Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001690.1 Kokia drynarioides strain JFW-HI SEQ_113369, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 49158
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:6915 original size:22 final size:21
Alignment explanation
Indices: 6890--6937 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
6880 ATAATCCGTT
*
6890 TCATCTCAATTCTATTTTCATA
1 TCATCTC-ATTCTAGTTTCATA
* *
6912 TCATTCTCATTTTAGTTTCATT
1 TCA-TCTCATTCTAGTTTCATA
6934 TCAT
1 TCAT
6938 GATCAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 17 0.77
23 4 0.18
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.54
Consensus pattern (21 bp):
TCATCTCATTCTAGTTTCATA
Found at i:7136 original size:10 final size:10
Alignment explanation
Indices: 7121--7155 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
7111 ATTAACTAAA
7121 TCATTCAAAC
1 TCATTCAAAC
7131 TCATTCAAAC
1 TCATTCAAAC
*
7141 TCATGCAAAAC
1 TCATTC-AAAC
7152 TCAT
1 TCAT
7156 AAAAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.40, C:0.29, G:0.03, T:0.29
Consensus pattern (10 bp):
TCATTCAAAC
Found at i:9081 original size:17 final size:17
Alignment explanation
Indices: 9061--9093 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9051 TTAGTTTTTA
*
9061 CTTATTTTTCTTTTATG
1 CTTATTTTTATTTTATG
9078 CTTATTTTTATTTTAT
1 CTTATTTTTATTTTAT
9094 TTTGCTAGTA
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:0.15, C:0.09, G:0.03, T:0.73
Consensus pattern (17 bp):
CTTATTTTTATTTTATG
Found at i:10349 original size:27 final size:27
Alignment explanation
Indices: 10319--10374 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
10309 AGATTTCATC
10319 CAACCTTACCGTATGATTCCGTCAATA
1 CAACCTTACCGTATGATTCCGTCAATA
* *
10346 CAACCTTGCCGTATGATTCCGTTAATA
1 CAACCTTACCGTATGATTCCGTCAATA
10373 CA
1 CA
10375 TGGCACTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (27 bp):
CAACCTTACCGTATGATTCCGTCAATA
Found at i:11729 original size:15 final size:15
Alignment explanation
Indices: 11709--11740 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11699 GCTAACAACC
11709 TCCTATTTTGTAACT
1 TCCTATTTTGTAACT
*
11724 TCCTATTTTGTTACT
1 TCCTATTTTGTAACT
11739 TC
1 TC
11741 ATAGCTTAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.22, G:0.06, T:0.56
Consensus pattern (15 bp):
TCCTATTTTGTAACT
Found at i:15857 original size:30 final size:31
Alignment explanation
Indices: 15823--16006 Score: 168
Period size: 30 Copynumber: 6.2 Consensus size: 31
15813 TGAAAATCAC
15823 ATTTTGA-CCTTAAACATTTTCTAAAATTAT
1 ATTTTGACCCTTAAACATTTTCTAAAATTAT
*
15853 ATTTTGACCAC--AAA-ATTTTCCAAAATTAT
1 ATTTTGACC-CTTAAACATTTTCTAAAATTAT
* *
15882 ATATTGACCCTTAAA-ATTTTCTCAAATTAT
1 ATTTTGACCCTTAAACATTTTCTAAAATTAT
* * *
15912 ATTTTAACCCTTAAAC-TTTTCCAAAATTAC
1 ATTTTGACCCTTAAACATTTTCTAAAATTAT
* * * *
15942 ATTTTAACCCCTAAAC-TTTTCTAAAATCAC
1 ATTTTGACCCTTAAACATTTTCTAAAATTAT
* * * * *
15972 ATTTTTACCCTCAAAC-TTCTCAAAAATCAT
1 ATTTTGACCCTTAAACATTTTCTAAAATTAT
16002 ATTTT
1 ATTTT
16007 TGCTCCTGAA
Statistics
Matches: 131, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
28 1 0.01
29 22 0.17
30 106 0.81
31 1 0.01
32 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (31 bp):
ATTTTGACCCTTAAACATTTTCTAAAATTAT
Found at i:16007 original size:30 final size:30
Alignment explanation
Indices: 15912--16189 Score: 211
Period size: 30 Copynumber: 9.5 Consensus size: 30
15902 CTCAAATTAT
* * * * *
15912 ATTTTAACCCTTAAACTTTTCCAAAATTAC
1 ATTTTTACCCTCAAACTTCTCAAAAATCAC
* * *
15942 ATTTTAACCC-CTAAACTTTTCTAAAATCAC
1 ATTTTTACCCTC-AAACTTCTCAAAAATCAC
*
15972 ATTTTTACCCTCAAACTTCTCAAAAATCAT
1 ATTTTTACCCTCAAACTTCTCAAAAATCAC
* *
16002 ATTTTTGCTCCT-GAA-TT-TCAAAACATCAC
1 ATTTTTAC-CCTCAAACTTCTCAAAA-ATCAC
* * *
16031 A-TTTTGCCCTCGAATTTC-CAAAAATCAC
1 ATTTTTACCCTCAAACTTCTCAAAAATCAC
* *
16059 A-TTTTGCCCTCGAACTT-TCAAAAATCAC
1 ATTTTTACCCTCAAACTTCTCAAAAATCAC
* *
16087 AATTTTGCCC-CTAAACTT-TCAAAAATCAC
1 ATTTTTACCCTC-AAACTTCTCAAAAATCAC
* * *
16116 A-TTTTACCATCAAACTTCTCAAAAATTAT
1 ATTTTTACCCTCAAACTTCTCAAAAATCAC
* * *
16145 ATTTTTACCCTCGAACTTCTTAAAAATTACC
1 ATTTTTACCCTCAAACTTCTCAAAAATCA-C
16176 A-TTTTACCCTCAAA
1 ATTTTTACCCTCAAA
16190 AATCCAAAAA
Statistics
Matches: 213, Mismatches: 21, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
27 3 0.01
28 60 0.28
29 50 0.23
30 95 0.45
31 5 0.02
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (30 bp):
ATTTTTACCCTCAAACTTCTCAAAAATCAC
Found at i:16035 original size:28 final size:28
Alignment explanation
Indices: 15959--16186 Score: 194
Period size: 28 Copynumber: 7.9 Consensus size: 28
15949 CCCCTAAACT
* * *
15959 TTTCTAAAATCACATTTTTACCCTCAAAC
1 TTTCAAAAATCACA-TTTTGCCCTCGAAC
*
15988 TTCTCAAAAATCATATTTTTGCTCCT-GAA-
1 TT-TCAAAAATCACA-TTTTGC-CCTCGAAC
16017 TTTCAAAACATCACATTTTGCCCTCGAA-
1 TTTCAAAA-ATCACATTTTGCCCTCGAAC
16045 TTTCCAAAAATCACATTTTGCCCTCGAAC
1 TTT-CAAAAATCACATTTTGCCCTCGAAC
*
16074 TTTCAAAAATCACAATTTTGCCC-CTAAAC
1 TTTCAAAAATCAC-ATTTTGCCCTC-GAAC
* * *
16103 TTTCAAAAATCACATTTTACCATCAAAC
1 TTTCAAAAATCACATTTTGCCCTCGAAC
* * *
16131 TTCTCAAAAATTATATTTTTACCCTCGAAC
1 TT-TCAAAAATCACA-TTTTGCCCTCGAAC
* * *
16161 TTCTTAAAAATTACCATTTTACCCTC
1 TT-TCAAAAATCA-CATTTTGCCCTC
16187 AAAAATCCAA
Statistics
Matches: 173, Mismatches: 14, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.02
28 61 0.35
29 53 0.31
30 52 0.30
31 4 0.02
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (28 bp):
TTTCAAAAATCACATTTTGCCCTCGAAC
Found at i:16063 original size:57 final size:57
Alignment explanation
Indices: 15959--16120 Score: 181
Period size: 57 Copynumber: 2.8 Consensus size: 57
15949 CCCCTAAACT
* * * *
15959 TTTCTAAAATCACATTTTTACCCTCAAACTTCTCAAAAATCATATTTTTGCTCCT-GAA-
1 TTTCAAAAATCACA-TTTTGCCCTCAAATTTC-CAAAAATCACATTTTTGC-CCTCGAAC
*
16017 TTTCAAAACATCACATTTTGCCCTCGAATTTCCAAAAATCACA-TTTTGCCCTCGAAC
1 TTTCAAAA-ATCACATTTTGCCCTCAAATTTCCAAAAATCACATTTTTGCCCTCGAAC
16074 TTTCAAAAATCACAATTTTGCCC-CTAAACTTT-CAAAAATCACATTTT
1 TTTCAAAAATCAC-ATTTTGCCCTC-AAA-TTTCCAAAAATCACATTTT
16121 ACCATCAAAC
Statistics
Matches: 91, Mismatches: 6, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
55 3 0.03
56 15 0.16
57 40 0.44
58 27 0.30
59 6 0.07
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (57 bp):
TTTCAAAAATCACATTTTGCCCTCAAATTTCCAAAAATCACATTTTTGCCCTCGAAC
Found at i:16132 original size:57 final size:56
Alignment explanation
Indices: 15929--16141 Score: 159
Period size: 57 Copynumber: 3.7 Consensus size: 56
15919 CCCTTAAACT
* * * *
15929 TTTCC-AAAATTACATTTTAACC-CCTAAACTTTTCTAAAATCACATTTTTACCCTCAAA
1 TTTCCAAAAATCACATTTT-ACCATC-AAAC-TTTCAAAAATCACA-TTTTGCCCTCAAA
* * ** * *
15987 CTTCTCAAAAATCATATTTTTGC-TCCTGAA-TTTCAAAACATCACATTTTGCCCTCGAA
1 TTTC-CAAAAATCACATTTTACCAT-C-AAACTTTCAAAA-ATCACATTTTGCCCTCAAA
* * *
16045 TTTCCAAAAATCACATTTTGCCCTCGAACTTTCAAAAATCACAATTTTGCCC-CTAAA
1 TTTCCAAAAATCACATTTTACCATCAAACTTTCAAAAATCAC-ATTTTGCCCTC-AAA
16102 CTTT-CAAAAATCACATTTTACCATCAAACTTCTCAAAAAT
1 -TTTCCAAAAATCACATTTTACCATCAAACTT-TCAAAAAT
16142 TATATTTTTA
Statistics
Matches: 127, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
56 9 0.07
57 59 0.46
58 36 0.28
59 8 0.06
60 15 0.12
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (56 bp):
TTTCCAAAAATCACATTTTACCATCAAACTTTCAAAAATCACATTTTGCCCTCAAA
Found at i:20833 original size:17 final size:17
Alignment explanation
Indices: 20813--20889 Score: 57
Period size: 17 Copynumber: 5.1 Consensus size: 17
20803 CCAATTTTAA
20813 ATTTTAAAATTT-AATTT
1 ATTTT-AAATTTAAATTT
*
20830 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
20847 A--TT-AATTT--A--T
1 ATTTTAAATTTAAATTT
20857 -T-TTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
20872 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
20889 A
1 A
20890 AAATTAATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
10 3 0.06
11 5 0.10
12 1 0.02
13 1 0.02
14 4 0.08
15 3 0.06
16 6 0.12
17 25 0.52
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:20854 original size:25 final size:25
Alignment explanation
Indices: 20806--20900 Score: 99
Period size: 25 Copynumber: 3.9 Consensus size: 25
20796 ATTGAACCCA
*
20806 ATTTTAAATTTTAAA-AT-TTAATTT
1 ATTTTAAA-TTTAAATTTATTAATTT
*
20830 ATTTTAAGTTTAAATTTATTAATTT
1 ATTTTAAATTTAAATTTATTAATTT
*
20855 ATTTTAAATTTAAATTTATT--TTG
1 ATTTTAAATTTAAATTTATTAATTT
* *
20878 AATTTAAATTTAAAATTAATTAA
1 ATTTTAAATTT-AAATTTATTAA
20901 ATGTCAAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
23 18 0.30
24 16 0.27
25 26 0.43
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTTTAAATTTAAATTTATTAATTT
Found at i:20893 original size:7 final size:6
Alignment explanation
Indices: 20808--20896 Score: 60
Period size: 6 Copynumber: 14.8 Consensus size: 6
20798 TGAACCCAAT
* * *
20808 TTTAAA TTTTAAAA TTT-AA TTT-AT TTTAAG TTTAAA TTTATTAA TTT-AT
1 TTTAAA -TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA
* * *
20857 TTTAAA TTTAAA TTT-AT TTTGAA TTTAAA TTTAAA ATTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
20897 TTAAATGTCA
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
5 17 0.25
6 36 0.54
7 6 0.09
8 8 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:21469 original size:11 final size:11
Alignment explanation
Indices: 21455--21480 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21445 AAATGTCTAC
21455 TAAATAAATAA
1 TAAATAAATAA
21466 TAAATAAATAA
1 TAAATAAATAA
21477 TAAA
1 TAAA
21481 AAGTGGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:27924 original size:9 final size:9
Alignment explanation
Indices: 27892--27977 Score: 79
Period size: 9 Copynumber: 9.4 Consensus size: 9
27882 ATAAATAAAT
*
27892 AAAATAAAG
1 AAAAGAAAG
27901 AAAAGAAAG
1 AAAAGAAAG
*
27910 AAAAAAGAATAA
1 --AAAAGAA-AG
27922 AAAAGAAAG
1 AAAAGAAAG
27931 AAAAGAAAG
1 AAAAGAAAG
27940 AAAAGAAAAG
1 AAAAG-AAAG
*
27950 GAAA-AAAG
1 AAAAGAAAG
*
27958 AAAA-AAGG
1 AAAAGAAAG
27966 AAAA-AAAG
1 AAAAGAAAG
27974 AAAA
1 AAAA
27978 TAGAAAAGGA
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
8 21 0.32
9 23 0.35
10 14 0.21
11 7 0.11
12 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:27933 original size:30 final size:30
Alignment explanation
Indices: 27873--27985 Score: 115
Period size: 30 Copynumber: 3.7 Consensus size: 30
27863 CGGATTCAAT
* *
27873 AAAGAAAAAATAAATAAATAAAATAAAGAAAAG
1 AAAGAAAAGA-AAAT-AA-AAAAGAAAGAAAAG
27906 AAAGAAAA-AAGAATAAAAAAGAAAGAAAAG
1 AAAGAAAAGAA-AATAAAAAAGAAAGAAAAG
* *
27936 AAAGAAAAGAAAAGGAAAAAAGAAA-AAAGG
1 AAAGAAAAGAAAA-TAAAAAAGAAAGAAAAG
*
27966 AAA-AAAAGAAAATAGAAAAG
1 AAAGAAAAGAAAATAAAAAAG
27986 GAGAGGTCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
28 6 0.08
29 9 0.12
30 30 0.42
31 15 0.21
32 4 0.06
33 8 0.11
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (30 bp):
AAAGAAAAGAAAATAAAAAAGAAAGAAAAG
Found at i:27940 original size:34 final size:33
Alignment explanation
Indices: 27892--27982 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 33
27882 ATAAATAAAT
*
27892 AAAATAAAGAAAAGAAAGAAAAAAGAATAAAAAAG
1 AAAA-AAAG-AAAGAAAGAAAAAAGAAGAAAAAAG
*
27927 AAAGAAAAGAAAGAAA-AGAAAAG--GAAAAAAG
1 AAA-AAAAGAAAGAAAGAAAAAAGAAGAAAAAAG
* * *
27958 AAAAAAGGAAAAAAAGAAAATAGAA
1 AAAAAAAGAAAGAAAGAAAAAAGAA
27983 AAGGAGAGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
30 10 0.22
31 15 0.33
33 6 0.13
34 7 0.15
35 7 0.15
36 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (33 bp):
AAAAAAAGAAAGAAAGAAAAAAGAAGAAAAAAG
Found at i:27942 original size:39 final size:39
Alignment explanation
Indices: 27873--27976 Score: 115
Period size: 39 Copynumber: 2.6 Consensus size: 39
27863 CGGATTCAAT
* *
27873 AAAGAAAAAATAAATAAATAAAATAAAGAAAAG-AAA-GAAA
1 AAAG-AAAAA-AAAGAAA-AAAAGAAAGAAAAGAAAAGGAAA
27913 AAAGAATAAAAAAGAAAGAAAAGAAAGAAAAGAAAAGGAAA
1 AAAGAA-AAAAAAGAAA-AAAAGAAAGAAAAGAAAAGGAAA
*
27954 AAAG-AAAAAAGGAAAAAAAGAAA
1 AAAGAAAAAAAAGAAAAAAAGAAA
27977 ATAGAAAAGG
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
38 8 0.14
39 30 0.53
40 11 0.19
41 8 0.14
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (39 bp):
AAAGAAAAAAAAGAAAAAAAGAAAGAAAAGAAAAGGAAA
Found at i:27984 original size:14 final size:13
Alignment explanation
Indices: 27906--27984 Score: 63
Period size: 14 Copynumber: 5.6 Consensus size: 13
27896 TAAAGAAAAG
27906 AAAGAAAAAAGAA
1 AAAGAAAAAAGAA
27919 TAAA-AAAGAAAG-A
1 -AAAGAAA-AAAGAA
27932 AAAGAAAGAAAAGAA
1 AAAG-AA-AAAAGAA
*
27947 AAGGAAAAAAGAAA
1 AAAGAAAAAAG-AA
27961 AAAGGAAAAAAAGAA
1 AAA-G-AAAAAAGAA
27976 AATAGAAAA
1 AA-AGAAAA
27985 GGAGAGGTCT
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
12 3 0.06
13 9 0.17
14 23 0.43
15 11 0.20
16 8 0.15
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.03
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:29131 original size:49 final size:49
Alignment explanation
Indices: 29013--29381 Score: 296
Period size: 49 Copynumber: 7.5 Consensus size: 49
29003 ATGTAATTGA
* * * *
29013 AAAGATTGAGGCCGCAACGGTGAATCC-GGTACCATGAA-ATGTGATGGG
1 AAAGATTGAGGCCGCAATGGCGAA-CCTGGTACCATGAAGATTTGAAGGG
* * * * *
29061 AAAGATTGAAGCCGCAGTGGCGAACCCGGTACCATGAAGATTTTAAGGT
1 AAAGATTGAGGCCGCAATGGCGAACCTGGTACCATGAAGATTTGAAGGG
* * * *
29110 AAAGATTGAGGCCGTAATGGCGAACCTAGTACCTTAGAAGATATGAA-GG
1 AAAGATTGAGGCCGCAATGGCGAACCTGGTACCAT-GAAGATTTGAAGGG
* * *
29159 AAAGATTGAGGCTGTAATGGCGAACCTGGTACCATGAAGATTTTAAGGG
1 AAAGATTGAGGCCGCAATGGCGAACCTGGTACCATGAAGATTTGAAGGG
* * * * * *
29208 AAAGGTTGAGGCCGCAACGGTGAACTTGGTACCTTGGAAGATATGAAGGG
1 AAAGATTGAGGCCGCAATGGCGAACCTGGTACCAT-GAAGATTTGAAGGG
* * * * * *
29258 AAAGGTTGAGGCCTCAATGGGGAATCTGGTACCATGAAGATTTTAAAGG
1 AAAGATTGAGGCCGCAATGGCGAACCTGGTACCATGAAGATTTGAAGGG
* * * * ** * * * * *
29307 AAAGGTT-AGGGCTGTAACGGTAAACTTGATACCTTAGAAGATATGAAAGG
1 AAAGATTGA-GGCCGCAATGGCGAACCTGGTACCAT-GAAGATTTGAAGGG
* *
29357 AAAGGTTGAGGCCGCAACGGCGAAC
1 AAAGATTGAGGCCGCAATGGCGAAC
29382 TCAGTACCTT
Statistics
Matches: 257, Mismatches: 56, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
47 2 0.01
48 41 0.16
49 132 0.51
50 81 0.32
51 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (49 bp):
AAAGATTGAGGCCGCAATGGCGAACCTGGTACCATGAAGATTTGAAGGG
Found at i:29260 original size:50 final size:49
Alignment explanation
Indices: 28898--29391 Score: 268
Period size: 50 Copynumber: 10.0 Consensus size: 49
28888 GAGAAAAACG
* * * *
28898 TGAAGATTTGAAGGG-AAGGATTGA-GCTAGCAACGACGAA-TCCGGTACCT
1 TGAAGATATGAAGGGAAAGG-TTGAGGC-CGCAACGGCGAACT-TGGTACCT
* * * ** * * *
28947 TAGAAGATGTGACGGGAAGGGTTGAGGCCATAACGGTGAACCTGATACCT
1 T-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTTGGTACCT
* * * * * * * *
28997 CAGAAGATGT-AATTGAAAAGATTGAGGCCGCAACGGTGAA-TCCGGTACCA
1 -TGAAGATATGAA-GGGAAAGGTTGAGGCCGCAACGGCGAACT-TGGTACCT
* * * * ** ** *
29047 TGAA-ATGTGATGGGAAAGATTGAAGCCGCAGTGGCGAACCCGGTACCA
1 TGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTTGGTACCT
* * * * * * * *
29095 TGAAGATTTTAAGGTAAAGATTGAGGCCGTAATGGCGAACCTAGTACCT
1 TGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTTGGTACCT
* * * * * *
29144 TAGAAGATATGAA-GGAAAGATTGAGGCTGTAATGGCGAACCTGGTACCA
1 T-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTTGGTACCT
* * *
29193 TGAAGATTTTAAGGGAAAGGTTGAGGCCGCAACGGTGAACTTGGTACCT
1 TGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTTGGTACCT
* * * *
29242 TGGAAGATATGAAGGGAAAGGTTGAGGCCTCAATGGGGAA-TCTGGTACCA
1 T-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACT-TGGTACCT
* * * * * ** *
29292 TGAAGATTTTAAAGGAAAGGTT-AGGGCTGTAACGGTAAACTTGATACCT
1 TGAAGATATGAAGGGAAAGGTTGA-GGCCGCAACGGCGAACTTGGTACCT
* **
29341 TAGAAGATATGAAAGGAAAGGTTGAGGCCGCAACGGCGAACTCAGTACCT
1 T-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTTGGTACCT
29391 T
1 T
29392 AGAAAACAAG
Statistics
Matches: 344, Mismatches: 83, Indels: 35
0.74 0.18 0.08
Matches are distributed among these distances:
48 47 0.14
49 139 0.40
50 152 0.44
51 6 0.02
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (49 bp):
TGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTTGGTACCT
Found at i:29309 original size:99 final size:99
Alignment explanation
Indices: 29013--29381 Score: 392
Period size: 99 Copynumber: 3.8 Consensus size: 99
29003 ATGTAATTGA
* * * * * *
29013 AAAGATTGAGGCCGCAACGGTGAA-TCCGGTACCAT-GAA-ATGTGATGGGAAAGATTGAAGCCG
1 AAAGATTGAGGCCGCAACGGTGAACT-TGGTACCTTAGAAGATATGAAGGGAAAGATTGAGGCCT
* *
29075 CAGTGGCGAACCCGGTACCATGAAGATTTT-AAGG
65 CAATGGCGAACCTGGTACCATGAAGATTTTAAAGG
* * * * *
29109 TAAAGATTGAGGCCGTAATGGCGAACCTAGTACCTTAGAAGATATGAA-GGAAAGATTGAGG-CT
1 -AAAGATTGAGGCCGCAACGGTGAACTTGGTACCTTAGAAGATATGAAGGGAAAGATTGAGGCCT
* *
29172 GTAATGGCGAACCTGGTACCATGAAGATTTTAAGGG
65 -CAATGGCGAACCTGGTACCATGAAGATTTTAAAGG
* * *
29208 AAAGGTTGAGGCCGCAACGGTGAACTTGGTACCTTGGAAGATATGAAGGGAAAGGTTGAGGCCTC
1 AAAGATTGAGGCCGCAACGGTGAACTTGGTACCTTAGAAGATATGAAGGGAAAGATTGAGGCCTC
* *
29273 AATGGGGAATCTGGTACCATGAAGATTTTAAAGG
66 AATGGCGAACCTGGTACCATGAAGATTTTAAAGG
* * * * * * * *
29307 AAAGGTT-AGGGCTGTAACGGTAAACTTGATACCTTAGAAGATATGAAAGGAAAGGTTGAGGCCG
1 AAAGATTGA-GGCCGCAACGGTGAACTTGGTACCTTAGAAGATATGAAGGGAAAGATTGAGGCCT
*
29371 CAACGGCGAAC
65 CAATGGCGAAC
29382 TCAGTACCTT
Statistics
Matches: 227, Mismatches: 37, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
97 28 0.12
98 83 0.37
99 114 0.50
100 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (99 bp):
AAAGATTGAGGCCGCAACGGTGAACTTGGTACCTTAGAAGATATGAAGGGAAAGATTGAGGCCTC
AATGGCGAACCTGGTACCATGAAGATTTTAAAGG
Found at i:29612 original size:41 final size:41
Alignment explanation
Indices: 29552--29646 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
29542 CAACATCATT
*
29552 CAATCTTTTACCCTTAATCAAGAA-GGTCAGATTGAAAATTC
1 CAATCTTTTACCCTTAATCAAGAAGGGT-AGAATGAAAATTC
* * * *
29593 CAGTCTTTTACTCTTAATCAAGAAGGGTAGAATGAAGATTT
1 CAATCTTTTACCCTTAATCAAGAAGGGTAGAATGAAAATTC
29634 CAATCTTTTACCC
1 CAATCTTTTACCC
29647 CGAGCCTAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
41 43 0.93
42 3 0.07
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34
Consensus pattern (41 bp):
CAATCTTTTACCCTTAATCAAGAAGGGTAGAATGAAAATTC
Found at i:29684 original size:39 final size:39
Alignment explanation
Indices: 29635--29942 Score: 132
Period size: 39 Copynumber: 7.9 Consensus size: 39
29625 TGAAGATTTC
* *
29635 AATCTTTTACCCCGAGCCTAAGGCGGATCACCATCAGCT
1 AATCTCTTACCCCGAGCCTAAGGCAGATCACCATCAGCT
* *
29674 AATCTCTTA-CCCAAGCCTAGGGCAGATTGCAACCATC--C-
1 AATCTCTTACCCCGAGCCTAAGGCAGA-T-C-ACCATCAGCT
* * * *
29712 GATCTTTTTCCTCGAGCCTAAGGCAGATCACCATCAG-T
1 AATCTCTTACCCCGAGCCTAAGGCAGATCACCATCAGCT
* * * ** *
29750 CAATCTCTTACCCCGAGCCTAGGGTAGATTACCGCCA-TT
1 -AATCTCTTACCCCGAGCCTAAGGCAGATCACCATCAGCT
* * * ** * * *
29789 CGATCTTTTACCCCAAGCCTGGGGTAGATCACCATTAGCC
1 -AATCTCTTACCCCGAGCCTAAGGCAGATCACCATCAGCT
* ** * ** *
29829 AATCTTTTACCTTGAGCCTAGGGCAGAT-TGCAGTCA-TT
1 AATCTCTTACCCCGAGCCTAAGGCAGATCACCA-TCAGCT
* * * *
29867 CGATCTTTTTCCCCGAG-CTTAGAGCAGATCACCATCAGCCT
1 -AATCTCTTACCCCGAGCCTAAG-GCAGATCACCATCAG-CT
* * * *
29908 -ATCTCTTAGCCTGAGCCTGAGGCAGATCAGCATCA
1 AATCTCTTACCCCGAGCCTAAGGCAGATCACCATCA
29943 ACCACCTGAT
Statistics
Matches: 197, Mismatches: 55, Indels: 34
0.69 0.19 0.12
Matches are distributed among these distances:
36 6 0.03
37 1 0.01
38 26 0.13
39 150 0.76
40 7 0.04
41 7 0.04
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (39 bp):
AATCTCTTACCCCGAGCCTAAGGCAGATCACCATCAGCT
Found at i:29818 original size:78 final size:78
Alignment explanation
Indices: 29636--29934 Score: 334
Period size: 78 Copynumber: 3.8 Consensus size: 78
29626 GAAGATTTCA
* * *
29636 ATCTTTTACCCCGAGCCTAAGGCGGATCACCATCAGCTAATCTCTTA-CCCAAGCCTAGGGCAGA
1 ATCTTTTACCCCGAGCCTAAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
* *
29700 TTGCAACCATCCG
66 TTGCAGCCATTCG
* * * *
29713 ATCTTTTTCCTCGAGCCTAAGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTAGGGTAGA
1 ATCTTTTACCCCGAGCCTAAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
* *
29778 TTACCGCCATTCG
66 TTGCAGCCATTCG
* ** * * * **
29791 ATCTTTTACCCCAAGCCTGGGGTAGATCACCATTAGCCAATCTTTTACCTTGAGCCTAGGGCAGA
1 ATCTTTTACCCCGAGCCTAAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
*
29856 TTGCAGTCATTCG
66 TTGCAGCCATTCG
* * * * *
29869 ATCTTTTTCCCCGAG-CTTAGAGCAGATCACCATCAGCCTATCTCTTAGCCTGAGCCT-GAGGCA
1 ATCTTTTACCCCGAGCCTAAG-GCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAG-GGCA
29932 GAT
64 GAT
29935 CAGCATCAAC
Statistics
Matches: 183, Mismatches: 36, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
77 46 0.25
78 137 0.75
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (78 bp):
ATCTTTTACCCCGAGCCTAAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
TTGCAGCCATTCG
Found at i:30410 original size:209 final size:209
Alignment explanation
Indices: 30046--30552 Score: 673
Period size: 209 Copynumber: 2.4 Consensus size: 209
30036 AATGGTCGTT
* * *
30046 TTCCTGATGAGATACAGAGAAGTGGATTAAAACAAGTGATGCGATCATCTTCCTCATGAGATGCA
1 TTCCTGATGAGATACAGAGAAGTGGATTTAAACAAGTGATGCGATCATCTTCCTAATGAGATACA
* * * *
30111 GAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGAGTGAAACTTCGATCCTCAGCTTCCTG
66 GAGAAGTAAACCAAATCAATGAAACAAAGCTCAATATGAGCGAAACTTCGAACCTCAGCTTCCTA
* * * * *
30176 ATGATGTACTGAGAAGCAAGTCGAAGCAATAAAATGGT-AGTCTTCCAGATGAGATACAGAGAAG
131 ATGATGTACTGAAAAACAAGTCGAAGCAATAAAACGGTCA-TCGTCCAGATGAGACACAGAGAAG
30240 TGGACCAAATCCGAC
195 TGGACCAAATCCGAC
* * *
30255 TTCCTGATGAGATACAGAGAAGTGGATTTAAATAATTGATGCGATCATCTTCCTAATGAGATACT
1 TTCCTGATGAGATACAGAGAAGTGGATTTAAACAAGTGATGCGATCATCTTCCTAATGAGATACA
* *
30320 GAGGAA-TAAACCAAATTAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACC-CGAGCTTCC
66 GA-GAAGTAAACCAAATCAATGAAACAAAGCTCAATATGAGCGAAACTTCGAACCTC-AGCTTCC
** *
30383 TAATGA-GATACTGAAAAACGGGTCGAAGCAATAAAACGGTCATCGTCCTGATGAGACACAGAGA
129 TAATGATG-TACTGAAAAACAAGTCGAAGCAATAAAACGGTCATCGTCCAGATGAGACACAGAGA
*
30447 AGTGGACCAAATCCGTC
193 AGTGGACCAAATCCGAC
** * * * *
30464 TTCCTGATGAGATACAGAGAAGCAGA-CTAAAGCAAGTGATGCGGTCATCTTCCTGATGAGATAT
1 TTCCTGATGAGATACAGAGAAGTGGATTTAAA-CAAGTGATGCGATCATCTTCCTAATGAGATAC
*
30528 AGAGAAGTAGACCAAATCAAATGAA
65 AGAGAAGTAAACCAAATC-AATGAA
30553 GAAAATGCGA
Statistics
Matches: 259, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
208 9 0.03
209 240 0.93
210 10 0.04
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (209 bp):
TTCCTGATGAGATACAGAGAAGTGGATTTAAACAAGTGATGCGATCATCTTCCTAATGAGATACA
GAGAAGTAAACCAAATCAATGAAACAAAGCTCAATATGAGCGAAACTTCGAACCTCAGCTTCCTA
ATGATGTACTGAAAAACAAGTCGAAGCAATAAAACGGTCATCGTCCAGATGAGACACAGAGAAGT
GGACCAAATCCGAC
Found at i:31060 original size:6 final size:6
Alignment explanation
Indices: 31034--31161 Score: 57
Period size: 6 Copynumber: 21.8 Consensus size: 6
31024 TGAACCCAAT
* * * *
31034 TTTAAA TTTTAA TTT-AT TTTAAG TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * * * * * ** * *
31080 CTTATT TTTGAG TTTAAA TTT-AT TTTAAG TTTAAA CTTATT TTTGAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
31127 TTTAAA TTT-AT TTTGAA TTTAAA TTTAAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA
31162 TTAAATATCC
Statistics
Matches: 87, Mismatches: 30, Indels: 10
0.69 0.24 0.08
Matches are distributed among these distances:
5 16 0.18
6 65 0.75
7 6 0.07
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:31095 original size:18 final size:17
Alignment explanation
Indices: 31032--31153 Score: 147
Period size: 17 Copynumber: 7.1 Consensus size: 17
31022 ATTGAACCCA
* *
31032 ATTTTAAATTTTAATTT
1 ATTTTAAGTTTAAATTT
31049 ATTTTAAGTTTAAATTT
1 ATTTTAAGTTTAAATTT
* *
31066 ATTTTAAATTTAAACTT
1 ATTTTAAGTTTAAATTT
*
31083 ATTTTTGAGTTTAAATTT
1 A-TTTTAAGTTTAAATTT
*
31101 ATTTTAAGTTTAAACTT
1 ATTTTAAGTTTAAATTT
*
31118 ATTTTTGAGTTTAAATTT
1 A-TTTTAAGTTTAAATTT
31136 ATTTTGAA-TTTAAATTT
1 ATTTT-AAGTTTAAATTT
31153 A
1 A
31154 AAATTTAATT
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
17 60 0.67
18 30 0.33
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTTTAAGTTTAAATTT
Found at i:31101 original size:35 final size:35
Alignment explanation
Indices: 31032--31149 Score: 184
Period size: 35 Copynumber: 3.4 Consensus size: 35
31022 ATTGAACCCA
* * *
31032 ATTTTAAATTTTAATTTA-TTTTAAGTTTAAATTT
1 ATTTTAAATTTAAACTTATTTTTGAGTTTAAATTT
31066 ATTTTAAATTTAAACTTATTTTTGAGTTTAAATTT
1 ATTTTAAATTTAAACTTATTTTTGAGTTTAAATTT
*
31101 ATTTTAAGTTTAAACTTATTTTTGAGTTTAAATTT
1 ATTTTAAATTTAAACTTATTTTTGAGTTTAAATTT
*
31136 ATTTTGAATTTAAA
1 ATTTTAAATTTAAA
31150 TTTAAAATTT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
34 16 0.21
35 61 0.79
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (35 bp):
ATTTTAAATTTAAACTTATTTTTGAGTTTAAATTT
Found at i:31120 original size:52 final size:52
Alignment explanation
Indices: 31032--31153 Score: 165
Period size: 52 Copynumber: 2.3 Consensus size: 52
31022 ATTGAACCCA
* * *
31032 ATTTTAAATTTTAATTTATTTTAAGTTTAAATTTA-TTTTAAATTTAAACTT
1 ATTTTGAATTTAAATTTATTTTAAGTTTAAACTTATTTTTAAATTTAAACTT
* * * *
31083 ATTTTTGAGTTTAAATTTATTTTAAGTTTAAACTTATTTTTGAGTTTAAATTT
1 A-TTTTGAATTTAAATTTATTTTAAGTTTAAACTTATTTTTAAATTTAAACTT
31136 ATTTTGAATTTAAATTTA
1 ATTTTGAATTTAAATTTA
31154 AAATTTAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
51 1 0.02
52 46 0.75
53 14 0.23
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (52 bp):
ATTTTGAATTTAAATTTATTTTAAGTTTAAACTTATTTTTAAATTTAAACTT
Found at i:31736 original size:11 final size:11
Alignment explanation
Indices: 31722--31747 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31712 ATTAAATAGC
31722 ATAATAAATAA
1 ATAATAAATAA
31733 ATAATAAATAA
1 ATAATAAATAA
31744 ATAA
1 ATAA
31748 ATAAGAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAATAAATAA
Found at i:38237 original size:50 final size:50
Alignment explanation
Indices: 38164--38785 Score: 336
Period size: 50 Copynumber: 12.6 Consensus size: 50
38154 CAGGTTTGAC
* * *
38164 AGGG-AAGGATTGAGGCCGCAACGGCGAATCCGGTACGTTAAAAGATGTGA
1 AGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCTAAAAAGATGTGA
* *
38214 AGGGAAAGGTTGAGGCCACAACGGTGAACCCGGTACCTAAAAAGATGTGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAAAAGATGTGA
* * ** **
38264 TGGGAAAGGTTGAGGCCGTAACATCGAACCCGGTACC-ATGAAGA-GATGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAAAAGATG-TGA
* * * *
38313 AGGG-AAGGATTGAGGCTGCGACGACGAATCCGGTACCTAAAAAGATGTGA
1 AGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCTAAAAAGATGTGA
* * * * ** *
38363 TGGGAAAGGTTGAGGTCGCATCGACGAACCCAATACCTAAGAAGATGTGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAAAAGATGTGA
* * ** * * * * **
38413 TGAGACGGGTTGATGCCGCAACGGCTAACCCAGTACC-ATAAAGATACGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAAAAGATGTGA
* * * ** **
38462 ATGGAAAGGTTGAGTCCGTAACGGCGAACCCGGTACC-ATGAAGATACGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAAAAGATGTGA
* * * ** * * ** ***
38511 AGGAAAAAGTTGAGGCCGCAACGGTGAAGTCGATATC-ACGAAGACACGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAAAAGATGTGA
* * * ** * *
38560 AGGGAAAAGTTGAGGCCGTAATGGCGAACTTGATACCTAAGAAGATGTGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAAAAGATGTGA
* * * * * * * * **
38610 TGAGAAAGCTTGAGGCTGCAATGGTGAATCCGATACC-ATGAAGA-GAT-A
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAAAAGATG-TGA
* * * * *
38658 AGGG-AAGGATTGAGGTCGCGACGGCGAATCCGGCACCTTAGAAA-ATGTGA
1 AGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACC-TAAAAAGATGTGA
* * ** ** * *
38708 TGGGAAAGGTTAAGGCCGCAACGGTAAACCCGGTACC-ATGAATATAT-A
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAAAAGATGTGA
* * *
38756 AGGGAAAGGTTGAGGTCGTAATGGCGAACC
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACC
38786 TAGCACCTTA
Statistics
Matches: 438, Mismatches: 119, Indels: 32
0.74 0.20 0.05
Matches are distributed among these distances:
47 3 0.01
48 57 0.13
49 158 0.36
50 207 0.47
51 13 0.03
ACGTcount: A:0.34, C:0.18, G:0.32, T:0.17
Consensus pattern (50 bp):
AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAAAAGATGTGA
Found at i:38443 original size:149 final size:149
Alignment explanation
Indices: 38164--38533 Score: 375
Period size: 149 Copynumber: 2.5 Consensus size: 149
38154 CAGGTTTGAC
* * *
38164 AGGGAAGGATTGAGGCCGCAACGGCGAATCCGGTACGTTAAAAGATGTGAAGGGAAAGGTTGAGG
1 AGGGAAGGATTGAGGCCGCAACGACGAATCCGGTACCTAAAAAGATGTGAAGGGAAAGGTTGAGG
** ** * * *
38229 CCACAACGGTGAACCCGGTACCTAAAAAGATGTGATGGGAAAGGTTGAGGCCGTAACATCGAACC
66 CCACAACGACGAACCCAATACCTAAAAAGATGTGATGAGAAAGGTTGAGGCCGCAACAGCGAACC
* *
38294 CGGTACCATGAAGAGATGA
131 CAGTACCATAAAGAGATGA
* * *
38313 AGGGAAGGATTGAGGCTGCGACGACGAATCCGGTACCTAAAAAGATGTGATGGGAAAGGTTGAGG
1 AGGGAAGGATTGAGGCCGCAACGACGAATCCGGTACCTAAAAAGATGTGAAGGGAAAGGTTGAGG
* * * * ** * * *
38378 TCGCATCGACGAACCCAATACCTAAGAAGATGTGATGAGACGGGTTGATGCCGCAACGGCTAACC
66 CCACAACGACGAACCCAATACCTAAAAAGATGTGATGAGAAAGGTTGAGGCCGCAACAGCGAACC
* *
38443 CAGTACCATAAAGATACGA
131 CAGTACCATAAAGAGATGA
* * * * * ** ** * *
38462 ATGGAAAGG-TTGAGTCCGTAACGGCGAACCCGGTACC-ATGAAGATACGAAGGAAAAAGTTGAG
1 A-GGGAAGGATTGAGGCCGCAACGACGAATCCGGTACCTAAAAAGATGTGAAGGGAAAGGTTGAG
*
38525 GCCGCAACG
65 GCCACAACG
38534 GTGAAGTCGA
Statistics
Matches: 178, Mismatches: 42, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
148 26 0.15
149 146 0.82
150 6 0.03
ACGTcount: A:0.34, C:0.19, G:0.32, T:0.16
Consensus pattern (149 bp):
AGGGAAGGATTGAGGCCGCAACGACGAATCCGGTACCTAAAAAGATGTGAAGGGAAAGGTTGAGG
CCACAACGACGAACCCAATACCTAAAAAGATGTGATGAGAAAGGTTGAGGCCGCAACAGCGAACC
CAGTACCATAAAGAGATGA
Found at i:38485 original size:49 final size:49
Alignment explanation
Indices: 38421--38588 Score: 151
Period size: 49 Copynumber: 3.4 Consensus size: 49
38411 GATGAGACGG
* * *
38421 GTTGATGCCGCAACGGCTAACCCAGTACCATAAAGATACGAATGG-AAAG
1 GTTGAGGCCGCAACGGCGAACCCAGTACCATAAAGATACGAA-GGAAAAA
* * * *
38470 GTTGAGTCCGTAACGGCGAACCCGGTACCATGAAGATACGAAGGAAAAA
1 GTTGAGGCCGCAACGGCGAACCCAGTACCATAAAGATACGAAGGAAAAA
* ** * ** * *
38519 GTTGAGGCCGCAACGGTGAAGTC-GATATCACGAAGACACGAAGGGAAAA
1 GTTGAGGCCGCAACGGCGAACCCAG-TACCATAAAGATACGAAGGAAAAA
* *
38568 GTTGAGGCCGTAATGGCGAAC
1 GTTGAGGCCGCAACGGCGAAC
38589 TTGATACCTA
Statistics
Matches: 97, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
48 3 0.03
49 94 0.97
ACGTcount: A:0.35, C:0.20, G:0.30, T:0.15
Consensus pattern (49 bp):
GTTGAGGCCGCAACGGCGAACCCAGTACCATAAAGATACGAAGGAAAAA
Found at i:38661 original size:98 final size:98
Alignment explanation
Indices: 38516--38784 Score: 258
Period size: 98 Copynumber: 2.7 Consensus size: 98
38506 TACGAAGGAA
* * * * *
38516 AAAGTTGAGGCCGCAACGGTGAAGT-CGATATCACGAAGACACGAAGGGAAAAGTTGAGGCCGTA
1 AAAGTTGAGGCCGCAACGGTGAA-TCCGATACCATGAAGACA-TAAGGGAAAGGTTGAGGTCGTA
* * *
38580 ATGGCGAACT-TGATACCTAAGAAGATGTGATGAG
64 ATGGCGAACTCCGACACCTAAGAAAATGTGATGAG
* * * **
38614 AAAGCTTGAGGCTGCAATGGTGAATCCGATACCATGAAGAGATAAGGG-AAGGATTGAGGTCGCG
1 AAAG-TTGAGGCCGCAACGGTGAATCCGATACCATGAAGACATAAGGGAAAGG-TTGAGGTCGTA
* * * *
38678 ACGGCGAA-TCCGGCACCTTAGAAAATGTGATGGG
64 ATGGCGAACTCCGACACCTAAGAAAATGTGATGAG
* * * * * *
38712 AAAGGTTAAGGCCGCAACGGTAAACCCGGTACCATGAATATATAAGGGAAAGGTTGAGGTCGTAA
1 AAA-GTTGAGGCCGCAACGGTGAATCCGATACCATGAAGACATAAGGGAAAGGTTGAGGTCGTAA
38777 TGGCGAAC
65 TGGCGAAC
38785 CTAGCACCTT
Statistics
Matches: 136, Mismatches: 28, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
97 4 0.03
98 97 0.71
99 35 0.26
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (98 bp):
AAAGTTGAGGCCGCAACGGTGAATCCGATACCATGAAGACATAAGGGAAAGGTTGAGGTCGTAAT
GGCGAACTCCGACACCTAAGAAAATGTGATGAG
Found at i:39318 original size:16 final size:16
Alignment explanation
Indices: 39297--39333 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
39287 ACTACAAAAC
39297 GCAAACATTTAAACCT
1 GCAAACATTTAAACCT
39313 GCAAACATTTAAACCT
1 GCAAACATTTAAACCT
*
39329 ACAAA
1 GCAAA
39334 ACGCAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.24, G:0.05, T:0.22
Consensus pattern (16 bp):
GCAAACATTTAAACCT
Found at i:39832 original size:13 final size:12
Alignment explanation
Indices: 39807--39841 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
39797 AATAAATGCA
39807 TAATAAGTAATAT
1 TAATAA-TAATAT
39820 TAAATAATAATAT
1 T-AATAATAATAT
39833 TAATAATAA
1 TAATAATAA
39842 AAATAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.38
13 8 0.38
14 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:40968 original size:59 final size:59
Alignment explanation
Indices: 40797--41179 Score: 295
Period size: 59 Copynumber: 6.5 Consensus size: 59
40787 AAAAATCACA
* * * * * * *
40797 TTAACCCCAAACTTTTTAAAAATTATA-TTTTAACCCTCAAACTTTTCTAAAATTATATTT
1 TTAACCCTAAACTTTTCAAAAATTACATTTTTACCCCT-AAACTTCTCAAAAATTACA-TT
* * * * * * *
40857 TTACCCCTAAAATTTTCCAAAATTATA-TTTTAACCCTAACACTTTTCCAAAATTACATT
1 TTAACCCTAAACTTTTCAAAAATTACATTTTTACCCCTAA-ACTTCTCAAAAATTACATT
* *
40916 TTAACCCTAAACTTTTCCAAAATTACATTTTTACCCCTAAACTTCTCAAAAATCACATT
1 TTAACCCTAAACTTTTCAAAAATTACATTTTTACCCCTAAACTTCTCAAAAATTACATT
** * *
40975 TTGCCCCTAAA--TTTCAAAAATCT-CATTTTTACCCCTAAATTTC-CAAAAATCACATT
1 TTAACCCTAAACTTTTCAAAAAT-TACATTTTTACCCCTAAACTTCTCAAAAATTACATT
* ** * * **
41031 TTTACCTCCGAACTTCTCAAAAATCACATTTTTACCCCCGAACTTCTCAAAAATTACAATT
1 TTAACC-CTAAACTTTTCAAAAATTACATTTTTACCCCTAAACTTCTCAAAAATTAC-ATT
* *
41092 TT-ACCCTCAAACTTCTCAAAAATTACCA-TTTTACCCAC-GAA-TATC-CAAAAATTATCATT
1 TTAACCCT-AAACTTTTCAAAAATTA-CATTTTTACCC-CTAAACT-TCTCAAAAATTA-CATT
* * *
41151 TT-CCCCTAAAATTTCCAAAAATTACATTT
1 TTAACCCTAAACTTTTCAAAAATTACATTT
41180 CAACCTCAAA
Statistics
Matches: 273, Mismatches: 35, Indels: 32
0.80 0.10 0.09
Matches are distributed among these distances:
56 17 0.06
57 33 0.12
58 17 0.06
59 99 0.36
60 99 0.36
61 8 0.03
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.37
Consensus pattern (59 bp):
TTAACCCTAAACTTTTCAAAAATTACATTTTTACCCCTAAACTTCTCAAAAATTACATT
Found at i:40976 original size:29 final size:29
Alignment explanation
Indices: 40787--41179 Score: 290
Period size: 30 Copynumber: 13.4 Consensus size: 29
40777 TATTTTCTTT
* * * *
40787 AAAAATCACA-TTAACCCC-AAACTTTTT
1 AAAAATTACATTTTACCCCTAAACTTCTC
* * *
40814 AAAAATTATATTTTAACCCTCAAACTTTTC
1 AAAAATTACATTTTACCCCT-AAACTTCTC
* * * *
40844 TAAAATTATATTTTTACCCCTAAAATTTTC
1 AAAAATTACA-TTTTACCCCTAAACTTCTC
* * * *
40874 CAAAATTATATTTTAACCCTAACACTTTTC
1 AAAAATTACATTTTACCCCTAA-ACTTCTC
* * *
40904 CAAAATTACATTTTAACCCTAAACTTTTC
1 AAAAATTACATTTTACCCCTAAACTTCTC
*
40933 CAAAATTACATTTTTACCCCTAAACTTCTC
1 AAAAATTACA-TTTTACCCCTAAACTTCTC
* *
40963 AAAAATCACATTTTGCCCCTAAA-TT-TC
1 AAAAATTACATTTTACCCCTAAACTTCTC
*
40990 AAAAATCT-CATTTTTACCCCTAAATTTC-C
1 AAAAAT-TACA-TTTTACCCCTAAACTTCTC
* *
41019 AAAAATCACATTTTTACCTCC-GAACTTCTC
1 AAAAATTACA-TTTTACC-CCTAAACTTCTC
* **
41049 AAAAATCACATTTTTACCCCCGAACTTCTC
1 AAAAATTACA-TTTTACCCCTAAACTTCTC
41079 AAAAATTACAATTTTA-CCCTCAAACTTCTC
1 AAAAATTAC-ATTTTACCCCT-AAACTTCTC
*
41109 AAAAATTACCATTTTACCCAC-GAA-TATC-C
1 AAAAATTA-CATTTTACCC-CTAAACT-TCTC
*
41138 AAAAATTATCATTTT-CCCCTAAAATT-TCC
1 AAAAATTA-CATTTTACCCCTAAACTTCT-C
41167 AAAAATTACATTT
1 AAAAATTACATTT
41180 CAACCTCAAA
Statistics
Matches: 314, Mismatches: 28, Indels: 47
0.81 0.07 0.12
Matches are distributed among these distances:
27 19 0.06
28 31 0.10
29 95 0.30
30 155 0.49
31 13 0.04
32 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (29 bp):
AAAAATTACATTTTACCCCTAAACTTCTC
Found at i:41208 original size:29 final size:29
Alignment explanation
Indices: 41155--41227 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
41145 ATCATTTTCC
*
41155 CCTAAAATTTCCAAAAATTACATTTCAA-
1 CCTAAATTTTCCAAAAATTACATTTCAAT
* *
41183 CCTCAAATTTTCCAAAAGTT-CAATTTTAAT
1 CCT-AAATTTTCCAAAAATTAC-ATTTCAAT
41213 CCTAAATTTTCCAAA
1 CCTAAATTTTCCAAA
41228 TTCCTCGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.10
29 32 0.82
30 3 0.08
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (29 bp):
CCTAAATTTTCCAAAAATTACATTTCAAT
Done.