Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008270.1 Hibiscus syriacus cultivar Beakdansim tig00110927_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: 726180
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:448438 original size:21 final size:21
Alignment explanation
Indices: 448412--448479 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
448402 ATTTTTGTTT
448412 TTATTATTATTATTAAAATTA
1 TTATTATTATTATTAAAATTA
*
448433 TTATTATTATTATTAATATTA
1 TTATTATTATTATTAAAATTA
*
448454 -TATATATTATTATT-AAATAA
1 TTAT-TATTATTATTAAAATTA
448474 TTATTA
1 TTATTA
448480 CAATCCCAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 9 0.21
21 33 0.79
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTATTATTATTAAAATTA
Found at i:448479 original size:3 final size:3
Alignment explanation
Indices: 448412--448468 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
448402 ATTTTTGTTT
** *
448412 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA ATA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
448460 TTA TTA TTA
1 TTA TTA TTA
448469 AATAATTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:450010 original size:24 final size:24
Alignment explanation
Indices: 449963--450008 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
449953 TTTAGCCATA
449963 AATATATATATTTATATAATAAAT
1 AATATATATATTTATATAATAAAT
* *
449987 AATATTTAT-TTTATTTAATAAA
1 AATATATATATTTATATAATAAA
450009 ATCTTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AATATATATATTTATATAATAAAT
Found at i:450172 original size:20 final size:19
Alignment explanation
Indices: 450147--450188 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
450137 CTATTTTATA
450147 AATTATATATTAATTATTTT
1 AATTATATATTAATT-TTTT
* *
450167 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
450186 AAT
1 AAT
450189 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:450175 original size:119 final size:119
Alignment explanation
Indices: 450045--450282 Score: 311
Period size: 120 Copynumber: 2.0 Consensus size: 119
450035 TTTAATCCCG
* * *
450045 TTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGAACAGTCTTAAAACAACTGGATGTCCAT
1 TTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAACAGTCTTAAAACAACTAGAAGT-CAT
* *
450108 TTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATATATTAATTA
65 TTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATATATAAATTA
* * * ** *
450163 TTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCAT
1 TTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAACAGTCTTAAAACAACTAGAAGTCAT
**
450228 TTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATATAAATTA
65 TTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATATAAATTA
450283 ATATATTTTT
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
118 6 0.06
119 29 0.28
120 47 0.46
121 21 0.20
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.45
Consensus pattern (119 bp):
TTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAACAGTCTTAAAACAACTAGAAGTCATT
TTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATATAAATTA
Found at i:452301 original size:2 final size:2
Alignment explanation
Indices: 452294--452329 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
452284 TCTTTTGCTT
452294 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
452330 ATTATTTACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:459157 original size:30 final size:30
Alignment explanation
Indices: 459121--459180 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
459111 TCCGAAGGAC
*
459121 CTATCCAAATATTCCAAAGAACATAGGTAA
1 CTATCCAAATATCCCAAAGAACATAGGTAA
* * * *
459151 CTATCCATATGTCCCGAAGGACATAGGTAA
1 CTATCCAAATATCCCAAAGAACATAGGTAA
459181 ACTGTCCATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (30 bp):
CTATCCAAATATCCCAAAGAACATAGGTAA
Found at i:459192 original size:31 final size:31
Alignment explanation
Indices: 459136--459211 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
459126 CAAATATTCC
*
459136 AAAGAACATAGGT-AACTATCCATATGTCCCG
1 AAAG-ACATAGGTAAACTATCCATATGTCCAG
* * *
459167 AAGGACATAGGTAAACTGTCCATATGTCTAG
1 AAAGACATAGGTAAACTATCCATATGTCCAG
459198 AAAGACATAGGTAA
1 AAAGACATAGGTAA
459212 CCCTCGACTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 8 0.21
31 31 0.79
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (31 bp):
AAAGACATAGGTAAACTATCCATATGTCCAG
Found at i:459710 original size:15 final size:15
Alignment explanation
Indices: 459692--459722 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
459682 GTAATCACAT
459692 ATCCTCACATCAATC
1 ATCCTCACATCAATC
459707 ATCCTCACATCAATC
1 ATCCTCACATCAATC
459722 A
1 A
459723 CATACTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.39, G:0.00, T:0.26
Consensus pattern (15 bp):
ATCCTCACATCAATC
Found at i:460848 original size:18 final size:18
Alignment explanation
Indices: 460825--460861 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
460815 TATTTCCTTA
460825 CTATAAAGACCATTTTGT
1 CTATAAAGACCATTTTGT
460843 CTATAAAGACCATTTTGT
1 CTATAAAGACCATTTTGT
460861 C
1 C
460862 CTTCAATTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (18 bp):
CTATAAAGACCATTTTGT
Found at i:464384 original size:20 final size:20
Alignment explanation
Indices: 464354--464427 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
464344 GCAGCCTTCG
*
464354 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* * **
464374 TGCATCAATGCACTACCTTGA
1 TGCATCGATGCAC-AGCAGGA
*
464395 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGCAGGA
464415 TGCATCGATGCAC
1 TGCATCGATGCAC
464428 TAAGTGCATT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:464495 original size:22 final size:23
Alignment explanation
Indices: 464460--464504 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
464450 GCATGGATGC
464460 ACTGCATGGTGCATCGATGCACT
1 ACTGCATGGTGCATCGATGCACT
*
464483 ACTGCA-GGTGCATGGATGCACT
1 ACTGCATGGTGCATCGATGCACT
464505 GTAGGGATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.24
Consensus pattern (23 bp):
ACTGCATGGTGCATCGATGCACT
Found at i:464517 original size:21 final size:21
Alignment explanation
Indices: 464449--464567 Score: 145
Period size: 21 Copynumber: 5.7 Consensus size: 21
464439 GGTGTTTGAG
*
464449 TGCATGGATGCACTGCATGG-
1 TGCATGGATGCACTGCAGGGA
*
464469 TGCATCGATGCACTACTGCA-GG-
1 TGCATGGATG--C-ACTGCAGGGA
*
464491 TGCATGGATGCACTGTAGGGA
1 TGCATGGATGCACTGCAGGGA
464512 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
464533 TGCATGGATGTACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
464554 TGCATGGAAGCACT
1 TGCATGGATGCACT
464568 TTGAAACCCT
Statistics
Matches: 87, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
19 5 0.06
20 12 0.14
21 52 0.60
22 12 0.14
23 6 0.07
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:464522 original size:63 final size:63
Alignment explanation
Indices: 464449--464567 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
464439 GGTGTTTGAG
* *
464449 TGCATGGATGCACTGCATGG-TGCATCGATGCACTACTGCA-GG-TGCATGGATGCACTGTAGGG
1 TGCATGGATGCACTGCAGGGATGCATCGATG---TACTGCAGGGATGCATGGAAGCACTGTAGGG
464511 A
63 A
*
464512 TGCATGGATGCACTGCAGGGATGCATGGATGTACTGCAGGGATGCATGGAAGCACT
1 TGCATGGATGCACTGCAGGGATGCATCGATGTACTGCAGGGATGCATGGAAGCACT
464568 TTGAAACCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
61 7 0.14
62 2 0.04
63 32 0.64
64 9 0.18
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (63 bp):
TGCATGGATGCACTGCAGGGATGCATCGATGTACTGCAGGGATGCATGGAAGCACTGTAGGGA
Found at i:464668 original size:29 final size:29
Alignment explanation
Indices: 464636--464698 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
464626 GAAACCTTTT
464636 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTGAA-AAATT-AATTAAAGTCCAA
* *
464666 AAATATTTTGTAAAATTAATTAAAGTCCAA
1 AAA-ACTTTGAAAAATTAATTAAAGTCCAA
464696 AAA
1 AAA
464699 CCATTTTGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 19 0.66
31 6 0.21
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAACTTTGAAAAATTAATTAAAGTCCAA
Found at i:465910 original size:22 final size:21
Alignment explanation
Indices: 465885--465947 Score: 56
Period size: 23 Copynumber: 3.0 Consensus size: 21
465875 TTTAAATCAA
465885 AATTTTCTTTTTCAAAACTTT
1 AATTTTCTTTTTCAAAACTTT
* * * *
465906 CAATTTTTATTTTTGAAAGCTCT
1 -AA-TTTTCTTTTTCAAAACTTT
*
465929 AA-TTCCTTTTTCAAAACTT
1 AATTTTCTTTTTCAAAACTT
465948 CATTTTGGCT
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 12 0.39
22 4 0.13
23 15 0.48
ACGTcount: A:0.29, C:0.16, G:0.03, T:0.52
Consensus pattern (21 bp):
AATTTTCTTTTTCAAAACTTT
Found at i:467421 original size:22 final size:23
Alignment explanation
Indices: 467386--467430 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
467376 GCATGGATGC
467386 ACTGCATGGTGCATCGATGCACT
1 ACTGCATGGTGCATCGATGCACT
*
467409 ACTGCA-GGTGCATGGATGCACT
1 ACTGCATGGTGCATCGATGCACT
467431 GTAGGGATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.24
Consensus pattern (23 bp):
ACTGCATGGTGCATCGATGCACT
Found at i:467443 original size:21 final size:20
Alignment explanation
Indices: 467374--467472 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
467364 CGGTGTTTGA
*
467374 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
467394 GTGCATCGATGCACTACTGCA-G
1 GTGCATGGATG--C-ACTGCAGG
*
467416 GTGCATGGATGCACTGTAGG
1 GTGCATGGATGCACTGCAGG
467436 GATGCATGGATGCACTGCAGG
1 G-TGCATGGATGCACTGCAGG
467457 GATGCATGGATGCACT
1 G-TGCATGGATGCACT
467473 TTGAAACCCT
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.07
20 13 0.19
21 34 0.49
22 12 0.17
23 6 0.09
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:467573 original size:29 final size:29
Alignment explanation
Indices: 467541--467603 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
467531 GAAACCTTTT
467541 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTGAA-AAATT-AATTCAAGTCCAA
* *
467571 AAATATTTTGTAAAATTAATTCAAGTCCAA
1 AAA-ACTTTGAAAAATTAATTCAAGTCCAA
467601 AAA
1 AAA
467604 CCATTTTGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 19 0.66
31 6 0.21
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAACTTTGAAAAATTAATTCAAGTCCAA
Found at i:468312 original size:30 final size:31
Alignment explanation
Indices: 468277--468338 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
468267 GAAGGACCTA
* *
468277 TCCATATGTTCCGGAGAACATAGGT-AACTG
1 TCCATATGTCCCGAAGAACATAGGTAAACTG
*
468307 TCCATATGTCCCGAAGGACATAGGTAAACTG
1 TCCATATGTCCCGAAGAACATAGGTAAACTG
468338 T
1 T
468339 ATATATATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTAAACTG
Found at i:472362 original size:23 final size:23
Alignment explanation
Indices: 472309--472362 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
472299 CTGAGTGACA
* *
472309 TATGAGATTTGTCCCGAAGGACC
1 TATGAAATATGTCCCGAAGGACC
**
472332 TACAAAATATGTCCCGAAGGACC
1 TATGAAATATGTCCCGAAGGACC
472355 TATGAAAT
1 TATGAAAT
472363 CCTCGACTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (23 bp):
TATGAAATATGTCCCGAAGGACC
Found at i:477421 original size:21 final size:20
Alignment explanation
Indices: 477335--477492 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
477325 AAATGACCAA
**
477335 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
477354 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
477374 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
477394 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
477415 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
477436 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
477456 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
477477 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
477493 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:477485 original size:20 final size:20
Alignment explanation
Indices: 477460--477652 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
477450 GATTTTCCAG
* ** *
477460 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
477480 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
477500 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
477520 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
477540 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
477560 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
477580 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
477600 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
477621 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
477641 AATCGCAACGCG
1 AATCGCAACGCG
477653 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:478071 original size:33 final size:33
Alignment explanation
Indices: 478032--478102 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
478022 TTCACTTAGA
478032 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
478065 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
478098 TTTCA
1 TTTCA
478103 AGTTAGTATT
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:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:478208 original size:21 final size:20
Alignment explanation
Indices: 478182--478288 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
478172 TGCAGAAGAG
478182 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
478203 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
478223 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
478245 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
478259 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
478278 TCGCAACGAGA
1 TCGCAACGAGA
478289 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:478262 original size:14 final size:14
Alignment explanation
Indices: 478243--478299 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
478233 GAAAAATGAA
478243 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
478257 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
478276 AATCGCAACGAGAG
1 AATCGCAACGAGAG
478290 AATCGCAACG
1 AATCGCAACG
478300 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:478274 original size:33 final size:33
Alignment explanation
Indices: 478236--478315 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
478226 GCAACGAGAA
478236 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
478269 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
478302 AAACCAAAATCGCA
1 AAATGAAAATCGCA
478316 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:478333 original size:19 final size:19
Alignment explanation
Indices: 478311--478438 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
478301 GAAACCAAAA
*
478311 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
478330 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
478344 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
478363 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
478377 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
478397 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
478417 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
478437 TC
1 TC
478439 AAGCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:478352 original size:14 final size:14
Alignment explanation
Indices: 478333--478389 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
478323 TTTCATTTCG
478333 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
478347 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
478366 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
478380 CGTTGCGATT
1 CGTTGCGATT
478390 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:478358 original size:33 final size:33
Alignment explanation
Indices: 478316--478438 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
478306 CAAAATCGCA
478316 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
478349 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
478382 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
478423 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
478439 AAGCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:478400 original size:21 final size:21
Alignment explanation
Indices: 478374--478438 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
478364 CGCGTTGCGA
478374 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
478395 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
478415 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
478436 TTC
1 TTC
478439 AAGCAAAAGA
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:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:480281 original size:93 final size:93
Alignment explanation
Indices: 480122--480437 Score: 623
Period size: 93 Copynumber: 3.4 Consensus size: 93
480112 TAGATTGCTT
*
480122 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
480187 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
480215 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
480280 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
480308 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
480373 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
480401 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
480438 AATACCCTGA
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:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:480572 original size:14 final size:14
Alignment explanation
Indices: 480553--480609 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
480543 CGAAACTTAA
480553 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
480567 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
480586 AATCGCAACGACAG
1 AATCGCAACGAGAG
480600 AATCGCAACG
1 AATCGCAACG
480610 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:480591 original size:19 final size:18
Alignment explanation
Indices: 480567--480658 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
480557 GCAACGAGAG
480567 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
480586 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
480600 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
480619 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
480633 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
480652 AATCGCA
1 AATCGCA
480659 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:480593 original size:33 final size:33
Alignment explanation
Indices: 480535--480658 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
480525 TAGTTTACTT
* * *
480535 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
480569 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
480602 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
480635 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
480659 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:480635 original size:14 final size:14
Alignment explanation
Indices: 480584--480642 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
480574 ACGCGAAATG
480584 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
480598 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
480617 AAAATCGCAACGAC
1 AAAATCGCAACGAC
480631 AAAATCGCAACG
1 AAAATCGCAACG
480643 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:480676 original size:19 final size:19
Alignment explanation
Indices: 480654--480826 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
480644 GAAACCAAAA
*
480654 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
480673 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
480687 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
480706 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
480722 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
480739 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
480758 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
480777 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
480796 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
480816 TCGTGTTGCGA
1 TCGCGTTGCGA
480827 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 17 0.13
16 8 0.06
17 8 0.06
19 81 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:480695 original size:14 final size:14
Alignment explanation
Indices: 480676--480732 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
480666 TTTCATTTCG
480676 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
480690 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
480707 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
480723 CGTTGCGATT
1 CGTTGCGATT
480733 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:480784 original size:38 final size:38
Alignment explanation
Indices: 480654--480826 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
480644 GAAACCAAAA
*
480654 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
480689 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
480722 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
480758 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
480796 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
480827 AAGTAAACTA
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 52 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:482769 original size:14 final size:14
Alignment explanation
Indices: 482750--482785 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
482740 ATTGTTTAAT
482750 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
482764 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
482778 TGATTTGT
1 TGATTTGT
482786 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:482900 original size:19 final size:19
Alignment explanation
Indices: 482876--482963 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
482866 GCATTATGTT
482876 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
482895 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
482912 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
482928 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
482947 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
482964 CTAGATAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 16 0.26
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:482995 original size:53 final size:53
Alignment explanation
Indices: 482876--482978 Score: 181
Period size: 53 Copynumber: 2.0 Consensus size: 53
482866 GCATTATGTT
482876 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
* *
482928 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACTAGATAATCGCAAT
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAAT
482979 TCGATTTTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 19 0.40
53 29 0.60
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (53 bp):
GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:483061 original size:72 final size:69
Alignment explanation
Indices: 482980--483266 Score: 268
Period size: 72 Copynumber: 4.1 Consensus size: 69
482970 AATCGCAATT
482980 CGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGATTTTC-TTTCG--TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
483045 -CGCATTG
62 CCGCATTG
* * * *
483052 CGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-T-TGCATTGCGATTTTCA
1 CGATTTTC-TTTCG--TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCT-CGTTGCGATTTTCA
483113 TTTCCGCATTG
59 TTTCCGCATTG
* *
483124 CGA--TTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 CGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATT
483187 TCCGCATTG
61 TCCGCATTG
* * * *
483196 CGATTTTC-TT-GTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGT
1 CGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGC
*
483259 GTTG
66 ATTG
483263 CGAT
1 CGAT
483267 AGTCAAATGC
Statistics
Matches: 183, Mismatches: 16, Indels: 37
0.78 0.07 0.16
Matches are distributed among these distances:
65 9 0.05
66 3 0.02
67 31 0.17
68 2 0.01
69 8 0.04
70 9 0.05
71 18 0.10
72 89 0.49
73 7 0.04
74 7 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (69 bp):
CGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGC
ATTG
Found at i:483102 original size:105 final size:109
Alignment explanation
Indices: 482980--483247 Score: 421
Period size: 105 Copynumber: 2.5 Consensus size: 109
482970 AATCGCAATT
*
482980 CGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGATTTTCATTTTGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
483045 CGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-TTG
66 CGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTG
483085 CGATTTTCATTTTGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGATTTTCATTTTGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
*
483150 CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTG
66 CGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-ATTG
*
483196 CGATTTTC---TTG--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 CGATTTTCATTTTGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
483248 GTAATTTCCG
Statistics
Matches: 154, Mismatches: 3, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
105 119 0.77
106 14 0.09
107 3 0.02
108 5 0.03
109 2 0.01
111 11 0.07
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (109 bp):
CGATTTTCATTTTGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
CGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTG
Found at i:483262 original size:53 final size:52
Alignment explanation
Indices: 482980--483247 Score: 402
Period size: 53 Copynumber: 5.1 Consensus size: 52
482970 AATCGCAATT
482980 CGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTG
483033 CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTG
*
483085 CGATTTTCATTTTGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTG
*
483138 CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTG
1 CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTG
*
483196 CGATTTTC--TT-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTG
483243 CGATT
1 CGATT
483248 GTAATTTCCG
Statistics
Matches: 203, Mismatches: 5, Indels: 20
0.89 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 61 0.30
53 106 0.52
54 3 0.01
55 3 0.01
56 4 0.02
58 11 0.05
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (52 bp):
CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTG
Found at i:485752 original size:24 final size:24
Alignment explanation
Indices: 485718--485764 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
485708 CTGAAACATC
485718 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
485742 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
485765 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:486484 original size:20 final size:20
Alignment explanation
Indices: 486456--486684 Score: 253
Period size: 20 Copynumber: 11.4 Consensus size: 20
486446 AAATTTCAGT
* * *
486456 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
486476 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
486496 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
486516 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
486536 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
486556 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
486576 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
486596 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
486616 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
486636 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
486656 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
486676 GTTGCGATT
1 GTTGCGATT
486685 CTGGAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:496783 original size:20 final size:21
Alignment explanation
Indices: 496758--496809 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
496748 TTTTCCTAAT
*
496758 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
496778 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
496799 TCGCAATGCGA
1 TCGCAATGCGA
496810 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:496826 original size:20 final size:20
Alignment explanation
Indices: 496798--496932 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
496788 AATTGGGAAA
496798 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
496818 ATCGTAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
496838 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
496859 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
496879 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * * *
496899 TTTGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
496919 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
496933 TTTCAAAGCG
Statistics
Matches: 92, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.04
20 63 0.68
21 23 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:496860 original size:61 final size:61
Alignment explanation
Indices: 496795--496932 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 61
496785 GCGAATTGGG
* * * *
496795 AAAATCGCAATGCGATACTGACTATCGTAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * * *
496856 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTTGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
496917 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
496933 TTTCAAAGCG
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:497128 original size:22 final size:22
Alignment explanation
Indices: 497100--497143 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
497090 CACTCTCTCA
497100 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
497122 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
497144 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:497451 original size:20 final size:20
Alignment explanation
Indices: 497397--497455 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
497387 GCGATTCTCT
**
497397 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
497417 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
497437 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
497456 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:498796 original size:18 final size:18
Alignment explanation
Indices: 498775--498819 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
498765 TCCACTTCGG
*
498775 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
498793 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
498811 GAGCCATCA
1 GAGCCATCA
498820 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:499355 original size:19 final size:20
Alignment explanation
Indices: 499301--499367 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
499291 TAGTTTACTT
* *
499301 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
499321 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
499341 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
499360 TCGCAACG
1 TCGCAACG
499368 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:499394 original size:19 final size:19
Alignment explanation
Indices: 499340--499401 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
499330 GGAAATGGCT
499340 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
499359 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
499373 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
499392 ATCGCAATGC
1 ATCGCAATGC
499402 AATTTGTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 10 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 20 0.56
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:499434 original size:14 final size:14
Alignment explanation
Indices: 499415--499472 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
499405 TTGTGTTTCG
499415 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
499429 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
499445 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
499461 CGTTGCGATTTT
1 CGTTGCGATTTT
499473 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:499479 original size:33 final size:33
Alignment explanation
Indices: 499410--499521 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
499400 GCAATTTGTG
*
499410 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
499442 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* *
499475 TTTCGCATTGCGATTTTGTTGTTGCAATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
499508 TTTTGCATTGCGAT
1 TTTCGCATTGCGAT
499522 AGCCATTTCC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 26 0.35
33 49 0.65
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:499491 original size:19 final size:18
Alignment explanation
Indices: 499431--499490 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 18
499421 GATTTTGTCG
499431 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
*
499449 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
499463 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
499482 TTGCGATTT
1 TTGCGATTT
499491 TGTTGTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 6 0.17
15 3 0.09
16 4 0.11
17 4 0.11
18 12 0.34
19 6 0.17
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.48
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:499540 original size:20 final size:20
Alignment explanation
Indices: 499515--499558 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
499505 TCATTTTGCA
499515 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* *
499535 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGCG
499555 TTGC
1 TTGC
499559 AATTTTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:500024 original size:42 final size:42
Alignment explanation
Indices: 499927--500015 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
499917 GACTCACCTG
* * *
499927 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCTCTA
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
* * *
499969 TCCTCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTC
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
500011 TCATC
1 TCATC
500016 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.44, G:0.13, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
Found at i:501449 original size:14 final size:14
Alignment explanation
Indices: 501430--501465 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
501420 ATTGTTTAAT
501430 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
501444 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
501458 TGATTTGT
1 TGATTTGT
501466 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:501624 original size:19 final size:19
Alignment explanation
Indices: 501602--501650 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
501592 ATCGCAACGA
*
501602 GAAAATCGTAATGCAAAAT
1 GAAAATCGCAATGCAAAAT
*
501621 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCAAAAT
501640 GAAAATCGCAA
1 GAAAATCGCAA
501651 CGAAAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.51, C:0.14, G:0.18, T:0.16
Consensus pattern (19 bp):
GAAAATCGCAATGCAAAAT
Found at i:501701 original size:20 final size:20
Alignment explanation
Indices: 501676--501726 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
501666 GCGATTTTCA
501676 TTTCGCATTGCGATAGCCAG
1 TTTCGCATTGCGATAGCCAG
* *
501696 TTTCGCGTTGCGATAGCCAT
1 TTTCGCATTGCGATAGCCAG
501716 TTTCGCATTGC
1 TTTCGCATTGC
501727 AATTTCCCCG
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:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (20 bp):
TTTCGCATTGCGATAGCCAG
Found at i:501967 original size:20 final size:20
Alignment explanation
Indices: 501942--502053 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
501932 TTTGAAGATG
501942 ATTGCGATTTTCAGAATCTC
1 ATTGCGATTTTCAGAATCTC
***
501962 ATTGCGAAAGTCAGAATCTC
1 ATTGCGATTTTCAGAATCTC
* * **
501982 GTTGCGATTTTGTATTATCTC
1 ATTGCGATTTT-CAGAATCTC
* ** * *
502003 GTTGCGATAGTCAGTATCGC
1 ATTGCGATTTTCAGAATCTC
*
502023 ATTGCGATTTTCCA-AATTCGC
1 ATTGCGATTTT-CAGAA-TCTC
502044 ATTGCGATTT
1 ATTGCGATTT
502054 ACTTATTCGC
Statistics
Matches: 70, Mismatches: 19, Indels: 5
0.74 0.20 0.05
Matches are distributed among these distances:
20 39 0.56
21 31 0.44
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTGCGATTTTCAGAATCTC
Found at i:502063 original size:20 final size:21
Alignment explanation
Indices: 502019--502070 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
502009 ATAGTCAGTA
*
502019 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
502040 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
502060 TCGCATTGCGA
1 TCGCATTGCGA
502071 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:502882 original size:24 final size:24
Alignment explanation
Indices: 502855--502908 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
502845 GTATTCGAAA
*
502855 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATATTGGTCAATACTCGGAC
*
502879 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACTCGGAC
502903 TTTGAT
1 TTTGAT
502909 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCGGAC
Found at i:505445 original size:33 final size:33
Alignment explanation
Indices: 505398--505524 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
505388 GGAAATTACT
505398 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
505431 ATCGTAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
505463 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
505497 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
505525 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:505481 original size:66 final size:66
Alignment explanation
Indices: 505399--505531 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
505389 GAAATTACTA
* *
505399 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
505464 T
66 T
*
505465 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
505530 T
66 T
505531 T
1 T
505532 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:507134 original size:21 final size:21
Alignment explanation
Indices: 507068--507134 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
507058 GTGAATCGGG
*
507068 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
507088 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
507110 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
507131 CTCT
1 CTCT
507135 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:507153 original size:42 final size:41
Alignment explanation
Indices: 507068--507190 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
507058 GTGAATCGGG
* * * *
507068 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
507110 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
507152 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
507191 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:507584 original size:91 final size:90
Alignment explanation
Indices: 507408--507592 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
507398 ATTTCAAACT
*
507408 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
507473 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGAAACCGAATAAATTTAC
*
507501 TTCAACCAAAAGATAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
507565 GTATTGGCAGAAACCGAATAAATTTAC
64 GAATTGGCAGAAACCGAATAAATTTAC
507592 T
1 T
507593 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 41 0.48
93 18 0.21
95 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGAAACCGAATAAATTTAC
Found at i:509352 original size:33 final size:33
Alignment explanation
Indices: 509295--509393 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
509285 ACGAGATAAT
*
509295 GAGAATCGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
509329 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
509362 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
509394 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 48 0.77
34 14 0.23
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:509397 original size:52 final size:52
Alignment explanation
Indices: 509270--509448 Score: 204
Period size: 52 Copynumber: 3.4 Consensus size: 52
509260 TCTTTTGGTT
* * * *
509270 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGCG-GAAAT-GACTATCGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGAGAG-AATCG-C-AACGC
**
509324 --AATGAGAGAATCGCAACGCGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 GAAATGA-A-AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
509376 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
509428 GAAATGAAAATCGCAATGCGA
1 GAAATGAAAATCGCAACGCGA
509449 TTTTGGTTTC
Statistics
Matches: 110, Mismatches: 9, Indels: 14
0.83 0.07 0.11
Matches are distributed among these distances:
52 70 0.64
53 21 0.19
54 19 0.17
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.13
Consensus pattern (52 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:509441 original size:19 final size:19
Alignment explanation
Indices: 509270--509448 Score: 127
Period size: 19 Copynumber: 10.1 Consensus size: 19
509260 TCTTTTGGTT
*
509270 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
509289 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
509309 GGAAATGACTATCGCAA--T
1 -GAAATGAAAATCGCAACGC
*
509327 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
509343 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
509360 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
509376 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
509395 GAAATGAAAATCGCAA--T
1 GAAATGAAAATCGCAACGC
*
509412 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
509428 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
509447 GA
1 GA
509449 TTTTGGTTTC
Statistics
Matches: 125, Mismatches: 18, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
14 28 0.22
15 3 0.02
16 4 0.03
17 4 0.03
18 3 0.02
19 54 0.43
20 27 0.22
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:509477 original size:19 final size:19
Alignment explanation
Indices: 509444--509510 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
509434 AAAATCGCAA
**
509444 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
509463 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
509482 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
509502 TGCGATTTT
1 TGCGATTTT
509511 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:510078 original size:20 final size:20
Alignment explanation
Indices: 510029--510142 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
510019 CGCTATGTAA
* * *
510029 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
510049 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
510069 ATCTCATTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
510090 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
510110 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
510130 ATCGCATTGCGAT
1 ATCGCATTGCGAT
510143 TTTCCCAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.78
21 13 0.16
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:510127 original size:61 final size:61
Alignment explanation
Indices: 510029--510145 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
510019 CGCTATGTAA
* * * *
510029 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCATTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
510090 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
510146 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:510161 original size:61 final size:61
Alignment explanation
Indices: 510029--510163 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
510019 CGCTATGTAA
* * * * ** *
510029 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCATTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
510090 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
510152 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
510164 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:512154 original size:22 final size:21
Alignment explanation
Indices: 512137--512185 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
512127 TGTGTACTTT
512137 TAATCCCAAAATTTTGTATAA
1 TAATCCCAAAATTTTGTATAA
* *
512158 TATTCCCAAAATTTATATATAA
1 TAATCCCAAAATTT-TGTATAA
512180 TTAATC
1 -TAATC
512186 AATTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 6 0.26
23 4 0.17
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (21 bp):
TAATCCCAAAATTTTGTATAA
Found at i:512164 original size:21 final size:22
Alignment explanation
Indices: 512140--512180 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
512130 GTACTTTTAA
*
512140 TCCCAAAATTT-TGTATAATAT
1 TCCCAAAATTTATATATAATAT
512161 TCCCAAAATTTATATATAAT
1 TCCCAAAATTTATATATAAT
512181 TAATCAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.41
Consensus pattern (22 bp):
TCCCAAAATTTATATATAATAT
Found at i:512531 original size:18 final size:19
Alignment explanation
Indices: 512494--512533 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
512484 ATTTTATTTT
**
512494 TTTAATTTTTTAAAGTATA
1 TTTAATTTTTTAAAAAATA
512513 TTTAA-TTTTTAAAAAATA
1 TTTAATTTTTTAAAAAATA
512531 TTT
1 TTT
512534 TTAGGGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTAATTTTTTAAAAAATA
Found at i:513334 original size:28 final size:29
Alignment explanation
Indices: 513289--513372 Score: 143
Period size: 28 Copynumber: 2.9 Consensus size: 29
513279 TCCCAACACA
*
513289 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
513318 TAGGTCG-CATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
513346 TAGGTCGCCATGCACTCCGGGTGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
513373 ACCCTCGTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
28 27 0.52
29 25 0.48
ACGTcount: A:0.13, C:0.35, G:0.31, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:513424 original size:23 final size:23
Alignment explanation
Indices: 513390--513449 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
513380 TTCGGCTGCC
*
513390 CTCGGATTCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
*
513413 CTCGGCTGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
513436 TTCGGATGGCCTCG
1 CTCGGATGCCCTCG
513450 GATGCTCTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.10, C:0.38, G:0.27, T:0.25
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:513462 original size:20 final size:20
Alignment explanation
Indices: 513437--513474 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
513427 CATAGCTCGT
*
513437 TCGGATGGCCTCGGATGCTC
1 TCGGATAGCCTCGGATGCTC
513457 TCGGATAGCCTCGGATGC
1 TCGGATAGCCTCGGATGC
513475 CCAGCGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.29, G:0.34, T:0.24
Consensus pattern (20 bp):
TCGGATAGCCTCGGATGCTC
Found at i:513550 original size:29 final size:29
Alignment explanation
Indices: 513513--513570 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
513503 GCTATCTCTT
513513 GTAGCTCG-CCGGAAAGACATGGCGACCTA
1 GTAGCTCGCCCGG-AAGACATGGCGACCTA
* *
513542 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
513571 CGGCCAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:515326 original size:2 final size:2
Alignment explanation
Indices: 515319--515373 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
515309 AGTTCACAGT
515319 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
515361 GA GA GA GA GA GA G
1 GA GA GA GA GA GA G
515374 CATTCTTAGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:516619 original size:22 final size:22
Alignment explanation
Indices: 516577--516617 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
516567 TTTGAAATTT
*
516577 AAAAATTGTTATATATTTTTAA
1 AAAAATTCTTATATATTTTTAA
516599 AAAAATTC-TATATATTTTT
1 AAAAATTCTTATATATTTTT
516618 TATTGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
AAAAATTCTTATATATTTTTAA
Found at i:516796 original size:34 final size:30
Alignment explanation
Indices: 516766--516826 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
516756 ACAATTTAAG
*
516766 ACAAAATGGTTTTTGGACTTGAATTGAATTT-
1 ACAAAAT-ATTTTTGGACTT-AATTGAATTTA
516797 ACAAAATATTTTTGGACTTAATTGAATTTA
1 ACAAAATATTTTTGGACTTAATTGAATTTA
516827 TTCAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
ACAAAATATTTTTGGACTTAATTGAATTTA
Found at i:516837 original size:29 final size:30
Alignment explanation
Indices: 516766--516826 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 30
516756 ACAATTTAAG
*
516766 ACAAAATGGTTTTTGGACTTGAATTGAATTT
1 ACAAAAT-ATTTTTGGACTTGAATTGAATTT
516797 ACAAAATATTTTTGGACTT-AATTGAATTT
1 ACAAAATATTTTTGGACTTGAATTGAATTT
516826 A
1 A
516827 TTCAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
ACAAAATATTTTTGGACTTGAATTGAATTT
Found at i:517432 original size:34 final size:32
Alignment explanation
Indices: 517392--517461 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
517382 TTTTGTAAAG
* *
517392 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
517426 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
517458 GGGA
1 GGGA
517462 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:520309 original size:34 final size:30
Alignment explanation
Indices: 520271--520339 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
520261 TTGATATAAC
520271 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
520305 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
520334 AATTTA
1 AATTTA
520340 TTCAAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:520350 original size:29 final size:30
Alignment explanation
Indices: 520280--520339 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
520270 CAATTTAAGG
520280 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
520311 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
520340 TTCAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:520530 original size:20 final size:20
Alignment explanation
Indices: 520505--520577 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
520495 ATACACTTAG
520505 TGCATCGATGCATCCTTCCA
1 TGCATCGATGCATCCTTCCA
520525 TGCATCGATGCATCCTGT-CA
1 TGCATCGATGCATCCT-TCCA
*
520545 TGCATCGATGCATCCTGCCA
1 TGCATCGATGCATCCTTCCA
*
520565 TGCATCCATGCAT
1 TGCATCGATGCAT
520578 AAAGGCTGCA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 48 0.98
21 1 0.02
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.29
Consensus pattern (20 bp):
TGCATCGATGCATCCTTCCA
Found at i:521733 original size:16 final size:17
Alignment explanation
Indices: 521699--521734 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
521689 CTTCTTCTTA
*
521699 TTTCTAGTTTTATATTT
1 TTTCAAGTTTTATATTT
521716 TTTCAAGTTTTA-ATTT
1 TTTCAAGTTTTATATTT
521732 TTT
1 TTT
521735 GATTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTCAAGTTTTATATTT
Found at i:528610 original size:20 final size:20
Alignment explanation
Indices: 528585--528622 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
528575 TTTTGGTGCA
*
528585 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
528605 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
528623 TTTGAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:528663 original size:19 final size:19
Alignment explanation
Indices: 528587--528669 Score: 55
Period size: 19 Copynumber: 4.2 Consensus size: 19
528577 TTGGTGCAGA
528587 GGGAATCGATACCCCC-ATG
1 GGGAATCGATACCCCCTA-G
* *
528606 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAATCGATACCCCC--T--AG
*
528630 GGGAA-CTGATTCCCCCTAG
1 GGGAATC-GATACCCCCTAG
528649 GGGAATCGATACCCCCT-G
1 GGGAATCGATACCCCCTAG
528667 GGG
1 GGG
528670 TTCTGGATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
18 4 0.08
19 16 0.30
20 15 0.28
21 1 0.02
22 1 0.02
23 14 0.26
24 1 0.02
25 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.29, T:0.18
Consensus pattern (19 bp):
GGGAATCGATACCCCCTAG
Found at i:539955 original size:41 final size:42
Alignment explanation
Indices: 539847--539955 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
539837 TTTTGCGGCA
* * * * *
539847 TTTGTGAGTAAAAACACCATTGTATACTTAATTATTAGTAGTG
1 TTTGTGA-TAAAAACGCCACTATATACATAATTATTAGTAGCG
*
539890 TTTGTGAGAAAAACGCCACTATATACATAATTATTAGT-GACG
1 TTTGTGATAAAAACGCCACTATATACATAATTATTAGTAG-CG
539932 TTTGT-ATAAAAACGCCACTATATA
1 TTTGTGATAAAAACGCCACTATATA
539956 TCATCACAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 19 0.33
42 32 0.55
43 7 0.12
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (42 bp):
TTTGTGATAAAAACGCCACTATATACATAATTATTAGTAGCG
Found at i:540588 original size:2 final size:2
Alignment explanation
Indices: 540581--540611 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
540571 TTATTATTAT
540581 TA TA TA 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
540612 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:540616 original size:2 final size:2
Alignment explanation
Indices: 540611--540639 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
540601 TATATATATA
540611 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
540640 ATTTTATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:540755 original size:23 final size:23
Alignment explanation
Indices: 540712--540755 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
540702 TTGGAAAATA
**
540712 TTGAGGATCCCTGTGGATATTTT
1 TTGAGGATCCCCATGGATATTTT
*
540735 TTGAGGATCCCCATGGTTATT
1 TTGAGGATCCCCATGGATATT
540756 CACACGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (23 bp):
TTGAGGATCCCCATGGATATTTT
Found at i:541445 original size:119 final size:119
Alignment explanation
Indices: 541232--541471 Score: 437
Period size: 119 Copynumber: 2.0 Consensus size: 119
541222 GAACTAGAAC
541232 AAGGTTTAATATGATTACGCTAATTTTAAAAATGATTTAAATTACATATTTTACAAATAAAAAAT
1 AAGGTTTAATATGATTACGCTAATTTTAAAAATGATTTAAATTACATATTTTACAAATAAAAAAT
*
541297 TAATAATGCATAAATAAAGTTTTTAGCTTTTCCTTTCTTTATTGTGCACATGAT
66 TAATAATGCATAAATAAAGTTTTTAGCTTTTCCTTTCTTTATTGTGCACACGAT
541351 AAGGTTTAATATGATTACGCTAA-TTTAAAAATGATTTAAATTACATATTTTACAAATAAAAAAA
1 AAGGTTTAATATGATTACGCTAATTTTAAAAATGATTTAAATTACATATTTTACAAAT-AAAAAA
* *
541415 TTGATAATGCATAAATAAAGTTTTTTGCTTTTCCTTTCTTTATTGTGCACACGAT
65 TTAATAATGCATAAATAAAGTTTTTAGCTTTTCCTTTCTTTATTGTGCACACGAT
541470 AA
1 AA
541472 AATGCATATT
Statistics
Matches: 117, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
118 34 0.29
119 83 0.71
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.41
Consensus pattern (119 bp):
AAGGTTTAATATGATTACGCTAATTTTAAAAATGATTTAAATTACATATTTTACAAATAAAAAAT
TAATAATGCATAAATAAAGTTTTTAGCTTTTCCTTTCTTTATTGTGCACACGAT
Found at i:542089 original size:17 final size:19
Alignment explanation
Indices: 542056--542094 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
542046 ATATATAACT
542056 TATAGAACATTAAATA-TAA
1 TATAGAACA-TAAATATTAA
542075 TATAGAACA-AAATATTAA
1 TATAGAACATAAATATTAA
542093 TA
1 TA
542095 ATACAGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
TATAGAACATAAATATTAA
Found at i:542643 original size:24 final size:24
Alignment explanation
Indices: 542605--542674 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
542595 CAAATCAGAG
* *
542605 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
542629 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
542653 TCCATGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
542675 CTATTTATAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:542674 original size:48 final size:47
Alignment explanation
Indices: 542580--542674 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 47
542570 ATTAAAACAT
* * * ** *
542580 AATTTAGGTCAAGTACAAATCAGAGTCCATGTCAAGTATCATATAAA
1 AATTCAGGTCAAATACAAATCAGAATCCATGTCAAAAATCAGATAAA
*
542627 AATTCAGGTCAAATATCATATCAGAATCCATGTCAAAAATCAGATAAA
1 AATTCAGGTCAAATA-CAAATCAGAATCCATGTCAAAAATCAGATAAA
542675 CTATTTATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 13 0.32
48 27 0.68
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (47 bp):
AATTCAGGTCAAATACAAATCAGAATCCATGTCAAAAATCAGATAAA
Found at i:543408 original size:29 final size:29
Alignment explanation
Indices: 543350--543503 Score: 163
Period size: 29 Copynumber: 5.3 Consensus size: 29
543340 CGTTTTACAG
** * *
543350 AAATAGCACCCTTTTTAAAATAAA-TACCA
1 AAATAGCA-CCTTTTCGAATTAAATTCCCA
*
543379 AAATAGCACCTTTTCGAATTAAAGTCCCA
1 AAATAGCACCTTTTCGAATTAAATTCCCA
* *
543408 AAATAACA-CTTTTTGAATTAAATTCCCA
1 AAATAGCACCTTTTCGAATTAAATTCCCA
* *
543436 AAATATCA-CTTTTCTGAATTAAATTCTCA
1 AAATAGCACCTTTTC-GAATTAAATTCCCA
543465 AAATAGCACCTTTTCTGAA-TAAATTCCCA
1 AAATAGCACCTTTTC-GAATTAAATTCCCA
*
543494 AAATATCACC
1 AAATAGCACC
543504 AAAATTGAAT
Statistics
Matches: 109, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
28 42 0.39
29 57 0.52
30 10 0.09
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (29 bp):
AAATAGCACCTTTTCGAATTAAATTCCCA
Found at i:543467 original size:57 final size:57
Alignment explanation
Indices: 543368--543502 Score: 177
Period size: 57 Copynumber: 2.4 Consensus size: 57
543358 CCCTTTTTAA
* *
543368 AATAAA-TACCAAAATAGCACCTTTTCGAATTAAAGTCCCAAAATAACA-CTTTT-TG
1 AATAAATTCCCAAAATATCA-CTTTTCGAATTAAAGTCCCAAAATAACACCTTTTCTG
* * *
543423 AATTAAATTCCCAAAATATCACTTTTCTGAATTAAATTCTCAAAATAGCACCTTTTCTG
1 AA-TAAATTCCCAAAATATCACTTTTC-GAATTAAAGTCCCAAAATAACACCTTTTCTG
543482 AATAAATTCCCAAAATATCAC
1 AATAAATTCCCAAAATATCAC
543503 CAAAATTGAA
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
55 2 0.03
56 10 0.14
57 30 0.43
58 24 0.34
59 4 0.06
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (57 bp):
AATAAATTCCCAAAATATCACTTTTCGAATTAAAGTCCCAAAATAACACCTTTTCTG
Found at i:543512 original size:29 final size:29
Alignment explanation
Indices: 543480--543561 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
543470 GCACCTTTTC
* *
543480 TGAATAAATTCCCAAAATATCACCAAAAT
1 TGAATTAATTCCCAGAATATCACCAAAAT
543509 TGAATTAATTCCCAGAATATCACCAAAAT
1 TGAATTAATTCCCAGAATATCACCAAAAT
543538 TGAATTAATTCCCAGAATATCACC
1 TGAATTAATTCCCAGAATATCACC
543562 GGTCAACGGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.27
Consensus pattern (29 bp):
TGAATTAATTCCCAGAATATCACCAAAAT
Found at i:543519 original size:58 final size:57
Alignment explanation
Indices: 543394--543516 Score: 142
Period size: 58 Copynumber: 2.1 Consensus size: 57
543384 GCACCTTTTC
* * ***
543394 GAATTAAAGTCCCAAAATAACACTTTTTGAATTAAATTCCCAAAATATCACTTTTCT
1 GAATTAAATTCTCAAAATAACACTTTTTGAATTAAATTCCCAAAATATCACAAATCT
*
543451 GAATTAAATTCTCAAAATAGCACCTTTTCTGAA-TAAATTCCCAAAATATCACCAAAAT-T
1 GAATTAAATTCTCAAAATAACA-CTTTT-TGAATTAAATTCCCAAAATATCA-C-AAATCT
543510 GAATTAA
1 GAATTAA
543517 TTCCCAGAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
57 19 0.34
58 23 0.41
59 13 0.23
60 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.33
Consensus pattern (57 bp):
GAATTAAATTCTCAAAATAACACTTTTTGAATTAAATTCCCAAAATATCACAAATCT
Found at i:543584 original size:17 final size:17
Alignment explanation
Indices: 543562--543594 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
543552 GAATATCACC
543562 GGTCAACGGTCGGGTCT
1 GGTCAACGGTCGGGTCT
543579 GGTCAACGGTCGGGTC
1 GGTCAACGGTCGGGTC
543595 AAAACCGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.24, G:0.42, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCT
Found at i:549873 original size:24 final size:24
Alignment explanation
Indices: 549835--549904 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
549825 CAAATCAGAG
* *
549835 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
549859 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
549883 TCCATGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
549905 CTATTTATAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:549904 original size:48 final size:47
Alignment explanation
Indices: 549810--549904 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 47
549800 ATTAAAACAT
* * ** *
549810 AATTCAGGTCAAGTACAAATCAGAGTCCATGTCAAGTATCATATAAA
1 AATTCAGGTCAAATACAAATCAGAATCCATGTCAAAAATCAGATAAA
*
549857 AATTCAGGTCAAATATCATATCAGAATCCATGTCAAAAATCAGATAAA
1 AATTCAGGTCAAATA-CAAATCAGAATCCATGTCAAAAATCAGATAAA
549905 CTATTTATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
47 14 0.34
48 27 0.66
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (47 bp):
AATTCAGGTCAAATACAAATCAGAATCCATGTCAAAAATCAGATAAA
Found at i:550680 original size:28 final size:29
Alignment explanation
Indices: 550622--550692 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 29
550612 TTTTTAAAAC
*
550622 AATTACCAAAATAGCACCTTTTCGAATTA
1 AATTCCCAAAATAGCACCTTTTCGAATTA
*
550651 AATTCCCAAAATAGCA-TTTTTCGAATTA
1 AATTCCCAAAATAGCACCTTTTCGAATTA
550679 AATTCCCAAAATAG
1 AATTCCCAAAATAG
550693 AAAATAGCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 25 0.62
29 15 0.38
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (29 bp):
AATTCCCAAAATAGCACCTTTTCGAATTA
Found at i:550718 original size:37 final size:35
Alignment explanation
Indices: 550658--550728 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 35
550648 TTAAATTCCC
*
550658 AAAATAGCATTTTTCGAATTAAATTCCCAAAATAG
1 AAAATAGCATTTTTCGAATTAAATTCCAAAAATAG
550693 AAAATAGCACCTTTTTCTGAA-TAAATTCCAAAAATA
1 AAAATAGCA--TTTTTC-GAATTAAATTCCAAAAATA
550729 TCACCAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 9 0.28
37 20 0.62
38 3 0.09
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAATAGCATTTTTCGAATTAAATTCCAAAAATAG
Found at i:550742 original size:29 final size:29
Alignment explanation
Indices: 550710--550791 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
550700 CACCTTTTTC
* *
550710 TGAATAAATTCCAAAAATATCACCAAAAT
1 TGAATTAATTCCAAGAATATCACCAAAAT
*
550739 TGAATTAATT-CACTGAATATCACCAAAAT
1 TGAATTAATTCCA-AGAATATCACCAAAAT
** *
550768 CAAATTAATTCCCAGAATATCACC
1 TGAATTAATTCCAAGAATATCACC
550792 GGTCAACTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 2 0.05
29 41 0.93
30 1 0.02
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.27
Consensus pattern (29 bp):
TGAATTAATTCCAAGAATATCACCAAAAT
Found at i:550814 original size:17 final size:17
Alignment explanation
Indices: 550792--550831 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
550782 GAATATCACC
*
550792 GGTCAACTGTCGGGTCG
1 GGTCAACGGTCGGGTCG
550809 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
550826 GGTCAA
1 GGTCAA
550832 AACCGGTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.23, G:0.42, T:0.20
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:551715 original size:6 final size:6
Alignment explanation
Indices: 551706--551731 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
551696 AAAGGGAGAA
551706 GGTAGG GGTAGG GGTAGG GGTAGG GG
1 GGTAGG GGTAGG GGTAGG GGTAGG GG
551732 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.69, T:0.15
Consensus pattern (6 bp):
GGTAGG
Found at i:551759 original size:14 final size:16
Alignment explanation
Indices: 551736--551768 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
551726 TAGGGGAATT
551736 TTTTTAAAAATA-ATA
1 TTTTTAAAAATATATA
551751 TTTTTAAAATATATATA
1 TTTTTAAAA-ATATATA
551768 T
1 T
551769 ATATATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.56
16 3 0.19
17 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTTAAAAATATATA
Found at i:556862 original size:18 final size:18
Alignment explanation
Indices: 556839--556873 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
556829 ACTGAATATT
556839 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
556857 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
556874 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:560955 original size:21 final size:21
Alignment explanation
Indices: 560929--560984 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
560919 CTTTGTCTAA
560929 TAATTCTTGTAATTATATCTT
1 TAATTCTTGTAATTATATCTT
560950 TAATTCTTGTAATTATATCTT
1 TAATTCTTGTAATTATATCTT
560971 TAATTCTTGTAATT
1 TAATTCTTGTAATT
560985 CTTTTGGAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.05, T:0.57
Consensus pattern (21 bp):
TAATTCTTGTAATTATATCTT
Found at i:563874 original size:2 final size:2
Alignment explanation
Indices: 563869--563911 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
563859 TCACACAATA
563869 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
563911 A
1 A
563912 ATGTACATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.