Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 92 of 126
Found at i:28400670 original size:17 final size:18
Alignment explanation
Indices: 28400648--28400688 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
28400638 ATGATCAATT
* *
28400648 TTTTTAAGGGAAA-AATA
1 TTTTTAAAGAAAATAATA
28400665 TTTTTAAAGAAAATAATA
1 TTTTTAAAGAAAATAATA
28400683 TTTTTA
1 TTTTTA
28400689 GATTCACGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (18 bp):
TTTTTAAAGAAAATAATA
Found at i:28408215 original size:21 final size:20
Alignment explanation
Indices: 28408175--28408244 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
28408165 ATTATATTGT
28408175 TGTTTTGGTGCTATTTTTTTAC
1 TGTTTTGGTGC--TTTTTTTAC
* * *
28408197 TGTTTTTGTGTTGTTTTTTAT
1 TGTTTTGGTGCT-TTTTTTAC
*
28408218 TGTTTTGGTGCTTTTTCTAC
1 TGTTTTGGTGCTTTTTTTAC
28408238 TGTTTTG
1 TGTTTTG
28408245 ATTGTTGTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 14 0.35
21 17 0.43
22 9 0.22
ACGTcount: A:0.06, C:0.07, G:0.20, T:0.67
Consensus pattern (20 bp):
TGTTTTGGTGCTTTTTTTAC
Found at i:28408223 original size:43 final size:44
Alignment explanation
Indices: 28408174--28408292 Score: 129
Period size: 43 Copynumber: 2.7 Consensus size: 44
28408164 AATTATATTG
*
28408174 TTGTTTTGGTGCTATTTTTTTACTGTTTTTGTGTTGTTTT-TTA
1 TTGTTTTGGTGCTATTTTTTTACTGTTTTTGTGTTGTTTTCGTA
* *
28408217 TTGTTTTGGTGC--TTTTTCTACTG-TTTTGATTGTTGTTTTCGTG
1 TTGTTTTGGTGCTATTTTTTTACTGTTTTTG--TGTTGTTTTCGTA
* * *
28408260 TTGTTTTGTTGTTATTTTTGTTACTATTTTTGT
1 TTGTTTTGGTGCTATTTTT-TTACTGTTTTTGT
28408293 TGCTATTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
40 5 0.08
41 10 0.16
42 9 0.15
43 23 0.37
45 6 0.10
46 4 0.06
47 5 0.08
ACGTcount: A:0.07, C:0.06, G:0.19, T:0.68
Consensus pattern (44 bp):
TTGTTTTGGTGCTATTTTTTTACTGTTTTTGTGTTGTTTTCGTA
Found at i:28408280 original size:12 final size:12
Alignment explanation
Indices: 28408263--28408306 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
28408253 TTTCGTGTTG
*
28408263 TTTTGTTGTTAT
1 TTTTGTTGCTAT
*
28408275 TTTTGTTACTAT
1 TTTTGTTGCTAT
28408287 TTTTGTTGCTAT
1 TTTTGTTGCTAT
28408299 TTTTGTTG
1 TTTTGTTG
28408307 TTTCTAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.09, C:0.05, G:0.16, T:0.70
Consensus pattern (12 bp):
TTTTGTTGCTAT
Found at i:28409113 original size:3 final size:3
Alignment explanation
Indices: 28409105--28409188 Score: 70
Period size: 3 Copynumber: 29.3 Consensus size: 3
28409095 TTTAAGCAGT
* *
28409105 AGA AGA AGA AG- AGA AAA AGA A-A A-A AGA AG- AGA AGGA AG- AGG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA
* * * *
28409146 AGG AGG AGG AGG AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
28409189 AGAGAAGAGA
Statistics
Matches: 73, Mismatches: 3, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
2 10 0.14
3 60 0.82
4 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:28409347 original size:12 final size:12
Alignment explanation
Indices: 28409330--28409355 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28409320 AGGTTGAGGG
28409330 ATTTAGAGATGT
1 ATTTAGAGATGT
28409342 ATTTAGAGATGT
1 ATTTAGAGATGT
28409354 AT
1 AT
28409356 GGCTAACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (12 bp):
ATTTAGAGATGT
Found at i:28411835 original size:21 final size:23
Alignment explanation
Indices: 28411809--28411856 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
28411799 AGTTGATTTG
*
28411809 AAAAAA-TAAATATAAATTATAA
1 AAAAAATTAAATATAAATGATAA
*
28411831 AAAAAATTGAATATAAATGATAA
1 AAAAAATTAAATATAAATGATAA
28411854 AAA
1 AAA
28411857 TTTTAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (23 bp):
AAAAAATTAAATATAAATGATAA
Found at i:28411903 original size:20 final size:20
Alignment explanation
Indices: 28411873--28411914 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
28411863 AAAGTAAATA
28411873 TAAAAATATTTT-TAAGTTT
1 TAAAAATATTTTATAAGTTT
*
28411892 TAAAATATATTTTATAATTTT
1 TAAAA-ATATTTTATAAGTTT
28411913 TA
1 TA
28411915 GAATTATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TAAAAATATTTTATAAGTTT
Found at i:28412341 original size:15 final size:15
Alignment explanation
Indices: 28412321--28412354 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28412311 TTTATCGGAT
28412321 TATTTCACTAATTAA
1 TATTTCACTAATTAA
**
28412336 TATTTCTTTAATTAA
1 TATTTCACTAATTAA
28412351 TATT
1 TATT
28412355 ATATTTAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTCACTAATTAA
Found at i:28412866 original size:17 final size:16
Alignment explanation
Indices: 28412826--28412867 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
28412816 AAAGATTTTA
*
28412826 ACTTTTACTCAAAAAT
1 ACTTTTAATCAAAAAT
28412842 ACTTTTTAATCCAAAAAT
1 AC-TTTTAAT-CAAAAAT
28412860 ACTTTTAA
1 ACTTTTAA
28412868 AAAACAATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 12 0.52
18 9 0.39
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (16 bp):
ACTTTTAATCAAAAAT
Found at i:28413251 original size:24 final size:24
Alignment explanation
Indices: 28413189--28413251 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
28413179 ATACATTAGA
* * *
28413189 TTAAAAAGTGAACCGATCCTTTTG
1 TTAAAAATTGATCCGATCCTTCTG
*
28413213 TTAAAAATTTTATCC-ATCTCTTCTG
1 TTAAAAA-TTGATCCGATC-CTTCTG
28413238 TTAAAAATTGATCC
1 TTAAAAATTGATCC
28413252 TTATACGTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 16 0.50
25 16 0.50
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (24 bp):
TTAAAAATTGATCCGATCCTTCTG
Found at i:28416781 original size:22 final size:24
Alignment explanation
Indices: 28416756--28416813 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
28416746 AGGTTTTTTC
28416756 ATATTAAT-TTTTATT-TTTTAAA
1 ATATTAATATTTTATTATTTTAAA
* * *
28416778 ATATTTATATTATATTATTTTAAT
1 ATATTAATATTTTATTATTTTAAA
28416802 AT-TTAATATTTT
1 ATATTAATATTTT
28416814 TATACATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 7 0.24
23 14 0.48
24 8 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
ATATTAATATTTTATTATTTTAAA
Found at i:28416952 original size:18 final size:18
Alignment explanation
Indices: 28416926--28416961 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28416916 AATGTGTTCT
*
28416926 AAATTACATAATATATAA
1 AAATAACATAATATATAA
*
28416944 AAATAACATAATGTATAA
1 AAATAACATAATATATAA
28416962 TATTATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (18 bp):
AAATAACATAATATATAA
Found at i:28417468 original size:15 final size:17
Alignment explanation
Indices: 28417432--28417468 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
28417422 TTGAATTTTT
28417432 TTAATGATAACAAATCA
1 TTAATGATAACAAATCA
*
28417449 TTAATG-TATCAAAT-A
1 TTAATGATAACAAATCA
28417464 TTAAT
1 TTAAT
28417469 ATTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 7 0.37
17 6 0.32
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (17 bp):
TTAATGATAACAAATCA
Found at i:28421250 original size:71 final size:71
Alignment explanation
Indices: 28421120--28421394 Score: 358
Period size: 71 Copynumber: 3.9 Consensus size: 71
28421110 TTTCACATAT
* *
28421120 AGTGACTCACGATGCTGTAGAGAATCCACAACAAATGCAGGATCTCAACCATC-GAACCAGTTTC
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCAG-ACCAGTTTC
28421184 ACTTTAC
65 ACTTTAC
* * * *
28421191 TGCGACTTACGATGCTGTAGAGAATCCGCAACAAATGCAAGATC-AAAGCCATCAGACCAGTTTC
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAA-CCATCAGACCAGTTTC
28421255 ACTTTAC
65 ACTTTAC
* * * * **
28421262 AGTAACTCAAGATGCTGTAGAGAATCCGCAACAAATGCAATATCTCAACCATCAAACCAGTTAAA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCAGACCAGTTTCA
28421327 CTTTAC
66 CTTTAC
* * * * *
28421333 GGTGACTCACGATGCTGTAGAGAATTCGTAATAAATGCAAGATCTCAACCATCGGACC-GTTT
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCAGACCAGTTT
28421395 TCTATCTTTG
Statistics
Matches: 175, Mismatches: 26, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
70 5 0.03
71 167 0.95
72 3 0.02
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (71 bp):
AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCAGACCAGTTTCA
CTTTAC
Found at i:28424867 original size:23 final size:22
Alignment explanation
Indices: 28424840--28424886 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
28424830 TTATTATTTG
28424840 TTTGTTCTG-TCTTTATCTTTGTC
1 TTTGTTCTGCTCTTT-TCTTT-TC
28424863 TTTGTTCTGCTCTTTTCTTTTC
1 TTTGTTCTGCTCTTTTCTTTTC
28424885 TT
1 TT
28424887 CTTTTTGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.17
23 14 0.61
24 5 0.22
ACGTcount: A:0.02, C:0.19, G:0.11, T:0.68
Consensus pattern (22 bp):
TTTGTTCTGCTCTTTTCTTTTC
Found at i:28425746 original size:49 final size:49
Alignment explanation
Indices: 28425602--28426266 Score: 382
Period size: 49 Copynumber: 13.6 Consensus size: 49
28425592 TCGAGGTAAA
* * *** * *
28425602 AGATTCGCTGTTGCGGCTTCAATCTTTCCCTTAATGTTTTTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGTTTCTGAGGTACC
* * * * * * * *
28425651 AGGTTTGCCATTGTGACTTAAA-CTTTCCC-TCTATATCTTC-GTGGTACC
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCAGC-ATGT-TTCTGAGGTACC
* * * * *
28425699 AGATTTGCCGTTGCGGGTTCAATCTTTCCCAGGATGTTTCTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGTTTCTGAGGTACC
* * * * ** * *
28425748 AGGTTCACCGTTGCGACTTAAACCTTTCCCTCCATATCTTC-GTGGTACC
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGT-TTCTGAGGTACC
* * * *
28425797 AGATTCGCCATTGCGGCTTCAATCTTTCTCAGCATGTTTCTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGTTTCTGAGGTACC
* * * ** * * *
28425846 AGGTTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTC-GTGGTATC
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGT-TTCTGAGGTACC
* * * * * *
28425895 AGATTCACCATTACGGCTTCAATCTTTCCTAGCATGTTTCTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGTTTCTGAGGTACC
* * * ** * *
28425944 AGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTC-GTGGTACC
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGT-TTCTGAGGTACC
* * *
28425993 AGATTCGCCGTTGCGGCTTTAATCTTTCCCAGCATGTTTTTGAGGTA-T
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGTTTCTGAGGTACC
* * * * ** * *
28426041 AAAGTTCGTCGTTGCGACTTAAACCTTTCCCTTCATATCTTC-GTGGTACC
1 AGA-TTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGT-TTCTGAGGTACC
* * * *
28426091 AGATTCGTCGTTGCAGCTTCAATCTTT-CCAGCATGTTTTTGAGGTA-C
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGTTTCTGAGGTACC
* ** * * * * ** *
28426138 AAAGTTCATCATTGTGACTTAAACCTTTCCCTCCATATCTTC--ATGGTACC
1 AGA-TTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGT-TTCTGA-GGTACC
* * *
28426188 AGATTCGCCGTTGCGGCTTCAATCTTTCCCAGCATGTTTTTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGTTTCTGAGGTACC
* * * * *
28426237 AGGTTCGCCGTTACGACTTCAACCTTTCCC
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCC
28426267 TCCAAACCTG
Statistics
Matches: 447, Mismatches: 147, Indels: 44
0.70 0.23 0.07
Matches are distributed among these distances:
47 6 0.01
48 76 0.17
49 346 0.77
50 19 0.04
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (49 bp):
AGATTCGCCGTTGCGGCTTAAATCTTTCCCAGCATGTTTCTGAGGTACC
Found at i:28425819 original size:98 final size:98
Alignment explanation
Indices: 28425602--28426270 Score: 982
Period size: 98 Copynumber: 6.8 Consensus size: 98
28425592 TCGAGGTAAA
* *** * * *
28425602 AGATTCGCTGTTGCGGCTTCAATCTTTCCCTTAATGTTTTTGAGGTACAAGGTTTGCCATTGTGA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCAGCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGA
*
28425667 CTTAAA-CTTTCCCTCTATATCTTCGTGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * * *
28425699 AGATTTGCCGTTGCGGGTTCAATCTTTCCCAGGATGTTTCTGAGGTACAAGGTTCACCGTTGCGA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCAGCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGA
28425764 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * *
28425797 AGATTCGCCATTGCGGCTTCAATCTTTCTCAGCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCAGCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGA
* *
28425862 CTTAAACCTTTCCCTTCATATCTTCGTGGTATC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * * *
28425895 AGATTCACCATTACGGCTTCAATCTTTCCTAGCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCAGCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGA
28425960 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * *
28425993 AGATTCGCCGTTGCGGCTTTAATCTTTCCCAGCATGTTTTTGAGGTATAAAGTTCGTCGTTGCGA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCAGCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGA
*
28426058 CTTAAACCTTTCCCTTCATATCTTCGTGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * ** * *
28426091 AGATTCGTCGTTGCAGCTTCAATCTTT-CCAGCATGTTTTTGAGGTACAAAGTTCATCATTGTGA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCAGCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGA
*
28426155 CTTAAACCTTTCCCTCCATATCTTCATGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
*
28426188 AGATTCGCCGTTGCGGCTTCAATCTTTCCCAGCATGTTTTTGAGGTACAAGGTTCGCCGTTACGA
1 AGATTCGCCGTTGCGGCTTCAATCTTTCCCAGCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGA
*
28426253 CTTCAACCTTTCCCTCCA
66 CTTAAACCTTTCCCTCCA
28426271 AACCTGTAGA
Statistics
Matches: 516, Mismatches: 54, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
97 149 0.29
98 367 0.71
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (98 bp):
AGATTCGCCGTTGCGGCTTCAATCTTTCCCAGCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGA
CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
Found at i:28434123 original size:23 final size:23
Alignment explanation
Indices: 28434080--28434123 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
28434070 TGTCATTAAA
* *
28434080 ATGCAATGCGAATGAATGCATGT
1 ATGCAATGCGAAAGAAGGCATGT
28434103 ATGCAATGC-AAGAGAAGGCAT
1 ATGCAATGCGAA-AGAAGGCAT
28434124 TGTTTCTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (23 bp):
ATGCAATGCGAAAGAAGGCATGT
Found at i:28438491 original size:19 final size:19
Alignment explanation
Indices: 28438464--28438506 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
28438454 TTTTTCTGAA
*
28438464 ATGCTCTCAAAAACTCTTC
1 ATGCCCTCAAAAACTCTTC
28438483 ATGCCCTCAAAAACTCTTC
1 ATGCCCTCAAAAACTCTTC
28438502 ATGCC
1 ATGCC
28438507 TGACCATGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.35, G:0.07, T:0.28
Consensus pattern (19 bp):
ATGCCCTCAAAAACTCTTC
Found at i:28438933 original size:17 final size:18
Alignment explanation
Indices: 28438908--28438941 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28438898 ATGCCGTCTT
*
28438908 TTTATATTA-TTTATTTG
1 TTTAAATTACTTTATTTG
28438925 TTTAAATTACTTTATTT
1 TTTAAATTACTTTATTT
28438942 TGAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTAAATTACTTTATTTG
Found at i:28441212 original size:17 final size:17
Alignment explanation
Indices: 28441190--28441260 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 17
28441180 AATAAGTTTG
*
28441190 AATTTATTTTAAATTCA
1 AATTTATTTTAAATTTA
* * *
28441207 AATTTATTTTGAGTTTG
1 AATTTATTTTAAATTTA
**
28441224 AATTTACCTTAAATTTA
1 AATTTATTTTAAATTTA
*
28441241 AATTTATTTTAAATTAA
1 AATTTATTTTAAATTTA
28441258 AAT
1 AAT
28441261 GAAATTAAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:28441227 original size:34 final size:34
Alignment explanation
Indices: 28441184--28441250 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
28441174 TTTTTAAATA
**
28441184 AGTTTGAATTTATTTTAAATTCAAATTTATTTTG
1 AGTTTGAATTTACCTTAAATTCAAATTTATTTTG
*
28441218 AGTTTGAATTTACCTTAAATTTAAATTTATTTT
1 AGTTTGAATTTACCTTAAATTCAAATTTATTTT
28441251 AAATTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.55
Consensus pattern (34 bp):
AGTTTGAATTTACCTTAAATTCAAATTTATTTTG
Found at i:28441339 original size:29 final size:29
Alignment explanation
Indices: 28441294--28441367 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
28441284 TCCAAAGTCC
* * **
28441294 AGACTCAATTACTAACCCATTTACACTTA
1 AGACCCAATTACAAACCCATTTACACCCA
28441323 AGACCCAATTACAAACCCATTTACACCCA
1 AGACCCAATTACAAACCCATTTACACCCA
28441352 A-AGCCCAATTACAAAC
1 AGA-CCCAATTACAAAC
28441368 AAGCCTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 1 0.03
29 39 0.98
ACGTcount: A:0.42, C:0.32, G:0.04, T:0.22
Consensus pattern (29 bp):
AGACCCAATTACAAACCCATTTACACCCA
Found at i:28441399 original size:26 final size:26
Alignment explanation
Indices: 28441363--28441414 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
28441353 AGCCCAATTA
*
28441363 CAAACAAGCCTAAATAGGCCAAACAC
1 CAAACAAGCCTAAATAGCCCAAACAC
*
28441389 CAAACAGGCCTAAATAGCCCAAACAC
1 CAAACAAGCCTAAATAGCCCAAACAC
28441415 TACACCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.33, G:0.12, T:0.08
Consensus pattern (26 bp):
CAAACAAGCCTAAATAGCCCAAACAC
Found at i:28441995 original size:9 final size:9
Alignment explanation
Indices: 28441981--28442015 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
28441971 TTAAATGATT
28441981 TTAATAACA
1 TTAATAACA
28441990 TTAATAACA
1 TTAATAACA
*
28441999 TTAATAATA
1 TTAATAACA
*
28442008 ATAATAAC
1 TTAATAAC
28442016 GAGTTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (9 bp):
TTAATAACA
Found at i:28443257 original size:29 final size:29
Alignment explanation
Indices: 28443223--28443316 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
28443213 CCGAATCTCT
** *
28443223 AAAAATTACCATTTTACCCTTGAGT-GTCC
1 AAAAATTACCATTTTACCCCCGA-TCATCC
*
28443252 AAAAATTTCCATTTTACCCCCGATCATCC
1 AAAAATTACCATTTTACCCCCGATCATCC
* *
28443281 TAAAATTACCATTTTACCCCCGGGT-ATCC
1 AAAAATTACCATTTTACCCCC-GATCATCC
28443310 AAAAATT
1 AAAAATT
28443317 GCATTTTTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.02
29 52 0.95
30 2 0.04
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.32
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCGATCATCC
Found at i:28444047 original size:119 final size:119
Alignment explanation
Indices: 28443836--28444073 Score: 458
Period size: 119 Copynumber: 2.0 Consensus size: 119
28443826 AATGTATACA
*
28443836 AATAATTTTAAAACAAAACGAGGCAATATTCATTCGTGTGAAAACTTCGAAAAACCATGCCCTAA
1 AATAATTTTAAAACAAAACGAGGCAATATTCATTCGTGTGAAAACTTCGAAAAACCACGCCCTAA
28443901 CGTGCTGGGTATGATTTTCGTATAATCCACGCAATCGAATATCCTCTTTAAAGT
66 CGTGCTGGGTATGATTTTCGTATAATCCACGCAATCGAATATCCTCTTTAAAGT
28443955 AATAATTTTAAAACAAAACGAGGCAATATTCATTCGTGTGAAAACTTCGAAAAACCACGCCCTAA
1 AATAATTTTAAAACAAAACGAGGCAATATTCATTCGTGTGAAAACTTCGAAAAACCACGCCCTAA
*
28444020 CGTGCTGGGTGTGATTTTCGTATAATCCACGCAATCGAATATCCTCTTTAAAGT
66 CGTGCTGGGTATGATTTTCGTATAATCCACGCAATCGAATATCCTCTTTAAAGT
28444074 CTTCCCAAAA
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 117 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (119 bp):
AATAATTTTAAAACAAAACGAGGCAATATTCATTCGTGTGAAAACTTCGAAAAACCACGCCCTAA
CGTGCTGGGTATGATTTTCGTATAATCCACGCAATCGAATATCCTCTTTAAAGT
Found at i:28446199 original size:24 final size:24
Alignment explanation
Indices: 28446172--28446217 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
28446162 ATGTAAACAT
*
28446172 TAAAATAATGT-TAAGATTATTATA
1 TAAAA-AATGTATAAAATTATTATA
28446196 TAAAAAATGTATAAAATTATTA
1 TAAAAAATGTATAAAATTATTA
28446218 AATATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (24 bp):
TAAAAAATGTATAAAATTATTATA
Found at i:28452822 original size:27 final size:26
Alignment explanation
Indices: 28452783--28452834 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
28452773 AGAAAAAAAA
28452783 ATGAGAAAAAGTGGTAGTGGATGAAG
1 ATGAGAAAAAGTGGTAGTGGATGAAG
*
28452809 ATGAGGAATAAGTGGTAGTGGATGAA
1 ATGA-GAAAAAGTGGTAGTGGATGAA
28452835 AAAGGAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.21
Consensus pattern (26 bp):
ATGAGAAAAAGTGGTAGTGGATGAAG
Found at i:28461469 original size:64 final size:64
Alignment explanation
Indices: 28461363--28461490 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
28461353 TTGTTTAAGC
*
28461363 TTTCGGGTTTTTAAAGAAAGTGCATATTTGGTGAGTGTTTTGGAATCGCTACTCATAGATGATT
1 TTTCAGGTTTTTAAAGAAAGTGCATATTTGGTGAGTGTTTTGGAATCGCTACTCATAGATGATT
28461427 TTTCAGGTTTTTAAAGAAAGTGCATATTTGGTGAGTGTTTTGGAATCGCTACTCATAGATGATT
1 TTTCAGGTTTTTAAAGAAAGTGCATATTTGGTGAGTGTTTTGGAATCGCTACTCATAGATGATT
28461491 CATTGTGTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (64 bp):
TTTCAGGTTTTTAAAGAAAGTGCATATTTGGTGAGTGTTTTGGAATCGCTACTCATAGATGATT
Found at i:28461688 original size:23 final size:23
Alignment explanation
Indices: 28461581--28461691 Score: 125
Period size: 23 Copynumber: 4.8 Consensus size: 23
28461571 AATATCAATA
*
28461581 AATATGATTTAT-CATCAAATATT
1 AATATGATTTATGC-TTAAATATT
* *
28461604 AATATGATTTGTGCTCAAATATT
1 AATATGATTTATGCTTAAATATT
* *
28461627 AATGTGATTTATGATTAAATATT
1 AATATGATTTATGCTTAAATATT
* * *
28461650 AGTGTAATTTATGCTTAAATATT
1 AATATGATTTATGCTTAAATATT
*
28461673 AATATGATTTGTGCTTAAA
1 AATATGATTTATGCTTAAA
28461692 GAATTATGAT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
23 74 0.99
24 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (23 bp):
AATATGATTTATGCTTAAATATT
Found at i:28464376 original size:2 final size:2
Alignment explanation
Indices: 28464369--28464447 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
28464359 GCTCAAAATA
28464369 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28464411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28464448 AGGATTTATT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28466032 original size:23 final size:23
Alignment explanation
Indices: 28465988--28466032 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28465978 TTAATGTTCA
**
28465988 CAAACATGTTCATTTAACTTAAT
1 CAAACATGTTCATCGAACTTAAT
28466011 CAAACATGTTCA-CGAACATTAA
1 CAAACATGTTCATCGAAC-TTAA
28466033 ACGAACATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (23 bp):
CAAACATGTTCATCGAACTTAAT
Found at i:28474251 original size:58 final size:58
Alignment explanation
Indices: 28474179--28474298 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 58
28474169 ACCCATTAAC
* * * *
28474179 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTTATTCTTTAAA-AACACTTAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATATTATTC-CTAAATAACACTCAT
28474237 AAACTAAACCCAAATATTTTTAAACCCAAATATAATATTATTCCTAAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATATTATTCCTAAATAACACTCAT
28474295 AAAC
1 AAAC
28474299 AACTTCCTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
57 4 0.07
58 53 0.93
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATATTATTCCTAAATAACACTCAT
Found at i:28476340 original size:5 final size:5
Alignment explanation
Indices: 28476330--28476363 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
28476320 TTGAAATGTA
28476330 AATTT AATTT AATTT AATTT AATTT -ATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT
28476364 TATGGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
AATTT
Found at i:28482983 original size:30 final size:31
Alignment explanation
Indices: 28482947--28483004 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
28482937 AATTGATTTT
28482947 TTTTAATTATTTTACAAG-GGTTTAATTAAA
1 TTTTAATTATTTTACAAGAGGTTTAATTAAA
**
28482977 TTTTAATTATTTTATGAGAGGTTTAATT
1 TTTTAATTATTTTACAAGAGGTTTAATT
28483005 GATTTTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (31 bp):
TTTTAATTATTTTACAAGAGGTTTAATTAAA
Found at i:28483012 original size:31 final size:30
Alignment explanation
Indices: 28482946--28483012 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
28482936 TAATTGATTT
28482946 TTTTTAATTATTTTACAAGGGTTTAATTAA
1 TTTTTAATTATTTTACAAGGGTTTAATTAA
* ** *
28482976 ATTTTAATTATTTTATGAGAGGTTTAATTGA
1 TTTTTAATTATTTTACAAG-GGTTTAATTAA
28483007 TTTTTA
1 TTTTTA
28483013 GAAAAAATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.55
Consensus pattern (30 bp):
TTTTTAATTATTTTACAAGGGTTTAATTAA
Found at i:28483321 original size:9 final size:9
Alignment explanation
Indices: 28483271--28483321 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
28483261 TTAAAAGTTA
28483271 TATAAAAAT
1 TATAAAAAT
*
28483280 TATTAAAAT
1 TATAAAAAT
*
28483289 GATAATTAAAT
1 TATAA--AAAT
28483300 TATAAAAACT
1 TATAAAAA-T
28483310 TATAAAAAT
1 TATAAAAAT
28483319 TAT
1 TAT
28483322 TTAAAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 18 0.51
10 9 0.26
11 8 0.23
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (9 bp):
TATAAAAAT
Found at i:28483332 original size:29 final size:28
Alignment explanation
Indices: 28483270--28483332 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
28483260 ATTAAAAGTT
*
28483270 ATATAAAAATTATTAAAATGATAATTAAA
1 ATATAAAAATTATAAAAAT-ATAATTAAA
* *
28483299 TTATAAAAACTTATAAAAAT-TATTTAAAA
1 ATATAAAAA-TTATAAAAATATAATT-AAA
28483328 ATATA
1 ATATA
28483333 GAATAGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 4 0.14
29 15 0.54
30 9 0.32
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
ATATAAAAATTATAAAAATATAATTAAA
Found at i:28483585 original size:29 final size:29
Alignment explanation
Indices: 28483553--28483612 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
28483543 AGAAAGTGGT
*
28483553 AATTT-TTTTAAAAATTATT-AGAAATTATA
1 AATTTATTATAAAAATT-TTCA-AAATTATA
28483582 AATTTATTATAAAAATTTTCAAAATTATA
1 AATTTATTATAAAAATTTTCAAAATTATA
28483611 AA
1 AA
28483613 AATAGATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
AATTTATTATAAAAATTTTCAAAATTATA
Found at i:28484425 original size:33 final size:33
Alignment explanation
Indices: 28484382--28484461 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 33
28484372 GAGAGGACAA
* * *
28484382 CAAGGAGAGCTCGCAATACCAACTCGCACGATC
1 CAAGGGGAGCTCGCAATACCAACTCACACGAGC
* * *
28484415 CAAGGGGAGCTTGCAATATCAGCTCACACGAGC
1 CAAGGGGAGCTCGCAATACCAACTCACACGAGC
*
28484448 CAAGAGGAG-TCGCA
1 CAAGGGGAGCTCGCA
28484462 GTTTTAGTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 4 0.10
33 35 0.90
ACGTcount: A:0.33, C:0.29, G:0.26, T:0.12
Consensus pattern (33 bp):
CAAGGGGAGCTCGCAATACCAACTCACACGAGC
Found at i:28484603 original size:21 final size:21
Alignment explanation
Indices: 28484572--28484629 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
28484562 TCGGAATGTC
28484572 AGTCCTATGAACAGTG-AGATCA
1 AGTCC-ATGAACAGTGAAG-TCA
*
28484594 AGTCCATGAATAGTGAAGTCA
1 AGTCCATGAACAGTGAAGTCA
*
28484615 AAT-CATGAACAGTGA
1 AGTCCATGAACAGTGA
28484630 TCATATGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 11 0.34
21 14 0.44
22 7 0.22
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
AGTCCATGAACAGTGAAGTCA
Found at i:28494988 original size:14 final size:15
Alignment explanation
Indices: 28494963--28494997 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
28494953 AAATGAAAAT
*
28494963 ATAAAGTAAAAACTA
1 ATAAACTAAAAACTA
28494978 A-AAACTAAAAACTA
1 ATAAACTAAAAACTA
28494992 ATAAAC
1 ATAAAC
28494998 GATATGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.69, C:0.11, G:0.03, T:0.17
Consensus pattern (15 bp):
ATAAACTAAAAACTA
Found at i:28527037 original size:5 final size:6
Alignment explanation
Indices: 28527015--28527044 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28527005 AAGAGTGTTT
*
28527015 GAAAAA GAAAAA CAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
28527045 TATGATGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:28527602 original size:16 final size:15
Alignment explanation
Indices: 28527581--28527614 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
28527571 CGATTAAAAT
28527581 TAATAAAATAAATGAA
1 TAATAAAATAAAT-AA
28527597 TAATAAAATAAATAA
1 TAATAAAATAAATAA
28527612 TAA
1 TAA
28527615 AGAACTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
TAATAAAATAAATAA
Found at i:28529051 original size:4 final size:4
Alignment explanation
Indices: 28529042--28529066 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28529032 AATTGATCTG
28529042 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
28529067 TTGTTAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:28550796 original size:20 final size:22
Alignment explanation
Indices: 28550760--28550800 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
28550750 CAGCAAATGA
28550760 TTTAAAATTATTAAAATTATTT
1 TTTAAAATTATTAAAATTATTT
28550782 TTTAAAA-TA-TAAAATTATT
1 TTTAAAATTATTAAAATTATT
28550801 AATTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAAAATTATTAAAATTATTT
Found at i:28550820 original size:27 final size:27
Alignment explanation
Indices: 28550762--28550829 Score: 93
Period size: 27 Copynumber: 2.4 Consensus size: 27
28550752 GCAAATGATT
28550762 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATT--AATTATTTTTTAAAATA
*
28550791 TAAAATTATTAATT-TTTTTTGAAATAA
1 TAAAATTATTAATTATTTTTTAAAAT-A
28550818 TAAAATTATTAA
1 TAAAATTATTAA
28550830 ATAATTCTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 10 0.27
27 17 0.46
29 10 0.27
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
TAAAATTATTAATTATTTTTTAAAATA
Found at i:28550865 original size:12 final size:12
Alignment explanation
Indices: 28550848--28550885 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
28550838 AATTTCCAGT
*
28550848 TTCATCATCATC
1 TTCATCATCTTC
28550860 TTCATCATCTTC
1 TTCATCATCTTC
*
28550872 TTCTTCATCTTC
1 TTCATCATCTTC
28550884 TT
1 TT
28550886 TTTCATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.53
Consensus pattern (12 bp):
TTCATCATCTTC
Found at i:28550890 original size:12 final size:12
Alignment explanation
Indices: 28550852--28550892 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
28550842 TCCAGTTTCA
* *
28550852 TCATCATCTTCA
1 TCATCTTCTTCT
28550864 TCATCTTCTTCT
1 TCATCTTCTTCT
*
28550876 TCATCTTCTTTT
1 TCATCTTCTTCT
28550888 TCATC
1 TCATC
28550893 ATTTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.54
Consensus pattern (12 bp):
TCATCTTCTTCT
Found at i:28551810 original size:28 final size:28
Alignment explanation
Indices: 28551712--28551810 Score: 130
Period size: 28 Copynumber: 3.5 Consensus size: 28
28551702 ATTAAAATTA
28551712 TTTAATAATTTTATTATTTTGAAAAAATAAT
1 TTTAATAATTTTA-TATTTT--AAAAATAAT
28551743 TTTAATAATTTTATA-TTTAAAGAATAA-
1 TTTAATAATTTTATATTTTAAA-AATAAT
* *
28551770 TTTAAAAAATTTATATTTTAAAAATAAT
1 TTTAATAATTTTATATTTTAAAAATAAT
28551798 TTTAATAATTTTA
1 TTTAATAATTTTA
28551811 AATCATTTGC
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
27 21 0.34
28 22 0.36
29 3 0.05
30 2 0.03
31 13 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTAATAATTTTATATTTTAAAAATAAT
Found at i:28565628 original size:18 final size:18
Alignment explanation
Indices: 28565605--28565641 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28565595 ACAATTCATA
28565605 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
28565623 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
28565641 T
1 T
28565642 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:28572724 original size:6 final size:6
Alignment explanation
Indices: 28572703--28572737 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
28572693 AAATAATCCT
*
28572703 AAATCGA AAATAA AAATCA AAATCA AAATCA AAAT
1 AAATC-A AAATCA AAATCA AAATCA AAATCA AAAT
28572738 TGAATAAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.69, C:0.11, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:28572753 original size:47 final size:46
Alignment explanation
Indices: 28572682--28572793 Score: 109
Period size: 47 Copynumber: 2.4 Consensus size: 46
28572672 AAACAGTAGC
* * *
28572682 AATCAAAATCGAAATAATCCTAAATCGAAAATAAAAATCAAAATCAA
1 AATCAAAATTG-AATAAACCTAAATCAAAAATAAAAATCAAAATCAA
* * * * *
28572729 AATCAAAATTGAATAAACCATAAATTAAAAATCACAATCAATATCGA
1 AATCAAAATTGAATAAACC-TAAATCAAAAATAAAAATCAAAATCAA
*
28572776 CATC-AAATTCGAATAAAC
1 AATCAAAATT-GAATAAAC
28572794 ACAAAATAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
46 12 0.22
47 42 0.78
ACGTcount: A:0.58, C:0.16, G:0.04, T:0.21
Consensus pattern (46 bp):
AATCAAAATTGAATAAACCTAAATCAAAAATAAAAATCAAAATCAA
Found at i:28573163 original size:30 final size:31
Alignment explanation
Indices: 28573096--28573163 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
28573086 ATCTAATTTC
*
28573096 AGTGACTATTTTGTCACTTTTCAATAACTTT
1 AGTGACTATTTTGTCACTTTTCAATAACTTG
*
28573127 AGTGACTATTTTGTCACATTTTC-A-AAGTTG
1 AGTGACTATTTTGTCAC-TTTTCAATAACTTG
28573157 AGTGACT
1 AGTGACT
28573164 GTTGTGTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 11 0.32
31 18 0.53
32 5 0.15
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (31 bp):
AGTGACTATTTTGTCACTTTTCAATAACTTG
Found at i:28574741 original size:26 final size:26
Alignment explanation
Indices: 28574710--28574762 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28574700 TATTTATGAG
28574710 GCCATCGCATATGATTAAACCTTATT
1 GCCATCGCATATGATTAAACCTTATT
28574736 GCCATCGCATATGATTAAACCTTATT
1 GCCATCGCATATGATTAAACCTTATT
28574762 G
1 G
28574763 GAAGTTACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (26 bp):
GCCATCGCATATGATTAAACCTTATT
Found at i:28582496 original size:13 final size:13
Alignment explanation
Indices: 28582478--28582510 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
28582468 ACCACTCAAC
28582478 ATTGAGATACCTT
1 ATTGAGATACCTT
28582491 ATTGAGATACCTT
1 ATTGAGATACCTT
*
28582504 TTTGAGA
1 ATTGAGA
28582511 AAAAAGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (13 bp):
ATTGAGATACCTT
Found at i:28584234 original size:20 final size:21
Alignment explanation
Indices: 28584194--28584233 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28584184 TGCAAGAAAT
*
28584194 TTGAAAC-AACAAAAGTAAAA
1 TTGAAACAAATAAAAGTAAAA
28584214 TTGAAACAAATAAAAGTAAA
1 TTGAAACAAATAAAAGTAAA
28584234 TAAACAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.65, C:0.07, G:0.10, T:0.17
Consensus pattern (21 bp):
TTGAAACAAATAAAAGTAAAA
Found at i:28598621 original size:18 final size:18
Alignment explanation
Indices: 28598600--28598634 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28598590 TAAATAATAA
* *
28598600 AATATTATTATTTATTAT
1 AATAATATTATTAATTAT
28598618 AATAATATTATTAATTA
1 AATAATATTATTAATTA
28598635 ATATATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATAATATTATTAATTAT
Found at i:28598624 original size:21 final size:20
Alignment explanation
Indices: 28598581--28598639 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
28598571 CTCTTATATT
28598581 TTATTATATTAAATAATAAAATA
1 TTATTA-ATT-AAT-ATAAAATA
* *
28598604 TTATTATTTATTATAATAATA
1 TTATTAATTAATATAA-AATA
28598625 TTATTAATTAATATA
1 TTATTAATTAATATA
28598640 TATTTTGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 19 0.61
22 2 0.06
23 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTAATTAATATAAAATA
Found at i:28600506 original size:22 final size:23
Alignment explanation
Indices: 28600481--28600529 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
28600471 TCTTGTTTTC
*
28600481 TTTTCTTTA-T-AATTTTGTTCGA
1 TTTTCTTTATTAAATTCTGTTC-A
*
28600503 TTTTTTTTATTAAATTCTGTTCA
1 TTTTCTTTATTAAATTCTGTTCA
28600526 TTTT
1 TTTT
28600530 GTTATTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 6 0.26
24 9 0.39
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.67
Consensus pattern (23 bp):
TTTTCTTTATTAAATTCTGTTCA
Found at i:28608869 original size:16 final size:18
Alignment explanation
Indices: 28608845--28608881 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
28608835 TAATTTATTA
*
28608845 TTATTAATT-TAAAAT-T
1 TTATAAATTATAAAATAT
28608861 TTATAAATTATAAAATAT
1 TTATAAATTATAAAATAT
28608879 TTA
1 TTA
28608882 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 6 0.33
18 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATAAATTATAAAATAT
Found at i:28608883 original size:16 final size:16
Alignment explanation
Indices: 28608850--28608894 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
28608840 TATTATTATT
*
28608850 AATT-TAAAATTTTATA
1 AATTATAAAATATT-TA
28608866 AATTATAAAATATTTA
1 AATTATAAAATATTTA
28608882 AA-TA-AAAATATTT
1 AATTATAAAATATTT
28608895 TTATTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 9 0.33
15 2 0.07
16 8 0.30
17 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTATAAAATATTTA
Found at i:28610235 original size:13 final size:13
Alignment explanation
Indices: 28610217--28610244 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28610207 ACTCTATTTT
28610217 TTTAGGATTATTA
1 TTTAGGATTATTA
28610230 TTTAGGATTATTA
1 TTTAGGATTATTA
28610243 TT
1 TT
28610245 ATATTGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (13 bp):
TTTAGGATTATTA
Found at i:28610362 original size:25 final size:23
Alignment explanation
Indices: 28610318--28610364 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
28610308 CCAACTAGGA
28610318 AATTATTGTTTAGATTTAATTTT
1 AATTATTGTTTAGATTTAATTTT
*
28610341 AATTATCTTTTTAGAGTTTAATTT
1 AATTAT-TGTTTAGA-TTTAATTT
28610365 GGATCCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.60
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTTT
Found at i:28613845 original size:9 final size:9
Alignment explanation
Indices: 28613831--28613856 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28613821 CCAATTTTGT
28613831 TTTTATTTA
1 TTTTATTTA
28613840 TTTTATTTA
1 TTTTATTTA
28613849 TTTTATTT
1 TTTTATTT
28613857 TCTTGCATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTATTTA
Found at i:28614799 original size:105 final size:105
Alignment explanation
Indices: 28614617--28614818 Score: 298
Period size: 105 Copynumber: 1.9 Consensus size: 105
28614607 TTATGGAAAA
* * * *
28614617 AATAAATTAGGAGTATGTTGGGTTGAGTAACTGGGATCGAGTGCTTGGGTTGTCATTTCATTTTA
1 AATAAATTAGGAGTATGTTGGGCTGAGTAACTGAGATCGAGTGCTTGGGTTGTCATTCCATTTCA
* *
28614682 CGTCAAAAGGGCCAATAAATTCTTAAGTAAAAATGATGAT
66 CATCAAAAGGGCCAATAAATTCTTAAGGAAAAATGATGAT
* * *
28614722 AATAAATT-GAGAGTGTGTTGGGCTGAGTAACTGAGATGGGGTGCTTGGGTTGTCATTCCATTTC
1 AATAAATTAG-GAGTATGTTGGGCTGAGTAACTGAGATCGAGTGCTTGGGTTGTCATTCCATTTC
*
28614786 ACATCAAAAGGGCCAATATATTCTTAAGGAAAA
65 ACATCAAAAGGGCCAATAAATTCTTAAGGAAAA
28614819 GGAAAAAAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
104 1 0.01
105 85 0.99
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (105 bp):
AATAAATTAGGAGTATGTTGGGCTGAGTAACTGAGATCGAGTGCTTGGGTTGTCATTCCATTTCA
CATCAAAAGGGCCAATAAATTCTTAAGGAAAAATGATGAT
Found at i:28618932 original size:2 final size:2
Alignment explanation
Indices: 28618925--28618958 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28618915 ACTTATTTTA
28618925 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28618959 ATTAAGATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28627884 original size:21 final size:21
Alignment explanation
Indices: 28627855--28627947 Score: 116
Period size: 21 Copynumber: 4.4 Consensus size: 21
28627845 GTGAAAATCG
28627855 TGATATGTGTTATGTGATCTA
1 TGATATGTGTTATGTGATCTA
28627876 TGGA-ATGTGTTATGTGATCTA
1 T-GATATGTGTTATGTGATCTA
* *
28627897 TGATATGTGCTATGTGATTTA
1 TGATATGTGTTATGTGATCTA
* * *
28627918 TTATAAGTGTTATGTGATGTA
1 TGATATGTGTTATGTGATCTA
*
28627939 TAATATGTG
1 TGATATGTG
28627948 ATTTCATCTC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.26, C:0.03, G:0.25, T:0.46
Consensus pattern (21 bp):
TGATATGTGTTATGTGATCTA
Found at i:28628219 original size:47 final size:47
Alignment explanation
Indices: 28628079--28628208 Score: 138
Period size: 46 Copynumber: 2.8 Consensus size: 47
28628069 TAAGTGAAAT
* * * * * * *
28628079 TATGTGATATGTGAGCATAATACATGCTAAAATGTG-GAAATCGTGA
1 TATGTGATATGTGAGCATGACAAATGCTAAAAAGTGAAAAATCATAA
* *
28628125 TATATGATATGTGAGCATGACACATGCTAAAAAGTGAAAAATCATAA
1 TATGTGATATGTGAGCATGACAAATGCTAAAAAGTGAAAAATCATAA
* *
28628172 TATGTGATATGTGGGGATGA-AAATGCTAAAAATGTGA
1 TATGTGATATGTGAGCATGACAAATGCTAAAAA-GTGA
28628209 TAAGTGATAA
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
46 43 0.61
47 28 0.39
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (47 bp):
TATGTGATATGTGAGCATGACAAATGCTAAAAAGTGAAAAATCATAA
Found at i:28628321 original size:25 final size:25
Alignment explanation
Indices: 28628274--28628355 Score: 107
Period size: 25 Copynumber: 3.4 Consensus size: 25
28628264 AAGGAGGAAG
*
28628274 CTATGTGGCAG-TTTTACTACAAAA
1 CTATGTGGCAGTTTTTACTGCAAAA
*
28628298 CTATGTGGTAGTTTTTACTGCAAAA
1 CTATGTGGCAGTTTTTACTGCAAAA
*
28628323 CTATGTGGCAGTTTAT-CTGCAAAAA
1 CTATGTGGCAGTTTTTACTGC-AAAA
28628348 C-ATGTGGC
1 CTATGTGGC
28628356 CATTATTGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
24 21 0.40
25 31 0.60
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (25 bp):
CTATGTGGCAGTTTTTACTGCAAAA
Found at i:28630645 original size:26 final size:28
Alignment explanation
Indices: 28630610--28630685 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 28
28630600 AAATGATTTA
28630610 AAAATTATTAAAATAATTTTT-AAT-AT
1 AAAATTATTAAAATAATTTTTAAATAAT
* *
28630636 AAAATTATTAAATTTATTTTTTTGAAATAAT
1 AAAATTATTAAA-ATA-ATTTTT-AAATAAT
28630667 AAAATTATT-AAATAATTTT
1 AAAATTATTAAAATAATTTT
28630686 AATTTTCAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
26 12 0.29
27 2 0.05
28 9 0.22
29 2 0.05
30 5 0.12
31 11 0.27
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
AAAATTATTAAAATAATTTTTAAATAAT
Found at i:28631649 original size:20 final size:22
Alignment explanation
Indices: 28631624--28631665 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
28631614 AAATAATTTT
28631624 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
28631644 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
28631666 TCAAAATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:28631653 original size:29 final size:31
Alignment explanation
Indices: 28631590--28631662 Score: 123
Period size: 29 Copynumber: 2.4 Consensus size: 31
28631580 ATTAAAATTA
28631590 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTATTATTTCAAAAAAATAAT
*
28631621 TTTAATAATTTTA-TATTT-TAAAAAATAAT
1 TTTAATAATTTTATTATTTCAAAAAAATAAT
28631650 TTTAATAATTTTA
1 TTTAATAATTTTA
28631663 AAATCAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 23 0.56
30 5 0.12
31 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTAATAATTTTATTATTTCAAAAAAATAAT
Found at i:28636174 original size:28 final size:28
Alignment explanation
Indices: 28636141--28636201 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
28636131 AATGTGAGGC
28636141 TTTGTGGTTGAATCAT-TTAAAGTGAGCA
1 TTTGTGGTTGAATC-TGTTAAAGTGAGCA
* * *
28636169 TTTGTGGTTGACTCTGTTCAAGTGAGCC
1 TTTGTGGTTGAATCTGTTAAAGTGAGCA
28636197 TTTGT
1 TTTGT
28636202 AACATCCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.43
Consensus pattern (28 bp):
TTTGTGGTTGAATCTGTTAAAGTGAGCA
Found at i:28644213 original size:9 final size:9
Alignment explanation
Indices: 28644185--28644227 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
28644175 TAAAATGGTA
*
28644185 ATATTAAAT
1 ATATTAATT
*
28644194 A-ATTTATT
1 ATATTAATT
*
28644202 ATAATAATT
1 ATATTAATT
28644211 ATATTAATT
1 ATATTAATT
28644220 ATATTAAT
1 ATATTAAT
28644228 AACTTATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
8 6 0.21
9 22 0.79
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATATTAATT
Found at i:28644221 original size:21 final size:22
Alignment explanation
Indices: 28644197--28644242 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
28644187 ATTAAATAAT
*
28644197 TTATTA-TAATAATTATATTA-A
1 TTATTATTAATAACT-TATTATA
28644218 TTA-TATTAATAACTTATTATA
1 TTATTATTAATAACTTATTATA
28644239 TTAT
1 TTAT
28644243 AAAATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATTATTAATAACTTATTATA
Found at i:28644243 original size:21 final size:21
Alignment explanation
Indices: 28644203--28644243 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28644193 TAATTTATTA
*
28644203 TAATAATTATATTAATTATAT
1 TAATAACTATATTAATTATAT
28644224 TAATAACT-TATTATATTATA
1 TAATAACTATATTA-ATTATA
28644244 AAATATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATAACTATATTAATTATAT
Found at i:28644308 original size:21 final size:22
Alignment explanation
Indices: 28644277--28644317 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28644267 TGTTTAATAT
28644277 TATTGAATATTATAATATTTGA
1 TATTGAATATTATAATATTTGA
*
28644299 TATT-AATATTTTAATATTT
1 TATTGAATATTATAATATTT
28644318 TTAAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
TATTGAATATTATAATATTTGA
Found at i:28648563 original size:29 final size:28
Alignment explanation
Indices: 28648497--28648572 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 28
28648487 GTAAGATGGG
* *
28648497 AGAAAAC-GAGGAAAAAAAAATTGTTTA
1 AGAAAACGGAAGAGAAAAAAATTGTTTA
** * *
28648524 CTAATATGGAAGAGAAAAAAATTGGTTTA
1 AGAAAACGGAAGAGAAAAAAATT-GTTTA
*
28648553 AGAAAACGGAAAAGAAAAAA
1 AGAAAACGGAAGAGAAAAAA
28648573 GGAGCTATTA
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
27 3 0.08
28 13 0.36
29 20 0.56
ACGTcount: A:0.59, C:0.04, G:0.20, T:0.17
Consensus pattern (28 bp):
AGAAAACGGAAGAGAAAAAAATTGTTTA
Found at i:28653799 original size:18 final size:19
Alignment explanation
Indices: 28653778--28653821 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
28653768 TTTTAACTAA
*
28653778 TAATTATAATTTAAATCT-
1 TAATTATAATTTAAATATG
**
28653796 TAATTATTTTTTAAATATG
1 TAATTATAATTTAAATATG
28653815 TAATTAT
1 TAATTAT
28653822 CACAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TAATTATAATTTAAATATG
Found at i:28653837 original size:45 final size:44
Alignment explanation
Indices: 28653788--28653878 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 44
28653778 TAATTATAAT
**
28653788 TTAAATCT-TAATTATTTTTTAAATATGTAATTATCACAAATTTTA
1 TTAAAT-TATAATTA-TTTTTAAATACATAATTATCACAAATTTTA
* * *
28653833 TTAAATTATAATTATTTTTGAATACATAGTTATCACAACTTTTA
1 TTAAATTATAATTATTTTTAAATACATAATTATCACAAATTTTA
28653877 TT
1 TT
28653879 TTATTTCAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
44 28 0.70
45 12 0.30
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (44 bp):
TTAAATTATAATTATTTTTAAATACATAATTATCACAAATTTTA
Found at i:28654142 original size:22 final size:22
Alignment explanation
Indices: 28654097--28654142 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
28654087 ACCTATAGTA
*
28654097 AAATAGGAATATTTAATTATAT
1 AAATAGGAATATTTAATTAAAT
* **
28654119 AAATATGAATATTTGTTTAAAT
1 AAATAGGAATATTTAATTAAAT
28654141 AA
1 AA
28654143 TGCTTAGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATAGGAATATTTAATTAAAT
Found at i:28655585 original size:5 final size:5
Alignment explanation
Indices: 28655575--28655610 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
28655565 AATACTAATA
* *
28655575 ATTAT ATTAT ATTAT ATTAT ATGAT ATTCT ATTAT A
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
28655611 AATAAATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (5 bp):
ATTAT
Found at i:28656063 original size:61 final size:62
Alignment explanation
Indices: 28655987--28656105 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 62
28655977 ATTAATACAA
* * * * * * *
28655987 AATAGTATCTAAATATTAATTTGGT-AAAAATAAAGTTAAATGATTGCAATATCTAAGTATG
1 AATAGTATATAAATATTAAATAGATAAAAAATAAACTTAAATAATTACAATATCTAAGTATG
28656048 AATAGTATATAAATATTAAATAGATAAAAAAATAAACTTAAATAATTACAATATCTAA
1 AATAGTATATAAATATTAAATAGAT-AAAAAATAAACTTAAATAATTACAATATCTAA
28656106 TACAAATTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
61 21 0.43
63 28 0.57
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (62 bp):
AATAGTATATAAATATTAAATAGATAAAAAATAAACTTAAATAATTACAATATCTAAGTATG
Found at i:28659028 original size:21 final size:21
Alignment explanation
Indices: 28658990--28659029 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28658980 TACTAATAAC
* *
28658990 TCTCAATTTTAGGATTTAAGG
1 TCTCAAGTTTAAGATTTAAGG
*
28659011 TCTCAAGTTTAAGTTTTAA
1 TCTCAAGTTTAAGATTTAA
28659030 TATTTTAGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (21 bp):
TCTCAAGTTTAAGATTTAAGG
Found at i:28660321 original size:28 final size:28
Alignment explanation
Indices: 28660281--28660335 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
28660271 GAGTAGTTTT
28660281 CTATATTATAGGAAGTTGA-AGACGAATC
1 CTATATTATAGGAAGTTGAGAG-CGAATC
*
28660309 CTATATTATAGGAATTTGAGAGCGAAT
1 CTATATTATAGGAAGTTGAGAGCGAAT
28660336 AGGAGTAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (28 bp):
CTATATTATAGGAAGTTGAGAGCGAATC
Found at i:28661881 original size:106 final size:106
Alignment explanation
Indices: 28661691--28661897 Score: 283
Period size: 106 Copynumber: 2.0 Consensus size: 106
28661681 GGATAAACCG
* * ** *
28661691 CAATAAATGAGACCAGCTCTAGTTGGATTAACCAACTGTTTTGCGCTTAGCACTAGACTGATAAA
1 CAATAAATGAGACCAGCTCTAGTTAGATTAACCAACGGTTTTGCGCCCAGCACTAGACGGATAAA
* *
28661756 TCGAAAAATGTGTGTCCAGCACTAG-CAAGTTAAACTAACAA
66 CCGAAAAATGTGTGCCCAGCACTAGTC-AGTTAAACTAACAA
* * *
28661797 CAATAAGTGAGTCCAGCTCTAGTTAGATTAACCAACGGTTTTGCGCCCAGCGCTAGTA-GGATAA
1 CAATAAATGAGACCAGCTCTAGTTAGATTAACCAACGGTTTTGCGCCCAGCACTAG-ACGGATAA
*
28661861 ACCGACAAATGTGTGCCCAGCACTAGTCAGTTAAACT
65 ACCGAAAAATGTGTGCCCAGCACTAGTCAGTTAAACT
28661898 GACGAAATAA
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
106 86 0.98
107 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (106 bp):
CAATAAATGAGACCAGCTCTAGTTAGATTAACCAACGGTTTTGCGCCCAGCACTAGACGGATAAA
CCGAAAAATGTGTGCCCAGCACTAGTCAGTTAAACTAACAA
Found at i:28668431 original size:26 final size:27
Alignment explanation
Indices: 28668385--28668436 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
28668375 TCCAACATCA
* *
28668385 AATACATCATTAACAATAACCTATTTC
1 AATACATCATTAACAACAACCAATTTC
28668412 AATAC-TCATTCAA-AACAACCAATTT
1 AATACATCATT-AACAACAACCAATTT
28668437 GAAGCTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (27 bp):
AATACATCATTAACAACAACCAATTTC
Found at i:28669326 original size:106 final size:106
Alignment explanation
Indices: 28669140--28669345 Score: 283
Period size: 106 Copynumber: 1.9 Consensus size: 106
28669130 GATAAACCGT
* * *
28669140 AATAAGTGATCCCAGCTCTAGTTGGATTAACCAACGATTTTGCACCCAACGCTAGTTGAATAAAC
1 AATAAGTGAACCCAACTCTAGTTGGAGTAACCAACGATTTTGCACCCAACGCTAGTTGAATAAAC
** *
28669205 TGACAAATGTGTGCCCAGCACTAGT-ACGTTAAACTAAAAAC
66 TGACAAATGCATGCCCAACACTAGTCA-GTTAAACTAAAAAC
* * *
28669246 AATAAGTGAACCCAACTCTAGTTGGAGTAACCAACGGTTTTGCACCCAGCGTTAGTCTG-ATAAA
1 AATAAGTGAACCCAACTCTAGTTGGAGTAACCAACGATTTTGCACCCAACGCTAGT-TGAATAAA
28669310 -TCGACAAATGCATGCCCAACACTAGTCAGTTAAACT
65 CT-GACAAATGCATGCCCAACACTAGTCAGTTAAACT
28669346 GACGAAATAA
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
105 1 0.01
106 84 0.95
107 3 0.03
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (106 bp):
AATAAGTGAACCCAACTCTAGTTGGAGTAACCAACGATTTTGCACCCAACGCTAGTTGAATAAAC
TGACAAATGCATGCCCAACACTAGTCAGTTAAACTAAAAAC
Found at i:28674215 original size:43 final size:43
Alignment explanation
Indices: 28674157--28674254 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
28674147 GGCCTGCTTC
* *
28674157 CACGAGCTGTAGGTCGAGATGTTAGGCTACACGATGCTGCTCA
1 CACGAGCTGTGGGTCGAGATGTTAGGCTACACAATGCTGCTCA
* *
28674200 CACGAGTTGTGGGTCGAGATGTTAGGCTACACAATGCTGCTCC
1 CACGAGCTGTGGGTCGAGATGTTAGGCTACACAATGCTGCTCA
28674243 CACGAGCTGTGG
1 CACGAGCTGTGG
28674255 AGAATCCGCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (43 bp):
CACGAGCTGTGGGTCGAGATGTTAGGCTACACAATGCTGCTCA
Found at i:28674431 original size:132 final size:132
Alignment explanation
Indices: 28674194--28674473 Score: 436
Period size: 132 Copynumber: 2.1 Consensus size: 132
28674184 TACACGATGC
* * * * *
28674194 TGCTCACACGAGTTGTGGGTCGAGATGTTAGGCTACACAATGCTGCTCCCACGAGCTGTGGAGAA
1 TGCTCACACGAGCTGTGGGTCGAGACGTTAAGCTACACAATGCTGCTCACACGAGCTGTAGAGAA
* * *
28674259 TCCGCAATCAATGCAGGACCTCAGCCATCGGTAGGACATCTAAGACCAGCACCCATATAACTTGT
66 TCCGCAACCAATGCAGGACCTCAGCCATCGGTAGGACATCTAAGACCAACACCCATATAACCTGT
28674324 AA
131 AA
* * * *
28674326 TGCTCACATGAGCTGTGGGTCGAGACGTTAAGCTACACGATGCTGCTTACATGAGCTGTAGAGAA
1 TGCTCACACGAGCTGTGGGTCGAGACGTTAAGCTACACAATGCTGCTCACACGAGCTGTAGAGAA
*
28674391 TCCGCAACCAATGCAGGACCTCAGCCATCGTTAGGACATCTAAGACCAACACCCATATAACCTGT
66 TCCGCAACCAATGCAGGACCTCAGCCATCGGTAGGACATCTAAGACCAACACCCATATAACCTGT
28674456 AA
131 AA
28674458 TGCTCACACG-GCTGTG
1 TGCTCACACGAGCTGTG
28674474 AAATGGGCCT
Statistics
Matches: 134, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
131 6 0.04
132 128 0.96
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (132 bp):
TGCTCACACGAGCTGTGGGTCGAGACGTTAAGCTACACAATGCTGCTCACACGAGCTGTAGAGAA
TCCGCAACCAATGCAGGACCTCAGCCATCGGTAGGACATCTAAGACCAACACCCATATAACCTGT
AA
Found at i:28678800 original size:16 final size:16
Alignment explanation
Indices: 28678779--28678813 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28678769 CATAAAGGAT
*
28678779 AAAATAAACCAAAATA
1 AAAATAAAACAAAATA
28678795 AAAATAAAACAAAATA
1 AAAATAAAACAAAATA
28678811 AAA
1 AAA
28678814 GTCCATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (16 bp):
AAAATAAAACAAAATA
Found at i:28680903 original size:218 final size:216
Alignment explanation
Indices: 28680504--28681061 Score: 701
Period size: 218 Copynumber: 2.6 Consensus size: 216
28680494 TGTTTTTCTT
**
28680504 TTGTTTTAAAAAATTTAAGACAATGTTCTTTTATTTTAGGGAATTCGAAAAGTGGTGTCCTAACG
1 TTGTTTTAAAAAATAAAAG-CAATGTTCTTTTATTTTAGGGAATTCGAAAAGT-GTGTCCTAACG
** * * * * *
28680569 TACTCGGTACGATTTTTTTCGAACCTAAATAATCGAACATCCTATTTGAAATCTATAATCGCTAT
64 TGTTGGGTACGATTTTTTTCGAACCTAAATAATCGAATATCCTA-TTAAAATCGATAATCGCCAT
* * * *
28680634 TTTTACTTGTAAATTACATGGGTATATCAATCTTTTTGCAAAGCATTTTTAACGAAATAAAATGT
128 TTTTACTTGTAAATTACATGGATATATCAATCTTTTTACAAAACATTTTTAACAAAATAAAATGT
28680699 ATATC-GTTTTTTAA-AAGCATAAA
193 ATATCAGTTTTTTAATAA-CATAAA
28680722 TTGTTTTGAAAAAATAAAAGCAATGTTCTTTTATTTTAGGGAATTCGAAAAGTGATGTCCTAACG
1 TTGTTTT-AAAAAATAAAAGCAATGTTCTTTTATTTTAGGGAATTCGAAAAGTG-TGTCCTAACG
* *
28680787 TGTTGGGTACGATTTTTCTTCGAACTTAAATAATCGAATATCCTATGTAAAATCGATAATCTCCA
64 TGTTGGGTACGATTTTT-TTCGAACCTAAATAATCGAATATCCTAT-TAAAATCGATAATCGCCA
* * * *
28680852 TTTTTACTTGTAAATTACATGGATTTATCCATC-TTTTACAAAACGTTTTTAATAAAATAAAATG
127 TTTTTACTTGTAAATTACATGGATATATCAATCTTTTTACAAAACATTTTTAACAAAATAAAATG
* *
28680916 TATATCATTTTTTTAATTACATAAA
192 TATATCAGTTTTTTAATAACATAAA
* * * * * * * *
28680941 TTGTTTT-AAAAATAAAGGTAATGTTATTCTATTTTAAGGATTTCGAGAAATTGTGCCCTAACGT
1 TTGTTTTAAAAAATAAAAGCAATGTTCTTTTATTTTAGGGAATTCGA-AAAGTGTGTCCTAACGT
* * * *
28681005 GTTGGGTATGATTTTTTTTGAACCTAAATAATTGAGTATCCTACTTAAAATCGATAA
65 GTTGGGTACGATTTTTTTCGAACCTAAATAATCGAATATCCTA-TTAAAATCGATAA
28681062 ATGCTAAATG
Statistics
Matches: 298, Mismatches: 34, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
216 35 0.12
217 60 0.20
218 102 0.34
219 100 0.34
220 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (216 bp):
TTGTTTTAAAAAATAAAAGCAATGTTCTTTTATTTTAGGGAATTCGAAAAGTGTGTCCTAACGTG
TTGGGTACGATTTTTTTCGAACCTAAATAATCGAATATCCTATTAAAATCGATAATCGCCATTTT
TACTTGTAAATTACATGGATATATCAATCTTTTTACAAAACATTTTTAACAAAATAAAATGTATA
TCAGTTTTTTAATAACATAAA
Found at i:28686204 original size:45 final size:45
Alignment explanation
Indices: 28686140--28686414 Score: 345
Period size: 45 Copynumber: 6.1 Consensus size: 45
28686130 TACATCACCT
* *
28686140 CATCCAATCTTTTACCCCTAGTCAAGAGGGGCATATTAAAGCCAC
1 CATCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
* * * *
28686185 CATCCAATCTTTTACCCCTAAGTTAAGAGAGACAGATTGAAGTCAC
1 CATCCAATCTTTTACCCCT-AGTCAAGAGGGGCAGATTGAAGCCAC
* * * * *
28686231 TATCCAATCTTTTACCCCTAATTAAGAAGGGCAAATTGAAGCCAC
1 CATCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
* *
28686276 CATTCAATCTTTTACCCTTAGTCAAGAGGGGCAGATTGAAGCCAC
1 CATCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
* * * * *
28686321 TATCCAATCTTTTACCACT-GATCAAGAGGGACAAATTGAAACCAC
1 CATCCAATCTTTTACCCCTAG-TCAAGAGGGGCAGATTGAAGCCAC
* *
28686366 CATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCTAC
1 CATCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
28686411 CATC
1 CATC
28686415 TCACAGAAGT
Statistics
Matches: 193, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
44 1 0.01
45 154 0.80
46 38 0.20
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (45 bp):
CATCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
Found at i:28686413 original size:135 final size:136
Alignment explanation
Indices: 28686144--28686413 Score: 389
Period size: 135 Copynumber: 2.0 Consensus size: 136
28686134 TCACCTCATC
* * *
28686144 CAATCTTTTACCCCTAGTCAAGAGGGGCATATTAAAGCCACCATCCAATCTTTTACCCCTAAGTT
1 CAATCTTTTACCCCTAGTCAAGAGGGGCAGATTAAAGCCACCATCCAATCTTTTACCACTAAGTC
* ** * *
28686209 AAGAGAGACAGATTGAAGTCACTATCCAATCTTTTACCCCTAATTAAGAAGGGCAAATTGAAGCC
66 AAGAGAGACAAATTGAAACCACCATCCAATCTTTTACCCCTAATCAAGAAGGGCAAATTGAAGCC
28686274 ACCATT
131 ACCATT
* * * *
28686280 CAATCTTTTACCCTTAGTCAAGAGGGGCAGATTGAAGCCACTATCCAATCTTTTACCACTGA-TC
1 CAATCTTTTACCCCTAGTCAAGAGGGGCAGATTAAAGCCACCATCCAATCTTTTACCACTAAGTC
* * * *
28686344 AAGAGGGACAAATTGAAACCACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCT
66 AAGAGAGACAAATTGAAACCACCATCCAATCTTTTACCCCTAATCAAGAAGGGCAAATTGAAGCC
28686409 ACCAT
131 ACCAT
28686414 CTCACAGAAG
Statistics
Matches: 118, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
135 62 0.53
136 56 0.47
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (136 bp):
CAATCTTTTACCCCTAGTCAAGAGGGGCAGATTAAAGCCACCATCCAATCTTTTACCACTAAGTC
AAGAGAGACAAATTGAAACCACCATCCAATCTTTTACCCCTAATCAAGAAGGGCAAATTGAAGCC
ACCATT
Found at i:28686857 original size:17 final size:17
Alignment explanation
Indices: 28686835--28686870 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28686825 GCTCAAGGAT
* *
28686835 AAAATAAACCAAAATAA
1 AAAATAAAACAAAACAA
28686852 AAAATAAAACAAAACAA
1 AAAATAAAACAAAACAA
28686869 AA
1 AA
28686871 CAAAAGTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (17 bp):
AAAATAAAACAAAACAA
Found at i:28686869 original size:22 final size:22
Alignment explanation
Indices: 28686833--28686875 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28686823 TGGCTCAAGG
* * *
28686833 ATAAAATAAACCAAAATAAAAA
1 ATAAAACAAAACAAAACAAAAA
28686855 ATAAAACAAAACAAAACAAAA
1 ATAAAACAAAACAAAACAAAA
28686876 GTCCATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.09
Consensus pattern (22 bp):
ATAAAACAAAACAAAACAAAAA
Found at i:28688504 original size:26 final size:27
Alignment explanation
Indices: 28688474--28688527 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
28688464 AAATTGAGTG
28688474 TACATTTATTTAAGGTTTTTTTT-TTT
1 TACATTTATTTAAGGTTTTTTTTCTTT
28688500 TACATTTATTTAAGGTTTTTTTTCTTT
1 TACATTTATTTAAGGTTTTTTTTCTTT
28688527 T
1 T
28688528 GTAAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.19, C:0.06, G:0.07, T:0.69
Consensus pattern (27 bp):
TACATTTATTTAAGGTTTTTTTTCTTT
Found at i:28688837 original size:221 final size:217
Alignment explanation
Indices: 28688584--28689145 Score: 691
Period size: 221 Copynumber: 2.6 Consensus size: 217
28688574 ATTATTTTTT
** * * *
28688584 TTGTTTTAAAAAATTTAGGACAATGTTCTTTTATTTTAAAGATTTCGAAAAGTGGTTCCCTAACG
1 TTGTTTT-AAAAATAAAGG-CAATGTTCTTTTATTTTAAGGAATTCGAAAAGTGGTGCCCTAACG
* * * ** *
28688649 TGTTGAGTACGATTTTTCTCCGGACCTAAATAATCGAATATTCTATTTCAAATCGATAATTGCTA
64 TATTGAGTACGATTTTTCTCCGAACCTAAATAATCGAATATCCTATTTCAAATCGATAATCACCA
* * *
28688714 TTTTTACTTGTAAATTACATGGGTATATCAATCTTTTTGCAAAGCATTTTTAACGAAATAAAATG
129 TTTTTACTTGTAAATTACATGGATATATCAATC-TTTTGCAAAACATTTTTAACAAAATAAAATG
*
28688779 TATATC-TTTTTTTAAATGCATAAA
193 TATATCATTTTTTTAAATACATAAA
* *
28688803 TTGTTTTTAAAAA-AAATGAAAGCAATGTTCTTTTATTTTAGGGAATTCGAAAAGTGGTGCCTTA
1 TTG-TTTTAAAAATAAA-G---GCAATGTTCTTTTATTTTAAGGAATTCGAAAAGTGGTGCCCTA
* *
28688867 ACGTATTGGGTACGATTTTTCTTCGAACCTAAATAATCGAATATCCTATTTCAAATCGATAATCA
61 ACGTATTGAGTACGATTTTTCTCCGAACCTAAATAATCGAATATCCTATTTCAAATCGATAATCA
* * * * *
28688932 CCATTTTTACTTGTAAATTTCGTGGATTTATCCATCTTTTGCAAAACATTTTTAATAAAATAAAA
126 CCATTTTTACTTGTAAATTACATGGATATATCAATCTTTTGCAAAACATTTTTAACAAAATAAAA
28688997 TGTATATCATTTTTTTAAATACATAAA
191 TGTATATCATTTTTTTAAATACATAAA
* *
28689024 TTGTTTTAAAAATAAAGGCAATGTTCTTTTATTTTAAGGAATTCGAGAAA-TTGTGCCCTAGCGT
1 TTGTTTTAAAAATAAAGGCAATGTTCTTTTATTTTAAGGAATTCGA-AAAGTGGTGCCCTAACGT
* * * * ** * * *
28689088 ATTGGGTATGGTTTTTTATTTGAACCTAAATAATTGAGTATCCTACTT-AAATCGATAA
65 ATTGAGTA-CGATTTTTCTCCGAACCTAAATAATCGAATATCCTATTTCAAATCGATAA
28689146 ATGTTCAATG
Statistics
Matches: 299, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
217 57 0.19
218 36 0.12
219 9 0.03
220 48 0.16
221 148 0.49
222 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (217 bp):
TTGTTTTAAAAATAAAGGCAATGTTCTTTTATTTTAAGGAATTCGAAAAGTGGTGCCCTAACGTA
TTGAGTACGATTTTTCTCCGAACCTAAATAATCGAATATCCTATTTCAAATCGATAATCACCATT
TTTACTTGTAAATTACATGGATATATCAATCTTTTGCAAAACATTTTTAACAAAATAAAATGTAT
ATCATTTTTTTAAATACATAAA
Found at i:28689202 original size:109 final size:110
Alignment explanation
Indices: 28689042--28689249 Score: 276
Period size: 109 Copynumber: 1.9 Consensus size: 110
28689032 AAAATAAAGG
* * * * *
28689042 CAATGTTCTTTTATTTTAAGGAATTCGAGAAATTGTGCCCTAGCGTATTGGGTATG-GTTTTTTA
1 CAATGTTCTGTTATTTTAAGGAACTCGAAAAATCGTGCCCTAACGTATTGGGTATGTGTTTTTTA
**
28689106 TTTGAACCTAAATAATTGAGTATCCTACTTAAATCGATAAATGTT
66 TTTGAACCTAAATAATTGAACATCCTACTTAAATCGATAAATGTT
* *
28689151 CAATGTTCTGTTATTTT-AGGAGACTCGAAAAATCGTGCCCTAACGTGTTGGGTATGTTTTTTTT
1 CAATGTTCTGTTATTTTAAGGA-ACTCGAAAAATCGTGCCCTAACGTATTGGGTATG-TGTTTTT
* * *
28689215 TCTTTGAACCTAAGTAATTGAACATCCTATTTAAA
64 TATTTGAACCTAAATAATTGAACATCCTACTTAAA
28689250 ATCTTATTAG
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
108 4 0.05
109 45 0.54
111 35 0.42
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (110 bp):
CAATGTTCTGTTATTTTAAGGAACTCGAAAAATCGTGCCCTAACGTATTGGGTATGTGTTTTTTA
TTTGAACCTAAATAATTGAACATCCTACTTAAATCGATAAATGTT
Found at i:28689933 original size:158 final size:157
Alignment explanation
Indices: 28689552--28690156 Score: 958
Period size: 157 Copynumber: 3.8 Consensus size: 157
28689542 GGTTTCGACA
* ** * * * *
28689552 CTGCTCACACGAGCTGTGGAGAATCCGCAACCAATGCAGGACCTCAGCCATCGATAAGACATCTA
1 CTGCTCACACGAGCTGTAGAGAATCTACAACCAATGCAGGACCTCAGTCATAGGTAGGACATCTA
* * * * *
28689617 AGACCAGCACCCATATAACTTATAATGCTCACACGAGCTGTGAAATGGACCTGCTCACTCGAGCT
66 AGACCAGCACCCATATAACCTATAATACTCACACGAGCAGTGAAATGGGCCTGCTCACACGAGCT
* *
28689682 GCGTGTCGAGATGTTAGGCTAACGATG
131 GTGGGTCGAGATGTTAGGCTAACGATG
*
28689709 CTGCTCACACGAGCTGTAGAGAATCTACAACCAATGCAGGACCTCAATCATAGGTAGGACATCTA
1 CTGCTCACACGAGCTGTAGAGAATCTACAACCAATGCAGGACCTCAGTCATAGGTAGGACATCTA
** * * *
28689774 AGACCAGCAATCATATAACCTGTAATACTCACACGAGCAGTGAAATGGGCCTGCTCACACAAGTT
66 AGACCAGCACCCATATAACCTATAATACTCACACGAGCAGTGAAATGGGCCTGCTCACACGAGCT
28689839 GTGGGTCGAGATGTTAGGCTACACGATG
131 GTGGGTCGAGATGTTAGGCTA-ACGATG
*
28689867 CTGCTCACACGAGCTGTAAAGAATCTACAACCAATGCAGGACCTCAGTCATAGGTAGGACATCTA
1 CTGCTCACACGAGCTGTAGAGAATCTACAACCAATGCAGGACCTCAGTCATAGGTAGGACATCTA
* * *
28689932 AGACCAGCACCCATATAACCTTTAATACTCACACGACCAGTGAAATGGGCCTGCTCACTCGAGCT
66 AGACCAGCACCCATATAACCTATAATACTCACACGAGCAGTGAAATGGGCCTGCTCACACGAGCT
*
28689997 GTGGTTCGAGATGTTAGGCTAACGATG
131 GTGGGTCGAGATGTTAGGCTAACGATG
* *
28690024 CTACTCACACGAGCTGTAGAGAATCTACAACCAATGTAGGACCTCAGTCATAGGTAGGACATCTA
1 CTGCTCACACGAGCTGTAGAGAATCTACAACCAATGCAGGACCTCAGTCATAGGTAGGACATCTA
28690089 AGACCAGCACCCATATAACCTATAATACTCACACGAGCAGTGAAATGGGCCTGCTCACACGAGCT
66 AGACCAGCACCCATATAACCTATAATACTCACACGAGCAGTGAAATGGGCCTGCTCACACGAGCT
28690154 GTG
131 GTG
28690157 AAGAATCCGC
Statistics
Matches: 411, Mismatches: 36, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
157 264 0.64
158 147 0.36
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (157 bp):
CTGCTCACACGAGCTGTAGAGAATCTACAACCAATGCAGGACCTCAGTCATAGGTAGGACATCTA
AGACCAGCACCCATATAACCTATAATACTCACACGAGCAGTGAAATGGGCCTGCTCACACGAGCT
GTGGGTCGAGATGTTAGGCTAACGATG
Found at i:28690124 original size:315 final size:315
Alignment explanation
Indices: 28689552--28690148 Score: 991
Period size: 315 Copynumber: 1.9 Consensus size: 315
28689542 GGTTTCGACA
** * *
28689552 CTGCTCACACGAGCTGTGGAGAATCCGCAACCAATGCAGGACCTCAGCCATCGATAAGACATCTA
1 CTGCTCACACGAGCTGTAAAGAATCCACAACCAATGCAGGACCTCAGCCATAGATAAGACATCTA
* * *
28689617 AGACCAGCACCCATATAACTTATAATGCTCACACGAGCTGTGAAATGGACCTGCTCACTCGAGCT
66 AGACCAGCACCCATATAACTTATAATACTCACACGACCAGTGAAATGGACCTGCTCACTCGAGCT
*
28689682 GCGTGTCGAGATGTTAGGCTAACGATGCTGCTCACACGAGCTGTAGAGAATCTACAACCAATGCA
131 GCGTGTCGAGATGTTAGGCTAACGATGCTACTCACACGAGCTGTAGAGAATCTACAACCAATGCA
* *
28689747 GGACCTCAATCATAGGTAGGACATCTAAGACCAGCAATCATATAACCTGTAATACTCACACGAGC
196 GGACCTCAATCATAGGTAGGACATCTAAGACCAGCAACCATATAACCTATAATACTCACACGAGC
28689812 AGTGAAATGGGCCTGCTCACACAAGTTGTGGGTCGAGATGTTAGGCTACACGATG
261 AGTGAAATGGGCCTGCTCACACAAGTTGTGGGTCGAGATGTTAGGCTACACGATG
* * * *
28689867 CTGCTCACACGAGCTGTAAAGAATCTACAACCAATGCAGGACCTCAGTCATAGGTAGGACATCTA
1 CTGCTCACACGAGCTGTAAAGAATCCACAACCAATGCAGGACCTCAGCCATAGATAAGACATCTA
*
28689932 AGACCAGCACCCATATAACCTT-TAATACTCACACGACCAGTGAAATGGGCCTGCTCACTCGAGC
66 AGACCAGCACCCATATAA-CTTATAATACTCACACGACCAGTGAAATGGACCTGCTCACTCGAGC
*
28689996 TGTG-GTTCGAGATGTTAGGCTAACGATGCTACTCACACGAGCTGTAGAGAATCTACAACCAATG
130 TGCGTG-TCGAGATGTTAGGCTAACGATGCTACTCACACGAGCTGTAGAGAATCTACAACCAATG
* * *
28690060 TAGGACCTCAGTCATAGGTAGGACATCTAAGACCAGCACCCATATAACCTATAATACTCACACGA
194 CAGGACCTCAATCATAGGTAGGACATCTAAGACCAGCAACCATATAACCTATAATACTCACACGA
28690125 GCAGTGAAATGGGCCTGCTCACAC
259 GCAGTGAAATGGGCCTGCTCACAC
28690149 GAGCTGTGAA
Statistics
Matches: 261, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
314 1 0.00
315 257 0.98
316 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (315 bp):
CTGCTCACACGAGCTGTAAAGAATCCACAACCAATGCAGGACCTCAGCCATAGATAAGACATCTA
AGACCAGCACCCATATAACTTATAATACTCACACGACCAGTGAAATGGACCTGCTCACTCGAGCT
GCGTGTCGAGATGTTAGGCTAACGATGCTACTCACACGAGCTGTAGAGAATCTACAACCAATGCA
GGACCTCAATCATAGGTAGGACATCTAAGACCAGCAACCATATAACCTATAATACTCACACGAGC
AGTGAAATGGGCCTGCTCACACAAGTTGTGGGTCGAGATGTTAGGCTACACGATG
Found at i:28694865 original size:29 final size:29
Alignment explanation
Indices: 28694796--28694906 Score: 96
Period size: 31 Copynumber: 3.7 Consensus size: 29
28694786 ATCTCAACAT
* * *
28694796 TATACATGAAGTTTGATTTAATGTGTAATTG
1 TATACATGAACTTTAATTT-A-GTGCAATTG
*
28694827 TATACATGAACTTTAATTTAGTGCAATTA
1 TATACATGAACTTTAATTTAGTGCAATTG
* * * * *
28694856 TATACGTGAAATTCTAATTGTGGTTCAAATG
1 TATACATGAACTT-TAATT-TAGTGCAATTG
28694887 TATACATGAAACTTTAATTT
1 TATACATG-AACTTTAATTT
28694907 TGATTTAATC
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
29 18 0.28
30 7 0.11
31 36 0.55
32 4 0.06
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.42
Consensus pattern (29 bp):
TATACATGAACTTTAATTTAGTGCAATTG
Found at i:28695266 original size:3 final size:3
Alignment explanation
Indices: 28695258--28695285 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28695248 TACATTAGAA
28695258 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28695286 TGAATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:28696202 original size:12 final size:12
Alignment explanation
Indices: 28696185--28696209 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28696175 ATTTTCTTTA
28696185 AATAAAAATATC
1 AATAAAAATATC
28696197 AATAAAAATATC
1 AATAAAAATATC
28696209 A
1 A
28696210 TGTAATGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAAAATATC
Found at i:28710586 original size:23 final size:22
Alignment explanation
Indices: 28710551--28710596 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
28710541 TTTGATAATA
*
28710551 TGTTTTGATATAACAAATTAAAG
1 TGTTTTGAAATAA-AAATTAAAG
* *
28710574 TGTTTTTAAATAAAAGTTAAAG
1 TGTTTTGAAATAAAAATTAAAG
28710596 T
1 T
28710597 TGAACATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.41
Consensus pattern (22 bp):
TGTTTTGAAATAAAAATTAAAG
Found at i:28710844 original size:21 final size:21
Alignment explanation
Indices: 28710818--28710880 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
28710808 TCAAACAAAC
28710818 ACAAAAAGTATCGACACCTTT
1 ACAAAAAGTATCGACACCTTT
* *
28710839 ACAAAAAGTATCAACACCTTC
1 ACAAAAAGTATCGACACCTTT
*
28710860 ACAAAAAGTATCGATACCTTT
1 ACAAAAAGTATCGACACCTTT
28710881 TATCAAGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (21 bp):
ACAAAAAGTATCGACACCTTT
Found at i:28713214 original size:19 final size:19
Alignment explanation
Indices: 28713190--28713238 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
28713180 GAAATTGGGA
*
28713190 TTTCTTTGTTTTCATTGAT
1 TTTCTTTGTTTTAATTGAT
* *
28713209 TTTCTTTATTTTAATTGGT
1 TTTCTTTGTTTTAATTGAT
*
28713228 TTTCATTGTTT
1 TTTCTTTGTTT
28713239 CACTATTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.12, C:0.08, G:0.10, T:0.69
Consensus pattern (19 bp):
TTTCTTTGTTTTAATTGAT
Found at i:28722774 original size:4 final size:4
Alignment explanation
Indices: 28722765--28722802 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
28722755 TTTATAAATG
28722765 TAAA TAAA TAAA TAAA TAAA TAAA -ATAA TAAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TA-AA T-AAA TAAA T
28722803 TTTATTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 1 0.03
4 26 0.84
5 3 0.10
6 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:28722866 original size:25 final size:25
Alignment explanation
Indices: 28722838--28722885 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
28722828 TACAAACAAG
28722838 CCCAAATACACCCACAAGCCCAATA
1 CCCAAATACACCCACAAGCCCAATA
* *
28722863 CCCAAATACCCCCACTAGCCCAA
1 CCCAAATACACCCACAAGCCCAA
28722886 ATTTTACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.48, G:0.04, T:0.08
Consensus pattern (25 bp):
CCCAAATACACCCACAAGCCCAATA
Found at i:28723998 original size:30 final size:30
Alignment explanation
Indices: 28723962--28724114 Score: 179
Period size: 30 Copynumber: 5.2 Consensus size: 30
28723952 ACTTTGTTTT
* * * * *
28723962 AAAATTATTTTTTGATCCTAAAACTATCCA
1 AAAATTATGTTTTGACCCTTAAACTTTCTA
*
28723992 AAAATTATGTTTTGACCCTTAAGCTTTCTA
1 AAAATTATGTTTTGACCCTTAAACTTTCTA
* *
28724022 AAAA-T-TGTTTT-A-CCTCCAAACTATCTA
1 AAAATTATGTTTTGACCCT-TAAACTTTCTA
*
28724049 AAAATTATGTTTTGACCCCTAAACTTTCTA
1 AAAATTATGTTTTGACCCTTAAACTTTCTA
*
28724079 AAAATTATGATTTGACCCTTAAACTTTCTA
1 AAAATTATGTTTTGACCCTTAAACTTTCTA
28724109 AAAATT
1 AAAATT
28724115 CAAATTTGAC
Statistics
Matches: 104, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
26 3 0.03
27 13 0.12
28 7 0.07
29 7 0.07
30 72 0.69
31 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.40
Consensus pattern (30 bp):
AAAATTATGTTTTGACCCTTAAACTTTCTA
Found at i:28724133 original size:29 final size:30
Alignment explanation
Indices: 28724059--28724185 Score: 163
Period size: 30 Copynumber: 4.3 Consensus size: 30
28724049 AAAATTATGT
*
28724059 TTTGACCCCTAAACTTTCTAAAAATT-ATGA
1 TTTGACCCCTAAACTTTCTAAAAATTCA-AA
*
28724089 TTTGACCCTTAAACTTTCTAAAAATTCAAA
1 TTTGACCCCTAAACTTTCTAAAAATTCAAA
28724119 TTTGACCCCT-AACTTT-TCAAAAATTCAAA
1 TTTGACCCCTAAACTTTCT-AAAAATTCAAA
* *
28724148 TTT-AACCCTCAAACTTTCCAAAAATTCAAA
1 TTTGACCCCT-AAACTTTCTAAAAATTCAAA
28724178 TTTGACCC
1 TTTGACCC
28724186 GATTTAAATG
Statistics
Matches: 85, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
28 6 0.07
29 20 0.24
30 55 0.65
31 4 0.05
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.35
Consensus pattern (30 bp):
TTTGACCCCTAAACTTTCTAAAAATTCAAA
Found at i:28724162 original size:59 final size:60
Alignment explanation
Indices: 28724059--28724185 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 60
28724049 AAAATTATGT
* * * *
28724059 TTTGACCCCTAAACTTTCTAAAAATTATGATTTGACCCTTAAACTTTCTAAAAATTCAAA
1 TTTGACCCCTAAACTTTCTAAAAATTATAATTTAACCCTCAAACTTTCCAAAAATTCAAA
28724119 TTTGACCCCT-AACTTT-TCAAAAATTCA-AATTTAACCCTCAAACTTTCCAAAAATTCAAA
1 TTTGACCCCTAAACTTTCT-AAAAATT-ATAATTTAACCCTCAAACTTTCCAAAAATTCAAA
28724178 TTTGACCC
1 TTTGACCC
28724186 GATTTAAATG
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
58 1 0.02
59 49 0.80
60 11 0.18
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.35
Consensus pattern (60 bp):
TTTGACCCCTAAACTTTCTAAAAATTATAATTTAACCCTCAAACTTTCCAAAAATTCAAA
Found at i:28730050 original size:39 final size:37
Alignment explanation
Indices: 28729984--28730075 Score: 89
Period size: 39 Copynumber: 2.4 Consensus size: 37
28729974 CCAGAATGGC
* *
28729984 ACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGT-GA
1 ACCCAGTGTCTCATCGGATAGTCCGAAG---TAAAGTGGA
* *
28730023 ACCCAGTGTCTCATCGGCCTAG-CCGAAGTAAAGTGGT
1 ACCCAGTGTCTCATCGG-ATAGTCCGAAGTAAAGTGGA
*
28730060 ACCCAGTATCTCATCG
1 ACCCAGTGTCTCATCG
28730076 AATCTATCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
36 6 0.13
37 16 0.35
39 21 0.46
40 3 0.07
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (37 bp):
ACCCAGTGTCTCATCGGATAGTCCGAAGTAAAGTGGA
Found at i:28742879 original size:86 final size:86
Alignment explanation
Indices: 28742734--28742906 Score: 292
Period size: 86 Copynumber: 2.0 Consensus size: 86
28742724 CGACATACCA
28742734 AGTTAACTATGACACTATGCCCCAAAGGGTTCGTGACTAGCATATCAAATTCAGTCGACTCAACG
1 AGTTAACTATGACACTATGCCCCAAAGGGTTCGTGACTAGCATATCAAATTCAGTCGACTCAACG
* *
28742799 ACCAATTTCTTATTAGTGGCT
66 AACAATTTCTTATCAGTGGCT
* * *
28742820 AGTTAATTATGACACTTTGCCCCAAAGGGTTCGTGACTTGCATATCAAATTCAGTCGACTCAACG
1 AGTTAACTATGACACTATGCCCCAAAGGGTTCGTGACTAGCATATCAAATTCAGTCGACTCAACG
*
28742885 AATAATTTCTTATCAGTGGCT
66 AACAATTTCTTATCAGTGGCT
28742906 A
1 A
28742907 AAGCAGTGCA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (86 bp):
AGTTAACTATGACACTATGCCCCAAAGGGTTCGTGACTAGCATATCAAATTCAGTCGACTCAACG
AACAATTTCTTATCAGTGGCT
Found at i:28749024 original size:30 final size:30
Alignment explanation
Indices: 28748980--28749133 Score: 125
Period size: 30 Copynumber: 5.2 Consensus size: 30
28748970 ACTTTGTTTT
* *
28748980 AAAATT-TTTTTTGACCCCCAAA-TTGTCTA
1 AAAATTATGTTTTGACCCCCAAACTT-TCCA
**
28749009 AAAATTATGTTTTGACCCTTAAACTTTCCA
1 AAAATTATGTTTTGACCCCCAAACTTTCCA
* * * ** *
28749039 AAAATTATTTTTTTACACTTAAACTGTCC-
1 AAAATTATGTTTTGACCCCCAAACTTTCCA
*
28749068 AAAATTATGTGTTGACCCCCAAACTTTCCA
1 AAAATTATGTTTTGACCCCCAAACTTTCCA
* * * ***
28749098 AAAATTATGATTTAATCGTTAAACTTTCCA
1 AAAATTATGTTTTGACCCCCAAACTTTCCA
28749128 AAAATT
1 AAAATT
28749134 CAAATTTGAC
Statistics
Matches: 100, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
29 28 0.28
30 70 0.70
31 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (30 bp):
AAAATTATGTTTTGACCCCCAAACTTTCCA
Found at i:28749041 original size:29 final size:30
Alignment explanation
Indices: 28749008--28749133 Score: 146
Period size: 30 Copynumber: 4.2 Consensus size: 30
28748998 CAAATTGTCT
28749008 AAAAATTATGTTTTGACCCTTAAACTTTCC
1 AAAAATTATGTTTTGACCCTTAAACTTTCC
* * * *
28749038 AAAAATTATTTTTTTACACTTAAACTGTCC
1 AAAAATTATGTTTTGACCCTTAAACTTTCC
* **
28749068 -AAAATTATGTGTTGACCCCCAAACTTTCC
1 AAAAATTATGTTTTGACCCTTAAACTTTCC
* * * *
28749097 AAAAATTATGATTTAATCGTTAAACTTTCC
1 AAAAATTATGTTTTGACCCTTAAACTTTCC
28749127 AAAAATT
1 AAAAATT
28749134 CAAATTTGAC
Statistics
Matches: 77, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
29 22 0.29
30 55 0.71
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.38
Consensus pattern (30 bp):
AAAAATTATGTTTTGACCCTTAAACTTTCC
Found at i:28749120 original size:59 final size:59
Alignment explanation
Indices: 28749009--28749130 Score: 158
Period size: 59 Copynumber: 2.1 Consensus size: 59
28748999 AAATTGTCTA
* ** **
28749009 AAAATTATGTTTTGACCCTTAAACTTTCCAAAAATTATTTTTTTACACTTAAACTGTCC
1 AAAATTATGTGTTGACCCCCAAACTTTCCAAAAATTATTGATTTACACTTAAACTGTCC
*
28749068 AAAATTATGTGTTGACCCCCAAACTTTCCAAAAATTA-TGATTTA-ATCGTTAAACTTTCC
1 AAAATTATGTGTTGACCCCCAAACTTTCCAAAAATTATTGATTTACA-C-TTAAACTGTCC
28749127 AAAA
1 AAAA
28749131 ATTCAAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
57 1 0.02
58 6 0.11
59 48 0.87
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.38
Consensus pattern (59 bp):
AAAATTATGTGTTGACCCCCAAACTTTCCAAAAATTATTGATTTACACTTAAACTGTCC
Done.