Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001778.1 Hibiscus syriacus cultivar Beakdansim tig00003592_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: 88898
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:369 original size:3 final size:3
Alignment explanation
Indices: 363--464 Score: 149
Period size: 3 Copynumber: 35.3 Consensus size: 3
353 TACCCATATC
* *
363 ATT ATT ATT ATT ATT A-T ATT ATT ATC ATC ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
410 ATT ATT A-T ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATC A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
455 ATT ATT ATT A
1 ATT ATT ATT A
465 AATATATATT
Statistics
Matches: 91, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
2 7 0.08
3 84 0.92
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:386 original size:20 final size:20
Alignment explanation
Indices: 363--464 Score: 138
Period size: 20 Copynumber: 5.0 Consensus size: 20
353 TACCCATATC
363 ATTATTATTATTATTA-TATT
1 ATTA-TATTATTATTATTATT
*
383 ATTATCATCATTATTATTATT
1 ATTAT-ATTATTATTATTATT
404 ATTATTATTATTA-TATTATT
1 ATTA-TATTATTATTATTATT
424 ATTATATTATTATTATTATT
1 ATTATATTATTATTATTATT
444 ATTATCA-TATTATTATTATT
1 ATTAT-ATTATTATTATTATT
464 A
1 A
465 AATATATATT
Statistics
Matches: 75, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
19 9 0.12
20 50 0.67
21 15 0.20
22 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATATTATTATTATTATT
Found at i:399 original size:23 final size:23
Alignment explanation
Indices: 363--464 Score: 152
Period size: 23 Copynumber: 4.3 Consensus size: 23
353 TACCCATATC
363 ATTATTATTATTATTATATTATT
1 ATTATTATTATTATTATATTATT
386 ATCATCATTATTATTATTATTATTATT
1 AT--T-ATTATTATTATTA-TATTATT
413 ATTA-TATTATTATTATATTATT
1 ATTATTATTATTATTATATTATT
*
435 ATTATTATTATTATCATATTATT
1 ATTATTATTATTATTATATTATT
458 ATTATTA
1 ATTATTA
465 AATATATATT
Statistics
Matches: 73, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
22 11 0.15
23 37 0.51
24 1 0.01
25 2 0.03
26 13 0.18
27 9 0.12
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTATTATTATTATTATATTATT
Found at i:473 original size:20 final size:19
Alignment explanation
Indices: 358--475 Score: 115
Period size: 17 Copynumber: 6.4 Consensus size: 19
348 TTTTTTACCC
358 ATATCATTATTATTATT-AT
1 ATAT-ATTATTATTATTAAT
* * *
377 -TATATTATTATCATCATT
1 ATATATTATTATTATTAAT
*
395 AT-TATTATTATTATTATT
1 ATATATTATTATTATTAAT
413 AT-TA-TATTATTATT-AT
1 ATATATTATTATTATTAAT
*
429 AT-TATTATTATTATTATT
1 ATATATTATTATTATTAAT
447 ATCATATTATTATTATTAAAT
1 AT-ATATTATTATTATT-AAT
468 ATATATTA
1 ATATATTA
476 AATACATATA
Statistics
Matches: 84, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
16 5 0.06
17 30 0.36
18 25 0.30
19 1 0.01
20 19 0.23
21 4 0.05
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATATTATTATTATTAAT
Found at i:1878 original size:13 final size:13
Alignment explanation
Indices: 1860--1905 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
1850 TTATATAAAA
1860 TAAATATTTATTT
1 TAAATATTTATTT
*
1873 TAAATAAATTATTT
1 TAAAT-ATTTATTT
1887 T-AATATTTATTT
1 TAAATATTTATTT
*
1899 TTAATAT
1 TAAATAT
1906 CGAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:3383 original size:35 final size:33
Alignment explanation
Indices: 3299--3384 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 33
3289 ATTTGATATT
*
3299 TAATACAACAAACTTACAATAAGAATTAAATGG
1 TAATACAACAAAATTACAATAAGAATTAAATGG
* *
3332 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 T-AAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
3370 TAATA-AACAAAATTA
1 TAATACAACAAAATTA
3385 ACTAAAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
33 1 0.02
34 3 0.07
35 24 0.55
36 1 0.02
37 5 0.11
38 10 0.23
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (33 bp):
TAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:4038 original size:20 final size:18
Alignment explanation
Indices: 3989--4040 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
3979 AAAGGCGATG
3989 GCGACATCATATATGGTT
1 GCGACATCATATATGGTT
4007 GCGACATCATATATGGTT
1 GCGACATCATATATGGTT
* *
4025 GTGGCATCATATATGG
1 GCGACATCATATATGG
4041 CTACGGTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (18 bp):
GCGACATCATATATGGTT
Found at i:5495 original size:111 final size:108
Alignment explanation
Indices: 5346--5564 Score: 368
Period size: 111 Copynumber: 2.0 Consensus size: 108
5336 ATTACAAAAA
* *
5346 TTAATTCTTAATAATAATCATATTTAAATGAATCAACTAATTATTACTAATAATTTAAATTAAAT
1 TTAATTCTTAATAATAATCATATTTAAATAAATCAACTAAATATTACTAATAATTTAAATTAAAT
*
5411 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
5454 TTAATTCTTAATCTAATAATCATGCA-TTAAATAAATCAACTAAATATTACTAATAATTTAAATT
1 TTAATTCTTAA--TAATAATCAT--ATTTAAATAAATCAACTAAATATTACTAATAATTTAAATT
5518 AAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
62 AAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
5565 ATGATTTTCA
Statistics
Matches: 104, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
108 11 0.11
110 10 0.10
111 82 0.79
112 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (108 bp):
TTAATTCTTAATAATAATCATATTTAAATAAATCAACTAAATATTACTAATAATTTAAATTAAAT
TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:7758 original size:22 final size:22
Alignment explanation
Indices: 7732--7775 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
7722 CTATGTGTAT
7732 CGATGCACATTCAATGTGCACC
1 CGATGCACATTCAATGTGCACC
7754 CGATGCACATTCAATGTGCACC
1 CGATGCACATTCAATGTGCACC
7776 TATGCATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (22 bp):
CGATGCACATTCAATGTGCACC
Found at i:10879 original size:20 final size:20
Alignment explanation
Indices: 10838--10880 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
10828 ACCGACGTGT
*
10838 CACATATTTGTCCCGATGAC
1 CACATATTTGTCCCGAAGAC
10858 CACATA-TTGTCCCGAAGAAC
1 CACATATTTGTCCCGAAG-AC
10878 CAC
1 CAC
10881 GTAAAACCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.30, C:0.33, G:0.14, T:0.23
Consensus pattern (20 bp):
CACATATTTGTCCCGAAGAC
Found at i:11040 original size:21 final size:21
Alignment explanation
Indices: 11016--11066 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
11006 CATAGAATTT
*
11016 GTTCACATTCA-TTGGTTCAAA
1 GTTCACATTCACTT-ATTCAAA
11037 GTTCACATTCACTTATTCAAA
1 GTTCACATTCACTTATTCAAA
*
11058 GCTCACATT
1 GTTCACATT
11067 TCCATAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (21 bp):
GTTCACATTCACTTATTCAAA
Found at i:11446 original size:22 final size:20
Alignment explanation
Indices: 11399--11452 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
11389 CATGCTTGGA
*
11399 GGTATCGGTACCACCCTAAG
1 GGTATCGATACCACCCTAAG
*
11419 GGTATCGATACCACCCTTCAGG
1 GGTATCGATACCACCC-T-AAG
11441 GGTATCGATACC
1 GGTATCGATACC
11453 TCTGCATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 15 0.50
21 1 0.03
22 14 0.47
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (20 bp):
GGTATCGATACCACCCTAAG
Found at i:11569 original size:21 final size:21
Alignment explanation
Indices: 11543--11602 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 21
11533 ATTCGATGTT
11543 TTAAGGGTATCGATACCATC-C
1 TTAA-GGTATCGATACCATCTC
*
11564 TTAAGGTATCAATACCCATCTC
1 TTAAGGTATCGATA-CCATCTC
11586 TTAAGGTATCGATACCA
1 TTAAGGTATCGATACCA
11603 CTATCAACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.26
21 12 0.34
22 14 0.40
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (21 bp):
TTAAGGTATCGATACCATCTC
Found at i:14553 original size:74 final size:75
Alignment explanation
Indices: 14406--14555 Score: 223
Period size: 74 Copynumber: 2.0 Consensus size: 75
14396 AAAGTTAATG
* *
14406 TAAATAATTTTTAATTTTTAATCAAATTTTAGTAATCCCAAAACAGTTAGTATAAATAGTTTGAG
1 TAAATAATTTTAAATTTTTAATCAAATTTTAATAAT--C-AAACAGTTAGTATAAATAGTTTGAG
14471 GATAAAATTAGTA
63 GATAAAATTAGTA
14484 TAAATAATTTTAAATTTTTAATCAAACTTTTAATAAT-AAA-AGTTAGTATAAATAGTTTGAGGA
1 TAAATAATTTTAAATTTTTAATCAAA-TTTTAATAATCAAACAGTTAGTATAAATAGTTTGAGGA
*
14547 TGAAATTAG
65 TAAAATTAG
14556 AATGTTTAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
74 31 0.46
75 3 0.04
78 25 0.37
79 9 0.13
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.40
Consensus pattern (75 bp):
TAAATAATTTTAAATTTTTAATCAAATTTTAATAATCAAACAGTTAGTATAAATAGTTTGAGGAT
AAAATTAGTA
Found at i:17573 original size:36 final size:36
Alignment explanation
Indices: 17521--17594 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
17511 GGTTCTATTG
**
17521 TAATATTTTATTCTTGAAGAATAAGACT-TCACAACT
1 TAATATTTTAGGCTTGAAGAATAAGACTGT-ACAACT
17557 TAATATTTTAGGCTTGAAGAATAAGACTGTACAACT
1 TAATATTTTAGGCTTGAAGAATAAGACTGTACAACT
17593 TA
1 TA
17595 TTATATTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 34 0.97
37 1 0.03
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (36 bp):
TAATATTTTAGGCTTGAAGAATAAGACTGTACAACT
Found at i:19089 original size:55 final size:55
Alignment explanation
Indices: 18960--19260 Score: 414
Period size: 55 Copynumber: 5.5 Consensus size: 55
18950 TTTATTAAGA
* * * * *
18960 TGCACACATAGTGCCTATACAG-TAGTTCATTAACTCATGATGAATT-TCGTGG-GT
1 TGCACACATAGTGCATGTACGGTTA-TTCATCAACTCATGATGAATTCT-GTGGATT
**
19014 TGCACACATAGTGTTTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
*
19069 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* *
19124 TGCACACATAGAGCATGTACGATTATTCATCAACTCATGATGAATTCTGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* *
19179 TACACACATAGTGTC-TGTACGGTTATTCATCAACTCATGATGAATT-TCGTTGATT
1 TGCACACATAGTG-CATGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGATT
*
19234 TGCACACATAGTGCCTGTACGGTTATT
1 TGCACACATAGTGCATGTACGGTTATT
19261 TGTTGAAAAC
Statistics
Matches: 224, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
54 44 0.20
55 179 0.80
56 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (55 bp):
TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
Found at i:23959 original size:31 final size:31
Alignment explanation
Indices: 23923--23981 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
23913 AACTTAAAAG
* *
23923 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
23954 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
23982 ACATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:24032 original size:22 final size:22
Alignment explanation
Indices: 24006--24048 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
23996 TAATAAATTA
24006 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
24028 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
24049 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:24057 original size:22 final size:22
Alignment explanation
Indices: 24008--24056 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
23998 ATAAATTATT
**
24008 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
24030 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
24053 TAAA
1 TAAA
24057 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:24060 original size:54 final size:54
Alignment explanation
Indices: 23996--24841 Score: 444
Period size: 54 Copynumber: 15.6 Consensus size: 54
23986 ACAACTACAA
23996 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
24050 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** **
24107 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
* *
24162 -AACTACA--A--T--AATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
24210 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-C---C
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *** * * *
24260 --ATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
* * * ** * *
24311 -AAT--A-T-TTTAAAATAAATCAATTCATA--CT--AATAAAT-TATTTAAAA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
24355 TAAATAAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATTAATCC
1 T-AATAAAT---TA-TTTAAAATAAATCAA-TC---C--AT--A-T-TTTAAAATAAATCAATCC
24420 ATAC
51 ATAC
*
24424 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCATTCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*** * * *
24478 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
* ** * ** * * *
24531 -CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT-TA-AA
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATAC
** ** *
24580 TCAATCCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-CA-AC
1 T-AATAAATTA-TTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCCATAC
* * * * *
24639 TCATACAACTA--CAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATAT
1 TAATA-AATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
24693 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
24747 TAATAAATTATTTAAAATAAATTAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATAC
*
24811 TAATAAATTATTTAAAATAAATCAATTCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
24842 CAACTACAAT
Statistics
Matches: 625, Mismatches: 86, Indels: 160
0.72 0.10 0.18
Matches are distributed among these distances:
43 6 0.01
44 3 0.00
45 2 0.00
46 3 0.00
48 111 0.18
49 13 0.02
50 13 0.02
51 4 0.01
52 13 0.02
53 12 0.02
54 220 0.35
55 46 0.07
56 7 0.01
57 20 0.03
58 45 0.07
59 9 0.01
60 10 0.02
62 2 0.00
63 3 0.00
64 61 0.10
65 2 0.00
66 1 0.00
68 14 0.02
69 5 0.01
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:24066 original size:32 final size:30
Alignment explanation
Indices: 24028--24912 Score: 405
Period size: 32 Copynumber: 32.4 Consensus size: 30
24018 CAATCCATAT
24028 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
*
24060 TTTAAAATAAATCAATCCATAC-AACTACAA
1 TTTAAAATAAATCAATCCATACTAA-TAAAA
24090 --T--AATAAATCAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
24108 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
*
24140 TTTAAAATAAATCAATCCATAC-AACTACAA
1 TTTAAAATAAATCAATCCATACTAA-TAAAA
*
24170 --T--AATAAATCAAT---T-C--AT--AT
1 TTTAAAATAAATCAATCCATACTAATAAAA
24188 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
24220 TTTAAAATAAATCAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
*
24242 TTTAAAATAAATCAATCCATA--AAT--TA
1 TTTAAAATAAATCAATCCATACTAATAAAA
* *
24268 TTTAAAATAAATCAATCTATAC-AACTACAA
1 TTTAAAATAAATCAATCCATACTAA-TAAAA
24298 --T--AATAAATCAAT-CA-A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
*
24316 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
*
24348 TTTAAAATAAATAAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
*
24370 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
*
24402 TTTAAAATAAATTAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
24434 TTTAAAATAAATCAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
*
24456 TTTAAAATAAATCATTCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
*
24488 TTTAAAATAAATCAATCCATAC-AACTACAA
1 TTTAAAATAAATCAATCCATACTAA-TAAAA
24518 --T--AATAAATCAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
24536 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
24568 TTTAAAATTAAATCAATCC--A-T-AT----
1 TTTAAAA-TAAATCAATCCATACTAATAAAA
24591 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
*
24623 TTTAAAATAAATCAA-CTCATAC-AACTACAA
1 TTTAAAATAAATCAATC-CATACTAA-TAAAA
24653 --T--AATAAATCAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
* *
24671 TTTAAAATAAATCAATTCATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
24703 TTTAAAATAAATCAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
*
24725 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
*
24757 TTTAAAATAAATTAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
24789 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
* *
24821 TTTAAAATAAATCAATTCATAC-AACTACAA
1 TTTAAAATAAATCAATCCATACTAA-TAAAA
24851 --T--AATAAATCAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
*
24869 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
24901 TTTAAAATAAAT
1 TTTAAAATAAAT
24913 TATTTTAAAA
Statistics
Matches: 679, Mismatches: 28, Indels: 292
0.68 0.03 0.29
Matches are distributed among these distances:
18 1 0.00
20 7 0.01
21 1 0.00
22 157 0.23
23 15 0.02
24 17 0.03
25 11 0.02
26 110 0.16
27 3 0.00
28 17 0.03
29 6 0.01
30 12 0.02
31 12 0.02
32 299 0.44
33 11 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (30 bp):
TTTAAAATAAATCAATCCATACTAATAAAA
Found at i:24101 original size:80 final size:80
Alignment explanation
Indices: 24011--24817 Score: 519
Period size: 80 Copynumber: 10.0 Consensus size: 80
24001 AATTATTTAA
24011 AATAAATCAATCCATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCATACTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
*
24075 TCCATACAACTACAAT
66 TCCATACAA-TAAAAT
24091 AATAAATCAATCCATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCATACTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
*
24155 TCCATACAACTACAAT
66 TCCATACAA-TAAAAT
*
24171 AATAAATCAATTCATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCATACTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
* **
24235 TCCAT--ATTTTAA-
66 TCCATACAATAAAAT
* * *
24247 AATAAATCAATCCATAAATTATTTAAAATAAATCAATCTATAC-AACTACA--A--T--AATAAA
1 AATAAATCAATCCAT--ACT-TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAA
* * **
24305 TCAAT-CA-ATATTTTAA-
62 TCAATCCATACAATAAAAT
* ** * ** * ** **
24321 AATAAATCAATTCATACTAATAAATTATTTAAAATAAATA--AATCCA-TATTTTAAAATAAATC
1 AATAAATCAATCCATACTTTTAAAATAAAT-CAATCCATACTAATAAATTA-TTTAAAATAAATC
*
24383 AATTCATACTAATAAATTATTT
64 AATCCATAC-AATAAA--A--T
* ** * ** * ** **
24405 AAAATAAATTAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCA-TATTTTAAAATAAA
1 --AATAAATCAATCCATACTTTTAAAATAAAT-CAATCCATACTAATAAATTA-TTTAAAATAAA
*
24467 TCATTCCATACTAATAAATTATTT
62 TCAATCCATAC-AATAAA--A--T
*** * * * *
24491 AAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATC
1 --AATAAATCAATCCATACTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATC
24549 AATCCATACTAATAAATTATTT
64 AATCCATAC-AATAAA--A--T
24571 AAAATTAAATCAATCCATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 --AA-TAAATCAATCCATACTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
*
24635 CAA-CTCATACAACTACAAT
63 CAATC-CATACAA-TAAAAT
* *
24654 AATAAATCAATCCATA-TTTTAAAATAAATCAATTCATATTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCATACTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
***
24718 TCCATATTTTAAAAT
66 TCCATACAATAAAAT
* * * *
24733 AAATCAATTC-ATACTAATAAATTATTTAAAATAAATTAATCCATACTAATAAATTATTTAAAAT
1 -AAT-AAATCAAT-C-CAT--ACT-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT
24797 AAATCAATCCATACTAATAAA
59 AAATCAATCCATAC-AATAAA
24818 TTATTTAAAA
Statistics
Matches: 624, Mismatches: 58, Indels: 83
0.82 0.08 0.11
Matches are distributed among these distances:
70 3 0.00
71 10 0.02
72 8 0.01
73 2 0.00
74 33 0.05
76 26 0.04
77 5 0.01
78 4 0.01
79 11 0.02
80 284 0.46
81 32 0.05
82 5 0.01
83 3 0.00
84 11 0.02
85 4 0.01
86 156 0.25
87 27 0.04
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (80 bp):
AATAAATCAATCCATACTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
TCCATACAATAAAAT
Found at i:24137 original size:22 final size:23
Alignment explanation
Indices: 24062--24136 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
24052 ATAAATTATT
24062 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
24084 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
24110 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
24133 TAAA
1 TAAA
24137 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:24217 original size:22 final size:23
Alignment explanation
Indices: 24142--24216 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
24132 ATAAATTATT
24142 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
* **
24164 CTACAATAATAAATCAATTCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
24190 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
24213 TAAA
1 TAAA
24217 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:24246 original size:22 final size:22
Alignment explanation
Indices: 24220--24336 Score: 108
Period size: 22 Copynumber: 5.0 Consensus size: 22
24210 TAATAAATTA
24220 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
24242 TTTAAAATAAATCAATCCATAAATT
1 TTTAAAATAAATCAATCCAT--A-T
* *
24267 ATTTAAAATAAATCAATCTATACAAC
1 -TTTAAAATAAATCAATCCAT---AT
** *
24293 TACAATAATAAATCAATCAATAT
1 TTTAA-AATAAATCAATCCATAT
*
24316 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
24337 CTAATAAATT
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
22 34 0.44
23 4 0.05
24 1 0.01
25 4 0.05
26 33 0.42
27 2 0.03
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:24342 original size:18 final size:18
Alignment explanation
Indices: 24321--24399 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 18
24311 AATATTTTAA
24321 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
* * * *
24339 AATAAAT-TATTTAAAAT
1 AATAAATCAATTCATACT
* *
24356 AAATAAATCCATATT-TTA-A
1 -AATAAAT-CA-ATTCATACT
24375 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
24393 AATAAAT
1 AATAAAT
24400 TATTTAAAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
16 3 0.07
17 10 0.22
18 28 0.62
20 1 0.02
21 3 0.07
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:24374 original size:22 final size:22
Alignment explanation
Indices: 24348--24390 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
24338 TAATAAATTA
24348 TTTAAAATAAATAAATCCATAT
1 TTTAAAATAAATAAATCCATAT
* *
24370 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATAAATCCATA
24391 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:24410 original size:14 final size:14
Alignment explanation
Indices: 24393--24445 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
24383 AATTCATACT
24393 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
24407 AATAAATTAATCCATACT
1 AATAAATT-AT--TTA-A
24425 AATAAATTATTTAA
1 AATAAATTATTTAA
24439 AATAAAT
1 AATAAAT
24446 CAATCCATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 15 0.48
15 4 0.13
17 4 0.13
18 8 0.26
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:24459 original size:22 final size:22
Alignment explanation
Indices: 24434--24476 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
24424 TAATAAATTA
24434 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
24456 TTTAAAATAAATCATTCCATA
1 TTTAAAATAAATCAATCCATA
24477 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:24485 original size:22 final size:22
Alignment explanation
Indices: 24436--24484 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
24426 ATAAATTATT
**
24436 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
24458 TAAAATAAATCATTCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
24481 TAAA
1 TAAA
24485 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:24562 original size:18 final size:18
Alignment explanation
Indices: 24518--24620 Score: 52
Period size: 22 Copynumber: 5.4 Consensus size: 18
24508 ACAACTACAA
*
24518 TAATAAATCAATCCATATTT
1 TAATAAATCAATCCATA--C
24538 TAAAATAAATCAATCCATAC
1 T--AATAAATCAATCCATAC
* *
24558 TAATAAAT-TAT--TTA-
1 TAATAAATCAATCCATAC
* *
24572 AAATTAAATCAATCCATATTT
1 TAA-TAAATCAATCCATA--C
24593 TAAAATAAATCAATCCATAC
1 T--AATAAATCAATCCATAC
24613 TAATAAAT
1 TAATAAAT
24621 TATTTAAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 24
0.67 0.08 0.25
Matches are distributed among these distances:
14 2 0.03
15 7 0.11
16 2 0.03
17 2 0.03
18 16 0.25
20 3 0.05
22 30 0.47
23 2 0.03
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATAAATCAATCCATAC
Found at i:24565 original size:22 final size:23
Alignment explanation
Indices: 24490--24564 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
24480 ATAAATTATT
24490 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
24512 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
24538 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
24561 TAAA
1 TAAA
24565 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:24601 original size:22 final size:23
Alignment explanation
Indices: 24568--24611 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
24558 TAATAAATTA
24568 TTTAAAATTAAATCAATCCATAT
1 TTTAAAATTAAATCAATCCATAT
24591 TTTAAAA-TAAATCAATCCATA
1 TTTAAAATTAAATCAATCCATA
24612 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (23 bp):
TTTAAAATTAAATCAATCCATAT
Found at i:24620 original size:22 final size:22
Alignment explanation
Indices: 24570--24619 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
24560 ATAAATTATT
**
24570 TAAAATTAAATCAATCCATATTT
1 TAAAA-TAAATCAATCCATATAA
24593 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
24616 TAAA
1 TAAA
24620 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:24700 original size:22 final size:22
Alignment explanation
Indices: 24654--24699 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
24644 CAACTACAAT
*
24654 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTATAA
*
24676 AATAAATCAATTCATATTAATAA
1 AATAAATCAATCCATATT-ATAA
24699 A
1 A
24700 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAAATCAATCCATATTATAA
Found at i:24729 original size:22 final size:22
Alignment explanation
Indices: 24703--24745 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
24693 TAATAAATTA
24703 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
24725 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
24746 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:24754 original size:22 final size:22
Alignment explanation
Indices: 24705--24753 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
24695 ATAAATTATT
**
24705 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
24727 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
24750 TAAA
1 TAAA
24754 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:24765 original size:14 final size:14
Alignment explanation
Indices: 24748--24832 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 14
24738 AATTCATACT
24748 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
24762 AATAAATTAATCCATACT
1 AATAAATT-AT--TTA-A
24780 AATAAATTATTTAA
1 AATAAATTATTTAA
* * *
24794 AATAAATCAATCCATACT
1 AATAAAT-TAT--TTA-A
24812 AATAAATTATTTAA
1 AATAAATTATTTAA
24826 AATAAAT
1 AATAAAT
24833 CAATTCATAC
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
14 22 0.42
15 8 0.15
17 8 0.15
18 15 0.28
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:24785 original size:18 final size:18
Alignment explanation
Indices: 24762--24820 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
24752 AATTATTTAA
24762 AATAAATTAATCCATACT
1 AATAAATTAATCCATACT
* *
24780 AATAAATT-AT--TTA-A
1 AATAAATTAATCCATACT
*
24794 AATAAATCAATCCATACT
1 AATAAATTAATCCATACT
24812 AATAAATTA
1 AATAAATTA
24821 TTTAAAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
17 4 0.13
18 16 0.52
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAAATTAATCCATACT
Found at i:24880 original size:22 final size:22
Alignment explanation
Indices: 24852--24947 Score: 75
Period size: 22 Copynumber: 4.2 Consensus size: 22
24842 CAACTACAAT
24852 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
* **
24874 AATAAATCAATTCATACTAATAA
1 AATAAATCAATCCATA-TTTTAA
* ** * **
24897 ATTATTTAAAATAAATTATTTTAA
1 AATAAAT-CAATCCA-TATTTTAA
*
24921 AATAAATCAATCCATATTTTAT
1 AATAAATCAATCCATATTTTAA
24943 AATAA
1 AATAA
24948 TTTATTTTAA
Statistics
Matches: 53, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
22 27 0.51
23 12 0.23
24 12 0.23
25 2 0.04
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:24880 original size:355 final size:345
Alignment explanation
Indices: 23996--24947 Score: 1280
Period size: 355 Copynumber: 2.8 Consensus size: 345
23986 ACAACTACAA
* *
23996 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATAAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
* * **
24061 TTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAA
66 TTAAAATAAATTAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATATAATAAAATAAA
* * *
24119 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATTC
130 TAAATCCATACTAATAAACTA-TCAAAATAAATCAATCCAT--AACTACAATAATAAATCAATTC
24184 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAA
192 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAA
24249 TAAATCAATCCATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCAAT
257 TAAATCAATCCATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCAAT
24314 ATTTTAAAATAAATCAATTCATAC
322 ATTTTAAAATAAATCAATTCATAC
24338 TAATAAATTATTTAAAATAAATAAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATAAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
**
24403 TTAAAATAAATTAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
66 TTAAAATAAATTAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATAATAAAATAAAT
* * * * *
24468 CATTCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCA
131 AAATCCATACTAATAAACTA-TCAAAATAAATCAATCCAT--AACTACAATAATAAATCAATTCA
24533 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATTAAATCAATCCATATTTTAAAA
193 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAA-TAAATCAATCCATATTTTAAAA
24598 TAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA-CTCATACAACTACAATAATAAATC
257 TAAATCAAT-C---C--ATAAATTATTTAAAATAAATCAATCT-ATACAACTACAATAATAAATC
* *
24662 AATCCATATTTTAAAATAAATCAATTCATAT
315 AATCAATATTTTAAAATAAATCAATTCATAC
*
24693 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATAAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
24758 TTAAAATAAATTAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATT
66 TTAAAATAAATTAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-TAATAAA--A--
* * * **
24823 TAAAATAAAT-CA-ATTCATACAACTA-CAATAATAAATCAATCCAT-ATTTTAA-AATAAATCA
126 T-AAATAAATCCATACTAATA-AACTATCAA-AATAAATCAATCCATAACTACAATAATAAATCA
* * * *
24883 ATTCATA--CT--AATAAAT-TAT--TTA-AAATAAATTATTTTAAAATAAATCAATCCATATTT
188 ATTCATATTTTAAAATAAATCAATCCATACTAATAAATTA-TTTAAAATAAATCAATCCATATTT
*
24940 TATAATAA
252 TAAAATAA
24948 TTTATTTTAA
Statistics
Matches: 560, Mismatches: 26, Indels: 43
0.89 0.04 0.07
Matches are distributed among these distances:
342 86 0.15
343 2 0.00
344 1 0.00
346 1 0.00
347 33 0.06
348 143 0.26
349 31 0.06
350 3 0.01
351 7 0.01
353 2 0.00
354 2 0.00
355 204 0.36
356 9 0.02
358 3 0.01
359 20 0.04
360 7 0.01
361 6 0.01
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (345 bp):
TAATAAATTATTTAAAATAAATAAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
TTAAAATAAATTAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATAATAAAATAAAT
AAATCCATACTAATAAACTATCAAAATAAATCAATCCATAACTACAATAATAAATCAATTCATAT
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATCCATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCAATATTT
TAAAATAAATCAATTCATAC
Found at i:24921 original size:15 final size:15
Alignment explanation
Indices: 24892--25009 Score: 139
Period size: 15 Copynumber: 7.5 Consensus size: 15
24882 AATTCATACT
24892 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
24906 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
24921 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
24943 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
24958 AATAAATTATTTTAT
1 AATAAATTATTTTAA
24973 AATAAATTATTTTAA
1 AATAAATTATTTTAA
24988 AATAAATTATTTTAA
1 AATAAATTATTTTAA
25003 AATAAAT
1 AATAAAT
25010 AACCTTATTA
Statistics
Matches: 90, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
14 9 0.10
15 64 0.71
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:24937 original size:69 final size:67
Alignment explanation
Indices: 24852--24994 Score: 198
Period size: 67 Copynumber: 2.1 Consensus size: 67
24842 CAACTACAAT
*
24852 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTA-TTTAAAATAAATTAT
1 AATAAATCAATCCATATTTTAAAAT-AATCAATT-ATA-AAATAAATTATTTTAAAATAAATTAT
24916 TTTAA
63 TTTAA
* ** * *
24921 AATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTTTATAATAAATTATTTT
1 AATAAATCAATCCATATTTTAAAATAATCAATTATAAAATAAATTATTTTAAAATAAATTATTTT
24986 AA
66 AA
24988 AATAAAT
1 AATAAAT
24995 TATTTTAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 9 0.13
67 28 0.42
68 6 0.09
69 24 0.36
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (67 bp):
AATAAATCAATCCATATTTTAAAATAATCAATTATAAAATAAATTATTTTAAAATAAATTATTTT
AA
Found at i:27236 original size:37 final size:37
Alignment explanation
Indices: 27186--27267 Score: 155
Period size: 37 Copynumber: 2.2 Consensus size: 37
27176 TCAAAACGGA
*
27186 TAATCAAAACCATCCAAGAAGGGATCCTCTTCACAGG
1 TAATCAATACCATCCAAGAAGGGATCCTCTTCACAGG
27223 TAATCAATACCATCCAAGAAGGGATCCTCTTCACAGG
1 TAATCAATACCATCCAAGAAGGGATCCTCTTCACAGG
27260 TAATCAAT
1 TAATCAAT
27268 CTTCCATTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.22
Consensus pattern (37 bp):
TAATCAATACCATCCAAGAAGGGATCCTCTTCACAGG
Found at i:35912 original size:19 final size:19
Alignment explanation
Indices: 35888--35936 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
35878 AGAAAGCCTT
*
35888 AGAGAGAGGGGAAGGGAAG
1 AGAGAGAGAGGAAGGGAAG
*
35907 AGAGAGAGAGGAGGGGAAG
1 AGAGAGAGAGGAAGGGAAG
*
35926 GGAAGAGAGAG
1 AG-AGAGAGAG
35937 AGAGAGGGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (19 bp):
AGAGAGAGAGGAAGGGAAG
Found at i:35925 original size:24 final size:23
Alignment explanation
Indices: 35888--35944 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 23
35878 AGAAAGCCTT
35888 AGAGAGAGGGGAAGGGAAGAGAG
1 AGAGAGAGGGGAAGGGAAGAGAG
35911 AGAGAGGAGGGGAAGGGAAGAGAG
1 AGAGA-GAGGGGAAGGGAAGAGAG
35935 AGAGAGAGGG
1 AGAGAGAGGG
35945 AGGCATGCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 10 0.30
24 23 0.70
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (23 bp):
AGAGAGAGGGGAAGGGAAGAGAG
Found at i:36846 original size:19 final size:18
Alignment explanation
Indices: 36822--36857 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
36812 TAATTATTAT
36822 TATTATATATTTTTAATAA
1 TATTATAT-TTTTTAATAA
36841 TATTATATTTTTTAATA
1 TATTATATTTTTTAATA
36858 TTATATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATATTTTTTAATAA
Found at i:36858 original size:15 final size:16
Alignment explanation
Indices: 36792--36863 Score: 62
Period size: 15 Copynumber: 4.6 Consensus size: 16
36782 TTTTAATAAA
* *
36792 AATATTA-ATTATTAA
1 AATATTATATTTTTAT
*
36807 AATATTA-ATTATTAT
1 AATATTATATTTTTAT
*
36822 TAT-TATATATTTTTAAT
1 AATAT-TATATTTTT-AT
36839 AATATTATATTTTT-T
1 AATATTATATTTTTAT
36854 AATATTATAT
1 AATATTATAT
36864 AAATATGTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
14 1 0.02
15 29 0.59
16 5 0.10
17 13 0.27
18 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATATTATATTTTTAT
Found at i:36864 original size:17 final size:16
Alignment explanation
Indices: 36822--36864 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
36812 TAATTATTAT
36822 TATTATATATTTTTAA
1 TATTATATATTTTTAA
*
36838 TAATATTATATTTTTTAA
1 TATTA-TATA-TTTTTAA
36856 TATTATATA
1 TATTATATA
36865 AATATGTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 8 0.35
18 11 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTATATATTTTTAA
Found at i:37633 original size:30 final size:32
Alignment explanation
Indices: 37566--37635 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 32
37556 TTTAAAATAC
* *
37566 AAAAATATATTTAATTTATAATTCTATTATTT
1 AAAAATATATATAATTAATAATTCTATTATTT
*
37598 CAAAAT-TATATAATTAAT-ATT-TATTTATTT
1 AAAAATATATATAATTAATAATTCTA-TTATTT
37628 AAAAATAT
1 AAAAATAT
37636 CAGAAAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 2 0.06
30 14 0.44
31 11 0.34
32 5 0.16
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
AAAAATATATATAATTAATAATTCTATTATTT
Found at i:37840 original size:20 final size:21
Alignment explanation
Indices: 37817--37862 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
37807 TATTATATAT
**
37817 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
37837 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
37858 ATATT
1 ATATT
37863 ACTAAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:38733 original size:19 final size:21
Alignment explanation
Indices: 38709--38747 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
38699 GTATAGTTTG
38709 TTTTTTTTCTTT-TCTCTGTT
1 TTTTTTTTCTTTCTCTCTGTT
38729 TTTTTTTTCTTTCTCTCTG
1 TTTTTTTTCTTTCTCTCTG
38748 GTTCTGTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (21 bp):
TTTTTTTTCTTTCTCTCTGTT
Found at i:39354 original size:15 final size:14
Alignment explanation
Indices: 39265--39357 Score: 91
Period size: 15 Copynumber: 6.4 Consensus size: 14
39255 TAATATAAAT
*
39265 TAATAATAATAATAA
1 TAATAATAAT-ATGA
39280 TAATAATAATAATGA
1 TAATAATAAT-ATGA
39295 TAATAATAATAT--
1 TAATAATAATATGA
* *
39307 TAATAATAATAAGGG
1 TAATAATAAT-ATGA
*
39322 TAATAATAATATTAA
1 TAATAATAATA-TGA
39337 TAATAATAATATGGA
1 TAATAATAATAT-GA
39352 TAATAA
1 TAATAA
39358 AAAAATTTAG
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
12 10 0.15
13 1 0.01
14 4 0.06
15 52 0.78
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (14 bp):
TAATAATAATATGA
Found at i:39357 original size:3 final size:3
Alignment explanation
Indices: 39265--39347 Score: 112
Period size: 3 Copynumber: 27.7 Consensus size: 3
39255 TAATATAAAT
* *
39265 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*** *
39313 TAA TAA GGG TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
39348 TGGATAATAA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39801 original size:113 final size:113
Alignment explanation
Indices: 39603--40486 Score: 1331
Period size: 113 Copynumber: 7.8 Consensus size: 113
39593 TCTTGATGAG
* *
39603 TTCTTCTCATTACGAACTT-TCTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTAC-C
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTC
* * * *
39666 TGGCAATGTTGATCTATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
64 TGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
39716 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
39781 GAAAAGATGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
39829 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
39894 GAAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* *
39942 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
40007 GAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* * *
40055 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTCCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
40120 GAAAAGCTGTTCCATCAAATGACGGATTCAAGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
40168 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
40233 GAAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* *
40281 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
40346 GAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
40394 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
40459 GAAAAGATGATTCATCAAATGATGAATT
66 GAAAAGATGATCCATCAAATGATGAATT
40487 TGAATCTTTG
Statistics
Matches: 697, Mismatches: 72, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
112 1 0.00
113 695 1.00
114 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
Found at i:40223 original size:339 final size:339
Alignment explanation
Indices: 39603--40486 Score: 1522
Period size: 339 Copynumber: 2.6 Consensus size: 339
39593 TCTTGATGAG
* * *
39603 TTCTTCTCATTACGAACTTTC-TCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTAC-C
1 TTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT-CTC
* * * * * *
39666 TGGCAATGTTGATCTATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
64 TGGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGA
*
39731 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCAT
129 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGTTCCAT
* * *
39796 CAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
194 CAAATGACGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTT
39861 CAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATTCACCAAATGATGGATTCAGG
259 CAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATTCACCAAATGATGGATTCAGG
39926 TAAAAGGTTGAACAAA
324 TAAAAGGTTGAACAAA
39942 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
*
40007 GAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTTATTATGAAC
66 GAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
* * *
40072 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTCCTCTGGAAAAGCTGTTCCATCA
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGTTCCATCA
* ** *
40137 AATGACGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
196 AATGACGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
40202 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATTCACCAAATGATGGATTCAGGTA
261 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATTCACCAAATGATGGATTCAGGTA
40267 AAAGGTTGAACAAA
326 AAAGGTTGAACAAA
40281 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
40346 GAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
66 GAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
40411 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATT-CATC
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATG-TTCCATC
*
40475 AAATGATGAATT
195 AAATGACGAATT
40487 TGAATCTTTG
Statistics
Matches: 515, Mismatches: 27, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
338 5 0.01
339 508 0.99
340 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (339 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
GAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGTTCCATCA
AATGACGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATTCACCAAATGATGGATTCAGGTA
AAAGGTTGAACAAA
Found at i:40887 original size:84 final size:84
Alignment explanation
Indices: 40790--41097 Score: 589
Period size: 84 Copynumber: 3.7 Consensus size: 84
40780 ATGTTGATTC
40790 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAA
1 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAA
40855 ATTCATCTTCCAAATTCAA
66 ATTCATCTTCCAAATTCAA
*
40874 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAGGAACACTTCCAGAAGATGCTATTGAGCAA
1 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAA
40939 ATTCATCTTCCAAATTCAA
66 ATTCATCTTCCAAATTCAA
*
40958 TGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAA
1 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAA
41023 ATTCATCTTCCAAATTCAA
66 ATTCATCTTCCAAATTCAA
*
41042 TGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
41098 TCGAGTGTCC
Statistics
Matches: 221, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 221 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.26
Consensus pattern (84 bp):
TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAA
ATTCATCTTCCAAATTCAA
Found at i:41960 original size:11 final size:11
Alignment explanation
Indices: 41932--41966 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
41922 ACCTTGACCC
*
41932 TCCTTTTTTCT
1 TCCTTTTTTTT
41943 TCTCTTTTTTTT
1 TC-CTTTTTTTT
41955 TCCTTTTTTTT
1 TCCTTTTTTTT
41966 T
1 T
41967 TTTCTTCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TCCTTTTTTTT
Found at i:52620 original size:17 final size:17
Alignment explanation
Indices: 52580--52621 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
52570 ATACTTGCAA
*
52580 ATAAAACATATAAATATT
1 ATAAAA-ATATAAATATC
52598 ATAAAAATAATAAATA-C
1 ATAAAAAT-ATAAATATC
52615 ATAAAAA
1 ATAAAAA
52622 ATTTGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATATAAATATC
Found at i:53132 original size:30 final size:32
Alignment explanation
Indices: 53065--53134 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 32
53055 TTTAAAATAC
* *
53065 AAAAATATATTTAATTTATAATTCTATTATTT
1 AAAAATATATATAATTAATAATTCTATTATTT
*
53097 CAAAAT-TATATAATTAAT-ATT-TATTTATTT
1 AAAAATATATATAATTAATAATTCTA-TTATTT
53127 AAAAATAT
1 AAAAATAT
53135 CAGAAAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 2 0.06
30 14 0.44
31 11 0.34
32 5 0.16
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
AAAAATATATATAATTAATAATTCTATTATTT
Found at i:54222 original size:21 final size:21
Alignment explanation
Indices: 54195--54235 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
54185 TTGGTATAGT
54195 TTGTTTTTTTCTTT-TCTCTG
1 TTGTTTTTTTCTTTCTCTCTG
*
54215 TTTTTTTTTTCTTTCTCTCTG
1 TTGTTTTTTTCTTTCTCTCTG
54236 GTTCTGTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (21 bp):
TTGTTTTTTTCTTTCTCTCTG
Found at i:54839 original size:15 final size:14
Alignment explanation
Indices: 54753--54842 Score: 89
Period size: 15 Copynumber: 6.4 Consensus size: 14
54743 TAATATAAAT
54753 TAATAATAATA--A
1 TAATAATAATATGA
54765 TAATAATAATAATGA
1 TAATAATAAT-ATGA
54780 TAATAATAATAT--
1 TAATAATAATATGA
* *
54792 TAATAATAATAAGGG
1 TAATAATAAT-ATGA
*
54807 TAATAATAATATTAA
1 TAATAATAATA-TGA
54822 TAATAATAATATGGA
1 TAATAATAATAT-GA
54837 TAATAA
1 TAATAA
54843 AAAAATTTAG
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
12 20 0.31
13 2 0.03
14 4 0.06
15 39 0.60
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (14 bp):
TAATAATAATATGA
Found at i:54842 original size:3 final size:3
Alignment explanation
Indices: 54753--54832 Score: 106
Period size: 3 Copynumber: 26.7 Consensus size: 3
54743 TAATATAAAT
* *
54753 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*** *
54801 TAA GGG TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
54833 TGGATAATAA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:57089 original size:31 final size:31
Alignment explanation
Indices: 57054--57115 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
57044 CACGGAAGTA
*
57054 TGAAATATTTCTTGGCCACCTCGCAAGGAAC
1 TGAAATATTTCTTCGCCACCTCGCAAGGAAC
57085 TGAAATATTTCTTCGCCACCTCGCAAGGAAC
1 TGAAATATTTCTTCGCCACCTCGCAAGGAAC
57116 GTTATTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (31 bp):
TGAAATATTTCTTCGCCACCTCGCAAGGAAC
Found at i:57656 original size:14 final size:14
Alignment explanation
Indices: 57637--57690 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
57627 TATAAAAACA
* *
57637 AAATCAAAATGAGT
1 AAATCAAAATAAAT
57651 AAATCAAAATAAAT
1 AAATCAAAATAAAT
** *
57665 AAATCAAAGGAAAA
1 AAATCAAAATAAAT
57679 AAAT-AAAATAAA
1 AAATCAAAATAAA
57691 AAGAAAAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
13 6 0.18
14 27 0.82
ACGTcount: A:0.70, C:0.06, G:0.07, T:0.17
Consensus pattern (14 bp):
AAATCAAAATAAAT
Found at i:57687 original size:19 final size:18
Alignment explanation
Indices: 57656--57698 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
57646 TGAGTAAATC
* *
57656 AAAATAAATAAATCAAAGG
1 AAAA-AAATAAATAAAAAG
57675 AAAAAAATAAAATAAAAAG
1 AAAAAAAT-AAATAAAAAG
57694 AAAAA
1 AAAAA
57699 TGAGAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (18 bp):
AAAAAAATAAATAAAAAG
Found at i:57767 original size:22 final size:22
Alignment explanation
Indices: 57714--57760 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
57704 AAAAATGAGA
57714 AATAAGTAAATTAAAATAAAAAT
1 AATAA-TAAATTAAAATAAAAAT
*
57737 AGTAATAAA-TAATAATAAAAAT
1 AATAATAAATTAA-AATAAAAAT
57759 AA
1 AA
57761 ATATAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
21 3 0.14
22 14 0.67
23 4 0.19
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (22 bp):
AATAATAAATTAAAATAAAAAT
Found at i:57825 original size:37 final size:36
Alignment explanation
Indices: 57778--57897 Score: 133
Period size: 37 Copynumber: 3.4 Consensus size: 36
57768 AAAGTGTTTA
*
57778 AAAACTATATATTATAAATTTTTAAAAATGTTTTTTT
1 AAAACTATATATTATAAATTTTAAAAAAT-TTTTTTT
* *
57815 AAAACTATATATTATAAATTTTCAAAAATATTTTTT
1 AAAACTATATATTATAAATTTTAAAAAATTTTTTTT
*
57851 GAAA-T-T-TA-TAT-AATTTTCAAAAAAATATTTTTTT
1 AAAACTATATATTATAAATTTT--AAAAAAT-TTTTTTT
57885 AAAACTATATATT
1 AAAACTATATATT
57898 TTCAAAAATA
Statistics
Matches: 70, Mismatches: 6, Indels: 13
0.79 0.07 0.15
Matches are distributed among these distances:
31 6 0.09
32 3 0.04
33 8 0.11
34 10 0.14
35 2 0.03
36 10 0.14
37 30 0.43
38 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (36 bp):
AAAACTATATATTATAAATTTTAAAAAATTTTTTTT
Found at i:57874 original size:32 final size:31
Alignment explanation
Indices: 57825--57924 Score: 116
Period size: 33 Copynumber: 3.3 Consensus size: 31
57815 AAAACTATAT
57825 ATTATA-AATTTTCAAAAATATTTTTTGAAA
1 ATTATATAATTTTCAAAAATATTTTTTGAAA
* *
57855 TTTATATAATTTTCAAAAAAATATTTTTTTAAA
1 ATTATATAATTTTC--AAAAATATTTTTTGAAA
* **
57888 ACTATAT-ATTTTCAAAAATA-TTTTCAAAA
1 ATTATATAATTTTCAAAAATATTTTTTGAAA
57917 ATTATATA
1 ATTATATA
57925 TTATATAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
29 13 0.22
30 12 0.20
31 7 0.12
32 6 0.10
33 21 0.36
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (31 bp):
ATTATATAATTTTCAAAAATATTTTTTGAAA
Found at i:57910 original size:12 final size:12
Alignment explanation
Indices: 57893--57918 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
57883 TTAAAACTAT
57893 ATATTTTCAAAA
1 ATATTTTCAAAA
57905 ATATTTTCAAAA
1 ATATTTTCAAAA
57917 AT
1 AT
57919 TATATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATTTTCAAAA
Found at i:57925 original size:31 final size:30
Alignment explanation
Indices: 57826--57926 Score: 107
Period size: 30 Copynumber: 3.3 Consensus size: 30
57816 AAACTATATA
* *
57826 TTATAAATTTTCAAAAATATTTTTTGAAAT
1 TTATATATTTTCAAAAATATTTTTTAAAAT
57856 TTATATAATTTTCAAAAAAATATTTTTTTAAAA-
1 TTATAT-ATTTTC--AAAAATA-TTTTTTAAAAT
* * *
57889 CTATATATTTTCAAAAATA-TTTTCAAAAA
1 TTATATATTTTCAAAAATATTTTTTAAAAT
57918 TTATATATT
1 TTATATATT
57927 ATATAAGTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
28 8 0.13
29 8 0.13
30 12 0.20
31 6 0.10
32 6 0.10
33 12 0.20
34 9 0.15
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.49
Consensus pattern (30 bp):
TTATATATTTTCAAAAATATTTTTTAAAAT
Found at i:57992 original size:37 final size:37
Alignment explanation
Indices: 57896--58115 Score: 270
Period size: 37 Copynumber: 5.9 Consensus size: 37
57886 AAACTATATA
* *
57896 TTTTCAAAAATATTTTCAAAAATTATATATTATATAAG
1 TTTTCAAAAATGTTTT-AAAAACTATATATTATATAAG
57934 TTTTCAAAAATGTTTTCAAAAACTATATATTATATAAG
1 TTTTCAAAAATGTTTT-AAAAACTATATATTATATAAG
* **
57972 TTTTC-AAAATGATTTTAAAAATTATATATTATATATT
1 TTTTCAAAAATG-TTTTAAAAACTATATATTATATAAG
* *
58009 TTTTCTAAAATGTTTTAAAAATTATATATTATAT-AG
1 TTTTCAAAAATGTTTTAAAAACTATATATTATATAAG
*
58045 -TTTCAAAAGTGTTTTAAAAACTATATATTATATACA-
1 TTTTCAAAAATGTTTTAAAAACTATATATTATATA-AG
* *
58081 TTTTC-AAAATAATTTTATAAACTATATATTATATA
1 TTTTCAAAAAT-GTTTTAAAAACTATATATTATATA
58116 CGTATTTTCA
Statistics
Matches: 163, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
35 30 0.18
36 4 0.02
37 78 0.48
38 51 0.31
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTTCAAAAATGTTTTAAAAACTATATATTATATAAG
Found at i:58076 original size:72 final size:70
Alignment explanation
Indices: 57890--58115 Score: 272
Period size: 72 Copynumber: 3.1 Consensus size: 70
57880 TTTTTAAAAC
* * *
57890 TATATATTTTCAAAAATATTTTCAAAAATTATATATTATATAAGTTTTCAAAAATGTTTTCAAAA
1 TATATAGTTTC-AAAATGTTTT-AAAAATTATATATTATATAAATTTTC-AAAATGTTTT-AAAA
57955 ACTATATAT
62 ACTATATAT
**
57964 TATATAAGTTTTCAAAATGATTTTAAAAATTATATATTATATATTTTTTCTAAAATGTTTTAAAA
1 TATAT-AG-TTTCAAAATG-TTTTAAAAATTATATATTATATAAATTTTC-AAAATGTTTTAAAA
*
58029 ATTATATAT
62 ACTATATAT
* * * *
58038 TATATAGTTTCAAAAGTGTTTTAAAAACTATATATTATATACATTTTCAAAATAATTTTATAAAC
1 TATATAGTTTCAAAA-TGTTTTAAAAATTATATATTATATAAATTTTCAAAAT-GTTTTAAAAAC
58103 TATATAT
64 TATATAT
58110 TATATA
1 TATATA
58116 CGTATTTTCA
Statistics
Matches: 135, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
71 5 0.04
72 56 0.41
73 4 0.03
74 22 0.16
75 40 0.30
76 8 0.06
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (70 bp):
TATATAGTTTCAAAATGTTTTAAAAATTATATATTATATAAATTTTCAAAATGTTTTAAAAACTA
TATAT
Found at i:58144 original size:109 final size:111
Alignment explanation
Indices: 57890--58152 Score: 311
Period size: 109 Copynumber: 2.4 Consensus size: 111
57880 TTTTTAAAAC
* ** *
57890 TATATATTTTCAAAAATATTTTCAAAAATTATATATTATATAAGTTTTCAAAAATGTTTTCAAAA
1 TATATATTTTCTAAAACGTTTT-AAAAACTATATATTATAT-AGTTTTCAAAAATGTTTTCAAAA
* *
57955 ACTATATATTATATAAGTTTTCAAAATGATTTTAAAAATTATATATTA
64 ACTATATATTATATAAGTTTTCAAAATAATTTTAAAAACTATATATTA
* * * *
58003 TATATTTTTTCTAAAATGTTTTAAAAATTATATATTATATAG-TTTCAAAAGTGTTTT-AAAAAC
1 TATATATTTTCTAAAACGTTTTAAAAACTATATATTATATAGTTTTCAAAAATGTTTTCAAAAAC
*
58066 TATATATTATATACA-TTTTCAAAATAATTTTATAAACTATATATTA
66 TATATATTATATA-AGTTTTCAAAATAATTTTAAAAACTATATATTA
* ** *
58112 TATACGTATTTTC-AAACCG-TTTGCAAACTATATAATATATA
1 TATA--TATTTTCTAAAACGTTTTAAAAACTATATATTATATA
58153 TAGATATGTG
Statistics
Matches: 133, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
109 69 0.52
110 19 0.14
111 8 0.06
112 18 0.14
113 19 0.14
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (111 bp):
TATATATTTTCTAAAACGTTTTAAAAACTATATATTATATAGTTTTCAAAAATGTTTTCAAAAAC
TATATATTATATAAGTTTTCAAAATAATTTTAAAAACTATATATTA
Found at i:58581 original size:22 final size:24
Alignment explanation
Indices: 58528--58581 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
58518 ATCAATTTTA
58528 TAATATTTAATTAAATAATTATTT
1 TAATATTTAATTAAATAATTATTT
*
58552 TAATATTT-TTTAAA-AA-TATTT
1 TAATATTTAATTAAATAATTATTT
58573 TCAATATTT
1 T-AATATTT
58582 CATTTATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 6 0.21
22 9 0.32
23 5 0.18
24 8 0.29
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TAATATTTAATTAAATAATTATTT
Found at i:59807 original size:32 final size:32
Alignment explanation
Indices: 59771--59853 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
59761 ACTCATGTGC
*
59771 ATTATCTGAATGCAACACTAACTCTATTTTAA
1 ATTATCTGAATGCAACACTAACTATATTTTAA
* * **
59803 ATTATCTAAATGCAACACTGACTATATTTTGC
1 ATTATCTGAATGCAACACTAACTATATTTTAA
* *
59835 ATTATTTGAATACAACACT
1 ATTATCTGAATGCAACACT
59854 TGCTTTGTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.37
Consensus pattern (32 bp):
ATTATCTGAATGCAACACTAACTATATTTTAA
Found at i:59845 original size:64 final size:63
Alignment explanation
Indices: 59768--59889 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 63
59758 GACACTCATG
*
59768 TGCATTATCTGAATGCAACACTAACTCTATTTTAAATTATCTAAATGCAACACTGACTATATTT
1 TGCATTATCTGAATACAACACTAACTCTATTTTAAATTATCTAAATGCAACACT-ACTATATTT
* ** * * ** *
59832 TGCATTATTTGAATACAACACTTGCTTTGTTTTGCATTATTTAAATGCAACACTACTA
1 TGCATTATCTGAATACAACACTAACTCTATTTTAAATTATCTAAATGCAACACTACTA
59890 GTATATGATC
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
63 4 0.08
64 45 0.92
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (63 bp):
TGCATTATCTGAATACAACACTAACTCTATTTTAAATTATCTAAATGCAACACTACTATATTT
Found at i:61682 original size:16 final size:17
Alignment explanation
Indices: 61658--61690 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
61648 AAAGTGGAGA
*
61658 AAAGAAGAAGAAGAAAT
1 AAAGAAGAAAAAGAAAT
61675 AAAG-AGAAAAAGAAAT
1 AAAGAAGAAAAAGAAAT
61691 GAATAAGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (17 bp):
AAAGAAGAAAAAGAAAT
Found at i:65383 original size:12 final size:12
Alignment explanation
Indices: 65366--65391 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
65356 TCTAATTGAG
65366 ATGCCAAACTTT
1 ATGCCAAACTTT
65378 ATGCCAAACTTT
1 ATGCCAAACTTT
65390 AT
1 AT
65392 AGTAAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (12 bp):
ATGCCAAACTTT
Found at i:65545 original size:27 final size:27
Alignment explanation
Indices: 65515--65572 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
65505 AAAAACATAT
65515 TAATATCATCATTCTCAAGCGTTGAGA
1 TAATATCATCATTCTCAAGCGTTGAGA
65542 TAATATCATCATTCTCAAGCGTTGAGA
1 TAATATCATCATTCTCAAGCGTTGAGA
65569 TAAT
1 TAAT
65573 GGTAGAGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (27 bp):
TAATATCATCATTCTCAAGCGTTGAGA
Found at i:71181 original size:23 final size:23
Alignment explanation
Indices: 71155--71246 Score: 96
Period size: 23 Copynumber: 4.0 Consensus size: 23
71145 CACCACAACT
*
71155 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
71178 CGTAGAATTGCACCGAAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
* *
71201 TGTAGAATTGCACCGAAGTG-CA
1 CGTAGAAATGCACCGAAGTGCCA
* *
71223 GCATAGAAATACACCGAAGTGCCA
1 -CGTAGAAATGCACCGAAGTGCCA
71247 TATAAAATGT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
22 1 0.02
23 54 0.95
24 2 0.04
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:72480 original size:60 final size:60
Alignment explanation
Indices: 72413--72525 Score: 190
Period size: 60 Copynumber: 1.9 Consensus size: 60
72403 AATTTTAAGG
**
72413 GGGTGCATCGATACACTAACTGTGCATCGGTACACTCCTGGCATTCGATGTTTTTTAAAT
1 GGGTGCATCGATACACTAACTGTGCATCGGTACACTCAAGGCATTCGATGTTTTTTAAAT
* *
72473 GGGTGCATCGATGCACTAACTGTGCATCGGTATACTCAAGGCATTCGATGTTT
1 GGGTGCATCGATACACTAACTGTGCATCGGTACACTCAAGGCATTCGATGTTT
72526 CTTCTTTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (60 bp):
GGGTGCATCGATACACTAACTGTGCATCGGTACACTCAAGGCATTCGATGTTTTTTAAAT
Found at i:77271 original size:16 final size:17
Alignment explanation
Indices: 77252--77284 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
77242 CATATCTCTT
77252 ATCTCTT-GTTCATATG
1 ATCTCTTAGTTCATATG
77268 ATCTCTTACGTTCATAT
1 ATCTCTTA-GTTCATAT
77285 TCTATATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.48
Consensus pattern (17 bp):
ATCTCTTAGTTCATATG
Found at i:77660 original size:30 final size:30
Alignment explanation
Indices: 77620--77712 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 30
77610 CCGAAGGACC
77620 ACTATCCATATGTTCTGAAGAACATAGGTA
1 ACTATCCATATGTTCTGAAGAACATAGGTA
* * *
77650 ACTGTCCATATGTCCCT-AAGGACATAGGTAA
1 ACTATCCATATGT-TCTGAAGAACATAGGT-A
*
77681 ACTATCTATATG-TCTCGAA-ATACATAGGTA
1 ACTATCCATATGTTCT-GAAGA-ACATAGGTA
77711 AC
1 AC
77713 CCTCGACTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
29 2 0.04
30 26 0.51
31 23 0.45
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (30 bp):
ACTATCCATATGTTCTGAAGAACATAGGTA
Found at i:77706 original size:31 final size:30
Alignment explanation
Indices: 77620--77711 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 30
77610 CCGAAGGACC
77620 ACTATCCATATGT-TCTGAAGAACATAGGT-A
1 ACTATCCATATGTCTC-GAA-AACATAGGTAA
* * * *
77650 ACTGTCCATATGTCCCTAAGGACATAGGTAA
1 ACTATCCATATGTCTCGAA-AACATAGGTAA
*
77681 ACTATCTATATGTCTCGAAATACATAGGTAA
1 ACTATCCATATGTCTCGAAA-ACATAGGTAA
77712 CCCTCGACTC
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
30 23 0.46
31 27 0.54
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (30 bp):
ACTATCCATATGTCTCGAAAACATAGGTAA
Found at i:83797 original size:41 final size:41
Alignment explanation
Indices: 83752--83843 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
83742 TTCCATAATT
* * * *
83752 CAATTCAATTCGGTCATGAAAACATGTATTTATTCACAAAC
1 CAATTCAATTAGATAATGAAAACATGTATTAATTCACAAAC
** *
83793 CAATTCAATTAGATAATGGTAACATGTATTAATTCACAATC
1 CAATTCAATTAGATAATGAAAACATGTATTAATTCACAAAC
83834 CAATTCAATT
1 CAATTCAATT
83844 TAACCAATGC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (41 bp):
CAATTCAATTAGATAATGAAAACATGTATTAATTCACAAAC
Done.