Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002980.1 Hibiscus syriacus cultivar Beakdansim tig00006162_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: 95223
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:7314 original size:15 final size:15
Alignment explanation
Indices: 7280--7314 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
7270 ATCCGACTGC
7280 TGGAGAAGGAGAAGG
1 TGGAGAAGGAGAAGG
* *
7295 AGGAGAAGGAGATGG
1 TGGAGAAGGAGAAGG
7310 TGGAG
1 TGGAG
7315 CAAATAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.54, T:0.09
Consensus pattern (15 bp):
TGGAGAAGGAGAAGG
Found at i:12653 original size:27 final size:27
Alignment explanation
Indices: 12619--12679 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
12609 CAGCTGAAAA
12619 GAGCTTGAGTGAGAGGATTATATAGAG
1 GAGCTTGAGTGAGAGGATTATATAGAG
12646 GAGCTTGAGTGAGAGGATTATATAGAG
1 GAGCTTGAGTGAGAGGATTATATAGAG
*
12673 GAACTTG
1 GAGCTTG
12680 GGAGCATTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.05, G:0.36, T:0.26
Consensus pattern (27 bp):
GAGCTTGAGTGAGAGGATTATATAGAG
Found at i:15680 original size:18 final size:18
Alignment explanation
Indices: 15653--15699 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
15643 CAGCCCTGTC
*
15653 ATAA-AAACATATGAACA
1 ATAATAAACATATCAACA
* *
15670 ATAATAAACATTTCAAGA
1 ATAATAAACATATCAACA
15688 ATAATAAA-ATAT
1 ATAATAAACATAT
15700 ACATAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.62, C:0.09, G:0.04, T:0.26
Consensus pattern (18 bp):
ATAATAAACATATCAACA
Found at i:16118 original size:115 final size:115
Alignment explanation
Indices: 15916--16262 Score: 633
Period size: 115 Copynumber: 3.0 Consensus size: 115
15906 TTCTAAAACT
15916 TCGTCATGATTAATTCGGATCGATTTGCG-TCGCATATTTAGTTTTGGTAGGTGAGTCTCTCAAC
1 TCGTCATGATTAATTCGGATCGATTTGCGAT-GCATATTTAGTTTTGGTAGGTGAGTCTCTCAAC
*
15980 TAGAATTTTTTGTATATACAATTACTCAAGCTCCAAACATATTTAAACATA
65 TAGAATTTTTTGTATATACAATTACTCAAGCTCCAGACATATTTAAACATA
16031 TCGTCATGATTAATTCGGATCGATTTGCGATGCATATTTAGTTTTGGTAGGTGAGTCTCTCAACT
1 TCGTCATGATTAATTCGGATCGATTTGCGATGCATATTTAGTTTTGGTAGGTGAGTCTCTCAACT
16096 AGAATTTTTTGTATATACAATTACTCAAGCTCCAGACATATTTAAACATA
66 AGAATTTTTTGTATATACAATTACTCAAGCTCCAGACATATTTAAACATA
** *
16146 TCGTCATGATTAATTCGGATCGATTTGCGACACATATTTAGTTTTGGTAGGTGAGTCTATCAACT
1 TCGTCATGATTAATTCGGATCGATTTGCGATGCATATTTAGTTTTGGTAGGTGAGTCTCTCAACT
*
16211 AGAATTTTTTGTATATACAATTATTCAAGCTCCAGACATATTTAAACATA
66 AGAATTTTTTGTATATACAATTACTCAAGCTCCAGACATATTTAAACATA
16261 TC
1 TC
16263 AAACTTCTAA
Statistics
Matches: 226, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
115 225 1.00
116 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (115 bp):
TCGTCATGATTAATTCGGATCGATTTGCGATGCATATTTAGTTTTGGTAGGTGAGTCTCTCAACT
AGAATTTTTTGTATATACAATTACTCAAGCTCCAGACATATTTAAACATA
Found at i:18739 original size:18 final size:18
Alignment explanation
Indices: 18716--18758 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
18706 TGTGTCGTAA
18716 AAACATATCAACAATAAT
1 AAACATATCAACAATAAT
* *
18734 AAACATTTCAAGAATAAT
1 AAACATATCAACAATAAT
18752 AAA-ATAT
1 AAACATAT
18759 ACATCAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (18 bp):
AAACATATCAACAATAAT
Found at i:19847 original size:37 final size:37
Alignment explanation
Indices: 19753--19857 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
19743 CATTTTCGTC
*
19753 CTACTAGGATTCAAACTCCTAAAAATAAGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
19790 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
19827 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
19858 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:20328 original size:63 final size:65
Alignment explanation
Indices: 20213--20353 Score: 173
Period size: 63 Copynumber: 2.2 Consensus size: 65
20203 TATTATATGG
* * *
20213 ATATTTTATTTATTTATTTTTATTATTCATGTTGTTATTATTATATGTATATATATATATATTAA
1 ATATTTTATTTATTTATTTTTACTATTCATGTTATTATTATTATATATATATATATATATATTAA
* *
20278 ATTATTTTCATTTATTT-TTTTTACTA-T-ATTTTATTATTA-TATATATATATATATATTTATT
1 A-TATTTT-ATTTATTTATTTTTACTATTCATGTTATTATTATTATATATATATATATATATATT
*
20339 TA
64 AA
*
20341 ATATTTTACTTAT
1 ATATTTTATTTAT
20354 AAGTCTAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
61 5 0.07
62 6 0.09
63 22 0.33
64 10 0.15
65 2 0.03
66 14 0.21
67 8 0.12
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (65 bp):
ATATTTTATTTATTTATTTTTACTATTCATGTTATTATTATTATATATATATATATATATATTAA
Found at i:20536 original size:11 final size:11
Alignment explanation
Indices: 20520--20546 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20510 TATATTTATA
20520 TTTTTTTTGTT
1 TTTTTTTTGTT
20531 TTTTTTTTGTT
1 TTTTTTTTGTT
20542 TTTTT
1 TTTTT
20547 ATTCATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:20750 original size:36 final size:38
Alignment explanation
Indices: 20701--20776 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
20691 ATTGGGAGGG
*
20701 TAGCTTTTCTA-TTT-TTAAGTA-TTTGGTATATATATA
1 TAGCTTTTCTATTTTATTAA-TACTTTGATATATATATA
20737 TAGCTTATT-TATTTTATTAATACTTTGATATATATATA
1 TAGCTT-TTCTATTTTATTAATACTTTGATATATATATA
20775 TA
1 TA
20777 TATTTATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 8 0.23
37 7 0.20
38 20 0.57
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (38 bp):
TAGCTTTTCTATTTTATTAATACTTTGATATATATATA
Found at i:25153 original size:183 final size:183
Alignment explanation
Indices: 24845--25381 Score: 995
Period size: 183 Copynumber: 2.9 Consensus size: 183
24835 ATTAAATCCG
24845 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
24910 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
24975 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
25028 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
25093 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
25158 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
*
25211 TAAAGCTGAGCTATTCCACTAAGACAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
25276 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
* *
25340 TTTATCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
25382 TAAACCTGAT
Statistics
Matches: 345, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
182 1 0.00
183 344 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:26603 original size:36 final size:36
Alignment explanation
Indices: 26563--26678 Score: 97
Period size: 36 Copynumber: 3.1 Consensus size: 36
26553 ATACTTTGTC
26563 TCACTTGAGAATGTTTTTCTCGAAAGAAGATTTATT
1 TCACTTGAGAATGTTTTTCTCGAAAGAAGATTTATT
** * ** * * *
26599 TCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTC
1 TCACTTGAGAATGTTTTTCTCGAAAGAAGATTTATT
* ** *
26635 TCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTATT
1 TCACTTGAGAATGTTTT-TCTCGAAAGAA-G-ATTTATT
26674 TCACT
1 TCACT
26679 CAAGGCTATT
Statistics
Matches: 57, Mismatches: 20, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
36 40 0.70
37 7 0.12
38 1 0.02
39 9 0.16
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (36 bp):
TCACTTGAGAATGTTTTTCTCGAAAGAAGATTTATT
Found at i:26614 original size:72 final size:76
Alignment explanation
Indices: 26522--26682 Score: 217
Period size: 72 Copynumber: 2.2 Consensus size: 76
26512 ATGCAGATGA
* * * *
26522 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGAATGTTTT-TCTC
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGAACGTTTTCACTC
26584 GAAAGAA-G-AT
65 GAAAGAAGGCAT
* *
26594 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCG
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGAACGTTTTCACTCG
26658 AAAGAAGGCAT
66 AAAGAAGGCAT
26669 TTATTTCACTCAAG
1 TTATTTCACTCAAG
26683 GCTATTTTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
71 1 0.01
72 49 0.63
73 11 0.14
74 1 0.01
75 16 0.21
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (76 bp):
TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGAACGTTTTCACTCG
AAAGAAGGCAT
Found at i:26701 original size:72 final size:71
Alignment explanation
Indices: 26540--26703 Score: 172
Period size: 72 Copynumber: 2.3 Consensus size: 71
26530 CTCAAATTTG
* * *
26540 TTTTTCTTAAAACATA-CTTTGTCTCACTTGAGAATGTTTTTCTCGAAAGAAGATTTATTTCACT
1 TTTTTCTT-AAACA-AGATTTGTCTCACTTGAGAACGTTTTACTCGAAAGAAGATTTATTTCACT
* *
26604 CAAGATTG
64 CAAGACTA
* *
26612 TTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTATTTCA
1 TTTTTCTT-AAACAAGATTTGTCTCACTTGAGAACGTTTT-ACTCGAAAGAA-G-ATTTATTTCA
*
26677 CTCAAGGCTA
62 CTCAAGACTA
*
26687 TTTTT-TT-AAGAAGATTT
1 TTTTTCTTAAACAAGATTT
26704 TATCTTCTTG
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
71 1 0.01
72 43 0.54
73 10 0.13
74 3 0.04
75 22 0.28
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (71 bp):
TTTTTCTTAAACAAGATTTGTCTCACTTGAGAACGTTTTACTCGAAAGAAGATTTATTTCACTCA
AGACTA
Found at i:26753 original size:39 final size:39
Alignment explanation
Indices: 26710--26862 Score: 110
Period size: 39 Copynumber: 3.6 Consensus size: 39
26700 ATTTTATCTT
*
26710 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * *
26749 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGACAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-C
* *
26801 C-TGAGATAGTTTCCCTCGAAATAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* *
26839 CTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCCCTCGAAACA
26863 TAAACATTGA
Statistics
Matches: 87, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
38 2 0.02
39 44 0.51
40 5 0.06
41 2 0.02
42 1 0.01
48 1 0.01
49 2 0.02
50 4 0.05
51 24 0.28
52 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:26874 original size:104 final size:103
Alignment explanation
Indices: 26765--27084 Score: 482
Period size: 106 Copynumber: 3.1 Consensus size: 103
26755 ACAGTTTCTC
*
26765 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAATAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAA-AGAAAAT
26830 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
26869 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTC-C-TGAGATAGTTTCCCTCGAAA-AGAAA
26934 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
63 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * * * *
26975 TTGAAAACATTTCCCTTGAAATGAATTATATCTCGCTTGAGATAGTTTCCCTTGAAACG--AATT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAAAGAAAATT
* ** *
27038 TTGTCTCCCTTGAGAAAGTTTCTCTCCAAACATAAACT
66 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
27076 TTGAAAACA
1 TTGAAAACA
27085 ATTTAACGAA
Statistics
Matches: 200, Mismatches: 14, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
101 47 0.23
103 1 0.00
104 53 0.26
105 1 0.00
106 98 0.49
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (103 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAAAGAAAATT
TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:27031 original size:36 final size:36
Alignment explanation
Indices: 26984--27059 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
26974 ATTGAAAACA
* * *
26984 TTTCCCTTGAAATGAATTATATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTATATCTCCCTTGAGAAAG
* *
27020 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGAAAG
1 TTTCCCTTGAAACGAATTATATCTCCCTTGAGAAAG
27056 TTTC
1 TTTC
27060 TCTCCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTATATCTCCCTTGAGAAAG
Found at i:27446 original size:105 final size:105
Alignment explanation
Indices: 27259--27889 Score: 860
Period size: 105 Copynumber: 6.0 Consensus size: 105
27249 ATATCGTGAC
* * * * * * * * *
27259 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGATGGTTATCTACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
27324 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
27365 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCACTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
27430 ATTTCAGAGCCAATTTCAACTTCAAAACGAAAGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
27470 ACTTCAGACAACGCAAGTTCAATTTCACGACGAAGGGACCGCTGCTTGTTAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
27535 ATCTCAGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
27575 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
27640 ATCTCAGACCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
27680 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGATCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
27741 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
27780 ACTCGAGACAACACAAGTTCAACTTCACAAC-ATAGGGACGGCTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGA-AGGGACCGCTGCTTGTCAAC-AACAACTTCC
** * * *
27844 CGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
27886 ACTC
1 ACTC
27890 AGAACAATGC
Statistics
Matches: 471, Mismatches: 47, Indels: 14
0.89 0.09 0.03
Matches are distributed among these distances:
99 1 0.00
100 78 0.17
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 299 0.63
106 80 0.17
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:31520 original size:23 final size:23
Alignment explanation
Indices: 31487--31533 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
31477 AAATTTATGG
31487 TGTTCACTTAACATGCACAAACA
1 TGTTCACTTAACATGCACAAACA
* *
31510 TGTTCATTTAACATTCACAAACA
1 TGTTCACTTAACATGCACAAACA
31533 T
1 T
31534 ATTTGTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (23 bp):
TGTTCACTTAACATGCACAAACA
Found at i:31542 original size:23 final size:23
Alignment explanation
Indices: 31489--31567 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
31479 ATTTATGGTG
* *
31489 TTCACTTAACATGCACAAACATG
1 TTCATTTAACATGCACAAACATA
*
31512 TTCATTTAACATTCACAAACATA
1 TTCATTTAACATGCACAAACATA
** ** *
31535 TTTGTTTAATGTTG-ACAAATATA
1 TTCATTTAA-CATGCACAAACATA
31558 TTCATTTAAC
1 TTCATTTAAC
31568 GATCGTTTAA
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (23 bp):
TTCATTTAACATGCACAAACATA
Found at i:31576 original size:34 final size:34
Alignment explanation
Indices: 31538--31621 Score: 141
Period size: 34 Copynumber: 2.4 Consensus size: 34
31528 AAACATATTT
31538 GTTTAATGTTGACAAATATATTCATTTAACGATC
1 GTTTAATGTTGACAAATATATTCATTTAACGATC
* *
31572 GTTTAATGTTCACAAATATGTTCATTTAACGATC
1 GTTTAATGTTGACAAATATATTCATTTAACGATC
31606 GTTTAATGTTCGACAA
1 GTTTAATGTT-GACAA
31622 CCAACGATCT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 42 0.91
35 4 0.09
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (34 bp):
GTTTAATGTTGACAAATATATTCATTTAACGATC
Found at i:36301 original size:149 final size:149
Alignment explanation
Indices: 36051--36365 Score: 576
Period size: 149 Copynumber: 2.1 Consensus size: 149
36041 TATAATTGCA
* *
36051 CCGAAGTACCGCATAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
36116 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
* *
36181 CACAGAATATATATATATC
131 CAAAGAATATACATATATC
*
36200 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
36265 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
36330 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
36349 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
36366 CCCTCGACTC
Statistics
Matches: 160, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 160 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:37854 original size:21 final size:21
Alignment explanation
Indices: 37830--37874 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
37820 TTTTGTTCGT
* *
37830 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
37851 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
37872 TTG
1 TTG
37875 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:41165 original size:23 final size:23
Alignment explanation
Indices: 41139--41183 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
41129 TACCACAGCT
*
41139 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
41162 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
41184 ATATAACAAT
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:41401 original size:149 final size:149
Alignment explanation
Indices: 41151--41465 Score: 562
Period size: 149 Copynumber: 2.1 Consensus size: 149
41141 TATAATTGCA
41151 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTA
41215 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* *
41280 CCACAA-AATATATATTTATC
130 CCA-AAGAATATACATATATC
*
41300 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
41365 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
41430 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
41449 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
41466 CCCTCGACTC
Statistics
Matches: 160, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
148 3 0.02
149 157 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:42954 original size:21 final size:21
Alignment explanation
Indices: 42930--42974 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42920 TTTTGTTCGT
* *
42930 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
42951 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
42972 TTG
1 TTG
42975 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:43769 original size:37 final size:37
Alignment explanation
Indices: 43728--43837 Score: 166
Period size: 37 Copynumber: 3.0 Consensus size: 37
43718 AAACAAACGT
* * *
43728 TAGAGTTTTAGTAGGATTCAAATTCCCAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
43765 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAAGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* *
43802 TAAAGTTTTACTATGATTCAAACTCCTAAAAATAGG
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGG
43838 TTCCACACGC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:44256 original size:14 final size:15
Alignment explanation
Indices: 44223--44261 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
44213 TACATTTACG
* *
44223 TTTTAATTATTATTA
1 TTTTATTTATTATAA
44238 TTTTATTTATT-TAA
1 TTTTATTTATTATAA
44252 TTTTATTTAT
1 TTTTATTTAT
44262 ACGCACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTTATTATAA
Found at i:44461 original size:29 final size:28
Alignment explanation
Indices: 44422--44518 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 28
44412 GTTTTATTAA
44422 TTTATATATATATTTACTATTTTTTATGTT
1 TTTAT-TATATATTTA-TATTTTTTATGTT
*
44452 TTTATTATATATATAT-TATTTTTACT-TT
1 TTTATTATATATTTATAT-TTTTTA-TGTT
*
44480 TTTATTAT-TATTT-TATTTATT-TG-T
1 TTTATTATATATTTATATTTTTTATGTT
44504 TTTATTTATATATTT
1 TTTA-TTATATATTT
44519 TTTCTTCTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
24 6 0.10
25 4 0.07
26 10 0.17
27 6 0.10
28 17 0.29
29 10 0.17
30 5 0.09
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (28 bp):
TTTATTATATATTTATATTTTTTATGTT
Found at i:44475 original size:20 final size:20
Alignment explanation
Indices: 44450--44493 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
44440 ATTTTTTATG
44450 TTTTTA-TTATATATATATTA
1 TTTTTACTTATATAT-TATTA
* *
44470 TTTTTACTTTTTTATTATTA
1 TTTTTACTTATATATTATTA
44490 TTTT
1 TTTT
44494 ATTTATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTACTTATATATTATTA
Found at i:44496 original size:28 final size:26
Alignment explanation
Indices: 44442--44550 Score: 78
Period size: 28 Copynumber: 3.9 Consensus size: 26
44432 TATTTACTAT
* *
44442 TTTTTATGTTTTTATTATATATATATTA
1 TTTTTAT-TTTTTATTAT-TTTTTATTA
44470 TTTTTACTTTTTTATTATTATTTTATTTA
1 TTTTTA-TTTTTTATTATT-TTTTA-TTA
* * *
44499 TTTGTT-TTATTTATATATTTTTTCTTC
1 TTT-TTATTTTTTAT-TATTTTTTATTA
44526 TTTTTCATTTTTT-TATATTTTTTAT
1 TTTTT-ATTTTTTAT-TATTTTTTAT
44551 ATTACTTACT
Statistics
Matches: 67, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
26 2 0.03
27 17 0.25
28 35 0.52
29 11 0.16
30 2 0.03
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTTTATTTTTTATTATTTTTTATTA
Found at i:53924 original size:23 final size:23
Alignment explanation
Indices: 53893--53969 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
53883 ATCTTTATCC
*
53893 TTGT-GCATG-TTTTTCTATATTT
1 TTGTGGCATGCTTTTT-TCTATTT
**
53915 TTGTGGCATGCTTTTTTTCTGCTT
1 TTGTGGCATGC-TTTTTTCTATTT
*
53939 TTGTGGCATGCTTTTTTCTATTC
1 TTGTGGCATGCTTTTTTCTATTT
53962 TTGTGGCA
1 TTGTGGCA
53970 CGTTCCATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
22 4 0.09
23 22 0.48
24 15 0.33
25 5 0.11
ACGTcount: A:0.09, C:0.14, G:0.19, T:0.57
Consensus pattern (23 bp):
TTGTGGCATGCTTTTTTCTATTT
Found at i:53952 original size:13 final size:13
Alignment explanation
Indices: 53913--53953 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
53903 TTTTCTATAT
53913 TTTTGTGGCATGC
1 TTTTGTGGCATGC
**
53926 TTTT-TTTC-TGC
1 TTTTGTGGCATGC
53937 TTTTGTGGCATGC
1 TTTTGTGGCATGC
53950 TTTT
1 TTTT
53954 TTCTATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 7 0.32
12 4 0.18
13 11 0.50
ACGTcount: A:0.05, C:0.15, G:0.22, T:0.59
Consensus pattern (13 bp):
TTTTGTGGCATGC
Found at i:55376 original size:183 final size:183
Alignment explanation
Indices: 54990--55376 Score: 627
Period size: 183 Copynumber: 2.1 Consensus size: 183
54980 ATTAAATTTT
* * *
54990 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGCCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
55055 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
* *
55120 TATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTTAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
55173 AAATATTAAATATATTATATATAACATATGGCCT-AAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGCCTCAA-CCCAAACCATTTAAAACCCAATTAATA
* * *
55237 ATTTAATATCTAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAATT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAA-TTATATAAAATT
55302 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
129 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTT-AATTAAA
* *
55357 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
55377 AATTAGAAAA
Statistics
Matches: 190, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
182 2 0.01
183 122 0.64
184 66 0.35
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGCCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
Found at i:58473 original size:20 final size:20
Alignment explanation
Indices: 58450--58489 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
58440 TTAAATATTA
58450 ATTTTTAATAATAAAAAAAT
1 ATTTTTAATAATAAAAAAAT
* *
58470 ATTTTTATTATTAAAAAAAT
1 ATTTTTAATAATAAAAAAAT
58490 TGTTATGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTTTAATAATAAAAAAAT
Found at i:65232 original size:21 final size:21
Alignment explanation
Indices: 65208--65251 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
65198 ATGACGTTGG
65208 TGAATTCTTATTCG-ATTTTTT
1 TGAATT-TTATTCGAATTTTTT
* *
65229 TGAATTTTTTTTGAATTTTTT
1 TGAATTTTATTCGAATTTTTT
65250 TG
1 TG
65252 TTATTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.66
Consensus pattern (21 bp):
TGAATTTTATTCGAATTTTTT
Found at i:65239 original size:11 final size:11
Alignment explanation
Indices: 65223--65250 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
65213 TCTTATTCGA
65223 TTTTTTTGAAT
1 TTTTTTTGAAT
65234 TTTTTTTGAAT
1 TTTTTTTGAAT
65245 TTTTTT
1 TTTTTT
65251 GTTATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:74980 original size:21 final size:21
Alignment explanation
Indices: 74954--74996 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
74944 ATTCTCATTC
*
74954 TTAATTAATGTAAAATTATAT
1 TTAATTAATATAAAATTATAT
*
74975 TTAATTAATATTAAATTATAT
1 TTAATTAATATAAAATTATAT
74996 T
1 T
74997 AGTTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TTAATTAATATAAAATTATAT
Found at i:84568 original size:15 final size:16
Alignment explanation
Indices: 84547--84585 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
84537 TTAAATTAAG
84547 ACTAAAATTTTAAATT
1 ACTAAAATTTTAAATT
*
84563 -CTAAAA-ATTAAATT
1 ACTAAAATTTTAAATT
84577 ACTAAAATT
1 ACTAAAATT
84586 AAATAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (16 bp):
ACTAAAATTTTAAATT
Found at i:84573 original size:14 final size:14
Alignment explanation
Indices: 84556--84589 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
84546 GACTAAAATT
84556 TTAAATT-CTAAAAA
1 TTAAATTACT-AAAA
84570 TTAAATTACTAAAA
1 TTAAATTACTAAAA
84584 TTAAAT
1 TTAAAT
84590 AAATTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAATTACTAAAA
Found at i:86061 original size:29 final size:30
Alignment explanation
Indices: 86027--86098 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
86017 CCCGAAAGAC
86027 CTATCCAGAGGTCACAAAG-ACCCCGACAA
1 CTATCCAGAGGTCACAAAGAACCCCGACAA
* * *
86056 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCCCGACAA
* *
86086 CTGTCCATAGGTC
1 CTATCCAGAGGTC
86099 CCGAATAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCCCGACAA
Found at i:86863 original size:20 final size:22
Alignment explanation
Indices: 86838--86895 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
86828 TTCCCCTTTA
86838 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
*
86858 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
86881 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
86896 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:87006 original size:64 final size:64
Alignment explanation
Indices: 86872--87023 Score: 170
Period size: 64 Copynumber: 2.4 Consensus size: 64
86862 CATCGATGCA
*
86872 TTCTTTAACATG-TGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTC
1 TTCTTTAA-ATGATGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTTC
* * * * * *
86936 AT-TTTAAATGGATGCATCGATGTACT-CCTTATGCATCGATACACCATTTGCATTCGATG-TTT
1 TTCTTTAAAT-GATGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGATGTTTT
86998 C
64 C
86999 TTCTTTAAA-GAGTGCATCGATGCAC
1 TTCTTTAAATGA-TGCATCGATGCAC
87024 ATTCAATGTG
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
62 4 0.05
63 25 0.34
64 45 0.61
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (64 bp):
TTCTTTAAATGATGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTTC
Found at i:90003 original size:30 final size:30
Alignment explanation
Indices: 89934--90006 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
89924 TATCTAGAAA
*
89934 GTCACAAAG-ACC-CCGACAACTATCCAGAG
1 GTCACAAAGAACCTCAG-CAACTATCCAGAG
* *
89963 GTCATAAAGAACCTCAGCAACTATCCATAG
1 GTCACAAAGAACCTCAGCAACTATCCAGAG
* *
89993 GTCCCGAAGAACCT
1 GTCACAAAGAACCT
90007 AGGTAAACTG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 8 0.22
30 26 0.72
31 2 0.06
ACGTcount: A:0.37, C:0.32, G:0.16, T:0.15
Consensus pattern (30 bp):
GTCACAAAGAACCTCAGCAACTATCCAGAG
Found at i:90760 original size:20 final size:22
Alignment explanation
Indices: 90735--90792 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
90725 TTCCCCTTGA
90735 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
*
90755 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
90778 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
90793 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:90889 original size:64 final size:63
Alignment explanation
Indices: 90780--90920 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
90770 TCTTTAACAT
* * *
90780 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACTACCCATGCATCAATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * *
90843 GATGCATCGATGCACT-CCTTATGCATCAATGCACCATTTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCAATACACAAATTACATTCGATGTTTCATCTTTAAAGA
*
90907 GTGTATCGATGCAC
1 GTGCATCGATGCAC
90921 ATTGAATGTG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 20 0.31
64 45 0.69
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCAATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Done.