Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007242.1 Hibiscus syriacus cultivar Beakdansim tig00019192_pilon, 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: 62466
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:9628 original size:21 final size:22
Alignment explanation
Indices: 9603--9679 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 22
9593 ATACTTTTAT
*
9603 ATTTATGTCATAATT-TATTAA
1 ATTTATATCATAATTATATTAA
*
9624 ATTTATATGATAATTATATTTAA
1 ATTTATATCATAATTATA-TTAA
* *
9647 A---ATATAATATATTATATTAT
1 ATTTATATCATA-ATTATATTAA
9667 ATTATATATCATA
1 ATT-TATATCATA
9680 TTAAACTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
20 11 0.25
21 19 0.43
22 2 0.05
23 5 0.11
24 7 0.16
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (22 bp):
ATTTATATCATAATTATATTAA
Found at i:9674 original size:17 final size:17
Alignment explanation
Indices: 9648--9682 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9638 TATATTTAAA
*
9648 ATATAATATATTATATT
1 ATATAATATATCATATT
*
9665 ATATTATATATCATATT
1 ATATAATATATCATATT
9682 A
1 A
9683 AACTTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATAATATATCATATT
Found at i:15735 original size:21 final size:22
Alignment explanation
Indices: 15688--15737 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
15678 ATTTGTAAAT
15688 ATTAAATTTAAAAAATATATTC
1 ATTAAATTTAAAAAATATATTC
*
15710 A--AAATTTTAAAAA-ATATTC
1 ATTAAATTTAAAAAATATATTC
15729 ATTAAATTT
1 ATTAAATTT
15738 CTTAAAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 7 0.28
20 11 0.44
21 6 0.24
22 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTAAATTTAAAAAATATATTC
Found at i:15939 original size:13 final size:13
Alignment explanation
Indices: 15918--15981 Score: 74
Period size: 13 Copynumber: 4.9 Consensus size: 13
15908 ATAAAACAAC
15918 TAATCAAATCAAT
1 TAATCAAATCAAT
** *
15931 TTCTCAAATCAAC
1 TAATCAAATCAAT
*
15944 TAATCAAATTAAT
1 TAATCAAATCAAT
15957 TAATCAAATCAAT
1 TAATCAAATCAAT
* *
15970 TATTGAAATCAA
1 TAATCAAATCAA
15982 CTACCAGCTA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.33
Consensus pattern (13 bp):
TAATCAAATCAAT
Found at i:15943 original size:26 final size:26
Alignment explanation
Indices: 15914--15968 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
15904 CTATATAAAA
**
15914 CAACTAATCAAATCAATTTCTCAAAT
1 CAACTAATCAAATCAATTAATCAAAT
*
15940 CAACTAATCAAATTAATTAATCAAAT
1 CAACTAATCAAATCAATTAATCAAAT
15966 CAA
1 CAA
15969 TTATTGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (26 bp):
CAACTAATCAAATCAATTAATCAAAT
Found at i:21698 original size:2 final size:2
Alignment explanation
Indices: 21688--21719 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
21678 AAAGTTAAGA
*
21688 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21720 TTGAGTGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26911 original size:23 final size:25
Alignment explanation
Indices: 26879--26929 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
26869 TCATCATTAG
* *
26879 AATGATT-AAAATTTGACTCGATTT
1 AATGATTAAAAATTCGACTCGATCT
26903 AATG-TTAAAAATTCGACTCGATCT
1 AATGATTAAAAATTCGACTCGATCT
26927 AAT
1 AAT
26930 TCGACTCGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (25 bp):
AATGATTAAAAATTCGACTCGATCT
Found at i:28695 original size:31 final size:29
Alignment explanation
Indices: 28629--28695 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
28619 GAGTAACAAC
* * * *
28629 TCAGTGACCTAAAACTAATTTTATTAAGT
1 TCAGTGACCAAAAACTAAATGTATAAAGT
*
28658 TTAGTGACCAAAAAAGCTAAATGTATAAAGT
1 TCAGTGACC-AAAAA-CTAAATGTATAAAGT
28689 TCAGTGA
1 TCAGTGA
28696 TGAAATTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 8 0.27
30 4 0.13
31 18 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (29 bp):
TCAGTGACCAAAAACTAAATGTATAAAGT
Found at i:33629 original size:21 final size:20
Alignment explanation
Indices: 33603--33663 Score: 52
Period size: 23 Copynumber: 2.9 Consensus size: 20
33593 TTAAGAGTGT
33603 AATTTATTAAATAAAATATA
1 AATTTATTAAATAAAATATA
*
33623 GAATTTAATATATATAAAGAT-TA
1 -AATTT-AT-TAAATAAA-ATATA
**
33646 TTTTTATTAAATAAAATA
1 AATTTATTAAATAAAATA
33664 GAAAAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
19 2 0.06
20 7 0.22
21 7 0.22
22 5 0.16
23 9 0.28
24 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (20 bp):
AATTTATTAAATAAAATATA
Found at i:34886 original size:31 final size:31
Alignment explanation
Indices: 34846--34917 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
34836 GACGATAAAG
*
34846 TGATCATTTTATTATAAATCAATAATATTAA
1 TGATTATTTTATTATAAATCAATAATATTAA
34877 TGATTATTTTATTATAAATCAATAATATTAA
1 TGATTATTTTATTATAAATCAATAATATTAA
34908 TGATTGATTT
1 TGATT-ATTT
34918 GTTATTTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 35 0.90
32 4 0.10
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (31 bp):
TGATTATTTTATTATAAATCAATAATATTAA
Found at i:41422 original size:29 final size:29
Alignment explanation
Indices: 41390--41454 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
41380 TTTTTTTGTT
***
41390 AAAATAAAAATATAATTTATTTTTTAATC
1 AAAATAAAAATATAAAGAATTTTTTAATC
* * *
41419 AAAATAGATATTTAAAGAATTTTTTAATC
1 AAAATAAAAATATAAAGAATTTTTTAATC
41448 AAAATAA
1 AAAATAA
41455 GTATTCAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAATAAAAATATAAAGAATTTTTTAATC
Found at i:41459 original size:29 final size:29
Alignment explanation
Indices: 41408--41469 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
41398 AATATAATTT
*
41408 ATTTTTTAATCAAAATAGATATTTAAAGA
1 ATTTTTTAATCAAAATAGATATTCAAAGA
*
41437 ATTTTTTAATCAAAATA-AGTATTCAAAGT
1 ATTTTTTAATCAAAATAGA-TATTCAAAGA
41466 ATTT
1 ATTT
41470 AACTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (29 bp):
ATTTTTTAATCAAAATAGATATTCAAAGA
Found at i:43443 original size:222 final size:222
Alignment explanation
Indices: 42917--45150 Score: 3284
Period size: 222 Copynumber: 10.1 Consensus size: 222
42907 AAGAGGTGTC
* *
42917 GTCGATGGAGAAATTGGTGAAAGATAAATTGGAGGAAGTTGGATTGAAAGAGAAATATTTGGAGA
1 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAAGATTTGGAGA
* *
42982 GATGCTTGAGAGAGCATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAAG
66 AATGCTTGAGAGAGTATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAAG
* * *
43047 CGATTTATGGAGTTTGAGTTGGAATAAAAGGCTTCGAAAGAGCGTCTTCGAGATCTTGGAGTTTA
131 CGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAGAGAGTCTTCGAGATCTT-GAGTTTA
* *
43112 GTGTGAAACACCGCGAGGATGAGGTTAA
195 GTGTGAAACAACGTGAGGATGAGGTTAA
43140 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTG-AAGTAGAAAGATTTGGAG
1 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAG-AGAAAGATTTGGAG
* * * * *
43204 AGATGCTTGAGAGAGTATGAGTTGAAAGAAGAGCAATTTGGGCTGAAAGAAAAGAGTTTCAAGAA
65 AAATGCTTGAGAGAGTATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAA
* * * *
43269 GCAATTTATGGAGTTTGAGTTGGAAGAAGAGGCTTCGAAAGTA-AGTCTTCGAGATCTTGAGTGT
130 GCGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAG-AGAGTCTTCGAGATCTTGAGTTT
**
43333 AGTGTGAAACAATATGAGGATGAGGTTAA
194 AGTGTGAAACAACGTGAGGATGAGGTTAA
* *
43362 GTCGATGTAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAAGGTTTGGAGA
1 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAAGATTTGGAGA
* * * * *
43427 GATGCTTGAAAGAGTATGAGTTGAAAGAAGAGCAATTAGGGTCGAAAGATAAGAGTTTCGAGAAG
66 AATGCTTGAGAGAGTATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAAG
* * * * *
43492 AGATTTACAGAATTTGAGTTGGAAGAAAAGGCTTCGAAAGAGCGTCTTCGAGATCATGAGTTTAG
131 CGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAGAGAGTCTTCGAGATCTTGAGTTTAG
* *
43557 TGTGAAACACCGCGAGGATGAGGTTAA
196 TGTGAAACAACGTGAGGATGAGGTTAA
*
43584 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAGGAGAAAGATTTGGAGA
1 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAAGATTTGGAGA
* *
43649 AATGCTTGAGAGAGTATGAGTTGAAAGAAGAGCAATTCGGGTT-AAAGAAAAGAGTTTTGAGAAG
66 AATGCTTGAGAGAGTATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAAG
* * * * * *
43713 CGATTTATGGAGTTTGAGTTGGAAGAAAAGGATTTGAAAGAAAGTCTTCAAGATCTTGAGTTTAA
131 CGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAGAGAGTCTTCGAGATCTTGAGTTTAG
*
43778 TGTGAAACAAAGTGAGGATGAGGTTAA
196 TGTGAAACAACGTGAGGATGAGGTTAA
43805 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAAGATTTGGAGA
1 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAAGATTTGGAGA
* *
43870 AATGCTTGTTG-GAGTATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCAAGAA
66 AATGCTTG-AGAGAGTATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAA
* *
43934 GCGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAGAGCGTCTTCGAGATCGTGAGTTTA
130 GCGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAGAGAGTCTTCGAGATCTTGAGTTTA
*
43999 GTGTGAAAAAACGTGAGGATGAGGTTAA
195 GTGTGAAACAACGTGAGGATGAGGTTAA
* * *
44027 GTCGATGGATAAATTGATGAAAGATAAGTTGGAGGAAGTTGAATTGAAAGAGAAAGATTTGGAGA
1 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAAGATTTGGAGA
* * *
44092 AATGCTTGTTGA-AGTATGGGTTGAAAGAATAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAA
66 AATGCTTG-AGAGAGTATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAA
** * *
44156 ATGATTTATGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAGTA-AGTCTTTGAGATCTTGAGTTT
130 GCGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAG-AGAGTCTTCGAGATCTTGAGTTT
* *
44220 AGTGTAAAACAACGTGGGGATGAGGTTAA
194 AGTGTGAAACAACGTGAGGATGAGGTTAA
* * *
44249 GTCAATGGAGAAATTGGTGAAAAATAAGTTGGAGGAAGTTGGATTGAAGGAGAAAGATTTGGAGA
1 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAAGATTTGGAGA
*
44314 AATGCTTGCTG-GAGTATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAA
66 AATGCTTG-AGAGAGTATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAA
* * * *
44378 GCGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCAAAAGAGCGTTTTTGAGATCTTGAGTTTA
130 GCGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAGAGAGTCTTCGAGATCTTGAGTTTA
**
44443 GTGTGAAACGTCGTGAGGATGAGGTTAA
195 GTGTGAAACAACGTGAGGATGAGGTTAA
44471 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAA-AGTTTGGAG
1 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAAGA-TTTGGAG
* * * * *
44535 AGATGCTTGAAAGAGTATGAGTTGAAAGAAGAGCAATTAGGGTCGAAAGAGAAGAGTTTTGAGAA
65 AAATGCTTGAGAGAGTATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAA
* * * * ** *
44600 GAGATTTACAGAATTTGAGTTGGAAGAAAAGGCTTCGAAAAAGCTTCTTTGAGATCTTGAGTTTA
130 GCGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAGAGAGTCTTCGAGATCTTGAGTTTA
* *
44665 TTGTGAAACAACGTGGGGATGAGGTTAA
195 GTGTGAAACAACGTGAGGATGAGGTTAA
* * *
44693 GTCTACT-GAGAAATTGGTGAAAGATAAGTTGGAGGATGTTGGATTGAAGGAGAAAGATTTGGAG
1 GTCGA-TGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAAGATTTGGAG
* * * * *
44757 AAATGCTTGCTG-GAGTATGAATGGAAAGAAGAGAAATTTGGGTTGAAAGAGAAGAGTTTCGAGA
65 AAATGCTTG-AGAGAGTATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGA
* *
44821 AGCGATTTACGGAGTTTAAGTTGGAAGAAAAAGCTTCGAAAGA-ACGTCTTCGAGATCTTGAGTT
129 AGCGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAGAGA-GTCTTCGAGATCTTGAGTT
* *
44885 TAGTGTGAAACAACATGAGGACGAGGTTAA
193 TAGTGTGAAACAACGTGAGGATGAGGTTAA
* * * *
44915 GTCGATGGAGAAATTAGTAAAAGATAAGTTGGAGGAAGTTGGATTGAAGGAGAAAGACTTGGAGA
1 GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAAGATTTGGAGA
* * *
44980 AATGTTTGAGAGAGTATTGAGTTGAAAGAAGAGCAATTCGGGCTGAAAGAGAATAGTTTCGAGAA
66 AATGCTTGAGAGAGTA-TGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAA
* * * *
45045 GCGATTTATGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAGAGCGTCTTTGAGATCTTGAATTTA
130 GCGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAGAGAGTCTTCGAGATCTTGAGTTTA
**
45110 GTGTGAAACAACGCAAGGATGAGGTTAA
195 GTGTGAAACAACGTGAGGATGAGGTTAA
*
45138 GTCAATGGAGAAA
1 GTCGATGGAGAAA
45151 GATTTGGAGA
Statistics
Matches: 1813, Mismatches: 178, Indels: 40
0.89 0.09 0.02
Matches are distributed among these distances:
221 206 0.11
222 1294 0.71
223 312 0.17
224 1 0.00
ACGTcount: A:0.36, C:0.06, G:0.32, T:0.25
Consensus pattern (222 bp):
GTCGATGGAGAAATTGGTGAAAGATAAGTTGGAGGAAGTTGGATTGAAAGAGAAAGATTTGGAGA
AATGCTTGAGAGAGTATGAGTTGAAAGAAGAGCAATTCGGGTTGAAAGAGAAGAGTTTCGAGAAG
CGATTTACGGAGTTTGAGTTGGAAGAAAAGGCTTCGAAAGAGAGTCTTCGAGATCTTGAGTTTAG
TGTGAAACAACGTGAGGATGAGGTTAA
Found at i:51497 original size:20 final size:20
Alignment explanation
Indices: 51467--51546 Score: 133
Period size: 20 Copynumber: 4.0 Consensus size: 20
51457 AGCCGTTGGG
51467 GCCTAATGGTATCGATACTAT
1 GCCT-ATGGTATCGATACTAT
* *
51488 GCTTATGGTATCAATACTAT
1 GCCTATGGTATCGATACTAT
51508 GCCTATGGTATCGATACTAT
1 GCCTATGGTATCGATACTAT
51528 GCCTATGGTATCGATACTA
1 GCCTATGGTATCGATACTA
51547 CTATACAAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
20 52 0.95
21 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (20 bp):
GCCTATGGTATCGATACTAT
Found at i:55035 original size:18 final size:18
Alignment explanation
Indices: 55008--55043 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54998 ATTTATTGCA
55008 TATTAGCATAATCATCAT
1 TATTAGCATAATCATCAT
*
55026 TATTATCATAATCATCAT
1 TATTAGCATAATCATCAT
55044 CGTCTAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.42
Consensus pattern (18 bp):
TATTAGCATAATCATCAT
Found at i:55289 original size:56 final size:56
Alignment explanation
Indices: 55208--55333 Score: 153
Period size: 56 Copynumber: 2.2 Consensus size: 56
55198 TAGGAGTCTT
* * ** *
55208 GAAATCGAGTATATCTATAAATTGTTGTCATTAATAAGTATAAAAATAGGGCCCCC
1 GAAATCGAGTATATATATAAATTGTTGTCATTAAGAAACAAAAAAATAGGGCCCCC
* * ** *
55264 GAAATCGAGTATATATATCAGTTGTTGTCATTAAGAAACAAAAAAATAGGGGGCTC
1 GAAATCGAGTATATATATAAATTGTTGTCATTAAGAAACAAAAAAATAGGGCCCCC
*
55320 GAAATCGAATATAT
1 GAAATCGAGTATAT
55334 CTAGAAAATA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (56 bp):
GAAATCGAGTATATATATAAATTGTTGTCATTAAGAAACAAAAAAATAGGGCCCCC
Found at i:55628 original size:2 final size:2
Alignment explanation
Indices: 55621--55660 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
55611 CTATTTTAGA
55621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55661 GAATTATGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58331 original size:22 final size:22
Alignment explanation
Indices: 58284--58336 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
58274 CGTATAATTA
*
58284 TAAATTAATTAAAAATTTAAATG
1 TAAATT-ATTAAAAATTTAAAGG
*
58307 TAAATTATTTAAAA-TTAAAGGG
1 TAAATTATTAAAAATTTAAA-GG
58329 TAAATTAT
1 TAAATTAT
58337 ACTAGTGACC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 5 0.19
22 16 0.59
23 6 0.22
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.40
Consensus pattern (22 bp):
TAAATTATTAAAAATTTAAAGG
Found at i:59096 original size:22 final size:22
Alignment explanation
Indices: 59045--59084 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
59035 GATTAATGGT
59045 ATAATTTACCCTTTAAATTTAA
1 ATAATTTACCCTTTAAATTTAA
59067 ATAATTTA-CC-TTAAATTT
1 ATAATTTACCCTTTAAATTT
59085 TCAACTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAATTTACCCTTTAAATTTAA
Done.