Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 157 of 190
Found at i:25448466 original size:25 final size:26
Alignment explanation
Indices: 25448438--25448487 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
25448428 TCAAAATCCT
25448438 TTTAGAA-AAGTCAAAGAATTTTTAA
1 TTTAGAATAAGTCAAAGAATTTTTAA
* *
25448463 TTTAGAATTAAGTCAGAGTATTTTT
1 TTTAGAA-TAAGTCAAAGAATTTTT
25448488 TTTGAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
27 14 0.67
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (26 bp):
TTTAGAATAAGTCAAAGAATTTTTAA
Found at i:25448943 original size:13 final size:13
Alignment explanation
Indices: 25448925--25448950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25448915 AGGATGAACT
25448925 TTGAATTTTTTGG
1 TTGAATTTTTTGG
25448938 TTGAATTTTTTGG
1 TTGAATTTTTTGG
25448951 CAAGGTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (13 bp):
TTGAATTTTTTGG
Found at i:25451640 original size:18 final size:20
Alignment explanation
Indices: 25451617--25451653 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
25451607 GATCTAGTTC
25451617 TTATCTTT-T-TTATTTTTT
1 TTATCTTTCTATTATTTTTT
25451635 TTATCTTTCTATTATTTTT
1 TTATCTTTCTATTATTTTT
25451654 GAATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (20 bp):
TTATCTTTCTATTATTTTTT
Found at i:25456920 original size:20 final size:22
Alignment explanation
Indices: 25456895--25456939 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
25456885 ATTAGCTTTT
*
25456895 AAAATTCT-ATTTATT-TTTAA
1 AAAATTATAATTTATTATTTAA
*
25456915 AAAATTATAATTTTTTATTTAA
1 AAAATTATAATTTATTATTTAA
25456937 AAA
1 AAA
25456940 TAAAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 6 0.29
22 8 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATTATAATTTATTATTTAA
Found at i:25469214 original size:27 final size:27
Alignment explanation
Indices: 25469178--25469233 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
25469168 TTTTCTATAA
*
25469178 AAAAGTTTATGTATGGAAAAGTTTAAT
1 AAAAGTTTATATATGGAAAAGTTTAAT
*
25469205 AAAAGTTTATATATGGAAAATTTTAAT
1 AAAAGTTTATATATGGAAAAGTTTAAT
25469232 AA
1 AA
25469234 TGTGTACCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (27 bp):
AAAAGTTTATATATGGAAAAGTTTAAT
Found at i:25480447 original size:54 final size:53
Alignment explanation
Indices: 25480333--25480484 Score: 146
Period size: 54 Copynumber: 2.8 Consensus size: 53
25480323 ATCTAATTAT
** * * * **
25480333 TCCACCATTCGGGTCAAATTAGAAATATTTTCTT-GTTTTGAATTTCTAAATTC
1 TCCACCATTTAGGCCAATTTAGAAATATTTT-TTATTTTTTTATTTCTAAATTC
* * *
25480386 TCCACCATTTAGGCCTATTTAGAAAT-TCTTGTTTTTTTTTTTATTTCTAAATTT
1 TCCACCATTTAGGCCAATTTAGAAATAT-TT-TTTATTTTTTTATTTCTAAATTC
* * *
25480440 TTCACCATTTTGGTCAATTTAGAAATATTTTTTATTTTTTTATTT
1 TCCACCATTTAGGCCAATTTAGAAATATTTTTTATTTTTTTATTT
25480485 TTTGATTTCA
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
52 1 0.01
53 39 0.48
54 40 0.49
55 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.53
Consensus pattern (53 bp):
TCCACCATTTAGGCCAATTTAGAAATATTTTTTATTTTTTTATTTCTAAATTC
Found at i:25481004 original size:21 final size:21
Alignment explanation
Indices: 25480963--25481004 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
25480953 ATAAGAAAAC
* *
25480963 GGCTTAGCTTAACGACTAGAA
1 GGCTTAACTTAACGACAAGAA
25480984 GGCTTAACTTAACTG-CAAGAA
1 GGCTTAACTTAAC-GACAAGAA
25481005 AAAAAGCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (21 bp):
GGCTTAACTTAACGACAAGAA
Found at i:25481371 original size:13 final size:13
Alignment explanation
Indices: 25481353--25481384 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
25481343 CTGCCTATTT
25481353 TTTTTAATTTTAA
1 TTTTTAATTTTAA
*
25481366 TTTTTAATTTTAT
1 TTTTTAATTTTAA
25481379 TTTTTA
1 TTTTTA
25481385 TTAACAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTAATTTTAA
Found at i:25481707 original size:41 final size:41
Alignment explanation
Indices: 25481582--25481780 Score: 164
Period size: 41 Copynumber: 4.7 Consensus size: 41
25481572 AGTAGAGCCT
* ** * *
25481582 CACAACTTTGAAAAAATAAATACGACTTATCTAAACATAGGCTC
1 CACAACTTTG-AAAAATAAA-ATG-CTCCTCTAAACAAAGGCAC
* * * * *
25481626 AACGACTTCTGAAAAATAAATTAAGCTCTTCTAAATAAAGGCAC
1 CACAACTT-TGAAAAATAAA--ATGCTCCTCTAAACAAAGGCAC
* *
25481670 CACAACTTTAAAAAATAAAATGCTCCTCTAAACAAAGGTAC
1 CACAACTTTGAAAAATAAAATGCTCCTCTAAACAAAGGCAC
* * * * *
25481711 CATAACTTTTGAAAAATAAAATGCTCTTATAAATAGAGGCAC
1 CACAAC-TTTGAAAAATAAAATGCTCCTCTAAACAAAGGCAC
* *
25481753 TACAACTTTGAAAAATAAAATGTTCCTC
1 CACAACTTTGAAAAATAAAATGCTCCTC
25481781 AACAATCATG
Statistics
Matches: 125, Mismatches: 27, Indels: 9
0.78 0.17 0.06
Matches are distributed among these distances:
41 42 0.34
42 33 0.26
43 10 0.08
44 35 0.28
45 5 0.04
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.26
Consensus pattern (41 bp):
CACAACTTTGAAAAATAAAATGCTCCTCTAAACAAAGGCAC
Found at i:25481760 original size:42 final size:41
Alignment explanation
Indices: 25481630--25481774 Score: 173
Period size: 41 Copynumber: 3.4 Consensus size: 41
25481620 AGGCTCAACG
*
25481630 ACTTCTGAAAAATAAATTAAGCTCTTCTAAATAAAGGCACCACA
1 ACTT-TGAAAAATAAA--ATGCTCTTCTAAATAAAGGCACCACA
* * * * *
25481674 ACTTTAAAAAATAAAATGCTCCTCTAAACAAAGGTACCATA
1 ACTTTGAAAAATAAAATGCTCTTCTAAATAAAGGCACCACA
* * *
25481715 ACTTTTGAAAAATAAAATGCTCTTATAAATAGAGGCACTACA
1 AC-TTTGAAAAATAAAATGCTCTTCTAAATAAAGGCACCACA
25481757 ACTTTGAAAAATAAAATG
1 ACTTTGAAAAATAAAATG
25481775 TTCCTCAACA
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
41 39 0.45
42 33 0.38
43 10 0.12
44 4 0.05
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.26
Consensus pattern (41 bp):
ACTTTGAAAAATAAAATGCTCTTCTAAATAAAGGCACCACA
Found at i:25482030 original size:21 final size:21
Alignment explanation
Indices: 25482006--25482075 Score: 54
Period size: 22 Copynumber: 3.3 Consensus size: 21
25481996 GCATCCAACA
*
25482006 TTTAAAGATTTTCATTCAAAT
1 TTTAAAGATTTTCATTCAAAG
** *
25482027 TTTAGAA-ATTCACATCCAAAAG
1 TTTA-AAGATTTTCATTC-AAAG
*
25482049 TTTAAAGCTTTTCATTC-AAG
1 TTTAAAGATTTTCATTCAAAG
*
25482069 TTCAAAG
1 TTTAAAG
25482076 GTTCACACTT
Statistics
Matches: 37, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
20 9 0.24
21 13 0.35
22 15 0.41
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
TTTAAAGATTTTCATTCAAAG
Found at i:25482216 original size:79 final size:78
Alignment explanation
Indices: 25482067--25482258 Score: 264
Period size: 79 Copynumber: 2.5 Consensus size: 78
25482057 TTTTCATTCA
* * * * *
25482067 AGTTCAAAGGTTCACACTT-GACAAA-TTTGGGATTCAC-TCTCAAAGATTCTATTCGAAATTCA
1 AGTTTAAAGATTCACA-TTCGACAAATTTTAGGTTTCACACCTCAAAGATTCTATTCGAAATTCA
25482129 AAGATTCTCATTTG
65 AAGATTCTCATTTG
* *
25482143 AGTTTGAAGATTCACATTCGACAAATTTTAGGTTTCACACCTCAAAGATTCTCATTTGAAATTCA
1 AGTTTAAAGATTCACATTCGACAAATTTTAGGTTTCACACCTCAAAGATTCT-ATTCGAAATTCA
25482208 AAGATTCTCATTTG
65 AAGATTCTCATTTG
* *
25482222 AGTTTAAAGATTCACATTCGATAAATTTTGGGTTTCA
1 AGTTTAAAGATTCACATTCGACAAATTTTAGGTTTCA
25482259 AAGATTCTCA
Statistics
Matches: 102, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
75 2 0.02
76 19 0.19
77 10 0.10
78 12 0.12
79 59 0.58
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (78 bp):
AGTTTAAAGATTCACATTCGACAAATTTTAGGTTTCACACCTCAAAGATTCTATTCGAAATTCAA
AGATTCTCATTTG
Found at i:25482232 original size:20 final size:21
Alignment explanation
Indices: 25482184--25482239 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
25482174 GTTTCACACC
25482184 TCAAAGATTCTCATTTGAAAT
1 TCAAAGATTCTCATTTGAAAT
*
25482205 TCAAAGATTCTCATTTG-AGT
1 TCAAAGATTCTCATTTGAAAT
* *
25482225 TTAAAGATTCACATT
1 TCAAAGATTCTCATT
25482240 CGATAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (21 bp):
TCAAAGATTCTCATTTGAAAT
Found at i:25482263 original size:51 final size:51
Alignment explanation
Indices: 25482204--25482307 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
25482194 TCATTTGAAA
* *
25482204 TTCAAAGATTCTCATTTGAGTTTAAAGATTCACATTCGATAAATTTTGGGT
1 TTCAAAGATTCTCATTAGAATTTAAAGATTCACATTCGATAAATTTTGGGT
25482255 TTCAAAGATTCTCATTAGAATTTAAAGATTCACATTCGATAAATTTTGGGT
1 TTCAAAGATTCTCATTAGAATTTAAAGATTCACATTCGATAAATTTTGGGT
25482306 TT
1 TT
25482308 TACACCTCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (51 bp):
TTCAAAGATTCTCATTAGAATTTAAAGATTCACATTCGATAAATTTTGGGT
Found at i:25482346 original size:21 final size:21
Alignment explanation
Indices: 25482314--25482411 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
25482304 GTTTTACACC
*
25482314 TCAAAGATTCTCATTTGAAAT
1 TCAAAAATTCTCATTTGAAAT
* *
25482335 TTAAAAATTCTCATTTG-AGT
1 TCAAAAATTCTCATTTGAAAT
* *
25482355 TCGAAAATCCTCATTTGAAAT
1 TCAAAAATTCTCATTTGAAAT
* *
25482376 TCAAAGACTCTCATTTGAGAACT
1 TCAAAAATTCTCATTTGA-AA-T
*
25482399 T-AAAAATTTTCAT
1 TCAAAAATTCTCAT
25482412 CAAAAGATTC
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
20 16 0.27
21 31 0.52
22 11 0.18
23 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (21 bp):
TCAAAAATTCTCATTTGAAAT
Found at i:25482771 original size:23 final size:23
Alignment explanation
Indices: 25482745--25482788 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
25482735 TTAGAGCAAG
*
25482745 TTTCATCAATTGATCATCATTAT
1 TTTCATCAATTGATCACCATTAT
*
25482768 TTTCATCACTTGATCACCATT
1 TTTCATCAATTGATCACCATT
25482789 TATAGGCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45
Consensus pattern (23 bp):
TTTCATCAATTGATCACCATTAT
Found at i:25483542 original size:9 final size:9
Alignment explanation
Indices: 25483520--25483570 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
25483510 CTTTTCTTTC
25483520 TTTTTCATCAT
1 TTTTTCAT--T
25483531 TTTTTCATT
1 TTTTTCATT
25483540 TTTTTCATT
1 TTTTTCATT
*
25483549 TTTCCTT-TTT
1 TTT--TTCATT
25483559 TTTTTCATT
1 TTTTTCATT
25483568 TTT
1 TTT
25483571 GTTGTTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 2 0.06
9 18 0.51
10 5 0.14
11 10 0.29
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTCATT
Found at i:25483561 original size:17 final size:17
Alignment explanation
Indices: 25483527--25483560 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25483517 TTCTTTTTCA
*
25483527 TCATTTTTTCATTTTTT
1 TCATTTTTCCATTTTTT
25483544 TCATTTTTCC-TTTTTT
1 TCATTTTTCCATTTTTT
25483560 T
1 T
25483561 TTTCATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (17 bp):
TCATTTTTCCATTTTTT
Found at i:25483588 original size:17 final size:18
Alignment explanation
Indices: 25483566--25483603 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
25483556 TTTTTTTTCA
25483566 TTTTTGTTGTTTC-TTTT
1 TTTTTGTTGTTTCATTTT
*
25483583 TTTTTGTTTTTTCATTTT
1 TTTTTGTTGTTTCATTTT
25483601 TTT
1 TTT
25483604 CATCCATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.03, C:0.05, G:0.08, T:0.84
Consensus pattern (18 bp):
TTTTTGTTGTTTCATTTT
Found at i:25487951 original size:58 final size:59
Alignment explanation
Indices: 25487824--25487974 Score: 241
Period size: 58 Copynumber: 2.5 Consensus size: 59
25487814 TTGTGCAGGA
* *
25487824 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGGAAATTTTGATTTCCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATA---TTTTTTGGAAACTTTGATTTCCAAGG
*
25487886 AAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTGATTTCCAAGG
25487944 AAAATTGATACTTTCAACTTTTCCTCAAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA
25487975 AACCTTTTTT
Statistics
Matches: 86, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
58 54 0.63
62 32 0.37
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTGATTTCCAAGG
Found at i:25489886 original size:1 final size:1
Alignment explanation
Indices: 25489880--25489907 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
25489870 TTTATCCATT
25489880 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
25489908 CTAGTTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25493629 original size:58 final size:57
Alignment explanation
Indices: 25493525--25493821 Score: 253
Period size: 58 Copynumber: 5.1 Consensus size: 57
25493515 TTCTACAATC
* * *
25493525 AGAAACGTAATTTTTGTATGTTTATTTTTGTTAATTAAAGACTACGTTTTTAATTTA
1 AGAAACGTAATTTTTGTATGTTAATTTTTTTTAATTAAAGATTACGTTTTTAATTTA
* * *
25493582 AGAAACGCAGTTTTTGTATGTTAAATTTTTTTTAATTAAAGATTACGTTTAT-ATTTCA
1 AGAAACGTAATTTTTGTATGTT-AATTTTTTTTAATTAAAGATTACGTTTTTAATTT-A
* * *
25493640 A-AAA-ATATATTATTTGTATGTTTAATTTTTTTTCCAATT-AAGATCCACGTTTTTAGTTTA
1 AGAAACGTA-ATT-TTTGTATG-TTAATTTTTTTT--AATTAAAGAT-TACGTTTTTAATTTA
* * * * * *
25493700 AGAAATGTAATTTTTGTACGCTTAATTTTTTTTAATTAAAAACTA-TTTTTTCATTTTA
1 AGAAACGTAATTTTTGTATG-TTAATTTTTTTTAATTAAAGATTACGTTTTT-AATTTA
* * * * ** *
25493758 AGAAACGTAATCTTTGTATATTTAATTTTTTTCAATTAAAAATCGCGTTTTCAATTTA
1 AGAAACGTAATTTTTGTAT-GTTAATTTTTTTTAATTAAAGATTACGTTTTTAATTTA
*
25493816 AAAAAC
1 AGAAAC
25493822 TTAGATAGTG
Statistics
Matches: 193, Mismatches: 32, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
56 1 0.01
57 34 0.18
58 101 0.52
59 14 0.07
60 32 0.17
61 9 0.05
62 2 0.01
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.49
Consensus pattern (57 bp):
AGAAACGTAATTTTTGTATGTTAATTTTTTTTAATTAAAGATTACGTTTTTAATTTA
Found at i:25493774 original size:118 final size:116
Alignment explanation
Indices: 25493525--25493796 Score: 293
Period size: 118 Copynumber: 2.3 Consensus size: 116
25493515 TTCTACAATC
* * *
25493525 AGAAACGTAATTTTTGTATGTTT-ATTTTTGTT-AATTAAAGACTACGTTTTTAATTTAAGAAAC
1 AGAAACGTAATATTTGTATGTTTAATTTTTTTTCAATT-AAGACCACGTTTTTAATTTAAGAAAC
* * * *
25493588 GCAGTTTTTGTATGTTAAATTTTTTTTAATTAAAGATTACGTTTATATTTCA
65 GCAATTTTTGTACGTTAAATTTTTTTTAATTAAAAACTACGTTTATATTTCA
* ** * *
25493640 AAAAATATATTATTTGTATGTTTAATTTTTTTTCCAATTAAGATCCACGTTTTTAGTTTAAGAAA
1 AGAAACGTAATATTTGTATGTTTAATTTTTTTT-CAATTAAGA-CCACGTTTTTAATTTAAGAAA
* * * * *
25493705 TGTAATTTTTGTACGCTT-AATTTTTTTTAATTAAAAACTA-TTTTTTCATTTTA
64 CGCAATTTTTGTACG-TTAAATTTTTTTTAATTAAAAACTACGTTTAT-ATTTCA
* *
25493758 AGAAACGTAATCTTTGTATATTTAA-TTTTTTTCAATTAA
1 AGAAACGTAATATTTGTATGTTTAATTTTTTTTCAATTAA
25493797 AAATCGCGTT
Statistics
Matches: 128, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
115 18 0.14
116 15 0.12
117 15 0.12
118 78 0.61
119 2 0.02
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.51
Consensus pattern (116 bp):
AGAAACGTAATATTTGTATGTTTAATTTTTTTTCAATTAAGACCACGTTTTTAATTTAAGAAACG
CAATTTTTGTACGTTAAATTTTTTTTAATTAAAAACTACGTTTATATTTCA
Found at i:25494434 original size:57 final size:54
Alignment explanation
Indices: 25494373--25494569 Score: 170
Period size: 57 Copynumber: 3.6 Consensus size: 54
25494363 TATAAGTTTA
*
25494373 TTTTTTTAATTAAAATTACTTTTTCACTTTAAAACACGTAGTCTTTGTATGTTAAT
1 TTTTTTTAATTAAAATTAC-TTTTCACTTTAAAA-ATGTAGTCTTTGTATGTTAAT
* * * *
25494429 TTTTTTTAATTAAAA--A-TTAT-ATTTTCAAAATGTAGTTTTTGTATGTTTAA-
1 TTTTTTTAATTAAAATTACTTTTCACTTTAAAAATGTAGTCTTTGTATG-TTAAT
* * * * **
25494479 TTTTTTTAATTAAAGATCACGTTTGCACTTTATGAAATGTAATCTTTGTATAATAAT
1 TTTTTTTAATTAAA-ATTAC-TTTTCACTTTA-AAAATGTAGTCTTTGTATGTTAAT
* *
25494536 TTTTTTTAATTAAAAACTACATTGTCACTTTAAA
1 TTTTTTTAATT-AAAATTAC-TTTTCACTTTAAA
25494570 CAACATGGTC
Statistics
Matches: 111, Mismatches: 20, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
50 28 0.25
51 12 0.11
52 3 0.03
53 1 0.01
54 1 0.01
55 2 0.02
56 23 0.21
57 38 0.34
58 3 0.03
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.51
Consensus pattern (54 bp):
TTTTTTTAATTAAAATTACTTTTCACTTTAAAAATGTAGTCTTTGTATGTTAAT
Found at i:25494540 original size:107 final size:105
Alignment explanation
Indices: 25494356--25494551 Score: 268
Period size: 107 Copynumber: 1.8 Consensus size: 105
25494346 ATCACAATCT
* * * *
25494356 TAGTTTTTATAAGTTTATTTTTTTAATTAAAATTACTTTTTCACTTTAAAACACGTAGTCTTTGT
1 TAGTTTTTATAAGTTTATTTTTTTAATTAAAATCACGTTTGCACTTTAAAACACGTAATCTTTGT
**
25494421 ATGTTAATTTTTTTTAATTAAAAATTATATTTTCAAAATG
66 ATAATAATTTTTTTTAATTAAAAATTATATTTTCAAAATG
* * * *
25494461 TAGTTTTTGTATGTTTAATTTTTTTAATTAAAGATCACGTTTGCACTTTATGAA-ATGTAATCTT
1 TAGTTTTTATAAGTTT-ATTTTTTTAATTAAA-ATCACGTTTGCACTTTA-AAACACGTAATCTT
25494525 TGTATAATAATTTTTTTTAATTAAAAA
63 TGTATAATAATTTTTTTTAATTAAAAA
25494552 CTACATTGTC
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
105 14 0.18
106 15 0.19
107 47 0.60
108 2 0.03
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (105 bp):
TAGTTTTTATAAGTTTATTTTTTTAATTAAAATCACGTTTGCACTTTAAAACACGTAATCTTTGT
ATAATAATTTTTTTTAATTAAAAATTATATTTTCAAAATG
Found at i:25494695 original size:3 final size:3
Alignment explanation
Indices: 25494689--25494724 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
25494679 AATAATAATA
25494689 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25494725 TATTTTTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:25495092 original size:71 final size:71
Alignment explanation
Indices: 25494977--25495129 Score: 218
Period size: 71 Copynumber: 2.2 Consensus size: 71
25494967 ATGAGAGATT
* * ** *
25494977 AAAAAAAA-AAGAAGAAGACCCACCTAAAAAAAAGATTTTTAGAATCAAAATTTTTTTTCTTTTT
1 AAAAAAAAGAAGAAAAAAACCCACCTAAAAAAAAGATTTCCAGAATCAAAATTTTTTTTCTTTCT
25495041 GTAAAA
66 GTAAAA
* * *
25495047 AAAAAAAAGAAGAAAAAAACCCATCTAAAAAAAGGGTTTCCAGAATCAAAATTTTTTTTCTTTCT
1 AAAAAAAAGAAGAAAAAAACCCACCTAAAAAAAAGATTTCCAGAATCAAAATTTTTTTTCTTTCT
25495112 GTAAAA
66 GTAAAA
25495118 AAAAAAAGAGAA
1 AAAAAAA-AGAA
25495130 CACACAGTCC
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
70 8 0.11
71 61 0.84
72 4 0.05
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (71 bp):
AAAAAAAAGAAGAAAAAAACCCACCTAAAAAAAAGATTTCCAGAATCAAAATTTTTTTTCTTTCT
GTAAAA
Found at i:25495797 original size:3 final size:3
Alignment explanation
Indices: 25495778--25495825 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
25495768 TAAAGAGTTT
*
25495778 TTA TATA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25495824 TT
1 TT
25495826 TATGCATGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:25496085 original size:21 final size:21
Alignment explanation
Indices: 25496059--25496103 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25496049 TTTTTTCTTC
* *
25496059 AAAATTAATAAAACAATTAAT
1 AAAATTAATAAAAAAATGAAT
**
25496080 AAAATTTCTAAAAAAATGAAT
1 AAAATTAATAAAAAAATGAAT
25496101 AAA
1 AAA
25496104 GTGTGTGCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATTAATAAAAAAATGAAT
Found at i:25507930 original size:62 final size:62
Alignment explanation
Indices: 25507855--25507974 Score: 195
Period size: 62 Copynumber: 1.9 Consensus size: 62
25507845 CTGCTGAAAG
* *
25507855 GAGCTTTTCCAAGATAAGATTTTTTTAAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTAGAT
1 GAGCTTTTCCAAGATAAGATTTTTTTAAAAGTTATTGAACCTCTACTGAGAGGAGCTTAGAT
* * *
25507917 GAGCTTTTTCAAGATAAGATTTTTTTAAAAGTTATTGAACCTCTGCTGAGATGAGCTT
1 GAGCTTTTCCAAGATAAGATTTTTTTAAAAGTTATTGAACCTCTACTGAGAGGAGCTT
25507975 TTTTAAGATA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (62 bp):
GAGCTTTTCCAAGATAAGATTTTTTTAAAAGTTATTGAACCTCTACTGAGAGGAGCTTAGAT
Found at i:25508123 original size:99 final size:97
Alignment explanation
Indices: 25507910--25508298 Score: 379
Period size: 99 Copynumber: 4.0 Consensus size: 97
25507900 CTGAGAGGAG
* * * * *
25507910 CTTAGATGAGCTTTTTCAAGATAAGATTTTTTTAAAAGTTATTGAACCTCTGCTGAGATGAGCTT
1 CTTAGAGGAGCTTTTTCCAGAT-AGA--ATTTT-AAAGTTGTTGAACCTCTGCTGAAATGAGCTT
* ** *
25507975 TTTTAAGAT-A-AAGTTTAAAGTTTTTGAGCCTCT-
62 TTTCAAGATGATATCTTTAAAGTTGTTGAGCCTCTA
* * *
25508008 GTTGAGAGGAGTTTTTTCCA-A-AGAATTTTAAAGTTGTTGAACCTCTGCT-AAGATAAGCTTTT
1 CTT-AGAGGAGCTTTTTCCAGATAGAATTTTAAAGTTGTTGAACCTCTGCTGAA-ATGAGCTTTT
*
25508070 TCAAGATAAGAT-TTTTTAAAAAAGTTGTTGAGCCTCTA
64 TCAAGAT--GATATCTTT---AAAGTTGTTGAGCCTCTA
* * * *
25508108 CTTAGAGGAGCTTTTTCAAGATAAAATTTTAAAGTTGTTGAGCCTCTACTGAAATGAGCTTTTTC
1 CTTAGAGGAGCTTTTTCCAGATAGAATTTTAAAGTTGTTGAACCTCTGCTGAAATGAGCTTTTTC
* *
25508173 AACATGATATCTTTAAAGTTGTTGAGCCTTTA
66 AAGATGATATCTTTAAAGTTGTTGAGCCTCTA
* *
25508205 CTGAGATGAGC-TTTTCCAAGATGAGAATTTTAAAAGTTGTTGAACCTCTGCTGAAA-GAGCTTT
1 CTTAGAGGAGCTTTTTCC-AGAT-AGAATTTT-AAAGTTGTTGAACCTCTGCTGAAATGAGCTTT
25508268 TTCAAGA-GA-AT-TTTAAAGTTGTTGAGCCTCT
63 TTCAAGATGATATCTTTAAAGTTGTTGAGCCTCT
25508299 GCTCAAAAGA
Statistics
Matches: 244, Mismatches: 30, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
92 1 0.00
93 34 0.14
94 4 0.02
95 19 0.08
96 14 0.06
97 32 0.13
98 23 0.09
99 68 0.28
100 7 0.03
101 40 0.16
102 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (97 bp):
CTTAGAGGAGCTTTTTCCAGATAGAATTTTAAAGTTGTTGAACCTCTGCTGAAATGAGCTTTTTC
AAGATGATATCTTTAAAGTTGTTGAGCCTCTA
Found at i:25508207 original size:49 final size:48
Alignment explanation
Indices: 25507915--25508298 Score: 320
Period size: 49 Copynumber: 7.9 Consensus size: 48
25507905 AGGAGCTTAG
* * * *
25507915 ATGAGCTTTTTCAAGAT-AAGATTTTTTTAAAAGTTATTGAACCTCTGCTGAG
1 ATGAGCTTTTTCAAGATGAA-A---TTTT-AAAGTTGTTGAGCCTCTACTGAA
* * * ** *
25507967 ATGAGCTTTTTTAAGAT-AAAGTTTAAAGTTTTTGAGCCTCTGTTGAG
1 ATGAGCTTTTTCAAGATGAAATTTTAAAGTTGTTGAGCCTCTACTGAA
* * * *
25508014 AGGAGTTTTTTCCAA-A-G-AATTTTAAAGTTGTTGAACCTCTGCT-AA
1 ATGAGCTTTTT-CAAGATGAAATTTTAAAGTTGTTGAGCCTCTACTGAA
* * *
25508059 GATAAGCTTTTTCAAGAT-AAGATTTTTTAAAAAAGTTGTTGAGCCTCTACTTAG
1 -ATGAGCTTTTTCAAGATGAA-A--TTTT---AAAGTTGTTGAGCCTCTACTGAA
* *
25508113 AGGAGCTTTTTCAAGATAAAATTTTAAAGTTGTTGAGCCTCTACTGAA
1 ATGAGCTTTTTCAAGATGAAATTTTAAAGTTGTTGAGCCTCTACTGAA
* * * *
25508161 ATGAGCTTTTTCAACATGATATCTTTAAAGTTGTTGAGCCTTTACTGAG
1 ATGAGCTTTTTCAAGATGAAAT-TTTAAAGTTGTTGAGCCTCTACTGAA
* * *
25508210 ATGAGCTTTTCCAAGATGAGAATTTTAAAAGTTGTTGAACCTCTGCTGAA
1 ATGAGCTTTTTCAAGATGA-AATTTT-AAAGTTGTTGAGCCTCTACTGAA
25508260 A-GAGCTTTTTCAAGA-G-AATTTTAAAGTTGTTGAGCCTCT
1 ATGAGCTTTTTCAAGATGAAATTTTAAAGTTGTTGAGCCTCT
25508299 GCTCAAAAGA
Statistics
Matches: 277, Mismatches: 38, Indels: 41
0.78 0.11 0.12
Matches are distributed among these distances:
45 20 0.07
46 37 0.13
47 31 0.11
48 46 0.17
49 57 0.21
50 26 0.09
51 5 0.02
52 18 0.06
53 34 0.12
54 3 0.01
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (48 bp):
ATGAGCTTTTTCAAGATGAAATTTTAAAGTTGTTGAGCCTCTACTGAA
Found at i:25508240 original size:147 final size:145
Alignment explanation
Indices: 25507913--25508298 Score: 460
Period size: 147 Copynumber: 2.7 Consensus size: 145
25507903 AGAGGAGCTT
* *
25507913 AGATGAGCTTTTTCAAGATAAGATTTTTTTAAAAGTTATTGAACCTCTGCTGAGATGAGCTTTTT
1 AGATGAGCTTTTTCAAGATAAGA-TTTTTTAAAAGTTGTTGAACCTCTGCTGAGAAGAGCTTTTT
* * * ** * *
25507978 TAAGAT-AAAGTTTAAAGTTTTTGAGCCTCTGTTGAGAGGAGTTTTTTCCAAAGAATTTTAAAGT
65 CAAGATAAAATTTTAAAGTTGTTGAGCCTCTACTGAAAGGAGCTTTTTCCAAAGAATTTTAAAGT
*
25508042 TGTTGAACCTCTGCTA
130 TGTTGAACCTCTACTA
* * * * *
25508058 AGATAAGCTTTTTCAAGATAAGATTTTTTAAAAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTT
1 AGATGAGCTTTTTCAAGATAAGATTTTTT--AAAAGTTGTTGAACCTCTGCTGAGAAGAGCTTTT
*
25508123 TCAAGATAAAATTTTAAAGTTGTTGAGCCTCTACTGAAATGAGCTTTTT-CAACATGATATCTTT
64 TCAAGATAAAATTTTAAAGTTGTTGAGCCTCTACTGAAAGGAGCTTTTTCCAA-A-GA-AT-TTT
* * *
25508187 AAAGTTGTTGAGCCTTTACTG
125 AAAGTTGTTGAACCTCTACTA
* * *
25508208 AGATGAGCTTTTCCAAGATGAGA-ATTTTAAAAGTTGTTGAACCTCTGCTGA-AAGAGCTTTTTC
1 AGATGAGCTTTTTCAAGATAAGATTTTTTAAAAGTTGTTGAACCTCTGCTGAGAAGAGCTTTTTC
*
25508271 AAG--AGAATTTTAAAGTTGTTGAGCCTCT
66 AAGATAAAATTTTAAAGTTGTTGAGCCTCT
25508299 GCTCAAAAGA
Statistics
Matches: 207, Mismatches: 27, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
144 30 0.14
145 22 0.11
146 52 0.25
147 55 0.27
148 2 0.01
149 6 0.03
150 40 0.19
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (145 bp):
AGATGAGCTTTTTCAAGATAAGATTTTTTAAAAGTTGTTGAACCTCTGCTGAGAAGAGCTTTTTC
AAGATAAAATTTTAAAGTTGTTGAGCCTCTACTGAAAGGAGCTTTTTCCAAAGAATTTTAAAGTT
GTTGAACCTCTACTA
Found at i:25516891 original size:19 final size:18
Alignment explanation
Indices: 25516859--25516894 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25516849 ACTCATTCAA
25516859 TCATTTCTTCTTTCTTTT
1 TCATTTCTTCTTTCTTTT
*
25516877 TCATTCTCTTTTTTCTTT
1 TCATT-TCTTCTTTCTTT
25516895 ATCTTTCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (18 bp):
TCATTTCTTCTTTCTTTT
Found at i:25519785 original size:25 final size:25
Alignment explanation
Indices: 25519757--25519807 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
25519747 CAATTAAGTA
25519757 TATATTAGTCCTTTTAAATTATTTT
1 TATATTAGTCCTTTTAAATTATTTT
*
25519782 TATATTTGTCCTTTTAAATTATTTT
1 TATATTAGTCCTTTTAAATTATTTT
25519807 T
1 T
25519808 TAATAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.63
Consensus pattern (25 bp):
TATATTAGTCCTTTTAAATTATTTT
Found at i:25520280 original size:9 final size:8
Alignment explanation
Indices: 25520253--25520278 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
25520243 TAGGTATCAT
25520253 AATTAAAA
1 AATTAAAA
25520261 AATTAAAA
1 AATTAAAA
25520269 AATTAAAA
1 AATTAAAA
25520277 AA
1 AA
25520279 ATATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AATTAAAA
Found at i:25521014 original size:28 final size:27
Alignment explanation
Indices: 25520965--25521018 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
25520955 AATAATATCA
* * *
25520965 TTAATTTTTTATATTATTTTTAAATAT
1 TTAATTTATTATATAATATTTAAATAT
25520992 TTAATTTGATTATATAATATTTAAATA
1 TTAATTT-ATTATATAATATTTAAATA
25521019 AATATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
TTAATTTATTATATAATATTTAAATAT
Found at i:25521024 original size:12 final size:12
Alignment explanation
Indices: 25521007--25521046 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
25520997 TTGATTATAT
25521007 AATATTTAAATA
1 AATATTTAAATA
25521019 AATATTTTTAAATA
1 AATA--TTTAAATA
*
25521033 AATATTAAAATA
1 AATATTTAAATA
25521045 AA
1 AA
25521047 ATAAAAGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 13 0.52
14 12 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATATTTAAATA
Found at i:25521030 original size:14 final size:14
Alignment explanation
Indices: 25521011--25521038 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25521001 TTATATAATA
25521011 TTTAAATAAATATT
1 TTTAAATAAATATT
25521025 TTTAAATAAATATT
1 TTTAAATAAATATT
25521039 AAAATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAAATAAATATT
Found at i:25521182 original size:8 final size:7
Alignment explanation
Indices: 25521153--25521229 Score: 52
Period size: 7 Copynumber: 11.1 Consensus size: 7
25521143 GTTTGATTTG
25521153 AAATAATA
1 AAAT-ATA
25521161 AAATATA
1 AAATATA
25521168 AAATATA
1 AAATATA
25521175 AAAT-TA
1 AAATATA
*
25521181 TAAAT-TT
1 -AAATATA
** *
25521188 TGATTTA
1 AAATATA
*
25521195 AAAAATA
1 AAATATA
25521202 AAATATA
1 AAATATA
*
25521209 AAAAATA
1 AAATATA
25521216 AAA-ATA
1 AAATATA
*
25521222 AAAAATA
1 AAATATA
25521229 A
1 A
25521230 TGAAACTTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
6 10 0.18
7 42 0.75
8 4 0.07
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (7 bp):
AAATATA
Found at i:25521220 original size:42 final size:42
Alignment explanation
Indices: 25521136--25521218 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 42
25521126 ACTGAAATGC
* *
25521136 TTATAAAGTTTGATTTGAAATAATAAAATATAAAATATAAAA
1 TTATAAAGTTTGATTTGAAAAAATAAAATATAAAAAATAAAA
*
25521178 TTATAAATTTTGATTT-AAAAAATAAAATATAAAAAATAAAA
1 TTATAAAGTTTGATTTGAAAAAATAAAATATAAAAAATAAAA
25521219 ATAAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 23 0.61
42 15 0.39
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (42 bp):
TTATAAAGTTTGATTTGAAAAAATAAAATATAAAAAATAAAA
Found at i:25521222 original size:13 final size:14
Alignment explanation
Indices: 25521157--25521229 Score: 69
Period size: 14 Copynumber: 5.4 Consensus size: 14
25521147 GATTTGAAAT
25521157 AATAAAATATAAAA
1 AATAAAATATAAAA
* *
25521171 TATAAAAT-TATAA
1 AATAAAATATAAAA
* *** *
25521184 ATTTTGATTTAAAA
1 AATAAAATATAAAA
25521198 AATAAAATATAAAA
1 AATAAAATATAAAA
25521212 AATAAAA-ATAAAA
1 AATAAAATATAAAA
25521225 AATAA
1 AATAA
25521230 TGAAACTTAA
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
13 18 0.40
14 27 0.60
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (14 bp):
AATAAAATATAAAA
Found at i:25521551 original size:26 final size:25
Alignment explanation
Indices: 25521522--25521575 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
25521512 CCAACTATTC
* *
25521522 TTTCACTACATGGCCTTGTTTTTTAT
1 TTTCACCACATGGCCTT-TCTTTTAT
*
25521548 TTTCACCACTTGGCCTTTCTTTTAT
1 TTTCACCACATGGCCTTTCTTTTAT
25521573 TTT
1 TTT
25521576 TTTTATCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.13, C:0.22, G:0.09, T:0.56
Consensus pattern (25 bp):
TTTCACCACATGGCCTTTCTTTTAT
Found at i:25529030 original size:16 final size:17
Alignment explanation
Indices: 25529004--25529037 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
25528994 CTTACAAACT
*
25529004 TGAATTTCTTGTGAATC
1 TGAATTTCTTGTAAATC
25529021 TGAA-TTCTTGTAAATC
1 TGAATTTCTTGTAAATC
25529037 T
1 T
25529038 TCTAGTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (17 bp):
TGAATTTCTTGTAAATC
Found at i:25530138 original size:16 final size:16
Alignment explanation
Indices: 25530117--25530148 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25530107 ATTATGGATT
*
25530117 GAAATTTTTAGTGTTG
1 GAAATTTCTAGTGTTG
25530133 GAAATTTCTAGTGTTG
1 GAAATTTCTAGTGTTG
25530149 TTTGATTTAT
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:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (16 bp):
GAAATTTCTAGTGTTG
Found at i:25530652 original size:12 final size:12
Alignment explanation
Indices: 25530637--25530682 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
25530627 CTTTTTTTCT
25530637 TTTAATTTTTAG
1 TTTAATTTTTAG
25530649 TTTAATTTTTAG
1 TTTAATTTTTAG
* *
25530661 TTTTGATTTTTAT
1 -TTTAATTTTTAG
*
25530674 TTTGATTTT
1 TTTAATTTT
25530683 AATTTCCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
12 21 0.68
13 10 0.32
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (12 bp):
TTTAATTTTTAG
Found at i:25530658 original size:25 final size:25
Alignment explanation
Indices: 25530629--25530682 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
25530619 AGTTTGGCCT
*
25530629 TTTTTTCTTTTAATTTTTAGTTTAA
1 TTTTTACTTTTAATTTTTAGTTTAA
* * * *
25530654 TTTTTAGTTTTGATTTTTATTTTGA
1 TTTTTACTTTTAATTTTTAGTTTAA
25530679 TTTT
1 TTTT
25530683 AATTTCCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (25 bp):
TTTTTACTTTTAATTTTTAGTTTAA
Found at i:25530768 original size:8 final size:8
Alignment explanation
Indices: 25530755--25530812 Score: 66
Period size: 8 Copynumber: 7.4 Consensus size: 8
25530745 TATGATAAAA
25530755 TATATTAT
1 TATATTAT
25530763 TATATTAGT
1 TATATTA-T
* *
25530772 TACATGAT
1 TATATTAT
*
25530780 AATA-TAT
1 TATATTAT
25530787 TATATTAT
1 TATATTAT
25530795 TATATTAT
1 TATATTAT
25530803 TATATT-T
1 TATATTAT
25530810 TAT
1 TAT
25530813 TGCATAGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
7 9 0.21
8 27 0.64
9 6 0.14
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (8 bp):
TATATTAT
Found at i:25531843 original size:14 final size:14
Alignment explanation
Indices: 25531816--25531860 Score: 72
Period size: 15 Copynumber: 3.1 Consensus size: 14
25531806 TAAATCAAAT
25531816 TTTATTTCTTTAAAA
1 TTTATTT-TTTAAAA
25531831 TTTATTTTTTAAAAA
1 TTTATTTTTT-AAAA
25531846 TTTATTTTTTAAAA
1 TTTATTTTTTAAAA
25531860 T
1 T
25531861 ATTAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.28
15 21 0.72
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTATTTTTTAAAA
Found at i:25534995 original size:25 final size:24
Alignment explanation
Indices: 25534963--25535024 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 24
25534953 TATTAATATA
25534963 ATTATTAAAATATAAAAAATTATTT
1 ATTATTAAAATATAAAAAA-TATTT
**
25534988 ATTATTAAAGTATATTGAAAATATTT
1 ATTATTAAA--ATATAAAAAATATTT
25535014 ATTATTAAAAT
1 ATTATTAAAAT
25535025 TATTAATATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 2 0.06
25 9 0.27
26 14 0.42
27 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (24 bp):
ATTATTAAAATATAAAAAATATTT
Found at i:25535055 original size:23 final size:24
Alignment explanation
Indices: 25535021--25535070 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
25535011 TTTATTATTA
**
25535021 AAATTATTAATATCCAAAATAATT
1 AAATTATTAATATAAAAAATAATT
*
25535045 AAATT-TTAATATAAAAAATACTT
1 AAATTATTAATATAAAAAATAATT
25535068 AAA
1 AAA
25535071 ATAAAACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATTATTAATATAAAAAATAATT
Found at i:25535496 original size:15 final size:15
Alignment explanation
Indices: 25535446--25535503 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
25535436 TGAAATATTG
*
25535446 AAAATATTAATATTT
1 AAAATATTAAAATTT
*
25535461 AATAATATATAAAA-TA
1 AA-AATAT-TAAAATTT
25535477 AAAATATTAAAATTT
1 AAAATATTAAAATTT
* *
25535492 GAAATATCAAAA
1 AAAATATTAAAA
25535504 GACTTTGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 5 0.14
15 18 0.51
16 8 0.23
17 4 0.11
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (15 bp):
AAAATATTAAAATTT
Found at i:25536571 original size:21 final size:22
Alignment explanation
Indices: 25536546--25536587 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
25536536 GATAAAAAAA
*
25536546 AATTAGAAA-TATTAAAATTTG
1 AATTACAAATTATTAAAATTTG
25536567 AATTACAAATTTATTAAAATT
1 AATTACAAA-TTATTAAAATT
25536588 ATATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
AATTACAAATTATTAAAATTTG
Found at i:25537408 original size:18 final size:18
Alignment explanation
Indices: 25537387--25537435 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
25537377 TAAATATAAA
* *
25537387 AAATATGTTAAACGTGTT
1 AAATATGTTAAAAGTATT
25537405 AAATATGTTAAAAGTATT
1 AAATATGTTAAAAGTATT
*
25537423 AAACATGTTAAAA
1 AAATATGTTAAAA
25537436 TATGATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (18 bp):
AAATATGTTAAAAGTATT
Found at i:25539026 original size:12 final size:12
Alignment explanation
Indices: 25538980--25539032 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
25538970 TTTAATTCGT
25538980 TAATTTTTAAAATA
1 TAATTTTT--AATA
* *
25538994 TGATTTTTTATA
1 TAATTTTTAATA
*
25539006 TATTATTTTAATA
1 TAAT-TTTTAATA
25539019 TAATTTTTAATA
1 TAATTTTTAATA
25539031 TA
1 TA
25539033 TTTAAATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 15 0.47
13 10 0.31
14 7 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TAATTTTTAATA
Found at i:25539033 original size:14 final size:14
Alignment explanation
Indices: 25538980--25539033 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
25538970 TTTAATTCGT
*
25538980 TAATTTTTAAAATA
1 TAATTTTTAATATA
* *
25538994 TGATTTTTTATATA
1 TAATTTTTAATATA
*
25539008 TTA-TTTT-A-ATA
1 TAATTTTTAATATA
25539019 TAATTTTTAATATA
1 TAATTTTTAATATA
25539033 T
1 T
25539034 TTAAATAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.16
12 5 0.16
13 5 0.16
14 17 0.53
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TAATTTTTAATATA
Found at i:25540556 original size:32 final size:28
Alignment explanation
Indices: 25540520--25540584 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
25540510 ATAATAGTTT
25540520 TAAATATAACAACATGTGATATAAAAATTATA
1 TAAATATAA-AA-ATGTGA-ATAAAAA-TATA
* *
25540552 TAAATATAAAAATTTTAATAAAAATATA
1 TAAATATAAAAATGTGAATAAAAATATA
25540580 TAAAT
1 TAAAT
25540585 TTAGTCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 9 0.29
29 7 0.23
30 4 0.13
31 2 0.06
32 9 0.29
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (28 bp):
TAAATATAAAAATGTGAATAAAAATATA
Found at i:25541490 original size:2 final size:2
Alignment explanation
Indices: 25541483--25541511 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25541473 CCAAAGTAAG
25541483 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
25541512 ACCCTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:25542747 original size:26 final size:26
Alignment explanation
Indices: 25542718--25542774 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
25542708 TTTTACACTT
25542718 TATTTTTCCAAACTAAAATTCATAAG
1 TATTTTTCCAAACTAAAATTCATAAG
25542744 TATTTTTCCAAACTAAAATTCATAAG
1 TATTTTTCCAAACTAAAATTCATAAG
25542770 TATTT
1 TATTT
25542775 CAATCTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (26 bp):
TATTTTTCCAAACTAAAATTCATAAG
Found at i:25542918 original size:22 final size:22
Alignment explanation
Indices: 25542893--25542936 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
25542883 TGAAAAAGTA
25542893 CTTATTTAAATATCATTTGATT
1 CTTATTTAAATATCATTTGATT
25542915 CTTATTTAAATATCATTTGATT
1 CTTATTTAAATATCATTTGATT
25542937 AGATTAACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.55
Consensus pattern (22 bp):
CTTATTTAAATATCATTTGATT
Found at i:25546037 original size:50 final size:50
Alignment explanation
Indices: 25545972--25546072 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
25545962 ATCAATATTC
25545972 AATATCATTTTTTACAACTAGTAAGTACTAAAAGCACAACAATTGTTAGT
1 AATATCATTTTTTACAACTAGTAAGTACTAAAAGCACAACAATTGTTAGT
25546022 AATATGCA-TTTTTACAACTAGTAAGTACTAAAAGCACAACAATTGTTAGT
1 AATAT-CATTTTTTACAACTAGTAAGTACTAAAAGCACAACAATTGTTAGT
25546072 A
1 A
25546073 TTATTTGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 48 0.96
51 2 0.04
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.33
Consensus pattern (50 bp):
AATATCATTTTTTACAACTAGTAAGTACTAAAAGCACAACAATTGTTAGT
Found at i:25551266 original size:141 final size:142
Alignment explanation
Indices: 25551012--25551292 Score: 429
Period size: 141 Copynumber: 2.0 Consensus size: 142
25551002 AGTACAAATT
* *
25551012 ATTAGAACTTATTAATTGTCAGCTGCAATCATGGATGGCTAAGGTGTTTTAAAAGGGGAAAGCAA
1 ATTAGAACTCATTAACTGTCAGCTGCAATCATGGATGGCTAAGGTGTTTTAAAAGGGGAAAGCAA
* * *
25551077 AAAGAAAAGTGGAATGTGTTATATTGTCATCTATTCTACCAGTTTCATATCCCGA-TTTAGATCC
66 AAAGAAAAGAGGAATGTGTTATATTGTCATCTATTCTAACAGTTTCATATCCCGACTTTAGACCC
*
25551141 GTTTCTGCAATC
131 CTTTCTGCAATC
* * * *
25551153 ATTAGAACTCATTAACTGTCAGCTGCAATCATGGGTGGGTAAGGTGTTTTAAAGGGGGAAAGCGA
1 ATTAGAACTCATTAACTGTCAGCTGCAATCATGGATGGCTAAGGTGTTTTAAAAGGGGAAAGCAA
* * * *
25551218 AGAGAAGAGAGGAATGTGTTATATTGTCATCTATTCTAACATTTTCATATTCCGACTTTAGACCC
66 AAAGAAAAGAGGAATGTGTTATATTGTCATCTATTCTAACAGTTTCATATCCCGACTTTAGACCC
25551283 CTTTCTGCAA
131 CTTTCTGCAA
25551293 AAGCACTCAA
Statistics
Matches: 125, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
141 108 0.86
142 17 0.14
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.32
Consensus pattern (142 bp):
ATTAGAACTCATTAACTGTCAGCTGCAATCATGGATGGCTAAGGTGTTTTAAAAGGGGAAAGCAA
AAAGAAAAGAGGAATGTGTTATATTGTCATCTATTCTAACAGTTTCATATCCCGACTTTAGACCC
CTTTCTGCAATC
Found at i:25553715 original size:49 final size:48
Alignment explanation
Indices: 25553550--25553809 Score: 183
Period size: 49 Copynumber: 5.3 Consensus size: 48
25553540 TGTCTCTTTA
* * * * * * *
25553550 AAAAAATAATAGAATTATTAAAAGGAATATG-AAAGACAGTGTTTCTTT
1 AAAAAATAAAAAAATTATTAAAAAGAATAGGTAGAGAGAGTGTTTC-CT
** * * *
25553598 AAAGAAATAAAAATGTTATTAAAAAAGGAATAAGTA-ATGAGAAT-TTTTCT
1 AAA-AAATAAAAAAATTATT-AAAAA-GAATAGGTAGA-GAGAGTGTTTCCT
* **
25553648 CCAAAAATAGGAAAATTATTAAAAAGAATAGGTA-A-AGTAGTGTTTTCCT
1 -AAAAAATAAAAAAATTATTAAAAAGAATAGGTAGAGAG-AGTG-TTTCCT
* *
25553697 AAAAAAGTAAAAAAATTATCAAAAGGAATAGG-AGATGAGAGTGTTTCCT
1 AAAAAA-TAAAAAAATTATTAAAAAGAATAGGTAGA-GAGAGTGTTTCCT
* *
25553746 AAAAAATAGAAAAATTATTAAAAAGAATAGGT-GATGAGAGTGATTCCCT
1 AAAAAATAAAAAAATTATTAAAAAGAATAGGTAGA-GAGAGTG-TTTCCT
*
25553795 AAAAAATAAGAAAAT
1 AAAAAATAAAAAAAT
25553810 AAGTAATGAG
Statistics
Matches: 168, Mismatches: 29, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
46 2 0.01
47 2 0.01
48 50 0.30
49 74 0.44
50 21 0.12
51 14 0.08
52 5 0.03
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (48 bp):
AAAAAATAAAAAAATTATTAAAAAGAATAGGTAGAGAGAGTGTTTCCT
Found at i:25553848 original size:37 final size:38
Alignment explanation
Indices: 25553795--25553875 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 38
25553785 GTGATTCCCT
25553795 AAAAAATAAGAAAATAAGTAATGAGAGT-TTTTTTTTG
1 AAAAAATAAGAAAATAAGTAATGAGAGTATTTTTTTTG
* *
25553832 AAAAAATAAGAGAATAAGTAATGAGAGTATTTTTTTTT
1 AAAAAATAAGAAAATAAGTAATGAGAGTATTTTTTTTG
25553870 AAAAAA
1 AAAAAA
25553876 AAAATAGGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 27 0.66
38 14 0.34
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (38 bp):
AAAAAATAAGAAAATAAGTAATGAGAGTATTTTTTTTG
Found at i:25554848 original size:22 final size:22
Alignment explanation
Indices: 25554823--25554864 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
25554813 AAAAAATAGT
*
25554823 TTTTGTAAAAATAAATGTGGGC
1 TTTTATAAAAATAAATGTGGGC
25554845 TTTTATAAAAATAAATGTGG
1 TTTTATAAAAATAAATGTGG
25554865 AATACTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38
Consensus pattern (22 bp):
TTTTATAAAAATAAATGTGGGC
Found at i:25554873 original size:23 final size:22
Alignment explanation
Indices: 25554828--25554880 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
25554818 ATAGTTTTTG
** *
25554828 TAAAAATAAATGTGGGCTTTTA
1 TAAAAATAAATGTGGAATCTTA
25554850 TAAAAATAAATGTGGAATACTTA
1 TAAAAATAAATGTGGAAT-CTTA
*
25554873 TTAAAATA
1 TAAAAATA
25554881 TCAAGAGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (22 bp):
TAAAAATAAATGTGGAATCTTA
Found at i:25559878 original size:49 final size:49
Alignment explanation
Indices: 25559770--25560058 Score: 239
Period size: 49 Copynumber: 5.9 Consensus size: 49
25559760 TAGAATTGTC
* * * * *
25559770 AAAAGGAATATGG-AATGACAGTACTTCTTTAAAGGAATA-GAAAAGTTATT
1 AAAAGGAATA-GGTAATGAGAATATTTCCTTAAA-AAATAGGAAAA-TTATT
** * *
25559820 AAAAGGAATAAATAATGAGAATTTTTTCTTAAAAAATAGGAAAATTATT
1 AAAAGGAATAGGTAATGAGAATATTTCCTTAAAAAATAGGAAAATTATT
* ** * ** *
25559869 AAAATGAATAGGTAAATGAGTGT-TTTCCTAAAAAAATAAAAAAATTTATC
1 AAAAGGAATAGGT-AATGAGAATATTTCCTTAAAAAATAGGAAAA-TTATT
* * * *
25559919 AAAAGGAATA-GTGATGGGAATATTTCCCTAAAAAATAGAAAAATTATT
1 AAAAGGAATAGGTAATGAGAATATTTCCTTAAAAAATAGGAAAATTATT
* * * * * *
25559967 AATAGGAATAGTTAA-GAGAGTGTTTCCCTAAAAAATAAGAAAATTATT
1 AAAAGGAATAGGTAATGAGAATATTTCCTTAAAAAATAGGAAAATTATT
*
25560015 AAAAGGAATAGGTGATG-GAACTATTTCCTTAAAAAATAGGAAAA
1 AAAAGGAATAGGTAATGAGAA-TATTTCCTTAAAAAATAGGAAAA
25560059 ATAAGTATTG
Statistics
Matches: 188, Mismatches: 43, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
48 60 0.32
49 79 0.42
50 49 0.26
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (49 bp):
AAAAGGAATAGGTAATGAGAATATTTCCTTAAAAAATAGGAAAATTATT
Found at i:25559967 original size:98 final size:97
Alignment explanation
Indices: 25559849--25560060 Score: 286
Period size: 98 Copynumber: 2.2 Consensus size: 97
25559839 AATTTTTTCT
* * *
25559849 TAAAAAATAGGAAAATTATTAAAATGAATAGGTAA-ATGAGTGTTTTCCTAAAAAAATAAAAAAA
1 TAAAAAATAGAAAAATTATTAAAAGGAATAGGTAAGA-GAGTGTTTCCCT-AAAAAATAAAAAAA
25559913 TTTATCAAAAGGAATA-GTGATGGGAA-TATTTCCC
64 -TTATCAAAAGGAATAGGTGAT-GGAACTATTTCCC
* * *
25559947 TAAAAAATAGAAAAATTATTAATAGGAATAGTTAAGAGAGTGTTTCCCTAAAAAATAAGAAAATT
1 TAAAAAATAGAAAAATTATTAAAAGGAATAGGTAAGAGAGTGTTTCCCTAAAAAATAAAAAAATT
* *
25560012 ATTAAAAGGAATAGGTGATGGAACTATTTCCT
66 ATCAAAAGGAATAGGTGATGGAACTATTTCCC
25560044 TAAAAAATAGGAAAAAT
1 TAAAAAATA-GAAAAAT
25560061 AAGTATTGAG
Statistics
Matches: 102, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
96 18 0.18
97 34 0.33
98 49 0.48
99 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.28
Consensus pattern (97 bp):
TAAAAAATAGAAAAATTATTAAAAGGAATAGGTAAGAGAGTGTTTCCCTAAAAAATAAAAAAATT
ATCAAAAGGAATAGGTGATGGAACTATTTCCC
Found at i:25560100 original size:35 final size:36
Alignment explanation
Indices: 25560061--25560137 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 36
25560051 TAGGAAAAAT
*
25560061 AAGTATTGAGAGTATTTCTAAAAAAAAAAG-AGAAC
1 AAGTAATGAGAGTATTTCTAAAAAAAAAAGAAGAAC
* **
25560096 AAGTAATGAGAGTGTTTCTCTAAAAAAAAGAAGAAC
1 AAGTAATGAGAGTATTTCTAAAAAAAAAAGAAGAAC
25560132 AAGTAA
1 AAGTAA
25560138 AATGAATACT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 26 0.70
36 11 0.30
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.22
Consensus pattern (36 bp):
AAGTAATGAGAGTATTTCTAAAAAAAAAAGAAGAAC
Found at i:25560121 original size:36 final size:35
Alignment explanation
Indices: 25560061--25560137 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 35
25560051 TAGGAAAAAT
*
25560061 AAGTATTGAGAGTATTTCTAAAAAAAAA-AGAGAAC
1 AAGTAATGAGAGTATTTCTAAAAAAAAAGA-AGAAC
* *
25560096 AAGTAATGAGAGTGTTTCTCTAAAAAAAAGAAGAAC
1 AAGTAATGAGAGTATTTCT-AAAAAAAAAGAAGAAC
25560132 AAGTAA
1 AAGTAA
25560138 AATGAATACT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 17 0.46
36 19 0.51
37 1 0.03
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.22
Consensus pattern (35 bp):
AAGTAATGAGAGTATTTCTAAAAAAAAAGAAGAAC
Found at i:25560157 original size:35 final size:35
Alignment explanation
Indices: 25560118--25560199 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 35
25560108 TGTTTCTCTA
*
25560118 AAAAAAAG-AAGAACAAGTAAAATGAATACTTTCCT
1 AAAAAAAGTAA-AACAAGTAAAATAAATACTTTCCT
* * ** *
25560153 AAAAATAGTAAAATAAGTAATGTAAATATTTTCCT
1 AAAAAAAGTAAAACAAGTAAAATAAATACTTTCCT
25560188 AAAAAAA-TAAAA
1 AAAAAAAGTAAAA
25560200 GAATAAATCA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
34 5 0.13
35 32 0.82
36 2 0.05
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (35 bp):
AAAAAAAGTAAAACAAGTAAAATAAATACTTTCCT
Found at i:25568181 original size:22 final size:22
Alignment explanation
Indices: 25568156--25568200 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
25568146 ATAAAAAAAA
25568156 TAGATTCTACTAAAGTCTAAAC
1 TAGATTCTACTAAAGTCTAAAC
25568178 TAGATTCTACTAAAGTCTAAAC
1 TAGATTCTACTAAAGTCTAAAC
25568200 T
1 T
25568201 TTCCATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (22 bp):
TAGATTCTACTAAAGTCTAAAC
Found at i:25573261 original size:144 final size:143
Alignment explanation
Indices: 25572990--25573271 Score: 298
Period size: 144 Copynumber: 2.0 Consensus size: 143
25572980 TTTTTTATAC
* * * *
25572990 ATTAAAAACTTTGATCGCACCTTAAAATGTGTGAAATTACCAACTACCTTTTAGGAGTATTTTTC
1 ATTAAAAACCTTGATCGCACCTTAAAAGGTGTGAAATTACCAAATACCTTTTAGGAGTATTTTAC
* * * * * *
25573055 TAATTTGACCTTTAAGGGGTCGATTTTTCACGAAAACTTTCATAACATGATTTTATAATATTTCA
66 TAATTTGACCTTTAAGAGGTCGATTTGTCACCAAAACTTTCAGAACATAATTTCATAATATTTCA
25573120 CGATTTTTGAACT
131 CGATTTTTGAACT
* ** *
25573133 ATTAAAAACCTTGATTGCACCTTGGAAGGT-TGAAATTACCAAAATATCCTTTTAAGGGGTATTT
1 ATTAAAAACCTTGATCGCACCTTAAAAGGTGTGAAATTACC-AAATA-CCTTTT-AGGAGTATTT
* ** * * * ** *
25573197 TAGTAATTTGA-CTTTTTGAGTTTGGTTTGTCACCAAAACTTTCAGATTATAATTTCATATTATT
63 TACTAATTTGACCTTTAAGAGGTCGATTTGTCACCAAAACTTTCAGAACATAATTTCATAATATT
* *
25573261 TGAGGATTTTT
128 TCACGATTTTT
25573272 AGTGCTTGAA
Statistics
Matches: 111, Mismatches: 25, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
142 10 0.09
143 29 0.26
144 54 0.49
145 18 0.16
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (143 bp):
ATTAAAAACCTTGATCGCACCTTAAAAGGTGTGAAATTACCAAATACCTTTTAGGAGTATTTTAC
TAATTTGACCTTTAAGAGGTCGATTTGTCACCAAAACTTTCAGAACATAATTTCATAATATTTCA
CGATTTTTGAACT
Found at i:25573319 original size:66 final size:66
Alignment explanation
Indices: 25573236--25573364 Score: 224
Period size: 66 Copynumber: 2.0 Consensus size: 66
25573226 TCACCAAAAC
*
25573236 TTTCAGATTATAATTTCATATTATTTGAGGATTTTT-AGTGCTTGAAAATCATAAAAATGAAGAA
1 TTTCAGATTATAATTTCATATTATTTGAGAATTTTTCA-TGCTTGAAAATCATAAAAATGAAGAA
25573300 GG
65 GG
*
25573302 TTTCAGATTATGATTTCATATTATTTGAGAATTTTTCATGCTTGAAAATCATAAAAATGAAGA
1 TTTCAGATTATAATTTCATATTATTTGAGAATTTTTCATGCTTGAAAATCATAAAAATGAAGA
25573365 TCATAAAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 59 0.98
67 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (66 bp):
TTTCAGATTATAATTTCATATTATTTGAGAATTTTTCATGCTTGAAAATCATAAAAATGAAGAAG
G
Found at i:25573367 original size:15 final size:15
Alignment explanation
Indices: 25573344--25573379 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
25573334 TTTTCATGCT
*
25573344 TGAAAATCATAAAAA
1 TGAAGATCATAAAAA
25573359 TGAAGATCATAAAAA
1 TGAAGATCATAAAAA
25573374 TGAAGA
1 TGAAGA
25573380 AGGTTTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.61, C:0.06, G:0.14, T:0.19
Consensus pattern (15 bp):
TGAAGATCATAAAAA
Found at i:25573373 original size:81 final size:81
Alignment explanation
Indices: 25573278--25573445 Score: 327
Period size: 81 Copynumber: 2.1 Consensus size: 81
25573268 TTTTAGTGCT
*
25573278 TGAAAATCATAAAAATGAAGAAGGTTTCAGATTATGATTTCATATTATTTGAGAATTTTTCATGC
1 TGAAGATCATAAAAATGAAGAAGGTTTCAGATTATGATTTCATATTATTTGAGAATTTTTCATGC
25573343 TTGAAAATCATAAAAA
66 TTGAAAATCATAAAAA
25573359 TGAAGATCATAAAAATGAAGAAGGTTTCAGATTATGATTTCATATTATTTGAGAATTTTTCATGC
1 TGAAGATCATAAAAATGAAGAAGGTTTCAGATTATGATTTCATATTATTTGAGAATTTTTCATGC
25573424 TTGAAAATCATAAAAA
66 TTGAAAATCATAAAAA
25573440 TGAAGA
1 TGAAGA
25573446 AGGAATCATA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 86 1.00
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (81 bp):
TGAAGATCATAAAAATGAAGAAGGTTTCAGATTATGATTTCATATTATTTGAGAATTTTTCATGC
TTGAAAATCATAAAAA
Found at i:25575129 original size:7 final size:7
Alignment explanation
Indices: 25575119--25575266 Score: 71
Period size: 7 Copynumber: 21.3 Consensus size: 7
25575109 ACCACCCATA
25575119 AAACCCT
1 AAACCCT
*
25575126 AAACTCT
1 AAACCCT
**
25575133 AAATTCT
1 AAACCCT
25575140 AAATCACCT
1 AAA-C-CCT
*
25575149 TAACCCT
1 AAACCCT
*
25575156 AAATCCT
1 AAACCCT
25575163 AAA--CT
1 AAACCCT
25575168 AAAACTCC-
1 -AAAC-CCT
*
25575176 AAACCTT
1 AAACCCT
25575183 AAACCCT
1 AAACCCT
*
25575190 AAAGCCT
1 AAACCCT
25575197 AAA-CCT
1 AAACCCT
25575203 AAACCCT
1 AAACCCT
25575210 AAA-CCT
1 AAACCCT
*
25575216 AAA-CTT
1 AAACCCT
25575222 AAACCCT
1 AAACCCT
*
25575229 GAAATGATCC-
1 --AA--ACCCT
25575239 AAACCCT
1 AAACCCT
25575246 AAA-CC-
1 AAACCCT
*
25575251 AAACCCC
1 AAACCCT
25575258 AAACCCT
1 AAACCCT
25575265 AA
1 AA
25575267 CCTAGATGCT
Statistics
Matches: 110, Mismatches: 15, Indels: 32
0.70 0.10 0.20
Matches are distributed among these distances:
5 5 0.05
6 28 0.25
7 64 0.58
8 3 0.03
9 7 0.06
11 3 0.03
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:25575205 original size:13 final size:13
Alignment explanation
Indices: 25575145--25575219 Score: 64
Period size: 13 Copynumber: 5.6 Consensus size: 13
25575135 ATTCTAAATC
*
25575145 ACCTTAACCCTAA
1 ACCTAAACCCTAA
25575158 ATCCTAAA--CTAAA
1 A-CCTAAACCCT-AA
* *
25575171 ACTCCAAACCTTAA
1 AC-CTAAACCCTAA
*
25575185 ACCCTAAAGCCTAA
1 A-CCTAAACCCTAA
25575199 ACCTAAACCCTAA
1 ACCTAAACCCTAA
25575212 ACCTAAAC
1 ACCTAAAC
25575220 TTAAACCCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
12 3 0.06
13 27 0.55
14 17 0.35
15 2 0.04
ACGTcount: A:0.45, C:0.35, G:0.01, T:0.19
Consensus pattern (13 bp):
ACCTAAACCCTAA
Found at i:25582998 original size:18 final size:19
Alignment explanation
Indices: 25582962--25582999 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
25582952 ATGAAGGAAG
*
25582962 AATGGCACTTTTGTACTTT
1 AATGACACTTTTGTACTTT
25582981 AATGACACTTTT-TACTTT
1 AATGACACTTTTGTACTTT
25582999 A
1 A
25583000 TAGGGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (19 bp):
AATGACACTTTTGTACTTT
Found at i:25588201 original size:45 final size:46
Alignment explanation
Indices: 25588131--25588221 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 46
25588121 TTTTAAAGTG
* * **
25588131 ATTTTTTAAAATTATCCTGCCTATGTCTGTAAGAGTTTTTTCCAAA
1 ATTTTTTAAAATTATCATGCCTATGTCTATAAGAGCATTTTCCAAA
* *
25588177 ATTTTTTAAAGTT-TCATGCTTATGTCTATAAGAGCATTTTCCAAA
1 ATTTTTTAAAATTATCATGCCTATGTCTATAAGAGCATTTTCCAAA
25588222 GACAATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 27 0.69
46 12 0.31
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (46 bp):
ATTTTTTAAAATTATCATGCCTATGTCTATAAGAGCATTTTCCAAA
Found at i:25588378 original size:192 final size:186
Alignment explanation
Indices: 25588024--25588504 Score: 499
Period size: 192 Copynumber: 2.5 Consensus size: 186
25588014 ACCCAAGTCT
* * *
25588024 TTTTTCAAAGAGATTTTTAAAGTTTTCTGCCTATGTTAAT-AGAAGTCTTTTTCAAAGTCAAAAT
1 TTTTCCAAAGAAATTTTTAAAGTTTTCTGCCTATGTTAATAAG-AG-CTTTTTCAAAGTGAAAAT
* ** * *
25588088 TTTAAAGTTTCTTGCTTACATTAATAGGAGCCATTTT-AAAGTGATTTTTTAAAATTATCCTGCC
64 TTTAAAGTTTCCTGC-TATGTTAATAGAAGCCTTTTTCAAAGTGA--TTTTAAAATTATCCTGCC
* * * * * * *
25588152 TATGTCTGTAAGAGTTTTTTC-CAAAATTTTTTAAAGTTTCATGCTTATGTCTATAAGAGCA
126 TATGTCTATAACAGTTTTTTCAAAAAAATTTTAAAAGTTTC-TACCTATGTCTATAAGAGCA
* *
25588213 TTTTCCAAAGACAATTTTTTTAAAGTTTTCTGCATATGTTAATAAGAGCTGTTTTCAAAGTGAGA
1 TTTTCCAAAGA-AA--TTTTTAAAGTTTTCTGCCTATGTTAATAAGAGCT-TTTTCAAAGTGAAA
* *
25588278 TTTTTAAAGTTTCCTGTCTATGTTAATAGAAACCTTTTTCAAAGTGA-TTTAAAAGTT-TCCTGC
62 ATTTTAAAGTTTCCTG-CTATGTTAATAGAAGCCTTTTTCAAAGTGATTTTAAAA-TTATCCTGC
* * * *
25588341 CTTTGTTTATAACAGTTTTTTCAAAAGAAAATTTTAAAATTTTCTACCTATGTCTATAAGAGCT
125 CTATGTCTATAACAGTTTTTTC-AAA-AAAATTTTAAAAGTTTCTACCTATGTCTATAAGAGCA
* * * *
25588405 TTTTCTAAAGAAATTTTTAAAGTTTCCTACCTATGTTAATAAGAGCTTTCTCTAAA--GAAAATT
1 TTTTCCAAAGAAATTTTTAAAGTTTTCTGCCTATGTTAATAAGAGCTTTTTC-AAAGTGAAAATT
* * *
25588468 TTAAAGTTTTCTGCCTATGTTAGTAGAAGTCTTTTTC
65 TTAAAGTTTCCTG-CTATGTTAATAGAAGCCTTTTTC
25588505 CTACTTATGT
Statistics
Matches: 245, Mismatches: 35, Indels: 26
0.80 0.11 0.08
Matches are distributed among these distances:
187 37 0.15
188 4 0.02
189 44 0.18
190 32 0.13
191 6 0.02
192 98 0.40
193 24 0.10
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (186 bp):
TTTTCCAAAGAAATTTTTAAAGTTTTCTGCCTATGTTAATAAGAGCTTTTTCAAAGTGAAAATTT
TAAAGTTTCCTGCTATGTTAATAGAAGCCTTTTTCAAAGTGATTTTAAAATTATCCTGCCTATGT
CTATAACAGTTTTTTCAAAAAAATTTTAAAAGTTTCTACCTATGTCTATAAGAGCA
Found at i:25588408 original size:47 final size:46
Alignment explanation
Indices: 25588325--25588489 Score: 186
Period size: 47 Copynumber: 3.5 Consensus size: 46
25588315 TTCAAAGTGA
* * * * *
25588325 TTTAAAAGTTTCCTGCCTTTGTTTATAACAGTTTTTTCAAAAGAAAAT
1 TTTAAAA-TTTCCTACCTATG-TTATAAGAGCTTTTTCTAAAGAAAAT
* *
25588373 TTTAAAATTTTCTACCTATGTCTATAAGAGCTTTTTCTAAAGAAATT
1 TTTAAAATTTCCTACCTATGT-TATAAGAGCTTTTTCTAAAGAAAAT
* *
25588420 TTTAAAGTTTCCTACCTATGTTAATAAGAGCTTTCTCTAAAGAAAAT
1 TTTAAAATTTCCTACCTATGTT-ATAAGAGCTTTTTCTAAAGAAAAT
* * *
25588467 TTTAAAGTTTTCTGCCTATGTTA
1 TTTAAAATTTCCTACCTATGTTA
25588490 GTAGAAGTCT
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
46 3 0.03
47 92 0.90
48 7 0.07
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (46 bp):
TTTAAAATTTCCTACCTATGTTATAAGAGCTTTTTCTAAAGAAAAT
Found at i:25588427 original size:94 final size:93
Alignment explanation
Indices: 25588024--25588487 Score: 329
Period size: 94 Copynumber: 4.9 Consensus size: 93
25588014 ACCCAAGTCT
* *
25588024 TTTTTCAAAGAGATTTTTAAAGTTTTCTGCCTATGTTAAT-AGAAGTCTTTTTC-AAAGTCAAAA
1 TTTTTCAAAGAAATTTTTAAAGTTTCCTGCCTATGTTAATAAG-AGT-TTTTTCAAAAG--AAAA
* ** *
25588087 TTTTAAAG-TTTCTTGCTTACAT-TAATAGGAGCC
62 TTTTAAAGTTTTC-TGCCTATGTCT-ATAAGAG-C
* * * * * * **
25588120 ATTTT-AAAGTGATTTTTTAAAATTATCCTGCCTATGTCT-GTAAGAGTTTTTTC-CAA-AATTT
1 TTTTTCAAAG-AAATTTTTAAAGTT-TCCTGCCTATGT-TAATAAGAGTTTTTTCAAAAGAAAAT
*
25588181 TTTAAAG-TTTCATGCTTATGTCTATAAGAGC
63 TTTAAAGTTTTC-TGCCTATGTCTATAAGAGC
* * * * * *
25588212 ATTTTCCAAAGACAATTTTTTTAAAGTTTTCTGCATATGTTAATAAGAGCTGTTTTCAAAGTGAG
1 -TTTTTCAAAGA-AA--TTTTTAAAGTTTCCTGCCTATGTTAATAAGAG-TTTTTTCAAA-AGAA
* * * * *
25588277 ATTTTTAAAGTTTCCTGTCTATGT-TAATAGAAACC
60 AATTTTAAAGTTTTCTGCCTATGTCT-ATA-AGAGC
** * * * *
25588312 TTTTTCAAAGTGA-TTTAAAAGTTTCCTGCCTTTGTTTATAACAGTTTTTTCAAAAGAAAATTTT
1 TTTTTCAAAGAAATTTTTAAAGTTTCCTGCCTATGTTAATAAGAGTTTTTTCAAAAGAAAATTTT
* *
25588376 AAAATTTTCTACCTATGTCTATAAGAGC
66 AAAGTTTTCTGCCTATGTCTATAAGAGC
* * * *
25588404 TTTTTCTAAAGAAATTTTTAAAGTTTCCTACCTATGTTAATAAGAGCTTTCTCTAAAGAAAATTT
1 TTTTTC-AAAGAAATTTTTAAAGTTTCCTGCCTATGTTAATAAGAGTTTTTTCAAAAGAAAATTT
25588469 TAAAGTTTTCTGCCTATGT
65 TAAAGTTTTCTGCCTATGT
25588488 TAGTAGAAGT
Statistics
Matches: 284, Mismatches: 63, Indels: 44
0.73 0.16 0.11
Matches are distributed among these distances:
92 10 0.04
93 59 0.21
94 76 0.27
95 45 0.16
96 38 0.13
97 16 0.06
98 5 0.02
99 29 0.10
100 6 0.02
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (93 bp):
TTTTTCAAAGAAATTTTTAAAGTTTCCTGCCTATGTTAATAAGAGTTTTTTCAAAAGAAAATTTT
AAAGTTTTCTGCCTATGTCTATAAGAGC
Found at i:25588516 original size:74 final size:75
Alignment explanation
Indices: 25588427--25588576 Score: 196
Period size: 74 Copynumber: 2.0 Consensus size: 75
25588417 ATTTTTAAAG
*
25588427 TTTCCTACCTATGTTAATAAGAGCTTTCTCTAAAGA-AAATTTTAAAGTTTTCT-GCCTATGTTA
1 TTTCCTACCTATGTTAATAAGAGCTTTCTCTAAA-ATAAATTTTAAAGTTTCCTAGCCTATGTTA
*
25588490 GTAGAAGTCTT
65 ATAGAAGTCTT
* * * * * *
25588501 TTTCCTACTTATGTTAATAGGAGCTTTTTTTAAAATGATTTTTAAAGTTTCCTAGCCTATGTTAA
1 TTTCCTACCTATGTTAATAAGAGCTTTCTCTAAAATAAATTTTAAAGTTTCCTAGCCTATGTTAA
*
25588566 TAGGAGTCTT
66 TAGAAGTCTT
25588576 T
1 T
25588577 AAAAAAAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
73 1 0.02
74 44 0.68
75 20 0.31
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (75 bp):
TTTCCTACCTATGTTAATAAGAGCTTTCTCTAAAATAAATTTTAAAGTTTCCTAGCCTATGTTAA
TAGAAGTCTT
Found at i:25589328 original size:144 final size:143
Alignment explanation
Indices: 25589150--25589471 Score: 350
Period size: 144 Copynumber: 2.3 Consensus size: 143
25589140 ATCATAGAAA
* * * *
25589150 GTGTGAAATTACTAAAATACCTTTTAGA-AGTATTTTTATTATTTAACATTCCCAA-AT-TTTGA
1 GTGTGAAATTACTAAAATACCTTTTA-ATGGTATTTTCATGATTTAACATTCCCAAGATCATT--
** * * *
25589212 TTTTTGTGAAAAGC-TCCAGATCATGATTTAATATTATTTCATGATTTTTGGTACATTAAAAACC
63 TTTTTACGAAAA-CTTCCAGACCAT-ATTTAATAATATTTCATGATTTTTAGTACATTAAAAACC
* *
25589276 TTGATTATACCACAAAAT
126 TTGATTACACCACAAAAG
* * *
25589294 GTGTGAAATTACTAAACTACCTTTTAATGGTATTTTCATGATTTGACATTCCCAAGGTCATTTTT
1 GTGTGAAATTACTAAAATACCTTTTAATGGTATTTTCATGATTTAACATTCCCAAGATCATTTTT
* * * *
25589359 TTACGAAAACTTTCATACCATATTTTATAATATTTCATGATTTTTAGTATATTAAAAACCTTGAT
66 TTACGAAAACTTCCAGACCATATTTAATAATATTTCATGATTTTTAGTACATTAAAAACCTTGAT
* * *
25589424 TGCACCTCGAAAG
131 TACACCACAAAAG
*
25589437 GT-TGAAATTACCAAAATACCCTTTT-ATGGTATTTT
1 GTGTGAAATTACTAAAATA-CCTTTTAATGGTATTTT
25589472 AGTAATTTGA
Statistics
Matches: 150, Mismatches: 23, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
142 24 0.16
143 58 0.39
144 65 0.43
145 1 0.01
146 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (143 bp):
GTGTGAAATTACTAAAATACCTTTTAATGGTATTTTCATGATTTAACATTCCCAAGATCATTTTT
TTACGAAAACTTCCAGACCATATTTAATAATATTTCATGATTTTTAGTACATTAAAAACCTTGAT
TACACCACAAAAG
Found at i:25589536 original size:143 final size:143
Alignment explanation
Indices: 25589237--25589546 Score: 331
Period size: 143 Copynumber: 2.2 Consensus size: 143
25589227 CCAGATCATG
* * *
25589237 ATTTAATATTATTTCATGATTTTTGGTACATTAAAAACCTTGATTATACCACAAAATGTGTGAAA
1 ATTTAATATTATTTCATGATTTTTAGTACATTAAAAACCTTGATTACACCACAAAAGGTGTGAAA
* * * ***
25589302 TTACTAAACTACCTTTTAATGGTATTTTCATGATTTGACATTCCCAAGGTCATTTTTTTACGAAA
66 TTACCAAAATACCTTTTAATGGTATTTTCATAATTTGACATTCCCAAGGTCATTTTGCCACGAAA
*
25589367 ACTTTCATACCAT
131 ACTTTCAAACCAT
* * * * * *
25589380 ATTTTATAATATTTCATGATTTTTAGTATATTAAAAACCTTGATTGCACCTCGAAAGGT-TGAAA
1 ATTTAATATTATTTCATGATTTTTAGTACATTAAAAACCTTGATTACACCACAAAAGGTGTGAAA
* ** * *
25589444 TTACCAAAATACCCTTTT-ATGGTATTTT-AGTAATTTGACCTTCTTAAGGTTGA-TTTGCCATG
66 TTACCAAAATA-CCTTTTAATGGTATTTTCA-TAATTTGACATTCCCAAGG-TCATTTTGCCACG
**
25589506 AAAACTTTCAAATTAT
128 AAAACTTTCAAACCAT
* *
25589522 AATTTAATATTATTTAAAGATTTTT
1 -ATTTAATATTATTTCATGATTTTT
25589547 TGTGCTTTAA
Statistics
Matches: 136, Mismatches: 27, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
141 1 0.01
142 57 0.42
143 78 0.57
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (143 bp):
ATTTAATATTATTTCATGATTTTTAGTACATTAAAAACCTTGATTACACCACAAAAGGTGTGAAA
TTACCAAAATACCTTTTAATGGTATTTTCATAATTTGACATTCCCAAGGTCATTTTGCCACGAAA
ACTTTCAAACCAT
Found at i:25591194 original size:19 final size:19
Alignment explanation
Indices: 25591169--25591222 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
25591159 ATGCATTTTT
25591169 CATGAAACCCTAAATCA-C
1 CATGAAACCCTAAATCATC
* *
25591187 CAATGAAACCCCAAACCATC
1 C-ATGAAACCCTAAATCATC
*
25591207 CATTAAACCCTAAATC
1 CATGAAACCCTAAATC
25591223 GCCCTCCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 1 0.03
19 26 0.90
20 2 0.07
ACGTcount: A:0.44, C:0.35, G:0.04, T:0.17
Consensus pattern (19 bp):
CATGAAACCCTAAATCATC
Found at i:25591277 original size:19 final size:19
Alignment explanation
Indices: 25591192--25591297 Score: 63
Period size: 19 Copynumber: 5.6 Consensus size: 19
25591182 ATCACCAATG
* * *
25591192 AAACCCCAAACCATCCATT
1 AAACCCTAAACTATCCATC
** *
25591211 AAACCCTAAA-TCGCCCTCC
1 AAACCCTAAACTATCCAT-C
* * **
25591230 AAACCCTAAACCACCCAGG
1 AAACCCTAAACTATCCATC
* *
25591249 AAAACTTAAACTATCCATC
1 AAACCCTAAACTATCCATC
*
25591268 AAACCCTAAACTA-CCTACC
1 AAACCCTAAACTATCC-ATC
25591287 AAACCCTAAAC
1 AAACCCTAAAC
25591298 CACTCATGAA
Statistics
Matches: 63, Mismatches: 21, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
18 5 0.08
19 56 0.89
20 2 0.03
ACGTcount: A:0.42, C:0.40, G:0.03, T:0.15
Consensus pattern (19 bp):
AAACCCTAAACTATCCATC
Found at i:25591309 original size:19 final size:19
Alignment explanation
Indices: 25591168--25591309 Score: 62
Period size: 19 Copynumber: 7.5 Consensus size: 19
25591158 CATGCATTTT
*
25591168 TCATGAAACCCTAAATCAC
1 TCATGAAACCCTAAACCAC
*
25591187 -CAATGAAACCCCAAACCA-
1 TC-ATGAAACCCTAAACCAC
* *
25591205 TCCATTAAACCCTAAATCGCCC
1 T-CATGAAACCCTAAA-C-CAC
*
25591227 TC--CAAACCCTAAACCAC
1 TCATGAAACCCTAAACCAC
* * * * *
25591244 CCAGGAAAACTTAAACTA-
1 TCATGAAACCCTAAACCAC
* *
25591262 TCCATCAAACCCTAAACTAC
1 T-CATGAAACCCTAAACCAC
**
25591282 -CTACCAAACCCTAAACCAC
1 TC-ATGAAACCCTAAACCAC
25591301 TCATGAAAC
1 TCATGAAAC
25591310 TATAAACCCT
Statistics
Matches: 90, Mismatches: 21, Indels: 24
0.67 0.16 0.18
Matches are distributed among these distances:
17 3 0.03
18 3 0.03
19 78 0.87
20 3 0.03
21 2 0.02
22 1 0.01
ACGTcount: A:0.42, C:0.37, G:0.04, T:0.16
Consensus pattern (19 bp):
TCATGAAACCCTAAACCAC
Found at i:25591316 original size:57 final size:55
Alignment explanation
Indices: 25591173--25591317 Score: 148
Period size: 57 Copynumber: 2.5 Consensus size: 55
25591163 ATTTTTCATG
* ** * *
25591173 AAACCCTAAATCACCAATGAAACCCCAAACCATCCATTAAACCCTAAATCGCCCTCC
1 AAACCCTAAACCACC-ATGAAA-CTTAAACCATCCATCAAACCCTAAATCGACCTCC
* * *
25591230 AAACCCTAAACCACCCAGGAAAACTTAAACTATCCATCAAACCCTAAA-CTACCTACC
1 AAACCCTAAACCA-CCATG-AAACTTAAACCATCCATCAAACCCTAAATCGACCT-CC
25591287 AAACCCTAAACCACTCATGAAACTATAAACC
1 AAACCCTAAACCAC-CATGAAACT-TAAACC
25591318 CTAGACCCTA
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
56 10 0.14
57 58 0.79
58 5 0.07
ACGTcount: A:0.43, C:0.37, G:0.03, T:0.16
Consensus pattern (55 bp):
AAACCCTAAACCACCATGAAACTTAAACCATCCATCAAACCCTAAATCGACCTCC
Found at i:25591353 original size:16 final size:17
Alignment explanation
Indices: 25591322--25591355 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
25591312 TAAACCCTAG
*
25591322 ACCCTAAACTCTAAACC
1 ACCCTAAACCCTAAACC
25591339 ACCCT-AACCCTAAACC
1 ACCCTAAACCCTAAACC
25591355 A
1 A
25591356 AAGCTCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (17 bp):
ACCCTAAACCCTAAACC
Found at i:25591420 original size:7 final size:7
Alignment explanation
Indices: 25591312--25591400 Score: 53
Period size: 7 Copynumber: 12.7 Consensus size: 7
25591302 CATGAAACTA
25591312 TAAACCC
1 TAAACCC
*
25591319 TAGACCC
1 TAAACCC
*
25591326 TAAACTC
1 TAAACCC
25591333 TAAACCACCC
1 T-AA--ACCC
25591343 T-AACCC
1 TAAACCC
25591349 TAAA-CC
1 TAAACCC
25591355 -AAAGCTCC
1 TAAA-C-CC
25591363 -AAACCC
1 TAAACCC
**
25591369 T-AACAT
1 TAAACCC
*
25591375 TAAACCT
1 TAAACCC
25591382 TAAACCC
1 TAAACCC
25591389 TAAACCC
1 TAAACCC
25591396 TAAAC
1 TAAAC
25591401 GTTTTATTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
5 3 0.05
6 13 0.20
7 37 0.57
8 8 0.12
10 4 0.06
ACGTcount: A:0.43, C:0.38, G:0.02, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:25591952 original size:22 final size:23
Alignment explanation
Indices: 25591924--25591983 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
25591914 TTCATCTTGA
* * *
25591924 TCCAAAAACAAAA-TGCTTTGTT
1 TCCAAAAAAAAAATTGATTTGCT
25591946 TCCAAAAGAAAAAATTGATTTGCT
1 TCCAAAA-AAAAAATTGATTTGCT
25591970 TCCAAAAAAGAAAA
1 TCCAAAAAA-AAAA
25591984 GAAAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 7 0.22
23 7 0.22
24 18 0.56
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (23 bp):
TCCAAAAAAAAAATTGATTTGCT
Found at i:25593133 original size:17 final size:18
Alignment explanation
Indices: 25593097--25593147 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
25593087 AAATAATAAT
*
25593097 TTTTCATAATTAAATTTA
1 TTTTAATAATTAAATTTA
*
25593115 TTTTAATAA-TAATTTTA
1 TTTTAATAATTAAATTTA
*
25593132 TTAATAAATAATTAAA
1 TT--TTAATAATTAAA
25593148 ATGCACTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 9 0.35
18 8 0.31
19 6 0.23
20 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAATAATTAAATTTA
Found at i:25593893 original size:32 final size:33
Alignment explanation
Indices: 25593838--25593905 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
25593828 ATATTGACAC
*
25593838 ATTATTTTATATATTTATTTAAATATATTAATT
1 ATTATTTTATATATTTATATAAATATATTAATT
* *
25593871 ATTATATTTATA-A-TTATATAAATTTATTTATT
1 ATTAT-TTTATATATTTATATAAATATATTAATT
25593903 ATT
1 ATT
25593906 TTAAATGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 19 0.61
33 6 0.19
34 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
ATTATTTTATATATTTATATAAATATATTAATT
Found at i:25594552 original size:30 final size:29
Alignment explanation
Indices: 25594502--25594572 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
25594492 ATTGAATATA
25594502 AAATAAATTTTATCATATAATAAA-TAAAG
1 AAATAAATTTTATCATATAATAAACT-AAG
*
25594531 AAATAAA-TTTATCATATATAATAAACTAAT
1 AAATAAATTTTATC--ATATAATAAACTAAG
25594561 AAATAAATTTTA
1 AAATAAATTTTA
25594573 ATTATTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 6 0.16
29 7 0.19
30 19 0.51
31 5 0.14
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (29 bp):
AAATAAATTTTATCATATAATAAACTAAG
Found at i:25594553 original size:26 final size:28
Alignment explanation
Indices: 25594502--25594564 Score: 85
Period size: 26 Copynumber: 2.3 Consensus size: 28
25594492 ATTGAATATA
*
25594502 AAATAAATTTTATCATATAATAAATAAAG
1 AAATAAA-TTTATCATATAATAAATAAAC
25594531 AAATAAATTTATCATAT-AT-AATAAAC
1 AAATAAATTTATCATATAATAAATAAAC
*
25594557 TAATAAAT
1 AAATAAAT
25594565 AAATTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 13 0.41
27 2 0.06
28 10 0.31
29 7 0.22
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (28 bp):
AAATAAATTTATCATATAATAAATAAAC
Found at i:25596026 original size:22 final size:22
Alignment explanation
Indices: 25596000--25596041 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
25595990 CCCAAAATTA
25596000 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
25596022 ATAAAATATTATTTTTTAAA
1 ATAAAATATTATTTTTTAAA
25596042 TTTAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:25596054 original size:8 final size:8
Alignment explanation
Indices: 25596044--25596077 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
25596034 TTTTTAAATT
*
25596044 TAAATATT
1 TAAATATA
25596052 TAAATATA
1 TAAATATA
*
25596060 TAATTATA
1 TAAATATA
25596068 TAAATATA
1 TAAATATA
25596076 TA
1 TA
25596078 TAAATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
TAAATATA
Found at i:25613732 original size:2 final size:2
Alignment explanation
Indices: 25613725--25613752 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25613715 ATATGAATTT
25613725 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
25613753 ACAATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25613850 original size:27 final size:27
Alignment explanation
Indices: 25613808--25613868 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
25613798 GAAAGTTGCT
*
25613808 GGGAAGGAAAAAGAGTAAATATTTATA
1 GGGAAGGAAAAAGAGTAAATAGTTATA
* * * *
25613835 GGGAAGGGAAATGAGTAGATAGTTGTA
1 GGGAAGGAAAAAGAGTAAATAGTTATA
25613862 GGGAAGG
1 GGGAAGG
25613869 CTTACTTTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.38, T:0.20
Consensus pattern (27 bp):
GGGAAGGAAAAAGAGTAAATAGTTATA
Found at i:25617356 original size:123 final size:122
Alignment explanation
Indices: 25617090--25617455 Score: 403
Period size: 132 Copynumber: 2.9 Consensus size: 122
25617080 CTCTTACCTA
* ** * *
25617090 AAAAATGTGTATGCAAATACATATATTTAATGCATTCATATTCACAACTATTTACAAAATTTTAA
1 AAAAATGTGTATGCAAATATATATATGCAATGCATTCATATTCACAACCATTTACAAAATTTGAA
*
25617155 AAGCAAAGATTGCCCAAACAAATAATATAATATACATACAAAAATGTTTACATGGAT
66 AAGCAAAGATTGCCCAAACAAATAATATAATATACATACAAAAATGTTTACATGAAT
* * *
25617212 AAAAATGTGTATACAAATATATGTATGCAATGCATTCATTTTCACAACCATTTACAAAA-TTGAA
1 AAAAATGTGTATGCAAATATATATATGCAATGCATTCATATTCACAACCATTTACAAAATTTGAA
* *
25617276 AAGGCAAAGATTGCCTTAAACAAATAATATAATATACATACAAAAATGTTTATATGAAT
66 AA-GCAAAGATTGCC-CAAACAAATAATATAATATACATACAAAAATGTTTACATGAAT
* * * * *
25617335 AAAAATGTATATGCAAGTATATAATGCATGATAACAATAAGAATTCATATTCACAACTATGTACA
1 AAAAATGTGTATGCAA--ATAT-AT--AT-AT-GCAAT--GCATTCATATTCACAACCATTTACA
* * * * * *
25617400 AAA-CTGAAAATGCAAAGATTCTCCCAAGCTAATAAAATAATGTACATACAAAAATG
57 AAATTTGAAAA-GCAAAGATT-GCCCAAACAAATAATATAATATACATACAAAAATG
25617456 GATAAAAATT
Statistics
Matches: 205, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
121 6 0.03
122 64 0.31
123 54 0.26
125 4 0.02
126 2 0.01
128 1 0.00
129 2 0.01
130 4 0.02
132 66 0.32
133 2 0.01
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (122 bp):
AAAAATGTGTATGCAAATATATATATGCAATGCATTCATATTCACAACCATTTACAAAATTTGAA
AAGCAAAGATTGCCCAAACAAATAATATAATATACATACAAAAATGTTTACATGAAT
Found at i:25617546 original size:131 final size:134
Alignment explanation
Indices: 25617264--25617684 Score: 425
Period size: 138 Copynumber: 3.1 Consensus size: 134
25617254 CACAACCATT
* * * * * *
25617264 TACAAAATTGAAAAGGCAAAGATTGCCTTAAACAAATAATATAATATACATACAAAAATGTTTAT
1 TACAAAATTGAAAAGGCAAAGATTTCC-CAAACAAATAAAATAATGTACATAC--AAATATATAT
* * * *
25617329 ATGAATAAAAATGTATATGCAAGT--A--TAT--AATGCAT-GAT-AACAATAAGAATTCATATT
63 A-G-ATAAAAATGTATATGCAAATACATGTATCCAATACATAG-TGAAAAATAAGAATTCATATC
*
25617386 CACAACTATG
125 CAAAACTATG
* * * * *
25617396 TACAAAACTGAAAATGCAAAGATTCTCCCAAGCTAATAAAATAATGTACATAC-AA-A-A-ATGG
1 TACAAAATTGAAAAGGCAAAGATT-TCCCAAACAAATAAAATAATGTACATACAAATATATATAG
* *
25617457 ATAAAAATTTATATGCAAATACATGTATGCAATACATAGTGAAAAATAAGAATTCATATCCAAAA
65 ATAAAAATGTATATGCAAATACATGTATCCAATACATAGTGAAAAATAAGAATTCATATCCAAAA
25617522 CTATG
130 CTATG
* * *
25617527 TACAAAATTGAAGAGGCAAAGATTTTCCAAACAAATGAAATAATGTACATACAAAAATATTTATA
1 TACAAAATTGAAAAGGCAAAGATTTCCCAAACAAATAAAATAATGTACATAC--AAATA--TATA
* * *
25617592 TAGATAAAAATGTATATGCAAATACATGTATCCAATACGTAGTGAAAAACAAGAATTTATATCCA
62 TAGATAAAAATGTATATGCAAATACATGTATCCAATACATAGTGAAAAATAAGAATTCATATCCA
* *
25617657 TAGCTATG
127 AAACTATG
25617665 TACAAAATTGAAAAGGCAAA
1 TACAAAATTGAAAAGGCAAA
25617685 TAAAATAGTG
Statistics
Matches: 239, Mismatches: 33, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
124 18 0.08
125 1 0.00
126 3 0.01
128 3 0.01
129 2 0.01
130 31 0.13
131 48 0.20
132 42 0.18
133 4 0.02
134 1 0.00
137 1 0.00
138 85 0.36
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27
Consensus pattern (134 bp):
TACAAAATTGAAAAGGCAAAGATTTCCCAAACAAATAAAATAATGTACATACAAATATATATAGA
TAAAAATGTATATGCAAATACATGTATCCAATACATAGTGAAAAATAAGAATTCATATCCAAAAC
TATG
Found at i:25617863 original size:20 final size:20
Alignment explanation
Indices: 25617840--25617910 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
25617830 AAATGGAATA
*
25617840 ATGCATGAATGAATGCATGT
1 ATGCATGAATGAATGCATAT
*
25617860 ATGCATGAATGAATGCATCT
1 ATGCATGAATGAATGCATAT
*
25617880 ATGTATGAATGAATGCATAT
1 ATGCATGAATGAATGCATAT
25617900 ATGCATGAATG
1 ATGCATGAATG
25617911 CAATAAAAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.31
Consensus pattern (20 bp):
ATGCATGAATGAATGCATAT
Found at i:25618039 original size:23 final size:23
Alignment explanation
Indices: 25618011--25618071 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
25618001 ATTAGTATGC
25618011 ACATAATATATACAAGAAACAAT
1 ACATAATATATACAAGAAACAAT
25618034 ACATAATATATACAAGAAACAAT
1 ACATAATATATACAAGAAACAAT
* *
25618057 ATATAA-ATTTACAAG
1 ACATAATATATACAAG
25618072 CAGAATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 8 0.22
23 28 0.78
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (23 bp):
ACATAATATATACAAGAAACAAT
Found at i:25619198 original size:16 final size:18
Alignment explanation
Indices: 25619157--25619220 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
25619147 ACAATTATGT
25619157 AAATATATTATATCATGC
1 AAATATATTATATCATGC
25619175 AAATATATTATATCATGC
1 AAATATATTATATCATGC
** * *
25619193 AAATATAAAATACCATAC
1 AAATATATTATATCATGC
25619211 AAATATATTA
1 AAATATATTA
25619221 ATAACCATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.34
Consensus pattern (18 bp):
AAATATATTATATCATGC
Found at i:25619533 original size:20 final size:23
Alignment explanation
Indices: 25619510--25619561 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
25619500 TGCAAACAAA
*
25619510 CATGCAAT-TAAATA-T-ATAAT
1 CATGCAATAAAAATATTAATAAT
25619530 CATGCAAATAAAAATATTAATAAT
1 CATGC-AATAAAAATATTAATAAT
25619554 CATGCAAT
1 CATGCAAT
25619562 CACACAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.19
21 3 0.11
22 5 0.19
23 4 0.15
24 10 0.37
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.31
Consensus pattern (23 bp):
CATGCAATAAAAATATTAATAAT
Found at i:25619559 original size:44 final size:43
Alignment explanation
Indices: 25619510--25619699 Score: 158
Period size: 44 Copynumber: 4.3 Consensus size: 43
25619500 TGCAAACAAA
25619510 CATGCAATTAAATATATAATCATGCAAATAAAAATATTAATAAT
1 CATGCAATTAAATATATAATCATGCAAATAAAAATA-TAATAAT
* * * * * *
25619554 CATGCAATCACACAAATAA--AT--AAATTAATAATCACACAGTTAGA-
1 CATGCAATTAAATATATAATCATGCAAA-TAAAAAT-ATA-A--TA-AT
* *
25619598 CATGCAATCAAATATATAATCATGCAAATAATAATATTAATAAT
1 CATGCAATTAAATATATAATCATGCAAATAAAAATA-TAATAAT
* *
25619642 CATGTAATTAAATATATAATCATGCAAATAAAAATAT-ATAAAC
1 CATGCAATTAAATATATAATCATGCAAATAAAAATATAAT-AAT
*
25619685 CATGCAAATAAATAT
1 CATGCAATTAAATAT
25619700 GCAATTAAAT
Statistics
Matches: 117, Mismatches: 16, Indels: 27
0.73 0.10 0.17
Matches are distributed among these distances:
40 3 0.03
41 7 0.06
42 6 0.05
43 17 0.15
44 68 0.58
45 1 0.01
46 4 0.03
47 8 0.07
48 3 0.03
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (43 bp):
CATGCAATTAAATATATAATCATGCAAATAAAAATATAATAAT
Found at i:25619641 original size:24 final size:21
Alignment explanation
Indices: 25619598--25619696 Score: 103
Period size: 22 Copynumber: 4.6 Consensus size: 21
25619588 CACAGTTAGA
*
25619598 CATGC-AATCAAATATATAAT
1 CATGCAAATAAAATATATAAT
25619618 CATGCAAATAATAATATTAATAAT
1 CATGCAAATAA-AATA-T-ATAAT
* *
25619642 CATG-TAATTAAATATATAAT
1 CATGCAAATAAAATATATAAT
*
25619662 CATGCAAATAAAAATATATAAAC
1 CATGCAAAT-AAAATATAT-AAT
25619685 CATGCAAATAAA
1 CATGCAAATAAA
25619697 TATGCAATTA
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
20 14 0.21
21 8 0.12
22 19 0.29
23 16 0.24
24 9 0.14
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (21 bp):
CATGCAAATAAAATATATAAT
Found at i:25619692 original size:23 final size:22
Alignment explanation
Indices: 25619607--25619696 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 22
25619597 ACATGCAATC
*
25619607 AAATATATAATCATGCAAATAA
1 AAATATATAACCATGCAAATAA
* * * *
25619629 TAATATTAATAATCATG-TAAT-T
1 AAATA-T-ATAACCATGCAAATAA
*
25619651 AAATATATAATCATGCAAATAA
1 AAATATATAACCATGCAAATAA
25619673 AAATATATAAACCATGCAAATAA
1 AAATATAT-AACCATGCAAATAA
25619696 A
1 A
25619697 TATGCAATTA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
20 9 0.16
21 4 0.07
22 16 0.29
23 18 0.32
24 9 0.16
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (22 bp):
AAATATATAACCATGCAAATAA
Found at i:25619702 original size:35 final size:32
Alignment explanation
Indices: 25619663--25619726 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
25619653 ATATATAATC
25619663 ATGCAAATAAAAATATATAAACCATGCAAATAAAT
1 ATGC-AAT-AAAATATAT-AACCATGCAAATAAAT
* *
25619698 ATGCAATTAAATATATAATCATGCAAATA
1 ATGCAATAAAATATATAACCATGCAAATA
25619727 TTAATATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 12 0.44
33 8 0.30
34 3 0.11
35 4 0.15
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.27
Consensus pattern (32 bp):
ATGCAATAAAATATATAACCATGCAAATAAAT
Found at i:25619706 original size:55 final size:55
Alignment explanation
Indices: 25619636--25619855 Score: 307
Period size: 55 Copynumber: 4.0 Consensus size: 55
25619626 TAATAATATT
* * * *
25619636 AATAATCATGTAATTAAATATATAATCATGCAAATAAAAATATATAAACCATGCA
1 AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCA
* * * *
25619691 AATAAATATGCAATTAAATATATAATCATGCAAATATTAATATATCAATCAAGCA
1 AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCA
* * * * * *
25619746 AAT-AACATGTAATTAAATATATAACCATACAACTAATAATACATAAATCACGCA
1 AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCA
25619800 AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCA
1 AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCA
25619855 A
1 A
25619856 TCATGTAAAT
Statistics
Matches: 141, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
54 45 0.32
55 96 0.68
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (55 bp):
AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCA
Found at i:25619721 original size:20 final size:20
Alignment explanation
Indices: 25619598--25619746 Score: 92
Period size: 20 Copynumber: 7.3 Consensus size: 20
25619588 CACAGTTAGA
*
25619598 CATGCAATCAAATATATAAT
1 CATGCAATTAAATATATAAT
*
25619618 CATGCAAATAATAATATTAATAAT
1 CATGC-AATTA-AATA-T-ATAAT
*
25619642 CATGTAATTAAATATATAAT
1 CATGCAATTAAATATATAAT
* *
25619662 CATGCAAATAAAAATAT-AT
1 CATGCAATTAAATATATAAT
** * **
25619681 -AAACCATGCAA-ATA-AAT
1 CATGCAATTAAATATATAAT
25619698 -ATGCAATTAAATATATAAT
1 CATGCAATTAAATATATAAT
*
25619717 CATGCAAATATTAATATATCAAT
1 CATGC-AAT-TAAATATAT-AAT
*
25619740 CAAGCAA
1 CATGCAA
25619747 ATAACATGTA
Statistics
Matches: 99, Mismatches: 19, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
17 11 0.11
18 8 0.08
19 5 0.05
20 28 0.28
21 8 0.08
22 18 0.18
23 12 0.12
24 9 0.09
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.30
Consensus pattern (20 bp):
CATGCAATTAAATATATAAT
Found at i:25619740 original size:23 final size:22
Alignment explanation
Indices: 25619707--25619749 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
25619697 TATGCAATTA
*
25619707 AATATATAATCATGCAAATATT
1 AATATATAATCAAGCAAATATT
25619729 AATATATCAATCAAGCAAATA
1 AATATAT-AATCAAGCAAATA
25619750 ACATGTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (22 bp):
AATATATAATCAAGCAAATATT
Found at i:25619829 original size:20 final size:21
Alignment explanation
Indices: 25619801--25619856 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
25619791 AATCACGCAA
* *
25619801 ATAAACATGCAATTA-AATAT
1 ATAATCATGCAATAATAATAT
25619821 ATAATCATGCAAATAATAATAT
1 ATAATCATGC-AATAATAATAT
25619843 ATAAATCATGCAAT
1 AT-AATCATGCAAT
25619857 CATGTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.29
21 4 0.13
22 10 0.32
23 8 0.26
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (21 bp):
ATAATCATGCAATAATAATAT
Found at i:25619853 original size:23 final size:22
Alignment explanation
Indices: 25619801--25619855 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
25619791 AATCACGCAA
*
25619801 ATAAA-CATGC-AATTAAATAT
1 ATAAATCATGCAAATAAAATAT
25619821 AT-AATCATGCAAATAATAATAT
1 ATAAATCATGCAAATAA-AATAT
25619843 ATAAATCATGCAA
1 ATAAATCATGCAA
25619856 TCATGTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.07
20 7 0.23
21 4 0.13
22 7 0.23
23 10 0.33
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (22 bp):
ATAAATCATGCAAATAAAATAT
Found at i:25619881 original size:109 final size:105
Alignment explanation
Indices: 25619597--25619887 Score: 351
Period size: 109 Copynumber: 2.8 Consensus size: 105
25619587 ACACAGTTAG
*
25619597 ACATGCAATCAAATATATAATCATGCAAATAATAATAT-T-A--AT--AATCATGTAATTAAATA
1 ACATGCAATTAAATATATAATCATGCAAATAATAATATATAATCATGCAATCATGTAATTAAATA
* * * *
25619656 TATAATCATGCAAATAAAAATATATAAACCATGCAAATAA
66 TATAACCATACAAATAAAAATACATAAACCACGCAAATAA
* * *
25619696 ATATGCAATTAAATATATAATCATGCAAATATTAATATATCAATCAAGCAAATAACATGTAATTA
1 ACATGCAATTAAATATATAATCATGCAAATAATAATATAT-AATCATGC-AAT--CATGTAATTA
* * *
25619761 AATATATAACCATACAACTAATAATACATAAATCACGCAAATAA
62 AATATATAACCATACAAATAAAAATACATAAACCACGCAAATAA
*
25619805 ACATGCAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCAATCATGTAAATAATA
1 ACATGCAATTAAATATATAATCATGCAAATAATAATATAT-AATCATGCAATCATGT-AATTA-A
*
25619870 ATATATAAACCATGCAAA
63 ATATAT-AACCATACAAA
25619888 ATATGTAATT
Statistics
Matches: 161, Mismatches: 18, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
99 35 0.22
100 1 0.01
102 1 0.01
104 1 0.01
106 5 0.03
107 7 0.04
108 10 0.06
109 101 0.63
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (105 bp):
ACATGCAATTAAATATATAATCATGCAAATAATAATATATAATCATGCAATCATGTAATTAAATA
TATAACCATACAAATAAAAATACATAAACCACGCAAATAA
Found at i:25619890 original size:55 final size:53
Alignment explanation
Indices: 25619642--25619887 Score: 271
Period size: 55 Copynumber: 4.5 Consensus size: 53
25619632 TATTAATAAT
* *
25619642 CATGTAATTAAATATATAATCATGCAAATAAAAATATATAAACCATGCAAATAAA
1 CATGTAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCAAAT--A
* * * * *
25619697 TATGCAATTAAATATATAATCATGCAAATATTAATATATCAATCAAGCAAATAA
1 CATGTAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCAAAT-A
* * * * *
25619751 CATGTAATTAAATATATAACCATACAACTAATAATACATAAATCACGCAAATAAA
1 CATGTAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCAAAT--A
*
25619806 CATGCAATTAAATATATAATCATGCAAATAATAATATATAAATCATGC-AAT-
1 CATGTAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCAAATA
* *
25619857 CATGTAAATAATAATATATAAACCATGCAAA
1 CATGT-AATTA-AATATAT-AATCATGCAAA
25619888 ATATGTAATT
Statistics
Matches: 162, Mismatches: 25, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
51 4 0.02
52 4 0.02
53 7 0.04
54 58 0.36
55 89 0.55
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.28
Consensus pattern (53 bp):
CATGTAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCAAATA
Found at i:25619906 original size:32 final size:31
Alignment explanation
Indices: 25619823--25619886 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
25619813 TTAAATATAT
* *
25619823 AATCATGCAAATAATAATATATAAATCATGC
1 AATCATGTAAATAATAATATATAAACCATGC
25619854 AATCATGTAAATAATAATATATAAACCATGC
1 AATCATGTAAATAATAATATATAAACCATGC
25619885 AA
1 AA
25619887 AATATGTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (31 bp):
AATCATGTAAATAATAATATATAAACCATGC
Found at i:25621336 original size:26 final size:27
Alignment explanation
Indices: 25621307--25621357 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
25621297 AAGGAAATAG
* *
25621307 TAATTTATAGT-TCATTAATTTTTATT
1 TAATATATAGTATCATTAAATTTTATT
*
25621333 TAATATATAGTATTATTAAATTTTA
1 TAATATATAGTATCATTAAATTTTA
25621358 ATAAAAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (27 bp):
TAATATATAGTATCATTAAATTTTATT
Done.