Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 102 of 253
Found at i:31771866 original size:20 final size:20
Alignment explanation
Indices: 31771843--31771880 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31771833 TCAGCTCCAA
31771843 TCAGCTCACTTGAGCTCGTT
1 TCAGCTCACTTGAGCTCGTT
**
31771863 TCAGCTCGTTTGAGCTCG
1 TCAGCTCACTTGAGCTCG
31771881 ATTTAGCTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.29, G:0.24, T:0.34
Consensus pattern (20 bp):
TCAGCTCACTTGAGCTCGTT
Found at i:31784154 original size:20 final size:20
Alignment explanation
Indices: 31784131--31784177 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31784121 GGGTTAAGAT
*
31784131 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31784151 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31784171 TGAGCTG
1 TGAGCTG
31784178 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:31785895 original size:48 final size:48
Alignment explanation
Indices: 31785843--31785948 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
31785833 ATTGTCTTTC
*
31785843 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
31785891 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
31785939 TTTCTTTTTC
1 TTTCTTTTTC
31785949 CATGACACTT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:31788346 original size:22 final size:22
Alignment explanation
Indices: 31788295--31788346 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
31788285 TCCACGTCTT
* *
31788295 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTCTCTAA
31788317 -TTCATTTTCTCTTCTTTCTC-AA
1 TTTC-TTTTCT-TTCTTTCTCTAA
31788339 TTTCTTTT
1 TTTCTTTT
31788347 TCACTCTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 11 0.44
23 11 0.44
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTCTCTAA
Found at i:31788347 original size:23 final size:21
Alignment explanation
Indices: 31788295--31788348 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
31788285 TCCACGTCTT
*
31788295 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTT-TCTCTTTTTCTAA
*
31788317 -TTCATTTTCTCTTCTTTCTCAA
1 TTTCTTTTTCTCTT-TTTCT-AA
31788339 TTTCTTTTTC
1 TTTCTTTTTC
31788349 ACTCTCAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 5 0.19
21 11 0.42
22 2 0.08
23 8 0.31
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTCTTTTTCTCTTTTTCTAA
Found at i:31794542 original size:17 final size:18
Alignment explanation
Indices: 31794520--31794556 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31794510 TGGAATAAAC
31794520 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
31794537 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
31794555 TT
1 TT
31794557 CAGCTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:31796398 original size:18 final size:19
Alignment explanation
Indices: 31796372--31796413 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
31796362 TTAATCCAAA
*
31796372 TAATGAAACAAACTC-AAT
1 TAATTAAACAAACTCTAAT
* *
31796390 TAATTAAACTAAGTCTAAT
1 TAATTAAACAAACTCTAAT
31796409 TAATT
1 TAATT
31796414 CAGTTTGGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (19 bp):
TAATTAAACAAACTCTAAT
Found at i:31806515 original size:18 final size:18
Alignment explanation
Indices: 31806477--31806511 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31806467 TTTGTGCTGG
31806477 AATAAACTTAGGTTAATT
1 AATAAACTTAGGTTAATT
*
31806495 AATAAAGTTA-GTTAATT
1 AATAAACTTAGGTTAATT
31806512 TAATTTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (18 bp):
AATAAACTTAGGTTAATT
Found at i:31810105 original size:20 final size:22
Alignment explanation
Indices: 31810082--31810122 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
31810072 GTTATACAAG
31810082 TCAAAAAAATC-AAAA-AAAAT
1 TCAAAAAAATCGAAAAGAAAAT
31810102 TCAAAAAAATCGAAAAGAAAA
1 TCAAAAAAATCGAAAAGAAAA
31810123 AAAAATCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.73, C:0.10, G:0.05, T:0.12
Consensus pattern (22 bp):
TCAAAAAAATCGAAAAGAAAAT
Found at i:31810125 original size:18 final size:17
Alignment explanation
Indices: 31810104--31810139 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
31810094 AAAAAAATTC
31810104 AAAAAAATC-GAAAAGAA
1 AAAAAAATCTGAAAA-AA
31810121 AAAAAAATCTGAAAAAA
1 AAAAAAATCTGAAAAAA
31810138 AA
1 AA
31810140 GTGTTTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.78, C:0.06, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAAAATCTGAAAAAA
Found at i:31811206 original size:29 final size:29
Alignment explanation
Indices: 31811137--31811206 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
31811127 TTGAAAAGCA
* *
31811137 AAAAGAAAATGAGATTGAAAAAGAGAACG
1 AAAAGAAATTGAGAGTGAAAAAGAGAACG
*
31811166 AAAA-AAATTTGAGAGTGAAAAAGA-AGATG
1 AAAAGAAA-TTGAGAGTGAAAAAGAGA-ACG
31811195 AAAAGAAATTGA
1 AAAAGAAATTGA
31811207 AACAAAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 4 0.11
29 28 0.80
30 3 0.09
ACGTcount: A:0.61, C:0.01, G:0.23, T:0.14
Consensus pattern (29 bp):
AAAAGAAATTGAGAGTGAAAAAGAGAACG
Found at i:31813318 original size:30 final size:30
Alignment explanation
Indices: 31813223--31813319 Score: 74
Period size: 30 Copynumber: 3.2 Consensus size: 30
31813213 AGCTCACTCC
* *
31813223 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACAAGCTAAACCT
* * * *
31813253 TAGCTCAACTTCAGCTTA-AGAGTTTAATCC-
1 TAGCTCAACTTTAGCTCACA-AG-CTAAACCT
* *
31813283 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACAAGCTAAACCT
31813313 TAGCTCA
1 TAGCTCA
31813320 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
29 4 0.08
30 35 0.71
31 10 0.20
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACAAGCTAAACCT
Found at i:31824580 original size:18 final size:18
Alignment explanation
Indices: 31824540--31824588 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
31824530 GTTCATTTTT
*
31824540 CTTTCTTTCTTCACTCTCA
1 CTTTCTTT-TTCAATCTCA
* *
31824559 CTTTCTTTTTCAATTTCG
1 CTTTCTTTTTCAATCTCA
31824577 CTTTCCTTTTTC
1 CTTT-CTTTTTC
31824589 TCATTCTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.08, C:0.31, G:0.02, T:0.59
Consensus pattern (18 bp):
CTTTCTTTTTCAATCTCA
Found at i:31829370 original size:17 final size:19
Alignment explanation
Indices: 31829348--31829387 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
31829338 GCACACACAA
31829348 AATTAA-TTTAG-CAAATT
1 AATTAATTTTAGACAAATT
*
31829365 AATTAATTTTAGACACATT
1 AATTAATTTTAGACAAATT
31829384 AATT
1 AATT
31829388 TTCGGCTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
19 9 0.45
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (19 bp):
AATTAATTTTAGACAAATT
Found at i:31831790 original size:13 final size:12
Alignment explanation
Indices: 31831772--31831818 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
31831762 ACAAAAAAAT
31831772 AAAAAAAATTCGA
1 AAAAAAAATT-GA
*
31831785 AAAAAAAATTAA
1 AAAAAAAATTGA
*
31831797 AAAAAAAAGTGA
1 AAAAAAAATTGA
31831809 CAAAAAAAAT
1 -AAAAAAAAT
31831819 CGAGTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:31832889 original size:6 final size:6
Alignment explanation
Indices: 31832856--31832963 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
31832846 AAAGAAATTG
* * * ** *
31832856 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
31832903 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
31832954 AAAGAA AAAG
1 AAAGAA AAAG
31832964 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 26, Indels: 7
0.69 0.25 0.07
Matches are distributed among these distances:
5 3 0.04
6 59 0.81
7 7 0.10
8 4 0.05
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:31832917 original size:18 final size:18
Alignment explanation
Indices: 31832860--31832918 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
31832850 AAATTGAAAG
* *
31832860 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* * *
31832878 AGAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
31832896 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
31832914 AAAAG
1 AAAAG
31832919 TGAGAGAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.71, C:0.07, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:31832945 original size:14 final size:13
Alignment explanation
Indices: 31832924--31832961 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
31832914 AAAAGTGAGA
31832924 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
31832936 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
31832951 GAAAAAGAAAA
1 GAAAAAGAAAA
31832962 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:31832975 original size:21 final size:21
Alignment explanation
Indices: 31832925--31832975 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
31832915 AAAGTGAGAG
*
31832925 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
31832946 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
31832967 AAAAAGAAA
1 AAAAAGAAA
31832976 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:31832979 original size:27 final size:27
Alignment explanation
Indices: 31832877--31832981 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 27
31832867 AAAGAAAACG
* *
31832877 AAGAAGAAAAAGAAATTGCAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*** **
31832904 AAGAAATCGAAAAAGTGAGAGAAAAAGAAA
1 AAG-AA--GAAAAAAAAATTGAAAAAGAAA
* *
31832934 ATGAAGAAAAGAAAATTGAAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*
31832961 AAG-CGAAAAAAGAAATTGAAA
1 AAGAAGAAAAAA-AAATTGAAA
31832982 GAGAGCTTGA
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
26 6 0.10
27 30 0.51
28 2 0.03
29 2 0.03
30 19 0.32
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.09
Consensus pattern (27 bp):
AAGAAGAAAAAAAAATTGAAAAAGAAA
Found at i:31833015 original size:33 final size:33
Alignment explanation
Indices: 31832978--31833040 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
31832968 AAAAGAAATT
31832978 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
31833011 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
31833041 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:31836258 original size:20 final size:20
Alignment explanation
Indices: 31836235--31836288 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
31836225 AGTTTTTCCC
*
31836235 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
31836255 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
31836275 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
31836289 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:31836270 original size:30 final size:30
Alignment explanation
Indices: 31836235--31836308 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
31836225 AGTTTTTCCC
31836235 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
31836265 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
31836295 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
31836309 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:31836298 original size:20 final size:20
Alignment explanation
Indices: 31836235--31836299 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
31836225 AGTTTTTCCC
* * * *
31836235 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
31836255 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
31836274 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
31836295 AGCTC
1 AGCTC
31836300 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:31839674 original size:15 final size:15
Alignment explanation
Indices: 31839654--31839701 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
31839644 TCAAAGATGG
31839654 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
31839669 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
31839683 GTTTATGGATATAAA
1 GTTTATGGATATGAA
31839698 GTTT
1 GTTT
31839702 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:31839688 original size:14 final size:14
Alignment explanation
Indices: 31839648--31839691 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
31839638 AAGGATTCAA
31839648 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
31839662 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
31839677 AGATGGGTTTATGG
1 AGATGGGTTTATGG
31839691 A
1 A
31839692 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:31839717 original size:29 final size:29
Alignment explanation
Indices: 31839648--31839707 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
31839638 AAGGATTCAA
*
31839648 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
31839677 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
31839706 AG
1 AG
31839708 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:31843246 original size:18 final size:18
Alignment explanation
Indices: 31843205--31843250 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
31843195 TCTTTTTCAT
* *
31843205 TCTCTTTTTCAATCTGAT
1 TCTCTTTTTCAATCTCAA
* *
31843223 TTTCTTTTTCACTCTCAA
1 TCTCTTTTTCAATCTCAA
31843241 TCTCTTTTTC
1 TCTCTTTTTC
31843251 TTTGTCTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.02, T:0.59
Consensus pattern (18 bp):
TCTCTTTTTCAATCTCAA
Found at i:31843251 original size:24 final size:24
Alignment explanation
Indices: 31843176--31843253 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
31843166 CTTGTTCACA
*
31843176 TTCTTTCTCTCTCTCAAACTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
* * * **
31843200 TTCATTCTCTTTTTCAATCTGATT
1 TTCTTTCTCTCTCTCAATCTCTTT
* *
31843224 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
31843248 TTCTTT
1 TTCTTT
31843254 GTCTTTCATT
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.13, C:0.27, G:0.01, T:0.59
Consensus pattern (24 bp):
TTCTTTCTCTCTCTCAATCTCTTT
Found at i:31844324 original size:18 final size:16
Alignment explanation
Indices: 31844301--31844347 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 16
31844291 TATGTTCAAA
31844301 TTTTCAGATTTTGTTTTT
1 TTTTCA-ATTTT-TTTTT
31844319 TTTTCAA---TTTTTT
1 TTTTCAATTTTTTTTT
31844332 TTTTCAATTTTTTTTT
1 TTTTCAATTTTTTTTT
31844348 GAAACTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 12 0.46
14 1 0.04
16 6 0.23
17 1 0.04
18 6 0.23
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (16 bp):
TTTTCAATTTTTTTTT
Found at i:31844331 original size:12 final size:13
Alignment explanation
Indices: 31844314--31844347 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
31844304 TCAGATTTTG
31844314 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
31844327 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
31844340 TTTTTTTT
1 TTTTTTTT
31844348 GAAACTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:31844347 original size:17 final size:18
Alignment explanation
Indices: 31844301--31844335 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
31844291 TATGTTCAAA
31844301 TTTTCAGATTTTGTTTTT
1 TTTTCAGATTTTGTTTTT
31844319 TTTTCA-ATTTT-TTTTT
1 TTTTCAGATTTTGTTTTT
31844335 T
1 T
31844336 CAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTTCAGATTTTGTTTTT
Found at i:31844603 original size:14 final size:14
Alignment explanation
Indices: 31844563--31844606 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
31844553 AAGGATTCAA
31844563 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
31844577 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
31844592 AGATGGGTTTATGG
1 AGATGGGTTTATGG
31844606 A
1 A
31844607 TTTTGTAGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:31845040 original size:11 final size:11
Alignment explanation
Indices: 31845020--31845051 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
31845010 GGTCACATAG
*
31845020 TAAAGTGCTAT
1 TAAAGGGCTAT
31845031 TAAAGGGCTAT
1 TAAAGGGCTAT
31845042 TAAAGGGCTA
1 TAAAGGGCTA
31845052 ATTATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (11 bp):
TAAAGGGCTAT
Found at i:31848395 original size:8 final size:8
Alignment explanation
Indices: 31848366--31848416 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
31848356 ATGTATCGAC
31848366 AAAAGCCG
1 AAAAGCCG
* *
31848374 AAATGCCA
1 AAAAGCCG
31848382 AAAAGCCG
1 AAAAGCCG
*
31848390 AAAAGCTG
1 AAAAGCCG
*
31848398 AAATGCCG
1 AAAAGCCG
*
31848406 AAAAGCTG
1 AAAAGCCG
31848414 AAA
1 AAA
31848417 GTTTGGCTAC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.51, C:0.20, G:0.22, T:0.08
Consensus pattern (8 bp):
AAAAGCCG
Found at i:31848400 original size:24 final size:24
Alignment explanation
Indices: 31848366--31848416 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
31848356 ATGTATCGAC
31848366 AAAAGCCGAAATGCCAAAAAGCCG
1 AAAAGCCGAAATGCCAAAAAGCCG
* * *
31848390 AAAAGCTGAAATGCCGAAAAGCTG
1 AAAAGCCGAAATGCCAAAAAGCCG
31848414 AAA
1 AAA
31848417 GTTTGGCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.20, G:0.22, T:0.08
Consensus pattern (24 bp):
AAAAGCCGAAATGCCAAAAAGCCG
Found at i:31848702 original size:28 final size:29
Alignment explanation
Indices: 31848639--31848739 Score: 152
Period size: 28 Copynumber: 3.6 Consensus size: 29
31848629 TGAATATGAC
*
31848639 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
31848668 TGGGCCTAATGGGCCATATACA-GTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
31848696 TGGGCCTAATGGGCCATATAAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
31848724 TGGGCTTAATGGGCCA
1 TGGGCCTAATGGGCCA
31848740 GATACAGGTA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
28 43 0.65
29 23 0.35
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.28
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:31848703 original size:57 final size:56
Alignment explanation
Indices: 31848639--31848746 Score: 171
Period size: 57 Copynumber: 1.9 Consensus size: 56
31848629 TGAATATGAC
* *
31848639 TGGGCCTAACGGGCCATATAAATGTGATTTGGGCCTAATGGGCCATATACAGTGATT
1 TGGGCCTAACGGGCCATATAAATATGA-TTGGGCCTAATGGGCCAGATACAGTGATT
* *
31848696 TGGGCCTAATGGGCCATATAAATATGATTGGGCTTAATGGGCCAGATACAG
1 TGGGCCTAACGGGCCATATAAATATGATTGGGCCTAATGGGCCAGATACAG
31848747 GTATGTGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
56 22 0.47
57 25 0.53
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.27
Consensus pattern (56 bp):
TGGGCCTAACGGGCCATATAAATATGATTGGGCCTAATGGGCCAGATACAGTGATT
Found at i:31854719 original size:29 final size:29
Alignment explanation
Indices: 31854686--31854776 Score: 130
Period size: 29 Copynumber: 3.2 Consensus size: 29
31854676 TGAATATTAC
*
31854686 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
31854715 TGGGCCTAATGGGCCATATATAGGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
31854744 TGGGCCTAATGGGCCATATCAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
31854772 TGGGC
1 TGGGC
31854777 TTTATAGGCC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 6 0.11
29 49 0.89
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:31855778 original size:30 final size:29
Alignment explanation
Indices: 31855684--31855779 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
31855674 AGCTCACTCC
*
31855684 TAGCTCATATTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTAGCTCACGAGCTAAACCT
* * * * *
31855714 TA-CTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTT-AGCTCACGAGCTAAACCT
* *
31855743 CAGCTCAACTGTAGCTCACGAGCTAAAGCT
1 TAGCTCAACT-TAGCTCACGAGCTAAACCT
31855773 TAGCTCA
1 TAGCTCA
31855780 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
28 3 0.06
29 18 0.36
30 28 0.56
31 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (29 bp):
TAGCTCAACTTAGCTCACGAGCTAAACCT
Found at i:31857437 original size:21 final size:22
Alignment explanation
Indices: 31857411--31857460 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
31857401 AGTAGTTATA
31857411 AAAAAAGTAT-ATAAAAAAATC-
1 AAAAAAGTATGA-AAAAAAATCG
* *
31857432 AAAAAAATTTGAAAAAAAATCG
1 AAAAAAGTATGAAAAAAAATCG
31857454 AAAAAAG
1 AAAAAAG
31857461 AGAGAGGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.72, C:0.04, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAAAGTATGAAAAAAAATCG
Found at i:31858398 original size:21 final size:21
Alignment explanation
Indices: 31858372--31858421 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
31858362 ACATTCTTGT
31858372 AAAGAAAAAACAAAGAAAAG-A
1 AAAGAAAAAACAAA-AAAAGAA
* *
31858393 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAACAAAAAAAGAA
31858414 AAAGAAAA
1 AAAGAAAA
31858422 TGAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAACAAAAAAAGAA
Found at i:31858407 original size:6 final size:5
Alignment explanation
Indices: 31858372--31858439 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
31858362 ACATTCTTGT
* *
31858372 AAAGA AAAAA CAAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA
1 AAAGA AAAGA -AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA
31858419 AAATGA AATA-A AAAGA AAAGA
1 AAA-GA AA-AGA AAAGA AAAGA
31858440 GAGGCAAGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
4 4 0.08
5 29 0.56
6 18 0.35
7 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:31858412 original size:15 final size:14
Alignment explanation
Indices: 31858383--31858439 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
31858373 AAGAAAAAAC
31858383 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
31858399 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
31858414 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
31858430 AAAGAAAAGA
1 AAAGAAAAGA
31858440 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:31858517 original size:6 final size:6
Alignment explanation
Indices: 31858501--31858556 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
31858491 AAAAGCCTTT
* * * ** *
31858501 GAAAAA CAAAAA GAAAAA GAAAAA GAAAAT GAGATT GAAAAA GAAAAT
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
31858549 GAAAAA GA
1 GAAAAA GA
31858557 GTTTGAGAGA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (6 bp):
GAAAAA
Found at i:31858540 original size:24 final size:24
Alignment explanation
Indices: 31858513--31858575 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
31858503 AAAACAAAAA
*
31858513 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAAAGAGATT
* *
31858537 GAAAAAGAAAATGAAAAAGAGTTT
1 GAAAAAGAAAAAGAAAAAGAGATT
* *
31858561 GAGAGAGAAAAAGAA
1 GAAAAAGAAAAAGAA
31858576 TGTGAAAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAAGAGATT
Found at i:31858564 original size:30 final size:30
Alignment explanation
Indices: 31858508--31858589 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
31858498 TTTGAAAAAC
* **
31858508 AAAAAGAAAAAGAAAAAGAAAATGAGATTG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
***
31858538 AAAAAGAAAATGAAAAAGAGTTTGAGAGAG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
**
31858568 AAAAAGAATGTGAAAAAGAAAA
1 AAAAAGAAAATGAAAAAGAAAA
31858590 AAAAGTGGAA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAAGAAAATGAGAGAG
Found at i:31858587 original size:18 final size:18
Alignment explanation
Indices: 31858543--31858606 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
31858533 GATTGAAAAA
* * *
31858543 GAAAATGAAAAAGAGTTT
1 GAAAAAGAAAAAGAATGT
* *
31858561 GAGAGAGAAAAAGAATGT
1 GAAAAAGAAAAAGAATGT
*
31858579 GAAAAAGAAAAA-AAAGT
1 GAAAAAGAAAAAGAATGT
31858596 GGAAAAAGAAA
1 -GAAAAAGAAA
31858607 TTTAGATAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
17 4 0.11
18 33 0.89
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (18 bp):
GAAAAAGAAAAAGAATGT
Found at i:31867016 original size:16 final size:16
Alignment explanation
Indices: 31866997--31867038 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
31866987 AAGAGAAAAC
31866997 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
* *
31867013 AAAGAAAACAAAATAA
1 AAAGAAAAGAAAAGAA
31867029 AAAGAAAAGA
1 AAAGAAAAGA
31867039 GAGGCAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:31867115 original size:12 final size:12
Alignment explanation
Indices: 31867100--31867131 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
31867090 AAAAGCCTTT
31867100 GAAAATGAAAAA
1 GAAAATGAAAAA
*
31867112 GAAAAAGAAAAA
1 GAAAATGAAAAA
31867124 GAAAATGA
1 GAAAATGA
31867132 TATTGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (12 bp):
GAAAATGAAAAA
Found at i:31869326 original size:30 final size:31
Alignment explanation
Indices: 31869292--31869388 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
31869282 AGCTCACTCC
*
31869292 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
31869322 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
31869352 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
31869382 TAGCTCA
1 TAGCTCA
31869389 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:31872152 original size:13 final size:14
Alignment explanation
Indices: 31872116--31872150 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
31872106 CAAAAAAATC
31872116 AAAAAAAAA-TTGA
1 AAAAAAAAATTTGA
31872129 AAAAAAAAATTTGA
1 AAAAAAAAATTTGA
31872143 AAAAAAAA
1 AAAAAAAA
31872151 TTGCATACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (14 bp):
AAAAAAAAATTTGA
Found at i:31874416 original size:17 final size:18
Alignment explanation
Indices: 31874377--31874418 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
31874367 AAGAAGAAAA
31874377 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
31874394 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
31874411 TCAAAAGA
1 ACAAAAGA
31874419 AAAAGAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:31879375 original size:376 final size:376
Alignment explanation
Indices: 31878682--31879375 Score: 1316
Period size: 376 Copynumber: 1.8 Consensus size: 376
31878672 GCTCGTATCA
31878682 CTATCCATATTTTCACCTTAAAAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCC
1 CTATCCATATTTTCACCTTAAAAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCC
*
31878747 TGACGTTAAGTTCGTTTTCCATTCCCATCCTTCGACTTATTTTCTTGTTATTCCAAACCGAGCCA
66 TGACGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCA
31878812 TTTAACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACC
131 TTTAACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACC
31878877 TTCCGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTC
196 TTCCGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTC
*
31878942 GAACGACGATCGGGCAACTAAGTGAATTCGACTCATCATCCCGAGACGGATCACATCAGCGTCAA
261 GAACGACGATCGGGCAACTAAGTGAATTCGAATCATCATCCCGAGACGGATCACATCAGCGTCAA
31879007 TCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCAT
326 TCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCAT
* *
31879058 CTATCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCC
1 CTATCCATATTTTCACCTTAAAAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCC
*
31879123 TGACGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCTAAACCGAGCCA
66 TGACGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCA
31879188 TTTAACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACC
131 TTTAACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACC
31879253 TTCCGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTC
196 TTCCGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTC
* * *
31879318 GAACGACGATCGGGCAACTAAGTGAATTCGAATTATCATCTCGAGCCGGATCACATCA
261 GAACGACGATCGGGCAACTAAGTGAATTCGAATCATCATCCCGAGACGGATCACATCA
31879376 CAAGTTCGTG
Statistics
Matches: 310, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
376 310 1.00
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.33
Consensus pattern (376 bp):
CTATCCATATTTTCACCTTAAAAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCC
TGACGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCA
TTTAACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACC
TTCCGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTC
GAACGACGATCGGGCAACTAAGTGAATTCGAATCATCATCCCGAGACGGATCACATCAGCGTCAA
TCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCAT
Found at i:31880694 original size:30 final size:30
Alignment explanation
Indices: 31880660--31880756 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
31880650 AGCTCACTCC
*
31880660 TAGCTCACTTTCAACTCACGAGCTAAACCT
1 TAGCTCACTTTCAGCTCACGAGCTAAACCT
* * * * * *
31880690 TAGCTTAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGC-TCACTTTCAGCTCACGAGCTAAACCT
* *
31880720 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTC-ACTTTCAGCTCACGAGCTAAACCT
31880750 TAGCTCA
1 TAGCTCA
31880757 TTTTAGTTTA
Statistics
Matches: 48, Mismatches: 16, Indels: 7
0.68 0.23 0.10
Matches are distributed among these distances:
29 2 0.04
30 41 0.85
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCACTTTCAGCTCACGAGCTAAACCT
Found at i:31882707 original size:20 final size:20
Alignment explanation
Indices: 31882660--31882707 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
31882650 AGTAAGCTCG
31882660 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
31882680 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
31882700 GTTGAGCT
1 GTTGAGCT
31882708 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:31885165 original size:30 final size:31
Alignment explanation
Indices: 31885131--31885227 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
31885121 AGCTCACTCC
*
31885131 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
31885161 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
31885191 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
31885221 TAGCTCA
1 TAGCTCA
31885228 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:31887866 original size:18 final size:18
Alignment explanation
Indices: 31887843--31887906 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
31887833 TTTGATCAAA
31887843 CTCTTTTTCTTTCTCATT
1 CTCTTTTTCTTTCTCATT
**
31887861 CTCTTTTTCAATCTCATT
1 CTCTTTTTCTTTCTCATT
* *
31887879 -T-TGTTTC-CTCTC-TT
1 CTCTTTTTCTTTCTCATT
31887893 CCTCTTTTTCTTTC
1 -CTCTTTTTCTTTC
31887907 ATTTCTTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
14 2 0.06
15 4 0.11
16 6 0.17
17 6 0.17
18 18 0.50
ACGTcount: A:0.06, C:0.30, G:0.02, T:0.62
Consensus pattern (18 bp):
CTCTTTTTCTTTCTCATT
Found at i:31890248 original size:10 final size:10
Alignment explanation
Indices: 31890232--31890266 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
31890222 AACAGGAAAG
31890232 AAGCTAAAAC
1 AAGCTAAAAC
*
31890242 GAGCTAAAAC
1 AAGCTAAAAC
*
31890252 AAGCTGAAAC
1 AAGCTAAAAC
31890262 AAGCT
1 AAGCT
31890267 CAAGTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.51, C:0.20, G:0.17, T:0.11
Consensus pattern (10 bp):
AAGCTAAAAC
Found at i:31892540 original size:11 final size:10
Alignment explanation
Indices: 31892515--31892575 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
31892505 ACCAATAAAA
31892515 TAAA-TGAGC
1 TAAATTGAGC
*
31892524 TGAATTGTAGC
1 TAAATTG-AGC
31892535 TAAATTGAGC
1 TAAATTGAGC
**
31892545 TCGATTGAGC
1 TAAATTGAGC
31892555 TGAAA-TGAGC
1 T-AAATTGAGC
*
31892565 TCAATTGAGC
1 TAAATTGAGC
31892575 T
1 T
31892576 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:31892576 original size:20 final size:20
Alignment explanation
Indices: 31892516--31892576 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
31892506 CCAATAAAAT
*
31892516 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
31892536 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
31892557 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
31892577 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:31895717 original size:24 final size:23
Alignment explanation
Indices: 31895674--31895759 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 23
31895664 CTCGCAATAC
**
31895674 TTTTCACTTTTTTAACTTGATTTT
1 TTTTCACTTTTTT-TTTTGATTTT
31895698 TTTGTCACTTTTTTTTTTGATTTT
1 TTT-TCACTTTTTTTTTTGATTTT
* * *
31895722 TTTTGAATATTTTTTTTTGAATTTC
1 TTTTCACT-TTTTTTTTTG-ATTTT
* *
31895747 TTCTCTCTTTTTT
1 TTTTCACTTTTTT
31895760 AAATCCAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
23 3 0.06
24 29 0.58
25 18 0.36
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTTCACTTTTTTTTTTGATTTT
Found at i:31897124 original size:11 final size:10
Alignment explanation
Indices: 31897099--31897159 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
31897089 ACCAATAAAA
31897099 TAAA-TGAGC
1 TAAATTGAGC
*
31897108 TGAATTGTAGC
1 TAAATTG-AGC
31897119 TAAATTGAGC
1 TAAATTGAGC
**
31897129 TCGATTGAGC
1 TAAATTGAGC
31897139 TGAAA-TGAGC
1 T-AAATTGAGC
*
31897149 TCAATTGAGC
1 TAAATTGAGC
31897159 T
1 T
31897160 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:31897160 original size:20 final size:20
Alignment explanation
Indices: 31897100--31897160 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
31897090 CCAATAAAAT
*
31897100 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
31897120 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
31897141 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
31897161 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:31903222 original size:55 final size:55
Alignment explanation
Indices: 31903150--31903286 Score: 267
Period size: 55 Copynumber: 2.5 Consensus size: 55
31903140 TGCTTTCATT
31903150 AATGCCG-TCCATGCATGGGAACATCTCATTAAATCCATGTCTTTGCTTCCTTTA
1 AATGCCGTTCCATGCATGGGAACATCTCATTAAATCCATGTCTTTGCTTCCTTTA
31903204 AATGCCGTTCCATGCATGGGAACATCTCATTAAATCCATGTCTTTGCTTCCTTTA
1 AATGCCGTTCCATGCATGGGAACATCTCATTAAATCCATGTCTTTGCTTCCTTTA
31903259 AATGCCGTTCCATGCATGGGAACATCTC
1 AATGCCGTTCCATGCATGGGAACATCTC
31903287 CCTTGCTGCT
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
54 7 0.09
55 75 0.91
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (55 bp):
AATGCCGTTCCATGCATGGGAACATCTCATTAAATCCATGTCTTTGCTTCCTTTA
Found at i:31905693 original size:21 final size:21
Alignment explanation
Indices: 31905644--31905710 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
31905634 CCTCTTTGAA
* * *
31905644 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
31905667 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
31905688 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
31905709 CC
1 CC
31905711 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:31907030 original size:22 final size:22
Alignment explanation
Indices: 31906997--31907050 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
31906987 GATTGAGAGT
31906997 GAAAAAGAAATT-GAAGAAAGAA
1 GAAAAAGAAATTAGAA-AAAGAA
31907019 GAAAAATG-AATTAGAAAAAGAA
1 GAAAAA-GAAATTAGAAAAAGAA
31907041 -ACAAAAGAAA
1 GA-AAAAGAAA
31907051 AAGACGTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
21 2 0.07
22 22 0.79
23 4 0.14
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (22 bp):
GAAAAAGAAATTAGAAAAAGAA
Found at i:31911436 original size:12 final size:12
Alignment explanation
Indices: 31911421--31911451 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
31911411 TTCTTTTTGC
31911421 TTTTCAAAGGCT
1 TTTTCAAAGGCT
31911433 TTTTCAAAGGCT
1 TTTTCAAAGGCT
31911445 TTTTCAA
1 TTTTCAA
31911452 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:31911539 original size:15 final size:14
Alignment explanation
Indices: 31911499--31911555 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 14
31911489 CTCTTGCCTC
*
31911499 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
*
31911514 TCATTTCCTTTTTCT
1 TC-TTTTCTTTTTCT
31911529 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
31911546 TCTTTTCTTT
1 TCTTTTCTTT
31911556 GTTTTCTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
14 3 0.09
15 12 0.34
16 13 0.37
17 7 0.20
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:31911556 original size:21 final size:20
Alignment explanation
Indices: 31911523--31911566 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
31911513 TTCATTTCCT
31911523 TTTTCTTCTTTTGCTTTT-TC
1 TTTTCTTCTTTTG-TTTTCTC
*
31911543 TTTTCTTTTCTTTGTTTTCTC
1 TTTTCTTCT-TTTGTTTTCTC
31911564 TTT
1 TTT
31911567 ACAAGAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTTCTTCTTTTGTTTTCTC
Found at i:31912546 original size:12 final size:12
Alignment explanation
Indices: 31912471--31912546 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
31912461 GCACAAATCA
31912471 TTTTTTTTGAAACT
1 TTTTTTTTG-AA-T
31912485 TTTTTTGTTGAATTTT
1 TTTTTT-TTGAA---T
*
31912501 TTTGTTTTTCAAAT
1 TTT-TTTTT-GAAT
*
31912515 TTCTTTTCTGAAT
1 TT-TTTTTTGAAT
31912528 TTTTTTTTGAAT
1 TTTTTTTTGAAT
31912540 TTTTTTT
1 TTTTTTT
31912547 ATACTTGTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
12 16 0.31
13 5 0.10
14 15 0.29
15 4 0.08
16 6 0.12
17 5 0.10
ACGTcount: A:0.16, C:0.05, G:0.08, T:0.71
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:31915642 original size:30 final size:30
Alignment explanation
Indices: 31915607--31915670 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
31915597 AGCTCGAATT
*
31915607 AGCTCACA-TGAGCTTAATTTAACTTGTTTG
1 AGCTCA-ATTGAGCTTAATTTAACTCGTTTG
* * *
31915637 AGCTCAATTTAGCTTACTTTAGCTCGTTTG
1 AGCTCAATTGAGCTTAATTTAACTCGTTTG
31915667 AGCT
1 AGCT
31915671 TGGCTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (30 bp):
AGCTCAATTGAGCTTAATTTAACTCGTTTG
Found at i:31920692 original size:20 final size:20
Alignment explanation
Indices: 31920669--31920715 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31920659 GGGTTAAGAT
*
31920669 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31920689 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31920709 TGAGCTG
1 TGAGCTG
31920716 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:31922437 original size:48 final size:48
Alignment explanation
Indices: 31922385--31922490 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
31922375 TTGTCTTTTC
*
31922385 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
31922433 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
31922481 TTTCTTTTTC
1 TTTCTTTTTC
31922491 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:31923599 original size:12 final size:11
Alignment explanation
Indices: 31923571--31923598 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
31923561 TTTTTTTTCC
31923571 TTTTTTGAATT
1 TTTTTTGAATT
31923582 TTTTTTGAATT
1 TTTTTTGAATT
31923593 TTTTTT
1 TTTTTT
31923599 TTTTAAATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTGAATT
Found at i:31925103 original size:20 final size:20
Alignment explanation
Indices: 31925080--31925126 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31925070 GGGTTAAGAT
*
31925080 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31925100 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31925120 TGAGCTG
1 TGAGCTG
31925127 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:31933048 original size:23 final size:22
Alignment explanation
Indices: 31932996--31933048 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
31932986 TCCACGTCTT
*
31932996 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
31933018 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
31933041 TTTCTTTT
1 TTTCTTTT
31933049 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:31934352 original size:24 final size:23
Alignment explanation
Indices: 31934298--31934375 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
31934288 GGATAATTAA
**
31934298 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
31934321 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
31934345 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
31934366 GAAATAGTAT
1 GAAATGGTAT
31934376 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:31934360 original size:21 final size:21
Alignment explanation
Indices: 31934334--31934400 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
31934324 TTGGTATTTG
31934334 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
31934355 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
31934376 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
31934399 GG
1 GG
31934401 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:31939845 original size:14 final size:14
Alignment explanation
Indices: 31939826--31939885 Score: 68
Period size: 14 Copynumber: 4.4 Consensus size: 14
31939816 TGAATACAAA
31939826 TTTTTTTTGAATTT
1 TTTTTTTTGAATTT
** *
31939840 TTTTTTTCAAAATT
1 TTTTTTTTGAATTT
31939854 TTTTTTTTG-ATTT
1 TTTTTTTTGAATTT
* *
31939867 TTTTTGTTCAATTT
1 TTTTTTTTGAATTT
31939881 TTTTT
1 TTTTT
31939886 ACAATACCGT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
13 10 0.27
14 27 0.73
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (14 bp):
TTTTTTTTGAATTT
Found at i:31939868 original size:28 final size:26
Alignment explanation
Indices: 31939826--31939885 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
31939816 TGAATACAAA
*
31939826 TTTTTTTTGAATTTTTTTTTTCAAAATT
1 TTTTTTTTGAATTTTTTTGTTC--AATT
*
31939854 TTTTTTTTGATTTTTTTTGTTCAATT
1 TTTTTTTTGAATTTTTTTGTTCAATT
31939880 TTTTTT
1 TTTTTT
31939886 ACAATACCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 10 0.33
28 20 0.67
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (26 bp):
TTTTTTTTGAATTTTTTTGTTCAATT
Found at i:31940551 original size:12 final size:12
Alignment explanation
Indices: 31940530--31940586 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
31940520 GAAAATGAAG
31940530 AAAAGAAAATTGA
1 AAAAG-AAATTGA
31940543 AAAAGAAATTGA
1 AAAAGAAATTGA
* ** *
31940555 GATTGAGATTGA
1 AAAAGAAATTGA
31940567 GAAAA-AAATTGA
1 -AAAAGAAATTGA
31940579 AAAAGAAA
1 AAAAGAAA
31940587 AAGATGTTGA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
11 4 0.12
12 24 0.71
13 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.19, T:0.18
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:31943102 original size:23 final size:22
Alignment explanation
Indices: 31943076--31943128 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
31943066 TTGAGAGTGA
*
31943076 AAAAGAAATT-GAAGAAAGAAGAG
1 AAAAGAAATTAGAA-AAAGAA-AC
31943099 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
31943121 AAAAGAAA
1 AAAAGAAA
31943129 AAGACGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:31947150 original size:20 final size:19
Alignment explanation
Indices: 31947124--31947184 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
31947114 AACTCCGACC
31947124 AGCTCAATTGAGCTCATTT
1 AGCTCAATTGAGCTCATTT
* *
31947143 CCGCTCAATCGAGCTCAATTT
1 -AGCTCAATTGAGCTC-ATTT
*
31947164 AGCTACAATTCAGCTCATTT
1 AGCT-CAATTGAGCTCATTT
31947184 A
1 A
31947185 TTTTATTGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 21 0.62
21 13 0.38
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (19 bp):
AGCTCAATTGAGCTCATTT
Found at i:31947178 original size:11 final size:10
Alignment explanation
Indices: 31947123--31947180 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
31947113 CAACTCCGAC
31947123 CAGCTCAATT
1 CAGCTCAATT
* *
31947133 GAGCTCATTT
1 CAGCTCAATT
*
31947143 CCGCTCAA-T
1 CAGCTCAATT
31947152 CGAGCTCAATT
1 C-AGCTCAATT
*
31947163 TAGCTACAATT
1 CAGCT-CAATT
31947174 CAGCTCA
1 CAGCTCA
31947181 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 2 0.05
10 25 0.68
11 10 0.27
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:31948558 original size:12 final size:13
Alignment explanation
Indices: 31948534--31948559 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31948524 AAAAGAGATG
31948534 AAATTCAAAAAAA
1 AAATTCAAAAAAA
31948547 AAATTCAAAAAAA
1 AAATTCAAAAAAA
31948560 TTGAAAAAAG
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:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATTCAAAAAAA
Found at i:31949678 original size:27 final size:27
Alignment explanation
Indices: 31949647--31949759 Score: 97
Period size: 27 Copynumber: 4.1 Consensus size: 27
31949637 GAAAGAAAAC
31949647 AAAAAGAAAACGAAGAAAAAGAAATTG
1 AAAAAGAAAACGAAGAAAAAGAAATTG
* * * ** **
31949674 CAAAAGAAAAAGAAATCAAAAAGTGAGAG
1 AAAAAGAAAACG-AA-GAAAAAGAAATTG
*
31949703 AAAAAGAAAATGAAG-AAAAGAAAATTG
1 AAAAAGAAAACGAAGAAAAAG-AAATTG
31949730 AAAAAGAAAAGCG-A-AAAAAGAAATTG
1 AAAAAGAAAA-CGAAGAAAAAGAAATTG
31949756 AAAA
1 AAAA
31949760 GAGCTTGAAA
Statistics
Matches: 66, Mismatches: 15, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
26 15 0.23
27 28 0.42
28 5 0.08
29 18 0.27
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAACGAAGAAAAAGAAATTG
Found at i:31949723 original size:14 final size:14
Alignment explanation
Indices: 31949703--31949752 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
31949693 AAAGTGAGAG
31949703 AAAAAGAAAA-TGA
1 AAAAAGAAAAGTGA
*
31949716 AGAAAAGAAAATTG-
1 A-AAAAGAAAAGTGA
*
31949730 AAAAAGAAAAGCGA
1 AAAAAGAAAAGTGA
31949744 AAAAAGAAA
1 AAAAAGAAA
31949753 TTGAAAAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 11 0.34
14 19 0.59
15 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (14 bp):
AAAAAGAAAAGTGA
Found at i:31949736 original size:13 final size:13
Alignment explanation
Indices: 31949702--31949759 Score: 57
Period size: 13 Copynumber: 4.4 Consensus size: 13
31949692 AAAAGTGAGA
31949702 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
31949714 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
**
31949729 GAAAAAGAAAAGC
1 GAAAAAGAAAATT
31949742 GAAAAA-AGAAATT
1 GAAAAAGA-AAATT
31949755 GAAAA
1 GAAAA
31949760 GAGCTTGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 2 0.05
13 24 0.63
14 10 0.26
15 2 0.05
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.09
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:31951821 original size:10 final size:10
Alignment explanation
Indices: 31951805--31951862 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
31951795 CAACTCCGAC
31951805 CAGCTCAATT
1 CAGCTCAATT
* *
31951815 GAGCTCATTT
1 CAGCTCAATT
31951825 CAGCTCAA-T
1 CAGCTCAATT
31951834 CGAGCTCAATT
1 C-AGCTCAATT
*
31951845 TAGCTACAATT
1 CAGCT-CAATT
31951856 CAGCTCA
1 CAGCTCA
31951863 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:31951828 original size:20 final size:20
Alignment explanation
Indices: 31951805--31951865 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
31951795 CAACTCCGAC
31951805 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
31951825 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
31951846 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
31951866 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:31953792 original size:20 final size:20
Alignment explanation
Indices: 31953769--31953815 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
31953759 AGGTTAAGAT
*
31953769 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
31953789 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
31953809 TGAGCTG
1 TGAGCTG
31953816 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:31955536 original size:48 final size:48
Alignment explanation
Indices: 31955481--31955586 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
31955471 TTGTCTTTTC
*
31955481 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
31955529 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
31955577 TTTCTTTTTC
1 TTTCTTTTTC
31955587 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:31958212 original size:20 final size:20
Alignment explanation
Indices: 31958189--31958235 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
31958179 AGGTTAAGAT
*
31958189 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
31958209 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
31958229 TGAGCTG
1 TGAGCTG
31958236 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:31964201 original size:13 final size:13
Alignment explanation
Indices: 31964183--31964217 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
31964173 CGGCTAACCT
31964183 ACATAATTAAATA
1 ACATAATTAAATA
31964196 ACATAATTAAATA
1 ACATAATTAAATA
*
31964209 AAATAATTA
1 ACATAATTA
31964218 TTCATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:31964480 original size:20 final size:21
Alignment explanation
Indices: 31964437--31964484 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
31964427 AAAAGAAATG
* *
31964437 AGCTGAAACGAGCTAAATTCA
1 AGCTCAAACGAGATAAATTCA
31964458 AGCTCAAACGAGATAAA-TCA
1 AGCTCAAACGAGATAAATTCA
31964478 AGCTCAA
1 AGCTCAA
31964485 GTGAGCTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.17
Consensus pattern (21 bp):
AGCTCAAACGAGATAAATTCA
Found at i:31965505 original size:43 final size:42
Alignment explanation
Indices: 31965402--31965506 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 42
31965392 GATTTGAGAT
* **
31965402 TTACATGTAAGACCATGTC-GGGACATCGGCATCACATCTGA
1 TTACATGTAAGACCATATCTGGGACAGAGGCATCACATCTGA
* * * *
31965443 TTTCGTGTAAGACCCTATCTGGGACAGAGGCATC-GATACTGAA
1 TTACATGTAAGACCATATCTGGGACAGAGGCATCACAT-CTG-A
31965486 TTACATGTAAGACCATATCTG
1 TTACATGTAAGACCATATCTG
31965507 AGAGTCGACA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
41 17 0.33
42 15 0.29
43 19 0.37
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (42 bp):
TTACATGTAAGACCATATCTGGGACAGAGGCATCACATCTGA
Found at i:31965603 original size:28 final size:28
Alignment explanation
Indices: 31965563--31965620 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
31965553 CTGTCTGATG
31965563 ATAGAGTACAAGATATGGGAAAGAATAT
1 ATAGAGTACAAGATATGGGAAAGAATAT
31965591 ATAGAGTACAAGATATGGGAAAGAATAT
1 ATAGAGTACAAGATATGGGAAAGAATAT
31965619 AT
1 AT
31965621 TAAACGTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.24, T:0.22
Consensus pattern (28 bp):
ATAGAGTACAAGATATGGGAAAGAATAT
Found at i:31968843 original size:64 final size:63
Alignment explanation
Indices: 31968738--31968945 Score: 184
Period size: 67 Copynumber: 3.2 Consensus size: 63
31968728 CATCATGTGT
* * *
31968738 ACAAGAGAGCTACAAGACATTATTATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGA-TA-TATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATG
31968803 CAG
62 -AG
* * * * * *
31968806 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGTGTGGTTCCAGGTGAAAGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGGTACTAAGTG---TACACCATG-
*
31968871 AA
62 AG
* * * * *
31968873 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGTG
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGAG
31968935 TACAAGAGAGC
1 -ACAAGAGAGC
31968946 CGAACTATAT
Statistics
Matches: 114, Mismatches: 22, Indels: 13
0.77 0.15 0.09
Matches are distributed among these distances:
63 17 0.15
64 28 0.25
65 2 0.02
66 25 0.22
67 29 0.25
68 13 0.11
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (63 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGAG
Found at i:31974953 original size:21 final size:22
Alignment explanation
Indices: 31974914--31974956 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
31974904 ATGCATACTC
31974914 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
31974936 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
31974957 TGAGCTCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.35, C:0.33, G:0.07, T:0.26
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Found at i:31980596 original size:6 final size:6
Alignment explanation
Indices: 31980587--31980626 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
31980577 CAATTTTTTC
* *
31980587 TCAATA TCAATA TCAATA TCAATA TCAATC TCAATC TCAA
1 TCAATA TCAATA TCAATA TCAATA TCAATA TCAATA TCAA
31980627 ATTCTTTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (6 bp):
TCAATA
Found at i:31980677 original size:21 final size:20
Alignment explanation
Indices: 31980633--31980677 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
31980623 TCAAATTCTT
*
31980633 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
31980653 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
31980674 TTTC
1 TTTC
31980678 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:31980679 original size:27 final size:26
Alignment explanation
Indices: 31980615--31980680 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
31980605 TCAATATCAA
**
31980615 TCTCAATCTCAAATTCTTTTTCTTTT
1 TCTCAATCTCATTTTCTTTTTCTTTT
*
31980641 TCTCACTCTCATTTTCTTTTT-TTCTT
1 TCTCAATCTCATTTTCTTTTTCTT-TT
*
31980667 CTCTCAATTTCATT
1 -TCTCAATCTCATT
31980681 CAAGATTCGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 2 0.06
26 20 0.61
27 11 0.33
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (26 bp):
TCTCAATCTCATTTTCTTTTTCTTTT
Found at i:31981600 original size:30 final size:31
Alignment explanation
Indices: 31981565--31981635 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
31981555 TCAATCACTT
**
31981565 TTTTTTTTTCAATTTTG-ATTTTTTTTCTTC
1 TTTTTTTTTCAATTCCGAATTTTTTTTCTTC
* *
31981595 TTTTTTTTTTAATTCCGAATTTTTTTTTTTC
1 TTTTTTTTTCAATTCCGAATTTTTTTTCTTC
31981626 TTTTTTTTTC
1 TTTTTTTTTC
31981636 TTCAATACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (31 bp):
TTTTTTTTTCAATTCCGAATTTTTTTTCTTC
Found at i:31981699 original size:15 final size:15
Alignment explanation
Indices: 31981679--31981728 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
31981669 GAATACAAAC
31981679 TTTTTTTTTT-GAAT
1 TTTTTTTTTTCGAAT
*
31981693 TTTTTTTTTTCAAAT
1 TTTTTTTTTTCGAAT
31981708 TTTTTTTTTTCGAAT
1 TTTTTTTTTTCGAAT
31981723 TTTTTT
1 TTTTTT
31981729 ATATTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
14 10 0.30
15 23 0.70
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.78
Consensus pattern (15 bp):
TTTTTTTTTTCGAAT
Found at i:31983958 original size:20 final size:20
Alignment explanation
Indices: 31983912--31983958 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31983902 AGCTCGTTTC
*
31983912 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
31983932 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
31983952 CAGCTCA
1 CAGCTCA
31983959 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:31984261 original size:20 final size:20
Alignment explanation
Indices: 31984238--31984284 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31984228 GGGTTAAGAT
*
31984238 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31984258 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31984278 TGAGCTG
1 TGAGCTG
31984285 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:31986932 original size:9 final size:9
Alignment explanation
Indices: 31986920--31986953 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
31986910 CTTTTCACTT
31986920 TTTTTTTTC
1 TTTTTTTTC
31986929 TTTTTTTTAC
1 TTTTTTTT-C
31986939 -TTTTTTTC
1 TTTTTTTTC
31986947 TTTTTTT
1 TTTTTTT
31986954 GCTCACTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.04
9 21 0.91
10 1 0.04
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:31986940 original size:21 final size:21
Alignment explanation
Indices: 31986911--31986971 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
31986901 CTCACAAGAC
31986911 TTTTCACTTTTTTTTTTCTTT
1 TTTTCACTTTTTTTTTTCTTT
*
31986932 TTTTTACTTTTTTTCTTT-TTT
1 TTTTCACTTTTTTT-TTTCTTT
**
31986953 TGCTCACTTCTTTTTTTTC
1 TTTTCACTT-TTTTTTTTC
31986972 GAATTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 25 0.76
22 8 0.24
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTCACTTTTTTTTTTCTTT
Found at i:31989612 original size:20 final size:19
Alignment explanation
Indices: 31989589--31989653 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
31989579 AAGCTCAAAC
31989589 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
31989609 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
31989629 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
31989649 GAGCT
1 GAGCT
31989654 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:31991470 original size:33 final size:33
Alignment explanation
Indices: 31991432--31991494 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
31991422 GATTACTCAC
31991432 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
31991465 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
31991495 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:31991533 original size:18 final size:18
Alignment explanation
Indices: 31991509--31991552 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
31991499 TCTTTTTTCG
* *
31991509 CTTTTTCTTTTTCAATTT
1 CTTTTTCATTCTCAATTT
*
31991527 TTTTTTCATTCTCAATTT
1 CTTTTTCATTCTCAATTT
31991545 CTTTTTCA
1 CTTTTTCA
31991553 ATTTTTTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTTTCATTCTCAATTT
Found at i:31991557 original size:26 final size:26
Alignment explanation
Indices: 31991512--31991577 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
31991502 TTTTTCGCTT
*
31991512 TTTCTTTTTCAATTTTTTTTTCATTCTCAA
1 TTTCTTTTTCAA-TTTTTATTC--T-TCAA
* *
31991542 TTTCTTTTTCAATTTTTTTTCTTCAT
1 TTTCTTTTTCAATTTTTATTCTTCAA
31991568 TTTCTTTTTC
1 TTTCTTTTTC
31991578 TTTCGTCATC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
26 13 0.37
27 1 0.03
29 9 0.26
30 12 0.34
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTCTTTTTCAATTTTTATTCTTCAA
Found at i:31991576 original size:44 final size:45
Alignment explanation
Indices: 31991493--31991577 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 45
31991483 AAGCTCTCTT
** *
31991493 TCAATTTCTTTTTTCGCTTTTTCTTTTTCAATTTTTTTTTCATTC
1 TCAATTTCTTTTTTCAATTTTTCTTTTTCAATTTCTTTTTCATTC
*
31991538 TCAATTTC-TTTTTCAATTTTT-TTTCTTCATTTTCTTTTTC
1 TCAATTTCTTTTTTCAATTTTTCTTT-TTCAATTTCTTTTTC
31991578 TTTCGTCATC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 3 0.09
44 24 0.69
45 8 0.23
ACGTcount: A:0.12, C:0.18, G:0.01, T:0.69
Consensus pattern (45 bp):
TCAATTTCTTTTTTCAATTTTTCTTTTTCAATTTCTTTTTCATTC
Found at i:31992675 original size:11 final size:11
Alignment explanation
Indices: 31992667--31992695 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
31992657 CTTATTTTCG
31992667 ATTTTTTTTGA
1 ATTTTTTTTGA
31992678 ATTTTTTTTGA
1 ATTTTTTTTGA
31992689 ATTTTTT
1 ATTTTTT
31992696 CTTTTTTTTA
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:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:31992781 original size:12 final size:12
Alignment explanation
Indices: 31992766--31992797 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
31992756 CCAACTCAAA
31992766 TTTTTTTTTGA-
1 TTTTTTTTTGAC
31992777 TTTTTTTTTGAC
1 TTTTTTTTTGAC
31992789 TTTTTTTTT
1 TTTTTTTTT
31992798 CGTTACGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTGAC
Found at i:31994330 original size:20 final size:19
Alignment explanation
Indices: 31994307--31994371 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
31994297 AAGCTCAAAC
31994307 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
31994327 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
31994347 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
31994367 GAGCT
1 GAGCT
31994372 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:31994868 original size:20 final size:20
Alignment explanation
Indices: 31994845--31994891 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31994835 GGGTTAAGAT
*
31994845 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31994865 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31994885 TGAGCTG
1 TGAGCTG
31994892 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:32002012 original size:23 final size:22
Alignment explanation
Indices: 32001961--32002012 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
32001951 CCTCATCTTT
*
32001961 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
32001983 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
32002006 TTCTTTT
1 TTCTTTT
32002013 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:32005867 original size:21 final size:22
Alignment explanation
Indices: 32005828--32005871 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
32005818 ATGCATACTC
32005828 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
32005850 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
32005871 C
1 C
32005872 GAGCTCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Done.