Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold382
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: 2572505
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 3 of 16
Found at i:270519 original size:12 final size:12
Alignment explanation
Indices: 270502--270549 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
270492 ATGAATTACA
270502 TTTAAAAATATT
1 TTTAAAAATATT
270514 TTTAAAAATA-T
1 TTTAAAAATATT
270525 TTT-AAAATATT
1 TTTAAAAATATT
*
270536 TTGAAAAATATT
1 TTTAAAAATATT
270548 TT
1 TT
270550 ATATTAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
10 6 0.18
11 7 0.21
12 20 0.61
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (12 bp):
TTTAAAAATATT
Found at i:270531 original size:22 final size:22
Alignment explanation
Indices: 270501--270550 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
270491 GATGAATTAC
* *
270501 ATTTAAAAATATTTTTAAAAAT
1 ATTTTAAAATATTTTGAAAAAT
270523 ATTTTAAAATATTTTGAAAAAT
1 ATTTTAAAATATTTTGAAAAAT
270545 ATTTTA
1 ATTTTA
270551 TATTAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTTAAAATATTTTGAAAAAT
Found at i:270748 original size:17 final size:17
Alignment explanation
Indices: 270722--270762 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
270712 TATATATATT
*
270722 TTTTTATTTTTTAAAATA
1 TTTTT-TTTTATAAAATA
270740 TTTTTTTTTATAAAATA
1 TTTTTTTTTATAAAATA
270757 TTTTTT
1 TTTTTT
270763 AAATGAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTTTTATAAAATA
Found at i:271339 original size:24 final size:24
Alignment explanation
Indices: 271276--271339 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 24
271266 TAAATTTGAC
*
271276 ATTTGATATAATAAAAAATTATTAT
1 ATTTGATA-AATAATAAATTATTAT
** * *
271301 -TTTTTTAAA-ATTAAATTTTTAT
1 ATTTGATAAATAATAAATTATTAT
271323 ATTTGATAAATAATAAA
1 ATTTGATAAATAATAAA
271340 GTGTTTTTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
22 10 0.34
23 9 0.31
24 10 0.34
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (24 bp):
ATTTGATAAATAATAAATTATTAT
Found at i:271603 original size:16 final size:16
Alignment explanation
Indices: 271584--271618 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
271574 AATTACTCTC
*
271584 AAATTAAATTTTAATT
1 AAATTAAATTATAATT
*
271600 AAATTATATTATAATT
1 AAATTAAATTATAATT
271616 AAA
1 AAA
271619 ATACCTATTA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTAAATTATAATT
Found at i:272667 original size:19 final size:19
Alignment explanation
Indices: 272643--272681 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
272633 ATATATTTAT
*
272643 TTATTTAATTTACTTAAAC
1 TTATTTAATTTAATTAAAC
*
272662 TTATTTTATTTAATTAAAC
1 TTATTTAATTTAATTAAAC
272681 T
1 T
272682 ACGTCGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTTAATTTAATTAAAC
Found at i:276660 original size:13 final size:13
Alignment explanation
Indices: 276642--276667 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
276632 CAATTTTTTG
276642 TGTATCGATACAT
1 TGTATCGATACAT
276655 TGTATCGATACAT
1 TGTATCGATACAT
276668 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:276751 original size:20 final size:20
Alignment explanation
Indices: 276706--276778 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
276696 CTGCCAAGAA
***
276706 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
276727 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
276747 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
276767 ATGTATCGATAC
1 ATGTATCGATAC
276779 TTTTAAGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.64
21 14 0.31
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:276779 original size:20 final size:20
Alignment explanation
Indices: 276726--276781 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
276716 ACATCTTTTT
*
276726 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
276746 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
276765 TTATGTATCGATACTTT
1 -CATGTATCGATACTTT
276782 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:287421 original size:16 final size:16
Alignment explanation
Indices: 287400--287430 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
287390 TTTTCCAAAC
*
287400 AAAAAAAAGAAAAAAG
1 AAAAAAAACAAAAAAG
287416 AAAAAAAACAAAAAA
1 AAAAAAAACAAAAAA
287431 TCTTGGTGAG
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:0.90, C:0.03, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAAAAG
Found at i:288502 original size:32 final size:32
Alignment explanation
Indices: 288419--288515 Score: 124
Period size: 33 Copynumber: 3.0 Consensus size: 32
288409 AATTCCTCAA
*
288419 ATCTTTTTCCTTCAAAGTCCACGGCTCAGTGGC
1 ATCTTTTT-CTTCAAAGTCCACGACTCAGTGGC
*
288452 ATCTCTTTTCTTCAAAGTCCACGACTTAGTGGC
1 ATCT-TTTTCTTCAAAGTCCACGACTCAGTGGC
* *
288485 ATCTTTTTCTTTC-AAGTCCACAACTCTGTGG
1 ATCTTTTTC-TTCAAAGTCCACGACTCAGTGG
288516 TACCCTTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
32 20 0.35
33 33 0.58
34 4 0.07
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (32 bp):
ATCTTTTTCTTCAAAGTCCACGACTCAGTGGC
Found at i:288532 original size:27 final size:27
Alignment explanation
Indices: 288493--288607 Score: 95
Period size: 27 Copynumber: 4.0 Consensus size: 27
288483 GCATCTTTTT
* * * *
288493 CTTTCAAGTCCACAACTCTGTGGTACC
1 CTTTTAAGCCCACAACTCCGTGGCACC
288520 CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTC
1 CTTTTAAGCCCACAACTCCGTGGCA--C-----C
** *
288554 CTTCTTAAGTTCACAACTCCGTGGCAAC
1 CTT-TTAAGCCCACAACTCCGTGGCACC
288582 CTTTTAAGCCCACAACTCCGTGGCAC
1 CTTTTAAGCCCACAACTCCGTGGCAC
288608 TTTTTTTCCT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
27 41 0.59
28 4 0.06
29 1 0.01
34 4 0.06
35 20 0.29
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.30
Consensus pattern (27 bp):
CTTTTAAGCCCACAACTCCGTGGCACC
Found at i:288674 original size:66 final size:65
Alignment explanation
Indices: 288420--288751 Score: 321
Period size: 66 Copynumber: 5.2 Consensus size: 65
288410 ATTCCTCAAA
* ** * * * * * *
288420 TCTTTTTCCTTCAAAGTCCACGGCTCAGTGGCATCTCTTTTCTTCAAAGTCCACGACTTAGTGGC
1 TCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCT-TTTTCTT-TAAGCCCACAACTTCGTGGC
288485 A-
64 AC
* * * * *
288486 TCTTTTTCTTTC-AAGTCCACAACTCTGTGGTACC---CT-TTTAAGCCCACAACTCCGTGGCAC
1 TCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTTTAAGCCCACAACTTCGTGGCAC
* *
288546 TCTTTTTCCTTCTTAAGTTCACAACTCCGTGGCAACC----T-TTTAAGCCCACAACTCCGTGGC
1 TCTTTTTCCTTC-TAAGTCCACAACTCCGTGGC-ACCTTTTTCTTTAAGCCCACAACTTCGTGGC
288606 AC
64 AC
*
288608 TTTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCATTTAAGCCCACAACTTCGTGGCA
1 TCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTC-TTTAAGCCCACAACTTCGTGGCA
288673 C
65 C
*
288674 TCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTTTAAGTCCACAAC-TCTGTG
1 TCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTT-C--TTTAAGCCCACAACTTC-GTG
288738 GCA-
62 GCAC
*
288741 TCTTTCTCCTT
1 TCTTTTTCCTT
288752 TTCAAAAGCC
Statistics
Matches: 230, Mismatches: 23, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
59 16 0.07
60 16 0.07
61 20 0.09
62 52 0.23
63 3 0.01
64 1 0.00
65 17 0.07
66 73 0.32
67 13 0.06
68 19 0.08
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.36
Consensus pattern (65 bp):
TCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTTTAAGCCCACAACTTCGTGGCAC
Found at i:288752 original size:34 final size:33
Alignment explanation
Indices: 288419--288753 Score: 268
Period size: 34 Copynumber: 10.4 Consensus size: 33
288409 AATTCCTCAA
** ** *
288419 ATCTTTTTCCTTCAAAGTCCACGGCTCAGTGGC
1 ATCTTTTTCCTTTTAAGTCCACAACTCCGTGGC
** * **
288452 ATCTCTTTT-CTTCAAAGTCCACGACTTAGTGGC
1 ATCT-TTTTCCTTTTAAGTCCACAACTCCGTGGC
* * *
288485 ATCTTTTT-CTTTCAAGTCCACAACTCTGTGGT
1 ATCTTTTTCCTTTTAAGTCCACAACTCCGTGGC
*
288517 A-C-----CCTTTTAAGCCCACAACTCCGTGGC
1 ATCTTTTTCCTTTTAAGTCCACAACTCCGTGGC
*
288544 ACTCTTTTTCCTTCTTAAGTTCACAACTCCGTGGC
1 A-TCTTTTTCCTT-TTAAGTCCACAACTCCGTGGC
* *
288579 A------ACCTTTTAAGCCCACAACTCCGTGGC
1 ATCTTTTTCCTTTTAAGTCCACAACTCCGTGGC
* *
288606 ACTTTTTTTCCTTCTAAGTCCACAACTCCGTGGC
1 A-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGC
* * * *
288640 ACCTTTTT-CATTTAAGCCCACAACTTCGTGGC
1 ATCTTTTTCCTTTTAAGTCCACAACTCCGTGGC
*
288672 ACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGC
1 A-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGC
* *
288706 ACCTTTTTCCTTTTTAAGTCCACAACTCTGTGGC
1 ATCTTTTTCC-TTTTAAGTCCACAACTCCGTGGC
*
288740 ATCTTTCTCCTTTT
1 ATCTTTTTCCTTTT
288754 CAAAAGCCCA
Statistics
Matches: 246, Mismatches: 36, Indels: 40
0.76 0.11 0.12
Matches are distributed among these distances:
27 41 0.17
28 4 0.02
29 1 0.00
31 1 0.00
32 44 0.18
33 53 0.22
34 82 0.33
35 20 0.08
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.36
Consensus pattern (33 bp):
ATCTTTTTCCTTTTAAGTCCACAACTCCGTGGC
Found at i:288845 original size:49 final size:49
Alignment explanation
Indices: 288785--289850 Score: 1486
Period size: 49 Copynumber: 21.8 Consensus size: 49
288775 GGCATCTTCT
* * * *
288785 TTTAAGCCCAATATAGCTGGCATTGAATCAGCATATTGGCACCCTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* *
288834 TTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGG------CATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
*
288877 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTCATCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCT--TCATC
* *
288928 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
288976 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCATATTGGCACTTTCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
289025 TTTAAATCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
*
289074 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
289123 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATC-TCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
289171 TTTAAGTCCAATGTAGCTGGCCTTGACTTAGCATATTGGCACCTTCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* ** *
289220 TTTAAATCCAACATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
*
289269 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
289318 TTTAAGTCCAATGTAGCTTGCCTTGAATCAGCACATTGGCA-CTTCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
289366 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCATCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
289415 TTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACC-TCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
*
289463 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
*
289512 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * *
289561 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACCTTTATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* *
289610 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * *
289659 TTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* *
289708 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * *
289757 TTTAAGTCCAATATCGTTGGCCTTGACTCAGCATATTGGCGCCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
** * *
289806 ATTTTTAAAACCCAATGTCGTTGGCCTTGAATCAGCATATTGGCA
1 ---TTT-AAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCA
289851 TTCTTCTCAT
Statistics
Matches: 917, Mismatches: 84, Indels: 28
0.89 0.08 0.03
Matches are distributed among these distances:
43 40 0.04
48 176 0.19
49 620 0.68
51 45 0.05
52 3 0.00
53 33 0.04
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (49 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
Found at i:289171 original size:195 final size:196
Alignment explanation
Indices: 288785--289850 Score: 1621
Period size: 195 Copynumber: 5.5 Consensus size: 196
288775 GGCATCTTCT
* * * * *
288785 TTTAAGCCCAATATAGCTGGCATTGAATCAGCATATTGGCACCCTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGACTCAGCATATTGGCACCTTCATCTTTAAATCCAATGTAG
*
288850 CTGGCCTTAAATCAGCACATTGGCA---T---CTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
288909 ATATTGGCACCTCATCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TC
131 ATATTGGCACCT--TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTC
288973 ACC
194 ACC
* * * *
288976 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCATATTGGCACTTTCACCTTTAAATCCAATATAG
1 TTTAAGTCCAATATAGCTGGCCTTGACTCAGCATATTGGCACCTTCATCTTTAAATCCAATGTAG
*
289041 CTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
*
289106 ATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATC-TCAC
131 ATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAC
289170 C
196 C
* * * **
289171 TTTAAGTCCAATGTAGCTGGCCTTGACTTAGCATATTGGCACCTTCACCTTTAAATCCAACATAG
1 TTTAAGTCCAATATAGCTGGCCTTGACTCAGCATATTGGCACCTTCATCTTTAAATCCAATGTAG
*
289236 CTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
*
289301 ATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTTGCCTTGAATCAGCACATTGGCA-CTTCAC
131 ATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAC
289365 C
196 C
* * * *
289366 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCATCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGACTCAGCATATTGGCACCTTCATCTTTAAATCCAATGTAG
*
289431 CTAGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
*
289495 ATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCAC
131 ATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAC
289560 C
196 C
* * * *
289561 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACCTTTATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGACTCAGCATATTGGCACCTTCATCTTTAAATCCAATGTAG
* * * *
289626 CTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
* * *
289691 ATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
131 ATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAC
289756 C
196 C
* * * *
289757 TTTAAGTCCAATATCGTTGGCCTTGACTCAGCATATTGGCGCCTTCATCATTTTTAAAACCCAAT
1 TTTAAGTCCAATATAGCTGGCCTTGACTCAGCATATTGGCACCTTCATC---TTT-AAATCCAAT
* * *
289822 GTCGTTGGCCTTGAATCAGCATATTGGCA
62 GTAGCTGGCCTTGAATCAGCACATTGGCA
289851 TTCTTCTCAT
Statistics
Matches: 808, Mismatches: 54, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
191 79 0.10
194 95 0.12
195 415 0.51
196 139 0.17
197 45 0.06
199 3 0.00
200 32 0.04
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (196 bp):
TTTAAGTCCAATATAGCTGGCCTTGACTCAGCATATTGGCACCTTCATCTTTAAATCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
ATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAC
C
Found at i:290816 original size:52 final size:52
Alignment explanation
Indices: 290759--290884 Score: 225
Period size: 52 Copynumber: 2.4 Consensus size: 52
290749 CACTGATCTT
**
290759 TGTATCGATACATGCAGGCAAATTTTTCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
290811 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
290863 TGTATCGATACATGCAGGCAAA
1 TGTATCGATACATGCAGGCAAA
290885 ATTTCATATT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:292444 original size:326 final size:326
Alignment explanation
Indices: 291845--292498 Score: 1218
Period size: 326 Copynumber: 2.0 Consensus size: 326
291835 TATTAAAATG
* *
291845 CATGCTTGTTTGCCTTAAAGCAATTATTCAAATACCTCCCCAAGTTAAGTTCAAGCTAACCTCAA
1 CATGCATGTTTGCCTTAAAGCAAATATTCAAATACCTCCCCAAGTTAAGTTCAAGCTAACCTCAA
291910 GCAATAAGGATTAGCATGAATTTAAGCTTTTAATAAGCAACCATCACTCTTGGGGTAAATCAGGT
66 GCAATAAGGATTAGCATGAATTTAAGCTTTTAATAAGCAACCATCACTCTTGGGGTAAATCAGGT
291975 CTAGAATCATGTTTAAAACAAGTCCAAAATTTTGATTTTTGAACCAAAATGGCTTTCAATCATCC
131 CTAGAATCATGTTTAAAACAAGTCCAAAATTTTGATTTTTGAACCAAAATGGCTTTCAATCATCC
* *
292040 TTAAAATGTTTGTGCCTTGGTTTTGTATCAAATCAAGAGTGGTATTGATAAACGGGCTGTTTCAT
196 TTAAAATGTTTGCGCCTAGGTTTTGTATCAAATCAAGAGTGGTATTGATAAACGGGCTGTTTCAT
* * * *
292105 CGTCCCAAACTACTCCGGGGCAGTGCAAATGAGTTCATGATGCTCATACCACTCTCTCCTTTCGG
261 CATCCCAAACTACTCCGAGGCAGTGAAAATGAGTTCATGATGCTCATACCACTCTCTCCTTTCAG
292170 T
326 T
292171 CATGCATGTTTGCCTTAAAGCAAATATTCAAATACCTCCCCAAGTTAAGTTCAAGCTAACCTCAA
1 CATGCATGTTTGCCTTAAAGCAAATATTCAAATACCTCCCCAAGTTAAGTTCAAGCTAACCTCAA
292236 GCAATAAGGATTAGCATGAATTTAAGCTTTTAATAAGCAACCATCACTCTTGGGGTAAATCAGGT
66 GCAATAAGGATTAGCATGAATTTAAGCTTTTAATAAGCAACCATCACTCTTGGGGTAAATCAGGT
*
292301 CTGGAATCATGTTTAAAACAAGTCCAAAATTTTGATTTTTGAACCAAAATGGCTTTCAATCATCC
131 CTAGAATCATGTTTAAAACAAGTCCAAAATTTTGATTTTTGAACCAAAATGGCTTTCAATCATCC
292366 TTAAAATGTTTGCGCCTAGGTTTTGTATCAAATCAAGAGTGGTATTGATAAACGGGCTGTTTCAT
196 TTAAAATGTTTGCGCCTAGGTTTTGTATCAAATCAAGAGTGGTATTGATAAACGGGCTGTTTCAT
*
292431 CATCCCAAACTACTCCGAGGCAGTGAAAATGAGTTCGTGATGCTCATACCACTCTCTCCTTTCAG
261 CATCCCAAACTACTCCGAGGCAGTGAAAATGAGTTCATGATGCTCATACCACTCTCTCCTTTCAG
292496 T
326 T
292497 CA
1 CA
292499 CGAATGTTCG
Statistics
Matches: 318, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
326 318 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (326 bp):
CATGCATGTTTGCCTTAAAGCAAATATTCAAATACCTCCCCAAGTTAAGTTCAAGCTAACCTCAA
GCAATAAGGATTAGCATGAATTTAAGCTTTTAATAAGCAACCATCACTCTTGGGGTAAATCAGGT
CTAGAATCATGTTTAAAACAAGTCCAAAATTTTGATTTTTGAACCAAAATGGCTTTCAATCATCC
TTAAAATGTTTGCGCCTAGGTTTTGTATCAAATCAAGAGTGGTATTGATAAACGGGCTGTTTCAT
CATCCCAAACTACTCCGAGGCAGTGAAAATGAGTTCATGATGCTCATACCACTCTCTCCTTTCAG
T
Found at i:295162 original size:20 final size:20
Alignment explanation
Indices: 295137--295193 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
295127 TTTTACCCAG
*
295137 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTGA
* *
295157 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTGA
295177 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
295194 GTCTTTTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTGA
Found at i:295222 original size:71 final size:72
Alignment explanation
Indices: 295105--295254 Score: 248
Period size: 71 Copynumber: 2.1 Consensus size: 72
295095 TTTTACCCAG
*
295105 ATGTATCGATACATTCTATCTTTTTTACCCAGATGTATCGATACATTTTTTAATGTATCGATACA
1 ATGTATCGATACATTCTATCTTTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACA
295170 TGTATGA
66 TGTATGA
* * *
295177 ATGTATCGATACATTTTGTC-TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATATA
1 ATGTATCGATACATTCTATCTTTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACA
295241 TGTATGA
66 TGTATGA
*
295248 ATATATC
1 ATGTATC
295255 TAGTTAAAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
71 55 0.75
72 18 0.25
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (72 bp):
ATGTATCGATACATTCTATCTTTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACA
TGTATGA
Found at i:305009 original size:16 final size:16
Alignment explanation
Indices: 304990--305021 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
304980 ATAATTTTTA
*
304990 AAATTTAATATTTAAT
1 AAATTTAAAATTTAAT
305006 AAATTTAAAATTTAAT
1 AAATTTAAAATTTAAT
305022 TCTTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTTAAAATTTAAT
Found at i:307257 original size:135 final size:135
Alignment explanation
Indices: 307015--307286 Score: 499
Period size: 135 Copynumber: 2.0 Consensus size: 135
307005 TTCCACTGAA
307015 GTTGCCGATAATGTTGAAACTGAAGATGATCGGTTCCAAGAGGATGCAAATTTGAAGACAGGTGC
1 GTTGCCGATAATGTTGAAACTGAAGATGATCGGTTCCAAGAGGATGCAAATTTGAAGACAGGTGC
*
307080 AGCTGTAAATGAAGGGACTGAAGCCTCCATAGAGGGACTGCTAGTACAGCTGATGATGGCGTTGG
66 AGCTGTAAATGAAGGGACTGAAGCCTCCATAGAGGGACTGCTAGTACAGCTGATGATGGCATTGG
307145 CAGTT
131 CAGTT
* *
307150 GTTGCCGATAATGTTGAAACTGAAGATGATGGGTTCCAAGAGGATGTAAATTTGAAGACAGGTGC
1 GTTGCCGATAATGTTGAAACTGAAGATGATCGGTTCCAAGAGGATGCAAATTTGAAGACAGGTGC
* *
307215 AGCTGTAAATGAAGGTACTGAAGCCTCCATAGAGGGACTGCTAGTACAGCTGATGGTGGCATTGG
66 AGCTGTAAATGAAGGGACTGAAGCCTCCATAGAGGGACTGCTAGTACAGCTGATGATGGCATTGG
307280 CAGTT
131 CAGTT
307285 GT
1 GT
307287 GGAAGTGGTG
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 132 1.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (135 bp):
GTTGCCGATAATGTTGAAACTGAAGATGATCGGTTCCAAGAGGATGCAAATTTGAAGACAGGTGC
AGCTGTAAATGAAGGGACTGAAGCCTCCATAGAGGGACTGCTAGTACAGCTGATGATGGCATTGG
CAGTT
Found at i:310137 original size:26 final size:26
Alignment explanation
Indices: 310100--310149 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
310090 GTATGAGGTG
310100 TGATCCTCCATATATAAGGAAAAAAA
1 TGATCCTCCATATATAAGGAAAAAAA
* *
310126 TGATCCTTCATATGTAAGGAAAAA
1 TGATCCTCCATATATAAGGAAAAA
310150 CTTATAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (26 bp):
TGATCCTCCATATATAAGGAAAAAAA
Found at i:315788 original size:32 final size:33
Alignment explanation
Indices: 315734--315815 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 33
315724 TTAAATCCTT
*
315734 TTATAATATATT-ATTTTAATTTAATCATATTAAA
1 TTAT-ATATATTAAATTTAATTTAATCATA-TAAA
*
315768 -TA-AT-TATTAAATTTATATTTAATTATATAAA
1 TTATATATATTAAATTTA-ATTTAATCATATAAA
315799 TTATATATATTAAATTT
1 TTATATATATTAAATTT
315816 TAAATTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
30 4 0.10
31 11 0.27
32 12 0.29
33 4 0.10
34 10 0.24
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (33 bp):
TTATATATATTAAATTTAATTTAATCATATAAA
Found at i:315819 original size:21 final size:20
Alignment explanation
Indices: 315768--315822 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
315758 TCATATTAAA
315768 TAATTATTAAATT-TATATT
1 TAATTATTAAATTATATATT
315787 TAATTATATAAATTATATATAT
1 TAATTAT-TAAATTATATAT-T
315809 TAAATT-TTAAATTA
1 T-AATTATTAAATTA
315823 AATAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.22
20 6 0.19
21 12 0.38
22 3 0.09
23 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATTATTAAATTATATATT
Found at i:317874 original size:16 final size:16
Alignment explanation
Indices: 317855--317957 Score: 104
Period size: 16 Copynumber: 6.4 Consensus size: 16
317845 TAATCCAAAA
*
317855 TTAAAATAATTTAGAT
1 TTAAAATAATTTAAAT
317871 TTAAAATAATTTTAAA-
1 TTAAAATAA-TTTAAAT
317887 --AAAATAATTTAAAT
1 TTAAAATAATTTAAAT
*
317901 TTAAAATAATTTAAAA
1 TTAAAATAATTTAAAT
*
317917 TTAAAATAATTCAAACT
1 TTAAAATAATTTAAA-T
**
317934 AAAAAATAATTTGAGAAT
1 TTAAAATAATTT-A-AAT
317952 TTAAAA
1 TTAAAA
317958 AATCGAATTC
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
13 6 0.08
14 7 0.10
16 36 0.51
17 14 0.20
18 6 0.08
19 2 0.03
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (16 bp):
TTAAAATAATTTAAAT
Found at i:317893 original size:30 final size:31
Alignment explanation
Indices: 317851--317945 Score: 111
Period size: 30 Copynumber: 3.0 Consensus size: 31
317841 TGATTAATCC
*
317851 AAAATTAAAATAATTTAGATTTAAAATAATTT
1 AAAA-TAAAATAATTTAAATTTAAAATAATTT
*
317883 TAAA-AAAATAATTTAAATTTAAAATAATTT
1 AAAATAAAATAATTTAAATTTAAAATAATTT
* **
317913 AAAATTAAAATAATTCAAACTAAAAAATAATTT
1 AAAA-TAAAATAATTTAAA-TTTAAAATAATTT
317946 GAGAATTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
30 28 0.52
32 15 0.28
33 11 0.20
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (31 bp):
AAAATAAAATAATTTAAATTTAAAATAATTT
Found at i:318585 original size:3 final size:3
Alignment explanation
Indices: 318577--318620 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
318567 TTATCTTTGC
318577 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
318621 AGTACTAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:320922 original size:16 final size:16
Alignment explanation
Indices: 320901--320938 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
320891 AAAATATAAA
320901 TTATTTACTTGCTTAT
1 TTATTTACTTGCTTAT
*
320917 TTATTTACTTGTTTAT
1 TTATTTACTTGCTTAT
*
320933 GTATTT
1 TTATTT
320939 GGTTATCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.66
Consensus pattern (16 bp):
TTATTTACTTGCTTAT
Found at i:322902 original size:2 final size:2
Alignment explanation
Indices: 322890--322931 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
322880 GACTCAAACA
322890 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
322932 GAGAGAGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:322936 original size:2 final size:2
Alignment explanation
Indices: 322931--322956 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
322921 ATATATATAT
322931 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
322957 GGGAATGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:326454 original size:15 final size:15
Alignment explanation
Indices: 326434--326464 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
326424 ATACTTAATT
326434 ATGATATAATTGATA
1 ATGATATAATTGATA
326449 ATGATATAATTGATA
1 ATGATATAATTGATA
326464 A
1 A
326465 AATCTTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (15 bp):
ATGATATAATTGATA
Found at i:329869 original size:6 final size:6
Alignment explanation
Indices: 329855--329936 Score: 76
Period size: 6 Copynumber: 13.2 Consensus size: 6
329845 AAACCCTATT
* * *
329855 AAAGAA AAAGGA AAAGAA AAAGAA AAAGAA AAAGAA ATGAGAA AAGTAGTA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AA--AGAA
* *
329906 AGAGAA AAA-AA AAACAA AAAGAAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAG-AA AAAGAA A
329937 TGAGGGGTGA
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
5 5 0.08
6 42 0.68
7 11 0.18
8 4 0.06
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:330404 original size:94 final size:92
Alignment explanation
Indices: 330283--330457 Score: 287
Period size: 94 Copynumber: 1.9 Consensus size: 92
330273 ATCTGAATAC
* * * *
330283 AAATTTTGATCAAGTCAGATTTAATATCTTTTGATTTTAAATTTATTAATATATCACTATTTATA
1 AAATTTTGATCAAATCAAATTTAATATCCTTTGATCTTAAATTTATTAATATATCACTATTTA-A
330348 TTTTTTTTATTTTTATGGATACAAAAAAT
65 -TTTTTTTATTTTTATGGATACAAAAAAT
*
330377 AAATTTTGATCAAATCAAATTTAATATCCTTTGATCTTAAATTTATTAATATATTACTATTTAAT
1 AAATTTTGATCAAATCAAATTTAATATCCTTTGATCTTAAATTTATTAATATATCACTATTTAAT
330442 TTTTTTATTTTTATGG
66 TTTTTTATTTTTATGG
330458 GCTATATCAT
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
92 17 0.22
93 1 0.01
94 58 0.76
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.52
Consensus pattern (92 bp):
AAATTTTGATCAAATCAAATTTAATATCCTTTGATCTTAAATTTATTAATATATCACTATTTAAT
TTTTTTATTTTTATGGATACAAAAAAT
Found at i:331742 original size:152 final size:154
Alignment explanation
Indices: 331521--332116 Score: 554
Period size: 157 Copynumber: 3.9 Consensus size: 154
331511 AGTATCTTAG
* * * * * * *
331521 TAACCTTAATGGACTTAAAACTGATCATAAATGAGATGAACCTGTCCTAAATACACAGCTTTGGC
1 TAACCCTAATAGACTTAAAAATGATCATAAATGAAATGAACCTATCCTAAATGCACACCTTTGGC
* *
331586 ATAAAAGCATCCTAA-TGTCAACCTAAGA-TTTGATTCTAAAAAATTACAAAAATGCTCCTAGG-
66 ATAAAAGCAT-CTAAGTGACAACCTAAGATTTTG-TTCAAAAAAATTACAAAAATGC-CCTAGGT
* * * *
331648 GTATATCTTCGATATG-AA-AA-T-AGG
128 ATATATCTTCGACACGAAAGAATTCA-A
* * *
331672 TAGCCCTAATAGACTTAAAAATGATCATAAAATGAAATGAACTTATCTTAAATGCACACCTTTGG
1 TAACCCTAATAGACTTAAAAATGATCAT-AAATGAAATGAACCTATCCTAAATGCACACCTTTGG
* * ** *
331737 TATAAAAGCATCTAAGTGACAACCTATGATTTTGTTCAAAAAAATTATGAAAATGCCCTTGGTAT
65 CATAAAAGCATCTAAGTGACAACCTAAGATTTTGTTCAAAAAAATTACAAAAATGCCCTAGGTAT
* *
331802 ATATTTTTGACACGAAAGAATTCCAA
130 ATATCTTCGACACGAAAGAATT-CAA
* * *
331828 TAACCCTAATAGAATTAAAAATGATCATAAATGAAATAAACCTATCCTAAATGCACATCTTTGGC
1 TAACCCTAATAGACTTAAAAATGATCATAAATGAAATGAACCTATCCTAAATGCACACCTTTGGC
* * * * * *
331893 ATAAAAGCAT-TCAGGTGACAACTTATA-ATTATGTTCTAAAGAAAATTATAAAAATAACCTTA-
66 ATAAAAGCATCT-AAGTGACAACCTA-AGATTTTGTTC-AAA-AAAATTACAAAAAT-GCCCTAG
* * * *
331955 GAATATA-CTTTTGACACAAAAGGATTTCAA
126 GTATATATC-TTCGACACGAAA-GAATTCAA
* ** *
331985 TAACCCTAAAAGACTTAAAAATGATCATAAATGAGGTGAACCTATCCTAAATACACACCTTTGGC
1 TAACCCTAATAGACTTAAAAATGATCATAAATGAAATGAACCTATCCTAAATGCACACCTTTGGC
* * * *
332050 ATAAAAGCATCCT-AGTGACAATCTAAGACTTGGTT-ATAAAAAATTACAACAATGCCCTTAGG-
66 ATAAAAGCAT-CTAAGTGACAACCTAAGATTTTGTTCA-AAAAAATTACAAAAATGCCC-TAGGT
332112 ATATA
128 ATATA
332117 CCTTTAACAT
Statistics
Matches: 364, Mismatches: 59, Indels: 40
0.79 0.13 0.09
Matches are distributed among these distances:
151 33 0.09
152 81 0.22
153 6 0.02
154 5 0.01
155 82 0.23
156 33 0.09
157 116 0.32
158 7 0.02
159 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (154 bp):
TAACCCTAATAGACTTAAAAATGATCATAAATGAAATGAACCTATCCTAAATGCACACCTTTGGC
ATAAAAGCATCTAAGTGACAACCTAAGATTTTGTTCAAAAAAATTACAAAAATGCCCTAGGTATA
TATCTTCGACACGAAAGAATTCAA
Found at i:332477 original size:166 final size:163
Alignment explanation
Indices: 332244--332766 Score: 498
Period size: 166 Copynumber: 3.2 Consensus size: 163
332234 TCAATTAACC
* * * * * * *
332244 CCTTTAACTTTTGAAAATTTTATTTCGTATTCTACA--AAAAACCGAAAAGACACGAAAAGTTTT
1 CCTTGAACTTTTGAAAATTTCATTTCGTA--CTAGATGAAAAATCGAGAGGACACAAAAAGTTTT
* * * *
332307 GAAAATTTCTATACCTTTACGAAAGGTAATAGGAATAGTAGAAATCTTTGAAAATGACTAAAATG
64 GAAAATTT-TATACCCTTACGAAAGAT-ATAGGAATAATAGAAATCTTT-AAAATGATTAAAATG
* *
332372 ATAATTTTTCCTCTAAAAATTAAAATTTTCTATTTAAT
126 ATGATTTTACCTCTAAAAATTAAAATTTTCTATTTAAT
* *
332410 CCTTGAACTTTTGAAAATTTCATTTCGTACCAGATGAAAAATCGAGAGGACACAAAAAGTCTTGA
1 CCTTGAACTTTTGAAAATTTCATTTCGTACTAGATGAAAAATCGAGAGGACACAAAAAGTTTTGA
* * * * * *
332475 AAATTTTTATACCCTTGCGGAAGACCATAAGAATAATAGAAATATTTAAAAATGATTAAAATAAT
66 AAA-TTTTATACCCTTACGAAAGA-TATAGGAATAATAGAAATCTTT-AAAATGATTAAAATGAT
* * * * *
332540 GATTTTACCTCCAAAAGTTGAACTTTGCTATTTAATT
128 GATTTTACCTCTAAAAATTAAAATTTTCTATTTAA-T
* * * * * * *
332577 CC-TAAACTTTTAAAAATTTTATTTCGTACTTGATGGAAAATCGAGAGGATATGAAAAA-TTTTA
1 CCTTGAACTTTTGAAAATTTCATTTCGTACTAGATGAAAAATCGAGAGGACA-CAAAAAGTTTT-
* * * * * *
332640 AAAAATTTTATACCCCTATGGAAAGCTATAGGAATAATAGAAACCTTTAGAAATTATTAAAATGA
64 GAAAATTTTATACCCTTA-CGAAAGATATAGGAATAATAGAAATCTTTA-AAATGATTAAAATGA
* *
332705 TGATTTTACCTCTAAAAACTAAAA-TTTGTATTTAAT
127 TGATTTTACCTCTAAAAATTAAAATTTTCTATTTAAT
* *
332741 CCCTGAACTTTTCAAAATTTTCATTT
1 CCTTGAACTTTTGAAAA-TTTCATTT
332767 TAGTTCCTAC
Statistics
Matches: 288, Mismatches: 58, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
164 6 0.02
165 22 0.08
166 241 0.84
167 19 0.07
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (163 bp):
CCTTGAACTTTTGAAAATTTCATTTCGTACTAGATGAAAAATCGAGAGGACACAAAAAGTTTTGA
AAATTTTATACCCTTACGAAAGATATAGGAATAATAGAAATCTTTAAAATGATTAAAATGATGAT
TTTACCTCTAAAAATTAAAATTTTCTATTTAAT
Found at i:334496 original size:150 final size:150
Alignment explanation
Indices: 334272--334718 Score: 472
Period size: 150 Copynumber: 2.9 Consensus size: 150
334262 TGAAAAGCTC
* * * * * *
334272 ATAAAATTAATTG-AA-TCTTCAAAAACTGATTTAATATAAATTTAATAAAAATATTTAATGAAT
1 ATAAAATAAATTGAAATTTTTCAAAAA-TAATTTAATATGAA-TTAATAAATA-ATTGAA-GAAT
*
334335 TTTAAAAATTATAAACTTAGAAAAATCCTACAAAAAAATTACGGAGTAGAAAACTCCATATTTTA
62 TTTAAAAATTATAAACTCAGAAAAATCCTACAAAAAAATTACGGAGTAGAAAACTCCATATTTTA
* *
334400 AAAATAGAAAAAATTCTAAAACCC
127 AAAATAGAAAAAATGCTAAAACCA
* *
334424 ATAAAATATATT-AAATTCTTTCAAAAATAATTTAATATGAATTAATTAATAATTGAAGAATTTT
1 ATAAAATAAATTGAAATT-TTTCAAAAATAATTTAATATGAATTAATAAATAATTGAAGAATTTT
* * * * **
334488 AAAAATTATAAACTCAGAAAAATCTTACAAAAAAATTTACGGAGAAGAAAACTCTATATCTTAGT
65 AAAAATTATAAACTCAGAAAAATCCTACAAAAAAA-TTACGGAGTAGAAAACTCCATATTTTAAA
* * * *
334553 AACAGGAAAAATGCTTATACCA
129 AATAGAAAAAATGCTAAAACCA
* * *
334575 ATAAAATAAATTGAAATTTGT-AAAACTAATTTAATATGAATTAAAAAATAAAATGTGAAGAATT
1 ATAAAATAAATTGAAATTTTTCAAAAATAATTTAATATGAATTAATAAAT--AAT-TGAAGAATT
* * * * * *
334639 TTGAAAATTATAAACTGAGAAAAATCCTACTAGATAAATTTACAGG-GTAGAAAACTGCGTATTT
63 TTAAAAATTATAAACTCAGAAAAATCCTAC-A-AAAAAATTAC-GGAGTAGAAAACTCCATATTT
*
334703 TGAAAATAGAAAAAAT
125 TAAAAATAGAAAAAAT
334719 CCAAAAGAAA
Statistics
Matches: 243, Mismatches: 41, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
150 65 0.27
151 58 0.24
152 28 0.12
153 49 0.20
154 37 0.15
155 6 0.02
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (150 bp):
ATAAAATAAATTGAAATTTTTCAAAAATAATTTAATATGAATTAATAAATAATTGAAGAATTTTA
AAAATTATAAACTCAGAAAAATCCTACAAAAAAATTACGGAGTAGAAAACTCCATATTTTAAAAA
TAGAAAAAATGCTAAAACCA
Found at i:334715 original size:153 final size:147
Alignment explanation
Indices: 334272--334716 Score: 427
Period size: 153 Copynumber: 2.9 Consensus size: 147
334262 TGAAAAGCTC
* * * * *
334272 ATAAAATTAATTGAA-TCT-TCAAAAACTGATTTAATATAAATTTAATAAAA-ATATTTAATGAA
1 ATAAAATAAATTAAATTCTGTCAAAAA-TAATTTAATATGAA-TTAA-AAAATA-ATTGAA-GAA
* *
334334 TTTTAAAAATTATAAACTTAGAAAAATCCTACAAAAAAATTACGGAGTAGAAAACTCCATATTTT
61 TTTTAAAAATTATAAACTCAGAAAAATCCTACAAAAAATTTACGGAGTAGAAAACT-C-TATTTT
* * *
334399 AAAAATAGAAAAAATTCTAAAACCC
124 GAAAATAG-AAAAATGCTAAAACCA
* * **
334424 ATAAAATATATTAAATTCTTTCAAAAATAATTTAATATGAATTAATTAATAATTGAAGAATTTTA
1 ATAAAATAAATTAAATTCTGTCAAAAATAATTTAATATGAATTAAAAAATAATTGAAGAATTTTA
* *
334489 AAAATTATAAACTCAGAAAAATCTTACAAAAAAATTTACGGAGAAGAAAACTCTATATCTTAGTA
66 AAAATTATAAACTCAGAAAAATCCTAC-AAAAAATTTACGGAGTAGAAAACTCTAT-T-TT-G-A
* * * *
334554 ACA-GGAAAAATGCTTATACCA
126 AAATAGAAAAATGCTAAAACCA
*
334575 ATAAAATAAATTGAAATT-TGT-AAAACTAATTTAATATGAATTAAAAAATAAAATGTGAAGAAT
1 ATAAAATAAATT-AAATTCTGTCAAAAATAATTTAATATGAATTAAAAAAT--AAT-TGAAGAAT
* * *
334638 TTTGAAAATTATAAACTGAGAAAAATCCTACTAGATAAATTTACAGG-GTAGAAAACTGCGTATT
62 TTTAAAAATTATAAACTCAGAAAAATCCTAC-A-AAAAATTTAC-GGAGTAGAAAACT-C-TATT
334702 TTGAAAATAGAAAAA
122 TTGAAAATAGAAAAA
334717 ATCCAAAAGA
Statistics
Matches: 244, Mismatches: 32, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
149 3 0.01
150 60 0.25
151 56 0.23
152 29 0.12
153 62 0.25
154 27 0.11
155 4 0.02
156 3 0.01
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (147 bp):
ATAAAATAAATTAAATTCTGTCAAAAATAATTTAATATGAATTAAAAAATAATTGAAGAATTTTA
AAAATTATAAACTCAGAAAAATCCTACAAAAAATTTACGGAGTAGAAAACTCTATTTTGAAAATA
GAAAAATGCTAAAACCA
Found at i:335793 original size:4 final size:4
Alignment explanation
Indices: 335784--335810 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
335774 ATAAAATATA
335784 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
335811 AAGTCAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:337389 original size:16 final size:15
Alignment explanation
Indices: 337358--337398 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 15
337348 AAATTAGAAT
337358 TAAAAAATAAAAAATAA
1 TAAAAAAT--AAAATAA
337375 TAACAAAATAAAATAA
1 TAA-AAAATAAAATAA
337391 TAAAAAAT
1 TAAAAAAT
337399 TCTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 3 0.13
18 5 0.22
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAAAAATAAAATAA
Found at i:341477 original size:22 final size:19
Alignment explanation
Indices: 341447--341495 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
341437 TTAATGGCAT
341447 TCATATTCATGACATTCATTCA
1 TCATATTCAT-A-A-TCATTCA
*
341469 TCATTTTCATAATCATTCA
1 TCATATTCATAATCATTCA
341488 TCAGTATT
1 TCA-TATT
341496 TGCTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 4 0.17
21 1 0.04
22 9 0.38
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (19 bp):
TCATATTCATAATCATTCA
Found at i:349765 original size:42 final size:42
Alignment explanation
Indices: 349712--350791 Score: 1197
Period size: 42 Copynumber: 25.7 Consensus size: 42
349702 CTTTTTTGTT
*
349712 TTCCCTTAGTCTGCCTGTCGGTTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
349754 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
349796 ATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * * *
349838 AACCCTTAGTTTGCCTGTCGG-TTTCGTCCCTGGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTT-GACCCTGGAGACTTTTC
* * *
349880 TACCCTTAGTCTGCTTGTCGGCTTTGACCTTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
*
349922 TTCCCTTAGTCTACCTGTCGGCTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
349964 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
*
350006 TTCCCTTAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
*
350048 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
350090 TACCTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
350132 TATCCCTTAGTCTGCCTGTCGGTTTTTACCCTGGAGACTTTTT
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* **
350175 TTCCCTTAGTCTGCCTGCCCACTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * *
350217 ATCCCTCAGTCTGCCTATCGACTTTGACCGTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * * *
350259 AACCCTCAGTCTGCCTGTCGG-TTTCGTCCCTGGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTT-GACCCTGGAGACTTTTC
*
350301 TAT-CCTTAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTTC
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
**
350343 TTCCCTTAGTCTGCCTGTCCACTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * *
350385 ATCCCTCAGTCTGCCTATCAGCTTTAACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * * * *
350427 ATCCCTCAGTCTGCCTGTCGACTTCGTCCCTAGAGAC-TATC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** ** *
350468 -TCATTTAAAGTCTGTTTGTCGGCTTTGACCCTGGAGACTTTCC
1 TTCCCTT--AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * * * *
350511 TACCCTTCAGTCTACTTGTCGGCTTCGTCCTTGGAGACTTTTT
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* ** * * * * *
350554 TTCTCGCAGTTTGCCTATCGGCATTGTCCTTGGAGAC-TTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
350595 TTTACCATAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTTC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * * * *
350638 AACCCTCAGTCTGCTTGTTGGCTTTGACCGTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * *
350680 AACCCTCAGTCTGCCTGCCGGCTTTGA-CCTGGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCT-GGAGACTTTTC
* * * **
350722 TTATCCTTAGTCTACTTGTCGGCTTTGACTATGGA-AC-TTTC
1 TT-CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
350763 TTTCCCTAAGTCTGCCCGTTGGCTTTGAC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGAC
350792 TTGGGAGAAT
Statistics
Matches: 877, Mismatches: 144, Indels: 35
0.83 0.14 0.03
Matches are distributed among these distances:
40 3 0.00
41 39 0.04
42 729 0.83
43 102 0.12
44 4 0.00
ACGTcount: A:0.13, C:0.30, G:0.20, T:0.37
Consensus pattern (42 bp):
TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
Found at i:351174 original size:21 final size:21
Alignment explanation
Indices: 351150--351200 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
351140 AATAAAAGAT
*
351150 AATATAGAAATCAA-AAATAAA
1 AATATA-AAATAAATAAATAAA
351171 AATATAAAATAAATAAATAAA
1 AATATAAAATAAATAAATAAA
351192 TAA-ATAAAA
1 -AATATAAAA
351201 AGTCAGGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 6 0.22
21 19 0.70
22 2 0.07
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (21 bp):
AATATAAAATAAATAAATAAA
Found at i:351194 original size:12 final size:13
Alignment explanation
Indices: 351163--351199 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
351153 ATAGAAATCA
351163 AAAATAAA-AATAT
1 AAAATAAATAA-AT
351176 AAAATAAATAAAT
1 AAAATAAATAAAT
351189 -AAATAAATAAA
1 AAAATAAATAAA
351200 AAGTCAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.48
13 10 0.43
14 2 0.09
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:352778 original size:16 final size:15
Alignment explanation
Indices: 352747--352787 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 15
352737 AAATTAGAAT
352747 TAAAAAATAAAAAATAA
1 TAAAAAAT--AAAATAA
352764 TAACAAAATAAAATAA
1 TAA-AAAATAAAATAA
352780 TAAAAAAT
1 TAAAAAAT
352788 TCTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 3 0.13
18 5 0.22
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAAAAATAAAATAA
Found at i:356341 original size:9 final size:9
Alignment explanation
Indices: 356327--356382 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
356317 TTTGATTTTT
356327 AATAAAAAA
1 AATAAAAAA
356336 AAT-AAAAA
1 AATAAAAAA
*
356344 ATTAAAAAA
1 AATAAAAAA
356353 TAA-AAAAAA
1 -AATAAAAAA
* *
356362 AATAATAAT
1 AATAAAAAA
*
356371 AATAATAAA
1 AATAAAAAA
356380 AAT
1 AAT
356383 GATGATGATG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 9 0.23
9 29 0.74
10 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AATAAAAAA
Found at i:357402 original size:55 final size:54
Alignment explanation
Indices: 357324--357481 Score: 162
Period size: 55 Copynumber: 2.9 Consensus size: 54
357314 ATTGTTTTTT
* * *
357324 TTCAAGCCGTGAGCTTATTTTCATTGCTTGATCTTCCTTTGTTGCATTTTC-TTC
1 TTCATGCCGTGAGCTTGTTTTCATTGTTTGAT-TTCCTTTGTTGCATTTTCTTTC
* * * *
357378 TTCATGCCGTGGAGTTTGTTTTCATTTTTTGATTTTTCTTTGCTGCATGTTTTCTTTC
1 TTCATGCCGT-GAGCTTGTTTTCATTGTTTGA-TTTCCTTTGTTGCA--TTTTCTTTC
* *
357436 TTCATGTCGT-A-CTTGTATTCATTGTTTG-TTTCCTTTGTTGCATTTT
1 TTCATGCCGTGAGCTTGTTTTCATTGTTTGATTTCCTTTGTTGCATTTT
357482 TTTATTGCAT
Statistics
Matches: 86, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
51 4 0.05
53 12 0.14
54 9 0.10
55 42 0.49
56 2 0.02
57 5 0.06
58 12 0.14
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.56
Consensus pattern (54 bp):
TTCATGCCGTGAGCTTGTTTTCATTGTTTGATTTCCTTTGTTGCATTTTCTTTC
Found at i:358663 original size:97 final size:96
Alignment explanation
Indices: 358497--359429 Score: 933
Period size: 97 Copynumber: 9.7 Consensus size: 96
358487 AGAATACGTT
*
358497 AACCCCATTCCTCTG-AGGAGATACTCCAACCTCGCTTTTAAACTTATCAAAATTTAAATCTTAT
1 AACCCCATTCCTC-GAAGG-GATACTCCAACCTCGTTTTTAAACTTATCAAAATTTAAATCTTAT
* * *
358561 TTTTGGTTAAATTGTCATCATCAGGGATACTCC
64 TTTCGGTTAAATTGTCATCATCGGGGACACTCC
* * *
358594 AACCCCATTCCTCAAAAGGGATATTCCAACCTTGTTTTTAAACTTATCAAAATTTAAATCTTATT
1 AACCCCATTCCTC-GAAGGGATACTCCAACCTCGTTTTTAAACTTATCAAAATTTAAATCTTATT
* * *
358659 TTTGGTTAAATTGTCATTATCGGGGACATTCC
65 TTCGGTTAAATTGTCATCATCGGGGACACTCC
* * * * *
358691 AACCCTATTCCTTCGAGGGGATACTCTAACC-CTGCTTTTAAACTTATTAAAATTTAAATCTTAT
1 AACCCCATTCC-TCGAAGGGATACTCCAACCTC-GTTTTTAAACTTATCAAAATTTAAATCTTAT
* ***
358755 TTTCGGTTAAATTATCATCATCAAAGACACTCC
64 TTTCGGTTAAATTGTCATCATCGGGGACACTCC
* * **
358788 AACCCCATTCTTTCG-AGGAGATACTCCAATCTCACTTTTAAACTTATCAAAATTTAAATCTTAT
1 AACCCCATTC-CTCGAAGG-GATACTCCAACCTCGTTTTTAAACTTATCAAAATTTAAATCTTAT
* *
358852 TTTTGGTTAAATTGTCATAATCGGGGACACTCC
64 TTTCGGTTAAATTGTCATCATCGGGGACACTCC
** * * ** *
358885 AAAACCATTCTTCTAAGGGGATACTTTAACC-CTGCTTTTAAACTTATCAAAATTTAAATCTTAT
1 AACCCCATTCCTCGAA-GGGATACTCCAACCTC-GTTTTTAAACTTATCAAAATTTAAATCTTAT
* **
358949 TTTCGATTAAATTGTCATCATCGAAGACACTCC
64 TTTCGGTTAAATTGTCATCATCGGGGACACTCC
* * * *
358982 AACCCTATTCCTCTG-AGAGGATACTCTAATCTTGTTTTTAAACTTATCAAAA--T---TCTTAT
1 AACCCCATTCCTC-GAAG-GGATACTCCAACCTCGTTTTTAAACTTATCAAAATTTAAATCTTAT
* * * * *
359041 TTTTGGTTAAATTGTAATAATCGGGAACACTCT
64 TTTCGGTTAAATTGTCATCATCGGGGACACTCC
** * * *
359074 AACCATATTCCTCTAAGAGGATACTTCAATCC-CATTTTTAAACTTATC--AATTTAAATCTTAT
1 AACCCCATTCCTCGAAG-GGATACTCCAA-CCTCGTTTTTAAACTTATCAAAATTTAAATCTTAT
* *
359136 TTTCGGTTAAATTGTCATTATCGGGGATACTCC
64 TTTCGGTTAAATTGTCATCATCGGGGACACTCC
* * *
359169 AACCCTATTCTTCCGAGGGGATACTCCAACC-CTGTTTTTAAACTTATCAAAATTTAAATCTTAT
1 AACCCCATTCCT-CGAAGGGATACTCCAACCTC-GTTTTTAAACTTATCAAAATTTAAATCTTAT
* * *
359233 TTTCGGTTAAATTGTCATTAGCGGGGACATTCC
64 TTTCGGTTAAATTGTCATCATCGGGGACACTCC
* * * * **
359266 AACTCCATTCTTTTGAAGAGATACTTTAA-CTCCGTTTTTAAACTTATCAAAATTTAAATCTTAT
1 AACCCCATTC-CTCGAAGGGATACTCCAACCT-CGTTTTTAAACTTATCAAAATTTAAATCTTAT
* * *** *
359330 TTTCAGTTAAATTATCATCATCAAAGACACTCT
64 TTTCGGTTAAATTGTCATCATCGGGGACACTCC
* * * * *
359363 AACCCCATTCCTCCGAGGGGATATTCTAACCCCGTTTTTTAACTTATCAAAATTTAAATCTTATT
1 AACCCCATTCCT-CGAAGGGATACTCCAACCTCGTTTTTAAACTTATCAAAATTTAAATCTTATT
359428 TT
65 TT
359430 ATCCAAATTA
Statistics
Matches: 695, Mismatches: 113, Indels: 56
0.80 0.13 0.06
Matches are distributed among these distances:
90 2 0.00
92 70 0.10
93 1 0.00
94 3 0.00
95 68 0.10
96 12 0.02
97 527 0.76
98 12 0.02
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (96 bp):
AACCCCATTCCTCGAAGGGATACTCCAACCTCGTTTTTAAACTTATCAAAATTTAAATCTTATTT
TCGGTTAAATTGTCATCATCGGGGACACTCC
Found at i:358845 original size:194 final size:193
Alignment explanation
Indices: 358500--359429 Score: 1045
Period size: 194 Copynumber: 4.8 Consensus size: 193
358490 ATACGTTAAC
* *
358500 CCCATTCC-TCTGAGGAGATACTCCAA-CCTCGCTTTTAAACTTATCAAAATTTAAATCTTATTT
1 CCCATTCCTTCTGAGGGGATACTCTAACCCT-GCTTTTAAACTTATCAAAATTTAAATCTTATTT
* ** * * * * *
358563 TTGGTTAAATTGTCATCATCAGGGATACTCCAACCCCATTCCTCAAAAGG-GATATTCCAACCTT
65 TCGGTTAAATTGTCATCATCAAAGACACTCCAACCCCATTCTTC--GAGGAGATACTCCAACCTC
* *
358627 GTTTTTAAACTTATCAAAATTTAAATCTTATTTTTGGTTAAATTGTCATTATCGGGGACATTCCA
128 GTTTTTAAACTTATCAAAATTTAAATCTTATTTTTGGTTAAATTGTCATAATCGGGGACACTCCA
358692 A
193 A
*
358693 CCCTATTCCTTC-GAGGGGATACTCTAACCCTGCTTTTAAACTTATTAAAATTTAAATCTTATTT
1 CCC-ATTCCTTCTGAGGGGATACTCTAACCCTGCTTTTAAACTTATCAAAATTTAAATCTTATTT
* * *
358757 TCGGTTAAATTATCATCATCAAAGACACTCCAACCCCATTCTTTCGAGGAGATACTCCAATCTCA
65 TCGGTTAAATTGTCATCATCAAAGACACTCCAACCCCATTC-TTCGAGGAGATACTCCAACCTCG
*
358822 CTTTTAAACTTATCAAAATTTAAATCTTATTTTTGGTTAAATTGTCATAATCGGGGACACTCCAA
129 TTTTTAAACTTATCAAAATTTAAATCTTATTTTTGGTTAAATTGTCATAATCGGGGACACTCC-A
358887 A
193 A
* * *
358888 ACCATT-CTTCTAAGGGGATACTTTAACCCTGCTTTTAAACTTATCAAAATTTAAATCTTATTTT
1 CCCATTCCTTCTGAGGGGATACTCTAACCCTGCTTTTAAACTTATCAAAATTTAAATCTTATTTT
* * * * * * *
358952 CGATTAAATTGTCATCATCGAAGACACTCCAACCCTATTCCTCTGA-GAGGATACTCTAATCTTG
66 CGGTTAAATTGTCATCATCAAAGACACTCCAACCCCATTCTTC-GAGGA-GATACTCCAACCTCG
* * *
359016 TTTTTAAACTTATCAAAA--T---TCTTATTTTTGGTTAAATTGTAATAATCGGGAACACTCTAA
129 TTTTTAAACTTATCAAAATTTAAATCTTATTTTTGGTTAAATTGTCATAATCGGGGACACTCCAA
* * *
359076 CCATATTCC-TCTAAGAGGATACT-TCAATCCCAT--TTTTAAACTTATC--AATTTAAATCTTA
1 CC-CATTCCTTCTGAGGGGATACTCT-AA-CCC-TGCTTTTAAACTTATCAAAATTTAAATCTTA
* *** * * *
359135 TTTTCGGTTAAATTGTCATTATCGGGGATACTCCAACCCTATTCTTCCGAGGGGATACTCCAACC
62 TTTTCGGTTAAATTGTCATCATCAAAGACACTCCAACCCCATTCTT-CGAGGAGATACTCCAACC
* * * *
359200 -CTGTTTTTAAACTTATCAAAATTTAAATCTTATTTTCGGTTAAATTGTCATTAGCGGGGACATT
126 TC-GTTTTTAAACTTATCAAAATTTAAATCTTATTTTTGGTTAAATTGTCATAATCGGGGACACT
359264 CCAA
190 CCAA
* * * * *
359268 CTCCATT-CTTTTGAAGAGATACTTTAACTCC-GTTTTTAAACTTATCAAAATTTAAATCTTATT
1 C-CCATTCCTTCTGAGGGGATACTCTAAC-CCTGCTTTTAAACTTATCAAAATTTAAATCTTATT
* * * * * * * *
359331 TTCAGTTAAATTATCATCATCAAAGACACTCTAACCCCATTCCTCCGAGGGGATATTCTAACCCC
64 TTCGGTTAAATTGTCATCATCAAAGACACTCCAACCCCATT-CTTCGAGGAGATACTCCAACCTC
*
359396 GTTTTTTAACTTATCAAAATTTAAATCTTATTTT
128 GTTTTTAAACTTATCAAAATTTAAATCTTATTTT
359430 ATCCAAATTA
Statistics
Matches: 633, Mismatches: 72, Indels: 63
0.82 0.09 0.08
Matches are distributed among these distances:
187 84 0.13
188 6 0.01
189 68 0.11
190 4 0.01
191 3 0.00
192 65 0.10
193 16 0.03
194 373 0.59
195 14 0.02
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (193 bp):
CCCATTCCTTCTGAGGGGATACTCTAACCCTGCTTTTAAACTTATCAAAATTTAAATCTTATTTT
CGGTTAAATTGTCATCATCAAAGACACTCCAACCCCATTCTTCGAGGAGATACTCCAACCTCGTT
TTTAAACTTATCAAAATTTAAATCTTATTTTTGGTTAAATTGTCATAATCGGGGACACTCCAA
Found at i:359600 original size:69 final size:69
Alignment explanation
Indices: 359379--359601 Score: 293
Period size: 69 Copynumber: 3.2 Consensus size: 69
359369 ATTCCTCCGA
* * * *
359379 GGGGATATTCTAACCCCGTTTTTTAACTTATCAAAATTTAAATCTTATTTTATCCAAATTATCAT
1 GGGGATACTCCAACCCCGTTTTTAAACTTATCAAAATTTAAATCTTATTTTGTCCAAATTATCAT
359444 TGTC
66 TGTC
* * * *** *
359448 AGGGATATTTCAACATTGTTTTTAAACTTATCAAAATTTAAATCTTATTTTGTCCAAATTATCGT
1 GGGGATACTCCAACCCCGTTTTTAAACTTATCAAAATTTAAATCTTATTTTGTCCAAATTATCAT
359513 TGTC
66 TGTC
* * * * * *
359517 GGGAATACTCCAACCCCGTTTTTAAACTCATCGAAATTTAAGTCTTATTTTGTCTAAATTCTCAT
1 GGGGATACTCCAACCCCGTTTTTAAACTTATCAAAATTTAAATCTTATTTTGTCCAAATTATCAT
359582 TGTC
66 TGTC
359586 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
359602 TATTCCTCTG
Statistics
Matches: 131, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 131 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (69 bp):
GGGGATACTCCAACCCCGTTTTTAAACTTATCAAAATTTAAATCTTATTTTGTCCAAATTATCAT
TGTC
Found at i:360635 original size:19 final size:19
Alignment explanation
Indices: 360611--360649 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
360601 ATGAAATCAA
360611 TGCCTCAAACATCAAAGAT
1 TGCCTCAAACATCAAAGAT
360630 TGCCTCAAACATCAAAGAT
1 TGCCTCAAACATCAAAGAT
360649 T
1 T
360650 TCAATAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (19 bp):
TGCCTCAAACATCAAAGAT
Found at i:367060 original size:147 final size:150
Alignment explanation
Indices: 366807--367101 Score: 400
Period size: 148 Copynumber: 2.0 Consensus size: 150
366797 TGCATATTGC
* * * *
366807 ATGCCATTCTTTCTACACAACATATATGGAAGGACTAGTATTAACTTTATTTGGACCCTCTAAAA
1 ATGCCAATCTTTCTACACAACATATATGGAAAGACTAGAATTAACTTTATTGGGACCCTCTAAAA
* * * * * *
366872 TTAAAATTATTGACTCCACCACCTATCAAGATTTTGATTGATGTAGT-CAAATGAGTGAAATTTT
66 TTAAAATTATTGACTCCACCACCTATCAACATTATGATTGATGCAATCCAAATGAGCGAAATTCT
* *
366936 TCCCCATATCACCTGCAACT
131 ACCCCATATCACATGCAACT
* *
366956 ATGCCAATCTTTCTACACCACATTTAT-GAAAGACTAGAATTAACTTTATTGGGACCCT-TAAAA
1 ATGCCAATCTTTCTACACAACATATATGGAAAGACTAGAATTAACTTTATTGGGACCCTCTAAAA
* *
367019 TTAAAATT-TTTAGCTCCACCACTTATCAACATTATGATTGATGCAATCCAAATGAGCGAAATTC
66 TTAAAATTATTGA-CTCCACCACCTATCAACATTATGATTGATGCAATCCAAATGAGCGAAATTC
*
367083 TACCCTATATCACATGCAA
130 TACCCCATATCACATGCAA
367102 TTATTTCTCC
Statistics
Matches: 127, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
146 3 0.02
147 42 0.33
148 58 0.46
149 24 0.19
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (150 bp):
ATGCCAATCTTTCTACACAACATATATGGAAAGACTAGAATTAACTTTATTGGGACCCTCTAAAA
TTAAAATTATTGACTCCACCACCTATCAACATTATGATTGATGCAATCCAAATGAGCGAAATTCT
ACCCCATATCACATGCAACT
Found at i:369320 original size:79 final size:79
Alignment explanation
Indices: 369218--369571 Score: 363
Period size: 79 Copynumber: 4.5 Consensus size: 79
369208 GATAGAAACA
* *
369218 GGGTTAGAGTAT-CCCTCAGAAATAACAAGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTT
1 GGGTTGGAGTATCCCCTCAAAAATAACAAGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTT
369282 TAGAAATAAAACCG
66 TAGAAATAAAACCG
* * * * *
369296 CGGTTGGAGTATCCCCTTAAAAATAAC-AGGATTGAAGTATCCCCGATGGTGAAAAATTAGCGTT
1 GGGTTGGAGTATCCCCTCAAAAATAACAAGG-TTGGAGTATCCCCGATGGTGAAAAATCAGTGTT
*
369360 TTAGAAATAAAACTG
65 TTAGAAATAAAACCG
* * * * * *
369375 GGGTTGGAGTATCCCCT-AGGAAATAACGAGGTTGGAGTATCTCTGATGGTGGAAAATTAGTGTT
1 GGGTTGGAGTATCCCCTCA-AAAATAACAAGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTT
* *
369439 TTAGAAGTAAAATCG
65 TTAGAAATAAAACCG
* * * *** ** * * *
369454 GGGTTTGAGTATCCTCTCGAAAATAATGGGGTAAGAGTATTCTCGATGGTGGAAAATCAGTGTTT
1 GGGTTGGAGTATCCCCTCAAAAATAACAAGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTT
* **
369519 TAAAAATAAAATTG
66 TAGAAATAAAACCG
* * * *
369533 GGGTTGGAGTATCCTCTCGAAAATAACAGGGTTAGAGTA
1 GGGTTGGAGTATCCCCTCAAAAATAACAAGGTTGGAGTA
369572 CATCCCTCGA
Statistics
Matches: 233, Mismatches: 38, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
78 14 0.06
79 216 0.93
80 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCTCAAAAATAACAAGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTT
TAGAAATAAAACCG
Found at i:369399 original size:158 final size:158
Alignment explanation
Indices: 369218--369571 Score: 408
Period size: 158 Copynumber: 2.2 Consensus size: 158
369208 GATAGAAACA
*
369218 GGGTTAGAGTAT-CCCTCA-GAAATAACAAGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTT
1 GGGTTGGAGTATCCCCT-AGGAAATAACAAGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTT
* * *
369281 TTAGAAATAAAACCGCGGTTGGAGTATCCCCTTAAAAATAACAGGATTGA-AGTATCCCCGATGG
65 TTAGAAATAAAACCGCGGTTGGAGTATCCCCTCAAAAATAA-AGGAGTAAGAGTATCCCCGATGG
* *
369345 TGAAAAATTAGCGTTTTAGAAATAAAACTG
129 TGAAAAATCAGCGTTTTAAAAATAAAACTG
* * * * *
369375 GGGTTGGAGTATCCCCTAGGAAATAACGAGGTTGGAGTATCTCTGATGGTGGAAAATTAGTGTTT
1 GGGTTGGAGTATCCCCTAGGAAATAACAAGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTT
* * * * * * * * * *
369440 TAGAAGTAAAATCGGGGTTTGAGTATCCTCTCGAAAATAATGGGGTAAGAGTATTCTCGATGGTG
66 TAGAAATAAAACCGCGGTTGGAGTATCCCCTCAAAAATAAAGGAGTAAGAGTATCCCCGATGGTG
* * *
369505 GAAAATCAGTGTTTTAAAAATAAAATTG
131 AAAAATCAGCGTTTTAAAAATAAAACTG
* * * * *
369533 GGGTTGGAGTATCCTCTCGAAAATAACAGGGTTAGAGTA
1 GGGTTGGAGTATCCCCTAGGAAATAACAAGGTTGGAGTA
369572 CATCCCTCGA
Statistics
Matches: 164, Mismatches: 30, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
157 16 0.10
158 148 0.90
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (158 bp):
GGGTTGGAGTATCCCCTAGGAAATAACAAGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTT
TAGAAATAAAACCGCGGTTGGAGTATCCCCTCAAAAATAAAGGAGTAAGAGTATCCCCGATGGTG
AAAAATCAGCGTTTTAAAAATAAAACTG
Found at i:372629 original size:2 final size:2
Alignment explanation
Indices: 372622--372673 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
372612 CTTCCAGCAC
372622 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
372664 TA TA TA TA TA
1 TA TA TA TA TA
372674 ATGTTAACTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:381667 original size:18 final size:19
Alignment explanation
Indices: 381639--381694 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 19
381629 TTAAAAAAAT
381639 TCTCCCCCTTAAACGATTA
1 TCTCCCCCTTAAACGATTA
* *
381658 TCT-CCTCTTAAA--A-AA
1 TCTCCCCCTTAAACGATTA
381673 TCTCCCCCTTAAACGATTA
1 TCTCCCCCTTAAACGATTA
381692 TCT
1 TCT
381695 TCTCCCCCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
15 4 0.14
16 9 0.31
18 9 0.31
19 7 0.24
ACGTcount: A:0.29, C:0.34, G:0.04, T:0.34
Consensus pattern (19 bp):
TCTCCCCCTTAAACGATTA
Found at i:383568 original size:13 final size:13
Alignment explanation
Indices: 383550--383578 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
383540 AAATAGTACC
383550 CAATGTATCGATA
1 CAATGTATCGATA
383563 CAATGTATCGATA
1 CAATGTATCGATA
383576 CAA
1 CAA
383579 GAAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:389768 original size:20 final size:20
Alignment explanation
Indices: 389745--389782 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
389735 TCATGTATTG
389745 ATACAATGTATCGATACATT
1 ATACAATGTATCGATACATT
*
389765 ATACCATGTATCGATACA
1 ATACAATGTATCGATACA
389783 AATAGTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (20 bp):
ATACAATGTATCGATACATT
Found at i:389773 original size:33 final size:32
Alignment explanation
Indices: 389717--389783 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
389707 GTTACAAGCT
*
389717 ATGTATCGATACATTTCTTCATGTATTGATACA
1 ATGTATCGATACATTTC-TCATGTATCGATACA
389750 ATGTATCGATACATTATAC-CATGTATCGATACA
1 ATGTATCGATACATT-T-CTCATGTATCGATACA
389783 A
1 A
389784 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (32 bp):
ATGTATCGATACATTTCTCATGTATCGATACA
Found at i:389877 original size:20 final size:20
Alignment explanation
Indices: 389812--389885 Score: 87
Period size: 19 Copynumber: 3.7 Consensus size: 20
389802 CTGCCAGTTT
* *
389812 CATGTATCGATACAATTTGG
1 CATGTATCGATACAATGTAG
* *
389832 CCATGTATCGATATAATG-AA
1 -CATGTATCGATACAATGTAG
*
389852 CATGTATCGATACAAAGTAG
1 CATGTATCGATACAATGTAG
389872 CATGTATCGATACA
1 CATGTATCGATACA
389886 TCTGGGTGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
19 15 0.33
20 15 0.33
21 15 0.33
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATGTAG
Found at i:393567 original size:32 final size:33
Alignment explanation
Indices: 393524--393602 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
393514 TTCCAAAGCC
*
393524 GTTAACTTTGATTATAGAT-TTATACACTTTTG
1 GTTAACTTTGATCATAGATATTATACACTTTTG
* * *
393556 GTTAACCTTGATCATAGATATTATATATTTTTG
1 GTTAACTTTGATCATAGATATTATACACTTTTG
393589 GTTAACTTTGATCA
1 GTTAACTTTGATCA
393603 AAGTTCTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 17 0.41
33 24 0.59
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (33 bp):
GTTAACTTTGATCATAGATATTATACACTTTTG
Found at i:393776 original size:108 final size:108
Alignment explanation
Indices: 393562--393769 Score: 278
Period size: 108 Copynumber: 1.9 Consensus size: 108
393552 TTTGGTTAAC
* *
393562 CTTGATCATAGATATTATATATTTTTGGTTAACTTTGATCAAAGTTCTTAAAGTGGTTTGACATG
1 CTTGATCATAGATATTATATACTTTTGATTAACTTTGATCAAAGTTCTTAAAGTGGTTTGACATG
* *
393627 GTAGTTTGTTTTCTTCTTAAAAAAGAAAGTTCTTATGTTACAA
66 ATAGTTTGATTTCTTCTTAAAAAAGAAAGTTCTTATGTTACAA
* * * * * *
393670 CTTGATCATATATGTTATATACTTTTGATTAACTTTGATTAAA-TTTTCTAAGGTTGTTTGACAT
1 CTTGATCATAGATATTATATACTTTTGATTAACTTTGATCAAAGTTCT-TAAAGTGGTTTGACAT
*
393734 GATAGTTTGCATTT-TTCTT-AAAAAGAGAGTTCTTAT
65 GATAGTTTG-ATTTCTTCTTAAAAAAGAAAGTTCTTAT
393770 TTTTACAGCT
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
107 19 0.22
108 65 0.75
109 3 0.03
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (108 bp):
CTTGATCATAGATATTATATACTTTTGATTAACTTTGATCAAAGTTCTTAAAGTGGTTTGACATG
ATAGTTTGATTTCTTCTTAAAAAAGAAAGTTCTTATGTTACAA
Found at i:395992 original size:18 final size:17
Alignment explanation
Indices: 395962--396005 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
395952 AATGTTTATG
*
395962 TGTATTGTGTTTGTATT
1 TGTATTGTATTTGTATT
395979 TGTACTTGTATTTGTATAT
1 TGTA-TTGTATTTGTAT-T
395998 TGGTATTG
1 T-GTATTG
396006 CATTATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 11 0.48
19 5 0.22
20 3 0.13
ACGTcount: A:0.16, C:0.02, G:0.23, T:0.59
Consensus pattern (17 bp):
TGTATTGTATTTGTATT
Found at i:396159 original size:75 final size:77
Alignment explanation
Indices: 396071--396228 Score: 243
Period size: 76 Copynumber: 2.1 Consensus size: 77
396061 TATTGAAATA
*
396071 AATTTTAGATTTTTTAATAATG-AA-ACATTTATC-GCATAAAAATACAAAAAATTAAAATTTTT
1 AATTTTAGATTTTTTAATAATGAAATACAGTTATCAG-ATAAAAATA-AAAAAATTAAAATTTTT
396133 AATATTTATAGACT
64 AATATTTATAGACT
*
396147 AATTTTA-ATTTTTTAATAATGAAATACAGTTATCAGATAAAAATATAAAAATTAAAATTTTTAA
1 AATTTTAGATTTTTTAATAATGAAATACAGTTATCAGATAAAAATAAAAAAATTAAAATTTTTAA
396211 TATTTATAGACT
66 TATTTATAGACT
*
396223 ACTTTT
1 AATTTT
396229 CTTGGATAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
75 14 0.18
76 44 0.58
77 17 0.22
78 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (77 bp):
AATTTTAGATTTTTTAATAATGAAATACAGTTATCAGATAAAAATAAAAAAATTAAAATTTTTAA
TATTTATAGACT
Found at i:397783 original size:2 final size:2
Alignment explanation
Indices: 397776--397806 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
397766 GTCAAGAATG
*
397776 TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
397807 TATTCATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:398760 original size:46 final size:47
Alignment explanation
Indices: 398644--398761 Score: 121
Period size: 47 Copynumber: 2.5 Consensus size: 47
398634 GTGCTAGATG
*** * * * *
398644 GTTTGTAACTTTATCCATGCAAAAGTTACAAGTTGATTGTGAGGAGG
1 GTTTGTAACTTTATATGTGCAAAAGTTACAAGCTGATTGTAAAGAGA
* * *
398691 GTTTGTAACTTTATTTGTGCAAAAGTTACAAGCTGTTTGTAAAGATA
1 GTTTGTAACTTTATATGTGCAAAAGTTACAAGCTGATTGTAAAGAGA
* *
398738 G-TTGTACCTTTGTATGTGCAAAAG
1 GTTTGTAACTTTATATGTGCAAAAG
398762 CTATTATTGT
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
46 20 0.34
47 39 0.66
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (47 bp):
GTTTGTAACTTTATATGTGCAAAAGTTACAAGCTGATTGTAAAGAGA
Found at i:399558 original size:46 final size:46
Alignment explanation
Indices: 399516--399625 Score: 175
Period size: 46 Copynumber: 2.4 Consensus size: 46
399506 TAGTTTGCTA
* *
399516 GAGGGTTTGTAGCTTTCTCCATGCAAAAACTACTCATCGTTTGTTG
1 GAGGATTTATAGCTTTCTCCATGCAAAAACTACTCATCGTTTGTTG
* *
399562 GAGGATTTATAGCTTTCTCCATGCAAAAACTATTCATTGTTTGTTG
1 GAGGATTTATAGCTTTCTCCATGCAAAAACTACTCATCGTTTGTTG
*
399608 GAGGTTTTATAGCTTTCT
1 GAGGATTTATAGCTTTCT
399626 TTGTACAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (46 bp):
GAGGATTTATAGCTTTCTCCATGCAAAAACTACTCATCGTTTGTTG
Found at i:399635 original size:46 final size:45
Alignment explanation
Indices: 399519--399681 Score: 166
Period size: 46 Copynumber: 3.6 Consensus size: 45
399509 TTTGCTAGAG
* * *
399519 GGTTTGTAGCTTTCTCCATGCAAAAACTACTCATCGTTTGTTGGA
1 GGTTTATAGCTTTCTCCATACAAAAACTACTCATTGTTTGTTGGA
* *
399564 GGATTTATAGCTTTCTCCATGCAAAAACTATTCATTGTTTGTTGGA
1 GG-TTTATAGCTTTCTCCATACAAAAACTACTCATTGTTTGTTGGA
*** * *
399610 GGTTTTATAGCTTTCTTTGTACAAAAGCTACT-AGTTGTGTGTTGGA
1 GG-TTTATAGCTTTCTCCATACAAAAACTACTCA-TTGTTTGTTGGA
* * *
399656 TGGTTTATAACTTTATTCATACAAAA
1 -GGTTTATAGCTTTCTCCATACAAAA
399682 GTTACAAGTT
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
45 3 0.03
46 95 0.95
47 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (45 bp):
GGTTTATAGCTTTCTCCATACAAAAACTACTCATTGTTTGTTGGA
Found at i:399682 original size:46 final size:46
Alignment explanation
Indices: 399598--399691 Score: 109
Period size: 46 Copynumber: 2.0 Consensus size: 46
399588 AAACTATTCA
* * * ** *
399598 TTGTTTGTTGGAGGTTTTATAGCTTTCTTTGTACAAAAGCTACTAG
1 TTGTGTGTTGGAGGTTTTATAACTTTATTCATACAAAAGCTACAAG
*
399644 TTGTGTGTTGGATGG-TTTATAACTTTATTCATACAAAAGTTACAAG
1 TTGTGTGTTGGA-GGTTTTATAACTTTATTCATACAAAAGCTACAAG
399690 TT
1 TT
399692 ATTTGTGATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 38 0.95
47 2 0.05
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.45
Consensus pattern (46 bp):
TTGTGTGTTGGAGGTTTTATAACTTTATTCATACAAAAGCTACAAG
Found at i:407058 original size:13 final size:13
Alignment explanation
Indices: 407040--407067 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
407030 CATTCCCATA
407040 ATTAACTTGCAGG
1 ATTAACTTGCAGG
407053 ATTAACTTGCAGG
1 ATTAACTTGCAGG
407066 AT
1 AT
407068 GGTTAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (13 bp):
ATTAACTTGCAGG
Found at i:409596 original size:19 final size:21
Alignment explanation
Indices: 409565--409606 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
409555 GATATGAAAA
409565 GATTTATGCTTAT-CC-AAAT
1 GATTTATGCTTATACCTAAAT
409584 GATTGTATG-TTATACCTAAAT
1 GATT-TATGCTTATACCTAAAT
409605 GA
1 GA
409607 GAGAGCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (21 bp):
GATTTATGCTTATACCTAAAT
Found at i:410214 original size:83 final size:83
Alignment explanation
Indices: 410075--410241 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
410065 CTAGAAATAA
410075 TATTGATGTTTACTTACAACCTTTGATAAAAGAATTATGAGAAATTGGTATAAACATTTTTGATG
1 TATTGATGTTTACTTACAACCTTTGATAAAAGAATTATGAGAAATTGGTATAAACATTTTTGATG
410140 CTTTTGTTGGAGAGAATT
66 CTTTTGTTGGAGAGAATT
410158 TATTGATGTTTACTTACAACCTTTGATAAAAGAATTATGAGAAATTGGTATAAACATTTTTGATG
1 TATTGATGTTTACTTACAACCTTTGATAAAAGAATTATGAGAAATTGGTATAAACATTTTTGATG
410223 CTTTTGTTGGAGAGAATT
66 CTTTTGTTGGAGAGAATT
410241 T
1 T
410242 TCAATTACGT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (83 bp):
TATTGATGTTTACTTACAACCTTTGATAAAAGAATTATGAGAAATTGGTATAAACATTTTTGATG
CTTTTGTTGGAGAGAATT
Found at i:415694 original size:107 final size:107
Alignment explanation
Indices: 415502--415722 Score: 261
Period size: 107 Copynumber: 2.1 Consensus size: 107
415492 TTTTGTTAAC
* * *
415502 CTTGATCATAGATATTATAAACTTTTGGTTAACTCTGATCAAATTTTTTAAAGTGGTTTGACATG
1 CTTGATAATAGATATTATAAACTTTTGGTTAACTCTGATCAAATTTTCTAAAGTGGTTTGACATA
**
415567 GTAGTTTGCTTTTTCTTAAAAAAGAAA-GTTCTTATGTTACAA
66 ACAGTTTGCTTTTTCTTAAAAAA-AAAGGTTCTTATGTTACAA
* * * * * * *
415609 CTTGATAATAGATGTTATATACTTTTGGTTAATTTTG-CCTAAATTTTCTAAGGTTGTTTGACAT
1 CTTGATAATAGATATTATAAACTTTTGGTTAACTCTGATC-AAATTTTCTAAAGTGGTTTGACAT
415673 AACAGTTTG-TGCTTTTC-TAAAAAAAAAGGGTTCTTATGTTACAA
65 AACAGTTTGCT--TTTTCTTAAAAAAAAA-GGTTCTTATGTTACAA
415717 CTTGAT
1 CTTGAT
415723 TTATTTTATT
Statistics
Matches: 97, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
106 5 0.05
107 66 0.68
108 26 0.27
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.43
Consensus pattern (107 bp):
CTTGATAATAGATATTATAAACTTTTGGTTAACTCTGATCAAATTTTCTAAAGTGGTTTGACATA
ACAGTTTGCTTTTTCTTAAAAAAAAAGGTTCTTATGTTACAA
Found at i:418979 original size:32 final size:33
Alignment explanation
Indices: 418938--419000 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
418928 ACAATTGTGC
*
418938 ATGTATCGATACAATG-A-ACATGTATCGATATA
1 ATGTATCGATACAAAGCATA-ATGTATCGATATA
418970 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGCATAATGTATCGATA
419001 CATCTGGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATATA
Found at i:419956 original size:33 final size:33
Alignment explanation
Indices: 419893--419959 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
419883 CTAAGTGCAC
* *
419893 TAAAATGCTCATCCATGCGCTGCGAGAGTGAAG
1 TAAAATGCTCATCCATGCGCTACGAAAGTGAAG
* *
419926 TAAAGTGCTCA-CTCATGTGCTACGAAAGTGAAG
1 TAAAATGCTCATC-CATGCGCTACGAAAGTGAAG
419959 T
1 T
419960 GATCAACTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (33 bp):
TAAAATGCTCATCCATGCGCTACGAAAGTGAAG
Found at i:421456 original size:13 final size:13
Alignment explanation
Indices: 421438--421490 Score: 88
Period size: 13 Copynumber: 4.1 Consensus size: 13
421428 ATAGTAACCC
421438 ATGTATCAATACA
1 ATGTATCAATACA
421451 ATGTATCAATACA
1 ATGTATCAATACA
*
421464 ATTTATCAATACA
1 ATGTATCAATACA
*
421477 ATGTATCGATACA
1 ATGTATCAATACA
421490 A
1 A
421491 AGAACATTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:426988 original size:13 final size:13
Alignment explanation
Indices: 426970--426995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
426960 CAATTTTTTG
426970 TGTATCGATACAT
1 TGTATCGATACAT
426983 TGTATCGATACAT
1 TGTATCGATACAT
426996 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:427007 original size:32 final size:33
Alignment explanation
Indices: 426950--427013 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
426940 TACAAGCCAA
**
426950 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
426983 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
427014 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:429564 original size:13 final size:13
Alignment explanation
Indices: 429546--429583 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
429536 ATAATCCCCC
429546 TGTATCGATACAG
1 TGTATCGATACAG
*
429559 TGTATCGATACAT
1 TGTATCGATACAG
429572 TGTATCGATACA
1 TGTATCGATACA
429584 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:431682 original size:15 final size:15
Alignment explanation
Indices: 431662--431692 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
431652 ATTTCGTTTG
*
431662 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
431677 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
431692 G
1 G
431693 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:435778 original size:13 final size:13
Alignment explanation
Indices: 435760--435785 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
435750 CAATTTTTTG
435760 TGTATCGATACAT
1 TGTATCGATACAT
435773 TGTATCGATACAT
1 TGTATCGATACAT
435786 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:435802 original size:32 final size:33
Alignment explanation
Indices: 435740--435803 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
435730 TACAAGCCAA
**
435740 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
*
435773 TGTATCGATAC-ATACTTTGTGTATTGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
435804 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:437591 original size:20 final size:20
Alignment explanation
Indices: 437566--437623 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
437556 CTGCCAGTTT
*
437566 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGTA
*
437586 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
437605 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
437624 TTGATACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 15 0.44
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:439627 original size:2 final size:2
Alignment explanation
Indices: 439593--439642 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
439583 AAAGTTGAAA
* * * *
439593 AT AT AT AC AT AA AT AG AT AT A- AT AT AT AC 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 AT
439634 AT AT AT AT A
1 AT AT AT AT A
439643 AAGCACATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (2 bp):
AT
Found at i:444149 original size:17 final size:17
Alignment explanation
Indices: 444107--444149 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
444097 TGAGATTGAA
*
444107 TGTATGCAAGAGGAGTTT
1 TGTA-GCAAGAGGAGTTG
444125 TGCT-GCAAGAGGAGTTG
1 TG-TAGCAAGAGGAGTTG
444142 TGTAGCAA
1 TGTAGCAA
444150 TTCCTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 1 0.05
17 18 0.82
18 2 0.09
19 1 0.05
ACGTcount: A:0.28, C:0.09, G:0.35, T:0.28
Consensus pattern (17 bp):
TGTAGCAAGAGGAGTTG
Found at i:444670 original size:46 final size:46
Alignment explanation
Indices: 444620--444758 Score: 152
Period size: 46 Copynumber: 3.0 Consensus size: 46
444610 AGTTTGCTAA
* *
444620 AGGATTTGTAGCTTTCTCTACACAAAAACTACTCATTATTTGTTGG
1 AGGATTTATAGCTTTCTCTATACAAAAACTACTCATTATTTGTTGG
* * * * *
444666 AGGATTTATAGCTTTCTCTGTGCAAAAACTATTCATTGTTTGTTAG
1 AGGATTTATAGCTTTCTCTATACAAAAACTACTCATTATTTGTTGG
* * * * * * *
444712 AGGTTTTATGGCTTTCTCTATATAAAAGCTACTAAATATGTGTTGG
1 AGGATTTATAGCTTTCTCTATACAAAAACTACTCATTATTTGTTGG
444758 A
1 A
444759 TGGTCTGTAA
Statistics
Matches: 74, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (46 bp):
AGGATTTATAGCTTTCTCTATACAAAAACTACTCATTATTTGTTGG
Found at i:447057 original size:15 final size:15
Alignment explanation
Indices: 447037--447067 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
447027 CTGAAGTATA
447037 ATTTAAGTAATTCTT
1 ATTTAAGTAATTCTT
447052 ATTTAAGTAATTCTT
1 ATTTAAGTAATTCTT
447067 A
1 A
447068 CTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (15 bp):
ATTTAAGTAATTCTT
Found at i:447162 original size:31 final size:31
Alignment explanation
Indices: 447124--447185 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
447114 AGAAAGTAAG
447124 CGAAGTACCTTGATTCTAAAACCAAAATGCA
1 CGAAGTACCTTGATTCTAAAACCAAAATGCA
447155 CGAAGTACCTTGATTCTAAAACCAAAATGCA
1 CGAAGTACCTTGATTCTAAAACCAAAATGCA
447186 TATTAAGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (31 bp):
CGAAGTACCTTGATTCTAAAACCAAAATGCA
Found at i:455423 original size:87 final size:87
Alignment explanation
Indices: 455277--455443 Score: 318
Period size: 87 Copynumber: 1.9 Consensus size: 87
455267 TTGTGTCTCA
455277 AGTCTTTTACGTGAGCACTGCCCCTGCCTGAACCACCAATTGCTATTTGTAATTACAAACTTGTC
1 AGTCTTTTACGTGAGCACTGCCCCTGCCTGAACCACCAATTGCTATTTGTAATTACAAACTTGTC
455342 TCTTTTCATTAATTGACGACAG
66 TCTTTTCATTAATTGACGACAG
455364 AGTCTTTTACGTGAGCACTAG-CCCTGCCTGAACCACCAATTGCTATTTGTAATTACAAACTTGT
1 AGTCTTTTACGTGAGCACT-GCCCCTGCCTGAACCACCAATTGCTATTTGTAATTACAAACTTGT
455428 CTCTTTTCATTAATTG
65 CTCTTTTCATTAATTG
455444 CGAGGGGCCT
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
87 78 0.99
88 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (87 bp):
AGTCTTTTACGTGAGCACTGCCCCTGCCTGAACCACCAATTGCTATTTGTAATTACAAACTTGTC
TCTTTTCATTAATTGACGACAG
Found at i:457232 original size:865 final size:865
Alignment explanation
Indices: 455556--458133 Score: 4148
Period size: 879 Copynumber: 3.0 Consensus size: 865
455546 ATTTCACGTC
455556 GTTAAGCTCATAATTTTGAATATTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATTA
1 GTTAAGCTCATAATTTTGAATATTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATTA
* *
455621 AAAATTGTTAAAAATAAGTACAGATAATTTTTATTTTAATAAGACAACACTACACTAAAAAAAAT
66 AAAATTGTTAAAAATAAGTATAGATAATTTTTATTTTAATAAGGCAACACTACACT-AAAAAAAT
*
455686 ATTATTCACCAACACTTTTTTTTTTGGGGTTTAGTTTATAAAAGTGTTGGGTTTTCTCATTTAAT
130 ATTATTCACCAACACTTTTTTTTCT-GGG----GTTTATAAAAGTGTTGGGTTTTCTCATTTAAT
*
455751 TTTTTATTTTTCTTGCATAAATAAAGTGCCCTTGATAAGGACACATTAAGCCTGTATTAAAAAAA
190 TTTTTATTTTTCTTGCATAAATAAAGTGCCCTTGATAAGGACACATTAAGCCTATATTAAAAAAA
* *
455816 AATCCTTTCATTTACTGAAAACACATTTTAAACCCATTAAATTCTTAAGCCCAAAACAATTTTTT
255 AATCCTTTCATTTACTCAAAATACATTTTAAACCCATTAAATTCTTAAGCCCAAAACAATTTTTT
* *
455881 CATCTTATTGATAGCTTGCCCATTAACTTCTTGATCTAAATCTCTAAGTTTTTTTTGATAGCCAG
320 CATCTTATTGATAGCTTGCCCATTAACTTCTTGATCTAAATCTCTGAGTTTATTTTGATAGCCAG
** *
455946 CCGAAAATAGCTTTTATCATGATATGGCATGATAAGGATCGTATTAAAGATGGAAAGTATAGGCA
385 CCGAAAATAGCTTTTGCCATGATATGGCATGATAAGGGTCGTATTAAAGATGGAAAGTATAGGCA
* *
456011 TCCAGTTGATTCCCTTGTTTGGAAATCTTGTGATTTATAGTATCTTAATTTTGCTTTAGAT-CTT
450 TCCAGTTGATTCCCTTGCTTGGAAATCTTTTGATTTATAGTATCTTAATTTTGCTTTAGATCCTT
*
456075 CATAATGTTAGGCTAGGCTTGGCTACTAATGGATTTAATCCATTTAAGACAATAAATAATAAGTA
515 -ATAATGTTAGGCTAGGCTTGGCTACTAATGGATTTAATCCATTT-AGACAATGAATAATAAGTA
456140 TAGTGTTTGGCCTGTTATATTGATACCATACAATTTGCCTCCTTAGTTGTCTGTGAAAGAGTCAA
578 TAGTGTTTGGCCTGTTATATTGATACCATACAATTTGCCTCCTTAGTTGTCTGTGAAAGAGTCAA
456205 GTTTTATTCTTTCCTTAATGATTTCGTGTAAGAATAGACCTAGAAATAATATTGATGTTTACTTA
643 GTTTTATTCTTTCCTTAATGATTTCGTGTAAGAATAGACCTAGAAATAATATTGATGTTTACTTA
* *
456270 CAACCTTTGATACAAGAACTAAAAGAAATATGAGAAATTGGTGTAAACATTTTTGATGGTTTTGC
708 CAACCTTTGATACAAGAATTAAAAGAATTATGAGAAATTGGTGTAAACATTTTTGATGGTTTTGC
* * * *
456335 TAGAGAAAATTTTCAATTACTTATCGCTGTAAAATGGACAACAAATGACTTTCGATAAAACTTTA
773 TAGAGAGAATTTTCAATTACGTATCGCTGTAAAGTGGACAACAAATGACTTTCGATAAAAATTTA
*
456400 TATTCAAGTCTAATTTCACGTCGATAAG
838 TATTCAAGTATAATTTCACGTCGATAAG
*
456428 GTTAAGCTCATAAATTTGAATATTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATTA
1 GTTAAGCTCATAATTTTGAATATTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATTA
*
456493 AAAATTGTTAAAAATAAGTATAGATAATTTTTATTTTAATAAGGCAACACCACACTAAAAAAATT
66 AAAATTGTTAAAAATAAGTATAGATAATTTTTATTTTAATAAGGCAACACTACACTAAAAAAA-T
* *
456558 ATTATTCACCAACACTTTTTTTTCTAGGGTTTATAAAAGTATTGGGTTTTCTCATTTAA-TTTTT
130 ATTATTCACCAACACTTTTTTTTCTGGGGTTTATAAAAGTGTTGGGTTTTCTCATTTAATTTTTT
**
456622 ATTTTTCTTAGCATAAATAAAGTGCCCTTGATAAGGACACATTAAGCCTATATTAAAAAAAAAAG
195 ATTTTTCTT-GCATAAATAAAGTGCCCTTGATAAGGACACATTAAGCCTATATTAAAAAAAAATC
* * * *
456687 CTTTCATTTACTCAAAATACATTTTTAACCCACTAAATTCTCAAGCCCAAAACAATATTTTTTAT
259 CTTTCATTTACTCAAAATACATTTTAAACCCATTAAATTCTTAAGCCCAAAACAAT-TTTTTCAT
* * * *
456752 CTTATTGATAGCTTGCCCATTAACTTCTTGATCTATATCTTTGAGTTTATTTTGATAGCTAGTCG
323 CTTATTGATAGCTTGCCCATTAACTTCTTGATCTAAATCTCTGAGTTTATTTTGATAGCCAGCCG
* *
456817 AAAATAGCTTTTGCCATGATATGGCATGATAAGGGTCGTATTAAAGATGGAAAATATAGGGATCC
388 AAAATAGCTTTTGCCATGATATGGCATGATAAGGGTCGTATTAAAGATGGAAAGTATAGGCATCC
456882 AGTTGATTCCCTTGCTTGGAAATCTTTTGATTTATAGTATCTTAATTTTGCTTTAGATCCTTATA
453 AGTTGATTCCCTTGCTTGGAAATCTTTTGATTTATAGTATCTTAATTTTGCTTTAGATCCTTATA
* * * * *
456947 ATGTTAGGTTAGGCTTGGCTGCTGATGGATTTAATCCA-TT-GACAATGAATAATAAGTACAATG
518 ATGTTAGGCTAGGCTTGGCTACTAATGGATTTAATCCATTTAGACAATGAATAATAAGTATAGTG
*
457010 TTTGGCCTGTTATATTGATACCATACAATTTGCCTCCTTAGCTGTCTGTGAAAGAGTCAAGTTTT
583 TTTGGCCTGTTATATTGATACCATACAATTTGCCTCCTTAGTTGTCTGTGAAAGAGTCAAGTTTT
*
457075 ATTCTTTCCTTAATGATTTCGAGTAAGAATAGACCTAGAAATAATATTGATGTTTACTTACAACC
648 ATTCTTTCCTTAATGATTTCGTGTAAGAATAGACCTAGAAATAATATTGATGTTTACTTACAACC
* * *
457140 TTTGATACAAGAATTAAAAGAATTATGAGAAATTGGAGTAAACATTTTTGATTGTTTTGCTTGAG
713 TTTGATACAAGAATTAAAAGAATTATGAGAAATTGGTGTAAACATTTTTGATGGTTTTGCTAGAG
457205 AGAATTTTCAATTACGTATCGCTGTAAAGTGGACAACAAATGACTTTCTGGCAACAAATAACTTT
778 AGAATTTTCAATTACGTATCGCTGTAAAGTGGACAAC-AA--A-----T-G---------ACTTT
*
457270 CGATAAAAATTTATATTCAAGTATGATTTCACGTCGATAAG
825 CGATAAAAATTTATATTCAAGTATAATTTCACGTCGATAAG
* *
457311 GTTAAGCTCATAATTTTGAATGTTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATCA
1 GTTAAGCTCATAATTTTGAATATTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATTA
*
457376 AAAATTGCTAAAAATAAGTATAGATAATTTTTATTTTAATAAGG---CA-TACACTAAAAAAATA
66 AAAATTGTTAAAAATAAGTATAGATAATTTTTATTTTAATAAGGCAACACTACACTAAAAAAATA
* ***
457437 TTATTCACTAACAC-TTTTTTGGGGGGGTTTATAAAAGTGTTGGGTTTTCTCATTTAATTTTTTT
131 TTATTCACCAACACTTTTTTTTCTGGGGTTTATAAAAGTGTTGGGTTTTCTCATTTAA-TTTTTT
*
457501 GTTTTTCTTGGCATAAATAAAGTGCCCTTGATAAGGACACATTAAGCCTATATTAAAAAAAAATC
195 ATTTTTCTT-GCATAAATAAAGTGCCCTTGATAAGGACACATTAAGCCTATATTAAAAAAAAATC
* *
457566 CATTCATTTACTCAAAATACATTTTAAACCCATTAAATTCTTAAGCCCAAAATAATTTTTTCATC
259 CTTTCATTTACTCAAAATACATTTTAAACCCATTAAATTCTTAAGCCCAAAACAATTTTTTCATC
* * *
457631 TTATTGATAGCTTGCACGTTAACTTCTTGATCTAAATCTCTGAGTTTGTTTTGATAGCCAGCCGA
324 TTATTGATAGCTTGCCCATTAACTTCTTGATCTAAATCTCTGAGTTTATTTTGATAGCCAGCCGA
* * *
457696 AAATAGCTTTTGCCATGATATGGCATGATGAGGGTCATATTAAAGATTGGAAAGTATAGGCATCT
389 AAATAGCTTTTGCCATGATATGGCATGATAAGGGTCGTATTAAAGA-TGGAAAGTATAGGCATCC
457761 AGTTGATTCCCTTGCTTGGAAATCTTTTGATTTATAGTATCTTAATTTTGCTTTAGATCCTTATA
453 AGTTGATTCCCTTGCTTGGAAATCTTTTGATTTATAGTATCTTAATTTTGCTTTAGATCCTTATA
* *
457826 ATGTTAGGCTAAGCTTGGCTACTAAGGGATTTAATCCATTTAAGACAATGAATAATAAGTATAGT
518 ATGTTAGGCTAGGCTTGGCTACTAATGGATTTAATCCATTT-AGACAATGAATAATAAGTATAGT
* *
457891 GTTTGGCCTGTCATATTGATACCATACAATTTGCCTCCTTAGTTGTATGTGAAAGAGTCAAGTTT
582 GTTTGGCCTGTTATATTGATACCATACAATTTGCCTCCTTAGTTGTCTGTGAAAGAGTCAAGTTT
* *
457956 TATTCTTTCCTTAATGATTCCGTGCAAGAATAGACCTAGAAATAATATTGATGTTTACTTACAAC
647 TATTCTTTCCTTAATGATTTCGTGTAAGAATAGACCTAGAAATAATATTGATGTTTACTTACAAC
*
458021 CTTTGATACAAGAATTAAAAGAATTATGAGAAATTGGTGTAAACATTTTTGATGGTTTTGCTGGA
712 CTTTGATACAAGAATTAAAAGAATTATGAGAAATTGGTGTAAACATTTTTGATGGTTTTGCTAGA
*
458086 GAGAATTTTCAATTACGTATTGCTGTAAAGTGGACAACAAATGACTTT
777 GAGAATTTTCAATTACGTATCGCTGTAAAGTGGACAACAAATGACTTT
458134 TCGACATATA
Statistics
Matches: 1580, Mismatches: 98, Indels: 64
0.91 0.06 0.04
Matches are distributed among these distances:
864 5 0.00
865 242 0.15
866 16 0.01
867 135 0.09
868 221 0.14
869 3 0.00
871 9 0.01
872 142 0.09
873 2 0.00
874 2 0.00
877 38 0.02
878 125 0.08
879 243 0.15
880 4 0.00
881 2 0.00
882 243 0.15
883 148 0.09
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (865 bp):
GTTAAGCTCATAATTTTGAATATTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATTA
AAAATTGTTAAAAATAAGTATAGATAATTTTTATTTTAATAAGGCAACACTACACTAAAAAAATA
TTATTCACCAACACTTTTTTTTCTGGGGTTTATAAAAGTGTTGGGTTTTCTCATTTAATTTTTTA
TTTTTCTTGCATAAATAAAGTGCCCTTGATAAGGACACATTAAGCCTATATTAAAAAAAAATCCT
TTCATTTACTCAAAATACATTTTAAACCCATTAAATTCTTAAGCCCAAAACAATTTTTTCATCTT
ATTGATAGCTTGCCCATTAACTTCTTGATCTAAATCTCTGAGTTTATTTTGATAGCCAGCCGAAA
ATAGCTTTTGCCATGATATGGCATGATAAGGGTCGTATTAAAGATGGAAAGTATAGGCATCCAGT
TGATTCCCTTGCTTGGAAATCTTTTGATTTATAGTATCTTAATTTTGCTTTAGATCCTTATAATG
TTAGGCTAGGCTTGGCTACTAATGGATTTAATCCATTTAGACAATGAATAATAAGTATAGTGTTT
GGCCTGTTATATTGATACCATACAATTTGCCTCCTTAGTTGTCTGTGAAAGAGTCAAGTTTTATT
CTTTCCTTAATGATTTCGTGTAAGAATAGACCTAGAAATAATATTGATGTTTACTTACAACCTTT
GATACAAGAATTAAAAGAATTATGAGAAATTGGTGTAAACATTTTTGATGGTTTTGCTAGAGAGA
ATTTTCAATTACGTATCGCTGTAAAGTGGACAACAAATGACTTTCGATAAAAATTTATATTCAAG
TATAATTTCACGTCGATAAG
Found at i:458096 original size:882 final size:870
Alignment explanation
Indices: 455515--458134 Score: 4150
Period size: 882 Copynumber: 3.0 Consensus size: 870
455505 AATAATTTGA
*
455515 TTGA-TTT-GATAAAAATTTATACTCAAGTCTGATTTCACGTC------GTTAAGCTCATAATTT
1 TTGACTTTCGATAAAAATTTATATTCAAGTCTGATTTCACGTCGATAAGGTTAAGCTCATAATTT
455572 TGAATATTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATTAAAAATTGTTAAAAATA
66 TGAATATTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATTAAAAATTGTTAAAAATA
* *
455637 AGTACAGATAATTTTTATTTTAATAAGACAACACTACACTAAAAAAAATATTATTCACCAACACT
131 AGTATAGATAATTTTTATTTTAATAAG---GCACTACACT-AAAAAAATATTATTCACCAACAC-
**
455702 TTTTTTTTTGGGGTTTAGTTTATAAAAGTGTTGGGTTTTCTCATTTAATTTTTTATTTTTCTTGC
191 --TTTTTTTGGGG--GGGTTTATAAAAGTGTTGGGTTTTCTCATTTAATTTTTTATTTTTCTTGC
*
455767 ATAAATAAAGTGCCCTTGATAAGGACACATTAAGCCTGTATTAAAAAAAAATCCTTTCATTTACT
252 ATAAATAAAGTGCCCTTGATAAGGACACATTAAGCCTATATTAAAAAAAAATCCTTTCATTTACT
* *
455832 GAAAACACATTTTAAACCCATTAAATTCTTAAGCCCAAAACAATTTTTTCATCTTATTGATAGCT
317 CAAAATACATTTTAAACCCATTAAATTCTTAAGCCCAAAACAATTTTTTCATCTTATTGATAGCT
* * *
455897 TGCCCATTAACTTCTTGATCTAAATCTCTAAGTTTTTTTTGATAGCCAGCCGAAAATAGCTTTTA
382 TGCCCATTAACTTCTTGATCTAAATCTCTGAGTTTATTTTGATAGCCAGCCGAAAATAGCTTTTG
* *
455962 TCATGATATGGCATGATAAGGATCGTATTAAAGATGGAAAGTATAGGCATCCAGTTGATTCCCTT
447 CCATGATATGGCATGATAAGGGTCGTATTAAAGATGGAAAGTATAGGCATCCAGTTGATTCCCTT
* *
456027 GTTTGGAAATCTTGTGATTTATAGTATCTTAATTTTGCTTTAGAT-CTTCATAATGTTAGGCTAG
512 GCTTGGAAATCTTTTGATTTATAGTATCTTAATTTTGCTTTAGATCCTT-ATAATGTTAGGCTAG
*
456091 GCTTGGCTACTAATGGATTTAATCCATTTAAGACAATAAATAATAAGTATAGTGTTTGGCCTGTT
576 GCTTGGCTACTAATGGATTTAATCCATTTAAGACAATGAATAATAAGTATAGTGTTTGGCCTGTT
456156 ATATTGATACCATACAATTTGCCTCCTTAGTTGTCTGTGAAAGAGTCAAGTTTTATTCTTTCCTT
641 ATATTGATACCATACAATTTGCCTCCTTAGTTGTCTGTGAAAGAGTCAAGTTTTATTCTTTCCTT
456221 AATGATTTCGTGTAAGAATAGACCTAGAAATAATATTGATGTTTACTTACAACCTTTGATACAAG
706 AATGATTTCGTGTAAGAATAGACCTAGAAATAATATTGATGTTTACTTACAACCTTTGATACAAG
* * *
456286 AACTAAAAGAAATATGAGAAATTGGTGTAAACATTTTTGATGGTTTTGCTAGAGAAAATTTTCAA
771 AATTAAAAGAATTATGAGAAATTGGTGTAAACATTTTTGATGGTTTTGCTAGAGAGAATTTTCAA
* *
456351 TTACTTATCGCTGTAAAATGGACAAC-AA--A---
836 TTACGTATCGCTGTAAAGTGGACAACAAATGACTT
* * *
456380 -TGACTTTCGATAAAACTTTATATTCAAGTCTAATTTCACGTCGATAAGGTTAAGCTCATAAATT
1 TTGACTTTCGATAAAAATTTATATTCAAGTCTGATTTCACGTCGATAAGGTTAAGCTCATAATTT
456444 TGAATATTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATTAAAAATTGTTAAAAATA
66 TGAATATTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATTAAAAATTGTTAAAAATA
*
456509 AGTATAGATAATTTTTATTTTAATAAGGCAACACCACACTAAAAAAATTATTATTCACCAACACT
131 AGTATAGATAATTTTTATTTTAATAAGG---CACTACACTAAAAAAA-TATTATTCACCAACACT
**** *
456574 TTTTTTTCTAGGGTTTATAAAAGTATTGGGTTTTCTCATTTAA-TTTTTATTTTTCTTAGCATAA
192 TTTTTTGGGGGGGTTTATAAAAGTGTTGGGTTTTCTCATTTAATTTTTTATTTTTCTT-GCATAA
**
456638 ATAAAGTGCCCTTGATAAGGACACATTAAGCCTATATTAAAAAAAAAAGCTTTCATTTACTCAAA
256 ATAAAGTGCCCTTGATAAGGACACATTAAGCCTATATTAAAAAAAAATCCTTTCATTTACTCAAA
* * * *
456703 ATACATTTTTAACCCACTAAATTCTCAAGCCCAAAACAATATTTTTTATCTTATTGATAGCTTGC
321 ATACATTTTAAACCCATTAAATTCTTAAGCCCAAAACAAT-TTTTTCATCTTATTGATAGCTTGC
* * * *
456768 CCATTAACTTCTTGATCTATATCTTTGAGTTTATTTTGATAGCTAGTCGAAAATAGCTTTTGCCA
385 CCATTAACTTCTTGATCTAAATCTCTGAGTTTATTTTGATAGCCAGCCGAAAATAGCTTTTGCCA
* *
456833 TGATATGGCATGATAAGGGTCGTATTAAAGATGGAAAATATAGGGATCCAGTTGATTCCCTTGCT
450 TGATATGGCATGATAAGGGTCGTATTAAAGATGGAAAGTATAGGCATCCAGTTGATTCCCTTGCT
*
456898 TGGAAATCTTTTGATTTATAGTATCTTAATTTTGCTTTAGATCCTTATAATGTTAGGTTAGGCTT
515 TGGAAATCTTTTGATTTATAGTATCTTAATTTTGCTTTAGATCCTTATAATGTTAGGCTAGGCTT
* * * *
456963 GGCTGCTGATGGATTTAATCCA-TT--GACAATGAATAATAAGTACAATGTTTGGCCTGTTATAT
580 GGCTACTAATGGATTTAATCCATTTAAGACAATGAATAATAAGTATAGTGTTTGGCCTGTTATAT
*
457025 TGATACCATACAATTTGCCTCCTTAGCTGTCTGTGAAAGAGTCAAGTTTTATTCTTTCCTTAATG
645 TGATACCATACAATTTGCCTCCTTAGTTGTCTGTGAAAGAGTCAAGTTTTATTCTTTCCTTAATG
*
457090 ATTTCGAGTAAGAATAGACCTAGAAATAATATTGATGTTTACTTACAACCTTTGATACAAGAATT
710 ATTTCGTGTAAGAATAGACCTAGAAATAATATTGATGTTTACTTACAACCTTTGATACAAGAATT
* * *
457155 AAAAGAATTATGAGAAATTGGAGTAAACATTTTTGATTGTTTTGCTTGAGAGAATTTTCAATTAC
775 AAAAGAATTATGAGAAATTGGTGTAAACATTTTTGATGGTTTTGCTAGAGAGAATTTTCAATTAC
457220 GTATCGCTGTAAAGTGGACAACAAATGACTT
840 GTATCGCTGTAAAGTGGACAACAAATGACTT
*
457251 TCTGGCAACAAATAACTTTCGATAAAAATTTATATTCAAGTATGATTTCACGTCGATAAGGTTAA
1 T-T-G---------ACTTTCGATAAAAATTTATATTCAAGTCTGATTTCACGTCGATAAGGTTAA
* *
457316 GCTCATAATTTTGAATGTTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATCAAAAAT
55 GCTCATAATTTTGAATATTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATTAAAAAT
*
457381 TGCTAAAAATAAGTATAGATAATTTTTATTTTAATAAGGCA-TACACTAAAAAAATATTATTCAC
120 TGTTAAAAATAAGTATAGATAATTTTTATTTTAATAAGGCACTACACTAAAAAAATATTATTCAC
* *
457445 TAACAC-TTTTTTGGGGGGGTTTATAAAAGTGTTGGGTTTTCTCATTTAATTTTTTTGTTTTTCT
185 CAACACTTTTTTTGGGGGGGTTTATAAAAGTGTTGGGTTTTCTCATTTAA-TTTTTTATTTTTCT
*
457509 TGGCATAAATAAAGTGCCCTTGATAAGGACACATTAAGCCTATATTAAAAAAAAATCCATTCATT
249 T-GCATAAATAAAGTGCCCTTGATAAGGACACATTAAGCCTATATTAAAAAAAAATCCTTTCATT
*
457574 TACTCAAAATACATTTTAAACCCATTAAATTCTTAAGCCCAAAATAATTTTTTCATCTTATTGAT
313 TACTCAAAATACATTTTAAACCCATTAAATTCTTAAGCCCAAAACAATTTTTTCATCTTATTGAT
* * *
457639 AGCTTGCACGTTAACTTCTTGATCTAAATCTCTGAGTTTGTTTTGATAGCCAGCCGAAAATAGCT
378 AGCTTGCCCATTAACTTCTTGATCTAAATCTCTGAGTTTATTTTGATAGCCAGCCGAAAATAGCT
* * *
457704 TTTGCCATGATATGGCATGATGAGGGTCATATTAAAGATTGGAAAGTATAGGCATCTAGTTGATT
443 TTTGCCATGATATGGCATGATAAGGGTCGTATTAAAGA-TGGAAAGTATAGGCATCCAGTTGATT
457769 CCCTTGCTTGGAAATCTTTTGATTTATAGTATCTTAATTTTGCTTTAGATCCTTATAATGTTAGG
507 CCCTTGCTTGGAAATCTTTTGATTTATAGTATCTTAATTTTGCTTTAGATCCTTATAATGTTAGG
* *
457834 CTAAGCTTGGCTACTAAGGGATTTAATCCATTTAAGACAATGAATAATAAGTATAGTGTTTGGCC
572 CTAGGCTTGGCTACTAATGGATTTAATCCATTTAAGACAATGAATAATAAGTATAGTGTTTGGCC
* *
457899 TGTCATATTGATACCATACAATTTGCCTCCTTAGTTGTATGTGAAAGAGTCAAGTTTTATTCTTT
637 TGTTATATTGATACCATACAATTTGCCTCCTTAGTTGTCTGTGAAAGAGTCAAGTTTTATTCTTT
* *
457964 CCTTAATGATTCCGTGCAAGAATAGACCTAGAAATAATATTGATGTTTACTTACAACCTTTGATA
702 CCTTAATGATTTCGTGTAAGAATAGACCTAGAAATAATATTGATGTTTACTTACAACCTTTGATA
*
458029 CAAGAATTAAAAGAATTATGAGAAATTGGTGTAAACATTTTTGATGGTTTTGCTGGAGAGAATTT
767 CAAGAATTAAAAGAATTATGAGAAATTGGTGTAAACATTTTTGATGGTTTTGCTAGAGAGAATTT
*
458094 TCAATTACGTATTGCTGTAAAGTGGACAACAAATGACTT
832 TCAATTACGTATCGCTGTAAAGTGGACAACAAATGACTT
458133 TT
1 TT
458135 CGACATATAG
Statistics
Matches: 1611, Mismatches: 105, Indels: 62
0.91 0.06 0.03
Matches are distributed among these distances:
864 3 0.00
865 245 0.15
866 47 0.03
867 135 0.08
868 221 0.14
869 10 0.01
871 7 0.00
872 130 0.08
873 1 0.00
874 1 0.00
877 38 0.02
878 125 0.08
879 242 0.15
880 4 0.00
881 1 0.00
882 253 0.16
883 148 0.09
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.38
Consensus pattern (870 bp):
TTGACTTTCGATAAAAATTTATATTCAAGTCTGATTTCACGTCGATAAGGTTAAGCTCATAATTT
TGAATATTTAAAAATTTATGTTAGTAAATGAAATCATATTATTTTATTAAAAATTGTTAAAAATA
AGTATAGATAATTTTTATTTTAATAAGGCACTACACTAAAAAAATATTATTCACCAACACTTTTT
TTGGGGGGGTTTATAAAAGTGTTGGGTTTTCTCATTTAATTTTTTATTTTTCTTGCATAAATAAA
GTGCCCTTGATAAGGACACATTAAGCCTATATTAAAAAAAAATCCTTTCATTTACTCAAAATACA
TTTTAAACCCATTAAATTCTTAAGCCCAAAACAATTTTTTCATCTTATTGATAGCTTGCCCATTA
ACTTCTTGATCTAAATCTCTGAGTTTATTTTGATAGCCAGCCGAAAATAGCTTTTGCCATGATAT
GGCATGATAAGGGTCGTATTAAAGATGGAAAGTATAGGCATCCAGTTGATTCCCTTGCTTGGAAA
TCTTTTGATTTATAGTATCTTAATTTTGCTTTAGATCCTTATAATGTTAGGCTAGGCTTGGCTAC
TAATGGATTTAATCCATTTAAGACAATGAATAATAAGTATAGTGTTTGGCCTGTTATATTGATAC
CATACAATTTGCCTCCTTAGTTGTCTGTGAAAGAGTCAAGTTTTATTCTTTCCTTAATGATTTCG
TGTAAGAATAGACCTAGAAATAATATTGATGTTTACTTACAACCTTTGATACAAGAATTAAAAGA
ATTATGAGAAATTGGTGTAAACATTTTTGATGGTTTTGCTAGAGAGAATTTTCAATTACGTATCG
CTGTAAAGTGGACAACAAATGACTT
Found at i:458436 original size:206 final size:206
Alignment explanation
Indices: 458082--458494 Score: 826
Period size: 206 Copynumber: 2.0 Consensus size: 206
458072 ATGGTTTTGC
458082 TGGAGAGAATTTTCAATTACGTATTGCTGTAAAGTGGACAACAAATGACTTTTCGACATATAGAG
1 TGGAGAGAATTTTCAATTACGTATTGCTGTAAAGTGGACAACAAATGACTTTTCGACATATAGAG
458147 ATTTGTTTAGATGGGATATTAAAAGTCATTTTGCGTGTCCTTATTATGCTATGGAAACATGTTCT
66 ATTTGTTTAGATGGGATATTAAAAGTCATTTTGCGTGTCCTTATTATGCTATGGAAACATGTTCT
458212 TTATGGCTACATCATGGGGGTAAATATTGTTTCATGGGTCATCTTCGGTTTTTAGATATTATTCA
131 TTATGGCTACATCATGGGGGTAAATATTGTTTCATGGGTCATCTTCGGTTTTTAGATATTATTCA
458277 TGAATTTTGGA
196 TGAATTTTGGA
458288 TGGAGAGAATTTTCAATTACGTATTGCTGTAAAGTGGACAACAAATGACTTTTCGACATATAGAG
1 TGGAGAGAATTTTCAATTACGTATTGCTGTAAAGTGGACAACAAATGACTTTTCGACATATAGAG
458353 ATTTGTTTAGATGGGATATTAAAAGTCATTTTGCGTGTCCTTATTATGCTATGGAAACATGTTCT
66 ATTTGTTTAGATGGGATATTAAAAGTCATTTTGCGTGTCCTTATTATGCTATGGAAACATGTTCT
458418 TTATGGCTACATCATGGGGGTAAATATTGTTTCATGGGTCATCTTCGGTTTTTAGATATTATTCA
131 TTATGGCTACATCATGGGGGTAAATATTGTTTCATGGGTCATCTTCGGTTTTTAGATATTATTCA
458483 TGAATTTTGGA
196 TGAATTTTGGA
458494 T
1 T
458495 TGATCCTTCT
Statistics
Matches: 207, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
206 207 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.39
Consensus pattern (206 bp):
TGGAGAGAATTTTCAATTACGTATTGCTGTAAAGTGGACAACAAATGACTTTTCGACATATAGAG
ATTTGTTTAGATGGGATATTAAAAGTCATTTTGCGTGTCCTTATTATGCTATGGAAACATGTTCT
TTATGGCTACATCATGGGGGTAAATATTGTTTCATGGGTCATCTTCGGTTTTTAGATATTATTCA
TGAATTTTGGA
Found at i:463819 original size:16 final size:16
Alignment explanation
Indices: 463795--463825 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
463785 AAAAAATCTA
463795 AAATATTAGATTTAAG
1 AAATATTAGATTTAAG
*
463811 AAATTTTAGATTTAA
1 AAATATTAGATTTAA
463826 TTGTTGACCT
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:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
AAATATTAGATTTAAG
Found at i:463963 original size:156 final size:155
Alignment explanation
Indices: 463655--463963 Score: 469
Period size: 156 Copynumber: 2.0 Consensus size: 155
463645 CTTTTAGATC
* *
463655 AAATTTTAGGTTTAATTGTTGACCTTTCACCCTTCGGCAAGACTAGTATTGAAGCAATCCAAAAG
1 AAATTTTAGATTTAATTGTTGACCTTTCACCCTTCGGAAAGACTAGTATTGAAGCAATCCAAAAG
* ** * *
463720 AGCAAAATTTTACTCATATTGCAAGTAGTTTTTTTTTGTTATGAGATGACTCATAAATTTTTTTA
66 AGCAAAATTTTACCCATATTGCAAACAG-TTTTTTCTCTTATGAGATGACTCATAAATTTTTTTA
463785 AAAAAATCTAAAATATTAGATTTAAG
130 AAAAAATCTAAAATATTAGATTTAAG
* * *
463811 AAATTTTAGATTTAATTGTTGACCTTTCACCTTTTGGAAAAGAGTAGTATTGAAGCAATCCAAAA
1 AAATTTTAGATTTAATTGTTGACCTTTCACCCTTCGG-AAAGACTAGTATTGAAGCAATCCAAAA
463876 GAGCAAAATTTTACCCATATTGCAAACAG-TTTTTCTCTTATGAGATGACTCAT-AATTGTTTTT
65 GAGCAAAATTTTACCCATATTGCAAACAGTTTTTTCTCTTATGAGATGACTCATAAATT-TTTTT
*
463939 AAAAAAAATTTAAAATATTAGATTT
129 -AAAAAAATCTAAAATATTAGATTT
463964 GAGGTTTTGT
Statistics
Matches: 139, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
154 4 0.03
155 27 0.19
156 57 0.41
157 51 0.37
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (155 bp):
AAATTTTAGATTTAATTGTTGACCTTTCACCCTTCGGAAAGACTAGTATTGAAGCAATCCAAAAG
AGCAAAATTTTACCCATATTGCAAACAGTTTTTTCTCTTATGAGATGACTCATAAATTTTTTTAA
AAAAATCTAAAATATTAGATTTAAG
Found at i:464614 original size:21 final size:21
Alignment explanation
Indices: 464590--464632 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
464580 TAAAGTTGAA
464590 AATATATACATAAATAGATAT
1 AATATATACATAAATAGATAT
* *
464611 AATATATACATATATATATAT
1 AATATATACATAAATAGATAT
464632 A
1 A
464633 TAAAGCACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
AATATATACATAAATAGATAT
Found at i:468887 original size:33 final size:33
Alignment explanation
Indices: 468845--468914 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
468835 GGCAGTAGCT
468845 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
468878 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
468911 TACA
1 TACA
468915 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:468888 original size:13 final size:13
Alignment explanation
Indices: 468870--468894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
468860 CAAAAAAATA
468870 TGTATCGATACAT
1 TGTATCGATACAT
468883 TGTATCGATACA
1 TGTATCGATACA
468895 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:470618 original size:2 final size:2
Alignment explanation
Indices: 470611--470639 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
470601 TGATTCAACC
470611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
470640 GATTTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:472605 original size:17 final size:17
Alignment explanation
Indices: 472563--472605 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
472553 TGAGATTGAA
*
472563 TGTATGCAAGAGGAGTTT
1 TGTA-GCAAGAGGAGTTG
472581 TGCT-GCAAGAGGAGTTG
1 TG-TAGCAAGAGGAGTTG
472598 TGTAGCAA
1 TGTAGCAA
472606 TTCCTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 1 0.05
17 18 0.82
18 2 0.09
19 1 0.05
ACGTcount: A:0.28, C:0.09, G:0.35, T:0.28
Consensus pattern (17 bp):
TGTAGCAAGAGGAGTTG
Found at i:473117 original size:46 final size:46
Alignment explanation
Indices: 473076--473188 Score: 163
Period size: 46 Copynumber: 2.5 Consensus size: 46
473066 AGTTTGGTAA
* *
473076 AGGATTTGTAGCTTTCTCTGTGCAAAAACTACTCATTGTTTGTTGG
1 AGGATTTATAGCTTTCTCTATGCAAAAACTACTCATTGTTTGTTGG
** * *
473122 AGGATTTATAGCTTTCTCTATGTTAAAACTATTTATTGTTTGTTGG
1 AGGATTTATAGCTTTCTCTATGCAAAAACTACTCATTGTTTGTTGG
*
473168 AGGTTTTATAGCTTTCTCTAT
1 AGGATTTATAGCTTTCTCTAT
473189 ATAAAAGCTA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (46 bp):
AGGATTTATAGCTTTCTCTATGCAAAAACTACTCATTGTTTGTTGG
Found at i:473212 original size:46 final size:46
Alignment explanation
Indices: 473084--473220 Score: 129
Period size: 46 Copynumber: 3.0 Consensus size: 46
473074 AAAGGATTTG
* * * *
473084 TAGCTTTCTCTGTGCA-AAAACTA-CTCATTGTTTGTTGGAGGATTTA
1 TAGCTTTCTCTATG-ATAAAACTATCT-AATGTGTGTTGGAGGTTTTA
* * * *
473130 TAGCTTTCTCTATGTTAAAACTATTTATTGTTTGTTGGAGGTTTTA
1 TAGCTTTCTCTATGATAAAACTATCTAATGTGTGTTGGAGGTTTTA
473176 TAGCTTTCTCTAT-ATAAAAGCTA-CTAGATGTGTGTTGGATGGTTT
1 TAGCTTTCTCTATGATAAAA-CTATCTA-ATGTGTGTTGGA-GGTTT
473221 GTAACTTTAT
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
45 7 0.09
46 65 0.83
47 6 0.08
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (46 bp):
TAGCTTTCTCTATGATAAAACTATCTAATGTGTGTTGGAGGTTTTA
Found at i:474816 original size:15 final size:15
Alignment explanation
Indices: 474793--474823 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
474783 CATAATGTGA
*
474793 TTTTTCTTTTAAATG
1 TTTTCCTTTTAAATG
474808 TTTTCCTTTTAAATG
1 TTTTCCTTTTAAATG
474823 T
1 T
474824 GATTATGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTTCCTTTTAAATG
Found at i:475514 original size:15 final size:15
Alignment explanation
Indices: 475494--475529 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
475484 CTGAAGTATA
475494 ATTTAAGTAATTCTT
1 ATTTAAGTAATTCTT
475509 ATTTAAGTAATTCTT
1 ATTTAAGTAATTCTT
*
475524 ACTTAA
1 ATTTAA
475530 TTTTTATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (15 bp):
ATTTAAGTAATTCTT
Found at i:475619 original size:31 final size:31
Alignment explanation
Indices: 475581--475673 Score: 186
Period size: 31 Copynumber: 3.0 Consensus size: 31
475571 AGAAAGTAAG
475581 CGAAGTACCTTGATTCTAAAACCAAAATGCA
1 CGAAGTACCTTGATTCTAAAACCAAAATGCA
475612 CGAAGTACCTTGATTCTAAAACCAAAATGCA
1 CGAAGTACCTTGATTCTAAAACCAAAATGCA
475643 CGAAGTACCTTGATTCTAAAACCAAAATGCA
1 CGAAGTACCTTGATTCTAAAACCAAAATGCA
475674 TATTAGGGTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (31 bp):
CGAAGTACCTTGATTCTAAAACCAAAATGCA
Found at i:483403 original size:2 final size:2
Alignment explanation
Indices: 483390--483429 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
483380 CTTTCAACAC
*
483390 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
483430 GTTTTAACTT
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:485633 original size:28 final size:28
Alignment explanation
Indices: 485572--485653 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
485562 TTTTGGAGAT
*
485572 AATAACGGGGTTGGAGTGTTCCCTCG--GA
1 AATAACGGGGTTGGAGT-ATCCC-CGATGA
*
485600 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGGGGTTGGAGTATCCCCGATGA
* *
485628 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
485654 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 4 0.09
28 41 0.87
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (28 bp):
AATAACGGGGTTGGAGTATCCCCGATGA
Found at i:485795 original size:51 final size:51
Alignment explanation
Indices: 485633--485805 Score: 204
Period size: 52 Copynumber: 3.4 Consensus size: 51
485623 GATGAAATAA
* *
485633 CGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAAT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAAT
* * * * *
485685 CG-GTGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAAC
1 CGAG-GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAAT
* *** *
485737 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAAT
485788 CGAGGTTGGAGTATCCCC
1 CGAGGTTGGAGTATCCCC
485806 TCGGAAATAA
Statistics
Matches: 101, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
51 38 0.38
52 52 0.51
53 11 0.11
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAAT
Found at i:485826 original size:28 final size:27
Alignment explanation
Indices: 485791--485862 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
485781 ATAAAGTCGA
**
485791 GGTTGGAGTATCCCCTCGGAAATAACGG
1 GGTTGGAGTATCCCCGAGG-AATAACGG
* *
485819 GGTTGGAGTATCCCCGATGATTAACGG
1 GGTTGGAGTATCCCCGAGGAATAACGG
*
485846 GGTTGGAGTGTCCCCGA
1 GGTTGGAGTATCCCCGA
485863 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.24
Consensus pattern (27 bp):
GGTTGGAGTATCCCCGAGGAATAACGG
Found at i:485914 original size:54 final size:51
Alignment explanation
Indices: 485847--485977 Score: 131
Period size: 51 Copynumber: 2.5 Consensus size: 51
485837 GATTAACGGG
* ** *
485847 GTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTTG-AAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAATG---TTTTGAAAATAAAATCAGA
*
485901 GTTGGAGTATCCCCGATTAT-AGAAAATTAATGTTTTGAAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAATGTTTTGAAAATAAAATCAGA
* *
485952 GTTGGAATATCCTCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
485978 TTGAGCAACT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
50 5 0.08
51 29 0.45
52 4 0.06
53 9 0.14
54 18 0.28
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAATGTTTTGAAAATAAAATCAGA
Found at i:485928 original size:211 final size:211
Alignment explanation
Indices: 485580--485969 Score: 586
Period size: 211 Copynumber: 1.8 Consensus size: 211
485570 ATAATAACGG
* * *
485580 GGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
1 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
* *
485645 ATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCCCGATTAAA
66 ATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
** * * *
485710 GGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATT
131 GGAAAATTAATGTTTTGAAAATAAAACCAGAGTTGGAATATCCCCGATTATGAAAAATCAATATT
485775 TTGGAAATAAAGTCGA
196 TTGGAAATAAAGTCGA
* *
485791 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGT
1 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
* * *
485855 GTCCCCGATTGTGAAGAAATTGGTGTTTTTTTGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
66 ATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
* * *
485920 TA-GAAAATTAATGTTTTGAAAATAAAATCAGAGTTGGAATATCCTCGATT
129 AAGGAAAATTAATGTTTTGAAAATAAAACCAGAGTTGGAATATCCCCGATT
485970 GTGGAGAATT
Statistics
Matches: 159, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
210 28 0.18
211 93 0.58
212 38 0.24
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.30
Consensus pattern (211 bp):
GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
ATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
GGAAAATTAATGTTTTGAAAATAAAACCAGAGTTGGAATATCCCCGATTATGAAAAATCAATATT
TTGGAAATAAAGTCGA
Found at i:488346 original size:13 final size:13
Alignment explanation
Indices: 488328--488353 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
488318 ACAAAGATCC
488328 ATGTATCGATACA
1 ATGTATCGATACA
488341 ATGTATCGATACA
1 ATGTATCGATACA
488354 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:488349 original size:33 final size:33
Alignment explanation
Indices: 488307--488373 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
488297 AAAATTTCCA
***
488307 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
488340 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
488373 A
1 A
488374 TTTCCTTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:488417 original size:19 final size:18
Alignment explanation
Indices: 488393--488460 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
488383 TAGTAGCTAA
488393 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
488412 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
488427 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
*
488444 TTATGTATCAATACAAA
1 TTATGTATCGATACAAA
488461 TCATTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.57
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:488433 original size:13 final size:13
Alignment explanation
Indices: 488415--488439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
488405 ACAATACTTA
488415 TGTATCGATACAT
1 TGTATCGATACAT
488428 TGTATCGATACA
1 TGTATCGATACA
488440 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:488437 original size:32 final size:32
Alignment explanation
Indices: 488396--488458 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
488386 TAGCTAATTA
* *
488396 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCAATACAT
488428 TGTATCGATACAAAACTTATGTATCAATACA
1 TGTATCGATACAAAACTTATGTATCAATACA
488459 AATCATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCAATACAT
Found at i:488522 original size:21 final size:22
Alignment explanation
Indices: 488496--488553 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
488486 GTTGGGACCC
*
488496 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGTACAAA
*
488517 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTACAAA
488538 TGTATCGATACATTTG
1 TGTATCGATACATTTG
488554 GGATTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 26 0.81
22 2 0.06
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (22 bp):
TGTATCGATACATTTGTACAAA
Found at i:488679 original size:31 final size:32
Alignment explanation
Indices: 488627--488689 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
488617 AAAAGTCATA
*
488627 AAAATCTAAAAAAACCTTTTTCGCCGGGCGCC
1 AAAATCTAAAAAAACCATTTTCGCCGGGCGCC
* *
488659 AAAATCT-AAAAAAGCATTTTCGCTGGGCGCC
1 AAAATCTAAAAAAACCATTTTCGCCGGGCGCC
488690 GTTGGCGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (32 bp):
AAAATCTAAAAAAACCATTTTCGCCGGGCGCC
Found at i:489413 original size:55 final size:55
Alignment explanation
Indices: 489329--490006 Score: 989
Period size: 55 Copynumber: 12.3 Consensus size: 55
489319 ATAAACTGTA
* * * * * *
489329 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
489384 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
489439 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
489494 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTTTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
489549 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
489604 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
489659 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
489714 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
489769 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
489824 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
489879 TCCTACTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
489934 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
489989 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
490007 AAAAAGCAGA
Statistics
Matches: 576, Mismatches: 34, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
54 18 0.03
55 540 0.94
56 18 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:489493 original size:29 final size:28
Alignment explanation
Indices: 489403--489933 Score: 87
Period size: 28 Copynumber: 19.2 Consensus size: 28
489393 TTGAGGACTG
489403 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * ** *
489431 GAAAGGTGTCCTGC-TCTT-TG-GGGAATG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
489458 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
489486 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
489514 AAA-ATGCCACCAACTTTTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
489541 GAAAGGTGTCCTGC-TCTT-TGAGGACTGG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
*
489569 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * *
489596 AAGAGGTGTCCTGC-TCTT-TGAGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
489623 GAAGGCGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
489651 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
489678 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
489706 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
489734 AAA-ATGCCACCAACTTGGGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
489761 GAAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 -AAAGGTG-CCACCAACTTGTGTGGG-CTTT
*
489788 AAAGGTGCCACCAACTTATGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
489816 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
*
489844 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
* * * **
489871 GAAAGGTGTCCTA-C-TCTT-TGAGGACTGG
1 -AAAGGTG-CC-ACCAACTTGTGTGGGCTTT
*
489899 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
489926 AAGAGGTG
1 AA-AGGTG
489934 TCCTGCTCTT
Statistics
Matches: 329, Mismatches: 122, Indels: 102
0.59 0.22 0.18
Matches are distributed among these distances:
24 1 0.00
25 27 0.08
26 60 0.18
27 71 0.22
28 79 0.24
29 63 0.19
30 27 0.08
31 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (28 bp):
AAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:491767 original size:18 final size:18
Alignment explanation
Indices: 491736--491770 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
491726 CTGTAAAGTG
491736 GACAACAAACGACTTTCC
1 GACAACAAACGACTTTCC
* *
491754 GACAATAAATGACTTTC
1 GACAACAAACGACTTTC
491771 GATAAAAATT
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:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (18 bp):
GACAACAAACGACTTTCC
Done.