Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005420.1 Hibiscus syriacus cultivar Beakdansim tig00012433_pilon, 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: 63655
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2941 original size:3 final size:3
Alignment explanation
Indices: 2933--2966 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2923 AGAAAGAAAC
2933 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2967 TAAGGTGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:10563 original size:26 final size:26
Alignment explanation
Indices: 10529--10590 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
10519 ATGATCAATG
* *
10529 ATCACATCTTTGAAACAAATTCATCA
1 ATCAAATCTTTGAAACAAATTCACCA
10555 ATCAAATCTTTGAAACAAATTCACCA
1 ATCAAATCTTTGAAACAAATTCACCA
10581 ATCAAATCTT
1 ATCAAATCTT
10591 CATAAACAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.31
Consensus pattern (26 bp):
ATCAAATCTTTGAAACAAATTCACCA
Found at i:11916 original size:23 final size:23
Alignment explanation
Indices: 11853--11916 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
11843 TTATGTTTAA
*
11853 ATATATTTTAACTCATACATTTTT
1 ATATATTTTTAC-CATACATTTTT
* * *
11877 -TTTATTTTTTGATCATATATTTTT
1 ATATA-TTTTT-ACCATACATTTTT
11901 ATATATTTTTACCATA
1 ATATATTTTTACCATA
11917 ATGATATCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
23 8 0.26
24 19 0.61
25 4 0.13
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (23 bp):
ATATATTTTTACCATACATTTTT
Found at i:12614 original size:21 final size:21
Alignment explanation
Indices: 12590--12652 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
12580 AATGACATGC
* * *
12590 TAATTCACGGTGCTGACGTGG
1 TAATCCACAGTGCTGACGTGA
* * *
12611 TAATCCACTGTGCTAATGTGA
1 TAATCCACAGTGCTGACGTGA
*
12632 TAATCCACAGTGCTGATGTGA
1 TAATCCACAGTGCTGACGTGA
12653 CAGTCCATCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (21 bp):
TAATCCACAGTGCTGACGTGA
Found at i:12659 original size:21 final size:21
Alignment explanation
Indices: 12612--12659 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
12602 CTGACGTGGT
* *
12612 AATCCACTGTGCTAATGTGAT
1 AATCCACAGTGCTAATGTGAC
*
12633 AATCCACAGTGCTGATGTGAC
1 AATCCACAGTGCTAATGTGAC
*
12654 AGTCCA
1 AATCCA
12660 TCTACGATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (21 bp):
AATCCACAGTGCTAATGTGAC
Found at i:14364 original size:22 final size:22
Alignment explanation
Indices: 14336--14377 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
14326 GTTTTTCTAC
14336 TTTCGAATA-GAAAAGTAATAGT
1 TTTCGAATAGGAAAA-TAATAGT
14358 TTTCGAATAGGAAAATAATA
1 TTTCGAATAGGAAAATAATA
14378 CCTTTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.31
Consensus pattern (22 bp):
TTTCGAATAGGAAAATAATAGT
Found at i:14383 original size:23 final size:22
Alignment explanation
Indices: 14336--14383 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
14326 GTTTTTCTAC
*
14336 TTTCGAATAGAAAAGTAATAGT
1 TTTCGAATAGAAAAGTAATACT
14358 TTTCGAATAGGAAAA-TAATACCT
1 TTTCGAATA-GAAAAGTAATA-CT
14381 TTT
1 TTT
14384 GAAAACTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (22 bp):
TTTCGAATAGAAAAGTAATACT
Found at i:15177 original size:16 final size:17
Alignment explanation
Indices: 15146--15179 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
15136 GAAGACTGTT
15146 TTTGTATAACTTTAATG
1 TTTGTATAACTTTAATG
*
15163 TTTGTA-AATTTTAATG
1 TTTGTATAACTTTAATG
15179 T
1 T
15180 ATTTTGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.29, C:0.03, G:0.12, T:0.56
Consensus pattern (17 bp):
TTTGTATAACTTTAATG
Found at i:15549 original size:43 final size:42
Alignment explanation
Indices: 15509--15626 Score: 120
Period size: 41 Copynumber: 2.8 Consensus size: 42
15499 ATAGTGGCAT
15509 TTTTTTCAAACAAACGCCGCAAGAGAAAGTAATTTTGTGGCG
1 TTTTTTCAAACAAACGCCGCAAGAGAAAGTAATTTTGTGGCG
* *
15551 TTTTTT--AACAAACGACGCAATAG--AGTTATTATTTTGTGGCG
1 TTTTTTCAAACAAACGCCGCAAGAGAAAG-TA--ATTTTGTGGCG
* * *
15592 TTTTATCAAACAAGCACCGC-AGAAGAAAGTAATTT
1 TTTTTTCAAACAAACGCCGCAAG-AGAAAGTAATTT
15627 AACGGCGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 15 0.25
41 16 0.26
42 11 0.18
43 11 0.18
44 2 0.03
45 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (42 bp):
TTTTTTCAAACAAACGCCGCAAGAGAAAGTAATTTTGTGGCG
Found at i:15555 original size:83 final size:82
Alignment explanation
Indices: 15394--15738 Score: 291
Period size: 83 Copynumber: 4.2 Consensus size: 82
15384 GTTTATACAT
* * * * * * * *
15394 AAACACCGCAATAGTGTTAATATATAGTGG-TGTTTGATCATACAAACGCCGTAACAGAAAGTAA
1 AAACGCCGTAATAGGGTTATTATATAGTGGCT-TTTTATCAAACAAACGCCGCAAGAGAAAGTAA
* **
15458 TTTTGCGGATTTTTTTAC
65 TTTAGCGGCGTTTTTTAC
* * *
15476 GAACGCCGTAATAGGGTTACTATATAGTGGCATTTTTTTCAAACAAACGCCGCAAGAGAAAGTAA
1 AAACGCCGTAATAGGGTTATTATATAGTGGC-TTTTTATCAAACAAACGCCGCAAGAGAAAGTAA
* *
15541 TTTTGTGGCGTTTTTTAAC
65 TTTAGCGGCGTTTTTT-AC
* * * * * * * *
15560 AAACGACGCAATAGAGTTATTATTTTGTGGCGTTTTATCAAACAAGCACCGC-AGAAGAAAGTAA
1 AAACGCCGTAATAGGGTTATTATATAGTGGCTTTTTATCAAACAAACGCCGCAAG-AGAAAGTAA
*
15624 TTTAACGGCGTTTTTATAC
65 TTTAGCGGCGTTTTT-TAC
* * * * ** * *
15643 AAATGCCGTAATATGTTTATTATATAATGG-TGTTTTATCTTACAAATGCCGCAAAAGAAAGTAA
1 AAACGCCGTAATAGGGTTATTATATAGTGGCT-TTTTATCAAACAAACGCCGCAAGAGAAAGTAA
*
15707 TTTAGCGGCGTTTTTAAAC
65 TTTAGCGGCGTTTTT-TAC
*
15726 AAACACCGTAATA
1 AAACGCCGTAATA
15739 ATCATGTAAT
Statistics
Matches: 209, Mismatches: 47, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
82 27 0.13
83 153 0.73
84 29 0.14
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (82 bp):
AAACGCCGTAATAGGGTTATTATATAGTGGCTTTTTATCAAACAAACGCCGCAAGAGAAAGTAAT
TTAGCGGCGTTTTTTAC
Found at i:15757 original size:83 final size:81
Alignment explanation
Indices: 15374--15761 Score: 228
Period size: 83 Copynumber: 4.7 Consensus size: 81
15364 TAGACCTGAC
* * * * * * * * *
15374 ATTTTGCGGCGTTTATACATAAACACCGCAATAGTGTTAATATATAGTGGTGTTTGATCATACAA
1 ATTTAGCGGCGTTTTTAAACAAACACCGTAATAATATTAAT-T-TAGTGGTGTTTTATCAAACAA
* *
15439 ACGCCGTAACAGAAAGTA
64 ACGCCGCAAAAGAAAGTA
* * ** * * *** * *
15457 ATTTTGCGG-ATTTTTTTACGAACGCCGTAATAGGGTTACTATATAGTGGCAT-TTTTTTCAAAC
1 ATTTAGCGGCGTTTTTAAACAAACACCGTAATAATATTA--ATTTAGTGG--TGTTTTATCAAAC
*
15520 AAACGCCGCAAGAGAAAGTA
62 AAACGCCGCAAAAGAAAGTA
* * * * * *
15540 ATTTTGTGGCGTTTTTTAACAAACGA-CGCAATAGAGTTATT-ATTTTGTGGCGTTTTATCAAAC
1 ATTTAGCGGCGTTTTTAAACAAAC-ACCGTAATA-A--TATTAATTTAGTGGTGTTTTATCAAAC
* * *
15603 AAGCACCGCAGAAGAAAGTA
62 AAACGCCGCAAAAGAAAGTA
* * ** * * * **
15623 ATTTAACGGCGTTTTTATACAAATGCCGTAAT-ATGTTTATTATATAATGGTGTTTTATCTTACA
1 ATTTAGCGGCGTTTTTAAACAAACACCGTAATAAT-ATTA--ATTTAGTGGTGTTTTATCAAACA
*
15687 AATGCCGCAAAAGAAAGTA
63 AACGCCGCAAAAGAAAGTA
15706 ATTTAGCGGCGTTTTTAAACAAACACCGTAATAATCATGTAATTTAGTGGTGTTTT
1 ATTTAGCGGCGTTTTTAAACAAACACCGTAATAAT-AT-TAATTTAGTGGTGTTTT
15762 GCCATATTTA
Statistics
Matches: 229, Mismatches: 59, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
79 1 0.00
80 2 0.01
81 1 0.00
82 26 0.11
83 165 0.72
84 30 0.13
85 2 0.01
87 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (81 bp):
ATTTAGCGGCGTTTTTAAACAAACACCGTAATAATATTAATTTAGTGGTGTTTTATCAAACAAAC
GCCGCAAAAGAAAGTA
Found at i:17684 original size:31 final size:29
Alignment explanation
Indices: 17617--17687 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 29
17607 ATTAACCCAT
* *
17617 TCAATAATAAATAGTCATTTGAATCAATC
1 TCAATAATAAATAGTCATTTAAACCAATC
* * *
17646 GCTATAATGAAATAGTTATTTTAAACCAATC
1 TCAATAAT-AAATAGTCA-TTTAAACCAATC
17677 TCAATAATAAA
1 TCAATAATAAA
17688 AGAATTGATT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 6 0.18
30 11 0.33
31 16 0.48
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (29 bp):
TCAATAATAAATAGTCATTTAAACCAATC
Found at i:18640 original size:18 final size:18
Alignment explanation
Indices: 18617--18656 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
18607 TATTTGACTT
18617 ATCCTGCTCCTTCTCACC
1 ATCCTGCTCCTTCTCACC
18635 ATCCTGCTCCTTCTCACC
1 ATCCTGCTCCTTCTCACC
18653 ATCC
1 ATCC
18657 AACTTTTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.50, G:0.05, T:0.33
Consensus pattern (18 bp):
ATCCTGCTCCTTCTCACC
Found at i:24176 original size:44 final size:44
Alignment explanation
Indices: 24118--24259 Score: 176
Period size: 44 Copynumber: 3.2 Consensus size: 44
24108 AACACATTTA
* * *
24118 GCGGCCTTGGTATCCTAAAAACGGCGCTATATACCAGACCTATT
1 GCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGACCTATT
* * *
24162 GCGGCGTTTGTATCCTAAACACGCCGCTATATACCAGTCCTATA
1 GCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGACCTATT
* * * * * *
24206 GCAGCATTTGTACCCTGAAAACGCCGCTAAATACCATACCTATT
1 GCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGACCTATT
24250 GCGGCGTTTG
1 GCGGCGTTTG
24260 CATAAAAAAT
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 81 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (44 bp):
GCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGACCTATT
Found at i:24188 original size:89 final size:87
Alignment explanation
Indices: 24073--24259 Score: 198
Period size: 88 Copynumber: 2.1 Consensus size: 87
24063 CATATATTTA
* * * * *
24073 GCGGCGTTTGTATCTAAAAAATGCCGCTAAATATTAACA-CATTTAGCGGCCTTGGTATCCTAAA
1 GCGGCGTTTGTATCTAAAAAACGCCGCT--ATA-TAACAGCATATAGCAGCATTGGTACCCTAAA
* *
24137 AACGGCGCTATATACCAGACCTATT
63 AACGCCGCTAAATACCAGACCTATT
* * * * *
24162 GCGGCGTTTGTATCCT-AAACACGCCGCTATATACCAGTCCTATAGCAGCATTTGTACCCTGAAA
1 GCGGCGTTTGTAT-CTAAAAAACGCCGCTATATAACAG-CATATAGCAGCATTGGTACCCTAAAA
*
24226 ACGCCGCTAAATACCATACCTATT
64 ACGCCGCTAAATACCAGACCTATT
24250 GCGGCGTTTG
1 GCGGCGTTTG
24260 CATAAAAAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
86 4 0.05
87 3 0.04
88 50 0.61
89 23 0.28
90 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (87 bp):
GCGGCGTTTGTATCTAAAAAACGCCGCTATATAACAGCATATAGCAGCATTGGTACCCTAAAAAC
GCCGCTAAATACCAGACCTATT
Found at i:24309 original size:42 final size:41
Alignment explanation
Indices: 24223--24388 Score: 163
Period size: 42 Copynumber: 4.0 Consensus size: 41
24213 TTGTACCCTG
* * *
24223 AAAACGCCGCTAAATA-CCATACCTATTGCGGCGTTTGCATAA
1 AAAACGCCGCTAAATATCAACACCTATTACGGCGTTTG--TAA
* * *
24265 AAAATGCCGCGAAATATCAACACTTATTACGGCGTTTGTGAA
1 AAAACGCCGCTAAATATCAACACCTATTACGGCGTTTGT-AA
* * * * *
24307 AAAACGTCGCTAAATATTAACACCTATTGCGACGTTTTTAA
1 AAAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTAA
**
24348 GACAAACGCCGCTAAATATCAGTACCTATTACGGCGTTTGT
1 -A-AAACGCCGCTAAATATCAACACCTATTACGGCGTTTGT
24389 TTAACAAACG
Statistics
Matches: 99, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
41 3 0.03
42 48 0.48
43 48 0.48
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (41 bp):
AAAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTAA
Found at i:24375 original size:43 final size:42
Alignment explanation
Indices: 24223--24400 Score: 171
Period size: 43 Copynumber: 4.2 Consensus size: 42
24213 TTGTACCCTG
* * * *
24223 AAAACGCCGCTAAATA-CCATACCTATTGCGGCGTTTGCATAA
1 AAAACGCCGCTAAATATCAACACCTATTACGGCGTTTG-TTAA
* * * *
24265 AAAATGCCGCGAAATATCAACACTTATTACGGCGTTTGTGAA
1 AAAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTTAA
* * * *
24307 AAAACGTCGCTAAATATTAACACCTATTGCGACGTTT-TTAA
1 AAAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTTAA
**
24348 GACAAACGCCGCTAAATATCAGTACCTATTACGGCGTTTGTTTAA
1 -A-AAACGCCGCTAAATATCAACACCTATTACGGCGTTTG-TTAA
*
24393 CAAACGCC
1 AAAACGCC
24401 ACGAACTTTA
Statistics
Matches: 108, Mismatches: 23, Indels: 9
0.77 0.16 0.06
Matches are distributed among these distances:
41 3 0.03
42 47 0.44
43 54 0.50
45 4 0.04
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (42 bp):
AAAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTTAA
Found at i:24443 original size:12 final size:14
Alignment explanation
Indices: 24407--24443 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
24397 CGCCACGAAC
24407 TTTAGCGGCGCTAT
1 TTTAGCGGCGCTAT
24421 TTTCAGCGGCGC-AT
1 TTT-AGCGGCGCTAT
24435 TTT-GCGGCG
1 TTTAGCGGCG
24444 TTTTTCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
14 8 0.36
15 8 0.36
ACGTcount: A:0.11, C:0.24, G:0.32, T:0.32
Consensus pattern (14 bp):
TTTAGCGGCGCTAT
Found at i:24714 original size:51 final size:51
Alignment explanation
Indices: 24649--24748 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 51
24639 ACAGAAAAAG
* *
24649 TATAATAAAATTAAATATATGTTTTAGTAAAACTATAACAAATTTTGAGAT
1 TATAATAAAATTAAATATATGTTTTAATAAAACCATAACAAATTTTGAGAT
*
24700 TATAATAAATTTAAATATATGTTTTAATAAAACCATAACAAATTTTGAG
1 TATAATAAAATTAAATATATGTTTTAATAAAACCATAACAAATTTTGAG
24749 TATAATTCAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (51 bp):
TATAATAAAATTAAATATATGTTTTAATAAAACCATAACAAATTTTGAGAT
Found at i:24844 original size:17 final size:16
Alignment explanation
Indices: 24822--24862 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 16
24812 AGTCATCGAA
24822 ATTTTTAATTTTTTTAT
1 ATTTTTAA-TTTTTTAT
24839 ATTTTTAATTTTTTAT
1 ATTTTTAATTTTTTAT
24855 ATGTTTTA
1 AT-TTTTA
24863 TTAATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
ATTTTTAATTTTTTAT
Found at i:24934 original size:26 final size:26
Alignment explanation
Indices: 24891--24942 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
24881 CGCCTAGAAC
*
24891 TTTATAAGTTCGCTCTCATCTAAAAT
1 TTTATAAGTTCGCTCTCATATAAAAT
*
24917 TTTATAAGTTC-ATCCTCATATAAAAT
1 TTTATAAGTTCGCT-CTCATATAAAAT
24943 CTTGCATTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (26 bp):
TTTATAAGTTCGCTCTCATATAAAAT
Found at i:25834 original size:2 final size:2
Alignment explanation
Indices: 25827--25863 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25817 ACTTTAATCT
25827 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25864 TAGTGAATTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27325 original size:21 final size:21
Alignment explanation
Indices: 27282--27325 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
27272 CACTAAACAT
*
27282 TAAACCATAAACCATATACTA
1 TAAACCATAAACCATAAACTA
* * *
27303 TAAACCTTAAACCCTAAATTA
1 TAAACCATAAACCATAAACTA
27324 TA
1 TA
27326 CTTACATCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAACCATAAACCATAAACTA
Found at i:27392 original size:7 final size:7
Alignment explanation
Indices: 27380--27442 Score: 65
Period size: 7 Copynumber: 9.0 Consensus size: 7
27370 CAATGAATCC
27380 TAAACCT
1 TAAACCT
*
27387 TAAACCC
1 TAAACCT
*
27394 TAAATCT
1 TAAACCT
*
27401 TAAACCA
1 TAAACCT
*
27408 TAAACCA
1 TAAACCT
27415 TAAA-CT
1 TAAACCT
*
27421 ATAAACCA
1 -TAAACCT
27429 TAAACCT
1 TAAACCT
27436 TAAACCT
1 TAAACCT
27443 AATTATGTGA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
6 1 0.02
7 44 0.96
8 1 0.02
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAACCT
Found at i:27397 original size:14 final size:14
Alignment explanation
Indices: 27380--27442 Score: 72
Period size: 14 Copynumber: 4.5 Consensus size: 14
27370 CAATGAATCC
*
27380 TAAACCTTAAACCC
1 TAAACCTTAAACCA
*
27394 TAAATCTTAAACCA
1 TAAACCTTAAACCA
* *
27408 TAAACCATAAACTA
1 TAAACCTTAAACCA
* *
27422 TAAACCATAAACCT
1 TAAACCTTAAACCA
27436 TAAACCT
1 TAAACCT
27443 AATTATGTGA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:27404 original size:21 final size:21
Alignment explanation
Indices: 27375--27439 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
27365 ATTTGCAATG
* * *
27375 AATCCTAAACCTTAAACCCTA
1 AATCTTAAACCATAAACCATA
27396 AATCTTAAACCATAAACCATA
1 AATCTTAAACCATAAACCATA
*
27417 AA-CTATAAACCATAAACCTTA
1 AATCT-TAAACCATAAACCATA
27438 AA
1 AA
27440 CCTAATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 2 0.05
21 37 0.95
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (21 bp):
AATCTTAAACCATAAACCATA
Found at i:30371 original size:23 final size:24
Alignment explanation
Indices: 30336--30403 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
30326 AAATTCTAGT
* *
30336 TCGAGTTTGAATCGAGCTC-AAAA
1 TCGAGCTTCAATCGAGCTCGAAAA
***
30359 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAAAA
*
30383 TCAAGCTTCAATCGAGCTCGA
1 TCGAGCTTCAATCGAGCTCGA
30404 TTCTCGAGCG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
23 17 0.45
24 21 0.55
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (24 bp):
TCGAGCTTCAATCGAGCTCGAAAA
Found at i:30394 original size:24 final size:24
Alignment explanation
Indices: 30362--30418 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
30352 CTCAAAATCG
30362 AGCTTCAATCGAGCTCGAGTCTCA
1 AGCTTCAATCGAGCTCGAGTCTCA
* *
30386 AGCTTCAATCGAGCTCGATTCTCG
1 AGCTTCAATCGAGCTCGAGTCTCA
*
30410 AGCGTCAAT
1 AGCTTCAAT
30419 TCCTGAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (24 bp):
AGCTTCAATCGAGCTCGAGTCTCA
Found at i:30637 original size:16 final size:16
Alignment explanation
Indices: 30616--30646 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
30606 CCTTGTCAAT
30616 AATCCAAGCGGCCATA
1 AATCCAAGCGGCCATA
30632 AATCCAAGCGGCCAT
1 AATCCAAGCGGCCAT
30647 GGATTATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.32, G:0.19, T:0.13
Consensus pattern (16 bp):
AATCCAAGCGGCCATA
Found at i:31089 original size:2 final size:2
Alignment explanation
Indices: 31084--31109 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31074 TTTTTTCTGA
31084 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
31110 TAGTTCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35109 original size:31 final size:31
Alignment explanation
Indices: 34990--35110 Score: 143
Period size: 32 Copynumber: 3.8 Consensus size: 31
34980 CTAAGGTGAC
* *
34990 CCTTGGGTAAGCTCTTAGGCCCCAAGATATT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGATATT
* * * *
35021 CCTTTGGGTAGGCTCTCAGGCCCTAAGGTTCTT
1 CC-TTGGGTAGGCTCTAAGGCCCCAA-GATATT
* *
35054 CCTTGGGTAGGCTCTGAGGGCCCAAGATATT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGATATT
*
35085 CCTTGGGTAGGCTCTAAGTCCCCAAG
1 CCTTGGGTAGGCTCTAAGGCCCCAAG
35111 GTACTCCCTT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
31 29 0.39
32 40 0.53
33 6 0.08
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.28
Consensus pattern (31 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGATATT
Found at i:35130 original size:63 final size:64
Alignment explanation
Indices: 34989--35130 Score: 178
Period size: 63 Copynumber: 2.2 Consensus size: 64
34979 CCTAAGGTGA
* * * * * *
34989 CCCTTGGGTAAGCTCTTAGGCCCCAAGATATTCCTTTGGGTAGGCTCTCAGGCCCTAAGGTTCT
1 CCCTTAGGTAGGCTCTGAGGCCCCAAGATATTCCTTTGGGTAGGCTCTAAGGCCCCAAGGTACT
* * * *
35053 TCCTTGGGTAGGCTCTGAGGGCCCAAGATATTCC-TTGGGTAGGCTCTAAGTCCCCAAGGTACT
1 CCCTTAGGTAGGCTCTGAGGCCCCAAGATATTCCTTTGGGTAGGCTCTAAGGCCCCAAGGTACT
*
35116 CCCTTAGGTTGGCTC
1 CCCTTAGGTAGGCTC
35131 CTACGCCCAA
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
63 37 0.55
64 30 0.45
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (64 bp):
CCCTTAGGTAGGCTCTGAGGCCCCAAGATATTCCTTTGGGTAGGCTCTAAGGCCCCAAGGTACT
Found at i:36088 original size:15 final size:16
Alignment explanation
Indices: 36068--36100 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
36058 AATCATCTTT
36068 AAAAAA-TAATTTAAA
1 AAAAAAGTAATTTAAA
*
36083 AAAAAAGTATTTTAAA
1 AAAAAAGTAATTTAAA
36099 AA
1 AA
36101 TTACGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAAAAGTAATTTAAA
Found at i:36633 original size:59 final size:59
Alignment explanation
Indices: 36552--36663 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
36542 TATGGAGGTT
* * **
36552 ATTCTAAACTAATCCTCAAACTTTTTAATATTTTAATTTCATCCCTAAACTATCATCTC
1 ATTCTAAACTAATCCTCAAACTTTTGAACATTCCAATTTCATCCCTAAACTATCATCTC
* * *
36611 ATTCTAAATTAGTGCCT-AAACTTTTGAGCATTCCAATTTCATCCCTAAACTAT
1 ATTCTAAACTAAT-CCTCAAACTTTTGAACATTCCAATTTCATCCCTAAACTAT
36664 GACCCTAGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 42 0.93
60 3 0.07
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (59 bp):
ATTCTAAACTAATCCTCAAACTTTTGAACATTCCAATTTCATCCCTAAACTATCATCTC
Found at i:37916 original size:29 final size:26
Alignment explanation
Indices: 37883--37934 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
37873 ATACTTAATA
37883 AAAACACAAAAATATTTATTAAAAAACT
1 AAAA-ACAAAAATATTTA-TAAAAAACT
*
37911 AAAAACTAAAATATTTATAAAAAA
1 AAAAACAAAAATATTTATAAAAAA
37935 TCCGAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 12 0.52
28 4 0.17
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (26 bp):
AAAAACAAAAATATTTATAAAAAACT
Found at i:39359 original size:42 final size:42
Alignment explanation
Indices: 39280--39368 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
39270 GCCGAAACAT
* * * * *
39280 CCACCCAGGCCTCCGGTTATTAGCCCTCCTTATCATCCCAAA
1 CCACCCAGGCCTCCGGTGATTAACCCGCCGTACCATCCCAAA
* *
39322 CCACCCAGGCCTCCGGTGGTTAACCCGCCGTACCATCCTAAA
1 CCACCCAGGCCTCCGGTGATTAACCCGCCGTACCATCCCAAA
39364 CCACC
1 CCACC
39369 TAAACATCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.45, G:0.15, T:0.19
Consensus pattern (42 bp):
CCACCCAGGCCTCCGGTGATTAACCCGCCGTACCATCCCAAA
Found at i:39573 original size:114 final size:114
Alignment explanation
Indices: 39420--40148 Score: 1352
Period size: 114 Copynumber: 6.4 Consensus size: 114
39410 CCCCCTATGT
* * * *
39420 ACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTACACACCCAAGCCACCCTACGTACCGGTGCCCA
1 ACCCAAGCCTCCCGTTGTAAATCCTCCGCCTTACACACCCAAGCCACCCTACGTACCGGTGCCCA
39485 ACCCACCTTACGTACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
66 ACCCACCTTACGTACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
*
39534 ACCCAAGCCTCCCGTTGTAAATCCTCCGCCTTACACACCCAAACCACCCTACGTACCGGTGCCCA
1 ACCCAAGCCTCCCGTTGTAAATCCTCCGCCTTACACACCCAAGCCACCCTACGTACCGGTGCCCA
39599 ACCCACCTTACGTACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
66 ACCCACCTTACGTACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
*
39648 ACCCAGGCCTCCCGTTGTAAATCCTCCGCCTTACACACCCAAGCCACCCTACGTACCGGTGCCCA
1 ACCCAAGCCTCCCGTTGTAAATCCTCCGCCTTACACACCCAAGCCACCCTACGTACCGGTGCCCA
39713 ACCCACCTTACGTACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
66 ACCCACCTTACGTACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
39762 ACCCAAGCCTCCCGTTGTAAATCCTCCGCCTTACACACCCAAGCCACCCTACGTACCGGTGCCCA
1 ACCCAAGCCTCCCGTTGTAAATCCTCCGCCTTACACACCCAAGCCACCCTACGTACCGGTGCCCA
39827 ACCCACCTTACGTACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
66 ACCCACCTTACGTACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
39876 ACCCAAGCCTCCCGTTGTAAATCCTCCGCCTTACACACCCAAGCCACCCTACGTACCGGTGCCCA
1 ACCCAAGCCTCCCGTTGTAAATCCTCCGCCTTACACACCCAAGCCACCCTACGTACCGGTGCCCA
39941 ACCCACCTTACGTACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
66 ACCCACCTTACGTACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
*
39990 ACCCAAGCCTCCCGTTGTAAATCCTCCGCCTTACACACCCAAGCCACCCTACGTACCGGTGCCAA
1 ACCCAAGCCTCCCGTTGTAAATCCTCCGCCTTACACACCCAAGCCACCCTACGTACCGGTGCCCA
* *
40055 ACCCACCTTACGTACCCAAACCTCCGGTCATAAAGCCTCCGCCGTATAC
66 ACCCACCTTACGTACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
*
40104 ACCCAAGCCTCCTC-TTGTAAATCCTCCGCCTTATACACCCAAGCC
1 ACCCAAGCCTCC-CGTTGTAAATCCTCCGCCTTACACACCCAAGCC
40149 TCCTGTTGTA
Statistics
Matches: 602, Mismatches: 12, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
114 601 1.00
115 1 0.00
ACGTcount: A:0.24, C:0.45, G:0.13, T:0.18
Consensus pattern (114 bp):
ACCCAAGCCTCCCGTTGTAAATCCTCCGCCTTACACACCCAAGCCACCCTACGTACCGGTGCCCA
ACCCACCTTACGTACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
Found at i:40028 original size:36 final size:36
Alignment explanation
Indices: 39954--40184 Score: 169
Period size: 36 Copynumber: 6.2 Consensus size: 36
39944 CACCTTACGT
* * * *
39954 ACCCAAACCTCCGGTCGTAAAGCCTCCGCCTTATAC
1 ACCCAAGCCTCCCGTCGTAAATCCTCCGCCTTACAC
*
39990 ACCCAAGCCTCCCGTTGTAAATCCTCCGCCTTACAC
1 ACCCAAGCCTCCCGTCGTAAATCCTCCGCCTTACAC
* ** * * **
40026 ACCCAAGCCACCC-TACGTACCGGTGCCAAACCCACCTTACGT
1 ACCCAAGCCTCCCGT-CGTA--AAT-CC---TCCGCCTTACAC
* * * * * *
40068 ACCCAAACCTCCGGTCATAAAGCCTCCGCCGTATAC
1 ACCCAAGCCTCCCGTCGTAAATCCTCCGCCTTACAC
* *
40104 ACCCAAGCCTCCTC-TTGTAAATCCTCCGCCTTATAC
1 ACCCAAGCCTCC-CGTCGTAAATCCTCCGCCTTACAC
* * *
40140 ACCCAAGCCTCCTGTTGTAAATCCTCCCCCTTACAC
1 ACCCAAGCCTCCCGTCGTAAATCCTCCGCCTTACAC
40176 ACCCAAGCC
1 ACCCAAGCC
40185 ACCTTACGTA
Statistics
Matches: 150, Mismatches: 35, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
35 1 0.01
36 122 0.81
38 1 0.01
39 4 0.03
42 21 0.14
43 1 0.01
ACGTcount: A:0.25, C:0.44, G:0.12, T:0.20
Consensus pattern (36 bp):
ACCCAAGCCTCCCGTCGTAAATCCTCCGCCTTACAC
Found at i:40150 original size:21 final size:21
Alignment explanation
Indices: 40087--40151 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 21
40077 TCCGGTCATA
*
40087 AAGCCTCCGCCGTATACACCC
1 AAGCCTCCGCCTTATACACCC
* *
40108 AAGCCTCC-TCTTGT--A---
1 AAGCCTCCGCCTTATACACCC
*
40123 AATCCTCCGCCTTATACACCC
1 AAGCCTCCGCCTTATACACCC
40144 AAGCCTCC
1 AAGCCTCC
40152 TGTTGTAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 12
0.62 0.14 0.24
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
18 2 0.06
20 3 0.10
21 15 0.48
ACGTcount: A:0.23, C:0.45, G:0.11, T:0.22
Consensus pattern (21 bp):
AAGCCTCCGCCTTATACACCC
Found at i:41250 original size:16 final size:17
Alignment explanation
Indices: 41218--41250 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41208 TTATTGTTAT
*
41218 TTTATTATTTCAAATAA
1 TTTAATATTTCAAATAA
41235 TTTAATATTT-AAATAA
1 TTTAATATTTCAAATAA
41251 ATAATTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAATATTTCAAATAA
Found at i:43020 original size:2 final size:2
Alignment explanation
Indices: 43013--43047 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
43003 CATTTGAGTT
*
43013 TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43048 ATTAGTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43264 original size:17 final size:17
Alignment explanation
Indices: 43231--43264 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43221 CTTAGCATTG
* *
43231 ATATATATGTATGTTAT
1 ATATATATATATATTAT
43248 ATATATATATATATTAT
1 ATATATATATATATTAT
43265 GTTGAGTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATATATATATATATTAT
Found at i:47161 original size:20 final size:20
Alignment explanation
Indices: 47138--47176 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
47128 ATTCAATAAC
*
47138 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
47158 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
47177 TATGGGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:50943 original size:40 final size:43
Alignment explanation
Indices: 50838--50943 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 43
50828 TTCATATAAA
* * * *
50838 ATGTCCCGAAAGACCACGTAGAATTGTACCGAATGACCACATAT
1 ATGTCCCGAAGGACCTCGTAGAATTGTACCCAAGGACCACA-AT
* * *
50882 ATGT-CCGAAGGAGCTCATAGAA-TG-CCCCAAGGACCAC-AT
1 ATGTCCCGAAGGACCTCGTAGAATTGTACCCAAGGACCACAAT
50921 ATGTCCCGAAGGACCTCGTAGAA
1 ATGTCCCGAAGGACCTCGTAGAA
50944 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
39 6 0.12
40 16 0.31
41 10 0.19
42 2 0.04
43 14 0.27
44 4 0.08
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (43 bp):
ATGTCCCGAAGGACCTCGTAGAATTGTACCCAAGGACCACAAT
Found at i:58729 original size:31 final size:26
Alignment explanation
Indices: 58661--58725 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
58651 TACTTTTCGG
*
58661 TTCGGGTCGGGTTTTTAACTGTGATA
1 TTCGGGTCGGGTCTTTAACTGTGATA
*
58687 TTCGAGTCGGGTCTTTAACTGTGATA
1 TTCGGGTCGGGTCTTTAACTGTGATA
*
58713 TTCAGGTCGGGTC
1 TTCGGGTCGGGTC
58726 GGGTTTGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.38
Consensus pattern (26 bp):
TTCGGGTCGGGTCTTTAACTGTGATA
Found at i:59332 original size:18 final size:17
Alignment explanation
Indices: 59295--59341 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
59285 TATGGAATTG
*
59295 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
59312 GATTCTAATTCCTTCACA
1 GATTCCAATTCC-TCACA
59330 GATTCCAATTCC
1 GATTCCAATTCC
59342 CTCATAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:61966 original size:21 final size:22
Alignment explanation
Indices: 61933--61973 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
61923 CCAGGACAGG
61933 GAGTATCAATAC-TCCTTTAAT
1 GAGTATCAATACTTCCTTTAAT
**
61954 GAGTATCGGTACTTCCTTTA
1 GAGTATCAATACTTCCTTTA
61974 TAATGTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (22 bp):
GAGTATCAATACTTCCTTTAAT
Found at i:62713 original size:3 final size:3
Alignment explanation
Indices: 62705--62801 Score: 124
Period size: 3 Copynumber: 32.0 Consensus size: 3
62695 AAATTTAAAT
**
62705 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
62752 TTA TTA TTA TTA TAA TTA TTA TTA ATA TTA ATA TTA TATA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA
62799 TTA
1 TTA
62802 AATATTACAA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.02
3 73 0.90
4 6 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Done.