Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005591.1 Hibiscus syriacus cultivar Beakdansim tig00012985_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: 182235
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2213 original size:26 final size:27
Alignment explanation
Indices: 2177--2227 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2167 CCAGTCGACC
*
2177 TGAGTCAACTC-ATGAGTCTACCCGAT
1 TGAGTCAACTCAATGAGTCAACCCGAT
2203 TGAGTCAACTCAATGAGTCAACCCG
1 TGAGTCAACTCAATGAGTCAACCCG
2228 TGACTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (27 bp):
TGAGTCAACTCAATGAGTCAACCCGAT
Found at i:2221 original size:13 final size:13
Alignment explanation
Indices: 2177--2224 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
2167 CCAGTCGACC
2177 TGAGTCAACTC-A
1 TGAGTCAACTCAA
* * *
2189 TGAGTCTACCCGAT
1 TGAGTCAACTC-AA
2203 TGAGTCAACTCAA
1 TGAGTCAACTCAA
2216 TGAGTCAAC
1 TGAGTCAAC
2225 CCGTGACTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 9 0.32
13 10 0.36
14 9 0.32
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (13 bp):
TGAGTCAACTCAA
Found at i:4613 original size:218 final size:217
Alignment explanation
Indices: 4071--4724 Score: 1226
Period size: 218 Copynumber: 3.0 Consensus size: 217
4061 ATATGTGCTC
4071 TTTGGTTACCTGTTTTCACTGGAAATATAATCATTCATGATTTATGGATCATGGAATCAACTATT
1 TTTGGTTACCTGTTTTCACTGGAAATATAATCATTCATGATTTATGGATCATGGAATCAACTATT
*
4136 TACTATATGAACCGATTATTAGAATATTGTCTAGGTAGGATTTTGGAGTATGAAGGTTCAACTCT
66 TACTATATGAACCGATTATTAGAATATTGTCTAGGTAGGATTTTGGAGTATGGAGGTTCAACTCT
*
4201 GATCAAGTTTGTAATTCCTTACAGACCTAAGGTATTCCTTGGGTAGGCTCTAAGGCCCCAAGGCA
131 GATCAAGTTTGTAATTCCTTACAAACCTAAGGTATTCCTTGGGTAGGCTCTAAGGCCCCAAGGCA
*
4266 CTCCC-TAGTGTGGGAC--TAT
196 CTCCCTTAGTATGGGACTATAT
4285 TTTGGTTACCTGTTTTCACTGGAAA-ATAATCATTCATGATTTATGGATCATGGAATCAACTATT
1 TTTGGTTACCTGTTTTCACTGGAAATATAATCATTCATGATTTATGGATCATGGAATCAACTATT
4349 TACTATATGAACCGATTATTAGAATATTGTCTAGGTAGGATTTTGGAGTATGGAGGTTCAACTCT
66 TACTATATGAACCGATTATTAGAATATTGTCTAGGTAGGATTTTGGAGTATGGAGGTTCAACTCT
4414 GATCAAGTTTGTAATTCCTTACAAACCTAAGGTATTCCTTGGGTAGGCTCTAAGGCCCCAAGGCA
131 GATCAAGTTTGTAATTCCTTACAAACCTAAGGTATTCCTTGGGTAGGCTCTAAGGCCCCAAGGCA
4479 CTCCCTTAGTATGGGACTATAT
196 CTCCCTTAGTATGGGACTATAT
*
4501 TTTGGATACCTGTTTTCACTGGAAAATATAATCATTCATGATTTATGGATCATGGAATCAACTAT
1 TTTGGTTACCTGTTTTCACTGG-AAATATAATCATTCATGATTTATGGATCATGGAATCAACTAT
*
4566 TTACTATATGAACCGATTATTAGAATATTGTCTAGGTAGGATTTTGGAGTATGGAGGTTTAACTC
65 TTACTATATGAACCGATTATTAGAATATTGTCTAGGTAGGATTTTGGAGTATGGAGGTTCAACTC
4631 TGATCAAGTTTGTAATTCCTTACAAACCTAAGGTATTCCTTGGGTAGGCTCTAAGGCCCCAAGGC
130 TGATCAAGTTTGTAATTCCTTACAAACCTAAGGTATTCCTTGGGTAGGCTCTAAGGCCCCAAGGC
4696 ACTCCCTTAGTATGGGACTATAT
195 ACTCCCTTAGTATGGGACTATAT
4719 TTTGGT
1 TTTGGT
4725 GTACAGATGG
Statistics
Matches: 429, Mismatches: 6, Indels: 6
0.97 0.01 0.01
Matches are distributed among these distances:
213 172 0.40
214 35 0.08
216 24 0.06
217 3 0.01
218 195 0.45
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (217 bp):
TTTGGTTACCTGTTTTCACTGGAAATATAATCATTCATGATTTATGGATCATGGAATCAACTATT
TACTATATGAACCGATTATTAGAATATTGTCTAGGTAGGATTTTGGAGTATGGAGGTTCAACTCT
GATCAAGTTTGTAATTCCTTACAAACCTAAGGTATTCCTTGGGTAGGCTCTAAGGCCCCAAGGCA
CTCCCTTAGTATGGGACTATAT
Found at i:5804 original size:20 final size:20
Alignment explanation
Indices: 5779--5818 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5769 TAAAAAAATA
5779 AAAATTCATA-ATTTATTTTT
1 AAAATT-ATAGATTTATTTTT
*
5799 AAAATTATAGTTTTATTTTT
1 AAAATTATAGATTTATTTTT
5819 TCTTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
AAAATTATAGATTTATTTTT
Found at i:13348 original size:27 final size:27
Alignment explanation
Indices: 13313--13375 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
13303 ACACAAATAC
13313 AAAATTTTAATTAAAGGATGGACTAAT
1 AAAATTTTAATTAAAGGATGGACTAAT
13340 AAAATTTTAATTAAAGGATGGACTAAT
1 AAAATTTTAATTAAAGGATGGACTAAT
13367 AAAATTTTA
1 AAAATTTTA
13376 TGATAAAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.35
Consensus pattern (27 bp):
AAAATTTTAATTAAAGGATGGACTAAT
Found at i:15561 original size:2 final size:2
Alignment explanation
Indices: 15554--15592 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
15544 TCTTTCACTT
15554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15593 CTTAATAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19331 original size:15 final size:15
Alignment explanation
Indices: 19313--19360 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
19303 AAATAATATA
19313 TTAAAATTTTAATTT
1 TTAAAATTTTAATTT
*
19328 TTAAAA-TTTAATTA
1 TTAAAATTTTAATTT
* *
19342 TTAATAATATTAATAT
1 TTAA-AATTTTAATTT
19358 TTA
1 TTA
19361 TATGTTATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 8 0.30
16 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAAAATTTTAATTT
Found at i:27962 original size:55 final size:55
Alignment explanation
Indices: 27896--28003 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 55
27886 GCGTTCAGAT
*
27896 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAACCTAATTGAAGAAC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTAATTGAAGAAC
*
27951 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGA
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTAATTGAAGA
28004 CTGATCCACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (55 bp):
GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTAATTGAAGAAC
Found at i:28018 original size:55 final size:55
Alignment explanation
Indices: 27904--28026 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 55
27894 ATGATTCATG
* * **
27904 AAGAAGGACATCCGATGAATGAAGAAATTTGAACCTAATTGAAGAACGATTCATG
1 AAGAAGGACATCCGATGAATGAAGAAATTTGAAACTAATTGAAGAACGATCCACA
*
27959 AAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAG-ACTGATCCACA
1 AAGAAGGACATCCGATGAATGAAGAAATTTGAAACTAATTGAAGAAC-GATCCACA
*
28014 AAGAAAGACATCC
1 AAGAAGGACATCC
28027 TGAAGATGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
54 2 0.03
55 59 0.97
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.20
Consensus pattern (55 bp):
AAGAAGGACATCCGATGAATGAAGAAATTTGAAACTAATTGAAGAACGATCCACA
Found at i:28804 original size:72 final size:72
Alignment explanation
Indices: 28687--28837 Score: 266
Period size: 72 Copynumber: 2.1 Consensus size: 72
28677 CCCTATTACA
* * *
28687 CAAGAAAATATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAGTCAATGTGATGATAGC
1 CAAGAACATATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
28752 AAATGAT
66 AAATGAT
28759 CAAGAACATATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
1 CAAGAACATATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
*
28824 AACTGAT
66 AAATGAT
28831 CAAGAAC
1 CAAGAAC
28838 CTGTTAGGGG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 75 1.00
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (72 bp):
CAAGAACATATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
AAATGAT
Found at i:32491 original size:125 final size:125
Alignment explanation
Indices: 32254--32495 Score: 342
Period size: 125 Copynumber: 1.9 Consensus size: 125
32244 ATTGGGGCAT
**
32254 GACTAAACCCACATCATGTTGAGATGACAAGATTTGGACCAAGAAGTCATGAAGAATGAGCCTTA
1 GACTAAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGTCATGAAGAATGAGCCTTA
* * *
32319 CAAATTGAGATGATGGGGCATTTTGAAGGCCCGTACCAGTATGAGATAATGTCGGGGTAC
66 CAAATTGAGATGATGGAGCATTTTGAAGGCCCGTACCAGAATAAGATAATGTCGGGGTAC
* * *
32379 GACTGAACCCACATCATGTTGAGATGATAAGGTTCAGACCAAGAAGTCATTGAA-AATGAGCCTT
1 GACTAAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGTCA-TGAAGAATGAGCCTT
* * * * * *
32443 ATAATTTGAGGTGTTGGAGCATTTTGAAGGCTCGTACCTGAATAAGATAATGT
65 ACAAATTGAGATGATGGAGCATTTTGAAGGCCCGTACCAGAATAAGATAATGT
32496 TGCGGCATTA
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
125 98 0.96
126 4 0.04
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (125 bp):
GACTAAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGTCATGAAGAATGAGCCTTA
CAAATTGAGATGATGGAGCATTTTGAAGGCCCGTACCAGAATAAGATAATGTCGGGGTAC
Found at i:33745 original size:37 final size:37
Alignment explanation
Indices: 33693--33806 Score: 167
Period size: 37 Copynumber: 3.1 Consensus size: 37
33683 AAAGTCAAGT
*
33693 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
* *
33730 CTTCACCAAATAGTAGTGAAGCAAA-CCATCTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
* * *
33766 CTTCACCGAAGAGTAGTGAAGCATATCCTTTTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
33803 CTTC
1 CTTC
33807 TCAGAAGAGT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 31 0.46
37 37 0.54
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (37 bp):
CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
Found at i:33781 original size:36 final size:36
Alignment explanation
Indices: 33693--33832 Score: 149
Period size: 37 Copynumber: 3.8 Consensus size: 36
33683 AAAGTCAAGT
* *
33693 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAA-CCATCTTAAGC
*
33730 CTTCACCAAATAGTAGTGAAGCAAACCATCTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAACCATCTTAAGC
* * * *
33766 CTTCACCGAAGAGTAGTGAAGCATATCCTTTTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCA-AACCATCTTAAGC
* *
33803 CTTC-TCAGAAGAGT-GTTGGAGCAAACCATC
1 CTTCACCA-AAGAGTAG-TGAAGCAAACCATC
33833 AGACTATCAG
Statistics
Matches: 86, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
36 36 0.42
37 50 0.58
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (36 bp):
CTTCACCAAAGAGTAGTGAAGCAAACCATCTTAAGC
Found at i:33826 original size:73 final size:73
Alignment explanation
Indices: 33693--33832 Score: 185
Period size: 73 Copynumber: 1.9 Consensus size: 73
33683 AAAGTCAAGT
* *
33693 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTGAGCCTTCACCAAATAGTAGTGAAGCAAACCA
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCACCAAAGAGTAGTGAAGCAAACCA
33758 TCTTAAGC
66 TCTTAAGC
* * * * *
33766 CTTCACCGAAGAGTAGTGAAGCATATCCTTTTTAAGCCTTC-TCAGAAGAGT-GTTGGAGCAAAC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCACCA-AAGAGTAG-TGAAGCAAAC
33829 CATC
64 CATC
33833 AGACTATCAG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
72 3 0.05
73 55 0.95
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (73 bp):
CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCACCAAAGAGTAGTGAAGCAAACCA
TCTTAAGC
Found at i:34723 original size:54 final size:54
Alignment explanation
Indices: 34192--34704 Score: 882
Period size: 54 Copynumber: 9.5 Consensus size: 54
34182 GTAGTAAAGC
*
34192 AGAAGAAGATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
34246 AAAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
34300 AGAAGAAGATGTTCGAGTTACATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
34354 AAAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
34408 AAAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * *
34462 AGAAGAAGATATTCGAGTTCCATACTCCCTAGAGAAAGAGTGAGCGAACCTGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
34516 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * *
34570 AGAAGAAGATGCTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAATCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
34624 AGAAGAAGATGTTCGAGTTCCATACTCCGTAGATAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
34678 AGAAGAAGATGTTTGAGTTCCATACTC
1 AGAAGAAGATGTTCGAGTTCCATACTC
34705 TCTGAAGCAA
Statistics
Matches: 433, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 433 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
Found at i:34852 original size:106 final size:106
Alignment explanation
Indices: 34699--35100 Score: 425
Period size: 106 Copynumber: 3.8 Consensus size: 106
34689 TTTGAGTTCC
* * * * *
34699 ATACTCTCTGAAGCAATAGGGAGCGGACACATTTTATTGAAGA----TCGAGTCCTATACTCTCT
1 ATACTCTCTGAAGGAATAGGGAGCAGACA-AGTTTGTTGAAGATTGTTCGAGTCCTATACTCCCT
* * *
34760 GAAGGAATAGAGAGCGGACCCGTTTGCTGAATATCGAGTCCT
65 GAAGGAATAGAGAGCGGACACGTTTGTTGAATATCGAGTCTT
* *
34802 ATACTCTCTGAAGGAATAGGGAGCAGACAAGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTG
1 ATACTCTCTGAAGGAATAGGGAGCAGACAAGTTTGTTGAAGATTGTTCGAGTCCTATACTCCCTG
* *
34867 AAGGAATAGAGAGCGGACACGTTTATTGAAGATCGAGTCTT
66 AAGGAATAGAGAGCGGACACGTTTGTTGAATATCGAGTCTT
* ** * *
34908 ATACTCTCTGAAGGAATAGGGAGCAAACCCGTTTGTTGAAGATTATTCGAGTCTTATACTCCCTG
1 ATACTCTCTGAAGGAATAGGGAGCAGACAAGTTTGTTGAAGATTGTTCGAGTCCTATACTCCCTG
* * * *
34973 AAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTTGAGTCTT
66 AAGGAATAGAGAGCGGACACGTTTGTTG-A-A-T-ATCGAGTCTT
* * * * ** * * * *
35018 ATACTCCCTGAATGAATAGGGAACAGACACGTTTGCCGAAGATTGTCCGAGTCTTATAATCCCTA
1 ATACTCTCTGAAGGAATAGGGAGCAGACAAGTTTGTTGAAGATTGTTCGAGTCCTATACTCCCTG
* * *
35083 AAAGAATAGGGAGTGGAC
66 AAGGAATAGAGAGCGGAC
35101 CCGTCATTTG
Statistics
Matches: 254, Mismatches: 37, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
102 11 0.04
103 27 0.11
106 137 0.54
107 1 0.00
108 1 0.00
110 77 0.30
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (106 bp):
ATACTCTCTGAAGGAATAGGGAGCAGACAAGTTTGTTGAAGATTGTTCGAGTCCTATACTCCCTG
AAGGAATAGAGAGCGGACACGTTTGTTGAATATCGAGTCTT
Found at i:34871 original size:55 final size:54
Alignment explanation
Indices: 34682--35095 Score: 400
Period size: 55 Copynumber: 7.7 Consensus size: 54
34672 CCCGTAAGAA
* * * * * *
34682 GAAGATGTTTGAGT-TCCATACTCTCTGAAGCAATAGGGAGCGGACACATTTTATT
1 GAAGATGTTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCAGACAC-GTTTGTT
* * * * *
34737 GAAGA---TCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGCT
1 GAAGATGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTT
* * *
34788 G-A-AT-ATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACAAGTTTGTT
1 GAAGATGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTT
* * *
34839 GAAGATTGTTCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTATT
1 GAAGA-TGTTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTT
* *
34894 GAAGA---TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAAACCCGTTTGTT
1 GAAGATGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTT
* *
34945 GAAGATTATTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTGTT
1 GAAGA-TGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTT
* * * * **
35000 GAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAACAGACACGTTTGCC
1 GAAGA-TGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTT
* * * * *
35055 GAAGATTGTCCGAGTCTTATAATCCCTAAAAGAATAGGGAG
1 GAAGA-TGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAG
35096 TGGACCCGTC
Statistics
Matches: 306, Mismatches: 40, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
49 1 0.00
50 1 0.00
51 91 0.30
52 34 0.11
53 1 0.00
54 1 0.00
55 177 0.58
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (54 bp):
GAAGATGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTT
Found at i:46430 original size:20 final size:19
Alignment explanation
Indices: 46407--46445 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
46397 TTTTATTTAA
46407 AATAAAAAAATATAATTTTT
1 AATAAAAAAATA-AATTTTT
*
46427 AATAAAAAATTAAATTTTT
1 AATAAAAAAATAAATTTTT
46446 CTCAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAAAAAAATAAATTTTT
Found at i:55943 original size:35 final size:36
Alignment explanation
Indices: 55876--55947 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
55866 CATATCTCTT
55876 TTGATTGTCATTTTGATAAAGGAAAAGAAAGGAAGA
1 TTGATTGTCATTTTGATAAAGGAAAAGAAAGGAAGA
*
55912 TTGATTGAT-ATTTTGGTAAA-GAAAAGAAAGGAAGA
1 TTGATTG-TCATTTTGATAAAGGAAAAGAAAGGAAGA
55947 T
1 T
55948 GGAGCAAGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 16 0.47
36 17 0.50
37 1 0.03
ACGTcount: A:0.44, C:0.01, G:0.25, T:0.29
Consensus pattern (36 bp):
TTGATTGTCATTTTGATAAAGGAAAAGAAAGGAAGA
Found at i:56463 original size:34 final size:32
Alignment explanation
Indices: 56425--56515 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
56415 AATTACAACT
* *
56425 TCTCTCGATCTAACAAGGGGAAAACAATAACAAA
1 TCTCTCGA--TAAAAAGGAGAAAACAATAACAAA
* *
56459 TCTCTTGATAAAAAGGAGAAAACAATAACAAT
1 TCTCTCGATAAAAAGGAGAAAACAATAACAAA
*
56491 TCTCTTGATAAAAAGGAGAAAACAA
1 TCTCTCGATAAAAAGGAGAAAACAA
56516 CTCTAAAACT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 46 0.87
34 7 0.13
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.20
Consensus pattern (32 bp):
TCTCTCGATAAAAAGGAGAAAACAATAACAAA
Found at i:56480 original size:32 final size:32
Alignment explanation
Indices: 56439--56515 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
56429 TCGATCTAAC
*
56439 AAGGGGAAAACAATAACAAATCTCTTGATAAA
1 AAGGAGAAAACAATAACAAATCTCTTGATAAA
*
56471 AAGGAGAAAACAATAACAATTCTCTTGATAAA
1 AAGGAGAAAACAATAACAAATCTCTTGATAAA
56503 AAGGAGAAAACAA
1 AAGGAGAAAACAA
56516 CTCTAAAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.17
Consensus pattern (32 bp):
AAGGAGAAAACAATAACAAATCTCTTGATAAA
Found at i:63636 original size:18 final size:18
Alignment explanation
Indices: 63613--63647 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
63603 ATGATAGTCA
63613 CCTCTACATAAGCTTGAC
1 CCTCTACATAAGCTTGAC
* *
63631 CCTCTACCTAAGTTTGA
1 CCTCTACATAAGCTTGA
63648 GCTCTAGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.11, T:0.31
Consensus pattern (18 bp):
CCTCTACATAAGCTTGAC
Found at i:64432 original size:30 final size:31
Alignment explanation
Indices: 64396--64471 Score: 127
Period size: 30 Copynumber: 2.5 Consensus size: 31
64386 AATGAATAAT
64396 AGCTTAGCAAAGCTATTAGAGAG-AGGGTAA
1 AGCTTAGCAAAGCTATTAGAGAGAAGGGTAA
*
64426 AGCTTAGCAAAGCTATTAGAGAGAAAGGGTGA
1 AGCTTAGCAAAGCTATTAGAGAG-AAGGGTAA
64458 AGCTTAGCAAAGCT
1 AGCTTAGCAAAGCT
64472 TAGAATAGCG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
30 23 0.53
32 20 0.47
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (31 bp):
AGCTTAGCAAAGCTATTAGAGAGAAGGGTAA
Found at i:65575 original size:30 final size:31
Alignment explanation
Indices: 65539--65614 Score: 136
Period size: 30 Copynumber: 2.5 Consensus size: 31
65529 AATGAATAAT
65539 AGCTTAGCAAAGCTATTAGAGAG-AGGGTAA
1 AGCTTAGCAAAGCTATTAGAGAGAAGGGTAA
65569 AGCTTAGCAAAGCTATTAGAGAGAAAGGGTAA
1 AGCTTAGCAAAGCTATTAGAGAG-AAGGGTAA
65601 AGCTTAGCAAAGCT
1 AGCTTAGCAAAGCT
65615 TAGAATAGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 23 0.52
32 21 0.48
ACGTcount: A:0.41, C:0.12, G:0.28, T:0.20
Consensus pattern (31 bp):
AGCTTAGCAAAGCTATTAGAGAGAAGGGTAA
Found at i:66504 original size:35 final size:35
Alignment explanation
Indices: 66440--66517 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
66430 TCGTAAACGC
66440 TAAATGAA-CAAACATGAAAACCTTCAAAAATAAA
1 TAAATGAACCAAACATGAAAACCTTCAAAAATAAA
* * *
66474 TAAACGAACCAAACATTAACACCGTT-AAAAATAAA
1 TAAATGAACCAAACATGAAAACC-TTCAAAAATAAA
*
66509 CAAATGAAC
1 TAAATGAAC
66518 ATACCCTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 7 0.19
35 28 0.76
36 2 0.05
ACGTcount: A:0.59, C:0.18, G:0.06, T:0.17
Consensus pattern (35 bp):
TAAATGAACCAAACATGAAAACCTTCAAAAATAAA
Found at i:68270 original size:31 final size:32
Alignment explanation
Indices: 68203--68270 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
68193 CTTTCAAAAG
* * *
68203 TTACACAATGGTCATTAAATTTTATAGAACTA
1 TTACAAAATGATCATTAAATATTATAGAACTA
* *
68235 TTACAAAATGATCATTAAA-ATTATTGAACTT
1 TTACAAAATGATCATTAAATATTATAGAACTA
68266 TTACA
1 TTACA
68271 CTTATTATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (32 bp):
TTACAAAATGATCATTAAATATTATAGAACTA
Found at i:69281 original size:8 final size:8
Alignment explanation
Indices: 69268--69302 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
69258 AGTAATAAAC
69268 AGAGAGGG
1 AGAGAGGG
69276 AGAGAGGG
1 AGAGAGGG
*
69284 AGGGAGGG
1 AGAGAGGG
*
69292 AGGGAGGG
1 AGAGAGGG
69300 AGA
1 AGA
69303 ACTTGGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (8 bp):
AGAGAGGG
Found at i:69288 original size:4 final size:4
Alignment explanation
Indices: 69271--69301 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
69261 AATAAACAGA
*
69271 GAGG GAGA GAGG GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG
69302 AACTTGGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.71, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:75957 original size:35 final size:35
Alignment explanation
Indices: 75918--75986 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
75908 AAATTAGGGT
* * * *
75918 AAAATACTTTAATTATATTCTAAACCTCAAATTCC
1 AAAATACTTCAATTACATGCTAAACCCCAAATTCC
*
75953 AAAATACTTCAATTACATGCTCAACCCCAAATTC
1 AAAATACTTCAATTACATGCTAAACCCCAAATTC
75987 ATAGTTCATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.42, C:0.25, G:0.01, T:0.32
Consensus pattern (35 bp):
AAAATACTTCAATTACATGCTAAACCCCAAATTCC
Found at i:76744 original size:35 final size:35
Alignment explanation
Indices: 76687--76780 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 35
76677 CACAGTCATT
*
76687 AATTACATTCTCAACCCAAAATTCCAAAATACTTC
1 AATTACATTCTAAACCCAAAATTCCAAAATACTTC
* * *
76722 AATTATATTCTAAACCTC-AAATTCTAAAATATTTC
1 AATTACATTCTAAACC-CAAAATTCCAAAATACTTC
* * *
76757 AATTACATGCTCAACCCTAAATTC
1 AATTACATTCTAAACCCAAAATTC
76781 ATAGTTAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 1 0.02
35 48 0.96
36 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.01, T:0.33
Consensus pattern (35 bp):
AATTACATTCTAAACCCAAAATTCCAAAATACTTC
Found at i:77847 original size:12 final size:12
Alignment explanation
Indices: 77832--77862 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
77822 TGCAATTTTA
77832 AAAATAATAAAT
1 AAAATAATAAAT
77844 AAAAT-ATAAAT
1 AAAATAATAAAT
77855 AAAATAAT
1 AAAATAAT
77863 GGATAGATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:78023 original size:20 final size:20
Alignment explanation
Indices: 77994--78039 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
77984 AGCCTGAGCC
*
77994 ATAAAACAACAATACATAGT
1 ATAAATCAACAATACATAGT
78014 ATAAATCAACAATACATAGT
1 ATAAATCAACAATACATAGT
78034 ATAAAT
1 ATAAAT
78040 TAAAATATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.59, C:0.13, G:0.04, T:0.24
Consensus pattern (20 bp):
ATAAATCAACAATACATAGT
Found at i:79398 original size:227 final size:229
Alignment explanation
Indices: 78719--79431 Score: 1326
Period size: 229 Copynumber: 3.1 Consensus size: 229
78709 GTAAATTATC
* * * *
78719 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAATATATTTATTATTATCTTTAG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
*
78783 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
66 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
78848 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAGAATT
131 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAGAATT
78913 GAAACATAAATTACATAACTTTCAAAAAAGTATA
196 GAAACATAAATTACATAACTTTCAAAAAAGTATA
78947 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
79012 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
66 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
79077 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAGAATT
131 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAGAATT
79142 GAAACATAAATTACATAACTTTC-AAAAAGTATA
196 GAAACATAAATTACATAACTTTCAAAAAAGTATA
79175 TATCA-TTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
*
79239 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAATAATCAAATAA-TTT
66 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
* *
79303 TTGTGTAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACAGTATTAAAAGAATT
131 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAGAATT
79368 GAAACATAAATTACATAACTTTCAAAAAAGTATA
196 GAAACATAAATTACATAACTTTCAAAAAAGTATA
79402 TATCATTTTTATAAAAGTGTCCATACTTAT
1 TATCATTTTTATAAAAGTGTCCATACTTAT
79432 AAAAGTAGGT
Statistics
Matches: 474, Mismatches: 8, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
226 89 0.19
227 134 0.28
228 75 0.16
229 176 0.37
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (229 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAGAATT
GAAACATAAATTACATAACTTTCAAAAAAGTATA
Found at i:79740 original size:19 final size:19
Alignment explanation
Indices: 79694--79752 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
79684 TGTATCGATC
* *
79694 CAAAACGATATACCAGGTAA
1 CAAAATGATAAACC-GGTAA
79714 -AAATATGATAAACCGGTAA
1 CAAA-ATGATAAACCGGTAA
79733 CAAAATGATAAAACCGGTAA
1 CAAAATGAT-AAACCGGTAA
79753 AACGTTACCG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.17
Consensus pattern (19 bp):
CAAAATGATAAACCGGTAA
Found at i:79748 original size:20 final size:19
Alignment explanation
Indices: 79709--79754 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
79699 CGATATACCA
79709 GGTAAAAATATGATAAACC
1 GGTAAAAATATGATAAACC
79728 GGTAACAAA-ATGATAAAACC
1 GGTAA-AAATATGAT-AAACC
79748 GGTAAAA
1 GGTAAAA
79755 CGTTACCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAATATGATAAACC
Found at i:79928 original size:180 final size:180
Alignment explanation
Indices: 79498--79966 Score: 676
Period size: 180 Copynumber: 2.6 Consensus size: 180
79488 GATCCAAATT
* * * *
79498 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTAGGACAAAACCGGTAT-AGAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCA-AAATGAT
* * * *
79562 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACG-TACCGGATATATTTAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * *
79627 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTT
129 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTA
* *
79679 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGAT-AAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
79743 AAACCGGTAAAACGTTACCGGATATA-TAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACG-TACCGGATATATTTAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
79806 GTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTAA
130 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTT-A
* * *
79858 AAAAATATATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
79923 AAACCGGTAAAATGTACCGGATATATTTAAAGTGTCGATACTTT
66 AAACCGGTAAAACGTACCGGATATATTTAAAGTGTCGATACTTT
79967 CGTAAGTACG
Statistics
Matches: 258, Mismatches: 26, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
178 63 0.24
179 67 0.26
180 88 0.34
181 40 0.16
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (180 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGTACCGGATATATTTAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTA
Found at i:82640 original size:17 final size:18
Alignment explanation
Indices: 82618--82651 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
82608 TCAGCCGGTT
82618 CGGTTC-GAACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
82635 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
82652 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Found at i:83278 original size:60 final size:60
Alignment explanation
Indices: 83155--83329 Score: 187
Period size: 60 Copynumber: 2.9 Consensus size: 60
83145 AATATGATTC
* * * * * * *
83155 TCATTCTAAATTAG--ATCATAA-TTTTTAAATATTTTAATTTTATCCTTAAACTATGACTA
1 TCATTCTAAATTAGTCCTCA-AACTTTTTGAACATTTCAATTTCATCC-CAAACTATAACTA
* * * * *
83214 TCATTCTAACTTAGTCTTTAAAC-TTTTGGACATTTCAATTTCATCCCCAAACTATAACTT
1 TCATTCTAAATTAGTCCTCAAACTTTTTGAACATTTCAATTTCAT-CCCAAACTATAACTA
83274 TCATTCTAAATTAGTCCTCAAACTTTTTGAACATTTCAATTTCATCCCAAACTATA
1 TCATTCTAAATTAGTCCTCAAACTTTTTGAACATTTCAATTTCATCCCAAACTATA
83330 CGTATATACT
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
59 13 0.14
60 59 0.61
61 24 0.25
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCTCAAACTTTTTGAACATTTCAATTTCATCCCAAACTATAACTA
Found at i:83782 original size:16 final size:16
Alignment explanation
Indices: 83763--83795 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
83753 CAATTAATTC
83763 AAATGGAGTATTATAG
1 AAATGGAGTATTATAG
83779 AAATGGAGTATTATAG
1 AAATGGAGTATTATAG
83795 A
1 A
83796 GATCTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (16 bp):
AAATGGAGTATTATAG
Found at i:88060 original size:45 final size:47
Alignment explanation
Indices: 87987--88074 Score: 135
Period size: 45 Copynumber: 1.9 Consensus size: 47
87977 TTATTTTTCG
* *
87987 TTTTTTGAATAAATGCATGCGAACTAGATATCATGTGGTTAGGTTTA
1 TTTTTCGAATAAATGCATGCAAACTAGATATCATGTGGTTAGGTTTA
*
88034 TTTTTCGAAT-AA-GCATGCAAATTAGATATCATGTGGTTAGG
1 TTTTTCGAATAAATGCATGCAAACTAGATATCATGTGGTTAGG
88075 GTTTTTATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 27 0.71
46 2 0.05
47 9 0.24
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.39
Consensus pattern (47 bp):
TTTTTCGAATAAATGCATGCAAACTAGATATCATGTGGTTAGGTTTA
Found at i:90500 original size:9 final size:8
Alignment explanation
Indices: 90485--90511 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
90475 TTGCATATGC
90485 ATTTTTTT
1 ATTTTTTT
90493 ATTTTTTT
1 ATTTTTTT
90501 ATTTTTTT
1 ATTTTTTT
90509 ATT
1 ATT
90512 ATTTGTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
ATTTTTTT
Found at i:94454 original size:7 final size:8
Alignment explanation
Indices: 94433--94505 Score: 56
Period size: 8 Copynumber: 10.1 Consensus size: 8
94423 TGAAGAAGAG
94433 ATGAAAAA
1 ATGAAAAA
94441 ATG--AAA
1 ATGAAAAA
94447 A-GAAAAA
1 ATGAAAAA
94454 ATG---AA
1 ATGAAAAA
94459 ATGAAAAA
1 ATGAAAAA
*
94467 GTGAAAAA
1 ATGAAAAA
*
94475 A-GAAGAA
1 ATGAAAAA
94482 A-GAGAAAA
1 ATGA-AAAA
94490 ATG-AAAA
1 ATGAAAAA
94497 ATGAAAAA
1 ATGAAAAA
94505 A
1 A
94506 ATAAAATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
5 6 0.12
6 4 0.08
7 19 0.37
8 22 0.42
9 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.10
Consensus pattern (8 bp):
ATGAAAAA
Found at i:94496 original size:6 final size:7
Alignment explanation
Indices: 94437--94504 Score: 54
Period size: 7 Copynumber: 9.7 Consensus size: 7
94427 GAAGAGATGA
94437 AAAAATG
1 AAAAATG
94444 -AAAA-G
1 AAAAATG
94449 AAAAAATG
1 -AAAAATG
94457 --AAATG
1 AAAAATG
94462 AAAAAGTG
1 AAAAA-TG
*
94470 AAAAAAG
1 AAAAATG
*
94477 AAGAAAGAG
1 AA-AAA-TG
94486 AAAAATG
1 AAAAATG
94493 AAAAATG
1 AAAAATG
94500 AAAAA
1 AAAAA
94505 AATAAAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
5 6 0.12
6 4 0.08
7 23 0.45
8 14 0.27
9 4 0.08
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (7 bp):
AAAAATG
Found at i:94503 original size:13 final size:12
Alignment explanation
Indices: 94437--94496 Score: 61
Period size: 13 Copynumber: 4.9 Consensus size: 12
94427 GAAGAGATGA
94437 AAAAATGAAAAG
1 AAAAATGAAAAG
*
94449 AAAAAATGAAATG
1 -AAAAATGAAAAG
94462 AAAAAGTGAAAA-
1 AAAAA-TGAAAAG
*
94474 AAGAA-GAAAGAG
1 AAAAATGAAA-AG
94486 AAAAATGAAAA
1 AAAAATGAAAA
94497 ATGAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 4 0.10
11 1 0.03
12 14 0.36
13 20 0.51
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.08
Consensus pattern (12 bp):
AAAAATGAAAAG
Found at i:94505 original size:16 final size:16
Alignment explanation
Indices: 94457--94511 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
94447 AGAAAAAATG
94457 AAATGAAAAAGTG-AAA
1 AAATGAAAAA-TGAAAA
*
94473 AAA-GAAGAAA-GAGAA
1 AAATGAA-AAATGAAAA
94488 AAATGAAAAATGAAAA
1 AAATGAAAAATGAAAA
94504 AAAT-AAAA
1 AAATGAAAA
94512 TAAAAGGGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 1 0.03
15 15 0.45
16 17 0.52
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (16 bp):
AAATGAAAAATGAAAA
Found at i:95856 original size:37 final size:36
Alignment explanation
Indices: 95792--95866 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
95782 AAACAAGTCA
* *
95792 ATCTTAAGCCTTCACGAAGAGTGGTGAAGTAAA-TC
1 ATCTTAAGCCTTCACGAAGAGTAGTGAAGCAAACTC
*
95827 ATCTATAATCCTTCACGGAAGAGTAGTGAAGCAAACTC
1 ATCT-TAAGCCTTCAC-GAAGAGTAGTGAAGCAAACTC
95865 AT
1 AT
95867 TTTATGAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 4 0.12
36 10 0.29
37 16 0.47
38 4 0.12
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGAAGAGTAGTGAAGCAAACTC
Found at i:95933 original size:51 final size:51
Alignment explanation
Indices: 95873--96140 Score: 250
Period size: 55 Copynumber: 5.1 Consensus size: 51
95863 TCATTTTATG
*
95873 AAGATCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTA
1 AAGATCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTA
* * * *** * * *
95924 AAGATCGAGTCTTATACTCTTTGAAGGAATAGGGAGATTACACTTTTGTTG
1 AAGATCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTA
* * * * *
95975 AAGATCGGGTCCTATACTCCCTGAAAGAATAAAGAGCAGACCCGTTTGTTGA
1 AAGATCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTT-A
* * * *
96027 AGATTGTTCGAGTTCTATACTCTCTAAAGGAATATAGAGCGGACCCGTTT-TATGA
1 A-A--GATCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-T-A
* * *
96082 AGATTGATCGAGTCCTATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGTTG
1 A-A--GATCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTA
96136 AAGAT
1 AAGAT
96141 TGTTCGAGTC
Statistics
Matches: 175, Mismatches: 36, Indels: 12
0.78 0.16 0.05
Matches are distributed among these distances:
51 84 0.48
52 1 0.01
53 2 0.01
54 2 0.01
55 85 0.49
56 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (51 bp):
AAGATCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTA
Found at i:96060 original size:55 final size:55
Alignment explanation
Indices: 95987--96316 Score: 328
Period size: 55 Copynumber: 6.0 Consensus size: 55
95977 GATCGGGTCC
**
95987 TATACTCCCTGAAA-GAATAAAGAGCAGACCCGTTTGTTGAAGATTGTTCGAGT-T
1 TATACTCCCT-AAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCT
* * ** * * *
96041 CTATACTCTCTAAAGGAATATAGAGCGGACCCGTTT-TATGAAGATTGATCGAGTCC
1 -TATACTCCCTAAACGAATAGGGAGCAGACCCGTTTGT-TGAAGATTGTTCGAGTCT
* * *
96097 TATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTCT
1 TATACTCCCTAAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCT
** * * * *
96152 TATACTCCCCGAACGAATAGGGAACATACCCATTTGCTGAAGATTGTTCGAGTCT
1 TATACTCCCTAAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCT
* * * * * *
96207 TATACTCCTTGAACGAATAGGGAGCAGACACATTTGATGAAGATTGTGCGAGTCT
1 TATACTCCCTAAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCT
* * * *
96262 TATACTCCCTAAA-GAAATAGGGAGCGGACCCGTCAT-TTGAAGATTTTTCAAGTCT
1 TATACTCCCTAAACG-AATAGGGAGCAGACCCGT-TTGTTGAAGATTGTTCGAGTCT
96317 CGTTTATCCC
Statistics
Matches: 234, Mismatches: 35, Indels: 12
0.83 0.12 0.04
Matches are distributed among these distances:
54 5 0.02
55 227 0.97
56 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (55 bp):
TATACTCCCTAAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCT
Found at i:96127 original size:110 final size:109
Alignment explanation
Indices: 95875--96294 Score: 390
Period size: 110 Copynumber: 3.9 Consensus size: 109
95865 ATTTTATGAA
* * * * *
95875 GATCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTT-AA-A--GATCGAGTCT
1 GATCGAGTCCTATACTC-CTGAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCT
** * *** * * *
95936 TATACTCTTTGAAGGAATAGGGAGATTACACTTTTGTTG-A-A--
65 TATACTCCCTAAAGGAATAGGGAGCGGACCCGTTTGATGAAGATT
* * **
95977 GATCGGGTCCTATACTCCCTGAAAGAATAAAGAGCAGACCCGTTTGTTGAAGATTGTTCGAGT-T
1 GATCGAGTCCTATACT-CCTGAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCT
* ** *
96041 CTATACTCTCTAAAGGAATATAGAGCGGACCCGTTTTATGAAGATT
65 -TATACTCCCTAAAGGAATAGGGAGCGGACCCGTTTGATGAAGATT
*
96087 GATCGAGTCCTATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTCT
1 GATCGAGTCCTATACTC-CTGAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCT
** * * ** * *
96152 TATACTCCCCGAACGAATAGGGAACATACCCATTTGCTGAAGATT
65 TATACTCCCTAAAGGAATAGGGAGCGGACCCGTTTGATGAAGATT
* * * * * *
96197 GTTCGAGTCTTATACTCCTTGAACGAATAGGGAGCAGACACATTTGATGAAGATTGTGCGAGTCT
1 GATCGAGTCCTATACTCC-TGAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCT
*
96262 TATACTCCCTAAAGAAATAGGGAGCGGACCCGT
65 TATACTCCCTAAAGGAATAGGGAGCGGACCCGT
96295 CATTTGAAGA
Statistics
Matches: 256, Mismatches: 49, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
102 41 0.16
103 3 0.01
104 1 0.00
105 1 0.00
106 35 0.14
107 1 0.00
108 1 0.00
109 2 0.01
110 170 0.66
111 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (109 bp):
GATCGAGTCCTATACTCCTGAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCTT
ATACTCCCTAAAGGAATAGGGAGCGGACCCGTTTGATGAAGATT
Found at i:96249 original size:165 final size:164
Alignment explanation
Indices: 95877--96308 Score: 447
Period size: 165 Copynumber: 2.7 Consensus size: 164
95867 TTTATGAAGA
* *
95877 TCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTG-TTAA-A--GATCGAGTCTTA
1 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGATGAAGATTGATCGAGTCTTA
* * *** * * * * *
95938 TACTCTTTGAAGGAATAGGGAGATTACACTTTTGTTGAAGA---TCGGGTCCTATACTCCCTGAA
66 TACTCTCTGAAAGAATAGGGAGCGGACCCGTTTGTTGAAGATTTTCGAGTCTTATACTCCCCGAA
* * *
96000 AGAATAAAGAGCAGACCCGTTTGTTGAAGATTGT
131 AGAATAAAGAACAGACCCATTTGCTGAAGATTGT
* * * * *
96034 TCGAGT-TCTATACTCTCTAAAGGAATATAGAGCGGACCCGTTTTATGAAGATTGATCGAGTCCT
1 TCGAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGATGAAGATTGATCGAGTCTT
*
96098 ATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCCG
65 ATACTCTCTGAAAGAATAGGGAGCGGACCCGTTTGTTGAAGATT-TTCGAGTCTTATACTCCCCG
* ** *
96163 AACGAATAGGGAACATACCCATTTGCTGAAGATTGT
129 AAAGAATAAAGAACAGACCCATTTGCTGAAGATTGT
* * * *
96199 TCGAGTCTTATACTC-CTTGAACGAATAGGGAGCAGACACATTTGATGAAGATTG-TGCGAGTCT
1 TCGAGTCTTATACTCTC-TGAAGGAATAGAGAGCGGACACGTTTGATGAAGATTGAT-CGAGTCT
* *
96262 TATACTCCCT-AAAGAAATAGGGAGCGGACCCGTCAT-TTGAAGATTTT
64 TATACTCTCTGAAAG-AATAGGGAGCGGACCCGT-TTGTTGAAGATTTT
96309 TCAAGTCTCG
Statistics
Matches: 225, Mismatches: 36, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
157 38 0.17
158 3 0.01
159 1 0.00
161 45 0.20
164 7 0.03
165 129 0.57
166 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (164 bp):
TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGATGAAGATTGATCGAGTCTTA
TACTCTCTGAAAGAATAGGGAGCGGACCCGTTTGTTGAAGATTTTCGAGTCTTATACTCCCCGAA
AGAATAAAGAACAGACCCATTTGCTGAAGATTGT
Found at i:103110 original size:15 final size:15
Alignment explanation
Indices: 103090--103121 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
103080 TCACTGATTG
*
103090 AATTAAATTAGTTAA
1 AATTAAATTAATTAA
103105 AATTAAATTAATTAA
1 AATTAAATTAATTAA
103120 AA
1 AA
103122 AAATTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AATTAAATTAATTAA
Found at i:103368 original size:36 final size:36
Alignment explanation
Indices: 103315--103400 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
103305 GATTTTTGGA
*
103315 AGTAGTAAATTAATAATT-ATTAATATATTAGTAAATT
1 AGTAGT-AATTATTAATTGA-TAATATATTAGTAAATT
*
103352 AGTAGTAATTATTAATTGATAATCTATTAGTAAATT
1 AGTAGTAATTATTAATTGATAATATATTAGTAAATT
* *
103388 AGTAATTATTATT
1 AGTAGTAATTATT
103401 TATACTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 37 0.84
37 7 0.16
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.45
Consensus pattern (36 bp):
AGTAGTAATTATTAATTGATAATATATTAGTAAATT
Found at i:115166 original size:26 final size:27
Alignment explanation
Indices: 115113--115167 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
115103 AAAAATTAAA
* *
115113 ATTAAAATACTAAAAAAATATATGTAT
1 ATTAAAATACTAAAAAAATAAATATAT
* *
115140 ATTAAAA-ATTAAAAAATTAAATATAT
1 ATTAAAATACTAAAAAAATAAATATAT
115166 AT
1 AT
115168 CGTAAGCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (27 bp):
ATTAAAATACTAAAAAAATAAATATAT
Found at i:115205 original size:16 final size:16
Alignment explanation
Indices: 115184--115215 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
115174 CTATAAAAGG
115184 AAAAATTAAAAATATT
1 AAAAATTAAAAATATT
115200 AAAAATTAAAAATATT
1 AAAAATTAAAAATATT
115216 TTTAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATTAAAAATATT
Found at i:115961 original size:36 final size:36
Alignment explanation
Indices: 115912--115982 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
115902 TATAAAAAAG
*
115912 TAATAAGTTTATTC-TCCAAGTAACATGACTTATTAC
1 TAATAAGTGTATTCAT-CAAGTAACATGACTTATTAC
115948 TAATAAGTGTATTCATCAAGTAACATGACTTATTA
1 TAATAAGTGTATTCATCAAGTAACATGACTTATTA
115983 TTAGCATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (36 bp):
TAATAAGTGTATTCATCAAGTAACATGACTTATTAC
Found at i:117389 original size:16 final size:15
Alignment explanation
Indices: 117353--117399 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
117343 TCGTTATAAA
117353 TTTTATTATAATT-T
1 TTTTATTATAATTAT
117367 TTTTATTATAATTAT
1 TTTTATTATAATTAT
*
117382 TATTTATTATGATTAT
1 T-TTTATTATAATTAT
117398 TT
1 TT
117400 GAAAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 13 0.43
15 3 0.10
16 14 0.47
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:120756 original size:35 final size:34
Alignment explanation
Indices: 120671--120757 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
120661 AATATAATTT
*
120671 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
120705 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
120743 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
120758 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:121378 original size:18 final size:18
Alignment explanation
Indices: 121355--121389 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
121345 ATGTGGCGAT
121355 ATCATAAATGGCTGCGGC
1 ATCATAAATGGCTGCGGC
121373 ATCATAAATGGCTGCGG
1 ATCATAAATGGCTGCGG
121390 TGGCTGCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (18 bp):
ATCATAAATGGCTGCGGC
Found at i:124596 original size:21 final size:21
Alignment explanation
Indices: 124570--124612 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
124560 AACGAAGCCT
124570 AGCCATAAATGGTACTAGGAA
1 AGCCATAAATGGTACTAGGAA
124591 AGCCATAAATGGTACTAGGAA
1 AGCCATAAATGGTACTAGGAA
124612 A
1 A
124613 TATGTGGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (21 bp):
AGCCATAAATGGTACTAGGAA
Found at i:125632 original size:83 final size:82
Alignment explanation
Indices: 125479--125632 Score: 238
Period size: 83 Copynumber: 1.9 Consensus size: 82
125469 ATTTTAAACA
* *
125479 TTATATTTTATCTTTGTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAG
1 TTATATTTTATATTTGTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAA
*
125544 GATATTATTTTTATATT
66 AATATTATTTTTATATT
* *
125561 TTATATTTTATATTTGTTTTATGTATTTTAGTTTAAATATGTTTTAGTATTTTAATT-AGTATTT
1 TTATATTTTATATTTG-TTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGT-TTT
125625 AAAATATT
64 AAAATATT
125633 GTTTAAAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
82 18 0.28
83 47 0.72
ACGTcount: A:0.29, C:0.01, G:0.10, T:0.60
Consensus pattern (82 bp):
TTATATTTTATATTTGTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAA
AATATTATTTTTATATT
Found at i:128207 original size:2 final size:2
Alignment explanation
Indices: 128200--128241 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
128190 TTAATAATAA
128200 AT 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 AT
128242 TGATAAGCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128441 original size:30 final size:30
Alignment explanation
Indices: 128407--128495 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 30
128397 TTAATAATAA
128407 TAATAATAATAAAATTATATTTAATTATTT
1 TAATAATAATAAAATTATATTTAATTATTT
* *
128437 TAATAATTAA-AATAATTAT-TTTATTTAAATT
1 TAATAA-TAATAA-AATTATATTTAATT-ATTT
* *
128468 TAA-AATGATATAAATTA-ATTTTATTATT
1 TAATAATAATA-AAATTATATTTAATTATT
128496 AATTTAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
29 4 0.09
30 27 0.57
31 16 0.34
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TAATAATAATAAAATTATATTTAATTATTT
Found at i:129271 original size:17 final size:18
Alignment explanation
Indices: 129238--129272 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
129228 ATTCGAAAGG
*
129238 CAAATATATGGAAATGTT
1 CAAATATATGAAAATGTT
129256 CAAATATAT-AAAATGTT
1 CAAATATATGAAAATGTT
129273 TAATTTATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (18 bp):
CAAATATATGAAAATGTT
Found at i:132708 original size:39 final size:39
Alignment explanation
Indices: 132613--132708 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 39
132603 GTTTTCAATT
* * * *
132613 TTTTAACTTAATTAATAATATATATTAATTTTAGATTATC
1 TTTT-ACTTAATAAATAATATATATTAATTTTAAATGAAC
* *
132653 TTTTACTTAATTAATAATATATATT-ATTTTAAATGAAG
1 TTTTACTTAATAAATAATATATATTAATTTTAAATGAAC
132691 TTTATA-TTAAATAAATAA
1 TTT-TACTT-AATAAATAA
132709 AAATAAGTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
38 14 0.29
39 31 0.63
40 4 0.08
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (39 bp):
TTTTACTTAATAAATAATATATATTAATTTTAAATGAAC
Found at i:132810 original size:20 final size:19
Alignment explanation
Indices: 132781--132827 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
132771 TAAAATATAT
132781 TAAAAATAATAAATAATAAA
1 TAAAAATAATAAATAA-AAA
* *
132801 TAAAAGTAATAAGTAAAAA
1 TAAAAATAATAAATAAAAA
132820 TAAAAATA
1 TAAAAATA
132828 TTATTTCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (19 bp):
TAAAAATAATAAATAAAAA
Found at i:132812 original size:13 final size:13
Alignment explanation
Indices: 132784--132827 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
132774 AATATATTAA
132784 AAATAATAAATAAT
1 AAATAA-AAATAAT
*
132798 AAATAAAAGTAAT
1 AAATAAAAATAAT
*
132811 AAGTAAAAATAA-
1 AAATAAAAATAAT
132823 AAATA
1 AAATA
132828 TTATTTCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 4 0.15
13 16 0.62
14 6 0.23
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (13 bp):
AAATAAAAATAAT
Found at i:134063 original size:27 final size:27
Alignment explanation
Indices: 134025--134079 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
134015 TTTACATTAA
134025 ACCTTCTTAGAAAAAAATTATAAGTGT
1 ACCTTCTTAGAAAAAAATTATAAGTGT
134052 ACCTTCTTAGAAAAAAATTATAAGTGT
1 ACCTTCTTAGAAAAAAATTATAAGTGT
134079 A
1 A
134080 GTATAACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (27 bp):
ACCTTCTTAGAAAAAAATTATAAGTGT
Found at i:144509 original size:2 final size:2
Alignment explanation
Indices: 144502--144529 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
144492 AAACATTTGA
144502 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
144530 TAAAGTTTAT
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:145922 original size:16 final size:16
Alignment explanation
Indices: 145898--145934 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
145888 AGTAAATTAA
145898 ATTCAGGTTGCTTTCG
1 ATTCAGGTTGCTTTCG
*
145914 ATTCGGGTTGCTTTCG
1 ATTCAGGTTGCTTTCG
*
145930 GTTCA
1 ATTCA
145935 ACTAAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.19, G:0.27, T:0.43
Consensus pattern (16 bp):
ATTCAGGTTGCTTTCG
Found at i:147154 original size:16 final size:17
Alignment explanation
Indices: 147122--147285 Score: 80
Period size: 17 Copynumber: 9.9 Consensus size: 17
147112 AATCAAAGAA
147122 AAAAACAATAAATAAAT
1 AAAAACAATAAATAAAT
*
147139 AAAATCAATAAA-AAAT
1 AAAAACAATAAATAAAT
* *
147155 AAAAA-AA-AAGTAAAA
1 AAAAACAATAAATAAAT
* *
147170 AAAAAGAATAAATAACCT
1 AAAAACAATAAATAA-AT
* *
147188 AGAAA-AAT-AATACCAT
1 AAAAACAATAAATA-AAT
*
147204 -AAAA-TAT-AATAAA-
1 AAAAACAATAAATAAAT
147217 AGAAAACAATAAATAAAT
1 A-AAAACAATAAATAAAT
*
147235 AAAATCAATAAA-AAAGT
1 AAAAACAATAAATAAA-T
* *
147252 ACAAATAAAACAAATAAA-
1 A-AAA-ACAATAAATAAAT
*
147270 ACAAAATAATAAATAA
1 A-AAAACAATAAATAA
147286 CCTAAAAAAT
Statistics
Matches: 113, Mismatches: 20, Indels: 28
0.70 0.12 0.17
Matches are distributed among these distances:
14 3 0.03
15 23 0.20
16 20 0.18
17 46 0.41
18 13 0.12
19 5 0.04
20 3 0.03
ACGTcount: A:0.74, C:0.07, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAAACAATAAATAAAT
Found at i:147162 original size:11 final size:11
Alignment explanation
Indices: 147120--147174 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
147110 TAAATCAAAG
*
147120 AAAAAAACAAT
1 AAAAAAAAAAT
147131 AAATAAATAAAAT
1 AAA-AAA-AAAAT
* *
147144 CAATAAAAAAT
1 AAAAAAAAAAT
*
147155 AAAAAAAAAGT
1 AAAAAAAAAAT
147166 AAAAAAAAA
1 AAAAAAAAA
147175 GAATAAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 25 0.69
12 5 0.14
13 6 0.17
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.13
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:147197 original size:48 final size:46
Alignment explanation
Indices: 147120--147318 Score: 140
Period size: 48 Copynumber: 4.2 Consensus size: 46
147110 TAAATCAAAG
147120 AAAAAAACAATAAATAAATAAAATCAATAAAAAATAAAAAAAAAGTAA
1 AAAAAAACAATAAATAAATAAAA-CAATAAAAAATAAAAAAAAA-TAA
* * ** * *
147168 AAAAAAAGAATAAATAACCTAGAAA-AATAATACCATAAAATATAATAA
1 AAAAAAACAATAAATAA-ATA-AAACAATAA-AAAATAAAAAAAAATAA
* * *
147216 AAGAAAACAATAAATAAATAAAATCAATAAAAAAGTACAAATAAAACAA
1 AAAAAAACAATAAATAAATAAAA-CAATAAAAAA-TA-AAAAAAAATAA
*
147265 ATAAAACAA-AAT-AATAAAT--AAC-CTAAAAAATAATATAAAAAATATA
1 A-AAAA-AACAATAAATAAATAAAACAATAAAAAATAA-A-AAAAAATA-A
147311 ATAAAAAA
1 A-AAAAAA
147319 TATATATAAA
Statistics
Matches: 122, Mismatches: 17, Indels: 27
0.73 0.10 0.16
Matches are distributed among these distances:
43 1 0.01
44 3 0.02
45 15 0.12
46 11 0.09
47 6 0.05
48 46 0.38
49 29 0.24
50 9 0.07
51 2 0.02
ACGTcount: A:0.74, C:0.07, G:0.03, T:0.17
Consensus pattern (46 bp):
AAAAAAACAATAAATAAATAAAACAATAAAAAATAAAAAAAAATAA
Found at i:147237 original size:96 final size:98
Alignment explanation
Indices: 147123--147316 Score: 288
Period size: 96 Copynumber: 2.0 Consensus size: 98
147113 ATCAAAGAAA
*
147123 AAAACAATAAATAAATAAAATCAATAAAAAA-T-AAA-AAAA-AAGTAAAAAAAAAGAATAAATA
1 AAAACAATAAATAAATAAAATCAATAAAAAAGTAAAATAAAACAAATAAAAAAAAAGAATAAATA
*
147184 ACCTAGAAAAATAATACCATAAAATATAATAAAAG
66 ACCTA-AAAAATAATA-CAAAAAATATAATAAAAG
* *
147219 AAAACAATAAATAAATAAAATCAATAAAAAAGTACAAATAAAACAAATAAAACAAAATAATAAAT
1 AAAACAATAAATAAATAAAATCAATAAAAAAGTA-AAATAAAACAAATAAAAAAAAAGAATAAAT
*
147284 AACCTAAAAAATAATATAAAAAATATAATAAAA
65 AACCTAAAAAATAATACAAAAAATATAATAAAA
147317 AATATATATA
Statistics
Matches: 88, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
96 31 0.35
97 1 0.01
99 18 0.20
100 14 0.16
101 24 0.27
ACGTcount: A:0.73, C:0.07, G:0.03, T:0.18
Consensus pattern (98 bp):
AAAACAATAAATAAATAAAATCAATAAAAAAGTAAAATAAAACAAATAAAAAAAAAGAATAAATA
ACCTAAAAAATAATACAAAAAATATAATAAAAG
Found at i:147297 original size:12 final size:12
Alignment explanation
Indices: 147275--147330 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
147265 ATAAAACAAA
*
147275 ATAATAAATAAC
1 ATAAAAAATAAC
* *
147287 CTAAAAAATAAT
1 ATAAAAAATAAC
147299 ATAAAAAATATA-
1 ATAAAAAATA-AC
*
147311 ATAAAAAATATAT
1 ATAAAAAATA-AC
147324 ATAAAAA
1 ATAAAAA
147331 GAGAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
12 30 0.79
13 8 0.21
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (12 bp):
ATAAAAAATAAC
Found at i:147311 original size:14 final size:13
Alignment explanation
Indices: 147288--147330 Score: 72
Period size: 12 Copynumber: 3.5 Consensus size: 13
147278 ATAAATAACC
147288 TAAAAAATA-ATA
1 TAAAAAATATATA
147300 TAAAAAATATA-A
1 TAAAAAATATATA
147312 TAAAAAATATATA
1 TAAAAAATATATA
147325 TAAAAA
1 TAAAAA
147331 GAGAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 21 0.72
13 8 0.28
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAAATATATA
Found at i:147317 original size:13 final size:13
Alignment explanation
Indices: 147204--147330 Score: 55
Period size: 14 Copynumber: 9.2 Consensus size: 13
147194 ATAATACCAT
147204 AAAATATAATAAAA
1 AAAATATAAT-AAA
*
147218 GAAAACAATAAATAAA
1 -AAAA-TAT-AATAAA
*
147234 TAAAAT-CAATAAA
1 -AAAATATAATAAA
* *
147247 AAAGTACAAATAAA
1 AAAATA-TAATAAA
* *
147261 ACAAATAAAACAAA
1 A-AAATATAATAAA
*
147275 ATAATA-AATAACCTA
1 AAAATATAATAA---A
147290 AAAA-ATAATATAA
1 AAAATATAATA-AA
147303 AAAATATAAT-AA
1 AAAATATAATAAA
147315 AAAATATATATAAA
1 AAAATATA-ATAAA
147329 AA
1 AA
147331 GAGAAATAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
12 18 0.20
13 17 0.19
14 24 0.27
15 16 0.18
16 10 0.11
17 3 0.03
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.20
Consensus pattern (13 bp):
AAAATATAATAAA
Found at i:147338 original size:25 final size:24
Alignment explanation
Indices: 147288--147341 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
147278 ATAAATAACC
*
147288 TAAAAAATAATATAAAAAATATAA
1 TAAAAAATAATATAAAAAAGATAA
147312 TAAAAAATATATATAAAAAGAGA-AA
1 TAAAAAATA-ATATAAAAA-AGATAA
147337 TAAAA
1 TAAAA
147342 TAAAGGGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 9 0.33
25 16 0.59
26 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (24 bp):
TAAAAAATAATATAAAAAAGATAA
Found at i:147992 original size:3 final size:3
Alignment explanation
Indices: 147969--148029 Score: 56
Period size: 3 Copynumber: 20.0 Consensus size: 3
147959 TGTGGGGCCT
*
147969 ATA AAA ATA ATA A-A ATAA ATA ATA ATA ATA ATA ATAA ATAA ATA TATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT-A AT-A ATA -ATA
148017 AT- ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA
148030 TTTTTATAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
2 6 0.12
3 31 0.62
4 13 0.26
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:147999 original size:27 final size:26
Alignment explanation
Indices: 147969--148027 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
147959 TGTGGGGCCT
147969 ATAAAAAT-AATAAAATAAATAATAATA
1 ATAAAAATAAAT-AAATAAATAAT-ATA
* *
147996 ATAATAATAAATAAATATATAATATA
1 ATAAAAATAAATAAATAAATAATATA
148022 ATAAAA
1 ATAAAA
148028 TATTTTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 8 0.29
27 17 0.61
28 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (26 bp):
ATAAAAATAAATAAATAAATAATATA
Found at i:148001 original size:24 final size:22
Alignment explanation
Indices: 147968--148029 Score: 83
Period size: 21 Copynumber: 2.8 Consensus size: 22
147958 GTGTGGGGCC
*
147968 TATAAAAATAATAAAATAAATA
1 TATAATAATAATAAAATAAATA
147990 -ATAATAATAATAATAAATAAATA
1 TATAATAATAAT-A-AAATAAATA
148013 TATAAT-ATAATAAAATA
1 TATAATAATAATAAAATA
148030 TTTTTATAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 15 0.42
22 2 0.06
23 14 0.39
24 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
TATAATAATAATAAAATAAATA
Found at i:148030 original size:15 final size:15
Alignment explanation
Indices: 147975--148030 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
147965 GCCTATAAAA
147975 ATAATAAAATA-AAT
1 ATAATAAAATATAAT
*
147989 AATAATAATA-ATAAT
1 -ATAATAAAATATAAT
148004 A-AATAAATATATAAT
1 ATAATAAA-ATATAAT
148019 ATAATAAAATAT
1 ATAATAAAATAT
148031 TTTTATAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 5 0.14
14 3 0.09
15 21 0.60
16 6 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAATAAAATATAAT
Found at i:150150 original size:16 final size:17
Alignment explanation
Indices: 150125--150179 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
150115 AAGAACCCCA
*
150125 GGGTGGCACTT-TTGAG
1 GGGTGACACTTGTTGAG
*
150141 GGGTGACACTTGTATTAG
1 GGGTGACACTTGT-TGAG
*
150159 GGGTGACACTTGTGGAG
1 GGGTGACACTTGTTGAG
150176 GGGT
1 GGGT
150180 TGCCTGAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 10 0.30
17 7 0.21
18 16 0.48
ACGTcount: A:0.16, C:0.11, G:0.44, T:0.29
Consensus pattern (17 bp):
GGGTGACACTTGTTGAG
Found at i:150230 original size:49 final size:49
Alignment explanation
Indices: 150173--150267 Score: 165
Period size: 49 Copynumber: 1.9 Consensus size: 49
150163 GACACTTGTG
150173 GAGGGGTTGCCTGAGATACCCCG-GACACCATGGAGGTCCGCCCCTGGAT
1 GAGGGGTTGCCTGAGATACCCCGAG-CACCATGGAGGTCCGCCCCTGGAT
*
150222 GAGGGGTTGCTTGAGATACCCCGAGCACCATGGAGGTCCGCCCCTG
1 GAGGGGTTGCCTGAGATACCCCGAGCACCATGGAGGTCCGCCCCTG
150268 CTTAAGGACC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 43 0.98
50 1 0.02
ACGTcount: A:0.18, C:0.31, G:0.35, T:0.17
Consensus pattern (49 bp):
GAGGGGTTGCCTGAGATACCCCGAGCACCATGGAGGTCCGCCCCTGGAT
Found at i:159562 original size:23 final size:21
Alignment explanation
Indices: 159510--159571 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
159500 TTTTGGTGCA
*
159510 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
159530 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
159551 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
159572 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:159597 original size:20 final size:20
Alignment explanation
Indices: 159512--159597 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 20
159502 TTGGTGCAGA
* *
159512 GGGAATCGA-TCCCCCCTTG
1 GGGAACCGATTCCCCCCTAG
*
159531 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGATTCCCCC-CT--AG
*
159555 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCC-TAG
* *
159576 GGGAATCGATACCCCCCTAG
1 GGGAACCGATTCCCCCCTAG
159596 GG
1 GG
159598 TTCTGGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.23
21 23 0.43
22 1 0.02
23 16 0.30
24 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCTAG
Found at i:164537 original size:24 final size:24
Alignment explanation
Indices: 164520--164645 Score: 139
Period size: 24 Copynumber: 5.3 Consensus size: 24
164510 ATCAAAACAT
* *
164520 AATTCAGGTCAAGTATCAAATCAG
1 AATTCAAGTCAAGTATCAGATCAG
* *
164544 AATCCAAGTCATGTATCAGATCAG
1 AATTCAAGTCAAGTATCAGATCAG
* *
164568 AATCCAAGTCATGTATCAGATCAG
1 AATTCAAGTCAAGTATCAGATCAG
*
164592 AATTCATGTC-AGTATCAGATCAG
1 AATTCAAGTCAAGTATCAGATCAG
* * *
164615 AATTCAGGTCAGGTATCATAGT-AG
1 AATTCAAGTCAAGTATCAGA-TCAG
164639 AATTCAA
1 AATTCAA
164646 ATTGAAAATC
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
23 21 0.24
24 67 0.75
25 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (24 bp):
AATTCAAGTCAAGTATCAGATCAG
Found at i:164641 original size:47 final size:47
Alignment explanation
Indices: 164520--164645 Score: 148
Period size: 47 Copynumber: 2.6 Consensus size: 47
164510 ATCAAAACAT
*
164520 AATTCAGGTCAAGTATCAAATCAGAATCCAAGTCATGTATCAGATCAG
1 AATTCAGGTCAAGTATC-AATCAGAATTCAAGTCATGTATCAGATCAG
* * * *
164568 AATCCAAGTCATGTATCAGATCAGAATTCATGTCA-GTATCAGATCAG
1 AATTCAGGTCAAGTATCA-ATCAGAATTCAAGTCATGTATCAGATCAG
*
164615 AATTCAGGTCAGGTATCATAGT-AGAATTCAA
1 AATTCAGGTCAAGTATCA-A-TCAGAATTCAA
164646 ATTGAAAATC
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
47 37 0.56
48 29 0.44
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (47 bp):
AATTCAGGTCAAGTATCAATCAGAATTCAAGTCATGTATCAGATCAG
Found at i:166588 original size:218 final size:217
Alignment explanation
Indices: 166205--166833 Score: 1001
Period size: 218 Copynumber: 2.9 Consensus size: 217
166195 TTATGAATGA
* *
166205 CCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTTTCAATGAACCCTTT
1 CCCGAAGGACTTACAAATCAAGAAA-CCCCGAAGGCTTAGTTTCTTAGTTATCAATGAACCCCTT
* * *
166270 TATTAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAGAAAACCCCTAAAGGCTTAGTTT
65 TATTAGGCTTAGCTTCCTTTAACAGCTCTTTTGAGATAATTAGTAAACCCCCAAAGGCTTAGTTT
* * * * *
166335 CTAAAATCTCATTTGTAAACATCCTACATTGAAGGTCTTATGGATGACCCAAAGGATTTATCATC
130 CTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATC
166400 TTACTCGAAAGGCTTACAGATGG
195 TTACTCGAAAGGCTTACAGATGG
*
166423 CCCGAAGGACTTACAAATCAAGAAACCCTCGAAGGCTTAGTTTCTTAGTTATCAAGGAACCCCTT
1 CCCGAAGGACTTACAAATCAAGAAACCC-CGAAGGCTTAGTTTCTTAGTTATCAATGAACCCCTT
* *
166488 TGTTAGGCTTAGCTTCCTTTAATAGCTCTTTTGAGATAATTAGTAAACCCCCAAAGGCTTAGTTT
65 TATTAGGCTTAGCTTCCTTTAACAGCTCTTTTGAGATAATTAGTAAACCCCCAAAGGCTTAGTTT
*
166553 CTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGCTTTATCATC
130 CTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATC
* *
166618 TTGCTCGAAAGGCTTACAGATGT
195 TTACTCGAAAGGCTTACAGATGG
** * * * * *
166641 CCTAAAGGATTTATAAATCAAGAAACCCCGAAGGTTTAGTTTCTTGGTTGTCAATGAACCCCTTT
1 CCCGAAGGACTTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTTAGTTATCAATGAACCCCTTT
166706 ATTAGGCTTAGCTTCCTTTAACAGCTCTTTTGAGATAATTAGTAAA--CCCAAAGGCTTAGTTTC
66 ATTAGGCTTAGCTTCCTTTAACAGCTCTTTTGAGATAATTAGTAAACCCCCAAAGGCTTAGTTTC
* *
166769 TAAAATCTCATTTGAAAACATCCTGCACTGAAGATCTTATGGATAACCCGAAGGCTTTATCATCT
131 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCT
166834 AGGGAAATAG
Statistics
Matches: 381, Mismatches: 29, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
215 79 0.21
217 80 0.21
218 222 0.58
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (217 bp):
CCCGAAGGACTTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTTAGTTATCAATGAACCCCTTT
ATTAGGCTTAGCTTCCTTTAACAGCTCTTTTGAGATAATTAGTAAACCCCCAAAGGCTTAGTTTC
TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCT
TACTCGAAAGGCTTACAGATGG
Found at i:167504 original size:22 final size:22
Alignment explanation
Indices: 167479--167530 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
167469 TATAAATCTT
167479 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATATA
* * *
167501 TCATATTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATATA
167523 TCATCTTT
1 TCATCTTT
167531 AAAGAATGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:167535 original size:22 final size:22
Alignment explanation
Indices: 167473--167535 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
167463 AAATCCTATA
*
167473 AATCTTTCATCTTTGAAA-AGAG
1 AATCTATCATCTTT-AAAGAGAG
* * *
167495 AATATATCATATTTGAAGAGAG
1 AATCTATCATCTTTAAAGAGAG
167517 AATCTATCATCTTTAAAGA
1 AATCTATCATCTTTAAAGA
167536 ATGTAGATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 2 0.06
22 31 0.94
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (22 bp):
AATCTATCATCTTTAAAGAGAG
Found at i:167995 original size:54 final size:52
Alignment explanation
Indices: 167908--168065 Score: 185
Period size: 54 Copynumber: 3.0 Consensus size: 52
167898 ACTGGTTCAT
167908 AAAACATTTGACAACACATTCATCATTTTCTGTGGCTTCTGTACAGATGTTCGC
1 AAAA-ATTTGACAACACATTCATCATTTTCTGTGGCTTCTG-ACAGATGTTCGC
* * * *
167962 AAAAGATTTGACAACATATTCATCTTTTTCTGTGGCTTCTG-CACATATTCGC
1 AAAA-ATTTGACAACACATTCATCATTTTCTGTGGCTTCTGACAGATGTTCGC
* * * * *
168014 -AAATTTTGACAACACATTCATAATTTCCTGTGGTTTTTGCACAGATGTTCGC
1 AAAAATTTGACAACACATTCATCATTTTCTGTGGCTTCTG-ACAGATGTTCGC
168066 CAGTGAAGCT
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
50 29 0.33
51 3 0.03
52 18 0.20
54 38 0.43
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (52 bp):
AAAAATTTGACAACACATTCATCATTTTCTGTGGCTTCTGACAGATGTTCGC
Found at i:169267 original size:13 final size:14
Alignment explanation
Indices: 169240--169279 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
169230 TAACCTCTCT
169240 TTTTC-TCTCTTTTC
1 TTTTCTTCT-TTTTC
169254 TTTTCTT-TTTTTC
1 TTTTCTTCTTTTTC
169267 TTTTCTTCTTTTT
1 TTTTCTTCTTTTT
169280 GCTATTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 11 0.46
15 1 0.04
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTCTTCTTTTTC
Found at i:169483 original size:69 final size:72
Alignment explanation
Indices: 169358--169498 Score: 216
Period size: 69 Copynumber: 2.0 Consensus size: 72
169348 ATATAATAGT
* *
169358 ATAACAGACTAGCTGAATATTATCCATAAAGCTGGGGATATTAACCAATTGCTTTAGGGGGACAA
1 ATAACAGACTAGCTGAATATTATCCATAAAGCTCGGGAGATTAACCAATTGCTTTAGGGGGACAA
169423 CTCAAGC
66 CTCAAGC
* *
169430 ATAACAGACTAGCTG-A-ATTATCCATAAAG-TCGGGCGATTAACCAATTGCTTTAGGGGGGCAA
1 ATAACAGACTAGCTGAATATTATCCATAAAGCTCGGGAGATTAACCAATTGCTTTAGGGGGACAA
*
169492 CTTAAGC
66 CTCAAGC
169499 TTTATTGTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
69 35 0.55
70 13 0.20
71 1 0.02
72 15 0.23
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (72 bp):
ATAACAGACTAGCTGAATATTATCCATAAAGCTCGGGAGATTAACCAATTGCTTTAGGGGGACAA
CTCAAGC
Found at i:171546 original size:6 final size:6
Alignment explanation
Indices: 171532--171572 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
171522 CAAGGATACG
* *
171532 AATGTA AATGCA AATGCA AATGCAA AATGAA AATGCA AATG
1 AATGCA AATGCA AATGCA AATGC-A AATGCA AATGCA AATG
171573 TATGTATGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.20
Consensus pattern (6 bp):
AATGCA
Found at i:171730 original size:43 final size:42
Alignment explanation
Indices: 171650--171777 Score: 184
Period size: 43 Copynumber: 3.0 Consensus size: 42
171640 CGGTACATCA
171650 AATAAAACTTTACATATAGGGATAGCTTTCACTCCTAACTTC
1 AATAAAACTTTACATATAGGGATAGCTTTCACTCCTAACTTC
* *
171692 AATAAAACTTTACATATAGCGGATAACTTTCACTCCTAACTTT
1 AATAAAACTTTACATATAG-GGATAGCTTTCACTCCTAACTTC
* * * *
171735 AACAAAACTTTATATATAGGGGATAGTTTTCACTCTTAACTTC
1 AATAAAACTTTACATATA-GGGATAGCTTTCACTCCTAACTTC
171778 TCTAAAGCCA
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
42 19 0.25
43 56 0.74
44 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (42 bp):
AATAAAACTTTACATATAGGGATAGCTTTCACTCCTAACTTC
Found at i:172290 original size:36 final size:36
Alignment explanation
Indices: 172243--172312 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 36
172233 TCTTATCGTC
172243 GAATACTTTTGGTATCAATCTAACAAT-ATCTTTGGG
1 GAATACTTTTGGTATCAATCTAAC-ATGATCTTTGGG
172279 GAATACTTTTGGTATCAATCTAACATGATCTTTG
1 GAATACTTTTGGTATCAATCTAACATGATCTTTG
172313 TGTGCATAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATCTAACATGATCTTTGGG
Found at i:173703 original size:2 final size:2
Alignment explanation
Indices: 173696--173729 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
173686 ACTAAAGTAA
173696 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
173730 GGAGTTTATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:175670 original size:12 final size:12
Alignment explanation
Indices: 175650--175699 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
175640 AAAATCATTT
*
175650 AAATCTATTTTA
1 AAATTTATTTTA
175662 AAATTTATTTTA
1 AAATTTATTTTA
* *
175674 AAATATATATT-
1 AAATTTATTTTA
*
175685 -GATTTATTTTA
1 AAATTTATTTTA
175696 AAAT
1 AAAT
175700 ATGGATTGAT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
10 7 0.24
12 22 0.76
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
AAATTTATTTTA
Found at i:175689 original size:22 final size:22
Alignment explanation
Indices: 175664--176183 Score: 690
Period size: 22 Copynumber: 23.6 Consensus size: 22
175654 CTATTTTAAA
**
175664 ATTTATTTTAAAATATATATTG
1 ATTTATTTTAAAATATGGATTG
175686 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
175708 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
175730 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* * *
175752 ATTTATTTTTAAATATGAAAAT-
1 ATTTATTTTAAAATATG-GATTG
*
175774 ATTTATTTTTAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
175796 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
175818 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
175840 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
* *
175862 AATTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
**
175884 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
175905 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
* ***
175928 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
175950 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
175972 ATTTATTTTAAAATATGGAAATT-
1 ATTTATTTTAAAATATGG--ATTG
*
175995 -TTTATTTTAAAATATGGATAG
1 ATTTATTTTAAAATATGGATTG
*
176016 ATTTTTTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
176038 ACTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
176060 CTTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
176082 ATTTATTTTAAAATATGGGA-AA
1 ATTTATTTTAAAATAT-GGATTG
176104 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
176126 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
176148 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
176170 ATTTATTTTTAAAA
1 ATTTA-TTTTAAAA
176184 AAAATTATTA
Statistics
Matches: 438, Mismatches: 49, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
20 2 0.00
21 6 0.01
22 413 0.94
23 14 0.03
24 3 0.01
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:176265 original size:31 final size:31
Alignment explanation
Indices: 176207--176266 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
176197 TAGTTGTATG
*
176207 AATTATTTAAATTTCAGTATTATAAAACTAA
1 AATTATTTAAATTTCAGTATTACAAAACTAA
* *
176238 AATTATTTAAATTTCATTATTGCAAAACT
1 AATTATTTAAATTTCAGTATTACAAAACT
176267 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTACAAAACTAA
Done.