Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004533.1 Hibiscus syriacus cultivar Beakdansim tig00010011_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: 58205
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7775 original size:80 final size:81
Alignment explanation
Indices: 7657--7809 Score: 245
Period size: 80 Copynumber: 1.9 Consensus size: 81
7647 GTCTCTTGCA
* * *
7657 CAACTGGCTCGGTAGCTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
1 CAACAGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
*
7722 CGAACCATTCTCGGTG
66 CAAACCATTCTCGGTG
* *
7738 CAACAGGCTCAGTAACTT-CTGCTCTACACCTCTGTGAGAGCTTGTTGCTCCGCCATTTCGTGTG
1 CAACAGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
7802 CAAACCAT
66 CAAACCAT
7810 CTTTGCAACT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
80 51 0.77
81 15 0.23
ACGTcount: A:0.18, C:0.31, G:0.22, T:0.29
Consensus pattern (81 bp):
CAACAGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
CAAACCATTCTCGGTG
Found at i:7986 original size:55 final size:55
Alignment explanation
Indices: 7927--8061 Score: 218
Period size: 55 Copynumber: 2.5 Consensus size: 55
7917 TAGAATTAAC
* *
7927 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAA-AAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGCCAACAA-T
*
7982 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGCCAACTAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGCCAACAAT
*
8037 GACTGAGCACCTCTGTGCTTCAATC
1 GATTGAGCACCTCTGTGCTTCAATC
8062 TAAATTCTGG
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
55 74 0.99
56 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (55 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGCCAACAAT
Found at i:8025 original size:27 final size:27
Alignment explanation
Indices: 7930--8061 Score: 110
Period size: 27 Copynumber: 4.8 Consensus size: 27
7920 AATTAACGAT
7930 TGAGCACCTCTGTGCTTCAATCGAGAGC
1 TGAGCACCTCTGTGCTTCAATCGAGA-C
* ** * *
7958 TGA-CACCTCTGTG-TAGCCAAAAGTGAT
1 TGAGCACCTCTGTGCT--TCAATCGAGAC
7985 TGAGCACCTCTGTGCTTCAATCGAGAAC
1 TGAGCACCTCTGTGCTTCAATCGAG-AC
** *
8013 TGA-CACCTCTGTGCAGCCAA-CTATGAC
1 TGAGCACCTCTGTGC-TTCAATCGA-GAC
8040 TGAGCACCTCTGTGCTTCAATC
1 TGAGCACCTCTGTGCTTCAATC
8062 TAAATTCTGG
Statistics
Matches: 80, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
26 1 0.01
27 39 0.49
28 39 0.49
29 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (27 bp):
TGAGCACCTCTGTGCTTCAATCGAGAC
Found at i:14891 original size:41 final size:41
Alignment explanation
Indices: 14819--14906 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
14809 TTTTTTTTAT
** *
14819 CAAACGCTGCAAAAGAATCTTACTTTAGTGGCATTTGTATA
1 CAAACGCTGCAAAAGAATCAGAATTTAGTGGCATTTGTATA
* * * *
14860 CAAACGCTGCTAAAGACTCAGAATTTCGTGGCGTTTGTATA
1 CAAACGCTGCAAAAGAATCAGAATTTAGTGGCATTTGTATA
*
14901 AAAACG
1 CAAACG
14907 TAGCTATAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (41 bp):
CAAACGCTGCAAAAGAATCAGAATTTAGTGGCATTTGTATA
Found at i:15005 original size:41 final size:41
Alignment explanation
Indices: 14839--15180 Score: 226
Period size: 41 Copynumber: 8.6 Consensus size: 41
14829 AAAAGAATCT
* * * * *
14839 TACTTTAGTGGCATTTGTATACAAACGCTGCTAAAGACTCAG
1 TACTTTAGTGGCGTTTTTATACAAACTCCGCTATAGACTC-G
* * * * * *
14881 -AATTTCGTGGCGTTTGTATAAAAACGT-AGCTATAAACTCG
1 TACTTTAGTGGCGTTTTTATACAAAC-TCCGCTATAGACTCG
* * *
14921 TACTTTAGTCGCGCTTTTAT-CAAACGT-CGCTATAAACTCG
1 TACTTTAGTGGCGTTTTTATACAAAC-TCCGCTATAGACTCG
* *
14961 TACTTTAGTGGCATTTTTATACAAGCTCCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTTATACAAACTCCGCTATAGACTCG
** * * *
15002 TACTTTAGTTACGTTTTTATACAAACACCGGTATAGAATCG
1 TACTTTAGTGGCGTTTTTATACAAACTCCGCTATAGACTCG
* *
15043 -----TA---GCGTTTTTATAC-AAGTGTCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTTATACAAACT-CCGCTATAGACTCG
* ** * *
15076 TACTTCAGTGGTATTTTTATACAAA-TGCCGCTATAAACTCA
1 TACTTTAGTGGCGTTTTTATACAAACT-CCGCTATAGACTCG
* * * * * * *
15117 TATTTTAGTGACATTTTTATATAAACGCTGCTATAGACTTG
1 TACTTTAGTGGCGTTTTTATACAAACTCCGCTATAGACTCG
15158 TACTTTAGTGGCGTTTTTATACA
1 TACTTTAGTGGCGTTTTTATACA
15181 CATCATAATA
Statistics
Matches: 232, Mismatches: 53, Indels: 31
0.73 0.17 0.10
Matches are distributed among these distances:
32 2 0.01
33 22 0.09
36 2 0.01
38 1 0.00
40 37 0.16
41 166 0.72
42 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (41 bp):
TACTTTAGTGGCGTTTTTATACAAACTCCGCTATAGACTCG
Found at i:15152 original size:115 final size:115
Alignment explanation
Indices: 14946--15153 Score: 283
Period size: 115 Copynumber: 1.8 Consensus size: 115
14936 TTTATCAAAC
* * * *
14946 GTCGCTATAAACTCGTACTTTAGTGGCATTTTTATACAAGCTCCGCTATAGACTCGTACTTTAGT
1 GTCGCTATAAACTCGTACTTCAGTGGCATTTTTATACAAGATCCGCTATAAACTCATACTTTAGT
* * *
15011 TACGTTTTTATACAAACACCGGTATAGAATCGTAGCGTTTTTATACAAGT
66 GACATTTTTATACAAACACCGCTATAGAATCGTAGCGTTTTTATACAAGT
* * *
15061 GTCGCTATAGACTCGTACTTCAGTGGTATTTTTATACAA-ATGCCGCTATAAACTCATATTTTAG
1 GTCGCTATAAACTCGTACTTCAGTGGCATTTTTATACAAGAT-CCGCTATAAACTCATACTTTAG
* * *
15125 TGACATTTTTATATAAACGCTGCTATAGA
65 TGACATTTTTATACAAACACCGCTATAGA
15154 CTTGTACTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
114 1 0.01
115 78 0.99
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (115 bp):
GTCGCTATAAACTCGTACTTCAGTGGCATTTTTATACAAGATCCGCTATAAACTCATACTTTAGT
GACATTTTTATACAAACACCGCTATAGAATCGTAGCGTTTTTATACAAGT
Found at i:17279 original size:16 final size:15
Alignment explanation
Indices: 17258--17289 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
17248 AACAGAATTT
17258 TAGGTAAAATAACAAA
1 TAGGTAAAATAA-AAA
17274 TAGGTAAAATAAAAA
1 TAGGTAAAATAAAAA
17289 T
1 T
17290 TTTCCCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.22
Consensus pattern (15 bp):
TAGGTAAAATAAAAA
Found at i:21955 original size:3 final size:3
Alignment explanation
Indices: 21947--21991 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
21937 TATATACTCT
* *
21947 TGA TGA TGA TGG TAA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
21992 GAGTCATAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:22240 original size:25 final size:25
Alignment explanation
Indices: 22176--22241 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
22166 TAATTTATTT
22176 TGTTTGTTAA-TTTTTTATTACTTAG
1 TGTTT-TTAATTTTTTTATTACTTAG
** * *
22201 T-TGTTCAAATGTTTTTATTATTTAG
1 TGT-TTTTAATTTTTTTATTACTTAG
22226 TGTTTTTAATTTTTTT
1 TGTTTTTAATTTTTTT
22242 TTTGTTATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
24 3 0.10
25 27 0.87
26 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.67
Consensus pattern (25 bp):
TGTTTTTAATTTTTTTATTACTTAG
Found at i:25497 original size:21 final size:18
Alignment explanation
Indices: 25473--25511 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 18
25463 TTTTTTTCGA
25473 ATAATCATATATAAAATAAAT
1 ATAAT-ATAT-TAAAA-AAAT
25494 ATAATATATTAAAAAAAT
1 ATAATATATTAAAAAAAT
25512 TACCTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 4 0.22
21 5 0.28
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAATATATTAAAAAAAT
Found at i:32270 original size:32 final size:32
Alignment explanation
Indices: 32234--32303 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
32224 GTTTTTGGTT
* *
32234 AGATGAAAGGAGTTTGTTGTGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
*
32266 AGATGAAATGAGTGTGTTATGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
32298 AGATGA
1 AGATGA
32304 TGTGCACAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (32 bp):
AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
Found at i:32476 original size:88 final size:89
Alignment explanation
Indices: 32370--32549 Score: 231
Period size: 91 Copynumber: 2.0 Consensus size: 89
32360 GTGATGAGTT
** *
32370 CCATTGAAATTTAAAAAAAATCA-ACCATTGAACAACGGTCAATCCAACGGT-TAAAAAGTCAAA
1 CCATTGAAATTTAAAAAAAAT-ATACCATTGAACAACGGTCAATCCAACAATAAAAAAAGTCAAA
32433 ATTATACCT-GTTGGAACTCGTCACG
65 ATTAT-CCTCGTTGGAACTCGTCACG
** * *
32458 CCATTGAAATTTTTAAAAAATATTGATCGTTGAACAACGGTCAATCCAACAATAAAAAAAGTCAA
1 CCATTGAAATTTAAAAAAAATA-T-ACCATTGAACAACGGTCAATCCAACAATAAAAAAAGTCAA
*
32523 AATTATTCTCGTTGGAACTCGTCACG
64 AATTATCCTCGTTGGAACTCGTCACG
32549 C
1 C
32550 TGTTGCAACT
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
87 1 0.01
88 19 0.24
90 26 0.33
91 33 0.42
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (89 bp):
CCATTGAAATTTAAAAAAAATATACCATTGAACAACGGTCAATCCAACAATAAAAAAAGTCAAAA
TTATCCTCGTTGGAACTCGTCACG
Found at i:34468 original size:32 final size:32
Alignment explanation
Indices: 34427--34547 Score: 181
Period size: 32 Copynumber: 3.8 Consensus size: 32
34417 TCGAGGGTTA
34427 CTATGTCTTTCGGGACATATGGACAGGATTAC
1 CTATGTCTTTCGGGACATATGGACAGGATTAC
*
34459 CTATGTCTTTCGGGACATATGGATAGGATTAC
1 CTATGTCTTTCGGGACATATGGACAGGATTAC
* * *
34491 ATATGTCCTTCGGGACATATGGACAAGATTAC
1 CTATGTCTTTCGGGACATATGGACAGGATTAC
*
34523 CTATGT-TCTTCAGGACATATGGACA
1 CTATGTCT-TTCGGGACATATGGACA
34548 TTTACCTATG
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
32 80 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (32 bp):
CTATGTCTTTCGGGACATATGGACAGGATTAC
Found at i:34854 original size:2 final size:2
Alignment explanation
Indices: 34847--34881 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
34837 ATAATAATTG
34847 TA TA TA TA T- TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34882 GCATGTATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:35289 original size:21 final size:22
Alignment explanation
Indices: 35259--35307 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
35249 AAATTTACTA
*
35259 TAGCAAGGGTATCGGTA-CACTG
1 TAGC-AGGGTATCGATACCACTG
* *
35281 TAGCAGGGTGTCGATACCCCTG
1 TAGCAGGGTATCGATACCACTG
35303 TAGCA
1 TAGCA
35308 TTTTGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (22 bp):
TAGCAGGGTATCGATACCACTG
Found at i:35345 original size:12 final size:12
Alignment explanation
Indices: 35328--35363 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
35318 TTTTAACATT
35328 CGGTACTGTTCA
1 CGGTACTGTTCA
35340 CGGTACTGTTCA
1 CGGTACTGTTCA
* *
35352 TGTTACTGTTCA
1 CGGTACTGTTCA
35364 GTAATGTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (12 bp):
CGGTACTGTTCA
Found at i:35374 original size:22 final size:23
Alignment explanation
Indices: 35331--35374 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
35321 TAACATTCGG
*
35331 TACTGTTCACGGTACTGTTCATGT
1 TACTGTTCAC-GTAATGTTCATGT
35355 TACTGTTCA-GTAATGTTCAT
1 TACTGTTCACGTAATGTTCAT
35375 ACAATATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (23 bp):
TACTGTTCACGTAATGTTCATGT
Found at i:36031 original size:19 final size:20
Alignment explanation
Indices: 36007--36057 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
35997 AATGACCAAT
36007 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
36026 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
36046 AAAATCGCAACG
1 AAAATCGCAACG
36058 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:36051 original size:20 final size:20
Alignment explanation
Indices: 36007--36324 Score: 147
Period size: 20 Copynumber: 15.6 Consensus size: 20
35997 AATGACCAAT
* *
36007 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
36026 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
36046 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
36066 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
36086 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
36107 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
36130 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * * *
36150 TGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
36170 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
36190 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
36210 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
36233 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* ** * *
36253 AGAATCGCAATACGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
36273 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
36293 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
36313 AAAATCGCAACG
1 AAAATCGCAACG
36325 TTAAAAAGAA
Statistics
Matches: 242, Mismatches: 45, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
19 17 0.07
20 182 0.75
21 14 0.06
23 29 0.12
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:36183 original size:40 final size:40
Alignment explanation
Indices: 36132--36309 Score: 214
Period size: 40 Copynumber: 4.4 Consensus size: 40
36122 TTTAGAAGAA
* **
36132 AATCGCAATGCGATTGATTGAATCGCAATGCGATTGATTG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
*
36172 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
* * *
36212 AGTCGCAACGCGATTTAGA-AGAAAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGA-TT-GATAG--AATCGCAATGCGATTGAGAG
* * *
36255 AATCGCAATACGACTGAGAGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
*
36295 AATCGCAACGCGATT
1 AATCGCAATGCGATT
36310 TAGAAAATCG
Statistics
Matches: 117, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
40 78 0.67
41 6 0.05
42 4 0.03
43 29 0.25
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (40 bp):
AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
Found at i:36239 original size:83 final size:83
Alignment explanation
Indices: 36152--36314 Score: 254
Period size: 83 Copynumber: 2.0 Consensus size: 83
36142 CGATTGATTG
* ** * * * * *
36152 AATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
1 AATCGCAATGCGACTGAGAGAATCGCAATACGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
36217 CAACGCGATTTAGAAGAA
66 CAACGCGATTTAGAAGAA
36235 AATCGCAATGCGACTGAGAGAATCGCAATACGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAATACGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
36300 CAACGCGATTTAGAA
66 CAACGCGATTTAGAA
36315 AATCGCAACG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 72 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (83 bp):
AATCGCAATGCGACTGAGAGAATCGCAATACGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
CAACGCGATTTAGAAGAA
Found at i:36243 original size:103 final size:103
Alignment explanation
Indices: 36111--36324 Score: 311
Period size: 103 Copynumber: 2.1 Consensus size: 103
36101 GCTTCCAAGT
* ** * * **
36111 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTGATTGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATACGACTGAGAGAATC
* * * * *
36176 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
66 GCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAA
36214 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATACGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATACGACTGAGAGAATC
*
36279 GCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAA
66 GCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAA
36317 TCGCAACG
1 TCGCAACG
36325 TTAAAAAGAA
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (103 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATACGACTGAGAGAATC
GCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAA
Found at i:36334 original size:20 final size:20
Alignment explanation
Indices: 36311--36354 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
36301 AACGCGATTT
*
36311 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
36331 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
36351 AGAA
1 AGAA
36355 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:36442 original size:6 final size:6
Alignment explanation
Indices: 36431--36498 Score: 129
Period size: 6 Copynumber: 11.5 Consensus size: 6
36421 GACACGTATT
36431 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
36479 ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
36499 CGAGACGAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.08
6 57 0.92
ACGTcount: A:0.32, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:37187 original size:6 final size:6
Alignment explanation
Indices: 37171--37280 Score: 213
Period size: 6 Copynumber: 18.5 Consensus size: 6
37161 TCTCGTCTCG
37171 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
37218 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
37266 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
37281 AATACGTGTC
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.05
6 99 0.95
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:37382 original size:20 final size:20
Alignment explanation
Indices: 37357--37400 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
37347 TTTTTAACTA
*
37357 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
37377 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
37397 TTCT
1 TTCT
37401 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:37410 original size:20 final size:20
Alignment explanation
Indices: 37389--37563 Score: 179
Period size: 20 Copynumber: 8.6 Consensus size: 20
37379 CTTTTTAACG
*
37389 TTGCGATTTTCTAAATCGCG
1 TTGCGATTTTCTAAATCGCA
* * *
37409 TTGCAATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCA
* *
37429 TTGCGATTCTATAAATCGCA
1 TTGCGATTTTCTAAATCGCA
* * *
37449 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCA
37469 TTGCGATTTTCTTCTAAATCGCA
1 TTGCGA--TT-TTCTAAATCGCA
* *
37492 TTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCA
* *
37512 TTGCGATTCTATAAATCGCA
1 TTGCGATTTTCTAAATCGCA
* * *
37532 TTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTAAATCGCA
37552 TTGCGATTTTCT
1 TTGCGATTTTCT
37564 TCTAAATCGC
Statistics
Matches: 132, Mismatches: 20, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
20 113 0.86
21 2 0.02
22 2 0.02
23 15 0.11
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCTAAATCGCA
Found at i:37433 original size:40 final size:40
Alignment explanation
Indices: 37389--37563 Score: 251
Period size: 40 Copynumber: 4.3 Consensus size: 40
37379 CTTTTTAACG
* *
37389 TTGCGATTTTCTAAATCGCGTTGCAATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
37429 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCATTGCGATTCTCTCAATCGCA
37469 TTGCGATTTTCTTCTAAATCGCATTGCGATTCTCTCAATCGCA
1 TTGCGA--TT-TTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
37512 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTAAATCGCATTGCGATTCTCTCAATCGCA
37552 TTGCGATTTTCT
1 TTGCGATTTTCT
37564 TCTAAATCGC
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
40 80 0.67
41 2 0.02
42 2 0.02
43 35 0.29
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.38
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:37505 original size:83 final size:83
Alignment explanation
Indices: 37397--37580 Score: 332
Period size: 83 Copynumber: 2.2 Consensus size: 83
37387 CGTTGCGATT
* *
37397 TTCTAAATCGCGTTGCAATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
*
37462 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
*
37480 TTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
1 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
37545 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
37563 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
37581 ACTTGGAAGC
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 96 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
AATCGCATTGCGATTTTC
Found at i:37619 original size:20 final size:20
Alignment explanation
Indices: 37594--37647 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
37584 TGGAAGCTCG
*
37594 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
37614 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
37634 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
37648 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:38014 original size:27 final size:27
Alignment explanation
Indices: 37974--38039 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
37964 CCAACCTTCT
*
37974 CTCTC-TCCCCCTTCCCTATCCTTTCC
1 CTCTCGTCCCCCTTCCCTATCATTTCC
38000 CTCTCGTCCCCCTTCCCTATCATTTCC
1 CTCTCGTCCCCCTTCCCTATCATTTCC
*
38027 CTCTTGTCTCCCC
1 CTCTCGTC-CCCC
38040 AGCCCGATGC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 5 0.14
27 27 0.75
28 4 0.11
ACGTcount: A:0.05, C:0.55, G:0.03, T:0.38
Consensus pattern (27 bp):
CTCTCGTCCCCCTTCCCTATCATTTCC
Found at i:39731 original size:60 final size:60
Alignment explanation
Indices: 39637--39812 Score: 180
Period size: 60 Copynumber: 2.9 Consensus size: 60
39627 GGGGGACATT
** * * * *
39637 ATTGGAATGTTTGAAAGTTTGGTGACTAATTTAGAATAAGGGTCATGGTTTGA-GGATTAA
1 ATTGGAATGTTCAAAAGTTAGG-GACTAATTTAGAATAAGAGTCATAGTTTGAGGGATGAA
* **
39697 ATTGGAATGTTCAAAAGCTTAGGGACCAATTTAGAATGTGAGTCATAGTTT-AGGGATGAA
1 ATTGGAATGTTCAAAAG-TTAGGGACTAATTTAGAATAAGAGTCATAGTTTGAGGGATGAA
** *
39757 ATTTAAATGTTCAAAAGTATAGGGACTGATTT-GAAATAAGAGTCATAGTTTG-GGGA
1 ATTGGAATGTTCAAAAGT-TAGGGACTAATTTAG-AATAAGAGTCATAGTTTGAGGGA
39813 CTCATCTTGT
Statistics
Matches: 96, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
59 3 0.03
60 89 0.93
61 4 0.04
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.33
Consensus pattern (60 bp):
ATTGGAATGTTCAAAAGTTAGGGACTAATTTAGAATAAGAGTCATAGTTTGAGGGATGAA
Found at i:40133 original size:5 final size:5
Alignment explanation
Indices: 40125--40159 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
40115 GGAATTTAAT
40125 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
40160 ATTAATGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:40917 original size:23 final size:24
Alignment explanation
Indices: 40885--40970 Score: 88
Period size: 24 Copynumber: 3.6 Consensus size: 24
40875 AACATTAAAC
*
40885 AAATGCTAAACGAACATGTTCGT-A
1 AAAT-CTAAACGAACACGTTCGTGA
40909 AAATCTAAACGAACACG-TCTGTGA
1 AAATCTAAACGAACACGTTC-GTGA
* * *
40933 ACATATAAACGAACACATTCGTGA
1 AAATCTAAACGAACACGTTCGTGA
*
40957 ACAT-TAAACGAACA
1 AAATCTAAACGAACA
40971 TGTTTACGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
22 2 0.04
23 24 0.44
24 27 0.49
25 2 0.04
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (24 bp):
AAATCTAAACGAACACGTTCGTGA
Found at i:40982 original size:47 final size:46
Alignment explanation
Indices: 40891--40987 Score: 106
Period size: 47 Copynumber: 2.1 Consensus size: 46
40881 AAACAAATGC
** **
40891 TAAACGAACATGTTCGTAAAATCTAAACGAACACGTCTGTGAACATA
1 TAAACGAACACATTCGTAAAATCTAAACGAACACGTCTACGAACA-A
* * *
40938 TAAACGAACACATTCGTGAACAT-TAAACGAACATGTTTACGAACAA
1 TAAACGAACACATTCGT-AAAATCTAAACGAACACGTCTACGAACAA
40984 TAAA
1 TAAA
40988 TAAACAAACA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
46 5 0.12
47 33 0.79
48 4 0.10
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (46 bp):
TAAACGAACACATTCGTAAAATCTAAACGAACACGTCTACGAACAA
Found at i:41970 original size:19 final size:19
Alignment explanation
Indices: 41946--41998 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
41936 GCATGGCAGT
*
41946 CCGTGACACTGCCCTCTGC
1 CCGTGACACTGCCCTCCGC
41965 CCGTGACACTGCCCTCCGC
1 CCGTGACACTGCCCTCCGC
41984 CCGTGACACTGCCCT
1 CCGTGACACTGCCCT
41999 GCATGGCAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.11, C:0.49, G:0.21, T:0.19
Consensus pattern (19 bp):
CCGTGACACTGCCCTCCGC
Found at i:42166 original size:18 final size:18
Alignment explanation
Indices: 42143--42187 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
42133 GGAGGCACCG
42143 GGAGAAGAAAGAAA-AATA
1 GGAGAAGAAAGAAATAA-A
*
42161 GGAGAAGGAAGAAATAAA
1 GGAGAAGAAAGAAATAAA
42179 GGAAGAAGA
1 GG-AGAAGA
42188 CGAAGAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.04
Consensus pattern (18 bp):
GGAGAAGAAAGAAATAAA
Found at i:43914 original size:22 final size:22
Alignment explanation
Indices: 43888--43929 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
43878 ATATGAGGTT
43888 TGTCCCGAAAGACCTATGAATA
1 TGTCCCGAAAGACCTATGAATA
*
43910 TGTCCCGAATGACCTATGAA
1 TGTCCCGAAAGACCTATGAA
43930 ACCCTCGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (22 bp):
TGTCCCGAAAGACCTATGAATA
Found at i:44564 original size:19 final size:19
Alignment explanation
Indices: 44540--44590 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
44530 TTTTGAGGGG
*
44540 GTATCGATACACTGACTGT
1 GTATCGATACACTGACCGT
*
44559 GTATCGATACACTGCCCGT
1 GTATCGATACACTGACCGT
44578 GTATCGATACACT
1 GTATCGATACACT
44591 TATTTCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (19 bp):
GTATCGATACACTGACCGT
Found at i:47250 original size:2 final size:2
Alignment explanation
Indices: 47245--47276 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
47235 TAAAAAATTC
47245 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47277 CATACATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48154 original size:2 final size:2
Alignment explanation
Indices: 48147--48192 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
48137 CCTGTTTTTA
*
48147 AT AT AT AT AT AT AT AT AT AT AT AT AG 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
48189 AT AT
1 AT AT
48193 TGTGTTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Done.