Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003401.1 Hibiscus syriacus cultivar Beakdansim tig00007157_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: 73191
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:17901 original size:19 final size:19
Alignment explanation
Indices: 17876--17923 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
17866 AAATGATTTT
* *
17876 GTTTTGAAAGCTAAATT-A
1 GTTTTGAAAACAAAATTAA
17894 GATTTTGAAAACAAAATTAA
1 G-TTTTGAAAACAAAATTAA
17914 GTTTTGAAAA
1 GTTTTGAAAA
17924 ATGATTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 23 0.88
20 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (19 bp):
GTTTTGAAAACAAAATTAA
Found at i:18463 original size:2 final size:2
Alignment explanation
Indices: 18458--18483 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18448 GGTTCATCAT
18458 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
18484 ATGGTCAAAT
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):
TA
Found at i:26279 original size:2 final size:2
Alignment explanation
Indices: 26204--26262 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
26194 CCTTACACTG
26204 AT AT AT 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
26246 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
26263 CACACGAACC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28447 original size:117 final size:115
Alignment explanation
Indices: 28243--28493 Score: 310
Period size: 117 Copynumber: 2.2 Consensus size: 115
28233 AGTTTGAACA
* * * **
28243 AGTTCTTATCGTTATGAACTTATTCTCTATCAATGTTGATCCACCTCCTGTGATGGAATCAAACA
1 AGTTCTTCTCATTATGAACTCATTCTCTAGAAATGTTGATCCACCTCCTGTGATGGAATCAAACA
* * *
28308 AAGGTTGAAAAAACTCTTCTCATTTTAAACTTATTCTCCCTTATTAGATG
66 AAGGTTGAAAAAACTCTTCTCATTATAAACTTATTCTCCCTCATTAGACG
* *
28358 AGTTCTTCTCATTATTAACTCATTCTACTAGAAATGTTGATCCACCTCATTCTGTGATGG-AT-G
1 AGTTCTTCTCATTATGAACTCATTCT-CTAGAAATGTTGATCCACCTC---CTGTGATGGAATCA
* * * *
28421 AACCAAGGTT-AAAGAAACTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACG
62 AACAAAGGTTGAAA-AAACTCTTCTCATTATAAACTTATTCTCCCTCATTAGACG
28475 AGTTCTTCTCATTATGAAC
1 AGTTCTTCTCATTATGAAC
28494 CCTTCCTTCG
Statistics
Matches: 116, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
115 22 0.19
116 22 0.19
117 61 0.53
118 2 0.02
119 9 0.08
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (115 bp):
AGTTCTTCTCATTATGAACTCATTCTCTAGAAATGTTGATCCACCTCCTGTGATGGAATCAAACA
AAGGTTGAAAAAACTCTTCTCATTATAAACTTATTCTCCCTCATTAGACG
Found at i:29190 original size:35 final size:35
Alignment explanation
Indices: 29143--29215 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
29133 CGAAAGAATC
29143 AACTACTATTTAAATTTTGAAAGTTATAACCCTTT
1 AACTACTATTTAAATTTTGAAAGTTATAACCCTTT
*
29178 AACTACTCTTTAAATTTTGAAAGTTATAACCCTTT
1 AACTACTATTTAAATTTTGAAAGTTATAACCCTTT
29213 AAC
1 AAC
29216 AATTGTTAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.41
Consensus pattern (35 bp):
AACTACTATTTAAATTTTGAAAGTTATAACCCTTT
Found at i:33983 original size:2 final size:2
Alignment explanation
Indices: 33976--34012 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
33966 TAAACCTGAA
33976 AT AT AT AT 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 AT AT AT AT A
34013 ATGCATTACA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39434 original size:91 final size:89
Alignment explanation
Indices: 39279--39446 Score: 255
Period size: 91 Copynumber: 1.9 Consensus size: 89
39269 CATCGTTGGA
* * * *
39279 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTGTTGGATGAATTATTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTCGCTGGATGAATTATTCTCATTATGAAC
39344 TCTTCATTGGAAATACTGATGCAAGG
66 TCTTC--TGGAAATACTGATGCAAGG
* * *
39370 TTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTCGCTGGATGAGTTCTTCTTATTATGAAC
1 TTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTCGCTGGATGAATTATTCTCATTATGAAC
39435 TCTTCTGGAAAT
66 TCTTCTGGAAAT
39447 GTTGATCCAC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
89 7 0.10
91 63 0.90
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.42
Consensus pattern (89 bp):
TTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTCGCTGGATGAATTATTCTCATTATGAAC
TCTTCTGGAAATACTGATGCAAGG
Found at i:39563 original size:105 final size:105
Alignment explanation
Indices: 39372--39647 Score: 401
Period size: 105 Copynumber: 2.6 Consensus size: 105
39362 ATGCAAGGTT
* * * *
39372 GAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTCGCT-GGATGAGTTCTTCTTATTATGAACT
1 GAACAAGTTCTTCTCATTATGAAC-T-TTC-TCCT--TTAGGACGAGTTCTTCTCATTATGAACT
*
39436 CTTCTGGAAATGTTGATCCACCTCCTTCTGTGATGGACTTGAAAG
61 CTTCTGGAAATGTTGATCCACCTCCTTCTGTGATGAACTTGAAAG
* *
39481 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAATTCTTCTCATTATGAACTCTTTT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
* * * *
39546 GGAAATGTTGGTTCACCTCCTTCTGTGGTGAATTTGAAAG
66 GGAAATGTTGATCCACCTCCTTCTGTGATGAACTTGAAAG
39586 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCT
39648 CCATTAGAAA
Statistics
Matches: 154, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
104 1 0.01
105 122 0.79
106 4 0.03
107 3 0.02
108 1 0.01
109 23 0.15
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (105 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
GGAAATGTTGATCCACCTCCTTCTGTGATGAACTTGAAAG
Found at i:39830 original size:136 final size:136
Alignment explanation
Indices: 39586--40115 Score: 665
Period size: 136 Copynumber: 3.9 Consensus size: 136
39576 AATTTGAAAG
* * * *
39586 GAACAAGTTCTTCTCATTATGAAC-T-TTCT---CCTTTAGGACGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCCCTGTCGGATGAGTTCTTCTCATTATGAACT
* * *
39646 CTCCATTAGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATACCATGAATTGAGTGA
66 CTCCATTAGAAATGTCAATCCCTCAAGTGAGGCGTCACTGATTCAAAATGCCATGAATCGAGTGA
39711 TAGGTC
131 TAGGTC
* * * * * *
39717 AAACAAGTTCTTCTCATTATGAGCTTCTTCTCCCCCTGTTGGATGAGTTCATCTCATTTTGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCCCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * * *
39782 CTCTATTAGAAATGTCAATCCCTCAAGTGATGTGTCACTAATTTAAAATGCCATGAATCGAGTGA
66 CTCCATTAGAAATGTCAATCCCTCAAGTGAGGCGTCACTGATTCAAAATGCCATGAATCGAGTGA
39847 TAGGTC
131 TAGGTC
* ** ** * *
39853 GAACAAGCTCTTCTTATTATGAACTTCTTCTCCCTATGTCATATGAGTTCTTCTTATTATGATCT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCCCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * * * *
39918 CTCTATTAGAAATGTCAATCCTTCAAGTGAGGTGTCACTGATTCGAAATGTCACGAATCGAGTGA
66 CTCCATTAGAAATGTCAATCCCTCAAGTGAGGCGTCACTGATTCAAAATGCCATGAATCGAGTGA
39983 TAGGTC
131 TAGGTC
* * * *
39989 GAACAAACTCTTCTCATTATGAACTTCTTCTACCTCTATCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCCCTGTCGGATGAGTTCTTCTCATTATGAACT
* * ** *
40054 TTCCATTGGAAATGTCAATCCCTCAAGTGAGGCGTCACTGATTTGAAATGCCGTGAATCGAG
66 CTCCATTAGAAATGTCAATCCCTCAAGTGAGGCGTCACTGATTCAAAATGCCATGAATCGAG
40116 CAACGAAATT
Statistics
Matches: 341, Mismatches: 53, Indels: 5
0.85 0.13 0.01
Matches are distributed among these distances:
131 22 0.06
132 1 0.00
133 4 0.01
136 314 0.92
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCCCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTAGAAATGTCAATCCCTCAAGTGAGGCGTCACTGATTCAAAATGCCATGAATCGAGTGA
TAGGTC
Found at i:40368 original size:90 final size:90
Alignment explanation
Indices: 40207--40462 Score: 422
Period size: 90 Copynumber: 2.8 Consensus size: 90
40197 CTCAATTTTT
* * *
40207 ATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAACCAAGAAACCCCCGAAGCCTT
1 ATCCTGCACTGAAGGTCTTATGGATGGCCCGAAAGACTTACAAATCAAGAAACCCCCGAAGACTT
*
40272 ATTTTCTAAAATCTCATTTGAAAAC
66 AGTTTCTAAAATCTCATTTGAAAAC
40297 ATCCTGCACTGAAGGTCTTATGGATGGCCCGAAAGACTTACAAATCAAGAAACCCCCGAAGACTT
1 ATCCTGCACTGAAGGTCTTATGGATGGCCCGAAAGACTTACAAATCAAGAAACCCCCGAAGACTT
40362 AGTTTCTAAAATCTCATTTGAAAAC
66 AGTTTCTAAAATCTCATTTGAAAAC
* * * * * *
40387 ATCCTACACTAAAGATCCTATGGATGGCCCAAAAGACTTACAAATCAAGAAACCCCCGAAGGCTT
1 ATCCTGCACTGAAGGTCTTATGGATGGCCCGAAAGACTTACAAATCAAGAAACCCCCGAAGACTT
40452 AGTTTCTAAAA
66 AGTTTCTAAAA
40463 AACACATTAG
Statistics
Matches: 156, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 156 1.00
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (90 bp):
ATCCTGCACTGAAGGTCTTATGGATGGCCCGAAAGACTTACAAATCAAGAAACCCCCGAAGACTT
AGTTTCTAAAATCTCATTTGAAAAC
Found at i:45197 original size:6 final size:6
Alignment explanation
Indices: 45188--45213 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
45178 TAAAAATGTG
45188 AATGCA AATGCA AATGCA AATGCA AA
1 AATGCA AATGCA AATGCA AATGCA AA
45214 AGGTATCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (6 bp):
AATGCA
Found at i:49144 original size:119 final size:119
Alignment explanation
Indices: 48933--49169 Score: 465
Period size: 119 Copynumber: 2.0 Consensus size: 119
48923 CCTTTATACA
48933 GTTTGCTTGTTGAGAATTTGAAAAATGTGGAAATTCCTCGGAAAATGTTATTATTATTTTATTAA
1 GTTTGCTTGTTGAGAATTTGAAAAATGTGGAAATTCCTCGGAAAATGTTATTATTATTTTATTAA
48998 TACTGAAGACCGTATTGTTTGGTTATTGTGGTAGTTGTTGTTGGGGTATGTACT
66 TACTGAAGACCGTATTGTTTGGTTATTGTGGTAGTTGTTGTTGGGGTATGTACT
*
49052 GTTTGCTTGTTGAGAATTTGAAAAATGTGGAAATTCCTCGGAAAATGTTATTATTTTTTTATTAA
1 GTTTGCTTGTTGAGAATTTGAAAAATGTGGAAATTCCTCGGAAAATGTTATTATTATTTTATTAA
49117 TACTGAAGACCGTATTGTTTGGTTATTGTGGTAGTTGTTGTTGGGGTATGTAC
66 TACTGAAGACCGTATTGTTTGGTTATTGTGGTAGTTGTTGTTGGGGTATGTAC
49170 CTCCTGAACG
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 117 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (119 bp):
GTTTGCTTGTTGAGAATTTGAAAAATGTGGAAATTCCTCGGAAAATGTTATTATTATTTTATTAA
TACTGAAGACCGTATTGTTTGGTTATTGTGGTAGTTGTTGTTGGGGTATGTACT
Found at i:51078 original size:2 final size:2
Alignment explanation
Indices: 51071--51129 Score: 109
Period size: 2 Copynumber: 29.0 Consensus size: 2
51061 CTTGGCAGAC
51071 AT AT AT 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
51113 AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT -AT AT
51130 GCACCAAATA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 54 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52346 original size:2 final size:2
Alignment explanation
Indices: 52339--52364 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52329 AAGCATCATA
52339 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
52365 GGTTTTGTAA
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:52771 original size:13 final size:13
Alignment explanation
Indices: 52748--52825 Score: 102
Period size: 13 Copynumber: 6.0 Consensus size: 13
52738 AATGACGCGC
*
52748 AATGAGCGTCATA
1 AATGCGCGTCATA
* *
52761 AATGTGTGTCATA
1 AATGCGCGTCATA
*
52774 AATGCGCATCATA
1 AATGCGCGTCATA
52787 AATGCGCGTCATA
1 AATGCGCGTCATA
*
52800 AATGTGCGTCATA
1 AATGCGCGTCATA
*
52813 AATGCACGTCATA
1 AATGCGCGTCATA
52826 GATTTATGAC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 56 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:52825 original size:39 final size:39
Alignment explanation
Indices: 52748--52825 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
52738 AATGACGCGC
* *
52748 AATGAGCGTCATAAATGTGTGTCATAAATGCGCATCATA
1 AATGAGCGTCATAAATGTGCGTCATAAATGCACATCATA
* *
52787 AATGCGCGTCATAAATGTGCGTCATAAATGCACGTCATA
1 AATGAGCGTCATAAATGTGCGTCATAAATGCACATCATA
52826 GATTTATGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (39 bp):
AATGAGCGTCATAAATGTGCGTCATAAATGCACATCATA
Found at i:60378 original size:82 final size:81
Alignment explanation
Indices: 60237--60701 Score: 380
Period size: 82 Copynumber: 5.7 Consensus size: 81
60227 GATAAATTGG
* * * * **
60237 TTATTGCATACTACCATGATTGAATCCAATTGGATGATGAACTATTATAT-CATGTCTTGATTGA
1 TTATTGCATGCTACCATGATTGAATCAAATTGAATGATGAACTATTACATGC-TACCTTGATTGA
60301 ATTAAATCGAATGATGA
65 ATTAAATCGAATGATGA
* * * *
60318 TCTATTGCATGCTACCATGATCGAATCAAATTGAAGGATAAACTATTATATGCTACCTTGATTGA
1 T-TATTGCATGCTACCATGATTGAATCAAATTGAATGATGAACTATTACATGCTACCTTGATTGA
* * * *
60383 ATTGAACCAAATGTTGAA
65 ATTAAATCGAATGATG-A
* * * * *
60401 TTATTGCATGCTACCATGATCGAA-CTAATTGAATGATAAACTATTATAAGCTACCTTGATTGAA
1 TTATTGCATGCTACCATGATTGAATCAAATTGAATGATGAACTATTACATGCTACCTTGATTGAA
* *
60465 TTGAATCGAATGTTGAA
66 TTAAATCGAATGATG-A
* * * * * * *
60482 TTATTTCATGTTACCATGATTGAATCAAGTTGAATGATGATCTATTGCATGCTACCATGATCGAA
1 TTATTGCATGCTACCATGATTGAATCAAATTGAATGATGAACTATTACATGCTACCTTGATTGAA
* * *
60547 TCAAATTGAATGAAGAA
66 TTAAATCGAATGATG-A
* ** * ** * ** * * * * * * *
60564 CTATTATATGTTGTCTTGATTGAATTGAATCGAAT-AGTGAATTATTGCATGTTATCATGATCGA
1 TTATTGCATGCTACCATGATTGAATCAAATTGAATGA-TGAACTATTACATGCTACCTTGATTGA
*
60628 ATCAAGAT-GAATGATGA
65 ATTAA-ATCGAATGATGA
* *
60645 TTTATTGCATGCTACCATGATAGAATCAAGTTGAATGATGAACTATTACATGCTACC
1 -TTATTGCATGCTACCATGATTGAATCAAATTGAATGATGAACTATTACATGCTACC
60702 AAGATCGAAC
Statistics
Matches: 311, Mismatches: 65, Indels: 15
0.80 0.17 0.04
Matches are distributed among these distances:
81 76 0.24
82 229 0.74
83 6 0.02
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (81 bp):
TTATTGCATGCTACCATGATTGAATCAAATTGAATGATGAACTATTACATGCTACCTTGATTGAA
TTAAATCGAATGATGA
Found at i:60509 original size:163 final size:164
Alignment explanation
Indices: 60237--60547 Score: 394
Period size: 163 Copynumber: 1.9 Consensus size: 164
60227 GATAAATTGG
* * * * **
60237 TTATTGCATACTACCATGATTGAATCCAATTGGATGATGAACTATTATATCATGTCTTGATTGAA
1 TTATTGCATACTACCATGATCGAATCCAATTGAATGATAAACTATTATAGCATACCTTGATTGAA
*
60302 TTAAATCGAATGATGATCTATTGCATGCTACCATGATCGAATCAAATTGAAGGATAAACTATTAT
66 TTAAATCGAATGATGATCTATTGCATGCTACCATGATCGAATCAAATTGAAGGATAAACTATTAC
* *
60367 ATGCTACCTTGATTGAATTGAACCAAATGTTGAA
131 ATGCTACCATGATCGAATTGAACCAAATGTTGAA
* *
60401 TTATTGCATGCTACCATGATCGAA-CTAATTGAATGATAAACTATTATAAGC-TACCTTGATTGA
1 TTATTGCATACTACCATGATCGAATCCAATTGAATGATAAACTATTAT-AGCATACCTTGATTGA
* * * * * * * * *
60464 ATTGAATCGAATGTTGAAT-TATTTCATGTTACCATGATTGAATCAAGTTGAATGATGATCTATT
65 ATTAAATCGAATGATG-ATCTATTGCATGCTACCATGATCGAATCAAATTGAAGGATAAACTATT
*
60528 GCATGCTACCATGATCGAAT
129 ACATGCTACCATGATCGAAT
60548 CAAATTGAAT
Statistics
Matches: 124, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
163 98 0.79
164 26 0.21
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (164 bp):
TTATTGCATACTACCATGATCGAATCCAATTGAATGATAAACTATTATAGCATACCTTGATTGAA
TTAAATCGAATGATGATCTATTGCATGCTACCATGATCGAATCAAATTGAAGGATAAACTATTAC
ATGCTACCATGATCGAATTGAACCAAATGTTGAA
Found at i:60594 original size:123 final size:123
Alignment explanation
Indices: 60402--60701 Score: 426
Period size: 123 Copynumber: 2.4 Consensus size: 123
60392 AATGTTGAAT
*
60402 TATTGCATGCTACCATGATCGAA-CTAATTGAATGATA-AACTATTATAAGCTACCTTGATTGAA
1 TATTGCATGCTACCATGATCGAATCAAATTGAATGA-AGAACTATTATAAGCTACCTTGATTGAA
* * *
60465 TTGAATCGAAT-GTTGAATTATTTCATGTTACCATGATTGAATCAAGTTGAATGATGATC
65 TTGAATCGAATAG-TGAATTATTGCATGTTACCATGATCGAATCAAGATGAATGATGATC
* * **
60524 TATTGCATGCTACCATGATCGAATCAAATTGAATGAAGAACTATTATATGTTGTCTTGATTGAAT
1 TATTGCATGCTACCATGATCGAATCAAATTGAATGAAGAACTATTATAAGCTACCTTGATTGAAT
* *
60589 TGAATCGAATAGTGAATTATTGCATGTTATCATGATCGAATCAAGATGAATGATGATT
66 TGAATCGAATAGTGAATTATTGCATGTTACCATGATCGAATCAAGATGAATGATGATC
* * * * *
60647 TATTGCATGCTACCATGATAGAATCAAGTTGAATGATGAACTATTACATGCTACC
1 TATTGCATGCTACCATGATCGAATCAAATTGAATGAAGAACTATTATAAGCTACC
60702 AAGATCGAAC
Statistics
Matches: 158, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
122 24 0.15
123 133 0.84
124 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (123 bp):
TATTGCATGCTACCATGATCGAATCAAATTGAATGAAGAACTATTATAAGCTACCTTGATTGAAT
TGAATCGAATAGTGAATTATTGCATGTTACCATGATCGAATCAAGATGAATGATGATC
Found at i:60720 original size:41 final size:40
Alignment explanation
Indices: 60238--60721 Score: 299
Period size: 41 Copynumber: 11.8 Consensus size: 40
60228 ATAAATTGGT
* * *
60238 TATTGCATACTACCATGATTGAATCCAATTGGATGATGAAC
1 TATTGCATGCTACCATGATCGAAT-CAATTGAATGATGAAC
** ** * * * * *
60279 TATTATAT-CATGTCTTGATTGAATTAAATCGAATGATGATC
1 TATTGCATGC-TACCATGATCGAA-TCAATTGAATGATGAAC
* *
60320 TATTGCATGCTACCATGATCGAATCAAATTGAAGGATAAAC
1 TATTGCATGCTACCATGATCGAATC-AATTGAATGATGAAC
** * * * *** * *
60361 TATTATATGCTACCTTGATTGAATTGAACCAAATGTTGAAT
1 TATTGCATGCTACCATGATCGAA-TCAATTGAATGATGAAC
*
60402 TATTGCATGCTACCATGATCGAA-CTAATTGAATGATAAAC
1 TATTGCATGCTACCATGATCGAATC-AATTGAATGATGAAC
** * * * * * * *
60442 TATTATAAGCTACCTTGATTGAATTGAATCGAATGTTGAAT
1 TATTGCATGCTACCATGATCGAA-TCAATTGAATGATGAAC
* * * *
60483 TATTTCATGTTACCATGATTGAATCAAGTTGAATGATGATC
1 TATTGCATGCTACCATGATCGAATCAA-TTGAATGATGAAC
*
60524 TATTGCATGCTACCATGATCGAATCAAATTGAATGAAGAAC
1 TATTGCATGCTACCATGATCGAATC-AATTGAATGATGAAC
** * ** * * * * *
60565 TATTATATGTTGTCTTGATTGAATTGAATCGAAT-AGTGAAT
1 TATTGCATGCTACCATGATCGAA-TCAATTGAATGA-TGAAC
* * * **
60606 TATTGCATGTTATCATGATCGAATCAAGATGAATGATGATT
1 TATTGCATGCTACCATGATCGAATCAA-TTGAATGATGAAC
*
60647 TATTGCATGCTACCATGATAGAATCAAGTTGAATGATGAAC
1 TATTGCATGCTACCATGATCGAATCAA-TTGAATGATGAAC
* * *
60688 TATTACATGCTACCAAGATCGAACTCGATTGAAT
1 TATTGCATGCTACCATGATCGAA-TCAATTGAAT
60722 CGAAATCTTG
Statistics
Matches: 330, Mismatches: 98, Indels: 30
0.72 0.21 0.07
Matches are distributed among these distances:
40 36 0.11
41 284 0.86
42 10 0.03
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (40 bp):
TATTGCATGCTACCATGATCGAATCAATTGAATGATGAAC
Found at i:63145 original size:2 final size:2
Alignment explanation
Indices: 63097--63130 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
63087 CTTTTTCCTT
63097 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63131 CTTTTTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67176 original size:2 final size:2
Alignment explanation
Indices: 67169--67287 Score: 133
Period size: 2 Copynumber: 61.0 Consensus size: 2
67159 TGCGAGCAAA
*
67169 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
67210 AT AT AT AT AT AT AT AT AT AT AT AC AT ACT AT -T TT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
*
67250 AT AT AT -T AT AT AT ACT GAT TT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT AT
67288 GTGCGCGTAA
Statistics
Matches: 101, Mismatches: 7, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
1 6 0.06
2 90 0.89
3 4 0.04
4 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:67397 original size:2 final size:2
Alignment explanation
Indices: 67390--67416 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
67380 TTGATGTTAG
67390 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 T
67417 CATTGCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68500 original size:32 final size:32
Alignment explanation
Indices: 68459--68524 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
68449 CCTCCTTACT
68459 TTCATACTTTCATGGAGATGATGGACATATGG
1 TTCATACTTTCATGGAGATGATGGACATATGG
*
68491 TTCATACTTTCATGGAGATGATGGACATGTGG
1 TTCATACTTTCATGGAGATGATGGACATATGG
68523 TT
1 TT
68525 TACTACCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (32 bp):
TTCATACTTTCATGGAGATGATGGACATATGG
Found at i:72899 original size:22 final size:22
Alignment explanation
Indices: 72864--72919 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
72854 TCAAAATCTC
* * *
72864 CTTAAATTTGTAAATCTTAAAA
1 CTTAAATCTCTAAACCTTAAAA
**
72886 CTTAAATCTCTAAACCTTAATC
1 CTTAAATCTCTAAACCTTAAAA
*
72908 CCTAAATCTCTA
1 CTTAAATCTCTA
72920 CCCCTAATCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.38
Consensus pattern (22 bp):
CTTAAATCTCTAAACCTTAAAA
Done.