Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004319.1 Hibiscus syriacus cultivar Beakdansim tig00009470_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: 65315
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4112 original size:2 final size:2
Alignment explanation
Indices: 4093--4186 Score: 138
Period size: 2 Copynumber: 48.0 Consensus size: 2
4083 ATTTGATCTA
* *
4093 AT AT AA AT AT AA AT AT AT AT AT AT AT A- 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
* *
4134 A- AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AG 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
4175 AT AT AT AT AT AT
1 AT AT AT AT AT AT
4187 TAGGATTTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
1 2 0.02
2 80 0.98
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5996 original size:19 final size:20
Alignment explanation
Indices: 5960--5997 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5950 TACACCCCTA
*
5960 AAAAAGAGAAAGGGAAAGGG
1 AAAAAGAGAAAGCGAAAGGG
*
5980 AAAAAGA-AAAGCTAAAGG
1 AAAAAGAGAAAGCGAAAGG
5998 AGGGAAATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.63, C:0.03, G:0.32, T:0.03
Consensus pattern (20 bp):
AAAAAGAGAAAGCGAAAGGG
Found at i:12243 original size:20 final size:20
Alignment explanation
Indices: 12218--12255 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12208 CTGATACTGT
12218 ACCCTTCAGTATCGATACTA
1 ACCCTTCAGTATCGATACTA
**
12238 ACCCTTTGGTATCGATAC
1 ACCCTTCAGTATCGATAC
12256 CCCTTACCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (20 bp):
ACCCTTCAGTATCGATACTA
Found at i:13297 original size:21 final size:21
Alignment explanation
Indices: 13271--13325 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
13261 CGGAAAATTA
13271 CCCCCAACGACTCTATTCACT
1 CCCCCAACGACTCTATTCACT
13292 CCCCCAACGACTCTATTCACT
1 CCCCCAACGACTCTATTCACT
* *
13313 CCCACAACAACTC
1 CCCCCAACGACTC
13326 AAACGGTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.27, C:0.49, G:0.04, T:0.20
Consensus pattern (21 bp):
CCCCCAACGACTCTATTCACT
Found at i:20469 original size:21 final size:21
Alignment explanation
Indices: 20436--20485 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 21
20426 AATCCATCCA
20436 TAATAAGTAAGATAAAACATAC
1 TAATAA-TAAGATAAAACATAC
20458 TAATAATAAGATAAAACATAC
1 TAATAATAAGATAAAACATAC
20479 TAATAAT
1 TAATAAT
20486 GTGAGTTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.26
Consensus pattern (21 bp):
TAATAATAAGATAAAACATAC
Found at i:37658 original size:30 final size:29
Alignment explanation
Indices: 37606--37663 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
37596 TTATTTTATT
*
37606 ATTATTAAATTTATAAAAATTATTAAATA
1 ATTATTAAATTTATAAAAATTATAAAATA
* **
37635 ATTATTAAAATTTTTAATGATTATAAAAT
1 ATTATT-AAATTTATAAAAATTATAAAAT
37664 GGTAATCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
ATTATTAAATTTATAAAAATTATAAAATA
Found at i:39171 original size:15 final size:15
Alignment explanation
Indices: 39151--39190 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
39141 CTATAACAAG
39151 ATAGCACAACTTGTT
1 ATAGCACAACTTGTT
39166 ATAGCACAACTTGTT
1 ATAGCACAACTTGTT
*
39181 GTAGCA-AACT
1 ATAGCACAACT
39191 CTCAAGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (15 bp):
ATAGCACAACTTGTT
Found at i:45684 original size:20 final size:20
Alignment explanation
Indices: 45659--45751 Score: 89
Period size: 20 Copynumber: 4.6 Consensus size: 20
45649 GCAACAAAAT
*
45659 CGCAACACGATTCTGACTAA
1 CGCAACGCGATTCTGACTAA
*
45679 CGCAACGCGATTCTGACTAT
1 CGCAACGCGATTCTGACTAA
** *
45699 CGCAACGCGATAAT-ACAAAA
1 CGCAACGCGATTCTGAC-TAA
* *
45719 TCGCAACGCAATTCTGACTAT
1 -CGCAACGCGATTCTGACTAA
*
45740 CGCAATGCGATT
1 CGCAACGCGATT
45752 TTCCAAATTT
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.04
20 41 0.72
21 12 0.21
22 2 0.04
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (20 bp):
CGCAACGCGATTCTGACTAA
Found at i:46224 original size:19 final size:20
Alignment explanation
Indices: 46199--46289 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
46189 CTTATTTTGG
46199 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
46219 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
46239 ACGTTTTTCAAACTTTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
46263 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
46282 ATTTTTCA
1 ATTTTTCA
46290 AAATCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 30 0.50
20 7 0.12
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.36
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:46261 original size:44 final size:41
Alignment explanation
Indices: 46210--46291 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
46200 TTTTTCACTA
* *
46210 TCGCAACACTTTTTCACTATCGCAACAACACGTTTTTCAAACTT
1 TCGCAACACATTTTAACTATCGCAAC-ACA--TTTTTCAAACTT
46254 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
46292 ATCGCGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 3 0.08
44 24 0.67
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTT
Found at i:52700 original size:20 final size:20
Alignment explanation
Indices: 52675--52720 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
52665 TATCTTTTGG
52675 TTGTTTAC-GACTTTTTGCCA
1 TTGTTTACAG-CTTTTTGCCA
* *
52695 TTGTTTACAGTTTTTTGCCG
1 TTGTTTACAGCTTTTTGCCA
52715 TTGTTT
1 TTGTTT
52721 TTGTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.11, C:0.15, G:0.17, T:0.57
Consensus pattern (20 bp):
TTGTTTACAGCTTTTTGCCA
Found at i:57131 original size:131 final size:131
Alignment explanation
Indices: 56944--57258 Score: 319
Period size: 131 Copynumber: 2.4 Consensus size: 131
56934 TGTTCCACAA
** * ** * *
56944 CTCTTCAG-GTAAGATCAAATCTGAAAAAAGGGATATGCTCTGCTATTTTTTGGGGTATATCAGA
1 CTCTTCAGAG-AAGATCAAATCTGAAAAAAGGGATATGCTCCACTACTTTTCAGGGTAGATCAAA
* * * ** * **
57008 TCTAGAAACGTTGATTCAATTCAATGCTCTTCAGGGAAGATTTAATCGAGGTAT-ATTTGCTTCA
65 TATAGAAACATTAATTCAATTCAACACTCTTCAGGGAAGATTGAATAAAGGT-TGATTTGCTTCA
57072 CTG
129 CTG
* * * * *
57075 TTCTTTAGAGAATATCAAATCTGGAAAAAGGGATATGCTCCACTGCTTTTCAGGGTAGATCAAAT
1 CTCTTCAGAGAAGATCAAATCTGAAAAAAGGGATATGCTCCACTACTTTTCAGGGTAGATCAAAT
* * * * *
57140 ATGGAAACATTAATTCACTTCACCACTCTTTAGGGAAGATTGAATAAAGGTTGGTTTGCTTCACT
66 ATAGAAACATTAATTCAATTCAACACTCTTCAGGGAAGATTGAATAAAGGTTGATTTGCTTCACT
57205 G
131 G
* * * * * *
57206 CTCTTCAGAGAAGATCAAATTTGAAAAAATGGATCTACTCCGCTACTCTTCAG
1 CTCTTCAGAGAAGATCAAATCTGAAAAAAGGGATATGCTCCACTACTTTTCAG
57259 AAAGGAAAAA
Statistics
Matches: 146, Mismatches: 36, Indels: 4
0.78 0.19 0.02
Matches are distributed among these distances:
130 1 0.01
131 144 0.99
132 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (131 bp):
CTCTTCAGAGAAGATCAAATCTGAAAAAAGGGATATGCTCCACTACTTTTCAGGGTAGATCAAAT
ATAGAAACATTAATTCAATTCAACACTCTTCAGGGAAGATTGAATAAAGGTTGATTTGCTTCACT
G
Found at i:57671 original size:45 final size:45
Alignment explanation
Indices: 57597--58163 Score: 644
Period size: 45 Copynumber: 12.7 Consensus size: 45
57587 AAATATCATT
* * * * * *
57597 ACTAAAAGGTTGACTTCTTTTCCCCAGAAAGTCAAGAATGACATC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * * *
57642 ACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATAACATC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * * *
57687 ACTAAAAGTTTGACTCCTCTTCATGAGAAATTCAAGAAAGACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
57732 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * * * *
57777 ACTGAAAGATTGACTCCTCGTCATGA-AAATTCAAGAAGGACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * *
57821 ACTAAAAGATTGACTCATCTTCATGAGAAAGTCAAGAATGACATC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * ** * *
57866 ACT-AAAGAATTAACTCTTCTTCGTGATAAA-TAAAGAATGACAAC
1 ACTAAAAG-ATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * *
57910 ACTAAAAGATTGACTCCTCTCCACAAGAAAATCAAGAATGACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * * *
57955 ATTGAAAGATTGACTCCCCTTCACGAGAAAGTCAAGAATGAAAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * *
58000 TCTAAAAGATTGAATCCTCTTCAC--GAAAGTCAAGAATGAAAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * * * *
58043 ACTTAAAGGTTAACTCCTCTTCACAAGAAAGTC-ATAATGACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* *
58087 ACTAAAAGATTGACTCCCCTTCACGAGAAAGTCAAGGATGACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* *
58132 ACTAAAAGATT-AGCTCATCTTCATGAGAAAGT
1 ACTAAAAGATTGA-CTCCTCTTCACGAGAAAGT
58164 TAAGTTGAGG
Statistics
Matches: 444, Mismatches: 70, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
43 38 0.09
44 111 0.25
45 295 0.66
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (45 bp):
ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
Found at i:57843 original size:89 final size:90
Alignment explanation
Indices: 57622--58163 Score: 657
Period size: 89 Copynumber: 6.1 Consensus size: 90
57612 TCTTTTCCCC
* * * * *
57622 AGAAAGTCAAGAATGACATCACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAATAACATC
1 AGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
*
57687 ACTAAAAGTTTGACTCCTCTTCATG
66 ACTAAAAGATTGACTCCTCTTCATG
* *
57712 AGAAATTCAAGAAAGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
1 AGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* *
57777 ACTGAAAGATTGACTCCTCGTCATG
66 ACTAAAAGATTGACTCCTCTTCATG
* * * * *
57802 A-AAATTCAAGAAGGACAACACTAAAAGATTGACTCATCTTCATGAGAAAGTCAAGAATGACATC
1 AGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * *
57866 ACT-AAAGAATTAACTCTTCTTCGTG
66 ACTAAAAG-ATTGACTCCTCTTCATG
* * * * *
57891 ATAAA-TAAAGAATGACAACACTAAAAGATTGACTCCTCTCCACAAGAAAATCAAGAATGACAAC
1 AGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * * *
57955 ATTGAAAGATTGACTCCCCTTCACG
66 ACTAAAAGATTGACTCCTCTTCATG
* * * *
57980 AGAAAGTCAAGAATGAAAACTCTAAAAGATTGAATCCTCTTCAC--GAAAGTCAAGAATGAAAAC
1 AGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * * **
58043 ACTTAAAGGTTAACTCCTCTTCACA
66 ACTAAAAGATTGACTCCTCTTCATG
* * *
58068 AGAAAGTC-ATAATGACAACACTAAAAGATTGACTCCCCTTCACGAGAAAGTCAAGGATGACAAC
1 AGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
*
58132 ACTAAAAGATT-AGCTCATCTTCATG
66 ACTAAAAGATTGA-CTCCTCTTCATG
58157 AGAAAGT
1 AGAAAGT
58164 TAAGTTGAGG
Statistics
Matches: 387, Mismatches: 58, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
87 30 0.08
88 49 0.13
89 187 0.48
90 121 0.31
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.22
Consensus pattern (90 bp):
AGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
ACTAAAAGATTGACTCCTCTTCATG
Found at i:57857 original size:134 final size:135
Alignment explanation
Indices: 57597--58163 Score: 644
Period size: 134 Copynumber: 4.2 Consensus size: 135
57587 AAATATCATT
* * * * * * *
57597 ACTAAAAGGTTGACTTCTTTTCCCCAGAAAGTCAAGAATGACATCACTAAAAGGTTGACTCCTCT
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCTCT
* * * * * * * *
57662 TCGCGAGAAAGTCAAGAATAACATCACTAAAAGTTTGACTCCTCTTCATGAGAAATTCAAGAAAG
66 TCACGAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCCCTTCACGAGAAAGTCAAGAATG
57727 ACAAC
131 ACAAC
* *
57732 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACTGAAAGATTGACTCCTCG
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCTCT
* * * ** *
57797 TCATGA-AAATTCAAGAAGGACAACACTAAAAGATTGACTCATCTTCATGAGAAAGTCAAGAATG
66 TCACGAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCCCTTCACGAGAAAGTCAAGAATG
*
57861 ACATC
131 ACAAC
* * ** * *
57866 ACT-AAAGAATTAACTCTTCTTCGTGATAAA-TAAAGAATGACAACACTAAAAGATTGACTCCTC
1 ACTAAAAG-ATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCTC
* * * * *
57929 TCCACAAGAAAATCAAGAATGACAACATTGAAAGATTGACTCCCCTTCACGAGAAAGTCAAGAAT
65 TTCACGAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCCCTTCACGAGAAAGTCAAGAAT
*
57994 GAAAAC
130 GACAAC
* * * * * *
58000 TCTAAAAGATTGAATCCTCTTCAC--GAAAGTCAAGAATGAAAACACTTAAAGGTTAACTCCTCT
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCTCT
* * *
58063 TCACAAGAAAGTC-ATAATGACAACACTAAAAGATTGACTCCCCTTCACGAGAAAGTCAAGGATG
66 TCACGAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCCCTTCACGAGAAAGTCAAGAATG
58127 ACAAC
131 ACAAC
* *
58132 ACTAAAAGATT-AGCTCATCTTCATGAGAAAGT
1 ACTAAAAGATTGA-CTCCTCTTCACGAGAAAGT
58164 TAAGTTGAGG
Statistics
Matches: 362, Mismatches: 63, Indels: 15
0.82 0.14 0.03
Matches are distributed among these distances:
131 1 0.00
132 72 0.20
133 78 0.22
134 147 0.41
135 64 0.18
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (135 bp):
ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCTCT
TCACGAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCCCCTTCACGAGAAAGTCAAGAATG
ACAAC
Found at i:58245 original size:36 final size:37
Alignment explanation
Indices: 58183--58270 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 37
58173 GTTTCTAGGA
* *
58183 AAACAATCCTAAGAAGGACTAAAACAA-ATTTTAGAG
1 AAACGATCCTAAGAAAGACTAAAACAATATTTTAGAG
* ** *
58219 AAATGATCCTAAGAAAGACTCTAACAATTTTTTAGAG
1 AAACGATCCTAAGAAAGACTAAAACAATATTTTAGAG
*
58256 AAACGACCCTAAGAA
1 AAACGATCCTAAGAA
58271 GGGAAAAAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 22 0.51
37 21 0.49
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (37 bp):
AAACGATCCTAAGAAAGACTAAAACAATATTTTAGAG
Found at i:58292 original size:37 final size:37
Alignment explanation
Indices: 58251--58344 Score: 120
Period size: 36 Copynumber: 2.6 Consensus size: 37
58241 AACAATTTTT
* *
58251 TAGAGAAACGACCCTAAGAAGGGAAAAAGTGAATTTC
1 TAGAGAAACGATCCTAAGAAGGGAAAAAATGAATTTC
*
58288 TAGAGAAACCG-TCCTAGGAA-GGAAAAAATGAATTTC
1 TAGAGAAA-CGATCCTAAGAAGGGAAAAAATGAATTTC
* *
58324 TAGAAAAACCATCCTAAGAAG
1 TAGAGAAACGATCCTAAGAAG
58345 AACTAGAGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
35 1 0.02
36 30 0.62
37 15 0.31
38 2 0.04
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.17
Consensus pattern (37 bp):
TAGAGAAACGATCCTAAGAAGGGAAAAAATGAATTTC
Found at i:61026 original size:20 final size:20
Alignment explanation
Indices: 60992--61048 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 20
60982 CAGGCTCATA
* *
60992 GTATCGGTACCTCTACCATG
1 GTATCGATACTTCTACCATG
*
61012 GTATCGATACTTCTATACTATG
1 GTATCGATACTTC--TACCATG
61034 GTATCGATACTTCTA
1 GTATCGATACTTCTA
61049 TACTATGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 13 0.41
22 19 0.59
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (20 bp):
GTATCGATACTTCTACCATG
Found at i:61037 original size:22 final size:22
Alignment explanation
Indices: 61009--61065 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
60999 TACCTCTACC
61009 ATGGTATCGATACTTCTATACT
1 ATGGTATCGATACTTCTATACT
61031 ATGGTATCGATACTTCTATACT
1 ATGGTATCGATACTTCTATACT
*
61053 ATGGTATTGATAC
1 ATGGTATCGATAC
61066 CCCCTTTCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (22 bp):
ATGGTATCGATACTTCTATACT
Done.