Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 191 of 199
Found at i:55776284 original size:30 final size:30
Alignment explanation
Indices: 55776249--55776354 Score: 140
Period size: 30 Copynumber: 3.5 Consensus size: 30
55776239 GGCCAAAGTG
55776249 TAATTTTAGGAAAATTTAAGGGTTAAAATA
1 TAATTTTAGGAAAATTTAAGGGTTAAAATA
* * * * *
55776279 TAATTTCATGAAAGTTTATGGGTTAAAATG
1 TAATTTTAGGAAAATTTAAGGGTTAAAATA
* *
55776309 TAATTTTAGGAAAGTTTAAGGGTCAAAATA
1 TAATTTTAGGAAAATTTAAGGGTTAAAATA
*
55776339 TAATTTTAAGAAAATT
1 TAATTTTAGGAAAATT
55776355 CAGATGTCAA
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38
Consensus pattern (30 bp):
TAATTTTAGGAAAATTTAAGGGTTAAAATA
Found at i:55776367 original size:60 final size:60
Alignment explanation
Indices: 55776228--55776374 Score: 170
Period size: 60 Copynumber: 2.4 Consensus size: 60
55776218 CAAACATAGC
* * * * *
55776228 AAAATTCTTGGGGCCAAAGTGTAATTTTAGGAAAATTTAAGGGTTAAAATATAATTTCATG
1 AAAATTCAT-GGGTCAAAATGTAATTTTAGGAAAATTTAAGGGTCAAAATATAATTTCAAG
* * * * *
55776289 AAAGTTTATGGGTTAAAATGTAATTTTAGGAAAGTTTAAGGGTCAAAATATAATTTTAAG
1 AAAATTCATGGGTCAAAATGTAATTTTAGGAAAATTTAAGGGTCAAAATATAATTTCAAG
*
55776349 AAAATTCA-GATGTCAAAATGTAATTT
1 AAAATTCATG-GGTCAAAATGTAATTT
55776375 AAAAAATGCA
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
59 1 0.01
60 64 0.90
61 6 0.08
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.35
Consensus pattern (60 bp):
AAAATTCATGGGTCAAAATGTAATTTTAGGAAAATTTAAGGGTCAAAATATAATTTCAAG
Found at i:55780062 original size:101 final size:101
Alignment explanation
Indices: 55779935--55780119 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 101
55779925 AAAGTGATGG
*
55779935 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAT-G-ATGGGTCGCATATGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGGAAT-GGTCACATATGTAGT
55779998 ACTATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
64 ACTATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
* * *
55780036 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGAAATGGTCACATGTGTAGTG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGG-AATGGTCACATATGTAGTA
55780101 CTATGTGCAGGCTACTATG
65 CTATGTGCAGGCTACTATG
55780120 TGAGCCGGGT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
100 2 0.03
101 41 0.53
102 32 0.42
103 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.29
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGAATGGTCACATATGTAGTAC
TATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
Found at i:55780065 original size:51 final size:49
Alignment explanation
Indices: 55779930--55780117 Score: 207
Period size: 51 Copynumber: 3.7 Consensus size: 49
55779920 AAGTGAAAGT
*
55779930 GATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A
1 GATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA
* * * * *
55779978 TGATGGGTCGCATATGTAGTACTATGTGCAGGCTACTATGCGAACCGGATA
1 -GAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA
* * * *
55780029 GCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGA
1 G-AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT--A
* *
55780082 AATGGTCACATGTGTAGTGCTATGTGCAGGCTACTA
1 GATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
55780118 TGTGAGCCGG
Statistics
Matches: 113, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
49 3 0.03
50 39 0.35
51 69 0.61
52 1 0.01
53 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (49 bp):
GATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA
Found at i:55780292 original size:69 final size:69
Alignment explanation
Indices: 55780143--55780334 Score: 258
Period size: 69 Copynumber: 2.7 Consensus size: 69
55780133 ATTGACTATT
* * * *
55780143 AGGGGGTTGCTAAGTGTTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACTGTATC
1 AGGGGGTTGCTAAGTGCTGATT-CCC--C-CA-AGG-GGTTGCTAAGTGCTGATCCCACCGTATC
*
55780208 TTGAATATAA
60 TTAAATATAA
*
55780218 AGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATCCCACCGTATTTTAAAT
1 AGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATCCCACCGTATCTTAAAT
* *
55780283 GTGA
66 ATAA
55780287 AGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGAT
1 AGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGAT
55780335 TCCCCGAATC
Statistics
Matches: 109, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
69 80 0.73
70 2 0.02
71 2 0.02
72 1 0.01
74 3 0.03
75 21 0.19
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.31
Consensus pattern (69 bp):
AGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATCCCACCGTATCTTAAAT
ATAA
Found at i:55780360 original size:33 final size:33
Alignment explanation
Indices: 55780291--55780451 Score: 129
Period size: 33 Copynumber: 4.7 Consensus size: 33
55780281 ATGTGAAGGG
*
55780291 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
55780318 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
55780351 GGTTGCTAAGTGCTGATTCCACC-ATATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGA-ATC-----AT-TG---GT
*
55780394 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
55780427 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
55780452 TAACGGTTAA
Statistics
Matches: 110, Mismatches: 5, Indels: 31
0.75 0.03 0.21
Matches are distributed among these distances:
27 22 0.20
31 2 0.02
32 2 0.02
33 41 0.37
34 9 0.08
36 2 0.02
37 1 0.01
39 2 0.02
40 2 0.02
42 5 0.05
43 22 0.20
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:55780407 original size:103 final size:96
Alignment explanation
Indices: 55780220--55780415 Score: 284
Period size: 103 Copynumber: 2.0 Consensus size: 96
55780210 GAATATAAAG
*
55780220 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATCCCACCATATTTTAAATGT
*
55780285 GAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
66 GAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
* *
55780316 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATCTT
1 GGGGTTGCTAAGTGCTGATTCCCC----CA-AGG-GGTTGCTAAGTGCTGATCCCACCATAT-TT
*
55780381 TGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
59 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
55780416 GAATCACTGG
Statistics
Matches: 88, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
96 24 0.27
100 2 0.02
101 2 0.02
102 25 0.28
103 35 0.40
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (96 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATCCCACCATATTTTAAATGT
GAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:55781299 original size:49 final size:49
Alignment explanation
Indices: 55781227--55781320 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 49
55781217 CTTTCGATAA
* * * *
55781227 GTGATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATAAGTGATTACATATAAGACCATAGCTGGACTATGGCATCGGTAT
* * *
55781276 GTGATAAGTGATTACATGTAAGACCATAGTTGGACTATGGTATCG
1 GTGATAAGTGATTACATATAAGACCATAGCTGGACTATGGCATCG
55781321 AGAAAAAGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (49 bp):
GTGATAAGTGATTACATATAAGACCATAGCTGGACTATGGCATCGGTAT
Found at i:55781843 original size:2 final size:2
Alignment explanation
Indices: 55781836--55781874 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
55781826 TGTTAAGTCT
55781836 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
55781875 GTATTTATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55787408 original size:46 final size:46
Alignment explanation
Indices: 55787305--55787617 Score: 302
Period size: 46 Copynumber: 6.6 Consensus size: 46
55787295 TACGTATGAT
* *
55787305 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
55787348 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*** *
55787394 CACTTATCACTTTGTCACCACTT-ATCACTTG-TCCCTGATCAGATAAGTGTAGCTA-
1 CACTTATCACTTTGT---CACTTGATCA---GATAAGTG-T-AGCTAA----AGCTAC
* * *
55787449 AAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAACTAC
1 CA-CT--TA----TCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
55787502 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
55787546 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
55787592 CACTTATCACTTTGTCAC-TGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
55787618 AGTACTCAAA
Statistics
Matches: 225, Mismatches: 18, Indels: 52
0.76 0.06 0.18
Matches are distributed among these distances:
43 10 0.04
44 42 0.19
45 38 0.17
46 71 0.32
48 4 0.02
49 5 0.02
50 4 0.02
51 2 0.01
52 11 0.05
53 1 0.00
55 1 0.00
56 12 0.05
57 2 0.01
58 4 0.02
59 5 0.02
60 4 0.02
62 9 0.04
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:55787445 original size:62 final size:64
Alignment explanation
Indices: 55787346--55787473 Score: 233
Period size: 62 Copynumber: 2.0 Consensus size: 64
55787336 TAGCTAGGCT
*
55787346 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
1 ACCACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
55787410 ACCACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
1 ACCACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
55787472 AC
1 AC
55787474 TTGATCAGAT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 46 0.73
63 5 0.08
64 12 0.19
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (64 bp):
ACCACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
Found at i:55787493 original size:108 final size:107
Alignment explanation
Indices: 55787305--55787513 Score: 391
Period size: 108 Copynumber: 1.9 Consensus size: 107
55787295 TACGTATGAT
*
55787305 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGA
1 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGA
*
55787370 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC
66 TCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTCAC
55787412 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
1 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACTTG
55787477 ATCAGATAAGTGTAGCTAAAACTACCACTTATCACTT
65 ATCAGATAAGTGTAGCTAAAACTACCACTTATCACTT
55787514 GTCCCTGATC
Statistics
Matches: 99, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
107 36 0.36
108 63 0.64
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.33
Consensus pattern (107 bp):
CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGA
TCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTCAC
Found at i:55787563 original size:90 final size:90
Alignment explanation
Indices: 55787410--55787617 Score: 389
Period size: 90 Copynumber: 2.3 Consensus size: 90
55787400 TCACTTTGTC
55787410 ACCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 ACCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
55787475 TGATCAGATAAGTGTAGCTAAAACT
66 TGATCAGATAAGTGTAGCTAAAACT
55787500 ACCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 ACCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
*
55787565 TGATCAGATAAGTGTAGCTAAAGCT
66 TGATCAGATAAGTGTAGCTAAAACT
*
55787590 ACCACTTATCACTTTGTCACTGATCAGA
1 ACCACTTATCAC-TTGTCCCTGATCAGA
55787618 AGTACTCAAA
Statistics
Matches: 115, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
90 101 0.88
91 14 0.12
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (90 bp):
ACCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
TGATCAGATAAGTGTAGCTAAAACT
Found at i:55787565 original size:52 final size:47
Alignment explanation
Indices: 55787410--55787617 Score: 319
Period size: 46 Copynumber: 4.6 Consensus size: 47
55787400 TCACTTTGTC
*
55787410 ACCACTTATCAC-TTGTC-C-CTGATCAGATAAGTGTAGCTAAAGCT
1 ACCACTTATCACTTTGTCACTTTGATCAGATAAGTGTAGCTAAAGCT
*
55787454 ACCACTTATCACTTTGTCAC-TTGATCAGATAAGTGTAGCTAAAACT
1 ACCACTTATCACTTTGTCACTTTGATCAGATAAGTGTAGCTAAAGCT
*
55787500 ACCACTTATCAC-TTGTC-C-CTGATCAGATAAGTGTAGCTAAAGCT
1 ACCACTTATCACTTTGTCACTTTGATCAGATAAGTGTAGCTAAAGCT
55787544 ACCACTTATCACTTTGTCAC-TTGATCAGATAAGTGTAGCTAAAGCT
1 ACCACTTATCACTTTGTCACTTTGATCAGATAAGTGTAGCTAAAGCT
55787590 ACCACTTATCACTTTGTCAC--TGATCAGA
1 ACCACTTATCACTTTGTCACTTTGATCAGA
55787618 AGTACTCAAA
Statistics
Matches: 155, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
44 49 0.32
45 23 0.15
46 83 0.54
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (47 bp):
ACCACTTATCACTTTGTCACTTTGATCAGATAAGTGTAGCTAAAGCT
Found at i:55790314 original size:7 final size:7
Alignment explanation
Indices: 55790298--55790329 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
55790288 CTAAAGCTAC
*
55790298 CACTTAT
1 CACTTGT
55790305 CACTTGT
1 CACTTGT
55790312 CACTTGT
1 CACTTGT
55790319 CACTTGT
1 CACTTGT
55790326 CACT
1 CACT
55790330 GATTAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.31, G:0.09, T:0.41
Consensus pattern (7 bp):
CACTTGT
Found at i:55790356 original size:51 final size:51
Alignment explanation
Indices: 55790301--55790482 Score: 211
Period size: 51 Copynumber: 3.4 Consensus size: 51
55790291 AAGCTACCAC
* * * *
55790301 TTATCACTTGTCACTTGTCACTTGTCACTGATTAGATAAGTGTACCTGAAG
1 TTATCACTTATCACTTGTCACTTGTCACTGATAAGATAAGTGTAGCTAAAG
*
55790352 TTATCACTTATCACTTGCCACTTGCCACTTGCCACTGATAAGATAAGTGTAGCTAAAG
1 TTATCACTTATCACTTG-----T--CACTTGTCACTGATAAGATAAGTGTAGCTAAAG
* * * *
55790410 CTATCACTTATCACTTGCCATTTGTCACTGATCAGATAAGTGTAGCTAAAG
1 TTATCACTTATCACTTGTCACTTGTCACTGATAAGATAAGTGTAGCTAAAG
*
55790461 TTACCACTTATCACTTGTCACT
1 TTATCACTTATCACTTGTCACT
55790483 GATCAGAAGA
Statistics
Matches: 110, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
51 64 0.58
56 1 0.01
58 45 0.41
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (51 bp):
TTATCACTTATCACTTGTCACTTGTCACTGATAAGATAAGTGTAGCTAAAG
Found at i:55790360 original size:58 final size:58
Alignment explanation
Indices: 55790253--55790482 Score: 276
Period size: 58 Copynumber: 4.1 Consensus size: 58
55790243 TTGCGTATGA
* * *
55790253 TCACTTATCACTTGTCCCTGATCAGATAAGTGCAGCTAAAGCTACCACTTATCACTTG
1 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* * * * *
55790311 TCACTTGTCACTTGTCACTGATTAGATAAGTGTACCTGAAGTTATCACTTATCACTTG
1 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* * * * *
55790369 CCACTTGCCACTTGCCACTGATAAGATAAGTGTAGCTAAAGCTATCACTTATCACTTG
1 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* *
55790427 ---C----CATTTGTCACTGATCAGATAAGTGTAGCTAAAGTTACCACTTATCACTTG
1 TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
55790478 TCACT
1 TCACT
55790483 GATCAGAAGA
Statistics
Matches: 148, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
51 45 0.30
54 1 0.01
55 1 0.01
58 101 0.68
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (58 bp):
TCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
Found at i:55790373 original size:7 final size:7
Alignment explanation
Indices: 55790363--55790387 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55790353 TATCACTTAT
55790363 CACTTGC
1 CACTTGC
55790370 CACTTGC
1 CACTTGC
55790377 CACTTGC
1 CACTTGC
55790384 CACT
1 CACT
55790388 GATAAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.44, G:0.12, T:0.28
Consensus pattern (7 bp):
CACTTGC
Found at i:55796894 original size:30 final size:30
Alignment explanation
Indices: 55796854--55796977 Score: 128
Period size: 30 Copynumber: 4.2 Consensus size: 30
55796844 AAAATTTTAT
55796854 ATTTTAACCCCTAAAATTTTTCAAAATTAC
1 ATTTTAACCCCTAAAATTTTTCAAAATTAC
* * *
55796884 ATGTCAACCCCTAAACA-TTTT-GAAATTAC
1 ATTTTAACCCCTAAA-ATTTTTCAAAATTAC
* * * * *
55796913 ATTTTGACCCCTGAACTTTCTCGAAATTAC
1 ATTTTAACCCCTAAAATTTTTCAAAATTAC
*
55796943 ATTTTAACCCCT-AAATTTTCTCAAAATTAT
1 ATTTTAACCCCTAAAATTTT-TCAAAATTAC
55796973 ATTTT
1 ATTTT
55796978 GGCCCCAGAA
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
29 26 0.34
30 49 0.64
31 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.40
Consensus pattern (30 bp):
ATTTTAACCCCTAAAATTTTTCAAAATTAC
Found at i:55797521 original size:17 final size:16
Alignment explanation
Indices: 55797481--55797535 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 16
55797471 GTCTGAACGA
55797481 AGAAGAAG-AAAAAAG
1 AGAAGAAGAAAAAAAG
*
55797496 A-AAGGAGAAAAAAAG
1 AGAAGAAGAAAAAAAG
* *
55797511 AGAAGAA-AGAAGAAG
1 AGAAGAAGAAAAAAAG
55797526 -GAAGAAGAAA
1 AGAAGAAGAAA
55797536 GGGGGAAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 11 0.34
15 17 0.53
16 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
AGAAGAAGAAAAAAAG
Found at i:55797682 original size:16 final size:17
Alignment explanation
Indices: 55797661--55797692 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
55797651 GCAGCCCCCC
55797661 AAAAAAAGAA-AAGCAA
1 AAAAAAAGAAGAAGCAA
55797677 AAAAAAAGAAGAAGCA
1 AAAAAAAGAAGAAGCA
55797693 GGCCACTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAGAAGCAA
Found at i:55797863 original size:10 final size:10
Alignment explanation
Indices: 55797848--55797924 Score: 63
Period size: 10 Copynumber: 7.8 Consensus size: 10
55797838 AGCCCAGTCC
55797848 AAAAAAAGAG
1 AAAAAAAGAG
55797858 AAAAAAA-A-
1 AAAAAAAGAG
*
55797866 AGAAAAAGAG
1 AAAAAAAGAG
**
55797876 AGGAAAAGAG
1 AAAAAAAGAG
55797886 AAGAAAAA-AG
1 AA-AAAAAGAG
*
55797896 -AAAAAAGAA
1 AAAAAAAGAG
55797905 AAAAAAAGAAG
1 AAAAAAAG-AG
55797916 AAGAAAAAG
1 AA-AAAAAG
55797925 GGGGTTCAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
8 11 0.20
9 4 0.07
10 26 0.48
11 7 0.13
12 6 0.11
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:55797892 original size:28 final size:29
Alignment explanation
Indices: 55797848--55797923 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 29
55797838 AGCCCAGTCC
* *
55797848 AAAAAAAGAGAAAAAAAAAG-AAAAAGAG
1 AAAAAAAGAGAAGAAAAAAGAAAAAAGAA
**
55797876 AGGAAAAGAGAAGAAAAAAGAAAAAAGAA
1 AAAAAAAGAGAAGAAAAAAGAAAAAAGAA
55797905 AAAAAAAGAAGAAGAAAAA
1 AAAAAAAG-AGAAGAAAAA
55797924 GGGGGTTCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
28 17 0.43
29 13 0.32
30 10 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (29 bp):
AAAAAAAGAGAAGAAAAAAGAAAAAAGAA
Found at i:55798275 original size:16 final size:16
Alignment explanation
Indices: 55798256--55798322 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 16
55798246 AAAAAAATCC
*
55798256 TCGTGTTTCGAAATTT
1 TCGTGTTTCAAAATTT
55798272 TCGTGTCTTCAAAAAATTTT
1 TCGTGT-TTC--AAAA-TTT
*
55798292 CTCGTGTTTCAAAATTC
1 -TCGTGTTTCAAAATTT
55798309 TCGTGTTTTCAAAA
1 TCGTG-TTTCAAAA
55798323 ATAAGGAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
16 11 0.26
17 13 0.30
18 4 0.09
19 3 0.07
20 6 0.14
21 6 0.14
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (16 bp):
TCGTGTTTCAAAATTT
Found at i:55798323 original size:18 final size:17
Alignment explanation
Indices: 55798248--55798324 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 17
55798238 AAATTTTCAA
*
55798248 AAAAATCCTCGTGTTTC
1 AAAAATTCTCGTGTTTC
* *
55798265 -GAAATTTTCGTGTCTTC
1 AAAAATTCTCGTGT-TTC
55798282 AAAAAATTTTCTCGTGTTTC
1 -AAAAA--TTCTCGTGTTTC
55798302 -AAAATTCTCGTGTTTTC
1 AAAAATTCTCGTG-TTTC
55798319 AAAAAT
1 AAAAAT
55798325 AAGGAAACAA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
16 18 0.38
17 7 0.15
18 9 0.19
19 3 0.06
20 3 0.06
21 8 0.17
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.42
Consensus pattern (17 bp):
AAAAATTCTCGTGTTTC
Found at i:55798517 original size:18 final size:18
Alignment explanation
Indices: 55798453--55798634 Score: 138
Period size: 18 Copynumber: 10.3 Consensus size: 18
55798443 AAAAATCCAG
* *
55798453 TGTTTTCAAAAAATTCCA
1 TGTTTTCAAAAATTTTCA
* ** *
55798471 T-TTTCCAAATTTTTTCG
1 TGTTTTCAAAAATTTTCA
*
55798488 TGTTTTCTAAAAATTTTTA
1 TGTTTTC-AAAAATTTTCA
*
55798507 TG-TTTCAAAAATTTTCG
1 TGTTTTCAAAAATTTTCA
*
55798524 TGTTTTCAAAAATTTTCG
1 TGTTTTCAAAAATTTTCA
* *
55798542 TGTTTTCAACAATTTTCG
1 TGTTTTCAAAAATTTTCA
* * *
55798560 TATTTTCAAAAAATTTCG
1 TGTTTTCAAAAATTTTCA
* *
55798578 TGTTTTCAACAATTCTCA
1 TGTTTTCAAAAATTTTCA
* * * *
55798596 TG-TTTCTAGAATTCTCG
1 TGTTTTCAAAAATTTTCA
*
55798613 TG-TTTCAAAAATTTTCG
1 TGTTTTCAAAAATTTTCA
55798630 TGTTT
1 TGTTT
55798635 AAAAAAAATT
Statistics
Matches: 132, Mismatches: 28, Indels: 8
0.79 0.17 0.05
Matches are distributed among these distances:
17 50 0.38
18 73 0.55
19 9 0.07
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.49
Consensus pattern (18 bp):
TGTTTTCAAAAATTTTCA
Found at i:55798522 original size:36 final size:36
Alignment explanation
Indices: 55798482--55798634 Score: 177
Period size: 36 Copynumber: 4.3 Consensus size: 36
55798472 TTTCCAAATT
**
55798482 TTTTCGTGTTTTCTAAAAATTTTTATG-TTTCAAAAA
1 TTTTCGTGTTTTC-AAAAATTTTCGTGTTTTCAAAAA
*
55798518 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAACAA
1 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAA
* * *
55798554 TTTTCGTATTTTCAAAAAATTTCGTGTTTTCAACAA
1 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAA
* * * * *
55798590 TTCTCATG-TTTCTAGAATTCTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAA
55798624 TTTTCGTGTTT
1 TTTTCGTGTTT
55798635 AAAAAAAATT
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
34 14 0.14
35 26 0.26
36 60 0.60
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.50
Consensus pattern (36 bp):
TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAA
Found at i:55798577 original size:54 final size:54
Alignment explanation
Indices: 55798455--55798634 Score: 172
Period size: 54 Copynumber: 3.4 Consensus size: 54
55798445 AAATCCAGTG
* * * **
55798455 TTTTCAAAAAATTCCAT-TTTCCAAATTTTTTCGTGTTTTCTAAAAATTTT--TA
1 TTTTCAAAAAATTTCGTGTTTTCAAAAATTTTCGTGTTTTC-AAAAATTTTCGTA
* *
55798507 TGTTTCAAAAATTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAACAATTTTCGTA
1 T-TTTCAAAAAATTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATTTTCGTA
* * * * * *
55798562 TTTTCAAAAAATTTCGTGTTTTCAACAATTCTCATG-TTTCTAGAATTCTCGT-
1 TTTTCAAAAAATTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATTTTCGTA
* *
55798614 GTTTCAAAAATTTTCGTGTTT
1 TTTTCAAAAAATTTCGTGTTT
55798635 AAAAAAAATT
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
52 20 0.19
53 34 0.31
54 51 0.47
55 3 0.03
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (54 bp):
TTTTCAAAAAATTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATTTTCGTA
Found at i:55798640 original size:17 final size:17
Alignment explanation
Indices: 55798482--55798639 Score: 156
Period size: 18 Copynumber: 9.0 Consensus size: 17
55798472 TTTCCAAATT
55798482 TTTTCGTGTTTTCTAAAAA
1 TTTTCGTG-TTTC-AAAAA
**
55798501 TTTTTATGTTTCAAAAA
1 TTTTCGTGTTTCAAAAA
55798518 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
*
55798536 TTTTCGTGTTTTCAACAA
1 TTTTCGTG-TTTCAAAAA
*
55798554 TTTTCGTATTTTCAAAAA
1 TTTTCGT-GTTTCAAAAA
* *
55798572 ATTTCGTGTTTTCAACAA
1 TTTTCGTG-TTTCAAAAA
* * * *
55798590 TTCTCATGTTTCTAGAA
1 TTTTCGTGTTTCAAAAA
*
55798607 TTCTCGTGTTTCAAAAA
1 TTTTCGTGTTTCAAAAA
55798624 TTTTCGTGTTT-AAAAA
1 TTTTCGTGTTTCAAAAA
55798640 AAATTTTCTT
Statistics
Matches: 117, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
16 5 0.04
17 42 0.36
18 64 0.55
19 6 0.05
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (17 bp):
TTTTCGTGTTTCAAAAA
Found at i:55804308 original size:14 final size:14
Alignment explanation
Indices: 55804283--55804326 Score: 63
Period size: 13 Copynumber: 3.1 Consensus size: 14
55804273 CAATAATAAT
55804283 AACAAGAAAAACAAA
1 AACAA-AAAAACAAA
55804298 AACAAAAAAAC-AA
1 AACAAAAAAACAAA
*
55804311 AACAAAAAAATAAA
1 AACAAAAAAACAAA
55804325 AA
1 AA
55804327 AATAAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 12 0.44
14 10 0.37
15 5 0.19
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.02
Consensus pattern (14 bp):
AACAAAAAAACAAA
Found at i:55804312 original size:13 final size:13
Alignment explanation
Indices: 55804283--55804343 Score: 61
Period size: 13 Copynumber: 4.6 Consensus size: 13
55804273 CAATAATAAT
55804283 AACAAGAAAAACAAA
1 AACAA-AAAAAC-AA
55804298 AACAAAAAAACAA
1 AACAAAAAAACAA
*
55804311 AACAAAAAAATAA
1 AACAAAAAAACAA
* *
55804324 AA-AAATAAAGAA
1 AACAAAAAAACAA
*
55804336 AAGAAAAA
1 AACAAAAA
55804344 GAAAAGTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.24
13 20 0.49
14 6 0.15
15 5 0.12
ACGTcount: A:0.84, C:0.08, G:0.05, T:0.03
Consensus pattern (13 bp):
AACAAAAAAACAA
Found at i:55804325 original size:21 final size:22
Alignment explanation
Indices: 55804255--55804348 Score: 75
Period size: 23 Copynumber: 4.1 Consensus size: 22
55804245 TATTATGCCT
55804255 AAAAAA-AAGACAAAAAAACAATA
1 AAAAAACAAGA-AAAAAAA-AATA
* *
55804278 ATAATAACAAGAAAAACAAAAACA
1 A-AAAAACAAGAAAAA-AAAAATA
*
55804302 AAAAAACAA-AACAAAAAAATA
1 AAAAAACAAGAAAAAAAAAATA
* * *
55804323 AAAAAATAAAGAAAAGAAAAAGA
1 AAAAAA-CAAGAAAAAAAAAATA
55804346 AAA
1 AAA
55804349 GTCAAGATGA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
21 12 0.21
22 6 0.11
23 20 0.35
24 12 0.21
25 7 0.12
ACGTcount: A:0.82, C:0.07, G:0.05, T:0.05
Consensus pattern (22 bp):
AAAAAACAAGAAAAAAAAAATA
Found at i:55804328 original size:35 final size:34
Alignment explanation
Indices: 55804255--55804337 Score: 78
Period size: 35 Copynumber: 2.4 Consensus size: 34
55804245 TATTATGCCT
* * * *
55804255 AAAAAAAAGACAAAAAAACAATAATAATAACAAGA
1 AAAAAAAAAACAAAAAAACAATAACAA-AAAAAAA
* *
55804290 AAAACAAAAACAAAAAAACAA-AACAAAAAAATA
1 AAAAAAAAAACAAAAAAACAATAACAAAAAAAAA
* *
55804323 AAAAAATAAAGAAAA
1 AAAAAAAAAACAAAA
55804338 GAAAAAGAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 17 0.43
34 4 0.10
35 19 0.47
ACGTcount: A:0.82, C:0.08, G:0.04, T:0.06
Consensus pattern (34 bp):
AAAAAAAAAACAAAAAAACAATAACAAAAAAAAA
Found at i:55805325 original size:75 final size:73
Alignment explanation
Indices: 55805224--55805406 Score: 276
Period size: 75 Copynumber: 2.5 Consensus size: 73
55805214 TATTTTTGGA
*
55805224 AAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCACGGGTCATCCTGAGGTATTTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCACGGGTCATCCTGAGGTA-TTTTCAATT
*
55805289 TTTGTTTTTT
65 TATG-TTTTT
* * *
55805299 AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCATCCTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCACGGGTCATCCTGAGGTATTTTCAATTT
55805364 ATGTTTTT
66 ATGTTTTT
* * *
55805372 CAAAAATTAACTCATATTGCGAAAGGTGAGTTGAG
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
55805407 NNNNNNNNNN
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
73 35 0.36
74 12 0.12
75 51 0.52
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (73 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCACGGGTCATCCTGAGGTATTTTCAATTT
ATGTTTTT
Found at i:55807173 original size:78 final size:78
Alignment explanation
Indices: 55806997--55807590 Score: 703
Period size: 78 Copynumber: 7.6 Consensus size: 78
55806987 NNNNNNNTTT
* *
55806997 TGTTTTTC-GAAATCAACTCCATA-TGCGA-AGGTGAGTTGAG-CTCGGGTCACATGTCGAGGTA
1 TGTTTTTCAAAAATCAACT-CATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA
*
55807058 TTC-TTTAAATTGC
65 TTCTTTTAAATTTC
* *
55807071 --TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCGCATGCCGAGGTA
1 TGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA
*
55807134 TTCTTTTCAATTTC
65 TTCTTTTAAATTTC
* * *
55807148 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCTCACGCTGAGGTA-
1 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTAT
*
55807212 --TTTTAAATTTT
66 TCTTTTAAATTTC
* *
55807223 TGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTAT
1 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA-
55807288 TTCTTTTAAATTT-
65 TTCTTTTAAATTTC
* * * *
55807301 TTTTTTTCAGAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCGCATGCCGAGGTAT
1 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTAT
*
55807366 TCTTTTCAATTTC
66 TCTTTTAAATTTC
* * * *
55807379 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCTCACGCTGAGGTA-
1 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTAT
55807443 --TTTTAAATTTC
66 TCTTTTAAATTTC
* * * **
55807454 CGTTTTTCAAAAATGAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGTCACATGCCGAGGTAT
1 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA-
* *
55807519 TTCTTTTTAATTTT
65 TTCTTTTAAATTTC
*
55807533 TGCTTTTCAAAAAAAAAGAGAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 TGTTTTTC--------A-A-AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
55807591 TTGCACGCTG
Statistics
Matches: 446, Mismatches: 47, Indels: 39
0.84 0.09 0.07
Matches are distributed among these distances:
72 6 0.01
73 4 0.01
74 14 0.03
75 147 0.33
76 21 0.05
77 20 0.04
78 167 0.37
79 31 0.07
87 1 0.00
88 1 0.00
89 34 0.08
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (78 bp):
TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTAT
TCTTTTAAATTTC
Found at i:55807284 original size:153 final size:153
Alignment explanation
Indices: 55806997--55807590 Score: 656
Period size: 153 Copynumber: 3.8 Consensus size: 153
55806987 NNNNNNNTTT
*
55806997 TGTTTTTC-GAAATCAACTCCATA-TGCGA-AGGTGAGTTGAG-CTCGGGTCACATG-TCGAGGT
1 TGTTTTTCAAAAATCAACT-CATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCT-GAGGT
*
55807057 ATTCTTTAAA---TTGCTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGG
64 ATT-TTTAAATTTTTG-TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* *
55807119 TCGCATGCCGAGGTATTCTTTTCAATTTC
126 TCACATG-CGAGGTATTCTTTTAAATTTC
* *
55807148 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCTCACGCTGAGGTA-
1 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTAT
*
55807212 TTTTAAATTTTTGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGTCACA
66 TTTTAAATTTTTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
55807277 TGTCGAGGTATTTCTTTTAAATTT-
131 TG-CGAGGTA-TTCTTTTAAATTTC
* * * * *
55807301 TTTTTTTCAGAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCGCATGCCGAGGTAT
1 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTA-
* * * *
55807366 TCTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCT
65 T-TTTTAAATTTTTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
55807431 CACGCTGAGGTA---TTTTAAATTTC
129 CATGC-GAGGTATTCTTTTAAATTTC
* * * ** *
55807454 CGTTTTTCAAAAATGAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGTCACATGCCGAGGTAT
1 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTA-
* *
55807519 TTCTTTTTAATTTTTGCTTTTCAAAAAAAAAGAGAAATCAACTCATATTGCGAGAGGTGAGTTGA
65 -T-TTTTAAATTTTTGTTTTTC--------A-A-AAATCAACTCATATTGCGAGAGGTGAGTTGA
55807584 GCCTCGG
118 GCCTCGG
55807591 TTGCACGCTG
Statistics
Matches: 385, Mismatches: 33, Indels: 37
0.85 0.07 0.08
Matches are distributed among these distances:
151 12 0.03
152 30 0.08
153 178 0.46
154 54 0.14
155 5 0.01
156 67 0.17
162 1 0.00
163 1 0.00
164 37 0.10
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (153 bp):
TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTAT
TTTTAAATTTTTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
TGCGAGGTATTCTTTTAAATTTC
Found at i:55807464 original size:231 final size:232
Alignment explanation
Indices: 55806998--55807587 Score: 908
Period size: 231 Copynumber: 2.5 Consensus size: 232
55806988 NNNNNNTTTT
*
55806998 GTTTTTC-GAAATCAACTCCATA-TGCG-AAGGTGAGTTGAG-CTCGGGTCACATGTCGAGGTA-
1 GTTTTTCAAAAATCAACT-CATATTGCGAAAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTAT
** *
55807058 TTC-TTTAAA-TTGCTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTC
65 TTCTTTTAAATTTTTTTTTTCAAGAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTC
55807121 GCATGCCGAGGTATTCTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
130 GCATGCCGAGGTATTCTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
* **
55807186 TGAGCCTCGGGTCTCACGCTGAGGTATTTTAAATTTTT
195 TGAGCCTCGAGTCTCACGCTGAGGTATTTTAAATTTCC
55807224 GTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATT
1 GTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATT
55807289 TCTTTTAAATTTTTTTTTTC-AGAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCG
66 TCTTTTAAATTTTTTTTTTCAAGAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCG
55807353 CATGCCGAGGTATTCTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
131 CATGCCGAGGTATTCTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
55807418 GAGCCTCGAGTCTCACGCTGAGGTATTTTAAATTTCC
196 GAGCCTCGAGTCTCACGCTGAGGTATTTTAAATTTCC
* ** *
55807455 GTTTTTCAAAAATGAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGTCACATGCCGAGGTATT
1 GTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATT
* *
55807520 TCTTTTTAATTTTTGCTTTTCAAAAAAAAAGAGAAATCAACTCATATTGCGAGAGGTGAGTTGAG
66 TCTTTTAAATTTTT-TTTTTC--------A-AGAAATCAACTCATATTGCGAGAGGTGAGTTGAG
55807585 CCT
121 CCT
55807588 CGGTTGCACG
Statistics
Matches: 333, Mismatches: 13, Indels: 20
0.91 0.04 0.05
Matches are distributed among these distances:
226 11 0.03
227 13 0.04
228 13 0.04
229 21 0.06
230 3 0.01
231 222 0.67
232 13 0.04
242 37 0.11
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (232 bp):
GTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATT
TCTTTTAAATTTTTTTTTTCAAGAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCG
CATGCCGAGGTATTCTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
GAGCCTCGAGTCTCACGCTGAGGTATTTTAAATTTCC
Found at i:55807802 original size:30 final size:30
Alignment explanation
Indices: 55807762--55807894 Score: 119
Period size: 30 Copynumber: 4.4 Consensus size: 30
55807752 TGTGTTTAAA
55807762 AAAATTTACATTTTAACCCCTAAAATTTTTC
1 AAAA-TTACATTTTAACCCCTAAAATTTTTC
* * *
55807793 AAAATTACATATCAACCTCTAAACA-TTTT-
1 AAAATTACATTTTAACCCCTAAA-ATTTTTC
* * * * * *
55807822 GAAATTACATTTTGACCTCTGAACTTTCTC
1 AAAATTACATTTTAACCCCTAAAATTTTTC
*
55807852 GAAATTACATTTTAACCCCT-AAATTTTCTC
1 AAAATTACATTTTAACCCCTAAAATTTT-TC
*
55807882 AAAATTATATTTT
1 AAAATTACATTTT
55807895 GGCCTCAGAA
Statistics
Matches: 82, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
29 26 0.32
30 51 0.62
31 5 0.06
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.41
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAAATTTTTC
Found at i:55808423 original size:17 final size:17
Alignment explanation
Indices: 55808401--55808435 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55808391 GGTCTGAACG
55808401 AAGGAGAAGAAAAA-AGA
1 AAGGAGAA-AAAAAGAGA
55808418 AAGGAGAAAAAAAGAGA
1 AAGGAGAAAAAAAGAGA
55808435 A
1 A
55808436 GAAAGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AAGGAGAAAAAAAGAGA
Found at i:55808440 original size:24 final size:24
Alignment explanation
Indices: 55808408--55808477 Score: 65
Period size: 26 Copynumber: 2.9 Consensus size: 24
55808398 ACGAAGGAGA
*
55808408 AGAAAAAAGAAAGGAGAAAAAAAG
1 AGAAGAAAGAAAGGAGAAAAAAAG
55808432 AGAAGAAAGAAGAAGGA-AGAAAAAAG
1 AGAAGAAAG-A-AAGGAGA-AAAAAAG
* *
55808458 AG-GGAAAGAAA-AAGAAAAAA
1 AGAAGAAAGAAAGGAGAAAAAA
55808478 GAAAAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
22 6 0.15
23 3 0.08
24 9 0.23
25 7 0.18
26 14 0.36
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (24 bp):
AGAAGAAAGAAAGGAGAAAAAAAG
Found at i:55808463 original size:14 final size:14
Alignment explanation
Indices: 55808406--55808484 Score: 67
Period size: 14 Copynumber: 5.7 Consensus size: 14
55808396 GAACGAAGGA
55808406 GAAGAAAAAAGAAAG
1 GAAGAAAAAAG-AAG
55808421 G-AG-AAAAA-AAG
1 GAAGAAAAAAGAAG
*
55808432 AGAAGAAAGAAGAAG
1 -GAAGAAAAAAGAAG
*
55808447 GAAGAAAAAAGAGG
1 GAAGAAAAAAGAAG
*
55808461 GAA-AGAAAAAGAAA
1 GAAGA-AAAAAGAAG
*
55808475 AAAGAAAAAA
1 GAAGAAAAAA
55808485 ATTAAATCAG
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
11 3 0.06
12 1 0.02
13 8 0.15
14 35 0.67
15 5 0.10
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
GAAGAAAAAAGAAG
Found at i:55808485 original size:8 final size:7
Alignment explanation
Indices: 55808407--55808484 Score: 52
Period size: 7 Copynumber: 11.3 Consensus size: 7
55808397 AACGAAGGAG
55808407 AAGAAAA
1 AAGAAAA
*
55808414 AAGAAAG
1 AAGAAAA
*
55808421 GAGAAAA
1 AAGAAAA
* *
55808428 AA-AGAG
1 AAGAAAA
*
55808434 AAGAAAG
1 AAGAAAA
**
55808441 AAGAAGG
1 AAGAAAA
55808448 AAGAAAA
1 AAGAAAA
**
55808455 AAGAGGGA
1 AAGA-AAA
55808463 AAG-AAA
1 AAGAAAA
55808469 AAGAAAA
1 AAGAAAA
55808476 AAGAAAA
1 AAGAAAA
55808483 AA
1 AA
55808485 ATTAAATCAG
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
6 8 0.15
7 42 0.78
8 4 0.07
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:55808614 original size:17 final size:16
Alignment explanation
Indices: 55808582--55808615 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55808572 TAGCAGCCCA
55808582 AAAAAAAAAGAAAAGC
1 AAAAAAAAAGAAAAGC
*
55808598 AAAAAAGAAGAAGAAGC
1 AAAAAAAAAGAA-AAGC
55808615 A
1 A
55808616 GACCACTTAT
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:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAGC
Found at i:55808787 original size:11 final size:11
Alignment explanation
Indices: 55808771--55808853 Score: 75
Period size: 12 Copynumber: 7.7 Consensus size: 11
55808761 AGCCCAGTCC
55808771 AAAAAAAGAG-
1 AAAAAAAGAGA
55808781 AAAAAAA-A-A
1 AAAAAAAGAGA
*
55808790 AGAAAAAGAGA
1 AAAAAAAGAGA
**
55808801 GGAAAAA-AGA
1 AAAAAAAGAGA
55808811 AAAAAAAGAGA
1 AAAAAAAGAGA
*
55808822 AGAAAAAAGAAA
1 A-AAAAAAGAGA
55808834 AAAAAAAGAAGA
1 AAAAAAAG-AGA
*
55808846 AGAAAAAG
1 AAAAAAAG
55808854 GGGGTTCAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
9 7 0.12
10 16 0.27
11 18 0.30
12 19 0.32
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAGA
Found at i:55808806 original size:18 final size:18
Alignment explanation
Indices: 55808773--55808853 Score: 74
Period size: 18 Copynumber: 4.3 Consensus size: 18
55808763 CCCAGTCCAA
*
55808773 AAAAAGAGAAAAAAAAAAG
1 AAAAAGAG-AAGAAAAAAG
*
55808792 AAAAAGAGAGGAAAAAAG
1 AAAAAGAGAAGAAAAAAG
55808810 AAAAAAAAGAGAAGAAAAAAG
1 ---AAAAAGAGAAGAAAAAAG
* * *
55808831 AAAAAAAAAAG-AAGAAG
1 AAAAAGAGAAGAAAAAAG
55808848 AAAAAG
1 AAAAAG
55808854 GGGGTTCAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
17 10 0.19
18 17 0.33
19 8 0.15
21 17 0.33
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAGAAGAAAAAAG
Found at i:55808813 original size:24 final size:23
Alignment explanation
Indices: 55808771--55808852 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 23
55808761 AGCCCAGTCC
55808771 AAAAAA-AG-AGAAAAAA-AAAA
1 AAAAAAGAGAAGAAAAAAGAAAA
* *
55808791 GAAAAAGAGAGGAAAAAAG--AA
1 AAAAAAGAGAAGAAAAAAGAAAA
55808812 AAAAAAGAGAAGAAAAAAGAAAA
1 AAAAAAGAGAAGAAAAAAGAAAA
55808835 AAAAAAGAAGAAGAAAAA
1 AAAAAAG-AGAAGAAAAA
55808853 GGGGGTTCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
20 5 0.10
21 21 0.40
22 7 0.13
23 9 0.17
24 10 0.19
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AAAAAAGAGAAGAAAAAAGAAAA
Found at i:55809202 original size:16 final size:16
Alignment explanation
Indices: 55809183--55809249 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 16
55809173 AAAAAAATCC
*
55809183 TCGTGTTTCGAAATTT
1 TCGTGTTTCAAAATTT
55809199 TCGTGTCTTCAAAAAATTTT
1 TCGTGT-TTC--AAAA-TTT
*
55809219 CTCGTGTTTCAAAATTC
1 -TCGTGTTTCAAAATTT
55809236 TCGTGTTTTCAAAA
1 TCGTG-TTTCAAAA
55809250 ATAAGGCAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
16 11 0.26
17 13 0.30
18 4 0.09
19 3 0.07
20 6 0.14
21 6 0.14
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (16 bp):
TCGTGTTTCAAAATTT
Found at i:55809213 original size:37 final size:37
Alignment explanation
Indices: 55809172--55809250 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
55809162 TAAATTTTCA
* *
55809172 AAAAAAAATCCTCGTGTTTCGAAATTTTCGTGTCTTC
1 AAAAAAAATCCTCGTGTTTCAAAATTCTCGTGTCTTC
** * *
55809209 AAAAAATTTTCTCGTGTTTCAAAATTCTCGTGTTTTC
1 AAAAAAAATCCTCGTGTTTCAAAATTCTCGTGTCTTC
55809246 AAAAA
1 AAAAA
55809251 TAAGGCAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.39
Consensus pattern (37 bp):
AAAAAAAATCCTCGTGTTTCAAAATTCTCGTGTCTTC
Found at i:55809250 original size:18 final size:17
Alignment explanation
Indices: 55809175--55809251 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 17
55809165 ATTTTCAAAA
*
55809175 AAAAATCCTCGTGTTTC
1 AAAAATTCTCGTGTTTC
* *
55809192 -GAAATTTTCGTGTCTTC
1 AAAAATTCTCGTGT-TTC
55809209 AAAAAATTTTCTCGTGTTTC
1 -AAAAA--TTCTCGTGTTTC
55809229 -AAAATTCTCGTGTTTTC
1 AAAAATTCTCGTG-TTTC
55809246 AAAAAT
1 AAAAAT
55809252 AAGGCAACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
16 18 0.38
17 7 0.15
18 9 0.19
19 3 0.06
20 3 0.06
21 8 0.17
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.42
Consensus pattern (17 bp):
AAAAATTCTCGTGTTTC
Found at i:55809423 original size:36 final size:35
Alignment explanation
Indices: 55809380--55809555 Score: 171
Period size: 36 Copynumber: 5.0 Consensus size: 35
55809370 AAAAAATCCA
**
55809380 GTGTTTTCAAAAATTTCCAT-TTTCCAAATTTTTTTC
1 GTGTTTTCAAAAATTTCCATGTTT-CAAA-AATTTTC
**
55809416 GTGTTTTCTAAAAATTTCTGTGTTTCAAAAATTTTC
1 GTGTTTTC-AAAAATTTCCATGTTTCAAAAATTTTC
* *
55809452 GTGTTTTCAAAAATTTTCGTAT-TTTCAAAAAATTTC
1 GTGTTTTCAAAAA-TTTC-CATGTTTCAAAAATTTTC
* * * *
55809488 GTGTTTTCAACAA-TTCTCATGTTTCTAGAATTCTC
1 GTGTTTTCAAAAATTTC-CATGTTTCAAAAATTTTC
*
55809523 GTG-TTTCAAAAATTTCCGTGTTTCAAAAATTTT
1 GTGTTTTCAAAAATTTCCATGTTTCAAAAATTTT
55809556 GCTTCAAAAT
Statistics
Matches: 116, Mismatches: 18, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
34 26 0.22
35 21 0.18
36 50 0.43
37 16 0.14
38 3 0.03
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (35 bp):
GTGTTTTCAAAAATTTCCATGTTTCAAAAATTTTC
Found at i:55809441 original size:18 final size:19
Alignment explanation
Indices: 55809414--55809554 Score: 103
Period size: 18 Copynumber: 7.9 Consensus size: 19
55809404 CAAATTTTTT
55809414 TCGTGTTTTCTAAAAATTTC
1 TCGTG-TTTCTAAAAATTTC
55809434 T-GTGTTTC-AAAAATTT-
1 TCGTGTTTCTAAAAATTTC
55809450 TCGTGTTT-TCAAAAATTT-
1 TCGTGTTTCT-AAAAATTTC
* *
55809468 TCGTATTT-TCAAAAAATT-
1 TCGTGTTTCT-AAAAATTTC
*
55809486 TCGTGTTT-TCAACAA-TTC
1 TCGTGTTTCT-AAAAATTTC
* *
55809504 TCATGTTTCT-AGAA-TTC
1 TCGTGTTTCTAAAAATTTC
55809521 TCGTGTTTC-AAAAATTTC
1 TCGTGTTTCTAAAAATTTC
55809539 -CGTGTTTC-AAAAATTT
1 TCGTGTTTCTAAAAATTT
55809555 TGCTTCAAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
16 1 0.01
17 49 0.46
18 51 0.48
19 4 0.04
20 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (19 bp):
TCGTGTTTCTAAAAATTTC
Found at i:55809447 original size:17 final size:18
Alignment explanation
Indices: 55809384--55809554 Score: 135
Period size: 17 Copynumber: 9.7 Consensus size: 18
55809374 AATCCAGTGT
*
55809384 TTTCAAAAATTTC-CAT-
1 TTTCAAAAATTTCTCGTG
** *
55809400 TTTCCAAATTTTTTTCGTG
1 TTT-CAAAAATTTCTCGTG
55809419 TTTTCTAAAAATTTCT-GTG
1 -TTTC-AAAAATTTCTCGTG
55809438 TTTCAAAAATTT-TCGTG
1 TTTCAAAAATTTCTCGTG
*
55809455 TTTTCAAAAATTT-TCGTAT
1 -TTTCAAAAATTTCTCGT-G
*
55809474 TTTCAAAAAATT-TCGTG
1 TTTCAAAAATTTCTCGTG
* *
55809491 TTTTCAACAA-TTCTCATG
1 -TTTCAAAAATTTCTCGTG
* *
55809509 TTTCTAGAA-TTCTCGTG
1 TTTCAAAAATTTCTCGTG
55809526 TTTCAAAAATTTC-CGTG
1 TTTCAAAAATTTCTCGTG
55809543 TTTCAAAAATTT
1 TTTCAAAAATTT
55809555 TGCTTCAAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
16 4 0.03
17 57 0.45
18 52 0.41
19 4 0.03
20 10 0.08
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.48
Consensus pattern (18 bp):
TTTCAAAAATTTCTCGTG
Found at i:55810067 original size:26 final size:24
Alignment explanation
Indices: 55810031--55810081 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 24
55810021 CTCTACCAAA
55810031 ATTAAATTTAAATAATAAAAATATAT
1 ATTAAATTT-AATAAT-AAAATATAT
*
55810057 ATTAAATTTAATTATAAAATATAT
1 ATTAAATTTAATAATAAAATATAT
55810081 A
1 A
55810082 AATATCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
25 5 0.21
26 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATTAAATTTAATAATAAAATATAT
Found at i:55819525 original size:9 final size:9
Alignment explanation
Indices: 55819507--55819567 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
55819497 TTATCTAAAT
*
55819507 TTTTTAATA
1 TTTTTCATA
55819516 TTTTTCATA
1 TTTTTCATA
*
55819525 TATTTCTATAA
1 TTTTTC-AT-A
55819536 TTTTTCATA
1 TTTTTCATA
*
55819545 TTTCTACA-A
1 TTT-TTCATA
55819554 TTTTTTCATA
1 -TTTTTCATA
55819564 TTTT
1 TTTT
55819568 ATGATTTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
9 25 0.60
10 11 0.26
11 6 0.14
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTTCATA
Found at i:55819540 original size:20 final size:20
Alignment explanation
Indices: 55819515--55819564 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
55819505 ATTTTTTAAT
*
55819515 ATTTTTCATATATTTCTATA
1 ATTTTTCATATATTTCTACA
55819535 ATTTTTC--ATATTTCTACA
1 ATTTTTCATATATTTCTACA
55819553 ATTTTTTCATAT
1 A-TTTTTCATAT
55819565 TTTATGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 11 0.42
19 6 0.23
20 7 0.27
21 2 0.08
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTCATATATTTCTACA
Found at i:55819547 original size:18 final size:18
Alignment explanation
Indices: 55819524--55819575 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
55819514 TATTTTTCAT
55819524 ATATTTCTATAATTTTTC
1 ATATTTCTATAATTTTTC
*
55819542 ATATTTCTACAATTTTTTC
1 ATATTTCTATAA-TTTTTC
*
55819561 ATATTT-TATGATTTT
1 ATATTTCTATAATTTT
55819576 CATTGAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 4 0.13
18 14 0.47
19 12 0.40
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.62
Consensus pattern (18 bp):
ATATTTCTATAATTTTTC
Found at i:55819558 original size:19 final size:18
Alignment explanation
Indices: 55819524--55819566 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
55819514 TATTTTTCAT
*
55819524 ATATTTCTATAATTTTTC
1 ATATTTCTACAATTTTTC
55819542 ATATTTCTACAATTTTTTC
1 ATATTTCTACAA-TTTTTC
55819561 ATATTT
1 ATATTT
55819567 TATGATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTTCTACAATTTTTC
Found at i:55822171 original size:18 final size:21
Alignment explanation
Indices: 55822148--55822191 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
55822138 CATATACATG
55822148 CATACA-TTTT-A-TAATACA
1 CATACATTTTTAATTAATACA
55822166 CATACATTTTTAATTAATACA
1 CATACATTTTTAATTAATACA
55822187 CATAC
1 CATAC
55822192 TTACACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
19 4 0.17
20 1 0.04
21 12 0.52
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (21 bp):
CATACATTTTTAATTAATACA
Found at i:55822233 original size:2 final size:2
Alignment explanation
Indices: 55822226--55822255 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
55822216 CTATATGCAT
*
55822226 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55822256 CATAAGTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55823000 original size:106 final size:108
Alignment explanation
Indices: 55822736--55823044 Score: 338
Period size: 106 Copynumber: 2.9 Consensus size: 108
55822726 AAAAGAAAAT
* * * *
55822736 TTTCTAAATAAGGCAATGTTTTGCGTTTGGAAAATCGAGAAAATGTACCCTAACGTGTTGGGTTT
1 TTTCAAAACAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAACGTGTTGGGTTT
* * *
55822801 CGATTTCTAGTTCGACCAAAATAGCCAAATACCCTTTTTAAAC
66 CGATTACTAGTTCGACCAAAATAGCCAAATACCATTTTGAAAC
* * * * * * *
55822844 TTTCAAAATAAGACCATATTTCGCGTTTGGAAATTTGAGAAAATGTGCCCTAACATGTTGGGTTT
1 TTTCAAAACAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAACGTGTTGGGTTT
* * * * * *
55822909 CGATTACTCGTTTGGCC-AAATAGTCGAATATCATTTTGAAA-
66 CGATTACTAGTTCGACCAAAATAGCCAAATACCATTTTGAAAC
* * * *
55822950 TTTTAAAACGAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTCAAAACAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAACGTGTTGGGTTT
* * *
55823015 CGATTTA-TCGTTCGA-CTAAATAGCGAAATA
66 CGA-TTACTAGTTCGACCAAAATAGCCAAATA
55823045 TCCTCTTAAA
Statistics
Matches: 165, Mismatches: 34, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
105 1 0.01
106 73 0.44
107 22 0.13
108 69 0.42
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (108 bp):
TTTCAAAACAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAACGTGTTGGGTTT
CGATTACTAGTTCGACCAAAATAGCCAAATACCATTTTGAAAC
Found at i:55823910 original size:67 final size:68
Alignment explanation
Indices: 55823821--55823959 Score: 192
Period size: 69 Copynumber: 2.0 Consensus size: 68
55823811 GATTTTTTTC
* *
55823821 TTAAAGGATTATTAAACTTATAAACCTGTG-TTTTTTAAGGGATAAATCTTAAAGA-TATACATG
1 TTAAAGGATTATTAAACTTATAAACCTGTGTTTTTTTAAGGGATAAATATCAAA-ACTATACATG
55823884 AAAT
65 AAAT
* * *
55823888 TTAAGGGATTTTTAAACTTATAAACCTGTGTTTTTTTTTAGGGATAAATATCAAAACTATACATG
1 TTAAAGGATTATTAAACTTATAAACCTGTG-TTTTTTTAAGGGATAAATATCAAAACTATACATG
*
55823953 AACT
65 AAAT
55823957 TTA
1 TTA
55823960 GTCTAATGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
67 28 0.44
68 1 0.02
69 34 0.54
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.40
Consensus pattern (68 bp):
TTAAAGGATTATTAAACTTATAAACCTGTGTTTTTTTAAGGGATAAATATCAAAACTATACATGA
AAT
Found at i:55823982 original size:31 final size:29
Alignment explanation
Indices: 55823945--55824014 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
55823935 ATATCAAAAC
*
55823945 TATACATGAACTTTAGTCTAATGTGCAATTCT
1 TATACATGAACTTT-GACT-ATGTGCAATT-T
* *
55823977 T-TACATGTACTTTGACTTTGTGCAATTT
1 TATACATGAACTTTGACTATGTGCAATTT
55824005 TATACATGAA
1 TATACATGAA
55824015 ATTTTGATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 2 0.06
29 16 0.48
30 3 0.09
31 11 0.33
32 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (29 bp):
TATACATGAACTTTGACTATGTGCAATTT
Found at i:55826198 original size:13 final size:14
Alignment explanation
Indices: 55826170--55826218 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
55826160 TTTTAAAATA
55826170 TTTTTAAAATACTT
1 TTTTTAAAATACTT
**
55826184 TTTTTAAAATTTTTT
1 TTTTTAAAA-TACTT
*
55826199 ATTTTTAAAATAATT
1 -TTTTTAAAATACTT
55826214 TTTTT
1 TTTTT
55826219 GTATTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 14 0.48
15 6 0.21
16 9 0.31
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTAAAATACTT
Found at i:55831344 original size:23 final size:22
Alignment explanation
Indices: 55831306--55831348 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
55831296 AAATTATAAA
*
55831306 ATATAAAAAGATATATATGTTC
1 ATATAAAAAAATATATATGTTC
55831328 ATATAAGAAAAATATATATGT
1 ATATAA-AAAAATATATATGT
55831349 ATGTGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.35
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTTC
Found at i:55831526 original size:28 final size:26
Alignment explanation
Indices: 55831495--55831558 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 26
55831485 ATTTATAAAA
55831495 ATTAAAAAATATGTACGTCTATGTATAT
1 ATTAAAAAATATGTACG-C-ATGTATAT
*
55831523 ATT-ATAAA-ATGTACGCATGTATAT
1 ATTAAAAAATATGTACGCATGTATAT
55831547 ATATAACAAAAT
1 AT-TAA-AAAAT
55831559 TTGAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
24 10 0.33
25 2 0.07
26 8 0.27
27 7 0.23
28 3 0.10
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (26 bp):
ATTAAAAAATATGTACGCATGTATAT
Found at i:55831545 original size:24 final size:25
Alignment explanation
Indices: 55831505--55831552 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
55831495 ATTAAAAAAT
55831505 ATGTACGTCTATGTATATATTATAAA
1 ATGTACGTCTATGTATATA-TATAAA
55831531 ATGTACG-C-ATGTATATATATAA
1 ATGTACGTCTATGTATATATATAA
55831553 CAAAATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.23
24 9 0.41
25 1 0.05
26 7 0.32
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (25 bp):
ATGTACGTCTATGTATATATATAAA
Found at i:55831557 original size:26 final size:26
Alignment explanation
Indices: 55831505--55831558 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
55831495 ATTAAAAAAT
*
55831505 ATGTACGTCTATGTATATATTATAAA
1 ATGTACGTCTATGTATATATTACAAA
55831531 ATGTACG-C-ATGTATATATATAACAAA
1 ATGTACGTCTATGTATATAT-T-ACAAA
55831557 AT
1 AT
55831559 TTGAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 10 0.40
25 2 0.08
26 13 0.52
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (26 bp):
ATGTACGTCTATGTATATATTACAAA
Found at i:55833405 original size:13 final size:13
Alignment explanation
Indices: 55833387--55833411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55833377 CTTAACCAAC
55833387 AAACAAAAAAACA
1 AAACAAAAAAACA
55833400 AAACAAAAAAAC
1 AAACAAAAAAAC
55833412 CCTAGCCCTA
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:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACAAAAAAACA
Found at i:55834523 original size:15 final size:14
Alignment explanation
Indices: 55834492--55834533 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 14
55834482 TTTCGGTTTG
55834492 TTTGTT-TTATTA-
1 TTTGTTGTTATTAT
55834504 TTTGTTGTTATTAT
1 TTTGTTGTTATTAT
55834518 TGTTGTTGTTATTAT
1 T-TTGTTGTTATTAT
55834533 T
1 T
55834534 ATTATCACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.22
13 6 0.22
14 1 0.04
15 14 0.52
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (14 bp):
TTTGTTGTTATTAT
Found at i:55834683 original size:22 final size:22
Alignment explanation
Indices: 55834643--55834749 Score: 77
Period size: 22 Copynumber: 5.0 Consensus size: 22
55834633 TAATATTTTC
55834643 TTATTATGCGTTGTATTATTTATTG
1 TTATTAT-CGTTG--TTATTTATTG
55834668 TTATTATCGTTGTTATTTATTG
1 TTATTATCGTTGTTATTTATTG
55834690 ----T-T-GTTGTTA-TTATTG
1 TTATTATCGTTGTTATTTATTG
*
55834705 TTATTTATTGTT-TTATTTATTG
1 TTA-TTATCGTTGTTATTTATTG
* *
55834727 TTATTTATTGTTATTATGTTATT
1 TTA-TTATCGTTGTTAT-TTATT
55834750 TATTGATGTC
Statistics
Matches: 72, Mismatches: 0, Indels: 21
0.77 0.00 0.23
Matches are distributed among these distances:
15 6 0.08
16 7 0.10
17 1 0.01
18 1 0.01
20 1 0.01
21 4 0.06
22 31 0.43
23 4 0.06
24 10 0.14
25 7 0.10
ACGTcount: A:0.19, C:0.02, G:0.13, T:0.66
Consensus pattern (22 bp):
TTATTATCGTTGTTATTTATTG
Found at i:55834693 original size:25 final size:25
Alignment explanation
Indices: 55834665--55834743 Score: 101
Period size: 25 Copynumber: 3.3 Consensus size: 25
55834655 GTATTATTTA
*
55834665 TTGTTATTATCGTTGTTATTTATTG
1 TTGTTATTATCATTGTTATTTATTG
* *
55834690 TTGTTGTTATTATTGTTATTTATTG
1 TTGTTATTATCATTGTTATTTATTG
55834715 TT-TTATT-T-ATTGTTATTTATTG
1 TTGTTATTATCATTGTTATTTATTG
*
55834737 TTATTAT
1 TTGTTAT
55834744 GTTATTTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.33
23 5 0.10
24 4 0.08
25 24 0.49
ACGTcount: A:0.18, C:0.01, G:0.13, T:0.68
Consensus pattern (25 bp):
TTGTTATTATCATTGTTATTTATTG
Found at i:55834693 original size:37 final size:37
Alignment explanation
Indices: 55834652--55834752 Score: 107
Period size: 37 Copynumber: 2.6 Consensus size: 37
55834642 CTTATTATGC
55834652 GTTG-TATTATTTATTGTTA-TTATCGTTGTTATTTATT
1 GTTGTTATTA-TTATTGTTATTTATCGTT-TTATTTATT
* *
55834689 GTTGTTGTTATTATTGTTATTTATTGTTTTATTTATT
1 GTTGTTATTATTATTGTTATTTATCGTTTTATTTATT
* *
55834726 GTTATTTATTGTTATTATGTTATTTAT
1 GTT-GTTATTATTA-T-TGTTATTTAT
55834753 TGATGTCTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
37 25 0.46
38 18 0.33
39 1 0.02
40 10 0.19
ACGTcount: A:0.19, C:0.01, G:0.13, T:0.67
Consensus pattern (37 bp):
GTTGTTATTATTATTGTTATTTATCGTTTTATTTATT
Found at i:55834753 original size:22 final size:24
Alignment explanation
Indices: 55834658--55834749 Score: 104
Period size: 22 Copynumber: 4.0 Consensus size: 24
55834648 ATGCGTTGTA
55834658 TTATTTATTGTTATTATCG---TTG
1 TTATTTATTGTTATTAT-GTTATTG
* * *
55834680 TTATTTATTGTTGTTGTTATTATTG
1 TTATTTATTGTTATT-ATGTTATTG
55834705 TTATTTATTGTT-TTAT-TTATTG
1 TTATTTATTGTTATTATGTTATTG
55834727 TTATTTATTGTTATTATGTTATT
1 TTATTTATTGTTATTATGTTATT
55834750 TATTGATGTC
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
22 32 0.53
23 6 0.10
24 7 0.12
25 15 0.25
ACGTcount: A:0.18, C:0.01, G:0.12, T:0.68
Consensus pattern (24 bp):
TTATTTATTGTTATTATGTTATTG
Found at i:55843436 original size:2 final size:2
Alignment explanation
Indices: 55843425--55843453 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
55843415 ATTAGAGAAT
55843425 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55843454 AATCAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:55843575 original size:37 final size:35
Alignment explanation
Indices: 55843467--55843578 Score: 100
Period size: 39 Copynumber: 3.1 Consensus size: 35
55843457 CAGAAAAAAG
* * *
55843467 AATTATCAAAAAATATAAGAATTATTAAA-TATCAA
1 AATTATAAAAAAATATAAGATTTAATAAATTAT-AA
* * * *
55843502 AATAATAAAAATATATGAAAATTAATATAAACTTATAA
1 AATTATAAAAAAATAT-AAGATTTA-ATAAA-TTATAA
55843540 ATATTATAAAAAAATATAAGATTCTAATAAATTATAA
1 A-ATTATAAAAAAATATAAGATT-TAATAAATTATAA
55843577 AA
1 AA
55843579 AAATCTTTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
35 13 0.22
36 6 0.10
37 11 0.18
38 13 0.22
39 17 0.28
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (35 bp):
AATTATAAAAAAATATAAGATTTAATAAATTATAA
Found at i:55843597 original size:22 final size:23
Alignment explanation
Indices: 55843571--55843624 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
55843561 TTCTAATAAA
*
55843571 TTATAAAAAAATCT-TTAAAATT
1 TTATAAAAAAAACTATTAAAATT
*
55843593 TTATAAAAAAAAGTATTAAAATT
1 TTATAAAAAAAACTATTAAAATT
*
55843616 ATATAAAAA
1 TTATAAAAA
55843625 CCATCAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
TTATAAAAAAAACTATTAAAATT
Found at i:55843679 original size:39 final size:38
Alignment explanation
Indices: 55843598--55843696 Score: 101
Period size: 39 Copynumber: 2.5 Consensus size: 38
55843588 AAATTTTATA
*
55843598 AAAAAAAGTATTAAAATTATATAAAAACCATCAAAACAAT
1 AAAAAAA-TATTAAAATTATAT-AAAACCATAAAAACAAT
* **
55843638 AAAAATATATTAAAATTGATAT-AAACCTATAAAAATTAT
1 AAAAAAATATTAAAATT-ATATAAAACC-ATAAAAACAAT
55843677 AAAAAAATAATATAAAATTA
1 AAAAAAAT-AT-TAAAATTA
55843697 AACTAGACAG
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
38 5 0.10
39 25 0.50
40 13 0.26
41 7 0.14
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (38 bp):
AAAAAAATATTAAAATTATATAAAACCATAAAAACAAT
Found at i:55848314 original size:7 final size:7
Alignment explanation
Indices: 55848302--55848326 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55848292 TACGCTACTG
55848302 AATATAA
1 AATATAA
55848309 AATATAA
1 AATATAA
55848316 AATATAA
1 AATATAA
55848323 AATA
1 AATA
55848327 GATATTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATATAA
Found at i:55861855 original size:87 final size:87
Alignment explanation
Indices: 55861689--55861879 Score: 210
Period size: 87 Copynumber: 2.2 Consensus size: 87
55861679 CCAGTTTGTG
* **
55861689 GATGAACCACCAGTGTCTGCAGATAAACTACCAGTAGGTGATGAATGCACAATGTATTTGCAGAT
1 GATGAACCACCAGTGTTTGCAGATAAACTACCAGTAGGTGATGAATGCACAACATATTTGCAGAT
**
55861754 AAAAGTTGTCAGTAAGATT-GCA
66 AAAAGTACTCAGTAA-ATTCGCA
* * * *
55861776 GATGAACCACCAGTGTTTGTAGATAAACTGCCAGTAGGTTG-TGAGTGCACAACATAATTT-TAG
1 GATGAACCACCAGTGTTTGCAGATAAACTACCAGTAGG-TGATGAATGCACAACAT-ATTTGCAG
**
55861839 ATAAAAGCTACT-AGTAAATTCGTG
64 ATAAAAG-TACTCAGTAAATTCGCA
*
55861863 GATAAACCACCAGTGTT
1 GATGAACCACCAGTGTT
55861880 GCTGATTATT
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
86 3 0.03
87 77 0.88
88 8 0.09
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (87 bp):
GATGAACCACCAGTGTTTGCAGATAAACTACCAGTAGGTGATGAATGCACAACATATTTGCAGAT
AAAAGTACTCAGTAAATTCGCA
Found at i:55862025 original size:38 final size:38
Alignment explanation
Indices: 55861974--55862071 Score: 142
Period size: 38 Copynumber: 2.6 Consensus size: 38
55861964 ACAAGAACAA
*
55861974 TAGACATGCTTAACATGTATTCGGTTCAACAATAGTAG
1 TAGACATGCTTAACATGTATTCGGTTCAACAATAATAG
* * *
55862012 TAGACATGCTTAACATGTATTAGGTTTAATAATAATAG
1 TAGACATGCTTAACATGTATTCGGTTCAACAATAATAG
* *
55862050 TAGGCATGTTTAACATGTATTC
1 TAGACATGCTTAACATGTATTC
55862072 AATTTAATAG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (38 bp):
TAGACATGCTTAACATGTATTCGGTTCAACAATAATAG
Found at i:55862275 original size:13 final size:13
Alignment explanation
Indices: 55862257--55862281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55862247 GAATTAATAT
55862257 GTGTGAAAATTTC
1 GTGTGAAAATTTC
55862270 GTGTGAAAATTT
1 GTGTGAAAATTT
55862282 TATTGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:55863437 original size:43 final size:42
Alignment explanation
Indices: 55863374--55863499 Score: 130
Period size: 43 Copynumber: 2.9 Consensus size: 42
55863364 AGGATTCCGT
*
55863374 TATGTGTTATCGTGTAAGACCATGTCTGGGACGTTGGCATCAAC
1 TATGTGTTA-CGTGTAAGACCATGTTTGGGACGTTGGCATC-AC
* **
55863418 T-TGTGTTTACGTGTAAGACCCTGTTTGGGACAG-TGGCATCGT
1 TATGTG-TTACGTGTAAGACCATGTTTGGGAC-GTTGGCATCAC
* * *
55863460 TATGTGATTACATGTAAGACCACGTTTGGGATGTTGGCAT
1 TATGTG-TTACGTGTAAGACCATGTTTGGGACGTTGGCAT
55863500 TGTAAAATAT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
42 2 0.03
43 62 0.90
44 5 0.07
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (42 bp):
TATGTGTTACGTGTAAGACCATGTTTGGGACGTTGGCATCAC
Found at i:55864499 original size:23 final size:23
Alignment explanation
Indices: 55864464--55864780 Score: 393
Period size: 23 Copynumber: 13.7 Consensus size: 23
55864454 TAGGTATATA
*
55864464 TATATATGCTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* *
55864487 TATAAATGTTGTCCAATTTAGTG
1 TATAAATGCTGTCCAATTTGGTG
*
55864510 TATAAATTGCTGTCCAATTTAGTG
1 TATAAA-TGCTGTCCAATTTGGTG
*
55864534 TATATATGCT-TCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
*
55864556 TATAAAATGTTGTCCAATTTGGTG
1 TAT-AAATGCTGTCCAATTTGGTG
55864580 TATAAATGCTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
*
55864603 TATATATGCTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* *
55864626 TATATATGCTATCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* *
55864649 TATAAAATGCTATCCGATTTGGTG
1 TAT-AAATGCTGTCCAATTTGGTG
*
55864673 TATAAATGCTATCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* *
55864696 TATATATGCTGTCCAATTTGGTA
1 TATAAATGCTGTCCAATTTGGTG
* * * *
55864719 TATATATGCTGTCCGATTGGGTA
1 TATAAATGCTGTCCAATTTGGTG
* * *
55864742 TATAAATGATGTCCGATTTGATG
1 TATAAATGCTGTCCAATTTGGTG
* *
55864765 TATAAAAGCTATCCAA
1 TATAAATGCTGTCCAA
55864781 ACAGGGTAGA
Statistics
Matches: 262, Mismatches: 28, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
22 14 0.05
23 191 0.73
24 57 0.22
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (23 bp):
TATAAATGCTGTCCAATTTGGTG
Found at i:55864567 original size:70 final size:70
Alignment explanation
Indices: 55864464--55864780 Score: 397
Period size: 70 Copynumber: 4.6 Consensus size: 70
55864454 TAGGTATATA
* *
55864464 TATATATGCTGTCCAATTTGGTGTATAAATGTTGTCCAATTTAGTGTATAAATTGCTGTCCAATT
1 TATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATTGCTGTCCAATT
*
55864529 TAGTG
66 TGGTG
*
55864534 TATATATGCT-TCCAATTTGGTGTATAAAATGTTGTCCAATTTGGTGTATAAA-TGCTGTCCAAT
1 TATATATGCTGTCCAATTTGGTGTAT-AAATGCTGTCCAATTTGGTGTATAAATTGCTGTCCAAT
55864597 TTGGTG
65 TTGGTG
* * * * *
55864603 TATATATGCTGTCCAATTTGGTGTATATATGCTATCCAATTTGGTGTATAAAATGCTATCCGATT
1 TATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATTGCTGTCCAATT
55864668 TGGTG
66 TGGTG
* * * * * *
55864673 TATAAATGCTATCCAATTTGGTGTATATATGCTGTCCAATTTGGTATATATA-TGCTGTCCGATT
1 TATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATTGCTGTCCAATT
* *
55864737 GGGTA
66 TGGTG
* * * * * *
55864742 TATAAATGATGTCCGATTTGATGTATAAAAGCTATCCAA
1 TATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAA
55864781 ACAGGGTAGA
Statistics
Matches: 222, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
69 110 0.50
70 112 0.50
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (70 bp):
TATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATTGCTGTCCAATT
TGGTG
Found at i:55864641 original size:93 final size:92
Alignment explanation
Indices: 55864473--55864780 Score: 431
Period size: 93 Copynumber: 3.3 Consensus size: 92
55864463 ATATATATGC
* * * * *
55864473 TGTCCAATTTGGTGTATAAATGTTGTCCAATTTAGTGTATAAATTGCTGTCCAATTTAGTGTATA
1 TGTCCAATTTGGTGTATAAATGCTATCCAATTTGGTGTATATA-TGCTGTCCAATTTGGTGTATA
*
55864538 TATGCTTCCAATTTGGTGTATAAAATGT
65 TATGCTTCCAATTTGGTGTATAAAATGA
*
55864566 TGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATATATGCTGTCCAATTTGGTGTATAT
1 TGTCCAATTTGGTGTATAAATGCTATCCAATTTGGTGTATATATGCTGTCCAATTTGGTGTATAT
*
55864631 ATGCTATCCAATTTGGTGTATAAAATGC
66 ATGCT-TCCAATTTGGTGTATAAAATGA
* * *
55864659 TATCCGATTTGGTGTATAAATGCTATCCAATTTGGTGTATATATGCTGTCCAATTTGGTATATAT
1 TGTCCAATTTGGTGTATAAATGCTATCCAATTTGGTGTATATATGCTGTCCAATTTGGTGTATAT
*
55864724 ATGCTGTCCGA-TTGG-GTATATAAATGA
66 ATGCT-TCCAATTTGGTGTATA-AAATGA
* * *
55864751 TGTCCGATTTGATGTATAAAAGCTATCCAA
1 TGTCCAATTTGGTGTATAAATGCTATCCAA
55864781 ACAGGGTAGA
Statistics
Matches: 198, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
91 5 0.03
92 62 0.31
93 131 0.66
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (92 bp):
TGTCCAATTTGGTGTATAAATGCTATCCAATTTGGTGTATATATGCTGTCCAATTTGGTGTATAT
ATGCTTCCAATTTGGTGTATAAAATGA
Found at i:55864680 original size:116 final size:117
Alignment explanation
Indices: 55864464--55864780 Score: 435
Period size: 116 Copynumber: 2.7 Consensus size: 117
55864454 TAGGTATATA
* * *
55864464 TATATATGCTGTCCAATTTGGTGTATAAATGTTGTCCAATTTAGTGTATAAATTGCTGTCCAATT
1 TATATATGCTGTCCAATTTGGTGTATATATGCTGTCCAATTTGGTGTATAAA-TGCTGTCCAATT
* * * *
55864529 TAGTGTAT-ATATGCT-TCCAATTTGGTGTATAAAATGTTGTCCAATTTGGTG
65 TGGTGTATAAAATGCTATCCAATTTGGTGTATAAAATGCTATCCAATTTGGTG
* * *
55864580 TATAAATGCTGTCCAATTTGGTGTATATATGCTGTCCAATTTGGTGTATATATGCTATCCAATTT
1 TATATATGCTGTCCAATTTGGTGTATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTT
*
55864645 GGTGTATAAAATGCTATCCGATTTGGTGTAT-AAATGCTATCCAATTTGGTG
66 GGTGTATAAAATGCTATCCAATTTGGTGTATAAAATGCTATCCAATTTGGTG
* * * * * *
55864696 TATATATGCTGTCCAATTTGGTATATATATGCTGTCCGATTGGGTATATAAATGATGTCCGATTT
1 TATATATGCTGTCCAATTTGGTGTATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTT
*
55864761 GATGTATAAAA-GCTATCCAA
66 GGTGTATAAAATGCTATCCAA
55864781 ACAGGGTAGA
Statistics
Matches: 177, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
115 26 0.15
116 137 0.77
117 14 0.08
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (117 bp):
TATATATGCTGTCCAATTTGGTGTATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTT
GGTGTATAAAATGCTATCCAATTTGGTGTATAAAATGCTATCCAATTTGGTG
Found at i:55864776 original size:139 final size:139
Alignment explanation
Indices: 55864462--55864780 Score: 433
Period size: 139 Copynumber: 2.3 Consensus size: 139
55864452 ACTAGGTATA
* * * *
55864462 TATATATATGCTGTCCAATTTGGTGTATAAATGTTGTCCAATTTAGTGTATAAATTGCTGTCCAA
1 TATATATATGCTGTCCAATTTGGTGTATAAATGCTATCCAATTTAGTGTATAAAATGCTATCCAA
* * *
55864527 TTTAGTGTATATATGCTTCCAATTTGGTGTATAAAATGTTGTCCAATTTGGTGTATAAATGCTGT
66 TTTAGTGTATAAATGCTTCCAATTTGGTGTATAAAATGCTGTCCAATTTGGTATATAAATGCTGT
*
55864592 CCAATTTGG
131 CCAATTGGG
* * * *
55864601 TGTATATATGCTGTCCAATTTGGTGTATATATGCTATCCAATTTGGTGTATAAAATGCTATCCGA
1 TATATATATGCTGTCCAATTTGGTGTATAAATGCTATCCAATTTAGTGTATAAAATGCTATCCAA
* * *
55864666 TTTGGTGTATAAATGCTATCCAATTTGGTGTAT-ATATGCTGTCCAATTTGGTATATATATGCTG
66 TTTAGTGTATAAATGCT-TCCAATTTGGTGTATAAAATGCTGTCCAATTTGGTATATAAATGCTG
*
55864730 TCCGATTGGG
130 TCCAATTGGG
* * * * *
55864740 TATATAAATGATGTCCGATTTGATGTATAAAAGCTATCCAA
1 TATATATATGCTGTCCAATTTGGTGTATAAATGCTATCCAA
55864781 ACAGGGTAGA
Statistics
Matches: 156, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
139 141 0.90
140 15 0.10
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (139 bp):
TATATATATGCTGTCCAATTTGGTGTATAAATGCTATCCAATTTAGTGTATAAAATGCTATCCAA
TTTAGTGTATAAATGCTTCCAATTTGGTGTATAAAATGCTGTCCAATTTGGTATATAAATGCTGT
CCAATTGGG
Found at i:55866928 original size:3 final size:3
Alignment explanation
Indices: 55866916--55866990 Score: 61
Period size: 3 Copynumber: 25.7 Consensus size: 3
55866906 GTTAATATAG
* *
55866916 TAA T-A TAA TAA TAA TGAA TCAC TAA -AA -AA TAA -AA AAA TAA -AA
1 TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
*
55866958 AAGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
55866991 CAATTAACAA
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
2 10 0.16
3 44 0.72
4 7 0.11
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:55869227 original size:37 final size:37
Alignment explanation
Indices: 55869162--55869270 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
55869152 TACGTATGAT
* *
55869162 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
55869197 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
55869234 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
55869271 TAAAGCTATC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 10 0.14
36 3 0.04
37 56 0.81
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:55869313 original size:52 final size:52
Alignment explanation
Indices: 55869234--55869432 Score: 284
Period size: 52 Copynumber: 3.9 Consensus size: 52
55869224 TAAGTGTAGC
* * **
55869234 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
55869287 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
55869339 CAC---T---TTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
*
55869385 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCAC
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCAC
55869433 NNNNNNNNNN
Statistics
Matches: 131, Mismatches: 9, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
46 43 0.33
49 1 0.01
52 78 0.60
53 9 0.07
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:55869344 original size:98 final size:98
Alignment explanation
Indices: 55869234--55869432 Score: 362
Period size: 98 Copynumber: 2.0 Consensus size: 98
55869224 TAAGTGTAGC
* * *
55869234 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
55869299 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
55869332 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
55869397 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
55869430 CAC
1 CAC
55869433 NNNNNNNNNN
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (98 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:55872736 original size:22 final size:22
Alignment explanation
Indices: 55872709--55872759 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
55872699 CTCTCTAATC
55872709 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
*
55872731 CTCTCAATTTCCTTTCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
55872753 CTCTCAA
1 CTCTCAA
55872760 ACCCATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.41
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:55872984 original size:14 final size:15
Alignment explanation
Indices: 55872965--55872994 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
55872955 TTTGTAATTA
55872965 TTATTTAAG-ATTTT
1 TTATTTAAGTATTTT
55872979 TTATTTAAGTATTTT
1 TTATTTAAGTATTTT
55872994 T
1 T
55872995 AGATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TTATTTAAGTATTTT
Found at i:55873965 original size:7 final size:7
Alignment explanation
Indices: 55873953--55873977 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55873943 AGTCGATTGA
55873953 TATTTAG
1 TATTTAG
55873960 TATTTAG
1 TATTTAG
55873967 TATTTAG
1 TATTTAG
55873974 TATT
1 TATT
55873978 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:55874650 original size:18 final size:18
Alignment explanation
Indices: 55874629--55874663 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55874619 AAGTATGTTT
* *
55874629 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
55874647 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
55874664 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:55875186 original size:5 final size:5
Alignment explanation
Indices: 55875178--55875203 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55875168 AATTGAAAAC
55875178 CCTAA CCTAA CCTAA CCTAA CCTAA C
1 CCTAA CCTAA CCTAA CCTAA CCTAA C
55875204 TTAATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.42, G:0.00, T:0.19
Consensus pattern (5 bp):
CCTAA
Found at i:55875228 original size:29 final size:29
Alignment explanation
Indices: 55875188--55875546 Score: 535
Period size: 29 Copynumber: 12.8 Consensus size: 29
55875178 CCTAACCTAA
*
55875188 CCTAA-CCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
55875216 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
55875245 CCTAA-CCTAACCT--A--AA-TAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
*
55875268 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
* *
55875297 CCTAACCTTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
55875326 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
*
55875355 CCTAACCCTAACCTAAATTAACTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
*
55875384 CCTAACCCTAACCTAAATTAATTAAAAAT
1 CCTAACCCTAACCTAAATTAATTAAAAAC
*
55875413 CCTAACCCTAACCTAAATTAACTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
* *
55875442 CCTAACCCTCACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
55875471 CCTAA--C---CCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
*
55875495 CCTAACCCTAATCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAAATTAATTAAAAAC
*
55875524 CCTAACCCTAACCTAACTTAATT
1 CCTAACCCTAACCTAAATTAATT
55875547 TGATAAATTT
Statistics
Matches: 302, Mismatches: 17, Indels: 23
0.88 0.05 0.07
Matches are distributed among these distances:
23 12 0.04
24 32 0.11
26 2 0.01
27 1 0.00
28 15 0.05
29 240 0.79
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.25
Consensus pattern (29 bp):
CCTAACCCTAACCTAAATTAATTAAAAAC
Found at i:55875616 original size:56 final size:56
Alignment explanation
Indices: 55875544--55875727 Score: 284
Period size: 56 Copynumber: 3.3 Consensus size: 56
55875534 ACCTAACTTA
*
55875544 ATTTGATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTT
1 ATTTCATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTT
* **
55875600 ATTTCATAAATTTTACTAACCATTAATACAATTTTTGG-CTTAATAATTTTA-CAT
1 ATTTCATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTT
* *
55875654 ATTTTGAT-AATTTTACTAACCATTAACACAATTTCTGGACTTAATAATTTTAGTTT
1 A-TTTCATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTT
55875710 ATTTCATAAATTTTACTA
1 ATTTCATAAATTTTACTA
55875728 TTTCTTACAT
Statistics
Matches: 114, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
54 30 0.26
55 36 0.32
56 48 0.42
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (56 bp):
ATTTCATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTT
Found at i:55880794 original size:26 final size:26
Alignment explanation
Indices: 55880758--55880807 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
55880748 AGGTATATTA
55880758 TTTTTGTTTTT-TTTCTCTGCTTGTGC
1 TTTTTGTTTTTGTTTCTCTG-TTGTGC
55880784 TTTTTGTTTTTGTTTCTCTGTTGT
1 TTTTTGTTTTTGTTTCTCTGTTGT
55880808 TTTACAGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (26 bp):
TTTTTGTTTTTGTTTCTCTGTTGTGC
Found at i:55886305 original size:2 final size:2
Alignment explanation
Indices: 55886298--55886347 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
55886288 TTATTCATAG
55886298 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55886340 TA TA TA TA
1 TA TA TA TA
55886348 AAAGTCACCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55887401 original size:46 final size:46
Alignment explanation
Indices: 55887334--55887424 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
55887324 CATTTTCCTA
*
55887334 TAGAGTTGAGTGTTTTTCCTTCCTTTCAAAAATATAGTGAATTCTG
1 TAGAGTTGAGTGTTTTTCCTTCCTTTCAAAAATATAGTAAATTCTG
55887380 TAGAGTTGAGTGTTTTTCCTTCCTTTCAAAAATATAGTAAATTCT
1 TAGAGTTGAGTGTTTTTCCTTCCTTTCAAAAATATAGTAAATTCT
55887425 TCTCCACTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.44
Consensus pattern (46 bp):
TAGAGTTGAGTGTTTTTCCTTCCTTTCAAAAATATAGTAAATTCTG
Found at i:55887854 original size:67 final size:68
Alignment explanation
Indices: 55887740--55887871 Score: 230
Period size: 67 Copynumber: 1.9 Consensus size: 68
55887730 TTGCCTTCTA
*
55887740 ATATATCTCGTTCACTTATTTGCAACGCTTCCTCTCTCCAT-AAAAAAATTCTCTTCAATTCCAA
1 ATATATCTCGTTCACTTATTTGCAACGCTTCCTCTCTCCATAAAAAAAACTCTCTTCAATTCCAA
55887804 CTC
66 CTC
*
55887807 ATATATCTCGTTCACTTATTTGCAACGCTTCCTCTCTCCATTTAAAAAAACTCTCTTCAATTCCA
1 ATATATCTCGTTCACTTATTTGCAACGCTTCCTCTCTCCA-TAAAAAAAACTCTCTTCAATTCCA
55887872 GACTGTCGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
67 40 0.65
68 1 0.02
69 21 0.34
ACGTcount: A:0.28, C:0.30, G:0.05, T:0.38
Consensus pattern (68 bp):
ATATATCTCGTTCACTTATTTGCAACGCTTCCTCTCTCCATAAAAAAAACTCTCTTCAATTCCAA
CTC
Found at i:55888350 original size:106 final size:106
Alignment explanation
Indices: 55888208--55888420 Score: 327
Period size: 106 Copynumber: 2.0 Consensus size: 106
55888198 AAATATCGCT
* * *
55888208 AATTAAATCAAATTTTATGAAAAATGCCTTCATATTTCGAGTTAATCGGGAAGAAAATCATGCCT
1 AATTAAATCAAATTTTATGAAAAATGCCTTCATATTTCAAGTTAATCAGGAAGAAAATCATGCCC
* *
55888273 CGTAAGTTAGGGCACGATGTCTTGAATCCCCAAAAATAAGA
66 CGTAAGGTAGGGCACGATGTCTCGAATCCCCAAAAATAAGA
* * * *
55888314 AATTAAATCAAATTTTATGAAGAATGTCTTCGTATTTCAAGTTAATCAGGAAGAGAATCATGCCC
1 AATTAAATCAAATTTTATGAAAAATGCCTTCATATTTCAAGTTAATCAGGAAGAAAATCATGCCC
**
55888379 CGTAAGGTAGGGCACGATGTCTCGAATCCCTGAAAATAAGA
66 CGTAAGGTAGGGCACGATGTCTCGAATCCCCAAAAATAAGA
55888420 A
1 A
55888421 TGCTCATTTT
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 96 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (106 bp):
AATTAAATCAAATTTTATGAAAAATGCCTTCATATTTCAAGTTAATCAGGAAGAAAATCATGCCC
CGTAAGGTAGGGCACGATGTCTCGAATCCCCAAAAATAAGA
Found at i:55889852 original size:51 final size:51
Alignment explanation
Indices: 55889797--55889902 Score: 112
Period size: 50 Copynumber: 2.1 Consensus size: 51
55889787 TTTTAATCTG
55889797 ATTTTTCATCTAG-ATTT-ATCTTTTTCATTC-TTCTTTCTTTTTCTTATTTTC
1 ATTTTTCATCTAGAATTTGAT-TTTTTC-TTCTTTC-TTCTTTTTCTTATTTTC
* * * * *
55889848 A-TTTTGATCTTGAATTTGATTTTTTCTTCTTTCTTCTTTTTGTTTTTTTT
1 ATTTTTCATCTAGAATTTGATTTTTTCTTCTTTCTTCTTTTTCTTATTTTC
55889898 ATTTT
1 ATTTT
55889903 AATTTTTTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
50 27 0.59
51 17 0.37
52 2 0.04
ACGTcount: A:0.12, C:0.13, G:0.05, T:0.70
Consensus pattern (51 bp):
ATTTTTCATCTAGAATTTGATTTTTTCTTCTTTCTTCTTTTTCTTATTTTC
Found at i:55889909 original size:22 final size:22
Alignment explanation
Indices: 55889884--55889956 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
55889874 TTCTTTCTTC
* *
55889884 TTTTTGTTTTTTTTATTTTAAT
1 TTTTTGATTTTTTTACTTTAAT
*
55889906 TTTTTGATTTTTTTACTTTGA-
1 TTTTTGATTTTTTTACTTTAAT
* **
55889927 -TTTTGATTTTTTTTCTTCCA-
1 TTTTTGATTTTTTTACTTTAAT
55889947 TTTTTGATTT
1 TTTTTGATTT
55889957 GAGCCTTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 17 0.39
21 9 0.20
22 18 0.41
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (22 bp):
TTTTTGATTTTTTTACTTTAAT
Found at i:55889951 original size:21 final size:21
Alignment explanation
Indices: 55889906--55889956 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
55889896 TTATTTTAAT
**
55889906 TTTTTGATTTTTTTACTTTGA
1 TTTTTGATTTTTTTACTTCCA
*
55889927 -TTTTGATTTTTTTTCTTCCA
1 TTTTTGATTTTTTTACTTCCA
55889947 TTTTTGATTT
1 TTTTTGATTT
55889957 GAGCCTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.73
Consensus pattern (21 bp):
TTTTTGATTTTTTTACTTCCA
Found at i:55894105 original size:11 final size:12
Alignment explanation
Indices: 55894088--55894175 Score: 81
Period size: 12 Copynumber: 7.4 Consensus size: 12
55894078 ATATAGAAGC
*
55894088 AATAATATTAGT
1 AATAATAATAGT
55894100 -ATAATAATAGT
1 AATAATAATAGT
55894111 AATAATAAT-GAT
1 AATAATAATAG-T
* * *
55894123 AACACTAATAAT
1 AATAATAATAGT
*
55894135 AATAATAATAAT
1 AATAATAATAGT
*
55894147 AATAATAATAAT
1 AATAATAATAGT
* *
55894159 AATAGTAATAAT
1 AATAATAATAGT
55894171 AATAA
1 AATAA
55894176 ACTTAAATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
11 11 0.17
12 54 0.83
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (12 bp):
AATAATAATAGT
Found at i:55894188 original size:3 final size:3
Alignment explanation
Indices: 55894100--55894175 Score: 107
Period size: 3 Copynumber: 25.3 Consensus size: 3
55894090 TAATATTAGT
* * * *
55894100 ATA ATA ATA GTA ATA ATA ATG ATA ACA CTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
55894148 ATA ATA ATA ATA ATA GTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
55894176 ACTTAAATAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:55895844 original size:16 final size:16
Alignment explanation
Indices: 55895823--55895862 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
55895813 GGTTATTTAT
55895823 TTGGGCCTAGGCTAAA
1 TTGGGCCTAGGCTAAA
55895839 TTGGGCCTAGGCTAAA
1 TTGGGCCTAGGCTAAA
55895855 TTGGGCCT
1 TTGGGCCT
55895863 TTAAACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.28
Consensus pattern (16 bp):
TTGGGCCTAGGCTAAA
Found at i:55900261 original size:46 final size:47
Alignment explanation
Indices: 55900177--55900543 Score: 388
Period size: 46 Copynumber: 7.6 Consensus size: 47
55900167 TTTGAGTACT
* *
55900177 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCT-TTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
* * *
55900223 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCT-TCGGCTATACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTATCAGCTACACTTA
* *
55900275 TCTGATCAAGTGACAAAGTGATAAGTGATAGCT-TCGGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
*
55900321 TCTGACCAAGTGACAAAGTGATAAGTGATAGCT-TCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
*
55900367 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCT-TCGGCTACACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTATCAGCTACACTTA
* * *
55900419 TTTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCT-TCGGCTATACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTATCAGCTACACTTA
* *
55900471 TCTGATCAAGAGACAAAGTGATAAGTGATAGCT-TTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
*
55900517 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
55900544 GCTACACTTA
Statistics
Matches: 290, Mismatches: 19, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
46 157 0.54
52 133 0.46
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (47 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTATCAGCTACACTTA
Found at i:55900297 original size:98 final size:97
Alignment explanation
Indices: 55900177--55900543 Score: 492
Period size: 98 Copynumber: 3.7 Consensus size: 97
55900167 TTTGAGTACT
* *
55900177 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
55900242 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * *
55900275 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGACCAAGTGAC-----
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
55900335 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
55900367 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGTGA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
55900432 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * *
55900471 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
55900536 GATAAGTG
65 GA-AAGTG
55900544 GCTACACTTA
Statistics
Matches: 237, Mismatches: 18, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
92 43 0.18
98 141 0.59
99 10 0.04
104 43 0.18
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (97 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:55900534 original size:196 final size:196
Alignment explanation
Indices: 55900191--55900543 Score: 598
Period size: 196 Copynumber: 1.8 Consensus size: 196
55900181 ATCAAGTGAC
* * *
55900191 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * *
55900256 ATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
55900321 TCTGACCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGACCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
55900386 G
196 G
* * *
55900387 AAAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
55900452 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
55900517 TCTGATCAAGAGACAAAGTGATAAGTG
131 TCTGACCAAGAGACAAAGTGATAAGTG
55900544 GCTACACTTA
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
196 145 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGACCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:55900551 original size:37 final size:37
Alignment explanation
Indices: 55900507--55900635 Score: 240
Period size: 37 Copynumber: 3.5 Consensus size: 37
55900497 GATAGCTTTA
*
55900507 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
55900544 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
55900581 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
55900618 GCTACACTTATCTGATCA
1 GCTACACTTATCTGATCA
55900636 GGGACAAGTG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 90 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:55900580 original size:150 final size:149
Alignment explanation
Indices: 55900177--55900532 Score: 442
Period size: 144 Copynumber: 2.4 Consensus size: 149
55900167 TTTGAGTACT
* * * * *
55900177 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGACCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* * *
55900242 GAAAGTGATAAGTAATAGCTTCGGCTATACT----T-ATC---TGATCAAGTGACAAAGTGATAA
66 GAAAGTGATAACT-ATAGCTTCAGC-AAACTAAAGTGATCAAGTGA-CAAGTGACAAAGTGATAA
55900299 GTGATAGCTTCGGCTATACTTA
128 GTGATAGCTTCGGCTATACTTA
* *
55900321 TCTGACCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGACCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* * * * **
55900386 GAAAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGTGACAAGTGA-AAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGC-AAACTAAAGTGATCAAGTGACAAGTGACAAAGTGATAAG
55900450 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
* *
55900471 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 TCTGACCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAA
55900533 AGTGATAAGT
Statistics
Matches: 195, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
144 91 0.47
148 1 0.01
149 3 0.02
150 90 0.46
151 7 0.04
152 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (149 bp):
TCTGACCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
GAAAGTGATAACTATAGCTTCAGCAAACTAAAGTGATCAAGTGACAAGTGACAAAGTGATAAGTG
ATAGCTTCGGCTATACTTA
Found at i:55901887 original size:30 final size:30
Alignment explanation
Indices: 55901810--55901889 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
55901800 TTATACATAC
* *
55901810 ATATATATATCTATATCCATCATACATTTT
1 ATATATATATATATATACATCATACATTTT
*
55901840 AT-TAATATATATATATACGTCTATA-ATTTT
1 ATAT-ATATATATATATACATC-ATACATTTT
55901870 ATATATATATATATATACAT
1 ATATATATATATATATACAT
55901890 AATTACATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
29 1 0.02
30 38 0.88
31 4 0.09
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.47
Consensus pattern (30 bp):
ATATATATATATATATACATCATACATTTT
Found at i:55901901 original size:36 final size:36
Alignment explanation
Indices: 55901861--55901935 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
55901851 TATATACGTC
55901861 TATAAT-TTTATATATATATATATATACATA-ATTACA
1 TATAATATTTATAT-TATATATATATACATATA-TACA
* *
55901897 TATAATATTTATATTTTATATGTATACATATATACA
1 TATAATATTTATATTATATATATATACATATATACA
55901933 TAT
1 TAT
55901936 CCACTGTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 27 0.77
37 8 0.23
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (36 bp):
TATAATATTTATATTATATATATATACATATATACA
Found at i:55902107 original size:15 final size:15
Alignment explanation
Indices: 55902084--55902113 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55902074 AAAAGGAAGG
*
55902084 AAAATAAAGAAAGAA
1 AAAAGAAAGAAAGAA
55902099 AAAAGAAAGAAAGAA
1 AAAAGAAAGAAAGAA
55902114 GGGAAATAGA
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:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAAGAAAGAAAGAA
Found at i:55902639 original size:21 final size:21
Alignment explanation
Indices: 55902598--55902636 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
55902588 AATTTTCATA
55902598 TATATATATATTATATCTTAT
1 TATATATATATTATATCTTAT
55902619 TATATATATA-TATATCTT
1 TATATATATATTATATCTT
55902637 TATACACGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATATATATTATATCTTAT
Found at i:55902703 original size:67 final size:65
Alignment explanation
Indices: 55902583--55902744 Score: 195
Period size: 67 Copynumber: 2.5 Consensus size: 65
55902573 TTTATATTCA
* *
55902583 TTTTTAATTTTCATATATATATATATTATATCTTATTATATATATATATATCTTTATACACGTAT
1 TTTTTAATTTTCATATATATATATATTATATCTTATTATATATACATACATCTTTATACACGTAT
* *
55902648 TTTTTAATTTTCAGATATATATATATACTTTGTATCTTA-T-TATATACATACATCTTTATATAC
1 TTTTTAATTTTC--ATATATATATATA--TTATATCTTATTATATATACATACATCTTTATACAC
55902711 GTA-
62 GTAT
* * *
55902714 TTTTTCATTTACATATCTATATATATCTATA
1 TTTTTAATTTTCATATATATATATAT-TATA
55902745 CACATTTTTA
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.04
64 12 0.14
65 12 0.14
66 10 0.12
67 36 0.43
68 1 0.01
69 9 0.11
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (65 bp):
TTTTTAATTTTCATATATATATATATTATATCTTATTATATATACATACATCTTTATACACGTAT
Found at i:55902710 original size:69 final size:63
Alignment explanation
Indices: 55902583--55902744 Score: 175
Period size: 69 Copynumber: 2.5 Consensus size: 63
55902573 TTTATATTCA
* *
55902583 TTTTTAATTTTCATATATATATATATTATATCTTATTATATATATATATATCTTTATACACGTAT
1 TTTTTAATTTTCATATATATATATATTATATCTTATTATATACATACATATCTTTAT--ACGTAT
* *
55902648 TTTTTAATTTTCAGATATATATATATACTTTGTATCTTATTATATACATACATCT-TTATATACG
1 TTTTTAATTTTC--ATATATATATATA--TTATATCTTATTATATACATACATATCTT-TATACG
55902712 TA-
61 TAT
* * *
55902714 TTTTTCATTTACATATCTATATATATCTATA
1 TTTTTAATTTTCATATATATATATAT-TATA
55902745 CACATTTTTA
Statistics
Matches: 83, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
62 1 0.01
63 3 0.04
64 12 0.14
65 12 0.14
66 10 0.12
67 18 0.22
68 2 0.02
69 25 0.30
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (63 bp):
TTTTTAATTTTCATATATATATATATTATATCTTATTATATACATACATATCTTTATACGTAT
Done.