Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000382.1 Hibiscus syriacus cultivar Beakdansim tig00000698_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: 77621
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:2112 original size:105 final size:99
Alignment explanation
Indices: 1876--2117 Score: 317
Period size: 99 Copynumber: 2.4 Consensus size: 99
1866 CCAATTTCTT
* * *
1876 AACCAATTTCAACTTCACAGCGAATGATATTGGACCCAAGATAACACAAGCTCAACTTCACGGCG
1 AACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACGGCG
*
1941 AAGGGGCGGCTAATTGTCAACAAACAATTTTCAA
66 AAGGGGCGGCTAACTGTCAACAAACAATTTTCAA
* * * *
1975 ATCCAATTTCAACTTCACAGCGAAGGATATTGGACTGAAGACAGCACAAGCTTAACTTCACGGC-
1 AACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACGGCG
*
2039 AAGGGGCGGCTGACTGTCAACAAACAATTTTCCAGTTCCA
66 AAGGGGCGGCTAACTGTCAACAAACAATTTT-CA-----A
2079 GAACCAATTTCAACTTCAC-GACGAAGGATATTGGACTCA
1 -AACCAATTTCAACTTCACAG-CGAAGGATATTGGACTCA
2118 GAGCAATACA
Statistics
Matches: 124, Mismatches: 11, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
98 29 0.23
99 59 0.48
104 2 0.02
105 34 0.27
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (99 bp):
AACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACGGCG
AAGGGGCGGCTAACTGTCAACAAACAATTTTCAA
Found at i:4250 original size:13 final size:13
Alignment explanation
Indices: 4232--4258 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4222 TTCTTTTACA
4232 TTTATTTCTTTTT
1 TTTATTTCTTTTT
4245 TTTATTTCTTTTT
1 TTTATTTCTTTTT
4258 T
1 T
4259 AATTCATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTATTTCTTTTT
Found at i:10954 original size:16 final size:16
Alignment explanation
Indices: 10933--10971 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
10923 CATAAAAAAA
*
10933 AAACATTTCCATTAAG
1 AAACATATCCATTAAG
10949 AAACATATCCATTAAG
1 AAACATATCCATTAAG
10965 AAACATA
1 AAACATA
10972 ATAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (16 bp):
AAACATATCCATTAAG
Found at i:27902 original size:12 final size:12
Alignment explanation
Indices: 27885--27913 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
27875 CCCATGAATA
27885 ATTTGGAACTCT
1 ATTTGGAACTCT
27897 ATTTGGAACTCT
1 ATTTGGAACTCT
27909 ATTTG
1 ATTTG
27914 TAATGTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (12 bp):
ATTTGGAACTCT
Found at i:30512 original size:16 final size:16
Alignment explanation
Indices: 30493--30566 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 16
30483 TAACCCGATC
30493 CAAAAGTAACTCGAAT
1 CAAAAGTAACTCGAAT
*
30509 C-AAAGTTAAC-CTGAAC
1 CAAAAG-TAACTC-GAAT
* *
30525 CGAAAA-TAATTTGAAT
1 C-AAAAGTAACTCGAAT
30541 CAAAAGTAACAT-GAAT
1 CAAAAGTAAC-TCGAAT
30557 CAAAAGTAAC
1 CAAAAGTAAC
30567 CCAAATCCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
15 9 0.20
16 33 0.72
17 1 0.02
18 3 0.07
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.20
Consensus pattern (16 bp):
CAAAAGTAACTCGAAT
Found at i:31262 original size:18 final size:18
Alignment explanation
Indices: 31239--31274 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
31229 AACATATGGT
31239 TGAAATTT-TAATTAAAAA
1 TGAAATTTATAA-TAAAAA
31257 TGAAATTTATAATAAAAA
1 TGAAATTTATAATAAAAA
31275 AATATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (18 bp):
TGAAATTTATAATAAAAA
Found at i:31274 original size:19 final size:18
Alignment explanation
Indices: 31239--31275 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
31229 AACATATGGT
*
31239 TGAAATTTTAATTAAAAA
1 TGAAATTTTAATAAAAAA
31257 TGAAATTTATAATAAAAAA
1 TGAAATTT-TAATAAAAAA
31276 ATATTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TGAAATTTTAATAAAAAA
Found at i:34089 original size:23 final size:23
Alignment explanation
Indices: 34063--34131 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
34053 CACCACAGCT
*
34063 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
34086 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
34109 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
34132 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:34311 original size:103 final size:103
Alignment explanation
Indices: 34147--34359 Score: 347
Period size: 103 Copynumber: 2.1 Consensus size: 103
34137 TAATGTCCAT
* * * *
34147 AAGGACTACATATCATTCCTTAAGAATCATATATATATACTAGGGATCAAGTATGTATCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTATCTCACCA
*
34212 GACTTCACACATGTTCCAAAGAATATATATATG-TCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTTC-CG
* *
34250 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTATCTCACCA
34315 GACTTCACACATGTTCCAAAGAATACATATATGTTCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTTCCG
34353 AAGGACC
1 AAGGACC
34360 GCGTAGACCC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 100 0.98
104 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTATCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTTCCG
Found at i:36070 original size:21 final size:21
Alignment explanation
Indices: 36046--36090 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
36036 TTTTGTTCGT
* * *
36046 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGAGTACCGATTCCCC
*
36067 TTGAATGAGTACCGATTCCCC
1 TTGAAGGAGTACCGATTCCCC
36088 TTG
1 TTG
36091 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGAGTACCGATTCCCC
Found at i:39109 original size:23 final size:23
Alignment explanation
Indices: 39078--39146 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
39068 CACCACAGCT
* *
39078 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
39101 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
39124 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
39147 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:39325 original size:103 final size:103
Alignment explanation
Indices: 39162--39374 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
39152 TAATGTCCAT
* * * *
39162 AAGGACTACATATCATTCCTTAAGAATCATATATATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
39227 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
39265 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
39330 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
39368 AAGGACC
1 AAGGACC
39375 GCGTAGACCC
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:41085 original size:21 final size:21
Alignment explanation
Indices: 41061--41105 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
41051 TTTTGTTCGT
* *
41061 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
41082 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
41103 TTG
1 TTG
41106 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:47448 original size:27 final size:27
Alignment explanation
Indices: 47402--47455 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
47392 TGTTTTTGAA
* *
47402 ATCTATTATTTCCCTTTTCGGAAGCAG
1 ATCTATTATTTCCCTATTCGAAAGCAG
**
47429 ATCTATTATTTTTCTATTCGAAAGCAG
1 ATCTATTATTTCCCTATTCGAAAGCAG
47456 TAAAACACTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (27 bp):
ATCTATTATTTCCCTATTCGAAAGCAG
Found at i:50155 original size:2 final size:2
Alignment explanation
Indices: 50148--50184 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
50138 CTTTGCATGT
50148 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
50185 TGGTAAATTC
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:50473 original size:4 final size:4
Alignment explanation
Indices: 50464--50828 Score: 721
Period size: 4 Copynumber: 91.2 Consensus size: 4
50454 AACTATACCT
*
50464 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50512 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50560 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50608 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50656 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50704 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50752 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50800 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
50829 GTGCATATAC
Statistics
Matches: 359, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 359 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:50881 original size:2 final size:2
Alignment explanation
Indices: 50874--50902 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
50864 TATTTAAATA
50874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50903 ACAAGTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52915 original size:32 final size:32
Alignment explanation
Indices: 52872--52997 Score: 103
Period size: 32 Copynumber: 3.9 Consensus size: 32
52862 CTGATCTAAA
52872 CCAAAAATCAACCGATCCGATATTAACCCGAT
1 CCAAAAATCAACCGATCCGATATTAACCCGAT
* ** * *
52904 CCAAAACTCAACTAATTCGATATTGACTCCGAT
1 CCAAAAATCAACCGATCCGATATTAAC-CCGAT
* * * * *
52937 TC-GAAATCTAACTGAAT-CGATATTAACCTGAC
1 CCAAAAATC-AACCG-ATCCGATATTAACCCGAT
* *
52969 CCAAAAATCAATCGATCCAATATTAACCC
1 CCAAAAATCAACCGATCCGATATTAACCC
52998 AAATCAAAAA
Statistics
Matches: 71, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
31 2 0.03
32 43 0.61
33 24 0.34
34 2 0.03
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.24
Consensus pattern (32 bp):
CCAAAAATCAACCGATCCGATATTAACCCGAT
Found at i:59000 original size:43 final size:42
Alignment explanation
Indices: 58884--59010 Score: 121
Period size: 42 Copynumber: 3.0 Consensus size: 42
58874 ATTCTTGTCT
* * * *
58884 TGATTCTACATAGGATCCTCTAC-GAAGGGCATCATCCTCATCT
1 TGATTCTGCAT-GAATCCTCTACAGAA-GGCATCATCCTCGTCA
* * *
58927 TGGTTCTGCATGAATCCTCTACAGAGGGCATCATCCCCGTCA
1 TGATTCTGCATGAATCCTCTACAGAAGGCATCATCCTCGTCA
* ** *
58969 TGATTCTGCATGAAATCCTTTATGGAAGGCATAATCCTCGTC
1 TGATTCTGCATG-AATCCTCTACAGAAGGCATCATCCTCGTC
59011 CTGGTTTTCT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 34 0.50
43 34 0.50
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (42 bp):
TGATTCTGCATGAATCCTCTACAGAAGGCATCATCCTCGTCA
Found at i:61088 original size:18 final size:18
Alignment explanation
Indices: 61048--61101 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
61038 CTTCTGAAAA
* *
61048 TTTTAAATTTTTTATAGT
1 TTTTAAATATTTTATATT
*
61066 ATTTAAATATTTTATATT
1 TTTTAAATATTTTATATT
*
61084 TTTT-AATAATTTA-ATT
1 TTTTAAATATTTTATATT
61100 TT
1 TT
61102 ACACCTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 5 0.16
17 8 0.26
18 18 0.58
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTAAATATTTTATATT
Found at i:61830 original size:30 final size:30
Alignment explanation
Indices: 61794--61855 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
61784 AACACCATAT
*
61794 CAATTTGAAGTCCTTGAATAACTTTGTATG
1 CAATTTGAAGCCCTTGAATAACTTTGTATG
*
61824 CAATTTGAAGCCCTTGAATAAGTTTGTATG
1 CAATTTGAAGCCCTTGAATAACTTTGTATG
61854 CA
1 CA
61856 GTGACAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (30 bp):
CAATTTGAAGCCCTTGAATAACTTTGTATG
Found at i:64295 original size:28 final size:26
Alignment explanation
Indices: 64264--64315 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
64254 ATTAAAAATT
*
64264 TATTTTATTCCTTCTATTATTTAAAAGA
1 TATTTTAAT-CTTCTA-TATTTAAAAGA
*
64292 TATTTTAATCTTTTATATTTAAAA
1 TATTTTAATCTTCTATATTTAAAA
64316 AAGTGAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 5 0.23
28 8 0.36
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.56
Consensus pattern (26 bp):
TATTTTAATCTTCTATATTTAAAAGA
Found at i:65817 original size:17 final size:17
Alignment explanation
Indices: 65789--65823 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
65779 TTAAAGTACA
65789 AAAAAATGAAAGATAAAT
1 AAAAAATGAAAGA-AAAT
65807 AAAAAAT-AAAGAAAAT
1 AAAAAATGAAAGAAAAT
65823 A
1 A
65824 GTAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 5 0.29
18 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (17 bp):
AAAAAATGAAAGAAAAT
Found at i:67232 original size:23 final size:23
Alignment explanation
Indices: 67202--67256 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
67192 CTATGCAAAT
67202 TCTTGAACTATAAGTTCTTCTCA
1 TCTTGAACTATAAGTTCTTCTCA
67225 TCTTGAACTATAAGTTCTTCTCA
1 TCTTGAACTATAAGTTCTTCTCA
67248 TCTTGAACT
1 TCTTGAACT
67257 TCTTCTCCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.44
Consensus pattern (23 bp):
TCTTGAACTATAAGTTCTTCTCA
Found at i:67790 original size:139 final size:139
Alignment explanation
Indices: 67519--68602 Score: 1564
Period size: 139 Copynumber: 7.8 Consensus size: 139
67509 GGTGTTGTTC
* * * * *
67519 CAACTCCTTATTTGATGGAAACGAGCTAAAGTAGAACAAGTTCTTCTCATTATGAACTTCTTCTC
1 CAACTCCATATGTGAT-GAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
* *
67584 CCTCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATTTTGATCCATCGAGTGAGGT
65 CCTCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGT
**
67649 GTTTTTGATT
130 GTTGCTGATT
** * * *
67659 CAACTCTGTATATGATGAATCGAGCTAAGGTTGGACAAGTTCTTCTCATTATGAACTTCTTCTCT
1 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * *
67724 CTCATCGGATGAGTTCTTCTCATTATGAATTCTCCACCGTAAATGTTGATCCCTCGAGTGAGGTG
66 CTCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTG
67789 TTGCTGATT
131 TTGCTGATT
* *
67798 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTACTCATTATGAACTTTTTCTCC
1 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
** * * * *
67863 CTCATCGGAACAATTATTCTCATTATAAACTCTCCATTCGAAATGTTGATCCCTCGAGTGAGGTG
66 CTCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTG
67928 TTGCTGATT
131 TTGCTGATT
*
67937 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCC
1 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * *
68002 CTCATCGGATGAGTTCTTCTCATTATGAACTCTCAACTAGAAATATTGATCCCTCGAGTGAGGTG
66 CTCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTG
*
68067 TTGTTGATT
131 TTGCTGATT
* * * *
68076 CAATTCTATATGTGATGAATCGAGCTAAGGTT-AATAAGTTCTTATCATTATGAA---CTTCTCC
1 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * *
68137 CTCATCGGATGATTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTTGAGTGAGATG
66 CTCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTG
68202 TTGCTGATT
131 TTGCTGATT
* *
68211 CAACTCCATATGTGATGAATCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
1 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * * ** ** *
68276 CTTATTGAATGAGTTTTTCTCATTATGAACTCTCCACTATAAATGTTGATATCTCGTGTGAGGTG
66 CTCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTG
*
68341 TTGCTGAAT
131 TTGCTGATT
* *
68350 CAACTCCATATGTGATAAATCGAGCTAAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTCC
1 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * *
68415 CTTATCGGATGAGTTATTCTCATTATGAACTTTTCATTGGAAATGTTGATCCCTCGAGTGAGGTG
66 CTCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTG
*
68480 TTGCTCATT
131 TTGCTGATT
* * *
68489 CAACTCAATATGTGATGAATTGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCC
1 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* *
68554 CTCATCGGATGAGTTCTTCTCATTATAAACTCTCCACTGGAAATGTTGA
66 CTCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGA
68603 CTGGTTTATC
Statistics
Matches: 834, Mismatches: 106, Indels: 9
0.88 0.11 0.01
Matches are distributed among these distances:
135 101 0.12
136 20 0.02
138 19 0.02
139 681 0.82
140 13 0.02
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (139 bp):
CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
CTCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTG
TTGCTGATT
Found at i:68992 original size:95 final size:96
Alignment explanation
Indices: 68856--69052 Score: 238
Period size: 95 Copynumber: 2.0 Consensus size: 96
68846 TTTGAGAAGA
* * * *
68856 GATAAATTTTCGTTTCAAGTGAATAAATTTCAAAATATGTGTTCTAAGGGGAACTATTTC-AAGC
1 GATAAATTTTCGTTTCAAGTGAAAAAAATTCAAAATATGTGTTCCAAGGGGAAATATTTCAAAG-
*
68920 A-AAATTGATTTTAAGAAAAACCATCTCAAGT
65 AGAAATTGATTTGAAGAAAAACCATCTCAAGT
* * *
68951 GATAAATTTTTGGTTT-GAGTGAAAAAAATTCAAAATTTGTGTTCCAAGGGGAAATATTTCAAAA
1 GATAAA-TTTTCGTTTCAAGTGAAAAAAATTCAAAATATGTGTTCCAAGGGGAAATATTTC---A
*
69015 AAGATGAAATTGATTTGAAGAGAAACCATCTCAAGT
62 AAGA-GAAATTGATTTGAAGAAAAACCATCTCAAGT
69051 GA
1 GA
69053 GATAATAATT
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
95 44 0.51
96 8 0.09
98 1 0.01
99 3 0.03
100 30 0.35
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (96 bp):
GATAAATTTTCGTTTCAAGTGAAAAAAATTCAAAATATGTGTTCCAAGGGGAAATATTTCAAAGA
GAAATTGATTTGAAGAAAAACCATCTCAAGT
Found at i:69083 original size:100 final size:94
Alignment explanation
Indices: 68873--69089 Score: 233
Period size: 100 Copynumber: 2.2 Consensus size: 94
68863 TTTCGTTTCA
* * * * *
68873 AGTGAATAAATTTCAAAATATGTGTTCTAAGGGGAACTATTTCAAGCAAAATTGATTTTAAGAAA
1 AGTGAAAAAATTTCAAAATTTGTGTTCCAAGGGGAAATATTTCAAGCAAAATTGATTTGAAGAAA
* * *
68938 AACCATCTCAAGTGATAAATTTTTGGTTTG
66 AACCATCTCAAGTGAGAAATATTT-GTTCG
*
68968 AGTGAAAAAAATTCAAAATTTGTGTTCCAAGGGGAAATATTTCAAAAAAG-ATGAAATTGATTTG
1 AGTGAAAAAATTTCAAAATTTGTGTTCCAAGGGGAAATATTTC----AAGCA--AAATTGATTTG
*
69032 AAGAGAAACCATCTCAAGTGAGATAATAATTT-TTCG
60 AAGAAAAACCATCTCAAGTGAGA-AAT-ATTTGTTCG
69068 AGT-AAAACAATTTCAAAATTTG
1 AGTGAAAA-AATTTCAAAATTTG
69090 AGTTTCGAGG
Statistics
Matches: 102, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
95 38 0.37
98 1 0.01
99 7 0.07
100 50 0.49
101 3 0.03
102 3 0.03
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (94 bp):
AGTGAAAAAATTTCAAAATTTGTGTTCCAAGGGGAAATATTTCAAGCAAAATTGATTTGAAGAAA
AACCATCTCAAGTGAGAAATATTTGTTCG
Found at i:69472 original size:105 final size:101
Alignment explanation
Indices: 69273--69459 Score: 263
Period size: 105 Copynumber: 1.8 Consensus size: 101
69263 CGGGTGAAAT
* * * *
69273 AATTTGTGTTTCAAGGGAAATAGTCTCTAGTGAGACGAAATTTATTTTAAGAAAAGAATAATCTC
1 AATTTGTGTTTCAAGGGAAATAGTCTCAAGCGAGACAAAATTAATTTTAAGAAAAG-ATAATCTC
*
69338 GAGTGAGATCAATTTTGGTTTCAAGTGAAACAATTTCAA
65 AAGTGAGA-CAATTTT-GTTTCAAGTGAAACAATTTCAA
*
69377 AATTTGTGTTTCAAGGGAAAATTGTCTCAAGCGAGACAAAATTAATTTTAAGAAAAG-TAATCTC
1 AATTTGTGTTTCAAGGG-AAATAGTCTCAAGCGAGACAAAATTAATTTTAAGAAAAGATAATCTC
69441 AAGTGAGA-AATTTT-TTTCA
65 AAGTGAGACAATTTTGTTTCA
69460 TCTTTGCTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
99 5 0.07
101 6 0.08
103 14 0.18
104 17 0.22
105 34 0.45
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.34
Consensus pattern (101 bp):
AATTTGTGTTTCAAGGGAAATAGTCTCAAGCGAGACAAAATTAATTTTAAGAAAAGATAATCTCA
AGTGAGACAATTTTGTTTCAAGTGAAACAATTTCAA
Found at i:70313 original size:29 final size:29
Alignment explanation
Indices: 70234--70303 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
70224 ACTTGGGAAG
70234 GTAATGTGTTTCAGGTTAATTTTGAGAAA
1 GTAATGTGTTTCAGGTTAATTTTGAGAAA
70263 GTAATGTGTTTCAGGTTAATTTTGAGAAA
1 GTAATGTGTTTCAGGTTAATTTTGAGAAA
70292 GTAATGTGTTTC
1 GTAATGTGTTTC
70304 GTGCTAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.43
Consensus pattern (29 bp):
GTAATGTGTTTCAGGTTAATTTTGAGAAA
Found at i:70991 original size:25 final size:27
Alignment explanation
Indices: 70963--71012 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
70953 TTTGATATGT
* *
70963 TTTC-TTTCT-TCTTTTTCCTTTTTGC
1 TTTCTTTTCTCTCTTATTACTTTTTGC
70988 TTTCTTTTCTCTCTTATTACTTTTT
1 TTTCTTTTCTCTCTTATTACTTTTT
71013 TCTTCTGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 5 0.24
27 12 0.57
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTCTTTTCTCTCTTATTACTTTTTGC
Found at i:71023 original size:21 final size:21
Alignment explanation
Indices: 70994--71033 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
70984 TTGCTTTCTT
70994 TTCTCTCTTATTACTTTTTTC
1 TTCTCTCTTATTACTTTTTTC
* * *
71015 TTCTGTCTTTTTTCTTTTT
1 TTCTCTCTTATTACTTTTT
71034 CATTCTTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (21 bp):
TTCTCTCTTATTACTTTTTTC
Found at i:71070 original size:14 final size:15
Alignment explanation
Indices: 71048--71076 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
71038 CTTTTATCTC
71048 TCTTCTATTTTCTTT
1 TCTTCTATTTTCTTT
71063 TCTT-TATTTTCTTT
1 TCTTCTATTTTCTTT
71077 ATTTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (15 bp):
TCTTCTATTTTCTTT
Found at i:74938 original size:4 final size:4
Alignment explanation
Indices: 74929--74967 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
74919 TTCGGACATA
* * *
74929 AAAT AAAT AAAT AAAT AAGT AAAC AAAT AAAG AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
74968 GAAAAATTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:76746 original size:29 final size:29
Alignment explanation
Indices: 76690--76746 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
76680 ACTAACCTAT
* * * *
76690 TTTTTATTTTGTTTGATTTAGTCATTTAA
1 TTTTTAATTCGTTTAATTTAGCCATTTAA
*
76719 TTTTTAATTCGTTTAATTTAGCCCTTTA
1 TTTTTAATTCGTTTAATTTAGCCATTTA
76747 TTTCAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.61
Consensus pattern (29 bp):
TTTTTAATTCGTTTAATTTAGCCATTTAA
Done.