Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012247.1 Corchorus olitorius cultivar O-4 contig12280, 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: 39657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:226 original size:24 final size:24
Alignment explanation
Indices: 199--248 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
189 TTCTGAGTAC
*
199 TTTGCAACGGAATCAAAAACGAAA
1 TTTGCAACAGAATCAAAAACGAAA
* *
223 TTTGCAATAGAATCAAAAACGGAA
1 TTTGCAACAGAATCAAAAACGAAA
247 TT
1 TT
249 CTATCTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22
Consensus pattern (24 bp):
TTTGCAACAGAATCAAAAACGAAA
Found at i:4233 original size:82 final size:81
Alignment explanation
Indices: 4096--4256 Score: 286
Period size: 82 Copynumber: 2.0 Consensus size: 81
4086 ACTAGCAAAT
* *
4096 TTATTATCATTTGGAAGCGGATTTTGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAA
1 TTATTATCATTTGGAAGCGGATTTAGACACAGATATGTAGTTTCCGTGTTAAATTCCGTTT-CAA
4161 ATGAAATAAAAATTTTA
65 ATGAAATAAAAATTTTA
*
4178 TTATTATCATTTGGAAGCGGATTTAGACACAGATATGTAGTTTCCGTGTTAAATTCCGTTTCAAG
1 TTATTATCATTTGGAAGCGGATTTAGACACAGATATGTAGTTTCCGTGTTAAATTCCGTTTCAAA
4243 TGAAATAAAAATTT
66 TGAAATAAAAATTT
4257 ATTTAATCAA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 17 0.22
82 59 0.78
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (81 bp):
TTATTATCATTTGGAAGCGGATTTAGACACAGATATGTAGTTTCCGTGTTAAATTCCGTTTCAAA
TGAAATAAAAATTTTA
Found at i:6792 original size:6 final size:6
Alignment explanation
Indices: 6781--6816 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
6771 CTCCATCGGC
6781 ATATCT ATATCT ATATACT ATATCT ATATACT ATAT
1 ATATCT ATATCT ATAT-CT ATATCT ATAT-CT ATAT
6817 AAGTCTAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (6 bp):
ATATCT
Found at i:6803 original size:13 final size:13
Alignment explanation
Indices: 6781--6816 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
6771 CTCCATCGGC
6781 ATAT-CTATATCT
1 ATATACTATATCT
6793 ATATACTATATCT
1 ATATACTATATCT
6806 ATATACTATAT
1 ATATACTATAT
6817 AAGTCTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATACTATATCT
Found at i:7141 original size:25 final size:24
Alignment explanation
Indices: 7105--7151 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
7095 AATACTTACA
7105 TTAATTAAATTCTTAGGTATTTTC
1 TTAATTAAATTCTTAGGTATTTTC
7129 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
7152 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.53
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTC
Found at i:8200 original size:36 final size:36
Alignment explanation
Indices: 8153--8222 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
8143 GAGATTTTGG
* *
8153 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAAGCAAAATCACAAAAAATGTAATA
*
8189 AGAAATATGATAAGCAAAATCACAAAAGATGTAA
1 AGAAATATGATAAGCAAAATCACAAAAAATGTAA
8223 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.07, G:0.11, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAAGCAAAATCACAAAAAATGTAATA
Found at i:9591 original size:58 final size:58
Alignment explanation
Indices: 9488--9602 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
9478 ATAGCATCAT
*
9488 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
* * *
9546 GCCTCGGTCCGAAAACGTCTTTTTTAATGCATCTAAT-AAAGAACATGTCACTTGATA
1 GCCTCGGTCCGAAAACGTCTTTTTT-AGGCATCTAATAAAAAAACATGTCACTCGATA
9603 TTTGATTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 42 0.81
59 10 0.19
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (58 bp):
GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
Found at i:13119 original size:16 final size:16
Alignment explanation
Indices: 13095--13126 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13085 GATATAAGAT
*
13095 AAAATATGTATGCTAA
1 AAAAAATGTATGCTAA
13111 AAAAAATGTATGCTAA
1 AAAAAATGTATGCTAA
13127 TATAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.28
Consensus pattern (16 bp):
AAAAAATGTATGCTAA
Found at i:19171 original size:18 final size:18
Alignment explanation
Indices: 19140--19176 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
19130 GTGCCTTTCA
* *
19140 AGTTTGAGTTGCAATTTG
1 AGTTTCAGTGGCAATTTG
19158 AGTTTCAGTGGCAATTTG
1 AGTTTCAGTGGCAATTTG
19176 A
1 A
19177 AACTGATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (18 bp):
AGTTTCAGTGGCAATTTG
Found at i:22859 original size:27 final size:28
Alignment explanation
Indices: 22818--22872 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
22808 TGGCATATAC
*
22818 TCCCTTTGTTCCTTTTTACTTGTCCCTT
1 TCCCTTTGTTCCTTTTTAATTGTCCCTT
* *
22846 TCCC-TTGTTTCTTTTTAATTGTTCCTT
1 TCCCTTTGTTCCTTTTTAATTGTCCCTT
22873 ATATTTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.05, C:0.27, G:0.07, T:0.60
Consensus pattern (28 bp):
TCCCTTTGTTCCTTTTTAATTGTCCCTT
Found at i:28632 original size:13 final size:13
Alignment explanation
Indices: 28614--28638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28604 CTCTTACAAT
28614 ATACCAATACCTA
1 ATACCAATACCTA
28627 ATACCAATACCT
1 ATACCAATACCT
28639 TTTGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (13 bp):
ATACCAATACCTA
Found at i:28924 original size:13 final size:13
Alignment explanation
Indices: 28906--28955 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
28896 AATATAGTGT
28906 CAATACCTTCTGA
1 CAATACCTTCTGA
* *
28919 CAATACCTTTTGT
1 CAATACCTTCTGA
*
28932 CAATACCCTCTGA
1 CAATACCTTCTGA
* *
28945 TAATAACTTCT
1 CAATACCTTCT
28956 TGTAACACCC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (13 bp):
CAATACCTTCTGA
Found at i:28938 original size:26 final size:27
Alignment explanation
Indices: 28903--28966 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
28893 GACAATATAG
* *
28903 TGTCAATACCTTCTGACAATACCTT-T
1 TGTCAATACCCTCTGACAATAACTTCT
*
28929 TGTCAATACCCTCTGATAATAACTTCT
1 TGTCAATACCCTCTGACAATAACTTCT
*
28956 TGT-AACACCCT
1 TGTCAATACCCT
28967 ATGTTAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 29 0.88
27 4 0.12
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (27 bp):
TGTCAATACCCTCTGACAATAACTTCT
Found at i:30769 original size:39 final size:39
Alignment explanation
Indices: 30708--30834 Score: 137
Period size: 46 Copynumber: 3.1 Consensus size: 39
30698 AACTACCATA
* *
30708 TAGAGAATTCTTTTCTGAAGATGGGTGCTCATATAAGAGC
1 TAGAGTATTC-TTTCTGAAGATGGGTGCTCACATAAGAGC
*
30748 TAGAGTATTCTTTCTGAAGATGGGTGTTCACATAAGAGTTACTGC
1 TAGAGTATTCTTTCTGAAGATGGGTGCTCACAT-A-AG--A--GC
* *
30793 ATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAGGAGC
1 -TAGAGTATTCTTTCTGAAGATGGGTGCTCACATAAGAGC
30833 TA
1 TA
30835 CCGTATAGAG
Statistics
Matches: 74, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
39 23 0.31
40 12 0.16
41 2 0.03
42 1 0.01
43 1 0.01
44 1 0.01
45 3 0.04
46 31 0.42
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (39 bp):
TAGAGTATTCTTTCTGAAGATGGGTGCTCACATAAGAGC
Found at i:30819 original size:46 final size:46
Alignment explanation
Indices: 30748--30984 Score: 330
Period size: 46 Copynumber: 5.1 Consensus size: 46
30738 ATATAAGAGC
* * * ***
30748 TAGAGTATTCTTTCTGAAGATGGGTGTTCACATAAGAGTTACTGCA
1 TAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATA
* *
30794 TAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAGGAGCTACCGTA
1 TAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATA
* * *
30840 TAGAGTATTTTTTTTTCGAAGAAAGGTGCTCACATAAGAGCTACCATA
1 TAGAGTA-TTCTTTCT-GAAGAAGGGTGCTCACATAAGAGCTACCATA
30888 TAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATA
1 TAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATA
* *
30934 TAGAGTATTCTTTCTGAAAAAAGAGTGCTCACATAAGAGCTACCATA
1 TAGAGTATTCTTTCTG-AAGAAGGGTGCTCACATAAGAGCTACCATA
30981 TAGA
1 TAGA
30985 TTTCAAAAAT
Statistics
Matches: 172, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
46 93 0.54
47 44 0.26
48 35 0.20
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (46 bp):
TAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATA
Found at i:30927 original size:94 final size:91
Alignment explanation
Indices: 30700--30984 Score: 348
Period size: 94 Copynumber: 3.1 Consensus size: 91
30690 TTGCAATAAA
* * *
30700 CTACCATATAGAGAATTCTTTTCTGAAGATGGGTGCTCATATAAGAG----C--TAGAGTATTCT
1 CTACCATATAGAGTATTC-TTTCTGAAGAAGGGTGCTCACATAAGAGCTACCTATAGAGTATTCT
** *
30759 TTCTGAAGATGGGTGTTCACATAAGAG
65 TTCTGAAGAAAGGTGCTCACATAAGAG
* *** * *
30786 TTACTGCATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAGGAGCTACCGTATAGAGTATTTT
1 CTACCATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACC-TATAGAGTA-TTC
*
30851 TTTTTCGAAGAAAGGTGCTCACATAAGAG
64 TTTCT-GAAGAAAGGTGCTCACATAAGAG
30880 CTACCATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCATATAGAGTATTCT
1 CTACCATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACC-TATAGAGTATTCT
*
30945 TTCTGAAAAAAGAGTGCTCACATAAGAG
65 TTCTGAAGAAAG-GTGCTCACATAAGAG
30973 CTACCATATAGA
1 CTACCATATAGA
30985 TTTCAAAAAT
Statistics
Matches: 167, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
85 25 0.15
86 13 0.08
89 1 0.01
92 14 0.08
93 39 0.23
94 75 0.45
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (91 bp):
CTACCATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAGAGCTACCTATAGAGTATTCTT
TCTGAAGAAAGGTGCTCACATAAGAG
Found at i:31381 original size:30 final size:30
Alignment explanation
Indices: 31347--31407 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
31337 TTCCAGGACG
31347 TTGGAAGGAGGTGAGACTTCGCT-AACACCA
1 TTGGAAGGAGGTGAGACTTCG-TGAACACCA
31377 TTGGAAGGAGGTGAGACTTCGTGAACACCA
1 TTGGAAGGAGGTGAGACTTCGTGAACACCA
31407 T
1 T
31408 ATGCTTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.30, C:0.18, G:0.31, T:0.21
Consensus pattern (30 bp):
TTGGAAGGAGGTGAGACTTCGTGAACACCA
Found at i:31452 original size:44 final size:44
Alignment explanation
Indices: 31394--31581 Score: 155
Period size: 50 Copynumber: 4.4 Consensus size: 44
31384 GAGGTGAGAC
*
31394 TTCGTGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
1 TTCGCGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
*
31438 TTCGCGAACACCATATGCCTTTGACATTGAAAGA----G---G-
1 TTCGCGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
* * * * *
31474 --CACAAACACCATATG-TTTTAACGTTGAAAGAAGGTGATAGT
1 TTCGCGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
*
31515 TTCGCGAACACCATATGCCTTTGACATTGACATTGAAAGAGGGTGATAAT
1 TTCGCGAACACCATATG-C-TT----TTGACATTGAAAGAGGGTGATAGT
**
31565 TTCATGAACACCATATG
1 TTCGCGAACACCATATG
31582 TCGTTGACGT
Statistics
Matches: 112, Mismatches: 15, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
33 13 0.12
34 13 0.12
37 2 0.02
40 2 0.02
43 13 0.12
44 32 0.29
46 2 0.02
50 35 0.31
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (44 bp):
TTCGCGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
Found at i:31510 original size:77 final size:78
Alignment explanation
Indices: 31400--31544 Score: 256
Period size: 77 Copynumber: 1.9 Consensus size: 78
31390 AGACTTCGTG
* *
31400 AACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTTTCGCGAACACCATATGCCTTTGACAT
1 AACACCATATGCTTTTAACATTGAAAGAAGGTGATAGTTTCGCGAACACCATATGCCTTTGACAT
31465 TGAAAGAGGCACA
66 TGAAAGAGGCACA
*
31478 AACACCATATG-TTTTAACGTTGAAAGAAGGTGATAGTTTCGCGAACACCATATGCCTTTGACAT
1 AACACCATATGCTTTTAACATTGAAAGAAGGTGATAGTTTCGCGAACACCATATGCCTTTGACAT
31542 TGA
66 TGA
31545 CATTGAAAGA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
77 53 0.83
78 11 0.17
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (78 bp):
AACACCATATGCTTTTAACATTGAAAGAAGGTGATAGTTTCGCGAACACCATATGCCTTTGACAT
TGAAAGAGGCACA
Found at i:31784 original size:42 final size:42
Alignment explanation
Indices: 31737--31867 Score: 226
Period size: 42 Copynumber: 3.1 Consensus size: 42
31727 TTGACGCCAA
** * *
31737 ATGCCTTTATTGTCGCGAATACCATAACATATCGCGAGTACC
1 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
31779 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
1 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
31821 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
1 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
31863 ATGCC
1 ATGCC
31868 ACATGCCACT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (42 bp):
ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
Found at i:31801 original size:23 final size:23
Alignment explanation
Indices: 31768--31845 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 23
31758 CCATAACATA
*
31768 TCGCGAGTACCATGCCTTTAGCG
1 TCGCGAATACCATGCCTTTAGCG
* *
31791 TCGCGAATACCATACC---A-CA
1 TCGCGAATACCATGCCTTTAGCG
*
31810 TCGCGAGTACCATGCCTTTAGCG
1 TCGCGAATACCATGCCTTTAGCG
31833 TCGCGAATACCAT
1 TCGCGAATACCAT
31846 ACCACATCGC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 15 0.34
20 1 0.02
22 1 0.02
23 27 0.61
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (23 bp):
TCGCGAATACCATGCCTTTAGCG
Found at i:31815 original size:19 final size:19
Alignment explanation
Indices: 31749--31871 Score: 84
Period size: 19 Copynumber: 6.1 Consensus size: 19
31739 GCCTTTATTG
* *
31749 TCGCGAATACCATAACATA
1 TCGCGAATACCATACCACA
* * *
31768 TCGCGAGTACCATGCCTTTAGCG
1 TCGCGAATACCATACC---A-CA
31791 TCGCGAATACCATACCACA
1 TCGCGAATACCATACCACA
* * *
31810 TCGCGAGTACCATGCCTTTAGCG
1 TCGCGAATACCATACC---A-CA
31833 TCGCGAATACCATACCACA
1 TCGCGAATACCATACCACA
* *
31852 TCGCGAGTACCATGCCACA
1 TCGCGAATACCATACCACA
31871 T
1 T
31872 GCCACTGTAC
Statistics
Matches: 80, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
19 47 0.59
20 2 0.03
22 2 0.03
23 29 0.36
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (19 bp):
TCGCGAATACCATACCACA
Found at i:31935 original size:14 final size:14
Alignment explanation
Indices: 31916--32012 Score: 124
Period size: 14 Copynumber: 6.9 Consensus size: 14
31906 ATACTATATC
*
31916 GCGAATGCCACATT
1 GCGAATACCACATT
* *
31930 GTGAATACCACATC
1 GCGAATACCACATT
*
31944 GCGAATGCCACATT
1 GCGAATACCACATT
*
31958 GCGAATACCACATC
1 GCGAATACCACATT
*
31972 GCGAATGCCACATT
1 GCGAATACCACATT
31986 GCGAATACCACATT
1 GCGAATACCACATT
32000 G-GAAATACCACAT
1 GCG-AATACCACAT
32013 GCCTTTGATG
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
13 1 0.01
14 70 0.99
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.20
Consensus pattern (14 bp):
GCGAATACCACATT
Found at i:32012 original size:28 final size:28
Alignment explanation
Indices: 31904--31998 Score: 163
Period size: 28 Copynumber: 3.4 Consensus size: 28
31894 TTGGAAGAAG
* * *
31904 GAATACTATATCGCGAATGCCACATTGT
1 GAATACCACATCGCGAATGCCACATTGC
31932 GAATACCACATCGCGAATGCCACATTGC
1 GAATACCACATCGCGAATGCCACATTGC
31960 GAATACCACATCGCGAATGCCACATTGC
1 GAATACCACATCGCGAATGCCACATTGC
31988 GAATACCACAT
1 GAATACCACAT
31999 TGGAAATACC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (28 bp):
GAATACCACATCGCGAATGCCACATTGC
Found at i:32092 original size:53 final size:53
Alignment explanation
Indices: 32029--32172 Score: 207
Period size: 53 Copynumber: 2.7 Consensus size: 53
32019 GATGTTTGAA
* * * * *
32029 GCGAACGCCACATGCTTTTGATGTCGCCAATACCACATCGCAAATACCATATC
1 GCGAATGCCACATGCCTTTGACGTCGCGAATACCACATCGCAAATACCACATC
* * * *
32082 GCGAATGCCACATGCCTTTGACATCGCGAATACCATATTGGAAATACCACATC
1 GCGAATGCCACATGCCTTTGACGTCGCGAATACCACATCGCAAATACCACATC
32135 GCGAATGCCACATGCCTTTGACGTCGCGAATACCACAT
1 GCGAATGCCACATGCCTTTGACGTCGCGAATACCACAT
32173 GCCTTTGACG
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 80 1.00
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (53 bp):
GCGAATGCCACATGCCTTTGACGTCGCGAATACCACATCGCAAATACCACATC
Found at i:32111 original size:25 final size:25
Alignment explanation
Indices: 32079--32197 Score: 121
Period size: 25 Copynumber: 4.6 Consensus size: 25
32069 CAAATACCAT
*
32079 ATCGCGAATGCCACATGCCTTTGAC
1 ATCGCGAATACCACATGCCTTTGAC
* ** ***
32104 ATCGCGAATACCATATTGGAAATACCAC
1 ATCGCGAATACCACA-T-G-CCTTTGAC
*
32132 ATCGCGAATGCCACATGCCTTTGAC
1 ATCGCGAATACCACATGCCTTTGAC
*
32157 GTCGCGAATACCACATGCCTTTGAC
1 ATCGCGAATACCACATGCCTTTGAC
*
32182 GTCGCGAATACCACAT
1 ATCGCGAATACCACAT
32198 CACGAATGCC
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
25 55 0.73
26 2 0.03
27 2 0.03
28 16 0.21
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (25 bp):
ATCGCGAATACCACATGCCTTTGAC
Found at i:32117 original size:39 final size:39
Alignment explanation
Indices: 32063--32249 Score: 138
Period size: 39 Copynumber: 4.8 Consensus size: 39
32053 CGCCAATACC
* *
32063 ACATCGCAAATACCATATCGCGAATGCCACATGCCTTTG
1 ACATCGCGAATACCATATCGCGAATACCACATGCCTTTG
*
32102 ACATCGCGAATACCATATTG-GAAATACCACAT-CGC---G
1 ACATCGCGAATACCATATCGCG-AATACCACATGC-CTTTG
* * *
32138 A-AT-GCCACATGCCTTTGACGTCGCGAATACCACATGCCTTTG
1 ACATCGCGA-ATACC-AT-A--TCGCGAATACCACATGCCTTTG
* * * *
32180 ACGTCGCGAATACCACATCACGAATGCCACATGCCTTTG
1 ACATCGCGAATACCATATCGCGAATACCACATGCCTTTG
* * *
32219 ACGTCGCGAATA-CATATTGCAAATACCACAT
1 ACATCGCGAATACCATATCGCGAATACCACAT
32250 CGCGAATGCC
Statistics
Matches: 115, Mismatches: 19, Indels: 29
0.71 0.12 0.18
Matches are distributed among these distances:
34 3 0.03
35 6 0.05
36 3 0.03
37 1 0.01
38 16 0.14
39 73 0.63
40 2 0.02
41 1 0.01
42 2 0.02
43 5 0.04
44 3 0.03
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (39 bp):
ACATCGCGAATACCATATCGCGAATACCACATGCCTTTG
Found at i:32145 original size:14 final size:14
Alignment explanation
Indices: 32052--32147 Score: 56
Period size: 14 Copynumber: 7.1 Consensus size: 14
32042 GCTTTTGATG
*
32052 TCGCCAATACCACA
1 TCGCGAATACCACA
* *
32066 TCGCAAATACCATA
1 TCGCGAATACCACA
*
32080 TCGCGAATGCCACA
1 TCGCGAATACCACA
* ***
32094 T-GC--CTTTGACA
1 TCGCGAATACCACA
*
32105 TCGCGAATACCATA
1 TCGCGAATACCACA
*
32119 TTG-GAAATACCACA
1 TCGCG-AATACCACA
*
32133 TCGCGAATGCCACA
1 TCGCGAATACCACA
32147 T
1 T
32148 GCCTTTGACG
Statistics
Matches: 59, Mismatches: 18, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
11 5 0.08
12 2 0.03
13 3 0.05
14 48 0.81
15 1 0.02
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (14 bp):
TCGCGAATACCACA
Found at i:32250 original size:52 final size:53
Alignment explanation
Indices: 32188--32300 Score: 201
Period size: 52 Copynumber: 2.2 Consensus size: 53
32178 TGACGTCGCG
*
32188 AATACCACATCACGAATGCCACATGCCTTTGACGTCGCGAATA-CATATTGCA
1 AATACCACATCACGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
*
32240 AATACCACATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
1 AATACCACATCACGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
32293 AATACCAC
1 AATACCAC
32301 CACATGCTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 42 0.72
53 16 0.28
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (53 bp):
AATACCACATCACGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCA
Found at i:32276 original size:116 final size:117
Alignment explanation
Indices: 32066--32288 Score: 394
Period size: 116 Copynumber: 1.9 Consensus size: 117
32056 CAATACCACA
* * *
32066 TCGCAAATACCATATCGCGAATGCCACATGCCTTTGACATCGCGAATACCATATTGGAAATACCA
1 TCGCAAATACCACATCACGAATGCCACATGCCTTTGACATCGCGAATACCATATTGCAAATACCA
32131 CATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATGCCTTTGACG
66 CATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATGCCTTTGACG
* *
32183 TCGCGAATACCACATCACGAATGCCACATGCCTTTGACGTCGCGAATA-CATATTGCAAATACCA
1 TCGCAAATACCACATCACGAATGCCACATGCCTTTGACATCGCGAATACCATATTGCAAATACCA
32247 CATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACAT
66 CATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACAT
32289 TGCAAATACC
Statistics
Matches: 101, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
116 57 0.56
117 44 0.44
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.22
Consensus pattern (117 bp):
TCGCAAATACCACATCACGAATGCCACATGCCTTTGACATCGCGAATACCATATTGCAAATACCA
CATCGCGAATGCCACATGCCTTTGACGTCGCGAATACCACATGCCTTTGACG
Found at i:32281 original size:25 final size:25
Alignment explanation
Indices: 32200--32288 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 25
32190 TACCACATCA
32200 CGAATGCCACATGCCTTTGACGTCG
1 CGAATGCCACATGCCTTTGACGTCG
* * * *** *
32225 CGAAT-ACATATTGCAAATACCACATCG
1 CGAATGCCACA-TGC--CTTTGACGTCG
32252 CGAATGCCACATGCCTTTGACGTCG
1 CGAATGCCACATGCCTTTGACGTCG
*
32277 CGAATACCACAT
1 CGAATGCCACAT
32289 TGCAAATACC
Statistics
Matches: 45, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
24 3 0.07
25 25 0.56
27 14 0.31
28 3 0.07
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (25 bp):
CGAATGCCACATGCCTTTGACGTCG
Found at i:32558 original size:36 final size:38
Alignment explanation
Indices: 32518--32589 Score: 94
Period size: 39 Copynumber: 1.9 Consensus size: 38
32508 ACATAGAATG
* *
32518 TAGGCGTTGTAAG-CC-TTTTTTGAAGCTGCATAGCTA
1 TAGGCATTGTAAGCCCTTTTTTTAAAGCTGCATAGCTA
*
32554 TAGGCATTGTACGCCCTTTTTTTTAAAGCTGCATAG
1 TAGGCATTGTAAGCCC-TTTTTTTAAAGCTGCATAG
32590 GCTAGAAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 11 0.37
37 2 0.07
39 17 0.57
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (38 bp):
TAGGCATTGTAAGCCCTTTTTTTAAAGCTGCATAGCTA
Found at i:32764 original size:111 final size:111
Alignment explanation
Indices: 32585--32792 Score: 364
Period size: 111 Copynumber: 1.9 Consensus size: 111
32575 TTTAAAGCTG
*
32585 CATAGGCTAGAAGTATCAACAAAGAAGGGCACTCCTGGAGGTGCAACCAGTGCAGCACTCCTAAG
1 CATAGGCCAGAAGTATCAACAAAGAAGGGCACTCCTGGAGGTGCAACCAGTGCAGCACTCCTAAG
32650 GGTGCACTCACTCCAAGTCAAAATATAGATTTTTTTTAATGGGCTA
66 GGTGCACTCACTCCAAGTCAAAATATAGATTTTTTTTAATGGGCTA
* *
32696 CATAGGCCAGAA-TCATCAACAAGGAAGGGCACTCCTGGAGGTGCAACTAGTGCAGCACTCCTAA
1 CATAGGCCAGAAGT-ATCAACAAAGAAGGGCACTCCTGGAGGTGCAACCAGTGCAGCACTCCTAA
*
32760 GGGTGCACTCACTCCGAGTCAAAATATAGATTT
65 GGGTGCACTCACTCCAAGTCAAAATATAGATTT
32793 CTTTAACAAG
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
110 1 0.01
111 91 0.99
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (111 bp):
CATAGGCCAGAAGTATCAACAAAGAAGGGCACTCCTGGAGGTGCAACCAGTGCAGCACTCCTAAG
GGTGCACTCACTCCAAGTCAAAATATAGATTTTTTTTAATGGGCTA
Found at i:34885 original size:14 final size:13
Alignment explanation
Indices: 34853--34884 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
34843 TTTTCTAAAT
*
34853 AAAAAATTCAAAC
1 AAAAAATTCAAAA
34866 AAAAAATTCAAAA
1 AAAAAATTCAAAA
34879 AAAAAA
1 AAAAAA
34885 AACTGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATTCAAAA
Found at i:34910 original size:15 final size:17
Alignment explanation
Indices: 34880--34916 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
34870 AATTCAAAAA
34880 AAAAAAACTGAAAAACG
1 AAAAAAACTGAAAAACG
34897 AAAAAAA-TG-AAAACG
1 AAAAAAACTGAAAAACG
34912 AAAAA
1 AAAAA
34917 TGTGGTGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.76, C:0.08, G:0.11, T:0.05
Consensus pattern (17 bp):
AAAAAAACTGAAAAACG
Found at i:34916 original size:16 final size:18
Alignment explanation
Indices: 34879--34916 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
34869 AAATTCAAAA
34879 AAAAAAAACTGAAAAACG
1 AAAAAAAACTGAAAAACG
34897 -AAAAAAA-TG-AAAACG
1 AAAAAAAACTGAAAAACG
34912 AAAAA
1 AAAAA
34917 TGTGGTGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.32
16 6 0.32
17 7 0.37
ACGTcount: A:0.76, C:0.08, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAAAAAACTGAAAAACG
Found at i:36368 original size:87 final size:88
Alignment explanation
Indices: 36241--36462 Score: 234
Period size: 87 Copynumber: 2.5 Consensus size: 88
36231 GACCACTCTG
* * * ** * * *
36241 ATTTGAATTCAAAATATCCTCCACCACATCAGTTTCCAAAGATTTTGCATTATTACTAGCCATAA
1 ATTTGAATTCAAACTACCCTCCACCAAATCAGTTTCCAAAGATTTTGCACCATAACCACCCATAA
* *
36306 CTCCATTAGGAAGGTCAC-TAAA
66 CTCCATTAGAAAGATCACATAAA
* *
36328 ATTTGAATTCAAACTACCCTCTACCATAAT-ATTTTCCAAAGATTTTGCACCATAACCACCCATA
1 ATTTGAATTCAAACTACCCTCCACCA-AATCAGTTTCCAAAGATTTTGCACCATAACCACCCATA
**
36392 ACTCCATTAGAAAGATCACATTCA
65 ACTCCATTAGAAAGATCACATAAA
** ** * *
36416 A-TTGAATTCAAACTATTCTCCACCTTATCAGTTTCCACAGAATTTGC
1 ATTTGAATTCAAACTACCCTCCACCAAATCAGTTTCCAAAGATTTTGC
36463 GCCTAAAAAT
Statistics
Matches: 110, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
86 2 0.02
87 103 0.94
88 5 0.05
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.32
Consensus pattern (88 bp):
ATTTGAATTCAAACTACCCTCCACCAAATCAGTTTCCAAAGATTTTGCACCATAACCACCCATAA
CTCCATTAGAAAGATCACATAAA
Done.