Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009010.1 Hibiscus syriacus cultivar Beakdansim tig00112396_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: 114646
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:6211 original size:23 final size:23
Alignment explanation
Indices: 6185--6229 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6175 CACGAATGAT
*
6185 TTGTAATACCCAAAAATTTAGAA
1 TTGTAATACCAAAAAATTTAGAA
*
6208 TTGTAATACTAAAAAATTTAGA
1 TTGTAATACCAAAAAATTTAGA
6230 CAATGACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (23 bp):
TTGTAATACCAAAAAATTTAGAA
Found at i:8616 original size:45 final size:45
Alignment explanation
Indices: 8498--8620 Score: 167
Period size: 45 Copynumber: 2.8 Consensus size: 45
8488 GTAAACATGC
*
8498 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * * *
8542 AAATAAACTTACGAGCTTATGAAACAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
8587 AAATAAGCTTACAAGTTTATGGGATAAATGGTAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAA
8621 AAAAATTTAT
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
44 22 0.33
45 45 0.67
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:11168 original size:26 final size:26
Alignment explanation
Indices: 11138--11194 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
11128 AAAGATTAAG
11138 AGTTCTTGAATGGAATTTTAAAATAA
1 AGTTCTTGAATGGAATTTTAAAATAA
* *
11164 AGTTCTTGAATGGAATTTTGAAATAG
1 AGTTCTTGAATGGAATTTTAAAATAA
11190 AGTTC
1 AGTTC
11195 ATATTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (26 bp):
AGTTCTTGAATGGAATTTTAAAATAA
Found at i:18348 original size:19 final size:19
Alignment explanation
Indices: 18324--18363 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
18314 GCATCAATGA
18324 ACATGAAGTGTATCGATGC
1 ACATGAAGTGTATCGATGC
18343 ACATGAAGTGTATCGATGC
1 ACATGAAGTGTATCGATGC
18362 AC
1 AC
18364 TCCTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (19 bp):
ACATGAAGTGTATCGATGC
Found at i:19115 original size:20 final size:19
Alignment explanation
Indices: 19062--19120 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
19052 TCGAGGGATT
*
19062 ATCAGTGGTCCTTCAGGA-T
1 ATCAGTGGTCCTTC-GGACA
* *
19081 AT-AGTGGTTCATCGGAACA
1 ATCAGTGGTCCTTCGG-ACA
19100 ATCAGTGGTCCTTCGGGACA
1 ATCAGTGGTCCTTC-GGACA
19120 A
1 A
19121 ATATTCAGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
17 2 0.06
18 10 0.32
19 4 0.13
20 13 0.42
21 2 0.06
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (19 bp):
ATCAGTGGTCCTTCGGACA
Found at i:19379 original size:2 final size:2
Alignment explanation
Indices: 19372--19412 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
19362 TGCATTACTG
*
19372 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19413 TATGTCTCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:20030 original size:39 final size:39
Alignment explanation
Indices: 19972--20048 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
19962 GTTAACAAAC
* *
19972 GTCGCAAAAAGTTAGGTTATTTAGCGACATTTTTGTTAT
1 GTCGCAAAAAGTCAAGTTATTTAGCGACATTTTTGTTAT
* **
20011 GTCGCAAAAAGTCAAGTTATTTAGTGGTATTTTTGTTA
1 GTCGCAAAAAGTCAAGTTATTTAGCGACATTTTTGTTA
20049 CAAACACCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.42
Consensus pattern (39 bp):
GTCGCAAAAAGTCAAGTTATTTAGCGACATTTTTGTTAT
Found at i:20808 original size:21 final size:20
Alignment explanation
Indices: 20762--20808 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
20752 GAATAAAATC
*
20762 AAAAACAAAAACACTTATAA
1 AAAAACAAAAACACTAATAA
20782 ATAAAACAAAAAACACTAACTAA
1 A-AAAAC-AAAAACACTAA-TAA
20805 AAAA
1 AAAA
20809 GCTTAGGCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 1 0.04
21 5 0.22
22 13 0.57
23 4 0.17
ACGTcount: A:0.72, C:0.15, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAAACAAAAACACTAATAA
Found at i:25049 original size:30 final size:30
Alignment explanation
Indices: 25015--25119 Score: 133
Period size: 31 Copynumber: 3.5 Consensus size: 30
25005 TTTTTTCGTC
*
25015 TAAGTACCTAAAGTATTTTTTTGGTCAAAA
1 TAAGTACCTAAAGTATATTTTTGGTCAAAA
* * *
25045 TAAGTACTTAAACTTATATTTTTGGTAAAAA
1 TAAGTACCTAAA-GTATATTTTTGGTCAAAA
25076 TAAGTACCTAAA--ATATTTTTGGTCAAAA
1 TAAGTACCTAAAGTATATTTTTGGTCAAAA
* *
25104 TATGTACCAAAAGTAT
1 TAAGTACCTAAAGTAT
25120 TCAAATTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 25 0.39
30 13 0.20
31 26 0.41
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (30 bp):
TAAGTACCTAAAGTATATTTTTGGTCAAAA
Found at i:25120 original size:28 final size:28
Alignment explanation
Indices: 25015--25120 Score: 106
Period size: 28 Copynumber: 3.6 Consensus size: 28
25005 TTTTTTCGTC
* *
25015 TAAGTACCTAAAGTATTTTTTTGGTCAAAA
1 TAAGTACCTAAA--ATATTTTTGGTAAAAA
*
25045 TAAGTACTTAAACTTATATTTTTGGTAAAAA
1 TAAGTACCTAAA---ATATTTTTGGTAAAAA
*
25076 TAAGTACCTAAAATATTTTTGGTCAAAA
1 TAAGTACCTAAAATATTTTTGGTAAAAA
*
25104 TATGTACC-AAAAGTATT
1 TAAGTACCTAAAA-TATT
25121 CAAATTTTTC
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
27 4 0.06
28 26 0.39
30 11 0.16
31 26 0.39
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (28 bp):
TAAGTACCTAAAATATTTTTGGTAAAAA
Found at i:25249 original size:29 final size:29
Alignment explanation
Indices: 25203--25302 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 29
25193 CAAAAATTGG
* *
25203 ATACTTTATGTATCTATTTTGACCAAAAA
1 ATACTTTAGGTATTTATTTTGACCAAAAA
*
25232 ATACTTTAGGTATTTATTTTGACTAAAAAA
1 ATACTTTAGGTATTTATTTTGAC-CAAAAA
* ** *
25262 ATAAGTTTAAATACTTATTTTGACCAAAAA
1 AT-ACTTTAGGTATTTATTTTGACCAAAAA
* *
25292 CTAATTTAGGT
1 ATACTTTAGGT
25303 GCTTAAATGA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
29 27 0.47
30 13 0.23
31 17 0.30
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (29 bp):
ATACTTTAGGTATTTATTTTGACCAAAAA
Found at i:25477 original size:43 final size:42
Alignment explanation
Indices: 25406--25487 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 42
25396 AACTTCATAT
*
25406 TAACTATCTACAATACACTAAATCAACATATTACAATCAAGG
1 TAACAATCTACAATACACTAAATCAACATATTACAATCAAGG
*
25448 TAACAATCTACAAATACATTAAA-CTAACATATTACAATCA
1 TAACAATCTAC-AATACACTAAATC-AACATATTACAATCA
25488 TTCTTGAGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 11 0.31
43 25 0.69
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.27
Consensus pattern (42 bp):
TAACAATCTACAATACACTAAATCAACATATTACAATCAAGG
Found at i:26555 original size:2 final size:2
Alignment explanation
Indices: 26536--26608 Score: 58
Period size: 2 Copynumber: 35.5 Consensus size: 2
26526 TTTCTATAAC
* * * * * *
26536 TA TA TA TGA TA TA CA TA TA TA TT TC TT TA TA TA T- TT TCA TA TG
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
26579 TGA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
26609 CATGCATAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
1 1 0.02
2 53 0.91
3 4 0.07
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27073 original size:4 final size:4
Alignment explanation
Indices: 27064--27102 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
27054 AAAGCTGTCT
27064 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
27103 GGAAGGAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:40085 original size:18 final size:21
Alignment explanation
Indices: 40064--40110 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
40054 TATATTTTAA
40064 TTTATTAA-AA-T-AATATAT
1 TTTATTAATAACTCAATATAT
*
40082 TTTA-TAATAACTCACTATAT
1 TTTATTAATAACTCAATATAT
40102 TTTATTAAT
1 TTTATTAAT
40111 TAAATAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 3 0.12
18 6 0.25
19 1 0.04
20 10 0.42
21 4 0.17
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTATTAATAACTCAATATAT
Found at i:40091 original size:42 final size:41
Alignment explanation
Indices: 40036--40128 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
40026 AAACATATTA
* * * *
40036 ATATTTTAAAATAA-TTATTATATTTTAATTTATTAAAATAAT
1 ATATTTTAAAATAACTCACTATATTTT-ATTAATT-AAATAAC
*
40078 ATATTTTATAATAACTCACTATATTTTATTAATTAAATAAC
1 ATATTTTAAAATAACTCACTATATTTTATTAATTAAATAAC
*
40119 ATATTGTAAA
1 ATATTTTAAA
40129 GCTATAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 14 0.33
42 19 0.44
43 10 0.23
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (41 bp):
ATATTTTAAAATAACTCACTATATTTTATTAATTAAATAAC
Found at i:40866 original size:66 final size:67
Alignment explanation
Indices: 40777--40901 Score: 182
Period size: 67 Copynumber: 1.9 Consensus size: 67
40767 TTACACTCTT
* * *
40777 CTCCTTCTTCACTATTCA-CTTTTTTAATTTTAAATTCTA-ATGTACAGTGAAGACGGTAGAATT
1 CTCCATCTTCACTATTCATCTTTTTTAATTTTAAACT-TACATCTACAGTGAAGACGGTAGAATT
40840 AAA
65 AAA
* *
40843 CTCCATCTTCATTATTCATTTTTTTTAATTTTAAACTTACATCTACAGTGAAGACGGTA
1 CTCCATCTTCACTATTCATCTTTTTTAATTTTAAACTTACATCTACAGTGAAGACGGTA
40902 TGCCAAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
66 18 0.35
67 34 0.65
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (67 bp):
CTCCATCTTCACTATTCATCTTTTTTAATTTTAAACTTACATCTACAGTGAAGACGGTAGAATTA
AA
Found at i:42426 original size:258 final size:258
Alignment explanation
Indices: 41946--42439 Score: 631
Period size: 258 Copynumber: 1.9 Consensus size: 258
41936 TTCTATAGAC
* **
41946 TTTGAAGTAAAATTAAATAAAATAGAAATAATTATGGCCAATTTCATATAAAAAATATTTTAAGG
1 TTTGAAGTAAAATTAAATAAAATAGAAATAATTATGGCCAATTTCAAATAAAAAATACATTAAGG
* * * *
42011 ACTAAATTGAACAAGCATGAAATTAGAAAATGAAATTTAAATAAATTAAACAACATGCAAGGATC
66 ACTAAATTGAACAAACATAAAATTACAAAATGAAATTTAAACAAATTAAACAACATGCAAGGATC
* * *
42076 AAATTGAAACAACTGTAAAATGTAAATCTAAAATTAATATCACATTGAACTAAATTGAATTCATT
131 AAATTGAAACAACTGTAAAATATAAAGCTAAAATTAATATCAAATTGAACTAAATTGAATTCATT
*
42141 TAAAAAAATTGGTGATAATAATTTATAGGATTT-GAAATTAAGTTTATGATGGGATTTATAGG
196 TAAAAAAATTGATGATAATAATTTATAGGATTTGGAAATTAAGTTTATGATGGGATTTATAGG
* **
42203 TTTGGAGTAAAA-TAAA-AAAATAGAAATAATTATGGTCTGATTTCAAATAAAAATATAACATTA
1 TTTGAAGTAAAATTAAATAAAATAGAAATAATTATGG-CCAATTTCAAATAAAAA-AT-ACATTA
* * * * *
42266 AGGACTAAATTTAACAAACATAAAATTTCAAAGTGAAATTTAAACAAATTAAACAACATGTAGGG
63 AGGACTAAATTGAACAAACATAAAATTACAAAATGAAATTTAAACAAATTAAACAACATGCAAGG
* * * * * *
42331 ATCGAATTGAAATAATTGTAAATTATAAAGCTGAAATTAATATCAAATT-AGACTAAATTGCATT
128 ATCAAATTGAAACAACTGTAAAATATAAAGCTAAAATTAATATCAAATTGA-ACTAAATTGAATT
* * * *
42395 TATTT-TAAAAGTTGATGAATAA-AATTTTATAGGGTTTGGAAATTA
192 CATTTAAAAAAATTGATG-ATAATAA-TTTATAGGATTTGGAAATTA
42440 TGATATAATT
Statistics
Matches: 201, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
255 19 0.09
256 18 0.09
257 25 0.12
258 132 0.66
259 7 0.03
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (258 bp):
TTTGAAGTAAAATTAAATAAAATAGAAATAATTATGGCCAATTTCAAATAAAAAATACATTAAGG
ACTAAATTGAACAAACATAAAATTACAAAATGAAATTTAAACAAATTAAACAACATGCAAGGATC
AAATTGAAACAACTGTAAAATATAAAGCTAAAATTAATATCAAATTGAACTAAATTGAATTCATT
TAAAAAAATTGATGATAATAATTTATAGGATTTGGAAATTAAGTTTATGATGGGATTTATAGG
Found at i:44290 original size:64 final size:64
Alignment explanation
Indices: 44216--44392 Score: 266
Period size: 64 Copynumber: 2.8 Consensus size: 64
44206 TAAAATAAAT
* * *
44216 ACATCAAATGCAATTCGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGA-A
1 ACATCGAATGCAATTTGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAAT-ACA
44280 ACATCGAATGCAATTTGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATACA
1 ACATCGAATGCAATTTGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATACA
* * * * *
44344 ACATCGAATACATTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ACATCGAATGCAATTTGTGCATCGATGCATAAGTAGTGCATCGATGCAT
44393 ACCTTCATTA
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
63 1 0.01
64 103 0.99
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (64 bp):
ACATCGAATGCAATTTGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATACA
Found at i:45087 original size:31 final size:31
Alignment explanation
Indices: 45049--45111 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
45039 AGGGTCGAGG
*
45049 GTTTACCTATGTTCTTC-GGAACATATGGACT
1 GTTTACCTAGGTTCTTCGGGAAC-TATGGACT
*
45080 GTTTACCTAGGTTCTTCGGGATCTATGGACT
1 GTTTACCTAGGTTCTTCGGGAACTATGGACT
45111 G
1 G
45112 GTCCTTCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGGGAACTATGGACT
Found at i:48338 original size:64 final size:64
Alignment explanation
Indices: 48267--48473 Score: 267
Period size: 64 Copynumber: 3.2 Consensus size: 64
48257 ATACACAGGA
**
48267 AGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAAT-TCAATTCGTGCATCGATGCATAA
1 AGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGT-AATTCGTGCATCGATGCATAA
48329 GT
63 GT
*
48331 AGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGTAATTCGTGCATCGATGCATAAGT
1 AGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGTAATTCGTGCATCGATGCATAAGT
* * * * ** * *
48395 AGTGCATCGATGCATCCCAGTAATAATACAACATCGAATATATTTTATGCACCGATGCATCAGT
1 AGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGTAATTCGTGCATCGATGCATAAGT
48459 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
48474 ACCTTCATTA
Statistics
Matches: 128, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
64 121 0.95
65 7 0.05
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGTAATTCGTGCATCGATGCATAAGT
Found at i:49946 original size:23 final size:21
Alignment explanation
Indices: 49910--49955 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
49900 TTAATAGTAT
49910 TAATAATAATATTATAATAAA
1 TAATAATAATATTATAATAAA
*
49931 TAATAATGAATAATTATTATAAA
1 TAATAAT-AAT-ATTATAATAAA
49954 TA
1 TA
49956 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 3 0.14
23 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAATAATAATATTATAATAAA
Found at i:50345 original size:124 final size:123
Alignment explanation
Indices: 50151--50600 Score: 686
Period size: 124 Copynumber: 3.6 Consensus size: 123
50141 CGTCGTTAAT
* * * *
50151 TTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAA
1 TTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGC-TGGAATTGGATATCATTCGTCGTGAA
** *
50216 GTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGGGCACGATAT-CCTTCATCGTGAAG
65 GTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGCACGAT-TCCCTTCATCGTGAAG
* *
50275 TTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCTGTGAATTGGATATCATTCGTCGTGAA
1 TTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCTG-GAATTGGATATCATTCGTCGTGAA
* * *
50340 TTTGAAATCCAATCTAAAGATGAATGTTACTGGTAAACACGATTCCCTTCATCGTGAAG
65 GTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCATCGTGAAG
* *
50399 TTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCTAGGAATTGGACATCATTCGTCGTGAA
1 TTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCT-GGAATTGGATATCATTCGTCGTGAA
* *
50464 GTTGAAATCCAATCTAAAGATGAATGTTACTAGTGAGCACGATTCCCTTCGTCGTGAAG
65 GTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCATCGTGAAG
* *
50523 TTGAAACCATGGATGGCCCATTCGTTGTGAAGTTGAGCCTGAAATTGGATATCATTCGTCGTGAA
1 TTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAG-CTGGAATTGGATATCATTCGTCGTGAA
50588 GTTGAAATCCAAT
65 GTTGAAATCCAAT
50601 GTAAGTTACG
Statistics
Matches: 299, Mismatches: 23, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
123 2 0.01
124 294 0.98
125 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (123 bp):
TTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCTGGAATTGGATATCATTCGTCGTGAAG
TTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCATCGTGAAG
Found at i:50808 original size:253 final size:249
Alignment explanation
Indices: 50443--51424 Score: 988
Period size: 253 Copynumber: 3.9 Consensus size: 249
50433 GAGCTAGGAA
* * * * * * * *
50443 TTGGACATCATTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTAGTGAGCACGATT
1 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGTGCACGATT
* *
50508 CCCTTCGTCGTGAAGTTGAAACCATGGATGGCCCATTCGTTGTGAAGTTGAGCCTGAAATTGGAT
66 CCCTTCGTCGTGAAGTTGAAACCATGGATGGCCCCTTCGTCGTGAAGTTGAGCCTG-AATTGGAT
* *
50573 ATCATTCGTCGTGAAGTTGAAATCCAATGTAAGTTACGCTATTATGAGGCCAATATCCTTCGTTG
130 ATCCTTCGTCGTGAAGTTGAAATCCAA-GTAAGTTA-G-TATTATGAGTCCAATATCCTTCGTTG
** *
50638 TGAAGTTGAAATTAACTTTGAAACTGGAAAGTTTGTTGACAGATACTCCTTCTTTGAG
192 TGAAGTTGAAATTGGCTCTGAAACTGGAAAGTTTGTTGACAGATACTCCTTCTTTGAG
*
50696 TTGGATATCCTTCGTCGTGAAATTGAAATCCAATCTAGAGATGGATGCTGCTTGTGTGCACGATT
1 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGTGCACGATT
* ** *
50761 CCCTTCGTCGTGATGTTGAAACCGCGGGTGGCCCCTTCGTCGTGAAGTTGAGCCTGAAATTGGAT
66 CCCTTCGTCGTGAAGTTGAAACCATGGATGGCCCCTTCGTCGTGAAGTTGAGCCTG-AATTGGAT
* * * * * * *
50826 ATCCTTCATCGTGAAGTTAAAATCCAAGTAAGTT-GTATTGTTTCGAGTCAAATATTCTCCGTCG
130 ATCCTTCGTCGTGAAGTTGAAATCCAAGTAAGTTAGTA-T-TAT-GAGTCCAATATCCTTCGTTG
* * * ***
50890 TGAAGTTGAAATTGGCTCTGAAACTAGG-AAGCCCCTTCGTCATGA-AGTTGA-GCCTTAAATG-
192 TGAAGTTGAAATTGGCTCTGAAACT-GGAAAG----TTTGT--TGACAGAT-ACTCCTTCTTTGA
50951 G
249 G
*** * * *
50952 CACGATATCCTCCGTCGTGGAGTTGAAAT-C-A--T-G-GAT--AT-ATG---G-GT--ACGATA
1 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGTGCACGAT-
* * * * ** * *
51002 T-CCTCCGTCGTGGAGTTGAAATCGTATATGGCCCCTTCGTCGTGAAGTTGAGCCCTGACTTGAA
65 TCCCTTCGTCGTGAAGTTGAAACCATGGATGGCCCCTTCGTCGTGAAGTTGAG-CCTGAATTGGA
* * *
51066 TATCCTTCGTCGTGAAGTTGAAATCCAAGTATGTATTGT-TTCA--AGTCCAATATCCTTCGCTG
129 TATCCTTCGTCGTGAAGTTGAAATCCAAGTAAGT-TAGTATT-ATGAGTCCAATATCCTTCGTTG
* **
51128 TTAAGTTGAAATTGGCTCTGAAACTGGAAAGTTTGTTGACAGGCACTCCTTCTTTGAG
192 TGAAGTTGAAATTGGCTCTGAAACTGGAAAGTTTGTTGACAGATACTCCTTCTTTGAG
*
51186 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGTGTACGATT
1 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGTGCACGATT
* * *
51251 CTCTTCATCGTGAAGTTGAAACCATGGATGGCCCCTCCGTCGTGAAGTTGAGCCTTGAATTGGAT
66 CCCTTCGTCGTGAAGTTGAAACCATGGATGGCCCCTTCGTCGTGAAGTTGAGCC-TGAATTGGAT
* * * *
51316 ATCCTTCGTCGTGAAGTTGAAATCCAAGTAAGTT-GTATTGTTCCGAGTCCAATATCCTCCCTCG
130 ATCCTTCGTCGTGAAGTTGAAATCCAAGTAAGTTAGTATT-AT--GAGTCCAATATCCTTCGTTG
*
51380 TGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAG
192 TGAAGTTGAAATTGGCTCTGAAACT-GGAAA--GTTTGTTGACAG
51425 TCAGCCGCCC
Statistics
Matches: 591, Mismatches: 93, Indels: 88
0.77 0.12 0.11
Matches are distributed among these distances:
232 4 0.01
233 8 0.01
234 29 0.05
235 1 0.00
236 1 0.00
237 2 0.00
238 42 0.07
239 1 0.00
240 4 0.01
241 85 0.14
242 8 0.01
243 6 0.01
244 1 0.00
246 1 0.00
247 6 0.01
248 8 0.01
249 89 0.15
250 5 0.01
251 3 0.01
252 86 0.15
253 146 0.25
254 1 0.00
255 13 0.02
256 28 0.05
257 9 0.02
258 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (249 bp):
TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGTGCACGATT
CCCTTCGTCGTGAAGTTGAAACCATGGATGGCCCCTTCGTCGTGAAGTTGAGCCTGAATTGGATA
TCCTTCGTCGTGAAGTTGAAATCCAAGTAAGTTAGTATTATGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTCTGAAACTGGAAAGTTTGTTGACAGATACTCCTTCTTTGAG
Found at i:55176 original size:7 final size:7
Alignment explanation
Indices: 55164--55197 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
55154 TCTTAATTGC
55164 AAAAATT
1 AAAAATT
55171 AAAAATT
1 AAAAATT
*
55178 -TAAATT
1 AAAAATT
55184 AAAAATT
1 AAAAATT
55191 AAAAATT
1 AAAAATT
55198 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAAATT
Found at i:55182 original size:13 final size:13
Alignment explanation
Indices: 55166--55190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55156 TTAATTGCAA
55166 AAATTAAAAATTT
1 AAATTAAAAATTT
55179 AAATTAAAAATT
1 AAATTAAAAATT
55191 AAAAATTTAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTAAAAATTT
Found at i:55189 original size:20 final size:20
Alignment explanation
Indices: 55164--55207 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
55154 TCTTAATTGC
55164 AAAAATTAAAAATTTAAATT
1 AAAAATTAAAAATTTAAATT
*
55184 AAAAATTAAAAATTTAATTT
1 AAAAATTAAAAATTTAAATT
55204 AAAA
1 AAAA
55208 TAATTACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATTAAAAATTTAAATT
Found at i:55613 original size:28 final size:28
Alignment explanation
Indices: 55573--55628 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
55563 AACGCCGCTA
55573 TTGAATGTGTATTTAACGGCGTTTGTAT
1 TTGAATGTGTATTTAACGGCGTTTGTAT
* * *
55601 TTGATTGTTTATTTAGCGGCGTTTGTAT
1 TTGAATGTGTATTTAACGGCGTTTGTAT
55629 ACAAACGCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.18, C:0.07, G:0.25, T:0.50
Consensus pattern (28 bp):
TTGAATGTGTATTTAACGGCGTTTGTAT
Found at i:55655 original size:41 final size:41
Alignment explanation
Indices: 55601--55760 Score: 160
Period size: 41 Copynumber: 3.8 Consensus size: 41
55591 GCGTTTGTAT
* * * *
55601 TTGATTGTTTATTTAGCGGCGTTTGTATACAAACGCCACTA
1 TTGACTGTGTATTTAGCGGCGTTTCTTTACAAACGCCACTA
* ** *
55642 TTGACTGTGTATTTAGCGGC-TTTTTTTAACAAACAACGCTA
1 TTGACTGTGTATTTAGCGGCGTTTCTTT-ACAAACGCCACTA
* *
55683 TTGACTTTATATTTAGCGGCGTTTTTCTTTACAAACGCCACTA
1 TTGACTGTGTATTTAGCGGCG--TTTCTTTACAAACGCCACTA
* *
55726 TTGACTATGTATTTAGCGACGTTTTTCTTTACAAA
1 TTGACTGTGTATTTAGCGGCG--TTTCTTTACAAA
55761 TGTGGTTATT
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
40 5 0.05
41 46 0.46
43 42 0.42
44 6 0.06
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.41
Consensus pattern (41 bp):
TTGACTGTGTATTTAGCGGCGTTTCTTTACAAACGCCACTA
Found at i:55731 original size:43 final size:43
Alignment explanation
Indices: 55610--55760 Score: 184
Period size: 43 Copynumber: 3.6 Consensus size: 43
55600 TTTGATTGTT
* * *
55610 TATTTAGCGGCG--TTTGTATACAAACGCCACTATTGACTGTG
1 TATTTAGCGGCGTTTTTCTTTACAAACGCCACTATTGACTATG
* ** * * *
55651 TATTTAGCGGC-TTTTT-TTAACAAACAACGCTATTGACTTTA
1 TATTTAGCGGCGTTTTTCTTTACAAACGCCACTATTGACTATG
55692 TATTTAGCGGCGTTTTTCTTTACAAACGCCACTATTGACTATG
1 TATTTAGCGGCGTTTTTCTTTACAAACGCCACTATTGACTATG
*
55735 TATTTAGCGACGTTTTTCTTTACAAA
1 TATTTAGCGGCGTTTTTCTTTACAAA
55761 TGTGGTTATT
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
41 40 0.43
42 8 0.09
43 44 0.48
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40
Consensus pattern (43 bp):
TATTTAGCGGCGTTTTTCTTTACAAACGCCACTATTGACTATG
Found at i:59020 original size:23 final size:23
Alignment explanation
Indices: 58994--59038 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
58984 CACCACAGCT
*
58994 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
* *
59017 CGTAGAATTGCATCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
59039 ATATAATAAT
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:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:59276 original size:149 final size:147
Alignment explanation
Indices: 59006--59318 Score: 556
Period size: 149 Copynumber: 2.1 Consensus size: 147
58996 TATAATTGCA
* *
59006 CCGAAGTG-CCGCGTAGAATTGCATCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
*
59070 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
*
59135 CCATAGAATATATATATATC
130 CCACAG-A-ATATATATATC
59155 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
59220 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
59285 CACAGAATATATATATC
131 CACAGAATATATATATC
59302 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
59319 CCCTCGACTC
Statistics
Matches: 159, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
147 28 0.18
148 2 0.01
149 129 0.81
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (147 bp):
CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CACAGAATATATATATC
Found at i:60337 original size:16 final size:16
Alignment explanation
Indices: 60316--60346 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60306 TGTAATACAG
*
60316 ATAATCACATATAATT
1 ATAATCACACATAATT
60332 ATAATCACACATAAT
1 ATAATCACACATAAT
60347 CATGTCCATG
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATCACACATAATT
Found at i:60701 original size:44 final size:44
Alignment explanation
Indices: 60651--60753 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
60641 TGCACTCCTG
* * * **
60651 ATGCATCGATGCACTGAGGGCATTCGATGTTTATTTTATTAGAA
1 ATGCATCGATGCACTGACGACATTCGATGTTTATATTAAAAGAA
* * **
60695 ATGCATCGATGCACTGACGATATTCGATGTTTGTATTAAAATTA
1 ATGCATCGATGCACTGACGACATTCGATGTTTATATTAAAAGAA
60739 ATGCATCGATGCACT
1 ATGCATCGATGCACT
60754 CAATATGCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (44 bp):
ATGCATCGATGCACTGACGACATTCGATGTTTATATTAAAAGAA
Found at i:63984 original size:23 final size:23
Alignment explanation
Indices: 63958--64002 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
63948 CACCACAGCT
*
63958 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
63981 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
64003 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:64240 original size:149 final size:149
Alignment explanation
Indices: 63970--64284 Score: 596
Period size: 149 Copynumber: 2.1 Consensus size: 149
63960 TATAATTGCA
63970 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
64034 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* *
64099 TCATAGAATATATATATATC
130 CCACAGAATATATATATATC
64119 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
64184 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
64249 CACAGAATATATATATATC
131 CACAGAATATATATATATC
64268 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
64285 CCCTCGACTC
Statistics
Matches: 163, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.01
149 162 0.99
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CACAGAATATATATATATC
Found at i:65303 original size:16 final size:16
Alignment explanation
Indices: 65282--65312 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65272 TGTAATACAG
*
65282 ATAATCACATATAATT
1 ATAATCACACATAATT
65298 ATAATCACACATAAT
1 ATAATCACACATAAT
65313 CATGTCCATG
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATCACACATAATT
Found at i:65704 original size:63 final size:63
Alignment explanation
Indices: 65602--65756 Score: 193
Period size: 63 Copynumber: 2.5 Consensus size: 63
65592 GGAGGCATGT
* * * * * **
65602 ATCGATGCACTCCTGATGCATTGATGCACTGAGGGCATTCGATGTTCATTTTATTAGAAATGC
1 ATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAAATGC
** **
65665 ATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTAAAATTAATGC
1 ATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAAATGC
**
65728 ATCGATGCACTCAATATGCATCGATGCAC
1 ATCGATGCACTCCTTATGCATCGATGCAC
65757 CTTCAACACA
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 79 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (63 bp):
ATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAAATGC
Found at i:66799 original size:22 final size:22
Alignment explanation
Indices: 66772--66823 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
66762 TATTTTGATA
66772 AATTTAATGTTTATTTTATAAT
1 AATTTAATGTTTATTTTATAAT
66794 AATTTAATGTTTATTTTATAAT
1 AATTTAATGTTTATTTTATAAT
66816 AATTTAAT
1 AATTTAAT
66824 AAAATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
AATTTAATGTTTATTTTATAAT
Found at i:66829 original size:10 final size:11
Alignment explanation
Indices: 66784--66848 Score: 62
Period size: 11 Copynumber: 6.1 Consensus size: 11
66774 TTTAATGTTT
*
66784 ATTTTATAATA
1 ATTTAATAATA
** *
66795 ATTTAATGTTT
1 ATTTAATAATA
*
66806 ATTTTATAATA
1 ATTTAATAATA
66817 ATTTAATAA-A
1 ATTTAATAATA
*
66827 ATTTAATAATC
1 ATTTAATAATA
66838 A-TTAATAATA
1 ATTTAATAATA
66848 A
1 A
66849 ATTGATTAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
10 19 0.45
11 23 0.55
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:67309 original size:41 final size:41
Alignment explanation
Indices: 67258--67716 Score: 471
Period size: 41 Copynumber: 11.2 Consensus size: 41
67248 TTGTAAACAC
** *
67258 AAACGCCACTAAAACACGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTATAA
**
67299 AAACGCCACTAAA-TCATGAGTCTATAGCGGTATTTGTA-AA
1 AAACGCCACTAAAGT-ATGAGTCTATAGCGGCGTTTGTATAA
* * *
67339 AAACACCACTAAA-TCATGAGTCTATAGCGGCGTTTATAACAA
1 AAACGCCACTAAAGT-ATGAGTCTATAGCGGCGTTTGT-ATAA
* * *
67381 AAACGCCACTAAAGTATGAGTATTTAGCGGCGTTTATATAA
1 AAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTATAA
* *
67422 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTATAA
* *
67463 AAACGCCACTAAA-TCATGATTCTATAGCGGTGTTTGTATAA
1 AAACGCCACTAAAGT-ATGAGTCTATAGCGGCGTTTGTATAA
* * * *
67504 AAATGCCACTAAAGTAAGAGTCTTTTGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTATAA
* * *
67545 AAACGTCACTTAA-TCATGAGTCTATAGCGTCGTTTGTATAAA
1 AAACGCCACTAAAGT-ATGAGTCTATAGCGGCGTTTGTAT-AA
** * *
67587 AAACGCCACTAAAGTACAAGTCTATAACGGCGTTTCTATAA
1 AAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTATAA
** * * * *
67628 AAACATCACTAAATTA-CATTCTGTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTATAA
* * * * * *
67668 CAACGCCGCTATAGTAGGAGTCTTTAGCGGCGTTTGTTCTAA
1 AAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTG-TATAA
67710 AAACGCC
1 AAACGCC
67717 GCTACAAATG
Statistics
Matches: 349, Mismatches: 58, Indels: 21
0.82 0.14 0.05
Matches are distributed among these distances:
40 66 0.19
41 204 0.58
42 77 0.22
43 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTATAA
Found at i:69191 original size:2 final size:2
Alignment explanation
Indices: 69179--69215 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
69169 AAATAATTAT
*
69179 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
69216 TTTAAACCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:78148 original size:41 final size:41
Alignment explanation
Indices: 78102--78208 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 41
78092 GTGTAACCGG
*
78102 TTTCGGTTTGTAAAAAACCGGTTTTAAAAAAAACCGGATTT
1 TTTCGGTTTGTAAAAAACCGGTTTTAAAAAAAACCAGATTT
** * *
78143 TTTCGG--T-TAAAAAACCGGTTTTTTTAAAAAATCAGTTTT
1 TTTCGGTTTGTAAAAAACCGG-TTTTAAAAAAAACCAGATTT
78182 TTAGTCCGGTTTG-AAAAAACCGGTTTT
1 TT--T-CGGTTTGTAAAAAACCGGTTTT
78209 TAATCCGGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
38 11 0.20
39 18 0.33
41 7 0.13
42 3 0.06
43 4 0.07
44 11 0.20
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (41 bp):
TTTCGGTTTGTAAAAAACCGGTTTTAAAAAAAACCAGATTT
Found at i:79940 original size:4 final size:4
Alignment explanation
Indices: 79931--79958 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
79921 TTTTATAATC
79931 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
79959 CTTTCATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:82668 original size:11 final size:11
Alignment explanation
Indices: 82652--82691 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
82642 GATATGACAC
82652 AATATTTTATA
1 AATATTTTATA
*
82663 AATA-TTT-TC
1 AATATTTTATA
82672 AATATTTTATA
1 AATATTTTATA
82683 AATATTTTA
1 AATATTTTA
82692 GATATTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 5 0.20
10 6 0.24
11 14 0.56
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (11 bp):
AATATTTTATA
Found at i:82676 original size:20 final size:20
Alignment explanation
Indices: 82651--82699 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
82641 AGATATGACA
82651 CAATATTTTATAAATATTTT
1 CAATATTTTATAAATATTTT
82671 CAATATTTTATAAATATTTT
1 CAATATTTTATAAATATTTT
82691 -AGATATTTT
1 CA-ATATTTT
82700 CTTTGTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (20 bp):
CAATATTTTATAAATATTTT
Found at i:84376 original size:18 final size:15
Alignment explanation
Indices: 84338--84380 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 15
84328 ATTGATTGTT
84338 ATTAATTTAATATAA
1 ATTAATTTAATATAA
*
84353 AATAATTATATATAATAA
1 ATTAATT-TA-AT-ATAA
84371 ATTAATTTAA
1 ATTAATTTAA
84381 AAATATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 6 0.26
16 3 0.13
17 4 0.17
18 10 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAATTTAATATAA
Found at i:100098 original size:21 final size:21
Alignment explanation
Indices: 100049--100110 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
100039 ATTCCCCTGT
100049 GGGGGGAATCGGTTCCCTTCAA
1 GGGGGGAATCGGTTCCC-TCAA
* *
100071 AGGGGGAATCGGTTCCCTCAG
1 GGGGGGAATCGGTTCCCTCAA
*
100092 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
100111 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 20 0.56
22 16 0.44
ACGTcount: A:0.18, C:0.24, G:0.37, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:106818 original size:63 final size:63
Alignment explanation
Indices: 106711--106843 Score: 221
Period size: 63 Copynumber: 2.1 Consensus size: 63
106701 GGGGGTGAAA
* *
106711 CTTGGCAGAACTCTTCGGGCTCGATTAAGGAGAATATTACAGCTATTGGGCAGAGATTAGGTC
1 CTTGGCAGAACTCTTCGGGCTCGATTAAGGAGAAGATTACAGCTATTAGGCAGAGATTAGGTC
* * *
106774 TTTGGCAGAACTCTTCGGGCTTGATTAAGGAGAAGATTATAGCTATTAGGCAGAGATTAGGTC
1 CTTGGCAGAACTCTTCGGGCTCGATTAAGGAGAAGATTACAGCTATTAGGCAGAGATTAGGTC
106837 CTTGGCA
1 CTTGGCA
106844 TAATGAGAGA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (63 bp):
CTTGGCAGAACTCTTCGGGCTCGATTAAGGAGAAGATTACAGCTATTAGGCAGAGATTAGGTC
Found at i:112981 original size:37 final size:37
Alignment explanation
Indices: 112908--112982 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
112898 GTTGGAAAAT
* *
112908 ATTTATATATTTTATTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTATTTAAAAAATTGAAAATCATAAA
*
112945 ATTTATATAATTTCT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTT-TATTTAAAAAATTGAAAATCATAAA
112982 A
1 A
112983 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 18 0.55
39 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTATTTAAAAAATTGAAAATCATAAA
Done.