Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000288.1 Hibiscus syriacus cultivar Beakdansim tig00000530_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: 81307
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:3605 original size:13 final size:13
Alignment explanation
Indices: 3573--3614 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
3563 AAATAAAACT
* *
3573 TAATTAATAATAA
1 TAATTATTATTAA
3586 TAA-TATTATTAA
1 TAATTATTATTAA
3598 TAATTATTATTAA
1 TAATTATTATTAA
3611 TAAT
1 TAAT
3615 ATAAAAGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTATTATTAA
Found at i:8910 original size:45 final size:45
Alignment explanation
Indices: 8845--8932 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
8835 ACCCTAACTG
* *
8845 CATGATATCTAATTCATATAC-TTGTTTGAAAAACAAACATAACCA
1 CATGATATCTAATTCATATACATTATTTGAAAAA-AAAAATAACCA
* * *
8890 CATGATCTCTAGTTCGTATACATTTATTTGAAAAAAAAAATAA
1 CATGATATCTAATTCATATACA-TTATTTGAAAAAAAAAATAA
8933 ATTACTCAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 18 0.50
46 7 0.19
47 11 0.31
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (45 bp):
CATGATATCTAATTCATATACATTATTTGAAAAAAAAAATAACCA
Found at i:23753 original size:3 final size:3
Alignment explanation
Indices: 23745--23794 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
23735 AAAACTTAAT
* *
23745 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23793 TA
1 TA
23795 TAAAAAGGGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:25362 original size:60 final size:59
Alignment explanation
Indices: 25253--25376 Score: 173
Period size: 60 Copynumber: 2.1 Consensus size: 59
25243 GTATATATGT
*
25253 ATAGTTTGAGATAAAATTAAATGTTCAAAAAGTTTGAAGATCAATTTAGAATGA-AGGTC
1 ATAGTTTGAGATAAAATGAAATGTTCAAAAAGTTTGAAGATCAATTTAGAATGATA-GTC
*
25312 ATAGTTTGAGGATGAAAATGAAATGTTC-AAAAGTTTGAGGATTC-ATTTAGAATGATAGTC
1 ATAGTTTGA-GAT-AAAATGAAATGTTCAAAAAGTTTGAAGA-TCAATTTAGAATGATAGTC
25372 ATAGT
1 ATAGT
25377 ATAGGGATAA
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
59 9 0.15
60 34 0.58
61 16 0.27
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (59 bp):
ATAGTTTGAGATAAAATGAAATGTTCAAAAAGTTTGAAGATCAATTTAGAATGATAGTC
Found at i:25404 original size:60 final size:59
Alignment explanation
Indices: 25253--25420 Score: 166
Period size: 60 Copynumber: 2.8 Consensus size: 59
25243 GTATATATGT
* *
25253 ATAGTTTGA-GATAAAATTAAATGTTCAAAAAGTTTGAAGATCAATTTAGAATGAAGGTC
1 ATAGTTAGAGGATAAAATTAAATGTT-AAAAAGTTTGAGGATCAATTTAGAATGAAGGTC
* * *
25312 ATAGTTTGAGGATGAAAATGAAATGTTCAAAAGTTTGAGGATTC-ATTTAGAATGATA-GTC
1 ATAGTTAGAGGAT-AAAATTAAATGTTAAAAAGTTTGAGGA-TCAATTTAGAATGA-AGGTC
* * *
25372 ATAGTATAG-GGATAAAATTAAAATATTTAAAAGTTTAAGGA-CTAATTTA
1 ATAGT-TAGAGGATAAAATT-AAATGTTAAAAAGTTTGAGGATC-AATTTA
25421 AAATAAGAAT
Statistics
Matches: 93, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
58 1 0.01
59 14 0.15
60 61 0.66
61 17 0.18
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.33
Consensus pattern (59 bp):
ATAGTTAGAGGATAAAATTAAATGTTAAAAAGTTTGAGGATCAATTTAGAATGAAGGTC
Found at i:27859 original size:36 final size:36
Alignment explanation
Indices: 27809--27880 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
27799 TATATTTTCC
*
27809 TTAAAAAGCTATTAGGAGATTATACAGTCGGACTAA
1 TTAAAAAGCGATTAGGAGATTATACAGTCGGACTAA
*
27845 TTAAAAAGCGATTAGGAGATTATACAGTTGGACTAA
1 TTAAAAAGCGATTAGGAGATTATACAGTCGGACTAA
27881 GCATGCAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.28
Consensus pattern (36 bp):
TTAAAAAGCGATTAGGAGATTATACAGTCGGACTAA
Found at i:29843 original size:22 final size:21
Alignment explanation
Indices: 29810--29865 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
29800 AGAGTATGAA
*
29810 ATAAAATAATTAATGAAAAAT
1 ATAAAAAAATTAATGAAAAAT
*
29831 ATAAAAAAGATT-ATGTAAAAT
1 ATAAAAAA-ATTAATGAAAAAT
29852 ATAAAAAAAATTAA
1 AT-AAAAAAATTAA
29866 ATTTTTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (21 bp):
ATAAAAAAATTAATGAAAAAT
Found at i:41324 original size:39 final size:38
Alignment explanation
Indices: 41280--41384 Score: 95
Period size: 39 Copynumber: 2.7 Consensus size: 38
41270 GACTCCTCAA
*
41280 CTTTGTGCTCAGGGTAAATCCTTACTGCAGGATCCTCTG
1 CTTTGTGCTCAGGGTAAA-CCTTACTGCAGGATCATCTG
* * * * *
41319 GTTTGTGCAT-AGGATAAGACCTTATTACAGGCTCATCTG
1 CTTTGTGC-TCAGGGTAA-ACCTTACTGCAGGATCATCTG
* *
41358 CTTTGTGCACAGGGTAAGCCCTTACTG
1 CTTTGTGCTCAGGGTAA-ACCTTACTG
41385 GGTGTACAGG
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
39 49 0.96
40 2 0.04
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (38 bp):
CTTTGTGCTCAGGGTAAACCTTACTGCAGGATCATCTG
Found at i:47193 original size:18 final size:18
Alignment explanation
Indices: 47170--47204 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
47160 TATGTGATAT
*
47170 GTGGTCCTTCGGGACATA
1 GTGGTCCTCCGGGACATA
47188 GTGGTCCTCCGGGACAT
1 GTGGTCCTCCGGGACAT
47205 TTCTACGCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.26, G:0.34, T:0.26
Consensus pattern (18 bp):
GTGGTCCTCCGGGACATA
Found at i:47894 original size:21 final size:20
Alignment explanation
Indices: 47868--47907 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
47858 GAAATTTTGG
47868 TGCATCGATGCACTGTAGCAA
1 TGCATCGATGCAC-GTAGCAA
*
47889 TGCATCGATGCGCGTAGCA
1 TGCATCGATGCACGTAGCA
47908 CTGTTCATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (20 bp):
TGCATCGATGCACGTAGCAA
Found at i:53477 original size:18 final size:18
Alignment explanation
Indices: 53454--53488 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53444 TATGTGATAT
*
53454 GTGGTCCTTCGGGACATA
1 GTGGTCCTCCGGGACATA
53472 GTGGTCCTCCGGGACAT
1 GTGGTCCTCCGGGACAT
53489 TTCTACTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.26, G:0.34, T:0.26
Consensus pattern (18 bp):
GTGGTCCTCCGGGACATA
Found at i:54500 original size:21 final size:21
Alignment explanation
Indices: 54449--54513 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
54439 TTTCTTTGGG
* *
54449 CTTTTAATTATTTTTGTTTTT
1 CTTTTATTTATTTTTGATTTT
*
54470 CTTGTAATTTA-TTTTGCATTTT
1 CTT-TTATTTATTTTTG-ATTTT
54492 CTTTTATTT-TTTATTGAGTTTT
1 CTTTTATTTATTT-TTGA-TTTT
54514 ATGGATTGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.15, C:0.06, G:0.08, T:0.71
Consensus pattern (21 bp):
CTTTTATTTATTTTTGATTTT
Found at i:56123 original size:43 final size:43
Alignment explanation
Indices: 56059--56141 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
56049 ATCTTCCAAG
*
56059 AACGTATTTCATATGAAAAATCATAGAAACTTTAATATATAAT
1 AACGTATTTCATATGAAAAATCATAGAAAATTTAATATATAAT
* *
56102 AACGTATTTCATATGAGAAATCATATAAAATTTAATATAT
1 AACGTATTTCATATGAAAAATCATAGAAAATTTAATATAT
56142 TATTATAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.36
Consensus pattern (43 bp):
AACGTATTTCATATGAAAAATCATAGAAAATTTAATATATAAT
Found at i:56177 original size:17 final size:17
Alignment explanation
Indices: 56134--56165 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56124 ATATAAAATT
56134 TAAT-ATATTATTATAA
1 TAATAATATTATTATAA
56150 TAATAATATTATTATA
1 TAATAATATTATTATA
56166 TATATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATAATATTATTATAA
Found at i:56933 original size:22 final size:22
Alignment explanation
Indices: 56908--56950 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
56898 AATAATATTG
*
56908 AACATTTTGTCACTAAAAATAA
1 AACATTTGGTCACTAAAAATAA
56930 AACATTTGGTCACTAAAAATA
1 AACATTTGGTCACTAAAAATA
56951 CTTAATGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (22 bp):
AACATTTGGTCACTAAAAATAA
Found at i:58540 original size:23 final size:23
Alignment explanation
Indices: 58510--58566 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
58500 CTCGTATAAA
58510 TGCACCGAAGTACCACATAGAAT
1 TGCACCGAAGTACCACATAGAAT
* * *
58533 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTACCACATAGAAT
*
58556 TGCACTGAAGT
1 TGCACCGAAGT
58567 GCCATATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTACCACATAGAAT
Found at i:72992 original size:24 final size:22
Alignment explanation
Indices: 72965--73126 Score: 123
Period size: 24 Copynumber: 6.9 Consensus size: 22
72955 AAATAATGAC
72965 AAAAGAAAAAGAGAAAAAAAATAA
1 AAAAGAAAAA-AGAAAAAAAA-AA
* *
72989 AAAATAAAAAGGAAAAAAAAAAA
1 AAAAGAAAAAAG-AAAAAAAAAA
73012 AAAATGAAAAAAGAAGAAAATGAAAA
1 AAAA-GAAAAAAGAA-AAAA--AAAA
*
73038 AAATGAAAAAAAAGAAAAAAAGAAA
1 AAA--AGAAAAAAGAAAAAAA-AAA
73063 AAAA-AAAAAA-AAGAAAAAAGAA
1 AAAAGAAAAAAGAA-AAAAAA-AA
***
73085 AAAAGAAAAAATGTTGAAAAAAA
1 AAAAGAAAAAA-GAAAAAAAAAA
*
73108 AAAAG-AAAAAGAAATAAAA
1 AAAAGAAAAAAGAAAAAAAA
73127 GGGGGTTCAA
Statistics
Matches: 113, Mismatches: 12, Indels: 29
0.73 0.08 0.19
Matches are distributed among these distances:
21 8 0.07
22 22 0.19
23 23 0.20
24 33 0.29
25 6 0.05
26 11 0.10
27 9 0.08
28 1 0.01
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.06
Consensus pattern (22 bp):
AAAAGAAAAAAGAAAAAAAAAA
Found at i:73096 original size:55 final size:54
Alignment explanation
Indices: 72951--73126 Score: 178
Period size: 59 Copynumber: 3.2 Consensus size: 54
72941 TATTCGCTTG
* * * * *
72951 AAAAAAATAATGACAAAAGAAAAAGAGAAAAAA--AATAAAAAATAAAAAGGAAAA
1 AAAAAAAAAAAGAAAAAAGAAAAA-AGAAAAAATGAA-AAAAAAAAAAAAAGAAAA
73005 AAAAAAAAAAATGAAAAAAGAAGAAAATGAAAAAAATGAAAAAAAAGAAAAAAAGAAAA
1 AAAAAAAAAAA-GAAAAAAGAA-AAAA-G-AAAAAATGAAAAAAAA-AAAAAAAGAAAA
***
73064 AAAAAAAAAAAGAAAAAAGAAAAAAGAAAAAATG-TTGAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAGAAAAAAGAAAAAAGAAAAAATGAAAAAAAAAAAAAAAGAAAA
* *
73117 AGAAATAAAA
1 AAAAAAAAAA
73127 GGGGGTTCAA
Statistics
Matches: 105, Mismatches: 10, Indels: 15
0.81 0.08 0.12
Matches are distributed among these distances:
53 20 0.19
54 13 0.12
55 18 0.17
56 5 0.05
57 10 0.10
58 16 0.15
59 23 0.22
ACGTcount: A:0.82, C:0.01, G:0.11, T:0.06
Consensus pattern (54 bp):
AAAAAAAAAAAGAAAAAAGAAAAAAGAAAAAATGAAAAAAAAAAAAAAAGAAAA
Found at i:73103 original size:58 final size:59
Alignment explanation
Indices: 72981--73126 Score: 190
Period size: 59 Copynumber: 2.4 Consensus size: 59
72971 AAAAGAGAAA
72981 AAAAATAAAAAATAAAAAGGAAAAAAAAAAAAAAATGAAAAAAGAAGAAAATGAAAAAAATG
1 AAAAA-AAAAAA-AAAAA-GAAAAAAAAAAAAAAATGAAAAAAGAAGAAAATGAAAAAAATG
* *
73043 AAAAAAAAGAAAAAAAGAAAAAAAAAAAAAAA-GAAAAAAGAA-AAAA-GAAAAAATGTTG
1 AAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAATGAAAAAAGAAGAAAATGAAAAAA--ATG
*
73101 AAAAAAAAAAAGAAAAAGAAATAAAA
1 AAAAAAAAAAA-AAAAAGAAAAAAAA
73127 GGGGGTTCAA
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
56 7 0.09
57 4 0.05
58 22 0.29
59 29 0.38
60 5 0.06
61 5 0.06
62 5 0.06
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (59 bp):
AAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAATGAAAAAAGAAGAAAATGAAAAAAATG
Found at i:73105 original size:65 final size:65
Alignment explanation
Indices: 72965--73097 Score: 177
Period size: 65 Copynumber: 2.1 Consensus size: 65
72955 AAATAATGAC
* * * *
72965 AAAA-GAAAAAGA-GAAAAAAAATAAAAAATAAAAAGGAAAAAAAAAAAAAAATGAAAAAAGAAG
1 AAAATGAAAAAAATGAAAAAAAAGAAAAAATAAAAAGAAAAAAAAAAAAAAAAAGAAAAAAGAAG
73028 AAAATGAAAAAAATGAAAAAAAAGAAAAAA-AGAAAA-AAAAAAAAAAAGAAAAAAGAAAAAAGA
1 AAAATGAAAAAAATGAAAAAAAAGAAAAAATA-AAAAGAAAAAAAAAAA-AAAAAAGAAAAAAGA
73091 A-
64 AG
73092 AAAATG
1 AAAATG
73098 TTGAAAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
63 4 0.06
64 24 0.39
65 34 0.55
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (65 bp):
AAAATGAAAAAAATGAAAAAAAAGAAAAAATAAAAAGAAAAAAAAAAAAAAAAAGAAAAAAGAAG
Found at i:73111 original size:1 final size:1
Alignment explanation
Indices: 72978--73095 Score: 83
Period size: 1 Copynumber: 118.0 Consensus size: 1
72968 AGAAAAAGAG
* * ** ** * * ** **
72978 AAAAAAAATAAAAAATAAAAAGGAAAAAAAAAAAAAAATGAAAAAAGAAGAAAATGAAAAAAATG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
73043 AAAAAAAAGAAAAAAAGAAAAAAAAAAAAAAAGAAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
73096 TGTTGAAAAA
Statistics
Matches: 88, Mismatches: 29, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 88 1.00
ACGTcount: A:0.86, C:0.00, G:0.10, T:0.04
Consensus pattern (1 bp):
A
Found at i:74174 original size:16 final size:17
Alignment explanation
Indices: 74137--74171 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
74127 AGGTTTCCCA
74137 AAGATAGTTGAAGATTG
1 AAGATAGTTGAAGATTG
74154 AAGATA-TTGAAGCATTG
1 AAGATAGTTGAAG-ATTG
74171 A
1 A
74172 GATGAAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.29
Consensus pattern (17 bp):
AAGATAGTTGAAGATTG
Found at i:74440 original size:37 final size:37
Alignment explanation
Indices: 74390--74498 Score: 150
Period size: 37 Copynumber: 2.9 Consensus size: 37
74380 AAAACAAGTT
* * *
74390 AATCTTAAGCCTTCATGAAAGAGCAGTGAAGCAATTC
1 AATCTTAAGCCTTCACGGAAGAGCAGTGAAGCAAATC
*
74427 AATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
1 AATCTTAAGCCTTCACGGAAGAGCAGTGAAGCAAATC
74464 -ATCTATAAGCCTTCACGGAAGAGTC-GTGAAGCAAA
1 AATCT-TAAGCCTTCACGGAAGAG-CAGTGAAGCAAA
74499 CTCATTTTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
36 4 0.06
37 61 0.94
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (37 bp):
AATCTTAAGCCTTCACGGAAGAGCAGTGAAGCAAATC
Found at i:74589 original size:55 final size:55
Alignment explanation
Indices: 74514--74988 Score: 593
Period size: 55 Copynumber: 8.7 Consensus size: 55
74504 TTTATGAAGA
* * * * * ****
74514 TCGAGTCATATACTCTCTGAAGGAATAGGGAACAGACACATAAATTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
* * *
74569 TCGATTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTCGCTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
* * ** *
74624 TCGAGTCTTATACTCCATGAATGAATAGGGAGCAGACACGTTCACTGAAGATTAT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
*
74679 TCGAGT-TCTATACTCCCTG-AAGAATAGGGAGC-GAACCCGTTTGCTGAAGATTGT
1 TCGAGTCT-TATACTCCCTGAAAGAATAGGGAGCAG-ACACGTTTGCTGAAGATTGT
* *
74733 TCGAGTCTTATACTCCCTGAAAAAATAGGGAGC-GAACCCGTTTGCTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAG-ACACGTTTGCTGAAGATTGT
* * *
74788 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCGGACCCG-TTGTTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
* * * *
74842 TCGAGTCTTATACTCCCTGAAAGAATAGGAAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
* * *
74897 TCGAGTCTTATACTCTCTGAACGAATAGGGAGCAGACATGTTTGCTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
*
74952 TCGAGTCTTATACTTCCTG-AAGAAATAGGGAGCAGAC
1 TCGAGTCTTATACTCCCTGAAAG-AATAGGGAGCAGAC
74989 CCGTCATTTG
Statistics
Matches: 379, Mismatches: 34, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
53 1 0.00
54 100 0.26
55 277 0.73
56 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (55 bp):
TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
Found at i:74760 original size:109 final size:110
Alignment explanation
Indices: 74514--74988 Score: 593
Period size: 109 Copynumber: 4.3 Consensus size: 110
74504 TTTATGAAGA
* * * * * ** * *
74514 TCGAGTCATATACTCTCTGAAGGAATAGGGAACAGACACATAAATTGAAGATTGTTCGATTCTTA
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTACTGAAGATTGTTCGAGTCTTA
* *
74579 TACTCCCTGAATGAATAGGGAGCAGACACGTTCGCTGAAGATTGT
66 TACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
* * * *
74624 TCGAGTCTTATACTCCATGAATGAATAGGGAGCAGACACGTTCACTGAAGATTATTCGAGT-TCT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTACTGAAGATTGTTCGAGTCT-T
*
74688 ATACTCCCTGAA-GAATAGGGAGC-GAACCCGTTTGCTGAAGATTGT
65 ATACTCCCTGAACGAATAGGGAGCAG-ACACGTTTGCTGAAGATTGT
* * *
74733 TCGAGTCTTATACTCCCTGAAAAAATAGGGAGC-GAACCCGTTTGCTGAAGATTGTTCGAGTCTT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAG-ACACGTTTACTGAAGATTGTTCGAGTCTT
* * * *
74797 ATACTCCCTGAAAGAATAGGGAGCGGACCCG-TTGTTGAAGATTGT
65 ATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
* * * **
74842 TCGAGTCTTATACTCCCTGAAAGAATAGGAAGCGGACCCGTTTGTTGAAGATTGTTCGAGTCTTA
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTACTGAAGATTGTTCGAGTCTTA
* *
74907 TACTCTCTGAACGAATAGGGAGCAGACATGTTTGCTGAAGATTGT
66 TACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
*
74952 TCGAGTCTTATACTTCCTG-AAGAAATAGGGAGCAGAC
1 TCGAGTCTTATACTCCCTGAAAG-AATAGGGAGCAGAC
74989 CCGTCATTTG
Statistics
Matches: 323, Mismatches: 33, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
108 2 0.01
109 196 0.61
110 124 0.38
111 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (110 bp):
TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTACTGAAGATTGTTCGAGTCTTA
TACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
Found at i:74816 original size:164 final size:164
Alignment explanation
Indices: 74559--74988 Score: 625
Period size: 164 Copynumber: 2.6 Consensus size: 164
74549 ACACATAAAT
* * *
74559 TGAAGATTGTTCGATTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTCGCTGAAGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
* *
74624 TCGAGTCTTATACTCCATGAATGAATAGGGAGCAGACACGTTCACTGAAGATTATTCGAGT-TCT
66 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTT-ACTGAAGATTATTCGAGTCT-T
*
74688 ATACTCCCTG-AAGAATAGGGAGCGAACCCGTTTGC
129 ATACTCCCTGAAAGAATAGGAAGCGAACCCGTTTGC
* *
74723 TGAAGATTGTTCGAGTCTTATACTCCCTGAAAAAATAGGGAGC-GAACCCGTTTGCTGAAGATTG
1 TGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAG-ACACGTTTGCTGAAGATTG
* * ** *
74787 TTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTGTTGAAGATTGTTCGAGTCTTA
65 TTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTACTGAAGATTATTCGAGTCTTA
* *
74852 TACTCCCTGAAAGAATAGGAAGCGGACCCGTTTGT
130 TACTCCCTGAAAGAATAGGAAGCGAACCCGTTTGC
* * *
74887 TGAAGATTGTTCGAGTCTTATACTCTCTGAACGAATAGGGAGCAGACATGTTTGCTGAAGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
*
74952 TCGAGTCTTATACTTCCTG-AAGAAATAGGGAGCAGAC
66 TCGAGTCTTATACTCCCTGAAAG-AATAGGGAGCAGAC
74989 CCGTCATTTG
Statistics
Matches: 239, Mismatches: 22, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
163 30 0.13
164 208 0.87
165 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (164 bp):
TGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTACTGAAGATTATTCGAGTCTTAT
ACTCCCTGAAAGAATAGGAAGCGAACCCGTTTGC
Found at i:78894 original size:16 final size:17
Alignment explanation
Indices: 78853--78894 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
78843 TTTGGTTCAC
78853 GGAATAAAAGATTACCAGTG
1 GGAAT-AAAGATTACCA--G
78873 GGAATAAAGATTACCA-
1 GGAATAAAGATTACCAG
78889 GGAATA
1 GGAATA
78895 GGATTACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.27
19 11 0.50
20 5 0.23
ACGTcount: A:0.48, C:0.10, G:0.24, T:0.19
Consensus pattern (17 bp):
GGAATAAAGATTACCAG
Done.