Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003414.1 Hibiscus syriacus cultivar Beakdansim tig00007191_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: 72252
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3197 original size:27 final size:28
Alignment explanation
Indices: 3158--3212 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
3148 CGTCTTATGG
* *
3158 AGATTGCTCGGTTTTG-CCATCGCATAC
1 AGATTACTCGGTTTTGTCCATAGCATAC
*
3185 AGATTACTTGGTTTTGTCCATAGCATAC
1 AGATTACTCGGTTTTGTCCATAGCATAC
3213 TAATTGATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (28 bp):
AGATTACTCGGTTTTGTCCATAGCATAC
Found at i:4015 original size:31 final size:31
Alignment explanation
Indices: 3977--4040 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
3967 TTCAAAGGAT
3977 TAGTTCCTTTTGT-TTATTGAGTTGCCAAAAG
1 TAGTTCCTTTT-TATTATTGAGTTGCCAAAAG
*
4008 TAGTTCCTTTTTATTATTGTGTTGCCAAAAG
1 TAGTTCCTTTTTATTATTGAGTTGCCAAAAG
4039 TA
1 TA
4041 AAATCAAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (31 bp):
TAGTTCCTTTTTATTATTGAGTTGCCAAAAG
Found at i:4082 original size:45 final size:45
Alignment explanation
Indices: 4029--4158 Score: 160
Period size: 45 Copynumber: 2.9 Consensus size: 45
4019 TATTATTGTG
* * *
4029 TTGC-CAAAAGTAAAATCAAAGGATTAGTTCCTTTTGATTATCGAC
1 TTGCACAAAATTAAAATCAAATGATTAGTTCCTTTTGATTATC-AA
*
4074 TT-CACAAAATTAAAATCAAATGATTAGTTTCTTTTGATTACTCAA
1 TTGCACAAAATTAAAATCAAATGATTAGTTCCTTTTGATTA-TCAA
* *
4119 TTGCA-ACAATTAAAATCAAATGA-TAGTTCCTTTTTATTAT
1 TTGCACAAAATTAAAATCAAATGATTAGTTCCTTTTGATTAT
4159 TGAGTTGCTA
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
43 1 0.01
44 15 0.20
45 55 0.73
46 4 0.05
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (45 bp):
TTGCACAAAATTAAAATCAAATGATTAGTTCCTTTTGATTATCAA
Found at i:4405 original size:58 final size:58
Alignment explanation
Indices: 4277--4555 Score: 217
Period size: 58 Copynumber: 4.8 Consensus size: 58
4267 AAACTTAAAA
* * * * * **
4277 AAGGGAAATAAATCATTAGATTTATTTCATCGTTAGAATCTTGCATTGATTCTAACTTCAT
1 AAGGAAAATAAATCATTAAATTTATTTTAT--TGAGAATCTTG-AATGATTCTAACTTTGT
* * *
4338 AAGGAAAATAAATCATTGAATTTATTTTATTGAGAACCTTGAATGATTCTAAATTTGT
1 AAGGAAAATAAATCATTAAATTTATTTTATTGAGAATCTTGAATGATTCTAACTTTGT
* * * * *
4396 AAGGAAAATAAATCGTTAAATTTATTTTCTTGAAAATCTCGAA-GTATTCTATCTTT-T
1 AAGGAAAATAAATCATTAAATTTATTTTATTGAGAATCTTGAATG-ATTCTAACTTTGT
* ** * * * *
4453 AAAAGAAAATAAATTGTTAAAATTATTTTCTTGAGAATCTTAAATGATTCT-ATTTTGT
1 -AAGGAAAATAAATCATTAAATTTATTTTATTGAGAATCTTGAATGATTCTAACTTTGT
** * *
4511 AAATGG-AAATAAATTGTTAAACTTATTTTCTT-ATGAATCTTGAAT
1 -AA-GGAAAATAAATCATTAAATTTATTTTATTGA-GAATCTTGAAT
4556 AAAGAAATAA
Statistics
Matches: 183, Mismatches: 29, Indels: 15
0.81 0.13 0.07
Matches are distributed among these distances:
57 6 0.03
58 140 0.77
59 11 0.06
61 26 0.14
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (58 bp):
AAGGAAAATAAATCATTAAATTTATTTTATTGAGAATCTTGAATGATTCTAACTTTGT
Found at i:4565 original size:101 final size:101
Alignment explanation
Indices: 4454--4639 Score: 259
Period size: 101 Copynumber: 1.8 Consensus size: 101
4444 CTATCTTTTA
* * **
4454 AAAGAAAATAAATTGTTAAAATTATTTTCTTGAGAATCTTAAATGATTCTATTTTGTAAATGGAA
1 AAAGAAAATAAATTGTTAAAATTATTTTATTGAGAATATTAAATGATTCTATTTT-TAAAAAGAA
*
4519 ATAAAT-TGTTAAACTTATTTTCTTATGAATCTTGAAT
65 AT-AATCTGATAAACTTATTTTCTTATGAATCTTGAAT
* * *
4556 AAAG-AAATAAATTGTTGAATTTATTTTATTGAGAATATTTAATGATTCTATTTTTAAAAAGAAA
1 AAAGAAAATAAATTGTTAAAATTATTTTATTGAGAATATTAAATGATTCTATTTTTAAAAAGAAA
*
4620 TAATCTGATAAATTTATTTT
66 TAATCTGATAAACTTATTTT
4640 ATTGAGAATC
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
99 3 0.04
100 22 0.30
101 45 0.61
102 4 0.05
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.44
Consensus pattern (101 bp):
AAAGAAAATAAATTGTTAAAATTATTTTATTGAGAATATTAAATGATTCTATTTTTAAAAAGAAA
TAATCTGATAAACTTATTTTCTTATGAATCTTGAAT
Found at i:4634 original size:57 final size:58
Alignment explanation
Indices: 4556--4788 Score: 210
Period size: 57 Copynumber: 4.1 Consensus size: 58
4546 AATCTTGAAT
* * *
4556 AAAGAAATAAAT-TGTTGAATTTATTTTATTGAGAATATTTAATGATTCTATTTTTAA
1 AAAGAAATAAATCTGATAAATTTATTTTATTGAGAATATTTAATGATTATATTTTTAA
* * *
4613 AAAGAAAT-AATCTGATAAATTTATTTTATTGAGAATCTTAAATGATTATGTTTTCTAA
1 AAAGAAATAAATCTGATAAATTTATTTTATTGAGAATATTTAATGATTATATTTT-TAA
* * * *
4671 AAATAAATAAA--TAATTGAATTTATTTTCTT-AGGAATATTTAATGATTATATCTTTTAA
1 AAAGAAATAAATCTGA-TAAATTTATTTTATTGA-GAATATTTAATGATTATAT-TTTTAA
* * ** * * * *
4729 AATGAAATAAATC-GTTAAATTTA-TTCCTTGAGAATCTTGAATGATTTCTATTTTGAA
1 AAAGAAATAAATCTGATAAATTTATTTTATTGAGAATATTTAATGA-TTATATTTTTAA
4786 AAA
1 AAA
4789 ATGTTCCTGT
Statistics
Matches: 142, Mismatches: 24, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
56 3 0.02
57 70 0.49
58 64 0.45
59 5 0.04
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (58 bp):
AAAGAAATAAATCTGATAAATTTATTTTATTGAGAATATTTAATGATTATATTTTTAA
Found at i:4689 original size:115 final size:115
Alignment explanation
Indices: 4560--4774 Score: 301
Period size: 115 Copynumber: 1.9 Consensus size: 115
4550 TTGAATAAAG
** *
4560 AAATAAATTGTTGAATTTATTTTATT-GAGAATATTTAATGATTCTAT-TTTTAAAAAGAAAT-A
1 AAATAAATAATTGAATTTATTTTATTAG-GAATATTTAATGATTATATCTTTTAAAAAGAAATAA
*
4622 ATCTGATAAATTTATTTTATTGAGAATCTTAAATGATTATGTTTTCTAAAAAT
65 ATC-GATAAATTTA-TTCATTGAGAATCTTAAATGATTATGTTTTCTAAAAAT
* *
4675 AAATAAATAATTGAATTTATTTTCTTAGGAATATTTAATGATTATATCTTTTAAAATGAAATAAA
1 AAATAAATAATTGAATTTATTTTATTAGGAATATTTAATGATTATATCTTTTAAAAAGAAATAAA
* * *
4740 TCGTTAAATTTATTCCTTGAGAATCTTGAATGATT
66 TCGATAAATTTATTCATTGAGAATCTTAAATGATT
4775 TCTATTTTGA
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
115 61 0.69
116 23 0.26
117 4 0.05
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (115 bp):
AAATAAATAATTGAATTTATTTTATTAGGAATATTTAATGATTATATCTTTTAAAAAGAAATAAA
TCGATAAATTTATTCATTGAGAATCTTAAATGATTATGTTTTCTAAAAAT
Found at i:4695 original size:158 final size:159
Alignment explanation
Indices: 4401--4706 Score: 368
Period size: 158 Copynumber: 1.9 Consensus size: 159
4391 TTTGTAAGGA
* *
4401 AAATAAATCGTTAAATTTATTTTCTTGAAAATCTCGAAGTATTCTATCTTTTAAAAGAAAATAAA
1 AAATAAATCGTTAAATTTATTTTATTGAAAATATCGAAGTATTCTATCTTTTAAAAGAAAATAAA
* * * * ** **
4466 TTGTTAAAATTATTTTCTTGAGAATCTTAAATGATTCTATTTTGTAAATGGAAATAAATTGTTAA
66 TTGATAAAATTATTTTATTGAGAATCTTAAATGATTATATTTTCTAAAAAGAAATAAATAATTAA
*
4531 ACTTATTTTCTTATGAATCTTGAATAAAG
131 ACTTATTTTCTTAGGAATCTTGAATAAAG
* * * **
4560 AAATAAATTGTTGAATTTATTTTATTGAGAATATTTAA-TGATTCTAT-TTTTAAAA-AGAAAT-
1 AAATAAATCGTTAAATTTATTTTATTGAAAATATCGAAGT-ATTCTATCTTTTAAAAGA-AAATA
* * *
4621 AATCTGATAAATTTATTTTATTGAGAATCTTAAATGATTATGTTTTCTAAAAATAAATAAATAAT
64 AAT-TGATAAAATTATTTTATTGAGAATCTTAAATGATTATATTTTCTAAAAAGAAATAAATAAT
* *
4686 TGAATTTATTTTCTTAGGAAT
128 TAAACTTATTTTCTTAGGAAT
4707 ATTTAATGAT
Statistics
Matches: 123, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
157 4 0.03
158 81 0.66
159 38 0.31
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.44
Consensus pattern (159 bp):
AAATAAATCGTTAAATTTATTTTATTGAAAATATCGAAGTATTCTATCTTTTAAAAGAAAATAAA
TTGATAAAATTATTTTATTGAGAATCTTAAATGATTATATTTTCTAAAAAGAAATAAATAATTAA
ACTTATTTTCTTAGGAATCTTGAATAAAG
Found at i:4738 original size:216 final size:215
Alignment explanation
Indices: 4343--4770 Score: 469
Period size: 216 Copynumber: 2.0 Consensus size: 215
4333 TTCATAAGGA
* **
4343 AAATAAATCATTGAATTTATTTTATTGAGAACCTTGAATGATTCTAAATTTGTAAGGAAAATAAA
1 AAATAAATCATTGAATTTATTTTATTGAGAACATTGAATGATTCT-AATTTGTAAAAAAAATAAA
* * * * **
4408 TCGTTAAATTTATTTTCTTGAAAATCTCGAAGTATTCTATCTTTTAAAAGAAAATAAATTGTTAA
65 TCGATAAATTTATTTTATTGAAAATCTCAAAGTATTATATCTTTTAAAAGAAAATAAATAATTAA
* * *
4473 AATTATTTTCTTGAGAATCTTAAATGATTCTATTTTGTAAATGGAAATAAATTGTTAAACTTATT
130 AATTATTTTCTTGAGAATATTAAATGATTATATTTTGTAAATGGAAATAAATCGTTAAACTTA-T
*
4538 TTCTT-ATGAATCTTGAATAAAG
194 TCCTTGA-GAATCTTGAATAAAG
** * * *
4560 AAATAAATTGTTGAATTTATTTTATTGAGAATATTTAATGATTCT-ATTTTTAAAAAGAAAT-AA
1 AAATAAATCATTGAATTTATTTTATTGAGAACATTGAATGATTCTAATTTGTAAAAA-AAATAAA
* * *
4623 TCTGATAAATTTATTTTATTGAGAATCTTAAA-TGATTATGT-TTTCTAAAA-ATAAATAAATAA
65 TC-GATAAATTTATTTTATTGAAAATCTCAAAGT-ATTATATCTTT-TAAAAGA-AAATAAATAA
* * *
4685 TTGAATTTATTTTCTT-AGGAATATTTAATGATTATATCTTT-TAAAAT-GAAATAAATCGTTAA
126 TTAAAATTATTTTCTTGA-GAATATTAAATGATTATAT-TTTGT-AAATGGAAATAAATCGTTAA
*
4747 ATTTATTCCTTGAGAATCTTGAAT
188 ACTTATTCCTTGAGAATCTTGAAT
4771 GATTTCTATT
Statistics
Matches: 177, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
215 34 0.19
216 96 0.54
217 47 0.27
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.43
Consensus pattern (215 bp):
AAATAAATCATTGAATTTATTTTATTGAGAACATTGAATGATTCTAATTTGTAAAAAAAATAAAT
CGATAAATTTATTTTATTGAAAATCTCAAAGTATTATATCTTTTAAAAGAAAATAAATAATTAAA
ATTATTTTCTTGAGAATATTAAATGATTATATTTTGTAAATGGAAATAAATCGTTAAACTTATTC
CTTGAGAATCTTGAATAAAG
Found at i:4750 original size:58 final size:57
Alignment explanation
Indices: 4559--4753 Score: 216
Period size: 58 Copynumber: 3.4 Consensus size: 57
4549 CTTGAATAAA
* * * *
4559 GAAATAAATTGTTGAATTTATTTTATTGAGAATATTTAATGATTCTATTTTTAAAAA
1 GAAATAAATCGTTAAATTTATTTTATTGAGAATATTTAATGATTATATTTTTAAAAT
* * * *
4616 GAAAT-AATCTGATAAATTTATTTTATTGAGAATCTTAAATGATTATGTTTTCTAAAAAT
1 GAAATAAATC-GTTAAATTTATTTTATTGAGAATATTTAATGATTATATTTT-T-AAAAT
** * *
4675 -AAATAAATAATTGAATTTATTTTCTT-AGGAATATTTAATGATTATATCTTTTAAAAT
1 GAAATAAATCGTTAAATTTATTTTATTGA-GAATATTTAATGATTATAT-TTTTAAAAT
4732 GAAATAAATCGTTAAATTTATT
1 GAAATAAATCGTTAAATTTATT
4754 CCTTGAGAAT
Statistics
Matches: 112, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
56 3 0.03
57 46 0.41
58 53 0.47
59 10 0.09
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (57 bp):
GAAATAAATCGTTAAATTTATTTTATTGAGAATATTTAATGATTATATTTTTAAAAT
Found at i:4788 original size:115 final size:115
Alignment explanation
Indices: 4550--4788 Score: 290
Period size: 115 Copynumber: 2.1 Consensus size: 115
4540 CTTATGAATC
** *
4550 TTGAATAAAGAAATAAATTGTTGAATTTATTTTATTGAGAATATTTAATGATTCTATTTTTAAAA
1 TTGAA-AAAGAAATAAATAATTGAATTTATTTTATTGAGAATATTTAATGATTATATTTTTAAAA
* *
4615 AGAAATAATCTGATAAATTTATTTTATTGAGAATCTTAAATGATTATGTTT
65 AGAAATAATCTGATAAATTTATTTCATTGAGAATCTTAAATGATTATCTTT
* *
4666 TCT-AAAAATAAATAAATAATTGAATTTATTTTCTT-AGGAATATTTAATGATTATATCTTTTAA
1 T-TGAAAAAGAAATAAATAATTGAATTTATTTTATTGA-GAATATTTAATGATTATAT-TTTTAA
* * * *
4729 AATGAAATAAATC-GTTAAATTTA-TTCCTTGAGAATCTTGAATGATT-TCTATT
63 AAAGAAAT-AATCTGATAAATTTATTTCATTGAGAATCTTAAATGATTATCT-TT
4781 TTGAAAAA
1 TTGAAAAA
4789 ATGTTCCTGT
Statistics
Matches: 106, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
114 4 0.04
115 72 0.68
116 25 0.24
117 5 0.05
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (115 bp):
TTGAAAAAGAAATAAATAATTGAATTTATTTTATTGAGAATATTTAATGATTATATTTTTAAAAA
GAAATAATCTGATAAATTTATTTCATTGAGAATCTTAAATGATTATCTTT
Found at i:4842 original size:40 final size:39
Alignment explanation
Indices: 4798--4942 Score: 122
Period size: 40 Copynumber: 3.8 Consensus size: 39
4788 AATGTTCCTG
4798 TTTTGTAAAAGGAAATAAAGT-ATTGAATTTAAATTTCTTA
1 TTTTGTAAAA-GAAATAAA-TCATTGAATTTAAATTTCTTA
* **
4838 TTTTG--AAA-AAA-AAATCATTGAATTT-AGTTTCCAA
1 TTTTGTAAAAGAAATAAATCATTGAATTTAAATTTCTTA
* * **
4872 TTTTGTAAAATGAAATAAATCGTTGGATTTATTTTTCTTA
1 TTTTGTAAAA-GAAATAAATCATTGAATTTAAATTTCTTA
* * *
4912 TTTTATAAAAAGAAATAAATAATTAAATTTA
1 TTTTGT-AAAAGAAATAAATCATTGAATTTA
4943 TTTTCTTGAG
Statistics
Matches: 83, Mismatches: 14, Indels: 16
0.73 0.12 0.14
Matches are distributed among these distances:
34 12 0.14
35 12 0.14
36 6 0.07
38 6 0.07
39 12 0.14
40 31 0.37
41 4 0.05
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (39 bp):
TTTTGTAAAAGAAATAAATCATTGAATTTAAATTTCTTA
Found at i:5046 original size:96 final size:98
Alignment explanation
Indices: 4873--5136 Score: 270
Period size: 96 Copynumber: 2.7 Consensus size: 98
4863 AGTTTCCAAT
* *
4873 TTTGTAAAATGAAATAAATCGTTGGATTTATTTTTCTTATTTTATAAAAAGAAATAAATAATTAA
1 TTTGTAAAAAGAAATAAATCGTTGAATTTATTTTTCTTATTTTATAAAAAGAAATAAATAATTAA
*
4938 ATTTATTTTCTTGAGAATCTCACATAATGCTGG
66 ATTTATTTTCTTGAGAATCTCACATAATGATGG
* * ** ** *
4971 TTTGTAAAAGGAAATAATTTTTTGAATTTA-TTTTCTTA-TTTATAAAACA-AAATAAATCGTTG
1 TTTGTAAAAAGAAATAAATCGTTGAATTTATTTTTCTTATTTTATAAAA-AGAAATAAATAATTA
* * * *
5033 AA-TTATTTTTCTTGATAATCTTATATAATTATGG
65 AATTTA-TTTTCTTGAGAATCTCACATAATGATGG
* * * * * * *
5067 GTTGTAAAAAGAAATAAATCGTTGGATAT-TTTTTCTTGTTTTGT-AAAAGAAAATAAATCATTC
1 TTTGTAAAAAGAAATAAATCGTTGAATTTATTTTTCTTATTTTATAAAAAG-AAATAAATAATTA
5130 AATTTAT
65 AATTTAT
5137 ATTTTTGGAA
Statistics
Matches: 135, Mismatches: 24, Indels: 15
0.78 0.14 0.09
Matches are distributed among these distances:
95 4 0.03
96 76 0.56
97 27 0.20
98 28 0.21
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (98 bp):
TTTGTAAAAAGAAATAAATCGTTGAATTTATTTTTCTTATTTTATAAAAAGAAATAAATAATTAA
ATTTATTTTCTTGAGAATCTCACATAATGATGG
Found at i:5214 original size:60 final size:59
Alignment explanation
Indices: 5111--5264 Score: 163
Period size: 58 Copynumber: 2.6 Consensus size: 59
5101 CTTGTTTTGT
* * *
5111 AAAAGA-AAATAAATCATTCAATTTATATTTTTGGAAATTAAGTAAGATTATACTTTAAAA
1 AAAAGAGAAATAAATCATTAAATTTAT-TTTTTAGAAATCAAGTAAGATTATA-TTTAAAA
* * * ***
5171 AAAAGAGAAATAAATTATTAAATTTATTTTTTA-AGAATCAAGTATGATTCTATTTTGTA
1 AAAAGAGAAATAAATCATTAAATTTATTTTTTAGA-AATCAAGTAAGATTATATTTAAAA
*
5230 AGAA-AGAAATAAATCATTAAATTTATTTTTT-GAAA
1 AAAAGAGAAATAAATCATTAAATTTATTTTTTAGAAA
5265 ATTGTAATAT
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
57 2 0.03
58 27 0.34
59 8 0.10
60 25 0.31
61 18 0.22
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (59 bp):
AAAAGAGAAATAAATCATTAAATTTATTTTTTAGAAATCAAGTAAGATTATATTTAAAA
Found at i:7578 original size:21 final size:20
Alignment explanation
Indices: 7540--7578 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
7530 TAAATTTATT
*
7540 TTCTATATTAATTATAATCC
1 TTCTATATAAATTATAATCC
*
7560 TTCTATTATAAATTTTAAT
1 TTCTA-TATAAATTATAAT
7579 TATAATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (20 bp):
TTCTATATAAATTATAATCC
Found at i:10474 original size:17 final size:17
Alignment explanation
Indices: 10452--10486 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10442 ATGATAGCGT
*
10452 TTTTTTTAATATAACAA
1 TTTTTTGAATATAACAA
10469 TTTTTTGAATATAACAA
1 TTTTTTGAATATAACAA
10486 T
1 T
10487 AATGCAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTTTTGAATATAACAA
Found at i:11395 original size:17 final size:17
Alignment explanation
Indices: 11359--11405 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
11349 TTGCTGGAAA
11359 TTTATTTCTTTTTG-GAT
1 TTTA-TTCTTTTTGTGAT
11376 TTTATTCTTTTTGTG-T
1 TTTATTCTTTTTGTGAT
11392 TTT-TCTCTTTTTGT
1 TTTAT-TCTTTTTGT
11406 TTTGAACTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.04
16 22 0.79
17 5 0.18
ACGTcount: A:0.06, C:0.09, G:0.11, T:0.74
Consensus pattern (17 bp):
TTTATTCTTTTTGTGAT
Found at i:11708 original size:5 final size:6
Alignment explanation
Indices: 11676--11712 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
11666 ATAATGATAG
11676 AATGGA AATGGA AATGGA AATGGA AAT-GA AAT-GA AAT
1 AATGGA AATGGA AATGGA AATGGA AATGGA AATGGA AAT
11713 AAATAAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.19
Consensus pattern (6 bp):
AATGGA
Found at i:13340 original size:3 final size:3
Alignment explanation
Indices: 13332--13356 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13322 TCTCATTCCT
13332 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
13357 CTCCAAAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:17928 original size:22 final size:22
Alignment explanation
Indices: 17902--17972 Score: 142
Period size: 22 Copynumber: 3.2 Consensus size: 22
17892 GTCAAAGCTT
17902 GCTCTTTTGGTCTCAAATAGAA
1 GCTCTTTTGGTCTCAAATAGAA
17924 GCTCTTTTGGTCTCAAATAGAA
1 GCTCTTTTGGTCTCAAATAGAA
17946 GCTCTTTTGGTCTCAAATAGAA
1 GCTCTTTTGGTCTCAAATAGAA
17968 GCTCT
1 GCTCT
17973 AGAGGTGTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (22 bp):
GCTCTTTTGGTCTCAAATAGAA
Found at i:26447 original size:23 final size:23
Alignment explanation
Indices: 26421--26467 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
26411 AAATGTACCA
26421 AAAGACAGAAGAAAACGTGTCAT
1 AAAGACAGAAGAAAACGTGTCAT
* * *
26444 AAAGGCATATGAAAACGTGTCAT
1 AAAGACAGAAGAAAACGTGTCAT
26467 A
1 A
26468 TAGGCATACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (23 bp):
AAAGACAGAAGAAAACGTGTCAT
Found at i:26472 original size:23 final size:23
Alignment explanation
Indices: 26431--26475 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
26421 AAAGACAGAA
26431 GAAAACGTGTCATAAAGGCATAT
1 GAAAACGTGTCATAAAGGCATAT
*
26454 GAAAACGTGTCATATAGGCATA
1 GAAAACGTGTCATAAAGGCATA
26476 CTTATTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.22
Consensus pattern (23 bp):
GAAAACGTGTCATAAAGGCATAT
Found at i:27012 original size:3 final size:3
Alignment explanation
Indices: 27006--27126 Score: 147
Period size: 3 Copynumber: 39.7 Consensus size: 3
26996 TCATTTAAAT
* *
27006 TTA TTA TTA TTGA -AA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
27051 TTA TTA TAA TTA TAA TTA TTTA TTA TTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
27097 TTA TATA TTA TTA TTA TATA TT- TTA TTA TT
1 TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TT
27127 TAATAATAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
2 3 0.03
3 89 0.87
4 10 0.10
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:29095 original size:20 final size:21
Alignment explanation
Indices: 29072--29123 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
29062 AGAAATTAAA
29072 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
29092 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
29114 -ATT-ATTTATT
1 AATTCATTTATT
29124 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:37352 original size:75 final size:75
Alignment explanation
Indices: 37229--37393 Score: 312
Period size: 75 Copynumber: 2.2 Consensus size: 75
37219 CTGTATCAGC
37229 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
1 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
*
37294 TAACAAGAAG
66 TAACAAGAAA
37304 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
1 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
37369 TAACAAGAAA
66 TAACAAGAAA
37379 CAAATATTGGGGCAT
1 C-AATATTGGGGCAT
37394 GCTGAAAACC
Statistics
Matches: 88, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
75 75 0.85
76 13 0.15
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (75 bp):
CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
TAACAAGAAA
Found at i:37538 original size:74 final size:74
Alignment explanation
Indices: 37386--37547 Score: 202
Period size: 74 Copynumber: 2.2 Consensus size: 74
37376 AAACAAATAT
* * *
37386 TGGGGCATGCTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAATATTTATCA
1 TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
37451 GCAAAATGC
66 GCAAAATGC
* * ** *
37460 TGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAATTGTTGATGCATTTTGAACACTTGTAT
1 TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACA-TT-TAT
* *
37525 TAGC-CAATG-
64 CAGCAAAATGC
37534 TGGGGCATGCTGAA
1 TGGGGCATGCTGAA
37548 GGCCTATATC
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
74 64 0.84
75 6 0.08
76 6 0.08
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (74 bp):
TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
GCAAAATGC
Found at i:38933 original size:22 final size:22
Alignment explanation
Indices: 38865--38944 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
38855 TACATCTGCA
* *
38865 CTTTTTAAAGATAATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
** * * * *
38887 CACTTCAGAGATGACAAATTTT
1 CTTTTCAAAGATGATAGATTCT
*
38909 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
*
38931 CTTTTCAAAAATGA
1 CTTTTCAAAGATGA
38945 AAGCTTTATG
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (22 bp):
CTTTTCAAAGATGATAGATTCT
Found at i:39705 original size:76 final size:76
Alignment explanation
Indices: 39613--40786 Score: 2251
Period size: 76 Copynumber: 15.5 Consensus size: 76
39603 CTATTTCTCA
39613 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39678 AGCCTTCGGGT
66 AGCCTTCGGGT
39689 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39754 AGCCTTCGGGT
66 AGCCTTCGGGT
39765 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39830 AGCCTTCGGGT
66 AGCCTTCGGGT
39841 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39906 AGCCTTCGGGT
66 AGCCTTCGGGT
39917 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39982 AGCCTTCGGGT
66 AGCCTTCGGGT
39993 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40058 AGCCTTCGGGT
66 AGCCTTCGGGT
40069 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40134 AGCCTTCGGGT
66 AGCCTTCGGGT
40145 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40210 AGCCTTCGGGT
66 AGCCTTCGGGT
40221 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40286 AGCCTTCGGGT
66 AGCCTTCGGGT
40297 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40362 AGCCTTCGGGT
66 AGCCTTCGGGT
*
40373 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40438 AGCCTTCGGGT
66 AGCCTTCGGGT
40449 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40514 AGCCTTCGGGT
66 AGCCTTCGGGT
*
40525 CATCTGTAAGCCCTTCAGTGCATGATTTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40589 AGCCTTCGGGT
66 AGCCTTCGGGT
*
40600 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40665 AGCCTTCGGGT
66 AGCCTTCGGGT
* * * *
40676 CATCTGTAAGCCCTTCCGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTAATATTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
40741 AACCTTCGGGT
66 AGCCTTCGGGT
* *
40752 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAA
40787 CATTTCCATC
Statistics
Matches: 1083, Mismatches: 14, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 0.07
76 1009 0.93
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:40919 original size:3 final size:3
Alignment explanation
Indices: 40913--41037 Score: 162
Period size: 3 Copynumber: 40.7 Consensus size: 3
40903 TCATTTAAAT
* *
40913 TTA TTA TTA TTGA -AA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
40958 TTA TTA TAA TTA TAA TTA TTTA TTA TTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
41004 TTA TATA TTA TTA TTA TTA TATA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TT
41038 TAATAAATAA
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
2 1 0.01
3 96 0.90
4 10 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:41768 original size:13 final size:13
Alignment explanation
Indices: 41750--41778 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
41740 ACCACCGTTA
41750 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
41763 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
41776 CGG
1 CGG
41779 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:44063 original size:25 final size:27
Alignment explanation
Indices: 44017--44066 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
44007 TTCTAAAGTA
*
44017 TTTCAATTTTTAAAATATAATTTTTTT
1 TTTCAATTTTTAAAATAAAATTTTTTT
44044 TTTCAA-TTTT-AAATAAAATTTTT
1 TTTCAATTTTTAAAATAAAATTTTT
44067 AAAGTTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.55
26 4 0.18
27 6 0.27
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTCAATTTTTAAAATAAAATTTTTTT
Found at i:45727 original size:6 final size:6
Alignment explanation
Indices: 45716--45745 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
45706 TCAATCAATA
45716 AAATTT AAATTT AAATTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT
45746 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:49242 original size:16 final size:17
Alignment explanation
Indices: 49216--49248 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
49206 GTAAAATGAG
49216 TATTCAATCCTATTTAC
1 TATTCAATCCTATTTAC
49233 TATT-AATCCTATTTAC
1 TATTCAATCCTATTTAC
49249 CTAGATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTCAATCCTATTTAC
Found at i:50104 original size:23 final size:24
Alignment explanation
Indices: 50073--50130 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
50063 GCATACTTAT
*
50073 CATTTATTTTATTAGC-TTATATG
1 CATTCATTTTATTAGCTTTATATG
50096 CATTCATTTTATTAGCTTTATATG
1 CATTCATTTTATTAGCTTTATATG
50120 CATTCATTTTA
1 CATTCATTTTA
50131 GCTCTTAAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 15 0.45
24 18 0.55
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.55
Consensus pattern (24 bp):
CATTCATTTTATTAGCTTTATATG
Found at i:53423 original size:18 final size:17
Alignment explanation
Indices: 53400--53434 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53390 AAATTAGAAT
53400 TAATTTAAAATAATTTAA
1 TAATTTAAAAT-ATTTAA
*
53418 TAATTTTAAATATTTAA
1 TAATTTAAAATATTTAA
53435 AAATCTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTTAAAATATTTAA
Found at i:55066 original size:17 final size:17
Alignment explanation
Indices: 55044--55086 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
55034 GATTTAAATA
*
55044 TTATTATGTGGTATATG
1 TTATTATGCGGTATATG
55061 TTATTATGCGGTATATG
1 TTATTATGCGGTATATG
55078 TTATTATGC
1 TTATTATGC
55087 CAAATTTCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (17 bp):
TTATTATGCGGTATATG
Found at i:61412 original size:19 final size:19
Alignment explanation
Indices: 61368--61403 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
61358 TATGAACATT
*
61368 AATTTTATTATCTCTTTCC
1 AATTTTATTATCTCTCTCC
61387 AATTTTATTATCT-TCTC
1 AATTTTATTATCTCTCTC
61404 ACACTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 3 0.19
19 13 0.81
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTTTATTATCTCTCTCC
Found at i:61495 original size:8 final size:7
Alignment explanation
Indices: 61471--61503 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
61461 TTAACTAACT
61471 ATTTAAA
1 ATTTAAA
61478 ATTTAAA
1 ATTTAAA
61485 ATTTAAA
1 ATTTAAA
*
61492 AATT-AA
1 ATTTAAA
61498 ATTTAA
1 ATTTAA
61504 CAGCCTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTTAAA
Found at i:66904 original size:20 final size:19
Alignment explanation
Indices: 66879--66930 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
66869 TGATTCAATC
*
66879 AGTATCGATACCGAAGTGA
1 AGTATCGATACCGAAGGGA
66898 GAGTATCGATACCGAAGGGA
1 -AGTATCGATACCGAAGGGA
66918 AGGTATCGATACC
1 A-GTATCGATACC
66931 ATTTTAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (19 bp):
AGTATCGATACCGAAGGGA
Found at i:66978 original size:19 final size:19
Alignment explanation
Indices: 66954--66995 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
66944 ATGCAAGAAT
66954 GGTATCGATACCATGTG-AA
1 GGTATCGATACCAT-TGCAA
*
66973 GGTATCGGTACCATTGCAA
1 GGTATCGATACCATTGCAA
66992 GGTA
1 GGTA
66996 GTATCGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (19 bp):
GGTATCGATACCATTGCAA
Found at i:67540 original size:59 final size:59
Alignment explanation
Indices: 67468--67586 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
67458 TATTGGCATG
*
67468 AAAGGATGCCTTAGTTGAAATGCATATGGGTGCATTATCGGCATAAAAGAATAATACAT
1 AAAGGATGCCTTAGCTGAAATGCATATGGGTGCATTATCGGCATAAAAGAATAATACAT
*
67527 AAAGGATGCCTTAGCTGAAATGCATATGGGTGCATTATCGGCATAAAAGAATAATGCAT
1 AAAGGATGCCTTAGCTGAAATGCATATGGGTGCATTATCGGCATAAAAGAATAATACAT
67586 A
1 A
67587 TGGGTGCATT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.26
Consensus pattern (59 bp):
AAAGGATGCCTTAGCTGAAATGCATATGGGTGCATTATCGGCATAAAAGAATAATACAT
Done.