCGCAAAAAA-TAAATCAATTT-TAAAAAACAAAAT
66 AAAACGCCGCAAAAAAGTAAATCAATTTATAAAAAACAAAAT
*
48464215 AAAAAATTTTGTGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTT
1 AAAAAATTTTGTGCATAGCAAAACGGCGTCATTTTGTTCAAATTG--A-AATA----GCGGCG-T
* * **
48464280 TTTCAC-AAAAACG-CGTCAAAAGA-TAAA-CAA---A-AAAATAA-ATTAT
58 TTTCCCTAAAAACGCCG-CAAAAAAGTAAATCAATTTATAAAA-AACAAAAT
** ** * * ***
48464323 AAAAAAAATTGT--ATAGCAAAACGGCGCTGTTTTTGTTCAAAATGAAATAGCGTCGTTTTTAGT
1 AAAAAATTTTGTGCATAGCAAAACGGCG-TCATTTTGTTCAAATTGAAATAGCGGCGTTTTCCCT
*
48464386 AAAAATGCCGCAAAGAAA-TAAATCAATTTATAAAAAACAAAAT
65 AAAAACGCCGCAAA-AAAGTAAATCAATTTATAAAAAACAAAAT
*
48464429 AAATAATTTT
1 AAAAAATTTT
48464439 TAGCATGCCG
Statistics
Matches: 273, Mismatches: 33, Indels: 48
0.77 0.09 0.14
Matches are distributed among these distances:
99 5 0.02
100 15 0.05
101 8 0.03
102 3 0.01
104 4 0.01
105 61 0.22
106 44 0.16
107 54 0.20
108 44 0.16
109 2 0.01
111 5 0.02
112 22 0.08
113 6 0.02
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.29
Consensus pattern (107 bp):
AAAAAATTTTGTGCATAGCAAAACGGCGTCATTTTGTTCAAATTGAAATAGCGGCGTTTTCCCTA
AAAACGCCGCAAAAAAGTAAATCAATTTATAAAAAACAAAAT
Found at i:48466310 original size:30 final size:30
Alignment explanation
Indices: 48466267--48466327 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
48466257 TATAACTTGC
* *
48466267 ATAATTTACATAACTTATAAATTTTTAATAT
1 ATAACTTACATAACTTATAAATATTT-ATAT
*
48466298 ATAACTTA-ATAACTTATTAATATTTATAT
1 ATAACTTACATAACTTATAAATATTTATAT
48466327 A
1 A
48466328 CATTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 15 0.56
31 7 0.26
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (30 bp):
ATAACTTACATAACTTATAAATATTTATAT
Found at i:48466317 original size:23 final size:22
Alignment explanation
Indices: 48466276--48466320 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
48466266 CATAATTTAC
*
48466276 ATAACTTATAAATTTTTAATAT
1 ATAACTTATAAATTATTAATAT
*
48466298 ATAACTTAATAACTTATTAATAT
1 ATAACTT-ATAAATTATTAATAT
48466321 TTATATACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAACTTATAAATTATTAATAT
Found at i:48466378 original size:20 final size:19
Alignment explanation
Indices: 48466336--48466380 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
48466326 TACATTTTTA
*
48466336 ATATATTTATTAAAAATTT
1 ATATATTTATTAAAAACTT
*
48466355 ATATATTTTTTAAATAACTT
1 ATATATTTATTAAA-AACTT
48466375 ATATAT
1 ATATAT
48466381 AACTTTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATATTTATTAAAAACTT
Found at i:48466393 original size:9 final size:9
Alignment explanation
Indices: 48466379--48466532 Score: 85
Period size: 9 Copynumber: 17.7 Consensus size: 9
48466369 TAACTTATAT
*
48466379 ATAACTTTC
1 ATAACTTAC
48466388 ATAACTTAC
1 ATAACTTAC
*
48466397 ATAA-TAAC
1 ATAACTTAC
48466405 ATAATAACTTAC
1 ---ATAACTTAC
48466417 ATAA--TAC
1 ATAACTTAC
* *
48466424 ATAGCCTAC
1 ATAACTTAC
* *
48466433 ATGACTTGC
1 ATAACTTAC
48466442 ATAA--TAC
1 ATAACTTAC
*
48466449 ACAACTTAC
1 ATAACTTAC
*
48466458 ATAAATTAC
1 ATAACTTAC
48466467 ATAA--TAC
1 ATAACTTAC
*
48466474 ATAACTTTC
1 ATAACTTAC
48466483 ATAACTTAC
1 ATAACTTAC
*
48466492 ATTA--TAC
1 ATAACTTAC
*
48466499 ATAACTTAT
1 ATAACTTAC
*
48466508 A-AATCATATC
1 ATAA-CTTA-C
48466518 ATAACTTAC
1 ATAACTTAC
48466527 ATAACT
1 ATAACT
48466533 CAAATTTATC
Statistics
Matches: 109, Mismatches: 21, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
7 24 0.22
8 5 0.05
9 67 0.61
10 4 0.04
11 6 0.06
12 3 0.03
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:48466411 original size:20 final size:19
Alignment explanation
Indices: 48466388--48466426 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
48466378 TATAACTTTC
48466388 ATAACTTACATAATAACATA
1 ATAACTTACATAAT-ACATA
48466408 ATAACTTACATAATACATA
1 ATAACTTACATAATACATA
48466427 GCCTACATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAACTTACATAATACATA
Found at i:48466444 original size:25 final size:25
Alignment explanation
Indices: 48466400--48466503 Score: 111
Period size: 25 Copynumber: 4.2 Consensus size: 25
48466390 AACTTACATA
*
48466400 ATAACATA-ATAACTTACATAATAC
1 ATAACCTACATAACTTACATAATAC
* * *
48466424 ATAGCCTACATGACTTGCATAATAC
1 ATAACCTACATAACTTACATAATAC
* * *
48466449 ACAACTTACATAAATTACATAATAC
1 ATAACCTACATAACTTACATAATAC
* * *
48466474 ATAACTTTCATAACTTACATTATAC
1 ATAACCTACATAACTTACATAATAC
48466499 ATAAC
1 ATAAC
48466504 TTATAAATCA
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
24 6 0.09
25 59 0.91
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (25 bp):
ATAACCTACATAACTTACATAATAC
Found at i:48466680 original size:9 final size:9
Alignment explanation
Indices: 48466661--48466731 Score: 58
Period size: 9 Copynumber: 8.2 Consensus size: 9
48466651 CTTATATAGG
*
48466661 AACTTGCAT
1 AACTTACAT
*
48466670 AACTTATAT
1 AACTTACAT
*
48466679 AACTTA-AA
1 AACTTACAT
*
48466687 AACTTAGAT
1 AACTTACAT
48466696 AA--TACAT
1 AACTTACAT
* *
48466703 AGCCTACAT
1 AACTTACAT
*
48466712 AACTTATAT
1 AACTTACAT
48466721 AACTTACAT
1 AACTTACAT
48466730 AA
1 AA
48466732 TACACCACTT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
7 5 0.10
8 7 0.14
9 37 0.76
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:48469196 original size:43 final size:44
Alignment explanation
Indices: 48469074--48469198 Score: 148
Period size: 43 Copynumber: 2.9 Consensus size: 44
48469064 CGTTTTTAAA
* ** * *
48469074 AAAAGCACCGCT-AAAGGTCATGGTCTTTAGCGGCATTTGTGGG
1 AAAAGCGCCGCTAAAAGAACATGATCTTTAGCGGCGTTTGTGGG
* *
48469117 AAAAGCGCCGCTAAAAGAACATGACCTTTAGTGGCGTTTGT-GG
1 AAAAGCGCCGCTAAAAGAACATGATCTTTAGCGGCGTTTGTGGG
*
48469160 AGAAAGCGCCGC-CAAAGAACATGATCTTTAGCGGCGTTT
1 A-AAAGCGCCGCTAAAAGAACATGATCTTTAGCGGCGTTT
48469199 CCAAAAGAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
43 38 0.54
44 32 0.46
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (44 bp):
AAAAGCGCCGCTAAAAGAACATGATCTTTAGCGGCGTTTGTGGG
Found at i:48469572 original size:19 final size:20
Alignment explanation
Indices: 48469539--48469577 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
48469529 TAAACAATTG
*
48469539 TAAAAATTATGAAAAATATT
1 TAAAAATTATAAAAAATATT
48469559 TAAAAATT-TAAAAAATATT
1 TAAAAATTATAAAAAATATT
48469578 AAAGATCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAAATTATAAAAAATATT
Found at i:48482497 original size:88 final size:88
Alignment explanation
Indices: 48482396--48482603 Score: 355
Period size: 88 Copynumber: 2.4 Consensus size: 88
48482386 AAGATGGCAA
*
48482396 ATCTTATCCCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAATTAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAATTAT
*
48482461 AGTGGAGTGGATTAAAACTTCAG
66 AGTGGAGTGGATTAAAACCTCAG
*
48482484 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCTTGAAATTAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAATTAT
48482549 AGTGGAGTGGATTAAAACCTCAG
66 AGTGGAGTGGATTAAAACCTCAG
* * *
48482572 ATCTTATCTCTCTAAAGTTGCAG-AGAGCAGAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
48482604 CGCATCTAGT
Statistics
Matches: 114, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
87 8 0.07
88 106 0.93
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (88 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAATTAT
AGTGGAGTGGATTAAAACCTCAG
Found at i:48482675 original size:45 final size:45
Alignment explanation
Indices: 48482613--48482729 Score: 130
Period size: 45 Copynumber: 2.6 Consensus size: 45
48482603 TCGCATCTAG
* * *
48482613 TCTTATCTCCCTGAAGTTGCAGTGGA-TCAGACTAAGCAAAGCAAG
1 TCTTATCT-ACTGAAGTTGCAGTGGAGGCAGACTAAGCAAAGCAAA
* * *
48482658 TCTTATCCTACTGAAGTTGCAGT-GAGGCAGACTGAGGATAGCAAA
1 TCTTAT-CTACTGAAGTTGCAGTGGAGGCAGACTAAGCAAAGCAAA
*
48482703 TCTTATCTCCTTGAAGTTGCAGTGGAG
1 TCTTATCTAC-TGAAGTTGCAGTGGAG
48482730 TGGATTAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
44 5 0.08
45 51 0.84
46 5 0.08
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (45 bp):
TCTTATCTACTGAAGTTGCAGTGGAGGCAGACTAAGCAAAGCAAA
Found at i:48482762 original size:44 final size:44
Alignment explanation
Indices: 48482396--48482779 Score: 200
Period size: 44 Copynumber: 8.8 Consensus size: 44
48482386 AAGATGGCAA
* * *
48482396 ATCTTATCCCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT-A-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACC--TCAG
* * ** * *
48482440 ATCCTATCTCCCTGAAATTATAGTGGAGTGGATTAAAACTTCAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCTCAG
* *
48482484 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT-A-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACC--TCAG
* * * ** *
48482528 ATCCTATCTCCTTGAAATTATAGTGGAGTGGATTAAAACCTCAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCTCAG
* * * * *** *
48482572 ATCTTATCTCTCTAAAGTTGCAG-AGAGCAGA-TCGCATCT-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCTCAG
* **
48482613 -TCTTATCTCCCTGAAGTTGCAGTGGA-TCAGACTAAGCAA-AGCA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGT-AGATTAA--AACCTCAG
* * * ** *** *
48482656 AGTCTTATC-CTACTGAAGTTGCAGT-GAGGCAGACTGAGGATAGCAA
1 A-TCTTATCTC-CCTGAAGTTGCAGTGGA-GTAGA-TTAAAACCTCAG
* *
48482702 ATCTTATCTCCTTGAAGTTGCAGTGGAGTGGATTAAAACCTCAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCTCAG
* * *
48482746 ATCTTATCTCCCTGAAGTTACCGTGGAGCAGATT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT
48482780 GGTAGATCAA
Statistics
Matches: 248, Mismatches: 70, Indels: 44
0.69 0.19 0.12
Matches are distributed among these distances:
40 20 0.08
41 7 0.03
42 7 0.03
43 7 0.03
44 151 0.61
45 50 0.20
46 6 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCTCAG
Found at i:48483414 original size:19 final size:19
Alignment explanation
Indices: 48483390--48483518 Score: 204
Period size: 19 Copynumber: 6.7 Consensus size: 19
48483380 AATTTTTGAG
48483390 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
48483409 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
*
48483428 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
48483447 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
48483468 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
48483487 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
48483506 GATATGCAATCTT
1 GATATGCAATCTT
48483519 TAGAATATAT
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
19 84 0.82
21 18 0.18
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:48483455 original size:59 final size:57
Alignment explanation
Indices: 48483390--48483518 Score: 204
Period size: 59 Copynumber: 2.2 Consensus size: 57
48483380 AATTTTTGAG
*
48483390 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCCTAGATAT
* * *
48483447 GATATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATATAATCTTAGATAT
1 G--ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCCTAGATAT
48483506 GATATGCAATCTT
1 GATATGCAATCTT
48483519 TAGAATATAT
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
57 13 0.20
59 53 0.80
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (57 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCCTAGATAT
Found at i:48484179 original size:24 final size:24
Alignment explanation
Indices: 48484135--48484207 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
48484125 GTAATTATTT
*
48484135 TTATTTTATTTTATTTATATATAA
1 TTATTTTATTTTATATATATATAA
* *
48484159 TTATTTT-TTTTATAATCTATATATG
1 TTATTTTATTTTAT-ATATATATA-A
*
48484184 TTATATTTATCTTTGTATATATAT
1 TTAT-TTTAT-TTTATATATATAT
48484208 GTATGTATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 6 0.15
24 14 0.36
25 4 0.10
26 3 0.08
27 8 0.21
28 4 0.10
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (24 bp):
TTATTTTATTTTATATATATATAA
Found at i:48490794 original size:132 final size:132
Alignment explanation
Indices: 48490443--48491224 Score: 1185
Period size: 132 Copynumber: 5.9 Consensus size: 132
48490433 TTGACAGCGA
48490443 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
** * ** * * *
48490508 TCTACTTCCCTGGGCAGTAGTGGAATAGATTAAAGATAGCAGATCTTACCTTCCT--GCATTGAC
66 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA--G-T
* *
48490571 AGCGA
128 AGTGG
*
48490576 AGCAGATCGAAGATGGCGAATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* *
48490641 TCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
48490706 GG
131 GG
48490708 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
*
48490773 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
48490838 GG
131 GG
*
48490840 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
*
48490905 TCTACTTCCCTGGGCAACTGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
48490970 GG
131 GG
* * * * *
48490972 AGCAGATTGAAGATTGCGGATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCTAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * *
48491037 TCTGCTTCCCTAGGCAATAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
48491102 GG
131 GG
* * * *
48491104 AGTAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGTCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * * * * *
48491169 CCTA-TCTCCCTGGTCAGCAGCGGAATAGGTTGAAGATTGTAAG-TCTTATCTCCCTA
66 TCTACT-TCCCTGGGCAACAGTGGAATAGATTGAAGATT-TCAGATCTTATCTCCCTA
48491225 TAATTGCAGT
Statistics
Matches: 601, Mismatches: 44, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
131 1 0.00
132 481 0.80
133 116 0.19
135 3 0.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (132 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
GG
Found at i:48491134 original size:44 final size:44
Alignment explanation
Indices: 48490615--48491135 Score: 175
Period size: 44 Copynumber: 11.9 Consensus size: 44
48490605 CCTGTGGTTA
* ** * * *
48490615 TAGTGGAGTACATTGAAGCCAGT-AATTCTACTTCCCT-GGACAG
1 TAGTGGAGTAGATTGAAGATAGTGGATTTTACCTCCCTAGG-CAG
* * * * * * *
48490658 CAGTGGAATAGATTGAAGAT-TTCAGATCTTATCTCCCTAAGCAG
1 TAGTGGAGTAGATTGAAGATAGT-GGATTTTACCTCCCTAGGCAG
* * * * * *
48490702 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTA-
1 TAGTGGAGTAGATTGAAGATAGTGGATTTTACCTCCCT-AGG-CAG
* ** * * * * *
48490747 TAGTGGAGTACATTGAAGCCAGT-AATTCTACTTCCCTGGGCAA
1 TAGTGGAGTAGATTGAAGATAGTGGATTTTACCTCCCTAGGCAG
* * ** * * * *
48490790 CAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCCTAAGCAG
1 TAGTGGAGTAGATTGAAGATAGTGGATTTTACCTCCCTAGGCAG
* * * * * *
48490834 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTA-
1 TAGTGGAGTAGATTGAAGATAGTGGATTTTACCTCCCT-AGG-CAG
* ** * * * * * *
48490879 TAGTGGAGTACATTGAAGCCAAT-AATTCTACTTCCCTGGGCAAC
1 TAGTGGAGTAGATTGAAGATAGTGGATTTTACCTCCCTAGGC-AG
* * * * * *
48490923 T-GTGGAATAGATTGAAGAT-TTCAGATCTTATCTCCCTAAGCAG
1 TAGTGGAGTAGATTGAAGATAGT-GGATTTTACCTCCCTAGGCAG
* * * *
48490966 TAGTGGAGCAGATTGAAGATTGCGGATTTTACCTCCCTATGGTTA-
1 TAGTGGAGTAGATTGAAGATAGTGGATTTTACCTCCCTA-GG-CAG
* * * * * * * *
48491011 CAGTGGAGTACATTGAAGCTAGT-AATTCTGCTTCCCTAGGCAA
1 TAGTGGAGTAGATTGAAGATAGTGGATTTTACCTCCCTAGGCAG
* * * * * *
48491054 TAGTGGAATAGATTGAAGAT-TTCAGATCTTATCTCCCTAAGCAG
1 TAGTGGAGTAGATTGAAGATAGT-GGATTTTACCTCCCTAGGCAG
* *
48491098 TAGTGGAGTAGATCGAAGATGGTGGATTTTACCTCCCT
1 TAGTGGAGTAGATTGAAGATAGTGGATTTTACCTCCCT
48491136 GTGGTTACAG
Statistics
Matches: 327, Mismatches: 129, Indels: 43
0.66 0.26 0.09
Matches are distributed among these distances:
42 5 0.02
43 70 0.21
44 196 0.60
45 53 0.16
46 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (44 bp):
TAGTGGAGTAGATTGAAGATAGTGGATTTTACCTCCCTAGGCAG
Found at i:48491498 original size:19 final size:19
Alignment explanation
Indices: 48491452--48491545 Score: 152
Period size: 19 Copynumber: 4.8 Consensus size: 19
48491442 AATTTTTGAG
48491452 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
48491471 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
48491492 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
48491511 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
48491530 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
48491546 ATATATGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
19 50 0.72
21 19 0.28
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:48491531 original size:38 final size:39
Alignment explanation
Indices: 48491452--48491545 Score: 172
Period size: 38 Copynumber: 2.4 Consensus size: 39
48491442 AATTTTTGAG
48491452 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATAT-CAATCTTAGATAT
48491492 GATATGCAATCTTAGATATGATATAT-AATCTTAGATAT
1 GATATGCAATCTTAGATATGATATATCAATCTTAGATAT
48491530 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
48491546 ATATATGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 28 0.52
40 26 0.48
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (39 bp):
GATATGCAATCTTAGATATGATATATCAATCTTAGATAT
Found at i:48492715 original size:12 final size:13
Alignment explanation
Indices: 48492684--48492725 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
48492674 ATTATTTTTA
*
48492684 TTATGTATATTGATT
1 TTATTTATATT-A-T
48492699 TTATTTAT-TTAT
1 TTATTTATATTAT
48492711 TTATTTATATTAT
1 TTATTTATATTAT
48492724 TT
1 TT
48492726 CTAGGCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 9 0.36
13 7 0.28
14 2 0.08
15 7 0.28
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (13 bp):
TTATTTATATTAT
Found at i:48492773 original size:19 final size:20
Alignment explanation
Indices: 48492732--48492773 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
48492722 ATTTCTAGGC
* *
48492732 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
48492752 CATTGT-ATATTTAATATAG
1 CATTGTAATATTTAATATAG
48492771 CAT
1 CAT
48492774 CACATCATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:48493261 original size:98 final size:98
Alignment explanation
Indices: 48493092--48493286 Score: 345
Period size: 98 Copynumber: 2.0 Consensus size: 98
48493082 NNNNNAACAA
* * *
48493092 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTAGGTGTGATTTC
48493157 CTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 CTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
48493190 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTAGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTAGGTGTGATTTC
*
48493255 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 CTAAATCTTGGATAAGTGGATGTTCTTTTAAA
48493287 ATTTTATTGT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTAGGTGTGATTTC
CTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:48496221 original size:21 final size:20
Alignment explanation
Indices: 48496171--48496227 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
48496161 TAATAGAGGG
48496171 TAAAGAAATGAAATAATGACA
1 TAAAGAAAT-AAATAATGACA
*
48496192 TAAATAAATAAATAGATGA-A
1 TAAAGAAATAAATA-ATGACA
48496212 TAAAGAAAATAAATAA
1 TAAAG-AAATAAATAA
48496228 AAGGATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.21
Consensus pattern (20 bp):
TAAAGAAATAAATAATGACA
Found at i:48496235 original size:21 final size:21
Alignment explanation
Indices: 48496197--48496236 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
48496187 TGACATAAAT
* *
48496197 AAATAAATAGATGAATAAAGA
1 AAATAAATAAAAGAATAAAGA
*
48496218 AAATAAATAAAAGGATAAA
1 AAATAAATAAAAGAATAAA
48496237 ATAAAAATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.17
Consensus pattern (21 bp):
AAATAAATAAAAGAATAAAGA
Found at i:48496383 original size:2 final size:2
Alignment explanation
Indices: 48496376--48496406 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
48496366 ATAAGGGCAA
48496376 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 A
48496407 AATGCTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48496579 original size:59 final size:63
Alignment explanation
Indices: 48496478--48497051 Score: 451
Period size: 59 Copynumber: 9.0 Consensus size: 63
48496468 TAATAAATAA
* * *
48496478 AAATATAAAAAATATTAAATTTAAGTATTTTAAAAAATAAAAGAATAATAAATAAACT-GATAAA
1 AAATATAAATAATA-T-AATTTAAATA-TTTAAAAAGTAAAAGAATAATAAATAAA-TAGATAAA
48496542 AC
62 AC
* * *
48496544 AAATATAAAT-A-AT-A-TTAAATGTTTAAAAAGCAAAAGAATAACAAATAAAT--AT--AA-
1 AAATATAAATAATATAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAC
* *
48496598 AAA-AT--ATCA-AT--TTTAAATATTTAAAAAGCAAAAGAATAATAAATAAATAGATAAAAC
1 AAATATAAATAATATAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAC
* *
48496655 AAATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAAAT
1 AAATATAAATAATAT--AATTTAAATATTT-AAAAAGTAAAAG-------AAT-AATAAATAAAT
48496720 AGATAAAAC
55 AGATAAAAC
* * *
48496729 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGT--AA-AATAATATATAAATAAATAAAAC
1 AAATATAAATAATAT--AATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAC
* *
48496791 AAATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAGAT
1 AAATATAAATAATAT--AATTTAAATATTT-AAAAAGTAAAAGAAT----AATAAATAAATAGAT
48496856 AAAAC
59 AAAAC
* *
48496861 GAATATAAATAATATCAAATTTAAATATTTAAAAATTAAAAGAATAATAAATAAATAGAT-----
1 AAATATAAATAATAT--AATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAC
* *
48496921 -AATATAAATAATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
1 AAATATAAATAATAT--AATTTAAATATTTAAAAAGTAAAAGAAT----AATAAATAAATAGATA
48496985 AAAC
60 AAAC
* * * * *
48496989 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAACAAATAAATAAATAAA
1 AAATATAAATAATAT--AATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAA
48497052 TAGATAAAAC
Statistics
Matches: 435, Mismatches: 31, Indels: 85
0.79 0.06 0.15
Matches are distributed among these distances:
51 2 0.00
52 37 0.09
53 2 0.00
54 5 0.01
55 2 0.00
56 2 0.00
57 5 0.01
58 2 0.00
59 67 0.15
60 8 0.02
61 3 0.01
62 47 0.11
63 25 0.06
64 1 0.00
65 44 0.10
66 23 0.05
69 54 0.12
70 45 0.10
71 2 0.00
73 10 0.02
74 49 0.11
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (63 bp):
AAATATAAATAATATAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAC
Found at i:48496614 original size:52 final size:52
Alignment explanation
Indices: 48496437--48496646 Score: 249
Period size: 52 Copynumber: 3.8 Consensus size: 52
48496427 TATAAGTAAC
*
48496437 ATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAAAATATAAAAAAT
1 ATCAAATTTAAATATTTAAAAAGCAAAAGAATAATAAAT--AAATATAAAAAAT
* * **
48496491 ATTAAATTTAAGTATTTTAAAAAATAAAAGAATAATAAATAAACTGATAAAACAAAT
1 ATCAAATTTAAATA-TTTAAAAAGCAAAAGAATAATAAATAAA-T-AT-AAA-AAAT
* * *
48496548 ATAAATAATATTAAATGTTTAAAAAGCAAAAGAATAACAAATAAATATAAAAAAT
1 AT-CA-AAT-TTAAATATTTAAAAAGCAAAAGAATAATAAATAAATATAAAAAAT
*
48496603 ATCAATTTTAAATATTTAAAAAGCAAAAGAATAATAAATAAATA
1 ATCAAATTTAAATATTTAAAAAGCAAAAGAATAATAAATAAATA
48496647 GATAAAACAA
Statistics
Matches: 135, Mismatches: 13, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
52 35 0.26
53 5 0.04
54 14 0.10
55 32 0.24
56 6 0.04
57 8 0.06
58 2 0.01
59 28 0.21
60 5 0.04
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (52 bp):
ATCAAATTTAAATATTTAAAAAGCAAAAGAATAATAAATAAATATAAAAAAT
Found at i:48496635 original size:111 final size:116
Alignment explanation
Indices: 48496441--48496976 Score: 392
Period size: 136 Copynumber: 4.3 Consensus size: 116
48496431 AGTAACATCA
* * * *
48496441 AATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAAAATATAAAAAATATTAAATTTAAGTAT
1 AATTTAAATGTTTAAAAAGTAAAAGAATAACAAAT--AAATATAAAAAATATCAAATTTAAATAT
*
48496506 TTTAAAAAATAAAAGAATAATAAATAAACT-GATAAAACAAATATAAAT-A-AT
64 TTTAAAAAACAAAAGAATAATAAATAAA-TAGATAAAACAAATATAAATAATAT
* *
48496557 -A-TTAAATGTTTAAAAAGCAAAAGAATAACAAATAAATATAAAAAATATCAATTTTAAATA-TT
1 AATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAATATAAAAAATATCAAATTTAAATATTT
* *
48496619 TAAAAAGCAAAAGAATAATAAATAAATAGATAAAACAAATTTAAATAATAT
66 TAAAAAACAAAAGAATAATAAATAAATAGATAAAACAAATATAAATAATAT
* *
48496670 CAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAAATAGATAAAACAAATTT
1 --AATTTAAATGTTT-AAAAAGTAAAAGAATAACAAATAAAT--ATAAA-A-A-ATATCAAATTT
* * * *
48496735 AAATAATATCAAATTTAAATATTTAA-AAAGTAAAATAATATATAAATAAATAAAACAAATTTAA
58 --A-AATAT----TTTAAA-A---AACAAA--AGAATAATAAATAAATAGATAAAACAAATATAA
48496799 ATAATAT
110 ATAATAT
* * *
48496806 CAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATA-AATAGATAA-AACGAATATAA
1 --AATTTAAATGTTT-AAAAAGTAAAAGAATAACAAATAAATATAA-A-A-AATATCAAATTTAA
* * * * * *
48496869 ATAATATCAAATTTAAATATTTAAA-AATTAAAAGAAT-AATAAATAAATAGATAATATAAATAA
60 AT-ATTTTAAA---AAACA---AAAGAA-TAATA-AATAAATAGATAAA-ACA-AATATAAATAA
48496932 TAT
114 TAT
48496935 CAAATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAATA
1 --AATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAATA
48496977 AATACATAAA
Statistics
Matches: 354, Mismatches: 27, Indels: 66
0.79 0.06 0.15
Matches are distributed among these distances:
110 1 0.00
111 43 0.12
112 25 0.07
113 2 0.01
114 29 0.08
115 1 0.00
116 1 0.00
117 10 0.03
118 25 0.07
120 5 0.01
121 1 0.00
122 1 0.00
123 8 0.02
125 3 0.01
126 11 0.03
127 15 0.04
128 33 0.09
129 33 0.09
130 3 0.01
131 6 0.02
132 8 0.02
133 3 0.01
134 7 0.02
135 1 0.00
136 79 0.22
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (116 bp):
AATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAATATAAAAAATATCAAATTTAAATATTT
TAAAAAACAAAAGAATAATAAATAAATAGATAAAACAAATATAAATAATAT
Found at i:48496640 original size:26 final size:26
Alignment explanation
Indices: 48496554--48496642 Score: 65
Period size: 26 Copynumber: 3.4 Consensus size: 26
48496544 AAATATAAAT
* *
48496554 AATATTAAATGTTTAAAAAGCAAAAG
1 AATAATAAATATTTAAAAAGCAAAAG
* * * **
48496580 AATAACAAATAAATATAAAAA--ATATC
1 AATAATAAAT--ATTTAAAAAGCAAAAG
**
48496606 AATTTTAAATATTTAAAAAGCAAAAG
1 AATAATAAATATTTAAAAAGCAAAAG
48496632 AATAATAAATA
1 AATAATAAATA
48496643 AATAGATAAA
Statistics
Matches: 43, Mismatches: 16, Indels: 8
0.64 0.24 0.12
Matches are distributed among these distances:
24 8 0.19
26 28 0.65
28 7 0.16
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (26 bp):
AATAATAAATATTTAAAAAGCAAAAG
Found at i:48496666 original size:15 final size:16
Alignment explanation
Indices: 48496648--48497015 Score: 101
Period size: 16 Copynumber: 23.2 Consensus size: 16
48496638 AAATAAATAG
48496648 ATAA-AACAAATTTAA
1 ATAATAACAAATTTAA
*
48496663 ATAATATCAAATTTAA
1 ATAATAACAAATTTAA
** * * *
48496679 ATGTTTAAAAAAGTAAA
1 AT-AATAACAAATTTAA
*
48496696 AGAATAACAAA--TAA
1 ATAATAACAAATTTAA
* *
48496710 AT-A-AATAAA--TAG
1 ATAATAACAAATTTAA
48496722 ATAA-AACAAATTTAA
1 ATAATAACAAATTTAA
*
48496737 ATAATATCAAATTTAA
1 ATAATAACAAATTTAA
* * *
48496753 ATATTTAA-AAAGTAAA
1 ATA-ATAACAAATTTAA
*
48496769 ATAATATATAAA--TAA
1 ATAATA-ACAAATTTAA
48496784 ATAA-AACAAATTTAA
1 ATAATAACAAATTTAA
*
48496799 ATAATATCAAATTTAA
1 ATAATAACAAATTTAA
** * * *
48496815 ATGTTTAAAAAAGTAAA
1 AT-AATAACAAATTTAA
* *
48496832 AGAATAACAAATAAATAA
1 ATAATAACAAAT--TTAA
* *
48496850 ATAGATAAAACGAATATAA
1 ATA-AT--AACAAATTTAA
*
48496869 ATAATATCAAATTTAA
1 ATAATAACAAATTTAA
* *
48496885 ATATTTAA-AAATTAAA
1 ATA-ATAACAAATTTAA
* *
48496901 AGAATAATAAA--TAA
1 ATAATAACAAATTTAA
*
48496915 ATAGAT----AATATAA
1 ATA-ATAACAAATTTAA
*
48496928 ATAATATCAAATTTAA
1 ATAATAACAAATTTAA
** * *
48496944 ATGTTTAA-AAAGTAAA
1 AT-AATAACAAATTTAA
* *
48496960 AGAATAACAAATAAATAA
1 ATAATAACAAAT--TTAA
48496978 ATACATAAAACAAATTTAA
1 ATA-AT--AACAAATTTAA
*
48496997 ATAATATCAAATTTAA
1 ATAATAACAAATTTAA
48497013 ATA
1 ATA
48497016 TTTAAAAAGT
Statistics
Matches: 253, Mismatches: 66, Indels: 67
0.66 0.17 0.17
Matches are distributed among these distances:
11 2 0.01
12 11 0.04
13 17 0.07
14 8 0.03
15 33 0.13
16 113 0.45
17 27 0.11
18 12 0.05
19 17 0.07
21 13 0.05
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (16 bp):
ATAATAACAAATTTAA
Found at i:48496669 original size:52 final size:51
Alignment explanation
Indices: 48496560--48496663 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 51
48496550 AAATAATATT
* * * *
48496560 AAATGTTTAAAAAGCAAAAGAATAACAAATAAATATAAAAAATATCAATTTT
1 AAATATTTAAAAAGCAAAAGAATAACAAATAAATAGAAAAAACA-CAATTTA
* *
48496612 AAATATTTAAAAAGCAAAAGAATAATAAATAAATAGATAAAACA-AATTTA
1 AAATATTTAAAAAGCAAAAGAATAACAAATAAATAGAAAAAACACAATTTA
48496662 AA
1 AA
48496664 TAATATCAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 7 0.15
52 39 0.85
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.25
Consensus pattern (51 bp):
AAATATTTAAAAAGCAAAAGAATAACAAATAAATAGAAAAAACACAATTTA
Found at i:48496719 original size:74 final size:72
Alignment explanation
Indices: 48496635--48496945 Score: 387
Period size: 74 Copynumber: 4.4 Consensus size: 72
48496625 GCAAAAGAAT
*
48496635 AATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAA
1 AATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTT-AAAAAGTAAAAGAA
48496700 TAACAAATA
65 TAAC-AATA
48496709 AATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGT--AA-AAT
1 AATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAAT
48496771 ---AAT-
66 AACAATA
* *
48496774 -AT--ATAAATAAATAAAACAAATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAA
1 AATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTT-AAAAAGTAAAAGAA
48496836 TAAC---A
65 TAACAATA
* * *
48496841 AATAAATAAATAGATAAAACGAATATAAATAATATCAAATTTAAATATTTAAAAATTAAAAGAAT
1 AATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAAT
*
48496906 AATAAATA
66 AA-CAATA
* * *
48496914 AATAGATAATATAAATAATATCAAATTTAAAT
1 AATAAATAA-ATAGATAA-AACAAATTTAAAT
48496946 GTTTAAAAAG
Statistics
Matches: 206, Mismatches: 14, Indels: 33
0.81 0.06 0.13
Matches are distributed among these distances:
62 43 0.21
63 7 0.03
64 2 0.01
65 2 0.01
66 6 0.03
68 2 0.01
69 16 0.08
70 44 0.21
71 2 0.01
73 16 0.08
74 56 0.27
75 10 0.05
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (72 bp):
AATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAAT
AACAATA
Found at i:48496789 original size:136 final size:133
Alignment explanation
Indices: 48496590--48497051 Score: 675
Period size: 128 Copynumber: 3.5 Consensus size: 133
48496580 AATAACAAAT
* * * *
48496590 AAATATAAAAAATATCAATTTTAAATATTTAAAAAGCAAAAGAATAATAAATAAATAGATAAAAC
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAG--TAAGAATAATAAATAAATAAATAAAAC
48496655 AAATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAAAT
64 AAATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAAC----AAATAAATAAAT
48496720 AGATAAAAC
125 AGATAAAAC
* *
48496729 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAA-AATAATATATAAATAAATAAAACAA
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAGAATAATAAATAAATAAATAAAACAA
48496793 ATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAGATAA
66 ATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAGATAA
48496858 AAC
131 AAC
* * * * *
48496861 GAATATAAATAATATCAAATTTAAATATTTAAAAATTAA-AAGAAT-AATAAATAAAT-AGA-TA
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAGAATAATAAATAAATAAATAAAACAA
* *
48496922 ATATAAATAATATCAAATTTAAATGTTT-AAAAAGTAAAAGAATAACAAATAAATAAATACATAA
66 ATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAGATAA
48496986 AAC
131 AAC
* *
48496989 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAACAAATAAATAAATAAA
1 AAATATAAATAATATCAAATTTAAATATTTAAAAAGTA-A-GAATAATAAATAAATAAATAAA
48497052 TAGATAAAAC
Statistics
Matches: 297, Mismatches: 21, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
128 73 0.25
129 29 0.10
130 2 0.01
131 14 0.05
132 73 0.25
133 1 0.00
136 70 0.24
137 2 0.01
139 33 0.11
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (133 bp):
AAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAGAATAATAAATAAATAAATAAAACAA
ATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAGATAA
AAC
Found at i:48497047 original size:73 final size:69
Alignment explanation
Indices: 48496590--48497049 Score: 414
Period size: 62 Copynumber: 6.9 Consensus size: 69
48496580 AATAACAAAT
* * * * *
48496590 AAATATAAAAAATATCAATTTTAAATATTTAAAAAGCAAAAGAAT----AATAAATAAATAGATA
1 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
48496651 AAAC
66 AAAC
*
48496655 AAATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAAAT
1 AAATTTAAATAATATCAAATTTAAATATTT-AAAAAGTAAAAGAATAAC----AAATAAATAAAT
*
48496720 AGATAAAAC
61 ACATAAAAC
* *
48496729 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGT--AA-AAT----AATATATAAATAAATA
1 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
48496787 AAAC
66 AAAC
* *
48496791 AAATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAGAT
1 AAATTTAAATAATATCAAATTTAAATATTT-AAAAAGTAAAAGAATAACAAATAAATAAATACAT
48496856 AAAAC
65 AAAAC
* * * * *
48496861 GAATATAAATAATATCAAATTTAAATATTTAAAAATTAAAAGAATAATAAATAAATAGATA-ATA
1 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
48496925 TAAA-
66 -AAAC
* * ** * * *
48496929 TAATATCAAAT--T-T-AAATGTTTAAA-AAGT-AAAAG-AATAA-CA-AATAAATAAATACA--
1 AAAT-TTAAATAATATCAAA--TTTAAATATTTAAAAAGTAA-AAGAATAACAAATAAATAAATA
48496983 --TAAAAC
62 CATAAAAC
* *
48496989 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAACAAATAAATAAATA
1 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATA
48497050 AATAGATAAA
Statistics
Matches: 327, Mismatches: 34, Indels: 66
0.77 0.08 0.15
Matches are distributed among these distances:
59 8 0.02
60 5 0.02
61 7 0.02
62 50 0.15
63 29 0.09
64 5 0.02
65 49 0.15
66 20 0.06
67 7 0.02
68 6 0.02
69 35 0.11
70 48 0.15
71 2 0.01
73 7 0.02
74 49 0.15
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (69 bp):
AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
AAAC
Found at i:48497063 original size:73 final size:69
Alignment explanation
Indices: 48496590--48497049 Score: 396
Period size: 65 Copynumber: 6.9 Consensus size: 69
48496580 AATAACAAAT
* * * * *
48496590 AAATATAAAAAATATCAATTTTAAATATTTAAAAAGCAAAAGAAT----AATAAATAAATAGATA
1 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
48496651 AAAC
66 AAAC
*
48496655 AAATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAAAT
1 AAATTTAAATAATATCAAATTTAAATATTT-AAAAAGTAAAAGAATAAC----AAATAAATAAAT
*
48496720 AGATAAAAC
61 ACATAAAAC
* *
48496729 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGT--AA-AAT----AATATATAAATAAATA
1 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
48496787 AAAC
66 AAAC
* *
48496791 AAATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAGAT
1 AAATTTAAATAATATCAAATTTAAATATTT-AAAAAGTAAAAGAATAACAAATAAATAAATACAT
48496856 AAAAC
65 AAAAC
* * * * *
48496861 GAATATAAATAATATCAAATTTAAATATTTAAAAATTAAAAGAATAATAAATAAATAGATA-ATA
1 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
48496925 TAAA-
66 -AAAC
* * ** * * *
48496929 TAATATCAAAT--T-T-AAATGTTTAAA-AAGT-AAAAG-AATAA-CA-AATAAATAAATACATA
1 AAAT-TTAAATAATATCAAA--TTTAAATATTTAAAAAGTAA-AAGAATAACAAATAAATAAATA
* *
48496985 AAA----C
62 CATAAAAC
* *
48496989 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAACAAATAAATAAATA
1 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATA
48497050 AATAGATAAA
Statistics
Matches: 327, Mismatches: 35, Indels: 66
0.76 0.08 0.15
Matches are distributed among these distances:
59 5 0.02
60 3 0.01
61 7 0.02
62 50 0.15
63 31 0.09
64 6 0.02
65 51 0.16
66 20 0.06
67 7 0.02
68 6 0.02
69 35 0.11
70 48 0.15
71 2 0.01
73 7 0.02
74 49 0.15
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (69 bp):
AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
AAAC
Found at i:48497082 original size:73 final size:69
Alignment explanation
Indices: 48496590--48497049 Score: 476
Period size: 69 Copynumber: 6.9 Consensus size: 69
48496580 AATAACAAAT
* * * * *
48496590 AAATATAAAAAATATCAATTTTAAATATTTAAAAAGCAAAAGAAT----AATAAATAAATAGATA
1 AAATATAAATAAGATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
48496651 AAAC
66 AAAC
* * *
48496655 AAATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAAAT
1 AAATATAAATAAGATCAAATTTAAATATTT-AAAAAGTAAAAGAATAAC----AAATAAATAAAT
*
48496720 AGATAAAAC
61 ACATAAAAC
* * * *
48496729 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGT--AA-AAT----AATATATAAATAAATA
1 AAATATAAATAAGATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
48496787 AAAC
66 AAAC
* * * *
48496791 AAATTTAAATAATATCAAATTTAAATGTTTAAAAAAGTAAAAGAATAACAAATAAATAAATAGAT
1 AAATATAAATAAGATCAAATTTAAATATTT-AAAAAGTAAAAGAATAACAAATAAATAAATACAT
48496856 AAAAC
65 AAAAC
* * * *
48496861 GAATATAAATAATATCAAATTTAAATATTTAAAAATTAAAAGAAT----AATAAATAAATAGAT-
1 AAATATAAATAAGATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
48496921 ----
66 AAAC
* *
48496921 -AATATAAATAATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
1 AAATATAAATAAGATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
48496985 AAAC
66 AAAC
* * * *
48496989 AAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAGAGGAATAACAAATAAATAAATA
1 AAATATAAATAAGATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATA
48497050 AATAGATAAA
Statistics
Matches: 346, Mismatches: 22, Indels: 50
0.83 0.05 0.12
Matches are distributed among these distances:
59 42 0.12
62 47 0.14
63 21 0.06
65 43 0.12
66 17 0.05
69 70 0.20
70 48 0.14
71 2 0.01
73 7 0.02
74 49 0.14
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (69 bp):
AAATATAAATAAGATCAAATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATACATA
AAAC
Found at i:48498378 original size:45 final size:44
Alignment explanation
Indices: 48498215--48498384 Score: 173
Period size: 44 Copynumber: 3.8 Consensus size: 44
48498205 TCGTGACTTT
* * * * **
48498215 AATCTAGTCCACTGTAACTTCAAGGAGATAAGACTCACTATTTC
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGCTATTTC
* * *
48498259 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTG-TAGATTC
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGCTA-TTTC
* * * *
48498303 -ATCTTGCTCCACTGCATCTTTAGGAAGATAAGATTTGCTATCTTC
1 AATC-TACTCCACTGCAACTTCAGGGAGATAAGATTTGCTAT-TTC
*
48498348 AATCTACTCTACTGCAACTTCAGGGAGATAAGATTTG
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG
48498385 TGGCTTCACT
Statistics
Matches: 104, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
43 5 0.05
44 63 0.61
45 33 0.32
46 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGCTATTTC
Found at i:48509556 original size:21 final size:20
Alignment explanation
Indices: 48509506--48509562 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
48509496 TAATAAAGGG
48509506 TAAAGAAATGAAATAATGACA
1 TAAAGAAAT-AAATAATGACA
*
48509527 TAAATAAATAAATAGATGA-A
1 TAAAGAAATAAATA-ATGACA
48509547 TAAAGAAAATAAATAA
1 TAAAG-AAATAAATAA
48509563 AAAGACAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.21
Consensus pattern (20 bp):
TAAAGAAATAAATAATGACA
Found at i:48509797 original size:30 final size:30
Alignment explanation
Indices: 48509762--48509857 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
48509752 ATATCAAATT
*
48509762 TAAATATTTAAAAAGTAAAAGAATAATAAA
1 TAAATATTTAAAAAGCAAAAGAATAATAAA
** * *
48509792 TAAATAGATAAAAA-CAAATATAAATAAT-AT
1 TAAATATTTAAAAAGCAAA-A-GAATAATAAA
* *
48509822 TAAATGTTTAAAAAGCAAAAGAATAACAAA
1 TAAATATTTAAAAAGCAAAAGAATAATAAA
48509852 TAAATA
1 TAAATA
48509858 AATAAATAGA
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
29 8 0.16
30 32 0.64
31 10 0.20
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (30 bp):
TAAATATTTAAAAAGCAAAAGAATAATAAA
Found at i:48509862 original size:75 final size:73
Alignment explanation
Indices: 48509786--48510089 Score: 282
Period size: 70 Copynumber: 4.1 Consensus size: 73
48509776 GTAAAAGAAT
* *
48509786 AATAAATAAATAGATAAAAACAAATATAAATAATATTAAATGTTTAAAAAGCAAAAGAATAACAA
1 AATAAATAAATA-ATATAAA-AAATATAAATAAT-TTAAATGTTTAAAAAGTAAAAGAATAACAA
48509851 ATAAATAAATA
63 ATAAATAAATA
* * *
48509862 AATAGATAAAATAAATACTAAAAAATATACAAT--TTTAAATATTTAAAAAGTAAAAGAATAATA
1 AATAAAT-AAAT-AATA-TAAAAAATATA-AATAATTTAAATGTTTAAAAAGTAAAAGAATAACA
48509925 AATAAATAAATA
62 AATAAATAAATA
* * * *
48509937 GATAAA-ACA-AATATAAATAATAT-CA-AATTTAAATGTTTAAAAAAGTAAAAGAATAACAAAT
1 AATAAATAAATAATATAAAAAATATAAATAATTTAAATGTTT-AAAAAGTAAAAGAATAACAAAT
48509998 AAATAAATA
65 AAATAAATA
* * * * * * **
48510007 AATAGATAAAACAAATTTAAATAATAT-CA-AATTTAAATATTTAAAAAGTAAAAGAATAATGAA
1 AATAAAT-AAA-TAATATAAAAAATATAAATAATTTAAATGTTTAAAAAGTAAAAGAATAACAAA
*
48510070 TAAATACATA
64 TAAATAAATA
* *
48510080 GATAGATAAA
1 AATAAATAAA
48510090 ACAAATTTAA
Statistics
Matches: 196, Mismatches: 21, Indels: 26
0.81 0.09 0.11
Matches are distributed among these distances:
68 1 0.01
69 10 0.05
70 43 0.22
71 4 0.02
72 5 0.03
73 36 0.18
74 27 0.14
75 42 0.21
76 7 0.04
77 14 0.07
78 7 0.04
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (73 bp):
AATAAATAAATAATATAAAAAATATAAATAATTTAAATGTTTAAAAAGTAAAAGAATAACAAATA
AATAAATA
Found at i:48510065 original size:58 final size:59
Alignment explanation
Indices: 48510003--48510304 Score: 199
Period size: 58 Copynumber: 4.9 Consensus size: 59
48509993 CAAATAAATA
*
48510003 AATAAATAGATAAA-ACAAATTTAAATAATATCAAATTTAAATATTTAAAAAGTAAAAG
1 AATAAATAGATAAATACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAG
* * * * *
48510061 AAT-AAT-GAATAAATACATAGATAGATAA-AACAAATTTAAATGTTTAAAAAAGTAAAAG
1 AATAAATAG-ATAAATACAAATATAAATAATATCAAATTTAAATATTT-AAAAAGTAAAAG
* * * *
48510119 AATAACA-A-ATAAAT--AGATA-AAACAAATTTAAATATTTAAATATTTAAAAAGTAAAAG
1 AATAA-ATAGATAAATACAAATATAAA-TAATATCAA-ATTTAAATATTTAAAAAGTAAAAG
* * *
48510176 AATAATAAATAAATAAATAAATAGATAATATAAATAATATCAAATTTAAATGTTTAAAAAGTAAA
1 -------AATAAATAGATAAATACA-AATATAAATAATATCAAATTTAAATATTTAAAAAGTAAA
48510241 AG
58 AG
* *
48510243 AATAACAAATAAATAAATAGATAAAACAAATATAAATAATATCAATTTTAAATATTTAAAAA
1 AAT---AAATAGAT--A-A-AT---ACAAATATAAATAATATCAAATTTAAATATTTAAAAA
48510305 ATAGAGGAAT
Statistics
Matches: 190, Mismatches: 22, Indels: 53
0.72 0.08 0.20
Matches are distributed among these distances:
55 2 0.01
56 6 0.03
57 37 0.19
58 45 0.24
59 1 0.01
60 4 0.02
63 9 0.05
64 6 0.03
65 7 0.04
66 1 0.01
67 26 0.14
68 9 0.05
69 35 0.18
70 2 0.01
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.28
Consensus pattern (59 bp):
AATAAATAGATAAATACAAATATAAATAATATCAAATTTAAATATTTAAAAAGTAAAAG
Found at i:48510105 original size:131 final size:129
Alignment explanation
Indices: 48509921--48510307 Score: 474
Period size: 123 Copynumber: 3.0 Consensus size: 129
48509911 GTAAAAGAAT
* * *
48509921 AATAAATAAATAAATAGATAAA-ACA-AATATAAATAATATCAAATTTAAATGTTTAAAAAAGTA
1 AATAAA-AAATAAATAAATAAATACATAAGATAAATAATAACAAATTTAAATGTTTAAAAAAGTA
48509984 AAAGAATAACAAATAAATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTT
65 AAAGAATAAC----AAATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTT
48510049 AAAA
126 AAAA
* * *
48510053 AGTAAAAGAAT-AATGAATAAATACAT-AGATAGATAA-AACAAATTTAAATGTTTAAAAAAGTA
1 AATAAAA-AATAAATAAATAAATACATAAGATAAATAATAACAAATTTAAATGTTTAAAAAAGTA
* * **
48510115 AAAGAATAAC----AAATAAATAGATAAAACAAATTTAAAT-ATTTAAATATTTAAA-AAGTAAA
65 AAAGAATAACAAATAAATAAATAGATAAAACAAATTTAAATAATATCAA-ATTTAAATATTTAAA
48510174 A
129 A
* * * *
48510175 GAATAATAAATAAATAAATAAATAGATAATATAAATAATATCAAATTTAAATGTTT-AAAAAGTA
1 -AATAAAAAATAAATAAATAAATACATAAGATAAATAATAACAAATTTAAATGTTTAAAAAAGTA
* *
48510239 AAAGAATAACAAATAAATAAATAGATAAAACAAATATAAATAATATCAATTTTAAATATTTAAAA
65 AAAGAATAACAAATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAA
48510304 AATA
1 AATA
48510308 GAGGAATAAC
Statistics
Matches: 218, Mismatches: 23, Indels: 32
0.80 0.08 0.12
Matches are distributed among these distances:
122 14 0.06
123 52 0.24
124 26 0.12
125 16 0.07
128 36 0.17
129 11 0.05
131 44 0.20
132 19 0.09
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.28
Consensus pattern (129 bp):
AATAAAAAATAAATAAATAAATACATAAGATAAATAATAACAAATTTAAATGTTTAAAAAAGTAA
AAGAATAACAAATAAATAAATAGATAAAACAAATTTAAATAATATCAAATTTAAATATTTAAAA
Found at i:48510163 original size:115 final size:122
Alignment explanation
Indices: 48510029--48510280 Score: 333
Period size: 128 Copynumber: 2.1 Consensus size: 122
48510019 AAATTTAAAT
* * *
48510029 AATATCAA-ATTTAAATATTTAAAAAGTAAAAG-AAT-AATGAATAAATACATAGAT-AGAT-A-
1 AATATAAATATTTAAATATTTAAAAAGTAAAAGAAATAAATAAATAAATAAATAGATAAGATAAT
48510088 AA-A-CAAATTTAAATGTTTAAAAAAGTAAAAGAATAAC-AAATAAATAGATAAAACA
66 AATATCAAATTTAAATGTTT-AAAAAGTAAAAGAATAACAAAATAAATAGATAAAACA
* *
48510143 AATTTAAATATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAAATAAATAGATAATATA
1 AATATAAATATTTAAATATTTAAAAAGTAAAAG-A-AATAAATAAATAAATAAATAGATAAGAT-
48510208 AATAATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAATAAATAGATAAAACA
63 AATAATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAAC--A-AAATAAATAGATAAAACA
48510271 AATATAAATA
1 AATATAAATA
48510281 ATATCAATTT
Statistics
Matches: 117, Mismatches: 6, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
114 6 0.05
115 24 0.21
118 3 0.03
119 17 0.15
120 3 0.03
122 1 0.01
123 2 0.02
124 19 0.16
125 15 0.13
128 27 0.23
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.27
Consensus pattern (122 bp):
AATATAAATATTTAAATATTTAAAAAGTAAAAGAAATAAATAAATAAATAAATAGATAAGATAAT
AATATCAAATTTAAATGTTTAAAAAGTAAAAGAATAACAAAATAAATAGATAAAACA
Found at i:48510188 original size:4 final size:4
Alignment explanation
Indices: 48510179--48510212 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
48510169 GTAAAAGAAT
*
48510179 AATA AATA AATA AATA AATA GATA ATATA AATA A
1 AATA AATA AATA AATA AATA AATA A-ATA AATA A
48510213 TATCAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:48510301 original size:69 final size:67
Alignment explanation
Indices: 48510152--48510332 Score: 254
Period size: 69 Copynumber: 2.7 Consensus size: 67
48510142 AAATTTAAAT
* * *
48510152 ATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAAATAAATAGATAATATAAATAATATC
1 ATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATAAATAAAAAATATAAATAATATC
48510217 AA
66 AA
* *
48510219 ATTTAAATGTTTAAAAAGTAAAAGAATAACAAATAAATAAATAGATAAAACAAATATAAATAATA
1 ATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATAAAT-AAA-AAATATAAATAATA
48510284 TCAA
64 TCAA
* * * * *
48510288 TTTTAAATATTTAAAAAATAGAGGAATAACAAATAAATAGATAAA
1 ATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATAAA
48510333 ACAACTCATA
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
67 43 0.43
68 2 0.02
69 55 0.55
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.28
Consensus pattern (67 bp):
ATTTAAATATTTAAAAAGTAAAAGAATAACAAATAAATAAATAAATAAAAAATATAAATAATATC
AA
Found at i:48513314 original size:19 final size:20
Alignment explanation
Indices: 48513270--48513314 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
48513260 CAAAAATTAC
48513270 ATAAAAATATAAAATAATTT
1 ATAAAAATATAAAATAATTT
*
48513290 -TTAAAAT-TCAAAAT-ATTT
1 ATAAAAATAT-AAAATAATTT
48513308 ATAAAAA
1 ATAAAAA
48513315 AATCTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAAAATATAAAATAATTT
Found at i:48514981 original size:32 final size:33
Alignment explanation
Indices: 48514945--48515014 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
48514935 TTGTAGAATG
*
48514945 CTTAATTTACTT-TTTTAATTATTTTACGAGAA
1 CTTAATTAACTTATTTTAATTATTTTACGAGAA
*
48514977 CTTAATTAACTTATTTTAATTATTTTAGGAGAA
1 CTTAATTAACTTATTTTAATTATTTTACGAGAA
*
48515010 GTTAA
1 CTTAA
48515015 ATGATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 11 0.32
33 23 0.68
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (33 bp):
CTTAATTAACTTATTTTAATTATTTTACGAGAA
Found at i:48515126 original size:20 final size:19
Alignment explanation
Indices: 48515097--48515143 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
48515087 AGTTTTTAAA
*
48515097 TTTT-ATAACATTTAATACT
1 TTTTAATAACATTT-ATAAT
48515116 TTTTAATAACATTTATAAT
1 TTTTAATAACATTTATAAT
48515135 TTTCTAATA
1 TTT-TAATA
48515144 TTTTAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATAACATTTATAAT
Found at i:48515137 original size:19 final size:20
Alignment explanation
Indices: 48515097--48515162 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 20
48515087 AGTTTTTAAA
*
48515097 TTTT-ATAACATTTAATACT
1 TTTTAATAACATTTAATAAT
48515116 TTTTAATAACATTT-ATAAT
1 TTTTAATAACATTTAATAAT
*
48515135 TTTCTAAT-A-TTTTAATAAT
1 TTT-TAATAACATTTAATAAT
*
48515154 TTCTAATAA
1 TTTTAATAA
48515163 TTTTTAAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.17
19 20 0.50
20 13 0.32
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTTAATAACATTTAATAAT
Done.