Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002770.1 Hibiscus syriacus cultivar Beakdansim tig00005709_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: 72722
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:18953 original size:19 final size:18
Alignment explanation
Indices: 18889--18959 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
18879 ACAAAATGAA
18889 ATATATAAATAATAAATATAT
1 ATATATAAA-AAT-AATA-AT
** *
18910 ATATATAATTATAGTAAT
1 ATATATAAAAATAATAAT
*
18928 AAAATATAAAAATAATAAT
1 -ATATATAAAAATAATAAT
18947 GATATATGAAAAA
1 -ATATAT-AAAAA
18960 GAATTAAAAG
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
18 2 0.05
19 22 0.56
20 7 0.18
21 8 0.21
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (18 bp):
ATATATAAAAATAATAAT
Found at i:26771 original size:17 final size:17
Alignment explanation
Indices: 26722--26776 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
26712 ATTTAATCAT
*
26722 TAATTATTATT-TTAAGA
1 TAATTA-TATTATTAGGA
*
26739 CTAATTATATTATTAGTA
1 -TAATTATATTATTAGGA
26757 TAATTATA-TATTTAGGA
1 TAATTATATTA-TTAGGA
26774 TAA
1 TAA
26777 CTTTATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.06
17 20 0.62
18 10 0.31
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (17 bp):
TAATTATATTATTAGGA
Found at i:29085 original size:6 final size:6
Alignment explanation
Indices: 29074--29119 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
29064 TTCATACTTG
* *
29074 CATTTA CATTTA CATTTA CATTTA CATTTA CATTTA TATTTG CATT
1 CATTTA CATTTA CATTTA CATTTA CATTTA CATTTA CATTTA CATT
29120 CTCGCTTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.30, C:0.15, G:0.02, T:0.52
Consensus pattern (6 bp):
CATTTA
Found at i:31448 original size:85 final size:85
Alignment explanation
Indices: 31232--31553 Score: 441
Period size: 85 Copynumber: 3.8 Consensus size: 85
31222 GTATTTTTAA
* * * * * * *
31232 ATGACGTGTGCTTCAACGACACGCAATGTAAGTCATATATGCGTGACATAAATTTATGACACAAA
1 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
* *
31297 AATGTATGTCAAAC--AGATTT
66 AATGTGTGTC-ATCTTA-ATTT
* *
31317 ATGATGGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCAC
1 ATGA-CGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACAC
31382 AAATGTGTGTCATCTTAATTT
65 AAATGTGTGTCATCTTAATTT
* *
31403 ATGACGGGGGCTTTAATGACGCGCAATGTAAGTCATACACGCGTGTCATAAATTTATGACACACA
1 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
*
31468 AATGTGTGTCATATTAATTT
66 AATGTGTGTCATCTTAATTT
* * * *
31488 ATGACGGAGGCTTCAATGACGCGTAATGTAAGTCATACATGCGCGTCATAGATTTATGACACACA
1 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
31553 A
66 A
31554 TTGCACGTCA
Statistics
Matches: 212, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
85 142 0.67
86 69 0.33
87 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (85 bp):
ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
AATGTGTGTCATCTTAATTT
Found at i:32883 original size:2 final size:2
Alignment explanation
Indices: 32876--32907 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32866 TTATTAATTA
32876 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
32908 GCGACAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36076 original size:18 final size:17
Alignment explanation
Indices: 36048--36082 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
36038 TTAAGACTAC
*
36048 TTATAATATTAGTATAA
1 TTATAATATTAGGATAA
36065 TTATATATATTAGGATAA
1 TTATA-ATATTAGGATAA
36083 CTTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (17 bp):
TTATAATATTAGGATAA
Found at i:37770 original size:44 final size:44
Alignment explanation
Indices: 37707--37798 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
37697 AAAATTCTTT
*
37707 TATGGGTACATTGTACCGATGTTGTTCTTACAGTATCGATACTG
1 TATGGGTACATTATACCGATGTTGTTCTTACAGTATCGATACTG
37751 TATGGGTACATTATACCGATGTTGTTCTTACAGTATCGATACTG
1 TATGGGTACATTATACCGATGTTGTTCTTACAGTATCGATACTG
37795 TATG
1 TATG
37799 AAAAAGTACC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (44 bp):
TATGGGTACATTATACCGATGTTGTTCTTACAGTATCGATACTG
Found at i:37782 original size:22 final size:22
Alignment explanation
Indices: 37713--37782 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
37703 CTTTTATGGG
*
37713 TACATTGTACCGATGTTGTTCT
1 TACATTATACCGATGTTGTTCT
* ** **
37735 TACAGTAT--CGATACTGTATGGG
1 TACATTATACCGATGTTGT-T-CT
37757 TACATTATACCGATGTTGTTCT
1 TACATTATACCGATGTTGTTCT
37779 TACA
1 TACA
37783 GTATCGATAC
Statistics
Matches: 33, Mismatches: 11, Indels: 8
0.63 0.21 0.15
Matches are distributed among these distances:
20 7 0.21
21 1 0.03
22 17 0.52
23 1 0.03
24 7 0.21
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (22 bp):
TACATTATACCGATGTTGTTCT
Found at i:38308 original size:27 final size:27
Alignment explanation
Indices: 38278--38331 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
38268 TTCTCTTGTA
38278 AATATTAGTGTTTAGTGAGACCAATCT
1 AATATTAGTGTTTAGTGAGACCAATCT
*
38305 AATATTAGTGTTTAGTGAGCCCAATCT
1 AATATTAGTGTTTAGTGAGACCAATCT
38332 TTGTAAACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (27 bp):
AATATTAGTGTTTAGTGAGACCAATCT
Found at i:41960 original size:22 final size:22
Alignment explanation
Indices: 41935--41976 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41925 CGAATGACCT
*
41935 AAATTAAAAAACCCTAAATTTA
1 AAATCAAAAAACCCTAAATTTA
**
41957 AAATCATTAAACCCTAAATT
1 AAATCAAAAAACCCTAAATT
41977 ATTCTTCTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATCAAAAAACCCTAAATTTA
Found at i:44833 original size:12 final size:13
Alignment explanation
Indices: 44796--44840 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
44786 GTAATCCCCA
44796 CCCCGATTACCCG
1 CCCCGATTACCCG
44809 CCCCGATTACCCG
1 CCCCGATTACCCG
*
44822 CCTCGA-TACCCG
1 CCCCGATTACCCG
*
44834 ACCCGAT
1 CCCCGAT
44841 AAATATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.18, C:0.51, G:0.16, T:0.16
Consensus pattern (13 bp):
CCCCGATTACCCG
Found at i:44914 original size:19 final size:19
Alignment explanation
Indices: 44863--44929 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
44853 TAATTATTTT
* *
44863 TATATATATATAATATTAA
1 TATATATATTTAATATAAA
*
44882 TA-AAATTAATTTAA-ATAAA
1 TATATA-T-ATTTAATATAAA
*
44901 CTATATATATTTAATTTAAA
1 -TATATATATTTAATATAAA
44921 TATATATAT
1 TATATATAT
44930 ATATACCCGG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
18 2 0.05
19 22 0.58
20 12 0.32
21 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATATATTTAATATAAA
Found at i:47289 original size:17 final size:18
Alignment explanation
Indices: 47258--47295 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
47248 AGCATCTTTT
47258 AAAACAATTTTAAGA-AA
1 AAAACAATTTTAAGACAA
47275 AAAAC-ATTTTAAAGACAA
1 AAAACAATTTT-AAGACAA
47293 AAA
1 AAA
47296 TAAGTCAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 9 0.47
18 5 0.26
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAACAATTTTAAGACAA
Found at i:49647 original size:11 final size:11
Alignment explanation
Indices: 49631--49660 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
49621 TATAAATTAA
49631 GGAAATTTTAG
1 GGAAATTTTAG
49642 GGAAATTTTAG
1 GGAAATTTTAG
49653 GGAAATTT
1 GGAAATTT
49661 GCTCTTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (11 bp):
GGAAATTTTAG
Found at i:55879 original size:36 final size:35
Alignment explanation
Indices: 55833--55961 Score: 107
Period size: 36 Copynumber: 3.5 Consensus size: 35
55823 ACAAAAATTT
55833 ATCTCACTTGAGATTGTCTTTCTTAAAACAAGATTC
1 ATCTCACTTGAGATTGT-TTTCTTAAAACAAGATTC
* * * * *
55869 ATCTCGCTTGAGATAGTTTCACTTGAAATAGAA-ATCTT
1 ATCTCACTTGAGATTGTTT-TCTT-AAA-ACAAGAT-TC
* *
55907 ATCTCACTTCAAATTGTTTTTCTTAAAACAAGATTC
1 ATCTCACTTGAGATTG-TTTTCTTAAAACAAGATTC
** *
55943 ATCTTGCTTGAGATAGTTT
1 ATCTCACTTGAGATTGTTT
55962 CACTCGAAGA
Statistics
Matches: 70, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
35 5 0.07
36 33 0.47
37 10 0.14
38 19 0.27
39 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (35 bp):
ATCTCACTTGAGATTGTTTTCTTAAAACAAGATTC
Found at i:55929 original size:74 final size:74
Alignment explanation
Indices: 55796--55965 Score: 236
Period size: 74 Copynumber: 2.3 Consensus size: 74
55786 AACAAAAATT
* * * * *
55796 ATCTCGCTTGAGACAGTCTCA-TTTAATACAAAAATTTATCTCACTTGAGATTGTCTTTCTTAAA
1 ATCTCGCTTGAGATAGTTTCACTTGAATACAAAAATTTATCTCACTTCAAATTGTCTTTCTTAAA
55860 ACAAGATTC
66 ACAAGATTC
* * *
55869 ATCTCGCTTGAGATAGTTTCACTTGAA-ATAGAAATCTTATCTCACTTCAAATTGTTTTTCTTAA
1 ATCTCGCTTGAGATAGTTTCACTTGAATACAAAAAT-TTATCTCACTTCAAATTGTCTTTCTTAA
55933 AACAAGATTC
65 AACAAGATTC
*
55943 ATCTTGCTTGAGATAGTTTCACT
1 ATCTCGCTTGAGATAGTTTCACT
55966 CGAAGAATTT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
73 25 0.29
74 61 0.71
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (74 bp):
ATCTCGCTTGAGATAGTTTCACTTGAATACAAAAATTTATCTCACTTCAAATTGTCTTTCTTAAA
ACAAGATTC
Found at i:56019 original size:38 final size:38
Alignment explanation
Indices: 55869--56172 Score: 141
Period size: 38 Copynumber: 8.1 Consensus size: 38
55859 AACAAGATTC
* *
55869 ATCTCGCTTGAGATAGTTTCACTTG-AAATAGAAATCTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAAAT-GAAATTTT
* * * * ** * * *
55907 ATCTCACTTCAAATTGTTTTTCT-TAAAA-CAAGA-TTC
1 ATCTCGCTTGAGATAGTTTCACTCGAAAATGAA-ATTTT
* ***
55943 ATCTTGCTTGAGATAGTTTCACTCGAAGAAT-TTTTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAA-AATGAAATTTT
55981 ATCTCGCTTGAGATAGTTTCACTCGAAAATGAAATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAAATGAAATTTT
* * * ** * * *
56019 ATATCACTTAAGATTA-TTTTTCT-TAAAA-CAAA-TTC
1 ATCTCGCTTGAGA-TAGTTTCACTCGAAAATGAAATTTT
56054 ATCTCGCTTGAGATAGTTTCACTC-AAACCAT-AAATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAA--ATGAAATTTT
* * * *
56092 ATCTCACTTGAGATTGTTTTC-CT-TAAAA-AAAATTATT
1 ATCTCGCTTGAGATAG-TTTCACTCGAAAATGAAATT-TT
* * * * *
56129 TTCTTGCTTAATATAGTTTCACTCGAAACAAGAAATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAA-ATGAAATTTT
56168 ATCTC
1 ATCTC
56173 ACTCCAGATT
Statistics
Matches: 192, Mismatches: 52, Indels: 43
0.67 0.18 0.15
Matches are distributed among these distances:
34 2 0.01
35 20 0.10
36 32 0.17
37 28 0.15
38 93 0.48
39 12 0.06
40 5 0.03
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (38 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAAATGAAATTTT
Found at i:56279 original size:75 final size:73
Alignment explanation
Indices: 55978--56375 Score: 376
Period size: 76 Copynumber: 5.3 Consensus size: 73
55968 AAGAATTTTT
* *
55978 TTTATCTCGCTTGAGATAGTTTCACTCGAAA-ATGAAATTTTATATCACTTAAGATTATTTTTCT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAT--AATTTTATCTCACTTAAGATTGTTTTTCT
56042 TAAAACAAA-
64 TAAAACAAAC
* * *
56051 TTCATCTCGCTTGAGATAGTTTCACTC-AAACCATAAATTTTATCTCACTTGAGATTGTTTTCCT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAA-CAT-AATTTTATCTCACTTAAGATTGTTTTTCT
* *
56115 TAAAAAAAAT
64 TAAAACAAAC
* * * * * ** *
56125 TATTTTCTTGCTTAATATAGTTTCACTCGAAACAAGAAATTTTATCTCACTCCAGATTTTTTTCT
1 T-TTATCTCGCTTGAGATAGTTTCACTCGAAAC-A-TAATTTTATCTCACTTAAGATTGTTTT-T
56190 CTTAAAACAAAC
62 CTTAAAACAAAC
* *
56202 TTTATC-CTGCTTGAGACAGCTTTCACTCGAAACATAATTTTGATCTCACTTGAGATTGTTTTTC
1 TTTATCTC-GCTTGAGATAG-TTTCACTCGAAACATAATTTT-ATCTCACTTAAGATTGTTTTTC
*
56266 TTAAAACAGAC
63 TTAAAACAAAC
* * * * * * *
56277 TTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAATTTCATTTCACTTAAGATTGATTTTC
1 TTTATCTCGCTTGAGATAG-TTTCACTCGAAAC-A-TAATTTTATCTCACTTAAGATTGTTTTTC
56342 TTAAAGA-AAA-
63 TTAAA-ACAAAC
*
56352 TTTCATCTCGCTTGAGAAAGTTTC
1 TTT-ATCTCGCTTGAGATAGTTTC
56376 CCATGAAATA
Statistics
Matches: 269, Mismatches: 40, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
72 3 0.01
73 60 0.22
74 3 0.01
75 74 0.28
76 99 0.37
77 30 0.11
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (73 bp):
TTTATCTCGCTTGAGATAGTTTCACTCGAAACATAATTTTATCTCACTTAAGATTGTTTTTCTTA
AAACAAAC
Found at i:56305 original size:152 final size:149
Alignment explanation
Indices: 55982--56375 Score: 460
Period size: 152 Copynumber: 2.6 Consensus size: 149
55972 ATTTTTTTTA
* *
55982 TCTCGCTTGAGATAGTTTCACTCGAAA-ATGAAATTTTATATCACTTAAGATTATTTTTCTTAAA
1 TCTCGCTTGAGATAGTTTCACTCGAAACAAGAAATTTTATATCACTCAAGATTATTTTTCTTAAA
*
56046 ACAAATTCATCTCGCTTGAGATAGTTTCACTCAAACCATAAATTTTATCTCACTTGAGATTGTTT
66 ACAAATTCATCTCGCTTGAGACAGTTTCACTCAAACCATAAATTTTATCTCACTTGAGATTGTTT
* *
56111 TCCTTAAAAAAAATTATTT
131 TCCTTAAAAAAAACTATTG
* * * * * *
56130 TCTTGCTTAATATAGTTTCACTCGAAACAAGAAATTTTATCTCACTCCAGATTTTTTTCTCTTAA
1 TCTCGCTTGAGATAGTTTCACTCGAAACAAGAAATTTTATATCACTCAAGATTATTTT-TCTTAA
*
56195 AACAAACTTTATC-CTGCTTGAGACAGCTTTCACTCGAAA-CAT-AATTTTGATCTCACTTGAGA
65 AACAAA-TTCATCTC-GCTTGAGACAG-TTTCACTC-AAACCATAAATTTT-ATCTCACTTGAGA
* * *
56257 TTGTTTTTCTTAAAACAGACT-TTG
125 TTGTTTTCCTTAAAAAAAACTATTG
* * * * *
56281 TCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAATTTCATTTCACTTAAGATTGA-TTTTCTTA
1 TCTCGCTTGAGATAG-TTTCACTCGAAACAAGAAATTTTATATCACTCAAGATT-ATTTTTCTTA
*
56345 AAGA-AAATTTCATCTCGCTTGAGAAAGTTTC
64 AA-ACAAA-TTCATCTCGCTTGAGACAGTTTC
56376 CCATGAAATA
Statistics
Matches: 207, Mismatches: 28, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
148 24 0.12
149 25 0.12
150 17 0.08
151 59 0.29
152 79 0.38
153 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (149 bp):
TCTCGCTTGAGATAGTTTCACTCGAAACAAGAAATTTTATATCACTCAAGATTATTTTTCTTAAA
ACAAATTCATCTCGCTTGAGACAGTTTCACTCAAACCATAAATTTTATCTCACTTGAGATTGTTT
TCCTTAAAAAAAACTATTG
Found at i:59803 original size:15 final size:14
Alignment explanation
Indices: 59780--59848 Score: 61
Period size: 14 Copynumber: 4.8 Consensus size: 14
59770 ATAAATAACA
*
59780 TAAAATGAAAGGAC
1 TAAAATTAAAGGAC
*
59794 TAAAATTGAAAGGAA
1 TAAAATT-AAAGGAC
59809 TGAAAATTAAA-GAC
1 T-AAAATTAAAGGAC
59823 -ATAAATTAAAGGAC
1 TA-AAATTAAAGGAC
*
59837 TGAAATATAAAG
1 TAAAAT-TAAAG
59849 TTCATAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
12 1 0.02
13 8 0.18
14 15 0.33
15 15 0.33
16 6 0.13
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.20
Consensus pattern (14 bp):
TAAAATTAAAGGAC
Found at i:59816 original size:16 final size:15
Alignment explanation
Indices: 59779--59820 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
59769 AATAAATAAC
59779 ATAAAA-TGAAAGGA
1 ATAAAATTGAAAGGA
*
59793 CTAAAATTGAAAGGA
1 ATAAAATTGAAAGGA
59808 ATGAAAATT-AAAG
1 AT-AAAATTGAAAG
59821 ACATAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 13 0.54
16 6 0.25
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (15 bp):
ATAAAATTGAAAGGA
Found at i:59847 original size:28 final size:29
Alignment explanation
Indices: 59796--59875 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 29
59786 GAAAGGACTA
*
59796 AAATTGAAAGGAATGAAA-ATTAAAG-ACAT
1 AAATT-AAAGGACTGAAATA-TAAAGTACAT
*
59825 AAATTAAAGGACTGAAATATAAAGTTCAT
1 AAATTAAAGGACTGAAATATAAAGTACAT
* *
59854 AAAATAAA-GACTGAAATGTAAA
1 AAATTAAAGGACTGAAATATAAA
59876 TAAAATAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
28 29 0.64
29 16 0.36
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (29 bp):
AAATTAAAGGACTGAAATATAAAGTACAT
Found at i:63325 original size:28 final size:27
Alignment explanation
Indices: 63285--63342 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 27
63275 CCAGATTCGC
*
63285 AACGCGAACTTCGACTATCGCATTGCGA
1 AACGCGAACTTCGACTATCGCAATGC-A
63313 AACGCGAACTTCGACTATCGCAATGCA
1 AACGCGAACTTCGACTATCGCAATGCA
63340 AAC
1 AAC
63343 TTGGACTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (27 bp):
AACGCGAACTTCGACTATCGCAATGCA
Found at i:63349 original size:21 final size:21
Alignment explanation
Indices: 63319--63359 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
63309 GCGAAACGCG
63319 AACTTCGACTATCGCAATGCA
1 AACTTCGACTATCGCAATGCA
* *
63340 AACTTGGACTATTGCAATGC
1 AACTTCGACTATCGCAATGC
63360 GAATATGTAA
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:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (21 bp):
AACTTCGACTATCGCAATGCA
Found at i:63440 original size:90 final size:90
Alignment explanation
Indices: 63322--63507 Score: 218
Period size: 90 Copynumber: 2.0 Consensus size: 90
63312 AAACGCGAAC
* *
63322 TTCGACTATCGCAATGCAAACTTGGACTATTGCAATGCGA-ATATGT-AAA-TCGCAATGCGATA
1 TTCGACTATCGCAACGCAAACTTGGACTATCGC-ATGCGATATAT-TAAAATTCG--ATGCGATA
63384 GTCGAAGTTCGCGTTGCGA-TTTTCCAAA
62 GTCGAAGTTCGCGTTGCGATTTTTCCAAA
** * * * *
63412 TTCGACTATCGCAACGGGAACTTTGACTATCGCTTGCGATTTATTCAAAATTCGTTGCGATAGTC
1 TTCGACTATCGCAACGCAAACTTGGACTATCGCATGCGATATATT-AAAATTCGATGCGATAGTC
63477 GAAGTTCGCGTTGCGATTTTTTCCAAA
65 GAAGTTCGCGTTGCGA-TTTTTCCAAA
63504 TTCG
1 TTCG
63508 TTGCGATAGT
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
89 6 0.07
90 57 0.70
91 3 0.04
92 16 0.20
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (90 bp):
TTCGACTATCGCAACGCAAACTTGGACTATCGCATGCGATATATTAAAATTCGATGCGATAGTCG
AAGTTCGCGTTGCGATTTTTCCAAA
Found at i:63471 original size:21 final size:21
Alignment explanation
Indices: 63445--63514 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
63435 TGACTATCGC
63445 TTGCGATTTATTCAAAATTCG
1 TTGCGATTTATTCAAAATTCG
* * *
63466 TTGCGA--TAGTCGAAGTTCGCG
1 TTGCGATTTATTCAAAATT--CG
* *
63487 TTGCGATTTTTTCCAAATTCG
1 TTGCGATTTATTCAAAATTCG
63508 TTGCGAT
1 TTGCGAT
63515 AGTCCAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 8 0.21
21 23 0.61
23 7 0.18
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (21 bp):
TTGCGATTTATTCAAAATTCG
Found at i:63522 original size:19 final size:19
Alignment explanation
Indices: 63459--63522 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 19
63449 GATTTATTCA
*
63459 AAATTCGTTGCGATAGTCG
1 AAATTCGTTGCGATAGTCC
* **
63478 AAGTTCGCGTTGCGATTTTTTCC
1 AAATT--CGTTGCGA--TAGTCC
63501 AAATTCGTTGCGATAGTCC
1 AAATTCGTTGCGATAGTCC
63520 AAA
1 AAA
63523 ATCGCAACGA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 11 0.32
21 16 0.47
23 7 0.21
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (19 bp):
AAATTCGTTGCGATAGTCC
Found at i:63643 original size:5 final size:5
Alignment explanation
Indices: 63616--63665 Score: 73
Period size: 5 Copynumber: 9.4 Consensus size: 5
63606 GTATTACAAG
63616 GACCAC GACCAC GACCAC GACCC GACCC GACCC GACCC GACCC GACCC
1 GACC-C GACC-C GACC-C GACCC GACCC GACCC GACCC GACCC GACCC
63664 GA
1 GA
63666 GACGAGACGA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 28 0.64
6 16 0.36
ACGTcount: A:0.26, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:64235 original size:6 final size:5
Alignment explanation
Indices: 64167--64231 Score: 85
Period size: 5 Copynumber: 12.0 Consensus size: 5
64157 TCTCGTCTCA
64167 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG TGGTCG TGGTCG TGGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG -GGTCG -GGTCG -GGTCG
64220 TGGTCG TGGTCG
1 -GGTCG -GGTCG
64232 TGGTAATACG
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 30 0.51
6 29 0.49
ACGTcount: A:0.00, C:0.18, G:0.55, T:0.26
Consensus pattern (5 bp):
GGTCG
Found at i:64333 original size:21 final size:21
Alignment explanation
Indices: 64309--64380 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
64299 ATGCAATACT
64309 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
64330 ATCGCAACACGAACTTCGACT--
1 ATCGC-A-ACGAATTTGGAATAA
64351 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
64372 ATCGCAACG
1 ATCGCAACG
64381 CGAACTTCGA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 10 0.24
20 1 0.02
21 19 0.46
22 1 0.02
23 10 0.24
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:64365 original size:42 final size:42
Alignment explanation
Indices: 64306--64399 Score: 179
Period size: 42 Copynumber: 2.2 Consensus size: 42
64296 CAAATGCAAT
64306 ACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTCG
1 ACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTCG
*
64348 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTCG
64390 ACTATCGCAA
1 ACTATCGCAA
64400 TGCGAATATG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (42 bp):
ACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTCG
Found at i:64396 original size:21 final size:21
Alignment explanation
Indices: 64330--64405 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
64320 TTTGGAATAA
*
64330 ATCGCAACACGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * *
64351 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
64370 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
*
64393 ATCGCAATGCGAA
1 ATCGCAACGCGAA
64406 TATGTAAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 9 0.20
21 26 0.59
23 9 0.20
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:64478 original size:90 final size:92
Alignment explanation
Indices: 64358--64543 Score: 256
Period size: 90 Copynumber: 2.0 Consensus size: 92
64348 ACTATCGCAA
64358 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTA-A-A-TCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCG-AT-T-TACATATTCGCAA
* **
64420 TGCGATAGTCGAAGTTCGTGTTGCGATAGT
63 TGCGATAGTCCAAGTTCGCATTGCGATAGT
* *
64450 CGAATTTGG-A-AAATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGC
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGATTTACATATTCGCAATGC
*
64513 GATAGTCCAAGTTCGCATTGCGATATT
66 GATAGTCCAAGTTCGCATTGCGATAGT
64540 CGAA
1 CGAA
64544 GTTCGCGTTA
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
87 2 0.02
88 2 0.02
89 3 0.04
90 68 0.80
91 1 0.01
92 9 0.11
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (92 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGATTTACATATTCGCAATGC
GATAGTCCAAGTTCGCATTGCGATAGT
Found at i:64529 original size:21 final size:21
Alignment explanation
Indices: 64503--64549 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
64493 GATTTACATA
64503 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
64524 TTCGCATTGCGATATTCGAAG
1 TTCGCATTGCGATAGTCCAAG
64545 TTCGC
1 TTCGC
64550 GTTACAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:68840 original size:2 final size:2
Alignment explanation
Indices: 68833--68906 Score: 102
Period size: 2 Copynumber: 39.0 Consensus size: 2
68823 CATTGGCATC
* *
68833 AT AT AT AT -T A- AT AT GT AT AT AT AT AT -T TT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68871 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
68907 GTTTTTTATA
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
1 4 0.06
2 61 0.94
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (2 bp):
AT
Found at i:69211 original size:13 final size:13
Alignment explanation
Indices: 69193--69222 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
69183 TGTTTCTTTA
69193 TTTTATTTTATTT
1 TTTTATTTTATTT
69206 TTTTATTTTATTT
1 TTTTATTTTATTT
69219 TTTT
1 TTTT
69223 GTTATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTATTTTATTT
Done.