Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019826.1 Corchorus olitorius cultivar O-4 contig19859, 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: 53876
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:9620 original size:32 final size:32
Alignment explanation
Indices: 9561--9623 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
9551 AGCTTGGATT
**
9561 TGAACAAAAATTATTGAGCCATTATGCATGAC
1 TGAACAAAAATTATTGAGCCAGAATGCATGAC
9593 TGAACAAAAATTATTGA-CCAAGAATGCATGA
1 TGAACAAAAATTATTGAGCC-AGAATGCATGA
9624 TTAAATCAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 2 0.07
32 26 0.93
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.25
Consensus pattern (32 bp):
TGAACAAAAATTATTGAGCCAGAATGCATGAC
Found at i:10373 original size:52 final size:52
Alignment explanation
Indices: 10295--10398 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
10285 CCTTATAGCA
*
10295 CTGTTGTTTATGATTGCAGATCAATGCTCAATAAATTCCAGCTGAGGGAACT
1 CTGTTGTTTATGATTACAGATCAATGCTCAATAAATTCCAGCTGAGGGAACT
10347 CTGTTGTTTATGATTACAGATCAATGCTCAATAAATTCCAGCTGAGGGAACT
1 CTGTTGTTTATGATTACAGATCAATGCTCAATAAATTCCAGCTGAGGGAACT
10399 ATGGAAATGC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (52 bp):
CTGTTGTTTATGATTACAGATCAATGCTCAATAAATTCCAGCTGAGGGAACT
Found at i:11242 original size:125 final size:125
Alignment explanation
Indices: 11105--11603 Score: 896
Period size: 124 Copynumber: 4.0 Consensus size: 125
11095 CAATGACATT
*
11105 TTGGTTCTTTTTTTTCCCCTAAAACCACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCC
1 TTGGTTC-TTTTTTCCCCCTAAAACCACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCC
11170 TTCTTAAACATAACAACAATCATCCTTTGCTCCTCCATTTTTCTTCCTTAATAAGATCTTC
65 TTCTTAAACATAACAACAATCATCCTTTGCTCCTCCATTTTTCTTCCTTAATAAGATCTTC
*
11231 TTGGTTCTTTTTTTCCCCTAAAACCACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCT
1 TTGGTTCTTTTTTCCCCCTAAAACCACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCT
*
11296 TCTTAAACATAACAACAATCATCCTTTGCTCCTCCCTTTTTCTTCCTTAATAAGATCTTC
66 TCTTAAACATAACAACAATCATCCTTTGCTCCTCCATTTTTCTTCCTTAATAAGATCTTC
11356 TTGG-T-TTTTTTCCCCCTTAAAACCACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCC
1 TTGGTTCTTTTTTCCCCC-TAAAACCACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCC
11419 TTCTTAAACATAACAACAATCATCCTTTGCTCCTCCATTTTTCTTCCTTAATAAGATCTTC
65 TTCTTAAACATAACAACAATCATCCTTTGCTCCTCCATTTTTCTTCCTTAATAAGATCTTC
*
11480 TTGGTTC-TTTTTCCCCCTAAAACAACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCT
1 TTGGTTCTTTTTTCCCCCTAAAACCACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCT
* * *
11544 TCTTAAACATAACAACAATTATCCTTTGCTCCACCCTTTTTCTTCCTTAATAAGATCTTC
66 TCTTAAACATAACAACAATCATCCTTTGCTCCTCCATTTTTCTTCCTTAATAAGATCTTC
11604 ACCCTCTCCT
Statistics
Matches: 363, Mismatches: 7, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
123 10 0.03
124 214 0.59
125 132 0.36
126 7 0.02
ACGTcount: A:0.22, C:0.31, G:0.05, T:0.42
Consensus pattern (125 bp):
TTGGTTCTTTTTTCCCCCTAAAACCACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCT
TCTTAAACATAACAACAATCATCCTTTGCTCCTCCATTTTTCTTCCTTAATAAGATCTTC
Found at i:11616 original size:100 final size:100
Alignment explanation
Indices: 11504--11703 Score: 373
Period size: 100 Copynumber: 2.0 Consensus size: 100
11494 CCCTAAAACA
* *
11504 ACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATTATCCT
1 ACCCTCTCCTTGTTAATTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCT
11569 TTGCTCCACCCTTTTTCTTCCTTAATAAGATCTTC
66 TTGCTCCACCCTTTTTCTTCCTTAATAAGATCTTC
11604 ACCCTCTCCTTGTTAATTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCT
1 ACCCTCTCCTTGTTAATTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCT
*
11669 TTGCTCCTCCCTTTTTCTTCCTTAATAAGATCTTC
66 TTGCTCCACCCTTTTTCTTCCTTAATAAGATCTTC
11704 TTGGTTCTTT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.23, C:0.33, G:0.04, T:0.41
Consensus pattern (100 bp):
ACCCTCTCCTTGTTAATTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCT
TTGCTCCACCCTTTTTCTTCCTTAATAAGATCTTC
Found at i:11741 original size:126 final size:127
Alignment explanation
Indices: 11603--11954 Score: 643
Period size: 126 Copynumber: 2.8 Consensus size: 127
11593 ATAAGATCTT
*
11603 CACCCTCTCCTTGTTAATTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCC
1 CACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCC
*
11668 TTTGCTCCTCCCTTTTTCTTCCTTAATAAGATCTTCTTGGTTCTTTTTTTTCCCC-TAAAAC
66 TTTGCTCCTCCCTTTTTCTTCCTTAATAAGATCTTCTTGGTTCTTTTTTTGCCCCATAAAAC
11729 CACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCC
1 CACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCC
*
11794 TTTGCTCCTCCATTTTTCTTCCTTAATAAGATCTTCTTGGTTCTTTTTTTGCCCCATAAAAC
66 TTTGCTCCTCCCTTTTTCTTCCTTAATAAGATCTTCTTGGTTCTTTTTTTGCCCCATAAAAC
* *
11856 CACCATCTCCATGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCC
1 CACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCC
*
11921 TTTGCTCCTCCCTTTTTCTTCCTAAATAAGATCT
66 TTTGCTCCTCCCTTTTTCTTCCTTAATAAGATCT
11955 CCACAATCAT
Statistics
Matches: 218, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
126 117 0.54
127 101 0.46
ACGTcount: A:0.23, C:0.32, G:0.05, T:0.41
Consensus pattern (127 bp):
CACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCC
TTTGCTCCTCCCTTTTTCTTCCTTAATAAGATCTTCTTGGTTCTTTTTTTGCCCCATAAAAC
Found at i:11836 original size:350 final size:350
Alignment explanation
Indices: 11255--11954 Score: 1262
Period size: 350 Copynumber: 2.0 Consensus size: 350
11245 CCCCTAAAAC
*
11255 CACCCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCC
1 CACCCTCTCCTTGTTAATTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCC
11320 TTTGCTCCTCCCTTTTTCTTCCTTAATAAGATCTTCTTGGTTTTTTTCCCCCTTAAAACCACCCT
66 TTTGCTCCTCCCTTTTTCTTCCTTAATAAGATCTTCTTGGTTTTTTTCCCCCTTAAAACCACCCT
11385 CTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCTTTGCT
131 CTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCTTTGCT
* *
11450 CCTCCATTTTTCTTCCTTAATAAGATCTTCTTGGTTC-TTTTT-CCCCCTAAAACAACCCTCTCC
196 CCTCCATTTTTCTTCCTTAATAAGATCTTCTTGGTTCTTTTTTGCCCCATAAAACAACCATCTCC
* *
11513 TTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATTATCCTTTGCTCCAC
261 ATGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCTTTGCTCCAC
*
11578 CCTTTTTCTTCCTTAATAAGATCTT
326 CCTTTTTCTTCCTAAATAAGATCTT
11603 CACCCTCTCCTTGTTAATTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCC
1 CACCCTCTCCTTGTTAATTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCC
*
11668 TTTGCTCCTCCCTTTTTCTTCCTTAATAAGATCTTCTTGGTTCTTTTTTTTCCCC-TAAAACCAC
66 TTTGCTCCTCCCTTTTTCTTCCTTAATAAGATCTTCTTGG---TTTTTTTCCCCCTTAAAACCAC
11732 CCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCTTT
128 CCTCTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCTTT
*
11797 GCTCCTCCATTTTTCTTCCTTAATAAGATCTTCTTGGTTCTTTTTTTGCCCCATAAAACCACCAT
193 GCTCCTCCATTTTTCTTCCTTAATAAGATCTTCTTGGTTC-TTTTTTGCCCCATAAAACAACCAT
11862 CTCCATGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCTTTGCT
257 CTCCATGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCTTTGCT
*
11927 CCTCCCTTTTTCTTCCTAAATAAGATCT
322 CCACCCTTTTTCTTCCTAAATAAGATCT
11955 CCACAATCAT
Statistics
Matches: 337, Mismatches: 9, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
348 104 0.31
350 114 0.34
351 11 0.03
352 5 0.01
353 103 0.31
ACGTcount: A:0.22, C:0.32, G:0.05, T:0.41
Consensus pattern (350 bp):
CACCCTCTCCTTGTTAATTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCC
TTTGCTCCTCCCTTTTTCTTCCTTAATAAGATCTTCTTGGTTTTTTTCCCCCTTAAAACCACCCT
CTCCTTGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCTTTGCT
CCTCCATTTTTCTTCCTTAATAAGATCTTCTTGGTTCTTTTTTGCCCCATAAAACAACCATCTCC
ATGTTATTTCTCGTAAACCTTCTCTCATCCTTCTTAAACATAACAACAATCATCCTTTGCTCCAC
CCTTTTTCTTCCTAAATAAGATCTT
Found at i:12778 original size:9 final size:9
Alignment explanation
Indices: 12764--12815 Score: 59
Period size: 9 Copynumber: 5.7 Consensus size: 9
12754 ATGCTATGAA
12764 AATCCTGTG
1 AATCCTGTG
*
12773 AATCCTCTG
1 AATCCTGTG
*
12782 AATTCTGGTG
1 AATCCT-GTG
*
12792 AATCCTCTG
1 AATCCTGTG
*
12801 AATCCTGCG
1 AATCCTGTG
12810 AATCCT
1 AATCCT
12816 ACAGATCCTG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
9 28 0.80
10 7 0.20
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (9 bp):
AATCCTGTG
Found at i:13588 original size:31 final size:30
Alignment explanation
Indices: 13553--13631 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
13543 AACTACAAAA
* *
13553 TTGGTCCCTCAAGTGGAGCGAAACTA-GCATT
1 TTGGTCCCTCAAGTGGA--GAAAATATGCAAT
* * *
13584 TTGGTCCCCCAAGTTGA-AAAATATGTAAT
1 TTGGTCCCTCAAGTGGAGAAAATATGCAAT
13613 TTGGTCCCTCAAGTGGAGA
1 TTGGTCCCTCAAGTGGAGA
13632 TAACTGGGCA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 5 0.13
29 18 0.46
30 1 0.03
31 15 0.38
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (30 bp):
TTGGTCCCTCAAGTGGAGAAAATATGCAAT
Found at i:13731 original size:19 final size:19
Alignment explanation
Indices: 13706--13758 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
13696 GTCAAATATC
13706 ATATTTTTTATAAAAAAAT
1 ATATTTTTTATAAAAAAAT
* * *
13725 TTATTTTTTTTAAAAATAT
1 ATATTTTTTATAAAAAAAT
13744 ATATTTTTTA-AAAAA
1 ATATTTTTTATAAAAA
13759 TTGGGTGAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 5 0.17
19 24 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTTTTTATAAAAAAAT
Found at i:13739 original size:17 final size:17
Alignment explanation
Indices: 13719--13757 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
13709 TTTTTTATAA
* *
13719 AAAAATTTATTTTTTTT
1 AAAAATATATATTTTTT
13736 AAAAATATATATTTTTT
1 AAAAATATATATTTTTT
13753 AAAAA
1 AAAAA
13758 ATTGGGTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAAAATATATATTTTTT
Found at i:14660 original size:30 final size:31
Alignment explanation
Indices: 14624--14692 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
14614 GTGCAAATGG
14624 GTCCCTGAAGTGAACG-T-AGTGAGCAATTGA
1 GTCCCTGAAGTGAA-GTTAAGTGAGCAATTGA
* *
14654 GTCCCTGAAGTGAAGTTAATTGAGCAATTGG
1 GTCCCTGAAGTGAAGTTAAGTGAGCAATTGA
14685 GTCCCTGA
1 GTCCCTGA
14693 CTATTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 1 0.03
30 15 0.43
31 19 0.54
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (31 bp):
GTCCCTGAAGTGAAGTTAAGTGAGCAATTGA
Found at i:22329 original size:31 final size:31
Alignment explanation
Indices: 22192--22318 Score: 220
Period size: 31 Copynumber: 4.1 Consensus size: 31
22182 ACTAAATACT
*
22192 AAAAAAATCTCTTATGTTTTTCTTTTGTGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGTGAC
22223 AAAAAAATCCCTTATGTTTTTCTTTTCG-GAC
1 AAAAAAATCCCTTATGTTTTTCTTTT-GTGAC
22254 AAAAAAATCCCTTATGTTTTTCTTTTGTGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGTGAC
*
22285 AAAAAAATCCCTTATGTTTTTCTTTTGAGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGTGAC
22316 AAA
1 AAA
22319 TCAGTCCCTT
Statistics
Matches: 92, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
30 1 0.01
31 90 0.98
32 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.43
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGTGAC
Found at i:23139 original size:37 final size:38
Alignment explanation
Indices: 23058--23149 Score: 109
Period size: 37 Copynumber: 2.4 Consensus size: 38
23048 ATTTATATTC
23058 AAAGAAAGCTTATTTTCTGGAAAAAAAGAAAAGAAAAG
1 AAAGAAAGCTTATTTTCTGGAAAAAAAGAAAAGAAAAG
**
23096 AAAAGAAAGCTTATTTT-T-TTAAAAAAGAAGAAGAAGAAG
1 -AAAGAAAGCTTATTTTCTGGAAAAAAAGAA-AAGAA-AAG
*
23135 -AAGAATGCTTATTTT
1 AAAGAAAGCTTATTTT
23150 ATAGTATTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
37 23 0.48
38 6 0.12
39 19 0.40
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.25
Consensus pattern (38 bp):
AAAGAAAGCTTATTTTCTGGAAAAAAAGAAAAGAAAAG
Found at i:39943 original size:187 final size:187
Alignment explanation
Indices: 39606--40164 Score: 840
Period size: 187 Copynumber: 3.0 Consensus size: 187
39596 GATACCATGT
* * *
39606 AGAAGAATTG-TTAGAAAAGATAATTTACTTCTGTTGTATTTGGTATAATATATACAACAGTGTT
1 AGAAGAATTGATTGGGAAAGATAATTTACTTCTGTTATATTTGGTATAATATATACAACAGTGTT
* * *
39670 TTGATAGAAGTAAGATACATAGAAGTTTAAACTGTACAGAATGCTATCAACTATACAACTGAATC
66 TTGATAGAAGTAGGATACATAGAAGTTTAAACTATACAGAATGCTATCAACTATACAACCGAATC
* * ** * * *
39735 TTCTTAAATCAAATAATTTTAAATTTGAATGCTGCAGATAAATGAAGATAATTTATT
131 TTCTTAAATCAAATCATTTTAAATTTGAATGTTGTGGATAAATAAAGATCATTTATC
* *
39792 AGAGGAATTGCTTGGGAAAGATAATTTACTTCTGTTATATTTGGTATAATATATACAACAGTGTT
1 AGAAGAATTGATTGGGAAAGATAATTTACTTCTGTTATATTTGGTATAATATATACAACAGTGTT
39857 TTGATAGAAGTAGGATACATAGAAGTTTAAACTATACAGAATGCTATCAACTATACAACCGAATC
66 TTGATAGAAGTAGGATACATAGAAGTTTAAACTATACAGAATGCTATCAACTATACAACCGAATC
*
39922 TTCTTAAATCAAATCATTTTAAATTTGAATATTGTGGATAAATAAAGATCATTTATC
131 TTCTTAAATCAAATCATTTTAAATTTGAATGTTGTGGATAAATAAAGATCATTTATC
* *
39979 AGAAGAATTGATTGGGAAAGATAATTTATTTCTGTTATATTTGGTATAATATATA-TACAGCGTG
1 AGAAGAATTGATTGGGAAAGATAATTTACTTCTGTTATATTTGGTATAATATATACAACA--GTG
* * * ** *
40043 TTATGATAGAAGTAGGATACAT--ACGTTTAAACTATACGGGAA-GCTATCAGTTATACAAACGA
64 TTTTGATAGAAGTAGGATACATAGAAGTTTAAACTATAC-AGAATGCTATCAACTATACAACCGA
40105 ATCTTCTTAAATCAAATCATTTTAAATTTGAATGTTGTGGATAAATAAAGATCATTTATC
128 ATCTTCTTAAATCAAATCATTTTAAATTTGAATGTTGTGGATAAATAAAGATCATTTATC
40165 CTTTACACCA
Statistics
Matches: 343, Mismatches: 26, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
186 102 0.30
187 217 0.63
188 24 0.07
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (187 bp):
AGAAGAATTGATTGGGAAAGATAATTTACTTCTGTTATATTTGGTATAATATATACAACAGTGTT
TTGATAGAAGTAGGATACATAGAAGTTTAAACTATACAGAATGCTATCAACTATACAACCGAATC
TTCTTAAATCAAATCATTTTAAATTTGAATGTTGTGGATAAATAAAGATCATTTATC
Found at i:45246 original size:129 final size:129
Alignment explanation
Indices: 45016--45274 Score: 509
Period size: 129 Copynumber: 2.0 Consensus size: 129
45006 AAATTTGAAT
*
45016 TGGCTTCAGGACAGCTAATTAATATTGATAAGTCTGTTGTACTGTTTAGTAGTAATACGTCGGAT
1 TGGCTTCAGGACAGCTAATTAATATTGATAAGTCTATTGTACTGTTTAGTAGTAATACGTCGGAT
45081 TGTCTTCGTGATTCGATTATGCGGCGGCTAGGAGTTCAGAAAGTGTTAGAGAGATATAAGTATC
66 TGTCTTCGTGATTCGATTATGCGGCGGCTAGGAGTTCAGAAAGTGTTAGAGAGATATAAGTATC
45145 TGGCTTCAGGACAGCTAATTAATATTGATAAGTCTATTGTACTGTTTAGTAGTAATACGTCGGAT
1 TGGCTTCAGGACAGCTAATTAATATTGATAAGTCTATTGTACTGTTTAGTAGTAATACGTCGGAT
45210 TGTCTTCGTGATTCGATTATGCGGCGGCTAGGAGTTCAGAAAGTGTTAGAGAGATATAAGTATC
66 TGTCTTCGTGATTCGATTATGCGGCGGCTAGGAGTTCAGAAAGTGTTAGAGAGATATAAGTATC
45274 T
1 T
45275 TGGAATGCCA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.34
Consensus pattern (129 bp):
TGGCTTCAGGACAGCTAATTAATATTGATAAGTCTATTGTACTGTTTAGTAGTAATACGTCGGAT
TGTCTTCGTGATTCGATTATGCGGCGGCTAGGAGTTCAGAAAGTGTTAGAGAGATATAAGTATC
Found at i:52462 original size:26 final size:28
Alignment explanation
Indices: 52409--52463 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
52399 ATTGAGTCTA
52409 GACTCGAAACTGACTCGAAAAAACAAACT
1 GACTCGAAACTGACTC-AAAAAACAAACT
52438 GACTC-AAACTGACT-AAAAAACAAACT
1 GACTCGAAACTGACTCAAAAAACAAACT
52464 CAAATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 12 0.46
28 9 0.35
29 5 0.19
ACGTcount: A:0.51, C:0.24, G:0.11, T:0.15
Consensus pattern (28 bp):
GACTCGAAACTGACTCAAAAAACAAACT
Done.