Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003882.1 Hibiscus syriacus cultivar Beakdansim tig00008373_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: 49581
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2114 original size:14 final size:15
Alignment explanation
Indices: 2086--2118 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2076 GGAGATTGTT
2086 GAAACTTGTGCCACC
1 GAAACTTGTGCCACC
*
2101 GAAA-TTGTGGCACC
1 GAAACTTGTGCCACC
2115 GAAA
1 GAAA
2119 GTGAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (15 bp):
GAAACTTGTGCCACC
Found at i:7057 original size:20 final size:20
Alignment explanation
Indices: 6993--7065 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
6983 CAACTTAATT
6993 TCGAATTCGCAACAC-GAAAG
1 TCGAATTCGCAACACAG-AAG
* **
7013 -CTAATTTCGCAACACAG-TT
1 TCGAA-TTCGCAACACAGAAG
7032 TCCGAATTCGCAACACAGAAG
1 T-CGAATTCGCAACACAGAAG
7053 TCGAATTCGCAAC
1 TCGAATTCGCAAC
7066 TCGAAATTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
19 3 0.07
20 34 0.81
21 5 0.12
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (20 bp):
TCGAATTCGCAACACAGAAG
Found at i:7103 original size:41 final size:39
Alignment explanation
Indices: 7058--7185 Score: 103
Period size: 39 Copynumber: 3.2 Consensus size: 39
7048 AGAAGTCGAA
* *
7058 TTCGCAACTCGAAATTGACATTTCGCAACACGAATTTCTTT
1 TTCGCAACTCGAAATTGA-AATTCGCAACACGAATTT-ATT
** * *
7099 TTCGCAACTCGATTTTTAAATTCGCAACACGAGTTTATT
1 TTCGCAACTCGAAATTGAAATTCGCAACACGAATTTATT
* ** ** * * *
7138 TTCACAACTCGATTTTCTAATTCGCAACGCGAGTTTCGTT
1 TTCGCAACTCGAAATTGAAATTCGCAACACGAATTT-ATT
7178 TTCGCAAC
1 TTCGCAAC
7186 GCAAATTTTG
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
39 34 0.46
40 25 0.34
41 15 0.20
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (39 bp):
TTCGCAACTCGAAATTGAAATTCGCAACACGAATTTATT
Found at i:7130 original size:40 final size:39
Alignment explanation
Indices: 7079--7205 Score: 148
Period size: 40 Copynumber: 3.2 Consensus size: 39
7069 AAATTGACAT
* *
7079 TTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTTAAA
1 TTCGCAACACGAGTTTCATTTTCGCAACTCGATTTTT-AA
*
7119 TTCGCAACACGAGTTT-ATTTTCACAACTCGATTTTCTAA
1 TTCGCAACACGAGTTTCATTTTCGCAACTCGATTTT-TAA
* * * * *
7158 TTCGCAACGCGAGTTTCGTTTTCGCAACGCAAATTTTGAA
1 TTCGCAACACGAGTTTCATTTTCGCAACTC-GATTTTTAA
7198 TTCGCAAC
1 TTCGCAAC
7206 CCATCCTGCT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
39 34 0.45
40 36 0.48
41 5 0.07
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (39 bp):
TTCGCAACACGAGTTTCATTTTCGCAACTCGATTTTTAA
Found at i:7187 original size:20 final size:20
Alignment explanation
Indices: 7078--7185 Score: 76
Period size: 20 Copynumber: 5.5 Consensus size: 20
7068 GAAATTGACA
* *
7078 TTTCGCAACACGAATTTCTT
1 TTTCGCAACACGAGTTTCAT
* * * *
7098 TTTCGCAACTCGATTTTTAA
1 TTTCGCAACACGAGTTTCAT
*
7118 ATTCGCAACACGAGTTT-AT
1 TTTCGCAACACGAGTTTCAT
* * *
7137 TTTCACAACTCGATTTTC-T
1 TTTCGCAACACGAGTTTCAT
* * *
7156 AATTCGCAACGCGAGTTTCGT
1 -TTTCGCAACACGAGTTTCAT
7177 TTTCGCAAC
1 TTTCGCAAC
7186 GCAAATTTTG
Statistics
Matches: 67, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
19 15 0.22
20 51 0.76
21 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (20 bp):
TTTCGCAACACGAGTTTCAT
Found at i:7664 original size:17 final size:17
Alignment explanation
Indices: 7620--7669 Score: 84
Period size: 17 Copynumber: 2.9 Consensus size: 17
7610 GCTTTATGAT
7620 TCTTCTCTCTCTCTTTTG
1 TCTTCTCT-TCTCTTTTG
7638 TCTT-TCTTCTCTTTTG
1 TCTTCTCTTCTCTTTTG
7654 TCTTCTCTTCTCTTTT
1 TCTTCTCTTCTCTTTT
7670 TCATTGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 13 0.42
17 14 0.45
18 4 0.13
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.66
Consensus pattern (17 bp):
TCTTCTCTTCTCTTTTG
Found at i:7862 original size:22 final size:20
Alignment explanation
Indices: 7813--7867 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
7803 TTGAATTTAA
7813 AAATATCGAGTTGCGAAAAAG
1 AAAT-TCGAGTTGCGAAAAAG
* *
7834 AAATTCGTGTTGCGAAAATG
1 AAATTCGAGTTGCGAAAAAG
7854 TCAAATTCGAGTTG
1 --AAATTCGAGTTG
7868 TGAATTCGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.48
21 4 0.14
22 11 0.38
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (20 bp):
AAATTCGAGTTGCGAAAAAG
Found at i:7925 original size:40 final size:40
Alignment explanation
Indices: 7855--7931 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
7845 GCGAAAATGT
** **
7855 CAAATTCGAGTTGTGAATTCGACTTCTGTGTTACGAATTC
1 CAAATTCGAGTTGCAAATTCGAAATCTGTGTTACGAATTC
*
7895 CAAATTCGAGTTGCAAATTCGGAAAT-TGTGTTGCGAA
1 CAAATTCGAGTTGCAAATTC-GAAATCTGTGTTACGAA
7932 ATGGCTTTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 28 0.90
41 3 0.10
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (40 bp):
CAAATTCGAGTTGCAAATTCGAAATCTGTGTTACGAATTC
Found at i:10002 original size:22 final size:21
Alignment explanation
Indices: 9960--10003 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
9950 AAGAATATTG
*
9960 AATAATAATATTTTTAAAAAT
1 AATAATAATATTTATAAAAAT
*
9981 AATAATATATATTTATATAAAT
1 AATAATA-ATATTTATAAAAAT
10003 A
1 A
10004 TCTTAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATAATAATATTTATAAAAAT
Found at i:13453 original size:2 final size:2
Alignment explanation
Indices: 13446--13479 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
13436 AAAAGAAAAC
*
13446 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13480 AAACAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:13505 original size:2 final size:2
Alignment explanation
Indices: 13498--13532 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
13488 AGTAAGGTTA
13498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13533 TAATTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13536 original size:6 final size:7
Alignment explanation
Indices: 13446--13536 Score: 52
Period size: 8 Copynumber: 13.3 Consensus size: 7
13436 AAAAGAAAAC
13446 ATATAT-
1 ATATATA
13452 ATATATA
1 ATATATA
13459 TATATATA
1 -ATATATA
13467 ATATATA
1 ATATATA
13474 A-ATATA
1 ATATATA
*
13480 A-A-ACA
1 ATATATA
*
13485 A-AAAGTA
1 ATATA-TA
**
13492 AGGT-TA
1 ATATATA
13498 ATATATA
1 ATATATA
13505 TATATATA
1 -ATATATA
13513 TATATATA
1 -ATATATA
13521 TATATATA
1 -ATATATA
13529 ATAT-TA
1 ATATATA
13535 AT
1 AT
13537 TAAAAATAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
5 4 0.06
6 22 0.31
7 16 0.22
8 30 0.42
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (7 bp):
ATATATA
Found at i:13668 original size:41 final size:41
Alignment explanation
Indices: 13610--13693 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
13600 ATAATACTCA
13610 TTCACTATTTTAACCTAAACTAACAAGAATTAAGTCTAAAT
1 TTCACTATTTTAACCTAAACTAACAAGAATTAAGTCTAAAT
* *
13651 TTCATTATTTTAACCTAAACTAACCAGAATTAAGTCTAAAT
1 TTCACTATTTTAACCTAAACTAACAAGAATTAAGTCTAAAT
13692 TT
1 TT
13694 GAAAAATTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.37
Consensus pattern (41 bp):
TTCACTATTTTAACCTAAACTAACAAGAATTAAGTCTAAAT
Found at i:14024 original size:20 final size:20
Alignment explanation
Indices: 14001--14063 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
13991 ATCCTATCAA
* *
14001 TACTATAAGAATAGTATCGG
1 TACTATAAGAACAATATCGG
* *
14021 TACTGTATGAACAATATCGG
1 TACTATAAGAACAATATCGG
* *
14041 TACTATACGAACAATATAGG
1 TACTATAAGAACAATATCGG
14061 TAC
1 TAC
14064 GTATGAATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (20 bp):
TACTATAAGAACAATATCGG
Found at i:14063 original size:40 final size:39
Alignment explanation
Indices: 14001--14076 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 39
13991 ATCCTATCAA
* * *
14001 TACTATAAGAATAGTATCGGTACTGTATGAACAATATCGG
1 TACTATAAGAACAATATAGGTAC-GTATGAACAATATCGG
* *
14041 TACTATACGAACAATATAGGTACGTATGAATAATAT
1 TACTATAAGAACAATATAGGTACGTATGAACAATAT
14077 TGATACCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 12 0.39
40 19 0.61
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (39 bp):
TACTATAAGAACAATATAGGTACGTATGAACAATATCGG
Found at i:15773 original size:16 final size:16
Alignment explanation
Indices: 15752--15784 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
15742 CCCATTTATC
15752 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
15768 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
15784 A
1 A
15785 AAACACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:18088 original size:23 final size:22
Alignment explanation
Indices: 18036--18117 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 22
18026 ACATAACCCC
* **
18036 AGGGGGTATCGATTCCCCT-GT
1 AGGGGGAATCGATTCCCCTCAA
*
18057 GGGGGGAATCGATTCCCCTTCAA
1 AGGGGGAATCGATTCCCC-TCAA
* *
18080 AGGGGGAATCGGTT-CCCTCAT
1 AGGGGGAATCGATTCCCCTCAA
* *
18101 GGGGGGGATCGATTCCC
1 AGGGGGAATCGATTCCC
18118 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
21 30 0.62
22 6 0.12
23 12 0.25
ACGTcount: A:0.17, C:0.24, G:0.35, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTCAA
Found at i:34650 original size:39 final size:39
Alignment explanation
Indices: 34607--34708 Score: 195
Period size: 39 Copynumber: 2.6 Consensus size: 39
34597 AGGTAGCCTT
*
34607 TTACATTTTTCTTTTGGATAACTTTCGCTTTTTCAATTG
1 TTACATTTTTCTTTTGGATAACTTTCGCTTTTTCAATCG
34646 TTACATTTTTCTTTTGGATAACTTTCGCTTTTTCAATCG
1 TTACATTTTTCTTTTGGATAACTTTCGCTTTTTCAATCG
34685 TTACATTTTTCTTTTGGATAACTT
1 TTACATTTTTCTTTTGGATAACTT
34709 CCGCCTTTAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.56
Consensus pattern (39 bp):
TTACATTTTTCTTTTGGATAACTTTCGCTTTTTCAATCG
Found at i:37402 original size:23 final size:23
Alignment explanation
Indices: 37372--37433 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
37362 GCCCAATTTG
37372 GATCCATCTTTGCAGTACCGGGA
1 GATCCATCTTTGCAGTACCGGGA
37395 GATCCATCTTTGCAGTACCGGGA
1 GATCCATCTTTGCAGTACCGGGA
37418 GATCCATCTTTGCAGT
1 GATCCATCTTTGCAGT
37434 TTCATCACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (23 bp):
GATCCATCTTTGCAGTACCGGGA
Found at i:44037 original size:2 final size:2
Alignment explanation
Indices: 44030--44054 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44020 GAGGGAAATT
44030 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
44055 AACGCGGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:46118 original size:84 final size:84
Alignment explanation
Indices: 46008--46470 Score: 631
Period size: 84 Copynumber: 5.5 Consensus size: 84
45998 AACAGTTTCC
* * * * * *
46008 TGTTGGTAGATAGCTCTTCTCACCTTGAGCTATGCTACAAATGATCTGCCTTTGAGCTGAGTGTA
1 TGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
*
46073 ATCGAACTTGAAGGTCTTT
66 ATCGAACTCGAAGGTCTTT
* * * * * *
46092 TGTTGGCAGATAACCCTTATTGCCTTGAGCTAAGCTGCAAATGATGTGTCTTTCAGCTGAGTATA
1 TGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
* *
46157 ATCAAACTCGAATGTCTTT
66 ATCGAACTCGAAGGTCTTT
* * * * * *
46176 TGTTGGCAGATAACCCTTATCGCCTTGAGCTATGCCGTAAATGATATACCTTTGAGCTAAGTGTA
1 TGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
46241 ATCGAACTCGAAGGTCTTT
66 ATCGAACTCGAAGGTCTTT
* *
46260 TGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGATGCAAATGATGTGCCTTTGAGCTTAGTGTA
1 TGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
46325 ATCGAACTCGAAGGTCTTT
66 ATCGAACTCGAAGGTCTTT
* * *
46344 TGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGCTGCAAATTATGTGCCTTTGAGCTGAGTGTA
1 TGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
46409 ATCGAACTCGAAGGTC-TT
66 ATCGAACTCGAAGGTCTTT
** * * * *
46427 TGTCAGCAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGA
1 TGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGA
46471 ACATGATATC
Statistics
Matches: 332, Mismatches: 47, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
83 38 0.11
84 294 0.89
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (84 bp):
TGTTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
ATCGAACTCGAAGGTCTTT
Found at i:46700 original size:124 final size:124
Alignment explanation
Indices: 46480--46837 Score: 563
Period size: 124 Copynumber: 2.9 Consensus size: 124
46470 AACATGATAT
* * * * *
46480 CCTTCGTCGTGAAGTTGAAATCGTAGAGGGCCCATTCGTTGTGAAGTTGAACCTTGAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATA
*
46545 TCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGGCACGATTC
66 TCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATTC
* **
46604 CCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCATTGTGAAGTTGAGCCTTGAATTATATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* *
46669 TCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATAAATGTTACTGGTGAGCACGATTC
66 TCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATTC
* * * *
46728 CCTTCGTTGTGAAGTTGAAACTGTGGATTACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* *
46793 TCCTTCGTCGTGAAGTTGAAATCCAATCTCAAGATGAATGTTGCT
66 TCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCT
46838 TCGAGTCCAA
Statistics
Matches: 212, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
124 212 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (124 bp):
CCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATA
TCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATTC
Found at i:46948 original size:64 final size:64
Alignment explanation
Indices: 46840--47070 Score: 318
Period size: 64 Copynumber: 3.6 Consensus size: 64
46830 ATGTTGCTTC
** * ** * *
46840 GAGTCCAATATCCTTTGCCGTGAAGTTGAAATTGGTTCTAAATGAAACTGGGAAGTCGTTTGTT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTT
* * *
46904 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAATCGTTTGTT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTT
* * * *
46968 GAGTCCTATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTT
* *
47032 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTTACTCT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCT
47071 AAAAGCTGCA
Statistics
Matches: 146, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 146 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (64 bp):
GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTT
Found at i:46993 original size:128 final size:128
Alignment explanation
Indices: 46840--47070 Score: 372
Period size: 128 Copynumber: 1.8 Consensus size: 128
46830 ATGTTGCTTC
* ** * *
46840 GAGTCCAATATCCTTTGCCGTGAAGTTGAAATTGGTTCTAAATGAAACTGGGAAGTCGTTTGTTG
1 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTAAATGAAACTAGAAAGTCGTTTGTTG
46905 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAATCGTTTGTT
66 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAATCGTTTGTT
* * * *
46968 GAGTCCTATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTAAATGAAACTAGAAAGTCGTTTGTTG
*
47033 AGTCCAATATCCTTCATTGTGAAGTTGAAATTTACTCT
66 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCT
47071 AAAAGCTGCA
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
128 93 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (128 bp):
GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTAAATGAAACTAGAAAGTCGTTTGTTG
AGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAATCGTTTGTT
Done.