Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014863.1 Kokia drynarioides strain JFW-HI SEQ_129906, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 219092
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 109 characters in sequence are not A, C, G, or T
Found at i:5040 original size:17 final size:17
Alignment explanation
Indices: 5018--5077 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
5008 ATATCATTAA
5018 TTATTATGTGTTAATAT
1 TTATTATGTGTTAATAT
*
5035 TTATTAT-TTTTAATTAT
1 TTATTATGTGTTAA-TAT
* *
5052 TTTTTAGTTGAGTTAATAT
1 TTATTA--TGTGTTAATAT
5071 TTGATTA
1 TT-ATTA
5078 ATTCGTGCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
16 5 0.15
17 15 0.45
19 6 0.18
20 7 0.21
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (17 bp):
TTATTATGTGTTAATAT
Found at i:7305 original size:28 final size:28
Alignment explanation
Indices: 7273--7339 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
7263 TTTTACAAAT
* *
7273 TAAGTGATTTAACTTTCGAAAAAGAAAC
1 TAAGTGATTTAACATTCAAAAAAGAAAC
* *
7301 TAAGTAATTTAACATTCAAAAAAGAAAT
1 TAAGTGATTTAACATTCAAAAAAGAAAC
7329 TAAGTGATTTA
1 TAAGTGATTTA
7340 TCTAATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.31
Consensus pattern (28 bp):
TAAGTGATTTAACATTCAAAAAAGAAAC
Found at i:17978 original size:16 final size:16
Alignment explanation
Indices: 17957--17988 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17947 CAACTTGGTC
17957 CTTAGATTAGCTAGGT
1 CTTAGATTAGCTAGGT
17973 CTTAGATTAGCTAGGT
1 CTTAGATTAGCTAGGT
17989 AAGCTAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (16 bp):
CTTAGATTAGCTAGGT
Found at i:26187 original size:22 final size:22
Alignment explanation
Indices: 26162--26203 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
26152 ATAAATTTTG
26162 ATAAT-AAT-TAA-TATATATT
1 ATAATAAATATAATTATATATT
26181 ATAATAAATATAATTATATATT
1 ATAATAAATATAATTATATATT
26203 A
1 A
26204 GTTATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 3 0.15
22 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATAAATATAATTATATATT
Found at i:26190 original size:16 final size:15
Alignment explanation
Indices: 26165--26198 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
26155 AATTTTGATA
*
26165 ATAATTAATATATATT
1 ATAATAAATATA-ATT
26181 ATAATAAATATAATT
1 ATAATAAATATAATT
26196 ATA
1 ATA
26199 TATTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:45582 original size:22 final size:20
Alignment explanation
Indices: 45557--45605 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 20
45547 GAAAGACGAA
45557 GAAAAAGAAGAAGCG-AGAGGAG
1 GAAAAA-AAGAAG-GAAGA-GAG
45579 GAAAGAAAAGAAGGAAGAGAG
1 GAAA-AAAAGAAGGAAGAGAG
45600 GAAAAA
1 GAAAAA
45606 CTTACTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.08
21 8 0.32
22 13 0.52
23 2 0.08
ACGTcount: A:0.61, C:0.02, G:0.37, T:0.00
Consensus pattern (20 bp):
GAAAAAAAGAAGGAAGAGAG
Found at i:46998 original size:20 final size:21
Alignment explanation
Indices: 46973--47011 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46963 TGCATTTTTA
*
46973 GCATTTT-TAACTTAGTGACT
1 GCATTTTCTAACTCAGTGACT
46993 GCATTTTCTAACTCAGTGA
1 GCATTTTCTAACTCAGTGA
47012 TGTTAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGACT
Found at i:50831 original size:29 final size:30
Alignment explanation
Indices: 50769--50831 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
50759 AAATAAGCGG
* * * *
50769 TATATGTTGTATTTTATAAATAATTAGGGT
1 TATATGCTGTATTTTAAAAATAATTAAGGA
50799 TATATGCTG-ATTTTAAAAATAATTAAGGA
1 TATATGCTGTATTTTAAAAATAATTAAGGA
50828 TATA
1 TATA
50832 GGTCATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (30 bp):
TATATGCTGTATTTTAAAAATAATTAAGGA
Found at i:52987 original size:18 final size:18
Alignment explanation
Indices: 52964--53004 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
52954 CAGAAGGAGT
*
52964 AGCATACTGGCTCGTTAG
1 AGCATACTGGCTCGTAAG
52982 AGCATACTGGCTCGTAAG
1 AGCATACTGGCTCGTAAG
53000 AGCAT
1 AGCAT
53005 TTCTGGATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (18 bp):
AGCATACTGGCTCGTAAG
Found at i:53749 original size:21 final size:21
Alignment explanation
Indices: 53725--53765 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
53715 GAAGCATGAC
* * *
53725 TTGTTTCGGTAGAACTATCAT
1 TTGTATCGGTAAAAATATCAT
53746 TTGTATCGGTAAAAATATCA
1 TTGTATCGGTAAAAATATCA
53766 CTAGTATTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (21 bp):
TTGTATCGGTAAAAATATCAT
Found at i:53772 original size:21 final size:21
Alignment explanation
Indices: 53730--53777 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
53720 ATGACTTGTT
* * * *
53730 TCGGTAGAACTATCATTTGTA
1 TCGGTAAAAATATCACTAGTA
53751 TCGGTAAAAATATCACTAGTA
1 TCGGTAAAAATATCACTAGTA
*
53772 TTGGTA
1 TCGGTA
53778 GAACATCGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (21 bp):
TCGGTAAAAATATCACTAGTA
Found at i:55553 original size:29 final size:29
Alignment explanation
Indices: 55509--55564 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
55499 TCCCCCGAAT
*
55509 GACACATATCCATAATTATTTTTAAAATC
1 GACACATATCCATAATTATTTATAAAATC
*
55538 GACACATATCCCTAATTATTTATAAAA
1 GACACATATCCATAATTATTTATAAAA
55565 AATGGCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.36
Consensus pattern (29 bp):
GACACATATCCATAATTATTTATAAAATC
Found at i:56556 original size:16 final size:15
Alignment explanation
Indices: 56537--56578 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
56527 ATTGTTTGGG
56537 GATTTACAAAAGAACA
1 GATTTA-AAAAGAACA
56553 GATTATAAAAA-AACA
1 GATT-TAAAAAGAACA
*
56568 AATTTAAAAAG
1 GATTTAAAAAG
56579 GGAATCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 6 0.26
15 7 0.30
16 8 0.35
17 2 0.09
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (15 bp):
GATTTAAAAAGAACA
Found at i:66066 original size:99 final size:98
Alignment explanation
Indices: 65878--66496 Score: 380
Period size: 99 Copynumber: 6.3 Consensus size: 98
65868 TAAATATAGT
* * * * * * *
65878 GATGGGAAATG-TTGAGGCCGCAACGACGAACCCTGTATCTTAGAAGATGAGATGGGAAAGGATG
1 GATGGGAAA-GATTGAGGCCGCAACGGCGAA-CCAGTACCATA-AAGATGTGAAGGGAAAGGTTG
** * * * * *
65942 AGGCTGCAATGACGAATCTGATACCTTAGAAGATGT
63 AGGCCACAACGGCGAACCCGATACCTTAGAAGATGA
* * *
65978 TATGGGAAAGATTGAGGCTGCAACGGCGAATTCAGTACCATAAAGATGTGAAGGGAAAGGTTGAG
1 GATGGGAAAGATTGAGGCCGCAACGGCGAA-CCAGTACCATAAAGATGTGAAGGGAAAGGTTGAG
* * * *
66043 GCCACAACGGTGAACTCGATACCTTAGCAGATGT
65 GCCACAACGGCGAACCCGATACCTTAGAAGATGA
* ** * * ** * *
66077 GATGGGAAAGGTTGAGGTTGCAACGGTGAACCCAATACCACGAAGATATAAAGGGAAAGGTTGAG
1 GATGGGAAAGATTGAGGCCGCAACGGCGAA-CCAGTACCATAAAGATGTGAAGGGAAAGGTTGAG
* * *
66142 GCCGCAACGGCGAACCCGGTACCTTAGAAGGTGA
65 GCCACAACGGCGAACCCGATACCTTAGAAGATGA
* * * * * * * * * * *
66176 GATAGGAAAGGTTTAGGCCACAACGACAAACCCGGTACCTTAGAAGATGTTATGGGAAAGATTGA
1 GATGGGAAAGATTGAGGCCGCAACGGCGAA-CCAGTACCATA-AAGATGTGAAGGGAAAGGTTGA
*** * ** *
66241 GGTTGCAACGGTGAATTCGATACCATA-AAGAT-A
64 GGCCACAACGGCGAACCCGATACCTTAGAAGATGA
* * * * *
66274 CGAAGGGAAAGATTGAGGCAGCAACGGCAAACC-GATACCTTAGCAGATGTGATA-GGAAAGGTT
1 -GATGGGAAAGATTGAGGCCGCAACGGCGAACCAG-TACCATA-AAGATGTGA-AGGGAAAGGTT
* * *
66337 GAGG-CAGTAACGACGAACCCAATACCTTAGAAGATGA
62 GAGGCCA-CAACGGCGAACCCGATACCTTAGAAGATGA
* * * * *
66374 GATGAGAAAGATTGAGGCCGTAACGACGAACCAAATACCATGAAGA-GTTGAAGGGAAAGGTTGA
1 GATGGGAAAGATTGAGGCCGCAACGGCGAACC-AGTACCATAAAGATG-TGAAGGGAAAGGTTGA
* * * * *
66438 --TCGCAACGACAAACCCGATACCAT-GAAGA-GA
64 GGCCACAACGGCGAACCCGATACCTTAGAAGATGA
*
66469 TGAAGGGAAA-AGTTGAGGCCGCAACGGC
1 -GATGGGAAAGA-TTGAGGCCGCAACGGC
66497 AAACTTGATA
Statistics
Matches: 402, Mismatches: 102, Indels: 34
0.75 0.19 0.06
Matches are distributed among these distances:
95 3 0.01
96 26 0.06
97 18 0.04
98 48 0.12
99 231 0.57
100 76 0.19
ACGTcount: A:0.36, C:0.17, G:0.30, T:0.17
Consensus pattern (98 bp):
GATGGGAAAGATTGAGGCCGCAACGGCGAACCAGTACCATAAAGATGTGAAGGGAAAGGTTGAGG
CCACAACGGCGAACCCGATACCTTAGAAGATGA
Found at i:66332 original size:49 final size:49
Alignment explanation
Indices: 65876--66514 Score: 274
Period size: 50 Copynumber: 12.9 Consensus size: 49
65866 CCTAAATATA
* * * * * *
65876 GTGATGGGAAATGTTGAGGCCGCAACGACGAACCCTG-TATCTTAGAAGAT
1 GTGATAGGAAAGGTTGAGGCAGCAACGGC-AAACC-GATACCTTAGAAGAT
* * * * * * * *
65926 GAGATGGGAAAGGATGAGGCTGCAATGACGAATCTGATACCTTAGAAGAT
1 GTGATAGGAAAGGTTGAGGCAGCAACGGC-AAACCGATACCTTAGAAGAT
* * * * ** *
65976 GTTATGGGAAAGATTGAGGCTGCAACGGCGAATTC-AGTACCATA-AAGAT
1 GTGATAGGAAAGGTTGAGGCAGCAACGGC-AAACCGA-TACCTTAGAAGAT
** *
66025 GTGA-AGGGAAAGGTTGAGGCCA-CAACGGTGAACTCGATACCTTAGCAGAT
1 GTGATA-GGAAAGGTTGAGG-CAGCAACGGCAAAC-CGATACCTTAGAAGAT
* ** * * *
66075 GTGATGGGAAAGGTTGAGGTTGCAACGGTGAACCCAATACC--ACGAAGAT
1 GTGATAGGAAAGGTTGAGGCAGCAACGG-CAAACCGATACCTTA-GAAGAT
* * * * * *
66124 AT-AAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGGT
1 GTGATA-GGAAAGGTTGAGGCAGCAACGGC-AAACCGATACCTTAGAAGAT
* * * *
66174 GAGATAGGAAAGGTTTAGGCCA-CAACGACAAACCCGGTACCTTAGAAGAT
1 GTGATAGGAAAGGTTGAGG-CAGCAACGGCAAA-CCGATACCTTAGAAGAT
* * * ** * ** *
66224 GTTATGGGAAAGATTGAGGTTGCAACGGTGAATTCGATACCATA-AAGAT
1 GTGATAGGAAAGGTTGAGGCAGCAACGG-CAAACCGATACCTTAGAAGAT
** * *
66273 ACGA-AGGGAAAGATTGAGGCAGCAACGGCAAACCGATACCTTAGCAGAT
1 GTGATA-GGAAAGGTTGAGGCAGCAACGGCAAACCGATACCTTAGAAGAT
* * * *
66322 GTGATAGGAAAGGTTGAGGCAGTAACGACGAACCCAATACCTTAGAAGAT
1 GTGATAGGAAAGGTTGAGGCAGCAACGGC-AAACCGATACCTTAGAAGAT
* * * * * * * *
66372 GAGAT-GAGAAAGATTGAGGCCGTAACGACGAACCAAATACCAT-GAAGA-
1 GTGATAG-GAAAGGTTGAGGCAGCAACGGCAAACC-GATACCTTAGAAGAT
* * *
66420 GTTGA-AGGGAAAGGTTGA-TC-GCAACGACAAACCCGATACCAT-GAAGA-
1 G-TGATA-GGAAAGGTTGAGGCAGCAACGGCAAA-CCGATACCTTAGAAGAT
* * *
66467 GATGA-AGGGAAAAGTTGAGGCCGCAACGGCAAACTTGATACCTTAGAA
1 G-TGATA-GGAAAGGTTGAGGCAGCAACGGCAAAC-CGATACCTTAGAA
66515 AACAAGATGT
Statistics
Matches: 453, Mismatches: 102, Indels: 68
0.73 0.16 0.11
Matches are distributed among these distances:
47 37 0.08
48 20 0.04
49 161 0.36
50 227 0.50
51 8 0.02
ACGTcount: A:0.36, C:0.17, G:0.30, T:0.18
Consensus pattern (49 bp):
GTGATAGGAAAGGTTGAGGCAGCAACGGCAAACCGATACCTTAGAAGAT
Found at i:66391 original size:248 final size:248
Alignment explanation
Indices: 65889--66405 Score: 666
Period size: 248 Copynumber: 2.1 Consensus size: 248
65879 ATGGGAAATG
* * * ** *
65889 TTGAGGCCGCAACGACGAACCCTGTATCTTAGAAGATGAGATGGGAAAGGATGAGGCTGCAATGA
1 TTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGATGAGATAGGAAAGGATGAGGCCACAACGA
* * *
65954 CGAATCTGATACCTTAGAAGATGTTATGGGAAAGATTGAGGCTGCAACGGCGAATTCAGTACCAT
66 CAAACCCGATACCTTAGAAGATGTTATGGGAAAGATTGAGGCTGCAACGGCGAATTCAGTACCAT
** * ** *
66019 AAAGATGTGAAGGGAAAGGTTGAGGCCACAACGGTGAACTCGATACCTTAGCAGATGTGATGGGA
131 AAAGATACGAAGGGAAAGATTGAGGCCACAACGGCAAACTCGATACCTTAGCAGATGTGATAGGA
** ** * *
66084 AAGGTTGAGGTTGCAACGGTGAACCCAATACCACGAAGATATAAAGGGAAAGG
196 AAGGTTGAGGCAGCAACGACGAACCCAATACCACGAAGATATAAAGAGAAAGA
* * * *
66137 TTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGGTGAGATAGGAAAGGTTTAGGCCACAACGA
1 TTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGATGAGATAGGAAAGGATGAGGCCACAACGA
* * *
66202 CAAACCCGGTACCTTAGAAGATGTTATGGGAAAGATTGAGGTTGCAACGGTGAATTC-GATACCA
66 CAAACCCGATACCTTAGAAGATGTTATGGGAAAGATTGAGGCTGCAACGGCGAATTCAG-TACCA
66266 TAAAGATACGAAGGGAAAGATTGAGG-CAGCAACGGCAAAC-CGATACCTTAGCAGATGTGATAG
130 TAAAGATACGAAGGGAAAGATTGAGGCCA-CAACGGCAAACTCGATACCTTAGCAGATGTGATAG
* * *
66329 GAAAGGTTGAGGCAGTAACGACGAACCCAATACCTTA-GAAGATGA-GATGAGAAAGA
194 GAAAGGTTGAGGCAGCAACGACGAACCCAATACC--ACGAAGAT-ATAAAGAGAAAGA
*
66385 TTGAGGCCGTAACGACGAACC
1 TTGAGGCCGCAACGACGAACC
66406 AAATACCATG
Statistics
Matches: 231, Mismatches: 33, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
247 54 0.23
248 175 0.76
249 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.18
Consensus pattern (248 bp):
TTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGATGAGATAGGAAAGGATGAGGCCACAACGA
CAAACCCGATACCTTAGAAGATGTTATGGGAAAGATTGAGGCTGCAACGGCGAATTCAGTACCAT
AAAGATACGAAGGGAAAGATTGAGGCCACAACGGCAAACTCGATACCTTAGCAGATGTGATAGGA
AAGGTTGAGGCAGCAACGACGAACCCAATACCACGAAGATATAAAGAGAAAGA
Found at i:67809 original size:17 final size:18
Alignment explanation
Indices: 67775--67812 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
67765 GGGGATTTAC
* *
67775 AAAAGAACAGATTATAAA
1 AAAAAAACAAATTATAAA
67793 AAAAAAACAAATT-TAAA
1 AAAAAAACAAATTATAAA
67810 AAA
1 AAA
67813 GGAATCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAAAAACAAATTATAAA
Found at i:75462 original size:61 final size:62
Alignment explanation
Indices: 75346--75469 Score: 144
Period size: 61 Copynumber: 2.0 Consensus size: 62
75336 CGGTCAAATG
* * * *
75346 ACAAATTTAGCACTCTAATATTTACATATTTTATCAAATTAATCTTAAGTGTAAAAAATTTA
1 ACAAATTTAACACTCTAATATTTACAAAATTTATCAAATTAATCTTAAGTCTAAAAAATTTA
* * * * *
75408 ACAAATTTAATACTC-AATATTTACAAAATTTATCAATTTAGT-TCTAATTCTAAAAATTTTA
1 ACAAATTTAACACTCTAATATTTACAAAATTTATCAAATTAATCT-TAAGTCTAAAAAATTTA
75469 A
1 A
75470 GTATATATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
60 1 0.02
61 38 0.73
62 13 0.25
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.41
Consensus pattern (62 bp):
ACAAATTTAACACTCTAATATTTACAAAATTTATCAAATTAATCTTAAGTCTAAAAAATTTA
Found at i:77379 original size:15 final size:15
Alignment explanation
Indices: 77359--77389 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
77349 CGCGACAACA
77359 AATGGGGATGTCGTG
1 AATGGGGATGTCGTG
*
77374 AATGGGGATGTTGTG
1 AATGGGGATGTCGTG
77389 A
1 A
77390 CACCCTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.45, T:0.29
Consensus pattern (15 bp):
AATGGGGATGTCGTG
Found at i:77467 original size:13 final size:13
Alignment explanation
Indices: 77451--77505 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
77441 TACTTTTGAG
77451 AAGTATTTTTAAA
1 AAGTATTTTTAAA
* *
77464 AAGTGTTTTGAAA
1 AAGTATTTTTAAA
**
77477 AAGTGGTTTTAAA
1 AAGTATTTTTAAA
*
77490 AAGTACTTTTAAA
1 AAGTATTTTTAAA
77503 AAG
1 AAG
77506 CTTGGTTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.38
Consensus pattern (13 bp):
AAGTATTTTTAAA
Found at i:83347 original size:21 final size:21
Alignment explanation
Indices: 83295--83370 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
83285 CAACTAGGAG
*
83295 TTCTACCAATACACTTCTGAC
1 TTCTACCGATACACTTCTGAC
83316 TTCTACCGATACACTTCTGAC
1 TTCTACCGATACACTTCTGAC
** *
83337 TTCTATTGATACA-TCCTAGAC
1 TTCTACCGATACACTTCT-GAC
*
83358 TTTTACCGATACA
1 TTCTACCGATACA
83371 AAAAATTCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 3 0.06
21 44 0.94
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.36
Consensus pattern (21 bp):
TTCTACCGATACACTTCTGAC
Found at i:85618 original size:15 final size:15
Alignment explanation
Indices: 85598--85626 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
85588 ATTTCTATTA
85598 TTTCTTCTTTCTTTG
1 TTTCTTCTTTCTTTG
85613 TTTCTTCTTTCTTT
1 TTTCTTCTTTCTTT
85627 TTTTATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTCTTCTTTCTTTG
Found at i:86290 original size:3 final size:3
Alignment explanation
Indices: 86282--86318 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
86272 TACAAAACTA
*
86282 ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
86319 ATGAATTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:90636 original size:21 final size:22
Alignment explanation
Indices: 90612--90668 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
90602 TACTACAAAA
90612 TTCTACCGATACAAC-TAGGAC
1 TTCTACCGATACAACTTAGGAC
* * **
90633 TTCTACTGGTAC-ACTTCTGAC
1 TTCTACCGATACAACTTAGGAC
90654 TTCTACCGATACAAC
1 TTCTACCGATACAAC
90669 AAACTCTAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (22 bp):
TTCTACCGATACAACTTAGGAC
Found at i:92622 original size:112 final size:111
Alignment explanation
Indices: 92419--92634 Score: 324
Period size: 112 Copynumber: 1.9 Consensus size: 111
92409 TCGTTAGGGA
* * ** *
92419 ACAATTTATGTATAGATACCATATCGATGGCTGAGGTGTCGCATATGTTGCGAGTCCTAATCAGC
1 ACAATTTATGTACAGATACCATATCGATGGCTAAGGTACCACATATGTTGCGAGTCCTAATCAGC
* * *
92484 TTAGTGTGAGGAGCATCGTATACTGGTAACAGAAATGACATTGGTC
66 TTAGTGTGAGCAGCATCATATACTGGTAAAAGAAATGACATTGGTC
* **
92530 ACAATTATATGTACAGATACCATATCGATGGCTAAGGTACCACATATGTTGCGAGTCTTCGTCAG
1 ACAATT-TATGTACAGATACCATATCGATGGCTAAGGTACCACATATGTTGCGAGTCCTAATCAG
92595 CTTAGTGTGAGCAGCATCATATACTGGTAAAAGAAATGAC
65 CTTAGTGTGAGCAGCATCATATACTGGTAAAAGAAATGAC
92635 CTATGACCAA
Statistics
Matches: 93, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
111 6 0.06
112 87 0.94
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (111 bp):
ACAATTTATGTACAGATACCATATCGATGGCTAAGGTACCACATATGTTGCGAGTCCTAATCAGC
TTAGTGTGAGCAGCATCATATACTGGTAAAAGAAATGACATTGGTC
Found at i:93319 original size:258 final size:258
Alignment explanation
Indices: 92862--93378 Score: 1016
Period size: 258 Copynumber: 2.0 Consensus size: 258
92852 CGGGAGCTCG
92862 TTCGATAGTATTTGCATCACTTGGTTTTATGGCATGTACTAGAGTGATGTTATTTTTTAATGCTT
1 TTCGATAGTATTTGCATCACTTGGTTTTATGGCATGTACTAGAGTGATGTTATTTTTTAATGCTT
*
92927 GACTTTGAGTTAATTATTAAAATGTCACACTTGTGTTGAATGTTTTAACTCCTTCCAAATGGTTG
66 GACTTTGAGTTAATTATTAAAATGTCACACATGTGTTGAATGTTTTAACTCCTTCCAAATGGTTG
*
92992 TTTAATGTTAAGTATAGGTATTTGGCTTTCAAAATGTAATGCTATGTTTTGTTCTTGAACACTTG
131 TTTAATGTTAAGTATAGGTATTTGGCTTTCAAAATGTAATGCTATGTTTTGTTATTGAACACTTG
93057 TGTCCTCTATTTATACAATATGTTTATGAAATGCAGTTTGGTTGATGAACTTGTGTAAATAGT
196 TGTCCTCTATTTATACAATATGTTTATGAAATGCAGTTTGGTTGATGAACTTGTGTAAATAGT
93120 TTCGATAGTATTTGCATCACTTGGTTTTATGGCATGTACTAGAGTGATGTTATTTTTTAATGCTT
1 TTCGATAGTATTTGCATCACTTGGTTTTATGGCATGTACTAGAGTGATGTTATTTTTTAATGCTT
93185 GACTTTGAGTTAATTATTAAAATGTCACACATGTGTTGAATGTTTTAACTCCTTCCAAATGGTTG
66 GACTTTGAGTTAATTATTAAAATGTCACACATGTGTTGAATGTTTTAACTCCTTCCAAATGGTTG
93250 TTTAATGTTAAGTATAGGTATTTGGCTTTCAAAATGTAATGCTATGTTTTGTTATTGAACACTTG
131 TTTAATGTTAAGTATAGGTATTTGGCTTTCAAAATGTAATGCTATGTTTTGTTATTGAACACTTG
93315 TGTCCTCTATTTATACAATATGTTTATGAAATGCAGTTTGGTTGATGAACTTGTGTAAATAGT
196 TGTCCTCTATTTATACAATATGTTTATGAAATGCAGTTTGGTTGATGAACTTGTGTAAATAGT
93378 T
1 T
93379 GAATTTTGCT
Statistics
Matches: 257, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
258 257 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (258 bp):
TTCGATAGTATTTGCATCACTTGGTTTTATGGCATGTACTAGAGTGATGTTATTTTTTAATGCTT
GACTTTGAGTTAATTATTAAAATGTCACACATGTGTTGAATGTTTTAACTCCTTCCAAATGGTTG
TTTAATGTTAAGTATAGGTATTTGGCTTTCAAAATGTAATGCTATGTTTTGTTATTGAACACTTG
TGTCCTCTATTTATACAATATGTTTATGAAATGCAGTTTGGTTGATGAACTTGTGTAAATAGT
Found at i:95145 original size:28 final size:28
Alignment explanation
Indices: 95114--95175 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
95104 AAAATTTGAT
*
95114 TTTTGGATACTCGGAGGCAAAATGGTAA
1 TTTTGGATACTCGGAGGAAAAATGGTAA
*
95142 TTTTGGATGCTCGGAGGAAAAATGGTAA
1 TTTTGGATACTCGGAGGAAAAATGGTAA
95170 TTTTGG
1 TTTTGG
95176 GAAAGTTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.32
Consensus pattern (28 bp):
TTTTGGATACTCGGAGGAAAAATGGTAA
Found at i:95509 original size:30 final size:29
Alignment explanation
Indices: 95243--95641 Score: 206
Period size: 29 Copynumber: 13.7 Consensus size: 29
95233 TGGAAAAATC
* * **
95243 AGGGTCAAAATGGAATTTTAGGTAGTTCG
1 AGGGTAAAAATGGAATTTTAGGAAGTTTA
* * * **
95272 AGGGTAAAAACGTAATTTTTGGAAAATTA
1 AGGGTAAAAATGGAATTTTAGGAAGTTTA
* ** *
95301 TGGGTCAAAAATATAATTTTTGGAAGTTT-
1 AGGGT-AAAAATGGAATTTTAGGAAGTTTA
* * ***
95330 GGGGT-AAAATGGTAATTTTTGGAAAAAT-
1 AGGGTAAAAATGG-AATTTTAGGAAGTTTA
* *
95358 CGAGGTAAAAATGGAATTATT-GGAAGTTTG
1 AG-GGTAAAAATGGAATT-TTAGGAAGTTTA
*
95388 A-GGT-AAAATGGTAATTTCTA-GAAGTTTT
1 AGGGTAAAAATGG-AATTT-TAGGAAGTTTA
* *
95416 AGGGTTAAAAATAGAATCTTAGGAAGTTTA
1 AGGG-TAAAAATGGAATTTTAGGAAGTTTA
* * *** *
95446 AGGGTAAAAGTGTAATTTTTA-GAAAAATC
1 AGGGTAAAAATGGAA-TTTTAGGAAGTTTA
*
95475 AGGGTTAAAAATGGAATTTTAGAAAGTTTA
1 AGGG-TAAAAATGGAATTTTAGGAAGTTTA
* * *
95505 AGGGTAAAAATGTAATTTTTGGGAAGTTCA
1 AGGGTAAAAATGGAA-TTTTAGGAAGTTTA
*
95535 A-GGTCAAAAATGGAATTTTTGGAAGTTTA
1 AGGGT-AAAAATGGAATTTTAGGAAGTTTA
* * * *
95564 AGGGTAAAAATGTAATTTTCA-AAAATTTT
1 AGGGTAAAAATGGAATTTT-AGGAAGTTTA
*** * **
95593 AGGGTTAAAAAAATAATTTTGGGGGGTTTA
1 AGGG-TAAAAATGGAATTTTAGGAAGTTTA
*
95623 AGGGTAAAAATGTAATTTT
1 AGGGTAAAAATGGAATTTT
95642 TGGACAATTT
Statistics
Matches: 282, Mismatches: 66, Indels: 44
0.72 0.17 0.11
Matches are distributed among these distances:
27 13 0.05
28 29 0.10
29 126 0.45
30 108 0.38
31 6 0.02
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (29 bp):
AGGGTAAAAATGGAATTTTAGGAAGTTTA
Found at i:95643 original size:30 final size:30
Alignment explanation
Indices: 95272--95644 Score: 204
Period size: 30 Copynumber: 12.7 Consensus size: 30
95262 AGGTAGTTCG
* **
95272 AGGGTAAAAACGTAATTTTT-GGAAAATTA
1 AGGGTAAAAATGTAATTTTTGGGAAGTTTA
* *
95301 TGGGTCAAAAATATAATTTTT-GGAAGTTT-
1 AGGGT-AAAAATGTAATTTTTGGGAAGTTTA
* * ** **
95330 GGGGT-AAAATGGTAATTTTTGGAAAAATCG
1 AGGGTAAAAAT-GTAATTTTTGGGAAGTTTA
* * *
95360 A-GGTAAAAATGGAATTATT-GGAAGTTTG
1 AGGGTAAAAATGTAATTTTTGGGAAGTTTA
* * *
95388 A-GGT-AAAATGGTAATTTCT-AGAAGTTTT
1 AGGGTAAAAAT-GTAATTTTTGGGAAGTTTA
* *
95416 AGGGTTAAAAATAG-AA-TCTTAGGAAGTTTA
1 AGGG-TAAAAAT-GTAATTTTTGGGAAGTTTA
* * *** *
95446 AGGGTAAAAGTGTAATTTTT-AGAAAAATC
1 AGGGTAAAAATGTAATTTTTGGGAAGTTTA
* * *
95475 AGGGTTAAAAATGGAA-TTTTAGAAAGTTTA
1 AGGG-TAAAAATGTAATTTTTGGGAAGTTTA
*
95505 AGGGTAAAAATGTAATTTTTGGGAAGTTCA
1 AGGGTAAAAATGTAATTTTTGGGAAGTTTA
*
95535 A-GGTCAAAAATGGAATTTTT-GGAAGTTTA
1 AGGGT-AAAAATGTAATTTTTGGGAAGTTTA
*** * *
95564 AGGGTAAAAATGTAA-TTTTCAAAAATTTT
1 AGGGTAAAAATGTAATTTTTGGGAAGTTTA
** **
95593 AGGGTTAAAAAAATAA-TTTTGGGGGGTTTA
1 AGGG-TAAAAATGTAATTTTTGGGAAGTTTA
95623 AGGGTAAAAATGTAATTTTTGG
1 AGGGTAAAAATGTAATTTTTGG
95645 ACAATTTAGG
Statistics
Matches: 259, Mismatches: 65, Indels: 39
0.71 0.18 0.11
Matches are distributed among these distances:
27 10 0.04
28 36 0.14
29 95 0.37
30 112 0.43
31 6 0.02
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (30 bp):
AGGGTAAAAATGTAATTTTTGGGAAGTTTA
Found at i:95653 original size:59 final size:59
Alignment explanation
Indices: 95216--95654 Score: 353
Period size: 59 Copynumber: 7.5 Consensus size: 59
95206 AGACATTCGG
* * * * * **
95216 GGGT-AAAATGGTAA-TTTTGGAAAAATCAGGG-TCAAAATGGAATTTTAGGTAGTTCGA
1 GGGTAAAAAT-GTAATTTTTGGAAAATTTAGGGTTAAAAATAGAATTTTAGGAAGTTTAA
* * * * *
95273 GGGTAAAAACGTAATTTTTGGAAAA-TTATGGGTCAAAAATATAATTTTTGGAAGTTT-G
1 GGGTAAAAATGTAATTTTTGGAAAATTTA-GGGTTAAAAATAGAATTTTAGGAAGTTTAA
* * * *
95331 GGGT-AAAATGGTAATTTTTGGAAAA-ATCGAGG-TAAAAATGGAATTATT-GGAAGTTTGA
1 GGGTAAAAAT-GTAATTTTTGGAAAATTTAG-GGTTAAAAATAGAATT-TTAGGAAGTTTAA
* * ** *
95389 -GGT-AAAATGGTAATTTCTAGAAGTTTTAGGGTTAAAAATAGAATCTTAGGAAGTTTAA
1 GGGTAAAAAT-GTAATTTTTGGAAAATTTAGGGTTAAAAATAGAATTTTAGGAAGTTTAA
* * * * * *
95447 GGGTAAAAGTGTAATTTTTAGAAAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTTAA
1 GGGTAAAAATGTAATTTTTGGAAAATTTAGGGTTAAAAATAGAATTTTAGGAAGTTTAA
* * * * * * *
95506 GGGTAAAAATGTAATTTTTGGGAAGTTCAAGGTCAAAAATGGAATTTTTGGAAGTTTAA
1 GGGTAAAAATGTAATTTTTGGAAAATTTAGGGTTAAAAATAGAATTTTAGGAAGTTTAA
** * * * **
95565 GGGTAAAAATGTAA-TTTTCAAAAATTTTAGGGTTAAAAAAATAATTTTGGGGGGTTTAA
1 GGGTAAAAATGTAATTTTTGGAAAA-TTTAGGGTTAAAAATAGAATTTTAGGAAGTTTAA
*
95624 GGGTAAAAATGTAATTTTTGGACAATTTAGG
1 GGGTAAAAATGTAATTTTTGGAAAATTTAGG
95655 AACCTTCAGG
Statistics
Matches: 307, Mismatches: 60, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
57 57 0.19
58 69 0.22
59 170 0.55
60 11 0.04
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.33
Consensus pattern (59 bp):
GGGTAAAAATGTAATTTTTGGAAAATTTAGGGTTAAAAATAGAATTTTAGGAAGTTTAA
Found at i:102719 original size:2 final size:2
Alignment explanation
Indices: 102712--102745 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
102702 TTGTACAGTA
102712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
102746 TTCTCTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112074 original size:23 final size:25
Alignment explanation
Indices: 112036--112089 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
112026 TTATTACAAT
* *
112036 TTTTCTATTTACTTCTGTATTTTA-
1 TTTTCTATTTAATTCTCTATTTTAG
*
112060 TTTTCT-TTTAATTCTCTTTTTTAG
1 TTTTCTATTTAATTCTCTATTTTAG
112084 TTTTCT
1 TTTTCT
112090 GCAGGAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.13, C:0.13, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTTCTATTTAATTCTCTATTTTAG
Found at i:112740 original size:45 final size:45
Alignment explanation
Indices: 112682--112771 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
112672 ATTTCGCGTA
112682 TGGGATGGGAGAAGTTCTGTGACC-TCCCAGAGGGATATTTTTCGT
1 TGGGATGGGAGAAGTTCTGTGACCAT-CCAGAGGGATATTTTTCGT
112727 TGGGATGGGAGAAGTTCTGTGACCATCCAGAGGGATATTTTTCGT
1 TGGGATGGGAGAAGTTCTGTGACCATCCAGAGGGATATTTTTCGT
112772 CCCTAGTAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 43 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.33, T:0.31
Consensus pattern (45 bp):
TGGGATGGGAGAAGTTCTGTGACCATCCAGAGGGATATTTTTCGT
Found at i:122533 original size:3 final size:3
Alignment explanation
Indices: 122527--122603 Score: 59
Period size: 3 Copynumber: 26.0 Consensus size: 3
122517 TACTGTTTTG
* * *
122527 GTT GTT GTT -TT AG-T GTT GTT TTT GTT GTT ATT TTT GTT GTT GTT
1 GTT GTT GTT GTT -GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
* * * * *
122571 TTT GTT ATT ATT TTT GTT GTT TTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
122604 TTGCTATTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
2 3 0.05
3 56 0.95
ACGTcount: A:0.05, C:0.00, G:0.22, T:0.73
Consensus pattern (3 bp):
GTT
Found at i:122537 original size:21 final size:20
Alignment explanation
Indices: 122486--122538 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
122476 CTATATTGGT
122486 GTTGTTTTTTTTACAATTTTG
1 GTTG-TTTTTTTACAATTTTG
**
122507 G-TGCTTTTTTTACTGTTTTG
1 GTTG-TTTTTTTACAATTTTG
*
122527 GTTGTTGTTTTA
1 GTTGTTTTTTTA
122539 GTGTTGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.09, C:0.06, G:0.19, T:0.66
Consensus pattern (20 bp):
GTTGTTTTTTTACAATTTTG
Found at i:122543 original size:11 final size:12
Alignment explanation
Indices: 122520--122647 Score: 104
Period size: 12 Copynumber: 11.1 Consensus size: 12
122510 CTTTTTTTAC
*
122520 TGTTTTGGTTGT
1 TGTTTTTGTTGT
*
122532 TGTTTTAG-TGT
1 TGTTTTTGTTGT
122543 TGTTTTTGTTGT
1 TGTTTTTGTTGT
*
122555 TATTTTTGTTGT
1 TGTTTTTGTTGT
*
122567 TGTTTTTGTT-A
1 TGTTTTTGTTGT
*
122578 T-TATTT-TTGT
1 TGTTTTTGTTGT
122588 TGTTTTTGTTGT
1 TGTTTTTGTTGT
* *
122600 TG-TTTTGCTAT
1 TGTTTTTGTTGT
* * *
122611 TATTTTTGCTGC
1 TGTTTTTGTTGT
*
122623 TGTTTTGGTTGT
1 TGTTTTTGTTGT
* *
122635 TATTTTAGTTGT
1 TGTTTTTGTTGT
122647 T
1 T
122648 TGGATGTTAT
Statistics
Matches: 92, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
9 2 0.02
10 5 0.05
11 23 0.25
12 62 0.67
ACGTcount: A:0.06, C:0.02, G:0.22, T:0.70
Consensus pattern (12 bp):
TGTTTTTGTTGT
Found at i:122561 original size:24 final size:23
Alignment explanation
Indices: 122520--122605 Score: 104
Period size: 23 Copynumber: 3.8 Consensus size: 23
122510 CTTTTTTTAC
* * *
122520 TGTTTTGGTTGTTGTTTTAGTGT
1 TGTTTTTGTTGTTATTTTTGTGT
122543 TGTTTTTGTTGTTATTTTTGTTGT
1 TGTTTTTGTTGTTATTTTTG-TGT
*
122567 TGTTTTTGTTATTA-TTTT-TGT
1 TGTTTTTGTTGTTATTTTTGTGT
*
122588 TGTTTTTGTTGTTGTTTT
1 TGTTTTTGTTGTTATTTT
122606 GCTATTATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
21 15 0.27
22 3 0.05
23 21 0.38
24 16 0.29
ACGTcount: A:0.05, C:0.00, G:0.22, T:0.73
Consensus pattern (23 bp):
TGTTTTTGTTGTTATTTTTGTGT
Found at i:122589 original size:56 final size:56
Alignment explanation
Indices: 122528--122648 Score: 154
Period size: 56 Copynumber: 2.2 Consensus size: 56
122518 ACTGTTTTGG
* * * * *
122528 TTGTTGTTTTAG-TGTTGTTTTTGTTGTTATTTTTGTTGTTGTTTTTGTTATTATTT
1 TTGTTGTTTTAGTTGTTG-TTTTGCTATTATTTTTGCTGCTGTTTTGGTTATTATTT
* *
122584 TTGTTGTTTTTGTTGTTGTTTTGCTATTATTTTTGCTGCTGTTTTGGTTGTTATTT
1 TTGTTGTTTTAGTTGTTGTTTTGCTATTATTTTTGCTGCTGTTTTGGTTATTATTT
*
122640 TAGTTGTTT
1 TTGTTGTTT
122649 GGATGTTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
56 51 0.91
57 5 0.09
ACGTcount: A:0.07, C:0.02, G:0.21, T:0.70
Consensus pattern (56 bp):
TTGTTGTTTTAGTTGTTGTTTTGCTATTATTTTTGCTGCTGTTTTGGTTATTATTT
Found at i:122634 original size:32 final size:31
Alignment explanation
Indices: 122557--122635 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 31
122547 TTTGTTGTTA
* *
122557 TTTTTGTTGTTGTTTTTGTTATTATTTTTGTTG
1 TTTTTG-TGTTG-TTTTGCTATTATTTTTGCTG
122590 TTTTTGTTGTTGTTTTGCTATTATTTTTGCTG
1 TTTTTG-TGTTGTTTTGCTATTATTTTTGCTG
122622 CTGTTTTG-GTTGTT
1 -T-TTTTGTGTTGTT
122636 ATTTTAGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
32 24 0.57
33 13 0.31
34 5 0.12
ACGTcount: A:0.05, C:0.04, G:0.20, T:0.71
Consensus pattern (31 bp):
TTTTTGTGTTGTTTTGCTATTATTTTTGCTG
Found at i:124217 original size:29 final size:29
Alignment explanation
Indices: 124184--124304 Score: 129
Period size: 30 Copynumber: 4.1 Consensus size: 29
124174 ATTTATTTAG
* *
124184 AAATTTTGTTTTAACCCTCGAACTTTCCA
1 AAATTATGTTTTAACCCTCAAACTTTCCA
* *
124213 AAATTATATTTTAA-CCTCTTAACTTTCCAA
1 AAATTATGTTTTAACCCTC-AAACTTTCC-A
*
124243 AAATTATATTTTAACCC-CTAAACTTTCCAA
1 AAATTATGTTTTAACCCTC-AAACTTTCC-A
* *
124273 AAATTATGTTTTGACCCTCAAACTTTTCA
1 AAATTATGTTTTAACCCTCAAACTTTCCA
124302 AAA
1 AAA
124305 CTTCGATTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
28 4 0.05
29 24 0.30
30 50 0.62
31 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (29 bp):
AAATTATGTTTTAACCCTCAAACTTTCCA
Found at i:124248 original size:30 final size:30
Alignment explanation
Indices: 124204--124304 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
124194 TTAACCCTCG
* *
124204 AACTTTCC-AAAATTATATTTTAACCTCTT
1 AACTTTCCAAAAATTATATTTTAACCCCTA
124233 AACTTTCCAAAAATTATATTTTAACCCCTA
1 AACTTTCCAAAAATTATATTTTAACCCCTA
* *
124263 AACTTTCCAAAAATTATGTTTTGA-CCCTCA
1 AACTTTCCAAAAATTATATTTTAACCCCT-A
*
124293 AACTTTTCAAAA
1 AACTTTCCAAAA
124305 CTTCGATTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
29 12 0.18
30 53 0.82
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.39
Consensus pattern (30 bp):
AACTTTCCAAAAATTATATTTTAACCCCTA
Found at i:124314 original size:60 final size:59
Alignment explanation
Indices: 124204--124319 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 59
124194 TTAACCCTCG
* *
124204 AACTTTCCAAAATTATATTTTAACCTCTTAACTTTCCAAAAATTATATTTTAACCCCTA
1 AACTTTCCAAAATTATATTTTAACCTCTAAACTTTCCAAAAATTAGATTTTAACCCCTA
* * * * * *
124263 AACTTTCCAAAAATTATGTTTTGACC-CTCAAACTTTTCAAAACTTCGATTTTGACCC
1 AACTTTCC-AAAATTATATTTTAACCTCT-AAACTTTCCAAAAATTAGATTTTAACCC
124320 TCGAACCTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
59 10 0.21
60 37 0.79
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.39
Consensus pattern (59 bp):
AACTTTCCAAAATTATATTTTAACCTCTAAACTTTCCAAAAATTAGATTTTAACCCCTA
Found at i:124397 original size:29 final size:29
Alignment explanation
Indices: 124192--124402 Score: 117
Period size: 30 Copynumber: 7.1 Consensus size: 29
124182 AGAAATTTTG
* * * *
124192 TTTTAACCCTCGAACTTTCCAAAATTATA
1 TTTTGACCCTCAAACTTTCTAAAATTACA
* * * *
124221 TTTT-AACCTCTTAACTTTCCAAAAATTATA
1 TTTTGACCCTC-AAACTTT-CTAAAATTACA
* * **
124251 TTTTAACCC-CTAAACTTTCCAAAAATTATG
1 TTTTGACCCTC-AAACTTT-CTAAAATTACA
124281 TTTTGACCCTCAAACTTT-TCAAAACTT-CGA
1 TTTTGACCCTCAAACTTTCT-AAAA-TTAC-A
* * *
124311 TTTTGACCCTCGAACCTTCTAAAAATAGCA
1 TTTTGACCCTCAAACTTTCTAAAATTA-CA
* * *
124341 TTTTGA-CCTCAAATTTTTTGAAAGTTACA
1 TTTTGACCCTCAAACTTTCT-AAAATTACA
* * *
124370 TTTTGACCCCCAAACTTTCTAAATTTACG
1 TTTTGACCCTCAAACTTTCTAAAATTACA
124399 TTTT
1 TTTT
124403 CAACCCTTTT
Statistics
Matches: 146, Mismatches: 24, Indels: 24
0.75 0.12 0.12
Matches are distributed among these distances:
28 5 0.03
29 43 0.29
30 92 0.63
31 6 0.04
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (29 bp):
TTTTGACCCTCAAACTTTCTAAAATTACA
Found at i:129945 original size:30 final size:30
Alignment explanation
Indices: 129920--130110 Score: 212
Period size: 30 Copynumber: 6.5 Consensus size: 30
129910 TGAACTTCTA
*
129920 AAAAAATACATTTTAACCCTCGAACTTTCC
1 AAAAATTACATTTTAACCCTCGAACTTTCC
*
129950 AAAAATTACATTTTAACACTCGAAC-TTCC
1 AAAAATTACATTTTAACCCTCGAACTTTCC
* *
129979 AAAAATTACATTTTAATCCC-CAAAATTTCC
1 AAAAATTACATTTTAA-CCCTCGAACTTTCC
* * *
130009 AAAAAATACATTTTAACCCTTGAACTTTCA
1 AAAAATTACATTTTAACCCTCGAACTTTCC
*
130039 AAAAATTACATTTTAACCC-CTAAACTTTCC
1 AAAAATTACATTTTAACCCTC-GAACTTTCC
* * * *
130069 CAAAATCACATTTTAACCCT-AAACTCTCC
1 AAAAATTACATTTTAACCCTCGAACTTTCC
*
130098 AAAACTT-CATTTT
1 AAAAATTACATTTT
130111 TCGACCCCTT
Statistics
Matches: 136, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
28 6 0.04
29 38 0.28
30 92 0.68
ACGTcount: A:0.41, C:0.25, G:0.02, T:0.32
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCTCGAACTTTCC
Found at i:129991 original size:59 final size:57
Alignment explanation
Indices: 129907--130110 Score: 230
Period size: 59 Copynumber: 3.5 Consensus size: 57
129897 CTCAGGAGGT
* *
129907 CCCTGAACTTCTAAAAAAATACATTTTAACCCTCGAACTTTCCAAAAATTACATTTTAA
1 CCCTGAACTTC-AAAAAATTACATTTTAACCC-CAAACTTTCCAAAAATTACATTTTAA
* * * *
129966 CACTCGAACTTCCAAAAATTACATTTTAATCCCCAAAATTTCCAAAAAATACATTTTAA
1 CCCT-GAACTTCAAAAAATTACATTTTAA-CCCCAAACTTTCCAAAAATTACATTTTAA
* *
130025 CCCTTGAACTTTCAAAAAATTACATTTTAACCCCTAAACTTTCCCAAAATCACATTTTAA
1 CCC-TGAAC-TTCAAAAAATTACATTTTAACCCC-AAACTTTCCAAAAATTACATTTTAA
* * *
130085 CCCTAAACTCTCCAAAACTT-CATTTT
1 CCCTGAACT-TCAAAAAATTACATTTT
130111 TCGACCCCTT
Statistics
Matches: 124, Mismatches: 15, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
58 7 0.06
59 63 0.51
60 54 0.44
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.32
Consensus pattern (57 bp):
CCCTGAACTTCAAAAAATTACATTTTAACCCCAAACTTTCCAAAAATTACATTTTAA
Found at i:130099 original size:89 final size:89
Alignment explanation
Indices: 129920--130101 Score: 251
Period size: 89 Copynumber: 2.0 Consensus size: 89
129910 TGAACTTCTA
* *
129920 AAAAAATACATTTTAACCCTCGAACTTTCCAAAAATTACATTTTAACACTCGAACTTCCAAAAAT
1 AAAAAATACATTTTAACCCTCGAACTTTCAAAAAATTACATTTTAACACTCAAACTTCCAAAAAT
* *
129985 TACATTTTAATCCCCAAAATTTCC
66 CACATTTTAATCCCCAAAATCTCC
* * *
130009 AAAAAATACATTTTAACCCTTGAACTTTCAAAAAATTACATTTTAAC-CCCTAAACTTTCCCAAA
1 AAAAAATACATTTTAACCCTCGAACTTTCAAAAAATTACATTTTAACACTC-AAAC-TTCCAAAA
* *
130073 ATCACATTTTAA-CCCTAAACTCTCC
64 ATCACATTTTAATCCCCAAAATCTCC
130098 AAAA
1 AAAA
130102 CTTCATTTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
88 2 0.02
89 62 0.76
90 18 0.22
ACGTcount: A:0.42, C:0.25, G:0.02, T:0.31
Consensus pattern (89 bp):
AAAAAATACATTTTAACCCTCGAACTTTCAAAAAATTACATTTTAACACTCAAACTTCCAAAAAT
CACATTTTAATCCCCAAAATCTCC
Found at i:139348 original size:39 final size:39
Alignment explanation
Indices: 139305--139768 Score: 201
Period size: 39 Copynumber: 11.9 Consensus size: 39
139295 CTGATTATGA
* *
139305 GGCAGATCATAATCATCCAATCTTTTACCCTGAGCCTAG
1 GGCAGATCACAATCATCCAATCTCTTACCCTGAGCCTAG
* * *
139344 GGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTAG
1 GGCAGATCACAATCATCCAATCTCTTACCCTGAGCCTAG
* *** ** * *
139383 GACAGATTGTAGCCATTCAATCTTTTACTCC-GAGCCTAG
1 GGCAGATCACAATCATCCAATCTCTTAC-CCTGAGCCTAG
* * *
139422 GGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTCA-
1 GGCAGATCACAATCATCCAATCTCTTACCCTGAGCCT-AG
* ** ** * * *
139461 GGAAGATTGCAGCCATCCGATCTTTTA-CCTCGAGCCTGG
1 GGCAGATCACAATCATCCAATCTCTTACCCT-GAGCCTAG
* * *
139500 GGCAGATCATC-ATCAGCCAATCTCTTACCCCT-AGTCTGG
1 GGCAGATCA-CAATCATCCAATCTCTTA-CCCTGAGCCTAG
** * * * * *
139539 GGCAGATTGCAGTCATCCGATCTTTTACCCTGATCTTAG
1 GGCAGATCACAATCATCCAATCTCTTACCCTGAGCCTAG
* * * *
139578 GTCAGATCACTATCAGCCAATCTCTTA-CCTCGAACCT-G
1 GGCAGATCACAATCATCCAATCTCTTACCCT-GAGCCTAG
* ** * * * * * * * *
139616 AGGTAGATTGC-TTCCATTCGATCTTTTACTCTGAACTTGG
1 -GGCAGATCACAAT-CATCCAATCTCTTACCCTGAGCCTAG
* * * *
139656 GGCAGATCACTATCAGCTAATCTCTTACCCCGAGCCT-G
1 GGCAGATCACAATCATCCAATCTCTTACCCTGAGCCTAG
** * * * * *
139694 AGGCAGATTGCAGTCATTCGATCTTTTACTCC-GAGCCTGG
1 -GGCAGATCACAATCATCCAATCTCTTAC-CCTGAGCCTAG
* * *
139734 GGCAGATCACCATCAACCAATCTCTTACCATGAGC
1 GGCAGATCACAATCATCCAATCTCTTACCCTGAGC
139769 TTGGGGCGGA
Statistics
Matches: 298, Mismatches: 107, Indels: 40
0.67 0.24 0.09
Matches are distributed among these distances:
38 16 0.05
39 268 0.90
40 11 0.04
41 3 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (39 bp):
GGCAGATCACAATCATCCAATCTCTTACCCTGAGCCTAG
Found at i:139389 original size:78 final size:78
Alignment explanation
Indices: 139317--139824 Score: 560
Period size: 78 Copynumber: 6.5 Consensus size: 78
139307 CAGATCATAA
* *
139317 TCATCCAATCTTTTACCCTGAGCCTAGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCT-
1 TCATCCGATCTTTTACCCTGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTG
*
139381 AGGACAGATTGTAG
66 AGG-CAGATTGCAG
* * *
139395 CCATTCAATCTTTTACTCC-GAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCT
1 TCATCCGATCTTTTAC-CCTGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCT
* *
139459 CAGGAAGATTGCAG
65 GAGGCAGATTGCAG
* * * * *
139473 CCATCCGATCTTTTA-CCTCGAGCCTGGGGCAGATCATCATCAGCCAATCTCTTACCCCTAGTCT
1 TCATCCGATCTTTTACCCT-GAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCT
*
139537 GGGGCAGATTGCAG
65 GAGGCAGATTGCAG
* * * * * *
139551 TCATCCGATCTTTTACCCTGATCTTAGGTCAGATCACTATCAGCCAATCTCTTACCTCGAACCTG
1 TCATCCGATCTTTTACCCTGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTG
* *
139616 AGGTAGATTGC-T
66 AGGCAGATTGCAG
* * * * * * *
139628 TCCATTCGATCTTTTACTCTGAACTTGGGGCAGATCACTATCAGCTAATCTCTTACCCCGAGCCT
1 T-CATCCGATCTTTTACCCTGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCT
139693 GAGGCAGATTGCAG
65 GAGGCAGATTGCAG
* * * ** *
139707 TCATTCGATCTTTTACTCC-GAGCCTGGGGCAGATCACCATCAACCAATCTCTTACCATGAGCTT
1 TCATCCGATCTTTTAC-CCTGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCT
* *
139771 GGGGCGGATTGCAG
65 GAGGCAGATTGCAG
* * *
139785 -CAATCAGATCTTTTACCCCGAGCCTGGGGCAGATCACCAT
1 TC-ATCCGATCTTTTACCCTGAGCCTAGGGCAGATCACCAT
139825 TAACCGTTGA
Statistics
Matches: 369, Mismatches: 51, Indels: 20
0.84 0.12 0.05
Matches are distributed among these distances:
76 2 0.01
77 4 0.01
78 353 0.96
79 10 0.03
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (78 bp):
TCATCCGATCTTTTACCCTGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTG
AGGCAGATTGCAG
Found at i:139774 original size:39 final size:40
Alignment explanation
Indices: 139305--139829 Score: 132
Period size: 39 Copynumber: 13.4 Consensus size: 40
139295 CTGATTATGA
** * * *
139305 GGCAGATCATAATCATCCA-ATCTTTTACC-CTGAGCCTAG
1 GGCAGATCACCATCAACCAGATCTCTTACCAC-GAGCCTGG
* *
139344 GGCAGATCACCATCAACCA-ATCTCTTACCCCGAGCCTAG
1 GGCAGATCACCATCAACCAGATCTCTTACCACGAGCCTGG
* * * * *
139383 GACAGATTGTAGCCAT---TCA-ATCTTTTACTC-CGAGCCTAG
1 GGCAGA-T-CA-CCATCAACCAGATCTCTTAC-CACGAGCCTGG
* * **
139422 GGCAGATCACCATCAGCCA-ATCTCTTACCCCGAGCCTCA
1 GGCAGATCACCATCAACCAGATCTCTTACCACGAGCCTGG
* * *
139461 GGAAGATTGCAGCCAT---CC-GATCTTTTACCTCGAGCCTGG
1 GGCAGA-T-CA-CCATCAACCAGATCTCTTACCACGAGCCTGG
* * * * *
139500 GGCAGATCATCATCAGCCA-ATCTCTTACCCCTAGTCTGG
1 GGCAGATCACCATCAACCAGATCTCTTACCACGAGCCTGG
** * * * * *
139539 GGCAGAT-TGCAGTCATCC-GATCTTTTACC-CTGATCTTAG
1 GGCAGATCACCA-TCAACCAGATCTCTTACCAC-GAGCCTGG
* * * * * *
139578 GTCAGATCACTATCAGCCA-ATCTCTTACCTCGAACCTGA
1 GGCAGATCACCATCAACCAGATCTCTTACCACGAGCCTGG
* ** * ** * * * *
139617 GGTAGAT-TGCTTCCATTC-GATCTTTTACTC-TGAACTTGG
1 GGCAGATCACCAT-CAACCAGATCTCTTAC-CACGAGCCTGG
* * * * *
139656 GGCAGATCACTATCAGCTA-ATCTCTTACCCCGAGCCTGA
1 GGCAGATCACCATCAACCAGATCTCTTACCACGAGCCTGG
** ** *
139695 GGCAGAT-TGCAGTCATTC-GATCTTTTACTC-CGAGCCTGG
1 GGCAGATCACCA-TCAACCAGATCTCTTAC-CACGAGCCTGG
* *
139734 GGCAGATCACCATCAACCA-ATCTCTTACCATGAGCTTGG
1 GGCAGATCACCATCAACCAGATCTCTTACCACGAGCCTGG
* ** * * * *
139773 GGCGGAT-TGCAGCAATCAGATCTTTTACCCCGAGCCTGG
1 GGCAGATCACCATCAACCAGATCTCTTACCACGAGCCTGG
*
139812 GGCAGATCACCATTAACC
1 GGCAGATCACCATCAACC
139830 GTTGAAGCTA
Statistics
Matches: 350, Mismatches: 99, Indels: 73
0.67 0.19 0.14
Matches are distributed among these distances:
36 7 0.02
37 3 0.01
38 17 0.05
39 296 0.85
40 16 0.05
41 3 0.01
42 8 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (40 bp):
GGCAGATCACCATCAACCAGATCTCTTACCACGAGCCTGG
Found at i:141834 original size:31 final size:30
Alignment explanation
Indices: 141713--141910 Score: 195
Period size: 30 Copynumber: 6.6 Consensus size: 30
141703 CGAACTTCTA
* **
141713 AAAAATTACATTTTGA-CCTCCGAACTTTCC
1 AAAAATTACATTTTAACCCT-TAAACTTTCC
* *
141743 AAAAATTACA-TTTAACCCCTAAACTTTTTC
1 AAAAATTACATTTTAACCCTTAAAC-TTTCC
* * *
141773 -AAAATTATATTTTAACCCTTCAGCTTTCC
1 AAAAATTACATTTTAACCCTTAAACTTTCC
* *
141802 AAAAATTACATTTTTTATCCTTAAACTTTCC
1 AAAAATTACA-TTTTAACCCTTAAACTTTCC
*
141833 AAAAATTACATTTTGACCCTTAAACTTTCC
1 AAAAATTACATTTTAACCCTTAAACTTTCC
* * * *
141863 CAAAATCACATTTTAACCGTCAAACTTTCC
1 AAAAATTACATTTTAACCCTTAAACTTTCC
* *
141893 CAAAATCACATTTTAACC
1 AAAAATTACATTTTAACC
141911 TCAAACTCTC
Statistics
Matches: 141, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
29 19 0.13
30 96 0.68
31 26 0.18
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCTTAAACTTTCC
Found at i:141846 original size:61 final size:59
Alignment explanation
Indices: 141713--141910 Score: 195
Period size: 61 Copynumber: 3.3 Consensus size: 59
141703 CGAACTTCTA
* * * *
141713 AAAAATTACATTTTGA-CCTCCGAACTTTCCAAAAATTACA-TTTAACCCCTAAACTTTTTC
1 AAAAATTACATTTTAACCCTTC-AACTTTCCAAAAATTACATTTTAA-CCTTAAAC-TTTCC
* * *
141773 -AAAATTATATTTTAACCCTTCAGCTTTCCAAAAATTACATTTTTTATCCTTAAACTTTCC
1 AAAAATTACATTTTAACCCTTCAACTTTCCAAAAATTACA--TTTTAACCTTAAACTTTCC
* * * * *
141833 AAAAATTACATTTTGACCCTTAAACTTTCCCAAAATCACATTTTAACCGTCAAACTTTCC
1 AAAAATTACATTTTAACCCTTCAACTTTCCAAAAATTACATTTTAACC-TTAAACTTTCC
* *
141893 CAAAATCACATTTTAACC
1 AAAAATTACATTTTAACC
141911 TCAAACTCTC
Statistics
Matches: 114, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
59 37 0.32
60 33 0.29
61 40 0.35
62 4 0.04
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (59 bp):
AAAAATTACATTTTAACCCTTCAACTTTCCAAAAATTACATTTTAACCTTAAACTTTCC
Found at i:148121 original size:127 final size:127
Alignment explanation
Indices: 147895--148151 Score: 478
Period size: 127 Copynumber: 2.0 Consensus size: 127
147885 GGAATTGGGG
* *
147895 CAATTTTGGTATCTCCAGAAGCTAACCATTATCCTTTCACTAGTGAGCTTGACTTTGACTGTACA
1 CAATTTTGGTATCTCCAAAAGCTAACCATTATCCTTTCACTAGTGAGCTCGACTTTGACTGTACA
147960 AAAAACATGTCCAAATATGAAGCATGTATCATGGGACTCCGTGCAGCCATAGAACGAGAGAT
66 AAAAACATGTCCAAATATGAAGCATGTATCATGGGACTCCGTGCAGCCATAGAACGAGAGAT
*
148022 CAATTTTGGTATCTCCAAAAGCTAACCATTATTCTTTCACTAGTGAGCTCGACTTTGACTGTACA
1 CAATTTTGGTATCTCCAAAAGCTAACCATTATCCTTTCACTAGTGAGCTCGACTTTGACTGTACA
*
148087 AAAAACATGTCCAAATATGAAGCATGTATCATGGGACTCCGTGTAGCCATAGAACGAGAGAT
66 AAAAACATGTCCAAATATGAAGCATGTATCATGGGACTCCGTGCAGCCATAGAACGAGAGAT
148149 CAA
1 CAA
148152 AGTTTTAGAA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 126 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (127 bp):
CAATTTTGGTATCTCCAAAAGCTAACCATTATCCTTTCACTAGTGAGCTCGACTTTGACTGTACA
AAAAACATGTCCAAATATGAAGCATGTATCATGGGACTCCGTGCAGCCATAGAACGAGAGAT
Found at i:150548 original size:39 final size:38
Alignment explanation
Indices: 150449--150554 Score: 108
Period size: 39 Copynumber: 2.8 Consensus size: 38
150439 ATTTCGCAGG
* *
150449 TCTCTTACCCCTA-CATGGGGCAGATCGAAGCACCCAA
1 TCTCTTACCCCAATCATGGGGCAGATTGAAGCACCCAA
* * **
150486 TCTCTTACCCTAATCA-GAAGGCAGATTGAAGACAGGCAA
1 TCTCTTACCCCAATCATG-GGGCAGATTGAAG-CACCCAA
* *
150525 TCTCTTGCCCCGATCATGGGGCAGATTGAA
1 TCTCTTACCCCAATCATGGGGCAGATTGAA
150555 TGTACCCTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
37 12 0.22
38 13 0.24
39 29 0.53
40 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (38 bp):
TCTCTTACCCCAATCATGGGGCAGATTGAAGCACCCAA
Found at i:150602 original size:66 final size:66
Alignment explanation
Indices: 150491--150620 Score: 190
Period size: 66 Copynumber: 2.0 Consensus size: 66
150481 CCCAATCTCT
** * *
150491 TACCCTAATCAGAAGGCAGATTGAAGACAGGCAATCTCTTGCCCCGATCATGGGGCAGATTGAAT
1 TACCCTAATCAGAAGGCAGATTGAAGACAACCAATCTCTTACCCCGATCATGAGGCAGATTGAAT
150556 G
66 G
* *
150557 TACCCTAATCA-AAGGGAGGATTGAAGACAACCAATCTCTTACCCCGATCATGAGTCAGATTGAA
1 TACCCTAATCAGAAGGCA-GATTGAAGACAACCAATCTCTTACCCCGATCATGAGGCAGATTGAA
150621 GCTCCAATCT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 5 0.09
66 52 0.91
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (66 bp):
TACCCTAATCAGAAGGCAGATTGAAGACAACCAATCTCTTACCCCGATCATGAGGCAGATTGAAT
G
Found at i:150742 original size:77 final size:77
Alignment explanation
Indices: 150557--151534 Score: 1181
Period size: 77 Copynumber: 12.7 Consensus size: 77
150547 AGATTGAATG
* * **
150557 TACCCTAATCA-AAGGGAGGATTGAAGACAACCAATCTCTTACCCCGATCAT-GAGTCAGATTGA
1 TACCTTAATCAGAAGGCA-GATTGAAGACATGCAATCTCTTACCCCGATCATGGAG-CAGATTGA
150620 AGC-TCCAATCTTT
64 AGCATCCAATCTTT
* * *
150633 TACCTTAATCA-AAGGGTAGATTGAAGATATGCAATCTCTTACCCCGATCATGGAGCAAATTGAA
1 TACCTTAATCAGAA-GGCAGATTGAAGACATGCAATCTCTTACCCCGATCATGGAGCAGATTGAA
* *
150697 GCTTTCAATCTTT
65 GCATCCAATCTTT
* *
150710 TACCTTAATCAGAAGGCAGATTGAAGACATGCAATTTCTTACCCCGATCATGGGGCAGATTGAAG
1 TACCTTAATCAGAAGGCAGATTGAAGACATGCAATCTCTTACCCCGATCATGGAGCAGATTGAAG
150775 CATCCAATCTTT
66 CATCCAATCTTT
* * *
150787 TACCTTAATCAGAAGGCAGATTAAAGACACGCAATCTCTTACCTCGATCAT-GAGGCAGATTGAA
1 TACCTTAATCAGAAGGCAGATTGAAGACATGCAATCTCTTACCCCGATCATGGA-GCAGATTGAA
*
150851 GCATCCAATTTTT
65 GCATCCAATCTTT
* * * * * *
150864 TACCTTAATCAAAAGGAAGATTGAAGACACGCCAATCTCTTACCCCAATCATAGG-CCAAATTGA
1 TACCTTAATCAGAAGGCAGATTGAAGACATG-CAATCTCTTACCCCGATCAT-GGAGCAGATTGA
*
150928 AGCATCTAATCTTT
64 AGCATCCAATCTTT
* *
150942 TACCCTAATCA-AAGGGCAGATTGAAGACA-ACAAATCTCTTACCCCGATCATGCG-GCAGATTG
1 TACCTTAATCAGAA-GGCAGATTGAAGACATGC-AATCTCTTACCCCGATCATG-GAGCAGATTG
*
151004 AAGCATCCAATTTTT
63 AAGCATCCAATCTTT
* * * * * *
151019 TACCCTAATCAAAAGGCAGATTGAAGACA-GACAATATCTTACTCCAATCATGGGGCAGATTGAA
1 TACCTTAATCAGAAGGCAGATTGAAGACATG-CAATCTCTTACCCCGATCATGGAGCAGATTGAA
*
151083 GCATCCGATCTTT
65 GCATCCAATCTTT
* * * ** * *
151096 T-GCTCTAATTAGAGGGCAGATTGAAGACAACCAATTTCTTACCCCGATCATGGGGCAGATTGAA
1 TACCT-TAATCAGAAGGCAGATTGAAGACATGCAATCTCTTACCCCGATCATGGAGCAGATTGAA
151160 GCATCCAATCTTT
65 GCATCCAATCTTT
* * ** *
151173 TACCCTAATCAGAGGGCAGATTGAAGACAACCAATCTCTTACCCCGATCATTGG-GCTGATTGAA
1 TACCTTAATCAGAAGGCAGATTGAAGACATGCAATCTCTTACCCCGATCA-TGGAGCAGATTGAA
151237 GCATCCAATCTTT
65 GCATCCAATCTTT
* * * * *
151250 TACCTTAATCAGAGGGTAGATTGAAGACATGCAATCTCCTACCCCAATCAT-GAGGCAGATTAAA
1 TACCTTAATCAGAAGGCAGATTGAAGACATGCAATCTCTTACCCCGATCATGGA-GCAGATTGAA
151314 GCATCCAATCTTT
65 GCATCCAATCTTT
* * *
151327 TACCTTAATCAGAACGTAGATTGAAGACATGCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
1 TACCTTAATCAGAAGGCAGATTGAAGACATGCAATCTCTTACCCCGATCATGGAGCAGATTGAAG
151392 CATCCAATCTTT
66 CATCCAATCTTT
* * ***
151404 TAACTTAATCAGAAGGCAGATTGAAGACACTCCAATCTCTTACCCCGATCATGGTTTAGATTGAA
1 TACCTTAATCAGAAGGCAGATTGAAGACA-TGCAATCTCTTACCCCGATCATGGAGCAGATTGAA
*
151469 GCACCCAATCTTT
65 GCATCCAATCTTT
** *
151482 TACCTTAATCAGAAGGCAGATTGAAGACACACCAATCTCTTACCCCAATCATG
1 TACCTTAATCAGAAGGCAGATTGAAGACA-TGCAATCTCTTACCCCGATCATG
151535 AGGTAGATTG
Statistics
Matches: 797, Mismatches: 83, Indels: 42
0.86 0.09 0.05
Matches are distributed among these distances:
75 1 0.00
76 58 0.07
77 573 0.72
78 164 0.21
80 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (77 bp):
TACCTTAATCAGAAGGCAGATTGAAGACATGCAATCTCTTACCCCGATCATGGAGCAGATTGAAG
CATCCAATCTTT
Found at i:151236 original size:231 final size:231
Alignment explanation
Indices: 150449--151546 Score: 1340
Period size: 231 Copynumber: 4.8 Consensus size: 231
150439 ATTTCGCAGG
* * * *
150449 TCTCTTACCCCTA-CATGGGGCAGATCGAAGCACCCAATCTCTTACCCTAATCAGAAGGCAGATT
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAAGGCAGATT
** * *
150513 GAAGACAGGCAATCTCTTGCCCCGATCATGGGGCAGATTGAATG--T---A-C-----CC-TAAT
66 GAAGACAACCAATCTCTTACCCCGATCATTGGGCAGATTGAA-GCATCCAATCTTTTACCTTAAT
* * *
150566 CA-AAGGGAGGATTGAAGACA-ACCAATCTCTTACCCCGATCATGAGTCAGATTGAAGC-TCCAA
130 CAGAAGGCA-GATTGAAGACAGA-CAATCTCTTACCCCAATCATGAGGCAGATTGAAGCATCCAA
* * *
150628 TCTTTTACCTTAATCAAAGGGTAGATTGAAGATATGCAA
193 TCTTTTACCTTAATCAAAAGGTAGATTGAAGACATCCAA
* * * * *
150667 TCTCTTACCCCGATCATGGAGCAAATTGAAGCTTTCAATCTTTTACCTTAATCAGAAGGCAGATT
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAAGGCAGATT
** * *
150732 GAAGACATGCAATTTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATC
66 GAAGACAACCAATCTCTTACCCCGATCATTGGGCAGATTGAAGCATCCAATCTTTTACCTTAATC
* * * *
150797 AGAAGGCAGATTAAAGACACG-CAATCTCTTACCTCGATCATGAGGCAGATTGAAGCATCCAATT
131 AGAAGGCAGATTGAAGACA-GACAATCTCTTACCCCAATCATGAGGCAGATTGAAGCATCCAATC
* *
150861 TTTTACCTTAATCAAAAGGAAGATTGAAGACACGCCAA
195 TTTTACCTTAATCAAAAGGTAGATTGAAGACA-TCCAA
* * * * *
150899 TCTCTTACCCCAATCATAGGCCAAATTGAAGCATCTAATCTTTTACCCTAATCA-AAGGGCAGAT
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAA-GGCAGAT
* * *
150963 TGAAGACAACAAATCTCTTACCCCGATCA-TGCGGCAGATTGAAGCATCCAATTTTTTACCCTAA
65 TGAAGACAACCAATCTCTTACCCCGATCATTG-GGCAGATTGAAGCATCCAATCTTTTACCTTAA
* * * * *
151027 TCAAAAGGCAGATTGAAGACAGACAATATCTTACTCCAATCATGGGGCAGATTGAAGCATCCGAT
129 TCAGAAGGCAGATTGAAGACAGACAATCTCTTACCCCAATCATGAGGCAGATTGAAGCATCCAAT
* * * * * *
151092 CTTTT-GCTCTAATTAGAGGGCAGATTGAAGACAACCAA
194 CTTTTACCT-TAATCAAAAGGTAGATTGAAGACATCCAA
* *
151130 TTTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGATT
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAAGGCAGATT
*
151195 GAAGACAACCAATCTCTTACCCCGATCATTGGGCTGATTGAAGCATCCAATCTTTTACCTTAATC
66 GAAGACAACCAATCTCTTACCCCGATCATTGGGCAGATTGAAGCATCCAATCTTTTACCTTAATC
* * * *
151260 AGAGGGTAGATTGAAGACATG-CAATCTCCTACCCCAATCATGAGGCAGATTAAAGCATCCAATC
131 AGAAGGCAGATTGAAGACA-GACAATCTCTTACCCCAATCATGAGGCAGATTGAAGCATCCAATC
* * *
151324 TTTTACCTTAATCAGAACGTAGATTGAAGACATGCAA
195 TTTTACCTTAATCAAAAGGTAGATTGAAGACATCCAA
* *
151361 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTAACTTAATCAGAAGGCAGATT
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAAGGCAGATT
* ** *
151426 GAAGACACTCCAATCTCTTACCCCGATCA-TGGTTTAGATTGAAGCACCCAATCTTTTACCTTAA
66 GAAGACA-ACCAATCTCTTACCCCGATCATTGG-GCAGATTGAAGCATCCAATCTTTTACCTTAA
* *
151490 TCAGAAGGCAGATTGAAGACACACCAATCTCTTACCCCAATCATGAGGTAGATTGAA
129 TCAGAAGGCAGATTGAAGACAGA-CAATCTCTTACCCCAATCATGAGGCAGATTGAA
151547 ACACCCAAAC
Statistics
Matches: 756, Mismatches: 94, Indels: 45
0.84 0.11 0.05
Matches are distributed among these distances:
218 13 0.02
219 82 0.11
220 1 0.00
223 1 0.00
224 1 0.00
229 2 0.00
230 49 0.06
231 315 0.42
232 262 0.35
233 30 0.04
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (231 bp):
TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAAGGCAGATT
GAAGACAACCAATCTCTTACCCCGATCATTGGGCAGATTGAAGCATCCAATCTTTTACCTTAATC
AGAAGGCAGATTGAAGACAGACAATCTCTTACCCCAATCATGAGGCAGATTGAAGCATCCAATCT
TTTACCTTAATCAAAAGGTAGATTGAAGACATCCAA
Found at i:151581 original size:38 final size:38
Alignment explanation
Indices: 151461--151585 Score: 103
Period size: 38 Copynumber: 3.2 Consensus size: 38
151451 ATCATGGTTT
* * * * *
151461 AGATTGAAGCACCCAATCTTTTA-CCTTAATCAGAAGGC
1 AGATTGAAACACCCAATCTCTTACCCTTATTGAGGA-GC
** *
151499 AGATTGAAGACACACCAATCTCTTACCCCAATCATGA-G-GT
1 AGATTGAA-ACAC-CCAATCTCTTACCCTTAT--TGAGGAGC
*
151539 AGATTGAAACACCCAAACTCTTACCCTTATTGAGGAGC
1 AGATTGAAACACCCAATCTCTTACCCTTATTGAGGAGC
151577 AGATTGAAA
1 AGATTGAAA
151586 ACGCCATTCA
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
36 3 0.04
37 1 0.01
38 33 0.49
39 7 0.10
40 19 0.28
41 3 0.04
43 2 0.03
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (38 bp):
AGATTGAAACACCCAATCTCTTACCCTTATTGAGGAGC
Found at i:153128 original size:29 final size:29
Alignment explanation
Indices: 153037--153180 Score: 130
Period size: 30 Copynumber: 4.9 Consensus size: 29
153027 ATTTTATTTT
* * *
153037 AAAATTTTGTTTTAACCCTCAAACTTTCCA
1 AAAATTATATTTTGACCCT-AAACTTTCCA
* * * *
153067 AAACTTCTATTTCGACCCCTAAACTTTCTA
1 AAAATTATATTTTGA-CCCTAAACTTTCCA
153097 AAAATTATATTTTGACCCTAAACTTTCCA
1 AAAATTATATTTTGACCCTAAACTTTCCA
* * *
153126 AAAATTATGTTTTGACCCTTGAACCTTT-TA
1 AAAATTATATTTTGACCC-T-AAACTTTCCA
* *
153156 AAAATCACA-TTTGACCCTAAACTTT
1 AAAATTATATTTTGACCCTAAACTTT
153181 TTGAAAGTTA
Statistics
Matches: 94, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
27 6 0.06
28 1 0.01
29 38 0.40
30 39 0.41
31 10 0.11
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATTATATTTTGACCCTAAACTTTCCA
Found at i:153128 original size:59 final size:59
Alignment explanation
Indices: 153033--153180 Score: 158
Period size: 59 Copynumber: 2.5 Consensus size: 59
153023 CTCTATTTTA
* * * * *
153033 TTTT-AAAATTTTGTTTTAACCCTCAAACTTTCCAAAACTTCTATTTCGACCCCT-AAAC
1 TTTTAAAAATTATATTTTGACCCT-AAACTTTCCAAAAATTATATTTCGACCCCTGAAAC
* * * *
153091 TTTCTAAAAATTATATTTTGACCCTAAACTTTCCAAAAATTATGTTTTGACCCTTGAACC
1 TTT-TAAAAATTATATTTTGACCCTAAACTTTCCAAAAATTATATTTCGACCCCTGAAAC
* *
153151 TTTTAAAAATCACA-TTTGACCCTAAACTTT
1 TTTTAAAAATTATATTTTGACCCTAAACTTT
153181 TTGAAAGTTA
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
58 19 0.25
59 35 0.46
60 22 0.29
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (59 bp):
TTTTAAAAATTATATTTTGACCCTAAACTTTCCAAAAATTATATTTCGACCCCTGAAAC
Found at i:153197 original size:29 final size:29
Alignment explanation
Indices: 153046--153201 Score: 129
Period size: 29 Copynumber: 5.3 Consensus size: 29
153036 TAAAATTTTG
* * *
153046 TTTTAACCCTCAAACTTTCCAAAACTT-CTA
1 TTTTGACCCT-AAACTTTCTAAAAATTAC-A
* *
153076 TTTCGACCCCTAAACTTTCTAAAAATTATA
1 TTTTGA-CCCTAAACTTTCTAAAAATTACA
* **
153106 TTTTGACCCTAAACTTTCCAAAAATTATG
1 TTTTGACCCTAAACTTTCTAAAAATTACA
* *
153135 TTTTGACCCTTGAACCTTT-TAAAAATCACA
1 TTTTGACCC-T-AAACTTTCTAAAAATTACA
* * *
153165 -TTTGACCCTAAACTTTTTGAAAGTTACA
1 TTTTGACCCTAAACTTTCTAAAAATTACA
153193 TTTTGACCC
1 TTTTGACCC
153202 CCCGAACTTT
Statistics
Matches: 103, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
27 6 0.06
28 9 0.09
29 46 0.45
30 32 0.31
31 10 0.10
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.38
Consensus pattern (29 bp):
TTTTGACCCTAAACTTTCTAAAAATTACA
Found at i:153212 original size:58 final size:58
Alignment explanation
Indices: 153046--153212 Score: 140
Period size: 59 Copynumber: 2.8 Consensus size: 58
153036 TAAAATTTTG
* * * ** * *
153046 TTTTAACCCTCAAACTTTCCAAAACTT-CTATTTCGACCCCTAAACTTTCTAAAAATTATA
1 TTTTGACCCT-AAACTTTCCAAAAATTAC-ATTTTGACCCCCGAACTTT-TAAAAATCACA
** **
153106 TTTTGACCCTAAACTTTCCAAAAATTATGTTTTGACCCTTGAACCTTTTAAAAATCACA
1 TTTTGACCCTAAACTTTCCAAAAATTACATTTTGACCCCCGAA-CTTTTAAAAATCACA
*** *
153165 -TTTGACCCTAAACTTTTTGAAAGTTACATTTTGACCCCCCGAACTTTT
1 TTTTGACCCTAAACTTTCCAAAAATTACATTTTGA-CCCCCGAACTTTT
153213 TTAATTTACA
Statistics
Matches: 87, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
58 33 0.38
59 41 0.47
60 13 0.15
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (58 bp):
TTTTGACCCTAAACTTTCCAAAAATTACATTTTGACCCCCGAACTTTTAAAAATCACA
Found at i:154443 original size:35 final size:36
Alignment explanation
Indices: 154378--154453 Score: 127
Period size: 35 Copynumber: 2.1 Consensus size: 36
154368 CTATAATTCA
*
154378 GGTCGGGCTTAGACAAAATTTTAGGCCCATTTTTCG
1 GGTCGAGCTTAGACAAAATTTTAGGCCCATTTTTCG
*
154414 GGTCGAGCTTGGACAAAA-TTTAGGCCCATTTTTCG
1 GGTCGAGCTTAGACAAAATTTTAGGCCCATTTTTCG
154449 GGTCG
1 GGTCG
154454 GGCCGGACCT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 22 0.58
36 16 0.42
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (36 bp):
GGTCGAGCTTAGACAAAATTTTAGGCCCATTTTTCG
Found at i:158221 original size:20 final size:20
Alignment explanation
Indices: 158196--158235 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
158186 ACTCTACAAA
158196 AAAATAAAAACTGT-TACTTT
1 AAAATAAAAA-TGTCTACTTT
*
158216 AAAATAATAATGTCTACTTT
1 AAAATAAAAATGTCTACTTT
158236 TCTTTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAATAAAAATGTCTACTTT
Found at i:166811 original size:101 final size:101
Alignment explanation
Indices: 166636--166840 Score: 338
Period size: 101 Copynumber: 2.0 Consensus size: 101
166626 ACAGCAACAG
* * * *
166636 AAGGATTGCATGTCTGCAGGATATGCTTAATCCTAAAGTAGAAAAAAGATTTATCTAGGATGCAA
1 AAGGATAGCATGTCTGCAGGATAAGCTCAATCCTAAAGTAGAAAAAAGATTCATCTAGGATGCAA
*
166701 GATACTCTTCCCAGCATAATGCATGAAACTAGAACT
66 GATACTCTTCCCAACATAATGCATGAAACTAGAACT
* *
166737 AAGGATAGCATGTCTGCAGGATAAGCTCAATCCTTAAGTAGAAAAAATATTCATCTAGGATGCAA
1 AAGGATAGCATGTCTGCAGGATAAGCTCAATCCTAAAGTAGAAAAAAGATTCATCTAGGATGCAA
*
166802 GATACTCTTCGCAACATAATGCATGAAACTAGAACT
66 GATACTCTTCCCAACATAATGCATGAAACTAGAACT
166838 AAG
1 AAG
166841 AATAAGATCA
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 96 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (101 bp):
AAGGATAGCATGTCTGCAGGATAAGCTCAATCCTAAAGTAGAAAAAAGATTCATCTAGGATGCAA
GATACTCTTCCCAACATAATGCATGAAACTAGAACT
Found at i:171301 original size:32 final size:32
Alignment explanation
Indices: 171265--171366 Score: 91
Period size: 32 Copynumber: 3.2 Consensus size: 32
171255 TATAATAACA
171265 AATTTAACTCTTCACTGTTTATAGATTCTATC
1 AATTTAACTCTTCACTGTTTATAGATTCTATC
* * * * ** * * * *
171297 AATTTAA-TCCTAATTCTAAAAAAAATC-AAC
1 AATTTAACTCTTCACTGTTTATAGATTCTATC
171327 AAATTTAACTCTTCACTGTTTATAGATTCTATC
1 -AATTTAACTCTTCACTGTTTATAGATTCTATC
171360 AATTTAA
1 AATTTAA
171367 TCCTAATTCT
Statistics
Matches: 47, Mismatches: 20, Indels: 6
0.64 0.27 0.08
Matches are distributed among these distances:
30 2 0.04
31 18 0.38
32 25 0.53
33 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.41
Consensus pattern (32 bp):
AATTTAACTCTTCACTGTTTATAGATTCTATC
Found at i:171331 original size:63 final size:63
Alignment explanation
Indices: 171261--171398 Score: 276
Period size: 63 Copynumber: 2.2 Consensus size: 63
171251 TTGATATAAT
171261 AACAAATTTAACTCTTCACTGTTTATAGATTCTATCAATTTAATCCTAATTCTAAAAAAAATC
1 AACAAATTTAACTCTTCACTGTTTATAGATTCTATCAATTTAATCCTAATTCTAAAAAAAATC
171324 AACAAATTTAACTCTTCACTGTTTATAGATTCTATCAATTTAATCCTAATTCTAAAAAAAATC
1 AACAAATTTAACTCTTCACTGTTTATAGATTCTATCAATTTAATCCTAATTCTAAAAAAAATC
171387 AACAAATTTAAC
1 AACAAATTTAAC
171399 CACCAAACTT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 75 1.00
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (63 bp):
AACAAATTTAACTCTTCACTGTTTATAGATTCTATCAATTTAATCCTAATTCTAAAAAAAATC
Found at i:171334 original size:31 final size:31
Alignment explanation
Indices: 171297--171397 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 31
171287 AGATTCTATC
171297 AATTTAATCCTAATTCTAAAAAAAATCAACA
1 AATTTAATCCTAATTCTAAAAAAAATCAACA
* * * * ** * * * *
171328 AATTTAACTCTTCACTGTTTATAGATTCTATC-
1 AATTTAA-TCCTAATTCTAAAAAAAATC-AACA
171360 AATTTAATCCTAATTCTAAAAAAAATCAACA
1 AATTTAATCCTAATTCTAAAAAAAATCAACA
171391 AATTTAA
1 AATTTAA
171398 CCACCAAACT
Statistics
Matches: 47, Mismatches: 20, Indels: 6
0.64 0.27 0.08
Matches are distributed among these distances:
30 2 0.04
31 25 0.53
32 18 0.38
33 2 0.04
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.36
Consensus pattern (31 bp):
AATTTAATCCTAATTCTAAAAAAAATCAACA
Found at i:171444 original size:63 final size:63
Alignment explanation
Indices: 171289--171427 Score: 199
Period size: 63 Copynumber: 2.2 Consensus size: 63
171279 CTGTTTATAG
** *** * *
171289 ATTCTATCAATTTAATCCTAATTCTAAAAAAAATCAACAAATTTAACTCTTCACTGTTTATAG
1 ATTCTATCAATTTAATCCTAATTCTAAAAAAAATCAACAAATTTAACTCACCAAACTTTACAA
171352 ATTCTATCAATTTAATCCTAATTCTAAAAAAAATCAACAAATTTAAC-CACCAAACTTTACAA
1 ATTCTATCAATTTAATCCTAATTCTAAAAAAAATCAACAAATTTAACTCACCAAACTTTACAA
*
171414 ATTTTATCAATTTA
1 ATTCTATCAATTTA
171428 TTCTTGATTC
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
62 21 0.31
63 47 0.69
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.37
Consensus pattern (63 bp):
ATTCTATCAATTTAATCCTAATTCTAAAAAAAATCAACAAATTTAACTCACCAAACTTTACAA
Found at i:171521 original size:24 final size:23
Alignment explanation
Indices: 171476--171524 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
171466 ATCATTTTCG
* **
171476 AAAAAAATTACTTAAATTTTATA
1 AAAAAAATTACATAAAAATTATA
171499 AAAAAAATTACATACAAAATTATA
1 AAAAAAATTACATA-AAAATTATA
171523 AA
1 AA
171525 TAAATGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAAAATTACATAAAAATTATA
Found at i:172003 original size:35 final size:35
Alignment explanation
Indices: 171957--172023 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
171947 ATCAATGTTA
171957 AAAAAAAAAAATTGAAGTAGAAAATACGAAGGGTT
1 AAAAAAAAAAATTGAAGTAGAAAATACGAAGGGTT
171992 AAAAAAAAAAATTGAAGTAGAAAATACGAAGG
1 AAAAAAAAAAATTGAAGTAGAAAATACGAAGG
172024 AATGTGGCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.63, C:0.03, G:0.19, T:0.15
Consensus pattern (35 bp):
AAAAAAAAAAATTGAAGTAGAAAATACGAAGGGTT
Found at i:173835 original size:10 final size:10
Alignment explanation
Indices: 173822--173972 Score: 80
Period size: 10 Copynumber: 15.2 Consensus size: 10
173812 AAAAAACAAT
173822 AAAAATTAT-
1 AAAAATTATA
173831 AAAAATT-TA
1 AAAAATTATA
*
173840 ATAAAAGTATTA
1 A-AAAATTA-TA
*
173852 AAAAATTATT
1 AAAAATTATA
*
173862 AAAAATTGTA
1 AAAAATTATA
**
173872 AAATTTTATA
1 AAAAATTATA
**
173882 AAAAATCGTA
1 AAAAATTATA
173892 AAAAATTATA
1 AAAAATTATA
*
173902 AAACA-TAT-
1 AAAAATTATA
*
173910 AGAAA-TATA
1 AAAAATTATA
173919 GAAAATATT-TA
1 -AAAA-ATTATA
* *
173930 TAAAATTTTA
1 AAAAATTATA
* * *
173940 TAAAGTCATAA
1 AAAAATTAT-A
173951 AAAAATTATA
1 AAAAATTATA
*
173961 AAAAAATATA
1 AAAAATTATA
173971 AA
1 AA
173973 GTAATATAAA
Statistics
Matches: 106, Mismatches: 26, Indels: 19
0.70 0.17 0.13
Matches are distributed among these distances:
8 7 0.07
9 14 0.13
10 65 0.61
11 16 0.15
12 4 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (10 bp):
AAAAATTATA
Found at i:173970 original size:29 final size:30
Alignment explanation
Indices: 173937--174005 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
173927 TTATAAAATT
*
173937 TTATAAAGTCATAAAAAAATT-ATAAAAAAA
1 TTATAAAGTAAT-AAAAAATTCATAAAAAAA
* *
173967 -TATAAAGTAATATAAAATTCCTAAAAAAA
1 TTATAAAGTAATAAAAAATTCATAAAAAAA
173996 TTATAAAGTA
1 TTATAAAGTA
174006 TATTGTACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.21
29 18 0.53
30 9 0.26
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (30 bp):
TTATAAAGTAATAAAAAATTCATAAAAAAA
Found at i:174935 original size:18 final size:19
Alignment explanation
Indices: 174900--174940 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
174890 ATTAAATAGT
* *
174900 TCAAGTTATTTGAGTTAA-
1 TCAAGTTATTCGAATTAAC
174918 TCAAGTTATTCGAATTAAC
1 TCAAGTTATTCGAATTAAC
174937 TCAA
1 TCAA
174941 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (19 bp):
TCAAGTTATTCGAATTAAC
Found at i:175098 original size:70 final size:67
Alignment explanation
Indices: 175016--175145 Score: 197
Period size: 70 Copynumber: 1.9 Consensus size: 67
175006 TGATAAGAAA
* ** *
175016 AGGCAAAACTACGTCGTTTTGATAAATGTTTACATTTTCTAAAGTTAAAAGTCAAAATCATTAAG
1 AGGCAAAACTACGTCGTTTTAATAAATGTTTAC-TCAT-T-AAGTTAAAAGACAAAATCATTAAG
175081 TTAGC
63 TTAGC
175086 AGGCAAAACTACGTCGTTTTAATAAATGTTTACTCATTAAGTTAAAAGACAAAATCATTA
1 AGGCAAAACTACGTCGTTTTAATAAATGTTTACTCATTAAGTTAAAAGACAAAATCATTA
175146 TATTGTTTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
67 21 0.38
68 1 0.02
69 2 0.04
70 32 0.57
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (67 bp):
AGGCAAAACTACGTCGTTTTAATAAATGTTTACTCATTAAGTTAAAAGACAAAATCATTAAGTTA
GC
Found at i:177875 original size:43 final size:42
Alignment explanation
Indices: 177814--178131 Score: 422
Period size: 43 Copynumber: 7.4 Consensus size: 42
177804 GTGAATTTTT
*
177814 AATGGAAGACTTGTGTCTCTGTTAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTC-GTTAGAGCATAAGATTGTTTATA
*
177857 AATGGAAGCCTTATGTCTCGATTAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTCG-TTAGAGCATAAGATTGTTTATA
*
177900 AATTGAAGACTTATGTCTCTGTTAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTC-GTTAGAGCATAAGATTGTTTATA
*
177943 AATGGAATACTTATGTCTCAGTTAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTC-GTTAGAGCATAAGATTGTTTATA
* * *
177986 AATGGAAGACTTATGTCTCGACTAGAGCATAAGATTATTTGTA
1 AATGGAAGACTTATGTCTCG-TTAGAGCATAAGATTGTTTATA
* * *
178029 AATGGAAGACTTATGTCTCGGCTAGAGCATAAGATTATTTGTA
1 AATGGAAGACTTATGTCTC-GTTAGAGCATAAGATTGTTTATA
* * *
178072 AATGGAAGAACTTATGTCTCGGCTAGAGCGTAAGATT-TTTGGTA
1 AATGGAAG-ACTTATGTCTC-GTTAGAGCATAAGATTGTTT-ATA
178116 AATGGAAGAACTTATG
1 AATGGAAG-ACTTATG
178132 ACTTGGATAG
Statistics
Matches: 257, Mismatches: 12, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
42 2 0.01
43 207 0.81
44 48 0.19
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (42 bp):
AATGGAAGACTTATGTCTCGTTAGAGCATAAGATTGTTTATA
Found at i:181549 original size:116 final size:116
Alignment explanation
Indices: 181345--181577 Score: 457
Period size: 116 Copynumber: 2.0 Consensus size: 116
181335 GTTGGACATT
*
181345 TCAAATCTCACTGAAGGGTTAGTCTATGGCCTGAAGCTTGGACCTCTAGTTAGGACAGTGAAAAA
1 TCAAATCTCACTGAAGGGTTAGTCTATGGACTGAAGCTTGGACCTCTAGTTAGGACAGTGAAAAA
181410 GTAAGATTTTTTATTTGACAATAATGTCCGTACTTTTTTTAGCATGGTTAA
66 GTAAGATTTTTTATTTGACAATAATGTCCGTACTTTTTTTAGCATGGTTAA
181461 TCAAATCTCACTGAAGGGTTAGTCTATGGACTGAAGCTTGGACCTCTAGTTAGGACAGTGAAAAA
1 TCAAATCTCACTGAAGGGTTAGTCTATGGACTGAAGCTTGGACCTCTAGTTAGGACAGTGAAAAA
181526 GTAAGATTTTTTATTTGACAATAATGTCCGTACTTTTTTTAGCATGGTTAA
66 GTAAGATTTTTTATTTGACAATAATGTCCGTACTTTTTTTAGCATGGTTAA
181577 T
1 T
181578 TTTTATCTTG
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (116 bp):
TCAAATCTCACTGAAGGGTTAGTCTATGGACTGAAGCTTGGACCTCTAGTTAGGACAGTGAAAAA
GTAAGATTTTTTATTTGACAATAATGTCCGTACTTTTTTTAGCATGGTTAA
Found at i:184798 original size:39 final size:39
Alignment explanation
Indices: 184755--184834 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
184745 AGTTGTTCAA
184755 GAAAATCCAGAAATTATTGAACAACTAGTTGAACAACAT
1 GAAAATCCAGAAATTATTGAACAACTAGTTGAACAACAT
184794 GAAAATCCAGAAATTATTGAACAACTAGTTGAACAACAT
1 GAAAATCCAGAAATTATTGAACAACTAGTTGAACAACAT
184833 GA
1 GA
184835 TTGACAAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (39 bp):
GAAAATCCAGAAATTATTGAACAACTAGTTGAACAACAT
Found at i:186880 original size:40 final size:40
Alignment explanation
Indices: 186825--186938 Score: 183
Period size: 40 Copynumber: 2.9 Consensus size: 40
186815 AAGTTATGTT
* * *
186825 TGAATAAATTTAAGCTTCGGCTTAGCAGGCTATGAGCTGG
1 TGAATAAATTCAAGCTTCGGCTTAGCAGGCTAAGAGCCGG
* *
186865 TGAATAAAATCAAGCTTCGACTTAGCAGGCTAAGAGCCGG
1 TGAATAAATTCAAGCTTCGGCTTAGCAGGCTAAGAGCCGG
186905 TGAATAAATTCAAGCTTCGGCTTAGCAGGCTAAG
1 TGAATAAATTCAAGCTTCGGCTTAGCAGGCTAAG
186939 TGTAACAGCC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (40 bp):
TGAATAAATTCAAGCTTCGGCTTAGCAGGCTAAGAGCCGG
Found at i:188390 original size:36 final size:36
Alignment explanation
Indices: 188331--188430 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
188321 GGTAACAGGC
* *
188331 ATGAACTTTAGGTCAACAGGGAGTGAAATGAGCATA
1 ATGACCTTTAGGTCAACAGGGAGTAAAATGAGCATA
* * *
188367 ATGACCTTTCGGTCAACAAGGAGTAAAATGAGCATC
1 ATGACCTTTAGGTCAACAGGGAGTAAAATGAGCATA
188403 ATGACCTTTAGGTCAACAGGGAGTAAAA
1 ATGACCTTTAGGTCAACAGGGAGTAAAA
188431 CGAATAACGA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (36 bp):
ATGACCTTTAGGTCAACAGGGAGTAAAATGAGCATA
Found at i:189116 original size:21 final size:21
Alignment explanation
Indices: 189092--189143 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
189082 TAGAAGTAAG
* * *
189092 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCGATAGAACAGTC
*
189113 ACTTGTATCGATAGAACCGTC
1 ACTTGTATCGATAGAACAGTC
*
189134 ACTTGAATCG
1 ACTTGTATCG
189144 GTAAAAGTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (21 bp):
ACTTGTATCGATAGAACAGTC
Found at i:189474 original size:40 final size:40
Alignment explanation
Indices: 189430--189557 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 40
189420 AAGAGCCAAG
*
189430 GAATAAATTCAAGCTTTGGCTTAGTAGACTAAGAGCTGGT
1 GAATAAATTCAAGCTTTGGCTTAGCAGACTAAGAGCTGGT
* * * *
189470 GAATAAATTCAAGTTTTGACTTAGCA-AGCTACGAG-TCGCT
1 GAATAAATTCAAGCTTTGGCTTAGCAGA-CTAAGAGCT-GGT
* * *
189510 GAAT-AATTCAAGCTTTGGCTTAGCAGGCTATGAGCCGGT
1 GAATAAATTCAAGCTTTGGCTTAGCAGACTAAGAGCTGGT
*
189549 GAATGAATT
1 GAATAAATT
189558 AGTAACAAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
39 33 0.46
40 39 0.54
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (40 bp):
GAATAAATTCAAGCTTTGGCTTAGCAGACTAAGAGCTGGT
Found at i:193203 original size:6 final size:6
Alignment explanation
Indices: 193192--193242 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
193182 TGATCAAAAT
* * *
193192 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
193240 TGA
1 TGA
193243 TATGAATTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:197830 original size:57 final size:56
Alignment explanation
Indices: 197769--197895 Score: 125
Period size: 59 Copynumber: 2.2 Consensus size: 56
197759 AAATTAATGT
*
197769 TAAAAAATAACAACAAAAAA-GT-AATATATATATATATAATTAATACAA-GTAAAAAGA
1 TAAAAAATAACAACAAAAAAGGTAAAAATATATA-AT-TAATTAA-A-AAGGTAAAAAGA
* * *
197826 TAAAAATATATTCTATAAAAAAGGTAAAAATATATAATTAATTAAAAAGTGTAAAAAGA
1 TAAAAA-ATA-ACAACAAAAAAGGTAAAAATATATAATTAATTAAAAAG-GTAAAAAGA
197885 TAAATAAATAA
1 TAAA-AAATAA
197896 ATAAAAAAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
57 8 0.14
58 4 0.07
59 31 0.53
60 6 0.10
61 9 0.16
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (56 bp):
TAAAAAATAACAACAAAAAAGGTAAAAATATATAATTAATTAAAAAGGTAAAAAGA
Found at i:197872 original size:26 final size:24
Alignment explanation
Indices: 197818--197882 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
197808 TTAATACAAG
*
197818 TAAAAAGATAAAAATATATTCTAT
1 TAAAAAGGTAAAAATATATTCTAT
*
197842 AAAAAAGGTAAAAATATATAAT-TAAT
1 TAAAAAGGTAAAAATATAT--TCT-AT
197868 TAAAAAGTGTAAAAA
1 TAAAAAG-GTAAAAA
197883 GATAAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 17 0.50
25 1 0.03
26 9 0.26
27 7 0.21
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.28
Consensus pattern (24 bp):
TAAAAAGGTAAAAATATATTCTAT
Found at i:197900 original size:29 final size:26
Alignment explanation
Indices: 197843--197902 Score: 66
Period size: 29 Copynumber: 2.2 Consensus size: 26
197833 ATATTCTATA
* * *
197843 AAAAAGGTAAAAATATATAATTAATT
1 AAAAAGGTAAAAATAAATAAATAAAT
197869 AAAAAGTGTAAAAAGATAAATAAATAAAT
1 AAAAAG-GT-AAAA-ATAAATAAATAAAT
197898 AAAAA
1 AAAAA
197903 AACTATTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.21
27 2 0.07
28 4 0.14
29 16 0.57
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.23
Consensus pattern (26 bp):
AAAAAGGTAAAAATAAATAAATAAAT
Found at i:198254 original size:60 final size:61
Alignment explanation
Indices: 198140--198314 Score: 174
Period size: 63 Copynumber: 2.9 Consensus size: 61
198130 AACTTGATTT
* * * * * *
198140 TTTTTCTTAATTTGATACTTAAA-TTTTTGTTTGATCCAATTTGATATTTGAACTTAAC-AC
1 TTTTTCTTAATTTGGTACCTAAACTTTTT-TTAGATCCAATTTGGTACTTAAACTTAACTAC
* * * * **
198200 TTTTTCTTAATTTGGTACCTAAACTTTTTTTGGACCCAATTTGGTACCTAAACTTAGCTTTTT
1 TTTTTCTTAATTTGGTACCTAAACTTTTTTTAGATCCAATTTGGTACTTAAACTTAAC--TAC
* * *
198263 TTTTTCTTAATTTGGCACCTAAGCTTTTTTTAGATTCAATTTGGTACTTAAA
1 TTTTTCTTAATTTGGTACCTAAACTTTTTTTAGATCCAATTTGGTACTTAAA
198315 TTTATTAAAT
Statistics
Matches: 94, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
60 43 0.46
61 5 0.05
63 46 0.49
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.50
Consensus pattern (61 bp):
TTTTTCTTAATTTGGTACCTAAACTTTTTTTAGATCCAATTTGGTACTTAAACTTAACTAC
Found at i:198556 original size:30 final size:31
Alignment explanation
Indices: 198520--198655 Score: 106
Period size: 29 Copynumber: 4.5 Consensus size: 31
198510 GGACTCCAAA
*
198520 AAGTTTAAGTACCAACTTA-AAAAAAATGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
* *
198550 AAGTTTAGGTACCAAATTAGGAAAAAATGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
* * * *
198581 AAGTTTGAGAACTAAATTTGACCAAAAAA----
1 AAGTTTAAGTACCAAATTAGA--AAAAAATGTC
* * *
198610 AAGTTTAGGTATCAAATT--AAAAAAATATC
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
*
198639 AAGTTTAAATACCAAAT
1 AAGTTTAAGTACCAAAT
198656 ATTATATTAA
Statistics
Matches: 82, Mismatches: 17, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
25 6 0.07
27 1 0.01
29 27 0.33
30 17 0.21
31 25 0.30
33 6 0.07
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAATGTC
Found at i:198839 original size:15 final size:15
Alignment explanation
Indices: 198819--198847 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
198809 CATTATCCCT
198819 GGAACGAACTGTTGA
1 GGAACGAACTGTTGA
198834 GGAACGAACTGTTG
1 GGAACGAACTGTTG
198848 GGATCATGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (15 bp):
GGAACGAACTGTTGA
Found at i:200924 original size:3 final size:3
Alignment explanation
Indices: 200916--200940 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
200906 AAAACCAGGG
200916 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
200941 TAGGAAATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:203672 original size:17 final size:17
Alignment explanation
Indices: 203645--203678 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
203635 AAATAAAATT
203645 AGTTGTTATTTAAGATAA
1 AGTTGTTATTTAA-ATAA
203663 AGTT-TTATTTAAATAA
1 AGTTGTTATTTAAATAA
203679 CTACAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 8 0.50
18 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
AGTTGTTATTTAAATAA
Found at i:209167 original size:30 final size:30
Alignment explanation
Indices: 209131--209187 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
209121 AATTAAATTC
209131 AATTTGACAAGTCCATTTACAAGCCCATTT
1 AATTTGACAAGTCCATTTACAAGCCCATTT
*
209161 AATTTGAGAAGTCCATTTACAAGCCCA
1 AATTTGACAAGTCCATTTACAAGCCCA
209188 AATCTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (30 bp):
AATTTGACAAGTCCATTTACAAGCCCATTT
Found at i:209380 original size:18 final size:18
Alignment explanation
Indices: 209357--209405 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
209347 TGACCATTGA
*
209357 CTCCTCTGCCCAAGACTG
1 CTCCTCTGCCCAAGACCG
* * *
209375 CTCCTCTCCCCGAGGCCG
1 CTCCTCTGCCCAAGACCG
*
209393 TTCCTCTGCCCAA
1 CTCCTCTGCCCAA
209406 AGCAACCTGT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.49, G:0.16, T:0.22
Consensus pattern (18 bp):
CTCCTCTGCCCAAGACCG
Found at i:218938 original size:41 final size:41
Alignment explanation
Indices: 218881--218963 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
218871 AAAAGATGAG
218881 AATATCATCTTTTCTTCTCATAACCAACCGTCCATGCCTAT
1 AATATCATCTTTTCTTCTCATAACCAACCGTCCATGCCTAT
218922 AATATCATCTTTTCTTCTCATAACCAACCGTCCATGCCTAT
1 AATATCATCTTTTCTTCTCATAACCAACCGTCCATGCCTAT
218963 A
1 A
218964 TTCCCCATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.28, C:0.31, G:0.05, T:0.36
Consensus pattern (41 bp):
AATATCATCTTTTCTTCTCATAACCAACCGTCCATGCCTAT
Done.