Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016764.1 Corchorus olitorius cultivar O-4 contig16797, 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: 83277
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4557 original size:31 final size:31
Alignment explanation
Indices: 4519--4598 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
4509 GTTACTTTTG
**
4519 AGCATAAATCGGCCTTTGGTAAAAACTCTCT
1 AGCATAAATCGGCCTTTGGTAAAAACAATCT
4550 AGCATAAATCGGCCTTTGGTAAAAACAATCT
1 AGCATAAATCGGCCTTTGGTAAAAACAATCT
4581 AGCATAAATCGGCCTTTG
1 AGCATAAATCGGCCTTTG
4599 AACTAAATTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (31 bp):
AGCATAAATCGGCCTTTGGTAAAAACAATCT
Found at i:9858 original size:29 final size:29
Alignment explanation
Indices: 9802--9860 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
9792 TACTACTATT
* *
9802 AAATTTCTTTTCTATTTTTGTGCCAAAAA
1 AAATTTCTTTTCTATTTCTGTGACAAAAA
*
9831 AAATTTCTTTTCTATTTACTGT-ATAAAAA
1 AAATTTCTTTTCTATTT-CTGTGACAAAAA
9860 A
1 A
9861 TAAAAAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (29 bp):
AAATTTCTTTTCTATTTCTGTGACAAAAA
Found at i:14988 original size:7 final size:7
Alignment explanation
Indices: 14976--15012 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
14966 TTAATGTGGA
14976 TGGCTCT
1 TGGCTCT
14983 TGGCTCT
1 TGGCTCT
14990 TGGCTCT
1 TGGCTCT
14997 TGGCTCT
1 TGGCTCT
15004 TGGCTCT
1 TGGCTCT
15011 TG
1 TG
15013 CTTGGGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.00, C:0.27, G:0.30, T:0.43
Consensus pattern (7 bp):
TGGCTCT
Found at i:20856 original size:31 final size:31
Alignment explanation
Indices: 20820--20960 Score: 121
Period size: 31 Copynumber: 4.6 Consensus size: 31
20810 TACCGTACAG
20820 GTCCCTCTACTTACAAAAAGG-GATCAATTTGA
1 GTCCCTCTACTTACAAAAAGGTG-TCAA-TTGA
* * *
20852 -TCCCTTTA-TTATAAAAA-CTGTCAATTTG-
1 GTCCCTCTACTTACAAAAAGGTGTCAA-TTGA
* ***
20880 GTCCCTTTACTTACAATTTGGTGTCAATTGA
1 GTCCCTCTACTTACAAAAAGGTGTCAATTGA
***
20911 GTCCCTCTACTTACAATTTGGTGTCAATTGA
1 GTCCCTCTACTTACAAAAAGGTGTCAATTGA
20942 GTCCCTCTACTTAACAAAA
1 GTCCCTCTACTT-ACAAAA
20961 TCTATCAATT
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
29 16 0.17
30 17 0.18
31 55 0.60
32 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (31 bp):
GTCCCTCTACTTACAAAAAGGTGTCAATTGA
Found at i:21124 original size:12 final size:12
Alignment explanation
Indices: 21103--21143 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
21093 AGCTCACAAC
21103 AAAC-TCAACAG
1 AAACATCAACAG
*
21114 AAACATCAACAA
1 AAACATCAACAG
21126 AAACAT-AAGCAG
1 AAACATCAA-CAG
21138 AAACAT
1 AAACAT
21144 AAGCAACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.61, C:0.22, G:0.07, T:0.10
Consensus pattern (12 bp):
AAACATCAACAG
Found at i:21144 original size:12 final size:12
Alignment explanation
Indices: 21111--21148 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
21101 ACAAACTCAA
21111 CAGAAACATCAA-
1 CAGAAACAT-AAG
*
21123 CAAAAACATAAG
1 CAGAAACATAAG
21135 CAGAAACATAAG
1 CAGAAACATAAG
21147 CA
1 CA
21149 ACCTATGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 2 0.09
12 21 0.91
ACGTcount: A:0.61, C:0.21, G:0.11, T:0.08
Consensus pattern (12 bp):
CAGAAACATAAG
Found at i:21266 original size:29 final size:31
Alignment explanation
Indices: 21220--21296 Score: 113
Period size: 29 Copynumber: 2.5 Consensus size: 31
21210 TGACACCAAA
*
21220 TTGTAAGTAGAGGGACCAAATTGAT-AGTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
* *
21250 TTGT-AGTAGGGGGACCAAATTGATCCCTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
21280 TTGTAAGTAGAGGGACC
1 TTGTAAGTAGAGGGACC
21297 TGTACGGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 19 0.46
30 11 0.27
31 11 0.27
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.31
Consensus pattern (31 bp):
TTGTAAGTAGAGGGACCAAATTGATCACTTT
Found at i:27133 original size:42 final size:42
Alignment explanation
Indices: 27064--27144 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
27054 TTAAACGTGT
*
27064 TAATCGTGTCTTGACACGATTATGACACGAAACACGATTACCA
1 TAATCGTGTCTTGACACGATTAGGACACGAAACAC-ATTACCA
* *
27107 TAATCGTGTC-TGACACGATTCGGACACGAGACACATTA
1 TAATCGTGTCTTGACACGATTAGGACACGAAACACATTA
27145 AGCTAAACAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 4 0.11
42 21 0.60
43 10 0.29
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (42 bp):
TAATCGTGTCTTGACACGATTAGGACACGAAACACATTACCA
Found at i:35231 original size:8 final size:8
Alignment explanation
Indices: 35218--35242 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
35208 ATTAAAGCTC
35218 CAATTCTT
1 CAATTCTT
35226 CAATTCTT
1 CAATTCTT
35234 CAATTCTT
1 CAATTCTT
35242 C
1 C
35243 CTCTTGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (8 bp):
CAATTCTT
Found at i:36294 original size:41 final size:41
Alignment explanation
Indices: 36195--36387 Score: 221
Period size: 41 Copynumber: 4.7 Consensus size: 41
36185 TTAATTCAAG
* * ***
36195 GTGACAATTTCTGGTGTCAACAA-TAATTATAATTTACTGGA
1 GTGACAACTTCTGGTGTCAA-AAGTAATTTTAATTTACCAAA
*
36236 GTAAC-ACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAA
1 GTGACAACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAA
*
36276 GTGACAACTTCTGGTGTCAAAGGTAATTTTAATTTACC-AA
1 GTGACAACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAA
* ** *
36316 GATGACAACTTCTAGTGTCAGCAGTAATTTTAATTCACCAAA
1 G-TGACAACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAA
* * *
36358 ATGACAACTTCCGGTGTCAAAGGTAATTTT
1 GTGACAACTTCTGGTGTCAAAAGTAATTTT
36388 CAATATTATA
Statistics
Matches: 129, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.02
40 34 0.26
41 91 0.71
42 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (41 bp):
GTGACAACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAA
Found at i:36450 original size:15 final size:16
Alignment explanation
Indices: 36424--36453 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
36414 AGATAACAAT
36424 ATAAACAACTTAAGAA
1 ATAAACAACTTAAGAA
36440 ATAAA-AACTTAAGA
1 ATAAACAACTTAAGA
36454 TTGGAAGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (16 bp):
ATAAACAACTTAAGAA
Found at i:36810 original size:16 final size:16
Alignment explanation
Indices: 36789--36819 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36779 TGAAATCTTC
*
36789 TGATAATATTTTCTGT
1 TGATAATATTATCTGT
36805 TGATAATATTATCTG
1 TGATAATATTATCTG
36820 GAATATTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (16 bp):
TGATAATATTATCTGT
Found at i:37862 original size:17 final size:17
Alignment explanation
Indices: 37840--37877 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
37830 TTTTAAAACT
*
37840 ATTATTTTTAAATATAA
1 ATTATTTTTAAAAATAA
*
37857 ATTA-TTTTAAAAATAT
1 ATTATTTTTAAAAATAA
37873 ATTAT
1 ATTAT
37878 AAAGTAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATTTTTAAAAATAA
Found at i:37872 original size:18 final size:17
Alignment explanation
Indices: 37840--37877 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
37830 TTTTAAAACT
*
37840 ATTATTTTTAAATATAA
1 ATTATTTTAAAATATAA
*
37857 ATTATTTTAAAA-ATAT
1 ATTATTTTAAAATATAA
37873 ATTAT
1 ATTAT
37878 AAAGTAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATTTTAAAATATAA
Found at i:57687 original size:6 final size:6
Alignment explanation
Indices: 57678--57706 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
57668 ATATATATTG
57678 TTTTT- TTTTTC TTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
57707 ACAAAGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:59136 original size:17 final size:17
Alignment explanation
Indices: 59114--59147 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
59104 TGGGTGAGAA
59114 AAAACTTTCTCTACCCC
1 AAAACTTTCTCTACCCC
59131 AAAACTTTCTCTACCCC
1 AAAACTTTCTCTACCCC
59148 TCCCATGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.41, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAACTTTCTCTACCCC
Found at i:59524 original size:39 final size:39
Alignment explanation
Indices: 59481--59632 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
59471 CCACTCCAAC
*
59481 CCTTTTTCAATT-AAAAGTTTCTATTAAGTTAAATTTTCA
1 CCTTTTTC-ATTAAAAAATTTCTATTAAGTTAAATTTTCA
*
59520 CCTTTTTCATCAAAAAATTTCTATTAAGTTAAATTTTCA
1 CCTTTTTCATTAAAAAATTTCTATTAAGTTAAATTTTCA
*
59559 CATTTTTCATTAAAAAATTTCTATTAAGTTAAATTTTCA
1 CCTTTTTCATTAAAAAATTTCTATTAAGTTAAATTTTCA
*
59598 CCTTTTTCATTAAAAAATTTCTATTAAGTTGAATT
1 CCTTTTTCATTAAAAAATTTCTATTAAGTTAAATT
59633 GAAAATATGT
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 2 0.02
39 104 0.98
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (39 bp):
CCTTTTTCATTAAAAAATTTCTATTAAGTTAAATTTTCA
Found at i:61972 original size:12 final size:12
Alignment explanation
Indices: 61955--61987 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
61945 TTTAATTATA
61955 AATAAATGAATG
1 AATAAATGAATG
61967 AATAAATGAATG
1 AATAAATGAATG
61979 AATAAATGA
1 AATAAATGA
61988 TAATTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (12 bp):
AATAAATGAATG
Found at i:64175 original size:3 final size:3
Alignment explanation
Indices: 64169--64196 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
64159 AACAACAATA
64169 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
64197 ATTATCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:64214 original size:18 final size:18
Alignment explanation
Indices: 64193--64233 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
64183 GATGATGATG
64193 ATGAATTATCTAATAATA
1 ATGAATTATCTAATAATA
64211 ATGAATTATCTAATAATA
1 ATGAATTATCTAATAATA
64229 ATGAA
1 ATGAA
64234 ATTTCCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (18 bp):
ATGAATTATCTAATAATA
Found at i:65098 original size:181 final size:176
Alignment explanation
Indices: 64696--65142 Score: 495
Period size: 178 Copynumber: 2.5 Consensus size: 176
64686 CAAAATTTCG
* * * *
64696 GTTGTAGATCATGGAACAACCTTTTAAGAGACACTTGAATCATCTCAATCAAACA-CATGGAGCA
1 GTTGTAGATCATGGAACAACCTTTTAAAAGACACTTGAATCACCTCAATCAGACATC-TGAAGC-
* * * *
64760 AAAATTATGTAATATTAAGTAGATCGTACATTTCCGCTCACTGAAACAACTAATTCCGTAAGCAT
64 AAAATTATGTAATATTAAGTAGACCATACATTTCCGCTAACCGAAACAACTAATTCCGTAAGCA-
*
64825 TTTTTTTATAATTTAAACATTAAATTTAGCTTTCGAATCCCTCATAAAA
128 TTTTTTTATAATTGAAACATTAAATTTAGCTTTCGAATCCCTCATAAAA
*
64874 GTTGTAGATAATGGAACAACCTTTTAAAAGACACTTGAATCACCTCAATCAGACATCTGAAGCAA
1 GTTGTAGATCATGGAACAACCTTTTAAAAGACACTTGAATCACCTCAATCAGACATCTGAAGCAA
* * ***
64939 AAGTTATGTAATATTAAGTGGACCATACATATTCCCGTTAACCGAAACAACTAAATTTTTTTGAA
66 AA-TTATGTAATATTAAGTAGACCATACAT-TT-CCGCTAACCGAAACAACT-AA-TTCCGT-AA
* * * *
65004 GCA-TTTTTTATACTTGAAACATTAAATTTAGTTTTCGAGT-CCTCATGAAA
125 GCATTTTTTTATAATTGAAACATTAAATTTAGCTTTCGAATCCCTCATAAAA
* * * * * * * * *
65054 GTTGTAGATCATGAAACAATCTTCTAATAGACCACTTAAATCACCTTAATCGGATATCCGAAGAC
1 GTTGTAGATCATGGAACAACCTTTTAAAAGA-CACTTGAATCACCTCAATCAGACATCTGAAG-C
* * *
65119 AAAATTATATAATGTTAAATAGAC
64 AAAATTATGTAATATTAAGTAGAC
65143 TGTTTAACCA
Statistics
Matches: 227, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
177 4 0.02
178 80 0.35
179 3 0.01
180 50 0.22
181 77 0.34
182 8 0.04
183 5 0.02
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (176 bp):
GTTGTAGATCATGGAACAACCTTTTAAAAGACACTTGAATCACCTCAATCAGACATCTGAAGCAA
AATTATGTAATATTAAGTAGACCATACATTTCCGCTAACCGAAACAACTAATTCCGTAAGCATTT
TTTTATAATTGAAACATTAAATTTAGCTTTCGAATCCCTCATAAAA
Found at i:68522 original size:31 final size:32
Alignment explanation
Indices: 68473--68538 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
68463 GTTTACTAAG
*
68473 AAGATATAATAAT-GTTTTTCTACAAATTATA
1 AAGATATAATAATATTTTTTCTACAAATTATA
* * **
68504 AAGATTTAGTAATATTTTTTCTATGAATTATA
1 AAGATATAATAATATTTTTTCTACAAATTATA
68536 AAG
1 AAG
68539 GTTTTACATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 11 0.38
32 18 0.62
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (32 bp):
AAGATATAATAATATTTTTTCTACAAATTATA
Found at i:69385 original size:134 final size:131
Alignment explanation
Indices: 69128--69414 Score: 445
Period size: 134 Copynumber: 2.2 Consensus size: 131
69118 TTAATTAGTG
* *
69128 TATATTAGAATTTTTTATATATACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAA
1 TATATTAGAATTTTTTAAATATACTTTTATAGTTTTACTCAAATAAAAACTCTATTTTTATTTAA
* * *
69193 TTAAATACAATATCCTTATACCTTTTTTATTTTTACCATTTTACTATTTTCATTAAAAAAACTTT
66 TTAAATACAATATCCTTATACCTATTTTATTTTTACCATTTTACTAATTTAATT-AAAAAAC--T
*
69258 TATA
128 TAGA
69262 TATATTAGAATTTTTTAAATATACTTTTATAGTTTTACTCAAATAAAAACTCTATTTTTATTTAA
1 TATATTAGAATTTTTTAAATATACTTTTATAGTTTTACTCAAATAAAAACTCTATTTTTATTTAA
*
69327 TTAAAT-CTAATATCCTTATATCTATTTTATTTTTA-CATTTTACTAATTTAATTAAAAAACTTA
66 TTAAATAC-AATATCCTTATACCTATTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTA
69390 GA
130 GA
69392 TATATTAGAA-TTTTTAAAGTATA
1 TATATTAGAATTTTTTAAA-TATA
69415 TTTCTCAAAT
Statistics
Matches: 144, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
129 8 0.06
130 18 0.12
132 7 0.05
133 17 0.12
134 94 0.65
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (131 bp):
TATATTAGAATTTTTTAAATATACTTTTATAGTTTTACTCAAATAAAAACTCTATTTTTATTTAA
TTAAATACAATATCCTTATACCTATTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAG
A
Found at i:69622 original size:31 final size:31
Alignment explanation
Indices: 69565--69624 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
69555 ATTTTCTCGA
*
69565 GTCATTCGGGTCTCAGCTCATTTGGGTTTTG
1 GTCATTCGGGTCTCAGCTCATCTGGGTTTTG
*
69596 GTCATTCGGGTCTCAGGTC-TGCTGGGTTT
1 GTCATTCGGGTCTCAGCTCAT-CTGGGTTT
69625 AGGGTTAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.08, C:0.20, G:0.32, T:0.40
Consensus pattern (31 bp):
GTCATTCGGGTCTCAGCTCATCTGGGTTTTG
Found at i:77011 original size:5 final size:5
Alignment explanation
Indices: 77001--77045 Score: 83
Period size: 5 Copynumber: 9.2 Consensus size: 5
76991 TTCTTCTTCA
77001 TGTTT TGTTT TGTTT TGTTT TG-TT TGTTT TGTTT TGTTT TGTTT T
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT T
77046 TTTGCATCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.10
5 35 0.90
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
TGTTT
Found at i:77028 original size:19 final size:19
Alignment explanation
Indices: 77004--77049 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
76994 TTCTTCATGT
77004 TTTGTTTTGTTTTGTTTTG
1 TTTGTTTTGTTTTGTTTTG
77023 TTTGTTTTGTTTTGTTTTG
1 TTTGTTTTGTTTTGTTTTG
77042 TTT-TTTTG
1 TTTGTTTTG
77050 CATCCTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (19 bp):
TTTGTTTTGTTTTGTTTTG
Found at i:77033 original size:24 final size:23
Alignment explanation
Indices: 77001--77049 Score: 89
Period size: 24 Copynumber: 2.1 Consensus size: 23
76991 TTCTTCTTCA
77001 TGTTTTGTTTTGTTTTGTTTTGTT
1 TGTTTTGTTTTGTTTTGTTTT-TT
77025 TGTTTTGTTTTGTTTTGTTTTTT
1 TGTTTTGTTTTGTTTTGTTTTTT
77048 TG
1 TG
77050 CATCCTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (23 bp):
TGTTTTGTTTTGTTTTGTTTTTT
Found at i:77795 original size:32 final size:31
Alignment explanation
Indices: 77758--77838 Score: 83
Period size: 32 Copynumber: 2.6 Consensus size: 31
77748 TGCCCCCTCC
* * *
77758 TTCAGGTGGTAAGTTGTCTTAAATTTGTGAAG
1 TTCAGGGGGTAAGTTGTCCTAAATTTG-GAAA
* *
77790 TTCAGGGGGCTAA-CTGTCCTGAATTTGGAAA
1 TTCAGGGGG-TAAGTTGTCCTAAATTTGGAAA
*
77821 TTCAGGGGGCAAGTTGTC
1 TTCAGGGGGTAAGTTGTC
77839 GCGATTTGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
30 2 0.05
31 16 0.40
32 19 0.47
33 3 0.08
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.33
Consensus pattern (31 bp):
TTCAGGGGGTAAGTTGTCCTAAATTTGGAAA
Found at i:79433 original size:20 final size:20
Alignment explanation
Indices: 79372--79433 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
79362 GTTTATGTCC
* *
79372 GTTGAAATTAATTTGTTAGT
1 GTTGAAATTAATATGGTAGT
* * *
79392 GTTGATATT-CTAT-GT-TT
1 GTTGAAATTAATATGGTAGT
79409 GTTGAAATTAATATGGTAGT
1 GTTGAAATTAATATGGTAGT
79429 GTTGA
1 GTTGA
79434 TATTCTTATT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
17 9 0.29
18 4 0.13
19 4 0.13
20 14 0.45
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.48
Consensus pattern (20 bp):
GTTGAAATTAATATGGTAGT
Found at i:83250 original size:2 final size:2
Alignment explanation
Indices: 83243--83277 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
83233 GCATCTCTAC
83243 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.