Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011809.1 Kokia drynarioides strain JFW-HI SEQ_126804, 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: 56522
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 121 characters in sequence are not A, C, G, or T
Found at i:10829 original size:205 final size:205
Alignment explanation
Indices: 10477--10898 Score: 765
Period size: 205 Copynumber: 2.1 Consensus size: 205
10467 TCGATACGAA
*
10477 CAAATCAAACTCACGCTCGATACGAACAAATCCTCGAACCCCAGCTTCCTGATGAGACACTGAGA
1 CAAATCAAACTCACGCTCGATACGAACAAATCCTCGAACCCCAACTTCCTGATGAGACACTGAGA
* * *
10542 AGCAGGTCGAACTCATAAAAGGTTAGCTTCCTGATAAGATACGAATAAGTGGGCCAAAATTGTCT
66 AGCAGGTCGAACTCATAAAAGGTTAGCTTCCTGATAAGATACGAAGAAGTGGACCAAAATTATCT
10607 TCCTGATGAGATACAGAGAAGCGGATTAAAACAAACGACACGGTCATCTTCCTGATGAGATACTG
131 TCCTGATGAGATACAGAGAAGCGGATTAAAACAAACGACACGGTCATCTTCCTGATGAGATACTG
10672 AGAAGAAGAC
196 AGAAGAAGAC
10682 CAAATCAAACTCACGCTCGATACGAACAAATCCTCGAACCCCAACTTCCTGATGAGACACTGAGA
1 CAAATCAAACTCACGCTCGATACGAACAAATCCTCGAACCCCAACTTCCTGATGAGACACTGAGA
*
10747 AGCAGGTCGAAGTCATAAAAGGTTAGCTTCCTGATAAGATACGAAGAAGTGGACC-AAATTCATC
66 AGCAGGTCGAACTCATAAAAGGTTAGCTTCCTGATAAGATACGAAGAAGTGGACCAAAATT-ATC
* *
10811 TTCCTGATGAGATACAGAGAAGCGGATTAAAATAAACGACGCGGTCATCTTCCTGATGAGATACT
130 TTCCTGATGAGATACAGAGAAGCGGATTAAAACAAACGACACGGTCATCTTCCTGATGAGATACT
10876 GAGAAGAAGAC
195 GAGAAGAAGAC
10887 CAAATCAAACTC
1 CAAATCAAACTC
10899 NNNNNNNNNN
Statistics
Matches: 209, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
204 5 0.02
205 204 0.98
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (205 bp):
CAAATCAAACTCACGCTCGATACGAACAAATCCTCGAACCCCAACTTCCTGATGAGACACTGAGA
AGCAGGTCGAACTCATAAAAGGTTAGCTTCCTGATAAGATACGAAGAAGTGGACCAAAATTATCT
TCCTGATGAGATACAGAGAAGCGGATTAAAACAAACGACACGGTCATCTTCCTGATGAGATACTG
AGAAGAAGAC
Found at i:13989 original size:30 final size:29
Alignment explanation
Indices: 13925--14108 Score: 178
Period size: 29 Copynumber: 6.3 Consensus size: 29
13915 AAAGTTACCA
** *
13925 TTTAACCCCCGAACTTCTAAAAATCCCAT
1 TTTAACCCCAAAACTTCCAAAAATCCCAT
*
13954 TTTAACCCCAAAACTTTCAAAAATCCCATT
1 TTTAACCCCAAAACTTCCAAAAATCCCA-T
* *
13984 TTTAACCCTC-GAACTTCCAAAAATTCCA-
1 TTTAACCC-CAAAACTTCCAAAAATCCCAT
* *
14012 TTTGACCCCAAAACTTCCAAAAATTACCAT
1 TTTAACCCCAAAACTTCCAAAAA-TCCCAT
* * *
14042 TTT-ACCCCTAAATTTCTAAAAATCCCATT
1 TTTAACCCCAAAACTTCCAAAAATCCCA-T
* *
14071 TTTTACCCCAAAACTTCCAAAAATTACCAT
1 TTTAACCCCAAAACTTCCAAAAA-TCCCAT
14101 TTT-ACCCC
1 TTTAACCCC
14109 TGATGTTTAA
Statistics
Matches: 129, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
27 1 0.01
28 23 0.18
29 53 0.41
30 47 0.36
31 5 0.04
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (29 bp):
TTTAACCCCAAAACTTCCAAAAATCCCAT
Found at i:14068 original size:87 final size:88
Alignment explanation
Indices: 13905--14108 Score: 245
Period size: 87 Copynumber: 2.3 Consensus size: 88
13895 GAAGGTCCCT
* * ** * *
13905 AAACTATCCGAAAGTTACCATTTAACCCCCGAACTTCTAAAAATCCCATTTTAACCCCAAAACTT
1 AAACT-TCCAAAAATTACCATTTAACCCCAAAACTTCCAAAAATACCATTTTAACCCCAAAACTT
13970 TCAAAAATCCCATTTTTAACCCTC-
65 TCAAAAATCCCATTTTTAACCC-CA
* * *
13994 GAACTTCCAAAAATT-CCATTTGACCCCAAAACTTCCAAAAATTACCATTTT-ACCCCTAAA-TT
1 AAACTTCCAAAAATTACCATTTAACCCCAAAACTTCCAAAAA-TACCATTTTAACCCCAAAACTT
*
14056 TCTAAAAATCCCATTTTTTACCCCA
65 TC-AAAAATCCCATTTTTAACCCCA
*
14081 AAACTTCCAAAAATTACCATTTTACCCC
1 AAACTTCCAAAAATTACCATTTAACCCC
14109 TGATGTTTAA
Statistics
Matches: 99, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
86 5 0.05
87 63 0.64
88 27 0.27
89 4 0.04
ACGTcount: A:0.37, C:0.31, G:0.02, T:0.29
Consensus pattern (88 bp):
AAACTTCCAAAAATTACCATTTAACCCCAAAACTTCCAAAAATACCATTTTAACCCCAAAACTTT
CAAAAATCCCATTTTTAACCCCA
Found at i:14104 original size:59 final size:58
Alignment explanation
Indices: 13905--14111 Score: 247
Period size: 59 Copynumber: 3.5 Consensus size: 58
13895 GAAGGTCCCT
* * * *
13905 AAACTATCCGAAAGTTACCATTTAACCCCCGAACTTCTAAAAATCCCATTTTAACCCCA
1 AAACT-TCCAAAAATTACCATTTTACCCCTGAACTTCTAAAAATCCCATTTTAACCCCA
* * * * * *
13964 AAACTTTCAAAAA-TCCCATTTTTAACCCTCGAACTTCCAAAAATTCCA-TTTGACCCCA
1 AAACTTCCAAAAATTACCA-TTTTACCCCT-GAACTTCTAAAAATCCCATTTTAACCCCA
* * *
14022 AAACTTCCAAAAATTACCATTTTACCCCTAAATTTCTAAAAATCCCATTTTTTACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCTGAACTTCTAAAAATCCCA-TTTTAACCCCA
14081 AAACTTCCAAAAATTACCATTTTACCCCTGA
1 AAACTTCCAAAAATTACCATTTTACCCCTGA
14112 TGTTTAAAAT
Statistics
Matches: 124, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
57 18 0.15
58 42 0.34
59 64 0.52
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.29
Consensus pattern (58 bp):
AAACTTCCAAAAATTACCATTTTACCCCTGAACTTCTAAAAATCCCATTTTAACCCCA
Found at i:16794 original size:17 final size:17
Alignment explanation
Indices: 16756--16792 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
16746 TTTAATTTTT
16756 TAAATATTATAAATATA
1 TAAATATTATAAATATA
16773 TAAATCATTA-AAATA-A
1 TAAAT-ATTATAAATATA
16789 TAAA
1 TAAA
16793 ATAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 10 0.53
18 4 0.21
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATATTATAAATATA
Found at i:35355 original size:22 final size:23
Alignment explanation
Indices: 35327--35380 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
35317 ATTAACAGAT
* *
35327 TATTATTACAAGCAAAAA-AAAA
1 TATTATTAAAAACAAAAATAAAA
*
35349 TATTATTAAAAATAAAAATAAAA
1 TATTATTAAAAACAAAAATAAAA
35372 TCATTATTA
1 T-ATTATTA
35381 TAAATTCGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 15 0.56
23 5 0.19
24 7 0.26
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (23 bp):
TATTATTAAAAACAAAAATAAAA
Found at i:35377 original size:24 final size:22
Alignment explanation
Indices: 35340--35385 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
35330 TATTACAAGC
35340 AAAAAAAAATATTATTAAAAAT
1 AAAAAAAAATATTATTAAAAAT
*
35362 AAAAATAAAATCATTATTATAAAT
1 AAAAA-AAAAT-ATTATTAAAAAT
35386 TCGGGTCGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 5 0.24
24 11 0.52
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAAAAAATATTATTAAAAAT
Found at i:36948 original size:20 final size:18
Alignment explanation
Indices: 36920--36968 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
36910 TGGACACAAG
36920 GTATTGATACCATGCTTCAA
1 GTATTGATACCATG--TCAA
*
36940 GTATCGATACCCATGTCAA
1 GTATTGATA-CCATGTCAA
36959 GTATTGATAC
1 GTATTGATAC
36969 TGTTTTTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 12 0.46
20 8 0.31
21 5 0.19
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (18 bp):
GTATTGATACCATGTCAA
Found at i:40802 original size:67 final size:67
Alignment explanation
Indices: 40694--40820 Score: 186
Period size: 67 Copynumber: 1.9 Consensus size: 67
40684 CTTAATAAAT
** * *
40694 ATTATTAGGGCTGTTGCCCCTTCATATTCATAAGGGGTAGTA-TTAGACCTTTT-ATGTATTGGG
1 ATTATTAGAACTGTTACCCCTTCATATTCATAAGAGGTAGTATTTA-A-CTTTTCATGTATTGGG
40757 TCCA
64 TCCA
40761 ATTATTAGAACTGTTACCCCTTCATATTCATAAGAGGTAGTATTTAACTTTTCATGTATT
1 ATTATTAGAACTGTTACCCCTTCATATTCATAAGAGGTAGTATTTAACTTTTCATGTATT
40821 TGATTCAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
66 5 0.09
67 46 0.85
68 3 0.06
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (67 bp):
ATTATTAGAACTGTTACCCCTTCATATTCATAAGAGGTAGTATTTAACTTTTCATGTATTGGGTC
CA
Found at i:40936 original size:9 final size:9
Alignment explanation
Indices: 40917--40968 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
40907 ATAAATATCA
40917 TTAATTTAAT
1 TTAA-TTAAT
40927 TTAATTAAT
1 TTAATTAAT
* *
40936 TAAATTAGT
1 TTAATTAAT
40945 TTAATTAAT
1 TTAATTAAT
*
40954 TT-TTTAA-
1 TTAATTAAT
40961 TTAATTAA
1 TTAATTAA
40969 ATATATTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 2 0.06
8 8 0.23
9 21 0.60
10 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (9 bp):
TTAATTAAT
Found at i:40947 original size:18 final size:18
Alignment explanation
Indices: 40916--40954 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
40906 AATAAATATC
*
40916 ATTAATTTAATTTAATTA
1 ATTAAATTAATTTAATTA
*
40934 ATTAAATTAGTTTAATTA
1 ATTAAATTAATTTAATTA
40952 ATT
1 ATT
40955 TTTTAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTAAATTAATTTAATTA
Found at i:40962 original size:30 final size:31
Alignment explanation
Indices: 40916--40980 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
40906 AATAAATATC
40916 ATTAATTTAATTTAATTAATTAAAT-TAGTTTA
1 ATTAATTT-ATTTAATTAATTAAATATA-TTTA
40948 ATTAATTT-TTTAATTAATTAAATATATTTA
1 ATTAATTTATTTAATTAATTAAATATATTTA
40978 ATT
1 ATT
40981 TCCATATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 22 0.69
31 2 0.06
32 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (31 bp):
ATTAATTTATTTAATTAATTAAATATATTTA
Found at i:46087 original size:6 final size:6
Alignment explanation
Indices: 46039--46110 Score: 53
Period size: 6 Copynumber: 12.3 Consensus size: 6
46029 TCATTTTGGG
* ***
46039 TTTAAA TTT-AA TTTAAG TTTAAA CTTTTCT TTTAAA GTTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA -TTTAAA TTTAAA
*
46088 -TTAAA -TTAAA -TTGAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
46111 CAATTAAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
5 19 0.37
6 24 0.46
7 9 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:46098 original size:16 final size:16
Alignment explanation
Indices: 46077--46115 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
46067 CTTTTAAAGT
*
46077 TTAAATTTAAATTAAA
1 TTAAATTGAAATTAAA
*
46093 TTAAATTGAATTTAAA
1 TTAAATTGAAATTAAA
*
46109 TTCAATT
1 TTAAATT
46116 AAAAAAATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (16 bp):
TTAAATTGAAATTAAA
Found at i:46848 original size:15 final size:16
Alignment explanation
Indices: 46828--46868 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
46818 ACAATAACAT
*
46828 TAAATAATAAT-ATAG
1 TAAATAATAATAATAA
46843 TAAATAATAATAATAA
1 TAAATAATAATAATAA
*
46859 TAATTAATAA
1 TAAATAATAA
46869 CAAACAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
TAAATAATAATAATAA
Found at i:47859 original size:30 final size:29
Alignment explanation
Indices: 47825--48014 Score: 129
Period size: 29 Copynumber: 6.5 Consensus size: 29
47815 AATTGTCCAT
* * *
47825 AAATTATATTTTGACACTTAAATTTTCTAA
1 AAATTACATTTTTAC-CTTAAACTTTCTAA
* * *
47855 AAATTGCATTTTTACCCTCAAACTTCCTAA
1 AAATTACATTTTTA-CCTTAAACTTTCTAA
*
47885 AAATTACATTTTTACCCTAAACTTTC-AA
1 AAATTACATTTTTACCTTAAACTTTCTAA
** *
47913 AAATTACATTTTTACCCCCAAACTTTC-CA
1 AAATTACATTTTTA-CCTTAAACTTTCTAA
* * *
47942 AAATTCCATTTTTGACC-TCAA-TTTCACCAA
1 AAATTACATTTTT-ACCTTAAACTTT--CTAA
* ***
47972 AAAATACATTTTTACCCCCGAACTTTCT-A
1 AAATTACATTTTTA-CCTTAAACTTTCTAA
48001 AAATTACATTTTTA
1 AAATTACATTTTTA
48015 ACCTCGATTT
Statistics
Matches: 129, Mismatches: 22, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
27 3 0.02
28 18 0.14
29 51 0.40
30 51 0.40
31 3 0.02
32 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (29 bp):
AAATTACATTTTTACCTTAAACTTTCTAA
Found at i:47906 original size:29 final size:29
Alignment explanation
Indices: 47851--48014 Score: 140
Period size: 29 Copynumber: 5.6 Consensus size: 29
47841 CTTAAATTTT
*
47851 CTAAAAATTGCATTTTTACCCTCAAACTTC
1 CTAAAAATTACATTTTTACCCT-AAACTTC
*
47881 CTAAAAATTACATTTTTACCCTAAACTTT
1 CTAAAAATTACATTTTTACCCTAAACTTC
*
47910 C-AAAAATTACATTTTTACCCCCAAACTTTC
1 CTAAAAATTACATTTTTA-CCCTAAAC-TTC
* * *
47940 C--AAAATTCCATTTTTGA-CCTCAATTTC
1 CTAAAAATTACATTTTT-ACCCTAAACTTC
* * ** *
47967 ACCAAAAAATACATTTTTACCCCCGAACTTT
1 -CTAAAAATTACATTTTTA-CCCTAAACTTC
47998 CT-AAAATTACATTTTTA
1 CTAAAAATTACATTTTTA
48015 ACCTCGATTT
Statistics
Matches: 110, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
27 3 0.03
28 21 0.19
29 42 0.38
30 38 0.35
31 6 0.05
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (29 bp):
CTAAAAATTACATTTTTACCCTAAACTTC
Found at i:47987 original size:59 final size:60
Alignment explanation
Indices: 47853--48135 Score: 316
Period size: 59 Copynumber: 4.8 Consensus size: 60
47843 TAAATTTTCT
* * * *
47853 AAAAATT-GCATTTTTACCCTCAAAC-TTCCTAAAAATTACATTTTT-ACCCTAAACTTT---C
1 AAAAATTACCATTTTTACCCCCAAACTTTCC--AAAATTCCATTTTTGA-CCTCAA-TTTCACC
47911 AAAAATTA-CATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTCAATTTCACC
1 AAAAATTACCATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTCAATTTCACC
* * * * * *
47970 AAAAAATA-CATTTTTACCCCCGAACTTTCTAAAATTACATTTTTAACCTCGATTTCACC
1 AAAAATTACCATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTCAATTTCACC
* * * *
48029 AAAAATTACCA-TTTTACCCTCGAACTTTCCAAAATTCCATTTTTGAACTCGATTTCACC
1 AAAAATTACCATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTCAATTTCACC
* *
48088 AAAAATTACCA-TTTTACCCCCTAACTTCCCAAAATTCCATTTTTGACC
1 AAAAATTACCATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACC
48136 CTGATTTTTC
Statistics
Matches: 199, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
56 3 0.02
57 18 0.09
58 24 0.12
59 152 0.76
60 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (60 bp):
AAAAATTACCATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTCAATTTCACC
Found at i:48032 original size:29 final size:30
Alignment explanation
Indices: 47854--48137 Score: 147
Period size: 30 Copynumber: 9.6 Consensus size: 30
47844 AAATTTTCTA
* * *
47854 AAAATTGCATTTTTACCCTCAAAC-TTC-CTA
1 AAAATTACATTTTTACCCTC-GACTTTCAC-C
**
47884 AAAATTACATTTTTACCCTAAACTTTCA--
1 AAAATTACATTTTTACCCTCGACTTTCACC
* *
47912 AAAATTACATTTTTACCCCCAAACTTT--CC
1 AAAATTACATTTTTACCCTC-GACTTTCACC
* *
47941 AAAATTCCATTTTTGA-CCTC-AATTTCACC
1 AAAATTACATTTTT-ACCCTCGACTTTCACC
* * *
47970 AAAAAATACATTTTTACCCCCGAACTTT--CT
1 -AAAATTACATTTTTACCCTCG-ACTTTCACC
*
48000 AAAATTACATTTTTAACCTCGA-TTTCACC
1 AAAATTACATTTTTACCCTCGACTTTCACC
48029 AAAAATTACCA-TTTTACCCTCGAACTTT--CC
1 -AAAATTA-CATTTTTACCCTCG-ACTTTCACC
* *
48059 AAAATTCCATTTTTGA-ACTCGA-TTTCACC
1 AAAATTACATTTTT-ACCCTCGACTTTCACC
* *
48088 AAAAATTACCA-TTTTACCCCCTAAC-TTC-CC
1 -AAAATTA-CATTTTTACCCTC-GACTTTCACC
*
48118 AAAATTCCATTTTTGACCCT
1 AAAATTACATTTTT-ACCCT
48138 GATTTTTCCA
Statistics
Matches: 200, Mismatches: 25, Indels: 58
0.71 0.09 0.20
Matches are distributed among these distances:
27 10 0.05
28 24 0.12
29 74 0.37
30 76 0.38
31 9 0.05
32 7 0.04
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTTACCCTCGACTTTCACC
Found at i:48142 original size:59 final size:59
Alignment explanation
Indices: 47910--48160 Score: 330
Period size: 59 Copynumber: 4.3 Consensus size: 59
47900 CCTAAACTTT
* *
47910 CAAAAATTA-CATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTCAATTTCAC
1 CAAAAATTACCA-TTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCAC
* * * *
47969 CAAAAAATA-CATTTTTACCCCCGAACTTTCTAAAATTACATTTTTAACCTCGATTTCAC
1 CAAAAATTACCA-TTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCAC
* *
48028 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGAACTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCAC
* * **
48087 CAAAAATTACCATTTTACCCCCTAACTTCCCAAAATTCCATTTTTGACC-CTGATTTTTC
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTC-GATTTCAC
*
48146 C-AAAACTACCATTTT
1 CAAAAATTACCATTTT
48161 GCCTTCGAGT
Statistics
Matches: 171, Mismatches: 19, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
58 14 0.08
59 155 0.91
60 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCAC
Found at i:48148 original size:29 final size:29
Alignment explanation
Indices: 47884--48160 Score: 125
Period size: 29 Copynumber: 9.4 Consensus size: 29
47874 AAACTTCCTA
* * ** *
47884 AAAATTACATTTTTACCCT-AAACTTTCA
1 AAAATTCCATTTTTACCCTCGATTTTTCC
* * * **
47912 AAAATTACATTTTTACCCCCAAACTTTCC
1 AAAATTCCATTTTTACCCTCGATTTTTCC
* **
47941 AAAATTCCATTTTTGA-CCTCAATTTCACC
1 AAAATTCCATTTTT-ACCCTCGATTTTTCC
* * * ** *
47970 AAAAAATACATTTTTACCCCCGAACTTTCT
1 -AAAATTCCATTTTTACCCTCGATTTTTCC
* * **
48000 AAAATTACATTTTTAACCTCGATTTCACC
1 AAAATTCCATTTTTACCCTCGATTTTTCC
**
48029 AAAAATTACCA-TTTTACCCTCGAACTTTCC
1 -AAAATT-CCATTTTTACCCTCGATTTTTCC
* **
48059 AAAATTCCATTTTTGA-ACTCGATTTCACC
1 AAAATTCCATTTTT-ACCCTCGATTTTTCC
* * ** *
48088 AAAAATTACCA-TTTTACCCCCTAACTTCCC
1 -AAAATT-CCATTTTTACCCTCGATTTTTCC
48118 AAAATTCCATTTTTGACCCT-GATTTTTCC
1 AAAATTCCATTTTT-ACCCTCGATTTTTCC
*
48147 AAAACTACCATTTT
1 AAAA-TTCCATTTT
48161 GCCTTCGAGT
Statistics
Matches: 186, Mismatches: 49, Indels: 26
0.71 0.19 0.10
Matches are distributed among these distances:
28 24 0.13
29 89 0.48
30 68 0.37
31 5 0.03
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTCGATTTTTCC
Found at i:48149 original size:118 final size:117
Alignment explanation
Indices: 47861--48160 Score: 356
Period size: 118 Copynumber: 2.6 Consensus size: 117
47851 CTAAAAATTG
* * **
47861 CATTTTTACCCTCAAACTTCCTAAAAATTACATTTTTACCCTAAACTTT-CAAAAATTA-CATTT
1 CATTTTTACCCCCAAACTTCC-AAAAATTACATTTTTACCCTGATTTTTCCAAAAATTACCA-TT
*
47924 TTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTCAATTTCACCAAAAAATA
64 TTACCCCCAAACTTTCCAAAATTCCATTTTTGAACTCAATTTCACCAAAAAATA
* * * * **
47978 CATTTTTACCCCCGAACTTTCTAAAATTACATTTTTAACCTCGATTTCACCAAAAATTACCATTT
1 CATTTTTACCCCCAAACTTCCAAAAATTACATTTTTACCCT-GATTTTTCCAAAAATTACCATTT
* * * *
48043 TACCCTCGAACTTTCCAAAATTCCATTTTTGAACTCGATTTCACCAAAAATTA
65 TACCCCCAAACTTTCCAAAATTCCATTTTTGAACTCAATTTCACCAAAAAATA
* * * *
48096 CCA-TTTTACCCCCTAACTTCCCAAAATTCCATTTTTGACCCTGATTTTTCC-AAAACTACCATT
1 -CATTTTTACCCCCAAACTTCCAAAAATTACATTTTT-ACCCTGATTTTTCCAAAAATTACCATT
48159 TT
64 TT
48161 GCCTTCGAGT
Statistics
Matches: 155, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
116 18 0.12
117 33 0.21
118 96 0.62
119 8 0.05
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.37
Consensus pattern (117 bp):
CATTTTTACCCCCAAACTTCCAAAAATTACATTTTTACCCTGATTTTTCCAAAAATTACCATTTT
ACCCCCAAACTTTCCAAAATTCCATTTTTGAACTCAATTTCACCAAAAAATA
Found at i:50245 original size:18 final size:18
Alignment explanation
Indices: 50222--50264 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
50212 GAATTATTTT
50222 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
50240 TTAATTAAAAAATTTAAA
1 TTAATTAAAAAATTTAAA
50258 TTAATTA
1 TTAATTA
50265 TAACTGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:51486 original size:26 final size:26
Alignment explanation
Indices: 51437--51486 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
51427 AAATTTAAAT
* *
51437 TTAATACCTACTTGTTCAAAAAAAAA
1 TTAATACCTACATGTTAAAAAAAAAA
*
51463 TTAATACCTACAT-TTAAAATAAAA
1 TTAATACCTACATGTTAAAAAAAAA
51487 CTTCATTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (26 bp):
TTAATACCTACATGTTAAAAAAAAAA
Found at i:53279 original size:43 final size:43
Alignment explanation
Indices: 53019--53281 Score: 373
Period size: 43 Copynumber: 6.1 Consensus size: 43
53009 GAAAAATGCA
* * * **
53019 GCTATAGAACGTGGTCTTTAGCAGTGCTTTTCCCACAAACGAA
1 GCTAAAGAACGTGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * *
53062 GCTAAAGAACGTTGTCTTTAGCGGCGCTTTTCTCACAAGCGCC
1 GCTAAAGAACGTGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* *
53105 GATAAAGAACGTGGTCTTTAGCGGCGCTTTTCTCACAAACGCC
1 GCTAAAGAACGTGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
*
53148 GCTAATGAACGTGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
1 GCTAAAGAACGTGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * *
53191 ACTAAAGAACGTGGTCTTTAGTGACGCTTTTCCCACAAACGCC
1 GCTAAAGAACGTGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * *
53234 GCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACACC
1 GCTAAAGAACGTGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
53277 GCTAA
1 GCTAA
53282 CATTAACAAA
Statistics
Matches: 196, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 196 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (43 bp):
GCTAAAGAACGTGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
Found at i:56402 original size:34 final size:33
Alignment explanation
Indices: 56353--56417 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
56343 TAAATTTATT
* *
56353 TTAAAATTAAGTTTATTCTAAATTTAAATTTGG
1 TTAAAATTAAATTTATTATAAATTTAAATTTGG
56386 TTAAAATTTAAATTTATTATAAATTTAAATTT
1 TTAAAA-TTAAATTTATTATAAATTTAAATTT
56418 AAAATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 6 0.21
34 23 0.79
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (33 bp):
TTAAAATTAAATTTATTATAAATTTAAATTTGG
Found at i:56428 original size:17 final size:17
Alignment explanation
Indices: 56342--56418 Score: 93
Period size: 17 Copynumber: 4.5 Consensus size: 17
56332 CCCAATCAGC
* *
56342 TTAAATTTATTTTAAAA
1 TTAAATTTATTATAAAT
* *
56359 TTAAGTTTATTCTAAAT
1 TTAAATTTATTATAAAT
*
56376 TTAAATTTGGTTA-AAAT
1 TTAAATTT-ATTATAAAT
56393 TTAAATTTATTATAAAT
1 TTAAATTTATTATAAAT
56410 TTAAATTTA
1 TTAAATTTA
56419 AAATTTATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
16 3 0.06
17 46 0.90
18 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTATAAAT
Done.