Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014403.1 Kokia drynarioides strain JFW-HI SEQ_129441, 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: 141942
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Warning! 169 characters in sequence are not A, C, G, or T
Found at i:142 original size:30 final size:28
Alignment explanation
Indices: 67--267 Score: 129
Period size: 30 Copynumber: 6.8 Consensus size: 28
57 AAAGATCTTT
* * *
67 AAACTATCCAAAAATTATATTTCGACCCC
1 AAACT-TCCAAAAATTACATTTTGACCCA
* *
96 AAACTTCCTCAAAATTATATTTTTGACCTCA
1 AAACTTCC-AAAAATTACA-TTTTGACC-CA
*
127 AAACTTCCAAAAATTACCATTTT-ACCCTC
1 AAACTTCCAAAAATTA-CATTTTGACCC-A
*
156 AAACTTCCAAAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTACA-TTTTGACCC-A
* *
186 AAACTTCCAAATATTACCA-TTT-ACCCCC
1 AAACTTCCAAAAATTA-CATTTTGA-CCCA
* * * *
214 AAACATCCAAAAATTCCATTTTTTAACCCC
1 AAACTTCCAAAAATTACA--TTTTGACCCA
* *
244 GAACTTCCTAAAATTATCATTTTG
1 AAACTTCCAAAAATTA-CATTTTG
268 TCCTTAGGTA
Statistics
Matches: 139, Mismatches: 19, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
27 2 0.01
28 20 0.14
29 46 0.33
30 56 0.40
31 15 0.11
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.33
Consensus pattern (28 bp):
AAACTTCCAAAAATTACATTTTGACCCA
Found at i:169 original size:59 final size:58
Alignment explanation
Indices: 67--236 Score: 193
Period size: 59 Copynumber: 2.9 Consensus size: 58
57 AAAGATCTTT
* * * *
67 AAACTATCCAAAAATTA-TATTTCGACCCCAAACTTCCTCAAAATTATATTTTTGA-CCTCA
1 AAACT-TCCAAAAATTACCATTT-TACCCCAAACTTCC-AAAAATTACATTTTTGACCCT-A
*
127 AAACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTACCATTTTACCC-CAAACTTCCAAAAATTACATTTTTGACCCTA
* * *
186 AAACTTCCAAATATTACCA-TTTACCCCCAAACATCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATTACCATTTTA-CCCCAAACTTCCAAAAATTACATTTTT
237 TAACCCCGAA
Statistics
Matches: 99, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
58 27 0.27
59 51 0.52
60 21 0.21
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.32
Consensus pattern (58 bp):
AAACTTCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATTACATTTTTGACCCTA
Found at i:237 original size:59 final size:60
Alignment explanation
Indices: 114--266 Score: 199
Period size: 58 Copynumber: 2.6 Consensus size: 60
104 TCAAAATTAT
* *
114 ATTTTTGA-CCTCAAAACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCC
1 ATTTTTGACCCTCAAAACTTCCAAAAATTACCATTTTACCCCCAAACATCCAAAAATTCC
*
173 ATTTTTGACCCT-AAAACTTCCAAATATTACCA-TTTACCCCCAAACATCCAAAAATTCC
1 ATTTTTGACCCTCAAAACTTCCAAAAATTACCATTTTACCCCCAAACATCCAAAAATTCC
* * * *
231 ATTTTTTAACCC-C-GAACTTCCTAAAATTATCATTTT
1 A-TTTTTGACCCTCAAAACTTCCAAAAATTACCATTTT
267 GTCCTTAGGT
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
58 40 0.49
59 39 0.48
60 3 0.04
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (60 bp):
ATTTTTGACCCTCAAAACTTCCAAAAATTACCATTTTACCCCCAAACATCCAAAAATTCC
Found at i:12227 original size:50 final size:49
Alignment explanation
Indices: 12112--12600 Score: 351
Period size: 50 Copynumber: 9.8 Consensus size: 49
12102 TACCGCAAAA
* * * * *
12112 AAGGGAAATATTTAAGCCGTAACGTCTAATCCAGTACCATGAAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAAGAAGACATG
* *
12161 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACAGAATACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA-AGAAGACATG
* * * * *
12211 AAAGGAAAGATCTAAGCCGCAACGGC-AGATCCAATACCGTAA-AGAGATAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGA-ATCCAGTACC--AAGA-AGACATG
*
12262 AAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACAGAAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA-AGAAGACATG
* * *** * *
12312 AAGGGAAAGATCTAAACCGCAACGATAAATCCAATACTGCAA-AGAGACAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTAC--CAAGA-AGACATG
** * * *
12363 AAGGGAAAGATTTAAGCTACAACGGCGAATTCAGTACCATGAATACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAAGAAGACATG
* * * * *
12412 AAGGGAAAGATTTAGGACCGCAACGGTGGATCCAATACCACA-AAGATACA-A
1 AAGGGAAAGATTTAAG-CCGCAACGGCGAATCCAGTACCA-AGAAG--ACATG
* * * ** * * *
12463 AAGAGAAAGGTTTAAGTCGCAACGATGAA-CCGTGTACCTTAGAAGACAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACC-AAGAAGACATG
* * * * * **
12513 AAGGGAAAGATTTAAGTCGTAACGGTGAATTCAGTACCACGAAGATTTG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAAGAAGACATG
* * * *
12562 AAGGGGAAAGGTTTAAGTCGCAATGGCGAACCCAGTACC
1 AA-GGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACC
12601 TTAGAAACAT
Statistics
Matches: 343, Mismatches: 75, Indels: 43
0.74 0.16 0.09
Matches are distributed among these distances:
49 71 0.21
50 175 0.51
51 90 0.26
52 7 0.02
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAAGAAGACATG
Found at i:12291 original size:101 final size:101
Alignment explanation
Indices: 12154--12538 Score: 418
Period size: 101 Copynumber: 3.8 Consensus size: 101
12144 AGTACCATGA
* * *
12154 AGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACAGAATACATGAAAGGAAA
1 AGACAAGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACAGAATACATGAAGGGAAA
* *
12219 GATCTAAGCCGCAACGGCAGATCCAATACCGTAAAG
66 GATCTAAGCCGCAACGGTAGATCCAATACCGCAAAG
* * *
12255 AGATAAGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACAGAAGACATGAAGGGAAA
1 AGACAAGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACAGAATACATGAAGGGAAA
* * * *
12320 GATCTAAACCGCAACGATAAATCCAATACTGCAAAG
66 GATCTAAGCCGCAACGGTAGATCCAATACCGCAAAG
** * *
12356 AGACAAGAAGGGAAAGATTTAAGCTACAACGGCGAAT-TCAGTACCA-TGAATACATGAAGGGAA
1 AGACAAGAAGGGAAAGATTTAAGCCGCAACGACGAATCT-AGTACCACAGAATACATGAAGGGAA
* * * *
12419 AGATTTAGGACCGCAACGGTGGATCCAATACCACAAAG
65 AGATCTAAG-CCGCAACGGTAGATCCAATACCGCAAAG
* * * * * * ** * *
12457 ATACAA-AAGAGAAAGGTTTAAGTCGCAACGATGAACCGT-GTACCTTAGAAGACAAGAAGGGAA
1 AGACAAGAAGGGAAAGATTTAAGCCGCAACGACGAATC-TAGTACCACAGAATACATGAAGGGAA
* * *
12520 AGATTTAAGTCGTAACGGT
65 AGATCTAAGCCGCAACGGT
12539 GAATTCAGTA
Statistics
Matches: 236, Mismatches: 43, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
100 56 0.24
101 179 0.76
102 1 0.00
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (101 bp):
AGACAAGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACAGAATACATGAAGGGAAA
GATCTAAGCCGCAACGGTAGATCCAATACCGCAAAG
Found at i:12500 original size:100 final size:100
Alignment explanation
Indices: 12154--12600 Score: 373
Period size: 101 Copynumber: 4.5 Consensus size: 100
12144 AGTACCATGA
* * * * * * *
12154 AGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACAGAATACATGAAAGGAAA
1 AGACAAGAAGGGAAAGATTTAAGTCGCAACGACGAATCCAGTACCA-TGAAGACATGAAGGGAAA
* * **
12219 GATCTAAGCCGCAACGGCAGATCCAATACCGTAAAG
65 GATCTAAGCCGCAACGGTAAATCCAATACCACAAAG
* * *
12255 AGATAAGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACAGAAGACATGAAGGGAAA
1 AGACAAGAAGGGAAAGATTTAAGTCGCAACGACGAATCCAGTACCA-TGAAGACATGAAGGGAAA
* * **
12320 GATCTAAACCGCAACGATAAATCCAATACTGCAAAG
65 GATCTAAGCCGCAACGGTAAATCCAATACCACAAAG
* * * *
12356 AGACAAGAAGGGAAAGATTTAAG-CTACAACGGCGAATTCAGTACCATGAATACATGAAGGGAAA
1 AGACAAGAAGGGAAAGATTTAAGTC-GCAACGACGAATCCAGTACCATGAAGACATGAAGGGAAA
* * **
12420 GATTTAGGACCGCAACGGTGGATCCAATACCACAAAG
65 GATCTAAG-CCGCAACGGTAAATCCAATACCACAAAG
* * * * * * *
12457 ATACAA-AAGAGAAAGGTTTAAGTCGCAACGATGAA-CCGTGTACCTTAGAAGACAAGAAGGGAA
1 AGACAAGAAGGGAAAGATTTAAGTCGCAACGACGAATCC-AGTACCAT-GAAGACATGAAGGGAA
* * * * * * *
12520 AGATTTAAGTCGTAACGGTGAATTCAGTACCAC-GA-
64 AGATCTAAGCCGCAACGGTAAATCCAATACCACAAAG
*** * * * *
12555 AGATTTGAAGGGGAAAGGTTTAAGTCGCAATGGCGAACCCAGTACC
1 AGACAAGAA-GGGAAAGATTTAAGTCGCAACGACGAATCCAGTACC
12601 TTAGAAACAT
Statistics
Matches: 285, Mismatches: 53, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
98 2 0.01
99 4 0.01
100 97 0.34
101 182 0.64
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.16
Consensus pattern (100 bp):
AGACAAGAAGGGAAAGATTTAAGTCGCAACGACGAATCCAGTACCATGAAGACATGAAGGGAAAG
ATCTAAGCCGCAACGGTAAATCCAATACCACAAAG
Found at i:12862 original size:101 final size:101
Alignment explanation
Indices: 12687--12880 Score: 300
Period size: 101 Copynumber: 1.9 Consensus size: 101
12677 CTACAATGAC
* * *
12687 AAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAACATCAATTCCTATCCTC
1 AAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATAAAGCTTCAACATCAAATCCTATCCTC
* * *
12752 TTGAAGTTGCAGTAAAGTTGGATTAAAAATAATAGT
66 CTGAAGTTGCAGCAAAGTTGGAATAAAAATAATAGT
*
12788 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAACATCAAATCCTAT-CTC
1 AAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATAAAGCTTCAACATCAAATCCTATCCT-
*
12852 CCTGAAGTTGCAGCGAAGTTGGAATAAAA
65 CCTGAAGTTGCAGCAAAGTTGGAATAAAA
12881 TTACAGCAGT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 2 0.02
101 82 0.98
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (101 bp):
AAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATAAAGCTTCAACATCAAATCCTATCCTC
CTGAAGTTGCAGCAAAGTTGGAATAAAAATAATAGT
Found at i:13428 original size:194 final size:193
Alignment explanation
Indices: 13077--13692 Score: 692
Period size: 194 Copynumber: 3.1 Consensus size: 193
13067 ACAGTAAGGC
* * *
13077 GGTCATCTTCCTGATGAGATATAGAGAAGTATACCAACTCAATGCGAACAAATCTACGAACTCCA
1 GGTCATCTCCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAAC-CCA
* * * *
13142 ACTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGTTTCCTGATGAGATAC
65 GCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATAC
* * * * *
13207 TGGGAAGTGGACAAAATTCGCCTTCCTGATGAGGTATAGAGAAGCGGATTGAAACAAGTGAGGT
130 TGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAACAAGTGATGT
* * *
13271 GGTCATCTCCCTGATGAGATACAGGGAAGTATACCAACTTAATGCGAACAAATCTTCGAACCGTA
1 GGTCATCTCCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACC-CA
* *
13336 GCTTCCTGATGAGATACTAAGAAGTAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATAC
65 GCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATAC
* * * *
13401 TGAGAAATGGACCAAATTTGTCTTCCTGATGAGATACAGGGAAGCGGATTGAAACAAGTGATGT
130 TGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAACAAGTGATGT
* * ** * * * *
13465 GGTCATCTCTCTGATAAGGTATTGAGAAGAAGACTAAATCAAACCCACGCTCGATGTGAGCAAAT
1 GGTCATCTCCCTGATGA-G-ATACAG-AGAAG--T--AT---A-CCA-ACTCAATGCGAACAAAT
* * *
13530 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAACAATAAAGTGGTTAGCTTC
54 CTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
* * * * * * * * **
13595 TTGATGAGATACAGAGAAGTGAACCAAATCCGTCGTCCTGATGAAATATGGAGAAGTGGATCAAA
118 CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAA
*
13660 ACAAGTGATGC
183 ACAAGTGATGT
* *
13671 AGTCATCTTCCTGATGAGATAC
1 GGTCATCTCCCTGATGAGATAC
13693 TGAAAAGAAG
Statistics
Matches: 350, Mismatches: 58, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
193 1 0.00
194 186 0.53
195 1 0.00
196 4 0.01
197 4 0.01
199 1 0.00
201 2 0.01
204 3 0.01
205 4 0.01
206 142 0.41
207 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (193 bp):
GGTCATCTCCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCAG
CTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACT
GAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAACAAGTGATGT
Found at i:14039 original size:6 final size:6
Alignment explanation
Indices: 14028--14086 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
14018 ATTTATACAT
* * * * *
14028 AATTTA AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTAGA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATT-TA
14075 AATTTA AATTTA
1 AATTTA AATTTA
14087 TCATAAATTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
5 8 0.20
6 28 0.68
7 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:14051 original size:17 final size:17
Alignment explanation
Indices: 14031--14071 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
14021 TATACATAAT
14031 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
14048 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAA
14065 TTAAATT
1 TTAAATT
14072 AGAAATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:14096 original size:17 final size:17
Alignment explanation
Indices: 14017--14103 Score: 58
Period size: 17 Copynumber: 5.4 Consensus size: 17
14007 GTTGAAGTCC
14017 AATTTATACAT-AATTTA
1 AATTTAT-CATAAATTTA
** *
14034 AATTTATTTTAAAATTA
1 AATTTATCATAAATTTA
* **
14051 AGTTTATTTTAAATTTA
1 AATTTATCATAAATTTA
*
14068 AA--T-T-AGAAATTTA
1 AATTTATCATAAATTTA
*
14081 AATTTATCATAAATTTG
1 AATTTATCATAAATTTA
14098 AATTTA
1 AATTTA
14104 AAATATATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
15 2 0.04
16 2 0.04
17 41 0.75
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (17 bp):
AATTTATCATAAATTTA
Found at i:14881 original size:3 final size:3
Alignment explanation
Indices: 14868--14963 Score: 59
Period size: 3 Copynumber: 30.7 Consensus size: 3
14858 ACATTAACAT
* * **
14868 TAA TAAA TAA TAA TAA TAA TAA TGAC T-G TTT TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* * * * *
14914 TAA TAA TAA TAAA TGA CAT TAA TAA TAA CCAT TAA TAA TTAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA -TAA TAA TAA -TAA TAA TAA
14962 TA
1 TA
14964 TTTTAAGTTA
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
2 1 0.01
3 59 0.82
4 12 0.17
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:15839 original size:29 final size:30
Alignment explanation
Indices: 15797--15972 Score: 105
Period size: 29 Copynumber: 6.0 Consensus size: 30
15787 GGAGGTCCCT
15797 AAACTGTCCAAAAATTATA-TTTCAACCCC-
1 AAACT-TCCAAAAATTATATTTTCAACCCCA
* *
15826 AAACTTCCCCAAAATTATATTTTTAACCCCA
1 AAACTT-CCAAAAATTATATTTTCAACCCCA
* **
15857 AAACTTCCAAAAATTACCATTTT--ACCCTT
1 AAACTTCCAAAAATTA-TATTTTCAACCCCA
* ** ** ***
15886 AAACTTTCAAAAATTCCATTTTTGACCTTG
1 AAACTTCCAAAAATTATATTTTCAACCCCA
* * *
15916 AAACTTACAAAAATTATCATTTT-ATCGCC-
1 AAACTTCCAAAAATTAT-ATTTTCAACCCCA
* *
15945 AAACTTCAAAAAATTTTATTTT-AACCCC
1 AAACTTCCAAAAATTATATTTTCAACCCC
15973 GAATTTTCCC
Statistics
Matches: 117, Mismatches: 23, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
28 16 0.14
29 48 0.41
30 37 0.32
31 16 0.14
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.34
Consensus pattern (30 bp):
AAACTTCCAAAAATTATATTTTCAACCCCA
Found at i:15899 original size:59 final size:57
Alignment explanation
Indices: 15836--16000 Score: 154
Period size: 59 Copynumber: 2.8 Consensus size: 57
15826 AAACTTCCCC
*
15836 AAAATTATATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCCTTAAACTTTC-A
1 AAAATTATATTTTTAACCCCGAAACTTCCAAAAATTACCATTTTACCC--AAAC-TTCAA
** * ** * *
15895 AAAATTCCATTTTTGACCTTGAAACTTACAAAAATTATCATTTTATCGCCAAACTTCAA
1 AAAATTATATTTTTAACCCCGAAACTTCCAAAAATTACCATTTTA-C-CCAAACTTCAA
* ** **
15954 AAAATTTTA-TTTTAACCCCGAATTTTCCCGAAATTACCATTTTACCC
1 AAAATTATATTTTTAACCCCGAAACTTCCAAAAATTACCATTTTACCC
16001 CCGGATACCT
Statistics
Matches: 84, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
56 2 0.02
57 1 0.01
58 29 0.35
59 49 0.58
60 1 0.01
61 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (57 bp):
AAAATTATATTTTTAACCCCGAAACTTCCAAAAATTACCATTTTACCCAAACTTCAA
Found at i:19119 original size:18 final size:18
Alignment explanation
Indices: 19091--19134 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
19081 TTTTATTTTA
*
19091 AATATATAATTAATATATT
1 AATAAATAATTAA-ATATT
*
19110 -ATAAATAATTAAATTTT
1 AATAAATAATTAAATATT
19127 AATAAATA
1 AATAAATA
19135 GATTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAATAATTAAATATT
Found at i:20023 original size:20 final size:20
Alignment explanation
Indices: 19998--20056 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
19988 TTATATTCGT
19998 TTTATAATTTATATTTTA-AA
1 TTTATAA-TTATATTTTACAA
*
20018 TTTATAATTACTCTTTTAACAA
1 TTTATAATTA-TATTTT-ACAA
*
20040 TATATAATTATATTTTA
1 TTTATAATTATATTTTA
20057 TTTATAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.09
20 13 0.39
21 6 0.18
22 11 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATAATTATATTTTACAA
Found at i:24410 original size:29 final size:31
Alignment explanation
Indices: 24378--24440 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
24368 TAGATTTGCC
24378 TTTTAAAAATTTTAAAATTTACTTT-AATTT
1 TTTTAAAAATTTTAAAATTTACTTTAAATTT
* **
24408 TTTTAAAAA-TTTAAGATTTTTTTTAAATTT
1 TTTTAAAAATTTTAAAATTTACTTTAAATTT
24438 TTT
1 TTT
24441 AGAATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (31 bp):
TTTTAAAAATTTTAAAATTTACTTTAAATTT
Found at i:24441 original size:29 final size:30
Alignment explanation
Indices: 24378--24454 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
24368 TAGATTTGCC
*
24378 TTTTAAAAATTTTAAAATTTACTTTAATTT
1 TTTTAAAAATTTTAAAATTTACTTTAAATT
* **
24408 TTTTAAAAA-TTTAAGATTTTTTTTAAATT
1 TTTTAAAAATTTTAAAATTTACTTTAAATT
* *
24437 TTTT-AGAATTTTATAATT
1 TTTTAAAAATTTTAAAATT
24455 AGGATTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 3 0.08
29 27 0.69
30 9 0.23
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (30 bp):
TTTTAAAAATTTTAAAATTTACTTTAAATT
Found at i:24448 original size:20 final size:20
Alignment explanation
Indices: 24403--24448 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
24393 AATTTACTTT
24403 AATTTTTTTAAAAATTTAAG
1 AATTTTTTTAAAAATTTAAG
* ** *
24423 ATTTTTTTTAAATTTTTTAG
1 AATTTTTTTAAAAATTTAAG
24443 AATTTT
1 AATTTT
24449 ATAATTAGGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (20 bp):
AATTTTTTTAAAAATTTAAG
Found at i:24715 original size:31 final size:32
Alignment explanation
Indices: 24636--24716 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
24626 ATATTTAATT
*
24636 TTAAAAAATTGAGTGACTAAAATGAAAAAAAA
1 TTAAATAATTGAGTGACTAAAATGAAAAAAAA
* **
24668 TT-AATAATCGAGTGACTAAAAT-AAAATGAA
1 TTAAATAATTGAGTGACTAAAATGAAAAAAAA
24698 TTAAATAATTG-GATGACTA
1 TTAAATAATTGAG-TGACTA
24717 TTCTTGTACT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
30 9 0.21
31 31 0.74
32 2 0.05
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (32 bp):
TTAAATAATTGAGTGACTAAAATGAAAAAAAA
Found at i:30504 original size:31 final size:30
Alignment explanation
Indices: 30452--30520 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
30442 AAATAATATT
* *
30452 TCAATTACTAAATTTATGAAAAGTGATAAA
1 TCAATCACTAAATTTACGAAAAGTGATAAA
*
30482 TCAGTCACTAATATTTACGAAAAGTGATAAA
1 TCAATCACTAA-ATTTACGAAAAGTGATAAA
30513 TCAATCAC
1 TCAATCAC
30521 CCAAATTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.26
31 25 0.74
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.30
Consensus pattern (30 bp):
TCAATCACTAAATTTACGAAAAGTGATAAA
Found at i:30953 original size:96 final size:96
Alignment explanation
Indices: 30786--30980 Score: 345
Period size: 96 Copynumber: 2.0 Consensus size: 96
30776 AGGATTGAAA
30786 ATATTCGAAATTGGAGAATTATTGTAAAAATTTTCAACATTGCTAGAATGGTTAATAGAAGAGAA
1 ATATTCGAAATTGGAGAATTATTGTAAAAATTTTCAACATTGCTAGAATGGTTAATAGAAGAGAA
* *
30851 CTAGTCGAAGGTGTTCCATCGATTATAACGG
66 CCAGTCGAAGGTGTTCCATCGATTATAACAG
* *
30882 ATATTCGAAATTGGAGAATTATTGTGAAAATTTTCAACATTGCTATAATGGTTAATAGAAGAGAA
1 ATATTCGAAATTGGAGAATTATTGTAAAAATTTTCAACATTGCTAGAATGGTTAATAGAAGAGAA
*
30947 CCAGTCGAAGGTGTTCTATCGATTATAACAG
66 CCAGTCGAAGGTGTTCCATCGATTATAACAG
30978 ATA
1 ATA
30981 AATTTATTTT
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (96 bp):
ATATTCGAAATTGGAGAATTATTGTAAAAATTTTCAACATTGCTAGAATGGTTAATAGAAGAGAA
CCAGTCGAAGGTGTTCCATCGATTATAACAG
Found at i:32806 original size:15 final size:15
Alignment explanation
Indices: 32786--32814 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
32776 ATCCTATTAT
32786 ACTAGACAGAAAAAG
1 ACTAGACAGAAAAAG
32801 ACTAGACAGAAAAA
1 ACTAGACAGAAAAA
32815 ACAAACACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.14, G:0.17, T:0.07
Consensus pattern (15 bp):
ACTAGACAGAAAAAG
Found at i:34050 original size:51 final size:51
Alignment explanation
Indices: 33917--34095 Score: 207
Period size: 51 Copynumber: 3.5 Consensus size: 51
33907 TTTCATTTAA
* ** *
33917 TACTCACGATGACATATAGTCATCGGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACATTTAGTCATCGGACCT-TTAATCCATATAGG-ATTCATT
* * **
33970 TACTCACGATGACACTGAGTCATTAGACCTTTAATCCATCATA-GATTCATT
1 TACTCACGATGACATTTAGTCATCGGACCTTTAATCCAT-ATAGGATTCATT
* *
34021 TACTCACGATGACATTTAGCCATCGGACCTTTAATCCATAAAGGATTCATT
1 TACTCACGATGACATTTAGTCATCGGACCTTTAATCCATATAGGATTCATT
* * *
34072 TATTCACGATGGCACTTAGTCATC
1 TACTCACGATGACATTTAGTCATC
34096 AGATCTTTTC
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
50 2 0.02
51 68 0.64
52 8 0.08
53 28 0.26
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACATTTAGTCATCGGACCTTTAATCCATATAGGATTCATT
Found at i:38889 original size:29 final size:31
Alignment explanation
Indices: 38825--38893 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
38815 AATGGGCTCG
38825 AGTGACTGATTTGTCACTTTTTATAAATGTA
1 AGTGACTGATTTGTCACTTTTTATAAATGTA
* * *
38856 AGTGACTGCTTTGTTA-TTTTTA-AAA-GTTT
1 AGTGACTGATTTGTCACTTTTTATAAATG-TA
38885 AGTGACTGA
1 AGTGACTGA
38894 AATATAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 12 0.36
30 6 0.18
31 14 0.42
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.45
Consensus pattern (31 bp):
AGTGACTGATTTGTCACTTTTTATAAATGTA
Found at i:43122 original size:28 final size:28
Alignment explanation
Indices: 43082--43141 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
43072 TTTTTGTACC
* *
43082 AAATAAATTAATTGAAATTATAAACTAT
1 AAATAAATTAATTGAAATAACAAACTAT
* *
43110 AAATTAATTAATTGAAATAACAAATTAT
1 AAATAAATTAATTGAAATAACAAACTAT
43138 AAAT
1 AAAT
43142 CGACCTTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (28 bp):
AAATAAATTAATTGAAATAACAAACTAT
Found at i:46155 original size:13 final size:14
Alignment explanation
Indices: 46138--46179 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
46128 ATTTCAATTT
46138 TATTTTAATAATAA
1 TATTTTAATAATAA
*
46152 -ATTTTAAAAATAA
1 TATTTTAATAATAA
46165 TTATTTTAAATAATA
1 -TATTTT-AATAATA
46180 TTCTTCACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 12 0.52
15 5 0.22
16 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:46232 original size:15 final size:15
Alignment explanation
Indices: 46212--46268 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
46202 ATTCAATATT
46212 AATATTTTAATAATA
1 AATATTTTAATAATA
* *
46227 AATATTTATTACAATTAGA
1 AATA-TT-TT--AATAATA
*
46246 AATATATTAATAATA
1 AATATTTTAATAATA
46261 AATATTTT
1 AATATTTT
46269 GTAGTATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 16 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 9 0.28
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:46727 original size:14 final size:15
Alignment explanation
Indices: 46708--46738 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
46698 AAAAGAAAGT
46708 AAATTATTTTTC-AA
1 AAATTATTTTTCGAA
46722 AAATTATTTTTCGAA
1 AAATTATTTTTCGAA
46737 AA
1 AA
46739 CCATTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (15 bp):
AAATTATTTTTCGAA
Found at i:47343 original size:2 final size:2
Alignment explanation
Indices: 47336--47365 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47326 TGTAGCCTCT
47336 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
47366 NNNNNNNNNN
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:59227 original size:20 final size:20
Alignment explanation
Indices: 59195--59245 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
59185 GAAGCTTTCG
59195 TTTCCCT-TTTTTTTTCTTC
1 TTTCCCTCTTTTTTTTCTTC
* * *
59214 TTTCTCTCTTTTTTTTTTTN
1 TTTCCCTCTTTTTTTTCTTC
59234 TTTCCCTCTTTT
1 TTTCCCTCTTTT
59246 AGTTTATTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTCCCTCTTTTTTTTCTTC
Found at i:61620 original size:60 final size:61
Alignment explanation
Indices: 61515--61631 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 61
61505 GAGATTTTTC
* * * *
61515 AAAATTTTGAGGGTCTTAATTGAAATTTTCTAAAGCTTCAAGG-AAAAATAAAATTTTCCA
1 AAAATTTTGAGGGACCTAAATGAAATTTTCTAAAACTTCAAGGAAAAAATAAAATTTTCCA
* * * *
61575 AAAATTTTGAGGGACCTAAAT-AATTTTTTTAAAATTTCAAGGGAAAAAATCAAATTT
1 AAAATTTTGAGGGACCTAAATGAAATTTTCTAAAACTTCAA-GGAAAAAATAAAATTT
61632 CTCGAAATTG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
59 15 0.32
60 20 0.43
61 12 0.26
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.35
Consensus pattern (61 bp):
AAAATTTTGAGGGACCTAAATGAAATTTTCTAAAACTTCAAGGAAAAAATAAAATTTTCCA
Found at i:62852 original size:2 final size:2
Alignment explanation
Indices: 62845--62872 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62835 ACAGCTTAGT
62845 TA TA TA TA 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
62873 CACATATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65581 original size:2 final size:2
Alignment explanation
Indices: 65574--65601 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
65564 AGTTATAACA
65574 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
65602 GAACTCTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82413 original size:21 final size:19
Alignment explanation
Indices: 82381--82432 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
82371 GAATATAATG
* *
82381 AATCAGGTTTTTACCAGTTT
1 AATCTGGTTTTTACC-GGTT
82401 AATCTGGTCTTTTACCGGTT
1 AATCTGGT-TTTTACCGGTT
*
82421 AAACTGGTTTTT
1 AATCTGGTTTTT
82433 TATGGGTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 17 0.61
21 7 0.25
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.46
Consensus pattern (19 bp):
AATCTGGTTTTTACCGGTT
Found at i:84358 original size:32 final size:32
Alignment explanation
Indices: 84317--84379 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
84307 AACTGAAGTG
84317 GTGTTTCTTAACAAGTTGAGCCTGTATGAGTA
1 GTGTTTCTTAACAAGTTGAGCCTGTATGAGTA
**
84349 GTGTTTCTTAATGAGTTGAGCCTGTATGAGT
1 GTGTTTCTTAACAAGTTGAGCCTGTATGAGT
84380 GGCCCAGCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.40
Consensus pattern (32 bp):
GTGTTTCTTAACAAGTTGAGCCTGTATGAGTA
Found at i:93712 original size:31 final size:31
Alignment explanation
Indices: 93657--93723 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
93647 ATAAAACTCA
* * * *
93657 AAATTCAAAAATATAAATATTAAAATTGA-C
1 AAATTCAAAAATACAAAAACTAAAATTAATC
93687 AAATTCAAAAAATACAAAAACTAAAATTAATC
1 AAATTC-AAAAATACAAAAACTAAAATTAATC
93719 AAATT
1 AAATT
93724 AAGTATAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 6 0.19
31 19 0.61
32 6 0.19
ACGTcount: A:0.63, C:0.09, G:0.01, T:0.27
Consensus pattern (31 bp):
AAATTCAAAAATACAAAAACTAAAATTAATC
Found at i:99266 original size:13 final size:14
Alignment explanation
Indices: 99236--99275 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
99226 AATATACTGC
99236 AAATAAAAAAATTA
1 AAATAAAAAAATTA
*
99250 AAATGAAAAAATTA
1 AAATAAAAAAATTA
*
99264 AATTACAAAAAA
1 AAATA-AAAAAA
99276 GTGAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (14 bp):
AAATAAAAAAATTA
Found at i:110222 original size:3 final size:3
Alignment explanation
Indices: 110209--110257 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
110199 TTTCAATCTC
*
110209 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
110257 A
1 A
110258 TGACAATGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:116363 original size:2 final size:2
Alignment explanation
Indices: 116356--116389 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
116346 ACATCCTTAA
116356 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
116390 GCTATTATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:117105 original size:19 final size:19
Alignment explanation
Indices: 117081--117117 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
117071 ATCACATGGG
* *
117081 AAAAAATCAAAAATATTTT
1 AAAAAATAAAAAAAATTTT
117100 AAAAAATAAAAAAAATTT
1 AAAAAATAAAAAAAATTT
117118 ATATACAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAAATAAAAAAAATTTT
Found at i:117118 original size:18 final size:19
Alignment explanation
Indices: 117081--117118 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
117071 ATCACATGGG
* *
117081 AAAAAATCAAAAATATTTT
1 AAAAAATCAAAAAAAATTT
117100 AAAAAAT-AAAAAAAATTT
1 AAAAAATCAAAAAAAATTT
117118 A
1 A
117119 TATACAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAAATCAAAAAAAATTT
Found at i:117161 original size:18 final size:18
Alignment explanation
Indices: 117118--117162 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
117108 AAAAAAATTT
* *
117118 ATATACAATTTTTTAAAA
1 ATATAAAATTATTTAAAA
117136 ATAGTAAAATTATTTAAAA
1 ATA-TAAAATTATTTAAAA
*
117155 CTATAAAA
1 ATATAAAA
117163 ACAATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (18 bp):
ATATAAAATTATTTAAAA
Found at i:128220 original size:2 final size:2
Alignment explanation
Indices: 128213--128238 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
128203 TTCTTTTTGG
128213 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
128239 TTCAATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:137277 original size:19 final size:20
Alignment explanation
Indices: 137253--137299 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
137243 AAAATGTAAA
137253 AAAAATCCAGAAAATTCT-T
1 AAAAATCCAGAAAATTCTAT
*
137272 AAAAATCCAGAAGATTCTAT
1 AAAAATCCAGAAAATTCTAT
137292 AACAAATC
1 AA-AAATC
137300 GAAAAGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 17 0.68
20 3 0.12
21 5 0.20
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.23
Consensus pattern (20 bp):
AAAAATCCAGAAAATTCTAT
Found at i:140162 original size:9 final size:9
Alignment explanation
Indices: 140150--140211 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
140140 TTTTTTTACG
140150 ATTTTTATA
1 ATTTTTATA
140159 ATTTTTATTCA
1 ATTTTTA-T-A
* *
140170 AATTTAATA
1 ATTTTTATA
140179 ATTTTTATA
1 ATTTTTATA
* *
140188 ACTTTTATT
1 ATTTTTATA
* *
140197 TTTTTTATT
1 ATTTTTATA
140206 ATTTTT
1 ATTTTT
140212 TTTGCTACAT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
9 34 0.81
10 2 0.05
11 6 0.14
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTTTATA
Done.