Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007114.1 Hibiscus syriacus cultivar Beakdansim tig00018592_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: 98494
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:199 original size:22 final size:24
Alignment explanation
Indices: 171--246 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 24
161 AATACCAAAC
171 AATAACAAAACCGGTAGAAA-AA-
1 AATAACAAAACCGGTAGAAACAAT
*
193 AATAACAAAATCGGTA-AAACGCCCAAT
1 AATAACAAAACCGGTAGAAA----CAAT
*
220 AATAACAAAACCGGTAGAAATAAT
1 AATAACAAAACCGGTAGAAACAAT
244 AAT
1 AAT
247 GTTTCCGGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
21 3 0.07
22 15 0.34
24 6 0.14
26 2 0.05
27 15 0.34
28 3 0.07
ACGTcount: A:0.58, C:0.16, G:0.12, T:0.14
Consensus pattern (24 bp):
AATAACAAAACCGGTAGAAACAAT
Found at i:7843 original size:40 final size:40
Alignment explanation
Indices: 7788--7867 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
7778 TCTGTCTTTC
7788 AACTTTTTATTTACAAAGAAAAAATAAAGGAAGAATTGCT
1 AACTTTTTATTTACAAAGAAAAAATAAAGGAAGAATTGCT
7828 AACTTTTTATTTACAAAGAAAAAATAAAGGAAGAATTGCT
1 AACTTTTTATTTACAAAGAAAAAATAAAGGAAGAATTGCT
7868 GGAACGCAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (40 bp):
AACTTTTTATTTACAAAGAAAAAATAAAGGAAGAATTGCT
Found at i:11540 original size:19 final size:16
Alignment explanation
Indices: 11501--11532 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11491 AATAGATTAT
*
11501 ATTAATAAAATAAATA
1 ATTAATAAAAAAAATA
11517 ATTAATAAAAAAAATA
1 ATTAATAAAAAAAATA
11533 TATTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATTAATAAAAAAAATA
Found at i:12794 original size:60 final size:60
Alignment explanation
Indices: 12683--12795 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
12673 TATAAGATAC
* * *
12683 TACTTTATTGAGTCCCTTAACTATTAAAAGTCACAAAATGATGTCTTGACTATATAAAGT
1 TACTTTATTGAGTCCCTCAACTATTAAAAGTCACAAAATGATATCTCGACTATATAAAGT
* * *
12743 TACTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATGATTATC-CGACTAT
1 TACTTTATTGAGTCCCTCAACTATTAAAAGTCACAAAATGA-TATCTCGACTAT
12796 TTATTATATT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 43 0.93
61 3 0.07
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (60 bp):
TACTTTATTGAGTCCCTCAACTATTAAAAGTCACAAAATGATATCTCGACTATATAAAGT
Found at i:17359 original size:24 final size:24
Alignment explanation
Indices: 17326--17386 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
17316 TTCGGTAATC
* *
17326 CGTTCATTTATGTTCATTCAT-TT
1 CGTTCGTTTATATTCATTCATGTT
*
17349 ACGTTCGTTTATATTCATTTATGTT
1 -CGTTCGTTTATATTCATTCATGTT
17374 CGTTCGTTTATAT
1 CGTTCGTTTATAT
17387 CCAGGGACGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (24 bp):
CGTTCGTTTATATTCATTCATGTT
Found at i:25234 original size:16 final size:18
Alignment explanation
Indices: 25192--25236 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
25182 TCACGGAATG
25192 TAAGATTACCAGTGAGAA
1 TAAGATTACCAGTGAGAA
25210 TAAAAGATTACCAG-G-GAA
1 T--AAGATTACCAGTGAGAA
25228 TAAGATTAC
1 TAAGATTAC
25237 TGTGAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 5 0.20
19 1 0.04
20 11 0.44
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (18 bp):
TAAGATTACCAGTGAGAA
Found at i:25411 original size:37 final size:37
Alignment explanation
Indices: 25377--25446 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
25367 TACAAATTGT
25377 AAAATATTTATAT-ATTTTATTTAAAAAATTAAATTC
1 AAAATATTTATATAATTTTATTTAAAAAATTAAATTC
* * *
25413 ATAATATTTATATAATTTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTATTTAAAAAATTAAA
25447 AATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 12 0.40
37 18 0.60
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (37 bp):
AAAATATTTATATAATTTTATTTAAAAAATTAAATTC
Found at i:32668 original size:2 final size:2
Alignment explanation
Indices: 32661--32704 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
32651 ACCCGGTTTA
32661 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
32703 AT
1 AT
32705 TTTTTATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32837 original size:39 final size:39
Alignment explanation
Indices: 32736--32843 Score: 141
Period size: 39 Copynumber: 2.8 Consensus size: 39
32726 TTATTTATAA
*
32736 TTCTCAAATTATTTCAC-TCTAACATTCTAAATTCCTAAT
1 TTCTTAAATTATTTCACAT-TAACATTCTAAATTCCTAAT
* *
32775 TTCTTAAATT-TTACCACCA-TAACATTCTAAATTCTTAAT
1 TTCTTAAATTATT-TCA-CATTAACATTCTAAATTCCTAAT
32814 TTCTTAAATTATTTCACATTAACATTCTAA
1 TTCTTAAATTATTTCACATTAACATTCTAA
32844 TTTTTTTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
38 4 0.07
39 53 0.88
40 3 0.05
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.44
Consensus pattern (39 bp):
TTCTTAAATTATTTCACATTAACATTCTAAATTCCTAAT
Found at i:34271 original size:21 final size:21
Alignment explanation
Indices: 34245--34284 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
34235 TTGGTTATCG
34245 AACA-TTAAACAAACAAATACA
1 AACATTTAAA-AAACAAATACA
*
34266 AACATTTTAAAAACAAATA
1 AACATTTAAAAAACAAATA
34285 AACGAACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.20
Consensus pattern (21 bp):
AACATTTAAAAAACAAATACA
Found at i:36654 original size:17 final size:17
Alignment explanation
Indices: 36632--36666 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
36622 GGTAGAGAGA
36632 GAGAGAGTTACTGGTTT
1 GAGAGAGTTACTGGTTT
36649 GAGAGAGTTACTGGTTT
1 GAGAGAGTTACTGGTTT
36666 G
1 G
36667 CCTTTCTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.37, T:0.34
Consensus pattern (17 bp):
GAGAGAGTTACTGGTTT
Found at i:38004 original size:2 final size:2
Alignment explanation
Indices: 37999--38031 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
37989 TTACCTTGAT
37999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38032 GGTGTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39931 original size:39 final size:39
Alignment explanation
Indices: 39830--39937 Score: 132
Period size: 39 Copynumber: 2.8 Consensus size: 39
39820 TTATTTATAA
* *
39830 TTCTCAAATTATTTCGC-TCTAACATTCTAAATTCCTAAT
1 TTCTTAAATTATTTCACAT-TAACATTCTAAATTCCTAAT
* *
39869 TTCTTAAATT-TTACCACCA-TAACATTCTAAATTCTTAAT
1 TTCTTAAATTATT-TCA-CATTAACATTCTAAATTCCTAAT
39908 TTCTTAAATTATTTCACATTAACATTCTAA
1 TTCTTAAATTATTTCACATTAACATTCTAA
39938 TTTTTTTAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
38 4 0.07
39 52 0.88
40 3 0.05
ACGTcount: A:0.34, C:0.20, G:0.01, T:0.44
Consensus pattern (39 bp):
TTCTTAAATTATTTCACATTAACATTCTAAATTCCTAAT
Found at i:47789 original size:2 final size:2
Alignment explanation
Indices: 47782--47819 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47772 TATGTTCTGA
47782 AT AT AT AT AT AT AT AT AT AT AT AT 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
47820 GTATTTGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52830 original size:3 final size:3
Alignment explanation
Indices: 52822--52866 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
52812 TGGCATGACA
52822 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52867 ATAAAAATAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:53132 original size:15 final size:16
Alignment explanation
Indices: 53102--53135 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
53092 TTCTATTTTT
53102 ATTTTATATTTTAAATA
1 ATTTTATA-TTTAAATA
53119 ATTTTATA-TTAAATA
1 ATTTTATATTTAAATA
53134 AT
1 AT
53136 AATGATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTATATTTAAATA
Found at i:54201 original size:40 final size:40
Alignment explanation
Indices: 54142--54224 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
54132 AAACTTTACT
* * *
54142 TTTTCTCCTATTTCGCTCATTGTACTTTCAGTTTTTTTAA
1 TTTTCTCCTATTTCACTCATTGTACTTTCAATTTTTTCAA
54182 TTTTCTCCTATTTCACTCATTGTACTTTCAATTTTTTCAA
1 TTTTCTCCTATTTCACTCATTGTACTTTCAATTTTTTCAA
54222 TTT
1 TTT
54225 GCTCACTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.17, C:0.20, G:0.05, T:0.58
Consensus pattern (40 bp):
TTTTCTCCTATTTCACTCATTGTACTTTCAATTTTTTCAA
Found at i:54743 original size:3 final size:3
Alignment explanation
Indices: 54737--54763 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54727 AATAATAAAA
54737 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
54764 TGTAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:55732 original size:15 final size:15
Alignment explanation
Indices: 55712--55741 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55702 CTTTTCTTTG
55712 TTAAATTAAAATAAA
1 TTAAATTAAAATAAA
55727 TTAAATTAAAATAAA
1 TTAAATTAAAATAAA
55742 GTTAGTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAATTAAAATAAA
Found at i:57856 original size:21 final size:20
Alignment explanation
Indices: 57798--57856 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 20
57788 ATCACTTTTT
*
57798 AAAAGGATCGATCCCTCGGG
1 AAAAGGATCGATCCCTTGGG
57818 AGAAAGGATCGATCCCTTGGAG
1 A-AAAGGATCGATCCCTTGG-G
*
57840 AAAAAGATCGATCCCTT
1 AAAAGGATCGATCCCTT
57857 CTCTGTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 1 0.03
21 32 0.91
22 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (20 bp):
AAAAGGATCGATCCCTTGGG
Found at i:62444 original size:16 final size:16
Alignment explanation
Indices: 62419--62449 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62409 TCATCACCAC
62419 CATACATACATACATG
1 CATACATACATACATG
*
62435 CATACGTACATACAT
1 CATACATACATACAT
62450 AAACCGCCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (16 bp):
CATACATACATACATG
Found at i:63844 original size:21 final size:21
Alignment explanation
Indices: 63819--64032 Score: 293
Period size: 21 Copynumber: 10.2 Consensus size: 21
63809 AGTTGCTGCA
* *
63819 GGCGGCGAGAAGAAGGAAGGA
1 GGCGGCGAGAAAAAGGAAGGC
* *
63840 GGCGGTGAAAAAAAGGAAGGC
1 GGCGGCGAGAAAAAGGAAGGC
*
63861 GGCGGCGAGAAGAAGGAAGGC
1 GGCGGCGAGAAAAAGGAAGGC
*
63882 GGCGGTGAGAAAAAGGAAGGC
1 GGCGGCGAGAAAAAGGAAGGC
* *
63903 GGCGGTGAAAAAAAGGAAGGC
1 GGCGGCGAGAAAAAGGAAGGC
* *
63924 GGCGGTGAGAAGAAGGAAGGC
1 GGCGGCGAGAAAAAGGAAGGC
63945 GGCGGCGAGAAAAAGGAAGGC
1 GGCGGCGAGAAAAAGGAAGGC
*
63966 GGCGGCGAGAAAAAGGAAGGA
1 GGCGGCGAGAAAAAGGAAGGC
*
63987 GGCGGCGAGAAGAAGGAAGGC
1 GGCGGCGAGAAAAAGGAAGGC
* * *
64008 GGCGGTGAAAAAAAGGAAGGA
1 GGCGGCGAGAAAAAGGAAGGC
64029 GGCG
1 GGCG
64033 AGAAGAAGGA
Statistics
Matches: 172, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 172 1.00
ACGTcount: A:0.38, C:0.11, G:0.49, T:0.02
Consensus pattern (21 bp):
GGCGGCGAGAAAAAGGAAGGC
Found at i:63865 original size:42 final size:42
Alignment explanation
Indices: 63819--64044 Score: 332
Period size: 42 Copynumber: 5.5 Consensus size: 42
63809 AGTTGCTGCA
* *
63819 GGCGGCGAGAAGAAGGAAGGAGGCGGTGAAAAAAAGGAAGGC
1 GGCGGCGAGAAGAAGGAAGGCGGCGGTGAGAAAAAGGAAGGC
63861 GGCGGCGAGAAGAAGGAAGGCGGCGGTGAGAAAAAGGAAGGC
1 GGCGGCGAGAAGAAGGAAGGCGGCGGTGAGAAAAAGGAAGGC
* * * *
63903 GGCGGTGAAAAAAAGGAAGGCGGCGGTGAGAAGAAGGAAGGC
1 GGCGGCGAGAAGAAGGAAGGCGGCGGTGAGAAAAAGGAAGGC
* * *
63945 GGCGGCGAGAAAAAGGAAGGCGGCGGCGAGAAAAAGGAAGGA
1 GGCGGCGAGAAGAAGGAAGGCGGCGGTGAGAAAAAGGAAGGC
*
63987 GGCGGCGAGAAGAAGGAAGGCGGCGGTGAAAAAAAGGAA---
1 GGCGGCGAGAAGAAGGAAGGCGGCGGTGAGAAAAAGGAAGGC
*
64026 GGAGGCGAGAAGAAGGAAG
1 GGCGGCGAGAAGAAGGAAG
64045 ACGACGGACG
Statistics
Matches: 169, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 18 0.11
42 151 0.89
ACGTcount: A:0.39, C:0.10, G:0.48, T:0.02
Consensus pattern (42 bp):
GGCGGCGAGAAGAAGGAAGGCGGCGGTGAGAAAAAGGAAGGC
Found at i:63907 original size:63 final size:63
Alignment explanation
Indices: 63819--64032 Score: 338
Period size: 63 Copynumber: 3.4 Consensus size: 63
63809 AGTTGCTGCA
*
63819 GGCGGCGAGAAGAAGGAAGGAGGCGGTGAAAAAAAGGAAGGCGGCGGCGAGAAGAAGGAAGGC
1 GGCGGCGAGAAAAAGGAAGGAGGCGGTGAAAAAAAGGAAGGCGGCGGCGAGAAGAAGGAAGGC
* * *
63882 GGCGGTGAGAAAAAGGAAGGCGGCGGTGAAAAAAAGGAAGGCGGCGGTGAGAAGAAGGAAGGC
1 GGCGGCGAGAAAAAGGAAGGAGGCGGTGAAAAAAAGGAAGGCGGCGGCGAGAAGAAGGAAGGC
* * * *
63945 GGCGGCGAGAAAAAGGAAGGCGGCGGCGAGAAAAAGGAAGGAGGCGGCGAGAAGAAGGAAGGC
1 GGCGGCGAGAAAAAGGAAGGAGGCGGTGAAAAAAAGGAAGGCGGCGGCGAGAAGAAGGAAGGC
* *
64008 GGCGGTGAAAAAAAGGAAGGAGGCG
1 GGCGGCGAGAAAAAGGAAGGAGGCG
64033 AGAAGAAGGA
Statistics
Matches: 139, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 139 1.00
ACGTcount: A:0.38, C:0.11, G:0.49, T:0.02
Consensus pattern (63 bp):
GGCGGCGAGAAAAAGGAAGGAGGCGGTGAAAAAAAGGAAGGCGGCGGCGAGAAGAAGGAAGGC
Found at i:65596 original size:15 final size:15
Alignment explanation
Indices: 65573--65622 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
65563 CCGTAGGACC
65573 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
65588 ACTATGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
65603 ACTACGTCCCTAAGG
1 ACTACGTCCCGAAGG
65618 ACTAC
1 ACTAC
65623 AGAACCCTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.18
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:72312 original size:18 final size:17
Alignment explanation
Indices: 72285--72328 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
72275 GCTATATATA
*
72285 TCCCGTAGGACCACTACG
1 TCCCGAAGGA-CACTACG
72303 TCCCGAAGG--ACTACG
1 TCCCGAAGGACACTACG
72318 TCCCGAAGGAC
1 TCCCGAAGGAC
72329 TACAGAACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 15 0.65
18 8 0.35
ACGTcount: A:0.25, C:0.36, G:0.25, T:0.14
Consensus pattern (17 bp):
TCCCGAAGGACACTACG
Found at i:72317 original size:15 final size:15
Alignment explanation
Indices: 72297--72331 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
72287 CCGTAGGACC
72297 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
72312 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
72327 ACTAC
1 ACTAC
72332 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:84737 original size:20 final size:20
Alignment explanation
Indices: 84712--84751 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
84702 TTTTTTCCTT
84712 ATACCTTCCCTAGTATATCA
1 ATACCTTCCCTAGTATATCA
84732 ATACCTTCCCTAGTATATCA
1 ATACCTTCCCTAGTATATCA
84752 GAGTGAACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (20 bp):
ATACCTTCCCTAGTATATCA
Found at i:87799 original size:27 final size:24
Alignment explanation
Indices: 87757--87808 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 24
87747 CGAGTAAAAC
*
87757 GGTTCGGTTCGGTTCGGTTTTAAAT
1 GGTTCGGTTCGGTTC-GATTTAAAT
87782 GGTTCGGTTTTCGGTTCGATTTAAAT
1 GGTTCGG--TTCGGTTCGATTTAAAT
87808 G
1 G
87809 CTTCATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 9 0.38
27 8 0.33
ACGTcount: A:0.13, C:0.12, G:0.31, T:0.44
Consensus pattern (24 bp):
GGTTCGGTTCGGTTCGATTTAAAT
Found at i:87818 original size:26 final size:27
Alignment explanation
Indices: 87764--87818 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
87754 AACGGTTCGG
* * *
87764 TTCGGTTCGGTTTTAAATGGTTCGGTT
1 TTCGGTTCGGATTTAAATGCTTCAGTT
*
87791 TTCGGTTC-GATTTAAATGCTTCATTT
1 TTCGGTTCGGATTTAAATGCTTCAGTT
87817 TT
1 TT
87819 TTGATTCGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.15, C:0.13, G:0.22, T:0.51
Consensus pattern (27 bp):
TTCGGTTCGGATTTAAATGCTTCAGTT
Found at i:91693 original size:21 final size:21
Alignment explanation
Indices: 91645--91698 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
91635 CCCCTATGGG
* *
91645 GAGTATCGATACTCTTTCCTT
1 GAGTATCGATACTCTATCATT
*
91666 G-GTATCGATACTCTATGATT
1 GAGTATCGATACTCTATCATT
91686 GAGTATCGATACT
1 GAGTATCGATACT
91699 ACCCTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (21 bp):
GAGTATCGATACTCTATCATT
Done.