Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003987.1 Hibiscus syriacus cultivar Beakdansim tig00008677_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: 65322
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:2004 original size:17 final size:15
Alignment explanation
Indices: 1982--2021 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
1972 CTTAAATATG
1982 TTAAATATTATTAAAA
1 TTAAATATTA-TAAAA
*
1998 CTTAAATATTATAATA
1 -TTAAATATTATAAAA
2014 TTAAATAT
1 TTAAATAT
2022 GAATGCCTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATTATAAAA
Found at i:2076 original size:23 final size:23
Alignment explanation
Indices: 2049--2117 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
2039 ATGTAAAAAG
2049 AATAAATTCGACTATTTATAAAT
1 AATAAATTCGACTATTTATAAAT
2072 AATAAATTCGACTATTTATAAAT
1 AATAAATTCGACTATTTATAAAT
* *
2095 AATTAATTTGACTATTTATAAAT
1 AATAAATTCGACTATTTATAAAT
2118 TCGATTTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (23 bp):
AATAAATTCGACTATTTATAAAT
Found at i:2344 original size:68 final size:68
Alignment explanation
Indices: 2267--2400 Score: 259
Period size: 68 Copynumber: 2.0 Consensus size: 68
2257 TATTATTTTT
*
2267 AAAAAATAGGTTATTATTACAAAATCAAATTTATAAATACATAGAAATACATAAATTTTATAAAT
1 AAAAAATAGGTTATTATTACAAAATCAAATATATAAATACATAGAAATACATAAATTTTATAAAT
2332 TTA
66 TTA
2335 AAAAAATAGGTTATTATTACAAAATCAAATATATAAATACATAGAAATACATAAATTTTATAAAT
1 AAAAAATAGGTTATTATTACAAAATCAAATATATAAATACATAGAAATACATAAATTTTATAAAT
2400 T
66 T
2401 CGATTTAAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.34
Consensus pattern (68 bp):
AAAAAATAGGTTATTATTACAAAATCAAATATATAAATACATAGAAATACATAAATTTTATAAAT
TTA
Found at i:2637 original size:10 final size:10
Alignment explanation
Indices: 2622--2646 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2612 AAAATCAAAT
2622 ATATAAATAC
1 ATATAAATAC
2632 ATATAAATAC
1 ATATAAATAC
2642 ATATA
1 ATATA
2647 TGATTACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (10 bp):
ATATAAATAC
Found at i:5754 original size:33 final size:33
Alignment explanation
Indices: 5717--5832 Score: 193
Period size: 33 Copynumber: 3.6 Consensus size: 33
5707 AATTTTTTAT
*
5717 ATATAATATAACTTAAACTAGAAACAAAATATA
1 ATATAATATAACTTAAACTAGAAACAAACTATA
5750 ATATAATATAACTTAAACTAGAAACAAACTATA
1 ATATAATATAACTTAAACTAGAAACAAACTATA
*
5783 ATATAATATAACTTAAACT---AACAACCTATA
1 ATATAATATAACTTAAACTAGAAACAAACTATA
5813 ATATAATATAACTTAAACTA
1 ATATAATATAACTTAAACTA
5833 ACAAACTAAT
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
30 29 0.36
33 51 0.64
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (33 bp):
ATATAATATAACTTAAACTAGAAACAAACTATA
Found at i:5812 original size:30 final size:31
Alignment explanation
Indices: 5717--5845 Score: 181
Period size: 33 Copynumber: 4.1 Consensus size: 31
5707 AATTTTTTAT
*
5717 ATATAATATAACTTAAACTAGAAACAAAATATA
1 ATATAATATAACTTAAACT--AAACAAACTATA
5750 ATATAATATAACTTAAACTAGAAACAAACTATA
1 ATATAATATAACTTAAACT--AAACAAACTATA
*
5783 ATATAATATAACTTAAACT-AACAACCTATA
1 ATATAATATAACTTAAACTAAACAAACTATA
5813 ATATAATATAACTTAAACT-AACAAACTAATA
1 ATATAATATAACTTAAACTAAACAAACT-ATA
5844 AT
1 AT
5846 TACCAATTAC
Statistics
Matches: 92, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
30 36 0.39
31 5 0.05
33 51 0.55
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (31 bp):
ATATAATATAACTTAAACTAAACAAACTATA
Found at i:5884 original size:19 final size:20
Alignment explanation
Indices: 5860--5912 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
5850 AATTACCCGA
*
5860 TCCTTTC-TTCTTCTTCCTT
1 TCCTTTCTTTCTTCTCCCTT
5879 TCCTTTCTTTCTTCTCCCTT
1 TCCTTTCTTTCTTCTCCCTT
*
5899 T-GTTTCTTTCTTCT
1 TCCTTTCTTTCTTCT
5913 AATTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (20 bp):
TCCTTTCTTTCTTCTCCCTT
Found at i:5923 original size:19 final size:19
Alignment explanation
Indices: 5882--5925 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5872 CTTCCTTTCC
**
5882 TTTCTTTCTTCTCCCTTTG
1 TTTCTTTCTTCTAACTTTG
* *
5901 TTTCTTTCTTCTAATTTTT
1 TTTCTTTCTTCTAACTTTG
5920 TTTCTT
1 TTTCTT
5926 CATTCCCGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.05, C:0.23, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTCTTTCTTCTAACTTTG
Found at i:7041 original size:17 final size:17
Alignment explanation
Indices: 7019--7057 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
7009 ATGGTCGACT
*
7019 GTTGACTGTTGACCTG-C
1 GTTGACCGTTGA-CTGAC
7036 GTTGACCGTTGACTGAC
1 GTTGACCGTTGACTGAC
7053 GTTGA
1 GTTGA
7058 TCACTGTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.15, C:0.21, G:0.31, T:0.33
Consensus pattern (17 bp):
GTTGACCGTTGACTGAC
Found at i:10586 original size:29 final size:28
Alignment explanation
Indices: 10544--10762 Score: 185
Period size: 29 Copynumber: 7.6 Consensus size: 28
10534 TATCAACATT
*
10544 TTACACAATTATCACCCTTTTAAAAATAA
1 TTACA-AAATATCACCCTTTTAAAAATAA
10573 TTACAAAACTATCA-CCTTCTTAAAAATAA
1 TTACAAAA-TATCACCCTT-TTAAAAATAA
* * * *
10602 TTATGAAAATAGCACCTATTTTCAAAATAA
1 TTA-CAAAATATCACC-CTTTTAAAAATAA
* *
10632 TTACTAAAATATCA-CTTTTTAAAAAAAA
1 TTAC-AAAATATCACCCTTTTAAAAATAA
* * **
10660 TTACGAAATTATCACCTTTTTTTTTAAA-AA
1 TTAC-AAAATATCACC--CTTTTAAAAATAA
* *
10690 TTACAAAATAGC-CCCATTTTCAAAATAA
1 TTACAAAATATCACCC-TTTTAAAAATAA
*
10718 TTACCAAAATATCACCATTTTAAAAATAA
1 TTA-CAAAATATCACCCTTTTAAAAATAA
10747 TTACAAAATATCACCC
1 TTACAAAATATCACCC
10763 GGTCAACGGT
Statistics
Matches: 154, Mismatches: 23, Indels: 27
0.75 0.11 0.13
Matches are distributed among these distances:
27 7 0.05
28 47 0.31
29 57 0.37
30 33 0.21
31 10 0.06
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.34
Consensus pattern (28 bp):
TTACAAAATATCACCCTTTTAAAAATAA
Found at i:10662 original size:87 final size:85
Alignment explanation
Indices: 10553--10761 Score: 260
Period size: 87 Copynumber: 2.4 Consensus size: 85
10543 TTTACACAAT
* *
10553 TATCACCCTTTTAAAAATAATTACAAAACTATCACC-TTCTTAAAAATAATTATGAAAATAGCAC
1 TATCACCATTTTAAAAATAATTACAAAA-TATCACCTTTCTTAAAAA-AATTA-CAAAATAGC-C
* *
10617 CTATTTTCAAAATAATTACTAAAA
62 CCATTTTCAAAATAATTACCAAAA
* * * * **
10641 TATCA-CTTTTTAAAAAAAATTACGAAATTATCACCTTTTTTTTTAAAAATTACAAAATAGCCCC
1 TATCACCATTTTAAAAATAATTAC-AAAATATCACC-TTTCTTAAAAAAATTACAAAATAGCCCC
10705 ATTTTCAAAATAATTACCAAAA
64 ATTTTCAAAATAATTACCAAAA
10727 TATCACCATTTTAAAAATAATTACAAAATATCACC
1 TATCACCATTTTAAAAATAATTACAAAATATCACC
10762 CGGTCAACGG
Statistics
Matches: 105, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
86 38 0.36
87 47 0.45
88 13 0.12
89 7 0.07
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.34
Consensus pattern (85 bp):
TATCACCATTTTAAAAATAATTACAAAATATCACCTTTCTTAAAAAAATTACAAAATAGCCCCAT
TTTCAAAATAATTACCAAAA
Found at i:10839 original size:18 final size:18
Alignment explanation
Indices: 10795--10846 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
10785 GTCAACGGGT
10795 TGGGTCGGG-CGGGTCAA
1 TGGGTCGGGTCGGGTCAA
* *
10812 CGGGAT-GGGTCGAGTCAA
1 TGGG-TCGGGTCGGGTCAA
10830 TGGGTCGGGTCGGGTCA
1 TGGGTCGGGTCGGGTCA
10847 GAACCGGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.13, C:0.17, G:0.50, T:0.19
Consensus pattern (18 bp):
TGGGTCGGGTCGGGTCAA
Found at i:17949 original size:30 final size:29
Alignment explanation
Indices: 17913--18113 Score: 226
Period size: 29 Copynumber: 6.9 Consensus size: 29
17903 ATTATAACCC
* * * **
17913 TTTTAAAAATAATTACGAAACTAACATCTT
1 TTTTAAAAATAATTACAAAAATATCA-CCA
*
17943 TTTTAAAAATAATTACAAAAATATCACCT
1 TTTTAAAAATAATTACAAAAATATCACCA
* *
17972 TTTTCAAAATAATTACTAAAATATCA-CA
1 TTTTAAAAATAATTACAAAAATATCACCA
* * **
18000 TTTTAAAAA-AATTACGAAATTATCACTT
1 TTTTAAAAATAATTACAAAAATATCACCA
* *
18028 TTTTAAAAAAAAATTACAAAAATAGCACCA
1 TTTT-AAAAATAATTACAAAAATATCACCA
* *
18058 TTTTCAAAATAATTACCAAAATATCACCA
1 TTTTAAAAATAATTACAAAAATATCACCA
18087 TTTTAAAAATAATTACAAAAATATCAC
1 TTTTAAAAATAATTACAAAAATATCAC
18114 TCGATCAACG
Statistics
Matches: 145, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
27 14 0.10
28 13 0.09
29 77 0.53
30 41 0.28
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.33
Consensus pattern (29 bp):
TTTTAAAAATAATTACAAAAATATCACCA
Found at i:18062 original size:86 final size:87
Alignment explanation
Indices: 17913--18114 Score: 300
Period size: 86 Copynumber: 2.3 Consensus size: 87
17903 ATTATAACCC
* * * * *
17913 TTTTAAAAATAATTACGAAACTAACATCTTTTTTAAAAATAATTACAAAAATATCACCTTTTTCA
1 TTTTAAAAATAATTACGAAAATATCA-CTTTTTTAAAAAAAATTACAAAAATAGCACCATTTTCA
*
17978 AAATAATTACTAAAATATCA-CA
65 AAATAATTACCAAAATATCACCA
*
18000 TTTTAAAAA-AATTACGAAATTATCACTTTTTTAAAAAAAAATTACAAAAATAGCACCATTTTCA
1 TTTTAAAAATAATTACGAAAATATCACTTTTTT-AAAAAAAATTACAAAAATAGCACCATTTTCA
18064 AAATAATTACCAAAATATCACCA
65 AAATAATTACCAAAATATCACCA
*
18087 TTTTAAAAATAATTACAAAAATATCACT
1 TTTTAAAAATAATTACGAAAATATCACT
18115 CGATCAACGG
Statistics
Matches: 104, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
85 7 0.07
86 61 0.59
87 20 0.19
88 16 0.15
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.34
Consensus pattern (87 bp):
TTTTAAAAATAATTACGAAAATATCACTTTTTTAAAAAAAATTACAAAAATAGCACCATTTTCAA
AATAATTACCAAAATATCACCA
Found at i:18130 original size:7 final size:7
Alignment explanation
Indices: 18118--18152 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
18108 TATCACTCGA
18118 TCAACGG
1 TCAACGG
18125 TCAACGG
1 TCAACGG
*
18132 TCAATGG
1 TCAACGG
18139 TCAACGG
1 TCAACGG
18146 TCAACGG
1 TCAACGG
18153 GTCGGGTCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.17
Consensus pattern (7 bp):
TCAACGG
Found at i:18167 original size:18 final size:18
Alignment explanation
Indices: 18144--18179 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
18134 AATGGTCAAC
*
18144 GGTCAACGGGTCGGGTCG
1 GGTCAACGAGTCGGGTCG
18162 GGTCAACGAGTCGGGTCG
1 GGTCAACGAGTCGGGTCG
18180 TGTTGGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.22, G:0.47, T:0.17
Consensus pattern (18 bp):
GGTCAACGAGTCGGGTCG
Found at i:24412 original size:16 final size:16
Alignment explanation
Indices: 24387--24419 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
24377 TTAAAAATAA
*
24387 AATTTTAAATTTTTAT
1 AATTTCAAATTTTTAT
24403 AATTTCAAATTTTTAT
1 AATTTCAAATTTTTAT
24419 A
1 A
24420 TTAAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTCAAATTTTTAT
Found at i:24951 original size:16 final size:16
Alignment explanation
Indices: 24930--24974 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
24920 TTCATTTTCC
24930 TTTCTCTCCCTCTCAT
1 TTTCTCTCCCTCTCAT
24946 TTTCTCTCCCTCTCAT
1 TTTCTCTCCCTCTCAT
*
24962 TTTCTCCCCCTCT
1 TTTCTCTCCCTCT
24975 TTTTAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTCTCTCCCTCTCAT
Found at i:24978 original size:14 final size:14
Alignment explanation
Indices: 24929--24978 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
24919 TTTCATTTTC
*
24929 CTTTCTCTCCCTCT
1 CTTTTTCTCCCTCT
24943 CATTTTCTCTCCCTCT
1 C-TTTT-TCTCCCTCT
* *
24959 CATTTTCTCCCCCT
1 CTTTTTCTCCCTCT
24973 CTTTTT
1 CTTTTT
24979 AAAATCTAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 14 0.47
15 6 0.20
16 10 0.33
ACGTcount: A:0.04, C:0.44, G:0.00, T:0.52
Consensus pattern (14 bp):
CTTTTTCTCCCTCT
Found at i:26010 original size:34 final size:34
Alignment explanation
Indices: 25964--26071 Score: 107
Period size: 34 Copynumber: 3.2 Consensus size: 34
25954 AACTTAAATA
*
25964 AATTTTATTTTAATTTGAGATATTCAAAAGATAT
1 AATTATATTTTAATTTGAGATATTCAAAAGATAT
*
25998 AATTATATTTTAATATTCA-A-AGTT-AAATAGATAAT
1 AATTATATTTTAAT-TTGAGATA-TTCAAA-AGAT-AT
* **
26033 AAATACCTTTTAATTTGAGATATTCAAAAGA-AT
1 AATTATATTTTAATTTGAGATATTCAAAAGATAT
26066 AATTAT
1 AATTAT
26072 CATACTAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
33 10 0.17
34 23 0.39
35 22 0.37
36 4 0.07
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (34 bp):
AATTATATTTTAATTTGAGATATTCAAAAGATAT
Found at i:26024 original size:63 final size:66
Alignment explanation
Indices: 25883--26092 Score: 211
Period size: 69 Copynumber: 3.2 Consensus size: 66
25873 TCTTTTAGTG
* **
25883 TTCAAATTTAAATATATAAT-AATATCTTTTAATTTGAAATATTCAAAA-ATATAGA-TACCTTT
1 TTCAAA-TTAAATA-ATAATAAATA-CTTTTAATTTGAGATATTCAAAAGATATA-ATTATATTT
*
25945 TACTA
62 TAATA
**
25950 TTCAAACTTAAAT-A-AAT-TTTA-TTTTAATTTGAGATATTCAAAAGATATAATTATATTTTAA
1 TTCAAA-TTAAATAATAATAAATACTTTTAATTTGAGATATTCAAAAGATATAATTATATTTTAA
26011 TA
65 TA
**
26013 TTCAAAGTTAAATAGATAATAAATACCTTTTAATTTGAGATATTCAAAAGA-ATAATTATCATAC
1 TTCAAA-TTAAATA-ATAATAAATA-CTTTTAATTTGAGATATTCAAAAGATATAATTAT-ATTT
26077 TAATA
62 TAATA
26082 TTCAAATTAAA
1 TTCAAATTAAA
26093 GATATAAATT
Statistics
Matches: 122, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
62 22 0.18
63 26 0.21
64 5 0.04
65 2 0.02
66 3 0.02
67 14 0.11
68 13 0.11
69 37 0.30
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (66 bp):
TTCAAATTAAATAATAATAAATACTTTTAATTTGAGATATTCAAAAGATATAATTATATTTTAAT
A
Found at i:29971 original size:4 final size:5
Alignment explanation
Indices: 29946--29978 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
29936 ATCATATTAC
29946 TTTTA TTTTA TTTTA TTTTA -TTTA TTTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTT
29979 GCGTTGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.69
6 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:31082 original size:17 final size:18
Alignment explanation
Indices: 31060--31095 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31050 TATTCTATTG
31060 TTTTTTA-ATAAATTTTA
1 TTTTTTACATAAATTTTA
*
31077 TTTTTTACATACATTTTA
1 TTTTTTACATAAATTTTA
31095 T
1 T
31096 GTATAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTTTACATAAATTTTA
Found at i:33187 original size:43 final size:43
Alignment explanation
Indices: 33139--33222 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
33129 AATCTAAACT
* * *
33139 CCAAAGTAACAATCTACAAATAAATCAAACTAGCATATTACCA
1 CCAAAGTAACAATCCACAAATAAACCAAACTAACATATTACCA
* *
33182 CCAAAGTAACAATCCACAAATATACCAAATTAACATATTAC
1 CCAAAGTAACAATCCACAAATAAACCAAACTAACATATTAC
33223 AACAATTCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.51, C:0.24, G:0.04, T:0.21
Consensus pattern (43 bp):
CCAAAGTAACAATCCACAAATAAACCAAACTAACATATTACCA
Found at i:36883 original size:54 final size:54
Alignment explanation
Indices: 36820--36939 Score: 213
Period size: 54 Copynumber: 2.2 Consensus size: 54
36810 CATAACATAG
*
36820 AGGCATCGATACCATGGTGAGGGTATCGATACCGGGCTAAACCAAAGCTAATTT
1 AGGCATCGATACCATGGTGAGGGTATCGATACCAGGCTAAACCAAAGCTAATTT
*
36874 AGGCATCGATACCATGGTGAGGGTATCGATACCAGGCTAAACCAAATCTAATTT
1 AGGCATCGATACCATGGTGAGGGTATCGATACCAGGCTAAACCAAAGCTAATTT
*
36928 AGGTATCGATAC
1 AGGCATCGATAC
36940 ATTAAGGGGG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (54 bp):
AGGCATCGATACCATGGTGAGGGTATCGATACCAGGCTAAACCAAAGCTAATTT
Found at i:37554 original size:45 final size:45
Alignment explanation
Indices: 37499--37663 Score: 172
Period size: 45 Copynumber: 3.7 Consensus size: 45
37489 TATAAAAGAA
* *** * *
37499 AAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTG
1 AAATGCATATGGGTACATTATCAACATGAAAGCATGCTATAGTTG
* * * *
37544 AAATGTATATGAGTACATTATCAACA-GAAAAGCATACTTTAGTTG
1 AAATGCATATGGGTACATTATCAACATG-AAAGCATGCTATAGTTG
* * * *
37589 AAATGTATATGGGTACATTATCAACATGAAAGTATGTTAGAGTTG
1 AAATGCATATGGGTACATTATCAACATGAAAGCATGCTATAGTTG
*
37634 AAATGCATATGGGTGCATTATCAACA-GAAA
1 AAATGCATATGGGTACATTATCAACATGAAA
37664 AGTATACTAG
Statistics
Matches: 100, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
44 5 0.05
45 94 0.94
46 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATGCATATGGGTACATTATCAACATGAAAGCATGCTATAGTTG
Found at i:37681 original size:29 final size:29
Alignment explanation
Indices: 37644--37701 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
37634 AAATGCATAT
*
37644 GGGTGCATTATCAACAGAAAAGTATACTA
1 GGGTACATTATCAACAGAAAAGTATACTA
37673 GGGTACATTATCAACAGAAAAGTATACTA
1 GGGTACATTATCAACAGAAAAGTATACTA
37702 TGGTTGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (29 bp):
GGGTACATTATCAACAGAAAAGTATACTA
Found at i:37688 original size:74 final size:74
Alignment explanation
Indices: 37599--37746 Score: 219
Period size: 74 Copynumber: 2.0 Consensus size: 74
37589 AAATGTATAT
** *
37599 GGGTACATTATCAACATG-AAAGTATGTTA-GAGTTGAAATGCATATGGGTGCATTATCAACAGA
1 GGGTACATTATCAACA-GAAAAGTATACTATG-GTTGAAATGCATATGGGTACATTATCAACAGA
37662 AAAGTATACTA
64 AAAGTATACTA
*
37673 GGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTACATTATCAACAGAAA
1 GGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGCATATGGGTACATTATCAACAGAAA
*
37738 TGTATACTA
66 AGTATACTA
37747 TGGTTGAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
73 1 0.01
74 65 0.97
75 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (74 bp):
GGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGCATATGGGTACATTATCAACAGAAA
AGTATACTA
Found at i:37700 original size:119 final size:119
Alignment explanation
Indices: 37556--37792 Score: 343
Period size: 119 Copynumber: 2.0 Consensus size: 119
37546 ATGTATATGA
*
37556 GTACATTATCAACAGAAAAGCATACTTTAGTTGAAATGTATATGGGTACATTATCAACATGAAA-
1 GTACATTATCAACAGAAAAGCATACTATAGTTGAAATGTATATGGGTACATTATCAACA-GAAAT
** ** * *
37620 GTATGTTA-GAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGG
65 GTATACTATG-GTTGAAATGCATACCGATACATTATCAACAGAAAAGTATACTAGG
* *
37675 GTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTACATTATCAACAGAAATG
1 GTACATTATCAACAGAAAAGCATACTATAGTTGAAATGTATATGGGTACATTATCAACAGAAATG
* *
37740 TATACTATGGTTGAAATGTATACCGATACATTATTAACAGAAAAGTATACTAG
66 TATACTATGGTTGAAATGCATACCGATACATTATCAACAGAAAAGTATACTAG
37793 AGTTGAAATG
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
118 4 0.04
119 100 0.95
120 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (119 bp):
GTACATTATCAACAGAAAAGCATACTATAGTTGAAATGTATATGGGTACATTATCAACAGAAATG
TATACTATGGTTGAAATGCATACCGATACATTATCAACAGAAAAGTATACTAGG
Found at i:37731 original size:45 final size:45
Alignment explanation
Indices: 37673--37829 Score: 226
Period size: 45 Copynumber: 3.5 Consensus size: 45
37663 AAGTATACTA
37673 GGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATAT
1 GGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATAT
* *
37718 GGGTACATTATCAACAGAAATGTATACTATGGTTGAAATGTATAC
1 GGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATAT
* * * *
37763 CGATACATTATTAACAGAAAAGTATACTA-GAGTTGAAATGGATAT
1 GGGTACATTATCAACAGAAAAGTATACTATG-GTTGAAATGTATAT
* *
37808 GGGTGCATTATCAACAAAAAAG
1 GGGTACATTATCAACAGAAAAG
37830 ATGTTATAGT
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
44 1 0.01
45 97 0.99
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (45 bp):
GGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATAT
Found at i:38233 original size:2 final size:2
Alignment explanation
Indices: 38220--38263 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
38210 GAAGGAAATC
* *
38220 TA TA TA TG TA TA TA TA TA TA TG TA TA TA TA 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 TA TA
38262 TA
1 TA
38264 ATGTACAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38239 original size:14 final size:14
Alignment explanation
Indices: 38220--38263 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
38210 GAAGGAAATC
38220 TATATATGTATATA
1 TATATATGTATATA
38234 TATATATGTATATA
1 TATATATGTATATA
*
38248 TATATATATATATA
1 TATATATGTATATA
38262 TA
1 TA
38264 ATGTACAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (14 bp):
TATATATGTATATA
Found at i:41703 original size:2 final size:2
Alignment explanation
Indices: 41698--41727 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41688 ATAAAAATGG
41698 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
41728 TCTTATATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42232 original size:22 final size:22
Alignment explanation
Indices: 42189--42252 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
42179 GAGGGTCTAC
*
42189 GTGGTCCTTCGGGGACATATACA
1 GTGGTCCTTC-GGGACAAATACA
42212 GTGGTCCTTCGGGACAAATACA
1 GTGGTCCTTCGGGACAAATACA
42234 -TAGGTCCTTCGGGACAAAT
1 GT-GGTCCTTCGGGACAAAT
42253 TTCATATGCC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 1 0.03
22 28 0.72
23 10 0.26
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (22 bp):
GTGGTCCTTCGGGACAAATACA
Found at i:42569 original size:15 final size:16
Alignment explanation
Indices: 42540--42573 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
42530 TAGTGATAAT
*
42540 AATATGATTATTGATA
1 AATATGATTAATGATA
42556 AATATG-TTAATGATA
1 AATATGATTAATGATA
42571 AAT
1 AAT
42574 GTATAGGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (16 bp):
AATATGATTAATGATA
Found at i:43000 original size:18 final size:17
Alignment explanation
Indices: 42974--43026 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 17
42964 ATGAACGTTT
42974 TAAATTTTATGAATTTA
1 TAAATTTTATGAATTTA
* *
42991 TACATATTTATAAAATTTTA
1 TAAAT-TTTAT-GAA-TTTA
43011 TAAATTTTATGAATTT
1 TAAATTTTATGAATTT
43027 TATGAATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 7 0.24
20 8 0.28
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
TAAATTTTATGAATTTA
Found at i:43010 original size:10 final size:9
Alignment explanation
Indices: 42974--43035 Score: 63
Period size: 9 Copynumber: 6.8 Consensus size: 9
42964 ATGAACGTTT
42974 TAAATTTTA
1 TAAATTTTA
*
42983 TGAA-TTTA
1 TAAATTTTA
*
42991 TACATATTTA
1 TAAAT-TTTA
43001 TAAAATTTTA
1 T-AAATTTTA
43011 TAAATTTTA
1 TAAATTTTA
*
43020 TGAATTTTA
1 TAAATTTTA
*
43029 TGAATTT
1 TAAATTT
43036 CGGGTACTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.13
9 26 0.58
10 10 0.22
11 3 0.07
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (9 bp):
TAAATTTTA
Found at i:43027 original size:18 final size:18
Alignment explanation
Indices: 42974--43035 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
42964 ATGAACGTTT
42974 TAAATTTTATGAA-TTTA
1 TAAATTTTATGAATTTTA
* *
42991 TACATATTTATAAAATTTTA
1 TAAAT-TTTAT-GAATTTTA
43011 TAAATTTTATGAATTTTA
1 TAAATTTTATGAATTTTA
*
43029 TGAATTT
1 TAAATTT
43036 CGGGTACTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 4 0.11
18 18 0.49
19 7 0.19
20 8 0.22
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (18 bp):
TAAATTTTATGAATTTTA
Found at i:46966 original size:31 final size:31
Alignment explanation
Indices: 46928--46994 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
46918 AGTTACGTCG
* *
46928 GGGACCATATTGGAAACGGACTAAATGTTGA
1 GGGACCATATTGCAAACAGACTAAATGTTGA
*
46959 GGGACCATATTGCAAACAGACTAAATGTTGG
1 GGGACCATATTGCAAACAGACTAAATGTTGA
46990 GGGAC
1 GGGAC
46995 TGTATTACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (31 bp):
GGGACCATATTGCAAACAGACTAAATGTTGA
Found at i:47707 original size:32 final size:32
Alignment explanation
Indices: 47670--47857 Score: 236
Period size: 32 Copynumber: 5.9 Consensus size: 32
47660 ATTGACGCTC
*
47670 CTGTGCATTATCTGAATGCAACACTAACTTTG
1 CTGTGCATTATCTGAATGCAACACTGACTTTG
* *
47702 TTGTGCATTATCTGAATGCAACACTAACTTTG
1 CTGTGCATTATCTGAATGCAACACTGACTTTG
* *
47734 TTGTGCATTATCTGAATGTAACACTGACTCTT-
1 CTGTGCATTATCTGAATGCAACACTGACT-TTG
* * *
47766 CTGTGTATTATCTGAATACAACACTGA-TTATA
1 CTGTGCATTATCTGAATGCAACACTGACTT-TG
* *
47798 CTATGCATTATCTGAATGCAATACTGACTTTG
1 CTGTGCATTATCTGAATGCAACACTGACTTTG
* *
47830 CTGTGCATTATATAAATGCAACACTGAC
1 CTGTGCATTATCTGAATGCAACACTGAC
47858 ACTAATATAC
Statistics
Matches: 136, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.01
31 2 0.01
32 129 0.95
33 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (32 bp):
CTGTGCATTATCTGAATGCAACACTGACTTTG
Found at i:47805 original size:96 final size:96
Alignment explanation
Indices: 47642--47857 Score: 254
Period size: 96 Copynumber: 2.2 Consensus size: 96
47632 TATATGTTGA
* ** * * * * ** *
47642 GCATTATCTAAATGCGGCATTGACGCTCCTGTGCATTATCTGAATGCAACACTAACTTTGTTGTG
1 GCATTATATAAATGCAACACTGACTCTTCTGTGCATTATCTGAATACAACACTAACTTTACTATG
*
47707 CATTATCTGAATGCAACACTAACTTTGTTGT
66 CATTATCTGAATGCAACACTAACTTTGCTGT
* * * * *
47738 GCATTATCTGAATGTAACACTGACTCTTCTGTGTATTATCTGAATACAACACTGA-TTATACTAT
1 GCATTATATAAATGCAACACTGACTCTTCTGTGCATTATCTGAATACAACACTAACTT-TACTAT
* *
47802 GCATTATCTGAATGCAATACTGACTTTGCTGT
65 GCATTATCTGAATGCAACACTAACTTTGCTGT
47834 GCATTATATAAATGCAACACTGAC
1 GCATTATATAAATGCAACACTGAC
47858 ACTAATATAC
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
95 2 0.02
96 98 0.98
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (96 bp):
GCATTATATAAATGCAACACTGACTCTTCTGTGCATTATCTGAATACAACACTAACTTTACTATG
CATTATCTGAATGCAACACTAACTTTGCTGT
Found at i:55787 original size:18 final size:18
Alignment explanation
Indices: 55764--55817 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
55754 ATATGTAACT
55764 GATTTTAAAGATGATTGG
1 GATTTTAAAGATGATTGG
55782 GA-TTT-----TGATTGG
1 GATTTTAAAGATGATTGG
*
55794 GATTTTAAAGATGATTGC
1 GATTTTAAAGATGATTGG
55812 GATTTT
1 GATTTT
55818 GATTGCCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 12
0.69 0.02 0.29
Matches are distributed among these distances:
12 9 0.31
13 3 0.10
17 3 0.10
18 14 0.48
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.44
Consensus pattern (18 bp):
GATTTTAAAGATGATTGG
Found at i:55790 original size:12 final size:12
Alignment explanation
Indices: 55775--55799 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55765 ATTTTAAAGA
55775 TGATTGGGATTT
1 TGATTGGGATTT
55787 TGATTGGGATTT
1 TGATTGGGATTT
55799 T
1 T
55800 AAAGATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (12 bp):
TGATTGGGATTT
Found at i:55798 original size:30 final size:30
Alignment explanation
Indices: 55764--55822 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
55754 ATATGTAACT
*
55764 GATTTTAAAGATGATTGGGATTTTGATTGG
1 GATTTTAAAGATGATTGCGATTTTGATTGG
55794 GATTTTAAAGATGATTGCGATTTTGATTG
1 GATTTTAAAGATGATTGCGATTTTGATTG
55823 CCTTTCTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (30 bp):
GATTTTAAAGATGATTGCGATTTTGATTGG
Found at i:59182 original size:20 final size:20
Alignment explanation
Indices: 59157--59214 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
59147 ATTCATTTGA
59157 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
59177 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
59197 CTATTGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
59215 CGCAATGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:59399 original size:14 final size:14
Alignment explanation
Indices: 59380--59416 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
59370 CATCAATTAA
59380 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
59394 ACAAATCATCTTTT
1 ACAAATCAACATTT
59408 ACAAATCAA
1 ACAAATCAA
59417 TTAACAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:61290 original size:19 final size:18
Alignment explanation
Indices: 61260--61313 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
61250 AAATCGAACA
61260 AAATGACTATCGCAACGCGG
1 AAATG-CTATCGCAACGC-G
*
61280 AAATGCTATCGCAATGCG
1 AAATGCTATCGCAACGCG
**
61298 AAATGAAATCGCAACG
1 AAATGCTATCGCAACG
61314 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 14 0.47
19 11 0.37
20 5 0.17
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (18 bp):
AAATGCTATCGCAACGCG
Found at i:61322 original size:14 final size:14
Alignment explanation
Indices: 61303--61360 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
61293 ATGCGAAATG
61303 AAATCGCAACGACA
1 AAATCGCAACGACA
*
61317 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
61336 AAATCGCAACGACA
1 AAATCGCAACGACA
61350 AAATCGCAACG
1 AAATCGCAACG
61361 CGAAACACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:61328 original size:32 final size:33
Alignment explanation
Indices: 61287--61365 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
61277 CGGAAATGCT
61287 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
61319 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
61352 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
61366 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 16 0.36
33 29 0.64
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:61338 original size:19 final size:19
Alignment explanation
Indices: 61287--61344 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 19
61277 CGGAAATGCT
61287 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
61305 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
61319 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
61338 ATCGCAA
1 ATCGCAA
61345 CGACAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
14 10 0.31
16 4 0.12
18 8 0.25
19 10 0.31
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:61373 original size:33 final size:33
Alignment explanation
Indices: 61287--61376 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
61277 CGGAAATGCT
* *
61287 ATCGCAATGCGAAAT-GAAATCGCAACGACAAA
1 ATCGCAACGCGAAATCAAAATCGCAACGACAAA
* *
61319 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATCAAAATCGCAACGACAAA
61352 ATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAACGCGAAATCA-AAATCGCA
61377 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 16 0.30
33 37 0.70
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATCAAAATCGCAACGACAAA
Found at i:61411 original size:14 final size:14
Alignment explanation
Indices: 61388--61451 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 14
61378 TGCGATTTTC
61388 ATTTTG-CGTTGCG
1 ATTTTGTCGTTGCG
61401 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
61415 ATTTCATTTCGCATTGCG
1 ATTT--TGTCG--TTGCG
61433 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
61447 ATTTT
1 ATTTT
61452 CATTTCGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 6 0.14
14 21 0.48
16 8 0.18
18 9 0.20
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:61458 original size:33 final size:33
Alignment explanation
Indices: 61377--61467 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
61367 ACAAATCGCA
* *
61377 TTGCGATTTTCATTTTGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
61410 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
61442 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
61468 AGCCATTTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:61506 original size:21 final size:20
Alignment explanation
Indices: 61454--61507 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
61444 GCGATTTTCA
*
61454 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
61474 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
61494 TTTCCGTGTTGCGA
1 TTT-CGCGTTGCGA
61508 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:62027 original size:17 final size:18
Alignment explanation
Indices: 61986--62027 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
61976 CGATCAGATG
* *
61986 ATGGCTCTGGGTGAGGTG
1 ATGGCTCTGGGCGAGGTA
*
62004 ATAGCTCT-GGCGAGGTA
1 ATGGCTCTGGGCGAGGTA
62021 ATGGCTC
1 ATGGCTC
62028 CCGAAGTGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.17, C:0.17, G:0.40, T:0.26
Consensus pattern (18 bp):
ATGGCTCTGGGCGAGGTA
Found at i:63342 original size:20 final size:20
Alignment explanation
Indices: 63317--63359 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
63307 GAATAGTTTT
63317 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
63337 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
63357 GAA
1 GAA
63360 TTTGACTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:63365 original size:20 final size:20
Alignment explanation
Indices: 63327--63380 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
63317 GAAAATGAAA
* *
63327 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATATGACT
*
63347 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATATGACT
*
63367 ATCGCAACGAGAAT
1 ATCGCAACGCGAAT
63381 CGCAACGCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:63628 original size:22 final size:22
Alignment explanation
Indices: 63601--63644 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
63591 GATGGAGATA
63601 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
63623 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
63645 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:63865 original size:19 final size:20
Alignment explanation
Indices: 63804--63874 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
63794 CGCTTTGAAA
* *
63804 ATCGCATTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGT
63824 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
63844 ATCGCGTTGCGAAAGT-AGT
1 ATCGCGTTGCGAAAGTCAGT
*
63863 ATCTCGTTGCGA
1 ATCGCGTTGCGA
63875 TTTTGTATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 14 0.29
20 34 0.71
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGT
Found at i:63916 original size:20 final size:20
Alignment explanation
Indices: 63804--63915 Score: 102
Period size: 20 Copynumber: 5.6 Consensus size: 20
63794 CGCTTTGAAA
*
63804 ATCGCATTGCGAAAGTCAGA
1 ATCGCATTGCGAAAGTCAGT
*
63824 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGAAAGTCAGT
*
63844 ATCGCGTTGCGAAAGT-AGT
1 ATCGCATTGCGAAAGTCAGT
* * ** *
63863 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--AAGTCAGT
*
63884 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGAAAGTCAGT
*
63904 ATCACATTGCGA
1 ATCGCATTGCGA
63916 TTTCCCATTC
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 17 0.22
20 47 0.60
21 14 0.18
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (20 bp):
ATCGCATTGCGAAAGTCAGT
Done.