Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold305
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: 704983
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 4 of 5
Found at i:465460 original size:19 final size:19
Alignment explanation
Indices: 465413--465498 Score: 85
Period size: 19 Copynumber: 4.7 Consensus size: 19
465403 ATTTCAATAA
*
465413 TTTGTATCGATACATTCAGT
1 TTTGTATCGATACA-TAAGT
**
465433 AAATGTATCGATACATAAGT
1 -TTTGTATCGATACATAAGT
465453 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
465468 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
465485 TTTGTATCGATACA
1 TTTGTATCGATACA
465499 ATGTATCGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 23 0.43
20 4 0.07
21 12 0.22
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:465473 original size:13 final size:13
Alignment explanation
Indices: 465455--465479 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
465445 ACATAAGTTT
465455 TGTATCGATACAA
1 TGTATCGATACAA
465468 TGTATCGATACA
1 TGTATCGATACA
465480 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:465475 original size:32 final size:32
Alignment explanation
Indices: 465434--465506 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
465424 ACATTCAGTA
465434 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTTTTGTATCGATAC
465466 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTTTTGTATCGATAC
465498 AATGTATCG
1 AATGTATCG
465507 CTATGAAGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (32 bp):
AATGTATCGATACATAAGTTTTGTATCGATAC
Found at i:465549 original size:21 final size:21
Alignment explanation
Indices: 465523--465564 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
465513 AGCTACTGCC
465523 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
465544 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
465565 GTATTGATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:467987 original size:52 final size:52
Alignment explanation
Indices: 467922--468280 Score: 181
Period size: 51 Copynumber: 6.9 Consensus size: 52
467912 CAATTGTTCA
*
467922 TAATCGGGGATACTCCAACCTCGATTTTATTTTC-AAAACACCAATTTTCCTT
1 TAATCGAGGATACTCCAACCTCGATTTTATTTTCGAAAACACCAATTTTCC-T
* * *
467974 TAATCGAGAATACTCCGA-CTCCGATTTTA-TTTCGAAAAACATCAAGTTTTCAC-
1 TAATCGAGGATACTCCAACCT-CGATTTTATTTTCG-AAAACACCAA-TTTTC-CT
* * * **
468027 -AATCGAGGATACTCCAACCTC-A--TTATTTCATCGGGGATACTCCAA--CCCCGT
1 TAATCGAGGATACTCCAACCTCGATTTTATTT--TC--GAAAACACCAATTTTCC-T
* * ** * * * *** * *
468078 TACCTCCGAGAGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTTTCA
1 TA-AT-C--GAGGATACTCCAACCTCGATTTTATTTTCGAAAACACCAATTTTCCT
* * * *
468133 TAATCGAGGATACTCCAACCCCGATTTTA-TTTCTAAAACACTAATTTTCCA
1 TAATCGAGGATACTCCAACCTCGATTTTATTTTCGAAAACACCAATTTTCCT
* * * *
468184 CAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTCCTT
1 TAATCGAGGATACTCCAACCTCGATTTTATTTTCGAAAACACCAATTTTCC-T
* * *
468236 TAATCG-GGGTACTCCAA-CTCCGATTTTATTTCCAAAAACACCAAT
1 TAATCGAGGATACTCCAACCT-CGATTTTATTTTCGAAAACACCAAT
468281 GTTAGGATCT
Statistics
Matches: 233, Mismatches: 47, Indels: 54
0.70 0.14 0.16
Matches are distributed among these distances:
49 4 0.02
50 4 0.02
51 107 0.46
52 62 0.27
53 19 0.08
54 11 0.05
55 3 0.01
56 18 0.08
58 2 0.01
59 3 0.01
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (52 bp):
TAATCGAGGATACTCCAACCTCGATTTTATTTTCGAAAACACCAATTTTCCT
Found at i:468152 original size:51 final size:51
Alignment explanation
Indices: 468087--468272 Score: 185
Period size: 51 Copynumber: 3.6 Consensus size: 51
468077 TTACCTCCGA
* * * * * *
468087 GAGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTTTCATAATC
1 GAGGATACTCCAACCCCGGTTTTATTCCCAAAACACTAATTTTCCACAATC
* * *
468138 GAGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCACAATC
1 GAGGATACTCCAACCCCGGTTTTATTCCCAAAACACTAATTTTCCACAATC
* ** * **
468189 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GAGGATACTCCAACCCCGGTTTTATTCCCAAAACACTAATTTTCC-ACAATC
* * * *
468241 G-GGGTACTCCAACTCCGATTTTATTTCCAAAA
1 GAGGATACTCCAACCCCGGTTTTATTCCCAAAA
468273 ACACCAATGT
Statistics
Matches: 114, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
51 109 0.96
52 5 0.04
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
GAGGATACTCCAACCCCGGTTTTATTCCCAAAACACTAATTTTCCACAATC
Found at i:468221 original size:102 final size:102
Alignment explanation
Indices: 468089--468272 Score: 244
Period size: 102 Copynumber: 1.8 Consensus size: 102
468079 ACCTCCGAGA
* *** *
468089 GGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTTTC-ATAATCGAGGATACTCCAACC
1 GGATACTCCAACCCCGGCTTTATTCCCAAAACACCAATTTTCCTATAATCG-GGATACTCCAACC
*
468153 CCGATTTTATTTCTAAAACACTAATTTTCCACAATCGG
65 CCGATTTTATTTCCAAAACACTAATTTTCCACAATCGG
* ** * * *
468191 GGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGTACTCCAACTC
1 GGATACTCCAACCCCGGCTTTATTCCCAAAACACCAATTTTCCTATAATCGGGATACTCCAACCC
468256 CGATTTTATTTCCAAAA
66 CGATTTTATTTCCAAAA
468273 ACACCAATGT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
102 63 0.91
103 6 0.09
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (102 bp):
GGATACTCCAACCCCGGCTTTATTCCCAAAACACCAATTTTCCTATAATCGGGATACTCCAACCC
CGATTTTATTTCCAAAACACTAATTTTCCACAATCGG
Found at i:468594 original size:20 final size:20
Alignment explanation
Indices: 468571--468643 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
468561 ACAATTCAAA
468571 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*
468591 GTATCGATACATGAAAATG--AT
1 GTATCGATACATG---TTGCAAT
468612 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
468632 GTATCGATACAT
1 GTATCGATACAT
468644 AAAAAAGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
20 27 0.59
21 15 0.33
23 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:468615 original size:21 final size:21
Alignment explanation
Indices: 468589--468664 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
468579 ACATGTTGCA
468589 ATGTATCGATACATGAAAATG
1 ATGTATCGATACATGAAAATG
*
468610 ATGTATCGATACATG---TTG
1 ATGTATCGATACATGAAAATG
* *
468628 CAATGTATCGATACATAAAAAAG
1 --ATGTATCGATACATGAAAATG
468651 ATGTATCGATACAT
1 ATGTATCGATACAT
468665 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
18 2 0.04
20 14 0.30
21 29 0.63
23 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAATG
Found at i:468622 original size:41 final size:41
Alignment explanation
Indices: 468571--468664 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
468561 ACAATTCAAA
* *
468571 GTATCGATACATGTTGCAATGTATCGATACATGAAAATGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
468612 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
468653 GTATCGATACAT
1 GTATCGATACAT
468665 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:468721 original size:13 final size:13
Alignment explanation
Indices: 468703--468728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
468693 TACAGCAAGT
468703 ATGTATCGATACA
1 ATGTATCGATACA
468716 ATGTATCGATACA
1 ATGTATCGATACA
468729 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:470972 original size:21 final size:21
Alignment explanation
Indices: 470939--470983 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
470929 TTACAAGTTG
*
470939 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
470961 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
470981 AAA
1 AAA
470984 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:474892 original size:20 final size:21
Alignment explanation
Indices: 474823--474900 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
474813 AATGTCCAAA
*
474823 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
474843 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
474868 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
474888 TTGTATCGATACA
1 ATGTATCGATACA
474901 GGGTGATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 30 0.64
24 3 0.06
25 14 0.30
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:477374 original size:20 final size:20
Alignment explanation
Indices: 477351--477423 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
477341 ACAATTCAAA
477351 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*
477371 GTATCGATACATGAAAATG--AT
1 GTATCGATACATG---TTGCAAT
477392 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
477412 GTATCGATACAT
1 GTATCGATACAT
477424 AAAAAAGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
20 27 0.59
21 15 0.33
23 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:477395 original size:21 final size:21
Alignment explanation
Indices: 477369--477444 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
477359 ACATGTTGCA
477369 ATGTATCGATACATGAAAATG
1 ATGTATCGATACATGAAAATG
*
477390 ATGTATCGATACATG---TTG
1 ATGTATCGATACATGAAAATG
* *
477408 CAATGTATCGATACATAAAAAAG
1 --ATGTATCGATACATGAAAATG
477431 ATGTATCGATACAT
1 ATGTATCGATACAT
477445 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
18 2 0.04
20 14 0.30
21 29 0.63
23 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAATG
Found at i:477402 original size:41 final size:41
Alignment explanation
Indices: 477351--477444 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
477341 ACAATTCAAA
* *
477351 GTATCGATACATGTTGCAATGTATCGATACATGAAAATGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
477392 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
477433 GTATCGATACAT
1 GTATCGATACAT
477445 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:477501 original size:13 final size:13
Alignment explanation
Indices: 477483--477508 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
477473 TACAGCAAGT
477483 ATGTATCGATACA
1 ATGTATCGATACA
477496 ATGTATCGATACA
1 ATGTATCGATACA
477509 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:484938 original size:1 final size:1
Alignment explanation
Indices: 484934--485008 Score: 51
Period size: 1 Copynumber: 75.0 Consensus size: 1
484924 CATCCTCTGC
* * * * * * ** * *
484934 AAAAAAAAAAAAAGAAAAAAAAAGAAGAAAAAAAACAAACAAACAAAAACTAACAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
484999 CAAAAAAAAA
1 AAAAAAAAAA
485009 GGAGACAAAC
Statistics
Matches: 55, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.01
Consensus pattern (1 bp):
A
Found at i:484964 original size:26 final size:26
Alignment explanation
Indices: 484935--485031 Score: 83
Period size: 26 Copynumber: 3.8 Consensus size: 26
484925 ATCCTCTGCA
*
484935 AAAAAAAAAAAAGAAAAAAAAAGAAG
1 AAAAAAAAAAAACAAAAAAAAAGAAG
* **
484961 AAAAAAAACAAACAAACAAAAACTAA-
1 AAAAAAAAAAAACAAA-AAAAAAGAAG
* *
484987 CAAAAAAAAAACCAAAAAAAAAG--G
1 AAAAAAAAAAAACAAAAAAAAAGAAG
* * *
485011 AGACAAACAAAACAAAAAAAA
1 AAAAAAAAAAAACAAAAAAAA
485032 CAACAAAAAG
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
24 16 0.29
25 5 0.09
26 27 0.49
27 7 0.13
ACGTcount: A:0.82, C:0.10, G:0.06, T:0.01
Consensus pattern (26 bp):
AAAAAAAAAAAACAAAAAAAAAGAAG
Found at i:484981 original size:14 final size:14
Alignment explanation
Indices: 484964--485040 Score: 54
Period size: 14 Copynumber: 5.4 Consensus size: 14
484954 AAAGAAGAAA
484964 AAAAACAAACAAAC
1 AAAAACAAACAAAC
* *
484978 AAAAACTAACAAAAA
1 AAAAACAAAC-AAAC
484993 AAAAACCAAA-AAA-
1 AAAAA-CAAACAAAC
485006 AAAGGAGACAAACAAAAC
1 AAA--A-ACAAAC-AAAC
485024 AAAAA-AAAC-AAC
1 AAAAACAAACAAAC
485036 AAAAA
1 AAAAA
485041 GGGTCCGGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
12 8 0.15
13 3 0.06
14 16 0.31
15 14 0.27
16 5 0.10
17 3 0.06
18 3 0.06
ACGTcount: A:0.79, C:0.16, G:0.04, T:0.01
Consensus pattern (14 bp):
AAAAACAAACAAAC
Found at i:485040 original size:9 final size:9
Alignment explanation
Indices: 484933--485040 Score: 64
Period size: 9 Copynumber: 11.9 Consensus size: 9
484923 GCATCCTCTG
484933 CAAAAAAAA
1 CAAAAAAAA
484942 -AAAAAGAAA
1 CAAAAA-AAA
484951 -AAAAAAGAA
1 CAAAAAA-AA
*
484960 GAAAAAAAA
1 CAAAAAAAA
*
484969 C-AAACAAA
1 CAAAAAAAA
*
484977 CAAAAACTAA
1 CAAAAA-AAA
484987 CAAAAAAAA
1 CAAAAAAAA
484996 -AACCAAAAAA
1 CAA--AAAAAA
** *
485006 -AAAGGAGA
1 CAAAAAAAA
*
485014 CAAACAAAA
1 CAAAAAAAA
485023 CAAAAAAAA
1 CAAAAAAAA
485032 CAACAAAAA
1 CAA-AAAAA
485041 GGGTCCGGAT
Statistics
Matches: 78, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
8 18 0.23
9 33 0.42
10 27 0.35
ACGTcount: A:0.81, C:0.12, G:0.06, T:0.01
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:486500 original size:28 final size:28
Alignment explanation
Indices: 486464--486671 Score: 276
Period size: 28 Copynumber: 7.4 Consensus size: 28
486454 TCACATTTTC
* *
486464 AAAGCCCACAAGTCAATAGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
*
486492 AAAGCCCACAAGTTAGTGGCAACCTTTC-
1 AAAGCCCACAAGTCAGTGGCAACC-TTCA
486520 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
*
486548 AAAGCCCATAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* **
486576 AAAGCCCACAAGTCAGTGGCATCCTTTTT
1 AAAGCCCACAAGTCAGTGGCAACC-TTCA
*
486605 AAAGCCCACAAGTTAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* *
486633 AAAGCACACAAGTTAGT-GCAACCCTTTCA
1 AAAGCCCACAAGTCAGTGGCAA-CC-TTCA
486662 AAAGCCCACA
1 AAAGCCCACA
486672 CAAGTTGGTG
Statistics
Matches: 160, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
27 7 0.04
28 113 0.71
29 40 0.25
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.18
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:486858 original size:48 final size:48
Alignment explanation
Indices: 486698--487290 Score: 411
Period size: 49 Copynumber: 12.7 Consensus size: 48
486688 TCTTCTAATT
* * * **
486698 CCAATATCACTGGCCTTGAATCAACATATTGGCACTTTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTACT-TTTAAGA
* * * * * *
486747 CCAATGTCGTTGACCTTGAATCAGCACATTGGCACCTTCACCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ACTTTTAAGA
*
486796 CCAATATCGCTGGCCTTGAATCGGCATATTGGCACCTTACTTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTACTTTTAAGA
* *
486844 CCAATGTCGCTGGCCTTGAATCAGCATATTGG---C--AC----AAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTACTTTTAAGA
*
486883 CCAATAT-GCTGGCCTTGAATCAGCATATTGGCACCTTGCTTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTACTTTTAAGA
* *
486930 CCAATGTCGCTGGCCTTGAATCAGCATATTGG---C--AC----AAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTACTTTTAAGA
* *
486969 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGCTTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTACTTTTAAGA
* * * * *
487017 CCAATGTCGCTGGCCCTGAATCAGCACATCGG---C--A----TAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTACTTTTAAGA
* * * *
487056 CCAATATCGCTGACCTTGAATCAGCACATTGGCACCTT-CATCCTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTAC-T-TTTAAGA
* * * * * * *
487105 CCGATATCGTTGGCCTTGAATTAACATATTGACATCTTTAACATTTTCAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTT-AC-TTTT-AAGA
* * * *
487157 CCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTT-CATCCTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTAC-T-TTTAAGA
* * * * *
487206 CCGATATCGTTGGCCTTGAATCAACATATTGGCATCTTTAACATTCCTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTT-AC-TT-TTAAGA
* * **
487258 CCAATGTCACTGGCCTTGTCTCAGCA-ATTGGCA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA
487291 TTCTTCTTCA
Statistics
Matches: 425, Mismatches: 79, Indels: 78
0.73 0.14 0.13
Matches are distributed among these distances:
38 24 0.06
39 74 0.17
41 1 0.00
42 2 0.00
43 4 0.01
44 1 0.00
45 3 0.01
47 9 0.02
48 92 0.22
49 136 0.32
50 8 0.02
51 12 0.03
52 59 0.14
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (48 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTACTTTTAAGA
Found at i:487029 original size:87 final size:87
Alignment explanation
Indices: 486796--487093 Score: 499
Period size: 87 Copynumber: 3.4 Consensus size: 87
486786 ACCTTTAAGT
* *
486796 CCAATATCGCTGGCCTTGAATCGGCATATTGGCACCTTACTTTTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCTTTTAAGACCAATGTCGCTGGCCTT
486861 GAATCAGCATATTGGCACAAGC
66 GAATCAGCATATTGGCACAAGC
486883 CCAATAT-GCTGGCCTTGAATCAGCATATTGGCACCTTGCTTTTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCTTTTAAGACCAATGTCGCTGGCCTT
*
486947 GAATCAGCATATTGGCACAAGT
66 GAATCAGCATATTGGCACAAGC
* *
486969 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGCTTTTAAGACCAATGTCGCTGGCCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCTTTTAAGACCAATGTCGCTGGCCTT
* * *
487034 GAATCAGCACATCGGCATAAGC
66 GAATCAGCATATTGGCACAAGC
* *
487056 CCAATATCGCTGACCTTGAATCAGCACATTGGCACCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
487094 CATCCTTAAG
Statistics
Matches: 199, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
86 83 0.42
87 116 0.58
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCTTTTAAGACCAATGTCGCTGGCCTT
GAATCAGCATATTGGCACAAGC
Found at i:487076 original size:39 final size:39
Alignment explanation
Indices: 487012--487089 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
487002 ACCTTGCTTT
* *
487012 TAAGACCAATGTCGCTGGCCCTGAATCAGCACATCGGCA
1 TAAGACCAATATCGCTGACCCTGAATCAGCACATCGGCA
* * *
487051 TAAGCCCAATATCGCTGACCTTGAATCAGCACATTGGCA
1 TAAGACCAATATCGCTGACCCTGAATCAGCACATCGGCA
487090 CCTTCATCCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (39 bp):
TAAGACCAATATCGCTGACCCTGAATCAGCACATCGGCA
Found at i:487232 original size:101 final size:101
Alignment explanation
Indices: 487052--487250 Score: 362
Period size: 101 Copynumber: 2.0 Consensus size: 101
487042 ACATCGGCAT
*
487052 AAGCCCAATATCGCTGACCTTGAATCAGCACATTGGCACCTTCATCCTTAAGTCCGATATCGTTG
1 AAGCCCAATATCGCTGACCTTAAATCAGCACATTGGCACCTTCATCCTTAAGTCCGATATCGTTG
*
487117 GCCTTGAATTAACATATTGACATCTTTAACATTTTC
66 GCCTTGAATCAACATATTGACATCTTTAACATTTTC
*
487153 AAGCCCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCCTTAAGTCCGATATCGTTG
1 AAGCCCAATATCGCTGACCTTAAATCAGCACATTGGCACCTTCATCCTTAAGTCCGATATCGTTG
*
487218 GCCTTGAATCAACATATTGGCATCTTTAACATT
66 GCCTTGAATCAACATATTGACATCTTTAACATT
487251 CCTAAGACCA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 94 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (101 bp):
AAGCCCAATATCGCTGACCTTAAATCAGCACATTGGCACCTTCATCCTTAAGTCCGATATCGTTG
GCCTTGAATCAACATATTGACATCTTTAACATTTTC
Found at i:487262 original size:101 final size:100
Alignment explanation
Indices: 487051--487392 Score: 359
Period size: 101 Copynumber: 3.4 Consensus size: 100
487041 CACATCGGCA
* *
487051 TAAGCCCAATATCGCTGACCTTGAATCAGCACATTGGCACCTTCATCCTTAAGTCCGATATCGTT
1 TAAGCCCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCCTTAAGTCCGATATCGTT
* *
487116 GGCCTTGAATTAACATATTGACATCTTTAACATTT
66 GGCCTTGAATCAACATATTGACATCTTTAACATTC
487151 TCAAGCCCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCCTTAAGTCCGATATCGT
1 T-AAGCCCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCCTTAAGTCCGATATCGT
*
487216 TGGCCTTGAATCAACATATTGGCATCTTTAACATTCC
65 TGGCCTTGAATCAACATATTGACATCTTTAACATT-C
* * * *** * ** * *
487253 TAAGACCAATGTCACTGGCCTTGTCTCAGCA-ATTGGCA--TTC-TTCTTCAAGTCTAATGTCGG
1 TAAGCCCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCCTT-AAGTCCGATATCGT
* * * * ** *
487314 TGACCGTGAATCAGCACATTGACATCTTTTTTCTCATCTT
65 TGGCCTTGAATCAACATATTGACATC---TTTAACAT-TC
* * *
487354 TAAGCCCAATATCGTTGGCCGTAAATCAGCATATTGGCA
1 TAAGCCCAATATCGCTGGCCTTAAATCAGCACATTGGCA
487393 TCTTTATCAC
Statistics
Matches: 202, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
97 4 0.02
98 34 0.17
100 8 0.04
101 147 0.73
102 9 0.04
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (100 bp):
TAAGCCCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCCTTAAGTCCGATATCGTT
GGCCTTGAATCAACATATTGACATCTTTAACATTC
Found at i:488172 original size:13 final size:13
Alignment explanation
Indices: 488154--488179 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
488144 ACATTATTCC
488154 ATGTATCGATACA
1 ATGTATCGATACA
488167 ATGTATCGATACA
1 ATGTATCGATACA
488180 TGGATCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:493747 original size:13 final size:13
Alignment explanation
Indices: 493729--493753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
493719 ATGTTGCTTA
493729 GTATCGATACATT
1 GTATCGATACATT
493742 GTATCGATACAT
1 GTATCGATACAT
493754 AAACTGGCAG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:493845 original size:10 final size:10
Alignment explanation
Indices: 493830--493869 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
493820 AGTATCGATA
493830 CATCACTGTT
1 CATCACTGTT
493840 CATCACTGTT
1 CATCACTGTT
493850 C--C-CTGTT
1 CATCACTGTT
*
493857 CATCATTGTT
1 CATCACTGTT
493867 CAT
1 CAT
493870 GTATTACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
7 6 0.23
8 1 0.04
9 1 0.04
10 18 0.69
ACGTcount: A:0.17, C:0.30, G:0.10, T:0.42
Consensus pattern (10 bp):
CATCACTGTT
Found at i:493857 original size:17 final size:17
Alignment explanation
Indices: 493835--493867 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
493825 CGATACATCA
493835 CTGTTCATCACTGTTCC
1 CTGTTCATCACTGTTCC
*
493852 CTGTTCATCATTGTTC
1 CTGTTCATCACTGTTC
493868 ATGTATTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.30, G:0.12, T:0.45
Consensus pattern (17 bp):
CTGTTCATCACTGTTCC
Found at i:497529 original size:13 final size:13
Alignment explanation
Indices: 497511--497535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
497501 CAAAGATCAG
497511 TGTATCGATACAA
1 TGTATCGATACAA
497524 TGTATCGATACA
1 TGTATCGATACA
497536 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:497606 original size:19 final size:20
Alignment explanation
Indices: 497578--497630 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
497568 TAGCTTAAAT
497578 TGTATCGATACAAAAC-TTA
1 TGTATCGATACAAAACTTTA
* *
497597 TGTATTGATACAACACTTTA
1 TGTATCGATACAAAACTTTA
497617 TGTATCGATACAAA
1 TGTATCGATACAAA
497631 TCGTTGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (20 bp):
TGTATCGATACAAAACTTTA
Found at i:500962 original size:18 final size:17
Alignment explanation
Indices: 500941--500997 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
500931 ATTAATTTTT
500941 ATAAATAAGATTAATAAA
1 ATAAATAA-ATTAATAAA
* *
500959 ATAATATATATTATTAAA
1 ATAA-ATAAATTAATAAA
*
500977 ATATAATAAA-TAAAAAA
1 ATA-AATAAATTAATAAA
500994 ATAA
1 ATAA
500998 TTTAAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 1 0.03
17 8 0.25
18 19 0.59
19 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
ATAAATAAATTAATAAA
Found at i:503968 original size:21 final size:21
Alignment explanation
Indices: 503938--503994 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
503928 TTCACTTTTC
503938 ATTCTCCATTTTTCTCCAAAA
1 ATTCTCCATTTTTCTCCAAAA
* * *
503959 ATTCTTCATTTTTCTTCAAAT
1 ATTCTCCATTTTTCTCCAAAA
503980 ATTCTCCATTATTTC
1 ATTCTCCATT-TTTC
503995 CTTTCTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTCTCCATTTTTCTCCAAAA
Found at i:508065 original size:20 final size:20
Alignment explanation
Indices: 508042--508089 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
508032 TATTTCAGAA
508042 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
* *
508062 ATGTTTCGATACATTTACTT
1 ATGTATCGATACATTCACTT
508082 ATTGTATC
1 A-TGTATC
508090 AATATAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:512894 original size:21 final size:21
Alignment explanation
Indices: 512836--512900 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
512826 TTCACTTTTC
*
512836 ATTCTCCGTTCTTCTTCTAAT
1 ATTCTCCGTTCTTCTTTTAAT
*
512857 ATTCTTCGTTCTTCTTTTAAT
1 ATTCTCCGTTCTTCTTTTAAT
* *
512878 ATTCTCCATTCTTCTTTAAAT
1 ATTCTCCGTTCTTCTTTTAAT
512899 AT
1 AT
512901 CCTTCATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTCTCCGTTCTTCTTTTAAT
Found at i:512908 original size:21 final size:20
Alignment explanation
Indices: 512844--512908 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
512834 TCATTCTCCG
*
512844 TTCTTCTTCTAATATTCTTCG
1 TTCTTCTT-TAATATTCTTCA
*
512865 TTCTTCTTTTAATATTCTCCA
1 TTCTTC-TTTAATATTCTTCA
*
512886 TTCTTCTTTAAATATCCTTCA
1 TTCTTCTTT-AATATTCTTCA
512907 TT
1 TT
512909 ATTTCCTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.08
21 33 0.87
22 2 0.05
ACGTcount: A:0.18, C:0.23, G:0.02, T:0.57
Consensus pattern (20 bp):
TTCTTCTTTAATATTCTTCA
Found at i:513346 original size:3 final size:3
Alignment explanation
Indices: 513338--513366 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
513328 ATTTAAATAG
513338 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
513367 CCTTTAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:515280 original size:21 final size:20
Alignment explanation
Indices: 515245--515302 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
515235 ATCCGGGAAA
515245 ATTTTAAT-A-TTTTATATT
1 ATTTTAATGATTTTTATATT
* *
515263 ATTATTAATTATTTTTATAAT
1 ATT-TTAATGATTTTTATATT
*
515284 ATTTTTATGATTTTT-TATT
1 ATTTTAATGATTTTTATATT
515303 TATGTGTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 3 0.09
19 8 0.24
20 11 0.33
21 11 0.33
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTTAATGATTTTTATATT
Found at i:516755 original size:17 final size:19
Alignment explanation
Indices: 516723--516757 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
516713 AAAAAAATAA
516723 TTTAAGAAAACAATAATTT
1 TTTAAGAAAACAATAATTT
516742 TTTAA-AAAAC-ATAATT
1 TTTAAGAAAACAATAATT
516758 GCTGACCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (19 bp):
TTTAAGAAAACAATAATTT
Found at i:516813 original size:25 final size:25
Alignment explanation
Indices: 516784--516832 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
516774 TATAGGAAAT
516784 TTCATCTGTAATACTATTTAATAAA
1 TTCATCTGTAATACTATTTAATAAA
516809 TTCATCTGTAATACTATTTAATAA
1 TTCATCTGTAATACTATTTAATAA
516833 CGAATTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (25 bp):
TTCATCTGTAATACTATTTAATAAA
Found at i:517411 original size:29 final size:30
Alignment explanation
Indices: 517369--517464 Score: 89
Period size: 28 Copynumber: 3.4 Consensus size: 30
517359 TATCATATTC
*
517369 TTAAGTAAA-TTTTATA-TTTTAATTACAT
1 TTAAATAAATTTTTATATTTTTAATTACAT
517397 TTAAATAAATTTTTA-ATTTTTAATTTACA-
1 TTAAATAAATTTTTATATTTTTAA-TTACAT
* * *
517426 CT-AACAAATTTTT-TATTTTTAATT-TAT
1 TTAAATAAATTTTTATATTTTTAATTACAT
517453 ATTAAATAAATT
1 -TTAAATAAATT
517465 ATTAACTCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
26 1 0.02
27 2 0.04
28 28 0.51
29 19 0.35
30 5 0.09
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (30 bp):
TTAAATAAATTTTTATATTTTTAATTACAT
Found at i:517557 original size:25 final size:26
Alignment explanation
Indices: 517528--517580 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
517518 TTTTATTTAA
517528 TTAATTATT-TTTAATATAAA-ATATT
1 TTAATTATTATTT-ATATAAATATATT
517553 TTAATTATTATTTATATAAATATATT
1 TTAATTATTATTTATATAAATATATT
517579 TT
1 TT
517581 TTAAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTAATTATTATTTATATAAATATATT
Found at i:517562 original size:28 final size:29
Alignment explanation
Indices: 517523--517639 Score: 102
Period size: 28 Copynumber: 4.0 Consensus size: 29
517513 CTTTTTTTTA
517523 TTTAATTAATTATTTTTAATATAAA-ATAT
1 TTTAATT-ATTATTTTTAATATAAATATAT
517552 TTTAATTATTA--TTT-ATATAAATATATTT
1 TTTAATTATTATTTTTAATATAAATATA--T
*
517580 TTTAAATATTTTTATTGTTTAATATAAATATAAT
1 TTT--A-ATTATTATT-TTTAATATAAATAT-AT
*
517614 TTTAA-TAAT-TTTTTAATATAAATATA
1 TTTAATTATTATTTTTAATATAAATATA
517640 ACATTAATAA
Statistics
Matches: 74, Mismatches: 3, Indels: 24
0.73 0.03 0.24
Matches are distributed among these distances:
25 7 0.09
26 6 0.08
27 1 0.01
28 22 0.30
29 9 0.12
30 3 0.04
31 7 0.09
32 1 0.01
34 7 0.09
35 10 0.14
36 1 0.01
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
TTTAATTATTATTTTTAATATAAATATAT
Found at i:517587 original size:37 final size:38
Alignment explanation
Indices: 517544--517630 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 38
517534 ATTTTTAATA
*
517544 TAAAATATTTTAATTATTATTT-ATATAAATATATTTT
1 TAAAATATTTTAATTATTATTTAATATAAATATAATTT
* *
517581 TTAAATA-TTT--TTATTGTTTAATATAAATATAATTT
1 TAAAATATTTTAATTATTATTTAATATAAATATAATTT
*
517616 TAATAATTTTTTAAT
1 TAA-AATATTTTAAT
517631 ATAAATATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
34 8 0.20
35 16 0.40
36 6 0.15
37 9 0.22
39 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (38 bp):
TAAAATATTTTAATTATTATTTAATATAAATATAATTT
Found at i:517640 original size:28 final size:28
Alignment explanation
Indices: 517597--517654 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
517587 ATTTTTATTG
**
517597 TTTAATATAAATATAATTTTAATAATTT
1 TTTAATATAAATATAACATTAATAATTT
517625 TTTAATATAAATATAACATTAATAATTT
1 TTTAATATAAATATAACATTAATAATTT
517653 TT
1 TT
517655 AATTATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTAATATAAATATAACATTAATAATTT
Found at i:517653 original size:62 final size:62
Alignment explanation
Indices: 517532--517842 Score: 208
Period size: 62 Copynumber: 4.9 Consensus size: 62
517522 ATTTAATTAA
* *
517532 TTATT-TTTAATATAAA-AT-ATTTTAATTATTATTT-ATATAAATATATTTTTTAA-ATATTT
1 TTATTATTTAATATAAATATAATTTTAATTATTATTTAATATAAATATA-ATATTAATA-ATTT
* * * *
517591 TTATTGTTTAATATAAATATAATTTTAATAATTTTTTAATATAAATATAACATTAATAATTT
1 TTATTATTTAATATAAATATAATTTTAATTATTATTTAATATAAATATAATATTAATAATTT
* * * *
517653 TTAATTATTATTCAAAATAAATATAATTTCCTTTATATTTTATTCTTTAATATAAATTTAATTTT
1 TT-ATTA-T-TT-AATATAAATATAA--T--TTTA-A--TTATTATTTAATATAAATATAATATT
517718 AATAATTT
55 AATAATTT
* * * * * *
517726 TTA--ATATAATATAATTTTAATATTTTAATTATTATTCAATATAAATATAAT-TT-GTTATATT
1 TTATTATTTAATATAAATAT-A-ATTTTAATTATTATTTAATATAAATATAATATTAATAAT-TT
** * *
517787 TTATTATTTAATATAAATATAAATTTTAAAAATTTATTTTATATATATATATATAT
1 TTATTATTTAATATAAATAT-AATTTTAATTA-TTATTTAATATAAATATA-ATAT
517843 ATATTTCAAT
Statistics
Matches: 199, Mismatches: 29, Indels: 42
0.74 0.11 0.16
Matches are distributed among these distances:
59 5 0.03
60 14 0.07
61 9 0.05
62 52 0.26
63 44 0.22
64 4 0.02
65 7 0.04
66 12 0.06
67 9 0.05
68 3 0.02
69 2 0.01
70 5 0.03
71 1 0.01
72 1 0.01
73 31 0.16
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.55
Consensus pattern (62 bp):
TTATTATTTAATATAAATATAATTTTAATTATTATTTAATATAAATATAATATTAATAATTT
Found at i:517702 original size:101 final size:97
Alignment explanation
Indices: 517547--517837 Score: 374
Period size: 101 Copynumber: 2.9 Consensus size: 97
517537 TTTAATATAA
* *
517547 AATATTTTAATTATTATT-TATATAAATAT-ATTTTTTAAATATTTTTATTGTTTAATATAAATA
1 AATATTTTAATTATTATTCAATATAAATATAATTTTTT--ATA-TTTTATTATTTAATATAAATA
517610 TAATTTTAATAATTTTTTAATATAAATATAACATT
63 TAATTTTAATAATTTTTTAATATAAATATAACATT
* *
517645 AATAATTTTTAATTATTATTCAAAATAAATATAATTTCCTTTATATTTTATTCTTTAATATAAAT
1 AAT-A-TTTTAATTATTATTCAATATAAATATAATTT--TTTATATTTTATTATTTAATATAAAT
* **
517710 TTAATTTTAATAA-TTTTTAATAT-AATATAATTTT
62 ATAATTTTAATAATTTTTTAATATAAATATAACATT
*
517744 AATATTTTAATTATTATTCAATATAAATATAATTTGTTATATTTTATTATTTAATATAAATATAA
1 AATATTTTAATTATTATTCAATATAAATATAATTTTTTATATTTTATTATTTAATATAAATAT-A
* * *
517809 ATTTTAAAAATTTATTTTATATATATATA
65 ATTTTAATAATTT-TTTAATATAAATATA
517838 TATATATATT
Statistics
Matches: 170, Mismatches: 13, Indels: 19
0.84 0.06 0.09
Matches are distributed among these distances:
95 25 0.15
96 10 0.06
97 32 0.19
98 11 0.06
99 18 0.11
100 24 0.14
101 40 0.24
102 7 0.04
104 3 0.02
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (97 bp):
AATATTTTAATTATTATTCAATATAAATATAATTTTTTATATTTTATTATTTAATATAAATATAA
TTTTAATAATTTTTTAATATAAATATAACATT
Found at i:517746 original size:26 final size:26
Alignment explanation
Indices: 517693--517751 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 26
517683 CTTTATATTT
*
517693 TATTCTTTAATATAAATTTAATTTTAA
1 TATT-TTTAATATAAATATAATTTTAA
517720 TAATTTTTAATAT-AATATAATTTTAA
1 T-ATTTTTAATATAAATATAATTTTAA
517746 TATTTT
1 TATTTT
517752 AATTATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 5 0.17
26 13 0.43
27 9 0.30
28 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTTTTAATATAAATATAATTTTAA
Found at i:519669 original size:22 final size:22
Alignment explanation
Indices: 519644--519687 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
519634 AAATAGTAAT
*
519644 TTATAAAAAATTAAATTATATC
1 TTATAAAAAAGTAAATTATATC
*
519666 TTATCAAAAAGTAAATTATATC
1 TTATAAAAAAGTAAATTATATC
519688 ATAAGATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (22 bp):
TTATAAAAAAGTAAATTATATC
Found at i:520209 original size:16 final size:16
Alignment explanation
Indices: 520181--520215 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
520171 CGTCTAAAAA
520181 AAAGATAATATATAATT
1 AAAGATAATATAT-ATT
520198 AAAGAT-ATATATATT
1 AAAGATAATATATATT
520213 AAA
1 AAA
520216 TCATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 6 0.33
17 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
AAAGATAATATATATT
Found at i:520654 original size:42 final size:46
Alignment explanation
Indices: 520570--520667 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 46
520560 AATTTGCAAT
* *
520570 ATATAATTTTGTAATAATAAATTATTTAAAAATTAATTATAT-ATAA
1 ATATAAATTTGTAATAATAAATTATTTAAAAATTAATCATATAAT-A
520616 ATATAAATTT-TAATAA-AAA-TATATTAAAAA-TAA-CATATAATA
1 ATATAAATTTGTAATAATAAATTAT-TTAAAAATTAATCATATAATA
*
520658 ATAAAAATTT
1 ATATAAATTT
520668 ACTTAAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
42 14 0.30
43 8 0.17
44 10 0.21
45 6 0.13
46 9 0.19
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (46 bp):
ATATAAATTTGTAATAATAAATTATTTAAAAATTAATCATATAATA
Found at i:520872 original size:16 final size:15
Alignment explanation
Indices: 520853--520907 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
520843 TCAAATAAAG
520853 TTAAACTTTAAAAAAA
1 TTAAA-TTTAAAAAAA
* *
520869 TTAAATTTAAATAGA
1 TTAAATTTAAAAAAA
520884 TTCAAATTTAAAAAAAA
1 TT-AAATTT-AAAAAAA
520901 TTAAATT
1 TTAAATT
520908 AAATATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 10 0.30
16 16 0.48
17 7 0.21
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (15 bp):
TTAAATTTAAAAAAA
Found at i:520881 original size:32 final size:31
Alignment explanation
Indices: 520845--520912 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
520835 ACTTGAACTC
520845 AAATAAAGTT-AAACTTT-AAAAAAATTAAATTT
1 AAATAAA-TTCAAA-TTTAAAAAAAATTAAA-TT
*
520877 AAATAGATTCAAATTTAAAAAAAATTAAATT
1 AAATAAATTCAAATTTAAAAAAAATTAAATT
520908 AAATA
1 AAATA
520913 TAAAATAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
31 12 0.36
32 21 0.64
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (31 bp):
AAATAAATTCAAATTTAAAAAAAATTAAATT
Found at i:523514 original size:3 final size:3
Alignment explanation
Indices: 523506--523539 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
523496 TTACATTCAT
523506 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
523540 TGTATTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:523644 original size:3 final size:3
Alignment explanation
Indices: 523636--523673 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
523626 TAGCCCAAAG
523636 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
523674 TGTATTTATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:523800 original size:134 final size:134
Alignment explanation
Indices: 523506--523774 Score: 484
Period size: 134 Copynumber: 2.0 Consensus size: 134
523496 TTACATTCAT
523506 TAATAATAATAATAATAATAATAATAATAATAATTGTATTTATGATTATATAAAAATTAACTTAT
1 TAATAATAATAATAATAATAATAATAATAATAATTGTATTTATGATTATATAAAAATTAACTTAT
* *
523571 GGACTCACTACGACAGCCTAAGATAAAAAGTGGCATTTTAGCAAGCCCAAACCTTTAGCCCAAAG
66 GGACTCACTACGACAACCTAAGATAAAAAGTGGCATTTTAGCAAGCCCAAACCTTTAGCACAAAG
523636 ATAA
131 ATAA
523640 TAATAATAATAATAATAATAATAATAATAATAATTGTATTTATGATTATATAAAAATTAACTTAT
1 TAATAATAATAATAATAATAATAATAATAATAATTGTATTTATGATTATATAAAAATTAACTTAT
* * * *
523705 GGGCTCACTACGATAACCTAAGATAAAAAGTGGCATTTTATCAAGCCCAAACTTTTAGCACAAAG
66 GGACTCACTACGACAACCTAAGATAAAAAGTGGCATTTTAGCAAGCCCAAACCTTTAGCACAAAG
523770 ATAA
131 ATAA
523774 T
1 T
523775 TTAAATCATA
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
134 129 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (134 bp):
TAATAATAATAATAATAATAATAATAATAATAATTGTATTTATGATTATATAAAAATTAACTTAT
GGACTCACTACGACAACCTAAGATAAAAAGTGGCATTTTAGCAAGCCCAAACCTTTAGCACAAAG
ATAA
Found at i:525896 original size:23 final size:23
Alignment explanation
Indices: 525870--525915 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
525860 ATGTAAGGAT
525870 GAGAAGGAACTAATGCTTGATAC
1 GAGAAGGAACTAATGCTTGATAC
525893 GAGAAGGAACTAATGCTTGATAC
1 GAGAAGGAACTAATGCTTGATAC
525916 AATTACATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (23 bp):
GAGAAGGAACTAATGCTTGATAC
Found at i:527024 original size:15 final size:15
Alignment explanation
Indices: 527004--527036 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
526994 TGGGCAAATC
*
527004 GATAATAATGTTGAT
1 GATAATAATGATGAT
527019 GATAATAATGATGAT
1 GATAATAATGATGAT
527034 GAT
1 GAT
527037 GATGCTGACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.36
Consensus pattern (15 bp):
GATAATAATGATGAT
Found at i:527684 original size:85 final size:85
Alignment explanation
Indices: 527554--527748 Score: 198
Period size: 85 Copynumber: 2.3 Consensus size: 85
527544 AAAGTAAGAA
* * * *
527554 AGAATTTAGTAAAAGAAAAACTGATGAAATTTATACAAAACAAAAATTTGTGATAATCTA-TTTA
1 AGAATTTAGTAACAGAATAA-TGATGAAATTTATACAAAACAAAAAATTGTGATAAT-AAGTTTA
*
527618 TGACAAAATTTTAA-TTTGTGAC
64 TGACAAAA-TTTAATTTTGTAAC
* ** * *
527640 AGAATTTAGTAACAGAATAATGATGGAATTTATA-AGGGATAAAAAATTGTGATAGTAAGTTTAT
1 AGAATTTAGTAACAGAATAATGATGAAATTTATACA-AAACAAAAAATTGTGATAATAAGTTTAT
* *
527704 GACGAAATTTAATTTTGTAAT
65 GACAAAATTTAATTTTGTAAC
* *
527725 AGTATTTAGTAACAAGAATCATGA
1 AGAATTTAGTAAC-AGAATAATGA
527749 CAAACTTTAA
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
84 7 0.08
85 57 0.63
86 27 0.30
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (85 bp):
AGAATTTAGTAACAGAATAATGATGAAATTTATACAAAACAAAAAATTGTGATAATAAGTTTATG
ACAAAATTTAATTTTGTAAC
Found at i:528420 original size:78 final size:78
Alignment explanation
Indices: 528338--528481 Score: 209
Period size: 78 Copynumber: 1.8 Consensus size: 78
528328 TGTGAATCAC
* *
528338 AAAACAACCCTACTGACCATGTGTTGATATTAAAATGCCAACA-GAATCCTAAAAACTTAGATTT
1 AAAACAACCCTACTGACCATGTATTGATATGAAAATGCCAACATG-ATCCTAAAAACTTAGATTT
528402 ATCATTTTATTATT
65 ATCATTTTATTATT
** * * *
528416 AAAACAAGTCTAGTGACCATTTATTGATATGAAAATGCCAACATGATCCTAAAGACTTAGATTTA
1 AAAACAACCCTACTGACCATGTATTGATATGAAAATGCCAACATGATCCTAAAAACTTAGATTTA
528481 T
66 T
528482 TATGAAAAGC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 57 0.98
79 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (78 bp):
AAAACAACCCTACTGACCATGTATTGATATGAAAATGCCAACATGATCCTAAAAACTTAGATTTA
TCATTTTATTATT
Found at i:528506 original size:38 final size:39
Alignment explanation
Indices: 528443--528528 Score: 120
Period size: 38 Copynumber: 2.2 Consensus size: 39
528433 CATTTATTGA
*
528443 TATGAAAATGCCAACATGATCCTAAAGACTTAGATTTAT
1 TATGAAAATGCCAACATAATCCTAAAGACTTAGATTTAT
* *
528482 TATGAAAA-GCCAGCATAATCCTAAAGACTTGGATTTAT
1 TATGAAAATGCCAACATAATCCTAAAGACTTAGATTTAT
* *
528520 CATGGAAAT
1 TATGAAAAT
528529 TATCAAAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
38 33 0.80
39 8 0.20
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (39 bp):
TATGAAAATGCCAACATAATCCTAAAGACTTAGATTTAT
Found at i:528584 original size:39 final size:39
Alignment explanation
Indices: 528437--528589 Score: 107
Period size: 39 Copynumber: 3.9 Consensus size: 39
528427 AGTGACCATT
*
528437 TATTGATATGAAAATGCCAACATGATCCTAAAGACTTA-G
1 TATTAATATGAAAATGCCAACATGATCCTAAAGA-TTATG
* * * *
528476 -ATTTATTATGAAAA-GCCAGCATAATCCTAAAGACT-TG
1 TA-TTAATATGAAAATGCCAACATGATCCTAAAGATTATG
* * * ** * ** *
528513 GATTTATCATGGAAATTATCAAAATGGCCCTAATGATTATG
1 TATTAAT-AT-GAAAATGCCAACATGATCCTAAAGATTATG
*
528554 TATTAATATGAAAATGCCAGCATGATCCTAAAGATT
1 TATTAATATGAAAATGCCAACATGATCCTAAAGATT
528590 CGAATTTATC
Statistics
Matches: 80, Mismatches: 27, Indels: 14
0.66 0.22 0.12
Matches are distributed among these distances:
37 5 0.06
38 21 0.26
39 33 0.41
40 14 0.17
41 7 0.09
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (39 bp):
TATTAATATGAAAATGCCAACATGATCCTAAAGATTATG
Found at i:528823 original size:57 final size:58
Alignment explanation
Indices: 528695--528828 Score: 180
Period size: 58 Copynumber: 2.3 Consensus size: 58
528685 ACCCTAAGTC
* * * * * *
528695 ATATTAAATAACCAAAATGGCTTTAAAAGGATGAAAATTGCTAAAATGGCCCTAGATT
1 ATATTAAATAACCTAAATAGCCTTAAAAGGATGAAAATTGCTAAAATGACACTAGACT
* *
528753 ATGTTAAATAACCTAAATAGCCTTAAAATGATGAAAATTGC-AAAATGACACTAGACT
1 ATATTAAATAACCTAAATAGCCTTAAAAGGATGAAAATTGCTAAAATGACACTAGACT
528810 ATATTAAATAACCTCAAAT
1 ATATTAAATAACCT-AAAT
528829 GATGGAATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
57 26 0.39
58 40 0.61
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (58 bp):
ATATTAAATAACCTAAATAGCCTTAAAAGGATGAAAATTGCTAAAATGACACTAGACT
Found at i:528889 original size:58 final size:57
Alignment explanation
Indices: 528825--529015 Score: 172
Period size: 57 Copynumber: 3.3 Consensus size: 57
528815 AAATAACCTC
* * * * *
528825 AAATGATGGAATTTATTAAATTGACCGTATATTATGTTAAATAACCTAAATGGCTCC-A
1 AAATGATGGAAATTACTAAATTGACCCTAGATCATG-TAAATAACCTAAATGGC-CCTA
* *
528883 AAATGATGGAAATTGCTAAATTGACCCTAGATCATGTGAATAACCTAAATGGCCCTA
1 AAATGATGGAAATTACTAAATTGACCCTAGATCATGTAAATAACCTAAATGGCCCTA
* * * * ** *
528940 AAATGATCGAAATTGCTAAGA-TGACCCTAGATTATATAAAATAGTCT-AATGACCCTA
1 AAATGATGGAAATTACTAA-ATTGACCCTAGATCATGT-AAATAACCTAAATGGCCCTA
* * *
528997 AATTGATAGAAATAACTAA
1 AAATGATGGAAATTACTAA
529016 GATGATCTTA
Statistics
Matches: 112, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
56 2 0.02
57 73 0.65
58 37 0.33
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (57 bp):
AAATGATGGAAATTACTAAATTGACCCTAGATCATGTAAATAACCTAAATGGCCCTA
Found at i:529049 original size:57 final size:56
Alignment explanation
Indices: 528882--529050 Score: 144
Period size: 57 Copynumber: 3.0 Consensus size: 56
528872 AAATGGCTCC
* ** * * *
528882 AAAATGATGGAAATTGCTAA-ATTGACCCTAG-ATCATGTGAATAACCTAAATGGCCCT
1 AAAATGATAGAAATAACTAAGA-TGACCCTAGAAT-ATGTAAATAGCCT-AATGACCCT
* ** * * *
528939 AAAATGATCGAAATTGCTAAGATGACCCTAGATTATATAAAATAGTCTAATGACCCT
1 AAAATGATAGAAATAACTAAGATGACCCTAGAATATGT-AAATAGCCTAATGACCCT
* * *
528996 AAATTGATAGAAATAACTAAGATGATCTTAGAATATGTAAATAGCCTAGATGACC
1 AAAATGATAGAAATAACTAAGATGACCCTAGAATATGTAAATAGCCTA-ATGACC
529051 TTAGGAATGC
Statistics
Matches: 92, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
56 9 0.10
57 75 0.82
58 8 0.09
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (56 bp):
AAAATGATAGAAATAACTAAGATGACCCTAGAATATGTAAATAGCCTAATGACCCT
Found at i:529716 original size:11 final size:11
Alignment explanation
Indices: 529700--529748 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
529690 TAGAACAATG
*
529700 CTTTCTCCTTT
1 CTTTCTTCTTT
529711 CTTTCTTCTTT
1 CTTTCTTCTTT
* *
529722 TTTTTTTCTTT
1 CTTTCTTCTTT
*
529733 CTTTTATTCTTT
1 C-TTTCTTCTTT
529745 CTTT
1 CTTT
529749 TTTGTTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (11 bp):
CTTTCTTCTTT
Found at i:529742 original size:12 final size:12
Alignment explanation
Indices: 529707--529749 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
529697 ATGCTTTCTC
*
529707 CTTTC-TTTCTT
1 CTTTCTTTTATT
*
529718 CTTT-TTTTTTT
1 CTTTCTTTTATT
529729 CTTTCTTTTATT
1 CTTTCTTTTATT
529741 CTTTCTTTT
1 CTTTCTTTT
529750 TTGTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 13 0.46
12 15 0.54
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (12 bp):
CTTTCTTTTATT
Found at i:529761 original size:27 final size:25
Alignment explanation
Indices: 529707--529777 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 25
529697 ATGCTTTCTC
* *
529707 CTTTCTTTCTTCTTTTTTTTTTCTTT
1 CTTT-TTTTTTCTTTTTTTTTTCATT
529733 CTTTTATTCTTTCTTTTTTGTTTT-ATT
1 CTTTT-TT-TTTCTTTTTT-TTTTCATT
*
529760 CTTTTTTTTTCCTTTTTT
1 CTTTTTTTTTCTTTTTTT
529778 CTTGATGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 1 0.03
25 10 0.26
26 8 0.21
27 16 0.41
28 4 0.10
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.80
Consensus pattern (25 bp):
CTTTTTTTTTCTTTTTTTTTTCATT
Found at i:529775 original size:19 final size:18
Alignment explanation
Indices: 529723--529780 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 18
529713 TTCTTCTTTT
529723 TTTTTTCTTTCTTTTATTC
1 TTTTTT-TTTCTTTTATTC
*
529742 TTTCTTTTTTGTTTTATTC
1 TTT-TTTTTTCTTTTATTC
529761 TTTTTTTTTCCTTTT-TTC
1 TTTTTTTTT-CTTTTATTC
529779 TT
1 TT
529781 GATGTGAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 11 0.31
19 21 0.60
20 3 0.09
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTTTTCTTTTATTC
Found at i:531169 original size:159 final size:159
Alignment explanation
Indices: 530863--531185 Score: 515
Period size: 159 Copynumber: 2.0 Consensus size: 159
530853 CCTTTACTTA
530863 TGGAGAGATGCAACACCATATTCAATGAATTCTTGATTCAATTAAACTTGTTTGATAAATCTCAG
1 TGGAGAGATGCAACACCATATTCAATGAATTCTTGATTCAATTAAAC-T-TTTGATAAATCTCAG
* * *
530928 TCTATCTTTTGGATTATCAAAGGCAACCCTAATATTAGGTAGTCCCATATTATTCTATTCTTCAT
64 TCTAGCTTTTGGATGATCAAAGGCAACCCTAATATCAGGTAGTCCCATATTATTCTATTCTTCAT
530993 TAGGAGTTACAGAGTGCAACTTCAAAAATAT
129 TAGGAGTTACAGAGTGCAACTTCAAAAATAT
* *
531024 TGGAGAGATGTAATCACCATATTCAATGAATTCTTGATTCAATTAAAC-TTTGATAAATCT-TGT
1 TGGAGAGATGCAA-CACCATATTCAATGAATTCTTGATTCAATTAAACTTTTGATAAATCTCAG-
***
531087 TCTAGCTTTTGGATGATCAAAGGCAACCCTAATATCAGGTAGTCTTGTATTATTCTATTCTTCAT
64 TCTAGCTTTTGGATGATCAAAGGCAACCCTAATATCAGGTAGTCCCATATTATTCTATTCTTCAT
*
531152 TAGGAGTTACAGGGTGCAACTTCAAAAATAT
129 TAGGAGTTACAGAGTGCAACTTCAAAAATAT
531183 TGG
1 TGG
531186 GTTATTACCT
Statistics
Matches: 151, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
158 1 0.01
159 104 0.69
161 12 0.08
162 34 0.23
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (159 bp):
TGGAGAGATGCAACACCATATTCAATGAATTCTTGATTCAATTAAACTTTTGATAAATCTCAGTC
TAGCTTTTGGATGATCAAAGGCAACCCTAATATCAGGTAGTCCCATATTATTCTATTCTTCATTA
GGAGTTACAGAGTGCAACTTCAAAAATAT
Found at i:531816 original size:15 final size:14
Alignment explanation
Indices: 531791--531847 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 14
531781 GTAGATATTT
531791 TCTCATTTTTTTCTC
1 TCTC-TTTTTTTCTC
*
531806 ATTTCTTTTTTTCTC
1 -TCTCTTTTTTTCTC
*
531821 TCTCTTTTCTTTCTT
1 TCTCTTTT-TTTCTC
531836 TCTCTTCTTTTT
1 TCTCTT-TTTTT
531848 TTTTCTTCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.19
15 24 0.67
16 5 0.14
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.72
Consensus pattern (14 bp):
TCTCTTTTTTTCTC
Found at i:531824 original size:19 final size:19
Alignment explanation
Indices: 531802--531859 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
531792 CTCATTTTTT
531802 TCTCATTTCTTTTTTTCTC
1 TCTCATTTCTTTTTTTCTC
* *
531821 TCTCTTTTCTTTCTTTCTC
1 TCTCATTTCTTTTTTTCTC
531840 T-TC--TT-TTTTTTTCT-
1 TCTCATTTCTTTTTTTCTC
531854 TCTCAT
1 TCTCAT
531860 CAAGGTACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 10 0.30
16 2 0.06
18 2 0.06
19 18 0.55
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (19 bp):
TCTCATTTCTTTTTTTCTC
Found at i:531852 original size:15 final size:15
Alignment explanation
Indices: 531796--531853 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 15
531786 TATTTTCTCA
531796 TTTTTTTCTCATTTCTT
1 TTTTTTTCTC--TTCTT
531813 TTTTTCTCTCTCTT-TT
1 TTTTT-T-TCTCTTCTT
*
531829 CTTTCTTTCTCTTCTT
1 -TTTTTTTCTCTTCTT
531845 TTTTTTTCT
1 TTTTTTTCT
531854 TCTCATCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
15 14 0.40
16 5 0.14
17 11 0.31
18 1 0.03
19 4 0.11
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTCTCTTCTT
Found at i:535196 original size:6 final size:6
Alignment explanation
Indices: 535185--535218 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
535175 AAGTTTCTCC
535185 CTTTTT CTTTTT CTTTTT -TTTTT C-TTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
535219 TAAGTTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
CTTTTT
Found at i:535208 original size:17 final size:16
Alignment explanation
Indices: 535186--535219 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
535176 AGTTTCTCCC
535186 TTTTTCTTTTTCTTTTT
1 TTTTTC-TTTTCTTTTT
535203 TTTTTCTTTTCTTTTT
1 TTTTTCTTTTCTTTTT
535219 T
1 T
535220 AAGTTTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTCTTTTCTTTTT
Found at i:535761 original size:28 final size:28
Alignment explanation
Indices: 535706--535813 Score: 101
Period size: 28 Copynumber: 3.9 Consensus size: 28
535696 AAGTGTAACA
* * *
535706 AAAAATCCTATATATAAGAAGTTT-ATT
1 AAAAATTCTATATATAAAAATTTTAATT
* * *
535733 AAAAATTCTATCTGTAAAAGTTTTAATT
1 AAAAATTCTATATATAAAAATTTTAATT
*
535761 AAAAATTTTATATATAAAAATTTTAATT
1 AAAAATTCTATATATAAAAATTTTAATT
* * * * *
535789 GAAAATTTTTTATGTAAAAAGTTTA
1 AAAAATTCTATATATAAAAATTTTA
535814 CTTCATAAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
27 18 0.27
28 48 0.73
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (28 bp):
AAAAATTCTATATATAAAAATTTTAATT
Found at i:535769 original size:13 final size:14
Alignment explanation
Indices: 535747--535852 Score: 74
Period size: 14 Copynumber: 7.4 Consensus size: 14
535737 ATTCTATCTG
*
535747 TAAAAGTTTTAAT-
1 TAAAAATTTTAATA
535760 TAAAAATTTTATATA
1 TAAAAATTTTA-ATA
535775 TAAAAATTTTAAT-
1 TAAAAATTTTAATA
* * *
535788 TGAAAATTTTTTATG
1 T-AAAAATTTTAATA
* *
535803 TAAAAAGTTTACTTCA
1 TAAAAATTTTA-AT-A
*
535819 TAAAAAGTTTAAT-
1 TAAAAATTTTAATA
*
535832 TAAAAATTTCATATA
1 TAAAAATTTTA-ATA
535847 TAAAAA
1 TAAAAA
535853 GTGGTGACAA
Statistics
Matches: 74, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
13 20 0.27
14 23 0.31
15 20 0.27
16 11 0.15
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (14 bp):
TAAAAATTTTAATA
Found at i:535780 original size:15 final size:14
Alignment explanation
Indices: 535729--535852 Score: 85
Period size: 15 Copynumber: 8.6 Consensus size: 14
535719 ATAAGAAGTT
*
535729 TATTAAAAATTCTA
1 TATTAAAAATTTTA
* *
535743 TCTGTAAAAGTTTTA
1 TAT-TAAAAATTTTA
535758 -ATTAAAAATTTTA
1 TATTAAAAATTTTA
535771 TATATAAAAATTTTA
1 TAT-TAAAAATTTTA
* *
535786 -ATTGAAAATTTTT
1 TATTAAAAATTTTA
*
535799 TATGTAAAAAGTTTA
1 TAT-TAAAAATTTTA
*
535814 CT-TCATAAAAAGTTTA
1 -TAT--TAAAAATTTTA
*
535830 -ATTAAAAATTTCA
1 TATTAAAAATTTTA
535843 TATATAAAAA
1 TAT-TAAAAA
535853 GTGGTGACAA
Statistics
Matches: 87, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
13 28 0.32
14 11 0.13
15 36 0.41
16 12 0.14
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (14 bp):
TATTAAAAATTTTA
Found at i:536525 original size:15 final size:15
Alignment explanation
Indices: 536505--536535 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
536495 AATTAATCTT
536505 TTAAATCTATTTTTA
1 TTAAATCTATTTTTA
536520 TTAAATCTATTTTTA
1 TTAAATCTATTTTTA
536535 T
1 T
536536 GAGATTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAAATCTATTTTTA
Found at i:539109 original size:10 final size:11
Alignment explanation
Indices: 539090--539114 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
539080 GTGGAAACAA
539090 TTTTCTTTTTT
1 TTTTCTTTTTT
539101 TTTTCTTTTTT
1 TTTTCTTTTTT
539112 TTT
1 TTT
539115 GTGCACTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:541587 original size:14 final size:14
Alignment explanation
Indices: 541568--541614 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
541558 TTGATACATT
541568 ACTGTTCATGTATA
1 ACTGTTCATGTATA
541582 ACTGTTCA--T-TA
1 ACTGTTCATGTATA
*
541593 A-TGTTCATGTATC
1 ACTGTTCATGTATA
541606 ACTGTTCAT
1 ACTGTTCAT
541615 CATTGTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
10 6 0.21
11 3 0.11
12 2 0.07
13 2 0.07
14 15 0.54
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.45
Consensus pattern (14 bp):
ACTGTTCATGTATA
Found at i:541597 original size:24 final size:24
Alignment explanation
Indices: 541564--541628 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
541554 TTAATTGATA
*
541564 CATTACTGTTCATGTATAACTGTT
1 CATTAATGTTCATGTATAACTGTT
*
541588 CATTAATGTTCATGTATCACTGTT
1 CATTAATGTTCATGTATAACTGTT
* *
541612 CATCATTGTTCATGTAT
1 CATTAATGTTCATGTAT
541629 CGATACAGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (24 bp):
CATTAATGTTCATGTATAACTGTT
Found at i:543789 original size:20 final size:21
Alignment explanation
Indices: 543764--543812 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
543754 GGAGAAAATG
*
543764 AATGAGTTAGAAAA-GAAAAA
1 AATGAGTTACAAAATGAAAAA
*
543784 AATGAGTTACAAAATGAAAAT
1 AATGAGTTACAAAATGAAAAA
*
543805 GATGAGTT
1 AATGAGTT
543813 GGCTAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.55, C:0.02, G:0.20, T:0.22
Consensus pattern (21 bp):
AATGAGTTACAAAATGAAAAA
Found at i:543809 original size:21 final size:20
Alignment explanation
Indices: 543756--543812 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
543746 GAATTAGAGG
*
543756 AGAAAATGAATGAGTTAGAAA
1 AGAAAATG-ATGAGTTACAAA
**
543777 AGAAAAAAATGAGTTACAAA
1 AGAAAATGATGAGTTACAAA
543797 ATGAAAATGATGAGTT
1 A-GAAAATGATGAGTT
543813 GGCTAATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.21
Consensus pattern (20 bp):
AGAAAATGATGAGTTACAAA
Found at i:544364 original size:38 final size:38
Alignment explanation
Indices: 544313--544562 Score: 261
Period size: 38 Copynumber: 6.6 Consensus size: 38
544303 AATCATATTG
*
544313 AATTCCAAATTGAATTCTCTAATTACCAGCCATC-GACC
1 AATTCCAAATTGAATTCTCTAATTACCAGCCACCAG-CC
544351 AATTCCAAATTGAATTCTCTAATTACCAGCCACC-GACC
1 AATTCCAAATTGAATTCTCTAATTACCAGCCACCAG-CC
*** *
544389 AATTCCAAATTGAATTCTCTAGCCACCAGCCACTAGCC
1 AATTCCAAATTGAATTCTCTAATTACCAGCCACCAGCC
* * * *
544427 AATTCCAAATTGAATTCTCTAGTTGCTAGCTACCAGCC
1 AATTCCAAATTGAATTCTCTAATTACCAGCCACCAGCC
* * * ***
544465 TATTCCATATTGAATTCTCTAGTCGTCAGCCACCAGCC
1 AATTCCAAATTGAATTCTCTAATTACCAGCCACCAGCC
** ** *
544503 AATTCCAAATTGAATTCTCTAACCATAAGCTACCAGCC
1 AATTCCAAATTGAATTCTCTAATTACCAGCCACCAGCC
** *
544541 AATTTTAAATTAAATTCTCTAA
1 AATTCCAAATTGAATTCTCTAA
544563 CTGTCAGCCA
Statistics
Matches: 184, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
38 183 0.99
39 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30
Consensus pattern (38 bp):
AATTCCAAATTGAATTCTCTAATTACCAGCCACCAGCC
Found at i:544470 original size:114 final size:114
Alignment explanation
Indices: 544313--544562 Score: 297
Period size: 114 Copynumber: 2.2 Consensus size: 114
544303 AATCATATTG
* *
544313 AATTCCAAATTGAATTCTCTAATTACCAGCCATCGACCAATTCCAAATTGAATTCTCTAATTACC
1 AATTCCAAATTGAATTCTCTAATTACCAGCCACCGACCAATTCCAAATTGAATTCTCTAATCACC
* * *
544378 AGCCACC-GACCAATTCCAAATTGAATTCTCTAGCCACCAGCCACTAGCC
66 AGCCACCAG-CCAATTCCAAATTGAATTCTCTAACCACAAGCCACCAGCC
* * * * * * * **
544427 AATTCCAAATTGAATTCTCTAGTTGCTAGCTACC-AGCCTATTCCATATTGAATTCTCTAGTCGT
1 AATTCCAAATTGAATTCTCTAATTACCAGCCACCGA-CCAATTCCAAATTGAATTCTCTAATCAC
* *
544491 CAGCCACCAGCCAATTCCAAATTGAATTCTCTAACCATAAGCTACCAGCC
65 CAGCCACCAGCCAATTCCAAATTGAATTCTCTAACCACAAGCCACCAGCC
** *
544541 AATTTTAAATTAAATTCTCTAA
1 AATTCCAAATTGAATTCTCTAA
544563 CTGTCAGCCA
Statistics
Matches: 114, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
113 1 0.01
114 112 0.98
115 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30
Consensus pattern (114 bp):
AATTCCAAATTGAATTCTCTAATTACCAGCCACCGACCAATTCCAAATTGAATTCTCTAATCACC
AGCCACCAGCCAATTCCAAATTGAATTCTCTAACCACAAGCCACCAGCC
Found at i:544827 original size:38 final size:38
Alignment explanation
Indices: 544775--544879 Score: 111
Period size: 38 Copynumber: 2.8 Consensus size: 38
544765 GTATACCTTT
* ** *
544775 CAATTCCATATTGAATTCTCTAGTCGTCAACCACCAGG
1 CAATTCCAAATTGAATTCTCTAACCGTCAACCACCAGC
* * * *
544813 GAATTCCAAATTGAATTATCTAACCGTCAGCTACCAGC
1 CAATTCCAAATTGAATTCTCTAACCGTCAACCACCAGC
* * *
544851 CAATTTCAAATTAAATTCTCTAACTGTCA
1 CAATTCCAAATTGAATTCTCTAACCGTCA
544880 TCCAATTCAA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.30
Consensus pattern (38 bp):
CAATTCCAAATTGAATTCTCTAACCGTCAACCACCAGC
Found at i:545029 original size:311 final size:311
Alignment explanation
Indices: 544466--545085 Score: 1107
Period size: 311 Copynumber: 2.0 Consensus size: 311
544456 CTACCAGCCT
* *
544466 ATTCCATATTGAATTCTCTAGTCGTCAGCCACCAGCCAATTCCAAATTGAATTCTCTAACCATAA
1 ATTCCATATTGAATTCTCTAGTCGTCAACCACCAGCCAATTCCAAATTGAATTATCTAACCATAA
* *
544531 GCTACCAGCCAATTTTAAATTAAATTCTCTAACTGTCAGCCAATTTAATTTGAATTTGATTTGGT
66 GCTACCAGCCAATTTCAAATTAAATTCTCTAACTGTCAGCCAATTCAATTTGAATTTGATTTGGT
*
544596 TCATGTAGAAAAGATATACCAACAATTCTCCCCCTCCTGACTACATGGAGGACTCCACAATCCTG
131 TCATGTAGAAAAGATATACCAACAATTCTCCCCCTCCCGACTACATGGAGGACTCCACAATCCTG
544661 CTACTAATCGACAGCACTCAGACTTGTGTGGGCCAATGTCAAAGTCACTTGGTGGTGCTTAACAC
196 CTACTAATCGACAGCACTCAGACTTGTGTGGGCCAATGTCAAAGTCACTTGGTGGTGCTTAACAC
544726 TTTGTGACATTCATTGATGATCATTCAC-AGAAGACATGGGTATACCTTTCA
261 TTTGTGACATTCATTGATGATCATTCACGA-AAGACATGGGTATACCTTTCA
** * *
544777 ATTCCATATTGAATTCTCTAGTCGTCAACCACCAGGGAATTCCAAATTGAATTATCTAACCGTCA
1 ATTCCATATTGAATTCTCTAGTCGTCAACCACCAGCCAATTCCAAATTGAATTATCTAACCATAA
*
544842 GCTACCAGCCAATTTCAAATTAAATTCTCTAACTGTCATCCAATTCAATTTGAATTTGATTTGGT
66 GCTACCAGCCAATTTCAAATTAAATTCTCTAACTGTCAGCCAATTCAATTTGAATTTGATTTGGT
* *
544907 TCATGTAGAAAGGATATACCAACAATTCTCCCCCTCCCGACTACATGGAGGACTCCACAATCTTG
131 TCATGTAGAAAAGATATACCAACAATTCTCCCCCTCCCGACTACATGGAGGACTCCACAATCCTG
*
544972 CTACTAATCGACAGCACTCAGACTTGTGTGGGCCAATGTTAAAGTCACTTGGTGGTGCTTAACAC
196 CTACTAATCGACAGCACTCAGACTTGTGTGGGCCAATGTCAAAGTCACTTGGTGGTGCTTAACAC
545037 TTTGTGACATTCATTGATGATCATTCACGAAAGACATGGGTATACCTTT
261 TTTGTGACATTCATTGATGATCATTCACGAAAGACATGGGTATACCTTT
545086 TAAAATCCAA
Statistics
Matches: 295, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
311 294 1.00
312 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (311 bp):
ATTCCATATTGAATTCTCTAGTCGTCAACCACCAGCCAATTCCAAATTGAATTATCTAACCATAA
GCTACCAGCCAATTTCAAATTAAATTCTCTAACTGTCAGCCAATTCAATTTGAATTTGATTTGGT
TCATGTAGAAAAGATATACCAACAATTCTCCCCCTCCCGACTACATGGAGGACTCCACAATCCTG
CTACTAATCGACAGCACTCAGACTTGTGTGGGCCAATGTCAAAGTCACTTGGTGGTGCTTAACAC
TTTGTGACATTCATTGATGATCATTCACGAAAGACATGGGTATACCTTTCA
Found at i:547616 original size:38 final size:38
Alignment explanation
Indices: 547567--547762 Score: 259
Period size: 38 Copynumber: 5.2 Consensus size: 38
547557 CAAATTGAAT
* *
547567 TGGCTAACGATTAGAGAATTCAATTTGAAATTGGCTGG
1 TGGCTGACGATTAGAGAATTCAATTTGGAATTGGCTGG
* *
547605 CGGCTGACGATTAGAGAATTCAATTTGGAAGTGGCTGG
1 TGGCTGACGATTAGAGAATTCAATTTGGAATTGGCTGG
*
547643 TGGCTGACGACTAGAGAATTCAATTTGGAATTGG-TCGG
1 TGGCTGACGATTAGAGAATTCAATTTGGAATTGGCT-GG
*** *
547681 TGGCTGGTAATTAGAGAATTCAATTTGGAATTAGCTGG
1 TGGCTGACGATTAGAGAATTCAATTTGGAATTGGCTGG
*** *
547719 TGGCTGGTAATTAGAGAATTCAATTTGGAATTAGCTGG
1 TGGCTGACGATTAGAGAATTCAATTTGGAATTGGCTGG
547757 TGGCTG
1 TGGCTG
547763 GCGGTTGGTG
Statistics
Matches: 144, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
37 1 0.01
38 142 0.99
39 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.31, T:0.31
Consensus pattern (38 bp):
TGGCTGACGATTAGAGAATTCAATTTGGAATTGGCTGG
Found at i:548000 original size:15 final size:15
Alignment explanation
Indices: 547980--548009 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
547970 TATGTTATTT
547980 ACTTTTGGAGTTTTG
1 ACTTTTGGAGTTTTG
547995 ACTTTTGGAGTTTTG
1 ACTTTTGGAGTTTTG
548010 GGAAACACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.27, T:0.53
Consensus pattern (15 bp):
ACTTTTGGAGTTTTG
Found at i:549415 original size:121 final size:121
Alignment explanation
Indices: 549259--549499 Score: 321
Period size: 122 Copynumber: 2.0 Consensus size: 121
549249 GCTTTTTTTA
* *
549259 AATAAAAAGTTGGTATTATTTTGCATTAAAGAAG-AAAAAA-TTTAAAAATTAAATCTAGTTGAT
1 AATAAAAAGTTGGTATTATTTTGCATTAAAAAAGAAAAAAAGTTT-AAAATTAAATCTAATTGAT
* *
549322 TCATGTAATT-AATTCAAACAAATTT-TAAATTGGAAT-TTAGCATTCTTATTGGTTGAT
65 TCATGCAATTCAATTCAAACAAATTTATAAATTGAAATATTAGC--T-TTATTGGTTGAT
* * **
549379 AATAAAATGTTGGGTATTATTTTGCTTTAAAAAAGAAAAAAAGTTTAAAATTTGATCTAATTGAT
1 AATAAAAAGTT-GGTATTATTTTGCATTAAAAAAGAAAAAAAGTTTAAAATTAAATCTAATTGAT
*
549444 TCATGCAATTCAATTCAAATAAATTTATAAATTGAAATATTAGCTTTATTGGTTGA
65 TCATGCAATTCAATTCAAACAAATTTATAAATTGAAATATTAGCTTTATTGGTTGA
549500 CAACATTAGG
Statistics
Matches: 106, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
120 10 0.09
121 21 0.20
122 42 0.40
123 18 0.17
124 10 0.09
125 5 0.05
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (121 bp):
AATAAAAAGTTGGTATTATTTTGCATTAAAAAAGAAAAAAAGTTTAAAATTAAATCTAATTGATT
CATGCAATTCAATTCAAACAAATTTATAAATTGAAATATTAGCTTTATTGGTTGAT
Found at i:552393 original size:9 final size:9
Alignment explanation
Indices: 552378--552431 Score: 65
Period size: 9 Copynumber: 6.0 Consensus size: 9
552368 CCTTCATACC
552378 CAAAAAAAA
1 CAAAAAAAA
*
552387 TAAAAAAAA
1 CAAAAAAAA
552396 CCAAAAAAAA
1 -CAAAAAAAA
*
552406 CCAAAAAAA
1 CAAAAAAAA
*
552415 -TAAAAAAA
1 CAAAAAAAA
552423 CAAAAAAAA
1 CAAAAAAAA
552432 TCCAAGGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
8 7 0.18
9 23 0.61
10 8 0.21
ACGTcount: A:0.85, C:0.11, G:0.00, T:0.04
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:552419 original size:16 final size:16
Alignment explanation
Indices: 552399--552430 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
552389 AAAAAAACCA
552399 AAAAAAACCAAAAAAAT
1 AAAAAAA-CAAAAAAAT
552416 AAAAAAACAAAAAAA
1 AAAAAAACAAAAAAA
552431 ATCCAAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (16 bp):
AAAAAAACAAAAAAAT
Found at i:552419 original size:27 final size:28
Alignment explanation
Indices: 552380--552436 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
552370 TTCATACCCA
552380 AAAAAAATAAAAAAAACCAAAAAAAA-CC
1 AAAAAAATAAAAAAAA-CAAAAAAAATCC
552408 AAAAAAAT-AAAAAAACAAAAAAAATCC
1 AAAAAAATAAAAAAAACAAAAAAAATCC
552435 AA
1 AA
552437 GGAAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 9 0.32
27 11 0.39
28 8 0.29
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.05
Consensus pattern (28 bp):
AAAAAAATAAAAAAAACAAAAAAAATCC
Found at i:556365 original size:13 final size:13
Alignment explanation
Indices: 556347--556372 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
556337 ACAAAGATCC
556347 ATGTATCGATACA
1 ATGTATCGATACA
556360 ATGTATCGATACA
1 ATGTATCGATACA
556373 TTGAGTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:556448 original size:19 final size:19
Alignment explanation
Indices: 556424--556485 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
556414 AGCGATACAT
556424 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
556443 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
556456 TGTAT-GATACAACACTTA
1 TGTATCGATACAACACTTA
556474 TGTATCGATACA
1 TGTATCGATACA
556486 GTTACTGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
12 3 0.08
13 5 0.14
14 1 0.03
15 3 0.08
16 3 0.08
17 1 0.03
18 5 0.14
19 15 0.42
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:556468 original size:31 final size:32
Alignment explanation
Indices: 556411--556485 Score: 134
Period size: 31 Copynumber: 2.4 Consensus size: 32
556401 GCAGTAGCTT
*
556411 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
556443 TGTATCGATACATTGTAT-GATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
556474 TGTATCGATACA
1 TGTATCGATACA
556486 GTTACTGTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 25 0.60
32 17 0.40
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:557415 original size:49 final size:49
Alignment explanation
Indices: 557281--557445 Score: 141
Period size: 49 Copynumber: 3.3 Consensus size: 49
557271 TCAGGAATGT
* * * * * **
557281 TAAAGATGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGA
1 TAAAGATGCCAATGTGCTGATTCAAGACCAGCGACACCGGACTTAAAGA
** * * *
557330 TGACGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATACCGGACTTAAAGA
1 T-A--AAGATGCCAATGTGCTGATTCAAGACCAGCGACACCGGACTTAAAGA
* * * **
557382 TGAAGATGCCAATGTGTTGATTCAAGACTAGCGACATTGGACTTAAAGA
1 TAAAGATGCCAATGTGCTGATTCAAGACCAGCGACACCGGACTTAAAGA
*
557431 TAAAGATGTCAATGT
1 TAAAGATGCCAATGT
557446 TAAAGATGCC
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
49 52 0.55
50 1 0.01
52 42 0.44
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (49 bp):
TAAAGATGCCAATGTGCTGATTCAAGACCAGCGACACCGGACTTAAAGA
Found at i:557522 original size:49 final size:49
Alignment explanation
Indices: 557463--558251 Score: 667
Period size: 49 Copynumber: 16.8 Consensus size: 49
557453 GCCGAAGGCA
*
557463 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
* * *
557512 CCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGACGAAGGCG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT---GAAGGTG
* * *
557564 CCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
** * * *
557613 CTGATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATG-ATGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
* * * *
557661 CCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAAAGATGGTTGAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-G--AAGGTG
* * * * * *
557713 CCAATGTGTTGATTCAAGGCCAACGACATCGGTCTTAAAGATAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
* * * *
557762 CTAATATGCTGATTCAAGGCCAGCGATACTGGGC-T-----T----GTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
* * *
557801 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
* * * *
557850 CCAATATGCTGATTCAAAGCCAGCGATACTGGGC-T-----T----GTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
* * * *
557889 CCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGATAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
* ***
557938 CTAATATGCTGATTCAAGGCCAGC-A-A-T--AC-T--AG--GCTTGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
* * * * *
557977 CCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGA-CAATGAG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
* *
558025 CCAATATGCTGATTCAAGGCCAGTGATATTGGACTT--A-A--AA-GTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
* *
558068 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGGTG
*
558120 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
* *
558163 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGGTG
* *
558215 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
558252 GAAGGGTTGC
Statistics
Matches: 596, Mismatches: 90, Indels: 105
0.75 0.11 0.13
Matches are distributed among these distances:
39 87 0.15
40 3 0.01
41 3 0.01
42 1 0.00
43 76 0.13
44 5 0.01
45 5 0.01
46 3 0.01
47 4 0.01
48 79 0.13
49 169 0.28
51 2 0.00
52 159 0.27
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
Found at i:557541 original size:122 final size:122
Alignment explanation
Indices: 557323--557553 Score: 381
Period size: 122 Copynumber: 1.9 Consensus size: 122
557313 GATATTGGAC
*
557323 TTAAAGATGACGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATACCGGACTTAAAGATGAAGA
1 TTAAAGATGACGAAGGCACCAATATGCTGATTCAAGGCCAGCGATACCGGACTTAAAGATGAAGA
* * *
557388 TGCCAATGTGTTGATTCAAGACTAGCGACATTGGACTTAAAGATAAAGATGTCAATG
66 TGCCAATGTGCTGATTCAAGACCAGCAACATTGGACTTAAAGATAAAGATGTCAATG
* ** *
557445 TTAAAGATGCCGAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TTAAAGATGACGAAGGCACCAATATGCTGATTCAAGGCCAGCGATACCGGACTTAAAGATGAAGA
*
557510 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGAT
66 TGCCAATGTGCTGATTCAAGACCAGCAACATTGGACTTAAAGAT
557554 GACGAAGGCG
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
122 100 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (122 bp):
TTAAAGATGACGAAGGCACCAATATGCTGATTCAAGGCCAGCGATACCGGACTTAAAGATGAAGA
TGCCAATGTGCTGATTCAAGACCAGCAACATTGGACTTAAAGATAAAGATGTCAATG
Found at i:557822 original size:39 final size:39
Alignment explanation
Indices: 557759--557999 Score: 167
Period size: 39 Copynumber: 5.7 Consensus size: 39
557749 AAAGATAAAG
*
557759 GTGCTAATATGCTGATTCAAGGCCAGCGATACTGGGCTT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATACTGGGCTT
* * * *
557798 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATACTGGGC-T-----T
*
557843 AAAGGTGCCAATATGCTGATTCAAAGCCAGCGATACTGGGCTT
1 ----GTGCCAATATGCTGATTCAAGGCCAGCGATACTGGGCTT
* * * * *
557886 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATACTGGGC-T-----T
* * *
557931 AAAGGTGCTAATATGCTGATTCAAGGCCAGCAATACTAGGCTT
1 ----GTGCCAATATGCTGATTCAAGGCCAGCGATACTGGGCTT
*
557974 GTGCCAATGTGCTGATTCAAGGCCAG
1 GTGCCAATATGCTGATTCAAGGCCAG
558000 TGACATTGGA
Statistics
Matches: 156, Mismatches: 26, Indels: 40
0.70 0.12 0.18
Matches are distributed among these distances:
39 87 0.56
40 2 0.01
43 2 0.01
45 2 0.01
48 2 0.01
49 61 0.39
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (39 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATACTGGGCTT
Found at i:557859 original size:88 final size:88
Alignment explanation
Indices: 557710--558250 Score: 769
Period size: 88 Copynumber: 6.0 Consensus size: 88
557700 GATGGTTGAG
* * * *
557710 GTGCCAATGTGTTGATTCAAGGCCAACGACATCGGTCTTAAAGATAAAGGTGCTAATATGCTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGAT
557775 TCAAGGCCAGCGATACTGGGCTT
66 TCAAGGCCAGCGATACTGGGCTT
557798 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGAT
*
557863 TCAAAGCCAGCGATACTGGGCTT
66 TCAAGGCCAGCGATACTGGGCTT
* *
557886 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGATAAAGGTGCTAATATGCTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGAT
* *
557951 TCAAGGCCAGCAATACTAGGCTT
66 TCAAGGCCAGCGATACTGGGCTT
* * * * *
557974 GTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGA-CAATGAGCCAATATGCTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGAT
* * *
558038 TCAAGGCCAGTGATATTGGACTT
66 TCAAGGCCAGCGATACTGGGCTT
558061 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATA
1 ----GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT---AAAGGTGCCAATA
* *
558126 TGCTGATTCAAGGCCAGCGATATTGGACTT
59 TGCTGATTCAAGGCCAGCGATACTGGGCTT
558156 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATA
1 ----GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT---AAAGGTGCCAATA
*
558221 TGCTGATTCAAGGCCAGCGATATTGGGCTT
59 TGCTGATTCAAGGCCAGCGATACTGGGCTT
558251 AGAAGGGTTG
Statistics
Matches: 415, Mismatches: 30, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
87 34 0.08
88 207 0.50
91 42 0.10
95 132 0.32
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (88 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGAT
TCAAGGCCAGCGATACTGGGCTT
Found at i:558138 original size:52 final size:52
Alignment explanation
Indices: 558061--558251 Score: 258
Period size: 52 Copynumber: 3.9 Consensus size: 52
558051 TATTGGACTT
*
558061 AAAA-GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGA
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGA
* *
558112 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGA
*
558156 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGA
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGA
* *
558207 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTA
558252 GAAGGGTTGC
Statistics
Matches: 121, Mismatches: 9, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
43 38 0.31
44 1 0.01
46 1 0.01
49 1 0.01
51 5 0.04
52 75 0.62
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (52 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGA
Found at i:558202 original size:43 final size:43
Alignment explanation
Indices: 558113--558256 Score: 153
Period size: 43 Copynumber: 3.1 Consensus size: 43
558103 TAAAGATGAA
*
558113 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
558156 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-T-----T
* *
558205 GAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 ---AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
558251 AGAAGG
1 A-AAGG
558257 GTTGCCACCG
Statistics
Matches: 85, Mismatches: 6, Indels: 19
0.77 0.05 0.17
Matches are distributed among these distances:
43 39 0.46
44 5 0.06
46 1 0.01
49 1 0.01
51 1 0.01
52 38 0.45
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
Found at i:558293 original size:33 final size:33
Alignment explanation
Indices: 558251--558317 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
558241 TATTGGGCTT
*
558251 AGAAGGGTTGCCACCGACTTGTGTGAGCTTTAG
1 AGAAGGGTTGCCACCGACTTATGTGAGCTTTAG
* *
558284 AGAATGGTTGCCACCGACTTATGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTATGTGAGCTTTAG
558317 A
1 A
558318 AGGGGGTGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTATGTGAGCTTTAG
Found at i:558538 original size:34 final size:34
Alignment explanation
Indices: 558428--558548 Score: 167
Period size: 33 Copynumber: 3.6 Consensus size: 34
558418 AGATGCACAG
* ***
558428 GAAAAAAGTGCCACGGAGTTGTGGAC-TTAACTG
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAA
558461 GAAAAAAGTGCCACGGAGTTGTGGGCTTT-AAAA
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAA
*
558494 G-AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAA
*
558527 GAAAAAGGTGCCACGGAGTTGT
1 GAAAAAAGTGCCACGGAGTTGT
558549 CGACTTAAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
32 26 0.32
33 32 0.40
34 22 0.28
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (34 bp):
GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAA
Found at i:558566 original size:27 final size:27
Alignment explanation
Indices: 558528--558587 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
558518 CTTTAAAAAG
* *
558528 AAAAAGGTGCCACGGAGTTGTCGACTT
1 AAAAAGGTGCCACGGAGTTATAGACTT
* *
558555 AAAAGGGTGCCACGGTGTTATAGACTT
1 AAAAAGGTGCCACGGAGTTATAGACTT
558582 AAAAAG
1 AAAAAG
558588 AAAAAGAGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (27 bp):
AAAAAGGTGCCACGGAGTTATAGACTT
Found at i:558939 original size:32 final size:32
Alignment explanation
Indices: 558733--559334 Score: 635
Period size: 32 Copynumber: 18.9 Consensus size: 32
558723 TGGGGGCTTA
* * **
558733 AAGAAGAA-ATGCCACTGAGTCATGGACTTTA
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTGG
*
558764 AAG-AAAATATGCCACTGAGTCGTGGACTTTGGG
1 AAGAAAAAGATGCCACTGAGTCGTGGAC-TT-GG
*
558797 AAGAGAAAAGATGCCACTAAGTCGTGGACTTGG
1 AAGA-AAAAGATGCCACTGAGTCGTGGACTTGG
* * **
558830 -A-AAAGAGATGCCACTGAGTTGTGGACTTTA
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTGG
*
558860 AAGAAAAGCGATGCCACTGAGTCGTGGACTT--
1 AAGAAAA-AGATGCCACTGAGTCGTGGACTTGG
*
558891 -AGAAAAGAGATGCCACTAAGTCGTGGACTTGG
1 AAGAAAA-AGATGCCACTGAGTCGTGGACTTGG
* **
558923 AAGAAAAAGATGCCACTGAGTCATGGACTTTA
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTGG
* *
558955 AAGAAAAGGATGCCACTGAGTTGTGGACTT--
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTGG
* * **
558985 -AGAAAAGAGATGCTACTGAGTTGTGGACTTAC
1 AAGAAAA-AGATGCCACTGAGTCGTGGACTTGG
* *
559017 AGGAAAAAGGGATGCCACTGACTCGTGGACTTGG
1 AAGAAAAA--GATGCCACTGAGTCGTGGACTTGG
*
559051 AAGAAAAAGATGTCACTGAGTCGTGGACTTGG
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTGG
*
559083 AAGAAAAGGATGCCACTGAGTCGTGGACTT--
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTGG
* * *
559113 -AGAAAATAGATGCCACTAAGTTGTGGACTTTG
1 AAGAAAA-AGATGCCACTGAGTCGTGGACTTGG
*
559145 AAGAAAAAAGATGGCACTGAGTCGTGGACTTGG
1 AAG-AAAAAGATGCCACTGAGTCGTGGACTTGG
*
559178 AAGAAAAGGATGCCACTGAGTCGTGGACTT--
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTGG
**
559208 -AGAAAAGAGATGCCACTGAGTCGTGGACTTTA
1 AAGAAAA-AGATGCCACTGAGTCGTGGACTTGG
* * *
559240 AAGAAAAAAATGCCACTGTGTTGTGGACTTGG
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTGG
559272 AAGAAAAAAGATGCCACTGAGTCGTGGACTTGG
1 AAG-AAAAAGATGCCACTGAGTCGTGGACTTGG
**
559305 AAG-AAAAGAATGCCACTGAGTTATGGACTT
1 AAGAAAAAG-ATGCCACTGAGTCGTGGACTT
559335 CGAGAAGAGA
Statistics
Matches: 487, Mismatches: 56, Indels: 55
0.81 0.09 0.09
Matches are distributed among these distances:
29 18 0.04
30 117 0.24
31 28 0.06
32 172 0.35
33 98 0.20
34 32 0.07
35 22 0.05
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.22
Consensus pattern (32 bp):
AAGAAAAAGATGCCACTGAGTCGTGGACTTGG
Found at i:558958 original size:95 final size:95
Alignment explanation
Indices: 558733--559334 Score: 660
Period size: 95 Copynumber: 6.3 Consensus size: 95
558723 TGGGGGCTTA
* * *
558733 AAGAAGAA-ATGCCACTGAGTCATGGACTTTAAAG-AAAATATGCCACTGAGTCGTGGACTTTGG
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGAC-TT--
*
558796 GAAGAGAAA-AGATGCCACTAAGTCGTGGACTTGG
63 G-AGA-AAAGAGATGCCACTGAGTCGTGGACTTGG
* * *
558830 -A-AAAGAGATGCCACTGAGTTGTGGACTTTAAAGAAAAGCGATGCCACTGAGTCGTGGACTT-A
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTTAAAGAAAA-AGATGCCACTGAGTCGTGGACTTGA
*
558892 GAAAAGAGATGCCACTAAGTCGTGGACTTGG
65 GAAAAGAGATGCCACTGAGTCGTGGACTTGG
* * *
558923 AAGAAAAAGATGCCACTGAGTCATGGACTTTAAAGAAAAGGATGCCACTGAGTTGTGGACTT-AG
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTGAG
* * **
558987 AAAAGAGATGCTACTGAGTTGTGGACTTAC
66 AAAAGAGATGCCACTGAGTCGTGGACTTGG
* * ** *
559017 AGGAAAAAGGGATGCCACTGACTCGTGGACTTGGAAGAAAAAGATGTCACTGAGTCGTGGACTTG
1 AAGAAAAA--GATGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTT-
559082 GAAGAAAAG-GATGCCACTGAGTCGTGGACTT--
63 G-AGAAAAGAGATGCCACTGAGTCGTGGACTTGG
* * * *
559113 -AGAAAATAGATGCCACTAAGTTGTGGACTTTGAAGAAAAAAGATGGCACTGAGTCGTGGACTTG
1 AAGAAAA-AGATGCCACTGAGTCGTGGACTTTAAAG-AAAAAGATGCCACTGAGTCGTGGACTT-
559177 GAAGAAAAG-GATGCCACTGAGTCGTGGACTT--
63 G-AGAAAAGAGATGCCACTGAGTCGTGGACTTGG
* * *
559208 -AGAAAAGAGATGCCACTGAGTCGTGGACTTTAAAGAAAAAAATGCCACTGTGTTGTGGACTTGG
1 AAGAAAA-AGATGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTT-G
*
559272 AAGAAAAAAGATGCCACTGAGTCGTGGACTTGG
64 -AGAAAAGAGATGCCACTGAGTCGTGGACTTGG
**
559305 AAG-AAAAGAATGCCACTGAGTTATGGACTT
1 AAGAAAAAG-ATGCCACTGAGTCGTGGACTT
559335 CGAGAAGAGA
Statistics
Matches: 444, Mismatches: 43, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
92 3 0.01
93 28 0.06
94 111 0.25
95 152 0.34
96 75 0.17
97 27 0.06
98 41 0.09
99 7 0.02
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.22
Consensus pattern (95 bp):
AAGAAAAAGATGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTGAG
AAAAGAGATGCCACTGAGTCGTGGACTTGG
Found at i:559343 original size:127 final size:124
Alignment explanation
Indices: 558736--559345 Score: 701
Period size: 127 Copynumber: 4.8 Consensus size: 124
558726 GGGCTTAAAG
* ** * * *
558736 AAGAAATGCCACTGAGTCATGGACTTTAA-AGAAAATATGCCACTGAGTCGTGGACTTTGGGAAG
1 AAGAGATGCCACTGAGTTGTGGACTTGAAGAAAAAAGATGCCACTGAGTCGTGGAC-TT-GGAAG
* * * *
558800 AGAAAAGATGCCACTAAGTCGTGGACTTGGAAAAGAGATGCCACTGAGTTGTGGACTTTAAAGAA
64 A-AAAAGATGCCACTGAGTCGTGGACTTAGAGAAGAGATGCCACTGAGTCGTGGAC-TT--AGAA
* * * *
558865 AAGCGATGCCACTGAGTCGTGGACTT--AGAAAAGAGATGCCACTAAGTCGTGGACTTGGAAGAA
1 AAGAGATGCCACTGAGTTGTGGACTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTGGAAGAA
* * * *
558928 AAAGATGCCACTGAGTCATGGACTTTAAAGAAAAGGATGCCACTGAGTTGTGGACTTAGAA
66 AAAGATGCCACTGAGTCGTGGAC-TTAGAGAAGA-GATGCCACTGAGTCGTGGACTTAGAA
* * *
558989 AAGAGATGCTACTGAGTTGTGGACTT-ACAGGAAAAAGGGATGCCACTGACTCGTGGACTTGGAA
1 AAGAGATGCCACTGAGTTGTGGACTTGA-A-GAAAAA-AGATGCCACTGAGTCGTGGACTTGGAA
* * *
559053 GAAAAAGATGTCACTGAGTCGTGGACTTGGAAGAAAAGGATGCCACTGAGTCGTGGACTTAGAA
63 GAAAAAGATGCCACTGAGTCGTGGACTTAG-AGAAGA-GATGCCACTGAGTCGTGGACTTAGAA
* * *
559117 AATAGATGCCACTAAGTTGTGGACTTTGAAGAAAAAAGATGGCACTGAGTCGTGGACTTGGAAGA
1 AAGAGATGCCACTGAGTTGTGGAC-TTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTGGAAGA
* *
559182 AAAGGATGCCACTGAGTCGTGGACTTAGAAAAGAGATGCCACTGAGTCGTGGACTTTAAAGAA
65 AAAAGATGCCACTGAGTCGTGGACTTAGAGAAGAGATGCCACTGAGTCGTGGAC-TT--AGAA
* *
559245 AA-AAATGCCACTGTGTTGTGGACTTGGAAGAAAAAAGATGCCACTGAGTCGTGGACTTGGAAG-
1 AAGAGATGCCACTGAGTTGTGGACTT-GAAGAAAAAAGATGCCACTGAGTCGTGGACTTGGAAGA
** *
559308 AAAAGAATGCCACTGAGTTATGGACTTCGAGAAGAGAT
65 AAAAG-ATGCCACTGAGTCGTGGACTTAGAGAAGAGAT
559346 TTGAAGAATT
Statistics
Matches: 421, Mismatches: 45, Indels: 32
0.85 0.09 0.06
Matches are distributed among these distances:
124 27 0.06
125 42 0.10
126 27 0.06
127 163 0.39
128 135 0.32
129 26 0.06
130 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.22
Consensus pattern (124 bp):
AAGAGATGCCACTGAGTTGTGGACTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTGGAAGAA
AAAGATGCCACTGAGTCGTGGACTTAGAGAAGAGATGCCACTGAGTCGTGGACTTAGAA
Found at i:572112 original size:1 final size:1
Alignment explanation
Indices: 572106--572176 Score: 79
Period size: 1 Copynumber: 71.0 Consensus size: 1
572096 TGGCAATTGG
* * * ** * *
572106 AAAAAAAAAAAACAAAACAAAAAAAAAAGAAAAAAACCAAAAAAAAAACAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
572171 AAAAAA
1 AAAAAA
572177 GTGAAGATTT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.90, C:0.08, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:572148 original size:31 final size:29
Alignment explanation
Indices: 572105--572176 Score: 108
Period size: 31 Copynumber: 2.4 Consensus size: 29
572095 ATGGCAATTG
*
572105 GAAAAAAAAAAAACAAAACAAAAAAAAAA
1 GAAAAAAAAAAAAAAAAACAAAAAAAAAA
572134 GAAAAAAACCAAAAAAAAAACAAAAAAAAAA
1 GAAAAAAA--AAAAAAAAAACAAAAAAAAAA
*
572165 CAAAAAAAAAAA
1 GAAAAAAAAAAA
572177 GTGAAGATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 12 0.31
31 27 0.69
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (29 bp):
GAAAAAAAAAAAAAAAAACAAAAAAAAAA
Found at i:572148 original size:36 final size:35
Alignment explanation
Indices: 572108--572176 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 35
572098 GCAATTGGAA
572108 AAAAAAAAAACAAAACAAAAAA-AAAAGAAAAAAACC
1 AAAAAAAAAACAAAA-AAAAAACAAAA-AAAAAAACC
572144 AAAAAAAAAACAAAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAACAAAAAAAAAACAAAAAAAAAAA
572177 GTGAAGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
35 13 0.41
36 19 0.59
ACGTcount: A:0.90, C:0.09, G:0.01, T:0.00
Consensus pattern (35 bp):
AAAAAAAAAACAAAAAAAAAACAAAAAAAAAAACC
Found at i:572175 original size:11 final size:11
Alignment explanation
Indices: 572108--572175 Score: 100
Period size: 11 Copynumber: 5.9 Consensus size: 11
572098 GCAATTGGAA
572108 AAAAAAAAAAC
1 AAAAAAAAAAC
*
572119 AAAACAAAAAAA
1 AAAA-AAAAAAC
572131 AAAGAAAAAAACC
1 AAA-AAAAAAA-C
572144 AAAAAAAAAAC
1 AAAAAAAAAAC
572155 AAAAAAAAAAC
1 AAAAAAAAAAC
572166 AAAAAAAAAA
1 AAAAAAAAAA
572176 AGTGAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
11 26 0.50
12 22 0.42
13 4 0.08
ACGTcount: A:0.90, C:0.09, G:0.01, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:577927 original size:19 final size:19
Alignment explanation
Indices: 577903--577987 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
577893 AGCGATACAT
577903 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
577922 TGTATCGAT---GCA--T-
1 TGTATCGATACAACACTTA
*
577935 TGTATTGATACAACACTTA
1 TGTATCGATACAACACTTA
* *
577954 TGTATCGATACAATGACTGTT
1 TGTATCGATACAA-CACT-TA
577975 TGTATCGATACAA
1 TGTATCGATACAA
577988 ATTGTTGAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
13 8 0.15
14 1 0.02
16 4 0.08
18 1 0.02
19 21 0.40
20 3 0.06
21 14 0.27
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:577945 original size:32 final size:32
Alignment explanation
Indices: 577890--577965 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
577880 GCAGTAGCTT
*
577890 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
* *
577922 TGTATCGATGCATTGTATTGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
577954 TGTATCGATACA
1 TGTATCGATACA
577966 ATGACTGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:578756 original size:28 final size:28
Alignment explanation
Indices: 578724--579490 Score: 922
Period size: 28 Copynumber: 26.6 Consensus size: 28
578714 TCTTCAAAAT
*
578724 CCACAAATCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* *
578752 CCACAAGTTAGTGGCACCATTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
578780 CCACGAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
578808 CCACATAAGTCAATGGCACCCTTTCAAAGC
1 CCAC--AAGTCAGTGGCACCCTTTCAAAGC
*
578838 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
578866 CCACAAGTCAGTAGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* *
578894 CCACAAGTTAGTGGCACCCATTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
** *
578922 CCACACGAGTTGGTGGCAACTCTTTTCAAAGC
1 CCACA--AGTCAGTGGC-AC-CCTTTCAAAGC
* *
578954 CCACAAGTTAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
578982 CCACAAGTTAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* *
579010 CCACACGAGTCGGTGGCAACTCTTTTCAAAGC
1 CCACA--AGTCAGTGGC-AC-CCTTTCAAAGC
* *
579042 CCACATGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
579070 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
579098 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* *
579126 CCATAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * *
579154 CTACAAGTTAGTGGCACCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
579182 CCACAAGTTAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
579210 CCACAAGTCAGTGGCATTCCTTTCAAAGC
1 CCACAAGTCAGTGGCA-CCCTTTCAAAGC
*
579239 CCACAAGTTAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
579267 CCACAAGTCAGTGGCATTCCTTTCAAAGC
1 CCACAAGTCAGTGGCA-CCCTTTCAAAGC
* * * * *
579296 CCACGAGTCGGTGGAAAATCTTTTCAAAGC
1 CCACAAGTCAGTGG--CACCCTTTCAAAGC
* *
579326 TCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * *
579354 CCACAAGTCAATGGTACTCTTTCAAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
579382 CCACAAGTCAATGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* *
579410 CCACAAGTCAGTGGAACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
* * *
579439 CCACACGAGTCAATGGTAACTCTTTTCAAAGCC
1 CCACA--AGTCAGTGG-CAC-CCTTTCAAAG-C
*
579472 CACACAAGTTAGTGGCACC
1 C-CACAAGTCAGTGGCACC
579491 TTTTTAAAAA
Statistics
Matches: 648, Mismatches: 71, Indels: 38
0.86 0.09 0.05
Matches are distributed among these distances:
28 428 0.66
29 66 0.10
30 83 0.13
31 15 0.02
32 50 0.08
33 2 0.00
34 4 0.01
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (28 bp):
CCACAAGTCAGTGGCACCCTTTCAAAGC
Found at i:579323 original size:200 final size:197
Alignment explanation
Indices: 578724--579493 Score: 981
Period size: 200 Copynumber: 3.8 Consensus size: 197
578714 TCTTCAAAAT
* * * *
578724 CCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCATTTCAAAGCCCACGAGTC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTC
*
578789 AGTGGCACCCTTTCAAAGCCCACATAAGTCAATGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGC
66 AGTGGCACCCTTTCAAAGCCCAC--AAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGC
* * * *
578853 ATCCTTTCAAAGCCCACAAGTCAGTAGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCATTCA
129 ATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
578918 AAGC
194 AAGC
** *
578922 CCACACGAGTTGGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCATCC-TTTCAAAGCCCAC
1 CCACA--AGTCAGTGGC-A-TCCTTTCAAAGCCCACAAGTTAGTGGCA-CCTTTTCAAAGCCCAC
* * * *
578986 AAGTTAGTGGCACCCTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACATGTC
61 AAGTCAGTGGCACCCTTTCAAAGCCCACA--AGTCAGTGGC-ACTCCTTTCAAAGCCCACAAGTC
579051 AGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACC
123 AGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACC
579116 CTTTCAAAGC
188 CTTTCAAAGC
* * *
579126 CCATAAGTCAGTGGCATCCTTTCAAAGCCTACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTT
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTC
* * *
579191 AGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATTCCTTTCAAAGCCCACAAGTTAGTGGCAC
66 AGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAT
* * * * *
579256 CCTTTCAAAGCCCACAAGTCAGTGGCATTCCTTTCAAAGCCCACGAGTCGGTGGAAAATCTTTTC
131 CCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGG--CACCCTTTC
579321 AAAGC
193 AAAGC
* * * * *
579326 TCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGTA-CTCTTTCAAAGTCCACAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCT-TTTCAAAGCCCACAAGT
* * * *
579390 CAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGAACTCTTTTCAAAGCCCACACGAGTCAATGG
65 CAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA--AGTCAGTGG
* * *
579455 TAACTCTTTTCAAAGCCCACACAAGTTAGTGGCA-CCTTT
128 -CA-TCCTTTCAAAG-CC-CACAAGTCAGTGGCATCCTTT
579494 TTAAAAAAAG
Statistics
Matches: 503, Mismatches: 49, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
197 53 0.11
198 38 0.08
199 4 0.01
200 190 0.38
201 2 0.00
202 88 0.17
203 5 0.01
204 107 0.21
205 2 0.00
206 14 0.03
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (197 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTC
AGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAT
CCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
GC
Done.