Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 52 of 182
Found at i:16214541 original size:20 final size:21
Alignment explanation
Indices: 16214503--16214543 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16214493 CCTAACCCCT
*
16214503 AACCCCTAAACCTTGAATCCC
1 AACCCCTAAACCATGAATCCC
*
16214524 AACCCTTAAACCAT-AATCCC
1 AACCCCTAAACCATGAATCCC
16214544 TAGTCCCTAA
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:0.37, C:0.41, G:0.02, T:0.20
Consensus pattern (21 bp):
AACCCCTAAACCATGAATCCC
Found at i:16215508 original size:41 final size:41
Alignment explanation
Indices: 16215437--16215634 Score: 240
Period size: 41 Copynumber: 4.8 Consensus size: 41
16215427 TAAAATGTCC
* *
16215437 TTAGCGGCGCTTTTCCGGAAAACGCCGCTAAAGGCCAAAGCA
1 TTAGCGGCGCTTTTAC-AAAAACGCCGCTAAAGGCCAAAGCA
** *
16215479 TTAGCGATGCTTTTACAAAAACACCGCTAAAGGCCAAAGCA
1 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGGCCAAAGCA
* * *
16215520 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGCCCATAGAA
1 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGGCCAAAGCA
*
16215561 TTAGCGGCGCTTATT-CAAAAACGCCGCTAAA-GCCTACAGCA
1 TTAGCGGCGCTT-TTACAAAAACGCCGCTAAAGGCC-AAAGCA
*
16215602 TTAGCGGCGCTTCTTA-ATAAAACGCCACTAAAG
1 TTAGCGGCGCTT-TTACA-AAAACGCCGCTAAAG
16215635 ACCCGAAAGG
Statistics
Matches: 135, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
40 2 0.01
41 105 0.78
42 28 0.21
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGGCCAAAGCA
Found at i:16215758 original size:40 final size:39
Alignment explanation
Indices: 16215673--16215826 Score: 157
Period size: 40 Copynumber: 3.8 Consensus size: 39
16215663 GGGCTTTGGT
* ** *
16215673 TTTTTGCGGCGTTTTTTTTTAAAACCGCCGCTAATGGTTCT-
1 TTTTAGCGGCG-TTTTTAATAAAA-CGCCGCTAAT-GCTCTA
16215714 TTTTAGCGGCGTTTTTAATAAAACGCCGCTAATGCTCCTA
1 TTTTAGCGGCGTTTTTAATAAAACGCCGCTAATGCT-CTA
* * *
16215754 TTTTAGCGGCATTTTTAATAAAACGCCGCGAATGCTCGA
1 TTTTAGCGGCGTTTTTAATAAAACGCCGCTAATGCTCTA
* * *
16215793 TTTTTGCCGGCGTTTTTTATGAAAACGCCACTAA
1 TTTTAG-CGGCGTTTTTAAT-AAAACGCCGCTAA
16215827 AAGTGCCGCT
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 19 0.20
40 55 0.57
41 21 0.22
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (39 bp):
TTTTAGCGGCGTTTTTAATAAAACGCCGCTAATGCTCTA
Found at i:16216763 original size:42 final size:42
Alignment explanation
Indices: 16216705--16216823 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
16216695 GTTTACAAAC
*
16216705 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAATA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAATA
*
16216747 AAAAACGCCGCTAAAGACCATGTTCTTTAGTGGCGCTTAATA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAATA
* *
16216789 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
16216824 TTTTCTTCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAATA
Found at i:16216846 original size:84 final size:83
Alignment explanation
Indices: 16216710--16217081 Score: 368
Period size: 84 Copynumber: 4.4 Consensus size: 83
16216700 CAAACAAAAA
* * ** *** * * *
16216710 CGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCATGTTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTT
* * ** ** *
16216775 AGTGGCGCTTAATAAAAAA
65 AGCGGCGTTTTTTACTAAG
* * *
16216794 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTCTTCTAAGCGCCTCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTT-TTCTAAGCGCCGCTAAAGAACATGGTCTTT
*
16216859 AGCAGCG-TTTTTATCTAAG
65 AGCGGCGTTTTTTA-CTAAG
* * ** * *
16216878 CACCGCTAAAGAACATGTTCTTTCGCTACGTTTTTTATTAAGCGTCGCTAAAGAACATGGTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTT-CTAAGCGCCGCTAAAGAACATGGTCTTT
*
16216943 AGCGGCGTTTTTTTCTAAG
65 AGCGGCGTTTTTTACTAAG
* * ** * *
16216962 CACCACTAAAGAACATGGCCTTTAGCGGCGTTTTTTCTTAAGCTCCACTAAAGAACATGGTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTC-TAAGCGCCGCTAAAGAACATGGTCTTT
*
16217027 AGCGGCGTTTTTTTCTAAG
65 AGCGGCGTTTTTTACTAAG
*
16217046 CGCCGCTAAAGAACATGTTCTTTAGCAGCGTTTTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTT
16217082 TACAAAAAAC
Statistics
Matches: 239, Mismatches: 44, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
83 8 0.03
84 226 0.95
85 5 0.02
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (83 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTA
GCGGCGTTTTTTACTAAG
Found at i:16216887 original size:126 final size:126
Alignment explanation
Indices: 16216754--16217079 Score: 404
Period size: 126 Copynumber: 2.6 Consensus size: 126
16216744 ATAAAAAACG
* * ** * *
16216754 CCGCTAAAGACCATGTTCTTTAGTGGCGCTTAATAAAAAACGCCGCTAAAGAACATGGTCTTTAG
1 CCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTTAATAAGCGCCGCTAAAGAACATGGTCTTTAG
* * **
16216819 CGGCGTTTTCTTCTAAGCGCCTCTAAAGAACATGTTCTTTAGCAGCGTTTTTATC-TAAGCA
66 CGGCGTTTTCTTCTAAGCACCACTAAAGAACATGGCCTTTAGCAGCGTTTTT-TCTTAAGCA
* * * *
16216880 CCGCTAAAGAACATGTTCTTTCGCT-ACGTTTTTTATTAAGCGTCGCTAAAGAACATGGTCTTTA
1 CCGCTAAAGAACATGTTCTTTAG-TGGCGTTTTTTAATAAGCGCCGCTAAAGAACATGGTCTTTA
* * *
16216944 GCGGCGTTTTTTTCTAAGCACCACTAAAGAACATGGCCTTTAGCGGCGTTTTTTCTTAAGCT
65 GCGGCGTTTTCTTCTAAGCACCACTAAAGAACATGGCCTTTAGCAGCGTTTTTTCTTAAGCA
* * * ** *
16217006 CCACTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGTTCTTTAG
1 CCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTTAATAAGCGCCGCTAAAGAACATGGTCTTTAG
*
16217071 CAGCGTTTT
66 CGGCGTTTT
16217080 TTTACAAAAA
Statistics
Matches: 170, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
125 2 0.01
126 167 0.98
127 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (126 bp):
CCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTTAATAAGCGCCGCTAAAGAACATGGTCTTTAG
CGGCGTTTTCTTCTAAGCACCACTAAAGAACATGGCCTTTAGCAGCGTTTTTTCTTAAGCA
Found at i:16217082 original size:42 final size:42
Alignment explanation
Indices: 16216794--16217082 Score: 384
Period size: 42 Copynumber: 6.9 Consensus size: 42
16216784 TAATAAAAAA
*
16216794 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTCTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* * * *
16216836 CGCCTCTAAAGAACATGTTCTTTAGCAGCGTTTTTATCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* * * **
16216878 CACCGCTAAAGAACATGTTCTTTCGCTACGTTTTTTAT-TAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT-TCTAAG
*
16216920 CGTCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* * *
16216962 CACCACTAAAGAACATGGCCTTTAGCGGCG-TTTTTTCTTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTC-TAAG
* *
16217004 CTCCACTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* *
16217046 CGCCGCTAAAGAACATGTTCTTTAGCAGCGTTTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT
16217083 ACAAAAAACG
Statistics
Matches: 216, Mismatches: 27, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
41 8 0.04
42 200 0.93
43 8 0.04
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:16217448 original size:20 final size:21
Alignment explanation
Indices: 16217398--16217463 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
16217388 TTTTACTCTG
*
16217398 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
16217419 CTCCGCTTCCCTCGCT-CAGTC
1 CTCTGCTTCCCTCGCTGCAG-C
16217440 C-CTGCTTCCCTCGCTGTC-GC
1 CTCTGCTTCCCTCGCTG-CAGC
16217460 CTCT
1 CTCT
16217464 TCTTTAAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 18 0.47
21 19 0.50
22 1 0.03
ACGTcount: A:0.03, C:0.48, G:0.17, T:0.32
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:16219311 original size:9 final size:9
Alignment explanation
Indices: 16219297--16219330 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
16219287 TTATGTATTA
16219297 TGTAAGTAC
1 TGTAAGTAC
16219306 TGTAAGTAC
1 TGTAAGTAC
16219315 TGTAAGTTA-
1 TGTAAG-TAC
16219324 TGTAAGT
1 TGTAAGT
16219331 TACTTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 1 0.04
9 21 0.88
10 2 0.08
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (9 bp):
TGTAAGTAC
Found at i:16219326 original size:27 final size:27
Alignment explanation
Indices: 16219278--16219747 Score: 482
Period size: 27 Copynumber: 17.6 Consensus size: 27
16219268 TTAAAACGCC
16219278 AGTTATGT-A-TTATGT-A-TTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
16219301 AG-TACTGTAAG-TACTGTAAGTTATGTA
1 AGTTA-TGTAAGTTA-TGTAAGTTATGTA
*
16219328 AGTTACT-TAATTTATGTAAGTTATGTA
1 AGTTA-TGTAAGTTATGTAAGTTATGTA
* *
16219355 AGTTATGTAAGTTATTTAATTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
16219382 AGTTATGTAAGATAT-TTAGTTTATGTA
1 AGTTATGTAAGTTATGTAAG-TTATGTA
* *
16219409 ATTTATGTAAGTTATGTAAGTTATTTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
16219436 ATTTTTGTAAGTTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
16219463 AGTTATTTAATTTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* * *
16219490 AGATAT-TTAGTTTATGTAATTTATGTA
1 AGTTATGTAAG-TTATGTAAGTTATGTA
* * *
16219517 AGTTATGTAAGTTATTTAATTTTTGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
*
16219544 AGTTATGTAAGTTACT-TAATTTATGTA
1 AGTTATGTAAGTTA-TGTAAGTTATGTA
* *
16219571 AGTTATGTAAGTTATTTAAGTTATTTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* * *
16219598 ATTTATGTAAGTTATGTAAGATAT-TT
1 AGTTATGTAAGTTATGTAAGTTATGTA
*
16219624 AGTTTATGTAATTTATGTAAGTTATGTA
1 AG-TTATGTAAGTTATGTAAGTTATGTA
* * *
16219652 AGTTATTTAATTTTTGTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
16219679 AGTTACT-TAATTTTTGTAAGTTATGTA
1 AGTTA-TGTAAGTTATGTAAGTTATGTA
*
16219706 AGTTACT-TAATTTATGTAAGTTATGTA
1 AGTTA-TGTAAGTTATGTAAGTTATGTA
16219733 A-TTAATGTAAGTTAT
1 AGTT-ATGTAAGTTAT
16219748 TTAATTTGTG
Statistics
Matches: 387, Mismatches: 40, Indels: 36
0.84 0.09 0.08
Matches are distributed among these distances:
22 2 0.01
23 5 0.01
24 3 0.01
25 3 0.01
26 12 0.03
27 345 0.89
28 17 0.04
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.50
Consensus pattern (27 bp):
AGTTATGTAAGTTATGTAAGTTATGTA
Found at i:16219348 original size:36 final size:36
Alignment explanation
Indices: 16219278--16219747 Score: 469
Period size: 36 Copynumber: 13.2 Consensus size: 36
16219268 TTAAAACGCC
*
16219278 AGTTATGT-A-TTATGT-A-TTATGTAA-GTACTGTA
1 AGTTATGTAAGTTATGTAAGTTATGTAATTTA-TGTA
16219310 AG-TACTGTAAGTTATGTAAGTTACT-TAATTTATGTA
1 AGTTA-TGTAAGTTATGTAAGTTA-TGTAATTTATGTA
*
16219346 AGTTATGTAAGTTATGTAAGTTATTTAATTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTAATTTATGTA
* *
16219382 AGTTATGTAAGATAT-TTAGTTTATGTAATTTATGTA
1 AGTTATGTAAGTTATGTAAG-TTATGTAATTTATGTA
* * * *
16219418 AGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTAATTTATGTA
* * *
16219454 AGTTATGTAAGTTATTTAATTTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTAATTTATGTA
* * * *
16219490 AGATAT-TTAGTTTATGTAATTTATGTAAGTTATGTA
1 AGTTATGTAAG-TTATGTAAGTTATGTAATTTATGTA
* * * *
16219526 AGTTATTTAATTTTTGTAAGTTATGTAAGTTACT-TA
1 AGTTATGTAAGTTATGTAAGTTATGTAATTTA-TGTA
* * * *
16219562 ATTTATGTAAGTTATGTAAGTTATTTAAGTTATTTA
1 AGTTATGTAAGTTATGTAAGTTATGTAATTTATGTA
* * * *
16219598 ATTTATGTAAGTTATGTAAGATATTTAGTTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTAATTTATGTA
* * *
16219634 ATTTATGTAAGTTATGTAAGTTATTTAATTTTTGTA
1 AGTTATGTAAGTTATGTAAGTTATGTAATTTATGTA
* * *
16219670 AGTTATGTAAGTTACT-TAATTTTTGTAAGTTATGTA
1 AGTTATGTAAGTTA-TGTAAGTTATGTAATTTATGTA
* *
16219706 AGTTACT-TAATTTATGTAAGTTATGTAATTAATGTA
1 AGTTA-TGTAAGTTATGTAAGTTATGTAATTTATGTA
16219742 AGTTAT
1 AGTTAT
16219748 TTAATTTGTG
Statistics
Matches: 379, Mismatches: 41, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
31 2 0.01
32 5 0.01
33 1 0.00
34 6 0.02
35 11 0.03
36 342 0.90
37 12 0.03
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.50
Consensus pattern (36 bp):
AGTTATGTAAGTTATGTAAGTTATGTAATTTATGTA
Found at i:16219754 original size:63 final size:62
Alignment explanation
Indices: 16219315--16219754 Score: 612
Period size: 63 Copynumber: 7.0 Consensus size: 62
16219305 CTGTAAGTAC
* * *
16219315 TGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTA-TTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* * * *
16219378 TGTAAGTTATGTAAGATATTTAGTTTATGTAATTTATGTAAGTTATGTAAGTTATTTAATTTT
1 TGTAAGTTATGTAAGTTATTAAG-TTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* *
16219441 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGATATTTAGTTTA
1 TGTAAGTTATGTAAGTTAT-TAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* * *
16219504 TGTAATTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTACTTAATTTA
1 TGTAAGTTATGTAAGTTAT-TAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* *
16219567 TGTAAGTTATGTAAGTTATTTAAGTTATTTAATTTATGTAAGTTATGTAAGATATTTAGTTTA
1 TGTAAGTTATGTAAGTTA-TTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* * * *
16219630 TGTAATTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTACTTAATTTT
1 TGTAAGTTATGTAAGTTAT-TAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
* * *
16219693 TGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAA-TTAATGTAAGTTATTTAATTT
1 TGTAAGTTATGTAAGTTA-TTAAGTTATTTAATTTATGTAAGTT-ATGTAAGTTATTTAATTT
16219755 GTGAACCCTA
Statistics
Matches: 338, Mismatches: 33, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
62 6 0.02
63 327 0.97
64 5 0.01
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.51
Consensus pattern (62 bp):
TGTAAGTTATGTAAGTTATTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA
Found at i:16223237 original size:14 final size:15
Alignment explanation
Indices: 16223206--16223240 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
16223196 TTTGACCCCA
*
16223206 AAATCCCTAAACCTT
1 AAATCCCTAAACCCT
16223221 AAATCCC-AAACCCT
1 AAATCCCTAAACCCT
16223235 AAATCC
1 AAATCC
16223241 ATACAAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATCCCTAAACCCT
Found at i:16224669 original size:113 final size:112
Alignment explanation
Indices: 16224154--16224693 Score: 412
Period size: 115 Copynumber: 4.7 Consensus size: 112
16224144 ATGCATGGTT
* * * * *
16224154 AAGACCAAAACTTTACGTTTTGGTTAAGATATTTTCCGGCGCTTCTCAAAAAGTGCCACTAATAC
1 AAGA-CAAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCAAAAA-CGCCGCTAATAC
* * * * * *
16224219 TATACTTTAGTGGCGATTTCTC-GT-GGACGCCACTAATTCCATTATACATC
64 TATGCTTTAGCGGCG-TTTCCCTATATG-CGCCACTAATTCTA-TATACATC
* * * * * * *
16224269 AAGACTTAAACACTGCATTTTTGTTAATATATTTTGCGGCGCTTCTCAAAAAGCACCGCTAATAA
1 AAGAC-AAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCAAAAA-CGCCGCTAATAC
* * *
16224334 TATGCTTTAGCGGCG-TTCCCGTATAAGCGCCACTAAGTCTAATATACCTC
64 TATGCTTTAGCGGCGTTTCCC-TATATGCGCCACTAATTCT-ATATACATC
* * * * * *
16224384 ATGAAAAAACTCTGCGTTTTGG-TGAGCATATTTTGCGGCGCTTTTTGC-CAAGCGCCGCTAATA
1 AAGACAAAACTCTGCGTTTTGGTTAAG-ATATTTTGCGGCGC-TTCT-CAAAAACGCCGCTAATA
* * * * *** *
16224447 CTATGATGTAGCAGTGTTTTTTTAATATGCGCCACTAATAACTATATACATC
63 CTATGCTTTAGCGGCGTTTCCCT-ATATGCGCCACTAAT-TCTATATACATC
* ** * * ** *
16224499 GAGACAAAAACGT-TGCGTTTTGGTTACCAAATTTTGCGGTGCTTCTCTGAAACGCCGCTAATAG
1 AAGAC-AAAAC-TCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCAAAAACGCCGCTAATAC
* *
16224563 TATGCCTTAGCGGCGTGTTCCCT-T-TGCGCCACTAATTCTAGTATACCTC
64 TATGCTTTAGCGGCGT-TTCCCTATATGCGCCACTAATTCTA-TATACATC
* * * *
16224612 AAGACCAAACTCTACGTTTTGGTTCAGATATTTTGCGGCGCTTCTCACAAAACGCCGCTAATATT
1 AAGACAAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCA-AAAACGCCGCTAATACT
16224677 ATGCTTTAGCGGCGTTT
65 ATGCTTTAGCGGCGTTT
16224694 TCCATTAAAC
Statistics
Matches: 328, Mismatches: 78, Indels: 41
0.73 0.17 0.09
Matches are distributed among these distances:
111 1 0.00
112 37 0.11
113 58 0.18
114 52 0.16
115 143 0.44
116 35 0.11
117 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (112 bp):
AAGACAAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCAAAAACGCCGCTAATACTA
TGCTTTAGCGGCGTTTCCCTATATGCGCCACTAATTCTATATACATC
Found at i:16229918 original size:61 final size:58
Alignment explanation
Indices: 16229853--16229965 Score: 163
Period size: 61 Copynumber: 1.9 Consensus size: 58
16229843 GATTACCATA
* * *
16229853 ATATTAAATTTAATTTAATGTTTATCTTATAGATAAATATTCTATTAATTTAATAAGATTT
1 ATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAAGATTT
*
16229914 ATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATA
1 ATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
16229966 TTAAAGTGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
58 22 0.46
59 1 0.02
60 1 0.02
61 24 0.50
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (58 bp):
ATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAAGATTT
Found at i:16234778 original size:39 final size:37
Alignment explanation
Indices: 16234713--16234803 Score: 85
Period size: 39 Copynumber: 2.4 Consensus size: 37
16234703 CAGAATGGCA
* *
16234713 CCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGACG
1 CCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGACG
* ***
16234752 CCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGGTA
1 CCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGACG
*
16234789 CCCAGTACCTCATCG
1 CCCAGTGCCTCATCG
16234804 AATCTATCCG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
37 18 0.42
38 2 0.05
39 20 0.47
40 3 0.07
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (37 bp):
CCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGACG
Found at i:16235015 original size:23 final size:24
Alignment explanation
Indices: 16234971--16235016 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
16234961 TTTCTCACAT
* **
16234971 TTTCAATTCAATCATTTTTCCACC
1 TTTCAATTCAATAATTAATCCACC
16234995 TTTCAA-TCAATAATTAATCCAC
1 TTTCAATTCAATAATTAATCCAC
16235017 AATTCACACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTCAATTCAATAATTAATCCACC
Found at i:16235834 original size:20 final size:20
Alignment explanation
Indices: 16235811--16235848 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
16235801 TAAAAATCTA
*
16235811 TTTTTCCCTT-TTTCTTTCT
1 TTTTTTCCTTCTTTCTTTCT
*
16235830 TTTTTTTCTTCTTTCTTTC
1 TTTTTTCCTTCTTTCTTTC
16235849 CCCTGTTTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTCCTTCTTTCTTTCT
Found at i:16236427 original size:17 final size:17
Alignment explanation
Indices: 16236384--16236430 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
16236374 TAAAACCATA
16236384 ATAATATTTA-ATAATT
1 ATAATATTTATATAATT
* *
16236400 ATACTAATTATATACA-T
1 ATAATATTTATATA-ATT
16236417 ATAATATTTATATA
1 ATAATATTTATATA
16236431 TAACCTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 8 0.32
17 16 0.64
18 1 0.04
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAATATTTATATAATT
Found at i:16237899 original size:37 final size:37
Alignment explanation
Indices: 16237849--16237923 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
16237839 AATGGAAGTG
16237849 TGTGATGATTTTGATCTTCCTTGCTAGGTTTGTAAAC
1 TGTGATGATTTTGATCTTCCTTGCTAGGTTTGTAAAC
16237886 TGTGATGATTTTGATCTTCCTTGCTAGGTTTGTAAAC
1 TGTGATGATTTTGATCTTCCTTGCTAGGTTTGTAAAC
16237923 T
1 T
16237924 TAGACATGTT
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:0.19, C:0.13, G:0.21, T:0.47
Consensus pattern (37 bp):
TGTGATGATTTTGATCTTCCTTGCTAGGTTTGTAAAC
Found at i:16241588 original size:7 final size:7
Alignment explanation
Indices: 16241576--16241603 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
16241566 GCCAAGTTTA
16241576 GTTCAAT
1 GTTCAAT
16241583 GTTCAAT
1 GTTCAAT
16241590 GTTCAAT
1 GTTCAAT
16241597 GTTCAAT
1 GTTCAAT
16241604 TTATAGATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (7 bp):
GTTCAAT
Found at i:16244538 original size:115 final size:113
Alignment explanation
Indices: 16244389--16244658 Score: 285
Period size: 113 Copynumber: 2.4 Consensus size: 113
16244379 GTTTTATTTA
* * ** * * *
16244389 TTTATTCC-CAGGCAAATTCAAATTAATTCCCTCCTCATCTATTAGGAAACCGAAACTACTTTTA
1 TTTATTCCTAAGGCAACTTCAAATTAATTAGCTCCTCATCT-CT-GGAAACCAAAACTACTTTGA
* * *
16244453 ATATTTTGATCAAATAAAAAAAAAACAATTTTTTC-AGTTATTTTTTTCC-G
64 ATATTTTAATCAAA-AAAAAAAAAACAATTTTTTCAACTT-TTTTTTCCCTG
* * *
16244503 TTTATTCCTAATGCAACTTCAAATTAATTGGCTCCTCATCTCTGGGAACCAAAACTACTTTGAAT
1 TTTATTCCTAAGGCAACTTCAAATTAATTAGCTCCTCATCTCTGGAAACCAAAACTACTTTGAAT
* * * * * *
16244568 TTTTTAATTACAGAAAAAGAAACCATTTTTTCAACTTTTTTTTCCCTG
66 ATTTTAATCAAAAAAAAAAAAACAATTTTTTCAACTTTTTTTTCCCTG
* * *
16244616 TTTGTTTCTAAGGCAACTTCAAATTAATTAGCTTCTCATCTCT
1 TTTATTCCTAAGGCAACTTCAAATTAATTAGCTCCTCATCTCT
16244659 AACTACTTCT
Statistics
Matches: 130, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
112 25 0.19
113 69 0.53
114 9 0.07
115 27 0.21
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (113 bp):
TTTATTCCTAAGGCAACTTCAAATTAATTAGCTCCTCATCTCTGGAAACCAAAACTACTTTGAAT
ATTTTAATCAAAAAAAAAAAAACAATTTTTTCAACTTTTTTTTCCCTG
Found at i:16246595 original size:31 final size:32
Alignment explanation
Indices: 16246519--16246595 Score: 84
Period size: 36 Copynumber: 2.3 Consensus size: 32
16246509 AGTGCATTAG
* *
16246519 TCAGAATAGATCTGAAAGACTGCTGAACTGAA
1 TCAGAATAGATCCGAAAGACTACTGAACTGAA
*
16246551 TCAGCCAGGATAGATCCGAAAGGCTACTGAACTGAA
1 TCAG--A--ATAGATCCGAAAGACTACTGAACTGAA
16246587 T-AGAATAGA
1 TCAGAATAGA
16246596 GTTTGCTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
31 5 0.13
32 4 0.11
33 1 0.03
34 1 0.03
35 2 0.05
36 25 0.66
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (32 bp):
TCAGAATAGATCCGAAAGACTACTGAACTGAA
Found at i:16255563 original size:26 final size:26
Alignment explanation
Indices: 16255508--16255563 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
16255498 TACATCGTTC
** *
16255508 CTCACACGAGTTGTGAAATGGATCTA
1 CTCACACGAACTGTGAAATGGACCTA
* *
16255534 CTCACACGAACTGTGAAATGGGCCTG
1 CTCACACGAACTGTGAAATGGACCTA
16255560 CTCA
1 CTCA
16255564 TATGGGCTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (26 bp):
CTCACACGAACTGTGAAATGGACCTA
Found at i:16259125 original size:43 final size:43
Alignment explanation
Indices: 16259063--16259191 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 43
16259053 ATAGGATTTC
*
16259063 CGATATGTG-TTATCATGTAAGACCATGTCTGGGACGTTGGCAT
1 CGATATATGATTA-CATGTAAGACCATGTCTGGGACGTTGGCAT
* * * * * *
16259106 CGATTTATGTTTACGTGTAAGACCCTGTCTGGGACAG-CGACAT
1 CGATATATGATTACATGTAAGACCATGTCTGGGAC-GTTGGCAT
* *
16259149 CGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATATGATTACATGTAAGACCATGTCTGGGACGTTGGCAT
16259192 TGTACGAGTT
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
42 1 0.01
43 64 0.93
44 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
CGATATATGATTACATGTAAGACCATGTCTGGGACGTTGGCAT
Found at i:16262541 original size:24 final size:26
Alignment explanation
Indices: 16262506--16262555 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
16262496 CAGTTTATTC
16262506 TTTAAAGTTTCC-CCTC-TTTCACTG
1 TTTAAAGTTTCCACCTCTTTTCACTG
16262530 TTTAACAG-TTCCGACCTCTTTTCACT
1 TTTAA-AGTTTCC-ACCTCTTTTCACT
16262556 AAAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
24 9 0.41
25 2 0.09
26 4 0.18
27 7 0.32
ACGTcount: A:0.18, C:0.30, G:0.08, T:0.44
Consensus pattern (26 bp):
TTTAAAGTTTCCACCTCTTTTCACTG
Found at i:16263389 original size:8 final size:8
Alignment explanation
Indices: 16263376--16263400 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16263366 ATATATACTA
16263376 AATAAAAT
1 AATAAAAT
16263384 AATAAAAT
1 AATAAAAT
16263392 AATAAAAT
1 AATAAAAT
16263400 A
1 A
16263401 TCATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:16267478 original size:13 final size:13
Alignment explanation
Indices: 16267460--16267486 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16267450 TATAAATTTG
16267460 GCCCATTGTAATT
1 GCCCATTGTAATT
16267473 GCCCATTGTAATT
1 GCCCATTGTAATT
16267486 G
1 G
16267487 GACTTTATTG
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:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (13 bp):
GCCCATTGTAATT
Found at i:16270672 original size:28 final size:29
Alignment explanation
Indices: 16270649--16270710 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
16270639 AAAAAACTAA
16270649 AAAAATC-TTTAAAAAA-ATATAAAAATAT
1 AAAAATCTTTTAAAAAAGATAT-AAAATAT
16270677 AAAAA-CTTTTAAAAAAGATATAAAATAT
1 AAAAATCTTTTAAAAAAGATATAAAATAT
16270705 AAAAAT
1 AAAAAT
16270711 TAAGATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
27 1 0.03
28 26 0.84
29 4 0.13
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (29 bp):
AAAAATCTTTTAAAAAAGATATAAAATAT
Found at i:16270672 original size:29 final size:29
Alignment explanation
Indices: 16270640--16270709 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
16270630 GTAAAAACAA
16270640 AAAAACTAAAAAAA-TCTTTAAAAAA-ATAT
1 AAAAA-TAAAAAAACT-TTTAAAAAAGATAT
*
16270669 AAAAATATAAAAACTTTTAAAAAAGATAT
1 AAAAATAAAAAAACTTTTAAAAAAGATAT
16270698 AAAATATAAAAA
1 AAAA-ATAAAAA
16270710 TTAAGATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 16 0.44
29 14 0.39
30 6 0.17
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.24
Consensus pattern (29 bp):
AAAAATAAAAAAACTTTTAAAAAAGATAT
Found at i:16281901 original size:34 final size:34
Alignment explanation
Indices: 16281858--16281924 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
16281848 CTTTGAATAC
16281858 ATAATTTATTCATCAATTAATTCCACTCCTAATT
1 ATAATTTATTCATCAATTAATTCCACTCCTAATT
16281892 ATAATTTATTCATCAATTAATTCCACTCCTAAT
1 ATAATTTATTCATCAATTAATTCCACTCCTAAT
16281925 ATTTTTAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (34 bp):
ATAATTTATTCATCAATTAATTCCACTCCTAATT
Found at i:16282929 original size:43 final size:43
Alignment explanation
Indices: 16282868--16283012 Score: 290
Period size: 43 Copynumber: 3.4 Consensus size: 43
16282858 TAATCAACCG
16282868 CGCACACTTAGTGCCAATCTCATGCCCGTGAACCCTTATTGCC
1 CGCACACTTAGTGCCAATCTCATGCCCGTGAACCCTTATTGCC
16282911 CGCACACTTAGTGCCAATCTCATGCCCGTGAACCCTTATTGCC
1 CGCACACTTAGTGCCAATCTCATGCCCGTGAACCCTTATTGCC
16282954 CGCACACTTAGTGCCAATCTCATGCCCGTGAACCCTTATTGCC
1 CGCACACTTAGTGCCAATCTCATGCCCGTGAACCCTTATTGCC
16282997 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
16283013 TGCATTTCAA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 102 1.00
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.25
Consensus pattern (43 bp):
CGCACACTTAGTGCCAATCTCATGCCCGTGAACCCTTATTGCC
Found at i:16283205 original size:29 final size:29
Alignment explanation
Indices: 16283142--16283209 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
16283132 TAATCAACCG
16283142 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
16283171 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
16283200 CGCACACTTA
1 CGCACACTTA
16283210 CCTTTCCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:16283216 original size:174 final size:174
Alignment explanation
Indices: 16282999--16283358 Score: 675
Period size: 174 Copynumber: 2.1 Consensus size: 174
16282989 TTATTGCCCG
*
16282999 CACACTTAGTGCCATGCATTTCAAGTTCGCACACTTCCCTTTCCCGCTGTCCAAAATCGACTCGG
1 CACACTTAGTGCCATGCATTTCAAGTTCGCACACTTACCTTTCCCGCTGTCCAAAATCGACTCGG
16283064 TAAGGTCGCACCCTTAATGTAAATAATTTATAGAAAATAGATATTGGGTTCGCACACATAGTGCT
66 TAAGGTCGCACCCTTAATGTAAATAATTTATAGAAAATAGATATTGGGTTCGCACACATAGTGCT
16283129 TAATAATCAACCGCGCACACTTAGTGCCATGCACTTTAAACTCA
131 TAATAATCAACCGCGCACACTTAGTGCCATGCACTTTAAACTCA
16283173 CACACTTAGTGCCATGCATTTCAAGTTCGCACACTTACCTTTCCCGCTGTCCAAAATCGACTCGG
1 CACACTTAGTGCCATGCATTTCAAGTTCGCACACTTACCTTTCCCGCTGTCCAAAATCGACTCGG
*
16283238 TAAGGTCGCACCCTTAATGTAAATAATTTATAGAAAATATATATTGGGTTCGCACACATAGTGCT
66 TAAGGTCGCACCCTTAATGTAAATAATTTATAGAAAATAGATATTGGGTTCGCACACATAGTGCT
* *
16283303 TAATAATCAACCGCGCACACTTAGTGCCATGTACTTTAAACTCG
131 TAATAATCAACCGCGCACACTTAGTGCCATGCACTTTAAACTCA
*
16283347 CACATTTAGTGC
1 CACACTTAGTGC
16283359 TGTACAATTT
Statistics
Matches: 181, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 181 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (174 bp):
CACACTTAGTGCCATGCATTTCAAGTTCGCACACTTACCTTTCCCGCTGTCCAAAATCGACTCGG
TAAGGTCGCACCCTTAATGTAAATAATTTATAGAAAATAGATATTGGGTTCGCACACATAGTGCT
TAATAATCAACCGCGCACACTTAGTGCCATGCACTTTAAACTCA
Found at i:16283350 original size:29 final size:30
Alignment explanation
Indices: 16283311--16283389 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
16283301 CTTAATAATC
16283311 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
* *
16283341 AACTCGCACATTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
16283370 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
16283390 ATCTCATGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 31 0.76
30 4 0.10
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:16288195 original size:27 final size:27
Alignment explanation
Indices: 16288149--16288201 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
16288139 AAATGGTAGG
16288149 TAAGATCTTAAAGACGAACCTAAATCT
1 TAAGATCTTAAAGACGAACCTAAATCT
* *
16288176 TAAGATCTTAAGGACTAACCTAAATC
1 TAAGATCTTAAAGACGAACCTAAATC
16288202 CAAATGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26
Consensus pattern (27 bp):
TAAGATCTTAAAGACGAACCTAAATCT
Found at i:16288653 original size:25 final size:24
Alignment explanation
Indices: 16288607--16288653 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
16288597 ATAAATATAA
**
16288607 AACATTAAAATATAGTGCATAATT
1 AACATTAAAATATAAAGCATAATT
*
16288631 AACATTAAATATATAAAGTATAA
1 AACATTAAA-ATATAAAGCATAA
16288654 ATGCAAGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (24 bp):
AACATTAAAATATAAAGCATAATT
Found at i:16289178 original size:20 final size:20
Alignment explanation
Indices: 16289155--16289198 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
16289145 ATGGTTAAAA
16289155 AAAAATTAAAACTTTGT-TTT
1 AAAAATTAAAACTTT-TCTTT
* *
16289175 AAAATTTTAAACTTTTCTTT
1 AAAAATTAAAACTTTTCTTT
16289195 AAAA
1 AAAA
16289199 TGACTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAAATTAAAACTTTTCTTT
Found at i:16289409 original size:155 final size:154
Alignment explanation
Indices: 16289143--16289568 Score: 506
Period size: 156 Copynumber: 2.8 Consensus size: 154
16289133 GCTTATTTCA
* * *
16289143 AAATGGTTAAAAAAAAATTAAAACTTTGTTTTAAAATTTTAAACTTTTCTTTAAAATGACTTAAA
1 AAATAGTTCAAAAAAAATTAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGAC-TAAA
*
16289208 AAAAC-ATATTTTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTTTTTTAAAAAAATACTAATT
65 AAAACTATATTTTTATTTTTCAAAATCTAAACTTTCTCC--TTTTTTTTTAAAAAAACACTAATT
* * * * *
16289272 TTATTAAAGTTTGAAGTTTTTATTTTT
128 TTATTAAAGATTAAAGCTTTTACTTTG
*
16289299 ACATAGTTTCAAAAAAAA-TAAAACTTTGTTTTAAAATTTTACAA-TTTCCTTTAAAATGACT-A
1 AAATAG-TTCAAAAAAAATTAAAACTTTGTTTTAAAATTTTA-AACTTTCCTTTAAAATGACTAA
*
16289361 AAAAACTATATTTTTATTTTTCAAAATCTAAACTTTCT-CTTTTATTTTTAAAAAAACACTATTT
64 AAAAACTATATTTTTATTTTTCAAAATCTAAACTTTCTCCTTTT-TTTTTAAAAAAACACTAATT
*
16289425 TTCTTAAAGATTAAAGCTTTTACTTTG
128 TTATTAAAGATTAAAGCTTTTACTTTG
* * * * * *
16289452 AAATAGTTGAAAACAAAATTAAAACTTTATTTTAAAAATTTAAATTTTCTTTTAAAATAACTAAA
1 AAATAGTTCAAAA-AAAATTAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACTAAA
* * * * * **
16289517 ATAAAATAAAATATTATTTATCAAAATCTAAAC--TCTGTTTTTTTTTTAAAAA
65 A-AAACTATATTTTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTTTTAAAAA
16289569 TTACAACTTT
Statistics
Matches: 236, Mismatches: 24, Indels: 22
0.84 0.09 0.08
Matches are distributed among these distances:
152 10 0.04
153 50 0.21
154 57 0.24
155 39 0.17
156 68 0.29
157 12 0.05
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (154 bp):
AAATAGTTCAAAAAAAATTAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACTAAAA
AAACTATATTTTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTTTTAAAAAAACACTAATTTTA
TTAAAGATTAAAGCTTTTACTTTG
Found at i:16289491 original size:20 final size:20
Alignment explanation
Indices: 16289466--16289508 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16289456 AGTTGAAAAC
16289466 AAAATTAAAACTTTATTTTA
1 AAAATTAAAACTTTATTTTA
* * *
16289486 AAAATTTAAATTTTCTTTTA
1 AAAATTAAAACTTTATTTTA
16289506 AAA
1 AAA
16289509 TAACTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATTAAAACTTTATTTTA
Found at i:16291537 original size:28 final size:28
Alignment explanation
Indices: 16291495--16291625 Score: 156
Period size: 28 Copynumber: 4.7 Consensus size: 28
16291485 AACACATCAA
* * *
16291495 GAAATAATAAGCCTTTGTGGCGAACAAT
1 GAAAGAATAAACCTTTGTGGCGAACTAT
*
16291523 GAAAGAATAAACCTTTGTGGCAAACTAT
1 GAAAGAATAAACCTTTGTGGCGAACTAT
*
16291551 GAAAGAATAAGCCTTTGTGGCGAACTAT
1 GAAAGAATAAACCTTTGTGGCGAACTAT
* ** *
16291579 GAAGGAATAAACCTTTGTGATGAGCTAT
1 GAAAGAATAAACCTTTGTGGCGAACTAT
* *
16291607 GAAAG-ATTAGCCTTTGTGG
1 GAAAGAATAAACCTTTGTGG
16291626 TGGACTCCGT
Statistics
Matches: 88, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 11 0.12
28 77 0.88
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.27
Consensus pattern (28 bp):
GAAAGAATAAACCTTTGTGGCGAACTAT
Found at i:16291587 original size:56 final size:56
Alignment explanation
Indices: 16291495--16291625 Score: 183
Period size: 56 Copynumber: 2.4 Consensus size: 56
16291485 AACACATCAA
* *
16291495 GAAATAATAAGCCTTTGTGGCGAACAATGAAAGAATAAACCTTTGTGGCAAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACAATGAAAGAATAAACCTTTGTGACAAACTAT
* * ** *
16291551 GAAAGAATAAGCCTTTGTGGCGAACTATGAAGGAATAAACCTTTGTGATGAGCTAT
1 GAAAGAATAAGCCTTTGTGGCGAACAATGAAAGAATAAACCTTTGTGACAAACTAT
*
16291607 GAAAG-ATTAGCCTTTGTGG
1 GAAAGAATAAGCCTTTGTGG
16291626 TGGACTCCGT
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
55 13 0.19
56 54 0.81
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.27
Consensus pattern (56 bp):
GAAAGAATAAGCCTTTGTGGCGAACAATGAAAGAATAAACCTTTGTGACAAACTAT
Found at i:16293232 original size:17 final size:17
Alignment explanation
Indices: 16293210--16293243 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16293200 GTAAATAATG
*
16293210 TTATTATTATAATTATA
1 TTATTATAATAATTATA
*
16293227 TTATTATAATATTTATA
1 TTATTATAATAATTATA
16293244 AAACATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTATAATAATTATA
Found at i:16295027 original size:18 final size:18
Alignment explanation
Indices: 16295004--16295044 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
16294994 AATTTGATCC
16295004 ACACGACCTCAGTTTGTT
1 ACACGACCTCAGTTTGTT
16295022 ACACGACCTCAGTTTGTT
1 ACACGACCTCAGTTTGTT
16295040 ACACG
1 ACACG
16295045 TCCTAACTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (18 bp):
ACACGACCTCAGTTTGTT
Found at i:16298204 original size:15 final size:15
Alignment explanation
Indices: 16298186--16298214 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16298176 AGAAGTTGTT
16298186 TGTAGTTGATGTTGG
1 TGTAGTTGATGTTGG
16298201 TGTAGTTGATGTTG
1 TGTAGTTGATGTTG
16298215 AATTTCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.48
Consensus pattern (15 bp):
TGTAGTTGATGTTGG
Found at i:16302723 original size:15 final size:15
Alignment explanation
Indices: 16302682--16302728 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
16302672 TTGGTTTCAA
16302682 TTATTATTTCAATATGT
1 TTATTATTT-AATAT-T
*
16302699 TTAATT-TTTATTATT
1 TT-ATTATTTAATATT
16302714 TTATTATTTAATATT
1 TTATTATTTAATATT
16302729 CGATATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 3 0.12
15 11 0.42
16 4 0.15
17 5 0.19
18 3 0.12
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (15 bp):
TTATTATTTAATATT
Found at i:16306549 original size:27 final size:27
Alignment explanation
Indices: 16306519--16306696 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
16306509 ATATTGAGTC
* * * *
16306519 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
16306546 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16306573 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
16306601 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
16306628 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
16306655 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16306682 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16306697 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:16306658 original size:82 final size:81
Alignment explanation
Indices: 16306540--16306695 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16306530 TGCTATATAA
* *
16306540 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16306605 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
16306622 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16306686 CACTTAGTGC
65 CACTTAGTGC
16306696 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:16312790 original size:30 final size:30
Alignment explanation
Indices: 16312734--16312790 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
16312724 TAAACCTTTT
*
16312734 CACTTTCCTCCCAAAATTTTTACTCCCTCA
1 CACTTTCCTCCCAAAACTTTTACTCCCTCA
* *
16312764 CACTTTCC-CCTCATAACTTTTGCTCCC
1 CACTTTCCTCC-CAAAACTTTTACTCCC
16312791 CTCCCATCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.09
30 21 0.91
ACGTcount: A:0.19, C:0.42, G:0.02, T:0.37
Consensus pattern (30 bp):
CACTTTCCTCCCAAAACTTTTACTCCCTCA
Found at i:16313196 original size:38 final size:37
Alignment explanation
Indices: 16313142--16313221 Score: 92
Period size: 38 Copynumber: 2.2 Consensus size: 37
16313132 GGTATCAATT
*
16313142 TCACATTTTATCTTTAAGATAATTTTT-ATTAAAAAA
1 TCACATTTTATCTTTAAAATAATTTTTAATTAAAAAA
* * *
16313178 TCACATTTTTTACATTTAAAATATTTTTTAATTTAAAAA
1 TCACATTTTAT-C-TTTAAAATAATTTTTAATTAAAAAA
16313217 T-ACAT
1 TCACAT
16313222 AGTGACGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 10 0.27
37 1 0.03
38 17 0.46
39 9 0.24
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (37 bp):
TCACATTTTATCTTTAAAATAATTTTTAATTAAAAAA
Found at i:16313218 original size:18 final size:18
Alignment explanation
Indices: 16313182--16313215 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
16313172 AAAAAATCAC
16313182 ATTTTTTACATTTAAAAT
1 ATTTTTTACATTTAAAAT
16313200 ATTTTTTA-ATTTAAAA
1 ATTTTTTACATTTAAAA
16313216 ATACATAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTTACATTTAAAAT
Found at i:16313852 original size:42 final size:42
Alignment explanation
Indices: 16313709--16313892 Score: 181
Period size: 43 Copynumber: 4.3 Consensus size: 42
16313699 TATGTGGAAA
* * * * * *
16313709 AAACGCCGCTATAGAACATGACATTTAACGACGTTTTTCACAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGACG-CTTTCCCAC
* * ** *
16313752 AAATGTCATTATAGAACATGACCTTTAGC-AGCGCTTTCCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGA-CGCTTT-CCCAC
*
16313795 AAACGCCGCTCAAGAACATGACCTTTAGCGACGCTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGACGCTTTCCCAC
* * **
16313837 AAACACCACTAAAGAACATGACCTTTAGCGGTGCTCTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGACGCT-TTCCCAC
16313880 AAACGCCGCTAAA
1 AAACGCCGCTAAA
16313893 AAATATGGTC
Statistics
Matches: 115, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
42 39 0.34
43 75 0.65
44 1 0.01
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGACGCTTTCCCAC
Found at i:16323191 original size:41 final size:41
Alignment explanation
Indices: 16323130--16323477 Score: 419
Period size: 41 Copynumber: 8.5 Consensus size: 41
16323120 CATATAGTGG
* * *
16323130 CGTTTTTTAAGAAGCACCGCTAATGCTCGGGCCGTTAGCGA
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
**
16323171 CGTTTTTGAAGAAGCGCCGCTAATGCTCTAGCCTTTAGCGA
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
* * * * * *
16323212 CATTTTTTAAGCAGTGTCGCTAATGCTCTGGCCTTTAGCGA
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
* * * * * *
16323253 CGTTTCTTCAA-AAACGCCGCTACTGCTGGGGTCTTTAGCGG
1 CGTTT-TTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
* * *
16323294 CGTTTTTGAAGCAGCACCGCTAATGCTCGGGCCTTTAGCGG
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
* * * *
16323335 CATTTTTGAAGAAGCGCCGCTAATACTCGGGCCCTTAGCGG
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
* * *
16323376 TGTTTTTGAAGAAGCGCCGCTAATGGTCGGGCCTTTAGCGG
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
*
16323417 CGTTTTTGAGGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
*
16323458 CGTTTTTGTAGAAGCGCCGC
1 CGTTTTTGAAGAAGCGCCGC
16323478 AAAAACATTT
Statistics
Matches: 260, Mismatches: 45, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
40 4 0.02
41 252 0.97
42 4 0.02
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (41 bp):
CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
Found at i:16323883 original size:14 final size:15
Alignment explanation
Indices: 16323855--16323887 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
16323845 AAGGTTTATA
16323855 GATTATGGAATTAGG
1 GATTATGGAATTAGG
16323870 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
16323884 GATT
1 GATT
16323888 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:16323929 original size:7 final size:7
Alignment explanation
Indices: 16323919--16324020 Score: 60
Period size: 7 Copynumber: 14.1 Consensus size: 7
16323909 AAGGTTTATT
16323919 GGTTAGG
1 GGTTAGG
16323926 GGTTAGG
1 GGTTAGG
*
16323933 GGTTAGA
1 GGTTAGG
*
16323940 GGTTAGA
1 GGTTAGG
*
16323947 AGTTAGG
1 GGTTAGG
* *
16323954 AGTTTAAG
1 -GGTTAGG
* *
16323962 GTTTATTG
1 GGTTA-GG
*
16323970 GTTTAGG
1 GGTTAGG
*
16323977 GATTAGG
1 GGTTAGG
16323984 GGTTAGG
1 GGTTAGG
*
16323991 GGTTTGG
1 GGTTAGG
* *
16323998 GATTTAAG
1 G-GTTAGG
16324006 GGTTAGG
1 GGTTAGG
*
16324013 AGTTAGG
1 GGTTAGG
16324020 G
1 G
16324021 ATTTAGTGTT
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
7 60 0.81
8 14 0.19
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (7 bp):
GGTTAGG
Found at i:16324008 original size:22 final size:22
Alignment explanation
Indices: 16323969--16324025 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
16323959 AAGGTTTATT
*
16323969 GGTTTAGGGA-TTAGGGGTTAGG
1 GGTTT-GGGATTTAAGGGTTAGG
16323991 GGTTTGGGATTTAAGGGTTAGG
1 GGTTTGGGATTTAAGGGTTAGG
* *
16324013 AGTTAGGGATTTA
1 GGTTTGGGATTTA
16324026 GTGTTTTGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (22 bp):
GGTTTGGGATTTAAGGGTTAGG
Found at i:16324713 original size:16 final size:16
Alignment explanation
Indices: 16324692--16324747 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
16324682 ACTTAGTAAT
16324692 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
*
16324708 TAAAAGATACTATTAA
1 TAAAAGATACAATTAA
* * *
16324724 GAAATAAATA-AATAAA
1 TAAA-AGATACAATTAA
16324740 TAAAAGAT
1 TAAAAGAT
16324748 GTGAGATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 3 0.09
16 25 0.78
17 4 0.12
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (16 bp):
TAAAAGATACAATTAA
Found at i:16325111 original size:24 final size:24
Alignment explanation
Indices: 16325063--16325108 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
16325053 CACTTAGCCG
16325063 AAATTCCCCCCAAATTTCTCCCCA
1 AAATTCCCCCCAAATTTCTCCCCA
* *
16325087 AAATTCCCCTCGAATTT-TCCCC
1 AAATTCCCCCCAAATTTCTCCCC
16325109 CAATTCTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.26, C:0.43, G:0.02, T:0.28
Consensus pattern (24 bp):
AAATTCCCCCCAAATTTCTCCCCA
Found at i:16326532 original size:22 final size:22
Alignment explanation
Indices: 16326507--16326548 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16326497 CGCTGTTATT
*
16326507 ATATAATATATAACTTACATTA
1 ATATAATACATAACTTACATTA
*
16326529 ATATTATACATAACTTACAT
1 ATATAATACATAACTTACAT
16326549 AACTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATAATACATAACTTACATTA
Found at i:16326852 original size:25 final size:25
Alignment explanation
Indices: 16326818--16327043 Score: 341
Period size: 25 Copynumber: 9.1 Consensus size: 25
16326808 TTAATATATT
16326818 TAATACATAACTTACATAACTTACA
1 TAATACATAACTTACATAACTTACA
16326843 TAATACATAACTTACATAACTTACA
1 TAATACATAACTTACATAACTTACA
16326868 TAATACATAACTTACATAACTTACA
1 TAATACATAACTTACATAACTTACA
* * *
16326893 TAATACATAACTTACTTAATTTTCA
1 TAATACATAACTTACATAACTTACA
*
16326918 TAATAAATAACTTACATAACTTACA
1 TAATACATAACTTACATAACTTACA
16326943 TAATACATAACTTACATAACTTACA
1 TAATACATAACTTACATAACTTACA
* * *
16326968 TAATACACAACTTACATAATTTTCA
1 TAATACATAACTTACATAACTTACA
*
16326993 TAATACATAACTTACATAA-TATTCA
1 TAATACATAACTTACATAACT-TACA
*
16327018 TAATAAATAACTTACATAA--TACA
1 TAATACATAACTTACATAACTTACA
16327041 TAA
1 TAA
16327044 CTTACATAGC
Statistics
Matches: 186, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
23 6 0.03
24 1 0.01
25 179 0.96
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (25 bp):
TAATACATAACTTACATAACTTACA
Found at i:16332606 original size:19 final size:19
Alignment explanation
Indices: 16332582--16332618 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16332572 GTAAATATTT
*
16332582 TTATCATTTTGACTTTTAA
1 TTATCATTTTAACTTTTAA
16332601 TTATCATTTTAACTTTTA
1 TTATCATTTTAACTTTTA
16332619 TCATTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.11, G:0.03, T:0.59
Consensus pattern (19 bp):
TTATCATTTTAACTTTTAA
Found at i:16332864 original size:43 final size:43
Alignment explanation
Indices: 16332801--16333025 Score: 220
Period size: 43 Copynumber: 5.2 Consensus size: 43
16332791 TCTGCCAAAA
* * * *
16332801 TTAGCGGCGTTTTTTA-AAAAAGCGCCGTTAAAGGTC-GTTGTCA
1 TTAGCGGCG-TTTGTAGAAAAAGCGCCGCTAAAGGTCAG-GGTCT
* * *
16332844 TTAGCGGCGTTTGTAGAAAAAATCACCGCTAAAGGTCAAGGTCT
1 TTAGCGGCGTTTGTAG-AAAAAGCGCCGCTAAAGGTCAGGGTCT
* * * **
16332888 TTAGCGGCGCTTGTGGAAAGAGTTCCGCTAAAGGTCAGGGTCT
1 TTAGCGGCGTTTGTAGAAAAAGCGCCGCTAAAGGTCAGGGTCT
* * *
16332931 TTAGCGGCGATTGTAGGAAAAGCGCCGCTAAAGATCAGGGTCT
1 TTAGCGGCGTTTGTAGAAAAAGCGCCGCTAAAGGTCAGGGTCT
* * * * *
16332974 TTAGCGGCGTTTGTCGAACAAGTGCTGCTAAAGGTCATGGTCT
1 TTAGCGGCGTTTGTAGAAAAAGCGCCGCTAAAGGTCAGGGTCT
*
16333017 TTAGTGGCG
1 TTAGCGGCG
16333026 CAATCCCAAA
Statistics
Matches: 149, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
42 5 0.03
43 110 0.74
44 34 0.23
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (43 bp):
TTAGCGGCGTTTGTAGAAAAAGCGCCGCTAAAGGTCAGGGTCT
Found at i:16339856 original size:21 final size:22
Alignment explanation
Indices: 16339808--16339858 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
16339798 GGTTTTTGAC
16339808 AGAAGAAAGAAAGAAGAAAAAA
1 AGAAGAAAGAAAGAAGAAAAAA
* * *
16339830 ATAAGAAAGGAA-AAGAAAAAG
1 AGAAGAAAGAAAGAAGAAAAAA
*
16339851 GGAAGAAA
1 AGAAGAAA
16339859 AGGAGGGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (22 bp):
AGAAGAAAGAAAGAAGAAAAAA
Found at i:16343652 original size:21 final size:22
Alignment explanation
Indices: 16343604--16343654 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
16343594 GGTTTTTGAC
16343604 AGAAGAAAGAAAGAAGAAAAAA
1 AGAAGAAAGAAAGAAGAAAAAA
* * *
16343626 ATAAGAAAGGAA-AAGAAAAAG
1 AGAAGAAAGAAAGAAGAAAAAA
*
16343647 GGAAGAAA
1 AGAAGAAA
16343655 AGGAGGGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (22 bp):
AGAAGAAAGAAAGAAGAAAAAA
Found at i:16347643 original size:18 final size:17
Alignment explanation
Indices: 16347609--16347658 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
16347599 TATTCTAGAA
16347609 AATTTTTAACTTTTTTTA-
1 AATTTTTAA--TTTTTTAG
16347627 ATATTCTTTAATTTTTTAG
1 A-ATT-TTTAATTTTTTAG
16347646 AATTTTTAATTTT
1 AATTTTTAATTTT
16347659 AAAAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.31
18 11 0.38
19 4 0.14
20 5 0.17
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (17 bp):
AATTTTTAATTTTTTAG
Found at i:16347696 original size:18 final size:19
Alignment explanation
Indices: 16347673--16347709 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16347663 AATTTTAAAA
16347673 TATAAAT-TTTTGAATTTT
1 TATAAATATTTTGAATTTT
16347691 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
16347710 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:16347710 original size:18 final size:18
Alignment explanation
Indices: 16347673--16347726 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
16347663 AATTTTAAAA
16347673 TATAAAT-TTTTGAATTTT
1 TATAAATATTTTGAA-TTT
16347691 TATAAATATTTTGAATTT
1 TATAAATATTTTGAATTT
* *
16347709 TAAAAATTATTTTAAATT
1 TATAAA-TATTTTGAATT
16347727 ATTTTGTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TATAAATATTTTGAATTT
Found at i:16347719 original size:19 final size:18
Alignment explanation
Indices: 16347647--16347726 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 18
16347637 ATTTTTTAGA
*
16347647 ATTTTTAATTTTAAAAA-
1 ATTTTGAATTTTAAAAAT
** *
16347664 ATTTT-AA-AATATAAAT
1 ATTTTGAATTTTAAAAAT
*
16347680 -TTTTGAATTTTTATAAAT
1 ATTTTGAA-TTTTAAAAAT
16347698 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAA-T
*
16347717 ATTTTAAATT
1 ATTTTGAATT
16347727 ATTTTGTAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
15 9 0.18
16 4 0.08
17 5 0.10
18 15 0.30
19 17 0.34
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTTGAATTTTAAAAAT
Found at i:16347826 original size:18 final size:18
Alignment explanation
Indices: 16347803--16347841 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
16347793 ATACTAATTC
*
16347803 ATTATTTGAGTTATTCAA
1 ATTATTTGACTTATTCAA
*
16347821 ATTATTTGACTTATTCTA
1 ATTATTTGACTTATTCAA
16347839 ATT
1 ATT
16347842 GTAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (18 bp):
ATTATTTGACTTATTCAA
Found at i:16348488 original size:111 final size:111
Alignment explanation
Indices: 16348294--16348514 Score: 352
Period size: 111 Copynumber: 2.0 Consensus size: 111
16348284 CTTATTATTT
* * * * *
16348294 AAATCTTCATTTCGAGAAAACGACACGTCATATCCAATATATTAGGACATGACGTATCGAATGCC
1 AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGGACACGACGTATCAAATGCC
*
16348359 CGAAAGTGAGTTTTTGGTTTATGCGTTTTGATTGTAGAAAATTTTA
66 CGAAAGTGAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTTA
* * *
16348405 AAATCTTCATTTCGAGAAAACGACACATCACATTCAATACATTAGGACACGGCGTATCAAATTCC
1 AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGGACACGACGTATCAAATGCC
*
16348470 CGAAAGTGAGTTTTTGGTTTATTCGCTTTGATTGTAGAAAATTTT
66 CGAAAGTGAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTT
16348515 CGATTATTTA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 100 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (111 bp):
AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGGACACGACGTATCAAATGCC
CGAAAGTGAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTTA
Found at i:16350371 original size:17 final size:17
Alignment explanation
Indices: 16350351--16350383 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16350341 TTGATTTGGT
16350351 TTTATTTTA-TTTATTTG
1 TTTA-TTTAGTTTATTTG
16350368 TTTATTTAGTTTATTT
1 TTTATTTAGTTTATTT
16350384 CACTAACGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTATTTAGTTTATTTG
Found at i:16355974 original size:6 final size:6
Alignment explanation
Indices: 16355963--16355998 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
16355953 AATAATTGAA
* *
16355963 GATATT GATATT GATATT GATATT TATATT TATATT
1 GATATT GATATT GATATT GATATT GATATT GATATT
16355999 CAAGAGGGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (6 bp):
GATATT
Found at i:16358045 original size:20 final size:20
Alignment explanation
Indices: 16357987--16358045 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
16357977 GAGTGTAAAA
*
16357987 ATTAAAAATTAAAAAATAATTT
1 ATTAAAAATT-ATAAA-AATTT
* *
16358009 ATTAACAATTATTAAAATTT
1 ATTAAAAATTATAAAAATTT
16358029 A-TAAAAATATATAAAAA
1 ATTAAAAAT-TATAAAAA
16358046 AATTCAAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 6 0.19
20 13 0.42
21 3 0.10
22 9 0.29
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAAAAATTATAAAAATTT
Found at i:16375457 original size:16 final size:18
Alignment explanation
Indices: 16375422--16375458 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
16375412 TCGACTGTGG
*
16375422 ATTACGGGTTTTATAAAA
1 ATTACGGGTTTTAGAAAA
16375440 ATTA-GGGTTTT-GAAAA
1 ATTACGGGTTTTAGAAAA
16375456 ATT
1 ATT
16375459 GATTGATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.41
Consensus pattern (18 bp):
ATTACGGGTTTTAGAAAA
Found at i:16396572 original size:71 final size:70
Alignment explanation
Indices: 16396438--16396701 Score: 248
Period size: 70 Copynumber: 3.8 Consensus size: 70
16396428 ACAACATTTG
* * * ** * ** * * * *
16396438 TGTCATACTAAGGTTCGTAAGATAAAAAATTGCAGCCACCAACATAGCTAGTGAAAGCAAAGCTC
1 TGTCATACTAAGGCTCGCAGGATAAAAAAACGTAGCCTTCAACAAAGTTAGCGAGAGCAAAGCTC
16396503 CCAAC
66 CCAAC
* *
16396508 TGTCATACTAAGACTCGCAGGATAAAAAAATCGTAGCCTTCAACACAGTTAGCGAGAGCAAAGCT
1 TGTCATACTAAGGCTCGCAGGATAAAAAAA-CGTAGCCTTCAACAAAGTTAGCGAGAGCAAAGCT
* *
16396573 CCTAGC
65 CCCAAC
* * *
16396579 TCTCATACTAAGGCTCGCAGGAT-AAAAAACGGCAGCCTTCAACAAAGTTAGCGAGAGCAAAAC-
1 TGTCATACTAAGGCTCGCAGGATAAAAAAAC-GTAGCCTTCAACAAAGTTAGCGAGAGCAAAGCT
* *
16396642 ACCAAGT
65 CCCAA-C
* * *
16396649 TGTCATACTAAGGCTCGCAGAAT-AAAAACCGTAGCCTCCAA-AATAGTTAGCGA
1 TGTCATACTAAGGCTCGCAGGATAAAAAAACGTAGCCTTCAACAA-AGTTAGCGA
16396702 AAGTTAAAAA
Statistics
Matches: 161, Mismatches: 29, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
68 2 0.01
69 21 0.13
70 87 0.54
71 51 0.32
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (70 bp):
TGTCATACTAAGGCTCGCAGGATAAAAAAACGTAGCCTTCAACAAAGTTAGCGAGAGCAAAGCTC
CCAAC
Found at i:16396655 original size:70 final size:69
Alignment explanation
Indices: 16396503--16396701 Score: 249
Period size: 70 Copynumber: 2.9 Consensus size: 69
16396493 AGCAAAGCTC
* *
16396503 CCAA-CTGTCATACTAAGACTCGCAGGATAAAAAAATCGTAGCCTTCAACACAGTTAGCGAGAGC
1 CCAAGCTGTCATACTAAGGCTCGCAGGAT-AAAAAA-CGTAGCCTTCAACAAAGTTAGCGAGAGC
* *
16396567 AAAGCT
64 AAAACA
* * *
16396573 CCTAGCTCTCATACTAAGGCTCGCAGGATAAAAAACGGCAGCCTTCAACAAAGTTAGCGAGAGCA
1 CCAAGCTGTCATACTAAGGCTCGCAGGATAAAAAAC-GTAGCCTTCAACAAAGTTAGCGAGAGCA
16396638 AAACA
65 AAACA
* * * *
16396643 CCAAGTTGTCATACTAAGGCTCGCAGAATAAAAACCGTAGCCTCCAA-AATAGTTAGCGA
1 CCAAGCTGTCATACTAAGGCTCGCAGGATAAAAAACGTAGCCTTCAACAA-AGTTAGCGA
16396702 AAGTTAAAAA
Statistics
Matches: 112, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
68 2 0.02
69 19 0.17
70 69 0.62
71 22 0.20
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (69 bp):
CCAAGCTGTCATACTAAGGCTCGCAGGATAAAAAACGTAGCCTTCAACAAAGTTAGCGAGAGCAA
AACA
Found at i:16429778 original size:21 final size:21
Alignment explanation
Indices: 16429754--16429794 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16429744 GGTGGATCAG
*
16429754 CTCTTATGAGCTTCTGTTCAA
1 CTCTTACGAGCTTCTGTTCAA
*
16429775 CTCTTACGAGCTTTTGTTCA
1 CTCTTACGAGCTTCTGTTCA
16429795 GCTTTCAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.44
Consensus pattern (21 bp):
CTCTTACGAGCTTCTGTTCAA
Found at i:16430801 original size:13 final size:14
Alignment explanation
Indices: 16430775--16430809 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
16430765 AACCCGCCCC
*
16430775 ATATACATATACAG
1 ATATACAGATACAG
16430789 ATA-ACAGATACAG
1 ATATACAGATACAG
16430802 ATATACAG
1 ATATACAG
16430810 TGTTAACGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.23
Consensus pattern (14 bp):
ATATACAGATACAG
Found at i:16434339 original size:16 final size:16
Alignment explanation
Indices: 16434318--16434348 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16434308 AAACATTATA
*
16434318 AATTAATTAATTTTCC
1 AATTAAATAATTTTCC
16434334 AATTAAATAATTTTC
1 AATTAAATAATTTTC
16434349 TCAACCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAAATAATTTTCC
Found at i:16445347 original size:20 final size:20
Alignment explanation
Indices: 16445322--16445388 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
16445312 TTGTACGAGA
16445322 TTGCACTTTGGTGCCTCTAT
1 TTGCACTTTGGTGCCTCTAT
* *
16445342 TTGCACTTCGGTGCCTCTAA
1 TTGCACTTTGGTGCCTCTAT
16445362 TTGCACAATTT--TGCCTCTAT
1 TTGCAC--TTTGGTGCCTCTAT
16445382 TTGCACT
1 TTGCACT
16445389 ACAGTGCCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.02
20 38 0.93
22 2 0.05
ACGTcount: A:0.15, C:0.27, G:0.16, T:0.42
Consensus pattern (20 bp):
TTGCACTTTGGTGCCTCTAT
Found at i:16445396 original size:20 final size:20
Alignment explanation
Indices: 16445332--16445397 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
16445322 TTGCACTTTG
* *
16445332 GTGCCTCTATTTGCACTTCG
1 GTGCCTCTATTTGCACTACA
* * **
16445352 GTGCCTCTAATTGCACAATT
1 GTGCCTCTATTTGCACTACA
*
16445372 TTGCCTCTATTTGCACTACA
1 GTGCCTCTATTTGCACTACA
16445392 GTGCCT
1 GTGCCT
16445398 ATGAATAGTA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.38
Consensus pattern (20 bp):
GTGCCTCTATTTGCACTACA
Found at i:16453726 original size:6 final size:6
Alignment explanation
Indices: 16453715--16453742 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
16453705 TAACAGATAG
16453715 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
16453743 TAGCTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:16455341 original size:124 final size:124
Alignment explanation
Indices: 16455007--16455381 Score: 567
Period size: 123 Copynumber: 3.0 Consensus size: 124
16454997 TTAGGGTTTC
* *** * *
16455007 AGGTCTTGGAAGAAATAATTTCGAGTTGACATTTCTGATCAAATAGTATAAAATCGCTTCTAGCA
1 AGGTCATGGAAGAAATAATTT-TTTTTGACGTTTCTGAACAAATAGTATAAAATCGCTTCTAGCA
* * *
16455072 TGATGCTATTTGAGAAGAATTTGTGAAATCCCGCCCTCGTGGACGCGCTTTTGCTACAGT
65 GGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
*
16455132 AGGTCATGGAAGAAAT-TTTTTTTTTGACGTTTCTGAACAAATAGTATAAAAAT-GCTTCTAGCA
1 AGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAACAAATAGTAT-AAAATCGCTTCTAGCA
*
16455195 GGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
65 GGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
*
16455255 CA-GTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
1 -AGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAACAAATAGTATAAAATCGCTTCTAGCA
* *
16455319 GGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGATTTTACTACAGT
65 GGATGCTATTTGAGAAGAATTTGT-AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
16455380 AG
1 AG
16455382 CATGTTTGGG
Statistics
Matches: 228, Mismatches: 16, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
123 107 0.47
124 73 0.32
125 48 0.21
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (124 bp):
AGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAACAAATAGTATAAAATCGCTTCTAGCAG
GATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
Found at i:16457974 original size:23 final size:23
Alignment explanation
Indices: 16457944--16458160 Score: 252
Period size: 23 Copynumber: 9.6 Consensus size: 23
16457934 CATGACCAAA
16457944 GGTTTTTAATTAAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
*
16457967 GGTTTTTAATTTAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
16457990 GGTTTTTAATTAAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
* * *
16458013 GG-TTTGAGGGTT-AA--GGGTTAG
1 GGTTTTTA--ATTAAATTAGGTTAG
16458034 GGTTTTTAATTAAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
* *
16458057 GG-TTTTAGGGTT-AA--GGGTTAG
1 GGTTTTTA--ATTAAATTAGGTTAG
*
16458078 GGTTTTTAATTAAATCAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
*
16458101 GGTTTTTAATTAAATTAGGTTAA
1 GGTTTTTAATTAAATTAGGTTAG
16458124 GGTTTTTAATTAAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAG
*
16458147 GATTTTTAAGTTAA
1 GGTTTTTAA-TTAA
16458161 GGGTATTAAT
Statistics
Matches: 165, Mismatches: 16, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
20 4 0.02
21 20 0.12
22 18 0.11
23 115 0.70
24 8 0.05
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (23 bp):
GGTTTTTAATTAAATTAGGTTAG
Found at i:16458033 original size:21 final size:21
Alignment explanation
Indices: 16458007--16458083 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
16457997 AATTAAATTA
*
16458007 GGTTAGGGTTTGAGGGTTAAG
1 GGTTAGGGTTTTAGGGTTAAG
* *
16458028 GGTTAGGGTTTTTA--ATTAAATTA
1 GGTTAGGG-TTTTAGGGTT-AA--G
16458051 GGTTAGGGTTTTAGGGTTAAG
1 GGTTAGGGTTTTAGGGTTAAG
16458072 GGTTAGGGTTTT
1 GGTTAGGGTTTT
16458084 TAATTAAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 2 0.04
21 22 0.49
22 9 0.20
23 10 0.22
24 2 0.04
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.42
Consensus pattern (21 bp):
GGTTAGGGTTTTAGGGTTAAG
Found at i:16458047 original size:44 final size:44
Alignment explanation
Indices: 16457944--16458152 Score: 253
Period size: 44 Copynumber: 4.7 Consensus size: 44
16457934 CATGACCAAA
** *
16457944 GGTTTTTAATTAAATTAGGTTAGGGTTTTTA-ATTTAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAGGG-TTTTAGGGTTAA--GGGTTAG
*
16457990 GGTTTTTAATTAAATTAGGTTAGGGTTTGAGGGTTAAGGGTTAG
1 GGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTTAAGGGTTAG
16458034 GGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTTAAGGGTTAG
1 GGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTTAAGGGTTAG
* * * *
16458078 GGTTTTTAATTAAATCAGGTTAGGGTTTTTA--ATTAAATTAGGTTAA
1 GGTTTTTAATTAAATTAGGTTAGGG-TTTTAGGGTT-AA--GGGTTAG
*
16458124 GGTTTTTAATTAAATTAGGTTAGGATTTT
1 GGTTTTTAATTAAATTAGGTTAGGGTTTT
16458153 TAAGTTAAGG
Statistics
Matches: 147, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
43 2 0.01
44 75 0.51
45 13 0.09
46 57 0.39
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (44 bp):
GGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTTAAGGGTTAG
Found at i:16458099 original size:67 final size:66
Alignment explanation
Indices: 16457944--16458160 Score: 228
Period size: 67 Copynumber: 3.2 Consensus size: 66
16457934 CATGACCAAA
*
16457944 GGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTAAATTAGG
1 GGTTTTTAATTAAA-TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTTTAATTAAA-TAGG
16458009 TTAG
63 TTAG
* * * * *
16458013 GG-TTTGAGGGTT-AA-GGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTT-AA-GG
1 GGTTTTTA--ATTAAATAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTA--ATTAAATAG
16458073 GTTAG
62 GTTAG
*
16458078 GGTTTTTAATTAAATCAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTTTTAATTAAATTAGG
1 GGTTTTTAATTAAAT-AGGTTAGGGTTTTTAATTAAATTAGGTT-AGGGTTTTAATTAAA-TAGG
16458143 TTAG
63 TTAG
*
16458147 GATTTTTAAGTTAA
1 GGTTTTTAA-TTAA
16458161 GGGTATTAAT
Statistics
Matches: 122, Mismatches: 13, Indels: 25
0.76 0.08 0.16
Matches are distributed among these distances:
64 2 0.02
65 10 0.08
66 11 0.09
67 61 0.50
68 14 0.11
69 18 0.15
70 6 0.05
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (66 bp):
GGTTTTTAATTAAATAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTAATTAAATAGGTTA
G
Found at i:16458212 original size:9 final size:9
Alignment explanation
Indices: 16458191--16458232 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
16458181 ATTCTCAAAT
16458191 AATA-TCAA
1 AATATTCAA
* *
16458199 TATATTTAA
1 AATATTCAA
16458208 AATATTCAA
1 AATATTCAA
16458217 AATATTCAA
1 AATATTCAA
16458226 AATATTC
1 AATATTC
16458233 TATTTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
8 3 0.10
9 26 0.90
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (9 bp):
AATATTCAA
Found at i:16458259 original size:25 final size:25
Alignment explanation
Indices: 16458230--16458347 Score: 131
Period size: 25 Copynumber: 4.9 Consensus size: 25
16458220 ATTCAAAATA
16458230 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
16458255 TTCTATTTTATTACATCAAAT-AA-
1 TTCTATTTTATTACATCAAATAAAC
** * * * *
16458278 TATC-A--AAATAAC-TAAAAAAAAT
1 T-TCTATTTTATTACATCAAATAAAC
16458300 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
16458325 TTCTATTTTATTACATCAAATAA
1 TTCTATTTTATTACATCAAATAA
16458348 TATCAAAATA
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
20 4 0.05
21 8 0.11
22 2 0.03
23 2 0.03
24 8 0.11
25 51 0.68
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.42
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:16458307 original size:70 final size:71
Alignment explanation
Indices: 16458224--16458357 Score: 261
Period size: 70 Copynumber: 1.9 Consensus size: 71
16458214 CAAAATATTC
16458224 AAAATATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
1 AAAATATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
16458289 CTAAAA
66 CTAAAA
16458295 AAAAT-TTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
1 AAAATATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
16458358 TTCAAAATAT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
70 58 0.92
71 5 0.08
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.40
Consensus pattern (71 bp):
AAAATATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
CTAAAA
Found at i:16458799 original size:18 final size:18
Alignment explanation
Indices: 16458776--16458815 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
16458766 GACTCGAAAA
*
16458776 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
16458794 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
16458812 AGGA
1 AGGA
16458816 AACGCACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:16459477 original size:7 final size:7
Alignment explanation
Indices: 16459467--16459491 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16459457 TATATACATG
16459467 ATACTAA
1 ATACTAA
16459474 ATACTAA
1 ATACTAA
16459481 ATACTAA
1 ATACTAA
16459488 ATAC
1 ATAC
16459492 CAATCGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACTAA
Found at i:16462110 original size:22 final size:22
Alignment explanation
Indices: 16462085--16462157 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
16462075 CTCAAACTAA
16462085 TATTTTTATATATATACATATT
1 TATTTTTATATATATACATATT
* **
16462107 TATTTTTGATA-ATGTATTTA-T
1 TATTTTT-ATATATATACATATT
* *
16462128 TATTTTTA-ATCTATACATATA
1 TATTTTTATATATATACATATT
16462149 TATATTTTA
1 TAT-TTTTA
16462158 AAAACAAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
19 1 0.03
20 6 0.15
21 11 0.28
22 18 0.46
23 3 0.08
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (22 bp):
TATTTTTATATATATACATATT
Found at i:16462542 original size:17 final size:17
Alignment explanation
Indices: 16462520--16462554 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
16462510 TCCTTATGTA
16462520 TATTTGTTTCAT-TTATT
1 TATTTGTTT-ATATTATT
16462537 TATTTGTTTATATTATT
1 TATTTGTTTATATTATT
16462554 T
1 T
16462555 CTATGCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.71
Consensus pattern (17 bp):
TATTTGTTTATATTATT
Found at i:16471246 original size:13 final size:13
Alignment explanation
Indices: 16471228--16471280 Score: 88
Period size: 13 Copynumber: 4.1 Consensus size: 13
16471218 AGGTAGAGCC
16471228 AGTGCTTTTGAGA
1 AGTGCTTTTGAGA
* *
16471241 AGTGCTTTTCAAA
1 AGTGCTTTTGAGA
16471254 AGTGCTTTTGAGA
1 AGTGCTTTTGAGA
16471267 AGTGCTTTTGAGA
1 AGTGCTTTTGAGA
16471280 A
1 A
16471281 ATTTGAGTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.38
Consensus pattern (13 bp):
AGTGCTTTTGAGA
Found at i:16472588 original size:19 final size:19
Alignment explanation
Indices: 16472542--16472590 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
16472532 AACAGCTTCA
* *
16472542 AAATATTAAACAGAAGAGG
1 AAATATAAAACAGAAGAAG
*
16472561 AACTAATAAAACAGAAGAAG
1 AAAT-ATAAAACAGAAGAAG
16472581 AAATATAAAA
1 AAATATAAAA
16472591 GAAACTCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.65, C:0.06, G:0.14, T:0.14
Consensus pattern (19 bp):
AAATATAAAACAGAAGAAG
Found at i:16474652 original size:6 final size:6
Alignment explanation
Indices: 16474645--16474689 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
16474635 TATTGCATTA
*
16474645 TTATTA TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTA
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTA
16474690 CGTTTTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (6 bp):
TTATTG
Found at i:16474752 original size:26 final size:26
Alignment explanation
Indices: 16474723--16474772 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
16474713 ATATACACAC
16474723 GCATAGTTT-TTAATATATATATATAT
1 GCATAGTTTCTTAATA-ATATATATAT
* *
16474749 GCATATTTTCTTTATAATATATAT
1 GCATAGTTTCTTAATAATATATAT
16474773 GTATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (26 bp):
GCATAGTTTCTTAATAATATATATAT
Found at i:16474757 original size:24 final size:25
Alignment explanation
Indices: 16474730--16474783 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
16474720 CACGCATAGT
16474730 TTTTAATATAT-ATATATATGCATA
1 TTTTAATATATAATATATATGCATA
* * *
16474754 TTTT-CTTTATAATATATATGTATA
1 TTTTAATATATAATATATATGCATA
16474778 TTTTAA
1 TTTTAA
16474784 ACTTTTGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (25 bp):
TTTTAATATATAATATATATGCATA
Found at i:16474884 original size:26 final size:27
Alignment explanation
Indices: 16474855--16474923 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 27
16474845 ATATACATGT
*
16474855 ATACATATATACATT-TACATTTTATA
1 ATACATATATACATTCCACATTTTATA
* *
16474881 ATACATATATATATTCCATATTTTATA
1 ATACATATATACATTCCACATTTTATA
*
16474908 ATCCATGCATATACAT
1 ATACAT--ATATACAT
16474924 GCATTTTCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 14 0.40
27 14 0.40
29 7 0.20
ACGTcount: A:0.41, C:0.14, G:0.01, T:0.43
Consensus pattern (27 bp):
ATACATATATACATTCCACATTTTATA
Found at i:16475087 original size:17 final size:18
Alignment explanation
Indices: 16475062--16475095 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16475052 TTTTCAAAAT
*
16475062 TTATTTATATAT-CATAC
1 TTATATATATATACATAC
16475079 TTATATATATATACATA
1 TTATATATATATACATA
16475096 GTTTGTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATATATATATACATAC
Found at i:16476109 original size:16 final size:16
Alignment explanation
Indices: 16476076--16476109 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16476066 ACCTGTTGTT
* *
16476076 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
16476092 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
16476108 AA
1 AA
16476110 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:16478937 original size:21 final size:21
Alignment explanation
Indices: 16478911--16478951 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16478901 AGACGAGCAA
* *
16478911 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
16478932 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
16478952 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:16480890 original size:16 final size:16
Alignment explanation
Indices: 16480857--16480890 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16480847 GGAAATTGTT
* *
16480857 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
16480873 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
16480889 AA
1 AA
16480891 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:16483718 original size:21 final size:21
Alignment explanation
Indices: 16483692--16483732 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16483682 AGACGAGCAA
* *
16483692 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
16483713 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
16483733 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:16485671 original size:16 final size:16
Alignment explanation
Indices: 16485638--16485671 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16485628 GGAGATTGTT
* *
16485638 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
16485654 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
16485670 AA
1 AA
16485672 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:16497269 original size:17 final size:16
Alignment explanation
Indices: 16497247--16497281 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
16497237 TTTACAAAAT
16497247 TTGAATTTATTTCTCAA
1 TTGAATTTATTTC-CAA
16497264 TTGAATTTATTTCCAA
1 TTGAATTTATTTCCAA
16497280 TT
1 TT
16497282 TATTTAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (16 bp):
TTGAATTTATTTCCAA
Found at i:16502770 original size:34 final size:34
Alignment explanation
Indices: 16502732--16502804 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
16502722 TTGGTGATAC
* * *
16502732 TGTTTTTGTGCTGTTTTTTATGTTGTTTTGA-TGT
1 TGTTTTGGTGCTGCTTTTTATGGTGTTTT-ATTGT
*
16502766 TGTTTTGGTGCTGCTTTTTGTGGTGTTTTATTGT
1 TGTTTTGGTGCTGCTTTTTATGGTGTTTTATTGT
16502800 TGTTT
1 TGTTT
16502805 CGCAGTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 1 0.03
34 33 0.97
ACGTcount: A:0.04, C:0.04, G:0.26, T:0.66
Consensus pattern (34 bp):
TGTTTTGGTGCTGCTTTTTATGGTGTTTTATTGT
Found at i:16502887 original size:12 final size:12
Alignment explanation
Indices: 16502870--16502896 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16502860 AGAACTTTTG
16502870 TTTTATTATTAA
1 TTTTATTATTAA
16502882 TTTTATTATTAA
1 TTTTATTATTAA
16502894 TTT
1 TTT
16502897 AGTTCTAACT
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTATTATTAA
Found at i:16503013 original size:23 final size:22
Alignment explanation
Indices: 16502985--16503051 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 22
16502975 AGTATCATTT
16502985 TTTATTTGTTTATTATTTTAATA
1 TTTATTTGTTTATTATTTTAA-A
16503008 TTTA-TT-TTTATGT-TTTTAAA
1 TTTATTTGTTTAT-TATTTTAAA
*
16503028 TGTATTTGATTTATTATATTTAAA
1 TTTATTTG-TTTATTAT-TTTAAA
16503052 AAAATTATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
20 4 0.11
21 13 0.35
22 4 0.11
23 10 0.27
24 6 0.16
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (22 bp):
TTTATTTGTTTATTATTTTAAA
Found at i:16503062 original size:13 final size:13
Alignment explanation
Indices: 16503044--16503084 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
16503034 TGATTTATTA
16503044 TATTTAAAAAAAT
1 TATTTAAAAAAAT
*
16503057 TATTTAATAAAAT
1 TATTTAAAAAAAT
* *
16503070 AATCTAAAAAAAT
1 TATTTAAAAAAAT
16503083 TA
1 TA
16503085 ATATGGGCCG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
TATTTAAAAAAAT
Found at i:16507160 original size:51 final size:51
Alignment explanation
Indices: 16507074--16507241 Score: 259
Period size: 51 Copynumber: 3.3 Consensus size: 51
16507064 ACTTCTGATC
*
16507074 AGTGACAAGTGATAAGT-AGTAGCTTCAGCTGCACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGA-TAGCTTCAGCTACACTTATCTGATCAGTGACA
*
16507125 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
* * *
16507176 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGA-A
1 AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
16507226 GAGTGACAAGTGATAA
1 -AGTGACAAGTGATAA
16507242 ATGTGATCTG
Statistics
Matches: 109, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
50 1 0.01
51 107 0.98
52 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
Found at i:16510628 original size:16 final size:16
Alignment explanation
Indices: 16510607--16510642 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
16510597 TTTGGTTCGC
16510607 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
16510623 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
16510639 TGTA
1 TGTA
16510643 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:16510707 original size:44 final size:45
Alignment explanation
Indices: 16510623--16510713 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
16510613 GGATTAGAGG
* * *
16510623 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
16510668 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
16510712 TG
1 TG
16510714 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:16513440 original size:16 final size:17
Alignment explanation
Indices: 16513421--16513461 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
16513411 TTGAAGATGC
16513421 AAATTAAATT-TTA-TA
1 AAATTAAATTATTAGTA
*
16513436 AAAAT-AATTATTAGTA
1 AAATTAAATTATTAGTA
16513452 AAATTAAATT
1 AAATTAAATT
16513462 CAAGATGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 4 0.19
15 7 0.33
16 6 0.29
17 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AAATTAAATTATTAGTA
Found at i:16515382 original size:21 final size:22
Alignment explanation
Indices: 16515339--16515387 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
16515329 AAGCAGATGG
16515339 AGCCACTGCAAATAAATTATAT
1 AGCCACTGCAAATAAATTATAT
* * *
16515361 AGCCACTGGAAA-CAATTGTAT
1 AGCCACTGCAAATAAATTATAT
16515382 AGCCAC
1 AGCCAC
16515388 AAGCAATGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (22 bp):
AGCCACTGCAAATAAATTATAT
Found at i:16515583 original size:26 final size:26
Alignment explanation
Indices: 16515554--16515607 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
16515544 TTGTTTTCTG
16515554 ATTTAACAATCAATATTCATGTCTCT
1 ATTTAACAATCAATATTCATGTCTCT
16515580 ATTTAACAATCAATATTCATGTCTCT
1 ATTTAACAATCAATATTCATGTCTCT
16515606 AT
1 AT
16515608 CTTCTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.43
Consensus pattern (26 bp):
ATTTAACAATCAATATTCATGTCTCT
Found at i:16517232 original size:12 final size:11
Alignment explanation
Indices: 16517196--16517248 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
16517186 ATTTTTTAAA
16517196 TTTTAAAATAT
1 TTTTAAAATAT
* *
16517207 TCTAAAAATAT
1 TTTTAAAATAT
16517218 TTTTAAAATACTT
1 TTTTAAAATA--T
*
16517231 TTTTTAAAT-T
1 TTTTAAAATAT
16517241 TTTTAAAA
1 TTTTAAAA
16517249 AAATTGGTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
10 8 0.24
11 17 0.50
13 9 0.26
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:16520464 original size:25 final size:24
Alignment explanation
Indices: 16520422--16520528 Score: 101
Period size: 25 Copynumber: 4.3 Consensus size: 24
16520412 AAGCTCATGC
* *
16520422 GAGCCAATATCGGGAAGCTCTGGA
1 GAGCCATTAACGGGAAGCTCTGGA
16520446 GAGCCATTAATCGGGAAGCTCAT-GA
1 GAGCCATTAA-CGGGAAGCTC-TGGA
16520471 GAGCCAATTAACGGGAAGCTC-GTGA
1 GAGCC-ATTAACGGGAAGCTCTG-GA
* * **
16520496 GAGCCAAATAACGGAAAGCTCAAGA
1 GAGCC-ATTAACGGGAAGCTCTGGA
16520521 GAGCCATT
1 GAGCCATT
16520529 TATTGGGATT
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
24 10 0.14
25 55 0.77
26 6 0.08
ACGTcount: A:0.35, C:0.21, G:0.29, T:0.16
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCTGGA
Found at i:16520475 original size:49 final size:50
Alignment explanation
Indices: 16520411--16520526 Score: 148
Period size: 50 Copynumber: 2.3 Consensus size: 50
16520401 TCAAATTCGA
* * *
16520411 GAAGCTCATGCGAGCCAA-TATCGGGAAGCTC-TGGAGAGCC-ATTAATCGG
1 GAAGCTCATGAGAGCCAATTAACGGGAAGCTCGT-GAGAGCCAAATAA-CGG
16520460 GAAGCTCATGAGAGCCAATTAACGGGAAGCTCGTGAGAGCCAAATAACGG
1 GAAGCTCATGAGAGCCAATTAACGGGAAGCTCGTGAGAGCCAAATAACGG
* *
16520510 AAAGCTCAAGAGAGCCA
1 GAAGCTCATGAGAGCCA
16520527 TTTATTGGGA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
49 17 0.29
50 37 0.63
51 5 0.08
ACGTcount: A:0.34, C:0.22, G:0.29, T:0.15
Consensus pattern (50 bp):
GAAGCTCATGAGAGCCAATTAACGGGAAGCTCGTGAGAGCCAAATAACGG
Done.