Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004061.1 Hibiscus syriacus cultivar Beakdansim tig00008883_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: 74669
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:10799 original size:43 final size:42
Alignment explanation
Indices: 10683--11129 Score: 314
Period size: 43 Copynumber: 10.4 Consensus size: 42
10673 TATACGGTTA
* * * *
10683 AATTATAAAAGTAAAAAAGTATGATTAAAAAATATTAGGGACCTC
1 AATTATAAAGGTAAAAATG-A-GATTGAAAAA-ATTAGGGGCCTC
*
10728 AATTATAAAGGTAAAAATGAGATT-AAAAAATGAGGGGTCCT-
1 AATTATAAAGGTAAAAATGAGATTGAAAAAATTAGGGG-CCTC
* * * *
10769 AATTTTAAAGGTAAAAAGTGAGATTGAAAAAGTTAAGGGCCTA
1 AATTATAAAGGTAAAAA-TGAGATTGAAAAAATTAGGGGCCTC
* *
10812 AATTATATAA-GTAAAAAAT-AGGATTGAAAAAGTTAGGGGCCTT
1 AATTATA-AAGGT-AAAAATGA-GATTGAAAAAATTAGGGGCCTC
* * **
10855 AATTATAAAGGTAAAAAGTGAGACT-AAAAAACTAGGGGTATC
1 AATTATAAAGGTAAAAA-TGAGATTGAAAAAATTAGGGGCCTC
* * * * *
10897 GATTATAAAGTTAGAAAACGAGATTGAAAAAATTAGGTGCATC
1 AATTATAAAGGTA-AAAATGAGATTGAAAAAATTAGGGGCCTC
* *
10940 AATTATAAAGGTAGATAAATGAGATTAAAAACAATTAGGAG-CTC
1 AATTATAAAGGTA-A-AAATGAGATTGAAAA-AATTAGGGGCCTC
* * ** * ** * *
10984 AATTATAAAGCTAGAAAGTGAGATTGAAAACCTTAAGATCATA
1 AATTATAAAGGTA-AAAATGAGATTGAAAAAATTAGGGGCCTC
* * * * *
11027 AATTATAAATGTAAAAGTGATATTGAAAAAATTAAGAGCCTC
1 AATTATAAAGGTAAAAATGAGATTGAAAAAATTAGGGGCCTC
* * * * *
11069 AATTATAAAGATAAAAAAGTAGGATT-ACAAAAATTAGAGACATC
1 AATTATAAAGGTAAAAATG-A-GATTGA-AAAAATTAGGGGCCTC
*
11113 AATTATAAAGATAAAAA
1 AATTATAAAGGTAAAAA
11130 ATAAAATTTT
Statistics
Matches: 327, Mismatches: 57, Indels: 37
0.78 0.14 0.09
Matches are distributed among these distances:
41 22 0.07
42 97 0.30
43 114 0.35
44 69 0.21
45 25 0.08
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.25
Consensus pattern (42 bp):
AATTATAAAGGTAAAAATGAGATTGAAAAAATTAGGGGCCTC
Found at i:10842 original size:129 final size:127
Alignment explanation
Indices: 10681--11129 Score: 405
Period size: 129 Copynumber: 3.5 Consensus size: 127
10671 ATTATACGGT
*
10681 TAAATTATAAAAGTAAAAAAGTATGATTAAAAAATATTAGGGACCTCAATTATAAAGGTAAAAAT
1 TAAATTAT-AAAGTAAAAAAGTAGGATTAAAAAA-ATTAGGGACCTCAATTATAAAGGTAAAAAT
* * *
10746 GAGATTAAAAAATGAGGGGTCCT-AATTTTAAAGGTAAAAAGTGAGATTGAAAAAGTTAAGGGCC
64 GAGATTAAAAAAT-AGGGGTCATAAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAAGGGCC
* * * *
10810 TAAATTATATAAGTAAAAAA-TAGGATTGAAAAAGTTAGGGGCCTTAATTATAAAGGTAAAAAGT
1 TAAATTATA-AAGTAAAAAAGTAGGATTAAAAAAATTAGGGACCTCAATTATAAAGGTAAAAA-T
* ** * *
10874 GAGACTAAAAAACTAGGGGT-ATCGATTATAAAGTTAGAAAA-CGAGATTGAAAAAATT-AGGTG
64 GAGATTAAAAAA-TAGGGGTCATAAATTATAAAGGTA-AAAAGTGAGATTGAAAAAATTAAGG-G
*
10936 CA
126 CC
* * * *
10938 TCAATTATAAAGGTAGATAAA-T-GAGATTAAAAACAATTA-GGAGCTCAATTATAAAGCTAGAA
1 TAAATTATAAA-GTA-AAAAAGTAG-GATTAAAAA-AATTAGGGACCTCAATTATAAAGGTA-AA
* ** * * * *
11000 AGTGAGATTGAAAACCTTA-AGATCATAAATTATAAATGT-AAAAGTGATATTGAAAAAATTAAG
61 AATGAGATT-AAAA-AATAGGGGTCATAAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAAG
*
11063 AGCC
124 GGCC
* * * * *
11067 TCAATTATAAAGATAAAAAAGTAGGATTACAAAAATTAGAGACATCAATTATAAAGATAAAAA
1 TAAATTATAAAG-TAAAAAAGTAGGATTAAAAAAATTAGGGACCTCAATTATAAAGGTAAAAA
11130 ATAAAATTTT
Statistics
Matches: 258, Mismatches: 42, Indels: 41
0.76 0.12 0.12
Matches are distributed among these distances:
127 32 0.12
128 85 0.33
129 114 0.44
130 27 0.10
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.25
Consensus pattern (127 bp):
TAAATTATAAAGTAAAAAAGTAGGATTAAAAAAATTAGGGACCTCAATTATAAAGGTAAAAATGA
GATTAAAAAATAGGGGTCATAAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAAGGGCC
Found at i:10864 original size:86 final size:85
Alignment explanation
Indices: 10683--11013 Score: 220
Period size: 85 Copynumber: 3.9 Consensus size: 85
10673 TATACGGTTA
* * *
10683 AATTATAAAAGTAAAAAAGT-ATGATTAAAAAATATTAGGGACCTCAATTATAAAGGTAAAAATG
1 AATTATAAAGGT-AAAAAGTGA-GATTAAAAAATATAAGGGACCTAAATTATAAAGGTAAAAATG
10747 AGATTAAAAAATGAGGGGTCCT
64 AGATTAAAAAATGAGGGGTCCT
* *
10769 AATTTTAAAGGTAAAAAGTGAGATTGAAAAAGT-TAAGGG-CCTAAATTATATAA-GTAAAAAAT
1 AATTATAAAGGTAAAAAGTGAGATT-AAAAAATATAAGGGACCTAAATTATA-AAGGT-AAAAAT
* *
10831 -AGGATTGAAAAAGTTAGGGG-CCTT
63 GA-GATT-AAAAAATGAGGGGTCC-T
* * * ** * *
10855 AATTATAAAGGTAAAAAGTGAGACTAAAAAA-CTAGGGGTA--TCGATTATAAAGTTAGAAAACG
1 AATTATAAAGGTAAAAAGTGAGATTAAAAAATATAAGGG-ACCTAAATTATAAAGGTA-AAAATG
* * *
10917 AGATTGAAAAAATTAGGTG-CAT
64 AGATT-AAAAAATGAGGGGTCCT
* * * *
10939 CAATTATAAAGGTAGATAAA-TGAGATTAAAAACA-ATTA-GGAGCTCAATTATAAAGCTAGAAA
1 -AATTATAAAGGTA-A-AAAGTGAGATTAAAAA-ATATAAGGGACCTAAATTATAAAGGTA-AAA
* *
11001 GTGAGATTGAAAA
61 ATGAGATTAAAAA
11014 CCTTAAGATC
Statistics
Matches: 199, Mismatches: 27, Indels: 38
0.75 0.10 0.14
Matches are distributed among these distances:
84 17 0.09
85 83 0.42
86 71 0.36
87 28 0.14
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (85 bp):
AATTATAAAGGTAAAAAGTGAGATTAAAAAATATAAGGGACCTAAATTATAAAGGTAAAAATGAG
ATTAAAAAATGAGGGGTCCT
Found at i:11102 original size:44 final size:43
Alignment explanation
Indices: 11053--11173 Score: 136
Period size: 43 Copynumber: 2.8 Consensus size: 43
11043 GTGATATTGA
**
11053 AAAAATTAAGAGCCTCAATTATAAAGATAAAAAAGTAGGATTAC
1 AAAAATTAAGAGCCTCAATTATAAAGATAAAAAA-TAAAATTAC
* **
11097 AAAAATT-AGAGACATCAATTATAAAGATAAAAAATAAAATTTT
1 AAAAATTAAGAG-CCTCAATTATAAAGATAAAAAATAAAATTAC
* * * *
11140 AAAAACTAAAAGACTCAATTATAAAAATAAAAAA
1 AAAAATTAAGAGCCTCAATTATAAAGATAAAAAA
11174 ATATAATGGA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
43 34 0.52
44 31 0.48
ACGTcount: A:0.61, C:0.07, G:0.08, T:0.23
Consensus pattern (43 bp):
AAAAATTAAGAGCCTCAATTATAAAGATAAAAAATAAAATTAC
Found at i:11172 original size:22 final size:22
Alignment explanation
Indices: 11106--11172 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
11096 CAAAAATTAG
*
11106 AGACATCAATTATAAAGATAAAA
1 AGAC-TCAATTATAAAAATAAAA
* *
11129 A-A-TAAAATTTTAAAAACT-AAA
1 AGACT-CAATTATAAAAA-TAAAA
11150 AGACTCAATTATAAAAATAAAA
1 AGACTCAATTATAAAAATAAAA
11172 A
1 A
11173 AATATAATGG
Statistics
Matches: 34, Mismatches: 5, Indels: 11
0.68 0.10 0.22
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 17 0.50
23 2 0.06
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.24
Consensus pattern (22 bp):
AGACTCAATTATAAAAATAAAA
Found at i:11187 original size:43 final size:44
Alignment explanation
Indices: 11106--11189 Score: 109
Period size: 43 Copynumber: 1.9 Consensus size: 44
11096 CAAAAATTAG
* **
11106 AGACATCAATTATAAAGATAAAAAATAAAATTTTAAAAACTAAA
1 AGACATCAATTATAAAAATAAAAAATAAAATTGGAAAAACTAAA
*
11150 AGAC-TCAATTATAAAAATAAAAAAATATAA-TGGAAAAACT
1 AGACATCAATTATAAAAAT-AAAAAATAAAATTGGAAAAACT
11190 TTGGACCCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 21 0.60
44 14 0.40
ACGTcount: A:0.63, C:0.07, G:0.06, T:0.24
Consensus pattern (44 bp):
AGACATCAATTATAAAAATAAAAAATAAAATTGGAAAAACTAAA
Found at i:12681 original size:28 final size:28
Alignment explanation
Indices: 12650--12706 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
12640 GTTTACATAT
*
12650 GTCATCAAGTCAATGTTTAAAACATTAA
1 GTCATCAAATCAATGTTTAAAACATTAA
12678 GTCATCAAATCAATGTTTAAAACATTAA
1 GTCATCAAATCAATGTTTAAAACATTAA
12706 G
1 G
12707 CTATCGAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (28 bp):
GTCATCAAATCAATGTTTAAAACATTAA
Found at i:13822 original size:21 final size:20
Alignment explanation
Indices: 13798--13846 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
13788 ACTTTTTGGA
13798 AAACTGTCTTG-GAAAGTTTCG
1 AAACT-TCTTGAGAAA-TTTCG
13819 AAAC-TCTTGTAGAAATTTCG
1 AAACTTCTTG-AGAAATTTCG
13839 AAACTTCT
1 AAACTTCT
13847 GGTCAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 5 0.20
20 9 0.36
21 11 0.44
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
AAACTTCTTGAGAAATTTCG
Found at i:14356 original size:2 final size:2
Alignment explanation
Indices: 14344--14374 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
14334 GTCACATTAC
*
14344 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14375 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:14379 original size:2 final size:2
Alignment explanation
Indices: 14374--14408 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14364 ATATATATAT
14374 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
14409 TAAAGAAAGA
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16677 original size:22 final size:23
Alignment explanation
Indices: 16645--16688 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16635 TGTATAGTAA
*
16645 AATTTTAAA-TTTGTTTTTTTAG
1 AATTTTAAATTTTATTTTTTTAG
*
16667 AATTTTTAATTTTATTTTTTTA
1 AATTTTAAATTTTATTTTTTTA
16689 TATTATTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (23 bp):
AATTTTAAATTTTATTTTTTTAG
Found at i:19235 original size:21 final size:22
Alignment explanation
Indices: 19186--19235 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
19176 AAAAAAAAAA
*
19186 ATATACATATTTAAGAAAATGT
1 ATATAAATATTTAAGAAAATGT
* * *
19208 ATTTAAATATTTTA-AAAATTT
1 ATATAAATATTTAAGAAAATGT
19229 ATATAAA
1 ATATAAA
19236 AACAATGTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (22 bp):
ATATAAATATTTAAGAAAATGT
Found at i:22134 original size:12 final size:12
Alignment explanation
Indices: 22117--22151 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
22107 TCTATTGTGT
22117 AAAAAATGAAAA
1 AAAAAATGAAAA
22129 AAAAAATGAAAA
1 AAAAAATGAAAA
22141 AAAAAATGAAA
1 AAAAAATGAAA
22152 GAGCCCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (12 bp):
AAAAAATGAAAA
Found at i:22667 original size:55 final size:53
Alignment explanation
Indices: 22524--22816 Score: 347
Period size: 53 Copynumber: 5.5 Consensus size: 53
22514 GGGTCCGTTT
* * **** *
22524 CCTCTTG-TTCAGGGATTAAGGAACTCAAACAATCTTCTAAAAATGGGTTCGCTC
1 CCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTGCCTACGGGTTCGCTC
* * * * * *
22578 CCTATTTCTTCAGGGAGTAGAAATCGAACGATCTTCT-CTTTACGGGTCCGCTC
1 CCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGC-CTACGGGTTCGCTC
* * *
22631 CCTCTTGCTTAATGGAGCGTAGAACTCGAACAATCTTCTGCTTACGGGTTCGCTC
1 CCTCTTGCTTCA-GG-GAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTC
*
22686 CCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCTCTC
1 CCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTC
* * *
22739 CCTCTTGCTTCAGGGAGTAGAACTCGAACTATCTTTTGCCTACGGGTTTGCTC
1 CCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTC
22792 CCTCTTGCTTCAGGGAGTAGAACTC
1 CCTCTTGCTTCAGGGAGTAGAACTC
22817 AAAAAAATCT
Statistics
Matches: 208, Mismatches: 26, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
53 144 0.69
54 10 0.05
55 53 0.25
56 1 0.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (53 bp):
CCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTC
Found at i:22697 original size:108 final size:106
Alignment explanation
Indices: 22568--22813 Score: 341
Period size: 108 Copynumber: 2.3 Consensus size: 106
22558 TTCTAAAAAT
* * * *
22568 GGGTTCGCTCCCTATTTCTTCAGGGAGTAGAAATCGAACGATCTTCT-CTTTACGGGTCCGCTCC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAAATCGAACAATCTTCTGC-CTACGGGTCCGCTCC
* *
22632 CTCTTGCTTAATGGAGCGTAGAACTCGAACAATCTTCTGCTTAC
65 CTCTTGCTTAA-GG-GAGTAGAACTCGAACAATCTTCTGCCTAC
* * *
22676 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCTCTCCC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAAATCGAACAATCTTCTGCCTACGGGTCCGCTCCC
* * *
22741 TCTTGCTTCAGGGAGTAGAACTCGAACTATCTTTTGCCTAC
66 TCTTGCTTAAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
*
22782 GGGTTTGCTCCCTCTTGCTTCAGGGAGTAGAA
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAA
22814 CTCAAAAAAA
Statistics
Matches: 124, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
106 56 0.45
107 2 0.02
108 65 0.52
109 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (106 bp):
GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAAATCGAACAATCTTCTGCCTACGGGTCCGCTCCC
TCTTGCTTAAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
Found at i:23379 original size:80 final size:80
Alignment explanation
Indices: 23241--23453 Score: 336
Period size: 80 Copynumber: 2.7 Consensus size: 80
23231 GCTCGAAAGA
* * *
23241 CTTACAAATAACCCAAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACT
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACT
**
23306 ACTCTTCGGTGAAGG
66 ACTCTTCCATGAAGG
*
23321 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACT
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACT
23386 ACTCTTCCATGAAGG
66 ACTCTTCCATGAAGG
* * * *
23401 CTTACAAATTTCCTGAAGGATTTAATCATCATGCTTGAAAGACTTATTGATGG
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
23454 CTCGAAGGAC
Statistics
Matches: 123, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 123 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (80 bp):
CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACT
ACTCTTCCATGAAGG
Found at i:23474 original size:42 final size:42
Alignment explanation
Indices: 23415--23496 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
23405 CAAATTTCCT
* * *
23415 GAAGGATTTAATCATCATGCTTGAAAGACTTATTGATGGCTC
1 GAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGGCTC
*
23457 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGC
1 GAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGGC
23497 ACTTACTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (42 bp):
GAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGGCTC
Found at i:23479 original size:22 final size:21
Alignment explanation
Indices: 23425--23488 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
23415 GAAGGATTTA
*
23425 ATCATCATGCTTGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* *
23446 AT--TGATGGCTCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
23466 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
23488 A
1 A
23489 CTGATGGCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 3 0.09
20 11 0.32
21 5 0.15
22 12 0.35
23 3 0.09
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:23543 original size:135 final size:135
Alignment explanation
Indices: 23362--23631 Score: 380
Period size: 135 Copynumber: 2.0 Consensus size: 135
23352 TGCTCGAAAG
* * *
23362 ACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATT-TCCTGAAGGATTTAA
1 ACTTACTGATGGGTTCGCTTCACTACTCTACCATGAAGGCTTACAAATTACCCT-AAGGATTTAA
* * * * * * *
23426 TCATCATGCTTGAAAGACTTATTGATGGCTCGAAGGACTTCATCATCATGCTCGAAAGACTTACT
65 TCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAAGCATCATACCCGAAAGACTTACT
23491 GATGGC
130 GATGGC
* *
23497 ACTTACTTATGGGTTCGCTTCACTACTCTACCGTGAAGGCTTACAAATTACCCTAAGGATTTAAT
1 ACTTACTGATGGGTTCGCTTCACTACTCTACCATGAAGGCTTACAAATTACCCTAAGGATTTAAT
* * * *
23562 CATTATGCTCGAAATACTTACTGATGGCCCTAAGGATTTAAGCATCATACCCGAAAGACTTACTG
66 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAAGCATCATACCCGAAAGACTTACTG
23627 ATGGC
131 ATGGC
23632 CCAAAGGACT
Statistics
Matches: 118, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
135 115 0.97
136 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (135 bp):
ACTTACTGATGGGTTCGCTTCACTACTCTACCATGAAGGCTTACAAATTACCCTAAGGATTTAAT
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAAGCATCATACCCGAAAGACTTACTG
ATGGC
Found at i:23595 original size:42 final size:42
Alignment explanation
Indices: 23547--23644 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
23537 TTACAAATTA
* * * * *
23547 CCCTAAGGATTTAATCATTATGCTCGAAATACTTACTGATGG
1 CCCTAAGGATTTAAGCATCATACCCGAAAGACTTACTGATGG
23589 CCCTAAGGATTTAAGCATCATACCCGAAAGACTTACTGATGG
1 CCCTAAGGATTTAAGCATCATACCCGAAAGACTTACTGATGG
* *
23631 CCCAAAGGACTTAA
1 CCCTAAGGATTTAA
23645 ATTGTTTACT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (42 bp):
CCCTAAGGATTTAAGCATCATACCCGAAAGACTTACTGATGG
Found at i:35021 original size:41 final size:41
Alignment explanation
Indices: 34976--35062 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
34966 ATTCACGTTG
*
34976 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * *
35017 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
35058 CATTT
1 CATTT
35063 ACAGTTGTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (41 bp):
CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:35191 original size:6 final size:6
Alignment explanation
Indices: 35180--35313 Score: 177
Period size: 6 Copynumber: 24.5 Consensus size: 6
35170 GACACGTATT
35180 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
35228 ACCACG ACCACG ACCACG ACCA-G ACCA-G ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
35271 ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
35311 ACC
1 ACC
35314 CGAGACGAGA
Statistics
Matches: 127, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
5 63 0.50
6 64 0.50
ACGTcount: A:0.28, C:0.54, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:35214 original size:30 final size:28
Alignment explanation
Indices: 35180--35316 Score: 182
Period size: 25 Copynumber: 5.0 Consensus size: 28
35170 GACACGTATT
35180 ACCACGACCACGACCACGACCACGACCACG
1 ACCACGACCACGACCACGACC-CGACC-CG
35210 ACCACGACCACGACCACGACCACGACCACG
1 ACCACGACCACGACCACGACC-CGACC-CG
35240 ACCACGACCA-GACCA-GACCCGACCCG
1 ACCACGACCACGACCACGACCCGACCCG
35266 ACC-CGACC-CGACC-CGACCCGACCCG
1 ACCACGACCACGACCACGACCCGACCCG
35291 ACC-CGACC-CGACC-CGACCCGACCCG
1 ACCACGACCACGACCACGACCCGACCCG
35316 A
1 A
35317 GACGAGACGA
Statistics
Matches: 105, Mismatches: 0, Indels: 9
0.92 0.00 0.08
Matches are distributed among these distances:
25 46 0.44
26 5 0.05
27 5 0.05
28 4 0.04
29 5 0.05
30 40 0.38
ACGTcount: A:0.28, C:0.53, G:0.18, T:0.00
Consensus pattern (28 bp):
ACCACGACCACGACCACGACCCGACCCG
Found at i:35268 original size:15 final size:17
Alignment explanation
Indices: 35180--35313 Score: 176
Period size: 15 Copynumber: 8.2 Consensus size: 17
35170 GACACGTATT
35180 ACCACGACCACGACCACG
1 ACCACGACCACGACC-CG
35198 ACCACGACCACGACCACG
1 ACCACGACCACGACC-CG
35216 ACCACGACCACGACCACG
1 ACCACGACCACGACC-CG
*
35234 ACCACGACCACGACCAG
1 ACCACGACCACGACCCG
35251 ACCA-GACC-CGACCCG
1 ACCACGACCACGACCCG
35266 ACC-CGACC-CGACCCG
1 ACCACGACCACGACCCG
35281 ACC-CGACC-CGACCCG
1 ACCACGACCACGACCCG
35296 ACC-CGACC-CGACCCG
1 ACCACGACCACGACCCG
35311 ACC
1 ACC
35314 CGAGACGAGA
Statistics
Matches: 113, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
15 53 0.47
16 4 0.04
17 5 0.04
18 51 0.45
ACGTcount: A:0.28, C:0.54, G:0.18, T:0.00
Consensus pattern (17 bp):
ACCACGACCACGACCCG
Found at i:35322 original size:5 final size:5
Alignment explanation
Indices: 35314--35344 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
35304 CGACCCGACC
35314 CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
35345 GCGGCGGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.35, C:0.23, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:35847 original size:6 final size:6
Alignment explanation
Indices: 35831--35874 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
35821 TCTCGTCTCG
35831 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
35875 AATGGTAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:35880 original size:6 final size:6
Alignment explanation
Indices: 35871--35901 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
35861 GTCGTGGTCG
35871 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
35902 ACGTGTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:35880 original size:12 final size:12
Alignment explanation
Indices: 35841--35892 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
35831 GGTCGGGTCG
**
35841 TGGTCGTGGTCG
1 TGGTCGTGGTAA
**
35853 TGGTCGTGGTCG
1 TGGTCGTGGTAA
35865 TGGTCGTGGTAA
1 TGGTCGTGGTAA
**
35877 TGGTAATGGTAA
1 TGGTCGTGGTAA
35889 TGGT
1 TGGT
35893 AATGGTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.12, C:0.10, G:0.44, T:0.35
Consensus pattern (12 bp):
TGGTCGTGGTAA
Found at i:35880 original size:18 final size:18
Alignment explanation
Indices: 35841--35880 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
35831 GGTCGGGTCG
**
35841 TGGTCGTGGTCGTGGTCG
1 TGGTCGTGGTCGTGGTAA
35859 TGGTCGTGGTCGTGGTAA
1 TGGTCGTGGTCGTGGTAA
35877 TGGT
1 TGGT
35881 AATGGTAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.12, G:0.47, T:0.35
Consensus pattern (18 bp):
TGGTCGTGGTCGTGGTAA
Found at i:36007 original size:19 final size:19
Alignment explanation
Indices: 35983--36048 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
35973 TTTACGATCA
35983 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
36002 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
36024 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
36043 CAACGA
1 CAACGA
36049 CAACTGTAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:36040 original size:41 final size:40
Alignment explanation
Indices: 35992--36333 Score: 307
Period size: 41 Copynumber: 8.1 Consensus size: 40
35982 ACAACGAATT
* *
35992 TGGAAAATCGCAACGACAACTGTAGACTATCGCAA-CGAATT
1 TGGAAAATCGCAACG-CGACTGTAGACTATCGCAACCGAA-A
*
36033 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGACTGTAGACTATCGCAAC-CGAAA
*
36075 CGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGTAGACTATCGCAAC-CGAAA
* * *
36116 TGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACGCCAAA
1 TGGAAAATCGCAACGCGACTGT-AGACTATCGCAAC-CGAAA
36157 TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGTAGACTATCGCAAC-CGAAA
*
36198 TGGAAAATCGCAAAGCGATTTTCTTGCGATTTTCA-ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGA----C-T--G----T-AGACTATCGCAAC-CGAAA
* * *
36250 TGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACGCCAAA
1 TGGAAAATCGCAACGCGACTGT-AGACTATCGCAAC-CGAAA
* *
36291 TGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACCCGAAA
1 TGGAAAATCGCAACGCGACTGT-AGACTATCGCAA-CCGAAA
36332 TG
1 TG
36334 CAACGCGAAT
Statistics
Matches: 268, Mismatches: 16, Indels: 34
0.84 0.05 0.11
Matches are distributed among these distances:
40 1 0.00
41 207 0.77
42 16 0.06
43 4 0.01
45 1 0.00
46 1 0.00
47 1 0.00
48 1 0.00
52 35 0.13
53 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.19
Consensus pattern (40 bp):
TGGAAAATCGCAACGCGACTGTAGACTATCGCAACCGAAA
Found at i:36086 original size:20 final size:20
Alignment explanation
Indices: 36061--36215 Score: 125
Period size: 20 Copynumber: 7.6 Consensus size: 20
36051 ACTGTAGACT
*
36061 ATCGCAACGCGAAACGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
36081 ATCGCAACGCG-ACTGTAGACT
1 ATCGCAACGCGAAATG--GAAA
36102 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
36122 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
36143 ATCGCAACGCCAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
36163 ATCGCAACGCG-ACTGTAGACT
1 ATCGCAACGCGAAATG--GAAA
36184 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
36204 ATCGCAAAGCGA
1 ATCGCAACGCGA
36216 TTTTCTTGCG
Statistics
Matches: 102, Mismatches: 26, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
19 5 0.05
20 51 0.50
21 40 0.39
22 6 0.06
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:36261 original size:20 final size:20
Alignment explanation
Indices: 36236--36308 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
36226 ATTTTCAACT
36236 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
36256 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
36277 ATCGCAACGCCAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
36297 ATCGCAACGCGA
1 ATCGCAACGCGA
36309 TTTTCAACTA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 26 0.65
21 14 0.35
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:36292 original size:93 final size:93
Alignment explanation
Indices: 36130--36313 Score: 307
Period size: 93 Copynumber: 2.0 Consensus size: 93
36120 AAATCGCAAC
*
36130 GCGATTTTCAACTATCGCAACGCCAAATGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCG
1 GCGATTTTCAACTATCGCAACGCCAAATGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCC
36195 AAATGGAAAATCGCAAAGCGATTTTCTT
66 AAATGGAAAATCGCAAAGCGATTTTCTT
* * *
36223 GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACGC
1 GCGATTTTCAACTATCGCAACGCCAAATGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGC
*
36287 CAAATGGAAAATCGCAACGCGATTTTC
65 CAAATGGAAAATCGCAAAGCGATTTTC
36314 AACTATCGCA
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
93 84 0.99
94 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (93 bp):
GCGATTTTCAACTATCGCAACGCCAAATGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCC
AAATGGAAAATCGCAAAGCGATTTTCTT
Found at i:36337 original size:21 final size:21
Alignment explanation
Indices: 36231--36337 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 21
36221 TTGCGATTTT
36231 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
36252 GAA-AATCGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
36272 CAACTATCGCAACGCCAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
36293 GAA-AATCGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
36313 CAACTATCGCAACCCGAAATG
1 CAACTATCGCAACGCGAAATG
36334 CAAC
1 CAAC
36338 GCGAATTTGC
Statistics
Matches: 61, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
20 29 0.48
21 32 0.52
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.18
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:43043 original size:14 final size:14
Alignment explanation
Indices: 43024--43053 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43014 TTTAGATTTT
*
43024 TTAAAATTACATTA
1 TTAAAAATACATTA
43038 TTAAAAATACATTA
1 TTAAAAATACATTA
43052 TT
1 TT
43054 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:43177 original size:25 final size:26
Alignment explanation
Indices: 43138--43213 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 26
43128 TGATAGAGTT
*
43138 TATGG-TTTAAGGTTTAAGGTTTAGG
1 TATGGATTTAGGGTTTAAGGTTTAGG
* *
43163 TA-GGATTTAGGGTTTATGGTGTAGG
1 TATGGATTTAGGGTTTAAGGTTTAGG
* *
43188 TATTGGGTATTAGGATTTAAGGTTTA
1 TA-TGGAT-TTAGGGTTTAAGGTTTA
43214 AGTTATACAC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
24 2 0.05
25 21 0.52
27 3 0.08
28 14 0.35
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (26 bp):
TATGGATTTAGGGTTTAAGGTTTAGG
Found at i:44720 original size:11 final size:11
Alignment explanation
Indices: 44704--44739 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
44694 GCATGAATGG
44704 CATGATCGAGT
1 CATGATCGAGT
44715 CATGAT-G-G-
1 CATGATCGAGT
44723 CATGATCGAGT
1 CATGATCGAGT
44734 CATGAT
1 CATGAT
44740 GACATTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.27
9 2 0.09
10 2 0.09
11 12 0.55
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (11 bp):
CATGATCGAGT
Found at i:44724 original size:19 final size:19
Alignment explanation
Indices: 44695--44740 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
44685 TCTTGAATTG
44695 CATGAATGGCATGATCGAGT
1 CATG-ATGGCATGATCGAGT
44715 CATGATGGCATGATCGAGT
1 CATGATGGCATGATCGAGT
44734 CATGATG
1 CATGATG
44741 ACATTTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26
Consensus pattern (19 bp):
CATGATGGCATGATCGAGT
Found at i:49604 original size:127 final size:127
Alignment explanation
Indices: 49378--49784 Score: 690
Period size: 127 Copynumber: 3.2 Consensus size: 127
49368 GTACTATTCA
* *
49378 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
*
49443 TATTATGTCACTTATGTCCCCTGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
*
49505 CGTGAAGACGCGTTCCCGGGGACGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
* *
49570 TATTATGTCACTTATGTCCCCCAGGAACTATTCATATCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* ** *
49632 CATGAAGGTGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
*
49697 TATTATGTCACTTATGTCCCTCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
*
49759 CGTGAA-AGCGCGTTTCCGGGGGCGCG
1 CGTGAAGA-CGCGTTCCCGGGGGCGCG
49785 TTCCTGGGGA
Statistics
Matches: 260, Mismatches: 19, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
127 260 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (127 bp):
CGTGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
Found at i:50241 original size:34 final size:34
Alignment explanation
Indices: 50203--50303 Score: 157
Period size: 34 Copynumber: 3.0 Consensus size: 34
50193 GAATTTAATG
*
50203 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
* * *
50237 TTAAATTTCGAATAATATTATTTGTATTTTAATT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
*
50271 TTAAATTTCGAATGCTATAATTTGTATTTTAAA
1 TTAAATTTCGAATACTATAATTTGTATTTTAAA
50304 AACATTTATT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.51
Consensus pattern (34 bp):
TTAAATTTCGAATACTATAATTTGTATTTTAAAT
Found at i:50852 original size:21 final size:20
Alignment explanation
Indices: 50825--50894 Score: 104
Period size: 21 Copynumber: 3.4 Consensus size: 20
50815 GGTATAAAAC
*
50825 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
50845 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
50866 CCCTGCGGGCTAGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
50887 CCCTGCGG
1 -CCTGCGG
50895 AGATGACATA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
20 3 0.06
21 41 0.87
22 3 0.06
ACGTcount: A:0.20, C:0.26, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:50966 original size:42 final size:42
Alignment explanation
Indices: 50887--50971 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
50877 AGGAATGTAA
* * *
50887 CCCTGCGGAGATGACATATGAACTGGTGGGCTTGGCATATAC
1 CCCTGAGGAGATGACATATGAACTGGAGGGCTGGGCATATAC
* * * * *
50929 CCCTGAGGATATGGCATCTGAAGTGGAGGGCTGGGCATGTAC
1 CCCTGAGGAGATGACATATGAACTGGAGGGCTGGGCATATAC
50971 C
1 C
50972 ATTGTGGCAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.22
Consensus pattern (42 bp):
CCCTGAGGAGATGACATATGAACTGGAGGGCTGGGCATATAC
Found at i:52773 original size:32 final size:32
Alignment explanation
Indices: 52703--52784 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
52693 AAATTTAAAT
*
52703 AAATAATAATTATATAAATATTATTTTAATAA
1 AAATAATAATTATATAAATATTATTATAATAA
* *
52735 AAATAATATTTATATAATTA-TATTA-ATATAA
1 AAATAATAATTATATAAATATTATTATA-ATAA
* *
52766 AATATAATAACTATTTAAA
1 AA-ATAATAATTATATAAA
52785 AAAATAACTG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 1 0.02
31 10 0.24
32 30 0.73
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
AAATAATAATTATATAAATATTATTATAATAA
Found at i:53699 original size:12 final size:12
Alignment explanation
Indices: 53682--53774 Score: 59
Period size: 12 Copynumber: 7.9 Consensus size: 12
53672 TAGGTTCAAA
53682 TTCGAGTTTGAG
1 TTCGAGTTTGAG
*
53694 TTCGAGCTTGA-
1 TTCGAGTTTGAG
* * *
53705 ATCGAGCTCT-AA
1 TTCGAG-TTTGAG
53717 TTCGAGTTTGAG
1 TTCGAGTTTGAG
*
53729 TTCGAGCTTGA-
1 TTCGAGTTTGAG
* * *
53740 ATCGAGCTCT-AA
1 TTCGAG-TTTGAG
53752 TTCGAGTTTGAG
1 TTCGAGTTTGAG
*
53764 TTCGAGCTTGA
1 TTCGAGTTTGA
53775 ATCGAGCTCA
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
11 16 0.27
12 44 0.73
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (12 bp):
TTCGAGTTTGAG
Found at i:53711 original size:11 final size:11
Alignment explanation
Indices: 53695--53853 Score: 79
Period size: 11 Copynumber: 13.6 Consensus size: 11
53685 GAGTTTGAGT
53695 TCGAGCTTGAA
1 TCGAGCTTGAA
53706 TCGAGCTCT-AA
1 TCGAGCT-TGAA
* *
53717 TTCGAGTTTGAGT
1 -TCGAGCTTGA-A
53730 TCGAGCTTGAA
1 TCGAGCTTGAA
53741 TCGAGCTCT-AA
1 TCGAGCT-TGAA
* *
53752 TTCGAGTTTGAGT
1 -TCGAGCTTGA-A
53765 TCGAGCTTGAA
1 TCGAGCTTGAA
**
53776 TCGAGCTCAAAA
1 TCGAGCT-TGAA
*
53788 TCGAGCTTCAA
1 TCGAGCTTGAA
* * *
53799 TTGAGCTCGAGTC
1 TCGAGCTTGA--A
*
53812 TCGAGCTTCAA
1 TCGAGCTTGAA
* *
53823 TCGAGCTCGAGTC
1 TCGAGCTTGA--A
*
53836 TCGAGCTTTAA
1 TCGAGCTTGAA
53847 TCGAGCT
1 TCGAGCT
53854 CCTAAATTTT
Statistics
Matches: 109, Mismatches: 26, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
11 51 0.47
12 43 0.39
13 15 0.14
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:53726 original size:35 final size:35
Alignment explanation
Indices: 53680--53792 Score: 208
Period size: 35 Copynumber: 3.2 Consensus size: 35
53670 TGTAGGTTCA
53680 AATTCGAGTTTGAGTTCGAGCTTGAATCGAGCTCT
1 AATTCGAGTTTGAGTTCGAGCTTGAATCGAGCTCT
53715 AATTCGAGTTTGAGTTCGAGCTTGAATCGAGCTCT
1 AATTCGAGTTTGAGTTCGAGCTTGAATCGAGCTCT
*
53750 AATTCGAGTTTGAGTTCGAGCTTGAATCGAGCTCA
1 AATTCGAGTTTGAGTTCGAGCTTGAATCGAGCTCT
*
53785 AAATCGAG
1 AATTCGAG
53793 CTTCAATTGA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 76 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (35 bp):
AATTCGAGTTTGAGTTCGAGCTTGAATCGAGCTCT
Found at i:53790 original size:47 final size:47
Alignment explanation
Indices: 53739--53830 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 47
53729 TTCGAGCTTG
* * *
53739 AATCGAGC-TCTAATTCGAGTTTGAGT-TCGAGCTTGAATCGAGCTCAA
1 AATCGAGCTTC-AATT-GAGCTCGAGTCTCGAGCTTCAATCGAGCTCAA
53786 AATCGAGCTTCAATTGAGCTCGAGTCTCGAGCTTCAATCGAGCTC
1 AATCGAGCTTCAATTGAGCTCGAGTCTCGAGCTTCAATCGAGCTC
53831 GAGTCTCGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 8 0.20
47 30 0.75
48 2 0.05
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (47 bp):
AATCGAGCTTCAATTGAGCTCGAGTCTCGAGCTTCAATCGAGCTCAA
Found at i:53818 original size:24 final size:24
Alignment explanation
Indices: 53761--53854 Score: 120
Period size: 24 Copynumber: 4.0 Consensus size: 24
53751 ATTCGAGTTT
*
53761 GAGT-TCGAGCTTGAATCGAGCTC
1 GAGTCTCGAGCTTCAATCGAGCTC
*** *
53784 -AAAATCGAGCTTCAATTGAGCTC
1 GAGTCTCGAGCTTCAATCGAGCTC
53807 GAGTCTCGAGCTTCAATCGAGCTC
1 GAGTCTCGAGCTTCAATCGAGCTC
*
53831 GAGTCTCGAGCTTTAATCGAGCTC
1 GAGTCTCGAGCTTCAATCGAGCTC
53855 CTAAATTTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
22 1 0.02
23 17 0.28
24 42 0.70
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (24 bp):
GAGTCTCGAGCTTCAATCGAGCTC
Found at i:55283 original size:26 final size:26
Alignment explanation
Indices: 55247--55300 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
55237 CTTATTCCAG
* *
55247 TAGCTGGTTTGACCAATTGATTTGAT
1 TAGCTGGTTTGACAAATTAATTTGAT
* *
55273 TAGCTGTTTTGAGAAATTAATTTGAT
1 TAGCTGGTTTGACAAATTAATTTGAT
55299 TA
1 TA
55301 ATTGTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.44
Consensus pattern (26 bp):
TAGCTGGTTTGACAAATTAATTTGAT
Found at i:56378 original size:12 final size:12
Alignment explanation
Indices: 56362--56412 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
56352 CACATATGCG
* *
56362 TATACGTATATG
1 TATACATATATA
* *
56374 TATACGTATACA
1 TATACATATATA
56386 TATACATATATA
1 TATACATATATA
*
56398 TATACATATACA
1 TATACATATATA
56410 TAT
1 TAT
56413 TGTAATAACA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (12 bp):
TATACATATATA
Found at i:56395 original size:18 final size:18
Alignment explanation
Indices: 56353--56412 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
56343 ACTAGAGAGC
* *
56353 ACATATGCGTATACGTAT
1 ACATATACGTATACATAT
**
56371 ATGTATACGTATACATAT
1 ACATATACGTATACATAT
**
56389 ACATATATATATACATAT
1 ACATATACGTATACATAT
56407 ACATAT
1 ACATAT
56413 TGTAATAACA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (18 bp):
ACATATACGTATACATAT
Found at i:56400 original size:6 final size:6
Alignment explanation
Indices: 56374--56412 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
56364 TACGTATATG
* *
56374 TATACG TATACA TATACA TATATA TATACA TATACA TAT
1 TATACA TATACA TATACA TATACA TATACA TATACA TAT
56413 TGTAATAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (6 bp):
TATACA
Found at i:59693 original size:13 final size:13
Alignment explanation
Indices: 59675--59702 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
59665 ATCTTAAATC
59675 ATCAAACTGATTG
1 ATCAAACTGATTG
59688 ATCAAACTGATTG
1 ATCAAACTGATTG
59701 AT
1 AT
59703 ATAACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATCAAACTGATTG
Found at i:60442 original size:26 final size:27
Alignment explanation
Indices: 60408--60467 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
60398 TACTAGGTAT
*
60408 GGAATACAAAATAC-AAAATCATGTAA
1 GGAACACAAAATACAAAAATCATGTAA
60434 GGAACACAAAATACAAAAATCATGTAA
1 GGAACACAAAATACAAAAATCATGTAA
60461 GGAACAC
1 GGAACAC
60468 TCAACTTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 13 0.41
27 19 0.59
ACGTcount: A:0.57, C:0.15, G:0.13, T:0.15
Consensus pattern (27 bp):
GGAACACAAAATACAAAAATCATGTAA
Found at i:61665 original size:2 final size:2
Alignment explanation
Indices: 61658--61691 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
61648 AATTTGAAAC
61658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61692 CTTGCTGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.