Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004948.1 Hibiscus syriacus cultivar Beakdansim tig00011123_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: 63192
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:617 original size:76 final size:77
Alignment explanation
Indices: 526--686 Score: 272
Period size: 76 Copynumber: 2.1 Consensus size: 77
516 AATCCGGACC
* *
526 TACTATCAAATTTTGTTTTATATAAAATGATAAG-ACACCTGTACGTTTATACATGGACCACTAT
1 TACTATAAAATTTTGTTTTATATAAAATGATAAGAACACCTGCACGTTTATACATGGACCACTA-
590 ATAATATTATT-G
65 ATAATATTATTCG
*
602 TACTATAAAATTTTGTTTTATATAAAATGATAAGAACACCTGCACTTTTATACATGGACCACTAA
1 TACTATAAAATTTTGTTTTATATAAAATGATAAGAACACCTGCACGTTTATACATGGACCACTAA
667 TAATATTATTCG
66 TAATATTATTCG
679 TACTATAA
1 TACTATAA
687 TTTATAAAAG
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
76 44 0.55
77 36 0.45
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (77 bp):
TACTATAAAATTTTGTTTTATATAAAATGATAAGAACACCTGCACGTTTATACATGGACCACTAA
TAATATTATTCG
Found at i:2936 original size:278 final size:280
Alignment explanation
Indices: 2407--3201 Score: 827
Period size: 278 Copynumber: 2.8 Consensus size: 280
2397 TTTGTAATTG
* * * **
2407 TATAGAGTTTGCAGTAAATTACAAAAATATAAATAATTATGGGCTAATTTAAAATAAAAATATAC
1 TATAGGGTTTGGAGTAAATTA-AAAAATAAAAATAATTATGGGCTAATTTAGGATAAAAA-A-AC
* **
2472 TATTAA-AGACTAAATTGAAC-CAACATTAAATTAAAAACTAAAATTTAAACGAATTAAACAACA
63 TATTAAGA-ACTAAATTGAACAC-ACATGAAATTAAAAACTAAAATTTAAATAAATTAAACAACA
* * * * * ** *
2535 CACAAGGATCAATTAAAACAATTATAAAATGTGAAGTTAAAAATTAATAAAAAATT-GACAAAAT
126 CACAAGGATCAATTGAAATAATTGTAAAATGTAAAGTT-GAAATTAATATCAAATTGGACTAAAT
* * * *
2599 TGAATTCATTTTAAAAGTTGGTGAACAAAAGTTTATATGGTTTAGATATTATGATAATTTATAGA
190 TGAATTCATTTGAAAAGTT-GTGAACAAAAGTTTATAAGATTTAGATATGATGATAATTTATAGA
*
2664 GTTTGAAATGAAGTTTATGATATGATT
254 GTTTGAAATGAAATTTATGATATGATT
* *
2691 TATATGGTTTGGAGTAAATTAAAAAATAGAAATAATTATGGGCTAATTTAGGAT-AAAAAA-TAT
1 TATAGGGTTTGGAGTAAATTAAAAAATAAAAATAATTATGGGCTAATTTAGGATAAAAAAACTAT
* * * * **
2754 TAAGAACT-AATTGAACACACATGAAATTAGAAACTAAAATTCAAATAAATTAAACAAAACGCCT
66 TAAGAACTAAATTGAACACACATGAAATTAAAAACTAAAATTTAAATAAATTAAACAACACACAA
* *
2818 GGATCGAATTGAAATAATTGTAAAATGTAAAGCTGAAATTAATATCAAATTGGACTAAATTGCAT
131 GGATC-AATTGAAATAATTGTAAAATGTAAAGTTGAAATTAATATCAAATTGGACTAAATTGAAT
*
2883 TCATTTGAAAAGTAT-TGAAC-AAAGTTTATAAGATTTAGAGATATGAT-ATAATTTATAGGGTT
195 TCATTTGAAAAGT-TGTGAACAAAAGTTTATAAGATTT--AGATATGATGATAATTTATAGAGTT
* *
2945 TGAATTGAAATTTATGATATGGTT
257 TGAAATGAAATTTATGATATGATT
* * * *
2969 TATAGGGTTTGGAGTAGATTATAGAAAAAAATAAAAAAAATATATGGGTTAATTTTGGATCAAAA
1 TATAGGGTTTGGAGTA-A--AT--TAAAAAATAAAAATAAT-TATGGGCTAATTTAGGAT-AAAA
* ** * * * * * * *
3034 CAAACTTTTGCGTACTAAATTGAACAAACATGAAACTACAATA-TGAAATTTGAATAAATTAAAT
59 -AAACTATTAAGAACTAAATTGAACACACATGAAATTA-AAAACTAAAATTTAAATAAATTAAAC
* * *
3098 AACATACAAGGATCAAATTGAAATAATTGTAAAATGTAAATTTGAAATTAATATCAAATTGGAAT
122 AACACACAAGGATC-AATTGAAATAATTGTAAAATGTAAAGTTGAAATTAATATCAAATTGGACT
* * * *
3163 AAATTAAATTCATTTTAAATGTTAGTAAACAAAAGTTTA
186 AAATTGAATTCATTTGAAAAGTT-GTGAACAAAAGTTTA
3202 ACATCTTAAT
Statistics
Matches: 424, Mismatches: 65, Indels: 37
0.81 0.12 0.07
Matches are distributed among these distances:
277 14 0.03
278 119 0.28
279 65 0.15
280 3 0.01
281 3 0.01
282 4 0.01
283 44 0.10
284 34 0.08
286 3 0.01
287 3 0.01
288 8 0.02
289 110 0.26
290 6 0.01
291 8 0.02
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.32
Consensus pattern (280 bp):
TATAGGGTTTGGAGTAAATTAAAAAATAAAAATAATTATGGGCTAATTTAGGATAAAAAAACTAT
TAAGAACTAAATTGAACACACATGAAATTAAAAACTAAAATTTAAATAAATTAAACAACACACAA
GGATCAATTGAAATAATTGTAAAATGTAAAGTTGAAATTAATATCAAATTGGACTAAATTGAATT
CATTTGAAAAGTTGTGAACAAAAGTTTATAAGATTTAGATATGATGATAATTTATAGAGTTTGAA
ATGAAATTTATGATATGATT
Found at i:12822 original size:17 final size:17
Alignment explanation
Indices: 12775--12825 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
12765 AATAAATTTA
12775 ATTTAATTTAAATATAT
1 ATTTAATTTAAATATAT
*
12792 ATATAATATT---TATAT
1 ATTTAAT-TTAAATATAT
12807 ATTTAATTTAAATATAT
1 ATTTAATTTAAATATAT
12824 AT
1 AT
12826 ACTCGGCCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.07
15 11 0.39
17 13 0.46
18 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTAATTTAAATATAT
Found at i:18900 original size:30 final size:31
Alignment explanation
Indices: 18861--18981 Score: 73
Period size: 31 Copynumber: 3.9 Consensus size: 31
18851 GAATGACCTA
* * * *
18861 TCCAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* *
18891 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
** ** ** * *
18922 TCCATATATTTCTTAGAACATAGGTAAGCTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* * * *
18953 TCCATATGTCCCGAAGAACATAGGTAAAC
1 TCCATAGGTCACAAAGAACCTAGGTAAAC
18982 CCTCGACTCT
Statistics
Matches: 70, Mismatches: 20, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
30 19 0.27
31 51 0.73
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:18924 original size:31 final size:31
Alignment explanation
Indices: 18886--18981 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 31
18876 GAACCTCGGC
* *
18886 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* ** **
18917 AACTGTCCATATATTTCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
*
18948 AGCTGTCCATATGTCCCGAAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
18979 AAC
1 AAC
18982 CCTCGACTCT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:25643 original size:18 final size:18
Alignment explanation
Indices: 25620--25654 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
25610 ATCAAGAGTA
25620 GAAAAATTATCTTATCTT
1 GAAAAATTATCTTATCTT
25638 GAAAAATTATCTTATCT
1 GAAAAATTATCTTATCT
25655 CCACTCATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (18 bp):
GAAAAATTATCTTATCTT
Found at i:28779 original size:6 final size:6
Alignment explanation
Indices: 28768--28796 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
28758 TTAAGATTCC
28768 ATTTGG ATTTGG ATTTGG ATTTGG ATTTG
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTG
28797 AATTAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (6 bp):
ATTTGG
Found at i:28807 original size:18 final size:18
Alignment explanation
Indices: 28768--28818 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
28758 TTAAGATTCC
* * *
28768 ATTTGGATTTGGATTTGG
1 ATTTGGATTTGAATTAGA
28786 ATTTGGATTTGAATTAGA
1 ATTTGGATTTGAATTAGA
**
28804 ATTTTCATTTGAATT
1 ATTTGGATTTGAATT
28819 TGGGTTGAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.22, T:0.51
Consensus pattern (18 bp):
ATTTGGATTTGAATTAGA
Found at i:31358 original size:15 final size:16
Alignment explanation
Indices: 31330--31376 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
31320 GGGTCGGTAT
*
31330 ATATATTTAA-ATTAA
1 ATATATATAATATTAA
*
31345 ATATATA-AATATTAT
1 ATATATATAATATTAA
31360 ATATATATAAT-TTAA
1 ATATATATAATATTAA
31375 AT
1 AT
31377 TAAATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.07
15 22 0.81
16 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATATAATATTAA
Found at i:31379 original size:35 final size:34
Alignment explanation
Indices: 31327--31402 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 34
31317 ATCGGGTCGG
31327 TATATATATTTAAATTAAATATATAAATATTATA
1 TATATATATTTAAATTAAATATATAAATATTATA
* *
31361 TATATATAATTTAAATTAAATTTATTAATATTATA
1 TATATAT-ATTTAAATTAAATATATAAATATTATA
31396 TATATAT
1 TATATAT
31403 TTATAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 7 0.18
35 32 0.82
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
TATATATATTTAAATTAAATATATAAATATTATA
Found at i:31424 original size:35 final size:34
Alignment explanation
Indices: 31327--31427 Score: 116
Period size: 35 Copynumber: 2.9 Consensus size: 34
31317 ATCGGGTCGG
* * *
31327 TATATATATTTAAATTAAATATATAAATATTATA
1 TATATATATTTAAAATAAATTTATTAATATTATA
*
31361 TATATATAATTTAAATTAAATTTATTAATATTATA
1 TATATAT-ATTTAAAATAAATTTATTAATATTATA
31396 TATATAT-TTATAAAATAATTATTT-TTAATATT
1 TATATATATT-TAAAATAA--ATTTATTAATATT
31428 TATCGGACCG
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
33 2 0.03
34 14 0.23
35 40 0.67
36 4 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TATATATATTTAAAATAAATTTATTAATATTATA
Found at i:31848 original size:41 final size:41
Alignment explanation
Indices: 31791--31897 Score: 205
Period size: 41 Copynumber: 2.6 Consensus size: 41
31781 TCGAGGAGAA
31791 ATGGCTTATCTGAGGAATTAAGGATTTGGTTTGCAACAAAG
1 ATGGCTTATCTGAGGAATTAAGGATTTGGTTTGCAACAAAG
31832 ATGGCTTATCTGAGGAATTAAGGATTTGGTTTGCAACAAAG
1 ATGGCTTATCTGAGGAATTAAGGATTTGGTTTGCAACAAAG
*
31873 ATGGCTTATCTGAGGGATTAAGGAT
1 ATGGCTTATCTGAGGAATTAAGGAT
31898 AGCATTCAGG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.32
Consensus pattern (41 bp):
ATGGCTTATCTGAGGAATTAAGGATTTGGTTTGCAACAAAG
Found at i:34229 original size:106 final size:106
Alignment explanation
Indices: 34058--34704 Score: 1039
Period size: 106 Copynumber: 6.2 Consensus size: 106
34048 AGCCGATATT
* *
34058 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACTAAGGGACCGC
1 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* *
34123 TGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTT
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
34164 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
34229 TGGTTGTCAACAAACAACCTCCCAATTTCAGAGCCAATTTC
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
* *
34270 AACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGC
1 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* *
34335 TGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTT
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
* *
34376 AACTTCATAGCGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
34441 TGGTTGTCAACAAACAACCTCCCAATTTCAGAGCCAATTTC
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
* * *
34482 AACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGATCGC
1 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
34547 TGGTTGTCAACAAACAA-----C---TTC----CCAATTTC
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
* *
34576 AACTTCACAGCGAAAGATATTGGACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
34641 TGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTC
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
*
34682 AACTTCACAACGAAGGATATTGG
1 AACTTCACAGCGAAGGATATTGG
34705 CCTCGAAACA
Statistics
Matches: 500, Mismatches: 29, Indels: 24
0.90 0.05 0.04
Matches are distributed among these distances:
94 85 0.17
98 3 0.01
99 1 0.00
101 1 0.00
102 3 0.01
106 407 0.81
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (106 bp):
AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
Found at i:34540 original size:43 final size:42
Alignment explanation
Indices: 34479--34634 Score: 114
Period size: 43 Copynumber: 3.4 Consensus size: 42
34469 CAGAGCCAAT
34479 TTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACA-CGAAGGATATTGGACTCCAGACAACGCAAG
* ** ** * * *
34522 TTCAACTTCACGATGAAGGGATCGCTGGTTGTCAACAAACAACTTCCCAAT
1 TTCAACTTCAC-ACGAA-GGAT-ATTGG-ACTC--CAGACAA---CGCAAG
* *
34573 TTCAACTTCACAGCGAAAGATATTGGACTCCAGATAACGCAAG
1 TTCAACTTCACA-CGAAGGATATTGGACTCCAGACAACGCAAG
34616 TTCAACTTCACGACGAAGG
1 TTCAACTTCAC-ACGAAGG
34635 GACCGCTGGT
Statistics
Matches: 83, Mismatches: 19, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
43 34 0.41
44 6 0.07
45 3 0.04
46 7 0.08
48 8 0.10
49 3 0.04
50 4 0.05
51 18 0.22
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (42 bp):
TTCAACTTCACACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:36258 original size:19 final size:19
Alignment explanation
Indices: 36236--36294 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
36226 TCGTTTATTA
*
36236 TTATTATTACATATATTTT
1 TTATTATTATATATATTTT
36255 TTATTATTATAT-TA-TTT
1 TTATTATTATATATATTTT
36272 TTATTATATATATATATATTT
1 TTATTAT-TATATATAT-TTT
36293 TT
1 TT
36295 TCTCATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
17 10 0.29
18 7 0.20
19 13 0.37
21 5 0.14
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTATTATATATATTTT
Found at i:36258 original size:22 final size:21
Alignment explanation
Indices: 36233--36295 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
36223 ATTTCGTTTA
36233 TTATTATTATTACATATATTTT
1 TTATTATTATTA-ATATATTTT
36255 TTATTATTA-T-AT-TA-TTT
1 TTATTATTATTAATATATTTT
36272 TTATTA-TATATATATATATTTT
1 TTATTATTAT-TA-ATATATTTT
36294 TT
1 TT
36296 CTCATATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
16 2 0.06
17 9 0.26
18 3 0.09
19 2 0.06
20 2 0.06
21 3 0.09
22 14 0.40
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATTATTATTAATATATTTT
Found at i:36277 original size:14 final size:15
Alignment explanation
Indices: 36234--36280 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
36224 TTTCGTTTAT
*
36234 TATTA-TTATTACATA
1 TATTATTTATTA-TTA
*
36249 TATTTTTTATTATTA
1 TATTATTTATTATTA
36264 TATTATTT-TTATTA
1 TATTATTTATTATTA
36278 TAT
1 TAT
36281 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 9 0.32
15 13 0.46
16 6 0.21
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTATTTATTATTA
Found at i:36289 original size:39 final size:39
Alignment explanation
Indices: 36233--36312 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
36223 ATTTCGTTTA
*
36233 TTATTATTATTACATATATTTTTTATTATTATAT-TATTT
1 TTATTATTATTACATATATTTTTTATCA-TATATGTATTT
* *
36272 TTATTA-TATATATATATATTTTTTCTCATATATGTATTT
1 TTATTATTAT-TACATATATTTTTTATCATATATGTATTT
36311 TT
1 TT
36313 CACAATCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 8 0.22
39 28 0.78
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (39 bp):
TTATTATTATTACATATATTTTTTATCATATATGTATTT
Found at i:36304 original size:22 final size:20
Alignment explanation
Indices: 36246--36295 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
36236 TTATTATTAC
36246 ATATA-TTTTTTAT-TAT-T
1 ATATATTTTTTTATATATAT
36263 ATATTATTTTTATTATATATAT
1 ATA-TATTTTT-TTATATATAT
36285 ATATATTTTTT
1 ATATATTTTTT
36296 CTCATATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.11
18 2 0.07
19 4 0.14
20 5 0.18
21 10 0.36
22 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATATATTTTTTTATATATAT
Found at i:36757 original size:68 final size:68
Alignment explanation
Indices: 36648--36779 Score: 228
Period size: 68 Copynumber: 1.9 Consensus size: 68
36638 CGGTTGCGAC
* * * *
36648 AGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTTTGTCAAATGCACA
1 AGGCCTCAAAGACACTTAGACTTTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCACA
36713 ATT
66 ATT
36716 AGGCCTCAAAGACACTTAGACTTTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCAC
1 AGGCCTCAAAGACACTTAGACTTTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCAC
36780 GGTTAAGCAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (68 bp):
AGGCCTCAAAGACACTTAGACTTTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCACA
ATT
Found at i:40745 original size:81 final size:81
Alignment explanation
Indices: 40610--41012 Score: 495
Period size: 81 Copynumber: 5.0 Consensus size: 81
40600 ATCGGTTAAA
*
40610 CAATTGTACAGTTAGGCCATTATTATTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGAATA
1 CAATTGTACAGTTAGGCCATTATTCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGAATA
40675 ATTGGCACATTTCTAC
66 ATTGGCACATTTCTAC
*
40691 CAATTGTACAGTTAGGCCATTATTCTTTTACTCAACGGTGTCTAACCGTTCATCTAACT-GACAT
1 CAATTGTACAGTTAGGCCATTATTCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGA-AT
*
40755 AATTGGAACATTTCTAC
65 AATTGGCACATTTCTAC
* ** * * * * *
40772 CAATTGCACAACTAGGCCATTGTTCTTTTACTCAACGATGTTTAATCTTTCATCTAACTGGATTA
1 CAATTGTACAGTTAGGCCATTATTCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGAATA
*
40837 ATTGGCACCTTTCTAC
66 ATTGGCACATTTCTAC
* * *** ** * *
40853 TAATT-TCACAATTAGGTTGTTATTCTTTTACTCAACGGTGTTTAACATTTCATCTAACTAGCAT
1 CAATTGT-ACAGTTAGGCCATTATTCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGAAT
* * *
40917 AACTGGAACCTTTCTAC
65 AATTGGCACATTTCTAC
* * * * *
40934 CAATTGCATAGTTAGGACATTATTCTTTTACTCAACGGTGTTTAATCGTTCATCTAACTGGCATA
1 CAATTGTACAGTTAGGCCATTATTCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGAATA
* *
40999 AATGACACATTTCT
66 ATTGGCACATTTCT
41013 GTCAAATGCA
Statistics
Matches: 274, Mismatches: 44, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
80 2 0.01
81 270 0.99
82 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (81 bp):
CAATTGTACAGTTAGGCCATTATTCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGAATA
ATTGGCACATTTCTAC
Found at i:41060 original size:68 final size:67
Alignment explanation
Indices: 40982--41169 Score: 304
Period size: 68 Copynumber: 2.8 Consensus size: 67
40972 TGTTTAATCG
*
40982 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCAGAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACAC-TTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
41047 CCT
65 CCT
* * *
41050 TTCATCTAACTGGCATAAATGATACCTTCTTGTCAAATGCACAGTTAGGCCTCCAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACTTTC-TGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
41115 CCT
65 CCT
*
41118 TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACA-CTTTCTGTCAAATGCACAGTTAGGCCT
41170 ATTAATCTTT
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
67 3 0.03
68 104 0.94
69 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (67 bp):
TTCATCTAACTGGCATAAATGACACTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGC
CT
Found at i:41962 original size:75 final size:73
Alignment explanation
Indices: 41855--42019 Score: 231
Period size: 75 Copynumber: 2.2 Consensus size: 73
41845 CGATACTTCT
* * *
41855 ATACTATGATACCGATACCCCCTTCCAGTATCGATACCAATTTTAGGTTCGATGTTGCCTGGTAT
1 ATACTATGGTATCGATACCCCCTTCCAGTATCGATACCAATTTTAGCTTCGATGTTGCCTGGTAT
*
41920 TGAGACTACC
66 CGAGAC--CC
* *
41930 ATACTATGGTATCGATACCCCCTTTCAGTATCGATACCAATTTTAGCTTCGATGTTGCTTGGTAT
1 ATACTATGGTATCGATACCCCCTTCCAGTATCGATACCAATTTTAGCTTCGATGTTGCCTGGTAT
*
41995 CGATACCC
66 CGAGACCC
* *
42003 TTACAATGGTATCGATA
1 ATACTATGGTATCGATA
42020 GTGCCTCGTC
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
73 17 0.21
75 64 0.79
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (73 bp):
ATACTATGGTATCGATACCCCCTTCCAGTATCGATACCAATTTTAGCTTCGATGTTGCCTGGTAT
CGAGACCC
Found at i:44959 original size:31 final size:31
Alignment explanation
Indices: 44918--44977 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
44908 GGAAAAAAAA
* * *
44918 TCAATTAAACTCTTATTTCCGAAAAATTTGT
1 TCAAATAAACTCTTAATTACGAAAAATTTGT
* *
44949 TCAAATAAACTTTTAATTATGAAAAATTT
1 TCAAATAAACTCTTAATTACGAAAAATTT
44978 AAAATGTTGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (31 bp):
TCAAATAAACTCTTAATTACGAAAAATTTGT
Found at i:46772 original size:16 final size:16
Alignment explanation
Indices: 46751--46784 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
46741 ATGAAATGAA
*
46751 AGTGAGAGAATGAGAT
1 AGTGAGAGAATAAGAT
46767 AGTGAGAGAATAAGAT
1 AGTGAGAGAATAAGAT
46783 AG
1 AG
46785 AAGATTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.35, T:0.18
Consensus pattern (16 bp):
AGTGAGAGAATAAGAT
Found at i:47020 original size:2 final size:2
Alignment explanation
Indices: 47015--47040 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47005 TATATATATA
47015 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
47041 AAAACTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:55225 original size:54 final size:54
Alignment explanation
Indices: 55060--55249 Score: 228
Period size: 52 Copynumber: 3.5 Consensus size: 54
55050 TGTATGAGTA
* *
55060 TGTATCGGTACACTGAGGAGTGTATCGATACACTCAAAACATAGAATACCATTTG
1 TGTATCGGTACACTGAGGAGTGTATCAATACACTCAAAACATCGAATA-CATTTG
* * *
55115 TGTATCGGTACACT---GAGTGTATCGATACACTCAAAACATC-ATATGTCATTTA
1 TGTATCGGTACACTGAGGAGTGTATCAATACACTCAAAACATCGA-AT-ACATTTG
* * * *
55167 TGTATCAGTACACTGAGGAGTGTATCAATGCCCT-TAAACATCGAATACAATTTG
1 TGTATCGGTACACTGAGGAGTGTATCAATACACTCAAAACATCGAATAC-ATTTG
55221 TGTATCGGTACACTGAGGAGTGTATCAAT
1 TGTATCGGTACACTGAGGAGTGTATCAAT
55250 CCCCAGTTAT
Statistics
Matches: 117, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
51 1 0.01
52 45 0.38
53 1 0.01
54 41 0.35
55 29 0.25
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (54 bp):
TGTATCGGTACACTGAGGAGTGTATCAATACACTCAAAACATCGAATACATTTG
Found at i:55624 original size:21 final size:21
Alignment explanation
Indices: 55600--55648 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
55590 TGTTAGGAAT
55600 ATATGAACTTTGAA-CATGTGA
1 ATATGAACTTTGAATCA-GTGA
55621 ATATGAACTTTGAATCAGTGA
1 ATATGAACTTTGAATCAGTGA
*
55642 ATGTGAA
1 ATATGAA
55649 TATACTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (21 bp):
ATATGAACTTTGAATCAGTGA
Found at i:55823 original size:21 final size:21
Alignment explanation
Indices: 55799--55839 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
55789 TCGGGATAAT
55799 TATGTGGCACTTCGGTGCAAA
1 TATGTGGCACTTCGGTGCAAA
55820 TATGTGGCACTTCGGTGCAA
1 TATGTGGCACTTCGGTGCAA
55840 CCCTACTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGTGGCACTTCGGTGCAAA
Found at i:55853 original size:16 final size:16
Alignment explanation
Indices: 55828--55860 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55818 AATATGTGGC
*
55828 ACTTCGGTGCAACCCT
1 ACTTCAGTGCAACCCT
55844 ACTTCAGTGCAACCCT
1 ACTTCAGTGCAACCCT
55860 A
1 A
55861 TACGGCACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.36, G:0.15, T:0.24
Consensus pattern (16 bp):
ACTTCAGTGCAACCCT
Done.