Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1024
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1774716
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 201941 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:1989 original size:2 final size:2
Alignment explanation
Indices: 1982--2029 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1972 TCAGAATGAT
1982 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2024 TC TC TC
1 TC TC TC
2030 CAAGCATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4285 original size:16 final size:17
Alignment explanation
Indices: 4262--4300 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4252 AATTATTTAC
*
4262 ATTTTTTTTATTTAA-TA
1 ATTTTTTTT-TTGAACTA
4279 ATTTTTTTTTTGAACTA
1 ATTTTTTTTTTGAACTA
4296 ATTTT
1 ATTTT
4301 AAAAAATGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
ATTTTTTTTTTGAACTA
Found at i:7720 original size:45 final size:45
Alignment explanation
Indices: 7646--8072 Score: 547
Period size: 45 Copynumber: 9.5 Consensus size: 45
7636 CTACCCTATC
* * * *
7646 ATTAGTCCCACCCAATCAATA-TAAACTAGCATCCTTTTCCCTCTG
1 ATTAGTCCCACCCAATCATTAGT-AGCTAGCCTCCTTTTCCCTGTG
* *
7691 ATTAATCCCACCCAATCATTAGTAGCTAGCTTCCTTTTCCCTGTG
1 ATTAGTCCCACCCAATCATTAGTAGCTAGCCTCCTTTTCCCTGTG
* * * * *
7736 ATTAGTCCCATCAAACCATTAGTAGCTAGCCTCCTATTCCCTGTC
1 ATTAGTCCCACCCAATCATTAGTAGCTAGCCTCCTTTTCCCTGTG
* * * **
7781 ATTAGTCCCACTCAATCATTCGTAGGTAGCCTCCTTTTCCCTGCC
1 ATTAGTCCCACCCAATCATTAGTAGCTAGCCTCCTTTTCCCTGTG
* * * **
7826 ATTAG-CCCTACCAAATCATTAGTAGCTAGCCTCTTTTTCCCCGCC
1 ATTAGTCCC-ACCCAATCATTAGTAGCTAGCCTCCTTTTCCCTGTG
* * **
7871 ATTAG-CCCTACCAAATCATTAGTAGCTAGCCTCTTTTTCCCTGCC
1 ATTAGTCCC-ACCCAATCATTAGTAGCTAGCCTCCTTTTCCCTGTG
*
7916 ATTAGTCCCACTCAATCATTAGTAGCT-GACCTCCTTTTCCCTGTG
1 ATTAGTCCCACCCAATCATTAGTAGCTAG-CCTCCTTTTCCCTGTG
7961 ATTAGTCCCACCCAATCATTAGTAGCTAGCCTCCTTTTCCCTGTG
1 ATTAGTCCCACCCAATCATTAGTAGCTAGCCTCCTTTTCCCTGTG
8006 ATTAGTCCCACCCAATCATTAGTAGCTAGCCTCCTTTTCCCTGTG
1 ATTAGTCCCACCCAATCATTAGTAGCTAGCCTCCTTTTCCCTGTG
*
8051 ATTAGTCCCACCCAAACATTAG
1 ATTAGTCCCACCCAATCATTAG
8073 ATGCGAGCCA
Statistics
Matches: 343, Mismatches: 34, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
44 4 0.01
45 334 0.97
46 5 0.01
ACGTcount: A:0.23, C:0.33, G:0.11, T:0.33
Consensus pattern (45 bp):
ATTAGTCCCACCCAATCATTAGTAGCTAGCCTCCTTTTCCCTGTG
Found at i:13861 original size:1 final size:1
Alignment explanation
Indices: 13855--13892 Score: 67
Period size: 1 Copynumber: 38.0 Consensus size: 1
13845 ATGACAACCG
*
13855 CCCCCCCCCCCCCCCCCCCCCCCCTCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
13893 AGTTCATAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:15333 original size:21 final size:21
Alignment explanation
Indices: 15307--15360 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
15297 CTTTTTAATT
15307 TCTCATAGCATAGCAAACAAA
1 TCTCATAGCATAGCAAACAAA
* ***
15328 TCTCATAGCATTGCACTGAAA
1 TCTCATAGCATAGCAAACAAA
15349 TCTCATAGCATA
1 TCTCATAGCATA
15361 TCATTAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (21 bp):
TCTCATAGCATAGCAAACAAA
Found at i:15779 original size:147 final size:147
Alignment explanation
Indices: 15571--15836 Score: 362
Period size: 147 Copynumber: 1.8 Consensus size: 147
15561 TGGCACTTGA
* * * *
15571 CAGTGACCTTGACCTTGCCCGAATAACCTTGGGTCAAGATCATTGCACATCTGCATTTCATAAGC
1 CAGTGACCTTGACCTTGCCCGAATAACCTTGGGTCAAAAACATAGCACATCTGCATATCATAAGC
* * *
15636 AATCTTTGTGTGAAATAAGAACTT-TCAATAG-TTCACTATAAGAGAGATATGGACAAGACACGC
66 AATCTTTCTGTGAAATAAGAACTTCT-AAT-GTTTCACCATAAGAAAGATATGGACAAGACACGC
15699 ATTTTTGCACTTTTACTGC
129 ATTTTTGCACTTTTACTGC
*
15718 CAGTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAAAACA-AGACACATCCT-C-TGATCATA
1 CAGTGACCTTGACCTTGCCCGAATAACCTTGGGTCAAAAACATAG-CACAT-CTGCAT-ATCATA
* *
15780 AGCAATCTTTCTGTGAAGTAAGAACTTCTAATGTTTCTCCATAAGAAAGATATGGAC
63 AGCAATCTTTCTGTGAAATAAGAACTTCTAATGTTTCACCATAAGAAAGATATGGAC
15837 GGGCACAAAT
Statistics
Matches: 104, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
146 3 0.03
147 98 0.94
148 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (147 bp):
CAGTGACCTTGACCTTGCCCGAATAACCTTGGGTCAAAAACATAGCACATCTGCATATCATAAGC
AATCTTTCTGTGAAATAAGAACTTCTAATGTTTCACCATAAGAAAGATATGGACAAGACACGCAT
TTTTGCACTTTTACTGC
Found at i:18801 original size:7 final size:7
Alignment explanation
Indices: 18755--18802 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
18745 TGTTAACTGA
18755 CCCCCAC
1 CCCCCAC
*
18762 CCCCCCC
1 CCCCCAC
18769 CCCCCAC
1 CCCCCAC
* *
18776 CACCCTC
1 CCCCCAC
*
18783 CGCCCNAC
1 C-CCCCAC
18791 CCCCCAC
1 CCCCCAC
18798 CCCCC
1 CCCCC
18803 CCATTCTTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
7 28 0.88
8 4 0.12
ACGTcount: A:0.10, C:0.83, G:0.02, T:0.02
Consensus pattern (7 bp):
CCCCCAC
Found at i:32186 original size:4 final size:4
Alignment explanation
Indices: 32169--32202 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
32159 AAAGTTTACA
*
32169 GACG GACA GACG GACG GACG GACG GAC- GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GACG GAC
32203 AAAATGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.29, C:0.26, G:0.44, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:33444 original size:2 final size:2
Alignment explanation
Indices: 33437--33500 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
33427 CTTTATGCAT
* *
33437 GA GA GA GA GA TA GA GA GA GA CA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
33479 GA GA GA GA GA GA GA AA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
33501 CTCTAAAGGA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.52, C:0.02, G:0.45, T:0.02
Consensus pattern (2 bp):
GA
Found at i:33626 original size:2 final size:2
Alignment explanation
Indices: 33613--33656 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
33603 ATATGATCTG
* *
33613 TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
33655 TC
1 TC
33657 ATAAAGAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.45, G:0.02, T:0.52
Consensus pattern (2 bp):
TC
Found at i:33812 original size:2 final size:2
Alignment explanation
Indices: 33805--33853 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
33795 AAATGTTACA
*
33805 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
33847 TC TC TC T
1 TC TC TC T
33854 GATGAAAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:33902 original size:190 final size:186
Alignment explanation
Indices: 33575--33932 Score: 467
Period size: 190 Copynumber: 1.9 Consensus size: 186
33565 CTTATGAGAC
* * *
33575 TGTAAACAAAATGAAGAGCCAAAAATCAATATGATCTGTCTCTGTCTCTCTCTCTCTCTCTCTCT
1 TGTAAACAAAATAAAGAGCCAAAAATCAATATGATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
* *
33640 CTCTTTCTCTCTCTCTCATAAAGAAAGGAAAGTACATGTATTAATCTCAAAAAAGCTTCCACTAA
66 CTCTCTCTCTCTCTCTCATAAAGAAAGGAAAGTACA--TATTAATCCCAAAAAAGCTTCCACTAA
*
33705 CACCACTCAGT-TGAATTGAGCTACATACTGCTCATCAAGCGCTGTCTATGTTTATAAGTT
129 AACCACTCA-TCTGAATT--GCTACATACTGCTCATCAAGCGCTGTCTATGTTTATAAGTT
* *
33765 TGTAAACAAAGTAAAGAGCCAAAAATCAATAAATGTTACATCTCTCTCTCTCTCTCTTTCTCTCT
1 TGTAAACAAAATAAAGAGCCAAAAATCAAT--ATG----ATCTCTCTCTCTCTCTCTCTCTCTCT
* * *
33830 CTCTCTCTCTCTCTCTCTCTCTC-TGATGAAAGGAAAGT-C-T-TT-ATCCCCCAAAAAGCTTCC
60 CTCTCTCTCTCTCTCTCTCTCTCATAAAGAAAGGAAAGTACATATTAAT-CCCAAAAAAGCTTCC
33890 ACTAAAACCACTCATCTGAATTGCTACATACTGCTCATCAAGC
124 ACTAAAACCACTCATCTGAATTGCTACATACTGCTCATCAAGC
33933 ACTTCCTCAT
Statistics
Matches: 149, Mismatches: 11, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
188 21 0.14
189 3 0.02
190 62 0.42
191 1 0.01
192 3 0.02
194 1 0.01
195 13 0.09
196 45 0.30
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (186 bp):
TGTAAACAAAATAAAGAGCCAAAAATCAATATGATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
CTCTCTCTCTCTCTCTCATAAAGAAAGGAAAGTACATATTAATCCCAAAAAAGCTTCCACTAAAA
CCACTCATCTGAATTGCTACATACTGCTCATCAAGCGCTGTCTATGTTTATAAGTT
Found at i:39010 original size:17 final size:17
Alignment explanation
Indices: 38990--39022 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
38980 AACCCTCAGT
38990 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
39007 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
39023 ACAATACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCCGATAACTGGTC
Found at i:40362 original size:4 final size:4
Alignment explanation
Indices: 40336--40377 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
40326 ATCACATTTT
* * *
40336 GTCC GT-C GTCC GTCT GTCC GTCT GTCT GTCC GTCC GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
40378 TGTAAACTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.33
Consensus pattern (4 bp):
GTCC
Found at i:41070 original size:168 final size:168
Alignment explanation
Indices: 40628--41028 Score: 732
Period size: 168 Copynumber: 2.4 Consensus size: 168
40618 AAGGAAAATN
* *
40628 TGACCCAGGGGTCATGAATTTCACAATTTTGGTAG-AGAGCCTCATTGACATCATAATCATGCAT
1 TGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAAGAG-TTCATGGACATCATAATCATGCAT
*
40692 TTTGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTTAGATTTAATACATTTTTAC
65 TTTGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTAC
40757 TATATGACCACATTGGCCCCACCCTAGAGCCTCAACCCA
130 TATATGACCACATTGGCCCCACCCTAGAGCCTCAACCCA
*
40796 TGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAAGAGTTCATGGACACCATAATCATGCATT
1 TGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAAGAGTTCATGGACATCATAATCATGCATT
40861 TTGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACT
66 TTGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACT
40926 ATATGACCACATTGGCCCCACCCTAGAGCCTCAACCCA
131 ATATGACCACATTGGCCCCACCCTAGAGCCTCAACCCA
* *
40964 TGATCCAGGGGTCATGAATTTCACAATTTTGGTAGAAGAGTTCATGGACATCATAACCATGCATT
1 TGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAAGAGTTCATGGACATCATAATCATGCATT
41029 CAGTTTTTTC
Statistics
Matches: 225, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
168 221 0.98
169 4 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (168 bp):
TGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAAGAGTTCATGGACATCATAATCATGCATT
TTGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACT
ATATGACCACATTGGCCCCACCCTAGAGCCTCAACCCA
Found at i:43019 original size:46 final size:46
Alignment explanation
Indices: 42966--43191 Score: 210
Period size: 46 Copynumber: 4.9 Consensus size: 46
42956 GATTCTCGGG
* * *
42966 TGATCTATT-AAACTAAACAAATTGCAAGAAAACCATGGTCCTGGAA
1 TGATCTATTGTAACT-AACAAATTGCAACAAAACCATGGTCCTGGTA
*
43012 TGATCTATTGTAACTAA-AAACT-CATATCAAAACCATGGTCCTGGTA
1 TGATCTATTGTAACTAACAAATTGCA-A-CAAAACCATGGTCCTGGTA
* * * * *
43058 TGATCTGTTGTAACTAACAACTCGTATCAAAACCATGGTCCTGGTA
1 TGATCTATTGTAACTAACAAATTGCAACAAAACCATGGTCCTGGTA
* * * * * *
43104 TGATCTGTTGTGACTAACAACTCGTATCAAAACCATGGTCCTGGTA
1 TGATCTATTGTAACTAACAAATTGCAACAAAACCATGGTCCTGGTA
* * *
43150 TGAACTGTTGTAACTAAC-AACT-CATATCAAAACCATGGTCCT
1 TGATCTATTGTAACTAACAAATTGCA-A-CAAAACCATGGTCCT
43192 TATATGACCT
Statistics
Matches: 155, Mismatches: 18, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
44 3 0.02
45 6 0.04
46 139 0.90
47 6 0.04
48 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (46 bp):
TGATCTATTGTAACTAACAAATTGCAACAAAACCATGGTCCTGGTA
Found at i:43204 original size:46 final size:46
Alignment explanation
Indices: 42994--43191 Score: 333
Period size: 46 Copynumber: 4.3 Consensus size: 46
42984 AAATTGCAAG
* * *
42994 AAAACCATGGTCCTGGAATGATCTATTGTAACTAAAAACTCATATC
1 AAAACCATGGTCCTGGTATGATCTGTTGTAACTAACAACTCATATC
*
43040 AAAACCATGGTCCTGGTATGATCTGTTGTAACTAACAACTCGTATC
1 AAAACCATGGTCCTGGTATGATCTGTTGTAACTAACAACTCATATC
* *
43086 AAAACCATGGTCCTGGTATGATCTGTTGTGACTAACAACTCGTATC
1 AAAACCATGGTCCTGGTATGATCTGTTGTAACTAACAACTCATATC
*
43132 AAAACCATGGTCCTGGTATGAACTGTTGTAACTAACAACTCATATC
1 AAAACCATGGTCCTGGTATGATCTGTTGTAACTAACAACTCATATC
43178 AAAACCATGGTCCT
1 AAAACCATGGTCCT
43192 TATATGACCT
Statistics
Matches: 144, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 144 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (46 bp):
AAAACCATGGTCCTGGTATGATCTGTTGTAACTAACAACTCATATC
Found at i:44490 original size:12 final size:12
Alignment explanation
Indices: 44467--44507 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
44457 AACAATCCCT
44467 TCTCTC-AT-TC
1 TCTCTCTATCTC
44477 TCTCTCTATCTC
1 TCTCTCTATCTC
*
44489 TCTCTCTATCTA
1 TCTCTCTATCTC
44501 TCTCTCT
1 TCTCTCT
44508 CTACCTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 6 0.21
11 2 0.07
12 20 0.71
ACGTcount: A:0.10, C:0.39, G:0.00, T:0.51
Consensus pattern (12 bp):
TCTCTCTATCTC
Found at i:54939 original size:18 final size:18
Alignment explanation
Indices: 54916--54953 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
54906 GTACGGTAAT
54916 AAACTCTCTCTCTCTCTC
1 AAACTCTCTCTCTCTCTC
*
54934 AAACTCTCTCTCTTTCTC
1 AAACTCTCTCTCTCTCTC
54952 AA
1 AA
54954 TTTGATAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.39
Consensus pattern (18 bp):
AAACTCTCTCTCTCTCTC
Found at i:59915 original size:16 final size:16
Alignment explanation
Indices: 59894--59941 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
59884 ATGGTATCAG
59894 GAGAAAACGTACCCAA
1 GAGAAAACGTACCCAA
*
59910 GAGAAAACGTACCCAG
1 GAGAAAACGTACCCAA
59926 GAGAAAACGTACCCAA
1 GAGAAAACGTACCCAA
59942 TTTAACGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.48, C:0.25, G:0.21, T:0.06
Consensus pattern (16 bp):
GAGAAAACGTACCCAA
Found at i:60558 original size:31 final size:31
Alignment explanation
Indices: 60520--60582 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
60510 TATTTTCATA
*
60520 GGGTACGTTTTCTCTTAGAGAAAACGTACCC
1 GGGTACGTTTTCTCCTAGAGAAAACGTACCC
*
60551 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCTAGAGAAAACGTACCC
60582 G
1 G
60583 TTAAATTGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (31 bp):
GGGTACGTTTTCTCCTAGAGAAAACGTACCC
Found at i:60610 original size:16 final size:16
Alignment explanation
Indices: 60591--60636 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
60581 CGTTAAATTG
60591 GGTACGTTTTCTCCTC
1 GGTACGTTTTCTCCTC
60607 GGTACGTTTTCTCCTC
1 GGTACGTTTTCTCCTC
60623 GGTACGTTTTCTCC
1 GGTACGTTTTCTCC
60637 GGCATTCCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.07, C:0.30, G:0.20, T:0.43
Consensus pattern (16 bp):
GGTACGTTTTCTCCTC
Found at i:62946 original size:12 final size:12
Alignment explanation
Indices: 62929--62953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62919 TAATAAACTC
62929 TCTCTCTCTCAA
1 TCTCTCTCTCAA
62941 TCTCTCTCTCAA
1 TCTCTCTCTCAA
62953 T
1 T
62954 TTGATAAGTG
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:0.16, C:0.40, G:0.00, T:0.44
Consensus pattern (12 bp):
TCTCTCTCTCAA
Found at i:64378 original size:6 final size:6
Alignment explanation
Indices: 64369--64403 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
64359 TTTTTCACTT
* *
64369 TTCTTA TTCTTA TTCTTA TTATTA TTATTA TTCTT
1 TTCTTA TTCTTA TTCTTA TTCTTA TTCTTA TTCTT
64404 TTTTTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (6 bp):
TTCTTA
Found at i:66719 original size:437 final size:433
Alignment explanation
Indices: 65922--67194 Score: 1549
Period size: 437 Copynumber: 2.9 Consensus size: 433
65912 CTGATATCAG
* *
65922 GAAAAAGGGGCTGGCCCCTAAAATTAGGGACCTAGAAGGCTCTAAAGTC-TTTTACCCATAGCTC
1 GAAAAAGGGGCTGGCCCCT-AAATTAGGGACCTAGAGGGCTCTAAAGTCTTTTTA-CTATAGCTC
* * * *
65986 TTCACCGAGGGATATTTTGTAATAGATTATAGAAGCAAATATGTTTATCTTACAAATATGAAGCC
64 TTTACTGAGGGATATTTTGTAATAAATTATAGAAGCAAATATGTTTATCTTACAATTATGAAGCC
* * * * * **
66051 AAGCAGTGTAACGATTTTCTCATATGTTACGTTATTAGGGGTTTTTAGGGGTCAGAAG-TCCAAA
129 AAGCAGTGTAACGATTTTCTCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCAAAAGTTAAAAA
* * *
66115 ACTTTGACCACCTATATCTCAAAACGGAAAAATATTTTGAAATGCAGTATAAAAGAAAAGATGCT
194 AC-TTGATCACCCATATCTCAAAA-GGAAAAATATTTTGTAATGCAGTATAAAAGAAAAGATGCT
* * * **
66180 CAAAATGATGTACTTAATACCATGCAACCTAAAAAATTAGGTTCAGCGGCCCCAATAAGGAGATA
257 CAAAATGATGTTCTCAATA-AATGCAACCT-AAAAATTTCGTTCAGCGGCCCCAATAAGGAGATA
* *
66245 AGGGACCGGCCCCTAAAACATTCTTTCTCAGATATCTCAAGAATGGTAACGAATTTCTGAACACT
320 AGGGACCGGCCCCTAAAACATTCTTTCTCAGATATCTCAAGAACGGTAACGAATTTCTAAACACT
* * *
66310 TGTTGAACAAAATGTCTTTATAATCAAATGACCTTTCATTTGATACCAA
385 TGTTGAACAAAATGTCTGTAGAATCAAATGACCTTTCATTTGAAACCAA
* * *
66359 GAAAAAGAGGCTGGCCCCTAATATTAGGGACCTAGAGGGCTCTAAAGCCTTTTTACTATAGTTCT
1 GAAAAAGGGGCTGGCCCCTAA-ATTAGGGACCTAGAGGGCTCTAAAGTCTTTTTACTATAGCTCT
* *
66424 TTACTGAGGGATATTTTGTAATAAATTAAAGAAGCAAATATGTTTATCTTACAGTTATGAAGCCA
65 TTACTGAGGGATATTTTGTAATAAATTATAGAAGCAAATATGTTTATCTTACAATTATGAAGCCA
*
66489 AGCAGTATAACGATTTTCTCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCAAAAGTTAAAAAA
130 AGCAGTGTAACGATTTTCTCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCAAAAGTTAAAAAA
* * *
66554 CTTGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTATGAAAGAAAAGTTGTTCA
195 CTTGATCACCCATATCTCA-AAAGGAAAAATATTTTGTAATGCAGTATAAAAGAAAAGATGCTCA
* * * * *
66619 AAATGATGTTCTCAACAAATTGCAACCGTCAAAATTTCGTTGAACGGCCCCTAA-AAGAAGATAA
259 AAATGATGTTCTCAATAAA-TGCAACC-TAAAAATTTCGTTCAGCGGCCCC-AATAAGGAGATAA
* *
66683 GGGACCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAA-AACGGTAACGAATTTCTAAACACT
321 GGGACCGGCCCCTAAAACATTCTTTCTCAGATATCT-CAAGAACGGTAACGAATTTCTAAACACT
* * * * *
66747 TGTTGAACAAAATTTGTGTAGAATTAAATGACCTTTTATTTGAAAGCAA
385 TGTTGAACAAAATGTCTGTAGAATCAAATGACCTTTCATTTGAAACCAA
* * * * * *
66796 GAAAAAGGGGCTGGCCCCTCAAATTAGGGGACC-AAAGGACTCTAAAATCTTTAATA-TGTAGCC
1 GAAAAAGGGGCTGGCCCCT-AAATTA-GGGACCTAGAGGGCTCTAAAGTCTTT-TTACTATAGCT
* * * * * * *
66859 CTTTACTGAGAGATATTTTGTGAA-ATATTATAGAAGCAAATGTGTTTATCTTATAATTCTGTAT
63 CTTTACTGAGGGATATTTTGT-AATAAATTATAGAAGCAAATATGTTTATCTTACAATTATGAAG
* * * * * * *
66923 TCAAGCAATGTTATGATTTTATCATGTGTTACATAATTAAGGGTTTTTAGGGGCCAAAAGTCAAA
127 CCAAGCAGTGTAACGATTTTCTCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCAAAAGTTAAA
* * *
66988 AAATTTGATCACCCTTATCTCAAAAAGAAAAAATATTTTGTAATGCAGTATAAAAGAAAAGATGC
192 AAACTTGATCACCCATATCTC-AAAAGGAAAAATATTTTGTAATGCAGTATAAAAGAAAAGATGC
* * * * **
67053 TCAAAATAATG-TCCCTAATAACATGCAACCTTACAATTTTTTTTCAGCGGCCCCAATAAGGAGA
256 TCAAAATGATGTTCTC-AATAA-ATGCAACC-TAAAAATTTCGTTCAGCGGCCCCAATAAGGAGA
* * * * *
67117 TAA-GGTCCGGCCCCTAAAATATTCTTTTTGAGATATC-CTAAGAACGGTGACGAATTTCTAAAC
318 TAAGGGACCGGCCCCTAAAACATTCTTTCTCAGATATCTC-AAGAACGGTAACGAATTTCTAAAC
*
67180 ACTTGTTGGACAAAA
382 ACTTGTTGAACAAAA
67195 CTCTTACACC
Statistics
Matches: 719, Mismatches: 99, Indels: 37
0.84 0.12 0.04
Matches are distributed among these distances:
434 1 0.00
435 2 0.00
436 70 0.10
437 612 0.85
438 34 0.05
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (433 bp):
GAAAAAGGGGCTGGCCCCTAAATTAGGGACCTAGAGGGCTCTAAAGTCTTTTTACTATAGCTCTT
TACTGAGGGATATTTTGTAATAAATTATAGAAGCAAATATGTTTATCTTACAATTATGAAGCCAA
GCAGTGTAACGATTTTCTCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCAAAAGTTAAAAAAC
TTGATCACCCATATCTCAAAAGGAAAAATATTTTGTAATGCAGTATAAAAGAAAAGATGCTCAAA
ATGATGTTCTCAATAAATGCAACCTAAAAATTTCGTTCAGCGGCCCCAATAAGGAGATAAGGGAC
CGGCCCCTAAAACATTCTTTCTCAGATATCTCAAGAACGGTAACGAATTTCTAAACACTTGTTGA
ACAAAATGTCTGTAGAATCAAATGACCTTTCATTTGAAACCAA
Found at i:68065 original size:3 final size:3
Alignment explanation
Indices: 68050--68079 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
68040 TCGAATCTAG
*
68050 TTC TTC TTA TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
68080 ATCCAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:68985 original size:440 final size:438
Alignment explanation
Indices: 68100--69358 Score: 2119
Period size: 440 Copynumber: 2.9 Consensus size: 438
68090 GTCCAGGCCG
68100 TAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGAAACATAGGTAGATGGTATTGAGAAGG
1 TAACTT-AATACCCTTTGACATTAAGACTTCAAACTTG-AACATAGGTAGATGGTATTGAGAAGG
* * *
68165 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTGTTTAGTTCTTCAAGGTCAAGCTTTTAATAAA
64 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTAATAAA
*
68230 AAATATTGTCGGGACCATAACACAATACTCCTTTAACATACAGACTTTTAACTTGTATCATAGAT
129 AAATATTGTCGGGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGAT
68295 AGATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTAATTTCA
194 AGATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTT-ATTTCA
* *
68360 AGGTCATATTTA-ATAAAACTTCATTGTTCAACTTCTGAATATACTTTGACAGAAGGACTTCAAA
258 AGGTCATA-TTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAA
* * *
68424 CTTTAAACAAAGAACAACAAAAATACACTTAAGTGTACTATTGAATAATATTTGACCTTGACCTT
322 CTTTAAACAAAGAACAATAAAAATACACTTAGGTGTACTATTGAATAATATTTGACATTGACCTT
68489 GTTTTACTCAAGGTCAAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA
387 GTTTTACTCAAGGTCAAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA
*
68541 TAACTTAATTACCCTTTGACATTAAGACTTCAAACTTAGAACATGGGTAGATGGTATTGAGAAGG
1 TAACTTAA-TACCCTTTGACATTAAGACTTCAAACTT-GAACATAGGTAGATGGTATTGAGAAGG
** *
68606 AGTGCACGCCACCAAAAGTTCCGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTGATAAA
64 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTAATAAA
* *
68671 AAATGTTGTCGGGACCATAACACAAGACTCCTATAACATACAGACTTTTAACTTGTATCATAGAT
129 AAATATTGTCGGGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGAT
*
68736 AAATGGTATATAACCTAGTTGAACCTTACCAAAA-TTTTGACCTTGACCTAGAATTTTCATTTCA
194 AGATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTT-ATTTCA
68800 AGGTCATATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAAC
258 AGGTCATATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAAC
* *
68865 TTTAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGATATTGACCTTG
323 TTTAAACAAAGAACAATAAAAATACACTTAGGTGTACTATTGAATAATATTTGACATTGACCTTG
*
68930 TTTTACTCAAGGTCGAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA
388 TTTTACTCAAGGTCAAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA
*
68981 TAACTTTAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTATATGGTATTGAGAAGG
1 TAAC-TTAATACCCTTTGACATTAAGACTTCAAACTT-GAACATAGGTAGATGGTATTGAGAAGG
* *
69046 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTATTTCAAGGTCAAGCTTTTCATAAA
64 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTAATAAA
*
69111 AAATATTGTCGGGACCATAACACAAGACTCCTTTAATATACAGACTTTTAACTTGTATCAT-GAA
129 AAATATTGTCGGGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAG-A
* * * *
69175 TAGACGGTATATTACCTAGTTGAACCTTACCAAAATTTTTGACATTGACCTAAAAATTTTATTTC
193 TAGATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCT-AGAATTTTATTTC
* * * *
69240 AAAGTCAAATTAGGAAAAACTTCATTGTTCAACTCCTGAATATGCTTTGACAGAAGGACTTCAAA
257 AAGGTCATATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAA
69305 CTTTAAACAAAGAACAATAAAAATACACTTAGGTGTACTATTGAATAATATTTG
322 CTTTAAACAAAGAACAATAAAAATACACTTAGGTGTACTATTGAATAATATTTG
69359 TTAAATTTGC
Statistics
Matches: 771, Mismatches: 40, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
439 4 0.01
440 409 0.53
441 350 0.45
442 8 0.01
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (438 bp):
TAACTTAATACCCTTTGACATTAAGACTTCAAACTTGAACATAGGTAGATGGTATTGAGAAGGAG
TGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTAATAAAAA
ATATTGTCGGGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGATAG
ATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTATTTCAAGG
TCATATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAACTTT
AAACAAAGAACAATAAAAATACACTTAGGTGTACTATTGAATAATATTTGACATTGACCTTGTTT
TACTCAAGGTCAAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA
Found at i:69716 original size:16 final size:16
Alignment explanation
Indices: 69695--69729 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
69685 AAAATACCCG
69695 GTAATTTGTGAAACTA
1 GTAATTTGTGAAACTA
69711 GTAATTTGTGAAACTA
1 GTAATTTGTGAAACTA
69727 GTA
1 GTA
69730 TTTTTAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (16 bp):
GTAATTTGTGAAACTA
Found at i:71173 original size:75 final size:75
Alignment explanation
Indices: 71045--71194 Score: 264
Period size: 75 Copynumber: 2.0 Consensus size: 75
71035 AAGGAGAAAA
* * *
71045 GTGCAAAGCTGCGAACTACAGACCTGTTTCTCTCACAGTAGTCATATGTAAGATACTAGCACACA
1 GTGCAAAGCTGCCAACTACAGACCTGTTTCTCTCACAGTAGTCATATGCAAGATACTAGAACACA
71110 TAATATGCAG
66 TAATATGCAG
*
71120 GTGCAAAGCTGCCAACTACAGACCTGTTTCTCTCACAGTAGTCATATGCAAGATCCTAGAACACA
1 GTGCAAAGCTGCCAACTACAGACCTGTTTCTCTCACAGTAGTCATATGCAAGATACTAGAACACA
71185 TAATATGCAG
66 TAATATGCAG
71195 TAGCATTTCC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (75 bp):
GTGCAAAGCTGCCAACTACAGACCTGTTTCTCTCACAGTAGTCATATGCAAGATACTAGAACACA
TAATATGCAG
Found at i:81142 original size:69 final size:69
Alignment explanation
Indices: 81066--81316 Score: 263
Period size: 69 Copynumber: 3.6 Consensus size: 69
81056 TTCAGTTAAG
* * *
81066 TCTTGCCGCTTCTCCCTTCTAAAGCTTGTTTCTTTCTGTCTTATGTTGCTGCGACCTTCTTCACT
1 TCTTGCCGCTTCTCTCTTCTAAAGCTTGTTTCTTTCTGTCTAATGTTGCTGCGAACTTCTTCACT
* *
81131 TAAG
66 CAAC
* * * * * *
81135 TTTTGCCGGTTCTCTCTTCTGGAA-CTTGTGTT-TTTTTGTCTAATGTTGTTACGAACTTCTTCA
1 TCTTGCCGCTTCTCTCTTCT-AAAGCTTGT-TTCTTTCTGTCTAATGTTGCTGCGAACTTCTTCA
81198 CTCAAC
64 CTCAAC
** * * * * *
81204 TCTTGTAGCTTCTCTCTTCCAGAGCTTGTGTCTTTCTCTCTAATGTTGGTGCGAACTTCTTCACT
1 TCTTGCCGCTTCTCTCTTCTAAAGCTTGTTTCTTTCTGTCTAATGTTGCTGCGAACTTCTTCACT
81269 CAAC
66 CAAC
* * ** *
81273 TTTTGTCGCTTCTCTCTTCTGGACCTTGTTTCTTTCTGTCTAAT
1 TCTTGCCGCTTCTCTCTTCTAAAGCTTGTTTCTTTCTGTCTAAT
81317 TTGGTCAGAA
Statistics
Matches: 148, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
68 2 0.01
69 142 0.96
70 4 0.03
ACGTcount: A:0.12, C:0.26, G:0.15, T:0.47
Consensus pattern (69 bp):
TCTTGCCGCTTCTCTCTTCTAAAGCTTGTTTCTTTCTGTCTAATGTTGCTGCGAACTTCTTCACT
CAAC
Found at i:88238 original size:168 final size:168
Alignment explanation
Indices: 87994--88467 Score: 797
Period size: 168 Copynumber: 2.8 Consensus size: 168
87984 CATGTGAGGA
* * * *
87994 AAAAACTGAATGCATGGTTATGATGTCCATGAGGCCCTCTACCAAAATTGTGAAATTTATGGCCC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGGCCC
*
88059 CTGGGTCAGGGGTTCTGGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATC
*
88124 TTAGAAAATCTTCTTCTCTACTACCATATATATTTGTT
131 TTAGAAAATCTTCTTCTCTACTACCATATACATTTGTT
* * * *
88162 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTTCCTTAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGGCCC
* * *
88227 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCAAATATGGCCAAACAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATC
*
88292 TTAGAAAATCTTCTTCTCTACTCCCATATACATTTGTT
131 TTAGAAAATCTTCTTCTCTACTACCATATACATTTGTT
88330 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGGCCC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGGCCC
88395 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATG-ATTTAAAT
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTA-TTAAAT
*
88459 ATTAGAAAA
130 CTTAGAAAA
88468 AAAAGAAAAG
Statistics
Matches: 283, Mismatches: 22, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
167 1 0.00
168 282 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (168 bp):
AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGGCCC
CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATC
TTAGAAAATCTTCTTCTCTACTACCATATACATTTGTT
Found at i:89875 original size:169 final size:169
Alignment explanation
Indices: 89596--89934 Score: 660
Period size: 169 Copynumber: 2.0 Consensus size: 169
89586 TTATTGGAAA
*
89596 TAACGTGGACTTTTTTGGAAAATGTTATAGCTTGAAAATGGACAGAAATAATTACAAAAAGTTTC
1 TAACGTGGACTTTTTTGGAAAATGTTATAGCTTGAAAATGGACAGAAATAATTACAAAAAGTATC
89661 TAAAATGATATATTGACTGATATATGTATTATAGGGGGTTAATTAGATCTTACCCATGGAGTCAT
66 TAAAATGATATATTGACTGATATATGTATTATAGGGGGTTAATTAGATCTTACCCATGGAGTCAT
89726 CCCCACCCCCAGAAATTGGAAGTGCCCAAATATCTTGGT
131 CCCCACCCCCAGAAATTGGAAGTGCCCAAATATCTTGGT
*
89765 TAACGTGGACTTTTTTGGAAAATGTTGTAGCTTGAAAATGGACAGAAATAATTACAAAAAGTATC
1 TAACGTGGACTTTTTTGGAAAATGTTATAGCTTGAAAATGGACAGAAATAATTACAAAAAGTATC
89830 TAAAATGATATATTGACTGATATATGTATTATAGGGGGTTAATTAGATCTTACCCATGGAGTCAT
66 TAAAATGATATATTGACTGATATATGTATTATAGGGGGTTAATTAGATCTTACCCATGGAGTCAT
89895 CCCCACCCCCAGAAATTGGAAGTGCCCAAATATCTTGGT
131 CCCCACCCCCAGAAATTGGAAGTGCCCAAATATCTTGGT
89934 T
1 T
89935 GACCTCCCTA
Statistics
Matches: 168, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 168 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (169 bp):
TAACGTGGACTTTTTTGGAAAATGTTATAGCTTGAAAATGGACAGAAATAATTACAAAAAGTATC
TAAAATGATATATTGACTGATATATGTATTATAGGGGGTTAATTAGATCTTACCCATGGAGTCAT
CCCCACCCCCAGAAATTGGAAGTGCCCAAATATCTTGGT
Found at i:90142 original size:11 final size:11
Alignment explanation
Indices: 90126--90173 Score: 69
Period size: 12 Copynumber: 4.2 Consensus size: 11
90116 GGTTCACCTG
90126 ATGTATAGATA
1 ATGTATAGATA
90137 ATGTATAGATA
1 ATGTATAGATA
*
90148 TATGAATAGATA
1 -ATGTATAGATA
90160 ATGTATAAGATA
1 ATGTAT-AGATA
90172 AT
1 AT
90174 CTGAAATCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 16 0.48
12 17 0.52
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (11 bp):
ATGTATAGATA
Found at i:103369 original size:188 final size:187
Alignment explanation
Indices: 103048--103424 Score: 718
Period size: 188 Copynumber: 2.0 Consensus size: 187
103038 TACTAATTAC
103048 TGCGTCTTGTCAGCAGTGATAATTTGAGCTTTGGTCCAAACACTGTTTCACTTGCTGATTACCAA
1 TGCGTCTTGTCAGCAGTGATAATTTGAGCTTTGGTCCAAACACTGTTTCACTTGCTGATTACCAA
* *
103113 CTGCATAGAAGAGTTGATTAAAATCAATTCCCAAAATGGTAAATTCTCGAGTATTATGTTATTTG
66 CTGCATAGAAGAGTTGATTAAAATCAATTCCCAAAATGGTAAATTCTCGAGTAGTATGTTAATTG
103178 ATTAGATAAGATGATTTTATTTTATTTTTGAGTATTATGTTAATTGATTAGATAAGA
131 ATTAGATAAGATGATTTTATTTTATTTTTGAGTATTATGTTAATTGATTAGATAAGA
103235 TGNCGTCTTGTCAGCAGTGATAATTTGAGCTTTGGTCCAAACACTGTTTCACTTGCTGATTACCA
1 TG-CGTCTTGTCAGCAGTGATAATTTGAGCTTTGGTCCAAACACTGTTTCACTTGCTGATTACCA
*
103300 ATTGCATAGAAGAGTTGATTAAAATCAATTCCCAAAATGGTAAATTCTCGAGTAGTATGTTAATT
65 ACTGCATAGAAGAGTTGATTAAAATCAATTCCCAAAATGGTAAATTCTCGAGTAGTATGTTAATT
103365 GATTAGATAAGATGATTTTATTTTATTTTTGAGTATTATGTTAATTGATTAGATAAGA
130 GATTAGATAAGATGATTTTATTTTATTTTTGAGTATTATGTTAATTGATTAGATAAGA
103423 TG
1 TG
103425 GTTTTTTTTT
Statistics
Matches: 186, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
187 2 0.01
188 184 0.99
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.39
Consensus pattern (187 bp):
TGCGTCTTGTCAGCAGTGATAATTTGAGCTTTGGTCCAAACACTGTTTCACTTGCTGATTACCAA
CTGCATAGAAGAGTTGATTAAAATCAATTCCCAAAATGGTAAATTCTCGAGTAGTATGTTAATTG
ATTAGATAAGATGATTTTATTTTATTTTTGAGTATTATGTTAATTGATTAGATAAGA
Found at i:103569 original size:50 final size:50
Alignment explanation
Indices: 103510--103675 Score: 296
Period size: 50 Copynumber: 3.3 Consensus size: 50
103500 TTTACCAGAT
*
103510 CTCTGGTATAAATAACGCGTCATCAGTGGACCCGGTTTTTGTGTACATGAA
1 CTCT-GTATAAATAACGCGTCATCAGTGGACCCTGTTTTTGTGTACATGAA
103561 CTCTGTATAAATAACGCGTCATCAGTGGACCCTGTTTTTGTGTACATGAA
1 CTCTGTATAAATAACGCGTCATCAGTGGACCCTGTTTTTGTGTACATGAA
* *
103611 CTCTGCATAAATAACGCGTCATCAGTGGACCCTGTTTCTGTGTACATGAA
1 CTCTGTATAAATAACGCGTCATCAGTGGACCCTGTTTTTGTGTACATGAA
103661 CTCTGTATAAATAAC
1 CTCTGTATAAATAAC
103676 CCTTATCAAT
Statistics
Matches: 111, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
50 107 0.96
51 4 0.04
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (50 bp):
CTCTGTATAAATAACGCGTCATCAGTGGACCCTGTTTTTGTGTACATGAA
Found at i:108964 original size:167 final size:163
Alignment explanation
Indices: 108683--109566 Score: 1149
Period size: 162 Copynumber: 5.4 Consensus size: 163
108673 GTCGCATTTA
* * *
108683 TCTCGGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCAGAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTT-AGGCATGCCATAT
*
108748 CGTGGGATATATTTTTGTACCGATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGA-GACTTTG-TT-TTTT
* *
108813 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATC
127 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
*
108850 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAATATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGT-TAGGCATGCCATAT
* *
108915 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTGTGTTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGA-GACTTTGTTT-TTTT
* *
108980 TAGCCAAAATTTTCAAACAAATTTTTGTCAAAGAAT
128 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
109016 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAAGCATGCTC-TA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGT-TAGGCATGC-CATA
* * * * *
109080 TCGTTGG----ATTTTTGAACCAATCGGACGTCAACTTCCTGTTTAATTAGTACTTTGTTTATTT
64 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAG-ACTTTGTTTTTTT
* * *
109141 TAGCCAAAATTGTCAAATAAATTTCCGTCAAAGATT
128 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * *
109177 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGACATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTG-TTAGGCATGCCATAT
** * * * ** *
109242 TTTGGGGTTTATTTTTGTATCAATCGGACGTCAACTTCCTGTTTTATAATGAC--TGTTTTTTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGA-GACTTTGTTTTTTTT
*
109305 AGCCAAAATTCTCAAACAAATTTTCGTCAAAGATT
129 AGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
** * * * *
109340 TCTCAGCAGGTATTTATCACAGATGTTTG-AAGTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTT-AGGCATGCCATAT
* *
109404 CGTGGGATATTTTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAG-ACTTTGTTTTTTTT
*
109469 AGCCAAAATTTTCAAACAAATTTTCCTC--AGATT
129 AGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
** * *
109502 TCTCAGCAGTTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTG-TTAGGCATGCCATAT
109567 ATTTCTGGGA
Statistics
Matches: 630, Mismatches: 70, Indels: 38
0.85 0.09 0.05
Matches are distributed among these distances:
160 1 0.00
161 97 0.15
162 144 0.23
163 94 0.15
164 37 0.06
165 38 0.06
166 104 0.17
167 114 0.18
168 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (163 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTAGGCATGCCATATC
GTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGACTTTGTTTTTTTTAG
CCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:109428 original size:327 final size:329
Alignment explanation
Indices: 108683--109566 Score: 1252
Period size: 327 Copynumber: 2.7 Consensus size: 329
108673 GTCGCATTTA
* *
108683 TCTCGGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCAGAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
* *
108748 CGTGGGATATATTTTTGTACCGATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGCTTATTT
66 CGTGGGATAT-TTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGA-GTACTTTG-TT-TAT
* * *
108812 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATCTCTCAGCAACTATTTATCGCAGATGCT
127 TTTAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCT
* * *
108877 TGAAATTTTTACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAG
192 TGAAATTTTAACACACTATTTGTTTAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAG
* * *
108942 ACGTCAACTTCCTGTTAAATGACGACTGTGTTTATTTTTAGCCAAAATTTTCAAACAAATTTTTG
257 ACGTCAACTTCCTGTTAAATAACGAC-GTGTTTATTTTTAGCCAAAATTCTCAAACAAATTTTCG
109007 TCAAAGAAT
321 TCAAAGAAT
* *
109016 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAA-GCATGCTC-T
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGT-TAAGGCATGC-CAT
* * * *
109079 ATCGTTGG--A-TTTTTGAACCAATCGGACGTCAACTTCCTGTTTAATTAGTACTTTGTTTATTT
64 ATCGTGGGATATTTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTT
* *
109141 TAGCCAAAATTGTCAAATAAATTTCCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTG
129 TAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTG
* ** * * * *
109206 AAATTTTAACACACTATTTGTTTAGACATGCCATATTTTGGGGTTTATTTTTGTATCAATCGGAC
194 AAATTTTAACACACTATTTGTTTAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGAC
** *
109271 GTCAACTTCCTGTTTTATAATGAC-TGTTT-TTTTTAGCCAAAATTCTCAAACAAATTTTCGTCA
259 GTCAACTTCCTGTTAAATAACGACGTGTTTATTTTTAGCCAAAATTCTCAAACAAATTTTCGTCA
*
109334 AAGATT
324 AAGAAT
** * * *
109340 TCTCAGCAGGTATTTATCACAGATGTTTG-AAGTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
109404 CGTGGGATATTTTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTT
66 CGTGGGATA-TTTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTT
**
109469 AGCCAAAATTTTCAAACAAATTTTCC-TC--AGATTTCTCAGCAGTTATTTATCGCAGATGCTTG
130 AGCCAAAATTTTCAAACAAA-TTTCCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTG
109531 AAATTTTAACACACTATTTGTTTAGGCATGCCATAT
194 AAATTTTAACACACTATTTGTTTAGGCATGCCATAT
109567 ATTTCTGGGA
Statistics
Matches: 493, Mismatches: 48, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
322 4 0.01
323 32 0.06
324 61 0.12
325 73 0.15
327 210 0.43
328 8 0.02
329 40 0.08
331 1 0.00
333 60 0.12
334 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (329 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
CGTGGGATATTTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTA
GCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTGAA
ATTTTAACACACTATTTGTTTAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGACGT
CAACTTCCTGTTAAATAACGACGTGTTTATTTTTAGCCAAAATTCTCAAACAAATTTTCGTCAAA
GAAT
Found at i:110936 original size:36 final size:36
Alignment explanation
Indices: 110883--111136 Score: 375
Period size: 36 Copynumber: 7.0 Consensus size: 36
110873 GGTATCATTA
*
110883 GTGTCTGTTCTGAAAAAAACTTCTTGGTAGTCTCTGG
1 GTGTCTGTTCTG-AAGAAACTTCTTGGTAGTCTCTGG
* *
110920 GTGTCTGTTCTGAAAAAACTTCTTGGTAGTTTCTGG
1 GTGTCTGTTCTGAAGAAACTTCTTGGTAGTCTCTGG
110956 GTGTCTGTTCTGAAGAAACTTCTTGGTAGTCTCTGG
1 GTGTCTGTTCTGAAGAAACTTCTTGGTAGTCTCTGG
110992 GTGTCTGTTCTGAAGAAACTTCTTGGTAGTCTCTGG
1 GTGTCTGTTCTGAAGAAACTTCTTGGTAGTCTCTGG
* * * *
111028 GTGTCTGTTCTGAAGAAACTTATAGGAAGTCTTTGG
1 GTGTCTGTTCTGAAGAAACTTCTTGGTAGTCTCTGG
*
111064 GTGTCTGTTCTGAAG-AACTTTCTTGGCAGTCTCTGG
1 GTGTCTGTTCTGAAGAAAC-TTCTTGGTAGTCTCTGG
* * * *
111100 GTGTCTGTTCCGAAGAAACTTCTAGGCAATCTCTGG
1 GTGTCTGTTCTGAAGAAACTTCTTGGTAGTCTCTGG
111136 G
1 G
111137 CCTCTGAATA
Statistics
Matches: 201, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
35 3 0.01
36 183 0.91
37 15 0.07
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (36 bp):
GTGTCTGTTCTGAAGAAACTTCTTGGTAGTCTCTGG
Found at i:113455 original size:69 final size:69
Alignment explanation
Indices: 113343--113481 Score: 242
Period size: 69 Copynumber: 2.0 Consensus size: 69
113333 CTTGCAAACA
* *
113343 TCACTTATGAGATAACGCAGGGAAACGTTCAGACCATTTATAATTTTGCAAAAACTCAATTATAT
1 TCACTTATGAGATAACGCAGGGAAACGTTCAGACCATTAATAATTTTGCAAAAACTCAATTATAC
113408 GGAT
66 GGAT
* *
113412 TCACTTATGAGATAACGCAGGGAAACTTTCAGACCATTAATAATTTTGCAAAAATTCAATTATAC
1 TCACTTATGAGATAACGCAGGGAAACGTTCAGACCATTAATAATTTTGCAAAAACTCAATTATAC
113477 GGAT
66 GGAT
113481 T
1 T
113482 GGTTGTCCTT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (69 bp):
TCACTTATGAGATAACGCAGGGAAACGTTCAGACCATTAATAATTTTGCAAAAACTCAATTATAC
GGAT
Found at i:114438 original size:13 final size:13
Alignment explanation
Indices: 114420--114445 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
114410 TAAAATTAAA
114420 AATCATCTACCAT
1 AATCATCTACCAT
114433 AATCATCTACCAT
1 AATCATCTACCAT
114446 GTCAGAGAGA
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:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (13 bp):
AATCATCTACCAT
Found at i:126729 original size:1 final size:1
Alignment explanation
Indices: 126725--126750 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
126715 ATTTTAGTAT
126725 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
126751 AAAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:131456 original size:105 final size:105
Alignment explanation
Indices: 131274--131483 Score: 420
Period size: 105 Copynumber: 2.0 Consensus size: 105
131264 TTCAATTGCA
131274 CTTTCACCCTCTTCTTTTGCGAAATTTAAATATTTCAAGCATTGTCTCTGTCATCTGTCTGGTAT
1 CTTTCACCCTCTTCTTTTGCGAAATTTAAATATTTCAAGCATTGTCTCTGTCATCTGTCTGGTAT
131339 GAATATTTTAATTTTTGTGTAGACATGGTAGATTTTAGTG
66 GAATATTTTAATTTTTGTGTAGACATGGTAGATTTTAGTG
131379 CTTTCACCCTCTTCTTTTGCGAAATTTAAATATTTCAAGCATTGTCTCTGTCATCTGTCTGGTAT
1 CTTTCACCCTCTTCTTTTGCGAAATTTAAATATTTCAAGCATTGTCTCTGTCATCTGTCTGGTAT
131444 GAATATTTTAATTTTTGTGTAGACATGGTAGATTTTAGTG
66 GAATATTTTAATTTTTGTGTAGACATGGTAGATTTTAGTG
131484 TCCATCCTCA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.46
Consensus pattern (105 bp):
CTTTCACCCTCTTCTTTTGCGAAATTTAAATATTTCAAGCATTGTCTCTGTCATCTGTCTGGTAT
GAATATTTTAATTTTTGTGTAGACATGGTAGATTTTAGTG
Found at i:136099 original size:1 final size:1
Alignment explanation
Indices: 136095--136125 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
136085 TTGAAAGTTT
*
136095 GGGGGGGGGGGGGGGGGGGGGGGGGGAGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
136126 AGACTCATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:141483 original size:166 final size:166
Alignment explanation
Indices: 141189--141650 Score: 552
Period size: 166 Copynumber: 2.8 Consensus size: 166
141179 GTGAATATGC
* * * * * * * * * *
141189 AAAATAAGCAAAGTCGACATTTAACAGTAAGCTGGCATCTGATTGGTACAGAAATATCTCCCACA
1 AAAATAAACAAAATCGCCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACG
* * * * * *
141254 ATATGACATGCCTAAAGAAAAAGTGTGTTAAAATCTCAAGCATCTGCGATAAATAGCTGCTGAGA
66 ATATGGCATGCCTATACAAAAACTGTGTAAAAATCTCAAGCATCTGCGATAAATAGTTGCTGAGA
* * ** *
141319 AATCTTTTAGGAAAATTTGTTTGAAAATTT-TGGCTG
131 AATCTCTAACAAAAATTTGTTTGAAAATTTGT-GCTA
* *
141355 AAAGTAAACAAAATCGCCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCAACG
1 AAAATAAACAAAATCGCCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACG
* * *
141420 ATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGA
66 ATATGGCATGCCTATACAAAAACTGTGTAAAAATCTCAAGCATCTGCGATAAATAGTTGCTGAGA
*
141485 ATTCTCTAACAAAAATTTGTTTGAAAATTTGTGCTA
131 AATCTCTAACAAAAATTTGTTTGAAAATTTGTGCTA
* * * * * * *
141521 AAAATAAGCAAAGTCGTCATATAACAGGAAGTTGACGTCCGATTGGTACAACAATATATCCCATG
1 AAAATAAACAAAATCGCCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACG
* *
141586 ATATGGCATGCCT-TAACAAACACTGT-TAAAAAATGTCAAGCATCTGCGATAAATAGTTGCTGA
66 ATATGGCATGCCTAT-ACAAAAACTGTGT-AAAAATCTCAAGCATCTGCGATAAATAGTTGCTGA
141649 GA
129 GA
141651 TAAATGCGAC
Statistics
Matches: 254, Mismatches: 39, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
165 2 0.01
166 251 0.99
167 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (166 bp):
AAAATAAACAAAATCGCCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACG
ATATGGCATGCCTATACAAAAACTGTGTAAAAATCTCAAGCATCTGCGATAAATAGTTGCTGAGA
AATCTCTAACAAAAATTTGTTTGAAAATTTGTGCTA
Found at i:144132 original size:15 final size:15
Alignment explanation
Indices: 144112--144152 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
144102 AGTATGAGGA
144112 AACATCCGAAATTCC
1 AACATCCGAAATTCC
* * *
144127 AACATCAGAGATTTC
1 AACATCCGAAATTCC
144142 AACATCCGAAA
1 AACATCCGAAA
144153 AGAAAAATTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
AACATCCGAAATTCC
Found at i:150966 original size:14 final size:14
Alignment explanation
Indices: 150947--150976 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
150937 AAAATGTATC
*
150947 TTCCAGTATTTATT
1 TTCCAGTATTGATT
150961 TTCCAGTATTGATT
1 TTCCAGTATTGATT
150975 TT
1 TT
150977 TTTTAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (14 bp):
TTCCAGTATTGATT
Found at i:154215 original size:24 final size:24
Alignment explanation
Indices: 154188--154255 Score: 136
Period size: 24 Copynumber: 2.8 Consensus size: 24
154178 CAAACAAACA
154188 TCACGACGGTGAAAACCAGATTAG
1 TCACGACGGTGAAAACCAGATTAG
154212 TCACGACGGTGAAAACCAGATTAG
1 TCACGACGGTGAAAACCAGATTAG
154236 TCACGACGGTGAAAACCAGA
1 TCACGACGGTGAAAACCAGA
154256 GTGTGATAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (24 bp):
TCACGACGGTGAAAACCAGATTAG
Found at i:155819 original size:74 final size:74
Alignment explanation
Indices: 155704--155851 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
155694 AGCAACTTTC
155704 ATCCTCGATGTTTTTCCACTTTGACGACGATTAAGAAGTGTTATTTGACATGAAATAACTTTAGC
1 ATCCTCGATGTTTTTCCACTTTGACGACGATTAAGAAGTGTTATTTGACATGAAATAACTTTAGC
155769 CAGTTCATA
66 CAGTTCATA
155778 ATCCTCGATGTTTTTCCACTTTGACGACGATTAAGAAGTGTTATTTGACATGAAATAACTTTAGC
1 ATCCTCGATGTTTTTCCACTTTGACGACGATTAAGAAGTGTTATTTGACATGAAATAACTTTAGC
155843 CAGTTCATA
66 CAGTTCATA
155852 CTATACTTTC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (74 bp):
ATCCTCGATGTTTTTCCACTTTGACGACGATTAAGAAGTGTTATTTGACATGAAATAACTTTAGC
CAGTTCATA
Found at i:164850 original size:36 final size:36
Alignment explanation
Indices: 164803--164877 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
164793 TCTCACATTA
*
164803 ATGTTCCATACATCATATACTTCTCTTTTTACAGAC
1 ATGTTCCATACATCATAAACTTCTCTTTTTACAGAC
*
164839 ATGTTCCATACATCATAAACTTCTCTTTTTTCAGAC
1 ATGTTCCATACATCATAAACTTCTCTTTTTACAGAC
164875 ATG
1 ATG
164878 GACATTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (36 bp):
ATGTTCCATACATCATAAACTTCTCTTTTTACAGAC
Found at i:187528 original size:2 final size:2
Alignment explanation
Indices: 187523--187559 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
187513 TATATATATA
187523 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
187560 AACTTAAGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:192555 original size:2 final size:2
Alignment explanation
Indices: 192548--192607 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
192538 CACAGTGAGA
*
192548 CT CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
192590 CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
192608 GCAGATTGAC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:195272 original size:168 final size:168
Alignment explanation
Indices: 194525--195262 Score: 1086
Period size: 168 Copynumber: 4.4 Consensus size: 168
194515 NNNNNNNNNN
* * *
194525 CCCTGACCAAGGGGTCATGAATTTCACAATTAAGGTAGGGGGCTTCATGGAAATCATAACCATGC
1 CCCTGACCAAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAACCATGC
* *
194590 ATTTAGTTTTTAACAAATATATATGGAAGTAGAGAAAAAGATTTTCTAAGATTTAATACATTTTT
66 ATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTT
194655 ACTATTTGGCCATATTGGCCCCACCCTAGAGACTGAAC
131 ACTATTTGGCCATATTGGCCCCACCCTAGAGACTGAAC
* * * * * *
194693 CCCTGACCAAGGGGTCAAGAATTTCACAATTTTGATAGAGGGCCTCATGGACATCATAATCGTGC
1 CCCTGACCAAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAACCATGC
*
194758 ATTTAGTTTTTAACAAATATATATGAG-AGTAGAGAAGAAGATTTTCTAAGATTAAATACATTTT
66 ATTTAGTTTTTAACAAATATATATG-GTAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTT
*
194822 TACTTTTTGGCCATATTGGCCCCACCCTAGAGACTGAAC
130 TACTATTTGGCCATATTGGCCCCACCCTAGAGACTGAAC
* * * *
194861 CCCTGACCAAGGGGTCGTGAATTTCACAATTTAAGTGGAGGGCTTCATGGACATCATAACCATAC
1 CCCTGACCAAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAACCATGC
* * *
194926 ATTTAGTTTTTAACAAATATATATGATAGTAGAAAAGAAGATTTTATAAGATTTAATACATTTTT
66 ATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTT
* *
194991 AATATTTGGCCATATTGGCCCCACCCTAGAGCCTGAAC
131 ACTATTTGGCCATATTGGCCCCACCCTAGAGACTGAAC
* * * *
195029 CCCTCACCCAGGGGTCATGATTTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAATCATGC
1 CCCTGACCAAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAACCATGC
* *
195094 ATTTAGTTTTTAA-AATATATTTATGGTAGTTGAGAAGAAGATTTTCTAAGATTTAATACATTTT
66 ATTTAGTTTTTAACAA-ATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTT
* * ** *
195158 TACTATATGGCCATATTGGCCCCACCATAGACCCAGAAC
130 TACTATTTGGCCATATTGGCCCCACCCTAGAGACTGAAC
* ** * *
195197 CCCTGACCCAGGGACCATAAATTTCACAATTTTGGTAGAGGGCCTT-ATGGACATCATAACCATG
1 CCCTGACCAAGGGGTCATGAATTTCACAATTTAGGTAGAGGG-CTTCATGGACATCATAACCATG
195261 CA
65 CA
195263 ACCAGTTTTT
Statistics
Matches: 512, Mismatches: 54, Indels: 8
0.89 0.09 0.01
Matches are distributed among these distances:
167 2 0.00
168 506 0.99
169 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (168 bp):
CCCTGACCAAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAACCATGC
ATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTT
ACTATTTGGCCATATTGGCCCCACCCTAGAGACTGAAC
Found at i:195485 original size:7 final size:7
Alignment explanation
Indices: 195473--195503 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
195463 ATAATTGTTA
195473 ACGCACG
1 ACGCACG
195480 ACGCACG
1 ACGCACG
*
195487 GCGCACG
1 ACGCACG
195494 ACGCACG
1 ACGCACG
195501 ACG
1 ACG
195504 ACGGACGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.42, G:0.32, T:0.00
Consensus pattern (7 bp):
ACGCACG
Found at i:199125 original size:17 final size:17
Alignment explanation
Indices: 199103--199154 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 17
199093 ATCAGTTCGC
199103 TATATCCGTAAATTAGT
1 TATATCCGTAAATTAGT
*
199120 TATATCCG--AATTCGT
1 TATATCCGTAAATTAGT
* *
199135 TATAACCGTCAAATTTGT
1 TATATCCGT-AAATTAGT
199153 TA
1 TA
199155 AGAATTTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 13 0.45
17 8 0.28
18 8 0.28
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
TATATCCGTAAATTAGT
Found at i:199610 original size:11 final size:11
Alignment explanation
Indices: 199594--199618 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
199584 ATTTTTTTGC
199594 TTTGGTTTGTT
1 TTTGGTTTGTT
199605 TTTGGTTTGTT
1 TTTGGTTTGTT
199616 TTT
1 TTT
199619 TAATCTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (11 bp):
TTTGGTTTGTT
Found at i:203566 original size:87 final size:87
Alignment explanation
Indices: 203437--203602 Score: 260
Period size: 87 Copynumber: 1.9 Consensus size: 87
203427 CTCACTGCTG
* * **
203437 TACTGCTATCTGAACGGAGAGGTCAGAATTATCTCTGTCACGTTATTTATAAAGCTGTCATTGTA
1 TACTGCTATCTCAACGGAGAGGTCAGAATTATCTCTGTCACGTAATCAATAAAGCTGTCATTGTA
203502 TCTTCATCTCACTGTTGTACAC
66 TCTTCATCTCACTGTTGTACAC
* * * *
203524 TACTGCTATCTCAACGGAGGGGTCAGAATTATCTCTGTCACGTAATCAATAAATCTGTCATTTTG
1 TACTGCTATCTCAACGGAGAGGTCAGAATTATCTCTGTCACGTAATCAATAAAGCTGTCATTGTA
203589 TCTTCATCTCACTG
66 TCTTCATCTCACTG
203603 CTTTACTGCT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (87 bp):
TACTGCTATCTCAACGGAGAGGTCAGAATTATCTCTGTCACGTAATCAATAAAGCTGTCATTGTA
TCTTCATCTCACTGTTGTACAC
Found at i:206423 original size:35 final size:35
Alignment explanation
Indices: 206377--206519 Score: 214
Period size: 35 Copynumber: 4.1 Consensus size: 35
206367 GAAGTCTTAT
*
206377 TTAATGCTCCTCAAAGCGTCATAAATTGTAGGTCC
1 TTAATACTCCTCAAAGCGTCATAAATTGTAGGTCC
*
206412 TTAATGCTCCTCAAAGCGTCATAAATTGTAGGTCC
1 TTAATACTCCTCAAAGCGTCATAAATTGTAGGTCC
* ** *
206447 TTAATACACCTCAAAAAGTCATACATTGTAGGTCC
1 TTAATACTCCTCAAAGCGTCATAAATTGTAGGTCC
**
206482 TTAATACTCCTCAAAGCGTCATTCATTGTAGGTCC
1 TTAATACTCCTCAAAGCGTCATAAATTGTAGGTCC
206517 TTA
1 TTA
206520 GTCTGCTCTG
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 99 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (35 bp):
TTAATACTCCTCAAAGCGTCATAAATTGTAGGTCC
Found at i:219564 original size:17 final size:17
Alignment explanation
Indices: 219542--219574 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
219532 ATTTTGGAAC
219542 TGTATAATGACCTGATA
1 TGTATAATGACCTGATA
*
219559 TGTATAATGTCCTGAT
1 TGTATAATGACCTGAT
219575 GACCTGATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (17 bp):
TGTATAATGACCTGATA
Found at i:220107 original size:2 final size:2
Alignment explanation
Indices: 220100--220142 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
220090 TTAATACTGT
220100 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
220142 T
1 T
220143 GAAACAGCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:222154 original size:36 final size:36
Alignment explanation
Indices: 222086--222155 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
222076 AATCACTCAG
* *
222086 CAGCTATTCGCACGACCGTCGTGTATTCACTCTCGT
1 CAGCTATTCGCAAGACCGTCGTCTATTCACTCTCGT
* ** *
222122 CAGCTATTCGCAAGACTGTTTTCTATTTACTCTC
1 CAGCTATTCGCAAGACCGTCGTCTATTCACTCTC
222156 ATTTATTTGC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.36
Consensus pattern (36 bp):
CAGCTATTCGCAAGACCGTCGTCTATTCACTCTCGT
Found at i:242343 original size:2 final size:2
Alignment explanation
Indices: 242336--242376 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
242326 TATACCACAT
242336 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
242377 GGAGTTCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:245053 original size:16 final size:16
Alignment explanation
Indices: 245017--245052 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
245007 NNNNNNNNNN
245017 GGGGGAGGGGGGGGAG
1 GGGGGAGGGGGGGGAG
*
245033 TGGGGAGGGGGGGG-G
1 GGGGGAGGGGGGGGAG
245048 GGGGG
1 GGGGG
245053 GTGCGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.08, C:0.00, G:0.89, T:0.03
Consensus pattern (16 bp):
GGGGGAGGGGGGGGAG
Found at i:258817 original size:33 final size:33
Alignment explanation
Indices: 258775--258839 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
258765 GGTGGGTGTC
258775 AAGTTTTCATATATTGGAAGAAAAAAATGGAAT
1 AAGTTTTCATATATTGGAAGAAAAAAATGGAAT
* *
258808 AAGTTTTCATATTTTTGAAGAAAAAAATGGAA
1 AAGTTTTCATATATTGGAAGAAAAAAATGGAA
258840 ATTCCTATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.48, C:0.03, G:0.17, T:0.32
Consensus pattern (33 bp):
AAGTTTTCATATATTGGAAGAAAAAAATGGAAT
Found at i:259989 original size:59 final size:59
Alignment explanation
Indices: 259910--260050 Score: 246
Period size: 59 Copynumber: 2.4 Consensus size: 59
259900 TTACAGTACT
*
259910 GTTGTATTTACTCAAGAGTATCATTGCCATAATTTTGTTAACCTGAACATAAAATTACA
1 GTTGTATTTACTCAATAGTATCATTGCCATAATTTTGTTAACCTGAACATAAAATTACA
* * *
259969 GTTGTATTTACTCAATAGTATTATTGCTATTATTTTGTTAACCTGAACATAAAATTACA
1 GTTGTATTTACTCAATAGTATCATTGCCATAATTTTGTTAACCTGAACATAAAATTACA
260028 GTTGTATTTACTCAATAGTATCA
1 GTTGTATTTACTCAATAGTATCA
260051 GCTATTCAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 77 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (59 bp):
GTTGTATTTACTCAATAGTATCATTGCCATAATTTTGTTAACCTGAACATAAAATTACA
Found at i:262405 original size:25 final size:25
Alignment explanation
Indices: 262374--262424 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
262364 TCCAACTTTA
* *
262374 AACCAGTACAGTAATTTATTAATTT
1 AACCAGTACACTAATTTACTAATTT
262399 AACCAGTACACTAATTTACTAATTT
1 AACCAGTACACTAATTTACTAATTT
262424 A
1 A
262425 CAGAGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (25 bp):
AACCAGTACACTAATTTACTAATTT
Found at i:277271 original size:21 final size:21
Alignment explanation
Indices: 277245--277297 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
277235 NNNNNNNNNT
277245 ATCTGACAAGTCGACATCAA-G
1 ATCTGACAAGTCGACAT-AACG
*
277266 ATCTGACAAGTCGACATAACT
1 ATCTGACAAGTCGACATAACG
277287 ATCTGACAAGT
1 ATCTGACAAGT
277298 GGTGGCAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (21 bp):
ATCTGACAAGTCGACATAACG
Found at i:278890 original size:225 final size:224
Alignment explanation
Indices: 278499--278947 Score: 880
Period size: 225 Copynumber: 2.0 Consensus size: 224
278489 TGATCAAATC
*
278499 CAATAAAGCCCGAAGGGCTTTATGATAGATTTGATCAAGCCCCGACCAAAATTATCATCTCATAA
1 CAATAAAGCCCAAAGGGCTTTATGATAGATTTGATCAAGCCCCGACCAAAATTATCATCTCATAA
278564 TATTCAAAGAATGATTCCTTATTACTTACATTTATATAATTTTAAACTATCTTACTATTAAATAT
66 TATTCAAAGAATGATTCCTTATTACTTACATTTATATAATTTTAAACTATCTTACTATTAAATAT
278629 TTAAATATAAATTAAATATAAATAAGCAAACCCCACTGGTGCCTCAATTTGGCTTTATGAGTTAT
131 TTAAATATAAATTAAATATAAATAAGCAAACCCCACTGGTGCCTCAATTTGGCTTTATGAGTTAT
278694 ATTGTACAAATTGATACGTAGTACAAGCA
196 ATTGTACAAATTGATACGTAGTACAAGCA
278723 NCAATAAAGCCCAAAGGGCTTTATGATAGATTTGATCAAGCCCCGACCAAAATTATCATCTCATA
1 -CAATAAAGCCCAAAGGGCTTTATGATAGATTTGATCAAGCCCCGACCAAAATTATCATCTCATA
278788 ATATTCAAAGAATGATTCCTTATTACTTACATTTATATAATTTTAAACTATCTTACTATTAAATA
65 ATATTCAAAGAATGATTCCTTATTACTTACATTTATATAATTTTAAACTATCTTACTATTAAATA
278853 TTTAAATATAAATTAAATATAAATAAGCAAACCCCACTGGTGCCTCAATTTGGCTTTATGAGTTA
130 TTTAAATATAAATTAAATATAAATAAGCAAACCCCACTGGTGCCTCAATTTGGCTTTATGAGTTA
278918 TATTGTACAAATTGATACGTAGTACAAGCA
195 TATTGTACAAATTGATACGTAGTACAAGCA
278948 AAGACATAGG
Statistics
Matches: 223, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
225 223 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (224 bp):
CAATAAAGCCCAAAGGGCTTTATGATAGATTTGATCAAGCCCCGACCAAAATTATCATCTCATAA
TATTCAAAGAATGATTCCTTATTACTTACATTTATATAATTTTAAACTATCTTACTATTAAATAT
TTAAATATAAATTAAATATAAATAAGCAAACCCCACTGGTGCCTCAATTTGGCTTTATGAGTTAT
ATTGTACAAATTGATACGTAGTACAAGCA
Found at i:284937 original size:165 final size:163
Alignment explanation
Indices: 284390--284976 Score: 638
Period size: 172 Copynumber: 3.5 Consensus size: 163
284380 ACACTATGTA
* * * * * **
284390 AAACTTGATCTCCCTATTGGGGCCAAACCCTACTCAAGGGGACCATGACTTGAACAAACTAGAAT
1 AAACTTGATCCCCCTACTGTGGCCCAACCCTACCCCCGGGGACCATGACTTGAACAAACTAGAAT
* * ** * * **
284455 CTACACTACCTGAGGATGCTTCCATTTTAATTTGAACTTTTCTAGCGTAATTGTTTTTGAGAAGA
66 CTACACTACCTGAGGATGCTTCCATTTCAATTTGAGC-TTTCTCCCCTGATACTTTTTGAGAAGA
* * *
284520 A-AGTTTAAACATTTTCTCTATATATTCCTATGTA
130 AGA-TTTAAAGATTTTCTCTATATATTCCTATCTG
* * * * * * * * * * *
284554 AAACTTCATCCCTCTATTGAGACCCTACCCTACCCCCGGGAACCAAGATTTGAACAAACTTGAAA
1 AAACTTGATCCCCCTACTGTGGCCCAACCCTACCCCCGGGGACCATGACTTGAACAAACTAGAAT
* * * *
284619 CTACACTTCCAGATGATGCTTTCATTTCAATTTGAGCTTTCCTCCCCTGATACTTTTTGAGAAGA
66 CTACACTACCTGAGGATGCTTCCATTTCAATTTGAGCTTT-CTCCCCTGATACTTTTTGAGAAGA
* * *
284684 AGA-CTAAAGATTTTCTCTTTATATTCTTTATATTCCTTTG
130 AGATTTAAAGATTTTCTCTATATATTC---CTA-T-C--TG
* * *
284724 TAAAATTTGATCCCCCCACTGTGGCCCAACCCTACCCCCGGGGACCATGATTTGAACAAACTAGA
1 --AAACTTGATCCCCCTACTGTGGCCCAACCCTACCCCCGGGGACCATGACTTGAACAAACTAGA
* * * *
284789 ATCTACATTACCTGAGGATGCTTCCATTTCATTTTGAGGTATTCTCCCCTGATACTTTTTAAGAA
64 ATCTACACTACCTGAGGATGCTTCCATTTCAATTTGAGCT-TTCTCCCCTGATACTTTTTGAGAA
284854 GAAGATTTTAAAGATTTTCTCTATATATTCCTATCTG
128 GAAGA-TTTAAAGATTTTCTCTATATATTCCTATCTG
284891 AAACTTGATCCCCCTACTGTGGCCCAACCCTACCCCCGGGGACCATGACTTGAACAAACTAGAAT
1 AAACTTGATCCCCCTACTGTGGCCCAACCCTACCCCCGGGGACCATGACTTGAACAAACTAGAAT
*
284956 CTAGACTACCTGAGGATGCTT
66 CTACACTACCTGAGGATGCTT
284977 TCCCCCTACT
Statistics
Matches: 348, Mismatches: 61, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
163 23 0.07
164 100 0.29
165 82 0.24
166 2 0.01
167 3 0.01
169 1 0.00
170 2 0.01
171 2 0.01
172 110 0.32
173 2 0.01
174 21 0.06
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (163 bp):
AAACTTGATCCCCCTACTGTGGCCCAACCCTACCCCCGGGGACCATGACTTGAACAAACTAGAAT
CTACACTACCTGAGGATGCTTCCATTTCAATTTGAGCTTTCTCCCCTGATACTTTTTGAGAAGAA
GATTTAAAGATTTTCTCTATATATTCCTATCTG
Found at i:285251 original size:278 final size:280
Alignment explanation
Indices: 284741--285511 Score: 1253
Period size: 278 Copynumber: 2.8 Consensus size: 280
284731 TGATCCCCCC
* * * * * * *
284741 ACTGTGGCCCAACCCTACCCCCGGGGACCATGATTTGAACAAACTAGAATCTACA-TTACCTGAG
1 ACTGTGACCCTACCCTACCCCCGGGAACCAAGATTTGAACAAACTTGAAACTACACTT-CCTGAT
* * * * * *
284805 GATGCTTCCATTTCATTTTGAGGTATT-CTCCCCTGATACTTTTTAAGAAGAAGATTTTAAAGAT
65 GATGCTTCCAATTCAATTTGAGCT-TTCCTCCCCTGAAACCTTTTGAGAAGAAGATTTTAAAGAT
* * *
284869 TTTCTCTATATATTCCTATCTGAAACTTGATCCCCCTACTGTGGCCCAACCCTACCCCCGGGGAC
129 TTTCTCTATATATTCCTATGTAAAACTTGATCCCCCTACTGTGGCCCTACCCTACCCCCGGGGAC
* *
284934 CATGACTTGAACAAACTAGAATCTAGACTACCTGAGGATGCTTTCCCCCTACTTGTTCTTCATTT
194 CATGATTTGAACAAACTAGAATCTACACTACCTGAGGATGCTTTCCCCCTACTTGTTCTTCATTT
284999 TCTCTATATATTCCTATGTAAA
259 TCTCTATATATTCCTATGTAAA
285021 ACTGTGACCCTACCCTACCCCCGGGAACCAAGATTTGAACAAACTTGAAACTACACTTCCTGATG
1 ACTGTGACCCTACCCTACCCCCGGGAACCAAGATTTGAACAAACTTGAAACTACACTTCCTGATG
285086 ATGCTTCCAATTCAATTTGAGCTTTCCT-CCC-GAAACCTTTTGAGAAGAAGATTTTAAAGATTT
66 ATGCTTCCAATTCAATTTGAGCTTTCCTCCCCTGAAACCTTTTGAGAAGAAGATTTTAAAGATTT
* *
285149 TCTTTATATATTCCTATGTAAAACTTGATCCCCCTACTGTGGCCCTACCCTTCCCCCGGGGACCA
131 TCTCTATATATTCCTATGTAAAACTTGATCCCCCTACTGTGGCCCTACCCTACCCCCGGGGACCA
285214 TGATTTGAACAAACTAGAATCTACACTACCTGAGGATGCTTTCCCCCTACTTGTTCTTCATTTTC
196 TGATTTGAACAAACTAGAATCTACACTACCTGAGGATGCTTTCCCCCTACTTGTTCTTCATTTTC
285279 TCTATATATTCCTATGTAAA
261 TCTATATATTCCTATGTAAA
* * *
285299 ACTGTAACCCTACCCTACCCCCGGGAACCAAGATTTAAACAAACTTGAAACAACACTTCCTGATG
1 ACTGTGACCCTACCCTACCCCCGGGAACCAAGATTTGAACAAACTTGAAACTACACTTCCTGATG
*
285364 ATGCTTCCAATTCAATTTGAGCTTTCCTCCCCTGACACCTTTTGAGAAGAAGATTTTAAAGATTT
66 ATGCTTCCAATTCAATTTGAGCTTTCCTCCCCTGAAACCTTTTGAGAAGAAGATTTTAAAGATTT
* * *
285429 CCTCTATATATTCCTATGTAAAACTTGATCCCCCTACTGTGGCCCTACCCTACCCCAGGGAACCA
131 TCTCTATATATTCCTATGTAAAACTTGATCCCCCTACTGTGGCCCTACCCTACCCCCGGGGACCA
285494 TGATTTGAACAAACTAGA
196 TGATTTGAACAAACTAGA
285512 TAAATTTCAT
Statistics
Matches: 458, Mismatches: 29, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
278 262 0.57
279 8 0.02
280 186 0.41
281 2 0.00
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (280 bp):
ACTGTGACCCTACCCTACCCCCGGGAACCAAGATTTGAACAAACTTGAAACTACACTTCCTGATG
ATGCTTCCAATTCAATTTGAGCTTTCCTCCCCTGAAACCTTTTGAGAAGAAGATTTTAAAGATTT
TCTCTATATATTCCTATGTAAAACTTGATCCCCCTACTGTGGCCCTACCCTACCCCCGGGGACCA
TGATTTGAACAAACTAGAATCTACACTACCTGAGGATGCTTTCCCCCTACTTGTTCTTCATTTTC
TCTATATATTCCTATGTAAA
Found at i:290970 original size:20 final size:20
Alignment explanation
Indices: 290942--290984 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
290932 TATCATATTG
* *
290942 ATACAATTTCATGTGATATA
1 ATACAATTTCATATAATATA
* *
290962 ATACTATTTTATATAATATA
1 ATACAATTTCATATAATATA
290982 ATA
1 ATA
290985 GTACAGGTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (20 bp):
ATACAATTTCATATAATATA
Found at i:292225 original size:15 final size:15
Alignment explanation
Indices: 292205--292324 Score: 65
Period size: 15 Copynumber: 8.3 Consensus size: 15
292195 ATTTAACTGT
292205 ATATCATATTATACA
1 ATATCATATTATACA
**
292220 ATATCATAATTATATT
1 ATATCAT-ATTATACA
292236 ATA-CA-A-TAT-C-
1 ATATCATATTATACA
* * *
292246 ATATCATATGATTCG
1 ATATCATATTATACA
*
292261 ATATGATA-TATTACA
1 ATATCATATTA-TACA
* * *
292276 ATAGCATGTGATACA
1 ATATCATATTATACA
* *
292291 ATAAT-GTATTCTACA
1 AT-ATCATATTATACA
292306 ATATCATATTATACA
1 ATATCATATTATACA
292321 ATAT
1 ATAT
292325 TGTATCATAA
Statistics
Matches: 76, Mismatches: 19, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
10 3 0.04
11 2 0.03
12 4 0.05
13 3 0.04
14 4 0.05
15 49 0.64
16 11 0.14
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (15 bp):
ATATCATATTATACA
Found at i:292306 original size:30 final size:30
Alignment explanation
Indices: 292272--292329 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
292262 TATGATATAT
*
292272 TACAATAGCATGTGATACAATAATGTATTC
1 TACAATAGCATATGATACAATAATGTATTC
* * *
292302 TACAATATCATATTATACAATATTGTAT
1 TACAATAGCATATGATACAATAATGTAT
292330 CATAATATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (30 bp):
TACAATAGCATATGATACAATAATGTATTC
Found at i:292332 original size:20 final size:20
Alignment explanation
Indices: 292307--292344 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
292297 TATTCTACAA
*
292307 TATCATATTATACAATATTG
1 TATCATAATATACAATATTG
292327 TATCATAATATACAATAT
1 TATCATAATATACAATAT
292345 ATACTATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (20 bp):
TATCATAATATACAATATTG
Found at i:298146 original size:8 final size:8
Alignment explanation
Indices: 298133--298157 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
298123 AAATAAATCA
298133 AAGGCCTG
1 AAGGCCTG
298141 AAGGCCTG
1 AAGGCCTG
298149 AAGGCCTG
1 AAGGCCTG
298157 A
1 A
298158 GCGGCACATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.36, T:0.12
Consensus pattern (8 bp):
AAGGCCTG
Found at i:299457 original size:41 final size:41
Alignment explanation
Indices: 299410--299492 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
299400 CTAGTCCGGC
299410 AGGACTAATGCATAAAAAAGTTAGTGTCGACCCCTGTTTTA
1 AGGACTAATGCATAAAAAAGTTAGTGTCGACCCCTGTTTTA
299451 AGGACTAATGCATAAAAAAGTTAGTGTCGACCCCTGTTTTA
1 AGGACTAATGCATAAAAAAGTTAGTGTCGACCCCTGTTTTA
299492 A
1 A
299493 AACGAATACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (41 bp):
AGGACTAATGCATAAAAAAGTTAGTGTCGACCCCTGTTTTA
Found at i:308094 original size:16 final size:16
Alignment explanation
Indices: 308052--308094 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
308042 TACAGTGAAG
**
308052 TCGTACCCAAACCCAC
1 TCGTACCCAAACAAAC
*
308068 TCGCACCCAAACAAAC
1 TCGTACCCAAACAAAC
*
308084 TCGTACTCAAA
1 TCGTACCCAAA
308095 TGGTCCGGTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.42, G:0.07, T:0.14
Consensus pattern (16 bp):
TCGTACCCAAACAAAC
Found at i:314080 original size:42 final size:42
Alignment explanation
Indices: 314021--314299 Score: 450
Period size: 42 Copynumber: 6.5 Consensus size: 42
314011 NNNNNNNNNN
314021 ATGAGTTCACGGGCCTCATATCTTATATTATATAGAGTGTCG
1 ATGAGTTCACGGGCCTCATATCTTATATTATATAGAGTGTCG
*
314063 ATGAGTTCAAGGGCCTCATATCTTATATTATATAGAGTGTCG
1 ATGAGTTCACGGGCCTCATATCTTATATTATATAGAGTGTCG
*
314105 ATGAGTTCACGGGCCTCATATCTTTTATTATATAGAGTGTCG
1 ATGAGTTCACGGGCCTCATATCTTATATTATATAGAGTGTCG
314147 ATGAGTTCACGGGCCTCATATCTTACATGTATATTATATAGAGTGTCG
1 ATGAGTTCACGGGCCTCATA---T-C-T-TATATTATATAGAGTGTCG
*
314195 ATGAGTTCACGGGCCTTATATCTTATATTATATAGAGTGTCG
1 ATGAGTTCACGGGCCTCATATCTTATATTATATAGAGTGTCG
* *
314237 ATGAGTTCACGGGCCTCATATCTTATTTTATATAGAGTGTCA
1 ATGAGTTCACGGGCCTCATATCTTATATTATATAGAGTGTCG
*
314279 ATGAGCTCACGGGCCTCATAT
1 ATGAGTTCACGGGCCTCATAT
314300 TTTAAGTACT
Statistics
Matches: 222, Mismatches: 9, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
42 179 0.81
43 1 0.00
44 1 0.00
45 2 0.01
46 1 0.00
47 1 0.00
48 37 0.17
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (42 bp):
ATGAGTTCACGGGCCTCATATCTTATATTATATAGAGTGTCG
Found at i:314252 original size:132 final size:127
Alignment explanation
Indices: 314021--314300 Score: 456
Period size: 132 Copynumber: 2.2 Consensus size: 127
314011 NNNNNNNNNN
314021 ATGAGTTCACGGGCCTCATA-TCTTATATTATATAGAGTGTCGATGAGTTCAAGGGCCTCATATC
1 ATGAGTTCACGGGCCTCATATTCTTATATTATATAGAGTGTCGATGAGTTCAAGGGCCTCATATC
*
314085 TTATATTATATAGAGTGTCGATGAGTTCACGGGCCTCATATCTT-TTATTATATAGAGTGTCG
66 TTATATTATATAGAGTGTCGATGAGTTCACGGGCCTCATATCTTATT-TTATATAGAGTGTCA
* *
314147 ATGAGTTCACGGGCCTCATATCTTACATGTATATTATATAGAGTGTCGATGAGTTCACGGGCCTT
1 ATGAGTTCACGGGCCTCATA--TT-C-T-TATATTATATAGAGTGTCGATGAGTTCAAGGGCCTC
314212 ATATCTTATATTATATAGAGTGTCGATGAGTTCACGGGCCTCATATCTTATTTTATATAGAGTGT
61 ATATCTTATATTATATAGAGTGTCGATGAGTTCACGGGCCTCATATCTTATTTTATATAGAGTGT
314277 CA
126 CA
*
314279 ATGAGCTCACGGGCCTCATATT
1 ATGAGTTCACGGGCCTCATATT
314301 TTAAGTACTG
Statistics
Matches: 143, Mismatches: 4, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
126 20 0.14
129 1 0.01
130 3 0.02
131 1 0.01
132 116 0.81
133 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (127 bp):
ATGAGTTCACGGGCCTCATATTCTTATATTATATAGAGTGTCGATGAGTTCAAGGGCCTCATATC
TTATATTATATAGAGTGTCGATGAGTTCACGGGCCTCATATCTTATTTTATATAGAGTGTCA
Found at i:314369 original size:132 final size:132
Alignment explanation
Indices: 314021--314345 Score: 406
Period size: 132 Copynumber: 2.5 Consensus size: 132
314011 NNNNNNNNNN
* * * *
314021 ATGAGTTCACGGGCCTCATATCTT--A--TAT--TATATAGAGTGTCGATGAGTTCAAGGGCCTC
1 ATGAGCTCACGGGCCTCATATCTTACATGTATAGTATACAGAGTGTCGATGAGTTCACGGGCCTT
* *
314080 ATATCTTATATTATATAGAGTGTCGATGAGTTCACGGGCCTCATATCTTTTATTATATAGAGTGT
66 AAATCTTATATTATATAGAGAGTCGATGAGTTCACGGGCCTCATATCTTTTATTATATAGAGTGT
*
314145 CG
131 CA
* * *
314147 ATGAGTTCACGGGCCTCATATCTTACATGTATATTATATAGAGTGTCGATGAGTTCACGGGCCTT
1 ATGAGCTCACGGGCCTCATATCTTACATGTATAGTATACAGAGTGTCGATGAGTTCACGGGCCTT
* *
314212 ATATCTTATATTATATAGAGTGTCGATGAGTTCACGGGCCTCATATCTTATT-TTATATAGAGTG
66 AAATCTTATATTATATAGAGAGTCGATGAGTTCACGGGCCTCATATCTT-TTATTATATAGAGTG
314276 TCA
130 TCA
* *
314279 ATGAGCTCACGGGCCTCATATTTTA-A-GTACT-GT-T-CAGAGTGTCGATGAAG-TCATGGGCC
1 ATGAGCTCACGGGCCTCATATCTTACATGTA-TAGTATACAGAGTGTCGATG-AGTTCACGGGCC
314338 TTAAATCT
64 TTAAATCT
314346 AGTTTAGAGT
Statistics
Matches: 181, Mismatches: 9, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
126 24 0.13
128 28 0.15
129 3 0.02
130 7 0.04
131 2 0.01
132 115 0.64
133 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (132 bp):
ATGAGCTCACGGGCCTCATATCTTACATGTATAGTATACAGAGTGTCGATGAGTTCACGGGCCTT
AAATCTTATATTATATAGAGAGTCGATGAGTTCACGGGCCTCATATCTTTTATTATATAGAGTGT
CA
Found at i:325059 original size:2 final size:2
Alignment explanation
Indices: 325052--325100 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
325042 TATTTATTAA
325052 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
325094 TC TC TC T
1 TC TC TC T
325101 GAGGTCCAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:325402 original size:52 final size:52
Alignment explanation
Indices: 325324--325424 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
325314 TGGACCTGAA
*
325324 TCACTAGCAGTCAACTTCAGATCATGAAAAGGATGAACCGGATTCGTTTGAG
1 TCACTAGCAGACAACTTCAGATCATGAAAAGGATGAACCGGATTCGTTTGAG
* * * *
325376 TCACTAGCGGACAACTTCCGGTCATGAAAAGGATGAACCGGATTGGTTT
1 TCACTAGCAGACAACTTCAGATCATGAAAAGGATGAACCGGATTCGTTT
325425 AGTTCGTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (52 bp):
TCACTAGCAGACAACTTCAGATCATGAAAAGGATGAACCGGATTCGTTTGAG
Found at i:327651 original size:19 final size:19
Alignment explanation
Indices: 327629--327667 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
327619 CCCATTCTTC
*
327629 GAATGGCGCCCGAGTTAAT
1 GAATGGAGCCCGAGTTAAT
*
327648 GAATTGAGCCCGAGTTAAT
1 GAATGGAGCCCGAGTTAAT
327667 G
1 G
327668 CAGGTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (19 bp):
GAATGGAGCCCGAGTTAAT
Found at i:332971 original size:2 final size:2
Alignment explanation
Indices: 332964--333024 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
332954 ATAGCATCAA
332964 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
333006 CT CT CT CT CT CA CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
333025 ATCAAACGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.02, C:0.51, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:339396 original size:2 final size:2
Alignment explanation
Indices: 339389--339482 Score: 179
Period size: 2 Copynumber: 47.0 Consensus size: 2
339379 CAGTCATATA
339389 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
339431 AG AG AG AG AG AG AN AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
339473 AG AG AG AG AG
1 AG AG AG AG AG
339483 CGTTGAAATG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.50, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:358729 original size:2 final size:2
Alignment explanation
Indices: 358722--358787 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
358712 ACCATAAACA
358722 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
358764 TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC
358788 CAATATATCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:361165 original size:2 final size:2
Alignment explanation
Indices: 361160--361255 Score: 142
Period size: 2 Copynumber: 49.0 Consensus size: 2
361150 AATATATGCA
** *
361160 TC TC TC TC AA TC TC TT TC -C TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
361201 TC TC TC TC TC TC TC TC TC TC TC TC -C CC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
361242 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
361256 ATTTTCTGTA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
1 2 0.02
2 83 0.98
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:369686 original size:8 final size:8
Alignment explanation
Indices: 369666--369742 Score: 72
Period size: 8 Copynumber: 9.8 Consensus size: 8
369656 TACACAAGNG
369666 ATAAGGTTT
1 ATAAGG-TT
369675 ATAAGGTT
1 ATAAGGTT
369683 ATAAGG--
1 ATAAGGTT
*
369689 ATAATGTTT
1 ATAA-GGTT
369698 ATAAGGTT
1 ATAAGGTT
*
369706 ATAAGGAT
1 ATAAGGTT
*
369714 ATAAGGGT
1 ATAAGGTT
369722 ATAAGG--
1 ATAAGGTT
369728 ATAAGGATT
1 ATAAGG-TT
369737 ATAAGG
1 ATAAGG
369743 GTCAATATGT
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
6 10 0.17
7 1 0.02
8 31 0.53
9 16 0.28
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (8 bp):
ATAAGGTT
Found at i:369697 original size:23 final size:23
Alignment explanation
Indices: 369665--369714 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
369655 ATACACAAGN
369665 GATAAGGTTTATAAGGTTATAAG
1 GATAAGGTTTATAAGGTTATAAG
*
369688 GATAATGTTTATAAGGTTATAAG
1 GATAAGGTTTATAAGGTTATAAG
369711 GATA
1 GATA
369715 TAAGGGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (23 bp):
GATAAGGTTTATAAGGTTATAAG
Found at i:370555 original size:9 final size:8
Alignment explanation
Indices: 370527--370617 Score: 86
Period size: 8 Copynumber: 11.8 Consensus size: 8
370517 TTCTATAAGG
370527 ATAAGGTT
1 ATAAGGTT
370535 ATAAGG--
1 ATAAGGTT
370541 ATAAGGTTT
1 ATAAGG-TT
370550 ATAAGGTT
1 ATAAGGTT
370558 ATAAGG--
1 ATAAGGTT
*
370564 ATAATGTTT
1 ATAA-GGTT
370573 ATAAGGTT
1 ATAAGGTT
*
370581 ATAAGGAT
1 ATAAGGTT
*
370589 ATAAGGGT
1 ATAAGGTT
370597 ATAAGG--
1 ATAAGGTT
370603 ATAAGGATT
1 ATAAGG-TT
370612 ATAAGG
1 ATAAGG
370618 GTCAATATGT
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
6 16 0.23
7 1 0.01
8 37 0.53
9 16 0.23
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (8 bp):
ATAAGGTT
Found at i:370555 original size:23 final size:23
Alignment explanation
Indices: 370527--370589 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
370517 TTCTATAAGG
370527 ATAAGGTTATAAGGATAAGGTTT
1 ATAAGGTTATAAGGATAAGGTTT
*
370550 ATAAGGTTATAAGGATAATGTTT
1 ATAAGGTTATAAGGATAAGGTTT
370573 ATAAGGTTATAAGGATA
1 ATAAGGTTATAAGGATA
370590 TAAGGGTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (23 bp):
ATAAGGTTATAAGGATAAGGTTT
Found at i:371430 original size:9 final size:8
Alignment explanation
Indices: 371402--371492 Score: 86
Period size: 8 Copynumber: 11.8 Consensus size: 8
371392 TTCTATAAGG
371402 ATAAGGTT
1 ATAAGGTT
371410 ATAAGG--
1 ATAAGGTT
371416 ATAAGGTTT
1 ATAAGG-TT
371425 ATAAGGTT
1 ATAAGGTT
371433 ATAAGG--
1 ATAAGGTT
*
371439 ATAATGTTT
1 ATAA-GGTT
371448 ATAAGGTT
1 ATAAGGTT
*
371456 ATAAGGAT
1 ATAAGGTT
*
371464 ATAAGGGT
1 ATAAGGTT
371472 ATAAGG--
1 ATAAGGTT
371478 ATAAGGATT
1 ATAAGG-TT
371487 ATAAGG
1 ATAAGG
371493 GTCAATATGT
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
6 16 0.23
7 1 0.01
8 37 0.53
9 16 0.23
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (8 bp):
ATAAGGTT
Found at i:371430 original size:23 final size:23
Alignment explanation
Indices: 371402--371464 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
371392 TTCTATAAGG
371402 ATAAGGTTATAAGGATAAGGTTT
1 ATAAGGTTATAAGGATAAGGTTT
*
371425 ATAAGGTTATAAGGATAATGTTT
1 ATAAGGTTATAAGGATAAGGTTT
371448 ATAAGGTTATAAGGATA
1 ATAAGGTTATAAGGATA
371465 TAAGGGTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (23 bp):
ATAAGGTTATAAGGATAAGGTTT
Found at i:372305 original size:9 final size:8
Alignment explanation
Indices: 372277--372367 Score: 86
Period size: 8 Copynumber: 11.8 Consensus size: 8
372267 TTCTATAAGG
372277 ATAAGGTT
1 ATAAGGTT
372285 ATAAGG--
1 ATAAGGTT
372291 ATAAGGTTT
1 ATAAGG-TT
372300 ATAAGGTT
1 ATAAGGTT
372308 ATAAGG--
1 ATAAGGTT
*
372314 ATAATGTTT
1 ATAA-GGTT
372323 ATAAGGTT
1 ATAAGGTT
*
372331 ATAAGGAT
1 ATAAGGTT
*
372339 ATAAGGGT
1 ATAAGGTT
372347 ATAAGG--
1 ATAAGGTT
372353 ATAAGGATT
1 ATAAGG-TT
372362 ATAAGG
1 ATAAGG
372368 GTCAATATGT
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
6 16 0.23
7 1 0.01
8 37 0.53
9 16 0.23
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (8 bp):
ATAAGGTT
Found at i:372305 original size:23 final size:23
Alignment explanation
Indices: 372277--372339 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
372267 TTCTATAAGG
372277 ATAAGGTTATAAGGATAAGGTTT
1 ATAAGGTTATAAGGATAAGGTTT
*
372300 ATAAGGTTATAAGGATAATGTTT
1 ATAAGGTTATAAGGATAAGGTTT
372323 ATAAGGTTATAAGGATA
1 ATAAGGTTATAAGGATA
372340 TAAGGGTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (23 bp):
ATAAGGTTATAAGGATAAGGTTT
Found at i:380246 original size:15 final size:15
Alignment explanation
Indices: 380228--380257 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
380218 TTTTTTTCTT
*
380228 TATATTTTTTTTTAA
1 TATAATTTTTTTTAA
380243 TATAATTTTTTTTAA
1 TATAATTTTTTTTAA
380258 AGATAGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATAATTTTTTTTAA
Found at i:382662 original size:2 final size:2
Alignment explanation
Indices: 382655--382712 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
382645 AATTATTCTC
382655 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
382696 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
382713 AATGTTTGCA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:385387 original size:2 final size:2
Alignment explanation
Indices: 385382--385425 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
385372 ATATATGTAT
385382 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
385424 GA
1 GA
385426 TATTTGACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:397389 original size:17 final size:17
Alignment explanation
Indices: 397367--397400 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
397357 ATCGCATAGC
397367 ACCCTAACTCCGTCACT
1 ACCCTAACTCCGTCACT
397384 ACCCTAACTCCGTCACT
1 ACCCTAACTCCGTCACT
397401 TTCGGGAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.47, G:0.06, T:0.24
Consensus pattern (17 bp):
ACCCTAACTCCGTCACT
Found at i:407528 original size:17 final size:18
Alignment explanation
Indices: 407501--407534 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
407491 AAAGAATTTT
407501 TTATTTCAATACAAATTA
1 TTATTTCAATACAAATTA
*
407519 TTATTT-AATACGAATT
1 TTATTTCAATACAAATT
407535 TACTTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (18 bp):
TTATTTCAATACAAATTA
Found at i:410026 original size:2 final size:2
Alignment explanation
Indices: 410019--410067 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
410009 ATCTTTAATA
410019 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
410061 TC TC TC T
1 TC TC TC T
410068 TGTAACAATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:418078 original size:174 final size:172
Alignment explanation
Indices: 417761--418096 Score: 433
Period size: 174 Copynumber: 1.9 Consensus size: 172
417751 ACTCTGAATA
** * *
417761 TTCCTATGTAAAAATTTGAACCCCCCCCCCCCTTGTAGACCCGTCCTACCCCTGGTAGTCATGAT
1 TTCCTATGTAAAAATTTGAACCCCCCCCCCCCTTGTAGACCCACCCTACCCCTGGGAGTCATAAT
* * * * * * **
417826 TTTCACAACTTTGAATCTACAATACTTTAGGGTGTCTCCATATAAGTTTCAACTTTCCTGGCTGA
66 TCTCACAACTTTGAATCTACAATACCTGAGGATGTCTCCACAAAAGTTTCAACTTTCCTGGCCAA
* *
417891 TTGGTTTTTGAGAAGAAGA-TTTTAAAGGATTTACTCTATTTT
131 ATGGTTCTTGAGAAGAAGATTTTTAAA-GATTTACTCTATTTT
* * * *
417933 TTCCTATGTAAAAATTTGACCCCCCCCCCCCCAATTGTGGCCCCACCCTACCCCTGGGGGTCATA
1 TTCCTATGTAAAAATTTGAACCCCCCCCCCCC--TTGTAGACCCACCCTACCCCTGGGAGTCATA
* * *
417998 ATTCTCACAACTTTGAATCTACACTACCTGAGGATG-CTTCCACAAAAGTTTCAGCTTTTCTGGC
64 ATTCTCACAACTTTGAATCTACAATACCTGAGGATGTC-TCCACAAAAGTTTCAACTTTCCTGGC
418062 CAAATGGTTCTTGAGAAGAAGATTTTTAAAGATTT
128 CAAATGGTTCTTGAGAAGAAGATTTTTAAAGATTT
418097 CTCAAAATTT
Statistics
Matches: 139, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
172 31 0.22
173 1 0.01
174 100 0.72
175 7 0.05
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (172 bp):
TTCCTATGTAAAAATTTGAACCCCCCCCCCCCTTGTAGACCCACCCTACCCCTGGGAGTCATAAT
TCTCACAACTTTGAATCTACAATACCTGAGGATGTCTCCACAAAAGTTTCAACTTTCCTGGCCAA
ATGGTTCTTGAGAAGAAGATTTTTAAAGATTTACTCTATTTT
Found at i:421063 original size:60 final size:61
Alignment explanation
Indices: 420998--421119 Score: 219
Period size: 60 Copynumber: 2.0 Consensus size: 61
420988 AAATAAATTG
* *
420998 GTTTATCTATACGCGTGTCATTTCTAGTCAAAAATCAAACGTTCTACACTTCAAAA-AAAA
1 GTTTATCTATACGCGTGTAATTTCTAGTCAAAAATCAAACGTTCTACACTCCAAAAGAAAA
421058 GTTTATCTATACGCGTGTAATTTCTAGTCAAAAATCAAACGTTCTACACTCCAAAAGAAAA
1 GTTTATCTATACGCGTGTAATTTCTAGTCAAAAATCAAACGTTCTACACTCCAAAAGAAAA
421119 G
1 G
421120 AATCCCCAGC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 54 0.92
61 5 0.08
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (61 bp):
GTTTATCTATACGCGTGTAATTTCTAGTCAAAAATCAAACGTTCTACACTCCAAAAGAAAA
Found at i:422845 original size:29 final size:29
Alignment explanation
Indices: 422803--422861 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
422793 CCCTCGACTT
422803 GACGGAAAAGGCCGAGTGATGCTCCGATG
1 GACGGAAAAGGCCGAGTGATGCTCCGATG
*
422832 GACGGAAAAGGCCGAGTGATGTTCCGATG
1 GACGGAAAAGGCCGAGTGATGCTCCGATG
422861 G
1 G
422862 GTATACCACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.39, T:0.15
Consensus pattern (29 bp):
GACGGAAAAGGCCGAGTGATGCTCCGATG
Found at i:443432 original size:273 final size:269
Alignment explanation
Indices: 442949--443471 Score: 985
Period size: 273 Copynumber: 1.9 Consensus size: 269
442939 TAACTCAACG
442949 TAAAATATCATATAATTTCTCAGTTTGTAAAAAAATCTAGGTAAAAACAAGAATATCGAAGCAAA
1 TAAAATATCATATAATTTCTCAGTTTGTAAAAAAATCTAGGTAAAAACAAGAATATCGAAGCAAA
443014 CATGCTAATATAAACATGACTATGCAATATTCAAAGAATTTTCTACAGTAAAAGATTATTACAGT
66 CATGCTAATATAAACATGACTATGCAATATTCAAAGAATTTTCTACAGTAAAAGATTATTACAGT
443079 GAGCATATATGCGATAAAAATGTACACTTACCAGCTAGTACACTGAAGTCAATAACATTCCCCTT
131 GAGCATATATGCGATAAAAATGTACACTTACCAGCTAGTACACTGAAGTCAATAACATTCCCCTT
443144 TTCCTCAAAGTTTACTACACTCTTGAAATTATTTTGAATTATGTTAGCAACAAATTGTTTTTAAT
196 TTCCTCAAAGTTTACTACACTCTTGAAATTATTTTGAATTATGTTAGCAACAAATTGTTTTTAAT
443209 AATTCTACC
261 AATTCTACC
443218 TAAAATATCATATAATTTCTCCA-TTTGTAAAAAAATCTAGGTAAAAACAAGAATATCGAAGCAA
1 TAAAATATCATATAATTTCT-CAGTTTGTAAAAAAATCTAGGTAAAAACAAGAATATCGAAGCAA
443282 ACATGCTAATATAAACATGACTATGCAATATTCAAAGAATTTAATTTCTACAGTAAAAGATTATT
65 ACATGCTAATATAAACATGACTATGCAATATTCAAAGAA--T--TTTCTACAGTAAAAGATTATT
*
443347 ACAGTGAGCATATATGCTATAAAAATGTACACTTACCAGCTAGTACACTGAAGTCAATAACATTC
126 ACAGTGAGCATATATGCGATAAAAATGTACACTTACCAGCTAGTACACTGAAGTCAATAACATTC
443412 CCCTTTTCCTCAAAGTTTACTACACTCTTGAAATTATTTTGAATTATGTTAGCAACAAAT
191 CCCTTTTCCTCAAAGTTTACTACACTCTTGAAATTATTTTGAATTATGTTAGCAACAAAT
443472 CAAAATCAAT
Statistics
Matches: 248, Mismatches: 1, Indels: 6
0.97 0.00 0.02
Matches are distributed among these distances:
269 100 0.40
270 2 0.01
271 1 0.00
273 145 0.58
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (269 bp):
TAAAATATCATATAATTTCTCAGTTTGTAAAAAAATCTAGGTAAAAACAAGAATATCGAAGCAAA
CATGCTAATATAAACATGACTATGCAATATTCAAAGAATTTTCTACAGTAAAAGATTATTACAGT
GAGCATATATGCGATAAAAATGTACACTTACCAGCTAGTACACTGAAGTCAATAACATTCCCCTT
TTCCTCAAAGTTTACTACACTCTTGAAATTATTTTGAATTATGTTAGCAACAAATTGTTTTTAAT
AATTCTACC
Found at i:444645 original size:14 final size:14
Alignment explanation
Indices: 444626--444655 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
444616 AAAAGAAATA
*
444626 TTGAAATTTGAATT
1 TTGAAATATGAATT
444640 TTGAAATATGAATT
1 TTGAAATATGAATT
444654 TT
1 TT
444656 TTCTTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TTGAAATATGAATT
Found at i:445028 original size:11 final size:11
Alignment explanation
Indices: 445012--445036 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
445002 AGTCTTTGTC
445012 TCAATCAAAGG
1 TCAATCAAAGG
445023 TCAATCAAAGG
1 TCAATCAAAGG
445034 TCA
1 TCA
445037 GTAAACCGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (11 bp):
TCAATCAAAGG
Found at i:448659 original size:2 final size:2
Alignment explanation
Indices: 448652--448682 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
448642 CATTATACTC
448652 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
448683 CACACACAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:448919 original size:14 final size:14
Alignment explanation
Indices: 448900--448926 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
448890 AGAGCACAGT
448900 TTGGGTAAGCAATG
1 TTGGGTAAGCAATG
448914 TTGGGTAAGCAAT
1 TTGGGTAAGCAAT
448927 CCTCCAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (14 bp):
TTGGGTAAGCAATG
Found at i:451553 original size:26 final size:25
Alignment explanation
Indices: 451509--451557 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
451499 TCAAATTAAT
*
451509 ATATATATATATATATTTTGTTCAAA
1 ATATATATATACATATTTT-TTCAAA
* *
451535 ATATATATGTACATGTTTTTTCA
1 ATATATATATACATATTTTTTCA
451558 GCCACTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (25 bp):
ATATATATATACATATTTTTTCAAA
Found at i:452392 original size:21 final size:21
Alignment explanation
Indices: 452366--452486 Score: 118
Period size: 21 Copynumber: 5.8 Consensus size: 21
452356 TACAAGATAA
452366 ACGATAGGATAGGATTCACGC
1 ACGATAGGATAGGATTCACGC
*
452387 ACGATAGGATAGGATTAACGC
1 ACGATAGGATAGGATTCACGC
* * * *
452408 ACGATAGAACAGTATACACGC
1 ACGATAGGATAGGATTCACGC
* * *
452429 ACGATACGATAGCATTAACGC
1 ACGATAGGATAGGATTCACGC
* * *
452450 ACGATA-GAGCAGTATACACGC
1 ACGATAGGA-TAGGATTCACGC
*
452471 ACGATACGATAGGATT
1 ACGATAGGATAGGATT
452487 GATAAACGAT
Statistics
Matches: 79, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
20 2 0.03
21 75 0.95
22 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (21 bp):
ACGATAGGATAGGATTCACGC
Found at i:452497 original size:42 final size:42
Alignment explanation
Indices: 452382--452486 Score: 183
Period size: 42 Copynumber: 2.5 Consensus size: 42
452372 GGATAGGATT
*
452382 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
1 CACGCACGATACGATAGGATTAACGCACGATAGAACAGTATA
* *
452424 CACGCACGATACGATAGCATTAACGCACGATAGAGCAGTATA
1 CACGCACGATACGATAGGATTAACGCACGATAGAACAGTATA
452466 CACGCACGATACGATAGGATT
1 CACGCACGATACGATAGGATT
452487 GATAAACGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (42 bp):
CACGCACGATACGATAGGATTAACGCACGATAGAACAGTATA
Found at i:453553 original size:21 final size:21
Alignment explanation
Indices: 453529--453600 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
453519 CGATAAACCT
*
453529 GATATGATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
453550 GATAGGATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
* * * *
453571 AACAGTA-TACACGCACGATAC
1 GATAGGATTA-ACGCACGATAG
453592 GATAGGATT
1 GATAGGATT
453601 GATACACGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 2 0.05
21 38 0.93
22 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.21
Consensus pattern (21 bp):
GATAGGATTAACGCACGATAG
Found at i:455361 original size:11 final size:11
Alignment explanation
Indices: 455345--455437 Score: 89
Period size: 11 Copynumber: 8.2 Consensus size: 11
455335 ACAAAACAGA
* *
455345 GTTAGGTTTGG
1 GTTAGGGTTAG
455356 GTTAGGGTTAG
1 GTTAGGGTTAG
* *
455367 TTTTGGGTTAGGG
1 GTTAGGGTTA--G
455380 GTTAGGGTTAG
1 GTTAGGGTTAG
*
455391 TTTAGGGTTAG
1 GTTAGGGTTAG
455402 GATTAGGGTTAG
1 G-TTAGGGTTAG
*
455414 TTTAGGG-TAGG
1 GTTAGGGTTA-G
455425 GTTAGGGTTAG
1 GTTAGGGTTAG
455436 GT
1 GT
455438 AACCATTGTA
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
10 2 0.03
11 44 0.66
12 12 0.18
13 9 0.13
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (11 bp):
GTTAGGGTTAG
Found at i:455363 original size:6 final size:6
Alignment explanation
Indices: 455345--455436 Score: 86
Period size: 6 Copynumber: 16.0 Consensus size: 6
455335 ACAAAACAGA
* * *
455345 GTTA-G GTTTGG GTTAGG GTTA-G TTTTGG GTTAGGG GTTAGG GTTA-G
1 GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTTA-GG GTTAGG GTTAGG
* * *
455391 TTTAGG GTTAGG ATTAGG GTTA-G TTTAGG G-TAGG GTTAGG GTTAGG
1 GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG
455437 TAACCATTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
5 19 0.28
6 44 0.64
7 6 0.09
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (6 bp):
GTTAGG
Found at i:455371 original size:17 final size:18
Alignment explanation
Indices: 455345--455413 Score: 70
Period size: 17 Copynumber: 3.9 Consensus size: 18
455335 ACAAAACAGA
455345 GTTAGGTTTGGGTTA-GG
1 GTTAGGTTTGGGTTAGGG
*
455362 GTTAGTTTTGGGTTAGGG
1 GTTAGGTTTGGGTTAGGG
* * *
455380 GTTAGGGTTAGTTTA-GG
1 GTTAGGTTTGGGTTAGGG
*
455397 GTTAGGATTAGGGTTAG
1 GTTAGG-TTTGGGTTAG
455414 TTTAGGGTAG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
17 22 0.55
18 18 0.45
ACGTcount: A:0.16, C:0.00, G:0.43, T:0.41
Consensus pattern (18 bp):
GTTAGGTTTGGGTTAGGG
Found at i:455375 original size:23 final size:23
Alignment explanation
Indices: 455349--455435 Score: 131
Period size: 23 Copynumber: 3.8 Consensus size: 23
455339 AACAGAGTTA
* *
455349 GGTTTGGGTTAGGGTTAGTTTTG
1 GGTTAGGGTTAGGGTTAGTTTAG
455372 GGTTAGGGGTTAGGGTTAGTTTAG
1 GGTTA-GGGTTAGGGTTAGTTTAG
*
455396 GGTTAGGATTAGGGTTAGTTTAG
1 GGTTAGGGTTAGGGTTAGTTTAG
455419 GG-TAGGGTTAGGGTTAG
1 GGTTAGGGTTAGGGTTAG
455436 GTAACCATTG
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
22 14 0.24
23 23 0.39
24 22 0.37
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (23 bp):
GGTTAGGGTTAGGGTTAGTTTAG
Found at i:455435 original size:17 final size:17
Alignment explanation
Indices: 455354--455436 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 17
455344 AGTTAGGTTT
** *
455354 GGGTTAGGGTTAGTTTT
1 GGGTTAGGGTTAGGGTA
455371 GGGTTAGGGGTTAGGGTTA
1 GGGTTA-GGGTTAGGG-TA
* *
455390 -GTTTAGGGTTAGGATTA
1 GGGTTAGGGTTAGG-GTA
*
455407 GGGTTA-GTTTAGGGTA
1 GGGTTAGGGTTAGGGTA
455423 GGGTTAGGGTTAGG
1 GGGTTAGGGTTAGG
455437 TAACCATTGT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
16 8 0.15
17 28 0.54
18 15 0.29
19 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.46, T:0.37
Consensus pattern (17 bp):
GGGTTAGGGTTAGGGTA
Found at i:455450 original size:9 final size:9
Alignment explanation
Indices: 455436--455471 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
455426 TTAGGGTTAG
*
455436 GTAACCATT
1 GTAACCAAT
455445 GTAACCAAT
1 GTAACCAAT
*
455454 GTTACCAAT
1 GTAACCAAT
455463 GTAACCAAT
1 GTAACCAAT
455472 TTAAAAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (9 bp):
GTAACCAAT
Found at i:455732 original size:92 final size:92
Alignment explanation
Indices: 455473--455925 Score: 734
Period size: 92 Copynumber: 4.9 Consensus size: 92
455463 GTAACCAATT
* * * *
455473 TAAAA-AAGACCCCCTGC-AAATCATGAAAATGAC-TGTCACCACTGTTACC-CTATGTCACAAA
1 TAAAATAAGACCCCCTGCTAAA-CA-GAAAAAGGCTTGTCACCTCTGTTACCTCT-TGTCACCAA
* * * *
455534 GAGAATAGAGCTGTTACCATTGTAACCAAA
63 TAGAATATAGCTGTAACCATTGTAACCACA
*
455564 TAAAATAAGACCCCCTGCTAAACAGAAAAAAGGCTTGTCACCTCTGTTACCGCTTGTCACCAATA
1 TAAAATAAGACCCCCTGCTAAACAG-AAAAAGGCTTGTCACCTCTGTTACCTCTTGTCACCAATA
455629 GAATATAGCTGTAACCATTGTAACCACA
65 GAATATAGCTGTAACCATTGTAACCACA
455657 TAAAATAAGACCCCCTGCTAAACAGAAAAAGGCTTGTCACCTCTGTTACCTCTTGTCACCAATAG
1 TAAAATAAGACCCCCTGCTAAACAGAAAAAGGCTTGTCACCTCTGTTACCTCTTGTCACCAATAG
455722 AATATAGCTGTAACCATTGTAACCACA
66 AATATAGCTGTAACCATTGTAACCACA
455749 TAAAATAAGACCCCCTGCTAAACAGAAAAAGGCTTGTCACCTCTGTTACCTCTTGTCACCAATAG
1 TAAAATAAGACCCCCTGCTAAACAGAAAAAGGCTTGTCACCTCTGTTACCTCTTGTCACCAATAG
455814 AATATAGCTGTAACCATTGTAACCACA
66 AATATAGCTGTAACCATTGTAACCACA
* * *
455841 TAAAATAAGACCCCCAGCTAAACAGAAAAAGGCTCGTCACCTCTGTTACCTTTTGTCACCAATAG
1 TAAAATAAGACCCCCTGCTAAACAGAAAAAGGCTTGTCACCTCTGTTACCTCTTGTCACCAATAG
455906 AATATAGCTGTAACCATTGT
66 AATATAGCTGTAACCATTGT
455926 TACTGGATGA
Statistics
Matches: 345, Mismatches: 12, Indels: 9
0.94 0.03 0.02
Matches are distributed among these distances:
91 6 0.02
92 260 0.75
93 77 0.22
94 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (92 bp):
TAAAATAAGACCCCCTGCTAAACAGAAAAAGGCTTGTCACCTCTGTTACCTCTTGTCACCAATAG
AATATAGCTGTAACCATTGTAACCACA
Found at i:459923 original size:9 final size:9
Alignment explanation
Indices: 459871--459908 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
459861 AAGGGGGCTC
459871 TTATAATGA
1 TTATAATGA
459880 TTATAATGA
1 TTATAATGA
*
459889 TTAT-ATTA
1 TTATAATGA
459897 -TATAATGA
1 TTATAATGA
459905 TTAT
1 TTAT
459909 TATAATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
7 3 0.12
8 6 0.24
9 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (9 bp):
TTATAATGA
Done.