Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 60 of 433
Found at i:17105583 original size:13 final size:13
Alignment explanation
Indices: 17105565--17105599 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
17105555 AGTAATCGAA
17105565 CACGGGCGTGTGC
1 CACGGGCGTGTGC
17105578 CACGGGCGTGTGC
1 CACGGGCGTGTGC
17105591 CACGGGCGT
1 CACGGGCGT
17105600 CTCCCTGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.09, C:0.31, G:0.46, T:0.14
Consensus pattern (13 bp):
CACGGGCGTGTGC
Found at i:17110604 original size:40 final size:40
Alignment explanation
Indices: 17110555--17110657 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
17110545 ATCTCGGTAT
17110555 TGCACACTTAGTGCC-TCATATAGCCGAA-GCTATTTC-AAC
1 TGCACACTTAGTGCCAT-ATATAGCC-AAGGCTATTTCGAAC
* *
17110594 TCGCACACTTAGTGCCATTTGTAGCCAAGGCTATTTCGAAC
1 T-GCACACTTAGTGCCATATATAGCCAAGGCTATTTCGAAC
*
17110635 TGCACACTTACTGCCGA-ATATAG
1 TGCACACTTAGTGCC-ATATATAG
17110658 TCAATAATCA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
39 3 0.06
40 45 0.83
41 6 0.11
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (40 bp):
TGCACACTTAGTGCCATATATAGCCAAGGCTATTTCGAAC
Found at i:17113615 original size:40 final size:40
Alignment explanation
Indices: 17113489--17113617 Score: 156
Period size: 40 Copynumber: 3.2 Consensus size: 40
17113479 ATGCTGGAAA
* *
17113489 TTATATCCGGGTTAAGA-CCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
17113528 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
17113568 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
17113608 TTATATCCGG
1 TTATATCCGG
17113618 TTGTATTCCG
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 18 0.24
40 57 0.76
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:17119999 original size:62 final size:61
Alignment explanation
Indices: 17119917--17120040 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 61
17119907 CGGGATTTAG
*
17119917 CCGGATATAGCAACTCGCAAATGCCTTCGGACTTAGCCCGG-ATAAGTAACTAGCACAAATGC
1 CCGGATATAGCAACTAGCAAATGCCTTCGGACTTAG--CGGTATAAGTAACTAGCACAAATGC
*
17119979 CCGGATATAGTAACTAGCAAATGCCTTCGGACTTAGCGGTATAAGTAACTAGCACAAATGC
1 CCGGATATAGCAACTAGCAAATGCCTTCGGACTTAGCGGTATAAGTAACTAGCACAAATGC
17120040 C
1 C
17120041 TTCGGGACTT
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
60 3 0.05
61 22 0.37
62 34 0.58
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (61 bp):
CCGGATATAGCAACTAGCAAATGCCTTCGGACTTAGCGGTATAAGTAACTAGCACAAATGC
Found at i:17120009 original size:26 final size:24
Alignment explanation
Indices: 17119952--17120003 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 24
17119942 TTCGGACTTA
17119952 GCCCGGATAAGTAACTAGCACAAAT
1 GCCCGGATAAGTAACTAG-ACAAAT
17119977 GCCCGGATATAGTAACTAG-CAAAT
1 GCCCGGATA-AGTAACTAGACAAAT
17120001 GCC
1 GCC
17120004 TTCGGACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 8 0.31
25 9 0.35
26 9 0.35
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (24 bp):
GCCCGGATAAGTAACTAGACAAAT
Found at i:17120121 original size:79 final size:79
Alignment explanation
Indices: 17119977--17120180 Score: 346
Period size: 79 Copynumber: 2.6 Consensus size: 79
17119967 TAGCACAAAT
17119977 GCCCGGATATAGTAACTAG--CAAATGCCTTCGGACTTAG-CGG-TATAAGTAACTAGCACAAAT
1 GCCCGGATATAGTAACTAGCACAAATGCCTTCGGACTTAGCCGGTTATAAGTAACTAGCACAAAT
17120038 GCCTTCGGGACTTA
66 GCCTTCGGGACTTA
17120052 GCCCGGATATAGTAACTAGCACAAATGCCTTCGGACTTAGCCCGGTTAT-AGTAACTAGCACAAA
1 GCCCGGATATAGTAACTAGCACAAATGCCTTCGGACTTAG-CCGGTTATAAGTAACTAGCACAAA
17120116 TGCCTTCGGGACTTA
65 TGCCTTCGGGACTTA
17120131 GCCCGGATATAGTAACTAGCACAAATGCCTTCGGATCTTAGTCCGGTTAT
1 GCCCGGATATAGTAACTAGCACAAATGCCTTCGGA-CTTAG-CCGGTTAT
17120181 CATCCGAATA
Statistics
Matches: 122, Mismatches: 1, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
75 19 0.16
77 19 0.16
79 68 0.56
80 16 0.13
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (79 bp):
GCCCGGATATAGTAACTAGCACAAATGCCTTCGGACTTAGCCGGTTATAAGTAACTAGCACAAAT
GCCTTCGGGACTTA
Found at i:17120171 original size:40 final size:39
Alignment explanation
Indices: 17119977--17120176 Score: 311
Period size: 40 Copynumber: 5.2 Consensus size: 39
17119967 TAGCACAAAT
17119977 GCCCGGATATAGTAACTAG--CAAATGCCTTCGGACTTA
1 GCCCGGATATAGTAACTAGCACAAATGCCTTCGGACTTA
17120014 G--CGG-TATAAGTAACTAGCACAAATGCCTTCGGGACTTA
1 GCCCGGATAT-AGTAACTAGCACAAATGCCTTC-GGACTTA
17120052 GCCCGGATATAGTAACTAGCACAAATGCCTTCGGACTTA
1 GCCCGGATATAGTAACTAGCACAAATGCCTTCGGACTTA
*
17120091 GCCCGGTTATAGTAACTAGCACAAATGCCTTCGGGACTTA
1 GCCCGGATATAGTAACTAGCACAAATGCCTTC-GGACTTA
17120131 GCCCGGATATAGTAACTAGCACAAATGCCTTCGGATCTTA
1 GCCCGGATATAGTAACTAGCACAAATGCCTTCGGA-CTTA
*
17120171 GTCCGG
1 GCCCGG
17120177 TTATCATCCG
Statistics
Matches: 151, Mismatches: 3, Indels: 15
0.89 0.02 0.09
Matches are distributed among these distances:
34 3 0.02
35 12 0.08
37 12 0.08
38 8 0.05
39 41 0.27
40 72 0.48
41 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (39 bp):
GCCCGGATATAGTAACTAGCACAAATGCCTTCGGACTTA
Found at i:17121597 original size:13 final size:13
Alignment explanation
Indices: 17121581--17121608 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17121571 TTTATTATTT
17121581 TTAACACAAAATA
1 TTAACACAAAATA
17121594 TTAACACAAAATA
1 TTAACACAAAATA
17121607 TT
1 TT
17121609 TATAATATGT
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:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (13 bp):
TTAACACAAAATA
Found at i:17128181 original size:40 final size:40
Alignment explanation
Indices: 17128107--17128244 Score: 165
Period size: 40 Copynumber: 3.5 Consensus size: 40
17128097 AACCCAAGTA
* *
17128107 CCTTCGGGAT-TTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTC-GGATCTTAGTCCGGATATAGTAACTAGCACAAATG
* * *
17128146 CCTTTGGATCTTAGTCCGGTTATAGTAACTAGCACAAATA
1 CCTTCGGATCTTAGTCCGGATATAGTAACTAGCACAAATG
* * *
17128186 CCTTCGGGA-CTTAGCCCGAATATAGTAACTAGCACTAATG
1 CCTTC-GGATCTTAGTCCGGATATAGTAACTAGCACAAATG
17128226 CCTTCGGATCTTAGTCCGG
1 CCTTCGGATCTTAGTCCGG
17128245 TTATCATCCG
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
38 4 0.05
39 11 0.13
40 64 0.78
41 3 0.04
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (40 bp):
CCTTCGGATCTTAGTCCGGATATAGTAACTAGCACAAATG
Found at i:17129670 original size:13 final size:13
Alignment explanation
Indices: 17129654--17129681 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17129644 TTTATTATTT
17129654 TTAACACAAAATA
1 TTAACACAAAATA
17129667 TTAACACAAAATA
1 TTAACACAAAATA
17129680 TT
1 TT
17129682 TATAATATGT
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:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (13 bp):
TTAACACAAAATA
Found at i:17132198 original size:40 final size:40
Alignment explanation
Indices: 17132131--17132295 Score: 208
Period size: 40 Copynumber: 4.2 Consensus size: 40
17132121 ACTCAAGTAT
* *
17132131 CTTCGGGATTTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGC
** *
17132170 CTTCGGGTTTTAGCCCGGATATAGCAACTCTCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * *
17132210 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* *
17132250 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGC
17132290 CTTCGG
1 CTTCGG
17132296 ATCTTAGTCC
Statistics
Matches: 109, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
39 14 0.13
40 93 0.85
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:17132248 original size:80 final size:79
Alignment explanation
Indices: 17132131--17132307 Score: 232
Period size: 80 Copynumber: 2.2 Consensus size: 79
17132121 ACTCAAGTAT
* ***
17132131 CTTCGGGAT-TTAGCCGGATATAACAACTCGCACAAATGCCTTCGGGTTTTAGCCCGGATATAGC
1 CTTCGGG-TCTTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGC
*
17132195 AACTCTCACAAATGC
65 AACTCGCACAAATGC
*
17132210 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAG
1 CTTCGGGTCTTAG-CCGGATATAA-CAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAG
*
17132274 CAACTCGCACGAATGC
64 CAACTCGCACAAATGC
*
17132290 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAG-CCGG
17132308 TTATCATCCG
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
78 1 0.01
79 11 0.13
80 73 0.85
81 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
CTTCGGGTCTTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGCA
ACTCGCACAAATGC
Found at i:17137759 original size:27 final size:28
Alignment explanation
Indices: 17137657--17137766 Score: 147
Period size: 27 Copynumber: 4.1 Consensus size: 28
17137647 TGCTCTACAT
* * *
17137657 GGGTATTTTGGTAATTTTACACTAC-AA
1 GGGTATTTCGGTAATTTTACACAACTAG
* *
17137684 GGGTATTTCAGTAATTTTACACTA-TAG
1 GGGTATTTCGGTAATTTTACACAACTAG
17137711 GGGTATTTCGGTAATTTTACA-AACTAG
1 GGGTATTTCGGTAATTTTACACAACTAG
17137738 GGGTATTTCGGTAATTTTACA-AACTAG
1 GGGTATTTCGGTAATTTTACACAACTAG
17137765 GG
1 GG
17137767 CTTTAACGAC
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
26 1 0.01
27 75 0.99
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (28 bp):
GGGTATTTCGGTAATTTTACACAACTAG
Found at i:17144539 original size:40 final size:40
Alignment explanation
Indices: 17144412--17144541 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
17144402 ATGCTGGAAA
* * * *
17144412 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
17144452 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
17144492 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
17144532 TTATATCCGG
1 TTATATCCGG
17144542 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:17149239 original size:68 final size:70
Alignment explanation
Indices: 17149167--17149364 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
17149157 ACACCCTGTA
* * * *
17149167 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
17149229 ATAAAT
65 ATAAAT
*
17149235 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
17149300 ATAAAT
65 ATAAAT
*
17149306 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
17149365 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:17149278 original size:41 final size:41
Alignment explanation
Indices: 17149233--17149350 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
17149223 TGAAAGATAA
17149233 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
17149274 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
17149304 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
17149345 ATGTAG
1 ATGTAG
17149351 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:17149290 original size:71 final size:71
Alignment explanation
Indices: 17149201--17149364 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
17149191 GAGATGTATC
17149201 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
17149266 AGGACA
66 AGGACA
17149272 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
17149337 AGGACA
66 AGGACA
17149343 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
17149365 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:17155944 original size:68 final size:70
Alignment explanation
Indices: 17155872--17156069 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
17155862 ACACCCTGTA
* * * *
17155872 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
17155934 ATAAAT
65 ATAAAT
*
17155940 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
17156005 ATAAAT
65 ATAAAT
*
17156011 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
17156070 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:17155983 original size:41 final size:41
Alignment explanation
Indices: 17155938--17156055 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
17155928 TGAAAGATAA
17155938 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
17155979 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
17156009 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
17156050 ATGTAG
1 ATGTAG
17156056 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:17155995 original size:71 final size:71
Alignment explanation
Indices: 17155906--17156069 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
17155896 GAGATGTATC
17155906 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
17155971 AGGACA
66 AGGACA
17155977 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
17156042 AGGACA
66 AGGACA
17156048 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
17156070 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:17161017 original size:46 final size:46
Alignment explanation
Indices: 17160870--17161073 Score: 187
Period size: 46 Copynumber: 4.4 Consensus size: 46
17160860 GTGTGTGAGT
* *** *
17160870 TAGTGTAAGACATGTCTGGGACATGCATCGGCCACCTTA-TTAGAGC
1 TAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA-AGC
* * * * *
17160916 TAATGTAAGACTATGTCTGGGACATGGCATTGGCATTGAGACGAAAGC
1 TAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCCTCGAGACGTAAGC
*
17160964 TAGTGTAAGACATGTCTGAGACATGCATCGGCCTCGAGACGTAAGC
1 TAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTAAGC
* * * * ** *
17161010 CAGTGTAAGACATGTTTGGGACATGACATC-GACTTGAGATATGAGC
1 TAGTGTAAGACATGTCTGGGACATG-CATCGGCCTCGAGACGTAAGC
17161056 TAGTGTAAGACCATGTCT
1 TAGTGTAAGA-CATGTCT
17161074 AAGACATGGC
Statistics
Matches: 127, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
46 70 0.55
47 35 0.28
48 21 0.17
49 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (46 bp):
TAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTAAGC
Found at i:17162714 original size:13 final size:13
Alignment explanation
Indices: 17162698--17162730 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17162688 TTTAATTAAA
*
17162698 TTAGTTAATTAGT
1 TTAGATAATTAGT
17162711 TTAGATAATTAGT
1 TTAGATAATTAGT
17162724 TTA-ATAA
1 TTAGATAA
17162731 ACAAACCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:17170632 original size:40 final size:40
Alignment explanation
Indices: 17170557--17170761 Score: 317
Period size: 40 Copynumber: 5.2 Consensus size: 40
17170547 CGGATGATAA
* *
17170557 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
*
17170597 CGAAGGCATTTGTGCGAGTTACTATATCCGAGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
17170637 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
17170677 CGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* *
17170717 CGAAGGCATTTGTGCGAG-TAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCC
17170756 CGAAGG
1 CGAAGG
17170762 TACATGGTTT
Statistics
Matches: 156, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 16 0.10
40 139 0.89
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:17173493 original size:40 final size:40
Alignment explanation
Indices: 17173448--17173614 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
17173438 CGGAATATAA
17173448 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
17173488 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
17173528 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
17173568 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
17173607 CCGGATAT
1 CCGGATAT
17173615 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:17181512 original size:40 final size:40
Alignment explanation
Indices: 17181467--17181633 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
17181457 CGGAATATAA
17181467 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
17181507 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
17181547 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
17181587 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
17181626 CCGGATAT
1 CCGGATAT
17181634 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:17185194 original size:60 final size:60
Alignment explanation
Indices: 17185100--17185221 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
17185090 TTGCAAAAGA
17185100 AAAACCATCAATTTAAGGTGTGTGAATAAAGAGGTAATCCGAGTTGAGTCTACTGACTTG
1 AAAACCATCAATTTAAGGTGTGTGAATAAAGAGGTAATCCGAGTTGAGTCTACTGACTTG
*
17185160 AAAACCATCAATTTAAGGTGTGTGAATAATGAGGTAATCCGAGTTGAGTCTACTGACTTG
1 AAAACCATCAATTTAAGGTGTGTGAATAAAGAGGTAATCCGAGTTGAGTCTACTGACTTG
17185220 AA
1 AA
17185222 TAGGTTGCCA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (60 bp):
AAAACCATCAATTTAAGGTGTGTGAATAAAGAGGTAATCCGAGTTGAGTCTACTGACTTG
Found at i:17189230 original size:40 final size:40
Alignment explanation
Indices: 17189156--17189320 Score: 219
Period size: 40 Copynumber: 4.2 Consensus size: 40
17189146 CGGATGATAA
* * * *
17189156 CGAAGGCATTTGTACTAGTGACTA-ATTCCAGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
17189196 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
17189236 CGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
17189276 CGAAGGCATTTGAGCGAG-TAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCC
17189315 CGAAGG
1 CGAAGG
17189321 TACTTGGTTT
Statistics
Matches: 115, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
39 16 0.14
40 98 0.85
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:17191284 original size:68 final size:70
Alignment explanation
Indices: 17191212--17191409 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
17191202 ACACCCTGTA
* * * *
17191212 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
17191274 ATAAAT
65 ATAAAT
*
17191280 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
17191345 ATAAAT
65 ATAAAT
*
17191351 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
17191410 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:17191323 original size:41 final size:41
Alignment explanation
Indices: 17191278--17191395 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
17191268 TGAAAGATAA
17191278 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
17191319 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
17191349 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
17191390 ATGTAG
1 ATGTAG
17191396 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:17191335 original size:71 final size:71
Alignment explanation
Indices: 17191246--17191409 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
17191236 GAGATGTATC
17191246 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
17191311 AGGACA
66 AGGACA
17191317 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
17191382 AGGACA
66 AGGACA
17191388 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
17191410 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:17198852 original size:68 final size:70
Alignment explanation
Indices: 17198780--17198977 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
17198770 ACACCCTGTA
* * * *
17198780 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
17198842 ATAAAT
65 ATAAAT
*
17198848 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
17198913 ATAAAT
65 ATAAAT
*
17198919 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
17198978 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:17198891 original size:41 final size:41
Alignment explanation
Indices: 17198846--17198963 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
17198836 TGAAAGATAA
17198846 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
17198887 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
17198917 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
17198958 ATGTAG
1 ATGTAG
17198964 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:17198903 original size:71 final size:71
Alignment explanation
Indices: 17198814--17198977 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
17198804 GAGATGTATC
17198814 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
17198879 AGGACA
66 AGGACA
17198885 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
17198950 AGGACA
66 AGGACA
17198956 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
17198978 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:17202471 original size:13 final size:13
Alignment explanation
Indices: 17202455--17202487 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17202445 TTTAATTAAA
*
17202455 TTAGTTAATTAGT
1 TTAGATAATTAGT
17202468 TTAGATAATTAGT
1 TTAGATAATTAGT
17202481 TTA-ATAA
1 TTAGATAA
17202488 ACAAACCCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:17209555 original size:47 final size:46
Alignment explanation
Indices: 17209480--17209654 Score: 180
Period size: 47 Copynumber: 3.7 Consensus size: 46
17209470 ATTTGTGTGT
17209480 GAGCTAGTGTAAGA-CATGTCTGGGACATGCATCGACCAGCTTATGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGACCAG-TTATGA
* *
17209526 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCTA-TTAGATGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGACCAGTT--ATGA
* * * *
17209573 TAG-TCAGTGTAAGACAATGTCTGGGACATGGCATCGACTTGAGATAT--
1 GAGCT-AGTGTAAGACCATGTCTGGGACAT-GCATCGAC--CAGTTATGA
*
17209620 GAGCTAGTGTAAGACCATGTCTGGGATATGACATC
1 GAGCTAGTGTAAGACCATGTCTGGGACATG-CATC
17209655 AGCACCTTAC
Statistics
Matches: 109, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
45 2 0.02
46 16 0.15
47 79 0.72
48 8 0.07
49 2 0.02
50 1 0.01
51 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (46 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGACCAGTTATGA
Found at i:17211402 original size:85 final size:85
Alignment explanation
Indices: 17211259--17211428 Score: 322
Period size: 85 Copynumber: 2.0 Consensus size: 85
17211249 TTTTGCAACC
*
17211259 TGGACTCTAATACCACTAAATGTAACACCTAAAACCTGGCCTAAATGTTAGACCCGAATCTAGCA
1 TGGACTCTAATACCACTAAATGTAACACCCAAAACCTGGCCTAAATGTTAGACCCGAATCTAGCA
17211324 TGTCATATTGAAGTGTCTTT
66 TGTCATATTGAAGTGTCTTT
*
17211344 TGGACTCTAATACCACTAAATGTAACACCCAAAACCTGGCCTAAATGTTAGGCCCGAATCTAGCA
1 TGGACTCTAATACCACTAAATGTAACACCCAAAACCTGGCCTAAATGTTAGACCCGAATCTAGCA
17211409 TGTCATATTGAAGTGTCTTT
66 TGTCATATTGAAGTGTCTTT
17211429 CGAAAATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (85 bp):
TGGACTCTAATACCACTAAATGTAACACCCAAAACCTGGCCTAAATGTTAGACCCGAATCTAGCA
TGTCATATTGAAGTGTCTTT
Found at i:17212390 original size:22 final size:22
Alignment explanation
Indices: 17212359--17212415 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
17212349 AATACAATTG
*
17212359 GCACAAAGCCATAGTTAAGATA
1 GCACAGAGCCATAGTTAAGATA
* * * *
17212381 GCACAGAGCCATATTTAGGCTG
1 GCACAGAGCCATAGTTAAGATA
17212403 GCACAGAGCCATA
1 GCACAGAGCCATA
17212416 AACAGATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.18
Consensus pattern (22 bp):
GCACAGAGCCATAGTTAAGATA
Found at i:17212543 original size:50 final size:50
Alignment explanation
Indices: 17212448--17212544 Score: 142
Period size: 50 Copynumber: 1.9 Consensus size: 50
17212438 CGTCCGCCGG
*
17212448 TCCACAGTCGTCTCGTGCGACCCGTGAGACCTTAACAGAGCAATACTGGA
1 TCCACAGTCGTCTCGTGCGACCCGTGAGACCCTAACAGAGCAATACTGGA
* * *
17212498 TCCATAGTCGTCTCGTGCGACCCGTGCGACCCTATCAGAAG-AATACT
1 TCCACAGTCGTCTCGTGCGACCCGTGAGACCCTAACAG-AGCAATACT
17212545 TCCTCTATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 40 0.95
51 2 0.05
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.22
Consensus pattern (50 bp):
TCCACAGTCGTCTCGTGCGACCCGTGAGACCCTAACAGAGCAATACTGGA
Found at i:17212892 original size:82 final size:82
Alignment explanation
Indices: 17212767--17212922 Score: 199
Period size: 82 Copynumber: 1.9 Consensus size: 82
17212757 TTACACTATA
** *
17212767 AGGGTATTTCAGTAATTTTACACTTCTAAGGTACTTCGGTAATTTCACAAA-TGGAGGGTATTTC
1 AGGGTATTTCAGTAATTTTACAAATCTAAGGTACTTCGATAATTTCACAAACT-GAGGGTATTTC
17212831 AATAATTTTACAAACCTG
65 AATAATTTTACAAACCTG
* * * *
17212849 AGGGTATTTCAGTAATTTTACAAATC-ATGGGTATTTCGATAATTTTATAAACTGAGGGTATTTC
1 AGGGTATTTCAGTAATTTTACAAATCTA-AGGTACTTCGATAATTTCACAAACTGAGGGTATTTC
**
17212913 GGTAATTTTA
65 AATAATTTTA
17212923 TAATCCGAGG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 1 0.02
82 61 0.97
83 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (82 bp):
AGGGTATTTCAGTAATTTTACAAATCTAAGGTACTTCGATAATTTCACAAACTGAGGGTATTTCA
ATAATTTTACAAACCTG
Found at i:17212925 original size:27 final size:26
Alignment explanation
Indices: 17212743--17212922 Score: 162
Period size: 27 Copynumber: 6.7 Consensus size: 26
17212733 ACTATAAGGT
* *
17212743 GTATTTCGGTAATTTTACACTATAAGG
1 GTATTTCGGTAATTTTACA-AATGAGG
* ** * *
17212770 GTATTTCAGTAATTTTACACTTCTAAG
1 GTATTTCGGTAATTTTACAAAT-GAGG
* *
17212797 GTACTTCGGTAATTTCACAAATGGAGG
1 GTATTTCGGTAATTTTACAAAT-GAGG
**
17212824 GTATTTCAATAATTTTACAAACCTGAGG
1 GTATTTCGGTAATTTTACAAA--TGAGG
* *
17212852 GTATTTCAGTAATTTTACAAATCATGG
1 GTATTTCGGTAATTTTACAAATGA-GG
* *
17212879 GTATTTCGATAATTTTATAAACTGAGG
1 GTATTTCGGTAATTTTACAAA-TGAGG
17212906 GTATTTCGGTAATTTTA
1 GTATTTCGGTAATTTTA
17212923 TAATCCGAGG
Statistics
Matches: 124, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
26 3 0.02
27 94 0.76
28 26 0.21
29 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (26 bp):
GTATTTCGGTAATTTTACAAATGAGG
Found at i:17222759 original size:18 final size:18
Alignment explanation
Indices: 17222714--17222762 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
17222704 TATCCTCCTG
17222714 ATTT-TGTTTTTATTTCA
1 ATTTATGTTTTTATTTCA
* *
17222731 ATTGA-GTTTTTTTTTTCA
1 ATTTATG-TTTTTATTTCA
17222749 ATTTATGTTTTTAT
1 ATTTATGTTTTTAT
17222763 ATTCTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
17 4 0.16
18 20 0.80
19 1 0.04
ACGTcount: A:0.18, C:0.04, G:0.08, T:0.69
Consensus pattern (18 bp):
ATTTATGTTTTTATTTCA
Found at i:17222828 original size:13 final size:13
Alignment explanation
Indices: 17222791--17222820 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17222781 ATTATTCATT
*
17222791 TTTTAGCATATTA
1 TTTTAACATATTA
17222804 TTTTAACATATTA
1 TTTTAACATATTA
17222817 TTTT
1 TTTT
17222821 GAACTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (13 bp):
TTTTAACATATTA
Found at i:17225804 original size:33 final size:34
Alignment explanation
Indices: 17225726--17225819 Score: 111
Period size: 34 Copynumber: 2.8 Consensus size: 34
17225716 GTTTCAGTTA
* * *
17225726 GGGCCTTAGCCTATTTCAGTGA-CAGTATCAATCT
1 GGGCCTAAGCCCATTTCAGT-ATCAGTATCAATCG
*
17225760 GGGCCTGAGCCCATTTCAGTATCAGTATCAAT-G
1 GGGCCTAAGCCCATTTCAGTATCAGTATCAATCG
* *
17225793 GGGCCTAAGCCCATTACAGAATCAGTA
1 GGGCCTAAGCCCATTTCAGTATCAGTA
17225820 CAGTATGCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
33 25 0.47
34 28 0.53
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (34 bp):
GGGCCTAAGCCCATTTCAGTATCAGTATCAATCG
Found at i:17229607 original size:43 final size:43
Alignment explanation
Indices: 17229545--17229826 Score: 375
Period size: 43 Copynumber: 6.6 Consensus size: 43
17229535 TATGTGACAC
* *
17229545 CGATATGTGATTACGTGTAAGACCGCGTCTGGGACGTTGGTAT
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
* * * *
17229588 GGATATGTGATTATGTGTAAGACCACATTTGGGACGTTGGCAT
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
* * * * * *
17229631 TGATATGTGATTACGTGTAAGACCGCATCTGGGATGTTAGCAC
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
* *
17229674 CGATATGTGATTATGTGTAAGACCACGTCTGGGACATTGGCAT
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
* *
17229717 CGATATGTGATTACGTGCAAGACCACGTTTGGGACGTTGGCAT
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
17229760 CGATATGTGATTACGTGTAAAACCACGTCTGGGATGTTGGCAA
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
* *
17229803 CGATATGTGTTTACGAGTAAGACC
1 CGATATGTGATTACGTGTAAGACC
17229827 CTGTCTAAGA
Statistics
Matches: 206, Mismatches: 33, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 206 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (43 bp):
CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:17229772 original size:129 final size:129
Alignment explanation
Indices: 17229542--17229826 Score: 426
Period size: 129 Copynumber: 2.2 Consensus size: 129
17229532 GTATATGTGA
* * * * * *
17229542 CACCGATATGTGATTACGTGTAAGACCGCGTCTGGGACGTTGGTATGGATATGTGATTATGTGTA
1 CACCGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTACGTGCA
* * *
17229607 AGACCACATTTGGGACGTTGGCATTGATATGTGATTACGTGTAAGACCGCATCTGGGATGTTAG
66 AGACCACATTTGGGACGTTGGCATCGATATGTGATTACGTGTAAAACCACATCTGGGATGTTAG
*
17229671 CACCGATATGTGATTATGTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTACGTGCA
1 CACCGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTACGTGCA
* * *
17229736 AGACCACGTTTGGGACGTTGGCATCGATATGTGATTACGTGTAAAACCACGTCTGGGATGTTGG
66 AGACCACATTTGGGACGTTGGCATCGATATGTGATTACGTGTAAAACCACATCTGGGATGTTAG
* * *
17229800 CAACGATATGTGTTTACGAGTAAGACC
1 CACCGATATGTGATTACGTGTAAGACC
17229827 CTGTCTAAGA
Statistics
Matches: 139, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
129 139 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (129 bp):
CACCGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTACGTGCA
AGACCACATTTGGGACGTTGGCATCGATATGTGATTACGTGTAAAACCACATCTGGGATGTTAG
Found at i:17238077 original size:2 final size:2
Alignment explanation
Indices: 17238070--17238095 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17238060 ACCAGAACAG
17238070 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
17238096 GTGGTGAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17242091 original size:30 final size:30
Alignment explanation
Indices: 17242055--17242117 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
17242045 CCTTTTCATA
17242055 TTTCATATTTCATAATACTGGGCCGAAGCC
1 TTTCATATTTCATAATACTGGGCCGAAGCC
*
17242085 TTTCATATTTCATATTACTGGGCCGAAGCC
1 TTTCATATTTCATAATACTGGGCCGAAGCC
17242115 TTT
1 TTT
17242118 ACTGTAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (30 bp):
TTTCATATTTCATAATACTGGGCCGAAGCC
Found at i:17242334 original size:24 final size:24
Alignment explanation
Indices: 17242307--17242472 Score: 255
Period size: 24 Copynumber: 7.0 Consensus size: 24
17242297 GCTTTATCAT
* * *
17242307 ATAACTGGAGGCCT-AGCCTTTTTA
1 ATAACTGG-GGCATAAGCCCTTTTG
* **
17242331 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTG
17242355 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTG
17242378 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
17242402 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
17242426 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
17242450 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
17242473 TCACTTCCTC
Statistics
Matches: 134, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
23 26 0.19
24 108 0.81
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:17242406 original size:71 final size:71
Alignment explanation
Indices: 17242306--17242472 Score: 255
Period size: 71 Copynumber: 2.3 Consensus size: 71
17242296 TGCTTTATCA
* *
17242306 TATAACTGGAGGCCT-AGCCTTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGG-GGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
17242370 GCCCTTT
65 GCCCTTT
* * **
17242377 TATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAG
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAG
17242442 CCCTTT
66 CCCTTT
17242448 TGATAACTGGGGCATAAGCCCTTTT
1 T-ATAACTGGGGCATAAGCCCTTTT
17242473 TCACTTCCTC
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
70 4 0.05
71 61 0.69
72 23 0.26
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (71 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAG
CCCTTT
Found at i:17242548 original size:20 final size:20
Alignment explanation
Indices: 17242523--17242582 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
17242513 TATGATTACC
17242523 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
* *
17242543 TCATGTGCATAGCATACATT
1 TCATGTGCATATCATACATA
17242563 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
17242583 CCATATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:17242652 original size:24 final size:25
Alignment explanation
Indices: 17242625--17242671 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
17242615 ATACATAAAC
*
17242625 CCTAGGGG-ATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
17242649 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
17242672 CATATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:17243928 original size:27 final size:27
Alignment explanation
Indices: 17243907--17244380 Score: 489
Period size: 27 Copynumber: 17.7 Consensus size: 27
17243897 AAGGGTATTT
*
17243907 TAGTAATTTTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
*
17243934 TAGTAA-TCTGTAAATCAAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* *
17243960 CAGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
*
17243987 TGGTAATTCTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
** *
17244014 CGGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* *
17244041 -CGATAATTATGTAAATCG-GGGTAAAA
1 TAG-TAATTCTGTAAATCGAGGGTAAAA
* * *
17244067 TGGTAATTATGTAAAT-TAGGGGTAAAA
1 TAGTAATTCTGTAAATCGA-GGGTAAAA
* *
17244094 CAGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
17244121 TAGTAATTCTGTAAA-CTGAGGGTAAAA
1 TAGTAATTCTGTAAATC-GAGGGTAAAA
**
17244148 CGGTAATTCTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
** * **
17244175 CGGTAATTTTACAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
** *
17244202 CGGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
17244229 TAGTAATTCTGTAAA-CTGAGGGTAAAA
1 TAGTAATTCTGTAAATC-GAGGGTAAAA
**
17244256 CGGTAATTCTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
** * **
17244283 CGGTAATTTTACAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* **
17244310 T-GATAATTTTACAAATCGAGGGTAAAA
1 TAG-TAATTCTGTAAATCGAGGGTAAAA
* *
17244337 CAGTAATTCTATAAA-CTGAGGGTAAAA
1 TAGTAATTCTGTAAATC-GAGGGTAAAA
*
17244364 -GGTAATTCTGTAAATCG
1 TAGTAATTCTGTAAATCG
17244381 GGAATACTTT
Statistics
Matches: 390, Mismatches: 43, Indels: 29
0.84 0.09 0.06
Matches are distributed among these distances:
26 62 0.16
27 324 0.83
28 4 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
TAGTAATTCTGTAAATCGAGGGTAAAA
Found at i:17244020 original size:54 final size:54
Alignment explanation
Indices: 17243908--17244380 Score: 573
Period size: 54 Copynumber: 8.8 Consensus size: 54
17243898 AGGGTATTTT
* * ** *
17243908 AGTAATTTTGTAAATCGAGGGTAAAATAGTAA-TCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC
*
17243961 AGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC
* * * *
17244015 GGTAATTCTATAAATCGAGGGTAAAACGATAATTATGTAAATCG-GGGTAAAAT
1 AGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC
* * * * * * *
17244068 GGTAATTATGTAAAT-TAGGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTATAAATCGA-GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC
*
17244122 AGTAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATC-GAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC
* * * * *
17244176 GGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC
*
17244230 AGTAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATC-GAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC
* * * * * * **
17244284 GGTAATTTTACAAATCGAGGGTAAAATGATAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC
17244338 AGTAATTCTATAAA-CTGAGGGTAAAA-GGTAATTCTGTAAATCG
1 AGTAATTCTATAAATC-GAGGGTAAAACGGTAATTCTGTAAATCG
17244381 GGAATACTTT
Statistics
Matches: 361, Mismatches: 50, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
52 1 0.00
53 87 0.24
54 270 0.75
55 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (54 bp):
AGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:17244181 original size:81 final size:81
Alignment explanation
Indices: 17243909--17244380 Score: 607
Period size: 81 Copynumber: 5.9 Consensus size: 81
17243899 GGGTATTTTA
* * * * * *
17243909 GTAATTTTGTAAATCGAGGGTAAAATAGTAA-TCTGTAAATCAAGGGTAAAACAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
17243973 AATCGAGGGTAAAATG
66 AATCGAGGGTAAAATG
* * *
17243989 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACGATAATTATGTA
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
17244054 AATCG-GGGTAAAATG
66 AATCGAGGGTAAAATG
* * **
17244069 GTAATTATGTAAAT-TAGGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGT
1 GTAATTCTGTAAATCGA-GGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGT
*
17244133 AAA-CTGAGGGTAAAACG
65 AAATC-GAGGGTAAAATG
* * * *
17244150 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
*
17244215 AATCGAGGGTAAAATA
66 AATCGAGGGTAAAATG
* * * **
17244231 GTAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTAC
1 GTAATTCTGTAAATC-GAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGT
17244295 AAATCGAGGGTAAAATG
65 AAATCGAGGGTAAAATG
* * **
17244312 ATAATTTTACAAATCGAGGGTAAAACAGTAATTCTATAAA-CTGAGGGTAAAA-GGTAATTCTGT
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATC-GAGGGTAAAACGGTAATTCTGT
17244375 AAATCG
65 AAATCG
17244381 GGAATACTTT
Statistics
Matches: 341, Mismatches: 42, Indels: 18
0.85 0.10 0.04
Matches are distributed among these distances:
79 2 0.01
80 113 0.33
81 223 0.65
82 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (81 bp):
GTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
AATCGAGGGTAAAATG
Found at i:17246718 original size:17 final size:18
Alignment explanation
Indices: 17246686--17246719 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17246676 CTCTCCTAAA
17246686 ACGATTCCGATCTTTCTC
1 ACGATTCCGATCTTTCTC
*
17246704 ACGATTCTG-TCTTTCT
1 ACGATTCCGATCTTTCT
17246720 GTATGCTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.15, C:0.29, G:0.12, T:0.44
Consensus pattern (18 bp):
ACGATTCCGATCTTTCTC
Found at i:17259049 original size:40 final size:40
Alignment explanation
Indices: 17258983--17259149 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
17258973 AAATTGAATG
* * *
17258983 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
17259022 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
17259062 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
17259102 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
17259142 ATATCCGG
1 ATATCCGG
17259150 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:17262806 original size:19 final size:19
Alignment explanation
Indices: 17262782--17262823 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
17262772 AACTTTTTCC
17262782 TTTTTTGCGATTTA-TGCCT
1 TTTTTTGCGATTTAGT-CCT
17262801 TTTTTTGCGATTTAGTCCT
1 TTTTTTGCGATTTAGTCCT
17262820 TTTT
1 TTTT
17262824 CGCAATCGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.62
Consensus pattern (19 bp):
TTTTTTGCGATTTAGTCCT
Found at i:17266300 original size:111 final size:111
Alignment explanation
Indices: 17266106--17266328 Score: 410
Period size: 111 Copynumber: 2.0 Consensus size: 111
17266096 AATAACATCA
* * *
17266106 AGTTGGTTATAAAGCAATGGCCTTTAATCATCAAAGGACAGTTTCTACATACTTGGTCCACTAAT
1 AGTTGGCTAGAAAGCAATGACCTTTAATCATCAAAGGACAGTTTCTACATACTTGGTCCACTAAT
17266171 ACATGCTTGCCTAACGGGTTAGACACTTTTATTACAAACTTAGTGG
66 ACATGCTTGCCTAACGGGTTAGACACTTTTATTACAAACTTAGTGG
*
17266217 AGTTGGCTAGAAAGTAATGACCTTTAATCATCAAAGGACAGTTTCTACATACTTGGTCCACTAAT
1 AGTTGGCTAGAAAGCAATGACCTTTAATCATCAAAGGACAGTTTCTACATACTTGGTCCACTAAT
17266282 ACATGCTTGCCTAACGGGTTAGACACTTTTATTACAAACTTAGTGG
66 ACATGCTTGCCTAACGGGTTAGACACTTTTATTACAAACTTAGTGG
17266328 A
1 A
17266329 CTCTACGAAC
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (111 bp):
AGTTGGCTAGAAAGCAATGACCTTTAATCATCAAAGGACAGTTTCTACATACTTGGTCCACTAAT
ACATGCTTGCCTAACGGGTTAGACACTTTTATTACAAACTTAGTGG
Found at i:17268229 original size:55 final size:55
Alignment explanation
Indices: 17268157--17268275 Score: 134
Period size: 55 Copynumber: 2.2 Consensus size: 55
17268147 CGTGTACGAC
* * * * *
17268157 ACTGACTTTAGGGCACGGCCATGACATACGCCTATGTGGCCTATCCATGGGCAAT
1 ACTGACTTTAGGACACGGCCATGACACACGCCCATGTGGCCTAACCATGGACAAT
* * * *
17268212 ACTGACTTATA-GACACGGCTATGGCACACGCCCGTGTGGCCTAACCGTGGACAAT
1 ACTGACTT-TAGGACACGGCCATGACACACGCCCATGTGGCCTAACCATGGACAAT
17268267 ACTGA-TTTA
1 ACTGACTTTA
17268276 AAAGTTTAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
53 2 0.04
54 2 0.04
55 48 0.89
56 2 0.04
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (55 bp):
ACTGACTTTAGGACACGGCCATGACACACGCCCATGTGGCCTAACCATGGACAAT
Found at i:17269247 original size:91 final size:94
Alignment explanation
Indices: 17269083--17269301 Score: 239
Period size: 91 Copynumber: 2.3 Consensus size: 94
17269073 CTCCATCGAC
* ** * * * *
17269083 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCATGTATACGTGCTGATGCATGTCCT
1 GCCGATGCCATGTCCCAGACATCGTCTTACACTAGCTAACATGCATACGGGCCGATGCATGTCCC
17269148 AGACATGTCTTACACTAGCACGAAACTTA
66 AGACATGTCTTACACTAGCACGAAACTTA
*
17269177 GCCGATG-CATGTCCCAGACA-CGTCTTACACTGGCTAACAT-CAT-CGAGGCCGATGCATGTCC
1 GCCGATGCCATGTCCCAGACATCGTCTTACACTAGCTAACATGCATACG-GGCCGATGCATGTCC
* * ** *
17269238 CAGAGATGTCTTACACTGGCACTCACCTCTA
65 CAGACATGTCTTACACTAGCACGAAACT-TA
* * *
17269269 CGCCAATGCCATGTCCCAGACGTGGTCTTACAC
1 -GCCGATGCCATGTCCCAGACATCGTCTTACAC
17269302 AGGCTATCTT
Statistics
Matches: 104, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
90 2 0.02
91 37 0.36
92 18 0.17
93 19 0.18
94 19 0.18
95 9 0.09
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (94 bp):
GCCGATGCCATGTCCCAGACATCGTCTTACACTAGCTAACATGCATACGGGCCGATGCATGTCCC
AGACATGTCTTACACTAGCACGAAACTTA
Found at i:17269282 original size:47 final size:44
Alignment explanation
Indices: 17269042--17269301 Score: 157
Period size: 47 Copynumber: 5.5 Consensus size: 44
17269032 TTGCCGCTGC
* * *
17269042 CATGTCCCAGACATGGTCTTACGCTGGATATCTC-CATCGACGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGG-CA-CTCAC-TCTA-GCCGATG
* ** * * *
17269090 CCATGTCCCAGACATGGTCTTACACTAGCTTTCATGTATACGTGCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCACTCA-CTCTA---GCCGATG
* * **
17269140 CATGTCCTAGACATGTCTTACACTAGCACGAAACT-TAGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCAC-TCACTCTAGCCGATG
* *
17269184 CATGTCCCAGACACGTCTTACACTGGCTAACATCA-TCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGC--AC-TCACTCTA-GCCGATG
* *
17269231 CATGTCCCAGAGATGTCTTACACTGGCACTCACCTCTACGCCAATG
1 CATGTCCCAGACATGTCTTACACTGGCACTCA-CTCTA-GCCGATG
*
17269277 CCATGTCCCAGACGTGGTCTTACAC
1 -CATGTCCCAGACAT-GTCTTACAC
17269302 AGGCTATCTT
Statistics
Matches: 167, Mismatches: 31, Indels: 27
0.74 0.14 0.12
Matches are distributed among these distances:
44 33 0.20
45 3 0.02
46 13 0.08
47 48 0.29
48 25 0.15
49 39 0.23
50 6 0.04
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTGGCACTCACTCTAGCCGATG
Found at i:17269328 original size:94 final size:94
Alignment explanation
Indices: 17269081--17269392 Score: 310
Period size: 94 Copynumber: 3.3 Consensus size: 94
17269071 ATCTCCATCG
* *
17269081 ACGCCGATGCCATGTCCCAGACATGGTCTTACACTA-GCTTTCATGTATACGTGCTGATGCATGT
1 ACGCCGATGCCATGTCCCAGACATGGTCTTACAC-AGGCTATCATG-ATGCG-GCTGATGCATGT
* **
17269145 CCTAGACATGTCTTACACTAGCACGAAACT-T
63 CCCAGACATGTCTTACACTAGCACTCAACTCT
* * * * * *
17269176 A-GCCGATG-CATGTCCCAGACA-CGTCTTACACTGGCTAACATCATCGAGGCCGATGCATGTCC
1 ACGCCGATGCCATGTCCCAGACATGGTCTTACACAGGCTATCATGAT-GCGGCTGATGCATGTCC
* * *
17269238 CAGAGATGTCTTACACTGGCACTCACCTCT
65 CAGACATGTCTTACACTAGCACTCAACTCT
* * * *
17269268 ACGCCAATGCCATGTCCCAGACGTGGTCTTACACAGGCTATCTTGATGCGGCTAATGCATGTCCC
1 ACGCCGATGCCATGTCCCAGACATGGTCTTACACAGGCTATCATGATGCGGCTGATGCATGTCCC
* ** * * *
17269333 AGATACATCTTACACTAGCCCTCATCTCA
66 AGACATGTCTTACACTAGCACTCAACTCT
* * *
17269362 ATGTCGATGCCATGTCCCAAACATGGTCTTA
1 ACGCCGATGCCATGTCCCAGACATGGTCTTA
17269393 TACTGGCTCT
Statistics
Matches: 175, Mismatches: 36, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
91 37 0.21
92 18 0.10
93 19 0.11
94 82 0.47
95 19 0.11
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (94 bp):
ACGCCGATGCCATGTCCCAGACATGGTCTTACACAGGCTATCATGATGCGGCTGATGCATGTCCC
AGACATGTCTTACACTAGCACTCAACTCT
Found at i:17276854 original size:34 final size:33
Alignment explanation
Indices: 17276806--17276870 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
17276796 GTGTTTGCAT
17276806 ACTGTACTGAAATAGGCTAAGGTCC-AGACTGCC
1 ACTGTACTGAAATAGGCTAAGG-CCTAGACTGCC
* *
17276839 ACTGATACTGCAATAGGCTTAGGCCTAGACTG
1 ACTG-TACTGAAATAGGCTAAGGCCTAGACTG
17276871 TTATTACTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 6 0.21
34 22 0.79
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (33 bp):
ACTGTACTGAAATAGGCTAAGGCCTAGACTGCC
Found at i:17279748 original size:40 final size:40
Alignment explanation
Indices: 17279696--17279788 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 40
17279686 CTCGGTATCT
*
17279696 CACACTTAGTGCC-TCATATAGCCAAAGCTATTTC-AACTCG
1 CACAATTAGTGCCAT-ATATAGCCAAAGCTATTTCGAACT-G
* * *
17279736 CACAGTTAGTGCCATTTGTAGCCAAAGCTATTTCGAACTG
1 CACAATTAGTGCCATATATAGCCAAAGCTATTTCGAACTG
17279776 CACAATTAGTGCC
1 CACAATTAGTGCC
17279789 GAATATCGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 42 0.89
41 5 0.11
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (40 bp):
CACAATTAGTGCCATATATAGCCAAAGCTATTTCGAACTG
Found at i:17285979 original size:36 final size:36
Alignment explanation
Indices: 17285932--17286008 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 36
17285922 AGTTAATTGC
*
17285932 ACATGGACATGC-GACACGGCCGTGTGAACCACACGG
1 ACATGGACATGCAG-CACGGCCATGTGAACCACACGG
*
17285968 ACATGGCCATGCAGCACGGCCATGTGAACCACACGG
1 ACATGGACATGCAGCACGGCCATGTGAACCACACGG
17286004 ACATG
1 ACATG
17286009 TCTATGGCCG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 37 0.97
37 1 0.03
ACGTcount: A:0.29, C:0.31, G:0.29, T:0.12
Consensus pattern (36 bp):
ACATGGACATGCAGCACGGCCATGTGAACCACACGG
Found at i:17286008 original size:17 final size:17
Alignment explanation
Indices: 17285954--17286009 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
17285944 GACACGGCCG
17285954 TGTGAACCACACGGACA
1 TGTGAACCACACGGACA
** *
17285971 TG-GCCATGCAGCACGGCCA
1 TGTG--AACCA-CACGGACA
17285990 TGTGAACCACACGGACA
1 TGTGAACCACACGGACA
17286007 TGT
1 TGT
17286010 CTATGGCCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
16 1 0.03
17 12 0.41
18 6 0.21
19 9 0.31
20 1 0.03
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (17 bp):
TGTGAACCACACGGACA
Found at i:17302877 original size:24 final size:24
Alignment explanation
Indices: 17302824--17302869 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
17302814 TCGACAATCC
17302824 ACTTTTCGGCTTTTTAGCCTTTCG
1 ACTTTTCGGCTTTTTAGCCTTTCG
17302848 ACTTTTCGGCTTTTTAGCCTTT
1 ACTTTTCGGCTTTTTAGCCTTT
17302870 GTAGTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (24 bp):
ACTTTTCGGCTTTTTAGCCTTTCG
Found at i:17305020 original size:37 final size:37
Alignment explanation
Indices: 17304978--17305049 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
17304968 AAAACATAAT
17304978 TATATTCGCCACCATTTAGTAAAGATATTATTTTGAA
1 TATATTCGCCACCATTTAGTAAAGATATTATTTTGAA
17305015 TATATTCGCCACCATTTAGTAAAGATATTATTTTG
1 TATATTCGCCACCATTTAGTAAAGATATTATTTTG
17305050 GAGATAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (37 bp):
TATATTCGCCACCATTTAGTAAAGATATTATTTTGAA
Found at i:17308957 original size:80 final size:80
Alignment explanation
Indices: 17308825--17309126 Score: 491
Period size: 80 Copynumber: 3.8 Consensus size: 80
17308815 AACCCAAGTA
* * * * * * *
17308825 CCTTCGGGATTTAG-CCGGTTATAGCAACTCGTACAAATGCCTTCGGGA-CTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTC-GGATCTTAGTCCGGTTATA
17308888 GTAACTAGCACAAATG
65 GTAACTAGCACAAATG
*
17308904 CCTTCGGGACTTAGCCCAGATATAGTAACTAGCACAAATGCCTTCGGATCTTAGTCCGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGATCTTAGTCCGGTTATAG
17308969 TAACTAGCACAAATG
66 TAACTAGCACAAATG
*
17308984 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGATCTTAGTTCGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGATCTTAGTCCGGTTATAG
17309049 TAACTAGCACAAATG
66 TAACTAGCACAAATG
*
17309064 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACTAATGCCTTCGGATCTTAGTCCGGTTAT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGATCTTAGTCCGGTTAT
17309127 CATCCGAATA
Statistics
Matches: 209, Mismatches: 12, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
79 16 0.08
80 193 0.92
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGATCTTAGTCCGGTTATAG
TAACTAGCACAAATG
Found at i:17309117 original size:40 final size:40
Alignment explanation
Indices: 17308825--17309110 Score: 425
Period size: 40 Copynumber: 7.2 Consensus size: 40
17308815 AACCCAAGTA
* * * * *
17308825 CCTTCGGGATTTAG-CCGGTTATAGCAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
17308864 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
*
17308904 CCTTCGGGACTTAGCCCAGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
* *
17308944 CCTTC-GGATCTTAGTCCGGTTATAGTAACTAGCACAAATG
1 CCTTCGGGA-CTTAGCCCGGATATAGTAACTAGCACAAATG
17308984 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
** *
17309024 CCTTC-GGATCTTAGTTCGGTTATAGTAACTAGCACAAATG
1 CCTTCGGGA-CTTAGCCCGGATATAGTAACTAGCACAAATG
*
17309064 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACTAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
17309104 CCTTCGG
1 CCTTCGG
17309111 ATCTTAGTCC
Statistics
Matches: 224, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
39 19 0.08
40 199 0.89
41 6 0.03
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
Found at i:17310547 original size:13 final size:13
Alignment explanation
Indices: 17310531--17310558 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17310521 TTTATTATTT
17310531 TTAACACAAAATA
1 TTAACACAAAATA
17310544 TTAACACAAAATA
1 TTAACACAAAATA
17310557 TT
1 TT
17310559 TATAATATGT
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:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (13 bp):
TTAACACAAAATA
Found at i:17317188 original size:40 final size:41
Alignment explanation
Indices: 17317054--17317193 Score: 216
Period size: 40 Copynumber: 3.5 Consensus size: 41
17317044 AACCCAAGTA
* *
17317054 CCTTCGGGAT-TTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGATCTTAGCCCGGATATAGTAACTAGCACAAATG
17317093 CCTTCGGGATCTTAGCCCGGATTATAGTAACTAGCACAAATG
1 CCTTCGGGATCTTAGCCCGGA-TATAGTAACTAGCACAAATG
17317135 CCTTCGGGA-CTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGATCTTAGCCCGGATATAGTAACTAGCACAAATG
*
17317175 CCTTC-GGATCTTAGTCCGG
1 CCTTCGGGATCTTAGCCCGG
17317194 TTATCATCCG
Statistics
Matches: 94, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
39 13 0.14
40 38 0.40
41 16 0.17
42 27 0.29
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (41 bp):
CCTTCGGGATCTTAGCCCGGATATAGTAACTAGCACAAATG
Found at i:17319497 original size:27 final size:27
Alignment explanation
Indices: 17319467--17319520 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
17319457 GTCTTGGTCG
17319467 AACAAGAAGAAAAATAAAATATAATAA
1 AACAAGAAGAAAAATAAAATATAATAA
*
17319494 AACAAGAAGAAGAATAAAATATAATAA
1 AACAAGAAGAAAAATAAAATATAATAA
17319521 CATTTTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (27 bp):
AACAAGAAGAAAAATAAAATATAATAA
Found at i:17321610 original size:30 final size:30
Alignment explanation
Indices: 17321539--17321610 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
17321529 CACACAAGTA
* * *
17321539 GGCCACACGCCCGTGTGAGCCATATGGGCT
1 GGCCACACGCCTGTGTGAGCCAAATGAGCT
17321569 GGCCACACGCCTGTGTGAGCCAAATGAGCT
1 GGCCACACGCCTGTGTGAGCCAAATGAGCT
17321599 GGCCACACGCCT
1 GGCCACACGCCT
17321611 ATATGCTAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.19, C:0.35, G:0.31, T:0.15
Consensus pattern (30 bp):
GGCCACACGCCTGTGTGAGCCAAATGAGCT
Found at i:17328084 original size:28 final size:28
Alignment explanation
Indices: 17328026--17328106 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
17328016 CTGCCAGAAC
* * * *
17328026 AGAT-ATTGTGACAGAGTCACCAGATAC
1 AGATAATTGTGGCAGAGCCACCAGAAAT
* *
17328053 AGATAATTGTGGCAGGGCCACTAGAAAT
1 AGATAATTGTGGCAGAGCCACCAGAAAT
*
17328081 AGATATTTGTGGCAGAGCCACCAGAA
1 AGATAATTGTGGCAGAGCCACCAGAA
17328107 CGATTCCTCC
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 4 0.09
28 40 0.91
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (28 bp):
AGATAATTGTGGCAGAGCCACCAGAAAT
Found at i:17329364 original size:18 final size:18
Alignment explanation
Indices: 17329305--17329364 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
17329295 AGCTATAGAG
17329305 GAAAAGAAGAAGAAGAAGAA
1 GAAAAGAAGAAG-AGAA-AA
* **
17329325 GAAATAGATGAAGAGATGA
1 GAAA-AGAAGAAGAGAAAA
17329344 GAAAAGAAGAAGAGAAAA
1 GAAAAGAAGAAGAGAAAA
17329362 GAA
1 GAA
17329365 TTGTCAGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 14 0.42
19 5 0.15
20 7 0.21
21 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (18 bp):
GAAAAGAAGAAGAGAAAA
Found at i:17332373 original size:27 final size:27
Alignment explanation
Indices: 17332167--17332446 Score: 260
Period size: 27 Copynumber: 10.4 Consensus size: 27
17332157 ACCAAATCAT
* *
17332167 CAAAATACCCCT-AGTTTGTAAAATTAA
1 CAAAATACCCTTGA-TTTGTAAAATTAC
* **
17332194 CAAAATACCCTTGGTTTACAAAATTAC
1 CAAAATACCCTTGATTTGTAAAATTAC
* *
17332221 CAAAATACCCCTGGTTTGTAAAATTAC
1 CAAAATACCCTTGATTTGTAAAATTAC
* * * *
17332248 TACAATACCCTT-AGTTTATAAAATCAC
1 CAAAATACCCTTGA-TTTGTAAAATTAC
*
17332275 CAAAATACCCTTGGTTTGTAAAATTAC
1 CAAAATACCCTTGATTTGTAAAATTAC
* *
17332302 CAAAATACCCCTGGTTTGTAAAATTAC
1 CAAAATACCCTTGATTTGTAAAATTAC
*
17332329 CAAAATACTCCTAG-TTTGTAAAATTAC
1 CAAAATAC-CCTTGATTTGTAAAATTAC
* *
17332356 CAAACTACCCTTGATTTGTGAAATTAC
1 CAAAATACCCTTGATTTGTAAAATTAC
* * ** *
17332383 TAAAATACCCTCGACCTGTAAAATTAT
1 CAAAATACCCTTGATTTGTAAAATTAC
** * * *
17332410 TGAAATAACCTCGACTTGTAAAATTAC
1 CAAAATACCCTTGATTTGTAAAATTAC
*
17332437 CAAAGTACCC
1 CAAAATACCC
17332447 CGATTTACAG
Statistics
Matches: 208, Mismatches: 40, Indels: 10
0.81 0.16 0.04
Matches are distributed among these distances:
26 4 0.02
27 201 0.97
28 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
CAAAATACCCTTGATTTGTAAAATTAC
Found at i:17332408 original size:81 final size:80
Alignment explanation
Indices: 17332167--17332392 Score: 326
Period size: 81 Copynumber: 2.8 Consensus size: 80
17332157 ACCAAATCAT
* **
17332167 CAAAATACCCCTAGTTTGTAAAATTAACAAAATACCCTTGGTTTACAAAATTACCAAAATACCCC
1 CAAAATA-CCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCC
17332232 TGGTTTGTAAAATTAC
65 TGGTTTGTAAAATTAC
* * * *
17332248 TACAATACCCTTAGTTTATAAAATCACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCC
1 CAAAATACCC-TAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCC
17332313 TGGTTTGTAAAATTAC
65 TGGTTTGTAAAATTAC
* * * *
17332329 CAAAATACTCCTAGTTTGTAAAATTACCAAACTACCCTTGATTTGTGAAATTACTAAAATACCC
1 CAAAATAC-CCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCC
17332393 TCGACCTGTA
Statistics
Matches: 128, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
80 3 0.02
81 123 0.96
82 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.31
Consensus pattern (80 bp):
CAAAATACCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCT
GGTTTGTAAAATTAC
Found at i:17332416 original size:81 final size:79
Alignment explanation
Indices: 17332169--17332446 Score: 315
Period size: 81 Copynumber: 3.4 Consensus size: 79
17332159 CAAATCATCA
* **
17332169 AAATACCCCTAGTTTGTAAAATTAACAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTG
1 AAATA-CCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTG
17332234 GTTTGTAAAATTACT
65 GTTTGTAAAATTACT
* *
17332249 ACAATACCCTTAGTTTATAAAATCACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCT
1 A-AATACCC-TAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCT
*
17332314 GGTTTGTAAAATTACCA
64 GGTTTGTAAAATTA-CT
* * * *
17332331 AAATACTCCTAGTTTGTAAAATTACCAAACTACCCTTGATTTGTGAAATTACTAAAATA-CCCTC
1 AAATAC-CCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCT-
*** *
17332395 GACCTGTAAAATTATT
64 GGTTTGTAAAATTACT
* * * *
17332411 GAAATAACCTCGACTTGTAAAATTACCAAAGTACCC
1 -AAATACCCTAG-TTTGTAAAATTACCAAAATACCC
17332447 CGATTTACAG
Statistics
Matches: 170, Mismatches: 21, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
80 12 0.07
81 154 0.91
82 4 0.02
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (79 bp):
AAATACCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTGG
TTTGTAAAATTACT
Found at i:17332521 original size:27 final size:28
Alignment explanation
Indices: 17332483--17332733 Score: 295
Period size: 27 Copynumber: 9.3 Consensus size: 28
17332473 TCGATTTACA
*
17332483 AAATTACCGAAATACCCTTGTAGGGTAG
1 AAATTACCGAAATACCCCTGTAGGGTAG
* * *
17332511 AAATT-CTGAAATACCCTTGGAGGGTAG
1 AAATTACCGAAATACCCCTGTAGGGTAG
* * *
17332538 AAA-TACCAAAATACCCCTGTAAGGTAT
1 AAATTACCGAAATACCCCTGTAGGGTAG
17332565 AAA-TACCGAAATACCCCTGTAGGGTA-
1 AAATTACCGAAATACCCCTGTAGGGTAG
**
17332591 AAATTACTAAAATACCCCTGTAGGGTAG
1 AAATTACCGAAATACCCCTGTAGGGTAG
* *
17332619 -AATTACCGAAATACCCTTGTAAGGTAG
1 AAATTACCGAAATACCCCTGTAGGGTAG
*
17332646 AAA-TACCGAAATACCCCTATAGGGTA-
1 AAATTACCGAAATACCCCTGTAGGGTAG
*
17332672 AAATTACTGAAATACCCCTGTAGGGTAG
1 AAATTACCGAAATACCCCTGTAGGGTAG
* * *
17332700 -AATTACCGAGATACCCTTGTGGGGTA-
1 AAATTACCGAAATACCCCTGTAGGGTAG
17332726 AAATTACC
1 AAATTACC
17332734 ATTTTACCCT
Statistics
Matches: 191, Mismatches: 25, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.04
27 177 0.93
28 7 0.04
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (28 bp):
AAATTACCGAAATACCCCTGTAGGGTAG
Found at i:17332716 original size:81 final size:81
Alignment explanation
Indices: 17332487--17332719 Score: 360
Period size: 81 Copynumber: 2.9 Consensus size: 81
17332477 TTTACAAAAT
* * * * *
17332487 TACCGAAATACCCTTGTAGGGTAGAAATT-CTGAAATACCCTTGGAGGGTAGAAATACCAAAATA
1 TACCGAAATACCCCTGTAGGGTA-AAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATA
* *
17332551 CCCCTGTAAGGTATAAA
65 CCCTTGTAAGGTAGAAA
*
17332568 TACCGAAATACCCCTGTAGGGTAAAATTACTAAAATACCCCTGTAGGGTAGAATTACCGAAATAC
1 TACCGAAATACCCCTGTAGGGTAAAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATAC
17332633 CCTTGTAAGGTAGAAA
66 CCTTGTAAGGTAGAAA
* *
17332649 TACCGAAATACCCCTATAGGGTAAAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAGATAC
1 TACCGAAATACCCCTGTAGGGTAAAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATAC
17332714 CCTTGT
66 CCTTGT
17332720 GGGGTAAAAT
Statistics
Matches: 140, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
80 5 0.04
81 135 0.96
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (81 bp):
TACCGAAATACCCCTGTAGGGTAAAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATAC
CCTTGTAAGGTAGAAA
Found at i:17333255 original size:6 final size:6
Alignment explanation
Indices: 17333246--17333429 Score: 90
Period size: 6 Copynumber: 29.8 Consensus size: 6
17333236 TTGCATTCAC
* * * * *
17333246 ATTCTG ATTCTA ATTATG -TTACCTG ATACTA ATTCTG ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * *
17333296 ATTCTG ATTCTG GTTCTG ATTTTG ATTCT- ATTATCTG ATACTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-T-TCTG ATTCTG ATTCTG
* * * * *
17333345 ATTCTG -TTACCTA ATTTTA ATTCTG ATTCTG ATTTTG ATTCTG -TCACCTG
1 ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG
** * *
17333395 ATAATG ATTCTG ATTCTG ATTCTC ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
17333430 AGTTTTGATA
Statistics
Matches: 132, Mismatches: 31, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
5 8 0.06
6 104 0.79
7 13 0.10
8 7 0.05
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:17333305 original size:25 final size:25
Alignment explanation
Indices: 17333246--17333313 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
17333236 TTGCATTCAC
* * *
17333246 ATTCTGATTCTAATTATGTTACCTG
1 ATTCTGATTCTGATTCTGTTACCTA
* *
17333271 ATACTAATTCTGATTCTGTTACCTA
1 ATTCTGATTCTGATTCTGTTACCTA
*
17333296 ATTCTGATTCTGGTTCTG
1 ATTCTGATTCTGATTCTG
17333314 ATTTTGATTC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTGTTACCTA
Found at i:17333344 original size:62 final size:62
Alignment explanation
Indices: 17333266--17333412 Score: 222
Period size: 62 Copynumber: 2.4 Consensus size: 62
17333256 TAATTATGTT
* * * *
17333266 ACCTGATACTAATTCTGATTCTGTTACCTAATTCTGATTCTGGTTCTGATTTTGATTCTATT
1 ACCTGATACTGATTCTGATTCTGTTACCTAATTCTAATTCTGATTCTGATTTTGATTCTATC
* * *
17333328 ATCTGATACTGATTCTGATTCTGTTACCTAATTTTAATTCTGATTCTGATTTTGATTCTGTC
1 ACCTGATACTGATTCTGATTCTGTTACCTAATTCTAATTCTGATTCTGATTTTGATTCTATC
*
17333390 ACCTGATAATGATTCTGATTCTG
1 ACCTGATACTGATTCTGATTCTG
17333413 ATTCTCATTT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 76 1.00
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.48
Consensus pattern (62 bp):
ACCTGATACTGATTCTGATTCTGTTACCTAATTCTAATTCTGATTCTGATTTTGATTCTATC
Found at i:17333370 original size:37 final size:37
Alignment explanation
Indices: 17333329--17333417 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
17333319 GATTCTATTA
* * **
17333329 TCTGATACTGATTCTGATTCTGTTACCTAATTTTAAT
1 TCTGATTCTGATTCTGATTCTGTCACCTAATAATAAT
* * *
17333366 TCTGATTCTGATTTTGATTCTGTCACCTGATAATGAT
1 TCTGATTCTGATTCTGATTCTGTCACCTAATAATAAT
17333403 TCTGATTCTGATTCT
1 TCTGATTCTGATTCT
17333418 CATTTTGATT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.48
Consensus pattern (37 bp):
TCTGATTCTGATTCTGATTCTGTCACCTAATAATAAT
Found at i:17334144 original size:29 final size:28
Alignment explanation
Indices: 17334097--17334156 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
17334087 AAAAAATGTC
*
17334097 AATTTTGGATTAAATTGTGAAA-TGTGGA
1 AATTTTGGATTAAAATGTGAAATTGT-GA
*
17334125 AATTTTGTGGTTAAAATGTGAAATTGTGA
1 AATTTTG-GATTAAAATGTGAAATTGTGA
17334154 AAT
1 AAT
17334157 ATATGGGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 18 0.64
30 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (28 bp):
AATTTTGGATTAAAATGTGAAATTGTGA
Found at i:17334165 original size:29 final size:29
Alignment explanation
Indices: 17334106--17334165 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
17334096 CAATTTTGGA
* *
17334106 TTAAATTGTGAAATGTGGAAATTTTGTGG
1 TTAAAATGTGAAATGTGGAAATTATGTGG
17334135 TTAAAATGTGAAAT-TGTGAAATATATG-GG
1 TTAAAATGTGAAATGTG-GAAAT-TATGTGG
17334164 TT
1 TT
17334166 GTGTGAGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.07
29 22 0.81
30 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (29 bp):
TTAAAATGTGAAATGTGGAAATTATGTGG
Found at i:17335374 original size:43 final size:43
Alignment explanation
Indices: 17335309--17335422 Score: 120
Period size: 43 Copynumber: 2.7 Consensus size: 43
17335299 GCTGGTGAAT
* * * *
17335309 AATATTATAGGGCTTCGGGCCTAGCAGGCTATAATGCTAGTGA
1 AATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCAGTGA
* * * *
17335352 GATAATATCGGGCTTCGAGCCTAGTAGGCTATCATGCCGGTGA
1 AATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCAGTGA
* * * *
17335395 AATGATATCGAGCTTCAAGCCTACCAGG
1 AATAATATCGGGCTTCGAGCCTAGCAGG
17335423 AGAAATGCCG
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (43 bp):
AATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCAGTGA
Found at i:17335473 original size:41 final size:40
Alignment explanation
Indices: 17335428--17335505 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
17335418 CCAGGAGAAA
* **
17335428 TGCCGATGAATGAGTTCAGACTTAAAGTCTAGCAGGCTTCG
1 TGCCGATG-ATGAATTCAGACTTAAAACCTAGCAGGCTTCG
* **
17335469 TGCCGGTGATGAATTCAGGTTTAAAACCTAGCAGGCT
1 TGCCGATGATGAATTCAGACTTAAAACCTAGCAGGCT
17335506 AAATGCCGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
40 24 0.77
41 7 0.23
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (40 bp):
TGCCGATGATGAATTCAGACTTAAAACCTAGCAGGCTTCG
Found at i:17350537 original size:46 final size:46
Alignment explanation
Indices: 17350469--17350605 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 46
17350459 TATATATACA
* * * *
17350469 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
17350515 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
17350561 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCATATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
17350606 ATACATGTTC
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.35
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:17350639 original size:47 final size:47
Alignment explanation
Indices: 17350579--17350769 Score: 274
Period size: 47 Copynumber: 4.1 Consensus size: 47
17350569 ACACATTTCG
* * * * **
17350579 CATTAGCCATTCGGCCTTACCATATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * * * *
17350626 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCGCATTTATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
17350673 CATTGGCCATTCGGCCTTATCACACATACGCATGCTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
17350720 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
17350767 CAT
1 CAT
17350770 AAAATCCTAA
Statistics
Matches: 130, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 130 1.00
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:17350743 original size:22 final size:22
Alignment explanation
Indices: 17350622--17350696 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
17350612 GTTCACATTC
17350622 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
17350644 ATCTCATATATG-CATGTTC-GCATTT
1 ATCACAT-T-GGCCA--TTCGGC-CTT
17350669 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
17350691 ATCACA
1 ATCACA
17350697 CATACGCATG
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 17 0.43
23 6 0.15
24 6 0.15
25 11 0.28
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:17357325 original size:17 final size:18
Alignment explanation
Indices: 17357303--17357336 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17357293 CACATTGAAG
17357303 TGTTTT-AGTGAAAACCT
1 TGTTTTCAGTGAAAACCT
*
17357320 TGTTTTCATTGAAAACC
1 TGTTTTCAGTGAAAACC
17357337 CTTCTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (18 bp):
TGTTTTCAGTGAAAACCT
Found at i:17358499 original size:29 final size:29
Alignment explanation
Indices: 17358459--17358563 Score: 192
Period size: 29 Copynumber: 3.6 Consensus size: 29
17358449 TTCATATGGC
* *
17358459 CCCAAATCACATTCGTATGGCCTATTAGG
1 CCCAAATCACATTCATATGGCCCATTAGG
17358488 CCCAAATCACATTCATATGGCCCATTAGG
1 CCCAAATCACATTCATATGGCCCATTAGG
17358517 CCCAAATCACATTCATATGGCCCATTAGG
1 CCCAAATCACATTCATATGGCCCATTAGG
17358546 CCCAAATCACATTCATAT
1 CCCAAATCACATTCATAT
17358564 ACATGCTTTC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 74 1.00
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.26
Consensus pattern (29 bp):
CCCAAATCACATTCATATGGCCCATTAGG
Found at i:17360497 original size:47 final size:46
Alignment explanation
Indices: 17360378--17360551 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
17360368 GGGATATTTG
*
17360378 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGA
* * *
17360425 -GCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATG---CGA
*
17360471 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGA
* * *
17360518 -AC-GCCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
17360552 TATGGGCGGG
Statistics
Matches: 109, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
43 4 0.04
45 32 0.29
46 34 0.31
47 33 0.30
48 2 0.02
50 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGA
Found at i:17360545 original size:45 final size:46
Alignment explanation
Indices: 17360382--17360556 Score: 225
Period size: 45 Copynumber: 3.8 Consensus size: 46
17360372 TATTTGGGCA
*
17360382 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
17360428 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
17360473 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
17360521 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17360557 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 38 0.34
46 29 0.26
47 29 0.26
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:17363531 original size:15 final size:15
Alignment explanation
Indices: 17363511--17363579 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
17363501 GTATCTTGGG
17363511 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
17363526 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
17363541 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
17363556 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
17363571 TTTCTTTAT
1 TTTCTTTAT
17363580 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:17363580 original size:30 final size:30
Alignment explanation
Indices: 17363502--17363589 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
17363492 CATAGTATCG
* * * *
17363502 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
17363532 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
17363562 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
17363590 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:17365573 original size:46 final size:46
Alignment explanation
Indices: 17365506--17365681 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
17365496 TATTTGGGCA
*
17365506 TCCGAACTCGTTGAGTTGAGTCCGAGTTTACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
17365552 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
* * *
17365599 TCCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
17365645 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17365682 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 64 0.60
47 31 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:17365661 original size:93 final size:93
Alignment explanation
Indices: 17365502--17365673 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
17365492 GGGATATTTG
* * * *
17365502 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTTACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
17365567 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
17365595 GGCATCCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
17365660 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
17365674 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:17367610 original size:28 final size:28
Alignment explanation
Indices: 17367545--17367645 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
17367535 ATAGTGAATC
*
17367545 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
17367574 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
17367602 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
17367632 CGCACACTTAGTGC
1 CGCACACTTAGTGC
17367646 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:17375567 original size:28 final size:28
Alignment explanation
Indices: 17375502--17375602 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
17375492 ATAGTGAATC
*
17375502 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
17375531 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
17375559 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
17375589 CGCACACTTAGTGC
1 CGCACACTTAGTGC
17375603 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:17378372 original size:7 final size:7
Alignment explanation
Indices: 17378360--17378385 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17378350 ATGCTTGTGA
17378360 TGCCACT
1 TGCCACT
17378367 TGCCACT
1 TGCCACT
17378374 TGCCACT
1 TGCCACT
17378381 TGCCA
1 TGCCA
17378386 ATTCTTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.42, G:0.15, T:0.27
Consensus pattern (7 bp):
TGCCACT
Found at i:17385108 original size:27 final size:27
Alignment explanation
Indices: 17385067--17385120 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
17385057 TGTCATGTGA
* *
17385067 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
17385094 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
17385121 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:17385455 original size:49 final size:49
Alignment explanation
Indices: 17385366--17385460 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
17385356 ATCATTGTGA
* * *
17385366 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
*
17385415 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATA
17385461 GCCTTGTCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
Found at i:17387739 original size:41 final size:42
Alignment explanation
Indices: 17387628--17387739 Score: 145
Period size: 43 Copynumber: 2.7 Consensus size: 42
17387618 ACACATATCG
* * *
17387628 TACAATGCCAATGTCCCAGATGTGGTCTTACATGCCATCACA
1 TACAATGCCAATGTCCCAGATATGGTCTTACATGCAATCAAA
* * *
17387670 TATCGATGCCACTGTCCCAGATAGGGTCTTACATG-AATCAAA
1 TA-CAATGCCAATGTCCCAGATATGGTCTTACATGCAATCAAA
*
17387712 TACAATGCCAATGTCCCAGACATGGTCT
1 TACAATGCCAATGTCCCAGATATGGTCT
17387740 AGCACATAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 22 0.37
42 9 0.15
43 28 0.47
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (42 bp):
TACAATGCCAATGTCCCAGATATGGTCTTACATGCAATCAAA
Found at i:17387773 original size:43 final size:42
Alignment explanation
Indices: 17387632--17387775 Score: 116
Period size: 43 Copynumber: 3.4 Consensus size: 42
17387622 ATATCGTACA
* * * *
17387632 ATGCCAATGTCCCAGA-TGTGGTCTTACATGCCATCACATATCG
1 ATGCCAACGTCCCAGACAG-GGTCTCACATG-AATCACATATCG
* * * *
17387675 ATGCC-ACTGTCCCAGATAGGGTCTTACATGAATCAAATA-CA
1 ATGCCAAC-GTCCCAGACAGGGTCTCACATGAATCACATATCG
* *
17387716 ATGCCAATGTCCCAGACATGGTCTAGCACAT-AATCACATATCG
1 ATGCCAACGTCCCAGACAGGGTCT--CACATGAATCACATATCG
*
17387759 ATGCCAACGGCCCAGAC
1 ATGCCAACGTCCCAGAC
17387776 GTTGTCTTAC
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
41 20 0.24
42 17 0.21
43 44 0.54
44 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACAGGGTCTCACATGAATCACATATCG
Found at i:17397946 original size:24 final size:24
Alignment explanation
Indices: 17397919--17397967 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
17397909 AGTTATAATT
17397919 ATATTTTTATAAATAATAAGAAAA
1 ATATTTTTATAAATAATAAGAAAA
17397943 ATATTTTTATAAATAATAAGAAAA
1 ATATTTTTATAAATAATAAGAAAA
17397967 A
1 A
17397968 AATAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
ATATTTTTATAAATAATAAGAAAA
Found at i:17409786 original size:27 final size:26
Alignment explanation
Indices: 17409738--17409797 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
17409728 GCGAAGCTGC
*
17409738 CAGATATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGACAAAGCCACCAGA-A
* * *
17409765 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACAAAGCCACCAGAA
17409791 CAGATAT
1 CAGATAT
17409798 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACAAAGCCACCAGAA
Found at i:17409801 original size:2 final size:2
Alignment explanation
Indices: 17409794--17409825 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17409784 ACCAGAACAG
17409794 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
17409826 GTGGCGAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17424643 original size:27 final size:27
Alignment explanation
Indices: 17424613--17424665 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
17424603 GTCTTGGTCG
*
17424613 AACAAGAAGAAAAATAAAATATAATAA
1 AACAAAAAGAAAAATAAAATATAATAA
*
17424640 AACAAAAAGAAGAATAAAATATAATA
1 AACAAAAAGAAAAATAAAATATAATA
17424666 GCATTTTTAA
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:0.74, C:0.04, G:0.08, T:0.15
Consensus pattern (27 bp):
AACAAAAAGAAAAATAAAATATAATAA
Found at i:17429077 original size:18 final size:19
Alignment explanation
Indices: 17429042--17429078 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17429032 TCACAAAAAA
17429042 TTCATAATGTCATGTACCT
1 TTCATAATGTCATGTACCT
17429061 TTCATAATGTC-TGTACCT
1 TTCATAATGTCATGTACCT
17429079 GGTCCTGAAT
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:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (19 bp):
TTCATAATGTCATGTACCT
Found at i:17431423 original size:7 final size:7
Alignment explanation
Indices: 17431411--17431448 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
17431401 ATTTCTAATG
17431411 ATCCCTC
1 ATCCCTC
17431418 ATCCCTC
1 ATCCCTC
*
17431425 ATCACTC
1 ATCCCTC
17431432 ATCCCTC
1 ATCCCTC
17431439 ATCCCTC
1 ATCCCTC
17431446 ATC
1 ATC
17431449 ATTCATCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.18, C:0.53, G:0.00, T:0.29
Consensus pattern (7 bp):
ATCCCTC
Found at i:17431435 original size:21 final size:21
Alignment explanation
Indices: 17431411--17431455 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
17431401 ATTTCTAATG
17431411 ATCCCTCATCCCTCATCACTC
1 ATCCCTCATCCCTCATCACTC
*
17431432 ATCCCTCATCCCTCATCATTC
1 ATCCCTCATCCCTCATCACTC
17431453 ATC
1 ATC
17431456 ATTCTCTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.49, G:0.00, T:0.31
Consensus pattern (21 bp):
ATCCCTCATCCCTCATCACTC
Found at i:17433253 original size:28 final size:27
Alignment explanation
Indices: 17433198--17433286 Score: 117
Period size: 28 Copynumber: 3.3 Consensus size: 27
17433188 AGCATGGCTG
* *
17433198 CCAGAACAGAT-ATTGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
17433224 CCAGATACAGATAATTGTGGCAGGGCCA
1 CCAGA-ACAGATAATTGTGGCAGAGCCA
*
17433252 CCAGAAACAGATATTTGTGGCAGAGCCA
1 CCAG-AACAGATAATTGTGGCAGAGCCA
17433280 CCAGAAC
1 CCAGAAC
17433287 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.09
27 9 0.16
28 40 0.73
29 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:17433711 original size:16 final size:15
Alignment explanation
Indices: 17433690--17433723 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
17433680 CCACAAAATA
17433690 TTGGCTTTTCGGCATT
1 TTGGCTTTTCGGC-TT
17433706 TTGGCTTTTCGGCTT
1 TTGGCTTTTCGGCTT
17433721 TTG
1 TTG
17433724 CCGATCTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.03, C:0.18, G:0.26, T:0.53
Consensus pattern (15 bp):
TTGGCTTTTCGGCTT
Found at i:17441133 original size:28 final size:27
Alignment explanation
Indices: 17441078--17441166 Score: 101
Period size: 28 Copynumber: 3.3 Consensus size: 27
17441068 AGCATGGCTG
* *
17441078 CCAGAACAGAT-ATTGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
17441104 CCAGATACAGATAATTGTGGCA-AGGCCA
1 CCAGA-ACAGATAATTGTGGCAGA-GCCA
* *
17441132 CCAGAAATAGATATTTGTGGCAGAGCCA
1 CCAG-AACAGATAATTGTGGCAGAGCCA
17441160 CCAGAAC
1 CCAGAAC
17441167 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
26 5 0.09
27 9 0.17
28 37 0.70
29 2 0.04
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:17441326 original size:26 final size:26
Alignment explanation
Indices: 17441273--17441328 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
17441263 CAACCCTAGA
* *
17441273 GGTATAATGGTCATTTTGCACCTAAG
1 GGTATAATGGTAATTTTGCAACTAAG
*
17441299 GGTATAATGGTAATTTT-CATACTTAG
1 GGTATAATGGTAATTTTGCA-ACTAAG
17441325 GGTA
1 GGTA
17441329 CTTTAGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.38
Consensus pattern (26 bp):
GGTATAATGGTAATTTTGCAACTAAG
Found at i:17441604 original size:8 final size:8
Alignment explanation
Indices: 17441578--17441607 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
17441568 CAAAATGCCG
17441578 GCTTTTCA
1 GCTTTTCA
*
17441586 GCATTTCA
1 GCTTTTCA
17441594 GCTTTTCA
1 GCTTTTCA
17441602 GCTTTT
1 GCTTTT
17441608 GCCGATCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.50
Consensus pattern (8 bp):
GCTTTTCA
Found at i:17445530 original size:27 final size:27
Alignment explanation
Indices: 17445507--17445839 Score: 416
Period size: 27 Copynumber: 12.4 Consensus size: 27
17445497 ACCAAATCAT
17445507 CAAAATACCCCTGGTTTGTAAAATTAC
1 CAAAATACCCCTGGTTTGTAAAATTAC
* ** *
17445534 CAAAATACCCTTGGTTTACAAAATTAT
1 CAAAATACCCCTGGTTTGTAAAATTAC
17445561 CAAAATACCCCTGGTTTGTAAAATTAC
1 CAAAATACCCCTGGTTTGTAAAATTAC
* * * * *
17445588 TACAATACCCTTGGTTTATAAAATCAC
1 CAAAATACCCCTGGTTTGTAAAATTAC
*
17445615 CAAAATACCCTTGG-TTGTAAAATTAC
1 CAAAATACCCCTGGTTTGTAAAATTAC
* **
17445641 CAAAATACCCTTGGTTTACAAAATTAC
1 CAAAATACCCCTGGTTTGTAAAATTAC
**
17445668 CAAAATACCCCTAATTTGTAAAATTAC
1 CAAAATACCCCTGGTTTGTAAAATTAC
* * *
17445695 TAAAATACCCTTGGTTTATAAAATTAC
1 CAAAATACCCCTGGTTTGTAAAATTAC
17445722 CAAAATACCCCTGGTTTGTAAAATTAC
1 CAAAATACCCCTGGTTTGTAAAATTAC
*
17445749 CAAAATACCCCTGGTTTGTAAAATTAT
1 CAAAATACCCCTGGTTTGTAAAATTAC
*
17445776 CAAAATACCCCTAGTTTGTAAAATTAC
1 CAAAATACCCCTGGTTTGTAAAATTAC
* ** * *
17445803 CAAACTACCATTGATTTGTGAAATTAC
1 CAAAATACCCCTGGTTTGTAAAATTAC
**
17445830 TGAAATACCC
1 CAAAATACCC
17445840 TCGACCTGTA
Statistics
Matches: 260, Mismatches: 45, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
26 24 0.09
27 236 0.91
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
CAAAATACCCCTGGTTTGTAAAATTAC
Done.