Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002107.1 Hibiscus syriacus cultivar Beakdansim tig00004310_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: 55861
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:1415 original size:12 final size:12
Alignment explanation
Indices: 1400--1424 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1390 CGTGGCTTCC
1400 GACGAGGATCGT
1 GACGAGGATCGT
1412 GACGAGGATCGT
1 GACGAGGATCGT
1424 G
1 G
1425 TCGTGCATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.44, T:0.16
Consensus pattern (12 bp):
GACGAGGATCGT
Found at i:1516 original size:29 final size:29
Alignment explanation
Indices: 1454--1588 Score: 110
Period size: 29 Copynumber: 4.5 Consensus size: 29
1444 AACCCAACCA
* * **
1454 TAGGTCGCCAAGCACTCCAAGCGACCTAC
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
*
1483 AAGGTCGCCATGCACTCCCAGCGACCTTG
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
** * *
1512 TAGGTCGCCAAACAATCCC-GACGACCAAGATGG
1 TAGGTCGCCATGCACTCCCAG-CGACC----TTG
* * *
1545 TAGGTCGCCATGTACGCCCAGCGACCTTA
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
1574 TAGGTCGCCATGCAC
1 TAGGTCGCCATGCAC
1589 GCCGGCGTCC
Statistics
Matches: 82, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
28 1 0.01
29 59 0.72
33 21 0.26
34 1 0.01
ACGTcount: A:0.25, C:0.35, G:0.24, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCTTG
Found at i:2254 original size:21 final size:20
Alignment explanation
Indices: 2207--2254 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
2197 ACAGAAATTT
2207 AGTTAATTAGTTGTTAGTATA
1 AGTT-ATTAGTTGTTAGTATA
* *
2228 AATTATTAGTTTGTTAGTTTA
1 AGTTATTAG-TTGTTAGTATA
2249 AGTTAT
1 AGTTAT
2255 ATTTATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (20 bp):
AGTTATTAGTTGTTAGTATA
Found at i:2267 original size:27 final size:28
Alignment explanation
Indices: 2213--2285 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
2203 ATTTAGTTAA
* * *
2213 TTAGTTGTTAGTATA-AATTATTAGTTTG
1 TTAGTT-TAAGTATATATTTATTAATTTG
2241 TTAGTTTAAGT-TATATTTATTAATTTG
1 TTAGTTTAAGTATATATTTATTAATTTG
2268 TTAGTTTAAGTATATATT
1 TTAGTTTAAGTATATATT
2286 AGATTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
26 2 0.05
27 26 0.65
28 12 0.30
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (28 bp):
TTAGTTTAAGTATATATTTATTAATTTG
Found at i:5358 original size:60 final size:59
Alignment explanation
Indices: 5286--6037 Score: 908
Period size: 58 Copynumber: 13.2 Consensus size: 59
5276 TTTATAAGAT
*
5286 TTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATTTGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAA--TGA
*
5347 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
5405 TTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATGAT--T--TGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
5456 -TAGTAATGATTAGTAATAATGAAATTATTATT-ATA-TTAATGATTTGATATTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
* *
5512 TTTAGTAATGATTAGT-ATAATGAAATTATTATTAATATTTAATTA-TTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
5570 TTTAGTAATG-TTAGT-ATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
5628 TTTAGTAATGA-TAGTAATAATGAAATTATTATTAATATTT-ATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
5686 TTTAGTAAT-ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
5745 TTTAATAATGATTAGT-ATAATGAAATTATTATTAAT-TTTAATGATTTGATA-TAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
5802 TTTAGTAATGATTAGTAATAATGAAA--ATTA-TCA-ATTT--T-A--TGAT--T--TGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
* *
5849 -TAGTAATGATTAGTAATAATGAAATCATTATTAAT-TTTAATGATTTAATA-TAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
5905 TTTAG-AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGTTAATG
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG--A-T-A-G-TAATG
5969 A
59 A
*
5970 TTAGTAATGATTAGTAATAATG-AA--ATTATTAAT-TTTAATAATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
6025 TTAGTAATAATTA
1 TTAGTAATGATTA
6038 AATTATTAAT
Statistics
Matches: 626, Mismatches: 19, Indels: 98
0.84 0.03 0.13
Matches are distributed among these distances:
45 24 0.04
47 7 0.01
48 9 0.01
49 33 0.05
50 6 0.01
51 5 0.01
52 5 0.01
53 5 0.01
54 2 0.00
55 27 0.04
56 12 0.02
57 103 0.16
58 163 0.26
59 79 0.13
60 95 0.15
61 12 0.02
62 10 0.02
64 6 0.01
65 23 0.04
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (59 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
Found at i:5390 original size:35 final size:35
Alignment explanation
Indices: 5350--5452 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 35
5340 AATTTGATAG
5350 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAATTTT
* * * *
5385 TAATGATT--TGAT-A-GTAATGA-T-TT-A---G
1 TAATGATTAGTAATAATGAAATTATTATTAATTTT
5410 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAATTTT
5445 TAATGATT
1 TAATGATT
5453 TGATAGTAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
25 8 0.16
27 3 0.06
28 2 0.04
29 7 0.14
30 2 0.04
31 7 0.14
32 2 0.04
33 3 0.06
35 16 0.32
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.48
Consensus pattern (35 bp):
TAATGATTAGTAATAATGAAATTATTATTAATTTT
Found at i:5507 original size:14 final size:14
Alignment explanation
Indices: 5488--5514 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5478 AATTATTATT
5488 ATATTAATGATTTG
1 ATATTAATGATTTG
5502 ATATTAATGATTT
1 ATATTAATGATTT
5515 AGTAATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (14 bp):
ATATTAATGATTTG
Found at i:5537 original size:57 final size:59
Alignment explanation
Indices: 5456--6302 Score: 1058
Period size: 58 Copynumber: 15.2 Consensus size: 59
5446 AATGATTTGA
* *
5456 TAGTAATGATTAGTAATAATGAAATTATTATT-ATATTAATGATTTGATATTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATT
* *
5514 TAGTAATGATTAGT-ATAATGAAATTATTATTAATATTTAATTA-TTGATATTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTTAATGATTTGATAGTAATGATT
5572 TAGTAATG-TTAGT-ATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAA-TTTTAATGATTTGATAGTAATGATT
*
5630 TAGTAATGA-TAGTAATAATGAAATTATTATTAATATTT-ATGATTTGATATTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTTAATGATTTGATAGTAATGATT
*
5688 TAGTAAT-ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTTAATGATTTGATAGTAATGATT
*
5747 TAATAATGATTAGT-ATAATGAAATTATTATTAATTTTAATGATTTGATA-TAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATT
*
5804 TAGTAATGATTAGTAATAATGAAA--ATTATCAA-TTT--T-A--TGAT--T--TGA--
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATT
* *
5849 TAGTAATGATTAGTAATAATGAAATCATTATTAATTTTAATGATTTAATA-TAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATT
5907 TAG-AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGTTAATGAT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAA-TTTTAATGATTTGATAGTAATG---AT--T
5971 TAGTAATGATTAGTAATAATG-AA--ATTATTAATTTTAAT-A----AT--T--TGA--
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATT
* *
6016 TAGTAATGATTAGTAATAATTAAATTATTA--ATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATT
*
6073 TAGTAATGATTAGT-ATAATGAAATTATTA--ATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATT
6129 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAA-TTTTAATGATTTGATAGTAATGATT
6189 TAGTAATGATTAGT-ATAATGAAATTATTA-TAATTTTAATGATTTGATAGTAATGA-T
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATT
6245 TAGTAAT-A--A-TAAT--T---ATTATTA-T-A-TTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATT
6292 TAGTAATGATT
1 TAGTAATGATT
6303 GATAGTAATG
Statistics
Matches: 718, Mismatches: 16, Indels: 118
0.84 0.02 0.14
Matches are distributed among these distances:
45 44 0.06
46 32 0.04
47 20 0.03
48 16 0.02
49 2 0.00
50 5 0.01
51 4 0.01
52 4 0.01
53 8 0.01
54 2 0.00
55 7 0.01
56 75 0.10
57 151 0.21
58 167 0.23
59 95 0.13
60 46 0.06
61 7 0.01
62 10 0.01
64 6 0.01
65 17 0.02
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (59 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATT
Found at i:5685 original size:14 final size:14
Alignment explanation
Indices: 5662--5747 Score: 50
Period size: 14 Copynumber: 5.9 Consensus size: 14
5652 ATTATTATTA
*
5662 ATATTTATGATTTG
1 ATATTAATGATTTG
5676 ATATTAATGATTTAG
1 ATATTAATGATTT-G
* * *
5691 TAATATTAGTAATAATG
1 --ATATTAATGAT-TTG
* * *
5708 AAATT-ATTA-TTA
1 ATATTAATGATTTG
5720 ATATTTAATGATTTG
1 ATA-TTAATGATTTG
5735 ATATTAATGATTT
1 ATATTAATGATTT
5748 AATAATGATT
Statistics
Matches: 53, Mismatches: 12, Indels: 14
0.67 0.15 0.18
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 27 0.51
15 10 0.19
17 10 0.19
18 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (14 bp):
ATATTAATGATTTG
Found at i:5853 original size:45 final size:47
Alignment explanation
Indices: 5804--5906 Score: 158
Period size: 45 Copynumber: 2.2 Consensus size: 47
5794 TATAATGATT
*
5804 TAGTAATGATTAGTAATAATGAAA-ATTATCAATTTT-ATGATTTGA
1 TAGTAATGATTAGTAATAATGAAACATTATCAATTTTAATGATTTAA
*
5849 TAGTAATGATTAGTAATAATGAAATCATTATTAATTTTAATGATTTAA
1 TAGTAATGATTAGTAATAATGAAA-CATTATCAATTTTAATGATTTAA
5897 TA-TAATGATT
1 TAGTAATGATT
5907 TAGAATGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
45 24 0.45
47 19 0.36
48 10 0.19
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.44
Consensus pattern (47 bp):
TAGTAATGATTAGTAATAATGAAACATTATCAATTTTAATGATTTAA
Found at i:6021 original size:45 final size:47
Alignment explanation
Indices: 5971--6135 Score: 210
Period size: 56 Copynumber: 3.4 Consensus size: 47
5961 TGTTAATGAT
*
5971 TAGTAATGA-TTAGTAATAATGAAATTATTAA-TTTTAATAATTTGA
1 TAGTAATGATTTAGTAATAATGAAATTATTAATTTTTAATGATTTGA
*
6016 TAGTAATGA-TTAGTAATAATTAAATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTTAGTAATAATGAAATTATTAATTTTTAATGATTTGA
6062 TAGTAATGATTTAGTAATGATTAGTATAATGAAATTATTAATTTTTAATGATTTGA
1 TAGTAATGA-TT--T-A-G--TA--ATAATGAAATTATTAATTTTTAATGATTTGA
6118 TAGTAATGATTTAGTAAT
1 TAGTAATGATTTAGTAAT
6136 GATTAGTAAT
Statistics
Matches: 106, Mismatches: 3, Indels: 20
0.82 0.02 0.16
Matches are distributed among these distances:
45 30 0.28
46 22 0.21
47 2 0.02
48 1 0.01
49 2 0.02
50 1 0.01
51 2 0.02
52 2 0.02
53 1 0.01
54 2 0.02
55 2 0.02
56 39 0.37
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (47 bp):
TAGTAATGATTTAGTAATAATGAAATTATTAATTTTTAATGATTTGA
Found at i:6055 original size:32 final size:31
Alignment explanation
Indices: 6019--6114 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 31
6009 AATTTGATAG
6019 TAATGATTAGTAATAATTAAATTATTAATTTT
1 TAATGATTAGT-ATAATTAAATTATTAATTTT
* * * **
6051 TAATGATTTG-AT-AGT-AATGA-T--TTAG
1 TAATGATTAGTATAATTAAATTATTAATTTT
*
6076 TAATGATTAGTATAATGAAATTATTAATTTT
1 TAATGATTAGTATAATTAAATTATTAATTTT
6107 TAATGATT
1 TAATGATT
6115 TGATAGTAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 13
0.66 0.15 0.18
Matches are distributed among these distances:
25 11 0.23
26 2 0.04
27 2 0.04
28 8 0.17
29 3 0.06
30 2 0.04
31 10 0.21
32 9 0.19
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (31 bp):
TAATGATTAGTATAATTAAATTATTAATTTT
Found at i:6057 original size:559 final size:546
Alignment explanation
Indices: 5287--6302 Score: 1574
Period size: 559 Copynumber: 1.8 Consensus size: 546
5277 TTATAAGATT
* * *
5287 TAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATTTGATAGTA
1 TAGTAATGATTAGTAATAATGAAATCATTATTAATATTTAATGATTTAATAGTAATTT-ATAGTA
5352 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGAT
65 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGAT
*
5417 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATT
130 TAGTAATAATGAAA-TATTATTAATTTTTAATAATTTGATAGTAATGATTAGTAATAATGAAATT
*
5482 ATTATTATATTAATGATTTGATATTAATGATTTAGTAATGATTAGTATAATGAAATTATTATTAA
194 ATTATTATATTAATGATTTGATAGTAATGATTTAGTAATGATTAGTATAATG-AA--ATTATTAA
* *
5547 TATTTAATTA-TTGATATTAATGATTTAGTAATG-TTAGT-ATAATGAAATTATTATTAATTTTT
256 TATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT
5609 AATGATTTGATAGTAATGATTTAGTAATGA-TAGTAATAATGAAATTATTATTAATATTTATGAT
321 AATGATTTGATAGTAATGATTTAGTAATGATTAGT-ATAATGAAATTATTA-TAAT-TTTA--A-
5673 TTGATATTAATGATTTAGTAAT-ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGAT
380 -TG--ATT--TGA--TAGTAATGATTAGTAATAAT--AATTATTATT-ATATTTAATGATTTGAT
*
5737 ATTAATGATTTAATAATGATTAGTATAATGAAATTATTATTAATTTTAATGATTTGATATAATGA
435 AGTAATGATTTAATAATGATTAGTATAATGAAATTATTATTAATTTTAATGATTTGATATAATGA
5802 TTTAGTAATGATTAGTAATAATGAAAATTATCAATTTTATGATTTGA
500 TTTAGTAATGATTAGTAATAATGAAAATTATCAATTTTATGATTTGA
5849 TAGTAATGATTAGTAATAATGAAATCATTATTAAT-TTTAATGATTTAATA-TAATGATT-TAG-
1 TAGTAATGATTAGTAATAATGAAATCATTATTAATATTTAATGATTTAATAGTAAT--TTATAGT
5910 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGTTAATGATTAGT
64 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATG---AT--TTAGT
*
5975 AATGATTAGTAATAATG-AA-ATTATTAA-TTTTAATAATTTGATAGTAATGATTAGTAATAATT
124 AATGATTAGTAATAATGAAATATTATTAATTTTTAATAATTTGATAGTAATGATTAGTAATAATG
6037 AAATTATTAATT-T-TTAATGATTTGATAGTAATGATTTAGTAATGATTAGTATAATGAAATTAT
189 AAATTATT-ATTATATTAATGATTTGATAGTAATGATTTAGTAATGATTAGTATAATGAAATTAT
*
6100 TAATTTTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT
253 TAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT
6165 TTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTATAATGAAATTATTATAATTTTAATGA
318 TTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTATAATGAAATTATTATAATTTTAATGA
*
6230 TTTGATAGTAATGATTAGTAATAATAATTATTATTATATTTAATGATTTGATAGTAATGATTTAG
383 TTTGATAGTAATGATTAGTAATAATAATTATTATTATATTTAATGATTTGATAGTAATGATTTAA
6295 TAATGATT
448 TAATGATT
6303 GATAGTAATG
Statistics
Matches: 430, Mismatches: 11, Indels: 43
0.89 0.02 0.09
Matches are distributed among these distances:
545 36 0.08
546 10 0.02
547 7 0.02
548 12 0.03
549 3 0.01
551 3 0.01
553 2 0.00
555 1 0.00
556 16 0.04
557 26 0.06
558 11 0.03
559 164 0.38
560 53 0.12
561 25 0.06
562 37 0.09
563 2 0.00
564 22 0.05
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (546 bp):
TAGTAATGATTAGTAATAATGAAATCATTATTAATATTTAATGATTTAATAGTAATTTATAGTAA
TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGATT
AGTAATAATGAAATATTATTAATTTTTAATAATTTGATAGTAATGATTAGTAATAATGAAATTAT
TATTATATTAATGATTTGATAGTAATGATTTAGTAATGATTAGTATAATGAAATTATTAATATTT
AATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGA
TTTGATAGTAATGATTTAGTAATGATTAGTATAATGAAATTATTATAATTTTAATGATTTGATAG
TAATGATTAGTAATAATAATTATTATTATATTTAATGATTTGATAGTAATGATTTAATAATGATT
AGTATAATGAAATTATTATTAATTTTAATGATTTGATATAATGATTTAGTAATGATTAGTAATAA
TGAAAATTATCAATTTTATGATTTGA
Found at i:6087 original size:10 final size:11
Alignment explanation
Indices: 6062--6203 Score: 55
Period size: 11 Copynumber: 12.5 Consensus size: 11
6052 AATGATTTGA
6062 TAGTAATGATT
1 TAGTAATGATT
6073 TAGTAATGA-T
1 TAGTAATGATT
*
6083 TAGTATAATGAAAT
1 TAG--TAATG-ATT
*
6097 TATTAAT--TT
1 TAGTAATGATT
6106 T--TAATGATTT
1 TAGTAATGA-TT
6116 GATAGTAATGATT
1 --TAGTAATGATT
6129 TAGTAATGATT
1 TAGTAATGATT
* *
6140 AGTAATAATGAAAT
1 --TAGTAATG-ATT
* * *
6154 TATTATTAATT
1 TAGTAATGATT
*
6165 T-TTAATGATTT
1 TAGTAATGA-TT
6176 GATAGTAATGATT
1 --TAGTAATGATT
6189 TAGTAATGA-T
1 TAGTAATGATT
6199 TAGTA
1 TAGTA
6204 TAATGAAATT
Statistics
Matches: 102, Mismatches: 11, Indels: 37
0.68 0.07 0.25
Matches are distributed among these distances:
7 4 0.04
9 2 0.02
10 17 0.17
11 34 0.33
12 15 0.15
13 13 0.13
14 17 0.17
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:6142 original size:21 final size:20
Alignment explanation
Indices: 6118--6203 Score: 52
Period size: 21 Copynumber: 4.2 Consensus size: 20
6108 AATGATTTGA
6118 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
6139 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * * *
6157 TATTAATTTTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
6178 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
6199 TAGTA
1 TAGTA
6204 TAATGAAATT
Statistics
Matches: 45, Mismatches: 14, Indels: 12
0.63 0.20 0.17
Matches are distributed among these distances:
18 12 0.27
19 2 0.04
20 4 0.09
21 20 0.44
22 7 0.16
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (20 bp):
TAGTAATATTTAGTAATGAT
Found at i:6171 original size:46 final size:49
Alignment explanation
Indices: 6121--6298 Score: 181
Period size: 46 Copynumber: 3.6 Consensus size: 49
6111 GATTTGATAG
6121 TAATGA-TT-TAGTAATGA-TTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTTATAGTAATGATTTAGTAATAATGAAATTATTATTAATTTT
* * *
6167 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTATAATGAAATTATTATAATTT
1 TAATGATTT-ATAGTAATGATTTAGTAAT-AAT-G-A-AAT--TATTATTA-ATTTT
*
6224 TAATGATTTGATAGTAATGA-TTAGTAATAAT--AATTATTATT-ATATT
1 TAATGATTT-ATAGTAATGATTTAGTAATAATGAAATTATTATTAATTTT
6270 TAATGATTTGATAGTAATGATTTAGTAAT
1 TAATGATTT-ATAGTAATGATTTAGTAAT
6299 GATTGATAGT
Statistics
Matches: 113, Mismatches: 7, Indels: 23
0.79 0.05 0.16
Matches are distributed among these distances:
46 29 0.26
47 10 0.09
48 6 0.05
49 9 0.08
50 11 0.10
51 2 0.02
52 1 0.01
53 1 0.01
54 3 0.03
55 2 0.02
56 15 0.13
57 24 0.21
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (49 bp):
TAATGATTTATAGTAATGATTTAGTAATAATGAAATTATTATTAATTTT
Found at i:6252 original size:219 final size:219
Alignment explanation
Indices: 5341--6302 Score: 1154
Period size: 219 Copynumber: 4.3 Consensus size: 219
5331 TTTGATAGTA
*
5341 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
1 ATTTGATAGTAATGATTAGTAATAAT-TAA--ATTATTAATTTTTAATGATTTGATAGTAATGAT
* *
5406 TTAGTAATGATTAGTAATAATGAAATTATTA--TTAAT-TTTTAAT-G-ATTTGA--TAGTAATG
63 TTAGTAATGATTAGTAATAATGAAATTATTATTTTAATGATTTAATAGTA-ATGATTTAGTAATG
* *
5464 ATTAGTAATAATGAAATTATTATT-A-TATTAATGATTTGATATTAATGATTTAGTAATGATTAG
127 ATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGATTAG
*
5527 TATAATGAAATTATTATTAATATTTAATT
192 TATAATGAAATTATTATTAAT-TTTAATG
*
5556 A-TTGATATTAATGATTTAGTAATGTTAGTATAATGAAATTATTATTAATTTTTAATGATTTGAT
1 ATTTGATAGTAATGA-TTAGTAA---TA--AT--T--AA--ATTATTAATTTTTAATGATTTGAT
* * *
5620 AGTAATGATTTAGTAATGA-TAGTAATAATGAAATTATTATTAATATTTATGATTTGATATTAAT
54 AGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTA-T--T-TTAATGATTTAATAGTAAT
* *
5684 GATTTAGTAAT-ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTT
115 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTT
*
5748 AATAATGATTAGTATAATGAAATTATTATTAATTTTAATG
180 AGTAATGATTAGTATAATGAAATTATTATTAATTTTAATG
* * * * * *
5788 ATTTGATA-TAATGATTTAGTAATGATTAGTAATAATGAAAATTATCAAT--TTT-AT-G-ATTT
1 ATTTGATAGTAATGA-TTAGTAATAATTA--AATTAT--TAATTTTTAATGATTTGATAGTA-AT
5847 GA--TAGTAATGATTAGTAATAATGAAATCATTATTAATTTTAATGATTTAATA-TAATGATTTA
60 GATTTAGTAATGATTAGTAATAATG-AA--ATTATT-ATTTTAATGATTTAATAGTAATGATTTA
5909 G-AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGTTAATGATTA
121 GTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATG---AT--TTA
*
5973 GTAATGATTAGTAATAATG-AA--ATTATTAATTTTAATA
181 GTAATGATTAGT-ATAATGAAATTATTATTAATTTTAATG
6010 ATTTGATAGTAATGATTAGTAATAATTAAATTATTAATTTTTAATGATTTGATAGTAATGATTTA
1 ATTTGATAGTAATGATTAGTAATAATTAAATTATTAATTTTTAATGATTTGATAGTAATGATTTA
*
6075 GTAATGATTAGT-ATAATGAAATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGAT
66 GTAATGATTAGTAATAATGAAATTATT-A-TTTTAATGATTTAATAGTAATGATTTAGTAATGAT
6139 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTA
129 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTA
6204 TAATGAAATTATTA-TAATTTTAATG
194 TAATGAAATTATTATTAATTTTAATG
*
6229 ATTTGATAGTAATGATTAGTAATAA-T-AATTATTATTATATTTAATGATTTGATAGTAATGATT
1 ATTTGATAGTAATGATTAGTAATAATTAAATTATTA--ATTTTTAATGATTTGATAGTAATGATT
6292 TAGTAATGATT
64 TAGTAATGATT
6303 GATAGTAATG
Statistics
Matches: 658, Mismatches: 33, Indels: 108
0.82 0.04 0.14
Matches are distributed among these distances:
214 12 0.02
215 8 0.01
217 14 0.02
218 31 0.05
219 139 0.21
220 48 0.07
221 24 0.04
222 76 0.12
223 128 0.19
224 31 0.05
225 16 0.02
227 2 0.00
228 4 0.01
229 6 0.01
230 3 0.00
231 25 0.04
232 29 0.04
233 62 0.09
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (219 bp):
ATTTGATAGTAATGATTAGTAATAATTAAATTATTAATTTTTAATGATTTGATAGTAATGATTTA
GTAATGATTAGTAATAATGAAATTATTATTTTAATGATTTAATAGTAATGATTTAGTAATGATTA
GTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTATA
ATGAAATTATTATTAATTTTAATG
Found at i:6297 original size:11 final size:11
Alignment explanation
Indices: 6281--6317 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
6271 AATGATTTGA
6281 TAGTAATGATT
1 TAGTAATGATT
6292 TAGTAATGATT
1 TAGTAATGATT
6303 GATAGTAATGATT
1 --TAGTAATGATT
6316 TA
1 TA
6318 CGACTTGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 13 0.54
13 11 0.46
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:6305 original size:24 final size:25
Alignment explanation
Indices: 6270--6317 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
6260 TTATTATATT
6270 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
6295 TAATGA-TTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
6318 CGACTTGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:6310 original size:13 final size:13
Alignment explanation
Indices: 6270--6315 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
6260 TTATTATATT
6270 TAATGATTTGATAG
1 TAATGA-TTGATAG
6284 TAATGATT--TAG
1 TAATGATTGATAG
6295 TAATGATTGATAG
1 TAATGATTGATAG
6308 TAATGATT
1 TAATGATT
6316 TACGACTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.37
13 13 0.43
14 6 0.20
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (13 bp):
TAATGATTGATAG
Found at i:8664 original size:30 final size:30
Alignment explanation
Indices: 8621--8723 Score: 106
Period size: 30 Copynumber: 3.4 Consensus size: 30
8611 TCCCTTAAAC
*
8621 AACTAAT-AACTATTCTTTAATATAACGTT-
1 AACTAATAAACTATTCTTTAATATAA-ATTA
8650 AACTAATAAACTATTCTTTAATATAAATTA
1 AACTAATAAACTATTCTTTAATATAAATTA
*
8680 AACTAATAAA-TGATT-TTTAATTATAATTTA
1 AACTAATAAACT-ATTCTTTAA-TATAAATTA
* *
8710 CTACTAAAAAACTA
1 -AACTAATAAACTA
8724 ATTAACTAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
29 15 0.23
30 39 0.61
31 9 0.14
32 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.40
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTAATATAAATTA
Found at i:8926 original size:21 final size:21
Alignment explanation
Indices: 8902--8941 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
8892 TTTCTATATG
8902 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
8923 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
8942 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:9022 original size:18 final size:18
Alignment explanation
Indices: 8969--9023 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
8959 TTGTTTTACC
*
8969 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
8987 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
8999 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
9016 CTAATTTA
1 CTAATTTA
9024 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:9082 original size:35 final size:37
Alignment explanation
Indices: 9043--9114 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 37
9033 TCTTTTATAT
9043 AACTT-AA-ACTAATAAACT-ATTTTTTATTATAATAA
1 AACTTAAACACTAATAAACTAATTTTTTA-TATAATAA
9078 AACTTAAACTACTAATAAACTAATTTTTTATATAATA
1 AACTTAAAC-ACTAATAAACTAATTTTTTATATAATA
9115 TAAATTCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
35 5 0.15
36 2 0.06
38 18 0.55
39 8 0.24
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.42
Consensus pattern (37 bp):
AACTTAAACACTAATAAACTAATTTTTTATATAATAA
Found at i:9174 original size:27 final size:29
Alignment explanation
Indices: 9139--9203 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
9129 AAAATATAAC
*
9139 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
9166 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
9194 TTAATTATTT
1 TTAAATATTT
9204 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:9521 original size:12 final size:11
Alignment explanation
Indices: 9494--9527 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
9484 TCACGGGCTA
9494 CAATAATGCAG
1 CAATAATGCAG
*
9505 CAATAAGTGCTG
1 CAATAA-TGCAG
9517 CAATAATGCAG
1 CAATAATGCAG
9528 TTGATTTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.21
Consensus pattern (11 bp):
CAATAATGCAG
Found at i:9669 original size:29 final size:29
Alignment explanation
Indices: 9622--9734 Score: 174
Period size: 29 Copynumber: 3.9 Consensus size: 29
9612 AAAGGCATAG
*
9622 GTCGTTGGGA-TCCCTTGGCGACCTACAAT
1 GTCGCTGGGATTCCC-TGGCGACCTACAAT
* *
9651 GTCGCTGGGATGCCCTGGCAACCTACAAT
1 GTCGCTGGGATTCCCTGGCGACCTACAAT
9680 GTCGCTGGGATTCCCTGGCGACCTACAAT
1 GTCGCTGGGATTCCCTGGCGACCTACAAT
*
9709 GTCGCTGGGATTCCCTGGCTACCTAC
1 GTCGCTGGGATTCCCTGGCGACCTAC
9735 CCACGTTGCA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
29 74 0.96
30 3 0.04
ACGTcount: A:0.17, C:0.31, G:0.27, T:0.25
Consensus pattern (29 bp):
GTCGCTGGGATTCCCTGGCGACCTACAAT
Found at i:10073 original size:29 final size:29
Alignment explanation
Indices: 10047--10104 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
10037 GCTGGGCGTG
10047 CATGG-AGGTCGCTGGGCGTGCATGGCGA
1 CATGGTAGGTCGCTGGGCGTGCATGGCGA
* * *
10075 CCTGGTAGGTCGGTGGGCTTGCATGGCGA
1 CATGGTAGGTCGCTGGGCGTGCATGGCGA
10104 C
1 C
10105 CTACCCCCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.12, C:0.22, G:0.45, T:0.21
Consensus pattern (29 bp):
CATGGTAGGTCGCTGGGCGTGCATGGCGA
Found at i:23882 original size:19 final size:20
Alignment explanation
Indices: 23860--23903 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
23850 TACATTATAT
*
23860 TTTTTTTGAATTTTATT-CA
1 TTTTTTTCAATTTTATTGCA
* *
23879 TTTTATTCATTTTTATTGCA
1 TTTTTTTCAATTTTATTGCA
23899 TTTTT
1 TTTTT
23904 ATTTATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTTTTCAATTTTATTGCA
Found at i:23902 original size:11 final size:10
Alignment explanation
Indices: 23870--23911 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
23860 TTTTTTTGAA
23870 TTTTATTCA-
1 TTTTATTCAT
23879 TTTTATTCAT
1 TTTTATTCAT
23889 TTTTATTGCAT
1 TTTTATT-CAT
*
23900 TTTTATTTAT
1 TTTTATTCAT
23910 TT
1 TT
23912 AAAAATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 9 0.30
10 11 0.37
11 10 0.33
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTATTCAT
Found at i:24492 original size:2 final size:2
Alignment explanation
Indices: 24485--24544 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
24475 TCTTTCTTCA
24485 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
24527 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
24545 GATTTTTGAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26396 original size:20 final size:20
Alignment explanation
Indices: 26371--26428 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
26361 ATCCTATTCC
26371 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
26391 CTGGTAATCTTACATTCTCA
1 CTGGTAATCTTACATTCCCA
*
26411 CTGGTAATCTTATATTCC
1 CTGGTAATCTTACATTCC
26429 GTGAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:31415 original size:40 final size:40
Alignment explanation
Indices: 31370--31461 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
31360 CAAAACTTGC
* * *
31370 GAAGCAACAGATTC-AACGAAGAGGGAGTGAGATTGGCGAA
1 GAAGCAGCAGATTCGAA-GAAGAGGGAGTGAGATCGGCAAA
* * *
31410 TAAGCAGTAGATTCGGAGAAGAGGGAGTGAGATCGGCAAA
1 GAAGCAGCAGATTCGAAGAAGAGGGAGTGAGATCGGCAAA
31450 GAAGCAGCAGAT
1 GAAGCAGCAGAT
31462 GGGTTTAGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 42 0.98
41 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.36, T:0.13
Consensus pattern (40 bp):
GAAGCAGCAGATTCGAAGAAGAGGGAGTGAGATCGGCAAA
Found at i:31451 original size:20 final size:20
Alignment explanation
Indices: 31388--31451 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
31378 AGATTCAACG
* *
31388 AAGAGGGAGTGAGATTGGCG
1 AAGAGGGAGTGAGATCGGCA
* * *
31408 AATAAGCAGT-AGATTCGG-A
1 AAGAGGGAGTGAGA-TCGGCA
31427 GAAGAGGGAGTGAGATCGGCA
1 -AAGAGGGAGTGAGATCGGCA
31448 AAGA
1 AAGA
31452 AGCAGCAGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
19 3 0.09
20 25 0.78
21 4 0.12
ACGTcount: A:0.38, C:0.08, G:0.41, T:0.14
Consensus pattern (20 bp):
AAGAGGGAGTGAGATCGGCA
Found at i:31858 original size:41 final size:41
Alignment explanation
Indices: 31759--31860 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
31749 GTATCTTATT
* * * *
31759 ACGGAGTTTGTTTAAAAA-GCTACTAAAGGAGTAGTCTGTA
1 ACGGCGTTTGTTTAAAAACGCTACTAAAGCAGAAGTCTATA
* * *
31799 GCGGCGTTTGTTTGAAAACGCTACTAAATCAGAAGTCTATA
1 ACGGCGTTTGTTTAAAAACGCTACTAAAGCAGAAGTCTATA
*
31840 ACGGCGTTTGTTCAAAAACGC
1 ACGGCGTTTGTTTAAAAACGC
31861 CAATAAAATA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 15 0.29
41 36 0.71
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (41 bp):
ACGGCGTTTGTTTAAAAACGCTACTAAAGCAGAAGTCTATA
Found at i:31925 original size:42 final size:43
Alignment explanation
Indices: 31764--31927 Score: 121
Period size: 41 Copynumber: 4.0 Consensus size: 43
31754 TTATTACGGA
* * * * *
31764 GTTTGTTT-AAAAA-GCTACTAAAGGA-GTAGTCTGTAGCGGC
1 GTTTGTTTGAAAAACGCCACTAAAGTACGAAGTCTATAGCGAC
* * *
31804 GTTTGTTTG-AAAACGCTACTAAA-T-CAGAAGTCTATAACGGC
1 GTTTGTTTGAAAAACGCCACTAAAGTAC-GAAGTCTATAGCGAC
* * * * *
31845 GTTTG-TTCAAAAACGCCAATAAAATAC-AAATATATAGCGAC
1 GTTTGTTTGAAAAACGCCACTAAAGTACGAAGTCTATAGCGAC
* *
31886 GTTTGTTTGAAAAATGCCACTAAAGTACG-AGTCTTTAGCGAC
1 GTTTGTTTGAAAAACGCCACTAAAGTACGAAGTCTATAGCGAC
31928 ATTTTATCAT
Statistics
Matches: 97, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
40 14 0.14
41 53 0.55
42 29 0.30
43 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (43 bp):
GTTTGTTTGAAAAACGCCACTAAAGTACGAAGTCTATAGCGAC
Found at i:32610 original size:25 final size:24
Alignment explanation
Indices: 32582--32644 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 24
32572 TATATATATA
32582 TATATATTAACTTAAAAAT-ATTT
1 TATATATTAACTTAAAAATAATTT
* *
32605 TTTATATTAACTTATTAAATATATTT
1 TATATATTAACTTA-AAAATA-ATTT
32631 TAT-TATTAACTTAA
1 TATATATTAACTTAA
32645 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 13 0.39
24 4 0.12
25 10 0.30
26 6 0.18
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (24 bp):
TATATATTAACTTAAAAATAATTT
Found at i:32610 original size:27 final size:28
Alignment explanation
Indices: 32548--32661 Score: 87
Period size: 27 Copynumber: 4.0 Consensus size: 28
32538 TATCTTAGTG
* * *
32548 TATAAATACTTAAATTCATAATATTATATAT
1 TATATATACTT-AATTAAAAATATT-T-TAT
32579 ATATATATA-TTAACTTAAAAATATTTT-T
1 -TATATATACTTAA-TTAAAAATATTTTAT
*
32607 TATAT-TAACTT-ATTAAATATATTTTAT
1 TATATAT-ACTTAATTAAAAATATTTTAT
32634 TAT-TA-ACTTAATTTAAAAATATTTTAT
1 TATATATACTTAA-TTAAAAATATTTTAT
32661 T
1 T
32662 TTTATTTTCA
Statistics
Matches: 70, Mismatches: 5, Indels: 19
0.74 0.05 0.20
Matches are distributed among these distances:
25 4 0.06
26 15 0.21
27 26 0.37
28 3 0.04
29 1 0.01
30 3 0.04
31 11 0.16
32 7 0.10
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (28 bp):
TATATATACTTAATTAAAAATATTTTAT
Found at i:32678 original size:27 final size:27
Alignment explanation
Indices: 32588--32661 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
32578 TATATATATA
* *
32588 TTAACTTAAAAATATTTTTTATATTAAC
1 TTAATTTAAAAATATTTTAT-TATTAAC
*
32616 TT-A-TTAAATATATTTTATTATTAAC
1 TTAATTTAAAAATATTTTATTATTAAC
32641 TTAATTTAAAAATATTTTATT
1 TTAATTTAAAAATATTTTATT
32662 TTTATTTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 9 0.22
26 14 0.34
27 16 0.39
28 2 0.05
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAATTTAAAAATATTTTATTATTAAC
Found at i:33666 original size:13 final size:14
Alignment explanation
Indices: 33639--33667 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33629 TGATTTTTTA
33639 TATTTTAAAATTAT
1 TATTTTAAAATTAT
33653 TATTTTAAAA-TAT
1 TATTTTAAAATTAT
33666 TA
1 TA
33668 AAAACAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTTTAAAATTAT
Found at i:33922 original size:2 final size:2
Alignment explanation
Indices: 33917--33941 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33907 CAATCAGAAT
33917 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
33942 TAAGATGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44044 original size:2 final size:2
Alignment explanation
Indices: 44035--44342 Score: 102
Period size: 2 Copynumber: 162.0 Consensus size: 2
44025 ATGAAGCAAT
44035 TA TA -A 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
* * * * *
44076 TA TA TA T- TA T- TA TCA TG TA CA T- TA TA CT- TA TG CA TA CA -A
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA -TA TA TA TA TA TA TA
*
44115 TA TA -A GTA TA TA CT- TA TA TA -A GTA TA CA T- TA TA CT- TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* * * *
44154 -A TA TA TG TA TT TA -A TA TA TA TA -A GA -A TA AA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
44193 TA -A GTA TA TA TA TA TA TA TA -A TA TA CA -A T- TA TA CA TA TGA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* *
44233 GTA TA TA -A TA TA TA -A GA -A TA TA AA T- TA TA TA -A TA TA -A
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
44270 GTA TA TA -A TA TA TA -A GA -A TA TA AA CTA TA TA -A TA TA -A GTA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
* *
44310 TA TA -A TA TA TA TG TA TA TA AA CTA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
44343 GGCATATAAA
Statistics
Matches: 232, Mismatches: 28, Indels: 92
0.66 0.08 0.26
Matches are distributed among these distances:
1 31 0.13
2 182 0.78
3 18 0.08
4 1 0.00
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (2 bp):
TA
Found at i:44336 original size:37 final size:37
Alignment explanation
Indices: 44113--44362 Score: 216
Period size: 37 Copynumber: 6.8 Consensus size: 37
44103 TTATGCATAC
* * *
44113 AATATAAGTATATACTTATATAAGTATACATTATACT-TAT
1 AATATAAGTATATA-ATATATAAG-A-ATA-TAAACTATAT
* *
44153 AATATATGTATTTAATATATATA-AGA-ATAAA-TATACT
1 AATATAAGTATATAATATATA-AGA-ATATAAACTATA-T
*
44190 -ATATAAGTATAT-ATATATATATAATATACAA-T-TAT
1 AATATAAGTATATAATATATA-AGAATATA-AACTATAT
* *
44225 ACATATGAGTATATAATATATAAGAATATAAATTATAT
1 A-ATATAAGTATATAATATATAAGAATATAAACTATAT
44263 AATATAAGTATATAATATATAAGAATATAAACTATAT
1 AATATAAGTATATAATATATAAGAATATAAACTATAT
* *
44300 AATATAAGTATATAATATATATGTATATAAACTATAT
1 AATATAAGTATATAATATATAAGAATATAAACTATAT
* * *
44337 AGTATAGGCATAT-A-A-ATAAGAATATA
1 AATATAAGTATATAATATATAAGAATATA
44363 TATTCATATA
Statistics
Matches: 181, Mismatches: 18, Indels: 28
0.80 0.08 0.12
Matches are distributed among these distances:
34 9 0.05
35 13 0.07
36 24 0.13
37 103 0.57
38 13 0.07
39 6 0.03
40 13 0.07
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (37 bp):
AATATAAGTATATAATATATAAGAATATAAACTATAT
Found at i:44417 original size:20 final size:21
Alignment explanation
Indices: 44392--44436 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
44382 GTATGATGCA
*
44392 TGTATAT-ACTTATGTGTGTG
1 TGTATATAACGTATGTGTGTG
44412 TGTATATACACGTATGTGTGTG
1 TGTATATA-ACGTATGTGTGTG
44434 TGT
1 TGT
44437 GCATGTATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
22 15 0.68
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.47
Consensus pattern (21 bp):
TGTATATAACGTATGTGTGTG
Found at i:44611 original size:14 final size:14
Alignment explanation
Indices: 44516--44732 Score: 101
Period size: 14 Copynumber: 15.1 Consensus size: 14
44506 AGAAAAAATA
*
44516 ATATACGTATATAT
1 ATATAAGTATATAT
44530 AT-TAA-TATTATAT
1 ATATAAGTA-TATAT
**
44543 ATATACTTATGCATAT
1 ATATAAGTAT--ATAT
*
44559 GTAT-AGTTATATAT
1 ATATAAG-TATATAT
* *
44573 ATAAAAGCATATAT
1 ATATAAGTATATAT
44587 ATATAAG--TATAT
1 ATATAAGTATATAT
*
44599 ACATAAGTATATAT
1 ATATAAGTATATAT
* * * *
44613 GTATGA-TTTATGT
1 ATATAAGTATATAT
* *
44626 ACATAAGTATAAAT
1 ATATAAGTATATAT
44640 ATATAAGTATAAAGTAT
1 ATATAAGTAT--A-TAT
44657 AGAATATAAGTATATAT
1 ---ATATAAGTATATAT
*
44674 AAGTATAA-AATATAT
1 -A-TATAAGTATATAT
*
44689 ACATAAGTATATAT
1 ATATAAGTATATAT
44703 ATAT-A-TATAAGTAT
1 ATATAAGTAT-A-TAT
*
44717 ATGTAAGTATATAT
1 ATATAAGTATATAT
44731 AT
1 AT
44733 GTGATGTATG
Statistics
Matches: 153, Mismatches: 28, Indels: 44
0.68 0.12 0.20
Matches are distributed among these distances:
12 16 0.10
13 23 0.15
14 65 0.42
15 14 0.09
16 19 0.12
17 5 0.03
18 1 0.01
20 10 0.07
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.40
Consensus pattern (14 bp):
ATATAAGTATATAT
Found at i:44643 original size:57 final size:56
Alignment explanation
Indices: 44581--44778 Score: 200
Period size: 57 Copynumber: 3.4 Consensus size: 56
44571 ATATAAAAGC
*
44581 ATATATATATAAGTATATACATAAGTATATATGTATGATTTATGTACATAAGTATAA
1 ATATATATATAAGTATATA-ATAAGTATATATGTATGATATATGTACATAAGTATAA
* * * * *
44638 ATATATAAGTATAAAGTATAGAATATAAGTATATATAAGTATAAAATATATACATAAGTATAT
1 ATATAT-A-TAT-AAGTATA-TA-ATAAGTATATAT--GTATGATATATGTACATAAGTATAA
* * * * *
44701 ATATATATATAAGTATAT-GTAAGTATATATATGTGATGTATGTACACAAGTATATA
1 ATATATATATAAGTATATAATAAGTATATATGTATGATATATGTACATAAGTATA-A
44757 TATATATATATAAGTATATAAT
1 -ATATATATATAAGTATATAAT
44779 TAAACATGAG
Statistics
Matches: 114, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
55 17 0.15
57 35 0.31
58 2 0.02
59 3 0.03
60 14 0.12
61 16 0.14
62 1 0.01
63 26 0.23
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.39
Consensus pattern (56 bp):
ATATATATATAAGTATATAATAAGTATATATGTATGATATATGTACATAAGTATAA
Found at i:45318 original size:12 final size:13
Alignment explanation
Indices: 45296--45325 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
45286 TAAAACTAAT
45296 TTAATGATTATAA
1 TTAATGATTATAA
45309 TTAA-GATTATAA
1 TTAATGATTATAA
45321 TTAAT
1 TTAAT
45326 ATAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (13 bp):
TTAATGATTATAA
Found at i:45552 original size:16 final size:16
Alignment explanation
Indices: 45531--45565 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
45521 TCAATTACAT
*
45531 GTCAGGTTCATATCAG
1 GTCAGGTTCATAACAG
*
45547 GTCAGGTTGATAACAG
1 GTCAGGTTCATAACAG
45563 GTC
1 GTC
45566 GGGTAATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (16 bp):
GTCAGGTTCATAACAG
Found at i:50312 original size:29 final size:29
Alignment explanation
Indices: 50269--50363 Score: 154
Period size: 29 Copynumber: 3.3 Consensus size: 29
50259 GAATTCTACA
* *
50269 GGCGACCTCGTAGGTCGCCATGGCATCCG
1 GGCGACCTTGGAGGTCGCCATGGCATCCG
50298 GGCGACCTTGGAGGTCGCCATGGCATCCG
1 GGCGACCTTGGAGGTCGCCATGGCATCCG
*
50327 GGCGACCTTGGAGGTCGCCATGGCATCCA
1 GGCGACCTTGGAGGTCGCCATGGCATCCG
*
50356 AGCGACCT
1 GGCGACCT
50364 GTGTGGTGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.16, C:0.33, G:0.35, T:0.17
Consensus pattern (29 bp):
GGCGACCTTGGAGGTCGCCATGGCATCCG
Found at i:50455 original size:20 final size:20
Alignment explanation
Indices: 50430--50467 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
50420 TGGGGGAGTT
*
50430 GTGGGAGCTGTGCATGGGAC
1 GTGGGAACTGTGCATGGGAC
50450 GTGGGAACTGTGCATGGG
1 GTGGGAACTGTGCATGGG
50468 GCATGGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.50, T:0.21
Consensus pattern (20 bp):
GTGGGAACTGTGCATGGGAC
Found at i:50474 original size:20 final size:20
Alignment explanation
Indices: 50431--50474 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
50421 GGGGGAGTTG
* *
50431 TGGGAGCTGTGCATGGGACG
1 TGGGAACTGTGCATGGGACA
*
50451 TGGGAACTGTGCATGGGGCA
1 TGGGAACTGTGCATGGGACA
50471 TGGG
1 TGGG
50475 GGAGTTGTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.50, T:0.20
Consensus pattern (20 bp):
TGGGAACTGTGCATGGGACA
Found at i:50486 original size:51 final size:51
Alignment explanation
Indices: 50417--50523 Score: 214
Period size: 51 Copynumber: 2.1 Consensus size: 51
50407 ATTGGAGCAT
50417 GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
1 GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
50468 GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
1 GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
50519 GCATG
1 GCATG
50524 CACGTCGAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.16, C:0.12, G:0.50, T:0.21
Consensus pattern (51 bp):
GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
Found at i:50506 original size:20 final size:20
Alignment explanation
Indices: 50481--50518 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
50471 TGGGGGAGTT
*
50481 GTGGGAGCTGTGCATGGGAC
1 GTGGGAACTGTGCATGGGAC
50501 GTGGGAACTGTGCATGGG
1 GTGGGAACTGTGCATGGG
50519 GCATGCACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.50, T:0.21
Consensus pattern (20 bp):
GTGGGAACTGTGCATGGGAC
Found at i:51016 original size:21 final size:21
Alignment explanation
Indices: 50991--51034 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
50981 AATCTAGTTA
50991 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
51012 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
51033 AT
1 AT
51035 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:51044 original size:28 final size:28
Alignment explanation
Indices: 51011--51101 Score: 155
Period size: 28 Copynumber: 3.2 Consensus size: 28
51001 TAGTATAAAT
*
51011 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTATTAGTTTAAGTTATATTA
51039 TATTAGTTTATTAGTTTAAGTTATATTA
1 TATTAGTTTATTAGTTTAAGTTATATTA
51067 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAG-T-TATATTA
51097 TATTA
1 TATTA
51102 TATAAAAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
28 47 0.78
29 1 0.02
30 12 0.20
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (28 bp):
TATTAGTTTATTAGTTTAAGTTATATTA
Found at i:51052 original size:8 final size:8
Alignment explanation
Indices: 51010--51084 Score: 53
Period size: 8 Copynumber: 10.4 Consensus size: 8
51000 TTAGTATAAA
51010 TTATTAGT
1 TTATTAGT
*
51018 TTGTTAGT
1 TTATTAGT
51026 TTA--AG-
1 TTATTAGT
51031 TTA-TA-T
1 TTATTAGT
51037 TATATTAGT
1 T-TATTAGT
51046 TTATTAGT
1 TTATTAGT
51054 TTA--AG-
1 TTATTAGT
51059 TTA-TA-T
1 TTATTAGT
51065 TATATTAGT
1 T-TATTAGT
51074 TTATTAGT
1 TTATTAGT
51082 TTA
1 TTA
51085 AGTTATATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
5 6 0.11
6 8 0.15
7 4 0.07
8 33 0.60
9 4 0.07
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (8 bp):
TTATTAGT
Found at i:51117 original size:56 final size:55
Alignment explanation
Indices: 51011--51121 Score: 127
Period size: 56 Copynumber: 2.0 Consensus size: 55
51001 TAGTATAAAT
* * ** **
51011 TATTAGTTTGTTAGTTTAAGTTATATTATATTAGTTTATTAGTTTAAGTTATATTA
1 TATTAGTTTATTAGTTTAAGTTATATTATATTAGTATAAAAAATTAAGTTA-ATTA
51067 TATTAGTTTATTAGTTTAAGTTATATATTATATTA-TATAAAAAATT-AGTTAATTA
1 TATTAGTTTATTAGTTTAAG-T-TATATTATATTAGTATAAAAAATTAAGTTAATTA
51122 GTTTCTTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
55 4 0.09
56 24 0.51
57 7 0.15
58 12 0.26
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (55 bp):
TATTAGTTTATTAGTTTAAGTTATATTATATTAGTATAAAAAATTAAGTTAATTA
Found at i:51162 original size:43 final size:48
Alignment explanation
Indices: 51061--51174 Score: 130
Period size: 50 Copynumber: 2.4 Consensus size: 48
51051 AGTTTAAGTT
51061 ATATTATATTAGTTTATTAGTTTAAGTTATATATTATATTATATAAAAAA
1 ATATTA-ATTAGTTTATTAGTTTAAGTTATATA-TATATTATATAAAAAA
* *
51111 TTAGTTAATTAGTTTCTTAGTTTAAGTTAT-TA-A-A-TATA-AAAAAA
1 ATA-TTAATTAGTTTATTAGTTTAAGTTATATATATATTATATAAAAAA
* *
51155 ATATTAATTAATTTGTTAGT
1 ATATTAATTAGTTTATTAGT
51175 GTCTTTAAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
43 15 0.26
44 8 0.14
45 4 0.07
46 1 0.02
47 1 0.02
49 2 0.03
50 24 0.41
51 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (48 bp):
ATATTAATTAGTTTATTAGTTTAAGTTATATATATATTATATAAAAAA
Found at i:51652 original size:20 final size:21
Alignment explanation
Indices: 51608--51652 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
51598 AAATATTGTG
**
51608 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
51629 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
51649 TTTA
1 TTTA
51653 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:51942 original size:26 final size:25
Alignment explanation
Indices: 51913--51971 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
51903 AAATCATATT
*
51913 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
51939 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
51965 ATTATTA
1 ATTATTA
51972 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:55448 original size:15 final size:16
Alignment explanation
Indices: 55414--55453 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
55404 TTTACAACAC
55414 TAAACTT-TAATATAA
1 TAAACTTATAATATAA
55429 T-AACTTATAATA-AA
1 TAAACTTATAATATAA
*
55443 TAAACTAATAA
1 TAAACTTATAA
55454 ACTAGCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAACTTATAATATAA
Found at i:55548 original size:32 final size:33
Alignment explanation
Indices: 55506--55583 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 33
55496 ACTAAACCCT
* *
55506 TAAAC-AACTAATAAAATATTTTTTTA-TATAC
1 TAAACTAACTAATAAAATATTTTTTCATTATAA
*
55537 TAAACTAACTAAT-AACTATTTTTTCATTATAA
1 TAAACTAACTAATAAAATATTTTTTCATTATAA
*
55569 TATACT-ACTAATAAA
1 TAAACTAACTAATAAA
55584 CTTACTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 22 0.55
32 18 0.45
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (33 bp):
TAAACTAACTAATAAAATATTTTTTCATTATAA
Found at i:55751 original size:41 final size:42
Alignment explanation
Indices: 55641--55755 Score: 110
Period size: 42 Copynumber: 2.7 Consensus size: 42
55631 ACTATTTAAC
*
55641 TAACACAAACTAATTAAATAATTTTT-TTTATATAACTAACTA
1 TAACA-AAACTAATTAAATAATTTTTAATTATATAACTAACTA
* * * *
55683 TTAACAAAACAAACTAAAATTATTTTTTAATTATATAACTATC-A
1 -TAACAAAACTAA-TTAAA-TAATTTTTAATTATATAACTAACTA
*
55727 -AACATATACTAATTAAATAATTTTTAATT
1 TAACA-AAACTAATTAAATAATTTTTAATT
55756 TATGTATACT
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
41 11 0.19
42 14 0.24
43 14 0.24
44 8 0.14
45 12 0.20
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (42 bp):
TAACAAAACTAATTAAATAATTTTTAATTATATAACTAACTA
Found at i:55849 original size:16 final size:18
Alignment explanation
Indices: 55811--55851 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
55801 TAAACTAATT
*
55811 AAATTTATAATAATAAAC
1 AAATTTATAATAATAAAA
*
55829 TAATTTA-AAT-ATAAAA
1 AAATTTATAATAATAAAA
55845 AAATTTA
1 AAATTTA
55852 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 11 0.55
17 3 0.15
18 6 0.30
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTTATAATAATAAAA
Done.