Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007876.1 Hibiscus syriacus cultivar Beakdansim tig00110252_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: 99081
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:675 original size:20 final size:20
Alignment explanation
Indices: 604--675 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
594 TTTCAGAACT
*
604 TTTCAAATTCATAA-TTTA-
1 TTTCAGATTCATAACTTTAC
*
622 TTTCAGATTCATAGCTTTAC
1 TTTCAGATTCATAACTTTAC
642 TTTCAGATTCATAACTTTAC
1 TTTCAGATTCATAACTTTAC
*
662 TTTTAGATTCATAA
1 TTTCAGATTCATAA
676 TTTCATGTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.25
19 4 0.08
20 32 0.67
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.47
Consensus pattern (20 bp):
TTTCAGATTCATAACTTTAC
Found at i:942 original size:32 final size:31
Alignment explanation
Indices: 896--979 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 31
886 TAATTATTTT
* * *
896 TAATATTTGTTATTAAGAGTTTAATCTTTCTC
1 TAATATTTATTATTAAGAGCTCAAT-TTTCTC
* * *
928 TAATATTTACTATTATGAGCTCAATTTTTTC
1 TAATATTTATTATTAAGAGCTCAATTTTCTC
* *
959 TAATAATTATTATTAGGAGCT
1 TAATATTTATTATTAAGAGCT
980 TACTCTTATA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 23 0.53
32 20 0.47
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.50
Consensus pattern (31 bp):
TAATATTTATTATTAAGAGCTCAATTTTCTC
Found at i:2630 original size:27 final size:27
Alignment explanation
Indices: 2574--2630 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
2564 CACCACATGA
*
2574 TCCAGCACTACCTCATGTTCCACCGTT
1 TCCAGCACTACCTCATGTTCCACCGCT
** *
2601 TCCAGCACTTTCTCATGTTCCACTGCT
1 TCCAGCACTACCTCATGTTCCACCGCT
2628 TCC
1 TCC
2631 TTGATTTGCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.16, C:0.40, G:0.11, T:0.33
Consensus pattern (27 bp):
TCCAGCACTACCTCATGTTCCACCGCT
Found at i:9283 original size:223 final size:222
Alignment explanation
Indices: 8896--9340 Score: 773
Period size: 223 Copynumber: 2.0 Consensus size: 222
8886 ACCCGGAATA
* * *
8896 AAGGACCATATTTTAGAATTAAAGACCATTTCTTCCCAAGTTACCATAAAACTTGAGCATTGTCC
1 AAGGACCATATTATAGAATTAAAGACCATTTCTTCCCAAGCTACCATAAAACTTGAGCATTATCC
8961 TGCAAAACCGAACAAACTCCCCACATTTTCAGAAATTTGTTCCAAAGATTCCATGCCACAGTACA
66 TGCAAAACCGAACAAACTCCCCACATTTTCAGAAATTTGTTCCAAAGATTCCATGCCACAGTACA
** *
9026 AGTGAAAAATAAATGTGTTGAAGATTCAGCCTCCTCTTTACAAAACGGGCAAGCAACATCAACAA
131 AGTGAAAAATAAATGTACTGAAGATTCAGCCTCCTCTTTACAAAACGAGCAAGCAACATCAACAA
9091 TAGCTGAAACTCCTCTCCTTTGTAATT
196 TAGCTGAAACTCCTCTCCTTTGTAATT
* *
9118 AAGGACCATATTATAGAATTGAGGACCATTTCTTCCCAAGCTACCATAAAACTTTGAGCATTATC
1 AAGGACCATATTATAGAATTAAAGACCATTTCTTCCCAAGCTACCATAAAAC-TTGAGCATTATC
* *
9183 CTGCAGAACCGAACAAACTCCCCACATTTTCAGAAATTTGTTCCAAAGATTCCATGCCACAGTGC
65 CTGCAAAACCGAACAAACTCCCCACATTTTCAGAAATTTGTTCCAAAGATTCCATGCCACAGTAC
* *
9248 AAGTGAAAAATAAATGTACTGGAGATTCAGCCTCCTCTTTACAAAACGAGCTAGCAACATCAACA
130 AAGTGAAAAATAAATGTACTGAAGATTCAGCCTCCTCTTTACAAAACGAGCAAGCAACATCAACA
9313 ATAGCTGAAACTCCTCTCCTTTGTAATT
195 ATAGCTGAAACTCCTCTCCTTTGTAATT
9341 TTTGCTTTAC
Statistics
Matches: 210, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
222 48 0.23
223 162 0.77
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (222 bp):
AAGGACCATATTATAGAATTAAAGACCATTTCTTCCCAAGCTACCATAAAACTTGAGCATTATCC
TGCAAAACCGAACAAACTCCCCACATTTTCAGAAATTTGTTCCAAAGATTCCATGCCACAGTACA
AGTGAAAAATAAATGTACTGAAGATTCAGCCTCCTCTTTACAAAACGAGCAAGCAACATCAACAA
TAGCTGAAACTCCTCTCCTTTGTAATT
Found at i:12517 original size:2 final size:2
Alignment explanation
Indices: 12510--12549 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12500 TTCTTATCAA
12510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12550 CAAGGCATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19132 original size:29 final size:28
Alignment explanation
Indices: 19099--19197 Score: 69
Period size: 29 Copynumber: 3.4 Consensus size: 28
19089 AGAGAATCAT
19099 AGTTTAGGGATGAAATTATAATGTTCAAA
1 AGTTTAGGGATGAAATTA-AATGTTCAAA
* * *
19128 AGTTTAAGGACT-AATTTAGAATGAGATTC-AT
1 AGTTTAGGGA-TGAAATTA-AAT--G-TTCAAA
*
19159 AGTTT-GAGGATGAAATTGAAATATTCAAA
1 AGTTTAG-GGATGAAATT-AAATGTTCAAA
19188 AGTTTAGGGA
1 AGTTTAGGGA
19198 CCAATTTGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 18
0.67 0.10 0.23
Matches are distributed among these distances:
28 3 0.06
29 26 0.49
30 3 0.06
31 17 0.32
32 4 0.08
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.33
Consensus pattern (28 bp):
AGTTTAGGGATGAAATTAAATGTTCAAA
Found at i:19144 original size:60 final size:59
Alignment explanation
Indices: 19047--19221 Score: 203
Period size: 60 Copynumber: 2.9 Consensus size: 59
19037 TGAATTTGGA
* * *
19047 GATGAAATTGGAATATTAAAAAGTTTTGGGACCAATTTAGAAAGAGAATCATAGTTT-AGG
1 GATGAAATT-AAATATTCAAAAGTTTAGGGACCAATTTAGAAAGAGAATCATAGTTTGA-G
* * * * *
19107 GATGAAATTATAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGATTCATAGTTTGAG
1 GATGAAATTA-AATATTCAAAAGTTTAGGGACCAATTTAGAAAGAGAATCATAGTTTGAG
*
19167 GATGAAATTGAAATATTCAAAAGTTTAGGGACCAATTT-GAAATGAG-GTCATAGTT
1 GATGAAATT-AAATATTCAAAAGTTTAGGGACCAATTTAGAAA-GAGAATCATAGTT
19222 GGGGACATAT
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
59 11 0.11
60 85 0.87
61 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.32
Consensus pattern (59 bp):
GATGAAATTAAATATTCAAAAGTTTAGGGACCAATTTAGAAAGAGAATCATAGTTTGAG
Found at i:28086 original size:20 final size:20
Alignment explanation
Indices: 28058--28110 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
28048 AAATCGCATT
* *
28058 GCGATAGTCAAATTCTCAAC
1 GCGAAAGTCAAATTCGCAAC
28078 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
28098 GCGAAAGTCAAAT
1 GCGAAAGTCAAAT
28111 GTTTTTACGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:28095 original size:40 final size:40
Alignment explanation
Indices: 28034--28110 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
28024 TCCAATTTCA
** *
28034 CAACGCGAATATGTAAATCGCATTGCGATAGTCAAATTCT
1 CAACGCGAATATGTAAATCGCAACGCGAAAGTCAAATTCT
28074 CAACGCGAA-A-GTCAAATTCGCAACGCGAAAGTCAAAT
1 CAACGCGAATATGT-AAA-TCGCAACGCGAAAGTCAAAT
28111 GTTTTTACGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.06
39 4 0.12
40 26 0.81
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (40 bp):
CAACGCGAATATGTAAATCGCAACGCGAAAGTCAAATTCT
Found at i:30775 original size:42 final size:42
Alignment explanation
Indices: 30728--30846 Score: 125
Period size: 42 Copynumber: 2.8 Consensus size: 42
30718 GATGCACCTA
* * * *
30728 TCATCATTCAAGAGGCGCCTTCTATCGTTCAAGAGGCCCATC-
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCA-CG
**
30770 TCATCA-TCGAAGAATCCCCTCCCACCGTTCAAGAGGCCCACG
1 TCATCATTC-AAGAGGCCCCTCCCACCGTTCAAGAGGCCCACG
* * *
30812 TCATCGTTCAAGAGGTCCCTCCCACTGTTCAAGAG
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAG
30847 CCCGATTCAT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
41 3 0.05
42 58 0.92
43 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCACG
Found at i:30841 original size:21 final size:20
Alignment explanation
Indices: 30786--30846 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
30776 TCGAAGAATC
*
30786 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACTGTTCAAGAGG
* *
30806 CCCACGTCA-TCGTTCAAGAGG
1 CCCTC-CCACT-GTTCAAGAGG
30827 TCCCTCCCACTGTTCAAGAG
1 -CCCTCCCACTGTTCAAGAG
30847 CCCGATTCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 4 0.12
21 23 0.72
22 5 0.16
ACGTcount: A:0.21, C:0.39, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACTGTTCAAGAGG
Found at i:32358 original size:18 final size:18
Alignment explanation
Indices: 32335--32370 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
32325 AAGCCGGTTG
32335 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
*
32353 TGATTGTGATTTTGATTT
1 TGATTGGGATTTTGATTT
32371 CCTTTTGCTT
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:0.17, C:0.00, G:0.25, T:0.58
Consensus pattern (18 bp):
TGATTGGGATTTTGATTT
Found at i:34832 original size:12 final size:12
Alignment explanation
Indices: 34811--34844 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
34801 GGTTGTGGGT
*
34811 TTTGAGATTGTG
1 TTTGATATTGTG
34823 TTTGATATTGTG
1 TTTGATATTGTG
*
34835 TTTGGTATTG
1 TTTGATATTG
34845 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:35432 original size:14 final size:15
Alignment explanation
Indices: 35396--35433 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
35386 GAAATCATTG
35396 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
35411 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
35426 AAAAATTA
1 AAAAATTA
35434 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:35611 original size:20 final size:20
Alignment explanation
Indices: 35585--35647 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
35575 AATTCTTTTA
35585 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
* * ***
35605 TGAATTTGACTATCACGTTG
1 CGAATTTGACTTTTGTGTTG
*
35625 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTTTGTGTTG
35645 CGA
1 CGA
35648 TTTACAGATT
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (20 bp):
CGAATTTGACTTTTGTGTTG
Found at i:38149 original size:38 final size:40
Alignment explanation
Indices: 38100--38264 Score: 170
Period size: 38 Copynumber: 4.3 Consensus size: 40
38090 CAAAGATTAC
*
38100 ATATATTATATACGTTTTCAAAAAACCA-TTTT-AAAAACT
1 ATATA-TATATATGTTTTCAAAAAACCATTTTTCAAAAACT
* *
38139 ATATATATATATGTTTTCAAAAAA-TATGTTTTTCAAAAATT
1 ATATATATATATGTTTTCAAAAAACCA--TTTTTCAAAAACT
*
38180 ATAT-TATATATGTTTTC-AAAAACCATTTTT-TAAAAC-
1 ATATATATATATGTTTTCAAAAAACCATTTTTCAAAAACT
***
38216 -TATATAT-TATGTTTTCAAAAATTTA-TTTTCAAAAACT
1 ATATATATATATGTTTTCAAAAAACCATTTTTCAAAAACT
38253 ATATATATATAT
1 ATATATATATAT
38265 ATTGTATATT
Statistics
Matches: 105, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
35 16 0.15
36 13 0.12
37 5 0.05
38 30 0.29
39 13 0.12
40 18 0.17
41 10 0.10
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (40 bp):
ATATATATATATGTTTTCAAAAAACCATTTTTCAAAAACT
Found at i:38167 original size:15 final size:16
Alignment explanation
Indices: 38147--38177 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38137 CTATATATAT
38147 ATATG-TTTTCAAAAA
1 ATATGTTTTTCAAAAA
38162 ATATGTTTTTCAAAAA
1 ATATGTTTTTCAAAAA
38178 TTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (16 bp):
ATATGTTTTTCAAAAA
Found at i:38266 original size:78 final size:81
Alignment explanation
Indices: 38084--38266 Score: 215
Period size: 78 Copynumber: 2.3 Consensus size: 81
38074 CAATATAATA
* *
38084 TATTTTCAAAGATTACATATATTATATACGTTTTCAAAAAACCATTTTAAAAACTATATATATAT
1 TATTTTCAAA-AATATATATATTATATACGTTTTCAAAAAACCATTTTAAAAAC-ATATATATAT
38149 ATGTTTTCAAAAAATATG
64 ATGTTTTCAAAAAATATG
* *
38167 T-TTTTC-AAAA-AT-TATATTATATATGTTTTC-AAAAACCATTTTTTAAAAC-TATATAT-TA
1 TATTTTCAAAAATATATATATTATATACGTTTTCAAAAAACCA-TTTTAAAAACATATATATATA
38225 TGTTTTC-AAAAAT-T-
65 TGTTTTCAAAAAATATG
38239 TATTTTCAAAAACTATATATATATATAT
1 TATTTTCAAAAA-TATATATAT-TATAT
38267 TGTATATTTT
Statistics
Matches: 89, Mismatches: 4, Indels: 19
0.79 0.04 0.17
Matches are distributed among these distances:
72 1 0.01
73 6 0.07
74 10 0.11
75 9 0.10
76 9 0.10
77 13 0.15
78 31 0.35
79 1 0.01
80 1 0.01
81 2 0.02
82 5 0.06
83 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (81 bp):
TATTTTCAAAAATATATATATTATATACGTTTTCAAAAAACCATTTTAAAAACATATATATATAT
GTTTTCAAAAAATATG
Found at i:39881 original size:9 final size:8
Alignment explanation
Indices: 39862--39897 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
39852 AACCAAAATG
39862 AAAATAAA
1 AAAATAAA
39870 AAAATAAA
1 AAAATAAA
39878 AAAATAAAA
1 AAAAT-AAA
39887 AAAATAAA
1 AAAATAAA
39895 AAA
1 AAA
39898 TATATGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:39899 original size:16 final size:17
Alignment explanation
Indices: 39862--39897 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
39852 AACCAAAATG
39862 AAAAT-AAAAAAATAAA
1 AAAATAAAAAAAATAAA
39878 AAAATAAAAAAAATAAA
1 AAAATAAAAAAAATAAA
39895 AAA
1 AAA
39898 TATATGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAATAAAAAAAATAAA
Found at i:39947 original size:21 final size:22
Alignment explanation
Indices: 39921--39968 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
39911 GCTATATAAT
39921 ATATAATATA-TTTCAAAAATA
1 ATATAATATATTTTCAAAAATA
* *
39942 ATATAATATATTTTCAAAGATT
1 ATATAATATATTTTCAAAAATA
39964 ATATA
1 ATATA
39969 TATTATATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATAATATATTTTCAAAAATA
Found at i:39971 original size:21 final size:22
Alignment explanation
Indices: 39916--39976 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
39906 TTATAGCTAT
39916 ATAATATATAATATATTTCAAAA
1 ATAATATAT-ATATATTTCAAAA
*
39939 ATAATATA-ATATATTTTCAAAG
1 ATAATATATATATA-TTTCAAAA
*
39961 ATTATATATATTATAT
1 ATAATATATA-TATAT
39977 ACGTTTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 5 0.15
22 14 0.42
23 10 0.30
24 4 0.12
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (22 bp):
ATAATATATATATATTTCAAAA
Found at i:40031 original size:42 final size:42
Alignment explanation
Indices: 39951--40033 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
39941 AATATAATAT
* * *
39951 ATTTTCAAAGATTATATATATTATATACGTTTTCAAAAAATC
1 ATTTTAAAAGATTATATATATTATATACATTATCAAAAAATC
*
39993 ATTTTAAAAG-TTATATATATATATATATATATAT-AAAAAAT
1 ATTTTAAAAGATTATATATAT-TATATACAT-TATCAAAAAAT
40034 ATGTTTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
41 10 0.29
42 23 0.66
43 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (42 bp):
ATTTTAAAAGATTATATATATTATATACATTATCAAAAAATC
Found at i:40052 original size:25 final size:24
Alignment explanation
Indices: 40024--40071 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40014 TATATATATA
40024 TATAAAAAATATGTTTTTCAAAAAT
1 TATAAAAAATATG-TTTTCAAAAAT
** *
40049 TATATTATATATGTTTTCAAAAA
1 TATAAAAAATATGTTTTCAAAAA
40072 CCATTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (24 bp):
TATAAAAAATATGTTTTCAAAAAT
Found at i:43179 original size:11 final size:10
Alignment explanation
Indices: 43155--43208 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 10
43145 TATATACACG
43155 TATTTTTA--
1 TATTTTTATT
43163 TATTTTTATAT
1 TATTTTTAT-T
43174 TATTTTTATT
1 TATTTTTATT
*
43184 T-TCTTTACTT
1 TATTTTTA-TT
43194 TATTTTTATT
1 TATTTTTATT
43204 T-TTTT
1 TATTTT
43209 CTTAATACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 8 0.21
9 9 0.23
10 8 0.21
11 14 0.36
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (10 bp):
TATTTTTATT
Found at i:43190 original size:20 final size:19
Alignment explanation
Indices: 43155--43208 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
43145 TATATACACG
*
43155 TATTTTTATATTTTTA-TAT
1 TATTTTTATTTTTTTACT-T
43174 TATTTTTATTTTCTTTACTT
1 TATTTTTATTTT-TTTACTT
43194 TATTTTTATTTTTTT
1 TATTTTTATTTTTTT
43209 CTTAATACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 14 0.44
20 17 0.53
21 1 0.03
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (19 bp):
TATTTTTATTTTTTTACTT
Found at i:48656 original size:84 final size:83
Alignment explanation
Indices: 48485--49456 Score: 996
Period size: 83 Copynumber: 11.7 Consensus size: 83
48475 TAAAAGACAA
* * * * *
48485 CATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
48550 CTCAGCTCCAAGGCACAT
66 CTCAGCTCCAAGGCACAT
* * * * * * * *
48568 CATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
* *
48633 GCTCAACTCCAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* *
48652 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACTAAAGA-CTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
48716 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * * * *
48735 CATTTGTAGCATAGCTTAAGTCAATAAGGGCTATCTG-C--CAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
* *
48797 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCCAAGGCACAT
* * * * * * * * * *
48816 CATTTACAGTATAACTCAAGGCTATAAGGGTTATCTGTCACCAAATACCTTCGAGTTCAACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
*
48881 CTCAGCTCCAAGGCATAT
66 CTCAGCTCCAAGGCACAT
** * * * *
48899 CATTTGCAATATAACTTGAGTTGAGAAGGGTTATCTGCCAACAAAGACCTTCAAGTTCAACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
*
48964 CTCAGCTCCAAGACACAT
66 CTCAGCTCCAAGGCACAT
* * * * *
48982 CATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTG-C--CAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
* * *
49044 CTCAGCTTCGAGAGCACAC
66 CTCAGCTCCAAG-GCACAT
* ** * * * * *
49063 CATTTACAATATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
*
49128 GCTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * * * *
49147 CATTTGCAGCATAACTTAAGTCGAGAATGGTTATCTGCCAACCAAATACTTTTGAGTTCGACTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
49212 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * * *
49231 CATTTGTAGCATAGCTTAAGTCAAGAAGGGTTATCTG-C--TAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
* * * *
49293 CTCAACTTCGAGTGCATAT
66 CTCAGCTCCAAG-GCACAT
* * * *
49312 CATTTACAGCATAACTCAAG--GATGAAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAACTTAAGTCGA-G-AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTA
*
49375 CGCTCAGCTCTAAGGCACAT
64 CGCTCAGCTCCAAGGCACAT
* *
49395 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTTCGAGTTCGA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACC-TTCGAGTTCGA
49457 TTTCATTCAG
Statistics
Matches: 724, Mismatches: 143, Indels: 42
0.80 0.16 0.05
Matches are distributed among these distances:
79 6 0.01
80 75 0.10
81 105 0.15
82 5 0.01
83 245 0.34
84 244 0.34
85 44 0.06
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (83 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACAT
Found at i:48887 original size:164 final size:164
Alignment explanation
Indices: 48485--49456 Score: 1004
Period size: 164 Copynumber: 5.9 Consensus size: 164
48475 TAAAAGACAA
* * * *
48485 CATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACA
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* * *
48550 CTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAG
66 CTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCAAGAAGGGCTATCTGCC--C-AAAG
* *
48615 ACCTTTGAGTTCGACTACGCTCAACTCCAAGGCATAT
128 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
* * * * *
48652 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACTAAAGA-CTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTAC
* * *
48716 GCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCAATAAGGGCTATCTG-CCAAAGAC
65 GCTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCAAGAAGGGCTATCTGCCCAAAGAC
* * * * * *
48780 CCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
130 CTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATAT
* * * * * * *
48816 CATTTACAGTATAACTCAAGGCTATAAGGGTTATCTGTCACCAAATACCTTCGAGTTCAACTACG
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* * * * ** *
48881 CTCAGCTCCAAGGCATATCATTTGCAATATAACTTGAGTTGAGAAGGGTTATCTGCCAACAAAGA
66 CTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCAAGAAGGGCTATCTGCC--CAAAGA
* * * *
48946 CCTTCAAGTTCAACTACGCTCAGCTCCAAGACACAT
129 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
* * * * * * *
48982 CATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTG---CCAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* * * * * * * * * *
49044 CTCAGCTTCGAGAGCACACCATTTACAATATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAA
66 CTCAGCTCCAAG-GCACATCATTTGCAACATAGCTTAAGTCAAGAAGGGCTATCTG-C-CC-AAA
49109 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
127 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
* * * * * * *
49147 CATTTGCAGCATAACTTAAGTCGAGAATGGTTATCTGCCAACCAAATACTTTTGAGTTCGACTAT
1 CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTAC
* * * *
49212 GCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCAAGAAGGGTTATCTG-CTAAAGAC
65 GCTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCAAGAAGGGCTATCTGCCCAAAGAC
* * * * * *
49276 CCTCGAGTTCGATTACACTCAACTTCGAGTGCATAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAG-GCATAT
* * *
49312 CATTTACAGCATAACTCAAGGATGA-AAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGG-CGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTAC
* * *
49376 GCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAA
65 GCTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCAAGAAGGGCTATCTG-C--CCAAA
49441 GACCTTTCGAGTTCGA
127 GACC-TTCGAGTTCGA
49457 TTTCATTCAG
Statistics
Matches: 660, Mismatches: 124, Indels: 40
0.80 0.15 0.05
Matches are distributed among these distances:
163 60 0.09
164 239 0.36
165 110 0.17
166 42 0.06
167 123 0.19
168 48 0.07
169 38 0.06
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (164 bp):
CATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCAAGAAGGGCTATCTGCCCAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
Found at i:48964 original size:247 final size:248
Alignment explanation
Indices: 48508--49456 Score: 1339
Period size: 247 Copynumber: 3.8 Consensus size: 248
48498 ACTCAAGGCT
* * * * *
48508 AGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATT
1 AGAAGGGATATCTG-C--CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
* * * * * * * *
48572 TGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACTACGCTC
63 TACAACATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTC
* * *
48637 AACTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACTAAAGA-C
127 AGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
*
48701 TTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCA
192 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCA
* *
48758 ATAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
1 AGAAGGGATATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
** * * *
48823 AGTATAACTCAAGGCTATAAGGGTTATCTGTCACCAAATACCTTCGAGTTCAACTACGCTCAGCT
66 AACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
** * * *
48888 CCAAGGCATATCATTTGCAATATAACTTGAGTTGAGAAGGGTTATCTGCCAA-CAAAGACCTTCA
131 CCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCG
* * * *
48952 AGTTCAACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCG
196 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCA
* *
49005 AGAAGGGATATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGAGCACACCATTTAC
1 AGAAGGGATATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
*
49070 AATATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGC
66 AACATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGC
* * * *
49135 TCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAATGGTTATCTGCCAACCAAATACTTTT
130 TCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTC
*
49200 GAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCA
195 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCA
* * * * *
49254 AGAAGGGTTATCTGCTAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGTGCATATCATTTAC
1 AGAAGGGATATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
* *
49319 AGCATAACTCAAGGAT-GAAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
66 AACATAACTCAAGGCTAG-AAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* * * *
49383 TCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTT
130 TCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC-TT
49448 CGAGTTCGA
194 CGAGTTCGA
49457 TTTCATTCAG
Statistics
Matches: 622, Mismatches: 71, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
246 5 0.01
247 249 0.40
248 200 0.32
249 156 0.25
250 12 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (248 bp):
AGAAGGGATATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
AACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
CCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCG
AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCA
Found at i:60563 original size:37 final size:38
Alignment explanation
Indices: 60493--60579 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 38
60483 TTATTAAATT
* *
60493 TTTTATATTTTCAATTTTATAAAACAAATTATATAA-A
1 TTTTATAATTTAAATTTTATAAAACAAATTATATAATA
*
60530 TTTTATGAATTTAAATTTTTTAAAGA-AAA-TATATAATA
1 TTTTAT-AATTTAAATTTTATAAA-ACAAATTATATAATA
*
60568 TTTTCTAATTTA
1 TTTTATAATTTA
60580 TTAAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
37 19 0.44
38 23 0.53
39 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (38 bp):
TTTTATAATTTAAATTTTATAAAACAAATTATATAATA
Found at i:64364 original size:41 final size:41
Alignment explanation
Indices: 64276--64432 Score: 118
Period size: 42 Copynumber: 3.8 Consensus size: 41
64266 AATTGATACT
* * * *
64276 TTAGCGGCGTTTTTAGTAAAAACGCTGCAATAGAGTTGACA
1 TTAGCGGCGTTTTTAGCAAAAACGCCGCAATAGAGTGGAAA
* *
64317 TATAGCGGCGTTTTTA-CAAAAATGCCGCAATAGGGTGGCAAA
1 T-TAGCGGCGTTTTTAGCAAAAACGCCGCAATAGAGTGG-AAA
* * * * * * ***
64359 TTAGCGGCGTTTATACCACAAACGCCACAATAAAATAGTTCA
1 TTAGCGGCGTTTTTAGCAAAAACGCCGCAATAGAGT-GGAAA
* **
64401 TTTGCGGCGTTTTTATTAAAAACGCCGCAATA
1 TTAGCGGCGTTTTTAGCAAAAACGCCGCAATA
64433 TTCTGATATA
Statistics
Matches: 90, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
41 31 0.34
42 58 0.64
43 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (41 bp):
TTAGCGGCGTTTTTAGCAAAAACGCCGCAATAGAGTGGAAA
Found at i:66357 original size:28 final size:28
Alignment explanation
Indices: 66326--66379 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
66316 TTATGAGTGC
66326 ATATAATAT-TTGTCATGGAAGTTTATCA
1 ATAT-ATATCTTGTCATGGAAGTTTATCA
* *
66354 ATATTTCTCTTGTCATGGAAGTTTAT
1 ATATATATCTTGTCATGGAAGTTTAT
66380 ATTTTCTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (28 bp):
ATATATATCTTGTCATGGAAGTTTATCA
Found at i:72824 original size:21 final size:21
Alignment explanation
Indices: 72806--72891 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
72796 ATGAAGCAAA
*
72806 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
72827 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
72848 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
72869 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
72890 GG
1 GG
72892 CAGAACAGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 1 0.02
21 55 0.98
ACGTcount: A:0.37, C:0.20, G:0.42, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:72892 original size:21 final size:21
Alignment explanation
Indices: 72814--72902 Score: 90
Period size: 21 Copynumber: 4.2 Consensus size: 21
72804 AAGGAAACAG
* *
72814 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * * *
72836 -TAGAGCAGCAGCGGAAGCAG
1 AGAGAGAAGCAGCGGCAGCAC
72856 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
* *
72877 AGAGAGAGGCAGCGGCAGAAC
1 AGAGAGAAGCAGCGGCAGCAC
72898 AGAGA
1 AGAGA
72903 TAAGTAATGT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.38, C:0.20, G:0.40, T:0.01
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:73444 original size:43 final size:42
Alignment explanation
Indices: 73242--73510 Score: 143
Period size: 43 Copynumber: 6.2 Consensus size: 42
73232 CATACATTTA
* * * * *
73242 GCGGCGTTTTTAATAAAAACGCCGCAAAATCTCAATACATATTCT
1 GCGGCG-TTTTAATGAAAACGCCGCTAAATATCAAAACCTA-T-T
* * * * * ** *
73287 GCGGCGTTTTTAGGAAAACGCCGGTAAAAATAAAAATTTACT
1 GCGGCGTTTTAATGAAAACGCCGCTAAATATCAAAACCTATT
* *
73329 GCGGCGTTTTGGAA-GAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTT--AATGAAAACGCCGCTAAATATCAA-AACCTATT
* * * *
73372 GCGGCGTTTGT-CTGCCAAATGCCGTTAAATATCAAAACCTATT
1 GCGGCGTTT-TAATG-AAAACGCCGCTAAATATCAAAACCTATT
* * *
73415 GCGGCGTTTTAATGATAAACGCCGCTAAATATCAATACATTTT
1 GCGGCGTTTTAATGA-AAACGCCGCTAAATATCAAAACCTATT
* * * ***
73458 GCTGCGTTTGT--TGAACAATCGCCGCTATATGTTGTAACCTATT
1 GCGGCGTTT-TAATGAA-AA-CGCCGCTAAATATCAAAACCTATT
73501 GCGGCGTTTT
1 GCGGCGTTTT
73511 TTTTGTTGAA
Statistics
Matches: 170, Mismatches: 42, Indels: 27
0.71 0.18 0.11
Matches are distributed among these distances:
41 1 0.01
42 20 0.12
43 116 0.68
44 27 0.16
45 6 0.04
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (42 bp):
GCGGCGTTTTAATGAAAACGCCGCTAAATATCAAAACCTATT
Found at i:73576 original size:13 final size:13
Alignment explanation
Indices: 73534--73575 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
73524 CGCCGCAAAC
73534 TTTAGCGGCGCTATT
1 TTTAGCGGCG--ATT
73549 TTTAGCGGCGA-T
1 TTTAGCGGCGATT
73561 TTTAGCGGC-ATT
1 TTTAGCGGCGATT
73573 TTT
1 TTT
73576 TTTTACGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.04
12 14 0.54
13 1 0.04
15 10 0.38
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43
Consensus pattern (13 bp):
TTTAGCGGCGATT
Found at i:74306 original size:35 final size:36
Alignment explanation
Indices: 74264--74338 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 36
74254 AAGGAAAATA
*
74264 TTGTCATC-TTGTATAAA-TTGGATATGTTGTCATAT
1 TTGTCATCTTTGTATAAATTTAGATATGTTGTCAT-T
* *
74299 TTGTCATCTTTTTATAAATTTAGATGTGTTGTCATT
1 TTGTCATCTTTGTATAAATTTAGATATGTTGTCATT
74335 TTGT
1 TTGT
74339 AAACTTTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 8 0.23
36 13 0.37
37 14 0.40
ACGTcount: A:0.23, C:0.08, G:0.16, T:0.53
Consensus pattern (36 bp):
TTGTCATCTTTGTATAAATTTAGATATGTTGTCATT
Found at i:74548 original size:12 final size:11
Alignment explanation
Indices: 74530--74694 Score: 51
Period size: 11 Copynumber: 13.9 Consensus size: 11
74520 GTAGGTTCAA
*
74530 ATTCGAGTTTG
1 ATTCGAGCTTG
74541 AGTTCGAGCTTG
1 A-TTCGAGCTTG
* *
74553 ATTCGAACTTAA
1 ATTCGAGCTT-G
* *
74565 AATCGAGCTTC
1 ATTCGAGCTTG
* *
74576 AATCGAGCTCG
1 ATTCGAGCTTG
*
74587 AGTCTCGAGCTTC
1 A-T-TCGAGCTTG
* *
74600 AATCGAGCTCG
1 ATTCGAGCTTG
*
74611 AGTCTCGAGCTTC
1 A-T-TCGAGCTTG
* *
74624 AATCGAGCTCG
1 ATTCGAGCTTG
*
74635 AGTCTCGAGCTTC
1 A-T-TCGAGCTTG
* *
74648 AATCGAGCTCG
1 ATTCGAGCTTG
*
74659 AGTCTCGAGCTTC
1 A-T-TCGAGCTTG
* *
74672 AATCGAGCTCG
1 ATTCGAGCTTG
74683 AGTCTCGAGCTT
1 A-T-TCGAGCTT
74695 CAATCGAGTT
Statistics
Matches: 108, Mismatches: 34, Indels: 22
0.66 0.21 0.13
Matches are distributed among these distances:
11 51 0.47
12 18 0.17
13 39 0.36
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.28
Consensus pattern (11 bp):
ATTCGAGCTTG
Found at i:74597 original size:24 final size:24
Alignment explanation
Indices: 74567--74702 Score: 272
Period size: 24 Copynumber: 5.7 Consensus size: 24
74557 GAACTTAAAA
74567 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
74591 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
74615 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
74639 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
74663 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
74687 TCGAGCTTCAATCGAG
1 TCGAGCTTCAATCGAG
74703 TTCCTGAAAT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 112 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (24 bp):
TCGAGCTTCAATCGAGCTCGAGTC
Found at i:91167 original size:22 final size:22
Alignment explanation
Indices: 91142--91216 Score: 141
Period size: 22 Copynumber: 3.4 Consensus size: 22
91132 TCATTTCTTT
91142 AGGCCTTGTTGAATAAATGTTC
1 AGGCCTTGTTGAATAAATGTTC
91164 AGGCCTTGTTGAATAAATGTTC
1 AGGCCTTGTTGAATAAATGTTC
91186 AGGCCTTGTTGAATAAATGTTC
1 AGGCCTTGTTGAATAAATGTTC
91208 AGGCGCTTG
1 AGGC-CTTG
91217 AGGTGAAAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 48 0.92
23 4 0.08
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (22 bp):
AGGCCTTGTTGAATAAATGTTC
Done.