Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007924.1 Hibiscus syriacus cultivar Beakdansim tig00110330_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: 1741266
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 7
Found at i:222451 original size:2 final size:2
Alignment explanation
Indices: 222444--222497 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
222434 TTTATAAGCA
222444 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
222486 AT AT AT AT AT AT
1 AT AT AT AT AT AT
222498 TACCAAGTGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:224778 original size:7 final size:7
Alignment explanation
Indices: 224768--224792 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
224758 TATAATTTGG
224768 AATTCGA
1 AATTCGA
224775 AATTCGA
1 AATTCGA
224782 AATTCGA
1 AATTCGA
224789 AATT
1 AATT
224793 TAAGATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (7 bp):
AATTCGA
Found at i:224856 original size:21 final size:19
Alignment explanation
Indices: 224822--224861 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
224812 ATTAAACAAA
*
224822 TATTATAAAATTTATATTT
1 TATTATAAAATTTAAATTT
224841 TATTATAAATAATTTAAATTT
1 TATTAT-AA-AATTTAAATTT
224862 GTTTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTATAAAATTTAAATTT
Found at i:225502 original size:30 final size:31
Alignment explanation
Indices: 225452--225510 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
225442 TGGCAGAGAA
* *
225452 ACTAAAATCGGATGGATCGATAATGTTAGGG
1 ACTAAAATCGAATGGATCGATAACGTTAGGG
225483 ACTAAAATCGAAT-GATCGATAACGTTAG
1 ACTAAAATCGAATGGATCGATAACGTTAG
225511 AGATCATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (31 bp):
ACTAAAATCGAATGGATCGATAACGTTAGGG
Found at i:228544 original size:630 final size:630
Alignment explanation
Indices: 227341--228576 Score: 2163
Period size: 630 Copynumber: 2.0 Consensus size: 630
227331 TGAGGCTGAT
227341 TTATTTGAGATTTTATCTGTCTTATACGTGGGTTTTGGGGACAAAAGATGAAAAACCTTCATTAT
1 TTATTTGAGATTTTATCTGTCTTATACGTGGGTTTTGGGGACAAAAGATGAAAAACCTT-ATTAT
*
227406 CTTCTCATTATTTTCTTATATCTTTTCATTTTTCCTATTTCCTCTCCAAGTGTCATAACTAAAGG
65 CTTCTCATTATTTTCTTATATCTTTTCATTTTTCCTATTTCCTCTACAAGTGTCATAACTAAAGG
* * *
227471 TAAGTTTCTTGAGCCCTTTTATGCTTATGTTAAACTTCATATTCGTCCGAACCACTCTAGAAAAC
130 TAAGTTTCTTGAGCCCTTTTATACTTATGTTAAACTTCAAATTCGTCCAAACCACTCTAGAAAAC
*
227536 TTGTTTTGAAGATTCAAAGCCTTGGGTTTCCTTTTTTGCTAGAAAAAAGTGGATAAGCAACCAAG
195 TTGTTTTGAAGATTCAAAGCCTTGGGTTTCCTTTTTTGCTAGAAAAAAGTGAATAAGCAACCAAG
227601 TTCTAGAGGAGAGTGTGGTTAACTAAAGGAGATTCATTTCGGGCTTCTAACATAATGTAGTATAT
260 TTCTAGAGGAGAGTGTGGTTAACTAAAGGAGATTCATTTCGGGCTTCTAACATAATGTAGTATAT
227666 TTCTAATCTTTTGCGGTGTTAAGACTTTCATGCATGTACTAACTGCTTAGTATCATATCTTACAA
325 TTCTAATCTTTTGCGGTGTTAAGACTTTCATGCATGTACTAACTGCTTAGTATCATATCTTACAA
227731 CATGCTTGTGTTTATAAGACTCATAATGATGTTCTAGATTATATATTATATTGTTGGGCTTCTTA
390 CATGCTTGTGTTTATAAGACTCATAATGATGTTCTAGATTATATATTATATTGTTGGGCTTCTTA
227796 AGCTCAACATTCAGATTTTTTCGTTTGTTGGTTATTAGCTTGAGCTGTTCGTAGAGCACTATCAC
455 AGCTCAACATTCAGATTTTTTCGTTTGTTGGTTATTAGCTTGAGCTGTTCGTAGAGCACTATCAC
* *
227861 AATAGGACTTCTAGCATCGCTTCCAAAGTACTATACTATAGCTTTAGTAAACATGTGTGTCACTC
520 AATAAGACTTCTAACATCGCTTCCAAAGTACTATACTATAGCTTTAGTAAACATGTGTGTCACTC
227926 CCTTAACATGCATTCATACCCTCTAGCAAGTGTCATCTTCTTCTCA
585 CCTTAACATGCATTCATACCCTCTAGCAAGTGTCATCTTCTTCTCA
*
227972 TTATTTGAGATTTTGTCTGTCTTATACGTGGGTTTTGGGGACAAAAGATGAAAAACC-T-TTATC
1 TTATTTGAGATTTTATCTGTCTTATACGTGGGTTTTGGGGACAAAAGATGAAAAACCTTATTATC
* * * *
228035 TTCTTATTATTTTCTTCTCTCTTTTTCCTTTTTTCCTATTTCCTCTACAAGTGTCATAACTAAAG
66 TTCTCATTATTTTCTTATATC-TTTT-CATTTTTCCTATTTCCTCTACAAGTGTCATAACTAAAG
* * *
228100 GTAAGTTTCTTGAGCCCTTTTATACTTCTGTTAAACTTCAAATTCGTTCAAACCACTCTAGCAAA
129 GTAAGTTTCTTGAGCCCTTTTATACTTATGTTAAACTTCAAATTCGTCCAAACCACTCTAGAAAA
*
228165 CTTGTTTTGAAGATTCAAAGCCTTGGGTTTCCTTTTTTGCTAGAAAAAGGTGAATAAGCAACCAA
194 CTTGTTTTGAAGATTCAAAGCCTTGGGTTTCCTTTTTTGCTAGAAAAAAGTGAATAAGCAACCAA
* * * *
228230 GTTCTAGATGAGAGTGTTGGTTAACTAAAGGAGCTTTATTTCGGGTTTCTAACATAATGTAGTAT
259 GTTCTAGAGGAGAGTG-TGGTTAACTAAAGGAGATTCATTTCGGGCTTCTAACATAATGTAGTAT
* *
228295 ATTTCTAATCTTTTGTGGTGTTAAGACTTTCATGCATGTACTAACTGCTTAGTATCATATCTTAT
323 ATTTCTAATCTTTTGCGGTGTTAAGACTTTCATGCATGTACTAACTGCTTAGTATCATATCTTAC
* *
228360 AGCATGCTTGTGTTTATAAGACTCATAATGATGTTCTAGATTATCTATTATATTGTTGGGCTTCT
388 AACATGCTTGTGTTTATAAGACTCATAATGATGTTCTAGATTATATATTATATTGTTGGGCTTCT
*
228425 TAAGCTCAACATTCAGA-TTTTTCGTTTGTTGGTTATTAGCTTGAGTTGTTCGTAGAGCACTATC
453 TAAGCTCAACATTCAGATTTTTTCGTTTGTTGGTTATTAGCTTGAGCTGTTCGTAGAGCACTATC
* * *
228489 ACAATAAGACTTCTAACATCTCTTCCAAAGTATTGTACTATAGCTTTAGTAAACATGTGTGTCAC
518 ACAATAAGACTTCTAACATCGCTTCCAAAGTACTATACTATAGCTTTAGTAAACATGTGTGTCAC
228554 TCCCTTAACATGCATTCATACCC
583 TCCCTTAACATGCATTCATACCC
228577 GAATACAAGC
Statistics
Matches: 574, Mismatches: 28, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
628 23 0.04
629 4 0.01
630 303 0.53
631 244 0.43
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (630 bp):
TTATTTGAGATTTTATCTGTCTTATACGTGGGTTTTGGGGACAAAAGATGAAAAACCTTATTATC
TTCTCATTATTTTCTTATATCTTTTCATTTTTCCTATTTCCTCTACAAGTGTCATAACTAAAGGT
AAGTTTCTTGAGCCCTTTTATACTTATGTTAAACTTCAAATTCGTCCAAACCACTCTAGAAAACT
TGTTTTGAAGATTCAAAGCCTTGGGTTTCCTTTTTTGCTAGAAAAAAGTGAATAAGCAACCAAGT
TCTAGAGGAGAGTGTGGTTAACTAAAGGAGATTCATTTCGGGCTTCTAACATAATGTAGTATATT
TCTAATCTTTTGCGGTGTTAAGACTTTCATGCATGTACTAACTGCTTAGTATCATATCTTACAAC
ATGCTTGTGTTTATAAGACTCATAATGATGTTCTAGATTATATATTATATTGTTGGGCTTCTTAA
GCTCAACATTCAGATTTTTTCGTTTGTTGGTTATTAGCTTGAGCTGTTCGTAGAGCACTATCACA
ATAAGACTTCTAACATCGCTTCCAAAGTACTATACTATAGCTTTAGTAAACATGTGTGTCACTCC
CTTAACATGCATTCATACCCTCTAGCAAGTGTCATCTTCTTCTCA
Found at i:230350 original size:23 final size:23
Alignment explanation
Indices: 230332--230415 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
230322 CTCGTATAAA
230332 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
230355 TGCACCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
230378 TGTACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
230401 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
230416 TATAAGATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:230426 original size:46 final size:46
Alignment explanation
Indices: 230335--230445 Score: 136
Period size: 46 Copynumber: 2.4 Consensus size: 46
230325 GTATAAATGC
*
230335 ACCGAAGTGCCACGTAGAATTGCACCGAAGTGCCGCATAGAATTGT
1 ACCGAAGTGCCACGTAGAATTGCACCGAAGTGCCACATAGAATTGT
* * *
230381 ACCGAAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA-AGATTGT
1 ACCGAAGTGCCACGTAGAATTGCACCGAAGTGCCACATAGA-ATTGT
* *
230427 CCCTAAG-GACCACGTAGAA
1 ACCGAAGTG-CCACGTAGAA
230446 AATTTCCTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
45 2 0.04
46 54 0.96
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (46 bp):
ACCGAAGTGCCACGTAGAATTGCACCGAAGTGCCACATAGAATTGT
Found at i:230671 original size:30 final size:31
Alignment explanation
Indices: 230637--230696 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
230627 ATATTGTATA
*
230637 AACATATAATTTTC-AT-ACCTTTATCACATG
1 AACATATAATGTTCTATCA-CTTTATCACATG
*
230667 AACATATCATGTTCTATCACTTTATCACAT
1 AACATATAATGTTCTATCACTTTATCACAT
230697 AGCTTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 13 0.50
32 1 0.04
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (31 bp):
AACATATAATGTTCTATCACTTTATCACATG
Found at i:237302 original size:23 final size:23
Alignment explanation
Indices: 237276--237320 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
237266 CACCACAGCT
*
237276 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
237299 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
237321 GCATAAATTG
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:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:237332 original size:22 final size:22
Alignment explanation
Indices: 237279--237348 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
237269 CACAGCTCGT
237279 ATAAA-TGCACCGAAGTGCCAC
1 ATAAATTGCACCGAAGTGCCAC
* *
237300 GTAGAATTGCACCGAAGTGCCGC
1 ATA-AATTGCACCGAAGTGCCAC
*
237323 ATAAATTGCACCGTAA-TGCCAT
1 ATAAATTGCACCG-AAGTGCCAC
237345 ATAA
1 ATAA
237349 GATTATCCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.05
22 20 0.49
23 19 0.46
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (22 bp):
ATAAATTGCACCGAAGTGCCAC
Found at i:237600 original size:30 final size:31
Alignment explanation
Indices: 237566--237624 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
237556 TATTGTATAG
237566 ACATATAAT-TTCCATTC-CTTTATCACATGA
1 ACATATAATGTTCCA-TCACTTTATCACATGA
* *
237596 ACATATCATGTTCTATCACTTTATCACAT
1 ACATATAATGTTCCATCACTTTATCACAT
237625 AGCTTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (31 bp):
ACATATAATGTTCCATCACTTTATCACATGA
Found at i:238063 original size:63 final size:64
Alignment explanation
Indices: 237969--238124 Score: 167
Period size: 64 Copynumber: 2.4 Consensus size: 64
237959 AATGAAGGTA
* **
237969 TGCATCGATGCAC-CACACCATGCATCGATGCA-TAAAT-CCTATTCGATGTTTATA-TTTAAGG
1 TGCATCGATGCACTC-CA-TATGCATCGATGCACT-AATGCC-ATTCGATGTTTATATTTTAAAA
*
238030 GGG
62 GAG
* * *
238033 TGCATCGATGCACTCCTTATGCATCGATGCACTAATGGCATTCGATGTTTGTATTTTAAAAGAG
1 TGCATCGATGCACTCCATATGCATCGATGCACTAATGCCATTCGATGTTTATATTTTAAAAGAG
* *
238097 TGCATCGATGCACTTCATGTGCATCGAT
1 TGCATCGATGCACTCCATATGCATCGAT
238125 ACACCTTGAA
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
63 29 0.37
64 48 0.62
65 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (64 bp):
TGCATCGATGCACTCCATATGCATCGATGCACTAATGCCATTCGATGTTTATATTTTAAAAGAG
Found at i:238665 original size:13 final size:13
Alignment explanation
Indices: 238647--238672 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
238637 TCTCACGGGG
238647 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
238660 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
238673 GAAATCTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:239353 original size:16 final size:17
Alignment explanation
Indices: 239303--239353 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
239293 TAACAATAAC
*
239303 TTAT-TAATGTTTTTTAT
1 TTATATAATGATTTTT-T
239320 TTATATAATGA-TTTTT
1 TTATATAATGATTTTTT
*
239336 TTATATTAT-ATTTTTT
1 TTATATAATGATTTTTT
239352 TT
1 TT
239354 CTTACATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 1 0.03
16 16 0.53
17 8 0.27
18 5 0.17
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (17 bp):
TTATATAATGATTTTTT
Found at i:243389 original size:14 final size:14
Alignment explanation
Indices: 243370--243409 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
243360 ACTTTAAAAG
243370 TTTATTTTAATTAT
1 TTTATTTTAATTAT
* *
243384 TTTATTATAATAAT
1 TTTATTTTAATTAT
*
243398 ATTATTTTAATT
1 TTTATTTTAATT
243410 TTTATATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATTTTAATTAT
Found at i:243437 original size:20 final size:17
Alignment explanation
Indices: 243396--243438 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
243386 TATTATAATA
*
243396 ATATTATTTTAATTTTT
1 ATATTATTTTAAATTTT
*
243413 ATATTATATTTAAAATTT
1 ATATTAT-TTTAAATTTT
243431 -TATTATTT
1 ATATTATTT
243439 GGAAGTGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 13 0.57
18 8 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATTATTTTAAATTTT
Found at i:250979 original size:2 final size:2
Alignment explanation
Indices: 250972--251005 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
250962 TTAATATTTA
250972 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
251006 GTATGTATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:253368 original size:9 final size:9
Alignment explanation
Indices: 253354--253385 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
253344 ACAAACATCA
253354 CTTCTCTTC
1 CTTCTCTTC
253363 CTTCTCTTC
1 CTTCTCTTC
253372 CTTCTCTTC
1 CTTCTCTTC
253381 CTTCT
1 CTTCT
253386 TTTCTGGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (9 bp):
CTTCTCTTC
Found at i:257967 original size:831 final size:817
Alignment explanation
Indices: 256359--257991 Score: 2452
Period size: 831 Copynumber: 2.0 Consensus size: 817
256349 ATTGTATGTG
256359 ATTATTATTTTTTATGTTTTTTTTTATATTATGTCTTTTTTTTTACTTTTCTCATTTTTAAATAA
1 ATTATTATTTTTTATG-TTTTTTTTATATTATGTCTTTTTTTTTACTTTTCTCATTTTTAAATAA
* * * * *
256424 AAATTTTTGTCTTTGTGACACGTTTTTTTCTGTTCTTGTGTTACGTTCCTTATGATTTTCGGTAA
65 AAATTTATGTCTTTGTGACACGTTTTTCTCTGCTCTTGTGTCACGTTCCTTATGATTTTCGATAA
* * * *
256489 GTTTTTCGCATACTTCTGCGATCGTGTTAGTGCTTCCACAAAGATTTTCACGATATTTGTTTTCT
130 GTTTTTCACATACTTCTGCGATCGTGTTAGTGCTTCCACAAAGATTCTCACGACATTTATTTTCT
* * * * * * *
256554 GATTGGCTTGTCAGTTGACACATTATTAAATCACCTTTTTTGTAAATGGTCGTTAGTATATATAA
195 GATCGGCTTATCAGTGGACACATTATTAAATCACATCTTTTGTAAATGGTCGTTAGCAGATATAA
*
256619 TCAGAATTGTGTAGCGAATCATTCTATCAAATTATTTGGTTCGCTCACCACTCTTTTACATCGTA
260 TCAGAATTATGTAGCGAATCATTCTATCAAATTATTTGGTTCGCTCACCACTCTTTTACATCGTA
* * * *
256684 AAGCGTCTCGTTCGACAGAGACAATGAGTTTTATGAAGGTTATTGATTGTTTTGATGTTTAGAAT
325 AAGCGTCTCGTTCGACAGAAACAATGAGTTTTATGAAGGTTATGGATTGTATTGATGTTTAGAAA
256749 GTTTCATTCTCTTCGTATCTTTAGGTTTAATATTTTTATTTTATGTATGAGTTTTTGGCTACCAT
390 GTTTCATTCTCTTCGTATCTTTAGGTTTAATATTTTTATTTTATGTATGAGTTTTTGGCTACCAT
* * *
256814 TGTCTCCAATTTTCTCTTTAAATGAGTTGTAATTTTGATTCTTTCATTTTTATTAATGAAATTTA
455 TGTCTCCAATTTTCTCTTTAAATGAGTTGTAATTTTGAGTCTCTCAGTTTTATTAATGAAATTTA
* * *
256879 GTTTGTATTGTAAAAAAAAAGAAGAACAAAGACTAATATGATAAAAAAAATTAAATATGAAACGT
520 GTTCGCATTGTAAAAAAAAAGAAGAACAAACACTAATATGATAAAAAAAATTAAATATGAAACGT
* * * * * *
256944 AAAATTTATTGAATTATTTTGAACTATGACCAAATTAATAAAATATATAAGTTTTACGATTAAAA
585 AAAATTTATTAAATTATTTCGAACCACGACCAAATTAATAAAATATAAAAGTTTTAAGATTAAAA
* *
257009 TTATTATACGAGTTGAAGCCACTATTTCATCTAATATTTAAAAGGCCACGACATGTTTATAATAA
650 TTATTATACAAGTTGAAACCACTATTTCATCTAATATTTAAAAGGCCACGACATGTTTATAATAA
257074 TATTTTATTTTATTGGTCAAATTATAATATTTTATTTAAAGAAAATGACTCGTGCATTACCAAAT
715 TATTTTATTTTATTGGTCAAATTATAATATTTTATTTAAAGAAAATGACTCGTGCATTACCAAAT
257139 ACATACATATTGAGTGTATTTTTTTATTACTGTTGATA
780 ACATACATATTGAGTGTATTTTTTTATTACTGTTGATA
257177 ATTATTATTTTCTTA-G-TTTTTTTATATTATGTCTTTGTTTTTTTTCTTGACTTTTCTCATTTT
1 ATTATTATTTT-TTATGTTTTTTTTATATTATGTC-----TTTTTTT-TT-ACTTTTCTCATTTT
* * * *
257240 TAAATAAGAATTTATGTTTTTGTGACACGTTTTTCTCTGCTCTTGTGTCATGTTCCTTATGGTTT
58 TAAATAAAAATTTATGTCTTTGTGACACGTTTTTCTCTGCTCTTGTGTCACGTTCCTTATGATTT
** * * * * **
257305 TCGATAAGTTTTTCATTTACTTTTGTGGTCGTGTTGGTG-TTTTACAAAGATTCTCACGACATTT
123 TCGATAAGTTTTTCACATACTTCTGCGATCGTGTTAGTGCTTCCACAAAGATTCTCACGACATTT
* * *
257369 ATTTTCTGATCGGCTTATCGGTGGGCACATATTATTAGATCACATCTTTTGTAAATGGTCGTTAG
188 ATTTTCTGATCGGCTTATCAGT-GG-ACACATTATTAAATCACATCTTTTGTAAATGGTCGTTAG
* * *
257434 CCGATATAATCAGAATTATGTAGCGAATTATTCTATCAAATTATTTGGTTTGCTCACCACTCCTT
251 CAGATATAATCAGAATTATGTAGCGAATCATTCTATCAAATTATTTGGTTCGCTCACCACT-C-T
* * *
257499 TTATCACATCGTAAAGTGTCTCGTTCGACATAAACAATTAGTTTTATGAAGGTTACTGGATTGTA
314 TT-T-ACATCGTAAAGCGTCTCGTTCGACAGAAACAATGAGTTTTATGAAGGTTA-TGGATTGTA
*
257564 TTGATGTTTAGAAAGTTTCATTTTCTTCGTATCTTTAGGTTTAATATTTTTATTTTATGTATGAG
376 TTGATGTTTAGAAAGTTTCATTCTCTTCGTATCTTTAGGTTTAATATTTTTATTTTATGTATGAG
* * *
257629 TTTTTGG-TGACCATTGTCTCCAATTTTCTTTTTAGATGCA-TTGTAATTTTGAGTC-CTCCGTT
441 TTTTTGGCT-ACCATTGTCTCCAATTTTCTCTTTAAATG-AGTTGTAATTTTGAGTCTCTCAGTT
257691 TTATTAATGAAATTTAGTTCGCATTGTAAAAAAAAAAGAGAAGAACAAACACTAATATGAT-AAA
504 TTATTAATGAAATTTAGTTCGCATTGT--AAAAAAAA-AGAAGAACAAACACTAATATGATAAAA
257755 AAAATTAAATATGAAACGTAAAATTTATTAAATTATTTCGAACCACGACCAAATTAATAAAATAT
566 AAAATTAAATATGAAACGTAAAATTTATTAAATTATTTCGAACCACGACCAAATTAATAAAATAT
257820 AAAAGTTTTAAGATTAAAATTATTATACCAAGTTGAAACCACTATTTCATCTAATATTTAAAAGG
631 AAAAGTTTTAAGATTAAAATTATTATA-CAAGTTGAAACCACTATTTCATCTAATATTTAAAAGG
257885 CCACGACATGTTTATAATAATATTTTATTTTATTGGTCAAATTATAATATTTTATTTAAAGAAAA
695 CCACGACATGTTTATAATAATATTTTATTTTATTGGTCAAATTATAATATTTTATTTAAAGAAAA
** *
257950 TGACTCGTGTGTTACCAAATACGTACATATTGAGTGTATTTT
760 TGACTCGTGCATTACCAAATACATACATATTGAGTGTATTTT
257992 ACTCTTATAA
Statistics
Matches: 731, Mismatches: 63, Indels: 29
0.89 0.08 0.04
Matches are distributed among these distances:
816 17 0.02
818 12 0.02
819 3 0.00
821 7 0.01
822 41 0.06
823 103 0.14
824 90 0.12
825 1 0.00
826 3 0.00
827 1 0.00
828 76 0.10
829 118 0.16
830 98 0.13
831 161 0.22
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.44
Consensus pattern (817 bp):
ATTATTATTTTTTATGTTTTTTTTATATTATGTCTTTTTTTTTACTTTTCTCATTTTTAAATAAA
AATTTATGTCTTTGTGACACGTTTTTCTCTGCTCTTGTGTCACGTTCCTTATGATTTTCGATAAG
TTTTTCACATACTTCTGCGATCGTGTTAGTGCTTCCACAAAGATTCTCACGACATTTATTTTCTG
ATCGGCTTATCAGTGGACACATTATTAAATCACATCTTTTGTAAATGGTCGTTAGCAGATATAAT
CAGAATTATGTAGCGAATCATTCTATCAAATTATTTGGTTCGCTCACCACTCTTTTACATCGTAA
AGCGTCTCGTTCGACAGAAACAATGAGTTTTATGAAGGTTATGGATTGTATTGATGTTTAGAAAG
TTTCATTCTCTTCGTATCTTTAGGTTTAATATTTTTATTTTATGTATGAGTTTTTGGCTACCATT
GTCTCCAATTTTCTCTTTAAATGAGTTGTAATTTTGAGTCTCTCAGTTTTATTAATGAAATTTAG
TTCGCATTGTAAAAAAAAAGAAGAACAAACACTAATATGATAAAAAAAATTAAATATGAAACGTA
AAATTTATTAAATTATTTCGAACCACGACCAAATTAATAAAATATAAAAGTTTTAAGATTAAAAT
TATTATACAAGTTGAAACCACTATTTCATCTAATATTTAAAAGGCCACGACATGTTTATAATAAT
ATTTTATTTTATTGGTCAAATTATAATATTTTATTTAAAGAAAATGACTCGTGCATTACCAAATA
CATACATATTGAGTGTATTTTTTTATTACTGTTGATA
Found at i:258264 original size:24 final size:23
Alignment explanation
Indices: 258213--258261 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
258203 AAATTATGCA
*
258213 TTTAGTACTTAAACTATCATTTT
1 TTTAATACTTAAACTATCATTTT
*
258236 TTTAATACTTAAACTTTCATTTT
1 TTTAATACTTAAACTATCATTTT
258259 TTT
1 TTT
258262 TAAAATCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTAATACTTAAACTATCATTTT
Found at i:258792 original size:87 final size:87
Alignment explanation
Indices: 258683--258862 Score: 243
Period size: 87 Copynumber: 2.1 Consensus size: 87
258673 ATTTTAAAAA
* * * * *
258683 AATTAAAAGTTTAGATACTAAAATAGATAAAAACTAATAGTTTATGTACTAAACGCACAATTTAC
1 AATTAAAAGTTTAGATAATAAAACAGATAAAAACTAATAGTTTAGGCACTAAACACACAATTTAC
*
258748 CTTATTATTTACAGTATGTACT
66 CCTATTATTTACAGTATGTACT
* * * *
258770 AATTAAAAGTTTAGGTAATAAAACAGATTAAAATTAATAGTTTAGGCACTAAACACATAATTTAC
1 AATTAAAAGTTTAGATAATAAAACAGATAAAAACTAATAGTTTAGGCACTAAACACACAATTTAC
**
258835 CCTATTATTTATTGTATGTACT
66 CCTATTATTTACAGTATGTACT
*
258857 AGTTAA
1 AATTAA
258863 TCCACTGTAA
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (87 bp):
AATTAAAAGTTTAGATAATAAAACAGATAAAAACTAATAGTTTAGGCACTAAACACACAATTTAC
CCTATTATTTACAGTATGTACT
Found at i:261822 original size:2 final size:2
Alignment explanation
Indices: 261815--261842 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
261805 TTTCTTTTTA
261815 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
261843 TAGTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:261913 original size:2 final size:2
Alignment explanation
Indices: 261906--261933 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
261896 ATTAAAACTA
261906 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
261934 TAAAAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:263485 original size:25 final size:25
Alignment explanation
Indices: 263439--263486 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
263429 TACCGTTAAA
* * **
263439 AATTTAAAGTTAAGTTTTTAAAAAC
1 AATTGAAAGTTAAGATACTAAAAAC
263464 AATTGAAAGTTAAGATACTAAAA
1 AATTGAAAGTTAAGATACTAAAA
263487 TGGGTCAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.33
Consensus pattern (25 bp):
AATTGAAAGTTAAGATACTAAAAAC
Found at i:267635 original size:21 final size:21
Alignment explanation
Indices: 267611--267750 Score: 67
Period size: 21 Copynumber: 6.6 Consensus size: 21
267601 CCTAATATAT
267611 TAATATTTTAAATAATTAAAA
1 TAATATTTTAAATAATTAAAA
*
267632 TAATATATTTATAATAA-T-ATA
1 TAATAT-TTTA-AATAATTAAAA
* *
267653 TTATATTTTAAA-AGATTAAAT
1 TAATATTTTAAATA-ATTAAAA
** **
267674 TAATATATTT-TGT-ATTCAATT
1 TAATAT-TTTAAATAATT-AAAA
*
267695 TAATATTTTTAATAATT-AAA
1 TAATATTTTAAATAATTAAAA
* *
267715 TAATATATTTCAATACTATAAAAA
1 TAATAT-TTTAAATA--ATTAAAA
*
267739 TAAAATTTTAAA
1 TAATATTTTAAA
267751 ATATTATATA
Statistics
Matches: 89, Mismatches: 16, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
18 1 0.01
19 3 0.03
20 18 0.20
21 36 0.40
22 11 0.12
23 12 0.13
24 8 0.09
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (21 bp):
TAATATTTTAAATAATTAAAA
Found at i:267645 original size:20 final size:21
Alignment explanation
Indices: 267611--267729 Score: 77
Period size: 21 Copynumber: 5.7 Consensus size: 21
267601 CCTAATATAT
267611 TAATAT-TTTAAATAATTAAAA
1 TAATATATTT-AATAATTAAAA
*
267632 TAATATATTT-ATAA-TAATA
1 TAATATATTTAATAATTAAAA
* * *
267651 TATTATATTTTAAAAGATTAAAT
1 TAATATA-TTTAATA-ATTAAAA
** **
267674 TAATATATTTTGT-ATTCAATT
1 TAATATATTTAATAATT-AAAA
*
267695 TAATATTTTTAATAATT-AAA
1 TAATATATTTAATAATTAAAA
267715 TAATATATTTCAATA
1 TAATATATTT-AATA
267730 CTATAAAAAT
Statistics
Matches: 74, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
19 10 0.14
20 20 0.27
21 25 0.34
22 10 0.14
23 9 0.12
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TAATATATTTAATAATTAAAA
Found at i:267664 original size:42 final size:42
Alignment explanation
Indices: 267603--267724 Score: 135
Period size: 42 Copynumber: 2.9 Consensus size: 42
267593 GACCCAATCC
267603 TAATATATTAATATTTTAAATAATTAAAATAATATATTTATAA
1 TAATATATT-ATATTTTAAATAATTAAAATAATATATTTATAA
* * *
267646 TAATATATTATATTTTAAA-AGATTAAATTAATATATTTTGTAT
1 TAATATATTATATTTTAAATA-ATTAAAATAATATA-TTTATAA
* *
267689 TCAAT-T-TAATATTTTTAATAATT-AAATAATATATTT
1 T-AATATATTATATTTTAAATAATTAAAATAATATATTT
267725 CAATACTATA
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
40 3 0.04
41 10 0.14
42 36 0.52
43 17 0.25
44 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (42 bp):
TAATATATTATATTTTAAATAATTAAAATAATATATTTATAA
Found at i:269607 original size:28 final size:29
Alignment explanation
Indices: 269576--269635 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
269566 AAAATTTTGT
*
269576 TTTTAAATTAATAT-GTTTTTTTGACAAA
1 TTTTAAATTAATATAATTTTTTTGACAAA
**
269604 TTTTAAATTAATATAATTTTTTTTTCAAA
1 TTTTAAATTAATATAATTTTTTTGACAAA
269633 TTT
1 TTT
269636 GAGATAATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTTAAATTAATATAATTTTTTTGACAAA
Found at i:271339 original size:29 final size:29
Alignment explanation
Indices: 271262--271342 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
271252 ACTCAATAAA
* * *
271262 ATAACTTTTT-ATAATTATACATCATTTT
1 ATAACTTTTTAATAATTAAAAATTATTTT
*
271290 ATAA-TTTTTAATAATCAAAAAATTATTTT
1 ATAACTTTTTAATAAT-TAAAAATTATTTT
*
271319 ATAACTTTTTAATAGTTAAAAATT
1 ATAACTTTTTAATAATTAAAAATT
271343 CAATAAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
27 5 0.11
28 9 0.20
29 20 0.45
30 10 0.23
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.49
Consensus pattern (29 bp):
ATAACTTTTTAATAATTAAAAATTATTTT
Found at i:271679 original size:20 final size:20
Alignment explanation
Indices: 271627--271679 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
271617 TCATCATTTA
** *
271627 AAAATAATTCAATTTTTATT
1 AAAATAATTTTATTTGTATT
* *
271647 AAACT-AGTTTATTTGTATT
1 AAAATAATTTTATTTGTATT
271666 AAAATAATTTTATT
1 AAAATAATTTTATT
271680 ATTTAATGTC
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (20 bp):
AAAATAATTTTATTTGTATT
Found at i:272190 original size:23 final size:23
Alignment explanation
Indices: 272164--272215 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
272154 ATATTATACG
* * *
272164 ATAAAGTTTCAAAATATTTTTAT
1 ATAAAATTTAAAAATATTTTTAA
*
272187 ATAATAATTTAAAAATGTTTTTAA
1 ATAA-AATTTAAAAATATTTTTAA
272211 ATAAA
1 ATAAA
272216 TAAATAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
ATAAAATTTAAAAATATTTTTAA
Found at i:272223 original size:24 final size:24
Alignment explanation
Indices: 272174--272224 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
272164 ATAAAGTTTC
* *
272174 AAAATATTTTTATATAATAATTTA
1 AAAATATTTTTAAATAATAATATA
*
272198 AAAATGTTTTTAAATAAATAA-ATA
1 AAAATATTTTTAAAT-AATAATATA
272222 AAA
1 AAA
272225 CCAATATTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
AAAATATTTTTAAATAATAATATA
Found at i:283113 original size:13 final size:13
Alignment explanation
Indices: 283095--283121 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
283085 TTTAGATTGA
283095 TATAAAGTAAATT
1 TATAAAGTAAATT
283108 TATAAAGTAAATT
1 TATAAAGTAAATT
283121 T
1 T
283122 CAACAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (13 bp):
TATAAAGTAAATT
Found at i:284531 original size:2 final size:2
Alignment explanation
Indices: 284488--284518 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
284478 ATTTTATAAC
*
284488 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
284519 TTTTTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:307552 original size:11 final size:11
Alignment explanation
Indices: 307520--307553 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
307510 TTAGAGAGTA
*
307520 TTTCCTTTTCT
1 TTTCCTTTTTT
*
307531 TTTCTTTTTTT
1 TTTCCTTTTTT
307542 TTTCCTTTTTT
1 TTTCCTTTTTT
307553 T
1 T
307554 GGATATACGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTCCTTTTTT
Found at i:307962 original size:19 final size:19
Alignment explanation
Indices: 307940--307977 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
307930 CAATAAGATT
307940 TGAATTTCTAGATAATTTC
1 TGAATTTCTAGATAATTTC
*
307959 TGAATTTCTAGATTATTTC
1 TGAATTTCTAGATAATTTC
307978 AAGAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (19 bp):
TGAATTTCTAGATAATTTC
Found at i:320693 original size:29 final size:31
Alignment explanation
Indices: 320659--320738 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
320649 ATCTTTTAAT
*
320659 TTTAGATAGAATAT-AATTTGA-CCCTAAAC
1 TTTAGATAAAATATCAATTTGACCCCTAAAC
*
320688 TTTAGATAAAATATCATTTTGACCCCTAAAC
1 TTTAGATAAAATATCAATTTGACCCCTAAAC
320719 TTT-GTATAAAATATCAATTT
1 TTTAG-ATAAAATATCAATTT
320739 AACACATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
29 13 0.29
30 7 0.16
31 25 0.56
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (31 bp):
TTTAGATAAAATATCAATTTGACCCCTAAAC
Found at i:321376 original size:157 final size:158
Alignment explanation
Indices: 321194--321511 Score: 629
Period size: 157 Copynumber: 2.0 Consensus size: 158
321184 TCGGTAAAGT
321194 TTGGTAAAATAATCGGATATTCAAATCAAATAAAAAAGTTACAAAAATTTGAAGAATGATAGTAT
1 TTGGTAAAATAATCGGATATTCAAATCAAATAAAAAAGTTACAAAAATTTGAAGAATGATAGTAT
321259 GAGTTTAGAAATGTTGTTTTAGTATTTTTGATGTGAAGAATTCAAAGTAGATTAGTCGGATTAAA
66 GAGTTTAGAAATGTTGTTTTAGTATTTTTGATGTGAAGAATTCAAAGTAGATTAGTCGGATTAAA
321324 AGGATTGAC-TTGTTTTTAGTGAAACAG
131 AGGATTGACTTTGTTTTTAGTGAAACAG
321351 TTGGTAAAATAATCGGATATTCAAATCAAATAAAAAAGTTACAAAAATTTGAAGAATGATAGTAT
1 TTGGTAAAATAATCGGATATTCAAATCAAATAAAAAAGTTACAAAAATTTGAAGAATGATAGTAT
321416 GAGTTTAGAAATGTTGTTTTAGTATTTTTGATGTGAAGAATTCAAAGTAGATTAGTCGGATTAAA
66 GAGTTTAGAAATGTTGTTTTAGTATTTTTGATGTGAAGAATTCAAAGTAGATTAGTCGGATTAAA
321481 AGGATTGACTTTGTTTTTAGTGAAACAG
131 AGGATTGACTTTGTTTTTAGTGAAACAG
321509 TTG
1 TTG
321512 AATTAAAGAC
Statistics
Matches: 160, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
157 139 0.87
158 21 0.13
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.36
Consensus pattern (158 bp):
TTGGTAAAATAATCGGATATTCAAATCAAATAAAAAAGTTACAAAAATTTGAAGAATGATAGTAT
GAGTTTAGAAATGTTGTTTTAGTATTTTTGATGTGAAGAATTCAAAGTAGATTAGTCGGATTAAA
AGGATTGACTTTGTTTTTAGTGAAACAG
Found at i:332055 original size:22 final size:23
Alignment explanation
Indices: 332030--332094 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 23
332020 AAACAATCCA
332030 AAAACATGCCA-AAAAGCATAAG
1 AAAACATGCCATAAAAGCATAAG
** * *
332052 AAAATGTGTCATAAATGCATAAG
1 AAAACATGCCATAAAAGCATAAG
*
332075 -AAACATGTCATACAAA-CATA
1 AAAACATGCCATA-AAAGCATA
332095 CTTATTTAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
22 22 0.65
23 12 0.35
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.18
Consensus pattern (23 bp):
AAAACATGCCATAAAAGCATAAG
Found at i:332830 original size:16 final size:16
Alignment explanation
Indices: 332811--332842 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
332801 ACATGTGTCA
332811 TTTAATATTAGTGTTT
1 TTTAATATTAGTGTTT
332827 TTTAATATTAGTGTTT
1 TTTAATATTAGTGTTT
332843 GAGCACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (16 bp):
TTTAATATTAGTGTTT
Found at i:338219 original size:21 final size:21
Alignment explanation
Indices: 338195--338236 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
338185 TATTGTCCTG
*
338195 AATCTGATAGGAAGTGCATGA
1 AATCTGACAGGAAGTGCATGA
338216 AATCTGACAGGAAGTGCATGA
1 AATCTGACAGGAAGTGCATGA
338237 TAGCAACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (21 bp):
AATCTGACAGGAAGTGCATGA
Found at i:348111 original size:18 final size:18
Alignment explanation
Indices: 348083--348148 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
348073 TGTCAACTTG
* *
348083 CCAATTTGCCAACTTGAA
1 CCAACTTGCCAACTTGGA
*
348101 TCAACTTGCCAACTTGGA
1 CCAACTTGCCAACTTGGA
348119 CCAACTTGCCAACTTGGA
1 CCAACTTGCCAACTTGGA
348137 CCAACTTGCCAA
1 CCAACTTGCCAA
348149 TGTTTGGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.24
Consensus pattern (18 bp):
CCAACTTGCCAACTTGGA
Found at i:348111 original size:26 final size:28
Alignment explanation
Indices: 348075--348126 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
348065 ACACAAGTTG
*
348075 TCAACTTGCCAA-TTTG-CCAACTTGAA
1 TCAACTTGCCAACTTGGACCAACTTGAA
348101 TCAACTTGCCAACTTGGACCAACTTG
1 TCAACTTGCCAACTTGGACCAACTTG
348127 CCAACTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 12 0.52
27 3 0.13
28 8 0.35
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (28 bp):
TCAACTTGCCAACTTGGACCAACTTGAA
Found at i:348113 original size:8 final size:8
Alignment explanation
Indices: 348076--348148 Score: 74
Period size: 8 Copynumber: 8.4 Consensus size: 8
348066 CACAAGTTGT
348076 CAACTTGC
1 CAACTTGC
*
348084 CAATTTGC
1 CAACTTGC
*
348092 CAACTTGAAT
1 CAACTTG--C
348102 CAACTTGC
1 CAACTTGC
348110 CAACTTGGAC
1 CAACTT-G-C
348120 CAACTTGC
1 CAACTTGC
348128 CAACTTGGAC
1 CAACTT-G-C
348138 CAACTTGC
1 CAACTTGC
348146 CAA
1 CAA
348149 TGTTTGGTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
8 30 0.55
9 4 0.07
10 21 0.38
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.25
Consensus pattern (8 bp):
CAACTTGC
Found at i:348122 original size:10 final size:10
Alignment explanation
Indices: 348091--348144 Score: 62
Period size: 10 Copynumber: 5.8 Consensus size: 10
348081 TGCCAATTTG
*
348091 CCAACTTGAA
1 CCAACTTGGA
*
348101 TCAACTT-G-
1 CCAACTTGGA
348109 CCAACTTGGA
1 CCAACTTGGA
348119 CCAACTT-G-
1 CCAACTTGGA
348127 CCAACTTGGA
1 CCAACTTGGA
348137 CCAACTTG
1 CCAACTTG
348145 CCAATGTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
8 13 0.35
9 3 0.08
10 21 0.57
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (10 bp):
CCAACTTGGA
Found at i:352469 original size:20 final size:20
Alignment explanation
Indices: 352408--352636 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
352398 GATTTTCAAG
* ** *
352408 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
352428 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
352448 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
352468 AACCACAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
352488 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
352508 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
352528 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
352548 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
352568 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
352588 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
352608 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
352628 AATCACAAC
1 AATCGCAAC
352637 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:353368 original size:24 final size:24
Alignment explanation
Indices: 353329--353375 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
353319 AAATTTGGTC
353329 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
353353 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
353376 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:355907 original size:33 final size:33
Alignment explanation
Indices: 355856--356107 Score: 179
Period size: 34 Copynumber: 7.2 Consensus size: 33
355846 CGGAAATTAC
* *
355856 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
*
355889 AATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
* * *
355923 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
355962 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
* *
355995 AATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
* * *
356029 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
356068 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
356101 AATCGCA
1 AATCGCA
356108 TTGCGATTCT
Statistics
Matches: 171, Mismatches: 27, Indels: 43
0.71 0.11 0.18
Matches are distributed among these distances:
32 9 0.05
33 47 0.27
34 59 0.35
35 2 0.01
36 2 0.01
38 7 0.04
39 35 0.20
40 10 0.06
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:355933 original size:53 final size:53
Alignment explanation
Indices: 355870--356107 Score: 449
Period size: 53 Copynumber: 4.5 Consensus size: 53
355860 GCAACGAGAG
* * *
355870 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
355923 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
355976 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
356029 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
356082 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
356108 TTGCGATTCT
Statistics
Matches: 182, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 182 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:356147 original size:53 final size:52
Alignment explanation
Indices: 356084--356199 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
356074 GAAATGAAAA
*
356084 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
356136 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
356189 TCGCATTGCGA
1 TCGCATTGCGA
356200 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:356162 original size:19 final size:19
Alignment explanation
Indices: 356122--356209 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
356112 GATTCTCTCG
356122 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
356142 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
356161 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
356175 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
356194 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
356210 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:356319 original size:14 final size:14
Alignment explanation
Indices: 356300--356336 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
356290 CATCAATTAC
356300 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
356314 ACAAATCATCTTTT
1 ACAAATCAACTTTT
356328 ACAAATCAA
1 ACAAATCAA
356337 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:358302 original size:19 final size:19
Alignment explanation
Indices: 358260--358432 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
358250 TAGTTTACTT
* *
358260 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
358280 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
358299 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
358318 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
358337 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
358356 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
* *
358370 TCACAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
358389 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
358403 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
358422 TCGCAATGCGA
1 TCGCAACGCGA
358433 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 17 0.13
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 81 0.64
20 12 0.10
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:358386 original size:33 final size:33
Alignment explanation
Indices: 358335--358427 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
358325 GCGAAATGAA
358335 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* * *
358368 AATCACAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
358401 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
358428 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:358429 original size:52 final size:52
Alignment explanation
Indices: 358294--358432 Score: 156
Period size: 52 Copynumber: 2.7 Consensus size: 52
358284 AACGCGAAAT
* * * *
358294 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAATGAAAATCGCAACGA
* ** * *
358346 GA-AAT-GAAAATCGCAACGACAGAATCACAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAATGAAAATCGCAACGA
*
358398 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
358433 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 43 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.10
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAATGAAAATCGCAACGA
Found at i:358463 original size:14 final size:14
Alignment explanation
Indices: 358444--358502 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
358434 TTTGGTTTCG
358444 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
358458 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
358475 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
358491 CGTTGCGATTTT
1 CGTTGCGATTTT
358503 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:358470 original size:33 final size:33
Alignment explanation
Indices: 358428--358521 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
358418 AAAATCGCAA
358428 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
*
358461 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
**
358494 TGCGATTTTCATTTCGCGTTGCGATTTT
1 TGCGATTTTGGTTTCGCGTTGCGATTTT
358522 AAGTTTCGTG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.07, C:0.17, G:0.28, T:0.48
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
Found at i:358482 original size:19 final size:18
Alignment explanation
Indices: 358428--358537 Score: 92
Period size: 19 Copynumber: 6.3 Consensus size: 18
358418 AAAATCGCAA
358428 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
358447 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
358461 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
358480 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
358494 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
358513 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
358533 TGCGA
1 TGCGA
358538 AAGTAAACTA
Statistics
Matches: 74, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
14 23 0.31
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 32 0.43
20 12 0.16
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:358794 original size:93 final size:93
Alignment explanation
Indices: 358635--358950 Score: 623
Period size: 93 Copynumber: 3.4 Consensus size: 93
358625 TCAGGGTATT
358635 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
358700 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
358728 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
358793 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
358821 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
358886 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
358914 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
358951 AAGCAATCTA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 222 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:360668 original size:20 final size:20
Alignment explanation
Indices: 360637--360743 Score: 104
Period size: 19 Copynumber: 5.7 Consensus size: 20
360627 TTTTGGTTGA
360637 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
360657 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
360677 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
360696 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
360711 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
360730 AATGAAAATCGCAA
1 AATGAAAATCGCAA
360744 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 30 0.41
20 17 0.23
21 12 0.16
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:360689 original size:21 final size:21
Alignment explanation
Indices: 360635--360699 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
360625 TCTTTTGGTT
360635 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
360656 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
360676 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
360697 GAA
1 GAA
360700 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:360796 original size:21 final size:21
Alignment explanation
Indices: 360771--360841 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
360761 GTTGTGATTC
360771 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
360792 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
360813 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
360834 TCTCGTTG
1 TCTCGTTG
360842 TGACTCTTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 6 0.15
21 29 0.71
22 6 0.15
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.49
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:360966 original size:33 final size:33
Alignment explanation
Indices: 360924--360994 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
360914 AATACTAACT
360924 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
360957 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
360990 TGAAA
1 TGAAA
360995 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:361399 original size:20 final size:20
Alignment explanation
Indices: 361374--361566 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
361364 CTTTAAAAAT
361374 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
361394 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
361414 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
361435 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
361455 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
361475 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
361495 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
361515 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
361535 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
361555 CGCGTTGCGATT
1 CGCGTTGCGATT
361567 CTGGAAAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
20 134 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:368408 original size:16 final size:16
Alignment explanation
Indices: 368383--368423 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
368373 TTGCTCGTTG
368383 AATG-TAGGCACATTA
1 AATGCTAGGCACATTA
368398 AATGCTAGGCACATTA
1 AATGCTAGGCACATTA
368414 AATGCTAGGC
1 AATGCTAGGC
368424 TACTAGAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (16 bp):
AATGCTAGGCACATTA
Found at i:371466 original size:14 final size:14
Alignment explanation
Indices: 371443--371480 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
371433 TCTGTCTATA
*
371443 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
371456 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
371471 TGCAGGGATT
1 TGCAGGGATT
371481 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:373544 original size:21 final size:20
Alignment explanation
Indices: 373517--373634 Score: 67
Period size: 21 Copynumber: 5.8 Consensus size: 20
373507 AATCAGTTTC
*
373517 CAAAATCGCAACGCGATTTTT
1 CAAAATCGCAACGCGA-ATTT
* * * * *
373538 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGA-ATTT
* ** *
373559 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGAATTT
*
373579 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGAATTT
* **
373600 GAAAATCGCAACGCGAA-CA
1 CAAAATCGCAACGCGAATTT
373619 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
373635 TATCCGTAAA
Statistics
Matches: 73, Mismatches: 22, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
19 1 0.01
20 31 0.42
21 41 0.56
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGAATTT
Found at i:373608 original size:20 final size:20
Alignment explanation
Indices: 373583--373777 Score: 122
Period size: 20 Copynumber: 9.7 Consensus size: 20
373573 GATTTTCAAT
*
373583 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
*
373603 AATCGCAACGCGAACAC-ATA
1 AATCGCAACGCGAATACGA-A
* * *
373623 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * *
373643 AATCGCAACGTGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* ** *
373664 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAATACGAA
* * * *
373684 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * * *
373704 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
** *
373724 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAATAC-GAA
* * *
373745 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
373765 AATCGCAACGCGA
1 AATCGCAACGCGA
373778 TATTTAAAGC
Statistics
Matches: 140, Mismatches: 31, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
19 1 0.01
20 109 0.78
21 30 0.21
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:373666 original size:61 final size:61
Alignment explanation
Indices: 373583--373776 Score: 248
Period size: 61 Copynumber: 3.2 Consensus size: 61
373573 GATTTTCAAT
* ** *
373583 AATCGCAACGCGAATATG-AAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
373643 AATCGCAACGTGTATCCGTAAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
373704 TATCGCAACGCGTATCCGT-AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
373765 AATCGCAACGCG
1 AATCGCAACGCG
373777 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
60 28 0.25
61 84 0.75
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (61 bp):
AATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:373673 original size:81 final size:80
Alignment explanation
Indices: 373583--373777 Score: 239
Period size: 81 Copynumber: 2.4 Consensus size: 80
373573 GATTTTCAAT
* * *
373583 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCG
1 AATCGCAACGCGTATACGTAAATCGCAACGCGAAC-CATAAATCGCAACGCGTATCCGTAAATCG
* * *
373648 CAACG-TGTATCCGTAA
65 CAACGAT-AATACATAA
** * * * *
373664 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTAAATCG
1 AATCGCAACGCGTATACGTAAATCGCAACGCG-AACCATAAATCGCAACGCGTATCCGTAAATCG
373729 CAACGATAATACATAA
65 CAACGATAATACATAA
*
373745 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATACGTAAATCGCAACGCGA
373778 TATTTAAAGC
Statistics
Matches: 98, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
80 1 0.01
81 94 0.96
82 3 0.03
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (80 bp):
AATCGCAACGCGTATACGTAAATCGCAACGCGAACCATAAATCGCAACGCGTATCCGTAAATCGC
AACGATAATACATAA
Found at i:373674 original size:41 final size:41
Alignment explanation
Indices: 373622--373774 Score: 211
Period size: 41 Copynumber: 3.8 Consensus size: 41
373612 GCGAACACAT
373622 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
** * *
373663 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT-
1 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
* * * *
373703 ATATCGCAACGCGTATCCGTAAATCGCAACGAT-AATACATA
1 AAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGTA
373744 AAATCGCAACGCGTATCCGTAAATCGCAACG
1 AAATCGCAACGCGTATCCGTAAATCGCAACG
373775 CGATATTTAA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 31 0.32
41 66 0.68
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (41 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
Found at i:374200 original size:33 final size:33
Alignment explanation
Indices: 374158--374228 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
374148 TTCACTTAGA
374158 TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
***
374191 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
374224 TTTCA
1 TTTCA
374229 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
Found at i:374368 original size:14 final size:14
Alignment explanation
Indices: 374349--374403 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
374339 AGAATGACTG
374349 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
374363 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
374382 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
374396 TCGCAACG
1 TCGCAACG
374404 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:374386 original size:33 final size:33
Alignment explanation
Indices: 374349--374419 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
374339 AGAATGACTG
**
374349 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
374382 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
374415 TCGCA
1 TCGCA
374420 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:374437 original size:19 final size:19
Alignment explanation
Indices: 374415--374512 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
374405 GAAACCAAAA
*
374415 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
374434 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
374448 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
374467 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
374481 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
374500 TCGCGTTGCGATT
1 TCGCGTTGCGATT
374513 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:374456 original size:14 final size:14
Alignment explanation
Indices: 374437--374526 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
374427 TTTCATTTCG
374437 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
374451 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
374470 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
374484 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
374501 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
374517 CGTTGCGATT
1 CGTTGCGATT
374527 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:374462 original size:33 final size:33
Alignment explanation
Indices: 374420--374534 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
374410 CAAAATCGCA
374420 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
374453 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
374486 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
374519 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
374535 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:376438 original size:92 final size:93
Alignment explanation
Indices: 376232--376609 Score: 726
Period size: 93 Copynumber: 4.1 Consensus size: 93
376222 TAGATTGCTT
*
376232 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
376297 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
376325 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
376389 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
376417 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
376480 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
376508 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
376573 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
376601 AGTAAATTT
1 AGTAAATTT
376610 ATCCATTCAA
Statistics
Matches: 282, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
91 91 0.32
92 91 0.32
93 100 0.35
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:376678 original size:20 final size:19
Alignment explanation
Indices: 376653--376750 Score: 93
Period size: 19 Copynumber: 5.4 Consensus size: 19
376643 TAGTTTACTT
*
376653 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
376673 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
376691 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
*
376710 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACTAAAA
*
376724 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
376743 TCGCAACG
1 TCGCAACG
376751 ACAAGATCGC
Statistics
Matches: 65, Mismatches: 5, Indels: 17
0.75 0.06 0.20
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 2 0.03
18 18 0.28
19 20 0.31
20 13 0.20
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:376712 original size:19 final size:18
Alignment explanation
Indices: 376653--376779 Score: 108
Period size: 18 Copynumber: 7.3 Consensus size: 18
376643 TAGTTTACTT
*
376653 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC--AAAA
*
376673 TCGCAACGCGAAACCAAA
1 TCGCAACGCGAAACAAAA
*
376691 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
376710 TCGCAA--CG--ACAGAA
1 TCGCAACGCGAAACAAAA
376724 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
*
376743 TCGCAA--CG--ACAAGA
1 TCGCAACGCGAAACAAAA
*
376757 TCGCAACGCGAAACCAAA
1 TCGCAACGCGAAACAAAA
376775 TCGCA
1 TCGCA
376780 TTGCGATTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 26 0.30
19 19 0.22
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (18 bp):
TCGCAACGCGAAACAAAA
Found at i:376731 original size:33 final size:32
Alignment explanation
Indices: 376687--376779 Score: 143
Period size: 33 Copynumber: 2.9 Consensus size: 32
376677 AACGCGAAAC
**
376687 CAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAATCGCAACGCGAAACCAAAATCGCAACGA
376719 CAGAATCGCAACGCGAAACCAAAATCGCAACGA
1 CA-AATCGCAACGCGAAACCAAAATCGCAACGA
376752 CAAGATCGCAACGCGAAACC-AAATCGCA
1 CAA-ATCGCAACGCGAAACCAAAATCGCA
376780 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
32 11 0.19
33 46 0.81
ACGTcount: A:0.45, C:0.29, G:0.18, T:0.08
Consensus pattern (32 bp):
CAAATCGCAACGCGAAACCAAAATCGCAACGA
Found at i:376802 original size:19 final size:19
Alignment explanation
Indices: 376775--376909 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
376765 CGAAACCAAA
*
376775 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
376794 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
**
376810 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
376827 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
376843 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
376860 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
376879 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
376899 TCGTGTTGCGA
1 TCGCGTTGCGA
376910 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 16 0.17
16 10 0.11
17 10 0.11
19 47 0.49
20 12 0.13
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:376816 original size:14 final size:14
Alignment explanation
Indices: 376797--376853 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
376787 TTTCATTTCG
376797 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
376811 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
376828 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
376844 CGTTGCGATT
1 CGTTGCGATT
376854 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:376822 original size:33 final size:33
Alignment explanation
Indices: 376780--376872 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
376770 CCAAATCGCA
*
376780 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
**
376813 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
376846 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
376873 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:378830 original size:13 final size:14
Alignment explanation
Indices: 378814--378848 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
378804 ATTGTTTAAT
378814 TGATTTGT-AAAGA
1 TGATTTGTAAAAGA
*
378827 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
378841 TGATTTGT
1 TGATTTGT
378849 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:379023 original size:20 final size:19
Alignment explanation
Indices: 378955--379037 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
378945 AAAAATGACT
378955 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
378974 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
378988 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
379007 ATCGCAATTCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
379027 ATCGCAATGCG
1 ATCGCAATGCG
379038 TTTATAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 20 0.37
20 18 0.33
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:379086 original size:33 final size:33
Alignment explanation
Indices: 379044--379440 Score: 303
Period size: 33 Copynumber: 11.5 Consensus size: 33
379034 TGCGTTTATA
379044 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
379077 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
379113 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
379148 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT--ATCTCG--TTGCGATTTTC
*
379186 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
379226 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
379257 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
379290 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
379324 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
379357 ATTTCCGCATTGCGATTTTCAT-GTTGCGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
* *
379391 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
379425 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
379441 GTATTTTCCG
Statistics
Matches: 322, Mismatches: 19, Indels: 46
0.83 0.05 0.12
Matches are distributed among these distances:
31 9 0.03
32 6 0.02
33 105 0.33
34 92 0.29
35 14 0.04
36 13 0.04
37 5 0.02
38 63 0.20
39 6 0.02
40 9 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:379090 original size:19 final size:19
Alignment explanation
Indices: 379066--379440 Score: 415
Period size: 19 Copynumber: 21.4 Consensus size: 19
379056 GATTATCTCG
379066 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
379085 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
379104 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
379118 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
379137 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
379156 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
379175 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
379194 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
379213 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
379227 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
379246 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
379265 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
379279 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
379299 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
379313 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
379332 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
379346 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
379366 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
379380 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
379400 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
379414 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
379433 TTGCGATT
1 TTGCGATT
379441 GTATTTTCCG
Statistics
Matches: 306, Mismatches: 12, Indels: 76
0.78 0.03 0.19
Matches are distributed among these distances:
14 58 0.19
16 35 0.11
17 27 0.09
18 8 0.03
19 142 0.46
20 36 0.12
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:379106 original size:52 final size:52
Alignment explanation
Indices: 379044--379412 Score: 493
Period size: 52 Copynumber: 7.0 Consensus size: 52
379034 TGCGTTTATA
*
379044 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
379096 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
379148 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
379205 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
379257 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
* * * * * *
379310 ATGTTGGGATTTTC-ATT-TCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 AT-TTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
379357 ATTTCCGCATTGCGATTTTCAT-GTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
379411 AT
1 AT
379413 GTTGGGATTT
Statistics
Matches: 284, Mismatches: 15, Indels: 34
0.85 0.05 0.10
Matches are distributed among these distances:
46 5 0.02
47 18 0.06
48 8 0.03
49 2 0.01
50 5 0.02
51 5 0.02
52 133 0.47
53 28 0.10
54 25 0.09
55 9 0.03
56 2 0.01
57 44 0.15
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:379383 original size:14 final size:14
Alignment explanation
Indices: 379366--379426 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 14
379356 CATTTCCGCA
379366 TTGCGATTTTCATG
1 TTGCGATTTTCATG
379380 TTGCGATTTTCATTTCCG
1 TTGCGATTTTCA--T--G
379398 CATTGCGATTTTCATG
1 --TTGCGATTTTCATG
*
379414 TTGGGATTTTCAT
1 TTGCGATTTTCAT
379427 TTCGCGTTGC
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
14 24 0.60
16 2 0.05
18 2 0.05
20 12 0.30
ACGTcount: A:0.15, C:0.16, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTCATG
Found at i:381736 original size:12 final size:12
Alignment explanation
Indices: 381719--381743 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
381709 TCTTCGGGGA
381719 CTTTTTCTTCTT
1 CTTTTTCTTCTT
381731 CTTTTTCTTCTT
1 CTTTTTCTTCTT
381743 C
1 C
381744 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:381952 original size:24 final size:24
Alignment explanation
Indices: 381918--381964 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
381908 CTGAAACATC
381918 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
381942 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
381965 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:382669 original size:20 final size:20
Alignment explanation
Indices: 382641--383031 Score: 441
Period size: 20 Copynumber: 19.4 Consensus size: 20
382631 AAATTTCAGT
* * * *
382641 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
382661 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
382681 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
382701 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
382721 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
382741 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
382761 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
382781 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
382801 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
382821 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
382841 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
382861 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
382882 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
382902 GTTGCGATATACGGATACGT
1 GTTGCGATTTACGGATACGC
* **
382922 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
382942 GTTGCGATTTTACGGATACAC
1 GTTGCGA-TTTACGGATACGC
382963 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
382983 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
383003 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
383023 GTTGCGATT
1 GTTGCGATT
383032 ATTGAAAATC
Statistics
Matches: 321, Mismatches: 38, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
19 7 0.02
20 276 0.86
21 36 0.11
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:383050 original size:81 final size:81
Alignment explanation
Indices: 382646--383050 Score: 389
Period size: 81 Copynumber: 5.0 Consensus size: 81
382636 TCAGTGTTGT
* * * * * * *
382646 GATTTACAGATTCTCGTTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTCGTTGCGATT
1 GATTTACGGATACGCGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACGCGTTGCGATT
* *
382710 TACGGATTATCG--TTGC
65 TA-TGAATATCGCATTGC
*
382726 GATTTACGGATACGCGTTGCGATTTACGGATTA-TCGTTGCGATTTACGGATACGCGTTGCGATT
1 GATTTACGGATACGCGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACGCGTTGCGATT
* *
382790 TACGGATA-CGCATTGC
65 TATGAATATCGCATTGC
*
382806 GATTTACGGATACGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTT
1 GATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGA-TT
*
382871 TATGTATTATCG--TTGC
65 TATG-AATATCGCATTGC
* ** **
382887 GATTTACGGATACGCGTTGCGATATACGGATACGTATTGCGATTTACCCATACGCGTTGCGATTT
1 GATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGA-TT
* * * *
382952 TACGGATA-CACGTTGC
65 TATGAATATCGCATTGC
* * * ** *
382968 GATTTACGGATACGCGTTGCGATTTATGTG-TTCGCGTTGCGATTTTCATATTCGCGTTGCGA-T
1 GATTTACGGATACGCGTTGCGATTTACG-GATACGCGTTGCGATTTACGGATACGCGTTGCGATT
* *
383031 TATTGAAAATCGCAATGC
65 TA-TGAATATCGCATTGC
383049 GA
1 GA
383051 ATTTGTACTA
Statistics
Matches: 276, Mismatches: 38, Indels: 21
0.82 0.11 0.06
Matches are distributed among these distances:
78 2 0.01
79 9 0.03
80 127 0.46
81 133 0.48
82 3 0.01
83 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.35
Consensus pattern (81 bp):
GATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTT
ATGAATATCGCATTGC
Found at i:383688 original size:40 final size:39
Alignment explanation
Indices: 383639--383767 Score: 113
Period size: 40 Copynumber: 3.3 Consensus size: 39
383629 GTTCACCAAG
*
383639 AAATAAGTTGCGATCTAGAATGTTAATATTTTTATTAATA
1 AAATGAGTTGCG-TCTAGAATGTTAATATTTTTATTAATA
* * * ** * *
383679 AAATGAGTTGCGTCCAAGAAT-ATCAT-GGTTCAGTAAT-
1 AAATGAGTTGCGT-CTAGAATGTTAATATTTTTATTAATA
*
383716 AAAT-ATGTTGCGGTCTGGAATGTTAATATTTTTATTAATA
1 AAATGA-GTTGC-GTCTAGAATGTTAATATTTTTATTAATA
383756 AAATGAGTTGCG
1 AAATGAGTTGCG
383768 CCCAAGAATA
Statistics
Matches: 66, Mismatches: 16, Indels: 15
0.68 0.16 0.15
Matches are distributed among these distances:
36 1 0.02
37 14 0.21
38 12 0.18
39 12 0.18
40 26 0.39
41 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (39 bp):
AAATGAGTTGCGTCTAGAATGTTAATATTTTTATTAATA
Found at i:383737 original size:153 final size:152
Alignment explanation
Indices: 383533--383867 Score: 474
Period size: 153 Copynumber: 2.2 Consensus size: 152
383523 AGAAATACGA
* * *
383533 TTGCACCTAAGAATATCATGGTTCACTAAGAAATATGTTGTGATTTTGAATGTTAATATTTTTAT
1 TTGCACC-AAGAATATCATGGTTCACTAAGAAATATGTTGCGATCTGGAATGTTAATATTTTTAT
* *
383598 TAATAAAATGGGTTGCG-CAAAAAATATCCTGGTTCACCAAGAAATAAGTTGCGATCTAGAATGT
65 TAATAAAATGAGTTGCGCCAAAAAATAT-CTGGTTCACCAAGAAATAAGTTGCGATCTAGAATAT
* *
383662 TAATATTTTTATTAATAAAATGAG
129 TAACATTTATATTAATAAAATGAG
* * * *
383686 TTGCGTCCAAGAATATCATGGTTCAGTAATAAATATGTTGCGGTCTGGAATGTTAATATTTTTAT
1 TTGC-ACCAAGAATATCATGGTTCACTAAGAAATATGTTGCGATCTGGAATGTTAATATTTTTAT
* * * * * *
383751 TAATAAAATGAGTTGCGCCCAAGAATATCTTGTTCACTAAGAAATATGTTGCGATCTATAATATT
65 TAATAAAATGAGTTGCGCCAAAAAATATCTGGTTCACCAAGAAATAAGTTGCGATCTAGAATATT
383816 AACATTTATATTAATAAAATGAG
130 AACATTTATATTAATAAAATGAG
*
383839 TTGCACCAAGAATGTCATGGTTCACTAAG
1 TTGCACCAAGAATATCATGGTTCACTAAG
383868 TGTTAACTAA
Statistics
Matches: 159, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
152 21 0.13
153 128 0.81
154 10 0.06
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (152 bp):
TTGCACCAAGAATATCATGGTTCACTAAGAAATATGTTGCGATCTGGAATGTTAATATTTTTATT
AATAAAATGAGTTGCGCCAAAAAATATCTGGTTCACCAAGAAATAAGTTGCGATCTAGAATATTA
ACATTTATATTAATAAAATGAG
Found at i:383742 original size:77 final size:76
Alignment explanation
Indices: 383541--383867 Score: 449
Period size: 76 Copynumber: 4.3 Consensus size: 76
383531 GATTGCACCT
* * *
383541 AAGAATATCATGGTTCACTAAGAAATATGTTGTGATTTTGAATGTTAATATTTTTATTAATAAAA
1 AAGAATATCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAA
* *
383606 TGGGTTGCGCA
66 TGAGTTGCGCC
* * * *
383617 AAAAATATCCTGGTTCACCAAGAAATAAGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAA
1 AAGAATATCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAA
383682 TGAGTTGCGTCC
66 TGAGTTGCG-CC
* * * *
383694 AAGAATATCATGGTTCAGTAATAAATATGTTGCGGTCTGGAATGTTAATATTTTTATTAATAAAA
1 AAGAATATCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAA
383759 TGAGTTGCGCCC
66 TGAGTTGCG-CC
* * * * *
383771 AAGAATATC-TTGTTCACTAAGAAATATGTTGCGATCTATAATATTAACATTTATATTAATAAAA
1 AAGAATATCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAA
*
383835 TGAGTTGCACC
66 TGAGTTGCGCC
*
383846 AAGAATGTCATGGTTCACTAAG
1 AAGAATATCATGGTTCACTAAG
383868 TGTTAACTAA
Statistics
Matches: 219, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
75 10 0.05
76 131 0.60
77 78 0.36
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.36
Consensus pattern (76 bp):
AAGAATATCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAA
TGAGTTGCGCC
Found at i:389035 original size:77 final size:77
Alignment explanation
Indices: 388885--389179 Score: 315
Period size: 77 Copynumber: 3.8 Consensus size: 77
388875 TCTTCCGCAA
* ** *
388885 CACTAAGAAATAGGTTGA-GATCTAGAATGTTAATATTTTTACTAATAAAATATGTTACACCCAA
1 CACTAAGAAATAGGTT-ACGATCTAGAATGTTAATATTTTTATTAATAAAATGGGTTGCACCCAA
*
388949 TAATGTCATGGTT
65 GAATGTCATGGTT
* * * * **
388962 CACTAAGAAATAGGTTACGATTTGGAATGTTAATATTTTTATTAATAAAACGGGTTGCTCTAAAG
1 CACTAAGAAATAGGTTACGATCTAGAATGTTAATATTTTTATTAATAAAATGGGTTGCACCCAAG
*
389027 AATATCATGGTT
66 AATGTCATGGTT
*** * * * * *
389039 TTGTAAGAAATAAGTTGCGATATAGAATGTTAATATTTTTATTAACAAAATGGATTGCACCCAAG
1 CACTAAGAAATAGGTTACGATCTAGAATGTTAATATTTTTATTAATAAAATGGGTTGCACCCAAG
*
389104 AATGTCATGATT
66 AATGTCATGGTT
* * * * * * *
389116 TACTAAGAAATAGATTGCGATCTGGAATGTTAAAATTTTTATT-ATAAATTGGGTTGCACACAAG
1 CACTAAGAAATAGGTTACGATCTAGAATGTTAATATTTTTATTAATAAAATGGGTTGCACCCAAG
389180 TATCGATAGT
Statistics
Matches: 179, Mismatches: 38, Indels: 3
0.81 0.17 0.01
Matches are distributed among these distances:
76 18 0.10
77 161 0.90
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (77 bp):
CACTAAGAAATAGGTTACGATCTAGAATGTTAATATTTTTATTAATAAAATGGGTTGCACCCAAG
AATGTCATGGTT
Found at i:389253 original size:20 final size:20
Alignment explanation
Indices: 389228--389281 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
389218 GAATGCTGTA
*
389228 AAGTATCAATATTTTTTCAC
1 AAGTATCAATACTTTTTCAC
**
389248 AAGTATTGATACTTTTTCAC
1 AAGTATCAATACTTTTTCAC
*
389268 AAGTATCGATACTT
1 AAGTATCAATACTT
389282 CTATAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (20 bp):
AAGTATCAATACTTTTTCAC
Found at i:389378 original size:77 final size:76
Alignment explanation
Indices: 389285--389803 Score: 542
Period size: 77 Copynumber: 6.8 Consensus size: 76
389275 GATACTTCTA
* * * * *
389285 TAATAAAAATTTTAACATTCTAGATCGTAACATATTTCTTAATGAAACATGATATTCTTGAGTAC
1 TAATAAAAATATTAACATTCTAGATCGCAACATATTTCTTAGTGAACCATGACATTCTTG-GTAC
389350 AACCCATTTTAT
65 AACCCATTTTAT
* * **
389362 TAATAAAAATATTAACATTCCAGATCGCAACATATTTATTAGTGAACCATGACATTCTTAGGCGC
1 TAATAAAAATATTAACATTCTAGATCGCAACATATTTCTTAGTGAACCATGACATTCTT-GGTAC
389427 -ACCTCATTTTAT
65 AACC-CATTTTAT
* * * * * *
389439 TAATAAAAATGTTAACATTCCATATCACAATC-TATTTTTTAGTGAACCATGACATTTTTGG-AC
1 TAATAAAAATATTAACATTCTAGATCGCAA-CATATTTCTTAGTGAACCATGACATTCTTGGTAC
* *
389502 GTAACCTATTTTGT
65 --AACCCATTTTAT
* * * * * * *
389516 TAATAAAAATATTAACATTCCATATCACAACTTATTTCTTACTGAACCATGATATTCTTTGGAAC
1 TAATAAAAATATTAACATTCTAGATCGCAACATATTTCTTAGTGAACCATGACATTC-TTGGTAC
*
389581 AATCCATTTTAT
65 AACCCATTTTAT
* * * * * **
389593 TAATAAAAATATTAACATTCTAAATCGCACCCTATTTCTTAGTGAACCATGATATTATTAGGTGT
1 TAATAAAAATATTAACATTCTAGATCGCAACATATTTCTTAGTGAACCATGACATTCTT-GGTAC
*
389658 AACCTATTTTAT
65 AACCCATTTTAT
* * * *
389670 TAGTAAAAATATTAACATTCTAGATCCCAACCTATTTCTTAGTGAACCATGACATTCTTGGTGCA
1 TAATAAAAATATTAACATTCTAGATCGCAACATATTTCTTAGTGAACCATGACATTCTTGGTACA
*
389735 ACTCATTTTAT
66 ACCCATTTTAT
* * * * *
389746 TAATAAAAATATTAATATT-TCAGATCGCAACTTATTTCTTAATAAATCATGACATTCT
1 TAATAAAAATATTAACATTCT-AGATCGCAACATATTTCTTAGTGAACCATGACATTCT
389804 GTAGTTTTGA
Statistics
Matches: 378, Mismatches: 53, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
75 2 0.01
76 71 0.19
77 294 0.78
78 9 0.02
79 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (76 bp):
TAATAAAAATATTAACATTCTAGATCGCAACATATTTCTTAGTGAACCATGACATTCTTGGTACA
ACCCATTTTAT
Found at i:389688 original size:231 final size:230
Alignment explanation
Indices: 389285--389803 Score: 668
Period size: 231 Copynumber: 2.3 Consensus size: 230
389275 GATACTTCTA
* * * * *
389285 TAATAAAAATTTTAACATTCTAGATCGTAACATATTTCTTAATGAAACATGATATTCTTGAGTAC
1 TAATAAAAATATTAACATTCCAGATCGCAACTTATTTCTTAATGAAACATGATATTCTTGAGAAC
*
389350 AACCCATTTTATTAATAAAAATATTAACATTCCAGATCGCAACATATTTATTAGTGAACCATGAC
66 AACCCATTTTATTAATAAAAATATTAACATTCCAAATCGCAACATATTTATTAGTGAACCATGAC
* * * * * *
389415 ATTCTTAGGCGCACCTCATTTTATTAATAAAAATGTTAACATTCCATATCACAATCTATTTTTTA
131 ATTATTAGGCGAACCTCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTA
* * *
389480 GTGAACCATGACATTTTTGGACGTAAC-CTATTTTGT
196 GTGAACCATGACATTCTTGG-CGCAACTC-ATTTTAT
* * * *
389516 TAATAAAAATATTAACATTCCATATCACAACTTATTTCTTACTGAACCATGATATTCTTTG-GAA
1 TAATAAAAATATTAACATTCCAGATCGCAACTTATTTCTTAATGAAACATGATATTC-TTGAGAA
* * * * *
389580 CAATCCATTTTATTAATAAAAATATTAACATTCTAAATCGCACCCTATTTCTTAGTGAACCATGA
65 CAACCCATTTTATTAATAAAAATATTAACATTCCAAATCGCAACATATTTATTAGTGAACCATGA
* * * * *
389645 TATTATTAGGTGTAACCT-ATTTTATTAGTAAAAATATTAACATTCTAGATCCCAACCTATTTCT
130 CATTATTAGGCG-AACCTCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCT
*
389709 TAGTGAACCATGACATTCTTGGTGCAACTCATTTTAT
194 TAGTGAACCATGACATTCTTGGCGCAACTCATTTTAT
* * *
389746 TAATAAAAATATTAATATTTCAGATCGCAACTTATTTCTTAAT-AAATCATGACATTCT
1 TAATAAAAATATTAACATTCCAGATCGCAACTTATTTCTTAATGAAA-CATGATATTCT
389804 GTAGTTTTGA
Statistics
Matches: 247, Mismatches: 37, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
229 3 0.01
230 57 0.23
231 180 0.73
232 7 0.03
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (230 bp):
TAATAAAAATATTAACATTCCAGATCGCAACTTATTTCTTAATGAAACATGATATTCTTGAGAAC
AACCCATTTTATTAATAAAAATATTAACATTCCAAATCGCAACATATTTATTAGTGAACCATGAC
ATTATTAGGCGAACCTCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTA
GTGAACCATGACATTCTTGGCGCAACTCATTTTAT
Found at i:393714 original size:30 final size:30
Alignment explanation
Indices: 393678--393749 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
393668 CCCGAAGGAC
393678 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
393708 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
393738 CTGTCCATAGGT
1 CTATCCAGAGGT
393750 TCCGAAGAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:393840 original size:32 final size:31
Alignment explanation
Indices: 393789--393906 Score: 157
Period size: 32 Copynumber: 3.7 Consensus size: 31
393779 ATTCCTTAGA
393789 ACATAGGTATACTGTCCATATGTCTCGAAAG
1 ACATAGGTATACTGTCCATATGTCTCGAAAG
* ***
393820 ACATAGGTAATTCTGTCCATATGT-TCCTTAG
1 ACATAGGT-ATACTGTCCATATGTCTCGAAAG
393851 AACATAGGTATACTGTCCATATGTCTCGAAAG
1 -ACATAGGTATACTGTCCATATGTCTCGAAAG
*
393883 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGT-ATACTGTCCATATGT
393907 TCCGTAGAAC
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
31 34 0.46
32 40 0.54
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (31 bp):
ACATAGGTATACTGTCCATATGTCTCGAAAG
Found at i:393849 original size:63 final size:63
Alignment explanation
Indices: 393761--393926 Score: 298
Period size: 63 Copynumber: 2.7 Consensus size: 63
393751 CCGAAGAACC
* *
393761 TAGGTAA-ACTGTCCATATATTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
393823 TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
*
393886 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
1 TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATAC
393927 CCTCAACTAT
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 7 0.07
63 93 0.93
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
Found at i:393919 original size:32 final size:32
Alignment explanation
Indices: 393737--393923 Score: 199
Period size: 31 Copynumber: 5.9 Consensus size: 32
393727 ATCCTCGGTA
* * *
393737 ACTGTCCATAGGTTCCGAAGAACCTAGGTAA-
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
393768 ACTGTCCATATATTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
*
393799 ACTGTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
* *
393831 TCTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
*
393862 ACTGTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
*
393894 TCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTTCCGTAGAACATAGGTA
393924 TACCCTCAAC
Statistics
Matches: 129, Mismatches: 16, Indels: 21
0.78 0.10 0.13
Matches are distributed among these distances:
30 9 0.07
31 66 0.51
32 46 0.36
33 8 0.06
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:398197 original size:21 final size:21
Alignment explanation
Indices: 398166--398216 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
398156 GTCCGAGTTA
* *
398166 CCCGTGACGGCCGCAATAGCG
1 CCCGCGACGGCCACAATAGCG
*
398187 TCCGCGACGGCCACAATAGCG
1 CCCGCGACGGCCACAATAGCG
398208 CCCGCGACG
1 CCCGCGACG
398217 ACCTCAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.41, G:0.31, T:0.08
Consensus pattern (21 bp):
CCCGCGACGGCCACAATAGCG
Found at i:398224 original size:21 final size:21
Alignment explanation
Indices: 398179--398224 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
398169 GTGACGGCCG
* *
398179 CAATAGCGTCCGCGACGGCCA
1 CAATAGCGCCCGCGACGACCA
*
398200 CAATAGCGCCCGCGACGACCT
1 CAATAGCGCCCGCGACGACCA
398221 CAAT
1 CAAT
398225 CACGGTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.39, G:0.24, T:0.11
Consensus pattern (21 bp):
CAATAGCGCCCGCGACGACCA
Found at i:401554 original size:18 final size:19
Alignment explanation
Indices: 401533--401574 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
401523 TTTAATTATT
*
401533 TTTTATTTGTTTAT-AATA
1 TTTTATTTATTTATAAATA
* *
401551 TTTTTTTTATTTTTAAATA
1 TTTTATTTATTTATAAATA
401570 TTTTA
1 TTTTA
401575 GATTGCGTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTATTTATTTATAAATA
Found at i:401569 original size:19 final size:19
Alignment explanation
Indices: 401523--401573 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
401513 ATTTTTTGAA
*
401523 TTTAATTATTTTTTATTTG
1 TTTAAATATTTTTTATTTG
*
401542 TTTATAATATTTTTT-TTATT
1 TTTA-AATATTTTTTATT-TG
401562 TTTAAATATTTT
1 TTTAAATATTTT
401574 AGATTGCGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTAAATATTTTTTATTTG
Found at i:404382 original size:21 final size:21
Alignment explanation
Indices: 404358--404401 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
404348 AAAATATTTG
*
404358 ATTA-AATAATCTGAATAGAAA
1 ATTATAATAATATGAATA-AAA
*
404379 ATTATAATTATATGAATAAAA
1 ATTATAATAATATGAATAAAA
404400 AT
1 AT
404402 AAGTTGAGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (21 bp):
ATTATAATAATATGAATAAAA
Found at i:407620 original size:6 final size:6
Alignment explanation
Indices: 407606--407643 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
407596 ACTTGTTAAA
*
407606 CCTCAT CCTCGT CCTCAT CCTCAT CCTCAT CCTCAT CC
1 CCTCAT CCTCAT CCTCAT CCTCAT CCTCAT CCTCAT CC
407644 ACCATAACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.13, C:0.53, G:0.03, T:0.32
Consensus pattern (6 bp):
CCTCAT
Found at i:416396 original size:25 final size:28
Alignment explanation
Indices: 416325--416401 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 28
416315 ATACATATTT
* * * *
416325 TTTGTAATAAATATAATAATTAATATAT
1 TTTGTAATAAAAACAATAGTTAATATAC
416353 TTTGTAATAAAAACAATAGTTAATATAC
1 TTTGTAATAAAAACAATAGTTAATATAC
416381 TTT-T-ATAAAAA-AATAGTTAAT
1 TTTGTAATAAAAACAATAGTTAAT
416402 TTTAATGATT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
25 10 0.22
26 7 0.16
27 1 0.02
28 27 0.60
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.42
Consensus pattern (28 bp):
TTTGTAATAAAAACAATAGTTAATATAC
Found at i:416648 original size:15 final size:15
Alignment explanation
Indices: 416628--416659 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
416618 ATTTTTGAAA
416628 CTATTGTAATTTTGT
1 CTATTGTAATTTTGT
416643 CTATTGTAATTTTGT
1 CTATTGTAATTTTGT
416658 CT
1 CT
416660 CTCTCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.09, G:0.12, T:0.59
Consensus pattern (15 bp):
CTATTGTAATTTTGT
Found at i:420222 original size:51 final size:51
Alignment explanation
Indices: 420167--420270 Score: 183
Period size: 51 Copynumber: 2.0 Consensus size: 51
420157 GAACTGTGGT
*
420167 ATGTTGGA-TTTGATTAGTTCTTATAAATATTGTCGCTTTTGTTTCAATTTA
1 ATGTTGGATTTTGATTAGTTCTTATAAAT-CTGTCGCTTTTGTTTCAATTTA
420218 ATGTTGGATTTTGATTAGTTCTTATAAATCTGTCGCTTTTGTTTCAATTTA
1 ATGTTGGATTTTGATTAGTTCTTATAAATCTGTCGCTTTTGTTTCAATTTA
420269 AT
1 AT
420271 TAATGTAAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 31 0.61
52 20 0.39
ACGTcount: A:0.23, C:0.09, G:0.15, T:0.53
Consensus pattern (51 bp):
ATGTTGGATTTTGATTAGTTCTTATAAATCTGTCGCTTTTGTTTCAATTTA
Found at i:423498 original size:155 final size:154
Alignment explanation
Indices: 423220--423607 Score: 527
Period size: 155 Copynumber: 2.5 Consensus size: 154
423210 CCTGATTTCA
* * * * * *
423220 TTATTTCTTCAATTCCTCCTTCA-TTTAAGTC-TTTTTTACCAAATTTGAAC-CTTGCTCTTAAA
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCTTTTTTTACCAAATTTGACCACATGCTCATAAA
*
423282 CCATAGTAGAATGCATGTGTACTTTCAATTCCTCTTTTTGATAACAATTTTAATTTTTCAATTTA
66 CCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAATTTTAATTTTTCAATTTA
* *
423347 TTCCTTCAATTTTTCATAATCTCC
131 GTCCTTCAATTTTTAATAATCTCC
*
423371 TTATTTCTTCAATTCGTCATTTATTTTAAGTCTGTTTTTTACCAAATTTGAGCCACATGCTCCTA
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCT-TTTTTTACCAAATTTGA-CCACATGCTCATA
*
423436 AACCATAGTAGAATACAT-TGTACTTTCAATTCCTC-TTTTGATAACAATTTTTTATTTTTCAAT
64 AACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAA-TTTTAATTTTTCAAT
*
423499 TTAGTCCTTCAATTTTTAATATTCTCC
128 TTAGTCCTTCAATTTTTAATAATCTCC
* *
423526 TTATTTCTTCAATT-GTCATTTATTTTAAGTTCGTTTTTTTTATCAAATTTAAACCACATGCTCA
1 TTATTTCTTCAATTCGTCATTTATTTTAAG-TC--TTTTTTTACCAAATTT-GACCACATGCTCA
* *
423590 TATACCATAATAGAATAC
62 TAAACCATAGTAGAATAC
423608 CTATGTAACT
Statistics
Matches: 211, Mismatches: 16, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
151 20 0.09
152 8 0.04
154 44 0.21
155 72 0.34
156 65 0.31
157 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.47
Consensus pattern (154 bp):
TTATTTCTTCAATTCGTCATTTATTTTAAGTCTTTTTTTACCAAATTTGACCACATGCTCATAAA
CCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAATTTTAATTTTTCAATTTA
GTCCTTCAATTTTTAATAATCTCC
Found at i:423862 original size:2 final size:2
Alignment explanation
Indices: 423855--423898 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
423845 ATATGAAAGA
* *
423855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
423897 AT
1 AT
423899 GGTTAGATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:427011 original size:27 final size:27
Alignment explanation
Indices: 426800--427018 Score: 216
Period size: 27 Copynumber: 8.2 Consensus size: 27
426790 AGAGGTATGT
*
426800 TGATCCCAGGGATCAACAGAGGA-ATGC
1 TGATCCCAGGGACCAACAGA-GACATGC
* * *
426827 -AACCCCAGGGACCAACAGAGAAATGC
1 TGATCCCAGGGACCAACAGAGACATGC
426853 TGATCCCAGGGACCAACAGAGACATGC
1 TGATCCCAGGGACCAACAGAGACATGC
* *
426880 TGATCCC-GGGA-CTACAGAGACATGT
1 TGATCCCAGGGACCAACAGAGACATGC
* *** *
426905 TGATCCAAGGGATGTACACAGACATGC
1 TGATCCCAGGGACCAACAGAGACATGC
*
426932 TGAT-CCACGGGACCTACAGAGACATGC
1 TGATCCCA-GGGACCAACAGAGACATGC
* *
426959 TGATCCTAGAGG-CCAACATAGACATGC
1 TGATCCCAG-GGACCAACAGAGACATGC
* * *
426986 TGATCCTAGGGACCAACAGAGGCATGT
1 TGATCCCAGGGACCAACAGAGACATGC
427013 TGATCC
1 TGATCC
427019 AAGAGGCCGT
Statistics
Matches: 162, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
25 20 0.12
26 32 0.20
27 106 0.65
28 4 0.02
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (27 bp):
TGATCCCAGGGACCAACAGAGACATGC
Found at i:428734 original size:20 final size:21
Alignment explanation
Indices: 428709--428748 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
428699 CTCTATATAT
*
428709 TATTTTCT-TTTAATTAAATC
1 TATTTTCTATTTAATAAAATC
*
428729 TATTTTTTATTTAATAAAAT
1 TATTTTCTATTTAATAAAAT
428749 AATATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTCTATTTAATAAAATC
Found at i:428779 original size:16 final size:17
Alignment explanation
Indices: 428738--428780 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
428728 CTATTTTTTA
428738 TTTAATAAA-ATAATAT
1 TTTAATAAATATAATAT
*
428754 TTTAAT-AATATTAT-T
1 TTTAATAAATATAATAT
428769 TTTAATAAATAT
1 TTTAATAAATAT
428781 GTTATTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:429231 original size:29 final size:29
Alignment explanation
Indices: 429198--429284 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 29
429188 ATTGAGTCTC
429198 TTGACTATTAAAAGTTATAAAATGATCCA
1 TTGACTATTAAAAGTTATAAAATGATCCA
** * *
429227 TTGACTA-TAAAGAGTTGATTTATTGAGTCCC
1 TTGACTATTAAA-AGTT-ATAAAATGA-TCCA
* *
429258 TTGACTATTAAAAGTTACAACATGATC
1 TTGACTATTAAAAGTTATAAAATGATC
429285 ACTCGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
28 4 0.09
29 13 0.29
30 10 0.22
31 14 0.31
32 4 0.09
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (29 bp):
TTGACTATTAAAAGTTATAAAATGATCCA
Done.