Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 100 of 105
Found at i:18288447 original size:20 final size:20
Alignment explanation
Indices: 18288424--18288469 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
18288414 TCTAAAGTTA
*
18288424 ATAAATTATTATTTTTAAAT
1 ATAAATAATTATTTTTAAAT
*
18288444 ATAAA-AATTATTTTTTAAT
1 ATAAATAATTATTTTTAAAT
18288463 ATAAATA
1 ATAAATA
18288470 TAAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAATAATTATTTTTAAAT
Found at i:18288606 original size:15 final size:16
Alignment explanation
Indices: 18288588--18288621 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18288578 GATTTGATTC
*
18288588 AAAATCATATTTTAAA
1 AAAATCAAATTTTAAA
18288604 AAAAT-AAATTTTAAA
1 AAAATCAAATTTTAAA
18288619 AAA
1 AAA
18288622 TCGAATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATCAAATTTTAAA
Found at i:18292212 original size:18 final size:19
Alignment explanation
Indices: 18292191--18292226 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
18292181 GATTAATCAA
*
18292191 ATTAATTTGATT-TAATCG
1 ATTAATTCGATTCTAATCG
18292209 ATTAATTCGATTCTAATC
1 ATTAATTCGATTCTAATC
18292227 AAATTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.47
Consensus pattern (19 bp):
ATTAATTCGATTCTAATCG
Found at i:18295861 original size:22 final size:22
Alignment explanation
Indices: 18295819--18295862 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
18295809 AATTTTTTTA
**
18295819 TTTTATTAAATTTATTTATAAT
1 TTTTATTAAATTTATAAATAAT
18295841 TTTTATTAAAATTT-TAAATAAT
1 TTTTATT-AAATTTATAAATAAT
18295863 ATCATTTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTATTAAATTTATAAATAAT
Found at i:18298487 original size:27 final size:26
Alignment explanation
Indices: 18298455--18298506 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
18298445 AATTTTGTCA
*
18298455 TTATATTTTAATTTTATCAACTTTTTT
1 TTATATTTCAATTTTATCAA-TTTTTT
*
18298482 TTATATTTCAATTTTATTAATTTTT
1 TTATATTTCAATTTTATCAATTTTT
18298507 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (26 bp):
TTATATTTCAATTTTATCAATTTTTT
Found at i:18306772 original size:25 final size:28
Alignment explanation
Indices: 18306708--18306773 Score: 66
Period size: 30 Copynumber: 2.4 Consensus size: 28
18306698 ATGAACTATT
*
18306708 TTTTAAAAATTAATTTAATATTAATCGAA
1 TTTT-AAATTTAATTTAATATTAATCGAA
*
18306737 TTTTATTAATTTAATTTAAT-TT-AT-TAA
1 TTTTA--AATTTAATTTAATATTAATCGAA
18306764 TTTTAAATTT
1 TTTTAAATTT
18306774 TTATATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
25 5 0.15
27 7 0.21
28 3 0.09
29 6 0.18
30 12 0.36
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTTAAATTTAATTTAATATTAATCGAA
Found at i:18306812 original size:21 final size:22
Alignment explanation
Indices: 18306767--18306822 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
18306757 TTATTAATTT
* *
18306767 TAAATTTTTATATATTATTTTAA
1 TAAATTTTT-TATAGTATTTAAA
18306790 TAAATTTTTTAT-GTATTTAAA
1 TAAATTTTTTATAGTATTTAAA
*
18306811 T-AGTTTTTTATA
1 TAAATTTTTTATA
18306823 TAAAATAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 9 0.31
21 8 0.28
22 3 0.10
23 9 0.31
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
TAAATTTTTTATAGTATTTAAA
Found at i:18307294 original size:18 final size:19
Alignment explanation
Indices: 18307273--18307314 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
18307263 TTAAATCGAA
* *
18307273 TTATATAT-TTTTTATTTT
1 TTATATATATTTTAAATTT
18307291 TTATATATATTTTAAATTT
1 TTATATATATTTTAAATTT
18307310 TTATA
1 TTATA
18307315 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATATATATTTTAAATTT
Found at i:18307309 original size:20 final size:20
Alignment explanation
Indices: 18307274--18307311 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18307264 TAAATCGAAT
**
18307274 TATATATTTTTTATTTTTTA
1 TATATATTTTAAATTTTTTA
18307294 TATATATTTTAAATTTTT
1 TATATATTTTAAATTTTT
18307312 ATAAAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TATATATTTTAAATTTTTTA
Found at i:18307394 original size:32 final size:31
Alignment explanation
Indices: 18307317--18307394 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 31
18307307 TTTTTATAAA
* * *
18307317 ATAAAAATAATAATTTTATATCAAAATCTAT
1 ATAAAATTAAAAATTTTATATCAAAATATAT
* * *
18307348 TTAAAATATTAAAATTTTATATTAAAATAATAT
1 ATAAAAT-TAAAAATTTTATATCAAAAT-ATAT
18307381 ATAAAATTAAAAAT
1 ATAAAATTAAAAAT
18307395 CAGTAAATCA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
31 5 0.14
32 23 0.62
33 9 0.24
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (31 bp):
ATAAAATTAAAAATTTTATATCAAAATATAT
Found at i:18308101 original size:16 final size:16
Alignment explanation
Indices: 18308080--18308137 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
18308070 TATTTATTTG
18308080 TATATATTTATATAAT
1 TATATATTTATATAAT
*
18308096 TATATATTTAAAT-A-
1 TATATATTTATATAAT
*
18308110 TATATATTTA-AAAAT
1 TATATATTTATATAAT
* *
18308125 AATATTTTTATAT
1 TATATATTTATAT
18308138 TTAAAAAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 1 0.03
14 11 0.32
15 9 0.26
16 13 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATTTATATAAT
Found at i:18308113 original size:14 final size:14
Alignment explanation
Indices: 18308080--18308131 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
18308070 TATTTATTTG
*
18308080 TATATATTTATATAA
1 TATATATTTAAAT-A
18308095 TTATATATTTAAATA
1 -TATATATTTAAATA
*
18308110 TATATATTTAAAAA
1 TATATATTTAAATA
18308124 TA-ATATTT
1 TATATATTT
18308132 TTATATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 6 0.18
14 15 0.44
15 1 0.03
16 12 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATATTTAAATA
Found at i:18308137 original size:21 final size:22
Alignment explanation
Indices: 18308112--18308153 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
18308102 TTTAAATATA
18308112 TATATTT-AAAAATAATATTTT
1 TATATTTAAAAAATAATATTTT
*
18308133 TATATTTAAAAAATCATATTT
1 TATATTTAAAAAATAATATTT
18308154 CATTAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TATATTTAAAAAATAATATTTT
Found at i:18309009 original size:12 final size:12
Alignment explanation
Indices: 18308986--18309028 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
18308976 ATTAAAATTT
18308986 TATATT-AATAA
1 TATATTAAATAA
18308997 TATATTAAATAA
1 TATATTAAATAA
*
18309009 TATA-TATATATA
1 TATATTAAATA-A
18309021 TATATTAA
1 TATATTAA
18309029 TGATGGGGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 11 0.41
12 14 0.52
13 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATTAAATAA
Found at i:18310322 original size:22 final size:22
Alignment explanation
Indices: 18310297--18310367 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
18310287 AAAACTTGAA
* *
18310297 GTTTGGGTTTTGGATTTTAGGG
1 GTTTGGATTTAGGATTTTAGGG
* * **
18310319 GTTTGGATTTAAGAGTTTAAAG
1 GTTTGGATTTAGGATTTTAGGG
*
18310341 GTTTGAGATTTCGGATTTTAGGG
1 GTTTG-GATTTAGGATTTTAGGG
18310364 GTTT
1 GTTT
18310368 TAGATTTTAG
Statistics
Matches: 37, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 21 0.57
23 16 0.43
ACGTcount: A:0.18, C:0.01, G:0.34, T:0.46
Consensus pattern (22 bp):
GTTTGGATTTAGGATTTTAGGG
Found at i:18310325 original size:15 final size:15
Alignment explanation
Indices: 18310305--18310442 Score: 82
Period size: 16 Copynumber: 9.0 Consensus size: 15
18310295 AAGTTTGGGT
18310305 TTTGGATTTTAGGGG
1 TTTGGATTTTAGGGG
* *
18310320 TTTGGA-TTTAAGAG
1 TTTGGATTTTAGGGG
** * * *
18310334 TTTAAAGGTTT-GAGA
1 TTTGGA-TTTTAGGGG
18310349 TTTCGGATTTTAGGGG
1 TTT-GGATTTTAGGGG
* *
18310365 TTTTAGATTTTAGGGT
1 -TTTGGATTTTAGGGG
*
18310381 TTTCGAATTTTAGGGG
1 TTT-GGATTTTAGGGG
* *
18310397 TTTGGATTTAAGGGA
1 TTTGGATTTTAGGGG
* **
18310412 TTTCAGATTTTAGGAT
1 TTT-GGATTTTAGGGG
18310428 TTTGGATTTTAGGGG
1 TTTGGATTTTAGGGG
18310443 CTTTTAGAAA
Statistics
Matches: 88, Mismatches: 28, Indels: 14
0.68 0.22 0.11
Matches are distributed among these distances:
14 10 0.11
15 36 0.41
16 39 0.44
17 3 0.03
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.46
Consensus pattern (15 bp):
TTTGGATTTTAGGGG
Found at i:18310360 original size:23 final size:23
Alignment explanation
Indices: 18310308--18310383 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
18310298 TTTGGGTTTT
18310308 GGATTTTAGGGGTTTG-GATTTA
1 GGATTTTAGGGGTTTGAGATTTA
* * ** *
18310330 AGAGTTTAAAGGTTTGAGATTTC
1 GGATTTTAGGGGTTTGAGATTTA
*
18310353 GGATTTTAGGGGTTTTAGATTTTA
1 GGATTTTAGGGGTTTGAGA-TTTA
*
18310377 GGGTTTT
1 GGATTTT
18310384 CGAATTTTAG
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
22 12 0.30
23 19 0.47
24 9 0.22
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (23 bp):
GGATTTTAGGGGTTTGAGATTTA
Found at i:18310375 original size:16 final size:16
Alignment explanation
Indices: 18310354--18310450 Score: 92
Period size: 15 Copynumber: 6.1 Consensus size: 16
18310344 TGAGATTTCG
18310354 GATTTTAGGGGTTTTA
1 GATTTTAGGGGTTTTA
*
18310370 GATTTTA-GGGTTTTC
1 GATTTTAGGGGTTTTA
*
18310385 GAATTTTAGGGG-TTTG
1 G-ATTTTAGGGGTTTTA
* * *
18310401 GATTTAAGGGATTTCA
1 GATTTTAGGGGTTTTA
* *
18310417 GATTTTA-GGATTTTG
1 GATTTTAGGGGTTTTA
18310432 GATTTTAGGGGCTTTTA
1 GATTTTAGGGG-TTTTA
18310449 GA
1 GA
18310451 AACCTAGGAT
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
15 29 0.45
16 27 0.42
17 9 0.14
ACGTcount: A:0.21, C:0.03, G:0.30, T:0.46
Consensus pattern (16 bp):
GATTTTAGGGGTTTTA
Found at i:18310422 original size:31 final size:30
Alignment explanation
Indices: 18310347--18310441 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 30
18310337 AAAGGTTTGA
*
18310347 GATTTCGGATTTTAGGGGTTTTAGATTTTAGG
1 GATTTC-GATTTTAGGGG-TTTGGATTTTAGG
* *
18310379 GTTTTCGAATTTTAGGGGTTTGGATTTAAGG
1 GATTTCG-ATTTTAGGGGTTTGGATTTTAGG
**
18310410 GATTTCAGATTTTAGGATTTTGGATTTTAGG
1 GATTTC-GATTTTAGGGGTTTGGATTTTAGG
18310441 G
1 G
18310442 GCTTTTAGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
31 38 0.70
32 16 0.30
ACGTcount: A:0.20, C:0.03, G:0.31, T:0.46
Consensus pattern (30 bp):
GATTTCGATTTTAGGGGTTTGGATTTTAGG
Found at i:18310434 original size:7 final size:8
Alignment explanation
Indices: 18310353--18310440 Score: 58
Period size: 7 Copynumber: 11.2 Consensus size: 8
18310343 TTGAGATTTC
18310353 GGATTTTA
1 GGATTTTA
*
18310361 GGGGTTTTA
1 -GGATTTTA
18310370 -GATTTTA
1 GGATTTTA
* *
18310377 GGGTTTTC
1 GGATTTTA
*
18310385 GAATTTTA
1 GGATTTTA
**
18310393 GGGGTTT-
1 GGATTTTA
*
18310400 GGATTTAA
1 GGATTTTA
*
18310408 GGGATTTCA
1 -GGATTTTA
18310417 -GATTTTA
1 GGATTTTA
18310424 GGATTTT-
1 GGATTTTA
18310431 GGATTTTA
1 GGATTTTA
18310439 GG
1 GG
18310441 GGCTTTTAGA
Statistics
Matches: 59, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
7 23 0.39
8 22 0.37
9 14 0.24
ACGTcount: A:0.20, C:0.02, G:0.31, T:0.47
Consensus pattern (8 bp):
GGATTTTA
Found at i:18311923 original size:27 final size:27
Alignment explanation
Indices: 18311875--18311937 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
18311865 CTCATTTTTT
* *
18311875 TTATTATTATTATATTTTTTAAAATTA
1 TTATTATTATTATATTTATTAAAACTA
18311902 TTATTATTATTGATA-TTATTAAAACTA
1 TTATTATTATT-ATATTTATTAAAACTA
*
18311929 TTAATATTA
1 TTATTATTA
18311938 AACTGAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
TTATTATTATTATATTTATTAAAACTA
Found at i:18313498 original size:10 final size:9
Alignment explanation
Indices: 18313460--18313530 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 9
18313450 TTAATATAAC
18313460 TATTAAAA-
1 TATTAAAAT
18313468 TATTAAAAAT
1 TATT-AAAAT
*
18313478 TATT--TAT
1 TATTAAAAT
18313485 TATTAAAAT
1 TATTAAAAT
*
18313494 ATATTGAAAT
1 -TATTAAAAT
*
18313504 TATT--TAT
1 TATTAAAAT
18313511 TATTAAAAT
1 TATTAAAAT
*
18313520 TATTAATAT
1 TATTAAAAT
18313529 TA
1 TA
18313531 AAAAAGCATT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
7 12 0.24
8 4 0.08
9 22 0.44
10 12 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (9 bp):
TATTAAAAT
Found at i:18313510 original size:26 final size:26
Alignment explanation
Indices: 18313460--18313530 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
18313450 TTAATATAAC
*
18313460 TATTAAAATAT-TAAAAATTATTTAT
1 TATTAAAATATATTAAAATTATTTAT
*
18313485 TATTAAAATATATTGAAATTATTTAT
1 TATTAAAATATATTAAAATTATTTAT
*
18313511 TATTAAAAT-TATTAATATTA
1 TATTAAAATATATTAAAATTA
18313531 AAAAAGCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 20 0.49
26 21 0.51
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
TATTAAAATATATTAAAATTATTTAT
Found at i:18313534 original size:16 final size:16
Alignment explanation
Indices: 18313494--18313533 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
18313484 TTATTAAAAT
*
18313494 ATATTGAAATTATTTA
1 ATATTAAAATTATTTA
*
18313510 TTATTAAAATTA-TTA
1 ATATTAAAATTATTTA
18313525 ATATTAAAA
1 ATATTAAAA
18313534 AAGCATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATATTAAAATTATTTA
Found at i:18313581 original size:19 final size:18
Alignment explanation
Indices: 18313504--18313591 Score: 60
Period size: 19 Copynumber: 4.9 Consensus size: 18
18313494 ATATTGAAAT
*
18313504 TATTTATTATTAAAAT--
1 TATTTAATATTAAAATAA
18313520 TA-TTAATATTAAAA-AA
1 TATTTAATATTAAAATAA
* *
18313536 GCA-TTATATTTTAATAATAA
1 -TATTTA-ATATTAA-AATAA
*
18313556 TATTTAATATTAAAATAT
1 TATTTAATATTAAAATAA
*
18313574 TATGTTAATATAAAAATA
1 TAT-TTAATATTAAAATA
18313592 CTTAAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
15 11 0.19
16 2 0.04
17 4 0.07
18 13 0.23
19 22 0.39
20 5 0.09
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (18 bp):
TATTTAATATTAAAATAA
Found at i:18313646 original size:16 final size:15
Alignment explanation
Indices: 18313621--18313735 Score: 57
Period size: 15 Copynumber: 7.8 Consensus size: 15
18313611 TTATTCTTTA
18313621 TATTAT-ATATTAATG
1 TATTATAATATT-ATG
*
18313636 TATTATAATATTATT
1 TATTATAATATTATG
18313651 TATTAGTAATATTTAT-
1 TATTA-TAATA-TTATG
* *
18313667 TACTATATTA-TAT-
1 TATTATAATATTATG
* * *
18313680 TAGTATTATATTATT
1 TATTATAATATTATG
18313695 TATTAATAATA-TAT-
1 TATT-ATAATATTATG
*
18313709 TATT-TATTCATATAT-
1 TATTATAAT-AT-TATG
18313724 TATTATAATATT
1 TATTATAATATT
18313736 TATTAATGAA
Statistics
Matches: 80, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
12 3 0.04
13 11 0.14
14 8 0.10
15 32 0.40
16 22 0.28
17 4 0.05
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.57
Consensus pattern (15 bp):
TATTATAATATTATG
Found at i:18313691 original size:44 final size:44
Alignment explanation
Indices: 18313621--18313892 Score: 210
Period size: 44 Copynumber: 6.2 Consensus size: 44
18313611 TTATTCTTTA
* * *
18313621 TATT-ATATATTA-ATGTATTATAATATTATTTATTAGTAATATT
1 TATTAATATATTATAT-TAGTATTATATTATTTATTAATAATATT
*
18313664 TATTACTATATTATATTAGTATTATATTATTTATTAATAATATAT
1 TATTAATATATTATATTAGTATTATATTATTTATTAATAATAT-T
* * *
18313709 TATT--TAT-TCATA-TATTATTATAATATTTATTAATGAA-A-T
1 TATTAATATATTATATTAGTATTATATTATTTATTAAT-AATATT
* * *
18313748 TAATAATAT-TTATCATTA-TATTAT-TTATTAATATAATATTATT
1 TATTAATATATTAT-ATTAGTATTATATTATTTAT-TAATAATATT
* *
18313791 TACTAATATTAATATATTAGTA-TATATTTATTTA-TAATAATATT
1 TATTAATA-TATTATATTAGTATTATA-TTATTTATTAATAATATT
* * * *
18313835 TATTAATATATTATTATTAATATTATTTTAATATATAATAATATTATT
1 TATTAATATATTA-TATTAGTATTATATT-AT-T-TATTAATAATATT
18313883 TATTAATATA
1 TATTAATATA
18313893 ATATTATTTA
Statistics
Matches: 186, Mismatches: 21, Indels: 39
0.76 0.09 0.16
Matches are distributed among these distances:
39 4 0.02
41 34 0.18
42 18 0.10
43 21 0.11
44 64 0.34
45 17 0.09
46 7 0.04
47 2 0.01
48 19 0.10
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (44 bp):
TATTAATATATTATATTAGTATTATATTATTTATTAATAATATT
Found at i:18313707 original size:18 final size:18
Alignment explanation
Indices: 18313672--18314018 Score: 136
Period size: 18 Copynumber: 18.7 Consensus size: 18
18313662 TTTATTACTA
* *
18313672 TATTATATTAGTATTATAT
1 TATT-TATTAATAATATAT
18313691 TATTTATTAATAATATAT
1 TATTTATTAATAATATAT
*
18313709 TATTTATTCATATATTATTATAA
1 TATTTATT-A-ATA--A-TATAT
*
18313732 TATTTATTAATGAAATTAATAA
1 TATTTATTAAT--AA-T-ATAT
*
18313754 TATTTA-TCAT--TATAT
1 TATTTATTAATAATATAT
18313769 TATTTATTAAT-ATAATAT
1 TATTTATTAATAAT-ATAT
*
18313787 TATTTACTAAT-AT-TA-
1 TATTTATTAATAATATAT
* *
18313802 -ATATATTAGT-ATATATT
1 TATTTATTAATAATATA-T
18313819 TATTTA-TAATAATATTTAT
1 TATTTATTAATAATA--TAT
* * *
18313838 TAATATATTATTATTAATAT
1 T-ATTTATTAATAAT-ATAT
*
18313858 TATTTTAATATATAATAATAT
1 TA-TTTATTA-ATAAT-ATAT
18313879 TATTTATTAAT-ATAATAT
1 TATTTATTAATAAT-ATAT
18313897 TATTTA-TAA-ACATATAT
1 TATTTATTAATA-ATATAT
* * *
18313914 TATAATATTATTTAT-TAAT
1 TAT-TTATTAATAATAT-AT
* **
18313933 AATTT-TTGTTAATATAT
1 TATTTATTAATAATATAT
*
18313950 TA--TATTAATAGTATAT
1 TATTTATTAATAATATAT
18313966 TATTTATTAATATAATATTATT
1 TATTTATT-A-ATAATA-TA-T
18313988 TATTTATTAAT-ATAATAT
1 TATTTATTAATAAT-ATAT
*
18314006 TATTTATAAATAA
1 TATTTATTAATAA
18314019 AATTATGTTC
Statistics
Matches: 256, Mismatches: 33, Indels: 78
0.70 0.09 0.21
Matches are distributed among these distances:
14 9 0.04
15 12 0.05
16 17 0.07
17 23 0.09
18 78 0.30
19 24 0.09
20 32 0.12
21 26 0.10
22 22 0.09
23 13 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
TATTTATTAATAATATAT
Found at i:18313775 original size:122 final size:122
Alignment explanation
Indices: 18313643--18313985 Score: 302
Period size: 122 Copynumber: 2.8 Consensus size: 122
18313633 ATGTATTATA
*
18313643 ATATTATTTATT-A-GTAATATT-TATTACT-ATATTATATTAGTATTA-TAT-TATTTATTAAT
1 ATATTATTTATTAATATAATATTAT-TTACTAATATTA-A-TA-TATTAGTATATATTTATTAAT
*
18313702 AATATATTATTTATTCATATATTATTA-TAATATT-TATTAATGAAATTAATAATATTTATCATT
62 AATA-A-TATTTATTAATATATTATTATTAATATTATATTAAT-AAA-TAATAATATTTATCATT
*
18313765 ATATTATTTATTAATATAATATTATTTACTAATATTAATATATTAGTATATATTTATTTATAATA
1 ATATTATTTATTAATATAATATTATTTACTAATATTAATATATTAGTATATATTTATTAATAATA
* * *
18313830 ATATTTATTAATATATTATTATTAATATTATTTTAATATATAATAATA-TTATTTATT
66 ATATTTATTAATATATTATTATTAATATTATATTAATAAATAATAATATTTA-TCATT
* * * * * * *
18313887 AATATAATATTATTTATA-AACA-TATATTA-TAATATT-ATTTATTAATA-ATTTTTGTTAAT-
1 -ATATTAT-TTATTAATATAATATTAT-TTACTAATATTAATATATTAGTATATATTTATTAATA
* * * *
18313946 ATATTATATTAATAGTATATTATTTATTAATATAATATTA
63 ATAATAT-TTATTAATATATTA-TTATTAATATTATATTA
18313986 TTTATTTATT
Statistics
Matches: 188, Mismatches: 19, Indels: 29
0.80 0.08 0.12
Matches are distributed among these distances:
119 6 0.03
120 21 0.11
121 27 0.14
122 58 0.31
123 28 0.15
124 41 0.22
125 7 0.04
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (122 bp):
ATATTATTTATTAATATAATATTATTTACTAATATTAATATATTAGTATATATTTATTAATAATA
ATATTTATTAATATATTATTATTAATATTATATTAATAAATAATAATATTTATCATT
Found at i:18314038 original size:87 final size:85
Alignment explanation
Indices: 18313875--18314047 Score: 215
Period size: 87 Copynumber: 2.0 Consensus size: 85
18313865 ATATATAATA
* * * *
18313875 ATATTATTTATTAATATAATATTATTTATAAACATATATTATAATATTATTTATTAATAATTTTT
1 ATATTATTTATTAATATAATATTATTTAT-AACATATAATATAATATTATTTATAAATAAATTAT
* *
18313940 GTTAATATATTATATTAATAGT
65 GTTAAAATATTA-ATAAATAGT
**
18313962 ATATTATTTATTAATATAATATTATTTAT-TTAT-TAATATAATATTATTTATAAATAAAATTAT
1 ATATTATTTATTAATATAATATTATTTATAACATATAATATAATATTATTTATAAAT-AAATTAT
18314025 GTTCAAAAGTATTAATAAATAGT
65 GTT-AAAA-TATTAATAAATAGT
18314048 TGTATTCGGA
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
84 20 0.27
85 10 0.13
86 11 0.15
87 34 0.45
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (85 bp):
ATATTATTTATTAATATAATATTATTTATAACATATAATATAATATTATTTATAAATAAATTATG
TTAAAATATTAATAAATAGT
Found at i:18314170 original size:22 final size:22
Alignment explanation
Indices: 18314122--18314170 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
18314112 CAGAAAAATA
* *
18314122 AAATCATTTTTCATTAATTAAT
1 AAATTATTTTTCATTAATCAAT
* *
18314144 AAATTATTTTTCGTTGATCAAT
1 AAATTATTTTTCATTAATCAAT
*
18314166 TAATT
1 AAATT
18314171 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (22 bp):
AAATTATTTTTCATTAATCAAT
Found at i:18314214 original size:14 final size:14
Alignment explanation
Indices: 18314195--18314229 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
18314185 ATTTAAAATA
*
18314195 TAAAAATTATTTTT
1 TAAAAATTATTATT
18314209 TAAAAATTATTATT
1 TAAAAATTATTATT
18314223 TACAAAA
1 TA-AAAA
18314230 CAAACGAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (14 bp):
TAAAAATTATTATT
Found at i:18314871 original size:15 final size:14
Alignment explanation
Indices: 18314842--18314895 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
18314832 CTAATATATA
*
18314842 TTATTT-TTATTAT
1 TTATTTATTTTTAT
18314855 TTATTTAGTTTTTAT
1 TTATTTA-TTTTTAT
*
18314870 TTATATATATTTTA-
1 TTATTTAT-TTTTAT
18314884 -TATTTATTTTTA
1 TTATTTATTTTTA
18314896 AAAAATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
12 5 0.14
13 12 0.34
14 1 0.03
15 17 0.49
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (14 bp):
TTATTTATTTTTAT
Found at i:18314909 original size:16 final size:18
Alignment explanation
Indices: 18314888--18314925 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18314878 ATTTTATATT
18314888 TATTTT-TA-AAAAATAA
1 TATTTTATATAAAAATAA
*
18314904 TATTTTATATTAAAATAA
1 TATTTTATATAAAAATAA
18314922 TATT
1 TATT
18314926 ATATTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 2 0.11
18 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTTATATAAAAATAA
Found at i:18314910 original size:21 final size:21
Alignment explanation
Indices: 18314886--18314938 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
18314876 ATATTTTATA
18314886 TTTATTTTTAAAA-AATAATAT
1 TTTA-TTTTAAAATAATAATAT
* *
18314907 TTTATATTAAAATAATATTAT
1 TTTATTTTAAAATAATAATAT
*
18314928 ATTAATTTTAA
1 -TTTATTTTAA
18314939 GTTAAATCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTATTTTAAAATAATAATAT
Found at i:18314927 original size:16 final size:17
Alignment explanation
Indices: 18314897--18314932 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
18314887 TTATTTTTAA
18314897 AAAATAATATTTTATATT
1 AAAATAATA-TTTATATT
18314915 AAAATAATA-TTATATT
1 AAAATAATATTTATATT
18314931 AA
1 AA
18314933 TTTTAAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATAATATTTATATT
Found at i:18315229 original size:2 final size:2
Alignment explanation
Indices: 18315222--18315248 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18315212 ACACTAATGC
18315222 TA 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 TA T
18315249 TGACCATTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18319418 original size:18 final size:17
Alignment explanation
Indices: 18319397--18319439 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
18319387 ATTATTTATT
18319397 TATTTAAT-TTTATGTTTA
1 TATTTAATATTT-T-TTTA
18319415 TATTTATATATTTTTTTA
1 TATTTA-ATATTTTTTTA
18319433 TATTTAA
1 TATTTAA
18319440 AAATAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 3 0.13
20 3 0.13
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTTAATATTTTTTTA
Found at i:18319460 original size:19 final size:20
Alignment explanation
Indices: 18319431--18319468 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
18319421 TATATTTTTT
18319431 TATATTTAAAAATAATATTG
1 TATATTTAAAAATAATATTG
18319451 TATA-TTAAAAATAATATT
1 TATATTTAAAAATAATATT
18319469 AAATAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TATATTTAAAAATAATATTG
Found at i:18319478 original size:29 final size:32
Alignment explanation
Indices: 18319440--18319500 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 32
18319430 TTATATTTAA
18319440 AAATAATATTGT-ATAT-T-AAAAA-TAATATT
1 AAATAATATT-TAATATGTAAAAAATTAATATT
18319469 AAATAATATTTAATATGTAAAAAATTAATATT
1 AAATAATATTTAATATGTAAAAAATTAATATT
18319501 TTATTACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 1 0.04
29 14 0.50
30 1 0.04
31 5 0.18
32 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (32 bp):
AAATAATATTTAATATGTAAAAAATTAATATT
Found at i:18326887 original size:25 final size:25
Alignment explanation
Indices: 18326858--18326913 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
18326848 TAATAATAAT
18326858 AATTATTATAATTATAATTGAAAAA
1 AATTATTATAATTATAATTGAAAAA
18326883 AATTATTATAATTATAATTGAAAAA
1 AATTATTATAATTATAATTGAAAAA
18326908 AATTAT
1 AATTAT
18326914 AAATAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
AATTATTATAATTATAATTGAAAAA
Found at i:18327740 original size:29 final size:29
Alignment explanation
Indices: 18327703--18327762 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
18327693 AATTAATAAA
* *
18327703 TTTATAATTTAAGTATCAAATTAAATATT
1 TTTAAAATTTAAATATCAAATTAAATATT
*
18327732 TTTAAAATTTAAATATCATATTAAATATT
1 TTTAAAATTTAAATATCAAATTAAATATT
18327761 TT
1 TT
18327763 ATTACAGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (29 bp):
TTTAAAATTTAAATATCAAATTAAATATT
Found at i:18333704 original size:22 final size:23
Alignment explanation
Indices: 18333674--18333716 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
18333664 TTTTTGTTTT
*
18333674 TTTTAAATATTTTTTAATAAAAA
1 TTTTAAATATATTTTAATAAAAA
18333697 TTTT-AATATATTTTAATAAA
1 TTTTAAATATATTTTAATAAA
18333717 TTTATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAAATATATTTTAATAAAAA
Found at i:18336141 original size:10 final size:10
Alignment explanation
Indices: 18336128--18336161 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
18336118 TCCTTTGTGC
18336128 CTCTTTCTCT
1 CTCTTTCTCT
18336138 CTCTTTCTCT
1 CTCTTTCTCT
* *
18336148 CTCTCTCACT
1 CTCTTTCTCT
18336158 CTCT
1 CTCT
18336162 GTGATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.03, C:0.44, G:0.00, T:0.53
Consensus pattern (10 bp):
CTCTTTCTCT
Found at i:18339812 original size:11 final size:11
Alignment explanation
Indices: 18339798--18339837 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
18339788 TTTTAAATAC
18339798 AATATAAAAAT
1 AATATAAAAAT
18339809 AATATAAAAA-
1 AATATAAAAAT
*
18339819 AATTATGAAAAT
1 AA-TATAAAAAT
18339831 AATATAA
1 AATATAA
18339838 TTTAAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 2 0.08
11 21 0.84
12 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:18340850 original size:22 final size:21
Alignment explanation
Indices: 18340793--18340850 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
18340783 ATAACTATTT
*
18340793 TATATATA-AATTTATTTAAA
1 TATATATATAATTTATTAAAA
*
18340813 TATAT-TAAAATTTTTATTAAAA
1 TATATATATAA--TTTATTAAAA
18340835 TAATATATATAATTTA
1 T-ATATATATAATTTA
18340851 AAATTTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
19 2 0.06
20 7 0.23
22 14 0.45
23 4 0.13
24 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATATATAATTTATTAAAA
Found at i:18340930 original size:32 final size:35
Alignment explanation
Indices: 18340889--18340955 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 35
18340879 ATCAAACTAA
** *
18340889 AAAATTTGATTTGAA-TTAGATTAA-TTTTAAAAT
1 AAAATTTGATTCAAATTTAGATCAATTTTTAAAAT
18340922 AAAA-TTGATTCAAATTTAGATCAATTTTTAAAAT
1 AAAATTTGATTCAAATTTAGATCAATTTTTAAAAT
18340956 TTATAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 8 0.28
33 12 0.41
34 9 0.31
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (35 bp):
AAAATTTGATTCAAATTTAGATCAATTTTTAAAAT
Found at i:18342831 original size:3 final size:3
Alignment explanation
Indices: 18342823--18342860 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
18342813 AATAATTAAC
18342823 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18342861 AGACAATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:18351541 original size:74 final size:74
Alignment explanation
Indices: 18351420--18351559 Score: 217
Period size: 74 Copynumber: 1.9 Consensus size: 74
18351410 GCAATTAGTA
* * * *
18351420 AACATAGAAATAATTTTTGTGAAATGAACAAATACAAATGCATGCACAACATTTTAGCAACAACT
1 AACATAGAAACAATTTATGTGAAATAAACAAATACAAATGCATGCACAAAATTTTAGCAACAACT
18351485 GAAACCAGT
66 GAAACCAGT
* * *
18351494 AACATAGAAACAATTTATGTGACATAAACAAGTAGAAATGCATGCACAAAATTTTAGCAACAACT
1 AACATAGAAACAATTTATGTGAAATAAACAAATACAAATGCATGCACAAAATTTTAGCAACAACT
18351559 G
66 G
18351560 GAACTGCAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.24
Consensus pattern (74 bp):
AACATAGAAACAATTTATGTGAAATAAACAAATACAAATGCATGCACAAAATTTTAGCAACAACT
GAAACCAGT
Found at i:18354761 original size:23 final size:22
Alignment explanation
Indices: 18354721--18354774 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
18354711 AAAAAATATA
*
18354721 AAAAAAAT-ATAATTTAAAATTTT
1 AAAAAAATCATAATAT-AAA-TTT
18354744 AAAAAAATCATAA-ATAAATTT
1 AAAAAAATCATAATATAAATTT
*
18354765 AATAAAATCA
1 AAAAAAATCA
18354775 AAAAATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 12 0.43
22 3 0.11
23 9 0.32
24 4 0.14
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAAAAATCATAATATAAATTT
Found at i:18356680 original size:148 final size:148
Alignment explanation
Indices: 18356325--18356766 Score: 647
Period size: 149 Copynumber: 3.0 Consensus size: 148
18356315 AGCCACAGAC
* * *
18356325 CATGGTAACCAAAAACCAAGC-AACTAATGCAGATTCAAGAAAATCTTTGCACTTCGAAGTAAAA
1 CATGGTAATCAAAAACCAA-CTAACTAATGCAGATTCGAGAAAATCTTTGCACTTCCAAGT--AA
* * *
18356389 AAAAAATTTACAAAGGAACTCAACTATAGCTCCAATTCGTGACCTTCATCTATTTCATCTCATGA
63 AAATAATTTACAAAGGAACTCAACCATAGCTCCAATTCGTGCCCTTCATCTATTTCATCTCATGA
*
18356454 GGCATCGGCCACGACCACAAA
128 GGCATCAGCCACGACCACAAA
18356475 CATGGTAATCAAAAACCAACTAACTAATGCAGATTCGAGAAAAATCTTTGCACTTCCAAGTAAAA
1 CATGGTAATCAAAAACCAACTAACTAATGCAGATTCGAG-AAAATCTTTGCACTTCCAAGTAAAA
* * * *
18356540 ATAATTTACAAAGGAACTGAACCATAGCTCCAATTCGTGCCCTTCGTCTGTTTCATCTCAAGAGG
65 ATAATTTACAAAGGAACTCAACCATAGCTCCAATTCGTGCCCTTCATCTATTTCATCTCATGAGG
*
18356605 CATCAGCCACGACCAC-GA
130 CATCAGCCACGACCACAAA
18356623 CATGGTAATCAAAAACCAACTAACTAATGCAGATTCGAGAAATATCTTTGCACTTCCAAGTAAAA
1 CATGGTAATCAAAAACCAACTAACTAATGCAGATTCGAGAAA-ATCTTTGCACTTCCAAGTAAAA
* * * *
18356688 ATAAATTTACAATGGAACTCAACTC-TAGCTCCAATTCATACCCTTCATCTATTTGATCTCATGA
65 AT-AATTTACAAAGGAACTCAAC-CATAGCTCCAATTCGTGCCCTTCATCTATTTCATCTCATGA
*
18356752 GGCATCTGCCACGAC
128 GGCATCAGCCACGAC
18356767 TTCCAACAGC
Statistics
Matches: 266, Mismatches: 21, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
147 3 0.01
148 64 0.24
149 143 0.54
150 36 0.14
151 20 0.08
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (148 bp):
CATGGTAATCAAAAACCAACTAACTAATGCAGATTCGAGAAAATCTTTGCACTTCCAAGTAAAAA
TAATTTACAAAGGAACTCAACCATAGCTCCAATTCGTGCCCTTCATCTATTTCATCTCATGAGGC
ATCAGCCACGACCACAAA
Found at i:18358710 original size:10 final size:10
Alignment explanation
Indices: 18358695--18358719 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18358685 ATGAGACCTG
18358695 TTCTCCGATC
1 TTCTCCGATC
18358705 TTCTCCGATC
1 TTCTCCGATC
18358715 TTCTC
1 TTCTC
18358720 AAGTGCATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.40, G:0.08, T:0.44
Consensus pattern (10 bp):
TTCTCCGATC
Found at i:18359382 original size:20 final size:20
Alignment explanation
Indices: 18359341--18359397 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
18359331 ATAAATTTAA
* *
18359341 ATAAACAAACTCTAAATGAAT
1 ATAAATAAACT-TAAATAAAT
18359362 ATAAATAAACTTAAATAAAT
1 ATAAATAAACTTAAATAAAT
18359382 ATAAATAAATCTTAAA
1 ATAAATAAA-CTTAAA
18359398 ATAAGATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (20 bp):
ATAAATAAACTTAAATAAAT
Found at i:18360611 original size:28 final size:28
Alignment explanation
Indices: 18360558--18360611 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
18360548 TAAGAATTTT
*
18360558 ATATAAAAATTATATATTATTATTTATG
1 ATATAAAAATTAAATATTATTATTTATG
18360586 ATATAAAAATATGAAATA-TATT-TTTA
1 ATATAAAAAT-T-AAATATTATTATTTA
18360612 ATTTCATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 14 0.61
29 5 0.22
30 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (28 bp):
ATATAAAAATTAAATATTATTATTTATG
Found at i:18361362 original size:50 final size:50
Alignment explanation
Indices: 18361287--18361388 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
18361277 AGGTATATTA
* *
18361287 TTCTCTTCGAATTTGAAAGTAGGGGTTGAGATTATTTTTGTTGATGGTGT
1 TTCTCTTCGAATTTGAAAGTAGGGGTTGAAATTATTTTTGTTGACGGTGT
*
18361337 TTCTCTTCGAATTTGAAAGTGGGGGTTGAAATTATTTTTGTTGACGGTGT
1 TTCTCTTCGAATTTGAAAGTAGGGGTTGAAATTATTTTTGTTGACGGTGT
18361387 TT
1 TT
18361389 TTAGGTATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.46
Consensus pattern (50 bp):
TTCTCTTCGAATTTGAAAGTAGGGGTTGAAATTATTTTTGTTGACGGTGT
Found at i:18362387 original size:2 final size:2
Alignment explanation
Indices: 18362380--18362406 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18362370 CAAGAAAGCA
18362380 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
18362407 AAATATAGTA
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18363773 original size:28 final size:27
Alignment explanation
Indices: 18363698--18363773 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 27
18363688 ATTAATTAAA
*
18363698 TTTTAATTTTAATTTTAAT-AAATTTT
1 TTTTAATTATAATTTTAATAAAATTTT
* * *
18363724 ATTTAATATAAAATTTTTATAAAATTATT
1 TTTTAAT-TATAATTTTAATAAAATT-TT
*
18363753 TTTTAATTATAATTATAATAA
1 TTTTAATTATAATTTTAATAA
18363774 TTTTTTAATC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 6 0.15
27 9 0.23
28 16 0.41
29 8 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTAATTATAATTTTAATAAAATTTT
Found at i:18363780 original size:23 final size:23
Alignment explanation
Indices: 18363750--18363800 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
18363740 TTATAAAATT
* * *
18363750 ATTTTTTAATTATAATTATAATA
1 ATTTTTTAATCACAATCATAATA
18363773 ATTTTTTAATCACAATCATAATA
1 ATTTTTTAATCACAATCATAATA
18363796 ATTTT
1 ATTTT
18363801 AATTATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTTTTAATCACAATCATAATA
Found at i:18366033 original size:23 final size:22
Alignment explanation
Indices: 18366006--18366061 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 22
18365996 TCTGAAATTA
18366006 ATAAAATATTATTTTTAAAAAAT
1 ATAAAATATTATTTTT-AAAAAT
*
18366029 ATAAAAATATTATTTTTTAAAAT
1 AT-AAAATATTATTTTTAAAAAT
18366052 ATAAATATAT
1 ATAAA-ATAT
18366062 AGTTATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 3 0.10
23 13 0.43
24 14 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAAATATTATTTTTAAAAAT
Found at i:18366037 original size:24 final size:23
Alignment explanation
Indices: 18366008--18366061 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
18365998 TGAAATTAAT
18366008 AAAATATTATTTTTAAAAAATATA
1 AAAATATTATTTTT-AAAAATATA
*
18366032 AAAATATTATTTTTTAAAATATA
1 AAAATATTATTTTTAAAAATATA
*
18366055 AATATAT
1 AAAATAT
18366062 AGTTATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATATTATTTTTAAAAATATA
Found at i:18367427 original size:13 final size:13
Alignment explanation
Indices: 18367406--18367443 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
18367396 ATATAATTTT
18367406 TATATAAAATATAA
1 TATA-AAAATATAA
18367420 TATAAAAATATAA
1 TATAAAAATATAA
*
18367433 TATATAAATAT
1 TATAAAAATAT
18367444 TTTATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TATAAAAATATAA
Found at i:18367449 original size:13 final size:13
Alignment explanation
Indices: 18367386--18367450 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
18367376 TTTATATTTT
18367386 ATATTTATATATATA
1 ATATTT-TATATA-A
18367401 AT-TTTTATATAAA
1 ATATTTTATAT-AA
** *
18367414 ATATAATATAAAA
1 ATATTTTATATAA
**
18367427 ATATAATATATAA
1 ATATTTTATATAA
18367440 ATATTTTATAT
1 ATATTTTATAT
18367451 TAAAGAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
13 31 0.74
14 9 0.21
15 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTTTATATAA
Found at i:18368005 original size:28 final size:28
Alignment explanation
Indices: 18367941--18368006 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 28
18367931 TATATAATTT
*
18367941 ATAATTATTATTTTTAATTATAAAATATG
1 ATAATT-TTATTTTTAATTATAAAAGATG
18367970 ATATATTTTA-TTTTAATT-TAAAAGATTG
1 ATA-ATTTTATTTTTAATTATAAAAGA-TG
18367998 AATAATTTT
1 -ATAATTTT
18368007 TATATTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 6 0.18
28 15 0.45
29 9 0.27
30 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (28 bp):
ATAATTTTATTTTTAATTATAAAAGATG
Found at i:18368007 original size:29 final size:28
Alignment explanation
Indices: 18367941--18368009 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
18367931 TATATAATTT
* *
18367941 ATAATTATTATTTTTAATTATAAAATATG
1 ATAATTTTTA-TTTTAATTATAAAAGATG
18367970 AT-ATATTTTATTTTAATT-TAAAAGATTG
1 ATAAT-TTTTATTTTAATTATAAAAGA-TG
18367998 AATAATTTTTAT
1 -ATAATTTTTAT
18368010 ATTCAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 6 0.18
28 12 0.35
29 14 0.41
30 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
ATAATTTTTATTTTAATTATAAAAGATG
Found at i:18368416 original size:2 final size:2
Alignment explanation
Indices: 18368409--18368442 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
18368399 TTGGCCTAAC
18368409 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18368443 TATCCACTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:18376886 original size:19 final size:19
Alignment explanation
Indices: 18376847--18376889 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
18376837 CCAAACCAAA
* *
18376847 TTATATATATTTTTAGCTT
1 TTATATATATTTTAAACTT
*
18376866 TTATATATATTTTAAATTT
1 TTATATATATTTTAAACTT
18376885 TTATA
1 TTATA
18376890 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTATATATATTTTAAACTT
Found at i:18376889 original size:17 final size:19
Alignment explanation
Indices: 18376847--18376889 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
18376837 CCAAACCAAA
**
18376847 TTATATATATTTTTAGCTT
1 TTATATATATTTTTAAATT
18376866 TTATATATA-TTTTAAATT
1 TTATATATATTTTTAAATT
18376884 TT-TATA
1 TTATATA
18376890 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 9 0.41
19 9 0.41
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTATATATATTTTTAAATT
Found at i:18376952 original size:15 final size:15
Alignment explanation
Indices: 18376934--18376984 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
18376924 TAAATATATT
* *
18376934 AAAATTTTATATTAAA
1 AAAATATTAAATT-AA
*
18376950 AAAATATAAAATTAA
1 AAAATATTAAATTAA
*
18376965 AAAAAATTAAATTAA
1 AAAATATTAAATTAA
18376980 AAAAT
1 AAAAT
18376985 TGGTAAACTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
15 19 0.66
16 10 0.34
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATATTAAATTAA
Found at i:18376953 original size:16 final size:16
Alignment explanation
Indices: 18376934--18376983 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
18376924 TAAATATATT
* *
18376934 AAAATTTTATATTAAA
1 AAAATATTAAATTAAA
*
18376950 AAAATATAAAATTAAA
1 AAAATATTAAATTAAA
18376966 AAAA-ATTAAATTAAA
1 AAAATATTAAATTAAA
18376981 AAA
1 AAA
18376984 TTGGTAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATATTAAATTAAA
Found at i:18376959 original size:23 final size:22
Alignment explanation
Indices: 18376909--18376962 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
18376899 TAATAATATT
* *
18376909 ATATCAAAA-TTTATTTAAATAT
1 ATAT-AAAATTTTATTTAAAAAA
18376931 AT-TAAAATTTTATATTAAAAAA
1 ATATAAAATTTTAT-TTAAAAAA
18376953 ATATAAAATT
1 ATATAAAATT
18376963 AAAAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 6 0.22
22 10 0.37
23 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATAAAATTTTATTTAAAAAA
Found at i:18377664 original size:22 final size:21
Alignment explanation
Indices: 18377629--18377673 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
18377619 AAACCCTAAC
*
18377629 CCCTTTCCTCTCCTCTTTCCTT
1 CCCTTTCCTCTCCT-TTCCCTT
18377651 CCCTTTCCGT-TCCTTTCCCTT
1 CCCTTTCC-TCTCCTTTCCCTT
18377672 CC
1 CC
18377674 TTCCATCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 12 0.57
23 1 0.05
ACGTcount: A:0.00, C:0.51, G:0.02, T:0.47
Consensus pattern (21 bp):
CCCTTTCCTCTCCTTTCCCTT
Found at i:18379839 original size:2 final size:2
Alignment explanation
Indices: 18379834--18379858 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18379824 TTTTTTTCTT
18379834 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
18379859 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:18382422 original size:18 final size:18
Alignment explanation
Indices: 18382399--18382436 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
18382389 ACCAAATGAT
18382399 AAAAAGAAATTAAAAA-AA
1 AAAAAG-AATTAAAAATAA
*
18382417 AAAAAGGATTAAAAATAA
1 AAAAAGAATTAAAAATAA
18382435 AA
1 AA
18382437 CATCAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAAAGAATTAAAAATAA
Found at i:18386659 original size:24 final size:24
Alignment explanation
Indices: 18386629--18386674 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
18386619 AATTACTGTT
* *
18386629 TATTAAATTTTAAATAAATTTAAA
1 TATTAAATATTAAAAAAATTTAAA
18386653 TATTAAATATTAAAAAAATTTA
1 TATTAAATATTAAAAAAATTTA
18386675 TCTGTATCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TATTAAATATTAAAAAAATTTAAA
Found at i:18388149 original size:14 final size:17
Alignment explanation
Indices: 18388125--18388164 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
18388115 AATTTTTTCA
18388125 ATTTTTATTTTA-AC-TT
1 ATTTTT-TTTTATACATT
18388141 ATTTTTTTTTATACATT
1 ATTTTTTTTTATACATT
18388158 ATTTTTT
1 ATTTTTT
18388165 CAAACCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 8 0.36
17 9 0.41
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTTTTTATACATT
Found at i:18393387 original size:15 final size:14
Alignment explanation
Indices: 18393369--18393411 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
18393359 TATATTCGTT
18393369 TAAATTTTATTTATA
1 TAAA-TTTATTTATA
*
18393384 TAAATTTATTTAGA
1 TAAATTTATTTATA
18393398 TATAATTTATTTAT
1 TA-AATTTATTTAT
18393412 TATTTATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TAAATTTATTTATA
Found at i:18393424 original size:22 final size:23
Alignment explanation
Indices: 18393389--18393433 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
18393379 TTATATAAAT
*
18393389 TTATTTAGATAT-AATTTATTTA
1 TTATTTAGATATAAATTAATTTA
18393411 TTATTTATGA-ATAAATTAATTTA
1 TTATTTA-GATATAAATTAATTTA
18393434 ATTTAATACG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TTATTTAGATATAAATTAATTTA
Found at i:18394186 original size:7 final size:7
Alignment explanation
Indices: 18394174--18394199 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18394164 TCTGTCACCG
18394174 GCCAAAA
1 GCCAAAA
18394181 GCCAAAA
1 GCCAAAA
18394188 GCCAAAA
1 GCCAAAA
18394195 GCCAA
1 GCCAA
18394200 GAGACTAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.31, G:0.15, T:0.00
Consensus pattern (7 bp):
GCCAAAA
Found at i:18397854 original size:16 final size:15
Alignment explanation
Indices: 18397806--18397905 Score: 94
Period size: 16 Copynumber: 6.5 Consensus size: 15
18397796 GAAGATTCAA
*
18397806 ATTTTAGGGTTTTGG
1 ATTTTAGGGGTTTGG
*
18397821 A-TTTAAGGGTTTGG
1 ATTTTAGGGGTTTGG
*
18397835 ATTTTTGGGGTTTCGG
1 ATTTTAGGGGTTT-GG
18397851 ATTTTAGGAGGTTTGG
1 ATTTTAGG-GGTTTGG
* ** *
18397867 ATTTAAAGGATTTTAG
1 ATTT-TAGGGGTTTGG
18397883 ATTTTAGGGGTTTTGG
1 ATTTTAGGGG-TTTGG
18397899 ATTTTAG
1 ATTTTAG
18397906 AATTAGTGTT
Statistics
Matches: 67, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
14 12 0.18
15 13 0.19
16 34 0.51
17 8 0.12
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.48
Consensus pattern (15 bp):
ATTTTAGGGGTTTGG
Found at i:18399031 original size:21 final size:22
Alignment explanation
Indices: 18398990--18399031 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
18398980 TGTGGTTTTT
*
18398990 ATTTTTGTATTTATTTTTGTTG
1 ATTTTTGTATTTATTTCTGTTG
18399012 ATTTTT-T-TTTACTTTCTGTT
1 ATTTTTGTATTTA-TTTCTGTT
18399032 TTGGCATGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.74
Consensus pattern (22 bp):
ATTTTTGTATTTATTTCTGTTG
Found at i:18399291 original size:20 final size:20
Alignment explanation
Indices: 18399266--18399306 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
18399256 ATCCCAGTTT
18399266 TCTTTTTTCT-GTATTTTATA
1 TCTTTTTT-TAGTATTTTATA
18399286 TCTTTTTTTAGTATTTTATA
1 TCTTTTTTTAGTATTTTATA
18399306 T
1 T
18399307 TTTATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (20 bp):
TCTTTTTTTAGTATTTTATA
Found at i:18399330 original size:29 final size:26
Alignment explanation
Indices: 18399277--18399339 Score: 63
Period size: 29 Copynumber: 2.3 Consensus size: 26
18399267 CTTTTTTCTG
* * *
18399277 TATTTTATATCTTTTTTTAGTATTTT
1 TATTTTATATATTTTTTAAATATTTT
18399303 ATATTTTATATAATTTTTTAAATAATTTT
1 -TATTTTATAT-ATTTTTTAAAT-ATTTT
18399332 TAATTTTA
1 T-ATTTTA
18399340 ATTAAACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 10 0.33
28 9 0.30
29 11 0.37
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (26 bp):
TATTTTATATATTTTTTAAATATTTT
Found at i:18399593 original size:37 final size:38
Alignment explanation
Indices: 18399519--18399601 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 38
18399509 AAGTCAAGTG
* *
18399519 ATAAAGAAAACGATCAAGACGACACCGCAAGTTGAGAA
1 ATAAAGAAAACGATCAAGACAACACCGCAAGTCGAGAA
* * * **
18399557 GTAAA-AAAATGATCAGGACAACACCGTGAGTCGAGAA
1 ATAAAGAAAACGATCAAGACAACACCGCAAGTCGAGAA
18399594 ATAAAGAA
1 ATAAAGAA
18399602 TCGACTAGGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
37 30 0.83
38 6 0.17
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.12
Consensus pattern (38 bp):
ATAAAGAAAACGATCAAGACAACACCGCAAGTCGAGAA
Found at i:18401889 original size:12 final size:11
Alignment explanation
Indices: 18401863--18401906 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
18401853 AGATGTCTCT
18401863 TTTATTTTTTA
1 TTTATTTTTTA
18401874 TTTATTTTTTA
1 TTTATTTTTTA
*
18401885 CTTTATTTGTTTG
1 -TTTATTT-TTTA
18401898 TTT-TTTTTT
1 TTTATTTTTT
18401907 TTTTGTTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 3 0.10
11 14 0.47
12 10 0.33
13 3 0.10
ACGTcount: A:0.11, C:0.02, G:0.05, T:0.82
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:18401892 original size:23 final size:24
Alignment explanation
Indices: 18401863--18401907 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
18401853 AGATGTCTCT
18401863 TTTATTT-TTTATTTATTTTTTAC
1 TTTATTTGTTTATTTATTTTTTAC
* *
18401886 TTTATTTGTTTGTTTTTTTTTT
1 TTTATTTGTTTATTTATTTTTT
18401908 TTTGTTGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.11, C:0.02, G:0.04, T:0.82
Consensus pattern (24 bp):
TTTATTTGTTTATTTATTTTTTAC
Found at i:18402767 original size:198 final size:206
Alignment explanation
Indices: 18402413--18403018 Score: 778
Period size: 198 Copynumber: 2.9 Consensus size: 206
18402403 TGAAAATTAC
* *
18402413 CAATCATTAAACTACCAATTGAAAATTTGAAAGAGTATCTGATTTTTGAAATTCAAAGTAAATTT
1 CAATCATTAAATTACCAATTGAAAATTTGAAAGAGTATCTGATTTTTGAAATTCAAAATAAATTT
* *
18402478 TTAAAATTAATCTCTTTTGTTCTTTGCCCAAGAAGAGATTATCGATCCTTTAATGTATGAACTCA
66 TTAAAATTAATCTCTTTTGTTCTTTGCCCAAGAAGAGATTATCGACCCTTTAAAGTATGAACTCA
* * *
18402543 AACTCACATTCTTTAAAAGACTATGATTGATGAGTTCAATCATTTGAATGATTAG-TCT-AA-A-
131 AACTCACATTCTTTGAAAGGCTATGATTGATGAGTCCAATCATTTGAATGATTAGATCTAAAGAG
18402604 ATTTTG-A-CA
196 ATTTTGAATCA
*
18402613 C-A-CATTAAATTACCAATTGAAATTTTGAAAGAGTATCTGATTTTTGAAATTCAAAATAAATTT
1 CAATCATTAAATTACCAATTGAAAATTTGAAAGAGTATCTGATTTTTGAAATTCAAAATAAATTT
* * * *
18402676 TTAAAACTAATCTCTTTTGTTTTTTACCCAAGAAGAGATTATCGACCCTTTAAGGTATGAACTCA
66 TTAAAATTAATCTCTTTTGTTCTTTGCCCAAGAAGAGATTATCGACCCTTTAAAGTATGAACTCA
* *
18402741 AACTCACATTCTTTGAAAGGCTATGATTGATGAGTCCAATCTTTTGAGTGATTAGGGGCATGAAA
131 AACTCACATTCTTTGAAAGGCTATGATTGATGAGTCCAATCATTTGA---A-T----G-AT--TA
* *
18402806 GTATTTAAAAGAGTATTTTGAAAATTA
185 G-ATCT-AAAGAG-ATTTTG--AATCA
* * *
18402833 CTAATCATTAAATTACCAATGGAAAATTTGAAAGAGCATCTGATTTTTGAAATTCAGAATAAATT
1 C-AATCATTAAATTACCAATTGAAAATTTGAAAGAGTATCTGATTTTTGAAATTCAAAATAAATT
* * *
18402898 TTTAAAATTAATCTCTTTTGTTCTTTGCCCAAGAAGATATTATCAACCTTTTAAAGTATGAACTC
65 TTTAAAATTAATCTCTTTTGTTCTTTGCCCAAGAAGAGATTATCGACCCTTTAAAGTATGAACTC
* * *
18402963 AAAGTCACATTCTTTGAAAGGCTATGGTTGATGAGTCCAATCATTTGAGTGATTAG
130 AAACTCACATTCTTTGAAAGGCTATGATTGATGAGTCCAATCATTTGAATGATTAG
18403019 GGGCATGAAA
Statistics
Matches: 350, Mismatches: 31, Indels: 38
0.84 0.07 0.09
Matches are distributed among these distances:
198 161 0.46
199 1 0.00
200 1 0.00
201 1 0.00
202 1 0.00
206 1 0.00
207 2 0.01
209 2 0.01
211 2 0.01
212 2 0.01
213 2 0.01
214 3 0.01
215 1 0.00
216 6 0.02
219 2 0.01
220 2 0.01
222 1 0.00
223 159 0.45
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (206 bp):
CAATCATTAAATTACCAATTGAAAATTTGAAAGAGTATCTGATTTTTGAAATTCAAAATAAATTT
TTAAAATTAATCTCTTTTGTTCTTTGCCCAAGAAGAGATTATCGACCCTTTAAAGTATGAACTCA
AACTCACATTCTTTGAAAGGCTATGATTGATGAGTCCAATCATTTGAATGATTAGATCTAAAGAG
ATTTTGAATCA
Found at i:18402963 original size:421 final size:421
Alignment explanation
Indices: 18402179--18403018 Score: 1425
Period size: 421 Copynumber: 2.0 Consensus size: 421
18402169 ATGATCATGG
18402179 TAAAATTTTGACACACATTAAATTACCAATTAAAATTTTGAAAAGAGTATCTGATTTTTGAAATT
1 TAAAATTTTGACACACATTAAATTACCAATTAAAATTTTGAAAAGAGTATCTGATTTTTGAAATT
* * *
18402244 CAAAATAAATTTTTAAAATTAATCTCTTTTGGTCTTTGCCCAATAAGAGATTATCGACCCTTTAA
66 CAAAATAAATTTTTAAAACTAATCTCTTTTGGTCTTTACCCAAGAAGAGATTATCGACCCTTTAA
*
18402309 AGTATGAACTCAAAGTCACATTCTTTGAAAGGCTATGATTGATGAGTCCAATAATTTGAGTGATT
131 AGTATGAACTCAAACTCACATTCTTTGAAAGGCTATGATTGATGAGTCCAATAATTTGAGTGATT
*
18402374 AGGGGCATGAAAGTATTTAAAAGAGTATTTGAAAATTACCAATCATTAAACTACCAATTGAAAAT
196 AGGGGCATGAAAGTATTTAAAAGAGTATTTGAAAATTACCAATCATTAAACTACCAATGGAAAAT
*
18402439 TTGAAAGAGTATCTGATTTTTGAAATTCAAAGTAAATTTTTAAAATTAATCTCTTTTGTTCTTTG
261 TTGAAAGAGCATCTGATTTTTGAAATTCAAAGTAAATTTTTAAAATTAATCTCTTTTGTTCTTTG
* *
18402504 CCCAAGAAGAGATTATCGATCCTTTAATGTATGAACTCAAACTCACATTCTTTAAAAGACTATGA
326 CCCAAGAAGAGATTATCGAACCTTTAAAGTATGAACTCAAACTCACATTCTTTAAAAGACTATGA
*
18402569 TTGATGAGTTCAATCATTTGAATGATTAGTC
391 TTGATGAGTCCAATCATTTGAATGATTAGTC
*
18402600 TAAAATTTTGACACACATTAAATTACCAATTGAAATTTTG-AAAGAGTATCTGATTTTTGAAATT
1 TAAAATTTTGACACACATTAAATTACCAATTAAAATTTTGAAAAGAGTATCTGATTTTTGAAATT
* *
18402664 CAAAATAAATTTTTAAAACTAATCTCTTTTGTTTTTTACCCAAGAAGAGATTATCGACCCTTTAA
66 CAAAATAAATTTTTAAAACTAATCTCTTTTGGTCTTTACCCAAGAAGAGATTATCGACCCTTTAA
* **
18402729 GGTATGAACTCAAACTCACATTCTTTGAAAGGCTATGATTGATGAGTCCAATCTTTTGAGTGATT
131 AGTATGAACTCAAACTCACATTCTTTGAAAGGCTATGATTGATGAGTCCAATAATTTGAGTGATT
* *
18402794 AGGGGCATGAAAGTATTTAAAAGAGTATTTTGAAAATTACTAATCATTAAATTACCAATGGAAAA
196 AGGGGCATGAAAGTATTTAAAAGAGTA-TTTGAAAATTACCAATCATTAAACTACCAATGGAAAA
18402859 TTTGAAAGAGCATCTGATTTTTGAAATTCAGAA-TAAATTTTTAAAATTAATCTCTTTTGTTCTT
260 TTTGAAAGAGCATCTGATTTTTGAAATTCA-AAGTAAATTTTTAAAATTAATCTCTTTTGTTCTT
* * * *
18402923 TGCCCAAGAAGATATTATC-AACCTTTTAAAGTATGAACTCAAAGTCACATTCTTTGAAAGGCTA
324 TGCCCAAGAAGAGATTATCGAACC-TTTAAAGTATGAACTCAAACTCACATTCTTTAAAAGACTA
* *
18402987 TGGTTGATGAGTCCAATCATTTGAGTGATTAG
388 TGATTGATGAGTCCAATCATTTGAATGATTAG
18403019 GGGCATGAAA
Statistics
Matches: 393, Mismatches: 23, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
420 175 0.45
421 216 0.55
422 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (421 bp):
TAAAATTTTGACACACATTAAATTACCAATTAAAATTTTGAAAAGAGTATCTGATTTTTGAAATT
CAAAATAAATTTTTAAAACTAATCTCTTTTGGTCTTTACCCAAGAAGAGATTATCGACCCTTTAA
AGTATGAACTCAAACTCACATTCTTTGAAAGGCTATGATTGATGAGTCCAATAATTTGAGTGATT
AGGGGCATGAAAGTATTTAAAAGAGTATTTGAAAATTACCAATCATTAAACTACCAATGGAAAAT
TTGAAAGAGCATCTGATTTTTGAAATTCAAAGTAAATTTTTAAAATTAATCTCTTTTGTTCTTTG
CCCAAGAAGAGATTATCGAACCTTTAAAGTATGAACTCAAACTCACATTCTTTAAAAGACTATGA
TTGATGAGTCCAATCATTTGAATGATTAGTC
Found at i:18403003 original size:223 final size:223
Alignment explanation
Indices: 18402615--18403038 Score: 722
Period size: 223 Copynumber: 1.9 Consensus size: 223
18402605 TTTTGACACA
* * *
18402615 CATTAAATTACCAATTGAAATTTTGAAAGAGTATCTGATTTTTGAAATTCAAAATAAATTTTTAA
1 CATTAAATTACCAATGGAAAATTTGAAAGAGCATCTGATTTTTGAAATTCAAAATAAATTTTTAA
* * *
18402680 AACTAATCTCTTTTGTTTTTTACCCAAGAAGAGATTATCGACCCTTTAAGGTATGAACTCAAACT
66 AACTAATCTCTTTTGTTCTTTACCCAAGAAGAGATTATCAACCCTTTAAAGTATGAACTCAAACT
*
18402745 CACATTCTTTGAAAGGCTATGATTGATGAGTCCAATCTTTTGAGTGATTAGGGGCATGAAAGTAT
131 CACATTCTTTGAAAGGCTATGATTGATGAGTCCAATCATTTGAGTGATTAGGGGCATGAAAGTAT
18402810 TTAAAAGAGTATTTTGAAAATTACTAAT
196 TTAAAAGAGTATTTTGAAAATTACTAAT
*
18402838 CATTAAATTACCAATGGAAAATTTGAAAGAGCATCTGATTTTTGAAATTCAGAATAAATTTTTAA
1 CATTAAATTACCAATGGAAAATTTGAAAGAGCATCTGATTTTTGAAATTCAAAATAAATTTTTAA
* * * * *
18402903 AATTAATCTCTTTTGTTCTTTGCCCAAGAAGATATTATCAACCTTTTAAAGTATGAACTCAAAGT
66 AACTAATCTCTTTTGTTCTTTACCCAAGAAGAGATTATCAACCCTTTAAAGTATGAACTCAAACT
*
18402968 CACATTCTTTGAAAGGCTATGGTTGATGAGTCCAATCATTTGAGTGATTAGGGGCATGAAAGTAT
131 CACATTCTTTGAAAGGCTATGATTGATGAGTCCAATCATTTGAGTGATTAGGGGCATGAAAGTAT
18403033 TTAAAA
196 TTAAAA
18403039 AGGTGTTGAG
Statistics
Matches: 187, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
223 187 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (223 bp):
CATTAAATTACCAATGGAAAATTTGAAAGAGCATCTGATTTTTGAAATTCAAAATAAATTTTTAA
AACTAATCTCTTTTGTTCTTTACCCAAGAAGAGATTATCAACCCTTTAAAGTATGAACTCAAACT
CACATTCTTTGAAAGGCTATGATTGATGAGTCCAATCATTTGAGTGATTAGGGGCATGAAAGTAT
TTAAAAGAGTATTTTGAAAATTACTAAT
Found at i:18408996 original size:16 final size:16
Alignment explanation
Indices: 18408969--18409006 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
18408959 AAAGATTCGG
18408969 ATTTTA-GGGTTTTGA
1 ATTTTAGGGGTTTTGA
*
18408984 ATTTTAGGGGTTTTGG
1 ATTTTAGGGGTTTTGA
18409000 ATTTTAG
1 ATTTTAG
18409007 AATTAATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (16 bp):
ATTTTAGGGGTTTTGA
Found at i:18409553 original size:12 final size:12
Alignment explanation
Indices: 18409538--18409564 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
18409528 GTTGAACCGA
18409538 TTGAGGAACGGT
1 TTGAGGAACGGT
18409550 TTGAGGAACGGT
1 TTGAGGAACGGT
18409562 TTG
1 TTG
18409565 GACTTATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.41, T:0.30
Consensus pattern (12 bp):
TTGAGGAACGGT
Found at i:18410395 original size:15 final size:15
Alignment explanation
Indices: 18410372--18410403 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18410362 ATATGATTTT
18410372 TTAAATAATTTTTAA
1 TTAAATAATTTTTAA
*
18410387 TTAATTAATTTTTAA
1 TTAAATAATTTTTAA
18410402 TT
1 TT
18410404 TTAAGTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAAATAATTTTTAA
Found at i:18410434 original size:22 final size:21
Alignment explanation
Indices: 18410381--18410434 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
18410371 TTTAAATAAT
* *
18410381 TTTTAATTAATTAATTTTTAA
1 TTTTAATAAATCAATTTTTAA
18410402 TTTTAAGTAAATCAATTTATT-A
1 TTTTAA-TAAATCAATTT-TTAA
18410424 TTATTAATAAA
1 TT-TTAATAAA
18410435 CAAGAACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 6 0.21
22 16 0.57
23 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTAATAAATCAATTTTTAA
Found at i:18411731 original size:11 final size:11
Alignment explanation
Indices: 18411715--18411739 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18411705 CTAGATCTTT
18411715 TATGAAAATTA
1 TATGAAAATTA
18411726 TATGAAAATTA
1 TATGAAAATTA
18411737 TAT
1 TAT
18411740 TTTACCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
TATGAAAATTA
Found at i:18414304 original size:2 final size:2
Alignment explanation
Indices: 18414297--18414340 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
18414287 TTGTTTTATG
18414297 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18414339 TC
1 TC
18414341 GCTTTTATCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:18423176 original size:6 final size:6
Alignment explanation
Indices: 18423165--18423216 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
18423155 TATTATTTTT
*
18423165 AATATA AATATA AA-ATA AA-AT- AA-ATA AATATA AATATA AA-ATT
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
18423208 AAT-TA AATA
1 AATATA AATA
18423217 ATTATATATC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 4 0.10
5 17 0.43
6 19 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:18423189 original size:16 final size:16
Alignment explanation
Indices: 18423165--18423216 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
18423155 TATTATTTTT
18423165 AATATAAATATAAAATA
1 AATATAAA-ATAAAATA
18423182 AA-AT-AAATAAATATA
1 AATATAAAATAAA-ATA
* *
18423197 AATATAAAATTAATTA
1 AATATAAAATAAAATA
18423213 AATA
1 AATA
18423217 ATTATATATC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 10 0.33
17 8 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATATAAAATAAAATA
Found at i:18423197 original size:10 final size:10
Alignment explanation
Indices: 18423168--18423200 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
18423158 TATTTTTAAT
18423168 ATAAATATAAA
1 ATAAATAT-AA
18423179 ATAAA-ATAA
1 ATAAATATAA
18423188 ATAAATATAA
1 ATAAATATAA
18423198 ATA
1 ATA
18423201 TAAAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.33
10 9 0.43
11 5 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAAATATAA
Found at i:18423198 original size:26 final size:26
Alignment explanation
Indices: 18423165--18423222 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
18423155 TATTATTTTT
18423165 AATATAAATATAAAATAAAATAAATA
1 AATATAAATATAAAATAAAATAAATA
* *
18423191 AATATAAATATAAAATTAATTAAATA
1 AATATAAATATAAAATAAAATAAATA
*
18423217 ATTATA
1 AATATA
18423223 TATCTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
AATATAAATATAAAATAAAATAAATA
Found at i:18423217 original size:20 final size:20
Alignment explanation
Indices: 18423163--18423222 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
18423153 AATATTATTT
*
18423163 TTAATATAAATATAAAATAAAA
1 TTAAT-TAAATA-AATATAAAA
* *
18423185 TAAATAAATATAAATATAAAA
1 TTAATTAA-ATAAATATAAAA
*
18423206 TTAATTAAATAATTATA
1 TTAATTAAATAAATATA
18423223 TATCTTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 8 0.26
21 16 0.52
22 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TTAATTAAATAAATATAAAA
Found at i:18424247 original size:21 final size:22
Alignment explanation
Indices: 18424223--18424268 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
18424213 TTAATATAAA
* *
18424223 AAATATATTTTTTA-TTTTATT
1 AAATATATTTATAATTTTTATT
*
18424244 AAATTTATTTATAATTTTTATT
1 AAATATATTTATAATTTTTATT
18424266 AAA
1 AAA
18424269 ATTTTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
AAATATATTTATAATTTTTATT
Found at i:18425392 original size:2 final size:2
Alignment explanation
Indices: 18425385--18425423 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
18425375 GCGACTGATC
*
18425385 AT AT AT AT AA AT AT AT AT AT AT AT AT 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 AT A
18425424 AAAGAACTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:18426842 original size:2 final size:2
Alignment explanation
Indices: 18426837--18426861 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18426827 ACACACATAC
18426837 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
18426862 ACATAACTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18427002 original size:16 final size:16
Alignment explanation
Indices: 18426981--18427012 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18426971 TTTTTTTGTG
*
18426981 TACATTATATACAATA
1 TACATTATAAACAATA
18426997 TACATTATAAACAATA
1 TACATTATAAACAATA
18427013 CAAAAAGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (16 bp):
TACATTATAAACAATA
Found at i:18433875 original size:42 final size:42
Alignment explanation
Indices: 18433816--18433901 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
18433806 CAAATTTAGA
18433816 CGGTGTATAACACATGGTTTGCCATGATATGCCGTGTTGCAT
1 CGGTGTATAACACATGGTTTGCCATGATATGCCGTGTTGCAT
* *
18433858 CGGTGTATAACACATGGTTTGTCATGATATGCCGTGTTGTAT
1 CGGTGTATAACACATGGTTTGCCATGATATGCCGTGTTGCAT
18433900 CG
1 CG
18433902 ATTCATAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (42 bp):
CGGTGTATAACACATGGTTTGCCATGATATGCCGTGTTGCAT
Found at i:18434376 original size:13 final size:13
Alignment explanation
Indices: 18434358--18434382 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18434348 TATATATCTT
18434358 AAATATTAATTTC
1 AAATATTAATTTC
18434371 AAATATTAATTT
1 AAATATTAATTT
18434383 TTAAAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATATTAATTTC
Found at i:18437828 original size:15 final size:15
Alignment explanation
Indices: 18437810--18437847 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
18437800 TTTTCAAATA
*
18437810 CTTTGTTTTCTTTTC
1 CTTTGTTTTCCTTTC
*
18437825 CTTTGCTTTCCTTTC
1 CTTTGTTTTCCTTTC
18437840 CTTT-TTTT
1 CTTTGTTTT
18437848 TATTAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (15 bp):
CTTTGTTTTCCTTTC
Found at i:18439855 original size:12 final size:12
Alignment explanation
Indices: 18439838--18439863 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18439828 TATAGGGGCT
18439838 ATAAAAGGTTTA
1 ATAAAAGGTTTA
18439850 ATAAAAGGTTTA
1 ATAAAAGGTTTA
18439862 AT
1 AT
18439864 GAGTGTTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (12 bp):
ATAAAAGGTTTA
Found at i:18443677 original size:13 final size:13
Alignment explanation
Indices: 18443642--18443678 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
18443632 TTAAAGAATC
*
18443642 TTTTTTTCTATGGT
1 TTTTTTTGT-TGGT
18443656 TTTTTTTGTTGGT
1 TTTTTTTGTTGGT
18443669 TTTTTTTGTT
1 TTTTTTTGTT
18443679 TTAATTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.78
Consensus pattern (13 bp):
TTTTTTTGTTGGT
Found at i:18446568 original size:22 final size:24
Alignment explanation
Indices: 18446530--18446592 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 24
18446520 TTAATTTGTG
18446530 TTATTTA-TT-TTAA-AAATTA-A
1 TTATTTATTTATTAATAAATTATA
18446550 -TATTTATTTATTAATAAATTATTA
1 TTATTTATTTATTAATAAATTA-TA
18446574 TTATTTAATTTATTAATAA
1 TTATTT-ATTTATTAATAA
18446593 TATATAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.17
20 2 0.06
21 4 0.11
22 6 0.17
24 1 0.03
25 5 0.14
26 12 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTTATTTATTAATAAATTATA
Found at i:18458621 original size:11 final size:11
Alignment explanation
Indices: 18458602--18458630 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
18458592 AATGGAAATG
18458602 AAAAA-AAAAA
1 AAAAAGAAAAA
18458612 AAAAAGAAAAA
1 AAAAAGAAAAA
18458623 AAAAAGAA
1 AAAAAGAA
18458631 TGTGTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:18463042 original size:17 final size:17
Alignment explanation
Indices: 18463006--18463038 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18462996 TAGGTATATT
18463006 AAAAAAATTAGTAAAAGA
1 AAAAAAATTA-TAAAAGA
18463024 AAAAAAATT-TAAAAG
1 AAAAAAATTATAAAAG
18463039 GAAAGATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
AAAAAAATTATAAAAGA
Found at i:18466607 original size:14 final size:14
Alignment explanation
Indices: 18466541--18466618 Score: 57
Period size: 14 Copynumber: 5.2 Consensus size: 14
18466531 CTTCGAGCTC
*
18466541 AATTAAATTTTTTT
1 AATTAAATTTATTT
18466555 AATTCAAATTTAATTT
1 AATT-AAATTT-ATTT
* * *
18466571 GAAATAAAAATTAAATT
1 --AAT-TAAATTTATTT
*
18466588 ATTTAAATTTATTT
1 AATTAAATTTATTT
*
18466602 AATTAAATTTAATT
1 AATTAAATTTATTT
18466616 AAT
1 AAT
18466619 ATATAAAAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
14 27 0.55
15 8 0.16
16 3 0.06
17 3 0.06
18 8 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (14 bp):
AATTAAATTTATTT
Found at i:18466649 original size:25 final size:25
Alignment explanation
Indices: 18466621--18466669 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
18466611 TAATTAATAT
18466621 ATAAAAACAATAATT-TTTATATTTG
1 ATAAAAA-AATAATTATTTATATTTG
**
18466646 ATAAAAATTTAATTATTTATATTT
1 ATAAAAAAATAATTATTTATATTT
18466670 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
ATAAAAAAATAATTATTTATATTTG
Found at i:18466688 original size:20 final size:20
Alignment explanation
Indices: 18466650--18466699 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 20
18466640 TATTTGATAA
*
18466650 AAATTT-AATTATTTATATTT
1 AAATTTAAAATATTTATA-TT
18466670 AAATTTAAAATATTT-TATT
1 AAATTTAAAATATTTATATT
18466689 -AA-TTAAAATAT
1 AAATTTAAAATAT
18466700 AAAAATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 9 0.32
18 2 0.07
19 2 0.07
20 8 0.29
21 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATTTAAAATATTTATATT
Found at i:18466782 original size:48 final size:48
Alignment explanation
Indices: 18466693--18466785 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
18466683 TTTATTAATT
* *
18466693 AAAATATAAAAATTAAATTAAATTCATAAATTACTTAAATAAAATATA
1 AAAATATAAAAATTAAATTAAATTAATAAATTAATTAAATAAAATATA
** * *
18466741 AAAATATTTAAATTCAATTTAATTAATAAATTAA-TATAATAAAAT
1 AAAATATAAAAATTAAATTAAATTAATAAATTAATTA-AATAAAAT
18466786 TTGAGTTTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 2 0.05
48 36 0.95
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (48 bp):
AAAATATAAAAATTAAATTAAATTAATAAATTAATTAAATAAAATATA
Found at i:18467962 original size:37 final size:38
Alignment explanation
Indices: 18467906--18467981 Score: 118
Period size: 37 Copynumber: 2.0 Consensus size: 38
18467896 GAGGTGTACC
*
18467906 GGGCAACCCTTAAGGTAAATCAAAGGAATGATGACTGT
1 GGGCAACCCTTAAGATAAATCAAAGGAATGATGACTGT
* *
18467944 GGGC-ACCCTTAAGATAAATCAAGGGAATGATTACTGT
1 GGGCAACCCTTAAGATAAATCAAAGGAATGATGACTGT
18467981 G
1 G
18467982 TATGGGTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 31 0.89
38 4 0.11
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (38 bp):
GGGCAACCCTTAAGATAAATCAAAGGAATGATGACTGT
Found at i:18471176 original size:15 final size:15
Alignment explanation
Indices: 18471156--18471185 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18471146 GGCCGGAGTC
18471156 GGATGAAGATGAAGA
1 GGATGAAGATGAAGA
*
18471171 GGATGATGATGAAGA
1 GGATGAAGATGAAGA
18471186 TGATCCAGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.40, T:0.17
Consensus pattern (15 bp):
GGATGAAGATGAAGA
Found at i:18471515 original size:24 final size:23
Alignment explanation
Indices: 18471488--18471545 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
18471478 GTGGAAGTTC
*
18471488 ATGAGATTGGGGATAG-TGATGATG
1 ATGAGA-T-GGGATAGAGGATGATG
18471512 ATGAAGATGGGATAGAGGATGATG
1 ATG-AGATGGGATAGAGGATGATG
18471536 ATGATGATGG
1 ATGA-GATGG
18471546 CGAGGATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 8 0.27
24 19 0.63
25 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.41, T:0.26
Consensus pattern (23 bp):
ATGAGATGGGATAGAGGATGATG
Found at i:18471557 original size:24 final size:24
Alignment explanation
Indices: 18471497--18471545 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
18471487 CATGAGATTG
18471497 GGGATAG-TGATGATGATGAAGAT
1 GGGATAGATGATGATGATGAAGAT
* *
18471520 GGGATAGAGGATGATGATGATGAT
1 GGGATAGATGATGATGATGAAGAT
18471544 GG
1 GG
18471546 CGAGGATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (24 bp):
GGGATAGATGATGATGATGAAGAT
Found at i:18471836 original size:48 final size:48
Alignment explanation
Indices: 18471763--18471859 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
18471753 AGAGGAGGTG
* *
18471763 AGATTCCTTGTTTCTTGCAAAAATACTACCTCATGCTTCTATGGTTTA
1 AGATTCCTTATTTCTTGCAAAAATACTACCTCATGCTTCTATCGTTTA
*
18471811 AGATTCCTTATTTCTTGCAATAATACTACCTCATGCTTCTATCGTTTA
1 AGATTCCTTATTTCTTGCAAAAATACTACCTCATGCTTCTATCGTTTA
18471859 A
1 A
18471860 TCTAATTGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (48 bp):
AGATTCCTTATTTCTTGCAAAAATACTACCTCATGCTTCTATCGTTTA
Done.