Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 138 of 318
Found at i:42199835 original size:71 final size:71
Alignment explanation
Indices: 42199749--42199912 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
42199739 CGATTTGTCT
42199749 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42199814 CTTTCA
66 CTTTCA
42199820 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42199885 CTTTCA
66 CTTTCA
42199891 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
42199913 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:42199950 original size:71 final size:70
Alignment explanation
Indices: 42199749--42199946 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
42199739 CGATTTGTCT
* * * *
42199749 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
42199814 CTTTCA
65 CTTTCA
* * * *
42199820 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
42199885 CTTTCA
65 CTTTCA
* *
42199891 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
42199947 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:42207373 original size:71 final size:71
Alignment explanation
Indices: 42207318--42207481 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
42207308 CGATTTGTCT
42207318 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42207383 CTTTCA
66 CTTTCA
42207389 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42207454 CTTTCA
66 CTTTCA
42207460 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
42207482 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:42207519 original size:71 final size:70
Alignment explanation
Indices: 42207318--42207515 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
42207308 CGATTTGTCT
* * * *
42207318 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
42207383 CTTTCA
65 CTTTCA
* * * *
42207389 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
42207454 CTTTCA
65 CTTTCA
* *
42207460 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
42207516 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:42214700 original size:28 final size:28
Alignment explanation
Indices: 42214635--42214735 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
42214625 ATAGTGAATC
*
42214635 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
42214664 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
42214692 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
42214722 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42214736 CATACCCTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:42214784 original size:29 final size:29
Alignment explanation
Indices: 42214723--42214853 Score: 174
Period size: 29 Copynumber: 4.5 Consensus size: 29
42214713 TTTTAAACCC
*** *
42214723 GCACACTTAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
42214751 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
42214781 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
*
42214810 GCACACTTAGTGCCATATATTTTCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
42214839 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
42214854 ATCTCGTCAC
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
29 89 0.99
30 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:42219352 original size:28 final size:28
Alignment explanation
Indices: 42219312--42219410 Score: 101
Period size: 28 Copynumber: 3.5 Consensus size: 28
42219302 GTAATAAGCC
*
42219312 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
42219340 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* ** * * *
42219368 TGCACACTTAGTGCTATACCATTTGAACC
1 CGCACACTTAGTGCT-TAATAATCGAACT
42219397 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42219411 CAATTTGTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
27 2 0.03
28 36 0.62
29 18 0.31
30 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:42229531 original size:40 final size:40
Alignment explanation
Indices: 42229446--42229590 Score: 215
Period size: 40 Copynumber: 3.7 Consensus size: 40
42229436 ACTTGAGGTA
*
42229446 TTATCCGGGCTTAAAGACCCGCAGGCTAT--AGCTGGAATG
1 TTATCCGGGCTTAAAGACCCGCAGGCT-TCGTGCTGGAATG
*
42229485 TTATCCGGGCTTAAAGACCCACAGGCTTCGTGCTGGAATG
1 TTATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATG
* *
42229525 TTATCCGGGCTTAAAAACCCGTAGGCTTCGTGCTGGAATG
1 TTATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATG
*
42229565 TTATCCGGGC-TAGAGACCCGCAGGCT
1 TTATCCGGGCTTAAAGACCCGCAGGCT
42229591 ACGAGTTGGT
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
38 1 0.01
39 39 0.41
40 56 0.58
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATG
Found at i:42238459 original size:40 final size:40
Alignment explanation
Indices: 42238401--42238568 Score: 175
Period size: 40 Copynumber: 4.2 Consensus size: 40
42238391 CAATTGAATG
* *
42238401 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTG-CTT
*
42238442 -TATCCGGGCTAATACCCGAAGGC-ATTCGTGCAAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGCTT
* * *
42238481 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGT-CGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGC-TT
** *
42238521 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTGCTT
42238561 ATATCCGG
1 ATATCCGG
42238569 TTGTATTCCG
Statistics
Matches: 110, Mismatches: 9, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
39 8 0.07
40 98 0.89
41 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGCTT
Found at i:42238539 original size:80 final size:79
Alignment explanation
Indices: 42238401--42238568 Score: 230
Period size: 80 Copynumber: 2.1 Consensus size: 79
42238391 CAATTGAATG
* * *
42238401 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTTTATCCGGGCTAATACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGA-TTTATCCGGGCTAAGACCCGAAGGCA
*
42238466 TTCGTGCAAGTTGTT
65 TTCGTGCAAGTGGTT
* *
42238481 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGTCG-TTATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT-GATT-TATCCGGGCTAAGACCCGAAGGC
**
42238545 ATTCGTGCGTGTGGTT
64 ATTCGTGCAAGTGGTT
42238561 ATATCCGG
1 ATATCCGG
42238569 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 2 0.03
80 75 0.96
81 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATTTATCCGGGCTAAGACCCGAAGGCAT
TCGTGCAAGTGGTT
Found at i:42241874 original size:16 final size:17
Alignment explanation
Indices: 42241844--42241876 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
42241834 AGAAAAGACC
*
42241844 GAATCTGTGCTAGTGGT
1 GAATCTGTGCCAGTGGT
42241861 GAAT-TGTGCCAGTGGT
1 GAATCTGTGCCAGTGGT
42241877 TTGTGAATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.18, C:0.12, G:0.36, T:0.33
Consensus pattern (17 bp):
GAATCTGTGCCAGTGGT
Found at i:42245631 original size:39 final size:40
Alignment explanation
Indices: 42245507--42245675 Score: 216
Period size: 40 Copynumber: 4.2 Consensus size: 40
42245497 CGGGATTTAA
* * * * *
42245507 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
42245547 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42245587 CCGGATATATCAACTCGCACGAATGCCTTC-GGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42245626 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42245666 CCGGATATAT
1 CCGGATATAT
42245676 TTCCAATGTT
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 40 0.36
40 71 0.64
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:42245670 original size:79 final size:80
Alignment explanation
Indices: 42245507--42245675 Score: 216
Period size: 79 Copynumber: 2.1 Consensus size: 80
42245497 CGGGATTTAA
* * * * * * *
42245507 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAACCCGGATTTGGTGACTTGCACAAAGG
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCATAACCCGGATATGATAACTCGCACAAAGG
42245572 CCTTCGGGTCTTAGC
66 CCTTCGGGTCTTAGC
* * * *
42245587 CCGGATATATCAACTCGCACGAATGCCTTC-GGTCTTAGCCCGGATAT-ATCAACTCGCACGAAT
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCATAACCCGGATATGAT-AACTCGCACAAAG
42245650 GCCTTCGGGTCTTAGC
65 GCCTTCGGGTCTTAGC
42245666 CCGGATATAT
1 CCGGATATAT
42245676 TTCCAATGTT
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
78 1 0.01
79 49 0.64
80 27 0.35
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCATAACCCGGATATGATAACTCGCACAAAGG
CCTTCGGGTCTTAGC
Found at i:42253705 original size:40 final size:40
Alignment explanation
Indices: 42253597--42253766 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
42253587 CGGGATTTAA
* * * * *
42253597 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
42253637 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42253677 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42253717 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42253757 CCGGATATAT
1 CCGGATATAT
42253767 TTCCAATGTT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 112 0.99
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:42258501 original size:27 final size:27
Alignment explanation
Indices: 42258410--42258886 Score: 305
Period size: 27 Copynumber: 17.7 Consensus size: 27
42258400 ATACCCCTAG
* *
42258410 TTGTAAAATTACC-AAGGTACCCTCGGT
1 TTGTAAAATTACCGAA-ATACCCTCGAT
* * * *
42258437 TTATAAAATTACCAAAATATCATCGA-
1 TTGTAAAATTACCGAAATACCCTCGAT
** *
42258463 TTGTAAAATTACTAAAATACCTTCGAT
1 TTGTAAAATTACCGAAATACCCTCGAT
42258490 TTGTAAAATTACCGAAATACCCTC-AGT
1 TTGTAAAATTACCGAAATACCCTCGA-T
* ** **
42258517 TTGCAAAATTAGTGAAATACCCTTAAT
1 TTGTAAAATTACCGAAATACCCTCGAT
* * *
42258544 TTGTAAAATTACTGAAATCCCCTCGAC
1 TTGTAAAATTACCGAAATACCCTCGAT
* *
42258571 TTGTAAAATTACC-AAAGTACCCCCAAT
1 TTGTAAAATTACCGAAA-TACCCTCGAT
* * *
42258598 TTATAAAATTACCCAAATATCCTCGAT
1 TTGTAAAATTACCGAAATACCCTCGAT
*
42258625 TTGTAAAATTATCGAAATACCCTC-AGT
1 TTGTAAAATTACCGAAATACCCTCGA-T
* *
42258652 TTGCAAAATTACTGAAATATCCCT-G-T
1 TTGTAAAATTACCGAAATA-CCCTCGAT
** * **
42258678 AAGATAGAATTACC-ATTTTACCCTCGAT
1 TTG-TAAAATTACCGA-AATACCCTCGAT
** * **
42258706 TTACAGAATTACC-ATTTTACCCTCGAT
1 TTGTAAAATTACCGA-AATACCCTCGAT
** * *
42258733 TTACAAAATTACTGAAATACCCT-TAGT
1 TTGTAAAATTACCGAAATACCCTCGA-T
** *
42258760 TTACAAAATTACCAAAATACCCTCGAT
1 TTGTAAAATTACCGAAATACCCTCGAT
*** * *
42258787 CAATAAAATTACCAAAATACCC-CTGGT
1 TTGTAAAATTACCGAAATACCCTC-GAT
*
42258814 TTGTAAAATTACCAAAATACCC-CTGAT
1 TTGTAAAATTACCGAAATACCCTC-GAT
*
42258841 TTGTGAAATTACCGAAATACCC-CTGAT
1 TTGTAAAATTACCGAAATACCCTC-GAT
*
42258868 TTGTGAAATTACCGAAATA
1 TTGTAAAATTACCGAAATA
42258887 TCCTTGTAGG
Statistics
Matches: 366, Mismatches: 67, Indels: 34
0.78 0.14 0.07
Matches are distributed among these distances:
26 36 0.10
27 317 0.87
28 13 0.04
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
TTGTAAAATTACCGAAATACCCTCGAT
Found at i:42258904 original size:27 final size:27
Alignment explanation
Indices: 42258847--42259202 Score: 414
Period size: 27 Copynumber: 13.3 Consensus size: 27
42258837 TGATTTGTGA
**
42258847 AATTACCGAAATACCCCTG-ATTTGT-G
1 AATTACCGAAATACCCCTGTA-GGGTAG
* *
42258873 AAATTACCGAAATATCCTTGTAGGGTAG
1 -AATTACCGAAATACCCCTGTAGGGTAG
*
42258901 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42258928 AATTACCGGAATA-CCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42258954 AATTACCGGAATACCCCTGCAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42258981 AATTACCGGAATACCCCTGCAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42259008 AATTACCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
42259035 AATTATCGCAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
42259062 AATTACCGGAATACCCCTATGGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42259089 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42259116 AATTACCAAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
42259143 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * * *
42259170 AATTACTGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
42259196 AATTACC
1 AATTACC
42259203 ATTTTGCCCC
Statistics
Matches: 289, Mismatches: 37, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
26 41 0.14
27 246 0.85
28 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:42259647 original size:6 final size:6
Alignment explanation
Indices: 42259610--42259728 Score: 75
Period size: 6 Copynumber: 19.3 Consensus size: 6
42259600 TTGCATTCAC
* * * *
42259610 ATTCTG GTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
42259659 -TTACCTG ATACTG ATTTTG ATTCTG ATTTTG -TCATCTA ATTCTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
42259709 ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
42259729 AATGTTTCTT
Statistics
Matches: 86, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
5 6 0.07
6 68 0.79
7 9 0.10
8 3 0.03
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:42259652 original size:31 final size:31
Alignment explanation
Indices: 42259610--42259744 Score: 139
Period size: 31 Copynumber: 4.4 Consensus size: 31
42259600 TTGCATTCAC
* *
42259610 ATTCTGGTTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
*
42259641 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
* * * * * *
42259672 ATTTTGATTCTGATTTTGTCATCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
*
42259703 ATTCTGATTCTGATTCTAGTT--CTGATAATG
1 ATTCTGATTCTGATTCT-GTTACCTGATACTG
* *
42259733 TTTCTTATTCTG
1 ATTCTGATTCTG
42259745 TAATGGGTTA
Statistics
Matches: 87, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
30 16 0.18
31 69 0.79
32 2 0.02
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.51
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTG
Found at i:42261729 original size:27 final size:26
Alignment explanation
Indices: 42261693--42262173 Score: 301
Period size: 27 Copynumber: 17.8 Consensus size: 26
42261683 AATACCCCAG
* *
42261693 TTGTAAAATTACCAAAGTACCCCCGGT
1 TTGTAAAATTACCAAA-TACCCTCGAT
* * *
42261720 TTATAAAATTACCGAAATACCGTC-AA
1 TTGTAAAATTACC-AAATACCCTCGAT
* *
42261746 TTGTAAAATTACTAAAATACCCTCTAT
1 TTGTAAAATTAC-CAAATACCCTCGAT
42261773 TTGTAAAATTACCGAAATACCCTC-AGT
1 TTGTAAAATTACC-AAATACCCTCGA-T
**
42261800 TTGTAAAATTATTGAAATACCCTCGAT
1 TTGTAAAATTA-CCAAATACCCTCGAT
** *
42261827 TTGTAAAATTATTGAAATACCCTCGAC
1 TTGTAAAATTA-CCAAATACCCTCGAT
*
42261854 TTGTAAAATTACCAAAGTACCCCCGAT
1 TTGTAAAATTACCAAA-TACCCTCGAT
* *
42261881 TTATAAAATTACCTAAATATCCTCGAT
1 TTGTAAAATTACC-AAATACCCTCGAT
* *
42261908 TTGTAAAATTATCGAAATACCCT-TAGT
1 TTGTAAAATTA-CCAAATACCCTCGA-T
* *
42261935 TTGCAAAATTACTAAAATACCCTCGAT
1 TTGTAAAATTAC-CAAATACCCTCGAT
*
42261962 TTGTAAAATTACTGAAATACTCCT-G-T
1 TTGTAAAATTAC-CAAATAC-CCTCGAT
** * ** *
42261988 AAGATAGAATTACCATTTTACCCTTGAT
1 TTG-TAAAATTACCA-AATACCCTCGAT
** * **
42262016 TTACAGAATTACCATTTTACCCTCGAT
1 TTGTAAAATTACCA-AATACCCTCGAT
** * * *
42262043 TTACAAAATTACTGAAATACCCTTGGT
1 TTGTAAAATTAC-CAAATACCCTCGAT
** *
42262070 TTACAAAATTACCAAAATACCCTCAAT
1 TTGTAAAATTACC-AAATACCCTCGAT
*** *
42262097 CAATAAAATTACCAAAATACCC-CTGGT
1 TTGTAAAATTACC-AAATACCCTC-GAT
42262124 TTGTAAAATTACCGAAATACCC-CTGAT
1 TTGTAAAATTACC-AAATACCCTC-GAT
*
42262151 TTGTGAAATTACCGAAATACCCT
1 TTGTAAAATTACC-AAATACCCT
42262174 TGTAGGGTAG
Statistics
Matches: 371, Mismatches: 61, Indels: 43
0.78 0.13 0.09
Matches are distributed among these distances:
26 33 0.09
27 324 0.87
28 14 0.04
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (26 bp):
TTGTAAAATTACCAAATACCCTCGAT
Found at i:42261820 original size:54 final size:53
Alignment explanation
Indices: 42261673--42262173 Score: 338
Period size: 54 Copynumber: 9.3 Consensus size: 53
42261663 TTAGTTTACC
* * * * * *
42261673 AAATTACTGAAATACCC-C-AGTTGTAAAATTACCAAAGTACCCCCGGTTTATA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTACGAAA-TACCCTCGATTTGTA
* * * *
42261725 AAATTACCGAAATACCGTC-AATTGTAAAATTACTAAAATACCCTCTATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTAC-GAAATACCCTCGATTTGTA
*
42261778 AAATTACCGAAATACCCTC-AGTTTGTAAAATTATTGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGA-TTTGTAAAATTA-CGAAATACCCTCGATTTGTA
** * * * *
42261832 AAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCCGATTTATA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTACGAAA-TACCCTCGATTTGTA
* * * *
42261886 AAATTACCTAAATATCCTCGATTTGTAAAATTATCGAAATACCCT-TAGTTTGCA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTA-CGAAATACCCTCGA-TTTGTA
** **
42261940 AAATTACTAAAATACCCTCGATTTGTAAAATTACTGAAATACTCCT-G-TAAGATA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTAC-GAAATAC-CCTCGATTTG-TA
* ** * ** * * ** **
42261994 GAATTACC-ATTTTACCCTTGATTTACAGAATTACCATTTTACCCTCGATTTACA
1 AAATTACCGA-AATACCCTCGATTTGTAAAATTACGA-AATACCCTCGATTTGTA
* * * ** * * ***
42262048 AAATTACTGAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCAATCAATA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTA-CGAAATACCCTCGATTTGTA
* * *
42262102 AAATTACCAAAATACCC-CTGGTTTGTAAAATTACCGAAATACCC-CTGATTTGTG
1 AAATTACCGAAATACCCTC-GATTTGTAAAATTA-CGAAATACCCTC-GATTTGTA
42262156 AAATTACCGAAATACCCT
1 AAATTACCGAAATACCCT
42262174 TGTAGGGTAG
Statistics
Matches: 352, Mismatches: 77, Indels: 37
0.76 0.17 0.08
Matches are distributed among these distances:
52 15 0.04
53 57 0.16
54 268 0.76
55 12 0.03
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (53 bp):
AAATTACCGAAATACCCTCGATTTGTAAAATTACGAAATACCCTCGATTTGTA
Found at i:42261865 original size:81 final size:81
Alignment explanation
Indices: 42261673--42262173 Score: 382
Period size: 81 Copynumber: 6.2 Consensus size: 81
42261663 TTAGTTTACC
* * * *
42261673 AAATTACTGAAATACCC-C-AGTTGTAAAATTACCAAAGTACCCCCGGTTTATAAAATTACCGAA
1 AAATTACTGAAATACCCTCTATTTGTAAAATTACCAAAGTACCCTCGATTTATAAAATTACTGAA
* *
42261736 ATACCGTC-AATTGTA
66 ATACCCTCGATTTGTA
* * *
42261751 AAATTACTAAAATACCCTCTATTTGTAAAATTACCGAAA-TACCCTC-AGTTTGTAAAATTATTG
1 AAATTACTGAAATACCCTCTATTTGTAAAATTACC-AAAGTACCCTCGA-TTTATAAAATTACTG
42261814 AAATACCCTCGATTTGTA
64 AAATACCCTCGATTTGTA
* * * *
42261832 AAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCCGATTTATAAAATTACCT-A
1 AAATTACTGAAATACCCTCTATTTGTAAAATTACCAAAGTACCCTCGATTTATAAAATTA-CTGA
*
42261896 AATATCCTCGATTTGTA
65 AATACCCTCGATTTGTA
* * * *
42261913 AAATTA-TCGAAATACCCT-TAGTTTGCAAAATTACTAAAATACCCTCGATTTGTAAAATTACTG
1 AAATTACT-GAAATACCCTCTA-TTTGTAAAATTACCAAAGTACCCTCGATTTATAAAATTACTG
**
42261976 AAATACTCCT-G-TAAGATA
64 AAATAC-CCTCGATTTG-TA
* * ** ** * *** *
42261994 GAATTAC-CATTTTACCCT-TGATTTACAGAATTACCATTTTACCCTCGATTTACAAAATTACTG
1 AAATTACTGA-AATACCCTCT-ATTTGTAAAATTACCAAAGTACCCTCGATTTATAAAATTACTG
* * **
42262057 AAATACCCTTGGTTTACA
64 AAATACCCTCGATTTGTA
** * *** * * * *
42262075 AAATTACCAAAATACCCTCAATCAATAAAATTACCAAAATACCC-CTGGTTTGTAAAATTACCGA
1 AAATTACTGAAATACCCTCTATTTGTAAAATTACCAAAGTACCCTC-GATTTATAAAATTACTGA
*
42262139 AATACCC-CTGATTTGTG
65 AATACCCTC-GATTTGTA
*
42262156 AAATTACCGAAATACCCT
1 AAATTACTGAAATACCCT
42262174 TGTAGGGTAG
Statistics
Matches: 336, Mismatches: 65, Indels: 41
0.76 0.15 0.09
Matches are distributed among these distances:
78 16 0.05
79 1 0.00
80 55 0.16
81 256 0.76
82 8 0.02
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (81 bp):
AAATTACTGAAATACCCTCTATTTGTAAAATTACCAAAGTACCCTCGATTTATAAAATTACTGAA
ATACCCTCGATTTGTA
Found at i:42262187 original size:27 final size:27
Alignment explanation
Indices: 42262103--42262513 Score: 470
Period size: 27 Copynumber: 15.3 Consensus size: 27
42262093 CAATCAATAA
* ** *
42262103 AATTACCAAAATACCCCTGGT-TTGTAA
1 AATTACCGAAATACCCCT-GTAGGGTAG
**
42262130 AATTACCGAAATACCCCTG-ATTTGT-G
1 AATTACCGAAATACCCCTGTA-GGGTAG
*
42262156 AAATTACCGAAATACCCTTGTAGGGTAG
1 -AATTACCGAAATACCCCTGTAGGGTAG
*
42262184 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42262211 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42262238 AATTATCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
42262265 AATTATCGAAATACCCTTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * **
42262292 AATTATCGAAATACCCTTACAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
42262319 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42262346 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
42262373 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42262400 AATTACCGGAATACCTCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
42262427 AATTATCGAAATACCCCTGTAAGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
42262454 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * * *
42262481 AATTACTGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
42262507 AATTACC
1 AATTACC
42262514 ATTTTACCCC
Statistics
Matches: 337, Mismatches: 42, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
26 16 0.05
27 319 0.95
28 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:42262959 original size:6 final size:6
Alignment explanation
Indices: 42262944--42263040 Score: 74
Period size: 6 Copynumber: 15.8 Consensus size: 6
42262934 ATTCTGTTAC
* * * *
42262944 CTGATA CTGATT CTGATT TTGATT CTG-TT ACTTGATA CTGATT TTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT -C-TGATT CTGATT CTGATT
* *
42262993 CTGATT CTG-TCAC CTAATT CTGATT CTGATT CTGATT CT-AGTT CTGAT
1 CTGATT CTGAT--T CTGATT CTGATT CTGATT CTGATT CTGA-TT CTGAT
42263041 AATGTTTCTT
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
5 4 0.06
6 60 0.83
7 6 0.08
8 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.48
Consensus pattern (6 bp):
CTGATT
Found at i:42262972 original size:31 final size:31
Alignment explanation
Indices: 42262921--42263056 Score: 141
Period size: 31 Copynumber: 4.4 Consensus size: 31
42262911 TTGCATTCAC
*
42262921 ATTCTGATTTTTTATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
*
42262953 ATTCTGATTTTGATTCTGTTACTTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * * *
42262984 ATTTTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* *
42263015 ATTCTGATTCTGATTCTAGTT--CTGATAATG
1 ATTCTGATTTTGATTCT-GTTACCTGATACTG
* *
42263045 TTTCTTATTTTG
1 ATTCTGATTTTG
42263057 TAATTGGTTA
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
30 15 0.17
31 63 0.72
32 9 0.10
ACGTcount: A:0.19, C:0.15, G:0.14, T:0.52
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:42267771 original size:46 final size:46
Alignment explanation
Indices: 42267721--42267896 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
42267711 TGTTTGGGCA
42267721 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
42267767 TCCGAACTCGTTGAGTTGAGTCCGAGTT--C-GA-GAGATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAA--ATG
* *
42267812 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
42267860 -CCTGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42267897 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 1 0.01
43 7 0.06
44 1 0.01
45 4 0.04
46 61 0.55
47 27 0.24
48 2 0.02
49 1 0.01
50 6 0.05
51 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:42267876 original size:93 final size:93
Alignment explanation
Indices: 42267717--42267888 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
42267707 AGGATGTTTG
*
42267717 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCATTGAG
42267782 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
42267810 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CCTGAGCTCATTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC-GAACTCATTGA
42267874 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
42267889 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCATTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:42278302 original size:84 final size:84
Alignment explanation
Indices: 42278161--42278330 Score: 340
Period size: 84 Copynumber: 2.0 Consensus size: 84
42278151 GTCATTAAAA
42278161 AGCTCAAGAGCTTAGAGGATCAAAGTTGGATAGGGGAAAGGAAAAGGTAATCGAATAGCCGTTGA
1 AGCTCAAGAGCTTAGAGGATCAAAGTTGGATAGGGGAAAGGAAAAGGTAATCGAATAGCCGTTGA
42278226 AATCGTTCGACAACTTCCG
66 AATCGTTCGACAACTTCCG
42278245 AGCTCAAGAGCTTAGAGGATCAAAGTTGGATAGGGGAAAGGAAAAGGTAATCGAATAGCCGTTGA
1 AGCTCAAGAGCTTAGAGGATCAAAGTTGGATAGGGGAAAGGAAAAGGTAATCGAATAGCCGTTGA
42278310 AATCGTTCGACAACTTCCG
66 AATCGTTCGACAACTTCCG
42278329 AG
1 AG
42278331 GTAAGTTTTA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (84 bp):
AGCTCAAGAGCTTAGAGGATCAAAGTTGGATAGGGGAAAGGAAAAGGTAATCGAATAGCCGTTGA
AATCGTTCGACAACTTCCG
Found at i:42279453 original size:47 final size:47
Alignment explanation
Indices: 42279384--42279507 Score: 189
Period size: 47 Copynumber: 2.7 Consensus size: 47
42279374 TTTTATGTGT
* *
42279384 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATATGAACATGC
42279431 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATATGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATATGAACATGC
* * *
42279478 --ATATGTGGTAAAGCCGAATGGTCAATGTGA
1 ATATATGTGATAAGGCCGAATGGCCAATGTGA
42279508 AATATATATG
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 27 0.38
47 45 0.62
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.25
Consensus pattern (47 bp):
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATATGAACATGC
Found at i:42279463 original size:22 final size:22
Alignment explanation
Indices: 42279392--42279463 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
42279382 GTATATATGA
42279392 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
42279414 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
42279439 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
42279461 GAT
1 GAT
42279464 GAATATGAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:42279543 original size:50 final size:48
Alignment explanation
Indices: 42279432--42279610 Score: 215
Period size: 48 Copynumber: 3.8 Consensus size: 48
42279422 TGAACATGCA
* * * * *
42279432 TATATGTGATAAGGCCGAATGGCCAATGTG--ATGA-ATATGA-ACATG
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAAT-ATATATGAGATATG
* *
42279477 CATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATGTGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AGTGTGAAATATATA--TGAGATATG
*
42279527 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATG
42279575 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
42279611 GTAGGCGATG
Statistics
Matches: 118, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
45 25 0.21
46 1 0.01
47 5 0.04
48 45 0.38
49 3 0.03
50 38 0.32
51 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATG
Found at i:42279589 original size:48 final size:49
Alignment explanation
Indices: 42279478--42279614 Score: 224
Period size: 48 Copynumber: 2.8 Consensus size: 49
42279468 ATGAACATGC
* *
42279478 ATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATGTGAGATATGT
1 ATATGTGGTAAAGCCGAATGGCT-AGTGTGAAATATGTA-GTGAGATATGT
42279528 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA-TGAGATATGT
1 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGTGAGATATGT
42279576 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAG
1 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAG
42279615 GCGATGTGCG
Statistics
Matches: 83, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
48 48 0.58
50 34 0.41
51 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (49 bp):
ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGTGAGATATGT
Found at i:42279810 original size:37 final size:37
Alignment explanation
Indices: 42279760--42279835 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
42279750 GGAAATATAT
*
42279760 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
*
42279797 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
42279834 TC
1 TC
42279836 TGAGCTAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
Found at i:42282168 original size:40 final size:40
Alignment explanation
Indices: 42282041--42282170 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 40
42282031 ATGCTGGAAA
* * * *
42282041 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
42282081 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
* *
42282121 TTCTATCCGGGCTAAGACCTGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
42282161 TTATATCCGG
1 TTATATCCGG
42282171 TTATATTCCG
Statistics
Matches: 70, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
39 2 0.03
40 68 0.97
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:42291982 original size:22 final size:22
Alignment explanation
Indices: 42291951--42291994 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42291941 AATTATTAAC
*
42291951 ATAATGAATTTTAAATAATTTT
1 ATAATAAATTTTAAATAATTTT
* *
42291973 ATAATAAATTTTGATTAATTTT
1 ATAATAAATTTTAAATAATTTT
42291995 GATCATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
ATAATAAATTTTAAATAATTTT
Found at i:42298082 original size:2 final size:2
Alignment explanation
Indices: 42298075--42298109 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
42298065 TTTGAAAAAC
42298075 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 A
42298110 AATTTAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42301788 original size:71 final size:68
Alignment explanation
Indices: 42301700--42301892 Score: 271
Period size: 68 Copynumber: 2.8 Consensus size: 68
42301690 CGATTTGTCT
* * * *
42301700 CGTAGCTCTCTTGTCTACATGGTG-TCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTA
1 CGTAGCTCTCTTGTCTACATGG-GATACATC-C--CGAATCACACATGCGACCTAGCTACATTTA
42301764 TCTTTCA
62 TCTTTCA
* *
42301771 CGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACATGTGACCTAGCTACATTTATCTT
1 CGTAGCTCTCTTGTCTACATGGGATACATCCCGAATCACACATGCGACCTAGCTACATTTATCTT
42301836 TCA
66 TCA
* *
42301839 CGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACATGTGACCTAGCT
1 CGTAGCTCTCTTGTCTACATGGGATACATCCCGAATCACACATGCGACCTAGCT
42301893 GCTACATGGT
Statistics
Matches: 115, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
68 87 0.76
70 2 0.02
71 26 0.23
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (68 bp):
CGTAGCTCTCTTGTCTACATGGGATACATCCCGAATCACACATGCGACCTAGCTACATTTATCTT
TCA
Found at i:42301832 original size:68 final size:68
Alignment explanation
Indices: 42301737--42301892 Score: 294
Period size: 68 Copynumber: 2.3 Consensus size: 68
42301727 TTCACTTGGA
* *
42301737 ATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCC
42301802 CGT
66 CGT
42301805 ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCC
42301870 CGT
66 CGT
42301873 ATCACACATGTGACCTAGCT
1 ATCACACATGTGACCTAGCT
42301893 GCTACATGGT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 86 1.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (68 bp):
ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCC
CGT
Found at i:42301927 original size:68 final size:68
Alignment explanation
Indices: 42301737--42301920 Score: 244
Period size: 68 Copynumber: 2.7 Consensus size: 68
42301727 TTCACTTGGA
* * ** *
42301737 ATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATACATCTGTCACGTAGCTCTCTTGTCTACATGGGATACATCC
42301802 CGT
66 CGT
** *
42301805 ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATACATCTGTCACGTAGCTCTCTTGTCTACATGGGATACATCC
42301870 CGT
66 CGT
* * * *
42301873 ATCACACATGTGACCTAGCTGC-TACATGGTGTCTCGTAGCTTTCTTGT
1 ATCACACATGTGACCTAGCTACATACAT-CTGTCACGTAGCTCTCTTGT
42301921 ACACATGATG
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
67 3 0.03
68 103 0.97
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.34
Consensus pattern (68 bp):
ATCACACATGTGACCTAGCTACATACATCTGTCACGTAGCTCTCTTGTCTACATGGGATACATCC
CGT
Found at i:42310358 original size:54 final size:54
Alignment explanation
Indices: 42310300--42310411 Score: 125
Period size: 54 Copynumber: 2.1 Consensus size: 54
42310290 TACTGAAATG
**
42310300 CCCTCAAATTGTAAAATTACCAAAGTACCCTCGATTTATAAAATTACCGTTTTA
1 CCCTCAAATTACAAAATTACCAAAGTACCCTCGATTTATAAAATTACCGTTTTA
* * * **** * *
42310354 CCCTCGATTTACAAAATTATCGTTTTACCCTCGATTTATAGAATTACTGTTTTA
1 CCCTCAAATTACAAAATTACCAAAGTACCCTCGATTTATAAAATTACCGTTTTA
42310408 CCCT
1 CCCT
42310412 TGATTTACAG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (54 bp):
CCCTCAAATTACAAAATTACCAAAGTACCCTCGATTTATAAAATTACCGTTTTA
Found at i:42310455 original size:27 final size:27
Alignment explanation
Indices: 42310325--42310455 Score: 192
Period size: 27 Copynumber: 4.9 Consensus size: 27
42310315 ATTACCAAAG
* *
42310325 TACCCTCGATTTATAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
42310352 TACCCTCGATTTACAAAATTA-TCGTTT
1 TACCCTCGATTTACAAAATTACT-GTTT
* *
42310379 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
42310406 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
42310433 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAAAATTACT
42310456 AAAATACCAT
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
27 93 0.99
28 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTGTTT
Found at i:42310473 original size:54 final size:55
Alignment explanation
Indices: 42310359--42310481 Score: 151
Period size: 54 Copynumber: 2.3 Consensus size: 55
42310349 TTTTACCCTC
* * **** *
42310359 GATTTACAAAATTA-TCGTTTTACCCTCGATTTATAGAATTACTGTTTTACCCTT
1 GATTTACAAAATTACTCGTTTTACCCTCGATTTACAAAATTACTAAAATACCATT
*
42310413 GATTTACAGAATTACT-GTTTTACCCTCGATTTACAAAATTACTAAAATACCATT
1 GATTTACAAAATTACTCGTTTTACCCTCGATTTACAAAATTACTAAAATACCATT
*
42310467 GGTTTACAAAATTAC
1 GATTTACAAAATTAC
42310482 CAAAATACCC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 57 0.98
55 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (55 bp):
GATTTACAAAATTACTCGTTTTACCCTCGATTTACAAAATTACTAAAATACCATT
Found at i:42310491 original size:81 final size:81
Alignment explanation
Indices: 42310312--42310496 Score: 185
Period size: 81 Copynumber: 2.3 Consensus size: 81
42310302 CTCAAATTGT
* *
42310312 AAAATTACCAAAGTACCCTCGATTTATAAAATTACCGTTTTACCCTCGATTTACAAAATTATCGT
1 AAAATTACCAAAATACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTATCGT
** * *
42310377 TTTACCCTCGATTTAT
66 AATACCATCGATTTAC
* ***** * * *
42310393 AGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTA-C-T
1 AAAATTACCAAAATACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTATCGT
* *
42310456 AAAATACCATTGGTTTAC
66 --AATACCATCGATTTAC
42310474 AAAATTACCAAAATACCCTCGAT
1 AAAATTACCAAAATACCCTCGAT
42310497 CAGTAAAATT
Statistics
Matches: 79, Mismatches: 23, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
79 1 0.01
80 1 0.01
81 77 0.97
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTATCGT
AATACCATCGATTTAC
Found at i:42310539 original size:26 final size:26
Alignment explanation
Indices: 42310447--42310677 Score: 241
Period size: 27 Copynumber: 8.7 Consensus size: 26
42310437 CTCGATTTAC
* * * **
42310447 AAAATTACTAAAATACCATTGGTTTAC
1 AAAATTACCAAAATACC-CTAGTTTGT
* **
42310474 AAAATTACCAAAATACCCTCGATCAGT
1 AAAATTACCAAAATACCCTAG-TTTGT
*
42310501 AAAATTACCAAAATACCCTAGTCTGT
1 AAAATTACCAAAATACCCTAGTTTGT
* *
42310527 AAAATTACTAAAATACCCTGGTTTGT
1 AAAATTACCAAAATACCCTAGTTTGT
*
42310553 AAAATTA-CAGAAAT-CCCTCAATTTGT
1 AAAATTACCA-AAATACCCT-AGTTTGT
*
42310579 AAAATTACCAAAATACGCTTAGTTTGT
1 AAAATTACCAAAATAC-CCTAGTTTGT
42310606 AAAATTACCAAAATACCACTAGTTTGT
1 AAAATTACCAAAATACC-CTAGTTTGT
* * *
42310633 GAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCT-AGTTTGT
42310660 AAAATTACCAAAATACCC
1 AAAATTACCAAAATACCC
42310678 CTAATTTACA
Statistics
Matches: 173, Mismatches: 23, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
25 5 0.03
26 59 0.34
27 107 0.62
28 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (26 bp):
AAAATTACCAAAATACCCTAGTTTGT
Found at i:42310754 original size:26 final size:26
Alignment explanation
Indices: 42310717--42310766 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
42310707 GACTTTCTAA
42310717 AAATTATGGAAATACCATTGGTTTAC
1 AAATTATGGAAATACCATTGGTTTAC
*
42310743 AAATTACT-GAAATACCCTTGGTTT
1 AAATTA-TGGAAATACCATTGGTTT
42310767 GTAGATTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (26 bp):
AAATTATGGAAATACCATTGGTTTAC
Found at i:42310860 original size:26 final size:27
Alignment explanation
Indices: 42310810--42310879 Score: 90
Period size: 26 Copynumber: 2.6 Consensus size: 27
42310800 TGACTAAAAT
*
42310810 ACCCCTATTA-GGTAAAAAGACCGTAAA
1 ACCCCTA-TAGGGTAAAGAGACCGTAAA
42310837 ACCCCTATAGGGTAAAGAGA-CGTAAA
1 ACCCCTATAGGGTAAAGAGACCGTAAA
* *
42310863 GCCCCTGTAGGGTAAAG
1 ACCCCTATAGGGTAAAG
42310880 TGGTCGTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 23 0.59
27 16 0.41
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (27 bp):
ACCCCTATAGGGTAAAGAGACCGTAAA
Found at i:42310894 original size:27 final size:26
Alignment explanation
Indices: 42310820--42310905 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
42310810 ACCCCTATTA
* * *
42310820 GGTAAAAAGACCGTAAAACCCCTATAG
1 GGTAAAGAGA-CGTAAAGCCCCTGTAG
42310847 GGTAAAGAGACGTAAAGCCCCTGTAG
1 GGTAAAGAGACGTAAAGCCCCTGTAG
* * * *
42310873 GGTAAAGTGGTCGTAATGCCCCTGTAT
1 GGTAAAG-AGACGTAAAGCCCCTGTAG
42310900 GGTAAA
1 GGTAAA
42310906 ATGACGAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
26 21 0.41
27 30 0.59
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.20
Consensus pattern (26 bp):
GGTAAAGAGACGTAAAGCCCCTGTAG
Found at i:42311808 original size:25 final size:26
Alignment explanation
Indices: 42311711--42311808 Score: 171
Period size: 26 Copynumber: 3.8 Consensus size: 26
42311701 GAGGAAGTGC
*
42311711 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
42311737 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
42311763 AAAAGGGCTTATGCCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
42311789 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
42311809 ATTAAAAGAG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
25 10 0.14
26 59 0.86
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACTG
Found at i:42312013 original size:42 final size:42
Alignment explanation
Indices: 42311954--42312045 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
42311944 TAGTCTCCCC
* ** *
42311954 AAATGGGCTTGCATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
42311996 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
42312038 AAATGGGC
1 AAATGGGC
42312046 CTATGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:42312104 original size:31 final size:31
Alignment explanation
Indices: 42312069--42312147 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
42312059 CGTTTACAAT
42312069 AAAGGCTTCGGCCCAGTGAAATAAATTATGA
1 AAAGGCTTCGGCCCAGTGAAATAAATTATGA
* * *
42312100 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATAAATTATGA
42312131 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
42312148 ATATGTTGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATAAATTATGA
Found at i:42315458 original size:31 final size:31
Alignment explanation
Indices: 42315420--42315482 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
42315410 CCTTTTCATA
42315420 TTCATATTTCATAACACTGGGCCGAAGCCTT
1 TTCATATTTCATAACACTGGGCCGAAGCCTT
**
42315451 TTCATATTTCATATTACTGGGCCGAAGCCTT
1 TTCATATTTCATAACACTGGGCCGAAGCCTT
42315482 T
1 T
42315483 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (31 bp):
TTCATATTTCATAACACTGGGCCGAAGCCTT
Found at i:42315725 original size:24 final size:24
Alignment explanation
Indices: 42315674--42315815 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
42315664 GCTTTATCAT
*
42315674 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
42315699 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
42315723 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
42315746 ATAACT-GGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
42315769 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
42315793 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
42315816 TCACTTCCTC
Statistics
Matches: 109, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
22 16 0.15
23 12 0.11
24 69 0.63
25 12 0.11
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:42315762 original size:46 final size:48
Alignment explanation
Indices: 42315674--42315814 Score: 198
Period size: 46 Copynumber: 3.0 Consensus size: 48
42315664 GCTTTATCAT
* *
42315674 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
42315723 ATAACTGGGGCATAAGCCCTTTT-ATAACT-GGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
42315769 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
42315815 TTCACTTCCT
Statistics
Matches: 85, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
46 37 0.44
47 12 0.14
48 24 0.28
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:42315891 original size:20 final size:20
Alignment explanation
Indices: 42315866--42315925 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
42315856 TATGATTACC
42315866 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
42315886 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATA
*
42315906 TCATGTGCATCTCATACATA
1 TCATGTGCATATCATACATA
42315926 CCATATTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:42316000 original size:25 final size:25
Alignment explanation
Indices: 42315968--42316015 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42315958 ATACATAAAC
* * *
42315968 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
42315993 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
42316016 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:42323557 original size:31 final size:31
Alignment explanation
Indices: 42323519--42323581 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
42323509 CCTTTTCATA
42323519 TTCATATTTCATAACACTGGGCCGAAGCCTT
1 TTCATATTTCATAACACTGGGCCGAAGCCTT
**
42323550 TTCATATTTCATATTACTGGGCCGAAGCCTT
1 TTCATATTTCATAACACTGGGCCGAAGCCTT
42323581 T
1 T
42323582 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (31 bp):
TTCATATTTCATAACACTGGGCCGAAGCCTT
Found at i:42323824 original size:24 final size:24
Alignment explanation
Indices: 42323773--42323915 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
42323763 GCTTTATCAT
*
42323773 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
42323798 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
42323822 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
42323845 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
42323869 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
42323893 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
42323916 TCACTTCCTC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.68
25 12 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:42323852 original size:47 final size:48
Alignment explanation
Indices: 42323773--42323914 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
42323763 GCTTTATCAT
* *
42323773 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
42323822 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
42323869 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
42323915 TTCACTTCCT
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 44 0.51
48 31 0.36
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:42323873 original size:71 final size:72
Alignment explanation
Indices: 42323772--42323915 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
42323762 TGCTTTATCA
*
42323772 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
42323837 GCCCTTT
66 GCCCTTT
* * **
42323844 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
42323907 AGCCCTTT
65 AGCCCTTT
42323915 T
1 T
42323916 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 53 0.80
72 13 0.20
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (72 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
GCCCTTT
Found at i:42323991 original size:20 final size:20
Alignment explanation
Indices: 42323966--42324025 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
42323956 TATGATTACC
42323966 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
42323986 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATA
*
42324006 TCATGTGCATCTCATACATA
1 TCATGTGCATATCATACATA
42324026 CCATATTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:42324100 original size:25 final size:25
Alignment explanation
Indices: 42324068--42324115 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42324058 ATACATAAAC
* * *
42324068 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
42324093 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
42324116 CATTATAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:42330264 original size:79 final size:80
Alignment explanation
Indices: 42330124--42330276 Score: 195
Period size: 79 Copynumber: 1.9 Consensus size: 80
42330114 AGCCCAGTTA
* * * *
42330124 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGGACCAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATATAGTAACTAGCACCAAAGCCTTCGG
42330189 G-CTTAGCCTGGAAT
66 GACTTAGCCTGGAAT
** * *
42330203 TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA-CAAAGCCTTC
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGAATATAGTAAC-TAGCACCAAAGCCTTC
42330266 GGGACTTAGCC
64 GGGACTTAGCC
42330277 CGGACATCAT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
78 3 0.05
79 50 0.79
80 10 0.16
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATATAGTAACTAGCACCAAAGCCTTCGG
GACTTAGCCTGGAAT
Found at i:42330280 original size:40 final size:40
Alignment explanation
Indices: 42330077--42330280 Score: 202
Period size: 40 Copynumber: 5.1 Consensus size: 40
42330067 CGGAATTTAT
** * *
42330077 CCGGATATAGCT-ACTCGTTCAAATGCCTTTGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
42330117 CCAGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
42330157 CCGAATTTAGTAACTCGGACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42330196 CTGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
42330236 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42330276 CCGGA
1 CCGGA
42330281 CATCATTCGA
Statistics
Matches: 133, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
38 2 0.02
39 30 0.23
40 89 0.67
41 12 0.09
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42336394 original size:42 final size:42
Alignment explanation
Indices: 42336335--42336420 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
42336325 TCCATGTCTT
42336335 TGCCATAACACTTTCACTAAAGCTATGCTTTTCTTTCTCAAC
1 TGCCATAACACTTTCACTAAAGCTATGCTTTTCTTTCTCAAC
42336377 TGCCATAACACTTTCACTAAAGCTATGCTTTTCTTTCTCAAC
1 TGCCATAACACTTTCACTAAAGCTATGCTTTTCTTTCTCAAC
42336419 TG
1 TG
42336421 TTTCACTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (42 bp):
TGCCATAACACTTTCACTAAAGCTATGCTTTTCTTTCTCAAC
Found at i:42345352 original size:13 final size:13
Alignment explanation
Indices: 42345336--42345362 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42345326 TAAAAATTTA
42345336 AGTTAAAATAAGT
1 AGTTAAAATAAGT
42345349 AGTTAAAATAAGT
1 AGTTAAAATAAGT
42345362 A
1 A
42345363 AAATAAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (13 bp):
AGTTAAAATAAGT
Found at i:42350788 original size:42 final size:42
Alignment explanation
Indices: 42350741--42350847 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
42350731 TATTGGTCTC
42350741 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
42350783 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* *
42350825 GGCACTACGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
42350848 ATTGTACAGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:42350912 original size:27 final size:28
Alignment explanation
Indices: 42350855--42350924 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
42350845 AAAATTGTAC
**
42350855 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
42350883 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
42350910 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
42350925 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:42355417 original size:27 final size:26
Alignment explanation
Indices: 42355369--42355420 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
42355359 GCGAGGCTGG
*
42355369 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
42355395 CAGATATATGTGGCGACGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
42355421 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:42362868 original size:27 final size:26
Alignment explanation
Indices: 42362820--42362871 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
42362810 GCGAGGCTGG
*
42362820 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
42362846 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
42362872 TTGCAGGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:42370737 original size:47 final size:47
Alignment explanation
Indices: 42370678--42371399 Score: 1063
Period size: 47 Copynumber: 15.4 Consensus size: 47
42370668 GATGTACAAG
* *
42370678 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* *
42370725 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGAAGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
*
42370772 GTGTGTATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* * *
42370819 GTGTATATATGTGACAAGG-CTGAGTGGCCAACGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCT-AATGGCCAATGTGATGAATGTGAAA
* *
42370866 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* * * *
42370913 GTGTCTATATGTGATAAGGCCGAATGGACAATGTGAAGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
*
42370960 GTGTGTATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* * *
42371007 GTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* * *
42371054 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* *
42371101 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGAAGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
*
42371148 GTGTGTATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* * *
42371195 GTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* * *
42371242 GTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* * ** * *
42371289 GTGTATATATGAGATAAGACCTAATGGCTGATGTGATGGATGTGAAG
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
*
42371336 GTGTATATATGTGATAAGG--TGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCT-AATGGCCAATGTGATGAATGTGAAA
*
42371382 GTGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
42371400 TCCCGAAGGG
Statistics
Matches: 611, Mismatches: 61, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.00
46 41 0.07
47 567 0.93
48 2 0.00
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
Found at i:42370995 original size:188 final size:188
Alignment explanation
Indices: 42370678--42371399 Score: 1232
Period size: 188 Copynumber: 3.8 Consensus size: 188
42370668 GATGTACAAG
42370678 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
1 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
42370743 GCCGAATGGCCAATGTGAAGAATGTGAAAGTGTGTATATGTGATAAGGCCTAATGGCCAATGTGA
66 GCCGAATGGCCAATGTGAAGAATGTGAAAGTGTGTATATGTGATAAGGCCTAATGGCCAATGTGA
* *
42370808 TGAATGTGAAAGTGTATATATGTGACAAGGCTGAGTGGCCAACGTGATGAATGTGAAA
131 TGAATGTGAAAGTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAA
*
42370866 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTCTATATGTGATAAG
1 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
*
42370931 GCCGAATGGACAATGTGAAGAATGTGAAAGTGTGTATATGTGATAAGGCCTAATGGCCAATGTGA
66 GCCGAATGGCCAATGTGAAGAATGTGAAAGTGTGTATATGTGATAAGGCCTAATGGCCAATGTGA
42370996 TGAATGTGAAAGTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAA
131 TGAATGTGAAAGTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAA
*
42371054 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAAAGTGTATATATGTGATAAG
1 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
42371119 GCCGAATGGCCAATGTGAAGAATGTGAAAGTGTGTATATGTGATAAGGCCTAATGGCCAATGTGA
66 GCCGAATGGCCAATGTGAAGAATGTGAAAGTGTGTATATGTGATAAGGCCTAATGGCCAATGTGA
42371184 TGAATGTGAAAGTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAA
131 TGAATGTGAAAGTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAA
* * * * * *
42371242 GTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTATATATGAGATAAG
1 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
* * ** * * * *
42371307 ACCTAATGGCTGATGTGATGGATGTGAAGGTGTATATATGTGATAAGG--TGAATGGCCAATGTG
66 GCCGAATGGCCAATGTGAAGAATGTGAAAGTGTGTATATGTGATAAGGCCT-AATGGCCAATGTG
* *
42371370 ATGGATGTGAAAGTGTATAAATGTGATAAG
130 ATGAATGTGAAAGTGTATATATGTGATAAG
42371400 TCCCGAAGGG
Statistics
Matches: 509, Mismatches: 24, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
186 1 0.00
187 41 0.08
188 467 0.92
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (188 bp):
GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
GCCGAATGGCCAATGTGAAGAATGTGAAAGTGTGTATATGTGATAAGGCCTAATGGCCAATGTGA
TGAATGTGAAAGTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGAAA
Found at i:42374754 original size:27 final size:26
Alignment explanation
Indices: 42374706--42374757 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
42374696 GCGAGGCTGC
*
42374706 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
42374732 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
42374758 TTTCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:42377119 original size:16 final size:17
Alignment explanation
Indices: 42377098--42377130 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42377088 TTTGGTAGAA
*
42377098 ATAGATT-ATTGTCTTG
1 ATAGATTGATTGACTTG
42377114 ATAGATTGATTGACTTG
1 ATAGATTGATTGACTTG
42377131 CTCATATCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.45
Consensus pattern (17 bp):
ATAGATTGATTGACTTG
Found at i:42379608 original size:40 final size:40
Alignment explanation
Indices: 42379512--42379730 Score: 271
Period size: 40 Copynumber: 5.5 Consensus size: 40
42379502 CGAATGGTAT
* * * *
42379512 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAAA
*
42379553 CCGGG-TCAA-TCCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCT-AAGT-CCCGAAGGCATTTGTGCGAGTTACTAAAA
* *
42379593 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* *
42379633 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * * *
42379673 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
*
42379713 CCGGGCTATGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
42379731 ACAACCGAGC
Statistics
Matches: 159, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
40 134 0.84
41 25 0.16
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
Found at i:42379726 original size:120 final size:121
Alignment explanation
Indices: 42379512--42379730 Score: 316
Period size: 120 Copynumber: 1.8 Consensus size: 121
42379502 CGAATGGTAT
* *
42379512 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAATCCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGGTCAATCCCCGAAGGCAATT
* *
42379577 GTGCGAGTTACCAAAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
66 GTGCGAATTACCAAAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* * * *
42379633 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGG-CTAATTCCCGAAGGCAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGGTC-AATCCCCGAAGGCAAT
* * *
42379696 TGTGCGAATTACTATAACCGGGCTATGTCCCGAAG
65 TGTGCGAATTACCAAAACCGGGCTAAGTCCCGAAG
42379731 ACAACCGAGC
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
119 1 0.01
120 59 0.69
121 26 0.30
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (121 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGGTCAATCCCCGAAGGCAATT
GTGCGAATTACCAAAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
Found at i:42379765 original size:80 final size:80
Alignment explanation
Indices: 42379579--42379756 Score: 185
Period size: 80 Copynumber: 2.2 Consensus size: 80
42379569 AGGCATTTGT
* * * * * * * *
42379579 GCGAGTTACCAAAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAACCGGGTTAAGT
1 GCGAGTCACTAAATCCGGGCTAATTCCCGAAGGCAATTGTGCGAATTACCAAAACCGGGCTAAGT
* *** *
42379644 CCCGAAGGCATTTGT
66 CCCGAAGACAACCGA
* * * *
42379659 GCGAGTTACTAAATCCGGGCTAATTCCCGAAGGCAATTGTGCGAATTACTATAACCGGGCTATGT
1 GCGAGTCACTAAATCCGGGCTAATTCCCGAAGGCAATTGTGCGAATTACCAAAACCGGGCTAAGT
42379724 CCCGAAGACAACCGA
66 CCCGAAGACAACCGA
* *
42379739 GCGAGTCGCTATATCCGG
1 GCGAGTCACTAAATCCGG
42379757 TTAAATTCCG
Statistics
Matches: 80, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (80 bp):
GCGAGTCACTAAATCCGGGCTAATTCCCGAAGGCAATTGTGCGAATTACCAAAACCGGGCTAAGT
CCCGAAGACAACCGA
Found at i:42397274 original size:46 final size:45
Alignment explanation
Indices: 42397221--42397395 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
42397211 TATTTGGGCA
42397221 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
42397267 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
42397314 TCCGAGCT-GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
42397359 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42397396 CGGGTTACAT
Statistics
Matches: 109, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
44 1 0.01
45 11 0.10
46 77 0.71
47 11 0.10
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:42397387 original size:92 final size:93
Alignment explanation
Indices: 42397217--42397387 Score: 299
Period size: 92 Copynumber: 1.8 Consensus size: 93
42397207 AGGATATTTG
* *
42397217 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
42397282 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
42397310 GGCATCCGAGCT-GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
42397374 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
42397388 ACTTATGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 63 0.85
93 11 0.15
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:42400355 original size:15 final size:15
Alignment explanation
Indices: 42400335--42400403 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
42400325 GTATCTTGGG
42400335 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
42400350 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
42400365 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
42400380 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
42400395 TTTCTTTAT
1 TTTCTTTAT
42400404 TCGGTTTCTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:42400404 original size:30 final size:30
Alignment explanation
Indices: 42400326--42400412 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
42400316 CATAGTATCG
* * * * *
42400326 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGGTTTCTC
42400356 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGGTTTCTC
42400386 TATCTTGGATTTCTTTATTC--GGTTTCT
1 TATCTTGGATTTCTTTATTCTGGGTTTCT
42400413 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.14
29 1 0.02
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGGTTTCTC
Found at i:42402838 original size:46 final size:45
Alignment explanation
Indices: 42402785--42402960 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
42402775 TATTTGGGCA
42402785 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
42402831 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
42402878 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
42402924 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42402961 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:42402940 original size:93 final size:93
Alignment explanation
Indices: 42402781--42402952 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
42402771 AGGATATTTG
* *
42402781 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
42402846 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
42402874 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
42402939 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
42402953 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:42405791 original size:25 final size:25
Alignment explanation
Indices: 42405763--42405811 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
42405753 TTATAATATG
* * *
42405763 AAAAATAACTGTTTTGCCCCTAGGC
1 AAAAATAACCGTTATACCCCTAGGC
*
42405788 AAAAATGACCGTTATACCCCTAGG
1 AAAAATAACCGTTATACCCCTAGG
42405812 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (25 bp):
AAAAATAACCGTTATACCCCTAGGC
Found at i:42407453 original size:35 final size:35
Alignment explanation
Indices: 42407414--42407486 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
42407404 ACACATTCTT
42407414 TATTCTCGTCAGATCAATCTCACATAAATAATATA
1 TATTCTCGTCAGATCAATCTCACATAAATAATATA
42407449 TATTCTCGTCAGATCAATCTCACATAAATAATATA
1 TATTCTCGTCAGATCAATCTCACATAAATAATATA
42407484 TAT
1 TAT
42407487 ATCACATACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (35 bp):
TATTCTCGTCAGATCAATCTCACATAAATAATATA
Found at i:42409775 original size:35 final size:35
Alignment explanation
Indices: 42409729--42409798 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
42409719 GGTTACAAAA
42409729 ATGTAAAAATCTTCAAGAAAGACATTAAAATCACT
1 ATGTAAAAATCTTCAAGAAAGACATTAAAATCACT
42409764 ATGTAAAAATCTTCAAGAAAGACATTAAAATCACT
1 ATGTAAAAATCTTCAAGAAAGACATTAAAATCACT
42409799 TACTTGCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (35 bp):
ATGTAAAAATCTTCAAGAAAGACATTAAAATCACT
Found at i:42411716 original size:68 final size:67
Alignment explanation
Indices: 42411640--42411789 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
42411630 CATCATGTGT
* * * *
42411640 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
42411702 ATGTAG
62 ATGTAG
** * *
42411708 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
42411773 AG
66 AG
42411775 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
42411790 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:42411745 original size:64 final size:64
Alignment explanation
Indices: 42411664--42411847 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
42411654 AGACATTATG
* *
42411664 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
42411728 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
42411793 AA
63 AA
* * * *
42411795 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
42411848 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:42412940 original size:2 final size:2
Alignment explanation
Indices: 42412933--42412963 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42412923 TCATGACATG
42412933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42412964 GACTAGTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42420689 original size:25 final size:25
Alignment explanation
Indices: 42420661--42420709 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
42420651 TTATATTATG
* * *
42420661 AAAAATAACTGTTTTGCCCCTAGGC
1 AAAAATAACCGTTCTACCCCTAGGC
*
42420686 AAAAATGACCGTTCTACCCCTAGG
1 AAAAATAACCGTTCTACCCCTAGG
42420710 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (25 bp):
AAAAATAACCGTTCTACCCCTAGGC
Found at i:42420864 original size:24 final size:24
Alignment explanation
Indices: 42420833--42420878 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
42420823 AGGAAGTGAA
**
42420833 AAAGGGCTTTGCC-CCAGTTATTT
1 AAAGGGCTAGGCCTCCAGTTATTT
42420856 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAG-GGCTAGGCCTCCAGTTAT
42420879 ATGATAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 7 0.37
25 8 0.42
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (24 bp):
AAAGGGCTAGGCCTCCAGTTATTT
Found at i:42426732 original size:79 final size:79
Alignment explanation
Indices: 42426628--42426773 Score: 186
Period size: 79 Copynumber: 1.8 Consensus size: 79
42426618 GAATGTTCGA
* ** *
42426628 GTGATATCCGGGCTAAGCTCGAAGGCAATTGTGCAAGTTATGATATCCGGGCTAAG-CCCGAAGG
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAGTTACCATAACCGGGCTAAGTCCCGAAGG
42426692 CAATTGTGCAAATT
66 CAATTGTGCAAATT
* ** ** *
42426706 GTGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTACCATAACCGGGCTATGTCCCGAAG
1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCAAGTTACCATAACCGGGCTAAGTCCCGAAG
42426771 GCA
65 GCA
42426774 TTTGAACGAG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
78 16 0.29
79 30 0.54
80 10 0.18
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (79 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAGTTACCATAACCGGGCTAAGTCCCGAAGG
CAATTGTGCAAATT
Found at i:42426740 original size:40 final size:39
Alignment explanation
Indices: 42426628--42426732 Score: 165
Period size: 39 Copynumber: 2.7 Consensus size: 39
42426618 GAATGTTCGA
* *
42426628 GTGATATCCGGGCTAAGCTCGAAGGCAATTGTGCAAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
42426667 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
42426706 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
42426733 CTTTGTGCGG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
39 51 0.85
40 9 0.15
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:42430128 original size:17 final size:18
Alignment explanation
Indices: 42430090--42430129 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
42430080 CATAATGCAG
* *
42430090 GCCCATGTGGGCCTACAC
1 GCCCATGTGGGCCCACAA
42430108 GCCCATGT-GGCCCACAA
1 GCCCATGTGGGCCCACAA
42430125 GCCCA
1 GCCCA
42430130 AATCTGGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.20, C:0.42, G:0.25, T:0.12
Consensus pattern (18 bp):
GCCCATGTGGGCCCACAA
Found at i:42434007 original size:34 final size:34
Alignment explanation
Indices: 42433964--42434067 Score: 199
Period size: 34 Copynumber: 3.1 Consensus size: 34
42433954 CCTAAAAATG
*
42433964 TTACCTCACGTAACCAGAGCTCTCAGTTACTTAA
1 TTACCTCACGTAACCAGAGCTCTCAGTTACTGAA
42433998 TTACCTCACGTAACCAGAGCTCTCAGTTACTGAA
1 TTACCTCACGTAACCAGAGCTCTCAGTTACTGAA
42434032 TTACCTCACGTAACCAGAGCTCTCAGTTACTGAA
1 TTACCTCACGTAACCAGAGCTCTCAGTTACTGAA
42434066 TT
1 TT
42434068 TGGCGTATAG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (34 bp):
TTACCTCACGTAACCAGAGCTCTCAGTTACTGAA
Found at i:42439217 original size:40 final size:40
Alignment explanation
Indices: 42439138--42439292 Score: 240
Period size: 40 Copynumber: 3.9 Consensus size: 40
42439128 CGGTATAATA
* * * * *
42439138 CCAGCTCGTAGCCTGCAGGTCTCT-AGCCCAGATAACATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATAACATT
42439177 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATAACATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATAACATT
* *
42439217 CCAGCACAAAGCCTGCGGGTCTTGAAGCCCGGATAACATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATAACATT
42439257 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATAA
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATAA
42439293 TACCTCAAGT
Statistics
Matches: 106, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 20 0.19
40 86 0.81
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (40 bp):
CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATAACATT
Found at i:42442777 original size:40 final size:40
Alignment explanation
Indices: 42442712--42442850 Score: 208
Period size: 40 Copynumber: 3.5 Consensus size: 40
42442702 TTCTAGCACC
* * *
42442712 AGCCTGCGGGTCTCT-AGCCCAGATAACATTCCAGCATGA
1 AGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCACGA
* *
42442751 AGCCTGCGAGTTTTTAAGCCCGGATAACATTCCAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCACGA
* *
42442791 AGCCTGCGGGTCTTTAAGCCCGAAAAACATTCCAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCACGA
42442831 AGCCTGCGGGTCTTTAAGCC
1 AGCCTGCGGGTCTTTAAGCC
42442851 TAGAAAATAC
Statistics
Matches: 90, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 12 0.13
40 78 0.87
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (40 bp):
AGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCACGA
Found at i:42444863 original size:40 final size:40
Alignment explanation
Indices: 42444818--42444985 Score: 198
Period size: 40 Copynumber: 4.2 Consensus size: 40
42444808 CGGAATACAA
*
42444818 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
42444858 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* **
42444898 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
42444938 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTATTAGC
42444978 CCGGATAT
1 CCGGATAT
42444986 CATTCAATTG
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 108 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
Found at i:42444958 original size:80 final size:80
Alignment explanation
Indices: 42444818--42444985 Score: 232
Period size: 80 Copynumber: 2.1 Consensus size: 80
42444808 CGGAATACAA
* * *
42444818 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATG
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
*
42444883 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
** *
42444898 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGCCCGGATA-AA-GTCACTAGCACAAT
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACG--ACTAGCACAAA
*
42444961 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
42444978 CCGGATAT
1 CCGGATAT
42444986 CATTCAATTG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 1 0.01
79 2 0.03
80 75 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (80 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:42455549 original size:79 final size:81
Alignment explanation
Indices: 42455448--42455632 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
42455438 ACGACTCGCT
** * *
42455448 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
42455511 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
42455528 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
42455592 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
42455608 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42455633 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:42455632 original size:40 final size:39
Alignment explanation
Indices: 42455441--42455632 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
42455431 GGATATAACG
* ** * *
42455441 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
42455481 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
42455521 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
42455560 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
42455600 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
42455633 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:42463497 original size:39 final size:39
Alignment explanation
Indices: 42463454--42463592 Score: 140
Period size: 39 Copynumber: 3.5 Consensus size: 39
42463444 CGGATATAAC
*
42463454 GACTCGCTCAAATGCCTTCGGGAC-AAGCCC-GGTTATAGT
1 GACTCGCACAAATGCCTTCGGGACTAA-CCCGGGTT-TAGT
*
42463493 GACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGT
1 GACTCGCACAAATGCCTTCGGGAC-TAACCCGGGTTTAGT
* * * * *
42463533 AACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATT
1 GACTCGCACAAATGCCTTCGGGAC-TAACCCGGGTTTAGT
* *
42463572 AACTCGCACGAATGCCTTCGG
1 GACTCGCACAAATGCCTTCGG
42463593 ATCCTAGTCC
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
39 55 0.63
40 26 0.30
41 6 0.07
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
GACTCGCACAAATGCCTTCGGGACTAACCCGGGTTTAGT
Found at i:42463547 original size:40 final size:40
Alignment explanation
Indices: 42463455--42463645 Score: 194
Period size: 40 Copynumber: 4.8 Consensus size: 40
42463445 GGATATAACG
* * *
42463455 ACTCGCTCAAATGCCTTCGGGAC-AAGCCCGG-TTATAGTG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* * *
42463494 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
42463534 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * * *
42463573 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
*
42463613 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
42463646 CATCATTCGA
Statistics
Matches: 125, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
38 2 0.02
39 52 0.42
40 59 0.47
41 12 0.10
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:42463553 original size:79 final size:81
Alignment explanation
Indices: 42463462--42463645 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
42463452 ACGACTCGCT
* * *
42463462 CAAATGCCTTCGGGAC-AAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
42463524 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
42463541 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
42463605 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
42463621 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42463646 CATCATTCGA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 4 0.04
79 67 0.74
80 20 0.22
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:42468943 original size:24 final size:24
Alignment explanation
Indices: 42468916--42469026 Score: 204
Period size: 24 Copynumber: 4.6 Consensus size: 24
42468906 CTTATCATGT
42468916 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
42468940 TCGCACACATAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
42468964 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
42468988 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
42469012 TCACACACATAGTGC
1 TCGCACACATAGTGC
42469027 ATTTGAGATT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:42478526 original size:80 final size:80
Alignment explanation
Indices: 42478442--42478590 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
42478432 TATGGTAACC
* * * *
42478442 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
42478506 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
42478522 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
42478587 CCGG
66 CCGG
42478591 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:42478532 original size:40 final size:38
Alignment explanation
Indices: 42478483--42478590 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
42478473 ATCACGATTT
*
42478483 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
42478523 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
42478563 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
42478591 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:42486629 original size:80 final size:80
Alignment explanation
Indices: 42486545--42486693 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
42486535 TATGGTAACC
* * * *
42486545 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
42486609 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
42486625 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
42486690 CCGG
66 CCGG
42486694 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:42486635 original size:40 final size:38
Alignment explanation
Indices: 42486586--42486693 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
42486576 ATCACGATTT
*
42486586 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
42486626 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
42486666 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
42486694 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:42492157 original size:16 final size:17
Alignment explanation
Indices: 42492124--42492173 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
42492114 AAGCCGTACC
**
42492124 TTCGACTTTTCGAATTT
1 TTCGACTTTTCGGCTTT
*
42492141 TTGGA-TTTTCGGC-TT
1 TTCGACTTTTCGGCTTT
42492156 TTCGACTTTTCGGCTTT
1 TTCGACTTTTCGGCTTT
42492173 T
1 T
42492174 AAGCTTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.10, C:0.18, G:0.18, T:0.54
Consensus pattern (17 bp):
TTCGACTTTTCGGCTTT
Found at i:42492173 original size:24 final size:24
Alignment explanation
Indices: 42492124--42492173 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
42492114 AAGCCGTACC
*
42492124 TTCGACTTTTCGAATTTTTGGATT
1 TTCGACTTTTCGAATTTTCGGATT
* * *
42492148 TTCGGCTTTTCGACTTTTCGGCTT
1 TTCGACTTTTCGAATTTTCGGATT
42492172 TT
1 TT
42492174 AAGCTTTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.10, C:0.18, G:0.18, T:0.54
Consensus pattern (24 bp):
TTCGACTTTTCGAATTTTCGGATT
Found at i:42492179 original size:24 final size:24
Alignment explanation
Indices: 42492129--42492181 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
42492119 GTACCTTCGA
* **
42492129 CTTTTCGAATTTTTGGATTTTCGG
1 CTTTTCGAATTTTCGGATTTTAAG
* *
42492153 CTTTTCGACTTTTCGGCTTTTAAG
1 CTTTTCGAATTTTCGGATTTTAAG
42492177 CTTTT
1 CTTTT
42492182 TCCATTTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.55
Consensus pattern (24 bp):
CTTTTCGAATTTTCGGATTTTAAG
Found at i:42499810 original size:8 final size:8
Alignment explanation
Indices: 42499794--42499827 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
42499784 CTCTACAGTG
42499794 TTCGGCTT
1 TTCGGCTT
*
42499802 TTTGGCTT
1 TTCGGCTT
*
42499810 TTCAGCTT
1 TTCGGCTT
42499818 TTCGGCTT
1 TTCGGCTT
42499826 TT
1 TT
42499828 ACCCTTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.21, G:0.21, T:0.56
Consensus pattern (8 bp):
TTCGGCTT
Found at i:42507510 original size:326 final size:321
Alignment explanation
Indices: 42506910--42507550 Score: 953
Period size: 326 Copynumber: 2.0 Consensus size: 321
42506900 ATATGAAATG
42506910 TGTATATATGCCTTGATGGAATTGACTTGTGATGATTCAATGAAAATGTGATGATAGCTTTATAT
1 TGTATATATGCCTTGATGGAATTGACTTGTGATGATTCAATGAAAATGTGATGATAGCTTTATAT
* * * *
42506975 CTCGGAAGTCCTGGGTGACCTTGAGGTAGGATTCGGATATCATGACACCATGGTTAATGAGATCC
66 CTCGAAAGTCCTAGGTGACCCTGAGGTAGGATTCGGATATCAAGACACCATGGTTAATGAGATCC
** * * *
42507040 CGTGTAAGACCATGTTTGGGACTTGGCATCAGCATCAAGATGTGATCCCGTATAAGACCATGTCA
131 CGTGTAAGACCATGCCTGGGACATGGCATCAACATCAAGATGTGATCCCGTATAAGACCATATCA
* * *
42507105 GGGATATGGCTTCGGTATCGTTAAGTGATTTCGTGTAAGACCATATCTCGGACATGGCATTGATA
196 GGGATATGACTTCGGCATCGTTAAGTGATTTCGTGTAAGACCATATCTCGGACATGGCATAGATA
42507170 AGAGATCCCGTATAAGACCATATCTGGGACATGGCATC-GACATCAGTATGAGATCCTGATC
261 AGAGATCCCGTATAAGACCATATCTGGGACATGGCATCAG-CATCAGTATGAGATCCTGATC
*
42507231 TGTATATATGCCTTGATGGAATTGACTTGTGATGATTTAATGAAAATGTGATGATAGCTTT-TAT
1 TGTATATATGCCTTGATGGAATTGACTTGTGATGATTCAATGAAAATGTGATGATAGCTTTATAT
42507295 CTCGAAAGTCCTAGGTGACCCTGAGGAATGCTTAGGATTCGGATATCAAGACACCATGGTTAATG
66 CTCGAAAGTCCTAGGTGACCCTGA-G---G--TAGGATTCGGATATCAAGACACCATGGTTAATG
* * *
42507360 AGATCCCGTGTAAGACCATGCCTGGGACATGGCATCAACATCAATATGTGTTCCTGTATAAGACC
125 AGATCCCGTGTAAGACCATGCCTGGGACATGGCATCAACATCAAGATGTGATCCCGTATAAGACC
* * * * *
42507425 ATATTAGGGATATGACTTCGGCATCGTTAAGTGATTTTGTGTAAGACTATATTTGGGACATGGCA
190 ATATCAGGGATATGACTTCGGCATCGTTAAGTGATTTCGTGTAAGACCATATCTCGGACATGGCA
** * ** * *
42507490 TAGATGTGAGGTTTCGTATAAGACCATGTCTGGGACATGGCATCAGCATTAGTATGAGATC
255 TAGATAAGAGATCCCGTATAAGACCATATCTGGGACATGGCATCAGCATCAGTATGAGATC
42507551 TCATGTAAGA
Statistics
Matches: 285, Mismatches: 28, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
320 24 0.08
321 61 0.21
324 1 0.00
326 198 0.69
327 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (321 bp):
TGTATATATGCCTTGATGGAATTGACTTGTGATGATTCAATGAAAATGTGATGATAGCTTTATAT
CTCGAAAGTCCTAGGTGACCCTGAGGTAGGATTCGGATATCAAGACACCATGGTTAATGAGATCC
CGTGTAAGACCATGCCTGGGACATGGCATCAACATCAAGATGTGATCCCGTATAAGACCATATCA
GGGATATGACTTCGGCATCGTTAAGTGATTTCGTGTAAGACCATATCTCGGACATGGCATAGATA
AGAGATCCCGTATAAGACCATATCTGGGACATGGCATCAGCATCAGTATGAGATCCTGATC
Found at i:42507572 original size:90 final size:90
Alignment explanation
Indices: 42507464--42507716 Score: 269
Period size: 96 Copynumber: 2.7 Consensus size: 90
42507454 AGTGATTTTG
* *
42507464 TGTAAGACTATATTTGGGACATGGCATAGATGTGAGGTTTCGTATAAGACCATGTCTGGGACATG
1 TGTAAGACCATATCTGGGACATGGCATAGATGTGAGGTTTCGTATAAGACCATGTCTGGGACATG
42507529 GCATCAGCATT-AGTATGAGA-TCTCA
66 GCATCAGCATTGA-TATGAGACT-TCA
42507554 TGTAAGACCATATCTGGGATATGGCATTGGCATCA-ATGTGAGGTTTCGTATAAGACCATGTCTG
1 TGTAAGACCATATCTGGG--A---CA-TGGCAT-AGATGTGAGGTTTCGTATAAGACCATGTCTG
* *
42507618 GGACATGGCATCGGCATTGATATGAGACTTCC
59 GGACATGGCATCAGCATTGATATGAGACTTCA
* * * * * ** ** * *
42507650 TATAAGACCATATCTGGGATATGGTATCGATATGTTGTCCCATGTAAGACCATGTCTGGGACATG
1 TGTAAGACCATATCTGGGACATGGCATAGATGTGAGGTTTCGTATAAGACCATGTCTGGGACATG
42507715 GC
66 GC
42507717 TTTAGCACTC
Statistics
Matches: 138, Mismatches: 15, Indels: 20
0.80 0.09 0.12
Matches are distributed among these distances:
90 52 0.38
91 1 0.01
92 1 0.01
94 1 0.01
95 2 0.01
96 78 0.57
97 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (90 bp):
TGTAAGACCATATCTGGGACATGGCATAGATGTGAGGTTTCGTATAAGACCATGTCTGGGACATG
GCATCAGCATTGATATGAGACTTCA
Found at i:42507579 original size:48 final size:48
Alignment explanation
Indices: 42507506--42507678 Score: 179
Period size: 48 Copynumber: 3.6 Consensus size: 48
42507496 TGAGGTTTCG
* *
42507506 TATAAGACCATGTCTGGGACATGGCATCAGCATTAGTATGAGATCTCA
1 TATAAGACCATATCTGGGACATGGCATCGGCATTAGTATGAGATCTCA
* * * * * * * * *
42507554 TGTAAGACCATATCTGGGATATGGCATTGGCATCAATGTGAGGTTTCG
1 TATAAGACCATATCTGGGACATGGCATCGGCATTAGTATGAGATCTCA
* *
42507602 TATAAGACCATGTCTGGGACATGGCATCGGCATT-GATATGAGA-CTTCC
1 TATAAGACCATATCTGGGACATGGCATCGGCATTAG-TATGAGATC-TCA
* *
42507650 TATAAGACCATATCTGGGATATGGTATCG
1 TATAAGACCATATCTGGGACATGGCATCG
42507679 ATATGTTGTC
Statistics
Matches: 99, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
48 99 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (48 bp):
TATAAGACCATATCTGGGACATGGCATCGGCATTAGTATGAGATCTCA
Found at i:42507622 original size:96 final size:96
Alignment explanation
Indices: 42507485--42507673 Score: 303
Period size: 96 Copynumber: 2.0 Consensus size: 96
42507475 ATTTGGGACA
42507485 TGGCATAGATGTGAGGTTTCGTATAAGACCATGTCTGGGACATGGCATCAGCATT-AGTATGAGA
1 TGGCATAGATGTGAGGTTTCGTATAAGACCATGTCTGGGACATGGCATCAGCATTGA-TATGAGA
*
42507549 -TCTCATGTAAGACCATATCTGGGATATGGCAT
65 CT-TCATATAAGACCATATCTGGGATATGGCAT
*
42507581 TGGCATCA-ATGTGAGGTTTCGTATAAGACCATGTCTGGGACATGGCATCGGCATTGATATGAGA
1 TGGCAT-AGATGTGAGGTTTCGTATAAGACCATGTCTGGGACATGGCATCAGCATTGATATGAGA
*
42507645 CTTCCTATAAGACCATATCTGGGATATGG
65 CTTCATATAAGACCATATCTGGGATATGG
42507674 TATCGATATG
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
96 84 0.97
97 3 0.03
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (96 bp):
TGGCATAGATGTGAGGTTTCGTATAAGACCATGTCTGGGACATGGCATCAGCATTGATATGAGAC
TTCATATAAGACCATATCTGGGATATGGCAT
Found at i:42521122 original size:29 final size:29
Alignment explanation
Indices: 42521032--42521191 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
42521022 ACTCGATTTC
* * **
42521032 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
42521061 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
42521089 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
42521119 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
42521148 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
42521177 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
42521192 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:42525602 original size:29 final size:29
Alignment explanation
Indices: 42525568--42525661 Score: 152
Period size: 29 Copynumber: 3.2 Consensus size: 29
42525558 GTGACGAGAT
**
42525568 TGGCACTAAGTGTGTGTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
42525597 TGGCACTGAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
42525626 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
42525655 CGGCACT
1 TGGCACT
42525662 GGGTGTGCGA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:42525686 original size:58 final size:58
Alignment explanation
Indices: 42525564--42525698 Score: 166
Period size: 58 Copynumber: 2.3 Consensus size: 58
42525554 TACGGTGACG
** * *
42525564 AGAT-TGGCACTAAGTGTGTGTGCTGGAAATATATGGCACTGAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGAGTGTGCATGCTCGAA
* *
42525621 ATATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGAGTGTGC-ATGCTCGAA
* * *
42525679 GGGTATGGCACTATGTGTGC
1 AGATATGGCACTAAGTGTGC
42525699 GGGCTTAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
57 3 0.05
58 62 0.94
59 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGAGTGTGCATGCTCGAA
Found at i:42533578 original size:29 final size:29
Alignment explanation
Indices: 42533545--42533705 Score: 162
Period size: 29 Copynumber: 5.6 Consensus size: 29
42533535 GTGACGAGAT
42533545 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* *
42533574 TGGCACTGAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
42533603 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* ** * * ***
42533632 CGGCACTGGGTGTGCGAGCTTGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
42533661 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
42533690 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
42533706 AAATCGAGTA
Statistics
Matches: 110, Mismatches: 21, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
28 2 0.02
29 108 0.98
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:42538923 original size:21 final size:20
Alignment explanation
Indices: 42538897--42538937 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42538887 CTAAACCGAT
* *
42538897 AACTTATGAAATTTTTTGAAA
1 AACTTA-GAAAATTTTGGAAA
42538918 AACTTAGAAAATTTTGGAAA
1 AACTTAGAAAATTTTGGAAA
42538938 CTACAGGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (20 bp):
AACTTAGAAAATTTTGGAAA
Done.