Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006751.1 Hibiscus syriacus cultivar Beakdansim tig00016991_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: 108726
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:782 original size:4 final size:4
Alignment explanation
Indices: 773--822 Score: 59
Period size: 4 Copynumber: 12.2 Consensus size: 4
763 TAGGAGATGT
773 AATA AATA AATAA AATA AA-A AATA AA-A ATATA ATATA AATA AATA AATA
1 AATA AATA AAT-A AATA AATA AATA AATA A-ATA A-ATA AATA AATA AATA
822 A
1 A
823 GAAGAAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 5 0.12
4 26 0.62
5 11 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:837 original size:25 final size:23
Alignment explanation
Indices: 780--838 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
770 TGTAATAAAT
*
780 AAATAAAATAAAAAATAAAAATA
1 AAATAAAATAAAAAATAAAAAGA
* *
803 TAATATAAATAAATAAATAAGAAGA
1 AAATA-AAATAAA-AAATAAAAAGA
828 AAATGAAAATA
1 AAAT-AAAATA
839 TCTTTGACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 4 0.14
24 7 0.24
25 17 0.59
26 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (23 bp):
AAATAAAATAAAAAATAAAAAGA
Found at i:3722 original size:17 final size:17
Alignment explanation
Indices: 3692--3733 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3682 TACTGACATT
*
3692 TCTTT-GAGAGAAACTC
1 TCTTTCGAGAAAAACTC
3708 TCTTTCGAGAAAAACTC
1 TCTTTCGAGAAAAACTC
3725 -CTGTTCGAG
1 TCT-TTCGAG
3734 CAACAAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (17 bp):
TCTTTCGAGAAAAACTC
Found at i:9879 original size:23 final size:23
Alignment explanation
Indices: 9853--9908 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
9843 CCCTTTTGAT
*
9853 TTTTCATCTTGAACCCTATTTTC
1 TTTTCATCTTGAACCCCATTTTC
9876 TTTTCATCTTGAACCCCATTTTC
1 TTTTCATCTTGAACCCCATTTTC
9899 TTTTCATCTT
1 TTTTCATCTT
9909 TTTTCTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.16, C:0.27, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTTCATCTTGAACCCCATTTTC
Found at i:9924 original size:14 final size:15
Alignment explanation
Indices: 9894--9931 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
9884 TTGAACCCCA
9894 TTTTCTTTTCATCTT
1 TTTTCTTTTCATCTT
9909 TTTTCTTATT-AT-TT
1 TTTTCTT-TTCATCTT
9923 TTTTCTTTT
1 TTTTCTTTT
9932 TTGTTCATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 9 0.41
15 9 0.41
16 2 0.09
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTCATCTT
Found at i:13877 original size:24 final size:25
Alignment explanation
Indices: 13840--13886 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
13830 ATCATTTTAA
*
13840 TTACTTATCCATTTT-CATTATATCC
1 TTACTAATCCATTTTAC-TTATATCC
13865 TTACTAAT-CATTTTACTTATAT
1 TTACTAATCCATTTTACTTATAT
13887 TTCTTTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (25 bp):
TTACTAATCCATTTTACTTATATCC
Found at i:16848 original size:14 final size:14
Alignment explanation
Indices: 16829--16862 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
16819 GCTATAGTAT
16829 GGAAACGCATATAG
1 GGAAACGCATATAG
16843 GGAAACGCATATAG
1 GGAAACGCATATAG
16857 GGAAAC
1 GGAAAC
16863 TCATGAGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.29, T:0.12
Consensus pattern (14 bp):
GGAAACGCATATAG
Found at i:29875 original size:45 final size:45
Alignment explanation
Indices: 29826--29912 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 45
29816 TCAAAATAGC
*
29826 CTGAGTACATCGATGCATGGCT-TGTGCATCGATGCATCAAATCCA
1 CTGAGTACATCGATGCATGG-TATGTGCATCGATGCATAAAATCCA
*
29871 CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAAT
1 CTGAGTACATCGATGCATGGTATGTGCATCGATGCATAAAAT
29913 GCATTCGATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (45 bp):
CTGAGTACATCGATGCATGGTATGTGCATCGATGCATAAAATCCA
Found at i:29960 original size:20 final size:20
Alignment explanation
Indices: 29935--29972 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29925 CAAAATATTC
29935 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
* *
29955 ATTGGTGTATCGGTGCAT
1 ATTGGTGCATCGATGCAT
29973 CACTTTGAAA
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:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:32171 original size:20 final size:20
Alignment explanation
Indices: 32146--32197 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
32136 ACCAGACGGA
*
32146 TGCATCGATGCATGGTAGTG
1 TGCATCGATGCATGGCAGTG
32166 TGCATCGATGCATGGCAGTG
1 TGCATCGATGCATGGCAGTG
32186 TGCATCGATGCA
1 TGCATCGATGCA
32198 CAGTCAAGGC
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:0.19, G:0.33, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCATGGCAGTG
Found at i:35925 original size:23 final size:23
Alignment explanation
Indices: 35848--35931 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
35838 CAGAACCCAT
*
35848 GGAGGGTATCGATT-CCC-TCAA
1 GGAGGGAATCGATTCCCCTTCAA
* * *
35869 GGAGAGAATCGGTTCCCATTCAAA
1 GGAGGGAATCGATTCCCCTTC-AA
*
35893 GG-GGGAATCGATTCCCCTTCAT
1 GGAGGGAATCGATTCCCCTTCAA
*
35915 GGAGGGTATCGATTCCC
1 GGAGGGAATCGATTCCC
35932 TCTGCACTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 11 0.22
22 5 0.10
23 30 0.60
24 4 0.08
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (23 bp):
GGAGGGAATCGATTCCCCTTCAA
Found at i:41341 original size:19 final size:19
Alignment explanation
Indices: 41317--41394 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
41307 AATAGTCTGA
41317 GTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGGCTT
*
41336 GTGCATCGATGCATCAAATGCACTT
1 GTGCATCGATG---C--ATG-GCTT
41361 AGTGCATCGATGCATGG-TAT
1 -GTGCATCGATGCATGGCT-T
41381 GTGCATCGATGCAT
1 GTGCATCGATGCAT
41395 AAAATGCTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
19 26 0.53
20 1 0.02
21 3 0.06
22 1 0.02
23 1 0.02
24 3 0.06
25 3 0.06
26 11 0.22
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTT
Found at i:41365 original size:45 final size:45
Alignment explanation
Indices: 41316--41401 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
41306 AAATAGTCTG
*
41316 AGTGCATCGATGCATGGCT-TGTGCATCGATGCATCAAATGCACTT
1 AGTGCATCGATGCATGG-TATGTGCATCGATGCATAAAATGCACTT
41361 AGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGC
1 AGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGC
41402 TTTCGATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (45 bp):
AGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCACTT
Found at i:46172 original size:12 final size:12
Alignment explanation
Indices: 46155--46181 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
46145 CTAACATTAA
46155 AGACTTATAATC
1 AGACTTATAATC
46167 AGACTTATAATC
1 AGACTTATAATC
46179 AGA
1 AGA
46182 ATTACAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (12 bp):
AGACTTATAATC
Found at i:62723 original size:24 final size:25
Alignment explanation
Indices: 62696--62744 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
62686 GAAAGATAAT
62696 AAAG-TCCATATATCAA-TATTATTA
1 AAAGATCCATA-ATCAAGTATTATTA
*
62720 AAAGATCCATAGTCAAGTATTATTA
1 AAAGATCCATAATCAAGTATTATTA
62745 TGGGCATGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (25 bp):
AAAGATCCATAATCAAGTATTATTA
Found at i:75207 original size:16 final size:16
Alignment explanation
Indices: 75186--75216 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
75176 TGCCTTGTCT
75186 AATGAAGATGCTAGAC
1 AATGAAGATGCTAGAC
75202 AATGAAGATGCTAGA
1 AATGAAGATGCTAGA
75217 TAGCATGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.19
Consensus pattern (16 bp):
AATGAAGATGCTAGAC
Found at i:91609 original size:2 final size:2
Alignment explanation
Indices: 91598--91630 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
91588 TAAAGGTAAT
91598 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91631 CAATAAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:93743 original size:213 final size:216
Alignment explanation
Indices: 93372--93783 Score: 632
Period size: 213 Copynumber: 1.9 Consensus size: 216
93362 TAAGACCTAC
* * * * *
93372 GGGTAGGATGTTTTCACATGATTTTTAAAATATGAGAAAGTGATTTTCAAGGTTTCTCATTTTGT
1 GGGTAGGATGTCTTCACATGA-TTTTAAAATATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGT
* * *
93437 ATTTTCAGAAAATGAATTTTTTGAAAAATAAGAAAACGATTTCCAAAGTTTCTTACACAGTAGAC
65 ATTTTCAGAAAATGAAATTTTTGAAAAATAAGAAAACGATTTCCAAAGTCTCTTACACAGTAAAC
* *
93502 TATTTCCAAAATCGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCACGATGATTAAATCCT
130 TATTTCCAAAATCGGTAAGTCATTCGGGCCATCAATAAGCCTTTCGAGCACGATGATTAAATCCT
93567 TCGGGCTATCTATATGACCTTT
195 TCGGGCTATCTATATGACCTTT
93589 GGGTAGGATGTCTTCACATGA-TTT-AAA-ATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTA
1 GGGTAGGATGTCTTCACATGATTTTAAAATATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTA
* * * * *
93651 TTTTCAGAAGATGAAATTTTTGAAAAGTAAGAAAGCGATTTTCAAAGTCTCTTACCCAGTAAACT
66 TTTTCAGAAAATGAAATTTTTGAAAAATAAGAAAACGATTTCCAAAGTCTCTTACACAGTAAACT
* * *
93716 ATTTTCAAAATCGGTAAGTCCTTCGGGCCATCAATAAGCCTTTCGAGCATGATGATTAAATCCTT
131 ATTTCCAAAATCGGTAAGTCATTCGGGCCATCAATAAGCCTTTCGAGCACGATGATTAAATCCTT
93781 CGG
196 CGG
93784 CTCATCTGTC
Statistics
Matches: 177, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
213 151 0.85
214 3 0.02
215 3 0.02
217 20 0.11
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (216 bp):
GGGTAGGATGTCTTCACATGATTTTAAAATATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTA
TTTTCAGAAAATGAAATTTTTGAAAAATAAGAAAACGATTTCCAAAGTCTCTTACACAGTAAACT
ATTTCCAAAATCGGTAAGTCATTCGGGCCATCAATAAGCCTTTCGAGCACGATGATTAAATCCTT
CGGGCTATCTATATGACCTTT
Found at i:93833 original size:41 final size:42
Alignment explanation
Indices: 93755--93833 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
93745 ATCAATAAGC
93755 CTTTCGAGCATGATGATTAAATCCTTCGGCTCATCTGTCAGG
1 CTTTCGAGCATGATGATTAAATCCTTCGGCTCATCTGTCAGG
* * *
93797 CTTTCGAGACA-GATGA-TAAGTCCTTTGGGTCATCTGT
1 CTTTCGAG-CATGATGATTAAATCCTTCGGCTCATCTGT
93834 AAGACCTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 18 0.55
42 13 0.39
43 2 0.06
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.34
Consensus pattern (42 bp):
CTTTCGAGCATGATGATTAAATCCTTCGGCTCATCTGTCAGG
Found at i:94115 original size:259 final size:260
Alignment explanation
Indices: 93613--94121 Score: 761
Period size: 259 Copynumber: 2.0 Consensus size: 260
93603 CACATGATTT
* * * *
93613 AAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAGATGAAATTTTTGAAAAG
1 AAAATGAGAAAGCGATTTCCAAAGTTTATCATTTAGTATTTTCAAAAAATGAAATTTTTAAAAAG
* * * *
93678 TAAGAAAGCGATTTTCAAAGTCTCTTACCCAGTAAACTATTTTCAAAATCGGTAAGTCCTTCGGG
66 TAAGAAAGCGATTTCCAAACTCTCTTACCCAGTAAACTATTTCCAAAATCGATAAGTCCTTCGGG
* *
93743 CCATCAATAAGCCTTTCGAGCATGATGATTAAATCCTTCGGCTCATCTGTCAGGCTTTCGAGACA
131 CCATCAATAAGCCTTTCGAGCATGAGGATTAAATCCTTCGGCTCATCTGTCAGGCTTTCGAGAAA
* * * *
93808 GATGATAAGTCCTTTGGGTCATCTGTAAGACCTTTGGGCAAGATGCTTTCATATGATGTTTGTGA
196 GATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAAGATGCTTTCATATGATGTTTGTGA
*
93873 AAAATGAGAAAGTGATTTCCAAAGTTTAT-ATTTAGTATTTTCAAAAAATGAAATTTTTAAAAAG
1 AAAATGAGAAAGCGATTTCCAAAGTTTATCATTTAGTATTTTCAAAAAATGAAATTTTTAAAAAG
* *
93937 TAAGAAAGTGATTTCCAAACTTTCTTACCCAGTAAACTATTTCCAAAATCGATAAGTCCTTCGGG
66 TAAGAAAGCGATTTCCAAACTCTCTTACCCAGTAAACTATTTCCAAAATCGATAAGTCCTTCGGG
* ** * * * * *
94002 CCGTCCGTAAGTCTTTCGAGCATGAGGATTAAATCCTTCGGGTCATCTGTTAGTCTTTTGA-ATA
131 CCATCAATAAGCCTTTCGAGCATGAGGATTAAATCCTTCGGCTCATCTGTCAGGCTTTCGAGA-A
*
94066 AGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAATATGCTTTCATATG
195 AGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAAGATGCTTTCATATG
94122 GTATTTGTAA
Statistics
Matches: 222, Mismatches: 26, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
258 1 0.00
259 194 0.87
260 27 0.12
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (260 bp):
AAAATGAGAAAGCGATTTCCAAAGTTTATCATTTAGTATTTTCAAAAAATGAAATTTTTAAAAAG
TAAGAAAGCGATTTCCAAACTCTCTTACCCAGTAAACTATTTCCAAAATCGATAAGTCCTTCGGG
CCATCAATAAGCCTTTCGAGCATGAGGATTAAATCCTTCGGCTCATCTGTCAGGCTTTCGAGAAA
GATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAAGATGCTTTCATATGATGTTTGTGA
Found at i:94631 original size:89 final size:90
Alignment explanation
Indices: 94469--94941 Score: 462
Period size: 89 Copynumber: 5.3 Consensus size: 90
94459 ATAGATTGAT
* * * *
94469 AGAGGAGTCAATCTTTTAGTGTTGTC-TTCCTTGAATTTCTCATGAAAATGAGTCAGTC-TTTAG
1 AGAGGAGTCAATCTTTTAGTGTTGTCATT-CTTGACTTTCTCATGAAGAGGAGTCAATCTTTTAG
*
94532 TGTTGTCATTCTTGACTTACTCGTGA
65 TGTTGTCATTCTTGACTTTCTCGTGA
* * *
94558 AGAGGAGTCAATC-TTTAATATTGTCATTCTTGACTTTCTCATGAAGAGGAGTCGATCTTTTAGT
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGAAGAGGAGTCAATCTTTTAGT
* *
94622 ATTGTCATTCTTGATTTTCTCGTGA
66 GTTGTCATTCTTGACTTTCTCGTGA
* * * * * **
94647 AGA-GAATCCAATCATTTAGTGTTGTCATTCTTGACTTT-TCGTGAAGAGAAATTGATCTTTTAG
1 AGAGGAGT-CAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGAAGAGGAGTCAATCTTTTAG
* *
94710 TGTTTTCATTCTTGAGTTTCTCGTGA
65 TGTTGTCATTCTTGACTTTCTCGTGA
* * * * ** * * *
94736 AGAGAAGTCGACCTTTTAGTGTTGTGATTCTTGACTTTCTCGCGGAGAGGAGTCAACCTTTTAAT
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGAAGAGGAGTCAATCTTTTAGT
* *
94801 GATGTTATTCTTGAC-TT-TC-TGA
66 GTTGTCATTCTTGACTTTCTCGTGA
* * * * * *
94823 AGAGAAGTCAATCTTTTTGTGTTGTCCTTCTTCACTTTCT-A-GCAAATATGAGTCAATCTTTTA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATG--AAGAGGAGTCAATCTTTTA
* *
94886 GTGTTGTCCTTCTTGACTTTCTCATGA
64 GTGTTGTCATTCTTGACTTTCTCGTGA
* * * *
94913 AGAGGAGTAAACCTTTTATTGATGTCATT
1 AGAGGAGTCAATCTTTTAGTGTTGTCATT
94942 TAAACTTGAT
Statistics
Matches: 313, Mismatches: 60, Indels: 21
0.79 0.15 0.05
Matches are distributed among these distances:
85 1 0.00
87 65 0.21
88 41 0.13
89 128 0.41
90 78 0.25
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (90 bp):
AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGAAGAGGAGTCAATCTTTTAGT
GTTGTCATTCTTGACTTTCTCGTGA
Found at i:94641 original size:45 final size:45
Alignment explanation
Indices: 94469--94941 Score: 467
Period size: 45 Copynumber: 10.6 Consensus size: 45
94459 ATAGATTGAT
* *
94469 AGAGGAGTCAATCTTTTAGTGTTGTC-TTCCTTGAATTTCTCATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATT-CTTGACTTTCTCGTGA
* * * *
94514 AAATGAGTCAGTC-TTTAGTGTTGTCATTCTTGACTTACTCGTGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * *
94558 AGAGGAGTCAATC-TTTAATATTGTCATTCTTGACTTTCTCATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * *
94602 AGAGGAGTCGATCTTTTAGTATTGTCATTCTTGATTTTCTCGTGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* *
94647 AGA-GAATCCAATCATTTAGTGTTGTCATTCTTGACTTT-TCGTGA
1 AGAGGAGT-CAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * ** * *
94691 AGAGAAATTGATCTTTTAGTGTTTTCATTCTTGAGTTTCTCGTGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * * * * *
94736 AGAGAAGTCGACCTTTTAGTGTTGTGATTCTTGACTTTCTCGCGG
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * * *
94781 AGAGGAGTCAACCTTTTAATGATGTTATTCTTGAC-TT-TC-TGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * * * * **
94823 AGAGAAGTCAATCTTTTTGTGTTGTCCTTCTTCACTTTCTAGCAA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * * *
94868 ATATGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
* * * *
94913 AGAGGAGTAAACCTTTTATTGATGTCATT
1 AGAGGAGTCAATCTTTTAGTGTTGTCATT
94942 TAAACTTGAT
Statistics
Matches: 350, Mismatches: 70, Indels: 16
0.80 0.16 0.04
Matches are distributed among these distances:
42 28 0.08
43 4 0.01
44 114 0.33
45 204 0.58
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (45 bp):
AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGA
Found at i:94884 original size:132 final size:133
Alignment explanation
Indices: 94473--94941 Score: 414
Period size: 134 Copynumber: 3.5 Consensus size: 133
94463 ATTGATAGAG
* * * * * ** * *
94473 GAGTCAATCTTTTAGTGTTGTC-TTCCTTGAATTTCTCATGAAAATGAGTCAGTC-TTTAGTGTT
1 GAGTCGATCTTTTAGTGTTGTCATT-CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAATGAT
* * * * * *
94536 GTCATTCTTGACTTACTCGTGAAGAGGAGTCAATC-TTTAATATTGTCATTCTTGACTTTCT--C
65 GTCATTCTTGACTT-TTCGTGAAGAGAAATCAATCTTTTAGTGTTGTCATTCTTCACTTTCTAGC
94598 ATGAAGA
129 A--AAGA
* * * * * * *
94605 GGAGTCGATCTTTTAGTATTGTCATTCTTGATTTTCTCGTGAAGA-GAATCCAATCATTTAGTGT
1 -GAGTCGATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAGT-CAACCTTTTAATGA
** * * * * *
94669 TGTCATTCTTGACTTTTCGTGAAGAGAAATTGATCTTTTAGTGTTTTCATTCTTGAGTTTCTCGT
64 TGTCATTCTTGACTTTTCGTGAAGAGAAATCAATCTTTTAGTGTTGTCATTCTTCACTTTCTAGC
*
94734 GAAGA
129 AAAGA
* * * *
94739 GAAGTCGACCTTTTAGTGTTGTGATTCTTGACTTTCTCGCGGAGAGGAGTCAACCTTTTAATGAT
1 G-AGTCGATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAATGAT
* * * *
94804 GTTATTCTTGAC-TTTC-TGAAGAGAAGTCAATCTTTTTGTGTTGTCCTTCTTCACTTTCTAGCA
65 GTCATTCTTGACTTTTCGTGAAGAGAAATCAATCTTTTAGTGTTGTCATTCTTCACTTTCTAGCA
*
94867 AATA
130 AAGA
* * * * *
94871 TGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCATGAAGAGGAGTAAACCTTTTATTGAT
1 -GAGTCGATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAATGAT
94936 GTCATT
65 GTCATT
94942 TAAACTTGAT
Statistics
Matches: 275, Mismatches: 52, Indels: 19
0.79 0.15 0.05
Matches are distributed among these distances:
132 101 0.37
133 61 0.22
134 110 0.40
135 3 0.01
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (133 bp):
GAGTCGATCTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAATGATG
TCATTCTTGACTTTTCGTGAAGAGAAATCAATCTTTTAGTGTTGTCATTCTTCACTTTCTAGCAA
AGA
Done.