Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 171 of 222
Found at i:54924238 original size:15 final size:16
Alignment explanation
Indices: 54924218--54924259 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
54924208 TTGGCCAAAA
*
54924218 ACCGCTGGTTCT-GCT
1 ACCGCTGGTTCTAGCC
54924233 ACCGCTGGTT-TAGCC
1 ACCGCTGGTTCTAGCC
54924248 ACCGCTGGTTCT
1 ACCGCTGGTTCT
54924260 TCTAATGACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.10, C:0.33, G:0.26, T:0.31
Consensus pattern (16 bp):
ACCGCTGGTTCTAGCC
Found at i:54926764 original size:15 final size:15
Alignment explanation
Indices: 54926744--54926791 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
54926734 AGACACGGGC
54926744 TGTCACATGGCCGTG
1 TGTCACATGGCCGTG
54926759 TGTCACATGGCC-TG
1 TGTCACATGGCCGTG
* * *
54926773 -GTGACACGGTCGTG
1 TGTCACATGGCCGTG
54926787 TGTCA
1 TGTCA
54926792 TTTGTGAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 8 0.30
14 4 0.15
15 15 0.56
ACGTcount: A:0.15, C:0.25, G:0.33, T:0.27
Consensus pattern (15 bp):
TGTCACATGGCCGTG
Found at i:54933329 original size:20 final size:20
Alignment explanation
Indices: 54933306--54933343 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
54933296 TTCTACTCTG
*
54933306 TTCTGTTTTACTCTATTCTA
1 TTCTGATTTACTCTATTCTA
54933326 TTCTGATTTACTCTATTC
1 TTCTGATTTACTCTATTC
54933344 AGTTCAGTTC
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:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (20 bp):
TTCTGATTTACTCTATTCTA
Found at i:54938127 original size:27 final size:25
Alignment explanation
Indices: 54938075--54938124 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
54938065 GATAGGAGAA
54938075 AGAAATTTCTCTCTAATCTATGGTG
1 AGAAATTTCTCTCTAATCTATGGTG
54938100 AGAAATTTCTCTCTAATCTATGGTG
1 AGAAATTTCTCTCTAATCTATGGTG
54938125 TGAATGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (25 bp):
AGAAATTTCTCTCTAATCTATGGTG
Found at i:54938701 original size:69 final size:69
Alignment explanation
Indices: 54938567--54938991 Score: 341
Period size: 69 Copynumber: 6.2 Consensus size: 69
54938557 CATTCGTGTC
* ** * * * * * * * * *
54938567 ATATTAAGGTTTGCAGGTGAAGTGCCGTAACCTCTAAAACAGTTAGCGAGATCAATGCTCTCAAC
1 ATATTAAGGTTCGCAGGCAAAGAGCTGCAACCTCCAAAACAATTAGCAAGAGCAAAGCTCCCAAC
54938632 TATA
66 TATA
* * * * *
54938636 ATATTAAGGTTCGTAGGCAAAGAGCTGAAACCTTCAAAATAGTTAGCAAGAGCAAAGCTCCCAAC
1 ATATTAAGGTTCGCAGGCAAAGAGCTGCAACCTCCAAAACAATTAGCAAGAGCAAAGCTCCCAAC
54938701 TATA
66 TATA
* * * * *
54938705 ATATTGAGGTTCGCAGGCAAAGAGCTGCAACCTCCAAAACAATTAGCAAGAGAAAATCTCCTAGC
1 ATATTAAGGTTCGCAGGCAAAGAGCTGCAACCTCCAAAACAATTAGCAAGAGCAAAGCTCCCAAC
** *
54938770 CGTC
66 TATA
* * * * * * *
54938774 ATATGAAGGTTCGCAGGCAAAGAGCCGCAATCTCCAAAACAATTAGCAAGAGTAAAGGTGCCAGC
1 ATATTAAGGTTCGCAGGCAAAGAGCTGCAACCTCCAAAACAATTAGCAAGAGCAAAGCTCCCAAC
* *
54938839 TTTC
66 TATA
* * *
54938843 ATATTAAGGTTCACAGGCGAAGAG-TCGCAACCTCCAAAATAATTAGCGAA-AGCAAAGCTCCCA
1 ATATTAAGGTTCGCAGGCAAAGAGCT-GCAACCTCCAAAACAATTAGC-AAGAGCAAAGCTCCCA
* *
54938906 GCTATC
64 ACTATA
* * ** ** * * * * ** *
54938912 ATATTAAGATTCACAGGTGAAGAGCCACAACCTTCAAAATAGTTAGCTAGAGCAAAGCTGTCAAT
1 ATATTAAGGTTCGCAGGCAAAGAGCTGCAACCTCCAAAACAATTAGCAAGAGCAAAGCTCCCAAC
*
54938977 TGTA
66 TATA
54938981 ATATTAAGGTT
1 ATATTAAGGTT
54938992 TGTAGACGAA
Statistics
Matches: 290, Mismatches: 62, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
68 1 0.00
69 287 0.99
70 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (69 bp):
ATATTAAGGTTCGCAGGCAAAGAGCTGCAACCTCCAAAACAATTAGCAAGAGCAAAGCTCCCAAC
TATA
Found at i:54938820 original size:138 final size:138
Alignment explanation
Indices: 54938636--54938991 Score: 383
Period size: 138 Copynumber: 2.6 Consensus size: 138
54938626 CTCAACTATA
* * *
54938636 ATATTAAGGTTCGTAGGCAAAGAGCTGAAACCTTCAAAATAGTTAGCAAGAGCAAAGCTCCCAAC
1 ATATTAAGGTTCGCAGGCAAAGAGCCGCAACCTTCAAAATAGTTAGCAAGAGCAAAGCTCCCAAC
* * *
54938701 TATAATATTGAGGTTCGCAGGCAAAGAG-CTGCAACCTCCAAAACAATTAGC-AAGAGAAAATCT
66 TATAATATTAAGGTTCACAGGCAAAGAGTC-GCAACCTCCAAAACAATTAGCGAA-AGAAAAGCT
* *
54938764 CCTAGCCGTC
129 CCCAGCCATC
* * * * * * * * *
54938774 ATATGAAGGTTCGCAGGCAAAGAGCCGCAATCTCCAAAACAATTAGCAAGAGTAAAGGTGCCAGC
1 ATATTAAGGTTCGCAGGCAAAGAGCCGCAACCTTCAAAATAGTTAGCAAGAGCAAAGCTCCCAAC
* * * * *
54938839 TTTCATATTAAGGTTCACAGGCGAAGAGTCGCAACCTCCAAAATAATTAGCGAAAGCAAAGCTCC
66 TATAATATTAAGGTTCACAGGCAAAGAGTCGCAACCTCCAAAACAATTAGCGAAAGAAAAGCTCC
*
54938904 CAGCTATC
131 CAGCCATC
* * ** * * ** *
54938912 ATATTAAGATTCACAGGTGAAGAGCCACAACCTTCAAAATAGTTAGCTAGAGCAAAGCTGTCAAT
1 ATATTAAGGTTCGCAGGCAAAGAGCCGCAACCTTCAAAATAGTTAGCAAGAGCAAAGCTCCCAAC
*
54938977 TGTAATATTAAGGTT
66 TATAATATTAAGGTT
54938992 TGTAGACGAA
Statistics
Matches: 175, Mismatches: 41, Indels: 4
0.80 0.19 0.02
Matches are distributed among these distances:
138 172 0.98
139 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (138 bp):
ATATTAAGGTTCGCAGGCAAAGAGCCGCAACCTTCAAAATAGTTAGCAAGAGCAAAGCTCCCAAC
TATAATATTAAGGTTCACAGGCAAAGAGTCGCAACCTCCAAAACAATTAGCGAAAGAAAAGCTCC
CAGCCATC
Found at i:54953256 original size:9 final size:10
Alignment explanation
Indices: 54953225--54953259 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
54953215 AAAATCAATC
*
54953225 AAAAAATCCA
1 AAAAAATTCA
54953235 AAAAAATTCA
1 AAAAAATTCA
54953245 AAAAAATT-A
1 AAAAAATTCA
54953254 AAAAAA
1 AAAAAA
54953260 AAAAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAAATTCA
Found at i:54954215 original size:15 final size:15
Alignment explanation
Indices: 54954188--54954225 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
54954178 TTGAGTTAGA
54954188 AAAAATATGAAAAA-T
1 AAAAA-ATGAAAAAGT
*
54954203 GAAAAATGAAAAAGT
1 AAAAAATGAAAAAGT
54954218 AAAAAATG
1 AAAAAATG
54954226 GATAGGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (15 bp):
AAAAAATGAAAAAGT
Found at i:54955580 original size:86 final size:87
Alignment explanation
Indices: 54955432--54955673 Score: 351
Period size: 86 Copynumber: 2.8 Consensus size: 87
54955422 GATGAAACTA
* * *
54955432 TAAGTCCTAGCTCCCTGTACAGCAGTGGAATAGGCGGAAGATTGTAAATCCTAGCTTCCTGACCA
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCAGAAGATTGTAAATCCTAGCTCCCTGACCA
*
54955497 GCAACGGAATAGGTGGAAGA-C
66 GCAACAGAATAGGTGGAAGATC
* * *
54955518 TATGTCCTAACTCCCTGAACAGCAGTGGAATATGCAGAAGATTGTAAATCCTAGCTCCCTGACCA
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCAGAAGATTGTAAATCCTAGCTCCCTGACCA
** *
54955583 GCTGCAGAATAGGTGGAAGATTG
66 GCAACAGAATAGGTGGAAGA-TC
* * *
54955606 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGGAGAAGATTGTAAGTCCTAGCTCCCTGAGCA
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCAGAAGATTGTAAATCCTAGCTCCCTGACCA
54955671 GCA
66 GCA
54955674 GTGGAGCAGG
Statistics
Matches: 137, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 76 0.55
88 61 0.45
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (87 bp):
TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCAGAAGATTGTAAATCCTAGCTCCCTGACCA
GCAACAGAATAGGTGGAAGATC
Found at i:54955691 original size:44 final size:44
Alignment explanation
Indices: 54955432--54955678 Score: 293
Period size: 44 Copynumber: 5.7 Consensus size: 44
54955422 GATGAAACTA
* *
54955432 TAAGTCCTAGCTCCCTGTACAGCAGTGGAATAGGCGGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
* * * ** *
54955476 TAAATCCTAGCTTCCTGACCAGCAACGGAATAGGTGGAAGA--C
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
* * * **
54955518 TATGTCCTAACTCCCTGAACAGCAGTGGAATATGCAGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
* * * **
54955562 TAAATCCTAGCTCCCTGACCAGCTGCAGAATAGGTGGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
54955606 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGG-GAGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTG-GAAGATTG
*
54955650 TAAGTCCTAGCTCCCTGAGCAGCAGTGGA
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGA
54955679 GCAGGTTGAA
Statistics
Matches: 165, Mismatches: 35, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
42 31 0.19
43 1 0.01
44 133 0.81
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (44 bp):
TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
Found at i:54955778 original size:88 final size:88
Alignment explanation
Indices: 54955673--54955998 Score: 483
Period size: 88 Copynumber: 3.7 Consensus size: 88
54955663 CCTGAGCAGC
* * *
54955673 AGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGATAACAAAGCAGATCGAAGACA
1 AGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAGCGAAGCAGATCGAAGACA
54955738 CAAGCCTTGCCTCCCTCGGTTGT
66 CAAGCCTTGCCTCCCTCGGTTGT
* * *
54955761 AATGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACA
1 AGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAGCGAAGCAGATCGAAGACA
* *
54955826 CAAGCCTTGTCTCCCTCGATTGT
66 CAAGCCTTGCCTCCCTCGGTTGT
* * * *
54955849 AGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCAACGGCGAAGCAAATCTAAGACA
1 AGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAGCGAAGCAGATCGAAGACA
54955914 CAAGCCTTGCCTCCCTCGGTTGT
66 CAAGCCTTGCCTCCCTCGGTTGT
* * * * *
54955937 AGTGGAGCTGGTTGAAGATAGCATG-TCTTACCTTCCTGCATCGACAGTGAAGTAGATCGAAG
1 AGTGGAGCAGGTTGAAGATAGCA-GATCTTGCCTTCCTACATCGACAGCGAAGCAGATCGAAG
54955999 CCAATGGTCC
Statistics
Matches: 211, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
88 210 1.00
89 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (88 bp):
AGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAGCGAAGCAGATCGAAGACA
CAAGCCTTGCCTCCCTCGGTTGT
Found at i:54955791 original size:44 final size:44
Alignment explanation
Indices: 54955675--54955881 Score: 133
Period size: 44 Copynumber: 4.7 Consensus size: 44
54955665 TGAGCAGCAG
* *
54955675 TGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTAC-ATCGATAA
1 TGGAGCAGGTTGAAGATAGCAGATCTTGCCTCCCT-CGATTG-TAA
*** * * * * *
54955720 CAAAGCAGATCGAAGACA-CA-AGCCTTGCCTCCCTCGGTTGTAA
1 TGGAGCAGGTTGAAGATAGCAGA-TCTTGCCTCCCTCGATTGTAA
*
54955763 TGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCT-GCATTG-ACA
1 TGGAGCAGGTTGAAGATAGCAGATCTTGCCTCCCTCG-ATTGTA-A
* * * * * *
54955807 -GCGAAGCAGATCGAAGACA-CA-AGCCTTGTCTCCCTCGATTGTAG
1 TG-G-AGCAGGTTGAAGATAGCAGA-TCTTGCCTCCCTCGATTGTAA
54955851 TGGAGCAGGTTGAAGATAGCAGATCTTGCCT
1 TGGAGCAGGTTGAAGATAGCAGATCTTGCCT
54955882 TCCTACATCA
Statistics
Matches: 117, Mismatches: 31, Indels: 29
0.66 0.18 0.16
Matches are distributed among these distances:
43 33 0.28
44 55 0.47
45 29 0.25
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (44 bp):
TGGAGCAGGTTGAAGATAGCAGATCTTGCCTCCCTCGATTGTAA
Found at i:54961298 original size:20 final size:20
Alignment explanation
Indices: 54961275--54961315 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54961265 TTTGAATTGT
* *
54961275 TGCTAAACTATTTCATTGCA
1 TGCTAAACCATCTCATTGCA
54961295 TGCTAAACCATCTCATTGCA
1 TGCTAAACCATCTCATTGCA
54961315 T
1 T
54961316 TTTTCATTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (20 bp):
TGCTAAACCATCTCATTGCA
Found at i:54968482 original size:11 final size:13
Alignment explanation
Indices: 54968462--54968493 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54968452 AATAAATTAA
54968462 TAAAATATCAT-T
1 TAAAATATCATAT
54968474 TAAAA-ATCATAT
1 TAAAATATCATAT
54968486 TAAAATAT
1 TAAAATAT
54968494 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:54976866 original size:285 final size:285
Alignment explanation
Indices: 54976356--54976891 Score: 957
Period size: 285 Copynumber: 1.9 Consensus size: 285
54976346 TCCCATTCAC
*
54976356 CACATTAACTCTCCTTCTCTCACCTTCCTTGTTTCTCCATATGGCAAGTCACAGTGTAATAATAG
1 CACATTAACTCTCCTTCTCTCACCTTCCTTATTTCTCCATATGGCAAGTCACAGTGTAATAATAG
*
54976421 CAATTATGGTCAACTTATGAGTTTTTGTGCATTAATGATCAAGTGTTTCTATTTTTGTGACCTTA
66 CAATTATGGTCAACTTATGAGTTTTTGTGCACTAATGATCAAGTGTTTCTATTTTTGTGACCTTA
*
54976486 TTTTTGGATCACTTTGACTTTTTCAACATTTTCTCACTCATAATGCTTTTTTATTGATTTTGTAC
131 TTTTTGGATCACTTTGACTTTTTCAACATTTTCTCACTCATAATGCTTTTCTATTGATTTTGTAC
*
54976551 TTTTCCACTCGTTTTGACTTTTTCTAAAATTTTCTTTATTCGCATATTTGTAGCTTTAGCTATAA
196 TTTTCCACTCGTTTTGACTTTTTCTAAAATTTTCTTTATTCACATATTTGTAGCTTTAGCTATAA
54976616 TTAATATATCACACTTTTTTATTCG
261 TTAATATATCACACTTTTTTATTCG
* *
54976641 CACATTAACTCTTCTTCTCTCACCTTTCTTATTTCTCCATATGAG-AAGTCACAGTGTAATAATA
1 CACATTAACTCTCCTTCTCTCACCTTCCTTATTTCTCCATATG-GCAAGTCACAGTGTAATAATA
54976705 GCAATTATGGTCAACTTATGAGTTTTTGTGCACTAATGATCAAGTGTTTCTATTTTTGTGACCTT
65 GCAATTATGGTCAACTTATGAGTTTTTGTGCACTAATGATCAAGTGTTTCTATTTTTGTGACCTT
* * * *
54976770 ATTTTTGGATCACTTTGATTTTTTCAACCTTTTCTCACTCATAATTCTTTTCTATTGATTTTGTG
130 ATTTTTGGATCACTTTGACTTTTTCAACATTTTCTCACTCATAATGCTTTTCTATTGATTTTGTA
*
54976835 CTTTTCCACTCGTTTTGACTTTTTCTAAAATTTTCTTTATTCACATATTTTTAGCTT
195 CTTTTCCACTCGTTTTGACTTTTTCTAAAATTTTCTTTATTCACATATTTGTAGCTT
54976892 AACCATTATC
Statistics
Matches: 239, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
285 238 1.00
286 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.48
Consensus pattern (285 bp):
CACATTAACTCTCCTTCTCTCACCTTCCTTATTTCTCCATATGGCAAGTCACAGTGTAATAATAG
CAATTATGGTCAACTTATGAGTTTTTGTGCACTAATGATCAAGTGTTTCTATTTTTGTGACCTTA
TTTTTGGATCACTTTGACTTTTTCAACATTTTCTCACTCATAATGCTTTTCTATTGATTTTGTAC
TTTTCCACTCGTTTTGACTTTTTCTAAAATTTTCTTTATTCACATATTTGTAGCTTTAGCTATAA
TTAATATATCACACTTTTTTATTCG
Found at i:54979978 original size:40 final size:40
Alignment explanation
Indices: 54979691--54979962 Score: 508
Period size: 40 Copynumber: 6.8 Consensus size: 40
54979681 CATTTGAATG
54979691 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
54979731 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
54979771 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
54979811 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* *
54979851 ACATCCGGGCTAAGACCCGAAGGTATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
*
54979891 ACATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
*
54979931 ATATCCGGGCTAAGACCCGAGGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
54979963 TTGTGGTTAT
Statistics
Matches: 227, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 227 1.00
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
Found at i:54995156 original size:27 final size:27
Alignment explanation
Indices: 54995117--54995294 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
54995107 TTATTGAGCC
* * *
54995117 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* * *
54995144 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
*
54995171 CGCACACTTAGTGCCACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
** * *
54995199 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
54995226 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
*
54995253 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAGTC-AACT
*
54995280 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
54995295 GTACAATTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 102 0.80
28 26 0.20
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:54995256 original size:82 final size:81
Alignment explanation
Indices: 54995138--54995293 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
54995128 TGCTATATAA
* *
54995138 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCCACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54995203 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
54995220 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
*
54995284 CCCTTAGTGC
65 CACTTAGTGC
54995294 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.77
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:55007543 original size:14 final size:14
Alignment explanation
Indices: 55007524--55007550 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55007514 CATTTCTTGG
55007524 TCGGTTCAGTTCAC
1 TCGGTTCAGTTCAC
55007538 TCGGTTCAGTTCA
1 TCGGTTCAGTTCA
55007551 ACTGGACCAC
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:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (14 bp):
TCGGTTCAGTTCAC
Found at i:55008684 original size:30 final size:30
Alignment explanation
Indices: 55008650--55008706 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
55008640 ATTAAGAGAG
55008650 AAGTGATGGCTAAATATTGCAAGGGTTCAA
1 AAGTGATGGCTAAATATTGCAAGGGTTCAA
55008680 AAGTGATGGCTAAATATTGCAAGGGTT
1 AAGTGATGGCTAAATATTGCAAGGGTT
55008707 TAAATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (30 bp):
AAGTGATGGCTAAATATTGCAAGGGTTCAA
Found at i:55011341 original size:30 final size:30
Alignment explanation
Indices: 55011284--55011345 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
55011274 GCTTTTTGAA
* *
55011284 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAATTTTT
*
55011314 AATATTTATAAAAAGA-GCAACCAAATTTTT
1 AATATTTACAAAAAGAGGC-ACCAAATTTTT
55011344 AA
1 AA
55011346 AAATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAATTTTT
Found at i:55026020 original size:29 final size:30
Alignment explanation
Indices: 55025961--55026021 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
55025951 GCTTTTTGAA
* * *
55025961 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCAACCAAATTTT
*
55025991 AATATTTATAAAAAGA-GCAACCAAATTTT
1 AATATTTACAAAAAGAGGCAACCAAATTTT
55026020 AA
1 AA
55026022 AAATAATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCAACCAAATTTT
Found at i:55037100 original size:22 final size:22
Alignment explanation
Indices: 55037056--55037106 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
55037046 AATAGAAAAT
*
55037056 TGAAAGAAAAACTAAATACAAA
1 TGAAAGCAAAACTAAATACAAA
*
55037078 TGAAAGCAAAATTAAA-ACTAAA
1 TGAAAGCAAAACTAAATAC-AAA
*
55037100 TAAAAGC
1 TGAAAGC
55037107 TAAGTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.16
Consensus pattern (22 bp):
TGAAAGCAAAACTAAATACAAA
Found at i:55046207 original size:61 final size:61
Alignment explanation
Indices: 55046121--55046235 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
55046111 AATGTATGTT
* * *
55046121 TTGAGTTTTATAAGTTGAAATAAATTGCATAAATTATATATATATTTAGCCGAATATATATG
1 TTGAGTTTTATAAGTTGAAATAAATTGAATAAATTACATATAT-GTTAGCCGAATATATATG
* * *
55046183 TTGAG-TTTGTAAGTTG-AATGAAATTTAATGAATTACATATATGTTAGCCGAAT
1 TTGAGTTTTATAAGTTGAAAT-AAATTGAATAAATTACATATATGTTAGCCGAAT
55046236 GTATGTATTG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 13 0.28
61 28 0.61
62 5 0.11
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (61 bp):
TTGAGTTTTATAAGTTGAAATAAATTGAATAAATTACATATATGTTAGCCGAATATATATG
Found at i:55051237 original size:2 final size:2
Alignment explanation
Indices: 55051230--55051263 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55051220 TCCACTCGCT
55051230 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55051264 CTCAACTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55066395 original size:2 final size:2
Alignment explanation
Indices: 55066388--55066416 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55066378 TGTTTCTCTT
55066388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55066417 TCTTTTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55071722 original size:23 final size:24
Alignment explanation
Indices: 55071677--55071723 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
55071667 TATTTTAAGT
* *
55071677 TTAATCTTAATTAAATTTGATTAA
1 TTAATCTTAATCAAATTTAATTAA
*
55071701 TTAAT-TTAATCAAGTTTAATTAA
1 TTAATCTTAATCAAATTTAATTAA
55071724 GCTTTAATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
TTAATCTTAATCAAATTTAATTAA
Found at i:55075956 original size:68 final size:68
Alignment explanation
Indices: 55075839--55076010 Score: 227
Period size: 68 Copynumber: 2.5 Consensus size: 68
55075829 TATAAGACTA
* * *
55075839 TAAGACCATAGTTAGGCTATGGCAACATATGAAGTCCGCCAGGACAGTAAACATGTCATCATATA
1 TAAGACCATAGTTGGGCTATGGCAACATATGAAGTCCGACAGGACAGTAAACATGGCATCATATA
55075904 GTG
66 GTG
* * * * * * *
55075907 TAAGACCATAGCTGGGTTATGGAAACATATGAATTCTGACATGATAGTAAACATGGCATCATATA
1 TAAGACCATAGTTGGGCTATGGCAACATATGAAGTCCGACAGGACAGTAAACATGGCATCATATA
55075972 GTG
66 GTG
* * *
55075975 TAAGACTATAGTTGGGCTATGGCAATATATGTAGTC
1 TAAGACCATAGTTGGGCTATGGCAACATATGAAGTC
55076011 TGCCAAGACA
Statistics
Matches: 87, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 87 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (68 bp):
TAAGACCATAGTTGGGCTATGGCAACATATGAAGTCCGACAGGACAGTAAACATGGCATCATATA
GTG
Found at i:55083051 original size:22 final size:23
Alignment explanation
Indices: 55083018--55083070 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
55083008 ACCCCTTAAC
* *
55083018 TAACATTACCAAT-TCATAATT-
1 TAACATTCCCAATCTCAAAATTA
55083039 TAGACATTCCCAATCTCAAAATTA
1 TA-ACATTCCCAATCTCAAAATTA
55083063 TAACATTC
1 TAACATTC
55083071 AATCCAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 10 0.37
23 13 0.48
24 2 0.07
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.34
Consensus pattern (23 bp):
TAACATTCCCAATCTCAAAATTA
Found at i:55085292 original size:21 final size:21
Alignment explanation
Indices: 55085268--55085322 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
55085258 GTTTGCTTTT
*
55085268 AGTTTAGCTCTTATGAGCTTC
1 AGTTTAACTCTTATGAGCTTC
* * *
55085289 AG-TTAACTCATATGAGTTTT
1 AGTTTAACTCTTATGAGCTTC
*
55085309 AGTTTAACCCTTAT
1 AGTTTAACTCTTAT
55085323 AGGTTTCCGT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (21 bp):
AGTTTAACTCTTATGAGCTTC
Found at i:55100760 original size:50 final size:50
Alignment explanation
Indices: 55100705--55100830 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
55100695 CATTGAGGTT
* * * *
55100705 ATGAGAGGTCCCATGTAAGATCATATCTAGG-ACATGGCGTTGGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATATCT-GGAACATGGCATAGACACCAAG
* * * * *
55100755 ATGAGAGGCCCCTTGTAAGACCATGTCTGGAACATGGCATAGACACCGAT
1 ATGAGAGGTCCCATGTAAGACCATATCTGGAACATGGCATAGACACCAAG
**
55100805 ATGAGAACTCCCATGTAAGACCATAT
1 ATGAGAGGTCCCATGTAAGACCATAT
55100831 ATGGGATATG
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
49 2 0.03
50 59 0.97
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATATCTGGAACATGGCATAGACACCAAG
Found at i:55116868 original size:40 final size:40
Alignment explanation
Indices: 55116777--55116946 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 40
55116767 TCCTCGTTCA
* * * * *
55116777 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
55116816 AATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
55116856 AATGCCTTCGGGACTTAACCCAGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
55116896 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
55116936 AAGGCCTTCGG
1 AATGCCTTCGG
55116947 ATCTTAGTCC
Statistics
Matches: 116, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
39 33 0.28
40 83 0.72
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:55116959 original size:40 final size:40
Alignment explanation
Indices: 55116775--55116999 Score: 195
Period size: 40 Copynumber: 5.7 Consensus size: 40
55116765 GCTCCTCGTT
* * * * * *
55116775 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * *
55116815 C-AATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * *
55116854 CGAATGCCTTCGGGACTTAACCCAGATTTAATAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * *
55116894 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
** * * ** *
55116934 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCGCTTAGCA
1 CAAAGGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCA
*
55116975 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGA
55117000 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
39 36 0.23
40 112 0.70
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:55133604 original size:18 final size:18
Alignment explanation
Indices: 55133571--55133623 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
55133561 ATTCACCTAA
*
55133571 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
* *
55133590 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
*
55133608 ACCCAACCTAACCCAA
1 ACCCAACCCAACCCAA
55133624 CCCAATCATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:55133704 original size:25 final size:25
Alignment explanation
Indices: 55133676--55133730 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
55133666 AATTTCAATT
* *
55133676 ATGTGTTAATTTCAAA-ACTTATTTA
1 ATGTGGTAA-TTCAAAGACTTATGTA
*
55133701 ATGTTGGTGATTCAAAGACTTATGTA
1 ATG-TGGTAATTCAAAGACTTATGTA
55133727 ATGT
1 ATGT
55133731 TTTTAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (25 bp):
ATGTGGTAATTCAAAGACTTATGTA
Found at i:55133765 original size:9 final size:9
Alignment explanation
Indices: 55133751--55133835 Score: 100
Period size: 9 Copynumber: 9.4 Consensus size: 9
55133741 GTAGTGATTC
55133751 AATTCGGTT
1 AATTCGGTT
*
55133760 AATTCGGGT
1 AATTCGGTT
*
55133769 AATTCGGGT
1 AATTCGGTT
*
55133778 AATTCTGTT
1 AATTCGGTT
55133787 AATTCGGTT
1 AATTCGGTT
*
55133796 ACTTCAGG-T
1 AATTC-GGTT
*
55133805 AATTCAGTT
1 AATTCGGTT
*
55133814 AATTCGGAT
1 AATTCGGTT
55133823 AATTCGGTT
1 AATTCGGTT
55133832 AATT
1 AATT
55133836 TTTAACCAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
8 1 0.02
9 61 0.95
10 2 0.03
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:55135821 original size:26 final size:26
Alignment explanation
Indices: 55135792--55135845 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
55135782 TTTTTATAAT
*
55135792 TTTTAAATATAATTTTT-ATTTATTTA
1 TTTT-AATATAATTTTTAAATTATTTA
**
55135818 TTTTTTTATAATTTTTAAATTATTTA
1 TTTTAATATAATTTTTAAATTATTTA
55135844 TT
1 TT
55135846 AATATGGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
TTTTAATATAATTTTTAAATTATTTA
Found at i:55147704 original size:26 final size:24
Alignment explanation
Indices: 55147675--55147746 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 24
55147665 CTAAACCAAA
*
55147675 AAACTATAAAAATATTTAAAAATCCT
1 AAACT-TAAAAATA-TTAAAAACCCT
*
55147701 AAACCTTAATAATATT-AAAACCCT
1 AAA-CTTAAAAATATTAAAAACCCT
*
55147725 AAACCTAAAAATATTAAAAACC
1 AAACTTAAAAATATTAAAAACC
55147747 TTAACCCTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 10 0.25
24 16 0.40
25 2 0.05
26 10 0.25
27 2 0.05
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (24 bp):
AAACTTAAAAATATTAAAAACCCT
Found at i:55147741 original size:23 final size:24
Alignment explanation
Indices: 55147681--55147752 Score: 92
Period size: 23 Copynumber: 3.0 Consensus size: 24
55147671 CAAAAAACTA
55147681 TAAAAATATTTAAAAATCCTAAACCT
1 TAAAAATA-TTAAAAA-CCTAAACCT
* *
55147707 TAATAATATTAAAACCCTAAACC-
1 TAAAAATATTAAAAACCTAAACCT
*
55147730 TAAAAATATTAAAAACCTTAACC
1 TAAAAATATTAAAAACCTAAACC
55147753 CTAGGAGAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.49
24 8 0.20
25 6 0.15
26 7 0.17
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (24 bp):
TAAAAATATTAAAAACCTAAACCT
Found at i:55147755 original size:24 final size:24
Alignment explanation
Indices: 55147681--55147755 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
55147671 CAAAAAACTA
* *
55147681 TAAAAATATTTAAAAATCCTAAACCT
1 TAAAAATA-TTAAAAA-CCTTAACCC
* * *
55147707 TAATAATATT-AAAACCCTAAACC
1 TAAAAATATTAAAAACCTTAACCC
55147730 TAAAAATATTAAAAACCTTAACCC
1 TAAAAATATTAAAAACCTTAACCC
55147754 TA
1 TA
55147756 GGAGAGAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 14 0.35
24 17 0.43
25 2 0.05
26 7 0.17
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (24 bp):
TAAAAATATTAAAAACCTTAACCC
Found at i:55155520 original size:9 final size:9
Alignment explanation
Indices: 55155506--55155553 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
55155496 ATTCAATACT
55155506 TTAATTCGG
1 TTAATTCGG
*
55155515 TTAATTCAG
1 TTAATTCGG
*
55155524 TTAATTAGG
1 TTAATTCGG
**
55155533 TTAATTTAG
1 TTAATTCGG
*
55155542 TTAATCCGG
1 TTAATTCGG
55155551 TTA
1 TTA
55155554 TTTTTTTATG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (9 bp):
TTAATTCGG
Found at i:55155529 original size:18 final size:18
Alignment explanation
Indices: 55155506--55155553 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
55155496 ATTCAATACT
55155506 TTAATTCGGTTAATTCAG
1 TTAATTCGGTTAATTCAG
* *
55155524 TTAATTAGGTTAATTTAG
1 TTAATTCGGTTAATTCAG
*
55155542 TTAATCCGGTTA
1 TTAATTCGGTTA
55155554 TTTTTTTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (18 bp):
TTAATTCGGTTAATTCAG
Found at i:55170463 original size:25 final size:25
Alignment explanation
Indices: 55170429--55170480 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
55170419 GATACTTGTC
*
55170429 CACCTAAGTATCAATGGAAGTTATT
1 CACCTAAGTATCAATAGAAGTTATT
*
55170454 CACCTAAGTATCGATAGAAGTTATT
1 CACCTAAGTATCAATAGAAGTTATT
55170479 CA
1 CA
55170481 GACTTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (25 bp):
CACCTAAGTATCAATAGAAGTTATT
Found at i:55177103 original size:31 final size:30
Alignment explanation
Indices: 55177046--55177120 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 30
55177036 TTTCGTTAAA
* *
55177046 AAAAGTTATAATTTAATCACTTAATTATTC
1 AAAAGTTTTTATTTAATCACTTAATTATTC
55177076 AAAAGTTTTTATTTAAATCA-TTGAATTATTC
1 AAAAGTTTTTATTT-AATCACTT-AATTATTC
*
55177107 AAAAATTTTTATTT
1 AAAAGTTTTTATTT
55177121 TTTTTAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 14 0.35
31 26 0.65
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (30 bp):
AAAAGTTTTTATTTAATCACTTAATTATTC
Found at i:55178117 original size:16 final size:15
Alignment explanation
Indices: 55178090--55178119 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
55178080 ATATTATTAA
55178090 AAATTAAATGAAATC
1 AAATTAAATGAAATC
55178105 AAATTATAATGAAAT
1 AAATTA-AATGAAAT
55178120 TAATATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (15 bp):
AAATTAAATGAAATC
Found at i:55178520 original size:27 final size:27
Alignment explanation
Indices: 55178490--55178614 Score: 135
Period size: 27 Copynumber: 4.6 Consensus size: 27
55178480 AGGAAGGGTA
55178490 TCTCATAGGCGGCACCAAAGGTGCCTT
1 TCTCATAGGCGGCACCAAAGGTGCCTT
* * * *
55178517 TCTCATGGGCGGCACCGATGGTGCCAT
1 TCTCATAGGCGGCACCAAAGGTGCCTT
* * *
55178544 TCCCATGGGCGGCACCAAAGGTGCATT
1 TCTCATAGGCGGCACCAAAGGTGCCTT
* *
55178571 T-TCCATAGGCGGCACCGAATGTGCCTT
1 TCT-CATAGGCGGCACCAAAGGTGCCTT
* *
55178598 TCCCATAAGCGGCACCA
1 TCTCATAGGCGGCACCA
55178615 CTTATGTCAT
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
27 79 1.00
ACGTcount: A:0.21, C:0.31, G:0.27, T:0.21
Consensus pattern (27 bp):
TCTCATAGGCGGCACCAAAGGTGCCTT
Found at i:55178582 original size:54 final size:54
Alignment explanation
Indices: 55178493--55178614 Score: 167
Period size: 54 Copynumber: 2.3 Consensus size: 54
55178483 AAGGGTATCT
*
55178493 CATAGGCGGCACCAAAGGTGCCTTTCTCATGGGCGGCACCG-ATGGTGCCATTCC
1 CATAGGCGGCACCAAAGGTGCCTTTCTCATAGGCGGCACCGAAT-GTGCCATTCC
* * *
55178547 CATGGGCGGCACCAAAGGTGCATTT-TCCATAGGCGGCACCGAATGTGCCTTTCC
1 CATAGGCGGCACCAAAGGTGCCTTTCT-CATAGGCGGCACCGAATGTGCCATTCC
*
55178601 CATAAGCGGCACCA
1 CATAGGCGGCACCA
55178615 CTTATGTCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
53 1 0.02
54 57 0.95
55 2 0.03
ACGTcount: A:0.21, C:0.31, G:0.28, T:0.20
Consensus pattern (54 bp):
CATAGGCGGCACCAAAGGTGCCTTTCTCATAGGCGGCACCGAATGTGCCATTCC
Found at i:55178863 original size:3 final size:3
Alignment explanation
Indices: 55178855--55178884 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
55178845 GTTTTAGTTG
55178855 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55178885 GTTTTTAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:55179091 original size:45 final size:44
Alignment explanation
Indices: 55179026--55179129 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 44
55179016 TTATTACAGC
**
55179026 ATGTTTGGTTGGCTGTAATGGAATAGAGGCGTAATAGGTAATCTT
1 ATGTTTGGTTGAATGTAATGGAATAGAGGCGTAAT-GGTAATCTT
* *
55179071 TTGTTTGGTTGAATGTAATGGAATAGAGGCGTAATGGTATTCTT
1 ATGTTTGGTTGAATGTAATGGAATAGAGGCGTAATGGTAATCTT
55179115 ATGTTTGGTTGAATG
1 ATGTTTGGTTGAATG
55179130 GAATAGAGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 22 0.41
45 32 0.59
ACGTcount: A:0.25, C:0.05, G:0.31, T:0.39
Consensus pattern (44 bp):
ATGTTTGGTTGAATGTAATGGAATAGAGGCGTAATGGTAATCTT
Found at i:55179130 original size:39 final size:43
Alignment explanation
Indices: 55179039--55179146 Score: 143
Period size: 45 Copynumber: 2.6 Consensus size: 43
55179029 TTTGGTTGGC
*
55179039 TGTAATGGAATAGAGGCGTAATAGGTAATCTTTTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATCTTATGTTTGGTT--A
*
55179084 TGTAATGGAATAGAGGCGTAAT-GGTATTCTTATGTTTGG-T-
1 TGTAATGGAATAGAGGCGTAATAGGTAATCTTATGTTTGGTTA
*
55179124 TG-AATGGAATAGAGGTGTAATAG
1 TGTAATGGAATAGAGGCGTAATAG
55179147 CATAAGAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
39 18 0.31
40 3 0.05
43 1 0.02
44 15 0.25
45 22 0.37
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.36
Consensus pattern (43 bp):
TGTAATGGAATAGAGGCGTAATAGGTAATCTTATGTTTGGTTA
Found at i:55179275 original size:18 final size:19
Alignment explanation
Indices: 55179246--55179289 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
55179236 GCTTATTAAT
55179246 ATAAATAATATAT-AATTTA
1 ATAAA-AATATATGAATTTA
55179265 ATAAAAATATATGAATTTA
1 ATAAAAATATATGAATTTA
*
55179284 CTAAAA
1 ATAAAA
55179290 TCATAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAAAAATATATGAATTTA
Found at i:55187338 original size:316 final size:318
Alignment explanation
Indices: 55186376--55187781 Score: 2392
Period size: 317 Copynumber: 4.4 Consensus size: 318
55186366 GCATGTTGAA
* *
55186376 AAAAAAGTTAGTAAAATACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
*
55186441 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATCTCAGTGCATTATGTTTGAAA
66 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
* *
55186506 TTTATTAATTTAGTGTGTTTTTTTAAATTAATTTAGTGTAAAAAAAATCC-TTATTCCTACCATT
131 TTTATTAATTTAGTGTGTTTTTTTAAATTAATTTAGTGTAAAAAAAA-CCTTTATTCCTGCCCTT
*
55186570 TGCTCGTATTATTTTCCCAAATTTTATTACGT-TCAATAAAAAATATTATTTTCGTATTTTATTA
195 TGCTCGTATTATTTTCCCGAATTTTATTA-GTCTCAATAAAAAATATTATTTTCGTATTTTATTA
*
55186634 TTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTT
259 TTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
*
55186694 AAAATATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
55186759 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
66 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
* *
55186824 TTTATTAATTTAGTGT-TTTTTTTAAATAAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCTTT
131 TTTATTAATTTAGTGTGTTTTTTTAAATTAATTTAGTGTAAAAAAAACCTTTATTCCTGCCCTTT
** * *
55186888 GCTCGTATTATTTTCTTGAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTATT
196 GCTCGTATTATTTTCCCGAATTTTATTAGTCTCAATAAAAAATATTATTTTCGTATTTTATTATT
55186953 TTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
261 TTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
* * *
55187011 AAAAAATTTAGTAAAACACTATTACTTCGGCCATTTGTTCATATTTTTTTCTCCGCATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
* * *
55187076 TTTTAGAAAATATCATAATTTCTAATTTTATAA-TTTACATTATTTCAGTGCATTATGTTTAAAA
66 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
* * * * *
55187140 TTTATTATTTTAGTGTGTTTTTTAAAATTAATTTAGTGTAGAAAAAACCTTTATTCATGCACTTT
131 TTTATTAATTTAGTGTGTTTTTTTAAATTAATTTAGTGTAAAAAAAACCTTTATTCCTGCCCTTT
55187205 GCTCGTATTATTTTCCCGAATTTTATTAGTCTCAAT-AAAAATATTATTTTCGTATTTTATTATT
196 GCTCGTATTATTTTCCCGAATTTTATTAGTCTCAATAAAAAATATTATTTTCGTATTTTATTATT
* *
55187269 TTATATTATTTCAGTATATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTT
261 TTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
*
55187327 AAAATATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
55187392 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
66 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
* *
55187457 TTTATTAATTTAGTGT-ATTTTTTAAATTAATTTAGTGTAAAAAAAACTTTTATTCCTGCCCTTT
131 TTTATTAATTTAGTGTGTTTTTTTAAATTAATTTAGTGTAAAAAAAACCTTTATTCCTGCCCTTT
* *
55187521 ACTCGTATTATTTTCCCGAATTTTATTAGTCTCAATAAAAAATATTATTTTTGTATTTTATTATT
196 GCTCGTATTATTTTCCCGAATTTTATTAGTCTCAATAAAAAATATTATTTTCGTATTTTATTATT
*
55187586 TTATATTATTTCAGTACATTTTGTTTCAAATATTTGTATTATTTATTTCTAAATTTTT
261 TTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
* * **
55187644 AAAAAATTTAGTAAAACACTCTTACTTCGGTCATTTGTTCGGATTTTTTTCTCCACATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
* * *
55187709 TTTTAAAAAATATCATAATTTTTAATTTTATAATTTTACTTTATTTCAGTGCATTATGTTTGAAA
66 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
55187774 TTTATTAA
131 TTTATTAA
55187782 ATATACCATT
Statistics
Matches: 1024, Mismatches: 59, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
316 301 0.29
317 581 0.57
318 142 0.14
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (318 bp):
AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
TTTATTAATTTAGTGTGTTTTTTTAAATTAATTTAGTGTAAAAAAAACCTTTATTCCTGCCCTTT
GCTCGTATTATTTTCCCGAATTTTATTAGTCTCAATAAAAAATATTATTTTCGTATTTTATTATT
TTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
Found at i:55187590 original size:633 final size:635
Alignment explanation
Indices: 55186376--55187781 Score: 2462
Period size: 633 Copynumber: 2.2 Consensus size: 635
55186366 GCATGTTGAA
* * *
55186376 AAAAAAGTTAGTAAAATACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
* *
55186441 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATCTCAGTGCATTATGTTTGAAA
66 TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
* *
55186506 TTTATTAATTTAGTGTGTTTTTTTAAATTAATTTAGTGTAAAAAAAATCCTTATTCCTACCATTT
131 TTTATTAATTTAGTGTGTTTTTTAAAATTAATTTAGTGTAAAAAAAATCCTTATTCATACCATTT
55186571 GCTCGTATTATTTTCCCAAATTTTATTACGTTCAATAAAAAATATTATTTTCGTATTTTATTATT
196 GCTCGTATTATTTTCCCAAATTTTATTACGTTCAATAAAAAATATTATTTTCGTATTTTATTATT
55186636 TTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTTAAAATAT
261 TTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTTAAAATAT
55186701 TTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTACTTTAAA
326 TTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTACTTTAAA
55186766 AAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAATTTATTA
391 AAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAATTTATTA
* *
55186831 ATTTAGTGTTTTTTTTAAATAAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCTTTGCTCGTAT
456 ATTTAGTGTATTTTTTAAATAAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCTTTACTCGTAT
** *
55186896 TATTTTCTTGAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTATTTTATATTA
521 TATTTTCCCGAATTTTATTACTCTCAATAAAAAATATTATTTTCGTATTTTATTATTTTATATTA
*
55186961 TTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
586 TTTCAGTACATTTTGTTTCAAATATTTGTATTATTTATTTCTAAATTTTT
* *
55187011 AAAAAATTTAGTAAAACACTATTACTTCGGCCATTTGTTCATATTTTTTTCTCCGCATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
* *
55187076 TTTTAGAAAATATCATAATTTCTAATTTTATAA-TTTACATTATTTCAGTGCATTATGTTTAAAA
66 TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
* * *
55187140 TTTATTATTTTAGTGTGTTTTTTAAAATTAATTTAGTGTAGAAAAAA-CCTTTATTCAT-GCACT
131 TTTATTAATTTAGTGTGTTTTTTAAAATTAATTTAGTGTAAAAAAAATCC-TTATTCATACCA-T
*
55187203 TTGCTCGTATTATTTTCCCGAATTTTATTA-GTCTCAAT-AAAAATATTATTTTCGTATTTTATT
194 TTGCTCGTATTATTTTCCCAAATTTTATTACGT-TCAATAAAAAATATTATTTTCGTATTTTATT
*
55187266 ATTTTATATTATTTCAGTATATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTTAAAA
258 ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTTAAAA
55187331 TATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTACTTT
323 TATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTACTTT
55187396 AAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAATTTA
388 AAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAATTTA
* **
55187461 TTAATTTAGTGTATTTTTTAAATTAATTTAGTGTAAAAAAAACTTTTATTCCTGCCCTTTACTCG
453 TTAATTTAGTGTATTTTTTAAATAAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCTTTACTCG
* *
55187526 TATTATTTTCCCGAATTTTATTAGTCTCAATAAAAAATATTATTTTTGTATTTTATTATTTTATA
518 TATTATTTTCCCGAATTTTATTACTCTCAATAAAAAATATTATTTTCGTATTTTATTATTTTATA
55187591 TTATTTCAGTACATTTTGTTTCAAATATTTGTATTATTTATTTCTAAATTTTT
583 TTATTTCAGTACATTTTGTTTCAAATATTTGTATTATTTATTTCTAAATTTTT
* * *
55187644 AAAAAATTTAGTAAAACACTCTTACTTCGGTCATTTGTTCGGATTTTTTTCTCCACATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
* *
55187709 TTTTAAAAAATATCATAATTTTTAATTTTATAATTTTACTTTATTTCAGTGCATTATGTTTGAAA
66 TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
55187774 TTTATTAA
131 TTTATTAA
55187782 ATATACCATT
Statistics
Matches: 730, Mismatches: 37, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
633 488 0.67
634 151 0.21
635 91 0.12
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (635 bp):
AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
TTTATTAATTTAGTGTGTTTTTTAAAATTAATTTAGTGTAAAAAAAATCCTTATTCATACCATTT
GCTCGTATTATTTTCCCAAATTTTATTACGTTCAATAAAAAATATTATTTTCGTATTTTATTATT
TTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTTAAAATAT
TTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTACTTTAAA
AAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAATTTATTA
ATTTAGTGTATTTTTTAAATAAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCTTTACTCGTAT
TATTTTCCCGAATTTTATTACTCTCAATAAAAAATATTATTTTCGTATTTTATTATTTTATATTA
TTTCAGTACATTTTGTTTCAAATATTTGTATTATTTATTTCTAAATTTTT
Found at i:55188185 original size:24 final size:23
Alignment explanation
Indices: 55188149--55188267 Score: 103
Period size: 24 Copynumber: 5.5 Consensus size: 23
55188139 TCTTCTTCTT
*
55188149 TTTTTTTTC-TCTTCTCCTTTCC
1 TTTTCTTTCTTCTTCTCCTTTCC
* * *
55188171 TTTTCTTTCATTCTTTTTCATT-C
1 TTTTCTTTC-TTCTTCTCCTTTCC
55188194 -TTT-TTTCTTCTTCTCCTTTCC
1 TTTTCTTTCTTCTTCTCCTTTCC
*
55188215 TTTTCTTTC--CTTCT--TTTTC
1 TTTTCTTTCTTCTTCTCCTTTCC
*
55188234 -TTTCTTTCTTTCCTCTCCTTTCC
1 TTTTCTTTC-TTCTTCTCCTTTCC
55188257 TTTTCTTTCTT
1 TTTTCTTTCTT
55188268 TTTTTCTTCT
Statistics
Matches: 76, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
18 8 0.11
19 4 0.05
20 9 0.12
21 14 0.18
22 14 0.18
23 11 0.14
24 16 0.21
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTCTTTCTTCTTCTCCTTTCC
Found at i:55188213 original size:44 final size:41
Alignment explanation
Indices: 55188139--55188292 Score: 185
Period size: 44 Copynumber: 3.8 Consensus size: 41
55188129 CTTCCTCCCC
*
55188139 TCTTCTTCTT-TT-TTTTTTCTCTTCTCCTTTCCTTTTCTT
1 TCTTCTTTTTCTTCTTTTTTCTCTTCTCCTTTCCTTTTCTT
55188178 TCATTCTTTTTCATTCTTTTTTCTTCTTCTCCTTTCCTTTTCTT
1 TC-TTCTTTTTC-TTCTTTTTTC-TCTTCTCCTTTCCTTTTCTT
55188222 TCCTTCTTTTTCTTTCTTTCTTTC-C-TCTCCTTTCCTTTTCTT
1 T-CTTCTTTTTC-TTCTTT-TTTCTCTTCTCCTTTCCTTTTCTT
* *
55188264 TCTT-TTTTTCTTCTTCTTTC-CCTCTCCTT
1 TCTTCTTTTTCTTCTTTTTTCTCTTCTCCTT
55188293 CTCTTCCCCC
Statistics
Matches: 104, Mismatches: 3, Indels: 16
0.85 0.02 0.13
Matches are distributed among these distances:
38 5 0.05
39 14 0.13
40 13 0.12
41 3 0.03
42 20 0.19
43 8 0.08
44 36 0.35
45 5 0.05
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (41 bp):
TCTTCTTTTTCTTCTTTTTTCTCTTCTCCTTTCCTTTTCTT
Found at i:55188217 original size:5 final size:5
Alignment explanation
Indices: 55188207--55188265 Score: 52
Period size: 5 Copynumber: 12.4 Consensus size: 5
55188197 TTTCTTCTTC
* * * *
55188207 TCCTT TCCTT TTCTT TCC-T TCTTT TTCTT T-CTT T-CTT TCCTC TCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
*
55188254 TCCTT TTCTT TC
1 TCCTT TCCTT TC
55188266 TTTTTTTCTT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
4 11 0.26
5 32 0.74
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (5 bp):
TCCTT
Found at i:55188222 original size:10 final size:10
Alignment explanation
Indices: 55188209--55188284 Score: 61
Period size: 10 Copynumber: 7.6 Consensus size: 10
55188199 TCTTCTTCTC
55188209 CTTTCCTTTT
1 CTTTCCTTTT
55188219 CTTTCCTTCTT
1 CTTTCCTT-TT
*
55188230 -TTTCTTTCTTT
1 CTTTC-CT-TTT
* *
55188241 CTTTCCTCTC
1 CTTTCCTTTT
55188251 CTTTCCTTTT
1 CTTTCCTTTT
55188261 CTTT-CTTTT
1 CTTTCCTTTT
55188270 -TTT-CTTCTT
1 CTTTCCTT-TT
55188279 CTTTCC
1 CTTTCC
55188285 CTCTCCTTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
8 6 0.11
9 7 0.13
10 28 0.53
11 7 0.13
12 5 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:55188234 original size:14 final size:14
Alignment explanation
Indices: 55188171--55188275 Score: 74
Period size: 14 Copynumber: 7.5 Consensus size: 14
55188161 TCTCCTTTCC
*
55188171 TTTTCTTTCATTCT
1 TTTTCTTTCCTTCT
* *
55188185 TTTTCATT-CTTTT
1 TTTTCTTTCCTTCT
*
55188198 TTCTTCTTCTCCTTTCC
1 TT-TTCTT-TCC-TTCT
55188215 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
55188229 TTTTCTTTCTTTC-
1 TTTTCTTTCCTTCT
* * *
55188242 TTTCCTCTCCTTTCC
1 TTTTCTTTCC-TTCT
55188257 TTTTCTTT-CTT-T
1 TTTTCTTTCCTTCT
55188269 TTTTCTT
1 TTTTCTT
55188276 CTTCTTTCCC
Statistics
Matches: 71, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
12 7 0.10
13 14 0.20
14 30 0.42
15 10 0.14
16 6 0.08
17 4 0.06
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:55188275 original size:8 final size:9
Alignment explanation
Indices: 55188139--55188283 Score: 52
Period size: 10 Copynumber: 15.2 Consensus size: 9
55188129 CTTCCTCCCC
55188139 TCTTCTTCTT
1 TCTT-TTCTT
55188149 T-TTTT-TT
1 TCTTTTCTT
55188156 TCTCTTCTCCTT
1 TCT-TT-T-CTT
55188168 TCCTTTTCTT
1 T-CTTTTCTT
55188178 TCATTCTT-TT
1 TC-TT-TTCTT
*
55188188 TCATTCTTTTT
1 TC-TT-TTCTT
55188199 TCTTCTTC-T
1 TCTT-TTCTT
* *
55188208 CCTTTCCTT
1 TCTTTTCTT
*
55188217 T-TCTTTCCT
1 TCT-TTTCTT
55188226 TCTTTTTCTT
1 TC-TTTTCTT
55188236 TC-TTTCTT
1 TCTTTTCTT
* *
55188244 TCCTCTCCTT
1 T-CTTTTCTT
55188254 TCCTTTTCTT
1 T-CTTTTCTT
55188264 TCTTTT-TT
1 TCTTTTCTT
55188272 TCTTCTTCTT
1 TCTT-TTCTT
55188282 TC
1 TC
55188284 CCTCTCCTTC
Statistics
Matches: 107, Mismatches: 11, Indels: 34
0.70 0.07 0.22
Matches are distributed among these distances:
7 3 0.03
8 19 0.18
9 23 0.21
10 47 0.44
11 8 0.07
12 5 0.05
13 2 0.02
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (9 bp):
TCTTTTCTT
Found at i:55188294 original size:28 final size:28
Alignment explanation
Indices: 55188235--55188294 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
55188225 TTCTTTTTCT
* * *
55188235 TTCTTTCTTTCCTCTCCTTTCCTTTTCT
1 TTCTTTCTTTCCTCTCCTTTCCCTCTCC
* * *
55188263 TTCTTTTTTTCTTCTTCTTTCCCTCTCC
1 TTCTTTCTTTCCTCTCCTTTCCCTCTCC
55188291 TTCT
1 TTCT
55188295 CTTCCCCCCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (28 bp):
TTCTTTCTTTCCTCTCCTTTCCCTCTCC
Found at i:55192318 original size:69 final size:70
Alignment explanation
Indices: 55192170--55192309 Score: 239
Period size: 69 Copynumber: 2.0 Consensus size: 70
55192160 ATCGGATTTT
*
55192170 AAAAAAAA-GATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAA
1 AAAAAAAAGGATCATGCCCAATAAGTTAGGACACGA--TTTTCTTAATTCCCGAGATCGTTTAAA
55192234 ACTTGAG
64 ACTTGAG
55192241 AAAAAAAAGGATCATGCCCAATAAGTTAGGACACGA-TTTCTTAATTCCCGAGATCGTTTAAAAC
1 AAAAAAAAGGATCATGCCCAATAAGTTAGGACACGATTTTCTTAATTCCCGAGATCGTTTAAAAC
55192305 TTGAG
66 TTGAG
55192310 TTTAAAAAGA
Statistics
Matches: 67, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
69 33 0.49
71 8 0.12
72 26 0.39
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (70 bp):
AAAAAAAAGGATCATGCCCAATAAGTTAGGACACGATTTTCTTAATTCCCGAGATCGTTTAAAAC
TTGAG
Found at i:55192715 original size:16 final size:16
Alignment explanation
Indices: 55192694--55192724 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
55192684 AAGTAAAAGA
55192694 TATATATATGTATATG
1 TATATATATGTATATG
55192710 TATATATATGTATAT
1 TATATATATGTATAT
55192725 AAAAATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (16 bp):
TATATATATGTATATG
Found at i:55192848 original size:22 final size:23
Alignment explanation
Indices: 55192823--55192870 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
55192813 AATTATACAA
55192823 TATATAAAAAAAT-ATAAG-TATG
1 TATATAAAAAAATCA-AAGATATG
*
55192845 TATATATAAAAATCAAAGATATG
1 TATATAAAAAAATCAAAGATATG
55192868 TAT
1 TAT
55192871 GTAGAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.33
Consensus pattern (23 bp):
TATATAAAAAAATCAAAGATATG
Found at i:55193165 original size:3 final size:3
Alignment explanation
Indices: 55193157--55193231 Score: 71
Period size: 3 Copynumber: 24.3 Consensus size: 3
55193147 AAACTAATAC
* *
55193157 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AACCT AATT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA--T AA-T AAT
* * *
55193205 -TT AAT AAT AAT AAA AAT AAC AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
55193232 GGACTAAATT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 1 0.02
3 53 0.90
4 2 0.03
5 3 0.05
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:55195608 original size:9 final size:9
Alignment explanation
Indices: 55195591--55195628 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
55195581 AAAAATGGTA
55195591 AGAATTGAG
1 AGAATTGAG
*
55195600 AGAACTGAG
1 AGAATTGAG
*
55195609 AGAGTTGAG
1 AGAATTGAG
55195618 AGAATTGAG
1 AGAATTGAG
55195627 AG
1 AG
55195629 TTTAGAGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.42, C:0.03, G:0.37, T:0.18
Consensus pattern (9 bp):
AGAATTGAG
Found at i:55196624 original size:16 final size:17
Alignment explanation
Indices: 55196603--55196636 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
55196593 AAGTCAATAC
55196603 ACATCTTGTC-ACTTCA
1 ACATCTTGTCTACTTCA
*
55196619 ACATCTTTTCTACTTCA
1 ACATCTTGTCTACTTCA
55196636 A
1 A
55196637 GACGTTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.41
Consensus pattern (17 bp):
ACATCTTGTCTACTTCA
Found at i:55208973 original size:5 final size:5
Alignment explanation
Indices: 55208963--55208988 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55208953 AAAATGCATC
55208963 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
55208989 GAATAAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:55209076 original size:16 final size:16
Alignment explanation
Indices: 55209055--55209085 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55209045 GTAGGGAGGA
*
55209055 ACAAAAGAATAAAACG
1 ACAAAAGAAAAAAACG
55209071 ACAAAAGAAAAAAAC
1 ACAAAAGAAAAAAAC
55209086 ATCTTTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.13, G:0.10, T:0.03
Consensus pattern (16 bp):
ACAAAAGAAAAAAACG
Found at i:55211828 original size:34 final size:34
Alignment explanation
Indices: 55211785--55211851 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
55211775 AAACATGTTA
55211785 CTTTTAGCACTTATCATGAATAGAATAATTACCC
1 CTTTTAGCACTTATCATGAATAGAATAATTACCC
55211819 CTTTTAGCACTTATCATGAATAGAATAATTACC
1 CTTTTAGCACTTATCATGAATAGAATAATTACC
55211852 TTACTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (34 bp):
CTTTTAGCACTTATCATGAATAGAATAATTACCC
Found at i:55220063 original size:14 final size:14
Alignment explanation
Indices: 55220044--55220081 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
55220034 GCTCAATGAA
55220044 TTTTTTTTCTTTCCT
1 TTTTTTTTCTTT-CT
55220059 TTTTTTTTCTTTCT
1 TTTTTTTTCTTTCT
55220073 TCTTTTTTT
1 T-TTTTTTT
55220082 AGAACAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTTCTTTCT
Found at i:55223684 original size:32 final size:33
Alignment explanation
Indices: 55223640--55223701 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
55223630 TCGTGTGGCC
55223640 TTTTTTATTTTTTAAGTAAAATAAACAAACCGT
1 TTTTTTATTTTTTAAGTAAAATAAACAAACCGT
**
55223673 TTTTTTA-TTTTTATTTAAAATAAACAAAC
1 TTTTTTATTTTTTAAGTAAAATAAACAAAC
55223702 TAAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 20 0.74
33 7 0.26
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.48
Consensus pattern (33 bp):
TTTTTTATTTTTTAAGTAAAATAAACAAACCGT
Found at i:55226740 original size:19 final size:18
Alignment explanation
Indices: 55226714--55226756 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
55226704 ATTAGAATGT
*
55226714 AAAAATTAAATTAAAAAC
1 AAAAATTAAAATAAAAAC
*
55226732 AAAATATTAAAATAAAAAT
1 AAAA-ATTAAAATAAAAAC
55226751 AAAAAT
1 AAAAAT
55226757 GGCTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATTAAAATAAAAAC
Found at i:55227575 original size:20 final size:21
Alignment explanation
Indices: 55227536--55227576 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
55227526 CTTGCATGGT
55227536 ATGATTTTGAATTATGTTTTTA
1 ATGATTTT-AATTATGTTTTTA
*
55227558 ATGATTTT-ATTTTGTTTTT
1 ATGATTTTAATTATGTTTTT
55227577 GAGGTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.66
Consensus pattern (21 bp):
ATGATTTTAATTATGTTTTTA
Found at i:55231039 original size:4 final size:4
Alignment explanation
Indices: 55231030--55231076 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
55231020 TGAAGGATAA
55231030 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
55231077 ATCTACATCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:55231764 original size:16 final size:15
Alignment explanation
Indices: 55231724--55231777 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
55231714 TCGTTATGTT
55231724 TGTTCGCCATTTGGATG
1 TGTTCGCCATTT--ATG
*
55231741 -GTTTGCCATTTATG
1 TGTTCGCCATTTATG
55231755 TTGTTCGCCA--TATG
1 -TGTTCGCCATTTATG
55231769 TGTTCGCCA
1 TGTTCGCCA
55231778 ATGCATGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 9 0.27
14 7 0.21
16 17 0.52
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (15 bp):
TGTTCGCCATTTATG
Found at i:55232454 original size:19 final size:18
Alignment explanation
Indices: 55232412--55232453 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
55232402 TAAAATTTGA
*
55232412 AATTTTATAAATATTTTC
1 AATTTTAGAAATATTTTC
55232430 AATTTTAGAAATTATTTT-
1 AATTTTAGAAA-TATTTTC
55232448 AATTTT
1 AATTTT
55232454 TTTGTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
AATTTTAGAAATATTTTC
Found at i:55233970 original size:21 final size:21
Alignment explanation
Indices: 55233933--55233978 Score: 51
Period size: 21 Copynumber: 2.1 Consensus size: 21
55233923 ACAAAGTTTT
55233933 TTTTTATTTGATTTTTT-TCTAA
1 TTTTTATTT-ATTTTTTGT-TAA
55233955 TTTTTATTT-TTATTTTGTTAA
1 TTTTTATTTATT-TTTTGTTAA
55233976 TTT
1 TTT
55233979 GCTATTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.09
21 10 0.45
22 10 0.45
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.76
Consensus pattern (21 bp):
TTTTTATTTATTTTTTGTTAA
Found at i:55237271 original size:9 final size:9
Alignment explanation
Indices: 55237257--55237281 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55237247 AAAGACTATC
55237257 CATTTAGCA
1 CATTTAGCA
55237266 CATTTAGCA
1 CATTTAGCA
55237275 CATTTAG
1 CATTTAG
55237282 TCATATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (9 bp):
CATTTAGCA
Found at i:55252211 original size:9 final size:9
Alignment explanation
Indices: 55252197--55252222 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55252187 TCTTTCTTTC
55252197 TTTATTTTA
1 TTTATTTTA
55252206 TTTATTTTA
1 TTTATTTTA
55252215 TTTATTTT
1 TTTATTTT
55252223 GCTTAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:55252833 original size:29 final size:31
Alignment explanation
Indices: 55252772--55252837 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
55252762 ACAAAAGAAG
*
55252772 AAAAA-AGCTTGTTTAACAAAACGAGATAGA
1 AAAAAGAGCTTGTTTAACAAAACGAGATAAA
*
55252802 AAAAAGAGTTTGTTTAACAAAACGA-A-AAA
1 AAAAAGAGCTTGTTTAACAAAACGAGATAAA
55252831 AAAAAGA
1 AAAAAGA
55252838 AGAGCTGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 9 0.27
30 6 0.18
31 18 0.55
ACGTcount: A:0.59, C:0.08, G:0.15, T:0.18
Consensus pattern (31 bp):
AAAAAGAGCTTGTTTAACAAAACGAGATAAA
Found at i:55252835 original size:30 final size:29
Alignment explanation
Indices: 55252750--55252835 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 29
55252740 ACGGTTTCCA
* *
55252750 TTGTTTAATAGAAC-AAAAGAAGAAAAAAGC
1 TTGTTTAACAAAACGAAAA-AA-AAAAAAGC
* * *
55252780 TTGTTTAACAAAACGAGATAGAAAAAAGAGT
1 TTGTTTAACAAAACGA-A-AAAAAAAAAAGC
55252811 TTGTTTAACAAAACGAAAAAAAAAA
1 TTGTTTAACAAAACGAAAAAAAAAA
55252836 GAAGAGCTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 7 0.15
30 13 0.28
31 23 0.49
32 3 0.06
33 1 0.02
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.21
Consensus pattern (29 bp):
TTGTTTAACAAAACGAAAAAAAAAAAAGC
Found at i:55259146 original size:50 final size:50
Alignment explanation
Indices: 55259071--55259363 Score: 424
Period size: 50 Copynumber: 5.8 Consensus size: 50
55259061 ATTTGGGTAA
55259071 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
55259121 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
55259171 ATAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
55259221 AGAGGTCCCATATAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
55259271 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
55259321 AGAACATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
55259364 TGTTATGGTC
Statistics
Matches: 213, Mismatches: 29, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
50 180 0.85
51 33 0.15
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:55268848 original size:13 final size:13
Alignment explanation
Indices: 55268830--55268857 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55268820 ATGGTAAGAA
55268830 AATTTTTTTAATT
1 AATTTTTTTAATT
55268843 AATTTTTTTAATT
1 AATTTTTTTAATT
55268856 AA
1 AA
55268858 AACAATTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTTTTTTAATT
Found at i:55269388 original size:6 final size:6
Alignment explanation
Indices: 55269379--55269412 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
55269369 GCAAGTTCAA
*
55269379 GCTCAG GCTCAG GCTCAG GCTCAG GCTCAA GCTC
1 GCTCAG GCTCAG GCTCAG GCTCAG GCTCAG GCTC
55269413 GGGAGAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (6 bp):
GCTCAG
Found at i:55271438 original size:43 final size:42
Alignment explanation
Indices: 55271377--55271486 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
55271367 CAATACCATC
* *
55271377 GTCCCAAACATGGTCTTACATGTAA-TCAAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACA-GTAAGTCAAATA-CGATGCCAAT
* **
55271420 GTCCCAGACAGGGTCTTACACAAAGTCAAATACGATGCCAAT
1 GTCCCAGACATGGTCTTACAGTAAGTCAAATACGATGCCAAT
* *
55271462 GTTCCAGAAATGGTCTTACACGTAA
1 GTCCCAGACATGGTCTTACA-GTAA
55271487 ATCTCAAATC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
42 28 0.51
43 27 0.49
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACAGTAAGTCAAATACGATGCCAAT
Found at i:55273730 original size:28 final size:28
Alignment explanation
Indices: 55273698--55273758 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
55273688 GATGCACTTT
55273698 ACTTGAACCCGTGACCACAACATCGTCA
1 ACTTGAACCCGTGACCACAACATCGTCA
* * * *
55273726 ACTTGGAGCCGTGATCGCAACATCGTCA
1 ACTTGAACCCGTGACCACAACATCGTCA
55273754 ACTTG
1 ACTTG
55273759 GAGCCCAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (28 bp):
ACTTGAACCCGTGACCACAACATCGTCA
Found at i:55273759 original size:28 final size:28
Alignment explanation
Indices: 55273706--55273763 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
55273696 TTACTTGAAC
55273706 CCGTGACCACAACATCGTCAACTTGGAG
1 CCGTGACCACAACATCGTCAACTTGGAG
* *
55273734 CCGTGATCGCAACATCGTCAACTTGGAG
1 CCGTGACCACAACATCGTCAACTTGGAG
55273762 CC
1 CC
55273764 CAAGTTGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.19
Consensus pattern (28 bp):
CCGTGACCACAACATCGTCAACTTGGAG
Found at i:55274526 original size:13 final size:14
Alignment explanation
Indices: 55274497--55274543 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
55274487 CAAACTAAAA
*
55274497 TATAATCTTAAACAT
1 TATAATC-TAAATAT
55274512 TA-AATCTAAATAT
1 TATAATCTAAATAT
*
55274525 TATAA-ATAAATAT
1 TATAATCTAAATAT
55274538 TATAAT
1 TATAAT
55274544 ATACAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 20 0.71
14 6 0.21
15 2 0.07
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (14 bp):
TATAATCTAAATAT
Found at i:55274673 original size:19 final size:19
Alignment explanation
Indices: 55274649--55274693 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
55274639 ACTATAATCT
55274649 TAAACATTAAATCTAAAA-A
1 TAAACATTAAAT-TAAAATA
*
55274668 TAAACAATAAATTAAAATA
1 TAAACATTAAATTAAAATA
55274687 TAAACAT
1 TAAACAT
55274694 ACATATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAACATTAAATTAAAATA
Found at i:55289879 original size:16 final size:17
Alignment explanation
Indices: 55289858--55289890 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55289848 GCTTAAGTCA
*
55289858 TGTGTT-AAAGGACTTG
1 TGTGTTGAAAGAACTTG
55289874 TGTGTTGAAAGAACTTG
1 TGTGTTGAAAGAACTTG
55289891 ATAAGTGCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.06, G:0.30, T:0.36
Consensus pattern (17 bp):
TGTGTTGAAAGAACTTG
Found at i:55294614 original size:19 final size:19
Alignment explanation
Indices: 55294590--55294652 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
55294580 ATATCTGAAT
55294590 TGTGGAAGCATTCAAACTG
1 TGTGGAAGCATTCAAACTG
55294609 TGTGGAAGCATTCAAACTG
1 TGTGGAAGCATTCAAACTG
* *
55294628 TGTAGAAGCATTCAAACTA
1 TGTGGAAGCATTCAAACTG
55294647 TGTGGA
1 TGTGGA
55294653 TTTGCGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (19 bp):
TGTGGAAGCATTCAAACTG
Found at i:55295542 original size:27 final size:27
Alignment explanation
Indices: 55295512--55295600 Score: 133
Period size: 27 Copynumber: 3.3 Consensus size: 27
55295502 TTTGCATTTA
55295512 AGGGTTCACACAAGTAGGCTCGCACCT
1 AGGGTTCACACAAGTAGGCTCGCACCT
*
55295539 AGGGTTCACACAAGTAGGCTCACACCT
1 AGGGTTCACACAAGTAGGCTCGCACCT
* * *
55295566 AGGGTTCACACAAGTAAGGGTTGCATCT
1 AGGGTTCACACAAGT-AGGCTCGCACCT
55295594 AGGGTTC
1 AGGGTTC
55295601 GTATGTACAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 41 0.73
28 15 0.27
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (27 bp):
AGGGTTCACACAAGTAGGCTCGCACCT
Found at i:55295742 original size:35 final size:34
Alignment explanation
Indices: 55295701--55295793 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 34
55295691 GTTGATTCGA
**
55295701 ATAATTTGACTCGCATGTAGTATTAAAAGGCTGGC
1 ATAATTTGACTCGCATGTA-TATTAAAAGGCTCAC
* *
55295736 ATAATTTGACTCGCATATTATATTAAGAGGCTCAC
1 ATAATTTGACTCGCAT-GTATATTAAAAGGCTCAC
* *
55295771 ATAATTTGGCCCGCATGTCATAT
1 ATAATTTGACTCGCATGT-ATAT
55295794 CCTAGGGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
34 1 0.02
35 46 0.94
36 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (34 bp):
ATAATTTGACTCGCATGTATATTAAAAGGCTCAC
Found at i:55296720 original size:36 final size:32
Alignment explanation
Indices: 55296654--55296725 Score: 83
Period size: 36 Copynumber: 2.1 Consensus size: 32
55296644 CATAAAATAA
*
55296654 AAATATTTTTAGAAAAATTAATTTTATGGTTTT
1 AAATATTTTTAGAAAAATAAATTTTATGG-TTT
55296687 AAATAATTTTTAGGTAAAAATAAATATTT-TGGTTT
1 AAAT-ATTTTTA-G-AAAAATAAAT-TTTATGGTTT
55296722 AAAT
1 AAAT
55296726 TGGAATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
33 4 0.12
34 7 0.21
35 8 0.24
36 12 0.35
37 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (32 bp):
AAATATTTTTAGAAAAATAAATTTTATGGTTT
Found at i:55301789 original size:16 final size:16
Alignment explanation
Indices: 55301768--55301835 Score: 75
Period size: 16 Copynumber: 4.2 Consensus size: 16
55301758 TAAATTATTG
55301768 ATTACATCTCTATTCC
1 ATTACATCTCTATTCC
55301784 ATTACAGT-TCTATTCC
1 ATTACA-TCTCTATTCC
* * *
55301800 ATTACAGCTCTTTTCA
1 ATTACATCTCTATTCC
* *
55301816 ATTACAACCCTATTCC
1 ATTACATCTCTATTCC
55301832 ATTA
1 ATTA
55301836 TAGTGAACCA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
16 42 0.98
17 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTACATCTCTATTCC
Found at i:55304873 original size:5 final size:5
Alignment explanation
Indices: 55304863--55304895 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
55304853 AAGAGAGGAT
*
55304863 AAGGG AAGGG AAAGG AAGGG AAGGG AAGGG AAG
1 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAG
55304896 AGGGACGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (5 bp):
AAGGG
Found at i:55316466 original size:16 final size:18
Alignment explanation
Indices: 55316435--55316468 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
55316425 CCAATCAATA
55316435 CCACAACCCATTCATCAC
1 CCACAACCCATTCATCAC
55316453 CCAC-ACCC-TTCATCAC
1 CCACAACCCATTCATCAC
55316469 TACCATCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (18 bp):
CCACAACCCATTCATCAC
Found at i:55318305 original size:111 final size:111
Alignment explanation
Indices: 55318184--55318405 Score: 333
Period size: 111 Copynumber: 2.0 Consensus size: 111
55318174 TGGTAAATTT
*
55318184 GTTTTTAAATAATTGCT-CCCCTTAATGAAAA-TCATTTTGAATTTAAGGCCAAAATAAAAAG-A
1 GTTTTCAAATAATTGCTCCCCCTTAAT-AAAAGTCATTTTGAATTTAAGGCCAAAA-AAAAAGTA
* *
55318246 TTGACATACAATTAACGTTCATTTTTACTTTAAGAAAAATGGTCACATA
64 -TGACATACAATTAACATTCATTTTAACTTTAAGAAAAATGGTCACATA
*
55318295 GTTTTCAAATAATTGCTCCCCCTTAATAAAAGTTATTTTGAATTTAAGGCCAAAAAAAAAGTATG
1 GTTTTCAAATAATTGCTCCCCCTTAATAAAAGTCATTTTGAATTTAAGGCCAAAAAAAAAGTATG
* * *
55318360 ACATACAGTTGACATTCATTTTAACTTTAAGGAAAATGGTCACATA
66 ACATACAATTAACATTCATTTTAACTTTAAGAAAAATGGTCACATA
55318406 ATTTGCATAA
Statistics
Matches: 101, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
111 69 0.68
112 32 0.32
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (111 bp):
GTTTTCAAATAATTGCTCCCCCTTAATAAAAGTCATTTTGAATTTAAGGCCAAAAAAAAAGTATG
ACATACAATTAACATTCATTTTAACTTTAAGAAAAATGGTCACATA
Found at i:55321361 original size:13 final size:13
Alignment explanation
Indices: 55321325--55321372 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
55321315 TCTACATTGC
55321325 TTTTGAAAAGTGT
1 TTTTGAAAAGTGT
* *
55321338 TGTGGAAAAGTGT
1 TTTTGAAAAGTGT
* *
55321351 TTTTGAGAAGTGC
1 TTTTGAAAAGTGT
55321364 TTTTGAAAA
1 TTTTGAAAA
55321373 ATTTGAGTGT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.27, T:0.40
Consensus pattern (13 bp):
TTTTGAAAAGTGT
Found at i:55321566 original size:28 final size:30
Alignment explanation
Indices: 55321534--55321594 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
55321524 ATTATAACTT
*
55321534 ATTTTTAATATTT-TAA-T-ATATAATATTA
1 ATTTTAAATATTTCTAAGTAAT-TAATATTA
55321562 ATTTTAAATATTTCTAAGTAATTAATATTA
1 ATTTTAAATATTTCTAAGTAATTAATATTA
55321592 ATT
1 ATT
55321595 ATTTTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 12 0.41
29 3 0.10
30 12 0.41
31 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (30 bp):
ATTTTAAATATTTCTAAGTAATTAATATTA
Found at i:55321590 original size:30 final size:28
Alignment explanation
Indices: 55321534--55321594 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 28
55321524 ATTATAACTT
*
55321534 ATTTTTAATATTTTAATATATAATATTA
1 ATTTTAAATATTTTAATATATAATATTA
55321562 ATTTTAAATATTTCTAAGTA-ATTAATATTA
1 ATTTTAAATATTT-TAA-TATA-TAATATTA
55321592 ATT
1 ATT
55321595 ATTTTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 12 0.41
29 4 0.14
30 13 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTTTAAATATTTTAATATATAATATTA
Found at i:55323492 original size:14 final size:14
Alignment explanation
Indices: 55323475--55323507 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
55323465 TATTAAATTG
55323475 TAGAACTAAAATGC
1 TAGAACTAAAATGC
55323489 TAGAACTAAAATGC
1 TAGAACTAAAATGC
*
55323503 CAGAA
1 TAGAA
55323508 ATTGTTCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.18
Consensus pattern (14 bp):
TAGAACTAAAATGC
Found at i:55324647 original size:19 final size:20
Alignment explanation
Indices: 55324623--55324671 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
55324613 TTTTCTTACG
55324623 AGTATCGATATTTTATAAA-
1 AGTATCGATATTTTATAAAT
*
55324642 AGTATCGATATTTTTTAAAT
1 AGTATCGATATTTTATAAAT
*
55324662 GGTATCGATA
1 AGTATCGATA
55324672 CCAAATTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (20 bp):
AGTATCGATATTTTATAAAT
Found at i:55329394 original size:8 final size:8
Alignment explanation
Indices: 55329381--55329405 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
55329371 TATACTAAAC
55329381 AATAAAAT
1 AATAAAAT
55329389 AATAAAAT
1 AATAAAAT
55329397 AATAAAAT
1 AATAAAAT
55329405 A
1 A
55329406 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:55332499 original size:21 final size:21
Alignment explanation
Indices: 55332475--55332514 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55332465 TGAAGCAATT
* *
55332475 TTGACTTGTTTAAATGATATC
1 TTGACTTGATAAAATGATATC
55332496 TTGACTTGATAAAATGATA
1 TTGACTTGATAAAATGATA
55332515 AAAGACCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (21 bp):
TTGACTTGATAAAATGATATC
Found at i:55338396 original size:27 final size:28
Alignment explanation
Indices: 55338308--55338550 Score: 253
Period size: 28 Copynumber: 8.8 Consensus size: 28
55338298 AACACGTCAG
*
55338308 GAAAGAATAAGCCTTTGTGGTGAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAT
* *
55338336 GAAAGAATAAGCCTTTATGGCAAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAT
*
55338364 GAAAGAATAAGCCTTTG-GGAGAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAT
*
55338391 GAAAGAATAAGCCTTTGTGGTGAA-TAAT
1 GAAAGAATAAGCCTTTGTGGCGAACT-AT
*
55338419 GAAAGAATAAGCCCTTGT-GCGAA-TAAT
1 GAAAGAATAAGCCTTTGTGGCGAACT-AT
* *
55338446 AAAAGAATAAGCCTTTGT-GCGAACAAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAT
* * *
55338473 GAAAGACTAAGCCCTTGCGGCGAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAT
** * * *
55338501 CTAAGACTAAGCCCTTGTGGTGAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAT
* * * *
55338529 CAAAGACTAAGCCCTTATGGCG
1 GAAAGAATAAGCCTTTGTGGCG
55338551 GACTCCGTAT
Statistics
Matches: 187, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
27 71 0.38
28 116 0.62
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (28 bp):
GAAAGAATAAGCCTTTGTGGCGAACTAT
Found at i:55338400 original size:55 final size:56
Alignment explanation
Indices: 55338308--55338544 Score: 250
Period size: 55 Copynumber: 4.3 Consensus size: 56
55338298 AACACGTCAG
* * * * *
55338308 GAAAGAATAAGCCTTTGTGGTGAACTATGAAAGAATAAGCCTTTATGGCAAACTAT
1 GAAAGAATAAGCCCTTGCGGCGAACTATGAAAGAATAAGCCTTTGTGGCGAACTAT
* * *
55338364 GAAAGAATAAGCCTTTG-GGAGAACTATGAAAGAATAAGCCTTTGTGGTGAA-TAAT
1 GAAAGAATAAGCCCTTGCGGCGAACTATGAAAGAATAAGCCTTTGTGGCGAACT-AT
* * *
55338419 GAAAGAATAAGCCCTTG-TGCGAA-TAATAAAAGAATAAGCCTTTGT-GCGAACAAT
1 GAAAGAATAAGCCCTTGCGGCGAACT-ATGAAAGAATAAGCCTTTGTGGCGAACTAT
* ** * * *
55338473 GAAAGACTAAGCCCTTGCGGCGAACTATCTAAGACTAAGCCCTTGTGGTGAACTAT
1 GAAAGAATAAGCCCTTGCGGCGAACTATGAAAGAATAAGCCTTTGTGGCGAACTAT
* *
55338529 CAAAGACTAAGCCCTT
1 GAAAGAATAAGCCCTT
55338545 ATGGCGGACT
Statistics
Matches: 156, Mismatches: 19, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
54 24 0.15
55 92 0.59
56 40 0.26
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (56 bp):
GAAAGAATAAGCCCTTGCGGCGAACTATGAAAGAATAAGCCTTTGTGGCGAACTAT
Found at i:55338512 original size:82 final size:82
Alignment explanation
Indices: 55338308--55338519 Score: 205
Period size: 82 Copynumber: 2.6 Consensus size: 82
55338298 AACACGTCAG
* * * * * * * *
55338308 GAAAGAATAAGCCTTTGTGGTGAACT-ATGAAAGAATAAGCCTTTATGGCAAACT-ATGAAAGAA
1 GAAAGAATAAGCCCTTGCGGCGAA-TAATCAAAGAATAAGCCCTTGT-GCGAA-TAATAAAAGAA
*
55338371 TAAGCCTTTGGGAGAACTAT
63 TAAGCCTTTGGGAGAACAAT
* * * *
55338391 GAAAGAATAAGCCTTTGTGGTGAATAATGAAAGAATAAGCCCTTGTGCGAATAATAAAAGAATAA
1 GAAAGAATAAGCCCTTGCGGCGAATAATCAAAGAATAAGCCCTTGTGCGAATAATAAAAGAATAA
* *
55338456 GCCTTTGTGCGAACAAT
66 GCCTTTGGGAGAACAAT
* * *
55338473 GAAAGACTAAGCCCTTGCGGCGAACT-ATCTAAGACTAAGCCCTTGTG
1 GAAAGAATAAGCCCTTGCGGCGAA-TAATCAAAGAATAAGCCCTTGTG
55338520 GTGAACTATC
Statistics
Matches: 112, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
81 1 0.01
82 68 0.61
83 43 0.38
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (82 bp):
GAAAGAATAAGCCCTTGCGGCGAATAATCAAAGAATAAGCCCTTGTGCGAATAATAAAAGAATAA
GCCTTTGGGAGAACAAT
Found at i:55350068 original size:16 final size:16
Alignment explanation
Indices: 55350047--55350077 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55350037 GTTTCACTTT
55350047 GACTGCATAGCATTTA
1 GACTGCATAGCATTTA
*
55350063 GACTGCATGGCATTT
1 GACTGCATAGCATTT
55350078 CATTATAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (16 bp):
GACTGCATAGCATTTA
Found at i:55351659 original size:41 final size:41
Alignment explanation
Indices: 55351608--55351794 Score: 191
Period size: 41 Copynumber: 4.6 Consensus size: 41
55351598 TTTAAACAGA
* * ** *
55351608 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTTTAATTCCG
1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTAATTCAG
* *
55351649 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
* * * *
55351690 TTCATCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
* * * *
55351731 CTCACCGGCACTTAGCCTGCT-GGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGCTAGG-CTTATAG-CCTAATTCAG
55351772 TTCACCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAG
55351795 ACGTATAGTC
Statistics
Matches: 126, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
40 3 0.02
41 120 0.95
42 3 0.02
ACGTcount: A:0.20, C:0.29, G:0.21, T:0.29
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
Found at i:55351817 original size:41 final size:41
Alignment explanation
Indices: 55351649--55351807 Score: 212
Period size: 41 Copynumber: 3.9 Consensus size: 41
55351639 TTTAATTCCG
* * *
55351649 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
* * * *
55351690 TTCATCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
* *
55351731 CTCACCGGCACTTAGCCTGCTGGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAG-CCTGATTCAA
*
55351772 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGA
55351808 ATAATTTCAC
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
40 1 0.01
41 100 0.97
42 2 0.02
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.28
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
Found at i:55359559 original size:41 final size:41
Alignment explanation
Indices: 55359508--55359694 Score: 200
Period size: 41 Copynumber: 4.6 Consensus size: 41
55359498 TTTAAACAGA
* * ** *
55359508 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTTTAATTCCG
1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTAATTCAG
* *
55359549 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
* * *
55359590 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
* * * *
55359631 CTCACCGGCACTTAGCCTGCT-GGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGCTAGG-CTTATAG-CCTAATTCAG
55359672 TTCACCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAG
55359695 ACGTATAGTC
Statistics
Matches: 128, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
40 3 0.02
41 122 0.95
42 3 0.02
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
Found at i:55359717 original size:41 final size:41
Alignment explanation
Indices: 55359549--55359707 Score: 221
Period size: 41 Copynumber: 3.9 Consensus size: 41
55359539 TTTAATTCCG
* * *
55359549 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
* * *
55359590 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
* *
55359631 CTCACCGGCACTTAGCCTGCTGGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAG-CCTGATTCAA
*
55359672 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGA
55359708 ATAATTTCAC
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 1 0.01
41 102 0.97
42 2 0.02
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
Found at i:55364482 original size:6 final size:7
Alignment explanation
Indices: 55364459--55364499 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
55364449 AAAAGTGATG
55364459 TGAAAAA
1 TGAAAAA
55364466 TGAAAAGA
1 TGAAAA-A
55364474 TG-AAAA
1 TGAAAAA
55364480 TGAAAAA
1 TGAAAAA
55364487 TGAAAAA
1 TGAAAAA
*
55364494 AGAAAA
1 TGAAAA
55364500 TGGAGAGGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 3 0.10
7 25 0.81
8 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (7 bp):
TGAAAAA
Found at i:55364483 original size:21 final size:20
Alignment explanation
Indices: 55364459--55364501 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
55364449 AAAAGTGATG
*
55364459 TGAAAAATGAAAAGATGAAAA
1 TGAAAAATGAAAA-AAGAAAA
55364480 TGAAAAATGAAAAAAGAAAA
1 TGAAAAATGAAAAAAGAAAA
55364500 TG
1 TG
55364502 GAGAGGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (20 bp):
TGAAAAATGAAAAAAGAAAA
Found at i:55366011 original size:132 final size:132
Alignment explanation
Indices: 55365785--55366088 Score: 493
Period size: 132 Copynumber: 2.3 Consensus size: 132
55365775 TCCCTCGGTT
*
55365785 GTAGTGGAGCAGATCAAAGATGGC-GAATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAG
1 GTAGTGGAGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAG
* * *
55365849 CCAATAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAATATTTCAGATCTTGTCTCCCTAA
65 CCAATAATTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAA
55365914 GCA
130 GCA
* *
55365917 GTAGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGC
1 GTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGC
* *
55365982 CAGTAATTCTACTTCCCTAGGCAGTAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAG
66 CAATAATTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAG
55366047 CA
131 CA
* * *
55366049 GTAGCGGAGCAAATAAAAGATGGCAGATTTTACCTCCCTG
1 GTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTG
55366089 GGCAGCAGCG
Statistics
Matches: 159, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
132 158 0.99
133 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
GTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGC
CAATAATTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAG
CA
Found at i:55366050 original size:44 final size:44
Alignment explanation
Indices: 55365995--55366140 Score: 148
Period size: 44 Copynumber: 3.3 Consensus size: 44
55365985 TAATTCTACT
* *
55365995 TCCCTAGGCAGTAGCGGAATAGATTGAAGATTTCAAATCTTGTC
1 TCCCTAAGCAGTAGCGGAATAGATTGAAGATTTCAGATCTTGTC
** * ** ** * **
55366039 TCCCTAAGCAGTAGCGGAGCAAATAAAAGATGGCAGATTTTACC
1 TCCCTAAGCAGTAGCGGAATAGATTGAAGATTTCAGATCTTGTC
** * *
55366083 TCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAGATCTTGTC
1 TCCCTAAGCAGTAGCGGAATAGATTGAAGATTTCAGATCTTGTC
55366127 TCCCTAAGCAGTAG
1 TCCCTAAGCAGTAG
55366141 TGGAGCAGAT
Statistics
Matches: 73, Mismatches: 29, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
44 73 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (44 bp):
TCCCTAAGCAGTAGCGGAATAGATTGAAGATTTCAGATCTTGTC
Found at i:55366106 original size:88 final size:88
Alignment explanation
Indices: 55365986--55366176 Score: 276
Period size: 88 Copynumber: 2.2 Consensus size: 88
55365976 TGAAGCCAGT
* * * * *
55365986 AATTCTACTTCCCTAGGCAGTAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAGCAGT
1 AATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAAATCTTGTCTCCCTAAGCAGT
55366051 AGCGGAGCAAATAAAAGATGGCAG
66 AGCGGAGCAAATAAAAGATGG-AG
*
55366075 -ATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAGATCTTGTCTCCCTAAGCAGT
1 AATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAAATCTTGTCTCCCTAAGCAGT
* * * *
55366139 AGTGGAGCAGATCAAAGATGGTG
66 AGCGGAGCAAATAAAAGATGGAG
55366162 AATTTTACCTCCCTG
1 AATTTTACCTCCCTG
55366177 TGGTTACAGT
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
87 1 0.01
88 90 0.99
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
AATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAAATCTTGTCTCCCTAAGCAGT
AGCGGAGCAAATAAAAGATGGAG
Found at i:55366157 original size:132 final size:131
Alignment explanation
Indices: 55366054--55366703 Score: 663
Period size: 132 Copynumber: 5.0 Consensus size: 131
55366044 AAGCAGTAGC
* * * * * *
55366054 GGAGCAAATAAAAGATGGCAGATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAG
1 GGAGCAAATAAAAGACGACAGATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAG
55366119 ATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTAC
66 ATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT--
55366184 AGT
129 AGT
* * ** * *
55366187 GGAGTACATTGAAG-C--CAGTAATTCTACTTCCTTGGGCAGTAGTGGAATAGATTGAAGATTTC
1 GGAGCAAATAAAAGACGACAG--ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
55366249 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
64 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
55366314 ACAGT
129 --AGT
* * ** * * * * * *
55366319 GGAGTACATTGAAGCCAATA-ATTCTACTTCCCTGGGTAGTAGCGGAATAGATTGAAGATTTCAG
1 GGAGCAAATAAAAGACGACAGATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAG
55366383 ATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTAC
66 ATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT--
55366448 AGT
129 AGT
* * * ** *
55366451 GAAGTACATTGAAG-C--CAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAGGATTTC
1 GGAGCAAATAAAAGACGACAG--ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
* *
55366513 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTT
64 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
55366578 GCAGT
129 --AGT
* * ** *
55366583 GGAGTACATTGAAG-C--CAGTAATTCTA-TATCCCTGGGCAGCAGTGGAATAGATTAAAGA-TT
1 GGAGCAAATAAAAGACGACAG--ATTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTT
* * * * *
55366643 ---A-C--ATATCCCTAAGCAGTAGTGGAGCAGATCAATGATGG-CAGATTTTACCTCCCTGAGG
63 CAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGA-ATTTTACCTCCCTGTGG
55366701 TTA
127 TTA
55366704 CAGTGGAGTA
Statistics
Matches: 475, Mismatches: 32, Indels: 30
0.88 0.06 0.06
Matches are distributed among these distances:
123 1 0.00
124 1 0.00
125 51 0.11
127 1 0.00
128 1 0.00
129 1 0.00
130 3 0.01
131 4 0.01
132 400 0.84
133 11 0.02
135 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (131 bp):
GGAGCAAATAAAAGACGACAGATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAG
ATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTAG
T
Found at i:55366245 original size:220 final size:220
Alignment explanation
Indices: 55365854--55366308 Score: 752
Period size: 220 Copynumber: 2.1 Consensus size: 220
55365844 TGAAGCCAAT
* * *
55365854 AATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAATATTTCAGATCTTGTCTCCCTAAGCAGT
1 AATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAGATCTTGTCTCCCTAAGCAGT
*
55365919 AGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCCA
66 AGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
55365984 GTAATTCTACTTCCCTAGGCAGTAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAGCA
131 GTAATTCTACTTCCCTAGGCAGTAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAGCA
55366049 GTAGCGGAGCAAATAAAAGATGGCAG
196 GTAGCGGAGCAAATAAAAGATGG-AG
55366075 -ATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAGATCTTGTCTCCCTAAGCAGT
1 AATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAGATCTTGTCTCCCTAAGCAGT
**
55366139 AGTGGAGCAGATCAAAGATG-GTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
66 AGTGGAGCAGATCAAAGATGACAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
* * * *
55366203 AGTAATTCTACTTCCTTGGGCAGTAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGC
130 AGTAATTCTACTTCCCTAGGCAGTAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAGC
* * * *
55366268 AGTAGTGGAGCAGATCAAAGATGGTG
195 AGTAGCGGAGCAAATAAAAGATGGAG
55366294 AATTTTACCTCCCTG
1 AATTTTACCTCCCTG
55366309 TGGTTACAGT
Statistics
Matches: 218, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
219 2 0.01
220 216 0.99
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (220 bp):
AATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAGATCTTGTCTCCCTAAGCAGT
AGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
GTAATTCTACTTCCCTAGGCAGTAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAGCA
GTAGCGGAGCAAATAAAAGATGGAG
Done.