Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015113.1 Corchorus olitorius cultivar O-4 contig15146, 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: 8690
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Found at i:4735 original size:54 final size:54
Alignment explanation
Indices: 4596--4739 Score: 164
Period size: 54 Copynumber: 2.7 Consensus size: 54
4586 GTACAGGGGT
* * * *
4596 TTAAAATGACCCAATGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAACAGATC
1 TTAAGATGACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAAATCTAAACAGATC
* ***
4650 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAGTTGATC
1 TTAAGATGACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAAATCTAAACAGATC
* * * *
4704 TTAAGTTGATCTAGTGCGGT-TGTTCAAAGAAGTTTT
1 TTAAGATGACCCAGTGCGGTCT-TTCATAGAAGTTTT
4740 TATGATCAGA
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 77 0.99
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (54 bp):
TTAAGATGACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAAATCTAAACAGATC
Found at i:4765 original size:35 final size:34
Alignment explanation
Indices: 4730--6148 Score: 1274
Period size: 35 Copynumber: 39.8 Consensus size: 34
4720 CGGTTGTTCA
*
4730 AAGAAGTTTTTATGATCAGAGTTGATCTCGTTTC
1 AAGAAGTTTTTATGATCAGAGTTGATCTCATTTC
*
4764 AAGAAGTTTTTTATGATTAGAGTTGATCTCATTTCC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTT-C
* *
4800 AAGAAGTTTTCGATGATCAGAGTTGATTTCATTTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
4835 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTT-C
* *
4871 AAGAAGTTTTCGATGATCAGAGTCGATCTCATTTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
*
4906 AAGAAGATTTTTATGATCAGAGTTGATCTCGTTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
*
4941 AAGAAGTGTTTGATGATCAGAGTTGATCTCATTTCC
1 AAGAAGT-TTTTATGATCAGAGTTGATCTCATTT-C
**
4977 AAGAAGTGTTCGATGATCAGAGTTGATCTCATTTC
1 AAGAAGT-TTTTATGATCAGAGTTGATCTCATTTC
* * * *
5012 CATAAGTTTTTTTATGATCAGAGTTGGTCTCCTTTC
1 AAGAAG--TTTTTATGATCAGAGTTGATCTCATTTC
*
5048 AAGAAGTTTTCGT-TGATCAGAGTTGATCTCGTTTC
1 AAGAAGTTTT--TATGATCAGAGTTGATCTCATTTC
*
5083 AAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
* * *
5118 AAGAAGTTTTCGT-TGATCAGAGTTAATATCATTCC
1 AAGAAGTTTT--TATGATCAGAGTTGATCTCATTTC
**
5153 AAGAAGTGTTTTTTTATGATCAGAGTTGATCTTGTTTC
1 AAGAA--G--TTTTTATGATCAGAGTTGATCTCATTTC
* *
5191 AAGAAGTTTTTTATGATTAGAGTTGATCTCCTTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
5226 AAGAAGTTTTCGT-TGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTT--TATGATCAGAGTTGATCTCATTTC
* * *
5261 AATAAGTTTTTTTTATGATCAGAGTTGATCTCGTTCC
1 AAGAAG---TTTTTATGATCAGAGTTGATCTCATTTC
5298 AAGAAGCTTTTTATGATCAGAGTTGATCTTC-TTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATC-TCATTTC
5333 AAGAAGTTTTGGT-TGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTT--TATGATCAGAGTTGATCTCATTTC
* *** **
5368 CAGAAGTTTTTAT--TTTTA-TT--T-TTTTTATC
1 AAGAAGTTTTTATGATCAGAGTTGATCTCATT-TC
* * * ** * * * **
5397 AGAGTAGATCTCGT-TTCAAGAAGTT--TTTAAGATC
1 A-AGAAGTTTTTATGATC-AG-AGTTGATCTCATTTC
*** * *
5431 -AG-AGTTGACATCATTTCAAGAAGTTTTTATGATCATAGTTGATCTCCTTTC
1 AAGAAGTTTTTATGA--TC-AG-AG----T-TGATC-----TCA-----TTTC
* ** *
5482 AAGAAGTTTTCGATTTTCAGAGTTGATCTCGTTTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
*
5517 AAGAAGTTTTCGT-TGATCGGAGTTGATCTCATTTC
1 AAGAAGTTTT--TATGATCAGAGTTGATCTCATTTC
* * *
5552 AAGAAGTTTTTTTTTATCAGAGTTGATCTCGTTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
*
5587 AAGAAGTTTTTATGATCAGAGTTGATCTCAGTTC
1 AAGAAGTTTTTATGATCAGAGTTGATCTCATTTC
* * *
5621 AAGAAGTTTTTTTTATGATCAAAGTTGATCTCGTTTG
1 AAGAAG---TTTTTATGATCAGAGTTGATCTCATTTC
*
5658 AAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
5693 AAGAAGTTTTCGT-TGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTT--TATGATCAGAGTTGATCTCATTTC
5728 AAGAAGTTTTTTTTTTATGATCAGAGTTGATCTCATTTC
1 AAGAAG-----TTTTTATGATCAGAGTTGATCTCATTTC
*
5767 AAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
*
5802 AAGAAGTTTTCGT-TGATCATAGTTGATCTCATTTC
1 AAGAAGTTTT--TATGATCAGAGTTGATCTCATTTC
*
5837 AAGAAGGTTTTTTTTATGATCAGAGTTGATCTCATTCC
1 AAGAA-G---TTTTTATGATCAGAGTTGATCTCATTTC
* *
5875 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTCC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
*
5910 AAGAAGTTTTCAATGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
5945 AAGAAGTTTTTATGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTTATGATCAGAGTTGATCTCATTTC
* *
5979 AAGAAGTTTTCAATGATCAGAGTTGATCTCCTTTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
* * * *
6014 AAGAAGTTTTCGATGTTTAGAGTTGATCTCGTTTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
* *
6049 AAGAAGTTTTGATGATCAGAGTTGATCTTATTTC
1 AAGAAGTTTTTATGATCAGAGTTGATCTCATTTC
*
6083 AAGAAGTTTTTTTTATGATCAGAGTTGATCTTATTTC
1 AAGAAG---TTTTTATGATCAGAGTTGATCTCATTTC
6120 AAGAAGTTTTCTATGATCAGAGTTGATCT
1 AAGAAGTTTT-TATGATCAGAGTTGATCT
6149 TCACATTGAT
Statistics
Matches: 1173, Mismatches: 122, Indels: 179
0.80 0.08 0.12
Matches are distributed among these distances:
28 3 0.00
29 3 0.00
30 7 0.01
31 8 0.01
32 4 0.00
33 2 0.00
34 146 0.12
35 644 0.55
36 143 0.12
37 93 0.08
38 53 0.05
39 37 0.03
40 5 0.00
41 1 0.00
45 5 0.00
46 3 0.00
50 2 0.00
51 4 0.00
52 4 0.00
53 4 0.00
54 2 0.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.42
Consensus pattern (34 bp):
AAGAAGTTTTTATGATCAGAGTTGATCTCATTTC
Found at i:5053 original size:177 final size:174
Alignment explanation
Indices: 4730--6148 Score: 1766
Period size: 177 Copynumber: 8.0 Consensus size: 174
4720 CGGTTGTTCA
* *
4730 AAGAAGTTTTTATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTTATGATTAGAGTTGATCTCA
1 AAGAAGTTTTTATGATCAGAGTTGATCTCGTTTCAAGAAG-TTTTGATGATCAGAGTTGATCTCA
*
4795 TTTCCAAGAAGTTTTCGATGATCAGAGTTGATTTCATTTCAAGAAG-TTTTTTATGATCAGAGTT
65 TTT-CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTATGATCAGAGTT
* *
4859 GATCTCATTTCCAAGAAGTTTTCGATGATCAGAGTCGATCTCATTTC
129 GATCTCATTT-CAAGAAGTTTTCTATGATCAGAGTTGATCTCATTTC
4906 AAGAAGATTTTTATGATCAGAGTTGATCTCGTTTCAAGAAGTGTTTGATGATCAGAGTTGATCTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCGTTTCAAGAAGT-TTTGATGATCAGAGTTGATCTC
* * *
4971 ATTTCCAAGAAGTGTTCGATGATCAGAGTTGATCTCATTTCCATAAGTTTTTTTATGATCAGAGT
64 ATTT-CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTATGATCAGAGT
* * *
5036 TGGTCTCCTTTCAAGAAGTTTTCGT-TGATCAGAGTTGATCTCGTTTC
128 TGATCTCATTTCAAGAAGTTTTC-TATGATCAGAGTTGATCTCATTTC
* * * *
5083 AAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTTAATATC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCGTTTCAAGAAGTTTT-GATGATCAGAGTTGATCTC
* ** ** *
5148 ATTCCAAGAAGTGTTTTTTTATGATCAGAGTTGATCTTGTTTCAAGAAG-TTTTTTATGATTAGA
64 ATTTCAAGAA--G-TTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTATGATCAGA
*
5212 GTTGATCTCCTTTCAAGAAGTTTTCGT-TGATCAGAGTTGATCTCATTTC
126 GTTGATCTCATTTCAAGAAGTTTTC-TATGATCAGAGTTGATCTCATTTC
* * *
5261 AATAAGTTTTTTTTATGATCAGAGTTGATCTCGTTCCAAGAAGCTTTTTATGATCAGAGTTGATC
1 AAGAAG---TTTTTATGATCAGAGTTGATCTCGTTTCAAGAAG-TTTTGATGATCAGAGTTGATC
* * *
5326 TTC-TTTCAAGAAGTTTTGGTTGATCAGAGTTGATCTCATTTCCAGAAGTTTTTATTTTTATTTT
62 -TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAG---TT-TTTTTA----
* * * *
5390 TTTTATCAGAGTAGATCTCGTTTCAAGAAGTTTT-TAAGATCAGAGTTGA-CATCATTTC
118 --TGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTATGATCAGAGTTGATC-TCATTTC
* * ** *
5448 AAGAAGTTTTTATGATCATAGTTGATCTCCTTTCAAGAAGTTTTCGATTTTCAGAGTTGATCTCG
1 AAGAAGTTTTTATGATCAGAGTTGATCTCGTTTCAAGAAGTTTT-GATGATCAGAGTTGATCTCA
* * *
5513 TTTCAAGAAGTTTTCGTTGATCGGAGTTGATCTCATTTCAAGAAGTTTTTTT-TTATCAGAGTTG
65 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTATGATCAGAGTTG
* *
5577 ATCTCGTTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCAGTTC
130 ATCTCATTTCAAGAAGTTTTCTATGATCAGAGTTGATCTCATTTC
* * *
5621 AAGAAGTTTTTTTTATGATCAAAGTTGATCTCGTTTGAAGAAGTTTTTTATGATCAGAGTTGATC
1 AAGAAG---TTTTTATGATCAGAGTTGATCTCGTTTCAAGAAG-TTTTGATGATCAGAGTTGATC
* *
5686 TCCTTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTTTTATGATCA
62 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAG---TTTTTTTATGATCA
* *
5751 GAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTC
124 GAGTTGATCTCATTTCAAGAAGTTTTCTATGATCAGAGTTGATCTCATTTC
* * *
5802 AAGAAGTTTTCGT-TGATCATAGTTGATCTCATTTCAAGAAGGTTTTTTTTATGATCAGAGTTGA
1 AAGAAGTTTT--TATGATCAGAGTTGATCTCGTTTCAAGAA-G---TTTTGATGATCAGAGTTGA
* * **
5866 TCTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTCCAAGAAG-TTTTCAATGATCAG
60 TCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTATGATCAG
5930 AGTTGATCTCATTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
125 AGTTGATCTCATTTCAAGAAGTTTTCTATGATCAGAGTTGATCTCATTTC
* * * *
5979 AAGAAGTTTTCAATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGTTTAGAGTTGATCTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCGTTTCAAGAAGTTTT-GATGATCAGAGTTGATCTC
* *
6044 GTTTCAAGAAGTTTT-GATGATCAGAGTTGATCTTATTTCAAGAAGTTTTTTTTATGATCAGAGT
64 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAG-TTTTTTTATGATCAGAGT
*
6108 TGATCTTATTTCAAGAAGTTTTCTATGATCAGAGTTGATCT
128 TGATCTCATTTCAAGAAGTTTTCTATGATCAGAGTTGATCT
6149 TCACATTGAT
Statistics
Matches: 1101, Mismatches: 95, Indels: 94
0.85 0.07 0.07
Matches are distributed among these distances:
173 89 0.08
174 30 0.03
175 36 0.03
176 126 0.11
177 279 0.25
178 135 0.12
179 59 0.05
180 91 0.08
181 37 0.03
182 72 0.07
183 6 0.01
184 87 0.08
186 2 0.00
187 24 0.02
188 28 0.03
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.42
Consensus pattern (174 bp):
AAGAAGTTTTTATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTGATGATCAGAGTTGATCTCAT
TTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTATGATCAGAGTTGA
TCTCATTTCAAGAAGTTTTCTATGATCAGAGTTGATCTCATTTC
Found at i:5123 original size:70 final size:71
Alignment explanation
Indices: 4730--6148 Score: 1634
Period size: 70 Copynumber: 19.9 Consensus size: 71
4720 CGGTTGTTCA
* *
4730 AAGAAG-TTTTTATGATCAGAGTTGATCTCGTTTCAAGAAGTTTT-TTATGATTAGAGTTGATCT
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATCT
4793 CATTTCC
66 CATTT-C
** *
4800 AAGAAGTTTTCGATGATCAGAGTTGATTTCATTTCAAGAAGTTTT-TTATGATCAGAGTTGATCT
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATCT
4864 CATTTCC
66 CATTT-C
** * *
4871 AAGAAGTTTTCGATGATCAGAGTCGATCTCATTTCAAGAAGATTT-TTATGATCAGAGTTGATCT
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATCT
*
4935 CGTTTC
66 CATTTC
* * * *
4941 AAGAAGTGTTTGATGATCAGAGTTGATCTCATTTCCAAGAAGTGTTC-GATGATCAGAGTTGATC
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTT-CAAGAAGTTTTCTTATGATCAGAGTTGATC
5005 TCATTTC
65 TCATTTC
* * * * *
5012 CATAAGTTTTTTTATGATCAGAGTTGGTCTCCTTTCAAGAAGTTTTCGT-TGATCAGAGTTGATC
1 AAGAAG-TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATC
*
5076 TCGTTTC
65 TCATTTC
* * * *
5083 AAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGT-TGATCAGAGTTAATAT
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATCT
*
5147 CATTCC
66 CATTTC
** *
5153 AAGAAGTGTTTTTTTATGATCAGAGTTGATCTTGTTTCAAGAAGTTTT-TTATGATTAGAGTTGA
1 AAGAA--G-TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGA
*
5217 TCTCCTTTC
63 TCTCATTTC
* * *
5226 AAGAAGTTTTCGT-TGATCAGAGTTGATCTCATTTCAATAAGTTTTTTTTATGATCAGAGTTGAT
1 AAGAAGTTTT-TTATGATCAGAGTTGATCTCATTTCAAGAAG-TTTTCTTATGATCAGAGTTGAT
* *
5290 CTCGTTCC
64 CTCATTTC
* **
5298 AAGAAGCTTTTTATGATCAGAGTTGATCTTC-TTTCAAGAAGTTTTGGT-TGATCAGAGTTGATC
1 AAGAAGTTTTTTATGATCAGAGTTGATC-TCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATC
5361 TCATTTC
65 TCATTTC
* * * * *
5368 CAGAAGTTTTTATTTTTATTTTTTTTATCAGAGTAGATCTCGTTTCAAGAAG-TTT-TTAAGATC
1 AAGAAG----T-TTTTTA------TGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATC
5431 AGAGTTGA-CATCATTTC
55 AGAGTTGATC-TCATTTC
* * * **
5448 AAGAAG-TTTTTATGATCATAGTTGATCTCCTTTCAAGAAGTTTTC-GATTTTCAGAGTTGATCT
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATCT
*
5511 CGTTTC
66 CATTTC
* * * *
5517 AAGAAGTTTTCGT-TGATCGGAGTTGATCTCATTTCAAGAAGTTTT-TTTTTATCAGAGTTGATC
1 AAGAAGTTTT-TTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATC
*
5580 TCGTTTC
65 TCATTTC
* * *
5587 AAGAAG-TTTTTATGATCAGAGTTGATCTCAGTTCAAGAAGTTTTTTTTATGATCAAAGTTGATC
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG-TTTTCTTATGATCAGAGTTGATC
* *
5651 TCGTTTG
65 TCATTTC
* *
5658 AAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGT-TGATCAGAGTTGATCT
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATCT
5722 CATTTC
66 CATTTC
5728 AAGAAGTTTTTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTT-TTATGATCAGAGTTG
1 AAGAAG----TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTG
*
5792 ATCTCCTTTC
62 ATCTCATTTC
* * *
5802 AAGAAGTTTTCGT-TGATCATAGTTGATCTCATTTCAAGAAGGTTTTTTTTATGATCAGAGTTGA
1 AAGAAGTTTT-TTATGATCAGAGTTGATCTCATTTCAAGAA-G-TTTTCTTATGATCAGAGTTGA
*
5866 TCTCATTCC
63 TCTCATTTC
** * *
5875 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTCCAAGAAGTTTTC-AATGATCAGAGTTGATCT
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATCT
5939 CATTTC
66 CATTTC
*
5945 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTC-AATGATCAGAGTTGATCT
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATCT
*
6008 CCTTTC
66 CATTTC
** * * * *
6014 AAGAAGTTTTCGATGTTTAGAGTTGATCTCGTTTCAAGAAG-TTT-TGATGATCAGAGTTGATCT
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATCT
*
6077 TATTTC
66 CATTTC
*
6083 AAGAAGTTTTTTTTATGATCAGAGTTGATCTTATTTCAAGAAGTTTTC-TATGATCAGAGTTGAT
1 AAGAAG--TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGAT
6147 CT
64 CT
6149 TCACATTGAT
Statistics
Matches: 1171, Mismatches: 124, Indels: 106
0.84 0.09 0.08
Matches are distributed among these distances:
68 25 0.02
69 150 0.13
70 332 0.28
71 275 0.23
72 138 0.12
73 120 0.10
74 71 0.06
75 6 0.01
79 2 0.00
80 29 0.02
81 23 0.02
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.42
Consensus pattern (71 bp):
AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAGTTGATCT
CATTTC
Found at i:6098 original size:19 final size:19
Alignment explanation
Indices: 6074--6129 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 19
6064 TCAGAGTTGA
6074 TCTTATTTCAAGAAGTTTT
1 TCTTATTTCAAGAAGTTTT
* * **
6093 TTTTATGATC-AG-AGTTGA
1 TCTTAT-TTCAAGAAGTTTT
6111 TCTTATTTCAAGAAGTTTT
1 TCTTATTTCAAGAAGTTTT
6130 CTATGATCAG
Statistics
Matches: 26, Mismatches: 8, Indels: 6
0.65 0.20 0.15
Matches are distributed among these distances:
17 2 0.08
18 11 0.42
19 11 0.42
20 2 0.08
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (19 bp):
TCTTATTTCAAGAAGTTTT
Found at i:6684 original size:18 final size:17
Alignment explanation
Indices: 6646--6711 Score: 57
Period size: 18 Copynumber: 3.9 Consensus size: 17
6636 TTCCCAACCC
6646 TAGACAGACAGACAC-A
1 TAGACAGACAGACACAA
6662 -A-ACAGACAGACACAAA
1 TAGACAGACAGACAC-AA
* * *
6678 TAGACAGACACAGATAGA
1 TAGACAGACAGACACA-A
*
6696 GAGACAGACAGACACA
1 TAGACAGACAGACACA
6712 CATTAGAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
14 12 0.32
15 1 0.03
16 1 0.03
17 2 0.05
18 22 0.58
ACGTcount: A:0.53, C:0.23, G:0.20, T:0.05
Consensus pattern (17 bp):
TAGACAGACAGACACAA
Found at i:6694 original size:14 final size:14
Alignment explanation
Indices: 6651--6701 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
6641 AACCCTAGAC
*
6651 AGACAGACACAAAC
1 AGACAGACACAAAT
6665 AGACAGACACAAAT
1 AGACAGACACAAAT
*
6679 AGACAGACACAGAT
1 AGACAGACACAAAT
*
6693 AGAGAGACA
1 AGACAGACA
6702 GACAGACACA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.55, C:0.22, G:0.20, T:0.04
Consensus pattern (14 bp):
AGACAGACACAAAT
Done.