Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004468.1 Hibiscus syriacus cultivar Beakdansim tig00009847_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: 57282
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:12555 original size:38 final size:38
Alignment explanation
Indices: 12478--12555 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 38
12468 ATTGAACATG
* * * *
12478 ATATATTTTTATATAAATTATGTTGAAGTAAAATGTTA
1 ATATATTTTTAAATAAATTATGTTAAAATAAAATATTA
**
12516 ATATATTTTTTAAATAAATTATG-TAAAATTTAATATTA
1 ATATA-TTTTTAAATAAATTATGTTAAAATAAAATATTA
12554 AT
1 AT
12556 TAAAATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
38 17 0.52
39 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (38 bp):
ATATATTTTTAAATAAATTATGTTAAAATAAAATATTA
Found at i:12640 original size:15 final size:15
Alignment explanation
Indices: 12612--12686 Score: 68
Period size: 15 Copynumber: 5.2 Consensus size: 15
12602 TTATCGATGG
**
12612 ATTTTTATAAAAATA
1 ATTTTTATTTAAATA
12627 ATTTTTATTTAAAT-
1 ATTTTTATTTAAATA
* *
12641 A-TATTA-TT-GATGA
1 ATTTTTATTTAAAT-A
*
12654 ATTTTTATATAAATA
1 ATTTTTATTTAAATA
12669 ATTTTTATTTAAATA
1 ATTTTTATTTAAATA
12684 ATT
1 ATT
12687 AGAATTTCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
11 2 0.04
12 2 0.04
13 5 0.11
14 5 0.11
15 31 0.66
16 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
ATTTTTATTTAAATA
Found at i:12642 original size:42 final size:42
Alignment explanation
Indices: 12596--12687 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
12586 ATAATAAAAT
*
12596 AATATATTATCGATGGATTTTTATAAAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATAAAAATAATTTTTATTTA
* *
12638 AATATATTATTGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATAAAAATAATTTTTATTTA
12680 AATA-ATTA
1 AATATATTA
12688 GAATTTCACT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (42 bp):
AATATATTATCGATGAATTTTTATAAAAATAATTTTTATTTA
Found at i:13162 original size:64 final size:64
Alignment explanation
Indices: 13061--13188 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
13051 AATGTTATAT
*
13061 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGG
1 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGG
*
13125 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGG
1 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGG
13189 TAGCGCTTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (64 bp):
CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGG
Found at i:13645 original size:73 final size:72
Alignment explanation
Indices: 13520--13655 Score: 188
Period size: 73 Copynumber: 1.9 Consensus size: 72
13510 TATAAATGTA
* * *
13520 TCGACACTTTATGGTTGCACCCTTTTTGGTATTCATTCTGGACCAAAAGTATCGACACAAATTTA
1 TCGACACTTTATGGTTGCACCCTTTGTGGCATTCATACTGGACCAAAAGTATCGACACAAATTTA
13585 TCAAGTG
66 TCAAGTG
13592 TCGACACTTTATGCG-TGCACCTCGTTTGT-GCATTCATACTGGA-CAATAAGTATCGACACAAA
1 TCGACACTTTATG-GTTGCACC-C-TTTGTGGCATTCATACTGGACCAA-AAGTATCGACACAAA
13654 TT
62 TT
13656 ACACAAGTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
72 22 0.39
73 31 0.54
74 4 0.07
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (72 bp):
TCGACACTTTATGGTTGCACCCTTTGTGGCATTCATACTGGACCAAAAGTATCGACACAAATTTA
TCAAGTG
Found at i:13663 original size:73 final size:72
Alignment explanation
Indices: 13517--13677 Score: 186
Period size: 73 Copynumber: 2.2 Consensus size: 72
13507 TTTTATAAAT
* * *
13517 GTATCGACACTTTATGGTTGCACCCTTTTTGGTATTCATTCTGGACCAAAAGTATCGACACAAAT
1 GTATCGACACTTTATGGTTGCACCCTTTGTGGCATTCATACTGGACCAAAAGTATCGACACAAAT
*
13582 TTATCAA
66 TTAACAA
*
13589 GTGTCGACACTTTATGCG-TGCACCTCGTTTGT-GCATTCATACTGGA-CAATAAGTATCGACAC
1 GTATCGACACTTTATG-GTTGCACC-C-TTTGTGGCATTCATACTGGACCAA-AAGTATCGACAC
13651 AAA-TTACACAA
62 AAATTTA-ACAA
* *
13662 GTATCGATACATTATG
1 GTATCGACACTTTATG
13678 TTGACATGTT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
72 27 0.36
73 45 0.59
74 4 0.05
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (72 bp):
GTATCGACACTTTATGGTTGCACCCTTTGTGGCATTCATACTGGACCAAAAGTATCGACACAAAT
TTAACAA
Found at i:15950 original size:23 final size:23
Alignment explanation
Indices: 15924--15968 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
15914 CACCACAGCT
*
15924 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
* *
15947 CGTAGAATTTCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
15969 ATATAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:16328 original size:149 final size:149
Alignment explanation
Indices: 15936--16397 Score: 849
Period size: 149 Copynumber: 3.1 Consensus size: 149
15926 TATAATTGCA
* **
15936 CCGAAGTG-CCGCGTAGAATTTCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTA
16000 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* *
16065 CCACAGAATAT--ATATATC
130 CCAAAGAATATACATATGTC
16083 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
16148 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
16213 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
16232 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
16297 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
16362 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
16381 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
16398 CCCTCGACTC
Statistics
Matches: 307, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
146 1 0.00
147 134 0.44
149 172 0.56
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:16517 original size:14 final size:14
Alignment explanation
Indices: 16498--16525 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16488 AACTTGTAAT
16498 TCACGTATCACATA
1 TCACGTATCACATA
16512 TCACGTATCACATA
1 TCACGTATCACATA
16526 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:16949 original size:2 final size:2
Alignment explanation
Indices: 16942--17015 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
16932 TTTCTTAGAC
16942 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
16984 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
17016 TCACATGTTC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17984 original size:21 final size:21
Alignment explanation
Indices: 17960--18004 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17950 TGTTGTTCGT
* *
17960 TTGAAAGGGTATCGGTTCCCC
1 TTGAAAGGGTACCGATTCCCC
*
17981 TTGAATGGGTACCGATTCCCC
1 TTGAAAGGGTACCGATTCCCC
18002 TTG
1 TTG
18005 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAAGGGTACCGATTCCCC
Found at i:21078 original size:23 final size:23
Alignment explanation
Indices: 21052--21096 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
21042 CACCACAGCT
*
21052 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
21075 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
21097 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:21475 original size:149 final size:149
Alignment explanation
Indices: 21064--21524 Score: 831
Period size: 149 Copynumber: 3.1 Consensus size: 149
21054 TATAATTGCA
** *
21064 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATTTTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTA
21128 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* *
21193 CCACAGAATAT--ATATATC
130 CCAAAGAATATACATATGTC
21211 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATAT-ATGATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
21275 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
21340 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
21359 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
*
21424 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACTTGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
21489 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
21508 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
21525 CCCTCAACTC
Statistics
Matches: 304, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
146 99 0.33
147 35 0.12
148 43 0.14
149 127 0.42
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:21644 original size:14 final size:14
Alignment explanation
Indices: 21625--21652 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21615 AACTTGTAAT
21625 TCACGTATCACATA
1 TCACGTATCACATA
21639 TCACGTATCACATA
1 TCACGTATCACATA
21653 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:23059 original size:21 final size:21
Alignment explanation
Indices: 23035--23079 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23025 TGTTGTTCGT
* *
23035 TTGAAAGGGTATCGGTTCCCC
1 TTGAAAGGGTACCGATTCCCC
*
23056 TTGAATGGGTACCGATTCCCC
1 TTGAAAGGGTACCGATTCCCC
23077 TTG
1 TTG
23080 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAAGGGTACCGATTCCCC
Found at i:25349 original size:201 final size:201
Alignment explanation
Indices: 24575--25706 Score: 1924
Period size: 201 Copynumber: 5.7 Consensus size: 201
24565 TATTTAAATT
* *
24575 AGTATCGA-AAAAAATTAAA-AAGTGTCGATTCATGTTGTAGACCTATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* * *
24638 ATATTTATACCAGTTATATTGTAAATTTACCTATTATATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* *
24703 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCA-CCTTTTTGGTATCCATTTTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
24767 ACCAAA
196 ACCAAA
* * * *
24773 CGTATCGACACAAAATTAAACAAGTGTCGATACATATTGTAGATCTATTCTCTCATAAAATCGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
24838 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
24903 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
24968 ACCAAA
196 ACCAAA
** *
24974 AGTATCGACACAAAATTAAACAAGCATCGATACGTGTTGTAGACCTATTCTCTCATAAAACCGG-
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* *
25038 -----TATA-CGGATACATTGTAAATTTACCTATTACATTATACTTATTGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* * *
25097 GGATCGACACTTTTTGAAAATATATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTGTGA
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
25162 ACCAAA
196 ACCAAA
* * **
25168 AGTATCGACACAAAATTAAACAAGTATCGATATATGTTGTAGACCTATTCTCTCATAAAATTGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* *
25233 ATATTTATACCTGTTACATTGTAAATTTACCTATTACATTATACTTATTGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
25298 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTGTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
25363 ACCAAA
196 ACCAAA
25369 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
25434 ATATTTATACCGGCTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
25499 GGATCGACACTTTTTGAAAATGTATCGACACTTTATCCGTTCACCCTTTTTGGCATCCATTCTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
25564 ACCAAA
196 ACCAAA
*
25570 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGTT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
25635 ATATTTATACCGGTTACATTGTAAATTTGCCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
25700 GGATCGA
131 GGATCGA
25707 TAAATTTTAC
Statistics
Matches: 880, Mismatches: 44, Indels: 17
0.94 0.05 0.02
Matches are distributed among these distances:
194 180 0.20
195 4 0.00
198 7 0.01
199 10 0.01
200 149 0.17
201 530 0.60
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (201 bp):
AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
ACCAAA
Found at i:25384 original size:395 final size:397
Alignment explanation
Indices: 24575--25706 Score: 1878
Period size: 395 Copynumber: 2.8 Consensus size: 397
24565 TATTTAAATT
* *
24575 AGTATCGA-AAAAAATTAAA-AAGTGTCGATTCATGTTGTAGACCTATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGG-
* * * *
24638 ATATTTATACCAGTTATATTGTAAATTTACCTATTATATTATACTTATGGATGCATATGTTTCTG
65 ----TTATACCGGATACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* *
24703 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCA-CCTTTTTGGTATCCATTTTGG
126 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
* * *
24767 ACCAAACGTATCGACACAAAATTAAACAAGTGTCGATACATATTGTAGATCTATTCTCTCATAAA
191 ACCAAAAGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAA
24832 ATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATG
256 ATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATG
24897 TTTCTGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCA
321 TTTCTGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCA
24962 TTCTGGACCAAA
386 TTCTGGACCAAA
** *
24974 AGTATCGACACAAAATTAAACAAGCATCGATACGTGTTGTAGACCTATTCTCTCATAAAACCGG-
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
25038 TATA-CGGATACATTGTAAATTTACCTATTACATTATACTTATTGATGCATATGTTTCTGGGATC
66 TATACCGGATACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTGGGATC
* * *
25102 GACACTTTTTGAAAATATATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTGTGAACCAA
131 GACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGACCAA
* * *
25167 AAGTATCGACACAAAATTAAACAAGTATCGATATATGTTGTAGACCTATTCTCTCATAAAATTGG
196 AAGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGG
* *
25232 TATATTTATACCTGTTACATTGTAAATTTACCTATTACATTATACTTATTGATGCATATGTTTCT
261 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCT
*
25297 GGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTGTG
326 GGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTG
25362 GACCAAA
391 GACCAAA
25369 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGG-
*
25434 ATATTTATACCGGCTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
65 ----TTATACCGGATACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
25499 GGATCGACACTTTTTGAAAATGTATCGACACTTTATCCGTTCACCCTTTTTGGCATCCATTCTGG
126 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
25564 ACCAAAAGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAA
191 ACCAAAAGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAA
* * *
25629 ACCGTTATATTTATACCGGTTACATTGTAAATTTGCCTATTACATTATACTTATGGATGCATATG
256 ATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATG
25694 TTTCTGGGATCGA
321 TTTCTGGGATCGA
25707 TAAATTTTAC
Statistics
Matches: 683, Mismatches: 40, Indels: 17
0.92 0.05 0.02
Matches are distributed among these distances:
394 92 0.13
395 281 0.41
399 8 0.01
400 10 0.01
401 43 0.06
402 249 0.36
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (397 bp):
AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
TATACCGGATACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTGGGATC
GACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGACCAA
AAGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGG
TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCT
GGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTG
GACCAAA
Found at i:27802 original size:33 final size:33
Alignment explanation
Indices: 27765--27830 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
27755 CATCTTAAGA
*
27765 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
*
27798 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
27831 CCATCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:27889 original size:21 final size:21
Alignment explanation
Indices: 27864--27928 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
27854 CCCCTTATGC
*
27864 CTCTCAAGTGTATCTTCAACT
1 CTCTCAAGTTTATCTTCAACT
*
27885 CTCTCAAGTTTTTCTTCAACT
1 CTCTCAAGTTTATCTTCAACT
* *
27906 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTATCTTCAACT
27927 CT
1 CT
27929 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.18, C:0.31, G:0.08, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTTTATCTTCAACT
Found at i:31988 original size:3 final size:3
Alignment explanation
Indices: 31982--32026 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
31972 AATTTTTTTC
* *
31982 ATT ATT ATT ATT ATT ATT ATA AGT ATT ATT ATT ATT A-T ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
32027 ATAATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:32038 original size:15 final size:14
Alignment explanation
Indices: 31982--32038 Score: 64
Period size: 15 Copynumber: 4.1 Consensus size: 14
31972 AATTTTTTTC
31982 ATTATTAT--TATT
1 ATTATTATAATATT
31994 ATTATTATAAGTATT
1 ATTATTATAA-TATT
*
32009 ATTATTATTATATT
1 ATTATTATAATATT
*
32023 ATTAATAATAATATT
1 ATT-ATTATAATATT
32038 A
1 A
32039 CATGGCTCAG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
12 8 0.21
14 7 0.18
15 23 0.61
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATTATTATAATATT
Found at i:33152 original size:21 final size:21
Alignment explanation
Indices: 33126--33170 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
33116 GATTTCTGGG
* *
33126 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
33147 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
33168 CAA
1 CAA
33171 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:33779 original size:18 final size:18
Alignment explanation
Indices: 33756--33790 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33746 CTAGGAGATT
33756 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
33774 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
33791 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:35236 original size:149 final size:149
Alignment explanation
Indices: 34773--35225 Score: 861
Period size: 149 Copynumber: 3.0 Consensus size: 149
34763 GAGTCGAGGG
* *
34773 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
34838 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
34903 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
34922 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
34987 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
35052 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
35071 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
35136 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
35201 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
35220 TCTACG
1 TCTACG
35226 GGGCACTTCG
Statistics
Matches: 298, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 298 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:35248 original size:23 final size:23
Alignment explanation
Indices: 35204--35248 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
35194 ATCATTATAT
*
35204 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
35227 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
35249 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:38407 original size:21 final size:21
Alignment explanation
Indices: 38381--38425 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38371 GATTTCTGGG
* *
38381 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
38402 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
38423 CAA
1 CAA
38426 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:39029 original size:18 final size:18
Alignment explanation
Indices: 39006--39040 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38996 CTAGGAGATT
39006 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
39024 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
39041 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:39126 original size:21 final size:22
Alignment explanation
Indices: 39097--39140 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
39087 GTTGTATGAT
39097 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
39118 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
39140 A
1 A
39141 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:40441 original size:148 final size:149
Alignment explanation
Indices: 40032--40482 Score: 859
Period size: 149 Copynumber: 3.0 Consensus size: 149
40022 GAGTCGAGGG
* *
40032 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
40097 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
40162 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
40181 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
40246 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
40311 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
40330 TCTACGC-GTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
40394 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
40459 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
40478 TCTAC
1 TCTAC
40483 AGGGCACTTC
Statistics
Matches: 298, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
148 144 0.48
149 154 0.52
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:43623 original size:23 final size:22
Alignment explanation
Indices: 43579--43623 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
43569 GAATGTCATG
*
43579 GGGAACCGATACCCCCATAGGA
1 GGGAACCGATACCCCCAAAGGA
*
43601 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
43624 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:44960 original size:18 final size:18
Alignment explanation
Indices: 44937--44972 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
44927 AGGAATGATA
44937 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
44955 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
44973 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:44974 original size:62 final size:62
Alignment explanation
Indices: 44908--45095 Score: 146
Period size: 62 Copynumber: 3.1 Consensus size: 62
44898 TGATCCCTAG
44908 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGA
1 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGA
* * * * * *
44970 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCC--
1 CATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTT
**
45025 CTAG-
58 CGGGA
*
45029 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACATTGTGGTCCTTCGGGA
1 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGA
45091 CATAT
1 CATAT
45096 ATGTATTCTT
Statistics
Matches: 90, Mismatches: 17, Indels: 38
0.62 0.12 0.26
Matches are distributed among these distances:
57 6 0.07
58 7 0.08
59 18 0.20
60 12 0.13
61 12 0.13
62 22 0.24
63 7 0.08
64 6 0.07
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (62 bp):
CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGA
Found at i:44992 original size:121 final size:121
Alignment explanation
Indices: 44834--45197 Score: 685
Period size: 121 Copynumber: 3.0 Consensus size: 121
44824 CGAGGGTCTA
44834 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
*
44899 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
*
44955 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
45020 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
45076 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
*
45141 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTT-ATGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCA-GGACAT
45197 T
1 T
45198 ATTATATGGC
Statistics
Matches: 238, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
120 1 0.00
121 237 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
Found at i:45081 original size:18 final size:18
Alignment explanation
Indices: 45058--45093 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
45048 AGGAATGATA
45058 TGTGGTCCTTCAGGACAT
1 TGTGGTCCTTCAGGACAT
*
45076 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCAGGACAT
45094 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.22, G:0.31, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCAGGACAT
Found at i:45272 original size:23 final size:23
Alignment explanation
Indices: 45204--45264 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
45194 CATTATTATA
*
45204 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
45227 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
45250 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
45265 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:49028 original size:21 final size:21
Alignment explanation
Indices: 49002--49044 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
48992 TTATAGGCTC
* *
49002 GGGGAATTGGTACCCATTCAA
1 GGGGAATCGATACCCATTCAA
*
49023 GGGGAATCGATACCCCTTCAA
1 GGGGAATCGATACCCATTCAA
49044 G
1 G
49045 CGAATAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (21 bp):
GGGGAATCGATACCCATTCAA
Found at i:49115 original size:23 final size:22
Alignment explanation
Indices: 49071--49115 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
49061 AATGTCATGG
*
49071 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
49093 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
49116 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:50452 original size:18 final size:18
Alignment explanation
Indices: 50429--50464 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
50419 AAGAATGATA
*
50429 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCAGGACAT
50447 TGTGGTCCTTCAGGACAT
1 TGTGGTCCTTCAGGACAT
50465 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.22, G:0.31, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCAGGACAT
Found at i:50474 original size:121 final size:121
Alignment explanation
Indices: 50326--50689 Score: 622
Period size: 121 Copynumber: 3.0 Consensus size: 121
50316 CGAGGGTCTA
* *
50326 TGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
** * * *
50391 GATCCCTAGCATATGTATAAAAATCTTAAAGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
*
50447 TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
*
50512 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGATAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
50568 TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
*
50633 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTT-ATGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCA-GGACAT
50689 T
1 T
50690 ATTATATGGC
Statistics
Matches: 230, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 1 0.00
121 229 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (121 bp):
TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
Found at i:50573 original size:18 final size:17
Alignment explanation
Indices: 50546--50582 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
50536 CTTAAGGAAT
50546 GATATGTGGTCCTTCAG
1 GATATGTGGTCCTTCAG
50563 GATATTGTGGTCCTTCAG
1 GATA-TGTGGTCCTTCAG
50581 GA
1 GA
50583 CATATATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.19, C:0.16, G:0.30, T:0.35
Consensus pattern (17 bp):
GATATGTGGTCCTTCAG
Found at i:55416 original size:20 final size:20
Alignment explanation
Indices: 55393--55436 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
55383 ACATTTGTTT
*
55393 TTTTTATGTTTGCATTTGCA
1 TTTTTATATTTGCATTTGCA
* *
55413 TTTTTATATTTTCATTTTCA
1 TTTTTATATTTGCATTTGCA
55433 TTTT
1 TTTT
55437 CATTTTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTTTATATTTGCATTTGCA
Done.