Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 29
Found at i:406950 original size:3 final size:3
Alignment explanation
Indices: 406942--406981 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
406932 CCAAAAACAT
406942 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
406982 CCCAGATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:412127 original size:29 final size:29
Alignment explanation
Indices: 412095--412153 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
412085 ATCTTATTGT
412095 TAAGATGCTTTGACTTTGTCTTTATATCA
1 TAAGATGCTTTGACTTTGTCTTTATATCA
*
412124 TAAGATGCTTTGACTTTTTCTTTATATCA
1 TAAGATGCTTTGACTTTGTCTTTATATCA
412153 T
1 T
412154 CTCTATGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (29 bp):
TAAGATGCTTTGACTTTGTCTTTATATCA
Found at i:412397 original size:21 final size:21
Alignment explanation
Indices: 412370--412422 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
412360 AATCCAAATA
*
412370 TCAATCCTTTTTAAGAAGTGG
1 TCAATCCTTTTTAAGAAATGG
*
412391 TCGATCCTTTTTAAGAAATGG
1 TCAATCCTTTTTAAGAAATGG
412412 TCAATCCTTTT
1 TCAATCCTTTT
412423 AGCCAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (21 bp):
TCAATCCTTTTTAAGAAATGG
Found at i:413373 original size:22 final size:23
Alignment explanation
Indices: 413304--413374 Score: 69
Period size: 22 Copynumber: 3.1 Consensus size: 23
413294 TGGTAAAAGC
413304 AGAGAGATAATT-GAAAAAGTAT
1 AGAGAGATAATTAGAAAAAGTAT
* *
413326 AAAGAGATAAGCATTAGTAAAA--AT
1 AGAGAGAT-A--ATTAGAAAAAGTAT
413350 AGAGAGATAATTAG-AAAAGTAT
1 AGAGAGATAATTAGAAAAAGTAT
413372 AGA
1 AGA
413375 AGGATGAGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
20 4 0.10
21 5 0.12
22 12 0.30
23 2 0.05
24 9 0.22
25 3 0.08
26 5 0.12
ACGTcount: A:0.56, C:0.01, G:0.21, T:0.21
Consensus pattern (23 bp):
AGAGAGATAATTAGAAAAAGTAT
Found at i:413854 original size:2 final size:2
Alignment explanation
Indices: 413847--413888 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
413837 AAATATTTGA
413847 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
413889 TAAAGTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:416636 original size:64 final size:65
Alignment explanation
Indices: 416490--416616 Score: 186
Period size: 64 Copynumber: 2.0 Consensus size: 65
416480 CGAATGCATT
* ** *
416490 CCATGCACCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCATTTGATGCATCGATGCACAA
1 CCATGCACCGATGCA-TCAGGCTATTTTTCAAAACATCGAATGCATTTCATGCATCGATGCACAA
416554 G
65 G
*
416555 CCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTTCATGCATCGATGCACA
1 CCATGCACCGATGCATCAGGCTATTTTTCAAAACATCGAATGCATTTCATGCATCGATGCACA
416617 CTTGGTGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
64 37 0.66
65 19 0.34
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (65 bp):
CCATGCACCGATGCATCAGGCTATTTTTCAAAACATCGAATGCATTTCATGCATCGATGCACAAG
Found at i:422434 original size:20 final size:21
Alignment explanation
Indices: 422405--422460 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
422395 TTTGTGCTTC
*
422405 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
422425 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
422447 ATGCATCGATGCAT
1 ATGCATCGATGCAT
422461 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:425063 original size:19 final size:19
Alignment explanation
Indices: 425039--425077 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
425029 TCGAATGCAT
425039 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
425058 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
425077 T
1 T
425078 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:425094 original size:65 final size:63
Alignment explanation
Indices: 425025--425184 Score: 212
Period size: 65 Copynumber: 2.5 Consensus size: 63
425015 GAATTAATTG
* * *** *
425025 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGAATATTTTC-A
* * **
425090 AACATTGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTCA
425153 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
425185 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 31 0.37
64 10 0.12
65 42 0.51
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTCA
Found at i:432363 original size:21 final size:23
Alignment explanation
Indices: 432339--432389 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
432329 AGGGAATCGA
432339 TCCCCCCTT-AA-AGGAACCAAT
1 TCCCCCCTTGAAGAGGAACCAAT
* * *
432360 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCTTGAAGAGGAACCAAT
432383 TCCCCCC
1 TCCCCCC
432390 ACAGGGGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 8 0.33
22 2 0.08
23 14 0.58
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.20
Consensus pattern (23 bp):
TCCCCCCTTGAAGAGGAACCAAT
Found at i:432415 original size:20 final size:21
Alignment explanation
Indices: 432371--432410 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
432361 CCCCCTTTGA
*
432371 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
432392 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
432411 TAGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:434696 original size:34 final size:34
Alignment explanation
Indices: 434657--434741 Score: 170
Period size: 34 Copynumber: 2.5 Consensus size: 34
434647 AACAAAAAGG
434657 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
1 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
434691 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
1 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
434725 GGGAGAAGTGTTAAAGT
1 GGGAGAAGTGTTAAAGT
434742 AAGGGGGGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (34 bp):
GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
Found at i:442914 original size:29 final size:29
Alignment explanation
Indices: 442874--442933 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
442864 AATTTTCACC
442874 AAACTAAATTGATGTAAGCAATGACATCA
1 AAACTAAATTGATGTAAGCAATGACATCA
442903 AAACTAAATTGATGTAAGCAATGACATCA
1 AAACTAAATTGATGTAAGCAATGACATCA
442932 AA
1 AA
442934 TTAATTTAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.23
Consensus pattern (29 bp):
AAACTAAATTGATGTAAGCAATGACATCA
Found at i:447602 original size:29 final size:29
Alignment explanation
Indices: 447562--447621 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
447552 AATTTTCACC
447562 AAACTAAATTGATGTAAGCAATGACATCA
1 AAACTAAATTGATGTAAGCAATGACATCA
447591 AAACTAAATTGATGTAAGCAATGACATCA
1 AAACTAAATTGATGTAAGCAATGACATCA
447620 AA
1 AA
447622 TTAATTTAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.23
Consensus pattern (29 bp):
AAACTAAATTGATGTAAGCAATGACATCA
Found at i:448275 original size:24 final size:24
Alignment explanation
Indices: 448243--448294 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
448233 GCCTCTACCT
*
448243 CTATTACTATAAGTGAACCCAATA
1 CTATTACTACAAGTGAACCCAATA
*
448267 CTATTACTACAAGTGAACCCAGTA
1 CTATTACTACAAGTGAACCCAATA
448291 CTAT
1 CTAT
448295 CACTGCGAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (24 bp):
CTATTACTACAAGTGAACCCAATA
Found at i:457429 original size:2 final size:2
Alignment explanation
Indices: 457395--457420 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
457385 TATATTTTGA
457395 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
457421 TTGTATATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:458096 original size:18 final size:18
Alignment explanation
Indices: 458073--458110 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
458063 GTTAGAGATG
*
458073 TTTATACCTTATGAAACA
1 TTTATACCCTATGAAACA
*
458091 TTTATACCCTATTAAACA
1 TTTATACCCTATGAAACA
458109 TT
1 TT
458111 AGGAATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (18 bp):
TTTATACCCTATGAAACA
Found at i:459357 original size:19 final size:19
Alignment explanation
Indices: 459333--459381 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
459323 TTATATGTAT
459333 ATGTGATATGTTTAACATG
1 ATGTGATATGTTTAACATG
459352 ATGTGATATGTTTAACATG
1 ATGTGATATGTTTAACATG
* *
459371 TTGTTATATGT
1 ATGTGATATGT
459382 GTTGTGTGAT
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:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (19 bp):
ATGTGATATGTTTAACATG
Found at i:460734 original size:11 final size:11
Alignment explanation
Indices: 460720--460762 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
460710 ATTTTATGAA
460720 AGTACTGTAGT
1 AGTACTGTAGT
**
460731 AGTACTGTAAC
1 AGTACTGTAGT
*
460742 AGTATTGTAGT
1 AGTACTGTAGT
460753 AGTACTGTAG
1 AGTACTGTAG
460763 CAGGGAATCG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (11 bp):
AGTACTGTAGT
Found at i:460750 original size:22 final size:22
Alignment explanation
Indices: 460720--460761 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
460710 ATTTTATGAA
460720 AGTACTGTAGTAGTACTGTAAC
1 AGTACTGTAGTAGTACTGTAAC
*
460742 AGTATTGTAGTAGTACTGTA
1 AGTACTGTAGTAGTACTGTA
460762 GCAGGGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.36
Consensus pattern (22 bp):
AGTACTGTAGTAGTACTGTAAC
Found at i:462571 original size:21 final size:21
Alignment explanation
Indices: 462547--462586 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
462537 TTTTCAAAGG
462547 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
462568 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
462587 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:462636 original size:19 final size:19
Alignment explanation
Indices: 462612--462650 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
462602 TCGAATGCAT
462612 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
* *
462631 TCCATGTATCGATGCACTC
1 TCCATGCACCGATGCACTC
462650 T
1 T
462651 GCTTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.15, T:0.28
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:462674 original size:64 final size:64
Alignment explanation
Indices: 462592--462759 Score: 189
Period size: 64 Copynumber: 2.6 Consensus size: 64
462582 TCAATGAATA
* * * *
462592 AATTGAAACATCGAATGCATTCCATGCACCGATGCACTCTCCATGTATCGATGCACTC-TGCT-T
1 AATTAAAACATCGAATGCATT-CATGCATCGATGCACTCTCCATGCATCGATGCAC-CAGGCTAT
462655 T
64 T
* **
462656 AATTAAAACATCGAATGCATTTGATGCATCGATGCACAATCCATGCATCGATGCACCAGGCTATT
1 AATTAAAACATCGAATGCA-TTCATGCATCGATGCACTCTCCATGCATCGATGCACCAGGCTATT
* * *
462721 -TTTCAAACATCGAATGCACTTCATGCATTGATGCACTCT
1 AATTAAAACATCGAATGCA-TTCATGCATCGATGCACTCT
462760 TAGTGCACCG
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 1 0.01
64 82 0.94
65 4 0.05
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (64 bp):
AATTAAAACATCGAATGCATTCATGCATCGATGCACTCTCCATGCATCGATGCACCAGGCTATT
Found at i:468603 original size:23 final size:20
Alignment explanation
Indices: 468552--468611 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
468542 TTTAGTGCTG
*
468552 AGGGAATCGATTCCCCCTTT
1 AGGGAACCGATTCCCCCTTT
*
468572 AGGGAACCGATTCTCCCTTT
1 AGGGAACCGATTCCCCCTTT
468592 GAAGGGGAACCGATTCCCCC
1 --A-GGGAACCGATTCCCCC
468612 CATAGGGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 15 0.44
ACGTcount: A:0.22, C:0.32, G:0.23, T:0.23
Consensus pattern (20 bp):
AGGGAACCGATTCCCCCTTT
Found at i:468618 original size:21 final size:21
Alignment explanation
Indices: 468553--468654 Score: 98
Period size: 21 Copynumber: 4.8 Consensus size: 21
468543 TTAGTGCTGA
**
468553 GGGAATCGATTCCCCCTTTA-
1 GGGAATCGATTCCCCCCATAG
* * **
468573 GGGAACCGATTCTCCCTTTGAAG
1 GGGAATCGATTCCCCCCAT--AG
*
468596 GGGAACCGATTCCCCCCATAG
1 GGGAATCGATTCCCCCCATAG
*
468617 GGGAATCGATACCCCCCATAG
1 GGGAATCGATTCCCCCCATAG
*
468638 GGGAATCGATACCCCCC
1 GGGAATCGATTCCCCCC
468655 TGGGGTTCTG
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
20 17 0.24
21 38 0.53
22 1 0.01
23 16 0.22
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.20
Consensus pattern (21 bp):
GGGAATCGATTCCCCCCATAG
Found at i:477727 original size:19 final size:19
Alignment explanation
Indices: 477705--477752 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
477695 TATGTGTGTG
477705 TGTGATATGTTTAACATGT
1 TGTGATATGTTTAACATGT
477724 TGTGATATGTTTAACATGT
1 TGTGATATGTTTAACATGT
*
477743 TGTTATATGT
1 TGTGATATGT
477753 GTTGTGTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.50
Consensus pattern (19 bp):
TGTGATATGTTTAACATGT
Found at i:483292 original size:11 final size:11
Alignment explanation
Indices: 483276--483338 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
483266 GTATTATAAA
483276 ATTTTTAATAT
1 ATTTTTAATAT
483287 ATTTTTAA-A-
1 ATTTTTAATAT
483296 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
483307 ATCAATAATGT
1 ATTTTTAATAT
*
483318 ATTTTTACTAT
1 ATTTTTAATAT
483329 ATTTTTAATA
1 ATTTTTAATA
483339 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 8 0.21
11 26 0.67
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:483321 original size:22 final size:25
Alignment explanation
Indices: 483295--483349 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
483285 ATATTTTTAA
483295 AATTTTA-TA-ATTATCAATAATGT
1 AATTTTACTATATTATCAATAATGT
* * *
483318 ATTTTTACTATATTTTTAATAATGT
1 AATTTTACTATATTATCAATAATGT
483343 AATTTTA
1 AATTTTA
483350 AAAAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 6 0.23
24 2 0.08
25 18 0.69
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (25 bp):
AATTTTACTATATTATCAATAATGT
Found at i:483357 original size:25 final size:25
Alignment explanation
Indices: 483310--483357 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
483300 TATAATTATC
* ** *
483310 AATAATGTATTTTTACTATATTTTT
1 AATAATGTAATTTTAAAAAATTTTT
483335 AATAATGTAATTTTAAAAAATTT
1 AATAATGTAATTTTAAAAAATTT
483358 AAAATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (25 bp):
AATAATGTAATTTTAAAAAATTTTT
Found at i:486561 original size:2 final size:2
Alignment explanation
Indices: 486550--486585 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
486540 CACATGTTTA
486550 AT AT AT -T 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 A
486586 ATTTAAGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:490839 original size:23 final size:24
Alignment explanation
Indices: 490813--490888 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 24
490803 ACTTATCAAG
490813 ATAAAATATGAAT-TAT-TAATGTA
1 ATAAAATAT-AATATATATAATGTA
*
490836 ATAAAATCTATACTATATATAATGTA
1 ATAAAA--TATAATATATATAATGTA
* *
490862 ATAAAATCTATACTATATACAATGTA
1 ATAAAA--TATAATATATATAATGTA
490888 A
1 A
490889 ATACACGTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.13
24 2 0.04
25 6 0.13
26 33 0.70
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (24 bp):
ATAAAATATAATATATATAATGTA
Found at i:490861 original size:26 final size:26
Alignment explanation
Indices: 490829--490888 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
490819 TATGAATTAT
490829 TAATGTAATAAAATCTATACTATATA
1 TAATGTAATAAAATCTATACTATATA
490855 TAATGTAATAAAATCTATACTATATA
1 TAATGTAATAAAATCTATACTATATA
*
490881 CAATGTAA
1 TAATGTAA
490889 ATACACGTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (26 bp):
TAATGTAATAAAATCTATACTATATA
Found at i:498336 original size:18 final size:18
Alignment explanation
Indices: 498301--498358 Score: 98
Period size: 18 Copynumber: 3.1 Consensus size: 18
498291 CACGGAATGT
498301 AAGATTACCAGTGGGAATAA
1 AAGATTACCA--GGGAATAA
498321 AAGATTACCAGGGAATAA
1 AAGATTACCAGGGAATAA
498339 AAGATTACCAGGGAATAA
1 AAGATTACCAGGGAATAA
498357 AA
1 AA
498359 TTACTGGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 28 0.74
20 10 0.26
ACGTcount: A:0.50, C:0.10, G:0.22, T:0.17
Consensus pattern (18 bp):
AAGATTACCAGGGAATAA
Found at i:503450 original size:7 final size:7
Alignment explanation
Indices: 503438--503463 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
503428 AATTTGGTTT
503438 GTGTATA
1 GTGTATA
503445 GTGTATA
1 GTGTATA
503452 GTGTATA
1 GTGTATA
503459 GTGTA
1 GTGTA
503464 GAATTGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (7 bp):
GTGTATA
Found at i:504336 original size:20 final size:20
Alignment explanation
Indices: 504313--504466 Score: 247
Period size: 20 Copynumber: 7.7 Consensus size: 20
504303 CGCGAACACA
504313 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
504333 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
504353 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
504373 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
504393 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
504413 TAAATCGCAACG-ATAATCAG
1 TAAATCGCAACGCGT-ATCCG
504433 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
504453 TAAATCGCAACGCG
1 TAAATCGCAACGCG
504467 ATTTTTAAAG
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 1 0.01
20 120 0.98
21 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:504338 original size:40 final size:39
Alignment explanation
Indices: 504275--504467 Score: 224
Period size: 40 Copynumber: 4.8 Consensus size: 39
504265 GATTTTCAAG
* ** * * *
504275 AATCGCAACGCGAATATGAAAATCGTAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CGTA
* *
504315 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCGTA
* *
504355 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCGTA
* ** *
504395 TATCGCAACGCGTATCCGTAAATCGCAACGATAATCAGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCGTA
504435 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
504468 TTTTTAAAGC
Statistics
Matches: 132, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 129 0.98
41 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCGTA
Found at i:504358 original size:60 final size:60
Alignment explanation
Indices: 504275--504466 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
504265 GATTTTCAAG
* ** * * *
504275 AATCGCAACGCGAATATGAAAATCGTAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTA
* * *
504335 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACGTAAATCGCAACGCGTATCCGTA
* **
504395 TATCGCAACGCGTATCCGTAAATCGCAACGATAATCA-GTAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CACGTAAATCGCAACGCGTATCCGTA
504455 AATCGCAACGCG
1 AATCGCAACGCG
504467 ATTTTTAAAG
Statistics
Matches: 113, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
59 1 0.01
60 110 0.97
61 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTA
Found at i:504885 original size:33 final size:33
Alignment explanation
Indices: 504846--504916 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
504836 TTCACTTAGA
504846 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
504879 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
504912 TTTCA
1 TTTCA
504917 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:505022 original size:21 final size:20
Alignment explanation
Indices: 504996--505102 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
504986 TGCAGAAGAG
504996 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
505017 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
505037 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
505059 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
505073 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
505092 TCGCAACGAGA
1 TCGCAACGAGA
505103 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:505076 original size:14 final size:14
Alignment explanation
Indices: 505057--505113 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
505047 GAAAAATGAA
505057 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
505071 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
505090 AATCGCAACGAGAG
1 AATCGCAACGAGAG
505104 AATCGCAACG
1 AATCGCAACG
505114 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:505088 original size:33 final size:33
Alignment explanation
Indices: 505050--505129 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
505040 GCAACGAGAA
505050 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
505083 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
505116 AAACCAAAATCGCA
1 AAATGAAAATCGCA
505130 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:505147 original size:19 final size:19
Alignment explanation
Indices: 505125--505252 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
505115 GAAACCAAAA
*
505125 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
505144 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
505158 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
505177 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
505191 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
505211 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
505231 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
505251 TC
1 TC
505253 AACCAAAAGA
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:505166 original size:14 final size:14
Alignment explanation
Indices: 505147--505203 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
505137 TTTCATTTCG
505147 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
505161 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
505180 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
505194 CGTTGCGATT
1 CGTTGCGATT
505204 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:505172 original size:33 final size:33
Alignment explanation
Indices: 505130--505252 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
505120 CAAAATCGCA
505130 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
505163 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
505196 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
505237 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
505253 AACCAAAAGA
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:505214 original size:21 final size:21
Alignment explanation
Indices: 505188--505252 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
505178 CGCGTTGCGA
505188 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
505209 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
505229 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
505250 TTC
1 TTC
505253 AACCAAAAGA
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:507093 original size:93 final size:93
Alignment explanation
Indices: 506931--507246 Score: 605
Period size: 93 Copynumber: 3.4 Consensus size: 93
506921 TAGATTGCTT
* *
506931 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTC
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
506996 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
507024 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
507089 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
507117 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
507182 TTTGTCTTTGTTTTATCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
507210 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
507247 AATACCCTGA
Statistics
Matches: 220, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 220 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:507381 original size:14 final size:14
Alignment explanation
Indices: 507362--507418 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
507352 CGAAACTTAA
507362 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
507376 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
507395 AATCGCAACGACAG
1 AATCGCAACGAGAG
507409 AATCGCAACG
1 AATCGCAACG
507419 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:507400 original size:19 final size:18
Alignment explanation
Indices: 507376--507467 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
507366 GCAACGAGAG
507376 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
507395 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
507409 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
507428 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
507442 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
507461 AATCGCA
1 AATCGCA
507468 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:507402 original size:33 final size:33
Alignment explanation
Indices: 507344--507467 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
507334 TAGTTTACTT
* * *
507344 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
507378 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
507411 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
507444 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
507468 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:507444 original size:14 final size:14
Alignment explanation
Indices: 507393--507451 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
507383 ACGCGAAATG
507393 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
507407 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
507426 AAAATCGCAACGAC
1 AAAATCGCAACGAC
507440 AAAATCGCAACG
1 AAAATCGCAACG
507452 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:507485 original size:19 final size:19
Alignment explanation
Indices: 507463--507616 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
507453 GAAACCAAAA
*
507463 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
507482 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
507498 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
507515 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
507531 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
507548 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
507567 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
507586 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
507606 TCGTGTTGCGA
1 TCGCGTTGCGA
507617 AAGTAAACTA
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 15 0.14
16 10 0.09
17 10 0.09
19 60 0.56
20 12 0.11
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:507504 original size:14 final size:14
Alignment explanation
Indices: 507485--507541 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
507475 TTTCATTTCG
507485 CGTTGCGATTCTGT
1 CGTTGCGATTCTGT
*
507499 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TGT
507516 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTGT
507532 CGTTGCGATT
1 CGTTGCGATT
507542 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:0.21, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTGT
Found at i:507600 original size:38 final size:33
Alignment explanation
Indices: 507468--507598 Score: 190
Period size: 33 Copynumber: 3.8 Consensus size: 33
507458 CAAAATCGCA
507468 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
507501 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
507534 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCT-G----TCG
*
507572 TTGCGATTCTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
507599 TTAAGTTTCG
Statistics
Matches: 89, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
33 59 0.66
34 1 0.01
38 29 0.33
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:509560 original size:14 final size:14
Alignment explanation
Indices: 509541--509576 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
509531 ATTGTTTAAT
509541 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
509555 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
509569 TGATTTGT
1 TGATTTGT
509577 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:509691 original size:19 final size:19
Alignment explanation
Indices: 509667--509754 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
509657 ACATTATGTT
509667 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
509686 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
* *
509703 G--A-GAGAATTGCAATGC
1 GAAATGAAAATCGCAATGC
509719 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
509738 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
509755 CGAGAGAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
14 9 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 28 0.47
20 16 0.27
ACGTcount: A:0.48, C:0.15, G:0.23, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:509786 original size:53 final size:53
Alignment explanation
Indices: 509667--509773 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
509657 ACATTATGTT
*
509667 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATTGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
509719 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
509772 GA
1 GA
509774 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 19 0.36
53 34 0.64
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.14
Consensus pattern (53 bp):
GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:509826 original size:14 final size:14
Alignment explanation
Indices: 509807--509861 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
509797 CATTTCCGCA
509807 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
509821 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
509838 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
509854 TTGCGATT
1 TTGCGATT
509862 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:509832 original size:53 final size:53
Alignment explanation
Indices: 509821--509986 Score: 298
Period size: 53 Copynumber: 3.2 Consensus size: 53
509811 GATTCTCTCG
509821 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
509873 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
* * *
509926 TTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
509979 TTGCGATT
1 TTGCGATT
509987 CTCTCGTTGC
Statistics
Matches: 110, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 15 0.14
53 95 0.86
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (53 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:509871 original size:86 final size:90
Alignment explanation
Indices: 509769--510000 Score: 358
Period size: 86 Copynumber: 2.7 Consensus size: 90
509759 AGAATCGCAA
509769 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
509834 TTCGCATTGCGA-TTC-TCT-CG-T
66 TTCGCATTGCGATTTCATCTCCGAT
509855 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
509920 TTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGA-TTTCATCTCCG-AT
*
509947 TGCGATTTTC--TT-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
510001 GTAATTTCCG
Statistics
Matches: 138, Mismatches: 2, Indels: 12
0.91 0.01 0.08
Matches are distributed among these distances:
86 103 0.75
87 14 0.10
88 3 0.02
89 3 0.02
90 4 0.03
92 11 0.08
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (90 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTCATCTCCGAT
Found at i:510008 original size:33 final size:33
Alignment explanation
Indices: 509787--510000 Score: 227
Period size: 33 Copynumber: 6.2 Consensus size: 33
509777 TCATTTCGCA
509787 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
509821 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
509854 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
* * * * *
509891 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
* *
509926 TTGCGATTTTCATTTCCGCATTGCGATTTTCTTG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
509960 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
509993 TTGCGATT
1 TTGCGATT
510001 GTAATTTCCG
Statistics
Matches: 150, Mismatches: 17, Indels: 27
0.77 0.09 0.14
Matches are distributed among these distances:
31 4 0.03
32 6 0.04
33 78 0.52
34 31 0.21
35 4 0.03
36 3 0.02
37 2 0.01
38 2 0.01
39 8 0.05
40 3 0.02
41 9 0.06
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:510015 original size:53 final size:53
Alignment explanation
Indices: 509821--510019 Score: 196
Period size: 53 Copynumber: 3.8 Consensus size: 53
509811 GATTCTCTCG
* *
509821 TTGCGATTTTCA-TTTCGCATTGCGA-TTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTC-CGT-GTTGCGATTTTCATTTCGCA
* *
509873 TTGCGATTTTCATTTCCGCATTGCGA-TTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTC-CGT-GTTGCGATTTTCATTTCGCA
* * * * *
509926 TTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTCCGTGTTGCGATTTTCATTTCGCA
* *
509979 TTGCGATTCTCTC-GTTGCG-ATTGTAATTTCCGTGTTGCGAT
1 TTGCGATT-T-TCAGTTCCGCATTGCAATTTCCGTGTTGCGAT
510020 AGTCAAATGC
Statistics
Matches: 132, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
52 12 0.09
53 110 0.83
54 8 0.06
55 2 0.02
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCAGTTCCGCATTGCAATTTCCGTGTTGCGATTTTCATTTCGCA
Found at i:512296 original size:12 final size:12
Alignment explanation
Indices: 512279--512303 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
512269 TCTTCGGGGA
512279 CTTTTTCTTCTT
1 CTTTTTCTTCTT
512291 CTTTTTCTTCTT
1 CTTTTTCTTCTT
512303 C
1 C
512304 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:512512 original size:24 final size:24
Alignment explanation
Indices: 512478--512524 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
512468 CTGAAACATC
512478 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
512502 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
512525 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:513245 original size:20 final size:20
Alignment explanation
Indices: 513217--513465 Score: 250
Period size: 20 Copynumber: 12.4 Consensus size: 20
513207 AAATTTCAGT
* * *
513217 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
513237 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
513257 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
513277 GTTGCGATTTACTGATTATC
1 GTTGCGATTTACGGATTCGC
*
513297 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
513317 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
513337 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
513357 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
513377 GTTGTGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
513397 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
*
513417 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
513437 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
513457 GTTGCGATT
1 GTTGCGATT
513466 CTGTAAAATC
Statistics
Matches: 202, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:513483 original size:21 final size:20
Alignment explanation
Indices: 513459--513507 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
513449 ATATTCGCGT
513459 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
513480 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
513501 TGCGATT
1 TGCGATT
513508 GTCAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 18 0.75
22 3 0.12
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:515709 original size:30 final size:30
Alignment explanation
Indices: 515643--515712 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
515633 CATATTCTTT
* *
515643 TGTTTGTTTAAATTGTTTATGTTTGGTTTG
1 TGTTTGTTTAAATTGTTTATATTTGGTTTA
515673 TGTTTGTTTAAATT-TTTAATATTAT-GTTTA
1 TGTTTGTTTAAATTGTTT-ATATT-TGGTTTA
*
515703 TTTTTGTTTA
1 TGTTTGTTTA
515713 TTTAATTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.09
30 31 0.89
31 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.66
Consensus pattern (30 bp):
TGTTTGTTTAAATTGTTTATATTTGGTTTA
Found at i:523601 original size:30 final size:30
Alignment explanation
Indices: 523542--523630 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 30
523532 CCCGAAGGAC
* * * *
523542 CTATCCAGAGATCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
523571 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
523601 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
523631 ACTGTCCATA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 17 0.31
30 37 0.69
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:523637 original size:31 final size:30
Alignment explanation
Indices: 523565--523638 Score: 130
Period size: 30 Copynumber: 2.4 Consensus size: 30
523555 ACACAGACCC
*
523565 CGGTAACTATCCAGAGGTCATAAAGATCCT
1 CGGTAACTGTCCAGAGGTCATAAAGATCCT
523595 CGGTAACTGTCCAGAGGTCATAAAGATCCT
1 CGGTAACTGTCCAGAGGTCATAAAGATCCT
523625 CGGTAAACTGTCCA
1 CGGT-AACTGTCCA
523639 TATGTTCCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 33 0.79
31 9 0.21
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (30 bp):
CGGTAACTGTCCAGAGGTCATAAAGATCCT
Found at i:523666 original size:31 final size:31
Alignment explanation
Indices: 523626--523726 Score: 132
Period size: 31 Copynumber: 3.2 Consensus size: 31
523616 AAAGATCCTC
*
523626 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
523657 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
523688 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
523720 GGTAAAC
1 GGTAAAC
523727 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
31 33 0.56
32 26 0.44
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:524582 original size:21 final size:21
Alignment explanation
Indices: 524552--524596 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
524542 ATTCTGTCGT
* *
524552 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
524573 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
524594 TTG
1 TTG
524597 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:527551 original size:30 final size:30
Alignment explanation
Indices: 527492--527580 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
527482 CCCGAAGGAC
* * *
527492 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
527521 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
527551 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
527581 ACTGTCCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:527616 original size:31 final size:31
Alignment explanation
Indices: 527576--527676 Score: 132
Period size: 31 Copynumber: 3.2 Consensus size: 31
527566 AAAGATCCTC
*
527576 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
527607 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
527638 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
527670 GGTAAAC
1 GGTAAAC
527677 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
31 33 0.56
32 26 0.44
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:528456 original size:2 final size:2
Alignment explanation
Indices: 528449--528475 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
528439 ATACAATTCC
528449 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 T
528476 CTAACTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:528562 original size:29 final size:29
Alignment explanation
Indices: 528508--528563 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
528498 TTTCTCTTGT
* *
528508 TATCATATAAATCATTGCCATATAACACA
1 TATCATATAAATCATTACCACATAACACA
*
528537 TATCATATAAATTCA-TACCACCTAACA
1 TATCATATAAA-TCATTACCACATAACA
528564 TGTAATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (29 bp):
TATCATATAAATCATTACCACATAACACA
Found at i:528980 original size:21 final size:21
Alignment explanation
Indices: 528950--528994 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
528940 ATTCTGTCGT
* *
528950 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
528971 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
528992 TTG
1 TTG
528995 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:531084 original size:21 final size:21
Alignment explanation
Indices: 531060--531099 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
531050 AATATTCTAT
531060 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
531081 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
531100 AAATAGTCTT
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:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:534017 original size:49 final size:49
Alignment explanation
Indices: 533902--534017 Score: 187
Period size: 49 Copynumber: 2.4 Consensus size: 49
533892 TACATCTGTA
*
533902 ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACAGTCACAAAG
* ** *
533951 ACGTCAGATGTTATAAATCATCATCAATCGTAGCACCACAGTCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACAGTCACAAAG
534000 ACGTCAGACGTGCTAAAT
1 ACGTCAGACGTGCTAAAT
534018 GCTCCACCTC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.21
Consensus pattern (49 bp):
ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACAGTCACAAAG
Found at i:534153 original size:53 final size:53
Alignment explanation
Indices: 534080--534186 Score: 137
Period size: 53 Copynumber: 2.0 Consensus size: 53
534070 TAAATCATTT
* * * *
534080 ATCATTCACCTATCAGAATCTTTTTCAAATATCATC-AAAATCAAGTATCATAC
1 ATCATTCACCTATCAAAATCTTTTT-AAACATCAACAAAAATCAAGTATAATAC
*
534133 ATCATTCA-CTCATCAAAATCTTTTTAAACATTAACAAAAATCAAGTATAATAC
1 ATCATTCACCT-ATCAAAATCTTTTTAAACATCAACAAAAATCAAGTATAATAC
534186 A
1 A
534187 ATATAAATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 9 0.19
53 38 0.81
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.33
Consensus pattern (53 bp):
ATCATTCACCTATCAAAATCTTTTTAAACATCAACAAAAATCAAGTATAATAC
Found at i:536292 original size:29 final size:30
Alignment explanation
Indices: 536245--536305 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
536235 TTTTGGTCCT
**
536245 TAAACTTTTCAAAGTTTATACTTTAGCCAC
1 TAAACTTTTCAAAACTTATACTTTAGCCAC
* *
536275 TAAAC-TTTCAAAACTTATATTTTAGTCAC
1 TAAACTTTTCAAAACTTATACTTTAGCCAC
536304 TA
1 TA
536306 GACAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (30 bp):
TAAACTTTTCAAAACTTATACTTTAGCCAC
Found at i:538437 original size:18 final size:18
Alignment explanation
Indices: 538414--538450 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
538404 GTCAAGTTTT
538414 TGGTTAAAACCCTATTTC
1 TGGTTAAAACCCTATTTC
538432 TGGTTAAAACCCTATTTC
1 TGGTTAAAACCCTATTTC
538450 T
1 T
538451 TCTTCATTTT
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:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
TGGTTAAAACCCTATTTC
Found at i:541000 original size:20 final size:20
Alignment explanation
Indices: 540975--541012 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
540965 AAATTTATGA
540975 ATTGATGCACCGATGCACTC
1 ATTGATGCACCGATGCACTC
*
540995 ATTGATGCATCGATGCAC
1 ATTGATGCACCGATGCAC
541013 ACACCATTTC
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:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
ATTGATGCACCGATGCACTC
Found at i:541157 original size:64 final size:64
Alignment explanation
Indices: 541021--541177 Score: 219
Period size: 64 Copynumber: 2.4 Consensus size: 64
541011 ACACACCATT
* * *
541021 TCGAATGCATTTTATATGTATCGATGCACTGACATGCATCGATGCACTCAGGTTTTTATGAAAAC
1 TCGAATGCA-TTT-TATGCATCGATGCACAGACATGCATCGATGCACTCAGGTTGTTATGAAAAC
541086 A
64 A
*
541087 TTGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTT-T-AAAAC
1 TCGAATGCATTTTATGCATCGATGCACAGA-CATGCATCGATGCACTCAGG-TTGTTATGAAAAC
541150 A
64 A
*
541151 TCGAATGCATTTTATGCATCAATGCAC
1 TCGAATGCATTTTATGCATCGATGCAC
541178 GCACCCTTAG
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
64 47 0.57
65 24 0.29
66 12 0.14
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTATGCATCGATGCACAGACATGCATCGATGCACTCAGGTTGTTATGAAAACA
Found at i:545827 original size:153 final size:154
Alignment explanation
Indices: 545595--545902 Score: 609
Period size: 153 Copynumber: 2.0 Consensus size: 154
545585 TTTAAAGAAT
545595 ATAATATCTTATCTCACTAAACAAACTGATTGCGGGTACAATGACTATAACATAAAAAGATGAAT
1 ATAATATCTTATCTCACTAAACAAACTGATTGCGGGTACAATGACTATAACATAAAAAGATGAAT
545660 TTTCACACTAAAAATATCGTTAATTTAAGAATTATCAAATTATATTTGTTATGAAAT-AAATTTA
66 TTTCACACTAAAAATATCGTTAATTTAAGAATTATCAAATTATATTTGTTATGAAATAAAATTTA
545724 TTTCGAAAACAAATAAAGAAACAA
131 TTTCGAAAACAAATAAAGAAACAA
545748 ATAATATCTTATCTCACTAAACAAACTGATTGCGGGTACAATGACTATAACATAAAAAGATGAAT
1 ATAATATCTTATCTCACTAAACAAACTGATTGCGGGTACAATGACTATAACATAAAAAGATGAAT
545813 TTTCACACTAAAAATATCGTTAATTTAAGAATTATCAAATTATATTTGTTATGAAATAAAATTTA
66 TTTCACACTAAAAATATCGTTAATTTAAGAATTATCAAATTATATTTGTTATGAAATAAAATTTA
545878 TTTCGAAAACAAATAAAGAAACAA
131 TTTCGAAAACAAATAAAGAAACAA
545902 A
1 A
545903 AGGGTTACAA
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
153 122 0.79
154 32 0.21
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (154 bp):
ATAATATCTTATCTCACTAAACAAACTGATTGCGGGTACAATGACTATAACATAAAAAGATGAAT
TTTCACACTAAAAATATCGTTAATTTAAGAATTATCAAATTATATTTGTTATGAAATAAAATTTA
TTTCGAAAACAAATAAAGAAACAA
Found at i:552649 original size:21 final size:21
Alignment explanation
Indices: 552514--552673 Score: 193
Period size: 21 Copynumber: 7.6 Consensus size: 21
552504 TTGTACCAAG
**
552514 GACGAGAAGAGAATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
552535 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
552556 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
*
552577 GACGAGAAGGCCATTCATCAA
1 GACGAGAAGACCATTCATCAA
552598 GACGAGAAGACCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
552619 GACGAGAAGACCCTTCAT-AA
1 GACGAGAAGACCATTCATCAA
* *
552639 TGACGAGAAGACCCTTC-GCAAA
1 -GACGAGAAGACCATTCATC-AA
552661 GACGAGAAGACCA
1 GACGAGAAGACCA
552674 CATCGCATGG
Statistics
Matches: 127, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
20 3 0.02
21 121 0.95
22 3 0.02
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.15
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:555021 original size:2 final size:2
Alignment explanation
Indices: 555014--555040 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
555004 CATTTATCCT
555014 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 T
555041 CCCTTGTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:555287 original size:17 final size:16
Alignment explanation
Indices: 555267--555312 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
555257 AGAGAAATGT
*
555267 AGAAAGAGAAAAGGAAA
1 AGAAA-AGAAAAAGAAA
555284 AGAAAAGAAGAAAGAAA
1 AGAAAAGAA-AAAGAAA
555301 AGAAAAGAAAAA
1 AGAAAAGAAAAA
555313 ATTGAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAAAAGAAA
Found at i:555290 original size:5 final size:5
Alignment explanation
Indices: 555267--555311 Score: 54
Period size: 5 Copynumber: 8.2 Consensus size: 5
555257 AGAGAAATGT
555267 AGAAA GAGAAA AGGAAA AGAAA AGAAGAA AGAAA AGAAA AGAAA A
1 AGAAA -AGAAA A-GAAA AGAAA AG-A-AA AGAAA AGAAA AGAAA A
555312 AATTGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 20 0.56
6 12 0.33
7 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:555297 original size:12 final size:11
Alignment explanation
Indices: 555267--555311 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
555257 AGAGAAATGT
*
555267 AGAAAGAGAAA
1 AGAAAAAGAAA
*
555278 AGGAAAAGAAA
1 AGAAAAAGAAA
555289 AGAAGAAAGAAA
1 AGAA-AAAGAAA
555301 AG-AAAAGAAA
1 AGAAAAAGAAA
555311 A
1 A
555312 AATTGAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
10 8 0.27
11 13 0.43
12 9 0.30
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:557605 original size:42 final size:41
Alignment explanation
Indices: 557536--557637 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 41
557526 TGAAGTAAAT
* *
557536 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGG
1 CCATCAGTAAGCCTTCAGAGCAAGATGA-TAAATCCTCCGGG
* * * * *
557578 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGG
1 CCATCAGTAAGCCTTCAGAGCAAGATGATAAATCCTCCGGG
557619 CCATCCA-TAAGACCTTCAG
1 CCAT-CAGTAAG-CCTTCAG
557638 GTAGGATGTT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
41 18 0.38
42 30 0.62
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (41 bp):
CCATCAGTAAGCCTTCAGAGCAAGATGATAAATCCTCCGGG
Found at i:557791 original size:42 final size:41
Alignment explanation
Indices: 557725--557826 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 41
557715 TTGCCAATTT
* * * *
557725 ATAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGATG
1 ATAAATCCTCCGGGCCATCAGTAAGCCTTCAGAGCAAGATG
* * *
557766 ATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 A-TAAATCCTCCGGGCCATCAGTAAGCCTTCAGAGCAAGATG
* *
557808 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTCCGGGCCATC
557827 CATAAGACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (41 bp):
ATAAATCCTCCGGGCCATCAGTAAGCCTTCAGAGCAAGATG
Found at i:557982 original size:42 final size:41
Alignment explanation
Indices: 557930--558031 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 41
557920 TTCCCAATTT
* * *
557930 ATAAGTCCTCCGGGCCATCAGTAAGTCTTTCA-AGCATGATG
1 ATAAATCCTCCGGGCCATCAGTAAGCCTTT-AGAGCAAGATG
* *
557971 ATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 A-TAAATCCTCCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * *
558013 ATAAGTTCTTCGGGCCATC
1 ATAAATCCTCCGGGCCATC
558032 CATAAGACCT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (41 bp):
ATAAATCCTCCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:558211 original size:42 final size:41
Alignment explanation
Indices: 558145--558246 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 41
558135 TTCCCAATTT
* * * *
558145 ATAAGTCCTCCAGGCCATCAGTAAGCCTTCCGAGCATGATG
1 ATAAATCCTCCGGGCCATCAGTAAGCCTTCAGAGCAAGATG
* * *
558186 ATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 A-TAAATCCTCCGGGCCATCAGTAAGCCTTCAGAGCAAGATG
* *
558228 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTCCGGGCCATC
558247 CATAAGACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (41 bp):
ATAAATCCTCCGGGCCATCAGTAAGCCTTCAGAGCAAGATG
Found at i:558220 original size:215 final size:214
Alignment explanation
Indices: 557536--558914 Score: 2327
Period size: 214 Copynumber: 6.5 Consensus size: 214
557526 TGAAGTAAAT
557536 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
*
557601 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGTAGGATGTTTTCAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
* *
557666 TGAAAAATGATG--TT--G--GA--G--TTTTTGAAAACGAAGAAT-CGAGTTTCAAAATTTGCC
131 AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
557720 AATTTATAAGTCCTCCGGG
196 AATTTATAAGTCCTCCGGG
*
557739 CCATCAGTAAGTCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
557804 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
*
557869 TGAAAAAATGATG--TT--G--GA--G--TTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCC
131 AG-AAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCC
557924 CAATTTATAAGTCCTCCGGG
195 CAATTTATAAGTCCTCCGGG
* * *
557944 CCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
* *
558009 GATGATAAGTTCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTTAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
*
558074 AGAAAAATGATG-TTTAAGAAGATGTATTTTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTC
131 AGAAAAATGATGTTTTAAGAAGATGGA--TTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTC
*
558138 CCAATTTATAAGTCCTCCAGG
194 CCAATTTATAAGTCCTCCGGG
558159 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
558224 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
558289 AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
131 AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
558354 AATTTATAAGTCCTCCGGG
196 AATTTATAAGTCCTCCGGG
* * * * *
558373 CCATCAGTAAGTCTTTCAAGCATGATGCTTAAATCCTCCGGGTCATCTGTAAGCCTTTTGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
*
558438 GATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
*
558503 AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCTC
131 AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
558568 AATTTATAAGTCCTCCGGG
196 AATTTATAAGTCCTCCGGG
*
558587 CCATCAGTAAGCCTTCTGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
558652 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
*
558717 TGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
131 AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
*
558782 AATTTATAAATCCTCCGGG
196 AATTTATAAGTCCTCCGGG
* *
558801 CCATCATTAAGCCTTCCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
* *
558866 GATGATAAATCCTTCGGGTCC-TCCATAAGACCTTCGGGCAGGATGTTTT
66 GATGATAAGTCCTTCGGG-CCATCCATAAGACCTTCGGGTAGGATGTTTT
558915 TCACCAGGAT
Statistics
Matches: 1122, Mismatches: 39, Indels: 19
0.95 0.03 0.02
Matches are distributed among these distances:
203 130 0.12
204 44 0.04
205 165 0.15
207 1 0.00
209 2 0.00
214 573 0.51
215 194 0.17
216 13 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (214 bp):
CCATCAGTAAGCCTTCCGAGCATGATGATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAA
GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
AGAAAAATGATGTTTTAAGAAGATGGATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCCC
AATTTATAAGTCCTCCGGG
Found at i:558639 original size:42 final size:41
Alignment explanation
Indices: 558573--558674 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 41
558563 TTCTCAATTT
* *
558573 ATAAGTCCTCCGGGCCATCAGTAAGCCTTCT-GAGCATGATG
1 ATAAATCCTCCGGGCCATCAGTAAGCCTT-TAGAGCAAGATG
* *
558614 ATTAAATCCTCCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 A-TAAATCCTCCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* *
558656 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTCCGGGCCATC
558675 CATAAGACCT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 17 0.33
42 35 0.67
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (41 bp):
ATAAATCCTCCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:558854 original size:42 final size:41
Alignment explanation
Indices: 558787--558885 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 41
558777 TTCCCAATTT
* * * *
558787 ATAAATCCTCCGGGCCATCATTAAGCCTTCCGAGCATGATG
1 ATAAATCCTTCGGGTCATCATTAAGCCTTCAGAGCAAGATG
*
558828 ATTAAATCCTTCGGGTCATC-TGTAAGCCTTTAGAGCAAGATG
1 A-TAAATCCTTCGGGTCATCAT-TAAGCCTTCAGAGCAAGATG
558870 ATAAATCCTTCGGGTC
1 ATAAATCCTTCGGGTC
558886 CTCCATAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
41 17 0.33
42 34 0.67
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (41 bp):
ATAAATCCTTCGGGTCATCATTAAGCCTTCAGAGCAAGATG
Found at i:568558 original size:24 final size:24
Alignment explanation
Indices: 568514--568559 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
568504 GTTTAAGGTA
*
568514 TATTTTATTATATTTAATATTTTG
1 TATTTAATTATATTTAATATTTTG
568538 TATTTAATT-TATTTAAGTATTT
1 TATTTAATTATATTTAA-TATTT
568560 AAATTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TATTTAATTATATTTAATATTTTG
Found at i:568559 original size:17 final size:17
Alignment explanation
Indices: 568537--568574 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
568527 TTAATATTTT
*
568537 GTATTTAATTTATTTAA
1 GTATTTAAATTATTTAA
568554 GTATTTAAATTATTTAA
1 GTATTTAAATTATTTAA
568571 -TATT
1 GTATT
568575 GTATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
GTATTTAAATTATTTAA
Found at i:574277 original size:24 final size:24
Alignment explanation
Indices: 574244--574307 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
574234 ATATGAACAA
574244 AAATATAACATAATAAAAT-TTTTAC
1 AAATA-AACATAATAAAATGTTTT-C
* *
574269 ACATAAACAT-ATAATATGTTTTC
1 AAATAAACATAATAAAATGTTTTC
*
574292 AAATAATCATAATAAA
1 AAATAAACATAATAAA
574308 CAATAAGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 15 0.47
24 13 0.41
25 4 0.12
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (24 bp):
AAATAAACATAATAAAATGTTTTC
Found at i:575167 original size:22 final size:21
Alignment explanation
Indices: 575141--575181 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
575131 GCTGCGGAAA
575141 TGATGGTCTTGATGGATGAAGT
1 TGATGGTCTTGAT-GATGAAGT
*
575163 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
575182 ATAGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGT
Found at i:575574 original size:19 final size:20
Alignment explanation
Indices: 575536--575586 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
575526 GAAACCCCTT
*
575536 TGAAAGTACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
575556 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
575575 TGAAGATACATG
1 TGAAAATACATG
575587 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:579495 original size:22 final size:22
Alignment explanation
Indices: 579462--579527 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
579452 CCAATCCAAG
579462 CGGCTC-GATCGGCTCGGTCGGC
1 CGGCTCAG-TCGGCTCGGTCGGC
* **
579484 CGGCTCAGTCGGC-CAGCTCGAT
1 CGGCTCAGTCGGCTC-GGTCGGC
* *
579506 CGACTCAGTCAGCTCGGTCGGC
1 CGGCTCAGTCGGCTCGGTCGGC
579528 TCGATCGATC
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
21 1 0.03
22 30 0.91
23 2 0.06
ACGTcount: A:0.11, C:0.36, G:0.35, T:0.18
Consensus pattern (22 bp):
CGGCTCAGTCGGCTCGGTCGGC
Found at i:579541 original size:13 final size:13
Alignment explanation
Indices: 579523--579556 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
579513 GTCAGCTCGG
579523 TCGGCTC-GATCGA
1 TCGGCTCAG-TCGA
579536 TCGGCTCAGTCGA
1 TCGGCTCAGTCGA
579549 TCGGCTCA
1 TCGGCTCA
579557 ACTGGTTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 19 0.95
14 1 0.05
ACGTcount: A:0.15, C:0.32, G:0.29, T:0.24
Consensus pattern (13 bp):
TCGGCTCAGTCGA
Found at i:581171 original size:20 final size:19
Alignment explanation
Indices: 581134--581172 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
581124 AAGTAAAGAT
**
581134 GTGAAAACATATGTTATGC
1 GTGAAAACATATAATATGC
581153 GTGAAAATCATATAATATGC
1 GTGAAAA-CATATAATATGC
581173 AAGTGAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (19 bp):
GTGAAAACATATAATATGC
Found at i:582996 original size:330 final size:334
Alignment explanation
Indices: 582469--583138 Score: 1255
Period size: 330 Copynumber: 2.0 Consensus size: 334
582459 CAATAAAATA
582469 AGGGGTGTTTGGATTGGGGAATGTGGGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGT
1 AGGGGTGTTTGGATTGGGGAATGTGGGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGT
582534 TAGCCCGGGAATCCTATTCCCGGTAATGTAAGATTACCAATAGTGGATTTTTTGGGGTATATTAC
66 TAGCCCGGGAATCCTATTCCCGGTAATGTAAGATTACCAATAGTGGATTTTTTGGGGTATATTAC
582599 CGGGAATGTCATTACCTCCCTTTCCTTAGGTATTGTTGGATTACCGGCGTTTGGACTAAAATGCC
131 CGGGAATGTCATTACCTCCCTTTCCTTAGGTATTGTTGGATTACCGGCGTTTGGACTAAAATGCC
582664 CTTAAATTTTTATTTTTTTC-AAA-ATATTTATTCTGTCATCGAATAATAAAAATTTTACGAATG
196 CTTAAA-TTTT-TTTTTTTCAAAATATATTTATTCTGTCATCGAATAATAAAAATTTTACGAATG
582727 TTAAATTACAAATTTATCCTTAAATTATTTTAGA-TTACAAAAAAAAATCTATAATTAAAATTTT
259 TTAAATTACAAATTTATCCTTAAATTATTTTAGATTTACAAAAAAAAATCTATAATTAAAATTTT
582791 ATATAAAGTTC
324 ATATAAAGTTC
582802 AGGGGTGTTTGGATTGGGGAATGTGGGATTCCCATGGGAATGGAATCCACATT-CCCCG-TTGGT
1 AGGGGTGTTTGGATTGGGGAATGTGGGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGT
582865 TAGCCCGGGAATCCTATTCCCGG-AATGTAAGATTACCAATAGTGGATTTTTTGGGGTATA-TAC
66 TAGCCCGGGAATCCTATTCCCGGTAATGTAAGATTACCAATAGTGGATTTTTTGGGGTATATTAC
582928 CGGGAATGTCATTACCTCCCTTTCCTTAGGTATTGTTGGATTACCGGCGTTTTGGACTAAAATGC
131 CGGGAATGTCATTACCTCCCTTTCCTTAGGTATTGTTGGATTACCGGCG-TTTGGACTAAAATGC
582993 CCTTAAATTTTTTTTTTTCAAAATATATTTATTCTGTCATCGAATAATAAAAATTTTACGAATGT
195 CCTTAAATTTTTTTTTTTCAAAATATATTTATTCTGTCATCGAATAATAAAAATTTTACGAATGT
583058 TAAATTACAAATTTATCCTTAAATTATTTTAGATTTACAAAAAAAAATCTATAATTAAAATTTTA
260 TAAATTACAAATTTATCCTTAAATTATTTTAGATTTACAAAAAAAAATCTATAATTAAAATTTTA
583123 TATAAAGTTC
325 TATAAAGTTC
*
583133 AAGGGT
1 AGGGGT
583139 TTAAATAAAA
Statistics
Matches: 332, Mismatches: 1, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
328 8 0.02
329 59 0.18
330 133 0.40
331 74 0.22
332 5 0.02
333 53 0.16
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37
Consensus pattern (334 bp):
AGGGGTGTTTGGATTGGGGAATGTGGGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGT
TAGCCCGGGAATCCTATTCCCGGTAATGTAAGATTACCAATAGTGGATTTTTTGGGGTATATTAC
CGGGAATGTCATTACCTCCCTTTCCTTAGGTATTGTTGGATTACCGGCGTTTGGACTAAAATGCC
CTTAAATTTTTTTTTTTCAAAATATATTTATTCTGTCATCGAATAATAAAAATTTTACGAATGTT
AAATTACAAATTTATCCTTAAATTATTTTAGATTTACAAAAAAAAATCTATAATTAAAATTTTAT
ATAAAGTTC
Found at i:583702 original size:311 final size:318
Alignment explanation
Indices: 583132--583761 Score: 1195
Period size: 311 Copynumber: 2.0 Consensus size: 318
583122 ATATAAAGTT
583132 CAAGGGTTTAAATAAAATTTTACCCTTTCATTAAACTTTTTTTATTTTTAATTTTGTAAAAAATA
1 CAAGGGTTTAAATAAAATTTTACCCTTTCATTAAACTTTTTTTATTTTTAATTTTGTAAAAAATA
583197 TATAAATATTATGAATTTAATTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTAATATTA
66 TATAAATATTATGAATTTAATTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTAATATTA
583262 CACAAATATATAATTAAGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCATTTAACC
131 CACAAATATATAATTAAGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCATTTAACC
583327 AAACACGGTAATCTTACATTCCTGCTAAGCCAACCAAACACAAAATACAACATTCCCAGTAATGC
196 AAACACGGTAATCTTACATTCCTGCTAAGCCAACCAAACACAAAATACAACATTCCCAGTAATGC
583392 TATTCCTTGGTAATCTTACATTCCCACTGGTAATCTTATATTCCGTGAACCAAACGCA
261 TATTCCTTGGTAATCTTACATTCCCACTGGTAATCTTATATTCCGTGAACCAAACGCA
583450 CAAGGGTTTAAAT-AAATTTTACCCTTTCATTAAACTTTTTTTTATTTTTAATTTTGTAAAAAAT
1 CAAGGGTTTAAATAAAATTTTACCCTTTCATTAAAC-TTTTTTTATTTTTAATTTTGTAAAAAAT
583514 ATAT-AA-ATTATGAATTTAATTTTTTTAAAG-AAATATATAAATATTTTCCAACTTGTAATATT
65 ATATAAATATTATGAATTTAATTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTAATATT
583576 ACAC-AA-ATAT-ATTAAGACAATTTGGTC-AATATACATTCCAATAATCTTTTATTCATTTAAC
130 ACACAAATATATAATTAAGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCATTTAAC
583637 CAAACACGGTAATCTTACATTCCTGCTAAGCCAACCAAACACAAAATACAACATTCCCAGTAATG
195 CAAACACGGTAATCTTACATTCCTGCTAAGCCAACCAAACACAAAATACAACATTCCCAGTAATG
583702 CTATTCCTTGGTAATCTTACATTCCCACTGGTAATCTTATATTCCGTGAACCAAACGCA
260 CTATTCCTTGGTAATCTTACATTCCCACTGGTAATCTTATATTCCGTGAACCAAACGCA
583761 C
1 C
583762 CCTAAGGGTA
Statistics
Matches: 311, Mismatches: 0, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
311 159 0.51
312 17 0.05
313 4 0.01
314 2 0.01
315 36 0.12
316 24 0.08
317 24 0.08
318 45 0.14
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.37
Consensus pattern (318 bp):
CAAGGGTTTAAATAAAATTTTACCCTTTCATTAAACTTTTTTTATTTTTAATTTTGTAAAAAATA
TATAAATATTATGAATTTAATTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTAATATTA
CACAAATATATAATTAAGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCATTTAACC
AAACACGGTAATCTTACATTCCTGCTAAGCCAACCAAACACAAAATACAACATTCCCAGTAATGC
TATTCCTTGGTAATCTTACATTCCCACTGGTAATCTTATATTCCGTGAACCAAACGCA
Found at i:595560 original size:15 final size:15
Alignment explanation
Indices: 595540--595569 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
595530 CCTAAATACC
*
595540 TTTTTTTGCAATTTT
1 TTTTTTTGAAATTTT
595555 TTTTTTTGAAATTTT
1 TTTTTTTGAAATTTT
595570 GGCTTTTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.73
Consensus pattern (15 bp):
TTTTTTTGAAATTTT
Found at i:603283 original size:12 final size:12
Alignment explanation
Indices: 603257--603289 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
603247 AATTTTGGCC
603257 TTTTTTTTTGGT
1 TTTTTTTTTGGT
603269 TTTTTTTTT-GT
1 TTTTTTTTTGGT
603280 TTTTTGTTTT
1 TTTTT-TTTT
603290 TAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTGGT
Found at i:608954 original size:41 final size:41
Alignment explanation
Indices: 608821--608954 Score: 128
Period size: 41 Copynumber: 3.3 Consensus size: 41
608811 AGTGGCATTT
* * * *
608821 TTTTTATAAAAACGCCGCGACAAAGTAGTACTTTAGTGGCG
1 TTTTTATAAAAACGCCGCAATAGAGTTGTACTTTAGTGGCG
* * ** *
608862 TTTTTATACAAACGCCGCAATAG-GTT-CATCAATAATGGCG
1 TTTTTATAAAAACGCCGCAATAGAGTTGTA-CTTTAGTGGCG
* * * *
608902 TTTTTAAAAAAACGCCGTAATAGAGTTGTACTTTAGCGCCG
1 TTTTTATAAAAACGCCGCAATAGAGTTGTACTTTAGTGGCG
608943 TTTTTATAAAAA
1 TTTTTATAAAAA
608955 TACCGCAACA
Statistics
Matches: 71, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
39 1 0.01
40 30 0.42
41 39 0.55
42 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (41 bp):
TTTTTATAAAAACGCCGCAATAGAGTTGTACTTTAGTGGCG
Found at i:608961 original size:81 final size:81
Alignment explanation
Indices: 608821--609068 Score: 185
Period size: 81 Copynumber: 3.1 Consensus size: 81
608811 AGTGGCATTT
* * * * * * *
608821 TTTTTATAAAAACGCCGCGACAAAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCAATAGG
1 TTTTTAAAAAAACGCCGCAACAAAGTAGTACTTTAGCGCCGTTTTTATAAAAACACCGCAACAGG
*
608886 TTCATCAATAATGGCG
66 GTCATCAATAATGGCG
* * * * *
608902 TTTTTAAAAAAACGCCGTAATAGAGTTGTACTTTAGCGCCGTTTTTATAAAAATACCGCAACAGG
1 TTTTTAAAAAAACGCCGCAACAAAGTAGTACTTTAGCGCCGTTTTTATAAAAACACCGCAACAGG
** * *
608967 GTCATGTATAGTGGCA
66 GTCATCAATAATGGCG
** * * * ** * ** *
608983 TTTTTTGACAAATGCCGCTAA-AAAGTAGTACTGTAGCAG-TATTTTTATAAAACCGTCGCAATA
1 TTTTTAAAAAAACGCCGC-AACAAAGTAGTACTTTAGC-GCCGTTTTTATAAAAACACCGCAACA
***
609046 GGGTCATGTGTAATGGCG
64 GGGTCATCAATAATGGCG
609064 TTTTT
1 TTTTT
609069 TTGACAAACT
Statistics
Matches: 130, Mismatches: 35, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
81 127 0.98
82 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (81 bp):
TTTTTAAAAAAACGCCGCAACAAAGTAGTACTTTAGCGCCGTTTTTATAAAAACACCGCAACAGG
GTCATCAATAATGGCG
Found at i:609108 original size:81 final size:80
Alignment explanation
Indices: 608958--609112 Score: 190
Period size: 81 Copynumber: 1.9 Consensus size: 80
608948 ATAAAAATAC
* *
608958 CGCAACAGGGTCATGTATAGTGGCATTTTTTGACAAATGCCGCTAAAAAGTAGTACTGTAGCAGT
1 CGCAACAGGGTCATGTATAATGGCATTTTTTGACAAATGCCGCTAAAAAGTAGTACTGTAG-AGC
609023 ATTTTTATAAAACCGT
65 ATTTTTATAAAACCGT
* * * *
609039 CGCAATAGGGTCATGTGTAATGGCGTTTTTTTGACAAACT-CCGCTATAGAA-TAGTACTGTATG
1 CGCAACAGGGTCATGTATAATGGC-ATTTTTTGACAAA-TGCCGCTA-AAAAGTAGTACTGTA-G
609102 -GCATTTTTATA
62 AGCATTTTTATA
609113 CAAATGTCAC
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
81 31 0.48
82 28 0.44
83 5 0.08
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (80 bp):
CGCAACAGGGTCATGTATAATGGCATTTTTTGACAAATGCCGCTAAAAAGTAGTACTGTAGAGCA
TTTTTATAAAACCGT
Found at i:609116 original size:40 final size:40
Alignment explanation
Indices: 609058--609169 Score: 118
Period size: 41 Copynumber: 2.8 Consensus size: 40
609048 GTCATGTGTA
*
609058 ATGGCGTTTTTTTGACAAACT-CCGCTATAGAATAGTACTGT
1 ATGGCGTTTTTAT-ACAAA-TGCCGCTATAGAATAGTACTGT
* * * * * * *
609099 ATGGCATTTTTATACAAATGTCACTATAGACTTGTATTTT
1 ATGGCGTTTTTATACAAATGCCGCTATAGAATAGTACTGT
609139 AGTGGCGTTTTTATACAAATGCCGCTATAGA
1 A-TGGCGTTTTTATACAAATGCCGCTATAGA
609170 CTCATACTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
39 1 0.02
40 20 0.34
41 37 0.64
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (40 bp):
ATGGCGTTTTTATACAAATGCCGCTATAGAATAGTACTGT
Found at i:609156 original size:41 final size:41
Alignment explanation
Indices: 609100--609193 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
609090 TAGTACTGTA
* * **
609100 TGGCATTTTTATACAAATGTCACTATAGACTTGTA-TTTTAG
1 TGGCGTTTTTATACAAATGCCACTATAGACTCATACTTTT-G
*
609141 TGGCGTTTTTATACAAATGCCGCTATAGACTCATACTTTTG
1 TGGCGTTTTTATACAAATGCCACTATAGACTCATACTTTTG
609182 TGGCGTTTTTAT
1 TGGCGTTTTTAT
609194 TTACAAACGC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 43 0.91
42 4 0.09
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (41 bp):
TGGCGTTTTTATACAAATGCCACTATAGACTCATACTTTTG
Found at i:610668 original size:28 final size:28
Alignment explanation
Indices: 610631--610695 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
610621 TCAGGTTGTA
*
610631 TATTTCCTTGCTAATATATCTGTTTTAT
1 TATTTACTTGCTAATATATCTGTTTTAT
* *
610659 TATTTACTTGCTACTATATTTGTTTTAT
1 TATTTACTTGCTAATATATCTGTTTTAT
610687 TGA-TTACTT
1 T-ATTTACTT
610696 TTAAATATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (28 bp):
TATTTACTTGCTAATATATCTGTTTTAT
Found at i:613429 original size:29 final size:29
Alignment explanation
Indices: 613387--613443 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
613377 TTATCAACAA
*
613387 AACGACACTATAGATCTGACTTTTTGCGG
1 AACGACACTATAGATCTGACATTTTGCGG
*
613416 AACGCCACTATAGATCTGACATTTTGCG
1 AACGACACTATAGATCTGACATTTTGCG
613444 ACGTTTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (29 bp):
AACGACACTATAGATCTGACATTTTGCGG
Found at i:613515 original size:43 final size:42
Alignment explanation
Indices: 613423--613659 Score: 246
Period size: 42 Copynumber: 5.6 Consensus size: 42
613413 CGGAACGCCA
* * * * *
613423 CTATAGATCTGACATTTTGCGACGTTTGTTACAAAAATGTCA
1 CTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAATGCCG
613465 CTATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAATGCCG
1 CTATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAATGCCG
* * * *
613508 CTATAGATCTGACTTTTTGCGGCTTTTGTTCCAAAAAAGTCG
1 CTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAATGCCG
* * * * * *
613550 -TAGATATC-AACCTTTTGCGACATTTGTTCCAAAATTGCCG
1 CTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAATGCCG
* * * *
613590 CTATAGATATCGACCTTTT-AGGCATTTGTTCCAAAAACGCCG
1 CTATAGATCT-GACCTTTTGCGGCGTTTGTTCCAAAAATGCCG
*
613632 CTATAGATCTTGACCTATTGCGGCGTTT
1 CTATAGATC-TGACCTTTTGCGGCGTTT
613660 TTTGTTCTCA
Statistics
Matches: 159, Mismatches: 30, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
40 25 0.16
41 11 0.07
42 72 0.45
43 51 0.32
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (42 bp):
CTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAATGCCG
Found at i:613576 original size:40 final size:40
Alignment explanation
Indices: 613476--613631 Score: 111
Period size: 43 Copynumber: 3.8 Consensus size: 40
613466 TATAGATCTG
* * * *
613476 ACCTTTTGCGGCGTTTGTATCCAAAAATGCCGCTATAGATCT-G
1 ACCTTTTGC-GCATTTGT-TCCAAAAAAGCCG--ATAGATATCA
* * *
613519 ACTTTTTGCGGCTTTTGTTCCAAAAAAGTCG-TAGATATCA
1 ACCTTTTGC-GCATTTGTTCCAAAAAAGCCGATAGATATCA
** *
613559 ACCTTTTGCGACATTTGTTCCAAAATTGCCGCTATAGATATCG
1 ACCTTTTGCG-CATTTGTTCCAAAAAAGCCG--ATAGATATCA
*
613602 ACCTTTTAG-GCATTTGTTCCAAAAACGCCG
1 ACCTTTT-GCGCATTTGTTCCAAAAAAGCCG
613632 CTATAGATCT
Statistics
Matches: 93, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
39 7 0.08
40 24 0.26
42 29 0.31
43 32 0.34
44 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (40 bp):
ACCTTTTGCGCATTTGTTCCAAAAAAGCCGATAGATATCA
Found at i:630282 original size:14 final size:14
Alignment explanation
Indices: 630263--630291 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
630253 ACTTCACTTA
630263 AATAATGTCTTTCC
1 AATAATGTCTTTCC
630277 AATAATGTCTTTCC
1 AATAATGTCTTTCC
630291 A
1 A
630292 TTTTAGCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (14 bp):
AATAATGTCTTTCC
Found at i:632393 original size:16 final size:18
Alignment explanation
Indices: 632372--632404 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
632362 TTAAAATTTA
632372 AGGATCA-A-TTTAAGAT
1 AGGATCATAGTTTAAGAT
632388 AGGATCATAGTTTAAGA
1 AGGATCATAGTTTAAGA
632405 ATATGTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (18 bp):
AGGATCATAGTTTAAGAT
Found at i:635748 original size:9 final size:9
Alignment explanation
Indices: 635734--635822 Score: 61
Period size: 9 Copynumber: 9.3 Consensus size: 9
635724 GCGGCTGAAA
635734 ACCGGTTTG
1 ACCGGTTTG
635743 ACCGGTTTTG
1 ACCGG-TTTG
635753 AACCGGTTTG
1 -ACCGGTTTG
*
635763 ATCGGTTTTG
1 ACCGG-TTTG
* * *
635773 ACCTGCTCG
1 ACCGGTTTG
*
635782 AACCGGTCTG
1 -ACCGGTTTG
*
635792 ACCGGTCTG
1 ACCGGTTTG
*
635801 AATCGGTTTG
1 -ACCGGTTTG
*
635811 ACCGGTATG
1 ACCGGTTTG
635820 ACC
1 ACC
635823 CGACCCGACC
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
9 30 0.48
10 27 0.44
11 5 0.08
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:635758 original size:20 final size:20
Alignment explanation
Indices: 635733--635773 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
635723 AGCGGCTGAA
635733 AACCGGTTTGACCGGTTTTG
1 AACCGGTTTGACCGGTTTTG
*
635753 AACCGGTTTGATCGGTTTTG
1 AACCGGTTTGACCGGTTTTG
635773 A
1 A
635774 CCTGCTCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.37
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTTTG
Done.