Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006172.1 Hibiscus syriacus cultivar Beakdansim tig00014673_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: 90451
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6564 original size:20 final size:20
Alignment explanation
Indices: 6531--6581 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
6521 TGTTGTTGCT
*
6531 AATTTGGTAG-TGTTGCTACG
1 AATTTGGT-GCTGTTGCCACG
* *
6551 GATTTGGTGCTGTTGCCGCG
1 AATTTGGTGCTGTTGCCACG
6571 AATTTGGTGCT
1 AATTTGGTGCT
6582 ACTGTGTGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.14, C:0.14, G:0.33, T:0.39
Consensus pattern (20 bp):
AATTTGGTGCTGTTGCCACG
Found at i:7451 original size:257 final size:257
Alignment explanation
Indices: 6947--7481 Score: 739
Period size: 257 Copynumber: 2.1 Consensus size: 257
6937 ATGGTCCATA
* *
6947 TGAAAGCATCTTGCCC-AAGGGTGTATAGATGGCCCAAAGAATTTATCATCTTGTTCGAAAGACT
1 TGAAAACATCTTGCCCGAA-GGTGTATAGATGGCCCAAAGAACTTATCATCTTGTTCGAAAGACT
* * * *
7011 GACAAATGACCCGAAGGATTTAATCATCATGCTTGAAAGACTTATTGATGGACCGAATGACTTAC
65 GACAAATAACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGACCGAAGGACTTAC
* * *
7076 CAATTTTGGAAAAAGTTTACTGGGTTAGAAACTATGGAAATTTTTCTTACTTTTCAAAGATTTCA
130 CAATTTTGGAAAAAGTTTACTGGGTAAAAAACTATGGAAATTTTTCTTACTTTTCAAAAATTTCA
*
7141 TTTTCTAAAAATATTAAATGAGAAACTTTGAAAATTGCCTTTTTCATTTTTTT-AAA-ATCATG
195 TTTTCTAAAAATATTAAATGAGAAACTTTAAAAATTG-CTTTTTCATTTTTTTAAAACATCATG
* * *
7203 TGAAAACATCTTGCCCGAAGGTCTTATAGATGGCCTAAAGGACTTATCATCTTGCTT-GAAAGAC
1 TGAAAACATCTTGCCCGAAGGT-GTATAGATGGCCCAAAGAACTTATCATCTTG-TTCGAAAGAC
* *
7267 TGA-AAGATAACCTGAAGGATTTAATCATCATGCTCGAAAGATTTACTGATGG-CCAGAAGGACT
64 TGACAA-ATAACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGACC-GAAGGACT
* * *
7330 TACTAATTTTGGAAATAGTTTACTGGGTAAAAAACT-TGGAAATCGTTTTCTTACTTTTTAAAAA
127 TACCAATTTTGGAAAAAGTTTACTGGGTAAAAAACTATGGAAAT--TTTTCTTACTTTTCAAAAA
7394 TTTCATTTT-TAGAAAATATTAAATGAGAAACTTTAAAAATTG-TTTTCCTCA-TTTTTTAAAAC
190 TTTCATTTTCTA-AAAATATTAAATGAGAAACTTTAAAAATTGCTTTT--TCATTTTTTTAAAAC
7456 ATCATG
252 ATCATG
7462 TGAAAACATCTTGCCCGAAG
1 TGAAAACATCTTGCCCGAAG
7482 AATTTAATCA
Statistics
Matches: 249, Mismatches: 18, Indels: 21
0.86 0.06 0.07
Matches are distributed among these distances:
256 33 0.13
257 127 0.51
258 63 0.25
259 26 0.10
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (257 bp):
TGAAAACATCTTGCCCGAAGGTGTATAGATGGCCCAAAGAACTTATCATCTTGTTCGAAAGACTG
ACAAATAACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGACCGAAGGACTTACC
AATTTTGGAAAAAGTTTACTGGGTAAAAAACTATGGAAATTTTTCTTACTTTTCAAAAATTTCAT
TTTCTAAAAATATTAAATGAGAAACTTTAAAAATTGCTTTTTCATTTTTTTAAAACATCATG
Found at i:17650 original size:83 final size:80
Alignment explanation
Indices: 17560--17847 Score: 197
Period size: 83 Copynumber: 3.5 Consensus size: 80
17550 TGTAACAAAC
*
17560 GCCACTATAGATGAACCTTATTATGGCATTTGTATAAAAACACCGCTAATGTACTACTATGTTGC
1 GCCACTATAGATGAACCTTATTACGGCATTTGTATAAAAACACCGCT-ATGTACTA-TATGTTGC
*
17625 GACGTTAGTTGAAAAAAT
64 GGCGTT-GTTGAAAAAAT
* * * * * ** * * * *
17643 GCCACTATAGGTGAA-CTCTATTGCGACGTTTGTATAATAAGGCCACTGACGTATTAATTTGTTG
1 GCCACTATAGATGAACCT-TATTACGGCATTTGTATAAAAACACCGCT-ATGTACT-ATATGTTG
* *
17707 CGGCGTTTTTG-AAAAAC
63 CGGCGTTGTTGAAAAAAT
* * ** * * * * * *
17724 G-CACTATAGATTAACCCTATTATTGTATTTTTGTAAAAACACTGCTATAGTACTTATCTGGTGC
1 GCCACTATAGATGAACCTTATTACGGCATTTGTATAAAAACACCGCTAT-GTAC-TATATGTTGC
* *
17788 GGCGTTTGTTTAGAAAAT
64 GGCG-TTGTTGAAAAAAT
* * *
17806 GCCACTAAAGATGAACC-TATTGCGGCGTTTGTATAAAAACAC
1 GCCACTATAGATGAACCTTATTACGGCATTTGTATAAAAACAC
17848 TACGAAAATA
Statistics
Matches: 148, Mismatches: 49, Indels: 17
0.69 0.23 0.08
Matches are distributed among these distances:
79 1 0.01
80 41 0.28
81 12 0.08
82 28 0.19
83 65 0.44
84 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (80 bp):
GCCACTATAGATGAACCTTATTACGGCATTTGTATAAAAACACCGCTATGTACTATATGTTGCGG
CGTTGTTGAAAAAAT
Found at i:34880 original size:42 final size:42
Alignment explanation
Indices: 34797--34880 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
34787 TGTTTTGCAA
** * *
34797 GAAGCATGAGAACTAGAAAATTATGTGGTTAGGTCTCTATGT
1 GAAGCATGAGAACTAGAAAAGCATGAGGTTAGGTCTATATGT
* *
34839 GAAGCATGCGAACTAG-AAAGCATGAGGTTAGGATTTATATGT
1 GAAGCATGAGAACTAGAAAAGCATGAGGTTAGG-TCTATATGT
34881 TGAACGAAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 13 0.37
42 22 0.63
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.29
Consensus pattern (42 bp):
GAAGCATGAGAACTAGAAAAGCATGAGGTTAGGTCTATATGT
Found at i:38559 original size:11 final size:12
Alignment explanation
Indices: 38536--38576 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
38526 ATACTAATCC
38536 AAAGAAGAAAGA
1 AAAGAAGAAAGA
38548 AAAGAA-AAAGAA
1 AAAGAAGAAAG-A
*
38560 AAAGAGGAAA-A
1 AAAGAAGAAAGA
38571 AAAGAA
1 AAAGAA
38577 AGCAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 10 0.40
12 12 0.48
13 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAGAAGAAAGA
Found at i:41911 original size:261 final size:259
Alignment explanation
Indices: 41303--42265 Score: 1405
Period size: 261 Copynumber: 3.7 Consensus size: 259
41293 CATTGAATTT
* *
41303 TGAAAATGAGAAAGTGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTAAAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
* *
41368 AGTAAG-AAACGATTTCCAAAGTTTCCTACCCAGTAAATTATTTCCAAAATTTGTAAATCCTTCG
66 AGTAAGAAAACGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTCGTAAATCCTTCG
* * * * * *
41432 GGTCATCAGTAAGTCTTTCAAGCATGATCCTTAAACCCTT-TGAGCCATCTGTAAGTTTTCGAGC
131 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAG-GTCATCTGTAAGTTTTCGAGA
* *
41496 AAGATGATAAGTCATTCAGGCCATCCATAAGACCTTCGGGTAGGAT-TTTACACATGCTTTTCAC
195 AAGATGATAAGTCCTTC-GGCCATCCATAAGACCTTCGGGTAGGATGTTTACACATGATTTTCAC
*
41560 G
259 A
*
41561 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTGGAAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
* * *
41626 AGTAAGAAAACAATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTCATAAATCCTTTG
66 AGTAAGAAAACGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTCGTAAATCCTTCG
* *
41691 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGT
131 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGT-TTTCGAGA
* * *
41756 AAGATGATAAGTCCTTCGGATCATCCATAAGACCTTCGGGTAGGATGTTTGCACATGATTTTGAC
195 AAGATGATAAGTCCTTCGG-CCATCCATAAGACCTTCGGGTAGGATGTTTACACATGATTTTCAC
41821 A
259 A
*
41822 TGAAAATGAGAAAGTGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
*
41887 AGTAAGAAAACGATTTCGAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTCGTAAATCCTTCG
66 AGTAAGAAAACGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTCGTAAATCCTTCG
* **
41952 GGTCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTGTTTTAAGA
131 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGT-TTTCGAGA
* *
42017 AAGATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGTAGGATGTTTACACATGATTTTCAT
195 AAGATGATAAGTCC-TTCGGCCATCCATAAGACCTTCGGGTAGGATGTTTACACATGATTTTCAC
42082 A
259 A
* * ** * *
42083 CGAGAATGAGAAAGCGATTAAAAAAGTTTTTCATTTAATGTCTTCAGAAAATGAAATTTTTGAAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
* * * *
42148 AGTAAGAAAACGATTTCCAAAGTTTCTTACCC-GATAAATTATTTCCCAAATTTGTAAGTCCTTT
66 AGTAAGAAAACGATTTCCAAAGTTTCTTACCCAG-TAAATTATTTCCAAAATTCGTAAATCCTTC
* * * * * * * *
42212 GGGCCATAAGTAAGTTTTTCGAACAAGATG-ATAAGTCCTTCAGGTCATCCGTAA
130 GGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAA
42266 AACCTTTGGG
Statistics
Matches: 640, Mismatches: 58, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
258 68 0.11
259 104 0.16
260 71 0.11
261 393 0.61
262 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (259 bp):
TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
AGTAAGAAAACGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTCGTAAATCCTTCG
GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTTTTCGAGAA
AGATGATAAGTCCTTCGGCCATCCATAAGACCTTCGGGTAGGATGTTTACACATGATTTTCACA
Found at i:42463 original size:38 final size:38
Alignment explanation
Indices: 42412--42501 Score: 135
Period size: 38 Copynumber: 2.4 Consensus size: 38
42402 TGAATATAAG
* * * *
42412 TCAATCTTTGTTATCTTTGACTTCGTTGTGAAGAGAAT
1 TCAATATTTGTTATCCTTGACTTCCTTGTGAAGAGAAA
42450 TCAATATTTGTTATCCTTGACTTCCTTGTGAAGAGAAA
1 TCAATATTTGTTATCCTTGACTTCCTTGTGAAGAGAAA
*
42488 TCAATAATTGTTAT
1 TCAATATTTGTTAT
42502 ATCTAACTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (38 bp):
TCAATATTTGTTATCCTTGACTTCCTTGTGAAGAGAAA
Found at i:43069 original size:12 final size:12
Alignment explanation
Indices: 43058--43100 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
43048 TTATTTATTC
*
43058 TTATTATGATTC
1 TTATTATGATTA
43070 TTATTATGATTA
1 TTATTATGATTA
*
43082 TTATTATGGTTA
1 TTATTATGATTA
43094 TTATTAT
1 TTATTAT
43101 ATAATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.60
Consensus pattern (12 bp):
TTATTATGATTA
Found at i:43172 original size:17 final size:17
Alignment explanation
Indices: 43146--43181 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
43136 AACATATTAA
*
43146 ACCCGATCTAGGCCTAG
1 ACCCGATCTAGGCCCAG
*
43163 ACCCGTTCTAGGCCCAG
1 ACCCGATCTAGGCCCAG
43180 AC
1 AC
43182 AACCCAACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.39, G:0.22, T:0.17
Consensus pattern (17 bp):
ACCCGATCTAGGCCCAG
Found at i:44437 original size:29 final size:28
Alignment explanation
Indices: 44404--44471 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
44394 ATTTTGTAGT
44404 TTTA-TAATTTAA-TCTTTAAATTTATTATA
1 TTTATTAATTTAATTCTTT--ATTTA-TATA
*
44433 TTTATTATTTTAATTCTTTATTTATATA
1 TTTATTAATTTAATTCTTTATTTATATA
*
44461 TTTGTTAATTT
1 TTTATTAATTT
44472 TTACTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 13 0.38
29 9 0.26
30 7 0.21
31 5 0.15
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (28 bp):
TTTATTAATTTAATTCTTTATTTATATA
Found at i:46112 original size:20 final size:20
Alignment explanation
Indices: 46087--46124 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46077 GAAAAATATA
*
46087 AATTTTCTTATATTTTTTTG
1 AATTTTCTTAGATTTTTTTG
*
46107 AATTTTTTTAGATTTTTT
1 AATTTTCTTAGATTTTTT
46125 AAATTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (20 bp):
AATTTTCTTAGATTTTTTTG
Found at i:47150 original size:17 final size:18
Alignment explanation
Indices: 47106--47141 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
47096 GGTTGCACCA
47106 ACCAA-ACAA-CACTTCC
1 ACCAATACAATCACTTCC
47122 ACCAATACAATCACTTCC
1 ACCAATACAATCACTTCC
47140 AC
1 AC
47142 ATTATAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 4 0.22
18 9 0.50
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (18 bp):
ACCAATACAATCACTTCC
Found at i:48495 original size:29 final size:29
Alignment explanation
Indices: 48453--48510 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
48443 ACAACTTATT
*
48453 GTATCTACATTTTACTTCTATGACACTTC
1 GTATCTACATTTTACTTCTACGACACTTC
48482 GTATCTACATTTTACTTCTACGACACTTC
1 GTATCTACATTTTACTTCTACGACACTTC
48511 AATACTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.26, G:0.07, T:0.43
Consensus pattern (29 bp):
GTATCTACATTTTACTTCTACGACACTTC
Found at i:52177 original size:14 final size:15
Alignment explanation
Indices: 52158--52189 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52148 TAATTTTAAG
52158 AATTAATA-TAAAAA
1 AATTAATATTAAAAA
52172 AATTAATATTAAAAA
1 AATTAATATTAAAAA
52187 AAT
1 AAT
52190 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATTAATATTAAAAA
Found at i:52934 original size:26 final size:24
Alignment explanation
Indices: 52905--52953 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
52895 TATAACTTTT
*
52905 TCTCTTAACGTAAAATCTTGCTTCCG
1 TCTCCTAACG-AAAATCTT-CTTCCG
*
52931 TCTCCTATCGAAAATCTTCTTCC
1 TCTCCTAACGAAAATCTTCTTCC
52954 CATGCGTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 8 0.38
26 8 0.38
ACGTcount: A:0.22, C:0.31, G:0.08, T:0.39
Consensus pattern (24 bp):
TCTCCTAACGAAAATCTTCTTCCG
Found at i:56435 original size:41 final size:41
Alignment explanation
Indices: 56325--56443 Score: 118
Period size: 41 Copynumber: 2.9 Consensus size: 41
56315 GTTTGTATCC
* * *
56325 ACAAACG-CGCAATAGATTAGCACTTTAGAGGCGTTTTAAT
1 ACAAACGCCGCAAAAGATTAGCAATTTAGTGGCGTTTTAAT
* * *
56365 ACAAACGCCGTAAAAGAATT-GGACA-TTAGTGGCGTTTTCAT
1 ACAAACGCCGCAAAAG-ATTAGCA-ATTTAGTGGCGTTTTAAT
* * *
56406 AGAAACGCCGCAAAAGATTAGTAATTTAGTGGAGTTTT
1 ACAAACGCCGCAAAAGATTAGCAATTTAGTGGCGTTTT
56444 TGTAAAAACA
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
40 11 0.17
41 50 0.78
42 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (41 bp):
ACAAACGCCGCAAAAGATTAGCAATTTAGTGGCGTTTTAAT
Found at i:57013 original size:34 final size:32
Alignment explanation
Indices: 56950--57013 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 32
56940 CTCTTAGGAG
*
56950 TGTTTATAACTTCTTTCTTGTTTTGGTTGAGT
1 TGTTTATAACTTCTTTCTTGATTTGGTTGAGT
56982 TGTTTATAATCTT-TTCTCTCTGATTTGGTTGA
1 TGTTTATAA-CTTCTT-TCT-TGATTTGGTTGA
57014 AGATGAGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 11 0.39
33 6 0.21
34 11 0.39
ACGTcount: A:0.14, C:0.11, G:0.17, T:0.58
Consensus pattern (32 bp):
TGTTTATAACTTCTTTCTTGATTTGGTTGAGT
Found at i:65859 original size:44 final size:44
Alignment explanation
Indices: 65754--65930 Score: 252
Period size: 44 Copynumber: 4.1 Consensus size: 44
65744 ACAAACACCA
* *
65754 CTATATACCA-ACCTTTAGCGGCGTTTGTATACT-AAAATGCCA
1 CTATATACCAGACCTTTAGCGGCGTTTGTATACTAAAAACGCCG
* *
65796 CTATATACTAGACCTTTAGCGGCGTTTGTATACTAAAAACGACG
1 CTATATACCAGACCTTTAGCGGCGTTTGTATACTAAAAACGCCG
65840 CTATATACCAGACCTTTAGCGGCGTTTGTAT-CTTAAAAACGCCG
1 CTATATACCAGACCTTTAGCGGCGTTTGTATAC-TAAAAACGCCG
* * * *
65884 TTATATACCATACCTTTAGCGGCGTTTGCATCCTAAAAACGCCG
1 CTATATACCAGACCTTTAGCGGCGTTTGTATACTAAAAACGCCG
65928 CTA
1 CTA
65931 AATTTCAAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
42 9 0.07
43 24 0.20
44 87 0.72
45 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (44 bp):
CTATATACCAGACCTTTAGCGGCGTTTGTATACTAAAAACGCCG
Found at i:66018 original size:32 final size:32
Alignment explanation
Indices: 65961--66022 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
65951 CGTTTGTAAG
*
65961 ACAAATGCCGCTTAATATCAGTACCTATTGCA
1 ACAAATGCCGCTTAAGATCAGTACCTATTGCA
65993 ACAAATGCCGC-TATAGATC-GTTACCTATTG
1 ACAAATGCCGCTTA-AGATCAG-TACCTATTG
66023 AGGCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (32 bp):
ACAAATGCCGCTTAAGATCAGTACCTATTGCA
Found at i:67257 original size:14 final size:14
Alignment explanation
Indices: 67238--67271 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
67228 TGCCAGCACA
67238 TGTTATTCATTAAC
1 TGTTATTCATTAAC
67252 TGTTATTCATTAAC
1 TGTTATTCATTAAC
*
67266 TATTAT
1 TGTTAT
67272 GGTTACTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (14 bp):
TGTTATTCATTAAC
Found at i:68222 original size:21 final size:21
Alignment explanation
Indices: 68198--68267 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
68188 GCATTGCATT
68198 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
* ** **
68219 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAATTGAAAA
*
68239 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
68260 TCGCGTTG
1 TCGCGTTG
68268 TGATTTTTCA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.39
21 23 0.61
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:68293 original size:41 final size:41
Alignment explanation
Indices: 68194--68294 Score: 157
Period size: 41 Copynumber: 2.5 Consensus size: 41
68184 ATTCGCATTG
*
68194 CATTTCGCGTTGCGATAATTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
68235 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
**
68276 CATTTCTTGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
68295 CTATAGTTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.41
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:68453 original size:5 final size:5
Alignment explanation
Indices: 68431--68475 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
68421 CGTATTACCA
*
68431 CGACC ACGACC ACGACC CGACC CGACC CGACC CGACA CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGACC CGA
68476 GACCAGACGA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
5 26 0.70
6 11 0.30
ACGTcount: A:0.27, C:0.53, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:68997 original size:17 final size:17
Alignment explanation
Indices: 68975--69018 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
68965 TCTCGTCTCG
68975 GGTCGGGTCGGGGTCGT
1 GGTCGGGTCGGGGTCGT
*
68992 GGTCGGGTCGTGGTCGT
1 GGTCGGGTCGGGGTCGT
69009 GGTCGTGGTC
1 GGTCG-GGTC
69019 ATACGTGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.00, C:0.18, G:0.55, T:0.27
Consensus pattern (17 bp):
GGTCGGGTCGGGGTCGT
Found at i:69012 original size:23 final size:22
Alignment explanation
Indices: 68972--69018 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
68962 TCGTCTCGTC
68972 TCGGGTCGGGTCGGGGTCGTGG
1 TCGGGTCGGGTCGGGGTCGTGG
*
68994 TCGGGTCGTGGTCGTGGTCGTGG
1 TCGGGTCG-GGTCGGGGTCGTGG
69017 TC
1 TC
69019 ATACGTGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.00, C:0.19, G:0.53, T:0.28
Consensus pattern (22 bp):
TCGGGTCGGGTCGGGGTCGTGG
Found at i:69156 original size:22 final size:22
Alignment explanation
Indices: 69128--69221 Score: 131
Period size: 22 Copynumber: 4.4 Consensus size: 22
69118 AACTTGGAAA
69128 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
69150 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
69172 ATCGCAAC-A-AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
69191 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
69213 ATCGCAACG
1 ATCGCAACG
69222 CGAAATGGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 12 0.20
20 3 0.05
21 3 0.05
22 43 0.70
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:69263 original size:21 final size:21
Alignment explanation
Indices: 69237--69368 Score: 133
Period size: 21 Copynumber: 6.4 Consensus size: 21
69227 TGGAAAATCA
69237 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
69258 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
** ** * *
69279 CAACGCGAAATGGAA-AAGCG
1 CAACGCGATTTTCAACTATCG
69299 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
* ** ** *
69320 TAACGCGAAATGGAA-AATCG
1 CAACGCGATTTTCAACTATCG
*
69340 CAACGCGATTTTCAACTATTG
1 CAACGCGATTTTCAACTATCG
69361 CAACGCGA
1 CAACGCGA
69369 AATGCAACGC
Statistics
Matches: 84, Mismatches: 25, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 28 0.33
21 56 0.67
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (21 bp):
CAACGCGATTTTCAACTATCG
Found at i:69289 original size:62 final size:62
Alignment explanation
Indices: 69210--69327 Score: 209
Period size: 62 Copynumber: 1.9 Consensus size: 62
69200 ACAACTGTAG
*
69210 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCAACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAAGCACAACGCGATTTTCAACTATCGCAACGCGATTTTCA
* *
69272 ACTATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACTATCGTAACGCGA
1 ACTATCGCAACGCGAAATGGAAAAGCACAACGCGATTTTCAACTATCGCAACGCGA
69328 AATGGAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAAGCACAACGCGATTTTCAACTATCGCAACGCGATTTTCA
Found at i:69301 original size:41 final size:41
Alignment explanation
Indices: 69256--69372 Score: 207
Period size: 41 Copynumber: 2.9 Consensus size: 41
69246 TTTCAACTAT
69256 CGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAAG
1 CGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAAG
* *
69297 CGCAACGCGATTTTCAACTATCGTAACGCGAAATGGAAAAT
1 CGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAAG
*
69338 CGCAACGCGATTTTCAACTATTGCAACGCGAAATG
1 CGCAACGCGATTTTCAACTATCGCAACGCGAAATG
69373 CAACGCGAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (41 bp):
CGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAAG
Found at i:69302 original size:20 final size:20
Alignment explanation
Indices: 69275--69347 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
69265 ATTTTCAACT
69275 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
69295 AGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
69316 ATCGTAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
69336 ATCGCAACGCGA
1 ATCGCAACGCGA
69348 TTTTCAACTA
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 25 0.66
21 13 0.34
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:69376 original size:21 final size:21
Alignment explanation
Indices: 69210--69376 Score: 115
Period size: 21 Copynumber: 8.1 Consensus size: 21
69200 ACAACTGTAG
*
69210 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
69231 A-AATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
** *
69251 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
69272 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
69293 A-AAGCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
* *
69313 ACTATCGTAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
69334 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
69354 ACTATTGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
69375 AC
1 AC
69377 GCGAATTTGC
Statistics
Matches: 107, Mismatches: 36, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
20 42 0.39
21 65 0.61
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:72333 original size:15 final size:15
Alignment explanation
Indices: 72313--72342 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
72303 TTATACACAT
72313 TACTTGACAATAAAA
1 TACTTGACAATAAAA
*
72328 TACTTGGCAATAAAA
1 TACTTGACAATAAAA
72343 AAAAGTTAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (15 bp):
TACTTGACAATAAAA
Found at i:76502 original size:16 final size:16
Alignment explanation
Indices: 76481--76515 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
76471 AAGAATGGCC
76481 TAAGAAAATGATTCAT
1 TAAGAAAATGATTCAT
76497 TAAGAAAATGATTCAT
1 TAAGAAAATGATTCAT
76513 TAA
1 TAA
76516 CCTCATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.31
Consensus pattern (16 bp):
TAAGAAAATGATTCAT
Found at i:81901 original size:14 final size:14
Alignment explanation
Indices: 81872--81920 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
81862 AAGGAGAAGA
81872 TGAAAGAAAGTAAAG
1 TGAAA-AAAGTAAAG
*
81887 TGAAAAAAGTGAAG
1 TGAAAAAAGTAAAG
* *
81901 TAAAAAAAGTAAAT
1 TGAAAAAAGTAAAG
81915 TGAAAA
1 TGAAAA
81921 GTGGGATAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 24 0.83
15 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.16
Consensus pattern (14 bp):
TGAAAAAAGTAAAG
Done.