Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007075.1 Hibiscus syriacus cultivar Beakdansim tig00018463_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: 70376
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:7069 original size:35 final size:35
Alignment explanation
Indices: 7030--7124 Score: 103
Period size: 32 Copynumber: 2.9 Consensus size: 35
7020 GTTATTTTAT
*
7030 GTATTTATAAAATTTATATTAAATTATTTAAAAAA
1 GTATTTATAATATTTATATTAAATTATTTAAAAAA
* *
7065 GTATTTATAATA-TTATA--AAAATATTTTAAAAA
1 GTATTTATAATATTTATATTAAATTATTTAAAAAA
*
7097 -TATTTAT-TTATTTAT-TTAAAATTATTTA
1 GTATTTATAATATTTATATT-AAATTATTTA
7125 CTTATTTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
30 2 0.04
31 11 0.22
32 13 0.26
33 8 0.16
34 5 0.10
35 11 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (35 bp):
GTATTTATAATATTTATATTAAATTATTTAAAAAA
Found at i:7114 original size:22 final size:22
Alignment explanation
Indices: 7089--7132 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
7079 ATAAAAATAT
*
7089 TTTAAAAATATTTATTTATTTA
1 TTTAAAAATATTTACTTATTTA
*
7111 TTTAAAATTATTTACTTATTTA
1 TTTAAAAATATTTACTTATTTA
7133 AAATAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTAAAAATATTTACTTATTTA
Found at i:7121 original size:18 final size:18
Alignment explanation
Indices: 7100--7146 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
7090 TTAAAAATAT
7100 TTATTTATTTATTTAAAA
1 TTATTTATTTATTTAAAA
*
7118 TTATTTACTTATTTAAAA
1 TTATTTATTTATTTAAAA
*
7136 TAATATTATTT
1 TTAT-TTATTT
7147 TTAAATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTTATTTATTTAAAA
Found at i:8514 original size:29 final size:29
Alignment explanation
Indices: 8459--8519 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
8449 AAATCACCTT
*
8459 TTTCATCTTTATTTTTCTATCAGACACCC
1 TTTCATCTTTATTTTCCTATCAGACACCC
8488 TTTCATCTTTA-TTTCCTGATCTA-ACACCC
1 TTTCATCTTTATTTTCCT-ATC-AGACACCC
8517 TTT
1 TTT
8520 TCTACGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 5 0.17
29 23 0.79
30 1 0.03
ACGTcount: A:0.20, C:0.28, G:0.03, T:0.49
Consensus pattern (29 bp):
TTTCATCTTTATTTTCCTATCAGACACCC
Found at i:8699 original size:16 final size:16
Alignment explanation
Indices: 8674--8704 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8664 TTTTTGTGTG
8674 TGCATAAAAATCTTTC
1 TGCATAAAAATCTTTC
*
8690 TGCATTAAAATCTTT
1 TGCATAAAAATCTTT
8705 AAATATTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (16 bp):
TGCATAAAAATCTTTC
Found at i:25854 original size:13 final size:13
Alignment explanation
Indices: 25836--25860 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25826 CCCTGAGGTA
25836 AGAGAAAAAAATG
1 AGAGAAAAAAATG
25849 AGAGAAAAAAAT
1 AGAGAAAAAAAT
25861 TTAAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (13 bp):
AGAGAAAAAAATG
Found at i:26981 original size:42 final size:42
Alignment explanation
Indices: 26869--26990 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 42
26859 AGGTTTTTTT
* * * *
26869 ATGATTAAATCCTTCGGGGCA-TCAGTAAGTCTTCCAAGTATG
1 ATGATTAAATCCTTCGGGTCATTC-GTAAGTCTTTCGAGCATG
* * *
26911 ATGATTAAATCCTTTGGATCATTTGTAAGTCTTTCGAGCATG
1 ATGATTAAATCCTTCGGGTCATTCGTAAGTCTTTCGAGCATG
*
26953 ATGATTAAATCCTTCGGGTTATTCGTAAGTCTTTCGAG
1 ATGATTAAATCCTTCGGGTCATTCGTAAGTCTTTCGAG
26991 TAAGAAAATA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 67 0.99
43 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (42 bp):
ATGATTAAATCCTTCGGGTCATTCGTAAGTCTTTCGAGCATG
Found at i:29174 original size:243 final size:243
Alignment explanation
Indices: 28632--29282 Score: 885
Period size: 243 Copynumber: 2.7 Consensus size: 243
28622 GCTAAGTTTG
* *
28632 ATTTCCAAAGTTTTTTACTTAGTAAGTCCTCAAGGCCATCAGTAAGTTTTTCGAGCATGATGATT
1 ATTTCCAAAGTTTCTTACTTAGTAAGTCCTCAAGGCCATCAGTAAGTTTTCCGAGCATGATGATT
* * * * *
28697 AAATCCTTCGGGTCATCTGTAAGTCTTCCGAGCAATATGATAAGTCCTCTGGGCCATCTATAACT
66 AAATCCTTCGGGTCATATGTAAGTCTTCCGATCAAGATGATAAGTCCTCCGGGCCATCTATAATT
* *
28762 CCTCCGGGCATGATGTTTTCATATGATTTTTG--AAAAAAAATGAGAAAGTGATTTTCAAAGTTT
131 CCTCTGGGCATAATGTTTTCATATGATTTTTGAAAAAAAAAATGAGAAAGTGATTTTCAAAGTTT
* * * **
28825 CTAAATTAATCTTTTCTTAAAGTGAAATTTTTTAAAAGTAAGAAAGTG
196 ATAAATTAATCTTTTCTGAAAATGAAATTTTTTAAAAGTAAGAAAGCA
* * ** *
28873 ATTTCCAAAGTTCCTTACTTGGTAAGTCCTCTGGGCCATCAGTAAGTTTTCTGAGCATGATGATT
1 ATTTCCAAAGTTTCTTACTTAGTAAGTCCTCAAGGCCATCAGTAAGTTTTCCGAGCATGATGATT
* * * * *
28938 AAATCCTTCGGGTCATTTATAAGTCTTCCAATCAAGATGATAAGTCCTCCAGACCATCTATAATT
66 AAATCCTTCGGGTCATATGTAAGTCTTCCGATCAAGATGATAAGTCCTCCGGGCCATCTATAATT
* * * *
29003 CCTCTAGACATAATGTTTTCATATGCTTTTTGAAAAAAAAAATGAGAAATTGATTTTCAAAGTTT
131 CCTCTGGGCATAATGTTTTCATATGATTTTTGAAAAAAAAAATGAGAAAGTGATTTTCAAAGTTT
* * * *
29068 ATCATTTAATCTTTTCTGAAAATTAATTTTTTTAAAAGTAAGAAAGCA
196 ATAAATTAATCTTTTCTGAAAATGAAATTTTTTAAAAGTAAGAAAGCA
* * * **
29116 ATTTCCAAAGTTTCTTACTTAGTAGGTCTTCCAGGCCATCAGTAAGTCCTCCGAGCATGATGATT
1 ATTTCCAAAGTTTCTTACTTAGTAAGTCCTCAAGGCCATCAGTAAGTTTTCCGAGCATGATGATT
* * * *
29181 GAATCCTCCGTGTCATATGTAAGTCTTCCGATCAAGATGATAAGTCCCCCGGGCCATCTATAATT
66 AAATCCTTCGGGTCATATGTAAGTCTTCCGATCAAGATGATAAGTCCTCCGGGCCATCTATAATT
* * *
29246 CCTATGGGTATCATG-TTTCATATGATTTTTGAAAAAA
131 CCTCTGGGCATAATGTTTTCATATGATTTTTGAAAAAA
29283 TGAGAAAGCA
Statistics
Matches: 353, Mismatches: 55, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
241 141 0.40
242 21 0.06
243 191 0.54
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (243 bp):
ATTTCCAAAGTTTCTTACTTAGTAAGTCCTCAAGGCCATCAGTAAGTTTTCCGAGCATGATGATT
AAATCCTTCGGGTCATATGTAAGTCTTCCGATCAAGATGATAAGTCCTCCGGGCCATCTATAATT
CCTCTGGGCATAATGTTTTCATATGATTTTTGAAAAAAAAAATGAGAAAGTGATTTTCAAAGTTT
ATAAATTAATCTTTTCTGAAAATGAAATTTTTTAAAAGTAAGAAAGCA
Found at i:29310 original size:177 final size:177
Alignment explanation
Indices: 29108--29484 Score: 483
Period size: 177 Copynumber: 2.1 Consensus size: 177
29098 TTTAAAAGTA
* * * * *
29108 AGAAAGCAATTTCCAAAGTTTCTTACTTAGTAGGT-CTTCCAGGCC-ATCAGTAAGTCCTCCGAG
1 AGAAAGCAATTTTCAAAGTTTCTTACTTAGTAAGTCCTT--AGGCCTATCAATAAGTCCTCCAAA
* * * *
29171 CATGATGATTGAATCCTCCGTGTCATATGTAAGTCTTCCGATCAAGATGATAAGTCCCCCGGGCC
64 CATGATGATTAAATCCTCCGGGTCATATGTAAGTCTTCCGAGCAAGATGATAAGTCCCCCGGACC
* * *
29236 ATCTATAATTCCTAT-GGGTATCATG-TTTCATATGATTTTTGAAAAAATG
129 ATCTATAAGTCCT-TCAGGCATCATGTTTTCATATGATTTTTG-AAAAATG
* *
29285 AGAAAGCAATTTTGAAAGTTTCTTACTTAGTAAGTCCTTAGGCCTATCAATAAGTCTTCCAAACA
1 AGAAAGCAATTTTCAAAGTTTCTTACTTAGTAAGTCCTTAGGCCTATCAATAAGTCCTCCAAACA
* * * ***
29350 TGATGATTAAATCCTCTGGGTCATTTGTAAGTGTTCCGAGCAAGATGATAAGTCCTTTGGACCAT
66 TGATGATTAAATCCTCCGGGTCATATGTAAGTCTTCCGAGCAAGATGATAAGTCCCCCGGACCAT
* * *
29415 TTATTAGTCCTTCAGGCATGATGTTTTCATATGATTTTTGAAAAATG
131 CTATAAGTCCTTCAGGCATCATGTTTTCATATGATTTTTGAAAAATG
29462 AGAAAGCAATTTTCAAAGTTTCT
1 AGAAAGCAATTTTCAAAGTTTCT
29485 CATTTAATCT
Statistics
Matches: 172, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
176 6 0.03
177 147 0.85
178 19 0.11
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (177 bp):
AGAAAGCAATTTTCAAAGTTTCTTACTTAGTAAGTCCTTAGGCCTATCAATAAGTCCTCCAAACA
TGATGATTAAATCCTCCGGGTCATATGTAAGTCTTCCGAGCAAGATGATAAGTCCCCCGGACCAT
CTATAAGTCCTTCAGGCATCATGTTTTCATATGATTTTTGAAAAATG
Found at i:29679 original size:415 final size:418
Alignment explanation
Indices: 28873--29724 Score: 1068
Period size: 415 Copynumber: 2.0 Consensus size: 418
28863 TAAGAAAGTG
* * * * * * ** *
28873 ATTTCCAAAGTTCCTTACTTGGTAAGTCCTCTGGGCCATCAGTAAGTTTTCTGAGCATGATGATT
1 ATTTTCAAAGTTTCTTACTTAGTAAGTCCTCTAGGCCATCAATAAGTCTTCCAAACATGATGATT
* *
28938 AAATCCTTCGGGTCATTTATAAGTCTTCCAATCAAGATGATAAGTCCTCCAGACCATCTATAATT
66 AAATCCTTCGGGTCATTTATAAGTCTTCCAAGCAAGATGATAAGTCCTCCAGACCATCTATAAGT
* ***
29003 CCTCTAGACATAATGTTTTCATATGCTTTTTGAAAAAAAAAATGAGAAATTGATTTTCAAAGTTT
131 CCTCTAGACATAATGTTTTCATATGATTTTTG----AAAAAATGAGAAAGCAATTTTCAAAGTTT
* * * * * *
29068 ATCATTTAATCTTTTCTGAAAATTAATTTTTTTAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTA
192 ATCATTTAATCTTTTCTAAAAATGAAATTTTTGAAAAATAAGAAAGCAATTTCCAAAGCTTCTTA
* * * * * *
29133 CTTAGTAGGTCTTCCAGGCCATCAGTAAGTCCTCCGAGCATGATGATTGAATCCTCCGTGTCATA
257 CTTAGTAAGTCCTCCAAGCCATCAGTAAGTCCTCCGAGCATGATGATTAAATCATCCGGGTCATA
* * * *
29198 TGTAAGTCTTCCGATCAAGATGATAAGTCCCCCGGGCCATCTATAATTCCTATGGGTATCATGTT
322 TGTAAGTCTTCCGAGCAAAATGATAAGTCCCCCGGGCCATCTATAAGTCCTATGGGCATCATGTT
* *
29263 T-CATATGATTTTT-GAAAAAATGAGAAAGCA
387 TCCATATGATTTTTCAAAAAAATGAGAAAACA
*
29293 ATTTTGAAAGTTTCTTACTTAGTAAGTCCT-TAGGCCTATCAATAAGTCTTCCAAACATGATGAT
1 ATTTTCAAAGTTTCTTACTTAGTAAGTCCTCTAGGCC-ATCAATAAGTCTTCCAAACATGATGAT
* * * *** * *
29357 TAAATCC-TCTGGGTCATTTGTAAGTGTTCCGAGCAAGATGATAAGTCCTTTGGACCATTTATTA
65 TAAATCCTTC-GGGTCATTTATAAGTCTTCCAAGCAAGATGATAAGTCCTCCAGACCATCTATAA
* * *
29421 GTCCT-TCAGGCATGATGTTTTCATATGATTTTTG-AAAAATGAGAAAGCAATTTTCAAAGTTTC
129 GTCCTCT-AGACATAATGTTTTCATATGATTTTTGAAAAAATGAGAAAGCAATTTTCAAAGTTTA
* *
29484 TCATTTAATCTTTTCTAAAAATGAAATTTTTGAAAAATAAGAAAGTAATTTCCAAAGCTTGTTAC
193 TCATTTAATCTTTTCTAAAAATGAAATTTTTGAAAAATAAGAAAGCAATTTCCAAAGCTTCTTAC
* * * * * *
29549 TTAGTAAGTCCTCCAAGTCATTAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCT
258 TTAGTAAGTCCTCCAAGCCATCAGTAAGTCCTCCGAGCATGATGATTAAATCATCCGGGTCATAT
* * * * *
29614 GTAAGTCTTTCGAGCAAAATGATAAGTCCTCCGGGCCATCTATACGTCCTCTGGGCATGATGTTT
323 GTAAGTCTTCCGAGCAAAATGATAAGTCCCCCGGGCCATCTATAAGTCCTATGGGCATCATGTTT
29679 CCATATGATTTTTCAAAAAAATGAGAAAACA
388 CCATATGATTTTTCAAAAAAATGAGAAAACA
*
29710 ATTTTCTAAGTTTCT
1 ATTTTCAAAGTTTCT
29725 CATTTAATCA
Statistics
Matches: 367, Mismatches: 60, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
415 191 0.52
416 12 0.03
417 28 0.08
419 8 0.02
420 128 0.35
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (418 bp):
ATTTTCAAAGTTTCTTACTTAGTAAGTCCTCTAGGCCATCAATAAGTCTTCCAAACATGATGATT
AAATCCTTCGGGTCATTTATAAGTCTTCCAAGCAAGATGATAAGTCCTCCAGACCATCTATAAGT
CCTCTAGACATAATGTTTTCATATGATTTTTGAAAAAATGAGAAAGCAATTTTCAAAGTTTATCA
TTTAATCTTTTCTAAAAATGAAATTTTTGAAAAATAAGAAAGCAATTTCCAAAGCTTCTTACTTA
GTAAGTCCTCCAAGCCATCAGTAAGTCCTCCGAGCATGATGATTAAATCATCCGGGTCATATGTA
AGTCTTCCGAGCAAAATGATAAGTCCCCCGGGCCATCTATAAGTCCTATGGGCATCATGTTTCCA
TATGATTTTTCAAAAAAATGAGAAAACA
Found at i:30042 original size:239 final size:237
Alignment explanation
Indices: 29270--30301 Score: 1156
Period size: 238 Copynumber: 4.3 Consensus size: 237
29260 GTTTCATATG
* * ** **
29270 ATTTTTGAAAAAATGAGAAAGCAATTTTGAAAGTTTCTTACTTAGTAAGTCCTTAGGCCTATCAA
1 ATTTTTG-AAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACTTAGTAAGTCCTCCGGCC-ATCAA
* * * * * *
29335 TAAGTCTTCCAAACATGATGATTAAATC-CTCTGGGTCATTTGTAAGTGTTCCGAGCAAGATGAT
64 TAAGTCTTCCGAGCATGATGATTAAATCATTC-GGGTCATTTGTAAGTCTTTCGAGCAAGATAAT
** * * * *
29399 AAGTCCTTTGGACCATTTATTAGTCCTTCAGGCATGATGTTTTCATATGATTTTTGAAAAATGAG
128 AAGTCCTCCGGGCCATCTATAAGTCCTTCAGGCATAATGTTTTCATATGATTTTTGAAAAATGAG
* *
29464 AAAGCAATTTTCAAAGTTTCTCATTTAATCTTTTCTAAAAATGAA
193 AAAACAATTTTCAAAGTTTCTCATTTAATCTTTTCTAAAAGTGAA
* * * * * * * *
29509 ATTTTTGAAAAATAAGAAAGTAATTTCCAAAGCTTGTTACTTAGTAAGTCCTCCAAGTCATTAGT
1 ATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACTTAGTAAGTCCTCC-GGCCATCAAT
* * * *
29574 AAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAAATGATAA
65 AAGTCTTCCGAGCATGATGATTAAATCATTCGGGTCATTTGTAAGTCTTTCGAGCAAGATAATAA
* * * * *
29639 GTCCTCCGGGCCATCTATACGTCC-TCTGGGCATGATGTTTCCATATGATTTTTCAAAAAAATGA
130 GTCCTCCGGGCCATCTATAAGTCCTTC-AGGCATAATGTTTTCATATGATTTTT--GAAAAATGA
* * *
29703 GAAAACAATTTTCTAAGTTTCTCATTTAATCATTTCTGAAAGTGAA
192 GAAAACAATTTTCAAAGTTTCTCATTTAATCTTTTCTAAAAGTGAA
* * * * *
29749 TTTTTTGAAAAGTAAGAAAGTAATTTCCAAAGTTTCTTACTTAGTAAATCCTCCGGGCGAACAAT
1 ATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACTTAGTAAGTCCTCC-GGCCATCAAT
* * * *
29814 AAGTCTTTCGAGCATGATGACTAAATCATTCAGGTCATTTGTAAGTCTTTCGATCAAGATAATAA
65 AAGTCTTCCGAGCATGATGATTAAATCATTCGGGTCATTTGTAAGTCTTTCGAGCAAGATAATAA
* * * * * *
29879 GTCCTCTGGGTCTTCTATAAGTCCTTCAGGCATAATGTTTTCATTTGCTTTTTGAAAAGATGATA
130 GTCCTCCGGGCCATCTATAAGTCCTTCAGGCATAATGTTTTCATATGATTTTTGAAAA-ATGAGA
*** * *
29944 AAGTGATTTTCAAAGTTTCTCATTTAATCTTTTTTGAAAGTGAA
194 AAACAATTTTCAAAGTTTCTCATTTAATCTTTTCTAAAAGTGAA
* * * * *
29988 ATTTTTGAAATGTAAGAAAGCGATTTCTAAAGTTTCTTACTAAGTAAGTCCTCCGGCCCATCAGT
1 ATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACTTAGTAAGTCCTCCGG-CCATCAAT
* * * *
30053 AAGTCTTCCGAGCATGATGATTAAATCCTTCGGGTCATTTGCAAGTCTTTTGAGAAAGA-AGATA
65 AAGTCTTCCGAGCATGATGATTAAATCATTCGGGTCATTTGTAAGTCTTTCGAGCAAGATA-ATA
* * * *
30117 TA-TCCTCCGAGCCATCTATAAGACCTCCAGGAATAATGTTTTCATATGATTTTTGAAAAATGAG
129 -AGTCCTCCGGGCCATCTATAAGTCCTTCAGGCATAATGTTTTCATATGATTTTTGAAAAATGAG
*
30181 AAAACAATTTTCAAAGTTTCTCATTTAATCTTTTCTAAAAAG-AAA
193 AAAACAATTTTCAAAGTTTCTCATTTAATCTTTTCT-AAAAGTGAA
** * * * * * *
30226 ATGCTTGAAAAGTAATAAAGCGATTTCCAAAGTTTTTTACTTAGTAAGTCCTTCGGGACATCAGT
1 ATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACTTAGTAAGTCC-TCCGGCCATCAAT
*
30291 AAGTCTCCCGA
65 AAGTCTTCCGA
30302 ACAATTTGAT
Statistics
Matches: 668, Mismatches: 113, Indels: 25
0.83 0.14 0.03
Matches are distributed among these distances:
237 2 0.00
238 245 0.37
239 216 0.32
240 203 0.30
241 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (237 bp):
ATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACTTAGTAAGTCCTCCGGCCATCAATA
AGTCTTCCGAGCATGATGATTAAATCATTCGGGTCATTTGTAAGTCTTTCGAGCAAGATAATAAG
TCCTCCGGGCCATCTATAAGTCCTTCAGGCATAATGTTTTCATATGATTTTTGAAAAATGAGAAA
ACAATTTTCAAAGTTTCTCATTTAATCTTTTCTAAAAGTGAA
Found at i:30751 original size:44 final size:44
Alignment explanation
Indices: 30702--30854 Score: 207
Period size: 44 Copynumber: 3.5 Consensus size: 44
30692 CCTTGGCCTG
*
30702 TCCATCTCATAAGGAGTTGGATTAGCATCAACATTTCGCTCGAT
1 TCCATCACATAAGGAGTTGGATTAGCATCAACATTTCGCTCGAT
* * * **
30746 TCCATCACTTAAGGAGTTGGATGAGCATCAACATTTTGCTTTAT
1 TCCATCACATAAGGAGTTGGATTAGCATCAACATTTCGCTCGAT
* * *
30790 TCCATCACATAAGGAGTTGGATTAGCATCACCATTTCGTTCGTT
1 TCCATCACATAAGGAGTTGGATTAGCATCAACATTTCGCTCGAT
* *
30834 TCCATCACATATGGATTTGGA
1 TCCATCACATAAGGAGTTGGA
30855 ACATCAATAT
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 93 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (44 bp):
TCCATCACATAAGGAGTTGGATTAGCATCAACATTTCGCTCGAT
Found at i:30870 original size:88 final size:87
Alignment explanation
Indices: 30702--30861 Score: 234
Period size: 88 Copynumber: 1.9 Consensus size: 87
30692 CCTTGGCCTG
* *
30702 TCCATCTCATAAGGAGTTGGATTAGCATCAACATTTCGCTCGATTCCATCACTTAAGGAGTTGGA
1 TCCATCACATAAGGAGTTGGATTAGCATCAACATTTCGCTCGATTCCATCACATAAGGAGTTGGA
30767 TGAGCATCAACATTTTGCTTTAT
66 -GAGCATCAACATTTTGCTTTAT
* * * * *
30790 TCCATCACATAAGGAGTTGGATTAGCATCACCATTTCGTTCGTTTCCATCACATATGGATTTGGA
1 TCCATCACATAAGGAGTTGGATTAGCATCAACATTTCGCTCGATTCCATCACATAAGGAGTTGGA
30855 -A-CATCAA
66 GAGCATCAA
30862 TATTATTTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
85 6 0.09
86 1 0.02
88 58 0.89
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (87 bp):
TCCATCACATAAGGAGTTGGATTAGCATCAACATTTCGCTCGATTCCATCACATAAGGAGTTGGA
GAGCATCAACATTTTGCTTTAT
Found at i:37883 original size:16 final size:15
Alignment explanation
Indices: 37862--37891 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
37852 ACCGCAACGA
37862 TTAATATGTTATTTTG
1 TTAATATGTT-TTTTG
37878 TTAATATGTTTTTT
1 TTAATATGTTTTTT
37892 ACAATATGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (15 bp):
TTAATATGTTTTTTG
Found at i:45854 original size:30 final size:30
Alignment explanation
Indices: 45770--45997 Score: 172
Period size: 30 Copynumber: 7.7 Consensus size: 30
45760 TATTTAACAC
* * *
45770 TTGCTA-TTTAGACCCTTAAGTTTCAATTT
1 TTGCTATTTTAGTCCTTTAAGTTTCTATTT
* * *
45799 TTACTATCTTAGCCCTTTAAGTTTCTATTT
1 TTGCTATTTTAGTCCTTTAAGTTTCTATTT
* * **
45829 TTGCCATTTTATTCCTTTAAGTTTCTGGTT
1 TTGCTATTTTAGTCCTTTAAGTTTCTATTT
* * * *
45859 TTGCCATTTTATTCCTTTAAATTTATATTT
1 TTGCTATTTTAGTCCTTTAAGTTTCTATTT
* * * *
45889 TT-CTGTGTTAGTCCTTTAAGTTTATGTTT
1 TTGCTATTTTAGTCCTTTAAGTTTCTATTT
* * * **
45918 TTTCTATTTTAGTCCCTTAAATTTCTGGTT
1 TTGCTATTTTAGTCCTTTAAGTTTCTATTT
** * * * *
45948 TTGCTGGTTTAGCCCTTTAATTTTATGTTT
1 TTGCTATTTTAGTCCTTTAAGTTTCTATTT
*
45978 TTGCTATTTAAGTCCTTTAA
1 TTGCTATTTTAGTCCTTTAA
45998 ATCGAATATG
Statistics
Matches: 157, Mismatches: 40, Indels: 3
0.79 0.20 0.01
Matches are distributed among these distances:
29 28 0.18
30 129 0.82
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.55
Consensus pattern (30 bp):
TTGCTATTTTAGTCCTTTAAGTTTCTATTT
Found at i:45965 original size:89 final size:89
Alignment explanation
Indices: 45795--45997 Score: 219
Period size: 89 Copynumber: 2.3 Consensus size: 89
45785 TTAAGTTTCA
* * * * * *
45795 ATTTTTACTATCTTAGCCCTTTAAGTTTCTATTTTTGCCATTTTATTCCTTTAAGTTTCTGGTTT
1 ATTTTTGCTAT-TTAGTCCTTTAAGTTTATATTTTTGCCATTTTAGTCCCTTAAATTTCTGGTTT
* **
45860 TGCCATTTTATTCCTTTAAATTTAT
65 TGCCAGTTTAGCCCTTTAAATTTAT
* * * *
45885 ATTTTT-CTGTGTTAGTCCTTTAAGTTTATGTTTTTTCTATTTTAGTCCCTTAAATTTCTGGTTT
1 ATTTTTGCTAT-TTAGTCCTTTAAGTTTATATTTTTGCCATTTTAGTCCCTTAAATTTCTGGTTT
** *
45949 TGCTGGTTTAGCCCTTTAATTTTAT
65 TGCCAGTTTAGCCCTTTAAATTTAT
*
45974 GTTTTTGCTATTTAAGTCCTTTAA
1 ATTTTTGCTATTT-AGTCCTTTAA
45998 ATCGAATATG
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
89 74 0.80
90 19 0.20
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.57
Consensus pattern (89 bp):
ATTTTTGCTATTTAGTCCTTTAAGTTTATATTTTTGCCATTTTAGTCCCTTAAATTTCTGGTTTT
GCCAGTTTAGCCCTTTAAATTTAT
Found at i:46230 original size:5 final size:5
Alignment explanation
Indices: 46217--46252 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
46207 CGATTTTCAT
* *
46217 TTTTA TTTTG TTTTA TTTTA TTGTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
46253 CTTGGTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:51241 original size:36 final size:37
Alignment explanation
Indices: 51200--51345 Score: 145
Period size: 36 Copynumber: 4.0 Consensus size: 37
51190 ATAAAGTGTC
* * *
51200 GTCTCGCTAGAGACAGTTT-TCTTAGAAACAAATTTT
1 GTCTCGCTTGAGACAATTTCTCTAAGAAACAAATTTT
* *
51236 GTCTCGCTTGAGACAATCTTCTCTAAAAAAACAAATTGT
1 GTCTCGCTTGAGACAAT-TTCTCT-AAGAAACAAATTTT
* * *
51275 GTCTCGCTTGAGACAATTTCACTCA-AAACAAATTTC
1 GTCTCGCTTGAGACAATTTCTCTAAGAAACAAATTTT
* * * *
51311 GTTTCGCTTGAGAC-ATTTTTCTGAGATACAAATTT
1 GTCTCGCTTGAGACAATTTCTCTAAGAAACAAATTT
51346 CAACGTTGTT
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
35 7 0.08
36 46 0.50
37 3 0.03
38 8 0.09
39 28 0.30
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (37 bp):
GTCTCGCTTGAGACAATTTCTCTAAGAAACAAATTTT
Found at i:51278 original size:39 final size:35
Alignment explanation
Indices: 51225--51325 Score: 121
Period size: 39 Copynumber: 2.7 Consensus size: 35
51215 GTTTTCTTAG
*
51225 AAACAAATTTTGTCTCGCTTGAGACAATCTTCTCTAAAA
1 AAACAAA-TTTGTCTCGCTTGAGACAAT-TTCACT--AA
*
51264 AAACAAATTGTGTCTCGCTTGAGACAATTTCACTCA
1 AAACAAATT-TGTCTCGCTTGAGACAATTTCACTAA
*
51300 AAACAAATTTCGTTTCGCTTGAGACA
1 AAACAAATTT-GTCTCGCTTGAGACA
51326 TTTTTCTGAG
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
35 1 0.02
36 24 0.42
38 7 0.12
39 25 0.44
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.32
Consensus pattern (35 bp):
AAACAAATTTGTCTCGCTTGAGACAATTTCACTAA
Found at i:51304 original size:75 final size:74
Alignment explanation
Indices: 51168--51325 Score: 185
Period size: 75 Copynumber: 2.1 Consensus size: 74
51158 ACTATGAGCT
** * * * *
51168 CTTGAGATTATCTTCTTAAAAAATAAAGTGTCGTCTCGCTAGAGACAGTTTTCTTAGAAACAAAT
1 CTTGAGACAATCTTCTTAAAAAACAAAGTGTCGTCTCGCTAGAGACAATTTACTCAGAAACAAAT
*
51233 TTTGTCTCG
66 TTCGTCTCG
* *
51242 CTTGAGACAATCTTCTCTAAAAAAACAAATTGT-GTCTCGCTTGAGACAATTTCACTCA-AAACA
1 CTTGAGACAATCTTCT-T-AAAAAACAAAGTGTCGTCTCGCTAGAGACAATTT-ACTCAGAAACA
*
51305 AATTTCGTTTCG
63 AATTTCGTCTCG
51317 CTTGAGACA
1 CTTGAGACA
51326 TTTTTCTGAG
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
74 14 0.20
75 42 0.59
76 15 0.21
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (74 bp):
CTTGAGACAATCTTCTTAAAAAACAAAGTGTCGTCTCGCTAGAGACAATTTACTCAGAAACAAAT
TTCGTCTCG
Found at i:51654 original size:64 final size:65
Alignment explanation
Indices: 51471--51691 Score: 202
Period size: 66 Copynumber: 3.4 Consensus size: 65
51461 CAAAATTGAC
* * * * * * *
51471 AATCTTTGAGTCTTTTTCTCTTAAAACAAAATATTGTCT--CTTAAGATAGTTTCTCTTAAAACA
1 AATCTTTGAGTCTATTTCCCTTAAAAC-GAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAAC-
51534 AAAT
64 --AT
* **
51538 CATCTTTGAGTC-ATTTCCCTCGAAACGAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAA-A-
1 AATCTTTGAGTCTATTTCCCTTAAAACGAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAACAT
* * * *
51600 AATCTTTGAGTCTATTTCCCTTAAAAC-AAGGTTTTGTCTCCTTTGAGACTGTTTCCTTTGAAAC
1 AATCTTTGAGTCTATTTCCCTTAAAACGAA--TTTTGTCTCCCTTAAGACAGTTTCCCTTGAAAC
51664 AT
64 AT
* *
51666 CATCTTTGAGTCTGTTTCCCTTAAAA
1 AATCTTTGAGTCTATTTCCCTTAAAA
51692 TAATATCCAT
Statistics
Matches: 128, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
62 13 0.10
63 13 0.10
64 28 0.22
65 10 0.08
66 34 0.27
67 30 0.23
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.40
Consensus pattern (65 bp):
AATCTTTGAGTCTATTTCCCTTAAAACGAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAACAT
Found at i:51993 original size:131 final size:130
Alignment explanation
Indices: 51715--52179 Score: 467
Period size: 131 Copynumber: 3.6 Consensus size: 130
51705 GATGGTATGT
* * *
51715 CATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCATATCACGTAGGAGTCGTGT
1 CATCCTCATCGCGTAGGAACCATGTCATCCCCTGACCAGACCTCCTTATCACGTAGGAGTCGTGT
* * ** * * *
51780 -AAACCTAGATAACCAATCATCCTCATCATGTAGGAACTGAGTTATCATCCCTAAAGATGACATG
66 CAACCCTAGATAA-CAGTCATCCTCATCGCGTAGGAACGGAGTTATAATCCCTAAAGATGACATA
51844 C
130 C
** ** *
51845 CATCCTCATCGTATAGGAACCATGTCATCCAATGACCAGACCTCCTTATCACGTAGGAGTCATGT
1 CATCCTCATCGCGTAGGAACCATGTCATCCCCTGACCAGACCTCCTTATCACGTAGGAGTCGTGT
* *
51910 CAACCCTAGATAATCAGTCATCCTCATCGCGTAGGAACGGTGTTATAATCCCTAAAGATTATC-T
66 CAACCCTAGATAA-CAGTCATCCTCATCGCGTAGGAACGGAGTTATAATCCCTAAAGATGA-CAT
51974 AC
129 AC
* * * *
51976 CATCCTTATCGCGTAGGAACCGTGTCATCCCCTGACCATACCTCCTCATCACGTAGGAGTCGTGT
1 CATCCTCATCGCGTAGGAACCATGTCATCCCCTGACCAGACCTCCTTATCACGTAGGAGTCGTGT
* * * *
52041 C-ACCTTAGATAACATGTCGTCCTCATTGCGTAGGAATC-GAGTTATCACTATTCCTAAAGATGG
66 CAACCCTAGATAACA-GTCATCCTCATCGCGTAGGAA-CGGAGTTAT-A--ATCCCTAAAGAT-G
* **
52104 TC-TGT
125 ACATAC
* *** * * * *
52109 CGTCCTCATCAAATAGGAACCTTGTCATCCACC-GACCATATCTCCTCATCACGTAGGAGTCGTG
1 CATCCTCATCGCGTAGGAACCATGTCATCC-CCTGACCAGACCTCCTTATCACGTAGGAGTCGTG
52173 TC-ACCCT
65 TCAACCCT
52180 TAAATGACCA
Statistics
Matches: 282, Mismatches: 44, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
129 2 0.01
130 92 0.33
131 112 0.40
132 1 0.00
133 73 0.26
134 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.26
Consensus pattern (130 bp):
CATCCTCATCGCGTAGGAACCATGTCATCCCCTGACCAGACCTCCTTATCACGTAGGAGTCGTGT
CAACCCTAGATAACAGTCATCCTCATCGCGTAGGAACGGAGTTATAATCCCTAAAGATGACATAC
Found at i:52375 original size:3 final size:3
Alignment explanation
Indices: 52369--52441 Score: 96
Period size: 3 Copynumber: 24.3 Consensus size: 3
52359 CTAAAAAAAC
* *
52369 ATT ATT AATT A-T ATT ATT AATT A-T ATT ATT ACT ATT ATT ATT ACT
1 ATT ATT -ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
52414 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
52442 ATTTACAATT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.06
3 52 0.84
4 6 0.10
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:53006 original size:9 final size:9
Alignment explanation
Indices: 52992--53016 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52982 TAAAAACAAC
52992 AAAGAAAAA
1 AAAGAAAAA
53001 AAAGAAAAA
1 AAAGAAAAA
53010 AAAGAAA
1 AAAGAAA
53017 GGAAAGAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:53907 original size:30 final size:29
Alignment explanation
Indices: 53857--54057 Score: 147
Period size: 30 Copynumber: 6.8 Consensus size: 29
53847 TTATTTAACA
* * *
53857 TTTT-CTA-TTTAGACCCTTAAGTTTCAAT
1 TTTTGCTATTTTAGTCCTTTAAGTTT-AGT
* * *
53885 TTTTACTATTTTAGCCCTTTAAGTTTCTGT
1 TTTTGCTATTTTAGTCCTTTAAGTTT-AGT
* * * *
53915 TTTTGCCATTTTATTCCTTTAAATTT-TT
1 TTTTGCTATTTTAGTCCTTTAAGTTTAGT
* * * *
53943 GTTTTACTGTGTTAGTCCTTTAAGTTTATTT
1 -TTTTGCTATTTTAGTCCTTTAAGTTTA-GT
* *
53974 TTTTGCTATTTTAGTCCTTTAAATTTTTGT
1 TTTTGCTATTTTAGTCCTTT-AAGTTTAGT
* *
54004 TTTTGCTATCTTAGCCCTTTAAGTTTATGT
1 TTTTGCTATTTTAGTCCTTTAAGTTTA-GT
* *
54034 TTTTTCTATTTAAGTCCTTTAAGT
1 TTTTGCTATTTTAGTCCTTTAAGT
54058 CGAATATGAT
Statistics
Matches: 136, Mismatches: 30, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
28 5 0.04
29 28 0.21
30 96 0.71
31 7 0.05
ACGTcount: A:0.18, C:0.14, G:0.10, T:0.58
Consensus pattern (29 bp):
TTTTGCTATTTTAGTCCTTTAAGTTTAGT
Found at i:53969 original size:59 final size:60
Alignment explanation
Indices: 53884--54055 Score: 238
Period size: 59 Copynumber: 2.9 Consensus size: 60
53874 TAAGTTTCAA
* * * *
53884 TTTTTACTATTTTAGCCCTTTAAGTTTCTGTTTTTGCCATTTTATTCCTTTAAATTTTTG
1 TTTTTACTATCTTAGCCCTTTAAGTTTATGTTTTTGCTATTTTAGTCCTTTAAATTTTTG
* * * *
53944 -TTTTACTGTGTTAGTCCTTTAAGTTTATTTTTTTGCTATTTTAGTCCTTTAAATTTTTG
1 TTTTTACTATCTTAGCCCTTTAAGTTTATGTTTTTGCTATTTTAGTCCTTTAAATTTTTG
* * *
54003 TTTTTGCTATCTTAGCCCTTTAAGTTTATGTTTTTTCTATTTAAGTCCTTTAA
1 TTTTTACTATCTTAGCCCTTTAAGTTTATGTTTTTGCTATTTTAGTCCTTTAA
54056 GTCGAATATG
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
59 52 0.54
60 45 0.46
ACGTcount: A:0.17, C:0.13, G:0.10, T:0.59
Consensus pattern (60 bp):
TTTTTACTATCTTAGCCCTTTAAGTTTATGTTTTTGCTATTTTAGTCCTTTAAATTTTTG
Found at i:57029 original size:20 final size:23
Alignment explanation
Indices: 56995--57045 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
56985 TGAAGTCTGC
56995 TTTTCTTTCATCTTCACTC-TTA
1 TTTTCTTTCATCTTCACTCATTA
*
57017 -TTTCTTT-ATCTTCTCTCATTA
1 TTTTCTTTCATCTTCACTCATTA
57038 TTTTCTTT
1 TTTTCTTT
57046 TCACAATGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 9 0.35
21 10 0.38
22 7 0.27
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTCTTTCATCTTCACTCATTA
Found at i:63224 original size:31 final size:30
Alignment explanation
Indices: 63179--63255 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 30
63169 AGATAAGTCA
*
63179 TTTTATTATTTTATTATTT-TATTTTATTTACT
1 TTTTATT-TTTTATT-TTTCTA-TTTATATACT
*
63211 TTTTATTTTTTATTTTTCTATTTATATATT
1 TTTTATTTTTTATTTTTCTATTTATATACT
63241 TATTTA-TTTTTATTT
1 T-TTTATTTTTTATTT
63256 ATATTTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 21 0.51
31 13 0.32
32 7 0.17
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTATTTTTTATTTTTCTATTTATATACT
Found at i:63227 original size:8 final size:8
Alignment explanation
Indices: 63179--63251 Score: 60
Period size: 8 Copynumber: 9.2 Consensus size: 8
63169 AGATAAGTCA
*
63179 TTTTATTA
1 TTTTATTT
*
63187 TTTTATTA
1 TTTTATTT
63195 TTTTATTT
1 TTTTATTT
*
63203 TATTTA-CT
1 T-TTTATTT
63211 TTTTA-TT
1 TTTTATTT
63218 TTTTATTT
1 TTTTATTT
*
63226 TTCTATTT
1 TTTTATTT
* *
63234 ATATATTT
1 TTTTATTT
*
63242 ATTTATTT
1 TTTTATTT
63250 TT
1 TT
63252 ATTTATATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
7 10 0.18
8 41 0.75
9 4 0.07
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTATTT
Found at i:63246 original size:4 final size:4
Alignment explanation
Indices: 63196--63257 Score: 53
Period size: 4 Copynumber: 16.2 Consensus size: 4
63186 ATTTTATTAT
* *
63196 TTTA TTTTA TTTA CTT- TTTA TTT- TTTA TTT- TTCTA TTTA TATA TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA
63243 TTTA -TT- TTTA TTTA T
1 TTTA TTTA TTTA TTTA T
63258 ATTTTTTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
3 11 0.23
4 30 0.64
5 6 0.13
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:64036 original size:9 final size:9
Alignment explanation
Indices: 64024--64057 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
64014 AAAAAAGGAA
64024 AAAAATGAG
1 AAAAATGAG
**
64033 AAAAATGTT
1 AAAAATGAG
64042 AAAAATGAG
1 AAAAATGAG
64051 AAAAATG
1 AAAAATG
64058 TGAAGAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (9 bp):
AAAAATGAG
Found at i:64036 original size:18 final size:18
Alignment explanation
Indices: 64015--64055 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
64005 AAAATGTTCA
64015 AAAAAGGAAAAAAATGAG
1 AAAAAGGAAAAAAATGAG
* **
64033 AAAAATGTTAAAAATGAG
1 AAAAAGGAAAAAAATGAG
64051 AAAAA
1 AAAAA
64056 TGTGAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (18 bp):
AAAAAGGAAAAAAATGAG
Found at i:64056 original size:18 final size:18
Alignment explanation
Indices: 64024--64058 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
64014 AAAAAAGGAA
64024 AAAAATGAGAAAAATGTT
1 AAAAATGAGAAAAATGTT
64042 AAAAATGAGAAAAATGT
1 AAAAATGAGAAAAATGT
64059 GAAGAAAAAA
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:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (18 bp):
AAAAATGAGAAAAATGTT
Found at i:66955 original size:16 final size:15
Alignment explanation
Indices: 66932--66971 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
66922 TAAACATAAC
66932 AAAATATTATAACA-A
1 AAAATATTATAA-ATA
66947 AACAATATTATAAATA
1 AA-AATATTATAAATA
66963 AAAATATTA
1 AAAATATTA
66972 GATTTGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATATTATAAATA
Found at i:68274 original size:22 final size:22
Alignment explanation
Indices: 68151--68272 Score: 199
Period size: 22 Copynumber: 5.5 Consensus size: 22
68141 TTCAGTATTT
68151 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
68173 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
* * *
68195 GTCCTGAAGGACTACTAGATAC
1 GTCCCGAAGGACCACTGGATAC
*
68217 GTTCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
68239 GTCCCGAAGGACTACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
68261 GTCCCGAAGGAC
1 GTCCCGAAGGAC
68273 TAATATACCC
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 91 1.00
ACGTcount: A:0.28, C:0.29, G:0.27, T:0.16
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Done.