Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003919.1 Hibiscus syriacus cultivar Beakdansim tig00008472_pilon, whole genome shotgun sequence
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: 85083
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1692 original size:24 final size:24
Alignment explanation
Indices: 1664--1710 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1654 ATAAATAGAG
1664 ATATCAAAAATCAAAACAGAATTC
1 ATATCAAAAATCAAAACAGAATTC
* * *
1688 ATATCATATATCAGAACAGAATT
1 ATATCAAAAATCAAAACAGAATT
1711 TAGATCAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (24 bp):
ATATCAAAAATCAAAACAGAATTC
Found at i:1934 original size:16 final size:17
Alignment explanation
Indices: 1903--1944 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1893 TTATTACTGA
1903 CAGAATCATCAATTATT
1 CAGAATCATCAATTATT
*
1920 CAGAAT-ATGAATTATT
1 CAGAATCATCAATTATT
*
1936 -AGGATCATC
1 CAGAATCATC
1945 TTATTCGGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 4 0.19
16 11 0.52
17 6 0.29
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (17 bp):
CAGAATCATCAATTATT
Found at i:8884 original size:3 final size:3
Alignment explanation
Indices: 8876--8906 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
8866 CATTCTTCAT
*
8876 CTC CTC CTC CTC CTC CTC CTC CTC CGC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
8907 CTCTTTGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.68, G:0.03, T:0.29
Consensus pattern (3 bp):
CTC
Found at i:12288 original size:27 final size:27
Alignment explanation
Indices: 12228--12292 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
12218 GATATTATCA
*
12228 AGAGGACCCGACATGAACCCCCTCTCG
1 AGAGGACCCGACATGAACCCCCTCTCC
**
12255 ATCGGACCCGACATGAACCCCCTCTCC
1 AGAGGACCCGACATGAACCCCCTCTCC
12282 AGAGGACCCGA
1 AGAGGACCCGA
12293 ACTCGGAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.26, C:0.42, G:0.22, T:0.11
Consensus pattern (27 bp):
AGAGGACCCGACATGAACCCCCTCTCC
Found at i:16435 original size:32 final size:32
Alignment explanation
Indices: 16368--16477 Score: 103
Period size: 32 Copynumber: 3.4 Consensus size: 32
16358 TTGTATTCAA
* ** **
16368 ATAATGCATAACAGAGTCAGTGTGGCATTCGG
1 ATAATGCACAACAGAGTCAGTGTCACATTTAG
16400 ATAATGCACAACAGAGTCAGTGTCACATTTAG
1 ATAATGCACAACAGAGTCAGTGTCACATTTAG
**** * * * *
16432 ATAATGCATGGGAGTGTTAATGTTACATTTAG
1 ATAATGCACAACAGAGTCAGTGTCACATTTAG
16464 ATAATGCACAACAG
1 ATAATGCACAACAG
16478 TTATAATCAT
Statistics
Matches: 61, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (32 bp):
ATAATGCACAACAGAGTCAGTGTCACATTTAG
Found at i:19564 original size:19 final size:20
Alignment explanation
Indices: 19523--19572 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
19513 AAATAATTTT
* *
19523 ATTTTG-AAAGCAAAATTAG
1 ATTTTGAAAAACAAAATGAG
19542 ATTTTGAAAAACAAAATGA-
1 ATTTTGAAAAACAAAATGAG
19561 ATTTTTGAAAAA
1 A-TTTTGAAAAA
19573 TGATTTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (20 bp):
ATTTTGAAAAACAAAATGAG
Found at i:23191 original size:2 final size:2
Alignment explanation
Indices: 23184--23212 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23174 ATTATTATTA
23184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23213 AGATAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24950 original size:23 final size:22
Alignment explanation
Indices: 24914--24967 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
24904 GGGCCTGGTG
* *
24914 GGTTTGTTGTAAAACGGGCCTC
1 GGTTTGGTGAAAAACGGGCCTC
*
24936 AGGTTTGGTGAAAAATGGGCCTC
1 -GGTTTGGTGAAAAACGGGCCTC
24959 GAGTTTGGT
1 G-GTTTGGT
24968 CCTGTAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.20, C:0.13, G:0.35, T:0.31
Consensus pattern (22 bp):
GGTTTGGTGAAAAACGGGCCTC
Found at i:25019 original size:3 final size:3
Alignment explanation
Indices: 24994--25073 Score: 101
Period size: 3 Copynumber: 27.3 Consensus size: 3
24984 AAATATTTAT
* * * *
24994 TAA T-A TAA TAC TAA TAA -AA TAA TAA TAA TAA TTA TAA GAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
25040 TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
25074 TAAGGACATT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
2 4 0.06
3 61 0.94
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:29325 original size:37 final size:37
Alignment explanation
Indices: 29229--29333 Score: 122
Period size: 37 Copynumber: 2.8 Consensus size: 37
29219 CATTTTCGTC
* *
29229 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAATTCCTAAAAATAGGATAGAATT
* * *
29266 TTGCTAGGATTCAAACTT-CTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAA-TTCCTAAAAATAGGATAGAATT
* * *
29303 CTACTATGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAATTCCTAAAAATAGGAT
29334 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
36 2 0.04
37 53 0.95
38 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAATTCCTAAAAATAGGATAGAATT
Found at i:30036 original size:12 final size:11
Alignment explanation
Indices: 30014--30054 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
30004 TCTTTCTTTT
30014 TATTATTCTTG
1 TATTATTCTTG
30025 TATTATTACTTG
1 TATTATT-CTTG
* *
30037 TATTATTTTTA
1 TATTATTCTTG
30048 TATTATT
1 TATTATT
30055 TATTTGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:32425 original size:17 final size:19
Alignment explanation
Indices: 32398--32433 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
32388 TTACAATAAC
32398 ATAATAAATTT-TGCCAAA
1 ATAATAAATTTATGCCAAA
32416 ATAA-AAATTTATGCCAAA
1 ATAATAAATTTATGCCAAA
32434 TTTATTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (19 bp):
ATAATAAATTTATGCCAAA
Found at i:32586 original size:198 final size:197
Alignment explanation
Indices: 32233--32792 Score: 685
Period size: 198 Copynumber: 2.8 Consensus size: 197
32223 TGTAATGTCA
* * ** * *
32233 AAATTTATTTAGTCAAAATATTTTCTCAAAATAACAAATTATGACAAATTTAAATAGTTATAATA
1 AAATTTATTTAGTCAAAATATTTTGTCAAAATAAAAAATTATGACAAATTTATTTAATTAAAATA
* **
32298 ACAAATTT-TAATAAATATTAA-TTCATCAATATAAAAAATTAAGACAAATAATATTCTTTCACA
66 A-AAATTTATAACAAATATTAATTTC-TC-ATATAAAAAATTGTGACAAATAATATTCTTTCACA
* * * * *
32361 ATAACAAATTGTAACAAATTTATTTAGTTACAATAACATAATAAATTTTGCCAAAATAAAAATTT
128 ATAACAAATTGTAACAAAATTATTTAGTCACAATAACACAATAAATTTAGCCAAAATAAAAAGTT
32426 ATGCC
193 ATGCC
* * * * *
32431 AAATTTATTTTGTCACAATATTTTGTCAAAATAAAAAATTCTAACAAATTTATTTAATCAAAATA
1 AAATTTATTTAGTCAAAATATTTTGTCAAAATAAAAAATTATGACAAATTTATTTAATTAAAATA
* *
32496 ATAATTTATAACAAATATTAATTTCTCATCATAAAAAATTGTGACAAGTAATATTCTTTCACAAT
66 AAAATTTATAACAAATATTAATTTCTCAT-ATAAAAAATTGTGACAAATAATATTCTTTCACAAT
* * * ** ** *
32561 AACAAATTATAATAAAATGATTTAGTCACAATAACACGTTAAATTTAGTTAAAGTAAAAAGTTAT
130 AACAAATTGTAACAAAATTATTTAGTCACAATAACACAATAAATTTAGCCAAAATAAAAAGTTAT
*
32626 GTC
195 GCC
* * *
32629 AAATTTATTTCGTCATAATATTTTGTCAAAAT-AAAAATTGTGACAAATTTATTTAATTAAAATA
1 AAATTTATTTAGTCAAAATATTTTGTCAAAATAAAAAATTATGACAAATTTATTTAATTAAAATA
* *
32693 ACAATTTATAACAAATATTAATTTCTCATTATAAAAATAAAAATTGTGACAAAAAATATTCTTTC
66 AAAATTTATAACAAATATTAATTTCTCA-TAT----A-AAAAATTGTGACAAATAATATTCTTTC
*
32758 ACAATAACAAATTGTAACAAAATTATTTTGTCACA
125 ACAATAACAAATTGTAACAAAATTATTTAGTCACA
32793 GTAAAAAGTT
Statistics
Matches: 311, Mismatches: 42, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
197 65 0.21
198 186 0.60
199 3 0.01
201 1 0.00
202 56 0.18
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (197 bp):
AAATTTATTTAGTCAAAATATTTTGTCAAAATAAAAAATTATGACAAATTTATTTAATTAAAATA
AAAATTTATAACAAATATTAATTTCTCATATAAAAAATTGTGACAAATAATATTCTTTCACAATA
ACAAATTGTAACAAAATTATTTAGTCACAATAACACAATAAATTTAGCCAAAATAAAAAGTTATG
CC
Found at i:32798 original size:70 final size:69
Alignment explanation
Indices: 32656--32799 Score: 150
Period size: 70 Copynumber: 2.1 Consensus size: 69
32646 ATATTTTGTC
** *
32656 AAAATAAAAATTGTGACAAATTTATTTAATTAAAATAACAATTTATAACAAATATTAATTTCTCA
1 AAAATAAAAATTGTGACAAAAATATTT-ATTAAAATAACAAATTATAACAAATATTAATTTCTCA
*
32721 TTATA
65 TCATA
* * * *
32726 AAAATAAAAATTGTGACAAAAAATATTCT-TTCACAATAACAAATTGTAACAAA-ATTATTTTGT
1 AAAATAAAAATTGTGAC-AAAAATATT-TATT-AAAATAACAAATTATAACAAATATTAATTTCT
32789 CA-CAGTA
63 CATCA-TA
32796 AAAA
1 AAAA
32800 GTTATAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
69 1 0.02
70 35 0.56
71 25 0.40
72 1 0.02
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (69 bp):
AAAATAAAAATTGTGACAAAAATATTTATTAAAATAACAAATTATAACAAATATTAATTTCTCAT
CATA
Found at i:32923 original size:21 final size:19
Alignment explanation
Indices: 32898--32940 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
32888 TTGATGTTAT
*
32898 AATTTAACTTAATTGTGATGA
1 AATTT-ACTT-ATTGTGATAA
*
32919 AATTTACTTTTTGTGATAA
1 AATTTACTTATTGTGATAA
32938 AAT
1 AAT
32941 AATTACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 4 0.20
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.47
Consensus pattern (19 bp):
AATTTACTTATTGTGATAA
Found at i:48427 original size:3 final size:3
Alignment explanation
Indices: 48419--48495 Score: 99
Period size: 3 Copynumber: 26.7 Consensus size: 3
48409 TGCTTTGAGT
*
48419 GAA GAA GAA GAA -AA GAA GAA AAA TGAA GAA GAA GAA GAA -AA G-A
1 GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA
*
48462 GAA GAA GAA GAA GAA -AA TAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
48496 GCCGGTCAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
2 8 0.12
3 56 0.85
4 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:48455 original size:19 final size:19
Alignment explanation
Indices: 48425--48493 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
48415 GAGTGAAGAA
48425 GAAGAA-AAGAAGAAAAAT
1 GAAGAAGAAGAAGAAAAAT
48443 GAAGAAGAAGAAGAAAAGA-
1 GAAGAAGAAGAAGAAAA-AT
48462 GAAGAAGAAGAAG-AAAAT
1 GAAGAAGAAGAAGAAAAAT
48480 -AAGAAGAAGAAGAA
1 GAAGAAGAAGAAGAA
48494 GAGCCGGTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
17 13 0.28
18 10 0.21
19 23 0.49
20 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.03
Consensus pattern (19 bp):
GAAGAAGAAGAAGAAAAAT
Found at i:48652 original size:2 final size:2
Alignment explanation
Indices: 48645--48677 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
48635 TTTGTGACTT
48645 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48678 GAAATTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48723 original size:20 final size:21
Alignment explanation
Indices: 48679--48725 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
48669 TATATATATG
*
48679 AAATTATTAATTAAAATTTAA
1 AAATTATTAATTAAAATTAAA
* *
48700 AAATTATT-ATTTAAGTTAAA
1 AAATTATTAATTAAAATTAAA
48720 AAATTA
1 AAATTA
48726 ATTTAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATTATTAATTAAAATTAAA
Found at i:49569 original size:20 final size:21
Alignment explanation
Indices: 49513--49569 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
49503 TAAATTAAGT
*
49513 AAAATGATAAAATGAAGAAAAC
1 AAAATAATAAAAT-AAGAAAAC
*
49535 AAAGATAA-AATAATAAGTAAA-
1 AAA-ATAATAA-AATAAGAAAAC
49556 AAAATAATAAAATA
1 AAAATAATAAAATA
49570 TATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 8 0.27
21 5 0.17
22 11 0.37
23 6 0.20
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.18
Consensus pattern (21 bp):
AAAATAATAAAATAAGAAAAC
Found at i:49923 original size:2 final size:2
Alignment explanation
Indices: 49916--49944 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49906 CTTGTGTAGA
49916 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49945 ATAATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50146 original size:2 final size:2
Alignment explanation
Indices: 50139--50193 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
50129 GAACATACGC
50139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50181 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
50194 ACAAAATAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50230 original size:12 final size:11
Alignment explanation
Indices: 50202--50242 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
50192 TAACAAAATA
* *
50202 AATAATATAAA
1 AATAATACAAG
50213 AATAATACAAG
1 AATAATACAAG
50224 TAATAATACAAG
1 -AATAATACAAG
50236 AATAATA
1 AATAATA
50243 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:50347 original size:12 final size:12
Alignment explanation
Indices: 50325--50369 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
50315 GAATAAAAGG
50325 AAAATATAATAGT
1 AAAA-ATAATAGT
*
50338 AAAAATAATAAT
1 AAAAATAATAGT
*
50350 AAATATAATAGT
1 AAAAATAATAGT
*
50362 AATAATAA
1 AAAAATAA
50370 AACTGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:50975 original size:37 final size:37
Alignment explanation
Indices: 50934--51030 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
50924 TGATCTTATC
* * *
50934 TTTAGGAATTTAAATCATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCATATT
* * * * *
50971 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTTTT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCATATT
51008 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTGAATCCTAGTAG
51031 GACGAAAATG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAGAACTCTATCATATT
Found at i:51286 original size:22 final size:22
Alignment explanation
Indices: 51260--51310 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
51250 CAGCACGTGG
51260 CTTCTCGTTGCCCTTCAGTCTT
1 CTTCTCGTTGCCCTTCAGTCTT
* *
51282 CTTCTCGTTGCCCTTCGGTTTT
1 CTTCTCGTTGCCCTTCAGTCTT
51304 CTTCTCG
1 CTTCTCG
51311 GTTTAAAGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.02, C:0.35, G:0.16, T:0.47
Consensus pattern (22 bp):
CTTCTCGTTGCCCTTCAGTCTT
Found at i:52105 original size:106 final size:106
Alignment explanation
Indices: 51780--53260 Score: 2199
Period size: 106 Copynumber: 14.0 Consensus size: 106
51770 GCATTGTTCT
* ** *
51780 GAGTCCAATATCC-TCTG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTC-GCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC
* * * * *
51843 AACCAGCCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
51886 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAATT-TTT-TTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * *
51945 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
51987 G-GTTCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
52051 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
52092 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
52157 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
52198 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
52263 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
52304 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
52369 CCAGCGGTCTCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
52410 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
52475 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
52516 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
52581 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
52622 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
52687 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
52728 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
52793 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* **
52834 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGATAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
52899 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
52940 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
**
53005 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
53046 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
53111 CCAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
53152 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * *
53216 CTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
53257 GAGT
1 GAGT
53261 GGCACGATAT
Statistics
Matches: 1263, Mismatches: 102, Indels: 21
0.91 0.07 0.02
Matches are distributed among these distances:
100 74 0.06
101 7 0.01
102 7 0.01
104 5 0.00
105 54 0.04
106 1113 0.88
107 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:54093 original size:22 final size:22
Alignment explanation
Indices: 54067--54143 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
54057 TTATGTTTGG
54067 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
54089 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
54111 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
54133 TCAACGGTTTG
1 TCAAAGGTTTG
54144 ATGGGGTAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:54774 original size:22 final size:21
Alignment explanation
Indices: 54749--54828 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 21
54739 CTTTTTGTCC
54749 CTTTTTCTTTTTATTTTTGCTT
1 CTTTTTCTTTTT-TTTTTGCTT
*
54771 C-TTTTCTTTTTTGTTCTTGATT
1 CTTTTTCTTTTTT-TT-TTGCTT
*
54793 CTCTTTTTTATTTGTTTTTTGCTT
1 CT-TTTTCT-TTT-TTTTTTGCTT
*
54817 C-TTTGCTTTTTT
1 CTTTTTCTTTTTT
54829 GTTCTTGATT
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
20 3 0.06
21 15 0.32
22 11 0.23
24 11 0.23
25 5 0.11
26 2 0.04
ACGTcount: A:0.04, C:0.14, G:0.07, T:0.75
Consensus pattern (21 bp):
CTTTTTCTTTTTTTTTTGCTT
Found at i:54787 original size:15 final size:15
Alignment explanation
Indices: 54753--54834 Score: 62
Period size: 16 Copynumber: 5.3 Consensus size: 15
54743 TTGTCCCTTT
54753 TTCTTTT-TATTTTTG
1 TTCTTTTCT-TTTTTG
54768 CTTCTTTTCTTTTTTG
1 -TTCTTTTCTTTTTTG
*
54784 TTCTTGATTCTCTTTT-
1 TTCTT--TTCTTTTTTG
* *
54800 TT-ATTTGTTTTTTG
1 TTCTTTTCTTTTTTG
*
54814 CTTCTTTGCTTTTTTG
1 -TTCTTTTCTTTTTTG
54830 TTCTT
1 TTCTT
54835 GATTGGATCT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
13 7 0.13
15 13 0.25
16 24 0.45
17 9 0.17
ACGTcount: A:0.04, C:0.13, G:0.09, T:0.74
Consensus pattern (15 bp):
TTCTTTTCTTTTTTG
Found at i:54818 original size:24 final size:22
Alignment explanation
Indices: 54751--54831 Score: 85
Period size: 22 Copynumber: 3.6 Consensus size: 22
54741 TTTTGTCCCT
*
54751 TTTTC-TTTTTATTTTTGCTTC
1 TTTTCTTTTTTGTTTTTGCTTC
* *
54772 TTTTCTTTTTTGTTCTTGATTC
1 TTTTCTTTTTTGTTTTTGCTTC
54794 TCTTT-TTTATTTGTTTTTTGCTTC
1 T-TTTCTTT-TTTG-TTTTTGCTTC
*
54818 TTTGCTTTTTTGTT
1 TTTTCTTTTTTGTT
54832 CTTGATTGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
21 5 0.10
22 19 0.39
23 13 0.27
24 12 0.24
ACGTcount: A:0.04, C:0.12, G:0.09, T:0.75
Consensus pattern (22 bp):
TTTTCTTTTTTGTTTTTGCTTC
Found at i:58223 original size:19 final size:20
Alignment explanation
Indices: 58195--58232 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
58185 TACAGATGAT
*
58195 GGAAATAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
58214 GGAAAAAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
58233 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:59373 original size:9 final size:9
Alignment explanation
Indices: 59359--59431 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 9
59349 ATAGTAAGTA
59359 AAAATAAAT
1 AAAATAAAT
59368 AAAATATATAT
1 AAAATA-A-AT
*
59379 AAAA-AAGAA
1 AAAATAA-AT
* *
59388 AAAGAAAAAG
1 AAA-ATAAAT
59398 AAAATAAAT
1 AAAATAAAT
*
59407 AAAACAAAT
1 AAAATAAAT
59416 AAAA-AAAT
1 AAAATAAAT
59424 AATAATAA
1 AA-AATAA
59432 CAAAGTACGA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
8 6 0.12
9 29 0.56
10 9 0.17
11 8 0.15
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.16
Consensus pattern (9 bp):
AAAATAAAT
Found at i:59749 original size:2 final size:2
Alignment explanation
Indices: 59742--59770 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59732 TTTGTGTAGA
59742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59771 CTTTTAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59885 original size:15 final size:15
Alignment explanation
Indices: 59865--59896 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
59855 AAATATTTCA
*
59865 TTTTATCTTTTATTT
1 TTTTATCTTCTATTT
59880 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
59895 TT
1 TT
59897 ATTTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:59913 original size:20 final size:20
Alignment explanation
Indices: 59866--59919 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
59856 AATATTTCAT
59866 TTTATCTTTTATTTTTTTATC
1 TTTAT-TTTTATTTTTTTATC
59887 TTCTATTTTTATTTTTTTAT-
1 TT-TATTTTTATTTTTTTATC
*
59907 TGTTATTGTTATT
1 T-TTATTTTTATT
59920 ATCTTCTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.33
21 17 0.57
22 3 0.10
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.76
Consensus pattern (20 bp):
TTTATTTTTATTTTTTTATC
Found at i:59953 original size:11 final size:10
Alignment explanation
Indices: 59926--59965 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
59916 TATTATCTTC
59926 TTTAT-TTTA
1 TTTATATTTA
*
59935 TGTAT-TTTA
1 TTTATATTTA
59944 TTTATATTT-
1 TTTATATTTA
59953 TTTATATTTA
1 TTTATATTTA
59963 TTT
1 TTT
59966 TTGTGCCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 21 0.78
10 6 0.22
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (10 bp):
TTTATATTTA
Found at i:59955 original size:13 final size:12
Alignment explanation
Indices: 59864--59967 Score: 57
Period size: 12 Copynumber: 7.9 Consensus size: 12
59854 TAAATATTTC
*
59864 ATTTTATCTTTT
1 ATTTTATTTTTT
*
59876 ATTTTTTTATCTTCT
1 ATTTTATT-T-TT-T
59891 ATTTTTATTTTTTT
1 A-TTTTA-TTTTTT
*
59905 ATTGTTA-TTGTT
1 ATT-TTATTTTTT
* * *
59917 ATTATCTTCTTT
1 ATTTTATTTTTT
59929 ATTTTATGTATTTT
1 ATTTTAT-T-TTTT
59943 ATTTATATTTTTT
1 ATTT-TATTTTTT
59956 ATATTTATTTTT
1 AT-TTTATTTTT
59968 GTGCCTCTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 21
0.69 0.11 0.21
Matches are distributed among these distances:
11 1 0.01
12 21 0.30
13 17 0.24
14 17 0.24
15 7 0.10
16 5 0.07
17 2 0.03
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (12 bp):
ATTTTATTTTTT
Found at i:70899 original size:110 final size:110
Alignment explanation
Indices: 70701--70904 Score: 311
Period size: 110 Copynumber: 1.9 Consensus size: 110
70691 GCTTCCCAGT
* *
70701 TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * *
70766 CAATGAAGGGGCGACTGATTGTCAACAAATAACTTTTCAGTTTCA
66 CAACGAAGGGGCGACTAACTGTCAACAAATAACTTTTCAGTTTCA
* * *
70811 TTCAGAGTCAATTTCAACTTCACAGCGAATGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
*
70876 CAGCGAAGGGGC-AGCTAACTGTCAACAAA
66 CAACGAAGGGGCGA-CTAACTGTCAACAAA
70905 CAATTTCCAG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
109 1 0.01
110 83 0.99
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGACTAACTGTCAACAAATAACTTTTCAGTTTCA
Found at i:72315 original size:3 final size:3
Alignment explanation
Indices: 72309--72342 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
72299 TTTTTTTTTT
72309 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
72343 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:72347 original size:2 final size:2
Alignment explanation
Indices: 72340--72374 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
72330 TTATTATTAT
72340 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
72375 TATCTTCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:72492 original size:31 final size:30
Alignment explanation
Indices: 72445--72518 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
72435 TTTAATTCTT
*
72445 TTTTTA-TATATCATTATTAT-TTATATATA
1 TTTTTATTATATAATTA-TATGTTATATATA
72474 TTTTTATTACTATAATTATATGTTATATATA
1 TTTTTATTA-TATAATTATATGTTATATATA
*
72505 TTTATTATTTTATA
1 TTT-TTATTATATA
72519 TATTTCATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 6 0.15
30 5 0.13
31 23 0.59
32 5 0.13
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTTTATTATATAATTATATGTTATATATA
Found at i:72507 original size:41 final size:39
Alignment explanation
Indices: 72401--72516 Score: 96
Period size: 39 Copynumber: 3.0 Consensus size: 39
72391 TTTATTTCTT
* *
72401 TTCTAT-ATTCTATCGTTATATATATATATATATATTTAA
1 TTCTATAATTATAT-GTTATATATATTTATATATATTTAA
* ** * * *
72440 TTCTTTTTTTATATATCAT-TATTATTTATATATATTTTTA
1 TTCTATAATTATATGTTATATA-TATTTATATATA-TTTAA
72480 TTACTATAATTATATGTTATATATATTTAT-TAT-TTTA
1 TT-CTATAATTATATGTTATATATATTTATATATATTTA
72517 TATATTTCAT
Statistics
Matches: 59, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
38 5 0.08
39 19 0.32
40 14 0.24
41 19 0.32
42 2 0.03
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (39 bp):
TTCTATAATTATATGTTATATATATTTATATATATTTAA
Found at i:72546 original size:15 final size:15
Alignment explanation
Indices: 72526--72557 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
72516 ATATATTTCA
*
72526 TTTTATCTTTTATTT
1 TTTTATCTTCTATTT
72541 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
72556 TT
1 TT
72558 ATTTTTGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:72601 original size:18 final size:18
Alignment explanation
Indices: 72570--72609 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
72560 TTTTGTAATG
*
72570 TTATTGTTATTATCTTCT
1 TTATTGTTATTATCTTAT
72588 TTATT-TTATGTATCTTAT
1 TTATTGTTAT-TATCTTAT
72606 TTAT
1 TTAT
72610 ATTTTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (18 bp):
TTATTGTTATTATCTTAT
Found at i:72712 original size:29 final size:29
Alignment explanation
Indices: 72679--72741 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
72669 CTTTATCCTG
*
72679 TTTTATTTT-CTCTACTTTATTGTATTTAT
1 TTTTATTTTAC-CTACTTTATTGTATTCAT
* *
72708 TTTTATTTTACCTTCTTTATTTTATTCAT
1 TTTTATTTTACCTACTTTATTGTATTCAT
72737 TTTTA
1 TTTTA
72742 CTACATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (29 bp):
TTTTATTTTACCTACTTTATTGTATTCAT
Found at i:73976 original size:20 final size:20
Alignment explanation
Indices: 73951--74003 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
73941 AACAATGAAG
73951 TAGTACCGATACTGCTAAGT
1 TAGTACCGATACTGCTAAGT
*
73971 TAGTACCAATACTGCTAAGT
1 TAGTACCGATACTGCTAAGT
* *
73991 CAGTACTGATACT
1 TAGTACCGATACT
74004 ATCAAAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (20 bp):
TAGTACCGATACTGCTAAGT
Found at i:76081 original size:8 final size:8
Alignment explanation
Indices: 76070--76107 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
76060 AAAGAGAAAG
76070 AAAGAAGA
1 AAAGAAGA
76078 AAAGAAGA
1 AAAGAAGA
*
76086 AAAG-TGA
1 AAAGAAGA
76093 AGAAGAAGA
1 A-AAGAAGA
76102 AAAGAA
1 AAAGAA
76108 TAAGAAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 3 0.12
8 20 0.77
9 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (8 bp):
AAAGAAGA
Found at i:78185 original size:19 final size:19
Alignment explanation
Indices: 78161--78211 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
78151 TTCCCTATCG
*
78161 GTGCATCGATGCACTACCT
1 GTGCATCGGTGCACTACCT
78180 GTGCATCGGTGCACTACCT
1 GTGCATCGGTGCACTACCT
*
78199 GTTCATCGGTGCA
1 GTGCATCGGTGCA
78212 TAAATGACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.18, C:0.29, G:0.25, T:0.27
Consensus pattern (19 bp):
GTGCATCGGTGCACTACCT
Found at i:80051 original size:19 final size:19
Alignment explanation
Indices: 80018--80054 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
80008 ACGTGGTCTT
80018 ATCCGTCATATTCATACAC
1 ATCCGTCATATTCATACAC
80037 ATCCTGTCATA-TCATACA
1 ATCC-GTCATATTCATACA
80055 TTTGATCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.32
Consensus pattern (19 bp):
ATCCGTCATATTCATACAC
Found at i:80256 original size:23 final size:23
Alignment explanation
Indices: 80238--80390 Score: 279
Period size: 23 Copynumber: 6.7 Consensus size: 23
80228 CTCGTATAAA
80238 TGCACCGAAGTGCCACGTAGGAT
1 TGCACCGAAGTGCCACGTAGGAT
*
80261 TGCACCGAAGTGCCACGTAGTAT
1 TGCACCGAAGTGCCACGTAGGAT
80284 TGCACCGAAGTGCCACGTAGGAT
1 TGCACCGAAGTGCCACGTAGGAT
80307 TGCACCGAAGTGCCACGTAGGAT
1 TGCACCGAAGTGCCACGTAGGAT
80330 TGCACCGAAGTGCCACGTAGGAT
1 TGCACCGAAGTGCCACGTAGGAT
* *
80353 TGCACCGAAGTGCCACGTAGAAA
1 TGCACCGAAGTGCCACGTAGGAT
80376 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
80391 TATAAAATGT
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 126 1.00
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGGAT
Found at i:80914 original size:2 final size:2
Alignment explanation
Indices: 80901--80955 Score: 101
Period size: 2 Copynumber: 27.0 Consensus size: 2
80891 TACACATTTC
80901 AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80944 AT AT AT AT AT AT
1 AT AT AT AT AT AT
80956 CCTAATTACT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:82997 original size:10 final size:10
Alignment explanation
Indices: 82984--83018 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
82974 TTCATATCCA
82984 TTCATGTTCG
1 TTCATGTTCG
*
82994 TTCATGTCCG
1 TTCATGTTCG
83004 TTCATGTTCG
1 TTCATGTTCG
83014 TTCAT
1 TTCAT
83019 TTAAATGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (10 bp):
TTCATGTTCG
Found at i:82998 original size:20 final size:20
Alignment explanation
Indices: 82973--83018 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
82963 AATATAGTTT
82973 GTTCATATCCATTCATGTTC
1 GTTCATATCCATTCATGTTC
* *
82993 GTTCATGTCCGTTCATGTTC
1 GTTCATATCCATTCATGTTC
83013 GTTCAT
1 GTTCAT
83019 TTAAATGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.46
Consensus pattern (20 bp):
GTTCATATCCATTCATGTTC
Found at i:84527 original size:37 final size:37
Alignment explanation
Indices: 84455--84527 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
84445 TTATATTTTT
*
84455 AATTTTGTAAAAAAATTATATAAATATTATGAATTTA
1 AATTTTGTAAAAAAATTATATAAATATTATCAATTTA
*
84492 AATTTT-TAAAGAAAA-TATATAAATATTTTACAATTT
1 AATTTTGTAAA-AAAATTATATAAATATTAT-CAATTT
84528 GTAATATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (37 bp):
AATTTTGTAAAAAAATTATATAAATATTATCAATTTA
Done.