Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009277.1 Hibiscus syriacus cultivar Beakdansim tig00112960_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: 120430
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5464 original size:20 final size:21
Alignment explanation
Indices: 5435--5490 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
5425 TTTGTGCTTC
*
5435 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
5455 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
5477 ATGCATCGATGCAT
1 ATGCATCGATGCAT
5491 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:7059 original size:21 final size:21
Alignment explanation
Indices: 7017--7060 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
7007 ACCCCGGGAG
*
7017 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
7038 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
7059 CT
1 CT
7061 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:7863 original size:20 final size:21
Alignment explanation
Indices: 7826--7865 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
7816 AAATTAAGTT
7826 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
7847 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
7866 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:8120 original size:19 final size:19
Alignment explanation
Indices: 8096--8134 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
8086 TCGAATGCAT
8096 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
* *
8115 TCCATGCATCGATGTACTC
1 TCCATGCACCGATGCACTC
8134 T
1 T
8135 GAATATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.15, T:0.28
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:8151 original size:65 final size:64
Alignment explanation
Indices: 8033--8240 Score: 215
Period size: 65 Copynumber: 3.2 Consensus size: 64
8023 TATTCAAAGG
* * * ** *
8033 CATGCACCGATGCATCAGTACATGCATCGATGCATCAATGAAT-TAATT-GAACATCGAATGCAT
1 CATGCATCGATGCA-CAATCCATGCATCGATGCATC-A-GAATATTTTTCAAACATCGAATGCAT
*
8096 TC
63 TT
* ** * *
8098 CATGCACCGATGCACTCTCCATGCATCGATGTACTCTGAATA-TTTTCAAAACATCGAATGCATT
1 CATGCATCGATGCACAATCCATGCATCGATGCA-TCAGAATATTTTTC-AAACATCGAATGCATT
8162 T
64 T
* **
8163 GATGCATCGATGCACAATCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCATCGATGCACAATCCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTT
8227 CATGCATCGATGCA
1 CATGCATCGATGCA
8241 TACTTGGTGC
Statistics
Matches: 120, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
63 6 0.05
64 50 0.42
65 64 0.53
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (64 bp):
CATGCATCGATGCACAATCCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTT
Found at i:11000 original size:24 final size:24
Alignment explanation
Indices: 10956--11005 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
10946 ATAAAGAACC
*
10956 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
10980 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
11004 AA
1 AA
11006 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:14874 original size:3 final size:3
Alignment explanation
Indices: 14866--14903 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
14856 CTAAAATATA
*
14866 AAT AAT AAT AAT AAT AAT AAT AAA ACAT AA- AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA
14904 AATTAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:14884 original size:15 final size:15
Alignment explanation
Indices: 14865--14905 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
14855 CCTAAAATAT
*
14865 AAATAATAATA-ATA
1 AAATAATAAAACATA
14879 ATAATAATAAAACATA
1 A-AATAATAAAACATA
14895 AAATAATAAAA
1 AAATAATAAAA
14906 TTAAATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 19 0.79
16 4 0.17
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAATAAAACATA
Found at i:16195 original size:13 final size:13
Alignment explanation
Indices: 16165--16203 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
16155 ATATTATTAT
*
16165 TATAT-ATAAACG
1 TATATAATAAACA
*
16177 TATATAATTAACA
1 TATATAATAAACA
16190 TATATAATAAACA
1 TATATAATAAACA
16203 T
1 T
16204 CACTTGAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (13 bp):
TATATAATAAACA
Found at i:18585 original size:23 final size:22
Alignment explanation
Indices: 18543--18585 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
18533 TTTTTCTATT
*
18543 TTATTATCTAATTTTTTTTAAA
1 TTATTATCTAATTTTGTTTAAA
18565 TTATT-TCTAATATTTAGTTTA
1 TTATTATCTAAT-TTT-GTTTA
18586 TGTTTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTATCTAATTTTGTTTAAA
Found at i:18678 original size:114 final size:114
Alignment explanation
Indices: 18502--18714 Score: 302
Period size: 114 Copynumber: 1.9 Consensus size: 114
18492 TTACCGTGAA
* * * * *
18502 TAATGATGTTTAGCACCTAAACTATTAATTTTTTTTCTATTTTATTATCTAATTTTTTTTAAATT
1 TAATGATGTTTAACACCTAAACTATTAACTTTTGTTCTATTTTATTATCTAACTTTTCTTAAATT
** *
18567 ATTTCTAATATTTAGTTTATGTTTTAATTCGATATCACATCTCCTTCAG
66 ATACCTAACATTTAGTTTATGTTTTAATTCGATATCACATCTCCTTCAG
* * *
18616 TAATGATGTTTAATACCTAAACTATT-ACTTTTGTTCTATTTTGTTATTTAAACTTTTCTTAAAT
1 TAATGATGTTTAACACCTAAACTATTAACTTTTGTTCTATTTTATTATCT-AACTTTTCTTAAAT
*
18680 TATACCTAACATTTAGTTTATGTTTTAATTTGATA
65 TATACCTAACATTTAGTTTATGTTTTAATTCGATA
18715 CTCGCTATTA
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
113 19 0.22
114 67 0.78
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.53
Consensus pattern (114 bp):
TAATGATGTTTAACACCTAAACTATTAACTTTTGTTCTATTTTATTATCTAACTTTTCTTAAATT
ATACCTAACATTTAGTTTATGTTTTAATTCGATATCACATCTCCTTCAG
Found at i:19690 original size:2 final size:2
Alignment explanation
Indices: 19685--19727 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
19675 AAAAAATAAA
19685 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
19727 A
1 A
19728 AGTTTTGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20053 original size:2 final size:2
Alignment explanation
Indices: 20046--20071 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20036 TACTCACAAA
20046 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
20072 TCAATACTTG
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:20148 original size:16 final size:16
Alignment explanation
Indices: 20115--20148 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20105 CCCTATAGTC
*
20115 TTTTTTTCTCTTCGTT
1 TTTTTTTCTCTTCATT
*
20131 TTTTTTTCTTTTCATT
1 TTTTTTTCTCTTCATT
20147 TT
1 TT
20149 GGTTTGGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTTTCTCTTCATT
Found at i:20349 original size:15 final size:15
Alignment explanation
Indices: 20329--20363 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20319 TTCATGGCAT
*
20329 ATTTTTTATCGTTGG
1 ATTTTTTAGCGTTGG
*
20344 ATTTTTTAGGGTTGG
1 ATTTTTTAGCGTTGG
20359 ATTTT
1 ATTTT
20364 ATGTCGCCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.03, G:0.23, T:0.60
Consensus pattern (15 bp):
ATTTTTTAGCGTTGG
Found at i:26573 original size:21 final size:21
Alignment explanation
Indices: 26548--26627 Score: 142
Period size: 21 Copynumber: 3.8 Consensus size: 21
26538 TTAAGAATGC
*
26548 GATGATATAATATTATCTTAT
1 GATGATATAACATTATCTTAT
26569 GATGATATAACATTATCTTAT
1 GATGATATAACATTATCTTAT
26590 GATGATATAACATTATCTTAT
1 GATGATATAACATTATCTTAT
26611 GATGATATAAACATTAT
1 GATGATAT-AACATTAT
26628 TGTTAAAATT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
21 49 0.86
22 8 0.14
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (21 bp):
GATGATATAACATTATCTTAT
Found at i:27945 original size:25 final size:25
Alignment explanation
Indices: 27917--27967 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
27907 AGGCTGAATC
27917 ATTTTAATTGTATGATGAAGTCACG
1 ATTTTAATTGTATGATGAAGTCACG
27942 ATTTTAATTGTATGATGAAGTCACG
1 ATTTTAATTGTATGATGAAGTCACG
27967 A
1 A
27968 CAGGAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
ATTTTAATTGTATGATGAAGTCACG
Found at i:31176 original size:2 final size:2
Alignment explanation
Indices: 31169--31200 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31159 GATTATTAGA
31169 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
31201 TGAAACAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31629 original size:3 final size:3
Alignment explanation
Indices: 31608--31654 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
31598 CTAATTATAT
* *
31608 TTA TTA ATA TTA CTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31655 CAAATATTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:35677 original size:20 final size:20
Alignment explanation
Indices: 35652--35701 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
35642 TTTCTACGTT
*
35652 TTTGCATTTTCATTCATATC
1 TTTGCATTTTCATTCACATC
* **
35672 TTTGCATTTGCATTTGCATC
1 TTTGCATTTTCATTCACATC
35692 TTTGCATTTT
1 TTTGCATTTT
35702 TACGTTTGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.10, T:0.56
Consensus pattern (20 bp):
TTTGCATTTTCATTCACATC
Found at i:37684 original size:11 final size:9
Alignment explanation
Indices: 37658--37695 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
37648 TCTAAGTAAG
37658 AAGAAAAAA
1 AAGAAAAAA
*
37667 AAGAAAATA
1 AAGAAAAAA
*
37676 AAGAGAAAA
1 AAGAAAAAA
37685 AAGAAAAAA
1 AAGAAAAAA
37694 AA
1 AA
37696 AGAGGGATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:38207 original size:8 final size:8
Alignment explanation
Indices: 38160--38189 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
38150 AAAAAAGAAA
38160 AAAAAAGG
1 AAAAAAGG
38168 -AAAAAGG
1 AAAAAAGG
38175 AAAAAAGG
1 AAAAAAGG
38183 AAAAAAG
1 AAAAAAG
38190 ATGACAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:41271 original size:42 final size:43
Alignment explanation
Indices: 41211--41291 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 43
41201 ACAAATTTGT
* *
41211 AAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTA
1 AAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGCTTA
41254 AAAT-CTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
1 AAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
41292 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
42 32 0.89
43 4 0.11
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (43 bp):
AAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGCTTA
Found at i:41673 original size:248 final size:248
Alignment explanation
Indices: 41117--41811 Score: 1151
Period size: 249 Copynumber: 2.8 Consensus size: 248
41107 TGATAAAATA
* * * * * *
41117 ATTTTCAAAGTTTCTCATTTAATCTTTTTTAAAAAATGAAATTCTTGAAAAGTAAGAAGCTTCTT
1 ATTTTCAAAGTTTCTCATTTAA--TGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAAGTTTCTT
*
41182 ACCCAGTAAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATG
64 A-CCAGTAAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTATTAGTCTTTCGAGCATG
*
41247 ATGCTTAAAATCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGAGCCATCC
128 ATGCTTAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGAGCCATCC
* *
41312 GTAAAGCCTTTGGGTATAATGTTCATATATGATTTTCGCATGAAAATGAGATAGCG
193 GTAAAGCCTTTGGGTAGAATGTTCACATATGATTTTCGCATGAAAATGAGATAGCG
*
41368 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAAGTTTATTAC
1 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAAGTTTCTTAC
* *
41433 TCAGTAAAATATTTCCCACAAATTTGTAAATCCTTCAGGTCATCTATTAGTCTTTCGAGCATGAT
66 -CAGTAAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTATTAGTCTTTCGAGCATGAT
* * * *
41498 GCATAAAACCTTCAGGTCATCTGTCAGTCTTTCGAGCAATATGATAAGTCCTTAG-GGCATCCGT
130 GCTTAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGAGCCATCCGT
*
41562 AAAGCCTTTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCG
195 AAAGCCTTTGGGTAGAATGTTCACATATGATTTTCGCATGAAAATGAGATAGCG
41616 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAAGTTTCTTAC
1 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAAGTTTCTTAC
*
41681 CTAGTAAAGTATTT-CCACAAATTTGTAAATCCTTCGGGTCATCTATTACTCTTTCGAGCATGAT
66 C-AGTAAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTATTAGTCTTTCGAGCATGAT
*
41745 GCTTAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGAGCCATCTGT
130 GCTTAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGAGCCATCCGT
41810 AA
195 AA
41812 GACCTTCAGG
Statistics
Matches: 414, Mismatches: 27, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
247 101 0.24
248 144 0.35
249 147 0.36
251 22 0.05
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (248 bp):
ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAAGTTTCTTAC
CAGTAAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTATTAGTCTTTCGAGCATGATG
CTTAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGAGCCATCCGTA
AAGCCTTTGGGTAGAATGTTCACATATGATTTTCGCATGAAAATGAGATAGCG
Found at i:41776 original size:42 final size:42
Alignment explanation
Indices: 41706--41787 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
41696 CACAAATTTG
* * *
41706 TAAATCCTTCGGGTCATCTATTACTCTTTCGAGCATGATGCT
1 TAAAACCTTCGGGTCATCTATCACTCTTTCGAGCAAGATGCT
* *
41748 TAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
1 TAAAACCTTCGGGTCATCTATCACTCTTTCGAGCAAGATG
41788 ATAAGTCCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (42 bp):
TAAAACCTTCGGGTCATCTATCACTCTTTCGAGCAAGATGCT
Found at i:41992 original size:25 final size:27
Alignment explanation
Indices: 41963--42015 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
41953 CCGTTTCTGA
41963 TACTA-ATTATAT-TTATTAATATTAC
1 TACTATATTATATATTATTAATATTAC
*
41988 TACTATTATTATATATTATTATTATTAC
1 TACTA-TATTATATATTATTAATATTAC
42016 AAATATTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
27 7 0.29
28 12 0.50
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.55
Consensus pattern (27 bp):
TACTATATTATATATTATTAATATTAC
Found at i:42022 original size:25 final size:25
Alignment explanation
Indices: 41976--42023 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
41966 TAATTATATT
* *
41976 TATTAATATTACTACTATTATTATA
1 TATTAATATTACTACAAATATTATA
* *
42001 TATTATTATTATTACAAATATTA
1 TATTAATATTACTACAAATATTA
42024 CAAAATTGGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTAATATTACTACAAATATTATA
Found at i:42729 original size:22 final size:23
Alignment explanation
Indices: 42698--42743 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
42688 GACGGTAGTA
*
42698 AATAGTGATCGA-CGGTGATCGG
1 AATAGCGATCGACCGGTGATCGG
42720 AATAGCGATCGACCGGTGATCGG
1 AATAGCGATCGACCGGTGATCGG
42743 A
1 A
42744 GCTCCCTCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.28, C:0.17, G:0.35, T:0.20
Consensus pattern (23 bp):
AATAGCGATCGACCGGTGATCGG
Found at i:49558 original size:20 final size:20
Alignment explanation
Indices: 49533--49577 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
49523 CTCCTTAACA
49533 AAATTCAAAGTCTGACCATT
1 AAATTCAAAGTCTGACCATT
49553 AAATTCAAAGTCTGACCATT
1 AAATTCAAAGTCTGACCATT
49573 AAATT
1 AAATT
49578 TATCTAGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (20 bp):
AAATTCAAAGTCTGACCATT
Found at i:51719 original size:49 final size:49
Alignment explanation
Indices: 51645--51740 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 49
51635 ATAATTTATA
* **
51645 CCAGGGGCGGATCTCCATAGAGCCCGGGGTATCCCGGGCAACCCCTCAT
1 CCAGGGGCGGACCTCCATAGAGCCCGGGGTATCCCAAGCAACCCCTCAT
* * *
51694 CCAGGGGTGGACCTCCATGGTGCCCGGGGTATCCCAAGCAACCCCTC
1 CCAGGGGCGGACCTCCATAGAGCCCGGGGTATCCCAAGCAACCCCTC
51741 CACAAGTGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.18, C:0.38, G:0.30, T:0.15
Consensus pattern (49 bp):
CCAGGGGCGGACCTCCATAGAGCCCGGGGTATCCCAAGCAACCCCTCAT
Found at i:52819 original size:29 final size:29
Alignment explanation
Indices: 52729--52833 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 29
52719 TTGAAATTAG
* * *
52729 TTTGTGGATTAACTTAAAATGAGGATCATAG
1 TTTGAGGATTAAATTAAAATGA-G-TCATAA
* * * * *
52760 TTTTAGGATAAAATTAAAATG-TTAAAAAA
1 TTTGAGGATTAAATTAAAATGAGT-CATAA
*
52789 TTTGAGGATTAATTTAAAATGAGTCATAA
1 TTTGAGGATTAAATTAAAATGAGTCATAA
* *
52818 TTTAAGGATGAAATTA
1 TTTGAGGATTAAATTA
52834 GAACGTTTAA
Statistics
Matches: 55, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
28 1 0.02
29 36 0.65
30 1 0.02
31 17 0.31
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (29 bp):
TTTGAGGATTAAATTAAAATGAGTCATAA
Found at i:54374 original size:30 final size:31
Alignment explanation
Indices: 54318--54382 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
54308 CGCGTTAAAG
*
54318 TTTGATAAAAATTGTCAAGTTTAAGGGTTGA
1 TTTGATAAAAATTGTCAAGTTTAAGGGTTAA
54349 TTTGATAAAAA-TGTCAA-TTTGAAGGGTTAA
1 TTTGATAAAAATTGTCAAGTTT-AAGGGTTAA
54379 TTTG
1 TTTG
54383 TGCAATAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 3 0.09
30 18 0.56
31 11 0.34
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (31 bp):
TTTGATAAAAATTGTCAAGTTTAAGGGTTAA
Found at i:55189 original size:29 final size:29
Alignment explanation
Indices: 55124--55189 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 29
55114 CTCAGGACCC
* *
55124 TAATTTTTTATATTTACAGTTAGACCCCT
1 TAATTTTTTACATTTACAATTAGACCCCT
* * * **
55153 CAAGTTTTTACATTTATAATTAGAGTCCT
1 TAATTTTTTACATTTACAATTAGACCCCT
55182 TAATTTTT
1 TAATTTTT
55190 ATAATTTCAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.50
Consensus pattern (29 bp):
TAATTTTTTACATTTACAATTAGACCCCT
Found at i:55967 original size:27 final size:28
Alignment explanation
Indices: 55912--55967 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
55902 CCTTCTTATG
*
55912 ATTTGTTTATATATTTATTTAATATAAA
1 ATTTGTTTATATATTTATTTAATAAAAA
55940 ATTTGTTT-T-TAGTTTAATTT-ATAAAAA
1 ATTTGTTTATATA-TTT-ATTTAATAAAAA
55967 A
1 A
55968 GTATTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 2 0.08
27 11 0.44
28 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (28 bp):
ATTTGTTTATATATTTATTTAATAAAAA
Found at i:56655 original size:15 final size:16
Alignment explanation
Indices: 56626--56661 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
56616 TTCAATTCAA
56626 TTTTACTTTCTTTTAT
1 TTTTACTTTCTTTTAT
56642 TTTTACTTTC-TTTAT
1 TTTTACTTTCTTTTAT
56657 TTTTA
1 TTTTA
56662 ATCAAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTACTTTCTTTTAT
Found at i:56766 original size:15 final size:16
Alignment explanation
Indices: 56737--56772 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
56727 AATTTATTGG
56737 TTTTACTTTCTTTTAT
1 TTTTACTTTCTTTTAT
56753 TTTTACTTTC-TTTAT
1 TTTTACTTTCTTTTAT
56768 TTTTA
1 TTTTA
56773 ATCAAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTACTTTCTTTTAT
Found at i:56820 original size:111 final size:111
Alignment explanation
Indices: 56626--56847 Score: 444
Period size: 111 Copynumber: 2.0 Consensus size: 111
56616 TTCAATTCAA
56626 TTTTACTTTCTTTTATTTTTACTTTCTTTATTTTTAATCAAACAAAACTCCCCCTATTTCTATTT
1 TTTTACTTTCTTTTATTTTTACTTTCTTTATTTTTAATCAAACAAAACTCCCCCTATTTCTATTT
56691 TCTTTTGCAATTCACGCCTTGCCTTGGAACAAGACCAATTTATTGG
66 TCTTTTGCAATTCACGCCTTGCCTTGGAACAAGACCAATTTATTGG
56737 TTTTACTTTCTTTTATTTTTACTTTCTTTATTTTTAATCAAACAAAACTCCCCCTATTTCTATTT
1 TTTTACTTTCTTTTATTTTTACTTTCTTTATTTTTAATCAAACAAAACTCCCCCTATTTCTATTT
56802 TCTTTTGCAATTCACGCCTTGCCTTGGAACAAGACCAATTTATTGG
66 TCTTTTGCAATTCACGCCTTGCCTTGGAACAAGACCAATTTATTGG
56848 CAAATACGAT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.23, C:0.22, G:0.07, T:0.48
Consensus pattern (111 bp):
TTTTACTTTCTTTTATTTTTACTTTCTTTATTTTTAATCAAACAAAACTCCCCCTATTTCTATTT
TCTTTTGCAATTCACGCCTTGCCTTGGAACAAGACCAATTTATTGG
Found at i:57340 original size:38 final size:38
Alignment explanation
Indices: 57297--57372 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
57287 AGTCCCTTAG
57297 ACTTTCTACCAATCCCCATGATCATGCCATTGGATGAT
1 ACTTTCTACCAATCCCCATGATCATGCCATTGGATGAT
57335 ACTTTCTACCAATCCCCATGATCATGCCATTGGATGAT
1 ACTTTCTACCAATCCCCATGATCATGCCATTGGATGAT
57373 CTAATATGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (38 bp):
ACTTTCTACCAATCCCCATGATCATGCCATTGGATGAT
Found at i:59644 original size:18 final size:17
Alignment explanation
Indices: 59602--59644 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
59592 TGATTAAGCG
* *
59602 CTGAATAATTCAATGGT
1 CTGAATGATTCAAAGGT
59619 CTGAATGATTCAAAGGCT
1 CTGAATGATTCAAAGG-T
*
59637 CTGTATGA
1 CTGAATGA
59645 ATTGACTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (17 bp):
CTGAATGATTCAAAGGT
Found at i:66536 original size:20 final size:20
Alignment explanation
Indices: 66442--66810 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
66432 GATTTTCCAT
* ** *
66442 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
66462 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
66482 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
66502 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
66522 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
66542 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
66562 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
66582 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
66602 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
66622 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
66642 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
66662 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
66682 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
66702 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
66722 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
66742 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
66762 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
66782 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
66802 AATCACAAC
1 AATCGCAAC
66811 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:67523 original size:24 final size:24
Alignment explanation
Indices: 67484--67530 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
67474 AAATTTGGTC
67484 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
67508 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
67531 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:67722 original size:12 final size:12
Alignment explanation
Indices: 67705--67729 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
67695 ATATAATCCT
67705 GAAGAAGAAAAA
1 GAAGAAGAAAAA
67717 GAAGAAGAAAAA
1 GAAGAAGAAAAA
67729 G
1 G
67730 TCCCGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:70049 original size:19 final size:19
Alignment explanation
Indices: 70027--70351 Score: 412
Period size: 19 Copynumber: 18.4 Consensus size: 19
70017 CGGAAAATAC
*
70027 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
70046 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
70060 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
70079 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
70093 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
70112 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
70131 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
70145 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
70164 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
70183 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
70197 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
70216 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
70235 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
70254 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
70273 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
70292 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
70306 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
70325 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
70344 AATCGCAA
1 AATCGCAA
70352 CGAGATAATC
Statistics
Matches: 269, Mismatches: 12, Indels: 50
0.81 0.04 0.15
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 13 0.05
18 3 0.01
19 187 0.70
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:70073 original size:33 final size:34
Alignment explanation
Indices: 70027--70351 Score: 306
Period size: 33 Copynumber: 9.2 Consensus size: 34
70017 CGGAAAATAC
* *
70027 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
* *
70060 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
70093 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
* * * *
70131 AATCGCAACGAGAGAATCG-CAAT-GCGA-AATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGCAACAATGAA
* *
70164 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
*
70197 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
*
70235 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
*
70273 AATCGCAATGCGAAATGAAAATCGCAACGAA--AG
1 AATCGCAATGCGAAATGAAAATCGCAAC-AATGAA
70306 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
70344 AATCGCAA
1 AATCGCAA
70352 CGAGATAATC
Statistics
Matches: 246, Mismatches: 25, Indels: 37
0.80 0.08 0.12
Matches are distributed among these distances:
31 1 0.00
32 6 0.02
33 132 0.54
34 2 0.01
35 5 0.02
36 3 0.01
37 2 0.01
38 88 0.36
39 6 0.02
40 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACAATGAA
Found at i:70389 original size:52 final size:52
Alignment explanation
Indices: 70055--70373 Score: 557
Period size: 52 Copynumber: 6.0 Consensus size: 52
70045 AAATCCCAAC
70055 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
70107 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
70159 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
70211 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
70268 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
70320 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
70372 AT
1 AT
70374 TATAAACGCA
Statistics
Matches: 255, Mismatches: 7, Indels: 10
0.94 0.03 0.04
Matches are distributed among these distances:
52 200 0.78
53 2 0.01
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:70489 original size:19 final size:19
Alignment explanation
Indices: 70380--70481 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
70370 AAATTATAAA
70380 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
70399 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
70419 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
70435 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
70452 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
70471 CGCATTGCGAT
1 CGCATTGCGAT
70482 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:70607 original size:14 final size:14
Alignment explanation
Indices: 70588--70624 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
70578 CATCAATTAC
70588 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
70602 ACAAATCATCTTTT
1 ACAAATCAACTTTT
70616 ACAAATCAA
1 ACAAATCAA
70625 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:70653 original size:38 final size:38
Alignment explanation
Indices: 70605--70677 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
70595 AACTTTTACA
*
70605 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
70643 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
70678 ACACATACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:70691 original size:26 final size:26
Alignment explanation
Indices: 70662--70712 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
70652 TTACAAATCA
70662 ATTAAACAATCAAAAAACACATACAG
1 ATTAAACAATCAAAAAACACATACAG
***
70688 ATTATTGAATCAAAAAACACATACA
1 ATTAAACAATCAAAAAACACATACA
70713 AATCAACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.59, C:0.18, G:0.04, T:0.20
Consensus pattern (26 bp):
ATTAAACAATCAAAAAACACATACAG
Found at i:70762 original size:12 final size:13
Alignment explanation
Indices: 70710--70762 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
70700 AAAAACACAT
**
70710 ACAAATCAACTTTT
1 ACAAATCAA-TTAA
70724 ACAAATCAATTAA
1 ACAAATCAATTAA
*
70737 ACAAATCAA-AAA
1 ACAAATCAATTAA
70749 AC-AATCAATTAA
1 ACAAATCAATTAA
70761 AC
1 AC
70763 TATTGAATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 6 0.18
12 8 0.24
13 11 0.32
14 9 0.26
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (13 bp):
ACAAATCAATTAA
Found at i:72639 original size:14 final size:14
Alignment explanation
Indices: 72620--72676 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
72610 GCGAAATGAA
*
72620 AATCGCAACGACAG
1 AATCGCAACGAAAG
72634 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
72651 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
72667 AATCGCAACG
1 AATCGCAACG
72677 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:72647 original size:33 final size:33
Alignment explanation
Indices: 72601--72693 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
72591 GCGAAACCAA
*
72601 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
72634 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
72667 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
72694 TGCGATATAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:72658 original size:19 final size:19
Alignment explanation
Indices: 72564--72698 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
72554 TAGTTTACTT
* *
72564 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
72584 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
72603 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
72622 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
72636 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
72655 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
72669 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
72688 TCGCAATGCGA
1 TCGCAACGCGA
72699 TATACGGATA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:72719 original size:20 final size:20
Alignment explanation
Indices: 72694--72841 Score: 163
Period size: 20 Copynumber: 7.4 Consensus size: 20
72684 AAAATCGCAA
* *
72694 TGCGATATACGGATACACGT
1 TGCGATTTACGGATACGCGT
* *
72714 TGCGATATACGGATACGCAT
1 TGCGATTTACGGATACGCGT
**
72734 TGCGATTTACCCATACGCGT
1 TGCGATTTACGGATACGCGT
*
72754 TGCGATTTACGGATACACGT
1 TGCGATTTACGGATACGCGT
72774 TGCGATTTACGGATACGCGT
1 TGCGATTTACGGATACGCGT
* *
72794 TGCGATTTATGTG-TTCGCGT
1 TGCGATTTACG-GATACGCGT
* ** *
72814 TGCGATTTTCATATTCGCGT
1 TGCGATTTACGGATACGCGT
72834 TGCGATTT
1 TGCGATTT
72842 TGGAAAATCG
Statistics
Matches: 110, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
20 109 0.99
21 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (20 bp):
TGCGATTTACGGATACGCGT
Found at i:72858 original size:21 final size:20
Alignment explanation
Indices: 72834--72910 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
72824 ATATTCGCGT
72834 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
72855 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
72875 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
72897 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
72911 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:72921 original size:20 final size:20
Alignment explanation
Indices: 72896--72947 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
72886 AAGAATCGCG
*
72896 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
72916 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
72936 TTGCGATTCTGG
1 TTGCGATTCTGG
72948 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:73248 original size:23 final size:24
Alignment explanation
Indices: 73215--73270 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
73205 CGTTAAAATG
* **
73215 ATAAACAAACACAAATGAACGAAT
1 ATAAACGAACACAAACAAACGAAT
73239 -TAAACGAACACAAACAAACGAAT
1 ATAAACGAACACAAACAAACGAAT
73262 ATAAACGAA
1 ATAAACGAA
73271 TGTAAACGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.62, C:0.18, G:0.09, T:0.11
Consensus pattern (24 bp):
ATAAACGAACACAAACAAACGAAT
Found at i:73267 original size:10 final size:10
Alignment explanation
Indices: 73254--73287 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
73244 GAACACAAAC
73254 AAACGAATAT
1 AAACGAATAT
*
73264 AAACGAATGT
1 AAACGAATAT
*
73274 AAACGAACAT
1 AAACGAATAT
73284 AAAC
1 AAAC
73288 AAACAACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.59, C:0.15, G:0.12, T:0.15
Consensus pattern (10 bp):
AAACGAATAT
Found at i:73299 original size:33 final size:32
Alignment explanation
Indices: 73215--73299 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
73205 CGTTAAAATG
*
73215 ATAAACAAACACAAATGAACGAATTAAACGAAC
1 ATAAACAAACA-AAATAAACGAATTAAACGAAC
* *
73248 ACAAACAAACGAATATAAACGAATGTAAACGAAC
1 ATAAACAAAC-AAAATAAACGAAT-TAAACGAAC
*
73282 ATAAACAAACAACATAAA
1 ATAAACAAACAAAATAAA
73300 ATTAATTGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
33 26 0.58
34 19 0.42
ACGTcount: A:0.62, C:0.18, G:0.08, T:0.12
Consensus pattern (32 bp):
ATAAACAAACAAAATAAACGAATTAAACGAAC
Found at i:73509 original size:14 final size:14
Alignment explanation
Indices: 73481--73519 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
73471 GAGATTAGTC
*
73481 CGAATATAAACGAA
1 CGAACATAAACGAA
* *
73495 CGATCATAAATGAA
1 CGAACATAAACGAA
73509 CGAACATAAAC
1 CGAACATAAAC
73520 ATACGGATTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.54, C:0.18, G:0.13, T:0.15
Consensus pattern (14 bp):
CGAACATAAACGAA
Found at i:78206 original size:14 final size:14
Alignment explanation
Indices: 78187--78217 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
78177 TTGAAGCTGA
78187 ACTCTCTTGGTGTT
1 ACTCTCTTGGTGTT
78201 ACTCTCTTGGTGTT
1 ACTCTCTTGGTGTT
78215 ACT
1 ACT
78218 AAACCCGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.10, C:0.23, G:0.19, T:0.48
Consensus pattern (14 bp):
ACTCTCTTGGTGTT
Found at i:81555 original size:248 final size:248
Alignment explanation
Indices: 81001--81690 Score: 1114
Period size: 249 Copynumber: 2.8 Consensus size: 248
80991 TGAGAAAATA
* * * *
81001 ATTTTCAAAGTTTCTCATTTAATCTTTTTTAGAAAATGAAATTCTTGAAAAGTAAGAAGTTTCTT
1 ATTTTCAAAGTTTCTCATTTAA--TGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAAGTTTCTT
* *
81066 ACCCAGTAAAGTATTTCCCACAAATTTGTAAATACTTCGGGTCATCTGTTAGTCTTTCGAGCATG
64 A-CCAGTAAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTATTAGTCTTTCGAGCATG
* * *
81131 ATGCTTAAAATCTTCGGGTCATCTGTCACTCTTTCGACCAAGATGATAAGTCCTTAGGGCCATCC
128 ATGCTTAAAACCTTCGGGTCATCTGTCAATCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCC
* *
81196 GTAAAGCCTTTGGGTATAATGTTCATATATGATTTTCGCATGAAAATGAGATAGCG
193 GTAAAGCCTTTGGGTAGAATGTTCACATATGATTTTCGCATGAAAATGAGATAGCG
*
81252 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAAGTTTATTAC
1 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAAGTTTCTTAC
* *
81317 TCAGTAAAATATTTCCCACAAATTTGTAAATCCTTCAGGTCATCTATTAGTCTTTCGAGCATGAT
66 -CAGTAAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTATTAGTCTTTCGAGCATGAT
* * *
81382 GCATAAAACCTTCAGGTCATCTGTCAATCTTTCGAGCAATATGATAAGTCCTTAGGG-CATCCGT
130 GCTTAAAACCTTCGGGTCATCTGTCAATCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGT
*
81446 AAAGCCTTTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCG
195 AAAGCCTTTGGGTAGAATGTTCACATATGATTTTCGCATGAAAATGAGATAGCG
81500 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAAGTTTCTTAC
1 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAAGTTTCTTAC
*
81565 CTAGTAAAGTATTT-CCACAAATTTGTAAATCCTTCGGGTCATCTATTACTCTTTCGAGCATGAT
66 C-AGTAAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTATTAGTCTTTCGAGCATGAT
* * * *
81629 GCTTAAAACCTTCGGGTTATCTGTCAGTCTTTCGAGCAAGATGATAAGTCTTTAGAGCCATC
130 GCTTAAAACCTTCGGGTCATCTGTCAATCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATC
81691 TATAAGACCT
Statistics
Matches: 407, Mismatches: 29, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
247 99 0.24
248 138 0.34
249 148 0.36
251 22 0.05
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (248 bp):
ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAGAAGTTTCTTAC
CAGTAAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTATTAGTCTTTCGAGCATGATG
CTTAAAACCTTCGGGTCATCTGTCAATCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTA
AAGCCTTTGGGTAGAATGTTCACATATGATTTTCGCATGAAAATGAGATAGCG
Found at i:81660 original size:42 final size:42
Alignment explanation
Indices: 81590--81671 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
81580 CACAAATTTG
* * *
81590 TAAATCCTTCGGGTCATCTATTACTCTTTCGAGCATGATGCT
1 TAAAACCTTCGGGTCATCTATCACTCTTTCGAGCAAGATGCT
* * *
81632 TAAAACCTTCGGGTTATCTGTCAGTCTTTCGAGCAAGATG
1 TAAAACCTTCGGGTCATCTATCACTCTTTCGAGCAAGATG
81672 ATAAGTCTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (42 bp):
TAAAACCTTCGGGTCATCTATCACTCTTTCGAGCAAGATGCT
Found at i:81880 original size:3 final size:3
Alignment explanation
Indices: 81859--81905 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
81849 CTAATTATAT
* *
81859 TTA TTA ATA TTA CTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
81906 CAAATATTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:89458 original size:20 final size:20
Alignment explanation
Indices: 89433--89477 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
89423 CTCCTGAACA
*
89433 AAATTCAAAGTCTGACCATT
1 AAATTCAAAATCTGACCATT
89453 AAATTCAAAATCTGACCATT
1 AAATTCAAAATCTGACCATT
89473 AAATT
1 AAATT
89478 TATCTAGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (20 bp):
AAATTCAAAATCTGACCATT
Found at i:91517 original size:27 final size:27
Alignment explanation
Indices: 91479--91537 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
91469 ATATCAGGGG
* * *
91479 CGGATCTCCATGGAGCCCGGGGTATCC
1 CGGACCTCCATGGAGCCCAGAGTATCC
91506 CGGACCTCCATGGAGCCCAGAGTATCC
1 CGGACCTCCATGGAGCCCAGAGTATCC
91533 CGGAC
1 CGGAC
91538 AACCCCTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.36, G:0.31, T:0.15
Consensus pattern (27 bp):
CGGACCTCCATGGAGCCCAGAGTATCC
Found at i:92600 original size:23 final size:22
Alignment explanation
Indices: 92556--92600 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
92546 AACAAATTGA
*
92556 TAGTTTGGGATGAAATTGAAAT
1 TAGTTTGGGATGAAATTAAAAT
* *
92578 TAGTTTGTGGATTAACTTAAAAT
1 TAGTTTG-GGATGAAATTAAAAT
92601 GAGGATCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.36, C:0.02, G:0.22, T:0.40
Consensus pattern (22 bp):
TAGTTTGGGATGAAATTAAAAT
Found at i:94239 original size:30 final size:31
Alignment explanation
Indices: 94183--94247 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
94173 CGCGTTAAAG
*
94183 TTTGATAAAAATTGTCAAGTTTAAGGGTTGA
1 TTTGATAAAAATTGTCAAGTTTAAGGGTTAA
94214 TTTGATAAAAA-TGTCAA-TTTGAAGGGTTAA
1 TTTGATAAAAATTGTCAAGTTT-AAGGGTTAA
94244 TTTG
1 TTTG
94248 TGCAATAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 3 0.09
30 18 0.56
31 11 0.34
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (31 bp):
TTTGATAAAAATTGTCAAGTTTAAGGGTTAA
Found at i:96530 original size:15 final size:16
Alignment explanation
Indices: 96501--96533 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
96491 TTCAATTCAA
96501 TTTTACTTTCTTTTAT
1 TTTTACTTTCTTTTAT
96517 TTTTACTTTC-TTTAT
1 TTTTACTTTCTTTTAT
96532 TT
1 TT
96534 GTAATCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTACTTTCTTTTAT
Found at i:97104 original size:38 final size:38
Alignment explanation
Indices: 97061--97136 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
97051 AGTCCCTTAG
97061 ACTTTCTACCAATCCCCATGATCATGCCATTGGATGAT
1 ACTTTCTACCAATCCCCATGATCATGCCATTGGATGAT
97099 ACTTTCTACCAATCCCCATGATCATGCCATTGGATGAT
1 ACTTTCTACCAATCCCCATGATCATGCCATTGGATGAT
97137 CTAATATGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (38 bp):
ACTTTCTACCAATCCCCATGATCATGCCATTGGATGAT
Found at i:99418 original size:15 final size:15
Alignment explanation
Indices: 99398--99434 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
99388 ATGATTCAAA
99398 GGCTCTGTATGAATT
1 GGCTCTGTATGAATT
99413 GGCTCTGTATGAATT
1 GGCTCTGTATGAATT
99428 GGCTCTG
1 GGCTCTG
99435 AATGTGACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.38
Consensus pattern (15 bp):
GGCTCTGTATGAATT
Found at i:104256 original size:2 final size:2
Alignment explanation
Indices: 104249--104277 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
104239 CAGTTAAAAC
104249 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 A
104278 ATACACAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:106239 original size:23 final size:24
Alignment explanation
Indices: 106206--106261 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
106196 TGTTAAAATG
* **
106206 ATAAACAAACACAAATGAACGAA-
1 ATAAACGAACACAAACAAACGAAT
*
106229 CTAAACGAACACAAACAAACGAAT
1 ATAAACGAACACAAACAAACGAAT
106253 ATAAACGAA
1 ATAAACGAA
106262 TGTAAACGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.62, C:0.20, G:0.09, T:0.09
Consensus pattern (24 bp):
ATAAACGAACACAAACAAACGAAT
Found at i:106258 original size:10 final size:10
Alignment explanation
Indices: 106245--106278 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
106235 GAACACAAAC
106245 AAACGAATAT
1 AAACGAATAT
*
106255 AAACGAATGT
1 AAACGAATAT
*
106265 AAACGAACAT
1 AAACGAATAT
106275 AAAC
1 AAAC
106279 AAACAAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.59, C:0.15, G:0.12, T:0.15
Consensus pattern (10 bp):
AAACGAATAT
Found at i:106501 original size:14 final size:14
Alignment explanation
Indices: 106473--106511 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
106463 GAGATTAGTC
*
106473 CGAATATAAACGAA
1 CGAACATAAACGAA
* *
106487 CGATCATAAATGAA
1 CGAACATAAACGAA
106501 CGAACATAAAC
1 CGAACATAAAC
106512 ATACGGATTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.54, C:0.18, G:0.13, T:0.15
Consensus pattern (14 bp):
CGAACATAAACGAA
Found at i:107131 original size:13 final size:13
Alignment explanation
Indices: 107113--107150 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
107103 ATTTGACCGA
*
107113 AACCGATTACTTG
1 AACCGATTACCTG
107126 AACCGATTTACCTG
1 AACCGA-TTACCTG
107140 AACCGA-TACCT
1 AACCGATTACCT
107151 AAAATAGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 5 0.22
13 6 0.26
14 12 0.52
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (13 bp):
AACCGATTACCTG
Found at i:107141 original size:14 final size:14
Alignment explanation
Indices: 107113--107146 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
107103 ATTTGACCGA
*
107113 AACCGA-TTACTTG
1 AACCGATTTACCTG
107126 AACCGATTTACCTG
1 AACCGATTTACCTG
107140 AACCGAT
1 AACCGAT
107147 ACCTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (14 bp):
AACCGATTTACCTG
Found at i:114638 original size:11 final size:10
Alignment explanation
Indices: 114601--114634 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
114591 AATAATATAT
114601 ATATATATTTA
1 ATATA-ATTTA
114612 ATATTAATTTA
1 ATA-TAATTTA
114623 ATATAATTTA
1 ATATAATTTA
114633 AT
1 AT
114635 TATATTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.41
11 11 0.50
12 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATATAATTTA
Found at i:114687 original size:29 final size:30
Alignment explanation
Indices: 114644--114707 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
114634 TTATATTATA
* * *
114644 ATAATATTCTTATTTTAATAATTAA-TAAT
1 ATAATAATCTCATTTTAATAAATAATTAAT
*
114673 TTAATAATCTCATTTTAATAAATAATTAAT
1 ATAATAATCTCATTTTAATAAATAATTAAT
114703 ATAAT
1 ATAAT
114708 TTTTAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (30 bp):
ATAATAATCTCATTTTAATAAATAATTAAT
Found at i:114860 original size:25 final size:23
Alignment explanation
Indices: 114820--114876 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
114810 ATAAATTATT
114820 TTAATATTTTAAAAATAATAATA
1 TTAATATTTTAAAAATAATAATA
* *
114843 TTAATCTTTCTAATAAATAATATTA
1 TTAATATTT-TAA-AAATAATAATA
114868 TT--TATTTTA
1 TTAATATTTTA
114877 TTCAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.07
23 12 0.41
24 3 0.10
25 12 0.41
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAATATTTTAAAAATAATAATA
Found at i:115191 original size:2 final size:2
Alignment explanation
Indices: 115184--115211 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
115174 GACTAATTCA
115184 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
115212 TTAAATATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118980 original size:22 final size:22
Alignment explanation
Indices: 118955--118999 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
118945 TCCTCATATC
118955 CATGTCCGATATGTGTAGGGCA
1 CATGTCCGATATGTGTAGGGCA
118977 CATGTCCGATATGTGTAGGGCA
1 CATGTCCGATATGTGTAGGGCA
118999 C
1 C
119000 GGGTTGCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (22 bp):
CATGTCCGATATGTGTAGGGCA
Done.