Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023199.1 Corchorus olitorius cultivar O-4 contig23232, 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: 35849
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8786 original size:3 final size:3
Alignment explanation
Indices: 8778--8819 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
8768 TAAATAGCAA
8778 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
8820 TAAAAATAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:10599 original size:69 final size:72
Alignment explanation
Indices: 10511--10666 Score: 171
Period size: 72 Copynumber: 2.2 Consensus size: 72
10501 GTATGGGAGT
** * *
10511 GATTTGAATTCATCCATGT-G-A-AGTTAAAGAATGATAA-ATTAGAAGATCAAGG-TTGGAATG
1 GATTTGAATTCATATATGTGGCACAGTTAAAG-ATGA-AAGATGAGAAGATAAAGGCTTGGAATG
10571 AATTA-AAAA
64 AA-TAGAAAA
* * *
10580 GATTTGAATTCATATATGTGGCACATTTAAAGATTAAAGATGAGAATATAAAGGCTTGGAATGAA
1 GATTTGAATTCATATATGTGGCACAGTTAAAGATGAAAGATGAGAAGATAAAGGCTTGGAATGAA
10645 TAGAAAA
66 TAGAAAA
*
10652 GATTTGAAATCATAT
1 GATTTGAATTCATAT
10667 GGGCCAAATT
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
69 17 0.23
70 3 0.04
71 18 0.25
72 35 0.48
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (72 bp):
GATTTGAATTCATATATGTGGCACAGTTAAAGATGAAAGATGAGAAGATAAAGGCTTGGAATGAA
TAGAAAA
Found at i:16683 original size:15 final size:16
Alignment explanation
Indices: 16652--16690 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
16642 TTTATCGTTA
16652 TCTTTTTCGTTATTTT
1 TCTTTTTCGTTATTTT
16668 TCTTTTT-GTTTATTTT
1 TCTTTTTCG-TTATTTT
*
16684 TATTTTT
1 TCTTTTT
16691 TTTTCTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.79
Consensus pattern (16 bp):
TCTTTTTCGTTATTTT
Found at i:22837 original size:76 final size:75
Alignment explanation
Indices: 22708--22858 Score: 178
Period size: 76 Copynumber: 2.0 Consensus size: 75
22698 TGATGAGCTA
* * * * *
22708 TGACACAGCCTACCTGGGTGATCAGGCGAACCACATGGGTCCTCAGTCAAACCATGTGGGCACCC
1 TGACACAGCCCACCTGGGTCATCAAGCAAACCACATGGGTCCTCAGACAAACCATGTGGGC-CCC
22773 AGGTAGAGTCG
65 AGGTAGAGTCG
* * ** * *
22784 TGACACTGCCCACCTGGGTCCTCAAGCAAACCACATGGGTGTTCAGA-ACAACCATGTGTGCGCC
1 TGACACAGCCCACCTGGGTCATCAAGCAAACCACATGGGTCCTCAGACA-AACCATGTGGGCCCC
22848 AGGTAGAGTCG
65 AGGTAGAGTCG
22859 GGGACAGCCA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
75 14 0.22
76 49 0.78
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.18
Consensus pattern (75 bp):
TGACACAGCCCACCTGGGTCATCAAGCAAACCACATGGGTCCTCAGACAAACCATGTGGGCCCCA
GGTAGAGTCG
Found at i:29638 original size:26 final size:24
Alignment explanation
Indices: 29609--29671 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 24
29599 GAGGGAAAGA
29609 AAAAAGAAAAATGAAGAAGAGAA-TTG
1 AAAAAGAAAAA--AAGAA-AGAAGTTG
29635 AAAAAGAATAGAAAAGAAAGAAGTTG
1 AAAAAGAA-A-AAAAGAAAGAAGTTG
*
29661 AAAATGAAAAA
1 AAAAAGAAAAA
29672 GATGGAGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
24 2 0.06
25 5 0.15
26 23 0.70
27 1 0.03
28 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (24 bp):
AAAAAGAAAAAAAGAAAGAAGTTG
Found at i:30009 original size:13 final size:13
Alignment explanation
Indices: 29991--30019 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29981 GTGTGGCAAA
29991 AAAAAAAAGAAGG
1 AAAAAAAAGAAGG
30004 AAAAAAAAGAAGG
1 AAAAAAAAGAAGG
30017 AAA
1 AAA
30020 TGATAATGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAGG
Found at i:31082 original size:54 final size:54
Alignment explanation
Indices: 31024--31269 Score: 352
Period size: 54 Copynumber: 4.6 Consensus size: 54
31014 GACCTAGTGT
* * * ***
31024 GGTCTTTGATAAAAGTTTTCAGAGATCTAAACAGATCTT-AGGATGACCCTGTGC
1 GGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCA-GATGACCCTGTGC
* *
31078 GGTCTTTCATAAAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGACCCTGTGC
1 GGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGC
*
31132 GGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGACCCTGTGC
1 GGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGC
* *
31186 GGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTAAGA-GACCCTTTGC
1 GGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGC
* *
31239 GGTCTTTCATAGAAGCTTTCAGAGATCTAAG
1 GGTCTTTCATAGAAGTTTTCAGAGATTTAAG
31270 CCCTGGGCGG
Statistics
Matches: 179, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
53 38 0.21
54 140 0.78
55 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (54 bp):
GGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGC
Found at i:31285 original size:92 final size:93
Alignment explanation
Indices: 31178--31362 Score: 291
Period size: 92 Copynumber: 2.0 Consensus size: 93
31168 CTTCAGATGA
* * * **
31178 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTAAGA-GACCCTTTGCGGT
1 CCCTGGGCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTAAGATGACCCAGTGCGGT
31242 CTTTCATAGAAGCTTTCAGAGATCTAAG
66 CTTTCATAGAAGCTTTCAGAGATCTAAG
*
31270 CCCTGGGCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGT
1 CCCTGGGCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTAAGATGACCCAGTGCGGT
* *
31335 CTTTCATGGAAGTTTTCAGAGATCTAAG
66 CTTTCATAGAAGCTTTCAGAGATCTAAG
31363 TTGATTTAAG
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 47 0.56
93 37 0.44
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (93 bp):
CCCTGGGCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTAAGATGACCCAGTGCGGT
CTTTCATAGAAGCTTTCAGAGATCTAAG
Found at i:31335 original size:54 final size:54
Alignment explanation
Indices: 31276--31473 Score: 253
Period size: 54 Copynumber: 3.7 Consensus size: 54
31266 TAAGCCCTGG
*
31276 GCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGT
1 GCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTCAGATGACCTAGT
* * * *
31330 GCGGTCTTTCATGGAAGTTTTCAGAGATCTAAGTTGAT-TTAAGATGACCTTGT
1 GCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTCAGATGACCTAGT
*
31383 GCGGTCTTTCATAGAAGCTTTCAGAGA--TAAGTTGATCTTCAGATGA-TTAGGT
1 GCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTCAGATGACCTA-GT
** * *
31435 GTTGTCTTTCATAGAAGTTTTTAGAGATC-AGAGTTGATC
1 GCGGTCTTTCATAGAAGCTTTCAGAGATCTA-AGTTGATC
31474 CCCAGATGGT
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
51 10 0.08
52 33 0.26
53 38 0.30
54 44 0.35
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.36
Consensus pattern (54 bp):
GCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTCAGATGACCTAGT
Found at i:31388 original size:146 final size:146
Alignment explanation
Indices: 31124--31410 Score: 479
Period size: 146 Copynumber: 2.0 Consensus size: 146
31114 CTTCAGATGA
* * * * *
31124 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGACCCTGTGCGGT
1 CCCTGGGCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGT
*
31189 CTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTAAGAGACCCTTTGCGGTCTTTCATAGAAG
66 CTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGAGACCCTTTGCGGTCTTTCATAGAAG
31254 CTTTCAGAGATCTAAG
131 CTTTCAGAGATCTAAG
31270 CCCTGGGCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGT
1 CCCTGGGCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGT
*
31335 CTTTCATGGAAGTTTTCAGAGATCTAAGTTGAT-TTAAGATGA-CCTTGTGCGGTCTTTCATAGA
66 CTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGA-GACCCTT-TGCGGTCTTTCATAGA
31398 AGCTTTCAGAGAT
129 AGCTTTCAGAGAT
31411 AAGTTGATCT
Statistics
Matches: 132, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
145 10 0.08
146 122 0.92
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (146 bp):
CCCTGGGCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGT
CTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGAGACCCTTTGCGGTCTTTCATAGAAG
CTTTCAGAGATCTAAG
Found at i:31442 original size:105 final size:106
Alignment explanation
Indices: 31276--31472 Score: 292
Period size: 105 Copynumber: 1.9 Consensus size: 106
31266 TAAGCCCTGG
31276 GCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGTCTTTCA
1 GCGGTCTTTCATAGAAGCTTTCAGAGA-CTAAGTTGATCTTCAGATGACCCAGTGCGGTCTTTCA
*
31341 TGGAAGTTTTCAGAGATCTA-AGTTGATTTAAGATGACCTTGT
65 TAGAAGTTTTCAGAGATC-AGAGTTGATTTAAGATGACCTTGT
** **
31383 GCGGTCTTTCATAGAAGCTTTCAGAGA-TAAGTTGATCTTCAGATGA-TTAGGTGTTGTCTTTCA
1 GCGGTCTTTCATAGAAGCTTTCAGAGACTAAGTTGATCTTCAGATGACCCA-GTGCGGTCTTTCA
*
31446 TAGAAGTTTTTAGAGATCAGAGTTGAT
65 TAGAAGTTTTCAGAGATCAGAGTTGAT
31473 CCCCAGATGG
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
104 2 0.02
105 53 0.65
107 27 0.33
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (106 bp):
GCGGTCTTTCATAGAAGCTTTCAGAGACTAAGTTGATCTTCAGATGACCCAGTGCGGTCTTTCAT
AGAAGTTTTCAGAGATCAGAGTTGATTTAAGATGACCTTGT
Found at i:31505 original size:54 final size:54
Alignment explanation
Indices: 31288--31618 Score: 225
Period size: 54 Copynumber: 6.2 Consensus size: 54
31278 GGTCTTTCAT
* ** * * * *
31288 AGAAGCTTTCAGAGATCTA-AGTTGATCTTCAGATGACCCAGTGCGGTC-TTTCA
1 AGAAGTTTTCAGAGATC-AGAGTTGATCCCCAGATGATCTAGTGCGATCATTCCA
* *** * * * *
31341 TGGAAGTTTTCAGAGATCTA-AGTTGAT-TTAAGATGACCTTGTGCGGTC-TTTCA
1 -AGAAGTTTTCAGAGATC-AGAGTTGATCCCCAGATGATCTAGTGCGATCATTCCA
* ** * *
31394 TAGAAGCTTTCAGAGAT-A-AGTTGATCTTCAGATGAT-TAGGTGTTG-TC-TTTCA
1 -AGAAGTTTTCAGAGATCAGAGTTGATCCCCAGATGATCTA-GTG-CGATCATTCCA
* * * *
31446 TAGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGGTCCAGTGAGATCATTCCA
1 -AGAAGTTTTCAGAGATCAGAGTTGATCCCCAGATGATCTAGTGCGATCATTCCA
* * * **
31501 AGAAGTTTTGA-ATGATTAGAGTTGATCCCCAAATGATCTAGTGCGATCATTTTA
1 AGAAGTTTTCAGA-GATCAGAGTTGATCCCCAGATGATCTAGTGCGATCATTCCA
* **
31555 AGAAGTTTTCAGTGATCAGAGTTGATCCCCAGATGATCTAGTGCGGCCATTCCA
1 AGAAGTTTTCAGAGATCAGAGTTGATCCCCAGATGATCTAGTGCGATCATTCCA
31609 AGAAGTTTTC
1 AGAAGTTTTC
31619 CTTAATCAGA
Statistics
Matches: 232, Mismatches: 35, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
51 9 0.04
52 33 0.14
53 42 0.18
54 143 0.62
55 5 0.02
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (54 bp):
AGAAGTTTTCAGAGATCAGAGTTGATCCCCAGATGATCTAGTGCGATCATTCCA
Found at i:31627 original size:54 final size:54
Alignment explanation
Indices: 31447--31642 Score: 225
Period size: 54 Copynumber: 3.6 Consensus size: 54
31437 TGTCTTTCAT
* * * *
31447 AGAAGTTTTTAGA-GATCAGAGTTGATCCCCAGATGGTCCAGTGAGATCATTCCA
1 AGAAGTTTTCA-ATGATCAGAGTTGATCCCCAGATGATCTAGTGCGATCATTCCA
* * * **
31501 AGAAGTTTTGAATGATTAGAGTTGATCCCCAAATGATCTAGTGCGATCATTTTA
1 AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCGATCATTCCA
* **
31555 AGAAGTTTTCAGTGATCAGAGTTGATCCCCAGATGATCTAGTGCGGCCATTCCA
1 AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCGATCATTCCA
** * *
31609 AGAAGTTTTCCTTAATCAGAGTTGAT-TCCAGATG
1 AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATG
31643 GTTTTCAGTG
Statistics
Matches: 121, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
53 8 0.07
54 113 0.93
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (54 bp):
AGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCGATCATTCCA
Found at i:31711 original size:84 final size:84
Alignment explanation
Indices: 31559--31727 Score: 252
Period size: 84 Copynumber: 2.0 Consensus size: 84
31549 ATTTTAAGAA
* *
31559 GTTTTCAGTGATCAGAGTTGATCCCCAGATGATCTAGTGCGGCCATTCCAAGAAGTTTTCCTTAA
1 GTTTTCAGTGATCAGAGTTGATCCCCAGATGATCCAGTGCGGCCATTCCAAGAAGTTTT-CTGAA
*
31624 TCAGAGTTGAT-TCCAGATG
65 TCAGAGTTGATCCCCAGATG
* *
31643 GTTTTCAGTGATCGGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTT-TAGAG
1 GTTTTCAGTGATCAGAGTTGATCCCCAGATGATCCAGTGCGGCCATTCCAAGAAGTTTTCT-GA-
31707 ATCAGAGTTGATCCCCAGATG
64 ATCAGAGTTGATCCCCAGATG
31728 AACCGGTGCG
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
82 1 0.01
83 1 0.01
84 68 0.88
85 7 0.09
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
GTTTTCAGTGATCAGAGTTGATCCCCAGATGATCCAGTGCGGCCATTCCAAGAAGTTTTCTGAAT
CAGAGTTGATCCCCAGATG
Found at i:31715 original size:54 final size:54
Alignment explanation
Indices: 31643--31754 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
31633 ATTCCAGATG
* * * *
31643 GTTTTCAGTGATCGGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAA
1 GTTTTCAGAGATCAGAGTTGATCCCCAGATGAACCAGTGCGATCATTCCAAGAA
* * *
31697 GTTTTTAGAGATCAGAGTTGATCCCCAGATGAACCGGTGCGATCATTCCATGAA
1 GTTTTCAGAGATCAGAGTTGATCCCCAGATGAACCAGTGCGATCATTCCAAGAA
31751 GTTT
1 GTTT
31755 ATTTTTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (54 bp):
GTTTTCAGAGATCAGAGTTGATCCCCAGATGAACCAGTGCGATCATTCCAAGAA
Found at i:31799 original size:35 final size:35
Alignment explanation
Indices: 31760--32135 Score: 495
Period size: 35 Copynumber: 10.6 Consensus size: 35
31750 AGTTTATTTT
*
31760 TTTTTTATGATCAGAGTTGATCTCGTTTCAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
31795 TTTTTTTATGATCAGAGTTGATCTCATTCCAAGAAG
1 -TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
31831 TTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* *
31866 TTTTCGT-TGATTAGAGTTGATCTCATTTCAAGAAG
1 TTTT-TTATGATCAGAGTTGATCTCATTTCAAGAAG
*
31901 TTTTTGATGATCAGAGTTGATCTCA-TTCTAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTC-AAGAAG
* **
31936 TTTTTGATGATCAGAGTTGATCTTGTTTCAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* *
31971 TTTTTTATGATCAGAGTTGATCTCCTTTTAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* * * *
32006 TTTTTGATTATCAAAGTTGATCTCATTTCAAGAAA
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
32041 TTTTTGATGATCAGAGTTGATCTCATTTCAAGAAG
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
32076 TTTTTTTTTATGATCAGAGTTGATCTCATTCCAAGAAG
1 ---TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
** * *
32114 TTTTCAATGGTCACAGTTGATC
1 TTTTTTATGATCAGAGTTGATC
32136 CCCAAAAGAT
Statistics
Matches: 302, Mismatches: 31, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
34 3 0.01
35 229 0.76
36 37 0.12
38 33 0.11
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (35 bp):
TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
Found at i:32166 original size:54 final size:54
Alignment explanation
Indices: 32101--32568 Score: 448
Period size: 54 Copynumber: 8.7 Consensus size: 54
32091 AGAGTTGATC
* *
32101 TCATTCCAAGAAGTTTTCAATGGTCACAGTTGATCCCCAAAAGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * *
32155 TCATTCTAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAAAAGGTCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * *
32209 TCATTCCAAGAAGTTGTCAATGGTCAGAGTTGATCGCC-AAAGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * * *
32262 TCATTTCAAGAAGTTTT--ATGATCAGAGTTGATCCTCAGAAGATCCCGTGCGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAAAGATCCAGTGCGG
** * *
32314 TCATTCCAAGAAGTTTTTGATGATCAGAGTTGATCTCCAAATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * ** * * *
32368 TCCTTCCGAA-AAGTTTTCGAA-GTTCAGAGTTGATGTCCAGATGATTCAGTGCGG
1 TCATTCC-AAGAAGTTTTC-AATGATCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * * * * * * **
32422 TTC-TTCCTAGAAGTTTTCAAAGATCAAAGTTGATCTCCAGATGATCCGGTGTTG
1 -TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * * * * * * *
32476 ACGTTTCAAGAAATTTTCGAA-GATCAGAGTTGATCTCCAGATGATCCAGTGTGG
1 TCATTCCAAGAAGTTTTC-AATGATCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * * *
32530 TCGTT-CAAGAAGTTTCCGATGATCAGAGTTGATCTCCAA
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAA
32569 TTTGATCCAG
Statistics
Matches: 356, Mismatches: 47, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
51 16 0.04
52 30 0.08
53 61 0.17
54 242 0.68
55 7 0.02
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (54 bp):
TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAAAGATCCAGTGCGG
Found at i:32385 original size:213 final size:215
Alignment explanation
Indices: 32101--32579 Score: 540
Period size: 213 Copynumber: 2.2 Consensus size: 215
32091 AGAGTTGATC
* * * * * *
32101 TCATTCCAAGAAGTTTTCAATGGTCACAGTTGATCCCCAAAAGATCCAGTGCGGTCATTCTAAGA
1 TCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCCAAATGATCCAGTGCGGTCATTCGAAGA
*
32166 AGTTTTC-AATGGTCAGAGTTGATCCCCAAAAGGTCCAGTGCGG-TCATTCCAAGAAGTTGTCAA
66 AGTTTTCGAA-GGTCAGAGTTGATCCCCAAAAGATCCAGTGCGGTTC-TTCCAAGAAGTTGTCAA
* * * * * *
32229 TGGTCAGAGTTGATCGCCA-AAGATCCAGTGCGGTCATTTCAAGAAGTTTT-ATGATCAGAGTTG
129 AGATCAAAGTTGATCGCCAGAAGATCCAGTGCGGACATTTCAAGAAATTTTCAAGATCAGAGTTG
*
32292 ATC-CTCAGAAGATCCCGTGCGG
194 ATCTC-CAGAAGATCCAGTGCGG
* *
32314 TCATTCCAAGAAGTTTTTGATGATCAGAGTTGATCTCCAAATGATCCAGTGCGGTCCTTCCGAA-
1 TCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCCAAATGATCCAGTGCGGTCATT-CGAAG
* ** * * * * *
32378 AAGTTTTCGAAGTTCAGAGTTGATGTCCAGATGATTCAGTGCGGTTCTTCCTAGAAGTTTTCAAA
65 AAGTTTTCGAAGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGGTTCTTCCAAGAAGTTGTCAAA
* * * ** *
32443 GATCAAAGTTGATCTCCAGATGATCCGGTGTTGACGTTTCAAGAAATTTTCGAAGATCAGAGTTG
130 GATCAAAGTTGATCGCCAGAAGATCCAGTGCGGACATTTCAAGAAATTTTC-AAGATCAGAGTTG
* *
32508 ATCTCCAGATGATCCAGTGTGG
194 ATCTCCAGAAGATCCAGTGCGG
* * *
32530 TCGTT-CAAGAAGTTTCCGATGATCAGAGTTGATCTCCAATTTGATCCAGT
1 TCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCCAA-ATGATCCAGT
32580 ATGGTCACTT
Statistics
Matches: 222, Mismatches: 36, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
213 116 0.52
214 31 0.14
215 32 0.14
216 42 0.19
217 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (215 bp):
TCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCCAAATGATCCAGTGCGGTCATTCGAAGA
AGTTTTCGAAGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGGTTCTTCCAAGAAGTTGTCAAAG
ATCAAAGTTGATCGCCAGAAGATCCAGTGCGGACATTTCAAGAAATTTTCAAGATCAGAGTTGAT
CTCCAGAAGATCCAGTGCGG
Found at i:32434 original size:108 final size:107
Alignment explanation
Indices: 32101--32595 Score: 507
Period size: 108 Copynumber: 4.6 Consensus size: 107
32091 AGAGTTGATC
* * * *
32101 TCATTCCAAGAAGTTTTCAATGGTCACAGTTGATCCCCAAAAGATCCAGTGCGGTCA-TTCTAAG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAATGATCCAGTGCGGTCATTTC-AAG
* * *
32165 AAGTTTTCAATGGTCAGAGTTGATCCCCAAAAGGTCCAGTGCGG
65 AAGTTTTCAA-GATCAGAGTTGATCCCCAGAAGATCCAGTGCGG
* * *
32209 TCATTCCAAGAAGTTGTCAATGGTCAGAGTTGATCGCCAAA-GATCCAGTGCGGTCATTTCAAGA
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAATGATCCAGTGCGGTCATTTCAAGA
* * *
32273 AGTTTT-ATGATCAGAGTTGATCCTCAGAAGATCCCGTGCGG
66 AGTTTTCAAGATCAGAGTTGATCCCCAGAAGATCCAGTGCGG
** * *
32314 TCATTCCAAGAAGTTTTTGATGATCAGAGTTGATCTCCAAATGATCCAGTGCGGTCCTTCCGAA-
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAATGATCCAGTGCGGTCATTTC-AAG
* ** * *
32378 AAGTTTTCGAAGTTCAGAGTTGATGTCCAGATGATTCAGTGCGG
65 AAGTTTTC-AAGATCAGAGTTGATCCCCAGAAGATCCAGTGCGG
* * * * * ** * *
32422 TTC-TTCCTAGAAGTTTTCAAAGATCAAAGTTGATCTCCAGATGATCCGGTGTTGACGTTTCAAG
1 -TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAATGATCCAGTGCGGTCATTTCAAG
* * * *
32486 AAATTTTCGAAGATCAGAGTTGATCTCCAGATGATCCAGTGTGG
65 AAGTTTTC-AAGATCAGAGTTGATCCCCAGAAGATCCAGTGCGG
* * * * ** *
32530 TCGTT-CAAGAAGTTTCCGATGATCAGAGTTGATCTCCAATTTGATCCAGTATGGTCACTTCAAG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAA-ATGATCCAGTGCGGTCATTTCAAG
32594 AA
65 AA
32596 AGGTTTCCGT
Statistics
Matches: 324, Mismatches: 54, Indels: 18
0.82 0.14 0.05
Matches are distributed among these distances:
105 64 0.20
106 25 0.08
107 59 0.18
108 174 0.54
109 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (107 bp):
TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAATGATCCAGTGCGGTCATTTCAAGA
AGTTTTCAAGATCAGAGTTGATCCCCAGAAGATCCAGTGCGG
Found at i:32575 original size:54 final size:52
Alignment explanation
Indices: 32101--32652 Score: 425
Period size: 54 Copynumber: 10.3 Consensus size: 52
32091 AGAGTTGATC
* * * * *
32101 TCATTCCAAGAAGTTTTCAATGGTCACAGTTGATCCCCAAAAGATCCAGTGCGG
1 TCATT-CAAGAAGTTTTCGATGATCAGAGTTGATCTCC-AATGATCCAGTGCGG
* * * * *
32155 TCATTCTAAGAAGTTTTCAATGGTCAGAGTTGATCCCCAAAAGGTCCAGTGCGG
1 TCATTC-AAGAAGTTTTCGATGATCAGAGTTGATCTCC-AATGATCCAGTGCGG
* * * * *
32209 TCATTCCAAGAAGTTGTCAATGGTCAGAGTTGATCGCCAAAGATCCAGTGCGG
1 TCATT-CAAGAAGTTTTCGATGATCAGAGTTGATCTCCAATGATCCAGTGCGG
* *
32262 TCATTTCAAGAAGTTTT--ATGATCAGAGTTGATC-CTCAGAAGATCCCGTGCGG
1 TCA-TTCAAGAAGTTTTCGATGATCAGAGTTGATCTC-CA-ATGATCCAGTGCGG
*
32314 TCATTCCAAGAAGTTTTTGATGATCAGAGTTGATCTCCAAATGATCCAGTGCGG
1 TCATT-CAAGAAGTTTTCGATGATCAGAGTTGATCTCC-AATGATCCAGTGCGG
* * * * *
32368 TCCTTCCGAA-AAGTTTTCGAAGTTCAGAGTTGATGTCCAGATGATTCAGTGCGG
1 TCATT-C-AAGAAGTTTTCGATGATCAGAGTTGATCTCCA-ATGATCCAGTGCGG
* * * * * **
32422 TTC-TTCCTAGAAGTTTTCAAAGATCAAAGTTGATCTCCAGATGATCCGGTGTTG
1 -TCATT-CAAGAAGTTTTCGATGATCAGAGTTGATCTCCA-ATGATCCAGTGCGG
* * * * *
32476 ACGTTTCAAGAAATTTTCGAAGATCAGAGTTGATCTCCAGATGATCCAGTGTGG
1 TC-ATTCAAGAAGTTTTCGATGATCAGAGTTGATCTCCA-ATGATCCAGTGCGG
* * **
32530 TCGTTCAAGAAGTTTCCGATGATCAGAGTTGATCTCCAATTTGATCCAGTATGG
1 TCATTCAAGAAGTTTTCGATGATCAGAGTTGATCTCCAA--TGATCCAGTGCGG
* * **
32584 TCACTTCAAGAAAGGTTTCCG-TGATC-GAGGTTCCATCTTAAATGATCCAGTGCGG
1 TCA-TTCAAG-AA-GTTTTCGATGATCAGA-GTT-GATCTCCAATGATCCAGTGCGG
* *
32639 TTATTTAAGAAGTT
1 TCATTCAAGAAGTT
32653 CAAGTTTGAA
Statistics
Matches: 429, Mismatches: 46, Indels: 48
0.82 0.09 0.09
Matches are distributed among these distances:
50 1 0.00
51 19 0.04
52 31 0.07
53 65 0.15
54 260 0.61
55 30 0.07
56 10 0.02
57 13 0.03
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (52 bp):
TCATTCAAGAAGTTTTCGATGATCAGAGTTGATCTCCAATGATCCAGTGCGG
Done.