Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold302
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: 592491
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.31
Warning! 22277 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:3463 original size:17 final size:18
Alignment explanation
Indices: 3428--3465 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3418 CCCGGCGCAG
3428 AGGAACAAAACACGAACA
1 AGGAACAAAACACGAACA
3446 AGGAAGCAAAA-A-GAACA
1 AGGAA-CAAAACACGAACA
3463 AGG
1 AGG
3466 CTAACAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.61, C:0.16, G:0.24, T:0.00
Consensus pattern (18 bp):
AGGAACAAAACACGAACA
Found at i:3985 original size:26 final size:26
Alignment explanation
Indices: 3949--3999 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
3939 AGATTAAACA
*
3949 CTTAATTTGTTCTTTCCATCAAAGAT
1 CTTAACTTGTTCTTTCCATCAAAGAT
*
3975 CTTAACTTGTTCTTTCCATTAAAGA
1 CTTAACTTGTTCTTTCCATCAAAGA
4000 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (26 bp):
CTTAACTTGTTCTTTCCATCAAAGAT
Found at i:5815 original size:35 final size:35
Alignment explanation
Indices: 5726--5815 Score: 85
Period size: 35 Copynumber: 2.6 Consensus size: 35
5716 GTATATTCTA
* *
5726 TTTTGTCGATTTCTTAATCATATATATATCATTCT
1 TTTTGTCGATTTCTTAATCATATATATATCAATAT
* * * * *
5761 TTTTGTCG-TAATATAAATCAT-TAATGTATTAATAT
1 TTTTGTCGAT-TTCTTAATCATAT-ATATATCAATAT
5796 TTTTGTCGATTTCTTAATCA
1 TTTTGTCGATTTCTTAATCA
5816 CACATTTAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
34 2 0.05
35 39 0.93
36 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (35 bp):
TTTTGTCGATTTCTTAATCATATATATATCAATAT
Found at i:5968 original size:20 final size:21
Alignment explanation
Indices: 5943--5988 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
5933 TTTTTCATAA
*
5943 TTAAGTATTTAATTTA-GTGG
1 TTAAGTATTTAATTTATGTGC
* *
5963 TTAAGTGTTTTATTTATGTGC
1 TTAAGTATTTAATTTATGTGC
5984 TTAAG
1 TTAAG
5989 GTTTGGGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.26, C:0.02, G:0.20, T:0.52
Consensus pattern (21 bp):
TTAAGTATTTAATTTATGTGC
Found at i:6484 original size:273 final size:273
Alignment explanation
Indices: 5997--6537 Score: 922
Period size: 273 Copynumber: 2.0 Consensus size: 273
5987 AGGTTTGGGG
* *
5997 TTCAAGTCCCATTTTTGGAAATTTTGCTTTTTGTTTTGAATCAACCCTCACTTTCAAACTTTTGA
1 TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTCAAACTTTCGA
** **
6062 CTTAAGATTAATTTTGTGTAAACTTATATTAAGAATGAGCTTGTTGGTTTAATAGTTAAACTTTT
66 CTTAAGATTAATTTTGCATAAACTTATATTAAGAATGAGCTTACTGGTTTAATAGTTAAACTTTT
* * * *
6127 GTATACCCTTTGGTCTTATGTTCGAGTTTCTGCAAAAGCTATGAGAAAATATCTTATGCTAGTTT
131 GTATACCCTTTGCTCTTATGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
*
6192 ATAAAAATTAGTTTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAAATTT-TTTCACGTT
196 ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTT-AAAATTTCTTTCACGTT
6256 TTATTTCTTTCACA
260 TTATTTCTTTCACA
*
6270 TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTTAAACTTTCGA
1 TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTCAAACTTTCGA
* * *
6335 CTTAAGATTAATTTTGCATAAACTTGTGTTAAGAATGAGCTTACTGGTTTAATGGTTAAACTTTT
66 CTTAAGATTAATTTTGCATAAACTTATATTAAGAATGAGCTTACTGGTTTAATAGTTAAACTTTT
*
6400 GTATACCCTTTGCTCTTGTGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
131 GTATACCCTTTGCTCTTATGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
6465 ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
196 ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
6530 TATTTCTT
261 TATTTCTT
6538 CCTTTATCCT
Statistics
Matches: 251, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
272 7 0.03
273 244 0.97
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.46
Consensus pattern (273 bp):
TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTCAAACTTTCGA
CTTAAGATTAATTTTGCATAAACTTATATTAAGAATGAGCTTACTGGTTTAATAGTTAAACTTTT
GTATACCCTTTGCTCTTATGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
TATTTCTTTCACA
Found at i:7274 original size:42 final size:43
Alignment explanation
Indices: 7185--7275 Score: 105
Period size: 42 Copynumber: 2.1 Consensus size: 43
7175 ATGACATGGG
* * * * *
7185 TGTGTATCTAGACCGTGTGACTCTCTAACTTGAGTAACATGGT
1 TGTGTGTCTAGACCGTATAACTCTCTAACTTGAGTAACACGGC
*
7228 TGTGTGTC-AGACCGTATAACTCTCTAACTT-AGGTCACACGGC
1 TGTGTGTCTAGACCGTATAACTCTCTAACTTGA-GTAACACGGC
7270 TGTGTG
1 TGTGTG
7276 CCAGGTCGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.02
42 33 0.80
43 7 0.17
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (43 bp):
TGTGTGTCTAGACCGTATAACTCTCTAACTTGAGTAACACGGC
Found at i:9218 original size:20 final size:20
Alignment explanation
Indices: 9179--9224 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
9169 CCAATATGAT
*
9179 GTTCTTCAGGATTTCTTCAA
1 GTTCTTCAGAATTTCTTCAA
9199 GTTCTTCAGAAATTTC-TCAA
1 GTTCTTCAG-AATTTCTTCAA
9219 GATTCT
1 G-TTCT
9225 AAAAAGAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (20 bp):
GTTCTTCAGAATTTCTTCAA
Found at i:15934 original size:12 final size:12
Alignment explanation
Indices: 15917--15941 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15907 ACATCAATTC
15917 AATAATATACCA
1 AATAATATACCA
15929 AATAATATACCA
1 AATAATATACCA
15941 A
1 A
15942 TTGCATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAATATACCA
Found at i:16872 original size:19 final size:19
Alignment explanation
Indices: 16844--16901 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
16834 TACTAGCGTG
*
16844 CAAAACGCATCCTGGCGCA
1 CAAAATGCATCCTGGCGCA
* *
16863 -AAAAGTGCATACTGGCACA
1 CAAAA-TGCATCCTGGCGCA
*
16882 CAAAATACATCCTGGCGCA
1 CAAAATGCATCCTGGCGCA
16901 C
1 C
16902 GAAGCGCATA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 4 0.13
19 23 0.74
20 4 0.13
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (19 bp):
CAAAATGCATCCTGGCGCA
Found at i:16942 original size:19 final size:19
Alignment explanation
Indices: 16865--17026 Score: 85
Period size: 19 Copynumber: 8.4 Consensus size: 19
16855 CTGGCGCAAA
*
16865 AAGTGCATAC-TGGCACACA
1 AAGTGCAT-CTTGGCACACG
* * * *
16884 AAATACATCCTGGCGCACG
1 AAGTGCATCTTGGCACACG
* * *
16903 AAGCGCATATCTGGAACACG
1 AAGTGCATCT-TGGCACACG
*
16923 ATGTGCATCTTGGCACACG
1 AAGTGCATCTTGGCACACG
* *
16942 AAGTGCATAC-TGGCATACA
1 AAGTGCAT-CTTGGCACACG
* * **
16961 AAGTGCATCCTAGTGCACG
1 AAGTGCATCTTGGCACACG
* * * *
16980 AAGCGTATATCTGGCACATG
1 AAGTGCATCT-TGGCACACG
* *
17000 ATGTGTATCTTGGCACACG
1 AAGTGCATCTTGGCACACG
17019 AAGTGCAT
1 AAGTGCAT
17027 TATGAAGAAT
Statistics
Matches: 101, Mismatches: 37, Indels: 10
0.68 0.25 0.07
Matches are distributed among these distances:
18 2 0.02
19 72 0.71
20 27 0.27
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (19 bp):
AAGTGCATCTTGGCACACG
Found at i:16946 original size:77 final size:77
Alignment explanation
Indices: 16865--17026 Score: 243
Period size: 77 Copynumber: 2.1 Consensus size: 77
16855 CTGGCGCAAA
*
16865 AAGTGCATACTGGCACACAAAATACATCCTGGCGCACGAAGCGCATATCTGGAACACGATGTGCA
1 AAGTGCATACTGGCACACAAAATACATCCTAGCGCACGAAGCGCATATCTGGAACACGATGTGCA
16930 TCTTGGCACACG
66 TCTTGGCACACG
* * * * * * * *
16942 AAGTGCATACTGGCATACAAAGTGCATCCTAGTGCACGAAGCGTATATCTGGCACATGATGTGTA
1 AAGTGCATACTGGCACACAAAATACATCCTAGCGCACGAAGCGCATATCTGGAACACGATGTGCA
17007 TCTTGGCACACG
66 TCTTGGCACACG
17019 AAGTGCAT
1 AAGTGCAT
17027 TATGAAGAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (77 bp):
AAGTGCATACTGGCACACAAAATACATCCTAGCGCACGAAGCGCATATCTGGAACACGATGTGCA
TCTTGGCACACG
Found at i:17596 original size:2 final size:2
Alignment explanation
Indices: 17589--17613 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17579 CATATAATTA
17589 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17614 GGCTTACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21225 original size:11 final size:11
Alignment explanation
Indices: 21205--21246 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
21195 AAATTGCAAC
21205 AGAAAGAAAAA
1 AGAAAGAAAAA
21216 AGAAA-AAAAA
1 AGAAAGAAAAA
*
21226 TGAAAGAAAAA
1 AGAAAGAAAAA
*
21237 AGATAGAAAA
1 AGAAAGAAAA
21247 CTCTCTGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:21640 original size:132 final size:132
Alignment explanation
Indices: 21461--21741 Score: 413
Period size: 132 Copynumber: 2.1 Consensus size: 132
21451 ACAACTTCAA
* ***
21461 GGAGATAGGAA-TACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATTTGCCATCT
1 GGAGATA-GAATTACTGGCTTCAATGCACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCT
* * *
21525 TTGATCTACTCCACTACT-TCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGC
65 TCGATCTACTCCACTACTGT-CTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGC
*
21589 CTAG
129 CCAG
* *
21593 GGAGATAGAATTACTGGCTTCAATGCACTCCACTTTAACCTCAGGGAGGTAAAATCCACCCTCTT
1 GGAGATAGAATTACTGGCTTCAATGCACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTT
* * *
21658 CGATCTGCTCCACTACTGTCTAGGGAGATAATATCTGTAATATTCAATCTATTCTACTGCTGCCC
66 CGATCTACTCCACTACTGTCTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGCCC
21723 AG
131 AG
21725 GGAGATAGAATTACTGG
1 GGAGATAGAATTACTGG
21742 TCGATTTTCG
Statistics
Matches: 134, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
131 3 0.02
132 130 0.97
133 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (132 bp):
GGAGATAGAATTACTGGCTTCAATGCACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTT
CGATCTACTCCACTACTGTCTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGCCC
AG
Found at i:22673 original size:45 final size:44
Alignment explanation
Indices: 22602--22836 Score: 178
Period size: 45 Copynumber: 5.3 Consensus size: 44
22592 GCCAATACAT
* * *
22602 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTGTG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCGCCACCAGTATG
* * * *
22646 GCAAGACAAGATCTGGTATCTTTGATCTACTCCACTA-CAGTACAT-
1 G-AAGACAAGATCTGCTATCTTTGATCTACTTCGCCACCAGT--ATG
* * * * *
22691 GAAGACAAAATCT-ATTTTTTTCGATCTACTTCGCCACCAGTGTGG
1 GAAGACAAGATCTGCTATCTTT-GATCTACTTCGCCACCAGTAT-G
* * * * *
22736 GAAGACAAGATCTGGTACCTTTGATCTACTTC-ACGCTAGTACAT-
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCGCCACCAGT--ATG
* *
22780 GAAGATAAGATCTGCT-T-TCTGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCGCCACCAGTAT-G
22823 GAAGACAAGATCTG
1 GAAGACAAGATCTG
22837 TACAAGATCT
Statistics
Matches: 146, Mismatches: 32, Indels: 27
0.71 0.16 0.13
Matches are distributed among these distances:
41 2 0.01
42 12 0.08
43 24 0.16
44 46 0.32
45 56 0.38
46 6 0.04
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCGCCACCAGTATG
Found at i:22675 original size:89 final size:89
Alignment explanation
Indices: 22564--22836 Score: 381
Period size: 89 Copynumber: 3.1 Consensus size: 89
22554 TTAGGGAGAT
* * *
22564 AAGATCT-GTAATCTTCGATCTACTTTACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATC
1 AAGATCTGGT-ATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATC
*
22628 TACTTCGCCACCAGTGTGGCAAGAC
65 TACTTCGCCACCAGTGTGGGAAGAC
* ** * ** *
22653 AAGATCTGGTATCTTTGATCTACTCCACTACAGTACATGAAGACAAAATCTATTTTTTTCGATCT
1 AAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCT
22718 ACTTCGCCACCAGTGTGGGAAGAC
66 ACTTCGCCACCAGTGTGGGAAGAC
* * *
22742 AAGATCTGGTACCTTTGATCTACTTCACGCTAGTACATGAAGATAAGATCTGCTTTC-T-GATCT
1 AAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCT
*
22805 ACTTCGCCACCAGTATGGGAAGAC
66 ACTTCGCCACCAGTGTGGGAAGAC
22829 AAGATCTG
1 AAGATCTG
22837 TACAAGATCT
Statistics
Matches: 161, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
87 36 0.22
88 1 0.01
89 122 0.76
90 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (89 bp):
AAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCT
ACTTCGCCACCAGTGTGGGAAGAC
Found at i:22847 original size:42 final size:41
Alignment explanation
Indices: 22713--22839 Score: 112
Period size: 43 Copynumber: 3.0 Consensus size: 41
22703 TATTTTTTTC
*
22713 GATCTACTTCGCCACCAGTGTGGGAAGACAAGATCTGGTACCTTT
1 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCT-GTA-C--T
* * * *** * *
22758 GATCTACTTC-ACGCTAGTACATGAAGATAAGATCTGCTTTCT
1 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG--TACT
22800 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTAC
1 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTAC
22840 AAGATCTATT
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
41 2 0.03
42 11 0.18
43 20 0.32
44 18 0.29
45 11 0.18
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (41 bp):
GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTACT
Found at i:22926 original size:187 final size:178
Alignment explanation
Indices: 22564--23127 Score: 693
Period size: 178 Copynumber: 3.1 Consensus size: 178
22554 TTAGGGAGAT
* * * *
22564 AAGATCTGTAATCTTCGATCTACTTTACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCT
1 AAGATCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATAT
* * * * * * **
22629 ACTTCGCCACCAGTGTGGCAAGACAAGATCTGGTATCTTTGATCTACTCCACTACAGTACATGAA
66 ACTTCACCACCAATATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAA
* * * *
22694 GACAAAATCTA-TTTTTTTCGATCTACTTCGCCACCAGTGTGGGAAGAC
131 GACAAGATCTACTTTCTTT-GATCTGCTTCGCCACCAGTATGGGAAGAC
* * * * * *
22742 AAGATCTGGTACCTTTGATCTACTTCACGCTAGTACATGAAGATAAGATCTGCTTTC-T-GATCT
1 AAGATCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATAT
* * *
22805 ACTTCGCCACCAGTATGGGAAGACAAGATCTGTACAAGATCTATTGTCTTCGATCTACTTCACGC
66 ACTTCACCACCAATATGGGAAGACAAGATC--T----G-T-TA---TCTTTGATCTACTTCACGC
*
22870 CAGTATATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGAC
120 CAGTACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGAC
*
22929 AAGATCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATAT
1 AAGATCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATAT
* *
22994 ACTTCACCACCAATATGGGAAGATAAGATCTGTTATCTTTAATCTACTTCACGCCAGTACATGAA
66 ACTTCACCACCAATATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAA
* * * *
23059 GACAAGATCTGCTTTCTTCGATCTGTTTTGCCACCAGTATGGGAAGAC
131 GACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGAC
*
23107 AAGATCTATTATCTTTGATCT
1 AAGATCTGTTATCTTTGATCT
23128 TATCTATTTT
Statistics
Matches: 334, Mismatches: 38, Indels: 28
0.83 0.09 0.07
Matches are distributed among these distances:
176 33 0.10
177 1 0.00
178 141 0.42
181 2 0.01
182 2 0.01
183 1 0.00
184 2 0.01
187 114 0.34
188 7 0.02
189 31 0.09
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (178 bp):
AAGATCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATAT
ACTTCACCACCAATATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAA
GACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGAC
Found at i:22928 original size:45 final size:44
Alignment explanation
Indices: 22838--23127 Score: 244
Period size: 45 Copynumber: 6.5 Consensus size: 44
22828 CAAGATCTGT
* * * *
22838 ACAAGATCTATTGTCTTCGATCTACTTCACGCCAGTATATGAAG
1 ACAAGATCTATTATCTTTGATCTACTTCACACCAGTATAGGAAG
* * *
22882 ACAAGATCTACTT-TCTTTGATCTGCTTCGCCACCAGTATGGGAAG
1 ACAAGATCTA-TTATCTTTGATCTACTTC-ACACCAGTATAGGAAG
* * * * *
22927 ACAAGATCTGTTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTATTATCTTTGATCTACTTCACACCAGTATAGGAAG
* * * * * *
22971 ACAAGATCTGTTTTCTTCGATATACTTCACCACCAATATGGGAAG
1 ACAAGATCTATTATCTTTGATCTACTTCA-CACCAGTATAGGAAG
* * * * * *
23016 ATAAGATCTGTTATCTTTAATCTACTTCACGCCAGTACATGAAG
1 ACAAGATCTATTATCTTTGATCTACTTCACACCAGTATAGGAAG
* * ** *
23060 ACAAGATCTGCTT-TCTTCGATCTGTTTTGC-CACCAGTATGGGAAG
1 ACAAGATCT-ATTATCTTTGATCT-ACTT-CACACCAGTATAGGAAG
23105 ACAAGATCTATTATCTTTGATCT
1 ACAAGATCTATTATCTTTGATCT
23128 TATCTATTTT
Statistics
Matches: 195, Mismatches: 43, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
44 89 0.46
45 105 0.54
46 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (44 bp):
ACAAGATCTATTATCTTTGATCTACTTCACACCAGTATAGGAAG
Found at i:22959 original size:89 final size:89
Alignment explanation
Indices: 22564--23127 Score: 324
Period size: 89 Copynumber: 6.2 Consensus size: 89
22554 TTAGGGAGAT
* * * * *
22564 AAGATCTGTAATCTTCGATCTACTTTACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCT
1 AAGATCTATTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCT
* * *
22629 ACTTCGCCACCAGTGTGGCAAGAC
66 GCTTCGCCACCAGTATGGGAAGAC
** * ** * ** *
22653 AAGATCTGGTATCTTTGATCTACTCCACTACAGTACATGAAGACAAAATCTATTTTTTTCGATCT
1 AAGATCTATTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCT
* *
22718 ACTTCGCCACCAGTGTGGGAAGAC
66 GCTTCGCCACCAGTATGGGAAGAC
** * * *
22742 AAGATCTGGTACCTTTGATCTACTTCACGCTAGTACATGAAGATAAGATCTGCTTTC-T-GATCT
1 AAGATCTATTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCT
*
22805 ACTTCGCCACCAGTATGGGAAGAC
66 GCTTCGCCACCAGTATGGGAAGAC
** * * ** * * * * * *
22829 AAGATCTGTACAAGATCTATTG-TCTTCGATCTACTTCACG-CCA-GTATATGAAGA-CAAGATC
1 AAGATC--T--ATTATCT-TTGATCTAC-TTC-ACGCCA-GTACATGAAGA-CAAGATC-TGCT-
* * * * ** * * **
22890 TACTTTC--TTTG-ATCTGCTTCGCCACCA--GTATGGG
55 TTC-TTCGATCTGCTTC-GC--CACCAGTATGGGAAGAC
* * *
22924 AAGA-CAAGATCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTT
1 AAGATC----TAT--TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* * * * *
22988 CGATATACTTCACCACCAATATGGGAAGAT
60 CGATCTGCTTCGCCACCAGTATGGGAAGAC
* *
23018 AAGATCTGTTATCTTTAATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCT
1 AAGATCTATTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCT
* *
23083 GTTTTGCCACCAGTATGGGAAGAC
66 GCTTCGCCACCAGTATGGGAAGAC
23107 AAGATCTATTATCTTTGATCT
1 AAGATCTATTATCTTTGATCT
23128 TATCTATTTT
Statistics
Matches: 353, Mismatches: 91, Indels: 62
0.70 0.18 0.12
Matches are distributed among these distances:
87 34 0.10
88 1 0.00
89 213 0.60
91 9 0.03
92 17 0.05
93 13 0.04
94 28 0.08
95 23 0.07
96 10 0.03
97 5 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (89 bp):
AAGATCTATTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCT
GCTTCGCCACCAGTATGGGAAGAC
Found at i:23057 original size:276 final size:278
Alignment explanation
Indices: 22575--23113 Score: 803
Period size: 276 Copynumber: 1.9 Consensus size: 278
22565 AGATCTGTAA
* *
22575 TCTTCGATCTACTTTACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACC
* * *
22640 AGTGTGGCAAGACAAGATCTGGTATCTTTGATCTACTCCACTACAGTACATGAAGACAAAATCTA
66 AGTATGGCAAGACAAGATCTGGTATCTTTGATCTACTCCACGACAATACATGAAGACAAAATCTA
* * * * * *
22705 TTTTTTTCGATCTACTTCGCCACCAGTGTGGGAAGACAAGATCTGGTACCTTTGATCTACTTCAC
131 TTTTCTTCGATATACTTCACCACCAATATGGGAAGACAAGATCTGGTACCTTTAATCTACTTCAC
* *
22770 GCTAGTACATGAAGATAAGATCTGCTTTC-T-GATCTACTTCGCCACCAGTATGGGAAGACAAGA
196 GCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
22833 TCTGTACAAGATCTATTG
261 TCTGTACAAGATCTATTG
* * * *
22851 TCTTCGATCTACTTCACGCCAGTATATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACC
* * * * * *
22916 AGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
66 AGTATGGCAAGACAAGATCTGGTATCTTTGATCTACTCCACGACAATACATGAAGACAAAATCTA
* * *
22981 TTTTCTTCGATATACTTCACCACCAATATGGGAAGATAAGATCTGTTATCTTTAATCTACTTCAC
131 TTTTCTTCGATATACTTCACCACCAATATGGGAAGACAAGATCTGGTACCTTTAATCTACTTCAC
** *
23046 GCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGTTTTGCCACCAGTATGGGAAGACAAGA
196 GCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
23111 TCT
261 TCT
23114 ATTATCTTTG
Statistics
Matches: 232, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
276 198 0.85
277 1 0.00
278 33 0.14
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (278 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACC
AGTATGGCAAGACAAGATCTGGTATCTTTGATCTACTCCACGACAATACATGAAGACAAAATCTA
TTTTCTTCGATATACTTCACCACCAATATGGGAAGACAAGATCTGGTACCTTTAATCTACTTCAC
GCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
TCTGTACAAGATCTATTG
Found at i:23134 original size:19 final size:19
Alignment explanation
Indices: 23110--23146 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
23100 GGAAGACAAG
23110 ATCTATTATCTTTGATCTT
1 ATCTATTATCTTTGATCTT
*
23129 ATCTATTTTCTTTGATCT
1 ATCTATTATCTTTGATCT
23147 GCTTCGCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.16, G:0.05, T:0.59
Consensus pattern (19 bp):
ATCTATTATCTTTGATCTT
Found at i:23174 original size:64 final size:64
Alignment explanation
Indices: 23071--23191 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 64
23061 CAAGATCTGC
* * * *
23071 TTTCTTCGATCTGTTTTGCCACCAGTATGGGAAGACAAGATCTATTATCTTTGATCTTATCTAT
1 TTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTTATCTAT
* * *
23135 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCT
1 TTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCT
23192 ACTTCACGCC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (64 bp):
TTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTTATCTAT
Found at i:23263 original size:153 final size:153
Alignment explanation
Indices: 22976--23280 Score: 448
Period size: 153 Copynumber: 2.0 Consensus size: 153
22966 TGAAGACAAG
* * * *
22976 ATCTGTTTTCTTCGATATACTTCACCACCAATATGGGAAGATAAGATCTGTTATCTTTAATCTAC
1 ATCTATTTTCTTCGATATACTTCACCACCAATATGGGAAGACAAGATCTGGTATCTCTAATCTAC
* *
23041 TTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGTTTTGCCACCAGTATGGGAAGA
66 TTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGA
*
23106 CAAGATCTATTATCTTTGATCTT
131 CAAGATCTATTATCTCTGATCTT
* * * * * * *
23129 ATCTATTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTAC
1 ATCTATTTTCTTCGATATACTTCACCACCAATATGGGAAGACAAGATCTGGTATCTCTAATCTAC
* *
23194 TTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGG
66 TTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGA
* *
23259 CAAGATTTGTTATCTCTGATCT
131 CAAGATCTATTATCTCTGATCT
23281 ACTTCACGCC
Statistics
Matches: 134, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
153 134 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (153 bp):
ATCTATTTTCTTCGATATACTTCACCACCAATATGGGAAGACAAGATCTGGTATCTCTAATCTAC
TTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGA
CAAGATCTATTATCTCTGATCTT
Found at i:23264 original size:45 final size:44
Alignment explanation
Indices: 23135--23321 Score: 169
Period size: 44 Copynumber: 4.2 Consensus size: 44
23125 TCTTATCTAT
* * ** * *
23135 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGG
1 TTTCTTTGATCTACTTC-ACACCAGTACAGGAAGACAAGATCTGC
* * * *
23180 TATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
1 TTTCTTTGATCTACTTCACACCAGTACAGGAAGACAAGATCTGC
* * ** * *
23224 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATTTG-
1 TTTCTTTGATCTACTTC-ACACCAGTACAGGAAGACAAGATCTGC
* * *
23268 TTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
1 TT-TCTTTGATCTACTTCACACCAGTACAGGAAGACAAGATCTGC
23313 TTTCTTTGA
1 TTTCTTTGA
23322 ACCTGCTCCA
Statistics
Matches: 109, Mismatches: 30, Indels: 7
0.75 0.21 0.05
Matches are distributed among these distances:
44 61 0.56
45 48 0.44
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (44 bp):
TTTCTTTGATCTACTTCACACCAGTACAGGAAGACAAGATCTGC
Found at i:23286 original size:89 final size:89
Alignment explanation
Indices: 23135--23321 Score: 356
Period size: 89 Copynumber: 2.1 Consensus size: 89
23125 TCTTATCTAT
23135 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
1 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
23200 CCAGTACATGAAGACAAGATCTGC
66 CCAGTACATGAAGACAAGATCTGC
* *
23224 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATTTGTTATCTCTGATCTACTTCACG
1 TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
23289 CCAGTACATGAAGACAAGATCTGC
66 CCAGTACATGAAGACAAGATCTGC
23313 TTTCTTTGA
1 TTTCTTTGA
23322 ACCTGCTCCA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 96 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (89 bp):
TTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACG
CCAGTACATGAAGACAAGATCTGC
Found at i:25239 original size:13 final size:14
Alignment explanation
Indices: 25221--25269 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
25211 CCTTAGTCTC
25221 TCCATTTT-ACTTT
1 TCCATTTTCACTTT
*
25234 TCCATTTTTCAGTTT
1 TCCA-TTTTCACTTT
25249 T-CATTTTCACTTT
1 TCCATTTTCACTTT
*
25262 TTCATTTT
1 TCCATTTT
25270 TCATCTCGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 14 0.45
14 12 0.39
15 5 0.16
ACGTcount: A:0.14, C:0.20, G:0.02, T:0.63
Consensus pattern (14 bp):
TCCATTTTCACTTT
Found at i:25249 original size:7 final size:7
Alignment explanation
Indices: 25231--25273 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
25221 TCCATTTTAC
*
25231 TTTTCCA
1 TTTTTCA
25238 TTTTTCA
1 TTTTTCA
*
25245 GTTTTCA
1 TTTTTCA
25252 -TTTTCA
1 TTTTTCA
25258 CTTTTTCA
1 -TTTTTCA
25266 TTTTTCA
1 TTTTTCA
25273 T
1 T
25274 CTCGTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 6 0.19
7 20 0.62
8 6 0.19
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.65
Consensus pattern (7 bp):
TTTTTCA
Found at i:25253 original size:14 final size:15
Alignment explanation
Indices: 25231--25272 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
25221 TCCATTTTAC
25231 TTTTCCATTTTTCA-G
1 TTTT-CATTTTTCACG
*
25246 TTTTCA-TTTTCACT
1 TTTTCATTTTTCACG
25260 TTTTCATTTTTCA
1 TTTTCATTTTTCA
25273 TCTCGTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.25
14 8 0.33
15 10 0.42
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTTCATTTTTCACG
Found at i:30087 original size:13 final size:13
Alignment explanation
Indices: 30069--30099 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
30059 CTCAATTTTC
*
30069 TCTTTTCTTTCTT
1 TCTTTTCCTTCTT
30082 TCTTTTCCTTCTT
1 TCTTTTCCTTCTT
30095 TCTTT
1 TCTTT
30100 CTCTGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TCTTTTCCTTCTT
Found at i:31039 original size:31 final size:30
Alignment explanation
Indices: 30859--31288 Score: 170
Period size: 31 Copynumber: 14.1 Consensus size: 30
30849 NNNNNNNNNN
* **
30859 ATATACGAATCAATTCGGCAACT-TATATTC
1 ATATACGAATCAATTCGACAA-TATATAACC
*
30889 ATATAC-AATTCAATTTCAACAAATATATAA-C
1 ATATACGAA-TCAA-TTCGAC-AATATATAACC
* * * *
30920 ATGTACGAATTAATTTC-AGCAATGTACAACC
1 ATATACGAATCAA-TTCGA-CAATATATAACC
* *
30951 ATATACGAATCAATT-TAGCAACT-TATATCC
1 ATATACGAATCAATTCGA-CAA-TATATAACC
* * * *
30981 ATATATC-AAACAATTCGGCCATGTATAACC
1 ATATA-CGAATCAATTCGACAATATATAACC
* *
31011 ATACACGAATCAAGTTCGACAATATATAATC
1 ATATACGAATCAA-TTCGACAATATATAACC
* * * **
31042 ATATACAAATCCAATTCGGC-ATCCTATATTC
1 ATATACGAAT-CAATTCGACAAT-ATATAACC
*
31073 ATAAAC-AATTCAATATCGACAATATATAACC
1 ATATACGAA-TCAAT-TCGACAATATATAACC
* * * ** *
31104 ATGTACAAATTAATTTC-AGCAAGGTACAA-C
1 ATATACGAATCAA-TTCGA-CAATATATAACC
*
31134 ATATACGAATCAATTCGACAACT-TATATCC
1 ATATACGAATCAATTCGACAA-TATATAACC
* * * **
31164 ATATACCAAACAATTCGGCAAGGTATAACC
1 ATATACGAATCAATTCGACAATATATAACC
* *
31194 AT-TCACGAATCAAGTTCGGCAATATATAATC
1 ATAT-ACGAATCAA-TTCGACAATATATAACC
* * * **
31225 ATATACAAATCCAATTCGGC-ATCCTATATTC
1 ATATACGAAT-CAATTCGACAAT-ATATAACC
*
31256 ATAAAC-AATTCAATATCGACAATATATAACC
1 ATATACGAA-TCAAT-TCGACAATATATAACC
31287 AT
1 AT
31289 GTAAAAATTA
Statistics
Matches: 304, Mismatches: 62, Indels: 67
0.70 0.14 0.15
Matches are distributed among these distances:
29 14 0.05
30 122 0.40
31 146 0.48
32 22 0.07
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (30 bp):
ATATACGAATCAATTCGACAATATATAACC
Found at i:31192 original size:183 final size:184
Alignment explanation
Indices: 30859--31304 Score: 711
Period size: 183 Copynumber: 2.4 Consensus size: 184
30849 NNNNNNNNNN
* * * * * *
30859 ATATACGAAT-CAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAAATATATAA-CAT
1 ATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGAC-AATATATAACCAT
* * * *
30922 GTACGAATTAATTTCAGCAATGTACAACCATATACGAATCAATTTAGCAACTTATATCCATATAT
65 GTACAAATTAATTTCAGCAAGGTACAACCATATACGAATCAATTGAGCAACTTATATCCATATAC
* *
30987 CAAACAATTCGGCCATGTATAACCATACACGAATCAAGTTCGACAATATATAATC
130 CAAACAATTCGGCAAGGTATAACCATACACGAATCAAGTTCGACAATATATAATC
31042 ATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCATG
1 ATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCATG
31107 TACAAATTAATTTCAGCAAGGTACAA-CATATACGAATCAATTCGA-CAACTTATATCCATATAC
66 TACAAATTAATTTCAGCAAGGTACAACCATATACGAATCAATT-GAGCAACTTATATCCATATAC
* *
31170 CAAACAATTCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAATC
130 CAAACAATTCGGCAAGGTATAACCATACACGAATCAAGTTCGACAATATATAATC
31225 ATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCATG
1 ATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCATG
*
31290 TAAAAATTAATTTCA
66 TACAAATTAATTTCA
31305 ACAATGTATA
Statistics
Matches: 245, Mismatches: 15, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
183 181 0.74
184 64 0.26
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (184 bp):
ATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCATG
TACAAATTAATTTCAGCAAGGTACAACCATATACGAATCAATTGAGCAACTTATATCCATATACC
AAACAATTCGGCAAGGTATAACCATACACGAATCAAGTTCGACAATATATAATC
Found at i:31279 original size:62 final size:60
Alignment explanation
Indices: 30859--31284 Score: 237
Period size: 62 Copynumber: 7.0 Consensus size: 60
30849 NNNNNNNNNN
* * * *
30859 ATATACGAATCAATTCGGCAACTTATATTCATATAC-AATTCAATTTCAACAAATATATAA-C
1 ATATACAAATCAATTCGGCAACCTATATTCATAAACGAA-TCAA-TTCGAC-AATATATAATC
* * * * ** * ** * *
30920 ATGTACGAATTAATTTCAGCAATGTACAACCATATACGAATCAATT-TAGCAACT-TAT-ATCC
1 ATATACAAATCAA-TTCGGCAACCTATATTCATAAACGAATCAATTCGA-CAA-TATATAAT-C
* ** ** *
30981 ATATATCAAA-CAATTCGGCCATGTATAACCATACACGAATCAAGTTCGACAATATATAATC
1 ATATA-CAAATCAATTCGGCAACCTATATTCATAAACGAATCAA-TTCGACAATATATAATC
* *
31042 ATATACAAATCCAATTCGGCATCCTATATTCATAAAC-AATTCAATATCGACAATATATAACC
1 ATATACAAAT-CAATTCGGCAACCTATATTCATAAACGAA-TCAAT-TCGACAATATATAATC
* * * ** * * *
31104 ATGTACAAATTAATTTCAGCAAGGTACA-ACATATACGAATCAATTCGACAACT-TAT-ATCC
1 ATATACAAATCAA-TTCGGCAACCTATATTCATAAACGAATCAATTCGACAA-TATATAAT-C
** ** ** *
31164 ATATACCAAA-CAATTCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAATC
1 ATATA-CAAATCAATTCGGCAACCTATATTCATAAACGAATCAA-TTCGACAATATATAATC
*
31225 ATATACAAATCCAATTCGGCATCCTATATTCATAAAC-AATTCAATATCGACAATATATAA
1 ATATACAAAT-CAATTCGGCAACCTATATTCATAAACGAA-TCAAT-TCGACAATATATAA
31285 CCATGTAAAA
Statistics
Matches: 286, Mismatches: 51, Indels: 55
0.73 0.13 0.14
Matches are distributed among these distances:
59 14 0.05
60 71 0.25
61 76 0.27
62 123 0.43
63 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.29
Consensus pattern (60 bp):
ATATACAAATCAATTCGGCAACCTATATTCATAAACGAATCAATTCGACAATATATAATC
Found at i:35220 original size:31 final size:30
Alignment explanation
Indices: 35182--35867 Score: 279
Period size: 31 Copynumber: 22.4 Consensus size: 30
35172 GGCTGTTACA
*
35182 TCGGCAATGTATAACCATTTACGAATCAAGT
1 TCGGCAATGTATAACCATATACGAATCAA-T
* * *
35213 TCGGCAATGTATAATCATACACAAATCAAAT
1 TCGGCAATGTATAACCATATACGAATC-AAT
* * **
35244 TCGGCATTCTATATTCATA-ATC-AATTCAAT
1 TCGGCAATGTATAACCATATA-CGAA-TCAAT
* * * * *
35274 GTTGACAATATATAACCATGTACGAATTAATT
1 -TCGGCAATGTATAACCATATACGAATCAA-T
* *
35306 TCAGCAATGTACAACCATATACGAATCAAT
1 TCGGCAATGTATAACCATATACGAATCAAT
** * *
35336 TTAGCAACT-TATATCCATATATC-AAACAAT
1 TCGGCAA-TGTATAACCATATA-CGAATCAAT
*
35366 TCGGCAATGTATAACCATACACGAATCAAGT
1 TCGGCAATGTATAACCATATACGAATCAA-T
* * * *
35397 TCGACAATATATAATCATATACAAATCCAAT
1 TCGGCAATGTATAACCATATACGAAT-CAAT
* ** * *
35428 TCGGC-ATCCTATATTCATAAAC-AATTCAAA
1 TCGGCAAT-GTATAACCATATACGAA-TCAAT
* * * * *
35458 TCGACAATATATAACCATGTACAAATTAATT
1 TCGGCAATGTATAACCATATACGAATCAA-T
* * *
35489 TCAGCAAGGTACAA-CATATACGAATCAAT
1 TCGGCAATGTATAACCATATACGAATCAAT
* * * *
35518 TCGACAACT-TATATCCATATACCAAACAAT
1 TCGGCAA-TGTATAACCATATACGAATCAAT
*
35548 TCGGCAAGGTATAACCAT-TCACGAATCAAGT
1 TCGGCAATGTATAACCATAT-ACGAATCAA-T
* * *
35579 TCGGCAATATATAATCATATACAAATCCAAT
1 TCGGCAATGTATAACCATATACGAAT-CAAT
* ** *
35610 TCGGC-ATCCTATATTCATAAAC-AATTCAAT
1 TCGGCAAT-GTATAACCATATACGAA-TCAAT
* * * * *
35640 ATCGACAATATATAACCATGTACAAATTAAT
1 -TCGGCAATGTATAACCATATACGAATCAAT
* * *
35671 ATCAGCAAGGTACAA-CATATACGAATCAAT
1 -TCGGCAATGTATAACCATATACGAATCAAT
* * * * *
35701 TCGACAACT-TACATCCATATACCAAACAAT
1 TCGGCAA-TGTATAACCATATACGAATCAAT
** * *
35731 TCAACAAGGTATAACCAT-TCATGAATCAAGT
1 TCGGCAATGTATAACCATAT-ACGAATCAA-T
* * * *
35762 CCGGCAATATATAATCATATACAAATCCAAT
1 TCGGCAATGTATAACCATATACGAAT-CAAT
* * ** *
35793 TCAGC-ATCCTATATTCATAAAC-AATTCAAT
1 TCGGCAAT-GTATAACCATATACGAA-TCAAT
* * * *
35823 ATCGACAATATATAACCATGTACGAATTAATT
1 -TCGGCAATGTATAACCATATACGAATCAA-T
*
35855 TCAGCAATGTATA
1 TCGGCAATGTATA
35868 TAACATTTAT
Statistics
Matches: 484, Mismatches: 128, Indels: 86
0.69 0.18 0.12
Matches are distributed among these distances:
29 22 0.05
30 177 0.37
31 259 0.54
32 26 0.05
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (30 bp):
TCGGCAATGTATAACCATATACGAATCAAT
Found at i:35382 original size:60 final size:60
Alignment explanation
Indices: 35182--35867 Score: 374
Period size: 62 Copynumber: 11.2 Consensus size: 60
35172 GGCTGTTACA
* * * *
35182 TCGGCAATGTATAACCATTTACGAATCAAGTTCGGCAATGTATAAT-CATACACAAATCAAAT
1 TCGGCAATGTATAACCATATACGAATCAA-TTCGACAATATAT-ATCCATATACAAATC-AAT
* * ** * * * * *
35244 TCGGCATTCTATATTCATA-ATC-AATTCAATGTTGACAATATATAACCATGTACGAATTAATT
1 TCGGCAATGTATAACCATATA-CGAA-TCAAT-TCGACAATATATATCCATATACAAATCAA-T
* * *
35306 TCAGCAATGTACAACCATATACGAATCAATT-TAGCAACT-TATATCCATATATCAAA-CAAT
1 TCGGCAATGTATAACCATATACGAATCAATTCGA-CAA-TATATATCCATATA-CAAATCAAT
*
35366 TCGGCAATGTATAACCATACACGAATCAAGTTCGACAATATATAAT-CATATACAAATCCAAT
1 TCGGCAATGTATAACCATATACGAATCAA-TTCGACAATATAT-ATCCATATACAAAT-CAAT
* ** * * * * *
35428 TCGGC-ATCCTATATTCATAAAC-AATTCAAATCGACAATATATAACCATGTACAAATTAATT
1 TCGGCAAT-GTATAACCATATACGAA-TCAATTCGACAATATATATCCATATACAAATCAA-T
* * *
35489 TCAGCAAGGTACAA-CATATACGAATCAATTCGACAACT-TATATCCATATACCAAA-CAAT
1 TCGGCAATGTATAACCATATACGAATCAATTCGACAA-TATATATCCATATA-CAAATCAAT
* *
35548 TCGGCAAGGTATAACCAT-TCACGAATCAAGTTCGGCAATATATAAT-CATATACAAATCCAAT
1 TCGGCAATGTATAACCATAT-ACGAATCAA-TTCGACAATATAT-ATCCATATACAAAT-CAAT
* ** * * * *
35610 TCGGC-ATCCTATATTCATAAAC-AATTCAATATCGACAATATATAACCATGTACAAATTAAT
1 TCGGCAAT-GTATAACCATATACGAA-TCAAT-TCGACAATATATATCCATATACAAATCAAT
* * * *
35671 ATCAGCAAGGTACAA-CATATACGAATCAATTCGACAACT-TACATCCATATACCAAA-CAAT
1 -TCGGCAATGTATAACCATATACGAATCAATTCGACAA-TATATATCCATATA-CAAATCAAT
** * * * *
35731 TCAACAAGGTATAACCAT-TCATGAATCAAGTCCGGCAATATATAAT-CATATACAAATCCAAT
1 TCGGCAATGTATAACCATAT-ACGAATCAA-TTCGACAATATAT-ATCCATATACAAAT-CAAT
* * ** * * * * *
35793 TCAGC-ATCCTATATTCATAAAC-AATTCAATATCGACAATATATAACCATGTACGAATTAATT
1 TCGGCAAT-GTATAACCATATACGAA-TCAAT-TCGACAATATATATCCATATACAAATCAA-T
*
35855 TCAGCAATGTATA
1 TCGGCAATGTATA
35868 TAACATTTAT
Statistics
Matches: 481, Mismatches: 88, Indels: 110
0.71 0.13 0.16
Matches are distributed among these distances:
59 27 0.06
60 117 0.24
61 139 0.29
62 192 0.40
63 6 0.01
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (60 bp):
TCGGCAATGTATAACCATATACGAATCAATTCGACAATATATATCCATATACAAATCAAT
Found at i:35648 original size:183 final size:183
Alignment explanation
Indices: 35182--35861 Score: 1112
Period size: 183 Copynumber: 3.7 Consensus size: 183
35172 GGCTGTTACA
* * * * *
35182 TCGGCAATGTATAACCATTTACGAATCAAGTTCGGCAATGTATAATCATACACAAATCAAATTCG
1 TCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAATCATATACAAATCCAATTCG
* * * * *
35247 GCATTCTATATTCATAATCAATTCAATGTTGACAATATATAACCATGTACGAATTAATTTCAGCA
66 GCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCATGTACAAATTAATTTCAGCA
* * *
35312 ATGTACAACCATATACGAATCAATT-TAGCAACTTATATCCATATATCAAACAAT
131 AGGTACAA-CATATACGAATCAATTCGA-CAACTTATATCCATATACCAAACAAT
* * *
35366 TCGGCAATGTATAACCATACACGAATCAAGTTCGACAATATATAATCATATACAAATCCAATTCG
1 TCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAATCATATACAAATCCAATTCG
35431 GCATCCTATATTCATAAACAATTCAA-ATCGACAATATATAACCATGTACAAATTAATTTCAGCA
66 GCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCATGTACAAATTAATTTCAGCA
35495 AGGTACAACATATACGAATCAATTCGACAACTTATATCCATATACCAAACAAT
131 AGGTACAACATATACGAATCAATTCGACAACTTATATCCATATACCAAACAAT
35548 TCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAATCATATACAAATCCAATTCG
1 TCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAATCATATACAAATCCAATTCG
*
35613 GCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCATGTACAAATTAATATCAGCA
66 GCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCATGTACAAATTAATTTCAGCA
*
35678 AGGTACAACATATACGAATCAATTCGACAACTTACATCCATATACCAAACAAT
131 AGGTACAACATATACGAATCAATTCGACAACTTATATCCATATACCAAACAAT
** * * *
35731 TCAACAAGGTATAACCATTCATGAATCAAGTCCGGCAATATATAATCATATACAAATCCAATTCA
1 TCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAATCATATACAAATCCAATTCG
*
35796 GCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCATGTACGAATTAATTTCAGCA
66 GCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCATGTACAAATTAATTTCAGCA
35861 A
131 A
35862 TGTATATAAC
Statistics
Matches: 468, Mismatches: 26, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
182 129 0.28
183 256 0.55
184 83 0.18
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (183 bp):
TCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAATCATATACAAATCCAATTCG
GCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCATGTACAAATTAATTTCAGCA
AGGTACAACATATACGAATCAATTCGACAACTTATATCCATATACCAAACAAT
Found at i:37633 original size:100 final size:100
Alignment explanation
Indices: 37460--37659 Score: 382
Period size: 100 Copynumber: 2.0 Consensus size: 100
37450 AAATTTCATC
37460 AATTTATCAATCTAACAAGCGGATTTTTTCATATTTGTCATTGCTTATTAAAAAAATCCAACAAA
1 AATTTATCAATCTAACAAGCGGATTTTTTCATATTTGTCATTGCTTATTAAAAAAATCCAACAAA
37525 AATCACAAAGAAAACCTTCCCAATTTTTCTTGTGT
66 AATCACAAAGAAAACCTTCCCAATTTTTCTTGTGT
* *
37560 AATTTATCAATCTAACAAGTGGGTTTTTTCATATTTGTCATTGCTTATTAAAAAAATCCAACAAA
1 AATTTATCAATCTAACAAGCGGATTTTTTCATATTTGTCATTGCTTATTAAAAAAATCCAACAAA
37625 AATCACAAAGAAAACCTTCCCAATTTTTCTTGTGT
66 AATCACAAAGAAAACCTTCCCAATTTTTCTTGTGT
37660 GAGCCAAGGC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (100 bp):
AATTTATCAATCTAACAAGCGGATTTTTTCATATTTGTCATTGCTTATTAAAAAAATCCAACAAA
AATCACAAAGAAAACCTTCCCAATTTTTCTTGTGT
Found at i:37860 original size:26 final size:25
Alignment explanation
Indices: 37809--37861 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
37799 CTCTTATGAG
* *
37809 TTAATAAATTCTTTTTAAGTTTTTT
1 TTAATAAATTCTCTTGAAGTTTTTT
*
37834 TTAATAAATTTCTCTTGAA-TTTCTT
1 TTAATAAA-TTCTCTTGAAGTTTTTT
37859 TTA
1 TTA
37862 GAAGAGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.60
Consensus pattern (25 bp):
TTAATAAATTCTCTTGAAGTTTTTT
Found at i:37980 original size:22 final size:22
Alignment explanation
Indices: 37947--37995 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
37937 TAATCGTAAA
*
37947 TTTATTATTTTATTTTATTTAT
1 TTTATTATTTTATTTTAATTAT
37969 TTTAGTTA-TTTATTTTAATTAT
1 TTTA-TTATTTTATTTTAATTAT
37991 TTTAT
1 TTTAT
37996 CTGACTTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.84
23 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTATTATTTTATTTTAATTAT
Found at i:38081 original size:13 final size:13
Alignment explanation
Indices: 38063--38091 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38053 CCCTAAGTCA
38063 AATCCGTGACTTG
1 AATCCGTGACTTG
38076 AATCCGTGACTTG
1 AATCCGTGACTTG
38089 AAT
1 AAT
38092 AAACTTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (13 bp):
AATCCGTGACTTG
Found at i:38709 original size:12 final size:12
Alignment explanation
Indices: 38686--38719 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38676 TCTCAAGCAG
*
38686 TGAGGTTGGGGA
1 TGAGGATGGGGA
*
38698 TGGGGATGGGGA
1 TGAGGATGGGGA
38710 TGAGGATGGG
1 TGAGGATGGG
38720 TGTGGATGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.62, T:0.21
Consensus pattern (12 bp):
TGAGGATGGGGA
Found at i:39272 original size:29 final size:28
Alignment explanation
Indices: 39240--39345 Score: 158
Period size: 29 Copynumber: 3.7 Consensus size: 28
39230 AAAAATAAAA
*
39240 ATTTACCAAAATAGTACAACTTTTTTTTT
1 ATTTACCAAAATA-TACAAATTTTTTTTT
*
39269 ATTTACGAAAATATTACAAATTTTTTTTT
1 ATTTACCAAAATA-TACAAATTTTTTTTT
*
39298 ATTTACCAAAATATATAAATTTTTTTTT
1 ATTTACCAAAATATACAAATTTTTTTTT
39326 ATTTACCAAAATATATCAAA
1 ATTTACCAAAATATA-CAAA
39346 AAAAAAACAA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
28 29 0.41
29 41 0.59
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (28 bp):
ATTTACCAAAATATACAAATTTTTTTTT
Found at i:39431 original size:27 final size:27
Alignment explanation
Indices: 39401--39478 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
39391 CCCCAATGGT
*
39401 ATTGGCGGCACCAAAGGTGCCAAA-TAA
1 ATTGGCGGCACCAATGGTGCCAAAGT-A
* * *
39428 ATTGGTGGCACCATTGGTGCCAAAGTC
1 ATTGGCGGCACCAATGGTGCCAAAGTA
39455 ATTGGCGGCACC-ATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
39479 GGAAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 11 0.25
27 32 0.73
28 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.19
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGTA
Found at i:39566 original size:19 final size:19
Alignment explanation
Indices: 39544--39580 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39534 ATTCTCCTTC
* *
39544 AACTCTTTTTTTATTTAAT
1 AACTCTATTTTAATTTAAT
39563 AACTCTATTTTAATTTAA
1 AACTCTATTTTAATTTAA
39581 ATTAAGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (19 bp):
AACTCTATTTTAATTTAAT
Found at i:39978 original size:20 final size:19
Alignment explanation
Indices: 39939--39979 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
39929 ACTTAATAGT
* *
39939 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
39958 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
39978 TT
1 TT
39980 GAAGGGGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:40229 original size:37 final size:37
Alignment explanation
Indices: 40187--40257 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
40177 AGTATTACTT
*
40187 AATAGTTTATTAAATTAAAATAGATTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
40224 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
40258 AAAAAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:40262 original size:19 final size:19
Alignment explanation
Indices: 40187--40261 Score: 102
Period size: 18 Copynumber: 4.1 Consensus size: 19
40177 AGTATTACTT
40187 AATAG-TTTATTAAATTAA
1 AATAGATTTATTAAATTAA
* *
40205 AATAGATTTATTAAATGAG
1 AATAGATTTATTAAATTAA
40224 AATAG-TTTATTAAATTAA
1 AATAGATTTATTAAATTAA
*
40242 AATAGAGTTATTAAA-TAA
1 AATAGATTTATTAAATTAA
40260 AA
1 AA
40262 AAATGAGTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
18 26 0.52
19 24 0.48
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (19 bp):
AATAGATTTATTAAATTAA
Found at i:40269 original size:20 final size:19
Alignment explanation
Indices: 40193--40270 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 19
40183 ACTTAATAGT
* * *
40193 TTATTAAATTAAAATAGAT
1 TTATTAAATAAAAAAAGAG
* * * *
40212 TTATTAAATGAGAATAG-T
1 TTATTAAATAAAAAAAGAG
* *
40230 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
40249 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
40269 TT
1 TT
40271 GAAGGGGAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
18 16 0.32
19 29 0.58
20 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:40384 original size:27 final size:26
Alignment explanation
Indices: 40335--40412 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 26
40325 ATTTTTTTCC
40335 CTTTGGCACCATGGTGCCGCCAATGA
1 CTTTGGCACCATGGTGCCGCCAATGA
* *
40361 CTTTGGCACCAATGGTGCCACCAATTTA
1 CTTTGGCACC-ATGGTGCCGCCAA-TGA
*
40389 -TTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACC-ATGGTGCCGCCAAT
40413 ACCATTGGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
26 11 0.24
27 32 0.71
28 2 0.04
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.28
Consensus pattern (26 bp):
CTTTGGCACCATGGTGCCGCCAATGA
Found at i:40532 original size:28 final size:28
Alignment explanation
Indices: 40474--40571 Score: 146
Period size: 29 Copynumber: 3.5 Consensus size: 28
40464 TTTTTTATAT
40474 ATATTTTGGTAAAT-AAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
40500 TATATTTTGGTAAATAAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAAAAAAAAGTTGTA
*
40529 ATATTTTCGTAAATAAAAAAAAAGTTGTA
1 ATATTTTGGTAAAT-AAAAAAAAGTTGTA
*
40558 ATATTTTAGTAAAT
1 ATATTTTGGTAAAT
40572 TTTTATTTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
27 14 0.21
28 23 0.35
29 29 0.44
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:42028 original size:18 final size:18
Alignment explanation
Indices: 41998--42048 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
41988 TAGTTTACCC
* *
41998 TTTT-TATATTTTTGTAG
1 TTTTATATAATTTTGTAA
42015 TTTTATATAATTTTTTGTAA
1 TTTTATATAA--TTTTGTAA
*
42035 TTTTATATTATTTT
1 TTTTATATAATTTT
42049 TTTGATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 4 0.14
18 8 0.29
20 16 0.57
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTATATAATTTTGTAA
Found at i:42031 original size:20 final size:20
Alignment explanation
Indices: 42006--42050 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
41996 CCTTTTTATA
*
42006 TTTTTGTAGTTTTATATAAT
1 TTTTTGTAATTTTATATAAT
*
42026 TTTTTGTAATTTTATATTAT
1 TTTTTGTAATTTTATATAAT
42046 TTTTT
1 TTTTT
42051 TGATTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTTTGTAATTTTATATAAT
Found at i:42122 original size:29 final size:29
Alignment explanation
Indices: 42057--42111 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
42047 TTTTTGATTA
*
42057 ATTTGTAACAATATTTTTTGCACTTTTCC
1 ATTTTTAACAATATTTTTTGCACTTTTCC
42086 ATTTTTAACAAT-TTTTTT-CACTTTTC
1 ATTTTTAACAATATTTTTTGCACTTTTC
42112 TATATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 8 0.32
28 6 0.24
29 11 0.44
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (29 bp):
ATTTTTAACAATATTTTTTGCACTTTTCC
Found at i:42128 original size:27 final size:26
Alignment explanation
Indices: 42066--42128 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
42056 AATTTGTAAC
42066 AATATTTTTTGCACTTTTCCATTTTT
1 AATATTTTTTGCACTTTTCCATTTTT
* * *
42092 AACAATTTTTTTCACTTTTCTATATTTTT
1 AA-TATTTTTTGCACTTTTC--CATTTTT
42121 AATATTTT
1 AATATTTT
42129 AAATAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 2 0.07
27 15 0.50
28 5 0.17
29 8 0.27
ACGTcount: A:0.24, C:0.13, G:0.02, T:0.62
Consensus pattern (26 bp):
AATATTTTTTGCACTTTTCCATTTTT
Found at i:43483 original size:43 final size:43
Alignment explanation
Indices: 43423--43570 Score: 215
Period size: 43 Copynumber: 3.4 Consensus size: 43
43413 TGTCCCAAAC
* ***
43423 ATGGTCTTACATGGAAATCTTGTATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACA-CGAAATCTCAAATCGATGCCAATAGCCCAGCT
* * *
43467 ATAGTCTTACATGAAATCTCAAATCGATGCCAATAGCCCAGTT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
*
43510 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCGCAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
43553 ATGGTCTTACACGAAATC
1 ATGGTCTTACACGAAATC
43571 ACACCTCGGA
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
43 84 0.89
44 10 0.11
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:43785 original size:31 final size:31
Alignment explanation
Indices: 43680--43788 Score: 166
Period size: 31 Copynumber: 3.5 Consensus size: 31
43670 AACTAGTCTC
* * *
43680 AATTCGGCAATATATATCCATATACAAATCA
1 AATTCGACAATGTATATCTATATACAAATCA
*
43711 AATTCGACAATGAATATCTATATACAAATCA
1 AATTCGACAATGTATATCTATATACAAATCA
43742 AATTCGACAATGTATATCTATATACAAATCA
1 AATTCGACAATGTATATCTATATACAAATCA
43773 AATTCGGA-AATGTATA
1 AATTC-GACAATGTATA
43789 AAACATATAC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 70 0.97
32 2 0.03
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (31 bp):
AATTCGACAATGTATATCTATATACAAATCA
Found at i:48014 original size:6 final size:6
Alignment explanation
Indices: 48005--48075 Score: 76
Period size: 6 Copynumber: 12.3 Consensus size: 6
47995 CTAAGAAAAT
* * * * *
48005 AATAAA AAT--A ACTAAA AATAAC AATAAA CATAAT CAT-AA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
48050 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
48076 AACTTAATGG
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
4 3 0.06
5 3 0.06
6 48 0.89
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:48053 original size:23 final size:24
Alignment explanation
Indices: 48005--48075 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 24
47995 CTAAGAAAAT
* *
48005 AATAAAAAT--AACTAAAAATAAC
1 AATAAAAATAAAAATAAAAATAAA
* **
48027 AATAAACATAATCAT-AAAATAAA
1 AATAAAAATAAAAATAAAAATAAA
48050 AATAAAAATAAAAATAAAAATAAA
1 AATAAAAATAAAAATAAAAATAAA
48074 AA
1 AA
48076 AACTTAATGG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
22 8 0.21
23 19 0.50
24 11 0.29
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (24 bp):
AATAAAAATAAAAATAAAAATAAA
Found at i:48072 original size:29 final size:29
Alignment explanation
Indices: 48005--48074 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
47995 CTAAGAAAAT
* *
48005 AATAAAAAT-AACTAAAAATAACAATAAA
1 AATAAAAATAAAATAAAAATAAAAATAAA
* **
48033 CATAATCATAAAATAAAAATAAAAATAAA
1 AATAAAAATAAAATAAAAATAAAAATAAA
48062 AATAAAAATAAAA
1 AATAAAAATAAAA
48075 AAACTTAATG
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.19
Consensus pattern (29 bp):
AATAAAAATAAAATAAAAATAAAAATAAA
Found at i:49928 original size:15 final size:16
Alignment explanation
Indices: 49903--49932 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49893 GTTGACCTCT
49903 AAAAGACAAAAAAAGA
1 AAAAGACAAAAAAAGA
49919 AAAAGA-AAAAAAAG
1 AAAAGACAAAAAAAG
49933 CTGAAGATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAGACAAAAAAAGA
Found at i:53765 original size:14 final size:15
Alignment explanation
Indices: 53731--53765 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
53721 TAAATCCATT
53731 TTTATATTTAAGTAC
1 TTTATATTTAAGTAC
53746 TTTATATTTAAGTA-
1 TTTATATTTAAGTAC
53760 TTTATA
1 TTTATA
53766 CAATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (15 bp):
TTTATATTTAAGTAC
Found at i:56760 original size:31 final size:32
Alignment explanation
Indices: 56701--56765 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
56691 NNNNNNTTAC
56701 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
56733 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
56764 AA
1 AA
56766 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:57559 original size:15 final size:15
Alignment explanation
Indices: 57528--57582 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
57518 CATCATCATC
*
57528 ATAATAATAAATGAA
1 ATAATAATAAATAAA
57543 ATAATTAATAAA-AAA
1 ATAA-TAATAAATAAA
*
57558 ATATAGTATTAAATAAA
1 ATA-A-TAATAAATAAA
57575 ATAA-AATA
1 ATAATAATA
57583 CAATGAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
14 3 0.09
15 9 0.27
16 15 0.45
17 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (15 bp):
ATAATAATAAATAAA
Found at i:62288 original size:22 final size:22
Alignment explanation
Indices: 62259--62312 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
62249 GATATGCAAG
62259 GGTT-GAATGCCCTAATGTTTT
1 GGTTCGAATGCCCTAATGTTTT
62280 GGTTCGAATGCCCTAATGTTTT
1 GGTTCGAATGCCCTAATGTTTT
*
62302 GGGTCGAATGC
1 GGTTCGAATGC
62313 TCGATTTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.37
Consensus pattern (22 bp):
GGTTCGAATGCCCTAATGTTTT
Found at i:62740 original size:26 final size:26
Alignment explanation
Indices: 62704--62786 Score: 96
Period size: 26 Copynumber: 3.1 Consensus size: 26
62694 TATGCGTTAA
62704 TCTGTGTCAAGAATGAGCCTGTTGGT
1 TCTGTGTCAAGAATGAGCCTGTTGGT
62730 TCTGTGTCAAGAATGAGCCTG-TGCGTT
1 TCTGTGTCAAGAATGAGCCTGTTG-G-T
* * *
62757 AATCTGTGTCAAGAGTGGGCTTGTTGGT
1 --TCTGTGTCAAGAATGAGCCTGTTGGT
62785 TC
1 TC
62787 AATGGATAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
25 2 0.04
26 24 0.49
27 1 0.02
28 1 0.02
29 19 0.39
30 2 0.04
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.35
Consensus pattern (26 bp):
TCTGTGTCAAGAATGAGCCTGTTGGT
Found at i:67120 original size:23 final size:23
Alignment explanation
Indices: 67094--67137 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
67084 TAATTAGTAA
67094 TTTAAT-ATTTAATATTTTTTATT
1 TTTAATAATTT-ATATTTTTTATT
*
67117 TTTAATAATTTATTTTTTTTA
1 TTTAATAATTTATATTTTTTA
67138 AATTGATCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTAATAATTTATATTTTTTATT
Found at i:67122 original size:16 final size:17
Alignment explanation
Indices: 67101--67138 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
67091 TAATTTAATA
67101 TTTAAT-ATTT-TTTATT
1 TTTAATAATTTATTT-TT
67117 TTTAATAATTTATTTTT
1 TTTAATAATTTATTTTT
67134 TTTAA
1 TTTAA
67139 ATTGATCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 11 0.55
18 3 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTAATAATTTATTTTT
Found at i:67243 original size:27 final size:27
Alignment explanation
Indices: 67194--67252 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
67184 AGTGAATTCA
* * *
67194 AAATATATTTTAATTAGGAAATTGATT
1 AAATTTATTTTAATTAGAAAATTAATT
67221 AAATTTATTTTAATTA-AACAATTAATT
1 AAATTTATTTTAATTAGAA-AATTAATT
*
67248 TAATT
1 AAATT
67253 AAAATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (27 bp):
AAATTTATTTTAATTAGAAAATTAATT
Found at i:67251 original size:17 final size:17
Alignment explanation
Indices: 67229--67268 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
67219 TTAAATTTAT
67229 TTTAATTAAACA-ATTAA
1 TTTAATTAAA-ATATTAA
67246 TTTAATTAAAATATTAA
1 TTTAATTAAAATATTAA
67263 -TTAATT
1 TTTAATT
67269 GGATTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAATTAAAATATTAA
Found at i:68298 original size:17 final size:17
Alignment explanation
Indices: 68278--68314 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
68268 AATTTTTGAA
68278 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
*
68295 TTAGTGAATTTTGTGAT
1 TTAGTGAATTCTGTGAT
68312 TTA
1 TTA
68315 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:69608 original size:46 final size:46
Alignment explanation
Indices: 69555--69694 Score: 253
Period size: 46 Copynumber: 3.0 Consensus size: 46
69545 CCATTGCAAA
*
69555 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAATCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
69601 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* *
69647 TTGTGAAAAGTATGTATGGTATTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
69693 TT
1 TT
69695 ATAGCATTGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 91 1.00
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:70620 original size:23 final size:23
Alignment explanation
Indices: 70594--70644 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
70584 ACCAAAAATT
*
70594 ATGA-AAATTAAATTAGAAGCTGA
1 ATGAGAAATGAAATTA-AAGCTGA
* *
70617 ATGAGATATGAAATTAAAGTTGA
1 ATGAGAAATGAAATTAAAGCTGA
70640 ATGAG
1 ATGAG
70645 TCTATTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.22, T:0.27
Consensus pattern (23 bp):
ATGAGAAATGAAATTAAAGCTGA
Found at i:76837 original size:17 final size:17
Alignment explanation
Indices: 76808--76840 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
76798 ATGAATAAAA
76808 AATAATAATTTTTTTTG
1 AATAATAATTTTTTTTG
76825 AATAA-AATATTTTTTT
1 AATAATAAT-TTTTTTT
76841 ATATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
AATAATAATTTTTTTTG
Found at i:77610 original size:16 final size:16
Alignment explanation
Indices: 77567--77610 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
77557 AAAATCAAAT
*
77567 AAAATTTAATTATATA
1 AAAATTAAATTATATA
* *
77583 AAAGTTACATTATATA
1 AAAATTAAATTATATA
77599 AAAATTAAATTA
1 AAAATTAAATTA
77611 GTTAACAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTAAATTATATA
Found at i:77686 original size:38 final size:38
Alignment explanation
Indices: 77643--77724 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
77633 AAAAAGTCAG
77643 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
*
77681 TTATAATTAAATTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
77719 TTATAA
1 TTATAA
77725 ACTTATATGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:77832 original size:60 final size:60
Alignment explanation
Indices: 77756--77877 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
77746 ATATTAAACT
* * * * *
77756 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
*
77816 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
77876 AA
1 AA
77878 TATTCATACA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 4 0.07
60 51 0.93
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:77916 original size:19 final size:19
Alignment explanation
Indices: 77870--78055 Score: 108
Period size: 19 Copynumber: 9.8 Consensus size: 19
77860 ATTATAAAAT
77870 AATTACAATATTCATACAAACA
1 AATTACAATATTCATAC--A-A
77892 ATATTACAATATTCATACAA
1 A-ATTACAATATTCATACAA
*
77912 AATTACAATATTCATATAA
1 AATTACAATATTCATACAA
*
77931 AATTACAA-AAT--TACAA
1 AATTACAATATTCATACAA
*
77947 AATT-C-ATA---ATAAAA
1 AATTACAATATTCATACAA
77961 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* * *
77980 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-A-A
*
78000 AA-TACAAATTTAATT-ATAAAA
1 AATTAC-AA--T-ATTCATACAA
*
78021 TAATTACAATATTAATACAA
1 -AATTACAATATTCATACAA
78041 AATTACAATATTCAT
1 AATTACAATATTCAT
78056 TGGCGCCTCT
Statistics
Matches: 131, Mismatches: 14, Indels: 41
0.70 0.08 0.22
Matches are distributed among these distances:
14 9 0.07
15 3 0.02
16 11 0.08
17 3 0.02
18 9 0.07
19 50 0.38
20 14 0.11
21 3 0.02
22 6 0.05
23 21 0.16
25 2 0.02
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:77937 original size:27 final size:27
Alignment explanation
Indices: 77907--77982 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
77897 ACAATATTCA
77907 TACAAAATTACAATATTCATATAAAAT
1 TACAAAATTACAATATTCATATAAAAT
*
77934 TACAAAATTACAAAATTC--AT--AA-
1 TACAAAATTACAATATTCATATAAAAT
* *
77956 TAAAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATATAAAAT
77983 ACTAATCCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
22 16 0.40
23 2 0.05
24 1 0.03
25 2 0.05
26 2 0.05
27 17 0.43
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (27 bp):
TACAAAATTACAATATTCATATAAAAT
Found at i:78089 original size:27 final size:27
Alignment explanation
Indices: 78051--78117 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
78041 AATTACAATA
78051 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
*
78078 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
78105 TTCATTGGCGCCT
1 TTCATTGGCGCCT
78118 ACCTGATAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.12, C:0.33, G:0.24, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:82778 original size:2 final size:2
Alignment explanation
Indices: 82771--82795 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
82761 GAGAAGAACA
82771 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
82796 CACTGACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84282 original size:16 final size:17
Alignment explanation
Indices: 84257--84289 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
84247 TGTCTCCCCC
*
84257 TCTTCCCCAT-ATTCCT
1 TCTTCACCATCATTCCT
84273 TCTTCACCATCATTCCT
1 TCTTCACCATCATTCCT
84290 CTCACCCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.42
Consensus pattern (17 bp):
TCTTCACCATCATTCCT
Found at i:87835 original size:18 final size:18
Alignment explanation
Indices: 87814--87850 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
87804 TGAGTTTTCG
87814 AATTCGAATAATTTAAAT
1 AATTCGAATAATTTAAAT
*
87832 AATTCGAATAATTTGAAT
1 AATTCGAATAATTTAAAT
87850 A
1 A
87851 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (18 bp):
AATTCGAATAATTTAAAT
Found at i:91771 original size:14 final size:15
Alignment explanation
Indices: 91752--91783 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
91742 TTTTGATCAC
91752 ATAAAATT-AAATTA
1 ATAAAATTAAAATTA
91766 ATAAAATTAAAATTA
1 ATAAAATTAAAATTA
91781 ATA
1 ATA
91784 TAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAAATTAAAATTA
Found at i:92242 original size:40 final size:40
Alignment explanation
Indices: 92197--92292 Score: 94
Period size: 38 Copynumber: 2.4 Consensus size: 40
92187 TTATTTTAAA
92197 AATAATATTATTTTAATAAAT-TTAATATTTAATTTAAT-TT
1 AATAATATTATTTTAATAAATATT-ATA-TTAATTTAATATT
* * *
92237 AAT-A-ATTATGTTGATAAGTATTATATTAATTTAATATT
1 AATAATATTATTTTAATAAATATTATATTAATTTAATATT
92275 AA-AATAATTATGTTTAAT
1 AATAAT-ATTAT-TTTAAT
92293 CATAGTTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
37 10 0.22
38 20 0.44
39 3 0.07
40 8 0.18
41 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (40 bp):
AATAATATTATTTTAATAAATATTATATTAATTTAATATT
Found at i:92545 original size:128 final size:129
Alignment explanation
Indices: 92306--92558 Score: 343
Period size: 128 Copynumber: 2.0 Consensus size: 129
92296 AGTTTAACTC
* ** *
92306 TCTAAAATCTCCCTATATAAAGAGATAATTGGGTCATTATTTTACATGCACTTGAATTCAAGAGA
1 TCTAAAATCTCCCTATATAAAGAGATAATTGAGTCATTATTTTACACACACTTGAATTAAAGAGA
* * * *
92371 AAGTTTTAGAGAGAAAATTTTCTAAAGAAATTATTTTAGAAGATTTCTAGAGATATTTTTACTT
66 AAATTTTAGAGAGAAAATTATCTAAAGAAATTATTTAAGAAAATTTCTAGAGATATTTTTACTT
* * * *
92435 TCTAAACTCTTCCTATATAAAGAGAGTCA-TGAGTCA-TATTTTTCACACACTTGAATTAAAGA-
1 TCTAAAATCTCCCTATATAAAGAGA-TAATTGAGTCATTATTTTACACACACTTGAATTAAAGAG
92497 AAAATTTGT-GTAGAGAAAATTATCTAAAGAAATTATTTAAGAAAATTTCTAGAGATATTTTT
65 AAAATTT-TAG-AGAGAAAATTATCTAAAGAAATTATTTAAGAAAATTTCTAGAGATATTTTT
92559 TTATTTACAA
Statistics
Matches: 109, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
127 7 0.06
128 71 0.65
129 29 0.27
130 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (129 bp):
TCTAAAATCTCCCTATATAAAGAGATAATTGAGTCATTATTTTACACACACTTGAATTAAAGAGA
AAATTTTAGAGAGAAAATTATCTAAAGAAATTATTTAAGAAAATTTCTAGAGATATTTTTACTT
Found at i:97685 original size:34 final size:34
Alignment explanation
Indices: 97642--97709 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
97632 GCATTTTTGA
* *
97642 CACTGTACTGAGATGGGC-TAGGGCCCAA-ACTGT
1 CACTGTACTGAAAAGGGCTTA-GGCCCAAGACTGT
97675 CACTGATACTGAAAAGGGCTTAGGCCCAAGACTGT
1 CACTG-TACTGAAAAGGGCTTAGGCCCAAGACTGT
97710 TCAACTGTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.17
34 18 0.60
35 7 0.23
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (34 bp):
CACTGTACTGAAAAGGGCTTAGGCCCAAGACTGT
Found at i:100502 original size:17 final size:17
Alignment explanation
Indices: 100476--100574 Score: 59
Period size: 17 Copynumber: 5.8 Consensus size: 17
100466 ATTTATCTAC
*
100476 AAATTAAATATTAAATT
1 AAATTTAATATTAAATT
100493 AAATTTAATATTAAGA-T
1 AAATTTAATATTAA-ATT
100510 AACCACTTTAATATTAAATTT
1 AA--A-TTTAATATTAAA-TT
* *
100531 AAA---AA-ATTACTATC
1 AAATTTAATATTA-AATT
100545 AAA--TAAGTATTAAATT
1 AAATTTAA-TATTAAATT
100561 AAATTTAATATTAA
1 AAATTTAATATTAA
100575 TTTATTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
14 8 0.12
15 5 0.08
16 5 0.08
17 26 0.40
18 4 0.06
19 3 0.05
20 11 0.17
21 3 0.05
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATTTAATATTAAATT
Found at i:103794 original size:14 final size:14
Alignment explanation
Indices: 103756--103788 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
103746 TACATGTATG
*
103756 TAATTTAACAAATA
1 TAATCTAACAAATA
103770 TAATCTAACAAATA
1 TAATCTAACAAATA
103784 TAATC
1 TAATC
103789 ATACAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATCTAACAAATA
Found at i:106133 original size:27 final size:29
Alignment explanation
Indices: 106103--106158 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
106093 GCAAAGTCAC
*
106103 ATGTGCATATTTG-AC-AATCAAAATTTT
1 ATGTGCATAATTGCACAAATCAAAATTTT
*
106130 ATGTTCATAATTGCACAAAATCAAAATTT
1 ATGTGCATAATTGCAC-AAATCAAAATTT
106159 ACAAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.46
28 2 0.08
30 11 0.46
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (29 bp):
ATGTGCATAATTGCACAAATCAAAATTTT
Found at i:118737 original size:6 final size:6
Alignment explanation
Indices: 118726--118750 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
118716 AGATATGCCG
118726 ATATGT ATATGT ATATGT ATATGT A
1 ATATGT ATATGT ATATGT ATATGT A
118751 CGTATGTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (6 bp):
ATATGT
Found at i:120114 original size:2 final size:2
Alignment explanation
Indices: 120107--120157 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
120097 ATACATACAT
* * *
120107 AC AC AC AC AC GC AC GC AC GC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
120149 AC AC GC AC A
1 AC AC AC AC A
120158 TACATACATG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.43, C:0.49, G:0.08, T:0.00
Consensus pattern (2 bp):
AC
Found at i:121875 original size:9 final size:9
Alignment explanation
Indices: 121857--121896 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
121847 TTTGGTTAAA
121857 AATTAACCG
1 AATTAACCG
*
121866 AATTACCCG
1 AATTAACCG
121875 AATTAACCG
1 AATTAACCG
*
121884 AATTACCCG
1 AATTAACCG
121893 AATT
1 AATT
121897 GAATCATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:121880 original size:18 final size:18
Alignment explanation
Indices: 121857--121896 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
121847 TTTGGTTAAA
121857 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
121875 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
121893 AATT
1 AATT
121897 GAATCATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:122144 original size:39 final size:39
Alignment explanation
Indices: 122062--122178 Score: 200
Period size: 39 Copynumber: 3.0 Consensus size: 39
122052 ACTTAAGAGT
*
122062 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
122100 TAGACTTTAGTTTTAGTTTTATTGAGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
122139 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTATTTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
122178 T
1 T
122179 TGGGTTGGTA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
38 26 0.35
39 48 0.65
ACGTcount: A:0.18, C:0.03, G:0.28, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:122208 original size:18 final size:17
Alignment explanation
Indices: 122160--122209 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
122150 TTTAGTTTTA
*
122160 TTGGGTTGGGTATTTGGG
1 TTGGGTT-GGTAATTGGG
122178 TTGGGTTGGTAATTGGG
1 TTGGGTTGGTAATTGGG
*
122195 TTTGGTTGGATAATT
1 TTGGGTTGG-TAATT
122210 TTATTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (17 bp):
TTGGGTTGGTAATTGGG
Found at i:122839 original size:9 final size:9
Alignment explanation
Indices: 122822--122858 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
122812 TGAGTTTTTG
122822 AATTCGAAT
1 AATTCGAAT
*
122831 AACTCGAAT
1 AATTCGAAT
122840 AATTCGAAT
1 AATTCGAAT
122849 AATTCGAAT
1 AATTCGAAT
122858 A
1 A
122859 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:123688 original size:5 final size:5
Alignment explanation
Indices: 123678--123714 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
123668 AAAATTTTTT
* *
123678 ATTCG ATTCG ATTCG ATTTG ATTCG ATTTG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG AT
123715 CGAATGCTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (5 bp):
ATTCG
Found at i:123693 original size:10 final size:10
Alignment explanation
Indices: 123678--123714 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
123668 AAAATTTTTT
*
123678 ATTCGATTCG
1 ATTCGATTTG
123688 ATTCGATTTG
1 ATTCGATTTG
123698 ATTCGATTTG
1 ATTCGATTTG
123708 ATTCGAT
1 ATTCGAT
123715 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (10 bp):
ATTCGATTTG
Found at i:125112 original size:19 final size:20
Alignment explanation
Indices: 125084--125133 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
125074 TTAAATTTTT
*
125084 AAAA-ATTAAAAATCAT-TA
1 AAAATATTAAAAATAATATA
*
125102 AAATTATT-AAAATAATATA
1 AAAATATTAAAAATAATATA
125121 AAAATATTAAAAA
1 AAAATATTAAAAA
125134 ATATCTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.38
19 12 0.46
20 4 0.15
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATATTAAAAATAATATA
Found at i:125137 original size:10 final size:9
Alignment explanation
Indices: 125084--125133 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
125074 TTAAATTTTT
125084 AAAA-ATTA
1 AAAATATTA
125092 AAAATCATTA
1 AAAAT-ATTA
*
125102 AAATTATT-
1 AAAATATTA
125110 AAAATAATATA
1 AAAAT-AT-TA
125121 AAAATATTA
1 AAAATATTA
125130 AAAA
1 AAAA
125134 ATATCTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.23
9 11 0.31
10 11 0.31
11 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAATATTA
Found at i:129334 original size:124 final size:124
Alignment explanation
Indices: 129114--129369 Score: 512
Period size: 124 Copynumber: 2.1 Consensus size: 124
129104 NNNNNNNNNN
129114 AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGCAGAATGCTGTTTG
1 AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGCAGAATGCTGTTTG
129179 ATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCTGGAAG
66 ATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCTGGAAG
129238 AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGCAGAATGCTGTTTG
1 AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGCAGAATGCTGTTTG
129303 ATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCTGGAAG
66 ATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCTGGAAG
129362 AAATAATT
1 AAATAATT
129370 AATGCTGTTT
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 132 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (124 bp):
AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGCAGAATGCTGTTTG
ATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCTGGAAG
Found at i:129387 original size:78 final size:78
Alignment explanation
Indices: 129292--129447 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
129282 CTTTTAGCAG
129292 AATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCT
1 AATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCT
129357 GGAAGAAATAATT
66 GGAAGAAATAATT
129370 AATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCT
1 AATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCT
129435 GGAAGAAATAATT
66 GGAAGAAATAATT
129448 TCGAGTTGAC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (78 bp):
AATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCT
GGAAGAAATAATT
Found at i:129514 original size:202 final size:203
Alignment explanation
Indices: 129168--129563 Score: 713
Period size: 202 Copynumber: 2.0 Consensus size: 203
129158 CTTTTAGCAG
129168 AATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCT
1 AATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCT
*
129233 GGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGCAGAATGCT
66 GGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGAATGCT
* * *
129298 GTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAACA-ACTTTTGCTACAATAGGTCCTGGAAG
131 ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACACACTTTTGCTACAATAGGTCCTGGAAG
129362 AAATAATT
196 AAATAATT
129370 AATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCT
1 AATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCT
*
129435 GGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
66 GGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGAATGCT
* * *
129500 ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGTAGGTCCTGGAA
131 ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACACACTTTTGCTACAATAGGTCCTGGAA
129564 ATTGAGAGGA
Statistics
Matches: 185, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
202 162 0.88
203 23 0.12
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (203 bp):
AATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAACAACTTTTGCTACAATAGGTCCT
GGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGAATGCT
ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACACACTTTTGCTACAATAGGTCCTGGAAG
AAATAATT
Found at i:130585 original size:18 final size:19
Alignment explanation
Indices: 130542--130585 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
130532 ATTTTATTTA
130542 TGCATTTATTTTATTTTCT
1 TGCATTTATTTTATTTTCT
** *
130561 TAAATTTA-TTTATTTTTT
1 TGCATTTATTTTATTTTCT
130579 TGCATTT
1 TGCATTT
130586 TTGAATCTGT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (19 bp):
TGCATTTATTTTATTTTCT
Found at i:136128 original size:16 final size:17
Alignment explanation
Indices: 136109--136145 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
136099 TGCTTGATAG
136109 AGAAAAGAAAA-TAAAA
1 AGAAAAGAAAAGTAAAA
136125 AGAAAAGAAAAGTTAAAA
1 AGAAAAGAAAAG-TAAAA
136143 AGA
1 AGA
136146 GGGAGGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
18 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (17 bp):
AGAAAAGAAAAGTAAAA
Found at i:141087 original size:5 final size:5
Alignment explanation
Indices: 141077--141101 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
141067 GCTTTGCCTG
141077 CTATT CTATT CTATT CTATT CTATT
1 CTATT CTATT CTATT CTATT CTATT
141102 GTATCGGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
CTATT
Found at i:142786 original size:2 final size:2
Alignment explanation
Indices: 142779--142822 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
142769 AATCCATTAC
*
142779 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
142821 TA
1 TA
142823 CACCTTACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:146601 original size:26 final size:26
Alignment explanation
Indices: 146567--146616 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
146557 AAATGTCAAA
*
146567 TTTTTTTAATATTTATTGGATTAGAT
1 TTTTTTTAATATTTATAGGATTAGAT
*
146593 TTTTTTTAATATTTGTAGGATTAG
1 TTTTTTTAATATTTATAGGATTAG
146617 GTCAATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (26 bp):
TTTTTTTAATATTTATAGGATTAGAT
Found at i:149288 original size:18 final size:18
Alignment explanation
Indices: 149248--149288 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
149238 ACGACATTCC
*
149248 TGGAAAAAATTAAAAAAA
1 TGGACAAAATTAAAAAAA
* *
149266 AGGACAAAATTAAAAATA
1 TGGACAAAATTAAAAAAA
149284 TGGAC
1 TGGAC
149289 GAATTGAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.63, C:0.05, G:0.15, T:0.17
Consensus pattern (18 bp):
TGGACAAAATTAAAAAAA
Found at i:150905 original size:113 final size:113
Alignment explanation
Indices: 150697--150906 Score: 303
Period size: 113 Copynumber: 1.9 Consensus size: 113
150687 TCTTTTTCGT
* * * *
150697 TTTTCTTTTCTTAAGAATATATTAAACCTTTTGAAGCGAAGAGAGATGACAACCAAGTACCCCAC
1 TTTTCTTTTCTTAAGAATATATTAAACCTTTTGAAGCAAAAAGAGATGAAAACCAAGCACCCCAC
* * *
150762 ACTGGTTATTCAGCCCAACATACTCCTAATTTATTATATTTATATATG
66 ACCGGTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATG
* *
150810 TTTTCTTTTCTTAAGAATATATTGAACCTTTTGACGCAAAAAGAGATGAAAACCAAGCACCCCAC
1 TTTTCTTTTCTTAAGAATATATTAAACCTTTTGAAGCAAAAAGAGATGAAAACCAAGCACCCCAC
* * * *
150875 CCCGGTTACTCATCCCAACACATTCTTAATTT
66 ACCGGTTACTCAGCCCAACACACTCCTAATTT
150907 TTTTGTTTAA
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
113 84 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (113 bp):
TTTTCTTTTCTTAAGAATATATTAAACCTTTTGAAGCAAAAAGAGATGAAAACCAAGCACCCCAC
ACCGGTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATG
Found at i:153125 original size:11 final size:13
Alignment explanation
Indices: 153114--153156 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
153104 ATTATAATAT
153114 ATAA-ATGTTATA
1 ATAATATGTTATA
*
153126 ATAAGTATATTATA
1 ATAA-TATGTTATA
*
153140 TTAATATGTTATA
1 ATAATATGTTATA
153153 ATAA
1 ATAA
153157 ACATTAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 4 0.16
13 11 0.44
14 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
ATAATATGTTATA
Found at i:153162 original size:25 final size:26
Alignment explanation
Indices: 153110--153162 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
153100 TATTATTATA
*
153110 ATATATAAATGTTATAATAAGTATATT
1 ATATATAAATGTTATAATAAG-ACATT
153137 ATAT-TAATATGTTATAATAA-ACATT
1 ATATATAA-ATGTTATAATAAGACATT
153162 A
1 A
153163 AAAGAAAGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 3 0.12
27 16 0.67
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (26 bp):
ATATATAAATGTTATAATAAGACATT
Found at i:153232 original size:13 final size:13
Alignment explanation
Indices: 153211--153244 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
153201 TCTTCTACGC
153211 GAAACAAAAAAAA
1 GAAACAAAAAAAA
* *
153224 GAAAGAAAATAAA
1 GAAACAAAAAAAA
153237 GAAACAAA
1 GAAACAAA
153245 GCTAAGGTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.79, C:0.06, G:0.12, T:0.03
Consensus pattern (13 bp):
GAAACAAAAAAAA
Found at i:153408 original size:122 final size:123
Alignment explanation
Indices: 153190--153439 Score: 450
Period size: 122 Copynumber: 2.0 Consensus size: 123
153180 TTATTTTGGC
* * *
153190 TTTTTAGTTCATCTTCTACGCGAAACAAAAAAAAGAAAGAAAATAAAGAAACAAAGCTAAGGTTC
1 TTTTTACTCCATCTTCTACACGAAACAAAAAAAAGAAAGAAAATAAAGAAACAAAGCTAAGGTTC
153255 GGCCATTGTTAAGCTTGATTCAAGGTGAGTTCTAGCTCGG-TTTTAATAATTTTTATG
66 GGCCATTGTTAAGCTTGATTCAAGGTGAGTTCTAGCTCGGTTTTTAATAATTTTTATG
153312 ATTTTTACTCCATCTTCTACACGAAAC-AAAAAAAGAAAGAAAATAAAGAAACAAAGCTAAGGTT
1 -TTTTTACTCCATCTTCTACACGAAACAAAAAAAAGAAAGAAAATAAAGAAACAAAGCTAAGGTT
153376 CGGCCATTGTTAAGCTTGATTCAAGGTGAGTTCTAGCTCGGTTTTTAATAATTTTTATG
65 CGGCCATTGTTAAGCTTGATTCAAGGTGAGTTCTAGCTCGGTTTTTAATAATTTTTATG
153435 TTTTT
1 TTTTT
153440 GAGATCGTTG
Statistics
Matches: 123, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
122 83 0.67
123 40 0.33
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (123 bp):
TTTTTACTCCATCTTCTACACGAAACAAAAAAAAGAAAGAAAATAAAGAAACAAAGCTAAGGTTC
GGCCATTGTTAAGCTTGATTCAAGGTGAGTTCTAGCTCGGTTTTTAATAATTTTTATG
Found at i:154232 original size:43 final size:44
Alignment explanation
Indices: 154169--154279 Score: 140
Period size: 43 Copynumber: 2.6 Consensus size: 44
154159 AGGACTCTGA
*
154169 TATGTGTTTTCGTGTAAGACCAC-GTCTGGGAC-GTCGGCATCGAC
1 TATGTGTTTACGTGTAAGACCACTGTCTGGGACAGT-GGCATC-AC
*
154213 T-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAGTGGCATCAG
1 TATGTGTTTACGTGTAAGACCACTGTCTGGGACAGTGGCATCAC
* *
154255 TATGTGATTACATGTAAGACCACTG
1 TATGTGTTTACGTGTAAGACCACTG
154280 ATTATCCGTG
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
42 3 0.05
43 50 0.85
44 6 0.10
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (44 bp):
TATGTGTTTACGTGTAAGACCACTGTCTGGGACAGTGGCATCAC
Found at i:158993 original size:31 final size:31
Alignment explanation
Indices: 158955--159017 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
158945 TCAGAGGTTC
158955 GACAGTATTGGCGCAACATTGCAGCAAATCT
1 GACAGTATTGGCGCAACATTGCAGCAAATCT
158986 GACAGTATTGGCGCAACATTGCAGCAAATCT
1 GACAGTATTGGCGCAACATTGCAGCAAATCT
159017 G
1 G
159018 TCAGCATCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (31 bp):
GACAGTATTGGCGCAACATTGCAGCAAATCT
Found at i:163199 original size:13 final size:13
Alignment explanation
Indices: 163161--163238 Score: 60
Period size: 13 Copynumber: 6.3 Consensus size: 13
163151 AGCACTTAAA
*
163161 ATTTATGCATTTT
1 ATTTATACATTTT
*
163174 ATTT-T-TA-TTT
1 ATTTATACATTTT
163184 ATTTATACATTTT
1 ATTTATACATTTT
*
163197 ATTT-TATCAATTT
1 ATTTATA-CATTTT
*
163210 A-CTATATCA-TTT
1 ATTTATA-CATTTT
163222 ATTTATACATTTT
1 ATTTATACATTTT
163235 ATTT
1 ATTT
163239 TTATTTTATC
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 7 0.13
11 2 0.04
12 11 0.21
13 33 0.62
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (13 bp):
ATTTATACATTTT
Found at i:163209 original size:22 final size:23
Alignment explanation
Indices: 163160--163210 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
163150 TAGCACTTAA
* *
163160 AATTTATGCATTTTATTTTTATT
1 AATTTATACATTTTATTTTTATC
*
163183 TATTTATACATTTTA-TTTTATC
1 AATTTATACATTTTATTTTTATC
163205 AATTTA
1 AATTTA
163211 CTATATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (23 bp):
AATTTATACATTTTATTTTTATC
Found at i:163443 original size:16 final size:15
Alignment explanation
Indices: 163424--163453 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
163414 TCTTCATCTA
163424 TTTATTTATTCATTTG
1 TTTATTTA-TCATTTG
163440 TTTATTTATCATTT
1 TTTATTTATCATTT
163454 TAACGTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTATTTATCATTTG
Found at i:169460 original size:29 final size:29
Alignment explanation
Indices: 169418--169502 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
169408 CATTGAACCA
*
169418 ACAGGCTCACTCTTGACACAGATTAACGC
1 ACAGGCTCATTCTTGACACAGATTAACGC
169447 ACAGGCTCATTCTTGACACAG---AAC-C
1 ACAGGCTCATTCTTGACACAGATTAACGC
*
169472 AACAGACTCATTCTTGACACAGATTAACGC
1 -ACAGGCTCATTCTTGACACAGATTAACGC
169502 A
1 A
169503 TAAATAAACT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
25 1 0.02
26 23 0.47
29 24 0.49
30 1 0.02
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.21
Consensus pattern (29 bp):
ACAGGCTCATTCTTGACACAGATTAACGC
Done.