Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003556.1 Hibiscus syriacus cultivar Beakdansim tig00007505_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: 64836
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:391 original size:5 final size:5
Alignment explanation
Indices: 383--409 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
373 GGTTTGGTCT
383 GACCC GACCC GACCC GACCC GACCC GA
1 GACCC GACCC GACCC GACCC GACCC GA
410 TGTCCCAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.56, G:0.22, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:4823 original size:21 final size:22
Alignment explanation
Indices: 4799--4849 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
4789 GGTTCATGTA
4799 TTGAGATATTTTCA-AATTCTT
1 TTGAGATATTTTCATAATTCTT
* * *
4820 TTGA-ACATTTTGATGATTCTT
1 TTGAGATATTTTCATAATTCTT
*
4841 TTGGGATAT
1 TTGAGATAT
4850 GATATTTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 7 0.30
21 13 0.57
22 3 0.13
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (22 bp):
TTGAGATATTTTCATAATTCTT
Found at i:7994 original size:22 final size:22
Alignment explanation
Indices: 7966--8011 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
7956 TATAAAAAAT
*
7966 AAAAAT-ATTTTTATAAATTTTA
1 AAAAATAAATTTTAT-AATTTTA
*
7988 AAAAATAAATTTTATATTTTTA
1 AAAAATAAATTTTATAATTTTA
8010 AA
1 AA
8012 TAATTGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAAATAAATTTTATAATTTTA
Found at i:8114 original size:21 final size:22
Alignment explanation
Indices: 8074--8114 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
8064 TTTATTTTAT
* *
8074 AAAAATTAAAAATATTTAATAC
1 AAAAATAAAAAATATATAATAC
8096 AAAAATAAAAAATA-ATAAT
1 AAAAATAAAAAATATATAAT
8115 TTTTAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAATAAAAAATATATAATAC
Found at i:8128 original size:28 final size:28
Alignment explanation
Indices: 8072--8127 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
8062 CTTTTATTTT
*
8072 ATAAAAATTAAAAATATTTAATACAAAA
1 ATAAAAAATAAAAATATTTAATACAAAA
* *
8100 ATAAAAAATAATAATTTTTAA-ACAAAA
1 ATAAAAAATAAAAATATTTAATACAAAA
8127 A
1 A
8128 AATGGAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (28 bp):
ATAAAAAATAAAAATATTTAATACAAAA
Found at i:9736 original size:17 final size:17
Alignment explanation
Indices: 9714--9749 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
9704 AGAGTAATGC
*
9714 CCAGAGTTGTTCGAAAG
1 CCAGAGTTGTTCAAAAG
9731 CCAGAGTTGTTCAAAAG
1 CCAGAGTTGTTCAAAAG
9748 CC
1 CC
9750 GGAGCTGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (17 bp):
CCAGAGTTGTTCAAAAG
Found at i:13825 original size:19 final size:19
Alignment explanation
Indices: 13787--13825 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
13777 TCATCTATTT
* * *
13787 AATTAAATTTAATTAGATA
1 AATTAAAATTAATAAAATA
13806 AATTAAAATTAATAAAATA
1 AATTAAAATTAATAAAATA
13825 A
1 A
13826 GCTTCCTCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AATTAAAATTAATAAAATA
Found at i:14519 original size:31 final size:32
Alignment explanation
Indices: 14484--14554 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 32
14474 ACTCTACAAT
*
14484 TTATAAAATAATCGTTAAA-TTTCTTAAATAA
1 TTATAAAATAATCGTTAAATTTTATTAAATAA
* *
14515 TTAT-AAATTATCGTTAAATTTTATTAAATTA
1 TTATAAAATAATCGTTAAATTTTATTAAATAA
*
14546 TTACAAAAT
1 TTATAAAAT
14555 TATCAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.38
31 17 0.50
32 4 0.12
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (32 bp):
TTATAAAATAATCGTTAAATTTTATTAAATAA
Found at i:14531 original size:21 final size:20
Alignment explanation
Indices: 14498--14546 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
14488 AAAATAATCG
14498 TTAAATT-TCTTAAATAATTA
1 TTAAATTATCTTAAAT-ATTA
*
14518 -TAAATTATCGTTAAATTTTA
1 TTAAATTATC-TTAAATATTA
14538 TTAAATTAT
1 TTAAATTAT
14547 TACAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.24
20 5 0.20
21 14 0.56
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (20 bp):
TTAAATTATCTTAAATATTA
Found at i:14569 original size:31 final size:31
Alignment explanation
Indices: 14499--14585 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
14489 AAATAATCGT
* * * **
14499 TAAATTTCTTAAATAATTA-TAAATTATCGT
1 TAAATTTATTAAATTATTACAAAATTATCAA
14529 TAAATTTTATTAAATTATTACAAAATTATCAA
1 TAAA-TTTATTAAATTATTACAAAATTATCAA
* *
14561 TAAATTTATTGAATTGTTACAAAAT
1 TAAATTTATTAAATTATTACAAAAT
14586 AACAATTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 4 0.08
31 32 0.67
32 12 0.25
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (31 bp):
TAAATTTATTAAATTATTACAAAATTATCAA
Found at i:14601 original size:31 final size:31
Alignment explanation
Indices: 14535--14615 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
14525 TCGTTAAATT
* * *
14535 TTATTAAATTATTACAAAATTATCAATAAAT
1 TTATTGAATTATTACAAAATTAACAATAAAC
*
14566 TTATTGAATTGTTACAAAA-TAACAATTAAAC
1 TTATTGAATTATTACAAAATTAACAA-TAAAC
* *
14597 TTATTGAGTTATTGCAAAA
1 TTATTGAATTATTACAAAA
14616 ATGATCTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 5 0.12
31 37 0.88
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (31 bp):
TTATTGAATTATTACAAAATTAACAATAAAC
Found at i:15940 original size:22 final size:22
Alignment explanation
Indices: 15915--15961 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
15905 CTCCCCCCTC
15915 CACCCTATAAACCCTCCATCTA
1 CACCCTATAAACCCTCCATCTA
15937 CACCCTATAAACCCTCCATCTA
1 CACCCTATAAACCCTCCATCTA
15959 CAC
1 CAC
15962 GATCGCTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (22 bp):
CACCCTATAAACCCTCCATCTA
Found at i:19628 original size:19 final size:19
Alignment explanation
Indices: 19604--19653 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
19594 ATCAACTAAA
* *
19604 TCGCAATGCGATTTATAAT
1 TCGCAACGCGATTGATAAT
19623 TCGCAACGCGATTGATAAT
1 TCGCAACGCGATTGATAAT
19642 TCGCAACGCGAT
1 TCGCAACGCGAT
19654 CTCCGGTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (19 bp):
TCGCAACGCGATTGATAAT
Found at i:19715 original size:21 final size:21
Alignment explanation
Indices: 19686--19839 Score: 172
Period size: 21 Copynumber: 7.4 Consensus size: 21
19676 CCAGATTCGT
19686 AATGCGAACTTCGACTATCGC
1 AATGCGAACTTCGACTATCGC
* *
19707 AATGAGAACTTAGACTATCGC
1 AATGCGAACTTCGACTATCGC
* *
19728 AATACGAA-TAT-GTA-AATCGC
1 AATGCGAACT-TCG-ACTATCGC
*
19748 AATGCGATA-GTCGACTATCGC
1 AATGCGA-ACTTCGACTATCGC
*
19769 AATGCGAACTTCGACTATTGC
1 AATGCGAACTTCGACTATCGC
*
19790 AATGCGAACTTCAACTATCGC
1 AATGCGAACTTCGACTATCGC
*
19811 AATGCGAACTTGGACTATCGC
1 AATGCGAACTTCGACTATCGC
*
19832 ATTGCGAA
1 AATGCGAA
19840 TATGTAAATC
Statistics
Matches: 112, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
20 16 0.14
21 96 0.86
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (21 bp):
AATGCGAACTTCGACTATCGC
Found at i:19851 original size:83 final size:82
Alignment explanation
Indices: 19686--19858 Score: 201
Period size: 83 Copynumber: 2.1 Consensus size: 82
19676 CCAGATTCGT
*
19686 AATGCGAACTTCGACTATCGCAATGAGAACTTAGACTATCGCAATACGAATATGTAAATCGCAAT
1 AATGCGAACTTCGACTATCGCAATGAGAACTTAGACTATCGCAATACGAATATGGAAATCGCAAT
*
19751 GCGATAGTCGACTATCGC
66 GCGATAGTC-ACAATCGC
* * * *
19769 AATGCGAACTTCGACTATTGCAATGCGAACTTCA-ACTATCGCAATGCGAACT-TGGACTATCGC
1 AATGCGAACTTCGACTATCGCAATGAGAACTT-AGACTATCGCAATACGAA-TATGGA-AATCGC
*
19832 ATTGCGAATATGT-A-AATCGC
63 AATGCG-ATA-GTCACAATCGC
19852 AATGCGA
1 AATGCGA
19859 TAGTCAAAGT
Statistics
Matches: 78, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
83 60 0.77
84 13 0.17
85 3 0.04
86 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (82 bp):
AATGCGAACTTCGACTATCGCAATGAGAACTTAGACTATCGCAATACGAATATGGAAATCGCAAT
GCGATAGTCACAATCGC
Found at i:19878 original size:21 final size:21
Alignment explanation
Indices: 19854--19922 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
19844 TAAATCGCAA
*
19854 TGCGATAGTCAAAGTTCGCGT
1 TGCGATAATCAAAGTTCGCGT
*
19875 TGCGATAATCCAAGTTCGCGT
1 TGCGATAATCAAAGTTCGCGT
*
19896 TGCGATAATCTAAGTTCGCGT
1 TGCGATAATCAAAGTTCGCGT
19917 TGCGAT
1 TGCGAT
19923 TTATTCCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (21 bp):
TGCGATAATCAAAGTTCGCGT
Found at i:19901 original size:42 final size:41
Alignment explanation
Indices: 19854--19947 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 41
19844 TAAATCGCAA
*
19854 TGCGATAGTCAAAGTTCGCGTTGCGA-TAATCCAAGTTCGCGT
1 TGCGATAGTCAAAGTTCGCGTTGCGATTAATCCAAATT--CGT
* * *
19896 TGCGATAATCTAAGTTCGCGTTGCGATTTATTCCAAATTCGT
1 TGCGATAGTCAAAGTTCGCGTTGCGA-TTAATCCAAATTCGT
19938 TGCGATAGTC
1 TGCGATAGTC
19948 CAAAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
42 36 0.80
44 9 0.20
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (41 bp):
TGCGATAGTCAAAGTTCGCGTTGCGATTAATCCAAATTCGT
Found at i:20784 original size:21 final size:21
Alignment explanation
Indices: 20758--20804 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
20748 TAAATCACAA
*
20758 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCAAAGTTCGCAT
*
20779 TGCGATAGTCAAAGTTCGCGT
1 TGCGATAGTCAAAGTTCGCAT
20800 TGCGA
1 TGCGA
20805 ATCTGAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCAAAGTTCGCAT
Found at i:28216 original size:17 final size:17
Alignment explanation
Indices: 28189--28237 Score: 89
Period size: 17 Copynumber: 2.8 Consensus size: 17
28179 GATTTTCTTC
28189 AAATAATTTTCAAACGAA
1 AAAT-ATTTTCAAACGAA
28207 AAATATTTTCAAACGAA
1 AAATATTTTCAAACGAA
28224 AAATATTTTCAAAC
1 AAATATTTTCAAAC
28238 AAGATAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 27 0.87
18 4 0.13
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.31
Consensus pattern (17 bp):
AAATATTTTCAAACGAA
Found at i:29017 original size:117 final size:115
Alignment explanation
Indices: 28744--29045 Score: 311
Period size: 117 Copynumber: 2.6 Consensus size: 115
28734 AATGGAATGG
* * *
28744 TTCATAATGAGAAGAACTCATCTGATGAGGGAGAATAAGTTCCTAGTGAGAAGAACTTGTTTAAA
1 TTCATAATGAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCCTAATGAGAAGAACTTGTTCAAA
** * * ** *
28809 CTTGTCTTGTCCATCACAAAAGAATGAAGATCAACATTTTGAATGAAAGAG
66 CTTGT-TCATCCATCAAAAAAGAATGAAGATCAACATCTCCAATGAAAGAA
* * * * *
28860 TTCATAATGAGAATAAATCATCCGATGATGGCA-AAAAAGTTCATAATGAGAAGAACTTGTTCAA
1 TTCATAATGAGAAGAACTCATCTGATGA-GGGAGAAAAAGTTCCTAATGAGAAGAACTTGTTCAA
* ** *
28924 CCTTAGTTCATCCATCATAAAAAGAATGTGGATCAACATCTCCACT-AGAAGAA
65 ACTT-GTTCATCCATCA-AAAAAGAATGAAGATCAACATCTCCAATGA-AAGAA
* * * * * * *
28977 TTCATAATGAGAAGAACTCGTCTGGTGGGGGAGAAGAAGTTCCTAATGAAAATAACTTGTTCAAT
1 TTCATAATGAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCCTAATGAGAAGAACTTGTTCAAA
29042 CTTG
66 CTTG
29046 GTTCCTTCAT
Statistics
Matches: 150, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
116 68 0.45
117 82 0.55
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (115 bp):
TTCATAATGAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCCTAATGAGAAGAACTTGTTCAAA
CTTGTTCATCCATCAAAAAAGAATGAAGATCAACATCTCCAATGAAAGAA
Found at i:29313 original size:37 final size:36
Alignment explanation
Indices: 29181--29312 Score: 150
Period size: 37 Copynumber: 3.8 Consensus size: 36
29171 ACAAATCATA
* *
29181 TCTCACTTAAGATTG-TTTTCTTAAAACAAAGTTCG
1 TCTCACTTAAGATTGTTTTTCTTAAAACTAATTTCG
* *
29216 TATCACTT--GATAT-TTTTTCCTAAAA-TGAATTTCG
1 TCTCACTTAAGAT-TGTTTTTCTTAAAACT-AATTTCG
29250 T-TCACTTAAGATTGTTTTTCTTAAAAACTAATTTCG
1 TCTCACTTAAGATTGTTTTTCTT-AAAACTAATTTCG
*
29286 TCTCACTTGAGATTGTTTTTCTTAAAA
1 TCTCACTTAAGATTGTTTTTCTTAAAA
29313 AAATCGTCTC
Statistics
Matches: 82, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
33 9 0.11
34 19 0.23
35 17 0.21
36 16 0.20
37 21 0.26
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (36 bp):
TCTCACTTAAGATTGTTTTTCTTAAAACTAATTTCG
Found at i:29330 original size:70 final size:67
Alignment explanation
Indices: 29183--29330 Score: 147
Period size: 70 Copynumber: 2.1 Consensus size: 67
29173 AAATCATATC
* * *
29183 TCACTTAAGATTGTTTTCTTAAAACAAAGTTCGTATCACTTGATATTTTTTCCTAAAATGAATTT
1 TCACATAAGATTGTTTTCTTAAAACAAAGTTCGTATCACTTGAGATTTTTTCCTAAAA-GAATAT
29248 CGT
65 CGT
* * * * *
29251 TCACTTAAGATTGTTTTTCTTAAAAACTAATTTCGTCTCACTTGAGATTGTTTTTCTTAAAA-AA
1 TCACATAAGATTG-TTTTCTT-AAAACAAAGTTCGTATCACTTGAGA-T-TTTTTCCTAAAAGAA
29315 -ATCGT
62 TATCGT
*
29320 CTCGCATAAGA
1 -TCACATAAGA
29331 CAATTTCCTT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
68 13 0.19
69 11 0.16
70 31 0.46
71 1 0.01
72 11 0.16
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.43
Consensus pattern (67 bp):
TCACATAAGATTGTTTTCTTAAAACAAAGTTCGTATCACTTGAGATTTTTTCCTAAAAGAATATC
GT
Found at i:30580 original size:37 final size:41
Alignment explanation
Indices: 30489--30580 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
30479 TCATATTCCC
*
30489 ATAAAAAGAGACATTCTAATATGGGTAAATTATTGTGGACTTA
1 ATAAAAAGAGACATTATAATATGGGTAAATTATTGTGGA--TA
*
30532 AT-AAAAGAGACATTATAATATGGGTAAGTTA-T-T-GA-A
1 ATAAAAAGAGACATTATAATATGGGTAAATTATTGTGGATA
30568 ATAAAAAGAGACA
1 ATAAAAAGAGACA
30581 AAGGGGATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
36 3 0.07
37 10 0.22
39 2 0.04
40 1 0.02
41 1 0.02
42 27 0.59
43 2 0.04
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.28
Consensus pattern (41 bp):
ATAAAAAGAGACATTATAATATGGGTAAATTATTGTGGATA
Found at i:39595 original size:20 final size:20
Alignment explanation
Indices: 39553--39595 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
39543 TAGTCAGTAG
* *
39553 GTATCGATACCTAGAGGTTA
1 GTATCGATACCCAGAGGTCA
*
39573 GTATCGATACCCAGGGGTCA
1 GTATCGATACCCAGAGGTCA
39593 GTA
1 GTA
39596 CCAATACTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
GTATCGATACCCAGAGGTCA
Found at i:48636 original size:18 final size:18
Alignment explanation
Indices: 48613--48649 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
48603 TTCAGCGGCT
*
48613 GATGTGGTAGGTGACGTG
1 GATGTGGCAGGTGACGTG
*
48631 GATGTGGCAGGTGGCGTG
1 GATGTGGCAGGTGACGTG
48649 G
1 G
48650 CACCCTGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.08, G:0.54, T:0.24
Consensus pattern (18 bp):
GATGTGGCAGGTGACGTG
Found at i:48931 original size:19 final size:18
Alignment explanation
Indices: 48907--48948 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
48897 AGTTTTCTTC
48907 TTTTATATTCTTTTCTAGT
1 TTTTATATT-TTTTCTAGT
48926 TTTTATATTTTTTCTAGT
1 TTTTATATTTTTTCTAGT
48944 TTTTA
1 TTTTA
48949 CTTTCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTTATATTTTTTCTAGT
Found at i:54627 original size:42 final size:42
Alignment explanation
Indices: 54560--54768 Score: 339
Period size: 42 Copynumber: 5.0 Consensus size: 42
54550 TCTAGAGCCC
* *
54560 TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCATTT
1 TCTTCAGCAAATAAAGTATTCTGTTGATTGTCATCTCCATTT
*
54602 TCTTCAGCAAATAAAGCATTCTGTTGATTGTCATCTCCATTT
1 TCTTCAGCAAATAAAGTATTCTGTTGATTGTCATCTCCATTT
* *
54644 TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCA-TT
1 TCTTCAGCAAATAAAGTATTCTGTTGATTGTCATCTCCATTT
*
54685 TCTTCAGCAAATAAAGCATTCTGTTGATTGTCATCTCCATTT
1 TCTTCAGCAAATAAAGTATTCTGTTGATTGTCATCTCCATTT
* *
54727 TCTTCAGCAAATAATGTATTCTGTTGATTGTCATCTTCATTT
1 TCTTCAGCAAATAAAGTATTCTGTTGATTGTCATCTCCATTT
54769 GAGTTGGTTG
Statistics
Matches: 154, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
41 38 0.25
42 116 0.75
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.43
Consensus pattern (42 bp):
TCTTCAGCAAATAAAGTATTCTGTTGATTGTCATCTCCATTT
Found at i:54724 original size:83 final size:83
Alignment explanation
Indices: 54560--54768 Score: 373
Period size: 83 Copynumber: 2.5 Consensus size: 83
54550 TCTAGAGCCC
54560 TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCATTTTCTTCAGCAAATAAAGCATTCTG
1 TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCA-TTTCTTCAGCAAATAAAGCATTCTG
54625 TTGATTGTCATCTCCATTT
65 TTGATTGTCATCTCCATTT
54644 TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCATTTCTTCAGCAAATAAAGCATTCTGT
1 TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCATTTCTTCAGCAAATAAAGCATTCTGT
54709 TGATTGTCATCTCCATTT
66 TGATTGTCATCTCCATTT
* * * *
54727 TCTTCAGCAAATAATGTATTCTGTTGATTGTCATCTTCATTT
1 TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCATTT
54769 GAGTTGGTTG
Statistics
Matches: 121, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 82 0.68
84 39 0.32
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.43
Consensus pattern (83 bp):
TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCATTTCTTCAGCAAATAAAGCATTCTGT
TGATTGTCATCTCCATTT
Found at i:57213 original size:20 final size:19
Alignment explanation
Indices: 57190--57235 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
57180 CGATATACCA
57190 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
57210 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
57230 GGTAAA
1 GGTAAA
57236 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:57381 original size:20 final size:19
Alignment explanation
Indices: 57358--57404 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
57348 CGATATAACA
57358 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
57378 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
57398 GGTAAAA
1 GGTAAAA
57405 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:57406 original size:17 final size:19
Alignment explanation
Indices: 57367--57409 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
57357 AGGTAAAAAT
57367 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
57387 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
57404 ATGATA
1 ATGATA
57410 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:59753 original size:31 final size:33
Alignment explanation
Indices: 59718--59781 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 33
59708 AAATAGATGG
*
59718 AGTGGTGAAAGAAG-T-AGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
*
59749 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
59782 TATTAAGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 14 0.48
32 1 0.03
33 14 0.48
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
Found at i:61590 original size:19 final size:18
Alignment explanation
Indices: 61568--61623 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
61558 GTAGGGTTAA
61568 TTTGTATAAGATTTATAAT
1 TTTGTATAAGA-TTATAAT
* *
61587 TTTGTATACGATTATATT
1 TTTGTATAAGATTATAAT
* *
61605 TTTGTATATGAATATAAT
1 TTTGTATAAGATTATAAT
61623 T
1 T
61624 ATGAATGAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 22 0.69
19 10 0.31
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTGTATAAGATTATAAT
Found at i:62677 original size:198 final size:199
Alignment explanation
Indices: 61729--62880 Score: 2110
Period size: 197 Copynumber: 5.9 Consensus size: 199
61719 ACAATATGCC
61729 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
61794 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
61859 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
61924 GGAA
196 GGAA
61928 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
61993 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAA-CGGTACATTTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
62057 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
62121 GGAA
196 GGAA
62125 AACAGGGTGCA-CC--AAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
62186 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTTATGAGA
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTTATGAGA
62249 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
62314 TGG-A
195 TGGAA
62318 AACAGGGTGCACCCAT-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
62382 CAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAA-TATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
62445 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
62510 GGAA
196 GGAA
62514 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
62579 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAA-TATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
62643 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
62707 GGAA
196 GGAA
*
62711 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAATTGTCGATCCCAAAATCATCG-ACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
62775 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
62840 AATATGTCT--A-AATGTGTCG--ACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
62881 CTAATTTAAA
Statistics
Matches: 934, Mismatches: 6, Indels: 33
0.96 0.01 0.03
Matches are distributed among these distances:
192 59 0.06
193 95 0.10
194 66 0.07
195 116 0.12
196 105 0.11
197 233 0.25
198 159 0.17
199 101 0.11
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (199 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAA
Found at i:64362 original size:3 final size:3
Alignment explanation
Indices: 64343--64395 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
64333 GAAGCTGACA
* * *
64343 ATG AAG ATG ACG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AAG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
64391 ATG AT
1 ATG AT
64396 CAACAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.38, C:0.02, G:0.32, T:0.28
Consensus pattern (3 bp):
ATG
Done.