Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 102 of 135
Found at i:34964519 original size:12 final size:12
Alignment explanation
Indices: 34964481--34964541 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
34964471 AACAGTTACG
*
34964481 AAACAACA-ATA
1 AAACAACACAAA
*
34964492 AAACAACAC--C
1 AAACAACACAAA
34964502 AAACAACACAAA
1 AAACAACACAAA
*
34964514 AAACAACACCAA
1 AAACAACACAAA
* *
34964526 CAACAACACCAA
1 AAACAACACAAA
34964538 AAAC
1 AAAC
34964542 CTGTCAAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
10 9 0.21
11 8 0.19
12 25 0.60
ACGTcount: A:0.67, C:0.31, G:0.00, T:0.02
Consensus pattern (12 bp):
AAACAACACAAA
Found at i:34964530 original size:24 final size:22
Alignment explanation
Indices: 34964481--34964541 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 22
34964471 AACAGTTACG
*
34964481 AAACAACA-ATAAAACAACACC
1 AAACAACACAAAAAACAACACC
34964502 AAACAACACAAAAAACAACACC
1 AAACAACACAAAAAACAACACC
*
34964524 AACAACAACACCAAAAAC
1 -A-AACAACACAAAAAAC
34964542 CTGTCAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 8 0.23
22 12 0.34
23 1 0.03
24 14 0.40
ACGTcount: A:0.67, C:0.31, G:0.00, T:0.02
Consensus pattern (22 bp):
AAACAACACAAAAAACAACACC
Found at i:34977270 original size:34 final size:34
Alignment explanation
Indices: 34977232--34977297 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
34977222 ACCTTTCAAC
*
34977232 TCCCTTGACTTTTAACC-TTCCACTTTCCTTAATT
1 TCCCTTGACGTTTAACCGTT-CACTTTCCTTAATT
*
34977266 TCCCTTGACGTTTAACCGTTCATTTTCCTTAA
1 TCCCTTGACGTTTAACCGTTCACTTTCCTTAA
34977298 CCTTTCATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.18, C:0.30, G:0.06, T:0.45
Consensus pattern (34 bp):
TCCCTTGACGTTTAACCGTTCACTTTCCTTAATT
Found at i:34979997 original size:16 final size:17
Alignment explanation
Indices: 34979973--34980006 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
34979963 TTAAGGGGAG
*
34979973 AAAATAAATAG-TTGGA
1 AAAAGAAATAGATTGGA
34979989 AAAAGAAATAGATTGGA
1 AAAAGAAATAGATTGGA
34980006 A
1 A
34980007 TGAATTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (17 bp):
AAAAGAAATAGATTGGA
Found at i:34980754 original size:16 final size:16
Alignment explanation
Indices: 34980733--34980764 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34980723 GATTTTCACA
34980733 AAGACCTGATATTGAT
1 AAGACCTGATATTGAT
*
34980749 AAGACCTGGTATTGAT
1 AAGACCTGATATTGAT
34980765 TATGAAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (16 bp):
AAGACCTGATATTGAT
Found at i:34982385 original size:17 final size:17
Alignment explanation
Indices: 34982365--34982406 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
34982355 CTCTCTTGAC
*
34982365 CTTTAACCCTTCATTTT
1 CTTTAACCCTTCATATT
*
34982382 CTTTAACCTTTCATATT
1 CTTTAACCCTTCATATT
34982399 CTTGTAAC
1 CTT-TAAC
34982407 TACTATTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.50
Consensus pattern (17 bp):
CTTTAACCCTTCATATT
Found at i:34984125 original size:21 final size:21
Alignment explanation
Indices: 34984083--34984135 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
34984073 CAATCGACAC
34984083 AAAACCATC-AAACAAAACAG
1 AAAACCATCAAAACAAAACAG
* * *
34984103 AAAACCAACAAAACGAAATAG
1 AAAACCATCAAAACAAAACAG
34984124 AAAACCATCAAA
1 AAAACCATCAAA
34984136 GGTTGAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.66, C:0.23, G:0.06, T:0.06
Consensus pattern (21 bp):
AAAACCATCAAAACAAAACAG
Found at i:35002013 original size:52 final size:52
Alignment explanation
Indices: 35001912--35002015 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 52
35001902 TTCAATTACA
* * *
35001912 AATGGTAAGAAAATATTATTTAATAATTTAGTTTTAATCCGTTAATTATTAT
1 AATGGTAAGAAAATATTATTAAATAATTTAATTTTAATCAGTTAATTATTAT
* * *
35001964 AATGTTAAGAAAATATTATTAAATTATTTAATTTTAAAT-AGTTAGTTATTAT
1 AATGGTAAGAAAATATTATTAAATAATTTAATTTT-AATCAGTTAATTATTAT
35002016 GTTGTTCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
52 42 0.93
53 3 0.07
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (52 bp):
AATGGTAAGAAAATATTATTAAATAATTTAATTTTAATCAGTTAATTATTAT
Found at i:35002821 original size:21 final size:21
Alignment explanation
Indices: 35002797--35002870 Score: 116
Period size: 21 Copynumber: 3.5 Consensus size: 21
35002787 TTGTGCTAGC
35002797 TCTACCGATACAAGTATGATT
1 TCTACCGATACAAGTATGATT
35002818 TCTACCGATACAAGTATGATT
1 TCTACCGATACAAGTATGATT
35002839 TCTACCGATACAAGTCATGCA-T
1 TCTACCGATACAAGT-ATG-ATT
35002861 T-TACCGATAC
1 TCTACCGATAC
35002871 CAGAAACTCC
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
21 45 0.88
22 5 0.10
23 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (21 bp):
TCTACCGATACAAGTATGATT
Found at i:35002948 original size:21 final size:22
Alignment explanation
Indices: 35002924--35002986 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 22
35002914 CAATATAAGC
35002924 ATACAAACTACCGATACAT-CA
1 ATACAAACTACCGATACATACA
*
35002945 ATACTAATAACTACCGATACTTACA
1 ATAC--A-AACTACCGATACATACA
*
35002970 ATTC-AACTACCGATACA
1 ATACAAACTACCGATACA
35002987 ACTCAAGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
21 16 0.46
23 1 0.03
24 13 0.37
25 5 0.14
ACGTcount: A:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (22 bp):
ATACAAACTACCGATACATACA
Found at i:35004327 original size:2 final size:2
Alignment explanation
Indices: 35004322--35004349 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35004312 TATTTTAATT
35004322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35004350 GTCAATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35005905 original size:63 final size:61
Alignment explanation
Indices: 35005830--35005947 Score: 182
Period size: 63 Copynumber: 1.9 Consensus size: 61
35005820 TTGTAAAAAC
* * *
35005830 ACATACAACACCAGTTTATTTTACACAAGCACCACATCATGCGCAATCATTCCCTACAACA
1 ACATACAACACCACTTTATTTTACACAAGCACCACAACACGCGCAATCATTCCCTACAACA
*
35005891 ACATAACAATCACCACTTTATTTTATACAAGCACCACAACACGCGCAATCATTCCCT
1 ACAT-ACAA-CACCACTTTATTTTACACAAGCACCACAACACGCGCAATCATTCCCT
35005948 GTACCGGTAG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
61 4 0.08
62 4 0.08
63 43 0.84
ACGTcount: A:0.37, C:0.33, G:0.06, T:0.24
Consensus pattern (61 bp):
ACATACAACACCACTTTATTTTACACAAGCACCACAACACGCGCAATCATTCCCTACAACA
Found at i:35008317 original size:21 final size:21
Alignment explanation
Indices: 35008292--35008339 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
35008282 TAACAGTGAA
35008292 TAGGTAGTTAACAATATTAAT
1 TAGGTAGTTAACAATATTAAT
35008313 TAGGTAGTTAACAATATTAAT
1 TAGGTAGTTAACAATATTAAT
35008334 TAGGTA
1 TAGGTA
35008340 TGAAAATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.38
Consensus pattern (21 bp):
TAGGTAGTTAACAATATTAAT
Found at i:35012475 original size:30 final size:32
Alignment explanation
Indices: 35012439--35012510 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
35012429 AAGTTTCAAT
35012439 TCAGTCACTCAAC-TT-TCAAAAAATAACAAA
1 TCAGTCACTCAACATTATCAAAAAATAACAAA
** * *
35012469 TCAGTCACT-AACATTATTGAAAAGTGACAAA
1 TCAGTCACTCAACATTATCAAAAAATAACAAA
35012500 TCAGTCACTCA
1 TCAGTCACTCA
35012511 TTAACATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 3 0.09
30 11 0.31
31 20 0.57
32 1 0.03
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.25
Consensus pattern (32 bp):
TCAGTCACTCAACATTATCAAAAAATAACAAA
Found at i:35012568 original size:174 final size:174
Alignment explanation
Indices: 35012257--35012607 Score: 404
Period size: 174 Copynumber: 2.0 Consensus size: 174
35012247 AGTCACATTG
* * **
35012257 GTTTCATTTCAGTCACTCAACTTTACAAAAATAACAAAACAATCGCTAATGTTATCAAAAAGTGA
1 GTTTCAATTCAGTCACTCAACTTTACAAAAATAACAAAACAATCACTAACATTATCAAAAAGTGA
* ** * ** * *
35012322 CAAATCAGTCACTTATTAACATTTTTCGTTATTGTCTTAACGGCACGGGTGACGTGGCCAGTTAA
66 CAAATCAGTCACTCATTAACATTTTTCGTTAAAGACTTAACGGCACAAGTGACGTGACCAGTAAA
* * *
35012387 CTAGCTGATGT-GACCAGTTAACTGGCCACGTTGGACGAGGTAAA
131 CTAGCTGATGTAG-CCAGTTAACTGGCCAAGTTAGACGAGGCAAA
* * **
35012431 GTTTCAATTCAGTCACTCAACTTT-CAAAAAATAACAAATCAGTCACTAACATTATTGAAAAGTG
1 GTTTCAATTCAGTCACTCAACTTTAC-AAAAATAACAAAACAATCACTAACATTATCAAAAAGTG
* * *
35012495 ACAAATCAGTCACTCATTAACATTTTTTGTTACAAGAC-TAACGAG-ACAAGTGATGTGATCAGT
65 ACAAATCAGTCACTCATTAACATTTTTCGTTA-AAGACTTAACG-GCACAAGTGACGTGACCAGT
* * * *
35012558 AAATTAGCTGATGTAGTCAGTTAACTTGTCAAGTTAGACGAGGCAAA
128 AAACTAGCTGATGTAGCCAGTTAACTGGCCAAGTTAGACGAGGCAAA
35012605 GTT
1 GTT
35012608 GAATGACTTT
Statistics
Matches: 147, Mismatches: 26, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
173 1 0.01
174 142 0.97
175 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (174 bp):
GTTTCAATTCAGTCACTCAACTTTACAAAAATAACAAAACAATCACTAACATTATCAAAAAGTGA
CAAATCAGTCACTCATTAACATTTTTCGTTAAAGACTTAACGGCACAAGTGACGTGACCAGTAAA
CTAGCTGATGTAGCCAGTTAACTGGCCAAGTTAGACGAGGCAAA
Found at i:35015350 original size:35 final size:35
Alignment explanation
Indices: 35015311--35015444 Score: 153
Period size: 35 Copynumber: 3.8 Consensus size: 35
35015301 AGACACAGAA
*
35015311 GTTTGAGCATACTAGCTCGTTGAGCATAATAACTT
1 GTTTGAGCATACTGGCTCGTTGAGCATAATAACTT
* * * *
35015346 GTTTGAGCATGCTGGCTCGTTAAGCATACTGACTT
1 GTTTGAGCATACTGGCTCGTTGAGCATAATAACTT
* * *
35015381 GTTTGAGCATACTGGCTCGTTGAGCATACTGGA-TA
1 GTTTGAGCATACTGGCTCGTTGAGCATAAT-AACTT
* *
35015416 GTTTGAGCATAGTGGCTCATTAGAGCATA
1 GTTTGAGCATACTGGCTCGTT-GAGCATA
35015445 CTGGCTCGTA
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
35 78 0.90
36 9 0.10
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (35 bp):
GTTTGAGCATACTGGCTCGTTGAGCATAATAACTT
Found at i:35015353 original size:18 final size:18
Alignment explanation
Indices: 35015311--35015355 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
35015301 AGACACAGAA
* *
35015311 GTTTGAGCATACTAGCTC
1 GTTTGAGCATAATAACTC
*
35015329 G-TTGAGCATAATAACTT
1 GTTTGAGCATAATAACTC
35015346 GTTTGAGCAT
1 GTTTGAGCAT
35015356 GCTGGCTCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (18 bp):
GTTTGAGCATAATAACTC
Found at i:35015424 original size:70 final size:71
Alignment explanation
Indices: 35015311--35015447 Score: 190
Period size: 70 Copynumber: 1.9 Consensus size: 71
35015301 AGACACAGAA
* *
35015311 GTTTGAGCATACTAGCTCGTTGAGCATAATAACTTGTTTGAGCAT-GCTGGCTCGTTA-AGCATA
1 GTTTGAGCATACTAGCTCGTTGAGCATAATAACTAGTTTGAGCATAG-TGGCTCATTAGAGCATA
35015374 CTGACTT
65 CTGACTT
* * *
35015381 GTTTGAGCATACTGGCTCGTTGAGCATACTGGA-TAGTTTGAGCATAGTGGCTCATTAGAGCATA
1 GTTTGAGCATACTAGCTCGTTGAGCATAAT-AACTAGTTTGAGCATAGTGGCTCATTAGAGCATA
35015445 CTG
65 CTG
35015448 GCTCGTAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
70 48 0.81
71 11 0.19
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (71 bp):
GTTTGAGCATACTAGCTCGTTGAGCATAATAACTAGTTTGAGCATAGTGGCTCATTAGAGCATAC
TGACTT
Found at i:35015441 original size:18 final size:17
Alignment explanation
Indices: 35015348--35015451 Score: 84
Period size: 18 Copynumber: 5.9 Consensus size: 17
35015338 AATAACTTGT
* *
35015348 TTGAGCATGCTGGCTCG
1 TTGAGCATACTGGCTCA
* * **
35015365 TTAAGCATACTGACTTGT
1 TTGAGCATACTGGC-TCA
*
35015383 TTGAGCATACTGGCTCG
1 TTGAGCATACTGGCTCA
*
35015400 TTGAGCATACTGGAT-A
1 TTGAGCATACTGGCTCA
*
35015416 GTTTGAGCATAGTGGCTCA
1 --TTGAGCATACTGGCTCA
35015435 TTAGAGCATACTGGCTC
1 TT-GAGCATACTGGCTC
35015452 GTAAAAGCAT
Statistics
Matches: 68, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
17 28 0.41
18 39 0.57
19 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (17 bp):
TTGAGCATACTGGCTCA
Found at i:35015461 original size:36 final size:35
Alignment explanation
Indices: 35015386--35015467 Score: 83
Period size: 36 Copynumber: 2.3 Consensus size: 35
35015376 GACTTGTTTG
* ***
35015386 AGCATACTGGCTCGTTGAGCATACTGGATAGTTTG
1 AGCATACTGGCTCATTGAGCATACTGGATAGTAAA
* * *
35015421 AGCATAGTGGCTCATTAGAGCATACTGGCTCGTAAA
1 AGCATACTGGCTCATT-GAGCATACTGGATAGTAAA
35015457 AGCATTACTGG
1 AGCA-TACTGG
35015468 ATCACAAGAG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 14 0.38
36 18 0.49
37 5 0.14
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (35 bp):
AGCATACTGGCTCATTGAGCATACTGGATAGTAAA
Found at i:35022154 original size:35 final size:35
Alignment explanation
Indices: 35022108--35022215 Score: 171
Period size: 35 Copynumber: 3.1 Consensus size: 35
35022098 AGACGCGAAA
35022108 GTTTGAGCATACTGGCTCATTGAGCATACTGGCTC
1 GTTTGAGCATACTGGCTCATTGAGCATACTGGCTC
* * *
35022143 GTTTGAGCATACTGGGTCGTTGAGCATACTAGCTC
1 GTTTGAGCATACTGGCTCATTGAGCATACTGGCTC
*
35022178 GTTTGAGCATACTGGCTCATTAGAGAATACTGGCTC
1 GTTTGAGCATACTGGCTCATT-GAGCATACTGGCTC
35022214 GT
1 GT
35022216 AAGAGCATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 51 0.78
36 14 0.22
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.31
Consensus pattern (35 bp):
GTTTGAGCATACTGGCTCATTGAGCATACTGGCTC
Found at i:35022220 original size:18 final size:18
Alignment explanation
Indices: 35022108--35022215 Score: 148
Period size: 18 Copynumber: 6.1 Consensus size: 18
35022098 AGACGCGAAA
35022108 GTTTGAGCATACTGGCTC
1 GTTTGAGCATACTGGCTC
*
35022126 -ATTGAGCATACTGGCTC
1 GTTTGAGCATACTGGCTC
*
35022143 GTTTGAGCATACTGGGTC
1 GTTTGAGCATACTGGCTC
*
35022161 G-TTGAGCATACTAGCTC
1 GTTTGAGCATACTGGCTC
35022178 GTTTGAGCATACTGGCTC
1 GTTTGAGCATACTGGCTC
* * *
35022196 ATTAGAGAATACTGGCTC
1 GTTTGAGCATACTGGCTC
35022214 GT
1 GT
35022216 AAGAGCATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
17 31 0.40
18 47 0.60
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.31
Consensus pattern (18 bp):
GTTTGAGCATACTGGCTC
Found at i:35029464 original size:26 final size:25
Alignment explanation
Indices: 35029427--35029486 Score: 59
Period size: 26 Copynumber: 2.3 Consensus size: 25
35029417 AATATTTATA
35029427 TTATATCATTTTAATAT-TTAATAATT
1 TTATAT-ATTTTAATATATTAA-AATT
* *
35029453 TTATATATTTTTTATTTATTAAAATT
1 TTATATA-TTTTAATATATTAAAATT
35029479 TGTATATA
1 T-TATATA
35029487 GTCATCTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 1 0.03
26 18 0.62
27 10 0.34
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTATATATTTTAATATATTAAAATT
Found at i:35041366 original size:43 final size:42
Alignment explanation
Indices: 35041285--35041543 Score: 248
Period size: 43 Copynumber: 6.0 Consensus size: 42
35041275 AATGCTATCA
* * *
35041285 CCGCTATAGAACATGGTTTTTAACGGCGCTTTTCCCACAAACA
1 CCGCTATAGAACATGGTCTTTAGCGGC-CTTTTCCCACAAACG
* * * * *
35041328 CCGCTATAGACCATTGTCTTTAGTGGCCTTTTTTCCACAAATG
1 CCGCTATAGAACATGGTCTTTAGCGGCC-TTTTCCCACAAACG
* * * * *
35041371 CCGTTATAGAACATGGCCTCTAGCGGTGCTTTACCCACAAACG
1 CCGCTATAGAACATGGTCTTTAGCGG-CCTTTTCCCACAAACG
* **
35041414 CCGCTATAGAGCATGGTCTTTAGCGGTGTTTTTCCCACAAACG
1 CCGCTATAGAACATGGTCTTTAGCGG-CCTTTTCCCACAAACG
** **
35041457 CCAATATAGAACATGGTCTTTAGCGGCGCTTTTTGCACAAACG
1 CCGCTATAGAACATGGTCTTTAGCGGC-CTTTTCCCACAAACG
** * *
35041500 CCTTTATAGAACATGATCTTTAGCGGCGTTTTTCCCACAAACG
1 CCGCTATAGAACATGGTCTTTAGCGGC-CTTTTCCCACAAACG
35041543 C
1 C
35041544 GACTAACAGT
Statistics
Matches: 176, Mismatches: 37, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
42 1 0.01
43 174 0.99
44 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (42 bp):
CCGCTATAGAACATGGTCTTTAGCGGCCTTTTCCCACAAACG
Found at i:35041434 original size:86 final size:86
Alignment explanation
Indices: 35041289--35041543 Score: 312
Period size: 86 Copynumber: 3.0 Consensus size: 86
35041279 CTATCACCGC
* * * * * *
35041289 TATAGAACATGGTTTTTAACGGCGCTTTTCCCACAAACACCGCTATAGACCATTGTCTTTAGTGG
1 TATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACATGGTCTTTAGCGG
* * * **
35041354 CCTTTTTTCCACAAATGCCGT
66 CGTTTTTCCCACAAACGCCAA
* * * * *
35041375 TATAGAACATGGCCTCTAGCGGTGCTTTACCCACAAACGCCGCTATAGAGCATGGTCTTTAGCGG
1 TATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACATGGTCTTTAGCGG
*
35041440 TGTTTTTCCCACAAACGCCAA
66 CGTTTTTCCCACAAACGCCAA
** ** *
35041461 TATAGAACATGGTCTTTAGCGGCGCTTTTTGCACAAACGCCTTTATAGAACATGATCTTTAGCGG
1 TATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACATGGTCTTTAGCGG
35041526 CGTTTTTCCCACAAACGC
66 CGTTTTTCCCACAAACGC
35041544 GACTAACAGT
Statistics
Matches: 142, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
86 142 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (86 bp):
TATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACATGGTCTTTAGCGG
CGTTTTTCCCACAAACGCCAA
Found at i:35041524 original size:129 final size:129
Alignment explanation
Indices: 35041285--35041543 Score: 322
Period size: 129 Copynumber: 2.0 Consensus size: 129
35041275 AATGCTATCA
* ** * *
35041285 CCGCTATAGAACATGGTTTTTAACGGCGCTTTTCCCACAAACACCGCTATAGACCATTGTCTTTA
1 CCGCTATAGAACATGGTCTTTAACGGCGCTTTTCCCACAAACACCAATATAGAACATGGTCTTTA
* * * *
35041350 GTGGCCTTTTTTCCACAAATGCCGTTATAGAACATGGCCTCTAGCGGTGCTTTACCCACAAACG
66 GCGGCCTTTTTTCCACAAACGCCGTTATAGAACATGACCTCTAGCGGCGCTTTACCCACAAACG
* * * * *
35041414 CCGCTATAGAGCATGGTCTTTAGCGGTGTTTTTCCCACAAACGCCAATATAGAACATGGTCTTTA
1 CCGCTATAGAACATGGTCTTTAACGGCGCTTTTCCCACAAACACCAATATAGAACATGGTCTTTA
* * * * * *
35041479 GCGGCGC-TTTTTGCACAAACGCCTTTATAGAACATGATCTTTAGCGGCGTTTTTCCCACAAACG
66 GCGGC-CTTTTTTCCACAAACGCCGTTATAGAACATGACCTCTAGCGGCGCTTTACCCACAAACG
35041543 C
1 C
35041544 GACTAACAGT
Statistics
Matches: 109, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
129 108 0.99
130 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (129 bp):
CCGCTATAGAACATGGTCTTTAACGGCGCTTTTCCCACAAACACCAATATAGAACATGGTCTTTA
GCGGCCTTTTTTCCACAAACGCCGTTATAGAACATGACCTCTAGCGGCGCTTTACCCACAAACG
Found at i:35047738 original size:6 final size:6
Alignment explanation
Indices: 35047727--35047753 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
35047717 GTTAAATATT
35047727 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
35047754 TATCATCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:35047965 original size:12 final size:12
Alignment explanation
Indices: 35047948--35047988 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
35047938 TTATTTTTAA
35047948 TAATTAAATATT
1 TAATTAAATATT
35047960 TAATTAAATA--
1 TAATTAAATATT
35047970 TAATTAAATATT
1 TAATTAAATATT
35047982 TAATTAA
1 TAATTAA
35047989 TTAAATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.37
12 17 0.63
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TAATTAAATATT
Found at i:35047972 original size:22 final size:22
Alignment explanation
Indices: 35047947--35047988 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
35047937 GTTATTTTTA
35047947 ATAATTAAATATTTAATTAAAT
1 ATAATTAAATATTTAATTAAAT
35047969 ATAATTAAATATTTAATTAA
1 ATAATTAAATATTTAATTAA
35047989 TTAAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATTAAATATTTAATTAAAT
Found at i:35048023 original size:8 final size:8
Alignment explanation
Indices: 35048010--35048045 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
35048000 GGTTATTTTT
35048010 AATAATTA
1 AATAATTA
35048018 AATAATTA
1 AATAATTA
35048026 AATAATTA
1 AATAATTA
*
35048034 AACAATTA
1 AATAATTA
35048042 AATA
1 AATA
35048046 TTTGGGTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (8 bp):
AATAATTA
Found at i:35051415 original size:34 final size:31
Alignment explanation
Indices: 35051341--35051468 Score: 86
Period size: 34 Copynumber: 4.1 Consensus size: 31
35051331 CCGTTAATGC
** *
35051341 TATATT-TCTATATTATTTATTTTATTATTCTA
1 TATATTAT-TATATTATTTA-AATATTATTATA
*
35051373 TCTATTATTATATTATTCTTATAATATTATTATA
1 TATATTATTATATTA-T-TTA-AATATTATTATA
* *
35051407 TATTTTATTATTTTATTTAAATATTATT-TA
1 TATATTATTATATTATTTAAATATTATTATA
* **
35051437 -A-ATTATTATTTCTATTTAGTTATTATT-TA
1 TATATTATTATAT-TATTTAAATATTATTATA
35051466 TAT
1 TAT
35051469 TTAGTCTATT
Statistics
Matches: 80, Mismatches: 10, Indels: 13
0.78 0.10 0.13
Matches are distributed among these distances:
28 9 0.11
29 16 0.20
30 3 0.04
31 9 0.11
32 15 0.19
33 3 0.04
34 25 0.31
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (31 bp):
TATATTATTATATTATTTAAATATTATTATA
Found at i:35051432 original size:28 final size:29
Alignment explanation
Indices: 35051400--35051454 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
35051390 CTTATAATAT
**
35051400 TATTATATATTTTATTATTT-TATTTAAA
1 TATTATATAAATTATTATTTCTATTTAAA
*
35051428 TATTATTTAAATTATTATTTCTATTTA
1 TATTATATAAATTATTATTTCTATTTA
35051455 GTTATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (29 bp):
TATTATATAAATTATTATTTCTATTTAAA
Found at i:35051434 original size:3 final size:3
Alignment explanation
Indices: 35051351--35051423 Score: 50
Period size: 3 Copynumber: 25.3 Consensus size: 3
35051341 TATATTTCTA
* *
35051351 TAT TATT TAT T-T TAT TAT T-C TAT CTAT TAT TA- TAT TAT TCT TA-
1 TAT TA-T TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
*
35051394 TAA TAT TAT TAT ATAT T-T TAT TAT T-T TAT T
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT T
35051424 TAAATATTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
2 11 0.20
3 36 0.64
4 9 0.16
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:35051435 original size:11 final size:12
Alignment explanation
Indices: 35051419--35051447 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
35051409 TTTTATTATT
35051419 TTATTTAAA-TA
1 TTATTTAAATTA
35051430 TTATTTAAATTA
1 TTATTTAAATTA
35051442 TTATTT
1 TTATTT
35051448 CTATTTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTAAATTA
Found at i:35051436 original size:23 final size:22
Alignment explanation
Indices: 35051410--35051471 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
35051400 TATTATATAT
35051410 TTTATTATTTTATTTAAATATTA
1 TTTATTATTTTATTTAAAT-TTA
* **
35051433 TTTA-AATTATTATTTCTATTTA
1 TTTATTATT-TTATTTAAATTTA
*
35051455 GTTATTATTTATATTTA
1 TTTATTATTT-TATTTA
35051472 GTCTATTTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTATTATTTTATTTAAATTTA
Found at i:35051461 original size:17 final size:17
Alignment explanation
Indices: 35051439--35051507 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
35051429 ATTATTTAAA
*
35051439 TTATTATTTCTATTTAG
1 TTATTATTTATATTTAG
35051456 TTATTATTTATATTTAG
1 TTATTATTTATATTTAG
* *
35051473 -T-CTATTTAGAATTTA-
1 TTATTATTTA-TATTTAG
35051488 TTATTATTTA-ATTTAAG
1 TTATTATTTATATTT-AG
35051505 TTA
1 TTA
35051508 AATAGAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 10 0.23
16 8 0.19
17 25 0.58
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (17 bp):
TTATTATTTATATTTAG
Found at i:35051462 original size:29 final size:28
Alignment explanation
Indices: 35051411--35051465 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
35051401 ATTATATATT
35051411 TTATTATTTTATTTAAATATTATTTAAA
1 TTATTATTTTATTTAAATATTATTTAAA
**
35051439 TTATTATTTCTATTTAGTTATTATTTA
1 TTATTATTT-TATTTAAATATTATTTA
35051466 TATTTAGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (28 bp):
TTATTATTTTATTTAAATATTATTTAAA
Found at i:35052293 original size:40 final size:41
Alignment explanation
Indices: 35052214--35052367 Score: 195
Period size: 40 Copynumber: 3.8 Consensus size: 41
35052204 TATATTTCTA
* *
35052214 TTTACCTTTTGCAGCGTTTTTCCCATAAACGTCGTTATTGC
1 TTTACCTTTTGCGGCGTTTTTCCCATAAACGTCGCTATTGC
* **
35052255 TTTGCCTTTTGCGGCG-TTTTCCCATAAACACCGCTATTGCTC
1 TTTACCTTTTGCGGCGTTTTTCCCATAAACGTCGCTATTG--C
* * * *
35052297 TTTACCTATTGTGGGGTTTTTCTCATAAACGTCGCTATTGC
1 TTTACCTTTTGCGGCGTTTTTCCCATAAACGTCGCTATTGC
35052338 TTTACCTTTTGCGGCG-TTTTCCCATAAACG
1 TTTACCTTTTGCGGCGTTTTTCCCATAAACG
35052368 CTACTATTGC
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
40 33 0.35
41 28 0.30
42 13 0.14
43 20 0.21
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (41 bp):
TTTACCTTTTGCGGCGTTTTTCCCATAAACGTCGCTATTGC
Found at i:35052324 original size:43 final size:42
Alignment explanation
Indices: 35052214--35052386 Score: 174
Period size: 40 Copynumber: 4.2 Consensus size: 42
35052204 TATATTTCTA
* * * *
35052214 TTTACCTTTTGCAGCGTTTTTCCCATAAACGTCGTTATTG--C
1 TTTACCTATTGCGGCG-TTTTCCCATAAACGCCGCTATTGCTC
* * *
35052255 TTTGCCTTTTGCGGCGTTTTCCCATAAACACCGCTATTGCTC
1 TTTACCTATTGCGGCGTTTTCCCATAAACGCCGCTATTGCTC
* * * *
35052297 TTTACCTATTGTGGGGTTTTTCTCATAAACGTCGCTATTG--C
1 TTTACCTATTGCGGCG-TTTTCCCATAAACGCCGCTATTGCTC
* **
35052338 TTTACCTTTTGCGGCGTTTTCCCATAAACGCTACTATTGCTC
1 TTTACCTATTGCGGCGTTTTCCCATAAACGCCGCTATTGCTC
35052380 TTTACCT
1 TTTACCT
35052387 CCGCTATTGC
Statistics
Matches: 108, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
40 39 0.36
41 28 0.26
42 21 0.19
43 20 0.19
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (42 bp):
TTTACCTATTGCGGCGTTTTCCCATAAACGCCGCTATTGCTC
Found at i:35052353 original size:83 final size:83
Alignment explanation
Indices: 35052229--35052386 Score: 262
Period size: 83 Copynumber: 1.9 Consensus size: 83
35052219 CTTTTGCAGC
* * *
35052229 GTTTTTCCCATAAACGTCGTTATTGCTTTGCCTTTTGCGGCGTTTTCCCATAAACACCGCTATTG
1 GTTTTTCCCATAAACGTCGCTATTGCTTTACCTTTTGCGGCGTTTTCCCATAAACACCACTATTG
35052294 CTCTTTACCTATTGTGGG
66 CTCTTTACCTATTGTGGG
* * *
35052312 GTTTTTCTCATAAACGTCGCTATTGCTTTACCTTTTGCGGCGTTTTCCCATAAACGCTACTATTG
1 GTTTTTCCCATAAACGTCGCTATTGCTTTACCTTTTGCGGCGTTTTCCCATAAACACCACTATTG
35052377 CTCTTTACCT
66 CTCTTTACCT
35052387 CCGCTATTGC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 69 1.00
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (83 bp):
GTTTTTCCCATAAACGTCGCTATTGCTTTACCTTTTGCGGCGTTTTCCCATAAACACCACTATTG
CTCTTTACCTATTGTGGG
Found at i:35052608 original size:21 final size:20
Alignment explanation
Indices: 35052584--35052638 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
35052574 ATACAATGTG
35052584 TTAATATATAATTACAGA-TAT
1 TTAATATATAATTA-A-ATTAT
35052605 TTAATGAT-TATATTAAATTAT
1 TTAAT-ATATA-ATTAAATTAT
*
35052626 TTAAAATATAATT
1 TTAATATATAATT
35052639 TATATATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
20 6 0.21
21 17 0.59
22 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
TTAATATATAATTAAATTAT
Found at i:35062686 original size:109 final size:109
Alignment explanation
Indices: 35062493--35062809 Score: 456
Period size: 109 Copynumber: 2.9 Consensus size: 109
35062483 GGCAATATTC
* *
35062493 TTTTATTTAGGGAATTCGAGAAATTGTGCTCAAACATACTGGGCATGATTTTTTCTTTGAACCTA
1 TTTTATTTAGGGAATTCAAGAAATTGTGCTCAAACATACTGGGTATGATTTTTTCTTTGAACCTA
* **
35062558 AATAATC-AAGTATCCTATTTAAAATCAATAAATTTTTGATGTTA
66 AATAATCGAA-TATCCTATTTAAAATCAATAAATGTTCAATGTTA
*
35062602 TTTTATTTAGGGAATTCAAGAAATTGTGCTCAAACATTCTGGGTATGATTTTTTCTTTGAACCTA
1 TTTTATTTAGGGAATTCAAGAAATTGTGCTCAAACATACTGGGTATGATTTTTTCTTTGAACCTA
* * *
35062667 AATAATCGAATATCTTATTTAAAATCAATAAACGTTCAATGTTC
66 AATAATCGAATATCCTATTTAAAATCAATAAATGTTCAATGTTA
* * * *
35062711 TTTTATTTAAGGAATTCAAGAAATTATGCTCAAACGTACTAGGTATGATTTTTTTCTTTGAACCT
1 TTTTATTTAGGGAATTCAAGAAATTGTGCTCAAACATACTGGGTATGA-TTTTTTCTTTGAACCT
* * * *
35062776 AAGTAGTCGAATATCCTATTTGAAATCGATAAAT
65 AAATAATCGAATATCCTATTTAAAATCAATAAAT
35062810 ATCCTTTATC
Statistics
Matches: 186, Mismatches: 20, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
109 140 0.75
110 46 0.25
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (109 bp):
TTTTATTTAGGGAATTCAAGAAATTGTGCTCAAACATACTGGGTATGATTTTTTCTTTGAACCTA
AATAATCGAATATCCTATTTAAAATCAATAAATGTTCAATGTTA
Found at i:35067290 original size:35 final size:34
Alignment explanation
Indices: 35067203--35067291 Score: 90
Period size: 35 Copynumber: 2.6 Consensus size: 34
35067193 GATGTTTGCT
* * * *
35067203 CCCAGTGCTAGTTGGATTAACTGACGAATGTGTG
1 CCCAGCGCTAGTCGGATAAACTGACGAATGTGCG
* *
35067237 CCCAGCACTAGTCAGATAAACTGACAGAAAT-TGCG
1 CCCAGCGCTAGTCGGATAAACTGAC-G-AATGTGCG
*
35067272 CCTAGCGCTAGTCGGATAAA
1 CCCAGCGCTAGTCGGATAAA
35067292 TCGACGGTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
34 20 0.45
35 21 0.48
36 3 0.07
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.22
Consensus pattern (34 bp):
CCCAGCGCTAGTCGGATAAACTGACGAATGTGCG
Found at i:35078303 original size:12 final size:12
Alignment explanation
Indices: 35078286--35078311 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35078276 AAGTAAAGAA
35078286 ATAATAGCATTC
1 ATAATAGCATTC
35078298 ATAATAGCATTC
1 ATAATAGCATTC
35078310 AT
1 AT
35078312 CATGATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:35082022 original size:26 final size:24
Alignment explanation
Indices: 35081993--35082052 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
35081983 TTAGTTAGTA
*
35081993 TAAAATATTAACAATTTAAAATAAAT
1 TAAAA-ATTAACAAATT-AAATAAAT
* *
35082019 TAAAAAGTTAATAAATTAATTAAAT
1 TAAAAA-TTAACAAATTAAATAAAT
35082044 TAAAAATTA
1 TAAAAATTA
35082053 GAAAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 3 0.10
25 14 0.47
26 13 0.43
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
TAAAAATTAACAAATTAAATAAAT
Found at i:35082057 original size:8 final size:7
Alignment explanation
Indices: 35082015--35082065 Score: 50
Period size: 7 Copynumber: 6.7 Consensus size: 7
35082005 AATTTAAAAT
35082015 AAATTAA
1 AAATTAA
35082022 AAAGTTAA
1 AAA-TTAA
35082030 TAAATTAA
1 -AAATTAA
35082038 TTAAATTAA
1 --AAATTAA
35082047 AAATTAGA
1 AAATTA-A
35082055 AAA-TAA
1 AAATTAA
35082061 AAATT
1 AAATT
35082066 CTTACCACCT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 4 0.10
7 12 0.31
8 12 0.31
9 11 0.28
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (7 bp):
AAATTAA
Found at i:35095676 original size:13 final size:13
Alignment explanation
Indices: 35095660--35095685 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35095650 GAAGGAGAAG
35095660 GAAGAAGAAAAAA
1 GAAGAAGAAAAAA
35095673 GAAGAAGAAAAAA
1 GAAGAAGAAAAAA
35095686 AGAAAGAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAAAAA
Found at i:35099103 original size:21 final size:21
Alignment explanation
Indices: 35099079--35099121 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
35099069 CTTCTAGTTT
35099079 TGGTGAAA-CTGGTTCTGATTC
1 TGGT-AAAGCTGGTTCTGATTC
* *
35099100 TGGTAAAGTTGGTTCTGGTTC
1 TGGTAAAGCTGGTTCTGATTC
35099121 T
1 T
35099122 AGTTCTGGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.16, C:0.12, G:0.30, T:0.42
Consensus pattern (21 bp):
TGGTAAAGCTGGTTCTGATTC
Found at i:35099117 original size:27 final size:27
Alignment explanation
Indices: 35099087--35099138 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
35099077 TTTGGTGAAA
*
35099087 CTGGTTCT-GATTCTGGTAAAGTTGGTT
1 CTGGTTCTAG-TTCTGGCAAAGTTGGTT
35099114 CTGGTTCTAGTTCTGGCAAAGTTGG
1 CTGGTTCTAGTTCTGGCAAAGTTGG
35099139 AGTTTCAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.15, C:0.13, G:0.31, T:0.40
Consensus pattern (27 bp):
CTGGTTCTAGTTCTGGCAAAGTTGGTT
Found at i:35100973 original size:16 final size:15
Alignment explanation
Indices: 35100946--35100982 Score: 65
Period size: 16 Copynumber: 2.4 Consensus size: 15
35100936 TAATGTAAGC
35100946 TAAATTAAACTAAAT
1 TAAATTAAACTAAAT
35100961 TAAATTAAAACTAAAT
1 TAAATT-AAACTAAAT
35100977 TAAATT
1 TAAATT
35100983 CCTATGCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATTAAACTAAAT
Found at i:35109189 original size:106 final size:104
Alignment explanation
Indices: 35109049--35109255 Score: 310
Period size: 106 Copynumber: 2.0 Consensus size: 104
35109039 TTTACTAAAA
* *
35109049 ATAATTTAATATAATTATAATGATTTCATTAAATATTAAAACATGGAAGTTAATA-TCTTTTTGG
1 ATAATTTAATATAATTATAATGATTTCATAAAATATTAAAACATGGAAGATAATATTC-TTTTGG
*
35109113 AAAGGATATAATGTTTTATTAAACCTTCCATA-ATTTAAC
65 AAAGGATATAATGTTTTAATAAACCTTCCATATATTTAAC
* *
35109152 ATAATTATAATTATTAATTATAATGATTTCGTAAAATATTAAAATATGGAAGATAATATTCTTTT
1 ATAATT-TAA-TA-TAATTATAATGATTTCATAAAATATTAAAACATGGAAGATAATATTCTTTT
*
35109217 GGAAAGGATATAATGTTTTAATAAACTTTCCATATATTT
63 GGAAAGGATATAATGTTTTAATAAACCTTCCATATATTT
35109256 CTTTAAAGGA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
103 6 0.06
104 3 0.03
105 2 0.02
106 76 0.82
107 6 0.06
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (104 bp):
ATAATTTAATATAATTATAATGATTTCATAAAATATTAAAACATGGAAGATAATATTCTTTTGGA
AAGGATATAATGTTTTAATAAACCTTCCATATATTTAAC
Found at i:35109332 original size:123 final size:122
Alignment explanation
Indices: 35109186--35109552 Score: 565
Period size: 123 Copynumber: 3.0 Consensus size: 122
35109176 GATTTCGTAA
* *
35109186 AATATTAAAATATGGAAGATAATATTCTTTTGGAAAGGATATAATGTTTTAATAAACTTTCCATA
1 AATATTAAAACATGGAAGATAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACTTTCCATA
*
35109251 TATTTCTTTAAAGGAATATTTCCATTTTAATATTAGATATTATATAAAAGGAAATTG
66 TATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
* * *
35109308 AATATTAAAAACATGGAAGTTAATATCCTTTTCGAAAGGATATAATGTTTTAATAAACCTTCCAT
1 AATATT-AAAACATGGAAGATAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACTTTCCAT
* *
35109373 ATATTTCTTTAAAGGGATATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTG
65 ATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
* *
35109431 AATATTAAAACATGGAAAATAATATCCTTTTGGAAAGGATATAATGGTTTAATAAA-TCTTCCAT
1 AATATTAAAACATGGAAGATAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACT-TTCCAT
* * *
35109495 ATATTTCTCTAAAGATATATATTTCCATTTTAATATGAGATATTAAAATAAAAGGAAA
65 ATATTTCTTTAAAG-GA-ATATTTCCATTTTAATATGAGATATT-ATATAAAAGGAAA
35109553 GATAACAGAA
Statistics
Matches: 222, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
122 71 0.32
123 114 0.51
124 26 0.12
125 11 0.05
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (122 bp):
AATATTAAAACATGGAAGATAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACTTTCCATA
TATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
Found at i:35116946 original size:79 final size:79
Alignment explanation
Indices: 35116875--35117082 Score: 371
Period size: 79 Copynumber: 2.6 Consensus size: 79
35116865 AATAAAAGCT
* *
35116875 AATATCTTTTTGGAAAGAATATAATGTTTTAATAAACCTTTCATAATTTAACGTAATTATAATTA
1 AATATCCTTTTGGAAAGAATATAATGTTTTAATAAACCTTTCATAATTTAACATAATTATAATTA
35116940 ATAAAATGGAAGAC
66 ATAAAATGGAAGAC
*
35116954 AATATCCTTTTGGAAAGAATATAATGTTTTAATAAACATTTCATAATTTAACATAATTATAATTA
1 AATATCCTTTTGGAAAGAATATAATGTTTTAATAAACCTTTCATAATTTAACATAATTATAATTA
35117019 ATAAAATGGAAGAC
66 ATAAAATGGAAGAC
*
35117033 AATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTTCATATATTT
1 AATATCCTTTTGGAAAGAATATAATGTTTTAATAAACCTTTCATA-ATTT
35117083 TTTTAAAGGA
Statistics
Matches: 123, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 119 0.97
80 4 0.03
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (79 bp):
AATATCCTTTTGGAAAGAATATAATGTTTTAATAAACCTTTCATAATTTAACATAATTATAATTA
ATAAAATGGAAGAC
Found at i:35117328 original size:122 final size:122
Alignment explanation
Indices: 35117015--35117379 Score: 523
Period size: 123 Copynumber: 3.0 Consensus size: 122
35117005 CATAATTATA
*
35117015 ATTAATAAAATGGAAGACAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTTCATATA
1 ATTAA-AACATGGAAGACAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTTCATATA
* * * * * * *
35117080 TTTTTTTAAAGGAATTTTTCCACTTTAATATTAGATATAATATAAGAGGAAATTGAAT
65 TTTCTTTAAAGGAATATTTCCATTTTAATATAAGATATTATATAAAAGGAAATTAAAT
**
35117138 ATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTTCATATA
1 ATT-AAAACATGGAAGACAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTTCATATA
*
35117203 TTTCTTTAAAGGAATATTTCCTTTTTAATATAAGATATTATATAAAAGGAAATTAAAT
65 TTTCTTTAAAGGAATATTTCCATTTTAATATAAGATATTATATAAAAGGAAATTAAAT
* * *
35117261 ATTAAAACATGGAAGAGAATATCCTTTTGGAAAGGATATAATGTTTTAATAAATCTTCCATATAT
1 ATTAAAACATGGAAGACAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTTCATATAT
* * * *
35117326 TTCTTTAAAGATATATATTTCCATTTTAATATGATATATTAAAATAAAAGGAAA
66 TTCTTTAAAG-GA-ATATTTCCATTTTAATATAAGATATT-ATATAAAAGGAAA
35117380 GATAGCAAAA
Statistics
Matches: 218, Mismatches: 20, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
122 68 0.31
123 113 0.52
124 25 0.11
125 12 0.06
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.39
Consensus pattern (122 bp):
ATTAAAACATGGAAGACAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTTCATATAT
TTCTTTAAAGGAATATTTCCATTTTAATATAAGATATTATATAAAAGGAAATTAAAT
Found at i:35120029 original size:9 final size:9
Alignment explanation
Indices: 35120015--35120039 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
35120005 ATATAGTTTG
35120015 CATTTTATT
1 CATTTTATT
35120024 CATTTTATT
1 CATTTTATT
35120033 CATTTTA
1 CATTTTA
35120040 GTCCCTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (9 bp):
CATTTTATT
Found at i:35133633 original size:10 final size:9
Alignment explanation
Indices: 35133599--35133712 Score: 68
Period size: 10 Copynumber: 13.3 Consensus size: 9
35133589 TTAAATAAAC
*
35133599 TTATAAAAT
1 TTATAAAAA
*
35133608 TTAGTACAAA
1 TTA-TAAAAA
35133618 TTATAAAAA
1 TTATAAAAA
35133627 CTTATAAAAA
1 -TTATAAAAA
35133637 -TATAAAAA
1 TTATAAAAA
*
35133645 -TA-AATAA
1 TTATAAAAA
*
35133652 --ATAAAAC
1 TTATAAAAA
35133659 TTAT-AAAA
1 TTATAAAAA
35133667 TCT-TAAAAA
1 T-TATAAAAA
35133676 -T-TAAAAA
1 TTATAAAAA
*
35133683 TTATATAAAC
1 TTATA-AAAA
35133693 TTATAAAAA
1 TTATAAAAA
*
35133702 -TAGAAAAA
1 TTATAAAAA
35133710 TTA
1 TTA
35133713 GGAAAAAAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
6 1 0.01
7 14 0.17
8 23 0.27
9 22 0.26
10 24 0.29
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:35133686 original size:24 final size:25
Alignment explanation
Indices: 35133653--35133700 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
35133643 AATAAATAAA
*
35133653 TAAAACTTATA-AAATCTTA-AAAAT
1 TAAAAATTATATAAA-CTTATAAAAT
35133677 TAAAAATTATATAAACTTATAAAA
1 TAAAAATTATATAAACTTATAAAA
35133701 ATAGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (25 bp):
TAAAAATTATATAAACTTATAAAAT
Found at i:35133739 original size:65 final size:68
Alignment explanation
Indices: 35133595--35133742 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 68
35133585 AATGTTAAAT
* * *
35133595 AAACTTATAAAATTTAGTACAAATTATAAAAACTTATAAAAATATAAAAATAAATAAATAAAACT
1 AAACTTATAAAAATTAG-ACAAATTATAAAAACTTATAAAAATAGAAAAATAAAGAAATAAAACT
35133660 TATA
65 TATA
* * *
35133664 AAA-TCT-TAAAAATTA-A-AAATTATATAAACTTATAAAAATAGAAAAATTAGGAAA-AAAATC
1 AAACT-TATAAAAATTAGACAAATTATAAAAACTTATAAAAATAGAAAAATAAAGAAATAAAA-C
35133724 TTA-A
64 TTATA
35133728 AAACTTATAAAAATT
1 AAACTTATAAAAATT
35133743 CTAATTAAGT
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
64 9 0.13
65 46 0.67
66 1 0.01
68 9 0.13
69 4 0.06
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (68 bp):
AAACTTATAAAAATTAGACAAATTATAAAAACTTATAAAAATAGAAAAATAAAGAAATAAAACTT
ATA
Found at i:35134521 original size:5 final size:5
Alignment explanation
Indices: 35134511--35134538 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
35134501 TGTAATTGTC
35134511 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
35134539 ACCATCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:35137028 original size:16 final size:16
Alignment explanation
Indices: 35136997--35137033 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
35136987 ATGTGAAGAA
35136997 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
35137013 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
35137029 TATTA
1 TATTA
35137034 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:35137072 original size:16 final size:19
Alignment explanation
Indices: 35137047--35137102 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 19
35137037 TAAAATTGAA
35137047 ATATTAAATAATTTATTAA-
1 ATATT-AATAATTTATTAAG
35137066 A-A-TAATAAATTATATTAAG
1 ATATTAAT-AATT-TATTAAG
35137085 TATATTAATAATTTATTA
1 -ATATTAATAATTTATTA
35137103 TATGACTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.10
17 5 0.16
18 7 0.23
19 1 0.03
20 6 0.19
21 5 0.16
22 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATTAATAATTTATTAAG
Found at i:35144556 original size:20 final size:20
Alignment explanation
Indices: 35144520--35144569 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
35144510 ATTAGCATGA
35144520 TTTATATTAAGTGTAAATAG-G
1 TTTA-ATTAAGTGTAAA-AGTG
35144541 TTTAATTAAGAT-TAAAAGTG
1 TTTAATTAAG-TGTAAAAGTG
*
35144561 GTTAATTAA
1 TTTAATTAA
35144570 AGCTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (20 bp):
TTTAATTAAGTGTAAAAGTG
Found at i:35150249 original size:30 final size:30
Alignment explanation
Indices: 35150209--35150545 Score: 376
Period size: 30 Copynumber: 11.2 Consensus size: 30
35150199 AAGAAAACAT
* * *
35150209 ATTTTGACCCTTAAGCTTCTT-CGAAATTAC
1 ATTTTAACCCTTAAACTT-TTCCAAAATTAC
* *
35150239 ATTTTAACCCTCAAACTTTTCCAAAATGAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
** * *
35150269 ATTTTAA-CCTCTAATTTTTTCTAAAATTGC
1 ATTTTAACCCT-TAAACTTTTCCAAAATTAC
*
35150299 ATTTTAACCCCTAAACTTTTCCAAAATTAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
*
35150329 ATTTTAACCCTTAAACTTTTCCAAAATAAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
* * *
35150359 ATTTTAA-CCTTAAATTTTTCTAAAATTGC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
* *
35150388 ATTTTAACCCCTAAAACTTTTCCAAAGTTAC
1 ATTTTAA-CCCTTAAACTTTTCCAAAATTAC
*
35150419 ATTTTAACCCCTAAACTTTTCCAAAATTAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
35150449 ATTTTAA-CCTCTAAACTTTTCCAAAATTAC
1 ATTTTAACCCT-TAAACTTTTCCAAAATTAC
* * *
35150479 ATTTTAACCCCTAAACCTTTCCCAAAATCAC
1 ATTTTAACCCTTAAA-CTTTTCCAAAATTAC
* * * *
35150510 ATTTTCACCCCCTAAACTTTTCTAAATTTAC
1 ATTTT-AACCCTTAAACTTTTCCAAAATTAC
35150541 ATTTT
1 ATTTT
35150546 GATCCCGTAT
Statistics
Matches: 259, Mismatches: 39, Indels: 17
0.82 0.12 0.05
Matches are distributed among these distances:
29 32 0.12
30 156 0.60
31 62 0.24
32 9 0.03
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.39
Consensus pattern (30 bp):
ATTTTAACCCTTAAACTTTTCCAAAATTAC
Found at i:35150362 original size:90 final size:90
Alignment explanation
Indices: 35150232--35150545 Score: 461
Period size: 90 Copynumber: 3.5 Consensus size: 90
35150222 AGCTTCTTCG
* *
35150232 AAATTACATTTTAA-CCCTCAAACTTTTCCAAAATGACATTTTAACCTCTAATTTTTTCTAAAAT
1 AAATTACATTTTAACCCCT-AAACTTTTCCAAAATTACATTTTAACCTCTAAATTTTTCTAAAAT
35150296 TGCATTTTAACCCCTAAACTTTTCCA
65 TGCATTTTAACCCCTAAACTTTTCCA
* *
35150322 AAATTACATTTTAACCCTTAAACTTTTCCAAAATAACATTTTAACCT-TAAATTTTTCTAAAATT
1 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCTCTAAATTTTTCTAAAATT
35150386 GCATTTTAACCCCTAAAACTTTTCCA
66 GCATTTTAACCCCT-AAACTTTTCCA
* * *
35150412 AAGTTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCTCTAAACTTTTCCAAAATT
1 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCTCTAAATTTTTCTAAAATT
* *
35150477 ACATTTTAACCCCTAAACCTTTCCCA
66 GCATTTTAACCCCTAAA-CTTTTCCA
* * * *
35150503 AAATCACATTTTCACCCCCTAAACTTTTCTAAATTTACATTTT
1 AAATTACATTTT-AACCCCTAAACTTTTCCAAAATTACATTTT
35150546 GATCCCGTAT
Statistics
Matches: 204, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
89 30 0.15
90 99 0.49
91 48 0.24
92 27 0.13
ACGTcount: A:0.35, C:0.24, G:0.01, T:0.39
Consensus pattern (90 bp):
AAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCTCTAAATTTTTCTAAAATT
GCATTTTAACCCCTAAACTTTTCCA
Found at i:35164695 original size:30 final size:30
Alignment explanation
Indices: 35164661--35164983 Score: 366
Period size: 30 Copynumber: 10.8 Consensus size: 30
35164651 AAGAAATCAT
* * *
35164661 ATTTTGACCCTTAAGCTTCTCCACAATTAC
1 ATTTTGACCCTTAAACTTTTCCAAAATTAC
35164691 ATTTTGACCCTTAAACTTTTCCAAAATTAC
1 ATTTTGACCCTTAAACTTTTCCAAAATTAC
* *
35164721 ATTTTGACCCCTAAA-TTTTCTAAAATTAC
1 ATTTTGACCCTTAAACTTTTCCAAAATTAC
*
35164750 ATTTTG-CCCCTAAACTTTTCCAAAATTAC
1 ATTTTGACCCTTAAACTTTTCCAAAATTAC
* * * **
35164779 ATTTTAACCCTCAAAC-TTTCTAAAATTGT
1 ATTTTGACCCTTAAACTTTTCCAAAATTAC
* * *
35164808 ATTTT-AACCTCTAAACTTATCCAAAATTTC
1 ATTTTGACCCT-TAAACTTTTCCAAAATTAC
* * *
35164838 ATTTTAACCCTTAAACTTTTCTAAAATTAG
1 ATTTTGACCCTTAAACTTTTCCAAAATTAC
* *
35164868 ATTTTAACCCTTAAACTTTTCCAAAATTAA
1 ATTTTGACCCTTAAACTTTTCCAAAATTAC
* *
35164898 ATTTTAACCCTTAAAATTTTCCAAAATTAC
1 ATTTTGACCCTTAAACTTTTCCAAAATTAC
* * *
35164928 ATTTTGACCCCTAAACCTTTCCCAAAATCAC
1 ATTTTGACCCTTAAA-CTTTTCCAAAATTAC
* *
35164959 ATTTTCACCCCTAAACTTTTCCAAA
1 ATTTTGACCCTTAAACTTTTCCAAA
35164984 TTTATGTTTT
Statistics
Matches: 253, Mismatches: 34, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.05
29 56 0.22
30 155 0.61
31 30 0.12
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.39
Consensus pattern (30 bp):
ATTTTGACCCTTAAACTTTTCCAAAATTAC
Found at i:35166964 original size:11 final size:11
Alignment explanation
Indices: 35166948--35166976 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
35166938 TTTCCTTTTT
35166948 CACGATCGGGA
1 CACGATCGGGA
35166959 CACGATCGGGA
1 CACGATCGGGA
35166970 CACGATC
1 CACGATC
35166977 TTGATCTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.31, T:0.10
Consensus pattern (11 bp):
CACGATCGGGA
Found at i:35171621 original size:15 final size:14
Alignment explanation
Indices: 35171596--35171628 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
35171586 AAATATATTA
35171596 AAATATTAAAAAAT
1 AAATATTAAAAAAT
*
35171610 AAATATTCAAAAA-
1 AAATATTAAAAAAT
35171623 AAATAT
1 AAATAT
35171629 GATAATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATATTAAAAAAT
Found at i:35176396 original size:15 final size:14
Alignment explanation
Indices: 35176378--35176419 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
35176368 ATTTTAAATT
35176378 ATATTTTGAAATAAA
1 ATATTTT-AAATAAA
*
35176393 ATATTTTATATTAAA
1 ATATTTTA-AATAAA
35176408 ATATTTTAAATA
1 ATATTTTAAATA
35176420 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATATTTTAAATAAA
Found at i:35178348 original size:28 final size:29
Alignment explanation
Indices: 35178289--35178352 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 29
35178279 TCCATTTTAA
*
35178289 TAATTTTAATTTATTTTAAATTCGCCTTT
1 TAATTTTAATTTATTTTAAATTAGCCTTT
35178318 TAATTTT-ATTT-TTTTAAATTTAGTCC-TT
1 TAATTTTAATTTATTTTAAA-TTAG-CCTTT
35178346 TAATTTT
1 TAATTTT
35178353 TGGAAGCCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 7 0.22
28 16 0.50
29 9 0.28
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (29 bp):
TAATTTTAATTTATTTTAAATTAGCCTTT
Found at i:35178431 original size:13 final size:13
Alignment explanation
Indices: 35178413--35178437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35178403 TAAAGCCCCT
35178413 ATTTTATTTTAAA
1 ATTTTATTTTAAA
35178426 ATTTTATTTTAA
1 ATTTTATTTTAA
35178438 CCCTTAAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTATTTTAAA
Found at i:35178465 original size:30 final size:30
Alignment explanation
Indices: 35178422--35178679 Score: 279
Period size: 30 Copynumber: 8.6 Consensus size: 30
35178412 TATTTTATTT
** *
35178422 TAAAATTTTATTTTAACCCTTAAACTTTTT
1 TAAAATTACATTTTAACCCTTAAACTTTTC
* * *
35178452 TAGAATTACATTTTGATCCC-TAAACTTATC
1 TAAAATTACATTTT-AACCCTTAAACTTTTC
* *
35178482 TAAAATCACATTTTAACCCCT-AACTTTTC
1 TAAAATTACATTTTAACCCTTAAACTTTTC
* *
35178511 CAAAATTACATTTTAACCCCTAAACTTTTC
1 TAAAATTACATTTTAACCCTTAAACTTTTC
*
35178541 TAAAATTTCATTTTAACCCTTAAACTTTTC
1 TAAAATTACATTTTAACCCTTAAACTTTTC
* * *
35178571 CAAAATTACATTTTGACCCCTAAACTTTTC
1 TAAAATTACATTTTAACCCTTAAACTTTTC
* *
35178601 TAAAATCACATTTTAACCCTTCAAC-TTTC
1 TAAAATTACATTTTAACCCTTAAACTTTTC
* * *
35178630 TCAAAATCACATTTTGACCCTCAAACTTTTC
1 T-AAAATTACATTTTAACCCTTAAACTTTTC
* * *
35178661 CAAAATTATATTTTGACCC
1 TAAAATTACATTTTAACCC
35178680 CAAATTCACC
Statistics
Matches: 193, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
29 35 0.18
30 150 0.78
31 8 0.04
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (30 bp):
TAAAATTACATTTTAACCCTTAAACTTTTC
Found at i:35178495 original size:60 final size:60
Alignment explanation
Indices: 35178431--35178666 Score: 325
Period size: 60 Copynumber: 4.0 Consensus size: 60
35178421 TTAAAATTTT
** * * *
35178431 ATTTTAACCCTTAAACTTTTTTAGAATTACATTTTGATCCCTAAACTTATCTAAAATCAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTTTCTAAAATCAC
* * **
35178491 ATTTTAACCCCT-AACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATTTC
1 ATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTTTCTAAAATCAC
35178550 ATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTTTCTAAAATCAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTTTCTAAAATCAC
* * *
35178610 ATTTTAACCCTTCAAC-TTTCTCAAAATCACATTTTGA-CCCTCAAACTTTTCCAAAAT
1 ATTTTAACCCTTAAACTTTTC-CAAAATTACATTTTGACCCCT-AAACTTTTCTAAAAT
35178667 TATATTTTGA
Statistics
Matches: 157, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
59 58 0.37
60 99 0.63
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (60 bp):
ATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTTTCTAAAATCAC
Found at i:35178545 original size:119 final size:120
Alignment explanation
Indices: 35178422--35178679 Score: 369
Period size: 119 Copynumber: 2.2 Consensus size: 120
35178412 TATTTTATTT
** * *
35178422 TAAAATTTTATTTTAACCCTTAAACTTTTTTAGAATTACATTTTGATCCCTAAACTTATCTAAAA
1 TAAAATTTTATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTATCTAAAA
*
35178487 TCACATTTTAACCCCT-AACTTT-TCCAAAATTACATTTTAACCC-CTAAACTTTTC
66 TCACATTTTAACCCCTCAACTTTCT-CAAAATCACATTTTAACCCTC-AAACTTTTC
* *
35178541 TAAAATTTCATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTTTCTAAAA
1 TAAAATTTTATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTATCTAAAA
* *
35178606 TCACATTTTAACCCTTCAACTTTCTCAAAATCACATTTTGACCCTCAAACTTTTC
66 TCACATTTTAACCCCTCAACTTTCTCAAAATCACATTTTAACCCTCAAACTTTTC
* * *
35178661 CAAAATTATATTTTGACCC
1 TAAAATTTTATTTTAACCC
35178680 CAAATTCACC
Statistics
Matches: 123, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
119 74 0.60
120 47 0.38
121 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (120 bp):
TAAAATTTTATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTATCTAAAA
TCACATTTTAACCCCTCAACTTTCTCAAAATCACATTTTAACCCTCAAACTTTTC
Found at i:35187978 original size:37 final size:38
Alignment explanation
Indices: 35187887--35187989 Score: 91
Period size: 37 Copynumber: 2.7 Consensus size: 38
35187877 GACCTTGAGT
* * **
35187887 CGATGAGACACTGGGTATCATTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTA-C--CACTTTACTTCGGATAGAGC
** *
35187928 CGATGAGGTACTGGGTACCACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTACCACTTTACTTCGGATAGAGC
**
35187965 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTACCACTTTA
35187990 TTGCTTCGAA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
37 21 0.41
38 14 0.27
40 1 0.02
41 15 0.29
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (38 bp):
CGATGAGACACTGGGTACCACTTTACTTCGGATAGAGC
Found at i:35190651 original size:85 final size:85
Alignment explanation
Indices: 35190503--35190662 Score: 239
Period size: 85 Copynumber: 1.9 Consensus size: 85
35190493 CATCTTCCTG
* *
35190503 ATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGATCATCTTCCTAATGAGATACAGAGAAGT
1 ATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGATCATCTTCCTAATGAGATACAAAGAAGT
*
35190568 GGACCAAATCCGCCTTCTTA
66 AGACCAAATCCGCCTTCTTA
* * * * * *
35190588 ATGAGATACAGAGAAGTGGATTAAATCATTGAAGTGGTCATCTTCCTAATGAGATACAAAGAAGT
1 ATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGATCATCTTCCTAATGAGATACAAAGAAGT
35190653 AGACCAAATC
66 AGACCAAATC
35190663 AATGAAGCGA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 66 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (85 bp):
ATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGATCATCTTCCTAATGAGATACAAAGAAGT
AGACCAAATCCGCCTTCTTA
Found at i:35190812 original size:211 final size:208
Alignment explanation
Indices: 35190451--35190940 Score: 755
Period size: 211 Copynumber: 2.3 Consensus size: 208
35190441 CATCTTCCTG
*
35190451 AATCAATGAAACAAAGCTTAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAGAG
1 AATCAATGAAACGAAGCTTAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAGAG
*
35190516 AAGTGGGTCAAAGCAATAAAGCGATCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCGC
66 AAGTGGGTCAAAGCAATAAAGCGAGCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCGC
* * * * *
35190581 CTTCTTAATGAGATACAGAGAAGTGGATTAAATCATTGAAGTGGTCATCTTCCTAATGAGATACA
131 CTTCTTAAGGAGATACAGAGAAGTGGACTAAATCAATGAAGCGGGCATCTTCCTAATGAGATACA
35190646 AAGAAGTAGACCA
196 AAGAAGTAGACCA
* *
35190659 AATCAATGAAGCGAAGCTTAATACGACGAATGAGACTTCAAACCCCATCTTCATGATGAGATACA
1 AATCAATGAAACGAAGCTTAAT---ACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACA
* * *
35190724 GAGAAGTGGGTCAAAGCAATAAAGCGGGCATCTTCCTGATGAGATATAGAGAAGTGGACCAAATC
63 GAGAAGTGGGTCAAAGCAATAAAGCGAGCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATC
* * *
35190789 TGCCTTCTTGAGGAGATACAGAGAAGTGGACTAAATCAATGAAGCGGGCATCTTCCTGATGAGAT
128 CGCCTTCTTAAGGAGATACAGAGAAGTGGACTAAATCAATGAAGCGGGCATCTTCCTAATGAGAT
* *
35190854 ACAGAGAAGTAGACTA
193 ACAAAGAAGTAGACCA
* * * * *
35190870 AATCAATGAAACGAAGCTCAATACGAATGAGACTTCAAATCTCATCTTCCTAATGAGATATAGAG
1 AATCAATGAAACGAAGCTTAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAGAG
35190935 AAGTGG
66 AAGTGG
35190941 ACCAAATCCT
Statistics
Matches: 255, Mismatches: 24, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
208 64 0.25
211 191 0.75
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (208 bp):
AATCAATGAAACGAAGCTTAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAGAG
AAGTGGGTCAAAGCAATAAAGCGAGCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCGC
CTTCTTAAGGAGATACAGAGAAGTGGACTAAATCAATGAAGCGGGCATCTTCCTAATGAGATACA
AAGAAGTAGACCA
Found at i:35190814 original size:37 final size:37
Alignment explanation
Indices: 35190755--35190825 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
35190745 AAGCGGGCAT
* *
35190755 CTTCCTGATGAGATATAGAGAAGTGGACCAAATCTGC
1 CTTCCTGAGGAGATACAGAGAAGTGGACCAAATCTGC
* *
35190792 CTTCTTGAGGAGATACAGAGAAGTGGACTAAATC
1 CTTCCTGAGGAGATACAGAGAAGTGGACCAAATC
35190826 AATGAAGCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (37 bp):
CTTCCTGAGGAGATACAGAGAAGTGGACCAAATCTGC
Found at i:35190860 original size:85 final size:85
Alignment explanation
Indices: 35190707--35190873 Score: 246
Period size: 85 Copynumber: 2.0 Consensus size: 85
35190697 CAAACCCCAT
* * *
35190707 CTTCATGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGGCATCTTCCTGATGAGATATA
1 CTTCATGAGGAGATACAGAGAAGTGGCTCAAAGCAATAAAGCGGGCATCTTCCTGATGAGATACA
*
35190772 GAGAAGTGGACCAAATCTGC
66 GAGAAGTAGACCAAATCTGC
* * *
35190792 CTTCTTGAGGAGATACAGAGAAGTGGACT-AAATCAATGAAGCGGGCATCTTCCTGATGAGATAC
1 CTTCATGAGGAGATACAGAGAAGTGG-CTCAAAGCAATAAAGCGGGCATCTTCCTGATGAGATAC
*
35190856 AGAGAAGTAGACTAAATC
65 AGAGAAGTAGACCAAATC
35190874 AATGAAACGA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 72 0.99
86 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (85 bp):
CTTCATGAGGAGATACAGAGAAGTGGCTCAAAGCAATAAAGCGGGCATCTTCCTGATGAGATACA
GAGAAGTAGACCAAATCTGC
Found at i:35191038 original size:112 final size:112
Alignment explanation
Indices: 35190840--35191052 Score: 293
Period size: 112 Copynumber: 1.9 Consensus size: 112
35190830 AAGCGGGCAT
* * *
35190840 CTTCCTGATGAGATACAGAGAAGTAGACTAAATCAATGAAACGAAGCTCAATACGAATGAGACTT
1 CTTCCTGATGAGATACAGAGAAGTAAACCAAATCAATGAAACGAAGCTCAATACGAATCAGACTT
* * *
35190905 CAAATCTCATCTTCCTAATGAGATATAGAGAAGTGGACCAAATCCTC
66 CAAACCTCATCTTCCTAATGAGATACAAAGAAGTGGACCAAATCCTC
* * ** *
35190952 CTTCCTGATGAGATATAGAGAAGTAAACCAAGTCAATGAAGTGAAGCTCAATATGAATCAGACTT
1 CTTCCTGATGAGATACAGAGAAGTAAACCAAATCAATGAAACGAAGCTCAATACGAATCAGACTT
* *
35191017 CAAACC-CTATTTTCCTGATGAGATACAAAGAAGTGG
66 CAAACCTC-ATCTTCCTAATGAGATACAAAGAAGTGG
35191053 GTTAAAGCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
111 1 0.01
112 86 0.99
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (112 bp):
CTTCCTGATGAGATACAGAGAAGTAAACCAAATCAATGAAACGAAGCTCAATACGAATCAGACTT
CAAACCTCATCTTCCTAATGAGATACAAAGAAGTGGACCAAATCCTC
Found at i:35191117 original size:48 final size:48
Alignment explanation
Indices: 35191028--35191146 Score: 148
Period size: 48 Copynumber: 2.5 Consensus size: 48
35191018 AAACCCTATT
* *
35191028 TTCCTGATGAGATACAAAGAAGTGGGTTAAAGCAATAAAGCGATCATC
1 TTCCTGATGAGATACAAAGAAGTGGATTAAAGCAATAAAGCGATAATC
* * * * * *
35191076 TTCTTGATGAGATGCAAAGAAGTGGATTCAATCAATGAAGCGGTAATC
1 TTCCTGATGAGATACAAAGAAGTGGATTAAAGCAATAAAGCGATAATC
* *
35191124 TTCCTGATGAGATATAGAGAAGT
1 TTCCTGATGAGATACAAAGAAGT
35191147 AGACCAAATC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (48 bp):
TTCCTGATGAGATACAAAGAAGTGGATTAAAGCAATAAAGCGATAATC
Found at i:35191259 original size:171 final size:171
Alignment explanation
Indices: 35190952--35191259 Score: 476
Period size: 171 Copynumber: 1.8 Consensus size: 171
35190942 CCAAATCCTC
* *
35190952 CTTCCTGATGAGATATAGAGAAGTAAACCAAGTCAATGAAGTGAAGCTCAATATGAATCAGACTT
1 CTTCCTGATGAGATATAGAGAAGTAAACCAAATCAATGAAGCGAAGCTCAATATGAATCAGACTT
* * * * * *
35191017 CAAACCCTATTTTCCTGATGAGATACAAAGAAGTGGGTTAAAGCAATAAAGCGATCATCTTCTTG
66 CAAACCCTATCTTCCTGATGAAATACAAAGAAGTAGGTCAAAGCAATAAAGAGATCATCTTCTTA
35191082 ATGAGATGCAAAGAAGTGGATTCAATCAATGAAGCGGTAAT
131 ATGAGATGCAAAGAAGTGGATTCAATCAATGAAGCGGTAAT
* *
35191123 CTTCCTGATGAGATATAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATATGAATGAGACTT
1 CTTCCTGATGAGATATAGAGAAGTAAACCAAATCAATGAAGCGAAGCTCAATATGAATCAGACTT
* *
35191188 CAAATCCC-ATCTTCCTGATGAAATACAGAGAAGTAGGTCAAAGCAATAAAGAGGTCATCTT-TC
66 CAAA-CCCTATCTTCCTGATGAAATACAAAGAAGTAGGTCAAAGCAATAAAGAGATCATCTTCT-
35191251 TAATGAGAT
129 TAATGAGAT
35191260 ATAGAGAAGT
Statistics
Matches: 123, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
170 1 0.01
171 119 0.97
172 3 0.02
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (171 bp):
CTTCCTGATGAGATATAGAGAAGTAAACCAAATCAATGAAGCGAAGCTCAATATGAATCAGACTT
CAAACCCTATCTTCCTGATGAAATACAAAGAAGTAGGTCAAAGCAATAAAGAGATCATCTTCTTA
ATGAGATGCAAAGAAGTGGATTCAATCAATGAAGCGGTAAT
Found at i:35191319 original size:208 final size:209
Alignment explanation
Indices: 35191074--35191485 Score: 583
Period size: 208 Copynumber: 2.0 Consensus size: 209
35191064 AAAGCGATCA
* * * * *
35191074 TCTTCTTGATGAGATGCAAAGAAGTGGATTCAATCAATGAAGCGGTAATCTTCCTGATGAGATAT
1 TCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATGAAGCGATAATCTTCCTGATGAGATAC
* * * *
35191139 AGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATATGAATGAGACTTCAAATCCC-ATCTTCC
66 AGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATACGAATGAAACTTCAAACCCCTATCTTCC
* *
35191203 TGATGAAATACAGAGAAGTAGGTCAAAGCAATAAAGAGGTCATCTTTCTAATGAGATATAGAGAA
131 TGATGAAATACAGAGAAGTAGGTCAAAGCAATAAAGAGGTCATCTTCCTAATGAGATACAGAGAA
35191268 GTAGACCAAATCCG
196 GTAGACCAAATCCG
* *
35191282 TCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGATCATCTTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATGAAGCGATAATCTTCCTGATGAGATAC
* * * * * *
35191347 AGAGAAGTAGACTAAATCAATGAAGTAAAGTTCAATGCGAGTGAAACTTCAAACCCCTATCTTTC
66 AGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATACGAATGAAACTTCAAACCCCTATCTTCC
* * * * * * *
35191412 TGATGAGATACAGAGAAGTGGGTCGAAGTAATAAAGCGGTCATCTTCCTGATGTGATACAGAGAA
131 TGATGAAATACAGAGAAGTAGGTCAAAGCAATAAAGAGGTCATCTTCCTAATGAGATACAGAGAA
35191477 GTAGACCAA
196 GTAGACCAA
35191486 GAAATGAAGG
Statistics
Matches: 177, Mismatches: 26, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
208 106 0.60
209 71 0.40
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (209 bp):
TCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATGAAGCGATAATCTTCCTGATGAGATAC
AGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATACGAATGAAACTTCAAACCCCTATCTTCC
TGATGAAATACAGAGAAGTAGGTCAAAGCAATAAAGAGGTCATCTTCCTAATGAGATACAGAGAA
GTAGACCAAATCCG
Found at i:35191342 original size:85 final size:85
Alignment explanation
Indices: 35191188--35191364 Score: 230
Period size: 85 Copynumber: 2.1 Consensus size: 85
35191178 AATGAGACTT
* *
35191188 CAAATCCCATCTTCCTGATGAAATACAGAGAAGTAGGTCAAAGCAATAAAGAGGTCATCTTTCTA
1 CAAAT-CCATCTTCCTGATGAAATACAGAGAAGTAGGTCAAAGCAATAAAGAGATCATCTTCCTA
*
35191253 ATGAGATATAGAGAAGTAGAC
65 ATGAGATACAGAGAAGTAGAC
* * * * * * *
35191274 CAAATCCGTCTTCCTGATGAGATACAGAGAAGT-GGATTAAATCAATGAAGCGATCATCTTCCTG
1 CAAATCCATCTTCCTGATGAAATACAGAGAAGTAGG-TCAAAGCAATAAAGAGATCATCTTCCTA
35191338 ATGAGATACAGAGAAGTAGAC
65 ATGAGATACAGAGAAGTAGAC
*
35191359 TAAATC
1 CAAATC
35191365 AATGAAGTAA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
84 2 0.03
85 72 0.91
86 5 0.06
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (85 bp):
CAAATCCATCTTCCTGATGAAATACAGAGAAGTAGGTCAAAGCAATAAAGAGATCATCTTCCTAA
TGAGATACAGAGAAGTAGAC
Found at i:35193442 original size:13 final size:13
Alignment explanation
Indices: 35193424--35193448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35193414 TAAAGCCCCT
35193424 ATTTTATTTTAAA
1 ATTTTATTTTAAA
35193437 ATTTTATTTTAA
1 ATTTTATTTTAA
35193449 CCTTAAACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTATTTTAAA
Found at i:35193488 original size:30 final size:30
Alignment explanation
Indices: 35193465--35193689 Score: 251
Period size: 30 Copynumber: 7.6 Consensus size: 30
35193455 ACTTTTTTAG
* *
35193465 AATTACATTTTGACCCCTAAACTTATCCAG
1 AATTACATTTTGACCCCTAAACTTTTCCAA
* *
35193495 AATTACATTTTGA-CTCTTAACTTTTCCAA
1 AATTACATTTTGACCCCTAAACTTTTCCAA
35193524 AATTACATTTTGA-CCCTAAACTTTTCCAA
1 AATTACATTTTGACCCCTAAACTTTTCCAA
* * *
35193553 AATTTCATTTTAACCCTTAAACTTTTCCAA
1 AATTACATTTTGACCCCTAAACTTTTCCAA
* * *
35193583 AATTACATTTTAACCTCTAAACTTTTCTAA
1 AATTACATTTTGACCCCTAAACTTTTCCAA
* * *
35193613 AATCACATTTTAACCCCTAAAC-TTTCTTAA
1 AATTACATTTTGACCCCTAAACTTTTC-CAA
* * *
35193643 AATCACATTTT-AACCCTCAAACTTTTCTAA
1 AATTACATTTTGACCCCT-AAACTTTTCCAA
*
35193673 AATTATATTTTGACCCC
1 AATTACATTTTGACCCC
35193690 AAATTCATCG
Statistics
Matches: 171, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
29 59 0.35
30 104 0.61
31 8 0.05
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (30 bp):
AATTACATTTTGACCCCTAAACTTTTCCAA
Found at i:35194964 original size:20 final size:21
Alignment explanation
Indices: 35194941--35194991 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
35194931 TTTAAAATTA
*
35194941 TAATTATATTT-AATATAAAT
1 TAATAATATTTAAATATAAAT
*
35194961 TAATAATATTTAAATATAAAA
1 TAATAATATTTAAATATAAAT
*
35194982 TAAAAATATT
1 TAATAATATT
35194992 CTATTATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATAATATTTAAATATAAAT
Found at i:35198941 original size:15 final size:16
Alignment explanation
Indices: 35198923--35198961 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
35198913 ACATATTCAC
*
35198923 TTATTTTTTATTTT-T
1 TTATTTTATATTTTAT
35198938 TTATTTTATATTTTAT
1 TTATTTTATATTTTAT
35198954 TTCATTTT
1 TT-ATTTT
35198962 CTAATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 3 0.14
17 5 0.24
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTATATTTTAT
Found at i:35199814 original size:30 final size:31
Alignment explanation
Indices: 35199757--35199904 Score: 121
Period size: 30 Copynumber: 4.9 Consensus size: 31
35199747 CAAAAAATAT
35199757 ATTTTAACCC-CTAAA-TTTTCCAAAAATTTAG
1 ATTTTAACCCTC-AAACTTTT-CAAAAATTTAG
* * *
35199788 -TTTTGACCCTTAAACTTTTTAAAAA-TTAG
1 ATTTTAACCCTCAAACTTTTCAAAAATTTAG
* * *
35199817 ATTTTAACCCTCGAAC-TTTCCAAAATTTTG
1 ATTTTAACCCTCAAACTTTTCAAAAATTTAG
* * *
35199847 ATTTTGACCCTCGAACTTTTCAAAAATTCA-
1 ATTTTAACCCTCAAACTTTTCAAAAATTTAG
* *
35199877 AATTTAACCCTTAAACTTCTT-AAAAATT
1 ATTTTAACCCTCAAACTT-TTCAAAAATT
35199905 ACTTTTTGGT
Statistics
Matches: 94, Mismatches: 17, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
29 11 0.12
30 67 0.71
31 16 0.17
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.40
Consensus pattern (31 bp):
ATTTTAACCCTCAAACTTTTCAAAAATTTAG
Found at i:35199821 original size:60 final size:59
Alignment explanation
Indices: 35199745--35199894 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 59
35199735 CCCGATTTTG
* * *
35199745 TTCAAAAAATATATTTTAACCCCTAAATTTTCCAAAAATTTAG-TTTTGACCCTTAAACTT
1 TTCAAAAATTA-ATTTTAACCCCTAAACTTTCC-AAAATTTAGATTTTGACCCTCAAACTT
* * * *
35199805 TTTAAAAATTAGATTTTAA-CCCTCGAACTTTCCAAAATTTTGATTTTGACCCTCGAACTT
1 TTCAAAAATTA-ATTTTAACCCCT-AAACTTTCCAAAATTTAGATTTTGACCCTCAAACTT
* *
35199865 TTCAAAAATTCAAATTTAACCCTTAAACTT
1 TTCAAAAATT-AATTTTAACCCCTAAACTT
35199895 CTTAAAAATT
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
59 12 0.16
60 58 0.78
61 4 0.05
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (59 bp):
TTCAAAAATTAATTTTAACCCCTAAACTTTCCAAAATTTAGATTTTGACCCTCAAACTT
Found at i:35205497 original size:23 final size:23
Alignment explanation
Indices: 35205456--35205516 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
35205446 ATTTCACCCA
*
35205456 AAAAAATAA-AAAAGGGAAAGAAAG
1 AAAAAATAAGAAAA-AGAAA-AAAG
*
35205480 -AAAAATAAGAAAAAGAAAAGAG
1 AAAAAATAAGAAAAAGAAAAAAG
*
35205502 AAAAAAGAAGAAAAA
1 AAAAAATAAGAAAAA
35205517 AAGATAGGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 3 0.09
23 25 0.78
24 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (23 bp):
AAAAAATAAGAAAAAGAAAAAAG
Found at i:35205509 original size:20 final size:21
Alignment explanation
Indices: 35205471--35205520 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
35205461 ATAAAAAAGG
35205471 GAAAG-AAAGAAAAATAAGAA
1 GAAAGAAAAGAAAAATAAGAA
35205491 -AAAGAAAAGAGAAAA-AAGAA
1 GAAAGAAAAGA-AAAATAAGAA
35205511 GAAA-AAAAGA
1 GAAAGAAAAGA
35205521 TAGGGCGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 4 0.15
20 16 0.59
21 7 0.26
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (21 bp):
GAAAGAAAAGAAAAATAAGAA
Found at i:35206573 original size:50 final size:50
Alignment explanation
Indices: 35206501--35207018 Score: 330
Period size: 50 Copynumber: 10.5 Consensus size: 50
35206491 AGGAAACATA
* * * * *
35206501 AAGATATGAAAGGAAAGG-TTGAGGCCACAACAGCGAACCCGATACCTTAA
1 AAGATATG-ATGGGAAGGATTGAGGCCGCAACGGCGAACCCGATACCTTAG
* * * * *
35206551 AAGATTTGATGGGAAGGATTGAGGCCGTAACGGCGAA-TCAAGTACCAT-G
1 AAGATATGATGGGAAGGATTGAGGCCGCAACGGCGAACCCGA-TACCTTAG
* *
35206600 AAGATATGAAGGGAAAGG-TTGAGGCCGCAACAGG-GAACCTGATACCTTAG
1 AAGATATGATGGG-AAGGATTGAGGCCGCAAC-GGCGAACCCGATACCTTAG
* * * * *
35206650 AAGATGTGATGAGG-AGGATTAAGGCCACAACGGCGAATCC-AGTACCAT-G
1 AAGATATGATG-GGAAGGATTGAGGCCGCAACGGCGAACCCGA-TACCTTAG
* * * * * *
35206699 AAGATATAAAGGGAA-AAGTTGAGGCTGCAATGGCGAACCCGGTACCTTAG
1 AAGATATGATGGGAAGGA-TTGAGGCCGCAACGGCGAACCCGATACCTTAG
* * ** ** * *
35206749 AGGATATGATTGGAAGGATTGAGGTTGCAATAGCGAATCCGATACCAT-G
1 AAGATATGATGGGAAGGATTGAGGCCGCAACGGCGAACCCGATACCTTAG
* * * *
35206798 AAGATATGAAAGGAAAGG-TTGAGGCCGTAACGGTGAACCCTG-TACCTTAG
1 AAGATATG-ATGGGAAGGATTGAGGCCGCAACGGCGAACCC-GATACCTTAG
* * *
35206848 AAGATATAATGGGAAGGATTGAGGCCGCAATGGCGAACTCGATACCTTAG
1 AAGATATGATGGGAAGGATTGAGGCCGCAACGGCGAACCCGATACCTTAG
* * * * * ** *
35206898 AAGATATAATGGGAAGGATTGAAGCCACAACGACGAATCTTATACCAT-G
1 AAGATATGATGGGAAGGATTGAGGCCGCAACGGCGAACCCGATACCTTAG
* * * * * **
35206947 GAGATTTGGA-GGGAAAGG-TTAAAGCCGCAACGACGAACCTTATACCTTAG
1 AAGATAT-GATGGG-AAGGATTGAGGCCGCAACGGCGAACCCGATACCTTAG
* *
35206997 -AGATATTAAGGGAAGGATTGAG
1 AAGATATGATGGGAAGGATTGAG
35207019 TTCGCAATGA
Statistics
Matches: 359, Mismatches: 84, Indels: 51
0.73 0.17 0.10
Matches are distributed among these distances:
48 8 0.02
49 160 0.45
50 188 0.52
51 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (50 bp):
AAGATATGATGGGAAGGATTGAGGCCGCAACGGCGAACCCGATACCTTAG
Found at i:35206771 original size:149 final size:148
Alignment explanation
Indices: 35206501--35207032 Score: 377
Period size: 149 Copynumber: 3.6 Consensus size: 148
35206491 AGGAAACATA
* * * * * * *
35206501 AAGATATGAAAGGAAAGGTTGAGGCCACAACAGCGAACCC-GATACCTTAAAAGATTTGATGGGA
1 AAGATATGAAAGG-AAGGTTAAGGCCACAACGGCGAACCCAG-TACCATAGAAGATATAAAGGGA
* * * * * *
35206565 AGGATTGAGGCCGTAACGGCGAA-TCAAGTACCAT-GAAGATATGAA-GGGAAAGG-TTGAGGCC
64 AAGATTGAGGCCGCAATGGCGAACCCGA-TACCTTAGAAGATAT-AATGGG-AAGGATTGAGGCC
* *
35206626 GCAACAGGGAA-CCTGATACCTTAG
126 GCAACAGCGAATCC-GATACCAT-G
* * *
35206650 AAGATGTGATGAGG-AGGATTAAGGCCACAACGGCGAATCCAGTACCAT-GAAGATATAAAGGGA
1 AAGATATGA-AAGGAAGG-TTAAGGCCACAACGGCGAACCCAGTACCATAGAAGATATAAAGGGA
* * * * * **
35206713 AA-AGTTGAGGCTGCAATGGCGAACCCGGTACCTTAGAGGATATGATTGGAAGGATTGAGGTTGC
64 AAGA-TTGAGGCCGCAATGGCGAACCCGATACCTTAGAAGATATAATGGGAAGGATTGAGGCCGC
*
35206777 AATAGCGAATCCGATACCATG
128 AACAGCGAATCCGATACCATG
* ** * * * *
35206798 AAGATATGAAAGGAAAGGTTGAGGCCGTAACGGTGAACCCTGTACCTTAGAAGATATAATGGGAA
1 AAGATATGAAAGG-AAGGTTAAGGCCACAACGGCGAACCCAGTACCATAGAAGATATAAAGGGAA
* * * *
35206863 GGATTGAGGCCGCAATGGCGAACTCGATACCTTAGAAGATATAATGGGAAGGATTGAAGCCACAA
65 AGATTGAGGCCGCAATGGCGAACCCGATACCTTAGAAGATATAATGGGAAGGATTGAGGCCGCAA
**
35206928 C-GACGAATCTTATACCATG
130 CAG-CGAATCCGATACCATG
* * * * * * * * * *
35206947 GAGATTTGGAGGGAAAGGTTAAAGCCGCAACGACGAACCTTA-TACCTTAG-AGATATTAAGGGA
1 AAGATATGAAAGG-AAGGTTAAGGCCACAACGGCGAACC-CAGTACCATAGAAGATATAAAGGGA
* ** *
35207010 AGGATTGAGTTCGCAATGACGAA
64 AAGATTGAGGCCGCAATGGCGAA
35207033 TCTCATACCC
Statistics
Matches: 302, Mismatches: 66, Indels: 31
0.76 0.17 0.08
Matches are distributed among these distances:
147 4 0.01
148 105 0.35
149 186 0.62
150 7 0.02
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (148 bp):
AAGATATGAAAGGAAGGTTAAGGCCACAACGGCGAACCCAGTACCATAGAAGATATAAAGGGAAA
GATTGAGGCCGCAATGGCGAACCCGATACCTTAGAAGATATAATGGGAAGGATTGAGGCCGCAAC
AGCGAATCCGATACCATG
Found at i:35206891 original size:99 final size:100
Alignment explanation
Indices: 35206501--35206904 Score: 457
Period size: 99 Copynumber: 4.1 Consensus size: 100
35206491 AGGAAACATA
* * * *
35206501 AAGATATGAAAGGAAAGGTTGAGGCCACAACAGCGAACCC-GATACCTTAAAAGATTTGATGGGA
1 AAGATATGAAAGGAAAGGTTGAGGCCGCAACGGCGAACCCTGATACCTTAGAAGATATGATGGGA
* *
35206565 AGGATTGAGGCCGTAACGGCGAATCAAGTACCATG
66 AGGATTGAGGCCGCAACGGCGAATCGAGTACCATG
* *
35206600 AAGATATGAAGGGAAAGGTTGAGGCCGCAACAGG-GAA-CCTGATACCTTAGAAGATGTGATGAG
1 AAGATATGAAAGGAAAGGTTGAGGCCGCAAC-GGCGAACCCTGATACCTTAGAAGATATGATG-G
* * *
35206663 G-AGGATTAAGGCCACAACGGCGAATCCAGTACCATG
64 GAAGGATTGAGGCCGCAACGGCGAATCGAGTACCATG
* * * * * *
35206699 AAGATAT-AAAGGGAAAAGTTGAGGCTGCAATGGCGAACCC-GGTACCTTAGAGGATATGATTGG
1 AAGATATGAAA-GGAAAGGTTGAGGCCGCAACGGCGAACCCTGATACCTTAGAAGATATGATGGG
** **
35206762 AAGGATTGAGGTTGCAATAGCGAATCCGA-TACCATG
65 AAGGATTGAGGCCGCAACGGCGAAT-CGAGTACCATG
* * *
35206798 AAGATATGAAAGGAAAGGTTGAGGCCGTAACGGTGAACCCTG-TACCTTAGAAGATATAATGGGA
1 AAGATATGAAAGGAAAGGTTGAGGCCGCAACGGCGAACCCTGATACCTTAGAAGATATGATGGGA
* *
35206862 AGGATTGAGGCCGCAATGGCGAACTCGA-TACCTTAG
66 AGGATTGAGGCCGCAACGGCGAA-TCGAGTACCAT-G
35206898 AAGATAT
1 AAGATAT
35206905 AATGGGAAGG
Statistics
Matches: 257, Mismatches: 36, Indels: 23
0.81 0.11 0.07
Matches are distributed among these distances:
98 8 0.03
99 229 0.89
100 20 0.08
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.19
Consensus pattern (100 bp):
AAGATATGAAAGGAAAGGTTGAGGCCGCAACGGCGAACCCTGATACCTTAGAAGATATGATGGGA
AGGATTGAGGCCGCAACGGCGAATCGAGTACCATG
Found at i:35207025 original size:49 final size:49
Alignment explanation
Indices: 35206840--35207041 Score: 173
Period size: 49 Copynumber: 4.1 Consensus size: 49
35206830 GTGAACCCTG
* * *
35206840 TACCTTAGAAGATATAATGGGAAGGATTGAGGCCGCAATGGCGAA-CTCGA
1 TACCTTAGAAGATATAATGGGAAGGATTGA-GCCGCAACGACGAATCT-TA
*
35206890 TACCTTAGAAGATATAATGGGAAGGATTGAAGCCACAACGACGAATCTTA
1 TACCTTAGAAGATATAATGGGAAGGATTG-AGCCGCAACGACGAATCTTA
* * * * * *
35206940 TACCAT-GGAGATTTGGA-GGGAAAGG-TTAAAGCCGCAACGACGAACCTTA
1 TACCTTAGAAGATAT-AATGGG-AAGGATT-GAGCCGCAACGACGAATCTTA
* * *
35206989 TACCTTAG-AGATATTAA-GGGAAGGATTGAGTTCGCAATGACGAATCTCA
1 TACCTTAGAAGATA-TAATGGGAAGGATTGAG-CCGCAACGACGAATCTTA
35207038 TACC
1 TACC
35207042 CTAAAGAAGA
Statistics
Matches: 124, Mismatches: 19, Indels: 19
0.77 0.12 0.12
Matches are distributed among these distances:
48 6 0.05
49 62 0.50
50 53 0.43
51 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.22
Consensus pattern (49 bp):
TACCTTAGAAGATATAATGGGAAGGATTGAGCCGCAACGACGAATCTTA
Found at i:35207304 original size:78 final size:78
Alignment explanation
Indices: 35207163--35208107 Score: 1439
Period size: 78 Copynumber: 12.1 Consensus size: 78
35207153 AGAGCAAAGC
* * *
35207163 GAAGACA-TCCAATCTCTTACCCCGATCAT-GGGCAGAATGAAGCATCCAATCTTTTACCTTAAT
1 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAAT
*
35207226 CAAAAGGCAGATT
66 CAGAAGGCAGATT
* * * *
35207239 GAAGACACACCAATCTCTTACCCTGATCATGGGGTAGACTGAAGCATCAAATCTTTTACCCTAAT
1 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAAT
*
35207304 CAGAGGGCAGATT
66 CAGAAGGCAGATT
** * *
35207317 GAAGACACATAAATCTCTTATCCCGATCATGGCGCAGATTGAAGCATCCAATCTTTTACCCTAAT
1 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAAT
35207382 CAGAAGGCAGATT
66 CAGAAGGCAGATT
* *
35207395 GAAGACACACCAATCTCTTACCCCGATCAT-GGGCAGAATGAAGCATCCAATCTTTTACCTTAAT
1 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAAT
*
35207459 CAAAAGGCAGATT
66 CAGAAGGCAGATT
* * *
35207472 GAAGACACACCAATCTCTTACCCTGATCATGGGGTAGATTGAAGCATCAAATCTTTTACCCTAAT
1 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAAT
*
35207537 CAGAGGGCAGATT
66 CAGAAGGCAGATT
** * *
35207550 GAAGACACATAAATCTCTTATCCCGATCATGGCGCAGATTGAAGCATCCAATCTTTTACCCTAAT
1 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAAT
35207615 CAGAAGGCAGATT
66 CAGAAGGCAGATT
* *
35207628 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCCATCTTTTACCTTAAT
1 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAAT
35207693 CAGAAGGCAGATT
66 CAGAAGGCAGATT
*
35207706 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAAT
1 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAAT
35207771 CAGAAGGCAGATT
66 CAGAAGGCAGATT
* *
35207784 AAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGTATCCAATCTTTTACCCTAAT
1 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAAT
*
35207849 CAGAGGGCAGATT
66 CAGAAGGCAGATT
*
35207862 GAAGACACACCAATCTCTTACCCCGATCATGGGGTAGATTGAAGCATCCAATCTTTTACCCTAAT
1 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAAT
*
35207927 CAGAGGGCAGATT
66 CAGAAGGCAGATT
*
35207940 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAAT
1 GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAAT
* *
35208005 CAGAGGGCAAATT
66 CAGAAGGCAGATT
* *
35208018 -AAGGACACACTAATCTCTTACCCCGATCATGAGGCAGATTGAAGCCACCATCCAATCTTTTACC
1 GAA-GACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAG----CATCCAATCTTTTA-C
*
35208082 CCTAAATCAAGAGGGGCAGATT
60 CCT-AATC-AGA-AGGCAGATT
35208104 GAAG
1 GAAG
35208108 CTATCATCTC
Statistics
Matches: 796, Mismatches: 60, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
76 7 0.01
77 94 0.12
78 660 0.83
82 14 0.02
83 3 0.00
84 4 0.01
85 3 0.00
86 9 0.01
87 2 0.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (78 bp):
GAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAAT
CAGAAGGCAGATT
Found at i:35209130 original size:21 final size:22
Alignment explanation
Indices: 35209106--35209146 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
35209096 ACATATTCAC
*
35209106 TTATTTTTTATTTC-TTTTCTT
1 TTATATTTTATTTCATTTTCTT
35209127 TTATATTTTATTTCATTTTC
1 TTATATTTTATTTCATTTTC
35209147 GAATCAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATATTTTATTTCATTTTCTT
Found at i:35209883 original size:30 final size:30
Alignment explanation
Indices: 35209840--35210080 Score: 190
Period size: 30 Copynumber: 8.1 Consensus size: 30
35209830 AATTTCACAA
* *
35209840 AAAAATTA-GTTTTGACCCTCAATCTTTTT
1 AAAAATTACATTTTGACCCTCAAACTTTTT
**
35209869 AAAAATT-CAATTTTGACCCTCAAACTTTCC
1 AAAAATTAC-ATTTTGACCCTCAAACTTTTT
* * * *
35209899 AAAAACTT-GATTTCGACCCTCTAATTTTTT
1 AAAAA-TTACATTTTGACCCTCAAACTTTTT
* * *
35209929 AAAAATTACATTTTGACTCTCGAACTTTCT
1 AAAAATTACATTTTGACCCTCAAACTTTTT
* *
35209959 AAAAATTTA-AATTTGACCC-CTAAACTTCTT
1 AAAAA-TTACATTTTGACCCTC-AAACTTTTT
* ** *
35209989 AAAAATTACTTTTTGGTCCTCAAACTTCTT
1 AAAAATTACATTTTGACCCTCAAACTTTTT
* *
35210019 AAAAATCACA-TTTAACCCT-AAACTTTTT
1 AAAAATTACATTTTGACCCTCAAACTTTTT
* * *
35210047 GAAAATTACATTTTGACCCCCTAAACTTTCT
1 AAAAATTACATTTTGACCCTC-AAACTTTTT
35210078 AAA
1 AAA
35210081 TTTTTATTTT
Statistics
Matches: 164, Mismatches: 37, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
28 16 0.10
29 26 0.16
30 106 0.65
31 16 0.10
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCTCAAACTTTTT
Found at i:35211718 original size:17 final size:17
Alignment explanation
Indices: 35211696--35211735 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
35211686 TCTCCACCTT
* *
35211696 AACAAGAATTCTCTACG
1 AACAAGAACTCTCAACG
35211713 AACAAGAACTCTCAACG
1 AACAAGAACTCTCAACG
35211730 AACAAG
1 AACAAG
35211736 TTCTCCACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.25, G:0.12, T:0.15
Consensus pattern (17 bp):
AACAAGAACTCTCAACG
Found at i:35214309 original size:4 final size:4
Alignment explanation
Indices: 35214300--35214325 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
35214290 TGACTATATA
35214300 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
35214326 TGTATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:35214351 original size:28 final size:28
Alignment explanation
Indices: 35214320--35214378 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
35214310 ATAAATAAAT
* *
35214320 AAATAATGT-ATAAAATTATTAAATATTA
1 AAATAATATAATAAAATT-TTAAAAATTA
*
35214348 AAATAATATAATATAATTTTAAAAATTA
1 AAATAATATAATAAAATTTTAAAAATTA
35214376 AAA
1 AAA
35214379 AAAATCTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (28 bp):
AAATAATATAATAAAATTTTAAAAATTA
Found at i:35227502 original size:10 final size:10
Alignment explanation
Indices: 35227489--35227536 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
35227479 ATAATTTTAG
35227489 AAATTTTTTT
1 AAATTTTTTT
35227499 AAATTTTTTAT
1 AAATTTTTT-T
*
35227510 ATATTTTTTT
1 AAATTTTTTT
* *
35227520 AGATTTTTTA
1 AAATTTTTTT
35227530 AAATTTT
1 AAATTTT
35227537 ATAATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
AAATTTTTTT
Found at i:35227623 original size:35 final size:35
Alignment explanation
Indices: 35227555--35227624 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
35227545 TAAAAAATAT
*
35227555 AAAATTTGAAATTTTTATTAATATTTTGAATTTTA
1 AAAATTTGAAATTTTTATAAATATTTTGAATTTTA
* *
35227590 AAAATTTTAAATTTTT-TAAAATCATTTTGATTTTT
1 AAAATTTGAAATTTTTAT-AAAT-ATTTTGAATTTT
35227625 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
34 1 0.03
35 18 0.60
36 11 0.37
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (35 bp):
AAAATTTGAAATTTTTATAAATATTTTGAATTTTA
Found at i:35229713 original size:17 final size:18
Alignment explanation
Indices: 35229666--35229715 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 18
35229656 CAATTCGCAT
*
35229666 CAAACATCAGTTCATATG
1 CAAATATCAGTTCATATG
* * *
35229684 -AGATAACAATTCATA-G
1 CAAATATCAGTTCATATG
35229700 CAAATATCAGTTCATA
1 CAAATATCAGTTCATA
35229716 CTACATAATA
Statistics
Matches: 24, Mismatches: 7, Indels: 3
0.71 0.21 0.09
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (18 bp):
CAAATATCAGTTCATATG
Found at i:35235561 original size:9 final size:8
Alignment explanation
Indices: 35235494--35235563 Score: 54
Period size: 8 Copynumber: 8.8 Consensus size: 8
35235484 TAAATACAAT
*
35235494 TAATAACA
1 TAATAATA
*
35235502 TAATAAAA
1 TAATAATA
35235510 TAATAA-A
1 TAATAATA
**
35235517 TAGGAATA
1 TAATAATA
*
35235525 -AATAAAA
1 TAATAATA
35235532 TAATAATA
1 TAATAATA
*
35235540 TAATCATA
1 TAATAATA
35235548 GTAATAATGA
1 -TAATAAT-A
35235558 TAATAA
1 TAATAA
35235564 ATATCAATTA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
7 9 0.18
8 27 0.55
9 12 0.24
10 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (8 bp):
TAATAATA
Found at i:35235751 original size:19 final size:17
Alignment explanation
Indices: 35235704--35235761 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
35235694 AATACAGGAA
*
35235704 AAAAATGAAATAAAAAAT
1 AAAAAT-AAATAAACAAT
**
35235722 AGATTATAAATACAACATAT
1 A-AAAATAAATA-AACA-AT
35235742 AAAAATAAATAAACAAT
1 AAAAATAAATAAACAAT
35235759 AAA
1 AAA
35235762 TAAATAGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
17 5 0.16
18 10 0.31
19 14 0.44
20 3 0.09
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAATAAATAAACAAT
Found at i:35235767 original size:19 final size:19
Alignment explanation
Indices: 35235727--35235761 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35235717 AAAATAGATT
35235727 ATAAATACAACATATAAAA
1 ATAAATACAACATATAAAA
35235746 ATAAATA-AACA-ATAAA
1 ATAAATACAACATATAAA
35235762 TAAATAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (19 bp):
ATAAATACAACATATAAAA
Found at i:35242298 original size:64 final size:64
Alignment explanation
Indices: 35242223--35242359 Score: 211
Period size: 64 Copynumber: 2.1 Consensus size: 64
35242213 CGGTACTAGA
* * * *
35242223 TTAATATTTTTTTTCTCTAAGGAGTTGCCTAGGCGGCTCAAGTTACTGCTCAAGCGGCAATGTAG
1 TTAATATTTTTTATCT-TAAGGAGCTACCTAGGCGGCTCAAGTTACTGCTCAAGCAGCAATGTAG
* *
35242288 TTAATATTTTTTATGTTAAGGAGCTACCTAGGCGGCTCGAGTTACTGCTCAAGCAGCAATGTAG
1 TTAATATTTTTTATCTTAAGGAGCTACCTAGGCGGCTCAAGTTACTGCTCAAGCAGCAATGTAG
35242352 TTAATATT
1 TTAATATT
35242360 AATTTTGTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
64 52 0.79
65 14 0.21
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (64 bp):
TTAATATTTTTTATCTTAAGGAGCTACCTAGGCGGCTCAAGTTACTGCTCAAGCAGCAATGTAG
Found at i:35242369 original size:64 final size:64
Alignment explanation
Indices: 35242240--35242384 Score: 213
Period size: 64 Copynumber: 2.3 Consensus size: 64
35242230 TTTTTTTCTC
* * *
35242240 TAAGGAGTTGCCTAGGCGGCTCAAGTTACTGCTCAAGCGGCAATGTAGTTAATATTTTTTATGT
1 TAAGGAGCTGCCTAGGCGGCTCAAGTTACTGCTCAAGCAGCAATGTAGTTAATATTATTTATGT
* *
35242304 TAAGGAGCTACCTAGGCGGCTCGAGTTACTGCTCAAGCAGCAATGTAGTTAATATTAATTT-TGT
1 TAAGGAGCTGCCTAGGCGGCTCAAGTTACTGCTCAAGCAGCAATGTAGTTAATATT-ATTTATGT
35242368 TAA-GATGCTGCCTAGGC
1 TAAGGA-GCTGCCTAGGC
35242385 AAGACAAGCT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
63 2 0.03
64 68 0.93
65 3 0.04
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (64 bp):
TAAGGAGCTGCCTAGGCGGCTCAAGTTACTGCTCAAGCAGCAATGTAGTTAATATTATTTATGT
Found at i:35245439 original size:61 final size:62
Alignment explanation
Indices: 35245287--35245440 Score: 195
Period size: 61 Copynumber: 2.5 Consensus size: 62
35245277 ATAAATGCAA
* *
35245287 AAAGTTCCGATGACTTAAGTCATCGTGAGTATTGAATAAGAAATGAATCCTACTACGGATTT
1 AAAGGTCCGATGACTTATGTCATCGTGAGTATTGAATAAGAAATGAATCCTACTACGGATTT
* * * ** *
35245349 AAAGGTCCGACGACTTTGTGTCATCGTGAGTATTGAATGAG-AATGAATCCTGTTATGGA-TT
1 AAAGGTCCGATGAC-TTATGTCATCGTGAGTATTGAATAAGAAATGAATCCTACTACGGATTT
*
35245410 AAAGGTCCGATGACTCTATGTCATTGTGAGT
1 AAAGGTCCGATGACT-TATGTCATCGTGAGT
35245441 TATCAAATAT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
60 1 0.01
61 28 0.35
62 27 0.34
63 23 0.29
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (62 bp):
AAAGGTCCGATGACTTATGTCATCGTGAGTATTGAATAAGAAATGAATCCTACTACGGATTT
Found at i:35250803 original size:195 final size:194
Alignment explanation
Indices: 35250457--35250819 Score: 453
Period size: 195 Copynumber: 1.9 Consensus size: 194
35250447 GTAACAAATA
* * * * * * * * *
35250457 CTGCTCACATGAGTTGTTGAGGACTCGCAACATATGTGGTACCCCAGTCATCGGTATGATGTCTG
1 CTGCTCACATGAGCTGTCGAGGACTCGCAACAAATGCGGTACCCCAGCCATCGATACGATATATG
*** ** *
35250522 TTTGTAAATTATCCCCTAATGATGCTACTCACATGAGATGTCGAGAATATGCATTCAAGCATAAA
66 TGCATAAATTATCCCCTAACAATGCTACTCACATGAGATATCGAGAATATGCATTCAAGCATAAA
* *
35250587 TCCAACCCATCGTATGGCCTGTAATCCATT-TTAGGATTTCATATCTCTTTTTCGACTCATGATG
131 TCCAACCCATAGTAGGGCCTGTAATCCATTCTT-GGATTTCATATCTCTTTTTCGACTCATGATG
* *
35250651 CTGCTCACATGAGCTGTCGAGGACTCGCAACAAATGCGGTACCTCAGCCATCGATACGGTATATG
1 CTGCTCACATGAGCTGTCGAGGACTCGCAACAAATGCGGTACCCCAGCCATCGATACGATATATG
* * * * *
35250716 TGCATATAATTGTCCCCTGACAATGCTGCTCACATGAGCTATCGAGAATATGCACTT-ATGCATA
66 TGCATA-AATTATCCCCTAACAATGCTACTCACATGAGATATCGAGAATATGCA-TTCAAGCATA
35250780 AATCCCAA-CCATAGTAGGGCCTGTAATCCATTCTTGGATT
129 AAT-CCAACCCATAGTAGGGCCTGTAATCCATTCTTGGATT
35250820 CATTTCTTAT
Statistics
Matches: 141, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
194 57 0.40
195 76 0.54
196 8 0.06
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (194 bp):
CTGCTCACATGAGCTGTCGAGGACTCGCAACAAATGCGGTACCCCAGCCATCGATACGATATATG
TGCATAAATTATCCCCTAACAATGCTACTCACATGAGATATCGAGAATATGCATTCAAGCATAAA
TCCAACCCATAGTAGGGCCTGTAATCCATTCTTGGATTTCATATCTCTTTTTCGACTCATGATG
Found at i:35250840 original size:195 final size:194
Alignment explanation
Indices: 35250457--35250860 Score: 451
Period size: 195 Copynumber: 2.1 Consensus size: 194
35250447 GTAACAAATA
* * * * * * * * *
35250457 CTGCTCACATGAGTTGTTGAGGACTCGCAACATATGTGGTACCCCAGTCATCGGTATGATGTCTG
1 CTGCTCACATGAGCTGTCGAGGACTCGCAACAAATGCGGTACCCCAGCCATCGATACGATATATG
*** ** *
35250522 TTTGTAAATTATCCCCTAATGATGCTACTCACATGAGATGTCGAGAATATGCATTCAAGCATAAA
66 TGCATAAATTATCCCCTAACAATGCTACTCACATGAGATATCGAGAATATGCATTCAAGCATAAA
* * ** *
35250587 TCCAACCCATCGTATGGCCTGTAATCCATTTTAGGATTTCATATCTCTTTTTCGACTCATGATG
131 TCCAACCCATAGTAGGGCCTGTAATCCATTTTAGGATTTCATATCTCTTTTTCGACTCACAAAG
* *
35250651 CTGCTCACATGAGCTGTCGAGGACTCGCAACAAATGCGGTACCTCAGCCATCGATACGGTATATG
1 CTGCTCACATGAGCTGTCGAGGACTCGCAACAAATGCGGTACCCCAGCCATCGATACGATATATG
* * * * *
35250716 TGCATATAATTGTCCCCTGACAATGCTGCTCACATGAGCTATCGAGAATATGCACTT-ATGCATA
66 TGCATA-AATTATCCCCTAACAATGCTACTCACATGAGATATCGAGAATATGCA-TTCAAGCATA
35250780 AATCCCAA-CCATAGTAGGGCCTGTAATCCATTCTT-GGA-TTCAT-T-TCTTATTTCCCGACTC
129 AAT-CCAACCCATAGTAGGGCCTGTAATCCATT-TTAGGATTTCATATCTCTT-TTT--CGACTC
35250840 ACAAAG
189 ACAAAG
*
35250846 CTGCTCACACGAGCT
1 CTGCTCACATGAGCT
35250861 ATTGAGAATA
Statistics
Matches: 175, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
192 4 0.02
193 4 0.02
194 62 0.35
195 97 0.55
196 8 0.05
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (194 bp):
CTGCTCACATGAGCTGTCGAGGACTCGCAACAAATGCGGTACCCCAGCCATCGATACGATATATG
TGCATAAATTATCCCCTAACAATGCTACTCACATGAGATATCGAGAATATGCATTCAAGCATAAA
TCCAACCCATAGTAGGGCCTGTAATCCATTTTAGGATTTCATATCTCTTTTTCGACTCACAAAG
Found at i:35250922 original size:105 final size:105
Alignment explanation
Indices: 35250735--35250971 Score: 384
Period size: 105 Copynumber: 2.3 Consensus size: 105
35250725 TTGTCCCCTG
35250735 ACAATGCTGCTCACATGAGCTATCGAGAATATGCACTTATGCATAAATCCCAACCATAGTAGGGC
1 ACAATGCTGCTCACATGAGCTATCGAGAATATGCACTTATGCATAAATCCCAACCATAGTAGGGC
* * *
35250800 CTGTAATCCATTCTTGGATTCATTTCTTATTTCCCGACTC
66 CTATAATCCATTCTTGGATTCATTTCTCATTTCCCAACTC
* * * * *
35250840 ACAAAGCTGCTCACACGAGCTATTGAGAATATGCACTTATGCATAAATCCCAGCCATCGTAGGGC
1 ACAATGCTGCTCACATGAGCTATCGAGAATATGCACTTATGCATAAATCCCAACCATAGTAGGGC
*
35250905 CTATGATCCATTCTTGGATTCATTTCTCATTTCCCAACTC
66 CTATAATCCATTCTTGGATTCATTTCTCATTTCCCAACTC
*
35250945 ACAATGCTGCTCACATGAGCTGTCGAG
1 ACAATGCTGCTCACATGAGCTATCGAG
35250972 GACTTGCAAC
Statistics
Matches: 119, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 119 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (105 bp):
ACAATGCTGCTCACATGAGCTATCGAGAATATGCACTTATGCATAAATCCCAACCATAGTAGGGC
CTATAATCCATTCTTGGATTCATTTCTCATTTCCCAACTC
Found at i:35255511 original size:18 final size:18
Alignment explanation
Indices: 35255490--35255524 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35255480 TAACCCAATT
*
35255490 TAAATAATTAATTAAATC
1 TAAATAATTAATGAAATC
*
35255508 TAAATTATTAATGAAAT
1 TAAATAATTAATGAAAT
35255525 ATTTTATGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
TAAATAATTAATGAAATC
Found at i:35273943 original size:22 final size:22
Alignment explanation
Indices: 35273914--35273966 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
35273904 TTCTTTACGG
35273914 TATT-CTACAATTTAATTAGAT
1 TATTACTACAATTTAATTAGAT
*
35273935 TATTACTACAATTTAATTGGAT
1 TATTACTACAATTTAATTAGAT
35273957 TATTACTACA
1 TATTACTACA
35273967 TTATTTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (22 bp):
TATTACTACAATTTAATTAGAT
Found at i:35274875 original size:9 final size:9
Alignment explanation
Indices: 35274861--35274903 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
35274851 TATTTATCAC
*
35274861 ATCACATTT
1 ATCACATTA
*
35274870 ATCACATGA
1 ATCACATTA
*
35274879 GTCACATTA
1 ATCACATTA
*
35274888 ATCGCATTA
1 ATCACATTA
35274897 ATCACAT
1 ATCACAT
35274904 AAGTACATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (9 bp):
ATCACATTA
Found at i:35274970 original size:115 final size:118
Alignment explanation
Indices: 35274767--35275073 Score: 442
Period size: 126 Copynumber: 2.6 Consensus size: 118
35274757 CATTCTTTTA
* *
35274767 CACATTAATCGCATTAATCACATGAGTACTTAGCACAACACATATTAATCACATTTAATCACATT
1 CACATTAATCGCATTAATCACATGAGTACTAAGAACAACACATATTAATCACATTTAATCACATT
*
35274832 AGTGAAATGAATATTTCAGTA-TT-T-ATCAC-ATCACATTTATCACATGAGT
66 AGTGAAATGAATATTTCAATATTTATCATCACAATCACATTTATCACATGAGT
*
35274881 CACATTAATCGCATTAATCACATAAGTACATAAGAACAACACATATTAATCACATTTAATCACAT
1 CACATTAATCGCATTAATCACATGAGTAC-TAAGAACAACACATATTAATCACATTTAATCACAT
35274946 TAGTGAAATGAATATTTCAATATTTATCACATCACATATTAATCACATTTATCACATGAGT
65 TAGTGAAATGAATATTTCAATATTTAT--CATCAC-----AATCACATTTATCACATGAGT
* *
35275007 CACATTAATCGCATTAATCACATGAGTACTTAAGAAGAACACATATTAATCACATACTAATCACA
1 CACATTAATCGCATTAATCACATGAGTAC-TAAGAACAACACATATTAATCACAT-TTAATCACA
35275072 TT
64 TT
35275074 TAGTCACATT
Statistics
Matches: 172, Mismatches: 8, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
114 28 0.16
115 54 0.31
116 2 0.01
117 1 0.01
120 5 0.03
126 72 0.42
127 10 0.06
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.32
Consensus pattern (118 bp):
CACATTAATCGCATTAATCACATGAGTACTAAGAACAACACATATTAATCACATTTAATCACATT
AGTGAAATGAATATTTCAATATTTATCATCACAATCACATTTATCACATGAGT
Found at i:35275001 original size:9 final size:9
Alignment explanation
Indices: 35274983--35275029 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
35274973 CACATCACAT
35274983 ATTAATCAC
1 ATTAATCAC
*
35274992 ATTTATCAC
1 ATTAATCAC
* *
35275001 ATGAGTCAC
1 ATTAATCAC
*
35275010 ATTAATCGC
1 ATTAATCAC
35275019 ATTAATCAC
1 ATTAATCAC
35275028 AT
1 AT
35275030 GAGTACTTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.34
Consensus pattern (9 bp):
ATTAATCAC
Found at i:35275021 original size:27 final size:27
Alignment explanation
Indices: 35274967--35275033 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
35274957 ATATTTCAAT
* *
35274967 ATTTATCACATCA--CATATTAATCAC
1 ATTTATCACATGAGTCACATTAATCAC
*
35274992 ATTTATCACATGAGTCACATTAATCGC
1 ATTTATCACATGAGTCACATTAATCAC
*
35275019 ATTAATCACATGAGT
1 ATTTATCACATGAGT
35275034 ACTTAAGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
25 12 0.33
27 24 0.67
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.34
Consensus pattern (27 bp):
ATTTATCACATGAGTCACATTAATCAC
Found at i:35275118 original size:23 final size:23
Alignment explanation
Indices: 35275077--35275172 Score: 111
Period size: 23 Copynumber: 4.1 Consensus size: 23
35275067 TCACATTTAG
*
35275077 TCACATTTAATATTTAAGCATAAA
1 TCACA-TTAATATTTAAGCACAAA
* ** *
35275101 TCATATTAGCATTTAAGCATAAA
1 TCACATTAATATTTAAGCACAAA
* *
35275124 TTACATTAATGTTTAAGCACAAA
1 TCACATTAATATTTAAGCACAAA
*
35275147 TCACATTAATATTTAAACACAAA
1 TCACATTAATATTTAAGCACAAA
35275170 TCA
1 TCA
35275173 TATAAATCAT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
23 56 0.93
24 4 0.07
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (23 bp):
TCACATTAATATTTAAGCACAAA
Done.