Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008750.1 Hibiscus syriacus cultivar Beakdansim tig00111841_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3719443
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 18
Found at i:11302 original size:19 final size:20
Alignment explanation
Indices: 11263--11302 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
11253 ATATTACACT
*
11263 TAAAAAAAAAATGATGGAAAA
1 TAAAAAAAAAA-GATGAAAAA
11284 TAAAAAAAAAA-ATGAAAAA
1 TAAAAAAAAAAGATGAAAAA
11303 AGAAGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (20 bp):
TAAAAAAAAAAGATGAAAAA
Found at i:12307 original size:41 final size:41
Alignment explanation
Indices: 12257--12485 Score: 159
Period size: 41 Copynumber: 5.5 Consensus size: 41
12247 CAGACTTCCT
*
12257 CATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTC
1 CATCACGTAGGAACCGTGTCAACCATAGATAACCAGCCGTC
* ** ** *
12298 CATCACGTAGGAACCGTGTTATCACC-TTTATGGCCAGATCTC-TT
1 CATCACGTAGGAACCGTGTCA--ACCATAGATAACCAG--C-CGTC
12342 CATCACGTAGG--CCGTGTCAACCATAGATAACCAGCCGTCC
1 CATCACGTAGGAACCGTGTCAACCATAGATAACCAGCCGT-C
* * ** *
12382 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATCTC-TT
1 -CATCACGTAGGAACCGTGTCA--ACC-ATAGATAACCAG--C-CGTC
* *
12429 CATCACGTATGAGCCGTGTC-A--ATAGATAACCAGCCGTC
1 CATCACGTAGGAACCGTGTCAACCATAGATAACCAGCCGTC
12467 CATCACGTAGGAACCGTGT
1 CATCACGTAGGAACCGTGT
12486 TATCACCTTT
Statistics
Matches: 143, Mismatches: 27, Indels: 39
0.68 0.13 0.19
Matches are distributed among these distances:
37 1 0.01
38 20 0.14
39 2 0.01
40 12 0.08
41 37 0.26
42 14 0.10
43 11 0.08
44 13 0.09
45 4 0.03
46 26 0.18
48 2 0.01
49 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (41 bp):
CATCACGTAGGAACCGTGTCAACCATAGATAACCAGCCGTC
Found at i:12395 original size:85 final size:85
Alignment explanation
Indices: 12256--12529 Score: 411
Period size: 85 Copynumber: 3.3 Consensus size: 85
12246 CCAGACTTCC
12256 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCATCACGTAGGAACCGTGTTATC
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCATCACGTAGGAACCGTGTTATC
12321 ACCTTTATGGCCAGATCTCT
66 ACCTTTATGGCCAGATCTCT
12341 TCATCACGTA-G-GCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGT-C-CATCACGTAGGAACCGTGTTA
12404 TCACCTTTAGATGGCCAGATCTCT
64 TCACCTTT--ATGGCCAGATCTCT
*
12428 TCATCACGTATGAGCCGTGTC-A--ATAGATAACCAGCCGTCCATCACGTAGGAACCGTGTTATC
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCATCACGTAGGAACCGTGTTATC
*
12490 ACCTTTAGTGGCCAGA-GT-T
66 ACCTTTA-TGGCCAGATCTCT
* *
12509 TCATCA-GTATGAACCGTGTCA
1 TCATCACGTAGGAGCCGTGTCA
12530 TCCCCAGACC
Statistics
Matches: 179, Mismatches: 2, Indels: 20
0.89 0.01 0.10
Matches are distributed among these distances:
80 13 0.07
81 7 0.04
82 2 0.01
83 36 0.20
84 31 0.17
85 40 0.22
86 16 0.09
87 24 0.13
88 2 0.01
89 8 0.04
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (85 bp):
TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCATCACGTAGGAACCGTGTTATC
ACCTTTATGGCCAGATCTCT
Found at i:12898 original size:17 final size:16
Alignment explanation
Indices: 12860--12901 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
12850 TTTTTTTTTC
12860 CGTTATTTTATTATAT
1 CGTTATTTTATTATAT
**
12876 TATTATTATTATTATAT
1 CGTTATT-TTATTATAT
12893 CGTTATTTT
1 CGTTATTTT
12902 TTTTATTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (16 bp):
CGTTATTTTATTATAT
Found at i:12907 original size:17 final size:17
Alignment explanation
Indices: 12860--12907 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
12850 TTTTTTTTTC
12860 CGTTA-TTTTATTATAT
1 CGTTATTTTTATTATAT
** *
12876 TATTATTATTATTATAT
1 CGTTATTTTTATTATAT
*
12893 CGTTATTTTTTTTAT
1 CGTTATTTTTATTAT
12908 TATTAATTAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (17 bp):
CGTTATTTTTATTATAT
Found at i:12928 original size:29 final size:29
Alignment explanation
Indices: 12875--12931 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
12865 TTTTATTATA
*
12875 TTATTATTATTATTATATCGTTATTTTTT
1 TTATTATTATTATTACATCGTTATTTTTT
12904 TTATTATTAATTAATTACAT-G-TATTTTT
1 TTATTATT-ATT-ATTACATCGTTATTTTT
12932 GCAGGCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 15 0.60
30 4 0.16
31 6 0.24
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (29 bp):
TTATTATTATTATTACATCGTTATTTTTT
Found at i:21766 original size:30 final size:29
Alignment explanation
Indices: 21730--21795 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
21720 AAAGGACGAG
21730 TTTGTAACATATGAATAGTCGAG-TGACTAT
1 TTTGTAAC-TATGAATAGTCG-GTTGACTAT
* *
21760 TTTGTAACTTTTAATAGTCGGTTGACTAT
1 TTTGTAACTATGAATAGTCGGTTGACTAT
21789 TTTGTAA
1 TTTGTAA
21796 ATTTTAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 1 0.03
29 24 0.73
30 8 0.24
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (29 bp):
TTTGTAACTATGAATAGTCGGTTGACTAT
Found at i:21779 original size:29 final size:29
Alignment explanation
Indices: 21743--21806 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
21733 GTAACATATG
*
21743 AATAGTCGAG-TGACTATTTTGTAACTTTT
1 AATAGTCG-GTTGACTATTTTGTAAATTTT
21772 AATAGTCGGTTGACTATTTTGTAAATTTT
1 AATAGTCGGTTGACTATTTTGTAAATTTT
21801 AATAGT
1 AATAGT
21807 TAAAGGAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (29 bp):
AATAGTCGGTTGACTATTTTGTAAATTTT
Found at i:23559 original size:15 final size:17
Alignment explanation
Indices: 23539--23572 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
23529 TTAACTCGAG
23539 CTCAAAA-ATTAT-AAA
1 CTCAAAATATTATCAAA
23554 CTCAAAATATTATCAAA
1 CTCAAAATATTATCAAA
23571 CT
1 CT
23573 TAGTTCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (17 bp):
CTCAAAATATTATCAAA
Found at i:24216 original size:29 final size:30
Alignment explanation
Indices: 24158--24218 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
24148 ATTGAAAGGG
* *
24158 TATTAAAAATTTGAGGACTCAATTAAAATA
1 TATTAAAAATTTAACGACTCAATTAAAATA
*
24188 TATT-AAAATTTAACGAC-CAATTTAGAATA
1 TATTAAAAATTTAACGACTCAA-TTAAAATA
24217 TA
1 TA
24219 AGTATAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.11
29 20 0.74
30 4 0.15
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.34
Consensus pattern (30 bp):
TATTAAAAATTTAACGACTCAATTAAAATA
Found at i:27285 original size:12 final size:12
Alignment explanation
Indices: 27270--27315 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
27260 CGGTTTTTTT
*
27270 ACCGGATAAAAA
1 ACCGGTTAAAAA
27282 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
27297 ACCGGTTAAAAA
1 ACCGGTTAAAAA
27309 ACCGGTT
1 ACCGGTT
27316 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:27297 original size:15 final size:13
Alignment explanation
Indices: 27276--27316 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
27266 TTTTACCGGA
27276 TAAAAAACCGGTT
1 TAAAAAACCGGTT
27289 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
27303 TAAAAAACCGGTT
1 TAAAAAACCGGTT
27316 T
1 T
27317 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:29691 original size:33 final size:33
Alignment explanation
Indices: 29644--29738 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
29634 TTTCAATTAG
29644 CGAACTT-GAAGTTTTTAAGTATTTGAATTTAT
1 CGAACTTGGAAGTTTTTAAGTATTTGAATTTAT
29676 CGAACTTGGAAGTTTTTAAGTATTTGAATTTAT
1 CGAACTTGGAAGTTTTTAAGTATTTGAATTTAT
* * *
29709 CAAACTTGGAAGTATTTAAGTATTTCAATT
1 CGAACTTGGAAGTTTTTAAGTATTTGAATT
29739 ATGTTGAGTT
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 7 0.12
33 52 0.88
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (33 bp):
CGAACTTGGAAGTTTTTAAGTATTTGAATTTAT
Found at i:29767 original size:13 final size:13
Alignment explanation
Indices: 29724--29778 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
29714 TTGGAAGTAT
29724 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
29737 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
29751 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
29764 TTAAGTATTTGAA
1 TTAAGTATTTCAA
29777 TT
1 TT
29779 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:30000 original size:21 final size:21
Alignment explanation
Indices: 29974--30030 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
29964 TGGAGCGTGG
*
29974 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
29995 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
30016 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
30031 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:30247 original size:15 final size:15
Alignment explanation
Indices: 30194--30247 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
30184 ATCTGGAATA
30194 TTAAAATCGGTTTTT
1 TTAAAATCGGTTTTT
* *
30209 TTATAACCGGTTTTT
1 TTAAAATCGGTTTTT
30224 TTAAAAAAATCGGTTTTT
1 TT---AAAATCGGTTTTT
30242 TTAAAA
1 TTAAAA
30248 CCGAAACCGG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 19 0.59
18 13 0.41
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (15 bp):
TTAAAATCGGTTTTT
Found at i:32683 original size:18 final size:19
Alignment explanation
Indices: 32646--32683 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
32636 TATAACTTTA
32646 TTTCAATTATCGTAAACTTG
1 TTTCAATTATCG-AAACTTG
32666 TTTCAATTATCG-AACTTG
1 TTTCAATTATCGAAACTTG
32684 AAGTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTCAATTATCGAAACTTG
Found at i:32725 original size:33 final size:33
Alignment explanation
Indices: 32672--32770 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
32662 CTTGTTTCAA
32672 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
32704 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
32737 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
32770 T
1 T
32771 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:32799 original size:13 final size:13
Alignment explanation
Indices: 32756--32810 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
32746 TTGGAAGTAT
32756 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
32769 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
32783 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
32796 TTAAGTATTTGAA
1 TTAAGTATTTCAA
32809 TT
1 TT
32811 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:33035 original size:21 final size:21
Alignment explanation
Indices: 33006--33062 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
32996 TGGAGCGTGG
*
33006 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
* * *
33027 GGGATTCGGTTTCCTCTCATC
1 GGGAATCGGTTCCCTCTCATA
33048 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
33063 AAGTGTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.28, G:0.26, T:0.30
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:33266 original size:17 final size:18
Alignment explanation
Indices: 33246--33279 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33236 GTTTTTTTAT
33246 AACC-GGTTTTTTAAAAA
1 AACCAGGTTTTTTAAAAA
*
33263 AACCAGTTTTTTTAAAA
1 AACCAGGTTTTTTAAAA
33280 CCGAAACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (18 bp):
AACCAGGTTTTTTAAAAA
Found at i:33399 original size:15 final size:17
Alignment explanation
Indices: 33373--33404 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
33363 TTCTATGGGA
33373 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
33389 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
33405 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:35103 original size:76 final size:76
Alignment explanation
Indices: 35014--35166 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
35004 TCAAATAAGT
*
35014 CATTAAACAATGATTTTATATCAAATTTACCCTAAAACTTTTTAATTTAAAAATAGAAAAAAAAA
1 CATTAAACAATGATTTTATATCAAATTTACCCTAAAACTTTTTAATTTAAAAATACAAAAAAAAA
35079 CTATATCCACC
66 CTATATCCACC
35090 CATTAAACAATGATTTTATATCAAATTTACCCTAAAACTTTTTAATTTAAAAATACAAAAAAAAA
1 CATTAAACAATGATTTTATATCAAATTTACCCTAAAACTTTTTAATTTAAAAATACAAAAAAAAA
35155 CTATATCCACC
66 CTATATCCACC
35166 C
1 C
35167 TTATCAGACA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (76 bp):
CATTAAACAATGATTTTATATCAAATTTACCCTAAAACTTTTTAATTTAAAAATACAAAAAAAAA
CTATATCCACC
Found at i:36964 original size:44 final size:44
Alignment explanation
Indices: 36901--36996 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
36891 TTAATTATAC
* *
36901 ATCCAAAAGTAAAAAGAAATAAAGGAAAATGGAATCGGAAACTT
1 ATCCAAAAGTAAAAAGAAATAAACGAAAAAGGAATCGGAAACTT
36945 ATCCAAAAGTAAAAAGAAATAAACGAAAAAGGAATCGGAAACTT
1 ATCCAAAAGTAAAAAGAAATAAACGAAAAAGGAATCGGAAACTT
*
36989 ACCCAAAA
1 ATCCAAAA
36997 TCGATCGGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (44 bp):
ATCCAAAAGTAAAAAGAAATAAACGAAAAAGGAATCGGAAACTT
Found at i:40887 original size:26 final size:27
Alignment explanation
Indices: 40837--40887 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
40827 ATTAAGTGTC
** *
40837 GGTTTAGTGGGATTTTCTTTTGACTTT
1 GGTTTAGTGGGATTTTCGGTGGACTTT
40864 GGTTT-GTGGGATTTTCGGTGGACT
1 GGTTTAGTGGGATTTTCGGTGGACT
40888 GTTCGCAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.10, C:0.08, G:0.33, T:0.49
Consensus pattern (27 bp):
GGTTTAGTGGGATTTTCGGTGGACTTT
Found at i:41283 original size:3 final size:3
Alignment explanation
Indices: 41269--41331 Score: 67
Period size: 3 Copynumber: 20.3 Consensus size: 3
41259 AATTAAAATA
41269 AAT AATT AAT AAT AAT AAT AGA- AAT AAT AAT AAT AAT -AT AATT AAT
1 AAT AA-T AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AA-T AAT
*
41315 AAT ATT AAT AAAT AAT A
1 AAT AAT AAT -AAT AAT A
41332 TTTTTGACCC
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
2 3 0.06
3 39 0.75
4 10 0.19
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:41848 original size:31 final size:32
Alignment explanation
Indices: 41748--41888 Score: 128
Period size: 32 Copynumber: 4.5 Consensus size: 32
41738 TATGTATAAA
** * *
41748 TGTTTCAAGGGAAACCGACTCAAAGGTGATTT
1 TGTTTCAAAAGAAACAGACTCAAAGATGATTT
* * **
41780 TTTTTCAAAAGAAACAGACTCAAAGATAATGG
1 TGTTTCAAAAGAAACAGACTCAAAGATGATTT
* *
41812 CGTTTCAAAAGAAAC-GACTCAAAGATGGTTT
1 TGTTTCAAAAGAAACAGACTCAAAGATGATTT
*
41843 TGTTTCAAGAA-AAACAGACTCAATGAT--TTT
1 TGTTTCAA-AAGAAACAGACTCAAAGATGATTT
*
41873 ATGTTTCCAAAGAAAC
1 -TGTTTCAAAAGAAAC
41889 TGCCTCAAGG
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
30 5 0.06
31 34 0.39
32 49 0.56
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (32 bp):
TGTTTCAAAAGAAACAGACTCAAAGATGATTT
Found at i:42407 original size:36 final size:35
Alignment explanation
Indices: 42349--42462 Score: 140
Period size: 36 Copynumber: 3.2 Consensus size: 35
42339 TTGTATCTCA
*
42349 GAGAAAAA-TATCTCAAGCGAGACGAAATTTGTTTT
1 GAGAAAAATTGTCTCAAGCGAGAC-AAATTTGTTTT
* *
42384 GAGAGAAATTGTCTCCAGCGAGACAAAATTTGTTTT
1 GAGAAAAATTGTCTCAAGCGAGAC-AAATTTGTTTT
* *
42420 TAGAAAAATTGTCTCAAGCGAGACAAAGGTTGTTTTT
1 GAGAAAAATTGTCTCAAGCGAGACAAA-TTTG-TTTT
42457 GAGAAA
1 GAGAAA
42463 GCGATCTCAA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
35 10 0.15
36 48 0.72
37 9 0.13
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (35 bp):
GAGAAAAATTGTCTCAAGCGAGACAAATTTGTTTT
Found at i:42603 original size:37 final size:37
Alignment explanation
Indices: 42506--42603 Score: 92
Period size: 37 Copynumber: 2.6 Consensus size: 37
42496 GAAGCAAATT
*
42506 CAAAA-TTTGTATCTCAAAGGGAAAATGTCTCAAGCGAGA
1 CAAAATTTTGT-T-TCAAA-GGAAAATGTCTCAAACGAGA
* * * * *
42545 CAAAATTTAT-TTTCGACGGAAATTGTCTCAAATGATA
1 CAAAATTT-TGTTTCAAAGGAAAATGTCTCAAACGAGA
42582 CAAAATTTTGTTTCAAAGGAAA
1 CAAAATTTTGTTTCAAAGGAAA
42604 CAAACACAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
36 1 0.02
37 34 0.71
38 3 0.06
39 6 0.12
40 3 0.06
41 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAGGAAAATGTCTCAAACGAGA
Found at i:44050 original size:2 final size:2
Alignment explanation
Indices: 44043--44067 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44033 AGCTTTATTG
44043 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
44068 GGTAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50931 original size:23 final size:22
Alignment explanation
Indices: 50886--50968 Score: 87
Period size: 23 Copynumber: 3.8 Consensus size: 22
50876 TTAGTGCAGA
* * *
50886 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTAAAG
50908 GGGAACCGATTCCCCCTTTAAAG
1 GGGAACCGATTCCCCC-TTAAAG
* *
50931 GGGAACCGATTCCCCC-CATAG
1 GGGAACCGATTCCCCCTTAAAG
* *
50952 GGGAATCGATACCCCCT
1 GGGAACCGATTCCCCCT
50969 GAGGGTTCTG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 17 0.33
22 14 0.27
23 21 0.40
ACGTcount: A:0.25, C:0.33, G:0.24, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTAAAG
Found at i:52567 original size:18 final size:18
Alignment explanation
Indices: 52546--52585 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
52536 GAACAGCACA
52546 AGGAACAAGCACGAG-CAG
1 AGGAACAAGCAC-AGCCAG
52564 AGGAACAAGCACAGCCAG
1 AGGAACAAGCACAGCCAG
52582 AGGA
1 AGGA
52586 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.45, C:0.23, G:0.33, T:0.00
Consensus pattern (18 bp):
AGGAACAAGCACAGCCAG
Found at i:58111 original size:32 final size:32
Alignment explanation
Indices: 58068--58145 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 32
58058 TACAATCAAG
* *
58068 AGAAATAAGTTAGTGTACATAAACAAAAGGAA
1 AGAAATAAGTTAATGTACACAAACAAAAGGAA
*
58100 AGAAATTAGTTAATGTACACAAACAAAAGGAA
1 AGAAATAAGTTAATGTACACAAACAAAAGGAA
58132 AGAAATCAA-TTAAT
1 AGAAAT-AAGTTAAT
58146 ACAGGTGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 40 0.98
33 1 0.02
ACGTcount: A:0.56, C:0.08, G:0.15, T:0.21
Consensus pattern (32 bp):
AGAAATAAGTTAATGTACACAAACAAAAGGAA
Found at i:59218 original size:17 final size:18
Alignment explanation
Indices: 59196--59231 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
59186 GTGCACTAAG
59196 AGTGCA-TCGATGTATCA
1 AGTGCATTCGATGTATCA
*
59213 AGTGCATTCGATGTTTCA
1 AGTGCATTCGATGTATCA
59231 A
1 A
59232 AATAGACAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (18 bp):
AGTGCATTCGATGTATCA
Found at i:59330 original size:65 final size:65
Alignment explanation
Indices: 59197--59406 Score: 211
Period size: 65 Copynumber: 3.2 Consensus size: 65
59187 TGCACTAAGA
* *
59197 GTGCATCGATGTATCAAGTGCATTCGATG-TTTCAAAATAGACAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGACAGAGTGCATCGATGCATGGCTG
**
59261 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTA-AGTGCATCGATGCATGG-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGAC-AGAGTGCATCGATGCATGGC
*
59323 TAT
64 T-G
* **
59326 GTGCATCGATGCATGAAATGCATTCGATG--TTCAATTTA-ATTCATG-GTGCATCGATGCATGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGA--CA-GAGTGCATCGATGCATGG
*
59387 ATTG
63 -CTG
*
59391 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
59407 CTTTGAAAAT
Statistics
Matches: 123, Mismatches: 12, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 45 0.37
65 66 0.54
66 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGACAGAGTGCATCGATGCATGGCTG
Found at i:59777 original size:24 final size:25
Alignment explanation
Indices: 59770--59822 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
59760 CCTTTTAACA
59770 TTTTAACACTTAACACTTC-T-CCC
1 TTTTAACACTTAACACTTCTTCCCC
*
59793 TTTTAACATTTTAACACTTCTTCCCC
1 TTTTAACA-CTTAACACTTCTTCCCC
59819 TTTT
1 TTTT
59823 TGTTAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.31
24 10 0.38
25 1 0.04
26 7 0.27
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTTAACACTTAACACTTCTTCCCC
Found at i:59787 original size:31 final size:31
Alignment explanation
Indices: 59749--59811 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
59739 CCCCTTACTA
59749 TAACACTTCTCCCTTTTAACATTTTAACACT
1 TAACACTTCTCCCTTTTAACATTTTAACACT
59780 TAACACTTCTCCCTTTTAACATTTTAACACT
1 TAACACTTCTCCCTTTTAACATTTTAACACT
59811 T
1 T
59812 CTTCCCCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (31 bp):
TAACACTTCTCCCTTTTAACATTTTAACACT
Found at i:59800 original size:16 final size:16
Alignment explanation
Indices: 59749--59800 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
59739 CCCCTTACTA
59749 TAACACTTCTCCCTTT
1 TAACACTTCTCCCTTT
* ** **
59765 TAACA-TTTTAACACT
1 TAACACTTCTCCCTTT
59780 TAACACTTCTCCCTTT
1 TAACACTTCTCCCTTT
59796 TAACA
1 TAACA
59801 TTTTAACACT
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (16 bp):
TAACACTTCTCCCTTT
Found at i:60466 original size:21 final size:21
Alignment explanation
Indices: 60455--60506 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
60445 ATGAGCACGA
60455 GAAGAGCTAGGAGCAGCTCGT
1 GAAGAGCTAGGAGCAGCTCGT
60476 GAAGAGCTAGGAGCAGCTCGT
1 GAAGAGCTAGGAGCAGCTCGT
60497 GAAGAGCTAG
1 GAAGAGCTAG
60507 CTCCCGGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.17, G:0.38, T:0.13
Consensus pattern (21 bp):
GAAGAGCTAGGAGCAGCTCGT
Found at i:62129 original size:20 final size:21
Alignment explanation
Indices: 62077--62132 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
62067 TCACCTTCAT
62077 GGTGTATCGATGCACATTTAA
1 GGTGTATCGATGCACATTTAA
*
62098 GGATGCATCGATGCAC-TGTT-A
1 GG-TGTATCGATGCACAT-TTAA
62119 GGTGTATCGATGCA
1 GGTGTATCGATGCA
62133 TGAAGCACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 11 0.35
21 6 0.19
22 14 0.45
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (21 bp):
GGTGTATCGATGCACATTTAA
Found at i:68013 original size:46 final size:45
Alignment explanation
Indices: 67912--68014 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
67902 CACTAAGAGT
* * * *
67912 GCATCGATGCATCAAGTGTATTCGATGTTTCAAAATAGCCAGAGT
1 GCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGC
* *
67957 GCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGC
1 GCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGC
*
68003 GCATCAATGCAT
1 GCATCGATGCAT
68015 GGTATGTGCA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
45 25 0.51
46 21 0.43
47 3 0.06
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (45 bp):
GCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGC
Found at i:71697 original size:23 final size:23
Alignment explanation
Indices: 71645--71702 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
71635 GTAAAATGTA
71645 ATTAAAATAAATAATAATAATAGT
1 ATTAAAAT-AATAATAATAATAGT
* * *
71669 AGTAAAATAATAATAATATTATT
1 ATTAAAATAATAATAATAATAGT
71692 ATT-AAATAATA
1 ATTAAAATAATA
71703 TTTTGACACG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 8 0.27
23 15 0.50
24 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (23 bp):
ATTAAAATAATAATAATAATAGT
Found at i:85526 original size:2 final size:2
Alignment explanation
Indices: 85519--85553 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
85509 AAAAGAGTGT
85519 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
85554 GCTTTGAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:86452 original size:18 final size:17
Alignment explanation
Indices: 86412--86456 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
86402 CTCAAAATTA
*
86412 AATATTATTTTAAATAAT
1 AATATT-TTTTAAACAAT
*
86430 CATATTTTTTACAACAAT
1 AATATTTTTTA-AACAAT
86448 AATATTTTT
1 AATATTTTT
86457 ACGTCATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATTTTTTAAACAAT
Found at i:87578 original size:22 final size:22
Alignment explanation
Indices: 87550--87592 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
87540 ATCACTCCTT
87550 TAGGAAAAATAAGTTGCTTGCA
1 TAGGAAAAATAAGTTGCTTGCA
87572 TAGGAAAAATAAGTTGCTTGC
1 TAGGAAAAATAAGTTGCTTGC
87593 TCCAGTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (22 bp):
TAGGAAAAATAAGTTGCTTGCA
Found at i:93271 original size:21 final size:20
Alignment explanation
Indices: 93245--93297 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 20
93235 AAATTACATA
93245 ACTTTCAACAAAGTATCGAT
1 ACTTTCAACAAAGTATCGAT
* *
93265 ACATTTCTATAAAAAGTATCTAT
1 AC-TTTC-A-ACAAAGTATCGAT
93288 ACTTTCAACA
1 ACTTTCAACA
93298 TATCAGGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 5 0.19
23 13 0.48
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.34
Consensus pattern (20 bp):
ACTTTCAACAAAGTATCGAT
Found at i:93510 original size:23 final size:23
Alignment explanation
Indices: 93484--93550 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
93474 TATTAGTTAC
*
93484 CGCTTATATAATGTAATATGTAG
1 CGCTTATATAATGTAATAGGTAG
93507 CGCTTATATAATGTAATAGGTAG
1 CGCTTATATAATGTAATAGGTAG
* **
93530 CACTTATATAATAAAATAGGT
1 CGCTTATATAATGTAATAGGT
93551 TAATTACAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (23 bp):
CGCTTATATAATGTAATAGGTAG
Found at i:93598 original size:87 final size:87
Alignment explanation
Indices: 93507--93730 Score: 351
Period size: 87 Copynumber: 2.6 Consensus size: 87
93497 TAATATGTAG
*
93507 CGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTAC-AGGAAACATTATC
1 CGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTA-AAAACATTATC
*
93571 CAGCACAATAACATATTAGGTAC
65 AAGCACAATAACATATTAGGTAC
** *
93594 CGCTTATATAATGTAATTTGTAGCACATATATAATAAAATAGGTTAATTACTAAAAACATTATCA
1 CGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAAAAACATTATCA
*
93659 AGCACAATAACATATTAGGTAG
66 AGCACAATAACATATTAGGTAC
* * *
93681 CGCTTATATAACGTAATAGGTAGCATTTATTTAATAAAATAGGTTAATTA
1 CGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTA
93731 TTTAATTTCC
Statistics
Matches: 124, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
87 123 0.99
88 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.33
Consensus pattern (87 bp):
CGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAAAAACATTATCA
AGCACAATAACATATTAGGTAC
Found at i:93604 original size:110 final size:110
Alignment explanation
Indices: 93402--93637 Score: 366
Period size: 110 Copynumber: 2.1 Consensus size: 110
93392 ATAGGTAAAA
* * *
93402 ATATGATGAAATAGGTAGCGCTTATCTAATAAAATAGGTTAATTACTAGAAACATTATCAAGCAC
1 ATATAATGAAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCAC
* * *
93467 AATAACATATTAGTTACCGCTTATATAATGTAATATGTAGCGCTT
66 AATAACATATTAGGTACCGCTTATATAATGTAATATGTAGCACAT
* *
93512 ATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTAC-AGGAAACATTATCCAGCA
1 ATATAATGAAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTA-GAAACATTATCAAGCA
*
93576 CAATAACATATTAGGTACCGCTTATATAATGTAATTTGTAGCACAT
65 CAATAACATATTAGGTACCGCTTATATAATGTAATATGTAGCACAT
*
93622 ATATAATAAAATAGGT
1 ATATAATGAAATAGGT
93638 TAATTACTAA
Statistics
Matches: 114, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
109 1 0.01
110 113 0.99
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (110 bp):
ATATAATGAAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCAC
AATAACATATTAGGTACCGCTTATATAATGTAATATGTAGCACAT
Found at i:93710 original size:23 final size:23
Alignment explanation
Indices: 93665--93724 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
93655 ATCAAGCACA
* *
93665 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCACTTAT
* *
93688 ATAACGTAATAGGTAGCATTTAT
1 ATAACATAATAGGTAGCACTTAT
* * *
93711 TTAATAAAATAGGT
1 ATAACATAATAGGT
93725 TAATTATTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCACTTAT
Found at i:93996 original size:24 final size:24
Alignment explanation
Indices: 93969--94037 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
93959 AACATCAAAT
93969 ACAATAAAATAATATTATTTATTA
1 ACAATAAAATAATATTATTTATTA
93993 ACAA-AATAATAATATTATTT-TTA
1 ACAATAA-AATAATATTATTTATTA
*
94016 AAATATTAAAATAAT-TTATTTA
1 ACA-A-TAAAATAATATTATTTA
94038 ATATTATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 7 0.18
24 24 0.62
25 6 0.15
26 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (24 bp):
ACAATAAAATAATATTATTTATTA
Found at i:94062 original size:14 final size:14
Alignment explanation
Indices: 94019--94138 Score: 61
Period size: 14 Copynumber: 8.6 Consensus size: 14
94009 ATTTTTAAAA
*
94019 TATTAAAATAAT-T
1 TATTAAAATATTAT
*
94032 TATT-TAATATTATT
1 TATTAAAATATTA-T
94046 TATGT-AAATATTAT
1 TAT-TAAAATATTAT
94060 TATTAAAATATTA-
1 TATTAAAATATTAT
* *
94073 TATCTATAATTTTAT
1 TAT-TAAAATATTAT
* * *
94088 AAATAAAAAATTAT
1 TATTAAAATATTAT
* **
94102 GATTATTATATT-T
1 TATTAAAATATTAT
**
94115 TATTAAAATAAAAT
1 TATTAAAATATTAT
94129 TATTATAAAT
1 TATTA-AAAT
94139 TATATTTATT
Statistics
Matches: 79, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
12 5 0.06
13 16 0.20
14 45 0.57
15 13 0.16
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (14 bp):
TATTAAAATATTAT
Found at i:94087 original size:28 final size:28
Alignment explanation
Indices: 94052--94141 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 28
94042 TATTTATGTA
94052 AATATTATTATTAAAATATTAT-ATCTAT
1 AATATTATTATTAAAATATTATGAT-TAT
* * * *
94080 AATTTTATAAATAAAAAATTATGATTAT
1 AATATTATTATTAAAATATTATGATTAT
* ** *
94108 TATATT-TTATTAAAATAAAATTATTAT
1 AATATTATTATTAAAATATTATGATTAT
94135 AA-ATTAT
1 AATATTAT
94142 ATTTATTATT
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
26 3 0.06
27 17 0.36
28 25 0.53
29 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATTATTATTAAAATATTATGATTAT
Found at i:94144 original size:31 final size:31
Alignment explanation
Indices: 94081--94149 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
94071 TATATCTATA
*
94081 ATTTTA-TAAATAAAAAATTATGATTATTAT
1 ATTTTATTAAATAAAAAATTATGATAATTAT
* *
94111 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTATTAAATAAAAAATTATGAT-AATTAT
94142 A-TTTATTA
1 ATTTTATTA
94150 TTTTTTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTATTAAATAAAAAATTATGATAATTAT
Found at i:94917 original size:31 final size:31
Alignment explanation
Indices: 94854--94922 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
94844 TATATCTATA
*
94854 ATTTTA-TAAATAAAAAATTATGATTATTAT
1 ATTTTATTAAATAAAAAATTATGATAATTAT
* *
94884 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTATTAAATAAAAAATTATGAT-AATTAT
94915 A-TTTATTA
1 ATTTTATTA
94923 TTTATTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTATTAAATAAAAAATTATGATAATTAT
Found at i:95387 original size:200 final size:197
Alignment explanation
Indices: 95025--95692 Score: 858
Period size: 200 Copynumber: 3.4 Consensus size: 197
95015 CATATGTTAC
* * *
95025 ATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAAAC-AGTATAAACATACCGAT
1 ATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGT--ACTAGTATAAATATACCGGT
* * * ** *** * *
95089 TTTATAAGAGAATAGGTCTACATAATGTATCGACACAAATTAAAAATGTGTCGATACATTTTGTC
64 TTTATGAGAAAATAGGTCTACATAATGTATAGACACATTTTAAGTTTGTGTCGATACTTTTTTTC
* *
95154 CATAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCGACACATTTATTAAAAGTATCGATCCA
129 CAGAATGAATGCC-AACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCA
95219 AAAAA
193 AAAAA
* * * *
95224 CATCGAAACCAATAATTACAATGTAATAGGTAAATTTACAATGTACTTGGTAGAAATATATCGGT
1 -ATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAC-TAGTATAAATATACCGGT
*
95289 TTTATGAGAAAATATGTCTACATAATGTATAGACACATTTTAAGTTTGTGTCGATACTTTTTTTC
64 TTTATGAGAAAATAGGTCTACATAATGTATAGACACATTTTAAGTTTGTGTCGATACTTTTTTTC
* * * * **
95354 CAGAATGAATGTTCAACGAAGTGCACACATAAAGTGTTGATACATTTATTAAAAGTATATATCCA
129 CAGAATGAATG-CCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCA
95419 AAAAA
193 AAAAA
* *
95424 ATCGAAACCGGTAATTACAATGTAATATGTAAATTTACAATGTACCTAGTATAAATATACCGGTT
1 ATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTA-CTAGTATAAATATACCGGTT
* * * *
95489 TTATGAGAAAATAGGTCTACATAATGTATTGACACATTTTAAGTTTATGTCTATACTTTTTTTCT
65 TTATGAGAAAATAGGTCTACATAATGTATAGACACATTTTAAGTTTGTGTCGATACTTTTTTTCC
*
95554 AGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA--AAATTGTATCGATTCC
130 AGAATGAATG-CCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAA-AGTATCGA-TCC
95617 -AAAAA
192 AAAAAA
* * * * * *
95622 ATCGAAACCGATAATTATAATATAATAAGTAAATTTGCAATGTTACTGGTATAAATATATCGGTT
1 ATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATG-TACTAGTATAAATATACCGGTT
95687 TTATGA
65 TTATGA
95693 TAGAATATGT
Statistics
Matches: 409, Mismatches: 52, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
197 3 0.01
198 73 0.18
199 164 0.40
200 168 0.41
201 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (197 bp):
ATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACTAGTATAAATATACCGGTTT
TATGAGAAAATAGGTCTACATAATGTATAGACACATTTTAAGTTTGTGTCGATACTTTTTTTCCA
GAATGAATGCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCAAAA
AA
Found at i:95752 original size:23 final size:23
Alignment explanation
Indices: 95696--95752 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
95686 TTTATGATAG
*
95696 AATATGTCAATATAAGCGCTACCT
1 AATATGT-TATATAAGCGCTACCT
* **
95720 ATTACATTATATAAGCGCTACCT
1 AATATGTTATATAAGCGCTACCT
95743 AATATGTTAT
1 AATATGTTAT
95753 TGTGCTTGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (23 bp):
AATATGTTATATAAGCGCTACCT
Found at i:95796 original size:87 final size:87
Alignment explanation
Indices: 95705--95941 Score: 402
Period size: 87 Copynumber: 2.7 Consensus size: 87
95695 GAATATGTCA
*
95705 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTT
95770 CCAGTAATTAACCTATTTTATT
66 CCAGTAATTAACCTATTTTATT
* *
95792 ATATAAGCGCTACCTATTACATTATATAAACGCTATCTAATATGTTATTGTGCTTGATAATGTTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTT
95857 CCAGTAATTAACCTATTTTATT
66 CCAGTAATTAACCTATTTTATT
* * * * *
95879 ATATAAACGCTACCTATTACATTATATAAACGTTACCTAATTTGTTATTTTACTTGATAATAT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATAT
95942 CTCCGGTTAA
Statistics
Matches: 140, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 140 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTT
CCAGTAATTAACCTATTTTATT
Found at i:95806 original size:23 final size:23
Alignment explanation
Indices: 95780--95826 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
95770 CCAGTAATTA
** *
95780 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAACGCT
95803 ACCTATTACATTATATAAACGCT
1 ACCTATTACATTATATAAACGCT
95826 A
1 A
95827 TCTAATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.38
Consensus pattern (23 bp):
ACCTATTACATTATATAAACGCT
Found at i:95839 original size:23 final size:23
Alignment explanation
Indices: 95789--95833 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
95779 AACCTATTTT
* *
95789 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAACGCTACCTAATAC
*
95812 ATTATATAAACGCTATCTAATA
1 ATTATATAAACGCTACCTAATA
95834 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:95902 original size:23 final size:23
Alignment explanation
Indices: 95867--95917 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
95857 CCAGTAATTA
**
95867 ACCTATTTTATTATATAAACGCT
1 ACCTATTACATTATATAAACGCT
*
95890 ACCTATTACATTATATAAACGTT
1 ACCTATTACATTATATAAACGCT
95913 ACCTA
1 ACCTA
95918 ATTTGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAACGCT
Found at i:95926 original size:23 final size:23
Alignment explanation
Indices: 95867--95926 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
95857 CCAGTAATTA
*
95867 ACCTATTTTATTATATAAACGCT
1 ACCTAATTTATTATATAAACGCT
* *
95890 ACCT-ATTACATTATATAAACGTT
1 ACCTAATT-TATTATATAAACGCT
*
95913 ACCTAATTTGTTAT
1 ACCTAATTTATTAT
95927 TTTACTTGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 2 0.07
23 25 0.83
24 3 0.10
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (23 bp):
ACCTAATTTATTATATAAACGCT
Found at i:101034 original size:16 final size:16
Alignment explanation
Indices: 101010--101045 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
101000 ATAAAATTGT
* *
101010 AAAATTAACCCGAATC
1 AAAAGTAACCCGAACC
101026 AAAAGTAACCCGAACC
1 AAAAGTAACCCGAACC
101042 AAAA
1 AAAA
101046 ACAACTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.25, G:0.08, T:0.11
Consensus pattern (16 bp):
AAAAGTAACCCGAACC
Found at i:101109 original size:32 final size:33
Alignment explanation
Indices: 101053--101121 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
101043 AAAACAACTA
* *
101053 GAACCGAATTTTAACCAGATCTGAAAGTAACCC
1 GAACCGAATTTTAACCAGACCTGAAAGCAACCC
*
101086 GAACCGAA-TTTAACTC-GACCTGAAAGCAATCC
1 GAACCGAATTTTAAC-CAGACCTGAAAGCAACCC
101118 GAAC
1 GAAC
101122 GTGTTGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 23 0.72
33 9 0.28
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (33 bp):
GAACCGAATTTTAACCAGACCTGAAAGCAACCC
Found at i:107253 original size:23 final size:23
Alignment explanation
Indices: 107221--107301 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
107211 TTGGTGTAGA
*
107221 GGGAATCGATACCCCCCTTGAAG
1 GGGAACCGATACCCCCCTTGAAG
* *
107244 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCCCTTGAAG
*
107267 GGGAACCGAT-TCCCCCTT--AG
1 GGGAACCGATACCCCCCTTGAAG
*
107287 GGGAATCGATACCCC
1 GGGAACCGATACCCC
107302 TCATGGGTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 11 0.22
21 3 0.06
22 6 0.12
23 30 0.60
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (23 bp):
GGGAACCGATACCCCCCTTGAAG
Found at i:114243 original size:21 final size:21
Alignment explanation
Indices: 114214--114271 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
114204 ACATAAAATT
* *
114214 TGTCTCGAAGGACCACATATA
1 TGTCTCGAATGACCACATAGA
*
114235 TGTCCCGAATGACCACATAGA
1 TGTCTCGAATGACCACATAGA
114256 TGTCTCGAATGACCAC
1 TGTCTCGAATGACCAC
114272 TCCTTAAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (21 bp):
TGTCTCGAATGACCACATAGA
Found at i:126340 original size:21 final size:19
Alignment explanation
Indices: 126302--126347 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
126292 AATTAACCCT
126302 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
126322 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
126343 A-TAAT
1 ACTAAT
126348 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:138902 original size:13 final size:13
Alignment explanation
Indices: 138884--138909 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
138874 TTTTGAAAAA
138884 TCAAAATCATTTT
1 TCAAAATCATTTT
138897 TCAAAATCATTTT
1 TCAAAATCATTTT
138910 GTTTTTCAAA
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:0.00, T:0.46
Consensus pattern (13 bp):
TCAAAATCATTTT
Found at i:146768 original size:24 final size:24
Alignment explanation
Indices: 146741--146835 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
146731 AAACGGAGAT
146741 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
146765 ATCAGATATCAGAACAAAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
146789 ATCAGAAATCAGAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
146813 GTCATG-TATCAAAATAGAATTCA
1 ATCA-GAAATCAAAACAGAATTCA
146836 AGCCAGAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
24 57 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:146770 original size:12 final size:12
Alignment explanation
Indices: 146743--146812 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
146733 ACGGAGATAT
* *
146743 CAGAAATCAAAA
1 CAGAATTCAGAA
*
146755 CAGAATTCAGAT
1 CAGAATTCAGAA
146767 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
146779 CAAAATCCAGAT
1 CAGAATTCAGAA
*
146791 CAGAAATCAGAA
1 CAGAATTCAGAA
*
146803 CATAATTCAG
1 CAGAATTCAG
146813 GTCATGTATC
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:150647 original size:23 final size:23
Alignment explanation
Indices: 150597--150649 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
150587 TAAATTTATT
**
150597 TTTATTACATAATATTTTTTACA
1 TTTATTACATAATATTTTAAACA
150620 TTTATTACATAATATTTCTAAACA
1 TTTATTACATAATATTT-TAAACA
150644 -TTATTA
1 TTTATTA
150650 TATTTTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTATTACATAATATTTTAAACA
Found at i:161473 original size:13 final size:13
Alignment explanation
Indices: 161455--161495 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
161445 CAACCTGTTG
161455 ACTTTGACCGTTA
1 ACTTTGACCGTTA
* *
161468 ACTTTGACAGTTG
1 ACTTTGACCGTTA
*
161481 ACTTTGGCCGTTA
1 ACTTTGACCGTTA
161494 AC
1 AC
161496 CCGAAAAGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (13 bp):
ACTTTGACCGTTA
Found at i:165459 original size:29 final size:30
Alignment explanation
Indices: 165435--165490 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
165425 ACAATATTTT
*
165435 TTAATTTTTATTAAT-GAAAGAAATAATTC
1 TTAATTTTTAGTAATAGAAAGAAATAATTC
165464 TTAATTTTTAGTAATAG-AA-AAATAATT
1 TTAATTTTTAGTAATAGAAAGAAATAATT
165491 TGAATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 16 0.64
30 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (30 bp):
TTAATTTTTAGTAATAGAAAGAAATAATTC
Found at i:168495 original size:20 final size:20
Alignment explanation
Indices: 168470--168521 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
168460 TACTTTGAAC
168470 AGTTTCGAAACTATCTCAAG
1 AGTTTCGAAACTATCTCAAG
168490 AGTTTCGAAACTATCTCAAG
1 AGTTTCGAAACTATCTCAAG
*
168510 AGTTTCTAAACT
1 AGTTTCGAAACT
168522 TTACCTAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (20 bp):
AGTTTCGAAACTATCTCAAG
Found at i:169908 original size:17 final size:16
Alignment explanation
Indices: 169850--169901 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
169840 TTTATAGATG
* *
169850 AAATAATTTTAAATAT
1 AAATAATTTAAAATTT
*
169866 -ATTAATTATAAAATTT
1 AAATAATT-TAAAATTT
169882 AAATAATTTAAATATTT
1 AAATAATTTAAA-ATTT
169899 AAA
1 AAA
169902 ACATTTATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 6 0.21
16 10 0.34
17 13 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATAATTTAAAATTT
Found at i:170323 original size:25 final size:25
Alignment explanation
Indices: 170289--170346 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
170279 TTCAGGTTTC
*
170289 AGTCGGATTTTGTCAGGTTATGTCA
1 AGTCGGATTTTGTCAGGTTAGGTCA
170314 AGTCGGATTTTGTCAGGTTAGGTCA
1 AGTCGGATTTTGTCAGGTTAGGTCA
*
170339 AATCGGAT
1 AGTCGGAT
170347 ATAAGTTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.36
Consensus pattern (25 bp):
AGTCGGATTTTGTCAGGTTAGGTCA
Found at i:171424 original size:12 final size:12
Alignment explanation
Indices: 171399--171434 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
171389 CATAAGTATA
171399 TATGTATGATATG
1 TATGTAT-ATATG
171412 TATGTATATATG
1 TATGTATATATG
171424 TATGTATATAT
1 TATGTATATAT
171435 ATATAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (12 bp):
TATGTATATATG
Found at i:172294 original size:37 final size:37
Alignment explanation
Indices: 172253--172324 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
172243 TGATTTATTT
* *
172253 CCTTTTACAAAATAGGAAAATAAATCCAACGATTTAA
1 CCTTTTACAAAACAGAAAAATAAATCCAACGATTTAA
*
172290 CCTTTTACAAAACAGAAAAATTAATCCAACGATTT
1 CCTTTTACAAAACAGAAAAATAAATCCAACGATTT
172325 TTTTTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (37 bp):
CCTTTTACAAAACAGAAAAATAAATCCAACGATTTAA
Found at i:176815 original size:46 final size:44
Alignment explanation
Indices: 176762--176862 Score: 116
Period size: 46 Copynumber: 2.3 Consensus size: 44
176752 TTCATTAAAA
* *
176762 ATTAATTTACTAATAGATAATAAAAAAGATGA-TAAATTACTAATCT
1 ATTAATTTACTAATAAACAATAAAAAA-AT-ACTAAATTACTAAT-T
* *
176808 ATTAATTTTCTAATAAACAATAAAAAAATACTAAATTATTAATT
1 ATTAATTTACTAATAAACAATAAAAAAATACTAAATTACTAATT
*
176852 AGT-ATTTACTA
1 ATTAATTTACTA
176863 CACTCAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
43 7 0.15
44 4 0.08
45 13 0.27
46 24 0.50
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (44 bp):
ATTAATTTACTAATAAACAATAAAAAAATACTAAATTACTAATT
Found at i:181071 original size:8 final size:8
Alignment explanation
Indices: 181058--181085 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
181048 GAATGGAAGT
181058 GTGAAAGG
1 GTGAAAGG
181066 GTGAAAGG
1 GTGAAAGG
181074 GTGAAAGG
1 GTGAAAGG
181082 GTGA
1 GTGA
181086 TTTGGGGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.50, T:0.14
Consensus pattern (8 bp):
GTGAAAGG
Found at i:184131 original size:20 final size:23
Alignment explanation
Indices: 184085--184131 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 23
184075 ACACACTCAA
184085 AATATTATTTATATATTCATGTT
1 AATATTATTTATATATTCATGTT
*
184108 AATA-TATTT-TATATT-ATTTT
1 AATATTATTTATATATTCATGTT
184128 AATA
1 AATA
184132 AAATATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 6 0.26
22 5 0.22
23 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
AATATTATTTATATATTCATGTT
Found at i:184428 original size:29 final size:29
Alignment explanation
Indices: 184373--184428 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
184363 ATAAACGATT
* *
184373 AATATAATTTATAATAATTTTATTTAATA
1 AATAAAATTTATAATAATTTTACTTAATA
*
184402 AATAAAATTTTTAAT-ATTTTCACTTAA
1 AATAAAATTTATAATAATTTT-ACTTAA
184429 AATTGTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (29 bp):
AATAAAATTTATAATAATTTTACTTAATA
Found at i:191472 original size:2 final size:2
Alignment explanation
Indices: 191465--191500 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
191455 TTAGACTTTG
191465 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
191501 AAGAAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:192174 original size:16 final size:17
Alignment explanation
Indices: 192155--192191 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
192145 TAAAATATTA
192155 TTTT-AAATAATTAC-AT
1 TTTTAAAATAA-TACAAT
192171 TTTTAAAATAATACAAT
1 TTTTAAAATAATACAAT
192188 TTTT
1 TTTT
192192 TATCCCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTAAAATAATACAAT
Found at i:193240 original size:2 final size:2
Alignment explanation
Indices: 193233--193283 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
193223 CTTTTATTCT
193233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
193275 TA TA TA TA T
1 TA TA TA TA T
193284 TGGGTATTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:199919 original size:4 final size:4
Alignment explanation
Indices: 199910--199974 Score: 98
Period size: 4 Copynumber: 16.5 Consensus size: 4
199900 GAATATATTC
*
199910 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TAA TATTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA
199958 TTTA TTTA -TTA TTTA TT
1 TTTA TTTA TTTA TTTA TT
199975 CTTTATATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
3 5 0.09
4 48 0.86
5 3 0.05
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:199983 original size:16 final size:16
Alignment explanation
Indices: 199911--199991 Score: 73
Period size: 16 Copynumber: 5.2 Consensus size: 16
199901 AATATATTCT
199911 TTATTTAT-TTATTTA
1 TTATTTATATTATTTA
199926 TTTATTTAT-TTATTTA
1 -TTATTTATATTATTTA
*
199942 TAATATTAT-TTATTTA
1 TTAT-TTATATTATTTA
199958 TT-TATT-TATTATTTA
1 TTAT-TTATATTATTTA
* *
199973 TTCTTTATATTATATA
1 TTATTTATATTATTTA
199989 TTA
1 TTA
199992 GATAAAATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
14 1 0.02
15 18 0.32
16 38 0.67
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTTATATTATTTA
Found at i:204165 original size:17 final size:17
Alignment explanation
Indices: 204143--204183 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
204133 AACATTGCCC
204143 ATCTTCACAACAGATCA
1 ATCTTCACAACAGATCA
* *
204160 ATCTTCACAACATATCC
1 ATCTTCACAACAGATCA
204177 ATCTTCA
1 ATCTTCA
204184 ATTGGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.37, C:0.32, G:0.02, T:0.29
Consensus pattern (17 bp):
ATCTTCACAACAGATCA
Found at i:210260 original size:23 final size:23
Alignment explanation
Indices: 210234--210279 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
210224 CACTTTTATC
210234 TCGGTAAGAAGACAATCTTGTTT
1 TCGGTAAGAAGACAATCTTGTTT
**
210257 TCGGTAAGAAGGTAATCTTGTTT
1 TCGGTAAGAAGACAATCTTGTTT
210280 AGAACCATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (23 bp):
TCGGTAAGAAGACAATCTTGTTT
Found at i:211115 original size:17 final size:16
Alignment explanation
Indices: 211095--211134 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
211085 ACTTACTCTT
211095 TTTTTCTGTACTAATC
1 TTTTTCTGTACTAATC
* *
211111 ATTTTACTGTACTATTC
1 -TTTTTCTGTACTAATC
211128 TTTTTCT
1 TTTTTCT
211135 TGTATTGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.17, C:0.17, G:0.05, T:0.60
Consensus pattern (16 bp):
TTTTTCTGTACTAATC
Found at i:219686 original size:21 final size:21
Alignment explanation
Indices: 219643--219687 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
219633 TATCGCATTT
**
219643 CGATTTTCCAAATTCGCGTTG
1 CGATTTTCCAAATTCGCAATG
*
219664 CGATTTTCCTAATTCGCAATG
1 CGATTTTCCAAATTCGCAATG
219685 CGA
1 CGA
219688 ATACGTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (21 bp):
CGATTTTCCAAATTCGCAATG
Found at i:219702 original size:20 final size:20
Alignment explanation
Indices: 219677--219749 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
219667 TTTTCCTAAT
*
219677 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* *
219697 TCGCAATGCGAATACGTAAT
1 TCGCAACGCGAATACGTAAA
* *
219717 TTGCAACGCGAATATGTAAA
1 TCGCAACGCGAATACGTAAA
219737 TCGCAACGCGAAT
1 TCGCAACGCGAAT
219750 CTGACTATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:219717 original size:40 final size:40
Alignment explanation
Indices: 219673--219749 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
219663 GCGATTTTCC
* *
219673 TAATTCGCAATGCGAATACGTAAATCGCAATGCGAATACG
1 TAATTCGCAACGCGAATACGTAAATCGCAACGCGAATACG
* *
219713 TAATTTGCAACGCGAATATGTAAATCGCAACGCGAAT
1 TAATTCGCAACGCGAATACGTAAATCGCAACGCGAAT
219750 CTGACTATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (40 bp):
TAATTCGCAACGCGAATACGTAAATCGCAACGCGAATACG
Found at i:219760 original size:60 final size:62
Alignment explanation
Indices: 219696--219827 Score: 141
Period size: 60 Copynumber: 2.2 Consensus size: 62
219686 GAATACGTAA
*
219696 ATCGCAATGCGA-ATACGTAATT-T-GCAACGCGAATATGTA-AATCGCAACGCGAATCTGACT
1 ATCGCAATGCGAGATAC-TAATTATCGCAACGAGAATATG-ACAATCGCAACGCGAATCTGACT
* * * * * *
219756 ATCGCAA--CGAGATTCTGATTATCGCAACGAGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAATGCGAGATACTAATTATCGCAACGAGAATATGACAATCGCAACGCGAATCTGACT
219816 ATCGCAATGCGA
1 ATCGCAATGCGA
219828 TTCTGACTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
58 7 0.12
59 5 0.08
60 44 0.75
62 3 0.05
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (62 bp):
ATCGCAATGCGAGATACTAATTATCGCAACGAGAATATGACAATCGCAACGCGAATCTGACT
Found at i:219763 original size:40 final size:40
Alignment explanation
Indices: 219719--219838 Score: 116
Period size: 40 Copynumber: 3.0 Consensus size: 40
219709 TACGTAATTT
219719 GCAACGCGAATATGTA-AATCGCAACGCGAATCTGACTATC
1 GCAACGCGAATATG-ACAATCGCAACGCGAATCTGACTATC
* * * ** * *
219759 GCAACGAGATTCTGATTATCGCAACGAGATTCTGACTATC
1 GCAACGCGAATATGACAATCGCAACGCGAATCTGACTATC
* * * * *
219799 GCAACGCGATTCTGACTATCGCAATGCGATTCTGACTATC
1 GCAACGCGAATATGACAATCGCAACGCGAATCTGACTATC
219839 ACAATACTGA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
39 1 0.01
40 68 0.99
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (40 bp):
GCAACGCGAATATGACAATCGCAACGCGAATCTGACTATC
Found at i:219843 original size:20 final size:20
Alignment explanation
Indices: 219736--219838 Score: 161
Period size: 20 Copynumber: 5.2 Consensus size: 20
219726 GAATATGTAA
*
219736 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
* *
219756 ATCGCAACGAGATTCTGATT
1 ATCGCAACGCGATTCTGACT
*
219776 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
219796 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
219816 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
219836 ATC
1 ATC
219839 ACAATACTGA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:220709 original size:24 final size:24
Alignment explanation
Indices: 220682--220737 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
220672 CAGTATTCAA
220682 AATTTGATCTTGGTCAATACCCGG
1 AATTTGATCTTGGTCAATACCCGG
*
220706 AATTTGATCTTGGTCAATACTCGG
1 AATTTGATCTTGGTCAATACCCGG
*
220730 ATTTTGAT
1 AATTTGAT
220738 GATTTTTCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (24 bp):
AATTTGATCTTGGTCAATACCCGG
Found at i:223196 original size:20 final size:20
Alignment explanation
Indices: 223171--223219 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
223161 CAACGCAGAA
*
223171 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAAAATGACT
*
223191 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
223211 ATCACAACG
1 ATCGCAACG
223220 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:223284 original size:34 final size:34
Alignment explanation
Indices: 223191--223286 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
223181 GAATATGACT
** ** *
223191 ATCGCAACACGAAAATGACTATCACAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
223225 ATCGCAATGCG-AAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
223258 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
223287 CGAATTTAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 29 0.54
34 25 0.46
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:223340 original size:14 final size:14
Alignment explanation
Indices: 223321--223357 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
223311 TTCTTTTTCG
*
223321 CATTGCGATTCTCT
1 CATTGCGATCCTCT
223335 CATTGCGATCCTCT
1 CATTGCGATCCTCT
*
223349 CGTTGCGAT
1 CATTGCGAT
223358 AGTCATTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.38
Consensus pattern (14 bp):
CATTGCGATCCTCT
Found at i:223502 original size:14 final size:14
Alignment explanation
Indices: 223483--223519 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
223473 CATCAATTAA
223483 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
223497 ACAAATCATCTTTT
1 ACAAATCAACATTT
223511 ACAAATCAA
1 ACAAATCAA
223520 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:225001 original size:42 final size:42
Alignment explanation
Indices: 224922--225014 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
224912 CCTCTTCAAC
* * *
224922 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
224964 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
225006 GATGACAGG
1 GATGACAGG
225015 TGAGTCGGGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:225517 original size:20 final size:20
Alignment explanation
Indices: 225494--225562 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
225484 GAAACTTAAA
225494 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
225514 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
225534 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
225554 ATCGTAACG
1 ATCGCAACG
225563 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:225632 original size:20 final size:20
Alignment explanation
Indices: 225607--225743 Score: 95
Period size: 20 Copynumber: 7.5 Consensus size: 20
225597 GATTCTTTCG
225607 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
225627 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTTCGCA
225647 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
225661 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
225680 TTACGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
**
225694 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCA
225714 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
225734 TTGCGATAGT
1 TTGCGATAGT
225744 AAACTATTCT
Statistics
Matches: 95, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
14 13 0.14
16 12 0.13
17 6 0.06
18 5 0.05
19 6 0.06
20 53 0.56
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:225640 original size:53 final size:52
Alignment explanation
Indices: 225569--225743 Score: 137
Period size: 53 Copynumber: 3.3 Consensus size: 52
225559 AACGAGAGAA
* **
225569 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTCGC-TTGCGATTCTTTCGTTGCGATAGTCATTT
* * **
225622 TCGCATTGCGATAGTCATTTTTGCGTTGCGATT-TTGTTGTTGCGATTTTCA-TT
1 TCGCATTGCGATAGTCA-TTTCGC-TTGCGATTCTT-TCGTTGCGATAGTCATTT
* *
225675 TCGCATTACGAT--TC-TCTCG-TTGCGATAGTCATTTTCGTGTTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTCGCTTGCGAT--TC--TTTC--GTTGCGATAGTCATTT
225729 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
225744 AAACTATTCT
Statistics
Matches: 95, Mismatches: 15, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
47 7 0.07
49 4 0.04
51 3 0.03
52 2 0.02
53 40 0.42
54 38 0.40
56 1 0.01
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATAGTCATTTCGCTTGCGATTCTTTCGTTGCGATAGTCATTT
Found at i:225681 original size:87 final size:87
Alignment explanation
Indices: 225575--225740 Score: 278
Period size: 87 Copynumber: 1.9 Consensus size: 87
225565 AGAATCGCAA
* *
225575 TGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCAT
* *
225640 TTTTGCGTTGCGATTTTGTTGT
66 TTTCGCATTGCGATTTTGTTGT
**
225662 TGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATAGTCATTTTCGTGTTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCAT
225727 TTTCGCATTGCGAT
66 TTTCGCATTGCGAT
225741 AGTAAACTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (87 bp):
TGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCAT
TTTCGCATTGCGATTTTGTTGT
Found at i:225707 original size:33 final size:33
Alignment explanation
Indices: 225627--225708 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 33
225617 CATTTTCGCA
* * * * * *
225627 TTGCGATAGTCATTTTTGCGTTGCGATTTTGTTG
1 TTGCGATAGTCA-TTTCGCATTACGATTCTCTCG
**
225661 TTGCGATTTTCATTTCGCATTACGATTCTCTCG
1 TTGCGATAGTCATTTCGCATTACGATTCTCTCG
225694 TTGCGATAGTCATTT
1 TTGCGATAGTCATTT
225709 TCGTGTTGCG
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
33 28 0.74
34 10 0.26
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCATTACGATTCTCTCG
Found at i:227673 original size:20 final size:20
Alignment explanation
Indices: 227650--227699 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
227640 GTGAAAATCG
*
227650 CAACACGAAAATGACTATCA
1 CAACGCGAAAATGACTATCA
** *
227670 CAACGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCA
227690 CAACGCGAAA
1 CAACGCGAAA
227700 TGAAAATCGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCA
Found at i:228111 original size:22 final size:22
Alignment explanation
Indices: 228060--228114 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
228050 GATTTCGCCA
*
228060 GAGATGGAGACTGATATCGTCG
1 GAGATGGGGACTGATATCGTCG
* *
228082 GAGATGGGGACTGATTTTGTCG
1 GAGATGGGGACTGATATCGTCG
228104 GAGATGGGGAC
1 GAGATGGGGAC
228115 GGATGTCGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.11, G:0.42, T:0.24
Consensus pattern (22 bp):
GAGATGGGGACTGATATCGTCG
Found at i:228337 original size:20 final size:20
Alignment explanation
Indices: 228314--228366 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
228304 CGATAGTCAG
*
228314 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
228334 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
228354 ATTCGCATTGCGA
1 ATTCGCATTGCGA
228367 ATTAGGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:228387 original size:21 final size:21
Alignment explanation
Indices: 228363--228408 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
228353 TATTCGCATT
228363 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
228384 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
228405 GCGA
1 GCGA
228409 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:233656 original size:23 final size:23
Alignment explanation
Indices: 233604--233648 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
233594 ATTAAAAAAT
233604 AAATTATACGTTTAATACTTAAG
1 AAATTATACGTTTAATACTTAAG
*
233627 AAATTATATGTTTAATACTTAA
1 AAATTATACGTTTAATACTTAA
233649 ACTATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (23 bp):
AAATTATACGTTTAATACTTAAG
Found at i:233962 original size:19 final size:17
Alignment explanation
Indices: 233911--233964 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 17
233901 TAGATACAAA
*
233911 AATTAAATAAAAATAAT
1 AATTTAATAAAAATAAT
*
233928 AATTTAAGTATCAAATATAT
1 AATTTAA-TA-AAAATA-AT
233948 AATTTAGATAAAAATAA
1 AATTTA-ATAAAAATAA
233965 AATATATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 6 0.20
18 3 0.10
19 10 0.33
20 10 0.33
21 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AATTTAATAAAAATAAT
Found at i:236702 original size:44 final size:44
Alignment explanation
Indices: 236648--236778 Score: 176
Period size: 44 Copynumber: 3.0 Consensus size: 44
236638 TGCGGAAAGC
* * *
236648 GGTAAGGTCTTACCCTAGCACATAGTAGAGGAGCCTTCAGAAAT
1 GGTAAGGTCTTACCCTAGCACATAGCAAAGAAGCCTTCAGAAAT
*
236692 GGTAAGGTCTTACCCTTGCACATAGCAAAGAAGCCTTCAGAAAT
1 GGTAAGGTCTTACCCTAGCACATAGCAAAGAAGCCTTCAGAAAT
* *
236736 GGTAAGGTCTTACCCTTA-CACATAACAAATG-AGCCTTAAGAAA
1 GGTAAGGTCTTACCC-TAGCACATAGCAAA-GAAGCCTTCAGAAA
236779 CTTCCTCCAA
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
44 76 0.97
45 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (44 bp):
GGTAAGGTCTTACCCTAGCACATAGCAAAGAAGCCTTCAGAAAT
Found at i:236770 original size:88 final size:90
Alignment explanation
Indices: 236603--236778 Score: 207
Period size: 88 Copynumber: 2.0 Consensus size: 90
236593 TGTACACCCA
* *
236603 GTAAGGACTTACCCTGTGCACAAAGCCGAAGAGCCTGCGGAAAGCGGTAAGGTCTTACCCTAGCA
1 GTAAGGACTTACCCTGTGCACAAAGCCAAAGAGCCTGCAGAAAGCGGTAAGGTCTTACCCTAGCA
** * *
236668 CATAGTAGAGGAGCCTTCAGAAATG
66 CATAACAAAGGAGCCTTAAGAAATG
* * * *
236693 GTAAGGTCTTACCCT-TGCACATAG-CAAAGAAGCCTTCAGAAA-TGGTAAGGTCTTACCCTTA-
1 GTAAGGACTTACCCTGTGCACAAAGCCAAAG-AGCCTGCAGAAAGCGGTAAGGTCTTACCC-TAG
*
236754 CACATAACAAATGAGCCTTAAGAAA
64 CACATAACAAAGGAGCCTTAAGAAA
236779 CTTCCTCCAA
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
88 39 0.53
89 20 0.27
90 14 0.19
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (90 bp):
GTAAGGACTTACCCTGTGCACAAAGCCAAAGAGCCTGCAGAAAGCGGTAAGGTCTTACCCTAGCA
CATAACAAAGGAGCCTTAAGAAATG
Found at i:238546 original size:37 final size:37
Alignment explanation
Indices: 238495--238600 Score: 149
Period size: 37 Copynumber: 2.8 Consensus size: 37
238485 TATAGTATTG
238495 TATTTCAATTGAATATAAATTCATAATAATATATTCA
1 TATTTCAATTGAATATAAATTCATAATAATATATTCA
* **
238532 TATTTCAATAGAATATAAATTTGTAATAATATATTCA
1 TATTTCAATTGAATATAAATTCATAATAATATATTCA
* * *
238569 CATTTTAATTGAATATAAATTCTTAAATAATA
1 TATTTCAATTGAATATAAATTCAT-AATAATA
238601 GAACATTATC
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
37 53 0.88
38 7 0.12
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (37 bp):
TATTTCAATTGAATATAAATTCATAATAATATATTCA
Found at i:238760 original size:37 final size:37
Alignment explanation
Indices: 238717--238887 Score: 168
Period size: 37 Copynumber: 4.6 Consensus size: 37
238707 TATTCCAATC
*
238717 GAATATAAATTCATAATAATATATTCATATTTTTATT
1 GAATATAAATTCATAATAATATATTCATATTTTAATT
* * *
238754 GAATATAAATTCATAAGTAATAAATT--TGTGTTTAATC
1 GAATATAAATTCATAA-TAATATATTCATAT-TTTAATT
* * *
238791 AAATATAAATTTATAAATAATATATTCATA-TTTCATT
1 GAATATAAATTCAT-AATAATATATTCATATTTTAATT
** * *
238828 AGAATATAAATTTGTAATAGTATATTCACATTTTAATT
1 -GAATATAAATTCATAATAATATATTCATATTTTAATT
*
238866 GAATATAAATTCTTAAATAATA
1 GAATATAAATTCAT-AATAATA
238888 GAACATTATC
Statistics
Matches: 108, Mismatches: 18, Indels: 15
0.77 0.13 0.11
Matches are distributed among these distances:
36 2 0.02
37 71 0.66
38 34 0.31
39 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (37 bp):
GAATATAAATTCATAATAATATATTCATATTTTAATT
Found at i:238863 original size:75 final size:75
Alignment explanation
Indices: 238713--238887 Score: 189
Period size: 75 Copynumber: 2.3 Consensus size: 75
238703 ATTGTATTCC
* *
238713 AATCGAATATAAATTCAT-AATAATATATTCATATTTTTATTGAATATAAATTCATAAGTAATAA
1 AATCGAATATAAATTTATAAATAATATATTCATATTTTCATTGAATATAAATTCATAAGTAATAA
**
238777 ATTTGTGTTT
66 ATTCATGTTT
* ** *
238787 AATCAAATATAAATTTATAAATAATATATTCATA-TTTCATTAGAATATAAATTTGTAA-TAGTA
1 AATCGAATATAAATTTATAAATAATATATTCATATTTTCATT-GAATATAAATTCATAAGTAATA
*
238850 TATTCACAT-TTT
65 AATT--CATGTTT
*
238862 AATTGAATATAAATTCT-TAAATAATA
1 AATCGAATATAAATT-TATAAATAATA
238888 GAACATTATC
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
74 29 0.34
75 54 0.64
76 2 0.02
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (75 bp):
AATCGAATATAAATTTATAAATAATATATTCATATTTTCATTGAATATAAATTCATAAGTAATAA
ATTCATGTTT
Found at i:250728 original size:33 final size:32
Alignment explanation
Indices: 250689--250751 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
250679 TATATTCATA
250689 TTTTAATAAAATATAAATTCATAGATAATATAT
1 TTTTAATAAAATATAAATTCATA-ATAATATAT
* * *
250722 TTTTAATCATATATAAATTTATAATAATAT
1 TTTTAATAAAATATAAATTCATAATAATAT
250752 TCTATTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 7 0.26
33 20 0.74
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (32 bp):
TTTTAATAAAATATAAATTCATAATAATATAT
Found at i:250773 original size:34 final size:32
Alignment explanation
Indices: 250689--250788 Score: 103
Period size: 34 Copynumber: 3.0 Consensus size: 32
250679 TATATTCATA
* * *
250689 TTTTAATAAAATATAAATTCATAGATAATATAT
1 TTTTAATCACATATAAATTTATA-ATAATATAT
*
250722 TTTTAATCATATATAAATTTATAATAATAT-T
1 TTTTAATCACATATAAATTTATAATAATATAT
* *
250753 CTATTTCAATCCCATATAAATTTGTAATAATATAT
1 -T-TTT-AATCACATATAAATTTATAATAATATAT
250788 T
1 T
250789 GATATTTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
31 1 0.02
32 8 0.14
33 23 0.40
34 24 0.42
35 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (32 bp):
TTTTAATCACATATAAATTTATAATAATATAT
Done.