Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008360.1 Hibiscus syriacus cultivar Beakdansim tig00111099_pilon, whole genome shotgun sequence
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: 1563863
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:283004 original size:20 final size:20
Alignment explanation
Indices: 282979--283069 Score: 121
Period size: 20 Copynumber: 4.5 Consensus size: 20
282969 TTGAAATTCA
*
282979 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
282999 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
* **
283019 GAGTTGCGATTATGT-ATTATC
1 GCGTTGCGA-TA-GTCAGAATC
283040 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
283060 GCGTTGCGAT
1 GCGTTGCGAT
283070 TTACATATTC
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.70
21 14 0.23
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.29
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:283146 original size:20 final size:19
Alignment explanation
Indices: 283123--283168 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
283113 GGAAACTGAT
* *
283123 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
283143 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
283162 TTGCGAT
1 TTGCGAT
283169 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:283158 original size:19 final size:19
Alignment explanation
Indices: 283134--283170 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
283124 TGCGATACTG
*
283134 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
283153 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
283171 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:286178 original size:21 final size:22
Alignment explanation
Indices: 286125--286185 Score: 106
Period size: 23 Copynumber: 2.8 Consensus size: 22
286115 GGATTTTGAG
286125 GGAGGAGTATCGATACTGCCAA
1 GGAGGAGTATCGATACTGCCAA
286147 GGAGAGAGTATCGATACTGCCAA
1 GGAG-GAGTATCGATACTGCCAA
286170 GG-GGAGTATCGATACT
1 GGAGGAGTATCGATACT
286186 ACCCCTGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
21 13 0.34
22 5 0.13
23 20 0.53
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (22 bp):
GGAGGAGTATCGATACTGCCAA
Found at i:287700 original size:17 final size:17
Alignment explanation
Indices: 287678--287722 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
287668 TATCTTCAAC
287678 ATGCTTATGTTTATGAA
1 ATGCTTATGTTTATGAA
287695 ATGCTTATGTTTATGAA
1 ATGCTTATGTTTATGAA
*
287712 ATTCTTATGTT
1 ATGCTTATGTT
287723 GCTCTAGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.51
Consensus pattern (17 bp):
ATGCTTATGTTTATGAA
Found at i:290703 original size:4 final size:4
Alignment explanation
Indices: 290694--290779 Score: 52
Period size: 4 Copynumber: 21.2 Consensus size: 4
290684 TAGAGGGAAA
* * * * * *
290694 AAAT AAAT AAAT GAAAA AAAT GAAG AATAA AAAT AAGT AAAA AAAT -AA-
1 AAAT AAAT AAAT -AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT
*
290742 AAAT AAA- AGAAA AAAT AAAT AAAT AAAT AAAT GAAAT A
1 AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT -AAAT A
290780 TTAAATATAT
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
3 5 0.08
4 47 0.75
5 11 0.17
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:290726 original size:30 final size:29
Alignment explanation
Indices: 290690--290777 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
290680 GTGTTAGAGG
290690 GAAAAAATAAATAAATGAAAAAAATGAAGAA
1 GAAAAAATAAATAAAT-AAAAAAATGAA-AA
* * *
290721 -TAAAAATAAGTAAAAAAATAAAAAT-AAAA
1 GAAAAAATAAAT-AAATAA-AAAAATGAAAA
*
290750 GAAAAAATAAATAAATAAATAAATGAAA
1 GAAAAAATAAATAAATAAAAAAATGAAA
290778 TATTAAATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
28 5 0.11
29 10 0.22
30 22 0.48
31 9 0.20
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (29 bp):
GAAAAAATAAATAAATAAAAAAATGAAAA
Found at i:290742 original size:18 final size:18
Alignment explanation
Indices: 290719--290760 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
290709 AAAAATGAAG
*
290719 AATAAAAATAAGTA-AAAA
1 AATAAAAATAA-AAGAAAA
290737 AATAAAAATAAAAGAAAA
1 AATAAAAATAAAAGAAAA
290755 AATAAA
1 AATAAA
290761 TAAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (18 bp):
AATAAAAATAAAAGAAAA
Found at i:290791 original size:2 final size:2
Alignment explanation
Indices: 290784--290819 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
290774 GAAATATTAA
290784 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
290820 GAAAAATAGA
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:290937 original size:29 final size:29
Alignment explanation
Indices: 290872--290937 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
290862 ATGAAAATAT
*
290872 AATAT-AATATAAACAAATAAAAAAATCA
1 AATATAAAAATAAACAAATAAAAAAATCA
* * * * *
290900 AAAACAAAAATAAATAAATATATAAATCA
1 AATATAAAAATAAACAAATAAAAAAATCA
290929 AATATAAAA
1 AATATAAAA
290938 GTATACATAT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
28 3 0.10
29 26 0.90
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (29 bp):
AATATAAAAATAAACAAATAAAAAAATCA
Found at i:291680 original size:37 final size:37
Alignment explanation
Indices: 291639--291743 Score: 133
Period size: 37 Copynumber: 2.8 Consensus size: 37
291629 GTGCTTGTGG
* * *
291639 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTT-T
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGTAGAAATTCT
*
291676 ATCCTATTTTAAGGAGTTTGAATCCTAGCA-AAATTCT
1 ATCCTATTTT-AGGAGTTTGAATCCTAGTAGAAATTCT
291713 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTA-TTTTAGGAGTTTGAATCCTAGTAG
291744 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
36 7 0.12
37 48 0.81
38 4 0.07
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGTAGAAATTCT
Found at i:292580 original size:106 final size:106
Alignment explanation
Indices: 292395--293903 Score: 2380
Period size: 106 Copynumber: 14.3 Consensus size: 106
292385 TGCGGGTAGC
* * * *
292395 CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGG-GTCCAAGATCCTTCGCTGAGAAGTTGAAA
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
*
292459 TTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCATCGGT
65 TTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
* *
292501 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACGCTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
* *
292566 TGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGTGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
* *
292607 CCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
* * * *
292672 TGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGTGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
*
292713 CCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
292778 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
292819 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
* * *
292884 TGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGTGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
*
292925 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
* *
292990 TGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
293031 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
*
293096 TGGCTCTGAAATTGGGAAGTTATTTATTGACAACCAGCGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
* * *
293137 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
* *
293202 TTGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
* ** *
293243 CCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTGGAGTCCAATATCCTTCATTGTAAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
* *
293308 TGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
293349 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
*
293414 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAACGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
* * * *
293455 CCCTTCGTCGTGATGTTGAATTTGCGTTGTCTTGAGTCCAATATCCTTCACTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
*
293520 TGG----G--A-----AA-TTGTTTATTGACAACCAACGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
* * *
293549 CCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAG
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
* * *
293614 TGGCTCTGAAATTGAGAAGTCGTTTATTGACAACCAGTGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
*
293655 CCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
* * *
293720 TGGCTCTGAAATTGAGAAATTATTTATTGACAACCAGCGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
* * *
293761 CCCTTCGTCGTGAAATTGAACTTGCGTTGTCTGGAGTCCAATATCCTACGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
* *
293826 TGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGT
66 TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
* * *
293867 CCCTTC-ACTGTGAAGTTGAACTTGTGTTGTCTTGAGT
1 CCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTGGAGT
293904 GGCACGATAT
Statistics
Matches: 1300, Mismatches: 89, Indels: 28
0.92 0.06 0.02
Matches are distributed among these distances:
94 83 0.06
95 2 0.00
98 1 0.00
100 2 0.00
102 1 0.00
105 5 0.00
106 1206 0.93
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
TGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
Found at i:294732 original size:22 final size:22
Alignment explanation
Indices: 294706--294826 Score: 224
Period size: 22 Copynumber: 5.5 Consensus size: 22
294696 TTATGTTTGG
294706 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
294728 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
294750 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
294772 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
294794 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
294816 TCAACGGTTTG
1 TCAAAGGTTTG
294827 ATGGGGTAGC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 96 1.00
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:295525 original size:172 final size:173
Alignment explanation
Indices: 295222--295562 Score: 571
Period size: 172 Copynumber: 2.0 Consensus size: 173
295212 TAAATAGGCC
*
295222 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTG
*
295287 CTCAAAATGTCTCTCTCTTGATGCTCTATAATCTTCGAGTGAAGTGATTCAGTGATTCGAGAATG
64 CTCAAAATGTCTCTCTCTTGATGCTCTATAATCTTCGAGTGAAGTGATTCAATGATTCGAGAATG
295352 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGTCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGTCATTT
*
295397 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGTCTTC-A-A-TCCTGCT
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
* *
295459 CAAAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCGGGAATG
66 CAAAATG--TCTCTCTCTTGATGCTCTATAATCTTCGAGTGAAGTGATTCAATGATTCGAGAATG
*
295524 ATTGTGCTTGATCAATCTTATAGTTTGAAGCTTGATGTG
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTG
295563 CCAATTTTTT
Statistics
Matches: 158, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
170 14 0.09
172 92 0.58
174 1 0.01
175 51 0.32
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (173 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTGATGCTCTATAATCTTCGAGTGAAGTGATTCAATGATTCGAGAATGAT
TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGTCATTT
Found at i:295673 original size:16 final size:16
Alignment explanation
Indices: 295641--295680 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
295631 CTCTTTTTTC
295641 TTTGTT-TTTTGCTTT
1 TTTGTTCTTTTGCTTT
295656 TTTGCTTCTTTT-CTTT
1 TTTG-TTCTTTTGCTTT
295672 TTTGTTCTT
1 TTTGTTCTT
295681 GATTGGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.39
16 10 0.43
17 4 0.17
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (16 bp):
TTTGTTCTTTTGCTTT
Found at i:300280 original size:16 final size:15
Alignment explanation
Indices: 300210--300299 Score: 76
Period size: 16 Copynumber: 5.9 Consensus size: 15
300200 TGTTAGAGGG
* *
300210 AAAAATGAATAAAAG
1 AAAAATAAATAAAAA
*
300225 AAAAAT-AATGAAGAAT
1 AAAAATAAAT-AA-AAA
*
300241 AAAAATAAGTAAAAA
1 AAAAATAAATAAAAA
*
300256 AATAA-AAATAAAAGA
1 AAAAATAAATAAAA-A
300271 AAAAATAAATAAATAA
1 AAAAATAAATAAA-AA
*
300287 ATAAATAAATAAA
1 AAAAATAAATAAA
300300 TATTAATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.16
15 19 0.31
16 30 0.48
17 3 0.05
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAAATAAATAAAAA
Found at i:300282 original size:4 final size:4
Alignment explanation
Indices: 300243--300301 Score: 61
Period size: 4 Copynumber: 15.2 Consensus size: 4
300233 TGAAGAATAA
* * *
300243 AAAT AAGT AAAA AAAT -AA- AAAT AAA- AGAAA AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT
300289 AAAT AAAT AAAT A
1 AAAT AAAT AAAT A
300302 TTAATATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
3 5 0.11
4 40 0.87
5 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:315053 original size:31 final size:31
Alignment explanation
Indices: 315017--315093 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
315007 GTAAACACCA
* *
315017 TTTTTCAACACCAACACCTACCA-CCCTATTT
1 TTTTTCAACACCAACACCCACCATCAC-ATTT
315048 TTTTTCAACACCAACACCCACCATCACATTT
1 TTTTTCAACACCAACACCCACCATCACATTT
315079 TTTTTCAACACCAAC
1 TTTTTCAACACCAAC
315094 CTCATCATCC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 41 0.95
32 2 0.05
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (31 bp):
TTTTTCAACACCAACACCCACCATCACATTT
Found at i:328904 original size:133 final size:133
Alignment explanation
Indices: 328667--329314 Score: 994
Period size: 133 Copynumber: 4.8 Consensus size: 133
328657 GATTCTATCA
* * * *
328667 CAGAAGGAGGTAGATCAGCATCGACTTTT-GCTCGATTCTATCACAGAATGAGGTAGATCAGCAT
1 CAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAATGAGGTAGATCAGCAT
* * *
328731 CGACATCTCGTTCGATTCCATCACAAAAAGAGGTGGATCGACATTTTTATTTTCACTCAAATCCA
66 CGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCA
328796 TCG
131 TCG
*
328799 CAGAAGGAGTTGGATCAACGTCAACTTTTAGCTCGATTCTATCACAGAATGAGGTAGATCAGCAT
1 CAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAATGAGGTAGATCAGCAT
*
328864 CAACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGAC-TTTTTATTTTCGCTCAAATCCA
66 CGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCA
328928 TCG
131 TCG
* * *
328931 CAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGCAT
1 CAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAATGAGGTAGATCAGCAT
*
328996 CGACATCTCGTTCGATTCCATCACAGAAAGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCA
66 CGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCA
329061 TCG
131 TCG
*
329064 CAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAATGAGAAGGAGGTATAT
1 CAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAT------GAGGTAGAT
* * * *
329129 CAGCATCAACATCTCGTTCGATTCCATCACAAAAGGAGGTGAATCGACATTTTTATTTTTGCTCA
60 CAGCATCGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCA
329194 AATCCATCG
125 AATCCATCG
* * * ** *
329203 TAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAAAAG
1 CAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAATGAGGTAGATCAGCAT
* *
329268 CGACATCTCGTTCGATTCCATCATAGAAGGAGATGGATCGACATTTT
66 CGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTT
329315 AAATCCATTA
Statistics
Matches: 472, Mismatches: 36, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
132 149 0.32
133 200 0.42
139 123 0.26
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (133 bp):
CAGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAATGAGGTAGATCAGCAT
CGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCA
TCG
Found at i:329252 original size:44 final size:44
Alignment explanation
Indices: 328643--329306 Score: 374
Period size: 44 Copynumber: 14.9 Consensus size: 44
328633 AAGAGATTGT
* * *
328643 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCA
1 TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAGCA
* * * *
328687 TCGACTTTT-GCTCGATTCTATCACAGAATGAGGTAGATCAGCA
1 TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAGCA
* * * * * *
328730 TCGACATCTCGTTCGATTCCATCACAAAAAGAGGTGGATC-GACA
1 TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG-CA
** * * * * * * *
328774 TTTTTA-TTTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAACG
1 --TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAGCA
* * * *
328819 TCAACTTTTAGCTCGATTCTATCACAGAATGAGGTAGATCAGCA
1 TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAGCA
* * * *
328863 TCAACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATC-GACTT
1 TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG-C-A
** * * * * *
328908 TTTA-TTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCG
1 TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAGCA
* * * *
328951 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGCA
1 TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAGCA
* * * * *
328995 TCGACATCTCGTTCGATTCCATCACAGAAAGAGGTGGATC-GACA
1 TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG-CA
** * * * * *
329039 TTTTTA-TTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCG
1 --TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAGCA
* * *
329084 TCAACTTTTAGCTCGATTCTATCACAGAATGAGAAGGAGGTATATCAGCA
1 TCAACTTTTCGCTCGATTCCATCACAGAA-G-G-AGGTGG---ATCAGCA
* * * * *
329134 TCAACATCTCGTTCGATTCCATCACAAAAGGAGGTGAATC-GACA
1 TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAG-CA
** * * * ** * *
329178 TTTTTA-TTTTTGCTCAAATCCATCGTAGAAGGAGTTGGATCAGCG
1 --TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAGCA
* * * **
329223 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAAAA
1 TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAGCA
* * * * * * *
329267 GCGACATCTCGTTCGATTCCATCATAGAAGGAGATGGATC
1 TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATC
329307 GACATTTTAA
Statistics
Matches: 456, Mismatches: 138, Indels: 52
0.71 0.21 0.08
Matches are distributed among these distances:
43 52 0.11
44 273 0.60
45 83 0.18
46 9 0.02
47 8 0.02
48 1 0.00
49 1 0.00
50 29 0.06
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
TCAACTTTTCGCTCGATTCCATCACAGAAGGAGGTGGATCAGCA
Found at i:329650 original size:29 final size:31
Alignment explanation
Indices: 329571--329655 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
329561 GTAAACACCA
* * *
329571 TTTTTCAACACCAACACCTACCACCCCATTT
1 TTTTTCAACACCAACACCCACCATCACATTT
329602 TTTTTCAACACCAACACCCACCATCACA-TT
1 TTTTTCAACACCAACACCCACCATCACATTT
* *
329632 TTTTTCAAAACCAAC-CCCATCATC
1 TTTTTCAACACCAACACCCACCATC
329656 CCTTGTTCCC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 8 0.16
30 16 0.33
31 25 0.51
ACGTcount: A:0.32, C:0.40, G:0.00, T:0.28
Consensus pattern (31 bp):
TTTTTCAACACCAACACCCACCATCACATTT
Found at i:330793 original size:15 final size:15
Alignment explanation
Indices: 330775--330804 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
330765 TTTATTTTAC
330775 TTATATTATTATATA
1 TTATATTATTATATA
*
330790 TTATTTTATTATATA
1 TTATATTATTATATA
330805 CATAATATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATATTATTATATA
Found at i:332273 original size:31 final size:32
Alignment explanation
Indices: 332238--332305 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
332228 AATCAATTCG
* *
332238 GGTCGGGTC-AAATTGGATCCGTTGATTTTCA
1 GGTCGGGTCAAAATCGGATCCGTTGATGTTCA
* *
332269 GGTCGGGTCAAAATCGGATCGGTTGGTGTTCA
1 GGTCGGGTCAAAATCGGATCCGTTGATGTTCA
332301 GGTCG
1 GGTCG
332306 ATTAATCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 9 0.28
32 23 0.72
ACGTcount: A:0.18, C:0.16, G:0.35, T:0.31
Consensus pattern (32 bp):
GGTCGGGTCAAAATCGGATCCGTTGATGTTCA
Found at i:332487 original size:46 final size:46
Alignment explanation
Indices: 332353--332498 Score: 193
Period size: 46 Copynumber: 3.2 Consensus size: 46
332343 ATCGGTTCGA
* * *
332353 TTGGTTTTGGTTCAGGTCAAGCTTTAGATTTTCGGGACAATTCGGG
1 TTGGTTTTGGTTCAGATCAACCTTTAGATTTTCGGGTCAATTCGGG
* * * *
332399 TTTGTTTCGGTTCGGATCAACCTGTAGATTTTCGGGTCAATTCGGG
1 TTGGTTTTGGTTCAGATCAACCTTTAGATTTTCGGGTCAATTCGGG
* * *
332445 TTGGTTTTGGTTCAGATCAACCTTTAGATTTTCGAGTTAATTCTGG
1 TTGGTTTTGGTTCAGATCAACCTTTAGATTTTCGGGTCAATTCGGG
*
332491 TTGTTTTT
1 TTGGTTTT
332499 ATTGAAGTCA
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.44
Consensus pattern (46 bp):
TTGGTTTTGGTTCAGATCAACCTTTAGATTTTCGGGTCAATTCGGG
Found at i:333055 original size:16 final size:15
Alignment explanation
Indices: 333015--333055 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
333005 TTAAGTTCGG
333015 ATTGATTTCGGTTCA
1 ATTGATTTCGGTTCA
*
333030 AGTTGCTTTCGGTTCA
1 A-TTGATTTCGGTTCA
333046 TATTGATTTC
1 -ATTGATTTC
333056 AGTTAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.49
Consensus pattern (15 bp):
ATTGATTTCGGTTCA
Found at i:333452 original size:26 final size:26
Alignment explanation
Indices: 333422--333472 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
333412 CTAATACTTA
* *
333422 ATATATTGTGTTAAAATTATTTAAAC
1 ATATATTATGTTAAAATCATTTAAAC
* *
333448 ATATATTATTTTATAATCATTTAAA
1 ATATATTATGTTAAAATCATTTAAA
333473 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (26 bp):
ATATATTATGTTAAAATCATTTAAAC
Found at i:340150 original size:21 final size:19
Alignment explanation
Indices: 340126--340164 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
340116 GGAAACCACC
340126 CTTCTATCGTAGTTTCTCTTT
1 CTTCTATC-T-GTTTCTCTTT
*
340147 CTTCTCTCTGTTTCTCTT
1 CTTCTATCTGTTTCTCTT
340165 AAGGTTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.05, C:0.28, G:0.08, T:0.59
Consensus pattern (19 bp):
CTTCTATCTGTTTCTCTTT
Found at i:349245 original size:19 final size:20
Alignment explanation
Indices: 349209--349246 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
349199 ACCTTACTAA
*
349209 CTCTTTTCATTTTTTTTCCT
1 CTCTTTTCATTTTATTTCCT
349229 CTCTTTT-ATTTTATTTCC
1 CTCTTTTCATTTTATTTCC
349247 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (20 bp):
CTCTTTTCATTTTATTTCCT
Found at i:352686 original size:13 final size:14
Alignment explanation
Indices: 352662--352690 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
352652 AAAAAAATAA
352662 AAGAAGCAAAAAAG
1 AAGAAGCAAAAAAG
352676 AAGAA-CAAAAAAG
1 AAGAAGCAAAAAAG
352689 AA
1 AA
352691 CAAAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (14 bp):
AAGAAGCAAAAAAG
Found at i:354420 original size:106 final size:106
Alignment explanation
Indices: 354291--355459 Score: 1835
Period size: 106 Copynumber: 11.0 Consensus size: 106
354281 ATATCGTGCC
* * *
354291 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
*
354355 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
354397 ACTCCAGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
354462 AATTTCAGAGCCAATTTCAATTTCAC-GACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
* *
354503 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
354568 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
354609 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC-TCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC-
* * * *
354673 C-ATTTTAGAGCCAATTTTAACTTCACAACGAATGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
354714 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
354779 AATTTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
354820 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * **
354885 AATTTCGGAGCCAATTTCAACTTCACAACGAAAGATATTAT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
354926 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
354991 AATTTCGGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
355032 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* **
355097 AATTTTAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
355138 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
355203 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
355244 ACTCGAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
355309 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * ** * * *
355350 ACTCGAGACAACACAAGTTCAACTTCATAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
355415 GATTCCAGAGCCAATTGCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
355456 ACTC
1 ACTC
355460 GGAACAATGC
Statistics
Matches: 987, Mismatches: 69, Indels: 14
0.92 0.06 0.01
Matches are distributed among these distances:
105 102 0.10
106 882 0.89
107 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:356342 original size:37 final size:37
Alignment explanation
Indices: 356212--356314 Score: 190
Period size: 37 Copynumber: 2.8 Consensus size: 37
356202 TTTCGTCCTA
356212 CTAGGA-TCAAAACTCCTAAAAATAGGATAAAATTTTG
1 CTAGGATTC-AAACTCCTAAAAATAGGATAAAATTTTG
356249 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTTG
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTTG
356286 CTAGGATTCAAACTCCTAAAAATAGGATA
1 CTAGGATTCAAACTCCTAAAAATAGGATA
356315 GATTTCTACT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
37 63 0.97
38 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTTG
Found at i:357223 original size:18 final size:17
Alignment explanation
Indices: 357175--357220 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
357165 TTTGTATATA
*
357175 TATTTTTTTTCTTCATT
1 TATTTTTTTTATTCATT
357192 TATTTTATTTTATTCAATT
1 TATTTT-TTTTATTC-ATT
357211 TCATTTTTTT
1 T-ATTTTTTT
357221 ATTTGTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 7 0.28
20 5 0.20
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTTTTTTATTCATT
Found at i:369030 original size:23 final size:23
Alignment explanation
Indices: 369004--369051 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
368994 ATAAAGTACA
*
369004 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
369027 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
369050 AT
1 AT
369052 TGATCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:369562 original size:23 final size:23
Alignment explanation
Indices: 369527--369599 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
369517 ATACTTTACA
*
369527 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
369550 ATATAAACGCTACTTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
369573 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
369596 ATAT
1 ATAT
369600 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:369846 original size:24 final size:24
Alignment explanation
Indices: 369809--369861 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
369799 AATATTTGAT
369809 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
369833 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
369857 TATTT
1 TATTT
369862 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:370023 original size:17 final size:18
Alignment explanation
Indices: 370001--370043 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
369991 ATATATTCGG
370001 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
370018 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
370038 TATCAT
1 TATCAT
370044 ATTTTTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:370052 original size:20 final size:19
Alignment explanation
Indices: 370006--370053 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
369996 TTCGGTATCA
370006 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
370025 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
370046 TTTTACCG
1 TTTTACCG
370054 TTATATCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:370231 original size:20 final size:19
Alignment explanation
Indices: 370186--370231 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
370176 TCCGATAACG
*
370186 TTTTACCGGTTTTATCATT
1 TTTTACAGGTTTTATCATT
370205 TTCTTACAGGTTTTATCATAT
1 TT-TTACAGGTTTTATCAT-T
370226 TTTTAC
1 TTTTAC
370232 CTGGTATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.57
Consensus pattern (19 bp):
TTTTACAGGTTTTATCATT
Found at i:370322 original size:181 final size:181
Alignment explanation
Indices: 369973--370444 Score: 610
Period size: 181 Copynumber: 2.6 Consensus size: 181
369963 CGTACTTACG
* * * * * * *
369973 AAAGTATCGATATTTTCAATATATTCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATA-TCGATAACGTTTTACCGGTTTTATCATTTTCATACAGGTTT
* *
370038 TATCATATTTTTACC-GTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTAAAAGTATCGACACATTAT
370102 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
370153 AAAGTATCGACACTTTCAATATATCCGATAACGTTTTACCGGTTTTATCATTTTCTTACAGGTTT
1 AAAGTATCGACACTTTCAATATAT-CGATAACGTTTTACCGGTTTTATCATTTTCATACAGGTTT
* * * *
370218 TATCATATTTTTACCTGGTATATCGTTTTGAATCGATACATTTTTTAAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTAAAAGTATCGACACATTAT
* *
370283 AGGAC-TTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGG-CGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * * *
370335 AAAGTACCGACACTTTAAATGTATCTAGTAGCGCTTTACCGGTTTTATTA-TTTCAATACTGGTT
1 AAAGTATCGACACTTTCAATATATCGA-TAACGTTTTACCGGTTTTATCATTTTC-ATACAGGTT
* * * * *
370399 TTGTTATAGTTTTACCTGTTATATCATTTTGGATCGACATATTTTT
64 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTT
370445 AATTTGGATC
Statistics
Matches: 253, Mismatches: 33, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
179 1 0.00
180 70 0.28
181 95 0.38
182 87 0.34
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCGATAACGTTTTACCGGTTTTATCATTTTCATACAGGTTTT
ATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTAAAAGTATCGACACATTATA
GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:371047 original size:41 final size:41
Alignment explanation
Indices: 370993--371149 Score: 287
Period size: 41 Copynumber: 3.8 Consensus size: 41
370983 ATTCGCGTTG
* * *
370993 CATTTCGCATTGCGATAGTTGGAAATTGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
371034 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
371075 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
371116 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGC
371150 TATAGTTGAA
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 113 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:371155 original size:103 final size:103
Alignment explanation
Indices: 371038--371255 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
371028 ATTTTCCATT
371038 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
371103 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
66 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
* *
371141 TCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGTGATAGTTGAAAATCG
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
*
371206 CGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAA
66 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
371244 TCGCGTTGCGAT
1 TCGCGTTGCGAT
371256 TTTTTATTTC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (103 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:371186 original size:41 final size:41
Alignment explanation
Indices: 371141--371365 Score: 239
Period size: 41 Copynumber: 5.5 Consensus size: 41
371131 TAGTTGAAAA
*
371141 TCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
* *
371182 TCGCGTTGTGATAGTTGAAAATCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
**
371223 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTTATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
* *
371264 TCGCGTTGCGATAGTCT-ACAAT-GTCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-ATT
* * * *
371306 T--CGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-ATT
*
371347 T--CGTTGCGATAGTTAAAAA
1 TCGCGTTGCGATAGTTGAAAA
371366 AAAAATTTGT
Statistics
Matches: 167, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
40 20 0.12
41 143 0.86
42 4 0.02
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
Found at i:371293 original size:144 final size:144
Alignment explanation
Indices: 370997--371278 Score: 492
Period size: 144 Copynumber: 2.0 Consensus size: 144
370987 GCGTTGCATT
* * *
370997 TCGCATTGCGATAGTTGGAAATTGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
371062 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
66 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
371127 GCGATAGTTGAAAA
131 GCGATAGTTGAAAA
* *
371141 TCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGTGATAGTTGAAAATCG
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
* **
371206 CGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTTATTTCGCGTT
66 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
371271 GCGATAGT
131 GCGATAGT
371279 CTACAATGTC
Statistics
Matches: 130, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
144 130 1.00
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (144 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
GCGATAGTTGAAAA
Found at i:371311 original size:19 final size:19
Alignment explanation
Indices: 371287--371356 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
371277 GTCTACAATG
371287 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
371306 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
371327 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
371347 TCGTTGCGAT
1 TCGTTGCGAT
371357 AGTTAAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 20 0.50
20 5 0.12
21 5 0.12
22 10 0.25
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:371333 original size:144 final size:144
Alignment explanation
Indices: 370997--371337 Score: 422
Period size: 144 Copynumber: 2.4 Consensus size: 144
370987 GCGTTGCATT
* ** * * * *
370997 TCGCATTGCGATAGTTGGAAATTGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
1 TCGCGTTGCGATAGTTCAAAATCGCGTTGCGATTCTACAGTTCGCGTTGCGATAGTTGAAAATCG
371062 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
66 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
371127 GCGATAGTTGAAAA
131 GCGATAGTTGAAAA
* * * * * *
371141 TCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGTGATAGTTGAAAATCG
1 TCGCGTTGCGATAGTTCAAAATCGCGTTGCGATTCTACAGTTCGCGTTGCGATAGTTGAAAATCG
* **
371206 CGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTTATTTCGCGTT
66 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
*
371271 GCGATAGTCT-ACAA
131 GCGATAGT-TGAAAA
* * *
371285 T-GTCGTTGCGAT-TTTCCAAAT-TCGTTGCGATAGTCTACAGTT-GTCGTTGCGAT
1 TCG-CGTTGCGATAGTTCAAAATCGCGTTGCGAT--TCTACAGTTCG-CGTTGCGAT
371338 TTTCCAAATT
Statistics
Matches: 174, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
142 9 0.05
143 8 0.05
144 156 0.90
145 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (144 bp):
TCGCGTTGCGATAGTTCAAAATCGCGTTGCGATTCTACAGTTCGCGTTGCGATAGTTGAAAATCG
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
GCGATAGTTGAAAA
Found at i:371446 original size:6 final size:6
Alignment explanation
Indices: 371435--371466 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
371425 GACACGTATT
371435 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
371467 CGAGACGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:371957 original size:5 final size:5
Alignment explanation
Indices: 371947--371994 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
371937 CCGCCGCCGC
371947 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
371995 GGTCGTGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.00, C:0.40, G:0.21, T:0.40
Consensus pattern (5 bp):
CGTCT
Found at i:376558 original size:155 final size:155
Alignment explanation
Indices: 376276--376587 Score: 615
Period size: 155 Copynumber: 2.0 Consensus size: 155
376266 TAACAAAACT
376276 AACATTTGTTTTTCGCGTAATGTGGGTGTATGTTTGCAGGATAACATTAGTGCGGGGTTCCAATT
1 AACATTTGTTTTTCGCGTAATGTGGGTGTATGTTTGCAGGATAACATTAGTGCGGGGTTCCAATT
376341 TACGTGAGTGGACGATATGGGAAAATATCTGGGTGTTCCTTTGCTCTATAATAGAGTAACTCAGA
66 TACGTGAGTGGACGATATGGGAAAATATCTGGGTGTTCCTTTGCTCTATAATAGAGTAACTCAGA
*
376406 ACACTTGTCAATACCTTGTTCAAAA
131 ACACTTGTCAATACATTGTTCAAAA
376431 AACATTTGTTTTTCGCGTAATGTGGGTGTATGTTTGCAGGATAACATTAGTGCGGGGTTCCAATT
1 AACATTTGTTTTTCGCGTAATGTGGGTGTATGTTTGCAGGATAACATTAGTGCGGGGTTCCAATT
376496 TACGTGAGTGGACGATATGGGAAAATATCTGGGTGTTCCTTTGCTCTATAATAGAGTAACTCAGA
66 TACGTGAGTGGACGATATGGGAAAATATCTGGGTGTTCCTTTGCTCTATAATAGAGTAACTCAGA
376561 ACACTTGTCAATACATTGTTCAAAA
131 ACACTTGTCAATACATTGTTCAAAA
376586 AA
1 AA
376588 TGCGTGATCA
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 156 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (155 bp):
AACATTTGTTTTTCGCGTAATGTGGGTGTATGTTTGCAGGATAACATTAGTGCGGGGTTCCAATT
TACGTGAGTGGACGATATGGGAAAATATCTGGGTGTTCCTTTGCTCTATAATAGAGTAACTCAGA
ACACTTGTCAATACATTGTTCAAAA
Found at i:378201 original size:2 final size:2
Alignment explanation
Indices: 378194--378231 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
378184 TTTTAAGATA
378194 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
378232 TCTTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:381519 original size:5 final size:5
Alignment explanation
Indices: 381504--381594 Score: 71
Period size: 5 Copynumber: 18.0 Consensus size: 5
381494 AAGTAATGAA
* *
381504 AAAAT -AAAT AAAAT AAAAT AAACTATT AAAAA ACAAAT GAAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAA--A-T AAAAT A-AAAT AAAAT AAAAT
* * * *
381551 AAGAT AAGAT AAGAT -AAAG AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
381595 GAATTTAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
4 10 0.14
5 53 0.74
6 4 0.06
7 1 0.01
8 4 0.06
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:381581 original size:24 final size:24
Alignment explanation
Indices: 381547--381592 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
381537 CAAATGAAAT
* * *
381547 AAATAAGATAAGATAAGATAAAGA
1 AAATAAAATAAAATAAAATAAAGA
381571 AAATAAAATAAAATAAAATAAA
1 AAATAAAATAAAATAAAATAAA
381593 ATGAATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (24 bp):
AAATAAAATAAAATAAAATAAAGA
Found at i:381813 original size:2 final size:2
Alignment explanation
Indices: 381808--381889 Score: 148
Period size: 2 Copynumber: 41.5 Consensus size: 2
381798 AAGGGAAAAA
*
381808 AT AT AT AT AT AT AT AG AT AT -T 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
381849 AT AT 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 AT AT A
381890 CACACGTATA
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 76 0.99
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:381922 original size:14 final size:14
Alignment explanation
Indices: 381903--381951 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
381893 ACGTATAAAC
381903 AAATAATAGAAAAA
1 AAATAATAGAAAAA
* * *
381917 AAATAAAATAATAA
1 AAATAATAGAAAAA
*
381931 AAATAA-AGAAATA
1 AAATAATAGAAAAA
381944 AAATAATA
1 AAATAATA
381952 AAATGATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (14 bp):
AAATAATAGAAAAA
Found at i:381970 original size:22 final size:21
Alignment explanation
Indices: 381914--381954 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
381904 AATAATAGAA
381914 AAAAAATAAAATAATAAAAAT
1 AAAAAATAAAATAATAAAAAT
381935 AAAGAAATAAAATAATAAAA
1 AAA-AAATAAAATAATAAAA
381955 TGATTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (21 bp):
AAAAAATAAAATAATAAAAAT
Found at i:382019 original size:23 final size:23
Alignment explanation
Indices: 381993--382043 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
381983 ATTATATCGT
*
381993 ATAAATAAAAAATAAGA-AATAAA
1 ATAAA-AAAAAATAAAATAATAAA
* *
382016 ATAAAATAAAATAAAATAATAAT
1 ATAAAAAAAAATAAAATAATAAA
382039 ATAAA
1 ATAAA
382044 GATAAAAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (23 bp):
ATAAAAAAAAATAAAATAATAAA
Found at i:382029 original size:15 final size:16
Alignment explanation
Indices: 381916--382039 Score: 70
Period size: 14 Copynumber: 8.1 Consensus size: 16
381906 TAATAGAAAA
381916 AAAATAAAATAAT-A-
1 AAAATAAAATAATAAT
381930 AAAATAAAGA-AATAA-
1 AAAATAAA-ATAATAAT
*
381945 AATAATAAAATGAT--T
1 AA-AATAAAATAATAAT
381960 AAAATAAAAT-ATAAT
1 AAAATAAAATAATAAT
* * * **
381975 ATATATATATTATATCGT
1 A-AAATAAAATA-ATAAT
381993 ATAAATAAAA-AATAA-
1 A-AAATAAAATAATAAT
*
382008 GAAATAAAATAA-AAT
1 AAAATAAAATAATAAT
382023 AAAATAAAATAATAAT
1 AAAATAAAATAATAAT
382039 A
1 A
382040 TAAAGATAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
13 2 0.02
14 29 0.35
15 22 0.26
16 20 0.24
17 1 0.01
18 10 0.12
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAATAAAATAATAAT
Found at i:382042 original size:5 final size:5
Alignment explanation
Indices: 382009--382039 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
381999 AAAAAATAAG
382009 AAATA AAATA AAATA AAATA AAATA ATAATA
1 AAATA AAATA AAATA AAATA AAATA A-AATA
382040 TAAAGATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:382050 original size:96 final size:99
Alignment explanation
Indices: 381869--382064 Score: 233
Period size: 96 Copynumber: 2.0 Consensus size: 99
381859 ATATATATAT
* *
381869 ATATATATATATATATATATACACACGTATAAACAAATAATAGAAAAAAAATAAAATAATAAAAA
1 ATATATATATATATATATATACACACGTATAAACAAAAAATAGAAAAAAAATAAAATAAAAAAAA
*
381934 TAAAGAAATAAAATAATAAAATGATTAAAATAAA
66 TAAAGAAATAAAATAATAAAAGGATTAAAATAAA
* * * *
381968 ATATA-ATATATATATAT-TATA-TCGTATAAATAAAAAATAAGAAATAAAATAAAATAAAATAA
1 ATATATATATATATATATATACACACGTATAAACAAAAAAT-AGAAAAAAAATAAAATAAAA-AA
* * *
382030 AAT-AA-TAATATAAA-GATAAAAGGATTAAATTAAA
64 AATAAAGAAATA-AAATAATAAAAGGATTAAAATAAA
382064 A
1 A
382065 GGGAGACAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
96 36 0.43
97 26 0.31
98 17 0.20
99 5 0.06
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.27
Consensus pattern (99 bp):
ATATATATATATATATATATACACACGTATAAACAAAAAATAGAAAAAAAATAAAATAAAAAAAA
TAAAGAAATAAAATAATAAAAGGATTAAAATAAA
Found at i:383584 original size:12 final size:12
Alignment explanation
Indices: 383546--383584 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
383536 GTTTGGACCC
*
383546 TAAAA-AAAACA
1 TAAAAGAAAATA
383557 TAAAAGAAAATAA
1 TAAAAGAAAAT-A
383570 TAAAAGAAAATA
1 TAAAAGAAAATA
383582 TAA
1 TAA
383585 TAATAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 5 0.20
12 8 0.32
13 12 0.48
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (12 bp):
TAAAAGAAAATA
Found at i:383647 original size:36 final size:35
Alignment explanation
Indices: 383607--383944 Score: 208
Period size: 35 Copynumber: 9.6 Consensus size: 35
383597 TATAATAAAT
* *
383607 TATATAATACATATATTTCAAAATATTTTTTAAAAC
1 TATATATTATATAT-TTTCAAAATATTTTTTAAAAC
* * *
383643 TATATA-T-TATA-TTT-AAAAAAGTTTTCAAAAC
1 TATATATTATATATTTTCAAAATATTTTTTAAAAC
* * *
383674 TAT-TA-TATA-GTTTTC-AAA-ATGTTTTAAAAA
1 TATATATTATATATTTTCAAAATATTTTTTAAAAC
* * *
383704 TAT-TA-TATA-AGTTTTTTAAAAAACGTTTTTAAAAC
1 TATATATTATATA--TTTTCAAAATA-TTTTTTAAAAC
383739 TATATATTATATAATTATTCAAAA-ATGTTTTTAAAAAC
1 TATATATTATAT-ATT-TTCAAAATAT-TTTTT-AAAAC
*
383777 TATATATTATA-AGTTTTTAAAATGA--TTTTAAAAC
1 TATATATTATATA-TTTTCAAAAT-ATTTTTTAAAAC
* * *
383811 TATATGTTATATATTTTCTAAAAT-GTTTTAAAAAC
1 TATATATTATATATTTTC-AAAATATTTTTTAAAAC
* *
383846 TATATGTTATATAGTTTTCAAAA-ATATTTTAAAAAC
1 TATATATTATATA-TTTTCAAAATAT-TTTTTAAAAC
* *
383882 TATATATTACCCATATTTTCAAAATTTTTCTTTTAAAAAC
1 TATATATTA--TATATTTTCAAAA-TATT-TTTT-AAAAC
383922 TATATATTATATATATTTCAAAA
1 TATATATTATATAT-TTTCAAAA
383945 ACCGTTTGCA
Statistics
Matches: 244, Mismatches: 26, Indels: 61
0.74 0.08 0.18
Matches are distributed among these distances:
30 20 0.08
31 25 0.10
32 7 0.03
33 3 0.01
34 23 0.09
35 47 0.19
36 38 0.16
37 23 0.09
38 31 0.13
39 13 0.05
40 14 0.06
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (35 bp):
TATATATTATATATTTTCAAAATATTTTTTAAAAC
Found at i:383806 original size:35 final size:34
Alignment explanation
Indices: 383633--383890 Score: 223
Period size: 35 Copynumber: 7.6 Consensus size: 34
383623 TTCAAAATAT
* *
383633 TTTTTAAAACTATATATTAT-A--TTTAAAAAAG
1 TTTTAAAAACTATATATTATAAGTTTTAAAAATG
* *
383664 TTTTCAAAACTAT-TA-TAT-AGTTTTCAAAATG
1 TTTTAAAAACTATATATTATAAGTTTTAAAAATG
*
383695 TTTTAAAAA-TAT-TA-TATAAGTTTTTTAAAAAACG
1 TTTTAAAAACTATATATTATAAG--TTTT-AAAAATG
* *
383729 TTTTTAAAACTATATATTATATAATTATTCAAAAATG
1 TTTTAAAAACTATATATTATA-AGTT-TT-AAAAATG
*
383766 TTTTTAAAAACTATATATTATAAGTTTTTAAAATG
1 -TTTTAAAAACTATATATTATAAGTTTTAAAAATG
* *
383801 ATTTT-AAAACTATATGTTATATA-TTTTCTAAAATG
1 -TTTTAAAAACTATATATTATA-AGTTTT-AAAAATG
* *
383836 TTTTAAAAACTATATGTTATATAGTTTTCAAAAATA
1 TTTTAAAAACTATATATTATA-AGTTTT-AAAAATG
383872 TTTTAAAAACTATATATTA
1 TTTTAAAAACTATATATTA
383891 CCCATATTTT
Statistics
Matches: 193, Mismatches: 18, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
29 4 0.02
30 10 0.05
31 30 0.16
33 4 0.02
34 36 0.19
35 39 0.20
36 34 0.18
37 15 0.08
38 21 0.11
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (34 bp):
TTTTAAAAACTATATATTATAAGTTTTAAAAATG
Found at i:383809 original size:107 final size:102
Alignment explanation
Indices: 383633--383890 Score: 286
Period size: 107 Copynumber: 2.5 Consensus size: 102
383623 TTCAAAATAT
*
383633 TTTTTAAAACTATATATTATAT-TTA---AAAAA-GTTTTCAAAACTAT-TA-TATAGTTTTCAA
1 TTTTTAAAACTATATATTATATATTATTCAAAAATGTTTTAAAAACTATATATTATAGTTTTCAA
*
383691 AATGTTTTAAAA-ATA--TTATATAAGTTTTTTAAAAAACG
66 AATGTTTTAAAACATATGTTATAT-A-TTTTCT--AAAACG
383729 TTTTTAAAACTATATATTATATAATTATTCAAAAATGTTTTTAAAAACTATATATTATAAGTTTT
1 TTTTTAAAACTATATATTATAT-ATTATTCAAAAATG-TTTTAAAAACTATATATTAT-AGTTTT
* *
383794 TAAAATGATTTTAAAACTATATGTTATATATTTTCTAAAATG
63 CAAAATG-TTTTAAAAC-ATATGTTATATATTTTCTAAAACG
* * *
383836 TTTTAAAAACTATATGTTATATAGTT-TTCAAAAATATTTTAAAAACTATATATTA
1 TTTTTAAAACTATATATTATATA-TTATTCAAAAATGTTTTAAAAACTATATATTA
383891 CCCATATTTT
Statistics
Matches: 139, Mismatches: 7, Indels: 23
0.82 0.04 0.14
Matches are distributed among these distances:
96 22 0.16
98 3 0.02
101 5 0.04
102 1 0.01
103 12 0.09
104 2 0.01
105 22 0.16
106 22 0.16
107 35 0.25
109 8 0.06
110 1 0.01
111 6 0.04
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (102 bp):
TTTTTAAAACTATATATTATATATTATTCAAAAATGTTTTAAAAACTATATATTATAGTTTTCAA
AATGTTTTAAAACATATGTTATATATTTTCTAAAACG
Found at i:383909 original size:34 final size:34
Alignment explanation
Indices: 383674--383945 Score: 184
Period size: 36 Copynumber: 7.6 Consensus size: 34
383664 TTTTCAAAAC
*
383674 TATTATATAGTTTTCAAAATGTTTTAAAAA-TAT-
1 TATTATATAGTTTTCAAAA-ATTTTAAAAACTATA
* *
383707 TA-TATA-AGTTTTTTAAAAAACGTTTTTAAAACTATA
1 TATTATATAG--TTTTCAAAAA--TTTTAAAAACTATA
*
383743 TATTATATAATTATTCAAAAATGTTTTTAAAAACTATA
1 TATTATATAGTT-TTCAAAAA---TTTTAAAAACTATA
*
383781 TATTATA-AGTTTTTAAAATGATTTT-AAAACTATA
1 TATTATATAGTTTTCAAAA--ATTTTAAAAACTATA
* *
383815 TGTTATATA-TTTTCTAAAATGTTTTAAAAACTATA
1 TATTATATAGTTTTC-AAAA-ATTTTAAAAACTATA
*
383850 TGTTATATAGTTTTCAAAAATATTTTAAAAACTATA
1 TATTATATAGTTTTC-AAAA-ATTTTAAAAACTATA
* *
383886 TATTACCCATA-TTTTCAAAATTTTTCTTTTAAAAACTATA
1 TATTA--TATAGTTTTCAAAA-----ATTTTAAAAACTATA
383926 TATTATATA-TATTTCAAAAA
1 TATTATATAGT-TTTCAAAAA
383946 CCGTTTGCAA
Statistics
Matches: 195, Mismatches: 21, Indels: 45
0.75 0.08 0.17
Matches are distributed among these distances:
31 2 0.01
32 4 0.02
33 10 0.05
34 31 0.16
35 30 0.15
36 42 0.22
37 19 0.10
38 29 0.15
39 8 0.04
40 20 0.10
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (34 bp):
TATTATATAGTTTTCAAAAATTTTAAAAACTATA
Found at i:384760 original size:84 final size:82
Alignment explanation
Indices: 384601--385074 Score: 557
Period size: 84 Copynumber: 5.7 Consensus size: 82
384591 TTGAATATAA
* * **
384601 TCGAACTCGAAGGTC-TT--TAGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC-AAATGATGT
*
384663 GCCTTGGAGCTGAGCGGAG
65 GCCTT-GAGCTGAGCGTAG
** * * *
384682 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAG-CTTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGAC-TTAAGTTATGCTGCAAATGATG
384746 TGCCGTTGAGCTGAGCGTAG
64 TGCC-TTGAGCTGAGCGTAG
* * ** *
384766 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTGTATTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
384831 GCCTTGGAGCTGAGCGTAG
65 GCCTT-GAGCTGAGCGTAG
* *
384850 TCGAACTCGAAGGTCTTTTGTTGGCAGCTAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * *
384915 GCCCTCGAAGCTGAGTGTAA
65 G-CCTTG-AGCTGAGCGTAG
** * * *
384935 TCGAACTCGGGGGTC-TT--TGGCAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
384997 CCGTTGAGCTGAGCGTAG
66 CC-TTGAGCTGAGCGTAG
*
385015 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
1 TCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
385075 AGTTTGTTAA
Statistics
Matches: 332, Mismatches: 44, Indels: 31
0.82 0.11 0.08
Matches are distributed among these distances:
80 24 0.07
81 60 0.18
83 11 0.03
84 179 0.54
85 58 0.17
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (82 bp):
TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
CCTTGAGCTGAGCGTAG
Found at i:385030 original size:165 final size:164
Alignment explanation
Indices: 384598--385074 Score: 634
Period size: 165 Copynumber: 2.9 Consensus size: 164
384588 AAGTTGAATA
* *
384598 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAAATGATGT
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC-AAATGATGT
* * ** * *
384663 GCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAG-CTTTG
65 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGAC-TTA
* * *
384727 AGTTATGCTGTAAATGATGTGCCGTTGAGCTGAGCG
129 AGTTATGCTGCAAATGATGTGCCCTCGAGCTGAGCG
* * * * * **
384763 TAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTGTATTGCAAATGA
1 TAATCGAACTCGAAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* *
384828 TATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGCTAACCCTTCTCGACT
62 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACT
*
384893 TAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
127 TAAGTTATGCTGCAAATGATGTGCCCTCG-AGCTGAGCG
** *
384932 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* *
384997 CCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAA
66 CC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAA
385061 GTTATGCTGCAAAT
130 GTTATGCTGCAAAT
385075 AGTTTGTTAA
Statistics
Matches: 270, Mismatches: 35, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
165 127 0.47
166 2 0.01
167 2 0.01
168 87 0.32
169 52 0.19
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (164 bp):
TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAG
TTATGCTGCAAATGATGTGCCCTCGAGCTGAGCG
Found at i:388441 original size:18 final size:19
Alignment explanation
Indices: 388401--388445 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
388391 AGTTAATGTG
*
388401 AATGCAGAGAAAATAATAA
1 AATGCAAAGAAAATAATAA
388420 AATGCAAAGAAAATAA-AA
1 AATGCAAAGAAAATAATAA
388438 AATGCAAA
1 AATGCAAA
388446 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (19 bp):
AATGCAAAGAAAATAATAA
Found at i:390140 original size:5 final size:5
Alignment explanation
Indices: 390126--390214 Score: 69
Period size: 5 Copynumber: 18.0 Consensus size: 5
390116 AAAAGTAATG
* *
390126 AAAA- AAAAT AAAAT -AAAT AAAAATT AAAAA ACAAAT GAAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT -AAAA-T AAAAT A-AAAT AAAAT AAAAT
* * * *
390171 AAGAT AAGAT AAGAT -AAAG AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
390215 GAATTTAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
4 14 0.20
5 46 0.65
6 10 0.14
7 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:390201 original size:24 final size:24
Alignment explanation
Indices: 390167--390212 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
390157 CAAATGAAAT
* * *
390167 AAATAAGATAAGATAAGATAAAGA
1 AAATAAAATAAAATAAAATAAAGA
390191 AAATAAAATAAAATAAAATAAA
1 AAATAAAATAAAATAAAATAAA
390213 ATGAATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (24 bp):
AAATAAAATAAAATAAAATAAAGA
Found at i:390502 original size:31 final size:32
Alignment explanation
Indices: 390467--390530 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 32
390457 ACAAAGTAAT
390467 AGAAATAAAAGA-AATAAAAT-AATAAAAATAA
1 AGAAATAAAA-ATAATAAAATGAATAAAAATAA
*
390498 AGAAATAAAAATAATAAAATGATTAAAAATAA
1 AGAAATAAAAATAATAAAATGAATAAAAATAA
390530 A
1 A
390531 ATATAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 1 0.03
31 18 0.60
32 11 0.37
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (32 bp):
AGAAATAAAAATAATAAAATGAATAAAAATAA
Found at i:390503 original size:17 final size:17
Alignment explanation
Indices: 390483--390515 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
390473 AAAAGAAATA
390483 AAATAATAAA-AATAAAG
1 AAATAA-AAATAATAAAG
390500 AAATAAAAATAATAAA
1 AAATAAAAATAATAAA
390516 ATGATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATAAAAATAATAAAG
Found at i:390504 original size:14 final size:14
Alignment explanation
Indices: 390464--390608 Score: 75
Period size: 14 Copynumber: 9.7 Consensus size: 14
390454 TAAACAAAGT
390464 AATAGAAATAA-AAGA
1 AATA-AAATAATAA-A
390479 AATAAAATAATAAA
1 AATAAAATAATAAA
390493 AATAAAGA-AATAAAAA
1 AATAAA-ATAAT--AAA
*
390509 TAATAAAATGATTAAA
1 -AATAAAAT-AATAAA
390525 AATAAAAT-ATAATA
1 AATAAAATAATAA-A
* ** *
390539 TATATATGTAATCGTATA
1 -A-ATA--AAATAATAAA
390557 AATAAAA-AA-AAGA
1 AATAAAATAATAA-A
390570 AATAAAATAATAAA
1 AATAAAATAATAAA
*
390584 AATAAAATAATAAT
1 AATAAAATAATAAA
390598 AATAAAGATAA
1 AATAAA-ATAA
390609 AAGATTAAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 34
0.70 0.07 0.23
Matches are distributed among these distances:
12 1 0.01
13 11 0.11
14 41 0.40
15 22 0.21
16 13 0.13
17 7 0.07
18 6 0.06
19 2 0.02
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.23
Consensus pattern (14 bp):
AATAAAATAATAAA
Found at i:390598 original size:20 final size:19
Alignment explanation
Indices: 390463--390610 Score: 76
Period size: 20 Copynumber: 7.7 Consensus size: 19
390453 ATAAACAAAG
* *
390463 TAATAGAAATAAAA-GAAA
1 TAATAAAAATAAAATAAAA
*
390481 TAA-AATAATAAAAATAAAGA
1 TAATAAAAAT-AAAATAAA-A
390501 -AATAAAAAT--AATAAAA
1 TAATAAAAATAAAATAAAA
* *
390517 TGATTAAAAATAAAATATAA
1 T-AATAAAAATAAAATAAAA
* ** **
390537 TATATATATGTAATCGTATAAA
1 TA-ATAAAAATAA-AATA-AAA
390559 TAA-AAAAA-AGAAATAAAA
1 TAATAAAAATA-AAATAAAA
390577 TAATAAAAATAAAATAATAA
1 TAATAAAAATAAAATAA-AA
*
390597 TAATAAAGATAAAA
1 TAATAAAAATAAAA
390611 GATTAAATTA
Statistics
Matches: 96, Mismatches: 19, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
16 1 0.01
17 10 0.10
18 21 0.22
19 19 0.20
20 38 0.40
21 3 0.03
22 4 0.04
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (19 bp):
TAATAAAAATAAAATAAAA
Found at i:392385 original size:20 final size:19
Alignment explanation
Indices: 392349--392388 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
392339 GGACCCTAAA
392349 AAAACAAAAAAAAAATAAT
1 AAAACAAAAAAAAAATAAT
* *
392368 AAAAGAAAATAAATAATAAT
1 AAAACAAAA-AAAAAATAAT
392388 A
1 A
392389 CTGATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.15
Consensus pattern (19 bp):
AAAACAAAAAAAAAATAAT
Found at i:392418 original size:23 final size:22
Alignment explanation
Indices: 392376--392419 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
392366 ATAAAAGAAA
392376 ATAAATAATAATACTGATATAAT
1 ATAAATAATAATAC-GATATAAT
392399 ATAAATTATATAATAC-ATATA
1 ATAAA-TA-ATAATACGATATA
392420 TTTCAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 10 0.53
24 2 0.11
25 7 0.37
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAAATAATAATACGATATAAT
Found at i:392472 original size:31 final size:32
Alignment explanation
Indices: 392437--392579 Score: 120
Period size: 35 Copynumber: 4.5 Consensus size: 32
392427 ATATTTTTTT
*
392437 AACTATATATTATATTTAAAAAA-GTTTTCAA
1 AACTATATATTATATTTAAAAAACGTTTTTAA
** *
392468 AAC--TATATTATAGTTTTCAAAATG-TTTTAA
1 AACTATATATTATA-TTTAAAAAACGTTTTTAA
*
392498 AATTATATAAGTT-T-TTTAAAAAACGTTTTTAA
1 AACTATAT-A-TTATATTTAAAAAACGTTTTTAA
*
392530 AACTATATA-TATAATTTATTCAAAAATGTTTTTAA
1 AACTATATATTAT-ATTTA---AAAAACGTTTTTAA
392565 AACTATATATTATAT
1 AACTATATATTATAT
392580 AAGTTTTTAA
Statistics
Matches: 89, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
29 10 0.11
30 15 0.17
31 13 0.15
32 20 0.22
33 2 0.02
34 2 0.02
35 24 0.27
36 3 0.03
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (32 bp):
AACTATATATTATATTTAAAAAACGTTTTTAA
Found at i:392598 original size:35 final size:35
Alignment explanation
Indices: 392499--392678 Score: 121
Period size: 35 Copynumber: 5.1 Consensus size: 35
392489 ATGTTTTAAA
392499 ATTATATAAGTTTTTTAAAAAACGTTTTTAAAAC--TAT
1 ATTATATAAG-TTTTT--AAAA-GTTTTTAAAACTATAT
392536 A-TATATAA-TTTATTCAAAAATGTTTTTAAAACTATAT
1 ATTATATAAGTTT-TT--AAAA-GTTTTTAAAACTATAT
*
392573 ATTATATAAGTTTTTAAAAGATTTTAAAAC--TAT
1 ATTATATAAGTTTTTAAAAGTTTTTAAAACTATAT
*
392606 GTTATAT-A-TTTTCTAAAA-TTTTTAAAAACTATAT
1 ATTATATAAGTTTT-TAAAAGTTTTT-AAAACTATAT
* ** *
392640 GTT-TAT-AGTTTCAAAAAATATTTTAAAAACTATAT
1 ATTATATAAGTTTTTAAAAGT-TTTT-AAAACTATAT
392675 ATTA
1 ATTA
392679 CCCATATTTC
Statistics
Matches: 122, Mismatches: 8, Indels: 27
0.78 0.05 0.17
Matches are distributed among these distances:
31 8 0.07
32 11 0.09
33 17 0.14
34 13 0.11
35 45 0.37
36 11 0.09
37 5 0.04
38 9 0.07
39 3 0.02
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (35 bp):
ATTATATAAGTTTTTAAAAGTTTTTAAAACTATAT
Found at i:398033 original size:52 final size:52
Alignment explanation
Indices: 397971--398073 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
397961 TTATAATATT
397971 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
* *
398023 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATG
398074 TGTCCAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
Found at i:402613 original size:52 final size:52
Alignment explanation
Indices: 402551--402653 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
402541 TTATAATATT
402551 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
* *
402603 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATG
402654 TGTCCAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
Found at i:404150 original size:17 final size:18
Alignment explanation
Indices: 404128--404162 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
404118 AAAAATATAT
404128 TTAAATTGT-TTAAAAAA
1 TTAAATTGTATTAAAAAA
*
404145 TTAAATTTTATTAAAAAA
1 TTAAATTGTATTAAAAAA
404163 ATGCAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
TTAAATTGTATTAAAAAA
Found at i:408847 original size:2 final size:2
Alignment explanation
Indices: 408842--408866 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
408832 CCTTTTTTCC
408842 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
408867 TTAAATGCAT
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:415273 original size:21 final size:21
Alignment explanation
Indices: 415244--415664 Score: 253
Period size: 21 Copynumber: 19.8 Consensus size: 21
415234 TTTTCAAATT
415244 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * *
415265 CGTTACGATTTATTCCAAATTCG
1 CGTTGCGA--TAGTCCAAGTTCG
415288 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
*
415307 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
415328 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
415349 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
415370 CGTTGCGATTGT-GATTTA-TTCTAAG
1 CGTTGCGATAGTCCA---AGTTC---G
*
415395 TTCGTTGCGATAGTCGAAGTTCG
1 --CGTTGCGATAGTCCAAGTTCG
* * *
415418 TGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
415439 CGTTGCGATAGTCGAAATTCG
1 CGTTGCGATAGTCCAAGTTCG
*
415460 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* * *
415481 CGTTGTGATAGTCGAAGTTCA
1 CGTTGCGATAGTCCAAGTTCG
*
415502 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
415523 CGTTGTGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
415544 CGTTGCAATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
415565 CGTTGTGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
415586 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* ** *
415607 CGTTGTGATAGTCCAAAATCA
1 CGTTGCGATAGTCCAAGTTCG
*
415628 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
415649 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
415665 AATCGCAACG
Statistics
Matches: 315, Mismatches: 49, Indels: 74
0.72 0.11 0.17
Matches are distributed among these distances:
19 69 0.22
20 2 0.01
21 152 0.48
22 3 0.01
23 71 0.23
25 2 0.01
26 3 0.01
27 11 0.03
28 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:415314 original size:63 final size:61
Alignment explanation
Indices: 415242--415622 Score: 351
Period size: 63 Copynumber: 6.0 Consensus size: 61
415232 ATTTTTCAAA
* * *
415242 TTCGTTGCGATAGTCCAAGTTCGCGTTACGATTTATTCCAAATTCGCGTTGCGATAGTCCAAG
1 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGATAGTCCAAG
*
415305 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAG
* * *
415366 TTCGCGTTGCGATTGT-GATTTA-TTCTAAGTTCGTTGCGA--TAGTCGAAGTTCGTGTTGCGAT
1 TT--CGTTGCGATAGTCGA---AGTTC---G--CGTTGCGATTTATTCCAAGTTC--GTTGCGA-
* *
415427 TTATTCCAAA
53 -TAGTCCAAG
* * *
415437 TTCGTTGCGATAGTCGAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGTGATAGTCGAAG
1 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAG
* * * * *
415498 TTCACGTTGCGATAGTCGAAGTTCGCGTTGTGA--TAGTCGAAGTTCGCGTTGCAATTTATTCCA
1 TT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCCA
415561 AG
60 AG
* *
415563 TTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGTGATAGTCCAA
1 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
415623 AATCACGTTG
Statistics
Matches: 260, Mismatches: 32, Indels: 54
0.75 0.09 0.16
Matches are distributed among these distances:
61 42 0.16
62 2 0.01
63 132 0.51
64 3 0.01
65 30 0.12
67 12 0.05
68 3 0.01
69 26 0.10
70 2 0.01
71 8 0.03
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (61 bp):
TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAG
Found at i:415668 original size:42 final size:42
Alignment explanation
Indices: 415284--415661 Score: 503
Period size: 42 Copynumber: 8.9 Consensus size: 42
415274 TTATTCCAAA
*
415284 TTCGCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
415324 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
415366 TTCGCGTTGCGATTGTGATTTATTCTAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGC------GATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* * *
415414 TTCGTGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAA
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
415456 TTCGCGTTGCGATTTATTCCAAGTTCGTTGTGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* * * *
415498 TTCACGTTGCGA--TAGTCGAAGTTCGCGTTGTGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGATAGTCGAAG
* *
415540 TTCGCGTTGCAATTTATTCCAAGTTCGTTGTGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* * *
415582 TTCGCGTTGCGATTTATTCCAAGTTCGTTGTGATAGTCCAAA
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* *
415624 ATCACGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
415662 CAAAATCGCA
Statistics
Matches: 303, Mismatches: 23, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
40 21 0.07
42 233 0.77
44 9 0.03
48 40 0.13
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (42 bp):
TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
Found at i:416534 original size:21 final size:21
Alignment explanation
Indices: 416508--416561 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
416498 GTTTTCAGAT
416508 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
416529 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
416550 TCGCAATGCGAA
1 TCGCAACGCGAA
416562 TATGTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:417710 original size:64 final size:64
Alignment explanation
Indices: 417609--417738 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
417599 TACATGTCAC
417609 GAAAAAAGAAGGGGGGGGAAAAAACTCCTCCGTTGGTACGGATTAACAAAAGAGCGAGTTAAAA
1 GAAAAAAGAAGGGGGGGGAAAAAACTCCTCCGTTGGTACGGATTAACAAAAGAGCGAGTTAAAA
417673 GAAAAAAGAAGGGGGGGGAAAAAACTCCTCCGTTGGTACGGATTAACAAAAGAGCGAGTTAAAA
1 GAAAAAAGAAGGGGGGGGAAAAAACTCCTCCGTTGGTACGGATTAACAAAAGAGCGAGTTAAAA
417737 GA
1 GA
417739 TAACAAAATG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (64 bp):
GAAAAAAGAAGGGGGGGGAAAAAACTCCTCCGTTGGTACGGATTAACAAAAGAGCGAGTTAAAA
Found at i:430408 original size:20 final size:20
Alignment explanation
Indices: 430307--430480 Score: 153
Period size: 20 Copynumber: 8.7 Consensus size: 20
430297 AGTTTCCAAC
430307 TTCGCAACGCGAATATGT-AAA
1 TTCGCAACGCGAA-A-GTCAAA
*
430328 -TCGCAACAC-ATAAGTCAAA
1 TTCGCAACGCGA-AAGTCAAA
*
430347 TTCGCAACGCGAATTTGT-AAA
1 TTCGCAACGCGAA--AGTCAAA
* *
430368 -TCGTAACAC-AGAAGTCAAA
1 TTCGCAACGCGA-AAGTCAAA
* *
430387 TTCGCAACGCGATAGCCAAA
1 TTCGCAACGCGAAAGTCAAA
* *
430407 TTCGCAACGCGATAGTAAAA
1 TTCGCAACGCGAAAGTCAAA
*
430427 TTCGCAACGTGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
* *
430447 TTCACAACGCGAAAGTAAAA
1 TTCGCAACGCGAAAGTCAAA
430467 TTCGCAACGCGAAA
1 TTCGCAACGCGAAA
430481 CACAATATTA
Statistics
Matches: 124, Mismatches: 19, Indels: 21
0.76 0.12 0.13
Matches are distributed among these distances:
18 4 0.03
19 9 0.07
20 104 0.84
21 5 0.04
22 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:430635 original size:22 final size:22
Alignment explanation
Indices: 430590--430636 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
430580 CTACGGCGAT
*
430590 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACAAA
*
430612 ATCCGTCCCCATCTCCGGCAAA
1 ATCCGTCCCCATCTCCGACAAA
430634 ATC
1 ATC
430637 TGTCTATCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.45, G:0.13, T:0.19
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:431022 original size:20 final size:20
Alignment explanation
Indices: 430999--431048 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
430989 GAAAATTGCA
430999 TTGCGAATTTCATTTTCGCG
1 TTGCGAATTTCATTTTCGCG
*
431019 TTGCGATTTTCATTTTCGCG
1 TTGCGAATTTCATTTTCGCG
*
431039 TTGTGAATTT
1 TTGCGAATTT
431049 AAGTTTCAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.50
Consensus pattern (20 bp):
TTGCGAATTTCATTTTCGCG
Found at i:431055 original size:20 final size:20
Alignment explanation
Indices: 430999--431055 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
430989 GAAAATTGCA
* *
430999 TTGCGAATTTCATTTTCGCG
1 TTGCGAATTTAAGTTTCGCG
* * *
431019 TTGCGATTTTCATTTTCGCG
1 TTGCGAATTTAAGTTTCGCG
*
431039 TTGTGAATTTAAGTTTC
1 TTGCGAATTTAAGTTTC
431056 AGAAACTACT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (20 bp):
TTGCGAATTTAAGTTTCGCG
Found at i:433233 original size:21 final size:21
Alignment explanation
Indices: 433207--433319 Score: 147
Period size: 21 Copynumber: 5.4 Consensus size: 21
433197 CTATCATCAC
* * *
433207 TCAAGAGGCGCCTCCTATCGT
1 TCAAGAGGCCCCTCCCACCGT
* * *
433228 TCAAGAGGCCCCTCTCATC-A
1 TCAAGAGGCCCCTCCCACCGT
*
433248 TCGAAGAAGCCCCTCCCACCGT
1 TC-AAGAGGCCCCTCCCACCGT
433270 TCAAGAGGCCCCTCCCACCGT
1 TCAAGAGGCCCCTCCCACCGT
433291 TCAAGAGGCCCCTCCCACCGT
1 TCAAGAGGCCCCTCCCACCGT
433312 TCAAGAGG
1 TCAAGAGG
433320 TCTCGCCCGT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
20 2 0.02
21 77 0.95
22 2 0.02
ACGTcount: A:0.22, C:0.41, G:0.20, T:0.17
Consensus pattern (21 bp):
TCAAGAGGCCCCTCCCACCGT
Found at i:433334 original size:42 final size:42
Alignment explanation
Indices: 433207--433339 Score: 133
Period size: 42 Copynumber: 3.2 Consensus size: 42
433197 CTATCATCAC
* * * * * * *
433207 TCAAGAGGCGCCTCCTATCGTTCAAGAGGCCCCTCTCATC-A
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCGCCCACCGT
* *
433248 TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTCCCACCGT
1 TC-AAGAGGCCCCTCCCACCGTTCAAGAGGCCCCGCCCACCGT
* * **
433291 TCAAGAGGCCCCTCCCACCGTTCAAGAGGTCTCGCCCGTCGT
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCGCCCACCGT
433333 TCAAGAG
1 TCAAGAG
433340 CCCGATTCAT
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
41 2 0.03
42 73 0.95
43 2 0.03
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.18
Consensus pattern (42 bp):
TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCGCCCACCGT
Found at i:434789 original size:28 final size:27
Alignment explanation
Indices: 434747--434835 Score: 88
Period size: 27 Copynumber: 3.1 Consensus size: 27
434737 TTTTTGCTTA
434747 TTTAATTGATTTGTAAAAGTTTATTTG
1 TTTAATTGATTTGTAAAAGTTTATTTG
* *
434774 TTTAATTTGATGTGTAAATAAGAATTTTTTTTG
1 TTTAA-TTGATTTGT-AA-AAG---TTTATTTG
* *
434807 TTTCATTGATTTGTAAAAGTTGATTTG
1 TTTAATTGATTTGTAAAAGTTTATTTG
434834 TT
1 TT
434836 ATTTTAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
27 13 0.26
28 8 0.16
29 2 0.04
30 6 0.12
31 2 0.04
32 8 0.16
33 11 0.22
ACGTcount: A:0.28, C:0.01, G:0.16, T:0.55
Consensus pattern (27 bp):
TTTAATTGATTTGTAAAAGTTTATTTG
Found at i:434833 original size:60 final size:61
Alignment explanation
Indices: 434698--434835 Score: 181
Period size: 60 Copynumber: 2.2 Consensus size: 61
434688 TTTTACATTG
434698 AAAGTTGATTTGTTTAATTGATGAATAAATAAAAATTATTTTTTGCTTATTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAATAAATAAAAATTATTTTTTG--T-TTTAATTGATTTGTA
* ** * *
434762 AAAGTTTATTTGTTTAATTTGATGTGTAAATAAGAATT-TTTTTTG-TTTCATTGATTTGTA
1 AAAGTTGATTTGTTTAA-TTGATGAATAAATAAAAATTATTTTTTGTTTTAATTGATTTGTA
434822 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
434836 ATTTTAAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
60 27 0.40
64 23 0.34
65 17 0.25
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.52
Consensus pattern (61 bp):
AAAGTTGATTTGTTTAATTGATGAATAAATAAAAATTATTTTTTGTTTTAATTGATTTGTA
Found at i:435353 original size:18 final size:18
Alignment explanation
Indices: 435330--435365 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
435320 AAGTCGGTTG
*
435330 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
435348 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
435366 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:442174 original size:21 final size:20
Alignment explanation
Indices: 442106--442186 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 20
442096 TTGGTGCAGA
*
442106 GGGAATCGA-TCCCCCCAATG
1 GGGAACCGATTCCCCCCAA-G
*
442126 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGATTCCCCC---CAAG
442150 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCA-AG
* *
442171 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
442187 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.02
21 24 0.48
22 6 0.12
23 16 0.32
24 1 0.02
25 2 0.04
ACGTcount: A:0.25, C:0.36, G:0.25, T:0.15
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCAAG
Found at i:445960 original size:18 final size:18
Alignment explanation
Indices: 445937--445973 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
445927 CGAAATTTAT
445937 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
445955 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
445973 A
1 A
445974 CTCCAATTAC
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:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:446387 original size:25 final size:25
Alignment explanation
Indices: 446359--446408 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
446349 CATTATTTTC
*
446359 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
*
446384 CAAATAATGTACCCACAATAATGTT
1 CAAATAATGTACCCACAACAATGTT
446409 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:446403 original size:14 final size:13
Alignment explanation
Indices: 446358--446407 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
446348 ACATTATTTT
446358 CCAAATAATGTAC
1 CCAAATAATGTAC
*
446371 CCATAACAATGT--
1 CCA-AATAATGTAC
*
446383 TCAAATAATGTAC
1 CCAAATAATGTAC
446396 CCACAATAATGT
1 CCA-AATAATGT
446408 TTAATTGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
11 7 0.24
12 2 0.07
13 5 0.17
14 15 0.52
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (13 bp):
CCAAATAATGTAC
Found at i:448227 original size:97 final size:98
Alignment explanation
Indices: 448038--448230 Score: 343
Period size: 97 Copynumber: 2.0 Consensus size: 98
448028 AAGTTTACTT
448038 CAAGGTATCGACCTTTCAAATGTGCTCCATCAACTATAATAACTGGGCGCATGCAAGTAATAAAC
1 CAAGGTATCGACCTTTCAAATGTGCTCCATCAACTATAATAACTGGGCGCATGCAAGTAATAAAC
*
448103 GAACAAATCTACAATATCATATACACAATAATC
66 GAACAAATCTACAAAATCATATACACAATAATC
*
448136 CAAGGTATCGACCTTTCAAATGTGCTCCGTCAACTATAATAACT-GGCGCATGCAAGTAATAAAC
1 CAAGGTATCGACCTTTCAAATGTGCTCCATCAACTATAATAACTGGGCGCATGCAAGTAATAAAC
**
448200 GAATGAATCTACAAAATCATATACACAATAA
66 GAACAAATCTACAAAATCATATACACAATAA
448231 ATATAATTAT
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
97 48 0.53
98 43 0.47
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (98 bp):
CAAGGTATCGACCTTTCAAATGTGCTCCATCAACTATAATAACTGGGCGCATGCAAGTAATAAAC
GAACAAATCTACAAAATCATATACACAATAATC
Found at i:448995 original size:3 final size:3
Alignment explanation
Indices: 448987--449011 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
448977 TCTTCGGGGA
448987 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
449012 AGGGTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:450229 original size:20 final size:19
Alignment explanation
Indices: 450204--450251 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
450194 TAAATTCGTA
450204 TTGCGAATTCGAAAAGCTAG
1 TTGCGAATTCGAAAAGC-AG
* **
450224 TTGCGAATTTGAAATTCAG
1 TTGCGAATTCGAAAAGCAG
450243 TTGCGAATT
1 TTGCGAATT
450252 TGACTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.33
Consensus pattern (19 bp):
TTGCGAATTCGAAAAGCAG
Found at i:450267 original size:20 final size:20
Alignment explanation
Indices: 450242--450408 Score: 203
Period size: 20 Copynumber: 8.3 Consensus size: 20
450232 TTGAAATTCA
450242 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * *
450262 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
450282 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
* *
450302 GTTGCG-ATTT-ACAAATTGGT
1 GTTGCGAATTTGAC--TTTTGT
450322 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
450342 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
450362 GTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
450382 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
450402 GTTGCGA
1 GTTGCGA
450409 TTTACAAATT
Statistics
Matches: 122, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
18 2 0.02
19 4 0.03
20 110 0.90
21 4 0.03
22 2 0.02
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:450360 original size:100 final size:100
Alignment explanation
Indices: 450242--450428 Score: 347
Period size: 100 Copynumber: 1.9 Consensus size: 100
450232 TTGAAATTCA
*
450242 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGC
1 GTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGC
* *
450307 GATTTACAAATTGGTGTTGCGAATTTGACTTTTGT
66 GATTTACAAATTCGCGTTGCGAATTTGACTTTTGT
450342 GTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGC
1 GTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGC
450407 GATTTACAAATTCGCGTTGCGA
66 GATTTACAAATTCGCGTTGCGA
450429 TTTACAGATT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.20, C:0.13, G:0.25, T:0.42
Consensus pattern (100 bp):
GTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGC
GATTTACAAATTCGCGTTGCGAATTTGACTTTTGT
Found at i:450422 original size:40 final size:40
Alignment explanation
Indices: 450342--450428 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
450332 TGACTTTTGT
* *
450342 GTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTTATGTGTTGCAAATTTGACAATCGC
*
450382 GTTGCGAATTTGACTTATGTGTTGC-GATTT-ACAAATTCGC
1 GTTGCGAATTTGACTTATGTGTTGCAAATTTGAC-AA-TCGC
450422 GTTGCGA
1 GTTGCGA
450429 TTTACAGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 2 0.05
39 5 0.12
40 35 0.83
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (40 bp):
GTTGCGAATTTGACTTATGTGTTGCAAATTTGACAATCGC
Found at i:450425 original size:20 final size:20
Alignment explanation
Indices: 450402--450448 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
450392 TGACTTATGT
450402 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
450422 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
450442 GTTGCGA
1 GTTGCGA
450449 AATTGGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:450442 original size:60 final size:60
Alignment explanation
Indices: 450262--450449 Score: 172
Period size: 60 Copynumber: 3.1 Consensus size: 60
450252 TGACTTTTGT
* * * * *
450262 GTTGCGAATTTGAC-TATCGCGTTGCGAATTTGAC-TTATGTGTTGCGATTTACAAATTGGT
1 GTTGCGAATTTGACTTAT-GTGTTGCGAATTTGACATT-CGCGTTGCGATTTACAAATTCGC
* * * * * *
450322 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGTGTTGCAAATTTGAC-TA-TCGC
1 GTTGCGAATTTGACTTATGTGTTGCGAATTTGACATTCGCGTTGC-GATTT-ACAAATTCGC
*
450382 GTTGCGAATTTGACTTATGTGTTGCG-ATTT-ACAAATTCGCGTTGCGATTTACAGATTCGC
1 GTTGCGAATTTGACTTATGTGTTGCGAATTTGAC--ATTCGCGTTGCGATTTACAAATTCGC
450442 GTTGCGAA
1 GTTGCGAA
450450 ATTGGAAACT
Statistics
Matches: 108, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
58 4 0.04
59 9 0.08
60 84 0.78
61 9 0.08
62 2 0.02
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.40
Consensus pattern (60 bp):
GTTGCGAATTTGACTTATGTGTTGCGAATTTGACATTCGCGTTGCGATTTACAAATTCGC
Found at i:450446 original size:100 final size:100
Alignment explanation
Indices: 450223--450449 Score: 343
Period size: 100 Copynumber: 2.3 Consensus size: 100
450213 CGAAAAGCTA
* * *
450223 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGC
1 GTTGCGAATTTGACATTCGCGTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGC
* *
450287 GAATTTGACTTATGTGTTGCGATTTACAAATTGGT
66 GAATTTGACTTATGTGTTGCGATTTACAAATTCGC
* * *
450322 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGC
1 GTTGCGAATTTGACATTCGCGTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGC
450387 GAATTTGACTTATGTGTTGCGATTTACAAATTCGC
66 GAATTTGACTTATGTGTTGCGATTTACAAATTCGC
450422 GTTGCG-ATTT-ACAGATTCGCGTTGCGAA
1 GTTGCGAATTTGAC--ATTCGCGTTGCGAA
450450 ATTGGAAACT
Statistics
Matches: 115, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
98 2 0.02
99 19 0.17
100 94 0.82
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (100 bp):
GTTGCGAATTTGACATTCGCGTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGC
GAATTTGACTTATGTGTTGCGATTTACAAATTCGC
Found at i:450489 original size:20 final size:19
Alignment explanation
Indices: 450435--450489 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
450425 GCGATTTACA
450435 GATTCGCGTTGCGAAATTG
1 GATTCGCGTTGCGAAATTG
** * *
450454 GAAACTGGGTTACGAAATTG
1 GATTC-GCGTTGCGAAATTG
450474 GAGTTCGCGTTGCGAA
1 GA-TTCGCGTTGCGAA
450490 TTTATTGGTC
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
19 3 0.12
20 22 0.85
21 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (19 bp):
GATTCGCGTTGCGAAATTG
Found at i:451347 original size:78 final size:77
Alignment explanation
Indices: 451195--451349 Score: 247
Period size: 77 Copynumber: 2.0 Consensus size: 77
451185 ATCAGATGAG
* *
451195 ACGATGCGACGGAGGAGAAAGACAGCTCACAAGGGATAGCATACGATAAGAACTCTCTCGAAACC
1 ACGATGCAACGAAGGAGAAAGACAGCTCACAAGGGATAGCATACGATAAGAACTCTCTCGAAACC
451260 TTGATGGAACTT
66 TTGATGGAACTT
* * * *
451272 ACGATGCAACGAAGGAGAAAGACAGCTCCCGAGGGATAGTATATCGATAAGAACTCTCTCGAACC
1 ACGATGCAACGAAGGAGAAAGACAGCTCACAAGGGATAGCATA-CGATAAGAACTCTCTCGAAAC
451337 CTTGATGGAACTT
65 CTTGATGGAACTT
451350 TTATGTTCGG
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 38 0.54
78 33 0.46
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.18
Consensus pattern (77 bp):
ACGATGCAACGAAGGAGAAAGACAGCTCACAAGGGATAGCATACGATAAGAACTCTCTCGAAACC
TTGATGGAACTT
Found at i:457886 original size:19 final size:20
Alignment explanation
Indices: 457842--457887 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
457832 AACCGCTAAA
*
457842 GAACCGGTAGAATCGGTTGG
1 GAACCGGTAAAATCGGTTGG
*
457862 GAACCGGTAAAATCGG-TGT
1 GAACCGGTAAAATCGGTTGG
457881 GAACCGG
1 GAACCGG
457888 CGATTCAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.28, C:0.17, G:0.37, T:0.17
Consensus pattern (20 bp):
GAACCGGTAAAATCGGTTGG
Found at i:464161 original size:16 final size:16
Alignment explanation
Indices: 464137--464169 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
464127 TATCGTCGAC
*
464137 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
464153 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
464169 C
1 C
464170 ATGAATAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:464643 original size:36 final size:36
Alignment explanation
Indices: 464598--464669 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
464588 ACATCTACAA
*
464598 AAATTTTACCAAACTTTGAAAAACAT-TTTT-CAAAG
1 AAATTTTACCAAACTTT-AAAAAAATATTTTCCAAAG
464633 AAATATTTACCAAACTTTAAAAAAATATTTTCCAAAG
1 AAAT-TTTACCAAACTTTAAAAAAATATTTTCCAAAG
464670 TTAGTTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
35 11 0.33
36 17 0.52
37 5 0.15
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (36 bp):
AAATTTTACCAAACTTTAAAAAAATATTTTCCAAAG
Found at i:476788 original size:2 final size:2
Alignment explanation
Indices: 476783--476813 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
476773 CTGTGTGCGA
476783 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 A
476814 CCTGATTGTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:480003 original size:183 final size:183
Alignment explanation
Indices: 479695--480265 Score: 1038
Period size: 183 Copynumber: 3.1 Consensus size: 183
479685 TTAAAATTAG
*
479695 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
479760 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
479825 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
479878 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
479943 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
480008 CACTTTTTGACAATGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
480061 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* * * *
480126 ATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTTTTTTCAA--T
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG---TGTAAATGT
*
480189 CGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
128 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
480245 CGACACAATATTAAAAAGTGT
1 CGACACAATATTAAAAAGTGT
480266 GAAAACTTTG
Statistics
Matches: 377, Mismatches: 8, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
183 297 0.79
184 76 0.20
186 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (183 bp):
CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
Found at i:481169 original size:200 final size:200
Alignment explanation
Indices: 480869--481829 Score: 1018
Period size: 200 Copynumber: 4.7 Consensus size: 200
480859 TTATATACCA
* * *
480869 ATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
*
480934 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
* *
480999 TGTTTGCCATTCATTTTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTATCGACACATTATTTA
481064 GACAT
196 GACAT
481069 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* * *
481134 ATGGGTTTCGATGTTTATGGGATCAACACTTTTTATATATGGATCGACACTTTATTGTTGCACCA
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
*
481199 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTATCGACACATTATTTA
*
481264 GACCT
196 GACAT
* *
481269 ATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGAATGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
*
481334 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTTTAT-ATATGGA
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACAC--TTTATGGT-T-G-
* * ** *** * * * **
481398 TCGACACTTTATTG---TTGCACCCTGTTTG-CCATTCAT-TCTGGATCA-AAAATATCGACACA
126 -C-ACCCTGT-TTGCCATT-CATTCTG---GACCAAAAATATC--GA-CACAAACTA-CAAAAGT
* * * * * *
481457 AACTACA-A-AAGTGTCGATAT
180 ATCGACACATTA-TTTAGACAT
* * * * * * * ***
481477 ATTAT-T--T-AGACC--TATTCTCTCATAAAACCGGTATA-CTTGTACCGGTTAGATTGAAAAA
1 ATTCTCTCATAAAACCGGTATACT-T-GT---ACCGGT-TAGATTG-A-----AAAATT-ACCTA
*
481535 TTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATC
53 TTA-C-ATT--A-TA--CTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATC
* *
481600 GACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACAAAAAATATCGACACAAACTACAA
111 GACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAA
* *
481665 AAGTATCGATACATTATTTAGACTT
176 AAGTATCGACACATTATTTAGACAT
*
481690 ATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* * *
481755 TTAGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATTGACACTTTATGGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
481820 TGTTTGCCAT
131 TGTTTGCCAT
481830 ATTGTAAATT
Statistics
Matches: 623, Mismatches: 85, Indels: 106
0.77 0.10 0.13
Matches are distributed among these distances:
200 376 0.60
201 1 0.00
202 13 0.02
203 3 0.00
204 6 0.01
205 10 0.02
206 7 0.01
207 23 0.04
208 25 0.04
209 9 0.01
212 9 0.01
213 25 0.04
214 22 0.04
215 8 0.01
216 10 0.02
217 7 0.01
218 3 0.00
219 13 0.02
220 1 0.00
221 52 0.08
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTATCGACACATTATTTA
GACAT
Found at i:481378 original size:21 final size:21
Alignment explanation
Indices: 481353--481407 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
481343 GATGTTTATG
481353 GGATCGACACTTTTTATATAT
1 GGATCGACACTTTTTATATAT
481374 GGATCGACACTTTTTATATAT
1 GGATCGACACTTTTTATATAT
481395 GGATCGACACTTT
1 GGATCGACACTTT
481408 ATTGTTGCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (21 bp):
GGATCGACACTTTTTATATAT
Found at i:481431 original size:221 final size:221
Alignment explanation
Indices: 481153--481607 Score: 838
Period size: 221 Copynumber: 2.1 Consensus size: 221
481143 GATGTTTATG
*
481153 GGATCAACACTTTTTATATATGGATCGACACTTTATTGTTGCACCATGTTTGCCATTCATTCTGG
1 GGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCATGTTTGCCATTCATTCTGG
481218 ACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAA
66 ACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAA
*
481283 TCGGTATACTTGTACCGGTTAGAATGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
131 CCGGTATACTTGTACCGGTTAGAATGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
*
481348 TTATGGGATCGACACTTTTTATATAT
196 TTATCGGATCGACACTTTTTATATAT
*
481374 GGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGG
1 GGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCATGTTTGCCATTCATTCTGG
* * *
481439 ATCAAAAATATCGACACAAACTACAAAAGTGTCGATATATTATTTAGACCTATTCTCTCATAAAA
66 ACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAA
*
481504 CCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
131 CCGGTATACTTGTACCGGTTAGAATGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
481569 TTATCGGATCGACACTTTTTATATAT
196 TTATCGGATCGACACTTTTTATATAT
481595 GGATCGACACTTT
1 GGATCGACACTTT
481608 ATTGTTGCAC
Statistics
Matches: 226, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
221 226 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (221 bp):
GGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCATGTTTGCCATTCATTCTGG
ACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAA
CCGGTATACTTGTACCGGTTAGAATGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
TTATCGGATCGACACTTTTTATATAT
Found at i:481737 original size:421 final size:421
Alignment explanation
Indices: 480953--481807 Score: 1539
Period size: 421 Copynumber: 2.0 Consensus size: 421
480943 GATGTTTATG
*
480953 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTTTGG
1 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
481018 ACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
66 ACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
481083 CCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
131 CCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
*
481148 TTATGGGATCAACACTTTTTATATATGGATCGACACTTTATTGTTGCACCATGTTTGCCATTCAT
196 TTATCGGATCAACACTTTTTATATATGGATCGACACTTTATTGTTGCACCATGTTTGCCATTCAT
* *
481213 TCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACCTATTCTCTCA
261 TCTGGACAAAAAATATCGACACAAACTACAAAAGTATCGACACATTATTTAGACCTATTCTCTCA
* * *
481278 TAAAATCGGTATACTTGTACCGGTTAGAATGAAAAATTACCTATTACATTATACTTATGGGTTTC
326 TAAAACCGGTATACTTGTACCGATTAGAATGAAAAATTACCTATTACATTATACTTATAGGTTTC
481343 GATGTTTATGGGATCGACACTTTTTATATAT
391 GATGTTTATGGGATCGACACTTTTTATATAT
*
481374 GGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGG
1 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
* * * *
481439 ATCAAAAATATCGACACAAACTACAAAAGTGTCGATATATTATTTAGACCTATTCTCTCATAAAA
66 ACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
481504 CCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
131 CCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
* *
481569 TTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCAT
196 TTATCGGATCAACACTTTTTATATATGGATCGACACTTTATTGTTGCACCATGTTTGCCATTCAT
* *
481634 TCTGGACAAAAAATATCGACACAAACTACAAAAGTATCGATACATTATTTAGACTTATTCTCTCA
261 TCTGGACAAAAAATATCGACACAAACTACAAAAGTATCGACACATTATTTAGACCTATTCTCTCA
* *
481699 TAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACATTATACTTTTAGGTTTC
326 TAAAACCGGTATACTTGTACCGATTAGAATGAAAAATTACCTATTACATTATACTTATAGGTTTC
481764 GATGTTTATGGGATCGACACTTTTTATATAT
391 GATGTTTATGGGATCGACACTTTTTATATAT
*
481795 GGATTGACACTTT
1 GGATCGACACTTT
481808 ATGGTTGCAC
Statistics
Matches: 415, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
421 415 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (421 bp):
GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
ACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
CCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
TTATCGGATCAACACTTTTTATATATGGATCGACACTTTATTGTTGCACCATGTTTGCCATTCAT
TCTGGACAAAAAATATCGACACAAACTACAAAAGTATCGACACATTATTTAGACCTATTCTCTCA
TAAAACCGGTATACTTGTACCGATTAGAATGAAAAATTACCTATTACATTATACTTATAGGTTTC
GATGTTTATGGGATCGACACTTTTTATATAT
Found at i:482074 original size:18 final size:18
Alignment explanation
Indices: 482051--482111 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
482041 TCTCATTCAT
*
482051 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
482069 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
482088 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
482107 AATTA
1 AATTA
482112 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:482087 original size:19 final size:19
Alignment explanation
Indices: 482063--482111 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
482053 TTATATTCAC
482063 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
482082 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
482101 ATACAAAATTA
1 ATACAAAATTA
482112 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Done.