Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008770.1 Hibiscus syriacus cultivar Beakdansim tig00111873_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: 569103
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:213407 original size:87 final size:87
Alignment explanation
Indices: 213308--213497 Score: 276
Period size: 87 Copynumber: 2.2 Consensus size: 87
213298 TGTATTAGTT
* *
213308 ATACATACATATATATACTATATTAATATAAATTATAATATATAAACTATATA-TTTTAAATAAT
1 ATACATATATATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTT-AATAAT
*
213372 TTATACATATATAGTTTATATAC
65 TTATACATATATAGATTATATAC
* * * *
213395 ATACATATATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTT
1 ATACATATATATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTTAATAATT
213460 TATACATATATAGATTATATAC
66 TATACATATATAGATTATATAC
* *
213482 ATA-GTTTATATATATA
1 ATACATATATATATATA
213498 GTTCACATAA
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
86 11 0.12
87 78 0.84
88 4 0.04
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.45
Consensus pattern (87 bp):
ATACATATATATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTTAATAATT
TATACATATATAGATTATATAC
Found at i:213482 original size:17 final size:17
Alignment explanation
Indices: 213373--213484 Score: 54
Period size: 17 Copynumber: 6.5 Consensus size: 17
213363 TTAAATAATT
*
213373 TATACATATATAGTTTA
1 TATACATATATAGATTA
* *
213390 TATACATACATATATATA
1 TATACATATATAGAT-TA
213408 TATAC-TATATTA-ATATA
1 TATACATATA-TAGAT-TA
* * *
213425 AATA-ATATTTTATAAACTA
1 TATACATA---TATAGATTA
* *
213444 TATACTTTTTATAG-TT-
1 TATAC-ATATATAGATTA
213460 TATACATATATAGATTA
1 TATACATATATAGATTA
213477 TATACATA
1 TATACATA
213485 GTTTATATAT
Statistics
Matches: 71, Mismatches: 13, Indels: 22
0.67 0.12 0.21
Matches are distributed among these distances:
15 6 0.08
16 7 0.10
17 34 0.48
18 13 0.18
19 7 0.10
20 3 0.04
21 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.46
Consensus pattern (17 bp):
TATACATATATAGATTA
Found at i:213495 original size:17 final size:16
Alignment explanation
Indices: 213227--213497 Score: 78
Period size: 16 Copynumber: 16.3 Consensus size: 16
213217 TATTTCTTTA
* *
213227 ATATATATATATATAT
1 ATATACATATTTATAT
* *
213243 ATATATATATATATAT
1 ATATACATATTTATAT
* *
213259 ATATATATATATATAT
1 ATATACATATTTATAT
*
213275 ATATATATATTCTATAT
1 ATATACATATT-TATAT
* *
213292 AT-TACTTGTATTAGTTAT
1 ATATACATAT-TTA--TAT
* *
213310 ACATACATATATATACT
1 ATATACATATTTATA-T
213327 ATATTA-ATATAAATTATAAT
1 ATA-TACATAT---TTAT-AT
*
213347 ATATA-A-A-CTATAT
1 ATATACATATTTATAT
* * *
213360 ATTTTAAATAATTTATAC
1 A-TATACAT-ATTTATAT
213378 ATAT--ATAGTTTATAT
1 ATATACATA-TTTATAT
*
213393 ACATACATA--TATAT
1 ATATACATATTTATAT
*
213407 ATATACTATATTAATAT
1 ATATAC-ATATTTATAT
*
213424 AAATA-ATATTTTATAAACT
1 ATATACATA-TTTAT--A-T
*
213443 ATATAC-TTTTTATAGT
1 ATATACATATTTATA-T
* * *
213459 TTATACATATATAGATT
1 ATATACATATTTATA-T
213476 ATATACATAGTTTATAT
1 ATATACATA-TTTATAT
213493 ATATA
1 ATATA
213498 GTTCACATAA
Statistics
Matches: 194, Mismatches: 32, Indels: 57
0.69 0.11 0.20
Matches are distributed among these distances:
13 3 0.02
14 17 0.09
15 18 0.09
16 61 0.31
17 49 0.25
18 24 0.12
19 14 0.07
20 7 0.04
21 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (16 bp):
ATATACATATTTATAT
Found at i:213499 original size:13 final size:13
Alignment explanation
Indices: 213453--213500 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
213443 ATATACTTTT
213453 TATAGTTTATACATA
1 TATAGTTTAT--ATA
*
213468 TATAGATTATATA
1 TATAGTTTATATA
*
213481 CATAGTTTATATA
1 TATAGTTTATATA
213494 TATAGTT
1 TATAGTT
213501 CACATAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 20 0.69
15 9 0.31
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:213558 original size:18 final size:18
Alignment explanation
Indices: 213519--213572 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
213509 CATAATTTAT
* *
213519 ATATAGCTTATAATA-ATT
1 ATATAGTTTATAATATA-A
213537 ATATAGTTTATAATATAA
1 ATATAGTTTATAATATAA
213555 ATATAGTTTAT-ATATAA
1 ATATAGTTTATAATATAA
213572 A
1 A
213573 CTTATATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 7 0.21
18 25 0.76
19 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATAGTTTATAATATAA
Found at i:213596 original size:17 final size:17
Alignment explanation
Indices: 213544--213597 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
213534 ATTATATAGT
213544 TTATA-ATATAAATATA
1 TTATATATATAAATATA
213560 GTT-TATATATAAACTTATA
1 -TTATATATATAAA--TATA
*
213579 TTATATATATATATATA
1 TTATATATATAAATATA
213596 TT
1 TT
213598 TTTTTTCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 2 0.06
17 15 0.47
18 2 0.06
19 13 0.41
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TTATATATATAAATATA
Found at i:218085 original size:16 final size:16
Alignment explanation
Indices: 218056--218088 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
218046 CTACATGGGT
218056 GGTCATTTATATTTTA
1 GGTCATTTATATTTTA
218072 GGTCAATTTA-ATTTTA
1 GGTC-ATTTATATTTTA
218088 G
1 G
218089 CTACTGATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (16 bp):
GGTCATTTATATTTTA
Found at i:218591 original size:5 final size:5
Alignment explanation
Indices: 218581--218605 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
218571 ATAATAAAAA
218581 AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT
218606 TAAGTATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:223240 original size:13 final size:13
Alignment explanation
Indices: 223222--223247 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
223212 ATTATTTAAA
223222 TTTATTTTAAAAT
1 TTTATTTTAAAAT
223235 TTTATTTTAAAAT
1 TTTATTTTAAAAT
223248 ATGAATTGAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATTTTAAAAT
Found at i:223263 original size:22 final size:22
Alignment explanation
Indices: 223235--223883 Score: 851
Period size: 22 Copynumber: 29.5 Consensus size: 22
223225 ATTTTAAAAT
*
223235 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGGATTGA
*
223257 TTTATTTTAAAATATGGTTTGA
1 TTTATTTTAAAATATGGATTGA
*
223279 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGGATTGA
* * ***
223301 TTTATTTTAAATTATGAACAAA
1 TTTATTTTAAAATATGGATTGA
*
223323 TTTATTTTAAAATATAGATTGA
1 TTTATTTTAAAATATGGATTGA
223345 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
***
223367 TTTATTTTAAAATAT-GAAAAA
1 TTTATTTTAAAATATGGATTGA
223388 CTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
* ***
223411 TTTATTTTAAAATAT-AAAAAA
1 TTTATTTTAAAATATGGATTGA
223432 CTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
223455 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
* ***
223477 TTTATTTTAAAATATGAAAAAA
1 TTTATTTTAAAATATGGATTGA
**
223499 TTTATTTTAAAATATATATTGA
1 TTTATTTTAAAATATGGATTGA
***
223521 TTTATTTTAAAATAT-GAAAAA
1 TTTATTTTAAAATATGGATTGA
223542 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
223565 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
* ***
223587 TTTATTTTAAAATATGAAAAAA
1 TTTATTTTAAAATATGGATTGA
* **
223609 ATTATTTTAAAATATATATTGA
1 TTTATTTTAAAATATGGATTGA
* *
223631 TTTATTTTAAAATATGAATTAA
1 TTTATTTTAAAATATGGATTGA
223653 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
223675 TTTATTTTAAAATATGGATAGA
1 TTTATTTTAAAATATGGATTGA
223697 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
223719 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
**
223741 -TTATTTTAAAATATGGA-AAA
1 TTTATTTTAAAATATGGATTGA
223761 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
* **
223784 TTTATTTTAAAATATAGA-AAA
1 TTTATTTTAAAATATGGATTGA
223805 GTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
223828 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
223850 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
223872 TTTATTTTAAAA
1 TTTATTTTAAAA
223884 AAATTTATTA
Statistics
Matches: 543, Mismatches: 73, Indels: 22
0.85 0.11 0.03
Matches are distributed among these distances:
20 1 0.00
21 25 0.05
22 507 0.93
23 10 0.02
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTATTTTAAAATATGGATTGA
Found at i:233402 original size:54 final size:54
Alignment explanation
Indices: 233317--233474 Score: 164
Period size: 54 Copynumber: 3.0 Consensus size: 54
233307 TGATTGAGAA
* *
233317 ATCTGAGCAGAAGCCACATAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGAGCAGAAGCCACAGAAAAGGACGAATGTGTTGTCAAATGCTTTACGAAC
* * *
233371 ATCTGAGTAGAAGCCACAGAAAAGGACGAATGTGTTGTCAAGTG-TTT---TAC
1 ATCTGAGCAGAAGCCACAGAAAAGGACGAATGTGTTGTCAAATGCTTTACGAAC
** * * * * *
233421 ATCTGAGCAGAAATCACATG-ATATGATGCATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACA-GAAAAGGACGAATGTGTTGTCAAATGCTTTACGAAC
233475 TAGTTATTCT
Statistics
Matches: 85, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
50 36 0.42
51 4 0.05
53 3 0.04
54 42 0.49
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACAGAAAAGGACGAATGTGTTGTCAAATGCTTTACGAAC
Found at i:233870 original size:22 final size:22
Alignment explanation
Indices: 233841--233895 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
233831 ATCTACACTC
233841 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
233863 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
233885 TTCAAAGATGA
1 TTCAAAGATGA
233896 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:234636 original size:76 final size:76
Alignment explanation
Indices: 234510--235077 Score: 1012
Period size: 76 Copynumber: 7.5 Consensus size: 76
234500 CTATTTCCCA
234510 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
234575 AGCCTTAGGGT
66 AGCCTTAGGGT
234586 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
234651 AGCCTTAGGGT
66 AGCCTTAGGGT
*
234662 CATCTGTTAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
234727 AGCCTTAGGGT
66 AGCCTTAGGGT
* * **
234738 CATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTTGA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
234803 AGCCTTATGGT
66 AGCCTTAGGGT
*
234814 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
234879 AGCCTTAGGGT
66 AGCCTTAGGGT
*
234890 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTGAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
234955 AGCCTTAGGGT
66 AGCCTTAGGGT
*
234966 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCATTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
235031 AACCTTAGGGT
66 AGCCTTAGGGT
* *
235042 CATCTGTAAG-CCGTTCAGTGCATGATGTTTTCAAAA
1 CATCTGTAAGTCC-TACAGTGCATGATGTTTCCAAAA
235078 CCTTTGGGTC
Statistics
Matches: 471, Mismatches: 20, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
75 2 0.00
76 469 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:235070 original size:45 final size:45
Alignment explanation
Indices: 235019--235348 Score: 527
Period size: 45 Copynumber: 7.3 Consensus size: 45
235009 GGGAGCATTT
*
235019 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAG-CCGTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCC-TTCAGTGCA
*
235064 TGATGTTTTCAAAACCTTTGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
235109 TGATGTTTTTAAAATCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
235154 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
235199 TGATGTTATCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
235244 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTTAGAGCA
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* * *
235290 TGATGTTTTCAAAAACCTTTGAGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
235336 TGATGTTTTCAAA
1 TGATGTTTTCAAA
235349 CATTTCTGTC
Statistics
Matches: 266, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
45 180 0.68
46 86 0.32
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:235496 original size:3 final size:3
Alignment explanation
Indices: 235478--235550 Score: 78
Period size: 3 Copynumber: 24.7 Consensus size: 3
235468 TTTCATTAAA
* * * *
235478 ATT ATT CTT AATT ATT ATT TTT ATT ATT ATT AAT AAT A-T ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
235523 ATT ATT ATT ATT ATC ATT ATT -TT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
235551 AAATAAATAC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 4 0.07
3 54 0.90
4 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:235527 original size:26 final size:24
Alignment explanation
Indices: 235486--235550 Score: 87
Period size: 26 Copynumber: 2.7 Consensus size: 24
235476 AAATTATTCT
*
235486 TAATTATTATTTTTATTATTATTAA
1 TAATTATTATTATTATTATTATT-A
235511 TAATATATTATTATTATTATTATTA
1 TAAT-TATTATTATTATTATTATTA
*
235536 TCATTATT-TTATTAT
1 TAATTATTATTATTAT
235551 AAATAAATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 7 0.19
24 4 0.11
25 8 0.22
26 18 0.49
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TAATTATTATTATTATTATTATTA
Found at i:237147 original size:4 final size:4
Alignment explanation
Indices: 237140--237164 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
237130 TAATAAATAA
237140 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
237165 TTATCCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:239324 original size:2 final size:2
Alignment explanation
Indices: 239313--239342 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
239303 TGTTGATTAT
239313 TA TA -A TA 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
239343 TGAAACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:241584 original size:20 final size:20
Alignment explanation
Indices: 241559--241603 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
241549 CAAAGGTACT
241559 TTGATCCTATATAGATATAG
1 TTGATCCTATATAGATATAG
241579 TTGATCCTATATAGATATAG
1 TTGATCCTATATAGATATAG
241599 TTGAT
1 TTGAT
241604 GGATGAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (20 bp):
TTGATCCTATATAGATATAG
Found at i:249290 original size:11 final size:11
Alignment explanation
Indices: 249272--249310 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
249262 TAGATTAGGA
249272 TATTATTTTAT
1 TATTATTTTAT
* *
249283 TGTTATTTCAT
1 TATTATTTTAT
249294 TATTATTTTAT
1 TATTATTTTAT
249305 TCATTA
1 T-ATTA
249311 GTCATGTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:249309 original size:15 final size:17
Alignment explanation
Indices: 249279--249310 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
249269 GGATATTATT
249279 TTATTGTTATTTCATTA
1 TTATTGTTATTTCATTA
249296 TTATT-TTA-TTCATTA
1 TTATTGTTATTTCATTA
249311 GTCATGTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (17 bp):
TTATTGTTATTTCATTA
Found at i:249315 original size:22 final size:22
Alignment explanation
Indices: 249272--249315 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
249262 TAGATTAGGA
* *
249272 TATTATTTTATTGTTATTTCAT
1 TATTATTTTATTATTATGTCAT
249294 TATTATTTTATTCATTA-GTCAT
1 TATTATTTTATT-ATTATGTCAT
249316 GTAGAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (22 bp):
TATTATTTTATTATTATGTCAT
Found at i:252420 original size:72 final size:71
Alignment explanation
Indices: 252335--252545 Score: 191
Period size: 67 Copynumber: 3.0 Consensus size: 71
252325 CTTGAACTTT
*
252335 CGAGTCTAGTCGAACTCAGCTTTGAACTTTTCAAGTTGAGTCAAGCTCGACTCGTTTACAGCCCT
1 CGAGTCAAGTCGAACTCAGCTTTGAACTTTTCAAGTTGAGT-AAGCTCGACTCGTTTACAGCCCT
252400 AGAAAAG
65 AGAAAAG
* * * * * * *
252407 GGAGTCAAGTCGAACACAACTTTGAACTTTTTAAGTT-A--AA-CTCAACTCGTTTACAACCATA
1 CGAGTCAAGTCGAACTCAGCTTTGAACTTTTCAAGTTGAGTAAGCTCGACTCGTTTACAGCCCTA
*
252468 -AAATAA
66 GAAA-AG
* * * ** * * *
252474 CGAGTCAAGTCAAAATCAGCTTTGAACTTTTCTAGCCGAGTGAAGCTAGACTAGTTTACGGCACC
1 CGAGTCAAGTCGAACTCAGCTTTGAACTTTTCAAGTTGAGT-AAGCTCGACTCGTTTACAGC-CC
252539 -AGAAAAG
64 TAGAAAAG
252546 AGTGTGCTTT
Statistics
Matches: 106, Mismatches: 25, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
66 3 0.03
67 47 0.44
68 3 0.03
71 3 0.03
72 46 0.43
73 4 0.04
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (71 bp):
CGAGTCAAGTCGAACTCAGCTTTGAACTTTTCAAGTTGAGTAAGCTCGACTCGTTTACAGCCCTA
GAAAAG
Found at i:257759 original size:16 final size:16
Alignment explanation
Indices: 257738--257768 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
257728 GTTATGACCC
*
257738 AAGAGAATCGGAGAAG
1 AAGAGAATCGAAGAAG
257754 AAGAGAATCGAAGAA
1 AAGAGAATCGAAGAA
257769 ATAGAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.32, T:0.06
Consensus pattern (16 bp):
AAGAGAATCGAAGAAG
Found at i:262162 original size:19 final size:19
Alignment explanation
Indices: 262138--262175 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
262128 TTACTAATCT
262138 TGGGTGTGTTAAATATAGG
1 TGGGTGTGTTAAATATAGG
262157 TGGGTGTGTTAAATATAGG
1 TGGGTGTGTTAAATATAGG
262176 GTTATGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (19 bp):
TGGGTGTGTTAAATATAGG
Found at i:265034 original size:20 final size:17
Alignment explanation
Indices: 264994--265042 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 17
264984 GATGTCATCT
*
264994 AAAATATTTAAAAATAG
1 AAAATATTTAAAAATAA
265011 AAAATATTATAAACAAATAA
1 AAAATATT-T-AA-AAATAA
*
265031 AAAATAATTAAA
1 AAAATATTTAAA
265043 TTTATGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 9 0.33
18 3 0.11
19 3 0.11
20 12 0.44
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATATTTAAAAATAA
Found at i:265074 original size:25 final size:25
Alignment explanation
Indices: 265028--265081 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
265018 TATAAACAAA
**
265028 TAAAAAATAATTAAATTTATGAAAT
1 TAAAAAATAATTAAATAAATGAAAT
*
265053 TAAAAAA-AAGTTAAATAAATGAAGT
1 TAAAAAATAA-TTAAATAAATGAAAT
265078 TAAA
1 TAAA
265082 CAATTACCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (25 bp):
TAAAAAATAATTAAATAAATGAAAT
Found at i:265894 original size:12 final size:12
Alignment explanation
Indices: 265871--265905 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
265861 AATTTTTAAT
265871 ATAAATTTATTGA
1 ATAAA-TTATTGA
265884 ATAAATTATTGA
1 ATAAATTATTGA
265896 ATAAATTATT
1 ATAAATTATT
265906 TGATTTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (12 bp):
ATAAATTATTGA
Found at i:266648 original size:19 final size:19
Alignment explanation
Indices: 266625--266713 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
266615 GACTCAACCC
*
266625 ATTGACTTTGACCTGACTC-
1 ATTGACTTTGACCAGAC-CA
* *
266644 GTTGACTTTAACCAGACCA
1 ATTGACTTTGACCAGACCA
266663 ATTGACTTTGACCAGACCA
1 ATTGACTTTGACCAGACCA
*
266682 ATTGACTTTGACC-GACCC
1 ATTGACTTTGACCAGACCA
266700 ATTGACTTTGACCA
1 ATTGACTTTGACCA
266714 AAAAAGTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
18 18 0.29
19 44 0.71
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (19 bp):
ATTGACTTTGACCAGACCA
Found at i:270618 original size:54 final size:54
Alignment explanation
Indices: 270532--270786 Score: 334
Period size: 54 Copynumber: 4.7 Consensus size: 54
270522 CATTTTTATG
*
270532 TATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCA
1 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
* *
270586 TATTGACACTAAGTGTTCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
1 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
** * * * *
270640 TATCGGTACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAATGATCG
1 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
* * * ***
270694 TATCGACACTAAGTGTGCAACCCA-TAGAATTTATAATAAATTTATGAACGATTG
1 TATCGACACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCA
*
270748 TATCGGCACTAAGTGTGCAACCCAC-AGAATTCATAATAA
1 TATCGACACTAAGTGTGCAACCCACGA-AATTCATAATAA
270787 TCGACACTAA
Statistics
Matches: 178, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
54 178 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (54 bp):
TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
Found at i:270625 original size:27 final size:27
Alignment explanation
Indices: 270541--270626 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
270531 GTATCGACAC
*
270541 TAAGTGTGCAACCCACAAAATTCATAA
1 TAAGTGTTCAACCCACAAAATTCATAA
* * * * * * * *
270568 TAAGTTTATGAA-CGACCATATTGACAC
1 TAAGTGT-TCAACCCACAAAATTCATAA
*
270595 TAAGTGTTCAACCCACGAAATTCATAA
1 TAAGTGTTCAACCCACAAAATTCATAA
270622 TAAGT
1 TAAGT
270627 TTATGAACGA
Statistics
Matches: 40, Mismatches: 17, Indels: 4
0.66 0.28 0.07
Matches are distributed among these distances:
26 3 0.08
27 35 0.88
28 2 0.05
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.27
Consensus pattern (27 bp):
TAAGTGTTCAACCCACAAAATTCATAA
Found at i:270804 original size:37 final size:37
Alignment explanation
Indices: 270749--270823 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
270739 GAACGATTGT
*
270749 ATCGGCACTAAGTGTGCAACCCACAGAATTCATAATA
1 ATCGACACTAAGTGTGCAACCCACAGAATTCATAATA
**
270786 ATCGACACTAAGTGTGCAACCCATGGAATTCATAATA
1 ATCGACACTAAGTGTGCAACCCACAGAATTCATAATA
270823 A
1 A
270824 GTTTATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (37 bp):
ATCGACACTAAGTGTGCAACCCACAGAATTCATAATA
Found at i:270869 original size:91 final size:91
Alignment explanation
Indices: 270695--270877 Score: 258
Period size: 91 Copynumber: 2.0 Consensus size: 91
270685 GAATGATCGT
* ** * *
270695 ATCGACACTAAGTGTGCAACCCATAGAATTTATAATAAATTTATGAACGATTGTATCGGCACTAA
1 ATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAATTTATGAACGACCGTATCGACACAAA
*
270760 GTGTGCAACCCACAGAATTCATAATA
66 GTGTGCAACCAACAGAATTCATAATA
* * *
270786 ATCGACACTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAATGACCGTATCGACACAAA
1 ATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAATTTATGAACGACCGTATCGACACAAA
* * *
270851 GTTTGTAACCAACTGAATTCATAATA
66 GTGTGCAACCAACAGAATTCATAATA
270877 A
1 A
270878 GTTTATGAAC
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (91 bp):
ATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAATTTATGAACGACCGTATCGACACAAA
GTGTGCAACCAACAGAATTCATAATA
Found at i:270872 original size:54 final size:54
Alignment explanation
Indices: 270786--271042 Score: 265
Period size: 54 Copynumber: 4.8 Consensus size: 54
270776 ATTCATAATA
* *
270786 ATCGACACTAAGTGTGCAACCCA-TGGAATTCATAATAAGTTTATGAATGACCGT
1 ATCGACACTAAGTTTGCAACCCACT-GAATTCATAATAAGTTTATGAACGACCGT
* * * *
270840 ATCGACACAAAGTTTGTAACCAACTGAATTCATAATAAGTTTATGAACGACTGT
1 ATCGACACTAAGTTTGCAACCCACTGAATTCATAATAAGTTTATGAACGACCGT
* * *
270894 ATCGGCACTAAGTGTGCAACCCAC-GAAATTCATAATAAGTTTATGAACGAACGT
1 ATCGACACTAAGTTTGCAACCCACTG-AATTCATAATAAGTTTATGAACGACCGT
* * ** *
270948 ATC-AGCACTAAGTTTACAACCCACAT-AATTCATAATGAGTTTATGAATAATCGT
1 ATCGA-CACTAAGTTTGCAACCCAC-TGAATTCATAATAAGTTTATGAACGACCGT
* * *
271002 ATCGACACT-ACTTGTGCACCCCACTTAACTT-ATAATAAGTT
1 ATCGACACTAAGTT-TGCAACCCACTGAA-TTCATAATAAGTT
271043 ACAATAAATA
Statistics
Matches: 170, Mismatches: 24, Indels: 18
0.80 0.11 0.08
Matches are distributed among these distances:
53 5 0.03
54 161 0.95
55 4 0.02
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (54 bp):
ATCGACACTAAGTTTGCAACCCACTGAATTCATAATAAGTTTATGAACGACCGT
Found at i:270892 original size:27 final size:27
Alignment explanation
Indices: 270811--270892 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
270801 GCAACCCATG
* *
270811 GAATTCATAATAAGTTTATGAATGACC
1 GAATTCATAATAAGTTTATGAACGACT
* * * *
270838 GTA-TCGACACA-AAGTTTGT-AACCAACT
1 GAATTC-ATA-ATAAGTTTATGAA-CGACT
270865 GAATTCATAATAAGTTTATGAACGACT
1 GAATTCATAATAAGTTTATGAACGACT
270892 G
1 G
270893 TATCGGCACT
Statistics
Matches: 39, Mismatches: 10, Indels: 12
0.64 0.16 0.20
Matches are distributed among these distances:
26 5 0.13
27 29 0.74
28 5 0.13
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (27 bp):
GAATTCATAATAAGTTTATGAACGACT
Found at i:270910 original size:145 final size:145
Alignment explanation
Indices: 270647--270931 Score: 448
Period size: 145 Copynumber: 2.0 Consensus size: 145
270637 CCATATCGGT
* * *
270647 ACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAATGATCGTATCGACACTAAGTGTGC
1 ACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGACCGTATCGACACAAAGTGTGC
* * *
270712 AACCCATAGAATTTATAATAAATTTATGAACGATTGTATCGGCACTAAGTGTGCAACCCAC-AGA
66 AACCAATAGAATTCATAATAAATTTATGAACGACTGTATCGGCACTAAGTGTGCAACCCACGA-A
270776 ATTCATAATAATCGAC
130 ATTCATAATAATCGAC
* * *
270792 ACTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAATGACCGTATCGACACAAAGTTTGT
1 ACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGACCGTATCGACACAAAGTGTGC
*
270857 AACCAACT-GAATTCATAATAAGTTTATGAACGACTGTATCGGCACTAAGTGTGCAACCCACGAA
66 AACCAA-TAGAATTCATAATAAATTTATGAACGACTGTATCGGCACTAAGTGTGCAACCCACGAA
270921 ATTCATAATAA
130 ATTCATAATAA
270932 GTTTATGAAC
Statistics
Matches: 128, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
145 126 0.98
146 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (145 bp):
ACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGACCGTATCGACACAAAGTGTGC
AACCAATAGAATTCATAATAAATTTATGAACGACTGTATCGGCACTAAGTGTGCAACCCACGAAA
TTCATAATAATCGAC
Found at i:270931 original size:199 final size:199
Alignment explanation
Indices: 270590--270983 Score: 542
Period size: 199 Copynumber: 2.0 Consensus size: 199
270580 CGACCATATT
* ** *
270590 GACACTAAGTGTTCAACCCACGAAATTCATAATAAGTTTATGAACGACCATATCGGTACTAAGTG
1 GACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCATATCGACACAAAGTG
* * *
270655 TGCAACCCACGTAATTCATAATAAGTTTATGAATGATCGTATCGACACTAAGTGTGCAACCCATA
66 TGCAACCAACGTAATTCATAATAAGTTTATGAACGATCGTATCGACACTAAGTGTGCAACCCAGA
* ** * *
270720 GAATTTATAATAAATTTATGAACGATTGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAAT
131 GAATTCATAATAAATTTATGAACGAACGTATCAGCACTAAGTGTACAACCCACAGAATTCATAAT
270785 AATC
196 AATC
* * * * *
270789 GACACTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAATGACCGTATCGACACAAAGTT
1 GACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCATATCGACACAAAGTG
* *
270854 TGTAACCAAC-TGAATTCATAATAAGTTTATGAACGA-CTGTATCGGCACTAAGTGTGCAACCCA
66 TGCAACCAACGT-AATTCATAATAAGTTTATGAACGATC-GTATCGACACTAAGTGTGCAACCCA
* * *
270917 CGA-AATTCATAATAAGTTTATGAACGAACGTATCAGCACTAAGTTTACAACCCACATAATTCAT
129 -GAGAATTCATAATAAATTTATGAACGAACGTATCAGCACTAAGTGTACAACCCACAGAATTCAT
270981 AAT
193 AAT
270984 GAGTTTATGA
Statistics
Matches: 170, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
198 2 0.01
199 167 0.98
200 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (199 bp):
GACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCATATCGACACAAAGTG
TGCAACCAACGTAATTCATAATAAGTTTATGAACGATCGTATCGACACTAAGTGTGCAACCCAGA
GAATTCATAATAAATTTATGAACGAACGTATCAGCACTAAGTGTACAACCCACAGAATTCATAAT
AATC
Found at i:270939 original size:108 final size:108
Alignment explanation
Indices: 270786--271042 Score: 297
Period size: 108 Copynumber: 2.4 Consensus size: 108
270776 ATTCATAATA
* * * *
270786 ATCGACACTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAATGACCGTATC-GACACAA
1 ATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAACGTATCAG-CACAA
**
270850 AGTTTGTAACCAAC-TGAATTCATAATAAGTTTATGAACGACTGT
65 AGTTTACAACCAACAT-AATTCATAATAAGTTTATGAACGACTGT
* *
270894 ATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAACGTATCAGCACTAA
1 ATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAACGTATCAGCACAAA
* * * *
270959 GTTTACAACCCACATAATTCATAATGAGTTTATGAA-TAATCGT
66 GTTTACAACCAACATAATTCATAATAAGTTTATGAACGACT-GT
** * * *
271002 ATCGACACTACTTGTGCACCCCACTTAACTT-ATAATAAGTT
1 ATCGACACTAAGTGTGCAACCCAC-GAAATTCATAATAAGTT
271043 ACAATAAATA
Statistics
Matches: 127, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
107 2 0.02
108 119 0.94
109 6 0.05
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (108 bp):
ATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAACGTATCAGCACAAA
GTTTACAACCAACATAATTCATAATAAGTTTATGAACGACTGT
Found at i:270993 original size:253 final size:253
Alignment explanation
Indices: 270533--270994 Score: 678
Period size: 253 Copynumber: 1.8 Consensus size: 253
270523 ATTTTTATGT
* *
270533 ATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCATATTGACACTAA
1 ATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCATATCGACACAAA
* *
270598 GTGTTCAACCCACGAAATTCATAATAAGTTTATGAACGACCATATCGGTACTAAGTGTGCAACCC
66 GTGTTCAACCAACGAAATTCATAATAAGTTTATGAACGACCATATCGGCACTAAGTGTGCAACCC
* * * * * *
270663 ACGTAATTCATAATAAGTTTATGAATGATCGTATCGACACTAAGTGTGCAACCCATAGAATTTAT
131 ACGAAATTCATAATAAGTTTATGAACGAACGTATCGACACTAAGTGTACAACCCACAGAATTCAT
270728 AATAAATTTATGAACGATTGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATA
196 AATAAATTTATGAACGATTGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATA
*** * *
270786 ATCGACACTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAATGACCGTATCGACACAAA
1 ATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCATATCGACACAAA
* **
270851 GT-TTGTAACCAACTG-AATTCATAATAAGTTTATGAACGACTGTATCGGCACTAAGTGTGCAAC
66 GTGTT-CAACCAAC-GAAATTCATAATAAGTTTATGAACGACCATATCGGCACTAAGTGTGCAAC
* *
270914 CCACGAAATTCATAATAAGTTTATGAACGAACGTATC-AGCACTAAGTTTACAACCCACATAATT
129 CCACGAAATTCATAATAAGTTTATGAACGAACGTATCGA-CACTAAGTGTACAACCCACAGAATT
* *
270978 CATAATGAGTTTATGAA
193 CATAATAAATTTATGAA
270995 TAATCGTATC
Statistics
Matches: 184, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
252 3 0.02
253 180 0.98
254 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (253 bp):
ATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCATATCGACACAAA
GTGTTCAACCAACGAAATTCATAATAAGTTTATGAACGACCATATCGGCACTAAGTGTGCAACCC
ACGAAATTCATAATAAGTTTATGAACGAACGTATCGACACTAAGTGTACAACCCACAGAATTCAT
AATAAATTTATGAACGATTGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATA
Found at i:277118 original size:54 final size:54
Alignment explanation
Indices: 276752--277103 Score: 463
Period size: 54 Copynumber: 6.5 Consensus size: 54
276742 GCATTCTTAT
* * * **
276752 GTATCGACACTAAGTGTGCAACCCAC-AGAATTCATAATAAGTTTATAAATGATT
1 GTATCGGCACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACC
* * * *
276806 GTATCGGCACTAAATGTGCAACCCACGGAATTCATAATAAGTTTATGAACAACT
1 GTATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
* * * * *
276860 TTATTGACACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAATGACC
1 GTATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
* *
276914 GTATCGGCACTAAGTGTGCAACCCACGGAATTTATAATAAGTTTATGAACGACC
1 GTATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
276968 GTATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
1 GTATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
* * ** *
277022 GTATCGGTACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAATAATC
1 GTATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
* * * *
277076 GTATCAGCAGTACGTGTGCACCCCACGA
1 GTATCGGCACTAAGTGTGCAACCCACGA
277104 TACTTATAAT
Statistics
Matches: 264, Mismatches: 33, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
54 264 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
GTATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACC
Found at i:278450 original size:38 final size:38
Alignment explanation
Indices: 278396--278483 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
278386 ACCCGACTCG
* * **
278396 TTGACTTTAACCCGACCTGTTGACTTTAACCCAACCCA
1 TTGACTTTGACTCGACCCATTGACTTTAACCCAACCCA
* *
278434 TTGACTTTGACTCGACCCATTGACTTTGACCTAACCCA
1 TTGACTTTGACTCGACCCATTGACTTTAACCCAACCCA
* *
278472 TTAACTGTGACT
1 TTGACTTTGACT
278484 AGAGTTTACC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.32
Consensus pattern (38 bp):
TTGACTTTGACTCGACCCATTGACTTTAACCCAACCCA
Found at i:278461 original size:19 final size:19
Alignment explanation
Indices: 278382--278464 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
278372 ACCGGGTTTG
* *
278382 TTTGACCCGACTCGTTGAC
1 TTTGACCCGACCCATTGAC
* **
278401 TTTAACCCGACCTGTTGAC
1 TTTGACCCGACCCATTGAC
* *
278420 TTTAACCCAACCCATTGAC
1 TTTGACCCGACCCATTGAC
*
278439 TTTGACTCGACCCATTGAC
1 TTTGACCCGACCCATTGAC
278458 TTTGACC
1 TTTGACC
278465 TAACCCATTA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.31
Consensus pattern (19 bp):
TTTGACCCGACCCATTGAC
Found at i:278470 original size:19 final size:19
Alignment explanation
Indices: 278415--278473 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
278405 ACCCGACCTG
* *
278415 TTGACTTTAACCCAACCCA
1 TTGACTTTGACCTAACCCA
*
278434 TTGACTTTGA-CTCGACCCA
1 TTGACTTTGACCT-AACCCA
278453 TTGACTTTGACCTAACCCA
1 TTGACTTTGACCTAACCCA
278472 TT
1 TT
278474 AACTGTGACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 31 0.91
20 2 0.06
ACGTcount: A:0.25, C:0.32, G:0.10, T:0.32
Consensus pattern (19 bp):
TTGACTTTGACCTAACCCA
Found at i:279597 original size:26 final size:26
Alignment explanation
Indices: 279534--279597 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
279524 TCCGATATTC
279534 AAATGACTGAAATACCCCTAAACTCTA
1 AAATGACTGAAATA-CCCTAAACTCTA
* *
279561 AAAGGATTGAAATA-CCTAGAACTCTA
1 AAATGACTGAAATACCCTA-AACTCTA
*
279587 AGATGACTGAA
1 AAATGACTGAA
279598 GTAACCTCGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 4 0.13
26 15 0.48
27 12 0.39
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (26 bp):
AAATGACTGAAATACCCTAAACTCTA
Found at i:287073 original size:15 final size:15
Alignment explanation
Indices: 287053--287083 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
287043 AATTACGAAT
*
287053 TTCCATTGAAATATC
1 TTCCATTAAAATATC
287068 TTCCATTAAAATATC
1 TTCCATTAAAATATC
287083 T
1 T
287084 CATAGTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.42
Consensus pattern (15 bp):
TTCCATTAAAATATC
Found at i:289176 original size:20 final size:22
Alignment explanation
Indices: 289138--289177 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
289128 TTTTTGTAGA
289138 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
289160 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
289178 AGATATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:290434 original size:22 final size:22
Alignment explanation
Indices: 290392--290434 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
290382 ATTTTGAATT
* *
290392 AGCAAATATTTCAAATTTTTAG
1 AGCAAATACTTCAAATATTTAG
*
290414 AGCAAATACTTCAACTATTTA
1 AGCAAATACTTCAAATATTTA
290435 CTCCAAATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (22 bp):
AGCAAATACTTCAAATATTTAG
Found at i:293092 original size:2 final size:2
Alignment explanation
Indices: 293085--293151 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
293075 ACTAAAGATA
293085 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
293126 AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
293152 TTCTTCAAAC
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:293505 original size:20 final size:20
Alignment explanation
Indices: 293462--293508 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
293452 TTTCTTGTAG
* *
293462 TTTTGAAACTATCTCAAGAG
1 TTTTGAAACTATCCCAAGAA
* *
293482 TTTTGAAACTTTCCCCAGAA
1 TTTTGAAACTATCCCAAGAA
293502 TTTTGAA
1 TTTTGAA
293509 CATTTATGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (20 bp):
TTTTGAAACTATCCCAAGAA
Found at i:301850 original size:22 final size:23
Alignment explanation
Indices: 301806--301851 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
301796 ATAATTATGA
*
301806 AAAATATTAATTTATATATAAAT
1 AAAATATTAATTTATATAGAAAT
* *
301829 AAAATATT-TTTTATTTAGAAAT
1 AAAATATTAATTTATATAGAAAT
301851 A
1 A
301852 TCAGAAAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AAAATATTAATTTATATAGAAAT
Found at i:302099 original size:3 final size:3
Alignment explanation
Indices: 302091--302120 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
302081 TTTATGGCTA
*
302091 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
302121 TAAAAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:306005 original size:42 final size:42
Alignment explanation
Indices: 305937--306043 Score: 160
Period size: 42 Copynumber: 2.5 Consensus size: 42
305927 CTTTAGTGGG
* *
305937 TAGTAGGCGGGTGTGGATTTAAAAAGTGGTACCCGTCGCGGA
1 TAGTGGGCGGGTGTGGATTTGAAAAGTGGTACCCGTCGCGGA
* *
305979 TAGTGGGCGGGTGTGGATTTGGAAAGTGGTACCCGTTGCGGA
1 TAGTGGGCGGGTGTGGATTTGAAAAGTGGTACCCGTCGCGGA
*
306021 TAGTGGGCGGGTGATGGGTTTGA
1 TAGTGGGCGGGTG-TGGATTTGA
306044 GACCTTACCC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 51 0.88
43 7 0.12
ACGTcount: A:0.19, C:0.11, G:0.44, T:0.26
Consensus pattern (42 bp):
TAGTGGGCGGGTGTGGATTTGAAAAGTGGTACCCGTCGCGGA
Found at i:306778 original size:38 final size:38
Alignment explanation
Indices: 306723--306796 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
306713 GTTTGATTGG
306723 TTGGTCAAACTGCTATCTTTATTCTCTCGTATTTCCCA
1 TTGGTCAAACTGCTATCTTTATTCTCTCGTATTTCCCA
* *
306761 TTGGTCAAATTGTTATCTTTATTCTCTCGTATTTCC
1 TTGGTCAAACTGCTATCTTTATTCTCTCGTATTTCC
306797 GAACAGATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.49
Consensus pattern (38 bp):
TTGGTCAAACTGCTATCTTTATTCTCTCGTATTTCCCA
Found at i:311118 original size:39 final size:39
Alignment explanation
Indices: 311075--311166 Score: 139
Period size: 39 Copynumber: 2.4 Consensus size: 39
311065 GCAATCTATT
* * *
311075 GCAGCATACAAATAGAGATTGCTATCAATCTATTTATAA
1 GCAGCATAAAAATACAGATTGCAATCAATCTATTTATAA
* *
311114 GCAGCATAAAAATTCTGATTGCAATCAATCTATTTATAA
1 GCAGCATAAAAATACAGATTGCAATCAATCTATTTATAA
311153 GCAGCATAAAAATA
1 GCAGCATAAAAATA
311167 TTATGTATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (39 bp):
GCAGCATAAAAATACAGATTGCAATCAATCTATTTATAA
Found at i:316700 original size:19 final size:19
Alignment explanation
Indices: 316676--316716 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
316666 CTAACTTGTG
*
316676 GACTTTGACCCGACCCGTT
1 GACTTTGACACGACCCGTT
*
316695 GACTTTGACATGACCCGTT
1 GACTTTGACACGACCCGTT
316714 GAC
1 GAC
316717 CGTTGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.32, G:0.22, T:0.27
Consensus pattern (19 bp):
GACTTTGACACGACCCGTT
Found at i:317625 original size:18 final size:19
Alignment explanation
Indices: 317604--317650 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
317594 GTAAAAAGAT
*
317604 ATTAAAAT-AATAAAAGCG
1 ATTAAAATAAATAAAAGCA
317622 ATT-AAATAAATAAAAGCA
1 ATTAAAATAAATAAAAGCA
*
317640 ATTAAAGTAAA
1 ATTAAAATAAA
317651 AATAAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 6 0.24
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.23
Consensus pattern (19 bp):
ATTAAAATAAATAAAAGCA
Found at i:321618 original size:19 final size:19
Alignment explanation
Indices: 321566--321605 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
321556 AACTGTGTCA
321566 ACCCGACCCGTTGACTTTG
1 ACCCGACCCGTTGACTTTG
321585 ACCCGACCCGTTGACTTTG
1 ACCCGACCCGTTGACTTTG
321604 AC
1 AC
321606 TTGACCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.38, G:0.20, T:0.25
Consensus pattern (19 bp):
ACCCGACCCGTTGACTTTG
Found at i:322734 original size:21 final size:21
Alignment explanation
Indices: 322708--322752 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
322698 GATTTCTGGG
* *
322708 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
322729 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
322750 CAA
1 CAA
322753 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:324090 original size:30 final size:30
Alignment explanation
Indices: 324046--324169 Score: 205
Period size: 30 Copynumber: 4.1 Consensus size: 30
324036 TCGAGACATA
324046 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
324077 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
324107 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* **
324137 TGGACAGTTACCG-GGGTCTTGGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
324166 TGGA
1 TGGA
324170 TAGGTCCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
29 17 0.19
30 66 0.73
31 7 0.08
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:327623 original size:17 final size:18
Alignment explanation
Indices: 327601--327634 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
327591 GAATAAGTCA
327601 GAAAAT-GATTATTTTTT
1 GAAAATAGATTATTTTTT
*
327618 GAAAATATATTATTTTT
1 GAAAATAGATTATTTTT
327635 ATTATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
GAAAATAGATTATTTTTT
Found at i:329461 original size:21 final size:21
Alignment explanation
Indices: 329432--329592 Score: 80
Period size: 21 Copynumber: 7.8 Consensus size: 21
329422 TCCAATATTG
*
329432 CAAATTCGCGTTGCGATAGTT
1 CAAAATCGCGTTGCGATAGTT
* * *
329453 GAAAATCGCATTGCGAT-TTT
1 CAAAATCGCGTTGCGATAGTT
* **
329473 CTATTTCGCGTTGCGATAGTT
1 CAAAATCGCGTTGCGATAGTT
* * *
329494 GAAAATCGCGTTACGAT-TTT
1 CAAAATCGCGTTGCGATAGTT
****
329514 CCTTTTCGCGTTGCGATAG-T
1 CAAAATCGCGTTGCGATAGTT
* * *
329534 CTACAGT-GTCGTTGCGAT-TTT
1 C-AAAATCG-CGTTGCGATAGTT
* **
329555 CCATTTCGCGTTGCGATAGTT
1 CAAAATCGCGTTGCGATAGTT
*
329576 GAAAATCGCGTTGCGAT
1 CAAAATCGCGTTGCGAT
329593 TATCCATTTC
Statistics
Matches: 96, Mismatches: 37, Indels: 14
0.65 0.25 0.10
Matches are distributed among these distances:
20 40 0.42
21 56 0.58
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (21 bp):
CAAAATCGCGTTGCGATAGTT
Found at i:329493 original size:41 final size:41
Alignment explanation
Indices: 329436--329656 Score: 297
Period size: 41 Copynumber: 5.4 Consensus size: 41
329426 ATATTGCAAA
* *
329436 TTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTCTAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
* *
329477 TTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCTT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
* *
329518 TTCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCAT
*
329559 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTATCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
* *
329600 TTCGCGTTGCGATAG-TGTACAGT-GTCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTG-AAAATCG-CGTTGCGATTTTCCAT
329641 TTCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
329657 CTACAGTGTC
Statistics
Matches: 159, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
40 5 0.03
41 152 0.96
42 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
Found at i:329630 original size:21 final size:21
Alignment explanation
Indices: 329604--329675 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
329594 ATCCATTTCG
*
329604 CGTTGCGATAGTGTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
329625 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
329643 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
329666 CGTTGCGATA
1 CGTTGCGATA
329676 ATTTTCTCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 9 0.22
21 19 0.47
22 4 0.10
23 2 0.05
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:329655 original size:123 final size:123
Alignment explanation
Indices: 329436--329674 Score: 383
Period size: 123 Copynumber: 1.9 Consensus size: 123
329426 ATATTGCAAA
* *
329436 TTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTCTATTTCGCGTTGCGATAGTTGAAAATC
1 TTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTATCCATTTCGCGTTGCGATAGTTGAAAATC
*
329501 GCGTTACGATTTTCCTTTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCAT
66 GCGTTACGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCAT
* * *
329559 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTATCCATTTCGCGTTGCGATAG-TGTACAGT
1 TTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTATCCATTTCGCGTTGCGATAGTTG-AAAAT
*
329623 -GTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT
65 CG-CGTTACGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT
329675 AATTTTCTCT
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
122 3 0.03
123 104 0.97
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.38
Consensus pattern (123 bp):
TTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTATCCATTTCGCGTTGCGATAGTTGAAAATC
GCGTTACGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCAT
Found at i:329674 original size:82 final size:82
Alignment explanation
Indices: 329463--329656 Score: 343
Period size: 82 Copynumber: 2.4 Consensus size: 82
329453 GAAAATCGCA
* * * *
329463 TTGCGATTTTCTATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCTTTTCGCGTTGC
1 TTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTATCCATTTCGCGTTGC
329528 GATAGTCTACAGTGTCG
66 GATAGTCTACAGTGTCG
329545 TTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTATCCATTTCGCGTTGC
1 TTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTATCCATTTCGCGTTGC
*
329610 GATAGTGTACAGTGTCG
66 GATAGTCTACAGTGTCG
329627 TTGCGATTTTCCATTTCGCGTTGCGATAGT
1 TTGCGATTTTCCATTTCGCGTTGCGATAGT
329657 CTACAGTGTC
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 107 1.00
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (82 bp):
TTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTATCCATTTCGCGTTGC
GATAGTCTACAGTGTCG
Found at i:329737 original size:6 final size:6
Alignment explanation
Indices: 329726--329774 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
329716 GACACGTATT
329726 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
329774 A
1 A
329775 GACGGCGACG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:330293 original size:6 final size:6
Alignment explanation
Indices: 330262--330413 Score: 255
Period size: 6 Copynumber: 26.5 Consensus size: 6
330252 TCTCGTCTCG
330262 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
330306 GGTCGT GGTCG- GGTCGT GGTCGT GGTCG- GGTCGT GGTCGT GGTCG-
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
330351 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
330399 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
330414 AATACGTGTC
Statistics
Matches: 143, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
5 35 0.24
6 108 0.76
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:330543 original size:21 final size:21
Alignment explanation
Indices: 330500--330543 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
330490 TTTACTATAG
** *
330500 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
330521 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
330542 AC
1 AC
330544 GCGAATTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:330946 original size:16 final size:17
Alignment explanation
Indices: 330925--330962 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
330915 ATGTTATGGG
330925 GTAAAAATAT-ATTATT
1 GTAAAAATATAATTATT
*
330941 GTAAAACTATAATTATT
1 GTAAAAATATAATTATT
330958 -TAAAA
1 GTAAAA
330963 TAATATCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (17 bp):
GTAAAAATATAATTATT
Found at i:331340 original size:30 final size:30
Alignment explanation
Indices: 331279--331367 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
331269 TGCATTCAAG
* *
331279 TAATCTTATATTCCTC-TAACCAAA-CACTA
1 TAATTTTATATTCCTCTTAAACAAACCA-TA
331308 TAATTTTATATTCCTCTTAAACAAACCATA
1 TAATTTTATATTCCTCTTAAACAAACCATA
331338 TAATTTTATATTCCTCTTAAACAAACCATA
1 TAATTTTATATTCCTCTTAAACAAACCATA
331368 AAAGGCAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
29 15 0.27
30 39 0.70
31 2 0.04
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.38
Consensus pattern (30 bp):
TAATTTTATATTCCTCTTAAACAAACCATA
Found at i:332011 original size:24 final size:24
Alignment explanation
Indices: 331983--332038 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
331973 CTATTTTGTC
331983 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
332007 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
332031 GCTTCAAT
1 GCTTCAAT
332039 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:340129 original size:12 final size:12
Alignment explanation
Indices: 340112--340155 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
340102 ACGTTGGTTT
340112 ATATGTTCACTA
1 ATATGTTCACTA
** *
340124 ATATGTTCGTTT
1 ATATGTTCACTA
*
340136 ATGTGTTCACTA
1 ATATGTTCACTA
340148 ATATGTTC
1 ATATGTTC
340156 GTCTTGAGTT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.48
Consensus pattern (12 bp):
ATATGTTCACTA
Found at i:340142 original size:24 final size:24
Alignment explanation
Indices: 340108--340157 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
340098 GATCACGTTG
340108 GTTTATATGTTCACTAATATGTTC
1 GTTTATATGTTCACTAATATGTTC
*
340132 GTTTATGTGTTCACTAATATGTTC
1 GTTTATATGTTCACTAATATGTTC
340156 GT
1 GT
340158 CTTGAGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (24 bp):
GTTTATATGTTCACTAATATGTTC
Found at i:349969 original size:20 final size:20
Alignment explanation
Indices: 349940--349978 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
349930 ATTCCACAAC
*
349940 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
349960 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
349979 CATGGGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:356162 original size:21 final size:22
Alignment explanation
Indices: 356116--356173 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
356106 TTCCCTCCAG
356116 GGGGAATCGGTTCCCCTTCAAA
1 GGGGAATCGGTTCCCCTTCAAA
* *
356138 GGGGAATCGGTTCCCCTTTAAG
1 GGGGAATCGGTTCCCCTTCAAA
* *
356160 GGGGTATCGATTCC
1 GGGGAATCGGTTCC
356174 TCCTGCACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.26
Consensus pattern (22 bp):
GGGGAATCGGTTCCCCTTCAAA
Found at i:359995 original size:22 final size:21
Alignment explanation
Indices: 359954--359993 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
359944 AAGACTATTT
359954 TCATTTTTTAATTTTGAAATG
1 TCATTTTTTAATTTTGAAATG
359975 TCATTTTTGT-ATTTTGAAA
1 TCATTTTT-TAATTTTGAAA
359994 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATG
Found at i:362007 original size:20 final size:20
Alignment explanation
Indices: 361979--362022 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
361969 AAACCATTTA
361979 GGGGGATC-GTACCCTCTTG
1 GGGGGATCGGTACCCTCTTG
*
361998 GGGGGAATCGGTTCCCTCTTG
1 GGGGG-ATCGGTACCCTCTTG
362019 GGGG
1 GGGG
362023 AATAAGTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 3 0.14
21 14 0.64
ACGTcount: A:0.09, C:0.23, G:0.43, T:0.25
Consensus pattern (20 bp):
GGGGGATCGGTACCCTCTTG
Found at i:362023 original size:20 final size:21
Alignment explanation
Indices: 361990--362036 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
361980 GGGGATCGTA
**
361990 CCCTCTTGGGGGGAATCGGTT
1 CCCTCTTGGGGGGAATAAGTT
362011 CCCTCTT-GGGGGAATAAGTT
1 CCCTCTTGGGGGGAATAAGTT
362031 CCCTCT
1 CCCTCT
362037 GGGCAATCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.13, C:0.28, G:0.30, T:0.30
Consensus pattern (21 bp):
CCCTCTTGGGGGGAATAAGTT
Found at i:386772 original size:20 final size:20
Alignment explanation
Indices: 386722--386773 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
386712 AAACTCAAAT
* *
386722 ATCAA-AGTCAACGGTCAACT
1 ATCAATAGTCAA-AGTCAACA
*
386742 ATCAATGGTCAAAGTCAACA
1 ATCAATAGTCAAAGTCAACA
*
386762 ATTAATAGTCAA
1 ATCAATAGTCAA
386774 TGATCAACGG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.23
Consensus pattern (20 bp):
ATCAATAGTCAAAGTCAACA
Found at i:403520 original size:15 final size:15
Alignment explanation
Indices: 403500--403550 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
403490 TGGTGGCTTT
*
403500 GGTGGTTTGGCTTCA
1 GGTGGTCTGGCTTCA
* *
403515 GGTGGTGGTGGATTC-
1 GGTGGT-CTGGCTTCA
*
403530 GGCGGTCTGGCTTCA
1 GGTGGTCTGGCTTCA
403545 GGTGGT
1 GGTGGT
403551 GGTGGTTCTG
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 6 0.21
15 16 0.57
16 6 0.21
ACGTcount: A:0.06, C:0.14, G:0.47, T:0.33
Consensus pattern (15 bp):
GGTGGTCTGGCTTCA
Found at i:403524 original size:30 final size:30
Alignment explanation
Indices: 403507--403563 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
403497 TTTGGTGGTT
403507 TGGCTTCAGGTGGTGGTGGATTCGGCGGTC
1 TGGCTTCAGGTGGTGGTGGATTCGGCGGTC
403537 TGGCTTCAGGTGGTGGTGG-TTCTGGCG
1 TGGCTTCAGGTGGTGGTGGATTC-GGCG
403564 CCACTGGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.05, C:0.16, G:0.47, T:0.32
Consensus pattern (30 bp):
TGGCTTCAGGTGGTGGTGGATTCGGCGGTC
Found at i:406751 original size:29 final size:29
Alignment explanation
Indices: 406714--406787 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
406704 TAAGAGTATG
*
406714 CTCATAATAACAAATATTAAAAAATTAGA
1 CTCATAATAACAAATACTAAAAAATTAGA
406743 CCTC-TAATAA-AAAGTACTAAAAAATTAGA
1 -CTCATAATAACAAA-TACTAAAAAATTAGA
*
406772 CTCATAACAACAAATA
1 CTCATAATAACAAATA
406788 AATATTAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 6 0.15
29 27 0.69
30 6 0.15
ACGTcount: A:0.57, C:0.15, G:0.04, T:0.24
Consensus pattern (29 bp):
CTCATAATAACAAATACTAAAAAATTAGA
Found at i:406993 original size:30 final size:30
Alignment explanation
Indices: 406957--407053 Score: 97
Period size: 32 Copynumber: 3.1 Consensus size: 30
406947 AGTAGGCTCC
406957 TAATAATAAATATTAAAAAAATT-AAGCCCA
1 TAATAATAAATATTAAAAAAATTGAA-CCCA
*
406987 TAATAATAAATATTAGGAAAAAATTGAACCCC
1 TAATAATAAATATTA--AAAAAATTGAACCCA
** * *
407019 TAATAGCAAGTATTAAAAATAATTGGACCCTA
1 TAATAATAAATATTAAAAA-AATTGAACCC-A
407051 TAA
1 TAA
407054 CGGATATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
30 19 0.34
31 9 0.16
32 26 0.46
33 2 0.04
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.27
Consensus pattern (30 bp):
TAATAATAAATATTAAAAAAATTGAACCCA
Found at i:407358 original size:23 final size:23
Alignment explanation
Indices: 407303--407358 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
407293 GAAACAAATG
*
407303 TTAAATGAACATATTCGTGAATA
1 TTAAATGAATATATTCGTGAATA
* *
407326 TTAAATGAATATGTTTGTGAATA
1 TTAAATGAATATATTCGTGAATA
407349 TTAAATGAAT
1 TTAAATGAAT
407359 CGAACACGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (23 bp):
TTAAATGAATATATTCGTGAATA
Found at i:407890 original size:20 final size:20
Alignment explanation
Indices: 407849--407908 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
407839 AAATGACCAA
***
407849 CAAATTCGCAACACAAACTC
1 CAAATTCGCAACACAGTTTC
*
407869 CAATTTCGCAACACAGTTTC
1 CAAATTCGCAACACAGTTTC
*
407889 CAAATTCGCAACTCAGTTTC
1 CAAATTCGCAACACAGTTTC
407909 TGAAATCACA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.32, G:0.08, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACACAGTTTC
Found at i:407995 original size:20 final size:21
Alignment explanation
Indices: 407943--408105 Score: 92
Period size: 20 Copynumber: 8.0 Consensus size: 21
407933 TTCGAATGCG
* *
407943 ATTTCCAAATTCGTAACACGAA
1 ATTTCTAAATTCGCAACACG-A
*
407965 ATTTC-AAATTCGCAACTCG-
1 ATTTCTAAATTCGCAACACGA
*
407984 ATTTCTAAATTCGCAACGCGA
1 ATTTCTAAATTCGCAACACGA
**
408005 ATTTCT-TTTTCGCAACAC-A
1 ATTTCTAAATTCGCAACACGA
* *
408024 AGTTTCCT--TTTCGCAACAAGA
1 A-TTT-CTAAATTCGCAACACGA
* *
408045 TTTTCTAAA-TCGCAACATGA
1 ATTTCTAAATTCGCAACACGA
*** *
408065 ATTT-TGTTTTCGCAACTCGA
1 ATTTCTAAATTCGCAACACGA
* *
408085 TTTTC-GAATTCGCAACACGA
1 ATTTCTAAATTCGCAACACGA
408105 A
1 A
408106 ACACGAATTT
Statistics
Matches: 111, Mismatches: 21, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
19 10 0.09
20 75 0.68
21 21 0.19
22 5 0.05
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (21 bp):
ATTTCTAAATTCGCAACACGA
Found at i:408097 original size:60 final size:60
Alignment explanation
Indices: 407952--408101 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 60
407942 GATTTCCAAA
* * ** *
407952 TTCGTAACACGAAATTTCAAATTCGCAACTCGATTTCTAAATTCGCAACGCGAATTTCTTT
1 TTCGCAACAC-AAGTTTCAAATTCGCAACAAGATTTCTAAATTCGCAACACGAATTTCTTT
*** *
408013 TTCGCAACACAAGTTTCCTTTTCGCAACAAGATTTTCTAAA-TCGCAACATGAATTT-TGTT
1 TTCGCAACACAAGTTTCAAATTCGCAACAAGA-TTTCTAAATTCGCAACACGAATTTCT-TT
* * * *
408073 TTCGCAACTCGATTTTCGAATTCGCAACA
1 TTCGCAACACAAGTTTCAAATTCGCAACA
408102 CGAAACACGA
Statistics
Matches: 72, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
59 1 0.01
60 54 0.75
61 17 0.24
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (60 bp):
TTCGCAACACAAGTTTCAAATTCGCAACAAGATTTCTAAATTCGCAACACGAATTTCTTT
Found at i:408304 original size:14 final size:15
Alignment explanation
Indices: 408285--408322 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
408275 TCCGCATCTC
408285 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
408299 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
408315 TAATTTTT
1 TAATTTTT
408323 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:409082 original size:23 final size:23
Alignment explanation
Indices: 409055--409106 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
409045 GTATTCGAAA
409055 TTTGATCTTGGTCAATACCCGAC
1 TTTGATCTTGGTCAATACCCGAC
* *
409078 TTTGATCTTGGTCAATACTCGAT
1 TTTGATCTTGGTCAATACCCGAC
409101 TTTGAT
1 TTTGAT
409107 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (23 bp):
TTTGATCTTGGTCAATACCCGAC
Found at i:411379 original size:18 final size:17
Alignment explanation
Indices: 411353--411387 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
411343 AAGCAAAAGG
*
411353 AAATCAAATCGCAATCA
1 AAATCAAATCCCAATCA
411370 AAATCAAAATCCCAATCA
1 AAATC-AAATCCCAATCA
411388 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (17 bp):
AAATCAAATCCCAATCA
Found at i:411656 original size:20 final size:21
Alignment explanation
Indices: 411631--411671 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
411621 GTTGCGAAAG
*
411631 TCAAATTCGTAACGC-AAAAT
1 TCAAATTCGCAACGCGAAAAT
411651 TCAAATTCGCAACGCGAAAAT
1 TCAAATTCGCAACGCGAAAAT
411672 CGCAACGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (21 bp):
TCAAATTCGCAACGCGAAAAT
Found at i:413268 original size:21 final size:21
Alignment explanation
Indices: 413233--413330 Score: 126
Period size: 21 Copynumber: 4.7 Consensus size: 21
413223 GTGAATCGGG
**
413233 CTCTTGAACGGTGAGAGGGGC
1 CTCTTGAACAATGAGAGGGGC
*
413254 CTCTTAAACAATGAGAGGGGC
1 CTCTTGAACAATGAGAGGGGC
413275 CTCTTGAACAATGAGAGGGGC
1 CTCTTGAACAATGAGAGGGGC
* *
413296 ATCTTGAACGAT-AGGAGGGGC
1 CTCTTGAACAATGA-GAGGGGC
*
413317 CTCTTGAACGATGA
1 CTCTTGAACAATGA
413331 CAGGTGAAAG
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
20 1 0.01
21 66 0.97
22 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (21 bp):
CTCTTGAACAATGAGAGGGGC
Found at i:413452 original size:12 final size:12
Alignment explanation
Indices: 413433--413473 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
413423 GGGCCGCTAA
413433 AAATAAATTAAT
1 AAATAAATTAAT
* *
413445 ACATAAATTACT
1 AAATAAATTAAT
*
413457 AAATAAATAAAT
1 AAATAAATTAAT
413469 AAATA
1 AAATA
413474 TTGCCGAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:413607 original size:21 final size:21
Alignment explanation
Indices: 413583--413622 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
413573 GTAGAGCGGC
* *
413583 TACCTCATCACGTAAAGTAGA
1 TACCTCACCACATAAAGTAGA
413604 TACCTCACCACATAAAGTA
1 TACCTCACCACATAAAGTA
413623 TCATTTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.23
Consensus pattern (21 bp):
TACCTCACCACATAAAGTAGA
Found at i:413935 original size:42 final size:42
Alignment explanation
Indices: 413860--413958 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
413850 GTGATGGAAT
* * * *
413860 AGGTGATGGCTCTCGGTATGGAGGTGTATAATCGGCTCGATC
1 AGGTAATGGCTCTCGGTATCGAGCTGTAGAATCGGCTCGATC
*
413902 AGGTAATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
1 AGGTAATGGCTCTCGGTATCGAGCTGTAGAATCGGCTCGATC
* *
413944 AGGTCATGACTCTCG
1 AGGTAATGGCTCTCG
413959 AAGTGGGGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.27
Consensus pattern (42 bp):
AGGTAATGGCTCTCGGTATCGAGCTGTAGAATCGGCTCGATC
Found at i:415507 original size:20 final size:20
Alignment explanation
Indices: 415482--415520 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
415472 TAAAATCGCA
*
415482 TTGCGATTTTCATTTTCGTG
1 TTGCGAATTTCATTTTCGTG
415502 TTGCGAATTTCATTTTCGT
1 TTGCGAATTTCATTTTCGT
415521 ATTAAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.15, G:0.18, T:0.54
Consensus pattern (20 bp):
TTGCGAATTTCATTTTCGTG
Found at i:415529 original size:20 final size:20
Alignment explanation
Indices: 415489--415531 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
415479 GCATTGCGAT
* **
415489 TTTCATTTTCGTGTTGCGAA
1 TTTCATTTTCGTATTAAGAA
415509 TTTCATTTTCGTATTAAGAA
1 TTTCATTTTCGTATTAAGAA
415529 TTT
1 TTT
415532 AAGTTTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (20 bp):
TTTCATTTTCGTATTAAGAA
Found at i:415924 original size:22 final size:22
Alignment explanation
Indices: 415866--415934 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
415856 AGGGGGGTCG
* * *
415866 CCGGATATGGGGACAGATGTCG
1 CCGGAGATGGGGACGGATGTCA
*
415888 TCGGAGATGGGGACGGATGTCA
1 CCGGAGATGGGGACGGATGTCA
*
415910 CCGGAGATGGGGACGAATGTCA
1 CCGGAGATGGGGACGGATGTCA
415932 CCG
1 CCG
415935 TAGAGAGTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.23, C:0.19, G:0.42, T:0.16
Consensus pattern (22 bp):
CCGGAGATGGGGACGGATGTCA
Found at i:416087 original size:19 final size:19
Alignment explanation
Indices: 416063--416107 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
416053 AAAATTTACG
*
416063 TTGCGAAAATAAACGCGTT
1 TTGCGAAAATAAACGCGCT
416082 TTGCGAAAATAAACGCGCT
1 TTGCGAAAATAAACGCGCT
416101 TTGCGAA
1 TTGCGAA
416108 TTTGACTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (19 bp):
TTGCGAAAATAAACGCGCT
Found at i:416126 original size:20 final size:20
Alignment explanation
Indices: 416101--416151 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
416091 TAAACGCGCT
* *
416101 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTAACTTCTGAG
*
416121 TTGCGAATTTAATTTCTGAG
1 TTGCGAATTTAACTTCTGAG
416141 TTGCGAATTTA
1 TTGCGAATTTA
416152 GAAAATCGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTAACTTCTGAG
Found at i:419380 original size:21 final size:21
Alignment explanation
Indices: 419356--419396 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
419346 CATCAAAACC
419356 ATTAGCATTATCAACATCAAT
1 ATTAGCATTATCAACATCAAT
* *
419377 ATTAGCCTTATCAATATCAA
1 ATTAGCATTATCAACATCAA
419397 CTATATCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (21 bp):
ATTAGCATTATCAACATCAAT
Found at i:420521 original size:14 final size:14
Alignment explanation
Indices: 420502--420535 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
420492 ACTTGTAATA
420502 TAGTCCCCAATATT
1 TAGTCCCCAATATT
420516 TAGTCCCCAATATT
1 TAGTCCCCAATATT
420530 TAGTCC
1 TAGTCC
420536 ATTTGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.35
Consensus pattern (14 bp):
TAGTCCCCAATATT
Found at i:420640 original size:31 final size:30
Alignment explanation
Indices: 420567--420643 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
420557 CAGTTACGTC
*
420567 GGGGATCATATTGCAAACGGACTAAATGTT
1 GGGGATCATATTGCAAACAGACTAAATGTT
420597 GGGGATCATATTGCAAACAGACTAAATGTT
1 GGGGATCATATTGCAAACAGACTAAATGTT
**
420627 GAGGGATTGTATTGCAA
1 G-GGGATCATATTGCAA
420644 GTTTAAAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 30 0.70
31 13 0.30
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (30 bp):
GGGGATCATATTGCAAACAGACTAAATGTT
Found at i:420813 original size:2 final size:2
Alignment explanation
Indices: 420806--420837 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
420796 AATGTTGTAA
420806 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
420838 TATCGTTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:442447 original size:22 final size:22
Alignment explanation
Indices: 442414--442456 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
442404 AAACCAAAAG
442414 CACAGCTCCTAA-CAATATCCTC
1 CACAGCTCCTAACCAAT-TCCTC
442436 CACAG-TCACTAACCAATTCCT
1 CACAGCTC-CTAACCAATTCCT
442457 GACTTAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.11
22 13 0.68
23 4 0.21
ACGTcount: A:0.33, C:0.40, G:0.05, T:0.23
Consensus pattern (22 bp):
CACAGCTCCTAACCAATTCCTC
Found at i:446562 original size:28 final size:28
Alignment explanation
Indices: 446529--446613 Score: 161
Period size: 28 Copynumber: 3.0 Consensus size: 28
446519 TTTAATGGAA
*
446529 TTAAAGGCCATTAAACAGAGTTTAATCT
1 TTAAAGGCCATTAAACAAAGTTTAATCT
446557 TTAAAGGCCATTAAACAAAGTTTAATCT
1 TTAAAGGCCATTAAACAAAGTTTAATCT
446585 TTAAAGGCCATTAAACAAAGTTTAATCT
1 TTAAAGGCCATTAAACAAAGTTTAATCT
446613 T
1 T
446614 CTTTGAATCT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (28 bp):
TTAAAGGCCATTAAACAAAGTTTAATCT
Found at i:447940 original size:104 final size:104
Alignment explanation
Indices: 447754--447942 Score: 315
Period size: 104 Copynumber: 1.8 Consensus size: 104
447744 TCTACTGCAG
* *
447754 GTTGCTTGAACATAAACTTAGTAAAGCAACATAGACATGTTGAAGCAAAAGTCACATTTTTTCCC
1 GTTGCTTGAACATAAACTCAGTAAAGCAACATAGACATGTTAAAGCAAAAGTCACATTTTTTCCC
*
447819 TTTTGGAAAATATCAAAAGTAGCAAATTACTTACTACAA
66 TTTTGGAAAATAGCAAAAGTAGCAAATTACTTACTACAA
* * *
447858 GTTGTTTGAACATGAACTCGGTAAAGCAACATAGACATGTTAAAGCAAAAGTCACATTTTTTCCC
1 GTTGCTTGAACATAAACTCAGTAAAGCAACATAGACATGTTAAAGCAAAAGTCACATTTTTTCCC
*
447923 TTTTGGCAAATAGCAAAAGT
66 TTTTGGAAAATAGCAAAAGT
447943 TCTTTTCAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
104 78 1.00
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (104 bp):
GTTGCTTGAACATAAACTCAGTAAAGCAACATAGACATGTTAAAGCAAAAGTCACATTTTTTCCC
TTTTGGAAAATAGCAAAAGTAGCAAATTACTTACTACAA
Found at i:450681 original size:65 final size:65
Alignment explanation
Indices: 450605--450726 Score: 226
Period size: 65 Copynumber: 1.9 Consensus size: 65
450595 AAGGAGAAAC
* *
450605 ATAGAATCCAACGGACTCAACGAGCAATACTCAAAAGTGCATGATGAGGTAATGTTATTTCTAGG
1 ATAGAATCCAACGGACTCAACAAGCAATACTCAAAAGTGCATGATGAGGCAATGTTATTTCTAGG
450670 ATAGAATCCAACGGACTCAACAAGCAATACTCAAAAGTGCATGATGAGGCAATGTTA
1 ATAGAATCCAACGGACTCAACAAGCAATACTCAAAAGTGCATGATGAGGCAATGTTA
450727 GCTTTAGGAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (65 bp):
ATAGAATCCAACGGACTCAACAAGCAATACTCAAAAGTGCATGATGAGGCAATGTTATTTCTAGG
Found at i:453988 original size:118 final size:118
Alignment explanation
Indices: 453775--453989 Score: 340
Period size: 118 Copynumber: 1.8 Consensus size: 118
453765 AGACGATAAC
* * * * *
453775 ATAATCGGTTAATTGTTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATATAATG
1 ATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGATAGCACTTATATAACG
* * * *
453840 TGATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCCGACTATAGT
66 TAATAGGTAACGCATTATTAAAGCTGATGGGGCTTTGGAAATCCGACTATAGT
*
453893 ATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGATAGCACTTATGTAACG
1 ATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGATAGCACTTATATAACG
453958 TAATAGGTAACGCATTATTAAAGCTGATGGGG
66 TAATAGGTAACGCATTATTAAAGCTGATGGGG
453990 TCCTAGAGAT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
118 87 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (118 bp):
ATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGATAGCACTTATATAACG
TAATAGGTAACGCATTATTAAAGCTGATGGGGCTTTGGAAATCCGACTATAGT
Found at i:454021 original size:118 final size:118
Alignment explanation
Indices: 453767--454025 Score: 331
Period size: 118 Copynumber: 2.2 Consensus size: 118
453757 AAAAATATAG
* * *
453767 ACGATAACATAATCGGTTAATTGTTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTT
1 ACGATAACATAATCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGATAGCACTT
* * * * * * * *
453832 ATATAATGTGATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCCG
66 ATATAACGTAATAGGTAACGCATTATTAAAGCTGATGGGGCTCTAGAAATCCA
* ** *
453885 ACTATAGTATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGATAGCACTT
1 ACGATAACATAATCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGATAGCACTT
* *
453950 ATGTAACGTAATAGGTAACGCATTATTAAAGCTGATGGGG-TCCTAGAGATCCA
66 ATATAACGTAATAGGTAACGCATTATTAAAGCTGATGGGGCT-CTAGAAATCCA
* *
454003 ACGATAACAAAATAGGTTAATTA
1 ACGATAACATAATCGGTTAATTA
454026 CTTATTTTGT
Statistics
Matches: 117, Mismatches: 23, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
117 1 0.01
118 116 0.99
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (118 bp):
ACGATAACATAATCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGATAGCACTT
ATATAACGTAATAGGTAACGCATTATTAAAGCTGATGGGGCTCTAGAAATCCA
Found at i:454179 original size:226 final size:226
Alignment explanation
Indices: 453877--454361 Score: 738
Period size: 226 Copynumber: 2.1 Consensus size: 226
453867 TGGGGCTTTG
* * *
453877 GAAATCCGACTATAGTATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGA
1 GAAATCCGACGATAGCATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGA
* *
453942 TAGCACTTATGTAACGTAATAGGTAACGCATTATTAAAGCTGATGGGGTCC-TAGAGATCCAACG
66 TAGCACTTATGTAACGTAATAGGTAACGCATTATTAAAGCTGATGAGG-CCTTAGAAATCCAACG
* * *
454006 ATAACAAAATAGGTTAATTACTTATTTTGTTATTATTATTATCAACATATTAGGTAACGCCTAAA
130 ATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAA
* *
454071 ATATTACCAAAGTTTAAGCTAATGAAGCCTTA
195 ATATTAACAAAATTTAAGCTAATGAAGCCTTA
* *
454103 GAAATCCGACGATAGCATAACCGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
1 GAAATCCGACGATAGCATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGA
* * * * *
454168 TAGCGCTTATGTAACGTAATAGGTAGCTCATTATTAAAGCTGATGAGGCCTTAGAAATTCGACGA
66 TAGCACTTATGTAACGTAATAGGTAACGCATTATTAAAGCTGATGAGGCCTTAGAAATCCAACGA
454233 TAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAA
131 TAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAA
* * * *
454298 TGTTAACAAAATTTAAGTTGATGTAGCCTTA
196 TATTAACAAAATTTAAGCTAATGAAGCCTTA
* * *
454329 GGAATCCGACGATAACATAACCGGTTATTTACT
1 GAAATCCGACGATAGCATAACCGGTTAATTACT
454362 TGATTTGTTA
Statistics
Matches: 233, Mismatches: 25, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
225 2 0.01
226 231 0.99
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (226 bp):
GAAATCCGACGATAGCATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGA
TAGCACTTATGTAACGTAATAGGTAACGCATTATTAAAGCTGATGAGGCCTTAGAAATCCAACGA
TAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAA
TATTAACAAAATTTAAGCTAATGAAGCCTTA
Found at i:457215 original size:19 final size:20
Alignment explanation
Indices: 457191--457229 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
457181 ATTGTTATAT
457191 TGTCAT-GTATCGATACATG
1 TGTCATAGTATCGATACATG
457210 TGTCATAGGTATCGATACAT
1 TGTCATA-GTATCGATACAT
457230 TTTGAATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
21 12 0.67
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TGTCATAGTATCGATACATG
Found at i:457457 original size:449 final size:448
Alignment explanation
Indices: 456609--457677 Score: 1298
Period size: 447 Copynumber: 2.4 Consensus size: 448
456599 ATTGAATACT
*
456609 CTTACTGAAGTGTCGATACTTTTGTGTAAGGTATCGATACTTTCGAGACGTTTCGTTTTTTGTGT
1 CTTACTGAAGTGTCGATAATTTTGTGTAAGGTATCGATACTTTCGAGACGTTTCGTTTTTT-TGT
* * ** * * *
456674 AAACCAATATATTTTTATATGTTTTGTCATATTGAAACTCGTTTTGTCAATTTTTAACCTGTTAT
65 AAACCAATATCTCTTTATCGGTTTTATCATATTGAAACTAGTTTTGTCAATTTTCAACCTGTTAT
* * * *
456739 ATTGTCATGTATAGATACATTTGT-ATTAGGTATCGATACTTTCTACGTTCATCTAGTTTGGGAA
130 ATTGTCATGTATCGATACATGTGTCA-TAGGTATCGATACTTTCTACATGCATCTAGTTTGGGAA
* * * *
456803 GAATACTAGACAAACAATATCGATACATATACAAATAGTATCGTTACTTTACGTAAACGTATTTT
194 GAATACTAGACAAAAAATATCGATACACATACAAAAAGTATCGATACTTTACGTAAACGTATTTT
* *
456868 GTCATTAAACCAGTATATTTTTACAGCTTACATTGTAAATTTACCTATTACTTTAAAGTAATCGG
259 GTCATTAAACCAGTATATTTTTACAGCTTACATTATAAATTTACCTATTACTTTAAAGTAATCCG
* * ** ** *
456933 TTTTGAAGTTTTAAGAATTGATATTTTTCATACGTGTATCGATACTTTATAGGCGCAATTATGGA
324 TTTCGAAGTTTTAAGAATCGATATCCTTCATACAAGTATCGATACTTTATAGGAGCAATTATGGA
* *
456998 AACTGGTTTTGTCAATTTTGATGAACTTGTTATGTTA-TTTATATTTAATCGATACCATTACC
389 AACTGGTTTTGTCAA-TTT--TGAACCTGTTAAGTTATTTTATATTTAATCGATACCATTACC
* * *
457060 CTTACTAAAGTGTCGATAATTTTGTGTAAGGTACCGATACTTTCGAGACGTTTCATTTTTTTGTA
1 CTTACTGAAGTGTCGATAATTTTGTGTAAGGTATCGATACTTTCGAGACGTTTCGTTTTTTTGTA
* * * * * **
457125 AACCAGTAGCTCTTTACCGGTTTTATCATATTGAAACTAGTTTTATCAATTTTGAAATTGTTATA
66 AACCAATATCTCTTTATCGGTTTTATCATATTGAAACTAGTTTTGTCAATTTTCAACCTGTTATA
457190 TTGTCATGTATCGATACATGTGTCATAGGTATCGATACATTT-TGA-ATGCATCTAGTTTGGGAA
131 TTGTCATGTATCGATACATGTGTCATAGGTATCGATAC-TTTCT-ACATGCATCTAGTTTGGGAA
* * * * * ** *
457253 GCATATTGGA-AAAAAAGTATCGATACACATA-AAAAAGTATTGATACTTTATGTTTATGTATTT
194 GAATACTAGACAAAAAA-TATCGATACACATACAAAAAGTATCGATACTTTACGTAAACGTATTT
* * * *
457316 TTTCATTAAATCGGTATATTTTTACCGCTTACATTATAAATTTACCTATTACTTTAAAGTAATCC
258 TGTCATTAAACCAGTATATTTTTACAGCTTACATTATAAATTTACCTATTACTTTAAAGTAATCC
* * *
457381 GTTTCGAAGTTTTAAGAATCGATA-CCTTCA-ACAAAAGTATTGATATTTTATAGGAGCATTTAT
323 GTTTCGAAGTTTTAAGAATCGATATCCTTCATAC--AAGTATCGATACTTTATAGGAGCAATTAT
457444 GGAAA-TCGGTTTTGTCAATTTTGAACCTGTTAAGTTATTTTATATTTAATCGATACCATTACC
386 GGAAACT-GGTTTTGTCAATTTTGAACCTGTTAAGTTATTTTATATTTAATCGATACCATTACC
* * * * * * * * *
457507 CTTAATGAAGTATTGATATTTTTGT-TGAAGGTGTCGATACTTTTGAAATGTTTCGTTTTTGTGT
1 CTTACTGAAGTGTCGATAATTTTGTGT-AAGGTATCGATACTTTCGAGACGTTTCGTTTTTTTGT
* * * * * *
457571 AAATCACTATCTCTTTATCGATATTGA-CATATTGAAA-TCGGTTTTGTCAATTTTCAACCAGTT
65 AAACCAATATCTCTTTATCGGT-TTTATCATATTGAAACT-AGTTTTGTCAATTTTCAACCTGTT
* * *
457634 ATATTGTCATGTATCGATACATGTTTCTTAGGTACCGATACTTT
128 ATATTGTCATGTATCGATACATGTGTCATAGGTATCGATACTTT
457678 ATAGGTGCAA
Statistics
Matches: 529, Mismatches: 78, Indels: 27
0.83 0.12 0.04
Matches are distributed among these distances:
446 19 0.04
447 160 0.30
448 11 0.02
449 150 0.28
450 127 0.24
451 62 0.12
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (448 bp):
CTTACTGAAGTGTCGATAATTTTGTGTAAGGTATCGATACTTTCGAGACGTTTCGTTTTTTTGTA
AACCAATATCTCTTTATCGGTTTTATCATATTGAAACTAGTTTTGTCAATTTTCAACCTGTTATA
TTGTCATGTATCGATACATGTGTCATAGGTATCGATACTTTCTACATGCATCTAGTTTGGGAAGA
ATACTAGACAAAAAATATCGATACACATACAAAAAGTATCGATACTTTACGTAAACGTATTTTGT
CATTAAACCAGTATATTTTTACAGCTTACATTATAAATTTACCTATTACTTTAAAGTAATCCGTT
TCGAAGTTTTAAGAATCGATATCCTTCATACAAGTATCGATACTTTATAGGAGCAATTATGGAAA
CTGGTTTTGTCAATTTTGAACCTGTTAAGTTATTTTATATTTAATCGATACCATTACC
Found at i:457785 original size:28 final size:27
Alignment explanation
Indices: 457754--457825 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 27
457744 ATTTTAACCG
*
457754 TTTTGTCAAATTTTAACTAGTTTATAAA
1 TTTTGTCAAATTTTAACTAATTTA-AAA
*
457782 TTTTGTCAAATTTCAACTAATTTAAAA
1 TTTTGTCAAATTTTAACTAATTTAAAA
457809 TTTTGTCAAATTTTAAC
1 TTTTGTCAAATTTTAAC
457826 CGTTTTGTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 19 0.46
28 22 0.54
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.49
Consensus pattern (27 bp):
TTTTGTCAAATTTTAACTAATTTAAAA
Found at i:457851 original size:19 final size:18
Alignment explanation
Indices: 457736--457852 Score: 76
Period size: 19 Copynumber: 6.3 Consensus size: 18
457726 TTTAATCGAT
*
457736 TTTGTCAAATTTTAACCG
1 TTTGTCAAATTTTAACAG
457754 TTTTGTCAAATTTTAACTAG
1 -TTTGTCAAATTTTAAC-AG
* ** *
457774 TTTAT-AAATTTTGTCAA
1 TTTGTCAAATTTTAACAG
* * * *
457791 ATT-TCAACTAATTTAAAAT
1 TTTGTCAA--ATTTTAACAG
*
457810 TTTGTCAAATTTTAACCG
1 TTTGTCAAATTTTAACAG
457828 TTTTGTCAAATTTTAACTAG
1 -TTTGTCAAATTTTAAC-AG
457848 TTTGT
1 TTTGT
457853 GTACAATACT
Statistics
Matches: 74, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
16 1 0.01
17 5 0.07
18 14 0.19
19 48 0.65
20 6 0.08
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (18 bp):
TTTGTCAAATTTTAACAG
Found at i:459102 original size:12 final size:12
Alignment explanation
Indices: 459085--459132 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
459075 TAGTGGAGGC
* *
459085 GAAATTTAAATT
1 GAAATTGAAAAT
459097 GAAATTGAAAAT
1 GAAATTGAAAAT
* *
459109 GAAATTCAACAT
1 GAAATTGAAAAT
459121 GAAATTGAAAAT
1 GAAATTGAAAAT
459133 TACATAAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (12 bp):
GAAATTGAAAAT
Found at i:465618 original size:29 final size:30
Alignment explanation
Indices: 465586--465655 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
465576 TATCTCTTCA
465586 TTTTTTTAATTTATTAAATAT-TTTTATTT
1 TTTTTTTAATTTATTAAATATATTTTATTT
* * *
465615 TTTTCTTAAATTATTAAATATATTTTGTTT
1 TTTTTTTAATTTATTAAATATATTTTATTT
465645 TTTATTTTAAT
1 TTT-TTTTAAT
465656 ATAAACATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 19 0.56
30 10 0.29
31 5 0.15
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (30 bp):
TTTTTTTAATTTATTAAATATATTTTATTT
Found at i:465795 original size:32 final size:31
Alignment explanation
Indices: 465731--465891 Score: 129
Period size: 29 Copynumber: 5.2 Consensus size: 31
465721 ATATATTTAA
* *
465731 ATATTTTATTATTAATTT-AATATAAAAATAT
1 ATATTTTATTCTTATTTTAAAT-TAAAAATAT
*
465762 ATATTTTACTCTTATTTTAAATTAAAAAATATAT
1 ATATTTTATTCTTATTTTAAATT--AAAA-ATAT
* *
465796 AATATTTTATTATTATCTTT-ACTT-AAAA-AT
1 -ATATTTTATTCTTAT-TTTAAATTAAAAATAT
465826 ATATTTTATTCTTATTTTAAATT-AAAA-AT
1 ATATTTTATTCTTATTTTAAATTAAAAATAT
* * *
465855 ATATTTTATTATTATCTTAACTTTTAAAAA-AT
1 ATATTTTATTCTTATTTTAA--ATTAAAAATAT
465887 ATATT
1 ATATT
465892 AAAATATTAT
Statistics
Matches: 109, Mismatches: 11, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
28 3 0.03
29 41 0.38
30 2 0.02
31 19 0.17
32 17 0.16
33 4 0.04
34 4 0.04
35 16 0.15
36 3 0.03
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (31 bp):
ATATTTTATTCTTATTTTAAATTAAAAATAT
Found at i:465823 original size:66 final size:63
Alignment explanation
Indices: 465730--465858 Score: 188
Period size: 64 Copynumber: 2.0 Consensus size: 63
465720 AATATATTTA
465730 AATATTTTATTATTAATTTAATATAAAAATATATATTTTACTCTTATTTTAAATTAAAAAATATA
1 AATATTTTATTATTAATTTAATAT-AAAA-ATATATTTTACTCTTATTTTAAATT-AAAAATATA
465795 T
63 T
* * *
465796 AATATTTTATTATTATCTTTACT-TAAAAATATATTTTATTCTTATTTTAAATTAAAAATATAT
1 AATATTTTATTATTA-ATTTAATATAAAAATATATTTTACTCTTATTTTAAATTAAAAATATAT
465859 TTTATTATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
63 10 0.17
64 24 0.41
65 4 0.07
66 16 0.27
67 5 0.08
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (63 bp):
AATATTTTATTATTAATTTAATATAAAAATATATTTTACTCTTATTTTAAATTAAAAATATAT
Found at i:465918 original size:95 final size:95
Alignment explanation
Indices: 465731--465921 Score: 219
Period size: 95 Copynumber: 2.0 Consensus size: 95
465721 ATATATTTAA
* *
465731 ATATTTTATTATTAATTTAATATAAAAATATATATTTTACTCTTATTTTAAATTAAAAAATATAT
1 ATATTTTATTATTAATTTAATATAAAAATATATATTTTACTATTATCTTAAATTAAAAAATATAT
* * **
465796 AATATTTTATTATTATCTTTACTTAAAAAT
66 AAAATATTATTATTATCTTTAAATAAAAAT
* * * * *
465826 ATATTTTATTCTTATTTTAA-ATTAAAA-ATATATTTTATTATTATCTTAACTTTTAAAAAATAT
1 ATATTTTATTATTAATTTAATATAAAAATATATATTTTACTATTATCTTAA--ATTAAAAAATAT
465889 ATTAAAATATTA-TATATAT-TTTAAATAAAAAT
64 A-TAAAATATTATTAT-TATCTTTAAATAAAAAT
465921 A
1 A
465922 AGATTAAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
93 19 0.23
94 6 0.07
95 45 0.56
96 11 0.14
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (95 bp):
ATATTTTATTATTAATTTAATATAAAAATATATATTTTACTATTATCTTAAATTAAAAAATATAT
AAAATATTATTATTATCTTTAAATAAAAAT
Done.