Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006313.1 Hibiscus syriacus cultivar Beakdansim tig00015086_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: 63356
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:413 original size:16 final size:16
Alignment explanation
Indices: 392--422 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
382 ATTACTATAA
392 TATTAAAAATATATTT
1 TATTAAAAATATATTT
*
408 TATTAAAATTATATT
1 TATTAAAAATATATT
423 ATACATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTAAAAATATATTT
Found at i:455 original size:20 final size:19
Alignment explanation
Indices: 392--463 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 19
382 ATTACTATAA
392 TATTAAAA--ATATAT-TT
1 TATTAAAATTATATATATT
408 TATTAAAATTATATTATACATAT
1 TATTAAAATTATA-TAT--AT-T
431 T-TTAATAATTATATATATT
1 TATTAA-AATTATATATATT
*
450 TATTAAAATGATAT
1 TATTAAAATTATAT
464 TAAAATATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 15
0.74 0.02 0.24
Matches are distributed among these distances:
16 8 0.17
18 3 0.07
19 12 0.26
20 6 0.13
22 8 0.17
23 9 0.20
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (19 bp):
TATTAAAATTATATATATT
Found at i:10990 original size:15 final size:15
Alignment explanation
Indices: 10972--11001 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10962 GCACCTTTAC
10972 CTGGTCTTTCAGCAA
1 CTGGTCTTTCAGCAA
10987 CTGGTCTTTCAGCAA
1 CTGGTCTTTCAGCAA
11002 TTGACCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (15 bp):
CTGGTCTTTCAGCAA
Found at i:16230 original size:4 final size:4
Alignment explanation
Indices: 16221--16248 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
16211 GAGAATGAGT
16221 GGAG GGAG GGAG GGAG GGAG GGAG GGAG
1 GGAG GGAG GGAG GGAG GGAG GGAG GGAG
16249 ATGCCCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:16877 original size:2 final size:2
Alignment explanation
Indices: 16872--16906 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16862 ACATACACAT
16872 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
16907 TCAAAACCAT
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22042 original size:31 final size:31
Alignment explanation
Indices: 22006--22081 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
21996 TAAAAAAATG
* *
22006 AGATATTGTCACTTTCATTTTTATTTAATTA
1 AGATATAGTCACTTTCATTTTTATATAATTA
*
22037 AGATATAGTCACTTTCGTTTTTATATAATTA
1 AGATATAGTCACTTTCATTTTTATATAATTA
* *
22068 AGATGTGGTCACTT
1 AGATATAGTCACTT
22082 CGAGTTAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.49
Consensus pattern (31 bp):
AGATATAGTCACTTTCATTTTTATATAATTA
Found at i:23265 original size:15 final size:15
Alignment explanation
Indices: 23247--23278 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
23237 AGATAAAAAT
*
23247 AAAAGTAAAAAAGTA
1 AAAAGAAAAAAAGTA
23262 AAAAGAAAAAAAGTA
1 AAAAGAAAAAAAGTA
23277 AA
1 AA
23279 GTTTAATAGT
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:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (15 bp):
AAAAGAAAAAAAGTA
Found at i:24505 original size:10 final size:10
Alignment explanation
Indices: 24492--24535 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
24482 TAAGTTAATA
*
24492 AAATGAAATG
1 AAATAAAATG
*
24502 AAATAAAATA
1 AAATAAAATG
24512 AAATAAAATG
1 AAATAAAATG
24522 AAATAAAAT-
1 AAATAAAATG
24531 AAATA
1 AAATA
24536 TTAATAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
9 5 0.16
10 26 0.84
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (10 bp):
AAATAAAATG
Found at i:24511 original size:20 final size:20
Alignment explanation
Indices: 24488--24533 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
24478 AAATTAAGTT
*
24488 AATAAAATGAAATGAAATAA
1 AATAAAATAAAATGAAATAA
24508 AATAAAATAAAATGAAATAA
1 AATAAAATAAAATGAAATAA
24528 AATAAA
1 AATAAA
24534 TATTAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (20 bp):
AATAAAATAAAATGAAATAA
Found at i:24542 original size:15 final size:15
Alignment explanation
Indices: 24488--24535 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
24478 AAATTAAGTT
*
24488 AATAAAATGAAATGA
1 AATAAAATAAAATGA
*
24503 AATAAAATAAAATAA
1 AATAAAATAAAATGA
*
24518 AATGAAATAAAAT-A
1 AATAAAATAAAATGA
24532 AATA
1 AATA
24536 TTAATAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 4 0.14
15 25 0.86
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (15 bp):
AATAAAATAAAATGA
Found at i:24747 original size:110 final size:109
Alignment explanation
Indices: 24611--24842 Score: 239
Period size: 108 Copynumber: 2.1 Consensus size: 109
24601 AAACATTTTC
* *
24611 AAAACTATATATTATATAGTTTTCAAAAAATGATTTTAAAAATATTATA-TA-AGT-TTTCCAAA
1 AAAAATATATATTATATAGTTTTC--AAAATGATTTCAAAAATA-TATACTACA-TATTTCCAAA
* *
24673 ATGTTTTGTTAAAAC-TATATA-T-TATATAAATTTTCCCAAAATGTTTTTTAA
62 ATG--TT-TTAAAACTTATATATTGTATATAAATTTT-CAAAAACG--TTTTAA
*
24724 AAAAATATATA-T-TATA-TTTTCAAAATGATTTCAAAACTATATACTACATAATTTCCAAAATG
1 AAAAATATATATTATATAGTTTTCAAAATGATTTCAAAAATATATACTACAT-ATTTCCAAAATG
*
24786 TTTTAAAACTTATATATTGTATATAAGTTTTCAAAAACGTTTTAA
65 TTTTAAAACTTATATATTGTATATAAATTTTCAAAAACGTTTTAA
24831 AAAAACTATATA
1 AAAAA-TATATA
24843 ATACCTATTT
Statistics
Matches: 105, Mismatches: 6, Indels: 21
0.80 0.05 0.16
Matches are distributed among these distances:
107 22 0.21
108 33 0.31
109 8 0.08
110 27 0.26
111 4 0.04
112 1 0.01
113 10 0.10
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (109 bp):
AAAAATATATATTATATAGTTTTCAAAATGATTTCAAAAATATATACTACATATTTCCAAAATGT
TTTAAAACTTATATATTGTATATAAATTTTCAAAAACGTTTTAA
Found at i:24760 original size:73 final size:72
Alignment explanation
Indices: 24607--24789 Score: 198
Period size: 73 Copynumber: 2.6 Consensus size: 72
24597 ATAAAAACAT
* ** * *
24607 TTTCAAAACTATATATTATATAGTTTTCAAAAAATG-ATTTTAAAAATATTATATAAGTTTTCCA
1 TTTCAAAACTATATATTATATAATTTTCCCAAAATGTTTTTTAAAAAAATTATATAAGTTTTCCA
*
24671 AAATGTT
66 AAATGTA
*
24678 TTGTTAAAACTATATATTATATAAATTTTCCCAAAATGTTTTTTAAAAAAATATATATTATA-TT
1 TT-TCAAAACTATATATTATAT-AATTTTCCCAAAATGTTTTTTAAAAAAAT-TATA-TA-AGTT
24742 TT-CAAAATG-A
61 TTCCAAAATGTA
* *
24752 TTTCAAAACTATATACTACATAA-TTT-CCAAAATGTTTT
1 TTTCAAAACTATATATTATATAATTTTCCCAAAATGTTTT
24790 AAAACTTATA
Statistics
Matches: 96, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
70 12 0.12
71 5 0.05
72 20 0.21
73 28 0.29
74 13 0.14
75 11 0.11
76 6 0.06
77 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (72 bp):
TTTCAAAACTATATATTATATAATTTTCCCAAAATGTTTTTTAAAAAAATTATATAAGTTTTCCA
AAATGTA
Found at i:25921 original size:250 final size:250
Alignment explanation
Indices: 25558--26385 Score: 1041
Period size: 250 Copynumber: 3.3 Consensus size: 250
25548 TCGGGGGTCT
* * * * * *
25558 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
*
25622 CCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
66 TCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* *
25687 GCCCTCGAATCTGAGTGTAATCTAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
131 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
25752 ATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
196 ATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
25807 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
*** *
25872 TCGAACTCGGGGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
66 TCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
25937 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
131 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
*
26002 ATACTGCAAATGATGTGCCTTGGATCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
196 ATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
26057 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* * * * * * * *
26122 TCGAACTTAAGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTTAAGCTATTCTGCAAATGATG
66 TCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAG-CCTTGAGTTATGCTGCAAATGATG
* * * * *** * * *
26183 TG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTT
130 TGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTGG---CAGATAGCCCTTCTCGACTT
* * * * * * ** * * *
26247 GAGTTATGCTGTAAATGTTATGCCCTTAAAGCTGAGTGTAATCGAACT-TAAGGGTC--T--
191 AAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGG
* * * * * *
26304 TTGGCAGATAGCCCTTCTCGACTTTAAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTA
1 TTGGCAGATAACCCTTCTCGAC-TTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTA
* *
26368 GTCGAACTCGAAGGTCTT
65 ATCGAACTCAAAGGTCTT
26386 GGTGGCATGT
Statistics
Matches: 513, Mismatches: 56, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
246 40 0.08
247 73 0.14
248 23 0.04
249 54 0.11
250 299 0.58
251 24 0.05
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (250 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
TCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
ATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:26254 original size:166 final size:165
Alignment explanation
Indices: 25484--26385 Score: 946
Period size: 165 Copynumber: 5.4 Consensus size: 165
25474 TTATTGACAA
* * * * * * * * * * *
25484 ATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAACT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
** * * *
25549 CGGGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG
65 CGAAGGTCTTTTGGTCACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTG
* ** *
25610 -AGCTGAGCGTAGCCGAACTCAAAGGTCTTTTGGTCACAG
130 AAGCTGAGTGTAATCGAACTCAAGGGTC-TTTGG---CAG
* * * * * * * * * * *
25649 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAATCTGAGTGTAATCTAACT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
** * * *
25714 CGGGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTG
65 CGAAGGTCTTTTGGTCACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTG
* * *
25774 GAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGGTTGGCAG
130 AAGCTGAGTGTAATCGAACTC-AAGGGTC--T--TTGGCAG
* * * * * *
25814 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
** * * * * *
25879 CGGGGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCG
65 CGAAGGTCTTTTGGTCACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTG
**
25944 AAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
130 AAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAG
* *
25980 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGATCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
** *
26045 GAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCG
66 GAAGGTCTTTTGG-TCACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTG
*
26109 AAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAG
130 AAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAG
*
26145 ATAGCCCTTCTCGACTTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
1 ATAGCCCTTCTCGAC-TTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
* * * * * * * *
26210 CAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTA
65 CGAAGGTCTTTTGGTCACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTG
*
26275 AAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAG
130 AAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAG
*
26311 ATAGCCCTTCTCGACTTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
1 ATAGCCCTTCTCGAC-TTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
26376 CGAAGGTCTT
65 CGAAGGTCTT
26386 GGTGGCATGT
Statistics
Matches: 659, Mismatches: 64, Indels: 27
0.88 0.09 0.04
Matches are distributed among these distances:
164 9 0.01
165 322 0.49
166 257 0.39
167 5 0.01
168 5 0.01
169 35 0.05
170 26 0.04
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTTGGTCACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGA
AGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAG
Found at i:29767 original size:18 final size:19
Alignment explanation
Indices: 29726--29770 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
29716 AGTTAATGTG
29726 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
29745 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
29763 AATGCAAA
1 AATGCAAA
29771 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:31632 original size:15 final size:15
Alignment explanation
Indices: 31614--31645 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31604 AGATAAAAAT
*
31614 AAAAGTAAAAAAGTA
1 AAAAGAAAAAAAGTA
31629 AAAAGAAAAAAAGTA
1 AAAAGAAAAAAAGTA
31644 AA
1 AA
31646 GTTTAATAGT
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:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (15 bp):
AAAAGAAAAAAAGTA
Found at i:32873 original size:10 final size:10
Alignment explanation
Indices: 32860--32903 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
32850 TAAGTTAATA
*
32860 AAATGAAATG
1 AAATAAAATG
*
32870 AAATAAAATA
1 AAATAAAATG
32880 AAATAAAATG
1 AAATAAAATG
32890 AAATAAAAT-
1 AAATAAAATG
32899 AAATA
1 AAATA
32904 TTAATAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
9 5 0.16
10 26 0.84
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (10 bp):
AAATAAAATG
Found at i:32879 original size:20 final size:20
Alignment explanation
Indices: 32856--32901 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
32846 AAATTAAGTT
*
32856 AATAAAATGAAATGAAATAA
1 AATAAAATAAAATGAAATAA
32876 AATAAAATAAAATGAAATAA
1 AATAAAATAAAATGAAATAA
32896 AATAAA
1 AATAAA
32902 TATTAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (20 bp):
AATAAAATAAAATGAAATAA
Found at i:32910 original size:15 final size:15
Alignment explanation
Indices: 32856--32903 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
32846 AAATTAAGTT
*
32856 AATAAAATGAAATGA
1 AATAAAATAAAATGA
*
32871 AATAAAATAAAATAA
1 AATAAAATAAAATGA
*
32886 AATGAAATAAAAT-A
1 AATAAAATAAAATGA
32900 AATA
1 AATA
32904 TTAATAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 4 0.14
15 25 0.86
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (15 bp):
AATAAAATAAAATGA
Found at i:33130 original size:73 final size:72
Alignment explanation
Indices: 32977--33159 Score: 198
Period size: 73 Copynumber: 2.6 Consensus size: 72
32967 ATAAAAACAT
* ** * *
32977 TTTCAAAACTATATATTATATAGTTTTCAAAAAATG-ATTTTAAAAATATTATATAAGTTTTCCA
1 TTTCAAAACTATATATTATATAATTTTCCCAAAATGTTTTTTAAAAAAATTATATAAGTTTTCCA
*
33041 AAATGTT
66 AAATGTA
*
33048 TTGTTAAAACTATATATTATATAAATTTTCCCAAAATGTTTTTTAAAAAAATATATATTATA-TT
1 TT-TCAAAACTATATATTATAT-AATTTTCCCAAAATGTTTTTTAAAAAAAT-TATA-TA-AGTT
33112 TT-CAAAATG-A
61 TTCCAAAATGTA
* *
33122 TTTCAAAACTATATACTACATAA-TTT-CCAAAATGTTTT
1 TTTCAAAACTATATATTATATAATTTTCCCAAAATGTTTT
33160 AAAACTTATA
Statistics
Matches: 96, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
70 12 0.12
71 5 0.05
72 20 0.21
73 28 0.29
74 13 0.14
75 11 0.11
76 6 0.06
77 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (72 bp):
TTTCAAAACTATATATTATATAATTTTCCCAAAATGTTTTTTAAAAAAATTATATAAGTTTTCCA
AAATGTA
Found at i:37633 original size:15 final size:15
Alignment explanation
Indices: 37609--37642 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
37599 TGATTACATA
37609 TTTTAATA-TTTTAT
1 TTTTAATATTTTTAT
37623 TTTTAAATATTTTTAT
1 TTTT-AATATTTTTAT
37639 TTTT
1 TTTT
37643 TAAAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 4 0.22
16 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTAATATTTTTAT
Found at i:48328 original size:16 final size:16
Alignment explanation
Indices: 48292--48332 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
48282 AATTTCATCC
48292 TTATA-TTATATAATA
1 TTATATTTATATAATA
48307 TATATATTTATTATAA-A
1 T-TATATTTA-TATAATA
48324 TTATATTTA
1 TTATATTTA
48333 CATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 12 0.52
17 5 0.22
18 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTTATATAATA
Found at i:49340 original size:20 final size:19
Alignment explanation
Indices: 49305--49345 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
49295 TAATTATCTT
49305 TTTATATTACATTATAATA
1 TTTATATTACATTATAATA
* *
49324 TTTATATATATATTATATTA
1 TTTATAT-TACATTATAATA
49344 TT
1 TT
49346 ATTAGTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATTACATTATAATA
Found at i:49427 original size:18 final size:17
Alignment explanation
Indices: 49406--49449 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
49396 CTTATACGTT
49406 TTATTATATATATATATA
1 TTATTAT-TATATATATA
*
49424 TTATTATTGT-TAT-TA
1 TTATTATTATATATATA
49439 TTATTATTATA
1 TTATTATTATA
49450 CGTATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 11 0.48
16 3 0.13
17 2 0.09
18 7 0.30
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TTATTATTATATATATA
Found at i:49428 original size:3 final size:3
Alignment explanation
Indices: 49406--49448 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
49396 CTTATACGTT
*
49406 TTA TTA TATA TATA TATA TTA TTA TTG TTA TTA TTA TTA TTA T
1 TTA TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T
49449 ACGTATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 26 0.70
4 11 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:49449 original size:48 final size:51
Alignment explanation
Indices: 49364--49474 Score: 124
Period size: 46 Copynumber: 2.2 Consensus size: 51
49354 TTTACACTCG
*
49364 TATATATGTATTATTAGTATAGTATTATGTCACTTATACGTTTTATTATATATA
1 TATATAT-TATTATTAGTATAGTATTATGTCACTTATACG-TATA-TATATATA
* *
49418 TATATATTATTATT-GT-TATTATTAT-T-A-TTATACGTATATATATGTA
1 TATATATTATTATTAGTATAGTATTATGTCACTTATACGTATATATATATA
*
49464 TATATTTTATT
1 TATATATTATT
49475 TCTTTTTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
46 17 0.32
47 3 0.06
48 7 0.13
49 1 0.02
50 1 0.02
51 8 0.15
52 2 0.04
53 7 0.13
54 7 0.13
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (51 bp):
TATATATTATTATTAGTATAGTATTATGTCACTTATACGTATATATATATA
Found at i:49529 original size:18 final size:18
Alignment explanation
Indices: 49506--49565 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
49496 TTTTTATTTT
49506 TATTATTATTATTCTTTA
1 TATTATTATTATTCTTTA
** * *
49524 TATTATCCTTATTATTTC
1 TATTATTATTATTCTTTA
*
49542 TATTATTACTATTCTTTA
1 TATTATTATTATTCTTTA
49560 T-TTATT
1 TATTATT
49566 CATGTAATTA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTATTATTATTCTTTA
Found at i:60742 original size:1 final size:1
Alignment explanation
Indices: 60736--60764 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
60726 TCTTAAGTTG
60736 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
60765 CGTTTAGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:61826 original size:104 final size:105
Alignment explanation
Indices: 61546--62048 Score: 965
Period size: 104 Copynumber: 4.8 Consensus size: 105
61536 GGTTTTACCC
61546 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
61611 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
61651 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
61716 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTC-AATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
61755 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
61820 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTC-AATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
*
61859 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
61924 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
* *
61964 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAGGTTCAACTTCATGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
62029 CGAAGGGACCGCTGGTTGTC
66 CGAAGGGACCGCTGGTTGTC
62049 GATAAACAAT
Statistics
Matches: 393, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
104 207 0.53
105 186 0.47
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
Found at i:61965 original size:209 final size:209
Alignment explanation
Indices: 61546--62048 Score: 963
Period size: 209 Copynumber: 2.4 Consensus size: 209
61536 GGTTTTACCC
61546 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
61611 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAACGA
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAACGA
61676 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAA
131 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAA
61741 ACATTTCTCAATTT
196 ACATTTCTCAATTT
61755 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
61820 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTC-AATTTAGAGCCAATTTCAACTTCACAGCGA
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAACGA
61884 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAA
131 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAA
61949 ACATTTCTCAAATTT
196 ACATTTCTC-AATTT
* *
61964 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAGGTTCAACTTCATGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
62029 CGAAGGGACCGCTGGTTGTC
66 CGAAGGGACCGCTGGTTGTC
62049 GATAAACAAT
Statistics
Matches: 290, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
208 103 0.36
209 187 0.64
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (209 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAACGA
AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAA
ACATTTCTCAATTT
Found at i:62153 original size:20 final size:20
Alignment explanation
Indices: 62128--62169 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
62118 CCAGAACTCT
62128 GAGTTCGACTTCAACTTCAC
1 GAGTTCGACTTCAACTTCAC
* *
62148 GAGTTCGATTTCAATTTCAC
1 GAGTTCGACTTCAACTTCAC
62168 GA
1 GA
62170 CGAAGGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (20 bp):
GAGTTCGACTTCAACTTCAC
Found at i:62412 original size:16 final size:16
Alignment explanation
Indices: 62376--62416 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
62366 AATTTCATCC
62376 TTATA-TTATATAATA
1 TTATATTTATATAATA
62391 TATATATTTATTATAA-A
1 T-TATATTTA-TATAATA
62408 TTATATTTA
1 TTATATTTA
62417 CATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 12 0.52
17 5 0.22
18 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTTATATAATA
Done.