Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002468.1 Hibiscus syriacus cultivar Beakdansim tig00005048_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: 66441
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:17322 original size:20 final size:20
Alignment explanation
Indices: 17299--17345 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
17289 CCGCCACCCG
*
17299 CTGCCGCCGTCAGCAGTCCT
1 CTGCCACCGTCAGCAGTCCT
*
17319 CTGCCACTGTCAGCAGTCCT
1 CTGCCACCGTCAGCAGTCCT
17339 CTGCCAC
1 CTGCCAC
17346 ACTCCGACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.45, G:0.21, T:0.21
Consensus pattern (20 bp):
CTGCCACCGTCAGCAGTCCT
Found at i:26959 original size:32 final size:31
Alignment explanation
Indices: 26923--26990 Score: 73
Period size: 32 Copynumber: 2.2 Consensus size: 31
26913 TTCAATGGTC
* * *
26923 ATTTTGTATTAATTTGGTAAAGTATAATAATT
1 ATTTTATAATAATTTGATAAA-TATAATAATT
* *
26955 ATTTTATAATAGTTTGATAAATTTAATAATT
1 ATTTTATAATAATTTGATAAATATAATAATT
*
26986 TTTTT
1 ATTTT
26991 TGTAATCTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (31 bp):
ATTTTATAATAATTTGATAAATATAATAATT
Found at i:47376 original size:27 final size:28
Alignment explanation
Indices: 47345--47446 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 28
47335 CAGAAAATGA
*
47345 TTTTTGAAAA-ATTTATATATTATATAG
1 TTTTTGAAAACATTTATATAATATATAG
*
47372 TTTTTTGAAAATATTTTTAAAATATAATATATA-
1 -TTTTTGAAAACA--TTT---ATATAATATATAG
* * *
47405 ATTTTGAAAACATTTATATACTGTATAG
1 TTTTTGAAAACATTTATATAATATATAG
47433 TTTTT-AAAACATTT
1 TTTTTGAAAACATTT
47447 TGAAAACTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 15
0.74 0.07 0.18
Matches are distributed among these distances:
27 19 0.31
28 14 0.23
29 1 0.02
30 3 0.05
31 3 0.05
32 10 0.16
34 11 0.18
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (28 bp):
TTTTTGAAAACATTTATATAATATATAG
Found at i:47403 original size:41 final size:41
Alignment explanation
Indices: 47318--47406 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
47308 TTTTGACAAA
*
47318 ATATAATATATAATTTTCAGAAAATGATTTTTGAAAAATTT
1 ATATAATATATAATTTTCAGAAAATGATTTTTGAAAAATAT
* * **
47359 ATATATTATATAGTTTTTTGAAAAT-ATTTTT-AAAATATAAT
1 ATATAATATATAATTTTCAGAAAATGATTTTTGAAAA-AT-AT
47400 ATATAAT
1 ATATAAT
47407 TTTGAAAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
39 4 0.10
40 8 0.20
41 28 0.70
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (41 bp):
ATATAATATATAATTTTCAGAAAATGATTTTTGAAAAATAT
Found at i:47468 original size:36 final size:35
Alignment explanation
Indices: 47405--47640 Score: 208
Period size: 38 Copynumber: 6.8 Consensus size: 35
47395 ATAATATATA
*
47405 ATTTTGAAAACATTTATATACTGTATAGTTTTTAAAAC
1 ATTTTGAAAAC--TTATATA-TATATAGTTTTTAAAAC
47443 ATTTTGAAAACTTATATAGTATATAGTTTTTAAAAC
1 ATTTTGAAAACTTATATA-TATATAGTTTTTAAAAC
* * *
47479 GTTTT-TAAA--TATA-ATATATAGTTTTAAAAAAC
1 ATTTTGAAAACTTATATATATATAGTTTT-TAAAAC
* * *
47511 ATTTTTGAAAAATTATATAATATATAGTTTTAAAAAT
1 A-TTTTGAAAACTTATAT-ATATATAGTTTTTAAAAC
47548 AGTTTTTGAAAACTTATATA-ATAT--TTTTTAAAAC
1 A--TTTTGAAAACTTATATATATATAGTTTTTAAAAC
* *
47582 ATTTTGAAAAC-TATATAACATATAGTTTTGAAAAC
1 ATTTTGAAAACTTATAT-ATATATAGTTTTTAAAAC
*
47617 -TTTTTAAAA--TATA-ATATATAGTTT
1 ATTTTGAAAACTTATATATATATAGTTT
47641 AAAAAAATAT
Statistics
Matches: 172, Mismatches: 14, Indels: 31
0.79 0.06 0.14
Matches are distributed among these distances:
31 26 0.15
32 17 0.10
33 16 0.09
34 20 0.12
35 12 0.07
36 35 0.20
37 7 0.04
38 39 0.23
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (35 bp):
ATTTTGAAAACTTATATATATATAGTTTTTAAAAC
Found at i:47527 original size:69 final size:69
Alignment explanation
Indices: 47428--47672 Score: 263
Period size: 69 Copynumber: 3.6 Consensus size: 69
47418 TTATATACTG
* * * *
47428 TATAGTTTT-TAAAACATTTTGAAAACTTATATAGTATATAGTTTTTAAAACGTTTTT-AAATAT
1 TATAGTTTTAAAAAACATTTTGAAAAATTATATAATATATAGTTTTAAAAACGTTTTTAAAATAT
47491 AATA
66 AATA
*
47495 TATAGTTTTAAAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAATAGTTTTTGAAAA
1 TATAGTTTTAAAAAACA-TTTTGAAAAATTATATAATATATAGTTTTAAAAA-CGTTTTT-AAAA
47560 CT-T-ATA
63 -TATAATA
** * * *
47566 TAATA-TTTTTTAAAACATTTTG-AAAACTATATAACATATAGTTTTGAAAAC-TTTTTAAAATA
1 T-ATAGTTTTAAAAAACATTTTGAAAAATTATATAATATATAGTTTTAAAAACGTTTTTAAAATA
47628 TAATA
65 TAATA
* * * *
47633 TATAGTTTAAAAAAATATTTTGAAATA-TATATATTATATA
1 TATAGTTTTAAAAAACATTTTGAAAAATTATATAATATATA
47673 AATTATATTT
Statistics
Matches: 149, Mismatches: 18, Indels: 22
0.79 0.10 0.12
Matches are distributed among these distances:
65 1 0.01
66 8 0.05
67 42 0.28
68 9 0.06
69 56 0.38
70 11 0.07
71 14 0.09
72 7 0.05
73 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (69 bp):
TATAGTTTTAAAAAACATTTTGAAAAATTATATAATATATAGTTTTAAAAACGTTTTTAAAATAT
AATA
Found at i:47628 original size:24 final size:24
Alignment explanation
Indices: 47583--47629 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
47573 TTTTAAAACA
*
47583 TTTTGAAAACTATATAACATATAG
1 TTTTGAAAACTATATAAAATATAG
* *
47607 TTTTGAAAACTTTTTAAAATATA
1 TTTTGAAAACTATATAAAATATA
47630 ATATATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (24 bp):
TTTTGAAAACTATATAAAATATAG
Found at i:47699 original size:9 final size:8
Alignment explanation
Indices: 47687--47729 Score: 50
Period size: 9 Copynumber: 4.9 Consensus size: 8
47677 ATATTTAGTA
47687 TATTATTAT
1 TATT-TTAT
47696 TATTTTATT
1 TATTTTA-T
47705 TATTTTAT
1 TATTTTAT
47713 TCATTTTATT
1 T-ATTTTA-T
47723 TATTTTA
1 TATTTTA
47730 ATACATTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 5 0.16
9 24 0.77
10 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (8 bp):
TATTTTAT
Found at i:47704 original size:23 final size:22
Alignment explanation
Indices: 47678--47727 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
47668 ATATAAATTA
47678 TATTTAGTATATT-ATTATTATTT
1 TATTTAGTATATTCATT-TTA-TT
* *
47701 TATTTATTTTATTCATTTTATT
1 TATTTAGTATATTCATTTTATT
47723 TATTT
1 TATTT
47728 TAATACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TATTTAGTATATTCATTTTATT
Found at i:47708 original size:18 final size:18
Alignment explanation
Indices: 47687--47729 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
47677 ATATTTAGTA
47687 TATTATTATT-ATTTTATT
1 TATT-TTATTCATTTTATT
47705 TATTTTATTCATTTTATT
1 TATTTTATTCATTTTATT
47723 TATTTTA
1 TATTTTA
47730 ATACATTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTTATTCATTTTATT
Found at i:48988 original size:24 final size:23
Alignment explanation
Indices: 48957--49010 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
48947 TTATTTTCTA
*
48957 TTTTATTTTATTT-TTCTTCTTTT
1 TTTTATTTTATTTGAT-TTCTTTT
*
48980 TTTTCATTTTCTTTGATTTC-TTT
1 TTTT-ATTTTATTTGATTTCTTTT
49003 TTTTATTT
1 TTTTATTT
49011 ATTCTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.15
23 11 0.41
24 11 0.41
25 1 0.04
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (23 bp):
TTTTATTTTATTTGATTTCTTTT
Found at i:48998 original size:29 final size:28
Alignment explanation
Indices: 48950--49044 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 28
48940 TTATTAATTA
48950 TTTTCTATTTTATTTTATTTTTCTTCTTT-T
1 TTTTC-ATTTTA-TTTATTTTT-TTCTTTAT
*
48980 TTTTCATTTTCTTTGATTTCTTTT-TTTAT
1 TTTTCATTTTATTT-ATTT-TTTTCTTTAT
*
49009 TTATTCTTTTTATTTATTTTTTTCTTTGACT
1 TT-TTCATTTTATTTATTTTTTTCTTT-A-T
49040 TTTTC
1 TTTTC
49045 CCTCTCTCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
28 10 0.18
29 21 0.38
30 21 0.38
31 3 0.05
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.77
Consensus pattern (28 bp):
TTTTCATTTTATTTATTTTTTTCTTTAT
Found at i:49035 original size:18 final size:18
Alignment explanation
Indices: 48940--49035 Score: 63
Period size: 19 Copynumber: 5.0 Consensus size: 18
48930 TTTTTTAATA
* *
48940 TTATTAATTATTTTCTATT
1 TTATTTATTTTTTTCT-TT
48959 TTATTTTATTTTTCTTCTTT
1 TTA-TTTATTTTT-TTCTTT
*
48979 TT-TTTCATTTTCTTTGATTT
1 TTATTT-ATTTT-TTT-CTTT
48999 CTT-TTT-TTATTTATTCTTT
1 -TTATTTATT-TTT-TTCTTT
49018 TTATTTATTTTTTTCTTT
1 TTATTTATTTTTTTCTTT
49036 GACTTTTTCC
Statistics
Matches: 63, Mismatches: 4, Indels: 21
0.72 0.05 0.24
Matches are distributed among these distances:
18 11 0.17
19 22 0.35
20 21 0.33
21 9 0.14
ACGTcount: A:0.14, C:0.08, G:0.01, T:0.77
Consensus pattern (18 bp):
TTATTTATTTTTTTCTTT
Found at i:49219 original size:16 final size:14
Alignment explanation
Indices: 49192--49229 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
49182 TTTTTTTATT
49192 TTATTTATTAAATA
1 TTATTTATTAAATA
49206 TTATGTTATATAAATA
1 TTAT-TTAT-TAAATA
49222 TT-TTTATT
1 TTATTTATT
49230 TTTTATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 8 0.36
15 5 0.23
16 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
TTATTTATTAAATA
Found at i:54761 original size:84 final size:83
Alignment explanation
Indices: 54511--55388 Score: 729
Period size: 84 Copynumber: 10.5 Consensus size: 83
54501 TTTAAGACAA
* * ** * *
54511 CATTTGCAGTATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTAC
* **
54576 GCTCAGCTCCAATGTGCAT
65 GCTCAGCTCCAAGGCACAT
* * * * * * * *
54595 CATTTGCAGCATAGCTTAAGTCGAGAAGGGATAT-T-T-TCCAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * * *
54657 CTCAACTTCGAGGGCATAT
66 CTCAGC-TCCAAGGCACAT
* * * *
54676 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGTCCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTAC
* *
54741 GCTTAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* ** * *
54760 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTAC
54825 GCTCAGCTCCAAGGCTAGCTCCAAGGCGCAT
65 GCTCAGCTCCAA-G---G---C-A----CAT
* * * * ** * *
54856 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTACA
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* *
54918 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCCAAGGCACAT
* * * *
54937 CATTTGAAGCATAACTCAAGGCTAGAAGGGTTAT-TTTCCACCAAAGACCTTCGAGTTCAACTAC
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGT-CACCAAAGACCTTCGAGTTCGACTAC
*
55001 GCTAAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * * *
55020 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * *
55082 CTCAACTTCGAGGGCACAT
66 CTCAGC-TCCAAGGCACAT
* * * * * *
55101 TATTTACAACATAACTCAAGGCTAGAAGGATTATCTGTCACCAAAGACCTTTGAGTTCGACTACG
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
55166 CTCAGCTCCAAGGCACAT
66 CTCAGCTCCAAGGCACAT
* * * * * * ** *
55184 CATATGCAGCATAGCTTAAGTCGAGATGGGTTATCTG---CCAAAGACCCTCGAGTTCGGTTACA
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * *
55246 TTCAGCTTCGAGGACACAT
66 CTCAGCTCCAAGG-CACAT
** * * *
55265 CATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAGAAGACCTTTGAGTTCGACTAT
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCA-AAGACCTTCGAGTTCGACTAC
*
55330 GCTCAGCTCCAATGCACAT
65 GCTCAGCTCCAAGGCACAT
* *
55349 CATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCA
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCA
55389 ATAAAATTGT
Statistics
Matches: 621, Mismatches: 140, Indels: 66
0.75 0.17 0.08
Matches are distributed among these distances:
80 82 0.13
81 136 0.22
82 1 0.00
83 77 0.12
84 201 0.32
85 53 0.09
86 1 0.00
88 1 0.00
89 1 0.00
91 1 0.00
92 28 0.05
93 3 0.00
96 36 0.06
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACAT
Found at i:55116 original size:164 final size:163
Alignment explanation
Indices: 54841--55385 Score: 840
Period size: 164 Copynumber: 3.3 Consensus size: 163
54831 CTCCAAGGCT
* *
54841 AGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCG
1 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCG
54906 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGAAGCATAACTCAAGGCTAGAAGGGTTAT
66 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTT-AAGCATAACTCAAGGCTAGAAGGGTTAT
* * * *
54971 -TTTCCACCAAAGACCTTCGAGTTCAACTACGCTA
130 CTGT-CACCAAAGACCTTTGAGTTCGACTACGCTC
55005 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCG
1 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCG
* * * *
55070 AGTTCGATTACACTCAACTTCGAGGGCACATTATTTACAACATAACTCAAGGCTAGAAGGATTAT
66 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA-AGCATAACTCAAGGCTAGAAGGGTTAT
55135 CTGTCACCAAAGACCTTTGAGTTCGACTACGCTC
130 CTGTCACCAAAGACCTTTGAGTTCGACTACGCTC
* * *
55169 AGCTCCAAGGCACATCATATGCAGCATAGCTTAAGTCGAGATGGGTTATCTGCCAAAGACCCTCG
1 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCG
* * *
55234 AGTTCGGTTACATTCAGCTTCGAGGACACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTAT
66 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA-AGCATAACTCAAGGCTAGAAGGGTTAT
*
55299 CTGTCACCAGAAGACCTTTGAGTTCGACTATGCTC
130 CTGTCACCA-AAGACCTTTGAGTTCGACTACGCTC
* * * * *
55334 AGCTCCAATGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTG
1 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
55386 TCAATAAAAT
Statistics
Matches: 350, Mismatches: 28, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
163 1 0.00
164 277 0.79
165 72 0.21
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (163 bp):
AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCG
AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAAGCATAACTCAAGGCTAGAAGGGTTATC
TGTCACCAAAGACCTTTGAGTTCGACTACGCTC
Found at i:55136 original size:81 final size:81
Alignment explanation
Indices: 54853--55385 Score: 453
Period size: 81 Copynumber: 6.5 Consensus size: 81
54843 CTCCAAGGCG
* * * * * * *
54853 CATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACA
1 CATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACA
54918 CTCAGCTTCGAGGGCA
66 CTCAGCTTCGAGGGCA
** * * *
54934 CATCATTTGA-AGCATAACTCAAGGCTAGAAGGGTTATTTTCCACCAAAGACCTTCGAGTTCAAC
1 CATCATTT-ACAGCATAACTCAAGGCTAGAAGGGTTA---TCTGCCAAAGACCCTCGAGTTCGAT
* * * *
54998 TACGCTAAGC-TCCAAGGCA
62 TACACTCAGCTTCGAGGGCA
* * * * * *
55017 CATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACA
1 CATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACA
*
55082 CTCAACTTCGAGGGCA
66 CTCAGCTTCGAGGGCA
* * * * * *
55098 CATTATTTACAACATAACTCAAGGCTAGAAGGATTATCTGTCACCAAAGACCTTTGAGTTCGACT
1 CATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG---CCAAAGACCCTCGAGTTCGATT
* * *
55163 ACGCTCAGC-TCCAAGGCA
63 ACACTCAGCTTCGAGGGCA
* * * * * * * *
55181 CATCATATGCAGCATAGCTTAAGTCGAGATGGGTTATCTGCCAAAGACCCTCGAGTTCGGTTACA
1 CATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACA
* *
55246 TTCAGCTTCGAGGACA
66 CTCAGCTTCGAGGGCA
* * * *
55262 CATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAGAAGACCTTTGAGTTCGAC
1 CATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG---CCA-AAGACCCTCGAGTTCGAT
** * **
55327 TATGCTCAGC-TCCAATGCA
62 TACACTCAGCTTCGAGGGCA
* * *
55346 CATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTG
1 CATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
55386 TCAATAAAAT
Statistics
Matches: 348, Mismatches: 90, Indels: 25
0.75 0.19 0.05
Matches are distributed among these distances:
80 52 0.15
81 105 0.30
83 73 0.21
84 97 0.28
85 21 0.06
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (81 bp):
CATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACA
CTCAGCTTCGAGGGCA
Found at i:56104 original size:27 final size:27
Alignment explanation
Indices: 56073--56126 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
56063 TATTTTTAAA
56073 ATATAATATATAGTTTTGAAAACATTT
1 ATATAATATATAGTTTTGAAAACATTT
* * * *
56100 ATATACTGTATGGTTTTTAAAACATTT
1 ATATAATATATAGTTTTGAAAACATTT
56127 TGAAAACTTA
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:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (27 bp):
ATATAATATATAGTTTTGAAAACATTT
Found at i:56152 original size:36 final size:35
Alignment explanation
Indices: 56086--56411 Score: 244
Period size: 38 Copynumber: 9.2 Consensus size: 35
56076 TAATATATAG
* * *
56086 TTTTGAAAACATTTATATACTGTATGGTTTTTAAAACA
1 TTTTGAAAAC--TTATATA-TATATAGTTTTAAAAACA
* **
56124 TTTTGAAAACTTATATAGTATATAGTTTTTAAAATG
1 TTTTGAAAACTTATATA-TATATAGTTTTAAAAACA
* *
56160 TTTT-TAAA--TATA-ATATATAGTTTTAAAAATA
1 TTTTGAAAACTTATATATATATAGTTTTAAAAACA
* * *
56191 TTTTTGAAAAATTATATAATATATAGTTTAAAAAAATA
1 -TTTTGAAAACTTATAT-ATATATAGTTT-TAAAAACA
*
56229 TTTTGAAAAAATTATATAGTATATAGTTTTAAAAACA
1 TTTTG-AAAACTTATATA-TATATAGTTTTAAAAACA
** *
56266 TTTTTGAAAAAATATATAATATATAGTTTTAAAAATA
1 -TTTTGAAAACTTATAT-ATATATAGTTTTAAAAACA
*
56303 GTTTTTGAAAACTTATATA-ATAT--TTTTTAAAACA
1 --TTTTGAAAACTTATATATATATAGTTTTAAAAACA
* *
56337 TTTTGAAAAC-TATATAACATATAGTTTTGAAAAC-
1 TTTTGAAAACTTATAT-ATATATAGTTTTAAAAACA
* * *
56371 TTTTTAAAA--TATA-ATATATAGTTTAAAAAAATA
1 TTTTGAAAACTTATATATATATAGTTT-TAAAAACA
56404 TTTTGAAA
1 TTTTGAAA
56412 TATATATATT
Statistics
Matches: 245, Mismatches: 25, Indels: 41
0.79 0.08 0.13
Matches are distributed among these distances:
31 31 0.13
32 20 0.08
33 22 0.09
34 17 0.07
35 16 0.07
36 29 0.12
37 51 0.21
38 59 0.24
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (35 bp):
TTTTGAAAACTTATATATATATAGTTTTAAAAACA
Found at i:56207 original size:30 final size:31
Alignment explanation
Indices: 56054--56420 Score: 154
Period size: 31 Copynumber: 10.9 Consensus size: 31
56044 TATATAGTTT
*
56054 TTTTGAAAATATTTTTAAAATATAATATATAG
1 TTTTAAAAATATTTTT-AAATATAATATATAG
* * * * *
56086 TTTTGAAAACA--TTT--ATATACTGTATGG
1 TTTTAAAAATATTTTTAAATATAATATATAG
* * *
56113 TTTTTAAAACATTTTGAAAACTTATATAGTATATAG
1 TTTTAAAAATATTTT-TAAA--TATA-A-TATATAG
* *
56149 TTTTTAAAATGTTTTTAAATATAATATATAG
1 TTTTAAAAATATTTTTAAATATAATATATAG
56180 TTTTAAAAATATTTTTGAAAAATTATATAATATATAG
1 TTTTAAAAATATTTTT----AA--ATATAATATATAG
* *
56217 TTTAAAAAAATATTTTGAAAAAATTATATAGTATATAG
1 TTT-TAAAAATATTTT---TAAA-TATA-A-TATATAG
*
56255 TTTTAAAAACATTTTTGAAAAAATATATAATATATAG
1 TTTTAAAAATATTTTT-----AA-ATATAATATATAG
* *
56292 TTTTAAAAATAGTTTTTGAAA-ACTTATATAATAT
1 TTTTAAAAATA-TTTTT-AAATA-TAATAT-ATAG
* * * *
56326 TTTTTAAAACATTTTGAAAACTATATAACATATAG
1 TTTTAAAAATATTTT--TAA--ATATAATATATAG
* *
56361 TTTTGAAAACT-TTTTAAAATATAATATATAG
1 TTTT-AAAAATATTTTTAAATATAATATATAG
* *
56392 TTTAAAAAAATATTTTGAAATAT-ATATAT
1 TTT-TAAAAATATTTTTAAATATAATATAT
56421 TATATAAATT
Statistics
Matches: 260, Mismatches: 36, Indels: 79
0.69 0.10 0.21
Matches are distributed among these distances:
27 20 0.08
29 2 0.01
30 3 0.01
31 47 0.18
32 23 0.09
33 17 0.07
34 20 0.08
35 17 0.07
36 30 0.12
37 47 0.18
38 27 0.10
39 6 0.02
40 1 0.00
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (31 bp):
TTTTAAAAATATTTTTAAATATAATATATAG
Found at i:56382 original size:24 final size:24
Alignment explanation
Indices: 56337--56383 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
56327 TTTTAAAACA
*
56337 TTTTGAAAACTATATAACATATAG
1 TTTTGAAAACTATATAAAATATAG
* *
56361 TTTTGAAAACTTTTTAAAATATA
1 TTTTGAAAACTATATAAAATATA
56384 ATATATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (24 bp):
TTTTGAAAACTATATAAAATATAG
Found at i:56453 original size:9 final size:8
Alignment explanation
Indices: 56441--56480 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 8
56431 ATATTTAGTA
56441 TATTATTAT
1 TATT-TTAT
56450 TATTTT-T
1 TATTTTAT
56457 TATTTTAT
1 TATTTTAT
56465 TCATTTTAT
1 T-ATTTTAT
56474 TATTTTA
1 TATTTTA
56481 ATTCATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.24
8 10 0.34
9 12 0.41
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (8 bp):
TATTTTAT
Found at i:56484 original size:18 final size:16
Alignment explanation
Indices: 56441--56488 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
56431 ATATTTAGTA
56441 TATTATTATT-ATTTTT
1 TATT-TTATTCATTTTT
56457 TATTTTATTCATTTTAT
1 TATTTTATTCATTTT-T
56474 TATTTTAATTCATTT
1 TATTTT-ATTCATTT
56489 CAGTTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.17
16 9 0.31
17 7 0.24
18 8 0.28
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTATTCATTTTT
Found at i:57679 original size:17 final size:19
Alignment explanation
Indices: 57648--57691 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
57638 CTCTAAGTTG
*
57648 TTACTTTAT-TTTATTTT-
1 TTACTTTTTCTTTATTTTA
57665 TTA-TTTTTCTTTATTTTA
1 TTACTTTTTCTTTATTTTA
57683 TTACTTTTT
1 TTACTTTTT
57692 AAAATTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 3 0.13
19 5 0.22
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (19 bp):
TTACTTTTTCTTTATTTTA
Found at i:57751 original size:16 final size:17
Alignment explanation
Indices: 57720--57754 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
57710 ATATTATTAA
57720 TTATTTTCTATTTTATT
1 TTATTTTCTATTTTATT
*
57737 TTATTTT-TCTTTTATT
1 TTATTTTCTATTTTATT
57753 TT
1 TT
57755 TCATTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (17 bp):
TTATTTTCTATTTTATT
Found at i:57755 original size:17 final size:17
Alignment explanation
Indices: 57720--57780 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
57710 ATATTATTAA
*
57720 TTATTTTCTATTTTA-TT
1 TTATTTT-TCTTTTATTT
57737 TTATTTTTCTTTTATTT
1 TTATTTTTCTTTTATTT
*
57754 TTCA-TTTTCTTTGATTT
1 TT-ATTTTTCTTTTATTT
*
57771 CTTTTTTTTC
1 -TTATTTTTC
57781 CTTTGACTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 6 0.16
17 23 0.62
18 8 0.22
ACGTcount: A:0.11, C:0.10, G:0.02, T:0.77
Consensus pattern (17 bp):
TTATTTTTCTTTTATTT
Found at i:57834 original size:15 final size:15
Alignment explanation
Indices: 57814--57858 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
57804 TTTTCTTGTT
57814 TTTTTCTTTATTTAA
1 TTTTTCTTTATTTAA
* *
57829 TTTTTCTTTTTATTAT
1 TTTTTCTTTAT-TTAA
57845 TATTTTCTTTATTT
1 T-TTTTCTTTATTT
57859 TCATTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 10 0.40
16 6 0.24
17 9 0.36
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTATTTAA
Found at i:57849 original size:18 final size:19
Alignment explanation
Indices: 57828--57889 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
57818 TCTTTATTTA
57828 ATTTTTCTTT-TTATT-ATT
1 ATTTTTCTTTATT-TTCATT
57846 A-TTTTCTTTATTTTCATT
1 ATTTTTCTTTATTTTCATT
* * *
57864 ATTTTATATATATATTCATT
1 ATTTT-TCTTTATTTTCATT
57884 ATTTTT
1 ATTTTT
57890 ATTTGTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 10 0.27
18 7 0.19
19 4 0.11
20 16 0.43
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTCTTTATTTTCATT
Found at i:58154 original size:19 final size:20
Alignment explanation
Indices: 58130--58169 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
58120 TTTTGATTTA
58130 TTTTAT-TTTATTCTTT-ATT
1 TTTTATGTTT-TTCTTTGATT
58149 TTTTATGTTTTTCTTTGATT
1 TTTTATGTTTTTCTTTGATT
58169 T
1 T
58170 ATCTAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTATGTTTTTCTTTGATT
Found at i:61621 original size:15 final size:15
Alignment explanation
Indices: 61601--61638 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
61591 TATCCATCGT
61601 GAATATTGCTAGTAA
1 GAATATTGCTAGTAA
*
61616 GAATATTTCTAGTAA
1 GAATATTGCTAGTAA
*
61631 AAATATTG
1 GAATATTG
61639 ATGCAAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (15 bp):
GAATATTGCTAGTAA
Found at i:62511 original size:73 final size:73
Alignment explanation
Indices: 62392--62537 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
62382 TCTGTTCAGG
62392 TATAATCTTATACTTCCATGGATTTGCAGGCAGCTGGTACGGTAAATCTGTAAATGGTTACATTC
1 TATAATCTTATACTTCCATGGATTTGCAGGCAGCTGGTACGGTAAATCTGTAAATGGTTACATTC
62457 TCTGTAGC
66 TCTGTAGC
62465 TATAATCTTATACTTCCATGGATTTGCAGGCAGCTGGTACGGTAAATCTGTAAATGGTTACATTC
1 TATAATCTTATACTTCCATGGATTTGCAGGCAGCTGGTACGGTAAATCTGTAAATGGTTACATTC
62530 TCTGTAGC
66 TCTGTAGC
62538 AAGCACTACC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (73 bp):
TATAATCTTATACTTCCATGGATTTGCAGGCAGCTGGTACGGTAAATCTGTAAATGGTTACATTC
TCTGTAGC
Found at i:63890 original size:2 final size:2
Alignment explanation
Indices: 63883--63921 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
63873 TTTCATTGCT
63883 TA 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 TA T
63922 TGCCCTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.