Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 151 of 208
Found at i:49037666 original size:40 final size:40
Alignment explanation
Indices: 49037640--49037945 Score: 470
Period size: 40 Copynumber: 7.7 Consensus size: 40
49037630 TGATTACTCT
* * * *
49037640 TCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
* * * *
49037680 TCGAGG-TTTAGCACGGATATATTACTAGCACGAATGCTCT
1 TCG-GGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
* * *
49037720 TCGGAACTTAGCCCGGATACATCACTAGCACGAATGATCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
*
49037760 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGGTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
*
49037800 TCGGGACTTAGCCCGGATATATCTCTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
49037840 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
*
49037880 TCGGGACTTAGCCCAGATATATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
49037920 TCGGGACTTAGCCCGGATATATCACT
1 TCGGGACTTAGCCCGGATATATCACT
49037946 CTCAATTCTC
Statistics
Matches: 243, Mismatches: 21, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
39 1 0.00
40 240 0.99
41 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
Found at i:49039202 original size:37 final size:37
Alignment explanation
Indices: 49039160--49039238 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
49039150 TTATTACGAA
* * *
49039160 GTCTTACCCGGACATAATCTCCACACGAACTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAACTCATCGG
* *
49039197 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAACTCATCGG
49039234 GTCTT
1 GTCTT
49039239 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAACTCATCGG
Found at i:49039435 original size:47 final size:47
Alignment explanation
Indices: 49039357--49040396 Score: 1819
Period size: 47 Copynumber: 21.9 Consensus size: 47
49039347 CCCTTAGGGA
* * * * * *
49039357 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
49039404 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49039451 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
49039498 CTTATCACATATATATATACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
49039547 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49039596 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49039643 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49039690 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49039737 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49039784 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49039831 CCTATCACATATATAACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATAT-ACACTTTCACATTCATCACATCGGCCATTAGGC
49039879 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49039926 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49039973 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49040020 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49040067 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49040116 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49040163 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49040210 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49040257 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49040306 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49040353 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
49040397 CGCCATACTA
Statistics
Matches: 962, Mismatches: 24, Indels: 14
0.96 0.02 0.01
Matches are distributed among these distances:
47 734 0.76
48 46 0.05
49 182 0.19
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:49040210 original size:190 final size:190
Alignment explanation
Indices: 49039357--49040396 Score: 1854
Period size: 190 Copynumber: 5.5 Consensus size: 190
49039347 CCCTTAGGGA
* * * * * * * *
49039357 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
49039422 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCACATC
* *
49039487 GGCCATTAGGCCTTATCACATATATATATACTTTCACATTCATCACATTGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
49039547 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
49039612 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCACA
49039677 TCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49039737 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
49039802 TTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAACACTTTCACATTCATCACAT
66 TTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATAT-ACACTTTCACATTCATCACAT
49039867 CGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
130 CGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49039926 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
49039991 TTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCACATC
*
49040056 GGCCATTAGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
49040116 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
49040181 TTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCACATC
*
49040246 GGCCATTAGGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49040306 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
49040371 TTTCACATTCATCACATCGGCCATTA
66 TTTCACATTCATCACATCGGCCATTA
49040397 CGCCATACTA
Statistics
Matches: 824, Mismatches: 21, Indels: 10
0.96 0.02 0.01
Matches are distributed among these distances:
188 138 0.17
189 188 0.23
190 366 0.44
192 132 0.16
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (190 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:49043913 original size:26 final size:26
Alignment explanation
Indices: 49043884--49043935 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
49043874 AATAAAAGAA
49043884 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTTAATTAG
49043910 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTTAATTAG
49043936 CATTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTAG
Found at i:49045159 original size:50 final size:50
Alignment explanation
Indices: 49044978--49045174 Score: 216
Period size: 50 Copynumber: 3.8 Consensus size: 50
49044968 ATTTGGGAAA
* *
49044978 AGAGATCCCATGTAAGACCATGTCTGGGAAATGGCATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC---GA---TATG
* * *
49045034 AGAGGTCCCATGTAAGACCATGTCTGGGACAT-GCCTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
** *
49045083 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCATCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
** * * *
49045133 AGAACTCCCATGTAAAACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
49045175 GTACAAGAAA
Statistics
Matches: 121, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
49 33 0.27
50 47 0.39
52 2 0.02
55 9 0.07
56 30 0.25
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
Found at i:49047230 original size:75 final size:75
Alignment explanation
Indices: 49047107--49047248 Score: 266
Period size: 75 Copynumber: 1.9 Consensus size: 75
49047097 TGAAATGACC
* *
49047107 TACACCTTTAGGTTTCCTTTTGGTTCTCCCATTGGCTTGGGTTGAACCACCTTAGTTTATGGGCT
1 TACACCTTTAGGTTTCCTTTTGGTTCTCCCATTGCCTTCGGTTGAACCACCTTAGTTTATGGGCT
49047172 ATTAACGACG
66 ATTAACGACG
49047182 TACACCTTTAGGTTTCCTTTTGGTTCTCCCATTGCCTTCGGTTGAACCACCTTAGTTTATGGGCT
1 TACACCTTTAGGTTTCCTTTTGGTTCTCCCATTGCCTTCGGTTGAACCACCTTAGTTTATGGGCT
49047247 AT
66 AT
49047249 AATTATTGCA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (75 bp):
TACACCTTTAGGTTTCCTTTTGGTTCTCCCATTGCCTTCGGTTGAACCACCTTAGTTTATGGGCT
ATTAACGACG
Found at i:49047276 original size:12 final size:13
Alignment explanation
Indices: 49047251--49047280 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
49047241 TGGGCTATAA
49047251 TTATTGCATTTAT
1 TTATTGCATTTAT
49047264 TTATTGC-TTTAT
1 TTATTGCATTTAT
49047276 TTATT
1 TTATT
49047281 CATGTATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (13 bp):
TTATTGCATTTAT
Found at i:49051121 original size:104 final size:104
Alignment explanation
Indices: 49050936--49051149 Score: 419
Period size: 104 Copynumber: 2.0 Consensus size: 104
49050926 CTTACATCTT
49050936 AGGAGTCAAGATCTATAGAGATAGATCAAGACGACTACTAGGTCTAAGCAAAAGTACATACATAT
1 AGGA-TCAAGATCTATAGAGATAGATCAAGACGACTACTAGGTCTAAGCAAAAGTACATACATAT
49051001 ATAAAGTACTGAAAAGGTTCAGTATGAAAGAATCTAAGAG
65 ATAAAGTACTGAAAAGGTTCAGTATGAAAGAATCTAAGAG
49051041 AGGATCAAGATCTATAGAGATAGATCAAGACGACTACTAGGTCTAAGCAAAAGTACATACATATA
1 AGGATCAAGATCTATAGAGATAGATCAAGACGACTACTAGGTCTAAGCAAAAGTACATACATATA
49051106 TAAAGTACTGAAAAGGTTCAGTATGAAAGAATCTAAGAG
66 TAAAGTACTGAAAAGGTTCAGTATGAAAGAATCTAAGAG
49051145 AGGAT
1 AGGAT
49051150 TCCTACCTAT
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
104 105 0.96
105 4 0.04
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (104 bp):
AGGATCAAGATCTATAGAGATAGATCAAGACGACTACTAGGTCTAAGCAAAAGTACATACATATA
TAAAGTACTGAAAAGGTTCAGTATGAAAGAATCTAAGAG
Found at i:49054290 original size:24 final size:25
Alignment explanation
Indices: 49054262--49054309 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
49054252 TCTGACCCAA
*
49054262 TTTTACTGGAATATG-AATGGAACC
1 TTTTACTGGAATAAGTAATGGAACC
* *
49054286 TTTTAGTGGGATAAGTAATGGAAC
1 TTTTACTGGAATAAGTAATGGAAC
49054310 TTGGAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (25 bp):
TTTTACTGGAATAAGTAATGGAACC
Found at i:49056375 original size:24 final size:25
Alignment explanation
Indices: 49056347--49056393 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
49056337 TCCGACCCAA
*
49056347 TTTTACTGGAATATG-AATGGAAGC
1 TTTTACTGGAATAAGTAATGGAAGC
* *
49056371 TTTTAGTGGGATAAGTAATGGAA
1 TTTTACTGGAATAAGTAATGGAA
49056394 CTTGGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (25 bp):
TTTTACTGGAATAAGTAATGGAAGC
Found at i:49062651 original size:26 final size:26
Alignment explanation
Indices: 49062622--49062673 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
49062612 AATAAAATAA
49062622 AACATTCAATATTTCT-GTTTAATTAG
1 AACATTCAATATTT-TAGTTTAATTAG
49062648 AACATTCAATATTTTAGTTTAATTAG
1 AACATTCAATATTTTAGTTTAATTAG
49062674 CTTTACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTTAGTTTAATTAG
Found at i:49069759 original size:11 final size:11
Alignment explanation
Indices: 49069735--49069771 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
49069725 CCAAGCCAAT
*
49069735 AGGAGAACCAAA
1 AGGA-AACCTAA
49069747 AGGAAACCTAA
1 AGGAAACCTAA
49069758 AGGAAACCTAA
1 AGGAAACCTAA
49069769 AGG
1 AGG
49069772 TGTAAGCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.54, C:0.16, G:0.24, T:0.05
Consensus pattern (11 bp):
AGGAAACCTAA
Found at i:49073295 original size:26 final size:26
Alignment explanation
Indices: 49073266--49073315 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
49073256 TAAAAGAAAA
* *
49073266 CATTCAATATTTTAGTTTAATTAGAC
1 CATTCAATATATCAGTTTAATTAGAC
49073292 CATTCAATATATCAGTTTAATTAG
1 CATTCAATATATCAGTTTAATTAG
49073316 CATGAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (26 bp):
CATTCAATATATCAGTTTAATTAGAC
Found at i:49075409 original size:26 final size:26
Alignment explanation
Indices: 49075379--49075430 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
49075369 AATAAAAGAA
*
49075379 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
49075405 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
49075431 CATTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTCTAATTAG
Found at i:49076480 original size:40 final size:40
Alignment explanation
Indices: 49076435--49076641 Score: 252
Period size: 40 Copynumber: 5.2 Consensus size: 40
49076425 GGAATTTAGT
*
49076435 CGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCC
1 CGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGCC
* * * *
49076475 CGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACC
1 CGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGCC
* * * * *
49076515 CGGGTATAGCAATTCGCACAAATGCCTTCGGGTCTTAGCC
1 CGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGCC
* * * *
49076555 CGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACC
1 CGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGCC
* * * *
49076595 CGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCC
1 CGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGCC
49076635 CGGATAT
1 CGGATAT
49076642 CATTCAAATG
Statistics
Matches: 135, Mismatches: 32, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 135 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGCC
Found at i:49076583 original size:80 final size:80
Alignment explanation
Indices: 49076450--49076640 Score: 373
Period size: 80 Copynumber: 2.4 Consensus size: 80
49076440 ATAACCACAA
49076450 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACC
*
49076515 CGGGTATAGCAATTC
66 CGGGTATAGCAACTC
49076530 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACC
49076595 CGGGTATAGCAACTC
66 CGGGTATAGCAACTC
49076610 GCACAAATGCCTTCGGGTCTTAGCCCGGATA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATA
49076641 TCATTCAAAT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 110 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACC
CGGGTATAGCAACTC
Found at i:49094132 original size:26 final size:26
Alignment explanation
Indices: 49094102--49094153 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
49094092 AATAAAAGAA
*
49094102 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
49094128 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
49094154 CATTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTCTAATTAG
Found at i:49095205 original size:26 final size:26
Alignment explanation
Indices: 49095174--49095225 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
49095164 AATAAAAGAA
* *
49095174 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAACATTTCAGTCTAATTAG
49095200 AACATTCAACATTTCAGTCTAATTAG
1 AACATTCAACATTTCAGTCTAATTAG
49095226 CATTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (26 bp):
AACATTCAACATTTCAGTCTAATTAG
Found at i:49102898 original size:26 final size:26
Alignment explanation
Indices: 49102860--49102911 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
49102850 AATAAAAGAA
* *
49102860 AACATTCAATATTTCAGTATAATTAG
1 AACAGTCAATATTTCAATATAATTAG
* *
49102886 AACAGTCACTATTTCAATTTAATTAG
1 AACAGTCAATATTTCAATATAATTAG
49102912 CATTGATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (26 bp):
AACAGTCAATATTTCAATATAATTAG
Found at i:49104642 original size:26 final size:26
Alignment explanation
Indices: 49104604--49104655 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
49104594 AATAAAAGAA
* *
49104604 AACATTCATTATTTCAGTGTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
49104630 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
49104656 CATTGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTCTAATTAG
Found at i:49107838 original size:26 final size:26
Alignment explanation
Indices: 49107800--49107851 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
49107790 AATAGAAGAA
* *
49107800 AACATTCATTATTTCAGTGTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
49107826 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
49107852 CATTGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTCTAATTAG
Found at i:49114077 original size:26 final size:26
Alignment explanation
Indices: 49114047--49114098 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
49114037 AATAAAAGAA
*
49114047 AACATT-TAATATTTTAGTTTAATTAG
1 AACATTCT-ATATTTTAGTCTAATTAG
49114073 AACATTCTATATTTTAGTCTAATTAG
1 AACATTCTATATTTTAGTCTAATTAG
49114099 CATTAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.48
Consensus pattern (26 bp):
AACATTCTATATTTTAGTCTAATTAG
Found at i:49118269 original size:26 final size:26
Alignment explanation
Indices: 49118240--49118291 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
49118230 AATGAAAGAA
*
49118240 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
49118266 AACATTCAATATTTCAGTTGAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
49118292 CATTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTGAATTAG
Found at i:49120388 original size:26 final size:26
Alignment explanation
Indices: 49120359--49120410 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
49120349 AATAAAAGAA
*
49120359 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
49120385 AACATTCAATATTTCAGTTGAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
49120411 CATTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTGAATTAG
Found at i:49122505 original size:26 final size:26
Alignment explanation
Indices: 49122475--49122526 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
49122465 AATGAAAGAA
*
49122475 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
49122501 AACATTCAATATTTCAGTTGAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
49122527 CATTGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTGAATTAG
Found at i:49124610 original size:26 final size:26
Alignment explanation
Indices: 49124581--49124632 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
49124571 AATAAAAGAA
*
49124581 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
49124607 AACATTCAATATTTCAGTTGAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
49124633 CATTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTGAATTAG
Found at i:49126718 original size:26 final size:26
Alignment explanation
Indices: 49126689--49126740 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
49126679 AATAAAAGAA
49126689 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTTAATTAG
*
49126715 AACATTCAATATTTCAGTTTCATTAG
1 AACATTCAATATTTCAGTTTAATTAG
49126741 CATTTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTAG
Found at i:49127586 original size:26 final size:26
Alignment explanation
Indices: 49127557--49127608 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
49127547 AATAAAAGAA
*
49127557 AACATTCAATATTTCAATTTAATTAG
1 AACATTCAATATTTCAATTGAATTAG
*
49127583 AACATTCAATATTTCAGTTGAATTAG
1 AACATTCAATATTTCAATTGAATTAG
49127609 CATTGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAATTGAATTAG
Found at i:49131748 original size:26 final size:25
Alignment explanation
Indices: 49131719--49131771 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 25
49131709 TTACAATAAA
49131719 AGAAAATTCAATATTTCAGTTTAATT
1 AGAAAATTCAATATTTCAG-TTAATT
*
49131745 AGAACATTCAATATTTCAGTTAATT
1 AGAAAATTCAATATTTCAGTTAATT
49131770 AG
1 AG
49131772 CATTATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (25 bp):
AGAAAATTCAATATTTCAGTTAATT
Found at i:49133848 original size:25 final size:26
Alignment explanation
Indices: 49133808--49133858 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
49133798 CAATAAAGAA
49133808 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTTAATTAG
49133834 AACATTC-ATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTTAATTAG
49133859 CATTAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTAG
Found at i:49135930 original size:25 final size:25
Alignment explanation
Indices: 49135890--49135939 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
49135880 CAATAAAAGA
49135890 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTT-ATTAG
49135916 AACATTC-ATATTTCAGTTTATTAG
1 AACATTCAATATTTCAGTTTATTAG
49135940 CATTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.21
25 12 0.50
26 7 0.29
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (25 bp):
AACATTCAATATTTCAGTTTATTAG
Found at i:49138006 original size:26 final size:26
Alignment explanation
Indices: 49137977--49138028 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
49137967 AATAAAAGAA
* *
49137977 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAATCTAATTAG
49138003 AACATTCAATATTTCAATCTAATTAG
1 AACATTCAATATTTCAATCTAATTAG
49138029 CATTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAATCTAATTAG
Found at i:49139716 original size:19 final size:19
Alignment explanation
Indices: 49139674--49139710 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
49139664 ATTTTTTTTG
*
49139674 TTATAACTTTATAAAATAC
1 TTATAAATTTATAAAATAC
*
49139693 TTATAAATTTTTAAAATA
1 TTATAAATTTATAAAATA
49139711 TATATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATAAATTTATAAAATAC
Found at i:49140512 original size:20 final size:21
Alignment explanation
Indices: 49140487--49140530 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
49140477 TTCTCGTTAT
49140487 CTAATAA-AAATCTAAAATT-C
1 CTAATAATAAATC-AAAATTGC
49140507 CTAATAATAAATCAAAATTGC
1 CTAATAATAAATCAAAATTGC
49140528 CTA
1 CTA
49140531 TTTGATTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (21 bp):
CTAATAATAAATCAAAATTGC
Found at i:49141188 original size:19 final size:19
Alignment explanation
Indices: 49141166--49141229 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
49141156 GGTTACAAAC
49141166 TTTATCTGTTTTTTACATG
1 TTTATCTGTTTTTTACATG
***
49141185 TTTATCTCACAAATTTT-C-T-
1 TTTATCT---GTTTTTTACATG
49141204 TTTATCTGTTTTTTACATG
1 TTTATCTGTTTTTTACATG
49141223 TTTATCT
1 TTTATCT
49141230 CACAAAGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
16 4 0.12
17 1 0.03
18 1 0.03
19 21 0.64
20 1 0.03
21 1 0.03
22 4 0.12
ACGTcount: A:0.19, C:0.14, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTATCTGTTTTTTACATG
Found at i:49141246 original size:38 final size:38
Alignment explanation
Indices: 49141166--49141247 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 38
49141156 GGTTACAAAC
* *
49141166 TTTATCTGTTTTTTACATGTTTATCTCACAAATTTTCT
1 TTTATCTGTTTTTTACATGTTTATCTCACAAAGTTTCG
*
49141204 TTTATCTGTTTTTTACATGTTTATCTCACAAAGTTTGG
1 TTTATCTGTTTTTTACATGTTTATCTCACAAAGTTTCG
49141242 TTTATC
1 TTTATC
49141248 AATTGTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.56
Consensus pattern (38 bp):
TTTATCTGTTTTTTACATGTTTATCTCACAAAGTTTCG
Found at i:49150743 original size:3 final size:3
Alignment explanation
Indices: 49150735--49150814 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
49150725 GCACATTTTA
49150735 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
49150783 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
49150815 TATTTCTCCT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:49153813 original size:3 final size:3
Alignment explanation
Indices: 49153807--49153844 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
49153797 AATATTCCAA
49153807 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
49153845 AAAAAGAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:49156520 original size:22 final size:22
Alignment explanation
Indices: 49156497--49156539 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
49156487 TTGTTTTTTA
*
49156497 TTTAAAATAAATTCTAAAAATAT
1 TTTAAAA-AAATTATAAAAATAT
*
49156520 TTTTAAAAAATTATAAAAAT
1 TTTAAAAAAATTATAAAAAT
49156540 GCATGAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAAAAATTATAAAAATAT
Found at i:49161945 original size:48 final size:48
Alignment explanation
Indices: 49161889--49161984 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
49161879 GATAATGAAA
49161889 GGCACTAAATCTTTTATCATACAATATCCTGCAACATGATCAATCATT
1 GGCACTAAATCTTTTATCATACAATATCCTGCAACATGATCAATCATT
49161937 GGCACTAAATCTTTTATCATACAATATCCTGCAACATGATCAATCATT
1 GGCACTAAATCTTTTATCATACAATATCCTGCAACATGATCAATCATT
49161985 ATCTAAAAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33
Consensus pattern (48 bp):
GGCACTAAATCTTTTATCATACAATATCCTGCAACATGATCAATCATT
Found at i:49165392 original size:24 final size:24
Alignment explanation
Indices: 49165347--49165392 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
49165337 TCTTCACCCT
* *
49165347 CTTCATCATCATCATCATCCTCTC
1 CTTCATCATCACCATCACCCTCTC
* *
49165371 CTTCATCTTCACCCTCACCCTC
1 CTTCATCATCACCATCACCCTC
49165393 AGCCTCTCCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.35
Consensus pattern (24 bp):
CTTCATCATCACCATCACCCTCTC
Found at i:49165422 original size:18 final size:18
Alignment explanation
Indices: 49165373--49165429 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
49165363 ATCCTCTCCT
*
49165373 TCATCTTCACCCTCACCC
1 TCATCTTCACCATCACCC
* * *
49165391 TCAGCCTCTCCATCACCC
1 TCATCTTCACCATCACCC
*
49165409 TCATCTTCAGCATCACCC
1 TCATCTTCACCATCACCC
49165427 TCA
1 TCA
49165430 CTCTCATTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.19, C:0.51, G:0.04, T:0.26
Consensus pattern (18 bp):
TCATCTTCACCATCACCC
Found at i:49165430 original size:24 final size:24
Alignment explanation
Indices: 49165379--49165436 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
49165369 TCCTTCATCT
* * *
49165379 TCACCCTCACCCTCAGCCTCTCCA
1 TCACCCTCATCCTCAGCATCACCA
* *
49165403 TCACCCTCATCTTCAGCATCACCC
1 TCACCCTCATCCTCAGCATCACCA
*
49165427 TCACTCTCAT
1 TCACCCTCAT
49165437 TTTGACCATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.52, G:0.03, T:0.26
Consensus pattern (24 bp):
TCACCCTCATCCTCAGCATCACCA
Found at i:49170583 original size:2 final size:2
Alignment explanation
Indices: 49170578--49170668 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
49170568 AAGATTCTTT
49170578 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
49170620 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
49170662 TC TC TC T
1 TC TC TC T
49170669 TTGCATTTCG
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:49171108 original size:9 final size:9
Alignment explanation
Indices: 49171094--49171118 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
49171084 ATATAGGGAT
49171094 TAAAATGAA
1 TAAAATGAA
49171103 TAAAATGAA
1 TAAAATGAA
49171112 TAAAATG
1 TAAAATG
49171119 CAAACTATGT
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:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (9 bp):
TAAAATGAA
Found at i:49171652 original size:98 final size:98
Alignment explanation
Indices: 49171485--49171681 Score: 315
Period size: 98 Copynumber: 2.0 Consensus size: 98
49171475 ATGTGAACTA
* * *
49171485 TATATATATATGTTAGAAACATTGGATATCCTATTAATGGTCTCGGATAGAGTCGGGTATAGATG
1 TATATATATATGTTAGAAACATTGGATATCCTATTAAGGGTCTCGAATAGAGTCGGGCATAGATG
* *
49171550 GCATGTCATAGGATTAGTGTATGAGATTTTTAC
66 GCATGTCATAGGATTAGCGTACGAGATTTTTAC
*
49171583 TATATATATATGTTAGAAACATTGGATA-CCTTATTAAGGGTCTCGAATAGAGTTGGGCATAGAT
1 TATATATATATGTTAGAAACATTGGATATCC-TATTAAGGGTCTCGAATAGAGTCGGGCATAGAT
*
49171647 GGCATGTTATAGGATTAGCGTACGAGATTTTTAC
65 GGCATGTCATAGGATTAGCGTACGAGATTTTTAC
49171681 T
1 T
49171682 TCAGTTTATA
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 2 0.02
98 89 0.98
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (98 bp):
TATATATATATGTTAGAAACATTGGATATCCTATTAAGGGTCTCGAATAGAGTCGGGCATAGATG
GCATGTCATAGGATTAGCGTACGAGATTTTTAC
Found at i:49176708 original size:37 final size:40
Alignment explanation
Indices: 49176612--49176751 Score: 151
Period size: 40 Copynumber: 3.5 Consensus size: 40
49176602 AACATGCTAG
* *
49176612 TTTGGCACCCAGTGCCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAAATCGAAGTAATAA
* * *
49176652 TTTGACAACCAGTGTCTCATCGGCTAAATCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGATAAATCGAAGTAATAA
* * *
49176690 -TTGACACCCAATGCCTCATCGAATTAATCCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAAAT-CGAAGTAATAA
* * *
49176730 ATTCACACCCAGTGTCTCATCG
1 TTTGACACCCAGTGCCTCATCG
49176752 ACTCAAAGTC
Statistics
Matches: 82, Mismatches: 14, Indels: 7
0.80 0.14 0.07
Matches are distributed among these distances:
37 22 0.27
38 8 0.10
39 2 0.02
40 32 0.39
41 18 0.22
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGATAAATCGAAGTAATAA
Found at i:49176738 original size:41 final size:40
Alignment explanation
Indices: 49176617--49176752 Score: 136
Period size: 37 Copynumber: 3.5 Consensus size: 40
49176607 GCTAGTTTGG
* *
49176617 CACCCAGTGCCTCATCGGA-TAATTCGAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGAATTAA-TCGAAGTAATAAATTGA
* * ** *
49176657 CAACCAGTGTCTCATCGGCTAAATCGAAG---TAAATTGA
1 CACCCAGTGCCTCATCGAATTAATCGAAGTAATAAATTGA
* *
49176694 CACCCAATGCCTCATCGAATTAATCCGAAGTAATAAATTCA
1 CACCCAGTGCCTCATCGAATTAAT-CGAAGTAATAAATTGA
*
49176735 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
49176753 CTCAAAGTCG
Statistics
Matches: 77, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
37 25 0.32
38 5 0.06
40 22 0.29
41 25 0.32
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATTAATCGAAGTAATAAATTGA
Found at i:49176745 original size:78 final size:78
Alignment explanation
Indices: 49176617--49176769 Score: 211
Period size: 78 Copynumber: 2.0 Consensus size: 78
49176607 GCTAGTTTGG
* * * * * *
49176617 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAATTTGACAACCAGTGTCTCATCGGCT-AAA-
1 CACCCAATGCCTCATCGAATAATCCGAAGTAATAAATTCACAACCAGTGTCTCATCGACTCAAAG
49176680 TCGAAGTAAATTGA
66 TCGAAG-AAATTGA
*
49176694 CACCCAATGCCTCATCGAATTAATCCGAAGTAATAAATTCACACCCAGTGTCTCATCGACTCAAA
1 CACCCAATGCCTCATCGAA-TAATCCGAAGTAATAAATTCACAACCAGTGTCTCATCGACTCAAA
49176759 GTCGAAGAAAT
65 GTCGAAGAAAT
49176770 CCTTGAACTC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
77 17 0.26
78 36 0.55
79 7 0.11
80 6 0.09
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (78 bp):
CACCCAATGCCTCATCGAATAATCCGAAGTAATAAATTCACAACCAGTGTCTCATCGACTCAAAG
TCGAAGAAATTGA
Found at i:49177643 original size:16 final size:15
Alignment explanation
Indices: 49177622--49177652 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
49177612 CTTTTCTCCT
49177622 TCTTTCTTTCTCTTTC
1 TCTTTCTTTCT-TTTC
49177638 TCTTTCTTTCTTTTC
1 TCTTTCTTTCTTTTC
49177653 CCCCTGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTTTCTTTCTTTTC
Found at i:49183841 original size:21 final size:21
Alignment explanation
Indices: 49183802--49183841 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
49183792 ATAATATAAA
*
49183802 TTAAAAATTACAATTATTTTT
1 TTAAAAATTACAATGATTTTT
* *
49183823 TTAAAATTTATAATGATTT
1 TTAAAAATTACAATGATTT
49183842 ATCAAAGTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (21 bp):
TTAAAAATTACAATGATTTTT
Found at i:49188999 original size:8 final size:8
Alignment explanation
Indices: 49188986--49189016 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
49188976 TAGAAGCCAC
49188986 AATACTTA
1 AATACTTA
49188994 AATACTTA
1 AATACTTA
49189002 AATACTTA
1 AATACTTA
49189010 AATACTT
1 AATACTT
49189017 CACAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (8 bp):
AATACTTA
Found at i:49189379 original size:29 final size:27
Alignment explanation
Indices: 49189310--49189379 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 27
49189300 ATAAACACCC
*
49189310 AAAATTTATTTTAAAAATAAAAAATAA
1 AAAATATATTTTAAAAATAAAAAATAA
* * *
49189337 AAAAAAGTATTTTAAAATTAAAAAAATTA
1 AAAATA-TATTTTAAAAAT-AAAAAATAA
49189366 AAAATATATATTTA
1 AAAATATAT-TTTA
49189380 TTATATTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 4 0.11
28 14 0.40
29 17 0.49
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (27 bp):
AAAATATATTTTAAAAATAAAAAATAA
Found at i:49206750 original size:41 final size:43
Alignment explanation
Indices: 49206644--49206752 Score: 143
Period size: 43 Copynumber: 2.6 Consensus size: 43
49206634 GAGGTGTGAT
49206644 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTGAGAA
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTGAGAA
** *
49206687 AACGTGTAAGACCATGTCTGGGACATTGGCATCGTA-T-ATG-A
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTGA-GAA
* *
49206728 TTCGTATAAGACCCTGTCTGGGACA
1 TTCGTGTAAGACCATGTCTGGGACA
49206753 GTGATATTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 23 0.40
42 2 0.03
43 33 0.57
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.27
Consensus pattern (43 bp):
TTCGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTGAGAA
Found at i:49209334 original size:5 final size:5
Alignment explanation
Indices: 49209324--49209348 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
49209314 TAGGGTTCCG
49209324 CTTCT CTTCT CTTCT CTTCT CTTCT
1 CTTCT CTTCT CTTCT CTTCT CTTCT
49209349 TTATGCTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTTCT
Found at i:49214872 original size:11 final size:11
Alignment explanation
Indices: 49214855--49214896 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
49214845 TTTTTTTTTC
49214855 ACTATTTTGCT
1 ACTATTTTGCT
* *
49214866 ACAATTTTACT
1 ACTATTTTGCT
*
49214877 ACTATGTTGCT
1 ACTATTTTGCT
49214888 ACTATTTTG
1 ACTATTTTG
49214897 TTGTTATTGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.50
Consensus pattern (11 bp):
ACTATTTTGCT
Found at i:49214945 original size:17 final size:19
Alignment explanation
Indices: 49214912--49214946 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
49214902 ATTGTTTGGA
49214912 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
49214931 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
49214947 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:49228731 original size:25 final size:25
Alignment explanation
Indices: 49228648--49228731 Score: 62
Period size: 25 Copynumber: 3.4 Consensus size: 25
49228638 GCTCTCTCTC
**
49228648 GAGCCATATAACAGGAAGCTCATGT
1 GAGCCATATAACAGGAAGCTCATAA
* * ** * *
49228673 TAGCCATGTAATGGGAAGCTTATCCA
1 GAGCCATATAACAGGAAGCTCAT-AA
* *
49228699 -TGCTATATAACAGGAAGCTCATAA
1 GAGCCATATAACAGGAAGCTCATAA
49228723 GAGCCATAT
1 GAGCCATAT
49228732 TTAGGAAGCT
Statistics
Matches: 41, Mismatches: 16, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
24 1 0.02
25 40 0.98
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATAA
Found at i:49228859 original size:26 final size:26
Alignment explanation
Indices: 49228779--49228862 Score: 95
Period size: 26 Copynumber: 3.3 Consensus size: 26
49228769 AGCGAGCCAT
49228779 ATCGGGAAGCTCTAG-AGAGCCAT-TA
1 ATCGGGAAGCTC-AGAAGAGCCATATA
* *
49228804 ATCAGGAAGCTCAGAAAGAGCC-TTTA
1 ATCGGGAAGCTCAG-AAGAGCCATATA
49228830 ATCGGGAAGCTCACGAAGAGCCATAT-
1 ATCGGGAAGCTCA-GAAGAGCCATATA
49228856 ATCGGGA
1 ATCGGGA
49228863 CGCTAATAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.04
25 12 0.24
26 34 0.67
27 3 0.06
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (26 bp):
ATCGGGAAGCTCAGAAGAGCCATATA
Found at i:49230428 original size:59 final size:59
Alignment explanation
Indices: 49230339--49230457 Score: 184
Period size: 59 Copynumber: 2.0 Consensus size: 59
49230329 CTAACATACG
* * * * *
49230339 CAAACAAACAAATGTGTTATTGGCGGGGAAATGATCTAAGTCACGTTCCTGCCAGAAAA
1 CAAACAAACAAATGTGTTAGTGGCAGGGAAATGATCTAAGTCACATTCCTACAAGAAAA
*
49230398 CAAACAAACAAATGTGTTAGTGGCAGGGAAATGATCTCAGTCACATTCCTACAAGAAAA
1 CAAACAAACAAATGTGTTAGTGGCAGGGAAATGATCTAAGTCACATTCCTACAAGAAAA
49230457 C
1 C
49230458 TTTAGAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.21
Consensus pattern (59 bp):
CAAACAAACAAATGTGTTAGTGGCAGGGAAATGATCTAAGTCACATTCCTACAAGAAAA
Found at i:49242014 original size:18 final size:18
Alignment explanation
Indices: 49241991--49242053 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
49241981 TAAGTGCACT
49241991 TTAATTATTTTGTAAAAA
1 TTAATTATTTTGTAAAAA
* ** **
49242009 TTAATTATTTAAGTGCACT
1 TTAATTATTT-TGTAAAAA
49242028 TTAATTATTTTGTAAAAA
1 TTAATTATTTTGTAAAAA
49242046 TTAATTAT
1 TTAATTAT
49242054 CTTTTCGACA
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
18 21 0.62
19 13 0.38
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (18 bp):
TTAATTATTTTGTAAAAA
Found at i:49242027 original size:37 final size:37
Alignment explanation
Indices: 49241979--49242053 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
49241969 ATGTTCATAT
49241979 TTTAAGTGCACTTTAATTATTTTGTAAAAATTAATTA
1 TTTAAGTGCACTTTAATTATTTTGTAAAAATTAATTA
49242016 TTTAAGTGCACTTTAATTATTTTGTAAAAATTAATTA
1 TTTAAGTGCACTTTAATTATTTTGTAAAAATTAATTA
49242053 T
1 T
49242054 CTTTTCGACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.49
Consensus pattern (37 bp):
TTTAAGTGCACTTTAATTATTTTGTAAAAATTAATTA
Found at i:49242033 original size:19 final size:19
Alignment explanation
Indices: 49241979--49242037 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
49241969 ATGTTCATAT
49241979 TTTAAGTGCACTTTAATTA
1 TTTAAGTGCACTTTAATTA
* ** **
49241998 TTT-TGTAAAAATTAATTA
1 TTTAAGTGCACTTTAATTA
49242016 TTTAAGTGCACTTTAATTA
1 TTTAAGTGCACTTTAATTA
49242035 TTT
1 TTT
49242038 TGTAAAAATT
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (19 bp):
TTTAAGTGCACTTTAATTA
Found at i:49249725 original size:59 final size:57
Alignment explanation
Indices: 49249642--49249808 Score: 149
Period size: 58 Copynumber: 2.9 Consensus size: 57
49249632 AAGTTCCTAA
* *****
49249642 TTTATTAAATGAA-ACTATGAAAAAATAATTTGTATTTTCTTATTCAAAAGAACTTCTAT
1 TTTATTAAATGAACAATAT--AAAAATAATTTGTATAAAAATATTCAAAA-AACTTCTAT
* * * * *
49249701 TTTATTAAATGACACAATATAAAAATAATTTTTACAAAAATATTCAAAACACTTTTGT
1 TTTATTAAATGA-ACAATATAAAAATAATTTGTATAAAAATATTCAAAAAACTTCTAT
* * *
49249759 TTTATTAAATGAAGCAATATAAAAATAGTTTGTATAGATATATT-AAAAAA
1 TTTATTAAATGAA-CAATATAAAAATAATTTGTATAAAAATATTCAAAAAA
49249809 TCAATGCATG
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
57 6 0.07
58 43 0.49
59 34 0.39
60 1 0.01
61 4 0.05
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (57 bp):
TTTATTAAATGAACAATATAAAAATAATTTGTATAAAAATATTCAAAAAACTTCTAT
Found at i:49249802 original size:58 final size:59
Alignment explanation
Indices: 49249682--49249792 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 59
49249672 TGTATTTTCT
*
49249682 TATTCAAAAGAACTTCTATTTTATTAAATGACACAATATAAAAATAATTTTTACAAAAA
1 TATTCAAAAGAACTTCTATTTTATTAAATGACACAATATAAAAATAATTTGTACAAAAA
* * * *
49249741 TATTCAAAA-CACTTTTGTTTTATTAAATGA-AGCAATATAAAAATAGTTTGTA
1 TATTCAAAAGAACTTCTATTTTATTAAATGACA-CAATATAAAAATAATTTGTA
49249793 TAGATATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
57 1 0.02
58 36 0.78
59 9 0.20
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (59 bp):
TATTCAAAAGAACTTCTATTTTATTAAATGACACAATATAAAAATAATTTGTACAAAAA
Found at i:49251743 original size:10 final size:10
Alignment explanation
Indices: 49251728--49251753 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
49251718 TACCGACTGT
49251728 TATAAAAAAA
1 TATAAAAAAA
49251738 TATAAAAAAA
1 TATAAAAAAA
49251748 TATAAA
1 TATAAA
49251754 TTTAAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
TATAAAAAAA
Found at i:49251786 original size:19 final size:20
Alignment explanation
Indices: 49251759--49251797 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
49251749 ATAAATTTAA
*
49251759 ATTACATAA-ATGAAAAAAT
1 ATTAAATAATATGAAAAAAT
*
49251778 ATTAAATAATATTAAAAAAT
1 ATTAAATAATATGAAAAAAT
49251798 TGAAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (20 bp):
ATTAAATAATATGAAAAAAT
Found at i:49252088 original size:32 final size:32
Alignment explanation
Indices: 49252052--49252126 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
49252042 AATTTTTTTC
* *
49252052 ATGACCGTTGGCCCTAACAGTCAAATTTTTAA
1 ATGACCATTGGCCCCAACAGTCAAATTTTTAA
* **
49252084 ATGACCTTTGGCCCCAATTGTCAAATTTTTAA
1 ATGACCATTGGCCCCAACAGTCAAATTTTTAA
49252116 ATGACCATTGG
1 ATGACCATTGG
49252127 AGGTGACTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (32 bp):
ATGACCATTGGCCCCAACAGTCAAATTTTTAA
Found at i:49254913 original size:16 final size:16
Alignment explanation
Indices: 49254892--49254923 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49254882 GTTTTGTTGC
*
49254892 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
49254908 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
49254924 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:49258492 original size:21 final size:22
Alignment explanation
Indices: 49258466--49258509 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
49258456 TTGCAACTCC
*
49258466 AAAAAAC-ATGGTTTTTTCTAA
1 AAAAAACTAAGGTTTTTTCTAA
*
49258487 AAAAAACTAAGGTTTTTTGTAA
1 AAAAAACTAAGGTTTTTTCTAA
49258509 A
1 A
49258510 TAGAAACGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (22 bp):
AAAAAACTAAGGTTTTTTCTAA
Found at i:49259845 original size:12 final size:13
Alignment explanation
Indices: 49259828--49259874 Score: 62
Period size: 12 Copynumber: 3.8 Consensus size: 13
49259818 AAACCGAGCC
49259828 ATAAATATTTTTT
1 ATAAATATTTTTT
**
49259841 A-AAATATTTTCC
1 ATAAATATTTTTT
49259853 ATAAATA-TTTTT
1 ATAAATATTTTTT
49259865 ATAAATATTT
1 ATAAATATTT
49259875 ATGGAGTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 20 0.71
13 8 0.29
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (13 bp):
ATAAATATTTTTT
Found at i:49259857 original size:25 final size:25
Alignment explanation
Indices: 49259826--49259874 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
49259816 TTAAACCGAG
49259826 CCATAAATATTTTT-TAAAATATTTT
1 CCATAAATATTTTTAT-AAATATTTT
49259851 CCATAAATATTTTTATAAATATTT
1 CCATAAATATTTTTATAAATATTT
49259875 ATGGAGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (25 bp):
CCATAAATATTTTTATAAATATTTT
Found at i:49273163 original size:27 final size:27
Alignment explanation
Indices: 49273133--49273310 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
49273123 ATATTGAGTC
* * * *
49273133 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
49273160 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
49273187 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
49273215 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
49273242 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
49273269 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
49273296 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
49273311 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:49273272 original size:82 final size:81
Alignment explanation
Indices: 49273154--49273309 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
49273144 TGCTATATAA
* *
49273154 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
49273219 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
49273236 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
49273300 CACTTAGTGC
65 CACTTAGTGC
49273310 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:49273808 original size:12 final size:12
Alignment explanation
Indices: 49273791--49273816 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49273781 ATGGCATACT
49273791 TATGTATATATA
1 TATGTATATATA
49273803 TATGTATATATA
1 TATGTATATATA
49273815 TA
1 TA
49273817 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:49276982 original size:40 final size:40
Alignment explanation
Indices: 49276791--49276982 Score: 185
Period size: 40 Copynumber: 4.8 Consensus size: 40
49276781 TTGAATGATG
* * * * *
49276791 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTAAA
* * * * *
49276831 TCCGGACTAAGAT-TCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTACTAAA
*
49276871 TTCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
* * *
49276910 TTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTA-AA
* *
49276951 -CCGGGCTATGTCCCGAAGGCATTTGAACGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGT
49276983 AGCTATATCC
Statistics
Matches: 126, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
39 33 0.26
40 83 0.66
41 10 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
Found at i:49276997 original size:79 final size:79
Alignment explanation
Indices: 49276845--49277008 Score: 199
Period size: 79 Copynumber: 2.1 Consensus size: 79
49276835 GACTAAGATT
** *
49276845 CGAAGGCATTTGTGCGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTTGTACGAGTTACTAAA
1 CGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
* *
49276910 TTCGGGTTAAGTCC
66 TTCCGGTTAAATCC
* *
49276924 CGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 CGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CT
* *
49276987 ATA-TCCGGTTAAATTC
63 AAATTCCGGTTAAATCC
49277003 CGAAGG
1 CGAAGG
49277009 TACGTGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.66
80 23 0.32
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
CGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
TTCCGGTTAAATCC
Found at i:49284748 original size:39 final size:40
Alignment explanation
Indices: 49284645--49284868 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
49284635 TTGAATGATG
* * * * *
49284645 TCCGGGCTAAGTCCCGAA-AC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
49284684 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
49284724 TCCGGGCTAAG-CCCAAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
49284763 TCCGGGTTAAGTCCCGATGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
49284803 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
49284844 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
49284869 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
39 49 0.30
40 103 0.64
41 9 0.06
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:49284886 original size:80 final size:79
Alignment explanation
Indices: 49284683--49284891 Score: 221
Period size: 80 Copynumber: 2.6 Consensus size: 79
49284673 AAGTGACCAT
* ** * *
49284683 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGAT-ACTAATTCCGGGCTAAGCCCAAAGGCAT
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGCCCAAAGGCAT
49284746 TTGTGCGAGTTACTAA
64 TTGTGCGAGTTACTAA
* * ** * *
49284762 ATCCGGGTTAAGTCCCGATGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAG-CCCAAAGGCATT
49284827 TGTGCGAGTTACTATA
65 TGTGCGAGTTACTA-A
* *
49284843 A-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAA
49284892 ATTCCAAAGG
Statistics
Matches: 112, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.02
79 50 0.45
80 58 0.52
81 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGCCCAAAGGCATTT
GTGCGAGTTACTAA
Found at i:49299972 original size:46 final size:46
Alignment explanation
Indices: 49299909--49300074 Score: 164
Period size: 46 Copynumber: 3.6 Consensus size: 46
49299899 TTAGATTTTG
*
49299909 TTAC-AACAATTAATACAATTAATAATTTGATATAATTTGATAATT
1 TTACTAACAATTAATACAATTAACAATTTGATATAATTTGATAATT
* *
49299954 TTACTAACAATTAATACAATTAACAA-TT-A-ATAATTTTACTAACAAAATG
1 TTACTAACAATTAATACAATTAACAATTTGATATAATTTGA-T-----AATT
* * *
49300003 TTAGTAACAATTAAT--AATTAATAATTTGTTATAATTTGATAATT
1 TTACTAACAATTAATACAATTAACAATTTGATATAATTTGATAATT
* *
49300047 TTAGTAACAATTAATATAATTAACAATT
1 TTACTAACAATTAATACAATTAACAATT
49300075 AATAATTTTA
Statistics
Matches: 100, Mismatches: 9, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
43 8 0.08
44 20 0.20
45 6 0.06
46 30 0.30
47 8 0.08
48 2 0.02
49 18 0.18
50 8 0.08
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (46 bp):
TTACTAACAATTAATACAATTAACAATTTGATATAATTTGATAATT
Found at i:49299986 original size:53 final size:52
Alignment explanation
Indices: 49299914--49300082 Score: 157
Period size: 53 Copynumber: 3.4 Consensus size: 52
49299904 TTTTGTTACA
*
49299914 ACAATTAATACAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAAT
1 ACAATT-A-ACAATTAATAATTTG-TATAATTTGATAATTTTAGTAACAATTAAT
* * *
49299969 ACAATTAACAATTAATAATTT-TACTAA---CAAAATGTTAGTAACAA-T--T
1 ACAATTAACAATTAATAATTTGTA-TAATTTGATAATTTTAGTAACAATTAAT
49300015 --AA-T---AATTAATAATTTGTTATAATTTGATAATTTTAGTAACAATTAAT
1 ACAATTAACAATTAATAATTTG-TATAATTTGATAATTTTAGTAACAATTAAT
*
49300062 ATAATTAACAATTAATAATTT
1 ACAATTAACAATTAATAATTT
49300083 TACTAGCAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 32
0.70 0.05 0.24
Matches are distributed among these distances:
40 12 0.13
41 3 0.03
42 2 0.02
43 1 0.01
44 16 0.17
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 15 0.16
50 1 0.01
51 2 0.02
52 3 0.03
53 26 0.28
54 1 0.01
55 6 0.07
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (52 bp):
ACAATTAACAATTAATAATTTGTATAATTTGATAATTTTAGTAACAATTAAT
Found at i:49299996 original size:19 final size:19
Alignment explanation
Indices: 49299948--49299998 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
49299938 ATATAATTTG
49299948 ATAATTTTACTAACAATTA
1 ATAATTTTACTAACAATTA
*
49299967 ATACA----ATTAACAATTA
1 ATA-ATTTTACTAACAATTA
49299983 ATAATTTTACTAACAA
1 ATAATTTTACTAACAA
49299999 AATGTTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
15 1 0.04
16 13 0.52
19 10 0.40
20 1 0.04
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAATTTTACTAACAATTA
Found at i:49300036 original size:93 final size:94
Alignment explanation
Indices: 49299913--49300099 Score: 322
Period size: 93 Copynumber: 2.0 Consensus size: 94
49299903 ATTTTGTTAC
49299913 AACAATTAATACAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAAC
1 AACAATTAATA-AATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAAC
49299978 AATTAATAATTTTACTAACAAAATGTTAGT
65 AATTAATAATTTTACTAACAAAATGTTAGT
* * *
49300008 AACAATTAAT-AATTAATAATTTGTTATAATTTGATAATTTTAGTAACAATTAATATAATTAACA
1 AACAATTAATAAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACA
*
49300072 ATTAATAATTTTACTAGCAAAATGTTAG
66 ATTAATAATTTTACTAACAAAATGTTAG
49300100 ATTTTACAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
93 78 0.89
95 10 0.11
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (94 bp):
AACAATTAATAAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACA
ATTAATAATTTTACTAACAAAATGTTAGT
Found at i:49301728 original size:23 final size:22
Alignment explanation
Indices: 49301702--49301764 Score: 56
Period size: 25 Copynumber: 2.7 Consensus size: 22
49301692 TGACTTGAAA
49301702 TTTTATATAATAAAA-TATATATG
1 TTTTATATAATAAAAGTA-A-ATG
* *
49301725 TTTTATTTATAGCTAAAAGTAAATT
1 TTTTA--TATA-ATAAAAGTAAATG
49301750 TTTTATATAATAAAA
1 TTTTATATAATAAAA
49301765 AATTGCAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
22 5 0.15
23 9 0.27
25 11 0.33
26 6 0.18
27 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (22 bp):
TTTTATATAATAAAAGTAAATG
Found at i:49301809 original size:23 final size:23
Alignment explanation
Indices: 49301783--49301827 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
49301773 GAAATGTTAA
*
49301783 TTTAA-AAGTTTTTTATTTTTATT
1 TTTAAGAA-TTTTTTATATTTATT
49301806 TTTAAGAATTTTTTATATTTAT
1 TTTAAGAATTTTTTATATTTAT
49301828 ACATATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTAAGAATTTTTTATATTTATT
Found at i:49304551 original size:23 final size:23
Alignment explanation
Indices: 49304501--49304552 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
49304491 GTTAGGTGTC
* *
49304501 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
49304524 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
49304547 AGTATG
1 AGTATG
49304553 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:49308070 original size:14 final size:14
Alignment explanation
Indices: 49308051--49308079 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
49308041 ATCCCTAAAT
49308051 CCCTAACTCTTAAC
1 CCCTAACTCTTAAC
49308065 CCCTAACTCTTAAC
1 CCCTAACTCTTAAC
49308079 C
1 C
49308080 ATTAAACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.45, G:0.00, T:0.28
Consensus pattern (14 bp):
CCCTAACTCTTAAC
Found at i:49308100 original size:21 final size:20
Alignment explanation
Indices: 49308076--49308116 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
49308066 CCTAACTCTT
*
49308076 AACCATTAAACCTTAAATCCC
1 AACCATTAAACCAT-AATCCC
*
49308097 AACCCTTAAACCATAATCCC
1 AACCATTAAACCATAATCCC
49308117 TAAATCCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (20 bp):
AACCATTAAACCATAATCCC
Found at i:49308458 original size:7 final size:7
Alignment explanation
Indices: 49308348--49308493 Score: 73
Period size: 7 Copynumber: 20.6 Consensus size: 7
49308338 CTAGTTAATC
*
49308348 TAAACCC
1 TAAACCA
49308355 TAAACCA
1 TAAACCA
*
49308362 TAAA-CT
1 TAAACCA
*
49308368 TAAACCC
1 TAAACCA
49308375 TAAAACCA
1 T-AAACCA
*
49308383 TAAACCC
1 TAAACCA
*
49308390 TTAACACA
1 TAAAC-CA
*
49308398 T-AACCTT
1 TAAACC-A
*
49308405 TAAACCT
1 TAAACCA
49308412 TAAACCA
1 TAAACCA
* * *
49308419 -CAGCCTT
1 TAAACC-A
49308426 TAAACCA
1 TAAACCA
49308433 TAAACCA
1 TAAACCA
*
49308440 TAAACCG
1 TAAACCA
49308447 TAAACCA
1 TAAACCA
*
49308454 CAAACCA
1 TAAACCA
* *
49308461 TAACCCC
1 TAAACCA
49308468 TAAACCCA
1 TAAA-CCA
*
49308476 TAATCCA
1 TAAACCA
* *
49308483 AAAACCT
1 TAAACCA
49308490 TAAA
1 TAAA
49308494 ATGGTAACAC
Statistics
Matches: 103, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
6 9 0.09
7 74 0.72
8 20 0.19
ACGTcount: A:0.48, C:0.32, G:0.01, T:0.18
Consensus pattern (7 bp):
TAAACCA
Found at i:49308761 original size:41 final size:41
Alignment explanation
Indices: 49308704--49308784 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
49308694 ATTTTAAATC
49308704 CTTGAGCATTAGCGGCGCTTTCCAAAAAACGCCGCTAAAGA
1 CTTGAGCATTAGCGGCGCTTTCCAAAAAACGCCGCTAAAGA
*
49308745 CTTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAG
1 CTTGAGCATTAGCGGCGCTTTCCAAAAAACGCCGCTAAAG
49308785 CCCCGAAAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (41 bp):
CTTGAGCATTAGCGGCGCTTTCCAAAAAACGCCGCTAAAGA
Found at i:49308969 original size:41 final size:39
Alignment explanation
Indices: 49308848--49308973 Score: 146
Period size: 40 Copynumber: 3.2 Consensus size: 39
49308838 TGGAAATCAT
* * *
49308848 CGCTAATGCTTGGT-TTTAGCGGCGTTTTCCATAAAGCGC
1 CGCTAATGCTCGATCTTTAGCGGCGTTTTTCATAAA-CGC
* * *
49308887 CGCTAATACTCGATCTTTAGCGGCGTTTTTGGAAAAACGC
1 CGCTAATGCTCGATCTTTAGCGGCGTTTTT-CATAAACGC
*
49308927 CGCTAATGCTCGATCTTTAGCGGCGTTTTTTATCCAAACGC
1 CGCTAATGCTCGATCTTTAGCGGCGTTTTTCAT--AAACGC
49308968 CGCTAA
1 CGCTAA
49308974 AAATGCCACT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
39 12 0.16
40 46 0.62
41 16 0.22
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (39 bp):
CGCTAATGCTCGATCTTTAGCGGCGTTTTTCATAAACGC
Found at i:49313600 original size:35 final size:35
Alignment explanation
Indices: 49313553--49313636 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 35
49313543 TGCAATCCCT
* * *
49313553 CCAAAATACACCATTGCTCATAAGAGCTAGTCCAA
1 CCAAAACACACCAATGCTCAAAAGAGCTAGTCCAA
* **
49313588 CCGAAACACACCAATGCTCAAAAGAGCTAGTCCCT
1 CCAAAACACACCAATGCTCAAAAGAGCTAGTCCAA
49313623 CCAAAACACACCAA
1 CCAAAACACACCAA
49313637 ACAAAAAGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.42, C:0.33, G:0.11, T:0.14
Consensus pattern (35 bp):
CCAAAACACACCAATGCTCAAAAGAGCTAGTCCAA
Found at i:49317511 original size:16 final size:17
Alignment explanation
Indices: 49317480--49317512 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
49317470 TTCTAAAAAA
49317480 ATTTATGATAAAATATT
1 ATTTATGATAAAATATT
*
49317497 ATTTAT-ATGAAATATT
1 ATTTATGATAAAATATT
49317513 TGGTTGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
ATTTATGATAAAATATT
Found at i:49320429 original size:18 final size:18
Alignment explanation
Indices: 49320403--49320455 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
49320393 GCAATAAGAA
*
49320403 AACGTTTTG-AAATTGAAT
1 AACGATTTGTAAA-TGAAT
49320421 AACGATTTGTAAATGAAT
1 AACGATTTGTAAATGAAT
* * *
49320439 AATGTTTTGGAAATGAA
1 AACGATTTGTAAATGAA
49320456 CGACGCGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 27 0.90
19 3 0.10
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.36
Consensus pattern (18 bp):
AACGATTTGTAAATGAAT
Found at i:49322642 original size:20 final size:20
Alignment explanation
Indices: 49322617--49322694 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
49322607 ATGGATGCAT
*
49322617 AACAGGGGCACTGAAGTGTA
1 AACAGGGGCACCGAAGTGTA
* **
49322637 AACAGGGGCACCGTAGTGCG
1 AACAGGGGCACCGAAGTGTA
* * * *
49322657 AATAGAGACACAGAAGTGTA
1 AACAGGGGCACCGAAGTGTA
*
49322677 TACAGGGGCACCGAAGTG
1 AACAGGGGCACCGAAGTG
49322695 CAAATCTCGT
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.18, G:0.35, T:0.13
Consensus pattern (20 bp):
AACAGGGGCACCGAAGTGTA
Found at i:49325135 original size:8 final size:8
Alignment explanation
Indices: 49325124--49325155 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
49325114 TATGTTATTG
49325124 TATTATAT
1 TATTATAT
*
49325132 TATTATAC
1 TATTATAT
49325140 TATTATAT
1 TATTATAT
49325148 TATTATAT
1 TATTATAT
49325156 ATATAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:49325143 original size:16 final size:16
Alignment explanation
Indices: 49325124--49325154 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
49325114 TATGTTATTG
49325124 TATTATATTATTATAC
1 TATTATATTATTATAC
49325140 TATTATATTATTATA
1 TATTATATTATTATA
49325155 TATATAACAA
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:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTATATTATTATAC
Found at i:49326317 original size:22 final size:22
Alignment explanation
Indices: 49326300--49326353 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
49326290 TGGCACGTCA
* *
49326300 GTGCTTTCTGTTTAGCACATAT
1 GTGCTCTCTGTATAGCACATAT
*
49326322 GTGCTCTCTGTATAGCAC-TTT
1 GTGCTCTCTGTATAGCACATAT
*
49326343 ATGCTCTCTGT
1 GTGCTCTCTGT
49326354 TCATTAATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (22 bp):
GTGCTCTCTGTATAGCACATAT
Found at i:49328854 original size:29 final size:29
Alignment explanation
Indices: 49328789--49328852 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
49328779 TATAAAAGCT
* *
49328789 TATTCTTGTAAATTTTTCAAAAATTAGTC
1 TATTTTTGTAAATTTTTCAAAAATTAATC
49328818 TATTTTTGTAATATTTTT-AAAAA-TAATC
1 TATTTTTGTAA-ATTTTTCAAAAATTAATC
*
49328846 TTTTTTT
1 TATTTTT
49328853 TGCCTAACAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 10 0.32
29 15 0.48
30 6 0.19
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (29 bp):
TATTTTTGTAAATTTTTCAAAAATTAATC
Found at i:49335912 original size:32 final size:31
Alignment explanation
Indices: 49335819--49335948 Score: 107
Period size: 32 Copynumber: 4.3 Consensus size: 31
49335809 TTAATATTCT
* *
49335819 ATTTGGTACCTGAACTTGAC-TTTTTTTCTA
1 ATTTGGTACTTGAACTTGACATTTTTTCCTA
49335849 ATTTGGTACTT--A--T-ACATTTTTTTGTCC-A
1 ATTTGGTACTTGAACTTGACA--TTTTT-TCCTA
49335877 ATTTGGTACTTGAACTTGACATTTTTTCCCTA
1 ATTTGGTACTTGAACTTGACATTTTTT-CCTA
* * *
49335909 ATTTGATA-TCTGAAGTTGACATTTTTT-TTA
1 ATTTGGTACT-TGAACTTGACATTTTTTCCTA
49335939 ATTTGGTACT
1 ATTTGGTACT
49335949 CAATCTTTTT
Statistics
Matches: 81, Mismatches: 6, Indels: 25
0.72 0.05 0.22
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
28 18 0.22
29 2 0.02
30 21 0.26
31 9 0.11
32 25 0.31
33 3 0.04
ACGTcount: A:0.22, C:0.14, G:0.13, T:0.51
Consensus pattern (31 bp):
ATTTGGTACTTGAACTTGACATTTTTTCCTA
Found at i:49335970 original size:29 final size:31
Alignment explanation
Indices: 49335937--49336007 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
49335927 ACATTTTTTT
49335937 TAATTTGGTA-CTCAATCT-T-TTTTTGGGTC
1 TAATTTGGTACCT-AATCTCTATTTTTGGGTC
**
49335966 TAATTTGGTACCTAATCTCTATTTTTTTGTC
1 TAATTTGGTACCTAATCTCTATTTTTGGGTC
*
49335997 TGATTTGGTAC
1 TAATTTGGTAC
49336008 ATGAATTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 15 0.42
30 3 0.08
31 18 0.50
ACGTcount: A:0.18, C:0.14, G:0.15, T:0.52
Consensus pattern (31 bp):
TAATTTGGTACCTAATCTCTATTTTTGGGTC
Found at i:49340397 original size:21 final size:21
Alignment explanation
Indices: 49340372--49340413 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
49340362 TTTTCCAAAT
* *
49340372 ATATGTATTGGATTGAATTGA
1 ATATGAATTGGATTAAATTGA
*
49340393 ATATGAATTGTATTAAATTGA
1 ATATGAATTGGATTAAATTGA
49340414 GTTAAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (21 bp):
ATATGAATTGGATTAAATTGA
Found at i:49340796 original size:25 final size:24
Alignment explanation
Indices: 49340768--49340969 Score: 122
Period size: 25 Copynumber: 8.2 Consensus size: 24
49340758 CTTATGCTCA
*
49340768 TCCCGTTACATGGCTCTCACGAGCT
1 TCCCGTTA-ATGGCTCTCATGAGCT
* * *
49340793 TCCCGATATTGGCTCGCATGAGCT
1 TCCCGTTAATGGCTCTCATGAGCT
** * *
49340817 TTTCGATT-TTAGCTCTCCA-GAGCT
1 TCCCG-TTAATGGCTCT-CATGAGCT
* * * *
49340841 TCCCGATATTTAGCTCTCTTGAGCT
1 TCCCGTTA-ATGGCTCTCATGAGCT
*
49340866 TCCCGTTTATGGCTCGT-ATGAGCT
1 TCCCGTTAATGGCTC-TCATGAGCT
* * * *
49340890 TCCTGATAATTGGCTCACAAGAGCT
1 TCCCGTTAA-TGGCTCTCATGAGCT
*
49340915 TCCCGTTATATGGCTCACATGAGCT
1 TCCCGTTA-ATGGCTCTCATGAGCT
* * *
49340940 TCTCGTTACATGGCTCTAAAGAGCT
1 TCCCGTTA-ATGGCTCTCATGAGCT
49340965 TCCCG
1 TCCCG
49340970 ATTACATACT
Statistics
Matches: 136, Mismatches: 32, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
23 1 0.01
24 48 0.35
25 86 0.63
26 1 0.01
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.33
Consensus pattern (24 bp):
TCCCGTTAATGGCTCTCATGAGCT
Found at i:49340815 original size:24 final size:24
Alignment explanation
Indices: 49340778--49340941 Score: 116
Period size: 24 Copynumber: 6.7 Consensus size: 24
49340768 TCCCGTTACA
* *
49340778 TGGCTCTCACGAGCTTCCCGATAT
1 TGGCTCACATGAGCTTCCCGATAT
* ** *
49340802 TGGCTCGCATGAGCTTTTCGATTT
1 TGGCTCACATGAGCTTCCCGATAT
* *
49340826 TAGCTCTCCA-GAGCTTCCCGATATT
1 TGGCTC-ACATGAGCTTCCCGATA-T
* * * *
49340851 TAGCTCTCTTGAGCTTCCCG-TTT
1 TGGCTCACATGAGCTTCCCGATAT
** *
49340874 ATGGCTCGTATGAGCTTCCTGATAAT
1 -TGGCTCACATGAGCTTCCCGAT-AT
* *
49340900 TGGCTCACAAGAGCTTCCCGTTAT
1 TGGCTCACATGAGCTTCCCGATAT
49340924 ATGGCTCACATGAGCTTC
1 -TGGCTCACATGAGCTTC
49340942 TCGTTACATG
Statistics
Matches: 108, Mismatches: 25, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
23 1 0.01
24 53 0.49
25 53 0.49
26 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (24 bp):
TGGCTCACATGAGCTTCCCGATAT
Found at i:49340891 original size:49 final size:50
Alignment explanation
Indices: 49340768--49340941 Score: 133
Period size: 49 Copynumber: 3.5 Consensus size: 50
49340758 CTTATGCTCA
* * * * * *
49340768 TCCCGTTACATGGCTCTCACGAGCTTCCCGAT-ATTGGCTCGCATGAGCT
1 TCCCGTTATATGGCTCACATGAGCTTCCCGATAATTAGCTCACAAGAGCT
** * * * * **
49340817 TTTCGATT-T-TAGCTCTCCA-GAGCTTCCCGATATTTAGCTCTCTTGAGCT
1 TCCCG-TTATATGGCTC-ACATGAGCTTCCCGATAATTAGCTCACAAGAGCT
** * *
49340866 TCCCGTT-TATGGCTCGTATGAGCTTCCTGATAATTGGCTCACAAGAGCT
1 TCCCGTTATATGGCTCACATGAGCTTCCCGATAATTAGCTCACAAGAGCT
49340915 TCCCGTTATATGGCTCACATGAGCTTC
1 TCCCGTTATATGGCTCACATGAGCTTC
49340942 TCGTTACATG
Statistics
Matches: 97, Mismatches: 22, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
48 21 0.22
49 57 0.59
50 19 0.20
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (50 bp):
TCCCGTTATATGGCTCACATGAGCTTCCCGATAATTAGCTCACAAGAGCT
Found at i:49348271 original size:30 final size:30
Alignment explanation
Indices: 49348237--49348299 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
49348227 ACTTAACAAG
*
49348237 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATGAA
*
49348267 CAAATGCCTTTAAAATAATAACAAAATGAA
1 CAAATGCCTCTAAAATAATAACAAAATGAA
49348297 CAA
1 CAA
49348300 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.16, G:0.05, T:0.22
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATGAA
Found at i:49348352 original size:14 final size:14
Alignment explanation
Indices: 49348333--49348359 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49348323 CAAACAATAA
49348333 CAACAAAATAGTAG
1 CAACAAAATAGTAG
49348347 CAACAAAATAGTA
1 CAACAAAATAGTA
49348360 AAATGGTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (14 bp):
CAACAAAATAGTAG
Found at i:49350324 original size:12 final size:12
Alignment explanation
Indices: 49350302--49350336 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
49350292 AATATAAATA
49350302 AATAGGTAATAAT
1 AATA-GTAATAAT
49350315 AATAGTAATAAT
1 AATAGTAATAAT
*
49350327 AATAATAATA
1 AATAGTAATA
49350337 GGACTAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (12 bp):
AATAGTAATAAT
Found at i:49351965 original size:98 final size:97
Alignment explanation
Indices: 49351795--49351984 Score: 292
Period size: 98 Copynumber: 1.9 Consensus size: 97
49351785 GACCTGACAC
49351795 GATCTCCTCTACTGTAACTTAAAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAATCTCA
1 GATCTCCTCTACTGTAACTTAAAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAATCTCA
*
49351860 GACAGATAGGATTACTATCTTCAATCTAATGT
66 GACAGATAGGATTACTAGCTTCAATCTAATGT
* * * * *
49351892 GATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTGTAA-CTT
1 GATCTCCTCTACTGTAACTT-AAAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAATC-T
*
49351956 CAGAGAGATAGGATTACTAGCTTCAATCT
64 CAGACAGATAGGATTACTAGCTTCAATCT
49351985 GCTCCGCTGT
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
97 20 0.24
98 64 0.76
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (97 bp):
GATCTCCTCTACTGTAACTTAAAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAATCTCA
GACAGATAGGATTACTAGCTTCAATCTAATGT
Found at i:49352113 original size:175 final size:175
Alignment explanation
Indices: 49351892--49352222 Score: 515
Period size: 175 Copynumber: 1.9 Consensus size: 175
49351882 AATCTAATGT
* * * * *
49351892 GATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTGTAA-CTT
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTGATTTTAATCCACTCCACTATAATC-T
*
49351956 C-AGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTGAAA
65 CAAG-GAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAA
*
49352020 T-TCTTCGGTCTGTTCCACCGTAATCTCAGGGGAATAAGACCTAGTGC
129 TCT-TTCGGTCTGCTCCACCGTAATCTCAGGGGAATAAGACCTAGTGC
* *
49352067 GATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTGGTTTTAATCCACTCCACTATAATCTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTGATTTTAATCCACTCCACTATAATCTC
*
49352132 AAGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATC
66 AAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATC
*
49352197 TTTCGGTCTGCTCCACTGTAATCTCA
131 TTTCGGTCTGCTCCACCGTAATCTCA
49352223 AGGAGATAAG
Statistics
Matches: 142, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
175 138 0.97
176 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (175 bp):
GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTGATTTTAATCCACTCCACTATAATCTC
AAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATC
TTTCGGTCTGCTCCACCGTAATCTCAGGGGAATAAGACCTAGTGC
Found at i:49352216 original size:46 final size:44
Alignment explanation
Indices: 49351893--49352617 Score: 345
Period size: 44 Copynumber: 16.6 Consensus size: 44
49351883 ATCTAATGTG
* * ** * *
49351893 ATCTGCTCTACTGTAA-CTTCAGAGAGATAAGATCTTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGATCTTTCA
* * * *
49351937 ATCCGCTCCACTGTAA-CTTCAGAGAGATAGGATTACT-AGC-TTCA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGA-T-CTGATCTTTCA
* * *
49351981 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTGAAAT-TCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG--ATCT-TTCA
* * * * * * *
49352027 GTCTGTTCCACCGTAATCTCAGGG-GAATAAGACCT-A--GTGCG
1 ATCTGCTCCACTGTAATCTCAGGGAG-ATAAGATCTGATCTTTCA
* * * * *
49352068 ATCTACTCTACTGTAA-CTTTAGAGAGATAAGATCCTTGGT-TTT-A
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-C-TGATCTTTCA
** * * *
49352112 ATCCACTCCACTATAATCTCAAGGAGATAGGATTACT-ATC-TTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA-T-CTGATCTTTCA
* *
49352156 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATCTTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG--ATCTTTCA
* * *
49352202 GTCTGCTCCACTGTAATCTCAAGGAGATAAGATCTGAAATCTTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG--ATCTTTCA
* * * * *
49352248 GTCTACTCCACTGTAATCTCAGGGAGATAAGACCTGA---TGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGATCTTTCA
* * *
49352289 ATCTACTCTACTGTAA-CTTCAGGGAGATAAGATCCTTTAT-TTT-A
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-C-TGATCTTTCA
* * *
49352333 ATCCGCTCCACTGTAA-CTTCAGGGAGATAGGATAGTG-TC-TTCA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-CTGATCTTTCA
* * *
49352376 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTG-GC-CTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA--TCTGATCTTTCA
* *
49352420 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAATTCTTT-A
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT--GA-TCTTTCA
* * * * * * *
49352466 GTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTG---GTGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGATCTTTCA
* *
49352507 ATCTGCTCTACTGTAA-CTTCAGAGAGATAAGATC----CTTT-A
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGATCTTTCA
* * *
49352546 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACT-AT-ATTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA-T-CTGATCTTTCA
*
49352590 ATCTGCTCCGCTGTAATCTCAGGGAGAT
1 ATCTGCTCCACTGTAATCTCAGGGAGAT
49352618 NNNNNNNNNN
Statistics
Matches: 527, Mismatches: 106, Indels: 96
0.72 0.15 0.13
Matches are distributed among these distances:
39 26 0.05
40 7 0.01
41 82 0.16
42 12 0.02
43 40 0.08
44 203 0.39
45 13 0.02
46 143 0.27
47 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGATCTTTCA
Found at i:49352365 original size:221 final size:216
Alignment explanation
Indices: 49351936--49352617 Score: 873
Period size: 221 Copynumber: 3.1 Consensus size: 216
49351926 CTTTTATTTT
* * * * * * *
49351936 AATCCGCTCCACTGTAA-CTTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCT
1 AATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATT-CTGGCCTCAATCTGCTCCACTGTAATCT
* *
49352000 CAGGGAGATAAGATTTGAAAT-TCTTCGGTCTGTTCCACCGTAATCTCAGGG-GAATAAGACCT-
64 CAGGGAGATAAGATCTGAAATCT-TTCGGTCTGTTCCACTGTAATCTCAGGGAG-ATAAGACCTG
* * *
49352062 AGTGCGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTGGTTTTAATCCACTCCACTATA
127 A-TGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTT--TTTTAATCCGCTCCACTGTA
*
49352127 ATCTCAAGGAGATAGGATTACTATCTTC
189 ATCTCAGGGAGATAGGATTACTATCTTC
* * **
49352155 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-TCTGAAATCTTTCGGTCTGCTCCACTGTAAT
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTCTG---GC-CTCAATCTGCTCCACTGTAAT
* **
49352219 CTCAAGGAGATAAGATCTGAAATCTTTCGGTCTACTCCACTGTAATCTCAGGGAGATAAGACCTG
62 CTCAGGGAGATAAGATCTGAAATCTTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG
*
49352284 ATGCGATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
127 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCC-TT-TTTTAATCCGCTCCACTGTAA
* *
49352349 -CTTCAGGGAGATAGGA-TAGTGTCTTC
190 TC-TCAGGGAGATAGGATTACTATCTTC
*
49352375 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCTGCTCCACTGTAACCTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-TTCTGGCCTCAATCTGCTCCACTGTAATCTC
* * * *
49352440 AGGGAGATAAGATCTAAAATTCTTT-AGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGT
65 AGGGAGATAAGATCTGAAA-TCTTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGAT
*
49352504 GCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCC---TTTAATCCGCTCCACTGTAATCTC
129 GCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTTTTAATCCGCTCCACTGTAATCTC
*
49352566 AGGGAGATAGGATTACTATATTC
194 AGGGAGATAGGATTACTATCTTC
49352589 AATCTGCTCCGCTGTAATCTCAGGGAGAT
1 AATCTGCTCCGCTGTAATCTCAGGGAGAT
49352618 NNNNNNNNNN
Statistics
Matches: 409, Mismatches: 39, Indels: 35
0.85 0.08 0.07
Matches are distributed among these distances:
213 34 0.08
214 37 0.09
217 2 0.00
218 108 0.26
219 33 0.08
220 44 0.11
221 142 0.35
222 9 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (216 bp):
AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTCTGGCCTCAATCTGCTCCACTGTAATCTCA
GGGAGATAAGATCTGAAATCTTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTTTTAATCCGCTCCACTGTAATCTCAG
GGAGATAGGATTACTATCTTC
Found at i:49352428 original size:87 final size:82
Alignment explanation
Indices: 49352332--49352617 Score: 238
Period size: 87 Copynumber: 3.4 Consensus size: 82
49352322 CCTTTATTTT
* * *
49352332 AATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCAATCTGCTCCGCTGTAATCTCA
1 AATCTGCTCCACTGTAACTTCAGGGAGATA-GATA-T-TCTTTAATCTGCTCCACTGTAATCTCA
*
49352397 GGGAGATAAGATTTCTGGCCTC
63 GGGAGATAAGATTACTGG--TC
* * *
49352419 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAATTCTTTAGTCTGTTCCACTGTAATC
1 AATCTGCTCCACTGTAACTTCAGGGAGAT-AGA--T---ATTCTTTAATCTGCTCCACTGTAATC
* *
49352484 TCAGGGAAATAAGA--CCTGGTGC
60 TCAGGGAGATAAGATTACTGGT-C
* * * * * *
49352506 GATCTGCTCTACTGTAACTTCAGAGAGATA-AGATCCTTTAATCCGCTCCACTGTAATCTCAGGG
1 AATCTGCTCCACTGTAACTTCAGGGAGATAGATATTCTTTAATCTGCTCCACTGTAATCTCAGGG
* **
49352570 AGATAGGATTACTATATTC
66 AGATAAGATTAC--TGGTC
*
49352589 AATCTGCTCCGCTGTAA-TCTCAGGGAGAT
1 AATCTGCTCCACTGTAACT-TCAGGGAGAT
49352618 NNNNNNNNNN
Statistics
Matches: 161, Mismatches: 26, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
80 34 0.21
82 2 0.01
83 24 0.15
84 2 0.01
85 1 0.01
86 2 0.01
87 55 0.34
88 5 0.03
89 1 0.01
90 33 0.20
91 1 0.01
92 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (82 bp):
AATCTGCTCCACTGTAACTTCAGGGAGATAGATATTCTTTAATCTGCTCCACTGTAATCTCAGGG
AGATAAGATTACTGGTC
Found at i:49369353 original size:28 final size:28
Alignment explanation
Indices: 49369290--49369415 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
49369280 ATATTAAGTC
*
49369290 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
49369317 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
49369345 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * * *
49369373 TGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
49369402 CGCACACTTAGTGC
1 CGCACACTTAGTGC
49369416 CAATCTCATG
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.24
28 50 0.56
29 18 0.20
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:49369360 original size:55 final size:57
Alignment explanation
Indices: 49369289--49369415 Score: 186
Period size: 55 Copynumber: 2.3 Consensus size: 57
49369279 TATATTAAGT
* *
49369289 CCGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTATATAA-TCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAATTCAAAC
* * * *
49369344 TCGCACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTGTACAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAATTCAAAC
49369401 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
49369416 CAATCTCATG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
55 22 0.35
56 22 0.35
57 19 0.30
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.28
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAATTCAAAC
Found at i:49369879 original size:12 final size:12
Alignment explanation
Indices: 49369862--49369888 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
49369852 TGGGCATACT
49369862 TATGTATATATA
1 TATGTATATATA
49369874 TATGTATATATA
1 TATGTATATATA
49369886 TAT
1 TAT
49369889 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:49383708 original size:31 final size:30
Alignment explanation
Indices: 49383665--49384066 Score: 249
Period size: 31 Copynumber: 13.1 Consensus size: 30
49383655 ATATACCACA
* *
49383665 CAATTCGACAATGTATAACCATACACAAAT
1 CAATTCGGCAATGTATAACCATATACAAAT
*
49383695 CAAGTTCGGCAATGTATAATCATATACAAAT
1 CAA-TTCGGCAATGTATAACCATATACAAAT
* * ** * *
49383726 CAAATTCGGC-TTCCTATATTCATAAACAATT
1 C-AATTCGGCAAT-GTATAACCATATACAAAT
* * *
49383757 CAACTTCGACAATATATAACCATGTACAAAT
1 CAA-TTCGGCAATGTATAACCATATACAAAT
* * * *
49383788 TAATTCCAGCAATGTACAACCATATACGAAT
1 CAATT-CGGCAATGTATAACCATATACAAAT
** **
49383819 CAATTAAGCAACT-TATATTCATATACCAAA-
1 CAATTCGGCAA-TGTATAACCATATA-CAAAT
* * *
49383849 CAATTCGGCAATGCATAACCATACACGAAT
1 CAATTCGGCAATGTATAACCATATACAAAT
* *
49383879 CAAGTTCAGCAATGTATAATCATATACAAAT
1 CAA-TTCGGCAATGTATAACCATATACAAAT
* * * ** * *
49383910 CAAACTCGGC-TTCCTATATTCATAAACAATT
1 C-AATTCGGCAAT-GTATAACCATATACAAAT
* * *
49383941 CAATTTCGTCAATATATAACCATGTACAAAT
1 CAA-TTCGGCAATGTATAACCATATACAAAT
* * * *
49383972 TAATTCCAGCAATGTACAACCATATACGAAT
1 CAATT-CGGCAATGTATAACCATATACAAAT
* * *
49384003 CAATTCAGTAACT-TATATCCATATACAAAAT
1 CAATTCGGCAA-TGTATAACCATATAC-AAAT
*
49384034 -AATTCGGCAATGTATAACCATACACAAAT
1 CAATTCGGCAATGTATAACCATATACAAAT
49384063 CAAT
1 CAAT
49384067 ATATCCATAT
Statistics
Matches: 279, Mismatches: 73, Indels: 40
0.71 0.19 0.10
Matches are distributed among these distances:
29 9 0.03
30 85 0.30
31 179 0.64
32 6 0.02
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (30 bp):
CAATTCGGCAATGTATAACCATATACAAAT
Found at i:49383786 original size:93 final size:92
Alignment explanation
Indices: 49383665--49384066 Score: 377
Period size: 93 Copynumber: 4.4 Consensus size: 92
49383655 ATATACCACA
* * * *
49383665 CAATTCGACAATGTATAACCATACACAAATCAAGTT-CGGCAATGTATAATCATATACAAATCAA
1 CAATTCGACAATATATAACCATACACAAATCAA-TTCCAGCAATGTACAACCATATACAAATCAA
49383729 ATTCGGCTTCCTATATTCATAAACAATT
65 ATTCGGCTTCCTATATTCATAAACAATT
** * *
49383757 CAACTTCGACAATATATAACCATGTACAAATTAATTCCAGCAATGTACAACCATATACGAATC-A
1 CAA-TTCGACAATATATAACCATACACAAATCAATTCCAGCAATGTACAACCATATACAAATCAA
** ** * * *
49383821 ATTAAGCAACTTATATTCATATACCAA-A
65 ATTCGGCTTCCTATATTCATA-AACAATT
* ** * * *
49383849 CAATTCGGCAATGCATAACCATACACGAATCAAGTT-CAGCAATGTATAATCATATACAAATCAA
1 CAATTCGACAATATATAACCATACACAAATCAA-TTCCAGCAATGTACAACCATATACAAATCAA
*
49383913 ACTCGGCTTCCTATATTCATAAACAATT
65 ATTCGGCTTCCTATATTCATAAACAATT
* ** * *
49383941 CAATTTCGTCAATATATAACCATGTACAAATTAATTCCAGCAATGTACAACCATATACGAATC-A
1 CAA-TTCGACAATATATAACCATACACAAATCAATTCCAGCAATGTACAACCATATACAAATCAA
* * * * * *
49384005 ATTCAG-TAACTTATATCCATATACAAAAT
65 ATTCGGCT-TCCTATATTCATAAAC-AATT
* *
49384034 -AATTCGGCAATGTATAACCATACACAAATCAAT
1 CAATTCGACAATATATAACCATACACAAATCAAT
49384067 ATATCCATAT
Statistics
Matches: 245, Mismatches: 55, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
91 77 0.31
92 67 0.27
93 101 0.41
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (92 bp):
CAATTCGACAATATATAACCATACACAAATCAATTCCAGCAATGTACAACCATATACAAATCAAA
TTCGGCTTCCTATATTCATAAACAATT
Found at i:49383964 original size:184 final size:184
Alignment explanation
Indices: 49383649--49384065 Score: 708
Period size: 184 Copynumber: 2.3 Consensus size: 184
49383639 TCAACAATGA
* * * *
49383649 ATATCAATATACCACACAATTCGACAATGTATAACCATACACAAATCAAGTTCGGCAATGTATAA
1 ATATCCATATACCAAACAATTCGGCAATGTATAACCATACACAAATCAAGTTCAGCAATGTATAA
*
49383714 TCATATACAAATCAAATTCGGCTTCCTATATTCATAAACAATTCAACTTCGACAATATATAACCA
66 TCATATACAAATCAAACTCGGCTTCCTATATTCATAAACAATTCAACTTCGACAATATATAACCA
49383779 TGTACAAATTAATTCCAGCAATGTACAACCATATACGAATCAATTAAGCAACTT
131 TGTACAAATTAATTCCAGCAATGTACAACCATATACGAATCAATTAAGCAACTT
* * *
49383833 ATATTCATATACCAAACAATTCGGCAATGCATAACCATACACGAATCAAGTTCAGCAATGTATAA
1 ATATCCATATACCAAACAATTCGGCAATGTATAACCATACACAAATCAAGTTCAGCAATGTATAA
* *
49383898 TCATATACAAATCAAACTCGGCTTCCTATATTCATAAACAATTCAATTTCGTCAATATATAACCA
66 TCATATACAAATCAAACTCGGCTTCCTATATTCATAAACAATTCAACTTCGACAATATATAACCA
* *
49383963 TGTACAAATTAATTCCAGCAATGTACAACCATATACGAATCAATTCAGTAACTT
131 TGTACAAATTAATTCCAGCAATGTACAACCATATACGAATCAATTAAGCAACTT
* *
49384017 ATATCCATATACAAAATAATTCGGCAATGTATAACCATACACAAATCAA
1 ATATCCATATACCAAACAATTCGGCAATGTATAACCATACACAAATCAA
49384066 TATATCCATA
Statistics
Matches: 216, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
184 216 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.28
Consensus pattern (184 bp):
ATATCCATATACCAAACAATTCGGCAATGTATAACCATACACAAATCAAGTTCAGCAATGTATAA
TCATATACAAATCAAACTCGGCTTCCTATATTCATAAACAATTCAACTTCGACAATATATAACCA
TGTACAAATTAATTCCAGCAATGTACAACCATATACGAATCAATTAAGCAACTT
Done.