Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003620.1 Hibiscus syriacus cultivar Beakdansim tig00007658_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: 323556
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:214280 original size:3 final size:3
Alignment explanation
Indices: 214272--214347 Score: 107
Period size: 3 Copynumber: 24.7 Consensus size: 3
214262 TTATTTATTA
* *
214272 AAT AAT AAT ATAT AAT ATT AAT ATT AAT AAT AAAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
*
214319 AAT AAT AAT ACT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
214348 ATTTAAATGA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
3 59 0.91
4 6 0.09
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:217177 original size:87 final size:87
Alignment explanation
Indices: 217031--217193 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
217021 TATATTATAT
* *
217031 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGAAAATATTATCAAGTACAATAAAATATTAGGTAACGCTTATATAATGTAATAGAT
217096 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * *
217118 TATTTAACCGAAAATATTATCAAGTATAATAAAATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCGAAAATATTATCAAGTACAATAAAATATTAGGTAACGCTTATATAATGTAATAGAT
*
217183 AGCGTTTATAT
66 AGCGCTTATAT
217194 TGATCTATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (87 bp):
TATTTAACCGAAAATATTATCAAGTACAATAAAATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:221124 original size:184 final size:183
Alignment explanation
Indices: 220815--221376 Score: 982
Period size: 184 Copynumber: 3.1 Consensus size: 183
220805 TGTTTTTTCA
* *
220815 ATCGACACTTTTTTCATCCATTCTGGACATAAAGTTGTGACACAATATTAAAAAGTGTCGATATA
1 ATCGACACTTTTTTCATCCATTCTGGACATAAAGTAGCGACACAATATTAAAAAGTGTCGATATA
*
220880 GGTTGTAGACATATTCTCTCATAAAACCGGTATATCTATACCGGTTATATTACAAAATTACCTAT
66 GGTTGTAGACCTATTCTCTCATAAAA-CGGTATATCTATACCGGTTATATTACAAAATTACCTAT
* *
220945 TACATTATAATTATGAGTTCCGATGTTTTTTCAATCGATACTTTTTGAAAAGGT
130 TACATTATAATTATGGGTTCCGATGTTTTTTCAATCGACACTTTTTGAAAAGGT
*
220999 ATCGACACTTTTTTCATCCATTCTGGACATAAAGTAGCAACACAATATTAAAAAGTGTCGATATA
1 ATCGACACTTTTTTCATCCATTCTGGACATAAAGTAGCGACACAATATTAAAAAGTGTCGATATA
*
221064 GGTTGTATACCTATTCTCTCATAAAATCGGTATATCTATACCGGTTATATTACAAAATTACCTAT
66 GGTTGTAGACCTATTCTCTCATAAAA-CGGTATATCTATACCGGTTATATTACAAAATTACCTAT
*
221129 TACATTATAATTATGGGTTTCGATGTTTTTTCAATCGACACTTTTTGAAAAGGT
130 TACATTATAATTATGGGTTCCGATGTTTTTTCAATCGACACTTTTTGAAAAGGT
221183 ATCGACACTTTTTTCATCCATTCTGGACATAAAGTAGCGACACAATATTAAAAAGTGTCGATATA
1 ATCGACACTTTTTTCATCCATTCTGGACATAAAGTAGCGACACAATATTAAAAAGTGTCGATATA
* *
221248 AGTTGTAGACCTATTCTCTCATAAAACTGGTATATCTATACCAGTTATATTACAAAATTACCTAT
66 GGTTGTAGACCTATTCTCTCATAAAAC-GGTATATCTATACCGGTTATATTACAAAATTACCTAT
* *
221313 TACATTATAATTATGGGTTCCGATG-TTTTTCAATTGACACTTTTTGAAAATGT
130 TACATTATAATTATGGGTTCCGATGTTTTTTCAATCGACACTTTTTGAAAAGGT
221366 ATCGACACTTT
1 ATCGACACTTT
221377 ATGATGATAT
Statistics
Matches: 361, Mismatches: 16, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
183 38 0.11
184 323 0.89
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (183 bp):
ATCGACACTTTTTTCATCCATTCTGGACATAAAGTAGCGACACAATATTAAAAAGTGTCGATATA
GGTTGTAGACCTATTCTCTCATAAAACGGTATATCTATACCGGTTATATTACAAAATTACCTATT
ACATTATAATTATGGGTTCCGATGTTTTTTCAATCGACACTTTTTGAAAAGGT
Found at i:222776 original size:12 final size:12
Alignment explanation
Indices: 222755--222794 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
222745 CTTGTTTGGA
*
222755 TCATCATCATCG
1 TCATCTTCATCG
222767 TCATCTTCATCG
1 TCATCTTCATCG
* *
222779 TCAGCTTCATCT
1 TCATCTTCATCG
222791 TCAT
1 TCAT
222795 TAACCGCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:224608 original size:200 final size:200
Alignment explanation
Indices: 224261--225235 Score: 1625
Period size: 200 Copynumber: 4.9 Consensus size: 200
224251 ATATTTAAAT
* * * *
224261 TAGTATCGACACAAAATTAAAAAGTGTCAATACATATATTACACCTATTATCTCATAAAAACGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAACCGGT
224326 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* * *
224391 GGATCGAAACTTTTTATATATAGATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGG
131 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
224456 ACCAA
196 ACCAA
*
224461 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAAACCGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAACCGGT
224526 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* *
224591 GGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTGCCATTCATTCTGG
131 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
224656 ACCAA
196 ACCAA
* * * *
224661 TAGTATTGACACAAAATTAAAAAATGTCGATACATAT-TATATACCTAATCTCTCATAAAACCAG
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATAT-TACACCTAATCTCTCATAAAACCGG
*
224725 TATACTTATACTGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
65 TATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
*
224790 GGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
130 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
224855 GACCAA
195 GACCAA
*
224861 TAGTATCGACACAAAATTAAAAAGTGTCGATACATAT-TATATACCTAA--TCTC-T-----C--
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATAT-TACACCTAATCTCTCATAAAACCGG
*
224915 -ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTGTACTTATGGGTTTCGATGTTTCT
65 TATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
*
224979 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTGCCATTCATTCTG
130 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
225044 GACCAA
195 GACCAA
* *
225050 TAGTATCGACACAAAATTAGAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAATCGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAACCGGT
225115 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* * *
225180 GGATCGACACTTTTTATATATGGATCGAAATTTTATGGTTGCACCCTGTTTACCAT
131 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
225236 ATTGTAAATT
Statistics
Matches: 734, Mismatches: 28, Indels: 26
0.93 0.04 0.03
Matches are distributed among these distances:
189 175 0.24
190 1 0.00
191 4 0.01
192 2 0.00
197 2 0.00
198 4 0.01
199 1 0.00
200 545 0.74
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
TAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAACCGGT
ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
ACCAA
Found at i:225119 original size:389 final size:393
Alignment explanation
Indices: 224261--225235 Score: 1611
Period size: 389 Copynumber: 2.5 Consensus size: 393
224251 ATATTTAAAT
* * *
224261 TAGTATCGACACAAAATTAAAAAGTGTCAATACATATATTACACCTATTATCTCATAAAAACGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAAACGGT
224326 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* * *
224391 GGATCGAAACTTTTTATATATAGATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGG
131 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
*
224456 ACCAATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAAA
196 ACCAATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTA-TATCTCAT---A
224521 CCGGTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
257 -C-G-ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
224586 TTCTGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTGCCATTCAT
319 TTCTGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTGCCATTCAT
224651 TCTGGACCAA
384 TCTGGACCAA
* * * * *
224661 TAGTATTGACACAAAATTAAAAAATGTCGATACATAT-TATATACCTAATCTCTCATAAAACCAG
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATAT-TACACCTAATCTCTCATAAAAACGG
*
224725 TATACTTATACTGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
65 TATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
*
224790 GGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
130 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
*
224855 GACCAATAGTATCGACACAAAATTAAAAAGTGTCGATACATAT-TATATACCTA-ATCTC-T-C-
195 GACCAATAGTATCGACACAAAATTAAAAAGTGTCGATACATATAT-TACACCTATATCTCATACG
*
224915 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTGTACTTATGGGTTTCGATGTTTCTG
259 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* * *
224980 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTGCCATTCATTCTGG
324 GGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTGCCATTCATTCTGG
225045 ACCAA
389 ACCAA
* *
225050 TAGTATCGACACAAAATTAGAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAATCGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAAACGGT
225115 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* * *
225180 GGATCGACACTTTTTATATATGGATCGAAATTTTATGGTTGCACCCTGTTTACCAT
131 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
225236 ATTGTAAATT
Statistics
Matches: 542, Mismatches: 30, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
389 304 0.56
390 1 0.00
392 1 0.00
397 1 0.00
398 4 0.01
399 2 0.00
400 229 0.42
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (393 bp):
TAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAAACGGT
ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
ACCAATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATATCTCATACGAT
ACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGGG
ATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTGCCATTCATTCTGGAC
CAA
Found at i:225489 original size:19 final size:19
Alignment explanation
Indices: 225465--225513 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
225455 TTACATTCAC
225465 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
225484 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
225503 ATACAAAATTA
1 ATACAAAATTA
225514 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:227782 original size:20 final size:19
Alignment explanation
Indices: 227736--227782 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
227726 TCCGATAGCG
227736 TTTTACCGGTTTCATCATT
1 TTTTACCGGTTTCATCATT
* *
227755 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTCATCAT-T
227776 TTTTACC
1 TTTTACC
227783 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (19 bp):
TTTTACCGGTTTCATCATT
Found at i:227990 original size:183 final size:182
Alignment explanation
Indices: 227522--227995 Score: 781
Period size: 181 Copynumber: 2.6 Consensus size: 182
227512 CGTACTTACG
* * * *
227522 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGATTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGATAGCGTTTTACCGGTTTCATCATTTTGATACCGGTTT
*
227587 TATCATATTTTTACATGTTATATCGTTGTGGATCGATACA-TTTTTTTAAAGTATCGACACTTTA
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTTAAAGTATCGACACTTTA
*
227651 TAGGCGCTAAAATTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATAT
131 TAGGCGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATAT
*
227703 AAAGTATCGACACTTTTAATATATCCGATAGCGTTTTACCGGTTTCATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGATAGCGTTTTACCGGTTTCATCATTTTGATACCGGTTT
*
227768 TATCATATTTTTACCTGTTATATCGTTGTGCATCGATACATTTTTTTTAAAGTATCGACACTTTA
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTTAAAGTATCGACACTTTA
227833 TAGGCGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATATT
131 TAGGCGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATA-T
* * * * *
227886 AAAGTACCGACACTTTAAATATATCCGATACCGCTTTACCGGTTTCATC-TTTTCAATACCTGTT
1 AAAGTATCGACACTTTAAATATATCCGATAGCGTTTTACCGGTTTCATCATTTT-GATACCGGTT
* *
227950 TTGTCATAGTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
227996 AATTTGGATC
Statistics
Matches: 274, Mismatches: 16, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
181 99 0.36
182 78 0.28
183 97 0.35
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGATAGCGTTTTACCGGTTTCATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTTAAAGTATCGACACTTTA
TAGGCGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATAT
Found at i:229594 original size:105 final size:105
Alignment explanation
Indices: 229412--229608 Score: 349
Period size: 105 Copynumber: 1.9 Consensus size: 105
229402 TTAGGCTTGC
* *
229412 TTTGGTTTTTCTTTATGCATTTGATCTTACTTTTATCATCTGTTAGGCTTTTCTTGGAATCTTAA
1 TTTGGATTTTCTTTATGCATTTGATCTTACTTCTATCATCTGTTAGGCTTTTCTTGGAATCTTAA
229477 TTATCCGATTCTTAATTTGTTCATGTGTATCTGGTATACA
66 TTATCCGATTCTTAATTTGTTCATGTGTATCTGGTATACA
* *
229517 TTTGGATTTTCTTTATGCATTTGATGTTAGTTCTATCATCTGTTAGGCTTTTCTTGGAATCTTAA
1 TTTGGATTTTCTTTATGCATTTGATCTTACTTCTATCATCTGTTAGGCTTTTCTTGGAATCTTAA
*
229582 TTATCCGATTCTTACTTTGTTCATGTG
66 TTATCCGATTCTTAATTTGTTCATGTG
229609 ATTTTGGTTG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 87 1.00
ACGTcount: A:0.18, C:0.14, G:0.15, T:0.52
Consensus pattern (105 bp):
TTTGGATTTTCTTTATGCATTTGATCTTACTTCTATCATCTGTTAGGCTTTTCTTGGAATCTTAA
TTATCCGATTCTTAATTTGTTCATGTGTATCTGGTATACA
Found at i:238446 original size:2 final size:2
Alignment explanation
Indices: 238439--238482 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
238429 CGCATAATTT
238439 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
238481 TA
1 TA
238483 ATTGATGATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:244905 original size:18 final size:20
Alignment explanation
Indices: 244869--244906 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
244859 TTAAAGCCGA
244869 ATTCACATGTTGAAATATAT
1 ATTCACATGTTGAAATATAT
244889 ATTCAC-TGTTG-AATATAT
1 ATTCACATGTTGAAATATAT
244907 GAAAGGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 5 0.28
20 6 0.33
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (20 bp):
ATTCACATGTTGAAATATAT
Found at i:261693 original size:35 final size:34
Alignment explanation
Indices: 261653--261730 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 34
261643 AATAAAGTCC
*
261653 TCAATTTCATTCTAAACCCTAAATTTTAAAATAAT
1 TCAATTT-ATTCTAAACCCTAAATTCTAAAATAAT
* * *
261688 TCAATTATATTTTAAACCTTAAATTCTAAAATATT
1 TCAATT-TATTCTAAACCCTAAATTCTAAAATAAT
261723 TCAATTTA
1 TCAATTTA
261731 AGGTTTAGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 2 0.05
35 35 0.92
36 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (34 bp):
TCAATTTATTCTAAACCCTAAATTCTAAAATAAT
Found at i:261764 original size:35 final size:35
Alignment explanation
Indices: 261725--261799 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
261715 AAAATATTTC
* *
261725 AATTTAAGGTTTAGGATATAATTAAAGTATTTTGG
1 AATTTAAGGTTTAGAATATAATTAAAATATTTTGG
**
261760 AATTTGGGGTTTAGAATATAATTAAAATATTTTGG
1 AATTTAAGGTTTAGAATATAATTAAAATATTTTGG
261795 AATTT
1 AATTT
261800 TGAATATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATATAATTAAAATATTTTGG
Found at i:267675 original size:20 final size:20
Alignment explanation
Indices: 267650--267687 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
267640 TTTGGTTCAC
*
267650 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
267670 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
267688 GAAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:267693 original size:18 final size:19
Alignment explanation
Indices: 267652--267693 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
267642 TGGTTCACGG
* *
267652 AATATAAGATTACCAGTGGG
1 AATAAAAGATTACCAG-GGA
267672 AATAAAAGATTACCA-GGA
1 AATAAAAGATTACCAGGGA
267690 AATA
1 AATA
267694 GGATTACTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
20 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.19, T:0.21
Consensus pattern (19 bp):
AATAAAAGATTACCAGGGA
Found at i:267764 original size:35 final size:35
Alignment explanation
Indices: 267718--267798 Score: 153
Period size: 35 Copynumber: 2.3 Consensus size: 35
267708 GTTACATTGT
267718 AGTGTTTGGTTGGTTTGGCAAGAATATAAGATTAC
1 AGTGTTTGGTTGGTTTGGCAAGAATATAAGATTAC
*
267753 AGTGTTTGGTTGGTTTGGCAGGAATATAAGATTAC
1 AGTGTTTGGTTGGTTTGGCAAGAATATAAGATTAC
267788 AGTGTTTGGTT
1 AGTGTTTGGTT
267799 AAAGGAATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.25, C:0.05, G:0.31, T:0.40
Consensus pattern (35 bp):
AGTGTTTGGTTGGTTTGGCAAGAATATAAGATTAC
Found at i:267918 original size:17 final size:15
Alignment explanation
Indices: 267882--267912 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
267872 AAATTCTAAA
267882 TATTTATATAAAAAT
1 TATTTATATAAAAAT
267897 TATTTATATAAAAAT
1 TATTTATATAAAAAT
267912 T
1 T
267913 CTATTTGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTTATATAAAAAT
Found at i:269961 original size:24 final size:24
Alignment explanation
Indices: 269934--270040 Score: 119
Period size: 24 Copynumber: 4.5 Consensus size: 24
269924 GAAATCAAAA
*
269934 CAGATATCAGAACAGAATCTAGAT
1 CAGAAATCAGAACAGAATCTAGAT
*
269958 CAGAAATCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATCTAGAT
*
269982 CAGAAATCAGAACAGAAT-TCAGGT
1 CAGAAATCAGAACAGAATCT-AGAT
* * *
270006 CATATATCAGAACAGAATTCAAG-T
1 CAGAAATCAGAACAGAA-TCTAGAT
*
270030 CGGAAATCAGA
1 CAGAAATCAGA
270041 TAAAATATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
24 67 0.96
25 3 0.04
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATCTAGAT
Found at i:269961 original size:36 final size:35
Alignment explanation
Indices: 269920--270040 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 35
269910 AAAAGTAGAT
*
269920 ATCAGAAATCAAAACAGATATCAGAACAGAATCTAG
1 ATCAGAAATCAGAACAGATATCAGAACAGAATC-AG
*
269956 ATCAGAAATCAGAACAGA-ATCCAGATCAGAAATCAG
1 ATCAGAAATCAGAACAGATAT-CAGAACAG-AATCAG
* * ** *
269992 AACAGAATTCAGGTCATATATCAGAACAGAATTCA-
1 ATCAGAAATCAGAACAGATATCAGAACAGAA-TCAG
*
270027 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
270041 TAAAATATTT
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
35 5 0.07
36 57 0.84
37 6 0.09
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (35 bp):
ATCAGAAATCAGAACAGATATCAGAACAGAATCAG
Found at i:270003 original size:12 final size:12
Alignment explanation
Indices: 269922--270026 Score: 72
Period size: 12 Copynumber: 8.8 Consensus size: 12
269912 AAGTAGATAT
* *
269922 CAGAAATCAAAA
1 CAGAATTCAGAA
269934 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
*
269946 CAGAA-TCTAGAT
1 CAGAATTC-AGAA
*
269958 CAGAAATCAGAA
1 CAGAATTCAGAA
* *
269970 CAGAATCCAGAT
1 CAGAATTCAGAA
*
269982 CAGAAATCAGAA
1 CAGAATTCAGAA
**
269994 CAGAATTCAGGT
1 CAGAATTCAGAA
*
270006 CA-TATATCAGAA
1 CAGAAT-TCAGAA
270018 CAGAATTCA
1 CAGAATTCA
270027 AGTCGGAAAT
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
11 5 0.07
12 60 0.86
13 5 0.07
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:273755 original size:22 final size:18
Alignment explanation
Indices: 273708--273796 Score: 115
Period size: 18 Copynumber: 4.7 Consensus size: 18
273698 GTTCAGTATT
273708 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
273726 TGTCCCGAAGGACCACTGGA
1 TGTCCCGAAGGACCACT--A
*
273746 TACGTCCCGAATGACCACTA
1 T--GTCCCGAAGGACCACTA
*
273766 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
*
273784 TGTCCTGAAGGAC
1 TGTCCCGAAGGAC
273797 TAATATACCC
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
18 44 0.70
20 4 0.06
22 15 0.24
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:274431 original size:64 final size:64
Alignment explanation
Indices: 274350--274504 Score: 165
Period size: 64 Copynumber: 2.4 Consensus size: 64
274340 GACGGGGTAA
* * * *
274350 CGATGCACTACC-CATGCATCGGTGCATAAATCATATTCGATGTT-TGT-ATTTTAA-GCAGGTG
1 CGATGCACT-CCTTATGCATCGATGCATAAATCACATTCGATGTTAT-TAATTTAAATG-A-GTG
274411 CAT
62 CAT
* * **
274414 CGATGCACTCCTTATGCATTGATGCATTAATGGCATTCGATGTTCATTAATTTAAATGAGTGCAT
1 CGATGCACTCCTTATGCATCGATGCATAAATCACATTCGATGTT-ATTAATTTAAATGAGTGCAT
274479 CGATGCACTCCTTATGCATCGATGCA
1 CGATGCACTCCTTATGCATCGATGCA
274505 CCTTCAACAA
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
63 2 0.03
64 34 0.44
65 32 0.42
66 8 0.10
67 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (64 bp):
CGATGCACTCCTTATGCATCGATGCATAAATCACATTCGATGTTATTAATTTAAATGAGTGCAT
Found at i:275192 original size:2 final size:2
Alignment explanation
Indices: 275185--275222 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
275175 CTAAACAATA
275185 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
275223 CTTTATACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:281350 original size:64 final size:63
Alignment explanation
Indices: 281275--281436 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 63
281265 TCCCTTGACG
* * * * *
281275 GGTGCAACGATGCACTACTCATGCATC-AGTGCATAAAT-CCTATTCGATGTT-TGTATTTTAAG
1 GGTGCATCGATGCACTCCTTATGCATCGA-TGCATAAATGCC-ATTCGATGTTAT-TAATTTAAA
281337 T
63 T
* *
281338 AGGTGCATCGATGCACTCCTTATGCATCGATGCATTAATGGCATTCGATGTTCATTAATTTAAAT
1 -GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATGCCATTCGATGTT-ATTAATTTAAAT
281403 GAGTGCATCGATGCACTCCTTATGCATCGATGCA
1 G-GTGCATCGATGCACTCCTTATGCATCGATGCA
281437 CCTTCAACAA
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
64 43 0.50
65 42 0.49
66 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (63 bp):
GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATGCCATTCGATGTTATTAATTTAAAT
Found at i:282385 original size:2 final size:2
Alignment explanation
Indices: 282378--282417 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
282368 ACTTCATTCG
282378 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
282418 AGTGAAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:289919 original size:20 final size:21
Alignment explanation
Indices: 289896--289937 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
289886 GTTAAGATTT
* *
289896 TTAATTTCTT-AATTTTAATA
1 TTAATTTATTAAATTTCAATA
289916 TTAATTTATTAAATTTCAATA
1 TTAATTTATTAAATTTCAATA
289937 T
1 T
289938 AAAATATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTTATTAAATTTCAATA
Found at i:292402 original size:27 final size:28
Alignment explanation
Indices: 292356--292408 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
292346 TTATCTTTTC
292356 AATTTTATAAAAAAATTATATAAATTTA
1 AATTTTATAAAAAAATTATATAAATTTA
292384 AATTTT-TAAAGAAAA-TATATAAATT
1 AATTTTATAAA-AAAATTATATAAATT
292409 AATTATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
AATTTTATAAAAAAATTATATAAATTTA
Found at i:299351 original size:31 final size:31
Alignment explanation
Indices: 299316--299380 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
299306 AAATTGATTT
299316 TTTAATA-ATTTAAT-TTTGTAGTATTTTTATA
1 TTTAATATA-TTAATATTTGTAGTATTTTT-TA
* *
299347 TTTAATATATTAATATTTTTTGTATTTTTTA
1 TTTAATATATTAATATTTGTAGTATTTTTTA
299378 TTT
1 TTT
299381 TATTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (31 bp):
TTTAATATATTAATATTTGTAGTATTTTTTA
Found at i:300282 original size:26 final size:26
Alignment explanation
Indices: 300218--300273 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
300208 AATTTTACGA
*
300218 AAAAATAAAAATAAAAAATATTTTCT
1 AAAAACAAAAATAAAAAATATTTTCT
300244 AAAAACAAAAATAAAAAATATTTTCT
1 AAAAACAAAAATAAAAAATATTTTCT
300270 AAAA
1 AAAA
300274 CCCCTAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (26 bp):
AAAAACAAAAATAAAAAATATTTTCT
Found at i:304425 original size:41 final size:40
Alignment explanation
Indices: 304380--304556 Score: 106
Period size: 41 Copynumber: 4.2 Consensus size: 40
304370 ACAAACGCTT
*
304380 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
1 CAATAGATTATAAA-TTGGCGGCGATTTAGCCAAAACGCCG
* ** * * * *
304421 CAATATAGTGGTAAACTGGCAGCGTTTTTTA-CCACAAACGCCA
1 CAATAGA-TTATAAATTGGCGGCG--ATTTAGCCA-AAACGCCG
* * * * *
304464 CAATAAAGTATAAATTTTGCGGCGATTGAGTCAAAACGCCG
1 CAATAGATTATAAA-TTGGCGGCGATTTAGCCAAAACGCCG
** *
304505 CAATAGAGTGGTAAATTGGCGGCG-TTTTGACCAAAAACGCCG
1 CAATAGA-TTATAAATTGGCGGCGATTTAG-CC-AAAACGCCG
*
304547 CAATATATTA
1 CAATAGATTA
304557 CACATATAGT
Statistics
Matches: 97, Mismatches: 30, Indels: 18
0.67 0.21 0.12
Matches are distributed among these distances:
40 3 0.03
41 38 0.39
42 33 0.34
43 23 0.24
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (40 bp):
CAATAGATTATAAATTGGCGGCGATTTAGCCAAAACGCCG
Found at i:304483 original size:84 final size:83
Alignment explanation
Indices: 304329--304551 Score: 284
Period size: 84 Copynumber: 2.7 Consensus size: 83
304319 CGTTTTTAGA
* * * * * ** * *
304329 AAAACGCCGCAATAGGGTGCTAAATTAGCGGCGTTTATATCACAAACGCTTCAATAGATTATAAA
1 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTTACCACAAACGCCACAATAAAGTATAAA
*
304394 TTTTGCGGCGATTTAGCC
66 TTTTGCGGCGATTGAGCC
* * *
304412 AAAACGCCGCAATATAGTGGTAAACTGGCAGCGTTTTTTACCACAAACGCCACAATAAAGTATAA
1 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCG-TTTTTACCACAAACGCCACAATAAAGTATAA
*
304477 ATTTTGCGGCGATTGAGTC
65 ATTTTGCGGCGATTGAGCC
* * *
304496 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTGACCAAAAACGCCGCAATA
1 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTTACCACAAACGCCACAATA
304552 TATTACACAT
Statistics
Matches: 119, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
83 47 0.39
84 72 0.61
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (83 bp):
AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTTACCACAAACGCCACAATAAAGTATAAA
TTTTGCGGCGATTGAGCC
Found at i:304584 original size:84 final size:83
Alignment explanation
Indices: 304273--304595 Score: 251
Period size: 83 Copynumber: 3.9 Consensus size: 83
304263 TGATACTTTA
** * * * **
304273 GCGGCGTTTTTAGTAAAAACGCTGCAATATAATT-GACATATAGCGGCGTTT-TTAGAAAAACGC
1 GCGGCGTTTTTACCAAAAACGCCGCAATAT-ATTATAAATATAGCGGCGTTTGTT-CCAAAACGC
* * *
304336 CGCAATAGGGTGCTAAATTA
64 CGCAATAGAGTGGTAAATTG
* * * ** * * *
304356 GCGGCGTTTATATCACAAACGCTTCAATAGATTATAAATTTTGCGGCGATTTAG--CCAAAACGC
1 GCGGCGTTTTTACCAAAAACGCCGCAATATATTATAAATATAGCGGCG-TTT-GTTCCAAAACGC
* *
304419 CGCAATATAGTGGTAAACTG
64 CGCAATAGAGTGGTAAATTG
* * * * * * * * *
304439 GCAGCGTTTTTTACCACAAACGCCACAATAAAGTATAAATTTTGCGGCGATTGAGT-CAAAACGC
1 GCGGCG-TTTTTACCAAAAACGCCGCAATATATTATAAATATAGCGGCGTTTG-TTCCAAAACGC
304503 CGCAATAGAGTGGTAAATTG
64 CGCAATAGAGTGGTAAATTG
* * * *
304523 GCGGCGTTTTGACCAAAAACGCCGCAATATATTACACATATAGTGGCGTTTGTTCCTAAAACGCC
1 GCGGCGTTTTTACCAAAAACGCCGCAATATATTATAAATATAGCGGCGTTTGTTCC-AAAACGCC
304588 GCAATAGA
65 GCAATAGA
304596 ATAGTTCCTT
Statistics
Matches: 190, Mismatches: 40, Indels: 19
0.76 0.16 0.08
Matches are distributed among these distances:
82 5 0.03
83 99 0.52
84 86 0.45
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (83 bp):
GCGGCGTTTTTACCAAAAACGCCGCAATATATTATAAATATAGCGGCGTTTGTTCCAAAACGCCG
CAATAGAGTGGTAAATTG
Found at i:305317 original size:23 final size:21
Alignment explanation
Indices: 305270--305309 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
305260 CGAGCAATTA
305270 GTTTTTTACTGAACACGAAAT
1 GTTTTTTACTGAACACGAAAT
305291 GTTTTTTACTGAACACGAA
1 GTTTTTTACTGAACACGAA
305310 TGATGTTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
GTTTTTTACTGAACACGAAAT
Found at i:306552 original size:12 final size:12
Alignment explanation
Indices: 306535--306560 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
306525 TTTAGTTCAT
306535 CATTTCATCACC
1 CATTTCATCACC
306547 CATTTCATCACC
1 CATTTCATCACC
306559 CA
1 CA
306561 CTAAAACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.42, G:0.00, T:0.31
Consensus pattern (12 bp):
CATTTCATCACC
Found at i:309566 original size:21 final size:21
Alignment explanation
Indices: 309511--309587 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
309501 ATGAAGCAAG
*
309511 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* **
309532 AGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
309553 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
309574 GGCAGCACAGAGAG
1 GGAAGCAGAGAGAG
309588 AGGCATCGGC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.40, C:0.19, G:0.39, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:309588 original size:21 final size:21
Alignment explanation
Indices: 309514--309611 Score: 90
Period size: 21 Copynumber: 4.6 Consensus size: 21
309504 AAGCAAGGGA
*
309514 AACAGAGAG-AGCAGCAGCAG
1 AACAGAGAGAAGCAGCGGCAG
* *
309534 AAGCAGCTAGAGCAGCAGCGGAAG
1 AA-CAG--AGAGAAGCAGCGGCAG
* *
309558 CAGAGAGAGAAGCAGCGGCAG
1 AACAGAGAGAAGCAGCGGCAG
* * *
309579 CACAGAGAGAGGCATCGGCAG
1 AACAGAGAGAAGCAGCGGCAG
309600 AACAGAGAGAAG
1 AACAGAGAGAAG
309612 TAATATATCA
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 45 0.71
23 6 0.10
24 10 0.16
ACGTcount: A:0.41, C:0.19, G:0.38, T:0.02
Consensus pattern (21 bp):
AACAGAGAGAAGCAGCGGCAG
Found at i:310083 original size:43 final size:43
Alignment explanation
Indices: 309950--310180 Score: 145
Period size: 43 Copynumber: 5.3 Consensus size: 43
309940 CATACAGTTA
* *
309950 GCGGCGTTTTTGATA-AAAACGCCGCAAAATC-TCAAAACATATCCT
1 GCGGCGTTTTTGA-AGAAAACGCCGCTAAA-CATCAAAACCTAT--T
* * * * * * *
309995 GCGGCGTTTGT-AGGAAAACGCCGATAAAAATAAAAATCTACT
1 GCGGCGTTTTTGAAGAAAACGCCGCTAAACATCAAAACCTATT
*
310037 GCGGCGTTTTTGAAGAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTTTGAAGAAAACGCCGCTAAACATCAA-AACCTATT
** * * * *
310080 GCGGCGTTTGTCTG--CCAAATGCCGTTAAATATCAACACCTATT
1 GCGGCGTTT-T-TGAAGAAAACGCCGCTAAACATCAAAACCTATT
* * *
310123 GCGGCG-TTTT-AATGATAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTTTGAA-GA-AAACGCCGCTAAACATCAAAACCTATT
310166 GCGGCGTTTGTTGAA
1 GCGGCGTTT-TTGAA
310181 CAATCGCCGC
Statistics
Matches: 144, Mismatches: 28, Indels: 27
0.72 0.14 0.14
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 14 0.10
43 88 0.61
44 24 0.17
45 14 0.10
46 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (43 bp):
GCGGCGTTTTTGAAGAAAACGCCGCTAAACATCAAAACCTATT
Found at i:310189 original size:43 final size:43
Alignment explanation
Indices: 310036--310218 Score: 130
Period size: 43 Copynumber: 4.3 Consensus size: 43
310026 AAAAATCTAC
* * *
310036 TGCGGCGTTTT-TGAAGAAAACGCCGCTAAACATCAACGA-CTAT
1 TGCGGCGTTTTATGAA-CAATCGCCGCTAAATATCAAC-ACCTAT
* * *
310079 TGCGGCGTTTGTCTG-CCAAAT-GCCGTTAAATATCAACACCTAT
1 TGCGGCGTTT-TATGAAC-AATCGCCGCTAAATATCAACACCTAT
* *
310122 TGCGGCGTTTTAATGATA-AA-CGCCGCTAAATATCAATACCTTT
1 TGCGGCGTTTT-ATGA-ACAATCGCCGCTAAATATCAACACCTAT
* * **
310165 TGCGGCGTTTGT-TGAACAATCGCCGCTATATGTTGTA-ACCTAT
1 TGCGGCGTTT-TATGAACAATCGCCGCTAAAT-ATCAACACCTAT
310208 TGCGGCGTTTT
1 TGCGGCGTTTT
310219 TTTGTTGAAA
Statistics
Matches: 113, Mismatches: 15, Indels: 25
0.74 0.10 0.16
Matches are distributed among these distances:
41 1 0.01
42 8 0.07
43 96 0.85
44 6 0.05
45 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (43 bp):
TGCGGCGTTTTATGAACAATCGCCGCTAAATATCAACACCTAT
Done.