Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004249.1 Hibiscus syriacus cultivar Beakdansim tig00009317_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: 87826
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:6609 original size:2 final size:2
Alignment explanation
Indices: 6602--6632 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6592 CCACATAACT
6602 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 T
6633 CATGATCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11768 original size:40 final size:40
Alignment explanation
Indices: 11692--11773 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
11682 ATATCTAAAG
* * * *
11692 TTTAGTTTTTGTTTTATTTTAGTATCTCACCATTAAAAAC
1 TTTAGTTTTCGTTTCATTTTAGTACCCCACCATTAAAAAC
*
11732 TTTAGTTTTCGTTTCATTTTAGTACCCCA-CATTTAAAA-
1 TTTAGTTTTCGTTTCATTTTAGTACCCCACCATTAAAAAC
11770 TTTA
1 TTTA
11774 ACGTTATGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 4 0.11
39 8 0.22
40 25 0.68
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (40 bp):
TTTAGTTTTCGTTTCATTTTAGTACCCCACCATTAAAAAC
Found at i:25519 original size:15 final size:16
Alignment explanation
Indices: 25499--25534 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 16
25489 ATTTTTAATA
25499 AAATATATAAT-TTTT
1 AAATATATAATATTTT
25514 AAATATATAATAATTTT
1 AAATATATAAT-ATTTT
25531 AAAT
1 AAAT
25535 TTTCAAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
17 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATATAATATTTT
Found at i:27916 original size:17 final size:17
Alignment explanation
Indices: 27894--27932 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
27884 ATTGAGACCG
27894 TAGATGACTTAATGAGC
1 TAGATGACTTAATGAGC
*
27911 TAGATGACTTAGTGAGC
1 TAGATGACTTAATGAGC
27928 TAGAT
1 TAGAT
27933 CTATCAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (17 bp):
TAGATGACTTAATGAGC
Found at i:29369 original size:31 final size:31
Alignment explanation
Indices: 29304--29369 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
29294 TAATATACGA
* * *
29304 TCACTTTCGTTTTTATTTAATTAAGATATGG
1 TCACTTTCATTTTTATTTAATTAAAAAATGG
*
29335 TCACTTTCATTTTTATTTAATTAAAAAATTG
1 TCACTTTCATTTTTATTTAATTAAAAAATGG
29366 TCAC
1 TCAC
29370 CACGAGTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (31 bp):
TCACTTTCATTTTTATTTAATTAAAAAATGG
Found at i:29603 original size:25 final size:26
Alignment explanation
Indices: 29546--29639 Score: 88
Period size: 25 Copynumber: 3.7 Consensus size: 26
29536 AACATAAAAA
*
29546 ATAAAATATTTTTAAATTAAGTTAAT-G
1 ATAAAATATATTT-AA-TAAGTTAATAG
29573 ATAAAATATATTTAATAAGTTAATAG
1 ATAAAATATATTTAATAAGTTAATAG
* *
29599 A-AAAA-ATATTTTA-AAGTTAATAT
1 ATAAAATATATTTAATAAGTTAATAG
* *
29622 ATATATATATATATAATA
1 ATA-AAATATATTTAATA
29640 TTATGAATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
23 10 0.18
24 8 0.14
25 15 0.27
26 10 0.18
27 13 0.23
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (26 bp):
ATAAAATATATTTAATAAGTTAATAG
Found at i:31970 original size:21 final size:20
Alignment explanation
Indices: 31919--31974 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
31909 GGTATTGTTC
31919 ATAGTTTGGAAAC-TTTGTA
1 ATAGTTTGGAAACTTTTGTA
* *
31938 AGAGTTTGGAAACTTTTATTA
1 ATAGTTTGGAAACTTTT-GTA
*
31959 ATAGTTTTGAAACTTT
1 ATAGTTTGGAAACTTT
31975 GCACCCAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.39
20 3 0.10
21 16 0.52
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (20 bp):
ATAGTTTGGAAACTTTTGTA
Found at i:43113 original size:14 final size:14
Alignment explanation
Indices: 43094--43126 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
43084 TGGAGAGTAA
*
43094 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
43108 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
43122 TCCCT
1 TCCCT
43127 ACATAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Found at i:62983 original size:5 final size:5
Alignment explanation
Indices: 62848--62972 Score: 250
Period size: 5 Copynumber: 25.0 Consensus size: 5
62838 CTACAAAAAC
62848 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
62898 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
62948 ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT
62973 TATTTTATTT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 120 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:63433 original size:3 final size:3
Alignment explanation
Indices: 63420--63465 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
63410 GCTTAAAAAA
63420 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
63466 ACTATATTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:63531 original size:14 final size:14
Alignment explanation
Indices: 63512--63547 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
63502 CCCAAATGAG
63512 GCCCAATTGTCCGA
1 GCCCAATTGTCCGA
*
63526 GCCCAATTGTTCGA
1 GCCCAATTGTCCGA
63540 GCCCAATT
1 GCCCAATT
63548 ACATGAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (14 bp):
GCCCAATTGTCCGA
Found at i:64977 original size:12 final size:13
Alignment explanation
Indices: 64955--64983 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
64945 ATGATCGAAT
64955 TTTTAAATTTTAA
1 TTTTAAATTTTAA
64968 TTTT-AATTTTAA
1 TTTTAAATTTTAA
64980 TTTT
1 TTTT
64984 CACAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:71878 original size:73 final size:70
Alignment explanation
Indices: 71794--71965 Score: 175
Period size: 73 Copynumber: 2.4 Consensus size: 70
71784 TTTGTCTTGT
* *
71794 TTGAGACAATTTTTCCTGAAACAACATTGATCTCACTTGAGATTGTTTTCTCTAAAAACAAATTT
1 TTGAGACAATTTTTCCTGAAACAA-ATTG-TCTCACTTGAAATAGTTTTC-CTAAAAACAAATTT
*
71859 CATCTCGC
63 CATCTCAC
** * * *
71867 TTGAGACAA-TTTTCCCCAAATTTTGAAATTGTTTCACTTGAAATAGTTTTCCTAAAAACTAATT
1 TTGAGACAATTTTTCCTGAAA----CAAATTGTCTCACTTGAAATAGTTTTCCTAAAAACAAATT
*
71931 TCGTCTCAC
62 TCATCTCAC
*
71940 TTGAGACAATTTTCCCTTGAAACAAA
1 TTGAGACAATTTTTCC-TGAAACAAA
71966 AAAATTGGAA
Statistics
Matches: 80, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
71 3 0.04
72 9 0.11
73 37 0.46
74 22 0.28
75 7 0.09
76 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (70 bp):
TTGAGACAATTTTTCCTGAAACAAATTGTCTCACTTGAAATAGTTTTCCTAAAAACAAATTTCAT
CTCAC
Found at i:72737 original size:122 final size:123
Alignment explanation
Indices: 72466--72738 Score: 320
Period size: 122 Copynumber: 2.2 Consensus size: 123
72456 TTCTAGAACA
* * * *
72466 TCTTCAACACCAAATTATCTCCAGATTG-ATCCGACTTCCTTAATAATAAGGAACAACATCATCT
1 TCTTTAACACCAAATTATCTCCAGATTGAATCCGACTTCCTCAACAAGAAGGAACAACATCATCT
*
72530 TCAACAAACAATTTACCTGAAAGCGGCTAGAACTCTTCAACACGGATGAGCATAGTCG
66 TCAACAAACAATTTACCTAAAAGCGGCTAGAACTCTTCAACACGGATGAGCATAGTCG
** *** ** * *
72588 TCTTTAACACCGTATTATCTTTGGATTGAAT-CGGTTTCCTCAACCAGAAGGAACAACGTCATCT
1 TCTTTAACACCAAATTATCTCCAGATTGAATCCGACTTCCTCAACAAGAAGGAACAACATCATCT
* * * * *
72652 TCAACAAATAATTTATCTAAAAGCGG-TCAGATCTCTTCAACATGGATGAGTAGT-GTCG
66 TCAACAAACAATTTACCTAAAAGCGGCT-AGAACTCTTCAACACGGATGAGCA-TAGTCG
*
72710 TCTTTAACACCAAATTATATCCAGATTGA
1 TCTTTAACACCAAATTATCTCCAGATTGA
72739 CCCAAAGTCC
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
121 1 0.01
122 119 0.97
123 3 0.02
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (123 bp):
TCTTTAACACCAAATTATCTCCAGATTGAATCCGACTTCCTCAACAAGAAGGAACAACATCATCT
TCAACAAACAATTTACCTAAAAGCGGCTAGAACTCTTCAACACGGATGAGCATAGTCG
Found at i:72765 original size:122 final size:123
Alignment explanation
Indices: 72466--72774 Score: 313
Period size: 122 Copynumber: 2.5 Consensus size: 123
72456 TTCTAGAACA
* * * ** *
72466 TCTTCAACACCAAATTATCTCCAGATTGATCCGACTTCCTTAATAAT-AAGGAACAACATCATCT
1 TCTTTAACACCAAATTATCTCCAGATTGAACCGAATTCCTTAACCATGAAGGAACAACGTCATCT
*
72530 TCAACAAACAATTTACCTGAAAGCGGCTAGAACTCTTCAACACGGATGAGCATAGTCG
66 TCAACAAACAATTTACCTAAAAGCGGCTAGAACTCTTCAACACGGATGAGCATAGTCG
** *** * ** *
72588 TCTTTAACACCGTATTATCTTTGGATTGAATCGGTTTCCTCAACCA-GAAGGAACAACGTCATCT
1 TCTTTAACACCAAATTATCTCCAGATTGAACCGAATTCCTTAACCATGAAGGAACAACGTCATCT
* * * * *
72652 TCAACAAATAATTTATCTAAAAGCGG-TCAGATCTCTTCAACATGGATGAGTAGT-GTCG
66 TCAACAAACAATTTACCTAAAAGCGGCT-AGAACTCTTCAACACGGATGAGCA-TAGTCG
* * * * * * *
72710 TCTTTAACACCAAATTATATCCAGATTGACCCAAAGTCCTTGA-CATGAAGCAACAATGTCATCT
1 TCTTTAACACCAAATTATCTCCAGATTGAACCGAATTCCTTAACCATGAAGGAACAACGTCATCT
72774 T
66 T
72775 TAAATCCTCT
Statistics
Matches: 147, Mismatches: 36, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
121 3 0.02
122 143 0.97
123 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (123 bp):
TCTTTAACACCAAATTATCTCCAGATTGAACCGAATTCCTTAACCATGAAGGAACAACGTCATCT
TCAACAAACAATTTACCTAAAAGCGGCTAGAACTCTTCAACACGGATGAGCATAGTCG
Found at i:73686 original size:16 final size:16
Alignment explanation
Indices: 73665--73706 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
73655 AACAAACATA
*
73665 AAAAAACATTTCCATT
1 AAAAAACATATCCATT
73681 AAAAAACATATCCATT
1 AAAAAACATATCCATT
*
73697 AAGAAACATA
1 AAAAAACATA
73707 ATAAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAAAACATATCCATT
Found at i:74262 original size:4 final size:4
Alignment explanation
Indices: 74253--74295 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
74243 ATCATTGTTG
*
74253 ATTT ATTT ATTT ATTT ATTT AGTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
74296 GTTTCTCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:74428 original size:33 final size:32
Alignment explanation
Indices: 74382--74445 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
74372 AACCGCTAAC
74382 TTTTCTAACTTACTAAC-TTTTATTTTTATTGT
1 TTTTCTAACTTACTAACATTTTA-TTTTATTGT
74414 TTTTACTAACTTACTAACATTTTATTTTATTG
1 TTTT-CTAACTTACTAACATTTTATTTTATTG
74446 CACAAACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 4 0.13
33 21 0.70
34 5 0.17
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.59
Consensus pattern (32 bp):
TTTTCTAACTTACTAACATTTTATTTTATTGT
Found at i:74455 original size:33 final size:33
Alignment explanation
Indices: 74386--74456 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
74376 GCTAACTTTT
*****
74386 CTAACTTACTAACTTTTATTTTTATTGTTTTTA
1 CTAACTTACTAACTTTTATTTTTATTGCACAAA
74419 CTAACTTACTAACATTTTA-TTTTATTGCACAAA
1 CTAACTTACTAAC-TTTTATTTTTATTGCACAAA
74452 CTAAC
1 CTAAC
74457 CCGCTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 27 0.84
34 5 0.16
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.49
Consensus pattern (33 bp):
CTAACTTACTAACTTTTATTTTTATTGCACAAA
Found at i:74642 original size:15 final size:16
Alignment explanation
Indices: 74624--74658 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
74614 TTCCAATATT
74624 TTTAATTTTC-TGCAC
1 TTTAATTTTCATGCAC
*
74639 TTTAATTTTCATGCAT
1 TTTAATTTTCATGCAC
74655 TTTA
1 TTTA
74659 TTTCAATCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTAATTTTCATGCAC
Found at i:75909 original size:72 final size:72
Alignment explanation
Indices: 75792--75935 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
75782 CACCCTTCCC
* *
75792 CACACGTAATCGATTCCTGAACTCTTAAAAATGAATTTTTGGTAAAACACAGACAATTTTTTTGT
1 CACACGTAATCGATTCCCGAACTCTTAAAAATGAATTTTTGGTAAAACACAGACAATATTTTTGT
75857 GTTTTAA
66 GTTTTAA
75864 CACACGTAATCGATTCCCGAACTCTTAAAAATGAATTTTTGGTAAAACACAGACAATATTTTTGT
1 CACACGTAATCGATTCCCGAACTCTTAAAAATGAATTTTTGGTAAAACACAGACAATATTTTTGT
75929 GTTTTAA
66 GTTTTAA
75936 TGATTTTTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (72 bp):
CACACGTAATCGATTCCCGAACTCTTAAAAATGAATTTTTGGTAAAACACAGACAATATTTTTGT
GTTTTAA
Found at i:81043 original size:37 final size:37
Alignment explanation
Indices: 80946--81053 Score: 110
Period size: 37 Copynumber: 2.9 Consensus size: 37
80936 ACACATTTTC
*
80946 GTTCTACTAGGATTTAAACTT-CTAAAAATATGATAAA
1 GTTCTACTAGGATTTAAA-TTCCTAAAAATAGGATAAA
* * ** * * *
80983 ATTTTGTTAGGATTCAAACTCCTAAAAATAGGATAGA
1 GTTCTACTAGGATTTAAATTCCTAAAAATAGGATAAA
* *
81020 GTTCTACTAAGATTTAAATTCCTAAAGATAGGAT
1 GTTCTACTAGGATTTAAATTCCTAAAAATAGGAT
81054 CCACAAACAC
Statistics
Matches: 54, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
36 1 0.02
37 53 0.98
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (37 bp):
GTTCTACTAGGATTTAAATTCCTAAAAATAGGATAAA
Found at i:81450 original size:18 final size:17
Alignment explanation
Indices: 81411--81508 Score: 64
Period size: 18 Copynumber: 5.6 Consensus size: 17
81401 ATTATATAGA
81411 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
81427 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
81445 TATTATTATAT-ATATATAT
1 TATTATTAT-TCAT-T-TAT
81464 ATATTAAATTATTTCATTTAT
1 -TATT--ATTA-TTCATTTAT
81485 T-TT-TTATT-ATATT-T
1 TATTATTATTCAT-TTAT
81499 TATTATTATT
1 TATTATTATT
81509 ATATATATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 24
0.71 0.03 0.26
Matches are distributed among these distances:
14 4 0.06
15 6 0.09
16 11 0.16
17 8 0.12
18 15 0.22
19 6 0.09
20 5 0.07
21 3 0.04
22 6 0.09
23 3 0.04
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:81539 original size:22 final size:21
Alignment explanation
Indices: 81473--81539 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
81463 TATATTAAAT
*
81473 TATTTCATTT-ATTTTTTATTA
1 TATTTC-TTTAATATTTTATTA
* *
81494 TATTT-TATTATTATTATATATA
1 TATTTCT-TTAATATTTTAT-TA
81516 TATTTCTTTAATATTTTACTTA
1 TATTTCTTTAATATTTTA-TTA
81538 TA
1 TA
81540 AGTATAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 11 0.31
22 20 0.56
23 2 0.06
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTCTTTAATATTTTATTA
Found at i:83963 original size:56 final size:56
Alignment explanation
Indices: 83869--84012 Score: 189
Period size: 56 Copynumber: 2.6 Consensus size: 56
83859 AGGGCTCTCA
* ** * * * * **
83869 AAAAATAGGGACCTTGAAATCGAATATATTTATTAGTTGTTGTTATTAATACGTAT
1 AAAAATAAGGACCCCGAAATCGAATATATCTATCAGTTGTTGTCATTAAGAAATAT
*
83925 AAAAATAAGGGCCCCGAAATCGAATATATCTATCAGTTGTTGTCATTAAGAAATAT
1 AAAAATAAGGACCCCGAAATCGAATATATCTATCAGTTGTTGTCATTAAGAAATAT
*
83981 AAAAATAAGGATCCCGAAATCGAATATATCTA
1 AAAAATAAGGACCCCGAAATCGAATATATCTA
84013 AAAAATAGAG
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 76 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (56 bp):
AAAAATAAGGACCCCGAAATCGAATATATCTATCAGTTGTTGTCATTAAGAAATAT
Found at i:84158 original size:23 final size:23
Alignment explanation
Indices: 84132--84182 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
84122 TTATAATATG
*
84132 TAACTAATACTAGTTTTAATGTC
1 TAACGAATACTAGTTTTAATGTC
* * *
84155 TAACGCATATTAGTTTTAATGTG
1 TAACGAATACTAGTTTTAATGTC
84178 TAACG
1 TAACG
84183 CATATCGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (23 bp):
TAACGAATACTAGTTTTAATGTC
Found at i:84183 original size:23 final size:23
Alignment explanation
Indices: 84142--84187 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
84132 TAACTAATAC
84142 TAGTTTTAATGTCTAACGCATAT
1 TAGTTTTAATGTCTAACGCATAT
*
84165 TAGTTTTAATGTGTAACGCATAT
1 TAGTTTTAATGTCTAACGCATAT
84188 CGGAATTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (23 bp):
TAGTTTTAATGTCTAACGCATAT
Done.