Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000711.1 Hibiscus syriacus cultivar Beakdansim tig00001381_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: 55467
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:7735 original size:20 final size:22
Alignment explanation
Indices: 7689--7748 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 22
7679 ACCCTCATGA
*
7689 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTCT-AAG
7712 GGGAACCGATTCCCCC-CT-AG
1 GGGAACCGATTCCCCCTCTAAG
* *
7732 GGGAATCGATACCCCCT
1 GGGAACCGATTCCCCCT
7749 GGGGTTCTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 16 0.48
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTCTAAG
Found at i:11991 original size:25 final size:23
Alignment explanation
Indices: 11945--11994 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
11935 CAGGACATAC
*
11945 AGTGATCCTTCGGGATAATTCAT
1 AGTGATCCTTCGGGAAAATTCAT
*
11968 AGTGGTCCTTCGGGACAAATTTCAT
1 AGTGATCCTTCGGGA-AAA-TTCAT
11993 AG
1 AG
11995 CCCCTAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 14 0.61
24 2 0.09
25 7 0.30
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (23 bp):
AGTGATCCTTCGGGAAAATTCAT
Found at i:16555 original size:67 final size:68
Alignment explanation
Indices: 16443--16571 Score: 197
Period size: 67 Copynumber: 1.9 Consensus size: 68
16433 TAAATTATCG
* *
16443 AATTAAACTACCCAGGTCGATAGGTGTTACTCGCTTCGATAATTTAAATTAAATGGGCATTGCCT
1 AATTAAACTACCCAGGTCGATAGGTGTAACTCGCTTCGATAATTTAAATTAAATGGACATTGCCT
16508 TTT
66 TTT
* * * *
16511 AATTAAACTACCCAGGTGGATTGG-GTAACTCGCTTTGATAATTTATATTAAATGGACATTG
1 AATTAAACTACCCAGGTCGATAGGTGTAACTCGCTTCGATAATTTAAATTAAATGGACATTG
16572 TATTTAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
67 33 0.60
68 22 0.40
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (68 bp):
AATTAAACTACCCAGGTCGATAGGTGTAACTCGCTTCGATAATTTAAATTAAATGGACATTGCCT
TTT
Found at i:17756 original size:651 final size:638
Alignment explanation
Indices: 16536--17785 Score: 1802
Period size: 651 Copynumber: 1.9 Consensus size: 638
16526 GTGGATTGGG
* * * * *
16536 TAACTCGCTTTGATAATTTATATTAAATGGACATTGTATTTAATTTATTATGAGTAAATTTGAGT
1 TAACTCACTTCGATAATTTAAATTAAATGGACATTGTATTTAATTTATTACGAGTAAATTCGAGT
* * * *
16601 GATGCGAATGAGGTTTATCATGCTTGAAAAATAATTAAAAAAAAGTCATGCCATAGATGACACAA
66 GATGCGAATAAGGCTTATCATGCTTAAAAAATAATTAAAAAAAAGTCATGCCATAGATAACACAA
* *
16666 AGTCATTTAATCACAATTAAATTAATTAGTTCTGTTATCATTAATGTCAAAATTGTATTTACTAA
131 AGTCATTTAATCACAATTAAATAAATTAGTTCTGTTATCATTAATGCCAAAATTGTATTTACTAA
*
16731 TTAAGACATATTACATAATTAAATAAACACAAGTTCATAAAAAATAAATTTATAATTAAACATGG
196 TTAAGACATATTACAAAATTAAATAAACACAAGTTCATAAAAAATAAATTTATAATTAAACATGG
*
16796 TTTTAAAGAAATTTAACCATTACACAAATAAATAAAAACAAGGCATAAAATTTTTAATTTAATAA
261 TTTTAAAGAAATTTAACCATTACACAAATAAATAAAAACAAGGCATAAAAATTTTAATTTAATAA
*
16861 GAATTAAAAAGCAAATAACCAAATTAAAAAAGAACATGGATTTAATTGTATTAAAAATAAAATTA
326 GAATTAAAAAGCAAATAACCAAATTAAAAAAGAACATGAATTTAATTGTATTAAAAATAAAATTA
* * * * * *
16926 CATGGGTTAAATTGTGATTTCTAGAACCTAATTTGAGCATTTAGGGACCAAATTGTAAGGCTCTA
391 CAGGGGTCAAATTATGATTTCTAAAACCTAATTTGAGAATTTAAGGACCAAATTGTAAGGCTCTA
* ** * * * *
16991 AAATCGAAGATGGCCACGAAAAGAATTACCCCAATATTTTAAAACACGCGGTTCATCGAATCGAT
456 AAATCGAAGATGACCACGAAAAGAATTACCAAAACACTTTAAAACACGCGGTTCAACGAACCGAT
* * *
17056 TAAGTCATTGAATCGACCATTATAAAACCCCTAAAAGTCTGGTTTTTTCATTTCGTCCCCCCTCT
521 TAAGTCATTGAACCGACCACTATAAAACCCCTAAAAGTCT-GTTTTTTCATTTCG-ACCCCCTCT
*
17121 TTTTCATCCTTGTTTTCTCTCTAAGTCTCTCAAATCACAAATTAAATTAAATGGA
584 TTATCATCCTTGTTTTCTCTCTAAGTCTCTCAAATCACAAATTAAATTAAATGGA
* *
17176 TAACTCACTTCGATAATTTAAATTAAATAGG-CATTGTCTTTTAATTTATTACGGGT-AATGTCG
1 TAACTCACTTCGATAATTTAAATTAAAT-GGACATTGT-ATTTAATTTATTACGAGTAAAT-TCG
17239 AGTGATGCGAATAAGGCTTATCATGCTTAAAAAATAATTTTAAAAAAAA-TCATGCCATAGATAA
63 AGTGATGCGAATAAGGCTTATCATGCTTAAAAAATAA--TTAAAAAAAAGTCATGCCATAGATAA
* * *
17303 GATAGAGTCATTTAATCACAAATTAAATAAATTA-TTCAATGTTATCATTAATGCCAAAATTGTA
126 CACAAAGTCATTTAATCAC-AATTAAATAAATTAGTTC--TGTTATCATTAATGCCAAAATTGTA
* *
17367 TTTACTAATTAAGACATGTTACAAAATTAAATAAGCACAAGTTCATAAAAAACAAATAAATTT-T
188 TTTACTAATTAAGACATATTACAAAATTAAATAAACACAAGTTCAT---AAA-AAATAAATTTAT
*
17431 AATTAAACATGGTTTTAAAGAAATTTAACCATTACACAAATAAATAAATAAAAACATGGCATAAA
249 AATTAAACATGGTTTTAAAGAAATTTAACCATTACAC----AAATAAATAAAAACAAGGCATAAA
*
17496 AATTTTAATTTAATAAGAATT-AAAAGCAAATAACCAAATTAAAAAATAACATGAATTTAATTGT
310 AATTTTAATTTAATAAGAATTAAAAAGCAAATAACCAAATTAAAAAAGAACATGAATTTAATTGT
17560 ATT-AAAATAAAATTACAGGGGTCAAATTATGATTTCTAAAACCTAATTTGAGAATTTAAGGACC
375 ATTAAAAATAAAATTACAGGGGTCAAATTATGATTTCTAAAACCTAATTTGAGAATTTAAGGACC
*
17624 AAATTGTAAGGCTCTAAAATCTAACG-TGACCAC-ACAAAGAATTAGCCAAAACACTTTAAAACA
440 AAATTGTAAGGCTCTAAAATCGAA-GATGACCACGA-AAAGAATTA-CCAAAACACTTTAAAACA
* * *
17687 CGCGGGTTCAACGAACCGGTTCAA-TCATTGAACCGACCACTATAAAACTCCTAAAAATTCAT-T
502 CGC-GGTTCAACGAACCGATT-AAGTCATTGAACCGACCACTATAAAACCCCT-AAAAGTC-TGT
17750 TTTTTCATTTCGACCCCCTCTTTATCATCCTTGTTT
563 TTTTTCATTTCGACCCCCTCTTTATCATCCTTGTTT
17786 CCCCCGCACC
Statistics
Matches: 543, Mismatches: 44, Indels: 36
0.87 0.07 0.06
Matches are distributed among these distances:
640 34 0.06
641 53 0.10
642 33 0.06
643 23 0.04
644 67 0.12
647 41 0.08
648 11 0.02
649 93 0.17
650 84 0.15
651 95 0.17
652 8 0.01
653 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.32
Consensus pattern (638 bp):
TAACTCACTTCGATAATTTAAATTAAATGGACATTGTATTTAATTTATTACGAGTAAATTCGAGT
GATGCGAATAAGGCTTATCATGCTTAAAAAATAATTAAAAAAAAGTCATGCCATAGATAACACAA
AGTCATTTAATCACAATTAAATAAATTAGTTCTGTTATCATTAATGCCAAAATTGTATTTACTAA
TTAAGACATATTACAAAATTAAATAAACACAAGTTCATAAAAAATAAATTTATAATTAAACATGG
TTTTAAAGAAATTTAACCATTACACAAATAAATAAAAACAAGGCATAAAAATTTTAATTTAATAA
GAATTAAAAAGCAAATAACCAAATTAAAAAAGAACATGAATTTAATTGTATTAAAAATAAAATTA
CAGGGGTCAAATTATGATTTCTAAAACCTAATTTGAGAATTTAAGGACCAAATTGTAAGGCTCTA
AAATCGAAGATGACCACGAAAAGAATTACCAAAACACTTTAAAACACGCGGTTCAACGAACCGAT
TAAGTCATTGAACCGACCACTATAAAACCCCTAAAAGTCTGTTTTTTCATTTCGACCCCCTCTTT
ATCATCCTTGTTTTCTCTCTAAGTCTCTCAAATCACAAATTAAATTAAATGGA
Found at i:18792 original size:2 final size:2
Alignment explanation
Indices: 18787--18815 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18777 TTTCAAAATT
18787 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 T
18816 TCAAAATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18811 original size:37 final size:35
Alignment explanation
Indices: 18755--18823 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 35
18745 TTAATAATTA
* *
18755 ATATTATATACATTATATATGTTTTCAAAATTTAT
1 ATATTATATACATTATATATATATTCAAAATTTAT
*
18790 ATATATATATATATATATATATATATTCAAAATT
1 ATAT-TATATACAT-TATATATATATTCAAAATT
18824 ACATTATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 4 0.14
36 8 0.28
37 17 0.59
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (35 bp):
ATATTATATACATTATATATATATTCAAAATTTAT
Found at i:18836 original size:37 final size:36
Alignment explanation
Indices: 18758--18836 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 36
18748 ATAATTAATA
* * *
18758 TTATATACATTATATATGTTTTCAAAATTTATATAT
1 TTATATACATTATATATATATTCAAAATTCATATAT
* *
18794 ATATATATATATATATATATATTCAAAATTACAT-TAT
1 TTATATACAT-TATATATATATTCAAAATT-CATATAT
18831 TTATAT
1 TTATAT
18837 TTCGAAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
36 8 0.23
37 25 0.71
38 2 0.06
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (36 bp):
TTATATACATTATATATATATTCAAAATTCATATAT
Found at i:18837 original size:21 final size:22
Alignment explanation
Indices: 18798--18934 Score: 65
Period size: 25 Copynumber: 6.3 Consensus size: 22
18788 ATATATATAT
* *
18798 ATATATATATATATATATTCAAA
1 ATATACATATTTATAT-TTCAAA
*
18821 AT-TACATTATTTATATTTCGAA
1 ATATACA-TATTTATATTTCAAA
18843 ATATAC--A--TAT-TTTCAAA
1 ATATACATATTTATATTTCAAA
* * *
18860 ATATACTAAATATAATATTTTCGAA
1 ATATAC-ATAT-TTATA-TTTCAAA
*
18885 ATATACCACATGTTATATTTCAAA
1 ATATA-CATAT-TTATATTTCAAA
* **
18909 AAAT-CATATACAT-TTTCAAA
1 ATATACATATTTATATTTCAAA
18929 ATATAC
1 ATATAC
18935 TAAATATAAT
Statistics
Matches: 87, Mismatches: 15, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
17 12 0.14
18 3 0.03
20 12 0.14
21 3 0.03
22 14 0.16
23 15 0.17
24 9 0.10
25 18 0.21
26 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (22 bp):
ATATACATATTTATATTTCAAA
Found at i:18849 original size:23 final size:22
Alignment explanation
Indices: 18804--18854 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
18794 ATATATATAT
*
18804 ATATATATATATTCAAAATTAC
1 ATATTTATATATTCAAAATTAC
*
18826 ATTATTTATAT-TTCGAAATATAC
1 A-TATTTATATATTCAAAAT-TAC
18849 ATATTT
1 ATATTT
18855 TCAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATTTATATATTCAAAATTAC
Found at i:18880 original size:25 final size:25
Alignment explanation
Indices: 18841--18947 Score: 100
Period size: 25 Copynumber: 4.5 Consensus size: 25
18831 TTATATTTCG
18841 AAATATACATATTTTCAAAATATACT
1 AAATATA-ATATTTTCAAAATATACT
* *
18867 AAATATAATATTTTCGAAATATACC
1 AAATATAATATTTTCAAAATATACT
* * *
18892 ACATGTTATA-TTTCAAAA-A-A-T
1 AAATATAATATTTTCAAAATATACT
* *
18913 -CATAT-ACATTTTCAAAATATACT
1 AAATATAATATTTTCAAAATATACT
18936 AAATATAATATT
1 AAATATAATATT
18948 ATATAATGAA
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.03
20 12 0.19
21 1 0.02
22 2 0.03
23 2 0.03
24 11 0.17
25 27 0.42
26 7 0.11
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (25 bp):
AAATATAATATTTTCAAAATATACT
Found at i:27470 original size:6 final size:6
Alignment explanation
Indices: 27459--27492 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
27449 TACTACGATG
27459 TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA TTTG
1 TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA TTTG
27493 GTTTTTCTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (6 bp):
TTTGAA
Found at i:34290 original size:2 final size:2
Alignment explanation
Indices: 34283--34307 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34273 TTAAAAATTT
34283 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 T
34308 TTTTTGTCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35158 original size:17 final size:19
Alignment explanation
Indices: 35138--35181 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
35128 TAATAGTGAG
35138 TTATT-TAA-AATATATTT
1 TTATTATAATAATATATTT
*
35155 TTATTATAATTATATATTT
1 TTATTATAATAATATATTT
35174 TTATTATA
1 TTATTATA
35182 GTTTAAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 5 0.21
18 3 0.12
19 16 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTATAATAATATATTT
Found at i:36714 original size:43 final size:42
Alignment explanation
Indices: 36655--36769 Score: 130
Period size: 43 Copynumber: 2.7 Consensus size: 42
36645 TTTGTCATTT
* *
36655 TATAT-ATATATGTATAATAATATATATAGTATA-TATATATATA
1 TATATAATATAT-TATAATAATATATATA-TATATTA-AAACATA
36698 TATATAATATATTATAA-ATATATATATATATATTGAAAACATA
1 TATATAATATATTATAATA-ATATATATATATATT-AAAACATA
*
36741 TTTATAATATATTATAAT-ATATATATATA
1 TATATAATATATTATAATAATATATATATA
36770 GTTTTTTAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
42 16 0.25
43 41 0.64
44 7 0.11
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (42 bp):
TATATAATATATTATAATAATATATATATATATTAAAACATA
Found at i:36786 original size:2 final size:2
Alignment explanation
Indices: 36655--36769 Score: 104
Period size: 2 Copynumber: 61.0 Consensus size: 2
36645 TTTGTCATTT
*
36655 TA TA TA TA TA TG TA TA -A TA -A TA TA TA TA GTA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
36696 TA TA TA TA -A TA TA T- TA TA AA TA TA TA TA TA TA TA T- TGA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* * *
36735 AA CA TA TT TA TA -A TA TA T- TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36770 GTTTTTTAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
1 9 0.10
2 83 0.88
3 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:36812 original size:66 final size:66
Alignment explanation
Indices: 36674--36821 Score: 184
Period size: 64 Copynumber: 2.3 Consensus size: 66
36664 ATGTATAATA
*
36674 ATATA-TATAGTATA-TATATATATATATATAATATATTATAAATATATATATATATATTGAAAA
1 ATATATTATAATATATTATATATATATATATAATATATTATAAATATATATATATATATTGAAAA
36737 C
66 C
* *
36738 ATAT-TTATAATATATTATA-ATATATATAT-ATAGTTTTTTAAAT-TATATAGTATATATT-AA
1 ATATATTATAATATATTATATATATATATATAATA-TATTATAAATATATATA-TATATATTGAA
36798 AGTAC
64 A--AC
36803 ATATATTATAATATATTAT
1 ATATATTATAATATATTAT
36822 TAATTATTAA
Statistics
Matches: 74, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
63 12 0.16
64 38 0.51
65 10 0.14
66 14 0.19
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.47
Consensus pattern (66 bp):
ATATATTATAATATATTATATATATATATATAATATATTATAAATATATATATATATATTGAAAA
C
Found at i:36875 original size:14 final size:14
Alignment explanation
Indices: 36833--36875 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
36823 AATTATTAAT
36833 TTTTATTTCTATTTTA
1 TTTTATTT-T-TTTTA
*
36849 TTTTATCTTTTTTA
1 TTTTATTTTTTTTA
36863 TTTTATTTTTTTT
1 TTTTATTTTTTTT
36876 TGTTTCAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 17 0.68
15 1 0.04
16 7 0.28
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTTTTTTA
Found at i:36876 original size:5 final size:5
Alignment explanation
Indices: 36833--36875 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
36823 AATTATTAAT
*
36833 TTTTA TTTCTA TTTTA TTTTA TCTT- TTTTA TTTTA TTTT- TTTT
1 TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
36876 TGTTTCAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
4 7 0.21
5 22 0.65
6 5 0.15
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:37718 original size:36 final size:36
Alignment explanation
Indices: 37678--37746 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
37668 AAATGCCACC
*
37678 GAAATCTCAAGGGCCATTCGAAAAGGTAAAACCGCG
1 GAAATCTCAAGGGACATTCGAAAAGGTAAAACCGCG
37714 GAAATCTCAAGGGACATTCGAAAAGGTAAAACC
1 GAAATCTCAAGGGACATTCGAAAAGGTAAAACC
37747 CGAAGGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.14
Consensus pattern (36 bp):
GAAATCTCAAGGGACATTCGAAAAGGTAAAACCGCG
Found at i:38394 original size:18 final size:18
Alignment explanation
Indices: 38371--38412 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
38361 AACATGATAA
38371 TCGATTGGTACCGAAAGG
1 TCGATTGGTACCGAAAGG
*
38389 TCGATTGGTATCGAAAGG
1 TCGATTGGTACCGAAAGG
*
38407 GCGATT
1 TCGATT
38413 CAAGGGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.14, G:0.33, T:0.26
Consensus pattern (18 bp):
TCGATTGGTACCGAAAGG
Found at i:45347 original size:19 final size:18
Alignment explanation
Indices: 45325--45361 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
45315 AAAAAATAAA
*
45325 ATTCTCTATTATAAATTTT
1 ATTCTCAATTA-AAATTTT
45344 ATTCTCAATTAAAATTTT
1 ATTCTCAATTAAAATTTT
45362 CAATCTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTCTCAATTAAAATTTT
Found at i:46075 original size:16 final size:16
Alignment explanation
Indices: 46056--46086 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46046 TTCAGATTGC
*
46056 TTTCAGTTCGTGTTAA
1 TTTCAGTTCGAGTTAA
46072 TTTCAGTTCGAGTTA
1 TTTCAGTTCGAGTTA
46087 CTTTTGGATC
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:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTCAGTTCGAGTTAA
Found at i:48242 original size:4 final size:4
Alignment explanation
Indices: 48235--48318 Score: 77
Period size: 4 Copynumber: 21.0 Consensus size: 4
48225 GTTTTTTATA
* *
48235 ATTT ATTT ATTT -TATT ATTT -CTT GTTT ATTT ATTT ATTTT ATTT ATTT
1 ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT
*
48283 GTTT A-TT ATCTT ATTT ATTTT ATTT -TTT ATTT ATTT
1 ATTT ATTT AT-TT ATTT A-TTT ATTT ATTT ATTT ATTT
48319 GTTTTATCTC
Statistics
Matches: 67, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
3 9 0.13
4 45 0.67
5 13 0.19
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:48289 original size:36 final size:35
Alignment explanation
Indices: 48211--48322 Score: 122
Period size: 36 Copynumber: 3.1 Consensus size: 35
48201 TATTTTCATT
*
48211 TTTATTT-TTGTTTGGTTTTTTATAATTTATTTATTT-
1 TTTATTTCTTGTTT-ATTTTTTAT--TTTATTTATTTG
48247 TATTATTTCTTGTTTATTTATTTATTTTATTTATTTG
1 T-TTATTTCTTGTTTATTT-TTTATTTTATTTATTTG
*
48284 TTTATTATCTTATTTATTTTATT-TTTTATTTATTTG
1 TTTATT-TCTTGTTTATTTT-TTATTTTATTTATTTG
48320 TTT
1 TTT
48323 TATCTCTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
36 34 0.50
37 23 0.34
38 11 0.16
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (35 bp):
TTTATTTCTTGTTTATTTTTTATTTTATTTATTTG
Found at i:48335 original size:20 final size:20
Alignment explanation
Indices: 48235--48335 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
48225 GTTTTTTATA
*
48235 ATTTATTTATTTTATTATTT
1 ATTTATTTATTTTATTCTTT
* * *
48255 -CTTGTTTA-TTTATT-TAT
1 ATTTATTTATTTTATTCTTT
*
48272 -TTTATTTATTTGT-TT-ATT
1 ATTTATTTATTT-TATTCTTT
*
48290 ATCTTATTTATTTTATTTTTT
1 AT-TTATTTATTTTATTCTTT
*
48311 ATTTATTTGTTTTATCTCTTT
1 ATTTATTTATTTTAT-TCTTT
48332 -TTTA
1 ATTTA
48336 CTTCATGTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
17 8 0.12
18 11 0.17
19 9 0.14
20 28 0.44
21 8 0.12
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.74
Consensus pattern (20 bp):
ATTTATTTATTTTATTCTTT
Found at i:52138 original size:21 final size:21
Alignment explanation
Indices: 52112--52152 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52102 GCAAAAAAGA
* *
52112 TGGAAGAGAAGATTAAGATGT
1 TGGAAGACAAGATGAAGATGT
52133 TGGAAGACAAGATGAAGATG
1 TGGAAGACAAGATGAAGATG
52153 GTCAAAGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.34, T:0.20
Consensus pattern (21 bp):
TGGAAGACAAGATGAAGATGT
Done.