Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold193
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: 3104049
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 172765 characters in sequence are not A, C, G, or T
File 13 of 18
Found at i:2167031 original size:21 final size:21
Alignment explanation
Indices: 2167007--2167082 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
2166997 TACTTGGAAT
2167007 TATGTACAT-TAGACATGGCTA
1 TATGTACATATAGACAT-GCTA
*
2167028 TATGTACATATAGGCATGCTA
1 TATGTACATATAGACATGCTA
* * * ***
2167049 TACGTTCATATTGTTGTGCTA
1 TATGTACATATAGACATGCTA
*
2167070 TATGTATATATAG
1 TATGTACATATAG
2167083 CTAAGCTTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
21 37 0.86
22 6 0.14
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (21 bp):
TATGTACATATAGACATGCTA
Found at i:2178770 original size:25 final size:22
Alignment explanation
Indices: 2178723--2178770 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 22
2178713 TGAGATTAAA
*
2178723 ATTTTTATCAAAACATGGATTT
1 ATTTTTATCAAAACATGCATTT
2178745 ATTTTTATACAAAATTCATGCATTT
1 ATTTTTAT-CAAAA--CATGCATTT
2178770 A
1 A
2178771 AAGGGGATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
25 9 0.41
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (22 bp):
ATTTTTATCAAAACATGCATTT
Found at i:2179994 original size:2 final size:2
Alignment explanation
Indices: 2179983--2180023 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2179973 TTTGAACACT
2179983 TA TA TA -A 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 TA TA TA TA
2180024 CAAAGTTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2180279 original size:22 final size:21
Alignment explanation
Indices: 2180231--2180291 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
2180221 TATAGTAATG
*
2180231 CTATATATACATATCGTTTTTGT
1 CTATATATACATAT--TATTTGT
2180254 -TATATATACATATTATTTGT
1 CTATATATACATATTATTTGT
2180274 ACTATATATA-A-ATTATTT
1 -CTATATATACATATTATTT
2180292 TATTTGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 13 0.37
21 1 0.03
22 21 0.60
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.52
Consensus pattern (21 bp):
CTATATATACATATTATTTGT
Found at i:2180467 original size:17 final size:16
Alignment explanation
Indices: 2180446--2180484 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 16
2180436 CTATATATAC
2180446 ATATATTTATGTTATATGT
1 ATATA-TTAT-TTATAT-T
2180465 ATATATTATTTATATT
1 ATATATTATTTATATT
2180481 ATAT
1 ATAT
2180485 GTATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 4 0.20
19 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
ATATATTATTTATATT
Found at i:2180473 original size:13 final size:13
Alignment explanation
Indices: 2180457--2180495 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
2180447 TATATTTATG
2180457 TTATATGTATATA
1 TTATATGTATATA
2180470 -T-TAT-T-TATA
1 TTATATGTATATA
2180479 TTATATGTATATA
1 TTATATGTATATA
2180492 TTAT
1 TTAT
2180496 TTTATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
9 4 0.18
10 2 0.09
11 6 0.27
12 2 0.09
13 8 0.36
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (13 bp):
TTATATGTATATA
Found at i:2180477 original size:22 final size:22
Alignment explanation
Indices: 2180449--2180501 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
2180439 TATATACATA
*
2180449 TATTTATGTTATATGTATATAT
1 TATTTATATTATATGTATATAT
2180471 TATTTATATTATATGTATATAT
1 TATTTATATTATATGTATATAT
2180493 TATTT-TATT
1 TATTTATATT
2180502 TTAAGAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (22 bp):
TATTTATATTATATGTATATAT
Found at i:2180656 original size:22 final size:22
Alignment explanation
Indices: 2180630--2180713 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 22
2180620 CAAATTTAGG
2180630 ATATATGTATATATTATTTTTA
1 ATATATGTATATATTATTTTTA
* * * *
2180652 CTATATATA-ATA-TAGTTATA
1 ATATATGTATATATTATTTTTA
* * *
2180672 TTATATGTATTTATTATTTGTA
1 ATATATGTATATATTATTTTTA
**
2180694 ATATATGTACGTATTATTTT
1 ATATATGTATATATTATTTT
2180714 ATTTAAAAAT
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 13 0.28
21 5 0.11
22 29 0.62
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (22 bp):
ATATATGTATATATTATTTTTA
Found at i:2181355 original size:16 final size:17
Alignment explanation
Indices: 2181334--2181365 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2181324 ATTTAATTAT
2181334 TATTTAAAA-ATTTTTG
1 TATTTAAAATATTTTTG
2181350 TATTTAAAATATTTTT
1 TATTTAAAATATTTTT
2181366 TTAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TATTTAAAATATTTTTG
Found at i:2181856 original size:41 final size:41
Alignment explanation
Indices: 2181803--2181884 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
2181793 ACTGTAGCTG
2181803 AATGTCTGATGATCGATCGTAATATTATCATTAATGACTGA
1 AATGTCTGATGATCGATCGTAATATTATCATTAATGACTGA
2181844 AATGTCTGATGATCGATCGTAATATTATCATTAATGACTGA
1 AATGTCTGATGATCGATCGTAATATTATCATTAATGACTGA
2181885 GCAAATAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (41 bp):
AATGTCTGATGATCGATCGTAATATTATCATTAATGACTGA
Found at i:2182067 original size:25 final size:27
Alignment explanation
Indices: 2182032--2182083 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
2182022 GCATTACTTT
*
2182032 ATATTATTA-TTTTATAAATA-ATAAA
1 ATATTAATATTTTTATAAATATATAAA
*
2182057 ATATTAATATTTTTATAATTATATAAA
1 ATATTAATATTTTTATAAATATATAAA
2182084 TTTTAATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 8 0.35
26 10 0.43
27 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
ATATTAATATTTTTATAAATATATAAA
Found at i:2182181 original size:43 final size:41
Alignment explanation
Indices: 2182101--2182182 Score: 101
Period size: 43 Copynumber: 2.0 Consensus size: 41
2182091 GTTGTATAAT
* *
2182101 AATTTTTTAAATAAAATTAATAAATTAATTTAATATTATCA
1 AATTTTTTAAATAAAATTAATAAATCAATCTAATATTATCA
* * *
2182142 AATTTATTTAAGATAAGATTAATAGATCAATCTATTATTAT
1 AATTT-TTTAA-ATAAAATTAATAAATCAATCTAATATTAT
2182183 TGAGGTATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 5 0.15
42 5 0.15
43 24 0.71
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (41 bp):
AATTTTTTAAATAAAATTAATAAATCAATCTAATATTATCA
Found at i:2184625 original size:42 final size:42
Alignment explanation
Indices: 2184579--2186156 Score: 352
Period size: 42 Copynumber: 37.6 Consensus size: 42
2184569 GTCTATTAGT
* *
2184579 TTTGACCCTAGAGACTTTTTAACTTTCAGTCTACCTGTCGAC
1 TTTGACCCTAGAGACTTTTTAACCTTCAGTCTGCCTGTCGAC
* * * *
2184621 TTTGACCTTAGAGACTGTCTTT--TC-TCAAGTTTGCCTATC-AGC
1 TTTGACCCTAGAGACT-T-TTTAACCTTC-AGTCTGCCTGTCGA-C
* * * * *
2184663 TTTGACCTTGGAGAATTTTTTACCTTCAGTCTGCCTGTCGGC
1 TTTGACCCTAGAGACTTTTTAACCTTCAGTCTGCCTGTCGAC
* * * * * * *
2184705 TTTCACCTTAGAGACTGTCTCACC-TCTAGTCTACCTGTCAAC
1 TTTGACCCTAGAGACTTTTTAACCTTC-AGTCTGCCTGTCGAC
*
2184747 TTTGACCCTAGAGACTTTCTT-ACCTTCAGTCTGCCTATC-AGC
1 TTTGACCCTAGAGACTTT-TTAACCTTCAGTCTGCCTGTCGA-C
* * *** * **
2184789 TTTCACCCTAAAGA-TAGCCTCACC-TCAAGTCCACCTGTCGAC
1 TTTGACCCTAGAGACT-TTTTAACCTTC-AGTCTGCCTGTCGAC
* * * * * **
2184831 TTT-AGCCATTGAGA-TTTTCTTACCTTCAGTCTGTCTATCGGT
1 TTTGA-CCCTAGAGACTTTT-TAACCTTCAGTCTGCCTGTCGAC
* * *** *
2184873 TTTAACCTTAGAGACTACCTAACC-TCAAGTCTGCCTGTCAAC
1 TTTGACCCTAGAGACTTTTTAACCTTC-AGTCTGCCTGTCGAC
* * *
2184915 TTTGA-CTTGGAGACTTTCTT-ACCTTCAGTCTGCCTGTCGGC
1 TTTGACCCTAGAGACTTT-TTAACCTTCAGTCTGCCTGTCGAC
* * *
2184956 TTTGACCCTAGAGAC-TTTCATACCTTCAGTTTACCTGTC-AGC
1 TTTGACCCTAGAGACTTTTTA-ACCTTCAGTCTGCCTGTCGA-C
* * * ** * ** * *
2184998 TTTCACCTTGGAGACTTGCCTCACCTAAAGCCTGCCTGTTGAC
1 TTTGACCCTAGAGACTT-TTTAACCTTCAGTCTGCCTGTCGAC
* * * * *
2185041 TTTGACCGTAAAGACTTTCTT-ACCTTTAGTCTGCTTGTCGGC
1 TTTGACCCTAGAGACTTT-TTAACCTTCAGTCTGCCTGTCGAC
* * * * * *
2185083 TTTCACCCTGGAGACTGTCTCACC-TCAAGTCTACCTGTC-AGC
1 TTTGACCCTAGAGACTTTTTAACCTTC-AGTCTGCCTGTCGA-C
* * *
2185125 TTTGACCCTAAAGA-TTTTTATACCTTCAGTCTGCCTAT-TAGC
1 TTTGACCCTAGAGACTTTTTA-ACCTTCAGTCTGCCTGTCGA-C
* *** * * *
2185167 TTTGACCCTGGAGACTACCTAATC-TCAAGTTTGCCTGTCGGC
1 TTTGACCCTAGAGACTTTTTAACCTTC-AGTCTGCCTGTCGAC
* * * * * *
2185209 TTTGACCTTGGAGACTTACTT-GCCTTTAGTCTGCCTGTCGGC
1 TTTGACCCTAGAGACTT-TTTAACCTTCAGTCTGCCTGTCGAC
*** * *
2185251 TTTGACCCTAGAGACTGCCTCACC-TCAAGTCTGCCTATC-AGC
1 TTTGACCCTAGAGACTTTTTAACCTTC-AGTCTGCCTGTCGA-C
* * * *
2185293 TTTGACCCTAAAGACTTTTTTACCTTCAGTTTGCCTATCGAC
1 TTTGACCCTAGAGACTTTTTAACCTTCAGTCTGCCTGTCGAC
* * * ** * *
2185335 TTTGACCTTGGAGACCTTCTT-ATGTTCAGTCTGCTTATC-AGC
1 TTTGACCCTAGAGA-CTTTTTAACCTTCAGTCTGCCTGTCGA-C
*
2185377 TTTGACCCTAGAGA-TTGCCTT-ACC-TCAAGTCTGCCTGTCGAC
1 TTTGACCCTAGAGACTT--TTTAACCTTC-AGTCTGCCTGTCGAC
* * ** *
2185419 TTTGACCCTAGAGACTTTTTTACTTTCAAACT-ACTAGTC-AGC
1 TTTGACCCTAGAGACTTTTTAACCTTCAGTCTGCCT-GTCGA-C
* * *** * * * *
2185461 TTTGACCTTGGAGACTACCTCACC-TCAAGTTTGCTTGTCGGC
1 TTTGACCCTAGAGACTTTTTAACCTTC-AGTCTGCCTGTCGAC
* * * *
2185503 TTTGACCTTGGAGACTTTCTT-ACCTTCAGTCTACCAGTC-AGC
1 TTTGACCCTAGAGACTTT-TTAACCTTCAGTCTGCCTGTCGA-C
* * *** * * * *
2185545 TTTGACCTTGGAGACTGCCTCACCTTAAGTCTGCATGTCGCC
1 TTTGACCCTAGAGACTTTTTAACCTTCAGTCTGCCTGTCGAC
* * * * * * * * *
2185587 CTTAACCGT-GAAGACTTTTTTACCTTTAATCT-ACAGTCAAC
1 TTTGACCCTAG-AGACTTTTTAACCTTCAGTCTGCCTGTCGAC
* * * * * * *
2185628 TTTGACCTTGGAAACTGTCTCACC-TCAAGTCTGCCTATC-AGC
1 TTTGACCCTAGAGACTTTTTAACCTTC-AGTCTGCCTGTCGA-C
* * * *
2185670 TTTGACCCTTA-AGAATTTCTT-ACCTTCAGTCTACCAGTCAAC
1 TTTGACCC-TAGAGACTTT-TTAACCTTCAGTCTGCCTGTCGAC
* * * * * * * *
2185712 TTTGA-ACTTGAAGACTGTCTCACC-TCAAGTTTGCCTATCGGC
1 TTTGACCCTAG-AGACTTTTTAACCTTC-AGTCTGCCTGTCGAC
** *
2185754 TTTGACCCT-GAAGACTACCTT-ACC-TCAAGTCTGCCTGTCAAC
1 TTTGACCCTAG-AGACT-TTTTAACCTTC-AGTCTGCCTGTCGAC
* * * *** * * * *
2185796 TTTAACCTTGGAGACTGCCTCACCTCCAGTTTGCCTGTCGGC
1 TTTGACCCTAGAGACTTTTTAACCTTCAGTCTGCCTGTCGAC
* * * *
2185838 TTTGACCCTGGAGACTTTCTT-ACCTTTAGTCTACCTATC-AGC
1 TTTGACCCTAGAGACTTT-TTAACCTTCAGTCTGCCTGTCGA-C
* * * * * * *
2185880 TTTGACCCTAAAGTCTGTCTCACC-TCAAGTTTGCCTGTCGGC
1 TTTGACCCTAGAGACTTTTTAACCTTC-AGTCTGCCTGTCGAC
* * * * *
2185922 TTTAACCCTGGATACTTTCTT-ACCTTTAGTCTGCCTGTCGGC
1 TTTGACCCTAGAGACTTT-TTAACCTTCAGTCTGCCTGTCGAC
* * * *** * * *
2185964 TTTTACCTTAAAGACTGCCTAACC-TCAAGTCTGCTTGTTGGC
1 TTTGACCCTAGAGACTTTTTAACCTTC-AGTCTGCCTGTCGAC
* * * * * * *
2186006 TTTGACCTTGGAGACTTTTTTACCTTTAGTCTACTTATCTG-C
1 TTTGACCCTAGAGACTTTTTAACCTTCAGTCTGCCTGTC-GAC
** * * **
2186048 TTTGA-CCT-GAAGACTACCTT-ACC-TCAAGTTTGCCTATCGGT
1 TTTGACCCTAG-AGACT-TTTTAACCTTC-AGTCTGCCTGTCGAC
* * * * *
2186089 TTTAACCCTAGAGACTTTCTTACCCTTAAGTCTGCTTGTCGGC
1 TTTGACCCTAGAGACTTT-TTAACCTTCAGTCTGCCTGTCGAC
* *
2186132 TTTGACCCTAGAAACTTTTTCACCT
1 TTTGACCCTAGAGACTTTTTAACCT
2186157 CTTGTCTTCC
Statistics
Matches: 1102, Mismatches: 329, Indels: 210
0.67 0.20 0.13
Matches are distributed among these distances:
40 11 0.01
41 125 0.11
42 852 0.77
43 109 0.10
44 5 0.00
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.35
Consensus pattern (42 bp):
TTTGACCCTAGAGACTTTTTAACCTTCAGTCTGCCTGTCGAC
Found at i:2184928 original size:41 final size:41
Alignment explanation
Indices: 2184883--2184961 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
2184873 TTTAACCTTA
2184883 GAGACTACCTAACC-TCAAGTCTGCCTGTCAACTTTGACTTG
1 GAGACTACCTAACCTTC-AGTCTGCCTGTCAACTTTGACTTG
** * **
2184924 GAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGAC
1 GAGACTACCTAACCTTCAGTCTGCCTGTCAACTTTGAC
2184962 CCTAGAGACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 30 0.94
42 2 0.06
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (41 bp):
GAGACTACCTAACCTTCAGTCTGCCTGTCAACTTTGACTTG
Found at i:2186007 original size:84 final size:84
Alignment explanation
Indices: 2184510--2186138 Score: 1037
Period size: 84 Copynumber: 19.4 Consensus size: 84
2184500 ATGTCTTTTT
* * ** * * * * *
2184510 TTTCTTATCTTCAGTCTGCCAGTCAGCTTTGACCTTGGAGATTGCCTCACTTTAAGTCTGTCTAT
1 TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTGT
** * *
2184575 TAGTTTTGACCCTAGAGAC
66 CGGCTTTGACCCTGGAGAC
* * * * *** *
2184594 TTT-TTAACTTTCAGTCTACCTGTC-GACTTTGACCTTAGAGACTGTCTTTTCTCAAGTTTGCCT
1 TTTCTT-ACCTTCAGTCTGCCTGTCAG-CTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCT
* * * *
2184657 ATCAGCTTTGACCTTGGAGAA
64 GTCGGCTTTGACCCTGGAGAC
* * * * * * *
2184678 TTTTTTACCTTCAGTCTGCCTGTCGGCTTTCACCTTAGAGACTGTCTCACCTCTAGTCTACCTGT
1 TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTGT
** *
2184743 CAACTTTGACCCTAGAGAC
66 CGGCTTTGACCCTGGAGAC
* * * **
2184762 TTTCTTACCTTCAGTCTGCCTATCAGCTTTCACCCTAAAGA-TAGCCTCACCTCAAGTCCACCTG
1 TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTTAAAGACT-GCCTCACCTCAAGTCTGCCTG
* * * *
2184826 TCGACTTT-AGCCATTGAGAT
65 TCGGCTTTGA-CCCTGGAGAC
* * * * * * * *
2184846 TTTCTTACCTTCAGTCTGTCTATCGGTTTTAACCTTAGAGACTACCTAACCTCAAGTCTGCCTGT
1 TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTGT
** *
2184911 CAACTTTGA-CTTGGAGAC
66 CGGCTTTGACCCTGGAGAC
* * * * * * *
2184929 TTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCAT-ACCTTC-AGTTTACCT
1 TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTTAAAGAC-TGCCTCACC-TCAAGTCTGCCT
* * *
2184992 GTCAGCTTTCACCTTGGAGAC
64 GTCGGCTTTGACCCTGGAGAC
* * ** * * * ** * ** *
2185013 TTGCCTCACCTAAAGCCTGCCTGT-TGACTTTGACCGTAAAGACTTTCTTACCTTTAGTCTGCTT
1 TT-TCTTACCTTCAGTCTGCCTGTCAG-CTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCT
*
2185077 GTCGGCTTTCACCCTGGAGAC
64 GTCGGCTTTGACCCTGGAGAC
* * * * *** *
2185098 TGTCTCACC-TCAAGTCTACCTGTCAGCTTTGACCCTAAAGA-TTTTTATACCTTC-AGTCTGCC
1 TTTCTTACCTTC-AGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCT-CACC-TCAAGTCTGCC
* **
2185160 TATTAGCTTTGACCCTGGAGAC
63 TGTCGGCTTTGACCCTGGAGAC
** * * * * ** ** ** **
2185182 TACCTAATC-TCAAGTTTGCCTGTCGGCTTTGACCTTGGAGACTTACTTGCCTTTAGTCTGCCTG
1 TTTCTTACCTTC-AGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTG
*
2185246 TCGGCTTTGACCCTAGAGAC
65 TCGGCTTTGACCCTGGAGAC
** * * * *** * *
2185266 TGCCTCACC-TCAAGTCTGCCTATCAGCTTTGACCCTAAAGACTTTTTTACCTTC-AGTTTGCCT
1 TTTCTTACCTTC-AGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACC-TCAAGTCTGCCT
* * *
2185329 ATCGACTTTGACCTTGGAGAC
64 GTCGGCTTTGACCCTGGAGAC
* ** * * * * * *
2185350 CTTCTTATGTTCAGTCTGCTTATCAGCTTTGACCCTAGAGATTGCCTTACCTCAAGTCTGCCTGT
1 TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTGT
* *
2185415 CGACTTTGACCCTAGAGAC
66 CGGCTTTGACCCTGGAGAC
* * ** * ** * * *
2185434 TTTTTTACTTTCAAACT-ACTAGTCAGCTTTGACCTTGGAGACTACCTCACCTCAAGTTTGCTTG
1 TTTCTTACCTTCAGTCTGCCT-GTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTG
*
2185498 TCGGCTTTGACCTTGGAGAC
65 TCGGCTTTGACCCTGGAGAC
* * ** * *
2185518 TTTCTTACCTTCAGTCTACCAGTCAGCTTTGACCTTGGAGACTGCCTCACCTTAAGTCTGCATGT
1 TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTGT
* * * * *
2185583 CGCCCTTAACCGTGAAGAC
66 CGGCTTTGACCCTGGAGAC
* * * * * * * * *
2185602 TTTTTTACCTTTAATCT-ACAGTCAACTTTGACCTTGGAA-ACTGTCTCACCTCAAGTCTGCCTA
1 TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTT-AAAGACTGCCTCACCTCAAGTCTGCCTG
* ** *
2185665 TCAGCTTTGACCCTTAAGAA
65 TCGGCTTTGACCCTGGAGAC
* * * * * * * *
2185685 TTTCTTACCTTCAGTCTACCAGTCAACTTTGAACTTGAAGACTGTCTCACCTCAAGTTTGCCTAT
1 TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTGT
*
2185750 CGGCTTTGACCCTGAAGAC
66 CGGCTTTGACCCTGGAGAC
** * * ** * *
2185769 TACCTTACC-TCAAGTCTGCCTGTCAACTTTAACCTTGGAGACTGCCTCACCTCCAGTTTGCCTG
1 TTTCTTACCTTC-AGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTG
2185833 TCGGCTTTGACCCTGGAGAC
65 TCGGCTTTGACCCTGGAGAC
* * * * * * *
2185853 TTTCTTACCTTTAGTCTACCTATCAGCTTTGACCCTAAAGTCTGTCTCACCTCAAGTTTGCCTGT
1 TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTGT
* *
2185918 CGGCTTTAACCCTGGATAC
66 CGGCTTTGACCCTGGAGAC
* * * * *
2185937 TTTCTTACCTTTAGTCTGCCTGTCGGCTTTTACCTTAAAGACTGCCTAACCTCAAGTCTGCTTGT
1 TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTGT
* *
2186002 TGGCTTTGACCTTGGAGAC
66 CGGCTTTGACCCTGGAGAC
* * * * * * * * * * *
2186021 TTTTTTACCTTTAGTCTACTTATCTGCTTTGACC-TGAAGACTACCTTACCTCAAGTTTGCCTAT
1 TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTGT
* * *
2186085 CGGTTTTAACCCTAGAGAC
66 CGGCTTTGACCCTGGAGAC
* * *
2186104 TTTCTTACCCTTAAGTCTGCTTGTCGGCTTTGACC
1 TTTCTTA-CCTTCAGTCTGCCTGTCAGCTTTGACC
2186139 CTAGAAACTT
Statistics
Matches: 1238, Mismatches: 275, Indels: 64
0.79 0.17 0.04
Matches are distributed among these distances:
83 187 0.15
84 977 0.79
85 74 0.06
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.36
Consensus pattern (84 bp):
TTTCTTACCTTCAGTCTGCCTGTCAGCTTTGACCTTAAAGACTGCCTCACCTCAAGTCTGCCTGT
CGGCTTTGACCCTGGAGAC
Found at i:2186737 original size:16 final size:16
Alignment explanation
Indices: 2186712--2186772 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
2186702 CATAAAAAAG
*
2186712 AAAAAAATAATATAAT
1 AAAAATATAATATAAT
*
2186728 AAAAATATAAAATAATT
1 AAAAATATAATATAA-T
*
2186745 AAAAA-AT-ATATACAC
1 AAAAATATAATATA-AT
2186760 AAAAATAGTAATA
1 AAAAATA-TAATA
2186773 ACTAATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
15 9 0.25
16 17 0.47
17 7 0.19
18 3 0.08
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (16 bp):
AAAAATATAATATAAT
Found at i:2186749 original size:18 final size:17
Alignment explanation
Indices: 2186703--2186754 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 17
2186693 TTTCTTTGAC
*
2186703 ATAAAA-AAGAAAAAA-
1 ATAAAATAATAAAAAAT
*
2186718 ATAATATAAT-AAAAAT
1 ATAAAATAATAAAAAAT
2186734 ATAAAATAATTAAAAAAT
1 ATAAAATAA-TAAAAAAT
2186752 ATA
1 ATA
2186755 TACACAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 10 0.33
16 10 0.33
17 1 0.03
18 9 0.30
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (17 bp):
ATAAAATAATAAAAAAT
Found at i:2186749 original size:31 final size:36
Alignment explanation
Indices: 2186713--2186786 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 36
2186703 ATAAAAAAGA
*
2186713 AAAAAATAATATA-ATAAAAATA-TAA-AA-TAA-TT
1 AAAAAAT-ATATACACAAAAATAGTAATAACTAATTT
2186745 AAAAAATATATACACAAAAATAGTAATAACTAATTT
1 AAAAAATATATACACAAAAATAGTAATAACTAATTT
2186781 AAAAAA
1 AAAAAA
2186787 AAAATAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
31 5 0.14
32 15 0.42
33 3 0.08
34 2 0.06
35 3 0.08
36 8 0.22
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.26
Consensus pattern (36 bp):
AAAAAATATATACACAAAAATAGTAATAACTAATTT
Found at i:2186959 original size:60 final size:60
Alignment explanation
Indices: 2186888--2187000 Score: 190
Period size: 60 Copynumber: 1.9 Consensus size: 60
2186878 CTCATTGCAT
* * *
2186888 CCATATGTTCATTTCATGCATTGCATTGCTTTTCATACATGCTTTTTTTCATGTTTCACA
1 CCATAAGTTCATTTCATGCATTGCATTGCATTTCATACATGCTTTATTTCATGTTTCACA
*
2186948 CCATAAGTTCATTTCATGCATTGCATTGCATTTCATGCATGCTTTATTTCATG
1 CCATAAGTTCATTTCATGCATTGCATTGCATTTCATACATGCTTTATTTCATG
2187001 CATTTCACGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (60 bp):
CCATAAGTTCATTTCATGCATTGCATTGCATTTCATACATGCTTTATTTCATGTTTCACA
Found at i:2186981 original size:19 final size:17
Alignment explanation
Indices: 2186955--2187004 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
2186945 ACACCATAAG
2186955 TTCATTTCATGCATTGC
1 TTCATTTCATGCATTGC
2186972 ATTGCATTTCATGCA-TGC
1 -TT-CATTTCATGCATTGC
*
2186990 TTTATTTCATGCATT
1 TTCATTTCATGCATT
2187005 TCACGAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 10 0.34
17 3 0.10
18 5 0.17
19 11 0.38
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (17 bp):
TTCATTTCATGCATTGC
Found at i:2187024 original size:60 final size:59
Alignment explanation
Indices: 2186890--2187021 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 59
2186880 CATTGCATCC
* * *
2186890 ATATGTTCATTTCATGCATTGCATTGCTTTTCATACATGCTTTTTTTCATGTTTCACACC
1 ATAT-TTCATTTCATGCATTGCATTGCATTTCATACATGCTTTATTTCATGTTTCACACA
* *
2186950 ATAAGTTCATTTCATGCATTGCATTGCATTTCATGCATGCTTTATTTCATGCATTTCACGA-A
1 AT-ATTTCATTTCATGCATTGCATTGCATTTCATACATGCTTTATTTCATG--TTTCAC-ACA
2187012 ATATTTCATT
1 ATATTTCATT
2187022 CATTAATATG
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
60 45 0.73
61 8 0.13
62 8 0.13
63 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (59 bp):
ATATTTCATTTCATGCATTGCATTGCATTTCATACATGCTTTATTTCATGTTTCACACA
Found at i:2187725 original size:26 final size:26
Alignment explanation
Indices: 2187689--2187743 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
2187679 AGAAGAGTAG
**
2187689 AAAAAGAAAGGAGTCAAAACA-AAACA
1 AAAAAGAAAGGA-AAAAAACAGAAACA
*
2187715 AAAAAGGAAGGAAAAAAACAGAAACA
1 AAAAAGAAAGGAAAAAAACAGAAACA
2187741 AAA
1 AAA
2187744 CACCAAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.73, C:0.09, G:0.16, T:0.02
Consensus pattern (26 bp):
AAAAAGAAAGGAAAAAAACAGAAACA
Found at i:2187830 original size:19 final size:19
Alignment explanation
Indices: 2187806--2187884 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 19
2187796 AAACACCAAC
*
2187806 AGCAACGTCAGCAAGCAAT
1 AGCAACATCAGCAAGCAAT
* *
2187825 AGCAACATAAAC-AGCAAT
1 AGCAACATCAGCAAGCAAT
* *
2187843 CAGCAACATCAGCAACCAAA
1 -AGCAACATCAGCAAGCAAT
*
2187863 AGC-A-ATCAGCAAGCAAC
1 AGCAACATCAGCAAGCAAT
2187880 AGCAA
1 AGCAA
2187885 GCAACGGCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
17 14 0.29
18 8 0.17
19 22 0.46
20 4 0.08
ACGTcount: A:0.49, C:0.28, G:0.15, T:0.08
Consensus pattern (19 bp):
AGCAACATCAGCAAGCAAT
Found at i:2187847 original size:38 final size:37
Alignment explanation
Indices: 2187796--2187867 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
2187786 ACCAGAATCG
* * *
2187796 AAACACCAACAGCAACGTCAGCAAGCAATAGCAACAT
1 AAACACCAACAGCAACATCAGCAACCAAAAGCAACAT
*
2187833 AAACAGCAATCAGCAACATCAGCAACCAAAAGCAA
1 AAACACCAA-CAGCAACATCAGCAACCAAAAGCAA
2187868 TCAGCAAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 8 0.27
38 22 0.73
ACGTcount: A:0.51, C:0.29, G:0.12, T:0.07
Consensus pattern (37 bp):
AAACACCAACAGCAACATCAGCAACCAAAAGCAACAT
Found at i:2187872 original size:17 final size:17
Alignment explanation
Indices: 2187850--2187884 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2187840 AATCAGCAAC
2187850 ATCAGCAACCAAAAGCA
1 ATCAGCAACCAAAAGCA
* *
2187867 ATCAGCAAGCAACAGCA
1 ATCAGCAACCAAAAGCA
2187884 A
1 A
2187885 GCAACGGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.29, G:0.14, T:0.06
Consensus pattern (17 bp):
ATCAGCAACCAAAAGCA
Found at i:2187882 original size:10 final size:10
Alignment explanation
Indices: 2187862--2187897 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
2187852 CAGCAACCAA
2187862 AAGCAATCAGC
1 AAGCAA-CAGC
2187873 AAGCAACAGC
1 AAGCAACAGC
*
2187883 AAGCAACGGC
1 AAGCAACAGC
2187893 AAGCA
1 AAGCA
2187898 CCAGTAGCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.75
11 6 0.25
ACGTcount: A:0.47, C:0.28, G:0.22, T:0.03
Consensus pattern (10 bp):
AAGCAACAGC
Found at i:2187894 original size:27 final size:26
Alignment explanation
Indices: 2187813--2187884 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 26
2187803 AACAGCAACG
* *
2187813 TCAGCAAGCAATAGCAACATAAACAGCAA
1 TCAGCAA-CAACAGCAAC-CAAA-AGCAA
*
2187842 TCAGCAACATCAGCAACCAAAAGCAA
1 TCAGCAACAACAGCAACCAAAAGCAA
2187868 TCAGCAAGCAACAGCAA
1 TCAGCAA-CAACAGCAA
2187885 GCAACGGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 12 0.32
27 11 0.29
28 8 0.21
29 7 0.18
ACGTcount: A:0.50, C:0.28, G:0.14, T:0.08
Consensus pattern (26 bp):
TCAGCAACAACAGCAACCAAAAGCAA
Found at i:2193835 original size:164 final size:162
Alignment explanation
Indices: 2193560--2193869 Score: 401
Period size: 164 Copynumber: 1.9 Consensus size: 162
2193550 ATTACAGCCT
*
2193560 TAGAAAATGGCATTTTGCATGCCATATATGTACCCAAGATAACTGCCACATAACGAAATCTATGG
1 TAGAAAATGGCATTTTCCATGCCATATATGTACCCAAGATAACTGCCACATAACGAAATCTATGG
* * * *
2193625 TTAAAGGCTAGTAAGCATTCTGATGCTTAATGGCCATTTTTAGATCTTTGGTTGGTTTATTAAAT
66 TTAAAGGCTAGTAAGCATTCTGATGCTCAATGGCCATTTCTAGATCTTAGGTTAGTTTATTAAAT
*
2193690 GGTTAAGGCATCGTTCGAATGCACAACTTCCC
131 AGTTAAGGCATCGTTCGAATGCACAACTTCCC
* * * * *
2193722 TAGAAAATGGCATTTTCCATGCC-TCATGTGTGCCTAAGATAAGTGCC-CTATAAGGGAAATGCT
1 TAGAAAATGGCATTTTCCATGCCAT-ATATGTACCCAAGATAACTGCCAC-ATAA-CGAAAT-CT
* * * *
2193785 ATGGTTAAAGGCTAGTGAGCATT-TAGATGGTCGATGGCCATTTCTAGATCTTAGGTTAGTTTGT
62 ATGGTTAAAGGCTAGTAAGCATTCT-GATGCTCAATGGCCATTTCTAGATCTTAGGTTAGTTTAT
* *
2193849 TGAGTAGTTAAGGCATCGTTC
126 TAAATAGTTAAGGCATCGTTC
2193870 AAGTGCAATA
Statistics
Matches: 126, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
161 2 0.02
162 44 0.35
163 6 0.05
164 74 0.59
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (162 bp):
TAGAAAATGGCATTTTCCATGCCATATATGTACCCAAGATAACTGCCACATAACGAAATCTATGG
TTAAAGGCTAGTAAGCATTCTGATGCTCAATGGCCATTTCTAGATCTTAGGTTAGTTTATTAAAT
AGTTAAGGCATCGTTCGAATGCACAACTTCCC
Found at i:2195532 original size:21 final size:19
Alignment explanation
Indices: 2195494--2195532 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
2195484 AATCAATCTT
*
2195494 TTTAAAATGAGTTTTTAAA
1 TTTAAAATGAGGTTTTAAA
2195513 TTTAAAATGATAGGTTTTAA
1 TTTAAAATG--AGGTTTTAA
2195533 TCAGTGTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (19 bp):
TTTAAAATGAGGTTTTAAA
Found at i:2197589 original size:13 final size:13
Alignment explanation
Indices: 2197571--2197597 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2197561 ACATTATGCT
2197571 TTGTATCGATACA
1 TTGTATCGATACA
2197584 TTGTATCGATACA
1 TTGTATCGATACA
2197597 T
1 T
2197598 GTTAATTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2197611 original size:19 final size:19
Alignment explanation
Indices: 2197583--2197638 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
2197573 GTATCGATAC
**
2197583 ATTGTATCGATACATGTTA
1 ATTGTATCGATACATGACA
*
2197602 ATTGTGTCGATACATGGACA
1 ATTGTATCGATACAT-GACA
2197622 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
2197639 GATTGGCAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:2197626 original size:20 final size:20
Alignment explanation
Indices: 2197583--2197637 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2197573 GTATCGATAC
**
2197583 ATTGTATCGATACAT-GTTA
1 ATTGTATCGATACATGGACA
*
2197602 ATTGTGTCGATACATGGACA
1 ATTGTATCGATACATGGACA
2197622 ATTGTATCGATACATG
1 ATTGTATCGATACATG
2197638 AGATTGGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:2203752 original size:13 final size:13
Alignment explanation
Indices: 2203734--2203758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2203724 CAATATTCCT
2203734 TGTATCGATACAA
1 TGTATCGATACAA
2203747 TGTATCGATACA
1 TGTATCGATACA
2203759 TTGGGTACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2205711 original size:36 final size:35
Alignment explanation
Indices: 2205664--2205733 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
2205654 TGACAAAAGG
*
2205664 GGAGAATTGCTTTGATTAAG-GGGAAGAAAATTTTTT
1 GGAGAAATGCTTTGATTAAGAGGG-AG-AAATTTTTT
2205700 GGAGAAATGCTTTGATTAAGAGGGAGAAATTTTT
1 GGAGAAATGCTTTGATTAAGAGGGAGAAATTTTT
2205734 GAAATTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 8 0.25
36 21 0.66
37 3 0.09
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (35 bp):
GGAGAAATGCTTTGATTAAGAGGGAGAAATTTTTT
Found at i:2206345 original size:20 final size:20
Alignment explanation
Indices: 2206303--2206356 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
2206293 ACATTATGCT
**
2206303 TTGTATCGATACAT-GTTAA
1 TTGTATCGATACATGGACAA
2206322 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
2206342 TTGTATCGATACATG
1 TTGTATCGATACATG
2206357 AGATTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:2206424 original size:13 final size:13
Alignment explanation
Indices: 2206408--2206432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2206398 TGGTACAATG
2206408 TATCGATACATTA
1 TATCGATACATTA
2206421 TATCGATACATT
1 TATCGATACATT
2206433 GCTTGTAACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:2206496 original size:20 final size:20
Alignment explanation
Indices: 2206471--2206523 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
2206461 TTCAAATCTA
2206471 TGTATCGATACATTATGAAT
1 TGTATCGATACATTATGAAT
2206491 TGTATCGATACATTATGAAT
1 TGTATCGATACATTATGAAT
2206511 TGTATCGATACAT
1 TGTATCGATACAT
2206524 GGCTACGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTATGAAT
Found at i:2207491 original size:13 final size:13
Alignment explanation
Indices: 2207473--2207500 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2207463 GTAACTTGTG
2207473 CAATCATGATATT
1 CAATCATGATATT
2207486 CAATCATGATATT
1 CAATCATGATATT
2207499 CA
1 CA
2207501 CTTTGATAAA
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:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (13 bp):
CAATCATGATATT
Found at i:2207945 original size:21 final size:20
Alignment explanation
Indices: 2207919--2207971 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2207909 TTCTACAATT
2207919 TGTATCGATACAAATAGTAAA
1 TGTATCGATACAAA-AGTAAA
* *
2207940 TGTATCGATACATAAGTGAA
1 TGTATCGATACAAAAGTAAA
2207960 TGTATCGATACA
1 TGTATCGATACA
2207972 TGCCTGGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (20 bp):
TGTATCGATACAAAAGTAAA
Found at i:2207963 original size:20 final size:20
Alignment explanation
Indices: 2207919--2207992 Score: 85
Period size: 21 Copynumber: 3.6 Consensus size: 20
2207909 TTCTACAATT
* *
2207919 TGTATCGATACAAATAGTAAA
1 TGTATCGATACATA-AGTGAA
2207940 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
***
2207960 TGTATCGATACATGCCTGGAA
1 TGTATCGATACATAAGT-GAA
2207981 TGTATCGATACA
1 TGTATCGATACA
2207993 AAACCATTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 19 0.40
21 28 0.60
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:2208042 original size:20 final size:20
Alignment explanation
Indices: 2208017--2208115 Score: 69
Period size: 20 Copynumber: 4.9 Consensus size: 20
2208007 TCTAGAAAGG
2208017 AAATGTATCGATACATAAGT
1 AAATGTATCGATACATAAGT
*
2208037 AAATGTATTGATAC--AAGCT
1 AAATGTATCGATACATAAG-T
* *
2208056 CATAATTGTATCGATACATTATT
1 -A-AA-TGTATCGATACATAAGT
* * **
2208079 CATTGTATCGATACAT-TTT
1 AAATGTATCGATACATAAGT
*
2208098 TAATGTATCGATACATAA
1 AAATGTATCGATACATAA
2208116 AAGCAAATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
18 3 0.05
19 17 0.27
20 27 0.44
21 3 0.05
22 10 0.16
23 1 0.02
24 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (20 bp):
AAATGTATCGATACATAAGT
Found at i:2208106 original size:19 final size:20
Alignment explanation
Indices: 2208062--2208113 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
2208052 AGCTCATAAT
*
2208062 TGTATCGATACATTATTCAT
1 TGTATCGATACATTATTCAA
*
2208082 TGTATCGATACATT-TTTAA
1 TGTATCGATACATTATTCAA
2208101 TGTATCGATACAT
1 TGTATCGATACAT
2208114 AAAAGCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTATTCAA
Found at i:2210936 original size:19 final size:20
Alignment explanation
Indices: 2210912--2210963 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
2210902 CTGCCAGTTT
*
2210912 CATGTATCGATACAATG-AA
1 CATGTATCGATACAAAGCAA
2210931 CATGTATCGATACAAAGCAA
1 CATGTATCGATACAAAGCAA
*
2210951 TATGTATCGATAC
1 CATGTATCGATAC
2210964 TTCTAGGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (20 bp):
CATGTATCGATACAAAGCAA
Found at i:2210976 original size:20 final size:21
Alignment explanation
Indices: 2210953--2210991 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2210943 CAAAGCAATA
2210953 TGTATCGATAC-TTCTAGGCT
1 TGTATCGATACTTTCTAGGCT
2210973 TGTATCGATACTTTCTAGG
1 TGTATCGATACTTTCTAGG
2210992 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (21 bp):
TGTATCGATACTTTCTAGGCT
Found at i:2213585 original size:13 final size:13
Alignment explanation
Indices: 2213567--2213592 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2213557 ATAGTGCCCT
2213567 TGTATCGATACAA
1 TGTATCGATACAA
2213580 TGTATCGATACAA
1 TGTATCGATACAA
2213593 AGATACTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2217878 original size:3 final size:3
Alignment explanation
Indices: 2217870--2217906 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2217860 CAAGTCAACT
2217870 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
2217907 TATCTTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:2220327 original size:19 final size:22
Alignment explanation
Indices: 2220303--2220351 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2220293 TTGACGTATT
*
2220303 AAATTTTTT-A-TTATTAAT-A
1 AAATTTTTTAATTTATAAATAA
2220322 AAATTTATTTAATTTATAAATAA
1 AAATTT-TTTAATTTATAAATAA
2220345 AAATTTT
1 AAATTTT
2220352 AATTTTATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.24
20 3 0.12
21 1 0.04
22 8 0.32
23 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AAATTTTTTAATTTATAAATAA
Found at i:2221148 original size:13 final size:13
Alignment explanation
Indices: 2221130--2221157 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2221120 CAACTGACCT
2221130 GACCACGCATTAA
1 GACCACGCATTAA
2221143 GACCACGCATTAA
1 GACCACGCATTAA
2221156 GA
1 GA
2221158 GCGTACAGAA
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:0.39, C:0.29, G:0.18, T:0.14
Consensus pattern (13 bp):
GACCACGCATTAA
Found at i:2221245 original size:32 final size:33
Alignment explanation
Indices: 2221208--2221286 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 33
2221198 ATTAGAAAAT
* *
2221208 TTTAAATTTAA-TTTAATTATT-ATTAATTTAAA
1 TTTAAA-TTAATTTTAATTATTAAATAAATTAAA
2221240 TTTAAA-TAATTTTAATTATTAAATAAATTAAA
1 TTTAAATTAATTTTAATTATTAAATAAATTAAA
2221272 TTTAAA-T-ATTTTAAT
1 TTTAAATTAATTTTAAT
2221287 ATTTGAGTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 3 0.07
31 18 0.42
32 22 0.51
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTTAAATTAATTTTAATTATTAAATAAATTAAA
Found at i:2221254 original size:21 final size:19
Alignment explanation
Indices: 2221205--2221256 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 19
2221195 TTTATTAGAA
2221205 AATTTTAAATTTAATTTAAT
1 AATTTT-AATTTAATTTAAT
*
2221225 TATTATTAATTTAAATTTAAAT
1 AATT-TTAATTT-AATTT-AAT
2221247 AATTTTAATT
1 AATTTTAATT
2221257 ATTAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 8 0.30
21 13 0.48
22 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTTAATTTAATTTAAT
Found at i:2221254 original size:31 final size:31
Alignment explanation
Indices: 2221219--2221286 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2221209 TTAAATTTAA
* *
2221219 TTTAATTATT-ATTAATTTAAATTTAAATAAT
1 TTTAATTATTAAATAAATTAAATTTAAAT-AT
2221250 TTTAATTATTAAATAAATTAAATTTAAATAT
1 TTTAATTATTAAATAAATTAAATTTAAATAT
2221281 TTTAAT
1 TTTAAT
2221287 ATTTGAGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 18 0.53
32 16 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTAATTATTAAATAAATTAAATTTAAATAT
Found at i:2229924 original size:2 final size:2
Alignment explanation
Indices: 2229917--2229943 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2229907 CAAACCTTGA
2229917 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2229944 GTATCTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2230759 original size:2 final size:2
Alignment explanation
Indices: 2230754--2230782 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2230744 GTGTGTGTGT
2230754 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2230783 GAGCTTAATG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2233192 original size:6 final size:6
Alignment explanation
Indices: 2233183--2233214 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2233173 TCGGGTAAGT
2233183 TTTGGG TTTGGG -TTGGG TTTGGG TTTGGG TTT
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTT
2233215 TTTACTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (6 bp):
TTTGGG
Found at i:2233198 original size:11 final size:12
Alignment explanation
Indices: 2233183--2233214 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
2233173 TCGGGTAAGT
2233183 TTTGGGTTTGGG
1 TTTGGGTTTGGG
2233195 -TTGGGTTTGGG
1 TTTGGGTTTGGG
2233206 TTTGGGTTT
1 TTTGGGTTT
2233215 TTTACTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (12 bp):
TTTGGGTTTGGG
Found at i:2235554 original size:2 final size:2
Alignment explanation
Indices: 2235547--2235571 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2235537 TTTCTCCTCC
2235547 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
2235572 GTTGCCCGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2236725 original size:25 final size:25
Alignment explanation
Indices: 2236682--2236746 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
2236672 GACTCAACTT
2236682 ATTTTTAATTATATAATA-TATATTA
1 ATTTTTAATTATATAATATTATA-TA
*
2236707 ATTTTATATTTATAT-ATATTATATA
1 ATTTT-TAATTATATAATATTATATA
*
2236732 ATTTTT-ATCATATAA
1 ATTTTTAATTATATAA
2236747 AAATAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 5 0.15
24 2 0.06
25 15 0.44
26 12 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTTTAATTATATAATATTATATA
Found at i:2236762 original size:21 final size:22
Alignment explanation
Indices: 2236738--2236779 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2236728 TATAATTTTT
2236738 ATCATAT-AAAAATAAATATAC
1 ATCATATAAAAAATAAATATAC
*
2236759 ATCATGTAAAAAATAAATATA
1 ATCATATAAAAAATAAATATA
2236780 TAATATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (22 bp):
ATCATATAAAAAATAAATATAC
Found at i:2239418 original size:23 final size:23
Alignment explanation
Indices: 2239392--2239445 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
2239382 TTCATACCTA
*
2239392 ATAATATTT-TTATTTTTTATTTT
1 ATAA-ATTTATTATATTTTATTTT
*
2239415 ATAAATTTATTGTATTTTA-TTT
1 ATAAATTTATTATATTTTATTTT
2239437 -TAAATTTAT
1 ATAAATTTAT
2239446 AATCATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.32
22 7 0.25
23 12 0.43
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
ATAAATTTATTATATTTTATTTT
Found at i:2240022 original size:2 final size:2
Alignment explanation
Indices: 2240015--2240049 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
2240005 GCGGTGCATG
2240015 TA TA TA TA TA TA TA TA TA TA TA CTA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
2240050 GCGATGACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2240510 original size:13 final size:13
Alignment explanation
Indices: 2240417--2240528 Score: 69
Period size: 13 Copynumber: 8.7 Consensus size: 13
2240407 TTTATTTATA
2240417 AATATA-ATA-TT
1 AATATATATATTT
2240428 AATATATATGATTCT
1 AATATATAT-ATT-T
2240443 -ATA-ATATATTAT
1 AATATATATATT-T
*
2240455 ACATATTTATA-TT
1 A-ATATATATATTT
* *
2240468 AAAAGTATATATAT
1 AATA-TATATATTT
*
2240482 AATATA-ATATAT
1 AATATATATATTT
2240494 -ATATATGAT-TTT
1 AATATAT-ATATTT
2240506 AATATATATATTT
1 AATATATATATTT
2240519 AAGTATATAT
1 AA-TATATAT
2240529 TAAAAATATA
Statistics
Matches: 80, Mismatches: 7, Indels: 25
0.71 0.06 0.22
Matches are distributed among these distances:
11 11 0.14
12 18 0.22
13 27 0.34
14 19 0.24
15 5 0.06
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (13 bp):
AATATATATATTT
Found at i:2240514 original size:37 final size:37
Alignment explanation
Indices: 2240442--2240525 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 37
2240432 TATATGATTC
* *
2240442 TATAATATATTATACATATTTATATTAAAAGTATATA
1 TATAATATAATATACATATTGATATTAAAAGTATATA
* * *
2240479 TATAATATAATATATATATATGATTTTAATA-TATATA
1 TATAATATAATATACATAT-TGATATTAAAAGTATATA
*
2240516 TTTAAGTATA
1 TATAA-TATA
2240526 TATTAAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
37 27 0.69
38 12 0.31
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TATAATATAATATACATATTGATATTAAAAGTATATA
Found at i:2240525 original size:14 final size:15
Alignment explanation
Indices: 2240492--2240528 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2240482 AATATAATAT
2240492 ATATATATGATTTTA
1 ATATATATGATTTTA
2240507 ATATATAT-A-TTTA
1 ATATATATGATTTTA
2240520 AGTATATAT
1 A-TATATAT
2240529 TAAAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 8 0.38
15 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
ATATATATGATTTTA
Found at i:2241106 original size:15 final size:15
Alignment explanation
Indices: 2241069--2241106 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2241059 TCGAGTTTAA
2241069 ATCATTTTGGATTCG
1 ATCATTTTGGATTCG
2241084 AGTCATTTT-GAGTTCG
1 A-TCATTTTGGA-TTCG
2241100 ATCATTT
1 ATCATTT
2241107 CGAATTTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.47
Consensus pattern (15 bp):
ATCATTTTGGATTCG
Found at i:2241205 original size:31 final size:31
Alignment explanation
Indices: 2241170--2241229 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
2241160 ATCAATTGGG
2241170 TTTAACATTCGAGTTAAATCAAATTCAAGGA
1 TTTAACATTCGAGTTAAATCAAATTCAAGGA
2241201 TTTAACATTCGAGTTAAATCAAATTCAAG
1 TTTAACATTCGAGTTAAATCAAATTCAAG
2241230 TTATTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (31 bp):
TTTAACATTCGAGTTAAATCAAATTCAAGGA
Found at i:2241981 original size:16 final size:16
Alignment explanation
Indices: 2241960--2242008 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
2241950 TAATTATCTG
2241960 GATCATTTTGAGTTCA
1 GATCATTTTGAGTTCA
2241976 GATCATTTTGAGTTC-
1 GATCATTTTGAGTTCA
* *
2241991 GAATTATTTCGAGTTCA
1 G-ATCATTTTGAGTTCA
2242008 G
1 G
2242009 GTTATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.43
Consensus pattern (16 bp):
GATCATTTTGAGTTCA
Found at i:2242391 original size:22 final size:23
Alignment explanation
Indices: 2242340--2242394 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
2242330 TTTATATGCT
*
2242340 TAAATT-ATTATTAAAGATATTA
1 TAAATTAAATATTAAAGATATTA
* *
2242362 AAATATTAAATATTAAATAT-TTA
1 TAA-ATTAAATATTAAAGATATTA
2242385 TAAATTAAAT
1 TAAATTAAAT
2242395 CGAATTATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 9 0.33
23 8 0.30
24 10 0.37
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAATTAAATATTAAAGATATTA
Found at i:2242489 original size:19 final size:18
Alignment explanation
Indices: 2242457--2242492 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2242447 TTTAATTTAT
*
2242457 AAATTTAAATTATTATTA
1 AAATTTAAAATATTATTA
2242475 AAATATTAAAATATTATT
1 AAAT-TTAAAATATTATT
2242493 TTTATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTTAAAATATTATTA
Found at i:2243052 original size:29 final size:30
Alignment explanation
Indices: 2242988--2243052 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
2242978 TTTGATAATT
* *
2242988 TTAA-ATAAAATATAAATATAATATATTTA
1 TTAATATAAAATATAAATATAATAAATTAA
2243017 TTAAATATAAAA-AT-AATATAATAAATATAA
1 TT-AATATAAAATATAAATATAATAAAT-TAA
2243047 TTAATA
1 TTAATA
2243053 CAATTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
29 17 0.55
30 8 0.26
31 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
TTAATATAAAATATAAATATAATAAATTAA
Found at i:2243507 original size:2 final size:2
Alignment explanation
Indices: 2243500--2243528 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2243490 AGAAATATTC
2243500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2243529 ATAGAACTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2243768 original size:10 final size:11
Alignment explanation
Indices: 2243748--2243779 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
2243738 TTAATTGACG
2243748 AAAA-TATAAT
1 AAAATTATAAT
2243758 AAAATTA-AAT
1 AAAATTATAAT
2243768 AAAATTATAAT
1 AAAATTATAAT
2243779 A
1 A
2243780 CAAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATTATAAT
Found at i:2243788 original size:21 final size:21
Alignment explanation
Indices: 2243748--2243793 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
2243738 TTAATTGACG
*
2243748 AAAA-TATAATAAAATTAAAT
1 AAAATTATAATAAAATAAAAT
2243768 AAAATTATAATACAAA-AAAAT
1 AAAATTATAATA-AAATAAAAT
*
2243789 TAAAT
1 AAAAT
2243794 AAAGATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 4 0.18
21 15 0.68
22 3 0.14
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATTATAATAAAATAAAAT
Found at i:2245463 original size:14 final size:14
Alignment explanation
Indices: 2245446--2245490 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
2245436 TTTTTATAAT
2245446 TTAATTAAATTTAA
1 TTAATTAAATTTAA
*
2245460 TTAATTAAAATTT-T
1 TTAATT-AAATTTAA
*
2245474 TTATTTAAATTTAA
1 TTAATTAAATTTAA
2245488 TTA
1 TTA
2245491 TAAAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 6 0.23
14 14 0.54
15 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAATTAAATTTAA
Found at i:2245491 original size:14 final size:14
Alignment explanation
Indices: 2245450--2245491 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
2245440 TATAATTTAA
2245450 TTAAATTTAATTAAT
1 TTAAATTTAATT-AT
* *
2245465 TAAAATTT-TTTAT
1 TTAAATTTAATTAT
2245478 TTAAATTTAATTAT
1 TTAAATTTAATTAT
2245492 AAAATATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 9 0.41
14 6 0.27
15 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATTTAATTAT
Found at i:2245500 original size:28 final size:28
Alignment explanation
Indices: 2245445--2245500 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2245435 ATTTTTATAA
*
2245445 TTTAATTAAATTTAATTAATTAAAATTT
1 TTTAATTAAATTTAATTAATAAAAATTT
*
2245473 TTTATTTAAATTTAATT-ATAAAATATTT
1 TTTAATTAAATTTAATTAATAAAA-ATTT
2245501 ATAAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TTTAATTAAATTTAATTAATAAAAATTT
Found at i:2245505 original size:23 final size:23
Alignment explanation
Indices: 2245451--2245543 Score: 64
Period size: 23 Copynumber: 3.8 Consensus size: 23
2245441 ATAATTTAAT
*
2245451 TAAATTTAATTAATTAAAATTTTTTA
1 TAAATTTAATT-A-TAAAA-TATTTA
2245477 TTTAAATTTAATTATAAAATATTTA
1 --TAAATTTAATTATAAAATATTTA
* *
2245502 TAAAATTAATT-TAAAA-ATTAA
1 TAAATTTAATTATAAAATATTTA
* *
2245523 TATATTTTAAATAATAAAATA
1 TA-AATTT-AATTATAAAATA
2245544 AAATTTTACA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
21 6 0.11
22 8 0.15
23 13 0.24
24 5 0.09
25 6 0.11
26 5 0.09
27 1 0.02
28 11 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATTTAATTATAAAATATTTA
Found at i:2245520 original size:12 final size:13
Alignment explanation
Indices: 2245479--2245523 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
2245469 ATTTTTTATT
*
2245479 TAAATTTAA-TTA
1 TAAAATTAATTTA
2245491 TAAAA-T-ATTTA
1 TAAAATTAATTTA
2245502 TAAAATTAATTTA
1 TAAAATTAATTTA
2245515 -AAAATTAAT
1 TAAAATTAAT
2245524 ATATTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 1 0.03
11 9 0.31
12 14 0.48
13 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAAATTAATTTA
Found at i:2247004 original size:20 final size:20
Alignment explanation
Indices: 2246979--2247020 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2246969 CTCAATGGCT
* * *
2246979 AAAAAATAAAAGAAAGTAAA
1 AAAAAAAAAAAAAAACTAAA
2246999 AAAAAAAAAAAAAAACTAAA
1 AAAAAAAAAAAAAAACTAAA
2247019 AA
1 AA
2247021 TGAAAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.86, C:0.02, G:0.05, T:0.07
Consensus pattern (20 bp):
AAAAAAAAAAAAAAACTAAA
Found at i:2248467 original size:23 final size:22
Alignment explanation
Indices: 2248441--2248489 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
2248431 TTTTATAAAA
2248441 TTTTA-AAATGATTATTTAATATT
1 TTTTATAAATGATTATTT--TATT
*
2248464 TTTTATTAGATGATTATTTTATT
1 TTTTA-TAAATGATTATTTTATT
2248487 TTT
1 TTT
2248490 GAGTAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 12 0.52
25 11 0.48
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (22 bp):
TTTTATAAATGATTATTTTATT
Found at i:2248974 original size:32 final size:32
Alignment explanation
Indices: 2248892--2248975 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 32
2248882 TTTTAGATAA
2248892 AAATT-TTATAAATT-TAAATTTATTTAATTT
1 AAATTATTATAAATTATAAATTTATTTAATTT
* * *
2248922 AAATTACATT-TTAATAATAAATTT-TTTTATTT
1 AAATT--ATTATAAATTATAAATTTATTTAATTT
2248954 AAATTATTATAAATTTATAAAT
1 AAATTATTATAAA-TTATAAAT
2248976 ATTAATATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
30 8 0.19
31 3 0.07
32 23 0.53
33 9 0.21
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (32 bp):
AAATTATTATAAATTATAAATTTATTTAATTT
Found at i:2249585 original size:19 final size:20
Alignment explanation
Indices: 2249555--2249607 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
2249545 AAATTGATAA
2249555 ATAAAA-ATAAATAT-AAAT
1 ATAAAATATAAATATAAAAT
2249573 ATAAAATATAAATATAAAAT
1 ATAAAATATAAATATAAAAT
*
2249593 ATTTAAATATAAATA
1 A-TAAAATATAAATA
2249608 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 6 0.19
19 8 0.26
20 5 0.16
21 12 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAAAATATAAATATAAAAT
Found at i:2249594 original size:13 final size:13
Alignment explanation
Indices: 2249563--2249605 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
2249553 AAATAAAAAT
2249563 AAATATAAATATA
1 AAATATAAATATA
2249576 AAATATAAATATA
1 AAATATAAATATA
2249589 AAATATTTAAATATA
1 AAATA--TAAATATA
2249604 AA
1 AA
2249606 TAATATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 18 0.64
15 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATATAAATATA
Found at i:2249605 original size:6 final size:6
Alignment explanation
Indices: 2249551--2249607 Score: 64
Period size: 6 Copynumber: 9.2 Consensus size: 6
2249541 ATAAAAATTG
2249551 ATAAAT A-AAA- ATAAAT ATAAAT ATAAAAT ATAAAT ATAAAAT ATTTAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT AT-AAAT ATAAAT AT-AAAT A--TAAAT
2249601 ATAAAT A
1 ATAAAT A
2249608 ATATTTTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 1 0.02
5 6 0.13
6 21 0.47
7 11 0.24
8 5 0.11
9 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAAAT
Found at i:2249608 original size:19 final size:19
Alignment explanation
Indices: 2249556--2249621 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
2249546 AATTGATAAA
*
2249556 TAAAAATAAATATAAATA-T
1 TAAATATAAATA-AAATATT
*
2249575 AAAATATAAATATAAAATATT
1 TAAATAT-AA-ATAAAATATT
*
2249596 TAAATATAAATAATAT-TT
1 TAAATATAAATAAAATATT
2249614 TAAATATA
1 TAAATATA
2249622 TATTATATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 10 0.25
19 11 0.28
20 9 0.22
21 10 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATAAATAAAATATT
Found at i:2249617 original size:18 final size:18
Alignment explanation
Indices: 2249562--2249633 Score: 69
Period size: 18 Copynumber: 4.1 Consensus size: 18
2249552 TAAATAAAAA
* * *
2249562 TAAATATAAATATAAAATA
1 TAAATATAAATA-ATATTT
2249581 TAAATAT-AA-AATA-TT
1 TAAATATAAATAATATTT
2249596 TAAATATAAATAATATTT
1 TAAATATAAATAATATTT
* *
2249614 TAAATATATATTATATTT
1 TAAATATAAATAATATTT
2249632 TA
1 TA
2249634 TTTAAAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
15 8 0.17
16 4 0.09
17 5 0.11
18 22 0.48
19 7 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATATAAATAATATTT
Found at i:2249637 original size:22 final size:22
Alignment explanation
Indices: 2249609--2249653 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2249599 ATATAAATAA
*
2249609 TATTTTAAATATATATTATATTT
1 TATTTAAAAT-TATATTATATTT
*
2249632 TATTTAAAATTTTATTATATTT
1 TATTTAAAATTATATTATATTT
2249654 AATAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTAAAATTATATTATATTT
Found at i:2249652 original size:17 final size:18
Alignment explanation
Indices: 2249627--2249661 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2249617 ATATATATTA
*
2249627 TATTTTATTTAA-AATTT
1 TATTATATTTAATAATTT
2249644 TATTATATTTAATAATTT
1 TATTATATTTAATAATTT
2249662 ATAACGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTATATTTAATAATTT
Found at i:2253947 original size:3 final size:3
Alignment explanation
Indices: 2253941--2253984 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
2253931 ACCACCACCC
* * * *
2253941 CCT CCT CCT TCT TCT CCT CCT CCG CCT TCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CC
2253985 CCCACCCCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.61, G:0.02, T:0.36
Consensus pattern (3 bp):
CCT
Found at i:2253961 original size:15 final size:15
Alignment explanation
Indices: 2253941--2253982 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
2253931 ACCACCACCC
*
2253941 CCTCCTCCTTCTTCT
1 CCTCCTCCTCCTTCT
*
2253956 CCTCCTCCGCCTTCT
1 CCTCCTCCTCCTTCT
2253971 CCTCCTCCTCCT
1 CCTCCTCCTCCT
2253983 CCCCCACCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.00, C:0.60, G:0.02, T:0.38
Consensus pattern (15 bp):
CCTCCTCCTCCTTCT
Found at i:2253968 original size:18 final size:18
Alignment explanation
Indices: 2253941--2253981 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2253931 ACCACCACCC
* *
2253941 CCTCCTCCTTCTTCTCCT
1 CCTCCGCCTTCTCCTCCT
2253959 CCTCCGCCTTCTCCTCCT
1 CCTCCGCCTTCTCCTCCT
2253977 CCTCC
1 CCTCC
2253982 TCCCCCACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.61, G:0.02, T:0.37
Consensus pattern (18 bp):
CCTCCGCCTTCTCCTCCT
Found at i:2259036 original size:78 final size:78
Alignment explanation
Indices: 2258791--2259046 Score: 202
Period size: 78 Copynumber: 3.2 Consensus size: 78
2258781 GTTACCGATC
* *
2258791 TTATATAATTTATTTATAATATATATAAAAATGAATGTGGAAAATTTTTAAGTTAATCCAAATAC
1 TTATATAATTAATTTATAATATATATAAAAATGAATGTGAAAAATTTTTAAGTTAATCCAAATAC
2258856 TTATTGTTGTTTA
66 TTATTGTTGTTTA
* * * * * * * *
2258869 TTATATAATTAATTT-T--TCTTTTTAAAATTTTTTTATTGTTAATAAGATTTTATCACA-TTTA
1 TTATATAATTAATTTATAATATATATAAAA----ATGAATGTGAA-AA-ATTTT-T-A-AGTTAA
* * *
2258930 TCAATAAATA-TT-TTGTTACCG-ATC
57 TC--CAAATACTTATTGTT---GTTTA
* *
2258954 TTATATAATTTATTTATAATATATATAAAAATGAATGTGAAAAATTTTTGAGTTAATCCAAATAC
1 TTATATAATTAATTTATAATATATATAAAAATGAATGTGAAAAATTTTTAAGTTAATCCAAATAC
2259019 TTATTGTTGTTTA
66 TTATTGTTGTTTA
2259032 TTATATAATTAATTT
1 TTATATAATTAATTT
2259047 TTCTTTTTAA
Statistics
Matches: 130, Mismatches: 27, Indels: 42
0.65 0.14 0.21
Matches are distributed among these distances:
75 8 0.06
77 2 0.02
78 34 0.26
79 9 0.07
80 12 0.09
81 6 0.05
82 6 0.05
83 13 0.10
84 10 0.08
85 20 0.15
86 2 0.02
88 8 0.06
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (78 bp):
TTATATAATTAATTTATAATATATATAAAAATGAATGTGAAAAATTTTTAAGTTAATCCAAATAC
TTATTGTTGTTTA
Found at i:2259048 original size:163 final size:163
Alignment explanation
Indices: 2258778--2259106 Score: 622
Period size: 163 Copynumber: 2.0 Consensus size: 163
2258768 TGCGTTATAA
*
2258778 TTTGTTACCGATCTTATATAATTTATTTATAATATATATAAAAATGAATGTGGAAAATTTTTAAG
1 TTTGTTACCGATCTTATATAATTTATTTATAATATATATAAAAATGAATGTGAAAAATTTTTAAG
*
2258843 TTAATCCAAATACTTATTGTTGTTTATTATATAATTAATTTTTCTTTTTAAAATTTTTTTATTGT
66 TTAATCCAAATACTTATTGTTGTTTATTATATAATTAATTTTTCTTTTTAAAATTTTTCTATTGT
2258908 TAATAAGATTTTATCACATTTATCAATAAATAT
131 TAATAAGATTTTATCACATTTATCAATAAATAT
*
2258941 TTTGTTACCGATCTTATATAATTTATTTATAATATATATAAAAATGAATGTGAAAAATTTTTGAG
1 TTTGTTACCGATCTTATATAATTTATTTATAATATATATAAAAATGAATGTGAAAAATTTTTAAG
2259006 TTAATCCAAATACTTATTGTTGTTTATTATATAATTAATTTTTCTTTTTAAAATTTTTCTATTGT
66 TTAATCCAAATACTTATTGTTGTTTATTATATAATTAATTTTTCTTTTTAAAATTTTTCTATTGT
*
2259071 TAGTAAGATTTTATCACATTTATCAATAAATAT
131 TAATAAGATTTTATCACATTTATCAATAAATAT
2259104 TTT
1 TTT
2259107 AATTTTATTG
Statistics
Matches: 162, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.50
Consensus pattern (163 bp):
TTTGTTACCGATCTTATATAATTTATTTATAATATATATAAAAATGAATGTGAAAAATTTTTAAG
TTAATCCAAATACTTATTGTTGTTTATTATATAATTAATTTTTCTTTTTAAAATTTTTCTATTGT
TAATAAGATTTTATCACATTTATCAATAAATAT
Found at i:2262185 original size:33 final size:31
Alignment explanation
Indices: 2262105--2262168 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
2262095 ATAATTAAAT
* * *
2262105 TTAA-AATATTATATATATAAATTTTGATATA
1 TTAATAATAATAT-TATATAAATTTTAACATA
2262136 TTAATAATAATATTATATAAATTTTAACATA
1 TTAATAATAATATTATATAAATTTTAACATA
2262167 TT
1 TT
2262169 TATACATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (31 bp):
TTAATAATAATATTATATAAATTTTAACATA
Found at i:2262330 original size:24 final size:24
Alignment explanation
Indices: 2262303--2262366 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
2262293 AAATTTTAAC
2262303 ATATTTTTTATTTATATCATATTT
1 ATATTTTTTATTTATATCATATTT
**
2262327 ATATTATTTT-TTTATATTTTATTT
1 ATATT-TTTTATTTATATCATATTT
2262351 -TAATTTTTTATATTAT
1 AT-ATTTTTTAT-TTAT
2262367 GTTTGTATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 5 0.15
24 21 0.62
25 8 0.24
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (24 bp):
ATATTTTTTATTTATATCATATTT
Found at i:2262347 original size:20 final size:20
Alignment explanation
Indices: 2262324--2262364 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2262314 TTATATCATA
*
2262324 TTTATATTATTTTTTTATAT
1 TTTATATTAATTTTTTATAT
*
2262344 TTTATTTTAATTTTTTATAT
1 TTTATATTAATTTTTTATAT
2262364 T
1 T
2262365 ATGTTTGTAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATATTAATTTTTTATAT
Found at i:2262983 original size:19 final size:19
Alignment explanation
Indices: 2262961--2263007 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
2262951 TGTCACGTAA
*
2262961 TAATTTATTA-ATTTTTAT
1 TAATTTATTATATTTATAT
*
2262979 GTAATTTTTTATATTTATAT
1 -TAATTTATTATATTTATAT
2262999 TATATTTAT
1 TA-ATTTAT
2263008 ATTATTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TAATTTATTATATTTATAT
Found at i:2263013 original size:9 final size:11
Alignment explanation
Indices: 2262987--2263012 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2262977 ATGTAATTTT
2262987 TTATATTTATA
1 TTATATTTATA
2262998 TTATATTTATA
1 TTATATTTATA
2263009 TTAT
1 TTAT
2263013 TTTTGATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATATTTATA
Found at i:2267948 original size:2 final size:2
Alignment explanation
Indices: 2267941--2267970 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2267931 ACATGTTAGT
2267941 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
2267971 ATCTTATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2269934 original size:2 final size:2
Alignment explanation
Indices: 2269927--2269962 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2269917 CACAAAATGA
2269927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2269963 GTACACTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2270136 original size:11 final size:11
Alignment explanation
Indices: 2270086--2270132 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
2270076 GTGATATAAA
2270086 ATAAATAAAAT
1 ATAAATAAAAT
*
2270097 ATAAATATAAT
1 ATAAATAAAAT
*
2270108 ATAAAAAATAAT
1 ATAAATAA-AAT
*
2270120 ATGAATAAAAT
1 ATAAATAAAAT
2270131 AT
1 AT
2270133 GAATTCATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
ATAAATAAAAT
Found at i:2270338 original size:18 final size:20
Alignment explanation
Indices: 2270317--2270358 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
2270307 ATGAATCCTG
2270317 ATAAT-ATTATTTTTG-AAT
1 ATAATCATTATTTTTGTAAT
* *
2270335 ATAATCTTTCTTTTTGTAAT
1 ATAATCATTATTTTTGTAAT
2270355 ATAA
1 ATAA
2270359 CTTATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 8 0.40
20 7 0.35
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
ATAATCATTATTTTTGTAAT
Found at i:2272560 original size:21 final size:22
Alignment explanation
Indices: 2272536--2272576 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2272526 CAATCCCTTA
2272536 ATAAAAA-TAAAAAAATTAAAT
1 ATAAAAACTAAAAAAATTAAAT
2272557 ATAAAAACTAAAAAAATTAA
1 ATAAAAACTAAAAAAATTAA
2272577 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (22 bp):
ATAAAAACTAAAAAAATTAAAT
Found at i:2278082 original size:52 final size:51
Alignment explanation
Indices: 2277997--2278120 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
2277987 ATATGAAAAG
* *
2277997 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
2278048 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
2278100 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
2278121 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:2278133 original size:51 final size:51
Alignment explanation
Indices: 2277997--2278140 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
2277987 ATATGAAAAG
*
2277997 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
2278049 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
2278100 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2278141 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:2278147 original size:13 final size:13
Alignment explanation
Indices: 2278129--2278153 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2278119 CAAAGATCAG
2278129 TGTATCGATACAA
1 TGTATCGATACAA
2278142 TGTATCGATACA
1 TGTATCGATACA
2278154 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2278231 original size:33 final size:33
Alignment explanation
Indices: 2278194--2278260 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2278184 AGTAGCTTAA
2278194 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2278227 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2278260 A
1 A
2278261 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2278234 original size:13 final size:13
Alignment explanation
Indices: 2278216--2278240 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2278206 CAAAAAAATA
2278216 TGTATCGATACAT
1 TGTATCGATACAT
2278229 TGTATCGATACA
1 TGTATCGATACA
2278241 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2279224 original size:22 final size:22
Alignment explanation
Indices: 2279199--2279267 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
2279189 ATGCTGATTC
2279199 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * *
2279221 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTATAT-TG--GACTTA
2279242 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
2279264 AAGG
1 AAGG
2279268 TGAAGGTGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:2279293 original size:49 final size:49
Alignment explanation
Indices: 2279075--2279557 Score: 640
Period size: 49 Copynumber: 9.8 Consensus size: 49
2279065 GTGATAAAGA
* * * *
2279075 TGCCAATATG-TCGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
1 TGCCAATATGCT-GATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG
* * *
2279129 ATGTCAATGTGCTGATTCAAGGCCAGCTACATT-GATCTTAAAGATGGAAAAGG
1 -TGCCAATATGCTGATTCAAGGCCAGCTATATTGGA-CTTAAAGAT-G--AAGG
2279182 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
2279225 TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
*
2279274 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
*
2279323 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
2279372 TGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
2279421 TGCCAATATGGTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
2279470 TGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
2279519 TGCCAATATGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
2279558 GAAGGGTTGC
Statistics
Matches: 387, Mismatches: 32, Indels: 24
0.87 0.07 0.05
Matches are distributed among these distances:
43 41 0.11
48 1 0.00
49 269 0.70
52 32 0.08
53 8 0.02
54 2 0.01
55 33 0.09
56 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
Found at i:2279694 original size:56 final size:57
Alignment explanation
Indices: 2279562--2279758 Score: 245
Period size: 56 Copynumber: 3.4 Consensus size: 57
2279552 GGCTTAGAAG
* * * * *
2279562 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTGAA
1 GGTTGCCACTGAC-T-TGTGGGCTTTTG-AAAGGTTGCCACTGACTTGTGGGCTTTTAAA
2279621 GGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTTAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTAAA
**
2279677 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAGGT-TGCCACTGACTTGTGGGCTTTT--AAA
* *
2279737 GGGTGCCACTAACTTGTGGGCT
1 GGTTGCCACTGACTTGTGGGCT
2279759 GAAAAAGAAA
Statistics
Matches: 124, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
55 21 0.17
56 31 0.25
57 14 0.11
58 23 0.19
59 12 0.10
60 23 0.19
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.32
Consensus pattern (57 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTAAA
Found at i:2279716 original size:30 final size:30
Alignment explanation
Indices: 2279578--2279979 Score: 308
Period size: 30 Copynumber: 13.5 Consensus size: 30
2279568 CACCGACTTG
* * *
2279578 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
2279608 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
2279635 TGTGGGCTTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
2279663 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
2279691 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* *
2279721 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*** * * *
2279751 TGTGGGCTGAAAAAGAAAAAGAGTGCTA-TAGAGT
1 TGTGGGCT---TTTGAAAAGGA-TGCCACT-GACT
* ** * * *
2279785 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT----TTGAAAAGGA-TGCCACTGACT
* * *
2279820 TGTGGACTTTGGAAAA-GATGCCACCGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
** * *
2279849 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
2279879 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
2279906 TGTGGGCTTTTGAAAAGAATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
2279936 TGTGGGC-TTTGAAAAAAAATGCCACTGACT
1 TGTGGGCTTTTG-AAAAGGATGCCACTGACT
*
2279966 TGTGGACTTTTGAA
1 TGTGGGCTTTTGAA
2279980 GGGTGATGAA
Statistics
Matches: 311, Mismatches: 41, Indels: 40
0.79 0.10 0.10
Matches are distributed among these distances:
27 42 0.14
28 62 0.20
29 32 0.10
30 120 0.39
31 9 0.03
33 7 0.02
34 13 0.04
35 26 0.08
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (30 bp):
TGTGGGCTTTTGAAAAGGATGCCACTGACT
Found at i:2279921 original size:57 final size:57
Alignment explanation
Indices: 2279624--2279949 Score: 190
Period size: 57 Copynumber: 5.4 Consensus size: 57
2279614 CTTTGAAGGT
* * * **
2279624 TGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTT--TTAAAG-G
1 TGCCACTGACTTGTGGGC-TTTGAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGAG
* * ** *
2279679 TTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGG
1 -TGCCACTGACTTGTGGGC-TTTG--AAAGATGCCACCGACTTGTGGGCTTCGGAAAAGAG
* ** * ** * * *
2279740 TGCCACTAACTTGTGGGCTGAAAAAGAAAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGAAAA
1 TGCCACTGACTTGTGGGCT----TTG--AAAGA-TGCCACCGACTTGTGGGCTT-C----GGAAA
2279805 AGAG
54 AGAG
* * * *
2279809 TGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTT-G-AAAGATGCCACCGACTTGTGGGCTTCGGAAAAGAG
* * * * ** *
2279868 TGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGAA
1 TGCCACTGACTTGTGGGCTTTGAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGAG
2279925 TGCCACTGACTTGTGGGCTTTGAAA
1 TGCCACTGACTTGTGGGCTTTGAAA
2279950 AAAAATGCCA
Statistics
Matches: 211, Mismatches: 43, Indels: 31
0.74 0.15 0.11
Matches are distributed among these distances:
56 23 0.11
57 51 0.24
58 23 0.11
59 26 0.12
60 21 0.10
61 1 0.00
63 8 0.04
64 30 0.14
65 6 0.03
66 1 0.00
69 21 0.10
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (57 bp):
TGCCACTGACTTGTGGGCTTTGAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGAG
Found at i:2279959 original size:87 final size:87
Alignment explanation
Indices: 2279809--2279981 Score: 222
Period size: 87 Copynumber: 2.0 Consensus size: 87
2279799 AGAAAAAGAG
* * ***
2279809 TGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCAC
1 TGCCACGGACTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAAAAAAAATGCCAC
* *
2279874 TGATTTGTGGGC-TTTGAAGGT
66 TGACTTGTGGACTTTTGAAGGT
* * * * *
2279895 TGCCACTGACTTGTGGGCTTTTGAAAAGAATGCCACTGACTTGTGGGCTTTGAAAAAAAATGCCA
1 TGCCACGGACTTGTGGACTTTGGAAAAG-ATGCCACCGACTTGTGGGCTTCGAAAAAAAATGCCA
2279960 CTGACTTGTGGACTTTTGAAGG
65 CTGACTTGTGGACTTTTGAAGG
2279982 GTGATGAATG
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
86 24 0.33
87 41 0.56
88 8 0.11
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (87 bp):
TGCCACGGACTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAAAAAAAATGCCAC
TGACTTGTGGACTTTTGAAGGT
Found at i:2280888 original size:3 final size:3
Alignment explanation
Indices: 2280880--2280968 Score: 124
Period size: 3 Copynumber: 29.7 Consensus size: 3
2280870 AAATTAAGCT
*
2280880 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TTA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
* * * * *
2280928 TCA TCA TCA TCA TCG TCA TCG TCA TCG TGA ACA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
2280969 GAGCTGTCCA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.30, C:0.31, G:0.04, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:2282986 original size:18 final size:18
Alignment explanation
Indices: 2282943--2282980 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2282933 CAAATAAATG
* *
2282943 ATCATCATTTTCATCATC
1 ATCATCATATTCATAATC
2282961 ATCATCATATTCATAATC
1 ATCATCATATTCATAATC
2282979 AT
1 AT
2282981 ATTCATCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (18 bp):
ATCATCATATTCATAATC
Found at i:2291307 original size:43 final size:42
Alignment explanation
Indices: 2291252--2291363 Score: 129
Period size: 42 Copynumber: 2.6 Consensus size: 42
2291242 GAACGCCACG
* **
2291252 AAATTTTATAGTTTAGTGGCGTTTTCATT-GTTTAAACG-TCGCT
1 AAATTTTATAGTTTAGTGGCATTTT--TTAGCATAAACGCTC-CT
*
2291295 AAATTTTATAGTTTAATGGCATTTTTTAGCATAAACGCTCCT
1 AAATTTTATAGTTTAGTGGCATTTTTTAGCATAAACGCTCCT
* *
2291337 AAATTTTATAATTTAGCGGCATTTTTT
1 AAATTTTATAGTTTAGTGGCATTTTTT
2291364 TTAAAACGCT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.03
42 33 0.55
43 25 0.42
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (42 bp):
AAATTTTATAGTTTAGTGGCATTTTTTAGCATAAACGCTCCT
Found at i:2291981 original size:12 final size:10
Alignment explanation
Indices: 2291955--2292006 Score: 59
Period size: 10 Copynumber: 4.9 Consensus size: 10
2291945 GTTGCTCATA
2291955 TCTTCTTCTT
1 TCTTCTTCTT
2291965 TCTTCTTCTCT
1 TCTTCTTCT-T
*
2291976 TGCTTCTTCATA
1 T-CTTCTTC-TT
*
2291988 TCTTCGTCTT
1 TCTTCTTCTT
2291998 TCTTCTTCT
1 TCTTCTTCT
2292007 CTTACTTCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 18 0.51
11 8 0.23
12 8 0.23
13 1 0.03
ACGTcount: A:0.04, C:0.31, G:0.04, T:0.62
Consensus pattern (10 bp):
TCTTCTTCTT
Found at i:2291987 original size:33 final size:33
Alignment explanation
Indices: 2291950--2292014 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
2291940 TTGAAGTTGC
* *
2291950 TCATATCTTCTTCTTTCTTCTTCTCTTGCTTCT
1 TCATATCTTCGTCTTTCTTCTTCTCTTACTTCT
2291983 TCATATCTTCGTCTTTCTTCTTCTCTTACTTC
1 TCATATCTTCGTCTTTCTTCTTCTCTTACTTC
2292015 CTCTAACCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.08, C:0.31, G:0.03, T:0.58
Consensus pattern (33 bp):
TCATATCTTCGTCTTTCTTCTTCTCTTACTTCT
Found at i:2292009 original size:18 final size:18
Alignment explanation
Indices: 2291955--2292009 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
2291945 GTTGCTCATA
*
2291955 TCTTCTTCTTTCTTCTTC
1 TCTTCGTCTTTCTTCTTC
* *
2291973 TCTT-G-C-TTCTTCATA
1 TCTTCGTCTTTCTTCTTC
2291988 TCTTCGTCTTTCTTCTTC
1 TCTTCGTCTTTCTTCTTC
2292006 TCTT
1 TCTT
2292010 ACTTCCTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 11 0.38
16 2 0.07
17 1 0.03
18 15 0.52
ACGTcount: A:0.04, C:0.31, G:0.04, T:0.62
Consensus pattern (18 bp):
TCTTCGTCTTTCTTCTTC
Found at i:2295862 original size:19 final size:19
Alignment explanation
Indices: 2295819--2295873 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
2295809 TGCCAGTTTT
**
2295819 ATGTATCGATACAATTGCGC
1 ATGTATCGATACAA-TGAAC
2295839 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
* *
2295858 ATGTATTGATATAATG
1 ATGTATCGATACAATG
2295874 TATCGATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Done.