Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 86 of 335
Found at i:28406361 original size:37 final size:37
Alignment explanation
Indices: 28406319--28406393 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
28406309 AAAACATGTT
28406319 CCACTTTTGTCCAATACCCAATAATCACATAAAAAAG
1 CCACTTTTGTCCAATACCCAATAATCACATAAAAAAG
28406356 CCACTTTTGTCCAATACCCAATAATCACATAAAAAAG
1 CCACTTTTGTCCAATACCCAATAATCACATAAAAAAG
28406393 C
1 C
28406394 AAATACCTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.43, C:0.28, G:0.05, T:0.24
Consensus pattern (37 bp):
CCACTTTTGTCCAATACCCAATAATCACATAAAAAAG
Found at i:28410638 original size:18 final size:18
Alignment explanation
Indices: 28410617--28410676 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
28410607 AATAAATTAT
*
28410617 TAATTATATATATTTTTA
1 TAATTAAATATATTTTTA
* *
28410635 TAATTAAATTTATTTTTT
1 TAATTAAATATATTTTTA
28410653 TAA--AAATA-ATTATTTA
1 TAATTAAATATATT-TTTA
28410669 -AATTAAAT
1 TAATTAAAT
28410677 TCGGGTTAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 5 0.15
16 7 0.21
17 4 0.12
18 18 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTAAATATATTTTTA
Found at i:28411107 original size:24 final size:25
Alignment explanation
Indices: 28411070--28411125 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
28411060 ATGGACCAAC
* *
28411070 TTTTAACAATAAAAATGAATGTACT
1 TTTTAATAATAAAAATAAATGTACT
*
28411095 TTTTAATAA-AAAAATAAATTTACT
1 TTTTAATAATAAAAATAAATGTACT
28411119 TTTTAAT
1 TTTTAAT
28411126 CTAACATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (25 bp):
TTTTAATAATAAAAATAAATGTACT
Found at i:28416000 original size:12 final size:12
Alignment explanation
Indices: 28415983--28416013 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28415973 TATAAGATAT
28415983 TTGCATCATTGC
1 TTGCATCATTGC
28415995 TTGCATCATTGC
1 TTGCATCATTGC
*
28416007 ATGCATC
1 TTGCATC
28416014 TTACCGTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.39
Consensus pattern (12 bp):
TTGCATCATTGC
Found at i:28419765 original size:22 final size:20
Alignment explanation
Indices: 28419727--28419766 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
28419717 TCTTTACATA
28419727 AAAACAATATATTAATGTCG
1 AAAACAATATATTAATGTCG
28419747 AAAACATATATAATTAATGT
1 AAAACA-ATAT-ATTAATGT
28419767 ATTTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (20 bp):
AAAACAATATATTAATGTCG
Found at i:28420989 original size:29 final size:31
Alignment explanation
Indices: 28420940--28421019 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
28420930 AAATTTAATC
* *
28420940 AAATCAAAATTTAATATATAA-A-ATCACACA
1 AAATCAAAA-TTCATGTATAATATATCACACA
* **
28420970 AAATCAAAATTCATGTATAATATTTCACATT
1 AAATCAAAATTCATGTATAATATATCACACA
*
28421001 AAATCAAAGTTCATGTATA
1 AAATCAAAATTCATGTATA
28421020 GTTTAATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 9 0.21
30 10 0.24
31 23 0.55
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (31 bp):
AAATCAAAATTCATGTATAATATATCACACA
Found at i:28422674 original size:26 final size:28
Alignment explanation
Indices: 28422645--28422696 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
28422635 AGGTAAGTTC
*
28422645 TTATATTGATTAAATT-TTT-TTAATTG
1 TTATATTAATTAAATTGTTTATTAATTG
28422671 TTATATTAATTAAATTGTTTATTAAT
1 TTATATTAATTAAATTGTTTATTAAT
28422697 GTTGTGCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 15 0.65
27 3 0.13
28 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (28 bp):
TTATATTAATTAAATTGTTTATTAATTG
Found at i:28425385 original size:47 final size:49
Alignment explanation
Indices: 28425265--28425442 Score: 198
Period size: 45 Copynumber: 3.8 Consensus size: 49
28425255 TGTAACCCGC
* * *
28425265 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-CGTT-GCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
28425310 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
28425360 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
28425403 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
28425443 TCAACCATCC
Statistics
Matches: 112, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 36 0.32
46 29 0.26
47 30 0.27
48 3 0.03
49 1 0.01
50 5 0.04
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:28425430 original size:93 final size:92
Alignment explanation
Indices: 28425272--28425442 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 92
28425262 CGCCCATAAG
* *
28425272 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTGCATCCATAAGTGAACTCGGACTCAACTCAA
28425337 CGAGTTCGGATGCCTAGTTACATCTCA
66 CGAGTTCGGATGCCTAGTTACATCTCA
*
28425364 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATT-GCATCCATAAGTGAACTCGGACTCAACTCA
28425429 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
28425443 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 31 0.41
93 44 0.59
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (92 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA
Found at i:28432263 original size:40 final size:40
Alignment explanation
Indices: 28432204--28432372 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
28432194 CGGGACTTTA
* * *
28432204 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
28432244 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
28432284 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
28432324 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
28432364 CCCGGATAT
1 CCCGGATAT
28432373 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:28435747 original size:46 final size:46
Alignment explanation
Indices: 28435680--28435854 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
28435670 TGTAACCCGC
* * *
28435680 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
* *
28435726 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-ATTTGCAT
* * *
28435776 CTCA-CA---AACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
28435819 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
28435855 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 7 0.06
44 1 0.01
46 61 0.56
47 27 0.25
48 1 0.01
49 1 0.01
50 7 0.06
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
Found at i:28435796 original size:93 final size:93
Alignment explanation
Indices: 28435689--28435858 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 93
28435679 CCCATAAGCG
* * *
28435689 AACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
28435754 GAGTTCGGATGCCTAGTTACATCTCACA
66 GAGTTCGGATGCCTAGTTACATCTCACA
*
28435782 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
28435847 GAGTTCGGATGC
66 GAGTTCGGATGC
28435859 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCACA
Found at i:28441541 original size:30 final size:29
Alignment explanation
Indices: 28441505--28441565 Score: 113
Period size: 30 Copynumber: 2.1 Consensus size: 29
28441495 AGTTGGAAGT
28441505 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTT-AACTAGC
28441535 TTTGGCACTAAGTGTGCGATTTAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAACTAGC
28441564 TT
1 TT
28441566 CGGCTACTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGCGATTTAACTAGC
Found at i:28445900 original size:28 final size:28
Alignment explanation
Indices: 28445868--28445932 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
28445858 ATTTACTAGA
*
28445868 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
28445896 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
28445924 ATACCCCTA
1 ATACCCCTA
28445933 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:28446096 original size:27 final size:27
Alignment explanation
Indices: 28446038--28446127 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
28446028 AGGAAGCGTC
28446038 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
28446066 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
28446093 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
28446122 CTGGTG
1 CTGGTG
28446128 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:28446146 original size:55 final size:56
Alignment explanation
Indices: 28446038--28446152 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
28446028 AGGAAGCGTC
* *
28446038 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
28446093 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
28446149 CTGG
1 CTGG
28446153 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.58
56 21 0.40
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:28447239 original size:11 final size:10
Alignment explanation
Indices: 28447211--28447244 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
28447201 AGCCTGTAAG
28447211 TATTCTGAAT
1 TATTCTGAAT
*
28447221 TTTTCTGAAT
1 TATTCTGAAT
28447231 ATATTCTGAAT
1 -TATTCTGAAT
28447242 TAT
1 TAT
28447245 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:28453752 original size:28 final size:28
Alignment explanation
Indices: 28453720--28453784 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
28453710 ATTTACTAGA
*
28453720 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
28453748 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
28453776 ATACCCCTA
1 ATACCCCTA
28453785 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:28453931 original size:28 final size:27
Alignment explanation
Indices: 28453890--28453977 Score: 110
Period size: 25 Copynumber: 3.2 Consensus size: 27
28453880 AGGAAGCGTC
28453890 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
*
28453918 CTGGTGGCCCTGCCAC--ATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
28453943 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
28453972 CTGGTG
1 CTGGTG
28453978 ACTCTGTCAC
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
25 23 0.43
26 1 0.02
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:28453988 original size:29 final size:28
Alignment explanation
Indices: 28453900--28453988 Score: 94
Period size: 25 Copynumber: 3.2 Consensus size: 28
28453890 CTGGTGGCTA
* * *
28453900 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
28453928 TGCCAC---ATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
28453953 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
28453982 TGTCACA
1 TGCCACA
28453989 TTTTCTGTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
25 23 0.44
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:28454470 original size:18 final size:18
Alignment explanation
Indices: 28454431--28454471 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
28454421 TAATAAGGCC
* *
28454431 TTTTAATTATTTTTATGG
1 TTTTAATTACTTTTATGA
*
28454449 TTTTAATTACTTTTATTA
1 TTTTAATTACTTTTATGA
28454467 TTTTA
1 TTTTA
28454472 TTTTACTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAATTACTTTTATGA
Found at i:28456233 original size:43 final size:42
Alignment explanation
Indices: 28456170--28456293 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 42
28456160 TCTGAACTCA
* **
28456170 TTCACCGGCATTTCGCCTGCTAGGCTTGAAGCCCGATATCAT
1 TTCACCGGCATTTAGCCTGCTAGGCCCGAAGCCCGATATCAT
* * *
28456212 TTCACCGCCATTGTAGCCTGCTAGGCCCGAAGCCCAATATTAT
1 TTCACCGGCATT-TAGCCTGCTAGGCCCGAAGCCCGATATCAT
* *
28456255 CTCATCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
1 TTCACCGGCATT-TAGCCTGCTAGGCCCGAAGCCCGATA
28456294 ATATTATTCA
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
42 11 0.16
43 59 0.84
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.25
Consensus pattern (42 bp):
TTCACCGGCATTTAGCCTGCTAGGCCCGAAGCCCGATATCAT
Found at i:28457190 original size:2 final size:2
Alignment explanation
Indices: 28457178--28457206 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28457168 CCCTATAGAT
28457178 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28457207 AAATAACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28465034 original size:22 final size:22
Alignment explanation
Indices: 28464994--28465035 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28464984 ATATTTGAGC
**
28464994 ATTGGTATTGAATTTAAATTGA
1 ATTGGTATTGAATCCAAATTGA
*
28465016 ATTGGTATTTAATCCAAATT
1 ATTGGTATTGAATCCAAATT
28465036 TTAATTATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (22 bp):
ATTGGTATTGAATCCAAATTGA
Found at i:28468407 original size:14 final size:14
Alignment explanation
Indices: 28468383--28468420 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
28468373 ATTTTTAGAA
*
28468383 TTTTTAATTT-ATT
1 TTTTTATTTTAATT
28468396 TTTTATATTTTAATT
1 TTTT-TATTTTAATT
28468411 TTTTTATTTT
1 TTTTTATTTT
28468421 CAAATAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 11 0.50
15 7 0.32
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTTTAATT
Found at i:28471191 original size:17 final size:17
Alignment explanation
Indices: 28471169--28471232 Score: 92
Period size: 17 Copynumber: 3.6 Consensus size: 17
28471159 CAATAATATG
28471169 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
28471186 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
28471204 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
28471221 TGCAATCTTAGA
1 --CAATCTTAGA
28471233 AGATATAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.38
18 16 0.38
19 10 0.24
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:28471209 original size:18 final size:18
Alignment explanation
Indices: 28471167--28471232 Score: 107
Period size: 18 Copynumber: 3.7 Consensus size: 18
28471157 TTCAATAATA
28471167 TGCAATCTTAGATATGA-
1 TGCAATCTTAGATATGAT
*
28471184 TACAATCTTAGATATGAT
1 TGCAATCTTAGATATGAT
28471202 TGCAATCTTAGATATGAT
1 TGCAATCTTAGATATGAT
28471220 ATGCAATCTTAGA
1 -TGCAATCTTAGA
28471233 AGATATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.36
18 17 0.38
19 12 0.27
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (18 bp):
TGCAATCTTAGATATGAT
Found at i:28471546 original size:17 final size:17
Alignment explanation
Indices: 28471524--28471556 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28471514 TTTCCCTGAT
*
28471524 TTTTTTTATATTTTTAA
1 TTTTTTTATAATTTTAA
28471541 TTTTTTTATAATTTTA
1 TTTTTTTATAATTTTA
28471557 GTATCATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTATAATTTTAA
Found at i:28480546 original size:44 final size:45
Alignment explanation
Indices: 28480484--28480707 Score: 242
Period size: 45 Copynumber: 5.0 Consensus size: 45
28480474 GGAATGTGAT
* *
28480484 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
*
28480529 ATCTGCT-TCTTCAATCTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* *
28480573 ATCTGTTATCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * * * * *
28480618 ATCT-ATCATCTTGGATCTGCT--TCGATGTAA-ACACATGAAGGTCAG
1 ATCTGCT-ATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ATGCCAA
28480663 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCC
1 ATCTGCTA--TCTTCGATCTGCTCCCCGTCTAATACAGAGATGCC
28480708 TAATGACATC
Statistics
Matches: 146, Mismatches: 22, Indels: 20
0.78 0.12 0.11
Matches are distributed among these distances:
43 6 0.04
44 46 0.32
45 67 0.46
46 1 0.01
47 15 0.10
48 5 0.03
49 6 0.04
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (45 bp):
ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
Found at i:28485322 original size:18 final size:18
Alignment explanation
Indices: 28485280--28485345 Score: 107
Period size: 18 Copynumber: 3.7 Consensus size: 18
28485270 TTTCAATATA
28485280 TGCAATCTTAGATATGA-
1 TGCAATCTTAGATATGAT
*
28485297 TACAATCTTAGATATGAT
1 TGCAATCTTAGATATGAT
28485315 TGCAATCTTAGATATGAT
1 TGCAATCTTAGATATGAT
28485333 ATGCAATCTTAGA
1 -TGCAATCTTAGA
28485346 AGATATGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.36
18 17 0.38
19 12 0.27
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (18 bp):
TGCAATCTTAGATATGAT
Found at i:28485352 original size:17 final size:19
Alignment explanation
Indices: 28485277--28485345 Score: 117
Period size: 17 Copynumber: 3.8 Consensus size: 19
28485267 AATTTTCAAT
28485277 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
28485296 ATA--CAATCTTAGATATG
1 ATATGCAATCTTAGATATG
28485313 AT-TGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
28485331 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
28485346 AGATATGATT
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.34
18 16 0.34
19 15 0.32
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:28485371 original size:22 final size:22
Alignment explanation
Indices: 28485277--28485368 Score: 73
Period size: 17 Copynumber: 4.7 Consensus size: 22
28485267 AATTTTCAAT
28485277 ATATGCAATCTT---AGATATG
1 ATATGCAATCTTAGAAGATATG
28485296 ATA--CAATCTT---AGATATG
1 ATATGCAATCTTAGAAGATATG
28485313 AT-TGCAATCTT---AGATATG
1 ATATGCAATCTTAGAAGATATG
28485331 ATATGCAATCTTAGAAGATATG
1 ATATGCAATCTTAGAAGATATG
* *
28485353 ATTTTGTAATCTTAGA
1 A-TATGCAATCTTAGA
28485369 GATTTAATTT
Statistics
Matches: 64, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
17 16 0.25
18 16 0.25
19 12 0.19
22 8 0.12
23 12 0.19
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
ATATGCAATCTTAGAAGATATG
Found at i:28495937 original size:78 final size:78
Alignment explanation
Indices: 28495852--28496120 Score: 423
Period size: 78 Copynumber: 3.4 Consensus size: 78
28495842 ATTCAATGGA
* *
28495852 GAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTC
1 GAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTC
*
28495917 TGTATTAGACAGG
66 TGTATTAGACGGG
* *
28495930 GAGCAGATCGAAGACACAACAGATCTGACCTTCATTGAATCAGATCCAAGATGATTTGGCATCTC
1 GAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTC
* *
28495995 TGTATTATATGGG
66 TGTATTAGACGGG
*
28496008 GAGCAGATCAAAGACATAACAGAT-TGGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCT
1 GAGCAGATCGAAGACATAACAGATCT-GACCTTCATTGAAACAGATCCAAGATGATTTGGCATCT
28496072 CTGTATTAGACGGG
65 CTGTATTAGACGGG
* * *
28496086 GAGCAGATCGAAGACATAGCATAGCTGACCTTCAT
1 GAGCAGATCGAAGACATAACAGATCTGACCTTCAT
28496121 GTGTTTACAT
Statistics
Matches: 174, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
77 1 0.01
78 172 0.99
79 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (78 bp):
GAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTC
TGTATTAGACGGG
Found at i:28496213 original size:45 final size:45
Alignment explanation
Indices: 28496134--28496332 Score: 249
Period size: 45 Copynumber: 4.5 Consensus size: 45
28496124 TTTACATCGA
* *
28496134 AGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGG
1 AGCAGATCAAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
* * *
28496179 AACAAATCAGAGATAACAGATTTGGCATCTCTGTATTAGAC-GGG
1 AGCAGATCAAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
* ** ** ** *
28496223 ATCAGATTGAAGA-AGTAGATTTAACGTCTCTGTATTAGACGGGG
1 AGCAGATCAAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
*
28496267 AGCAGATCAAAGATAACAGATTTGGCGTCTCTGTATTAGACGGGG
1 AGCAGATCAAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
*
28496312 AGCAGATCAAAGATAGCAGAT
1 AGCAGATCAAAGATAACAGAT
28496333 ATCGCCTTCC
Statistics
Matches: 129, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
43 22 0.17
44 24 0.19
45 83 0.64
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.25
Consensus pattern (45 bp):
AGCAGATCAAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
Found at i:28496760 original size:18 final size:17
Alignment explanation
Indices: 28496737--28496770 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28496727 TTTCCCTGAT
*
28496737 TTTTTTTATATATTTTAA
1 TTTTTTAATA-ATTTTAA
28496755 TTTTTTAATAATTTTA
1 TTTTTTAATAATTTTA
28496771 GTATCATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAATAATTTTAA
Found at i:28503237 original size:52 final size:52
Alignment explanation
Indices: 28503088--28503238 Score: 158
Period size: 52 Copynumber: 2.9 Consensus size: 52
28503078 TAACATGCCA
* * *
28503088 ATGCCATATCCCAGATATGGTCTTATACGGAATCACATTATCACATCACACCG
1 ATGCCATAACCCAGCTATGGTCTTATACGGAAACACA-TATCACATCACACCG
* ** * * ***
28503141 ATGCCATAACCCAGCTATGGTCTTATACAGAAACTTAAAACACATTGTACCG
1 ATGCCATAACCCAGCTATGGTCTTATACGGAAACACATATCACATCACACCG
* * * *
28503193 ATGCCATAGCCCATCTATGGTCTTATATGGAAGCACATATCACATC
1 ATGCCATAACCCAGCTATGGTCTTATACGGAAACACATATCACATC
28503239 TTTTCCATCA
Statistics
Matches: 77, Mismatches: 21, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
52 46 0.60
53 31 0.40
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (52 bp):
ATGCCATAACCCAGCTATGGTCTTATACGGAAACACATATCACATCACACCG
Found at i:28509198 original size:99 final size:103
Alignment explanation
Indices: 28509073--28509275 Score: 247
Period size: 105 Copynumber: 2.0 Consensus size: 103
28509063 CACACATCAG
*
28509073 ACACCGAAGCCATAGCCCTGCCATGGTCTTACA-CGG-A-TC-AGATAACA-TG-CCGATGCCAT
1 ACACCGAAGCCATAGCCCAGCCATGGTCTTACATCGGAACTCGA-ATAACATTGACCGATGCCAT
* *
28509132 ATCCCAGATATGGTCTTATACGGAATCACATTATCACATC
65 AGCCCAGATATGGTCTTATACGGAAGCACA-TATCACATC
* * * * * *
28509172 ACACCGATGCCATAGCCCAGCTATGGTCTTATATGGGAACTCGAATCACATTGTATCGATGCCAT
1 ACACCGAAGCCATAGCCCAGCCATGGTCTTACATCGGAACTCGAATAACATTG-ACCGATGCCAT
*
28509237 AGCCCAGCTATGGTCTTATACGGAAGCACATATCACATC
65 AGCCCAGATATGGTCTTATACGGAAGCACATATCACATC
28509276 TTTTCTGTCA
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
99 29 0.33
100 2 0.02
101 1 0.01
102 7 0.08
103 3 0.03
104 9 0.10
105 36 0.41
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (103 bp):
ACACCGAAGCCATAGCCCAGCCATGGTCTTACATCGGAACTCGAATAACATTGACCGATGCCATA
GCCCAGATATGGTCTTATACGGAAGCACATATCACATC
Found at i:28509202 original size:53 final size:52
Alignment explanation
Indices: 28509122--28509275 Score: 186
Period size: 52 Copynumber: 2.9 Consensus size: 52
28509112 AGATAACATG
* *
28509122 CCGATGCCATATCCCAGATATGGTCTTATACGGAATCACATTATCACATCACA
1 CCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACA-TATCACATCACA
* * ***
28509175 CCGATGCCATAGCCCAGCTATGGTCTTATATGGGAACTC-GA-ATCACATTGTA
1 CCGATGCCATAGCCCAGCTATGGTCTTATA-CGGAA-TCACATATCACATCACA
* *
28509227 TCGATGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATC
1 CCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACATC
28509276 TTTTCTGTCA
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
50 1 0.01
51 5 0.06
52 44 0.52
53 28 0.33
54 5 0.06
55 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (52 bp):
CCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACATCACA
Found at i:28511695 original size:31 final size:31
Alignment explanation
Indices: 28511660--28511761 Score: 84
Period size: 34 Copynumber: 3.2 Consensus size: 31
28511650 ATGATGCTAG
28511660 AGATATTTTGA-TATTTTATAATTATTTAATT
1 AGATATTTT-ATTATTTTATAATTATTTAATT
** *
28511691 AGATA-AATATTATTTTATTAA-TATTTCAATA
1 AGATATTTTATTATTTTA-TAATTATTT-AATT
* *
28511722 AGATATTTATTATTATTTTATTATTATTTTATT
1 AGATA-TT-TTATTATTTTATAATTATTTAATT
28511755 AGTATAT
1 AG-ATAT
28511762 AAAGAAAGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
29 1 0.02
30 13 0.24
31 16 0.29
33 7 0.13
34 18 0.33
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (31 bp):
AGATATTTTATTATTTTATAATTATTTAATT
Found at i:28511715 original size:11 final size:11
Alignment explanation
Indices: 28511701--28511755 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
28511691 AGATAAATAT
28511701 TATTTTATTAA
1 TATTTTATTAA
* *
28511712 TATTTCAATAA
1 TATTTTATTAA
* *
28511723 GATATTTATTAT
1 TAT-TTTATTAA
*
28511735 TATTTTATTAT
1 TATTTTATTAA
28511746 TATTTTATTA
1 TATTTTATTA
28511756 GTATATAAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
11 29 0.81
12 7 0.19
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:28513627 original size:46 final size:46
Alignment explanation
Indices: 28513575--28513985 Score: 531
Period size: 46 Copynumber: 9.0 Consensus size: 46
28513565 GCTTGCTGAA
* *
28513575 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
28513621 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
28513667 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAAATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
28513713 ATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * * *
28513759 AGGAAATGAATAAAACCATGGTTG-AAGATACCATGGTAGCGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
28513804 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
28513850 ATGAGAA-GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGA-AATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
28513896 ATGAAAAGAATAAGACAATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
28513942 A-GAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
28513986 TCAAAGATAA
Statistics
Matches: 334, Mismatches: 27, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
45 42 0.13
46 290 0.87
47 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:28513919 original size:183 final size:183
Alignment explanation
Indices: 28513589--28513985 Score: 535
Period size: 183 Copynumber: 2.2 Consensus size: 183
28513579 AATGTGTAAG
* **
28513589 ACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
1 ACCATGGTTG-AAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGATACC
* ** *
28513654 ATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAAATGATATGAAA
65 ATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAAATGACATGAAA
* ** * * *
28513719 TGTGTAAGACCATGGTTGAAAGATATCATGGCAACATGACAGGAAATGAATAAA
130 AGAATAAGACAATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAA
* * *
28513773 ACCATGGTTGAAGATACCATGGTAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGATACCA
1 ACCATGGTTGAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGATACCA
* **
28513838 TGGCAACGTGACATGAGAA-GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAA
66 TGGCAACATGACATGA-AATGAATAAGACCATGGTTGAAAGATACCATGGCAAAATGACATGAAA
* *
28513902 AGAATAAGACAATGGTTGAAAGATACCATGGCAACATGATAGAAAATGAGTAAA
130 AGAATAAGACAATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAA
* * * *
28513956 ACCATAGTTGAAAGACACTATGGCATCATG
1 ACCATGGTTG-AAGATACCATGGCAACATG
28513986 TCAAAGATAA
Statistics
Matches: 184, Mismatches: 27, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
183 158 0.86
184 26 0.14
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.21
Consensus pattern (183 bp):
ACCATGGTTGAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGATACCA
TGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAAATGACATGAAAA
GAATAAGACAATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAA
Found at i:28514048 original size:77 final size:77
Alignment explanation
Indices: 28513921--28514078 Score: 307
Period size: 77 Copynumber: 2.1 Consensus size: 77
28513911 CAATGGTTGA
*
28513921 AAGATACCATGGCAACATGATAGAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
1 AAGATACCATGGCAACATGACAGAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
28513986 TCAAAGATAAAT
66 TCAAAGATAAAT
28513998 AAGATACCATGGCAACATGACAGAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
1 AAGATACCATGGCAACATGACAGAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
28514063 TCAAAGATAAAT
66 TCAAAGATAAAT
28514075 AAGA
1 AAGA
28514079 CCGTAGATAG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (77 bp):
AAGATACCATGGCAACATGACAGAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
TCAAAGATAAAT
Found at i:28514364 original size:16 final size:17
Alignment explanation
Indices: 28514343--28514375 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28514333 ATGATGGAGC
28514343 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
28514359 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
28514376 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:28519993 original size:20 final size:20
Alignment explanation
Indices: 28519970--28520007 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28519960 ACTTAATGTT
*
28519970 AATTAAGTAAAGGTTAATTA
1 AATTAAGTAAAGATTAATTA
*
28519990 AATTAATTAAAGATTAAT
1 AATTAAGTAAAGATTAAT
28520008 CTAAGTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (20 bp):
AATTAAGTAAAGATTAATTA
Found at i:28522414 original size:53 final size:53
Alignment explanation
Indices: 28522273--28522423 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
28522263 ACAAGTGTGC
* **
28522273 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
28522326 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
28522379 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
28522424 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:28526639 original size:203 final size:203
Alignment explanation
Indices: 28526280--28526888 Score: 1090
Period size: 203 Copynumber: 3.0 Consensus size: 203
28526270 TTAAAGAAAT
28526280 AAATA-ATAAA-ATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
1 AAATACATAAACATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
28526343 ATTACATTTAAGGGATCTATTAATACCAAGAAACTGGATGATAGTTAGAATAAGT-AGTGCTAGT
66 ATTACATTTAAGGGATCTATTAATACCAAGAAACTGGATGATAGTTAGAATAAGTGA-TGCTAGT
* *
28526407 ACTTCAAAATCTGTAAATACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAA
130 ACTTCAAAACCTGTAAGTACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAA
28526472 TGCTATAAC
195 TGCTATAAC
28526481 AAATACATAAACATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
1 AAATACATAAACATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
* *
28526546 ATTACATTTAAGGGATCTATTGATACCAAGAAACTGGATGATAGTTAGAATAAGTGAAGCTAGTA
66 ATTACATTTAAGGGATCTATTAATACCAAGAAACTGGATGATAGTTAGAATAAGTGATGCTAGTA
*
28526611 CTTCAAAACCTGTAAGTACTATAGAATATATGTTGTCAGGAGATAGATTATTTTTTAAAAATAAT
131 CTTCAAAACCTGTAAGTACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAAT
28526676 GCTATAAC
196 GCTATAAC
28526684 AAATACATAAACATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
1 AAATACATAAACATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
*
28526749 ATTACATTTAAGGGATCTATTAATACCAAG--A---GATGATAGTTAGAATAAGTGGTGCTAGTA
66 ATTACATTTAAGGGATCTATTAATACCAAGAAACTGGATGATAGTTAGAATAAGTGATGCTAGTA
28526809 CTTCAAAACCTGTAAGTACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAAT
131 CTTCAAAACCTGTAAGTACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAAT
*
28526874 GTTATAAC
196 GCTATAAC
28526882 AAATACA
1 AAATACA
28526889 AATGATAATT
Statistics
Matches: 395, Mismatches: 10, Indels: 9
0.95 0.02 0.02
Matches are distributed among these distances:
198 105 0.27
201 6 0.02
202 5 0.01
203 278 0.70
204 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (203 bp):
AAATACATAAACATTATTGAGCTTTTTAAACCTAATAAATTTACTACAGAAATTCAACCAAAATT
ATTACATTTAAGGGATCTATTAATACCAAGAAACTGGATGATAGTTAGAATAAGTGATGCTAGTA
CTTCAAAACCTGTAAGTACTATAGAATATATGTCGTCAGGAGATAGATTATTTTTTAAAAATAAT
GCTATAAC
Found at i:28527763 original size:16 final size:16
Alignment explanation
Indices: 28527729--28527762 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
28527719 TATACAAATC
*
28527729 AAAGAATTATTAGAAA
1 AAAGAATTAATAGAAA
28527745 AAAG-ATTAATAGAAA
1 AAAGAATTAATAGAAA
28527760 AAA
1 AAA
28527763 ACTAATAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.21
Consensus pattern (16 bp):
AAAGAATTAATAGAAA
Found at i:28528285 original size:2 final size:2
Alignment explanation
Indices: 28528253--28528277 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28528243 GATGTACTTT
28528253 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28528278 GCATATATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28530684 original size:17 final size:17
Alignment explanation
Indices: 28530642--28530684 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
28530632 TTTATTTTGG
*
28530642 TTTTTATTGTTTTCTAA
1 TTTTTTTTGTTTTCTAA
28530659 TTTTCTTTTGTTTT-TAA
1 TTTT-TTTTGTTTTCTAA
28530676 TTGTTTTTT
1 TT-TTTTTT
28530685 AGATTTCTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.77
Consensus pattern (17 bp):
TTTTTTTTGTTTTCTAA
Found at i:28530691 original size:28 final size:28
Alignment explanation
Indices: 28530630--28530692 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
28530620 AAGCTTTAAG
*
28530630 GATTTATTTTGGTTTTTATTGTTTTCTA
1 GATTTCTTTTGGTTTTTATTGTTTTCTA
*
28530658 -ATTTTCTTTT-GTTTTTAATTGTTTTTTA
1 GA-TTTCTTTTGGTTTTT-ATTGTTTTCTA
28530686 GATTTCT
1 GATTTCT
28530693 GGTGTTGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
27 7 0.23
28 22 0.73
29 1 0.03
ACGTcount: A:0.14, C:0.05, G:0.11, T:0.70
Consensus pattern (28 bp):
GATTTCTTTTGGTTTTTATTGTTTTCTA
Found at i:28530698 original size:28 final size:27
Alignment explanation
Indices: 28530641--28530698 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
28530631 ATTTATTTTG
**
28530641 GTTTTTATTGTTTTCTAATTTTCTTTT
1 GTTTTTATTGTTTTCTAATTTTCTGGT
*
28530668 GTTTTTAATTGTTTTTTAGA-TTTCTGGT
1 GTTTTT-ATTGTTTTCTA-ATTTTCTGGT
28530696 GTT
1 GTT
28530699 GTTACATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.23
28 19 0.73
29 1 0.04
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.69
Consensus pattern (27 bp):
GTTTTTATTGTTTTCTAATTTTCTGGT
Found at i:28551909 original size:25 final size:26
Alignment explanation
Indices: 28551883--28551931 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
28551873 TCATTTATTT
28551883 TTTTA-TTTTTTT-AATCAT-TAAAA
1 TTTTATTTTTTTTAAATCATCTAAAA
28551906 TTTTATTTTTTTTAAATCATCTAAAA
1 TTTTATTTTTTTTAAATCATCTAAAA
28551932 ATTGATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.22
24 7 0.30
25 6 0.26
26 5 0.22
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTATTTTTTTTAAATCATCTAAAA
Found at i:28555990 original size:23 final size:23
Alignment explanation
Indices: 28555964--28556018 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
28555954 TTAAGAATAA
28555964 ATTTATATTATTTTAAATTTAAT
1 ATTTATATTATTTTAAATTTAAT
* * **
28555987 ATTTA-ATAAATTTAAATTTTTT
1 ATTTATATTATTTTAAATTTAAT
28556009 ATTT-TATTAT
1 ATTTATATTAT
28556019 AAGTTTAAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTATATTATTTTAAATTTAAT
Found at i:28560734 original size:18 final size:19
Alignment explanation
Indices: 28560711--28560747 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28560701 GATATGATAC
*
28560711 TAAAAT-TATTAAAAAAAT
1 TAAAATATATAAAAAAAAT
28560729 TAAAATATATAAAAAAAAT
1 TAAAATATATAAAAAAAAT
28560748 CAGGGAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAATATATAAAAAAAAT
Found at i:28561071 original size:17 final size:18
Alignment explanation
Indices: 28561037--28561089 Score: 81
Period size: 17 Copynumber: 2.9 Consensus size: 18
28561027 AATCAAATAT
28561037 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
28561055 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
28561072 TCTAAGATTGCATATCAT
1 TCTAAGATTGCA-ATCAT
28561090 TGAAGATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:28561500 original size:45 final size:45
Alignment explanation
Indices: 28561464--28561662 Score: 174
Period size: 44 Copynumber: 4.4 Consensus size: 45
28561454 CTGCTCCTTA
*
28561464 TCTAATACAGAGGCGCCAAATCTGTTATCTTCGATCTGCTCCCCG
1 TCTAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCG
* * *
28561509 TCTAATACAGAGACGCCAAATCTGCT-TCTTC-AGTTTACTCCCCG
1 TCTAATACAGAGACGCCAAATCTGTTATCTTCGA-TCTGCTCCCCG
* * * *
28561553 TCTAATACAGAGATGCCAAATCTGTCATCTTGGATCTGCT--TCG
1 TCTAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCG
* * * * * *
28561596 ATGTAA-ACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCG
1 -TCTAATACAGA-G-ACGCCAAATCTG-T-TATCTTCGATCTGCTCCCCG
*
28561645 TCTAATACAGAGATGCCA
1 TCTAATACAGAGACGCCA
28561663 TATCATCTTG
Statistics
Matches: 119, Mismatches: 24, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
43 7 0.06
44 42 0.35
45 41 0.34
46 2 0.02
47 16 0.13
48 5 0.04
49 6 0.05
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (45 bp):
TCTAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCG
Found at i:28561735 original size:78 final size:78
Alignment explanation
Indices: 28561606--28561900 Score: 457
Period size: 78 Copynumber: 3.8 Consensus size: 78
28561596 ATGTAAACAC
*
28561606 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCATATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
*
28561671 TGAATCTGCTTCA
66 TGGATCTGCTTCA
* *
28561684 ATGAAGGTCCA-ATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
*
28561748 TTGGATCTACTTCA
65 TTGGATCTGCTTCA
* * *
28561762 ATGAAGGTCAGATCTGTTGTGTCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
28561827 TGGATCTGCTTCA
66 TGGATCTGCTTCA
** * **
28561840 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTTCGTCAAATATGGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
28561901 TGTTTCTTCA
Statistics
Matches: 198, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
77 2 0.01
78 194 0.98
79 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:28562163 original size:44 final size:44
Alignment explanation
Indices: 28562108--28562393 Score: 249
Period size: 44 Copynumber: 6.7 Consensus size: 44
28562098 GTCGAATATG
* * * * *
28562108 GAGATGGCAAATCTACTATCTCT-GATTTGCTCTCTGACCATACA
1 GAGATGCCAAATCTGCTATCT-TGGATCTGCTCCCTGACAATACA
* *
28562152 GAGATGCCAAATCTGCTATCTTCGATCTGCTCCCTGAAAATACA
1 GAGATGCCAAATCTGCTATCTTGGATCTGCTCCCTGACAATACA
* * * *
28562196 GGGATGTCAAATCTGCT-TCTTGGATTTGC-CCCTCGTCAAATAC-
1 GAGATGCCAAATCTGCTATCTTGGATCTGCTCCCT-GAC-AATACA
* * *
28562239 GAAGATGCCAAA--T-C-ATCTTGGATCTGCTCCCCGTCGAATACG
1 G-AGATGCCAAATCTGCTATCTTGGATCTGCTCCCTGAC-AATACA
* * *
28562281 GAGATGCCAAATAT-C-ATCTTTGATCTGCTCTCTGACAATACA
1 GAGATGCCAAATCTGCTATCTTGGATCTGCTCCCTGACAATACA
* * *
28562323 GAGACGCCAAATCTGCTATCTTTGATCTGCTCTCTGACAATACA
1 GAGATGCCAAATCTGCTATCTTGGATCTGCTCCCTGACAATACA
28562367 GAGATGCCAAA--T-C-ATCTTGGATCTGCT
1 GAGATGCCAAATCTGCTATCTTGGATCTGCT
28562394 TCAGCGTAAA
Statistics
Matches: 205, Mismatches: 26, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
40 13 0.06
41 31 0.15
42 27 0.13
43 33 0.16
44 101 0.49
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (44 bp):
GAGATGCCAAATCTGCTATCTTGGATCTGCTCCCTGACAATACA
Found at i:28562309 original size:127 final size:129
Alignment explanation
Indices: 28562147--28562393 Score: 324
Period size: 127 Copynumber: 1.9 Consensus size: 129
28562137 CTCTCTGACC
* * * *
28562147 ATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCCCTGAAAATACAGGGATGTCAAATCTGC
1 ATACAGAGATGCCAAATATGCTATCTTCGATCTGCTCCCTGAAAATACAGAGACGCCAAATCTGC
*
28562212 T-TCTTGGATTTGCCCCTCGTCA-AATAC-GAAGATGCCAAATCATCTTGGATCTGCTCCCCGTC
66 TATCTTGGATCTG-CCCTC-TCACAATACAG-AGATGCCAAATCATCTTGGATCTGCTCCCCGTC
28562274 GA
128 GA
* * * *
28562276 ATACGGAGATGCCAAATAT-C-ATCTTTGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGC
1 ATACAGAGATGCCAAATATGCTATCTTCGATCTGCTCCCTGAAAATACAGAGACGCCAAATCTGC
* * *
28562339 TATCTTTGATCTGCTCTCTGACAATACAGAGATGCCAAATCATCTTGGATCTGCT
66 TATCTTGGATCTGCCCTCTCACAATACAGAGATGCCAAATCATCTTGGATCTGCT
28562394 TCAGCGTAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
126 2 0.02
127 73 0.71
128 11 0.11
129 17 0.17
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (129 bp):
ATACAGAGATGCCAAATATGCTATCTTCGATCTGCTCCCTGAAAATACAGAGACGCCAAATCTGC
TATCTTGGATCTGCCCTCTCACAATACAGAGATGCCAAATCATCTTGGATCTGCTCCCCGTCGA
Found at i:28575525 original size:93 final size:93
Alignment explanation
Indices: 28575413--28575584 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
28575403 GCCCATAAGT
* *
28575413 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28575478 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
28575506 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28575571 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
28575585 CAAATATCCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:28575580 original size:46 final size:46
Alignment explanation
Indices: 28575405--28575580 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
28575395 TGTAACCCGC
* * *
28575405 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
28575451 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
28575501 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
28575544 CCATAAGTGAACTTGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28575581 TGCCCAAATA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 67 0.60
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:28576680 original size:19 final size:19
Alignment explanation
Indices: 28576648--28576693 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28576638 ACAACATATA
* * *
28576648 ATAATGTCACATTATTTAC
1 ATAATATCAAATTATTCAC
28576667 ATAATATCAAATTATTCAC
1 ATAATATCAAATTATTCAC
28576686 ATATATAT
1 ATA-ATAT
28576694 ATGCTTACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.41
Consensus pattern (19 bp):
ATAATATCAAATTATTCAC
Found at i:28579065 original size:15 final size:15
Alignment explanation
Indices: 28579040--28579103 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
28579030 AACAACAAAA
*
28579040 CCAAGATAAAGAAAC
1 CCAACATAAAGAAAC
28579055 CCAGA-ATAAAGAAAC
1 CCA-ACATAAAGAAAC
*
28579070 CCAACATAAAGAAAT
1 CCAACATAAAGAAAC
* *
28579085 CCAACATAAGGAAAT
1 CCAACATAAAGAAAC
28579100 CCAA
1 CCAA
28579104 ATTACAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.02
15 43 0.96
16 1 0.02
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (15 bp):
CCAACATAAAGAAAC
Found at i:28583416 original size:16 final size:16
Alignment explanation
Indices: 28583395--28583427 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28583385 GGTCCATAAA
28583395 TCATACTTTTACAAAT
1 TCATACTTTTACAAAT
28583411 TCATACTTTTACAAAT
1 TCATACTTTTACAAAT
28583427 T
1 T
28583428 TTTATTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (16 bp):
TCATACTTTTACAAAT
Found at i:28585634 original size:15 final size:15
Alignment explanation
Indices: 28585609--28585687 Score: 88
Period size: 15 Copynumber: 5.3 Consensus size: 15
28585599 AACAACAAAA
*
28585609 CCAAGATAAAGAAAC
1 CCAACATAAAGAAAC
28585624 CCAGA-ATAAAGAAAC
1 CCA-ACATAAAGAAAC
*
28585639 CCAACATAAAGAAAT
1 CCAACATAAAGAAAC
*
28585654 CCAACATAAAGAAAT
1 CCAACATAAAGAAAC
* * *
28585669 CCAAGATAAGGAAAT
1 CCAACATAAAGAAAC
28585684 CCAA
1 CCAA
28585688 ATTACAATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
14 1 0.02
15 57 0.97
16 1 0.02
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.10
Consensus pattern (15 bp):
CCAACATAAAGAAAC
Found at i:28585648 original size:30 final size:30
Alignment explanation
Indices: 28585609--28585687 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
28585599 AACAACAAAA
28585609 CCAAGATAAAGAAACCCAGA-ATAAAGAAAC
1 CCAAGATAAAGAAACCCA-ACATAAAGAAAC
* * *
28585639 CCAACATAAAGAAATCCAACATAAAGAAAT
1 CCAAGATAAAGAAACCCAACATAAAGAAAC
* *
28585669 CCAAGATAAGGAAATCCAA
1 CCAAGATAAAGAAACCCAA
28585688 ATTACAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.10
Consensus pattern (30 bp):
CCAAGATAAAGAAACCCAACATAAAGAAAC
Found at i:28589984 original size:30 final size:30
Alignment explanation
Indices: 28589950--28590006 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
28589940 CATAAATCAT
* *
28589950 ACTTTTACAAATTTTTA-TTTTGACCTCTAA
1 ACTTTCACAAATTTGTACTTTTG-CCTCTAA
*
28589980 ACTTTCACATATTTGTACTTTTGCCTC
1 ACTTTCACAAATTTGTACTTTTGCCTC
28590007 AAGGCTCGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.25, C:0.21, G:0.05, T:0.49
Consensus pattern (30 bp):
ACTTTCACAAATTTGTACTTTTGCCTCTAA
Found at i:28593702 original size:23 final size:23
Alignment explanation
Indices: 28593642--28593729 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
28593632 CAGAAGCAGT
28593642 TACAACACATAAAGTGCCTG-AA
1 TACAACACATAAAGTGCCTGAAA
* ****
28593664 -ACGACACACGGGGTGCCTGAAA
1 TACAACACATAAAGTGCCTGAAA
28593686 TACAACACATAAAGTGCCT-AATA
1 TACAACACATAAAGTGCCTGAA-A
* *
28593709 TACGACACATAGAGTGCCTGA
1 TACAACACATAAAGTGCCTGA
28593730 TCGGCAAAGC
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
21 14 0.28
22 4 0.08
23 31 0.62
24 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (23 bp):
TACAACACATAAAGTGCCTGAAA
Found at i:28593936 original size:16 final size:17
Alignment explanation
Indices: 28593910--28593948 Score: 62
Period size: 16 Copynumber: 2.3 Consensus size: 17
28593900 ATACATACAC
28593910 ATTCATCATTCAATTCA
1 ATTCATCATTCAATTCA
28593927 ATTC-TCATTCAATTCAA
1 ATTCATCATTCAATTC-A
28593944 ATTCA
1 ATTCA
28593949 GTTTTCCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTCATCATTCAATTCA
Found at i:28595673 original size:3 final size:3
Alignment explanation
Indices: 28595667--28595695 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28595657 AATAAGATTA
28595667 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28595696 AACAACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28607569 original size:2 final size:2
Alignment explanation
Indices: 28607562--28607592 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28607552 CGCAATTTAT
28607562 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28607593 TTGGTACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28610657 original size:23 final size:24
Alignment explanation
Indices: 28610600--28610656 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
28610590 TATCTCTTTG
28610600 TTTGTATTTTTAAAATATTTAGAT
1 TTTGTATTTTTAAAATATTTAGAT
* *
28610624 TTT-AATTTTTAAAATATATTA-TT
1 TTTGTATTTTTAAAATAT-TTAGAT
28610647 TTTGTATTTT
1 TTTGTATTTT
28610657 ATTTTTATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 17 0.61
24 11 0.39
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (24 bp):
TTTGTATTTTTAAAATATTTAGAT
Found at i:28610834 original size:137 final size:138
Alignment explanation
Indices: 28610597--28611212 Score: 877
Period size: 137 Copynumber: 4.5 Consensus size: 138
28610587 TTTTATCTCT
* * * * *
28610597 TTGTTTGTATTTTTAAAATATTTAGATTTTAATTTTTAAAATATATTATTTTTGTATTTTA-TTT
1 TTGTTTATATTTTTAAAATATTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTT
* *
28610661 TTATCTTATTTTAGTACATAATGTTTCAAATATATTA-TCTTAGTGTTTTTAAAATAACCCTAAT
66 TTATCTTATTTTAGTACATAATGTTTCAAATGTATTACT-TTAGTGTTTTTTAAATAACCCTAAT
28610725 TTTGTCCCA
130 TTTGTCCCA
* *
28610734 TTGTTTATATTTTTAAAATTTTTAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTT
1 TTGTTTATATTTTTAAAATATTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTT
* *
28610799 TTATCTTA-TTTAGTACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTATATAACTCTAATT
66 TTATCTTATTTTAGTACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTAAATAACCCTAATT
28610863 TTGTCCC-
131 TTGTCCCA
* *
28610870 TT-TATTAT-TTGTATCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTA
1 TTGT-TTATATT-T-T-TAAAATATTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTA
* * *
28610933 TTTTTTATCTTATTTTAGTAAATAATATTTCAAATGTATTACTTTAGTGTTTTTTATATAACCCT
62 TTTTTTATCTTATTTTAGTACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTAAATAACCCT
*
28610998 AATTTTGTCCTTTTA
127 AATTTTGTCC---CA
* * * * * * *
28611013 TTATTTGTATTTCTAAAATATTCGGATTTTAATTTTTAAAATATACTGTTTTCATATTTTA-TTT
1 TTGTTTATATTTTTAAAATATTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTT
*
28611077 TTATCTTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTAATT
66 TTATCTTATTTTAGTACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTAAATAACCCTAATT
28611142 TTGTCCCA
131 TTGTCCCA
*
28611150 TTGTTTATATTTTTAAAATTTTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATT
1 TTGTTTATATTTTTAAAATATTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATT
28611213 ATATTTTTTT
Statistics
Matches: 429, Mismatches: 36, Indels: 27
0.87 0.07 0.05
Matches are distributed among these distances:
135 3 0.01
136 7 0.02
137 168 0.39
138 69 0.16
139 59 0.14
140 70 0.16
141 44 0.10
143 6 0.01
144 3 0.01
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.57
Consensus pattern (138 bp):
TTGTTTATATTTTTAAAATATTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTT
TTATCTTATTTTAGTACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTAAATAACCCTAATT
TTGTCCCA
Found at i:28611072 original size:23 final size:24
Alignment explanation
Indices: 28611020--28611073 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
28611010 TTATTATTTG
*
28611020 TATTTCTAAAATATTCGGATTTTAA
1 TATTT-TAAAATATACGGATTTTAA
* *
28611045 T-TTTTAAAATATACTG-TTTTCA
1 TATTTTAAAATATACGGATTTTAA
28611067 TATTTTA
1 TATTTTA
28611074 TTTTTATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 6 0.24
23 15 0.60
24 3 0.12
25 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (24 bp):
TATTTTAAAATATACGGATTTTAA
Found at i:28611107 original size:279 final size:275
Alignment explanation
Indices: 28610597--28611212 Score: 884
Period size: 279 Copynumber: 2.2 Consensus size: 275
28610587 TTTTATCTCT
* * * *
28610597 TTGTTTGTATTTTTAAAATATTTAGATTTTAATTTTTAAAATATATTATTTTTGTATTTTA-TTT
1 TTGTTTATATTTTTAAAATATTTGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTT
* *
28610661 TTATCTTATTTTAGTACATAATGTTTCAAATATATTATCTTAGTGTTTTTAAAATAACCCTAATT
66 TTATCTTATTTTAGTAAATAATATTTCAAATATATTATCTTAGTGTTTTTAAAATAACCCTAATT
* * * * * *
28610726 TTGTCCCATTGTTTATATTTTTAAAATTTTTAGATTTTATTTTTTAAAATATACTATTTTCGTAT
131 TTGTCCCATTATTTATATTTCTAAAATATTCAGATTTTAATTTTTAAAATATACTATTTTCATAT
*
28610791 TTTATTTTTTATCTTATTTAGTACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTATATAAC
196 TTTATTTTTTATCTTATTTAGTACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTAAATAAC
*
28610856 TCTAATTTTGTCCC-
261 CCTAATTTTGTCCCA
*
28610870 TT-TATTAT-TTGTATCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTA
1 TTGT-TTATATT-T-T-TAAAATATTTGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTA
* * *
28610933 TTTTTTATCTTATTTTAGTAAATAATATTTCAAATGTATTA-CTTTAGTGTTTTTTATATAACCC
62 TTTTTTATCTTATTTTAGTAAATAATATTTCAAATATATTATC-TTAGTGTTTTTAAAATAACCC
* * * *
28610997 TAATTTTGTCCTTTTATTATTTGTATTTCTAAAATATTCGGATTTTAATTTTTAAAATATACTGT
126 TAATTTTGTCC---CATTATTTATATTTCTAAAATATTCAGATTTTAATTTTTAAAATATACTAT
*
28611062 TTTCATATTTTA-TTTTTATCTTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTT
188 TTTCATATTTTATTTTTTATCTTA-TTTAGTACATAATGTTTCAAATGTATTACTTTAGTGTTTT
28611126 TTAAATAACCCTAATTTTGTCCCA
252 TTAAATAACCCTAATTTTGTCCCA
* *
28611150 TTGTTTATATTTTTAAAATTTTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATT
1 TTGTTTATATTTTTAAAATATTTGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATT
28611213 ATATTTTTTT
Statistics
Matches: 304, Mismatches: 26, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
272 3 0.01
273 6 0.02
274 1 0.00
275 45 0.15
276 67 0.22
278 58 0.19
279 114 0.38
280 7 0.02
281 3 0.01
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.57
Consensus pattern (275 bp):
TTGTTTATATTTTTAAAATATTTGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTT
TTATCTTATTTTAGTAAATAATATTTCAAATATATTATCTTAGTGTTTTTAAAATAACCCTAATT
TTGTCCCATTATTTATATTTCTAAAATATTCAGATTTTAATTTTTAAAATATACTATTTTCATAT
TTTATTTTTTATCTTATTTAGTACATAATGTTTCAAATGTATTACTTTAGTGTTTTTTAAATAAC
CCTAATTTTGTCCCA
Found at i:28611274 original size:12 final size:12
Alignment explanation
Indices: 28611257--28611289 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
28611247 TATTTTTCAT
*
28611257 TAAAAAATAGTA
1 TAAAAAATAATA
28611269 T-AAAAATAATA
1 TAAAAAATAATA
28611280 TAAAAAATAA
1 TAAAAAATAA
28611290 AATACGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
TAAAAAATAATA
Found at i:28612470 original size:15 final size:16
Alignment explanation
Indices: 28612446--28612489 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
28612436 TTATTCGAAG
*
28612446 TGAAATAAAAT-ATTT
1 TGAAAAAAAATAATTT
28612461 TGAAAAAAAATAATTT
1 TGAAAAAAAATAATTT
28612477 TCGAAAAATAAAT
1 T-GAAAAA-AAAT
28612490 GAAATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 10 0.40
16 5 0.20
17 6 0.24
18 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (16 bp):
TGAAAAAAAATAATTT
Found at i:28614686 original size:10 final size:10
Alignment explanation
Indices: 28614671--28614730 Score: 77
Period size: 10 Copynumber: 6.0 Consensus size: 10
28614661 TAATTTTAGG
*
28614671 ATTTATCTTC
1 ATTTATCTTT
28614681 ATTTATCTTT
1 ATTTATCTTT
*
28614691 AATTATCTTT
1 ATTTATCTTT
*
28614701 AATTATCTTT
1 ATTTATCTTT
28614711 ATTTAT-TTGT
1 ATTTATCTT-T
28614721 ATTTATCTTT
1 ATTTATCTTT
28614731 TAGAATTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
9 2 0.04
10 41 0.91
11 2 0.04
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.65
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:28615502 original size:39 final size:39
Alignment explanation
Indices: 28615459--28615534 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
28615449 CGAAATCTCA
*
28615459 ATCAAAACTTTTAACTCTGTTTTTATTTTATTT-TTTTAG
1 ATCAAAACTTTTAACTCAGTTTTT-TTTTATTTCTTTTAG
* *
28615498 ATCAAAACTTTTAATTGAGTTTTTTTTTATTTCTTTT
1 ATCAAAACTTTTAACTCAGTTTTTTTTTATTTCTTTT
28615535 CCAGGTATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 8 0.24
39 25 0.76
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.61
Consensus pattern (39 bp):
ATCAAAACTTTTAACTCAGTTTTTTTTTATTTCTTTTAG
Found at i:28618508 original size:19 final size:19
Alignment explanation
Indices: 28618460--28618511 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
28618450 CAAATTTTTT
28618460 TTTTTTATTTTATTATTAC
1 TTTTTTATTTTATTATTAC
*
28618479 TCTTTCT-TTTTATTATTA-
1 T-TTTTTATTTTATTATTAC
28618497 TTTTATTATTTTATT
1 TTTT-TTATTTTATT
28618512 TTTGGATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 3 0.11
18 2 0.07
19 19 0.68
20 4 0.14
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTTTATTTTATTATTAC
Found at i:28619814 original size:96 final size:97
Alignment explanation
Indices: 28619646--28619827 Score: 276
Period size: 96 Copynumber: 1.9 Consensus size: 97
28619636 TTTAAGAATG
* * * * * *
28619646 TGTTGGGCTGAGTGACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTTAAAAGGTTCGAT
1 TGTTGGGCTGAGTAACCAGGGTGAGGTGCTTGACTGTCATCTCTCTTCGCGTCAAAAGATTCAAT
*
28619711 ATGTTCTTAAG-AAAAATAAAAATTAGGAGTA
66 ATATTCTTAAGCAAAAATAAAAATTAGGAGTA
*
28619742 TGTTGGGCTGAGTAACCAGGGTGGGGTGCTTGACTGTCATCTCTCTTCGCGTCAAAAGATTCAAT
1 TGTTGGGCTGAGTAACCAGGGTGAGGTGCTTGACTGTCATCTCTCTTCGCGTCAAAAGATTCAAT
*
28619807 ATATTCTTAAGCAACAATAAA
66 ATATTCTTAAGCAAAAATAAA
28619828 TAAATTAATT
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
96 68 0.89
97 8 0.11
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (97 bp):
TGTTGGGCTGAGTAACCAGGGTGAGGTGCTTGACTGTCATCTCTCTTCGCGTCAAAAGATTCAAT
ATATTCTTAAGCAAAAATAAAAATTAGGAGTA
Found at i:28620528 original size:20 final size:20
Alignment explanation
Indices: 28620505--28620552 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
28620495 TTATTTTCAT
28620505 TTATCTTTAATTATATT-TAA
1 TTATCTTTAATTAT-TTGTAA
* *
28620525 TTATCTTTATTTATTTGTAT
1 TTATCTTTAATTATTTGTAA
28620545 TTATCTTT
1 TTATCTTT
28620553 TAGAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATCTTTAATTATTTGTAA
Found at i:28628035 original size:18 final size:20
Alignment explanation
Indices: 28628003--28628053 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
28627993 ATATATATAA
*
28628003 ATTTTGAAAATTTTACAAA-T
1 ATTTTG-AAATTTTAAAAATT
28628023 ATTTTGAAA-TTTAAAAATT
1 ATTTTGAAATTTTAAAAATT
28628042 ATTTTG-AATTTT
1 ATTTTGAAATTTT
28628054 TTTTTGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.32
19 13 0.46
20 6 0.21
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (20 bp):
ATTTTGAAATTTTAAAAATT
Found at i:28629197 original size:14 final size:14
Alignment explanation
Indices: 28629179--28629212 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28629169 TTTAAAAATA
28629179 AAAAAATACAAAAAG
1 AAAAAA-ACAAAAAG
*
28629194 AAAAAAAGAAAAAG
1 AAAAAAACAAAAAG
28629208 AAAAA
1 AAAAA
28629213 GTAATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.85, C:0.03, G:0.09, T:0.03
Consensus pattern (14 bp):
AAAAAAACAAAAAG
Found at i:28630173 original size:39 final size:39
Alignment explanation
Indices: 28630118--28630192 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
28630108 TAGGCGAGCT
*
28630118 CAATATGAGGACACATAATACGTAATATGAGTTTGCGCC
1 CAATATGAAGACACATAATACGTAATATGAGTTTGCGCC
*
28630157 CAATATGAAGAGACATAATACGTAATATGAGTTTGC
1 CAATATGAAGACACATAATACGTAATATGAGTTTGC
28630193 CTACACATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (39 bp):
CAATATGAAGACACATAATACGTAATATGAGTTTGCGCC
Found at i:28631736 original size:20 final size:19
Alignment explanation
Indices: 28631707--28631748 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
28631697 AAAAATTCAG
28631707 TATTAAAAATTAGAAAAAA
1 TATTAAAAATTAGAAAAAA
* *
28631726 TATTAAAAAATTATAAAATA
1 TATT-AAAAATTAGAAAAAA
28631746 TAT
1 TAT
28631749 AGAATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
TATTAAAAATTAGAAAAAA
Found at i:28633049 original size:17 final size:15
Alignment explanation
Indices: 28633027--28633062 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
28633017 TAAATTTTCA
28633027 AAAATTAAAGAAAATTT
1 AAAATTAAA-AAAA-TT
28633044 AAAATTAAAAAAATT
1 AAAATTAAAAAAATT
28633059 AAAA
1 AAAA
28633063 GTTCATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 4 0.21
17 9 0.47
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (15 bp):
AAAATTAAAAAAATT
Found at i:28635652 original size:21 final size:21
Alignment explanation
Indices: 28635626--28635665 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28635616 GAACTAATAA
*
28635626 AAATAATTAAATTAACAAAAT
1 AAATAAATAAATTAACAAAAT
*
28635647 AAATAAATAAATTATCAAA
1 AAATAAATAAATTAACAAA
28635666 TGTTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATAAATAAATTAACAAAAT
Found at i:28636240 original size:25 final size:24
Alignment explanation
Indices: 28636212--28636261 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
28636202 TAATGATTAC
28636212 TTTAGC-ATTAAATATTTTTATTTTT
1 TTTAGCAATT-AA-ATTTTTATTTTT
* *
28636237 TTTATCAATTTAATTTTTATTTTT
1 TTTAGCAATTAAATTTTTATTTTT
28636261 T
1 T
28636262 GAGTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 13 0.59
25 6 0.27
26 3 0.14
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTAGCAATTAAATTTTTATTTTT
Found at i:28636984 original size:16 final size:16
Alignment explanation
Indices: 28636963--28636993 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28636953 TGAGGGCTAA
*
28636963 ATTTATCATTATACTT
1 ATTTATAATTATACTT
28636979 ATTTATAATTATACT
1 ATTTATAATTATACT
28636994 AGATTTATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTATAATTATACTT
Found at i:28637750 original size:2 final size:2
Alignment explanation
Indices: 28637743--28637778 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28637733 TAATACATTA
28637743 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
28637779 TTTACACTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28639728 original size:77 final size:74
Alignment explanation
Indices: 28639569--28639778 Score: 235
Period size: 77 Copynumber: 2.8 Consensus size: 74
28639559 CCTCGAAGGT
*
28639569 AATCTCGAGGCTCAACCCATTTTGTG--AACATGAATTTGACTTTTGATAAAATGAAAAATTAAA
1 AATCTCGAGGCTCAACCCATTTT-TGAAAACA-G-ATTTGACTTTTGATAAAATGAAAAATGAAA
*
28639632 AGGACATCAAAA
63 AAGACATCAAAA
* * *
28639644 ATGATCTCAAGGCTCAACCCATTTTTGAAAACAGATTTGAGTTTTAATAAAATGAAAAACTGAAA
1 A--ATCTCGAGGCTCAACCCATTTTTGAAAACAGATTTGACTTTTGATAAAATGAAAAA-TGAAA
*
28639709 AAGACTTCAACAGA
63 AAGACATCAA-A-A
* * * * *
28639723 AATCTCGAGGCTAAACTCATTTTTGAAAATAGATTCGACTTTTGGTAAAATGAAAA
1 AATCTCGAGGCTCAACCCATTTTTGAAAACAGATTTGACTTTTGATAAAATGAAAA
28639779 GAAAATACCT
Statistics
Matches: 114, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
75 1 0.01
76 25 0.22
77 81 0.71
78 5 0.04
79 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (74 bp):
AATCTCGAGGCTCAACCCATTTTTGAAAACAGATTTGACTTTTGATAAAATGAAAAATGAAAAAG
ACATCAAAA
Found at i:28640086 original size:76 final size:73
Alignment explanation
Indices: 28639939--28640094 Score: 192
Period size: 76 Copynumber: 2.1 Consensus size: 73
28639929 ACTAAATGGA
* *
28639939 AAGGCTCGATCCCTTTTTGAAAACAAATTCGATTTTGATAAAAGATAATTAAAAGGACCTCGACA
1 AAGGCTCGATCCCTTTTTGAAAACAAATTCGATTTTAATAAAAGAAAATTAAAAGGACCTCGACA
28640004 AAAATCTC
66 AAAATCTC
* *
28640012 AAGGCTTGA-CCCATTTTTAGAAAACAAATTCGATTTTTAATAAAAAGAAAATTGAAAA-GATCT
1 AAGGCTCGATCCC-TTTTT-GAAAACAAATTCGA-TTTTAAT-AAAAGAAAATT-AAAAGGACCT
*
28640075 CGACAACAATCT-
61 CGACAAAAATCTC
28640087 AGAGGCTC
1 A-AGGCTC
28640095 AACACTCTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
72 3 0.04
73 13 0.18
74 14 0.20
75 7 0.10
76 30 0.42
77 4 0.06
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (73 bp):
AAGGCTCGATCCCTTTTTGAAAACAAATTCGATTTTAATAAAAGAAAATTAAAAGGACCTCGACA
AAAATCTC
Found at i:28640366 original size:94 final size:94
Alignment explanation
Indices: 28640196--28640894 Score: 667
Period size: 94 Copynumber: 7.5 Consensus size: 94
28640186 ACATTTTGGT
* * * *
28640196 GAGATTTAAAAATATCCTTAAGAGA-GGTTTG-AAA-ATATCTCTAGGGA-A-AGTCGAAAGCAT
1 GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATA-T-GAAAGCAT
* * * *
28640256 CCTCAAGATA-GAGTTTGAAAATATCTCAATA
64 CTTCGAGAGAGGA-TTTGAAAATATCTCAAGA
* * * * *
28640287 GAGATCTAAAAGCATCCTTAATAGAGGGTTTGAAAATATATCTCATA-AGAGATTTGAAAGCATC
1 GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCA-AGGGAGATATGAAAGCATC
* * *
28640351 TTAGAGATAAGG-TTTGAAAATATCTCAACA
65 TTCGAGA-GAGGATTTGAAAATATCTCAAGA
* * * * * *
28640381 TAGATCTAAAAGCATCCTCAAGAGAGGGCTTGAAAATAAATCTCATA-GGAGATCTGGAAGCATC
1 GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCA-AGGGAGATATGAAAGCATC
* *
28640445 CTCGAGATAGGATTTGAAAATATCTCAAGA
65 TTCGAGAGAGGATTTGAAAATATCTCAAGA
* * ** * *
28640475 GAGATCAAAAAGCATCCTTGAGAGAGGGTTTGAAAATATATATCAAGGGAGATATAAAAGCATCC
1 GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGAAAGCAT-C
* *
28640540 TT-GAGGGAGGATTTGAAAATATCTCAAGG
65 TTCGAGAGAGGATTTGAAAATATCTCAAGA
* *
28640569 GAGATCTAAAAGTATCCTCAAAGAGAGGGTTTGAAAATATATTTCATA-GGAGATCTGAAAGCAT
1 GAGATCTAAAAGTATCCTC-AAGAGAGGGTTTGAAAATATATCTCA-AGGGAGATATGAAAGCAT
* * * * * *
28640633 CCTCGAGA-AGGGACTCGAAAGTATCTCCAGG
64 CTTCGAGAGA-GGATTTGAAAATATCTCAAGA
* * *
28640664 GAGATCTACAAA-TATCCTCAAGTGAGGGTTTGAAAATATATCTCAAGAGTGATATGAAAGCAT-
1 GAGATCTA-AAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGAAAGCATC
* ** * *
28640727 TCTCGAGGGAGGATTT-ATAAGCATCTCAGGG
65 T-TCGAGAGAGGATTTGA-AAATATCTCAAGA
*
28640758 GAGATCTAAAAGTATCCTTAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGAAAGCATCC
1 GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGAAAGCAT-C
* *
28640823 TT-AAGAGAGGA-TTCAAAAGTATCTCAAGA
65 TTCGAGAGAGGATTTGAAAA-TATCTCAAGA
* *
28640852 TAGATCTAAAAGTATCATCAAGAGAGGGTTTGAAAATATATCT
1 GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCT
28640895 AAAAGCATCT
Statistics
Matches: 507, Mismatches: 76, Indels: 47
0.80 0.12 0.07
Matches are distributed among these distances:
91 21 0.04
92 6 0.01
93 16 0.03
94 377 0.74
95 81 0.16
96 6 0.01
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.26
Consensus pattern (94 bp):
GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGAAAGCATCT
TCGAGAGAGGATTTGAAAATATCTCAAGA
Found at i:28640569 original size:23 final size:25
Alignment explanation
Indices: 28640543--28640608 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 25
28640533 AGCATCCTTG
28640543 AGGGAGGATTTGAAAATAT-CTC-A
1 AGGGAGGATTTGAAAATATCCTCAA
*
28640566 AGGGA-GATCT-AAAAGTATCCTCAA
1 AGGGAGGATTTGAAAA-TATCCTCAA
* *
28640590 AGAGAGGGTTTGAAAATAT
1 AGGGAGGATTTGAAAATAT
28640609 ATTTCATAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 4 0.12
22 7 0.21
23 8 0.24
24 5 0.15
25 6 0.18
26 4 0.12
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (25 bp):
AGGGAGGATTTGAAAATATCCTCAA
Found at i:28640576 original size:188 final size:187
Alignment explanation
Indices: 28640196--28640894 Score: 749
Period size: 188 Copynumber: 3.7 Consensus size: 187
28640186 ACATTTTGGT
* * * *
28640196 GAGATTTAAAAATATCCTTAAGAGA-GGTTTG-AAA-ATATCTC-TAGGGAAAGTC-GAAAGCAT
1 GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCATA-GGAGA-TCTGAAAGCAT
* * * *
28640256 CCTCAAGATA-GAGTTTGAAAATATCTCAATAGAGATCTAAAAGCATCCTTAATAGAGGGTTTGA
64 CCTCAAGATAGGA-TTTGAAAATATCTCAAGAGAGATCAAAAAGCATCCTCAAGAGAGGGTTTGA
* ** **
28640320 AAATATATCTCATA-AGAGATTTGAAAGCATCTTAGAGATAAGG-TTTGAAAATATCTCAACA
128 AAATATATCTCA-AGAGAGATATGAAAGCATCTT-GAG-GGAGGATTTGAAAATATCTCAAGG
* * * * *
28640381 TAGATCTAAAAGCATCCTCAAGAGAGGGCTTGAAAATAAATCTCATAGGAGATCTGGAAGCATCC
1 GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCATAGGAGATCTGAAAGCATCC
* **
28640446 TCGAGATAGGATTTGAAAATATCTCAAGAGAGATCAAAAAGCATCCTTGAGAGAGGGTTTGAAAA
66 TCAAGATAGGATTTGAAAATATCTCAAGAGAGATCAAAAAGCATCCTCAAGAGAGGGTTTGAAAA
* * *
28640511 TATATATCAAGGGAGATATAAAAGCATCCTTGAGGGAGGATTTGAAAATATCTCAAGG
131 TATATCTCAAGAGAGATATGAAAGCAT-CTTGAGGGAGGATTTGAAAATATCTCAAGG
*
28640569 GAGATCTAAAAGTATCCTCAAAGAGAGGGTTTGAAAATATATTTCATAGGAGATCTGAAAGCATC
1 GAGATCTAAAAGTATCCTC-AAGAGAGGGTTTGAAAATATATCTCATAGGAGATCTGAAAGCATC
* * * * * * * * *
28640634 CTCGAGA-AGGGACTCGAAAGTATCTCCAGGGAGATCTACAAA-TATCCTCAAGTGAGGGTTTGA
65 CTCAAGATA-GGATTTGAAAATATCTCAAGAGAGATC-AAAAAGCATCCTCAAGAGAGGGTTTGA
* * ** *
28640697 AAATATATCTCAAGAGTGATATGAAAGCATTCTCGAGGGAGGATTT-ATAAGCATCTCAGGG
128 AAATATATCTCAAGAGAGATATGAAAGCA-TCTTGAGGGAGGATTTGA-AAATATCTCAAGG
* *
28640758 GAGATCTAAAAGTATCCTTAAGAGAGGGTTTGAAAATATATCTCA-AGGGAGATATGAAAGCATC
1 GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCATA-GGAGATCTGAAAGCATC
* * * * * * *
28640822 CTTAAGAGAGGA-TTCAAAAGTATCTCAAGATAGATCTAAAAGTATCATCAAGAGAGGGTTTGAA
65 CTCAAGATAGGATTTGAAAA-TATCTCAAGAGAGATCAAAAAGCATCCTCAAGAGAGGGTTTGAA
28640886 AATATATCT
129 AATATATCT
28640895 AAAAGCATCT
Statistics
Matches: 435, Mismatches: 61, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
185 20 0.05
186 5 0.01
187 17 0.04
188 226 0.52
189 162 0.37
190 5 0.01
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.26
Consensus pattern (187 bp):
GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCATAGGAGATCTGAAAGCATCC
TCAAGATAGGATTTGAAAATATCTCAAGAGAGATCAAAAAGCATCCTCAAGAGAGGGTTTGAAAA
TATATCTCAAGAGAGATATGAAAGCATCTTGAGGGAGGATTTGAAAATATCTCAAGG
Found at i:28640784 original size:283 final size:282
Alignment explanation
Indices: 28640209--28640894 Score: 791
Period size: 283 Copynumber: 2.4 Consensus size: 282
28640199 ATTTAAAAAT
* * * * *
28640209 ATCCTTAAGAGA-GGTTTG-AAA-ATATCTCTAGGGA-A-AGTCGAAAGCATCCTCAAGATA-GA
1 ATCCTTAAGAGAGGGTTTGAAAATATATATCAAGGGAGATA-T-AAAAGCATCCTTAAGAGAGGA
* * * *
28640268 GTTTGAAAATATCTCAATAGAGATCTAAAAGCATCCTTAATAGAGGGTTTGAAAATATATCTCAT
64 -TTTGAAAATATCTCAAGAGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCAT
* * * * *
28640333 AAGAGATTTGAAAGCATCTTAGAGATAAGGTTTGAAAATATCTCAACATAGATCTAAAAGCATCC
128 AAGAGATCTGAAAGCATCCTAGAGATAAGGCTCGAAAATATCTCAACAGAGATCTAAAAGCATCC
* * *
28640398 TCAAGAGAGGGCTTGAAAATAAATCTCATAGGAGATCTGGAAGCATCCTCGAGATAGGATTTGAA
193 TCAAGAGAGGGCTTGAAAATAAATCTCATAGGAGATATGAAAGCATCCTCGAGAGAGGATTTGAA
*
28640463 AATATCTCAAGAGAGATCAAAAAGC
258 AACATCTCAAGAGAGATCAAAAAGC
* * *
28640488 ATCCTTGAGAGAGGGTTTGAAAATATATATCAAGGGAGATATAAAAGCATCCTTGAGGGAGGATT
1 ATCCTTAAGAGAGGGTTTGAAAATATATATCAAGGGAGATATAAAAGCATCCTTAAGAGAGGATT
* * *
28640553 TGAAAATATCTCAAGGGAGATCTAAAAGTATCCTCAAAGAGAGGGTTTGAAAATATATTTCATAG
66 TGAAAATATCTCAAGAGAGATCTAAAAGTATCCTC-AAGAGAGGGTTTGAAAATATATCTCATAA
* * * * ** *
28640618 GAGATCTGAAAGCATCCTCGAGA-AGGGACTCGAAAGTATCTCCAGGGAGATCTACAAA-TATCC
130 GAGATCTGAAAGCATCCTAGAGATAAGG-CTCGAAAATATCTCAACAGAGATCTA-AAAGCATCC
* * * * * *
28640681 TCAAGTGAGGGTTTGAAAATATATCTCA-AGAGTGATATGAAAGCATTCTCGAGGGAGGATTT-A
193 TCAAGAGAGGGCTTGAAAATAAATCTCATAG-GAGATATGAAAGCATCCTCGAGAGAGGATTTGA
* * * * *
28640744 TAAGCATCTCAGGGGAGATCTAAAAGT
257 -AAACATCTCAAGAGAGATCAAAAAGC
* *
28640771 ATCCTTAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGAAAGCATCCTTAAGAGAGGA-T
1 ATCCTTAAGAGAGGGTTTGAAAATATATATCAAGGGAGATATAAAAGCATCCTTAAGAGAGGATT
* * *
28640835 TCAAAAGTATCTCAAGATAGATCTAAAAGTATCATCAAGAGAGGGTTTGAAAATATATCT
66 TGAAAA-TATCTCAAGAGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCT
28640895 AAAAGCATCT
Statistics
Matches: 343, Mismatches: 52, Indels: 21
0.82 0.12 0.05
Matches are distributed among these distances:
279 11 0.03
280 6 0.02
281 3 0.01
282 92 0.27
283 227 0.66
284 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (282 bp):
ATCCTTAAGAGAGGGTTTGAAAATATATATCAAGGGAGATATAAAAGCATCCTTAAGAGAGGATT
TGAAAATATCTCAAGAGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATCTCATAAG
AGATCTGAAAGCATCCTAGAGATAAGGCTCGAAAATATCTCAACAGAGATCTAAAAGCATCCTCA
AGAGAGGGCTTGAAAATAAATCTCATAGGAGATATGAAAGCATCCTCGAGAGAGGATTTGAAAAC
ATCTCAAGAGAGATCAAAAAGC
Found at i:28640851 original size:23 final size:24
Alignment explanation
Indices: 28640825--28640878 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
28640815 AAGCATCCTT
28640825 AAGAGAGGAT-TCAAAAGTATC-TC
1 AAGAGAGGATCT-AAAAGTATCATC
*
28640848 AAGATA-GATCTAAAAGTATCATC
1 AAGAGAGGATCTAAAAGTATCATC
28640871 AAGAGAGG
1 AAGAGAGG
28640879 GTTTGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 12 0.46
23 13 0.50
24 1 0.04
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.20
Consensus pattern (24 bp):
AAGAGAGGATCTAAAAGTATCATC
Found at i:28647863 original size:40 final size:40
Alignment explanation
Indices: 28647808--28647888 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
28647798 ATGGAACTCT
28647808 ATCTAAATTGGCAAAATAACTTATTTGCTTGAGTATCTGC
1 ATCTAAATTGGCAAAATAACTTATTTGCTTGAGTATCTGC
*
28647848 ATCTAAATTGGCAAAATAACTTATTTTCTTGAGTATCTGC
1 ATCTAAATTGGCAAAATAACTTATTTGCTTGAGTATCTGC
28647888 A
1 A
28647889 GTATAACTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (40 bp):
ATCTAAATTGGCAAAATAACTTATTTGCTTGAGTATCTGC
Found at i:28649854 original size:25 final size:24
Alignment explanation
Indices: 28649826--28649875 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
28649816 ATTTTTATTT
28649826 TTATTAAAAATATT-TAACAATAATC
1 TTATT-AAAAT-TTATAACAATAATC
28649851 TTATTAAAATTTAATAACAATAATC
1 TTATTAAAATTT-ATAACAATAATC
28649876 ATCTATCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 2 0.09
24 5 0.22
25 16 0.70
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (24 bp):
TTATTAAAATTTATAACAATAATC
Found at i:28650016 original size:44 final size:46
Alignment explanation
Indices: 28649946--28650039 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 46
28649936 ATTACAACAT
28649946 CATTCCATTCAACCAAACACAAGAATT-CT-ATTACAGCTCTACTC
1 CATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTACTC
*** *
28649990 CATTCCATTCAACCAAACAGTTGAATTACTGATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTACTC
28650036 CATT
1 CATT
28650040 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 24 0.55
45 2 0.05
46 18 0.41
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (46 bp):
CATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTACTC
Found at i:28650042 original size:16 final size:16
Alignment explanation
Indices: 28650021--28650075 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
28650011 TGAATTACTG
28650021 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
28650037 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
* *
28650053 ATTACAACCCTATTCC
1 ATTACAGCTCTATTCC
28650069 ATTACAG
1 ATTACAG
28650076 TGAACCAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:28651915 original size:10 final size:10
Alignment explanation
Indices: 28651900--28651951 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
28651890 TTAATTTAGG
28651900 ATTTATTTTT
1 ATTTATTTTT
*
28651910 ATTTATCTTT
1 ATTTATTTTT
*
28651920 ATTTATCTTT
1 ATTTATTTTT
*
28651930 ATTTATTTGT
1 ATTTATTTTT
28651940 ATTTATCTTTT
1 ATTTAT-TTTT
28651951 A
1 A
28651952 GAATTTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
10 33 0.89
11 4 0.11
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:28652457 original size:30 final size:30
Alignment explanation
Indices: 28652421--28652489 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
28652411 CTAGCCTTTG
28652421 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* * *
28652451 CCACCACCTACTCCATTAGCCACACTTGTT
1 CCACCACCAACTCCACTAGCCACACTTGCT
28652481 CCACCACCA
1 CCACCACCA
28652490 CTTGTACCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.26, C:0.49, G:0.06, T:0.19
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:28653038 original size:23 final size:25
Alignment explanation
Indices: 28652945--28653076 Score: 82
Period size: 23 Copynumber: 5.6 Consensus size: 25
28652935 TTTTTTTTGT
* *
28652945 TATTAT-TATATTTC-TTAATATTA
1 TATTATGTATATATCATTAATACTA
* * * *
28652968 TATTATATATATATTC-TT-TTAATG
1 TATTATGTATATA-TCATTAATACTA
* * *
28652992 TATTAGGTATAT-TC-TAAATTCTA
1 TATTATGTATATATCATTAATACTA
*
28653015 TATTACGTATATAT-ATT-ATACTA
1 TATTATGTATATATCATTAATACTA
* *
28653038 TTTTATGTATATATCTTTAATACTA
1 TATTATGTATATATCATTAATACTA
*
28653063 TATTATTTATATAT
1 TATTATGTATATAT
28653077 TTTTTTTTCT
Statistics
Matches: 83, Mismatches: 19, Indels: 12
0.73 0.17 0.11
Matches are distributed among these distances:
22 3 0.04
23 36 0.43
24 22 0.27
25 22 0.27
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (25 bp):
TATTATGTATATATCATTAATACTA
Found at i:28653050 original size:25 final size:25
Alignment explanation
Indices: 28653012--28653076 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
28653002 ATTCTAAATT
*
28653012 CTATATTACGTATATATA-TT-ATA
1 CTATATTATGTATATATATTTAATA
* *
28653035 CTATTTTATGTATATATCTTTAATA
1 CTATATTATGTATATATATTTAATA
*
28653060 CTATATTATTTATATAT
1 CTATATTATGTATATAT
28653077 TTTTTTTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 15 0.43
24 2 0.06
25 18 0.51
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (25 bp):
CTATATTATGTATATATATTTAATA
Found at i:28653087 original size:80 final size:78
Alignment explanation
Indices: 28653003--28653161 Score: 185
Period size: 78 Copynumber: 2.0 Consensus size: 78
28652993 ATTAGGTATA
* *
28653003 TTCTAAAT-TCTATATTACGTATATATATTATACTATTTTATGTATATATCTTTAATACTATATT
1 TTCTAAATGT-TATATTACGTATATATATTA-ACTATATTATGTATATAT-TTTAACACTATATT
* *
28653067 ATTTATATATTTTTTT
63 ATGTACATATTTTTTT
* * * * * * *
28653083 TTCTACATGTTATCTTATGTATATATTTTAATTATATTATGTATGTATTTTTACACTATATTATG
1 TTCTAAATGTTATATTACGTATATATATTAACTATATTATGTATATATTTTAACACTATATTATG
28653148 TACATATTTTTTT
66 TACATATTTTTTT
28653161 T
1 T
28653162 ATATCTATTT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
78 27 0.40
79 15 0.22
80 24 0.36
81 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (78 bp):
TTCTAAATGTTATATTACGTATATATATTAACTATATTATGTATATATTTTAACACTATATTATG
TACATATTTTTTT
Found at i:28653117 original size:22 final size:23
Alignment explanation
Indices: 28653092--28653157 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 23
28653082 TTTCTACATG
*
28653092 TTATCTTATGTATATATTTTA-A
1 TTATATTATGTATATATTTTACA
*
28653114 TTATATTATGTATGTATTTTTACA
1 TTATATTATGTATATA-TTTTACA
* *
28653138 CTATATTATGTACATATTTT
1 TTATATTATGTATATATTTT
28653158 TTTTATATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 14 0.38
23 9 0.24
24 14 0.38
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATATTATGTATATATTTTACA
Found at i:28653147 original size:24 final size:23
Alignment explanation
Indices: 28653097--28653158 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
28653087 ACATGTTATC
*
28653097 TTATGTATATA-TTTTAATTATA
1 TTATGTATATATTTTTAACTATA
*
28653119 TTATGTATGTATTTTTACACTATA
1 TTATGTATATATTTTTA-ACTATA
*
28653143 TTATGTACATATTTTT
1 TTATGTATATATTTTT
28653159 TTTATATCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 10 0.29
23 5 0.15
24 19 0.56
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATGTATATATTTTTAACTATA
Found at i:28653197 original size:78 final size:78
Alignment explanation
Indices: 28653024--28653197 Score: 192
Period size: 78 Copynumber: 2.2 Consensus size: 78
28653014 ATATTACGTA
* * * * *
28653024 TATATATTATACTATTTTATGTATATATCTTTAATACTATATTATTTATATATTTTTTTTTCTAC
1 TATATATTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTTTATAC
*
28653089 ATGTTATCTTATG
66 ATGTTATCATATG
* * * *
28653102 TATATATTTTAATTATATTATGTATGTAT-TTTTACACTATATTATGTACATA-TTTTTTTTATA
1 TATATATTAT-ACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTTTATA
*
28653165 TCTATTTTATACATATG
65 -C-ATGTTAT-CATATG
28653182 TATATATTATA-TATAT
1 TATATATTATACTATAT
28653198 CTTAACATTA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
77 10 0.12
78 34 0.43
79 22 0.28
80 14 0.17
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (78 bp):
TATATATTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTTTATAC
ATGTTATCATATG
Found at i:28653249 original size:25 final size:24
Alignment explanation
Indices: 28653221--28653276 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
28653211 GTTATATTTT
*
28653221 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
28653246 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
28653269 CACTATTA
1 CACTATTA
28653277 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:28668154 original size:13 final size:13
Alignment explanation
Indices: 28668124--28668154 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28668114 CGCCGAGGTA
28668124 TTTTTAATTTCTG
1 TTTTTAATTTCTG
*
28668137 CTTTTAATTTCTG
1 TTTTTAATTTCTG
28668150 TTTTT
1 TTTTT
28668155 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:28668190 original size:86 final size:88
Alignment explanation
Indices: 28667980--28668412 Score: 333
Period size: 86 Copynumber: 4.8 Consensus size: 88
28667970 ATCTTTCAAA
* **
28667980 AAAAATCAACTCATATTGCGAGAA-GTGAGTTGGGCCTCAGGTCACACGCTGAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCGA-AAGGTGAGTTGAGCCTC-GG-GGCACGCTGAGGTATTTTCAAT
* *
28668044 TTCCGTTTTTTCAACTTATGCTTTTC
63 TTCTGTCTTTTCAACTTATGCTTTTC
* * * *
28668070 AAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGGCACGCCGAGGTATTTTTAATTTC
1 AAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTC
* * *
28668135 TG-CTTTT-AATTTCTGTTTTTC
66 TGTCTTTTCAACTTATGCTTTTC
* * *
28668156 AAAAATCAACTCATATTGCGAAAGGTAAGTTGAGCTTCAGGGCACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTC
* * *
28668221 T-TTTTTTCAATTTTTGCCTTACAAATTCTGC
66 TGTCTTTTCAACTTATG-C-T-----TT-T-C
** * * * *
28668252 TTTTCAAATCAACTCATATTGCGAGAA-GTGAGTTAAGTCTCAGGACACGCTGAGGTATTTTCAA
1 ---AAAAATCAACTCATATTGCGA-AAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAA
* * * *
28668316 TTT-TCGTTTTTTTAATTTATG-TTTCTAA
62 TTTCT-GTCTTTTCAACTTATGCTTT-T-C
* * * *
28668344 AAAAATCAACTCATATTGCGAGAA-GTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTT
1 AAAAATCAACTCATATTGCGA-AAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTT
*
28668408 TTGTC
65 CTGTC
28668413 AAAACTCAAC
Statistics
Matches: 284, Mismatches: 40, Indels: 39
0.78 0.11 0.11
Matches are distributed among these distances:
86 74 0.26
87 11 0.04
88 22 0.08
89 64 0.23
90 34 0.12
92 4 0.01
94 2 0.01
95 1 0.00
96 1 0.00
97 1 0.00
98 1 0.00
99 54 0.19
100 15 0.05
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (88 bp):
AAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTC
TGTCTTTTCAACTTATGCTTTTC
Found at i:28668233 original size:100 final size:100
Alignment explanation
Indices: 28668124--28668333 Score: 268
Period size: 99 Copynumber: 2.1 Consensus size: 100
28668114 CGCCGAGGTA
** * *
28668124 TTTTTAATTTCTG-CTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGA-AAGGTAAGTT
1 TTTTTAATTTCTGCCTTACAAATTCTGCTTTTC--AAATCAACTCATATTGCGAGAA-GTAAGTT
* *
28668187 GAG-CTTCAGGGCACGCTGAGGTATTTTCAA-TTTC-TT
63 AAGTC-TCAGGACACGCTGAGGTATTTTCAATTTTCGTT
* *
28668223 TTTTTCAATTTTTGCCTTACAAATTCTGCTTTTCAAATCAACTCATATTGCGAGAAGTGAGTTAA
1 TTTTT-AATTTCTGCCTTACAAATTCTGCTTTTCAAATCAACTCATATTGCGAGAAGTAAGTTAA
28668288 GTCTCAGGACACGCTGAGGTATTTTCAATTTTCGTT
65 GTCTCAGGACACGCTGAGGTATTTTCAATTTTCGTT
28668324 TTTTTAATTT
1 TTTTTAATTT
28668334 ATGTTTCTAA
Statistics
Matches: 97, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
99 56 0.58
100 19 0.20
101 22 0.23
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (100 bp):
TTTTTAATTTCTGCCTTACAAATTCTGCTTTTCAAATCAACTCATATTGCGAGAAGTAAGTTAAG
TCTCAGGACACGCTGAGGTATTTTCAATTTTCGTT
Found at i:28668514 original size:75 final size:75
Alignment explanation
Indices: 28668324--28668916 Score: 766
Period size: 75 Copynumber: 8.1 Consensus size: 75
28668314 AATTTTCGTT
* * * * *
28668324 TTTTTAATTTATGTTTCT-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* *
28668388 TGCTGAGGTA
66 CGTTGAGGTA
* * * * *
28668398 ATTTCAA--T-T-TTTGTC--AAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGGCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
28668457 CGTTGAGGTA
66 CGTTGAGGTA
* * *
28668467 TTTTCAATTTCAGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* *
28668532 CGCTGTGGTA
66 CGTTGAGGTA
* * * *
28668542 ATTTCAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
28668605 CGTTGAGGTA
66 CGTTGAGGTA
* *
28668615 TTTTCAATTTCTGTCTTTT-AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
1 TTTTCAATTTCTGT-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
28668679 ACGTTGAGGTA
65 ACGTTGAGGTA
* *
28668690 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAG--A
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
28668753 CGCTGAGGTA
66 CGTTGAGGTA
* * * *
28668763 ATTTCAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGGGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
28668826 CGTTAAGGTA
66 CGTTGAGGTA
* * *
28668836 TTTTCAATTTCTGTCTTT-AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
28668900 CGTTGAGGTA
66 CGTTGAGGTA
28668910 TTTTCAA
1 TTTTCAA
28668917 AAAAATCAAC
Statistics
Matches: 450, Mismatches: 54, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
69 53 0.12
70 4 0.01
71 40 0.09
72 1 0.00
73 115 0.26
74 69 0.15
75 168 0.37
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (75 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
CGTTGAGGTA
Found at i:28668619 original size:148 final size:148
Alignment explanation
Indices: 28668324--28669104 Score: 936
Period size: 148 Copynumber: 5.4 Consensus size: 148
28668314 AATTTTCGTT
* * * * * *
28668324 TTTTTAATTTATGTTTCT-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
* * * *
28668388 TGCTGAGGTAATTTCAA---TT-TTTGTCAAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCC
66 CGTTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
28668449 TCAAGGCACGTTGAGGTA
131 TCAAGACACGTTGAGGTA
* * * *
28668467 TTTTCAATTTCAGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
* * *
28668532 CGCTGTGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCC
66 CGTTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
28668597 TCAAGACACGTTGAGGTA
131 TCAAGACACGTTGAGGTA
*
28668615 TTTTCAATTTCTGTCTTTT-AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
1 TTTTCAATTTCTGT-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
* * * *
28668679 ACGTTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGA
65 ACGTTGAGGTAATTTCAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* *
28668744 ACCTCAAG--ACGCTGAGGTA
128 GCCTCAAGACACGTTGAGGTA
* * * **
28668763 ATTTCAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGGGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
* * * * * *
28668826 CGTTAAGGTATTTTCAATTTCTGTCTT-TAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAA
66 CGTTGAGGTAATTTCAATTTTTGT-TTGT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
28668890 CCTCAAGACACGTTGAGG--
129 CCTCAAGACACGTTGAGGTA
*
28668908 ---T--A-------TTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAG--A
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
*
28668959 CGTTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATT--GTGAGGTGAGTTGAGCC
66 CGTTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
28669022 TCAAGACACGTTGAGGTA
131 TCAAGACACGTTGAGGTA
* * *
28669040 TTTTAAATTTCTGTCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
1 TTTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
28669105 GCTGAGGTGT
Statistics
Matches: 554, Mismatches: 51, Indels: 62
0.83 0.08 0.09
Matches are distributed among these distances:
130 31 0.06
132 18 0.03
133 27 0.05
135 39 0.07
137 1 0.00
140 1 0.00
142 1 0.00
143 14 0.03
144 63 0.11
145 80 0.14
146 65 0.12
147 15 0.03
148 157 0.28
149 4 0.01
150 38 0.07
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (148 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
CGTTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
TCAAGACACGTTGAGGTA
Found at i:28668974 original size:59 final size:60
Alignment explanation
Indices: 28668854--28668975 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 60
28668844 TTCTGTCTTT
* *
28668854 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGTATTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGA-ACGTTGAGGTAATTTC
*
28668915 AAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAG-ACGTTGAGGTAATTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGAACGTTGAGGTAATTTC
28668974 AA
1 AA
28668976 TTTTTGTTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 17 0.29
61 41 0.71
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (60 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGAACGTTGAGGTAATTTC
Found at i:28669066 original size:206 final size:205
Alignment explanation
Indices: 28668704--28669104 Score: 723
Period size: 206 Copynumber: 1.9 Consensus size: 205
28668694 CAATTTCTGT
28668704 TTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAGACGCTGAGGTAATTTCA
1 TTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAGACGCTGAGGTAATTTCA
*
28668769 ATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGGGCCTCAAGACACGTTAAGG
66 ATTTTTGTTTGTCAAAAATCAACTCATATT-CGAGAGGTGAGTTGAGCCTCAAGACACGTTAAGG
*
28668834 TATTTTCAATTTCTGTCTTTAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
130 TATTTTAAATTTCTGTCTTTAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
28668899 ACGTTGAGGTA
195 ACGTTGAGGTA
*
28668910 TTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAGACGTTGAGGTAATTTCA
1 TTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAGACGCTGAGGTAATTTCA
* *
28668975 ATTTTTGTTTGTCAAAAATCAACTCATATT-GTGAGGTGAGTTGAGCCTCAAGACACGTTGAGGT
66 ATTTTTGTTTGTCAAAAATCAACTCATATTCGAGAGGTGAGTTGAGCCTCAAGACACGTTAAGGT
28669039 ATTTTAAATTTCTGTCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGA
131 ATTTTAAATTTCTGTCTTT--AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGA
28669104 C
194 C
28669105 GCTGAGGTGT
Statistics
Matches: 188, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
204 49 0.26
206 139 0.74
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (205 bp):
TTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAGACGCTGAGGTAATTTCA
ATTTTTGTTTGTCAAAAATCAACTCATATTCGAGAGGTGAGTTGAGCCTCAAGACACGTTAAGGT
ATTTTAAATTTCTGTCTTTAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
CGTTGAGGTA
Found at i:28669111 original size:74 final size:72
Alignment explanation
Indices: 28668910--28669134 Score: 278
Period size: 71 Copynumber: 3.1 Consensus size: 72
28668900 CGTTGAGGTA
* *
28668910 TTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAGACGTTGAGGTAATTTCA
1 TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGTTGAGGTATTTTCA
*
28668975 ATTTTTG
66 ATTTCTG
* *
28668982 TTTGTC--AAAAATCAACTCATATT--GTGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTT
1 TTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGTTGAGGTATTT
*
28669043 TAAATTTCTG
63 TCAATTTCTG
* * *
28669053 TCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTGTTTT
1 T-TTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGTTGAGGTATTTT
*
28669118 CCATTTCTG
64 CAATTTCTG
28669127 TTCTTCAA
1 TT-TTCAA
28669135 TTTTTATGTT
Statistics
Matches: 130, Mismatches: 13, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
69 19 0.15
71 41 0.32
72 5 0.04
73 5 0.04
74 40 0.31
76 20 0.15
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (72 bp):
TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGTTGAGGTATTTTCA
ATTTCTG
Done.