Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005702.1 Hibiscus syriacus cultivar Beakdansim tig00013335_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: 49178
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:4202 original size:20 final size:20
Alignment explanation
Indices: 4177--4228 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
4167 CGGTTGAATG
*
4177 GGTATCAATACCAGAAGGAT
1 GGTATCGATACCAGAAGGAT
4197 GGTATCGATACCAGAAGGAT
1 GGTATCGATACCAGAAGGAT
4217 GGTATCGATACC
1 GGTATCGATACC
4229 GTTGTTAAGA
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:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (20 bp):
GGTATCGATACCAGAAGGAT
Found at i:4893 original size:21 final size:21
Alignment explanation
Indices: 4852--4961 Score: 78
Period size: 21 Copynumber: 5.0 Consensus size: 21
4842 TCGAAGGTTT
* *
4852 TATGTGGTTCTTCGAG-ACAAA
1 TATGTGGTACTTCG-GTGCAAA
4873 TATGTGGTACTTCGGTGCAAA
1 TATGTGGTACTTCGGTGCAAA
* * *
4894 CCTATGTGGCACTTTGGTGTAAA
1 --TATGTGGTACTTCGGTGCAAA
* ** *
4917 TTTATGTGGTCCTTCGGAACAAT
1 --TATGTGGTACTTCGGTGCAAA
*
4940 TATGTGGCACTTCGGTGCAAA
1 TATGTGGTACTTCGGTGCAAA
4961 T
1 T
4962 TACGAGCTGT
Statistics
Matches: 67, Mismatches: 19, Indels: 6
0.73 0.21 0.07
Matches are distributed among these distances:
20 1 0.01
21 34 0.51
23 32 0.48
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (21 bp):
TATGTGGTACTTCGGTGCAAA
Found at i:4907 original size:23 final size:22
Alignment explanation
Indices: 4869--4963 Score: 88
Period size: 23 Copynumber: 4.3 Consensus size: 22
4859 TTCTTCGAGA
*
4869 CAAA-TATGTGGTACTTCGGTG
1 CAAATTATGTGGCACTTCGGTG
* *
4890 CAAACCTATGTGGCACTTTGGTG
1 CAAA-TTATGTGGCACTTCGGTG
* **
4913 TAAATTTATGTGGTC-CTTCGGAA
1 CAAA-TTATGTGG-CACTTCGGTG
4936 C-AATTATGTGGCACTTCGGTG
1 CAAATTATGTGGCACTTCGGTG
4957 CAAATTA
1 CAAATTA
4964 CGAGCTGTGG
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.02
21 19 0.33
22 7 0.12
23 30 0.52
24 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (22 bp):
CAAATTATGTGGCACTTCGGTG
Found at i:11778 original size:23 final size:23
Alignment explanation
Indices: 11752--11804 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
11742 TTAGGACAAA
11752 TATGTGGCACTTCGATGCAAACC
1 TATGTGGCACTTCGATGCAAACC
* * **
11775 TATGTGGCACTTTGGTGCAAATT
1 TATGTGGCACTTCGATGCAAACC
11798 TATGTGG
1 TATGTGG
11805 TCCTTCGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (23 bp):
TATGTGGCACTTCGATGCAAACC
Found at i:12308 original size:20 final size:20
Alignment explanation
Indices: 12271--12311 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
12261 CCTTTTGGTA
*
12271 TTTATGTAAATTATTATGTT
1 TTTATGTAAATAATTATGTT
12291 TTTATGTAAA-AATGTATGTT
1 TTTATGTAAATAAT-TATGTT
12311 T
1 T
12312 AATGATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (20 bp):
TTTATGTAAATAATTATGTT
Found at i:16994 original size:21 final size:21
Alignment explanation
Indices: 16965--17004 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16955 TATTGGTACC
*
16965 TAATTTATGAGGTTCGATACT
1 TAATCTATGAGGTTCGATACT
*
16986 TAATCTATGAGGTTTGATA
1 TAATCTATGAGGTTCGATA
17005 TGAAACATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.42
Consensus pattern (21 bp):
TAATCTATGAGGTTCGATACT
Found at i:18880 original size:20 final size:20
Alignment explanation
Indices: 18855--18892 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
18845 AGGTTTTCGA
18855 GATGAGCTGATGTTTCACGG
1 GATGAGCTGATGTTTCACGG
18875 GATGAGCTGATGTTTCAC
1 GATGAGCTGATGTTTCAC
18893 TAATATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
GATGAGCTGATGTTTCACGG
Found at i:19649 original size:45 final size:45
Alignment explanation
Indices: 19586--19973 Score: 537
Period size: 45 Copynumber: 8.6 Consensus size: 45
19576 CATTATTTTA
* * * * * *
19586 ATTTATGGCATTCGTTCATGCCTATAATGCACTGTTATGAATTTT
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTC
* * *
19631 ATTTATGGCATCCTTTCATGCCAATAATGCACTGTTATGCGTTTC
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTC
*
19676 ATTTATGGCATCCTTTCATGTCGATAATGCACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTC
** *
19721 ATTTAT-GCATCCTTTCATGTTGATAATGCACTGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTC
* * *
19765 ATTTATGGCATCCTTTCATTCCGATAATGCACCGTTATACGTTTC
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTC
* * *
19810 ATTTATGGCAACCTTTCATGTCGATAATGCACTGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTC
* **
19855 ATTTATGACATAATTTCATGCCGATAATTG-ACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCGATAA-TGCACCGTTATGCATTTC
19900 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTC
* *
19945 ATCTATAGCATCCTTTCATGCCGATAATG
1 ATTTATGGCATCCTTTCATGCCGATAATG
19974 AAAACATGTT
Statistics
Matches: 305, Mismatches: 35, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
44 44 0.14
45 259 0.85
46 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (45 bp):
ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTC
Found at i:19840 original size:134 final size:135
Alignment explanation
Indices: 19600--19973 Score: 563
Period size: 134 Copynumber: 2.8 Consensus size: 135
19590 ATGGCATTCG
* * * * *
19600 TTCATGCCTATAATGCACTGTTATGAATTTTATTTATGGCATCCTTTCATGCCAATAATGCACTG
1 TTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
19665 TTATGCGTTTCATTTATGGCATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATG-C
66 TTATGCGTTTCATTTATGGCATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGAC
**
19729 ATCCT
131 ATAAT
** *
19734 TTCATGTTGATAATGCACTGTTATGCATTTCATTTATGGCATCCTTTCATTCCGATAATGCACCG
1 TTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * *
19799 TTATACGTTTCATTTATGGCAACCTTTCATGTCGATAATGCACTGTTATGCATTTCATTTATGAC
66 TTATGCGTTTCATTTATGGCATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGAC
19864 ATAAT
131 ATAAT
*
19869 TTCATGCCGATAATTG-ACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
1 TTCATGCCGATAA-TGCACTGTTATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* * * *
19933 GTTATGCATTTCATCTATAGCATCCTTTCATGCCGATAATG
65 GTTATGCGTTTCATTTATGGCATCCTTTCATGTCGATAATG
19974 AAAACATGTT
Statistics
Matches: 215, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
134 117 0.54
135 96 0.45
136 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (135 bp):
TTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
TTATGCGTTTCATTTATGGCATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGAC
ATAAT
Found at i:25586 original size:45 final size:45
Alignment explanation
Indices: 25537--25872 Score: 354
Period size: 45 Copynumber: 7.7 Consensus size: 45
25527 TATAAGTTAT
* *
25537 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
** * * * * *
25582 TTTCATTTATGGCATTATTTCTTGCCAATAATGTACCGTTATTCG
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
** * *
25627 TTTCATTTATGGCATCCTACCATGTCGATAATGCATCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * * * * *
25672 TTTCATTTGTTGCATCCTTTCATGTCGATAATACACCGTTATACG
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
25717 TTTCATTTATGGTATCATTTCATGCCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
25762 TTTCATTTATGGAATCCTTTCATGCTGATAATGCACCGTTATG--
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
*
25805 ---CA-TT-T--CA---TTTCATGCCGATAATGCACCGTTATGTA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
25840 TTTCATTTATGGCTTCTTTTCATGCCGATAATG
1 TTTCATTTATGGCATCCTTTCATGCCGATAATG
25873 AAAATATATT
Statistics
Matches: 238, Mismatches: 41, Indels: 24
0.79 0.14 0.08
Matches are distributed among these distances:
33 25 0.11
36 1 0.00
38 3 0.01
39 4 0.02
40 3 0.01
42 1 0.00
45 201 0.84
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.42
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
Found at i:25816 original size:33 final size:33
Alignment explanation
Indices: 25779--25847 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
25769 TATGGAATCC
*
25779 TTTCATGCTGATAATGCACCGTTATGCATTTCA
1 TTTCATGCCGATAATGCACCGTTATGCATTTCA
*
25812 TTTCATGCCGATAATGCACCGTTATGTATTTCA
1 TTTCATGCCGATAATGCACCGTTATGCATTTCA
25845 TTT
1 TTT
25848 ATGGCTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.42
Consensus pattern (33 bp):
TTTCATGCCGATAATGCACCGTTATGCATTTCA
Found at i:29523 original size:14 final size:15
Alignment explanation
Indices: 29506--29538 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29496 GCAGACCATA
29506 ATTT-AAAACAACCT
1 ATTTAAAAACAACCT
*
29520 ATTTAAAAACAATCT
1 ATTTAAAAACAACCT
29535 ATTT
1 ATTT
29539 GTAGGCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTTAAAAACAACCT
Found at i:32754 original size:38 final size:38
Alignment explanation
Indices: 32640--32756 Score: 103
Period size: 38 Copynumber: 2.9 Consensus size: 38
32630 ACTAAATTTC
*
32640 AAATAAAAATTAATTAACCAAA-AATTAATAA-AATAAAT
1 AAATAAAAATTAATTAACCAAATAA--AAAAATAATAAAT
*
32678 AAATAACAATTAATTAACCTTCAAATTAAAATTTAAAATAATAAAT
1 AAATAAAAATTAATTAA-C--CAAA-T-AAA---AAAATAATAAAT
*
32724 TAATAAAAATTAATTAACCAAATAAAAAAATAA
1 AAATAAAAATTAATTAACCAAATAAAAAAATAA
32757 ATTTACCCTG
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
38 23 0.35
39 1 0.02
41 7 0.11
42 2 0.03
43 4 0.06
44 2 0.03
45 4 0.06
46 22 0.34
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (38 bp):
AAATAAAAATTAATTAACCAAATAAAAAAATAATAAAT
Found at i:33124 original size:18 final size:18
Alignment explanation
Indices: 33101--33202 Score: 75
Period size: 18 Copynumber: 5.6 Consensus size: 18
33091 GTAAGTTAGG
*
33101 ATTTTTTTTAATTAAGAT
1 ATTTTTTTAAATTAAGAT
*
33119 ATTTTTCTTAAATTAGGAT
1 ATTTTT-TTAAATTAAGAT
* *
33138 -TTTCTTTAAGATCT-AGTTT
1 ATTTTTTTAA-AT-TAAG-AT
* *
33157 TTTTTTTTAAATTAGGAT
1 ATTTTTTTAAATTAAGAT
*
33175 ATTTTTTTAAATTTAGAT
1 ATTTTTTTAAATTAAGAT
*
33193 -TTTTATTAAA
1 ATTTTTTTAAA
33203 CTCTAATCAA
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
17 13 0.20
18 30 0.45
19 15 0.23
20 8 0.12
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.59
Consensus pattern (18 bp):
ATTTTTTTAAATTAAGAT
Found at i:33196 original size:37 final size:36
Alignment explanation
Indices: 33096--33196 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 36
33086 AGAAGGTAAG
* *
33096 TTAGGATTTTTTTT-AATTAAGATATTTTTCTTAAA
1 TTAGGATTTTTTTTAAATTTAGATTTTTTTCTTAAA
* * * *
33131 TTAGGATTTTCTTTAAGATCTAGTTTTTTTTTTTAAA
1 TTAGGATTTTTTTTAA-ATTTAGATTTTTTTCTTAAA
33168 TTAGGATATTTTTTTAAATTTAGATTTTT
1 TTAGGAT-TTTTTTTAAATTTAGATTTTT
33197 ATTAAACTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 13 0.24
36 1 0.02
37 32 0.59
38 8 0.15
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (36 bp):
TTAGGATTTTTTTTAAATTTAGATTTTTTTCTTAAA
Found at i:34323 original size:30 final size:30
Alignment explanation
Indices: 34289--34369 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
34279 CGGGGATATG
34289 ATCCCATGCAGATGTCAAAAC-AGGGATAAA
1 ATCCCATGCAGATGTCAAAACGA-GGATAAA
* * **
34319 ATCCCATACAGATGTCTAAACGAGGATGTA
1 ATCCCATGCAGATGTCAAAACGAGGATAAA
*
34349 ATCCCATGAAGATGTCAAAAC
1 ATCCCATGCAGATGTCAAAAC
34370 CGAGAGTTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 42 0.98
31 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.20
Consensus pattern (30 bp):
ATCCCATGCAGATGTCAAAACGAGGATAAA
Found at i:35828 original size:30 final size:30
Alignment explanation
Indices: 35745--35863 Score: 100
Period size: 30 Copynumber: 4.0 Consensus size: 30
35735 AGAATGAGGT
* * *
35745 TATAATCTAATGCAAATGTCA-TACCGGGA
1 TATAATCTCATGCAAATGTCAGAACGGGGA
** *
35774 TATAATCAT-ATATAGATGTCAGAACGGGGA
1 TATAATC-TCATGCAAATGTCAGAACGGGGA
* **
35804 TATAATCTCATGCAAATGTTAGAACAAGGA
1 TATAATCTCATGCAAATGTCAGAACGGGGA
* *
35834 TATAATCCCATG-AAGATGTTAGAACGGGGA
1 TATAATCTCATGCAA-ATGTCAGAACGGGGA
35864 GTTCATCCCA
Statistics
Matches: 72, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
29 19 0.26
30 53 0.74
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (30 bp):
TATAATCTCATGCAAATGTCAGAACGGGGA
Found at i:35873 original size:30 final size:31
Alignment explanation
Indices: 35787--35863 Score: 104
Period size: 30 Copynumber: 2.5 Consensus size: 31
35777 AATCATATAT
* *
35787 AGATGTCAGAACGGGGATATAATCTCATGCA
1 AGATGTTAGAACGGGGATATAATCCCATGCA
**
35818 A-ATGTTAGAACAAGGATATAATCCCATG-A
1 AGATGTTAGAACGGGGATATAATCCCATGCA
35847 AGATGTTAGAACGGGGA
1 AGATGTTAGAACGGGGA
35864 GTTCATCCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 2 0.05
30 36 0.92
31 1 0.03
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (31 bp):
AGATGTTAGAACGGGGATATAATCCCATGCA
Found at i:42604 original size:21 final size:20
Alignment explanation
Indices: 42557--42605 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
42547 TAAAGTAGTT
* *
42557 ATCCAATTATGTGTAAAATA
1 ATCCAAATAAGTGTAAAATA
* *
42577 ATACAAATAAGTGTAACATTA
1 ATCCAAATAAGTGTAA-AATA
42598 ATCCAAAT
1 ATCCAAAT
42606 TAAATTAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (20 bp):
ATCCAAATAAGTGTAAAATA
Found at i:42791 original size:30 final size:30
Alignment explanation
Indices: 42757--42878 Score: 165
Period size: 30 Copynumber: 4.1 Consensus size: 30
42747 AACAAAACAA
* *
42757 AACGGAGATATAATCTCATGCAGATATCAG
1 AACGGAGATATAATCCCATGCAGATGTCAG
* *
42787 AACGGGGATATAATCCCATGTAGATGTCAG
1 AACGGAGATATAATCCCATGCAGATGTCAG
*
42817 AACGGAGATATAACCCCATGCAGATGTCAG
1 AACGGAGATATAATCCCATGCAGATGTCAG
* *
42847 AACGGGGAGT-TTATCCCATGCAGATGTCAG
1 AACGGAGA-TATAATCCCATGCAGATGTCAG
42877 AA
1 AA
42879 ATGCATCAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 80 0.99
31 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (30 bp):
AACGGAGATATAATCCCATGCAGATGTCAG
Found at i:42837 original size:60 final size:60
Alignment explanation
Indices: 42757--42878 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
42747 AACAAAACAA
* * *
42757 AACGGAGATATAATCTCATGCAGATATCAGAACGGGGA-TATAATCCCATGTAGATGTCAG
1 AACGGAGATATAACCCCATGCAGATATCAGAACGGGGAGT-TAATCCCATGCAGATGTCAG
* *
42817 AACGGAGATATAACCCCATGCAGATGTCAGAACGGGGAGTTTATCCCATGCAGATGTCAG
1 AACGGAGATATAACCCCATGCAGATATCAGAACGGGGAGTTAATCCCATGCAGATGTCAG
42877 AA
1 AA
42879 ATGCATCAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 55 0.98
61 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (60 bp):
AACGGAGATATAACCCCATGCAGATATCAGAACGGGGAGTTAATCCCATGCAGATGTCAG
Found at i:43451 original size:13 final size:13
Alignment explanation
Indices: 43433--43467 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
43423 GGTCTTTGGA
43433 AAAGTCAACGATC
1 AAAGTCAACGATC
*
43446 AAAGTCAACGGTC
1 AAAGTCAACGATC
43459 AAAGTCAAC
1 AAAGTCAAC
43468 AGTTAACGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.14
Consensus pattern (13 bp):
AAAGTCAACGATC
Found at i:45569 original size:110 final size:109
Alignment explanation
Indices: 45388--45588 Score: 312
Period size: 110 Copynumber: 1.8 Consensus size: 109
45378 CAAAAAAGAC
* *
45388 CCCAAAAAAGTATATATATAGCGGCGTTTTTCCAACAAACGCCACTATAGATGACCCATTGCGAC
1 CCCAAAAAAGTATATATATAGCGGCGTTTTTCCAACAAACACCACTATAGATGACCCATTACGAC
*
45453 GCTTTTTCAAAAAAACGCCACTATTATGCACAGCCCAAAACAATG
66 GTTTTTTC-AAAAAACGCCACTATTATGCACAGCCCAAAACAATG
* * *
45498 CCCAAAAAAGTATATATATAGTGGCGTTTTTCCAATAAACACCACTATAGATGGACCTATTACGA
1 CCCAAAAAAGTATATATATAGCGGCGTTTTTCCAACAAACACCACTATAGAT-GACCCATTACGA
*
45563 CGTTTTTTTCAAGAAACGCCACTATT
65 CG-TTTTTTCAAAAAACGCCACTATT
45589 GTGCCCCAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
110 49 0.60
111 27 0.33
112 6 0.07
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (109 bp):
CCCAAAAAAGTATATATATAGCGGCGTTTTTCCAACAAACACCACTATAGATGACCCATTACGAC
GTTTTTTCAAAAAACGCCACTATTATGCACAGCCCAAAACAATG
Done.