Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003069.1 Hibiscus syriacus cultivar Beakdansim tig00006396_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: 90827
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1445 original size:20 final size:19
Alignment explanation
Indices: 1413--1456 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1403 TTGTTTGTAA
1413 ATTTTTTATTCTCATTAAT
1 ATTTTTTATTCTCATTAAT
*
1432 -TTTTTTATACTCTCGTTAAT
1 ATTTTTTAT--TCTCATTAAT
1452 ATTTT
1 ATTTT
1457 AACTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.38
20 9 0.43
21 4 0.19
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTTATTCTCATTAAT
Found at i:1506 original size:20 final size:20
Alignment explanation
Indices: 1481--1540 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
1471 TTTTTTAAAA
1481 TATAATATTAAAATATATTT
1 TATAATATTAAAATATATTT
* * *
1501 TATAATTTTAGATTATATTT
1 TATAATATTAAAATATATTT
*
1521 GAT-ATATTAATACATATATT
1 TATAATATTAA-A-ATATATT
1541 ATTTAAAGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 5 0.16
20 20 0.65
21 6 0.19
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (20 bp):
TATAATATTAAAATATATTT
Found at i:18079 original size:55 final size:55
Alignment explanation
Indices: 18035--18412 Score: 589
Period size: 55 Copynumber: 6.9 Consensus size: 55
18025 AGTTTTCTCC
* * *
18035 CTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCACTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
*
18090 CTATTCCTTCAGAGAGTATAGAACTTGAACAATCTTCA-ACAAACGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGCTCT
* * **
18145 CTATTCCTTCAAAGAGTATAGAACTCGAACAATCTTAAGCAAACGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
* *
18200 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCATCA-ACAAACGGGTTCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGCTCT
* * *
18255 CTATTCCTTAAGAGAGCATAGAACTCAAACAATCTTCATAAAACGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
*
18310 CTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
*
18365 CTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
18413 TTGCTTCACT
Statistics
Matches: 295, Mismatches: 24, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
54 1 0.00
55 293 0.99
56 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (55 bp):
CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
Found at i:18429 original size:110 final size:110
Alignment explanation
Indices: 17966--18412 Score: 610
Period size: 110 Copynumber: 4.1 Consensus size: 110
17956 ATCTTCGAAT
* * * * * * * * * **
17966 AACGGGTCTGTTCCCTATTCCTTAAGGGATTATA-AGACTCGAACAATATTCAGCAAACGAGTTT
1 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCC
* * * *
18030 TCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAA
65 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
* *
18076 AACGGGTCCACTCTCTATTCCTTCAGAGAGTATAGAACTTGAACAATCTTCAACAAACGGGTCCG
1 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCG
* * **
18141 CTCTCTATTCCTTCAAAGAGTATAGAACTCGAACAATCTTAAGCA
66 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
* *
18186 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCATCAACAAACGGGTTCG
1 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCG
* * *
18251 CTCTCTATTCCTTAAGAGAGCATAGAACTCAAACAATCTTCATAA
66 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
*
18296 AACGGGTCCGCTCTCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCC
1 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCC
*
18360 GCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
65 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
18406 AACGGGT
1 AACGGGT
18413 TTGCTTCACT
Statistics
Matches: 296, Mismatches: 39, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
110 294 0.99
111 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (110 bp):
AACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCG
CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAA
Found at i:18472 original size:37 final size:37
Alignment explanation
Indices: 18412--18493 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
18402 ATAAAACGGG
* * *
18412 TTTGCTTCACTATTCTTCTGTGAAGGCTTATAGA-TGA
1 TTTGTTTCACTACTCTTCCGTGAAGGCTTA-AGATTGA
18449 TTTGTTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
1 TTTGTTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
*
18486 CTTGTTTC
1 TTTGTTTC
18494 GAAGGTCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 3 0.08
37 37 0.93
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (37 bp):
TTTGTTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
Found at i:19288 original size:23 final size:23
Alignment explanation
Indices: 19262--19306 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
19252 CACCACAGCT
*
19262 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
19285 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
19307 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:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:19449 original size:25 final size:25
Alignment explanation
Indices: 19421--19489 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
19411 TATATATATA
*
19421 TCCCGAATGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
19446 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
*
19471 TCCCGAAGGACCTCGTAGA
1 TCCCGAAGGACCGCGTAGA
19490 CCCTCTACCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:19991 original size:18 final size:19
Alignment explanation
Indices: 19954--19990 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19944 TTTTTTTATA
*
19954 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
19973 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
19991 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:21881 original size:29 final size:28
Alignment explanation
Indices: 21849--22032 Score: 106
Period size: 28 Copynumber: 7.1 Consensus size: 28
21839 TTGAACCCCC
*
21849 TTTTA-TTTTCTCTTTC-TTTTTTTCA-
1 TTTTATTTTTCTTTTTCATTTTTTTCAT
* *
21874 TCTT-TTTTCCTTTTT-A--TTTTTC-T
1 TTTTATTTTTCTTTTTCATTTTTTTCAT
21897 TTTTCA--TTT-TTTT-CAT-TTTT-CAT
1 TTTT-ATTTTTCTTTTTCATTTTTTTCAT
21920 TTTTCATTTTTCATTTTTCA--TTTTTCAT
1 TTTT-ATTTTTC-TTTTTCATTTTTTTCAT
21948 TTTTCATTTTTCATTTTTCA-TTTTTT-AT
1 TTTT-ATTTTTC-TTTTTCATTTTTTTCAT
21976 TTTTCATTTTTCATTTTTCA-TTTTTT-AT
1 TTTT-ATTTTTC-TTTTTCATTTTTTTCAT
*
22004 TTTT-TATTTT-TTATTCATTTTTTTCAT
1 TTTTAT-TTTTCTTTTTCATTTTTTTCAT
22031 TT
1 TT
22033 CTTTTTCAGG
Statistics
Matches: 135, Mismatches: 6, Indels: 34
0.77 0.03 0.19
Matches are distributed among these distances:
22 6 0.04
23 22 0.16
25 20 0.15
26 7 0.05
27 16 0.12
28 59 0.44
29 5 0.04
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTATTTTTCTTTTTCATTTTTTTCAT
Found at i:22018 original size:7 final size:7
Alignment explanation
Indices: 21877--22014 Score: 208
Period size: 7 Copynumber: 19.7 Consensus size: 7
21867 TTTTTCATCT
*
21877 TTTTTCC
1 TTTTTCA
21884 TTTTT-A
1 TTTTTCA
21890 TTTTTC-
1 TTTTTCA
21896 TTTTTCA
1 TTTTTCA
21903 TTTTTTTCA
1 --TTTTTCA
21912 TTTTTCA
1 TTTTTCA
21919 TTTTTCA
1 TTTTTCA
21926 TTTTTCA
1 TTTTTCA
21933 TTTTTCA
1 TTTTTCA
21940 TTTTTCA
1 TTTTTCA
21947 TTTTTCA
1 TTTTTCA
21954 TTTTTCA
1 TTTTTCA
21961 TTTTTCA
1 TTTTTCA
*
21968 TTTTTTA
1 TTTTTCA
21975 TTTTTCA
1 TTTTTCA
21982 TTTTTCA
1 TTTTTCA
21989 TTTTTCA
1 TTTTTCA
*
21996 TTTTTTA
1 TTTTTCA
*
22003 TTTTTTA
1 TTTTTCA
22010 TTTTT
1 TTTTT
22015 TATTCATTTT
Statistics
Matches: 123, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
6 11 0.09
7 105 0.85
9 7 0.06
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:22027 original size:21 final size:20
Alignment explanation
Indices: 21884--22032 Score: 165
Period size: 21 Copynumber: 7.1 Consensus size: 20
21874 TCTTTTTTCC
*
21884 TTTTTATTTTTCTTTTTCATT
1 TTTTTATTTTTATTTTTCA-T
21905 TTTTTCATTTTTCATTTTTCAT
1 TTTTT-ATTTTT-ATTTTTCAT
*
21927 TTTTCATTTTTCATTTTTCAT
1 TTTTTATTTTT-ATTTTTCAT
*
21948 TTTTCATTTTTCATTTTTCAT
1 TTTTTATTTTT-ATTTTTCAT
21969 TTTTTATTTTTCATTTTTCAT
1 TTTTTATTTTT-ATTTTTCAT
* *
21990 TTTTCATTTTTTATTTTTTAT
1 TTTTTA-TTTTTATTTTTCAT
*
22011 TTTTTATTCATT-TTTTTCAT
1 TTTTTATT-TTTATTTTTCAT
22031 TT
1 TT
22033 CTTTTTCAGG
Statistics
Matches: 116, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
20 11 0.09
21 82 0.71
22 16 0.14
23 7 0.06
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTATTTTTATTTTTCAT
Found at i:37899 original size:18 final size:18
Alignment explanation
Indices: 37876--37918 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
37866 TTACACACAG
**
37876 AAAAAAGGGGAGGGATCA
1 AAAAAAGGAAAGGGATCA
*
37894 AAAAAAAGAAAGGGATCA
1 AAAAAAGGAAAGGGATCA
37912 AAAAAAG
1 AAAAAAG
37919 AAAACAGGGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.63, C:0.05, G:0.28, T:0.05
Consensus pattern (18 bp):
AAAAAAGGAAAGGGATCA
Found at i:37914 original size:17 final size:18
Alignment explanation
Indices: 37886--37921 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
37876 AAAAAAGGGG
37886 AGGGATCAAAAAAAAGAA
1 AGGGATCAAAAAAAAGAA
37904 AGGGATC-AAAAAAAGAA
1 AGGGATCAAAAAAAAGAA
37921 A
1 A
37922 ACAGGGCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.67, C:0.06, G:0.22, T:0.06
Consensus pattern (18 bp):
AGGGATCAAAAAAAAGAA
Found at i:40913 original size:44 final size:48
Alignment explanation
Indices: 40847--40943 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 48
40837 TTATTTTCGT
40847 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
* * *
40894 TTTTT-GAAT-AA-GCATGCGAATTAGATATTATGCGGTTAGGATTTC
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
40939 TTTTT
1 TTTTT
40944 ATGGATAACA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
44 27 0.59
45 10 0.22
46 4 0.09
47 5 0.11
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:50629 original size:27 final size:27
Alignment explanation
Indices: 50594--50691 Score: 78
Period size: 27 Copynumber: 3.6 Consensus size: 27
50584 GCTTGAAGAA
*
50594 GAAATAAAAGAGAAAAGAA-GAAAAAAT
1 GAAAAAAAAGAGAAAA-AACGAAAAAAT
50621 GAAAAAAAATGATGGAAAAAACGAAAAGAA-
1 GAAAAAAAA-GA--GAAAAAACGAAAA-AAT
* *
50651 -AAAAAAAAGAGAAAAAATG-GAAAAT
1 GAAAAAAAAGAGAAAAAACGAAAAAAT
*
50676 GGAAGAAAAAGAGAAA
1 -GAAAAAAAAGAGAAA
50692 TAAAAGGAGG
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
24 2 0.03
25 2 0.03
26 8 0.14
27 21 0.36
28 4 0.07
29 10 0.17
30 10 0.17
31 2 0.03
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.06
Consensus pattern (27 bp):
GAAAAAAAAGAGAAAAAACGAAAAAAT
Found at i:51884 original size:51 final size:51
Alignment explanation
Indices: 51823--52360 Score: 693
Period size: 51 Copynumber: 10.4 Consensus size: 51
51813 AGTGAAGCAA
51823 ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
1 ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
*
51874 ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAACGG
1 ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
51925 ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
1 ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
*
51976 ACAAGTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
1 ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
*
52027 ACAAGTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
1 ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
* *
52078 ACAAGTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGG
1 ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
* * * * * * * *
52129 ACAAGTTCGTTGAAGATCGAGTTCTATACTCCCTGAACGGATAGGGAGCGA
1 ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
** * *
52180 ACACGTTTGTTAAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGG
1 ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
* * * * *
52231 AC-CTGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGG
1 ACAAT-TTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGG
** * * * * *
52286 ACCCGTTTTATTGAAGATTATTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAG
1 A-CAATTTTGTTGAAG---ATT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGG
*
52342 ACACATTTT-ATGAAGATTG
1 ACA-ATTTTGTTGAAGATTG
52361 TTCGAGTCTT
Statistics
Matches: 439, Mismatches: 37, Indels: 22
0.88 0.07 0.04
Matches are distributed among these distances:
50 1 0.00
51 347 0.79
52 3 0.01
54 2 0.00
55 37 0.08
56 47 0.11
57 1 0.00
59 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (51 bp):
ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
Found at i:52395 original size:55 final size:54
Alignment explanation
Indices: 52198--52396 Score: 224
Period size: 55 Copynumber: 3.6 Consensus size: 54
52188 GTTAAAGATT
* * * * *
52198 GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCT-TTTATTGAAGATTATTC
*
52253 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTATTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGA-CC-TTTTATTGAAGATTATTC
* * *
52309 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-C-TTTTATTGAAGATTATTC
*
52364 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAG
52397 GCTCGTCATT
Statistics
Matches: 126, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.01
55 70 0.56
56 53 0.42
57 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (54 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCTTTTATTGAAGATTATTC
Found at i:52411 original size:55 final size:54
Alignment explanation
Indices: 51943--52413 Score: 223
Period size: 51 Copynumber: 8.9 Consensus size: 54
51933 GTTGAAGATT
* * * *
51943 GAGTCCTATACTCTCTGAATGAATAGGGAGC-GGACAAGTTTGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGG-CACGTTT-TTGAAGATTATTC
* * * *
51994 GAGTCCTATACTCTCTGAATGAATAGGGAGC-GGACAAGTTTGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGG-CACGTTT-TTGAAGATTATTC
* * * *
52045 GAGTCCTATACTCTCTGAATGAATAGGGAGC-GGACAAGTTTGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGG-CACGTTT-TTGAAGATTATTC
* * * *
52096 GAGTCCTATACTCTCTGAATGAATAGAGAGC-GGACAAGTTCGTTGAAG---A-TC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGG-CACGTT-TTTGAAGATTATTC
* * * *
52147 GAGT-TCTATACTCCCTGAACGG-ATAGGGAGC-GAACACGTTTGTT-AA-A-GATT-
1 GAGTCT-TATACTCTCTGAA-GGAATAGAGAGCAG-GCACGTTT-TTGAAGATTATTC
* * * *
52198 GAGTCCTATACTCTCTGAAAGAATAGGGAGC-GG-ACCTGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCA-C-GTTT-TTGAAGATTATTC
*
52253 GAGT-TCTATACTCTCTGAAGGAATAGAGAGC-GGACCCGTTTTATTGAAGATTATTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGG-CACG-TTT-TTGAAGATTATTC
* * * * *
52309 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCACGTTTT-TGAAGATTATTC
* * *
52364 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATTTGAAGAT
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAGGCACGT-TTTTGAAGAT
52414 GTTTCAAGTC
Statistics
Matches: 360, Mismatches: 34, Indels: 48
0.81 0.08 0.11
Matches are distributed among these distances:
49 1 0.00
50 5 0.01
51 213 0.59
52 4 0.01
53 1 0.00
54 4 0.01
55 82 0.23
56 48 0.13
57 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (54 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCACGTTTTTGAAGATTATTC
Found at i:52424 original size:55 final size:54
Alignment explanation
Indices: 52199--52424 Score: 185
Period size: 55 Copynumber: 4.1 Consensus size: 54
52189 TTAAAGATTG
* * * * *
52199 AGTCCTATACTCTCTGAAAGAATAGGGAGC-GG-ACCTGTTTATTGAAGATTTTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCA-C-GTTT-TTGAAGATTATTCA
*
52254 AGT-TCTATACTCTCTGAAGGAATAGAGAGC-GGACCCGTTTTATTGAAGATTATTCA
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCAGG-CACG-TTT-TTGAAGATTATTCA
* * * * *
52310 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCACGTTTT-TGAAGATTATTCA
* * *
52365 AGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATTTGAAGATGT-TTCA
1 AGTCTTATACTCT-CTGAAGGAATAGAGAGCAGGCACGT-TTTTGAAGAT-TATTCA
52420 AGTCT
1 AGTCT
52425 CATTTATCCT
Statistics
Matches: 142, Mismatches: 19, Indels: 20
0.78 0.10 0.11
Matches are distributed among these distances:
54 2 0.01
55 89 0.63
56 49 0.35
57 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (54 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCACGTTTTTGAAGATTATTCA
Found at i:52761 original size:18 final size:18
Alignment explanation
Indices: 52738--52780 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
52728 TTACACACAG
**
52738 AAAAAAGGGGAGGGATCA
1 AAAAAAGGAAAGGGATCA
*
52756 AAAAAAAGAAAGGGATCA
1 AAAAAAGGAAAGGGATCA
52774 AAAAAAG
1 AAAAAAG
52781 AAAACAGGGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.63, C:0.05, G:0.28, T:0.05
Consensus pattern (18 bp):
AAAAAAGGAAAGGGATCA
Found at i:52776 original size:17 final size:18
Alignment explanation
Indices: 52748--52783 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
52738 AAAAAAGGGG
52748 AGGGATCAAAAAAAAGAA
1 AGGGATCAAAAAAAAGAA
52766 AGGGATC-AAAAAAAGAA
1 AGGGATCAAAAAAAAGAA
52783 A
1 A
52784 ACAGGGCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.67, C:0.06, G:0.22, T:0.06
Consensus pattern (18 bp):
AGGGATCAAAAAAAAGAA
Found at i:61086 original size:19 final size:19
Alignment explanation
Indices: 61062--61102 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
61052 TTCATAGGTG
61062 GCTGATAATTTGAATAATT
1 GCTGATAATTTGAATAATT
61081 GCTGATAATTTGAATAATT
1 GCTGATAATTTGAATAATT
61100 GCT
1 GCT
61103 ACCGCCAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (19 bp):
GCTGATAATTTGAATAATT
Found at i:64654 original size:20 final size:20
Alignment explanation
Indices: 64629--64676 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
64619 GTCAGAGTGT
*
64629 GGCGGCGGACGGCTGACGGC
1 GGCGGCGGACGGCGGACGGC
* *
64649 GGCGGCAGACGGCGGGCGGC
1 GGCGGCGGACGGCGGACGGC
*
64669 GGCAGCGG
1 GGCGGCGG
64677 CCAGCGGGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.10, C:0.29, G:0.58, T:0.02
Consensus pattern (20 bp):
GGCGGCGGACGGCGGACGGC
Found at i:64666 original size:17 final size:16
Alignment explanation
Indices: 64646--64677 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
64636 GACGGCTGAC
64646 GGCGGCGGCAGACGGCG
1 GGCGGCGGCAG-CGGCG
64663 GGCGGCGGCAGCGGC
1 GGCGGCGGCAGCGGC
64678 CAGCGGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.31, G:0.59, T:0.00
Consensus pattern (16 bp):
GGCGGCGGCAGCGGCG
Found at i:75665 original size:14 final size:14
Alignment explanation
Indices: 75646--75703 Score: 80
Period size: 14 Copynumber: 4.1 Consensus size: 14
75636 TTCGATTATA
*
75646 CGTTCGTTTATGTT
1 CGTTCATTTATGTT
*
75660 CGTTCGTTTATGTT
1 CGTTCATTTATGTT
*
75674 CGTCCATTTATGTT
1 CGTTCATTTATGTT
*
75688 CATTCATTTATGTT
1 CGTTCATTTATGTT
75702 CG
1 CG
75704 AACAGAGGGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.53
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:77115 original size:20 final size:20
Alignment explanation
Indices: 77091--77177 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
77081 GAATATGTAA
77091 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
77111 GTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
77131 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
77151 GTCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
77171 ATCGCAA
1 ATCGCAA
77178 TGCAATTTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:77135 original size:40 final size:40
Alignment explanation
Indices: 77091--77177 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
77081 GAATATGTAA
*
77091 ATCGCAACGCGATTCTGACTGTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACTGTCGCAACGAGATGCTGACT
*
77131 ATCGCAACGCGATTCTGACTGTCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACTGTCGCAACGAGATGCTGACT
77171 ATCGCAA
1 ATCGCAA
77178 TGCAATTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
ATCGCAACGCGATTCTGACTGTCGCAACGAGATGCTGACT
Found at i:77384 original size:22 final size:22
Alignment explanation
Indices: 77359--77401 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
77349 GGTAACATCC
77359 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
77381 GTCCCCGTCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
77402 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.42, G:0.19, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:77824 original size:20 final size:20
Alignment explanation
Indices: 77799--77851 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
77789 CGATTTTAGT
77799 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
77819 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
77839 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
77852 TTTAAGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:79786 original size:20 final size:20
Alignment explanation
Indices: 79761--79809 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
79751 TAGTTTACTT
* *
79761 TCGCAACGCGAAAATGACTA
1 TCGCAACGAGAAAATGACAA
**
79781 TCGCAACGAGAATTTGACAA
1 TCGCAACGAGAAAATGACAA
79801 TCGCAACGA
1 TCGCAACGA
79810 AAGAATCGCA
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:0.39, C:0.24, G:0.20, T:0.16
Consensus pattern (20 bp):
TCGCAACGAGAAAATGACAA
Found at i:79893 original size:18 final size:19
Alignment explanation
Indices: 79851--79897 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
79841 GCGATTCTCT
79851 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
79871 CGTTGCGATAGTCA-TTCG
1 CGTTGCGATAGTCATTTCG
*
79889 TGTTGCGAT
1 CGTTGCGAT
79898 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:80477 original size:21 final size:20
Alignment explanation
Indices: 80383--80484 Score: 64
Period size: 21 Copynumber: 4.9 Consensus size: 20
80373 CCTGATTCAT
80383 CTGTCATCGTTCAAGAGG-C
1 CTGTCATCGTTCAAGAGGCC
**
80402 CTCCCCTATCGTTCAAGAGGCCC
1 CT-GTC-ATCGTTCAAGAGG-CC
* ** *
80425 CTATCATCCCTCAAGAGTCC
1 CTGTCATCGTTCAAGAGGCC
*
80445 CAT-TCCACCGTTCAAGAGGCC
1 C-TGT-CATCGTTCAAGAGGCC
*
80466 ACTGTCATCGTTGAAGAGG
1 -CTGTCATCGTTCAAGAGG
80485 TCTCTCCCAA
Statistics
Matches: 62, Mismatches: 13, Indels: 14
0.70 0.15 0.16
Matches are distributed among these distances:
19 2 0.03
20 5 0.08
21 49 0.79
22 3 0.05
23 3 0.05
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.24
Consensus pattern (20 bp):
CTGTCATCGTTCAAGAGGCC
Found at i:81930 original size:14 final size:14
Alignment explanation
Indices: 81896--81957 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
81886 TTGCTTGTTT
*
81896 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
81910 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
81924 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
81939 TATTGATGTGTAAA
1 AATTGATTTGTAAA
81953 TAATT
1 -AATT
81958 ATTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:82109 original size:20 final size:20
Alignment explanation
Indices: 82056--82109 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
82046 AGGTACACTT
* **
82056 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
82076 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
82096 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
82110 TCAATTCGCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:82181 original size:20 final size:20
Alignment explanation
Indices: 82152--82430 Score: 227
Period size: 20 Copynumber: 14.8 Consensus size: 20
82142 ACGATTTTCT
* * *
82152 CGTTGTGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
82172 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
82192 CGTTGCGATACTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
82212 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
** * *
82232 TATTGC-A-A-T---TTTCT
1 CGTTGCGATAGTCAAATTCG
*
82246 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
82265 CCGTTGCGATAGTCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
* *
82286 CGTTGCGATAGACAAATTTG
1 CGTTGCGATAGTCAAATTCG
* *
82306 AGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
82320 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
82340 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
82360 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
82374 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
82394 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
82414 CGTTGTGATATTCAAAT
1 CGTTGCGATAGTCAAAT
82431 GAATGTGTAA
Statistics
Matches: 207, Mismatches: 32, Indels: 40
0.74 0.11 0.14
Matches are distributed among these distances:
14 30 0.14
15 1 0.00
16 3 0.01
17 2 0.01
18 2 0.01
19 2 0.01
20 165 0.80
21 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:82245 original size:94 final size:94
Alignment explanation
Indices: 82112--82314 Score: 291
Period size: 94 Copynumber: 2.2 Consensus size: 94
82102 CGCGAAAGTC
* * *
82112 AATTCGCGTTGCGATAGTCTAATACGCTTTACGATTTTCTCGTTGTGATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATACGCTTTACAATTTTCTCGTTGCGATAGTCAAATACCCGTTG
*
82177 CGATAATCAAATTCGCGTTGCGATACTCA
66 CGATAATCAAATTCGCGTTGCGATACACA
* * *
82206 AATTCGCGTTGCGATAGTCAAATTCG-TATTGCAATTTTCTCGTTGCGATAGTCAAATAGCCGTT
1 AATTCGCGTTGCGATAGTCAAATACGCT-TTACAATTTTCTCGTTGCGATAGTCAAATACCCGTT
* *
82270 GCGATAGTCAAATTCGCGTTGCGATAGACA
65 GCGATAATCAAATTCGCGTTGCGATACACA
* *
82300 AATTTGAGTTGCGAT
1 AATTCGCGTTGCGAT
82315 TTTTGCGTTG
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
93 1 0.01
94 96 0.99
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (94 bp):
AATTCGCGTTGCGATAGTCAAATACGCTTTACAATTTTCTCGTTGCGATAGTCAAATACCCGTTG
CGATAATCAAATTCGCGTTGCGATACACA
Found at i:82255 original size:74 final size:74
Alignment explanation
Indices: 82172--82368 Score: 274
Period size: 74 Copynumber: 2.7 Consensus size: 74
82162 GTCAAATACC
* * *
82172 CGTTGCGATAATCAAATTCGCGTTGCGATACTCAAATTCGCGTTGCGATAGTCAAATTCGTA-TT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCG-AGTT
82236 GCAATTTTCT-
65 GCAATTTT-TG
* *
82246 CGTTGCGATAGTCAAA-TAGCCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTTGAGTT
1 CGTTGCGATAGTCAAATTCG-CGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGAGTT
*
82310 GCGATTTTTG
65 GCAATTTTTG
* *
82320 CGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
82369 TTTTGAGTTG
Statistics
Matches: 110, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
73 4 0.04
74 104 0.95
75 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (74 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGAGTTG
CAATTTTTG
Found at i:82324 original size:54 final size:54
Alignment explanation
Indices: 82266--82418 Score: 234
Period size: 54 Copynumber: 2.8 Consensus size: 54
82256 GTCAAATAGC
* *
82266 CGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTTGAGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGAGTTGCGATTTTTG
* * *
82320 CGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGAGTTGCGATTTTTG
* * *
82374 AGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGAGTTG
82419 TGATATTCAA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 90 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.35
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGAGTTGCGATTTTTG
Found at i:82397 original size:74 final size:72
Alignment explanation
Indices: 82103--82430 Score: 231
Period size: 74 Copynumber: 4.4 Consensus size: 72
82093 AAATCGCAAC
* * * * * ** *
82103 GCGAAAGTCAATTCGCGTTGCGATAGTCTAATACGCTTTACGAT-TTTCTCGTTGTGATAGTCAA
1 GCGATAGTCAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATATTT-GAGTTGCGATA-TCAA
* *
82167 ATACCCGTT
64 ATTCGCGTT
* * * ** *
82176 GCGATAATCAAATTCGCGTTGCGATACTCAAATTCGCGTTGCGATAGTCAAATT-CG-TATTGCA
1 GCGATAGTC-AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATATTTGAGTTGCGATA-T-CA
* *
82239 ATTTTCTCGTT
63 A-ATTCGCGTT
* *
82250 GCGATAGTCAAATAGCCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTTGAGTTGCGAT
1 GCGATAGTCAATTCG-CGTTGCGATAGTCAAATTCGCGTTGCGAT------ATTTGAGTTGCGAT
*
82315 -T----TTTGCGTT
59 ATCAAATTCGCGTT
* *
82324 GCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTGCGATAATCAA
1 GCGATAGTCA-ATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATATTTGAGTTGCGAT-ATCAA
82389 ATTCGCGTT
64 ATTCGCGTT
* *
82398 GCGATAGTCAAATTCGCGTTGTGATATTCAAAT
1 GCGATAGTC-AATTCGCGTTGCGATAGTCAAAT
82431 GAATGTGTAA
Statistics
Matches: 199, Mismatches: 35, Indels: 41
0.72 0.13 0.15
Matches are distributed among these distances:
68 13 0.07
70 1 0.01
72 3 0.02
73 15 0.08
74 153 0.77
75 5 0.03
80 6 0.03
81 2 0.01
82 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (72 bp):
GCGATAGTCAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATATTTGAGTTGCGATATCAAAT
TCGCGTT
Found at i:82653 original size:140 final size:140
Alignment explanation
Indices: 82401--82670 Score: 522
Period size: 140 Copynumber: 1.9 Consensus size: 140
82391 TCGCGTTGCG
* *
82401 ATAGTCAAATTCGCGTTGTGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
82466 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
82531 AATACACATA
131 AATACACATA
82541 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
82606 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
82671 TACAACGTTT
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:82753 original size:18 final size:18
Alignment explanation
Indices: 82730--82764 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
82720 AAACCGGTTG
*
82730 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
82748 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
82765 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:85060 original size:24 final size:24
Alignment explanation
Indices: 85026--85079 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
85016 CTGAAACATC
*
85026 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
85050 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
85074 ATCAAA
1 ATCAAA
85080 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:85947 original size:20 final size:20
Alignment explanation
Indices: 85901--85971 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
85891 AAATTCAATG
* * *
85901 TTGCGACAGTCAAAATCGCG
1 TTGCGATAGTCATAATCGCA
*
85921 TTGCGATAGTCATAATAGCA
1 TTGCGATAGTCATAATCGCA
* *
85941 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
85961 TTGCGATAGTC
1 TTGCGATAGTC
85972 GAAAAATCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.02
20 39 0.95
21 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:87359 original size:40 final size:40
Alignment explanation
Indices: 87304--87386 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
87294 CAGTAACATA
87304 ATTCATGGATTTGTAGATGTAAACATTGTACATATGACCT
1 ATTCATGGATTTGTAGATGTAAACATTGTACATATGACCT
87344 ATTCATGGATTTGTAGATGTAAACATTGTACATATGACCT
1 ATTCATGGATTTGTAGATGTAAACATTGTACATATGACCT
87384 ATT
1 ATT
87387 AACAAATTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.39
Consensus pattern (40 bp):
ATTCATGGATTTGTAGATGTAAACATTGTACATATGACCT
Found at i:89694 original size:41 final size:42
Alignment explanation
Indices: 89647--89765 Score: 213
Period size: 41 Copynumber: 2.9 Consensus size: 42
89637 TTTCCCCGAA
89647 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATG-T
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
89688 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
* *
89730 TTCCCGTGTTTGTTTCTCGTAATTGGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
89766 TGTAATTCAT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
41 40 0.53
42 35 0.47
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
Found at i:90082 original size:28 final size:29
Alignment explanation
Indices: 90051--90106 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
90041 AATATTATAT
*
90051 AATAAAAATCTTTATATATTT-AATAATG
1 AATAAAAATATTTATATATTTAAATAATG
* *
90079 AATAATATTATTTATATATTTAAATAAT
1 AATAAAAATATTTATATATTTAAATAAT
90107 ATTTAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (29 bp):
AATAAAAATATTTATATATTTAAATAATG
Found at i:90518 original size:14 final size:14
Alignment explanation
Indices: 90499--90541 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
90489 CCAGAAATGT
90499 AATTCATTTTCCAG
1 AATTCATTTTCCAG
** *
90513 AATTCAAATTCCAAT
1 AATTCATTTTCC-AG
90528 AATTCATTTTCCAG
1 AATTCATTTTCCAG
90542 TTCCAGTAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (14 bp):
AATTCATTTTCCAG
Found at i:90522 original size:20 final size:20
Alignment explanation
Indices: 90485--90523 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
90475 CCGGAAAACG
**
90485 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
90505 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
90524 CAATAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:90539 original size:15 final size:15
Alignment explanation
Indices: 90498--90540 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
90488 TCCAGAAATG
90498 TAATTCATTTTCC-A
1 TAATTCATTTTCCAA
* **
90512 GAATTCAAATTCCAA
1 TAATTCATTTTCCAA
90527 TAATTCATTTTCCA
1 TAATTCATTTTCCA
90541 GTTCCAGTAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (15 bp):
TAATTCATTTTCCAA
Done.