Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020907.1 Corchorus olitorius cultivar O-4 contig20940, 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: 35465
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:798 original size:36 final size:36
Alignment explanation
Indices: 758--871 Score: 85
Period size: 36 Copynumber: 3.2 Consensus size: 36
748 GACCCATGGT
758 CCAAGATGTTAACAATACAAGCCCAAGCAAATAATG
1 CCAAGATGTTAACAATACAAGCCCAAGCAAATAATG
* ** ** *
794 CCAAGAAATGATTAGC-CCACTTG---AAGCACTATAA-G
1 CCAAG--ATG-TTAACAATACAAGCCCAAGCA-AATAATG
*
829 CCCAAGATGTTAACAATACAAACCCAAGCAAATAATG
1 -CCAAGATGTTAACAATACAAGCCCAAGCAAATAATG
866 CCAAGA
1 CCAAGA
872 AAAAATGATT
Statistics
Matches: 55, Mismatches: 13, Indels: 20
0.62 0.15 0.23
Matches are distributed among these distances:
33 4 0.07
34 5 0.09
35 6 0.11
36 24 0.44
37 6 0.11
38 6 0.11
39 4 0.07
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.17
Consensus pattern (36 bp):
CCAAGATGTTAACAATACAAGCCCAAGCAAATAATG
Found at i:917 original size:75 final size:72
Alignment explanation
Indices: 758--980 Score: 383
Period size: 72 Copynumber: 3.1 Consensus size: 72
748 GACCCATGGT
758 CCAAGATGTTAACAATACAAGCCCAAGCAAATAATGCCAAGAAATGATTAGCCCACTTGAAGCAC
1 CCAAGATGTTAACAATACAAGCCCAAGCAAATAATGCCAAGAAATGATTAGCCCACTTGAAGCAC
823 TATAAGC
66 TATAAGC
* *
830 CCAAGATGTTAACAATACAAACCCAAGCAAATAATGCCAAGAAAAAATGATTAGCCCACTTGAAA
1 CCAAGATGTTAACAATACAAGCCCAAGCAAATAATGCCAAG---AAATGATTAGCCCACTTGAAG
895 CACTATAAGC
63 CACTATAAGC
* *
905 CCAAGATGTTAACAATACAAGCCCGAGCAAATAATGCCAAGAAATGATCAGCCCACTTGAAGCAC
1 CCAAGATGTTAACAATACAAGCCCAAGCAAATAATGCCAAGAAATGATTAGCCCACTTGAAGCAC
970 TATAAGC
66 TATAAGC
977 CCAA
1 CCAA
981 ATGCAACAGG
Statistics
Matches: 142, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
72 73 0.51
75 69 0.49
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.17
Consensus pattern (72 bp):
CCAAGATGTTAACAATACAAGCCCAAGCAAATAATGCCAAGAAATGATTAGCCCACTTGAAGCAC
TATAAGC
Found at i:1066 original size:36 final size:38
Alignment explanation
Indices: 992--1072 Score: 141
Period size: 37 Copynumber: 2.2 Consensus size: 38
982 TGCAACAGGC
992 GAAAG-AGTTCCAAGCCAATTGGTTCGAAAATGGAAGA
1 GAAAGTAGTTCCAAGCCAATTGGTTCGAAAATGGAAGA
1029 GAAAGTAG-TCCAAGCCAATTGGTTCG-AAATGGAAGA
1 GAAAGTAGTTCCAAGCCAATTGGTTCGAAAATGGAAGA
1065 GAAAGTAG
1 GAAAGTAG
1073 CCTTATAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
36 18 0.42
37 23 0.53
38 2 0.05
ACGTcount: A:0.41, C:0.12, G:0.28, T:0.19
Consensus pattern (38 bp):
GAAAGTAGTTCCAAGCCAATTGGTTCGAAAATGGAAGA
Found at i:1479 original size:27 final size:27
Alignment explanation
Indices: 1441--1492 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1431 CAACTCTAAA
*
1441 AACTAAGAAAGACCTGTCTGAGGTCTG
1 AACTAAGAAAGACCAGTCTGAGGTCTG
*
1468 AACTGAAG-AAGACCAGTCTGTGGTC
1 AACT-AAGAAAGACCAGTCTGAGGTC
1493 GATTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (27 bp):
AACTAAGAAAGACCAGTCTGAGGTCTG
Found at i:1557 original size:33 final size:33
Alignment explanation
Indices: 1509--1757 Score: 224
Period size: 33 Copynumber: 7.5 Consensus size: 33
1499 AAAAACTAAG
* *
1509 AAAGACCTGTTTGAGGTCTAGAACTTGAAAGAT
1 AAAGACCTGTCTGAGGTCTGGAACTTGAAAGAT
* * * *
1542 AAAGTCCTGTCTGAGGTC--GAATTTAAAACTGAG
1 AAAGACCTGTCTGAGGTCTGGAACTTGAAA--GAT
* *
1575 GAACACCTGTCTGAGGTCTGGAAC-TGAAAGAT
1 AAAGACCTGTCTGAGGTCTGGAACTTGAAAGAT
* ** * * * *
1607 AAAAACCTGTCAAAGGTC-GAAAATTAAAACTGAG
1 AAAGACCTGTCTGAGGTCTGGAACTTGAAA--GAT
*
1641 AAAGACCTGTCTGAGGTCGGGAACTTGAAAGAT
1 AAAGACCTGTCTGAGGTCTGGAACTTGAAAGAT
* *
1674 AAAGACCTGTCTGAGGTC--GAAATT-AAAGCTGAG
1 AAAGACCTGTCTGAGGTCTGGAACTTGAAA---GAT
1707 AAAGACCTGTCTGAGGTCTGGAACTTGAAAGAT
1 AAAGACCTGTCTGAGGTCTGGAACTTGAAAGAT
1740 AAAGACCTGTCTGAGGTC
1 AAAGACCTGTCTGAGGTC
1758 GAATTAAAAA
Statistics
Matches: 172, Mismatches: 30, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
30 3 0.02
31 16 0.09
32 20 0.12
33 93 0.54
34 21 0.12
35 16 0.09
36 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.23
Consensus pattern (33 bp):
AAAGACCTGTCTGAGGTCTGGAACTTGAAAGAT
Found at i:1591 original size:66 final size:66
Alignment explanation
Indices: 1439--1772 Score: 439
Period size: 66 Copynumber: 5.1 Consensus size: 66
1429 GTCAACTCTA
* * * *
1439 AAAACTAAGAAAGACCTGTCTGAGGTCT-GAAC-TG-AAG---AAGACCAGTCTGTGGTCGATTT
1 AAAACTGAGAAAGACCTGTCTGAGGTCTGGAACTTGAAAGATAAAGACCTGTCTGAGGTCGAATT
1498 T
66 T
* * * *
1499 AAAAACTAAGAAAGACCTGTTTGAGGTCTAGAACTTGAAAGATAAAGTCCTGTCTGAGGTCGAAT
1 -AAAACTGAGAAAGACCTGTCTGAGGTCTGGAACTTGAAAGATAAAGACCTGTCTGAGGTCGAAT
1564 TT
65 TT
* * * ** *
1566 AAAACTGAGGAACACCTGTCTGAGGTCTGGAAC-TGAAAGATAAAAACCTGTCAAAGGTCGAAAA
1 AAAACTGAGAAAGACCTGTCTGAGGTCTGGAACTTGAAAGATAAAGACCTGTCTGAGGTCG-AAT
1630 TT
65 TT
* *
1632 AAAACTGAGAAAGACCTGTCTGAGGTCGGGAACTTGAAAGATAAAGACCTGTCTGAGGTCGAAAT
1 AAAACTGAGAAAGACCTGTCTGAGGTCTGGAACTTGAAAGATAAAGACCTGTCTGAGGTCGAATT
1697 T
66 T
*
1698 AAAGCTGAGAAAGACCTGTCTGAGGTCTGGAACTTGAAAGATAAAGACCTGTCTGAGGTCGAATT
1 AAAACTGAGAAAGACCTGTCTGAGGTCTGGAACTTGAAAGATAAAGACCTGTCTGAGGTCGAATT
*
1763 A
66 T
1764 AAAACTGAG
1 AAAACTGAG
1773 TAAGGATGAC
Statistics
Matches: 239, Mismatches: 26, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
61 27 0.11
62 4 0.02
63 2 0.01
64 3 0.01
65 23 0.10
66 137 0.57
67 43 0.18
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (66 bp):
AAAACTGAGAAAGACCTGTCTGAGGTCTGGAACTTGAAAGATAAAGACCTGTCTGAGGTCGAATT
T
Found at i:1824 original size:39 final size:39
Alignment explanation
Indices: 1777--2710 Score: 1125
Period size: 39 Copynumber: 23.9 Consensus size: 39
1767 ACTGAGTAAG
* ** *
1777 GATGACCTGTTTCCAGTCAACCTTGGA-AACTACTGAAAA
1 GATGGCCTGTTTCCAACCAA-CTTTGATAACTACTGAAAA
** ** * *
1816 GATTACCTGTTTCCAGTCAACTTT-ATTAAATGCTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGA-TAACTACTGAAAA
* *
1855 GATGGCCTGTTTCCAACCAACTTTGAAAACTATTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* * * * *
1894 GATGGTCTGTTTCTAACCAATTTTGAAAACTATTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* ** *
1933 GATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
*
1972 GATGGCCTGTTTCCAACCAACTTTGATAACTATTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* *
2011 GATGGCCTGTTTCCAACCAACTTTGATAAATGCTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* ** *
2050 GATGACCTGTTTCCAGTCAACTTTGATAACTATTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
*
2089 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* * ** *
2128 GATGACCTCTTTCCAGTCAACTTTGATAACTATTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
*
2167 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* ** * *
2206 GATGACCTGTTTCCAGTCAGCTTTGATAACTGCTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
*
2245 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* * ** * *
2284 GATGACTTGTTTCCAGTCAACTTTGATAACTATTGAAGA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
*
2323 GATGGCCTGTTTCCAACCAACTTTGATAACTATTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* * *
2362 GATGGCCTGTTACCAACCAGCTTTGATAACTGCTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* *
2401 GATGGCTTGTTTCCAACCAACTTTGATAACTGCTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
** ** * **
2440 GATGATCTGTTTCCAGTCAACTTTGATAACTATTGAAGC
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* *
2479 GATGGGCTGTTTCCAACCAACTTTGATAACTATTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* * *
2518 AATGACCTGTTTCCAACCAACTTTGATAACTGCTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* ** *
2557 GATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
*
2596 GATGGCCTGTTTCCAACCAACTTTGATAACTATTGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* * *
2635 GATGGCCTGTTTCCAACCAACTTTGATAAATGCCGAAAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
* * * ** *
2674 GATGACCTGGTTGCAGTCAACTTTGATAACTATTGAA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAA
2711 GAATTGAAAT
Statistics
Matches: 769, Mismatches: 123, Indels: 6
0.86 0.14 0.01
Matches are distributed among these distances:
37 1 0.00
38 3 0.00
39 764 0.99
40 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (39 bp):
GATGGCCTGTTTCCAACCAACTTTGATAACTACTGAAAA
Found at i:1864 original size:78 final size:78
Alignment explanation
Indices: 1777--2710 Score: 1269
Period size: 78 Copynumber: 12.0 Consensus size: 78
1767 ACTGAGTAAG
* ** * * *
1777 GATGACCTGTTTCCAGTCAACCTTGGA-AACTACTGAAAAGATTACCTGTTTCCAGTCAACTTT-
1 GATGGCCTGTTTCCAACCAA-CTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTG
* **
1840 ATTAAATGCTGAAAA
65 A-TAACTATTGAAAA
* ** ** * ** *
1855 GATGGCCTGTTTCCAACCAACTTTGAAAACTATTGAAAAGATGGTCTGTTTCTAACCAATTTTGA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
*
1920 AAACTATTGAAAA
66 TAACTATTGAAAA
* ** * **
1933 GATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAAGATGGCCTGTTTCCAACCAACTTTGA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
1998 TAACTATTGAAAA
66 TAACTATTGAAAA
*
2011 GATGGCCTGTTTCCAACCAACTTTGATAAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
2076 TAACTATTGAAAA
66 TAACTATTGAAAA
*
2089 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTCTTTCCAGTCAACTTTGA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
2154 TAACTATTGAAAA
66 TAACTATTGAAAA
*
2167 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAGCTTTGA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
**
2232 TAACTGCTGAAAA
66 TAACTATTGAAAA
*
2245 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACTTGTTTCCAGTCAACTTTGA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
*
2310 TAACTATTGAAGA
66 TAACTATTGAAAA
** * * ** *
2323 GATGGCCTGTTTCCAACCAACTTTGATAACTATTGAAAAGATGGCCTGTTACCAACCAGCTTTGA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
**
2388 TAACTGCTGAAAA
66 TAACTATTGAAAA
* *
2401 GATGGCTTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGATCTGTTTCCAGTCAACTTTGA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
**
2466 TAACTATTGAAGC
66 TAACTATTGAAAA
* ** * **
2479 GATGGGCTGTTTCCAACCAACTTTGATAACTATTGAAAAAATGACCTGTTTCCAACCAACTTTGA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
**
2544 TAACTGCTGAAAA
66 TAACTATTGAAAA
* ** * **
2557 GATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAAGATGGCCTGTTTCCAACCAACTTTGA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
2622 TAACTATTGAAAA
66 TAACTATTGAAAA
* * * *
2635 GATGGCCTGTTTCCAACCAACTTTGATAAATGCCGAAAAGATGACCTGGTTGCAGTCAACTTTGA
1 GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
2700 TAACTATTGAA
66 TAACTATTGAA
2711 GAATTGAAAT
Statistics
Matches: 754, Mismatches: 100, Indels: 4
0.88 0.12 0.00
Matches are distributed among these distances:
77 5 0.01
78 748 0.99
79 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (78 bp):
GATGGCCTGTTTCCAACCAACTTTGATAACTGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGA
TAACTATTGAAAA
Found at i:2829 original size:8 final size:7
Alignment explanation
Indices: 2818--3059 Score: 54
Period size: 8 Copynumber: 32.7 Consensus size: 7
2808 AATTGATGCC
2818 TTGAATGA
1 TTGAAT-A
*
2826 TTGAAAA
1 TTGAATA
*
2833 TTGAAGGA
1 TTGAA-TA
2841 TTGAAATA
1 TTG-AATA
2849 TTGAA-A
1 TTGAATA
*
2855 TTGAACCA
1 TTGAA-TA
*
2863 TTGAAGGA
1 TTGAA-TA
2871 TTGAAT-
1 TTGAATA
*
2877 TTGAAGAA
1 TTGAA-TA
2885 TTGAAATA
1 TTG-AATA
2893 TTGAA-A
1 TTGAATA
*
2899 TTGAAACA
1 TTG-AATA
*
2907 TTGAAGGA
1 TTGAA-TA
2915 TTGAAT-
1 TTGAATA
*
2921 TTGAAGAAA
1 TTG-A-ATA
*
2930 TTGAAAAA
1 TTG-AATA
2938 TTGAA-A
1 TTGAATA
*
2944 TTGAAGGA
1 TTGAA-TA
2952 TTGAAT-
1 TTGAATA
*
2958 TTGAAGAA
1 TTGAA-TA
2966 TTGAAATA
1 TTG-AATA
2974 TTGAA-A
1 TTGAATA
*
2980 TTGAAACA
1 TTG-AATA
*
2988 TTGAAGGA
1 TTGAA-TA
2996 TTGAAT-
1 TTGAATA
*
3002 TTGAAGAAA
1 TTG-A-ATA
*
3011 TTGAAAAA
1 TTG-AATA
3019 TTGAA-A
1 TTGAATA
*
3025 TTGAAGGA
1 TTGAA-TA
3033 TTGAAT-
1 TTGAATA
*
3039 TTGAAGAA
1 TTGAA-TA
3047 TTGAAATA
1 TTG-AATA
3055 TTGAA
1 TTGAA
3060 GAAAGACCAC
Statistics
Matches: 185, Mismatches: 20, Indels: 59
0.70 0.08 0.22
Matches are distributed among these distances:
6 47 0.25
7 28 0.15
8 92 0.50
9 18 0.10
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.31
Consensus pattern (7 bp):
TTGAATA
Found at i:2833 original size:56 final size:56
Alignment explanation
Indices: 2705--2838 Score: 180
Period size: 56 Copynumber: 2.4 Consensus size: 56
2695 TTTGATAACT
* * *
2705 ATTGAAGAATTGAAATTGAAGAAAGTCCACCCTAGATCATTGAAGTAAATTGATGC
1 ATTGAAGAATTGAAAATGAAGAAAGACCACACTAGATCATTGAAGTAAATTGATGC
* * *
2761 ATTGAAGAATTAAAAATGAAGAAAGACCACACTGGATCGTTGAAGTAAATTGATGC
1 ATTGAAGAATTGAAAATGAAGAAAGACCACACTAGATCATTGAAGTAAATTGATGC
*
2817 CTTGAATG-ATTGAAAATTGAAG
1 ATTGAA-GAATTGAAAA-TGAAG
2839 GATTGAAATA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
56 62 0.91
57 6 0.09
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (56 bp):
ATTGAAGAATTGAAAATGAAGAAAGACCACACTAGATCATTGAAGTAAATTGATGC
Found at i:2857 original size:14 final size:14
Alignment explanation
Indices: 2825--3053 Score: 99
Period size: 14 Copynumber: 16.1 Consensus size: 14
2815 GCCTTGAATG
2825 ATTGAAA-ATTGAA
1 ATTGAAATATTGAA
2838 GGATTGAAATATTGAA
1 --ATTGAAATATTGAA
**
2854 ATTGAACCATTGAA
1 ATTGAAATATTGAA
2868 GGATTG-AAT-TTGAAGA
1 --ATTGAAATATTG-A-A
2884 ATTGAAATATTGAA
1 ATTGAAATATTGAA
*
2898 ATTGAAACATTGAA
1 ATTGAAATATTGAA
2912 GGATTG-AAT-TTGAAGAA
1 --ATTGAAATATT---GAA
*
2929 ATTGAAAAATTGAA
1 ATTGAAATATTGAA
**
2943 ATTGAAGGATTGAA
1 ATTGAAATATTGAA
*
2957 TTTG--A-A--G-A
1 ATTGAAATATTGAA
2965 ATTGAAATATTGAA
1 ATTGAAATATTGAA
*
2979 ATTGAAACATTGAA
1 ATTGAAATATTGAA
2993 GGATTG-AAT-TTGAAGAA
1 --ATTGAAATATT---GAA
*
3010 ATTGAAAAATTGAA
1 ATTGAAATATTGAA
**
3024 ATTGAAGGATTGAA
1 ATTGAAATATTGAA
*
3038 TTTGAAGA-ATTGAA
1 ATTGAA-ATATTGAA
3052 AT
1 AT
3054 ATTGAAGAAA
Statistics
Matches: 166, Mismatches: 20, Indels: 57
0.68 0.08 0.23
Matches are distributed among these distances:
8 4 0.02
9 1 0.01
10 1 0.01
11 2 0.01
13 1 0.01
14 96 0.58
15 25 0.15
16 26 0.16
17 10 0.06
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.31
Consensus pattern (14 bp):
ATTGAAATATTGAA
Found at i:2858 original size:22 final size:22
Alignment explanation
Indices: 2825--3000 Score: 135
Period size: 22 Copynumber: 7.9 Consensus size: 22
2815 GCCTTGAATG
2825 ATTGAAAATTGAAGGATTGAAAT
1 ATTG-AAATTGAAGGATTGAAAT
** **
2848 ATTGAAATTGAACCATTGAAGG
1 ATTGAAATTGAAGGATTGAAAT
* *
2870 ATTGAATTTGAAGAATTGAAAT
1 ATTGAAATTGAAGGATTGAAAT
** **
2892 ATTGAAATTGAAACATTGAAGG
1 ATTGAAATTGAAGGATTGAAAT
* * *
2914 ATTGAATTTGAAGAAATTGAAAA
1 ATTGAAATTGAAG-GATTGAAAT
2937 ATTGAAATTGAAGGATTG-AAT
1 ATTGAAATTGAAGGATTGAAAT
**
2958 -TTGAAGAATTGAAATATTG-AA-
1 ATTG-A-AATTGAAGGATTGAAAT
2979 ATTGAAACATTGAAGGATTGAA
1 ATTG-AA-ATTGAAGGATTGAA
3001 TTTGAAGAAA
Statistics
Matches: 121, Mismatches: 26, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
20 3 0.02
21 4 0.03
22 91 0.75
23 23 0.19
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.31
Consensus pattern (22 bp):
ATTGAAATTGAAGGATTGAAAT
Found at i:2950 original size:81 final size:81
Alignment explanation
Indices: 2852--3059 Score: 398
Period size: 81 Copynumber: 2.5 Consensus size: 81
2842 TGAAATATTG
2852 AAATTGAACCATTGAAGGATTGAATTTGAAGAATTGAAATATTGAAATTGAAACATTGAAGGATT
1 AAATTGAA--ATTGAAGGATTGAATTTGAAGAATTGAAATATTGAAATTGAAACATTGAAGGATT
2917 GAATTTGAAGAAATTGAA
64 GAATTTGAAGAAATTGAA
2935 AAATTGAAATTGAAGGATTGAATTTGAAGAATTGAAATATTGAAATTGAAACATTGAAGGATTGA
1 AAATTGAAATTGAAGGATTGAATTTGAAGAATTGAAATATTGAAATTGAAACATTGAAGGATTGA
3000 ATTTGAAGAAATTGAA
66 ATTTGAAGAAATTGAA
3016 AAATTGAAATTGAAGGATTGAATTTGAAGAATTGAAATATTGAA
1 AAATTGAAATTGAAGGATTGAATTTGAAGAATTGAAATATTGAA
3060 GAAAGACCAC
Statistics
Matches: 125, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
81 117 0.94
83 8 0.06
ACGTcount: A:0.47, C:0.02, G:0.21, T:0.31
Consensus pattern (81 bp):
AAATTGAAATTGAAGGATTGAATTTGAAGAATTGAAATATTGAAATTGAAACATTGAAGGATTGA
ATTTGAAGAAATTGAA
Found at i:3120 original size:56 final size:57
Alignment explanation
Indices: 3039--3231 Score: 329
Period size: 56 Copynumber: 3.4 Consensus size: 57
3029 AGGATTGAAT
*
3039 TTGAAGAATTGAAATATTGAAGAAAGACCACACTGGATCATTGAAGTAAATTGATGCA
1 TTGAAGAATTGAAA-ATTGAAGAAAGACCACACTGGATCGTTGAAGTAAATTGATGCA
*
3097 TTGAAGAATTGAAAA-TGAAGAAAGACCACACTGGATCGTTGAAGTATATTGATGCA
1 TTGAAGAATTGAAAATTGAAGAAAGACCACACTGGATCGTTGAAGTAAATTGATGCA
3153 TTGAAGAATTGAAAA-TGAAGAAAGACCACACTGGATCGTTGAAGTAAATTGATGCA
1 TTGAAGAATTGAAAATTGAAGAAAGACCACACTGGATCGTTGAAGTAAATTGATGCA
3209 TTGAATG-ATTGAAAATTGAAGAA
1 TTGAA-GAATTGAAAATTGAAGAA
3232 TTGAAATATT
Statistics
Matches: 130, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
56 107 0.82
57 9 0.07
58 14 0.11
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.25
Consensus pattern (57 bp):
TTGAAGAATTGAAAATTGAAGAAAGACCACACTGGATCGTTGAAGTAAATTGATGCA
Found at i:3249 original size:22 final size:22
Alignment explanation
Indices: 3198--3332 Score: 128
Period size: 22 Copynumber: 6.1 Consensus size: 22
3188 TCGTTGAAGT
* *
3198 AAATTGATGCATTG-AATGATTG
1 AAATTGAAGAATTGAAAT-ATTG
3220 AAAATTGAAGAATTGAAATATTG
1 -AAATTGAAGAATTGAAATATTG
* **
3243 AAATTGAAGCATTGAAGGATTG
1 AAATTGAAGAATTGAAATATTG
* * *
3265 AATTTGAAAAATTGAAATATTT
1 AAATTGAAGAATTGAAATATTG
** **
3287 AAATTGAACCATTGAAGGATTG
1 AAATTGAAGAATTGAAATATTG
*
3309 AATTTGAAGAATTGAAATATTG
1 AAATTGAAGAATTGAAATATTG
3331 AA
1 AA
3333 GAAAGACCAC
Statistics
Matches: 89, Mismatches: 22, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
22 70 0.79
23 16 0.18
24 3 0.03
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.33
Consensus pattern (22 bp):
AAATTGAAGAATTGAAATATTG
Found at i:3291 original size:44 final size:44
Alignment explanation
Indices: 3197--3329 Score: 203
Period size: 44 Copynumber: 3.0 Consensus size: 44
3187 ATCGTTGAAG
* * *
3197 TAAATTGATGCATTGAATGATTGAAAATTGAAGAATTGAAATATT
1 TAAATTGAAGCATTGAAGGATTG-AATTTGAAGAATTGAAATATT
* *
3242 GAAATTGAAGCATTGAAGGATTGAATTTGAAAAATTGAAATATT
1 TAAATTGAAGCATTGAAGGATTGAATTTGAAGAATTGAAATATT
*
3286 TAAATTGAACCATTGAAGGATTGAATTTGAAGAATTGAAATATT
1 TAAATTGAAGCATTGAAGGATTGAATTTGAAGAATTGAAATATT
3330 GAAGAAAGAC
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 60 0.75
45 20 0.25
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (44 bp):
TAAATTGAAGCATTGAAGGATTGAATTTGAAGAATTGAAATATT
Found at i:4565 original size:20 final size:21
Alignment explanation
Indices: 4542--4581 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4532 TTTTGAGAAA
*
4542 AAAAAAC-ATTTTTTCTTTTG
1 AAAAAACAATTTCTTCTTTTG
*
4562 AAAAATCAATTTCTTCTTTT
1 AAAAAACAATTTCTTCTTTT
4582 TGGACAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (21 bp):
AAAAAACAATTTCTTCTTTTG
Found at i:4594 original size:21 final size:20
Alignment explanation
Indices: 4542--4595 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
4532 TTTTGAGAAA
* *
4542 AAAAAACATTTTTTCTTTTG
1 AAAAATCATTTCTTCTTTTG
4562 AAAAATCAATTTCTTCTTTTTG
1 AAAAATC-ATTTCTTC-TTTTG
* *
4584 GACAATCATTTC
1 AAAAATCATTTC
4596 ACCTTCAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 6 0.21
21 12 0.43
22 10 0.36
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (20 bp):
AAAAATCATTTCTTCTTTTG
Found at i:6087 original size:14 final size:14
Alignment explanation
Indices: 6068--6119 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
6058 AACCCTAACC
6068 TTTTTGAAAACTCA
1 TTTTTGAAAACTCA
*
6082 TTTTTGAAAAC-CT
1 TTTTTGAAAACTCA
6095 TTTCTTGAAAACAT-A
1 TTT-TTGAAAAC-TCA
6110 TTTTTGAAAA
1 TTTTTGAAAA
6120 ACCTCTTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 4 0.12
14 26 0.79
15 3 0.09
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (14 bp):
TTTTTGAAAACTCA
Found at i:6106 original size:28 final size:26
Alignment explanation
Indices: 6064--6119 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 26
6054 AAAAAACCCT
6064 AACCTTTTTGAAAAC-TCATTTTTGAA
1 AACCTTTTTGAAAACAT-ATTTTTGAA
6090 AACCTTTTCTTGAAAACATATTTTTGAA
1 AACC-TTT-TTGAAAACATATTTTTGAA
6118 AA
1 AA
6120 ACCTCTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 4 0.15
27 3 0.11
28 19 0.70
29 1 0.04
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (26 bp):
AACCTTTTTGAAAACATATTTTTGAA
Found at i:6579 original size:48 final size:48
Alignment explanation
Indices: 6498--6649 Score: 241
Period size: 48 Copynumber: 3.1 Consensus size: 48
6488 TTTGGGATTA
*
6498 TTATCTTTTTTTGTTCAAAACACGATTGCTTATTTAAAAGAATCTTGT
1 TTATCTTTTTTTTTTCAAAACACGATTGCTTATTTAAAAGAATCTTGT
* * * *
6546 TTATCTTTTTTTTTTCAAAACACAACTGATTATTCAAAAGAATCTTGT
1 TTATCTTTTTTTTTTCAAAACACGATTGCTTATTTAAAAGAATCTTGT
6594 TTATCTTTTTTTTTGTTCAAAACACGATTGCTTATTTAAAAGAATCTTGT
1 TTATC-TTTTTTTT-TTCAAAACACGATTGCTTATTTAAAAGAATCTTGT
6644 TTATCT
1 TTATCT
6650 CATTCAAACC
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
48 48 0.52
49 9 0.10
50 36 0.39
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.49
Consensus pattern (48 bp):
TTATCTTTTTTTTTTCAAAACACGATTGCTTATTTAAAAGAATCTTGT
Found at i:6629 original size:50 final size:50
Alignment explanation
Indices: 6503--6649 Score: 244
Period size: 50 Copynumber: 3.0 Consensus size: 50
6493 GATTATTATC
6503 TTTTTTTGTTCAAAACACGATTGCTTATTTAAAAGAATCTTGTTTATC-T
1 TTTTTTTGTTCAAAACACGATTGCTTATTTAAAAGAATCTTGTTTATCTT
* * * *
6552 TTTTTTT-TTCAAAACACAACTGATTATTCAAAAGAATCTTGTTTATCTT
1 TTTTTTTGTTCAAAACACGATTGCTTATTTAAAAGAATCTTGTTTATCTT
6601 TTTTTTTGTTCAAAACACGATTGCTTATTTAAAAGAATCTTGTTTATCT
1 TTTTTTTGTTCAAAACACGATTGCTTATTTAAAAGAATCTTGTTTATCT
6650 CATTCAAACC
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
48 36 0.41
49 15 0.17
50 37 0.42
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (50 bp):
TTTTTTTGTTCAAAACACGATTGCTTATTTAAAAGAATCTTGTTTATCTT
Found at i:8942 original size:35 final size:34
Alignment explanation
Indices: 8898--9019 Score: 129
Period size: 35 Copynumber: 3.4 Consensus size: 34
8888 GAACTGACGA
* *
8898 GAACATTCCCTAAATTGAAAACTAAAACCTGATGG
1 GAACTTTCCC-AATTTGAAAACTAAAACCTGATGG
* *
8933 GAACTTTCCCAATTTGAAAATTTGAAA-CTGGATGG
1 GAACTTTCCCAATTTGAAAA-CTAAAACCT-GATGG
* *
8968 GAACTTTCCCAATTTGAAAACTTAAAAACTTGGTGG
1 GAACTTTCCCAATTTGAAAAC-T-AAAACCTGATGG
9004 GAACTTTCCCCAATTT
1 GAACTTT-CCCAATTT
9020 TGACAATTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
34 11 0.15
35 39 0.53
36 14 0.19
37 9 0.12
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (34 bp):
GAACTTTCCCAATTTGAAAACTAAAACCTGATGG
Found at i:9056 original size:75 final size:69
Alignment explanation
Indices: 8898--9060 Score: 209
Period size: 75 Copynumber: 2.3 Consensus size: 69
8888 GAACTGACGA
*
8898 GAACATTCCCTAAATTGAAAACTAAAACCTGATGGGAACTTTCCCAATTTGAAAATTTGAAACTG
1 GAACATTCCC-AATTTGAAAACTAAAACCTGATGGGAACTTTCCCAATTTGAAAATTTGAAACTG
8963 GATGG
65 GATGG
* * * *
8968 GAACTTTCCCAATTTGAAAACTTAAAAACTTGGTGGGAACTTTCCCCAATTTTGACAATTTTGAA
1 GAACATTCCCAATTTGAAAAC-T-AAAACCTGATGGGAACTTT-CCCAA-TTTGA-AAATTTG-A
9033 AACTGGATGG
60 AACTGGATGG
*
9043 GAACATTCGCAATTTGAA
1 GAACATTCCCAATTTGAA
9061 GACTGGCTAA
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
69 10 0.12
70 10 0.12
71 17 0.21
72 5 0.06
73 5 0.06
74 6 0.08
75 27 0.34
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (69 bp):
GAACATTCCCAATTTGAAAACTAAAACCTGATGGGAACTTTCCCAATTTGAAAATTTGAAACTGG
ATGG
Found at i:9782 original size:21 final size:22
Alignment explanation
Indices: 9746--9797 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
9736 AGTTCTAAAT
*
9746 TTTAAAACTATAAA-TTAAATTA
1 TTTAAAA-TTTAAATTTAAATTA
9768 TTTAAAATTTAAATTTAAATTA
1 TTTAAAATTTAAATTTAAATTA
*
9790 -CTAAAATT
1 TTTAAAATT
9798 ACTATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAAAATTTAAATTTAAATTA
Found at i:15611 original size:27 final size:27
Alignment explanation
Indices: 15581--15656 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
15571 GTTAGGGTTA
15581 TCCAGGGGCATTTTGGTCATTTGCACG
1 TCCAGGGGCATTTTGGTCATTTGCACG
*
15608 TCCAGGGGCATTTTGGTCATTTGCTCG
1 TCCAGGGGCATTTTGGTCATTTGCACG
*
15635 TCCAGGGGCATTTTAGTCATTT
1 TCCAGGGGCATTTTGGTCATTT
15657 CAAGTACATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.37
Consensus pattern (27 bp):
TCCAGGGGCATTTTGGTCATTTGCACG
Found at i:16954 original size:14 final size:14
Alignment explanation
Indices: 16932--16965 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16922 CACAAAAAAA
* *
16932 ATCTCCCTACTCTC
1 ATCTTCCTACCCTC
16946 ATCTTCCTACCCTC
1 ATCTTCCTACCCTC
16960 ATCTTC
1 ATCTTC
16966 TCTCATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.47, G:0.00, T:0.38
Consensus pattern (14 bp):
ATCTTCCTACCCTC
Found at i:17005 original size:56 final size:56
Alignment explanation
Indices: 16923--17044 Score: 226
Period size: 56 Copynumber: 2.2 Consensus size: 56
16913 CAATCTTTAC
16923 ACAAAAAAAATCTCCCTACTCTCATCTTCCTACCCTCATCTTCTCTCATTCAACAA
1 ACAAAAAAAATCTCCCTACTCTCATCTTCCTACCCTCATCTTCTCTCATTCAACAA
*
16979 ACAAAAAAAATCTTCCTACTCTCATCTTCCTACCCTCATCTTCTCTCATTCAACAA
1 ACAAAAAAAATCTCCCTACTCTCATCTTCCTACCCTCATCTTCTCTCATTCAACAA
*
17035 ATAAAAAAAA
1 ACAAAAAAAA
17045 ATATTCTCTC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.37, C:0.34, G:0.00, T:0.30
Consensus pattern (56 bp):
ACAAAAAAAATCTCCCTACTCTCATCTTCCTACCCTCATCTTCTCTCATTCAACAA
Found at i:17007 original size:14 final size:14
Alignment explanation
Indices: 16988--17021 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
16978 AACAAAAAAA
*
16988 ATCTTCCTACTCTC
1 ATCTTCCTACCCTC
17002 ATCTTCCTACCCTC
1 ATCTTCCTACCCTC
17016 ATCTTC
1 ATCTTC
17022 TCTCATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.44, G:0.00, T:0.41
Consensus pattern (14 bp):
ATCTTCCTACCCTC
Found at i:17162 original size:75 final size:75
Alignment explanation
Indices: 16996--17218 Score: 357
Period size: 75 Copynumber: 3.0 Consensus size: 75
16986 AAATCTTCCT
16996 ACTCTCATCTTCCTACCCTCATCTTCTCTCATTCAACAAATAAAAAAAAATATTCTCTCTTGAGC
1 ACTCTCATCTTCCTACCCTCATCTTCTCTCATTCAACAAAT-AAAAAAAA-ATTCTCTCTTGAGC
* *
17061 TCTATTTAACAA
64 TCTCTTTAACAC
17073 ACTCTCATCTTCCTACCCTCATCTTCTCTCATTCAACAAATAAAAAAAAATTCTCTCTTGAGCTC
1 ACTCTCATCTTCCTACCCTCATCTTCTCTCATTCAACAAATAAAAAAAAATTCTCTCTTGAGCTC
*
17138 TCTTGAACAC
66 TCTTTAACAC
*
17148 ACTCTCATCTTCCTACCCTCATCTTCTCTCATTCAAC-----AAAAAAAATTGTCTCTTGAGCTC
1 ACTCTCATCTTCCTACCCTCATCTTCTCTCATTCAACAAATAAAAAAAAATTCTCTCTTGAGCTC
17208 TCTTTAACAC
66 TCTTTAACAC
17218 A
1 A
17219 TGATACACAC
Statistics
Matches: 141, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
70 32 0.23
75 60 0.43
76 8 0.06
77 41 0.29
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.35
Consensus pattern (75 bp):
ACTCTCATCTTCCTACCCTCATCTTCTCTCATTCAACAAATAAAAAAAAATTCTCTCTTGAGCTC
TCTTTAACAC
Found at i:22153 original size:15 final size:16
Alignment explanation
Indices: 22126--22167 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
22116 CAAGACATGT
* *
22126 TTTTCAAGAAAA-AGG
1 TTTTCAAAAAAATAGA
22141 TTTTCAAAAAAAATAGA
1 TTTTC-AAAAAAATAGA
22158 TTTTCAAAAA
1 TTTTCAAAAA
22168 GGATTTGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 5 0.22
16 11 0.48
17 7 0.30
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (16 bp):
TTTTCAAAAAAATAGA
Found at i:25120 original size:67 final size:67
Alignment explanation
Indices: 25020--25604 Score: 906
Period size: 67 Copynumber: 8.8 Consensus size: 67
25010 GAAGTACACT
* * *
25020 GGAAGACGGTTTGCTAGAAAAAATTTTCAAATGTTGATTGGAAGACAATCTTATTAAGGAGTACA
1 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACA
*
25085 CC
66 TC
* *
25087 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGACTGGAAGACAATCTCATTAAAGAATACA
1 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACA
*
25152 CC
66 TC
* *
25154 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTTATTAAGGAGTACA
1 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACA
*
25219 CC
66 TC
*
25221 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGACTGGAAGACAATCTCATTAAGGAATACA
1 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACA
25286 TC
66 TC
25288 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACA
1 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACA
25353 TC
66 TC
*
25355 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCAATAAGGAATACA
1 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACA
25420 TC
66 TC
*
25422 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCAATAAGGAATACA
1 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACA
25487 TC
66 TC
* * * ** * *
25489 GGAAGACAGTTTGCTAGAAGGAAGTTTCAAATGTTGATTCAAAAACAACCTCA--AAGGAATACA
1 GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACA
25552 TC
66 TC
* * * * * *
25554 GAAAGACGGTTTGTTAGAAAGGATTTTCAGAA-GATGATCGGAAGACGATCT
1 GGAAGACGGTTTGCTAGAAAGAATTTTCA-AATGTTGATTGGAAGACAATCT
25605 TGTCAAAGAA
Statistics
Matches: 482, Mismatches: 35, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
65 47 0.10
66 2 0.00
67 433 0.90
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27
Consensus pattern (67 bp):
GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACA
TC
Found at i:25689 original size:40 final size:39
Alignment explanation
Indices: 25630--25707 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
25620 CCAGAAAGTG
*
25630 GTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGACGATA
1 GTTTCTCAAAAAGTTTCAGAAGTTGATCGGAAGACGATA
*
25669 GTTTCTCGAAAAGGTTTCAGAAGTTGATCGGAAGACGAT
1 GTTTCTC-AAAAAGTTTCAGAAGTTGATCGGAAGACGAT
25708 CTTATTAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 7 0.19
40 29 0.81
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (39 bp):
GTTTCTCAAAAAGTTTCAGAAGTTGATCGGAAGACGATA
Found at i:26007 original size:51 final size:51
Alignment explanation
Indices: 25945--26326 Score: 590
Period size: 51 Copynumber: 7.5 Consensus size: 51
25935 TGATTTTGTC
*
25945 AAGATTAAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
* * *
25996 AAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGAAGGTCCTCTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
*
26047 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGTTCCTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
* * *
26098 AAGATTGAATTGGAAGATAGTTCAAAGGATAAGCGGAAGACGGTTCTCTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
* **
26149 AAGATTGAATTGGAAGACAGTTAAAAGGATAAGCGGAAGACTTTCCTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
26200 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
* * *
26251 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGAC-G-ACTCTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
* *
26300 AATATT-AGATTGGAAGACAATTCAAAG
1 AAGATTGA-ATTGGAAGACAGTTCAAAG
26327 AAGTTGATCC
Statistics
Matches: 304, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
48 1 0.00
49 28 0.09
50 1 0.00
51 274 0.90
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (51 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
Found at i:26357 original size:153 final size:153
Alignment explanation
Indices: 25945--26373 Score: 582
Period size: 153 Copynumber: 2.8 Consensus size: 153
25935 TGATTTTGTC
* * *
25945 AAGATTAAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGAATTGGA
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTACTCTTTAAGATTGAATTGGA
* *
26010 AGACAATTCAAAG-GATAAGCGGAAGAAGGTCCTCTTTAAGATTGAATTGGAAGACAGTTCAAAG
66 AGACAATTCAAAGAGATAAGCGGAAGACGATCCTC-TTAAGATTGAATTGGAAGACAGTTCAAAG
*
26074 GATAAGCGGAAGACGTTCCTTTTT
130 GATAAGCGGAAGACGGTCCTTTTT
* *
26098 AAGATTGAATTGGAAGATAGTTCAAAGGATAAGCGGAAGACGGTTCTCTTTAAGATTGAATTGGA
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTACTCTTTAAGATTGAATTGGA
* * ** *
26163 AGACAGTTAAAAG-GATAAGCGGAAGACTTTCCTTTTTAAGATTGAATTGGAAGACAGTTCAAAG
66 AGACAATTCAAAGAGATAAGCGGAAGACGATCC-TCTTAAGATTGAATTGGAAGACAGTTCAAAG
26227 GATAAGCGGAAGACGGTCCTTTTT
130 GATAAGCGGAAGACGGTCCTTTTT
* *
26251 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGAC-G-ACTCTTTAATATT-AGATTGG
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTACTCTTTAAGATTGA-ATTGG
* ** * *
26313 AAGACAATTCAAAGAAGTTGATCCGGAAGACGATACC-CTGAAGATGGAATTGGAAGACAGT
65 AAGACAATTCAAAG-AGAT-AAGCGGAAGACGAT-CCTCTTAAGATTGAATTGGAAGACAGT
26374 CTAAAGAAGT
Statistics
Matches: 245, Mismatches: 25, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
150 1 0.00
151 28 0.11
152 1 0.00
153 202 0.82
154 11 0.04
155 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (153 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTACTCTTTAAGATTGAATTGGA
AGACAATTCAAAGAGATAAGCGGAAGACGATCCTCTTAAGATTGAATTGGAAGACAGTTCAAAGG
ATAAGCGGAAGACGGTCCTTTTT
Found at i:26647 original size:27 final size:27
Alignment explanation
Indices: 26617--26692 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
26607 ATTAGGGTTA
*
26617 TCCAGGGGCATTTTGGTCATTTGCACG
1 TCCAGGGGCATTTTAGTCATTTGCACG
* *
26644 TCCAGGGGCATTTTTGTCATTTGCTCG
1 TCCAGGGGCATTTTAGTCATTTGCACG
26671 TCCAGGGGCATTTTAGTCATTT
1 TCCAGGGGCATTTTAGTCATTT
26693 CAAGTACATT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.38
Consensus pattern (27 bp):
TCCAGGGGCATTTTAGTCATTTGCACG
Found at i:27984 original size:14 final size:14
Alignment explanation
Indices: 27965--27995 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27955 CACAAAAAAA
*
27965 ATCTTCCTACTCTC
1 ATCTTCCTACCCTC
27979 ATCTTCCTACCCTC
1 ATCTTCCTACCCTC
27993 ATC
1 ATC
27996 CTTCTCATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.45, G:0.00, T:0.39
Consensus pattern (14 bp):
ATCTTCCTACCCTC
Found at i:30470 original size:75 final size:76
Alignment explanation
Indices: 30283--30496 Score: 361
Period size: 76 Copynumber: 2.9 Consensus size: 76
30273 AGTTACAACA
30283 CTTCCTACCCTCATCTTCTCTCATTCAACAAATAAAAAAAAAATT-TCTCTTGAGCTCTCTTTAA
1 CTTCCTACCCTCATCTTCTCTCATTCAACAAATAAAAAAAAAATTCTCTCTTGAGCTCTCTTTAA
*
30347 CACGCTCTCAT
66 CACACTCTCAT
*
30358 CTTCCTACCCTCATCTTCTCTCATTCAACAAATAAAAAAAAAATTCTCTCTTGAGCTCTCTTGAA
1 CTTCCTACCCTCATCTTCTCTCATTCAACAAATAAAAAAAAAATTCTCTCTTGAGCTCTCTTTAA
30423 CACACTCTCAT
66 CACACTCTCAT
30434 CTTCCTACCCTCATCTTCTCTCATTCAAC------AAAAAAAATTCTCTCTTGAGCTCTCTTTAA
1 CTTCCTACCCTCATCTTCTCTCATTCAACAAATAAAAAAAAAATTCTCTCTTGAGCTCTCTTTAA
30493 CACA
66 CACA
30497 TGATACACAC
Statistics
Matches: 135, Mismatches: 3, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
70 33 0.24
75 45 0.33
76 57 0.42
ACGTcount: A:0.30, C:0.32, G:0.04, T:0.34
Consensus pattern (76 bp):
CTTCCTACCCTCATCTTCTCTCATTCAACAAATAAAAAAAAAATTCTCTCTTGAGCTCTCTTTAA
CACACTCTCAT
Found at i:32979 original size:15 final size:15
Alignment explanation
Indices: 32944--32973 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32934 AGACGACACC
*
32944 ATTGGAGGTGCTGCT
1 ATTGGAGGTGGTGCT
32959 ATTGGAGGTGGTGCT
1 ATTGGAGGTGGTGCT
32974 GATGGAAGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.43, T:0.33
Consensus pattern (15 bp):
ATTGGAGGTGGTGCT
Done.