Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004764.1 Hibiscus syriacus cultivar Beakdansim tig00010746_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: 102610
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:387 original size:7 final size:7
Alignment explanation
Indices: 364--421 Score: 88
Period size: 7 Copynumber: 8.9 Consensus size: 7
354 GACACGTATT
364 ACCAC-G
1 ACCACGG
370 ACCAC-G
1 ACCACGG
376 ACCACGG
1 ACCACGG
383 ACCAC-G
1 ACCACGG
389 ACCACGG
1 ACCACGG
396 A-CACGG
1 ACCACGG
402 ACCACGG
1 ACCACGG
409 ACCACGG
1 ACCACGG
416 ACCACG
1 ACCACG
422 AGACGAGACG
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
6 23 0.47
7 26 0.53
ACGTcount: A:0.31, C:0.45, G:0.24, T:0.00
Consensus pattern (7 bp):
ACCACGG
Found at i:387 original size:13 final size:14
Alignment explanation
Indices: 364--421 Score: 88
Period size: 13 Copynumber: 4.4 Consensus size: 14
354 GACACGTATT
364 ACCAC-GACCAC-G
1 ACCACGGACCACGG
376 ACCACGGACCAC-G
1 ACCACGGACCACGG
389 ACCACGGA-CACGG
1 ACCACGGACCACGG
402 ACCACGGACCACGG
1 ACCACGGACCACGG
416 ACCACG
1 ACCACG
422 AGACGAGACG
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.19
13 24 0.56
14 11 0.26
ACGTcount: A:0.31, C:0.45, G:0.24, T:0.00
Consensus pattern (14 bp):
ACCACGGACCACGG
Found at i:2031 original size:2 final size:2
Alignment explanation
Indices: 2026--2068 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2016 TTTTAATCAG
2026 AT AT AT AT AT AT AT AT AT AT AT -T 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 AT
2067 AT
1 AT
2069 TATGGGTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2051 original size:21 final size:21
Alignment explanation
Indices: 2027--2071 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2017 TTTAATCAGA
2027 TATATATATATATATATATAT
1 TATATATATATATATATATAT
2048 TATATATATATATATATATAT
1 TATATATATATATATATATAT
2069 TAT
1 TAT
2072 GGGTTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATATATATATATATATAT
Found at i:17614 original size:33 final size:33
Alignment explanation
Indices: 17577--17642 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
17567 CTATTTGCAT
17577 GTTTAAGTACAATAAATATCAGCTTAAAAAGAA
1 GTTTAAGTACAATAAATATCAGCTTAAAAAGAA
*
17610 GTTTAAGTACAATAAGTATCAGCTTAAAAAGAA
1 GTTTAAGTACAATAAATATCAGCTTAAAAAGAA
17643 TACCTCCATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (33 bp):
GTTTAAGTACAATAAATATCAGCTTAAAAAGAA
Found at i:24087 original size:16 final size:17
Alignment explanation
Indices: 24056--24088 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
24046 AAAATTTTAA
*
24056 TTTAAACTTCTAAATTT
1 TTTAAAATTCTAAATTT
24073 TTTAAAATT-TAAATTT
1 TTTAAAATTCTAAATTT
24089 ACCCCAAACG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAAAATTCTAAATTT
Found at i:24684 original size:31 final size:31
Alignment explanation
Indices: 24619--24686 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
24609 GACTATAGAG
*
24619 TATTATTTTATTAAGTTTATCGATTATTATA
1 TATTATTTTATTAAGTTTATCGATTATTAAA
* * *
24650 TATTGTTTTATTAAGTTCT-TTGATTTTTAAA
1 TATTATTTTATTAAGTT-TATCGATTATTAAA
24681 TATTAT
1 TATTAT
24687 AAAATTATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.60
Consensus pattern (31 bp):
TATTATTTTATTAAGTTTATCGATTATTAAA
Found at i:30449 original size:50 final size:50
Alignment explanation
Indices: 30374--30468 Score: 190
Period size: 50 Copynumber: 1.9 Consensus size: 50
30364 AGGAAGCGAC
30374 AGCCTTTTTACCTTTGATTTCACTTTTAATCAATGCTCAAGTGTAGTGAT
1 AGCCTTTTTACCTTTGATTTCACTTTTAATCAATGCTCAAGTGTAGTGAT
30424 AGCCTTTTTACCTTTGATTTCACTTTTAATCAATGCTCAAGTGTA
1 AGCCTTTTTACCTTTGATTTCACTTTTAATCAATGCTCAAGTGTA
30469 AGATTGAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (50 bp):
AGCCTTTTTACCTTTGATTTCACTTTTAATCAATGCTCAAGTGTAGTGAT
Found at i:32632 original size:60 final size:59
Alignment explanation
Indices: 32483--32672 Score: 170
Period size: 60 Copynumber: 3.2 Consensus size: 59
32473 AATTTGGATG
* * * *
32483 AGTTTAGGGATAAAATTGTAATATTCAAAAGTTTGAGGACAAATTCAAGAA-GAGGGTCAT
1 AGTTTAGGGATAAAATTGAAATATTCAAAAGTTTAAGAAC-AATT-TAGAATGAGGGTCAT
* * *** * *
32543 AGTTTAAGGATGAAATT-AGAATGCACAAAAGTTTAAGAACTAGTTTGGAATGAGGGTCAT
1 AGTTTAGGGATAAAATTGA-AATATTCAAAAGTTTAAGAAC-AATTTAGAATGAGGGTCAT
* * *
32603 AGTTTGGGGATAAAATTGAAATATTCAAAAGTTTAAAGATCAATTTAAAATGAGGGAT-AT
1 AGTTTAGGGATAAAATTGAAATATTCAAAAGTTT-AAGAACAATTTAGAATGAGGG-TCAT
*
32663 AGTTTGGGGA
1 AGTTTAGGGA
32673 CATGTGATGC
Statistics
Matches: 103, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
59 3 0.03
60 93 0.90
61 7 0.07
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.29
Consensus pattern (59 bp):
AGTTTAGGGATAAAATTGAAATATTCAAAAGTTTAAGAACAATTTAGAATGAGGGTCAT
Found at i:34750 original size:27 final size:29
Alignment explanation
Indices: 34719--34778 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
34709 TCTTAATTTA
34719 AATA-TTGTAAATC-AAAAATAATATCAG
1 AATATTTGTAAATCAAAAAATAATATCAG
* *
34746 AATATTTGTAAATCAAAAAATAATGTCGG
1 AATATTTGTAAATCAAAAAATAATATCAG
34775 AATA
1 AATA
34779 ATTTCATCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 4 0.14
28 9 0.31
29 16 0.55
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (29 bp):
AATATTTGTAAATCAAAAAATAATATCAG
Found at i:35254 original size:2 final size:2
Alignment explanation
Indices: 35247--35298 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
35237 GCATACATAC
35247 AT 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 AT
35289 AT AT AT AT AT
1 AT AT AT AT AT
35299 GCAAAATTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38564 original size:36 final size:36
Alignment explanation
Indices: 38523--38598 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
38513 ATTTTCGGGA
*
38523 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
38559 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
38595 TTTT
1 TTTT
38599 TTTGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:39041 original size:15 final size:15
Alignment explanation
Indices: 39021--39050 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39011 TATCACAATC
39021 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
39036 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
39051 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:43573 original size:36 final size:36
Alignment explanation
Indices: 43532--43607 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
43522 ATTTTCGGGA
*
43532 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
43568 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
43604 TTTT
1 TTTT
43608 TTTGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:50073 original size:21 final size:21
Alignment explanation
Indices: 50026--50070 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
50016 CTTAAGTTAT
50026 GGTTAGGGCTAATGGTTTAGA
1 GGTTAGGGCTAATGGTTTAGA
50047 GGTTAGGGCTAATGGTTTA-A
1 GGTTAGGGCTAATGGTTTAGA
50067 GGTT
1 GGTT
50071 TAGAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.22, C:0.04, G:0.38, T:0.36
Consensus pattern (21 bp):
GGTTAGGGCTAATGGTTTAGA
Found at i:52244 original size:11 final size:12
Alignment explanation
Indices: 52214--52247 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
52204 GTTATTTAAA
52214 CGGGTATTGGGT
1 CGGGTATTGGGT
52226 CGGGTATTGGGT
1 CGGGTATTGGGT
52238 C-GGTATTGGG
1 CGGGTATTGGG
52248 CCGTGAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.09, C:0.09, G:0.50, T:0.32
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:52327 original size:24 final size:25
Alignment explanation
Indices: 52265--52327 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
52255 TCGGGCCGGG
52265 TATATA-TATATATATTTAAATTAAA
1 TATATATTATAT-TATTTAAATTAAA
*
52290 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
52314 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
52328 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 19 0.58
25 8 0.24
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:53238 original size:12 final size:12
Alignment explanation
Indices: 53218--53251 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
53208 GGTCACGTCC
*
53218 AAATTTTTTTTT
1 AAATATTTTTTT
53230 AAATA-TTTTTT
1 AAATATTTTTTT
53241 AAATATTTTTT
1 AAATATTTTTT
53252 ATTTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
AAATATTTTTTT
Found at i:53249 original size:10 final size:11
Alignment explanation
Indices: 53224--53252 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
53214 GTCCAAATTT
53224 TTTTTTAAATA
1 TTTTTTAAATA
53235 TTTTTTAAATA
1 TTTTTTAAATA
53246 TTTTTTA
1 TTTTTTA
53253 TTTTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:66245 original size:46 final size:46
Alignment explanation
Indices: 66179--66280 Score: 188
Period size: 46 Copynumber: 2.2 Consensus size: 46
66169 ATACTTTATT
66179 TTAACC-AAAGTTATTTTGTCAATGAGCTACGTAGCTTTGTTGACA
1 TTAACCAAAAGTTATTTTGTCAATGAGCTACGTAGCTTTGTTGACA
66224 TTAACCAAAAGTTATTTTGTCAATGAGCTACGTAGCTTTGTTGACA
1 TTAACCAAAAGTTATTTTGTCAATGAGCTACGTAGCTTTGTTGACA
*
66270 TGAACCAAAAG
1 TTAACCAAAAG
66281 AATTTTATGT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 6 0.11
46 49 0.89
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (46 bp):
TTAACCAAAAGTTATTTTGTCAATGAGCTACGTAGCTTTGTTGACA
Found at i:68576 original size:23 final size:23
Alignment explanation
Indices: 68547--68598 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
68537 ACTGTTATAT
68547 TATATTTCAAAAATATTAATTAA
1 TATATTTCAAAAATATTAATTAA
* * *
68570 TATATTTTAAATATATTTATTAA
1 TATATTTCAAAAATATTAATTAA
*
68593 AATATT
1 TATATT
68599 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TATATTTCAAAAATATTAATTAA
Found at i:68600 original size:11 final size:11
Alignment explanation
Indices: 68556--68633 Score: 54
Period size: 11 Copynumber: 7.0 Consensus size: 11
68546 TTATATTTCA
68556 AAAATATTAATT
1 AAAATATT-ATT
*
68568 AATATATT-TT
1 AAAATATTATT
68578 AAATATATTTATT
1 AAA-ATA-TTATT
68591 AAAATATTATT
1 AAAATATTATT
* *
68602 AGATTATTA-T
1 AAAATATTATT
* *
68612 ATAATAAT-TT
1 AAAATATTATT
68622 AATAATATTATT
1 AA-AATATTATT
68634 TCTATGAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
10 12 0.24
11 20 0.39
12 14 0.27
13 5 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (11 bp):
AAAATATTATT
Found at i:68764 original size:22 final size:22
Alignment explanation
Indices: 68736--68779 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
68726 TTGATTATTT
68736 TATTATAATATTAAAAATATAA
1 TATTATAATATTAAAAATATAA
* *
68758 TATTATATTATTAGAAATATAA
1 TATTATAATATTAAAAATATAA
68780 ATAAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTATAATATTAAAAATATAA
Found at i:68769 original size:30 final size:34
Alignment explanation
Indices: 68719--68788 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 34
68709 ATATTATTAT
* * *
68719 AATATAATTGATTATTTTATTA-TAATATTAA-A
1 AATATAATTGATTATATTATTAGAAATATAAATA
68751 AATATAA-T-ATTATATTATTAGAAATATAAATA
1 AATATAATTGATTATATTATTAGAAATATAAATA
68783 AATATA
1 AATATA
68789 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 11 0.33
31 8 0.24
32 14 0.42
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (34 bp):
AATATAATTGATTATATTATTAGAAATATAAATA
Found at i:70127 original size:10 final size:10
Alignment explanation
Indices: 70112--70145 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
70102 GGACCGGTTG
70112 AAAACCGGAA
1 AAAACCGGAA
70122 AAAACCAGG-A
1 AAAACC-GGAA
70132 AAAACCGGAA
1 AAAACCGGAA
70142 AAAA
1 AAAA
70146 TTGCCAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.65, C:0.18, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAACCGGAA
Found at i:72156 original size:32 final size:32
Alignment explanation
Indices: 72086--72163 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
72076 AAGGCTAATG
* * * *
72086 GACTAAAATCGAATGAGAGTTAACGGTTAAGA
1 GACTAAAATCGAATGAAAGTTAAAGATCAAGA
* *
72118 GACTAAAATCGAATGAAAGTTAAAGATCGAGG
1 GACTAAAATCGAATGAAAGTTAAAGATCAAGA
*
72150 GGCTAAAATCGAAT
1 GACTAAAATCGAAT
72164 ATATCAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (32 bp):
GACTAAAATCGAATGAAAGTTAAAGATCAAGA
Found at i:78305 original size:87 final size:87
Alignment explanation
Indices: 78159--78324 Score: 260
Period size: 87 Copynumber: 1.9 Consensus size: 87
78149 CATTTCATTG
* * *
78159 ATTTCAACATTGACTTTGACATCAATATTAGATAATAGTAGTAAGGTATATAACTTTATGTACTC
1 ATTTCAACATTGACTTTGACATCAATATAAGATAATAGTAGTAAGGCATAGAACTTTATGTACTC
78224 AGCATGAATTTGCTCAATAATC
66 AGCATGAATTTGCTCAATAATC
* ** *
78246 ATTTCAATATTGTTTTTGACATCAATATAAGATAATAGTAGTAAGGCATAGAACTTTATGTTCTC
1 ATTTCAACATTGACTTTGACATCAATATAAGATAATAGTAGTAAGGCATAGAACTTTATGTACTC
*
78311 AGGATGAATTTGCT
66 AGCATGAATTTGCT
78325 GGCTTTCTGA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (87 bp):
ATTTCAACATTGACTTTGACATCAATATAAGATAATAGTAGTAAGGCATAGAACTTTATGTACTC
AGCATGAATTTGCTCAATAATC
Found at i:79640 original size:2 final size:2
Alignment explanation
Indices: 79633--79679 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
79623 TGTATGTATG
79633 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
79675 TA TA T
1 TA TA T
79680 GGATTCACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:85946 original size:30 final size:29
Alignment explanation
Indices: 85910--85985 Score: 107
Period size: 30 Copynumber: 2.6 Consensus size: 29
85900 TTTAGAACCT
85910 AAAATCTTAAATCTTCCTTCAGACAAAAA
1 AAAATCTTAAATCTTCCTTCAGACAAAAA
* * *
85939 CAAAATCTTAAGTCATCCTTCAGACCAAAA
1 -AAAATCTTAAATCTTCCTTCAGACAAAAA
*
85969 TAAATCTTAAATCTTCC
1 AAAATCTTAAATCTTCC
85986 AATGAATATC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 14 0.35
30 26 0.65
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.29
Consensus pattern (29 bp):
AAAATCTTAAATCTTCCTTCAGACAAAAA
Found at i:88358 original size:24 final size:24
Alignment explanation
Indices: 88331--88389 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
88321 GCCATAACAT
88331 AAGAAGCTCACACTTTTTCCCTTC
1 AAGAAGCTCACACTTTTTCCCTTC
88355 AAGAAGCTCACACTTTTTCCCTTC
1 AAGAAGCTCACACTTTTTCCCTTC
* *
88379 AAAAACCTCAC
1 AAGAAGCTCAC
88390 TCTTCTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.34, G:0.07, T:0.29
Consensus pattern (24 bp):
AAGAAGCTCACACTTTTTCCCTTC
Found at i:89353 original size:35 final size:36
Alignment explanation
Indices: 89278--89354 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 36
89268 TTGTCATTAT
* * *
89278 ATTTTTTTAGATGATTATAATAACATTAAATTTATT
1 ATTTTTTTAGATGATTATAATAACATTAAAATAATC
* *
89314 ATTTTTTTA-AT-ATTTATTATAACTTTAAAATAATC
1 ATTTTTTTAGATGA-TTATAATAACATTAAAATAATC
89349 ATTTTT
1 ATTTTT
89355 AACAATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 1 0.03
35 25 0.71
36 9 0.26
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.56
Consensus pattern (36 bp):
ATTTTTTTAGATGATTATAATAACATTAAAATAATC
Found at i:94624 original size:31 final size:31
Alignment explanation
Indices: 94586--94649 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
94576 AACTCGTTAA
94586 CTTCAACAAATAAGCCCCATTCAATCTGTTT
1 CTTCAACAAATAAGCCCCATTCAATCTGTTT
94617 CTTCAACAAATAAGCCCCATTCAATCTGTTT
1 CTTCAACAAATAAGCCCCATTCAATCTGTTT
94648 CT
1 CT
94650 GACATGCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.33
Consensus pattern (31 bp):
CTTCAACAAATAAGCCCCATTCAATCTGTTT
Found at i:99496 original size:22 final size:22
Alignment explanation
Indices: 99443--99517 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 22
99433 GTTCAGTATT
*
99443 CGTCCTGAAGGACCACT--AT-
1 CGTCCCGAAGGACCACTAGATA
*
99462 -GTCCCGAATGACCACTAGATA
1 CGTCCCGAAGGACCACTAGATA
*
99483 CGTCTCGAAGGACCACTAGATA
1 CGTCCCGAAGGACCACTAGATA
99505 CGTCCCGAAGGAC
1 CGTCCCGAAGGAC
99518 TAATATACCC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 14 0.30
20 2 0.04
22 31 0.66
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (22 bp):
CGTCCCGAAGGACCACTAGATA
Found at i:100958 original size:64 final size:64
Alignment explanation
Indices: 100849--101008 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 64
100839 TTCTTTAACG
* * * * * * * **
100849 GTGCACCGATGCACTACTTGTGCATCGGTGCATAAAATACATTCGATGTTTC-AATATTAAGGT
1 GTGCATCGATGCACTACTTATGCATCGATACATTAATTGCATTCGATGTTTCTAATATTAAGAA
* *
100912 GATGCATCGATGCA-TGCCTTATGCATCGATACATTAATTGCATTCGATGTTTCTATTATTAAGA
1 G-TGCATCGATGCACT-ACTTATGCATCGATACATTAATTGCATTCGATGTTTCTAATATTAAGA
100976 A
64 A
*
100977 GTGCATCGATGCACTACTTGTGCATCGATACA
1 GTGCATCGATGCACTACTTATGCATCGATACA
101009 CCTTCAATAA
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
63 2 0.03
64 68 0.85
65 10 0.12
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTACTTATGCATCGATACATTAATTGCATTCGATGTTTCTAATATTAAGAA
Done.