Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000712.1 Hibiscus syriacus cultivar Beakdansim tig00001382_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: 63702
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:5690 original size:20 final size:21
Alignment explanation
Indices: 5649--5692 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
5639 TGATCGATTC
5649 CTTTCACAAAATGATAGATCT
1 CTTTCACAAAATGATAGATCT
*
5670 CTTTCACAAAA-GATTGATCT
1 CTTTCACAAAATGATAGATCT
5690 CTT
1 CTT
5693 ATGTCAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.36
Consensus pattern (21 bp):
CTTTCACAAAATGATAGATCT
Found at i:6383 original size:20 final size:20
Alignment explanation
Indices: 6360--6399 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6350 GGTAAATTAC
6360 GCATTTAGTATATAAACTAT
1 GCATTTAGTATATAAACTAT
*
6380 GCATTTAGTATCTAAACTAT
1 GCATTTAGTATATAAACTAT
6400 CAGTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (20 bp):
GCATTTAGTATATAAACTAT
Found at i:10200 original size:183 final size:183
Alignment explanation
Indices: 9868--10224 Score: 439
Period size: 183 Copynumber: 2.0 Consensus size: 183
9858 TTCACTAGCT
*
9868 TAACTTCTTCCCAGGAAGCATTTTTGGTTTCACTCTCTTCCTTCATCAGGGTTTCAGGGCAATTC
1 TAACTTCTTCCCAGGAAGCATTTTTGGTTTCACTCTCTTCCTTCATCAGGGTTTCAGGACAATTC
** * * * * *
9933 TCCTGTTTGCATTCTGAACTTTGGCCTGCTTCAATCACATGTGCTATTTCTGTGAATTCATGTTT
66 TCCTGTTTGCATTCTGAACTAAGGCCTGCTGCAATCACATGAGCTATTTCTCTGAATACATGTTC
* * * *
9998 CTCCCCAAACTCACAATGTAACTGGGCATCAACCAATCTTACCTGCCTCAATG
131 CTCCCCAAAATCACAATGTAACTGGGAAGCAACAAATCTTACCTGCCTCAATG
* * *
10051 TAACTTCTTCTC-GGCAAGCATTTTTGGTTTCCCTCTCTTCTTTCA-CAAGGGTTTCAGGACAAT
1 TAACTTCTTCCCAGG-AAGCATTTTTGGTTTCACTCTCTTCCTTCATC-AGGGTTTCAGGACAAT
* * * * * * **
10114 TTTCTTTTTTGCATTCTGTACTAAGGTCTGCTGCAATCTCATGAGCTATTTCTCTGGCTACATGT
64 TCTCCTGTTTGCATTCTGAACTAAGGCCTGCTGCAATCACATGAGCTATTTCTCTGAATACATGT
* ** *
10179 TCCTCGCCAAAATTGCAATGTAACTGGGAAGCATCAAATCTTACCT
129 TCCTCCCCAAAATCACAATGTAACTGGGAAGCAACAAATCTTACCT
10225 CATCAGAGTG
Statistics
Matches: 145, Mismatches: 27, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
182 3 0.02
183 142 0.98
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.37
Consensus pattern (183 bp):
TAACTTCTTCCCAGGAAGCATTTTTGGTTTCACTCTCTTCCTTCATCAGGGTTTCAGGACAATTC
TCCTGTTTGCATTCTGAACTAAGGCCTGCTGCAATCACATGAGCTATTTCTCTGAATACATGTTC
CTCCCCAAAATCACAATGTAACTGGGAAGCAACAAATCTTACCTGCCTCAATG
Found at i:16748 original size:5 final size:5
Alignment explanation
Indices: 16165--16741 Score: 810
Period size: 5 Copynumber: 115.0 Consensus size: 5
16155 TATAGTATTA
* * *
16165 TATAT TA-AGT TATAT TA-AT ATATAG TATAT TATA- AACATT TATAT
1 TATAT TATA-T TATAT TATAT -TATAT TATAT TATAT TATA-T TATAT
*
16210 TATAT TATA- TATA- TATAT T-TA- TATAGT ATATAT TATACAG TATAT
1 TATAT TATAT TATAT TATAT TATAT TATA-T -TATAT TAT--AT TATAT
* *
16255 TATAA TATAT TATAGT ACTATAT TATAT TATAT ATGTAT T-TAT ATATAT
1 TATAT TATAT TATA-T --TATAT TATAT TATAT -TATAT TATAT -TATAT
16304 TATAT TATAT TATAT TATAT TATAT TATAT TAT-T TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
16353 TATA- T-TAT TATAT TATAT TATAT TATAT TATAT TATA- TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
16400 TATAT TATAT TATAT TATTAT ATATAT ATATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TA-TAT -TATAT -TATAT TATAT TATAT TATAT
16448 TATAT TATAT ATATAT TATAT TATAT TATAT T-TAT TATA- T-TAT TATAT
1 TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
16496 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
16546 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
16596 TATAT TATAT TATAT TATAT TATAT TATA- TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
16645 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA- TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
16694 ATATAT ATATTAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 -TATAT -TA-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
16742 ATTATATGCA
Statistics
Matches: 528, Mismatches: 11, Indels: 66
0.87 0.02 0.11
Matches are distributed among these distances:
3 5 0.01
4 44 0.08
5 421 0.80
6 40 0.08
7 14 0.03
8 4 0.01
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:17181 original size:20 final size:21
Alignment explanation
Indices: 17140--17182 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17130 GAAGCAGTAT
17140 ACCAAGAAAATCAATAGAGAA
1 ACCAAGAAAATCAATAGAGAA
17161 ACCAAGAAAGA-CAAT-GAGAA
1 ACCAAGAAA-ATCAATAGAGAA
17181 AC
1 AC
17183 ATTGCATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 13 0.62
22 1 0.05
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.07
Consensus pattern (21 bp):
ACCAAGAAAATCAATAGAGAA
Found at i:24727 original size:2 final size:2
Alignment explanation
Indices: 24714--24750 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
24704 TTCTTCTTTC
* *
24714 AT AT AC AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24751 CACACACACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:24755 original size:2 final size:2
Alignment explanation
Indices: 24750--24776 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24740 ATATATATAT
24750 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
24777 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30395 original size:7 final size:7
Alignment explanation
Indices: 30383--30727 Score: 173
Period size: 7 Copynumber: 47.4 Consensus size: 7
30373 ATTGTTATAC
30383 TATATTA
1 TATATTA
30390 TATATTA
1 TATATTA
*
30397 TATAGTA
1 TATATTA
*
30404 TGGTATTA
1 T-ATATTA
*
30412 TATAACATA
1 TAT-A-TTA
*
30421 TATATTG
1 TATATTA
*
30428 TAATAGTA
1 T-ATATTA
30436 TATAGTATA
1 TATA-T-TA
30445 TAGTATTA
1 TA-TATTA
30453 TATA-T-
1 TATATTA
*
30458 TATGTTA
1 TATATTA
30465 TATTATTA
1 TA-TATTA
*
30473 TATAGTA
1 TATATTA
30480 TATATTA
1 TATATTA
30487 TATAACATT-
1 TAT---ATTA
30496 TATATTA
1 TATATTA
30503 TTCATATTA
1 -T-ATATTA
*
30512 TATATCA
1 TATATTA
30519 TATA--A
1 TATATTA
30524 TAT-TTA
1 TATATTA
*
30530 TATAGTA
1 TATATTA
30537 TATAATTA
1 TAT-ATTA
* *
30545 TACAGTA
1 TATATTA
30552 TATTATTA
1 TA-TATTA
30560 TATATTA
1 TATATTA
30567 TAGTACTATA
1 TA-TA-T-TA
30577 TTATATTA
1 -TATATTA
30585 TATA-TA
1 TATATTA
30591 T-TA-TA
1 TATATTA
30596 TGATATT-
1 T-ATATTA
30603 TATATTA
1 TATATTA
30610 TAGTA-TA
1 TA-TATTA
30617 TAT-TTA
1 TATATTA
*
30623 TATAGTA
1 TATATTA
30630 TATATGTA
1 TATAT-TA
30638 TTATATTA
1 -TATATTA
30646 TAGTA-TA
1 TA-TATTA
*
30653 GTATAGTA
1 -TATATTA
30661 TATATTTA
1 TATA-TTA
*
30669 TATAGTA
1 TATATTA
*
30676 AATATATA
1 TATAT-TA
30684 TATATTA
1 TATATTA
30691 TAGTATTA
1 TA-TATTA
*
30699 TTTATTA
1 TATATTA
30706 T-TA-TA
1 TATATTA
30711 TAT-TTA
1 TATATTA
30717 TTATATTA
1 -TATATTA
30725 TAT
1 TAT
30728 TATATTATGT
Statistics
Matches: 265, Mismatches: 29, Indels: 88
0.69 0.08 0.23
Matches are distributed among these distances:
5 15 0.06
6 28 0.11
7 113 0.43
8 72 0.27
9 26 0.10
10 9 0.03
11 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (7 bp):
TATATTA
Found at i:30410 original size:22 final size:21
Alignment explanation
Indices: 30369--30745 Score: 170
Period size: 20 Copynumber: 18.4 Consensus size: 21
30359 TTTTTATACA
*
30369 ATATATTGT-TATACTA-TATT
1 ATATATTATATATA-TAGTATT
*
30389 ATATATTATATAGTATGGTATT
1 ATATATTATATA-TATAGTATT
** *
30411 ATATAACATATATATTGTA--
1 ATATATTATATATATAGTATT
30430 ATAGTA-TATAGTATATAGTATT
1 ATA-TATTATA-TATATAGTATT
* *
30452 ATATATTATGT-TATATTATT
1 ATATATTATATATATAGTATT
* *
30472 ATATAGTATATAT-TA-TATA
1 ATATATTATATATATAGTATT
*
30491 ACAT-TTATAT-TATTCA-TATT
1 ATATATTATATATA-T-AGTATT
*
30511 ATATATCATATA-ATA-T-TT
1 ATATATTATATATATAGTATT
*
30529 ATATAGTATATAATTATACAGTA-T
1 ATATA-T-TAT-A-TATATAGTATT
30553 AT-TATTATATATTATAGTACTAT
1 ATATATTATATA-TATAGTA-T-T
*
30576 ATTATATTATATATATTA-TATG
1 A-TATATTATATATA-TAGTATT
30598 ATAT-TTATAT-TATAGTA-T
1 ATATATTATATATATAGTATT
30616 ATAT-TTATATAGTATA-TATGT
1 ATATATTATATA-TATAGTAT-T
*
30637 ATTATATTATA-GTATAGTA-T
1 A-TATATTATATATATAGTATT
* *
30657 AGTATA-TATTTATATAGTA-A
1 A-TATATTATATATATAGTATT
30677 ATATA-TATATATTATAGTATT
1 ATATATTATATA-TATAGTATT
*
30698 ATTTATTAT-TATATA-T-TT
1 ATATATTATATATATAGTATT
*
30716 ATTATATTATAT-TATATTATGT
1 A-TATATTATATATATAGTAT-T
30738 -TATATTAT
1 ATATATTAT
30746 TAATAATATT
Statistics
Matches: 281, Mismatches: 31, Indels: 90
0.70 0.08 0.22
Matches are distributed among these distances:
17 1 0.00
18 27 0.10
19 48 0.17
20 99 0.35
21 39 0.14
22 35 0.12
23 12 0.04
24 9 0.03
25 11 0.04
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (21 bp):
ATATATTATATATATAGTATT
Found at i:30470 original size:5 final size:5
Alignment explanation
Indices: 30453--30745 Score: 141
Period size: 5 Copynumber: 57.6 Consensus size: 5
30443 TATAGTATTA
* * *
30453 TATAT TATGT TATAT TAT-T ATATAGT ATATAT TATAT AACATT TATAT
1 TATAT TATAT TATAT TATAT -TATA-T -TATAT TATAT TATA-T TATAT
* * * *
30501 TAT-T CATAT TATAT ATCATAT AATAT T-TA- TATAG TATA- TA-AT TATACAG
1 TATAT TATAT TATAT -T-ATAT TATAT TATAT TATAT TATAT TATAT TAT--AT
30550 TATAT TAT-T ATATAT TATAGT ACTATAT TATAT TATA- TATAT TATAT
1 TATAT TATAT -TATAT TATA-T --TATAT TATAT TATAT TATAT TATAT
* * *
30597 GATATT TATAT TATAGT ATATAT T-TA- TATAG TATAT ATGTAT TATAT
1 TATA-T TATAT TATA-T -TATAT TATAT TATAT TATAT -TATAT TATAT
* * * *
30644 TATAG TATAG TATAG TATA- TAT-T TATA- TAGTAAA TATAT ATATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TA-T-AT TATAT -TATAT
* *
30689 TATAG TATTAT T-TAT TAT-T ATATAT T-TAT TATAT TATAT TATAT TATGT
1 TATAT TA-TAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT
30738 TATAT TAT
1 TATAT TAT
30746 TAATAATATT
Statistics
Matches: 229, Mismatches: 23, Indels: 72
0.71 0.07 0.22
Matches are distributed among these distances:
3 3 0.01
4 38 0.17
5 135 0.59
6 28 0.12
7 21 0.09
8 4 0.02
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (5 bp):
TATAT
Found at i:30532 original size:18 final size:17
Alignment explanation
Indices: 30478--30733 Score: 105
Period size: 18 Copynumber: 14.0 Consensus size: 17
30468 TATTATATAG
*
30478 TATATATTATATAACATT
1 TATATA-TATATAATATT
*
30496 TATAT-TAT-TCATA-T
1 TATATATATATAATATT
30510 TATATATCATATAATATT
1 TATATAT-ATATAATATT
*
30528 TATATAGTATATAAT-TA
1 TATATA-TATATAATATT
* *
30545 TACAGTATATTATTATATAT
1 TATA-TATA-TATAATAT-T
*
30565 TATAGTACTATATTATATT
1 TATA-TA-TATATAATATT
*
30584 ATATATATTATATGATATT
1 -TATATA-TATATAATATT
30603 TATAT-TATAGTATATATT
1 TATATATATA-TA-ATATT
30621 TATATAGTATATATGTATTATAT
1 TATATA-TATATA---A-TAT-T
* *
30644 TATAGTATAGTATAGTATA
1 TATA-TATA-TATAATATT
* *
30663 TATTTATATAGTAAATATA
1 TATATATATA-T-AATATT
*
30682 TATATATTATAGTATTATT
1 TATATA-TATA-TAATATT
30701 TAT-TAT-TAT-ATATT
1 TATATATATATAATATT
*
30715 TATTATATTATATTATATT
1 TA-TATA-TATATAATATT
30734 ATGTTATATT
Statistics
Matches: 190, Mismatches: 19, Indels: 57
0.71 0.07 0.21
Matches are distributed among these distances:
14 12 0.06
15 6 0.03
16 13 0.07
17 15 0.08
18 51 0.27
19 42 0.22
20 31 0.16
21 4 0.02
22 3 0.02
23 7 0.04
24 6 0.03
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (17 bp):
TATATATATATAATATT
Found at i:42515 original size:25 final size:25
Alignment explanation
Indices: 42478--42529 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
42468 TGATCGCTTA
* * *
42478 ATTTTGTATCATACTTTATAGTAAC
1 ATTTTGTAGCATACTCTATAATAAC
42503 ATTTTGTAGCATACTCTATAATAAC
1 ATTTTGTAGCATACTCTATAATAAC
42528 AT
1 AT
42530 CATTGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (25 bp):
ATTTTGTAGCATACTCTATAATAAC
Found at i:46357 original size:4 final size:4
Alignment explanation
Indices: 46348--46441 Score: 113
Period size: 4 Copynumber: 23.8 Consensus size: 4
46338 TTTAGAGGGA
* *
46348 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAAAG GAGA
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG G-AGG GAGG
* *
46397 GAGA G-GG GAGG GA-- GAGG GAGAG GAGA GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAGG GAGG GAG-G GAGG GAGG GAGG GAGG GAGG GAG
46442 AGGGAGAGAG
Statistics
Matches: 79, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.03
3 2 0.03
4 68 0.86
5 7 0.09
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:46450 original size:8 final size:8
Alignment explanation
Indices: 46341--46457 Score: 80
Period size: 8 Copynumber: 14.2 Consensus size: 8
46331 GCAAATATTT
46341 AGAGGGAG
1 AGAGGGAG
46349 AGGGAGGGAG
1 A--GAGGGAG
*
46359 GGAGGGAG
1 AGAGGGAG
*
46367 GGAGGGAG
1 AGAGGGAG
*
46375 GGAGGGAG
1 AGAGGGAG
*
46383 GGAGGGA-
1 AGAGGGAG
46390 A-AGGAGAG
1 AGAGG-GAG
46398 AGAGGG-G
1 AGAGGGAG
46405 AG-GGAGAG
1 AGAGG-GAG
*
46413 GGAGAGGAG
1 AGAG-GGAG
46422 AGAGGGAG
1 AGAGGGAG
*
46430 GGAGGGAGGG
1 AGAGGGA--G
46440 AGAGGGAG
1 AGAGGGAG
*
46448 AGAGAGAG
1 AGAGGGAG
46456 AG
1 AG
46458 CAAAACAAAA
Statistics
Matches: 91, Mismatches: 7, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
6 5 0.05
7 6 0.07
8 55 0.60
9 10 0.11
10 15 0.16
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (8 bp):
AGAGGGAG
Found at i:46454 original size:12 final size:12
Alignment explanation
Indices: 46341--46457 Score: 83
Period size: 12 Copynumber: 9.5 Consensus size: 12
46331 GCAAATATTT
*
46341 AGAGGGAGAGGG
1 AGAGAGAGAGGG
* *
46353 AGGGAGGGAGGG
1 AGAGAGAGAGGG
* *
46365 AGGGAGGGAGGG
1 AGAGAGAGAGGG
* *
46377 AGGGAGGGAGGG
1 AGAGAGAGAGGG
46389 AAAGGAGAGAGAGGG
1 --A-GAGAGAGAGGG
*
46404 -GAGGGAGAGGG
1 AGAGAGAGAGGG
46415 AGAGGAGAGAGGG
1 AGA-GAGAGAGGG
* *
46428 AGGGAGGGAGGG
1 AGAGAGAGAGGG
* *
46440 AGAGGGAGAGAG
1 AGAGAGAGAGGG
46452 AGAGAG
1 AGAGAG
46458 CAAAACAAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
11 10 0.12
12 56 0.65
13 10 0.12
14 1 0.01
15 9 0.10
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAGGG
Found at i:46704 original size:3 final size:3
Alignment explanation
Indices: 46689--46737 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
46679 TTTGTCCCAT
* *
46689 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46737 T
1 T
46738 AAAAAATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:46807 original size:21 final size:20
Alignment explanation
Indices: 46771--46829 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
46761 AATTTTATAG
* *
46771 GCCCAGATCTAGAACCCGGAG
1 GCCCAGATCCA-AACCCGGAA
* *
46792 GTCTAGATCCAAAACCCGGAA
1 GCCCAGATCC-AAACCCGGAA
46813 GCCCAGATCCAAACCCG
1 GCCCAGATCCAAACCCG
46830 ACCCAACACC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 7 0.23
21 23 0.74
22 1 0.03
ACGTcount: A:0.32, C:0.36, G:0.22, T:0.10
Consensus pattern (20 bp):
GCCCAGATCCAAACCCGGAA
Found at i:48025 original size:19 final size:18
Alignment explanation
Indices: 47996--48031 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
47986 TATTTTATGA
47996 ATTTTAATTTTAATTTAG
1 ATTTTAATTTTAATTTAG
*
48014 ATTTTAAATTTTATTTTA
1 ATTTT-AATTTTAATTTA
48032 TTATGTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTTAATTTTAATTTAG
Found at i:61123 original size:27 final size:26
Alignment explanation
Indices: 61093--61170 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 26
61083 GAAGGCACGT
*
61093 TGACTAGATCTTCTAGAAAACTGCCGC
1 TGACT-GACCTTCTAGAAAACTGCCGC
61120 TGACTGGACCTTCTAGAAAACTGCCGC
1 TGACT-GACCTTCTAGAAAACTGCCGC
61147 TGACTGAACCTTCTAG-AAACTGCC
1 TGACTG-ACCTTCTAGAAAACTGCC
61171 ACGTCAGACT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
26 9 0.19
27 39 0.81
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (26 bp):
TGACTGACCTTCTAGAAAACTGCCGC
Found at i:61563 original size:20 final size:20
Alignment explanation
Indices: 61538--61588 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
61528 TGAATATCAC
*
61538 CAATTGGAACACGTTAAATG
1 CAATTGGAACAAGTTAAATG
61558 CAATTGGAACAAGTTAAATG
1 CAATTGGAACAAGTTAAATG
*
61578 CAATTGTAACA
1 CAATTGGAACA
61589 TCCATTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (20 bp):
CAATTGGAACAAGTTAAATG
Done.