Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007143.1 Hibiscus syriacus cultivar Beakdansim tig00018680_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: 94151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2989 original size:59 final size:59
Alignment explanation
Indices: 2897--3016 Score: 204
Period size: 59 Copynumber: 2.0 Consensus size: 59
2887 AATAGATGGA
* *
2897 TAAGTGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGACTC
* *
2956 TAAGTGTCCTATCGAACCCTTCTAGTCACAATGAAAAGGAAAACTCGATAATATGACTC
1 TAAGTGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGACTC
3015 TA
1 TA
3017 TTCAACCCTC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (59 bp):
TAAGTGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGACTC
Found at i:9894 original size:15 final size:15
Alignment explanation
Indices: 9866--9910 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
9856 GAGTGACGTT
9866 TATTATAT-ATATTA
1 TATTATATAATATTA
9880 TA-TATAATAATATTA
1 TATTAT-ATAATATTA
*
9895 TATTATATATTATTA
1 TATTATATAATATTA
9910 T
1 T
9911 TTACAAAGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 3 0.11
14 4 0.15
15 17 0.63
16 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTATATAATATTA
Found at i:10298 original size:22 final size:22
Alignment explanation
Indices: 10267--10321 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
10257 AACACTCTAT
*
10267 GGTGAGTCACCACCATAGGTCC
1 GGTGACTCACCACCATAGGTCC
10289 GGTGACTCACCACCATAGGTCC
1 GGTGACTCACCACCATAGGTCC
10311 GGTGACTCACC
1 GGTGACTCACC
10322 GGATTTCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (22 bp):
GGTGACTCACCACCATAGGTCC
Found at i:11170 original size:18 final size:18
Alignment explanation
Indices: 11149--11238 Score: 62
Period size: 18 Copynumber: 4.9 Consensus size: 18
11139 TATTTTAGTC
11149 ATTAATTATTATAATAAG
1 ATTAATTATTATAATAAG
* *
11167 ATTAATTATAAT-AT-TG
1 ATTAATTATTATAATAAG
*
11183 GTATAATT-TTATATATTAAG
1 AT-TAATTATTATA-A-TAAG
*
11203 TTTAATT-TTATAATATAG
1 ATTAATTATTATAATA-AG
11221 TATTACATTATTATAATA
1 -ATTA-ATTATTATAATA
11239 GGACTACTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
16 5 0.09
17 9 0.16
18 15 0.27
19 14 0.25
20 5 0.09
21 8 0.14
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTAATTATTATAATAAG
Found at i:11804 original size:25 final size:26
Alignment explanation
Indices: 11745--11804 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
11735 ATAAATTTGT
* *
11745 TTTAATTTTTTTATTATTTTACTAAC
1 TTTAATTTTTTTATTATTGTACTAAA
**
11771 TTTTGTTTTTTTA-TATGTGTAC-AAA
1 TTTAATTTTTTTATTAT-TGTACTAAA
11796 TTTAATTTT
1 TTTAATTTT
11805 GGGTTATTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (26 bp):
TTTAATTTTTTTATTATTGTACTAAA
Found at i:17647 original size:57 final size:56
Alignment explanation
Indices: 17577--17690 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 56
17567 AACCTTGCTC
17577 GAGATCTGATTAGATGTGGAGACATGAAAGGAATTAGGATAAAATCCTTCTTGTGAA
1 GAGATCTGATTAGATGTGGAGACATGAAAGGAATTAGGAT-AAATCCTTCTTGTGAA
* *
17634 GAGATCTGATTAGATGTGGAGACATGAAAGGAATTAGGATAAATCTTTCTTTTGAA
1 GAGATCTGATTAGATGTGGAGACATGAAAGGAATTAGGATAAATCCTTCTTGTGAA
17690 G
1 G
17691 TGTTTCAAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 15 0.27
57 40 0.73
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (56 bp):
GAGATCTGATTAGATGTGGAGACATGAAAGGAATTAGGATAAATCCTTCTTGTGAA
Found at i:17985 original size:8 final size:8
Alignment explanation
Indices: 17972--17998 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
17962 TAAAGGATTG
17972 ATACATTC
1 ATACATTC
17980 ATACATTC
1 ATACATTC
17988 ATACATTC
1 ATACATTC
17996 ATA
1 ATA
17999 AAGGATCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (8 bp):
ATACATTC
Found at i:18584 original size:20 final size:20
Alignment explanation
Indices: 18559--18627 Score: 129
Period size: 20 Copynumber: 3.5 Consensus size: 20
18549 TTTATCACGA
*
18559 ATTTGTAAAGCCTTTGGGTC
1 ATTTGTAAAGCCTTCGGGTC
18579 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTTCGGGTC
18599 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTTCGGGTC
18619 ATTTGTAAA
1 ATTTGTAAA
18628 ATCCTTTGGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTTGTAAAGCCTTCGGGTC
Found at i:19301 original size:15 final size:15
Alignment explanation
Indices: 19270--19316 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
19260 GAGTGACGTT
*
19270 TATTATATATATGTTA
1 TATTATATA-ATATTA
19286 TA-TATAATAATATTA
1 TATTAT-ATAATATTA
*
19301 TATTATATATTATTA
1 TATTATATAATATTA
19316 T
1 T
19317 TTACAGAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TATTATATAATATTA
Found at i:21807 original size:29 final size:29
Alignment explanation
Indices: 21765--21823 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
21755 ATTTTCACCT
*
21765 AACTAAATTGATGTAAGCAGTGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
21794 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
21823 A
1 A
21824 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:26485 original size:29 final size:29
Alignment explanation
Indices: 26452--26510 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
26442 ATTTTCACCT
26452 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
26481 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
26510 A
1 A
26511 TTAATTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:30759 original size:24 final size:23
Alignment explanation
Indices: 30732--30805 Score: 66
Period size: 24 Copynumber: 3.3 Consensus size: 23
30722 GAATATTAAT
30732 TAAATTTATGAAAAATAACTGAAC
1 TAAATTTATGAAAAATAA-TGAAC
* * *
30756 TAAATTATTTG---AAT-ATTAAT
1 TAAATT-TATGAAAAATAATGAAC
30776 TAAATTTATGAAAAATAATTGAAC
1 TAAATTTATGAAAAATAA-TGAAC
30800 TAAATT
1 TAAATT
30806 ATTTGCAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
19 3 0.08
20 9 0.24
21 1 0.03
22 6 0.16
23 1 0.03
24 15 0.39
25 3 0.08
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (23 bp):
TAAATTTATGAAAAATAATGAAC
Found at i:30768 original size:44 final size:44
Alignment explanation
Indices: 30718--30810 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
30708 ATTATAGTTG
30718 ATTTGAATATTAATTAAATTTATGAAAAATAACTGAACTAAATT
1 ATTTGAATATTAATTAAATTTATGAAAAATAACTGAACTAAATT
*
30762 ATTTGAATATTAATTAAATTTATGAAAAATAATTGAACTAAATT
1 ATTTGAATATTAATTAAATTTATGAAAAATAACTGAACTAAATT
30806 ATTTG
1 ATTTG
30811 CAAAATCATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (44 bp):
ATTTGAATATTAATTAAATTTATGAAAAATAACTGAACTAAATT
Found at i:30822 original size:44 final size:44
Alignment explanation
Indices: 30718--30823 Score: 160
Period size: 44 Copynumber: 2.4 Consensus size: 44
30708 ATTATAGTTG
*
30718 ATTTGAATATTAATTAAATTTATGAAAAATAACTGAACTAAATT
1 ATTTGAATAATAATTAAATTTATGAAAAATAACTGAACTAAATT
* *
30762 ATTTGAATATTAATTAAATTTATGAAAAATAATTGAACTAAATT
1 ATTTGAATAATAATTAAATTTATGAAAAATAACTGAACTAAATT
*
30806 ATTTGCAA-AATCATTAAA
1 ATTTG-AATAATAATTAAA
30824 ATTCCTCTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 56 0.97
45 2 0.03
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (44 bp):
ATTTGAATAATAATTAAATTTATGAAAAATAACTGAACTAAATT
Found at i:33026 original size:17 final size:17
Alignment explanation
Indices: 32987--33025 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
32977 TTTTTATAAA
32987 TAAAAATATTATTTTTC
1 TAAAAATATTATTTTTC
33004 TAAAAATATTATTTTT-
1 TAAAAATATTATTTTTC
33020 TAAAAA
1 TAAAAA
33026 AGAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAAATATTATTTTTC
Found at i:33461 original size:15 final size:15
Alignment explanation
Indices: 33437--33468 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
33427 GTTTTAAAAA
33437 AATATATTTATTTTT
1 AATATATTTATTTTT
*
33452 AATATTTTTATTTTT
1 AATATATTTATTTTT
33467 AA
1 AA
33469 AATAACTTCT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATATATTTATTTTT
Found at i:56471 original size:24 final size:21
Alignment explanation
Indices: 56436--56478 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
56426 GGCACATTCT
*
56436 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
56459 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
56479 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:60129 original size:22 final size:22
Alignment explanation
Indices: 60104--60145 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
60094 CAATTCATTT
60104 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
60126 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
60146 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:60490 original size:10 final size:11
Alignment explanation
Indices: 60475--60501 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
60465 ATTTTTTTAG
60475 AAAAAAAAACA
1 AAAAAAAAACA
60486 AAAAAAAAACA
1 AAAAAAAAACA
60497 AAAAA
1 AAAAA
60502 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:64826 original size:22 final size:22
Alignment explanation
Indices: 64801--64843 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
64791 CAATTCATTT
64801 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
64823 ATCTTATTTTTATCTTGTTTT
1 ATCTTATTTTTATCTTGTTTT
64844 CAGCACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:67265 original size:2 final size:2
Alignment explanation
Indices: 67258--67296 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
67248 TATCTTATAA
67258 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
67297 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:67301 original size:2 final size:2
Alignment explanation
Indices: 67296--67350 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
67286 TCTCTCTCTC
67296 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67338 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
67351 GGGTATGGGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:80529 original size:38 final size:39
Alignment explanation
Indices: 80461--80534 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
80451 AAAATAATAA
*
80461 ATATATAATACTAAGTAAAACAATTAAAAAAATAAAGAT
1 ATATATAATACTAAGTAAAACAAATAAAAAAATAAAGAT
* *
80500 ATATATGATATTAAG-AAAA-AAATAGAAAAAATAAA
1 ATATATAATACTAAGTAAAACAAATA-AAAAAATAAA
80535 ATAAAGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 4 0.13
38 14 0.45
39 13 0.42
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (39 bp):
ATATATAATACTAAGTAAAACAAATAAAAAAATAAAGAT
Found at i:80711 original size:25 final size:23
Alignment explanation
Indices: 80667--80713 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
80657 AAATTAATAC
* *
80667 ATATATATATATAATGATATAAG
1 ATATATATATAAAATAATATAAG
80690 ATATATATAATAAAAATAATATAA
1 ATATATAT-AT-AAAATAATATAA
80714 TATAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATATATATAAAATAATATAAG
Found at i:80815 original size:13 final size:12
Alignment explanation
Indices: 80796--80828 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
80786 TATAAAAGTA
80796 AAATTAAAGGGT
1 AAATTAAAGGGT
80808 AAATTTAAA-GGT
1 AAA-TTAAAGGGT
80820 AAATTAAAG
1 AAATTAAAG
80829 ATTAAGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.26
12 9 0.47
13 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (12 bp):
AAATTAAAGGGT
Found at i:82415 original size:106 final size:105
Alignment explanation
Indices: 82091--82462 Score: 464
Period size: 106 Copynumber: 3.5 Consensus size: 105
82081 GTATTGTTCC
* * *
82091 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCT-CGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAAATGTTTGTTGACAG
* * * *
82156 CCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTC
65 CTAGCTGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
* * * * *
82197 GAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACT--AAAAAGTTGTTTTT
1 GAGTCCAATATCC-TCGCTGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAAA--TGTTTGT
* *
82260 TGATA-ATCAG-TCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
59 TGACAGCT-AGCT-GCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
* *
82307 GAGTCCAATATCACTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAAATATTTGTTGACAG
1 GAGTCCAATATC-CTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAAATGTTTGTTGACAG
82372 CTAGCTGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
65 CTAGCTGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
82413 GAGTCCAATATCCCTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAA
1 GAGTCCAATAT-CCTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAA
82463 GCCCCTTCGT
Statistics
Matches: 229, Mismatches: 22, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
106 132 0.58
107 4 0.02
108 7 0.03
110 85 0.37
111 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAAATGTTTGTTGACAGC
TAGCTGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
Found at i:83289 original size:64 final size:67
Alignment explanation
Indices: 83128--83300 Score: 228
Period size: 64 Copynumber: 2.6 Consensus size: 67
83118 AAGATATATG
* * * **
83128 GTGTTTCATGA-AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGAT
1 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT-TTTTAAGGGAAATAAATTCAAAGAT
83192 TTT
65 TTT
*
83195 GTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTTTTTTTAGGGGAAATAAATTCAAAGA-T
1 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTTTAAGGGAAATAAATTCAAAGATT
83258 TT
66 TT
* * *
83260 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATTTTTTT
1 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTT
83301 CAAGAGAACC
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
64 28 0.29
65 13 0.14
66 21 0.22
67 17 0.18
68 17 0.18
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (67 bp):
GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTTTAAGGGAAATAAATTCAAAGATT
TT
Found at i:83304 original size:36 final size:36
Alignment explanation
Indices: 83258--83376 Score: 141
Period size: 36 Copynumber: 3.3 Consensus size: 36
83248 ATTCAAAGAT
*
83258 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAA
* * *
83294 TTTTTTTCAAGAGAACCTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAA
* * * *
83330 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGA-TGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACT-AAA
83367 TTTGTTTCAA
1 TTTGTTTCAA
83377 ATAAAACATA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
36 40 0.59
37 28 0.41
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAA
Found at i:85450 original size:69 final size:69
Alignment explanation
Indices: 85339--85476 Score: 233
Period size: 69 Copynumber: 2.0 Consensus size: 69
85329 TGTCTCTCTC
*
85339 TTGATGCTCTATGATCTTCCAGTAGAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
1 TTGATGCTCTATGATCTTCCAGTAGAGTGATTCAGTGATTCAGAAATGAATGTGCTCGATCAATC
85404 TCAT
66 TCAT
* *
85408 TTGATGCTCTATGATCTTCGAGT-GAAGTGATTCAGTGATTCAGAAATGAATGTGCTTGATCAAT
1 TTGATGCTCTATGATCTTCCAGTAG-AGTGATTCAGTGATTCAGAAATGAATGTGCTCGATCAAT
85472 CTCAT
65 CTCAT
85477 AGTTTGAATC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 1 0.02
69 64 0.98
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCCAGTAGAGTGATTCAGTGATTCAGAAATGAATGTGCTCGATCAATC
TCAT
Found at i:85578 original size:26 final size:26
Alignment explanation
Indices: 85532--85599 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
85522 ATGCATATTG
**
85532 TCTTCTTTTTTT-T-TTCAATTTTCC
1 TCTTCTTTTTTTCTCTTTGATTTTCC
* *
85556 T-TTGTTTTTTTTCTCTTTGATTTTTC
1 TCTT-CTTTTTTTCTCTTTGATTTTCC
85582 TCTTCTTTTTTTCTCTTT
1 TCTTCTTTTTTTCTCTTT
85600 TTGTTCTGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 2 0.06
24 8 0.23
25 1 0.03
26 22 0.63
27 2 0.06
ACGTcount: A:0.04, C:0.18, G:0.03, T:0.75
Consensus pattern (26 bp):
TCTTCTTTTTTTCTCTTTGATTTTCC
Found at i:88980 original size:49 final size:50
Alignment explanation
Indices: 88885--88985 Score: 129
Period size: 49 Copynumber: 2.0 Consensus size: 50
88875 ATATAATACT
88885 AAGTAAAACAAATAAAAAAATAAATATATATGATAAGAAAAAAAAAA-AA
1 AAGTAAAACAAATAAAAAAATAAATATATATGATAAGAAAAAAAAAATAA
* *
88934 AAGTAAAA-AAAGTAAAAATATAATATATATAT-ATAA-ATAAATAAAAATAA
1 AAGTAAAACAAA-TAAAAAAATAA-ATATATATGATAAGA-AAAAAAAAATAA
88984 AA
1 AA
88986 TAGAATATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
48 4 0.09
49 30 0.65
50 12 0.26
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (50 bp):
AAGTAAAACAAATAAAAAAATAAATATATATGATAAGAAAAAAAAAATAA
Found at i:89007 original size:39 final size:40
Alignment explanation
Indices: 88962--89047 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 40
88952 TATAATATAT
88962 ATATATAAATAAATAA-AAATAAAATAGAATATTAAGAAAA
1 ATATATAAATAAA-AACAAATAAAATAGAATATTAAGAAAA
* ** *
89002 A-ATATATATAAAAACGTATAAAATATAATATTAAGAAAA
1 ATATATAAATAAAAACAAATAAAATAGAATATTAAGAAAA
89041 ATATATA
1 ATATATA
89048 CATAGCAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
38 2 0.05
39 32 0.80
40 6 0.15
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (40 bp):
ATATATAAATAAAAACAAATAAAATAGAATATTAAGAAAA
Found at i:89145 original size:15 final size:15
Alignment explanation
Indices: 89108--89153 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
89098 ATATATATAT
*
89108 ATATATATAATGATATA
1 ATATATATAAT-A-AAA
*
89125 AGATATATAATAAAA
1 ATATATATAATAAAA
89140 ATATATATAATAAA
1 ATATATATAATAAA
89154 TAAAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 15 0.58
16 1 0.04
17 10 0.38
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (15 bp):
ATATATATAATAAAA
Done.