Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008743.1 Hibiscus syriacus cultivar Beakdansim tig00111832_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: 979257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:935647 original size:14 final size:15
Alignment explanation
Indices: 935628--935661 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
935618 AATAAAAAAT
935628 ATTTTTTAT-TGAAA
1 ATTTTTTATCTGAAA
*
935642 ATTTTTTATCTTAAA
1 ATTTTTTATCTGAAA
935657 ATTTT
1 ATTTT
935662 ATAAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTTTTATCTGAAA
Found at i:943066 original size:6 final size:6
Alignment explanation
Indices: 943055--943082 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
943045 GCCGCTTTGG
943055 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
943083 CCTTTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:944820 original size:180 final size:180
Alignment explanation
Indices: 944518--944882 Score: 721
Period size: 180 Copynumber: 2.0 Consensus size: 180
944508 TTTTTTTATG
944518 GTATAAATTATTTTGTTTTAAGATTTATTATGTATTATTAAACTTTTTTCAATTATGTTTGTAAA
1 GTATAAATTATTTTGTTTTAAGATTTATTATGTATTATTAAACTTTTTTCAATTATGTTTGTAAA
944583 ATATTTATGGATTGTTAGTTTGTTACTTTGATGTTTAAACTGTGAAATTGATTCACATAATATTT
66 ATATTTATGGATTGTTAGTTTGTTACTTTGATGTTTAAACTGTGAAATTGATTCACATAATATTT
944648 TGTTATTTTTTAATTTGTTAATTTATATTAAGTTTTATATATTATTGTTA
131 TGTTATTTTTTAATTTGTTAATTTATATTAAGTTTTATATATTATTGTTA
944698 GTATAAATTATTTTGTTTTAAGATTTATTATGTATTATTAAACTTTTTTCAATTATGTTTGTAAA
1 GTATAAATTATTTTGTTTTAAGATTTATTATGTATTATTAAACTTTTTTCAATTATGTTTGTAAA
944763 ATATTTATGGATTGTTAGTTTGTTACTTTGATGTTTAAACTGTGAAATTGATTCACATAATATTT
66 ATATTTATGGATTGTTAGTTTGTTACTTTGATGTTTAAACTGTGAAATTGATTCACATAATATTT
944828 TGTTATTTTTTAATTTGTTAATTTATATTAAGTTTTATATATTATTGTTA
131 TGTTATTTTTTAATTTGTTAATTTATATTAAGTTTTATATATTATTGTTA
*
944878 TTATA
1 GTATA
944883 TTAAAATAAG
Statistics
Matches: 184, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 184 1.00
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (180 bp):
GTATAAATTATTTTGTTTTAAGATTTATTATGTATTATTAAACTTTTTTCAATTATGTTTGTAAA
ATATTTATGGATTGTTAGTTTGTTACTTTGATGTTTAAACTGTGAAATTGATTCACATAATATTT
TGTTATTTTTTAATTTGTTAATTTATATTAAGTTTTATATATTATTGTTA
Found at i:946778 original size:12 final size:12
Alignment explanation
Indices: 946753--946822 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
946743 ACGAAGATAT
* *
946753 CAGAAATCAAAA
1 CAGAATTCAGAA
946765 CAGAATTCAGAA
1 CAGAATTCAGAA
946777 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
946789 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
946801 CAAAAATCAGAA
1 CAGAATTCAGAA
946813 CAGAATTCAG
1 CAGAATTCAG
946823 GTCATTTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:946833 original size:24 final size:24
Alignment explanation
Indices: 946758--946845 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 24
946748 GATATCAGAA
* * *
946758 ATCAAAACAGAATTCAGAACAGAT
1 ATCAGAACAGAATTCAGATCAAAT
* *
946782 ATCAGAACAGAATCCAGATCAAAA
1 ATCAGAACAGAATTCAGATCAAAT
* **
946806 ATCAGAACAGAATTCAGGTCATTT
1 ATCAGAACAGAATTCAGATCAAAT
*
946830 ATCAGAACATAATTCA
1 ATCAGAACAGAATTCA
946846 AGTCGGAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCAAAT
Found at i:946856 original size:48 final size:48
Alignment explanation
Indices: 946751--946859 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 48
946741 AAACGAAGAT
* *
946751 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCAAG
* ** ** *
946799 ATCAAAAATCAGAACAGAATTCAGGTCATTTATCAGAACATAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAA-TCAAG
*
946848 -TCGGAAATCAGA
1 ATCAGAAATCAGA
946860 TAAAATATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 46 0.92
49 4 0.08
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCAAG
Found at i:947486 original size:15 final size:15
Alignment explanation
Indices: 947468--947503 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
947458 TATCCATTCC
*
947468 AGTCAATGGTCAACG
1 AGTCAACGGTCAACG
947483 AGTCAACGGTCAACG
1 AGTCAACGGTCAACG
*
947498 GGTCAA
1 AGTCAA
947504 GTCAACGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (15 bp):
AGTCAACGGTCAACG
Found at i:947509 original size:13 final size:14
Alignment explanation
Indices: 947476--947513 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
947466 CCAGTCAATG
*
947476 GTCAACGAGTCAAC
1 GTCAACGGGTCAAC
947490 GGTCAACGGGTCAA-
1 -GTCAACGGGTCAAC
947504 GTCAACGGGT
1 GTCAACGGGT
947514 TGGGTCGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
15 12 0.55
ACGTcount: A:0.29, C:0.24, G:0.32, T:0.16
Consensus pattern (14 bp):
GTCAACGGGTCAAC
Found at i:947525 original size:18 final size:18
Alignment explanation
Indices: 947504--947541 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
947494 AACGGGTCAA
*
947504 GTCAACGGGTTGGGTCGG
1 GTCAACGGGTCGGGTCGG
947522 GTCAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTCGG
947540 GT
1 GT
947542 TGTGACCGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.18, G:0.50, T:0.21
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCGG
Found at i:949696 original size:12 final size:12
Alignment explanation
Indices: 949671--949740 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
949661 ACGAAGATAT
* *
949671 CAGAAATCAAAA
1 CAGAATTCAGAA
949683 CAGAATTCAGAA
1 CAGAATTCAGAA
949695 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
949707 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
949719 CAAAAATCAGAA
1 CAGAATTCAGAA
949731 CAGAATTCAG
1 CAGAATTCAG
949741 GTCATTTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:949751 original size:24 final size:24
Alignment explanation
Indices: 949676--949763 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 24
949666 GATATCAGAA
* * *
949676 ATCAAAACAGAATTCAGAACAGAT
1 ATCAGAACAGAATTCAGATCAAAT
* *
949700 ATCAGAACAGAATCCAGATCAAAA
1 ATCAGAACAGAATTCAGATCAAAT
* **
949724 ATCAGAACAGAATTCAGGTCATTT
1 ATCAGAACAGAATTCAGATCAAAT
*
949748 ATCAGAACATAATTCA
1 ATCAGAACAGAATTCA
949764 AGTCGGAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCAAAT
Found at i:949774 original size:48 final size:48
Alignment explanation
Indices: 949669--949777 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 48
949659 AAACGAAGAT
* *
949669 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCAAG
* ** ** *
949717 ATCAAAAATCAGAACAGAATTCAGGTCATTTATCAGAACATAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAA-TCAAG
*
949766 -TCGGAAATCAGA
1 ATCAGAAATCAGA
949778 TAAAATATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 46 0.92
49 4 0.08
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCAAG
Found at i:950957 original size:43 final size:43
Alignment explanation
Indices: 950891--950976 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
950881 CGGTATTTCA
* **
950891 ATCTTTTTCCTCCATTCGGTCTTATTATTTAATTCCAAT-TTAT
1 ATCTTTTTCCTCCATCCAATCTTATTATTTAATT-CAATCTTAT
950934 ATCTTTTTCCTCCATCCAATCTTATTATTTAATTCAATCTTAT
1 ATCTTTTTCCTCCATCCAATCTTATTATTTAATTCAATCTTAT
950977 CATTTACTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
42 4 0.10
43 35 0.90
ACGTcount: A:0.23, C:0.22, G:0.02, T:0.52
Consensus pattern (43 bp):
ATCTTTTTCCTCCATCCAATCTTATTATTTAATTCAATCTTAT
Found at i:952319 original size:15 final size:15
Alignment explanation
Indices: 952299--952334 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
952289 GGTCAACTCC
952299 AGTCAACGGTCAACG
1 AGTCAACGGTCAACG
952314 AGTCAACGGTCAACG
1 AGTCAACGGTCAACG
*
952329 GGTCAA
1 AGTCAA
952335 GTCAACGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.28, T:0.14
Consensus pattern (15 bp):
AGTCAACGGTCAACG
Found at i:952320 original size:8 final size:7
Alignment explanation
Indices: 952300--952342 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
952290 GTCAACTCCA
952300 GTCAACG
1 GTCAACG
952307 GTCAACG
1 GTCAACG
952314 AGTCAACG
1 -GTCAACG
952322 GTCAACGG
1 GTCAAC-G
952330 GTCAA--
1 GTCAACG
952335 GTCAACG
1 GTCAACG
952342 G
1 G
952343 GTCGGGTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.16
7 14 0.44
8 13 0.41
ACGTcount: A:0.30, C:0.26, G:0.30, T:0.14
Consensus pattern (7 bp):
GTCAACG
Found at i:952340 original size:13 final size:13
Alignment explanation
Indices: 952307--952358 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
952297 CCAGTCAACG
*
952307 GTCAACGAGTCAA
1 GTCAACGGGTCAA
952320 CGGTCAACGGGTCAA
1 --GTCAACGGGTCAA
**
952335 GTCAACGGGTCGG
1 GTCAACGGGTCAA
952348 GTCAACGGGTC
1 GTCAACGGGTC
952359 TGGTAAACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
13 22 0.65
15 12 0.35
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (13 bp):
GTCAACGGGTCAA
Found at i:952353 original size:26 final size:26
Alignment explanation
Indices: 952321--952376 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
952311 ACGAGTCAAC
*
952321 GGTCAACGGGTCAAGTCAACGGGTCG
1 GGTCAACGGGTCAAGTAAACGGGTCG
**
952347 GGTCAACGGGTCTGGTAAACGGGTCG
1 GGTCAACGGGTCAAGTAAACGGGTCG
952373 GGTC
1 GGTC
952377 GGGTTGTGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.20, C:0.21, G:0.41, T:0.18
Consensus pattern (26 bp):
GGTCAACGGGTCAAGTAAACGGGTCG
Found at i:952358 original size:8 final size:8
Alignment explanation
Indices: 952300--952358 Score: 53
Period size: 8 Copynumber: 8.4 Consensus size: 8
952290 GTCAACTCCA
952300 GTCAAC-G
1 GTCAACGG
*
952307 GTCAACGA
1 GTCAACGG
952315 GTCAAC-G
1 GTCAACGG
952322 GTCAACGG
1 GTCAACGG
952330 GTCAA---
1 GTCAACGG
952335 GTCAACGG
1 GTCAACGG
952343 GT---CGG
1 GTCAACGG
952348 GTCAACGG
1 GTCAACGG
952356 GTC
1 GTC
952359 TGGTAAACGG
Statistics
Matches: 42, Mismatches: 2, Indels: 15
0.71 0.03 0.25
Matches are distributed among these distances:
5 10 0.24
7 12 0.29
8 20 0.48
ACGTcount: A:0.25, C:0.25, G:0.34, T:0.15
Consensus pattern (8 bp):
GTCAACGG
Found at i:952367 original size:13 final size:13
Alignment explanation
Indices: 952338--952375 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
952328 GGGTCAAGTC
*
952338 AACGGGTCGGGTC
1 AACGGGTCGGGTA
*
952351 AACGGGTCTGGTA
1 AACGGGTCGGGTA
952364 AACGGGTCGGGT
1 AACGGGTCGGGT
952376 CGGGTTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.45, T:0.18
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:958771 original size:19 final size:20
Alignment explanation
Indices: 958742--958779 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
958732 CAGAAATTGT
958742 TGAAGGTGTATCGATGCACA
1 TGAAGGTGTATCGATGCACA
958762 TGAA-GTGTATCGATGCAC
1 TGAAGGTGTATCGATGCAC
958780 TCCTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGTATCGATGCACA
Found at i:958886 original size:63 final size:63
Alignment explanation
Indices: 958747--958908 Score: 191
Period size: 63 Copynumber: 2.6 Consensus size: 63
958737 ATTGTTGAAG
* * *
958747 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCAC-CCTTTAAAATAAAAACATCGAATGTCATCA
* ** * **
958811 GTGTATCGATGCACAAGTAGTGCATCGATGCACCGC-TTAATATTCAAACATCGAATGTGATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACC-CTTTAAAATAAAAACATCGAATGTCATCA
* * *
958874 GTGTACCGATGCACAGGTAGTGCATAGATGCACCC
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCC
958909 GTCAAGGGAT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
62 1 0.01
63 53 0.62
64 31 0.36
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (63 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCTTTAAAATAAAAACATCGAATGTCATCA
Found at i:959484 original size:22 final size:22
Alignment explanation
Indices: 959456--959540 Score: 152
Period size: 22 Copynumber: 3.9 Consensus size: 22
959446 GAGGGTTTAT
959456 AGTGGTCCTTCGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
*
959478 AGTGGTCCTTCGGGAAGTATCC
1 AGTGGTCCTTCGGGACGTATCC
959500 AGTGGTCCTTCGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
*
959522 AGTGGTCCTTAGGGACGTA
1 AGTGGTCCTTCGGGACGTA
959541 ATGGTCATTC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.16, C:0.24, G:0.33, T:0.27
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACGTATCC
Found at i:960040 original size:3 final size:3
Alignment explanation
Indices: 960032--960126 Score: 156
Period size: 3 Copynumber: 31.7 Consensus size: 3
960022 TTTTTATCCA
* *
960032 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
960080 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
960125 TA
1 TA
960127 AATATATATT
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.02
3 81 0.94
4 3 0.03
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:960058 original size:21 final size:21
Alignment explanation
Indices: 960032--960137 Score: 139
Period size: 21 Copynumber: 5.1 Consensus size: 21
960022 TTTTTATCCA
960032 TATTATTATTATTAATATTAT
1 TATTATTATTATTAATATTAT
960053 TATTATTATTA-T--TATTAT
1 TATTATTATTATTAATATTAT
* *
960071 TATTACTATTATTATTATTAT
1 TATTATTATTATTAATATTAT
960092 TATTATTATTATT-ATATTAT
1 TATTATTATTATTAATATTAT
960112 TATTATTTATTATTAAATATATAT
1 TATTA-TTATTATT-AATAT-TAT
960136 TA
1 TA
960138 AACATATATA
Statistics
Matches: 75, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
18 16 0.21
19 1 0.01
20 12 0.16
21 37 0.49
23 4 0.05
24 5 0.07
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTATTATTATTAATATTAT
Found at i:960607 original size:18 final size:18
Alignment explanation
Indices: 960573--960607 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
960563 TGAAAAAAAA
*
960573 GGGACAGAGACAGAGAAC
1 GGGACAGAGACACAGAAC
*
960591 GGGACAGAGAGACAGAA
1 GGGACAGAGACACAGAA
960608 AAAAAAAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.40, T:0.00
Consensus pattern (18 bp):
GGGACAGAGACACAGAAC
Found at i:960619 original size:20 final size:20
Alignment explanation
Indices: 960594--960640 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
960584 AGAGAACGGG
960594 ACAGAGAGACAGAAAAAAAA
1 ACAGAGAGACAGAAAAAAAA
*
960614 AGAGAGAGACAGAAAAAAAA
1 ACAGAGAGACAGAAAAAAAA
960634 ACAGAGA
1 ACAGAGA
960641 AGATACAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.68, C:0.09, G:0.23, T:0.00
Consensus pattern (20 bp):
ACAGAGAGACAGAAAAAAAA
Found at i:973301 original size:19 final size:20
Alignment explanation
Indices: 973268--973309 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
973258 TTCAAGTTCA
*
973268 ATTTATTGGAGATTCAATTT
1 ATTTATTGGAAATTCAATTT
973288 ATTT-TTGGAAATTCAATTT
1 ATTTATTGGAAATTCAATTT
973307 ATT
1 ATT
973310 CTTTTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (20 bp):
ATTTATTGGAAATTCAATTT
Found at i:974171 original size:84 final size:84
Alignment explanation
Indices: 974072--974384 Score: 583
Period size: 84 Copynumber: 3.7 Consensus size: 84
974062 CATTAACTGA
974072 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
974137 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
974156 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
974221 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
974240 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
974305 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
* * * *
974324 AAGATGAATTTGC-CAATAGCATCTTTTGAAAGTGTTCTTTGAGTTATCTAATCTGGTTTGG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGG
974385 TAAAAATTAC
Statistics
Matches: 225, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
83 44 0.20
84 181 0.80
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (84 bp):
AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
AACCAATCATTGAATTTGG
Found at i:975575 original size:225 final size:224
Alignment explanation
Indices: 975103--975775 Score: 1011
Period size: 225 Copynumber: 3.0 Consensus size: 224
975093 CAAAGATTCA
* * *
975103 AATCTATCATTTGATGGATTATCTTTTCCAGA-GAAGGTTCATAATGAGAAGAACTCATCATCTG
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGGAA-GTTCATAATGAGAAGAA--C-TCATCTG
*
975167 AAGGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT-CTGAATTCATCACTT
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-TCCTGAATTCATCA-TT
* *
975231 GATGGATTATTTTTGCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAA-AAGGAAGAAGAAG
125 GATGGATCACTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
975294 TTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
189 TTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
975330 AATCCATCATTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAG-ACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
975394 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATCCATCATTTGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCA-TTGATGG
975459 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
130 ATCA-CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
975524 AATGAGAAGAATTTGTTCAACCTTTTACCTG
194 AATGAGAAGAATTTGTTCAACCTTTTACCTG
*
975555 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
975620 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTGATGGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCATTGATGGA
* * * *
975685 TCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAG-A-AAGTT
131 TC-ACTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTT
* * *
975747 CATAATAAGAAGAACTTGTTCAACTTTTT
191 CATAATGAGAAGAATTTGTTCAACCTTTT
975776 GCATAATTCT
Statistics
Matches: 416, Mismatches: 19, Indels: 23
0.91 0.04 0.05
Matches are distributed among these distances:
222 1 0.00
223 80 0.19
224 35 0.08
225 135 0.32
226 100 0.24
227 46 0.11
228 19 0.05
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (224 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCATTGATGGA
TCACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
TGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:975784 original size:112 final size:113
Alignment explanation
Indices: 975103--975777 Score: 1006
Period size: 113 Copynumber: 6.0 Consensus size: 113
975093 CAAAGATTCA
* * * *
975103 AATCTATCATTTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCATCTGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGA
* *
975168 AGGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTG
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * * *
975219 AATTCATCACTTGATGGATTA-TTTTTGCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAA-
1 AATCCATCATTTGATGGATCAGCTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
975281 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
*
975330 AATCCATCATTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAG-ACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
975394 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
975442 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
975507 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
975555 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
975620 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * * * *
975668 AATTCATCA-TTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTG
* * * *
975731 AAGAAGAAAG-A-AAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
975778 ATAATTCTAT
Statistics
Matches: 524, Mismatches: 26, Indels: 21
0.92 0.05 0.04
Matches are distributed among these distances:
111 82 0.16
112 165 0.31
113 213 0.41
114 2 0.00
115 38 0.07
116 24 0.05
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
Found at i:976102 original size:3 final size:3
Alignment explanation
Indices: 976094--976181 Score: 153
Period size: 3 Copynumber: 29.7 Consensus size: 3
976084 TTTTTATCCA
976094 TAT TAT TAT ATAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
976139 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
976182 AATATATATT
Statistics
Matches: 82, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.05
3 75 0.91
4 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:976672 original size:18 final size:19
Alignment explanation
Indices: 976647--976690 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 19
976637 CAGAGAACGG
976647 ACAGAGAGACAGAAAAAAA
1 ACAGAGAGACAGAAAAAAA
976666 A-AGAGAGACAGAAAAAAA
1 ACAGAGAGACAGAAAAAAA
976684 ACAGAGA
1 ACAGAGA
976691 AGATACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.68, C:0.09, G:0.23, T:0.00
Consensus pattern (19 bp):
ACAGAGAGACAGAAAAAAA
Done.