Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 98 of 132
Found at i:30066818 original size:24 final size:24
Alignment explanation
Indices: 30066786--30066833 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
30066776 TGTTTCTCTT
*
30066786 AAAATGTTTATAAAGAATATGAAA
1 AAAAAGTTTATAAAGAATATGAAA
*
30066810 AAAAAGTTTATAAAGAGTATGAAA
1 AAAAAGTTTATAAAGAATATGAAA
30066834 TGGTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (24 bp):
AAAAAGTTTATAAAGAATATGAAA
Found at i:30066970 original size:39 final size:40
Alignment explanation
Indices: 30066920--30067013 Score: 120
Period size: 39 Copynumber: 2.4 Consensus size: 40
30066910 TAAATTTATT
*
30066920 TTAGAAGTAATTTTCTATATTATAAGAAGTAAAGGAC-AA
1 TTAGGAGTAATTTTCTATATTATAAGAAGTAAAGGACGAA
* * * *
30066959 TTAGGAGTAATTTTCTATATTATAGGGAGTAGAGGGCGAA
1 TTAGGAGTAATTTTCTATATTATAAGAAGTAAAGGACGAA
*
30066999 -TAGGAGTAGTTTTCT
1 TTAGGAGTAATTTTCT
30067014 CATTTCGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
39 46 0.96
40 2 0.04
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.35
Consensus pattern (40 bp):
TTAGGAGTAATTTTCTATATTATAAGAAGTAAAGGACGAA
Found at i:30071772 original size:2 final size:2
Alignment explanation
Indices: 30071765--30071812 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
30071755 TACTAACACC
* *
30071765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30071807 TA TA TA
1 TA TA TA
30071813 CGCCTATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30071845 original size:15 final size:16
Alignment explanation
Indices: 30071816--30071846 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30071806 ATATATACGC
30071816 CTATTTATATTTTTAT
1 CTATTTATATTTTTAT
30071832 CTATTTAT-TTTTTAT
1 CTATTTATATTTTTAT
30071847 ATTTTCGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
CTATTTATATTTTTAT
Found at i:30072621 original size:30 final size:30
Alignment explanation
Indices: 30072587--30072821 Score: 162
Period size: 30 Copynumber: 7.9 Consensus size: 30
30072577 AAAGGTCCTT
* *
30072587 GAACTTTCTATAAATTACATTTTGACCCTC
1 GAACTTTCCAAAAATTACATTTTGACCCTC
** *
30072617 GAACTTTCCAAAAATTTGGA-TTTGAACCC-A
1 GAACTTTCCAAAAA-TTACATTTTG-ACCCTC
* * *
30072647 AAACTTTCCAAAAATAACATTTTG-TCCTC
1 GAACTTTCCAAAAATTACATTTTGACCCTC
* *
30072676 GAACTTTTCAAAAATCACATTTTGACCCTC
1 GAACTTTCCAAAAATTACATTTTGACCCTC
* ** *
30072706 GAACTTCCCAAAAATTTGGATTTT-ACCCTT
1 GAACTTTCCAAAAA-TTACATTTTGACCCTC
* *
30072736 GAACTTTCC-AAAATT-CAGATTTGACCCCC
1 GAACTTTCCAAAAATTACA-TTTTGACCCTC
* * * * *
30072765 AAACTTCCCAAAAATTTAAATTTAG-CCCCC
1 GAACTTTCCAAAAA-TTACATTTTGACCCTC
* *
30072795 GAACTTTTC-AAAATTTCATTTTGACCC
1 GAACTTTCCAAAAATTACATTTTGACCC
30072822 CATTTTTCCT
Statistics
Matches: 156, Mismatches: 37, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
27 1 0.01
28 14 0.09
29 45 0.29
30 77 0.49
31 18 0.12
32 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.34
Consensus pattern (30 bp):
GAACTTTCCAAAAATTACATTTTGACCCTC
Found at i:30072770 original size:89 final size:89
Alignment explanation
Indices: 30072598--30072779 Score: 215
Period size: 89 Copynumber: 2.0 Consensus size: 89
30072588 AACTTTCTAT
* *
30072598 AAATTACATTTTGACCCTCGAACTTTCCAAAAATTTGGATTTGAACCCAAAACTTTCCAAAAATA
1 AAATCACATTTTGACCCTCGAACTTCCCAAAAATTTGGATTTGAACCCAAAACTTTCCAAAAATA
* * * **
30072663 ACATTTTGTCCTCGAACTTTTCAA
66 ACATTTTGCCCCCAAACTTCCCAA
* ** *
30072687 AAATCACATTTTGACCCTCGAACTTCCCAAAAATTTGGATTT-TACCCTTGAACTTTCCAAAATT
1 AAATCACATTTTGACCCTCGAACTTCCCAAAAATTTGGATTTGAACCC-AAAACTTTCCAAAAAT
* *
30072751 CAGA-TTTGACCCCCAAACTTCCCAA
65 AACATTTTG-CCCCCAAACTTCCCAA
30072776 AAAT
1 AAAT
30072780 TTAAATTTAG
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
88 8 0.10
89 70 0.90
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.32
Consensus pattern (89 bp):
AAATCACATTTTGACCCTCGAACTTCCCAAAAATTTGGATTTGAACCCAAAACTTTCCAAAAATA
ACATTTTGCCCCCAAACTTCCCAA
Found at i:30072780 original size:59 final size:59
Alignment explanation
Indices: 30072601--30072822 Score: 198
Period size: 59 Copynumber: 3.7 Consensus size: 59
30072591 TTTCTATAAA
** * * *
30072601 TTACATTTTGACCCTCGAACTTTCCAAAAATTTGGATTTGAACCCAAAACTTTCCAAAAA-
1 TTACATTTT-ACCCTCGAACTTTCC-AAAATTCAGATTTGACCCCCAAACTTCCCAAAAAT
* ** * * * * *
30072661 TAACATTTTGTCCTCGAACTTTTCAAAAATCACATTTTGACCCTCGAACTTCCCAAAAAT
1 TTACATTTTACCCTCGAACTTTCCAAAATTCAGA-TTTGACCCCCAAACTTCCCAAAAAT
** *
30072721 TTGGATTTTACCCTTGAACTTTCCAAAATTCAGATTTGACCCCCAAACTTCCCAAAAAT
1 TTACATTTTACCCTCGAACTTTCCAAAATTCAGATTTGACCCCCAAACTTCCCAAAAAT
* * * *
30072780 TTA-AATTTAGCCCCCGAACTTTTCAAAATTTCA-TTTTGACCCC
1 TTACATTTTA-CCCTCGAACTTTCCAAAA-TTCAGATTTGACCCC
30072823 ATTTTTCCTT
Statistics
Matches: 128, Mismatches: 30, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
58 11 0.09
59 80 0.62
60 37 0.29
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.33
Consensus pattern (59 bp):
TTACATTTTACCCTCGAACTTTCCAAAATTCAGATTTGACCCCCAAACTTCCCAAAAAT
Found at i:30080831 original size:42 final size:39
Alignment explanation
Indices: 30080764--30080965 Score: 169
Period size: 39 Copynumber: 5.1 Consensus size: 39
30080754 CCCGACTACA
*
30080764 GGGCAAATTGA-AG-CATCCAATCTCTTACCCTAATCATG
1 GGGCAAATT-ACAGCCATCCAATCTCTTACCCTGATCATG
* *
30080802 GGGTAAATTACAGCCATTATCCAATCTCTTACCCCGATCATG
1 GGGCAAATTACAGCC---ATCCAATCTCTTACCCTGATCATG
* ** *
30080844 GGGCAGATTACAGCCATCTGATCTTTTA-CCTCGATCATG
1 GGGCAAATTACAGCCATCCAATCTCTTACCCT-GATCATG
* * * *
30080883 GAGCAGATTGCAGCCATCCAATCTCTTA-CCTCAATCATG
1 GGGCAAATTACAGCCATCCAATCTCTTACCCT-GATCATG
* * *
30080922 AGGCAAATTGCAGCCATCATCCAATCTCTTACCCCGATCATG
1 GGGCAAATTACAG-C--CATCCAATCTCTTACCCTGATCATG
30080964 GG
1 GG
30080966 TAGATTGCAG
Statistics
Matches: 133, Mismatches: 21, Indels: 16
0.78 0.12 0.09
Matches are distributed among these distances:
37 1 0.01
38 12 0.09
39 61 0.46
40 1 0.01
42 56 0.42
43 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (39 bp):
GGGCAAATTACAGCCATCCAATCTCTTACCCTGATCATG
Found at i:30080889 original size:39 final size:39
Alignment explanation
Indices: 30080820--30080981 Score: 175
Period size: 39 Copynumber: 4.1 Consensus size: 39
30080810 TACAGCCATT
* * *
30080820 ATCCAATCTCTTACCCCGATCATGGGGCAGATTACAGCC
1 ATCCAATCTCTTACCTCGATCATGGAGCAGATTGCAGCC
** *
30080859 ATCTGATCTTTTACCTCGATCATGGAGCAGATTGCAGCC
1 ATCCAATCTCTTACCTCGATCATGGAGCAGATTGCAGCC
* *
30080898 ATCCAATCTCTTACCTCAATCAT-GAGGCAAATTGCAGCCATC
1 ATCCAATCTCTTACCTCGATCATGGA-GCAGATTGCAG-C--C
* * *
30080940 ATCCAATCTCTTACCCCGATCATGG-GTAGATTGCAGTC
1 ATCCAATCTCTTACCTCGATCATGGAGCAGATTGCAGCC
30080978 ATCC
1 ATCC
30080982 GAAGCAATAA
Statistics
Matches: 102, Mismatches: 16, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
38 7 0.07
39 62 0.61
40 1 0.01
41 9 0.09
42 22 0.22
43 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (39 bp):
ATCCAATCTCTTACCTCGATCATGGAGCAGATTGCAGCC
Found at i:30080920 original size:78 final size:79
Alignment explanation
Indices: 30080820--30080981 Score: 202
Period size: 78 Copynumber: 2.1 Consensus size: 79
30080810 TACAGCCATT
* * * * * *
30080820 ATCCAATCTCTTACCCCGATCATGGGGCAGATTACAGCCATC-T-GATCTTTTACCTCGATCATG
1 ATCCAATCTCTTACCCCAATCATGAGGCAAATTACAGCCATCATCAATCTCTTACCCCGATCATG
30080883 GAGCAGATTGCAGCC
66 G-GCAGATTGCAGCC
* *
30080898 ATCCAATCTCTTACCTCAATCATGAGGCAAATTGCAGCCATCATCCAATCTCTTACCCCGATCAT
1 ATCCAATCTCTTACCCCAATCATGAGGCAAATTACAGCCATCAT-CAATCTCTTACCCCGATCAT
* *
30080963 GGGTAGATTGCAGTC
65 GGGCAGATTGCAGCC
30080978 ATCC
1 ATCC
30080982 GAAGCAATAA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
78 37 0.52
79 1 0.01
80 15 0.21
81 18 0.25
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (79 bp):
ATCCAATCTCTTACCCCAATCATGAGGCAAATTACAGCCATCATCAATCTCTTACCCCGATCATG
GGCAGATTGCAGCC
Found at i:30081313 original size:85 final size:85
Alignment explanation
Indices: 30081169--30081324 Score: 215
Period size: 85 Copynumber: 1.8 Consensus size: 85
30081159 ATCTTTCTGA
* * * * * *
30081169 TGAGATACAAAGAAGTGGGTCGAAGCAATAAAGTCGTCATCTTCCTAATGAGATGCAGAGAAGTG
1 TGAGATACAAAGAAGTGGATCAAAACAATAAAGTCGTCATATTCCTAATGAGATACAGAGAAGTA
30081234 GACCAAATCCGTCTTCTTGT
66 GACCAAATCCGTCTTCTTGT
* * *
30081254 TGAGATACAGAGAAGTGGATTAAAACAATGAAG-CTGTCATATTCCTAATGAGATACAGAGAAGT
1 TGAGATACAAAGAAGTGGATCAAAACAATAAAGTC-GTCATATTCCTAATGAGATACAGAGAAGT
30081318 AGACCAA
65 AGACCAA
30081325 TTCAATGAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 1 0.02
85 60 0.98
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (85 bp):
TGAGATACAAAGAAGTGGATCAAAACAATAAAGTCGTCATATTCCTAATGAGATACAGAGAAGTA
GACCAAATCCGTCTTCTTGT
Found at i:30081342 original size:208 final size:207
Alignment explanation
Indices: 30080983--30082004 Score: 1298
Period size: 208 Copynumber: 5.0 Consensus size: 207
30080973 CAGTCATCCG
* ** * * * *
30080983 AAGCAATAAAGTGGTCATCTTCCTGACAATATGCAGAGAAGTGAACCAAATCCGTCTTCCTGATG
1 AAGCAATAAAG-CGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCTTGATG
* * * *
30081048 AGATATAGAGAAGTGGATTAAAATAATGAAGCGGTCATCTTCCTGATGAGATATAGAGAAGTAGA
65 AGATATAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGA
* * * * *
30081113 TCAAATCTATGAAGTGAAGCTCAACATGAATGAGACTTCAAACCCCATCTTTCTGATGAGATACA
130 CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTTCTGATGAGATACA
* *
30081178 AAGAAGTGGGTCG
195 GAGAAGTGGGTCA
* * *
30081191 AAGCAATAAAGTCGTCATCTTCCTAATGAGATGCAGAGAAGTGGACCAAATCCGTCTTCTTGTTG
1 AAGCAATAAAG-CGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCTTGATG
* * * * * *
30081256 AGATACAGAGAAGTGGATTAAAACAATGAAGCTGTCATATTCCTAATGAGATACAGAGAAGTAGA
65 AGATATAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGA
* * ** * *
30081321 CCAATTCAATGAAACGAAGCTCAATATAAATGAGACTTCAAACCTCATCTTCCTGATGAGATACA
130 CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTTCTGATGAGATACA
30081386 GAGAAGTGGGTCA
195 GAGAAGTGGGTCA
* * * * * *
30081399 AAGTAATAAAGCGGTCATCTTCTTGATGAGATACAGAGAAGTGAATCAAATTCATCTT-TCTGAT
1 AAGCAATAAAGC-GTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCT-TGAT
* * *
30081463 GAGATATAGAGAAGTGGATTGAAACAATGAGGCGGTCATATTCTTGATGAGATACTGAGAAGTAG
64 GAGATATAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAG
*
30081528 ACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATC-TTCTTGATAAGATA
129 ACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTTC-TGATGAGATA
30081592 CAGAGAAGTGGGTCA
193 CAGAGAAGTGGGTCA
* * * ** * *
30081607 AAGCAATAAAGCGATCATCTTCCTGATAAGATACAAAAAAGAAGACTAAATTCGTCTTCTTGATG
1 AAGCAATAAAGCG-TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCTTGATG
* *
30081672 AGATATAGAGAAATGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAAA
65 AGATATAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGA
* *
30081737 CCAAATCAATGAAGCGATGCTCAATACGAATGAGACTTCAAACCTCATC-TTCTTGATGAGATAC
130 CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTTC-TGATGAGATAC
30081801 AGAGAAGTGGGT--
194 AGAGAAGTGGGTCA
** * *
30081813 ---C---AAA---TCATCTTCCCAATGAGATACAAAGAAGTGGACCAAATCCGTCTTCCTGATGA
1 AAGCAATAAAGCGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCTTGATGA
*
30081869 GATATAGAGAAGTGGATTGAAACAATGAGGCGATCATCTTCCTGATGAGATACAGAGAAGTAGAC
66 GATATAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGAC
** * * * *
30081934 CAAATCAATGAAGTAAAGCTCAATAAGAATGAGACTTCAAACCCCATCTTCCTTATGACATACAG
131 CAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTTCTGATGAGATACAG
30081999 AGAAGT
196 AGAAGT
30082005 TCATCTTCTT
Statistics
Matches: 721, Mismatches: 87, Indels: 24
0.87 0.10 0.03
Matches are distributed among these distances:
196 165 0.23
197 2 0.00
200 3 0.00
203 1 0.00
207 5 0.01
208 544 0.75
209 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (207 bp):
AAGCAATAAAGCGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCTTGATGA
GATATAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGAC
CAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTTCTGATGAGATACAG
AGAAGTGGGTCA
Found at i:30081474 original size:85 final size:85
Alignment explanation
Indices: 30081365--30081525 Score: 225
Period size: 85 Copynumber: 1.9 Consensus size: 85
30081355 ACTTCAAACC
* *
30081365 TCATCTTCCTGATGAGATACAGAGAAGTGG-GTCAAAGTAATAAAGCGGTCATCTTCTTGATGAG
1 TCATCTTCCTGATGAGATACAGAGAAGTGGAGTCAAA-CAATAAAGCGGTCATATTCTTGATGAG
30081429 ATACAGAGAAGTGAATCAAAT
65 ATACAGAGAAGTGAATCAAAT
* * * * * *
30081450 TCATCTTTCTGATGAGATATAGAGAAGTGGATTGAAACAATGAGGCGGTCATATTCTTGATGAGA
1 TCATCTTCCTGATGAGATACAGAGAAGTGGAGTCAAACAATAAAGCGGTCATATTCTTGATGAGA
*
30081515 TACTGAGAAGT
66 TACAGAGAAGT
30081526 AGACCAAATC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
85 62 0.94
86 4 0.06
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (85 bp):
TCATCTTCCTGATGAGATACAGAGAAGTGGAGTCAAACAATAAAGCGGTCATATTCTTGATGAGA
TACAGAGAAGTGAATCAAAT
Found at i:30081870 original size:37 final size:36
Alignment explanation
Indices: 30081781--30081884 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 36
30081771 ACTTCAAACC
* **
30081781 TCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAA
1 TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAA
** *
30081817 TCATCTTCCCAATGAGATACAAAGAAGTGGACCAAA
1 TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAA
* *
30081853 TCCGTCTTCCTGATGAGATATAGAGAAGTGGA
1 T-CATCTTCCTGATGAGATACAGAGAAGTGGA
30081885 TTGAAACAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
36 31 0.55
37 25 0.45
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (36 bp):
TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAA
Found at i:30082010 original size:28 final size:28
Alignment explanation
Indices: 30081978--30082032 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
30081968 CTTCAAACCC
*
30081978 CATCTTCCTT-ATGACATACAGAGAAGTT
1 CATCTT-CTTGATAACATACAGAGAAGTT
*
30082006 CATCTTCTTGATAAGATACAGAGAAGT
1 CATCTTCTTGATAACATACAGAGAAGT
30082033 AGACCAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (28 bp):
CATCTTCTTGATAACATACAGAGAAGTT
Found at i:30083658 original size:30 final size:30
Alignment explanation
Indices: 30083622--30083824 Score: 150
Period size: 29 Copynumber: 6.9 Consensus size: 30
30083612 AAGGTTCTCG
*
30083622 AACTTTCTAAAAATTCAAATTTGACCCCCA
1 AACTTTCCAAAAATTCAAATTTGACCCCCA
* * *
30083652 AACTTTCCAAAAA-TCATATCTTG-TCCTCA
1 AACTTTCCAAAAATTCAAAT-TTGACCCCCA
* * * *
30083681 AACTTCCCAAAAA-TCACACTTGACCCCCG
1 AACTTTCCAAAAATTCAAATTTGACCCCCA
* * **
30083710 AACTTTCCAAAAATTTAAAATTGACCCCTG
1 AACTTTCCAAAAATTCAAATTTGACCCCCA
***
30083740 AACTTTCC-AAAATTTGGATTTGA-CCCCA
1 AACTTTCCAAAAATTCAAATTTGACCCCCA
*
30083768 AAC-TTCCTAAAAATTCAAATTT-AGCCCCCG
1 AACTTTCC-AAAAATTCAAATTTGA-CCCCCA
* * **
30083798 AACTTTCTAAAATTTCATTTTTGACCC
1 AACTTTCCAAAAATTCAAATTTGACCC
30083825 TATTTTCCCT
Statistics
Matches: 136, Mismatches: 28, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
27 4 0.03
28 10 0.07
29 62 0.46
30 56 0.41
31 4 0.03
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (30 bp):
AACTTTCCAAAAATTCAAATTTGACCCCCA
Found at i:30083796 original size:88 final size:88
Alignment explanation
Indices: 30083620--30083814 Score: 223
Period size: 88 Copynumber: 2.2 Consensus size: 88
30083610 AGAAGGTTCT
* * * *
30083620 CGAACTTTCTAAAAATTCAAATTTGACCCCCAAACTTTCCAAAAATCATATCTTGTCCTCAAACT
1 CGAACTTTCTAAAAATTCAAAATTGACCCCCAAACTTTCCAAAAATCAGATCTTGACCCCAAACT
*
30083685 TCCCAAAAATCACACTTGACCCC
66 TCCCAAAAATCAAACTTGACCCC
* * ** * **
30083708 CGAACTTTCCAAAAATTTAAAATTGACCCCTGAACTTTCCAAAATTTGGAT-TTGACCCCAAACT
1 CGAACTTTCTAAAAATTCAAAATTGACCCCCAAACTTTCCAAAAATCAGATCTTGACCCCAAACT
* *
30083772 TCCTAAAAATTCAAA-TTTAGCCCC
66 TCCCAAAAA-TCAAACTTGA-CCCC
*
30083796 CGAACTTTCTAAAATTTCA
1 CGAACTTTCTAAAAATTCA
30083815 TTTTTGACCC
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
87 22 0.25
88 66 0.75
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.29
Consensus pattern (88 bp):
CGAACTTTCTAAAAATTCAAAATTGACCCCCAAACTTTCCAAAAATCAGATCTTGACCCCAAACT
TCCCAAAAATCAAACTTGACCCC
Found at i:30087091 original size:8 final size:8
Alignment explanation
Indices: 30087080--30087122 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
30087070 ATAAAAAAAT
30087080 TAATTTAA
1 TAATTTAA
30087088 TAATTTAA
1 TAATTTAA
30087096 TAATTATAA
1 TAATT-TAA
30087105 -AATTATAAA
1 TAATT-T-AA
30087114 TAATTTAA
1 TAATTTAA
30087122 T
1 T
30087123 TTCGACCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 22 0.69
9 6 0.19
10 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TAATTTAA
Found at i:30092479 original size:36 final size:35
Alignment explanation
Indices: 30092423--30092536 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 35
30092413 GGTAAACAGA
*
30092423 GAGTAAAATGAGCATAATGACCTTTAGGTCAATAG
1 GAGTAAAATGAGCATCATGACCTTTAGGTCAATAG
* * *
30092458 GTAGTAAAATAAGAATCATGACCTTTAGGTCAACAAG
1 G-AGTAAAATGAGCATCATGACCTTTAGGTCAA-TAG
*
30092495 GAGTAAAATGAGCATCATGACCTTTGGGTCAATAGG
1 GAGTAAAATGAGCATCATGACCTTTAGGTCAATA-G
30092531 GAGTAA
1 GAGTAA
30092537 GCATAACCTT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
35 2 0.03
36 63 0.93
37 3 0.04
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (35 bp):
GAGTAAAATGAGCATCATGACCTTTAGGTCAATAG
Found at i:30108814 original size:6 final size:6
Alignment explanation
Indices: 30108805--30108856 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
30108795 CAAATTTATT
* **
30108805 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTATCTT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA
30108854 TTT
1 TTT
30108857 GCTTTAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 4 0.11
6 29 0.78
8 4 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (6 bp):
TTTAAA
Found at i:30108826 original size:17 final size:18
Alignment explanation
Indices: 30108796--30108856 Score: 97
Period size: 17 Copynumber: 3.3 Consensus size: 18
30108786 AAATTGATTC
30108796 AAATTTATTTTTAAATTT
1 AAATTTATTTTTAAATTT
30108814 AAATTTA-TTTTAAATTT
1 AAATTTATTTTTAAATTT
30108831 AAATTTATCTTTTTAAATTT
1 AAATTTA--TTTTTAAATTT
30108851 AAATTT
1 AAATTT
30108857 GCTTTAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.43
18 7 0.17
20 16 0.40
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
AAATTTATTTTTAAATTT
Found at i:30108847 original size:37 final size:36
Alignment explanation
Indices: 30108796--30108873 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 36
30108786 AAATTGATTC
*
30108796 AAATTTATTTTTAAATTTAAATTTATTTTAAA-TTT
1 AAATTTATTTTTAAATTTAAATTTACTTTAAATTTT
*
30108831 AAATTTATCTTTTTAAATTTAAATTTGCTTTAAATTTT
1 AAATTTA--TTTTTAAATTTAAATTTACTTTAAATTTT
30108869 AAATT
1 AAATT
30108874 CAATCAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 7 0.18
37 23 0.61
38 8 0.21
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (36 bp):
AAATTTATTTTTAAATTTAAATTTACTTTAAATTTT
Found at i:30108864 original size:17 final size:17
Alignment explanation
Indices: 30108805--30108873 Score: 84
Period size: 17 Copynumber: 3.8 Consensus size: 17
30108795 CAAATTTATT
*
30108805 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAC
30108822 TTTAAATTTAAATTTATC
1 TTTAAATTTAAATTTA-C
*
30108840 TTTTTAAATTTAAATTTGC
1 --TTTAAATTTAAATTTAC
30108859 TTTAAATTTTAAATT
1 TTTAAA-TTTAAATT
30108874 CAATCAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
17 22 0.48
18 8 0.17
19 1 0.02
20 15 0.33
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (17 bp):
TTTAAATTTAAATTTAC
Found at i:30110748 original size:30 final size:30
Alignment explanation
Indices: 30110713--30110910 Score: 197
Period size: 30 Copynumber: 6.6 Consensus size: 30
30110703 AAACTATCCA
*
30110713 AAAATTATATTTTGACACCCGAAATTTTTC-
1 AAAATTATATTTTGAC-CCCTAAATTTTTCT
* * *
30110743 AAAATTATATTTTGACCTCAAAACTTTTTGT
1 AAAATTATATTTTGACCCCTAAA-TTTTTCT
* *
30110774 -AAATTACATTTTGACCCCTAAACTTTTCT
1 AAAATTATATTTTGACCCCTAAATTTTTCT
* **
30110803 AAAATTATATTTT-AACCCTAAAACTTTCT
1 AAAATTATATTTTGACCCCTAAATTTTTCT
* * *
30110832 ATAAGTTACATTTTAACCCCTAAATTTTTCT
1 A-AAATTATATTTTGACCCCTAAATTTTTCT
**
30110863 AAAATTATATTTTGA-CCCTAAAACTTTCT
1 AAAATTATATTTTGACCCCTAAATTTTTCT
* *
30110892 AAAATTACATTTTTACCCC
1 AAAATTATATTTTGACCCC
30110911 CAAGTTTCCA
Statistics
Matches: 138, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
29 49 0.36
30 75 0.54
31 14 0.10
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.42
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCTAAATTTTTCT
Found at i:30110785 original size:60 final size:59
Alignment explanation
Indices: 30110714--30110910 Score: 263
Period size: 60 Copynumber: 3.3 Consensus size: 59
30110704 AACTATCCAA
* * *
30110714 AAATTATATTTTGACACCCGAAATTTTTC-AAAATTATATTTTGA-CCTCAAAACTTTTTGT
1 AAATTACATTTTGAC-CCCTAAATTTTTCTAAAATTATATTTTGACCCT-AAAACTTTCT-T
* *
30110774 AAATTACATTTTGACCCCTAAACTTTTCTAAAATTATATTTTAACCCTAAAACTTTCTAT
1 AAATTACATTTTGACCCCTAAATTTTTCTAAAATTATATTTTGACCCTAAAACTTTCT-T
* * *
30110834 AAGTTACATTTTAACCCCTAAATTTTTCTAAAATTATATTTTGACCCTAAAACTTTCTA
1 AAATTACATTTTGACCCCTAAATTTTTCTAAAATTATATTTTGACCCTAAAACTTTCTT
*
30110893 AAATTACATTTTTACCCC
1 AAATTACATTTTGACCCC
30110911 CAAGTTTCCA
Statistics
Matches: 122, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
59 27 0.22
60 92 0.75
61 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.42
Consensus pattern (59 bp):
AAATTACATTTTGACCCCTAAATTTTTCTAAAATTATATTTTGACCCTAAAACTTTCTT
Found at i:30110964 original size:29 final size:28
Alignment explanation
Indices: 30110892--30111083 Score: 105
Period size: 29 Copynumber: 6.6 Consensus size: 28
30110882 AAAACTTTCT
* *
30110892 AAAATTA-CATTTTTACCCCCAAGTTT-CC
1 AAAATTACCA-TTTTA-CCCCGACTTTACC
*
30110920 ATAATT-CCATTTTTACCCTCGA-TTTCACC
1 AAAATTACCA-TTTTACCC-CGACTTT-ACC
*
30110949 AAAATTACCATTTTACCCCCGAACTTT-CT
1 AAAATTACCATTTTA-CCCCG-ACTTTACC
* *
30110978 AAAATT-CTATTTTAAACCCCGATTTTACC
1 AAAATTACCATTTT--ACCCCGACTTTACC
30111007 AAAAATTACCATTTTACCCCCGAACTTT-CC
1 -AAAATTACCATTTTA-CCCCG-ACTTTACC
* * *
30111037 AAAA-TCCCATTTTTGA-CCCAATTTTAACC
1 AAAATTACCA-TTTT-ACCCCGACTTT-ACC
30111066 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
30111084 TCGGGTATCT
Statistics
Matches: 130, Mismatches: 13, Indels: 41
0.71 0.07 0.22
Matches are distributed among these distances:
27 10 0.08
28 33 0.25
29 48 0.37
30 26 0.20
31 13 0.10
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCGACTTTACC
Found at i:30111030 original size:59 final size:57
Alignment explanation
Indices: 30110892--30111083 Score: 228
Period size: 58 Copynumber: 3.3 Consensus size: 57
30110882 AAAACTTTCT
* * * *
30110892 AAAATTA-CATTTTTACCCCC-AAGTTTCCATAATTCCATTTTTACCCTCGATTTCACC
1 AAAATTACCA-TTTTACCCCCGAACTTTCCAAAATTCCATTTTAACCC-CGATTTTACC
* *
30110949 AAAATTACCATTTTACCCCCGAACTTTCTAAAATTCTATTTTAAACCCCGATTTTACC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTT-AACCCCGATTTTACC
* * *
30111007 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTGA-CCCAATTTTAACC
1 -AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTT-ACC
30111066 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
30111084 TCGGGTATCT
Statistics
Matches: 118, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
57 17 0.14
58 54 0.46
59 43 0.36
60 4 0.03
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.35
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTAACCCCGATTTTACC
Found at i:30119590 original size:101 final size:100
Alignment explanation
Indices: 30119411--30119863 Score: 671
Period size: 101 Copynumber: 4.5 Consensus size: 100
30119401 GAAATACAAC
* * * * *
30119411 GGGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAGATACAGAAGGGAAAGGTCTAAG
1 GGGAAAGATCTAAGACCGCAATGGCAGATCCAGTACCGCAAAGACACAAAAGGGAAAGGTCTAAG
*
30119476 TCGCAACGACGGACCGTGTACCTCAGAAGCATGAAA
66 TCGCAACGGCGGACCGTGTACCTCAGAAGCATG-AA
*
30119512 GGGAAAGATCTAATACCGCAATGGCAGATCCAGTACCGCCAAA-ACACAAAAGGGAAAGGTCTAA
1 GGGAAAGATCTAAGACCGCAATGGCAGATCCAGTACCG-CAAAGACACAAAAGGGAAAGGTCTAA
*
30119576 GTTGCAACGGCGGACCGTGTACCTCAGAAGCATGAA
65 GTCGCAACGGCGGACCGTGTACCTCAGAAGCATGAA
* * *
30119612 GGGAAAGATCTAAGACCGCAACT-GCAGATCTAGTACCGCAAAGATACAATAGGGAAAGGTCTAA
1 GGGAAAGATCTAAGACCGCAA-TGGCAGATCCAGTACCGCAAAGACACAAAAGGGAAAGGTCTAA
*
30119676 GTCGCAACGGCGGACCGTGCACCTCAGAAGCATGAAA
65 GTCGCAACGGCGGACCGTGTACCTCAGAAGCATG-AA
*
30119713 GGGAAAGATCTAAGACTGCAATGGCAGATCCAGTACCGCCAAA-ACACAAAAGGGAAAGGTCTAA
1 GGGAAAGATCTAAGACCGCAATGGCAGATCCAGTACCG-CAAAGACACAAAAGGGAAAGGTCTAA
30119777 GTCGCAACGGCGGACCGTGTACCAT-AGAAGCATGAA
65 GTCGCAACGGCGGACCGTGTACC-TCAGAAGCATGAA
* * * *
30119813 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTAAAGATACAAAA
1 GGGAAAGATCTAAGACCGCAATGGCAGATCCAGTACCGCAAAGACACAAAA
30119864 AGTGCAATGG
Statistics
Matches: 320, Mismatches: 24, Indels: 17
0.89 0.07 0.05
Matches are distributed among these distances:
99 7 0.02
100 132 0.41
101 172 0.54
102 9 0.03
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.13
Consensus pattern (100 bp):
GGGAAAGATCTAAGACCGCAATGGCAGATCCAGTACCGCAAAGACACAAAAGGGAAAGGTCTAAG
TCGCAACGGCGGACCGTGTACCTCAGAAGCATGAA
Found at i:30119756 original size:201 final size:199
Alignment explanation
Indices: 30119411--30119862 Score: 771
Period size: 201 Copynumber: 2.2 Consensus size: 199
30119401 GAAATACAAC
30119411 GGGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAGATACAGAAGGGAAAGGTCTAAG
1 GGGAAAGATCTAAGACCGCAACG-CGGATCCAGTACCGCAAAGATACA-AAGGGAAAGGTCTAAG
* *
30119476 TCGCAACGACGGACCGTGTACCTCAGAAGCATGAAAGGGAAAGATCTAATACCGCAATGGCAGAT
64 TCGCAACGACGGACCGTGCACCTCAGAAGCATGAAAGGGAAAGATCTAAGACCGCAATGGCAGAT
*
30119541 CCAGTACCGCCAAAACACAAAAGGGAAAGGTCTAAGTTGCAACGGCGGACCGTGTACC-TCAGAA
129 CCAGTACCGCCAAAACACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCAT-AGAA
30119605 GCATGAA
193 GCATGAA
* *
30119612 GGGAAAGATCTAAGACCGCAACTGCAGATCTAGTACCGCAAAGATACAATAGGGAAAGGTCTAAG
1 GGGAAAGATCTAAGACCGCAAC-GCGGATCCAGTACCGCAAAGATACAA-AGGGAAAGGTCTAAG
* *
30119677 TCGCAACGGCGGACCGTGCACCTCAGAAGCATGAAAGGGAAAGATCTAAGACTGCAATGGCAGAT
64 TCGCAACGACGGACCGTGCACCTCAGAAGCATGAAAGGGAAAGATCTAAGACCGCAATGGCAGAT
30119742 CCAGTACCGCCAAAACACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCATAGAAG
129 CCAGTACCGCCAAAACACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCATAGAAG
30119807 CATGAA
194 CATGAA
*
30119813 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTAAAGATACAAA
1 GGGAAAGATCTAAGACCGCAAC-GCGGATCCAGTACCGCAAAGATACAAA
30119863 AAGTGCAATG
Statistics
Matches: 237, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
200 2 0.01
201 233 0.98
202 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.13
Consensus pattern (199 bp):
GGGAAAGATCTAAGACCGCAACGCGGATCCAGTACCGCAAAGATACAAAGGGAAAGGTCTAAGTC
GCAACGACGGACCGTGCACCTCAGAAGCATGAAAGGGAAAGATCTAAGACCGCAATGGCAGATCC
AGTACCGCCAAAACACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCATAGAAGCA
TGAA
Found at i:30120091 original size:17 final size:18
Alignment explanation
Indices: 30120069--30120108 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
30120059 AAATTGATTC
*
30120069 AAATTTATTTTAAA-TTT
1 AAATTTACTTTAAATTTT
*
30120086 AAATTTGCTTTAAATTTT
1 AAATTTACTTTAAATTTT
30120104 AAATT
1 AAATT
30120109 CAATCAAATT
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:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (18 bp):
AAATTTACTTTAAATTTT
Found at i:30120390 original size:25 final size:25
Alignment explanation
Indices: 30120344--30120391 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
30120334 CTGCTGTTGC
* *
30120344 CCACTAGCTCCACTCTATCCTGCCA
1 CCACCAGCTCCACTCTACCCTGCCA
30120369 CCACCAGCTCCAC-CTTACCCTGC
1 CCACCAGCTCCACTC-TACCCTGC
30120392 TACCGCCGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.19, C:0.52, G:0.08, T:0.21
Consensus pattern (25 bp):
CCACCAGCTCCACTCTACCCTGCCA
Found at i:30121109 original size:30 final size:30
Alignment explanation
Indices: 30121050--30121191 Score: 162
Period size: 30 Copynumber: 4.7 Consensus size: 30
30121040 CCCTAAACTG
* **
30121050 TCTAGAAATTATATTTTGACACTCGAACTTT
1 TCTA-AAATTATATTTTGACCCTAAAACTTT
*
30121081 TCCAAAATTATATTTTGACCCTAAAACTTT
1 TCTAAAATTATATTTTGACCCTAAAACTTT
* * *
30121111 T-TATAAATTACATTTTAACCCTAAAACTTA
1 TCTA-AAATTATATTTTGACCCTAAAACTTT
*
30121141 TCTAAAATTATATTTTTACCCTAAAAC-TT
1 TCTAAAATTATATTTTGACCCTAAAACTTT
* *
30121170 TCTAAAATTACATTTTTACCCT
1 TCTAAAATTATATTTTGACCCT
30121192 CAAGTTATCC
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
29 23 0.24
30 69 0.71
31 5 0.05
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (30 bp):
TCTAAAATTATATTTTGACCCTAAAACTTT
Found at i:30121139 original size:60 final size:59
Alignment explanation
Indices: 30121040--30121191 Score: 180
Period size: 60 Copynumber: 2.6 Consensus size: 59
30121030 CCTTAGAGGT
* * * * ** *
30121040 CCCT-AAACTGTCTAGAAATTATATTTTGACACTCGAACTTTTCCAAAATTATATTTTGA
1 CCCTAAAACTTTCTA-AAATTACATTTTAACCCTAAAACTTATCCAAAATTATATTTTGA
* * *
30121099 CCCTAAAACTTTTTATAAATTACATTTTAACCCTAAAACTTATCTAAAATTATATTTTTA
1 CCCTAAAACTTTCTA-AAATTACATTTTAACCCTAAAACTTATCCAAAATTATATTTTGA
*
30121159 CCCTAAAACTTTCTAAAATTACATTTTTACCCT
1 CCCTAAAACTTTCTAAAATTACATTTTAACCCT
30121192 CAAGTTATCC
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 21 0.27
60 58 0.73
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.41
Consensus pattern (59 bp):
CCCTAAAACTTTCTAAAATTACATTTTAACCCTAAAACTTATCCAAAATTATATTTTGA
Found at i:30121236 original size:29 final size:29
Alignment explanation
Indices: 30121115--30121306 Score: 83
Period size: 29 Copynumber: 6.6 Consensus size: 29
30121105 AACTTTTTAT
* * * * *
30121115 AAATTACATTTTAACCCTAAAACTTATCTA
1 AAATTCCATTTTTACCCT-CAAGTTATCCA
** * * *
30121145 AAATTATATTTTTACCCTAAAACTT-TCTA
1 AAATTCCATTTTTACCCT-CAAGTTATCCA
*
30121174 AAATTACATTTTTACCCTCAAGTTATCCA
1 AAATTCCATTTTTACCCTCAAGTTATCCA
* * * *
30121203 TAATTCCATTTTTGCCCTCGATTTCA-CCA
1 AAATTCCATTTTTACCCTCAAGTT-ATCCA
* * *
30121232 AAATTACCA-TTTTACCCTTGAACTT-TCTA
1 AAATT-CCATTTTTACCC-TCAAGTTATCCA
* *
30121261 AAATTCCATTTTAACCC-CAA-TTTTACCAA
1 AAATTCCATTTTTACCCTCAAGTTAT-CC-A
30121290 AAATTACCA-TTTTACCC
1 AAATT-CCATTTTTACCC
30121307 CCGAACTTTC
Statistics
Matches: 131, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
26 2 0.02
27 3 0.02
28 8 0.06
29 84 0.64
30 34 0.26
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.39
Consensus pattern (29 bp):
AAATTCCATTTTTACCCTCAAGTTATCCA
Found at i:30121266 original size:58 final size:57
Alignment explanation
Indices: 30121173--30121366 Score: 207
Period size: 58 Copynumber: 3.4 Consensus size: 57
30121163 AAAACTTTCT
* * *
30121173 AAAATTA-CATTTTTACCCTC-AAGTTATCCATAATTCCATTTTTGCCCTCGATTTCACC
1 AAAATTACCA-TTTTACCCTCGAACTT-TCCAAAATTCCATTTTTGCCC-CAATTTCACC
* * ** *
30121231 AAAATTACCATTTTACCCTTGAACTTTCTAAAATTCCATTTTAACCCCAATTTTACC
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGCCCCAATTTCACC
* * *
30121288 AAAAATTACCATTTTACCCCCGAACTTTCCAAAA-TCTCA-TTTTGACCCAATTTCAACA
1 -AAAATTACCATTTTACCCTCGAACTTTCCAAAATTC-CATTTTTGCCCCAATTTC-ACC
30121346 AAAATTACCATTTTACCCTCG
1 AAAATTACCATTTTACCCTCG
30121367 GGTATCCAAA
Statistics
Matches: 114, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
57 41 0.36
58 67 0.59
59 6 0.05
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (57 bp):
AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGCCCCAATTTCACC
Found at i:30121307 original size:29 final size:29
Alignment explanation
Indices: 30121260--30121360 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 29
30121250 TGAACTTTCT
30121260 AAAATTCCATTTTAACCCCAATTTTACCA
1 AAAATTCCATTTTAACCCCAATTTTACCA
* *
30121289 AAAATTACCATTTTACCCCCGAACTTT-CC-
1 AAAATT-CCATTTTAACCCC-AATTTTACCA
* * *
30121318 AAAA-TCTCATTTTGA-CCCAATTTCAACA
1 AAAATTC-CATTTTAACCCCAATTTTACCA
30121346 AAAATTACCATTTTA
1 AAAATT-CCATTTTA
30121361 CCCTCGGGTA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
26 4 0.07
27 5 0.09
28 11 0.19
29 17 0.30
30 15 0.26
31 5 0.09
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAATTCCATTTTAACCCCAATTTTACCA
Found at i:30128627 original size:18 final size:18
Alignment explanation
Indices: 30128584--30128644 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
30128574 TGTGAGTGTT
*
30128584 GAAGCAGAAGAAGAGAAAA
1 GAAGAAGAAGAAG-GAAAA
*
30128603 GAA-AAGAGGAAGGAAAA
1 GAAGAAGAAGAAGGAAAA
*
30128620 GAAGAAGAAGAAGAAAAA
1 GAAGAAGAAGAAGGAAAA
30128638 GAAGAAG
1 GAAGAAG
30128645 TTGTCCCGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 8 0.22
18 26 0.70
19 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.33, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAGAAGGAAAA
Found at i:30128629 original size:6 final size:6
Alignment explanation
Indices: 30128584--30128644 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
30128574 TGTGAGTGTT
* *
30128584 GAAGCA GAAGAA G-AGAA -AAGAA -AAGAG GAAGGAA -AAGAA GAAGAA
1 GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAA-GAA GAAGAA GAAGAA
*
30128629 GAAGAA AAAGAA GAAG
1 GAAGAA GAAGAA GAAG
30128645 TTGTCCCGAC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
5 15 0.33
6 29 0.63
7 2 0.04
ACGTcount: A:0.66, C:0.02, G:0.33, T:0.00
Consensus pattern (6 bp):
GAAGAA
Found at i:30132795 original size:20 final size:21
Alignment explanation
Indices: 30132770--30132808 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30132760 ATTGTATGAA
*
30132770 TATATG-ATTAAATATGCTTG
1 TATATGAATAAAATATGCTTG
30132790 TATATGAATAAAATATGCT
1 TATATGAATAAAATATGCT
30132809 GAAAATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (21 bp):
TATATGAATAAAATATGCTTG
Found at i:30134122 original size:28 final size:29
Alignment explanation
Indices: 30134089--30134160 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
30134079 TATTATGTAG
* *
30134089 ATAATATATATGTGTGGGCTTTATTTTAT
1 ATAATATATATGTATGGGCTTTATTATAT
*
30134118 A-AATATATATGCATGGGCTTTATTATAT
1 ATAATATATATGTATGGGCTTTATTATAT
*
30134146 ATAGTATATATGTAT
1 ATAATATATATGTAT
30134161 ATGCATGGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 25 0.68
29 12 0.32
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.47
Consensus pattern (29 bp):
ATAATATATATGTATGGGCTTTATTATAT
Found at i:30134480 original size:2 final size:2
Alignment explanation
Indices: 30134473--30134498 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30134463 GTATAATTTG
30134473 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
30134499 GTTAGTGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30135798 original size:16 final size:16
Alignment explanation
Indices: 30135777--30135841 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 16
30135767 TTAAACAATC
30135777 AGGCTTTGTGCCTAGT
1 AGGCTTTGTGCCTAGT
30135793 AGGCTTTGTGCCGGT-GTTTT
1 AGGCTTTGTGCC--TAG---T
30135813 CAGGCTTTGTGCCTAGT
1 -AGGCTTTGTGCCTAGT
*
30135830 AGGCTTCGTGCC
1 AGGCTTTGTGCC
30135842 GATGTTTTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
16 23 0.56
17 2 0.05
18 1 0.02
19 1 0.02
20 2 0.05
21 12 0.29
ACGTcount: A:0.09, C:0.22, G:0.32, T:0.37
Consensus pattern (16 bp):
AGGCTTTGTGCCTAGT
Found at i:30135819 original size:21 final size:21
Alignment explanation
Indices: 30135793--30135883 Score: 95
Period size: 21 Copynumber: 4.6 Consensus size: 21
30135783 TGTGCCTAGT
30135793 AGGCTTTGTGCCGGTGTTTTC
1 AGGCTTTGTGCCGGTGTTTTC
30135814 AGGCTTTGTGCC--TAG---T-
1 AGGCTTTGTGCCGGT-GTTTTC
* *
30135830 AGGCTTCGTGCCGATGTTTTC
1 AGGCTTTGTGCCGGTGTTTTC
*
30135851 AGGCTTCGTGCCGGTGTTTTC
1 AGGCTTTGTGCCGGTGTTTTC
*
30135872 TGGCTTTGTGCC
1 AGGCTTTGTGCC
30135884 TAGTAAGCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
16 11 0.19
17 2 0.03
18 1 0.02
19 1 0.02
20 2 0.03
21 42 0.71
ACGTcount: A:0.07, C:0.22, G:0.32, T:0.40
Consensus pattern (21 bp):
AGGCTTTGTGCCGGTGTTTTC
Found at i:30135825 original size:37 final size:37
Alignment explanation
Indices: 30135775--30135862 Score: 149
Period size: 37 Copynumber: 2.4 Consensus size: 37
30135765 ATTTAAACAA
* *
30135775 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTTT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGATGTTT
30135812 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGATGTTT
1 TCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGATGTTT
*
30135849 TCAGGCTTCGTGCC
1 TCAGGCTTTGTGCC
30135863 GGTGTTTTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.09, C:0.23, G:0.31, T:0.38
Consensus pattern (37 bp):
TCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGATGTTT
Found at i:30135862 original size:58 final size:58
Alignment explanation
Indices: 30135793--30135913 Score: 215
Period size: 58 Copynumber: 2.1 Consensus size: 58
30135783 TGTGCCTAGT
* *
30135793 AGGCTTTGTGCCGGTGTTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGATGTTTTC
1 AGGCTTCGTGCCGGTGTTTTCAGGCTTTGTGCCTAGTAAGCTTCGTGCCGATGTTTTC
*
30135851 AGGCTTCGTGCCGGTGTTTTCTGGCTTTGTGCCTAGTAAGCTTCGTGCCGATGTTTTC
1 AGGCTTCGTGCCGGTGTTTTCAGGCTTTGTGCCTAGTAAGCTTCGTGCCGATGTTTTC
30135909 AGGCT
1 AGGCT
30135914 ATGTGCCTAG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.09, C:0.21, G:0.31, T:0.39
Consensus pattern (58 bp):
AGGCTTCGTGCCGGTGTTTTCAGGCTTTGTGCCTAGTAAGCTTCGTGCCGATGTTTTC
Found at i:30135894 original size:37 final size:37
Alignment explanation
Indices: 30135851--30135975 Score: 178
Period size: 37 Copynumber: 3.4 Consensus size: 37
30135841 CGATGTTTTC
* *
30135851 AGGCTTCGTGCCGGTGTTTTCTGGCTTTGTGCCTAGT
1 AGGCTTCGTGCCGGTGTTTTCAGGCTATGTGCCTAGT
* *
30135888 AAGCTTCGTGCCGATGTTTTCAGGCTATGTGCCTAGT
1 AGGCTTCGTGCCGGTGTTTTCAGGCTATGTGCCTAGT
* * *
30135925 AGGCTTCGTGTCGGTGTATTCGGGCTATGTGCCTAGT
1 AGGCTTCGTGCCGGTGTTTTCAGGCTATGTGCCTAGT
*
30135962 AGGCTTTGTGCCGG
1 AGGCTTCGTGCCGG
30135976 CGATCCAAGA
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 77 1.00
ACGTcount: A:0.10, C:0.21, G:0.33, T:0.36
Consensus pattern (37 bp):
AGGCTTCGTGCCGGTGTTTTCAGGCTATGTGCCTAGT
Found at i:30135957 original size:95 final size:95
Alignment explanation
Indices: 30135778--30135950 Score: 274
Period size: 95 Copynumber: 1.8 Consensus size: 95
30135768 TAAACAATCA
* * * *
30135778 GGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCG
1 GGCTTTGTGCCTAGTAAGCTTCGTGCCGATGTTTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCG
*
30135843 ATGTTTTCAGGCTTCGTGCCGGTGTTTTCT
66 ATGTATTCAGGCTTCGTGCCGGTGTTTTCT
*
30135873 GGCTTTGTGCCTAGTAAGCTTCGTGCCGATGTTTTCAGGCTATGTGCCTAGTAGGCTTCGTGTCG
1 GGCTTTGTGCCTAGTAAGCTTCGTGCCGATGTTTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCG
* *
30135938 GTGTATTCGGGCT
66 ATGTATTCAGGCT
30135951 ATGTGCCTAG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 70 1.00
ACGTcount: A:0.09, C:0.21, G:0.32, T:0.38
Consensus pattern (95 bp):
GGCTTTGTGCCTAGTAAGCTTCGTGCCGATGTTTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCG
ATGTATTCAGGCTTCGTGCCGGTGTTTTCT
Found at i:30138928 original size:34 final size:34
Alignment explanation
Indices: 30138854--30138919 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
30138844 TGTGAAAGTG
*
30138854 AATATGTGAGTATGTTCTTTATGCCATGTGACAA
1 AATATGTGAGTATATTCTTTATGCCATGTGACAA
*
30138888 AATATGTGGGTATATT-TTTCATGCCATGTGAC
1 AATATGTGAGTATATTCTTT-ATGCCATGTGAC
30138920 TGATTATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 3 0.10
34 26 0.90
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.39
Consensus pattern (34 bp):
AATATGTGAGTATATTCTTTATGCCATGTGACAA
Found at i:30145099 original size:15 final size:15
Alignment explanation
Indices: 30145081--30145129 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
30145071 TCTTCTTTCT
*
30145081 CTTCTTCTCGTGCTC
1 CTTCATCTCGTGCTC
30145096 CTTCATCTCGTGCTC
1 CTTCATCTCGTGCTC
*
30145111 CTTCATCTCGTGCTT
1 CTTCATCTCGTGCTC
30145126 CTTC
1 CTTC
30145130 GTTGGCTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.04, C:0.39, G:0.12, T:0.45
Consensus pattern (15 bp):
CTTCATCTCGTGCTC
Found at i:30148614 original size:297 final size:296
Alignment explanation
Indices: 30148041--30148637 Score: 1052
Period size: 297 Copynumber: 2.0 Consensus size: 296
30148031 AAACAAGTAT
* *
30148041 GGCTCATTCCAATAATATTTTAAAGCATCCTTTAGATTTTGACTTTCCTAAGACATATTGCACTC
1 GGCTCATTCCAATAATATTTCAAAGCATCCTTTAGATTCTGACTTTCCTAAGACATATTGCACTC
**
30148106 AACGGTAGCTTACCACAAACTAGATAACTAACGACATCTGCATACCATGGAGATGTGTCAAAAAA
66 AACGGTAGCTTACCACAAACTAGATAACTAACGACATCTGCATACCATGGAGATGCATCAAAAAA
* * *
30148171 GAATAATTGCTCATTTGGAAATGCATCGATAATTTATGACTTATTACCATCTTCGCTTCTAGCTT
131 GAATAATTGCTCATCTGGAAATGCATCGATAATTTATGACTTATTACCATCTTCACTTCCAGCTT
30148236 CTAGACAAGATAAGTGGTCTACTACTTGAATTTCTGATCCTTTCTTGTCCTTGATCTCAACATCA
196 CTAGACAAGATAAGTGGTCTACTACTTGAATTTCTGATCCTTTCTTGTCCTTGATCTCAACATCA
30148301 AATTCTTGCTGCAAAAGGATCCATCTGATCAGCCTA
261 AATTCTTGCTGCAAAAGGATCCATCTGATCAGCCTA
30148337 GGCTCATTCCAATAATATTTCACAA-CATCCTTTAGAATTCTGACTTTCCTAAGACATATTGCAC
1 GGCTCATTCCAATAATATTTCA-AAGCATCCTTTAG-ATTCTGACTTTCCTAAGACATATTGCAC
* *
30148401 TCAACGGTAGCTTATCACAAACTAGATAACTAACTACATCTGCATACCATGGAGATGCATCAAAA
64 TCAACGGTAGCTTACCACAAACTAGATAACTAACGACATCTGCATACCATGGAGATGCATCAAAA
*
30148466 AAGAATAATTGCTCATCTGGAAATGCATCGATAATTTCTGACTTATTACCATCTTCACTTCCAGC
129 AAGAATAATTGCTCATCTGGAAATGCATCGATAATTTATGACTTATTACCATCTTCACTTCCAGC
* * *
30148531 TTCTAGACGAGATAAGTGGTCTGCTACTTGAATTTTTGATCCTTTCTTGTCCTTGATCTCAACAT
194 TTCTAGACAAGATAAGTGGTCTACTACTTGAATTTCTGATCCTTTCTTGTCCTTGATCTCAACAT
30148596 CAAATTCTTGCTGCAAAAGGATCCATCTGATCAGCCTA
259 CAAATTCTTGCTGCAAAAGGATCCATCTGATCAGCCTA
30148634 GGCT
1 GGCT
30148638 TGGCATCTTT
Statistics
Matches: 286, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
296 31 0.11
297 255 0.89
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (296 bp):
GGCTCATTCCAATAATATTTCAAAGCATCCTTTAGATTCTGACTTTCCTAAGACATATTGCACTC
AACGGTAGCTTACCACAAACTAGATAACTAACGACATCTGCATACCATGGAGATGCATCAAAAAA
GAATAATTGCTCATCTGGAAATGCATCGATAATTTATGACTTATTACCATCTTCACTTCCAGCTT
CTAGACAAGATAAGTGGTCTACTACTTGAATTTCTGATCCTTTCTTGTCCTTGATCTCAACATCA
AATTCTTGCTGCAAAAGGATCCATCTGATCAGCCTA
Found at i:30162987 original size:20 final size:21
Alignment explanation
Indices: 30162962--30163010 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
30162952 AGTTCATTTT
30162962 TTTATAAAAATACATA-AAAA
1 TTTATAAAAATACATACAAAA
*
30162982 TTTATAAAAATGCATACAAAA
1 TTTATAAAAATACATACAAAA
30163003 -TTATAAAA
1 TTTATAAAA
30163011 TATTAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (21 bp):
TTTATAAAAATACATACAAAA
Found at i:30169135 original size:78 final size:78
Alignment explanation
Indices: 30169046--30169199 Score: 290
Period size: 78 Copynumber: 2.0 Consensus size: 78
30169036 AACTATCTGA
**
30169046 CATCGAGACGATTGCACTCACAGAGGGGTGTAACGCTGTACTCACAAACAAATTACCAACAAAGA
1 CATCGAGACGATTGCACTCACAGAGGGGTACAACGCTGTACTCACAAACAAATTACCAACAAAGA
30169111 TGAAAGATCCTGG
66 TGAAAGATCCTGG
30169124 CATCGAGACGATTGCACTCACAGAGGGGTACAACGCTGTACTCACAAACAAATTACCAACAAAGA
1 CATCGAGACGATTGCACTCACAGAGGGGTACAACGCTGTACTCACAAACAAATTACCAACAAAGA
30169189 TGAAAGATCCT
66 TGAAAGATCCT
30169200 AGCAGTTTCA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (78 bp):
CATCGAGACGATTGCACTCACAGAGGGGTACAACGCTGTACTCACAAACAAATTACCAACAAAGA
TGAAAGATCCTGG
Found at i:30179852 original size:37 final size:37
Alignment explanation
Indices: 30179805--30179878 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
30179795 ATTTTGACAT
30179805 GTTTAAAATCATTTTAACTTGATTTGAAAATTGTTTC
1 GTTTAAAATCATTTTAACTTGATTTGAAAATTGTTTC
*
30179842 GTTTAAAATCATTTTAACTTGATTTGAAACTTGTTTC
1 GTTTAAAATCATTTTAACTTGATTTGAAAATTGTTTC
30179879 AAACTTTTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (37 bp):
GTTTAAAATCATTTTAACTTGATTTGAAAATTGTTTC
Found at i:30183066 original size:37 final size:36
Alignment explanation
Indices: 30182971--30183071 Score: 139
Period size: 36 Copynumber: 2.8 Consensus size: 36
30182961 GGTAACAGGC
* * * *
30182971 ATGACCATTAGGTTAACAGGGAGAAAAATGAGCATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
*
30183007 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATC
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
*
30183043 ATGACCTTTGGGGTCAACTGGGAGTAAAA
1 ATGACCTTT-GGGTCAACAGGGAGTAAAA
30183072 CGAATAATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 40 0.69
37 18 0.31
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.22
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
Found at i:30183765 original size:21 final size:21
Alignment explanation
Indices: 30183735--30183780 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
30183725 AGAGTTTTTA
* *
30183735 GTATCTGTAGTAGTATGACTT
1 GTATCAGTAGTAGTATCACTT
* *
30183756 GTATCAGTAGTTGTCTCACTT
1 GTATCAGTAGTAGTATCACTT
30183777 GTAT
1 GTAT
30183781 AGGTAGATCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (21 bp):
GTATCAGTAGTAGTATCACTT
Found at i:30198349 original size:14 final size:14
Alignment explanation
Indices: 30198332--30198365 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
30198322 AAATAAAATC
30198332 CTAAAAGGCTAAAA
1 CTAAAAGGCTAAAA
*
30198346 CTAAAAGTCTAAAA
1 CTAAAAGGCTAAAA
30198360 CTAAAA
1 CTAAAA
30198366 AATAAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.15, G:0.09, T:0.18
Consensus pattern (14 bp):
CTAAAAGGCTAAAA
Found at i:30199179 original size:15 final size:15
Alignment explanation
Indices: 30199130--30199179 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
30199120 ACCATTGTTC
30199130 AATTAAGCATAA-AA
1 AATTAAGCATAATAA
*
30199144 TAATTATAGTATAATTAA
1 -AATTA-AGCATAA-TAA
30199162 AATTAAGCATAATAA
1 AATTAAGCATAATAA
30199177 AAT
1 AAT
30199180 CATATTATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 11 0.37
16 12 0.40
17 5 0.17
18 2 0.07
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (15 bp):
AATTAAGCATAATAA
Found at i:30200363 original size:21 final size:19
Alignment explanation
Indices: 30200318--30200359 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
30200308 GATTTTTAGA
* *
30200318 TATTTTAATTGAGAGATAT
1 TATTCTAATTAAGAGATAT
30200337 TATTCTAATTAAGAGATAT
1 TATTCTAATTAAGAGATAT
30200356 TATT
1 TATT
30200360 TTCTTAGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TATTCTAATTAAGAGATAT
Found at i:30206675 original size:37 final size:37
Alignment explanation
Indices: 30206625--30206916 Score: 435
Period size: 37 Copynumber: 7.9 Consensus size: 37
30206615 GTGATTCACT
* *
30206625 GGCACAAAGCCTACTAGGTACAAAGCCCGAATA-AGCC
1 GGCACGAAGCCTACTAGGCACAAAGCCCGAATACA-CC
*
30206662 GGCACGAAGCCTACTAGGCACAAAGCCCGAATACATC
1 GGCACGAAGCCTACTAGGCACAAAGCCCGAATACACC
* * *
30206699 GACACAAAGCCTACTAGGCACAAAACCCGAATACACC
1 GGCACGAAGCCTACTAGGCACAAAGCCCGAATACACC
* *
30206736 GGCACGAAACCTACTAGGCACAAAGCTCGAGA-ACACC
1 GGCACGAAGCCTACTAGGCACAAAGCCCGA-ATACACC
*
30206773 GGCACGAAGCTTACTAGGCACAAAGCCCGAATACACC
1 GGCACGAAGCCTACTAGGCACAAAGCCCGAATACACC
30206810 GGCACGAAGCCTACTAGGCACAAAGCCCGAATACACC
1 GGCACGAAGCCTACTAGGCACAAAGCCCGAATACACC
*
30206847 GACACGAAGCCTACTAGGCACAAAGCCCGAATACACC
1 GGCACGAAGCCTACTAGGCACAAAGCCCGAATACACC
* * *
30206884 AGCACGAAGCCTATTAGGCACAAAGCCCAAATA
1 GGCACGAAGCCTACTAGGCACAAAGCCCGAATA
30206917 TTTAGATGTA
Statistics
Matches: 231, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
36 1 0.00
37 228 0.99
38 2 0.01
ACGTcount: A:0.38, C:0.33, G:0.20, T:0.10
Consensus pattern (37 bp):
GGCACGAAGCCTACTAGGCACAAAGCCCGAATACACC
Found at i:30206687 original size:16 final size:16
Alignment explanation
Indices: 30206625--30206722 Score: 52
Period size: 16 Copynumber: 5.5 Consensus size: 16
30206615 GTGATTCACT
30206625 GGCACAAAGCCTACTA
1 GGCACAAAGCCTACTA
* * *
30206641 GGTACAAAGCCCGAATAA
1 GGCACAAAG-CCTACT-A
*
30206659 GCCGGCACGAAGCCTACTA
1 ---GGCACAAAGCCTACTA
*
30206678 GGCACAAAGCCCGAATACATC
1 GGCACAAAG-CC---TAC-TA
*
30206699 GACACAAAGCCTACTA
1 GGCACAAAGCCTACTA
30206715 GGCACAAA
1 GGCACAAA
30206723 ACCCGAATAC
Statistics
Matches: 60, Mismatches: 12, Indels: 20
0.65 0.13 0.22
Matches are distributed among these distances:
16 24 0.40
17 9 0.15
18 1 0.02
19 1 0.02
20 9 0.15
21 16 0.27
ACGTcount: A:0.39, C:0.31, G:0.20, T:0.10
Consensus pattern (16 bp):
GGCACAAAGCCTACTA
Found at i:30206813 original size:21 final size:21
Alignment explanation
Indices: 30206789--30206894 Score: 65
Period size: 21 Copynumber: 5.5 Consensus size: 21
30206779 AAGCTTACTA
30206789 GGCACAAAGCCCGAATACACC
1 GGCACAAAGCCCGAATACACC
*
30206810 GGCACGAAG-CC---TACTA--
1 GGCACAAAGCCCGAATAC-ACC
30206826 GGCACAAAGCCCGAATACACC
1 GGCACAAAGCCCGAATACACC
* *
30206847 GACACGAAG-CC---TACTA--
1 GGCACAAAGCCCGAATAC-ACC
30206863 GGCACAAAGCCCGAATACACC
1 GGCACAAAGCCCGAATACACC
* *
30206884 AGCACGAAGCC
1 GGCACAAAGCC
30206895 TATTAGGCAC
Statistics
Matches: 63, Mismatches: 8, Indels: 28
0.64 0.08 0.28
Matches are distributed among these distances:
16 15 0.24
17 10 0.16
18 2 0.03
19 2 0.03
20 10 0.16
21 24 0.38
ACGTcount: A:0.37, C:0.36, G:0.21, T:0.07
Consensus pattern (21 bp):
GGCACAAAGCCCGAATACACC
Found at i:30220264 original size:13 final size:12
Alignment explanation
Indices: 30220248--30220277 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
30220238 AAAAAAATTC
30220248 AAAAAAATTTAGA
1 AAAAAAATTTA-A
30220261 AAAAAAATTTAA
1 AAAAAAATTTAA
30220273 AAAAA
1 AAAAA
30220278 TAAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (12 bp):
AAAAAAATTTAA
Found at i:30223196 original size:28 final size:29
Alignment explanation
Indices: 30223141--30223195 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 29
30223131 ATAAATATAG
30223141 CACAAAGACAAATATAATAAAAAGAAAAA
1 CACAAAGACAAATATAATAAAAAGAAAAA
*
30223170 CACAAA-ACAAATAT--TAAAAATAAAAA
1 CACAAAGACAAATATAATAAAAAGAAAAA
30223196 ATAAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 11 0.44
28 8 0.32
29 6 0.24
ACGTcount: A:0.73, C:0.11, G:0.04, T:0.13
Consensus pattern (29 bp):
CACAAAGACAAATATAATAAAAAGAAAAA
Found at i:30227611 original size:25 final size:25
Alignment explanation
Indices: 30227577--30227628 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
30227567 ATAATACGCA
30227577 TAACATGTTGCCTCATTAAAAATCT
1 TAACATGTTGCCTCATTAAAAATCT
*
30227602 TAACATGTTGTCTCATTAAAAATCT
1 TAACATGTTGCCTCATTAAAAATCT
30227627 TA
1 TA
30227629 CCAGGAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (25 bp):
TAACATGTTGCCTCATTAAAAATCT
Found at i:30229569 original size:31 final size:29
Alignment explanation
Indices: 30229497--30229569 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
30229487 ATTCCAATAA
* *
30229497 AAAATGTTTTAATTAATCAGGCTAGATAG
1 AAAATGTTTTAATTAATCAGGCTAAAAAG
30229526 AAAGGATGTTTTAATTAATCAGGCTAAACAAG
1 AAA--ATGTTTTAATTAATCAGGCTAAA-AAG
*
30229558 TAAAATATTTTA
1 -AAAATGTTTTA
30229570 GTAAATTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 3 0.08
31 29 0.78
32 2 0.05
33 3 0.08
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (29 bp):
AAAATGTTTTAATTAATCAGGCTAAAAAG
Found at i:30230299 original size:3 final size:3
Alignment explanation
Indices: 30230291--30230322 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
30230281 TAATTTACCC
30230291 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
30230323 CTGTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:30236293 original size:16 final size:17
Alignment explanation
Indices: 30236272--30236304 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
30236262 TCCCGTGAGT
*
30236272 TTTTTTTTTC-CTTTTA
1 TTTTTTTGTCACTTTTA
30236288 TTTTTTTGTCACTTTTA
1 TTTTTTTGTCACTTTTA
30236305 AGCTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTTTGTCACTTTTA
Found at i:30237901 original size:8 final size:7
Alignment explanation
Indices: 30237888--30237939 Score: 53
Period size: 6 Copynumber: 8.1 Consensus size: 7
30237878 AAATTTATTT
30237888 TAAATACA
1 TAAATA-A
30237896 TAAATAA
1 TAAATAA
30237903 T-AATAA
1 TAAATAA
30237909 T-AATAA
1 TAAATAA
30237915 T-AATAA
1 TAAATAA
30237921 T-AATAA
1 TAAATAA
30237927 T-AATAA
1 TAAATAA
30237933 T-AATAA
1 TAAATAA
30237939 T
1 T
30237940 TGTAGACCCA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 36 0.82
7 2 0.05
8 6 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (7 bp):
TAAATAA
Found at i:30237906 original size:3 final size:3
Alignment explanation
Indices: 30237898--30237939 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
30237888 TAAATACATA
30237898 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
30237940 TGTAGACCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:30238651 original size:16 final size:17
Alignment explanation
Indices: 30238622--30238655 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
30238612 AATTTTATAT
30238622 AAAATATATATTAATAA
1 AAAATATATATTAATAA
*
30238639 AAAATAT-TTTTAATAA
1 AAAATATATATTAATAA
30238655 A
1 A
30238656 TGGAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATATATATTAATAA
Found at i:30239068 original size:2 final size:2
Alignment explanation
Indices: 30239063--30239127 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
30239053 TTTTAGATAA
30239063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30239105 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
30239128 AAAATCTAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30251512 original size:6 final size:6
Alignment explanation
Indices: 30251501--30251529 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
30251491 ACAGCTTTCT
30251501 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
30251530 TTCCTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:30251813 original size:18 final size:16
Alignment explanation
Indices: 30251790--30251825 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
30251780 GTTTAAAATT
30251790 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
30251808 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
30251824 TT
1 TT
30251826 CTCATCGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:30252172 original size:30 final size:27
Alignment explanation
Indices: 30252107--30252175 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
30252097 CTTTTATAAA
*
30252107 TTTAAAATTTAGTCTCTATATTGTTAT
1 TTTAAAATTTAATCTCTATATTGTTAT
* *
30252134 TTTAAAAATTTAATCTCTCTACTTTTTAGAT
1 TTT-AAAATTTAATCTCTATA-TTGTT--AT
30252165 TTTAAAATTTA
1 TTTAAAATTTA
30252176 GATTCAACTG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 3 0.09
28 15 0.43
29 4 0.11
30 8 0.23
31 5 0.14
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (27 bp):
TTTAAAATTTAATCTCTATATTGTTAT
Found at i:30256379 original size:37 final size:39
Alignment explanation
Indices: 30256320--30256413 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 39
30256310 CTTAATCACT
* * *
30256320 TTAATATTAAATTAATATAATATT-TAT-CAAGATAAATA
1 TTAA-ATTAAATTAATAGAATATTATATACAAAATAAACA
* *
30256358 TTAGATTAAATTAATAGAATATTATCTACAAAATAAACA
1 TTAAATTAAATTAATAGAATATTATATACAAAATAAACA
30256397 TTAAATTAAATTTAATA
1 TTAAATTAAA-TTAATA
30256414 TTAAGATAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
37 18 0.38
38 5 0.11
39 18 0.38
40 6 0.13
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.39
Consensus pattern (39 bp):
TTAAATTAAATTAATAGAATATTATATACAAAATAAACA
Found at i:30256443 original size:20 final size:18
Alignment explanation
Indices: 30256396--30256444 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
30256386 CAAAATAAAC
30256396 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
30256413 ATTAAGA-TAATCATTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
30256433 ATTAAATTAATA
1 ATTAAATTAATA
30256445 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:30256553 original size:20 final size:20
Alignment explanation
Indices: 30256514--30256553 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
30256504 TTATTATATT
*
30256514 ATGCGAGGTGGGCTGAGATG
1 ATGCGAGGTGGGCGGAGATG
* *
30256534 ATGCGGGGTGGGCGGGGATG
1 ATGCGAGGTGGGCGGAGATG
30256554 GGGTGGGTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.10, G:0.57, T:0.17
Consensus pattern (20 bp):
ATGCGAGGTGGGCGGAGATG
Found at i:30256558 original size:15 final size:15
Alignment explanation
Indices: 30256538--30256567 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30256528 GAGATGATGC
30256538 GGGGTGGGCGGGGAT
1 GGGGTGGGCGGGGAT
*
30256553 GGGGTGGGTGGGGAT
1 GGGGTGGGCGGGGAT
30256568 TAGGCAAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.03, G:0.73, T:0.17
Consensus pattern (15 bp):
GGGGTGGGCGGGGAT
Found at i:30257468 original size:16 final size:16
Alignment explanation
Indices: 30257441--30257478 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
30257431 TTTTTTTCCT
*
30257441 TTTTTTTTGTAT-TTA
1 TTTTTATTGTATGTTA
30257456 TTATTTATTGTATGTTA
1 TT-TTTATTGTATGTTA
30257473 TTTTTA
1 TTTTTA
30257479 ACTTGTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 13 0.65
17 5 0.25
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (16 bp):
TTTTTATTGTATGTTA
Found at i:30259775 original size:339 final size:337
Alignment explanation
Indices: 30258786--30260217 Score: 1834
Period size: 330 Copynumber: 4.3 Consensus size: 337
30258776 TTCGGGTAAG
* * *
30258786 ATATTATAAATTTATATGATTTTGTACATATTAGTAATTCGTTTTATGTAATTTGT-A-TTTTTA
1 ATATTATAAATTTATATGATTTTGTACATATTATTAATTCGTTTTATGTAATTTTTGAGTTTTTT
* * * * * *
30258849 AATATATATTTATTATTATTTATTTTATTTTT-TTACGTGATATATTTTTATTATTTTAAATTCT
66 AATA-ATTTTTGTCATTATTTATTTTATTTTTGTCACGTGATATATTTTTATTATTTTTAATTAT
* * *
30258913 TTATCATGTTTATTTTAACTCTATCATAATAATTTAGTTTTAACTTTAATATCATTT-AAAAATT
130 TTATCATGTTTA-GTTAACTCTATCATAGTAATCTAGTTTTAACTTTAATATCATTTAAAAAATT
* * * *
30258977 TATTCTGATTTTACAAAAGATTCCAAAATTAATAGCCGAGAAAATTGTTGTATTTCAATTCCTCA
194 TAATCTGATTTTACAAAAGATTCCAAAATTAATTGCCGAGAAAATTGTTGTCTTTCCATTCCTCA
* **
30259042 AATTTTCACAATGTTTTGGTTTTCTAGAAATATGTTGATGTCATTTTTATTATGTTGGTGTTACT
259 ATTTTTCACAATGTTTTAATTTTCTAGAAATATGTTGATGTCATTTTTATTATGTTGGTGTTACT
30259107 TTCGTGAACTCAAA
324 TTCGTGAACTCAAA
* *
30259121 ATATTATAAATTTATATAATTTTGTACATATTATTAATTCGTTTTATGTAATTTTTGAGTTCTTT
1 ATATTATAAATTTATATGATTTTGTACATATTATTAATTCGTTTTATGTAATTTTTGAGTTTTTT
* *
30259186 AATATATTTTTGTCATTATTTATTTTATTTTTTTCACGTGATATATTTTTACT-TTTTT-A-TA-
66 AATA-ATTTTTGTCATTATTTATTTTATTTTTGTCACGTGATATATTTTTATTATTTTTAATTAT
* * *
30259247 --AT-GT-TTTAGTTAATTCTATCATAGTAGTCTAGTTTTAACTTTAATATCATTTAAAAAATTT
130 TTATCATGTTTAGTTAACTCTATCATAGTAATCTAGTTTTAACTTTAATATCATTTAAAAAATTT
30259308 AAT-TCGATTTTACAAAAGATTCCAAAATTAATTGCCGAGAAAATTGTTGTCTTTCCATTCCTCA
195 AATCT-GATTTTACAAAAGATTCCAAAATTAATTGCCGAGAAAATTGTTGTCTTTCCATTCCTCA
* * * *
30259372 ACTTTTCACAATATTTTGATTTTTTAGAAATATGTTGATGTCATTTTTATTATGTTGGTGTTACT
259 ATTTTTCACAATGTTTTAATTTTCTAGAAATATGTTGATGTCATTTTTATTATGTTGGTGTTACT
* *
30259437 TTCGTAAATTCAAA
324 TTCGTGAACTCAAA
30259451 ATATTATAAATTTATATGATTTTGTACATATTATTAATTCGTTTTATGTAATTTTTGAGTTTTTT
1 ATATTATAAATTTATATGATTTTGTACATATTATTAATTCGTTTTATGTAATTTTTGAGTTTTTT
*
30259516 AATTAATTTTTGTCATTATTTATTTTATTTTTGTCAGGTGATATATTTTTATTATTTTTAATTAT
66 AA-TAATTTTTGTCATTATTTATTTTATTTTTGTCACGTGATATATTTTTATTATTTTTAATTAT
* * * * * *
30259581 TTATCTTGTTTATGTTAACTCTATCGTACTAATTTAGTTTTAACTTTAATATCGTTTAAAAAAAT
130 TTATCATGTTTA-GTTAACTCTATCATAGTAATCTAGTTTTAACTTTAATATCATTTAAAAAATT
* ***
30259646 TAATCTGATTTTACAAAAGATTCTAAAATTAATTTTTGAGAAAATTGTTGTCTTTCCATTCCTCA
194 TAATCTGATTTTACAAAAGATTCCAAAATTAATTGCCGAGAAAATTGTTGTCTTTCCATTCCTCA
* *
30259711 ATTTTTCACAATGTTTTAATTTTCTAGAAATATGTTCATGTCATTTTTATTATGTTGATGTTACT
259 ATTTTTCACAATGTTTTAATTTTCTAGAAATATGTTGATGTCATTTTTATTATGTTGGTGTTACT
* *
30259776 TTTGTGAACTCAGA
324 TTCGTGAACTCAAA
* *
30259790 ATATTATAAATTTATTTGATTTTGTACATATTATTAA------TT-TG----TTTT-A----TCT
1 ATATTATAAATTTATATGATTTTGTACATATTATTAATTCGTTTTATGTAATTTTTGAGTTTTTT
* * * * *
30259839 AAT-A--TTTGACCTT-TTTAATATATTTTTGTCACGTGATATATTTTTATTATTTTTAAATTTT
66 AATAATTTTTGTCATTATTTATTTTATTTTTGTCACGTGATATATTTTTATTATTTTT-AA-TTA
* * * * ** * *
30259900 TTTATAATGTTTCAGGTAATTATATTGTAGTAATCTAGTTTTAACTTTAATATCGTTTCAAAAAT
129 TTTATCATGTTT-AGTTAACTCTATCATAGTAATCTAGTTTTAACTTTAATATCATTTAAAAAAT
* * * * * * *
30259965 TTAATATGATTTTACAAAAGATTTCAAAAGTAATTACCGAGAAAACTGCTCTCTTTCCATTCCTC
193 TTAATCTGATTTTACAAAAGATTCCAAAATTAATTGCCGAGAAAATTGTTGTCTTTCCATTCCTC
*
30260030 AATTTATCACAATGTTTTAATTTTCTAGAAATATGTTGATGTCATTTTTATTATGTTGGTGTTAC
258 AATTTTTCACAATGTTTTAATTTTCTAGAAATATGTTGATGTCATTTTTATTATGTTGGTGTTAC
*
30260095 TTTCGTGAAGTCAAA
323 TTTCGTGAACTCAAA
* * * * *
30260110 TTATTCTAAATTTATATGATTTTGTATATATTATTAATTTGTTTTATGTAACTTTTGAGTTTTTT
1 ATATTATAAATTTATATGATTTTGTACATATTATTAATTCGTTTTATGTAATTTTTGAGTTTTTT
* *
30260175 AAT-ATATTTTGTCATTATTTATTTTATTTCTGTCATGTGATAT
66 AATAAT-TTTTGTCATTATTTATTTTATTTTTGTCACGTGATAT
30260218 GTAACATCTC
Statistics
Matches: 958, Mismatches: 100, Indels: 73
0.85 0.09 0.06
Matches are distributed among these distances:
318 38 0.04
319 9 0.01
320 217 0.23
321 2 0.00
322 1 0.00
323 4 0.00
326 2 0.00
327 3 0.00
328 4 0.00
329 40 0.04
330 253 0.26
331 12 0.01
332 6 0.01
333 4 0.00
335 54 0.06
336 10 0.01
337 38 0.04
338 22 0.02
339 216 0.23
340 23 0.02
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (337 bp):
ATATTATAAATTTATATGATTTTGTACATATTATTAATTCGTTTTATGTAATTTTTGAGTTTTTT
AATAATTTTTGTCATTATTTATTTTATTTTTGTCACGTGATATATTTTTATTATTTTTAATTATT
TATCATGTTTAGTTAACTCTATCATAGTAATCTAGTTTTAACTTTAATATCATTTAAAAAATTTA
ATCTGATTTTACAAAAGATTCCAAAATTAATTGCCGAGAAAATTGTTGTCTTTCCATTCCTCAAT
TTTTCACAATGTTTTAATTTTCTAGAAATATGTTGATGTCATTTTTATTATGTTGGTGTTACTTT
CGTGAACTCAAA
Found at i:30269680 original size:22 final size:21
Alignment explanation
Indices: 30269629--30269677 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
30269619 GTGTCACCGT
*
30269629 GGAAAAAGTTTCTTCGATTTG
1 GGAAAAAGGTTCTTCGATTTG
30269650 GGAAAAAGGTTCTTCGATTTG
1 GGAAAAAGGTTCTTCGATTTG
30269671 GGAAAAA
1 GGAAAAA
30269678 AGGGAAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (21 bp):
GGAAAAAGGTTCTTCGATTTG
Found at i:30275488 original size:16 final size:17
Alignment explanation
Indices: 30275457--30275491 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30275447 TGCATAGGAA
*
30275457 TTTAACTTAGATTTAAT
1 TTTAACTTAGACTTAAT
30275474 TTTAACTTAG-CTTAAT
1 TTTAACTTAGACTTAAT
30275490 TT
1 TT
30275492 AATTTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAACTTAGACTTAAT
Found at i:30277716 original size:16 final size:17
Alignment explanation
Indices: 30277695--30277734 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
30277685 CATTGTCCCC
* *
30277695 AATGCACTGACATTA-A
1 AATGCAATGACAATAGA
30277711 AATGCAATGACAATAGA
1 AATGCAATGACAATAGA
30277728 AATGCAA
1 AATGCAA
30277735 CGATAATGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (17 bp):
AATGCAATGACAATAGA
Found at i:30277889 original size:15 final size:15
Alignment explanation
Indices: 30277857--30277885 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30277847 CTGCATGATG
30277857 CTTTTTCTTCCTCCT
1 CTTTTTCTTCCTCCT
30277872 CTTTTTC-TCCTCCT
1 CTTTTTCTTCCTCCT
30277886 TCTTGCGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
CTTTTTCTTCCTCCT
Found at i:30287927 original size:21 final size:22
Alignment explanation
Indices: 30287901--30287962 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
30287891 CAACTTTGCC
*
30287901 AGAACCAGTTTTACCGGAA-TT
1 AGAACCAGTTTTACCAGAACTT
**
30287922 AGAACCAACTTTACCAGAACTT
1 AGAACCAGTTTTACCAGAACTT
* *
30287944 -GAACCAGTTTCACTAGAAC
1 AGAACCAGTTTTACCAGAAC
30287963 CAAAATCGGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (22 bp):
AGAACCAGTTTTACCAGAACTT
Found at i:30294515 original size:25 final size:24
Alignment explanation
Indices: 30294463--30294522 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 24
30294453 AAATCATCTT
*
30294463 TTAATTTTTAATTTATTTAACTTA
1 TTAATTTTTAATTTATTTAAATTA
*
30294487 TTAACTTTTTAATTTATTTAAATTG
1 TTAA-TTTTTAATTTATTTAAATTA
30294512 TTAATATTTTA
1 TTAAT-TTTTA
30294523 TACTAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 5 0.16
25 27 0.84
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (24 bp):
TTAATTTTTAATTTATTTAAATTA
Found at i:30295491 original size:18 final size:18
Alignment explanation
Indices: 30295394--30295483 Score: 108
Period size: 18 Copynumber: 5.0 Consensus size: 18
30295384 ACAAGCTGAA
30295394 GAAGAAGAAGAAGATCCT
1 GAAGAAGAAGAAGATCCT
*
30295412 GAAGAAGAATAAGATCCT
1 GAAGAAGAAGAAGATCCT
* **
30295430 GAAGAAGAAGAGGATGTT
1 GAAGAAGAAGAAGATCCT
* *
30295448 GAATAAGAAGAAGATCTT
1 GAAGAAGAAGAAGATCCT
* *
30295466 AAAGAAGAAGAGGATCCT
1 GAAGAAGAAGAAGATCCT
30295484 AAGGAAGATC
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.49, C:0.08, G:0.28, T:0.16
Consensus pattern (18 bp):
GAAGAAGAAGAAGATCCT
Found at i:30303555 original size:12 final size:12
Alignment explanation
Indices: 30303535--30303599 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
30303525 GAGACTGATG
30303535 AGGAGAAAGAAGA
1 AGGA-AAAGAAGA
30303548 AGGAAAAGAAGA
1 AGGAAAAGAAGA
30303560 A-GAATAAGAAGAGGA
1 AGGAA-AAG-A-A-GA
*
30303575 AGGGAAAGAAGA
1 AGGAAAAGAAGA
* *
30303587 AAGAAAGGAAGA
1 AGGAAAAGAAGA
30303599 A
1 A
30303600 CCTACTGTCG
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
11 3 0.07
12 24 0.56
13 6 0.14
14 2 0.05
15 6 0.14
16 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (12 bp):
AGGAAAAGAAGA
Found at i:30304666 original size:5 final size:5
Alignment explanation
Indices: 30304646--30304685 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
30304636 CACATATAAA
*
30304646 AAAAG AAGACG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
30304686 AAGAAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.78, C:0.03, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:30305040 original size:13 final size:13
Alignment explanation
Indices: 30305022--30305046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30305012 CCCATTTTAT
30305022 CATTTTTAGCATG
1 CATTTTTAGCATG
30305035 CATTTTTAGCAT
1 CATTTTTAGCAT
30305047 TTTTAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:30312620 original size:21 final size:21
Alignment explanation
Indices: 30312595--30312646 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
30312585 AAATATAAGT
30312595 ATAAAAAATATAATT-AAGAAC
1 ATAAAAAATATAATTCAAG-AC
* *
30312616 ATAAATAACATAATTCAAGAC
1 ATAAAAAATATAATTCAAGAC
30312637 A-AAAAAATAT
1 ATAAAAAATAT
30312647 CACAAATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.27
21 16 0.62
22 3 0.12
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (21 bp):
ATAAAAAATATAATTCAAGAC
Found at i:30313201 original size:21 final size:21
Alignment explanation
Indices: 30313164--30313365 Score: 65
Period size: 20 Copynumber: 9.1 Consensus size: 21
30313154 AAAATGCATA
*
30313164 AAAAATAACATCC-AAACAAC
1 AAAAATAACAACCAAAACAAC
*
30313184 AAAAATAACAACCAAAACAATAGA
1 AAAAATAACAACCAAAAC-A-A-C
* *
30313208 AAAAATAAC-AGCAAAACACC
1 AAAAATAACAACCAAAACAAC
* *
30313228 ATTAAA-AACAACAAAAATAGCAAC
1 A-AAAATAACAAC-CAAA-A-CAAC
* *
30313252 AAAAATAACAGCAAAAACAACC
1 AAAAATAACAACCAAAACAA-C
*
30313274 AAAACAATAAAAAAAACCAAAACAGTA-
1 -AAA-AAT---AACAACCAAAACA--AC
* * *
30313301 AAAAACAAC-ACAAAAACAATAA
1 AAAAATAACAACCAAAAC-A-AC
* **
30313323 AAAAATAGCAACCAAAACAGT
1 AAAAATAACAACCAAAACAAC
*
30313344 AAAAA-AAGAACCAAAACAAC
1 AAAAATAACAACCAAAACAAC
30313364 AA
1 AA
30313366 TATAATTTTT
Statistics
Matches: 135, Mismatches: 26, Indels: 42
0.67 0.13 0.21
Matches are distributed among these distances:
20 29 0.21
21 25 0.19
22 18 0.13
23 26 0.19
24 21 0.16
25 2 0.01
26 3 0.02
27 10 0.07
29 1 0.01
ACGTcount: A:0.70, C:0.19, G:0.04, T:0.07
Consensus pattern (21 bp):
AAAAATAACAACCAAAACAAC
Found at i:30313225 original size:44 final size:41
Alignment explanation
Indices: 30313163--30313277 Score: 106
Period size: 44 Copynumber: 2.6 Consensus size: 41
30313153 AAAAATGCAT
* *
30313163 AAAAAATAACATCCAAACAACAAAAATAACAACCAAAACAATAG-
1 AAAAAATAACAGCAAAACAACAAAAA-AACAA-C-AAA-AATAGA
* *
30313207 AAAAAATAACAGCAAAACACCATTAAAAACAACAAAAATAGCA
1 AAAAAATAACAGCAAAACAACA-AAAAAACAACAAAAATAG-A
*
30313250 ACAAAAATAACAGCAAAAACAACCAAAA
1 A-AAAAATAACAGC-AAAACAACAAAAA
30313278 CAATAAAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
41 5 0.08
42 3 0.05
43 2 0.03
44 39 0.66
45 10 0.17
ACGTcount: A:0.69, C:0.20, G:0.03, T:0.08
Consensus pattern (41 bp):
AAAAAATAACAGCAAAACAACAAAAAAACAACAAAAATAGA
Found at i:30313251 original size:12 final size:12
Alignment explanation
Indices: 30313234--30313268 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
30313224 CACCATTAAA
30313234 AACAACAAAAAT
1 AACAACAAAAAT
*
30313246 AGCAACAAAAAT
1 AACAACAAAAAT
*
30313258 AACAGCAAAAA
1 AACAACAAAAA
30313269 CAACCAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.71, C:0.17, G:0.06, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:30313279 original size:18 final size:18
Alignment explanation
Indices: 30313258--30313361 Score: 66
Period size: 18 Copynumber: 5.2 Consensus size: 18
30313248 CAACAAAAAT
*
30313258 AACAGCAAAAACAACCAA
1 AACAGAAAAAACAACCAA
*
30313276 AACA-ATAAAAAAAACCAA
1 AACAGA-AAAAACAACCAA
30313294 AACAGTAAAAAACAACACAAA
1 AACAG-AAAAAACAAC-C-AA
*
30313315 AACAATAAAAAAATAGCAACCAA
1 AAC---AGAAAAA-A-CAACCAA
*
30313338 AACAGTAAAAAAAGAACCAA
1 AACAG--AAAAAACAACCAA
30313358 AACA
1 AACA
30313362 ACAATATAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
18 19 0.28
19 8 0.12
20 13 0.19
21 6 0.09
22 5 0.07
23 10 0.15
24 3 0.04
25 4 0.06
ACGTcount: A:0.71, C:0.19, G:0.05, T:0.05
Consensus pattern (18 bp):
AACAGAAAAAACAACCAA
Found at i:30313288 original size:44 final size:43
Alignment explanation
Indices: 30313208--30313339 Score: 116
Period size: 39 Copynumber: 3.1 Consensus size: 43
30313198 AAACAATAGA
*
30313208 AAAAATAACAGC-AAAACACCATTAAA-AACAACAAAAATAGCAAC
1 AAAAATAACAGCAAAAACACCA--AAACAATAA-AAAAATAGCAAC
*
30313252 AAAAATAACAGCAAAAACAACCAAAACAATAAAAAAA-ACCAA-
1 AAAAATAACAGCAAAAAC-ACCAAAACAATAAAAAAATAGCAAC
* * *
30313294 AACAGTAA-A--AAACAACACAAAAACAATAAAAAAATAGCAAC
1 AAAAATAACAGCAAA-AACACCAAAACAATAAAAAAATAGCAAC
*
30313335 CAAAA
1 AAAAA
30313340 CAGTAAAAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 15
0.75 0.09 0.15
Matches are distributed among these distances:
39 20 0.27
40 7 0.10
41 3 0.04
42 6 0.08
43 4 0.05
44 20 0.27
45 9 0.12
46 4 0.05
ACGTcount: A:0.70, C:0.19, G:0.04, T:0.07
Consensus pattern (43 bp):
AAAAATAACAGCAAAAACACCAAAACAATAAAAAAATAGCAAC
Found at i:30313305 original size:20 final size:20
Alignment explanation
Indices: 30313264--30313361 Score: 92
Period size: 21 Copynumber: 4.8 Consensus size: 20
30313254 AAATAACAGC
* *
30313264 AAAAACAACCAAAACA--AT
1 AAAAAAAACCAAAACAGTAA
30313282 AAAAAAAACCAAAACAGTAA
1 AAAAAAAACCAAAACAGTAA
* * *
30313302 AAAACAACACAAAAACAATAA
1 AAAA-AAAACCAAAACAGTAA
30313323 AAAAATAGCAACCAAAACAGTAA
1 AAAAA-A--AACCAAAACAGTAA
*
30313346 AAAAAGAACCAAAACA
1 AAAAAAAACCAAAACA
30313362 ACAATATAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
18 15 0.23
20 16 0.25
21 18 0.28
23 16 0.25
ACGTcount: A:0.72, C:0.18, G:0.04, T:0.05
Consensus pattern (20 bp):
AAAAAAAACCAAAACAGTAA
Found at i:30313326 original size:11 final size:11
Alignment explanation
Indices: 30313177--30313327 Score: 51
Period size: 12 Copynumber: 13.3 Consensus size: 11
30313167 AATAACATCC
30313177 AAACAACAAAA
1 AAACAACAAAA
*
30313188 ATAACAAC--CA
1 A-AACAACAAAA
*
30313198 AAACAATAGAAA
1 AAACAACA-AAA
* **
30313210 AAATAACAGCA
1 AAACAACAAAA
* *
30313221 AAACACCATTAA
1 AAACAACA-AAA
30313233 AAACAACAAAA
1 AAACAACAAAA
*
30313244 ATAGCAACAAAA
1 A-AACAACAAAA
*
30313256 ATAACAGC--AA
1 A-AACAACAAAA
30313266 AAACAACCAAAA
1 AAACAA-CAAAA
* *
30313278 CAATAA-AAAA
1 AAACAACAAAA
*
30313288 AACCAAAACAGTAAA
1 AA--ACAACA--AAA
*
30313303 AAACAACACAA
1 AAACAACAAAA
*
30313314 AAACAATAAAA
1 AAACAACAAAA
30313325 AAA
1 AAA
30313328 TAGCAACCAA
Statistics
Matches: 101, Mismatches: 25, Indels: 28
0.66 0.16 0.18
Matches are distributed among these distances:
9 9 0.09
10 11 0.11
11 25 0.25
12 45 0.45
13 6 0.06
15 5 0.05
ACGTcount: A:0.72, C:0.19, G:0.03, T:0.07
Consensus pattern (11 bp):
AAACAACAAAA
Found at i:30315273 original size:15 final size:15
Alignment explanation
Indices: 30315253--30315386 Score: 126
Period size: 15 Copynumber: 8.9 Consensus size: 15
30315243 ACCTTATATC
*
30315253 GCTGTACCAAATACT
1 GCTGTACCAAATGCT
* *
30315268 GTTGTACCGAATGCT
1 GCTGTACCAAATGCT
** *
30315283 GAAGTGCCAAATGCT
1 GCTGTACCAAATGCT
** *
30315298 GGGGTACCAAATGTT
1 GCTGTACCAAATGCT
*
30315313 GCTGTACCAAATGTT
1 GCTGTACCAAATGCT
* *
30315328 GCCGTACCAAATGTT
1 GCTGTACCAAATGCT
*
30315343 GCTGTACCAAATGTT
1 GCTGTACCAAATGCT
30315358 G-TGGTACCAAATGCT
1 GCT-GTACCAAATGCT
*
30315373 GCTTTACCAAATGC
1 GCTGTACCAAATGC
30315387 GGACGATAAA
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
14 1 0.01
15 98 0.98
16 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (15 bp):
GCTGTACCAAATGCT
Found at i:30315323 original size:30 final size:30
Alignment explanation
Indices: 30315253--30315386 Score: 142
Period size: 30 Copynumber: 4.5 Consensus size: 30
30315243 ACCTTATATC
* * *
30315253 GCTGTACCAAATACTGTTGTACCGAATGCT
1 GCTGTACCAAATGCTGTGGTACCAAATGCT
** * * *
30315283 GAAGTGCCAAATGCTGGGGTACCAAATGTT
1 GCTGTACCAAATGCTGTGGTACCAAATGCT
* ** *
30315313 GCTGTACCAAATGTTGCCGTACCAAATGTT
1 GCTGTACCAAATGCTGTGGTACCAAATGCT
*
30315343 GCTGTACCAAATGTTGTGGTACCAAATGCT
1 GCTGTACCAAATGCTGTGGTACCAAATGCT
*
30315373 GCTTTACCAAATGC
1 GCTGTACCAAATGC
30315387 GGACGATAAA
Statistics
Matches: 85, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 85 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (30 bp):
GCTGTACCAAATGCTGTGGTACCAAATGCT
Found at i:30318463 original size:15 final size:15
Alignment explanation
Indices: 30318445--30318596 Score: 162
Period size: 15 Copynumber: 10.1 Consensus size: 15
30318435 CCGCTACCTT
*
30318445 ATGCCGCTGTACCAA
1 ATGCTGCTGTACCAA
* * *
30318460 ATGCAGTTGTACCGA
1 ATGCTGCTGTACCAA
* *
30318475 ATGCTGCAGTGCCAA
1 ATGCTGCTGTACCAA
30318490 ATGCTGCTGTACCAA
1 ATGCTGCTGTACCAA
*
30318505 ATG-TCGCAGTACCAA
1 ATGCT-GCTGTACCAA
* *
30318520 ATGTTGTTGTACCAA
1 ATGCTGCTGTACCAA
* *
30318535 ATGTTGCGGTACCAA
1 ATGCTGCTGTACCAA
30318550 ATGCTGCTGTACCAA
1 ATGCTGCTGTACCAA
30318565 ATGCTGCTGTACCAA
1 ATGCTGCTGTACCAA
* * *
30318580 TTGTTACTGTACCAA
1 ATGCTGCTGTACCAA
30318595 AT
1 AT
30318597 ACGGACGATA
Statistics
Matches: 114, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
14 1 0.01
15 112 0.98
16 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (15 bp):
ATGCTGCTGTACCAA
Found at i:30318944 original size:11 final size:11
Alignment explanation
Indices: 30318928--30318963 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
30318918 GTATATAAAA
30318928 AATTTAAATTT
1 AATTTAAATTT
30318939 AATTTAAATTT
1 AATTTAAATTT
*
30318950 AATAATAAATTT
1 AAT-TTAAATTT
30318962 AA
1 AA
30318964 AAATAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:30318960 original size:12 final size:12
Alignment explanation
Indices: 30318932--30318971 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
30318922 ATAAAAAATT
*
30318932 TAAATTTAAT-T
1 TAAATTTAATAA
30318943 TAAATTTAATAA
1 TAAATTTAATAA
*
30318955 TAAATTTAAAAA
1 TAAATTTAATAA
30318967 TAAAT
1 TAAAT
30318972 AACAAGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAATTTAATAA
Found at i:30320685 original size:30 final size:29
Alignment explanation
Indices: 30320645--30320726 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
30320635 ACATTAACAA
*
30320645 GACACCCCCACATTTTCAAGTGGTTCTAG
1 GACACCCCCACATTTCCAAGTGGTTCTAG
30320674 GACACCCCCCACATTTCCAAGTGGTTCT--
1 GACA-CCCCCACATTTCCAAGTGGTTCTAG
* *
30320702 G-C-CCTCTACATTTCCAAGTGGTTCT
1 GACACCCCCACATTTCCAAGTGGTTCT
30320727 CTTGTCTCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
25 21 0.43
27 1 0.02
28 1 0.02
29 4 0.08
30 22 0.45
ACGTcount: A:0.21, C:0.34, G:0.16, T:0.29
Consensus pattern (29 bp):
GACACCCCCACATTTCCAAGTGGTTCTAG
Found at i:30328655 original size:10 final size:9
Alignment explanation
Indices: 30328593--30328635 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 9
30328583 AGCAACCATG
30328593 TTTTTTTCT
1 TTTTTTTCT
30328602 TCTTTTTCTCCT
1 T-TTTTT-T-CT
30328614 TTTTTTCTCT
1 TTTTTT-TCT
30328624 TTTTTTTCT
1 TTTTTTTCT
30328633 TTT
1 TTT
30328636 CGAACATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 7 0.23
10 13 0.42
11 8 0.26
12 3 0.10
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:30328680 original size:20 final size:20
Alignment explanation
Indices: 30328642--30328680 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30328632 TTTTCGAACA
*
30328642 TTTTGCTTTTTTTTCTTTTT
1 TTTTGCTTTCTTTTCTTTTT
30328662 TTTTGCTATTCTTTT-TTTT
1 TTTTGCT-TTCTTTTCTTTT
30328681 CTTCTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.03, C:0.10, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTGCTTTCTTTTCTTTTT
Found at i:30338447 original size:16 final size:17
Alignment explanation
Indices: 30338416--30338450 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30338406 TGCATAGGAA
*
30338416 TTTAACTTAGATTTAAT
1 TTTAACTTAGACTTAAT
30338433 TTTAACTTAG-CTTAAT
1 TTTAACTTAGACTTAAT
30338449 TT
1 TT
30338451 AATTTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAACTTAGACTTAAT
Found at i:30339993 original size:59 final size:60
Alignment explanation
Indices: 30339930--30340364 Score: 423
Period size: 59 Copynumber: 7.4 Consensus size: 60
30339920 TTTTTGACTC
* * * *
30339930 TCGAGGGGAAAAAT-GTAA-TTTTGG-GAAAATTTAGGGTTAAAAATGGGATTTTAGAAGGT
1 TCGAGGGGTAAAATGGTAATTTTTGGTG-AAA-CTAGGGTTAAAAATGGAATTTTAGAAAGT
* * * *
30339989 TCGA-GGGTAAAATGGTAATTTTTGGTGAAA-TCGGGGTTAAAAATGGGATTTTGGAAGGT
1 TCGAGGGGTAAAATGGTAATTTTTGGTGAAACT-AGGGTTAAAAATGGAATTTTAGAAAGT
* * * *
30340048 TCGA-GGGT-AAATCAGTAATTTATGGTGAAAC-CGAGGTTGAAAATGGAATTTTAGAAAGT
1 TCGAGGGGTAAAAT-GGTAATTTTTGGTGAAACTAG-GGTTAAAAATGGAATTTTAGAAAGT
* * * *
30340107 T-TAGGGGTAAAATGGTAATTTTTGGTGAAACTGGGGTTAAAAATGGAATTTTGGAAAGG
1 TCGAGGGGTAAAATGGTAATTTTTGGTGAAACTAGGGTTAAAAATGGAATTTTAGAAAGT
* * *
30340166 TC-AGGGGTAAAATGATAATTTTTGGTGAAA-TCGGGGTTAAAAATGAAATTTTAGAAAGT
1 TCGAGGGGTAAAATGGTAATTTTTGGTGAAACT-AGGGTTAAAAATGGAATTTTAGAAAGT
* * * * *
30340225 T-TAGGGGTAAAATGGTAATTTTTGGTGAAA-TCGAGGATAAAAATGAAATTTTGGAAAGT
1 TCGAGGGGTAAAATGGTAATTTTTGGTGAAACTAG-GGTTAAAAATGGAATTTTAGAAAGT
* * *
30340284 TTG-GGGGTAAAATGGTAATTTTGGGTGAAATCT-GGGTTAAAAATGGAATTTTAAAAAGT
1 TCGAGGGGTAAAATGGTAATTTTTGGTGAAA-CTAGGGTTAAAAATGGAATTTTAGAAAGT
** *
30340343 TTTAGGGGCAAAATGGTAATTT
1 TCGAGGGGTAAAATGGTAATTT
30340365 CTGGAAGTTT
Statistics
Matches: 325, Mismatches: 33, Indels: 35
0.83 0.08 0.09
Matches are distributed among these distances:
58 17 0.05
59 274 0.84
60 32 0.10
61 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (60 bp):
TCGAGGGGTAAAATGGTAATTTTTGGTGAAACTAGGGTTAAAAATGGAATTTTAGAAAGT
Found at i:30340058 original size:29 final size:30
Alignment explanation
Indices: 30339962--30340055 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
30339952 GGGAAAATTT
*
30339962 AGGGTTAAAAATGGGATTTTAGAAGGTTCG
1 AGGGTTAAAAATGGGATTTTGGAAGGTTCG
* *
30339992 AGGG-T-AAAATGGTAATTTTTGGTGAA--ATCG
1 AGGGTTAAAAATGG-GA-TTTT-G-GAAGGTTCG
30340022 -GGGTTAAAAATGGGATTTTGGAAGGTTCG
1 AGGGTTAAAAATGGGATTTTGGAAGGTTCG
30340051 AGGGT
1 AGGGT
30340056 AAATCAGTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
27 3 0.06
28 8 0.16
29 12 0.24
30 17 0.34
31 7 0.14
32 3 0.06
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (30 bp):
AGGGTTAAAAATGGGATTTTGGAAGGTTCG
Found at i:30340157 original size:30 final size:31
Alignment explanation
Indices: 30340115--30340335 Score: 109
Period size: 30 Copynumber: 7.4 Consensus size: 31
30340105 GTTTAGGGGT
30340115 AAAATGGTAATTTTTGGTGAAA-CTGGGGTTA
1 AAAATGG-AATTTTTGGTGAAAGCTGGGGTTA
*
30340146 AAAATGGAA-TTTT-G-GAAAGGTCAGGGG-T-
1 AAAATGGAATTTTTGGTGAAA-G-CTGGGGTTA
* *
30340174 AAAATGATAATTTTTGGTGAAATC-GGGGTTA
1 AAAATG-GAATTTTTGGTGAAAGCTGGGGTTA
* * *
30340205 AAAAT-GAAATTTT--AGAAAGTTTAGGGG-T-
1 AAAATGGAATTTTTGGTGAAAG-CT-GGGGTTA
* * *
30340233 AAAATGGTAATTTTTGGTGAAATC-GAGGATA
1 AAAATGG-AATTTTTGGTGAAAGCTGGGGTTA
* * *
30340264 AAAAT-GAAATTTT-G-GAAAGTTTGGGGGT-
1 AAAATGGAATTTTTGGTGAAAG-CTGGGGTTA
* *
30340292 AAAATGGTAATTTTGGGTGAAATCT-GGGTTA
1 AAAATGG-AATTTTTGGTGAAAGCTGGGGTTA
30340323 AAAATGGAATTTT
1 AAAATGGAATTTT
30340336 AAAAAGTTTT
Statistics
Matches: 142, Mismatches: 23, Indels: 51
0.66 0.11 0.24
Matches are distributed among these distances:
27 12 0.08
28 18 0.13
29 33 0.23
30 40 0.28
31 27 0.19
32 12 0.08
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (31 bp):
AAAATGGAATTTTTGGTGAAAGCTGGGGTTA
Found at i:30340206 original size:177 final size:177
Alignment explanation
Indices: 30339933--30340336 Score: 525
Period size: 177 Copynumber: 2.3 Consensus size: 177
30339923 TTGACTCTCG
* * * *
30339933 AGGGGAAAAAT-GTAATTTTGGG-AAAATTTAGGGTTAAAAATGGGATTTTAGAAGGTTCGAGGG
1 AGGGGTAAAATGGTAATTTTGGGTGAAATCT-GGGTTAAAAATGGAATTTTAGAAGGTTCGAGGG
* ** * *
30339996 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAGGTTCGA-GGGT-AAA
65 TAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAAGTT-GAGGGGTAAAA
* * *
30340059 TCAGTAATTTATGGTGAAACCGAGGTTGAAAATGGAATTTTAGAAAGTTT
129 T-AGTAATTTATGGTGAAACCGAGGATAAAAATGAAATTTTAGAAAGTTT
* *
30340109 AGGGGTAAAATGGTAATTTTTGGTGAAA-CTGGGGTTAAAAATGGAATTTTGGAAAGG-TC-AGG
1 AGGGGTAAAATGGTAATTTTGGGTGAAATCT-GGGTTAAAAATGGAATTTTAG-AAGGTTCGA-G
*
30340171 GGTAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAAGTTTAGGGGTAAA
63 GGTAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAAGTTGAGGGGTAAA
* * * *
30340236 ATGGTAATTTTTGGTGAAATCGAGGATAAAAATGAAATTTTGGAAAGTTT
128 ATAGTAATTTATGGTGAAACCGAGGATAAAAATGAAATTTTAGAAAGTTT
*
30340286 GGGGGTAAAATGGTAATTTTGGGTGAAATCTGGGTTAAAAATGGAATTTTA
1 AGGGGTAAAATGGTAATTTTGGGTGAAATCTGGGTTAAAAATGGAATTTTA
30340337 AAAAGTTTTA
Statistics
Matches: 198, Mismatches: 23, Indels: 13
0.85 0.10 0.06
Matches are distributed among these distances:
176 12 0.06
177 173 0.87
178 13 0.07
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (177 bp):
AGGGGTAAAATGGTAATTTTGGGTGAAATCTGGGTTAAAAATGGAATTTTAGAAGGTTCGAGGGT
AAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAAGTTGAGGGGTAAAATA
GTAATTTATGGTGAAACCGAGGATAAAAATGAAATTTTAGAAAGTTT
Found at i:30340394 original size:118 final size:117
Alignment explanation
Indices: 30339933--30340364 Score: 493
Period size: 118 Copynumber: 3.7 Consensus size: 117
30339923 TTGACTCTCG
* * ** * * *
30339933 AGGGGAAAAATG-TAATTTTGGG-AAAATTTAGGGTTAAAAATGGGATTTTAG-AAGGTTCGAGG
1 AGGGGTAAAATGATAATTTTGGGTGAAA-TCGGGGTTAAAAATGGAATTTTAGAAAGTTTAG-GG
**
30339995 GTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGG-AAGGTTC
64 GTAAAATGGTAATTTTTGGTGAAATCGGGG-TAAAAATGAAATTTTGGAAAGG-TC
* * * *
30340050 -GAGGGT-AAATCAGTAATTTAT-GGTGAAACCGAGGTTGAAAATGGAATTTTAGAAAGTTTAGG
1 AG-GGGTAAAATGA-TAATTT-TGGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGG
*
30340112 GGTAAAATGGTAATTTTTGGTGAAA-CTGGGGTTAAAAATGGAATTTTGGAAAGGTC
63 GGTAAAATGGTAATTTTTGGTGAAATC-GGGG-TAAAAATGAAATTTTGGAAAGGTC
* *
30340168 AGGGGTAAAATGATAATTTTTGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAAGTTTAGGGGT
1 AGGGGTAAAATGATAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
* * *
30340233 AAAATGGTAATTTTTGGTGAAATCGAGGATAAAAATGAAATTTTGGAAAGTTT
66 AAAATGGTAATTTTTGGTGAAATCG-GGGTAAAAATGAAATTTTGGAAAGGTC
* * * *
30340286 GGGGGTAAAATGGTAATTTTGGGTGAAATCTGGGTTAAAAATGGAATTTTAAAAAGTTTTAGGGG
1 AGGGGTAAAATGATAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAG-TTTAGGGG
*
30340351 CAAAATGGTAATTT
65 TAAAATGGTAATTT
30340365 CTGGAAGTTT
Statistics
Matches: 273, Mismatches: 28, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
116 5 0.02
117 5 0.02
118 219 0.80
119 44 0.16
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (117 bp):
AGGGGTAAAATGATAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
AAAATGGTAATTTTTGGTGAAATCGGGGTAAAAATGAAATTTTGGAAAGGTC
Found at i:30342250 original size:17 final size:16
Alignment explanation
Indices: 30342232--30342323 Score: 116
Period size: 17 Copynumber: 5.7 Consensus size: 16
30342222 TTAATATTAT
* *
30342232 TTTAAATATAATTAAA
1 TTTAAATTTAAATAAA
30342248 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
30342265 TTTAAA--TAAATAAA
1 TTTAAATTTAAATAAA
30342279 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
30342296 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
*
30342313 TTTAAAATTAA
1 TTTAAATTTAA
30342324 TTTAAACTTA
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
14 13 0.19
15 1 0.01
16 13 0.19
17 39 0.57
18 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:30342254 original size:6 final size:6
Alignment explanation
Indices: 30342243--30342335 Score: 79
Period size: 6 Copynumber: 15.8 Consensus size: 6
30342233 TTAAATATAA
* *
30342243 TTAAAT TTAAAT TTAAA- ATAAAT TTAAAT AAATAAAT TTAAAT TTAAGA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAA-AT
* * *
30342292 -TAAAT TTAAAT TTAAA- ATAAAT TTAAAA TT-AAT TTAAAC TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
30342336 AAATCAAAAG
Statistics
Matches: 70, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
4 1 0.01
5 15 0.21
6 48 0.69
7 1 0.01
8 5 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:30342255 original size:11 final size:11
Alignment explanation
Indices: 30342243--30342335 Score: 71
Period size: 11 Copynumber: 7.9 Consensus size: 11
30342233 TTAAATATAA
30342243 TTAAATTTAAAT
1 TTAAA-TTAAAT
*
30342255 TTAAAATAAAT
1 TTAAATTAAAT
30342266 TTAAATAAATAAAT
1 TTAAAT---TAAAT
* *
30342280 TTAAATTTAAG
1 TTAAATTAAAT
*
30342291 ATAAATTTAAAT
1 TTAAA-TTAAAT
*
30342303 TTAAAATAAAT
1 TTAAATTAAAT
30342314 TTAAAATT-AAT
1 TT-AAATTAAAT
30342325 TTAAACTTAAA
1 TTAAA-TTAAA
30342336 AAATCAAAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
10 3 0.05
11 31 0.48
12 19 0.30
14 11 0.17
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:30342336 original size:17 final size:17
Alignment explanation
Indices: 30342244--30342323 Score: 121
Period size: 17 Copynumber: 4.9 Consensus size: 17
30342234 TAAATATAAT
30342244 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
30342261 TAAATTTAAA--T-AAA
1 TAAATTTAAATTTAAAA
*
30342275 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAAA
30342292 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
30342309 TAAATTTAAAATTAA
1 TAAATTTAAATTTAA
30342324 TTTAAACTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
16 1 0.02
17 42 0.74
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:30344351 original size:16 final size:17
Alignment explanation
Indices: 30344330--30344376 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
30344320 CATTGTCCCC
* *
30344330 AATGCACTGACATTA-A
1 AATGCAATGACAATAGA
30344346 AATGCAATGACAATAGA
1 AATGCAATGACAATAGA
*
30344363 AATGCAACGACAAT
1 AATGCAATGACAAT
30344377 GTGCACTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (17 bp):
AATGCAATGACAATAGA
Found at i:30345215 original size:6 final size:6
Alignment explanation
Indices: 30345186--30345246 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
30345176 AAGCTTTGAT
* * **
30345186 TTTAAA ATTAAG TTTAAA -TT-AA TTTAAA TTTATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
30345232 TTT-GA TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
30345247 GTTAAATTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
4 2 0.05
5 8 0.19
6 32 0.76
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:30345240 original size:17 final size:17
Alignment explanation
Indices: 30345184--30345246 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
30345174 TTAAGCTTTG
* *
30345184 ATTTTAAAATTAAGTTT
1 ATTTTAAATTTAAATTT
**
30345201 AAATT-AATTTAAATTT
1 ATTTTAAATTTAAATTT
30345217 ATTTTTAAATTTAAATTT
1 A-TTTTAAATTTAAATTT
30345235 GA-TTTAAATTTA
1 -ATTTTAAATTTA
30345247 GTTAAATTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 10 0.27
17 15 0.41
18 11 0.30
19 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:30345253 original size:21 final size:20
Alignment explanation
Indices: 30345227--30345266 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
30345217 ATTTTTAAAT
*
30345227 TTAAATTTGATTTAAATTTAG
1 TTAAATTTGAATT-AATTTAG
30345248 TTAAATTTGAATTAATTTA
1 TTAAATTTGAATTAATTTA
30345267 AAACTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (20 bp):
TTAAATTTGAATTAATTTAG
Done.