Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 44 of 173
Found at i:11989077 original size:41 final size:41
Alignment explanation
Indices: 11988988--11989081 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
11988978 GCTAGCTACA
*
11988988 AAACGCCGCTAATGCTCCGGTCTTTAGCGGCGTTTTCTAAT
1 AAACGCCGCTAATGCTCCGGTCTTTAGCGGCGTTTTCTAAG
** * *
11989029 ATGCGCCGCTAATGCTGCGGTTTTTAGCGGCGCTTTT-TAAG
1 AAACGCCGCTAATGCTCCGGTCTTTAGCGGCG-TTTTCTAAG
11989070 AAACGCCGCTAA
1 AAACGCCGCTAA
11989082 AGACCTAAGC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 41 0.91
42 4 0.09
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (41 bp):
AAACGCCGCTAATGCTCCGGTCTTTAGCGGCGTTTTCTAAG
Found at i:11989097 original size:41 final size:41
Alignment explanation
Indices: 11989052--11989359 Score: 336
Period size: 41 Copynumber: 7.5 Consensus size: 41
11989042 GCTGCGGTTT
* *
11989052 TTAGCGGCGCTTTTTAAGAAACGCCGCTAAAGACCTAAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTAAGCA
* * *
11989093 TTAGCGGCGC-TTGTTAAGAAATGCCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTTG-TAAAAAACGCCGCTAAAGACCTAAGCA
* *
11989134 TTAGCGGCGCTTGGTAAAAAATGCCGCTAAAAGACCGT-AGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCT-AAAGACC-TAAGCA
*
11989176 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTCAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTAAGCA
** * * * *
11989217 TTAGCAACGCTTTGTAAAGAACGCCGCGAAAGACATAAGTA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTAAGCA
* *
11989258 TTAGCGGCGCTTTGTAAAAAACGTCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTAAGCA
* * * * *
11989299 TTAGCGGTGCATAT-TAGAAAACGCCGCGAAAGA-CTGTAGCA
1 TTAGCGGCGC-TTTGTAAAAAACGCCGCTAAAGACCT-AAGCA
*
11989340 TTAGCGGCGATTATGTAAAA
1 TTAGCGGCGCTT-TGTAAAA
11989360 GCACCGCTAA
Statistics
Matches: 226, Mismatches: 32, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
40 6 0.03
41 174 0.77
42 45 0.20
43 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTAAGCA
Found at i:11989218 original size:124 final size:122
Alignment explanation
Indices: 11989052--11989358 Score: 350
Period size: 124 Copynumber: 2.5 Consensus size: 122
11989042 GCTGCGGTTT
* * *
11989052 TTAGCGGCGCTTTTTAAGAAACGCCGCTAAAGACCTAAGCATTAGCGGCGC-TTGTTAAGAAATG
1 TTAGCGGCGC-TTTTAAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTTGTAAAG-AACG
* * * *
11989116 CCGCTAAAGACCTGAGCATTAGCGGCGCTTGGTAAAAAATGCCGCTAAAAGACC-GTAGCA
64 CCGCGAAAGACATAAGCATTAGCGGCGCTTGGTAAAAAACGCCGCT-AAAGACCTG-AGCA
* **
11989176 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTCAGCATTAGCAACGCTTTGTAAAGAACGC
1 TTAGCGGCGCTTT-TAAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTTGTAAAGAACGC
* * *
11989241 CGCGAAAGACATAAGTATTAGCGGCGCTTTGTAAAAAACGTCGCTAAAGACCTGAGCA
65 CGCGAAAGACATAAGCATTAGCGGCGCTTGGTAAAAAACGCCGCTAAAGACCTGAGCA
* * * * * *
11989299 TTAGCGGTGCATATTAGAAAACGCCGCGAAAGA-CTGTAGCATTAGCGGCGATTATGTAAA
1 TTAGCGGCGC-TTTTAAAAAACGCCGCTAAAGACCT-AAGCATTAGCGGCGCTT-TGTAAA
11989359 AGCACCGCTA
Statistics
Matches: 156, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
122 2 0.01
123 53 0.34
124 94 0.60
125 7 0.04
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (122 bp):
TTAGCGGCGCTTTTAAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTTGTAAAGAACGCC
GCGAAAGACATAAGCATTAGCGGCGCTTGGTAAAAAACGCCGCTAAAGACCTGAGCA
Found at i:11989562 original size:41 final size:41
Alignment explanation
Indices: 11989473--11989563 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
11989463 TTACATATAT
11989473 CGCCGCTAATGCTCGTATCTTTGGCGGCGTTTTTCGTAAAG
1 CGCCGCTAATGCTCGTATCTTTGGCGGCGTTTTTCGTAAAG
* * * * *
11989514 CGTCGCTAATGCTCG-ATTTTTTGTGGCGTTTTTTGTCCAAA-
1 CGCCGCTAATGCTCGTATCTTTGGCGGCGTTTTTCGT--AAAG
11989555 CGCCGCTAA
1 CGCCGCTAA
11989564 AAGCGCCGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
40 17 0.40
41 22 0.52
42 3 0.07
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.36
Consensus pattern (41 bp):
CGCCGCTAATGCTCGTATCTTTGGCGGCGTTTTTCGTAAAG
Found at i:11989572 original size:12 final size:12
Alignment explanation
Indices: 11989555--11989579 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11989545 TTTGTCCAAA
11989555 CGCCGCTAAAAG
1 CGCCGCTAAAAG
11989567 CGCCGCTAAAAG
1 CGCCGCTAAAAG
11989579 C
1 C
11989580 CTGTTTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.24, T:0.08
Consensus pattern (12 bp):
CGCCGCTAAAAG
Found at i:11997990 original size:31 final size:32
Alignment explanation
Indices: 11997916--11997991 Score: 104
Period size: 31 Copynumber: 2.4 Consensus size: 32
11997906 GTAAAAGTTA
* *
11997916 ATTTCAAATTTTTAATATTATTTAATATTTTT
1 ATTTCAATTTTTTAATATTAATTAATATTTTT
11997948 ATTTCAATTTTTTAAT-TTAATTAATATTTTT
1 ATTTCAATTTTTTAATATTAATTAATATTTTT
11997979 -TTAT-AATTTTTTA
1 ATT-TCAATTTTTTA
11997992 TAACAGTCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 11 0.27
31 15 0.37
32 15 0.37
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (32 bp):
ATTTCAATTTTTTAATATTAATTAATATTTTT
Found at i:11999953 original size:59 final size:59
Alignment explanation
Indices: 11999791--11999965 Score: 255
Period size: 58 Copynumber: 3.0 Consensus size: 59
11999781 ATTGATTTAT
* * *
11999791 TTTTGAATATATTTGTACAAATTGTTTTTATATTGTTTCATTTAATAAAACAAAAGTTC
1 TTTTGAATATATTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
*
11999850 TTTTGAA-ATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
1 TTTTGAATATATTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
** * *
11999908 TTTTGAATATGCTTGTACAAATTATTTTT-TCATTGTTTCATTTAATAAATTAGGAGTT
1 TTTTGAATATATTTGTACAAATTATTTTTAT-ATTGTTTCATTTAATAAAATAGAAGTT
11999966 ATTTCGATTT
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
58 55 0.52
59 51 0.48
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (59 bp):
TTTTGAATATATTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
Found at i:12002257 original size:22 final size:22
Alignment explanation
Indices: 12002232--12002279 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
12002222 ATATTTCCTT
12002232 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCCAAAATTCTC
12002254 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCCAAAATTCTC
12002276 TCAA
1 TCAA
12002280 ATCCATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (22 bp):
TCAATTTCCTTCCAAAATTCTC
Found at i:12003467 original size:7 final size:7
Alignment explanation
Indices: 12003455--12003479 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12003445 AGTTGATTGA
12003455 TATTTAG
1 TATTTAG
12003462 TATTTAG
1 TATTTAG
12003469 TATTTAG
1 TATTTAG
12003476 TATT
1 TATT
12003480 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:12004631 original size:25 final size:25
Alignment explanation
Indices: 12004597--12004717 Score: 110
Period size: 25 Copynumber: 5.0 Consensus size: 25
12004587 TATTTTGAAG
12004597 TTTATTTGATGTAAAAAAATAGAAT
1 TTTATTTGATGTAAAAAAATAGAAT
12004622 TTTATTTGATGTAATAAAAATAGAAAT
1 TTTATTTGATGTAA-AAAAATAG-AAT
* ** *
12004649 TTT-TTTGA-GT---TATTTTG-AT
1 TTTATTTGATGTAAAAAAATAGAAT
* * *
12004668 ATTATTTGATGTAATAAAATAGAAG
1 TTTATTTGATGTAAAAAAATAGAAT
*
12004693 TTTATTTGATGTAATAAAATAGAAT
1 TTTATTTGATGTAAAAAAATAGAAT
12004718 ATTTTGAATA
Statistics
Matches: 76, Mismatches: 12, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
19 4 0.05
20 5 0.07
21 5 0.07
24 3 0.04
25 40 0.53
26 13 0.17
27 6 0.08
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (25 bp):
TTTATTTGATGTAAAAAAATAGAAT
Found at i:12004676 original size:71 final size:67
Alignment explanation
Indices: 12004576--12004743 Score: 239
Period size: 71 Copynumber: 2.4 Consensus size: 67
12004566 TATTTGTACA
*
12004576 AATATTTTGAGTATTTTGA-AGTTTATTTGATGTAAAAAAATAGAATTTTATTTGATGTAATAAA
1 AATATTTTGAGTATTTTGATA--TTATTTGATGTAAAAAAATAGAAGTTTATTTGATGTAAT-AA
12004640 AATAG
63 AATAG
* *
12004645 AAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAA
1 -AA-TATTTTGAG-TATTTTGATATTATTTGATGTAAAAAAATAGAAGTTTATTTGATGTAATAA
12004710 AATAG
63 AATAG
*
12004715 AATATTTTGAATATTTTGATATTATTTGA
1 AATATTTTGAGTATTTTGATATTATTTGA
12004744 GAATTCTACT
Statistics
Matches: 90, Mismatches: 5, Indels: 9
0.87 0.05 0.09
Matches are distributed among these distances:
67 18 0.20
68 7 0.08
69 2 0.02
70 9 0.10
71 45 0.50
72 8 0.09
73 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (67 bp):
AATATTTTGAGTATTTTGATATTATTTGATGTAAAAAAATAGAAGTTTATTTGATGTAATAAAAT
AG
Found at i:12004790 original size:23 final size:23
Alignment explanation
Indices: 12004764--12005443 Score: 616
Period size: 23 Copynumber: 28.0 Consensus size: 23
12004754 AACCTAATTA
*
12004764 AATTGAAA-AGAAAACCCTAACGT
1 AATT-AAATAGAAAACCCTAACCT
*
12004787 AATTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
12004810 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
*
12004833 AATTAAAAAGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
****
12004856 AATTAAACCCTAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
12004879 AATTAAATTGAAAAGAAAACCCTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
* *
12004907 ACTTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
*
12004930 AATTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
**** *
12004953 AATTAAACCCTAAATCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
12004976 AATTAAATTGAAAAGAAAACCCTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
****
12005004 AATTAAACCCTAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
12005027 AATTAAATTGAAAAGAAAACCCTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
12005055 AATTAAATTGAAAAGAAAACCCTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
* *
12005083 AATTAAATTGAAAATCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
* *
12005106 AGTTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
12005129 AATTAAATTGAAAAGAAAACCCTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
12005157 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
**
12005180 AATTAAATTGAAAAGAAAACTTTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
*
12005208 AATTAAATTGAAAAACCCTAACCT
1 AATTAAATAG-AAAACCCTAACCT
*
12005232 AATTAAATTGAAAAACCCTAACCT
1 AATTAAATAG-AAAACCCTAACCT
*
12005256 AATTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
****
12005279 AATTAAACCCTAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
12005302 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
*
12005325 AATTAAATTGAAAAGAAAACCATAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
12005353 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
12005376 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
*
12005399 AATTAAAAAGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
*
12005422 AATTAAATTGAAAACCCTAACC
1 AATTAAATAGAAAACCCTAACC
12005444 CTAAACCCTT
Statistics
Matches: 565, Mismatches: 56, Indels: 72
0.82 0.08 0.10
Matches are distributed among these distances:
22 5 0.01
23 361 0.64
24 49 0.09
27 5 0.01
28 145 0.26
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (23 bp):
AATTAAATAGAAAACCCTAACCT
Found at i:12004827 original size:46 final size:46
Alignment explanation
Indices: 12004774--12005443 Score: 712
Period size: 51 Copynumber: 13.8 Consensus size: 46
12004764 AATTGAAAAG
*
12004774 AAAACCCTAACGTAATTAAATTGAAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
** ***
12004820 AAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTAAACCC
1 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
* * *
12004866 TAAACCCTAACCTAATTAAATTGAAAAGAAAACCCTAACCTACTTAAATTG
1 AAAACCCTAACCTAATTAAATT-----GAAAACCCTAACCTAATTAAATTA
***
12004917 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAACCC
1 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
* * ***
12004963 TAAATCCTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAATTAAACCC
1 AAAACCCTAACCTAATTAAATT-----GAAAACCCTAACCTAATTAAATTA
*
12005014 TAAACCCTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAATTAAATTGAAAA
1 AAAACCCTAACCTAATTAAATT-----GAAAACCCTAACCTAATTAAATT----A
* * *
12005069 GAAAACCCTAACCTAATTAAATTGAAAATCCTAACCTAGTTAAATTG
1 -AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
12005116 AAAACCCTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAATT-----GAAAACCCTAACCTAATTAAATTA
**
12005167 AAAACCCTAACCTAATTAAATTGAAAAGAAAACTTTAACCTAATTAAATTGA
1 AAAACCCTAACCTAATTAAATT-----GAAAACCCTAACCTAATTAAATT-A
*
12005219 AAAACCCTAACCTAATTAAATTGAAAAACCCTAACCTAATTAAATTG
1 AAAACCCTAACCTAATTAAATTG-AAAACCCTAACCTAATTAAATTA
****
12005266 AAAACCCTAACCTAATTAAACCCTAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
*
12005312 AAAACCCTAACCTAATTAAATTGAAAAGAAAACCATAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAATT-----GAAAACCCTAACCTAATTAAATTA
* *
12005363 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAA-AA
1 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
12005408 GAAAACCCTAACCTAATTAAATTGAAAACCCTAACC
1 -AAAACCCTAACCTAATTAAATTGAAAACCCTAACC
12005444 CTAAACCCTT
Statistics
Matches: 546, Mismatches: 50, Indels: 56
0.84 0.08 0.09
Matches are distributed among these distances:
45 1 0.00
46 215 0.39
47 21 0.04
48 20 0.04
51 245 0.45
52 23 0.04
56 21 0.04
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (46 bp):
AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
Found at i:12005379 original size:18 final size:20
Alignment explanation
Indices: 12005356--12005466 Score: 71
Period size: 23 Copynumber: 5.0 Consensus size: 20
12005346 ATAACCTAAT
12005356 TAAATTAAAAACCCTAACCTAA
1 TAAATTAAAAACCCTAACC--A
12005378 TTAAATTAAAAACCCTAACCTAA
1 -TAAATTAAAAACCCTAACC--A
*
12005401 TTAAA-AAGAAAACCCTAACCTAA
1 -TAAATTA-AAAACCCTAACC--A
* *
12005424 TTAAATTGAAAACCCTAACCC
1 -TAAATTAAAAACCCTAACCA
12005445 TAAACCCTTAAAAACCCTAACC
1 TAAA---TTAAAAACCCTAACC
12005467 CTTAATATTC
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
20 4 0.05
22 1 0.01
23 73 0.94
ACGTcount: A:0.50, C:0.26, G:0.02, T:0.22
Consensus pattern (20 bp):
TAAATTAAAAACCCTAACCA
Found at i:12005456 original size:74 final size:69
Alignment explanation
Indices: 12004773--12005443 Score: 678
Period size: 74 Copynumber: 9.2 Consensus size: 69
12004763 AAATTGAAAA
* * *
12004773 GAAAACCCTAACGTAATTAAATTGAAAACCCTAACCTAATTAAATTA-AAAACCCTAACCTAATT
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAA-AAGAAAACCCTAACCTAATT
**
12004837 AAAAA
65 AAATT
****
12004842 GAAAACCCTAACCTAATTAAACCCTAAACCCTAACCTAATTAAATTGAAAAGAAAACCCTAACCT
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATT--A---AAAAGAAAACCCTAACCT
*
12004907 ACTTAAATT
61 AATTAAATT
* **** *
12004916 GAAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAACCCTAAATCCTAACCTAATTA
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTA
12004981 AATT
66 AATT
****
12004985 GAAAAGAAAACCCTAACCTAATTAAACCCTAAACCCTAACCTAATTAAATTGAAAAGAAAACCCT
1 -----GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATT--A---AAAAGAAAACCCT
12005050 AACCTAATTAAATT
56 AACCTAATTAAATT
* * * **
12005064 GAAAAGAAAACCCTAACCTAATTAAATTGAAAATCCTAACCTAGTTAAATTGAAAACCCTAACCT
1 -----GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCT
12005129 AATTAAATT
61 AATTAAATT
**
12005138 GAAAAGAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTGAAAAGAAAACTTT
1 -----GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATT--A---AAAAGAAAACCCT
12005203 AACCTAATTAAATT
56 AACCTAATTAAATT
**
12005217 GAAAAACCCTAACCTAATTAAATTGAAAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAAT
1 G-AAAACCCTAACCTAATTAAATT-AAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAAT
**
12005282 TAAACC
64 TAAATT
** *
12005288 CTAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTGAAAAGAAAACCATAACCT
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATT--A---AAAAGAAAACCCTAACCT
12005353 AATTAAATT
61 AATTAAATT
*
12005362 AAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTA
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTA
12005427 AATT
66 AATT
12005431 GAAAACCCTAACC
1 GAAAACCCTAACC
12005444 CTAAACCCTT
Statistics
Matches: 514, Mismatches: 60, Indels: 56
0.82 0.10 0.09
Matches are distributed among these distances:
69 113 0.22
70 21 0.04
71 23 0.04
72 2 0.00
73 1 0.00
74 226 0.44
75 22 0.04
76 20 0.04
77 1 0.00
79 85 0.17
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (69 bp):
GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTA
AATT
Found at i:12005468 original size:16 final size:17
Alignment explanation
Indices: 12005440--12005471 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12005430 TGAAAACCCT
12005440 AACCCTAAACCCTTAAA
1 AACCCTAAACCCTTAAA
12005457 AACCCT-AACCCTTAA
1 AACCCTAAACCCTTAA
12005472 TATTCACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.19
Consensus pattern (17 bp):
AACCCTAAACCCTTAAA
Found at i:12005696 original size:115 final size:115
Alignment explanation
Indices: 12005485--12005700 Score: 330
Period size: 115 Copynumber: 1.9 Consensus size: 115
12005475 TCACATAATG
* * *
12005485 TTAGATTTGGAAAAATGTTTTTTCCTCGTACTAACAATTAATAATTTTATATAATTTGATAATTT
1 TTAGATTTGGAAAAATG-TTTTTCCTAGTACTAACAAATAATAATTTTATATAAATTGATAATTT
*
12005550 TACTAACAATTAATACAATTTATCGGATAATAATTTTACATTCACGTAACC
65 TACTAACAATTAATACAATTTATCGAATAATAATTTTACATTCACGTAACC
12005601 TTAGATTTGGAAAAATG-TTTTCACTAGTACTAACAAATAATAATTTTATATAAATTGA-AATTT
1 TTAGATTTGGAAAAATGTTTTTC-CTAGTACTAACAAATAATAATTTTATATAAATTGATAA-TT
*
12005664 TTACTAACCATTAATACAATTTATC-AATTAATAATTT
64 TTACTAACAATTAATACAATTTATCGAA-TAATAATTT
12005701 CACAAACTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
114 8 0.09
115 67 0.73
116 17 0.18
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (115 bp):
TTAGATTTGGAAAAATGTTTTTCCTAGTACTAACAAATAATAATTTTATATAAATTGATAATTTT
ACTAACAATTAATACAATTTATCGAATAATAATTTTACATTCACGTAACC
Found at i:12008838 original size:124 final size:124
Alignment explanation
Indices: 12008617--12008980 Score: 568
Period size: 123 Copynumber: 2.9 Consensus size: 124
12008607 CCCAAACATG
* *
12008617 CTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCTTA
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTT-ACAAATTCTTCTCAAATAGCATCTTG
12008682 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCATCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCATCCATGAC
* * *
12008742 CTACTGTAGCAAAAGCGCGTCTACGAGGGCGCGATTTTACAAATTATTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCTTGC
* * *
12008807 TAAAAGTGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAATTATTTTATCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCATCCATGAC
* * *
12008865 CTACTGTAGCAAAAACGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCTTGC
* * **
12008930 TAGAAGCGATTTTATACTATTTGATTAGAAACGTCAACTCAAAATTATTTC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTC
12008981 TTCCCGGACC
Statistics
Matches: 216, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
123 112 0.52
124 58 0.27
125 46 0.21
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCTTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCATCCATGAC
Found at i:12014050 original size:22 final size:20
Alignment explanation
Indices: 12014022--12014078 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 20
12014012 TAAAATTTAG
12014022 GATAATTATAATTTAATAAA
1 GATAATTATAATTTAATAAA
*
12014042 GTGATAATTACATATTT-A-AAA
1 --GATAATTATA-ATTTAATAAA
12014063 -ATAATTATAATTTAAT
1 GATAATTATAATTTAAT
12014079 TTTCAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
17 4 0.13
18 9 0.30
21 3 0.10
22 10 0.33
23 4 0.13
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (20 bp):
GATAATTATAATTTAATAAA
Found at i:12014124 original size:20 final size:20
Alignment explanation
Indices: 12014099--12014139 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12014089 TAACTAAAAA
*
12014099 TTTTAATATAAAAATATATT
1 TTTTAATATAAAAATAAATT
* *
12014119 TTTTAATTTTAAAATAAATT
1 TTTTAATATAAAAATAAATT
12014139 T
1 T
12014140 ATTACATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTAATATAAAAATAAATT
Found at i:12014270 original size:14 final size:15
Alignment explanation
Indices: 12014251--12014287 Score: 60
Period size: 13 Copynumber: 2.6 Consensus size: 15
12014241 CCTTATTATA
12014251 AAAAAAATTGAT-GT
1 AAAAAAATTGATAGT
12014265 -AAAAAATTGATAGT
1 AAAAAAATTGATAGT
12014279 AAAAAAATT
1 AAAAAAATT
12014288 CAGCTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.52
14 2 0.10
15 8 0.38
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (15 bp):
AAAAAAATTGATAGT
Found at i:12014739 original size:4 final size:4
Alignment explanation
Indices: 12014732--12014800 Score: 138
Period size: 4 Copynumber: 17.2 Consensus size: 4
12014722 TTTATTTATT
12014732 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12014780 TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG T
12014801 GTTATTTGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 65 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:12016714 original size:16 final size:16
Alignment explanation
Indices: 12016689--12016719 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12016679 TGAGAGTAAA
*
12016689 AGAGTTTTAGTGTGTG
1 AGAGTATTAGTGTGTG
12016705 AGAGTATTAGTGTGT
1 AGAGTATTAGTGTGT
12016720 AAATTACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (16 bp):
AGAGTATTAGTGTGTG
Found at i:12017358 original size:21 final size:20
Alignment explanation
Indices: 12017330--12017368 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
12017320 TCCAACAATA
12017330 TATTATTATTTTTCACTTAG
1 TATTATTATTTTTCACTTAG
*
12017350 TATTAATTATTTTTTACTT
1 TATT-ATTATTTTTCACTT
12017369 TGCATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.64
Consensus pattern (20 bp):
TATTATTATTTTTCACTTAG
Found at i:12017828 original size:37 final size:35
Alignment explanation
Indices: 12017787--12017876 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 35
12017777 ATTTAAATTG
**
12017787 TTAAATATATTAATATATATTAATTATATT-TAATAAT
1 TTAAATATATTAA-AT-TAAAAATTA-ATTATAATAAT
12017824 TTAAATA-A-TAAATTAAAAATTAATTATAATAAT
1 TTAAATATATTAAATTAAAAATTAATTATAATAAT
* *
12017857 TAAAATATATT-ATTTAAAAA
1 TTAAATATATTAAATTAAAAA
12017877 ATAAACATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
32 3 0.07
33 20 0.43
34 11 0.24
35 4 0.09
36 1 0.02
37 7 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
TTAAATATATTAAATTAAAAATTAATTATAATAAT
Found at i:12018731 original size:4 final size:4
Alignment explanation
Indices: 12018722--12018762 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
12018712 TATTTGGAAA
12018722 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC T
12018763 CTGCACTGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:12021013 original size:19 final size:19
Alignment explanation
Indices: 12020991--12021042 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
12020981 AAACAAAATA
*
12020991 GAAAATTTTGGGAAAACTT
1 GAAAATTTTGGAAAAACTT
12021010 GAAAATTTTGGAAAAACTT
1 GAAAATTTTGGAAAAACTT
12021029 GAAAATTTTGGAAA
1 GAAAATTTTGGAAA
12021043 CAAGGGTCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (19 bp):
GAAAATTTTGGAAAAACTT
Found at i:12027115 original size:15 final size:15
Alignment explanation
Indices: 12027068--12027116 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 15
12027058 TATGATTCTT
*
12027068 TTATTTTAA-TGTTA
1 TTATTTTAATTTTTA
12027082 TTATTTTAACCTTTATTA
1 TTATTTTAA--TTT-TTA
12027100 TTATTTTAATTTTTA
1 TTATTTTAATTTTTA
12027115 TT
1 TT
12027117 TAATATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 9 0.30
15 5 0.17
16 3 0.10
17 1 0.03
18 12 0.40
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTTTAATTTTTA
Found at i:12032312 original size:42 final size:42
Alignment explanation
Indices: 12032177--12032402 Score: 289
Period size: 42 Copynumber: 5.4 Consensus size: 42
12032167 TTTAAACAGA
* * * *
12032177 TTCACTGGCACTT-AGCCTGCTAGACTTAAAGCCTGAT-TCAG-
1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATAT-TGT
* * * * * *
12032218 TACACTGGCATTTAGCCTGCTAGACATATAGTCTGA-AATGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
*
12032259 TTCACCGGCATTAAGCATGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
* *
12032301 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
12032343 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
12032385 TTCACCGGCATTAAGCCT
1 TTCACCGGCATTAAGCCT
12032403 AATAGGCACT
Statistics
Matches: 163, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
40 3 0.02
41 59 0.36
42 101 0.62
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (42 bp):
TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
Found at i:12032924 original size:2 final size:2
Alignment explanation
Indices: 12032917--12032951 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12032907 AATCTTAAGT
12032917 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
12032952 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12034392 original size:25 final size:24
Alignment explanation
Indices: 12034339--12034427 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 24
12034329 CCGTTATTTA
*
12034339 GCTCTCATGAGCTTCCCGATTA-ATT
1 GCTCTCATGAGCTTCTC-ATTATA-T
*
12034364 GCTCTCTTGAGCTTCTCATTATAT
1 GCTCTCATGAGCTTCTCATTATAT
* **
12034388 GGCTCTCACGAGCTTCTCGGTATAT
1 -GCTCTCATGAGCTTCTCATTATAT
12034413 GCTCTCATGAGCTTC
1 GCTCTCATGAGCTTC
12034428 CTATTTATGG
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
24 19 0.35
25 36 0.65
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.37
Consensus pattern (24 bp):
GCTCTCATGAGCTTCTCATTATAT
Found at i:12053756 original size:22 final size:22
Alignment explanation
Indices: 12053725--12053854 Score: 133
Period size: 22 Copynumber: 5.9 Consensus size: 22
12053715 TTTATGGTGT
* *
12053725 ATTCTAATTTGGCATTTATGGC
1 ATTCTGATTTGGCCTTTATGGC
12053747 ATTCTGATTTGGCCTTTATGGC
1 ATTCTGATTTGGCCTTTATGGC
12053769 ATTCTGATTTGGCCTTTATGGC
1 ATTCTGATTTGGCCTTTATGGC
* *
12053791 ATTCTG-TTATGGCTTTTGTGGC
1 ATTCTGATT-TGGCCTTTATGGC
* * *
12053813 ATT-TTA-TTAGCCTTTGTGGTC
1 ATTCTGATTTGGCCTTTATGG-C
12053834 TAATT-TGATTTGGCCTTTATG
1 --ATTCTGATTTGGCCTTTATG
12053855 ACATATTCTG
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.11
21 5 0.05
22 62 0.67
23 5 0.05
24 10 0.11
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (22 bp):
ATTCTGATTTGGCCTTTATGGC
Found at i:12053843 original size:66 final size:67
Alignment explanation
Indices: 12053773--12053899 Score: 170
Period size: 68 Copynumber: 1.9 Consensus size: 67
12053763 TATGGCATTC
* * *
12053773 TGATTTGGCCTTTATGGC-ATTCTGTTATGGCTTT-TGTG-GCATTTTATTAGCCTTTGTGGTCT
1 TGATTTGGCCTTTATGACAATTCTGTTA-GCCTTTATG-GAACATTTTATTAGCCTTTGTGGTCT
12053835 AATT
64 AATT
*
12053839 TGATTTGGCCTTTATGACATATTCTGTTAGCCTTTATGGAACATTTTGTTAGCCTTTGTGG
1 TGATTTGGCCTTTATGACA-ATTCTGTTAGCCTTTATGGAACATTTTATTAGCCTTTGTGG
12053900 CATTCTGCTA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
66 17 0.32
67 6 0.11
68 30 0.57
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.48
Consensus pattern (67 bp):
TGATTTGGCCTTTATGACAATTCTGTTAGCCTTTATGGAACATTTTATTAGCCTTTGTGGTCTAA
TT
Found at i:12053873 original size:22 final size:22
Alignment explanation
Indices: 12053846--12053895 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
12053836 ATTTGATTTG
12053846 GCCTTTAT-G-ACATATTCTGTTA
1 GCCTTTATGGAACAT-TT-TGTTA
12053868 GCCTTTATGGAACATTTTGTTA
1 GCCTTTATGGAACATTTTGTTA
12053890 GCCTTT
1 GCCTTT
12053896 GTGGCATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 19 0.73
23 3 0.12
24 4 0.15
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (22 bp):
GCCTTTATGGAACATTTTGTTA
Found at i:12053911 original size:20 final size:21
Alignment explanation
Indices: 12053859--12053919 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
12053849 TTTATGACAT
*
12053859 ATTCTGTTAGCCTTTATGGAAC
1 ATTCTGTTAGCCTTTGTGG-AC
*
12053881 ATTTTGTTAGCCTTTGTGG-C
1 ATTCTGTTAGCCTTTGTGGAC
* *
12053901 ATTCTGCTAGCCTTAGTGG
1 ATTCTGTTAGCCTTTGTGG
12053920 TGTACTCTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 17 0.50
22 17 0.50
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (21 bp):
ATTCTGTTAGCCTTTGTGGAC
Found at i:12053912 original size:88 final size:86
Alignment explanation
Indices: 12053751--12053920 Score: 200
Period size: 88 Copynumber: 1.9 Consensus size: 86
12053741 TATGGCATTC
* * *
12053751 TGATTTGGCCTTTATGGCATTCTGATTTGGCCTTTATGGCATTCTGTTATGGCTTTTGTGGCATT
1 TGATTTGGCCTTTATGACATTCTGA-TTAGCCTTTATGGCATTCTGTTA-GGCCTTTGTGGCATT
* * *
12053816 TTATTAGCCTTTGTGGTCTAATT
64 CTACTAGCCTTAGTGGTCTAATT
*
12053839 TGATTTGGCCTTTATGACATATTCTG-TTAGCCTTTATGGAACATTTTGTTA-GCCTTTGTGGCA
1 TGATTTGGCCTTTATGAC--ATTCTGATTAGCCTTTATGG--CATTCTGTTAGGCCTTTGTGGCA
*
12053902 TTCTGCTAGCCTTAGTGGT
62 TTCTACTAGCCTTAGTGGT
12053921 GTACTCTATA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 55 0.79
90 15 0.21
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.46
Consensus pattern (86 bp):
TGATTTGGCCTTTATGACATTCTGATTAGCCTTTATGGCATTCTGTTAGGCCTTTGTGGCATTCT
ACTAGCCTTAGTGGTCTAATT
Found at i:12056234 original size:67 final size:63
Alignment explanation
Indices: 12056067--12056538 Score: 224
Period size: 64 Copynumber: 7.2 Consensus size: 63
12056057 TAAGATTGTA
* * * *
12056067 GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTAATTTAAGATCGCAACCTAAGTTC
1 GCTGATTTAAGATCAAAACTAATATTATTAAGGTTAGCTGATTTAAGATCGCAACCAAAGTTC
* * * * *
12056130 ACTCAATTTAAGATCATGAAC-AATTTTATT-TGAGTTAGCTGATTTAAGATCGCAACTTCGAAC
1 GCT-GATTTAAGATCA-AAACTAATATTATTAAG-GTTAGCTGATTTAAGATCGCAAC--C-AA-
12056193 AGCTT-
59 AG-TTC
* *
12056198 GCTGATTTAAGATCAAAACTAATATTATTAAGGTTAGTTGATTTAAGATCG-AAGCCTAAGTTC
1 GCTGATTTAAGATCAAAACTAATATTATTAAGGTTAGCTGATTTAAGATCGCAA-CCAAAGTTC
** * * * * * * *
12056261 ATTCGATTTAAGATCATGAAC-AATTTTGTT-TGAGATAGCTAATTTAATATCGCAACTCTGAAC
1 GCT-GATTTAAGATCA-AAACTAATATTATTAAG-GTTAGCTGATTTAAGATCGCAAC-C--AA-
**
12056324 AAATC
59 AGTTC
* * * * * *
12056329 GCTGATTTAAGATCACAATTGATATTATTAAGGTTAGTTGATTTAAGATTGCAACCAAAGTTT
1 GCTGATTTAAGATCAAAACTAATATTATTAAGGTTAGCTGATTTAAGATCGCAACCAAAGTTC
** * * * * *
12056392 ATTCGATTTAAGATCATGAAC-AATTTTATT-CGAGTTAGTTGATTTAAGATCGTAACTCTACAC
1 GCT-GATTTAAGATCA-AAACTAATATTATTAAG-GTTAGCTGATTTAAGATCGCAAC-C-A-A-
*
12056455 AGCTC
59 AGTTC
* * * * ** * * * *
12056460 ACTAAGTTAAGGTC-GCAGTCGATATTATTAAGGTTAGCTGATTTAAGATCCCAACCTAAGTTC
1 GCTGATTTAAGATCAAAACT-AATATTATTAAGGTTAGCTGATTTAAGATCGCAACCAAAGTTC
**
12056523 ATTTGATTTAAGATCA
1 -GCTGATTTAAGATCA
12056539 TGAAAAATTT
Statistics
Matches: 301, Mismatches: 74, Indels: 66
0.68 0.17 0.15
Matches are distributed among these distances:
62 2 0.01
63 15 0.05
64 128 0.43
65 15 0.05
66 11 0.04
67 112 0.37
68 16 0.05
69 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (63 bp):
GCTGATTTAAGATCAAAACTAATATTATTAAGGTTAGCTGATTTAAGATCGCAACCAAAGTTC
Found at i:12056244 original size:131 final size:131
Alignment explanation
Indices: 12056067--12056807 Score: 877
Period size: 131 Copynumber: 5.7 Consensus size: 131
12056057 TAAGATTGTA
* *
12056067 GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTAATTTAAGATCGCAACCTAAGTTCAC
1 GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTCAT
* * * *
12056132 TCAATTTAAGATCATGAACAATTTTATTTGAGTTAGCTGATTTAAGATCGCAACT-TCGAACAGC
66 TCGATTTAAGATCATGAACAATTTTATTCGAGTTAGCTAATTTAAAATCGCAACTCT-GAACAGC
*
12056196 TT
130 TC
* * *
12056198 GCTGATTTAAGATCAAAACTAATATTATTAAGGTTAGTTGATTTAAGATCG-AAGCCTAAGTTCA
1 GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTGATTTAAGATCGCAA-CCTAAGTTCA
* * * * **
12056262 TTCGATTTAAGATCATGAACAATTTTGTTTGAGATAGCTAATTTAATATCGCAACTCTGAACAAA
65 TTCGATTTAAGATCATGAACAATTTTATTCGAGTTAGCTAATTTAAAATCGCAACTCTGAACAGC
12056327 TC
130 TC
* * * * *
12056329 GCTGATTTAAGATCACAATTGATATTATTAAGGTTAGTTGATTTAAGATTGCAACCAAAGTTTAT
1 GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTCAT
* * * *
12056394 TCGATTTAAGATCATGAACAATTTTATTCGAGTTAGTTGATTTAAGATCGTAACTCT-ACACAGC
66 TCGATTTAAGATCATGAACAATTTTATTCGAGTTAGCTAATTTAAAATCGCAACTCTGA-ACAGC
12056458 TC
130 TC
* * * * * * *
12056460 ACTAAGTTAAGGTCGC-AGTCGATATTATTAAGGTTAGCTGATTTAAGATCCCAACCTAAGTTCA
1 GCTGATTTAAGATCACAACT-GATATTATTAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTCA
* * *
12056524 TTTGATTTAAGATCATGAAAAATTTTATTCGAGTTAGCTAATTTAAAATTGCAACTCTGAACAGC
65 TTCGATTTAAGATCATGAACAATTTTATTCGAGTTAGCTAATTTAAAATCGCAACTCTGAACAGC
12056589 TC
130 TC
* * * * * *
12056591 ACTAAGTTAAGGTCGC-AGTCGATATTATTAAGGTTAGCTGATTTAAGATC-CTAACCTAAGTTC
1 GCTGATTTAAGATCACAACT-GATATTATTAAGGTTAGCTGATTTAAGATCGC-AACCTAAGTTC
* * * *
12056654 ATTCGATTTAAGATCATGAAAAATTTTATTCGAGTTAGCTAATTTAAAATTGCAACTCTAAACAA
64 ATTCGATTTAAGATCATGAACAATTTTATTCGAGTTAGCTAATTTAAAATCGCAACTCTGAACAG
12056719 CT-
129 CTC
* * ** * * ** *
12056721 TCTGATTTAAGATCGCAGTTGATATTATCAAGGTTAGCTGATTCAAGATCATAACCGAAGTTCAC
1 GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTCA-
12056786 TT-GATTTAAGATCATGAACAAT
65 TTCGATTTAAGATCATGAACAAT
12056808 CTCACTTGTG
Statistics
Matches: 540, Mismatches: 60, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
130 76 0.14
131 460 0.85
132 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (131 bp):
GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTCAT
TCGATTTAAGATCATGAACAATTTTATTCGAGTTAGCTAATTTAAAATCGCAACTCTGAACAGCT
C
Found at i:12062789 original size:15 final size:15
Alignment explanation
Indices: 12062765--12062797 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12062755 CACTATGAGT
*
12062765 TCGCATGTAAGGCAC
1 TCGCACGTAAGGCAC
12062780 TCGCACGTAAGGCAC
1 TCGCACGTAAGGCAC
12062795 TCG
1 TCG
12062798 TACCCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.18
Consensus pattern (15 bp):
TCGCACGTAAGGCAC
Found at i:12065531 original size:17 final size:18
Alignment explanation
Indices: 12065511--12065544 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12065501 CAAATTACAT
12065511 AATTAACCGAA-TTAATC
1 AATTAACCGAAGTTAATC
*
12065528 AATTAACTGAAGTTAAT
1 AATTAACCGAAGTTAAT
12065545 AATCTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (18 bp):
AATTAACCGAAGTTAATC
Found at i:12071799 original size:5 final size:5
Alignment explanation
Indices: 12071791--12071824 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
12071781 ATTAGTAACT
12071791 TAAAA TAAAA TAAAA TAAAA TAAAA TAAATA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA-A TAA
12071825 CTAATATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:12077031 original size:19 final size:20
Alignment explanation
Indices: 12076985--12077033 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
12076975 ATTAAGTGTA
12076985 AATTCTTTTAAATCAACAACT
1 AATT-TTTTAAATCAACAACT
*
12077006 AATTTTTTAAATCCACAACT
1 AATTTTTTAAATCAACAACT
12077026 AATTTTTT
1 AATTTTTT
12077034 CTAGTTTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTTTTAAATCAACAACT
Found at i:12078894 original size:58 final size:58
Alignment explanation
Indices: 12078808--12078925 Score: 191
Period size: 58 Copynumber: 2.0 Consensus size: 58
12078798 TAAAATGAAA
* *
12078808 CTTAAAATATTAAAAACTAAAAATGTAATAAAAACATATAAAAGAGTTAGAAAAAAAG
1 CTTAAAATACTAAAAACTAAAAACGTAATAAAAACATATAAAAGAGTTAGAAAAAAAG
* * *
12078866 CTTAAACTACTAAAAACTGAAAACGTAATAAAAACATATAAAAGAGTTAGAAAACAAG
1 CTTAAAATACTAAAAACTAAAAACGTAATAAAAACATATAAAAGAGTTAGAAAAAAAG
12078924 CT
1 CT
12078926 CGTTAAACGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21
Consensus pattern (58 bp):
CTTAAAATACTAAAAACTAAAAACGTAATAAAAACATATAAAAGAGTTAGAAAAAAAG
Found at i:12082003 original size:12 final size:12
Alignment explanation
Indices: 12081986--12082010 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12081976 CAAAGTGAGT
12081986 AGAAAGAAAAAA
1 AGAAAGAAAAAA
12081998 AGAAAGAAAAAA
1 AGAAAGAAAAAA
12082010 A
1 A
12082011 TAAAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAA
Found at i:12082054 original size:13 final size:13
Alignment explanation
Indices: 12082036--12082060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12082026 TTTTGCACAA
12082036 AAAAATAAAATAG
1 AAAAATAAAATAG
12082049 AAAAATAAAATA
1 AAAAATAAAATA
12082061 AAATAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATAAAATAG
Found at i:12088173 original size:23 final size:23
Alignment explanation
Indices: 12088147--12088193 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
12088137 GTAATTATAA
*
12088147 ATACCTGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
12088170 ATACATTTGTAATTAATATATGT
1 ATACATGTGTAATAAATATATGT
12088193 A
1 A
12088194 CAGACTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:12089229 original size:25 final size:25
Alignment explanation
Indices: 12089201--12089310 Score: 108
Period size: 22 Copynumber: 4.6 Consensus size: 25
12089191 AATTTAGCGC
*
12089201 GCTCTATGATTATTAGCACATCAGT
1 GCTCTCTGATTATTAGCACATCAGT
* *
12089226 GCTCTCTGATTACTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACATCAGT
*
12089251 GCTCTCTG--T-TTAGCACATCTGT
1 GCTCTCTGATTATTAGCACATCAGT
* *
12089273 GCTCTC--AGTATT-GCACTTCAGT
1 GCTCTCTGATTATTAGCACATCAGT
12089295 GCTCTCTG-TTCATTAG
1 GCTCTCTGATT-ATTAG
12089311 TGCATAACAA
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
22 31 0.45
23 4 0.06
24 3 0.04
25 31 0.45
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.37
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACATCAGT
Found at i:12089257 original size:27 final size:25
Alignment explanation
Indices: 12089201--12089277 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
12089191 AATTTAGCGC
*
12089201 GCTCTATGATTATTAGCACATCAGT
1 GCTCTATGATTACTAGCACATCAGT
* *
12089226 GCTCTCTGATTACTAGCACGTCAGT
1 GCTCTATGATTACTAGCACATCAGT
* *
12089251 GCTCTCTG-TT--TAGCACATCTGT
1 GCTCTATGATTACTAGCACATCAGT
12089273 GCTCT
1 GCTCT
12089278 CAGTATTGCA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
22 15 0.32
24 2 0.04
25 30 0.64
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.36
Consensus pattern (25 bp):
GCTCTATGATTACTAGCACATCAGT
Found at i:12092299 original size:16 final size:18
Alignment explanation
Indices: 12092278--12092310 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12092268 ATTGACCTGT
12092278 AAAC-AACA-CAAAAAAG
1 AAACAAACAGCAAAAAAG
12092294 AAACAAACAGCAAAAAA
1 AAACAAACAGCAAAAAA
12092311 TGGAATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.76, C:0.18, G:0.06, T:0.00
Consensus pattern (18 bp):
AAACAAACAGCAAAAAAG
Found at i:12094790 original size:26 final size:26
Alignment explanation
Indices: 12094754--12094808 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
12094744 TATCAGGTCA
12094754 GTTCTAATCAGGAAATGTTATTATGG
1 GTTCTAATCAGGAAATGTTATTATGG
12094780 GTTCTAATCAGGAAATGTTATTATGG
1 GTTCTAATCAGGAAATGTTATTATGG
12094806 GTT
1 GTT
12094809 AAAGTCATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (26 bp):
GTTCTAATCAGGAAATGTTATTATGG
Found at i:12095616 original size:23 final size:23
Alignment explanation
Indices: 12095590--12095636 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
12095580 GTAATTATAA
12095590 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
12095613 ATACATTTGTAATTAATATATGT
1 ATACATGTGTAATAAATATATGT
12095636 A
1 A
12095637 CATACTTATT
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:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:12095786 original size:26 final size:27
Alignment explanation
Indices: 12095727--12095791 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
12095717 GAATGGAAAC
*
12095727 AGAATAGAAAAACGAAAACAGGGGAGAA
1 AGAA-AGAAAAACGAAAACAGGGAAGAA
12095755 AGGAAAGAAAAA-GAAAA-AGGGAAGGAA
1 A-GAAAGAAAAACGAAAACAGGGAA-GAA
12095782 AGAAAGAAAA
1 AGAAAGAAAA
12095792 TTTGGGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
26 14 0.41
27 9 0.26
28 8 0.24
29 3 0.09
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.02
Consensus pattern (27 bp):
AGAAAGAAAAACGAAAACAGGGAAGAA
Found at i:12098362 original size:16 final size:16
Alignment explanation
Indices: 12098337--12098371 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12098327 TTGTGTTTTG
*
12098337 TTTTGGCTGCATGACA
1 TTTTGACTGCATGACA
*
12098353 TTTTGACTGCATGGCA
1 TTTTGACTGCATGACA
12098369 TTT
1 TTT
12098372 CATCATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (16 bp):
TTTTGACTGCATGACA
Found at i:12100963 original size:6 final size:6
Alignment explanation
Indices: 12100954--12101004 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
12100944 AAAAATCAAA
*
12100954 AAAATG AAAATG AAAATG AAAATG ATGGAAA-G AAAAAG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG A---AAATG AAAATG AAAATG AAAATG
12101004 A
1 A
12101005 GAGGCCAAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 3 0.08
6 32 0.80
8 2 0.05
9 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:12102270 original size:6 final size:7
Alignment explanation
Indices: 12102243--12102268 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12102233 AATCAATTCT
12102243 TTTTTTA
1 TTTTTTA
12102250 TTTTTTA
1 TTTTTTA
12102257 TTTTTTA
1 TTTTTTA
12102264 TTTTT
1 TTTTT
12102269 ATATATATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:12103230 original size:45 final size:45
Alignment explanation
Indices: 12103174--12104031 Score: 1045
Period size: 45 Copynumber: 19.1 Consensus size: 45
12103164 AGAGTAGGTT
* *
12103174 GAAGATAGCAGATTTTGTCTTCCTGTATTGGCAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12103219 GAAGTTAGCAGATCTTGTCTCCCTGTATTGGCAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
12103264 GAAGATAGTAGGTCTTGTCTTCCTGTATTGGTAGTGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12103309 GAAGTTAGCAGATCTTGTCTTCCGGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12103354 GAAGATAGTAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
12103399 GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
12103444 GAAGATAGCAGATCTTATCTTCCTATATTAGCAGCGAAATAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
12103489 GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
12103534 GAAGATAGCAGATCTTGTCTTCCTATACTGGCAGCAAAGTATATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * * *
12103579 GAAGATAGCAAATCTTGTCTTTCTGTACTAGTAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *** * * * *
12103624 GAAGATACCAG-CCTTATCTTCCTG-AGCAGCAGTGGAGTAGGTT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
12103667 GAAAATAGTAGATCTTGTCTTCATATACTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
** *
12103712 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAATGAAGTATATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12103757 GAAGATAGCAGATCTTGTCTTCCTATATTAGCAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
12103802 GAAGATAGTAGATCTTGTCTTCCTGTATTGGTAGTGAAGTAGATA
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
12103847 GAAGATAACAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
12103892 CAAGATAGCAGATCTTGTCTTCCTGTATTAGCAGTGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
12103937 GAAGATAGCATATCTTGTCTTCCTATATTGACAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
12103982 GAAGATAACGGATCTTGTCTTCCTATACTGGTAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
12104027 GAAGA
1 GAAGA
12104032 CGGCGAGTCT
Statistics
Matches: 691, Mismatches: 120, Indels: 4
0.85 0.15 0.00
Matches are distributed among these distances:
43 19 0.03
44 19 0.03
45 653 0.95
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
Found at i:12104163 original size:44 final size:44
Alignment explanation
Indices: 12104115--12104294 Score: 114
Period size: 44 Copynumber: 4.1 Consensus size: 44
12104105 AGAATAGGTT
* *
12104115 GAAGATTGTAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATC
1 GAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATC
* * * * * *
12104159 GAAGATGGTAAATCTTATCTTCCC-AAGGTAGTAG-GGAAGTAGATT
1 GAAGATTGTAGATCCTATC-TCCCTAA-GCAGTAGTGG-AGCAGATC
* ***** * * * * *
12104204 TAAGCCACCAG-TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTT
1 GAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATC
* * *
12104247 GAAAATTGTAGATCCTGTCTCCCTAAGTAGTAGTGGAGCAGATC
1 GAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATC
12104291 GAAG
1 GAAG
12104295 GCAGCAAATC
Statistics
Matches: 97, Mismatches: 33, Indels: 12
0.68 0.23 0.08
Matches are distributed among these distances:
43 20 0.21
44 57 0.59
45 20 0.21
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (44 bp):
GAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATC
Found at i:12104467 original size:132 final size:132
Alignment explanation
Indices: 12104039--12104442 Score: 587
Period size: 132 Copynumber: 3.1 Consensus size: 132
12104029 AGACGGCGAG
* * *
12104039 TCTTATCTTCCCAAGGTAGTAGGGAAACAGATTTAAGCCACCAATCTTATCTCACTGAGCAGCAG
1 TCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGCAG
* * * * * *
12104104 TAGAATAGGTTGAAGATTGTAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTA
66 TAGAGTAGGTTGAAAATTGTAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGTAGCA
12104169 AA
131 AA
* *
12104171 TCTTATCTTCCCAAGGTAGTAGGGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAG
1 TCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGCAG
* * * *
12104236 TGGAGTAGGTTGAAAATTGTAGATCCTGTCTCCCTAAGTAGTAGTGGAGCAGATCGAAGGCAGCA
66 TAGAGTAGGTTGAAAATTGTAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGTAGCA
12104301 AA
131 AA
* * *
12104303 TCCTATCTTCCCAAGGTAGTAGGGAAGTAGATTTAAGCCACCAATCCCT-TCTCCCTGAG-ATAC
1 TCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAAT-CCTATCTCCCTGAGCA-GC
* *
12104366 AGTAGAGTAGGTTGAAAATTGTAGATCATGTATCCCTAAGCAGTAGTGGAGCAGATCAAAGGTAG
64 AGTAGAGTAGGTTGAAAATTGTAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGTAG
*
12104431 CGAA
129 CAAA
12104435 TCTTATCT
1 TCTTATCT
12104443 CCTTGGCATT
Statistics
Matches: 245, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
131 1 0.00
132 241 0.98
133 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (132 bp):
TCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGCAG
TAGAGTAGGTTGAAAATTGTAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGTAGCA
AA
Found at i:12104590 original size:44 final size:43
Alignment explanation
Indices: 12104539--12104696 Score: 147
Period size: 44 Copynumber: 3.6 Consensus size: 43
12104529 ATAACCAACC
*
12104539 TTATCTCCCTGAAGTTACAGTGGAGTCGGTTGAAGATATCAATA
1 TTATCTCCCTGAAGTTACAGTGGAGTCGATTGAAGATA-CAATA
* * * * *
12104583 TTATCTCCTTGAAGTTGCAGTGG-GGCAGATTGAAGTTACAAGTC
1 TTATCTCCCTGAAGTTACAGTGGAGTC-GATTGAAGATACAA-TA
* * * * *
12104627 TTATCTCCCTGCAGTTACAGTGGAGTAGACTGACGATGACGAATT
1 TTATCTCCCTGAAGTTACAGTGGAGTCGATTGAAGAT-AC-AATA
* *
12104672 TTGTCTCCCTGAAGTTGCAGTGGAG
1 TTATCTCCCTGAAGTTACAGTGGAG
12104697 CATATTAAAG
Statistics
Matches: 91, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
43 5 0.05
44 58 0.64
45 26 0.29
46 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
TTATCTCCCTGAAGTTACAGTGGAGTCGATTGAAGATACAATA
Found at i:12105101 original size:19 final size:19
Alignment explanation
Indices: 12105077--12105130 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
12105067 AATCTTGAAG
*
12105077 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAA
12105096 GATATGCAATCTTAGATAA
1 GATATGCAATCTTAGATAA
*
12105115 GATATGCAATTTTAGA
1 GATATGCAATCTTAGA
12105131 AGATAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAA
Found at i:12105156 original size:22 final size:22
Alignment explanation
Indices: 12105077--12105153 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 22
12105067 AATCTTGAAG
*
12105077 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAA
12105096 GATATGCAATCTT---AGATAA
1 GATATGCAATCTTAGAAGATAA
*
12105115 GATATGCAATTTTAGAAGATAA
1 GATATGCAATCTTAGAAGATAA
* *
12105137 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
12105154 GATTTAATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 30 0.61
22 8 0.16
23 11 0.22
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAA
Found at i:12106452 original size:25 final size:24
Alignment explanation
Indices: 12106424--12106560 Score: 149
Period size: 25 Copynumber: 5.7 Consensus size: 24
12106414 GAACTTTAGT
12106424 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTG-TTATTAGCACATCA
*
12106449 GTGCTCTCTGATTATTAGCA-AGTTA
1 GTGCTCTCTG-TTATTAGCACA-TCA
* *
12106474 GTGCTCTCTGATTACTAGCACGTCA
1 GTGCTCTCTG-TTATTAGCACATCA
*
12106499 GTGCTCTCTG-T-TTAGCACATCT
1 GTGCTCTCTGTTATTAGCACATCA
*
12106521 GTGCTCTCTG-TA-TAGCACTTCA
1 GTGCTCTCTGTTATTAGCACATCA
12106543 GTGCTCTCTGTTCATTAG
1 GTGCTCTCTGTT-ATTAG
12106561 TGCATAACAA
Statistics
Matches: 97, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
22 37 0.38
23 2 0.02
24 2 0.02
25 56 0.58
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (24 bp):
GTGCTCTCTGTTATTAGCACATCA
Found at i:12107549 original size:26 final size:26
Alignment explanation
Indices: 12107501--12107588 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 26
12107491 ACTCACCTAC
* *
12107501 AATAGTCCTTGCGGACTTATACTTGA
1 AATAGTCCTTGTGGACTCATACTTGA
* *
12107527 AATAGTCCTTGTGGACTCCTACTTGCT
1 AATAGTCCTTGTGGACTCATACTTG-A
* * * *
12107554 AACAATTCTTGTAGACTCATACTTGA
1 AATAGTCCTTGTGGACTCATACTTGA
12107580 AATAG-CCTT
1 AATAGTCCTT
12107589 TGCAGAATCT
Statistics
Matches: 48, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
25 3 0.06
26 25 0.52
27 20 0.42
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (26 bp):
AATAGTCCTTGTGGACTCATACTTGA
Found at i:12107660 original size:28 final size:27
Alignment explanation
Indices: 12107596--12107795 Score: 96
Period size: 28 Copynumber: 7.1 Consensus size: 27
12107586 CTTTGCAGAA
* * *
12107596 TCTTGCTTGAAAGATACTCCATGTGAAA
1 TCTTGCTTGAAAGATAATCCATGCG-AC
* *
12107624 TCCTACTTGAAAGATAATCCATGCAGAC
1 TCTTGCTTGAAAGATAATCCATGC-GAC
* * * **
12107652 TATTGCTTGAAAGGTAGTTTATGCAGAC
1 TCTTGCTTGAAAGATAATCCATGC-GAC
** * * * *
12107680 TCTTAATTGAAGGATAGTCCATGTGGTC
1 TCTTGCTTGAAAGATAATCCATG-CGAC
* * *
12107708 TCTTGCTTGATAGGTAATCCATGCGAAA
1 TCTTGCTTGAAAGATAATCCATGCG-AC
* * ** *
12107736 TATTACTTGAAAGATTGTCCATGCGAAA
1 TCTTGCTTGAAAGATAATCCATGCG-AC
*
12107764 TCTTGCTTGAAA-AGTAATCCATACGGAC
1 TCTTGCTTGAAAGA-TAATCCATGC-GAC
12107792 TCTT
1 TCTT
12107796 ACTTCTTGCG
Statistics
Matches: 125, Mismatches: 42, Indels: 10
0.71 0.24 0.06
Matches are distributed among these distances:
27 2 0.02
28 121 0.97
29 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (27 bp):
TCTTGCTTGAAAGATAATCCATGCGAC
Found at i:12110885 original size:28 final size:28
Alignment explanation
Indices: 12110853--12110924 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
12110843 TTTAATAAGT
*
12110853 TCGCACACTTAGTGCTTAATAATCAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
* * *
12110881 TCGCACACTTAGTGCTTGACCATTAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
12110909 TCGCACACTTAGTGCT
1 TCGCACACTTAGTGCT
12110925 AATCTCATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATCAAAC
Found at i:12125885 original size:95 final size:94
Alignment explanation
Indices: 12125676--12126018 Score: 235
Period size: 95 Copynumber: 3.7 Consensus size: 94
12125666 CAAATAGTAT
* *
12125676 CCACTG-AGGGGTGTCTACTTT-AAATTATTGAAATTTGGCTAAGT-CCTTTTAGAGACTAGTTG
1 CCACTGAAGGGGT-TCTACTTTAAAATTATTGAAATTTGGCTAAGTGCCTTATAGAGACTAATTG
* * **
12125738 TGTTTATTTTATTAACTTAGCGAGCAATGT
65 TGTTTATTTTATTAACTTAACAAGCAATAC
**
12125768 CCACT-AAGGGGCGTT-TGTTTTAAAATTATTGAAATTTGGCTAAGTGCCTTAATA-AG-CTAAC
1 CCACTGAA-GGG-GTTCTACTTTAAAATTATTGAAATTTGGCTAAGTGCCTT-ATAGAGACT-A-
*
12125829 ATT-T-TTTTTTTGCTATTAACTTAACAAGCAATAC
61 ATTGTGTTTATTT--TATTAACTTAACAAGCAATAC
* * * *
12125863 CCACTGAAGGGGTTCTACTTTAACATTACTGAAATTTGGCTAAGTG-CTT-TAGGAGGCTAGTAA
1 CCACTGAAGGGGTTCTACTTTAAAATTATTGAAATTTGGCTAAGTGCCTTATA-GAGACTA--AT
* * * * * * * *
12125926 CGTTTTTCTTCTATTAACTTAGCAAGTAGTAT
63 TGTGTTTATTTTATTAACTTAACAAGCAATAC
* * * * * * *
12125958 CCACTTAA-GGGTGTCTGCTTTAAAATTACTAAAATTTCGCTAAGTACCTTA-AGAGGCTAAT
1 CCACTGAAGGGGT-TCTACTTTAAAATTATTGAAATTTGGCTAAGTGCCTTATAGAGACTAAT
12126019 AGTATTTCTA
Statistics
Matches: 201, Mismatches: 29, Indels: 41
0.74 0.11 0.15
Matches are distributed among these distances:
92 12 0.06
93 36 0.18
94 23 0.11
95 118 0.59
96 7 0.03
97 5 0.02
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (94 bp):
CCACTGAAGGGGTTCTACTTTAAAATTATTGAAATTTGGCTAAGTGCCTTATAGAGACTAATTGT
GTTTATTTTATTAACTTAACAAGCAATAC
Found at i:12126049 original size:188 final size:187
Alignment explanation
Indices: 12125676--12126049 Score: 416
Period size: 190 Copynumber: 2.0 Consensus size: 187
12125666 CAAATAGTAT
* *
12125676 CCACTGAGGGGTGTCTACTTTAAATTATTGAAATTTGGCTAAGTCCTTTTAGAGACTAGTTGTGT
1 CCACTGAGGGGTGTCTACTTTAAATTACTGAAATTTGGCTAAGTCCTTTTAGAGACTAGTCGTGT
* * * * * * * *
12125741 TTATTTTATTAACTTAGCGAGCAATGTCCACTAAGGGGCGTTTGTTTTAAAATTATTGAAATTTG
66 TTATTCTATTAACTTAGCAAGCAATATCCACTAAGGGGCGTCTGCTTTAAAATTACTAAAATTTC
* * ** * * *
12125806 GCTAAGTGCCTTAATAAGCTAACATTTTTTTTTTGCTATTAACTTAACAAGCAATAC
131 GCTAAGTACCTTAAGAAGCTAACATAGTATTTCTACTATTAACTTAACAAGCAATAC
* *
12125863 CCACTGAAGGGGT-TCTACTTTAACATTACTGAAATTTGGCTAAGTGC-TTTAGGAGGCTAGTAA
1 CCACTG-AGGGGTGTCTACTTTAA-ATTACTGAAATTTGGCTAAGTCCTTTTA-GAGACTAGT--
* * * * *
12125926 CGTTTTTCTTCTATTAACTTAGCAAGTAGTATCCACTTAA-GGGTGTCTGCTTTAAAATTACTAA
61 CGTGTTTATTCTATTAACTTAGCAAGCAATATCCAC-TAAGGGGCGTCTGCTTTAAAATTACTAA
* * *
12125990 AATTTCGCTAAGTACCTTAAGAGGCT-A-ATAGTATTTCTACTATTAACTTAGCGAGCAATA
125 AATTTCGCTAAGTACCTTAAGAAGCTAACATAGTATTTCTACTATTAACTTAACAAGCAATA
12126050 TCCATTAAAA
Statistics
Matches: 154, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
187 20 0.13
188 61 0.40
189 1 0.01
190 69 0.45
191 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (187 bp):
CCACTGAGGGGTGTCTACTTTAAATTACTGAAATTTGGCTAAGTCCTTTTAGAGACTAGTCGTGT
TTATTCTATTAACTTAGCAAGCAATATCCACTAAGGGGCGTCTGCTTTAAAATTACTAAAATTTC
GCTAAGTACCTTAAGAAGCTAACATAGTATTTCTACTATTAACTTAACAAGCAATAC
Found at i:12129087 original size:13 final size:13
Alignment explanation
Indices: 12129069--12129099 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12129059 TCAACTATTT
12129069 TTCTTTTCTCTTC
1 TTCTTTTCTCTTC
*
12129082 TTCTTTTCTTTTC
1 TTCTTTTCTCTTC
12129095 TTCTT
1 TTCTT
12129100 ATTTTTAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTCTTTTCTCTTC
Found at i:12130488 original size:2 final size:2
Alignment explanation
Indices: 12130481--12130508 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12130471 GAAGGGAATA
12130481 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12130509 TCACTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12131418 original size:2 final size:2
Alignment explanation
Indices: 12131411--12131437 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12131401 GTCTAAAGTT
12131411 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
12131438 ACATTATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12135996 original size:27 final size:27
Alignment explanation
Indices: 12135966--12136034 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
12135956 TGGCATTTTA
*
12135966 ATAGCCTATGTGGCAAACTCTGAAAGG
1 ATAGCCTTTGTGGCAAACTCTGAAAGG
* *
12135993 ATAGCCTTTGTGGCGAACTCTGAATGG
1 ATAGCCTTTGTGGCAAACTCTGAAAGG
12136020 ATTA-CCTTTGTGGCA
1 A-TAGCCTTTGTGGCA
12136035 TACCCTGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 35 0.95
28 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (27 bp):
ATAGCCTTTGTGGCAAACTCTGAAAGG
Found at i:12138862 original size:23 final size:22
Alignment explanation
Indices: 12138836--12138884 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
12138826 AGTTAAACTG
*
12138836 CCAATATAAGTGCAGACAATCCA
1 CCAATAT-AGTGCAGACAAGCCA
*
12138859 CC-A-ATAGTGTAGACAAGCCA
1 CCAATATAGTGCAGACAAGCCA
12138879 CCAATA
1 CCAATA
12138885 ACGATAATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
20 15 0.68
21 3 0.14
22 2 0.09
23 2 0.09
ACGTcount: A:0.43, C:0.27, G:0.14, T:0.16
Consensus pattern (22 bp):
CCAATATAGTGCAGACAAGCCA
Found at i:12138872 original size:20 final size:20
Alignment explanation
Indices: 12138844--12138884 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12138834 TGCCAATATA
*
12138844 AGTGCAGACAATCCACCAAT
1 AGTGCAGACAAGCCACCAAT
*
12138864 AGTGTAGACAAGCCACCAAT
1 AGTGCAGACAAGCCACCAAT
12138884 A
1 A
12138885 ACGATAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.15
Consensus pattern (20 bp):
AGTGCAGACAAGCCACCAAT
Found at i:12143741 original size:6 final size:6
Alignment explanation
Indices: 12143730--12143777 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
12143720 TTATCTTATC
* * * *
12143730 CATCTT CATCTT CACCTT GAGCTC CATCTT CATCTT CATCTT CATCTT
1 CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT
12143778 GTTCCTCCGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.35, G:0.04, T:0.44
Consensus pattern (6 bp):
CATCTT
Found at i:12145906 original size:17 final size:17
Alignment explanation
Indices: 12145884--12145917 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12145874 AAAATTAGAG
12145884 AATTGAGAGAATGGATA
1 AATTGAGAGAATGGATA
*
12145901 AATTGAGAGAATTGATA
1 AATTGAGAGAATGGATA
12145918 GAACTATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (17 bp):
AATTGAGAGAATGGATA
Found at i:12150718 original size:10 final size:10
Alignment explanation
Indices: 12150658--12150770 Score: 53
Period size: 9 Copynumber: 11.6 Consensus size: 10
12150648 ATTAAATTAT
12150658 AATTAT-AAA
1 AATTATAAAA
12150667 AATTATAAAA
1 AATTATAAAA
*
12150677 GAATT-TATAA
1 -AATTATAAAA
*
12150687 AA-TATATAGA
1 AATTATA-AAA
*
12150697 AATATAGAAAAA
1 AAT-TA-TAAAA
12150709 AATTAT--AA
1 AATTATAAAA
* *
12150717 AATTTTATAA
1 AATTATAAAA
* *
12150727 AGTTGTAAGAA
1 AATTATAA-AA
12150738 AATTATAAAA
1 AATTATAAAA
*
12150748 AA-T-GAAAA
1 AATTATAAAA
12150756 AATTAT-AAA
1 AATTATAAAA
12150765 AATTAT
1 AATTAT
12150771 TATACCAAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
8 14 0.18
9 21 0.27
10 21 0.27
11 14 0.18
12 7 0.09
13 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (10 bp):
AATTATAAAA
Found at i:12150765 original size:8 final size:9
Alignment explanation
Indices: 12150658--12150770 Score: 52
Period size: 10 Copynumber: 11.7 Consensus size: 9
12150648 ATTAAATTAT
12150658 AATTATAAA
1 AATTATAAA
12150667 AATTATAAAA
1 AATTAT-AAA
12150677 GAATT-TATAA
1 -AATTATA-AA
12150687 AATATATAGAA
1 AAT-TATA-AA
* *
12150698 ATATAGAAAAA
1 A-AT-TATAAA
12150709 AATTAT-AA
1 AATTATAAA
*
12150717 AATTTTATAA
1 AATTATA-AA
* *
12150727 AGTTGTAAGAA
1 AATTAT-A-AA
12150738 AATTATAAAA
1 AATTAT-AAA
*
12150748 AATGA-AAA
1 AATTATAAA
12150756 AATTATAAA
1 AATTATAAA
12150765 AATTAT
1 AATTAT
12150771 TATACCAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
8 14 0.17
9 20 0.25
10 21 0.26
11 21 0.26
12 5 0.06
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (9 bp):
AATTATAAA
Found at i:12151051 original size:28 final size:28
Alignment explanation
Indices: 12150985--12151083 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 28
12150975 ATTTTACACT
** *
12150985 TTTTTATATTTTT-TTACAATTATTATTA
1 TTTTTATATTTTTATTA-AAAAATTAATA
* *
12151013 TCTCTA-ATTTTTATTAAAAAATTAATA
1 TTTTTATATTTTTATTAAAAAATTAATA
*
12151040 TTTTTATATTTTTTATT-AAAATTTAATAA
1 TTTTTATA-TTTTTATTAAAAAATTAAT-A
12151069 TTTCTTAT-TTTTTAT
1 TTT-TTATATTTTTAT
12151084 CTTTATCATT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
27 18 0.31
28 24 0.41
29 12 0.21
30 4 0.07
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTTATATTTTTATTAAAAAATTAATA
Found at i:12151056 original size:29 final size:28
Alignment explanation
Indices: 12151020--12151083 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
12151010 TTATCTCTAA
*
12151020 TTTTTATTAAAAAATTAAT-ATTTTTATAT
1 TTTTTATT-AAAAATTAATAATTTCT-TAT
*
12151049 TTTTTATTAAAATTTAATAATTTCTTAT
1 TTTTTATTAAAAATTAATAATTTCTTAT
12151077 TTTTTAT
1 TTTTTAT
12151084 CTTTATCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 19 0.59
29 13 0.41
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTTATTAAAAATTAATAATTTCTTAT
Found at i:12165593 original size:45 final size:45
Alignment explanation
Indices: 12165529--12165618 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
12165519 TGGTCAACAG
* * *
12165529 CACGATGGATCAAACAAAGTGGTGCTGATTTACTCGGGAATTCTA
1 CACGATGGACCAAACAAAGTGGTGCTGACTTACTCGGCAATTCTA
12165574 CACGATGGACCAAACAAAGTGGTGCTGACTTACTCGGCAATTCTA
1 CACGATGGACCAAACAAAGTGGTGCTGACTTACTCGGCAATTCTA
12165619 AGTATTGGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (45 bp):
CACGATGGACCAAACAAAGTGGTGCTGACTTACTCGGCAATTCTA
Found at i:12187437 original size:16 final size:16
Alignment explanation
Indices: 12187413--12187446 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12187403 AACCTGTAAC
*
12187413 CACGTTTACTTTTCAT
1 CACGCTTACTTTTCAT
12187429 CACGCTTACTTTTCAT
1 CACGCTTACTTTTCAT
12187445 CA
1 CA
12187447 ACCCTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.06, T:0.44
Consensus pattern (16 bp):
CACGCTTACTTTTCAT
Found at i:12189853 original size:30 final size:28
Alignment explanation
Indices: 12189796--12189865 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
12189786 TGATTTTTCC
*
12189796 CTTAAAATTTTTAGAAAACTTTAATTAAGCT
1 CTTAAAA-TTTTAGAAAACTCTAATTAA--T
* *
12189827 CTTAAAATTTTAGAAAAGTCTCATTAAT
1 CTTAAAATTTTAGAAAACTCTAATTAAT
*
12189855 CTCAAAATTTT
1 CTTAAAATTTT
12189866 TAAAAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.31
30 17 0.49
31 7 0.20
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (28 bp):
CTTAAAATTTTAGAAAACTCTAATTAAT
Found at i:12196341 original size:19 final size:19
Alignment explanation
Indices: 12196319--12196365 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
12196309 TATTTAAAAC
12196319 TTATAAAAAATAAAAATAT
1 TTATAAAAAATAAAAATAT
** *
12196338 TTATAAAATTTTAAAATAT
1 TTATAAAAAATAAAAATAT
*
12196357 ATATAAAAA
1 TTATAAAAA
12196366 TTGACAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTATAAAAAATAAAAATAT
Found at i:12216699 original size:44 final size:44
Alignment explanation
Indices: 12216591--12217341 Score: 439
Period size: 44 Copynumber: 16.9 Consensus size: 44
12216581 GATTCATCGT
* * *
12216591 TTTAATC-AGCTCCACTGCAACTTTAGGGAGAT-AGATTAGTAGC
1 TTTAATCTA-CTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
* * * * *
12216634 TTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGACTATTGGC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
*
12216678 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGA-T-TTGTC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
* * * *
12216720 ATCTTCAGTCTACTCCACTGCAACCTCAGGGAGATAAGACTTGTTATAGTAGA
1 -T-TT-AATCTACTCCACTGCAACTTCAGGGAGATAAGA----TTAT--TGGC
* * * * * * *
12216773 TTTAATCCGAC-CTACTGTAACTTCAGAGG-TATAGGATTCA-TCGT
1 TTTAAT-CTACTCCACTGCAACTTCAG-GGAGATAAGATT-ATTGGC
* * ** **
12216817 TTTAATCCACTCTACTGCAACTTCAGGGAGATAAGATTGGTATC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
* * * * * **
12216861 ATTAGTTTGCTCCACTGTAACTTCAGGGAGATAAGATT-TGTAAC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAT-TGGC
* * *
12216905 TTTAAT-TCGCTCCACTGCAACTTCAAGGAGATAGGATTATTGGC
1 TTTAATCT-ACTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
*****
12216949 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCACCATA
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATT-ATTGGC
* * * * * * *
12216994 TTCAGTTTGCCCCACTGCAACTTCAGGGGGATAAGACTATTGGC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
* * * **
12217038 TTTAATCTTCTTCACTGCAACTTCAAGGAGATAAGATT-TGTAAC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAT-TGGC
** * *
12217082 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGA
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
* *****
12217126 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATT-ATTGGC
* * * * * *
12217171 TTTAGTCTACCCCACTGTAATTTCAGAGG-GATAAGACTTGCTT-TC
1 TTTAATCTACTCCACTGCAACTTCAG-GGAGATAAGA-TT-ATTGGC
* * * * * **
12217216 TTCAGTCTGCTCTACTGCAACTTCAGGGAGATAAGACTT-GTAAC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGA-TTATTGGC
* ** * * *
12217260 TTTAATTTGTTCCATTGCAACTTTAGGGAGATATGATTATTGGC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
* * * *
12217304 TTTAATTTACTCCACTGTAACTTTAAGGAGATAAGATT
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATT
12217342 TGCCATCTTC
Statistics
Matches: 544, Mismatches: 132, Indels: 63
0.74 0.18 0.09
Matches are distributed among these distances:
42 4 0.01
43 38 0.07
44 339 0.62
45 126 0.23
46 6 0.01
47 1 0.00
50 20 0.04
51 8 0.01
52 1 0.00
53 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTATTGGC
Found at i:12216849 original size:226 final size:224
Alignment explanation
Indices: 12216498--12217210 Score: 747
Period size: 226 Copynumber: 3.2 Consensus size: 224
12216488 ATTTGTGGTT
* * *
12216498 TTAGTCTACTCCACTGCAACTTTAAGGAGATAAGACTTGTTATGGTAGATTTAATCCGACCTACT
1 TTAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTTATAGTAGATTTAATCCGACCTACT
* * *
12216563 GCAACTTCAAAGGTATAGGATTCATCGTTTTAAT-CAGCTCCACTGCAACTTTAGGGAGAT-AGA
66 GCAACTTCAGAGGTATAGGATTCATCGTTTTAATCCA-CTCTACTGCAACTTCAGGGAGATAAGA
* * * *
12216626 TTAGTAGCTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGACTATTGGCTTTAATCTACTCC
130 TTAGTAACTT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TATTGGCTTTAATCTGCTCC
*
12216691 ACTGCAACTTCAGGGAGATAAGATTTGTCATC
193 ACTGCAACTTCAGGGAGATAAGATTTGCCATC
*
12216723 TTCAGTCTACTCCACTGCAACCTCAGGGAGATAAGACTTGTTATAGTAGATTTAATCCGACCTAC
1 TT-AGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTTATAGTAGATTTAATCCGACCTAC
*
12216788 TGTAACTTCAGAGGTATAGGATTCATCGTTTTAATCCACTCTACTGCAACTTCAGGGAGATAAGA
65 TGCAACTTCAGAGGTATAGGATTCATCGTTTTAATCCACTCTACTGCAACTTCAGGGAGATAAGA
* * * * * *
12216853 TTGGTATCATTAGTTTGCTCCACTGTAACTTCAGGGAGATAAGAT-TTGTAACTTTAAT-TCGCT
130 TTAGTAAC-TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATATTG--GCTTTAATCT-GCT
* * *
12216916 CCACTGCAACTTCAAGGAGATAGGATTATTGGC-T-
191 CCACTGCAACTTCAGGGAGATAAGA-T-TTGCCATC
* *** * *
12216950 TTAATCTACTCCACTGCAACTTCAGGGAGATAAGA-TTCACCATATTCAG-TTT--GCC--CC-A
1 TTAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTT-GTTATAGT-AGATTTAATCCGACCTA
* * * * * * ** *
12217008 CTGCAACTTCAGGGGGATAAGACT-ATTGGCTTTAATCTTCT-TCACTGCAACTTCAAGGAGATA
64 CTGCAACTTCAGAGGTATAGGATTCA-TCGTTTTAATCCACTCT-ACTGCAACTTCAGGGAGATA
* * * *
12217071 AGATTTGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGATTTAATCTGC
127 AGATTAGTAAC-TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TATTGGCTTTAATCTGC
*
12217136 TCCACTGCAACTTCAGGGAGATAAGATTCGCCATC
190 TCCACTGCAACTTCAGGGAGATAAGATTTGCCATC
* * *
12217171 TTTAGTCTACCCCACTGTAATTTCAGAGG-GATAAGACTTG
1 -TTAGTCTACTCCACTGCAACTTCAG-GGAGATAAGACTTG
12217211 CTTTCTTCAG
Statistics
Matches: 411, Mismatches: 56, Indels: 45
0.80 0.11 0.09
Matches are distributed among these distances:
219 3 0.01
220 4 0.01
221 121 0.29
222 32 0.08
223 7 0.02
224 2 0.00
225 7 0.02
226 152 0.37
227 75 0.18
228 4 0.01
229 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (224 bp):
TTAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTTATAGTAGATTTAATCCGACCTACT
GCAACTTCAGAGGTATAGGATTCATCGTTTTAATCCACTCTACTGCAACTTCAGGGAGATAAGAT
TAGTAACTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATATTGGCTTTAATCTGCTCCACT
GCAACTTCAGGGAGATAAGATTTGCCATC
Found at i:12216922 original size:88 final size:88
Alignment explanation
Indices: 12216591--12217343 Score: 574
Period size: 88 Copynumber: 8.5 Consensus size: 88
12216581 GATTCATCGT
* * * * *
12216591 TTTAATCAGCTCCACTGCAACTTTAGGGAGAT-AGATTAGTAGCTTCAA-TCTGCTCCACTGCAA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTTAATTC-GCTCCACTGCAA
* * *
12216654 CTTCAAGAAGATAAGACTATTGGC
65 CTTCAGGGAGATAAGATTATTGGC
* * * * *
12216678 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTCA-TCTTCAGTCTACTCCACTGCA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACT-TTAATTC-GCTCCACTGCA
* * *
12216742 ACCTCAGGGAGATAAGACTTGTTATAGTAGA
64 ACTTCAGGGAGATAAGA----TTAT--TGGC
* * * * * ** *** * * *
12216773 TTTAATCCGAC-CTACTGTAACTTCAGAGG-TATAGGATTCATCGTTTTAATCCACTCTACTGCA
1 TTTAATCTG-CTCCACTGCAACTTCAG-GGAGATAAGATTTGTAACTTTAATTCGCTCCACTGCA
** **
12216836 ACTTCAGGGAGATAAGATTGGTATC
64 ACTTCAGGGAGATAAGATTATTGGC
* * * *
12216861 ATTAGTTTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTAACTTTAATTCGCTCCACTGCAAC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTTAATTCGCTCCACTGCAAC
* *
12216926 TTCAAGGAGATAGGATTATTGGC
66 TTCAGGGAGATAAGATTATTGGC
* * * * * *
12216949 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGA-TT-CACCATATTCAGTTTGCCCCACTGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC-T-TT-AATTCGCTCCACTGC
* *
12217012 AACTTCAGGGGGATAAGACTATTGGC
63 AACTTCAGGGAGATAAGATTATTGGC
* * * *
12217038 TTTAATCTTCTTCACTGCAACTTCAAGGAGATAAGATTTGTAACTTTAATCCGCTCCACTGCAAC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTTAATTCGCTCCACTGCAAC
* *
12217103 TTCAGGGAGATAGGATTATTGGA
66 TTCAGGGAGATAAGATTATTGGC
* * * * *
12217126 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTTAGTCTAC-C-CCACTGT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAACTTTAAT-T-CGCTCCACTGC
* * *
12217189 AATTTCAGAGG-GATAAGACTTGCTT-TC
63 AACTTCAG-GGAGATAAGA-TT-ATTGGC
* * * * * * *
12217216 TTCAGTCTGCTCTACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATTTGTTCCATTGCAAC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTTAATTCGCTCCACTGCAAC
* *
12217281 TTTAGGGAGATATGATTATTGGC
66 TTCAGGGAGATAAGATTATTGGC
* * * * *
12217304 TTTAATTTACTCCACTGTAACTTTAAGGAGATAAGATTTG
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
12217344 CCATCTTCTT
Statistics
Matches: 516, Mismatches: 121, Indels: 57
0.74 0.17 0.08
Matches are distributed among these distances:
86 2 0.00
87 38 0.07
88 212 0.41
89 146 0.28
90 45 0.09
91 5 0.01
93 3 0.01
94 26 0.05
95 35 0.07
96 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (88 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTTAATTCGCTCCACTGCAAC
TTCAGGGAGATAAGATTATTGGC
Found at i:12217059 original size:133 final size:132
Alignment explanation
Indices: 12216599--12217341 Score: 529
Period size: 133 Copynumber: 5.6 Consensus size: 132
12216589 GTTTTAATCA
* * * * *
12216599 GCTCCACTGCAACTTTAGGGAGAT-AGATTAGTAGCTTCAATCTGCTCCACTGCAACTTCAAGAA
1 GCTCCACTGCAACTTCAGGGAGATAAGACTATTAGCTTTAATCTGCTCCACTGCAACTTCAAGGA
* * * *
12216663 GATAAGACTATTGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAG
66 GATAAGATTATTGGCTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGA-TTGCCATATTCAG
*
12216728 TCT
130 TTT
* * * * * *
12216731 ACTCCACTGCAACCTCAGGGAGATAAGACTTGTTATAGTAGATTTAATCCGAC-CTACTGTAACT
1 GCTCCACTGCAACTTCAGGGAGATAAGAC----TAT--TAGCTTTAATCTG-CTCCACTGCAACT
* * * * * **
12216795 TCAGAGG-TATAGGATTCA-TCGTTTTAATCCACTCTACTGCAACTTCAGGGAGATAAGATTGGT
59 TCA-AGGAGATAAGATT-ATTGGCTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGATTGCC
12216858 ATCATT-AGTTT
122 AT-ATTCAGTTT
* * *
12216869 GCTCCACTGTAACTTCAGGGAGATAAGA-TTTGTAACTTTAAT-TCGCTCCACTGCAACTTCAAG
1 GCTCCACTGCAACTTCAGGGAGATAAGACTAT-TAGCTTTAATCT-GCTCCACTGCAACTTCAAG
* * *
12216932 GAGATAGGATTATTGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCACCATATTC
64 GAGATAAGATTATTGGCTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGATT-GCCATATTC
12216997 AGTTT
128 AGTTT
* * * * *
12217002 GCCCCACTGCAACTTCAGGGGGATAAGACTATTGGCTTTAATCTTCTTCACTGCAACTTCAAGGA
1 GCTCCACTGCAACTTCAGGGAGATAAGACTATTAGCTTTAATCTGCTCCACTGCAACTTCAAGGA
** * * ***** * *
12217067 GATAAGATT-TGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGATTTAA
66 GATAAGATTAT-TGGCTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGATTGCCATATTCAG
*
12217131 TCT
130 TTT
* *** * * * * * *
12217134 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTTAGTCTACCCCACTGTAATTTCAGAG
1 GCTCCACTGCAACTTCAGGGAGATAAGACT-ATTAGCTTTAATCTGCTCCACTGCAACTTCA-AG
* * * * ** * *
12217199 G-GATAAGACTTGCTT-TCTTCAGTCTGCTCTACTGCAACTTCAGGGAGATAAGACTTG-TA-AC
64 GAGATAAGA-TT-ATTGGCTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGA-TTGCCATA-
* *
12217260 TTTAATTT
125 TTCAGTTT
* * * * * * * * * *
12217268 GTTCCATTGCAACTTTAGGGAGATATGATTATTGGCTTTAATTTACTCCACTGTAACTTTAAGGA
1 GCTCCACTGCAACTTCAGGGAGATAAGACTATTAGCTTTAATCTGCTCCACTGCAACTTCAAGGA
12217333 GATAAGATT
66 GATAAGATT
12217342 TGCCATCTTC
Statistics
Matches: 486, Mismatches: 97, Indels: 56
0.76 0.15 0.09
Matches are distributed among these distances:
131 5 0.01
132 132 0.27
133 165 0.34
134 74 0.15
135 3 0.01
136 1 0.00
137 2 0.00
138 34 0.07
139 66 0.14
140 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (132 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTATTAGCTTTAATCTGCTCCACTGCAACTTCAAGGA
GATAAGATTATTGGCTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGATTGCCATATTCAGT
TT
Found at i:12217062 original size:177 final size:176
Alignment explanation
Indices: 12216830--12217341 Score: 636
Period size: 177 Copynumber: 2.9 Consensus size: 176
12216820 AATCCACTCT
* * * * * *
12216830 ACTGCAACTTCAG-GGAGATAAGA-TTGGTATCATTAGTTTGCTCCACTGTAACTTCAGGGAGAT
1 ACTGCAACTTCAGAGG-GATAAGACTTGCTTTAATCAGTCT-CT-CACTGCAACTTCAGGGAGAT
*
12216893 AAGATTTGTAACTTTAATTCGCTCCACTGCAACTTCAAGGAGATAGGATTATTGGCTTTAATCTA
63 AAGATTTGTAACTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTA
* *
12216958 CTCCACTGCAACTTCAGGGAGATAAGATTCACCATATTCAGTTTGCCCC
128 CTCCACTGCAACTTCAGGGAGATAAGATTCACCATATTCAGTCTACCCC
* * *
12217007 ACTGCAACTTCAGGGGGATAAGACTATTGGCTTTAATC-TTCT-TCACTGCAACTTCAAGGAGAT
1 ACTGCAACTTCAGAGGGATAAGAC--TT-GCTTTAATCAGTCTCTCACTGCAACTTCAGGGAGAT
* * *
12217070 AAGATTTGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGATTTAATCTG
63 AAGATTTGTAACTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTA
* * *
12217135 CTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTTAGTCTACCCC
128 CTCCACTGCAACTTCAGGGAGATAAGATTCACCATATTCAGTCTACCCC
* * **
12217184 ACTGTAATTTCAGAGGGATAAGACTTGCTTTCTTCAGTCTGCTCTACTGCAACTTCAGGGAGATA
1 ACTGCAACTTCAGAGGGATAAGACTTGCTTTAATCAGTCT-CTC-ACTGCAACTTCAGGGAGATA
* * * * * * *
12217249 AGACTTGTAACTTTAATTTGTTCCATTGCAACTTTAGGGAGATATGATTATTGGCTTTAATTTAC
64 AGATTTGTAACTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTAC
* * *
12217314 TCCACTGTAACTTTAAGGAGATAAGATT
129 TCCACTGCAACTTCAGGGAGATAAGATT
12217342 TGCCATCTTC
Statistics
Matches: 289, Mismatches: 37, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
174 7 0.02
175 5 0.02
177 166 0.57
178 102 0.35
180 4 0.01
181 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (176 bp):
ACTGCAACTTCAGAGGGATAAGACTTGCTTTAATCAGTCTCTCACTGCAACTTCAGGGAGATAAG
ATTTGTAACTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTACTC
CACTGCAACTTCAGGGAGATAAGATTCACCATATTCAGTCTACCCC
Found at i:12218662 original size:31 final size:30
Alignment explanation
Indices: 12218598--12218662 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
12218588 GGCCTCTCCA
* * *
12218598 TTTTTTATGACTCAAAGCACCTTTTACGTG
1 TTTTTTAGGACTCAAAGCACCCTTTACGGG
* *
12218628 TTTTTTAGGGACTCAAGGCACCCTTTGCGGG
1 TTTTTTA-GGACTCAAAGCACCCTTTACGGG
12218659 TTTT
1 TTTT
12218663 CACCTTGGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (30 bp):
TTTTTTAGGACTCAAAGCACCCTTTACGGG
Found at i:12220570 original size:48 final size:48
Alignment explanation
Indices: 12220515--12220613 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
12220505 AATTATTTGT
*
12220515 ATAGTATGATTATGAATGAAAGAATGATTTGGAAGAAAATCCAAAAGA
1 ATAGTATGATTATAAATGAAAGAATGATTTGGAAGAAAATCCAAAAGA
12220563 ATAGTATGATTATAAATGAAAGAATGATTTGGAAGAAAATCCAAAAGA
1 ATAGTATGATTATAAATGAAAGAATGATTTGGAAGAAAATCCAAAAGA
12220611 ATA
1 ATA
12220614 AAAGAAACAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.52, C:0.04, G:0.19, T:0.25
Consensus pattern (48 bp):
ATAGTATGATTATAAATGAAAGAATGATTTGGAAGAAAATCCAAAAGA
Found at i:12220602 original size:23 final size:23
Alignment explanation
Indices: 12220529--12220602 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 23
12220519 TATGATTATG
12220529 AATGAAAGAATGATTTGGAAGAA
1 AATGAAAGAATGATTTGGAAGAA
* * **
12220552 AATCCAAAAGAAT-AGTAT-GATTATA
1 AAT--GAAAGAATGA-TTTGGAAGA-A
12220577 AATGAAAGAATGATTTGGAAGAA
1 AATGAAAGAATGATTTGGAAGAA
12220600 AAT
1 AAT
12220603 CCAAAAGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
23 16 0.43
24 8 0.22
25 13 0.35
ACGTcount: A:0.53, C:0.03, G:0.20, T:0.24
Consensus pattern (23 bp):
AATGAAAGAATGATTTGGAAGAA
Found at i:12220610 original size:25 final size:25
Alignment explanation
Indices: 12220533--12220612 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 25
12220523 ATTATGAATG
12220533 AAAGAATGATTTGGAAGAAAATCCA
1 AAAGAATGATTTGGAAGAAAATCCA
* ** *
12220558 AAAGAAT-AGTAT-GATTATAAAT--G
1 AAAGAATGA-TTTGGAAGA-AAATCCA
12220581 AAAGAATGATTTGGAAGAAAATCCA
1 AAAGAATGATTTGGAAGAAAATCCA
12220606 AAAGAAT
1 AAAGAAT
12220613 AAAAGAAACA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
23 13 0.32
24 8 0.20
25 20 0.49
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.23
Consensus pattern (25 bp):
AAAGAATGATTTGGAAGAAAATCCA
Found at i:12225354 original size:4 final size:4
Alignment explanation
Indices: 12225340--12225375 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
12225330 ATGATAATAA
*
12225340 TAAT AAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
12225376 AGCAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
TAAT
Found at i:12227744 original size:20 final size:19
Alignment explanation
Indices: 12227707--12227746 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12227697 AATTTTAAAA
*
12227707 TATTTTTAAAATACTTTTT
1 TATTTTTAAAATAATTTTT
*
12227726 TATTTTTAAAATAAATTTT
1 TATTTTTAAAATAATTTTT
12227745 TA
1 TA
12227747 GTGTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTTAAAATAATTTTT
Found at i:12227753 original size:20 final size:19
Alignment explanation
Indices: 12227711--12227753 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12227701 TTAAAATATT
** *
12227711 TTTAAAATACTTTTTTATT
1 TTTAAAATAAATTTTTATG
12227730 TTTAAAATAAATTTTTAGTG
1 TTTAAAATAAATTTTTA-TG
12227750 TTTA
1 TTTA
12227754 TTAAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTAAAATAAATTTTTATG
Found at i:12232978 original size:4 final size:4
Alignment explanation
Indices: 12232969--12233008 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
12232959 TTCTTAATTT
*
12232969 ACAA ACAA ACAA ATAA ACAA ACAA ACAA ACAA A-AA ACAA A
1 ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA A
12233009 TGTTTTGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.78, C:0.20, G:0.00, T:0.03
Consensus pattern (4 bp):
ACAA
Found at i:12234326 original size:24 final size:24
Alignment explanation
Indices: 12234294--12234339 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
12234284 TATAACTTTT
12234294 TTTTTATTTACCAAAAAATATATA
1 TTTTTATTTACCAAAAAATATATA
*
12234318 TTTTTATTTACCAAAATATATA
1 TTTTTATTTACCAAAAAATATA
12234340 AAAAAACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTTTATTTACCAAAAAATATATA
Found at i:12234422 original size:27 final size:27
Alignment explanation
Indices: 12234380--12234432 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
12234370 TGATCAGGCC
12234380 AATTAAATTGGCGGCACCAAAGGTGCA
1 AATTAAATTGGCGGCACCAAAGGTGCA
* *
12234407 AATTAAATTGGTGGCACCAATGGTGC
1 AATTAAATTGGCGGCACCAAAGGTGC
12234433 CAAAGTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (27 bp):
AATTAAATTGGCGGCACCAAAGGTGCA
Found at i:12234443 original size:27 final size:28
Alignment explanation
Indices: 12234383--12234463 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 28
12234373 TCAGGCCAAT
* *
12234383 TAAATTGGCGGCACCAAAGGTG-CAAAT
1 TAAATTGGCGGCACCAATGGTGCCAAAG
*
12234410 TAAATTGGTGGCACCAATGGTGCCAAAG
1 TAAATTGGCGGCACCAATGGTGCCAAAG
* * *
12234438 T-CATTGGCAGCACC-ATGGAGCCAAAG
1 TAAATTGGCGGCACCAATGGTGCCAAAG
12234464 GAAAAAAAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
26 11 0.24
27 30 0.65
28 5 0.11
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (28 bp):
TAAATTGGCGGCACCAATGGTGCCAAAG
Found at i:12234569 original size:18 final size:19
Alignment explanation
Indices: 12234524--12234598 Score: 98
Period size: 19 Copynumber: 4.0 Consensus size: 19
12234514 TATTCTCCTT
* *
12234524 TAACTCTTTTTTTATTTAA
1 TAACTCTATTTTAATTTAA
12234543 TAACTCTATTTTAATTTAA
1 TAACTCTATTTTAATTTAA
* * *
12234562 TAA-ACTATTCTCATTTAA
1 TAACTCTATTTTAATTTAA
12234580 TAACTCTATTTTAATTTAA
1 TAACTCTATTTTAATTTAA
12234599 AAAAATATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
18 15 0.32
19 32 0.68
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (19 bp):
TAACTCTATTTTAATTTAA
Found at i:12234581 original size:37 final size:37
Alignment explanation
Indices: 12234537--12234607 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
12234527 CTCTTTTTTT
* *
12234537 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAAAAAAATATTCTC
12234574 ATTTAATAACTCTATTTTAATTTAAAAAAATATT
1 ATTTAATAACTCTATTTTAATTTAAAAAAATATT
12234608 AAGTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAAAAAAATATTCTC
Found at i:12234634 original size:19 final size:17
Alignment explanation
Indices: 12234590--12234628 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
12234580 TAACTCTATT
12234590 TTAA-TTTAAAAAAATA
1 TTAAGTTTAAAAAAATA
12234606 TTAAGTTTAAAAAAATA
1 TTAAGTTTAAAAAAATA
12234623 TTAAGT
1 TTAAGT
12234629 ACTTAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
TTAAGTTTAAAAAAATA
Found at i:12234962 original size:27 final size:27
Alignment explanation
Indices: 12234926--12234981 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
12234916 AATGACTTTA
* *
12234926 GCACCATTGGTGCCACTAATTTACTTG
1 GCACCATTGGTGCCACCAATTTAATTG
* *
12234953 GCACCTTTGGTGCCGCCAATTTAATTG
1 GCACCATTGGTGCCACCAATTTAATTG
12234980 GC
1 GC
12234982 CTGATCAAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (27 bp):
GCACCATTGGTGCCACCAATTTAATTG
Found at i:12239061 original size:5 final size:5
Alignment explanation
Indices: 12239051--12239075 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12239041 AAACAATACC
12239051 TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA
12239076 AGAATAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:12240547 original size:38 final size:36
Alignment explanation
Indices: 12240461--12240554 Score: 125
Period size: 38 Copynumber: 2.6 Consensus size: 36
12240451 GTTTTCTAGC
12240461 ATAATGGTTTGTCATGGGATATCTCTAGTTTTAAGG
1 ATAATGGTTTGTCATGGGATATCTCTAGTTTTAAGG
* * *
12240497 ATAGTAGCTTGTCATGGGATACGTCTCTAGTTTTAAGG
1 ATAATGGTTTGTCATGGGATA--TCTCTAGTTTTAAGG
* *
12240535 TTAATGGTTTGTCATAGGAT
1 ATAATGGTTTGTCATGGGAT
12240555 GTAAGCCTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 18 0.38
38 30 0.62
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (36 bp):
ATAATGGTTTGTCATGGGATATCTCTAGTTTTAAGG
Found at i:12241319 original size:16 final size:15
Alignment explanation
Indices: 12241294--12241323 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12241284 ATTAAGTTAA
12241294 TTAACTAAATGCAAG
1 TTAACTAAATGCAAG
12241309 TTAACCTAAATGCAA
1 TTAA-CTAAATGCAA
12241324 ATGAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (15 bp):
TTAACTAAATGCAAG
Found at i:12245027 original size:55 final size:55
Alignment explanation
Indices: 12244943--12245052 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
12244933 AAATACCAAG
12244943 AATGCTAAGGCCAATGTTGTTCTAGTTGAAGAAGATAAGAGAGAACCCGAGACAT
1 AATGCTAAGGCCAATGTTGTTCTAGTTGAAGAAGATAAGAGAGAACCCGAGACAT
12244998 AATGCTAAGGCCAATGTTGTTCTAGTTGAAGAAGATAAGAGAGAACCCGAGACAT
1 AATGCTAAGGCCAATGTTGTTCTAGTTGAAGAAGATAAGAGAGAACCCGAGACAT
12245053 TTGAGGAAGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (55 bp):
AATGCTAAGGCCAATGTTGTTCTAGTTGAAGAAGATAAGAGAGAACCCGAGACAT
Found at i:12247292 original size:27 final size:27
Alignment explanation
Indices: 12247243--12247295 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
12247233 AAAGGTAGAA
* *
12247243 TTTTAATTTTAGAGTGTATATTTAATC
1 TTTTAATTTTAGAATGTACATTTAATC
*
12247270 TTTTAATTTTAGAATGTCCATTTAAT
1 TTTTAATTTTAGAATGTACATTTAAT
12247296 TTTATTTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (27 bp):
TTTTAATTTTAGAATGTACATTTAATC
Found at i:12254057 original size:46 final size:45
Alignment explanation
Indices: 12254004--12254131 Score: 168
Period size: 45 Copynumber: 2.8 Consensus size: 45
12253994 CTAAACAATA
* * * *
12254004 ATGCTCCTAAGTACAAGCTTAAATTGTTCATCCAAAATAAATGATG
1 ATGCTCCTAAGCACGAGCTTAAACTGTTCATCCAAAAT-AATGATC
*
12254050 ATGCTCCTAAGCACGAGCTTAAACTGTT-AGCACAAAATAATGATC
1 ATGCTCCTAAGCACGAGCTTAAACTGTTCATC-CAAAATAATGATC
* *
12254095 ATACTCCTAAGCACGAGTTTAAACTGTTCATCCAAAA
1 ATGCTCCTAAGCACGAGCTTAAACTGTTCATCCAAAA
12254132 ACAGATGCTC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
45 39 0.54
46 33 0.46
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (45 bp):
ATGCTCCTAAGCACGAGCTTAAACTGTTCATCCAAAATAATGATC
Found at i:12254937 original size:43 final size:43
Alignment explanation
Indices: 12254890--12255005 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 43
12254880 TCGACGACTA
*
12254890 TTGAAGCGAAC-ATCATTGATTCAAGATCAAGTCTCAATGACCC
1 TTGAAGCAAACTA-CATTGATTCAAGATCAAGTCTCAATGACCC
* *
12254933 TTGAAGCAAACTACATTGATTCAAGATCAAGTCTCGATTACCC
1 TTGAAGCAAACTACATTGATTCAAGATCAAGTCTCAATGACCC
* * *
12254976 TTAAAGCAAACTATATT-ATCCCAAGATCAA
1 TTGAAGCAAACTACATTGAT-TCAAGATCAA
12255006 ATCTTGACAA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
42 2 0.03
43 62 0.95
44 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (43 bp):
TTGAAGCAAACTACATTGATTCAAGATCAAGTCTCAATGACCC
Found at i:12257336 original size:18 final size:18
Alignment explanation
Indices: 12257315--12257360 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
12257305 GTTATATTAA
12257315 ATTATTTAAATATAATTT
1 ATTATTTAAATATAATTT
* *
12257333 ATTA-TTATATTTAATTT
1 ATTATTTAAATATAATTT
12257350 -TT-TTTAAATAT
1 ATTATTTAAATAT
12257361 TTTATCAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
16 8 0.35
17 11 0.48
18 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTATTTAAATATAATTT
Found at i:12258842 original size:12 final size:12
Alignment explanation
Indices: 12258825--12258854 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12258815 GAGTCGTAGG
*
12258825 CACGACTATTGC
1 CACGACTATTGA
12258837 CACGACTATTGA
1 CACGACTATTGA
12258849 CACGAC
1 CACGAC
12258855 AGAAATTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (12 bp):
CACGACTATTGA
Found at i:12274067 original size:6 final size:6
Alignment explanation
Indices: 12274058--12274086 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12274048 ATCCTTTGCC
12274058 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
12274087 TATAGTGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:12275849 original size:16 final size:16
Alignment explanation
Indices: 12275808--12275862 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
12275798 CAATTGACTT
12275808 GAAATGACCCAAACTA
1 GAAATGACCCAAACTA
*
12275824 GAAATTACCCAACACT-
1 GAAATGACCCAA-ACTA
* *
12275840 GTAATGACCCGAATCTA
1 GAAATGACCC-AAACTA
12275857 -AAATGA
1 GAAATGA
12275863 TCTAAACATG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 26 0.84
17 5 0.16
ACGTcount: A:0.45, C:0.24, G:0.13, T:0.18
Consensus pattern (16 bp):
GAAATGACCCAAACTA
Found at i:12275876 original size:16 final size:16
Alignment explanation
Indices: 12275857--12275940 Score: 50
Period size: 16 Copynumber: 5.4 Consensus size: 16
12275847 CCCGAATCTA
12275857 AAATGATCTAAACATG
1 AAATGATCTAAACATG
* * *
12275873 AAATGAATCGAATC-TA
1 AAATG-ATCTAAACATG
* *
12275889 AAATGATCCAAACTTG
1 AAATGATCTAAACATG
* *
12275905 AACA--ATC-AGACTTG
1 AA-ATGATCTAAACATG
*
12275919 AAATGACCTAAACATG
1 AAATGATCTAAACATG
12275935 AAATGA
1 AAATGA
12275941 CCCGAGAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
13 1 0.02
14 8 0.15
15 11 0.21
16 25 0.48
17 7 0.13
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (16 bp):
AAATGATCTAAACATG
Found at i:12275878 original size:32 final size:32
Alignment explanation
Indices: 12275842--12275945 Score: 97
Period size: 32 Copynumber: 3.3 Consensus size: 32
12275832 CCAACACTGT
12275842 AATGACCCGAATCTAAAATGATCTAAACATGA
1 AATGACCCGAATCTAAAATGATCTAAACATGA
** * *
12275874 AATGAATCGAATCTAAAATGATCCAAACTTGA
1 AATGACCCGAATCTAAAATGATCTAAACATGA
* * * * *
12275906 ACA--ATCAGACT-TGAAATGACCTAAACATGA
1 A-ATGACCCGAATCTAAAATGATCTAAACATGA
12275936 AATGACCCGA
1 AATGACCCGA
12275946 GAATAACTAG
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
29 1 0.02
30 16 0.29
31 8 0.15
32 29 0.53
33 1 0.02
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.21
Consensus pattern (32 bp):
AATGACCCGAATCTAAAATGATCTAAACATGA
Found at i:12279252 original size:23 final size:23
Alignment explanation
Indices: 12279204--12279253 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
12279194 AATAAAATTT
* *
12279204 AATTTAAATGGTAAGTAAATTGA
1 AATTTAAATGGTAAATAAATTCA
*
12279227 AATTTAAATAGGTAAATACA-TCA
1 AATTTAAAT-GGTAAATAAATTCA
12279250 AATT
1 AATT
12279254 AAGAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.34
Consensus pattern (23 bp):
AATTTAAATGGTAAATAAATTCA
Found at i:12283389 original size:2 final size:2
Alignment explanation
Indices: 12283382--12283424 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
12283372 GAAAAACCCA
12283382 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12283424 T
1 T
12283425 TTTCAAGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:12295333 original size:11 final size:11
Alignment explanation
Indices: 12295307--12295341 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
12295297 CGAAATAGGG
12295307 GAAAAGAAAGAA
1 GAAAAGAAA-AA
12295319 GAAAAGAAAAA
1 GAAAAGAAAAA
12295330 GAAAAGGAAAAA
1 GAAAA-GAAAAA
12295342 CTAGGGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:12296525 original size:23 final size:23
Alignment explanation
Indices: 12296498--12296588 Score: 89
Period size: 23 Copynumber: 4.1 Consensus size: 23
12296488 AACTTTGCCG
**
12296498 ATCAGGCATTTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
* *
12296521 ATCAGGAACTTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
* * *
12296544 TTTAGGCACCTCATGTGTCGT-T
1 ATCAGGCACCTTATGTGTCGTAT
*
12296566 -TCAGACA-CTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
12296587 AT
1 AT
12296589 TGATCAGGTA
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
20 11 0.20
21 6 0.11
22 2 0.04
23 37 0.66
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (23 bp):
ATCAGGCACCTTATGTGTCGTAT
Done.