Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 79 of 144
Found at i:17602012 original size:21 final size:21
Alignment explanation
Indices: 17601981--17602035 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
17601971 ACACGTGGCA
17601981 AAAATAATAAAAAATAAAAAAT
1 AAAATAATAAAAAAT-AAAAAT
17602003 AAAA-AATAAAAAATAAAAAT
1 AAAATAATAAAAAATAAAAAT
*
17602023 AAAAGTTATAAAA
1 AAAA-TAATAAAA
17602036 TTTTAGTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 10 0.33
21 10 0.33
22 10 0.33
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (21 bp):
AAAATAATAAAAAATAAAAAT
Found at i:17602642 original size:29 final size:29
Alignment explanation
Indices: 17602600--17602662 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
17602590 AATAATACAA
* * *
17602600 ATACAGTTATAGATTTAGTCATGTCACAG
1 ATACAGTCACAGATATAGTCATGTCACAG
*
17602629 ATACAGTCACAGATATAGTCATGTCATAG
1 ATACAGTCACAGATATAGTCATGTCACAG
17602658 ATACA
1 ATACA
17602663 ATTACGGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (29 bp):
ATACAGTCACAGATATAGTCATGTCACAG
Found at i:17602680 original size:29 final size:29
Alignment explanation
Indices: 17602610--17602688 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 29
17602600 ATACAGTTAT
* * *
17602610 AGATTTAGTCATGTCACAGATACAGTCAC
1 AGATATAGACATGTCACAGATACAATCAC
* * *
17602639 AGATATAGTCATGTCATAGATACAATTAC
1 AGATATAGACATGTCACAGATACAATCAC
* *
17602668 GGATGTAGACATGAT-ACAGAT
1 AGATATAGACATG-TCACAGAT
17602689 GCAGTTACAG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 40 0.98
30 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (29 bp):
AGATATAGACATGTCACAGATACAATCAC
Found at i:17602858 original size:40 final size:40
Alignment explanation
Indices: 17602799--17602934 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 40
17602789 GACACATCGC
* *
17602799 AGTGTTTACAGTGTTACTGCTAGTTTAGTTGTAATCTTGT
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTTGTAATCTTGT
** * *
17602839 AGTGTTTACAGTGTCACTGCCGGTTCAATTG-AAGTCTTAT
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTTGTAA-TCTTGT
* * *
17602879 AGTGATAACAGTGTCACTG-TCAGTTCAGTTGTAATCTTGC
1 AGTGTTTACAGTGTCACTGCT-AGTTCAGTTGTAATCTTGT
17602919 AGTGTTTACAGTGTCA
1 AGTGTTTACAGTGTCA
17602935 TTACTGGTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 74 0.95
41 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (40 bp):
AGTGTTTACAGTGTCACTGCTAGTTCAGTTGTAATCTTGT
Found at i:17603423 original size:53 final size:53
Alignment explanation
Indices: 17603348--17603480 Score: 169
Period size: 53 Copynumber: 2.5 Consensus size: 53
17603338 TGTGTCTCAA
* * *
17603348 AACAGTATACACAGACCCTGACACACG-CTCATGTGTCAGCCCATGTGCCCCAG
1 AACAATATACACACACCTTGACACACGCCT-ATGTGTCAGCCCATGTGCCCCAG
* * * *
17603401 AACAATATGCACACACCTTGACACACACCTATGTGTCAGCCCGTGTGCCTCAG
1 AACAATATACACACACCTTGACACACGCCTATGTGTCAGCCCATGTGCCCCAG
* *
17603454 AATAACATACACACACCTTGACACACG
1 AACAATATACACACACCTTGACACACG
17603481 TCCGTATGCC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
53 66 0.97
54 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.16, T:0.18
Consensus pattern (53 bp):
AACAATATACACACACCTTGACACACGCCTATGTGTCAGCCCATGTGCCCCAG
Found at i:17603520 original size:43 final size:43
Alignment explanation
Indices: 17603462--17603612 Score: 203
Period size: 43 Copynumber: 3.5 Consensus size: 43
17603452 AGAATAACAT
* * * *
17603462 ACACACACCTTGACACACGTCCGTATGCCTCCAAACAGTATAC
1 ACACACACCCTGACACACGCCCATGTGCCTCCAAACAGTATAC
** * *
17603505 GTACATACCCTGACACACGCCCATGTGTCTCCAAACAGTATAC
1 ACACACACCCTGACACACGCCCATGTGCCTCCAAACAGTATAC
* * *
17603548 CCACACACCCTGACACATGTCCATGTGCCTCCAAACAGTATAC
1 ACACACACCCTGACACACGCCCATGTGCCTCCAAACAGTATAC
17603591 ACACACACCCTGACACACGCCC
1 ACACACACCCTGACACACGCCC
17603613 GTGTACCAGC
Statistics
Matches: 91, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.31, C:0.40, G:0.12, T:0.17
Consensus pattern (43 bp):
ACACACACCCTGACACACGCCCATGTGCCTCCAAACAGTATAC
Found at i:17604794 original size:21 final size:20
Alignment explanation
Indices: 17604753--17604795 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
17604743 TTAGGGATCC
* *
17604753 TTAACTTTAATGGTCAATGG
1 TTAAATTTAATGGTAAATGG
17604773 TTAAATTTAATGGTTAAATGG
1 TTAAATTTAATGG-TAAATGG
17604794 TT
1 TT
17604796 TTTTTGATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.44
Consensus pattern (20 bp):
TTAAATTTAATGGTAAATGG
Found at i:17604830 original size:19 final size:18
Alignment explanation
Indices: 17604808--17604935 Score: 73
Period size: 20 Copynumber: 6.8 Consensus size: 18
17604798 TTTGATGCAT
17604808 TTTATAATTTTTATAAAA
1 TTTATAATTTTTATAAAA
* **
17604826 GTTTACAATTTTTTATAACTT
1 -TTTATAA-TTTTTATAA-AA
* *
17604847 TTTATGATTTCTGTAAAAAA
1 TTTATAATTT-T-TATAAAA
* *
17604867 ATTATAATTTTTAATAAAC
1 TTTATAATTTTT-ATAAAA
*
17604886 TTTATATTTTTTATTAAAA
1 TTTATAATTTTTA-TAAAA
* *
17604905 TGTAATAATTCTTAT-AAA
1 T-TTATAATTTTTATAAAA
17604923 TTT-T-ATTTTTATA
1 TTTATAATTTTTATA
17604936 TTTTTTTGTC
Statistics
Matches: 81, Mismatches: 20, Indels: 19
0.68 0.17 0.16
Matches are distributed among these distances:
15 7 0.09
16 1 0.01
17 1 0.01
18 6 0.07
19 30 0.37
20 32 0.40
21 4 0.05
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTATAATTTTTATAAAA
Found at i:17605208 original size:88 final size:87
Alignment explanation
Indices: 17605046--17605313 Score: 317
Period size: 88 Copynumber: 3.1 Consensus size: 87
17605036 CCAAAAGACT
* * * * *
17605046 TTTTTGATGCA-TTTGACAGTTCAAATACTCAATTGAGTGA-AAAAAAATAGGGGATTAATTGCT
1 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGT-ACAAAAAAAAAGGGGCTTAATTGCT
*
17605109 TTTTTTGAAAAAGTTTGTGGGCC
65 TTTTTTGAAAAAGTTTGAGGGCC
* * *
17605132 TTTTTGATGCATTTTGAAAGTTTAAGCACCCAATTGAGTACAAAAAAGACAGGGGCTTAATTGCT
1 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTACAAAAAA-AAAGGGGCTTAATTGCT
* *
17605197 TTTTTTGAAAAAATTTGAGGGTC
65 TTTTTTGAAAAAGTTTGAGGGCC
** *
17605220 TTTTTGATGCATTTTGGTAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGTAAGGGCTTAATTG
1 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTACAAAAAAAAAG---GGGCTTAATTG
* * *
17605285 CATTTTTTAAAAAAGTTTTAGGG-C
63 CTTTTTTTGAAAAAGTTTGAGGGCC
17605309 TTTTT
1 TTTTT
17605314 ACACCCTTAA
Statistics
Matches: 156, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
86 12 0.08
87 31 0.20
88 77 0.49
89 6 0.04
90 30 0.19
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.37
Consensus pattern (87 bp):
TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTACAAAAAAAAAGGGGCTTAATTGCTT
TTTTTGAAAAAGTTTGAGGGCC
Found at i:17605898 original size:18 final size:18
Alignment explanation
Indices: 17605847--17605900 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
17605837 GACACATAAT
*
17605847 ATATATAAGTTAATAAAA
1 ATATATAAATTAATAAAA
* *
17605865 ATA-AAAAATCT-TTAAAA
1 ATATATAAAT-TAATAAAA
17605882 ATATATAAATTAATAAAA
1 ATATATAAATTAATAAAA
17605900 A
1 A
17605901 AGTATAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
ATATATAAATTAATAAAA
Found at i:17614222 original size:46 final size:44
Alignment explanation
Indices: 17614172--17614258 Score: 111
Period size: 46 Copynumber: 1.9 Consensus size: 44
17614162 ATATAGCTAT
*
17614172 AATGGAATAGAGCTGTAATAAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAT-AGTAATTCAA-TGTTTGGTTGAATGG
* * **
17614218 AATGGAATAGAATTGTAATAGTATTTTTATGTTTGGTTGAA
1 AATGGAATAGAACTGTAATAGTAATTCAATGTTTGGTTGAA
17614259 CGAAATGATG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 12 0.33
45 7 0.19
46 17 0.47
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.39
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTAATTCAATGTTTGGTTGAATGG
Found at i:17614423 original size:16 final size:16
Alignment explanation
Indices: 17614399--17614440 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
17614389 TAAAAAAAAA
*
17614399 TAATTTAATTA-TATTT
1 TAATATAATTATTA-TT
17614415 TAATATAATTATTATT
1 TAATATAATTATTATT
*
17614431 AAATATAATT
1 TAATATAATT
17614441 TAATAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATATAATTATTATT
Found at i:17614440 original size:55 final size:54
Alignment explanation
Indices: 17614351--17614526 Score: 174
Period size: 55 Copynumber: 3.0 Consensus size: 54
17614341 TGTTATTGTT
* ** * *
17614351 ATTAAATTTTAATAGGATTATTATTAAATGTAATTTAATAAAAAAAAATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAAAAAATAA-ATA
17614406 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAAAAATAAATA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAAT-AAAA-AAAAATAAATA
*
17614462 ATTTTATAACATTATTAATATAATTATTATTAAAATATGAA-TTAATAAAAATAATAATATATA
1 A--TTAT---ATT-TTAATATAATTATTATT-AAATAT-AATTTAATAAAAA-AA-AATAAATA
17614525 AT
1 AT
17614527 ATTTGAAAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
55 35 0.34
56 7 0.07
57 8 0.08
58 4 0.04
61 5 0.05
62 23 0.22
63 19 0.18
64 2 0.02
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.43
Consensus pattern (54 bp):
ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAAAAAATAAATA
Found at i:17615481 original size:21 final size:20
Alignment explanation
Indices: 17615431--17615484 Score: 99
Period size: 20 Copynumber: 2.6 Consensus size: 20
17615421 GTTCGATTCT
17615431 TTTATTTTGAATTTTCCTTA
1 TTTATTTTGAATTTTCCTTA
17615451 TTTATTTTGAATTTTCCTTA
1 TTTATTTTGAATTTTCCTTA
17615471 TTTATTTTTGAATT
1 TTTA-TTTTGAATT
17615485 ATGCTCAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 24 0.73
21 9 0.27
ACGTcount: A:0.20, C:0.07, G:0.06, T:0.67
Consensus pattern (20 bp):
TTTATTTTGAATTTTCCTTA
Found at i:17617061 original size:23 final size:23
Alignment explanation
Indices: 17616999--17617062 Score: 58
Period size: 25 Copynumber: 2.7 Consensus size: 23
17616989 TTGATATTTG
* *
17616999 TATATACATACACAAACATTATA
1 TATATACATACATATACATTATA
* *
17617022 TATATATATAAGTATATACGA-TATA
1 TATATACAT-A-CATATAC-ATTATA
17617047 TATATACATACATATA
1 TATATACATACATATA
17617063 TGCCCATACA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
23 13 0.41
24 2 0.06
25 16 0.50
26 1 0.03
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.36
Consensus pattern (23 bp):
TATATACATACATATACATTATA
Found at i:17617651 original size:24 final size:23
Alignment explanation
Indices: 17617607--17617651 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
17617597 GGTCCTTTCG
* *
17617607 TATTTTTCATTTGTTTCAAATGC
1 TATTTTTAATTTGTTTAAAATGC
*
17617630 TATTTTTAATTTATTTTAAAAT
1 TATTTTTAATTT-GTTTAAAAT
17617652 TACCCAGTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (23 bp):
TATTTTTAATTTGTTTAAAATGC
Found at i:17617864 original size:30 final size:29
Alignment explanation
Indices: 17617813--17617909 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
17617803 TTTTGATATG
* * *
17617813 CAAACCTTTCCATAATAACATTTTCACCCC
1 CAAACTTTTCCA-AATTACATTTTGACCCC
*
17617843 CAAACTTTTCCAAAGTTACATTTGGACCCC
1 CAAACTTTTCCAAA-TTACATTTTGACCCC
* * ** *
17617873 TAAACTTTTCTAAAATTGTATTTTGACCCT
1 CAAACTTTTC-CAAATTACATTTTGACCCC
17617903 CAAACTT
1 CAAACTT
17617910 CTTTAAAACT
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
29 2 0.04
30 49 0.91
31 3 0.06
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (29 bp):
CAAACTTTTCCAAATTACATTTTGACCCC
Found at i:17617917 original size:30 final size:29
Alignment explanation
Indices: 17617861--17617926 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
17617851 TCCAAAGTTA
* *
17617861 CATTTGGACCCCTAAACTTTTCTAAAATTG
1 CATTTTGA-CCCTAAACTTTTCTAAAACTG
*
17617891 TATTTTGACCCTCAAACTTCTT-TAAAACTG
1 CATTTTGACCCT-AAACTT-TTCTAAAACTG
17617921 CATTTT
1 CATTTT
17617927 CTTTAAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 4 0.13
30 24 0.80
31 2 0.07
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.41
Consensus pattern (29 bp):
CATTTTGACCCTAAACTTTTCTAAAACTG
Found at i:17617930 original size:17 final size:17
Alignment explanation
Indices: 17617908--17617943 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
17617898 ACCCTCAAAC
17617908 TTCTTTAAAACTGCATT
1 TTCTTTAAAACTGCATT
17617925 TTCTTTAAAACTGCATT
1 TTCTTTAAAACTGCATT
17617942 TT
1 TT
17617944 GACCCTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (17 bp):
TTCTTTAAAACTGCATT
Found at i:17617945 original size:47 final size:47
Alignment explanation
Indices: 17617883--17617972 Score: 144
Period size: 47 Copynumber: 1.9 Consensus size: 47
17617873 TAAACTTTTC
* *
17617883 TAAAATTGTATTTTGACCCTCAAACTTCTTTAAAACTGCATTTTCTT
1 TAAAACTGCATTTTGACCCTCAAACTTCTTTAAAACTGCATTTTCTT
* *
17617930 TAAAACTGCATTTTGACCCTCAAACTTCTTTCAAATTGCATTT
1 TAAAACTGCATTTTGACCCTCAAACTTCTTTAAAACTGCATTT
17617973 GACCCCTAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (47 bp):
TAAAACTGCATTTTGACCCTCAAACTTCTTTAAAACTGCATTTTCTT
Found at i:17618083 original size:63 final size:59
Alignment explanation
Indices: 17618016--17618133 Score: 173
Period size: 63 Copynumber: 1.9 Consensus size: 59
17618006 CCCAAAATTT
*
17618016 TTTAAAATTACATTTTGACCCCTAAATTTTTTTAAAAAAATCACATTTTAACCCTTAAATATC
1 TTTAAAATTACATTTTGACCCCTAAA-TTTTCT--AAAAATCACATTTTAA-CCTTAAATATC
* *
17618079 TTTAAAATTACATTTTGACCCTTAAATTTTCTCAAAATCACATTTTAACCTTAAA
1 TTTAAAATTACATTTTGACCCCTAAATTTTCTAAAAATCACATTTTAACCTTAAA
17618134 CCTTCCTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 7 0.13
60 15 0.29
62 5 0.10
63 25 0.48
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.42
Consensus pattern (59 bp):
TTTAAAATTACATTTTGACCCCTAAATTTTCTAAAAATCACATTTTAACCTTAAATATC
Found at i:17618092 original size:30 final size:29
Alignment explanation
Indices: 17617925--17618227 Score: 145
Period size: 30 Copynumber: 10.1 Consensus size: 29
17617915 AAACTGCATT
* * * *
17617925 TTCTTTAAAACTGCATTTTGACCCTCAAA
1 TTCTTTAAAATTACATTTTAACCCTTAAA
* * * * *
17617954 CTTCTTTCAAATTGCA-TTTGACCCCTAAC
1 -TTCTTTAAAATTACATTTTAACCCTTAAA
* * * **
17617983 TT-TTCCAAAATTTCATTTTGACCCCCAAAA
1 TTCTT-TAAAATTACATTTT-AACCCTTAAA
* * *
17618013 TTTTTTAAAATTACATTTTGACCCCTAAA
1 TTCTTTAAAATTACATTTTAACCCTTAAA
* *
17618042 TTTTTTTAAAAAAATCACATTTTAACCCTTAAA
1 -TTCTTT---AAAATTACATTTTAACCCTTAAA
*
17618075 TATCTTTAAAATTACATTTTGACCCTTAAA
1 T-TCTTTAAAATTACATTTTAACCCTTAAA
*
17618105 TT-TTCTCAAAATCACATTTTAA-CCTTAAA
1 TTCTT-T-AAAATTACATTTTAACCCTTAAA
* *
17618134 CCTTC-CTAAAATCACATTTTAACCC-TAAA
1 --TTCTTTAAAATTACATTTTAACCCTTAAA
* * * *
17618163 CTT-TCATAAAATTACCTTTTGACCCCTCCAAA
1 -TTCT-TTAAAATTACATTTT-AACCCT-TAAA
*
17618195 TTCTTCCAAAATTACATTTTAA-CCTTAAA
1 TTCTT-TAAAATTACATTTTAACCCTTAAA
17618224 TTCT
1 TTCT
17618228 CTGAAACTTC
Statistics
Matches: 215, Mismatches: 36, Indels: 45
0.73 0.12 0.15
Matches are distributed among these distances:
27 2 0.01
28 14 0.07
29 67 0.31
30 84 0.39
31 7 0.03
32 17 0.08
33 24 0.11
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (29 bp):
TTCTTTAAAATTACATTTTAACCCTTAAA
Found at i:17618144 original size:29 final size:28
Alignment explanation
Indices: 17618052--17618223 Score: 114
Period size: 29 Copynumber: 5.8 Consensus size: 28
17618042 TTTTTTTAAA
*
17618052 AAAATCACATTTTAACCCTTAAA-TATCTTT
1 AAAATCACATTTTAA-CCTTAAACT-TC-CT
* * * *
17618082 AAAATTACATTTTGACCCTTAAATTTTCT
1 AAAATCACATTTT-AACCTTAAACTTCCT
17618111 CAAAATCACATTTTAACCTTAAACCTTCCT
1 -AAAATCACATTTTAACCTTAAA-CTTCCT
* *
17618141 AAAATCACATTTTAACCCTAAACTTTCAT
1 AAAATCACATTTTAACCTTAAAC-TTCCT
* * * *
17618170 AAAATTACCTTTTGACCCCTCCAAATTCTTCC-
1 AAAATCACATTTT-A-ACCT-TAAA--CTTCCT
*
17618202 AAAATTACATTTTAACCTTAAA
1 AAAATCACATTTTAACCTTAAA
17618224 TTCTCTGAAA
Statistics
Matches: 113, Mismatches: 19, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
28 1 0.01
29 48 0.42
30 40 0.35
31 5 0.04
32 15 0.13
33 3 0.03
34 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (28 bp):
AAAATCACATTTTAACCTTAAACTTCCT
Found at i:17618250 original size:90 final size:87
Alignment explanation
Indices: 17618052--17618223 Score: 231
Period size: 90 Copynumber: 1.9 Consensus size: 87
17618042 TTTTTTTAAA
* * *
17618052 AAAATCACATTTTAACCCTTAAA-TATCTTTAAAATTACATTTTGACCCTTAAATTTTCTCAAAA
1 AAAATCACATTTTAACCC-TAAACTTTC-ATAAAATTACATTTTGACCCTCAAATTTTCTCAAAA
17618116 TCACATTTTAACCTTAAACCTTCCT
64 TCACATTTTAACCTTAAA-CTTCCT
*
17618141 AAAATCACATTTTAACCCTAAACTTTCATAAAATTACCTTTTGACCCCTCCAAATTCTTC-CAAA
1 AAAATCACATTTTAACCCTAAACTTTCATAAAATTACATTTTGA-CCCT-CAAATT-TTCTCAAA
*
17618205 ATTACATTTTAACCTTAAA
63 ATCACATTTTAACCTTAAA
17618224 TTCTCTGAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
88 19 0.26
89 25 0.34
90 27 0.36
91 3 0.04
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (87 bp):
AAAATCACATTTTAACCCTAAACTTTCATAAAATTACATTTTGACCCTCAAATTTTCTCAAAATC
ACATTTTAACCTTAAACTTCCT
Found at i:17638014 original size:40 final size:40
Alignment explanation
Indices: 17637959--17638041 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
17637949 TATTTTGCCT
*
17637959 AAAAAAAGAATCGAGATGAAAACCCGTAAAGGGCGTCTCG
1 AAAAAAAGAATCGAGATGAAAACCCATAAAGGGCGTCTCG
* * *
17637999 AAAAAAAGGATCGAGATGAAAACCCATAAAGGGCTTCTTG
1 AAAAAAAGAATCGAGATGAAAACCCATAAAGGGCGTCTCG
17638039 AAA
1 AAA
17638042 CCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (40 bp):
AAAAAAAGAATCGAGATGAAAACCCATAAAGGGCGTCTCG
Found at i:17639423 original size:122 final size:123
Alignment explanation
Indices: 17639101--17639429 Score: 376
Period size: 124 Copynumber: 2.7 Consensus size: 123
17639091 ACCGAATCCG
* * * *
17639101 TCTTCCAGATGAGATACAGAGAAGTGGATTAAAACAATGAAGCAGTTATCTTCTTGATGAAATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAAGCGGTTATCTTCCTGATGAGATAC
* ** *
17639166 ACAGAAGTAGACCAATTCAATGAAGTGAAGCTCAATGTGAGTGAAACTTCCAAACCTCA
66 A-AGAAGTAGACCAAATCAATGAAGTGAAGCTCAATACGAATGAAACTTCCAAACCTCA
** * * *
17639225 TCTTTTTTATGAGATACAGAGAAGTGGAATAAAACAATGAAGCGATTATCTTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAAGCGGTTATCTTCCTGATGAGATAC
* * * *
17639290 AAAATAGTAGACCAAATCAATTAAGTGAAGCTTAATACGAATGAGACTT-CAAACAC-CA
66 AAGA-AGTAGACCAAATCAATGAAGTGAAGCTCAATACGAATGAAACTTCCAAAC-CTCA
* * * * * * * *
17639348 TCTTCCTGATGAGATAC-GAAAAGTGGGTTAAAACAATAAAACGGTCATCTTCCTAATGTGATAT
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAAGCGGTTATCTTCCTGATGAGATAC
17639412 AGAGAAGTAGACCAAATC
66 A-AGAAGTAGACCAAATC
17639430 CGTCTTCTTG
Statistics
Matches: 171, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
122 51 0.30
123 25 0.15
124 95 0.56
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (123 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAAGCGGTTATCTTCCTGATGAGATAC
AAGAAGTAGACCAAATCAATGAAGTGAAGCTCAATACGAATGAAACTTCCAAACCTCA
Found at i:17641170 original size:30 final size:30
Alignment explanation
Indices: 17641121--17641385 Score: 202
Period size: 30 Copynumber: 8.9 Consensus size: 30
17641111 ATAGTTTACC
* * *
17641121 CCCAACCTTTTCCAGAATTGCATTTTGACT
1 CCCAAACTTCTCCAAAATTGCATTTTGACT
*
17641151 CCCAAACTTCTCCGAAATTGCATTTTGA-T
1 CCCAAACTTCTCCAAAATTGCATTTTGACT
* * *
17641180 CCCAAACTTTTCTAACATTGCATTTTG--T
1 CCCAAACTTCTCCAAAATTGCATTTTGACT
* *
17641208 CCATCAAACTTCTTCAAAATTGCATTTTAAC-
1 CC--CAAACTTCTCCAAAATTGCATTTTGACT
** * *
17641239 CTATAAACTTTTCCAAAATTACATTTTGAC-
1 C-CCAAACTTCTCCAAAATTGCATTTTGACT
*
17641269 CCCTAAACTTCTCCAAAATTGCATTTTGACA
1 CCC-AAACTTCTCCAAAATTGCATTTTGACT
* * * *
17641300 CTCAAACTTTTCCAAAATTACATTTTAAC-
1 CCCAAACTTCTCCAAAATTGCATTTTGACT
* * ** *
17641329 CCTTAAACTTTTCCAAAATCACATTTTAAC-
1 CC-CAAACTTCTCCAAAATTGCATTTTGACT
* *
17641359 CCTCAAATTTCTCCAAAATTACATTTT
1 CC-CAAACTTCTCCAAAATTGCATTTT
17641386 AACCCTTAAA
Statistics
Matches: 193, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
28 3 0.02
29 25 0.13
30 162 0.84
31 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (30 bp):
CCCAAACTTCTCCAAAATTGCATTTTGACT
Found at i:17641277 original size:60 final size:59
Alignment explanation
Indices: 17641127--17641445 Score: 263
Period size: 60 Copynumber: 5.3 Consensus size: 59
17641117 TACCCCCAAC
* * * * *
17641127 CTTTTCCAGAATTGCATTTTGACTCCC-AAACTTCTCCGAAATTGCATTTTGATCC-CAAA
1 CTTTTCCAAAATTACATTTTGAC-CCCTAAACTTCTTCAAAATTGCATTTT-AACCTCAAA
* * * * * *
17641186 CTTTTCTAACATTGCATTTTG-TCCATCAAACTTCTTCAAAATTGCATTTTAACCTATAAA
1 CTTTTCCAAAATTACATTTTGACCCCT-AAACTTCTTCAAAATTGCATTTTAACCT-CAAA
* *
17641246 CTTTTCCAAAATTACATTTTGACCCCTAAACTTCTCCAAAATTGCATTTTGACACTCAAA
1 CTTTTCCAAAATTACATTTTGACCCCTAAACTTCTTCAAAATTGCATTTTAAC-CTCAAA
* * **
17641306 CTTTTCCAAAATTACATTTTAACCCTTAAACTT-TTCCAAAATCACATTTTAACCCTCAAA
1 CTTTTCCAAAATTACATTTTGACCCCTAAACTTCTT-CAAAATTGCATTTTAA-CCTCAAA
* * * * * **
17641366 -TTTCTCCAAAATTACATTTTAACCCTTAAATTTTCCTAAAAATCACATTTTAACC-CTAAA
1 CTTT-TCCAAAATTACATTTTGACCCCTAAA-CTTCTTCAAAATTGCATTTTAACCTC-AAA
* * *
17641426 CCTTCCCAAAATCACATTTT
1 CTTTTCCAAAATTACATTTT
17641446 AACCTTAAAC
Statistics
Matches: 218, Mismatches: 29, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
57 2 0.01
58 3 0.01
59 44 0.20
60 143 0.66
61 25 0.11
62 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (59 bp):
CTTTTCCAAAATTACATTTTGACCCCTAAACTTCTTCAAAATTGCATTTTAACCTCAAA
Found at i:17641316 original size:90 final size:89
Alignment explanation
Indices: 17641127--17641457 Score: 300
Period size: 90 Copynumber: 3.7 Consensus size: 89
17641117 TACCCCCAAC
* * * * * * ** * *
17641127 CTTTTCCAGAATTGCATTTTGA-CTCCCAAACTTCTCCGAAATTGCATTTTGATCCC-AAACTTT
1 CTTTTCCAAAATTACATTTTAACCT-CTAAACTTTTCCAAAATCACATTTTGAACCCTAAACTTC
* * *
17641190 TCTAACATTGCATTTTGTCCATCAAA
65 TCCAAAATTGCATTTTGACC-TCAAA
* * * *
17641216 CTTCTT-CAAAATTGCATTTTAACCTATAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTC
1 CTT-TTCCAAAATTACATTTTAACCTCTAAACTTTTCCAAAATCACATTTTGAACCCTAAACTTC
17641280 TCCAAAATTGCATTTTGACACTCAAA
65 TCCAAAATTGCATTTTGAC-CTCAAA
*
17641306 CTTTTCCAAAATTACATTTTAACC-CTTAAACTTTTCCAAAATCACATTTT-AACCCTCAAATTT
1 CTTTTCCAAAATTACATTTTAACCTC-TAAACTTTTCCAAAATCACATTTTGAACCCT-AAACTT
* * *
17641369 CTCCAAAATTACATTTTAACCCTTAAA
64 CTCCAAAATTGCATTTTGA-CCTCAAA
* * * *
17641396 -TTTTCCTAAAAATCACATTTTAACC-CTAAACCTTCCCAAAATCACATTTT-AACCTTAAACTT
1 CTTTTCC--AAAATTACATTTTAACCTCTAAACTTTTCCAAAATCACATTTTGAACCCTAAACTT
17641458 TCATAAAATT
Statistics
Matches: 207, Mismatches: 25, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
89 60 0.29
90 128 0.62
91 19 0.09
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.37
Consensus pattern (89 bp):
CTTTTCCAAAATTACATTTTAACCTCTAAACTTTTCCAAAATCACATTTTGAACCCTAAACTTCT
CCAAAATTGCATTTTGACCTCAAA
Found at i:17641386 original size:30 final size:30
Alignment explanation
Indices: 17641211--17641532 Score: 224
Period size: 30 Copynumber: 10.8 Consensus size: 30
17641201 ATTTTGTCCA
* * *
17641211 TCAAACTTCTTCAAAATTGCATTTTAA-CC
1 TCAAATTTCTCCAAAATTACATTTTAACCC
* *
17641240 TATAAACTTT-TCCAAAATTACATTTTGACCC
1 T-CAAA-TTTCTCCAAAATTACATTTTAACCC
* * * *
17641271 -CTAAACTTCTCCAAAATTGCATTTTGACAC
1 TC-AAATTTCTCCAAAATTACATTTTAACCC
17641301 TCAAACTTT-TCCAAAATTACATTTTAACCC
1 TCAAA-TTTCTCCAAAATTACATTTTAACCC
* *
17641331 TTAAACTTT-TCCAAAATCACATTTTAACCC
1 TCAAA-TTTCTCCAAAATTACATTTTAACCC
17641361 TCAAATTTCTCCAAAATTACATTTTAACCC
1 TCAAATTTCTCCAAAATTACATTTTAACCC
* *
17641391 TTAAATTT-TCCTAAAAATCACATTTTAACCC
1 TCAAATTTCTCC--AAAATTACATTTTAACCC
* *
17641422 T-AAACCTTC-CCAAAATCACATTTTAA-CC
1 TCAAA-TTTCTCCAAAATTACATTTTAACCC
* * *
17641450 TTAAACTTTCAT--AAAATTTCCTTTTAACCC
1 TCAAA-TTTC-TCCAAAATTACATTTTAACCC
* * * *
17641480 CCGAA-TTCTTCCAAAATTATATTTTAA-TC
1 TCAAATTTC-TCCAAAATTACATTTTAACCC
*
17641509 TCATA-TTCTCCAAAACTT-CATTTT
1 TCAAATTTCTCCAAAA-TTACATTTT
17641533 TGACCCCATT
Statistics
Matches: 238, Mismatches: 36, Indels: 39
0.76 0.12 0.12
Matches are distributed among these distances:
28 19 0.08
29 51 0.21
30 139 0.58
31 29 0.12
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (30 bp):
TCAAATTTCTCCAAAATTACATTTTAACCC
Found at i:17641446 original size:60 final size:60
Alignment explanation
Indices: 17641213--17641458 Score: 279
Period size: 60 Copynumber: 4.1 Consensus size: 60
17641203 TTTGTCCATC
** * * * *
17641213 AAACTTCTT-CAAAATTGCATTTTAA-CCTATAAACTTTTCCAAAATTACATTTTGACCCCT
1 AAACTT-TTCCAAAATCACATTTTAACCCT-CAAACTTTCCCAAAATTACATTTTAACCCTT
* ** * * *
17641273 AAACTTCTCCAAAATTGCATTTTGACACTCAAACTTTTCCAAAATTACATTTTAACCCTT
1 AAACTTTTCCAAAATCACATTTTAACCCTCAAACTTTCCCAAAATTACATTTTAACCCTT
17641333 AAACTTTTCCAAAATCACATTTTAACCCTCAAA-TTTCTCCAAAATTACATTTTAACCCTT
1 AAACTTTTCCAAAATCACATTTTAACCCTCAAACTTTC-CCAAAATTACATTTTAACCCTT
* *
17641393 AAA-TTTTCCTAAAAATCACATTTTAACCCT-AAACCTTCCCAAAATCACATTTTAA-CCTT
1 AAACTTTTCC--AAAATCACATTTTAACCCTCAAACTTTCCCAAAATTACATTTTAACCCTT
17641452 AAACTTT
1 AAACTTT
17641459 CATAAAATTT
Statistics
Matches: 165, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
59 17 0.10
60 124 0.75
61 24 0.15
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (60 bp):
AAACTTTTCCAAAATCACATTTTAACCCTCAAACTTTCCCAAAATTACATTTTAACCCTT
Found at i:17644918 original size:56 final size:56
Alignment explanation
Indices: 17644858--17644984 Score: 125
Period size: 56 Copynumber: 2.3 Consensus size: 56
17644848 GTTCTTTTCT
* * * *
17644858 AGAGATAGCCACAAAGGTTTTC-CTCTCAGAGTATCGCCACAAA-GATGTTCTTTCAC
1 AGAGATAGCCACAAAGGCTTTCTCTCACAGAG-ATCACCACAAATGAT-TTCTTTAAC
* * * *
17644914 AGAGATCA-CCATAAATGCTTTCTTTCACAGAGATCACCACAAATGCTTTCTTTAAC
1 AGAGAT-AGCCACAAAGGCTTTCTCTCACAGAGATCACCACAAATGATTTCTTTAAC
*
17644970 AGAGATTGCCACAAA
1 AGAGATAGCCACAAA
17644985 TTCTTTTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
56 47 0.82
57 10 0.18
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (56 bp):
AGAGATAGCCACAAAGGCTTTCTCTCACAGAGATCACCACAAATGATTTCTTTAAC
Found at i:17644937 original size:28 final size:28
Alignment explanation
Indices: 17644905--17645045 Score: 129
Period size: 28 Copynumber: 5.0 Consensus size: 28
17644895 CACAAAGATG
*
17644905 TTCTTTCACAGAGATCACCATAAATGCT
1 TTCTTTCACAGAGATCACCACAAATGCT
17644933 TTCTTTCACAGAGATCACCACAAATGCT
1 TTCTTTCACAGAGATCACCACAAATGCT
* ** *
17644961 TTCTTTAACAGAGATTGCCACAAATTCT
1 TTCTTTCACAGAGATCACCACAAATGCT
* * * * *** *
17644989 TTTTTTAAAAAAGATTGTCACAAAGGCT
1 TTCTTTCACAGAGATCACCACAAATGCT
* * * *
17645017 TTCTTTAAAAAAGATCACCACAAAGGCT
1 TTCTTTCACAGAGATCACCACAAATGCT
17645045 T
1 T
17645046 CTTCATGAAA
Statistics
Matches: 98, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 98 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.32
Consensus pattern (28 bp):
TTCTTTCACAGAGATCACCACAAATGCT
Found at i:17659329 original size:33 final size:32
Alignment explanation
Indices: 17659229--17659334 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 32
17659219 ATATATTACA
17659229 ATTTTTTAATAAATAATAAATT-A--TTTTTG
1 ATTTTTTAATAAATAATAAATTAATTTTTTTG
* * * * *
17659258 AGTTTTTACTAATTTAA-AATTTATATATATTTTAG
1 ATTTTTTAATAA-ATAATAAATTA-AT-T-TTTTTG
17659293 ATTTTATTAATAAATAATAAATTAATTTTTTTG
1 ATTTT-TTAATAAATAATAAATTAATTTTTTTG
17659326 ATTTTTTAA
1 ATTTTTTAA
17659335 ACATTTGAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
29 14 0.24
30 3 0.05
31 1 0.02
32 4 0.07
33 10 0.17
34 1 0.02
35 14 0.24
36 11 0.19
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.56
Consensus pattern (32 bp):
ATTTTTTAATAAATAATAAATTAATTTTTTTG
Found at i:17659353 original size:68 final size:65
Alignment explanation
Indices: 17659211--17659358 Score: 183
Period size: 68 Copynumber: 2.2 Consensus size: 65
17659201 TATATTCACT
* *
17659211 ATTTATATATATATTACAATTTTTTAATAAATAATAAATTATTTTTGAGTTTTTACTAATTTAAA
1 ATTTATATATATTTTACAATTTTTTAATAAATAATAAATTATTTTTGAGTTTTTACAAATTTAAA
* *
17659276 ATTTATATATATTTTA-GATTTTATTAATAAATAATAAATTAATTTTTTTGATTTTTTA-AACAT
1 ATTTATATATATTTTACAATTTT-TTAATAAATAATAAATT-A--TTTTTGAGTTTTTACAA-AT
*
17659339 TTGAA
61 TTAAA
*
17659344 ATTTGTATATATTTT
1 ATTTATATATATTTT
17659359 TAAAAAATCT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
64 5 0.07
65 32 0.44
66 1 0.01
67 1 0.01
68 33 0.46
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (65 bp):
ATTTATATATATTTTACAATTTTTTAATAAATAATAAATTATTTTTGAGTTTTTACAAATTTAAA
Found at i:17659569 original size:22 final size:24
Alignment explanation
Indices: 17659528--17659580 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
17659518 AAAAATTATG
*
17659528 TTTTGTAAAATATATATTTTAA-A
1 TTTTTTAAAATATATATTTTAATA
*
17659551 TTTTTTAAAA-ATATTTTTTAATTA
1 TTTTTTAAAATATATATTTTAA-TA
17659575 TTTTTT
1 TTTTTT
17659581 TCTAATGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 9 0.35
24 7 0.27
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTTTTAAAATATATATTTTAATA
Found at i:17664359 original size:36 final size:36
Alignment explanation
Indices: 17664309--17664442 Score: 187
Period size: 36 Copynumber: 3.7 Consensus size: 36
17664299 AATATAATCA
* * *
17664309 GTCACTTGGCATGAAGAACATACACACATATTTTCT
1 GTCACATGGCATAAAGAACATACCCACATATTTTCT
* *
17664345 GTCACATGGTATGAAGAACATACCCACATATTTTCT
1 GTCACATGGCATAAAGAACATACCCACATATTTTCT
* *
17664381 GTCACATGACATAAAGATCATACCCACATATTTTCT
1 GTCACATGGCATAAAGAACATACCCACATATTTTCT
* *
17664417 GCCACATGGCATAAAAAACATACCCA
1 GTCACATGGCATAAAGAACATACCCA
17664443 TGTATTCACT
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 87 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.27
Consensus pattern (36 bp):
GTCACATGGCATAAAGAACATACCCACATATTTTCT
Found at i:17664563 original size:23 final size:23
Alignment explanation
Indices: 17664528--17664778 Score: 337
Period size: 23 Copynumber: 11.0 Consensus size: 23
17664518 ATCTTAATTC
* *
17664528 TTTAAGAACAAATCACATTACTA
1 TTTAAGCACAAATCACATTAATA
* * * *
17664551 TTTAATCATAAATAATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17664574 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17664597 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
17664620 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
17664643 TTT-AGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17664665 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
17664688 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
17664711 --TGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
17664732 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17664755 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
17664778 T
1 T
17664779 ATTTTTTTTG
Statistics
Matches: 203, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
21 21 0.10
22 21 0.10
23 161 0.79
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:17675072 original size:23 final size:23
Alignment explanation
Indices: 17675045--17675228 Score: 260
Period size: 23 Copynumber: 8.0 Consensus size: 23
17675035 TTTTAAAAGT
17675045 CAAATCACATTAATATTTAAGCA
1 CAAATCACATTAATATTTAAGCA
*
17675068 CAAATCATATTAATATTTAAGCA
1 CAAATCACATTAATATTTAAGCA
* *
17675091 CAAATTACATTAATATTTGAGCA
1 CAAATCACATTAATATTTAAGCA
*
17675114 CAAATCATATTAATATTTAAGCA
1 CAAATCACATTAATATTTAAGCA
* * *
17675137 TAAATCACATTAATACTTAAGCT
1 CAAATCACATTAATATTTAAGCA
* * *
17675160 TAACTCACATTAATATTTAATCA
1 CAAATCACATTAATATTTAAGCA
* *
17675183 TAAATCATATTAATATTTAAGCA
1 CAAATCACATTAATATTTAAGCA
17675206 CAAATCACATTAATATTTAAGCA
1 CAAATCACATTAATATTTAAGCA
17675229 TAGATATAAG
Statistics
Matches: 141, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 141 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (23 bp):
CAAATCACATTAATATTTAAGCA
Found at i:17678440 original size:13 final size:13
Alignment explanation
Indices: 17678422--17678446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17678412 GAACTTCAAA
17678422 AACGTGTTTTATG
1 AACGTGTTTTATG
17678435 AACGTGTTTTAT
1 AACGTGTTTTAT
17678447 TTTGCCTTCA
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
AACGTGTTTTATG
Found at i:17682917 original size:12 final size:12
Alignment explanation
Indices: 17682880--17682910 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
17682870 GATTGTGGAG
17682880 AATTCAAAAGAA
1 AATTCAAAAGAA
17682892 AATTCAAAAGAA
1 AATTCAAAAGAA
17682904 AATTCAA
1 AATTCAA
17682911 TTGAAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (12 bp):
AATTCAAAAGAA
Found at i:17686487 original size:17 final size:16
Alignment explanation
Indices: 17686456--17686486 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17686446 GTTAGAAATT
17686456 ATAATTTAAAATTTTC
1 ATAATTTAAAATTTTC
*
17686472 ATAATTTTAAATTTT
1 ATAATTTAAAATTTT
17686487 TAAAATATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
ATAATTTAAAATTTTC
Found at i:17687094 original size:32 final size:29
Alignment explanation
Indices: 17687005--17687096 Score: 85
Period size: 32 Copynumber: 3.0 Consensus size: 29
17686995 AAATTTTAAT
* *
17687005 AAATTTAGGTACCAAATTGAATTTAAAAA
1 AAATTTAGGTACCAAATTGAGTTAAAAAA
* * **
17687034 AAATCTTAGGTACTAAATTAAGAAAAAAATGTA
1 AAAT-TTAGGTACCAAATTGAGTTAAAAA---A
*
17687067 AAATTTAGATACCAAATTGAGTTAAAAAA
1 AAATTTAGGTACCAAATTGAGTTAAAAAA
17687096 A
1 A
17687097 TTTGAATACT
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
29 6 0.12
30 18 0.38
32 19 0.40
33 5 0.10
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (29 bp):
AAATTTAGGTACCAAATTGAGTTAAAAAA
Found at i:17688157 original size:21 final size:21
Alignment explanation
Indices: 17688132--17688171 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17688122 GAAATCCAAT
*
17688132 TTTATTTTTTTATTATTTTTA
1 TTTATTTATTTATTATTTTTA
17688153 TTTATTTATTTATTATTTT
1 TTTATTTATTTATTATTTT
17688172 ATGAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTATTTATTTATTATTTTTA
Found at i:17688292 original size:63 final size:64
Alignment explanation
Indices: 17688148--17688319 Score: 292
Period size: 63 Copynumber: 2.7 Consensus size: 64
17688138 TTTTTATTAT
17688148 TTTTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAGAATAATATTAATTTTG
1 TTTTA-TTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAGAATAATATTAATTTTG
* * *
17688213 TTTTATTATTTATTTATTATTGTATAAATATAAATAAATAAATGTAA-AATAATATTAATTTTG
1 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAGAATAATATTAATTTTG
*
17688276 TTTTATTATTTATTTATTATTTTATGAATATAGATAAATAAATA
1 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATA
17688320 AATAACAAAC
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
63 56 0.56
64 39 0.39
65 5 0.05
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (64 bp):
TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAGAATAATATTAATTTTG
Found at i:17700429 original size:40 final size:40
Alignment explanation
Indices: 17700385--17700610 Score: 187
Period size: 39 Copynumber: 5.7 Consensus size: 40
17700375 TGAAATCGGT
* *
17700385 AGATTGTAGACCATCCCATCTCTTACCCCGATCATGGGGC
1 AGATTGAAGACCATCCCATCTCTTACCCCGACCATGGGGC
* * * * **
17700425 AGATTGAAG-CAATTCAATCTTTTACCCTAACCA-GAGGGC
1 AGATTGAAGACCATCCCATCTCTTACCCCGACCATG-GGGC
17700464 AGATTGAAGACCATCCCATCTCTTACCCCGACCATGGGGC
1 AGATTGAAGACCATCCCATCTCTTACCCCGACCATGGGGC
** * * ***
17700504 AGATTGAAGTA--ATCTAATATTTTACCTTAACC--GGATGGC
1 AGATTGAAG-ACCATCCCATCTCTTACCCCGACCATGG--GGC
* *
17700543 AGATTGAAGACCATCCGATCTCTTATCCCGACCATGGGGC
1 AGATTGAAGACCATCCCATCTCTTACCCCGACCATGGGGC
* * *
17700583 AGATTGAA-ACAATCCAATCTTTTACCCC
1 AGATTGAAGACCATCCCATCTCTTACCCC
17700611 TAAAACTATA
Statistics
Matches: 143, Mismatches: 33, Indels: 21
0.73 0.17 0.11
Matches are distributed among these distances:
37 2 0.01
38 2 0.01
39 72 0.50
40 63 0.44
41 2 0.01
42 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (40 bp):
AGATTGAAGACCATCCCATCTCTTACCCCGACCATGGGGC
Found at i:17700492 original size:79 final size:79
Alignment explanation
Indices: 17700385--17700609 Score: 335
Period size: 79 Copynumber: 2.8 Consensus size: 79
17700375 TGAAATCGGT
* *
17700385 AGATTGTAGACCATCCCATCTCTTACCCCGATCATGGGGCAGATTGAAGCAATTCAATCTTTTAC
1 AGATTGAAGACCATCCCATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATTCAATCTTTTAC
17700450 CCTAACCAGAGGGC
66 CCTAACCAGAGGGC
* *
17700464 AGATTGAAGACCATCCCATCTCTTACCCCGACCATGGGGCAGATTGAAGTAA-TCTAATATTTTA
1 AGATTGAAGACCATCCCATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATTC-AATCTTTTA
* * *
17700528 CCTTAACCGGATGGC
65 CCCTAACCAGAGGGC
* * * *
17700543 AGATTGAAGACCATCCGATCTCTTATCCCGACCATGGGGCAGATTGAAACAATCCAATCTTTTAC
1 AGATTGAAGACCATCCCATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATTCAATCTTTTAC
17700608 CC
66 CC
17700610 CTAAAACTAT
Statistics
Matches: 130, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
78 2 0.02
79 127 0.98
80 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (79 bp):
AGATTGAAGACCATCCCATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATTCAATCTTTTAC
CCTAACCAGAGGGC
Found at i:17701209 original size:63 final size:63
Alignment explanation
Indices: 17701125--17701358 Score: 432
Period size: 63 Copynumber: 3.7 Consensus size: 63
17701115 TTCTTATTAT
17701125 TTTTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG
1 TTTTA-TTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG
*
17701189 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAATAATATTAATTTTG
1 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG
*
17701252 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAATAATATTAATTTTG
1 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG
*
17701315 TTTTATTATTTATTTATTATTTTATGAATATAGATAAATAAATA
1 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATA
17701359 ACAAATCAAA
Statistics
Matches: 167, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
63 162 0.97
64 5 0.03
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (63 bp):
TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG
Found at i:17702879 original size:20 final size:19
Alignment explanation
Indices: 17702837--17702879 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
17702827 TTCTATTTTG
* **
17702837 TTTTAATATAAATTTTATT
1 TTTTAATATAAATATTACA
17702856 TTTTAAATATAAATATTACA
1 TTTT-AATATAAATATTACA
17702876 TTTT
1 TTTT
17702880 GTTGATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTAATATAAATATTACA
Found at i:17703115 original size:13 final size:12
Alignment explanation
Indices: 17703085--17703119 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
17703075 AATAAAAAAA
17703085 TATTATTTTTTT
1 TATTATTTTTTT
*
17703097 TGTTATTTTTATT
1 TATTATTTTT-TT
17703110 TATTATTTTT
1 TATTATTTTT
17703120 CAAGATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (12 bp):
TATTATTTTTTT
Found at i:17703262 original size:25 final size:27
Alignment explanation
Indices: 17703225--17703275 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
17703215 TTACAATGTA
*
17703225 TTTTTAAATAATAATGATTTT-TTAAT
1 TTTTTAAATAATAATAATTTTATTAAT
*
17703251 TTTTTGAA-AATAATAATTTTATTAA
1 TTTTTAAATAATAATAATTTTATTAA
17703276 AATATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (27 bp):
TTTTTAAATAATAATAATTTTATTAAT
Found at i:17703269 original size:17 final size:17
Alignment explanation
Indices: 17703247--17703279 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17703237 AATGATTTTT
17703247 TAATTTT-TTGAAAATAA
1 TAATTTTATT-AAAATAA
17703264 TAATTTTATTAAAATA
1 TAATTTTATTAAAATA
17703280 TTTTAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TAATTTTATTAAAATAA
Found at i:17705649 original size:26 final size:26
Alignment explanation
Indices: 17705620--17705707 Score: 149
Period size: 26 Copynumber: 3.4 Consensus size: 26
17705610 AACAAACTTA
*
17705620 GTTTATGCTTGTATTTCATAAATTAT
1 GTTTATGTTTGTATTTCATAAATTAT
17705646 GTTTATGTTTGTATTTCATAAATTAT
1 GTTTATGTTTGTATTTCATAAATTAT
* *
17705672 GTTTATGTTTGTATTTAATTAATTAT
1 GTTTATGTTTGTATTTCATAAATTAT
17705698 GTTTATGTTT
1 GTTTATGTTT
17705708 AGGTTTTAGG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (26 bp):
GTTTATGTTTGTATTTCATAAATTAT
Found at i:17708701 original size:27 final size:27
Alignment explanation
Indices: 17708671--17708723 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
17708661 TGGCAGCACT
*
17708671 GGTGCTGCCTACCAAATGGGCACCATA
1 GGTGCCGCCTACCAAATGGGCACCATA
** *
17708698 GGTGCCGCCTGTCATATGGGCACCAT
1 GGTGCCGCCTACCAAATGGGCACCAT
17708724 TGCTGGTGCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.30, G:0.28, T:0.21
Consensus pattern (27 bp):
GGTGCCGCCTACCAAATGGGCACCATA
Found at i:17708734 original size:27 final size:27
Alignment explanation
Indices: 17708686--17708738 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
17708676 TGCCTACCAA
*
17708686 ATGGGCACCATAGGTGCCGCCTGTCAT
1 ATGGGCACCATAGCTGCCGCCTGTCAT
* **
17708713 ATGGGCACCATTGCTGGTGCCTGTCA
1 ATGGGCACCATAGCTGCCGCCTGTCA
17708739 AGTAGCCTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (27 bp):
ATGGGCACCATAGCTGCCGCCTGTCAT
Found at i:17715765 original size:41 final size:41
Alignment explanation
Indices: 17715720--17715870 Score: 196
Period size: 41 Copynumber: 3.7 Consensus size: 41
17715710 TATTACAGAT
** * *
17715720 TATGTGCCTCAAAGTAGTACACACACACCTTGACACACGCC
1 TATGTGCCTCAAAACAGTACACACACACCCTGACACATGCC
* * **
17715761 TATGTTCCTCAAAACAATATGCACACACCCTGACACATGCC
1 TATGTGCCTCAAAACAGTACACACACACCCTGACACATGCC
*
17715802 TATGTGCCTCAAAACAGTATACACACACCCTGACACATGCC
1 TATGTGCCTCAAAACAGTACACACACACCCTGACACATGCC
*
17715843 TGTGTGCCTTC-AAACAGTACACACACAC
1 TATGTGCC-TCAAAACAGTACACACACAC
17715871 ACACACCTTG
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 94 0.98
42 2 0.02
ACGTcount: A:0.33, C:0.34, G:0.13, T:0.21
Consensus pattern (41 bp):
TATGTGCCTCAAAACAGTACACACACACCCTGACACATGCC
Found at i:17723475 original size:19 final size:22
Alignment explanation
Indices: 17723437--17723476 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
17723427 TACAATCGAG
17723437 TTCATCATCATCACACATATAT
1 TTCATCATCATCACACATATAT
17723459 TTCAT-ATCATC-CA-ATATA
1 TTCATCATCATCACACATATA
17723477 GTTCTATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 6 0.33
22 5 0.28
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.38
Consensus pattern (22 bp):
TTCATCATCATCACACATATAT
Found at i:17723484 original size:18 final size:21
Alignment explanation
Indices: 17723435--17723484 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
17723425 ATTACAATCG
17723435 AGTTCATCATCATCACACATAT
1 AGTTCAT-ATCATCACACATAT
*
17723457 ATTTCATATCATC-CA-ATAT
1 AGTTCATATCATCACACATAT
17723476 AGTTC-TATC
1 AGTTCATATC
17723485 CAATTTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 4 0.15
19 8 0.31
20 2 0.08
21 6 0.23
22 6 0.23
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (21 bp):
AGTTCATATCATCACACATAT
Found at i:17724988 original size:16 final size:18
Alignment explanation
Indices: 17724947--17724997 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 18
17724937 CATAACACGT
17724947 TGAGATTCTTCGATACAC
1 TGAGATTCTTCGATACAC
*
17724965 TGAG--TCTT-GA-ACGC
1 TGAGATTCTTCGATACAC
17724979 TGAGATTCTTCGATACAC
1 TGAGATTCTTCGATACAC
17724997 T
1 T
17724998 AAGTCCGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 7 0.26
15 2 0.07
16 8 0.30
17 2 0.07
18 8 0.30
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (18 bp):
TGAGATTCTTCGATACAC
Found at i:17727877 original size:18 final size:20
Alignment explanation
Indices: 17727840--17727878 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
17727830 TCTTTAGATG
17727840 AGTGATTTCTCACTTGTTTTT
1 AGTGATTTCTCAC-TGTTTTT
17727861 AGTGATTTCT-A-TGTTTTT
1 AGTGATTTCTCACTGTTTTT
17727879 GAGTTCGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.59
Consensus pattern (20 bp):
AGTGATTTCTCACTGTTTTT
Found at i:17734575 original size:38 final size:38
Alignment explanation
Indices: 17734512--17734594 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
17734502 TGGAACACTA
17734512 TAAATATTTGAAAATGTTCCAACAATCTGCCCCCATTTT
1 TAAA-ATTTGAAAATGTTCCAACAATCTGCCCCCATTTT
*** * *
17734551 TAAAATTTGAAAATGTTTTGACAATTTTCCCCCATTTT
1 TAAAATTTGAAAATGTTCCAACAATCTGCCCCCATTTT
*
17734589 CAAAAT
1 TAAAAT
17734595 ATTTTAGATT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
38 34 0.89
39 4 0.11
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (38 bp):
TAAAATTTGAAAATGTTCCAACAATCTGCCCCCATTTT
Found at i:17741076 original size:12 final size:12
Alignment explanation
Indices: 17741059--17741083 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17741049 CTAGTTCCAC
17741059 TTAATAATATTT
1 TTAATAATATTT
17741071 TTAATAATATTT
1 TTAATAATATTT
17741083 T
1 T
17741084 CACAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAATAATATTT
Found at i:17741604 original size:20 final size:20
Alignment explanation
Indices: 17741576--17741622 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
17741566 AACATTATTT
*
17741576 TATTGTTTACATTAAAAT-AG
1 TATTATTTAC-TTAAAATAAG
*
17741596 TATTATTTACTTAATATAAG
1 TATTATTTACTTAAAATAAG
17741616 T-TTATTT
1 TATTATTT
17741623 TTTTAATGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (20 bp):
TATTATTTACTTAAAATAAG
Found at i:17752653 original size:15 final size:15
Alignment explanation
Indices: 17752633--17752691 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
17752623 AAAATATTTG
17752633 AAATATTTTAATATA
1 AAATATTTTAATATA
*
17752648 AAATATTTT-ATTTCA
1 AAATATTTTAATAT-A
*
17752663 AAATATAATTTAAAATA
1 AAATAT--TTTAATATA
17752680 AAATATTTTAAT
1 AAATATTTTAAT
17752692 GTAATTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 3 0.08
15 21 0.58
17 10 0.28
18 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATTTTAATATA
Found at i:17752739 original size:24 final size:24
Alignment explanation
Indices: 17752712--17752787 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 24
17752702 AAAAAATAAT
*
17752712 TATATTAATAATGTTATTAAATTA
1 TATATTAATAATATTATTAAATTA
* * * *
17752736 TATATGATTATTTTTATTAAA-T-
1 TATATTAATAATATTATTAAATTA
*
17752758 TATATTCA-AATATTATTAAATTA
1 TATATTAATAATATTATTAAATTA
*
17752781 TTTATTA
1 TATATTA
17752788 TCATTTTTAT
Statistics
Matches: 39, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
21 10 0.26
22 6 0.15
23 6 0.15
24 17 0.44
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (24 bp):
TATATTAATAATATTATTAAATTA
Found at i:17752778 original size:45 final size:46
Alignment explanation
Indices: 17752709--17752808 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 46
17752699 AATAAAAAAT
* *
17752709 AATTATATTAATAATGTTATTAAATTATATATGATTATTTTTATTA
1 AATTATATTAATAATATTATTAAATTATATATGATCATTTTTATTA
* * * *
17752755 AATTATATTCA-AATATTATTAAATTATTTATTATCATTTTTATTT
1 AATTATATTAATAATATTATTAAATTATATATGATCATTTTTATTA
17752800 AATTATATT
1 AATTATATT
17752809 TCATAATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 38 0.79
46 10 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (46 bp):
AATTATATTAATAATATTATTAAATTATATATGATCATTTTTATTA
Found at i:17753467 original size:36 final size:36
Alignment explanation
Indices: 17753427--17753499 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
17753417 AAAAGTAAAG
17753427 TCCAAATAGAACTAGACTTCTTTTATTTTAATTTAA
1 TCCAAATAGAACTAGACTTCTTTTATTTTAATTTAA
17753463 TCCAAATAGAACTAGACTTCTTTTATTTTAATTTAA
1 TCCAAATAGAACTAGACTTCTTTTATTTTAATTTAA
17753499 T
1 T
17753500 TAGAATAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (36 bp):
TCCAAATAGAACTAGACTTCTTTTATTTTAATTTAA
Found at i:17753504 original size:31 final size:31
Alignment explanation
Indices: 17753433--17753533 Score: 109
Period size: 36 Copynumber: 3.2 Consensus size: 31
17753423 AAAGTCCAAA
17753433 TAGAACTAGACTTCTTTTATTTTAATTTAAT
1 TAGAACTAGACTTCTTTTATTTTAATTTAAT
17753464 CCAAATAGAACTAGACTTCTTTTATTTTAATTTAAT
1 -----TAGAACTAGACTTCTTTTATTTTAATTTAAT
* * *
17753500 TAGAA-TA-A-GTCTTCTATTTTATTTTAAT
1 TAGAACTAGACTTCTTTTATTTTAATTTAAT
17753528 TAGAAC
1 TAGAAC
17753534 AAGGTGTTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
28 22 0.36
29 1 0.02
30 2 0.03
31 5 0.08
36 31 0.51
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.48
Consensus pattern (31 bp):
TAGAACTAGACTTCTTTTATTTTAATTTAAT
Found at i:17755097 original size:26 final size:26
Alignment explanation
Indices: 17755031--17755099 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
17755021 ATTGCGATAT
* * *
17755031 TGGCTCATAAGAGTAATATATTGCAC
1 TGGCTCGTAAGAGTGATATACTGCAC
*
17755057 TGGCTCGTAAGAGTGATATACTGTAC
1 TGGCTCGTAAGAGTGATATACTGCAC
*
17755083 TGGCTTGTAAGAGTGAT
1 TGGCTCGTAAGAGTGAT
17755100 TTAATAACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (26 bp):
TGGCTCGTAAGAGTGATATACTGCAC
Found at i:17755113 original size:26 final size:26
Alignment explanation
Indices: 17755031--17755117 Score: 86
Period size: 26 Copynumber: 3.3 Consensus size: 26
17755021 ATTGCGATAT
* * * *
17755031 TGGCTCATAAGAGTAATATATTGCAC
1 TGGCTCGTAAGAGTGATATAATGAAC
* *
17755057 TGGCTCGTAAGAGTGATATACTGTAC
1 TGGCTCGTAAGAGTGATATAATGAAC
* *
17755083 TGGCTTGTAAGAGTGATTTAAT-AAC
1 TGGCTCGTAAGAGTGATATAATGAAC
17755108 TAGGCTCGTA
1 T-GGCTCGTA
17755118 TGAGCTAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
25 3 0.06
26 48 0.94
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (26 bp):
TGGCTCGTAAGAGTGATATAATGAAC
Found at i:17757523 original size:20 final size:20
Alignment explanation
Indices: 17757498--17757537 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
17757488 TTCGAGAGGT
17757498 GGAGCTAACTATATGCTAAC
1 GGAGCTAACTATATGCTAAC
*
17757518 GGAGCTAATTATATGCTAAC
1 GGAGCTAACTATATGCTAAC
17757538 TCTTATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (20 bp):
GGAGCTAACTATATGCTAAC
Found at i:17769072 original size:28 final size:28
Alignment explanation
Indices: 17769026--17769080 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
17769016 TTTTTTTGTG
17769026 ATTTTATATTCCTTTTATATAGCCTTTT
1 ATTTTATATTCCTTTTATATAGCCTTTT
*
17769054 ATTTT-TATTTCTTTATATATAGCCTTT
1 ATTTTATATTCCTTT-TATATAGCCTTT
17769081 GTTTCTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.22, C:0.13, G:0.04, T:0.62
Consensus pattern (28 bp):
ATTTTATATTCCTTTTATATAGCCTTTT
Found at i:17772305 original size:17 final size:18
Alignment explanation
Indices: 17772268--17772307 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
17772258 TAACAAAATG
*
17772268 ATGCGATGATAAAATAAA
1 ATGCAATGATAAAATAAA
*
17772286 ATGCAATGATAATA-AAA
1 ATGCAATGATAAAATAAA
17772303 ATGCA
1 ATGCA
17772308 TTAAAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.23
Consensus pattern (18 bp):
ATGCAATGATAAAATAAA
Found at i:17773937 original size:12 final size:12
Alignment explanation
Indices: 17773916--17773944 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
17773906 GAGATGAAGG
17773916 TTTT-GGAGTGT
1 TTTTGGGAGTGT
17773927 TTTTGGGAGTGT
1 TTTTGGGAGTGT
17773939 TTTTGG
1 TTTTGG
17773945 ATGCACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.07, C:0.00, G:0.38, T:0.55
Consensus pattern (12 bp):
TTTTGGGAGTGT
Found at i:17783881 original size:20 final size:20
Alignment explanation
Indices: 17783853--17783892 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17783843 GCTTGTATGG
17783853 ATTTGCACTTCAATGCCTCT
1 ATTTGCACTTCAATGCCTCT
* *
17783873 ATTTTCACTTCGATGCCTCT
1 ATTTGCACTTCAATGCCTCT
17783893 GCTAGCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.30, G:0.10, T:0.42
Consensus pattern (20 bp):
ATTTGCACTTCAATGCCTCT
Found at i:17789259 original size:23 final size:24
Alignment explanation
Indices: 17789226--17789270 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
17789216 TTATGATAGT
* *
17789226 TATATTTAATTTT-ATCATTTTAA
1 TATATTAAATTTTCATAATTTTAA
17789249 TATATTAAATTTTCATAATTTT
1 TATATTAAATTTTCATAATTTT
17789271 TTAAGAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
TATATTAAATTTTCATAATTTTAA
Found at i:17790904 original size:29 final size:29
Alignment explanation
Indices: 17790860--17790940 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
17790850 TAATTGTACT
* * *
17790860 TTTATAAATATTCAATATGGTATCTATAC
1 TTTAAAAATATCCAATATGGTACCTATAC
*
17790889 TTTAAAAATATCCAATGTGGTACCTATAC
1 TTTAAAAATATCCAATATGGTACCTATAC
* *
17790918 TTTGAAAATGTCCAA-AGTGGTAC
1 TTTAAAAATATCCAATA-TGGTAC
17790941 TTGAACTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (29 bp):
TTTAAAAATATCCAATATGGTACCTATAC
Found at i:17791810 original size:20 final size:21
Alignment explanation
Indices: 17791785--17791838 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
17791775 ATTTAATTAA
17791785 TAAAATTATAAAATAT-TTTT
1 TAAAATTATAAAATATATTTT
*
17791805 TAAAATTAAAAAATATATTTT
1 TAAAATTATAAAATATATTTT
*
17791826 T-AAATTTTAAAAT
1 TAAAATTATAAAAT
17791839 TTAATTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 25 0.83
21 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAATTATAAAATATATTTT
Found at i:17792375 original size:41 final size:42
Alignment explanation
Indices: 17792325--17792405 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
17792315 CACTTTAATG
*
17792325 TCAACATAAAATTT-AAAAAGGTAATTAGAATTTTCAAAATA
1 TCAACATAAAATTTAAAAAAAGTAATTAGAATTTTCAAAATA
*
17792366 TCAATATAAAATTTAAAAAAAGTAATTAGAATTTTCAAAA
1 TCAACATAAAATTTAAAAAAAGTAATTAGAATTTTCAAAA
17792406 GAGTGATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
41 13 0.35
42 24 0.65
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (42 bp):
TCAACATAAAATTTAAAAAAAGTAATTAGAATTTTCAAAATA
Found at i:17792398 original size:20 final size:19
Alignment explanation
Indices: 17792334--17792399 Score: 53
Period size: 21 Copynumber: 3.3 Consensus size: 19
17792324 GTCAACATAA
*
17792334 AATTTAAAAAGGTAATTAG
1 AATTTAAAAAAGTAATTAG
* *
17792353 AATTTTCAAAATA-TCAATATAA
1 AA-TTT-AAAAAAGT-AAT-TAG
17792375 AATTTAAAAAAAGTAATTAG
1 AATTT-AAAAAAGTAATTAG
17792395 AATTT
1 AATTT
17792400 TCAAAAGAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 18 0.50
22 5 0.14
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.35
Consensus pattern (19 bp):
AATTTAAAAAAGTAATTAG
Found at i:17792405 original size:20 final size:20
Alignment explanation
Indices: 17792339--17792405 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 20
17792329 CATAAAATTT
17792339 AAAAAGGTAATTAGAATTTTC
1 AAAAA-GTAATTAGAATTTTC
* **
17792360 AAAATA-TCAATATAAAATTTAA
1 AAAA-AGT-AAT-TAGAATTTTC
17792382 AAAAAGTAATTAGAATTTTC
1 AAAAAGTAATTAGAATTTTC
17792402 AAAA
1 AAAA
17792406 GAGTGATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
20 12 0.33
21 11 0.31
22 13 0.36
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAAAGTAATTAGAATTTTC
Found at i:17815764 original size:17 final size:17
Alignment explanation
Indices: 17815744--17815782 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
17815734 TAATTGTCCA
17815744 TGCATTATTAATGTCAT
1 TGCATTATTAATGTCAT
* * *
17815761 TGCATTTTTATTGTCGT
1 TGCATTATTAATGTCAT
17815778 TGCAT
1 TGCAT
17815783 CTACATTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (17 bp):
TGCATTATTAATGTCAT
Found at i:17819342 original size:32 final size:29
Alignment explanation
Indices: 17819302--17819378 Score: 111
Period size: 28 Copynumber: 2.6 Consensus size: 29
17819292 TAATAATGTA
17819302 AAAAAAGAAAGAAAGAAAATGATGAAAGAATT
1 AAAAAAGAAAGAAAGAAAAT-A--AAAGAATT
*
17819334 AAAAAAGAAAGAAA-ATAATAAAAGAATT
1 AAAAAAGAAAGAAAGAAAATAAAAGAATT
17819362 AAAAAAGAAAGAAAGAA
1 AAAAAAGAAAGAAAGAA
17819379 TTACAAATGA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 22 0.52
29 1 0.02
30 1 0.02
31 4 0.10
32 14 0.33
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (29 bp):
AAAAAAGAAAGAAAGAAAATAAAAGAATT
Found at i:17819346 original size:28 final size:28
Alignment explanation
Indices: 17819309--17819375 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
17819299 GTAAAAAAAG
* *
17819309 AAAGAAAGAAAATGATGAAAGAATTAAA
1 AAAGAAAGAAAATAATAAAAGAATTAAA
17819337 AAAGAAAGAAAATAATAAAAGAATTAAA
1 AAAGAAAGAAAATAATAAAAGAATTAAA
17819365 AAAGAAAGAAA
1 AAAGAAAGAAA
17819376 GAATTACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (28 bp):
AAAGAAAGAAAATAATAAAAGAATTAAA
Found at i:17820511 original size:23 final size:23
Alignment explanation
Indices: 17820447--17820497 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
17820437 GAAAAAAATA
17820447 TATGTATAAGACTTTATAACCAT
1 TATGTATAAGACTTTATAACCAT
17820470 TATGTATAAGACTTTATAACCAT
1 TATGTATAAGACTTTATAACCAT
17820493 TATGT
1 TATGT
17820498 GTTAATTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (23 bp):
TATGTATAAGACTTTATAACCAT
Found at i:17824997 original size:31 final size:30
Alignment explanation
Indices: 17824960--17825021 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
17824950 AATAATGTAA
* *
17824960 AAAAAAAAGAAAAGAAAATGATGAAAGAATT
1 AAAAAAAAG-AAAGAAAATAATAAAAGAATT
17824991 AAAAAAAAGAAAGAAAATAATAAAAGAATT
1 AAAAAAAAGAAAGAAAATAATAAAAGAATT
17825021 A
1 A
17825022 GAAATGAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 20 0.69
31 9 0.31
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (30 bp):
AAAAAAAAGAAAGAAAATAATAAAAGAATT
Found at i:17845994 original size:17 final size:18
Alignment explanation
Indices: 17845908--17845996 Score: 65
Period size: 17 Copynumber: 4.7 Consensus size: 18
17845898 TAATATTTTA
17845908 ATAATTTAATATTAAATT
1 ATAATTTAATATTAAATT
* * **
17845926 -TAATTCAATGCTTATCTT
1 ATAATTTAAT-ATTAAATT
17845944 AATAGTATTTAATATTAAATT
1 -ATA--ATTTAATATTAAATT
*
17845965 GATTATCTTAATATTAAATT
1 -ATAAT-TTAATATTAAATT
17845985 -TAATTTAATATT
1 ATAATTTAATATT
17845997 TATATTGTAA
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
17 16 0.30
18 8 0.15
19 2 0.04
20 15 0.28
21 7 0.13
22 6 0.11
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (18 bp):
ATAATTTAATATTAAATT
Found at i:17846048 original size:62 final size:59
Alignment explanation
Indices: 17845972--17846088 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
17845962 ATTGATTATC
* * * * *
17845972 TTAATATTAAATTTAATTTAATATTTATATTGTAAATAAATATTCTATTATTTTAATAAGAT
1 TTAAGATTAAATTTAATCTAATATTTAT-CT-T-AATAAATATTATATTAATTTAATAAGAT
17846034 TTAAGATTAAATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATA
1 TTAAGATTAAATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATA
17846089 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 22 0.44
60 1 0.02
61 1 0.02
62 26 0.52
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAAGATTAAATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATAAGAT
Found at i:17851268 original size:16 final size:17
Alignment explanation
Indices: 17851240--17851273 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17851230 CAGACCGAGA
17851240 TACTAGAGTTTAAAGTT
1 TACTAGAGTTTAAAGTT
*
17851257 TACTAG-GTTTAAGGTT
1 TACTAGAGTTTAAAGTT
17851273 T
1 T
17851274 TGATCTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (17 bp):
TACTAGAGTTTAAAGTT
Found at i:17851743 original size:3 final size:3
Alignment explanation
Indices: 17851735--17851791 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
17851725 CAATGAATTT
*
17851735 ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17851783 ATA ATA ATA
1 ATA ATA ATA
17851792 TGGATATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17854810 original size:11 final size:10
Alignment explanation
Indices: 17854787--17854848 Score: 58
Period size: 11 Copynumber: 6.2 Consensus size: 10
17854777 TAAAATTATT
*
17854787 AAAAA-ATAC
1 AAAAATATAA
17854796 AAAAATATGAA
1 AAAAATAT-AA
17854807 AAAAATTATAA
1 AAAAA-TATAA
17854818 AAAAAT-T-A
1 AAAAATATAA
*
17854826 AAAATTATAA
1 AAAAATATAA
17854836 AAAATATATAA
1 AAAA-ATATAA
17854847 AA
1 AA
17854849 CTATTAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
8 6 0.14
9 7 0.16
10 8 0.18
11 20 0.45
12 3 0.07
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (10 bp):
AAAAATATAA
Found at i:17854814 original size:30 final size:29
Alignment explanation
Indices: 17854778--17854865 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
17854768 TTTTTCCCAT
*
17854778 AAAATTATTAAAAAA-TACAAAAATATGAAA
1 AAAATTATAAAAAAATTA-AAAAATAT-AAA
*
17854808 AAAATTATAAAAAAATTAAAAATTAT-AA
1 AAAATTATAAAAAAATTAAAAAATATAAA
** *
17854836 AAAATATATAAAACTATT-AAAATTATAAA
1 AAAAT-TATAAAAAAATTAAAAAATATAAA
17854865 A
1 A
17854866 TGTTATAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
28 15 0.29
29 13 0.25
30 21 0.41
31 2 0.04
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.27
Consensus pattern (29 bp):
AAAATTATAAAAAAATTAAAAAATATAAA
Found at i:17854819 original size:9 final size:9
Alignment explanation
Indices: 17854778--17854928 Score: 88
Period size: 9 Copynumber: 15.9 Consensus size: 9
17854768 TTTTTCCCAT
17854778 AAAATTATTA
1 AAAATTA-TA
* *
17854788 AAAAATACA
1 AAAATTATA
*
17854797 AAAATATGAAA
1 AAAAT-T-ATA
17854808 AAAATTATA
1 AAAATTATA
*
17854817 AAAA-AATTA
1 AAAATTA-TA
17854826 AAAATTATA
1 AAAATTATA
*
17854835 AAAAATATA
1 AAAATTATA
* *
17854844 TAAAACTATT
1 -AAAATTATA
17854854 AAAATTATA
1 AAAATTATA
*
17854863 AAATGTTATA
1 AAA-ATTATA
* *
17854873 AATATTAAA
1 AAAATTATA
*
17854882 AAAATTCTA
1 AAAATTATA
17854891 ATAAATTATA
1 A-AAATTATA
**
17854901 AAAAAAATA
1 AAAATTATA
17854910 TAAAATTAATA
1 -AAAATT-ATA
*
17854921 AAACTTAT
1 AAAATTAT
17854929 TTAAAATACT
Statistics
Matches: 107, Mismatches: 25, Indels: 19
0.71 0.17 0.13
Matches are distributed among these distances:
8 1 0.01
9 56 0.52
10 40 0.37
11 10 0.09
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:17854828 original size:29 final size:28
Alignment explanation
Indices: 17854778--17854865 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 28
17854768 TTTTTCCCAT
* *
17854778 AAAATTATTAAAAAATACAAAAATATGAAA
1 AAAATTATAAAAAAAT-TAAAAATAT-AAA
17854808 AAAATTATAAAAAAATTAAAAAT-TATAA
1 AAAATTATAAAAAAATTAAAAATATA-AA
** *
17854836 AAAATATATAAAACTATTAAAATTATAAA
1 AAAAT-TATAAAAAAATTAAAAATATAAA
17854865 A
1 A
17854866 TGTTATAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
27 1 0.02
28 8 0.16
29 24 0.48
30 17 0.34
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.27
Consensus pattern (28 bp):
AAAATTATAAAAAAATTAAAAATATAAA
Found at i:17854859 original size:28 final size:28
Alignment explanation
Indices: 17854778--17854923 Score: 102
Period size: 28 Copynumber: 5.1 Consensus size: 28
17854768 TTTTTCCCAT
* *
17854778 AAAATTATTAAAAAA-TACAAAAATATGAAA
1 AAAATTATAAAAAAATTA-AAAATTAT--AA
17854808 AAAATTATAAAAAAATTAAAAATTATAA
1 AAAATTATAAAAAAATTAAAAATTATAA
**
17854836 AAAATATATAAAACTATT-AAAATTATAA
1 AAAAT-TATAAAAAAATTAAAAATTATAA
** * *
17854864 AATGTTAT--AAATATTAAAAAAATTCTAA
1 AAAATTATAAAAAAATT--AAAAATTATAA
* *
17854892 TAAATTATAAAAAAAATATAAAATTAATAA
1 AAAATTATAAAAAAATTA-AAAATT-ATAA
17854922 AA
1 AA
17854924 CTTATTTAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
25 6 0.07
27 3 0.03
28 35 0.38
29 16 0.17
30 30 0.33
31 2 0.02
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (28 bp):
AAAATTATAAAAAAATTAAAAATTATAA
Found at i:17854875 original size:17 final size:18
Alignment explanation
Indices: 17854836--17854882 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
17854826 AAAATTATAA
17854836 AAAATATATAAAACTATT
1 AAAATATATAAAACTATT
*
17854854 AAAAT-TATAAAA-TGTT
1 AAAATATATAAAACTATT
17854870 ATAAATAT-TAAAA
1 A-AAATATATAAAA
17854883 AAATTCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.15
17 16 0.62
18 6 0.23
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAATATATAAAACTATT
Found at i:17854915 original size:19 final size:19
Alignment explanation
Indices: 17854808--17854923 Score: 65
Period size: 21 Copynumber: 5.6 Consensus size: 19
17854798 AAATATGAAA
*
17854808 AAAATTATAAAAAAATTA-
1 AAAATTATAAAAAAAATAT
*
17854826 AAAATTATAAAAAATATAT
1 AAAATTATAAAAAAAATAT
* *
17854845 AAAACTATTAAAATTATAAAATGTT
1 AAAATTA-T-AAA--A-AAAAT-AT
* *
17854870 ATAAA-TATTAAAAAAATTCT
1 A-AAATTA-TAAAAAAAATAT
17854890 AATAAATTATAAAAAAAATAT
1 -A-AAATTATAAAAAAAATAT
17854911 AAAATTAATAAAA
1 AAAATT-ATAAAA
17854924 CTTATTTAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
18 16 0.21
19 11 0.14
20 9 0.12
21 22 0.28
22 3 0.04
23 1 0.01
24 7 0.09
25 6 0.08
26 3 0.04
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (19 bp):
AAAATTATAAAAAAAATAT
Found at i:17854934 original size:29 final size:29
Alignment explanation
Indices: 17854901--17854958 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
17854891 ATAAATTATA
* * *
17854901 AAAAAAATATAAAATTAATAAAACTTATTT
1 AAAATAAT-TAAAATTAAAAAAACATATTT
*
17854931 AAAATACTTAAAATTAAAAAAACATATT
1 AAAATAATTAAAATTAAAAAAACATATT
17854959 GTAATTCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (29 bp):
AAAATAATTAAAATTAAAAAAACATATTT
Found at i:17857657 original size:33 final size:36
Alignment explanation
Indices: 17857615--17857680 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 36
17857605 TGTTTATGTG
* *
17857615 AAATTGAAGAGAAA-GAGAAGAG-AG-GCAAGGATC
1 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGGATC
17857648 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGG
1 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGG
17857681 GGTAAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 13 0.46
34 7 0.25
35 2 0.07
36 6 0.21
ACGTcount: A:0.53, C:0.06, G:0.32, T:0.09
Consensus pattern (36 bp):
AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGGATC
Found at i:17858730 original size:23 final size:23
Alignment explanation
Indices: 17858704--17858824 Score: 156
Period size: 23 Copynumber: 5.2 Consensus size: 23
17858694 ACACTAGCGC
17858704 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
17858727 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
17858750 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
17858775 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
17858798 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
17858821 GCTC
1 GCTC
17858825 AGTACTTTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
22 4 0.05
23 62 0.72
24 1 0.01
25 16 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:17858773 original size:48 final size:46
Alignment explanation
Indices: 17858704--17858824 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
17858694 ACACTAGCGC
* *
17858704 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GT
*
17858750 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
*
17858798 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
17858825 AGTACTTTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:17858853 original size:39 final size:39
Alignment explanation
Indices: 17858789--17858863 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
17858779 TCCGATTAGC
*
17858789 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
17858828 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
17858864 CTGTTGCCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:17865558 original size:13 final size:13
Alignment explanation
Indices: 17865540--17865565 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17865530 TATCTCCTTA
17865540 AATTTACTATTGT
1 AATTTACTATTGT
17865553 AATTTACTATTGT
1 AATTTACTATTGT
17865566 GCACTTTTGT
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:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
AATTTACTATTGT
Found at i:17870228 original size:22 final size:22
Alignment explanation
Indices: 17870200--17870255 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
17870190 CAATATTCAA
17870200 AAAATAACAACAAAATAATAGC
1 AAAATAACAACAAAATAATAGC
* * *
17870222 AATATAATAACAAAATGATAGC
1 AAAATAACAACAAAATAATAGC
*
17870244 AAAACAACAACA
1 AAAATAACAACA
17870256 TAAAAACAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.66, C:0.14, G:0.05, T:0.14
Consensus pattern (22 bp):
AAAATAACAACAAAATAATAGC
Found at i:17871766 original size:30 final size:30
Alignment explanation
Indices: 17871730--17871814 Score: 134
Period size: 30 Copynumber: 2.8 Consensus size: 30
17871720 GTAACCTTGA
*
17871730 TAAAATGTTAGCTTGTGTAAGCAACTTTGT
1 TAAAATGTCAGCTTGTGTAAGCAACTTTGT
17871760 TAAAATGTCAGCTTGTGTAAGCAACTTTGT
1 TAAAATGTCAGCTTGTGTAAGCAACTTTGT
** *
17871790 TAAAATGTCAATTTGTGTGAGCAAC
1 TAAAATGTCAGCTTGTGTAAGCAAC
17871815 CTTGATATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (30 bp):
TAAAATGTCAGCTTGTGTAAGCAACTTTGT
Found at i:17871829 original size:30 final size:30
Alignment explanation
Indices: 17871722--17871821 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
17871712 CCAGAAAGGT
* **
17871722 AACCTTGATAAAATGTTAGCTTGTGTAAGC
1 AACCTTGATAAAATGTCAATTTGTGTAAGC
* * **
17871752 AACTTTGTTAAAATGTCAGCTTGTGTAAGC
1 AACCTTGATAAAATGTCAATTTGTGTAAGC
* * *
17871782 AACTTTGTTAAAATGTCAATTTGTGTGAGC
1 AACCTTGATAAAATGTCAATTTGTGTAAGC
17871812 AACCTTGATA
1 AACCTTGATA
17871822 TATTGTCAGC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (30 bp):
AACCTTGATAAAATGTCAATTTGTGTAAGC
Found at i:17874252 original size:4 final size:4
Alignment explanation
Indices: 17874243--17874277 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
17874233 CAATCAGGTG
17874243 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
17874278 TATATATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:17875419 original size:20 final size:21
Alignment explanation
Indices: 17875374--17875421 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
17875364 TCGATCCATT
** *
17875374 TCAATTTTTATGATTTTTTTA
1 TCAATTTTTATGAAATTTATA
17875395 T-AATTTTTAT-AAATTTATA
1 TCAATTTTTATGAAATTTATA
17875414 TCAATTTT
1 TCAATTTT
17875422 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 7 0.30
20 15 0.65
21 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TCAATTTTTATGAAATTTATA
Found at i:17875431 original size:29 final size:30
Alignment explanation
Indices: 17875398--17875470 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 30
17875388 TTTTTTATAA
*
17875398 TTTTTATAAATTTATATCAATTTTAAT-TT
1 TTTTTATAAATTTATAACAATTTTAATATT
* *
17875427 TTTTT-TACAATTTTTAAGAATTTTAATACATT
1 TTTTTATA-AATTTATAACAATTTTAAT--ATT
17875459 TTTTTA-AAATTT
1 TTTTTATAAATTT
17875471 TAAATAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 2 0.06
29 21 0.58
31 5 0.14
32 8 0.22
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (30 bp):
TTTTTATAAATTTATAACAATTTTAATATT
Found at i:17875450 original size:20 final size:20
Alignment explanation
Indices: 17875375--17875450 Score: 50
Period size: 20 Copynumber: 3.9 Consensus size: 20
17875365 CGATCCATTT
* *
17875375 CAATTTTTATGATTTTTTTA
1 CAATTTTTAAGAATTTTTTA
* *
17875395 TAATTTTTATA-AA-TTTATA
1 CAATTTTTA-AGAATTTTTTA
***
17875414 TCAA-TTTTAATTTTTTTTTA
1 -CAATTTTTAAGAATTTTTTA
17875434 CAATTTTTAAGAATTTT
1 CAATTTTTAAGAATTTT
17875451 AATACATTTT
Statistics
Matches: 40, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
18 1 0.03
19 13 0.32
20 26 0.65
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (20 bp):
CAATTTTTAAGAATTTTTTA
Found at i:17875456 original size:21 final size:21
Alignment explanation
Indices: 17875432--17875473 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17875422 AATTTTTTTT
17875432 TACA-ATTTTTAAGAATTTTAA
1 TACATATTTTTAA-AATTTTAA
*
17875453 TACATTTTTTTAAAATTTTAA
1 TACATATTTTTAAAATTTTAA
17875474 ATAAGTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (21 bp):
TACATATTTTTAAAATTTTAA
Found at i:17875482 original size:21 final size:22
Alignment explanation
Indices: 17875437--17875487 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
17875427 TTTTTTACAA
*
17875437 TTTTTAAGAATTTTAATACATT
1 TTTTTAAGAATTTTAATACAGT
17875459 TTTTTAA-AATTTTAAATA-AGT
1 TTTTTAAGAATTTT-AATACAGT
17875480 TTTATTAA
1 TTT-TTAA
17875488 TTTGTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
TTTTTAAGAATTTTAATACAGT
Found at i:17875704 original size:20 final size:21
Alignment explanation
Indices: 17875659--17875706 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
17875649 TCAATCCATT
** *
17875659 TCAATTTTTATGATTTTTTTA
1 TCAATTTTTATGAGGTTTATA
17875680 T-AATTTTTAT-AGGTTTATA
1 TCAATTTTTATGAGGTTTATA
17875699 TCAATTTT
1 TCAATTTT
17875707 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 7 0.30
20 15 0.65
21 1 0.04
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.62
Consensus pattern (21 bp):
TCAATTTTTATGAGGTTTATA
Found at i:17875740 original size:21 final size:21
Alignment explanation
Indices: 17875716--17875757 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17875706 TAATTTTTTT
17875716 TACA-ATTTTTAAGAATTTTAA
1 TACATATTTTTAA-AATTTTAA
*
17875737 TACATTTTTTTAAAATTTTAA
1 TACATATTTTTAAAATTTTAA
17875758 ATAAGTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (21 bp):
TACATATTTTTAAAATTTTAA
Found at i:17875766 original size:21 final size:22
Alignment explanation
Indices: 17875721--17875771 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
17875711 TTTTTTACAA
*
17875721 TTTTTAAGAATTTTAATACATT
1 TTTTTAAGAATTTTAATACAGT
17875743 TTTTTAA-AATTTTAAATA-AGT
1 TTTTTAAGAATTTT-AATACAGT
17875764 TTTATTAA
1 TTT-TTAA
17875772 TTTGTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
TTTTTAAGAATTTTAATACAGT
Found at i:17875784 original size:10 final size:9
Alignment explanation
Indices: 17875674--17875913 Score: 81
Period size: 10 Copynumber: 24.8 Consensus size: 9
17875664 TTTTATGATT
17875674 TTTTTATAA
1 TTTTTATAA
*
17875683 TTTTTATAGG
1 TTTTTATA-A
*
17875693 TTTATATCAA
1 TTTTTAT-AA
* **
17875703 TTTTAATTT
1 TTTTTATAA
*
17875712 TTTTTACAA
1 TTTTTATAA
*
17875721 TTTTTAAGAA
1 TTTTT-ATAA
*
17875731 TTTTAATACA
1 TTTTTATA-A
*
17875741 TTTTTTTAAAA
1 --TTTTTATAA
*
17875752 TTTTAAATAA
1 TTTT-TATAA
*
17875762 GTTTTATTAA
1 TTTTTA-TAA
17875772 TTTGTTATAA
1 TTT-TTATAA
17875782 TTTTTAT--
1 TTTTTATAA
*
17875789 GTTTTATAA
1 TTTTTATAA
*
17875798 TATTTATAA
1 TTTTTATAA
*
17875807 GCTTTTATAA
1 -TTTTTATAA
17875817 TTTTTTATAA
1 -TTTTTATAA
*
17875827 TAATTTTCATAG
1 T--TTTT-ATAA
*
17875839 TTTTAATAA
1 TTTTTATAA
* *
17875848 GTTTATATCCA
1 -TTTTTAT-AA
*
17875859 TTTTAAT-A
1 TTTTTATAA
*
17875867 TTTTTAATAT
1 TTTTT-ATAA
17875877 TTTTTATAA
1 TTTTTATAA
*
17875886 TTTTTTTTATCA
1 ---TTTTTATAA
*
17875898 TTTTAATAA
1 TTTTTATAA
17875907 TTTTTAT
1 TTTTTAT
17875914 GAGAAAAATA
Statistics
Matches: 166, Mismatches: 43, Indels: 44
0.66 0.17 0.17
Matches are distributed among these distances:
7 6 0.04
8 5 0.03
9 58 0.35
10 69 0.42
11 10 0.06
12 18 0.11
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:17875910 original size:18 final size:18
Alignment explanation
Indices: 17875674--17875913 Score: 63
Period size: 18 Copynumber: 12.9 Consensus size: 18
17875664 TTTTATGATT
*
17875674 TTTTTATAATTTTTATAG
1 TTTTAATAATTTTTATAG
* * **
17875692 GTTTATATCAATTTTAATTT
1 TTTTA-AT-AATTTTTATAG
* *
17875712 TTTTTACAATTTTTA-AG
1 TTTTAATAATTTTTATAG
* *
17875729 AATTTTAATACATTTTTTTAAAA
1 --TTTTAATA-A--TTTTTATAG
* *
17875752 TTTTAAATAAGTTTTATTAA
1 TTTT-AATAATTTTTA-TAG
*
17875772 TTTGTTATAATTTTTAT-G
1 TTT-TAATAATTTTTATAG
*
17875790 TTTT-ATAATATTTATAAG
1 TTTTAATAATTTTTAT-AG
17875808 CTTTT-ATAATTTTT-TA-
1 -TTTTAATAATTTTTATAG
*
17875824 ---TAATAATTTTCATAG
1 TTTTAATAATTTTTATAG
*
17875839 TTTTAATAAGTTTATATCCA-
1 TTTTAATAA-TTTTTAT--AG
*
17875859 TTTTAAT-ATTTTTAATAT
1 TTTTAATAATTTTT-ATAG
*
17875877 TTTTTATAATTTTTTTTATCA-
1 TTTTAATAA---TTTTTAT-AG
17875898 TTTTAATAATTTTTAT
1 TTTTAATAATTTTTAT
17875914 GAGAAAAATA
Statistics
Matches: 165, Mismatches: 27, Indels: 60
0.65 0.11 0.24
Matches are distributed among these distances:
12 1 0.01
13 8 0.05
14 2 0.01
16 10 0.06
17 3 0.02
18 38 0.23
19 36 0.22
20 33 0.20
21 17 0.10
22 16 0.10
23 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTAATAATTTTTATAG
Found at i:17883291 original size:24 final size:24
Alignment explanation
Indices: 17883245--17883292 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
17883235 ATCATCTCAG
* **
17883245 ATTAAATTGAAATTTTATCATTTT
1 ATTAAATTAAAATTTTAAAATTTT
*
17883269 ATTAATTTAAAATTTTAAAATTTT
1 ATTAAATTAAAATTTTAAAATTTT
17883293 TAAAAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTAAATTAAAATTTTAAAATTTT
Found at i:17885622 original size:18 final size:18
Alignment explanation
Indices: 17885599--17885634 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
17885589 TTGAGGCATA
17885599 TTATTTATGGGTAAAATT
1 TTATTTATGGGTAAAATT
17885617 TTATTTATGGGTAAAATT
1 TTATTTATGGGTAAAATT
17885635 GTAGTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (18 bp):
TTATTTATGGGTAAAATT
Found at i:17901973 original size:21 final size:21
Alignment explanation
Indices: 17901930--17901987 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
17901920 TAAAAGCATG
* * * *
17901930 ACTTGTTTCGATAGAAGTGTC
1 ACTTGTATCGGTAGAACTATC
17901951 ACTTGTATCGGTAGAACTATC
1 ACTTGTATCGGTAGAACTATC
* *
17901972 ACTAGTATCAGTAGAA
1 ACTTGTATCGGTAGAA
17901988 GTCTGCTACT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACTATC
Done.