Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002894.1 Hibiscus syriacus cultivar Beakdansim tig00005980_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: 55425
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Found at i:3888 original size:22 final size:22
Alignment explanation
Indices: 3850--3892 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3840 TTTTTAATAT
*
3850 TATAATATAGTCAATTATATTA
1 TATAATATAGTAAATTATATTA
3872 TATAATATA-TAATATTATATT
1 TATAATATAGTAA-ATTATATT
3893 TTATTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TATAATATAGTAAATTATATTA
Found at i:4131 original size:17 final size:17
Alignment explanation
Indices: 4105--4159 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
4095 ATAATAATAT
*
4105 TAATTTTTTATGATAAA
1 TAATTATTTATGATAAA
*
4122 TAATTATTTATGAT-AT
1 TAATTATTTATGATAAA
* * *
4138 TAAATATTTGTAATAAA
1 TAATTATTTATGATAAA
4155 TAATT
1 TAATT
4160 TCTAAAAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTATTTATGATAAA
Found at i:4758 original size:22 final size:22
Alignment explanation
Indices: 4728--4770 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4718 AATTCTTTAA
*
4728 AAATCTAAAACATTAAAAAATG
1 AAATATAAAACATTAAAAAATG
* *
4750 AAATATAAAATATTAATAAAT
1 AAATATAAAACATTAAAAAAT
4771 ATAAAAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (22 bp):
AAATATAAAACATTAAAAAATG
Found at i:6506 original size:13 final size:13
Alignment explanation
Indices: 6488--6532 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
6478 AACATTGTGA
*
6488 AAAGAAAATAATG
1 AAAGAAAATAAAG
6501 AAAGAAAATAAAG
1 AAAGAAAATAAAG
* *
6514 AAAAAAAATAGAG
1 AAAGAAAATAAAG
6527 -AAGAAA
1 AAAGAAA
6533 GAAAAGCAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 5 0.18
13 23 0.82
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:7899 original size:24 final size:24
Alignment explanation
Indices: 7865--7943 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
7855 AGGTTTTAAT
7865 ATGTTAGTTTGGTGTATTTGTGGA
1 ATGTTAGTTTGGTGTATTTGTGGA
* **
7889 ATGTTACTTTGGT-T-TTAAT---
1 ATGTTAGTTTGGTGTATTTGTGGA
7908 ATGTTAGTTTGGTGTATTTGTGGA
1 ATGTTAGTTTGGTGTATTTGTGGA
* *
7932 TTGTTAATTTGG
1 ATGTTAGTTTGG
7944 AGTTTAGATT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
19 12 0.29
20 1 0.02
21 3 0.07
22 3 0.07
23 1 0.02
24 22 0.52
ACGTcount: A:0.18, C:0.01, G:0.28, T:0.53
Consensus pattern (24 bp):
ATGTTAGTTTGGTGTATTTGTGGA
Found at i:7913 original size:19 final size:19
Alignment explanation
Indices: 7847--7920 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 19
7837 ATTTGTGGAT
*
7847 TGTTACTTAGGTTTTAATA
1 TGTTACTTTGGTTTTAATA
* **
7866 TGTTAGTTTGGTGTATTTGTGGAA
1 TGTTACTTTGGT-T-TTAAT---A
7890 TGTTACTTTGGTTTTAATA
1 TGTTACTTTGGTTTTAATA
*
7909 TGTTAGTTTGGT
1 TGTTACTTTGGT
7921 GTATTTGTGG
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
19 22 0.52
20 1 0.02
21 3 0.07
22 3 0.07
23 1 0.02
24 12 0.29
ACGTcount: A:0.19, C:0.03, G:0.24, T:0.54
Consensus pattern (19 bp):
TGTTACTTTGGTTTTAATA
Found at i:7943 original size:43 final size:43
Alignment explanation
Indices: 7834--7943 Score: 193
Period size: 43 Copynumber: 2.6 Consensus size: 43
7824 TATTAGTTAA
*
7834 TGTATTTGTGGATTGTTACTTAGGTTTTAATATGTTAGTTTGG
1 TGTATTTGTGGATTGTTACTTTGGTTTTAATATGTTAGTTTGG
*
7877 TGTATTTGTGGAATGTTACTTTGGTTTTAATATGTTAGTTTGG
1 TGTATTTGTGGATTGTTACTTTGGTTTTAATATGTTAGTTTGG
*
7920 TGTATTTGTGGATTGTTAATTTGG
1 TGTATTTGTGGATTGTTACTTTGG
7944 AGTTTAGATT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.18, C:0.02, G:0.26, T:0.54
Consensus pattern (43 bp):
TGTATTTGTGGATTGTTACTTTGGTTTTAATATGTTAGTTTGG
Found at i:8616 original size:60 final size:60
Alignment explanation
Indices: 8551--8676 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
8541 ATAGTCCCCT
* ** * *
8551 GACTATAGGACATTTTTTTGTTGAGTC-CCTCAAC-AGTT-AAAAGTTATAAAATGGTCTCTC
1 GACTATAGGACAGTGCTTTGTTGAGTCTCC-CAACTA-TTCAAAA-TTATAAAATGGTCACCC
*
8611 GACTATAGGATAGTGCTTTGTTGAGTCTCCCAACTATTCAAAATTATAAAATGGTCACCC
1 GACTATAGGACAGTGCTTTGTTGAGTCTCCCAACTATTCAAAATTATAAAATGGTCACCC
8671 GACTAT
1 GACTAT
8677 TTATATGTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
60 50 0.88
61 7 0.12
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (60 bp):
GACTATAGGACAGTGCTTTGTTGAGTCTCCCAACTATTCAAAATTATAAAATGGTCACCC
Found at i:8864 original size:28 final size:28
Alignment explanation
Indices: 8813--8867 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
8803 CTCTGTTTAC
* *
8813 ATTATTTTGTTGAGCATGTGCTTGAAAT
1 ATTATGTTGTTGAGCATGTACTTGAAAT
8841 ATTATGTTGTTGAGC-TAGTACTTGAAA
1 ATTATGTTGTTGAGCAT-GTACTTGAAA
8868 GAAATGACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (28 bp):
ATTATGTTGTTGAGCATGTACTTGAAAT
Found at i:15131 original size:20 final size:20
Alignment explanation
Indices: 15101--15139 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
15091 TCAAAACATT
15101 AAAATTTAAAATTC-AAACG
1 AAAATTTAAAATTCTAAACG
15120 AAAATGTTAAAATTCTAAAC
1 AAAAT-TTAAAATTCTAAAC
15140 CGACTTATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAATTTAAAATTCTAAACG
Found at i:17034 original size:2 final size:2
Alignment explanation
Indices: 17027--17057 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17017 TGCAAAATCT
17027 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 T
17058 TTCCAATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29249 original size:113 final size:113
Alignment explanation
Indices: 28844--29326 Score: 570
Period size: 113 Copynumber: 4.2 Consensus size: 113
28834 AACTTTCAAC
* *
28844 AAAGTATCGATACATTTTTATAAAAAATATCTATACTTTCAACATATTAGGTAAATTTTACCGGT
1 AAAGTATCGATACATTTTTATAAAAAAGATCGATACTTTCAACATATTAGGTAAATTTTACCGGT
* * **
28909 TTTGTCATCATGAAACTGATTTTGTCATATTTTTACCAATTATATTGT
66 TTTGTCATAATGAAACTGATTTTGTCATACTTTTACCTGTTATATTGT
* * * ** * *
28957 AAAATATCGAT-CCTTTTTAATATATTAG---GATCCTTT---TATATTAGGTAAATTTTACCGG
1 AAAGTATCGATACATTTTT-ATAAAAAAGATCGATACTTTCAACATATTAGGTAAATTTTACCGG
* *
29015 TTTTGTCATAATGAAACTGGTTTTGTCATACTTTTACCTGTTATATTAT
65 TTTTGTCATAATGAAACTGATTTTGTCATACTTTTACCTGTTATATTGT
*
29064 AAAGTAAT-GATACATTTTTATCCTTTTTCAACATAAAAATGATCGATACTTTCAATATATTAGG
1 AAAGT-ATCGATACATTTTTA-------T----A-AAAAA-GATCGATACTTTCAACATATTAGG
*
29128 TAAATTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATACTTTTACCTGTTATATTGT
52 TAAATTTTACCGGTTTTGTCATAATGAAACTGATTTTGTCATACTTTTACCTGTTATATTGT
**
29190 AAAGTAAT-GATACATTTTTATAAAAAAGATCGATACTTTCAACATATCCGGTAAATTTTACCGG
1 AAAGT-ATCGATACATTTTTATAAAAAAGATCGATACTTTCAACATATTAGGTAAATTTTACCGG
* *
29254 TTTTGTCATAATGAAACTGATTTTGTCATATTTTTACTTGTTATATTGT
65 TTTTGTCATAATGAAACTGATTTTGTCATACTTTTACCTGTTATATTGT
29303 AAAGTATCGATACATTTTTATAAA
1 AAAGTATCGATACATTTTTATAAA
29327 GTATCGATAC
Statistics
Matches: 319, Mismatches: 28, Indels: 46
0.81 0.07 0.12
Matches are distributed among these distances:
107 72 0.23
108 8 0.03
110 6 0.02
112 8 0.03
113 116 0.36
114 6 0.02
115 1 0.00
118 1 0.00
119 3 0.01
120 1 0.00
123 7 0.02
126 90 0.28
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (113 bp):
AAAGTATCGATACATTTTTATAAAAAAGATCGATACTTTCAACATATTAGGTAAATTTTACCGGT
TTTGTCATAATGAAACTGATTTTGTCATACTTTTACCTGTTATATTGT
Found at i:29690 original size:87 final size:87
Alignment explanation
Indices: 29567--29771 Score: 293
Period size: 87 Copynumber: 2.4 Consensus size: 87
29557 ACAAATTAAA
* * * * *
29567 TAATTAACCTCTTTTATTATATAAGGGCTACCTATTACGTTATATAAACGCTACCAAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATACAAACGCTACCAAATATGTTA
* *
29632 TTGTGCTTGATAATGTTTCTAT
66 TTGTGCTTGATAATGTTTCCAG
* * *
29654 TAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATACAACCGGTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATACAAACGCTACCAAATATGTTA
*
29719 TTGTGTTTGATAATGTTTCCAG
66 TTGTGCTTGATAATGTTTCCAG
* *
29741 TAATTAACATATTTTATTATATAAGCACTAC
1 TAATTAACCTATTTTATTATATAAGCGCTAC
29772 CTCTGTGGAA
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 105 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (87 bp):
TAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATACAAACGCTACCAAATATGTTA
TTGTGCTTGATAATGTTTCCAG
Found at i:30301 original size:112 final size:112
Alignment explanation
Indices: 30089--30442 Score: 609
Period size: 112 Copynumber: 3.2 Consensus size: 112
30079 TAACTTTCAA
* * * *
30089 TAAAGTATCGATACATTTTTATAAAAAGTATCTATACTTTCAACATATTAGGTAAATTTTACCGG
1 TAAAGTATCGAT-CCTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGG
30154 TTTTGTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTG
65 TTTTGTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTG
*
30202 TAAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACTGGT
1 TAAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
*
30267 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTG
66 TTTGTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTG
*
30314 TAAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGAT
1 TAAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
* *
30379 TTTGTCATAATGAAATTGGTTTTGTCACATTTTTACTTGTTATATTG
66 TTTGTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTG
*
30426 TAAAGTATCGATACTTT
1 TAAAGTATCGATCCTTT
30443 ATAGGCGCTA
Statistics
Matches: 229, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
112 217 0.95
113 12 0.05
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (112 bp):
TAAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
TTTGTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTG
Found at i:30722 original size:87 final size:87
Alignment explanation
Indices: 30627--30833 Score: 279
Period size: 87 Copynumber: 2.4 Consensus size: 87
30617 ATAAATTAAA
* ** * * **
30627 TAATTAACATATTTTATTATATAAGTGCTATTTATTGCGTTATATAAACGCTACCTAATATGTTA
1 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGCCA
*
30692 TTGTGTTTAATAATGTTTCCAG
66 TTGTGATTAATAATGTTTCCAG
** * *
30714 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAGTGGTACTTAATATGCCA
1 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGCCA
*
30779 TTGTGATTGATAATGTTTCCAG
66 TTGTGATTAATAATGTTTCCAG
* *
30801 TAATTAACCTATTTTATTATATAAGCACTACCT
1 TAATTAACATATTTTATTATATAAGCGCTACCT
30834 CTGTGGAAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 105 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (87 bp):
TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGCCA
TTGTGATTAATAATGTTTCCAG
Found at i:32368 original size:23 final size:23
Alignment explanation
Indices: 32320--32369 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
32310 ACATATTTTA
* * *
32320 TTATATAAGTGTTACCTATTGCG
1 TTATATAAGCGTTACCTAATACG
*
32343 TTATATAAGCGTTACCTAATATG
1 TTATATAAGCGTTACCTAATACG
32366 TTAT
1 TTAT
32370 TGTGTTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (23 bp):
TTATATAAGCGTTACCTAATACG
Found at i:32409 original size:87 final size:87
Alignment explanation
Indices: 32304--32508 Score: 311
Period size: 87 Copynumber: 2.4 Consensus size: 87
32294 ACAAATTAAA
* * * * * *
32304 TAATTAACATATTTTATTATATAAGTGTTACCTATTGCGTTATATAAGCGTTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGTGCTACCTATTACATTAAATAAGCGGTACCTAATATGTTA
*
32369 TTGTGTTTGATAATGTTTCCAG
66 TTGTGCTTGATAATGTTTCCAG
* * *
32391 TAATTAACCTTTTTTATTATATAAGTGCTACCTATTACATTAAATAAGTGGTACTTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGTGCTACCTATTACATTAAATAAGCGGTACCTAATATGTTA
32456 TTGTGCTTGATAATGTTTCCAG
66 TTGTGCTTGATAATGTTTCCAG
*
32478 TAATTAACCTATTTTATTATATAAGTACTAC
1 TAATTAACCTATTTTATTATATAAGTGCTAC
32509 TTCTGTGGAA
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 106 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (87 bp):
TAATTAACCTATTTTATTATATAAGTGCTACCTATTACATTAAATAAGCGGTACCTAATATGTTA
TTGTGCTTGATAATGTTTCCAG
Found at i:33234 original size:23 final size:23
Alignment explanation
Indices: 33184--33228 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
33174 AACATATTTT
* * *
33184 ATTATATAAGTGCTACCTATTAC
1 ATTATATAAGCGATACCTAATAC
33207 ATTATATAAGCGATACCTAATA
1 ATTATATAAGCGATACCTAATA
33229 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGATACCTAATAC
Found at i:33340 original size:87 final size:87
Alignment explanation
Indices: 33082--33340 Score: 374
Period size: 87 Copynumber: 3.0 Consensus size: 87
33072 ACAAATTAAA
* ** * * *
33082 TAATTAACATATTTTATTATATAAGTGTTATTTATTGCGTTATATAAGCGCTACCTAATATGTTA
1 TAATTAACATATTTTATTATATAAGTGCTACCTATTACATTATATAAGCGATACCTAATATGTTA
* *
33147 TTGTGTTTAATAATGTTTCCAG
66 TTGTGATTAATAATGTTTCTAG
33169 TAATTAACATATTTTATTATATAAGTGCTACCTATTACATTATATAAGCGATACCTAATATGTTA
1 TAATTAACATATTTTATTATATAAGTGCTACCTATTACATTATATAAGCGATACCTAATATGTTA
* *
33234 TTGTGCTTGATAATGTTTCTAG
66 TTGTGATTAATAATGTTTCTAG
* * * * *
33256 TAATTAACCTATTTTATTTTATAAGCGCTACGTATTACATTATATAAGCGGTACCTAATATGTTA
1 TAATTAACATATTTTATTATATAAGTGCTACCTATTACATTATATAAGCGATACCTAATATGTTA
*
33321 TTGTGATTAATAATATTTCT
66 TTGTGATTAATAATGTTTCT
33341 GATTAAATGA
Statistics
Matches: 155, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 155 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (87 bp):
TAATTAACATATTTTATTATATAAGTGCTACCTATTACATTATATAAGCGATACCTAATATGTTA
TTGTGATTAATAATGTTTCTAG
Found at i:39406 original size:20 final size:20
Alignment explanation
Indices: 39376--39414 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39366 TCAAAACATT
39376 AAAATTTAAAATTC-AAACG
1 AAAATTTAAAATTCTAAACG
39395 AAAATGTTAAAATTCTAAAC
1 AAAAT-TTAAAATTCTAAAC
39415 CGACTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAATTTAAAATTCTAAACG
Found at i:41330 original size:2 final size:2
Alignment explanation
Indices: 41319--41391 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
41309 AACTTGCCAA
41319 AT AT -T AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
41360 AT AT AT 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 AT AT AT
41392 CCAATCAATT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:41788 original size:23 final size:24
Alignment explanation
Indices: 41753--41798 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
41743 AATTTTATTG
*
41753 AATTTTAAATTCA-ATTAATGAGA
1 AATTATAAATTCACATTAATGAGA
*
41776 AATTATAATTTCACCATTAATGA
1 AATTATAAATTCA-CATTAATGA
41799 ATTATGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (24 bp):
AATTATAAATTCACATTAATGAGA
Found at i:52803 original size:314 final size:307
Alignment explanation
Indices: 52233--52858 Score: 839
Period size: 314 Copynumber: 2.0 Consensus size: 307
52223 TACCCGCCGT
*
52233 TAAAAACTTAACGCGCTTAGTACATAAAATATTAGTTTTGGTATGTTTAGTACCTAAACTTTCAT
1 TAAAAACTTAACGCGCTTAGTACATAAAATATCAGTTTTGGTATGTTTAGTACCTAAACTTTCAT
* *
52298 TTTTTTTCAAACTTAACGTTAAATTTTGAAGGGTACTAAAATAAAACAAAAACCAAATTTTAAGT
66 TTTTTTTCAAACTTAACATTAAATTTTGAAGGGTACTAAAATAAAACAAAAACCAAACTTTAAGT
* * * *
52363 ACTTAAAAATTGAAAGTTTAGGTACTAAAATAGACGAAATTGATAGTTTAGTTATAAATGTGTAA
131 ACTTAAAAAATGAAAGTTTAGGTACTAAAATAGAC-AAATTGATAGTTTAGATATAAACGCGTAA
* *
52428 TTTATCTTTTTTATATATATACTTATCTCCTCGTAGTTTCAAATTATTAATAGAAGATAATAGGA
195 TTTATCTTTTTTATATAAATAATTATCTCCTCGTAGTTTCAAATTATTAATAGAAGATAATAGGA
*
52493 TGGAAATATTATACTTAT-AAAATAAGTACGTTAGTACTACTTT-TTAA
260 TGGAAATATTATACTTATAAAAATAAATACGTTAGTACTA-TTTATTAA
* * * * * *
52540 TAAAAAGTTAACGCGTTTAGTACTTAAAATATCAGTTTTGGTTTGTTTTAGTTCCTAAATTTTCA
1 TAAAAACTTAACGCGCTTAGTACATAAAATATCAGTTTTGGTATG-TTTAGTACCTAAACTTTCA
* * * * **
52605 TTTTTTTTCAAAATTTAATATTAAATTTTGAACGGGTACTAAAATGAAATAAAAATTAAACTTTA
65 TTTTTTTTC-AAACTTAACATTAAATTTTGAA-GGGTACTAAAATAAAACAAAAACCAAACTTTA
* * ** *
52670 AGTATGGTTGTAAAAAAAT-AAAGTTTAGGTATTAAAATA-A-ACCTTGCTAGTTTAGATACTAA
128 AGTA---CT-T-AAAAAATGAAAGTTTAGGTACTAAAATAGACAAATTGATAGTTTAGATA-TAA
*
52732 ACGCGTAATTTATCCTTTTTTATATGAAATAATTATCTCCTCGTAGTTTCAAATTATTAATAGAT
187 ACGCGTAATTTAT-CTTTTTTATAT-AAATAATTATCTCCTCGTAGTTTCAAATTATTAATAGAA
*
52797 GATAATAGGATGGAAATATTCTACTTATAAAAATAAATACGTTAGTACTATTTATTAA
250 GATAATAGGATGGAAATATTATACTTATAAAAATAAATACGTTAGTACTATTTATTAA
52855 TAAA
1 TAAA
52859 GAAATATTAT
Statistics
Matches: 277, Mismatches: 29, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
307 40 0.14
308 26 0.09
309 19 0.07
310 31 0.11
311 14 0.05
312 14 0.05
313 13 0.05
314 86 0.31
315 34 0.12
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (307 bp):
TAAAAACTTAACGCGCTTAGTACATAAAATATCAGTTTTGGTATGTTTAGTACCTAAACTTTCAT
TTTTTTTCAAACTTAACATTAAATTTTGAAGGGTACTAAAATAAAACAAAAACCAAACTTTAAGT
ACTTAAAAAATGAAAGTTTAGGTACTAAAATAGACAAATTGATAGTTTAGATATAAACGCGTAAT
TTATCTTTTTTATATAAATAATTATCTCCTCGTAGTTTCAAATTATTAATAGAAGATAATAGGAT
GGAAATATTATACTTATAAAAATAAATACGTTAGTACTATTTATTAA
Done.