Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000859.1 Hibiscus syriacus cultivar Beakdansim tig00001664_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: 105688
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2626 original size:2 final size:2
Alignment explanation
Indices: 2619--2667 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
2609 ATCATAACTC
* *
2619 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TCC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
2662 TA TA TA
1 TA TA TA
2668 CCATTTCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
2 42 0.98
3 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3120 original size:23 final size:23
Alignment explanation
Indices: 3102--3185 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
3092 CTCGTATAAT
*
3102 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAA
* *
3125 TGCACCGTAGTGCCGCGTAGAAA
1 TGCACCGAAGTGCCACGTAGAAA
* *
3148 TGCACCGAAGTGCCGCCTAGAAA
1 TGCACCGAAGTGCCACGTAGAAA
*
3171 TGCACCAAAGTGCCA
1 TGCACCGAAGTGCCA
3186 TATAAGATGT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.15
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAA
Found at i:5415 original size:2 final size:2
Alignment explanation
Indices: 5408--5442 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5398 TTGGGATATT
5408 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5443 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5447 original size:2 final size:2
Alignment explanation
Indices: 5442--5483 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5432 ACACACACAC
5442 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
5484 CATAAAGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8176 original size:11 final size:11
Alignment explanation
Indices: 8160--8185 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8150 GCTATTTTTT
8160 AAAAAAAACAA
1 AAAAAAAACAA
8171 AAAAAAAACAA
1 AAAAAAAACAA
8182 AAAA
1 AAAA
8186 TCCAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:15511 original size:5 final size:5
Alignment explanation
Indices: 15498--15536 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
15488 ACCACGACCA
* * *
15498 CGAGC CGAGT CGAGC CGTGC CGTGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
15537 ACGGACGGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.15, C:0.36, G:0.41, T:0.08
Consensus pattern (5 bp):
CGAGC
Found at i:30316 original size:2 final size:2
Alignment explanation
Indices: 30309--30339 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30299 AATGTGAGTG
30309 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
30340 GATGATGTAA
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:31329 original size:29 final size:29
Alignment explanation
Indices: 31286--31368 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
31276 CTCACCTAAC
*
31286 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
* *
31316 TAAATGATGTAAGCAATGGCATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
31345 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
31369 ATTTAGTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 43 0.91
30 4 0.09
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:34722 original size:15 final size:15
Alignment explanation
Indices: 34702--34731 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34692 CTTTCTCATA
34702 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
34717 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
34732 CTAGCCTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:36066 original size:29 final size:29
Alignment explanation
Indices: 36023--36105 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
36013 CTCACCTAAC
*
36023 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
* *
36053 TAAATGATGCAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
36082 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
36106 ATTTAGTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 43 0.91
30 4 0.09
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:39040 original size:84 final size:83
Alignment explanation
Indices: 38888--39455 Score: 607
Period size: 84 Copynumber: 6.7 Consensus size: 83
38878 TCTTACCTTG
* * * * * *
38888 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGGC
1 AGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGC
38953 AGATAACCCTTCTCGACTTA
64 AGATAACCCTTCTCGACTTA
* * * * *
38973 AGCTATACTGCAAATGATGTACCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACA
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCA
* * *
39038 GATAACCCTTCTAGCCTTG
65 GATAACCCTTCTCGACTTA
* * * * * * * *
39057 AGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGACTGGC
1 AGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG-GTGGC
* *
39122 AGATAGCCATTCTCGACTTA
64 AGATAACCCTTCTCGACTTA
* * * * * * *
39142 AGCTATGCTGCAAATGATATGTCGTT-GAACCGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGC
1 AGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGC
39206 AGATAACCCTTCTCGACTTA
64 AGATAACCCTTCTCGACTTA
* * * *
39226 AGTTATACTGCAAATGATATGCCATGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAG
* * * *
39291 ATAACCCTTATAGCCTTG
66 ATAACCCTTCTCGACTTA
* * * * * *
39309 AGTTATGCTGTAAATGATGTGCCTTGGAACTGAGCATCGTTGAACTCGAAGGTCTTTTGGTTGAC
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG-TGGC
39374 AGATAACCCTTCTCGACTTA
64 AGATAACCCTTCTCGACTTA
* * * *
39394 AGTTATGCTGCAAATAATGTGCCTTAGAGTTGAGCGTAGTCGAACTCGAAGGCCTTTGGTGG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGG
39456 GCACAATTCC
Statistics
Matches: 392, Mismatches: 84, Indels: 16
0.80 0.17 0.03
Matches are distributed among these distances:
83 75 0.19
84 164 0.42
85 153 0.39
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (83 bp):
AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAG
ATAACCCTTCTCGACTTA
Found at i:39059 original size:169 final size:167
Alignment explanation
Indices: 38864--39445 Score: 659
Period size: 169 Copynumber: 3.5 Consensus size: 167
38854 ACAATTTTAT
* * * * *
38864 TGACAGATATCCCTTCTTA-CCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TGACAGATAACCCTTC-TAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAA
*
38928 TCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGT
65 TCGAACTCGAAGGTCTT-GGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* *
38993 ACCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGG
129 -CCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
* * * * *
39033 TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAAT
* ** * *
39098 CGAACTCGAGGGTCTTTGACTGGCAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATATG
66 CGAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG--ATG
* * * *
39163 TCGTT-GAACCGAGCGTAGTCGAACTCAAAGGTCTTTTGT
128 TCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
* * * * * * *
39202 TGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATGCCAT-GGAGCTGAGCGTAGT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAAT
* * * * * * *
39266 CGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATGTGC
66 CGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT-C
* * *
39331 CTTGGAACTGAGCATCGTTGAACTCGAAGGTCTTTTGG
130 CTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
* * * * * *
39369 TTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAATGTGCCTTAG-AGTTGAGCGTAG
1 -TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAA
39433 TCGAACTCGAAGG
65 TCGAACTCGAAGG
39446 CCTTTGGTGG
Statistics
Matches: 354, Mismatches: 51, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
165 4 0.01
166 3 0.01
167 62 0.18
168 95 0.27
169 181 0.51
170 5 0.01
171 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (167 bp):
TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAAT
CGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTCC
TTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
Found at i:39218 original size:253 final size:252
Alignment explanation
Indices: 38928--39408 Score: 703
Period size: 252 Copynumber: 1.9 Consensus size: 252
38918 CTGAGTGTAA
* *
38928 TCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGT
1 TCGAACTCAAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATAT
* *
38993 ACCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGA
66 ACCATGGAGCTGAGCGTAGTCAAACTCGAAGGTC-TTTGGTGACAGATAACCCTTATAGCCTTGA
* ** * *
39058 GTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGACTGGC
130 GTTATGCTGTAAATGATGTGCCCTCGAA-CTGAGCATAATCGAACTCGAAGGTCTTTTGACTGAC
*
39122 AGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATATGTCGTTGAACCGAGCGTAG
194 AGATAACCATTCTCGACTTAAGCTATGCTGCAAATGATATGTCGTTGAACCGAGCGTAG
** *
39181 TCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATAT
1 TCGAACTCAAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATAT
* * * *
39246 GCCATGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTATAGCCTTGAG
66 ACCATGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAACCCTTATAGCCTTGAG
* * ** * **
39311 TTATGCTGTAAATGATGTGCCTTGGAACTGAGCATCGTTGAACTCGAAGGTCTTTTGGTTGACAG
131 TTATGCTGTAAATGATGTGCCCTCGAACTGAGCATAATCGAACTCGAAGGTCTTTTGACTGACAG
* *
39376 ATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
196 ATAACCATTCTCGACTTAAGCTATGCTGCAAAT
39409 AATGTGCCTT
Statistics
Matches: 201, Mismatches: 26, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
251 19 0.09
252 91 0.45
253 91 0.45
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (252 bp):
TCGAACTCAAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATAT
ACCATGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAACCCTTATAGCCTTGAG
TTATGCTGTAAATGATGTGCCCTCGAACTGAGCATAATCGAACTCGAAGGTCTTTTGACTGACAG
ATAACCATTCTCGACTTAAGCTATGCTGCAAATGATATGTCGTTGAACCGAGCGTAG
Found at i:39852 original size:110 final size:110
Alignment explanation
Indices: 39563--40043 Score: 713
Period size: 110 Copynumber: 4.4 Consensus size: 110
39553 CAAGTTGGTA
* * * ** *
39563 TTGTTTCGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAGTCG
1 TTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTG
* * *
39624 TTTGTTGACAGCCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTG
66 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTG
* *
39669 TTGTCTCGAGTCTAATAT-CATCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTG
1 TTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTG
* *
39733 TTTGTTGACAGGCATTCGCCCCTTCGCTGTGAAGTTGAACTTGTG
66 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTG
* * *
39778 TTGTCTTGAGT-TCAATATCCTTCGCTGTGAAGTTGAAATTAACTCTGAATGAAACTGAAAATTT
1 TTGTCTCGAGTCT-AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTT
*
39842 GTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAACTTTTG
65 GTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTG
* * *
39888 TTGTCTTGAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTG
1 TTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTG
*
39953 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
66 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTG
*
39998 TTATCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
1 TTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
40044 AAAGCTGCAA
Statistics
Matches: 340, Mismatches: 28, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
105 24 0.07
106 17 0.05
108 1 0.00
109 69 0.20
110 229 0.67
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (110 bp):
TTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTG
TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTG
Found at i:43823 original size:15 final size:15
Alignment explanation
Indices: 43791--43911 Score: 59
Period size: 16 Copynumber: 7.7 Consensus size: 15
43781 CAAAAGAAAG
43791 AAAAAAAATGAATGAAAT
1 AAAAAAAAT-AA--AAAT
43809 AAAAAAAATAAAAAT
1 AAAAAAAATAAAAAT
* *
43824 AAAAGAAGTAAAAAAT
1 AAAAAAAAT-AAAAAT
* *
43840 GAATAAAA-AAAAAT
1 AAAAAAAATAAAAAT
** **
43854 -AAAAAGTTAAATCTT
1 AAAAAAAATAAA-AAT
*
43869 AAAAATAAT-AAAAT
1 AAAAAAAATAAAAAT
*
43883 AAAAACAACTAAAAGAT
1 AAAAA-AAATAAAA-AT
43900 AAACAAAAATAA
1 AAA-AAAAATAA
43912 TACTAATTAA
Statistics
Matches: 76, Mismatches: 19, Indels: 17
0.68 0.17 0.15
Matches are distributed among these distances:
13 4 0.05
14 15 0.20
15 16 0.21
16 18 0.24
17 12 0.16
18 11 0.14
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (15 bp):
AAAAAAAATAAAAAT
Found at i:43835 original size:24 final size:25
Alignment explanation
Indices: 43787--43852 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
43777 GAATCAAAAG
* * *
43787 AAAGAAAAAAAATGAATGAAATAAA
1 AAAGAATAAAAATAAAAGAAATAAA
*
43812 AAA-AATAAAAATAAAAGAAGTAAA
1 AAAGAATAAAAATAAAAGAAATAAA
43836 AAATGAATAAAAA-AAAA
1 AAA-GAATAAAAATAAAA
43853 TAAAAAGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 20 0.57
25 7 0.20
26 8 0.23
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (25 bp):
AAAGAATAAAAATAAAAGAAATAAA
Found at i:43897 original size:38 final size:36
Alignment explanation
Indices: 43794--43913 Score: 86
Period size: 36 Copynumber: 3.3 Consensus size: 36
43784 AAGAAAGAAA
* * *
43794 AAAAATGAATGAAAT-AAAAAAAATAAAAATA-AAAG
1 AAAAAT-AATAAAATAAAAAAAAATAAAAAGATAAAC
* * *
43829 AAGTAAAAAAT-GAATAAAAAAAAATAAAAAGTTAAATC
1 AA--AAATAATAAAATAAAAAAAAATAAAAAGATAAA-C
* *
43867 TTAAAAATAATAAAATAAAAACAACT-AAAAGATAAAC
1 --AAAAATAATAAAATAAAAAAAAATAAAAAGATAAAC
43904 AAAAATAATA
1 AAAAATAATA
43914 CTAATTAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
35 15 0.22
36 17 0.25
37 7 0.10
38 15 0.22
39 11 0.16
40 2 0.03
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.17
Consensus pattern (36 bp):
AAAAATAATAAAATAAAAAAAAATAAAAAGATAAAC
Found at i:46280 original size:20 final size:20
Alignment explanation
Indices: 46255--46292 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
46245 GGTAAACACA
46255 TCGCAACGCGAATTTCGTTT
1 TCGCAACGCGAATTTCGTTT
46275 TCGCAACGCGAATTTCGT
1 TCGCAACGCGAATTTCGT
46293 AAATCGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (20 bp):
TCGCAACGCGAATTTCGTTT
Found at i:46300 original size:14 final size:14
Alignment explanation
Indices: 46273--46315 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
46263 CGAATTTCGT
**
46273 TTTCGCAACGCGAA
1 TTTCGCAAATCGAA
*
46287 TTTCGTAAATCGAA
1 TTTCGCAAATCGAA
46301 -TTCGCAAATCGAA
1 TTTCGCAAATCGAA
46314 TT
1 TT
46316 CGCTAATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (14 bp):
TTTCGCAAATCGAA
Found at i:46309 original size:13 final size:13
Alignment explanation
Indices: 46283--46318 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
46273 TTTCGCAACG
*
46283 CGAATTTCGTAAAT
1 CGAA-TTCGCAAAT
46297 CGAATTCGCAAAT
1 CGAATTCGCAAAT
46310 CGAATTCGC
1 CGAATTCGC
46319 TAATTTCGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (13 bp):
CGAATTCGCAAAT
Found at i:49901 original size:2 final size:2
Alignment explanation
Indices: 49894--49944 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
49884 CTTTAATCCC
49894 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
*
49936 AT AT GT AT A
1 AT AT AT AT A
49945 ATTGTGTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51294 original size:6 final size:6
Alignment explanation
Indices: 51283--51316 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
51273 ATAACCGGCC
* *
51283 GGATGG GGATGG GGATGG GGATAG GGATAG GGAT
1 GGATGG GGATGG GGATGG GGATGG GGATGG GGAT
51317 CGGAGAACCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.59, T:0.18
Consensus pattern (6 bp):
GGATGG
Found at i:52149 original size:14 final size:14
Alignment explanation
Indices: 52126--52166 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
52116 ATATATATAC
*
52126 AATATAATTTTAAT
1 AATATTATTTTAAT
52140 AATATTATTTT--T
1 AATATTATTTTAAT
*
52152 AATATTATATTAAT
1 AATATTATTTTAAT
52166 A
1 A
52167 TATACTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.48
14 12 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATATTATTTTAAT
Found at i:52589 original size:25 final size:26
Alignment explanation
Indices: 52552--52610 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
52542 TATTAGTTTA
* *
52552 GTTATATATAATTATTAAAAT-ATATT
1 GTTA-ATAAAATTATGAAAATAATATT
52578 GTTAATAAAATTATGAAAATAATATT
1 GTTAATAAAATTATGAAAATAATATT
52604 -TTAATAA
1 GTTAATAA
52611 TAATCTTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 21 0.70
26 9 0.30
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (26 bp):
GTTAATAAAATTATGAAAATAATATT
Found at i:53907 original size:21 final size:20
Alignment explanation
Indices: 53881--54201 Score: 136
Period size: 21 Copynumber: 15.3 Consensus size: 20
53871 CATATTCGCA
53881 TTGCGATAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTC-CG
*
53902 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTC-CG
* ** ***
53923 TTGCGA-A-TCTGGAAACTGAT
1 TTGCGATAGTC--CAAGTTCCG
**
53943 TTGCGATAGTCGGAGTTCGCG
1 TTGCGATAGTCCAAGTTC-CG
* * *
53964 TTGCGATTTATTACAAATT-CG
1 TTGCGA--TAGTCCAAGTTCCG
53985 TTGCGATAGTCCAAGTT-CG
1 TTGCGATAGTCCAAGTTCCG
* *
54004 TTGCGATAGTCGAAGTTCGAG
1 TTGCGATAGTCCAAGTTC-CG
** * *
54025 TTGTAATTTATTCTAAGTT-CG
1 TTGCGA--TAGTCCAAGTTCCG
*
54046 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTC-CG
* *
54067 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAGTTCCG
* *
54088 TTGCGATTTATTCCAAGTTTGCG
1 TTGCGA--TAGTCCAAG-TTCCG
* *
54111 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAGTTCCG
*
54132 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTC-CG
* *
54153 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAGTTCCG
54174 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTC-CG
54195 TTGCGAT
1 TTGCGAT
54202 TTATTCTAAA
Statistics
Matches: 232, Mismatches: 45, Indels: 46
0.72 0.14 0.14
Matches are distributed among these distances:
19 54 0.23
20 10 0.04
21 113 0.49
22 6 0.03
23 49 0.21
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTCCG
Found at i:54043 original size:42 final size:42
Alignment explanation
Indices: 53994--54222 Score: 341
Period size: 42 Copynumber: 5.4 Consensus size: 42
53984 GTTGCGATAG
* * **
53994 TCCAAGTTCGTTGCGATAGTCGAAGTTCGAGTTGTAATTTAT
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
54036 TCTAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * *
54078 TCCAAATTCGTTGCGATTTATTCCAAGTTTGCGTTGCGATTTAT
1 TCCAAATTCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTAT
54122 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
54164 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
54206 TCTAAATTCGTTGCGAT
1 TCCAAATTCGTTGCGAT
54223 TTATTCCAAA
Statistics
Matches: 171, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
42 132 0.77
44 39 0.23
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (42 bp):
TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:54132 original size:86 final size:84
Alignment explanation
Indices: 53994--54222 Score: 359
Period size: 86 Copynumber: 2.7 Consensus size: 84
53984 GTTGCGATAG
* * * ** *
53994 TCCAAGTTCGTTGCGATAGTCGAAGTTCGAGTTGTAATTTATTCTAAGTTCGTTGCGATAGTCGA
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCGATAGTCGA
54059 AGTTCGCGTTGCGATTTAT
66 AGTTCGCGTTGCGATTTAT
* * *
54078 TCCAAATTCGTTGCGATTTATTCCAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1 TCCAAATTCGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCGATAGTC
54143 GAAGTTCGCGTTGCGATTTAT
64 GAAGTTCGCGTTGCGATTTAT
54164 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCGAT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCGAT
54223 TTATTCCAAA
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
84 55 0.42
86 76 0.58
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (84 bp):
TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCGATAGTCGA
AGTTCGCGTTGCGATTTAT
Found at i:54143 original size:128 final size:125
Alignment explanation
Indices: 53962--54251 Score: 431
Period size: 128 Copynumber: 2.3 Consensus size: 125
53952 TCGGAGTTCG
* *
53962 CGTTGCGATTTATTACAAATTCGTTGCGA-TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGAGT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAAATTCGTTGCGATAGTCGAAGTTCGAGT
* * * *
54026 TGTAATTTATTCTAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
66 TGCAATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
54086 CGTTGCGATTTATTCCAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTTATTCCAA-ATT-CGTTGCGA-TTAGTCCAAATTCGTTGCGATAGTCGAAGTTCG
* * *
54151 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATT
63 AGTTGCAATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
54214 CGTTGCGATTTATTCCAAATTCGTTGCGA-TAGCCCAAA
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAAA
54252 ATTGCAACGA
Statistics
Matches: 148, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
124 24 0.16
125 2 0.01
126 16 0.11
127 2 0.01
128 104 0.70
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (125 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAAATTCGTTGCGATAGTCGAAGTTCGAGT
TGCAATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:54217 original size:21 final size:21
Alignment explanation
Indices: 53962--54243 Score: 224
Period size: 21 Copynumber: 13.4 Consensus size: 21
53952 TCGGAGTTCG
*
53962 CGTTGCGATTTATTACAAATT
1 CGTTGCGATTTATTCCAAATT
* *
53983 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
* * *
54002 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
** * *
54021 CGAGTTGTAATTTATTCTAAGTT
1 C--GTTGCGATTTATTCCAAATT
* * *
54044 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
54063 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
*
54086 CGTTGCGATTTATTCCAAGTTT
1 CGTTGCGATTTATTCCAA-ATT
54108 GCGTTGCGATTTATTCCAAATT
1 -CGTTGCGATTTATTCCAAATT
* * *
54130 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
54149 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
* *
54172 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
*
54191 CGCGTTGCGATTTATTCTAAATT
1 --CGTTGCGATTTATTCCAAATT
54214 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
54235 CGTTGCGAT
1 CGTTGCGAT
54244 AGCCCAAAAT
Statistics
Matches: 214, Mismatches: 29, Indels: 36
0.77 0.10 0.13
Matches are distributed among these distances:
19 53 0.25
21 105 0.49
22 4 0.02
23 52 0.24
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:55033 original size:6 final size:6
Alignment explanation
Indices: 55012--55060 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
55002 TCTCGCCTCG
55012 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
55058 GGT
1 GGT
55061 AATACGTGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.23
6 33 0.77
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:55209 original size:42 final size:42
Alignment explanation
Indices: 55150--55385 Score: 368
Period size: 42 Copynumber: 5.6 Consensus size: 42
55140 CGTTGCGATT
55150 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
55192 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
55234 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
55276 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* * *
55318 TTCGACTATCGCAACGAACTTGGACT--ATCGCAACGCGAAT
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
55358 TTGGAATAAATCGCAACGCGAACTTGGA
1 TTGGACT--ATCGCAA--CGAACTTGGA
55386 CTATCGCAAC
Statistics
Matches: 183, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
40 18 0.10
42 155 0.85
44 10 0.05
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
Found at i:55247 original size:63 final size:60
Alignment explanation
Indices: 55150--55412 Score: 289
Period size: 63 Copynumber: 4.2 Consensus size: 60
55140 CGTTGCGATT
*
55150 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTGGACTATCGCAACGAAC
* * *
55211 TTGGAATAAATCGCAACGCGAACTTGGACT-ATCGCAA--CGAATTTGGAATAAATCGCAACGCG
1 TTGGAAT--ATCGCAA--CGAACTTGGAATAATCGCAACGCGAACTTGGACT--ATCGCAA--CG
55273 AAC
58 AAC
* * *
55276 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTGGACTATCGCAACGAAC
* * *
55337 TTGGACTATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAAT
1 TTGGAATATCGCAA--CGAACTTGGAAT-AATCGCAACGCGAACTTGGACTATCGCAACGAAC
*
55400 TTGGAAAATCGCA
1 TTGGAATATCGCA
55413 TTGCGATAGT
Statistics
Matches: 172, Mismatches: 16, Indels: 26
0.80 0.07 0.12
Matches are distributed among these distances:
61 45 0.26
63 97 0.56
65 30 0.17
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (60 bp):
TTGGAATATCGCAACGAACTTGGAATAATCGCAACGCGAACTTGGACTATCGCAACGAAC
Found at i:55329 original size:105 final size:102
Alignment explanation
Indices: 55220--55412 Score: 316
Period size: 105 Copynumber: 1.9 Consensus size: 102
55210 CTTGGAATAA
55220 ATCGCAACGCGAACTTGGACTATCGCAA-CGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
1 ATCGCAA--CGAACTTGGACTATCGCAACCGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
55284 TCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
64 TCGCAACGAACTTGG-A-AAATCGCAACGCGAACTTCGACT
*
55325 ATCGCAACGAACTTGGACTATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTGGACTAT
1 ATCGCAACGAACTTGGACTATCGCAAC-CGAATTTGGAATAAATCGCAACGCGAACTTCGACTAT
*
55390 CGCAACGAATTTGGAAAATCGCA
65 CGCAACGAACTTGGAAAATCGCA
55413 TTGCGATAGT
Statistics
Matches: 84, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
103 27 0.32
104 1 0.01
105 56 0.67
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (102 bp):
ATCGCAACGAACTTGGACTATCGCAACCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATC
GCAACGAACTTGGAAAATCGCAACGCGAACTTCGACT
Found at i:59523 original size:6 final size:6
Alignment explanation
Indices: 59514--59579 Score: 60
Period size: 6 Copynumber: 10.3 Consensus size: 6
59504 ATAGATATAT
* * * *
59514 TAATTA TAATTA TAATTT TATTTA TATATATCA TATTTA TAAATTA TGATTA
1 TAATTA TAATTA TAATTA TAATTA TA-AT-T-A TAATTA T-AATTA TAATTA
59566 TAATTA TAATTA TA
1 TAATTA TAATTA TA
59580 TGAGTATACT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 36 0.75
7 7 0.15
8 2 0.04
9 3 0.06
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TAATTA
Found at i:59559 original size:40 final size:38
Alignment explanation
Indices: 59482--59580 Score: 101
Period size: 40 Copynumber: 2.6 Consensus size: 38
59472 TCATGTATTA
** *
59482 ATAATTATTTTTTTATTAT-TATATAGATATATTAATT
1 ATAATTATAATTTTATTATATATATAGATATATAAATT
* *
59519 ATAATTATAATTTTATTTATATATATCATATTTATAAATT
1 ATAATTATAATTTTA-TTATATATAT-AGATATATAAATT
* *
59559 ATGATTATAATTATAATTATAT
1 ATAATTATAATT-TTATTATAT
59581 GAGTATACTA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 13 0.25
38 4 0.08
39 5 0.10
40 27 0.53
41 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (38 bp):
ATAATTATAATTTTATTATATATATAGATATATAAATT
Found at i:59926 original size:21 final size:21
Alignment explanation
Indices: 59880--59933 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
59870 GATTTTGACT
*
59880 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAA
* * *
59901 TTCGCGTTGCGATTTTAGAAA
1 ATCGCATTGCGATTTTACAAA
*
59922 ATCGCAATGCGA
1 ATCGCATTGCGA
59934 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
ATCGCATTGCGATTTTACAAA
Found at i:60900 original size:24 final size:24
Alignment explanation
Indices: 60843--60902 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
60833 TAGTCAGTAT
* *
60843 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATATTGATCAATAC
* * *
60867 CCGGACTTTGATATTGATCAATAC
1 TCGAAATTTGATATTGATCAATAC
*
60891 TCGAATTTTGAT
1 TCGAAATTTGAT
60903 GATATTTCAG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATATTGATCAATAC
Found at i:61730 original size:23 final size:23
Alignment explanation
Indices: 61661--61814 Score: 260
Period size: 23 Copynumber: 6.8 Consensus size: 23
61651 TTGATATTTA
*
61661 TCCCGAAGGACCACATG-ATATG
1 TCCCGAAGGACCACTTGAATATG
61683 TCCCGAAGGACCACTTG-ATATG
1 TCCCGAAGGACCACTTGAATATG
*
61705 TCCCGTAGGACCACTTGAATATG
1 TCCCGAAGGACCACTTGAATATG
61728 TCCCGAAGGACCACTTGAATATG
1 TCCCGAAGGACCACTTGAATATG
61751 TCCCGAAGGACCACTTGAATATG
1 TCCCGAAGGACCACTTGAATATG
*
61774 TCCCGAAGGACCACGTG-ATATG
1 TCCCGAAGGACCACTTGAATATG
61796 TCCCGAAGGACCACTTGAA
1 TCCCGAAGGACCACTTGAA
61815 CCCTCGACTC
Statistics
Matches: 125, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
22 58 0.46
23 67 0.54
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (23 bp):
TCCCGAAGGACCACTTGAATATG
Found at i:61795 original size:68 final size:68
Alignment explanation
Indices: 61661--61814 Score: 258
Period size: 68 Copynumber: 2.3 Consensus size: 68
61651 TTGATATTTA
* * *
61661 TCCCGAAGGACCACATG-ATATGTCCCGAAGGACCACTTGATATGTCCCGTAGGACCACTTGAAT
1 TCCCGAAGGACCACTTGAATATGTCCCGAAGGACCACTTGATATGTCCCGAAGGACCACGTGAAT
61725 ATG
66 ATG
61728 TCCCGAAGGACCACTTGAATATGTCCCGAAGGACCACTTGAATATGTCCCGAAGGACCACGTG-A
1 TCCCGAAGGACCACTTGAATATGTCCCGAAGGACCACTTG-ATATGTCCCGAAGGACCACGTGAA
61792 TATG
65 TATG
61796 TCCCGAAGGACCACTTGAA
1 TCCCGAAGGACCACTTGAA
61815 CCCTCGACTC
Statistics
Matches: 82, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
67 16 0.20
68 46 0.56
69 20 0.24
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (68 bp):
TCCCGAAGGACCACTTGAATATGTCCCGAAGGACCACTTGATATGTCCCGAAGGACCACGTGAAT
ATG
Found at i:68641 original size:22 final size:22
Alignment explanation
Indices: 68610--68697 Score: 113
Period size: 22 Copynumber: 3.9 Consensus size: 22
68600 ATATTTATCT
* *
68610 CGAAGCACCACATGATATGTCC
1 CGAAGGACCACTTGATATGTCC
68632 CGAAGGACCACTTGATATGTCC
1 CGAAGGACCACTTGATATGTCC
* * *
68654 CGTAGGACCACTTAAATATGTCT
1 CGAAGGACCACTT-GATATGTCC
68677 CGAAGGACCACTTGAATATGT
1 CGAAGGACCACTTG-ATATGT
68698 GACCATGTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
22 32 0.56
23 25 0.44
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (22 bp):
CGAAGGACCACTTGATATGTCC
Found at i:69683 original size:20 final size:20
Alignment explanation
Indices: 69654--69750 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
69644 GTGATTTTCT
* *
69654 CGTTGGGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
69674 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
69694 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
69714 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
69734 CGTTTCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
69751 GAATGTGTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:69973 original size:140 final size:140
Alignment explanation
Indices: 69721--70003 Score: 503
Period size: 140 Copynumber: 2.0 Consensus size: 140
69711 TCGCGTTGCG
* * *
69721 ATAGTCAAATTCGCGTTTCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
* *
69786 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACTTAA
66 TAACAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
69851 AATACACATA
131 AATACACATA
*
69861 ATAGTCAAATTCATGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
1 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
*
69926 TAACAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAATTTTACACATAA
66 TAACAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
69991 AATACACATA
131 AATACACATA
70001 ATA
1 ATA
70004 CAACGTTTGC
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 136 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
TAACAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:70084 original size:18 final size:18
Alignment explanation
Indices: 70061--70095 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
70051 AAGCCGGTTG
70061 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
70079 TGATTGCGATTTTGATT
1 TGATTGAGATTTTGATT
70096 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:72668 original size:74 final size:75
Alignment explanation
Indices: 72547--72697 Score: 286
Period size: 74 Copynumber: 2.0 Consensus size: 75
72537 ATAGAAGAAT
72547 TGAAGGAAGAATTGATTATTTTCGGGCTTGAAATATAATTTCTGGGT-AGGGAATCGATACCCTA
1 TGAAGGAAGAATTGATTATTTTCGGGCTTGAAATATAATTTCTGGGTAAGGGAATCGATACCCTA
72611 TGAATGGGAA
66 TGAATGGGAA
72621 TGAAGGAAGAATTGATTATTTTCGGGCTTGAAATATAATTTCTGGGTAGAGGGAATCGATACCCT
1 TGAAGGAAGAATTGATTATTTTCGGGCTTGAAATATAATTTCTGGGTA-AGGGAATCGATACCCT
72686 ATGAATGGGAA
65 ATGAATGGGAA
72697 T
1 T
72698 CAATTCCCCC
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
74 47 0.63
76 28 0.37
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.31
Consensus pattern (75 bp):
TGAAGGAAGAATTGATTATTTTCGGGCTTGAAATATAATTTCTGGGTAAGGGAATCGATACCCTA
TGAATGGGAA
Found at i:73062 original size:14 final size:14
Alignment explanation
Indices: 73043--73076 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
73033 TATCAATTAA
73043 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
73057 ACAAATTAACTTTT
1 ACAAATCAACTTTT
73071 ACAAAT
1 ACAAAT
73077 AAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:74454 original size:21 final size:21
Alignment explanation
Indices: 74397--74463 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
74387 AACAGTCATA
*
74397 TTGAACGGTGGGAGG-GACCTC
1 TTGAACGATGGGAGGAG-CCTC
* **
74418 TTCAACGATGACAGGAGCCTC
1 TTGAACGATGGGAGGAGCCTC
*
74439 TTGAACGATGGGAGGAGACTC
1 TTGAACGATGGGAGGAGCCTC
74460 TTGA
1 TTGA
74464 GGGATTATAG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 36 0.97
22 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
TTGAACGATGGGAGGAGCCTC
Found at i:74461 original size:42 final size:42
Alignment explanation
Indices: 74397--74516 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 42
74387 AACAGTCATA
* *
74397 TTGAACGGTGGGAGG-GACCTCTTCAACGATGACAGGAGCCTC
1 TTGAACGATGGGAGGAGA-CTCTTGAACGATGACAGGAGCCTC
** * * *
74439 TTGAACGATGGGAGGAGACTCTTGAGGGATTATAGGGGCCTC
1 TTGAACGATGGGAGGAGACTCTTGAACGATGACAGGAGCCTC
* *
74481 TTGAACGATAGGA-GAGACATATTGAACGATGACAGG
1 TTGAACGATGGGAGGAGAC-TCTTGAACGATGACAGG
74517 TGAGTCGGGC
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
41 5 0.08
42 56 0.89
43 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.21
Consensus pattern (42 bp):
TTGAACGATGGGAGGAGACTCTTGAACGATGACAGGAGCCTC
Found at i:75029 original size:20 final size:20
Alignment explanation
Indices: 75006--75073 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
74996 GAAACTTAAA
* **
75006 ATCGCAACGTGAAAATGACT
1 ATCGCAACGCGAATTTGACT
75026 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
75046 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
75066 ATCGCAAC
1 ATCGCAAC
75074 AAGATAACCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:75106 original size:33 final size:33
Alignment explanation
Indices: 75069--75136 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
75059 TTTGACTATC
* * *
75069 GCAACAAGATAACCGTAATGCGAAA-TAAAAATT
1 GCAACAAGAAAACCGCAACGCGAAACT-AAAATT
*
75102 GCAACAAGAAAATCGCAACGCGAAACTAAAATT
1 GCAACAAGAAAACCGCAACGCGAAACTAAAATT
75135 GC
1 GC
75137 GTTGTGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.15
Consensus pattern (33 bp):
GCAACAAGAAAACCGCAACGCGAAACTAAAATT
Found at i:75197 original size:33 final size:34
Alignment explanation
Indices: 75135--75211 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 34
75125 AACTAAAATT
* * *
75135 GCGTTGTGATTTTCATTTTTGCATTGCGATTTTC
1 GCGTTGCGATTTTCATTTTCGCATTGCGATTATC
*
75169 GCGTTGCGATTTTTA-TTTCGCATTGCGATTATC
1 GCGTTGCGATTTTCATTTTCGCATTGCGATTATC
*
75202 CCGTTGCGAT
1 GCGTTGCGAT
75212 AGTCAAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
33 25 0.66
34 13 0.34
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (34 bp):
GCGTTGCGATTTTCATTTTCGCATTGCGATTATC
Found at i:75245 original size:20 final size:20
Alignment explanation
Indices: 75203--75271 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
75193 GCGATTATCC
75203 CGTTGCGATAGTCAAATTT--G
1 CGTTGCGATAGTC--ATTTCCG
*
75223 CGTTGTGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
75243 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
75263 CGTTGCGAT
1 CGTTGCGAT
75272 TTTAAGTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 4 0.09
20 40 0.91
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:77656 original size:20 final size:21
Alignment explanation
Indices: 77631--77695 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
77621 TCTGAGAGAT
77631 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
77651 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
* * *
77673 AGAGATGGGGACGGATGTCGCC
1 GGAGAT-GAGACGGATTTCGCC
77695 G
1 G
77696 TAGAGAGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 6 0.16
22 31 0.84
ACGTcount: A:0.22, C:0.17, G:0.43, T:0.18
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:77665 original size:22 final size:22
Alignment explanation
Indices: 77638--77695 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
77628 GATGGAGATA
77638 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
77660 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
77682 GACGGATGTCGCCG
1 GACGGATTTCGCCG
77696 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.43, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:77992 original size:19 final size:19
Alignment explanation
Indices: 77960--78007 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
77950 GGAAACTGAT
*
77960 TTGCGATATTAGAGATCGCG
1 TTGCGAT-TTAGAGATCGCA
77980 TTGCGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCA
77999 TTGCGATTT
1 TTGCGATTT
78008 TGTTGGTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (19 bp):
TTGCGATTTAGAGATCGCA
Found at i:84488 original size:29 final size:30
Alignment explanation
Indices: 84451--84539 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
84441 TTACTTTGTT
*
84451 TTAACTTATTAAATAT-TTTTATTTTTATC
1 TTAATTTATTAAATATATTTTATTTTTATC
* *
84480 TTAATTTATTAAATATATTTTGTTTTTATT
1 TTAATTTATTAAATATATTTTATTTTTATC
* * *
84510 TTAATATA-AAATATATATTTTATCTTTATC
1 TTAATTTATTAA-ATATATTTTATTTTTATC
84540 ATCACTTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 17 0.34
30 33 0.66
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (30 bp):
TTAATTTATTAAATATATTTTATTTTTATC
Found at i:84609 original size:26 final size:26
Alignment explanation
Indices: 84573--84626 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
84563 ATATCTTAAC
84573 TTGAAAAATATTTAAATATTTTACTA
1 TTGAAAAATATTTAAATATTTTACTA
84599 TTGAAAAATATTTAAATATTTTACTA
1 TTGAAAAATATTTAAATATTTTACTA
84625 TT
1 TT
84627 AATTTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (26 bp):
TTGAAAAATATTTAAATATTTTACTA
Found at i:87605 original size:22 final size:22
Alignment explanation
Indices: 87556--87609 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
87546 TTGCTATTTT
87556 TTTCAAAAAAAAAAGACAAAAA
1 TTTCAAAAAAAAAAGACAAAAA
** *
87578 AATCAAAACAAAAAAG-CCAAAA
1 TTTCAAAA-AAAAAAGACAAAAA
87600 TTTCAAAAAA
1 TTTCAAAAAA
87610 TTGTAAACGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 2 0.08
22 17 0.65
23 7 0.27
ACGTcount: A:0.70, C:0.13, G:0.04, T:0.13
Consensus pattern (22 bp):
TTTCAAAAAAAAAAGACAAAAA
Done.