Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008754.1 Hibiscus syriacus cultivar Beakdansim tig00111845_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: 290996
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:218059 original size:112 final size:112
Alignment explanation
Indices: 217691--218161 Score: 707
Period size: 111 Copynumber: 4.2 Consensus size: 112
217681 TTTCAAAAGT
* * * *
217691 ATCGATAC-TTATAATAAAGTAGCGACACTATT-AACATATCCGGTAGCGCTTTACCTATTTTGT
1 ATCGATACATTTTTATAAAGTATCGACACT-TTCAACATATCCGGTAGCGCTTTACCTGTTTTGT
* *
217754 CATTTATAGACCGGTTTTGTCA-TTTTTTACATGTTTTATTGTTATGG
65 CATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGG
* *
217801 ATCGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACTTGTTTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
*
217866 ATTTATAGACCGGTTTTGT-AATTTTTTACCTGTTATATTGTTATGG
66 ATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGG
* *
217912 ATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
217977 ATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGG
66 ATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGG
** * *
218024 ATATATATATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
* * * *
218089 ATTTATAGGCCGGTTTTATCATTTTTTTACTTGTTATATTGCTATGG
66 ATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGG
** *
218136 ATTAATATATTTTTATAAAGTATCGA
1 ATCGATACATTTTTATAAAGTATCGA
218162 TACAAACCGA
Statistics
Matches: 336, Mismatches: 21, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
110 10 0.03
111 172 0.51
112 154 0.46
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (112 bp):
ATCGATACATTTTTATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
ATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGG
Found at i:218091 original size:223 final size:223
Alignment explanation
Indices: 217691--218161 Score: 705
Period size: 223 Copynumber: 2.1 Consensus size: 223
217681 TTTCAAAAGT
* * *
217691 ATCGATAC-TTATAATAAAGTAGCGACACTATTAACATATCCGGTAGCGCTTTACCTATTTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTATTAACATATCCGGTAGCGCTTTACCTATTTTGTC
* *
217755 ATTTATAGACCGGTTTTGTCATTTTTTACATGTTTTATTGTTATGGATCGATACATTTTTATAAA
66 ATTTATAGACCGGTTTTGTCATTTTTTACATGTTATATTGTTATGGATAGATACATTTTTATAAA
* *
217820 GTATCGACACTATCAACATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGTTTTGT
131 GTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTAT
*
217885 -AATTTTTTACCTGTTATATTGTTATGG
196 CAATTTTTTACCTGTTATATTGCTATGG
* * *
217912 ATCGATACATTTTTATAAAGTATCGACACT-TTCAATATATCCGGTAGCGCTTTACTTGTTTTGT
1 ATCGATACATTTTTATAAAGTATCGACACTATT-AACATATCCGGTAGCGCTTTACCTATTTTGT
* * *
217976 CATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATATATATATTTTTATA
65 CATTTATAGACCGGTTTTGTCA-TTTTTTACATGTTATATTGTTATGGATAGATACATTTTTATA
* * *
218041 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGGCCGGTTTT
129 AAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
* *
218106 ATCATTTTTTTACTTGTTATATTGCTATGG
194 ATCAATTTTTTACCTGTTATATTGCTATGG
** *
218136 ATTAATATATTTTTATAAAGTATCGA
1 ATCGATACATTTTTATAAAGTATCGA
218162 TACAAACCGA
Statistics
Matches: 224, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
221 10 0.04
222 68 0.30
223 99 0.44
224 47 0.21
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (223 bp):
ATCGATACATTTTTATAAAGTATCGACACTATTAACATATCCGGTAGCGCTTTACCTATTTTGTC
ATTTATAGACCGGTTTTGTCATTTTTTACATGTTATATTGTTATGGATAGATACATTTTTATAAA
GTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTAT
CAATTTTTTACCTGTTATATTGCTATGG
Found at i:218334 original size:18 final size:20
Alignment explanation
Indices: 218293--218335 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
218283 GCGGTTCACG
218293 GAATGTAAGATTATCAATGA
1 GAATGTAAGATTATCAATGA
218313 GAATGTAAGATTA-CAA-GA
1 GAATGTAAGATTATCAATGA
218331 GAATG
1 GAATG
218336 AGAATGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.30
19 3 0.13
20 13 0.57
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.26
Consensus pattern (20 bp):
GAATGTAAGATTATCAATGA
Found at i:220542 original size:36 final size:35
Alignment explanation
Indices: 220460--220544 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 35
220450 AATTATATTT
*
220460 TAAACCCTAAATTCCAAAATACTTCAATTACATCA
1 TAAACCCCAAATTCCAAAATACTTCAATTACATCA
**
220495 TAAACATCAAATTCCAAAAATACTTCAATTACATGCA
1 TAAACCCCAAATTCC-AAAATACTTCAATTACAT-CA
*
220532 -CAACCCCAAATTC
1 TAAACCCCAAATTC
220545 ATAATCCATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 12 0.29
36 28 0.67
37 2 0.05
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (35 bp):
TAAACCCCAAATTCCAAAATACTTCAATTACATCA
Found at i:224444 original size:153 final size:148
Alignment explanation
Indices: 224145--224444 Score: 519
Period size: 148 Copynumber: 2.0 Consensus size: 148
224135 AAAAACTATT
* *
224145 TAAATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCG
1 TAAATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCG
*
224210 AAAATTCAATTCAATTCTACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAA
66 AAAATTCAATTCAATTCTACTTGATTTAAAATTTATAAACTCAAATCGAAAAAATTTCGAGTCAA
*
224275 TTATTTTATAAACTGAAC
131 CTATTTTATAAACTGAAC
224293 TAAATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCG
1 TAAATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCG
224358 AAAATTCAATTCAATTCAATTCGACTTGATTTAAAATTTATAAACTCAAATCGAAAAAATTTCGA
66 AAAATTCAATTCAATTC---T--ACTTGATTTAAAATTTATAAACTCAAATCGAAAAAATTTCGA
224423 GTCAACTATTTTATAAACTGAA
126 GTCAACTATTTTATAAACTGAA
224445 TTGAGTATTT
Statistics
Matches: 143, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
148 80 0.56
151 1 0.01
153 62 0.43
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.36
Consensus pattern (148 bp):
TAAATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCG
AAAATTCAATTCAATTCTACTTGATTTAAAATTTATAAACTCAAATCGAAAAAATTTCGAGTCAA
CTATTTTATAAACTGAAC
Found at i:224663 original size:35 final size:35
Alignment explanation
Indices: 224624--224702 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 35
224614 ATTGGGCATG
* *
224624 TAATTGATGTATTTTGGAATTTGAGGTTTAGAATA
1 TAATTGATGTATTTTAGAATTTGAGGTTTAAAATA
* ** * *
224659 TAATTGAAGTATTTTAGTTTTTGGGGTTTAAAATG
1 TAATTGATGTATTTTAGAATTTGAGGTTTAAAATA
224694 TAATTGATG
1 TAATTGATG
224703 ATTGTGTTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (35 bp):
TAATTGATGTATTTTAGAATTTGAGGTTTAAAATA
Found at i:225615 original size:34 final size:35
Alignment explanation
Indices: 225575--225640 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
225565 CTCCAACCAG
225575 ATATCTTTTAATATCT-AAAT-TTAAACATATAATA
1 ATATCTTTTAA-ATCTAAAATATTAAACATATAATA
*
225609 ATATCTTTTAAATTTAAAATATTAAACATATA
1 ATATCTTTTAAATCTAAAATATTAAACATATA
225641 TACACTCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 3 0.10
34 15 0.52
35 11 0.38
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (35 bp):
ATATCTTTTAAATCTAAAATATTAAACATATAATA
Found at i:225634 original size:83 final size:84
Alignment explanation
Indices: 225477--225634 Score: 248
Period size: 83 Copynumber: 1.9 Consensus size: 84
225467 TTGAGAGAGT
*
225477 TTTACTCCACCTAAATCTCTTTTAATATCTAAATTTAAAAAAGATAATAATATCTTTTAAATGTA
1 TTTACTCCACCTAAATATCTTTTAATATCTAAATTTAAAAAAGATAATAATATCTTTTAAATGTA
225542 AAATATTAAATCTGAGAAA
66 AAATATTAAATCTGAGAAA
* * * *
225561 TTTACTCCAACC-AGATATCTTTTAATATCTAAATTT-AAACATATAATAATATCTTTTAAATTT
1 TTTACTCC-ACCTAAATATCTTTTAATATCTAAATTTAAAAAAGATAATAATATCTTTTAAATGT
225624 AAAATATTAAA
65 AAAATATTAAA
225635 CATATATACA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
83 35 0.51
84 30 0.44
85 3 0.04
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (84 bp):
TTTACTCCACCTAAATATCTTTTAATATCTAAATTTAAAAAAGATAATAATATCTTTTAAATGTA
AAATATTAAATCTGAGAAA
Found at i:232557 original size:189 final size:189
Alignment explanation
Indices: 232237--232616 Score: 715
Period size: 189 Copynumber: 2.0 Consensus size: 189
232227 TCTAAATGAC
*
232237 CCAAAAAAATCCTTCTCTCTTCTCTAATCTCCTAAGATCGAAACCAGTTCATTATAAAATGAAGA
1 CCAAAAAAATCCTTCTCTCTTCTCTAATCTCCTAAGATCGAAACCAGTTCATCATAAAATGAAGA
**
232302 AAATTTTCTTTCTCCAAACACCATTAACGGTGGTTGGGAAAGTCGAAACTCAAACCCTTTGAACC
66 AAATTTTCTTTCTCCAAACACCATTAACGGTGGTTAAGAAAGTCGAAACTCAAACCCTTTGAACC
232367 CAAAACCTCATTCCTTTTAATCTAACCCTAAATCAAGATCCAAGATCAATATACAAGCT
131 CAAAACCTCATTCCTTTTAATCTAACCCTAAATCAAGATCCAAGATCAATATACAAGCT
*
232426 CCAAAAAAATCCTTCTCTCTTCTCTAATCTCCTAAGATCGAAATCAGTTCATCATAAAATGAAGA
1 CCAAAAAAATCCTTCTCTCTTCTCTAATCTCCTAAGATCGAAACCAGTTCATCATAAAATGAAGA
232491 AAATTTTCTTTCTCCAAACACCATTAACGGTGGTTAAGAAAGTCGAAACTCAAACCCTTTGAACC
66 AAATTTTCTTTCTCCAAACACCATTAACGGTGGTTAAGAAAGTCGAAACTCAAACCCTTTGAACC
*
232556 CAAAACCTCATTCCTTTTAATCTAACCCTAAATCGAGATCCAAGATCAATATACAAGCT
131 CAAAACCTCATTCCTTTTAATCTAACCCTAAATCAAGATCCAAGATCAATATACAAGCT
232615 CC
1 CC
232617 CTAAACGACC
Statistics
Matches: 186, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
189 186 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.28
Consensus pattern (189 bp):
CCAAAAAAATCCTTCTCTCTTCTCTAATCTCCTAAGATCGAAACCAGTTCATCATAAAATGAAGA
AAATTTTCTTTCTCCAAACACCATTAACGGTGGTTAAGAAAGTCGAAACTCAAACCCTTTGAACC
CAAAACCTCATTCCTTTTAATCTAACCCTAAATCAAGATCCAAGATCAATATACAAGCT
Found at i:234218 original size:19 final size:20
Alignment explanation
Indices: 234178--234218 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
234168 GTAGGAAAAG
234178 AATATTTTCTAAGGAGAGAA
1 AATATTTTCTAAGGAGAGAA
234198 AATATTTTC-AA-GAGAAGAA
1 AATATTTTCTAAGGAG-AGAA
234217 AA
1 AA
234219 CTTCTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 8 0.40
20 9 0.45
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (20 bp):
AATATTTTCTAAGGAGAGAA
Found at i:236835 original size:15 final size:15
Alignment explanation
Indices: 236815--236845 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
236805 TTTTAACCAT
*
236815 ACTCTCAAGCATTTG
1 ACTCTCAACCATTTG
236830 ACTCTCAACCATTTG
1 ACTCTCAACCATTTG
236845 A
1 A
236846 ACAATTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (15 bp):
ACTCTCAACCATTTG
Found at i:237266 original size:98 final size:98
Alignment explanation
Indices: 237097--237285 Score: 335
Period size: 98 Copynumber: 1.9 Consensus size: 98
237087 AGTTGCGTGC
* *
237097 TGAGTTTATCTCAATTATCAATGGACTAATTTTTAAGTACCACATGCTATTACTATTAGAAAATG
1 TGAGTCTATCTCAATTATCAATGGACTAATTTTTAAGTACCACATGCTATTACTACTAGAAAATG
*
237162 GATTATGAACTAGGTTGAGTATTTTTTTTACGA
66 GATTATGAACTAGGTTGAGCATTTTTTTTACGA
237195 TGAGTCTATCTCAATTATCAATGGACT-ATTTTCTAAGTACCACATGCTATTACTACTAGAAAAT
1 TGAGTCTATCTCAATTATCAATGGACTAATTTT-TAAGTACCACATGCTATTACTACTAGAAAAT
237259 GGATTATGAACTAGGTTGAGCATTTTT
65 GGATTATGAACTAGGTTGAGCATTTTT
237286 CTTTGAAAGG
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
97 5 0.06
98 82 0.94
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.39
Consensus pattern (98 bp):
TGAGTCTATCTCAATTATCAATGGACTAATTTTTAAGTACCACATGCTATTACTACTAGAAAATG
GATTATGAACTAGGTTGAGCATTTTTTTTACGA
Found at i:237315 original size:2 final size:2
Alignment explanation
Indices: 237308--237364 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
237298 GTAAGTTTTG
237308 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
237350 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
237365 TTAAGGGTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:243612 original size:17 final size:17
Alignment explanation
Indices: 243590--243631 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
243580 CACTATGATA
243590 TGCACAAGACCAGACAT
1 TGCACAAGACCAGACAT
243607 TGCACAAGACCAGACAT
1 TGCACAAGACCAGACAT
243624 TGCACAAG
1 TGCACAAG
243632 CAGTGGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.29, G:0.19, T:0.12
Consensus pattern (17 bp):
TGCACAAGACCAGACAT
Found at i:244334 original size:12 final size:12
Alignment explanation
Indices: 244317--244341 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
244307 GTCAAATAAT
244317 TTAGGCACCAAA
1 TTAGGCACCAAA
244329 TTAGGCACCAAA
1 TTAGGCACCAAA
244341 T
1 T
244342 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:251418 original size:16 final size:16
Alignment explanation
Indices: 251397--251429 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
251387 TTAACAGTGG
251397 TTGGGAAAGTCAAAAC
1 TTGGGAAAGTCAAAAC
*
251413 TTGGGAAAGTCGAAAC
1 TTGGGAAAGTCAAAAC
251429 T
1 T
251430 CAAACCCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.21
Consensus pattern (16 bp):
TTGGGAAAGTCAAAAC
Found at i:261226 original size:6 final size:6
Alignment explanation
Indices: 261215--261255 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
261205 TAACACCTCG
261215 TGCATT TGCATT TGCATT TGCATT TGCATTT TGCA-T TGCAT
1 TGCATT TGCATT TGCATT TGCATT TGCA-TT TGCATT TGCAT
261256 GTATTTGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (6 bp):
TGCATT
Found at i:263581 original size:6 final size:6
Alignment explanation
Indices: 263566--263660 Score: 54
Period size: 6 Copynumber: 15.2 Consensus size: 6
263556 AGAGAAATAT
* *
263566 AGAAAG AGAAAA AG-AAA AGATAAA A-AAAA ATG-AAA TGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGA-AAA AGAAAA A-GAAAA AGAAAA AGAAAA
* *
263613 TA-AAAA AGGAAA AGAAAG AGAAAA ATTGAAAA TGAGAAAA ATGAAAA
1 -AGAAAA AGAAAA AGAAAA AGAAAA A--GAAAA --AGAAAA A-GAAAA
263660 A
1 A
263661 AAGAATGAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
5 11 0.16
6 37 0.53
7 11 0.16
8 10 0.14
10 1 0.01
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (6 bp):
AGAAAA
Found at i:263590 original size:12 final size:11
Alignment explanation
Indices: 263545--263637 Score: 53
Period size: 12 Copynumber: 7.8 Consensus size: 11
263535 TTGACATCAT
*
263545 AAAGAGAAAGA
1 AAAGAAAAAGA
*
263556 AGAGAAATATAGA
1 AAAGAAA-A-AGA
263569 AAGAGAAAAAGA
1 AA-AGAAAAAGA
*
263581 AAAGATAAAAAA
1 AAAGA-AAAAGA
*
263593 AAATG-AAATGAA
1 AAA-GAAAAAG-A
*
263605 AAAGAAAATAAA
1 AAAGAAAA-AGA
*
263617 AAAGGAAAAGA
1 AAAGAAAAAGA
263628 AAGAGAAAAA
1 AA-AGAAAAA
263638 TTGAAAATGA
Statistics
Matches: 62, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
11 16 0.26
12 35 0.56
13 6 0.10
14 5 0.08
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:263607 original size:24 final size:23
Alignment explanation
Indices: 263575--263637 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
263565 TAGAAAGAGA
*
263575 AAAAG-AAAAGATAAAAAAAAATG
1 AAAAGAAAAAGA-AAAAAAAAAGG
*
263598 AAATGAAAAAGAAAATAAAAAAGG
1 AAAAGAAAAAGAAAA-AAAAAAGG
*
263622 AAAAGAAAGAGAAAAA
1 AAAAGAAAAAGAAAAA
263638 TTGAAAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 8 0.24
24 26 0.76
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (23 bp):
AAAAGAAAAAGAAAAAAAAAAGG
Found at i:263629 original size:29 final size:29
Alignment explanation
Indices: 263573--263629 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
263563 TATAGAAAGA
*
263573 GAAAAAGAAAAGATAAAAAAAAATGAAAT
1 GAAAAAGAAAAGATAAAAAAAAAAGAAAT
263602 GAAAAAG-AAA-ATAAAAAAGGAAAAGAAA
1 GAAAAAGAAAAGATAAAAAA--AAAAGAAA
263630 GAGAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 8 0.32
28 3 0.12
29 14 0.56
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (29 bp):
GAAAAAGAAAAGATAAAAAAAAAAGAAAT
Found at i:263660 original size:16 final size:16
Alignment explanation
Indices: 263630--263659 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
263620 GGAAAAGAAA
263630 GAGAAAAATTGAAAAT
1 GAGAAAAATTGAAAAT
263646 GAGAAAAA-TGAAAA
1 GAGAAAAATTGAAAA
263660 AAAGAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (16 bp):
GAGAAAAATTGAAAAT
Found at i:265137 original size:124 final size:125
Alignment explanation
Indices: 264917--265220 Score: 484
Period size: 124 Copynumber: 2.4 Consensus size: 125
264907 AAGTTGTGAT
* * * *
264917 ATGTTGGGGCACGAATGAACCCACATCATGTTGAGAAGACAAGATTCAGACCAAGGAGGCATTAA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCATGAA
* **
264982 GAATGAGCCTTACAATTTGAGGTGTTGGGGCATTTTG-ATTCCCGTACCAGTATAAGATA
66 GAATGAGCCTTACAATTTGAGGTGGTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
*
265041 ATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCATGAA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCATGAA
*
265106 GAATGAGCCTTACAATTTGAGGTGGTGGGGCATTTTGAAGGCCCGTACCAGTGTAAGATA
66 GAATGAGCCTTACAATTTGAGGTGGTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
* ** *
265166 ATGTTGGGGCGCGACCAAACCCACGTCATGTTGAGATGAAAAGATTCAGACCAAG
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAG
265221 AAATTATTGA
Statistics
Matches: 165, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
124 96 0.58
125 69 0.42
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (125 bp):
ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCATGAA
GAATGAGCCTTACAATTTGAGGTGGTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
Found at i:266104 original size:36 final size:36
Alignment explanation
Indices: 265948--266137 Score: 238
Period size: 36 Copynumber: 5.2 Consensus size: 36
265938 AAGTCAATCC
265948 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * *
265984 GAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* *
266020 GAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCA
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * *
266056 TAAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * * * *
266092 TAAGTCTTCACC-AAAAATTAGTGAAGCAGATCCATTT
1 TAAGCCTTCACCGGAGAA-TAGTGAAGCA-AACCATCT
266129 TAAGCCTTC
1 TAAGCCTTC
266138 TCAGAAGAGT
Statistics
Matches: 135, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
35 2 0.01
36 119 0.88
37 14 0.10
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (36 bp):
TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
Found at i:266584 original size:51 final size:51
Alignment explanation
Indices: 266519--266820 Score: 379
Period size: 51 Copynumber: 5.8 Consensus size: 51
266509 AAGATTATTT
*
266519 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGAAGATGTCC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCC
* * * *
266570 GGGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCC
* * * * *
266621 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCC
* * * * *
266672 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG-A-AGATGTCC
* * *
266725 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCT
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG---ATGTCC
* *
266779 GAGTTCCATACTCCCTAGAGAAATAGGGAGCGAACCCATTTG
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
266821 TTGAAGATTG
Statistics
Matches: 223, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
51 133 0.60
52 2 0.01
53 46 0.21
54 42 0.19
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (51 bp):
GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCC
Found at i:266966 original size:55 final size:53
Alignment explanation
Indices: 266820--267043 Score: 340
Period size: 53 Copynumber: 4.2 Consensus size: 53
266810 GAACCCATTT
* *
266820 GTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATC
1 GTTGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
* *
266873 GTTGAAGATTGTGGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATC
1 GTTGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
* * *
266926 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATT
1 GTTGAAGATTG-T-GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
* *
266981 GATGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATT
1 GTTGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
*
267034 GTTAAAGATT
1 GTTGAAGATT
267044 ATTCGAGTTC
Statistics
Matches: 157, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
53 109 0.69
54 2 0.01
55 46 0.29
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (53 bp):
GTTGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
Found at i:266987 original size:108 final size:108
Alignment explanation
Indices: 266820--267051 Score: 351
Period size: 108 Copynumber: 2.2 Consensus size: 108
266810 GAACCCATTT
* *
266820 GTTGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTTGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGATGAAGATT
* *
266883 GTGGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATC
66 GTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
* * * *
266926 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTGATGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGATGAAGATT
*
266991 GTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATT
66 GTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
* *
267034 GTTAAAGATTATTCGAGT
1 GTTGAAGATTGTTCGAGT
267052 TCCATACTCC
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
106 11 0.10
107 1 0.01
108 101 0.89
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (108 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGATGAAGATT
GTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
Found at i:267059 original size:108 final size:108
Alignment explanation
Indices: 266834--267079 Score: 334
Period size: 108 Copynumber: 2.3 Consensus size: 108
266824 AAGATTGTGG
* * *
266834 GTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTTGAAGATTGTGGGTCTTATACTCT
1 GTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATCGATGAAGATTGTGAGTCTTATACTCT
* * *
266899 CTGAAGATATAGGGGGCAGACACGATCGTTGAAGATTGTTCGA
66 CTGAAGAAATAGGGGGCAGACACGATCGTTAAAGATTATTCGA
* * * * *
266942 GTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTGATGAAGATTGTGAGTCTTATACTCT
1 GTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATCGATGAAGATTGTGAGTCTTATACTCT
*
267007 CTGAAGAAATAGGGGGCAGACACGATTGTTAAAGATTATTCGA
66 CTGAAGAAATAGGGGGCAGACACGATCGTTAAAGATTATTCGA
*
267050 GT-TCCATACTC-CTTGGAAGCAATAGGGAGC
1 GTCT-CATACTCTC-T-GAAGAAATAGGGAGC
267080 GAACCTATTT
Statistics
Matches: 122, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
107 2 0.02
108 107 0.88
109 13 0.11
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (108 bp):
GTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATCGATGAAGATTGTGAGTCTTATACTCT
CTGAAGAAATAGGGGGCAGACACGATCGTTAAAGATTATTCGA
Found at i:272661 original size:77 final size:79
Alignment explanation
Indices: 272562--272708 Score: 183
Period size: 77 Copynumber: 1.9 Consensus size: 79
272552 AATAAATTTC
**
272562 TTATTTAATTAATTCAAATTAAATAT-ACATT-AAAGACTTATAATCTGAATTAAAATC-TTTAA
1 TTATTTAATTAATTCAAATTAAATATCA-ATTAAAAGACTTATAATCAAAATTAAAATCTTTTAA
272624 TGTTTATTTAAAATA
65 TGTTTATTTAAAATA
* ** * * * *
272639 TTATTTAATTATTTTGAATTAAATATCAATTAAAAGAGTTGTAATCAAAATTACATTCTTTTAAT
1 TTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATCAAAATTAAAATCTTTTAAT
272704 GTTTA
66 GTTTA
272709 CTTATTATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
77 26 0.45
78 21 0.36
79 11 0.19
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (79 bp):
TTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATCAAAATTAAAATCTTTTAAT
GTTTATTTAAAATA
Found at i:276286 original size:19 final size:20
Alignment explanation
Indices: 276235--276287 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
276225 TGTCCTCACA
*
276235 TTTTCTTTTTCC-TCTCTTG
1 TTTTCTTTTTCCTTTTCTTG
* **
276254 TTTTCTCTCCCCTTTTCTT-
1 TTTTCTTTTTCCTTTTCTTG
276273 TTTTCTTTTTCCTTT
1 TTTTCTTTTTCCTTT
276288 GCCTCAGGGA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTCTTTTTCCTTTTCTTG
Found at i:286876 original size:5 final size:5
Alignment explanation
Indices: 286866--286899 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
286856 TGTTTAAAAG
*
286866 AAACA AAACAA AAATA AAACA AAACA AAACA AAA
1 AAACA AAAC-A AAACA AAACA AAACA AAACA AAA
286900 ATTGGTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (5 bp):
AAACA
Done.