Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000895.1 Hibiscus syriacus cultivar Beakdansim tig00001758_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: 69209
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:184 original size:23 final size:23
Alignment explanation
Indices: 158--226 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
148 TCACCATACT
*
158 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * * *
181 CGTAGAATTACACCGGAGTACCG
1 CGTAGAATTGCACCGAAGTGCCA
*
204 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
227 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:7641 original size:23 final size:23
Alignment explanation
Indices: 7615--7683 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
7605 CACCACAGCT
*
7615 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* **
7638 CGTAGAATTACACCGAAGTGCTG
1 CGTAGAATTGCACCGAAGTGCCA
* *
7661 TGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
7684 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:12221 original size:15 final size:15
Alignment explanation
Indices: 12201--12232 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12191 GCATCAAAAG
12201 TATGTCTTTATTAAT
1 TATGTCTTTATTAAT
12216 TATGTCTTTATTAAT
1 TATGTCTTTATTAAT
12231 TA
1 TA
12233 ATTTATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.59
Consensus pattern (15 bp):
TATGTCTTTATTAAT
Found at i:13158 original size:2 final size:2
Alignment explanation
Indices: 13151--13215 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
13141 GCCTTTTAAA
13151 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
13193 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
13216 ATTAGTTTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14774 original size:2 final size:2
Alignment explanation
Indices: 14767--14798 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14757 ACCATAATTG
14767 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
14799 AAGAGATGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21419 original size:11 final size:11
Alignment explanation
Indices: 21403--21427 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21393 TCGGGTCAAG
21403 TCAATATCAGA
1 TCAATATCAGA
21414 TCAATATCAGA
1 TCAATATCAGA
21425 TCA
1 TCA
21428 GTTGTTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (11 bp):
TCAATATCAGA
Found at i:27040 original size:23 final size:23
Alignment explanation
Indices: 27014--27104 Score: 119
Period size: 23 Copynumber: 4.0 Consensus size: 23
27004 CACCACAGCT
* * * *
27014 CGTATAATTGCACCGAAATGCCA
1 CGTAGAATTGCACCGGAGTGCCG
*
27037 CGTAAAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCG
*
27060 CGTAGAATTGCACCGGAGTGCTG
1 CGTAGAATTGCACCGGAGTGCCG
*
27083 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGGAGTGCC
27105 ATATAATAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCG
Found at i:27356 original size:30 final size:30
Alignment explanation
Indices: 27315--27383 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
27305 ACATAATTTG
* * *
27315 TATCACGTAGACATATTATTTTCC-TACCTT
1 TATCACATAGACATATCA-TTTCCATACATT
27345 TATCACATAGACATATCATTTCCATACATT
1 TATCACATAGACATATCATTTCCATACATT
27375 TATCACATA
1 TATCACATA
27384 ACTCATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 5 0.14
30 30 0.86
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.39
Consensus pattern (30 bp):
TATCACATAGACATATCATTTCCATACATT
Found at i:35615 original size:24 final size:24
Alignment explanation
Indices: 35588--35719 Score: 167
Period size: 24 Copynumber: 5.5 Consensus size: 24
35578 TAGAGTTGAT
35588 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
35612 TTCTGTTCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
35636 TTCTGATATGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
*
35660 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* * *
35684 TTTTGATATGATACTTGACATGAA
1 TTCTGATCTGATACTTGACATGGA
* *
35708 TTATGATTTGAT
1 TTCTGATCTGAT
35720 TTTTGATATA
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 93 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:37478 original size:17 final size:17
Alignment explanation
Indices: 37456--37491 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
37446 TTTTCAGAAT
*
37456 CGGACCGGTTAGCGAAC
1 CGGACCGGTTAACGAAC
37473 CGGACCGGTTAACGAAC
1 CGGACCGGTTAACGAAC
37490 CG
1 CG
37492 ATCATGCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.31, G:0.33, T:0.11
Consensus pattern (17 bp):
CGGACCGGTTAACGAAC
Found at i:38681 original size:16 final size:16
Alignment explanation
Indices: 38660--38693 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
38650 TTACTATTCA
*
38660 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
38676 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
38692 CG
1 CG
38694 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:39461 original size:15 final size:16
Alignment explanation
Indices: 39443--39475 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39433 GTGGCAGATC
39443 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
39458 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
39474 AA
1 AA
39476 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:46136 original size:5 final size:5
Alignment explanation
Indices: 46128--46152 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
46118 AAAAACAAAA
46128 TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT
46153 GAATAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:46235 original size:13 final size:13
Alignment explanation
Indices: 46217--46252 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
46207 ACTATATAAT
46217 ATATATATTTTAA
1 ATATATATTTTAA
*
46230 ATATATTTTTTAA
1 ATATATATTTTAA
46243 ACTATATATT
1 A-TATATATT
46253 ATATTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATATATTTTAA
Found at i:46387 original size:37 final size:35
Alignment explanation
Indices: 46205--46470 Score: 185
Period size: 36 Copynumber: 7.5 Consensus size: 35
46195 AATATGATAT
* * *
46205 AAACTATATAATATATATA-TTTT-AAATATATTTTTT
1 AAACTATATATTATATA-AGTTTTCAAA-AT-GTTTTA
* * *
46241 AAACTATATATTATAT---TTTTAAAAAAAGTTTTCT
1 AAACTATATATTATATAAGTTTT-CAAAATGTTTT-A
*
46275 AAACTATATATTATAT-AGATTTCAAAAATGATTTTA
1 AAACTATATATTATATAAGTTTTC-AAAATG-TTTTA
*
46311 AAA--A-ATATTATATAAGTTTTTTAAAAAATGTTTTTA
1 AAACTATATATTATATAAG--TTTT-CAAAATG-TTTTA
46347 AAACTATATATTATATAAGTTTTTCAAAATGTTTTAA
1 AAACTATATATTATATAAG-TTTTCAAAATGTTTT-A
* * * *
46384 AAACCATATATTGTATCAGTTTTCAAAGTGTTTTAA
1 AAACTATATATTATATAAGTTTTCAAAATGTTTT-A
* *
46420 AAGACTATATATTATATAA--TTTCAAAATGATTTC
1 AA-ACTATATATTATATAAGTTTTCAAAATGTTTTA
*
46454 AAACTATATAATATATA
1 AAACTATATATTATATA
46471 CATATATATA
Statistics
Matches: 192, Mismatches: 22, Indels: 35
0.77 0.09 0.14
Matches are distributed among these distances:
33 31 0.16
34 23 0.12
35 15 0.08
36 65 0.34
37 40 0.21
38 6 0.03
39 12 0.06
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (35 bp):
AAACTATATATTATATAAGTTTTCAAAATGTTTTA
Found at i:46944 original size:80 final size:80
Alignment explanation
Indices: 46842--48033 Score: 1435
Period size: 80 Copynumber: 14.8 Consensus size: 80
46832 CGAAATCGAA
* *
46842 AAGGTATTTGGCAGATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGA
1 AAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGA
46907 GTGTAATCGAACTCG
66 GTGTAATCGAACTCG
* * * *
46922 AAGG-CTTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTACCTTTCATCTG
1 AAGGTC-TTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTG
*
46986 AATGTAATCGAACTCG
65 AGTGTAATCGAACTCG
* *
47002 AAGGTCTTTGGTAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTCTGAGCTGA
1 AAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGA
* * *
47067 GCGTAACCAAACTCG
66 GTGTAATCGAACTCG
* * *
47082 AAGGTCTTTGGTAGATAACCCTTCTTGTCTTGAATTATGCTGCAAATGATGTG-CTTCTGAGCTG
1 AAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTT-TGAGCTG
*
47146 AATGTAATCGAACTCG
65 AGTGTAATCGAACTCG
* * * ** * *
47162 AAGGTCTTTGGAAGATAACCCTTCTTACATTGAGTTATATTGCAAATGATGTGCTTTTAAGCTGA
1 AAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGA
* *
47227 GTGTAATCAAACTCA
66 GTGTAATCGAACTCG
* * *
47242 AAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAATTATGCTGCAAATGATGTGCC-TTGAGCTGA
1 AAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGA
47306 GTGTAATCGAACTCG
66 GTGTAATCGAACTCG
* * * * *
47321 AAGGTCTTTGTTGACAGATAACCCTGCTAGCCTTGAGTTATGCTGTAAATGATATGCCTTTGAAC
1 AAGGTCTTTG--G-CAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGC
47386 TGAGTGTAATCGAACTCG
63 TGAGTGTAATCGAACTCG
* * * * *
47404 AAGGTCTTTGGCAGATAGCCCTTTTTGCCTTAAGCTATACTAG-AAATGATGTGCCTTT-AGCTG
1 AAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCT-GCAAATGATGTGCCTTTGAGCTG
* *
47467 AGTGTAATTGAGCTCG
65 AGTGTAATCGAACTCG
* ** * * *
47483 AATGTCTTTATTAACAGATAACCCTTCTAGCCTTGAGTTATGCAGCAAATGATGTGTCTTTGAGC
1 AAGGTC--T-TTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGC
*
47548 TGAGTGTAATTGAACTCG
63 TGAGTGTAATCGAACTCG
* * * * * * *
47566 AAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTATGCTGTAAATGATGCGTCTTTGATCCGA
1 AAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGA
* *
47631 GTGGAATTGAACTCG
66 GTGTAATCGAACTCG
* * *
47646 AAGGTCTTGTGTTGGCAGATAACCCTTATAGCCTTGAGTTATACTGCAAATGATGTGCCTTTGAG
1 AAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAG
47711 CTGAGTGTAATCGAACTCG
62 CTGAGTGTAATCGAACTCG
* * ** * * * *
47730 AAGGTCTTTGGCAAATATCTTTTCTTGCCTTAAGCTATGCTGCAAATGATATGCC-TTGAGATGA
1 AAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGA
*
47794 GTGTAATTGAACTCG
66 GTGTAATCGAACTCG
* * * * * *
47809 AAGGTCTTTATTGACATATAACGCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCTTTGAGC
1 AAGGTC--T-TTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGC
47874 TGAGTGTAATCGAACTCG
63 TGAGTGTAATCGAACTCG
* * *
47892 AAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTAA
1 AAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGA
* *
47956 GTGTAATCAAACTCA
66 GTGTAATCGAACTCG
** * **
47971 AAGGTCTTTGGCAGATAACCCTTCTTGTTTTGAGCTATGCTGCAAATGATGCACCTTTGAGCT
1 AAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCT
48034 ATGCTGCAAA
Statistics
Matches: 943, Mismatches: 146, Indels: 46
0.83 0.13 0.04
Matches are distributed among these distances:
79 153 0.16
80 511 0.54
81 12 0.01
82 113 0.12
83 87 0.09
84 67 0.07
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (80 bp):
AAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGA
GTGTAATCGAACTCG
Found at i:47410 original size:162 final size:162
Alignment explanation
Indices: 46853--48033 Score: 1515
Period size: 162 Copynumber: 7.3 Consensus size: 162
46843 AGGTATTTGG
* *
46853 CAGATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * * * *
46918 CTCGAAGG-CTTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTACCTTTCA
66 CTCGAAGGTC-TTTGGCAGATAGCCCTTCTTGCCTTAAGTTATGCTGCAAATGATGTGCC-TTGA
* *
46982 TCTGAATGTAATCGAACTCGAAGGTCTTTG--G-
129 GCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGA
* * * * * *
47013 TAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTCTGAGCTGAGCGTAACCAAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * * *
47078 CTCGAAGGTCTTTGGTAGATAACCCTTCTTGTCTTGAA-TTATGCTGCAAATGATGTGCTTCTGA
66 CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTT-AAGTTATGCTGCAAATGATGTGCCT-TGA
*
47142 GCTGAATGTAATCGAACTCGAAGGTCTTTG--GA
129 GCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGA
* ** * * *
47174 -AGATAACCCTTCTTA-CATTGAGTTATATTGCAAATGATGTGCTTTTAAGCTGAGTGTAATCAA
1 CAGATAACCCTTC-TAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGA
* *
47237 ACTCAAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAATTATGCTGCAAATGATGTGCCTTGAG
65 ACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTATGCTGCAAATGATGTGCCTTGAG
47302 CTGAGTGTAATCGAACTCGAAGGTCTTTGTTGA
130 CTGAGTGTAATCGAACTCGAAGGTCTTTGTTGA
* * * *
47335 CAGATAACCCTGCTAGCCTTGAGTTATGCTGTAAATGATATGCCTTTGAACTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * * *
47400 CTCGAAGGTCTTTGGCAGATAGCCCTTTTTGCCTTAAGCTATACTAG-AAATGATGTGCCTTTAG
66 CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTATGCT-GCAAATGATGTGCCTTGAG
* * * * *
47464 CTGAGTGTAATTGAGCTCGAATGTCTTTATTAA
130 CTGAGTGTAATCGAACTCGAAGGTCTTTGTTGA
* * *
47497 CAGATAACCCTTCTAGCCTTGAGTTATGCAGCAAATGATGTGTCTTTGAGCTGAGTGTAATTGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * * *
47562 CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTATGCTGTAAATGATGCGTCTTTGAT
66 CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTATGCTGCAAATGATGTG-CCTTGAG
* * * *
47627 CCGAGTGGAATTGAACTCGAAGGTCTTGTGTTGG
130 CTGAGTGTAATCGAACTCGAAGGTCTT-TGTTGA
* *
47661 CAGATAACCCTTATAGCCTTGAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * ** * * *
47726 CTCGAAGGTCTTTGGCAAATATCTTTTCTTGCCTTAAGCTATGCTGCAAATGATATGCCTTGAGA
66 CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTATGCTGCAAATGATGTGCCTTGAGC
* *
47791 TGAGTGTAATTGAACTCGAAGGTCTTTATTGA
131 TGAGTGTAATCGAACTCGAAGGTCTTTGTTGA
* * * *
47823 CATATAACGCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
47888 CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTATGCTGCAAATGATGTGCCTTGAGC
66 CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTATGCTGCAAATGATGTGCCTTGAGC
* * *
47953 TAAGTGTAATCAAACTCAAAGGTCTTTG--G-
131 TGAGTGTAATCGAACTCGAAGGTCTTTGTTGA
* ** * **
47982 CAGATAACCCTTCTTGTTTTGAGCTATGCTGCAAATGATGCACCTTTGAGCT
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCT
48034 ATGCTGCAAA
Statistics
Matches: 890, Mismatches: 117, Indels: 29
0.86 0.11 0.03
Matches are distributed among these distances:
159 77 0.09
160 246 0.28
161 8 0.01
162 390 0.44
163 57 0.06
164 112 0.13
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (162 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTATGCTGCAAATGATGTGCCTTGAGC
TGAGTGTAATCGAACTCGAAGGTCTTTGTTGA
Found at i:47797 original size:488 final size:481
Alignment explanation
Indices: 46853--48021 Score: 1565
Period size: 488 Copynumber: 2.4 Consensus size: 481
46843 AGGTATTTGG
* * *
46853 CAGATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * *
46918 CTCGAAGG-CTTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTACCTTTCA
66 CTCGAAGGTC-TTTGGCAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTT-A
* * * * *
46982 TCTGAATGTAATCGAACTCGAAGGTCTTTGGTAGATAACCCTTCTTGCCTTGAGTTATGCTGCAA
129 GCTGAGTGTAATCGAACTCGAAGGTCTTTAGTAGATAACCCTTCTAGCCTTGAGTTATGCAGCAA
* *
47047 ATGATGTGCCTCTGAGCTGAGCGTAACCAAACTCGAAGGTCTTTGGTAGATAACCCTTCTTGTCT
194 ATGATGTGCCTCTGAGCTGAGCGTAACCAAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCT
* * *
47112 TGAATTATGCTGCAAATGATGTGCTTCTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGGAAGA
259 TGAATTATGCTGCAAATGATGCGCTTCTGAGCCGAATGGAATCGAACTCGAAGGTCTTTGGAAGA
* * *
47177 TAACCCTTCTTACATTGAGTTATATTGCAAATGATGTGCTTTTAAGCTGAGTGTAATCAAACTCA
324 TAACCCTTCATACATTGAGTTATACTGCAAATGATGTGCCTTTAAGCTGAGTGTAATCAAACTCA
* * * *
47242 AAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAATTATGCTGCAAATGATGTGCCTTGAGCTGAG
389 AAGGTCTTTGGCAAATAGCCCTTCTTGCCTTAAACTATGCTGCAAATGATATGCCTTGAGATGAG
*
47307 TGTAATCGAACTCGAAGGTCTTTGTTGA
454 TGTAATCGAACTCGAAGGTCTTTATTGA
* * *
47335 CAGATAACCCTGCTAGCCTTGAGTTATGCTGTAAATGATATGCCTTTGAACTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* *
47400 CTCGAAGGTCTTTGGCAGATAGCCCTTTTTGCCTTAAGCTATACTAG-AAATGATGTGCCTTTAG
66 CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGCTATGCT-GCAAATGATGTGCCTTTAG
* * * *
47464 CTGAGTGTAATTGAGCTCGAATGTCTTTATTAACAGATAACCCTTCTAGCCTTGAGTTATGCAGC
130 CTGAGTGTAATCGAACTCGAAGGTCTTTAGT---AGATAACCCTTCTAGCCTTGAGTTATGCAGC
* * * *** *
47529 AAATGATGTGTCTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGC
192 AAATGATGTGCCTCTGAGCTGAGCGTAACCAAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGC
* * * *
47594 CTT-AAGTTATGCTGTAAATGATGCGTCTT-TGATCCGAGTGGAATTGAACTCGAAGGTCTTGTG
257 CTTGAA-TTATGCTGCAAATGATGCG-CTTCTGAGCCGAATGGAATCGAACTCGAAGGTC---T-
* * *
47657 TTGGCAGATAACCCTT-ATAGCCTTGAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAA
316 TTGGAAGATAACCCTTCATA-CATTGAGTTATACTGCAAATGATGTGCCTTTAAGCTGAGTGTAA
* * * ** *
47721 TCGAACTCGAAGGTCTTTGGCAAATATCTTTTCTTGCCTTAAGCTATGCTGCAAATGATATGCCT
380 TCAAACTCAAAGGTCTTTGGCAAATAGCCCTTCTTGCCTTAAACTATGCTGCAAATGATATGCCT
*
47786 TGAGATGAGTGTAATTGAACTCGAAGGTCTTTATTGA
445 TGAGATGAGTGTAATCGAACTCGAAGGTCTTTATTGA
* * *
47823 CATATAACGCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* *
47888 CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGTTATGCTGCAAATGATGTGCCTTGAGC
66 CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTAGC
* * * * * * ** * *
47953 TAAGTGTAATCAAACTCAAAGGTCTTTGGCAGATAACCCTTCTTGTTTTGAGCTATGCTGCAAAT
131 TGAGTGTAATCGAACTCGAAGGTCTTTAGTAGATAACCCTTCTAGCCTTGAGTTATGCAGCAAAT
48018 GATG
196 GATG
48022 CACCTTTGAG
Statistics
Matches: 596, Mismatches: 78, Indels: 23
0.86 0.11 0.03
Matches are distributed among these distances:
481 26 0.04
482 112 0.19
483 4 0.01
484 129 0.22
485 37 0.06
487 4 0.01
488 284 0.48
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (481 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTAGC
TGAGTGTAATCGAACTCGAAGGTCTTTAGTAGATAACCCTTCTAGCCTTGAGTTATGCAGCAAAT
GATGTGCCTCTGAGCTGAGCGTAACCAAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTG
AATTATGCTGCAAATGATGCGCTTCTGAGCCGAATGGAATCGAACTCGAAGGTCTTTGGAAGATA
ACCCTTCATACATTGAGTTATACTGCAAATGATGTGCCTTTAAGCTGAGTGTAATCAAACTCAAA
GGTCTTTGGCAAATAGCCCTTCTTGCCTTAAACTATGCTGCAAATGATATGCCTTGAGATGAGTG
TAATCGAACTCGAAGGTCTTTATTGA
Found at i:48037 original size:27 final size:27
Alignment explanation
Indices: 47999--48060 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
47989 CCCTTCTTGT
47999 TTTGAGCTATGCTGCAAATGATGCACC
1 TTTGAGCTATGCTGCAAATGATGCACC
48026 TTTGAGCTATGCTGCAAATGATGCACC
1 TTTGAGCTATGCTGCAAATGATGCACC
48053 TTTGAGCT
1 TTTGAGCT
48061 GAATGGAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (27 bp):
TTTGAGCTATGCTGCAAATGATGCACC
Found at i:48112 original size:107 final size:106
Alignment explanation
Indices: 47927--48140 Score: 277
Period size: 107 Copynumber: 2.0 Consensus size: 106
47917 TGCCTTAAGT
** * *
47927 TATGCTGCAAATGATGTGCCTTGAGCTAAGTGTAATCAAACTCAAAGGTCTTTGGCAGATAACCC
1 TATGCTGCAAATGATGCACCTTGAGCTAAGTGGAATCAAACTCAAAGGTCTTTGGCAAATAACCC
** *
47992 TTCTTGTTTTGAGCTATGCTGCAAATGATGCACCTTTGAGC
66 TTCTTGCCTTGAGCTATGCTACAAATGATGCACCTTTGAGC
* * **
48033 TATGCTGCAAATGATGCACCTTTGAGCTGAA-TGGAATCGAACTCGAAGGTCTTTGGCAAATAGG
1 TATGCTGCAAATGATGCACC-TTGAGCT-AAGTGGAATCAAACTCAAAGGTCTTTGGCAAATAAC
* **
48097 CCTTCTTGCCTTGAGCTATGCTACAAATGTTGTTCCTTTGAGC
64 CCTTCTTGCCTTGAGCTATGCTACAAATGATGCACCTTTGAGC
48140 T
1 T
48141 GAGTGTAATC
Statistics
Matches: 92, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
106 18 0.20
107 72 0.78
108 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (106 bp):
TATGCTGCAAATGATGCACCTTGAGCTAAGTGGAATCAAACTCAAAGGTCTTTGGCAAATAACCC
TTCTTGCCTTGAGCTATGCTACAAATGATGCACCTTTGAGC
Found at i:53052 original size:14 final size:14
Alignment explanation
Indices: 53033--53059 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53023 AAATAAAAAA
53033 TATTAATATAATAG
1 TATTAATATAATAG
53047 TATTAATATAATA
1 TATTAATATAATA
53060 AAATAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
TATTAATATAATAG
Found at i:54755 original size:37 final size:36
Alignment explanation
Indices: 54537--54838 Score: 186
Period size: 37 Copynumber: 8.5 Consensus size: 36
54527 AATATGATAT
* * **
54537 AAACTATATAATATATA-TATTTCTAAAATATTTTTT
1 AAACTATATATTATATAGTTTTTC-AAAATATTTTAA
* *
54573 AAACTATATA-T-TATA-TTTTT-AAAAAAGTTTTCA
1 AAACTATATATTATATAGTTTTTCAAAATA-TTTTAA
*
54606 AAACTATATATTATATAG-TATTCAAAAATGATTTTAA
1 AAACTATATATTATATAGTTTTTC-AAAAT-ATTTTAA
* * *
54643 AAA-TAT-TA-TATAT-GTTTTTAAGAAAATGTTTTTA
1 AAACTATATATTATATAGTTTTT--CAAAATATTTTAA
* * * * *
54677 AAATTTTAT-TTATATAATTTTTTCAAAAAATGTTTTTA
1 AAACTATATATTATAT-AGTTTTTC--AAAATATTTTAA
54715 AAACTATATATTATATAAGTTTTTCAAAATATTTTAA
1 AAACTATATATTATAT-AGTTTTTCAAAATATTTTAA
* * *
54752 AAACCATATATTATATCAG-TTTTCAAAGTGTTTTAA
1 AAACTATATATTATAT-AGTTTTTCAAAATATTTTAA
* *
54788 AAGACTATATATTATATA--ATTTCAAAATGA-TTT-C
1 AA-ACTATATATTATATAGTTTTTCAAAAT-ATTTTAA
*
54822 AAACTATATAATATATA
1 AAACTATATATTATATA
54839 TATAAAAATA
Statistics
Matches: 217, Mismatches: 29, Indels: 43
0.75 0.10 0.15
Matches are distributed among these distances:
32 5 0.02
33 29 0.13
34 27 0.12
35 28 0.13
36 37 0.17
37 52 0.24
38 25 0.12
39 14 0.06
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (36 bp):
AAACTATATATTATATAGTTTTTCAAAATATTTTAA
Found at i:66367 original size:18 final size:18
Alignment explanation
Indices: 66341--66385 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
66331 TTCACGAAAT
* * *
66341 ATAAAATTAACGGTGGGA
1 ATAAGATTAACGGCGGAA
*
66359 ATAAGATTACCGGCGGAA
1 ATAAGATTAACGGCGGAA
66377 ATAAGATTA
1 ATAAGATTA
66386 CTGAGAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.22
Consensus pattern (18 bp):
ATAAGATTAACGGCGGAA
Found at i:67447 original size:15 final size:15
Alignment explanation
Indices: 67429--67461 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
67419 AAATTCTAAA
67429 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
67444 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
67459 TAT
1 TAT
67462 ATTTGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Done.