Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 39 of 141
Found at i:11748508 original size:22 final size:21
Alignment explanation
Indices: 11748480--11748523 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
11748470 TGAAATCTGA
11748480 TTTTTTTTTCTTTTCGATTTCT
1 TTTTTTTTTCTTTTCG-TTTCT
*
11748502 TTTTTTTTTCTTTTTGTTTCT
1 TTTTTTTTTCTTTTCGTTTCT
11748523 T
1 T
11748524 CGATGTTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.82
Consensus pattern (21 bp):
TTTTTTTTTCTTTTCGTTTCT
Found at i:11749250 original size:17 final size:16
Alignment explanation
Indices: 11749217--11749251 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
11749207 ATATAATATA
11749217 TATTTTTAATGATTTT
1 TATTTTTAATGATTTT
11749233 TATTTTGTAATGTATTTT
1 TATTTT-TAATG-ATTTT
11749251 T
1 T
11749252 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (16 bp):
TATTTTTAATGATTTT
Found at i:11752314 original size:56 final size:50
Alignment explanation
Indices: 11752217--11752452 Score: 220
Period size: 50 Copynumber: 4.6 Consensus size: 50
11752207 CATTTGGGTA
* * * *
11752217 AAGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAGA-T
11752271 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 A--AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * * *
11752323 AAAAGGTCGCATGTAAGACCATGTCTGGGACATAGCGTTGGCACCAAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* ** * * * * * *
11752373 GAGAGGTCCCCCGTAAGACTATGTCTAGGACATGGCATGGGCACCTATAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* ** * *
11752423 GAGAACTCTCATGTAAGACCATATCTGGGA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGA
11752453 TATGACATTG
Statistics
Matches: 152, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
50 105 0.69
52 2 0.01
53 4 0.03
54 1 0.01
55 1 0.01
56 39 0.26
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:11752405 original size:100 final size:102
Alignment explanation
Indices: 11752226--11752465 Score: 263
Period size: 100 Copynumber: 2.3 Consensus size: 102
11752216 AAAGAGATCC
* *
11752226 CATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATTATGAGAGGTCCCATGTAAGA
1 CATGTAAGACCATGTCTGGGACATGACATTGGCACCA-T-AG--TATGAGAGGTCCCACGTAAGA
* * * *
11752291 CCATGTCTGGGACATGGCGTTGGCACCGAGAT-AAAAGGTCG
62 CCATGTCTAGGACATGGCATGGGCACCGAGATGAAAA-CTCG
* * *
11752332 CATGTAAGACCATGTCTGGGACAT-AGCGTTGGCACCA-AG-ATGAGAGGTCCCCCGTAAGACTA
1 CATGTAAGACCATGTCTGGGACATGA-CATTGGCACCATAGTATGAGAGGTCCCACGTAAGACCA
* * * *
11752394 TGTCTAGGACATGGCATGGGCACCTATATGAGAACTCT
65 TGTCTAGGACATGGCATGGGCACCGAGATGAAAACTCG
* *
11752432 CATGTAAGACCATATCTGGGATATGACATTGGCA
1 CATGTAAGACCATGTCTGGGACATGACATTGGCA
11752466 GTACAAGAAA
Statistics
Matches: 115, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
100 75 0.65
101 4 0.03
103 2 0.02
105 1 0.01
106 33 0.29
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (102 bp):
CATGTAAGACCATGTCTGGGACATGACATTGGCACCATAGTATGAGAGGTCCCACGTAAGACCAT
GTCTAGGACATGGCATGGGCACCGAGATGAAAACTCG
Found at i:11759021 original size:30 final size:32
Alignment explanation
Indices: 11758987--11759049 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
11758977 GAGTTCCTCG
11758987 ACAAATGAAAATAA-AA-TCTAGAATAAACTT
1 ACAAATGAAAATAACAAGTCTAGAATAAACTT
11759017 ACAAATGAAAATAACCTAAGTCTAGAATAAACT
1 ACAAATGAAAATAA-C-AAGTCTAGAATAAACT
11759050 AGAAAGAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 14 0.48
33 2 0.07
34 13 0.45
ACGTcount: A:0.57, C:0.13, G:0.08, T:0.22
Consensus pattern (32 bp):
ACAAATGAAAATAACAAGTCTAGAATAAACTT
Found at i:11766562 original size:29 final size:28
Alignment explanation
Indices: 11766528--11766616 Score: 84
Period size: 29 Copynumber: 3.3 Consensus size: 28
11766518 CCTTTCAAAA
11766528 TTCTCTCAAATCCATATTTAATTTCAAT
1 TTCTCTCAAATCCATATTTAATTTCAAT
* *
11766556 TTC-CTC---T-CA-ATTT-CTTTCCAAAA
1 TTCTCTCAAATCCATATTTAATTT-C-AAT
11766579 TTCTCTCAAATCCATATTTAATTTCAATT
1 TTCTCTCAAATCCATATTTAATTTCAA-T
11766608 TTCTCTCAA
1 TTCTCTCAA
11766617 TTTCCTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 19
0.67 0.06 0.27
Matches are distributed among these distances:
21 3 0.06
22 5 0.11
23 7 0.15
24 4 0.09
27 4 0.09
28 7 0.15
29 14 0.30
30 3 0.06
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.46
Consensus pattern (28 bp):
TTCTCTCAAATCCATATTTAATTTCAAT
Found at i:11766585 original size:51 final size:50
Alignment explanation
Indices: 11766513--11766620 Score: 189
Period size: 51 Copynumber: 2.1 Consensus size: 50
11766503 AATTCTCAAA
11766513 AATTTCCTTTCAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCTCTC
1 AATTT-CTTTCAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCTCTC
*
11766564 AATTTCTTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTTCTCTC
1 AATTTCTTT-CAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCTCTC
11766615 AATTTC
1 AATTTC
11766621 CTTTTTTAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
50 4 0.07
51 51 0.93
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (50 bp):
AATTTCTTTCAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCTCTC
Found at i:11767589 original size:20 final size:20
Alignment explanation
Indices: 11767553--11767590 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11767543 TAACGAGATA
11767553 AATTTTATATTACATTTTAC
1 AATTTTATATTACATTTTAC
*
11767573 AATTATTAT-TTAGATTTT
1 AATT-TTATATTACATTTT
11767591 TAAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (20 bp):
AATTTTATATTACATTTTAC
Found at i:11767773 original size:7 final size:7
Alignment explanation
Indices: 11767761--11767785 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11767751 AGTCGATTGA
11767761 TATTTAG
1 TATTTAG
11767768 TATTTAG
1 TATTTAG
11767775 TATTTAG
1 TATTTAG
11767782 TATT
1 TATT
11767786 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:11768463 original size:18 final size:18
Alignment explanation
Indices: 11768437--11768471 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11768427 AGGTGCGTTT
*
11768437 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
11768455 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
11768472 TCCTTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:11768968 original size:44 final size:46
Alignment explanation
Indices: 11768894--11768981 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 46
11768884 ATATTTTGAA
*
11768894 TATTTTGATATTATTTTATGTAAAAAAAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTGATGTAAAAAAAATAGAAATTTATTTGAGT
* *
11768939 TATTTTGATATTATTTGATGT-AATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAAAAAAAATAGAAATTTATTTGA
11768982 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (46 bp):
TATTTTGATATTATTTGATGTAAAAAAAATAGAAATTTATTTGAGT
Found at i:11768983 original size:25 final size:25
Alignment explanation
Indices: 11768949--11769110 Score: 221
Period size: 25 Copynumber: 6.7 Consensus size: 25
11768939 TATTTTGATA
11768949 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
11768974 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
** *
11768999 TT-TTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
*
11769017 ATTATTTGATGTAATAAAATAGAAAT
1 -TTATTTGATGTAATAAAATAGAAGT
11769043 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
11769068 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
11769093 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
11769111 ACCCTAACCT
Statistics
Matches: 121, Mismatches: 8, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 8 0.07
21 3 0.02
23 3 0.02
24 8 0.07
25 94 0.78
26 1 0.01
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:11768999 original size:69 final size:69
Alignment explanation
Indices: 11768904--11769075 Score: 290
Period size: 69 Copynumber: 2.5 Consensus size: 69
11768894 TATTTTGATA
* *
11768904 TTATTTTATGTAAAAAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTATTTGATGT-AATAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
*
11768969 GAAGT
65 GAAAT
11768974 TTATTTGATGTAATAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
1 TTATTTGATGTAATAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
11769039 AAAT
66 AAAT
*
11769043 TTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TTATTTGATGTAATAAAATAGAAATTT-TTTGA
11769076 TGTAATAAAA
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
69 82 0.85
70 15 0.15
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (69 bp):
TTATTTGATGTAATAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
AAAT
Found at i:11769196 original size:23 final size:23
Alignment explanation
Indices: 11769159--11769467 Score: 195
Period size: 23 Copynumber: 13.3 Consensus size: 23
11769149 ATAAAATAGA
11769159 AATTT-ATT-AAAACCCTAACCT
1 AATTTAATTAAAAACCCTAACCT
11769180 AATTTAATTAAAAACCCTAACCCT
1 AATTTAATTAAAAACCCTAA-CCT
*
11769204 -A---ACTTAAAAACCCTAAACCTT
1 AATTTAATTAAAAACCCT-AACC-T
* *
11769225 AA-CT--TTAAAAATCCTAACCT
1 AATTTAATTAAAAACCCTAACCT
11769245 AATTTAA-TACAAAACCCTAACCT
1 AATTTAATTA-AAAACCCTAACCT
11769268 AATTTAATTAAAAACCCTAACCCTAACCT
1 AATTTAATT--AAA----AACCCTAACCT
*
11769297 AATTTTATTAAAAACCCTAAACCTT
1 AATTTAATTAAAAACCCT-AACC-T
* *
11769322 AA-CT--TTAAAAATCCTAACCT
1 AATTTAATTAAAAACCCTAACCT
11769342 AATTTAA-TACAAAACCCTAACCT
1 AATTTAATTA-AAAACCCTAACCT
11769365 AATTTAATTAAAAACCCTAACC-
1 AATTTAATTAAAAACCCTAACCT
* *
11769387 -CTTTAACTTTAAAACCCTAACCCTT
1 AATTTAA-TTAAAAACCCTAA-CC-T
** *
11769412 AACTTTAA--AACCCTACTCCTAACTT
1 AA-TTTAATTAA--AAAC-CCTAACCT
*
11769437 AATTTAATTAAAAACCCTAAACT
1 AATTTAATTAAAAACCCTAACCT
*
11769460 AAGTTAAT
1 AATTTAAT
11769468 AATTTTACAT
Statistics
Matches: 230, Mismatches: 21, Indels: 72
0.71 0.07 0.22
Matches are distributed among these distances:
20 20 0.09
21 23 0.10
22 40 0.17
23 82 0.36
24 19 0.08
25 8 0.03
26 6 0.03
27 13 0.06
29 19 0.08
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (23 bp):
AATTTAATTAAAAACCCTAACCT
Found at i:11769295 original size:29 final size:29
Alignment explanation
Indices: 11769257--11769316 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
11769247 TTTAATACAA
11769257 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
11769286 AACCCTAACCTAATTTTATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
11769315 AA
1 AA
11769317 ACCTTAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:11769315 original size:97 final size:97
Alignment explanation
Indices: 11769207--11769388 Score: 364
Period size: 97 Copynumber: 1.9 Consensus size: 97
11769197 TAACCCTAAC
11769207 TTAAAAACCCTAAACCTTAACTTTAAAAATCCTAACCTAATTTAATACAAAACCCTAACCTAATT
1 TTAAAAACCCTAAACCTTAACTTTAAAAATCCTAACCTAATTTAATACAAAACCCTAACCTAATT
11769272 TAATTAAAAACCCTAACCCTAACCTAATTTTA
66 TAATTAAAAACCCTAACCCTAACCTAATTTTA
11769304 TTAAAAACCCTAAACCTTAACTTTAAAAATCCTAACCTAATTTAATACAAAACCCTAACCTAATT
1 TTAAAAACCCTAAACCTTAACTTTAAAAATCCTAACCTAATTTAATACAAAACCCTAACCTAATT
11769369 TAATTAAAAACCCTAACCCT
66 TAATTAAAAACCCTAACCCT
11769389 TTAACTTTAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 85 1.00
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (97 bp):
TTAAAAACCCTAAACCTTAACTTTAAAAATCCTAACCTAATTTAATACAAAACCCTAACCTAATT
TAATTAAAAACCCTAACCCTAACCTAATTTTA
Found at i:11769363 original size:68 final size:71
Alignment explanation
Indices: 11769286--11769458 Score: 228
Period size: 68 Copynumber: 2.5 Consensus size: 71
11769276 TAAAAACCCT
* *
11769286 AACCCTAACCTAATTTTATTAAAAACCCTAAACC-TTAACTTTAAAAATCCTAA-CC-TAA-TTT
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTTAACTTT-AAAACCCTAACCCTTAACTTT
*
11769347 AATACAA
65 AAAACAA
*
11769354 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTTTAACTTTAAAACCCTAACCCTTAACTTTA
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTTAACTTTAAAACCCTAACCCTTAACTTTA
**
11769419 AAACCC
66 AAACAA
* *
11769425 TACTCCTAACTTAATTTAATTAAAAACCCTAAAC
1 AAC-CCTAACCTAATTTAATTAAAAACCCTAAAC
11769459 TAAGTTAATA
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
68 41 0.45
69 10 0.11
70 3 0.03
71 9 0.10
72 28 0.31
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (71 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTTAACTTTAAAACCCTAACCCTTAACTTTA
AAACAA
Found at i:11769665 original size:116 final size:116
Alignment explanation
Indices: 11769461--11769816 Score: 658
Period size: 116 Copynumber: 3.1 Consensus size: 116
11769451 CCCTAAACTA
* * *
11769461 AGTTAATAATTTTACATTCACGTAATGTTAGATTTGGAAAACTGTTTTGACTGCTACTAACAATT
1 AGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
11769526 AATAATTTTATATAATTTGATAATTTTACGAACCATTAATAAAATTTTTAG
66 AATAATTTTATATAATTTGATAATTTTACGAACCATTAATAAAATTTTTAG
11769577 AGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
1 AGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
11769642 AATAATTTTATATAATTTGATAATTTTACGAACCATTAATAAAATTTTTAG
66 AATAATTTTATATAATTTGATAATTTTACGAACCATTAATAAAATTTTTAG
11769693 AGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
1 AGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
* * *
11769758 AATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTG
66 AATAATTTTATATAATTTGATAATTTTACGAACCATTAATAAAATTTTTAG
11769809 AGTTAATA
1 AGTTAATA
11769817 CAATTTATCA
Statistics
Matches: 234, Mismatches: 6, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
116 234 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (116 bp):
AGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
AATAATTTTATATAATTTGATAATTTTACGAACCATTAATAAAATTTTTAG
Found at i:11769833 original size:17 final size:18
Alignment explanation
Indices: 11769792--11769833 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
11769782 TTTACTAACC
* *
11769792 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
11769810 GTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
11769827 ATTAATA
1 ATTAATA
11769834 ATTGCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:11772150 original size:124 final size:126
Alignment explanation
Indices: 11771930--11772401 Score: 815
Period size: 126 Copynumber: 3.8 Consensus size: 126
11771920 CCCAAACATG
* *
11771930 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCCCAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
11771995 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAA-AATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
* *
11772054 CTACTGTAGCAAAAGCGCG-CTCACGAGGCCGCGATTTCACAAATTCTTCCCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
11772118 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
*
11772180 CTACTGTAGCAAAAGCGCGTCCACGAAGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
11772245 TAGAAGTGATTTTATACTATTTGCTAAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
*
11772306 ATACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
11772371 TAGAAGCGATTTTATACTATTTGATCAGAAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAA
11772402 ATTCAACTCG
Statistics
Matches: 328, Mismatches: 16, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
123 1 0.00
124 94 0.29
125 6 0.02
126 226 0.69
127 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
Found at i:11775808 original size:51 final size:48
Alignment explanation
Indices: 11775747--11775844 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
11775737 TGATCTAATT
* *
11775747 TTCTAAATCTACTTGCCAATCCTCCTTCTCACCATCATCCAAATGTAATCC
1 TTCTAAATCTACCTGCCAA---GCCTTCTCACCATCATCCAAATGTAATCC
*
11775798 TTCTAGATCTACCTGCCAAGCCTTCTCACCATCATCCAAATGTAATC
1 TTCTAAATCTACCTGCCAAGCCTTCTCACCATCATCCAAATGTAATC
11775845 TAGCAATGCC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
48 27 0.61
51 17 0.39
ACGTcount: A:0.28, C:0.35, G:0.06, T:0.32
Consensus pattern (48 bp):
TTCTAAATCTACCTGCCAAGCCTTCTCACCATCATCCAAATGTAATCC
Found at i:11778035 original size:22 final size:22
Alignment explanation
Indices: 11778005--11778058 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
11777995 CTGCCCTCGA
11778005 TGTCACGACACAAGACCTGATG
1 TGTCACGACACAAGACCTGATG
*
11778027 TGTCGCGACACAAGACCTGATG
1 TGTCACGACACAAGACCTGATG
11778049 TGTCACGACA
1 TGTCACGACA
11778059 TCGCTTCTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.19
Consensus pattern (22 bp):
TGTCACGACACAAGACCTGATG
Found at i:11780766 original size:24 final size:24
Alignment explanation
Indices: 11780705--11780759 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
11780695 AAAGAGATGG
11780705 AGATGAAAACGAGGGTGGAGATAA
1 AGATGAAAACGAGGGTGGAGATAA
* * * *
11780729 AGATGAAGATGAGGGTTGAGATCA
1 AGATGAAAACGAGGGTGGAGATAA
11780753 AGATGAA
1 AGATGAA
11780760 TAGGAGGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.36, T:0.16
Consensus pattern (24 bp):
AGATGAAAACGAGGGTGGAGATAA
Found at i:11782090 original size:20 final size:20
Alignment explanation
Indices: 11782047--11782091 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
11782037 TGTCGTTATG
*
11782047 TTTAAATCGATTCATTATTG
1 TTTAAATCGATTCATTATTA
* * *
11782067 TTTAAATCTATTCTTTGTTA
1 TTTAAATCGATTCATTATTA
11782087 TTTAA
1 TTTAA
11782092 CCTGATTCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTAAATCGATTCATTATTA
Found at i:11792006 original size:213 final size:214
Alignment explanation
Indices: 11791621--11792048 Score: 804
Period size: 213 Copynumber: 2.0 Consensus size: 214
11791611 GAGCATCTAA
11791621 CATTGCAGGAGATCCCGCTCCTTGTGCTGAATTAGATCCAACCTCCTCATGATCAAACAATGCCA
1 CATTGCAGGAGATCCCGCTCCTTGTGCTGAATTAGATCCAACCTCCTCATGATCAAACAATGCCA
*
11791686 CCATTCTAACACCACTCTCATTTTCAGGGTCGCTGTCGGAGGATGTAGCATCAATTAATGCCTGT
66 CCATTCTAACACCACTCTCATTTTCAAGGTCGCTGTCGGAGGATGTAGCATCAATTAATGCCTGT
* * *
11791751 AATGAAATTACATCATGACAAAGGGATGAAGCAAAAAATATGCATACCATTATCAGGTTTAATAT
131 AACGAAATTACATCATGACAAAGGAATGAAGCAAAAAATATGCATACCATCATCAGGTTTAATAT
11791816 AGCACGGTTCCAAATATTC
196 AGCACGGTTCCAAATATTC
11791835 CATTGCAGGAGAT-CCGCTCCTTGTGCTGAATTAGATCCAACCTCCTCATGATCAAACAATGCCA
1 CATTGCAGGAGATCCCGCTCCTTGTGCTGAATTAGATCCAACCTCCTCATGATCAAACAATGCCA
11791899 CCATTCTAACACCACTCTCATTTTCAAGGTCGCTGTCGGAGGATGTAGCATCAATTAATGCCTGT
66 CCATTCTAACACCACTCTCATTTTCAAGGTCGCTGTCGGAGGATGTAGCATCAATTAATGCCTGT
*
11791964 AACGAAATTACATCATGACAAAGGAATGAAGCAAACAATATGCATACCATCATCAGGTTTAATAT
131 AACGAAATTACATCATGACAAAGGAATGAAGCAAAAAATATGCATACCATCATCAGGTTTAATAT
11792029 AGCACGGTTCCAAATATTC
196 AGCACGGTTCCAAATATTC
11792048 C
1 C
11792049 CCATTTGGAA
Statistics
Matches: 209, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
213 196 0.94
214 13 0.06
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (214 bp):
CATTGCAGGAGATCCCGCTCCTTGTGCTGAATTAGATCCAACCTCCTCATGATCAAACAATGCCA
CCATTCTAACACCACTCTCATTTTCAAGGTCGCTGTCGGAGGATGTAGCATCAATTAATGCCTGT
AACGAAATTACATCATGACAAAGGAATGAAGCAAAAAATATGCATACCATCATCAGGTTTAATAT
AGCACGGTTCCAAATATTC
Found at i:11792645 original size:113 final size:111
Alignment explanation
Indices: 11792431--11792728 Score: 338
Period size: 113 Copynumber: 2.7 Consensus size: 111
11792421 CGAAAAAGAA
** * * *
11792431 AAAAAAAGGAAAAAAAAATTTTTGGGTGCAGGCCTGTCAATGGCCGACACCCA--AC-AGTAAAA
1 AAAAAAATAAAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGG-CG-CACCCAGTACAATTTAAA
* *
11792493 AAAAAATTTACTTTTTTTTTTCGTGTCAGAGTCAAATATAAATATAGG
64 AAAAAATTTACTTTCTTTTTTCGTGTCAGAGTCAAATATAAATATACG
11792541 AAAAAAATAAAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCAGGCACCCAGTACAATTTAAA
1 AAAAAAATAAAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGC--GCACCCAGTACAATTTAAA
* * *
11792606 AAAAAATATT-CTTTCTTTTTTCGTTTCAGAGTCAGATATAATTATACG
64 AAAAAAT-TTACTTTCTTTTTTCGTGTCAGAGTCAAATATAAATATACG
* *** *
11792654 AAAAAAATTTTAAAAAATTTTTGTTTGGGTGCTGGCCTGTCAATGGC-C-GCCAGTACAAATTTA
1 AAAAAAA--TAAAAAAAAAATT-TTTGGGTGCTGGCCTGTCAATGGCGCACCCAGTAC-AATTTA
11792717 AAAAAAAATTTA
62 AAAAAAAATTTA
11792729 ATTTTTTCGT
Statistics
Matches: 162, Mismatches: 15, Indels: 19
0.83 0.08 0.10
Matches are distributed among these distances:
109 1 0.01
110 46 0.28
111 1 0.01
112 11 0.07
113 68 0.42
114 2 0.01
115 9 0.06
116 24 0.15
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (111 bp):
AAAAAAATAAAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCGCACCCAGTACAATTTAAAAA
AAAATTTACTTTCTTTTTTCGTGTCAGAGTCAAATATAAATATACG
Found at i:11792991 original size:108 final size:111
Alignment explanation
Indices: 11792728--11793008 Score: 381
Period size: 108 Copynumber: 2.5 Consensus size: 111
11792718 AAAAAAATTT
*
11792728 AATTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAAGAATTTTTTTTTAAAATTTGTA
1 AATTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAAGAA-ATTTTTTT-AAATTTGTA
* *
11792793 CTGGGTGCCGGCCATTGACAGGCAACACCCAAAAAAAACTTTTTTTTTTA
64 CTAGGTGCCGGCCATTAACAGGC-ACACCCAAAAAAAAC-TTTTTTTTTA
*
11792843 AATTTTTTTCGTATATTTATATCTGACTTTGACACAAAAAAAAAGAAATTTTTTTAAA-TTGTAC
1 AA-TTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAAGAAATTTTTTTAAATTTGTAC
**
11792907 TAGGTGCCGGCCATTAACAGGC-CA-CCAACCAAAA-TTTTTTTTTA
65 TAGGTGCCGGCCATTAACAGGCACACCCAAAAAAAACTTTTTTTTTA
* **
11792951 AATTTTTTCCGTATATTTATATCTGACTCTGAAATGAAAAAAAAGTAAAATTTTTTTA
1 AATTTTTT-CGTATATTTATATCTGACTCTGACACAAAAAAAAAG--AAATTTTTTTA
11793009 CTGTTGGGTC
Statistics
Matches: 152, Mismatches: 10, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
107 6 0.04
108 44 0.29
110 19 0.12
111 2 0.01
113 26 0.17
114 3 0.02
115 9 0.06
116 43 0.28
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (111 bp):
AATTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAAGAAATTTTTTTAAATTTGTACT
AGGTGCCGGCCATTAACAGGCACACCCAAAAAAAACTTTTTTTTTA
Found at i:11797080 original size:26 final size:25
Alignment explanation
Indices: 11797059--11797107 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
11797049 TCTAAATTTC
11797059 ACCATAA-ATTTTTATAAATAAATAT
1 ACCATAACATTTTTAT-AATAAATAT
**
11797084 ATTATAACATTTTTATAATAAATA
1 ACCATAACATTTTTATAATAAATA
11797108 ACATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (25 bp):
ACCATAACATTTTTATAATAAATAT
Found at i:11797284 original size:20 final size:20
Alignment explanation
Indices: 11797255--11797306 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
11797245 CCTAACACCC
11797255 ATAT-ATTTTTAT-ACTTATA
1 ATATAATTTTTATAACTT-TA
*
11797274 ATATAATTTTTATAACTTTT
1 ATATAATTTTTATAACTTTA
11797294 ATAATAATTTTTA
1 AT-ATAATTTTTA
11797307 AAAATTGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 4 0.14
20 11 0.38
21 14 0.48
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATAATTTTTATAACTTTA
Found at i:11798989 original size:17 final size:18
Alignment explanation
Indices: 11798965--11799003 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
11798955 GTTTATGGGT
11798965 AAAAAAAATAGAAGAAA-AG
1 AAAAAAAA-A-AAGAAATAG
11798984 AAAAAAAAAAAGAAATAG
1 AAAAAAAAAAAGAAATAG
11799002 AA
1 AA
11799004 TGCTTGTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 5 0.26
19 8 0.42
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAAAGAAATAG
Found at i:11807360 original size:9 final size:8
Alignment explanation
Indices: 11807348--11807406 Score: 50
Period size: 9 Copynumber: 7.1 Consensus size: 8
11807338 TATGTATAAT
11807348 AAATATATA
1 AAAT-TATA
11807357 AAATTA-A
1 AAATTATA
*
11807364 TAATTATTA
1 AAATTA-TA
11807373 AAATCTATA
1 AAAT-TATA
11807382 AAATT-TA
1 AAATTATA
*
11807389 AATTTATA
1 AAATTATA
11807397 AAATATATA
1 AAAT-TATA
11807406 A
1 A
11807407 TAACATAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 12 0.29
8 8 0.20
9 19 0.46
10 2 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (8 bp):
AAATTATA
Found at i:11807376 original size:16 final size:17
Alignment explanation
Indices: 11807344--11807406 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 17
11807334 TATATATGTA
11807344 TAATAAATATATAAAAT
1 TAATAAATATATAAAAT
*
11807361 TAATAATTAT-TAAAAT
1 TAATAAATATATAAAAT
*
11807377 CT-ATAAA-AT-TTAAAT
1 -TAATAAATATATAAAAT
*
11807392 TTATAAAATATATAA
1 TAAT-AAATATATAA
11807407 TAACATAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 1 0.03
15 9 0.24
16 13 0.35
17 12 0.32
18 2 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATAAATATATAAAAT
Found at i:11807376 original size:25 final size:24
Alignment explanation
Indices: 11807348--11807406 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
11807338 TATGTATAAT
11807348 AAATATATAAAATTAATAA-TTATTA
1 AAATATATAAAATTAA-AATTTA-TA
* *
11807373 AAATCTATAAAATTTAAATTTATA
1 AAATATATAAAATTAAAATTTATA
11807397 AAATATATAA
1 AAATATATAA
11807407 TAACATAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
AAATATATAAAATTAAAATTTATA
Found at i:11807911 original size:22 final size:22
Alignment explanation
Indices: 11807869--11807912 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11807859 ATATAAACTG
*
11807869 TTAATATATTAACAATTTATAT
1 TTAATATATTAACAATATATAT
*
11807891 TTAAT-TATTAATACATATATAT
1 TTAATATATTAACA-ATATATAT
11807913 AAACCATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAATATATTAACAATATATAT
Found at i:11812212 original size:31 final size:31
Alignment explanation
Indices: 11812174--11812236 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
11812164 ACTAGTTAGA
*
11812174 TTCCTTACATTATATCGATGTGAACCGTACG
1 TTCCTTACACTATATCGATGTGAACCGTACG
11812205 TTCCTTACACTATATCGATGTGAACCGTACG
1 TTCCTTACACTATATCGATGTGAACCGTACG
11812236 T
1 T
11812237 ACAATCGTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (31 bp):
TTCCTTACACTATATCGATGTGAACCGTACG
Found at i:11817592 original size:31 final size:31
Alignment explanation
Indices: 11817557--11817620 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
11817547 AACATTTCAC
* * *
11817557 TAACACTTAGCCAACAAATCAATACCTCATT
1 TAACACTTAACCAAAAAATAAATACCTCATT
**
11817588 TAACACTTAATTAAAAAATAAATACCTCATT
1 TAACACTTAACCAAAAAATAAATACCTCATT
11817619 TA
1 TA
11817621 TTTTCTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.30
Consensus pattern (31 bp):
TAACACTTAACCAAAAAATAAATACCTCATT
Found at i:11818281 original size:13 final size:13
Alignment explanation
Indices: 11818263--11818289 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11818253 AGATGTCGTT
11818263 TGAATTGAATTGA
1 TGAATTGAATTGA
11818276 TGAATTGAATTGA
1 TGAATTGAATTGA
11818289 T
1 T
11818290 ATTATAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
TGAATTGAATTGA
Found at i:11820794 original size:25 final size:23
Alignment explanation
Indices: 11820757--11820803 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
11820747 AACCATTCAT
11820757 TCTTCACTTTTCTTTCACTTTTCTC
1 TCTTCACTTTTC-TTCA-TTTTCTC
11820782 TCTTCA-TTGTTCTTCATTTTCT
1 TCTTCACTT-TTCTTCATTTTCT
11820804 TCCCTATTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.09, C:0.28, G:0.02, T:0.62
Consensus pattern (23 bp):
TCTTCACTTTTCTTCATTTTCTC
Found at i:11824056 original size:50 final size:50
Alignment explanation
Indices: 11823991--11824327 Score: 383
Period size: 51 Copynumber: 6.7 Consensus size: 50
11823981 TATCATTCGA
*
11823991 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGG
* * *
11824041 TTCACGTAGTAGCCTTCACATAGTACTACACACGTTATCAAGTTTTACGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGG
* *
11824091 TTCACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTT-CGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACGG
* * * * *** *
11824142 TACACATAATAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA-CGG
* *
11824193 TCCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTCT-CGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACGG
* * * * * *
11824244 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACC-ATTATTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGT-TTTA-CGG
*
11824295 TACACGTAGTAGCCTTCACACAGTACTACACAC
1 TACACGTAGTAGCCTTCACATAGTACTACACAC
11824328 ATGTTCATCG
Statistics
Matches: 242, Mismatches: 36, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.00
49 6 0.02
50 85 0.35
51 143 0.59
52 5 0.02
53 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (50 bp):
TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGG
Found at i:11824227 original size:102 final size:102
Alignment explanation
Indices: 11823987--11824327 Score: 481
Period size: 102 Copynumber: 3.4 Consensus size: 102
11823977 CTTTTATCAT
* * *
11823987 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTTACGGTTCACGTAG
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAG
* * * * ***
11824050 TAGCCTTCACATAGTACTACACACGTTATCAAGTTTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * *
11824088 -CGGTTCACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAAT
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
11824152 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * *
11824189 TCGATCCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGT
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
*
11824254 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
*
11824291 TCGATACACGTAGTAGCCTTCACACAGTACTACACAC
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACAC
11824328 ATGTTCATCG
Statistics
Matches: 214, Mismatches: 23, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
100 38 0.18
101 43 0.20
102 133 0.62
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (102 bp):
TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:11827322 original size:30 final size:30
Alignment explanation
Indices: 11827288--11827348 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
11827278 CCAGGTTTTC
*
11827288 TTTCCCTTATAAGATATTAGATAGATTTGA
1 TTTCCCTAATAAGATATTAGATAGATTTGA
11827318 TTTCCCTAATAAGATATTAGATAGATTTGA
1 TTTCCCTAATAAGATATTAGATAGATTTGA
11827348 T
1 T
11827349 GGGAGAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (30 bp):
TTTCCCTAATAAGATATTAGATAGATTTGA
Found at i:11829942 original size:10 final size:10
Alignment explanation
Indices: 11829905--11829939 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
11829895 AACATGTTGG
11829905 ATTTTAATTA
1 ATTTTAATTA
11829915 ATTTTAATTA
1 ATTTTAATTA
*
11829925 ATTTTGATTA
1 ATTTTAATTA
11829935 ATTTT
1 ATTTT
11829940 GATCATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (10 bp):
ATTTTAATTA
Found at i:11833039 original size:71 final size:71
Alignment explanation
Indices: 11832841--11833046 Score: 234
Period size: 71 Copynumber: 2.9 Consensus size: 71
11832831 TGTCACGTCG
* * * * * * * ** *
11832841 GTGTCACGACACTGATGGCAATTTACTAACTTGGGTGAGTCTTTAGGGCTGTGTCGCAACATCCT
1 GTGTCATGACACCGAAGGCAACTTACTAGCTTGGGCGTGTCTTTAGGGCTGTGTCGTGACATCGT
*
11832906 TTGGTT
66 TTGGCT
* * * * *
11832912 GTGTCGTGACACCGAAGG-TAGTCTACTAGCTTGGGCATGTCTTTAGGGCTCTGTCGTGACATCG
1 GTGTCATGACACCGAAGGCAACT-TACTAGCTTGGGCGTGTCTTTAGGGCTGTGTCGTGACATCG
11832976 TTTGGCT
65 TTTGGCT
* *
11832983 GTGTCATGGCACCGAAGGCAACTTACTAGCTTGGGCGTGTCTTCAGGGCTGTGTCGTGACATCG
1 GTGTCATGACACCGAAGGCAACTTACTAGCTTGGGCGTGTCTTTAGGGCTGTGTCGTGACATCG
11833047 AAGGCAGTCT
Statistics
Matches: 111, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
70 2 0.02
71 107 0.96
72 2 0.02
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.31
Consensus pattern (71 bp):
GTGTCATGACACCGAAGGCAACTTACTAGCTTGGGCGTGTCTTTAGGGCTGTGTCGTGACATCGT
TTGGCT
Found at i:11840071 original size:25 final size:25
Alignment explanation
Indices: 11840042--11840102 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
11840032 TTTGGCTTGT
*
11840042 ATGAGCTTCCCGATTAATAGCTCTC
1 ATGAGCTTCCCGATTAACAGCTCTC
* * * *
11840067 TTGAGCTACCCGATTTACGGCTCTC
1 ATGAGCTTCCCGATTAACAGCTCTC
11840092 ATGAGCTTCCC
1 ATGAGCTTCCC
11840103 AATGACATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.31, G:0.18, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCGATTAACAGCTCTC
Found at i:11842284 original size:70 final size:71
Alignment explanation
Indices: 11842197--11842337 Score: 257
Period size: 71 Copynumber: 2.0 Consensus size: 71
11842187 GGTTACGTAT
*
11842197 GAGGAAGGATTAGCACCCTC-TAACGCCTAGAAATTGGTACCTAGTTGATTAATTAATGTCTTAG
1 GAGGAAGGATTAGCACCCTCGTAACGCCCAGAAATTGGTACCTAGTTGATTAATTAATGTCTTAG
11842261 TGTCGA
66 TGTCGA
*
11842267 GAGGAAGGATTAGCACCCTCGTAACGCCCAGAAATTGGTACCTAGTTGATTAGTTAATGTCTTAG
1 GAGGAAGGATTAGCACCCTCGTAACGCCCAGAAATTGGTACCTAGTTGATTAATTAATGTCTTAG
11842332 TGTCGA
66 TGTCGA
11842338 AAAAATAAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 20 0.29
71 48 0.71
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (71 bp):
GAGGAAGGATTAGCACCCTCGTAACGCCCAGAAATTGGTACCTAGTTGATTAATTAATGTCTTAG
TGTCGA
Found at i:11842986 original size:109 final size:109
Alignment explanation
Indices: 11842782--11843098 Score: 548
Period size: 109 Copynumber: 2.9 Consensus size: 109
11842772 GAAATTCAAG
* * * *
11842782 AGGATATTTGGCTATTTGGTTAAATGAG-AAAATCGAAACCCAGCACATTAGGGCACG-TTCCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
11842845 AAATTTCCAAACGCACAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
11842889 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
**
11842954 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGGA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
11842998 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
11843063 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAA
11843099 AATTTTCCTT
Statistics
Matches: 200, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
107 25 0.12
108 29 0.14
109 146 0.73
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (109 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
Found at i:11843245 original size:16 final size:16
Alignment explanation
Indices: 11843224--11843254 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11843214 ATATCATAGC
11843224 GAATAAATAAATAAAT
1 GAATAAATAAATAAAT
*
11843240 GAATAAATAACTAAA
1 GAATAAATAAATAAA
11843255 GCATAAAAAT
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:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (16 bp):
GAATAAATAAATAAAT
Found at i:11843436 original size:17 final size:18
Alignment explanation
Indices: 11843416--11843449 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11843406 TATATGTTTT
11843416 AAGGATAT-TAAATATAA
1 AAGGATATGTAAATATAA
*
11843433 AAGGTTATGTAAATATA
1 AAGGATATGTAAATATA
11843450 TATACACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (18 bp):
AAGGATATGTAAATATAA
Found at i:11843734 original size:13 final size:13
Alignment explanation
Indices: 11843716--11843746 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
11843706 ATGATGATGA
11843716 TAAATTAATTAAC
1 TAAATTAATTAAC
11843729 TAAATTAATTAAC
1 TAAATTAATTAAC
11843742 TAAAT
1 TAAAT
11843747 AATAAAATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAATTAATTAAC
Found at i:11843986 original size:70 final size:70
Alignment explanation
Indices: 11843873--11844012 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 70
11843863 AGGGTCAATT
*
11843873 CGAAATAATGGAAAACGAAAGGGATCAAATTACGACACGCGTAAAAAGGGAAGGACCGAAACAAT
1 CGAAATAATGGAAAACAAAAGGGATCAAATTACGACACGCGTAAAAAGGGAAGGACCGAAACAAT
11843938 AAATA
66 AAATA
*
11843943 CGAAATAATGGAAAACAAAAGGGATCAAATTACGACATGCGTAAAAAGGGAAGGACCGAAACAAT
1 CGAAATAATGGAAAACAAAAGGGATCAAATTACGACACGCGTAAAAAGGGAAGGACCGAAACAAT
11844008 AAATA
66 AAATA
11844013 AACCCACAGT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.52, C:0.14, G:0.22, T:0.12
Consensus pattern (70 bp):
CGAAATAATGGAAAACAAAAGGGATCAAATTACGACACGCGTAAAAAGGGAAGGACCGAAACAAT
AAATA
Found at i:11859901 original size:10 final size:10
Alignment explanation
Indices: 11859886--11859911 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
11859876 GATTTATGAT
11859886 AGAAACGAAG
1 AGAAACGAAG
11859896 AGAAACGAAG
1 AGAAACGAAG
11859906 AGAAAC
1 AGAAAC
11859912 ACTTACCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.27, T:0.00
Consensus pattern (10 bp):
AGAAACGAAG
Found at i:11881900 original size:21 final size:21
Alignment explanation
Indices: 11881874--11881933 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
11881864 GTAAATCGTC
*
11881874 AACAGAAGTTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
11881895 AACAGAAGCTCGA-AAGAGCTG
1 AACAGAAGCTC-ATAAGAGCTG
*
11881916 AACAGAAACTCATAAGAG
1 AACAGAAGCTCATAAGAG
11881934 TTTAATAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:11896429 original size:19 final size:21
Alignment explanation
Indices: 11896400--11896442 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
11896390 AAAATATCAT
11896400 TAATAATTTAAATTTTTA-AA
1 TAATAATTTAAATTTTTACAA
*
11896420 TAAT-ATTTAACTTTTTACAA
1 TAATAATTTAAATTTTTACAA
11896440 TAA
1 TAA
11896443 GTAAGAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATAATTTAAATTTTTACAA
Found at i:11897596 original size:11 final size:10
Alignment explanation
Indices: 11897571--11897629 Score: 59
Period size: 10 Copynumber: 6.1 Consensus size: 10
11897561 TTTATTTAAT
11897571 ATTTTTATAA
1 ATTTTTATAA
11897581 ATTTTTATAA
1 ATTTTTATAA
**
11897591 CGTTTTA-AA
1 ATTTTTATAA
11897600 A-TTTTATAA
1 ATTTTTATAA
*
11897609 ATTTTTTTAA
1 ATTTTTATAA
* *
11897619 TTTTTTTTAA
1 ATTTTTATAA
11897629 A
1 A
11897630 AAATAAGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 5 0.12
9 5 0.12
10 31 0.76
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:11902993 original size:18 final size:18
Alignment explanation
Indices: 11902972--11903047 Score: 73
Period size: 18 Copynumber: 4.2 Consensus size: 18
11902962 AGGTGACAAT
*
11902972 GAAGGCATAGGTGAGGAA
1 GAAGGCATAGATGAGGAA
*
11902990 GAAGGCGTAGATGAGGAA
1 GAAGGCATAGATGAGGAA
** * *
11903008 GAAGGCGCAAATGAGAAA
1 GAAGGCATAGATGAGGAA
*
11903026 GAAGGCACAG-TGGAGGAA
1 GAAGGCATAGAT-GAGGAA
11903044 GAAG
1 GAAG
11903048 ATACAGGTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
17 1 0.02
18 48 0.98
ACGTcount: A:0.42, C:0.08, G:0.42, T:0.08
Consensus pattern (18 bp):
GAAGGCATAGATGAGGAA
Found at i:11904862 original size:17 final size:18
Alignment explanation
Indices: 11904840--11904873 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11904830 ATATCGACAA
*
11904840 AAAAATTAAATA-TTTAC
1 AAAAATAAAATACTTTAC
11904857 AAAAATAAAATACTTTA
1 AAAAATAAAATACTTTA
11904874 AATTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATAAAATACTTTAC
Found at i:11907545 original size:16 final size:17
Alignment explanation
Indices: 11907520--11907562 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
11907510 AACTGTTATT
*
11907520 AATATATTTTAA-TAAA
1 AATATTTTTTAACTAAA
11907536 AATATTTTTTAACTTAAA
1 AATATTTTTTAAC-TAAA
*
11907554 TATATTTTT
1 AATATTTTT
11907563 AATGTTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
18 12 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATTTTTTAACTAAA
Found at i:11914418 original size:17 final size:18
Alignment explanation
Indices: 11914396--11914430 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11914386 ATTTAGACCA
11914396 TGTGGGCC-ACACGGGCG
1 TGTGGGCCTACACGGGCG
11914413 TGTGGGCCTACACGGGCG
1 TGTGGGCCTACACGGGCG
11914431 AACATCATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.11, C:0.29, G:0.46, T:0.14
Consensus pattern (18 bp):
TGTGGGCCTACACGGGCG
Found at i:11915404 original size:18 final size:18
Alignment explanation
Indices: 11915372--11915420 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
11915362 TAAAAAAATG
11915372 TTTGGAAATTGAATAACGA
1 TTTGGAAA-TGAATAACGA
* * *
11915391 TTTGTAAATGAATAATGT
1 TTTGGAAATGAATAACGA
11915409 TTTGGAAATGAA
1 TTTGGAAATGAA
11915421 AGACACGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (18 bp):
TTTGGAAATGAATAACGA
Found at i:11921814 original size:18 final size:18
Alignment explanation
Indices: 11921782--11921830 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
11921772 TAAAAAAATG
11921782 TTTGGAAATTGAATAACGA
1 TTTGGAAA-TGAATAACGA
* * *
11921801 TTTGTAAATGAATAATGT
1 TTTGGAAATGAATAACGA
11921819 TTTGGAAATGAA
1 TTTGGAAATGAA
11921831 CGACACGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (18 bp):
TTTGGAAATGAATAACGA
Found at i:11929389 original size:18 final size:18
Alignment explanation
Indices: 11929366--11929400 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11929356 AGAAATAGCT
* *
11929366 GCAAAATAATATATAAAA
1 GCAAAACAATAAATAAAA
11929384 GCAAAACAATAAATAAA
1 GCAAAACAATAAATAAA
11929401 TTCTCAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.17
Consensus pattern (18 bp):
GCAAAACAATAAATAAAA
Found at i:11932112 original size:3 final size:3
Alignment explanation
Indices: 11932104--11932156 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
11932094 CATATTCTAG
11932104 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11932152 TAT TA
1 TAT TA
11932157 CCTACTTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:11932515 original size:18 final size:17
Alignment explanation
Indices: 11932492--11932530 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
11932482 TGCTTTAATT
*
11932492 TTTTATTTGTTTATTTAC
1 TTTTATTTGTTGATTT-C
11932510 TTTTATTTGTTGATTTC
1 TTTTATTTGTTGATTTC
11932527 TTTT
1 TTTT
11932531 CATTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTATTTGTTGATTTC
Found at i:11932832 original size:111 final size:111
Alignment explanation
Indices: 11932638--11933035 Score: 660
Period size: 111 Copynumber: 3.6 Consensus size: 111
11932628 TATCAAAAAC
*
11932638 TAAAAAATTTTTC-AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGT
1 TAAAAAA-ATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGT
11932702 GCTGGGTGCCGATTTTTCTCGTTCAACCAAGTGGCTTAATATCCTTT
65 GCTGGGTGCCGATTTTTCTCGTTCAACCAAGTGGCTTAATATCCTTT
*
11932749 TAAAAAAATTTCAAAATATGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTG
1 TAAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTG
11932814 CTGGGTGCCGATTTTTCTCGTTCAACCAAGTGGCTTAATATCCTTT
66 CTGGGTGCCGATTTTTCTCGTTCAACCAAGTGGCTTAATATCCTTT
*
11932860 TAAAAAAATTTCAAAATATGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTG
1 TAAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTG
* * * *
11932925 CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATAT-CTTT
66 CTGGGTGCCGATTTTTCTCGTTCAACCAAGTGGCTTAATATCCTTT
* * * *
11932970 T-TAAAAATTTCAAAATAAGACAATGTTTTGCGTTTGGAAATTCGAG-GAACATGCCCTAATGTG
1 TAAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTG
11933033 CTG
66 CTG
11933036 AGTTTCGATT
Statistics
Matches: 275, Mismatches: 11, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
108 18 0.07
109 42 0.15
110 9 0.03
111 206 0.75
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (111 bp):
TAAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTG
CTGGGTGCCGATTTTTCTCGTTCAACCAAGTGGCTTAATATCCTTT
Found at i:11944904 original size:50 final size:50
Alignment explanation
Indices: 11944833--11945356 Score: 386
Period size: 50 Copynumber: 10.5 Consensus size: 50
11944823 AATTTAAAAT
* *
11944833 ATTGAAG-TCACAATGGCGAATCTTACTTCCCAGGCGATGCAGCGGAATAG
1 ATTGAAGCT-ACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAATAG
* * * **** *
11944883 ATTGAAGCTACGACGGTGAATCTCACTTCCCCA-AC-ATTGCAATTCAAAAG
1 ATTGAAGCTACAACGGTGAATCTTACTT-CCCAGGCGA-TGCAGCGGAATAG
*
11944933 ATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAATAG
1 ATTGAAGCTACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAATAG
* * * * *
11944983 ATTGAAGCTACAACGGTGAGTCTTCCTTCCCCGAC-ATTGCAGTC-AAATAG
1 ATTGAAGCTACAACGGTGAATCTTACTTCCCAGGCGA-TGCAG-CGGAATAG
* * ** * * * **
11945033 ATTGAAGCCACAATGGCAAATCTCACCTCCCTGGCGATGCAATGGAATAG
1 ATTGAAGCTACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAATAG
* * * * *
11945083 ATTGAAGCTACAACAGTGAATCTCACCTCCCTGGCGATGCAGTGGAATAG
1 ATTGAAGCTACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAATAG
* * * * *
11945133 ATTCAAGCTACAACGGTGAATCTTCCTTCCCCGAC-ATTGCAGTC-AAATAG
1 ATTGAAGCTACAACGGTGAATCTTACTTCCCAGGCGA-TGCAG-CGGAATAG
* * * *
11945183 ATTGAAGCTACAACAGTGAATCTCACCTCCCTA-GCGATGCAGTGGAATAG
1 ATTGAAGCTACAACGGTGAATCTTACTTCCC-AGGCGATGCAGCGGAATAG
* ** * * * *
11945233 ATTGAAGTTACAACGACGAATCTTCCTTCCCCGAC-ATTGCAGTC-AAATAG
1 ATTGAAGCTACAACGGTGAATCTTACTTCCCAGGCGA-TGCAG-CGGAATAG
* * * * * *
11945283 ATTGAAGCTACAACAGCGAATCTTACCTCCCTA-GCGATGCAGTGGAACAA
1 ATTGAAGCTACAACGGTGAATCTTACTTCCC-AGGCGATGCAGCGGAATAG
* *
11945333 ATTGAAGCTACGATGGTGAATCTT
1 ATTGAAGCTACAACGGTGAATCTT
11945357 GCTTTTCCTA
Statistics
Matches: 366, Mismatches: 88, Indels: 40
0.74 0.18 0.08
Matches are distributed among these distances:
49 8 0.02
50 348 0.95
51 10 0.03
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (50 bp):
ATTGAAGCTACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAATAG
Found at i:11944989 original size:100 final size:100
Alignment explanation
Indices: 11944816--11945313 Score: 429
Period size: 100 Copynumber: 5.0 Consensus size: 100
11944806 CGAAGAAATT
* * * *
11944816 ACATTGCAATTTAAAATATTGAAGTCACAATGGCGAATCTTACTTCCCAGGCGATGCAGCGGAAT
1 ACATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAAT
* * * *
11944881 AGATTGAAGCTACGACGGTGAATCTCACTTCCCCA
66 AGATTGAAGCTACAACAGTGAATCTCACCTCCCCG
*
11944916 ACATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAAT
1 ACATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAAT
* * *
11944981 AGATTGAAGCTACAACGGTGAGTCTTC-CTTCCCCG
66 AGATTGAAGCTACAACAGTGAATC-TCACCTCCCCG
* * * * * * **
11945016 ACATTGC-AGTCAAATAGATTGAAGCCACAATGGCAAATCTCACCTCCCTGGCGATGCAATGGAA
1 ACATTGCAATTCAAA-AGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAA
*
11945080 TAGATTGAAGCTACAACAGTGAATCTCACCTCCCTG
65 TAGATTGAAGCTACAACAGTGAATCTCACCTCCCCG
* * ** * * * * * * * *
11945116 GCGA-TGCAGTGGAATAGATTCAAGCTACAACGGTGAATCTTCCTTCCCCGAC-ATTGCAGTC-A
1 AC-ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGA-TGCAG-CGG
*
11945178 AATAGATTGAAGCTACAACAGTGAATCTCACCT-CCCT
63 AATAGATTGAAGCTACAACAGTGAATCTCACCTCCCCG
* ** * ** * * * *
11945215 AGCGA-TGCAGTGGAATAGATTGAAGTTACAACGACGAATCTTCCTTCCCCGAC-ATTGCAGTC-
1 A-C-ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGA-TGCAG-CG
* * *
11945277 AAATAGATTGAAGCTACAACAGCGAATCTTACCTCCC
62 GAATAGATTGAAGCTACAACAGTGAATCTCACCTCCC
11945314 TAGCGATGCA
Statistics
Matches: 340, Mismatches: 49, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
99 11 0.03
100 322 0.95
101 7 0.02
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (100 bp):
ACATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAAT
AGATTGAAGCTACAACAGTGAATCTCACCTCCCCG
Found at i:11945355 original size:150 final size:150
Alignment explanation
Indices: 11944833--11945306 Score: 496
Period size: 150 Copynumber: 3.2 Consensus size: 150
11944823 AATTTAAAAT
* * * * *
11944833 ATTGAAG-TCACAATGGCGAATCTTACTTCCCAGGCGA-TGCAG-CGGAATAGATTGAAGCTACG
1 ATTGAAGCT-ACAACGGCGAATCTTCCTTCCCAGAC-ATTGCAGTC-AAATAGATTGAAGCTACA
* * * ** * * * *
11944895 ACGGTGAATCTCACTTCCCCAAC-ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTAC
63 ACGGTGAATCTCACCTCCCTAGCGA-TGCAATGGAATAGATTGAAGCTACAACGATGAATCTTCC
11944959 TTCCCAGGCGATGCAG-CGGAATAG
127 TTCCCAGGCGATGCAGTC-GAATAG
* * * * *
11944983 ATTGAAGCTACAACGGTGAGTCTTCCTTCCCCGACATTGCAGTCAAATAGATTGAAGCCACAATG
1 ATTGAAGCTACAACGGCGAATCTTCCTTCCCAGACATTGCAGTCAAATAGATTGAAGCTACAACG
** * *
11945048 GCAAATCTCACCTCCCTGGCGATGCAATGGAATAGATTGAAGCTACAAC-AGTGAATC-TCACCT
66 GTGAATCTCACCTCCCTAGCGATGCAATGGAATAGATTGAAGCTACAACGA-TGAATCTTC-CTT
* *
11945111 CCCTGGCGATGCAGTGGAATAG
129 CCCAGGCGATGCAGTCGAATAG
* * * *
11945133 ATTCAAGCTACAACGGTGAATCTTCCTTCCCCGACATTGCAGTCAAATAGATTGAAGCTACAACA
1 ATTGAAGCTACAACGGCGAATCTTCCTTCCCAGACATTGCAGTCAAATAGATTGAAGCTACAACG
* * *
11945198 GTGAATCTCACCTCCCTAGCGATGCAGTGGAATAGATTGAAGTTACAACGACGAATCTTCCTTCC
66 GTGAATCTCACCTCCCTAGCGATGCAATGGAATAGATTGAAGCTACAACGATGAATCTTCCTTCC
* * *
11945263 CCGAC-ATTGCAGTCAAATAG
131 CAGGCGA-TGCAGTCGAATAG
*
11945283 ATTGAAGCTACAACAGCGAATCTT
1 ATTGAAGCTACAACGGCGAATCTT
11945307 ACCTCCCTAG
Statistics
Matches: 270, Mismatches: 44, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
149 3 0.01
150 261 0.97
151 6 0.02
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (150 bp):
ATTGAAGCTACAACGGCGAATCTTCCTTCCCAGACATTGCAGTCAAATAGATTGAAGCTACAACG
GTGAATCTCACCTCCCTAGCGATGCAATGGAATAGATTGAAGCTACAACGATGAATCTTCCTTCC
CAGGCGATGCAGTCGAATAG
Found at i:11945370 original size:100 final size:100
Alignment explanation
Indices: 11944878--11945356 Score: 461
Period size: 100 Copynumber: 4.8 Consensus size: 100
11944868 GATGCAGCGG
* * * * * * ** * *
11944878 AATAGATTGAAGCTACGACGGTGAATCTCACTTCCCCAAC-ATTGCAATTCAAAAGATTGAAGCC
1 AATAGATTGAAGCTACAACAGTGAATCTCACCTCCCTAGCGA-TGCAGTGGAATAGATTGAAGCT
* * * *
11944942 ACAACGGTGAATCTTACTTCCCAGGCGA-TGCAG-CGG
65 ACAACGGTGAATCTTCCTTCCCCGAC-ATTGCAGTC-A
* * * * **
11944978 AATAGATTGAAGCTACAACGGTGAGTCTTC-CTTCCC-CGAC-ATTGCAGTCAAATAGATTGAAG
1 AATAGATTGAAGCTACAACAGTGAATC-TCACCTCCCTAG-CGA-TGCAGTGGAATAGATTGAAG
* * ** * * * * **
11945040 CCACAATGGCAAATC-TCACCTCCCTGGCGA-TGCAATGG
63 CTACAACGGTGAATCTTC-CTTCCCCGAC-ATTGCAGTCA
* *
11945078 AATAGATTGAAGCTACAACAGTGAATCTCACCTCCCTGGCGATGCAGTGGAATAGATTCAAGCTA
1 AATAGATTGAAGCTACAACAGTGAATCTCACCTCCCTAGCGATGCAGTGGAATAGATTGAAGCTA
11945143 CAACGGTGAATCTTCCTTCCCCGACATTGCAGTCA
66 CAACGGTGAATCTTCCTTCCCCGACATTGCAGTCA
*
11945178 AATAGATTGAAGCTACAACAGTGAATCTCACCTCCCTAGCGATGCAGTGGAATAGATTGAAGTTA
1 AATAGATTGAAGCTACAACAGTGAATCTCACCTCCCTAGCGATGCAGTGGAATAGATTGAAGCTA
**
11945243 CAACGACGAATCTTCCTTCCCCGACATTGCAGTCA
66 CAACGGTGAATCTTCCTTCCCCGACATTGCAGTCA
* * * *
11945278 AATAGATTGAAGCTACAACAGCGAATCTTACCTCCCTAGCGATGCAGTGGAACAAATTGAAGCTA
1 AATAGATTGAAGCTACAACAGTGAATCTCACCTCCCTAGCGATGCAGTGGAATAGATTGAAGCTA
* *
11945343 CGATGGTGAATCTT
66 CAACGGTGAATCTT
11945357 GCTTTTCCTA
Statistics
Matches: 323, Mismatches: 47, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
99 4 0.01
100 313 0.97
101 6 0.02
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (100 bp):
AATAGATTGAAGCTACAACAGTGAATCTCACCTCCCTAGCGATGCAGTGGAATAGATTGAAGCTA
CAACGGTGAATCTTCCTTCCCCGACATTGCAGTCA
Found at i:11946788 original size:3 final size:3
Alignment explanation
Indices: 11946780--11946805 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11946770 CATATTCTAG
11946780 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
11946806 CCTACTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:11947164 original size:18 final size:17
Alignment explanation
Indices: 11947141--11947179 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
11947131 TGCTTTAATT
*
11947141 TTTTATTTGTTTATTTAC
1 TTTTATTTGTTGATTT-C
11947159 TTTTATTTGTTGATTTC
1 TTTTATTTGTTGATTTC
11947176 TTTT
1 TTTT
11947180 CATTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTATTTGTTGATTTC
Found at i:11949940 original size:28 final size:28
Alignment explanation
Indices: 11949900--11949959 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
11949890 TGAGTATACT
11949900 AATAAGATATATTACAATTTAAAAAGAG
1 AATAAGATATATTACAATTTAAAAAGAG
11949928 AATAAGATATATTACAATTTAAAAAGAG
1 AATAAGATATATTACAATTTAAAAAGAG
11949956 AATA
1 AATA
11949960 TGTGTTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.58, C:0.03, G:0.10, T:0.28
Consensus pattern (28 bp):
AATAAGATATATTACAATTTAAAAAGAG
Found at i:11954395 original size:46 final size:45
Alignment explanation
Indices: 11954226--11954395 Score: 198
Period size: 46 Copynumber: 3.7 Consensus size: 45
11954216 ATACGCCTAG
* *
11954226 AAATGAGTAAGACCATAGCTGAAAAATGCTATGGCATCATGATA-A
1 AAATGAGTAAGACCATAGCTGAAAGATGTTAT-GCATCATGATAGA
* * * * *
11954271 AGATGAGTAAGAACATAGTTAAAAGATGTTATTGCATCATAATAGA
1 AAATGAGTAAGACCATAGCTGAAAGATGTTA-TGCATCATGATAGA
* *
11954317 AAATGAGTAATACCATAGCTGAAAGATGTTATGACATCATGGTAGA
1 AAATGAGTAAGACCATAGCTGAAAGATGTTATG-CATCATGATAGA
* * *
11954363 AAATGAGTAAGACCATTGTTGAAAGACGTTATG
1 AAATGAGTAAGACCATAGCTGAAAGATGTTATG
11954396 GTATCCATGA
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
45 37 0.36
46 67 0.64
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGCTGAAAGATGTTATGCATCATGATAGA
Found at i:11954510 original size:27 final size:27
Alignment explanation
Indices: 11954480--11954548 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
11954470 GTAGTTCATC
* * *
11954480 GGGACACTAAAGATGGAATAGTCCGCT
1 GGGACACTAAACACGGAATAGTCCACT
**
11954507 GGGACACTAAACACGGGGTAGTCCACT
1 GGGACACTAAACACGGAATAGTCCACT
*
11954534 GGGACGCTAAACACG
1 GGGACACTAAACACG
11954549 CGGTAGACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.32, C:0.23, G:0.30, T:0.14
Consensus pattern (27 bp):
GGGACACTAAACACGGAATAGTCCACT
Found at i:11954553 original size:27 final size:27
Alignment explanation
Indices: 11954498--11954554 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
11954488 AAAGATGGAA
* *
11954498 TAGTCCGCTGGGACACTAAACACGGGG
1 TAGTCCACTGGGACACTAAACACGCGG
*
11954525 TAGTCCACTGGGACGCTAAACACGCGG
1 TAGTCCACTGGGACACTAAACACGCGG
11954552 TAG
1 TAG
11954555 ACAATTGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.16
Consensus pattern (27 bp):
TAGTCCACTGGGACACTAAACACGCGG
Found at i:11954563 original size:27 final size:27
Alignment explanation
Indices: 11954505--11954566 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
11954495 GAATAGTCCG
* * *
11954505 CTGGGACACTAAACACGGGGTAGTCCA
1 CTGGGACACTAAACACGCGGTAGACAA
*
11954532 CTGGGACGCTAAACACGCGGTAGACAA
1 CTGGGACACTAAACACGCGGTAGACAA
*
11954559 TTGGGACA
1 CTGGGACA
11954567 GTAACATGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.31, T:0.15
Consensus pattern (27 bp):
CTGGGACACTAAACACGCGGTAGACAA
Found at i:11958306 original size:46 final size:46
Alignment explanation
Indices: 11958187--11958306 Score: 172
Period size: 45 Copynumber: 2.7 Consensus size: 46
11958177 GCTATACGCC
11958187 TAGAA-ATGAGTTAGACCATAGCTGAAAGATGGTATGGCATCATAA
1 TAGAAGATGAGTTAGACCATAGCTGAAAGATGGTATGGCATCATAA
* ** * * *
11958232 TA-AAGATGAGTAAGACCATTTCTAAAAGATGTTATGGCATCATGA
1 TAGAAGATGAGTTAGACCATAGCTGAAAGATGGTATGGCATCATAA
11958277 TAGAAGATGAGTTAGACCATAGCTGAAAGA
1 TAGAAGATGAGTTAGACCATAGCTGAAAGA
11958307 CACCATGGCA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 2 0.03
45 38 0.60
46 23 0.37
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (46 bp):
TAGAAGATGAGTTAGACCATAGCTGAAAGATGGTATGGCATCATAA
Found at i:11958315 original size:46 final size:46
Alignment explanation
Indices: 11958187--11958321 Score: 166
Period size: 45 Copynumber: 3.0 Consensus size: 46
11958177 GCTATACGCC
* *
11958187 TAGAA-ATGAGTTAGACCATAGCTGAAAGATGGTATGGCATCATAA
1 TAGAAGATGAGTTAGACCATAGCTGAAAGATGCTATGGCATCATGA
* ** * *
11958232 TA-AAGATGAGTAAGACCATTTCTAAAAGATGTTATGGCATCATGA
1 TAGAAGATGAGTTAGACCATAGCTGAAAGATGCTATGGCATCATGA
** *
11958277 TAGAAGATGAGTTAGACCATAGCTGAAAGACACCATGGCATCATG
1 TAGAAGATGAGTTAGACCATAGCTGAAAGATGCTATGGCATCATG
11958322 TAAAAGTAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
44 2 0.03
45 38 0.51
46 34 0.46
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.24
Consensus pattern (46 bp):
TAGAAGATGAGTTAGACCATAGCTGAAAGATGCTATGGCATCATGA
Found at i:11963498 original size:112 final size:112
Alignment explanation
Indices: 11963301--11963529 Score: 424
Period size: 112 Copynumber: 2.0 Consensus size: 112
11963291 TCCATAGCTA
*
11963301 AGGGTGTGAAGTTTCGGCAACGCTTTGTCTTGTATGCATGGTACGTAATGTTGCCGCGTTTTTAG
1 AGGGTGTGAAGTTTCGACAACGCTTTGTCTTGTATGCATGGTACGTAATGTTGCCGCGTTTTTAG
*
11963366 TATTTTTTATGTTATTGAGTTTGTTTTACCTTAATTTAGCTAGCCCG
66 TATTTTTTATGTTATTGAGTTCGTTTTACCTTAATTTAGCTAGCCCG
11963413 AGGGTGTGAAGTTTCGACAACGCTTTGTCTTGTATGCATGGTACGTAATGTTGCCGCGTTTTTAG
1 AGGGTGTGAAGTTTCGACAACGCTTTGTCTTGTATGCATGGTACGTAATGTTGCCGCGTTTTTAG
11963478 TATTTTTTATGCTT-TTGAGTTCGTTTTACCTTAATTTAGCTAGCCCG
66 TATTTTTTATG-TTATTGAGTTCGTTTTACCTTAATTTAGCTAGCCCG
11963525 AGGGT
1 AGGGT
11963530 CAATTCGTAA
Statistics
Matches: 114, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
112 112 0.98
113 2 0.02
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.43
Consensus pattern (112 bp):
AGGGTGTGAAGTTTCGACAACGCTTTGTCTTGTATGCATGGTACGTAATGTTGCCGCGTTTTTAG
TATTTTTTATGTTATTGAGTTCGTTTTACCTTAATTTAGCTAGCCCG
Found at i:11964065 original size:14 final size:15
Alignment explanation
Indices: 11964041--11964069 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
11964031 AAGGACTAAA
11964041 TTATCATATAATGTT
1 TTATCATATAATGTT
11964056 TTAT-ATATAATGTT
1 TTATCATATAATGTT
11964070 AATAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (15 bp):
TTATCATATAATGTT
Found at i:11968778 original size:22 final size:21
Alignment explanation
Indices: 11968717--11968778 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 21
11968707 CTAGAAATGT
11968717 GTAAGACCATAGCTAAAAGATG
1 GTAAGACCATAGCT-AAAGATG
* * *
11968739 CTATGA-CATCATGATAAAGATGG
1 GTAAGACCAT-A-GCTAAAGAT-G
11968762 GTAAGACCATAGCTAAA
1 GTAAGACCATAGCTAAA
11968779 AGATTCTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
21 3 0.10
22 16 0.53
23 8 0.27
24 3 0.10
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (21 bp):
GTAAGACCATAGCTAAAGATG
Found at i:11968782 original size:23 final size:22
Alignment explanation
Indices: 11968717--11968782 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
11968707 CTAGAAATGT
11968717 GTAAGACCATAGCTAAAAGATG
1 GTAAGACCATAGCTAAAAGATG
* * *
11968739 CTATGA-CATCATGAT-AAAGATGG
1 GTAAGACCAT-A-GCTAAAAGAT-G
11968762 GTAAGACCATAGCTAAAAGAT
1 GTAAGACCATAGCTAAAAGAT
11968783 TCTATGGCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
21 3 0.09
22 13 0.39
23 14 0.42
24 3 0.09
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (22 bp):
GTAAGACCATAGCTAAAAGATG
Found at i:11968827 original size:46 final size:46
Alignment explanation
Indices: 11968711--11968888 Score: 205
Period size: 46 Copynumber: 3.9 Consensus size: 46
11968701 ATACGTCTAG
* *
11968711 AAATGTGTAAGACCATAGCTAAAAGATGCTATGACATCATGATA-A
1 AAATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCATGATAGA
* * * * *
11968756 AGATGGGTAAGACCATAGCTAAAAGATTCTATGGCATAATAATAGA
1 AAATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCATGATAGA
* * * *
11968802 AAATGAGTAAGACCGTAGTTGAAAGATGCTATGGCATCATGGTAGA
1 AAATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCATGATAGA
* * * * *
11968848 ATATGAGTAAGACCATAGTTGAAAGGTGCTATAGCATCATG
1 AAATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCATG
11968889 TAAAATCACG
Statistics
Matches: 113, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
45 38 0.34
46 75 0.66
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (46 bp):
AAATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCATGATAGA
Found at i:11972506 original size:50 final size:50
Alignment explanation
Indices: 11972452--11972593 Score: 266
Period size: 50 Copynumber: 2.8 Consensus size: 50
11972442 AATTCATGCA
11972452 TTATGTAACTCTCATGTTAGTTAAGTTTGCATCATAAATTATTACATGAT
1 TTATGTAACTCTCATGTTAGTTAAGTTTGCATCATAAATTATTACATGAT
11972502 TTATGTAACTCTCATGTTAGTTAAGTTTGCATCATAAATTATTACATGAT
1 TTATGTAACTCTCATGTTAGTTAAGTTTGCATCATAAATTATTACATGAT
11972552 TTATGTAACTCTCATGTTAGTTGAAGTTTGCATCATTAAATT
1 TTATGTAACTCTCATGTTAGTT-AAGTTTGCATCA-TAAATT
11972594 TAAGTCATGC
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
50 72 0.80
51 12 0.13
52 6 0.07
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (50 bp):
TTATGTAACTCTCATGTTAGTTAAGTTTGCATCATAAATTATTACATGAT
Found at i:11975426 original size:27 final size:27
Alignment explanation
Indices: 11975388--11975455 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
11975378 GTCGAGACAT
*
11975388 TAAAAGTGGGGTAGTCCACCAGGACG-A
1 TAAAAATGGGGTAGTCCACCAGGA-GAA
*
11975415 TAAAAATGGGGTAGTCCACCGGGAGAA
1 TAAAAATGGGGTAGTCCACCAGGAGAA
*
11975442 TAAAAACGGGGTAG
1 TAAAAATGGGGTAG
11975456 CCTTCCAGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 1 0.03
27 36 0.97
ACGTcount: A:0.37, C:0.15, G:0.34, T:0.15
Consensus pattern (27 bp):
TAAAAATGGGGTAGTCCACCAGGAGAA
Found at i:11975505 original size:27 final size:27
Alignment explanation
Indices: 11975475--11975529 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
11975465 ACACTAAATG
* *
11975475 TGGGGTAGTCTG-CTAGGATGATGAAAA
1 TGGGATAGTCTGTC-AGGATGATAAAAA
*
11975502 TGGGATGGTCTGTCAGGATGATAAAAA
1 TGGGATAGTCTGTCAGGATGATAAAAA
11975529 T
1 T
11975530 AAAATAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.31, C:0.07, G:0.35, T:0.27
Consensus pattern (27 bp):
TGGGATAGTCTGTCAGGATGATAAAAA
Found at i:11979162 original size:36 final size:35
Alignment explanation
Indices: 11979115--11979184 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
11979105 ATCTCCAGAA
*
11979115 CTTGGTAAATATGGAAAGTGATCTTCCAAAGATATG
1 CTTGGCAAATATGGAAAGTGATCTT-CAAAGATATG
* *
11979151 CTTGGCAAATATGGAAGGTGATCTTCAAATATAT
1 CTTGGCAAATATGGAAAGTGATCTTCAAAGATAT
11979185 ATGATCCTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 8 0.26
36 23 0.74
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (35 bp):
CTTGGCAAATATGGAAAGTGATCTTCAAAGATATG
Found at i:11985530 original size:14 final size:14
Alignment explanation
Indices: 11985511--11985552 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
11985501 AGATAAAAAT
11985511 AAATAAATCAATAA
1 AAATAAATCAATAA
**
11985525 AAATAAA-CAATTG
1 AAATAAATCAATAA
*
11985538 AAGTAAATCAATAA
1 AAATAAATCAATAA
11985552 A
1 A
11985553 CCAATCAGGA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (14 bp):
AAATAAATCAATAA
Found at i:11989849 original size:167 final size:166
Alignment explanation
Indices: 11989573--11989901 Score: 604
Period size: 167 Copynumber: 2.0 Consensus size: 166
11989563 ACTGCCAGAG
*
11989573 GAGGAAAGGAGTATAAAAATTCATTGTAGAAGCCCAACATGACCCCAGATGAGGTCGCGATCGGG
1 GAGGAAAGGAGTAGAAAAATTCATTGTAGAAGCCCAACATGACCCCAGATGAGGTCGCGATCGGG
* *
11989638 AGTACATACGTCAAGTTTATCATCATTAACTCCGACCCCAAATACTATACCGATGGGTGCACCAC
66 AGTACATACGTCAAGTTCATCATCATTAACTCCAACCCCAAATACTATACCGATGGGTGCACCAC
*
11989703 TTCCCGATCAATATGTTTTATATTTTTTCTCGTAGAA
131 TTCCCGATCAATATGTTTCATA-TTTTTCTCGTAGAA
11989740 GAGGAAAGGAGTAGAAAAATTCATTGTAGAAGCCCAACATGACCCCAGATGAGGTCGCGATCGGG
1 GAGGAAAGGAGTAGAAAAATTCATTGTAGAAGCCCAACATGACCCCAGATGAGGTCGCGATCGGG
*
11989805 AGTACATACGTCAAGTTCATCATCATTAACTCCAACCCCAAATACTATACTGATGGGTGCACCAC
66 AGTACATACGTCAAGTTCATCATCATTAACTCCAACCCCAAATACTATACCGATGGGTGCACCAC
11989870 TTCCCGATCAATATGTTTCATATTTTTCTCGT
131 TTCCCGATCAATATGTTTCATATTTTTCTCGT
11989902 GCTTTTACTA
Statistics
Matches: 157, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
166 10 0.06
167 147 0.94
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (166 bp):
GAGGAAAGGAGTAGAAAAATTCATTGTAGAAGCCCAACATGACCCCAGATGAGGTCGCGATCGGG
AGTACATACGTCAAGTTCATCATCATTAACTCCAACCCCAAATACTATACCGATGGGTGCACCAC
TTCCCGATCAATATGTTTCATATTTTTCTCGTAGAA
Found at i:11990406 original size:5 final size:5
Alignment explanation
Indices: 11990396--11990448 Score: 106
Period size: 5 Copynumber: 10.6 Consensus size: 5
11990386 AAATAAAAAA
11990396 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
11990446 ATT
1 ATT
11990449 TTTACATTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.21, C:0.00, G:0.19, T:0.60
Consensus pattern (5 bp):
ATTGT
Found at i:11990503 original size:72 final size:72
Alignment explanation
Indices: 11990421--11990644 Score: 286
Period size: 72 Copynumber: 3.0 Consensus size: 72
11990411 ATTGTATTGT
11990421 ATTGTATTGTATTGTATTGTATTGTATTTTTACATTAATAATATACTTATTTACAATTTACAAAA
1 ATTGT-TTGTATTGTATTGTATTGTATTTTTACATTAATAATATACTTATTTACAATTTACAAAA
11990486 AATGAAAA
65 AATGAAAA
*
11990494 ATTGTTTGTATTGTGTTGTATTGTATTTTTACATTAATAATATACTTATTTACAATTTACGAAAA
1 ATTGTTTGTATTGTATTGTATTGTATTTTTACATTAATAATATACTTATTTACAATTTAC--AAA
*
11990559 AAATAAAAAA
64 AAAT-GAAAA
* * ** * * * * *
11990569 ATTTATTTTTATTGTATCATATTGCATTTTTAAATCAATAATAAACTTATTTACAATTTACCCAA
1 A-TTGTTTGTATTGTATTGTATTGTATTTTTACATTAATAATATACTTATTTACAATTTA-CAAA
11990634 AAATGCAAAA
64 AAATG-AAAA
11990644 A
1 A
11990645 AAATTGTTTT
Statistics
Matches: 132, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
72 54 0.41
73 5 0.04
74 7 0.05
75 16 0.12
76 49 0.37
77 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.45
Consensus pattern (72 bp):
ATTGTTTGTATTGTATTGTATTGTATTTTTACATTAATAATATACTTATTTACAATTTACAAAAA
ATGAAAA
Found at i:11990644 original size:76 final size:74
Alignment explanation
Indices: 11990427--11990645 Score: 289
Period size: 76 Copynumber: 2.9 Consensus size: 74
11990417 TTGTATTGTA
11990427 TTGTATTGTATTGTATTGTATTTTTACATTAATAATATACTTATTTACAATTTA-CAAAAAATG-
1 TTGTATTGTATTGTATTGTATTTTTACATTAATAATATACTTATTTACAATTTACCAAAAAATGA
*
11990490 AAAAATTGT
66 AAAAATTAT
* * *
11990499 TTGTATTGTGTTGTATTGTATTTTTACATTAATAATATACTTATTTACAATTTACGAAAAAAATA
1 TTGTATTGTATTGTATTGTATTTTTACATTAATAATATACTTATTTACAATTTAC-CAAAAAATG
11990564 AAAAAATTTAT
65 AAAAAA-TTAT
* ** * * * * *
11990575 TTTTATTGTATCATATTGCATTTTTAAATCAATAATAAACTTATTTACAATTTACCCAAAAATGC
1 TTGTATTGTATTGTATTGTATTTTTACATTAATAATATACTTATTTACAATTTACCAAAAAATG-
11990640 AAAAAA
65 AAAAAA
11990646 AATTGTTTTG
Statistics
Matches: 127, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
72 53 0.42
74 7 0.06
75 11 0.09
76 56 0.44
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (74 bp):
TTGTATTGTATTGTATTGTATTTTTACATTAATAATATACTTATTTACAATTTACCAAAAAATGA
AAAAATTAT
Found at i:11993582 original size:41 final size:41
Alignment explanation
Indices: 11993458--11993648 Score: 217
Period size: 42 Copynumber: 4.6 Consensus size: 41
11993448 ACTGTGATAT
* *
11993458 GATTACGTGTAAGACCATGTCTGGAACATTGGCATCGTTATGT
1 GATT-CGTGTAAGACCATGTCTGG-ACATTGGCATCGATATGA
* * *
11993501 GATTCATGTAAGACTATGTCTGGGACATTGGCATCAATATGA
1 GATTCGTGTAAGACCATGTCT-GGACATTGGCATCGATATGA
11993543 GATTCGTGTAAGACCATGTCTGGACATTGGCATCGATATGA
1 GATTCGTGTAAGACCATGTCTGGACATTGGCATCGATATGA
*
11993584 GATTCGTGTAAGATCATAG-CTGG-CTATTGGCATCGATAT-A
1 GATTCGTGTAAGACCAT-GTCTGGAC-ATTGGCATCGATATGA
* * *
11993624 TGATAGCATGTAAGACCATATCTGG
1 -GAT-TCGTGTAAGACCATGTCTGG
11993649 GATATGACAT
Statistics
Matches: 129, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
40 2 0.02
41 56 0.43
42 65 0.50
43 6 0.05
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (41 bp):
GATTCGTGTAAGACCATGTCTGGACATTGGCATCGATATGA
Found at i:11993636 original size:83 final size:84
Alignment explanation
Indices: 11993465--11993648 Score: 218
Period size: 83 Copynumber: 2.2 Consensus size: 84
11993455 TATGATTACG
* *
11993465 TGTAAGACCATGTCTGGAACATTGGCATCGTTATGTGATTCATGTAAGACTATGTCTGGGACATT
1 TGTAAGACCATGTCTGGAACATTGGCATCGATATGAGATTCATGTAAGACTATGTCTGGGACATT
* *
11993530 GGCATCAATATGAGATTCG
66 GGCATCAATATGAGATGCA
*
11993549 TGTAAGACCATGTCTGG-ACATTGGCATCGATATGAGATTCGTGTAAGA-TCATAG-CT-GG-CT
1 TGTAAGACCATGTCTGGAACATTGGCATCGATATGAGATTCATGTAAGACT-AT-GTCTGGGAC-
*
11993609 ATTGGCATCGATAT-ATGATAGCA
63 ATTGGCATCAATATGA-GAT-GCA
*
11993632 TGTAAGACCATATCTGG
1 TGTAAGACCATGTCTGG
11993649 GATATGACAT
Statistics
Matches: 88, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
81 2 0.02
82 19 0.22
83 49 0.56
84 18 0.20
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (84 bp):
TGTAAGACCATGTCTGGAACATTGGCATCGATATGAGATTCATGTAAGACTATGTCTGGGACATT
GGCATCAATATGAGATGCA
Found at i:11997298 original size:27 final size:28
Alignment explanation
Indices: 11997260--11997333 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
11997250 AAACACACCA
* *
11997260 AAAAAGTAAGCCTTTGTAACGATTTA-T
1 AAAAAGAAAGCCTTTGTAACGATCTATT
*
11997287 AAAAAGAAAGCCTTTTGTAGCGATCTATT
1 AAAAAGAAAGCC-TTTGTAACGATCTATT
*
11997316 AAAAAGGGAAGCCTTTGT
1 AAAAA-GAAAGCCTTTGT
11997334 GGCAAACTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
27 11 0.28
28 12 0.30
29 11 0.28
30 6 0.15
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (28 bp):
AAAAAGAAAGCCTTTGTAACGATCTATT
Found at i:12004630 original size:15 final size:14
Alignment explanation
Indices: 12004610--12004657 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
12004600 TTTAAGAGTC
12004610 TAATATTTGTATTGT
1 TAATATTTGTATT-T
*
12004625 TAATATATTTTATTT
1 TAATAT-TTGTATTT
* *
12004640 GAAAATTTGTATTT
1 TAATATTTGTATTT
12004654 TAAT
1 TAAT
12004658 TTTTATAATG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 9 0.35
15 11 0.42
16 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (14 bp):
TAATATTTGTATTT
Found at i:12004634 original size:17 final size:16
Alignment explanation
Indices: 12004612--12004657 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
12004602 TAAGAGTCTA
12004612 ATATTTGTATTGTTAAT
1 ATATTTGTATT-TTAAT
*
12004629 ATATTT-TATTTGAA-
1 ATATTTGTATTTTAAT
12004643 A-ATTTGTATTTTAAT
1 ATATTTGTATTTTAAT
12004658 TTTTATAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 3 0.12
16 4 0.16
17 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
ATATTTGTATTTTAAT
Found at i:12005798 original size:17 final size:18
Alignment explanation
Indices: 12005763--12005797 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12005753 AATTTAACTT
12005763 TAATTAAATTTCTTAAAA
1 TAATTAAATTTCTTAAAA
* *
12005781 TAATTAATTTTTTTAAA
1 TAATTAAATTTCTTAAA
12005798 TTATAAACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAAATTTCTTAAAA
Found at i:12006728 original size:20 final size:20
Alignment explanation
Indices: 12006703--12006742 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12006693 TAACGAGACC
*
12006703 GCTGATGTGGCAAGTTAACT
1 GCTGATGTAGCAAGTTAACT
*
12006723 GCTGATGTAGCCAGTTAACT
1 GCTGATGTAGCAAGTTAACT
12006743 TGCCACGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (20 bp):
GCTGATGTAGCAAGTTAACT
Found at i:12006843 original size:3 final size:3
Alignment explanation
Indices: 12006824--12006864 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
12006814 CCCTTAACAG
* *
12006824 AGA AAA AGA ATA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
12006865 CTGAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:12013359 original size:3 final size:3
Alignment explanation
Indices: 12013340--12013423 Score: 141
Period size: 3 Copynumber: 28.0 Consensus size: 3
12013330 TTTTATAGTC
* * *
12013340 TCT TAT TCT TTT TCT TCT TCT ACT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
12013388 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
12013424 CTGTTAAGGG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:12013644 original size:30 final size:31
Alignment explanation
Indices: 12013579--12013646 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
12013569 ATTGTTAATC
* *
12013579 AGTGACTATTTTGTCACTTTTTTATAACGTT
1 AGTGACTATTTTGTCACTTTTTCATAAAGTT
*
12013610 AGTGACTATTTTGTTA-TTTTTCA-AAAGTT
1 AGTGACTATTTTGTCACTTTTTCATAAAGTT
12013639 GAGTGACT
1 -AGTGACT
12013647 GGAATAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.15
30 13 0.39
31 15 0.45
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (31 bp):
AGTGACTATTTTGTCACTTTTTCATAAAGTT
Found at i:12015002 original size:2 final size:2
Alignment explanation
Indices: 12014997--12015036 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
12014987 TTATGCATTC
*
12014997 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12015037 GAGTGCATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12015657 original size:31 final size:30
Alignment explanation
Indices: 12015617--12015691 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 30
12015607 AAATGGTATG
* *
12015617 TTTGGTACAAATGAATTACCGAAATGGG-TCA
1 TTTGCTACAAAT-AAATACCGAAATGGGCT-A
12015648 TTTGCTACAAAAATAAATACCGAAATGGGCTA
1 TTTGCTAC--AAATAAATACCGAAATGGGCTA
*
12015680 CTTGCTACAAAT
1 TTTGCTACAAAT
12015692 TTTTACAGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 4 0.11
31 7 0.18
32 22 0.58
33 5 0.13
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (30 bp):
TTTGCTACAAATAAATACCGAAATGGGCTA
Found at i:12017088 original size:28 final size:28
Alignment explanation
Indices: 12017025--12017088 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
12017015 ATATTCAATA
*
12017025 CATGTTATTTTAATTGTGTTACTACCTC
1 CATGTTATTTTAATCGTGTTACTACCTC
* *
12017053 TATATTATTTTAATCGTGTTACTACCTC
1 CATGTTATTTTAATCGTGTTACTACCTC
12017081 CATGTTAT
1 CATGTTAT
12017089 CAATTGTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.50
Consensus pattern (28 bp):
CATGTTATTTTAATCGTGTTACTACCTC
Found at i:12018215 original size:17 final size:18
Alignment explanation
Indices: 12018195--12018229 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12018185 ATCCATCTTC
*
12018195 AATAA-TAAATTTGTAAA
1 AATAATTAAATTTCTAAA
12018212 AATAATTAAATTTCTAAA
1 AATAATTAAATTTCTAAA
12018230 TATTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
AATAATTAAATTTCTAAA
Found at i:12020707 original size:48 final size:50
Alignment explanation
Indices: 12020642--12020783 Score: 146
Period size: 48 Copynumber: 2.9 Consensus size: 50
12020632 AGCCATGTAA
* *
12020642 CGGGAAGCTCCGGAGAGCCATTAACGGGAAGCTCATACA-AGCCAAT-AT
1 CGGGAAGCTCCGAAGAGCCATTAACGGGAAGCTCATAAAGAGCCAATAAT
* ** * **
12020690 CGGGAAGCTCCAAAGAGCCATTAACGAAAAGCTCACAAAGAGCCTTTAAT
1 CGGGAAGCTCCGAAGAGCCATTAACGGGAAGCTCATAAAGAGCCAATAAT
* * *
12020740 TGGGAAGCTCACGAAGAGCCATATATCGGGACGCTCAT-AAGAGC
1 CGGGAAGCTC-CGAAGAGCCAT-TAACGGGAAGCTCATAAAGAGC
12020784 TACGGTGTGT
Statistics
Matches: 75, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
48 33 0.44
49 5 0.07
50 11 0.15
51 16 0.21
52 10 0.13
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.15
Consensus pattern (50 bp):
CGGGAAGCTCCGAAGAGCCATTAACGGGAAGCTCATAAAGAGCCAATAAT
Found at i:12020733 original size:25 final size:26
Alignment explanation
Indices: 12020694--12020761 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
12020684 CAATATCGGG
12020694 AAGCTC-CAAAGAGCCATTAA-CGAA
1 AAGCTCACAAAGAGCCATTAATCGAA
* * **
12020718 AAGCTCACAAAGAGCCTTTAATTGGG
1 AAGCTCACAAAGAGCCATTAATCGAA
*
12020744 AAGCTCACGAAGAGCCAT
1 AAGCTCACAAAGAGCCAT
12020762 ATATCGGGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
24 6 0.17
25 13 0.36
26 17 0.47
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (26 bp):
AAGCTCACAAAGAGCCATTAATCGAA
Found at i:12020770 original size:26 final size:25
Alignment explanation
Indices: 12020631--12020776 Score: 127
Period size: 24 Copynumber: 5.8 Consensus size: 25
12020621 AAGTTCATGT
**
12020631 GAGCCATGTAACGGGAAGCTC-CGGA
1 GAGCCAT-TAACGGGAAGCTCACAAA
* *
12020656 GAGCCATTAACGGGAAGCTCATACA
1 GAGCCATTAACGGGAAGCTCACAAA
* *
12020681 -AGCCAATATCGGGAAGCTC-CAAA
1 GAGCCATTAACGGGAAGCTCACAAA
**
12020704 GAGCCATTAACGAAAAGCTCACAAA
1 GAGCCATTAACGGGAAGCTCACAAA
* * *
12020729 GAGCCTTTAATTGGGAAGCTCACGAA
1 GAGCCATTAA-CGGGAAGCTCACAAA
* *
12020755 GAGCCATATATCGGGACGCTCA
1 GAGCCAT-TAACGGGAAGCTCA
12020777 TAAGAGCTAC
Statistics
Matches: 96, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
23 2 0.02
24 45 0.47
25 21 0.22
26 26 0.27
27 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (25 bp):
GAGCCATTAACGGGAAGCTCACAAA
Found at i:12021249 original size:21 final size:21
Alignment explanation
Indices: 12021215--12021264 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
12021205 TATACGAATG
*
12021215 AATTAACA-TCAATTTAATAC
1 AATTAACATTCAATTCAATAC
* *
12021235 AATTTACATTCAATTCAATCC
1 AATTAACATTCAATTCAATAC
*
12021256 AATTCACAT
1 AATTAACAT
12021265 CTTAGGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTAACATTCAATTCAATAC
Found at i:12022624 original size:20 final size:20
Alignment explanation
Indices: 12022601--12022639 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12022591 TACCGATACT
*
12022601 TTTCTTAAGGTATCAATATA
1 TTTCCTAAGGTATCAATATA
12022621 TTTCCTAAGGTATCAATAT
1 TTTCCTAAGGTATCAATAT
12022640 TCATGCTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (20 bp):
TTTCCTAAGGTATCAATATA
Found at i:12027377 original size:41 final size:41
Alignment explanation
Indices: 12027316--12027394 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
12027306 TTTGATATGG
* * **
12027316 TCTTTAGCAGCGTTTTTGGGGAAAGCGTCGCTAAAGGTTGT
1 TCTTTAGCAGCATTTGTGGGGAAAGCACCGCTAAAGGTTGT
12027357 TCTTTAGCAGCATTTGTGGGGAAAGCACCGCTAAAGGT
1 TCTTTAGCAGCATTTGTGGGGAAAGCACCGCTAAAGGT
12027395 AATGTCTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (41 bp):
TCTTTAGCAGCATTTGTGGGGAAAGCACCGCTAAAGGTTGT
Found at i:12028623 original size:25 final size:25
Alignment explanation
Indices: 12028595--12028645 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
12028585 CAGCGAGTGT
* * *
12028595 GCCACAAGGGTTTTCTAGAGAATTC
1 GCCACAAAGGCTTTCTACAGAATTC
*
12028620 GCCACAAAGGCTTTCTACATAATTC
1 GCCACAAAGGCTTTCTACAGAATTC
12028645 G
1 G
12028646 TGTTTACTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (25 bp):
GCCACAAAGGCTTTCTACAGAATTC
Found at i:12034723 original size:23 final size:23
Alignment explanation
Indices: 12034668--12034754 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 23
12034658 TATTAACAAG
12034668 GTTCGTGAACATGTTCAATTATAT
1 GTTCGTGAACATGTTCAATTA-AT
* * * *
12034692 GTCCATGAACAAGTTCATTTAAT
1 GTTCGTGAACATGTTCAATTAAT
12034715 GTTCGTGAACATGTTCAATTAA-
1 GTTCGTGAACATGTTCAATTAAT
**
12034737 GTTAAATGAACATGTTCA
1 GTT-CGTGAACATGTTCA
12034755 TGAACACTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 3 0.06
23 32 0.62
24 17 0.33
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (23 bp):
GTTCGTGAACATGTTCAATTAAT
Found at i:12037308 original size:25 final size:25
Alignment explanation
Indices: 12037272--12037373 Score: 88
Period size: 25 Copynumber: 4.2 Consensus size: 25
12037262 ACACATCGCA
*
12037272 GCTCTTAT-GAGCTTCTCGA-TATATG
1 GCTCTT-TGGAGCTTCCCGATTA-ATG
*
12037297 GCTCTTTGGAGCTTCCCGATTAAAG
1 GCTCTTTGGAGCTTCCCGATTAATG
**
12037322 GCTCTTTGTGAGCTTCTTGATTAAT-
1 GCTCTTTG-GAGCTTCCCGATTAATG
**
12037347 GCTCTCCGGAGCTTCCCGA-T-ATG
1 GCTCTTTGGAGCTTCCCGATTAATG
12037370 GCTC
1 GCTC
12037374 GCTTGAACTT
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.03
23 5 0.08
24 10 0.16
25 32 0.50
26 15 0.23
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.36
Consensus pattern (25 bp):
GCTCTTTGGAGCTTCCCGATTAATG
Found at i:12037421 original size:25 final size:24
Alignment explanation
Indices: 12037393--12037446 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
12037383 TTCCGATATA
*
12037393 TGGCTATCCAAAGCTTCCTGATTAT
1 TGGCTATCCAAAGCTACCTG-TTAT
* * *
12037418 TGGCTCTTCAGAGCTACCTGTTAT
1 TGGCTATCCAAAGCTACCTGTTAT
12037442 TGGCT
1 TGGCT
12037447 TGCATTAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (24 bp):
TGGCTATCCAAAGCTACCTGTTAT
Found at i:12042976 original size:69 final size:69
Alignment explanation
Indices: 12042856--12043031 Score: 196
Period size: 69 Copynumber: 2.5 Consensus size: 69
12042846 AAGATGTGAT
* * *
12042856 TGTGGTGGTGGATGAATATAACTTTTTGTATGTCA-TAGAGCGTTGTCACTTTGTCTATGTGTAA
1 TGTGGTGGTGGAT-AATATAACTTTTTGTATGTAATTTGAGCGTTGTCACTTTGTCAATGTGTAA
*
12042920 ATGTA
65 ATGGA
* * * * *
12042925 TGTGGTGGTGAACTAATATAACTTTTTGTATGTAATTTTAG-GTTG-CTACTTTTTGAATGTTTA
1 TGTGGTGGTGGA-TAATATAACTTTTTGTATGTAATTTGAGCGTTGTC-ACTTTGTCAATGTGTA
*
12042988 AATGGG
64 AATGGA
*
12042994 TGTGGTGGTGGAGTATTATAACTTTTTGTATGTAATTT
1 TGTGGTGGTGGA-TAATATAACTTTTTGTATGTAATTT
12043032 CAGGATGATA
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
68 1 0.01
69 86 0.95
70 4 0.04
ACGTcount: A:0.23, C:0.06, G:0.25, T:0.45
Consensus pattern (69 bp):
TGTGGTGGTGGATAATATAACTTTTTGTATGTAATTTGAGCGTTGTCACTTTGTCAATGTGTAAA
TGGA
Found at i:12043570 original size:10 final size:10
Alignment explanation
Indices: 12043542--12043600 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
12043532 AATAAAATAT
*
12043542 TTTAA-ATAT
1 TTTAATATAA
*
12043551 TTTAAAATAA
1 TTTAATATAA
12043561 TTTAATATAAA
1 TTTAATAT-AA
** *
12043572 AATAA-AAAA
1 TTTAATATAA
12043581 TTTAATATAA
1 TTTAATATAA
12043591 TTTAATATAA
1 TTTAATATAA
12043601 AATATTAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 10 0.26
10 24 0.62
11 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TTTAATATAA
Found at i:12043573 original size:40 final size:40
Alignment explanation
Indices: 12043524--12043600 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
12043514 CATTTCAGAA
* *
12043524 AATATAAAAATAAAATATTTTAA-ATATTTTAAAATAATTT
1 AATATAAAAATAAAA-AATTTAATATAATTTAAAATAATTT
*
12043564 AATATAAAAATAAAAAATTTAATATAATTTAATATAA
1 AATATAAAAATAAAAAATTTAATATAATTTAAAATAA
12043601 AATATTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 6 0.18
40 27 0.82
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (40 bp):
AATATAAAAATAAAAAATTTAATATAATTTAAAATAATTT
Found at i:12043611 original size:30 final size:30
Alignment explanation
Indices: 12043533--12043611 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 30
12043523 AAATATAAAA
12043533 ATAAAATATTTTAAATATTTTAAAATAATTTAAT
1 ATAAAATA--TTAAA-A-TTTAAAATAATTTAAT
* *
12043567 ATAAAA-ATAAAAAATTTAATATAATTTAAT
1 ATAAAATAT-TAAAATTTAAAATAATTTAAT
12043597 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
12043612 AATATTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 26 0.65
31 4 0.10
32 3 0.08
33 1 0.03
34 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
ATAAAATATTAAAATTTAAAATAATTTAAT
Found at i:12045311 original size:2 final size:2
Alignment explanation
Indices: 12045304--12045342 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12045294 GATCCTATTT
12045304 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
12045343 TTTGACATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Done.