Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 8 of 22
Found at i:4033253 original size:124 final size:125
Alignment explanation
Indices: 4033007--4033290 Score: 277
Period size: 124 Copynumber: 2.3 Consensus size: 125
4032997 AAATACTTTA
* * * * *
4033007 AACATGGTGTGTAATAATTTTTTTTTTTCAACATAGCATATAACTTGGTCTCTATCTTTGTATTT
1 AACATGATGTGTAATAA--TTTTTTTTTCAACATAACATATAACTTGATCTCTATATTTGTACTT
* * ** * * *
4033072 CACTATAGCATAAATTTTTAGAATTAAGTATATTAAACATGATGTATAATAACTTTTTTTT-
64 CACTAGAGCATAAATTCTTAGAATTAAACACATTAAACATGATGTATAACAAATTTTTTTTC
* * * *
4033133 AATATGATGTGTAATAATTTTTTTTTCAACTTAACGTGTAACTTGATCTCTATATTTGTACTTCA
1 AACATGATGTGTAATAATTTTTTTTTCAACATAACATATAACTTGATCTCTATATTTGTACTTCA
** * * *
4033198 CTACGA-CAT-AATTCTTAGCGTTAAACACCTTAAACATGGTGTGTAACAATATTTTTTTTCC
66 CTA-GAGCATAAATTCTTAGAATTAAACACATTAAACATGATGTATAACAA-ATTTTTTTT-C
* * * *
4033259 AACATGGTGTTTAATAATATTTTTTTGAACAT
1 AACATGATGTGTAATAATTTTTTTTTCAACAT
4033291 GGTATGTAAC
Statistics
Matches: 127, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
123 30 0.24
124 55 0.43
125 1 0.01
126 41 0.32
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (125 bp):
AACATGATGTGTAATAATTTTTTTTTCAACATAACATATAACTTGATCTCTATATTTGTACTTCA
CTAGAGCATAAATTCTTAGAATTAAACACATTAAACATGATGTATAACAAATTTTTTTTC
Found at i:4033281 original size:27 final size:27
Alignment explanation
Indices: 4033230--4033311 Score: 92
Period size: 27 Copynumber: 2.9 Consensus size: 27
4033220 AAACACCTTA
4033230 AACATGGTGTGTAACAATATTTTTTTTCC
1 AACATGGTGTGTAACAATA--TTTTTTCC
* * **
4033259 AACATGGTGTTTAATAATATTTTTTTG
1 AACATGGTGTGTAACAATATTTTTTCC
*
4033286 AACATGGTATGTAACAATATTATTTT
1 AACATGGTGTGTAACAATATT-TTTT
4033312 TTAAGTATGA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 24 0.53
28 4 0.09
29 17 0.38
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (27 bp):
AACATGGTGTGTAACAATATTTTTTCC
Found at i:4033311 original size:29 final size:29
Alignment explanation
Indices: 4033230--4033313 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
4033220 AAACACCTTA
4033230 AACATGGTGTGTAACAATATTTTTTTTCC
1 AACATGGTGTGTAACAATATTTTTTTTCC
* * *
4033259 AACATGGTGTTTAATAATA-TTTTTTT-G
1 AACATGGTGTGTAACAATATTTTTTTTCC
*
4033286 AACATGGTATGTAACAATATTATTTTTT
1 AACATGGTGTGTAACAATATT-TTTTTT
4033314 AAGTATGAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.34
28 8 0.17
29 23 0.49
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (29 bp):
AACATGGTGTGTAACAATATTTTTTTTCC
Found at i:4051502 original size:3 final size:3
Alignment explanation
Indices: 4051494--4051520 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4051484 TCCCCATATG
4051494 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
4051521 CTCGTTGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:4051806 original size:2 final size:2
Alignment explanation
Indices: 4051799--4051829 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4051789 AATTGATTAT
4051799 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4051830 ATACAGAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4057897 original size:2 final size:2
Alignment explanation
Indices: 4057890--4057915 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4057880 CTAATTATTG
4057890 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
4057916 GAGTAACTCC
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:4069263 original size:2 final size:2
Alignment explanation
Indices: 4069256--4069290 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4069246 AGTTCACAGG
4069256 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4069291 CACAATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4073470 original size:12 final size:12
Alignment explanation
Indices: 4073453--4073477 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4073443 GATAAAATTA
4073453 TACTCTCTGTTT
1 TACTCTCTGTTT
4073465 TACTCTCTGTTT
1 TACTCTCTGTTT
4073477 T
1 T
4073478 GCTCCAACAA
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:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (12 bp):
TACTCTCTGTTT
Found at i:4074282 original size:1 final size:1
Alignment explanation
Indices: 4074276--4074332 Score: 114
Period size: 1 Copynumber: 57.0 Consensus size: 1
4074266 CATCAAGGAA
4074276 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
4074333 ATAGAGTTCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:4080277 original size:2 final size:2
Alignment explanation
Indices: 4080270--4080297 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4080260 CGTTAAATCA
4080270 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
4080298 TGCGTATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4080492 original size:17 final size:16
Alignment explanation
Indices: 4080466--4080504 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
4080456 TTAAAATCTC
*
4080466 AATATATTTTGAATAA
1 AATATATTTTAAATAA
*
4080482 TATATATTTTTAAATAA
1 AATATA-TTTTAAATAA
4080499 AATATA
1 AATATA
4080505 CATTTTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
AATATATTTTAAATAA
Found at i:4085765 original size:29 final size:29
Alignment explanation
Indices: 4085716--4085771 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
4085706 ATGTAAGGCG
*
4085716 GATATTTTAAAAATATTTTTTATATATAA
1 GATATTTTAAAAATATATTTTATATATAA
* *
4085745 GATATTTTTGAAAATA-ATTTTTTATAT
1 GATA-TTTTAAAAATATATTTTATATAT
4085772 TTTTAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (29 bp):
GATATTTTAAAAATATATTTTATATATAA
Found at i:4085827 original size:18 final size:18
Alignment explanation
Indices: 4085776--4085827 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 18
4085766 TTATATTTTT
* *
4085776 AATTATTTTTAATTAAAA
1 AATTATTTTTAATGATAA
*
4085794 AATTTAATTTT-A-GATAA
1 AA-TTATTTTTAATGATAA
4085811 AATTATTTTTAATGATA
1 AATTATTTTTAATGATA
4085828 TCGATTCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.26
17 6 0.22
18 7 0.26
19 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
AATTATTTTTAATGATAA
Found at i:4089426 original size:22 final size:22
Alignment explanation
Indices: 4089381--4089426 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4089371 TGTTGATAGG
*
4089381 ATTAAATATGAAATATATTAAA
1 ATTAAATATGAAATATAATAAA
4089403 ATTAAATAT-AAATATAATATAA
1 ATTAAATATGAAATATAATA-AA
4089425 AT
1 AT
4089427 ATTATTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
ATTAAATATGAAATATAATAAA
Found at i:4089838 original size:18 final size:18
Alignment explanation
Indices: 4089791--4089843 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
4089781 TCATGTATAC
4089791 ACATTTAAACACGATAAT
1 ACATTTAAACACGATAAT
* * *
4089809 ACGA-TTATACACGTTTAT
1 AC-ATTTAAACACGATAAT
4089827 ACATTTAAACACGATAA
1 ACATTTAAACACGATAA
4089844 CAAAATTAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (18 bp):
ACATTTAAACACGATAAT
Found at i:4111962 original size:15 final size:15
Alignment explanation
Indices: 4111944--4111981 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4111934 TTTGTATATA
4111944 TTATAATTAATAA-TT
1 TTATAATT-ATAATTT
4111959 TTATAAATTATAATTT
1 TTAT-AATTATAATTT
4111975 TTATAAT
1 TTATAAT
4111982 GTTAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATAATTATAATTT
Found at i:4111976 original size:16 final size:16
Alignment explanation
Indices: 4111944--4111980 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4111934 TTTGTATATA
4111944 TTAT-AATTAATAATT
1 TTATAAATTAATAATT
4111959 TTATAAATT-ATAATTT
1 TTATAAATTAATAA-TT
4111975 TTATAA
1 TTATAA
4111981 TGTTAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATAAATTAATAATT
Found at i:4112916 original size:341 final size:348
Alignment explanation
Indices: 4112042--4112916 Score: 978
Period size: 341 Copynumber: 2.5 Consensus size: 348
4112032 TATATAAATA
*
4112042 ATAGTAAT-TATATTCTCTATAAATGAACCCAACATATATAAAGTATAGATATT-AAAAACATTA
1 ATAGTAATATAT-TTCT-TATAAATGAA-CCAAAATATATAAAGTAT--ATATTAAAAAACATTA
* * * * * *
4112105 GAATTTAATTAATAATCATAGTTTTATTAATTAATTTAATTAATTATGTGAGTTCGTCTTTAATT
61 CAAATTAATTAATAATCATAATTTTATAAATTAATTTAATTAATTATATGAGTTTGTCTTTAATT
* * *
4112170 ACATGAAATTAAAAAAAAACTAAATT-TCAAAACTATTGTAATCTCACAACTTCTTTTTAAATAA
126 ACATGAAATTAAAAAAATACTAAATTCTCAAAACTATTATAATCTCACAACTTCTTCTTAAATAA
* * * *
4112234 TTAAATTTATATATTATAAGTTTATATAAATAAAAATATGTATATTATAATTAATAATTTTATAA
191 TT--ATGTATATATTATAAGTTTATACAAATAAAAATATATATATTATAATTAATAATTTTACAA
*
4112299 GTTAAAATATTTGTAATGTTAATACAAAATAGAAAATAAATATGCTTATATTTAAAGTATATATA
254 GTTAAAATATTTGTAATGTTAATACAAAATAGAAAATAAATATACTTATATTTAAAGTATATATA
* *
4112364 TGTGTACACACACTAAAAGTATTTTACTATATGTAT
319 ---GT--A-ACACTAAAAGTATTTTACTATATGAAC
*
4112400 ATTAGTAATTATATTAT-TTATAAATGAACTCAAAATATATAAAGTAAATATATTAAAAGACATT
1 A-TAGTAA-TATATT-TCTTATAAATGAAC-CAAAATATATAAAGT--ATATATTAAAAAACATT
** * * * *
4112464 ACAAGGTCATTAATAATCATAATTTTGTAAATTAATTTAATTAATTATATGACTTTGTCCTTAAT
60 ACAAATTAATTAATAATCATAATTTTATAAATTAATTTAATTAATTATATGAGTTTGTCTTTAAT
* *
4112529 TACATGAAATTAAAAAAAATACT-AAGTCTCAAAACTATTTTAATCTCACAACTTC-TCTT-AA-
125 TACATGAAATT-AAAAAAATACTAAATTCTCAAAACTATTATAATCTCACAACTTCTTCTTAAAT
* * ** *
4112590 GATT-TGTA-A-ATTGTAAGTTTATACAAATAAAGGTGTATATATTATAATTAATAATTTTACAA
189 AATTATGTATATATTATAAGTTTATACAAATAAAAATATATATATTATAATTAATAATTTTACAA
* * *
4112652 GTTATAAAT-TTTGTAATGTTAATATAAAATAGAAAGTAAATATATTTATATTTAAAGT-T-TAT
254 GTTA-AAATATTTGTAATGTTAATACAAAATAGAAAATAAATATACTTATATTTAAAGTATATAT
*
4112714 A-T-ATACTAAAAGTATTAGTGTA-TATAT-AAC
318 AGTAACACTAAAAGTATT--T-TACTATATGAAC
* * * *
4112744 ATAGTATATATATTTCTTATAAATGAATCCAATATATATAATGTATATATTAAAAAATATTATAA
1 ATAGTA-ATATATTTCTTATAAATGAA-CCAAAATATATAAAGTATATATTAAAAAACATTACAA
* * * *
4112809 ATTAATTAATAATAATAATTTAATGAATTAATTTAATTAAATATATGAGTTTGTCTTTAATTACA
64 ATTAATTAATAATCATAATTTTATAAATTAATTTAATTAATTATATGAGTTTGTCTTTAATTACA
*
4112874 TGAAATTAAAAAAATAGTTAAATTCT-AAAACTATTATAATCTC
129 TGAAATTAAAAAAATA-CTAAATTCTCAAAACTATTATAATCTC
4112917 CAAGACTTTC
Statistics
Matches: 447, Mismatches: 51, Indels: 55
0.81 0.09 0.10
Matches are distributed among these distances:
340 9 0.02
341 97 0.22
342 6 0.01
343 48 0.11
344 4 0.01
345 6 0.01
346 2 0.00
347 1 0.00
351 4 0.01
352 1 0.00
353 95 0.21
354 5 0.01
355 3 0.01
358 5 0.01
359 37 0.08
360 82 0.18
361 42 0.09
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (348 bp):
ATAGTAATATATTTCTTATAAATGAACCAAAATATATAAAGTATATATTAAAAAACATTACAAAT
TAATTAATAATCATAATTTTATAAATTAATTTAATTAATTATATGAGTTTGTCTTTAATTACATG
AAATTAAAAAAATACTAAATTCTCAAAACTATTATAATCTCACAACTTCTTCTTAAATAATTATG
TATATATTATAAGTTTATACAAATAAAAATATATATATTATAATTAATAATTTTACAAGTTAAAA
TATTTGTAATGTTAATACAAAATAGAAAATAAATATACTTATATTTAAAGTATATATAGTAACAC
TAAAAGTATTTTACTATATGAAC
Found at i:4113166 original size:19 final size:19
Alignment explanation
Indices: 4113131--4113169 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4113121 GTAATAATAT
*
4113131 TTTTTAATATAGTTATTAA
1 TTTTTAATATAATTATTAA
4113150 TTTTTAATA-AATATATTAA
1 TTTTTAATATAAT-TATTAA
4113169 T
1 T
4113170 ATTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTTAATATAATTATTAA
Found at i:4113191 original size:15 final size:16
Alignment explanation
Indices: 4113165--4113195 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4113155 AATAAATATA
4113165 TTAATATTAATTATTT
1 TTAATATTAATTATTT
4113181 TTAAT-TTAATTATTT
1 TTAATATTAATTATTT
4113196 AAATAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATATTAATTATTT
Found at i:4134454 original size:2 final size:2
Alignment explanation
Indices: 4134449--4134474 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4134439 AGAGAATTAA
4134449 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
4134475 GTGTGTGTGT
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:4135631 original size:2 final size:2
Alignment explanation
Indices: 4135624--4135666 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4135614 GTTTTATGGA
4135624 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
4135666 A
1 A
4135667 AAAGACTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4164338 original size:28 final size:28
Alignment explanation
Indices: 4164298--4164381 Score: 159
Period size: 28 Copynumber: 3.0 Consensus size: 28
4164288 TTTATGAGAA
*
4164298 AAAGAAAAATAATACAGGCTAGCTGCCT
1 AAAGAAAAATAATACAGGCTAGCAGCCT
4164326 AAAGAAAAATAATACAGGCTAGCAGCCT
1 AAAGAAAAATAATACAGGCTAGCAGCCT
4164354 AAAGAAAAATAATACAGGCTAGCAGCCT
1 AAAGAAAAATAATACAGGCTAGCAGCCT
4164382 TACAGTATAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.15
Consensus pattern (28 bp):
AAAGAAAAATAATACAGGCTAGCAGCCT
Found at i:4170976 original size:29 final size:30
Alignment explanation
Indices: 4170921--4170991 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
4170911 AATCAGGAAG
*
4170921 AACTTACTCCAATTTTGAGGCCGAGATAAA
1 AACTAACTCCAATTTTGAGGCCGAGATAAA
*
4170951 AACTAACTCCAA-TTTGA-GCGCTAGATAAA
1 AACTAACTCCAATTTTGAGGC-CGAGATAAA
* *
4170980 ATCTAATTCCAA
1 AACTAACTCCAA
4170992 GATAAAAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 2 0.06
29 23 0.64
30 11 0.31
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (30 bp):
AACTAACTCCAATTTTGAGGCCGAGATAAA
Found at i:4174287 original size:6 final size:6
Alignment explanation
Indices: 4174266--4174307 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
4174256 TTATCACAGG
* * *
4174266 GTGTGT GTGCGT GCGTGT GCGTGT GTGTGT GTGTGT GTGTGT
1 GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT
4174308 TGCATATATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.07, G:0.50, T:0.43
Consensus pattern (6 bp):
GTGTGT
Found at i:4174293 original size:4 final size:4
Alignment explanation
Indices: 4174266--4174307 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
4174256 TTATCACAGG
* * *
4174266 GTGT GTGT GCGT GCGT GTGC GTGT GTGT GTGT GTGT GTGT GT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GT
4174308 TGCATATATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.00, C:0.07, G:0.50, T:0.43
Consensus pattern (4 bp):
GTGT
Found at i:4174307 original size:10 final size:10
Alignment explanation
Indices: 4174266--4174304 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
4174256 TTATCACAGG
4174266 GTGTGTGTGC
1 GTGTGTGTGC
*
4174276 GTGCGTGTGC
1 GTGTGTGTGC
*
4174286 GTGTGTGTGT
1 GTGTGTGTGC
4174296 GTGTGTGTG
1 GTGTGTGTG
4174305 TGTTGCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.00, C:0.08, G:0.51, T:0.41
Consensus pattern (10 bp):
GTGTGTGTGC
Found at i:4196458 original size:61 final size:60
Alignment explanation
Indices: 4196377--4196511 Score: 166
Period size: 61 Copynumber: 2.2 Consensus size: 60
4196367 AAAGAAAAAC
* * * *
4196377 TTTTAAACA-TTTTGAGTATTTCAGAGT-AGTTTTTGATACATAAAGAAAATCTTTTGAACG
1 TTTT-AACATTTTTAAGTATTTCAGAGTGA-TTTTTGATAAATAAAGAAAAACTTTTGAACA
* *
4196437 TTTTGAACATTTTTAAGTATTTCGGAGTGATTTTTGATAAATAAAGAAAAACTTTTGTACA
1 TTTT-AACATTTTTAAGTATTTCAGAGTGATTTTTGATAAATAAAGAAAAACTTTTGAACA
4196498 TTTTAAGCATTTTT
1 TTTTAA-CATTTTT
4196512 CGTTAAGTAG
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
60 10 0.15
61 54 0.83
62 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.44
Consensus pattern (60 bp):
TTTTAACATTTTTAAGTATTTCAGAGTGATTTTTGATAAATAAAGAAAAACTTTTGAACA
Found at i:4196657 original size:22 final size:21
Alignment explanation
Indices: 4196632--4196689 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
4196622 TATGTTATTA
*
4196632 ATTTTTAAGAATTGTGTGATT
1 ATTTTTAAGTATTGTGTGATT
*
4196653 GATTTTTAGGTATTGTGTGATT
1 -ATTTTTAAGTATTGTGTGATT
4196675 AGTTTTTAAGTATTG
1 A-TTTTTAAGTATTG
4196690 CACTACTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.53
Consensus pattern (21 bp):
ATTTTTAAGTATTGTGTGATT
Found at i:4196757 original size:22 final size:23
Alignment explanation
Indices: 4196731--4196809 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 23
4196721 TTAATATGAT
4196731 ATTGTGTGACTAGTT-GATAAG-C
1 ATTGTGTGACTAGTTAG-TAAGAC
*
4196753 ATTGTGTGACTTGTTAGTAAGAC
1 ATTGTGTGACTAGTTAGTAAGAC
* * * **
4196776 ATTGCGTTACTAGTTAGCAAGGT
1 ATTGTGTGACTAGTTAGTAAGAC
4196799 ATTGTGTGACT
1 ATTGTGTGACT
4196810 TAAGCATCGT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 18 0.39
23 28 0.61
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (23 bp):
ATTGTGTGACTAGTTAGTAAGAC
Found at i:4196791 original size:23 final size:23
Alignment explanation
Indices: 4196731--4196792 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
4196721 TTAATATGAT
*
4196731 ATTGTGTGACTAGTT-GATAAGC
1 ATTGCGTGACTAGTTAGATAAGC
* *
4196753 ATTGTGTGACTTGTTAG-TAAGAC
1 ATTGCGTGACTAGTTAGATAAG-C
*
4196776 ATTGCGTTACTAGTTAG
1 ATTGCGTGACTAGTTAG
4196793 CAAGGTATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 18 0.53
23 16 0.47
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.39
Consensus pattern (23 bp):
ATTGCGTGACTAGTTAGATAAGC
Found at i:4211563 original size:29 final size:29
Alignment explanation
Indices: 4211502--4211563 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 29
4211492 ATTAAATTAT
4211502 ATTATAATATTTATTTTATAATAAATCAC
1 ATTATAATATTTATTTTATAATAAATCAC
*
4211531 --TATAATATATTA-TTT-TAATGTAATCAC
1 ATTATAATAT-TTATTTTATAAT-AAATCAC
4211558 ATTATA
1 ATTATA
4211564 GTTAATGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
26 4 0.14
27 17 0.61
28 3 0.11
29 4 0.14
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (29 bp):
ATTATAATATTTATTTTATAATAAATCAC
Found at i:4211863 original size:33 final size:33
Alignment explanation
Indices: 4211819--4211884 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
4211809 TATAATGTAG
*
4211819 AAAATTTTATT-AAAATGTAAAAATAAAATATAT
1 AAAATTATATTAAAAAT-TAAAAATAAAATATAT
4211852 AAAATTATATTAAAAATTAAAAATAAAATATAT
1 AAAATTATATTAAAAATTAAAAATAAAATATAT
4211885 GATATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (33 bp):
AAAATTATATTAAAAATTAAAAATAAAATATAT
Found at i:4222310 original size:2 final size:2
Alignment explanation
Indices: 4222305--4222331 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4222295 ATTAGGAGAG
4222305 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 A
4222332 AAAGTTATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4222514 original size:25 final size:25
Alignment explanation
Indices: 4222443--4222518 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 25
4222433 ATCTTAATTT
* *
4222443 TATTCATAGTCTAATTTTAATTAAAA
1 TATT-ATAATCTAACTTTAATTAAAA
* * * * *
4222469 TATCCATGATTTAACTCTAATTAAGA
1 TAT-TATAATCTAACTTTAATTAAAA
4222495 TATTATAATCTAACTTTAATTAAA
1 TATTATAATCTAACTTTAATTAAA
4222519 TAATTTATAT
Statistics
Matches: 37, Mismatches: 12, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
25 16 0.43
26 21 0.57
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (25 bp):
TATTATAATCTAACTTTAATTAAAA
Found at i:4244630 original size:21 final size:21
Alignment explanation
Indices: 4244592--4244631 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4244582 TGTATCGAAC
*
4244592 ATAACATTAATATTCATATTA
1 ATAACATTAAAATTCATATTA
4244613 ATAACA-TAAAATTCCATAT
1 ATAACATTAAAATT-CATAT
4244632 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAACATTAAAATTCATATTA
Found at i:4262406 original size:2 final size:2
Alignment explanation
Indices: 4262399--4262427 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4262389 ACGAAAAATA
4262399 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 A
4262428 CATAAGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4267477 original size:24 final size:22
Alignment explanation
Indices: 4267437--4267485 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 22
4267427 AAACACGTTC
*
4267437 CCATCTTCATCACCATCATCAT
1 CCATCTTCAGCACCATCATCAT
4267459 CCATCATTCAGCATCCATCATCAT
1 CCATC-TTCAGCA-CCATCATCAT
4267483 CCA
1 CCA
4267486 CCATCCATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.21
23 6 0.25
24 13 0.54
ACGTcount: A:0.29, C:0.41, G:0.02, T:0.29
Consensus pattern (22 bp):
CCATCTTCAGCACCATCATCAT
Found at i:4267480 original size:17 final size:17
Alignment explanation
Indices: 4267437--4267498 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
4267427 AAACACGTTC
*
4267437 CCATCTTCAT-CACCAT
1 CCATCATCATCCACCAT
* *
4267453 CATCATCCATCATTCAGCAT
1 C--CAT-CATCATCCACCAT
4267473 CCATCATCATCCACCAT
1 CCATCATCATCCACCAT
4267490 CCATCATCA
1 CCATCATCA
4267499 GGGAAACCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.03
17 20 0.53
18 6 0.16
19 5 0.13
20 6 0.16
ACGTcount: A:0.29, C:0.42, G:0.02, T:0.27
Consensus pattern (17 bp):
CCATCATCATCCACCAT
Found at i:4267497 original size:24 final size:24
Alignment explanation
Indices: 4267444--4267497 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
4267434 TTCCCATCTT
* *
4267444 CATCA-CCATCATCATCCATCATT
1 CATCATCCATCATCATCCACCATC
*
4267467 CAGCATCCATCATCATCCACCATC
1 CATCATCCATCATCATCCACCATC
4267491 CATCATC
1 CATCATC
4267498 AGGGAAACCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.30, C:0.43, G:0.02, T:0.26
Consensus pattern (24 bp):
CATCATCCATCATCATCCACCATC
Found at i:4282902 original size:16 final size:17
Alignment explanation
Indices: 4282875--4282906 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4282865 ATTTTTTTAA
4282875 TAAAAGATAAAAAATTC
1 TAAAAGATAAAAAATTC
4282892 TAAAA-ATAAAAAATT
1 TAAAAGATAAAAAATT
4282907 ATAATTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (17 bp):
TAAAAGATAAAAAATTC
Found at i:4298698 original size:2 final size:2
Alignment explanation
Indices: 4298691--4298715 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4298681 ATATGTGTAT
4298691 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 T
4298716 CAAGATTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4311203 original size:15 final size:15
Alignment explanation
Indices: 4311175--4311251 Score: 65
Period size: 16 Copynumber: 5.3 Consensus size: 15
4311165 AATCTCTTTT
4311175 ATTTAAAATATTAATA
1 ATTT-AAATATTAATA
*
4311191 ATTTAAATTTTAAT-
1 ATTTAAATATTAATA
*
4311205 ATTT-TATA-T-ATA
1 ATTTAAATATTAATA
*
4311217 ATTTAAATATT-ATT
1 ATTTAAATATTAATA
4311231 ATGATTAAATATTAATA
1 AT--TTAAATATTAATA
4311248 ATTT
1 ATTT
4311252 TAATTAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
11 2 0.04
12 5 0.10
13 5 0.10
14 9 0.18
15 11 0.22
16 13 0.27
17 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (15 bp):
ATTTAAATATTAATA
Found at i:4311254 original size:16 final size:16
Alignment explanation
Indices: 4311175--4311254 Score: 59
Period size: 15 Copynumber: 5.4 Consensus size: 16
4311165 AATCTCTTTT
*
4311175 ATTTAAAATATTAATA
1 ATTTTAAATATTAATA
*
4311191 A-TTTAAATTTTAAT-
1 ATTTTAAATATTAATA
4311205 ATTTT--ATA-T-ATA
1 ATTTTAAATATTAATA
*
4311217 A-TTTAAATATT-ATT
1 ATTTTAAATATTAATA
*
4311231 ATGATTAAATATTAATA
1 AT-TTTAAATATTAATA
4311248 ATTTTAA
1 ATTTTAA
4311255 TTAATTTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
11 5 0.10
12 2 0.04
13 5 0.10
14 5 0.10
15 14 0.29
16 14 0.29
17 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (16 bp):
ATTTTAAATATTAATA
Found at i:4311450 original size:16 final size:17
Alignment explanation
Indices: 4311438--4311475 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
4311428 GTATTAAAAC
4311438 TTTAA-AATTTTAATAA
1 TTTAATAATTTTAATAA
* *
4311454 TTTAATAATTTTTATTA
1 TTTAATAATTTTAATAA
4311471 TTTAA
1 TTTAA
4311476 GTATTAGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATAATTTTAATAA
Found at i:4312082 original size:19 final size:19
Alignment explanation
Indices: 4312058--4312126 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 19
4312048 TTAAAATATT
4312058 AATATTAAGTTATAAATAA
1 AATATTAAGTTATAAATAA
4312077 AATATTAATAGTT-TAAAATATTA
1 AATATT-A-AGTTAT-AAATA--A
* *
4312100 AAAATTAAATTATAAATAA
1 AATATTAAGTTATAAATAA
4312119 AATATTAA
1 AATATTAA
4312127 TATTCAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
19 14 0.34
20 2 0.05
21 17 0.41
22 2 0.05
23 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AATATTAAGTTATAAATAA
Found at i:4312086 original size:42 final size:43
Alignment explanation
Indices: 4312028--4312130 Score: 156
Period size: 42 Copynumber: 2.4 Consensus size: 43
4312018 ATTCCAACTT
* * *
4312028 TAAATAAAATGTTAATATTTTTAAAATATT-AATATTAAGTTA
1 TAAATAAAATATTAATATTTTTAAAATATTAAAAATTAAATTA
*
4312070 TAAATAAAATATTAATA-GTTTAAAATATTAAAAATTAAATTA
1 TAAATAAAATATTAATATTTTTAAAATATTAAAAATTAAATTA
4312112 TAAATAAAATATTAATATT
1 TAAATAAAATATTAATATT
4312131 CAAATTATCA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
41 11 0.20
42 43 0.80
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (43 bp):
TAAATAAAATATTAATATTTTTAAAATATTAAAAATTAAATTA
Found at i:4312280 original size:27 final size:26
Alignment explanation
Indices: 4312244--4312300 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
4312234 TATTAACAAT
4312244 TAAATCATCAATTATTAATATTTTAAA
1 TAAATCATCAATTATTAATA-TTTAAA
*
4312271 TAAATTATCAATTATTAATATTTAAA
1 TAAATCATCAATTATTAATATTTAAA
4312297 -AAAT
1 TAAAT
4312301 AAAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 6 0.21
27 19 0.66
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAATCATCAATTATTAATATTTAAA
Found at i:4312375 original size:46 final size:40
Alignment explanation
Indices: 4312267--4312389 Score: 115
Period size: 41 Copynumber: 2.9 Consensus size: 40
4312257 ATTAATATTT
4312267 TAAATAAATTATCAATTATTAATATTTAAA-AAATAAAATAA
1 TAAA-AAATTATC-ATTATTAATATTTAAATAAATAAAATAA
* *
4312308 TAAAAAATTAATCA-TAATAATATTTAAATTAAATAAAATAT
1 TAAAAAATT-ATCATTATTAATATTTAAA-TAAATAAAATAA
*
4312349 TAATATTTAGATTATCTATTATTAATATTTTAAATAAATAA
1 TAA-A---AAATTATC-ATTATTAATA-TTTAAATAAATAA
4312390 TCAATTACTT
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
39 13 0.19
40 6 0.09
41 20 0.29
42 1 0.01
44 3 0.04
45 5 0.07
46 14 0.21
47 6 0.09
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (40 bp):
TAAAAAATTATCATTATTAATATTTAAATAAATAAAATAA
Found at i:4342777 original size:28 final size:29
Alignment explanation
Indices: 4342714--4342811 Score: 110
Period size: 28 Copynumber: 3.4 Consensus size: 29
4342704 CGTTGATATA
* * *
4342714 ATATTTAAATAAGTTTTTATATTATTA-A
1 ATATTTAAATAAATTTTTATATTTTTATT
* *
4342742 AAAATTAAATAAATTTTTAT-TTTTTATT
1 ATATTTAAATAAATTTTTATATTTTTATT
*
4342770 ATATTTAATTAAATTTTTATATTTTTATT
1 ATATTTAAATAAATTTTTATATTTTTATT
*
4342799 TTGATTTAAATAA
1 AT-ATTTAAATAA
4342812 GTTATTTTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
27 5 0.09
28 34 0.60
29 9 0.16
30 9 0.16
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (29 bp):
ATATTTAAATAAATTTTTATATTTTTATT
Found at i:4343103 original size:20 final size:23
Alignment explanation
Indices: 4343078--4343123 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
4343068 CATAAGAGCT
4343078 TATTTAACT-AA-A-AATAAAAA
1 TATTTAACTGAATACAATAAAAA
*
4343098 TATTTAATTGAATACAATAAAAA
1 TATTTAACTGAATACAATAAAAA
4343121 TAT
1 TAT
4343124 ATAGATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 2 0.09
22 1 0.05
23 11 0.50
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
TATTTAACTGAATACAATAAAAA
Found at i:4343544 original size:19 final size:20
Alignment explanation
Indices: 4343522--4343563 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
4343512 TTTAATTTTA
4343522 TATTATGATTTTA-TTTTGT
1 TATTATGATTTTATTTTTGT
* *
4343541 TATTTTTATTTTATTTTTGT
1 TATTATGATTTTATTTTTGT
4343561 TAT
1 TAT
4343564 CTTTTTAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (20 bp):
TATTATGATTTTATTTTTGT
Found at i:4343560 original size:20 final size:20
Alignment explanation
Indices: 4343529--4343568 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4343519 TTATATTATG
4343529 ATTTTATTTTGTTAT-TTTT
1 ATTTTATTTTGTTATCTTTT
4343548 ATTTTATTTTTGTTATCTTTT
1 ATTTTA-TTTTGTTATCTTTT
4343569 TAAGTGTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.78
Consensus pattern (20 bp):
ATTTTATTTTGTTATCTTTT
Found at i:4348869 original size:23 final size:24
Alignment explanation
Indices: 4348843--4348896 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
4348833 CACATATACA
4348843 TATTTTTTATA-TTTATCT-ATTTC
1 TATTTTTTATATTTTAT-TAATTTC
* *
4348866 TA-TTTTCATATTTTATTAATTTT
1 TATTTTTTATATTTTATTAATTTC
4348889 TATTTTTT
1 TATTTTTT
4348897 TCCAAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 8 0.32
23 13 0.52
24 4 0.16
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (24 bp):
TATTTTTTATATTTTATTAATTTC
Found at i:4371236 original size:15 final size:15
Alignment explanation
Indices: 4371216--4371246 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4371206 TTTCATCTAT
*
4371216 TTCTTCTTGTTTTTC
1 TTCTTCTTATTTTTC
4371231 TTCTTCTTATTTTTC
1 TTCTTCTTATTTTTC
4371246 T
1 T
4371247 GGGAAGAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.74
Consensus pattern (15 bp):
TTCTTCTTATTTTTC
Found at i:4374620 original size:31 final size:30
Alignment explanation
Indices: 4374585--4374690 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
4374575 ATTATTAATA
*
4374585 ATAAATATTTATTTGACTCAAAATATAAAAT
1 ATAAAGATTTATTTGACTCAAAATA-AAAAT
* * *
4374616 ATAAAGATTTATTTGATTTAAAATAAAAGT
1 ATAAAGATTTATTTGACTCAAAATAAAAAT
* * * *
4374646 ATAATGACTTAATTGTACTC--AATAAAAGT
1 ATAAAGATTTATTTG-ACTCAAAATAAAAAT
* *
4374675 ATAAGGGTTTATTTGA
1 ATAAAGATTTATTTGA
4374691 ATTTTTTTTA
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
28 1 0.02
29 20 0.33
30 16 0.26
31 24 0.39
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (30 bp):
ATAAAGATTTATTTGACTCAAAATAAAAAT
Found at i:4375564 original size:2 final size:2
Alignment explanation
Indices: 4375557--4375601 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
4375547 TATAAATTAA
*
4375557 AT AT AT AT AT A- AT AT TT AT AT A- AT -T 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
4375596 AT AT AT
1 AT AT AT
4375602 TCATAATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4375909 original size:18 final size:19
Alignment explanation
Indices: 4375886--4375924 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4375876 AAAAAATATT
4375886 ATATATT-TAATATAAAAA
1 ATATATTATAATATAAAAA
* *
4375904 ATATATTATTATTTAAAAA
1 ATATATTATAATATAAAAA
4375923 AT
1 AT
4375925 TAATTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATATTATAATATAAAAA
Found at i:4375910 original size:25 final size:22
Alignment explanation
Indices: 4375872--4375919 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 22
4375862 TTTCTAATAC
4375872 ATATAAAAAATATTATATATTTA
1 ATATAAAAAATATTAT-TATTTA
4375895 ATATAAAAAATATATTATTATTTA
1 ATAT-AAAAA-ATATTATTATTTA
4375919 A
1 A
4375920 AAAATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.17
24 12 0.52
25 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATAAAAAATATTATTATTTA
Found at i:4375932 original size:17 final size:19
Alignment explanation
Indices: 4375875--4375934 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
4375865 CTAATACATA
*
4375875 TAAAAAATATTATATATTTAATA
1 TAAAAAATA-TA-ATA-TT-ATT
*
4375898 TAAAAAATATATTATTATT
1 TAAAAAATATAATATTATT
4375917 TAAAAAAT-TAAT-TTATT
1 TAAAAAATATAATATTATT
4375934 T
1 T
4375935 TTTAAATGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 6 0.18
18 3 0.09
19 10 0.29
20 2 0.06
21 2 0.06
22 2 0.06
23 9 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAAAATATAATATTATT
Found at i:4400824 original size:18 final size:18
Alignment explanation
Indices: 4400803--4400845 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
4400793 TATTTCTTTA
4400803 ATATATT-TTTTATATTAT
1 ATATATTATTTTA-ATTAT
4400821 ATAT-TTATTTTAATTAT
1 ATATATTATTTTAATTAT
4400838 A-ATATTAT
1 ATATATTAT
4400846 AAAATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.09
17 12 0.52
18 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATATTATTTTAATTAT
Found at i:4404764 original size:21 final size:21
Alignment explanation
Indices: 4404753--4404796 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
4404743 ATTGAATTGG
*
4404753 TTTTAGAGTTTAATGCATCGA
1 TTTTAGAGTTTAATGAATCGA
4404774 TTTTAGAGTTGT--TGAATCGA
1 TTTTAGAGTT-TAATGAATCGA
4404794 TTT
1 TTT
4404797 AGGGGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 10 0.48
22 1 0.05
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.48
Consensus pattern (21 bp):
TTTTAGAGTTTAATGAATCGA
Found at i:4404885 original size:21 final size:21
Alignment explanation
Indices: 4404836--4404886 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
4404826 TCAAACCACT
*
4404836 TTTAAGG-GTTGTTAAATTCA
1 TTTAAGGATTTGTTAAATTCA
* *
4404856 TTTTAGGATTTGTTAAATTGA
1 TTTAAGGATTTGTTAAATTCA
4404877 TTTAAGGATT
1 TTTAAGGATT
4404887 GAATTGGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (21 bp):
TTTAAGGATTTGTTAAATTCA
Found at i:4410837 original size:2 final size:2
Alignment explanation
Indices: 4410830--4410865 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4410820 AATATAAAAA
4410830 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4410866 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4410870 original size:2 final size:2
Alignment explanation
Indices: 4410865--4410892 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4410855 TCTCTCTCTC
4410865 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4410893 AGAGTCACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4413023 original size:9 final size:9
Alignment explanation
Indices: 4413009--4413042 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
4412999 AGCTGTTTAC
*
4413009 ATGATTGAT
1 ATGATTAAT
4413018 ATGATTAAT
1 ATGATTAAT
4413027 ATGATTAA-
1 ATGATTAAT
4413035 ATGATTAA
1 ATGATTAA
4413043 ATTGAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (9 bp):
ATGATTAAT
Found at i:4415094 original size:19 final size:18
Alignment explanation
Indices: 4415067--4415109 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
4415057 TGAAAAATGG
*
4415067 AAAAGAAATACATAATATA
1 AAAAGAAATAAATAA-ATA
*
4415086 AAAATAAATAAATAAATA
1 AAAAGAAATAAATAAATA
4415104 AAAAGA
1 AAAAGA
4415110 GGGTTTTCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (18 bp):
AAAAGAAATAAATAAATA
Found at i:4415708 original size:16 final size:17
Alignment explanation
Indices: 4415689--4415729 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
4415679 AATTTTATTT
4415689 TTATTAATTTTAA-AAA
1 TTATTAATTTTAATAAA
4415705 TTATT-A-TTTAATAAA
1 TTATTAATTTTAATAAA
4415720 TTA-TAATTTT
1 TTATTAATTTT
4415730 TATTTTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.27
15 8 0.36
16 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATTAATTTTAATAAA
Found at i:4416677 original size:17 final size:15
Alignment explanation
Indices: 4416646--4416684 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
4416636 TGAAAAAAGG
4416646 ATAATAATTAATGAA
1 ATAATAATTAATGAA
4416661 ATAATACATTAAATGAA
1 ATAATA-ATT-AATGAA
4416678 AT-ATAAT
1 ATAATAAT
4416685 AAATTTCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 8 0.36
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (15 bp):
ATAATAATTAATGAA
Found at i:4418760 original size:83 final size:82
Alignment explanation
Indices: 4418673--4418844 Score: 175
Period size: 83 Copynumber: 2.1 Consensus size: 82
4418663 GATGTTTAAG
* * * * * *
4418673 TTTAAAAGTTTATATTC-TAATGAAGTATAAAAATAGAGATCAACTTATATGATATGTTGAAAAA
1 TTTAAAAGTTTA-ACTCGTAATGAAATACAAAAATAGAAATCAACTTACAAGATATGTTG-AAAA
**
4418737 AAAATTATTACATGTTATA
64 AAAATTATTACACATTATA
** * * * *
4418756 TTTAAGTGTTTAACTCGTAATGAAATACAAATATATAAATCAAGTTACAAGTTATGTTGAAAAAA
1 TTTAAAAGTTTAACTCGTAATGAAATACAAAAATAGAAATCAACTTACAAGATATGTTGAAAAAA
*
4418821 ATTTATTACACATTATA
66 AATTATTACACATTATA
*
4418838 TTGAAAA
1 TTTAAAA
4418845 AAAAGTTTTT
Statistics
Matches: 70, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
82 27 0.39
83 43 0.61
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (82 bp):
TTTAAAAGTTTAACTCGTAATGAAATACAAAAATAGAAATCAACTTACAAGATATGTTGAAAAAA
AATTATTACACATTATA
Found at i:4418964 original size:27 final size:27
Alignment explanation
Indices: 4418932--4418997 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
4418922 AAACTTTGTA
*
4418932 TTGAAAAAAAAGTTATTATACATCATG
1 TTGAAAAAAAAGTTATTACACATCATG
** *
4418959 TTGAAAAATAAA-TTATTACATGTTATG
1 TTGAAAAA-AAAGTTATTACACATCATG
4418986 TTGAAAAAAAAG
1 TTGAAAAAAAAG
4418998 AAAAATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 3 0.09
27 27 0.82
28 3 0.09
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (27 bp):
TTGAAAAAAAAGTTATTACACATCATG
Found at i:4419113 original size:70 final size:70
Alignment explanation
Indices: 4419022--4419165 Score: 202
Period size: 70 Copynumber: 2.1 Consensus size: 70
4419012 CCCTTACTGA
*
4419022 AAGTATTTAACTTCAAAAGTTTATATTGTAATGAAAT-CAAAAGATAGAGATAAAATTACATGTC
1 AAGTATTTAACTTCAAAAGTTTATATTGTAATAAAATAC-AAAGATAGAGATAAAATTACATGTC
*
4419086 ATGTTT
65 ATATTT
* * * *
4419092 AAGTATTTAACTAT-AAGAGTTTATATTTTAATAAAATACAAAGATAGAGATTAAGTTACATGTC
1 AAGTATTTAACT-TCAAAAGTTTATATTGTAATAAAATACAAAGATAGAGATAAAATTACATGTC
4419156 ATATTT
65 ATATTT
4419162 AAGT
1 AAGT
4419166 CATGTTATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
70 64 0.97
71 2 0.03
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.37
Consensus pattern (70 bp):
AAGTATTTAACTTCAAAAGTTTATATTGTAATAAAATACAAAGATAGAGATAAAATTACATGTCA
TATTT
Found at i:4419735 original size:2 final size:2
Alignment explanation
Indices: 4419728--4419760 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4419718 TTAAAGTGTA
4419728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4419761 GGATCACAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4431064 original size:18 final size:19
Alignment explanation
Indices: 4431034--4431069 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
4431024 TTTAATTTTT
4431034 TTATTTTTAATTTATATTA
1 TTATTTTTAATTTATATTA
4431053 TTATTTTT-ATTTATATT
1 TTATTTTTAATTTATATT
4431070 TTTTATACTA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTTTTAATTTATATTA
Found at i:4443789 original size:42 final size:42
Alignment explanation
Indices: 4443742--4443824 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
4443732 AATCAAGGCC
** *
4443742 GAAAAATAAGAGAAGTAGAGAGTTTCTAGCTGCAGCGAGACA
1 GAAAAATAAGAGAAACAGAGAGTTGCTAGCTGCAGCGAGACA
* * *
4443784 GAAAAATAGGAGAAACATAGAGTTGCTCGCTGCAGCGAGAC
1 GAAAAATAAGAGAAACAGAGAGTTGCTAGCTGCAGCGAGAC
4443825 CCCATTTTCG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.41, C:0.14, G:0.29, T:0.16
Consensus pattern (42 bp):
GAAAAATAAGAGAAACAGAGAGTTGCTAGCTGCAGCGAGACA
Found at i:4450746 original size:17 final size:16
Alignment explanation
Indices: 4450724--4450758 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4450714 CAACTTATTT
4450724 ATCAATTAAAAGTAAAA
1 ATCAATTAAAA-TAAAA
*
4450741 ATCAATTCAAATAAAA
1 ATCAATTAAAATAAAA
4450757 AT
1 AT
4450759 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.63, C:0.09, G:0.03, T:0.26
Consensus pattern (16 bp):
ATCAATTAAAATAAAA
Found at i:4451909 original size:25 final size:25
Alignment explanation
Indices: 4451879--4451934 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
4451869 TTGCCGTATG
**
4451879 AATTTTAACATTTCTTTTTCAAATA
1 AATTTTAACATTTCTCATTCAAATA
* * *
4451904 AATTTTAATATTTGTCATTCAAATG
1 AATTTTAACATTTCTCATTCAAATA
4451929 AATTTT
1 AATTTT
4451935 GTACCAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.52
Consensus pattern (25 bp):
AATTTTAACATTTCTCATTCAAATA
Found at i:4462619 original size:13 final size:12
Alignment explanation
Indices: 4462598--4462635 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
4462588 GCCGGCTGAC
4462598 TAAGAAAAAAAA
1 TAAGAAAAAAAA
*
4462610 TAATGAAAAAAAG
1 TAA-GAAAAAAAA
4462623 TAA-AAAAAAAA
1 TAAGAAAAAAAA
4462634 TA
1 TA
4462636 TTTTAAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 9 0.39
12 3 0.13
13 11 0.48
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (12 bp):
TAAGAAAAAAAA
Found at i:4466695 original size:2 final size:2
Alignment explanation
Indices: 4466688--4466717 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4466678 ACTTAAAAGA
*
4466688 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4466718 CAAAACTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4468476 original size:2 final size:2
Alignment explanation
Indices: 4468469--4468502 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4468459 GTTCAGATTC
4468469 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
4468503 TCTATTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4472562 original size:5 final size:5
Alignment explanation
Indices: 4472541--4472578 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
4472531 GAAACCGAAT
* *
4472541 GGTTC GGATC AGTTC GGTTC GGTTC GGTTC GGTTC GGT
1 GGTTC GGTTC GGTTC GGTTC GGTTC GGTTC GGTTC GGT
4472579 GGAGTTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.05, C:0.18, G:0.39, T:0.37
Consensus pattern (5 bp):
GGTTC
Found at i:4474723 original size:4 final size:4
Alignment explanation
Indices: 4474714--4474744 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
4474704 ACAGCAAATT
4474714 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
4474745 AAAGGGTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:4481235 original size:53 final size:54
Alignment explanation
Indices: 4481172--4481279 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
4481162 AGGAAAAAGT
4481172 CATTAGTTTTTCATCGGATTC-AACGGTAGCCGTAGGCTTCCAGGACTGAAGCA
1 CATTAGTTTTTCATCGGATTCAAACGGTAGCCGTAGGCTTCCAGGACTGAAGCA
4481225 CATTAGTTTTTCATCGGATTCAAACGGTAGCCGTAGGCTTCCAGGACTGAAGCA
1 CATTAGTTTTTCATCGGATTCAAACGGTAGCCGTAGGCTTCCAGGACTGAAGCA
4481279 C
1 C
4481280 TAAGTGCCGC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 21 0.39
54 33 0.61
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (54 bp):
CATTAGTTTTTCATCGGATTCAAACGGTAGCCGTAGGCTTCCAGGACTGAAGCA
Found at i:4488405 original size:62 final size:62
Alignment explanation
Indices: 4488216--4488407 Score: 185
Period size: 62 Copynumber: 3.1 Consensus size: 62
4488206 CCTCTTTAAC
* * * * * * *
4488216 AATTTTTAAATTTTTATAATTTATATGTATTTTTTA-AAATATTTTTAATTTCGTC-TT-CAAT
1 AATTTTTAAA-TTTTCTAACTTATTTTTAATTTTTAGAAAT-TTTATAATTTCATCATTACAAT
* * * *
4488277 AATTTTTAAATTTTGTAACTTATTTTTAATTTTTAGGAATTTTATAATTTCCTCATTACAAA
1 AATTTTTAAATTTTCTAACTTATTTTTAATTTTTAGAAATTTTATAATTTCATCATTACAAT
* * * * *
4488339 AATTTTTAAATTTTCTAA-TATATTTTTATTTTTTTGAAATTTTATAATTTTATCTTTATAAT
1 AATTTTTAAATTTTCTAACT-TATTTTTAATTTTTAGAAATTTTATAATTTCATCATTACAAT
4488401 AATTTTT
1 AATTTTT
4488408 TATTTAGTTG
Statistics
Matches: 109, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
60 32 0.29
61 16 0.15
62 61 0.56
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (62 bp):
AATTTTTAAATTTTCTAACTTATTTTTAATTTTTAGAAATTTTATAATTTCATCATTACAAT
Found at i:4504924 original size:21 final size:21
Alignment explanation
Indices: 4504898--4504937 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
4504888 TTTAGTTAGG
4504898 GGTCTTACAAGGTCAAGAAAA
1 GGTCTTACAAGGTCAAGAAAA
4504919 GGTCTTACAAGGTCAAGAA
1 GGTCTTACAAGGTCAAGAA
4504938 GAGATTATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (21 bp):
GGTCTTACAAGGTCAAGAAAA
Found at i:4505448 original size:26 final size:26
Alignment explanation
Indices: 4505411--4505460 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
4505401 CCGACAGAGC
*
4505411 AAAGAAGGGTTGCTCTTTAGTTTTAA
1 AAAGAAGAGTTGCTCTTTAGTTTTAA
*
4505437 AAAGAAGAGTTGCTCTTTGGTTTT
1 AAAGAAGAGTTGCTCTTTAGTTTT
4505461 TAGTTAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (26 bp):
AAAGAAGAGTTGCTCTTTAGTTTTAA
Found at i:4507238 original size:14 final size:14
Alignment explanation
Indices: 4507219--4507261 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
4507209 TTATGCTGCA
4507219 TATCTTTTTTGTTT
1 TATCTTTTTTGTTT
*
4507233 TATC-TTTTTCTTT
1 TATCTTTTTTGTTT
4507246 TATACTTTGTTTGTTT
1 TAT-CTTT-TTTGTTT
4507262 CTTTGTCTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 11 0.46
14 5 0.21
15 2 0.08
16 6 0.25
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.74
Consensus pattern (14 bp):
TATCTTTTTTGTTT
Found at i:4513024 original size:8 final size:8
Alignment explanation
Indices: 4513011--4513076 Score: 54
Period size: 7 Copynumber: 9.0 Consensus size: 8
4513001 AAAATTTATG
4513011 TAAATTTA
1 TAAATTTA
4513019 TAAA-TTA
1 TAAATTTA
4513026 TAAATTTA
1 TAAATTTA
4513034 T--ATTT-
1 TAAATTTA
*
4513039 TTAATTTA
1 TAAATTTA
**
4513047 -AAAAATA
1 TAAATTTA
4513054 TAAATTTA
1 TAAATTTA
4513062 TAAA-TTA
1 TAAATTTA
*
4513069 TGAATTTA
1 TAAATTTA
4513077 AATTTAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
5 1 0.02
6 4 0.09
7 21 0.46
8 20 0.43
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (8 bp):
TAAATTTA
Found at i:4513031 original size:15 final size:15
Alignment explanation
Indices: 4513011--4513076 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
4513001 AAAATTTATG
4513011 TAAATTTATAAATTA
1 TAAATTTATAAATTA
*
4513026 TAAATTTAT--ATTT
1 TAAATTTATAAATTA
* * *
4513039 TTAATTTAAAAAATA
1 TAAATTTATAAATTA
4513054 TAAATTTATAAATTA
1 TAAATTTATAAATTA
*
4513069 TGAATTTA
1 TAAATTTA
4513077 AATTTAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
13 10 0.25
15 30 0.75
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
TAAATTTATAAATTA
Found at i:4513057 original size:35 final size:36
Alignment explanation
Indices: 4513017--4513087 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
4513007 TATGTAAATT
* *
4513017 TATAAA-TTATAAATTTAT-ATTTTTAATTTAAAAAA
1 TATAAATTTATAAA-TTATGAATTTAAATTTAAAAAA
4513052 TATAAATTTATAAATTATGAATTTAAATTTAAAAAA
1 TATAAATTTATAAATTATGAATTTAAATTTAAAAAA
4513088 ACATACCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 10 0.31
36 22 0.69
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (36 bp):
TATAAATTTATAAATTATGAATTTAAATTTAAAAAA
Found at i:4516505 original size:5 final size:5
Alignment explanation
Indices: 4516492--4516526 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
4516482 CTCAAAGACA
*
4516492 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
4516527 CTGTATACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:4521726 original size:2 final size:2
Alignment explanation
Indices: 4521719--4521746 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4521709 AATTGTTTTG
4521719 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4521747 TGTTACATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4529038 original size:31 final size:31
Alignment explanation
Indices: 4529003--4529099 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
4528993 TATTATCTTT
* *
4529003 TAAAAAATAAATT-AAAATATAATATATAATA
1 TAAAAAATAAATTAAAAATA-AAAATAAAATA
* *
4529034 TAAAAATTATATTAAAAATAAAAATAAAATA
1 TAAAAAATAAATTAAAAATAAAAATAAAATA
* * *
4529065 TATAAAATTATAATAAAAAATAAAAATAAACTA
1 TA-AAAAATA-AATTAAAAATAAAAATAAAATA
4529098 TA
1 TA
4529100 TGATATTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
31 22 0.39
32 13 0.23
33 21 0.38
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (31 bp):
TAAAAAATAAATTAAAAATAAAAATAAAATA
Found at i:4529057 original size:6 final size:6
Alignment explanation
Indices: 4529046--4529094 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
4529036 AAAATTATAT
* *
4529046 TAAAAA TAAAAA TAAAATA TATAAAA TTATAA TAAAAAA TAAAAA TAAA
1 TAAAAA TAAAAA TAAAA-A TA-AAAA TAAAAA T-AAAAA TAAAAA TAAA
4529095 CTATATGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 24 0.67
7 9 0.25
8 3 0.08
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
TAAAAA
Found at i:4529065 original size:20 final size:20
Alignment explanation
Indices: 4529042--4529113 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
4529032 TATAAAAATT
4529042 ATATTAAAAATAAAAATAAA
1 ATATTAAAAATAAAAATAAA
* *
4529062 ATA-TATAAAATTATAATAAA
1 ATATTA-AAAATAAAAATAAA
* * **
4529082 A-AATAAAAATAAACTATATG
1 ATATTAAAAATAAA-AATAAA
4529102 ATATTAAAAATA
1 ATATTAAAAATA
4529114 TATTTAAGAG
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
19 9 0.22
20 22 0.55
21 9 0.22
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (20 bp):
ATATTAAAAATAAAAATAAA
Found at i:4529065 original size:38 final size:36
Alignment explanation
Indices: 4529011--4529117 Score: 107
Period size: 33 Copynumber: 2.9 Consensus size: 36
4529001 TTTAAAAAAT
*
4529011 AAATTAAAATATAATATATAATATAAAAATTATATTAA
1 AAATAAAAATA-AATATAT-ATATAAAAATTATATTAA
*
4529049 AAATAAAAAT-AA-A-ATATAT-AAAATTATAATAAA
1 AAATAAAAATAAATATATATATAAAAATTAT-ATTAA
4529082 AAATAAAAATAAACTATATGATATTAAAAA-TATATT
1 AAATAAAAATAAA-TATAT-ATA-TAAAAATTATATT
4529118 TAAGAGATGA
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
32 8 0.14
33 18 0.31
34 4 0.07
35 1 0.02
36 3 0.05
37 2 0.03
38 14 0.24
39 4 0.07
40 4 0.07
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (36 bp):
AAATAAAAATAAATATATATATAAAAATTATATTAA
Found at i:4529084 original size:33 final size:32
Alignment explanation
Indices: 4529016--4529100 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 32
4529006 AAAATAAATT
* * *
4529016 AAAATATAATATATAATATA-AAAATTATATTA
1 AAAATA-AAAATAAAATATATAAAATTATATAA
4529048 AAAATAAAAATAAAATATATAAAATTATAATAA
1 AAAATAAAAATAAAATATATAAAATTAT-ATAA
*
4529081 AAAATAAAAATAAACTATAT
1 AAAATAAAAATAAAATATAT
4529101 GATATTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
31 11 0.23
32 14 0.30
33 22 0.47
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (32 bp):
AAAATAAAAATAAAATATATAAAATTATATAA
Found at i:4529994 original size:29 final size:29
Alignment explanation
Indices: 4529962--4530052 Score: 69
Period size: 31 Copynumber: 3.0 Consensus size: 29
4529952 TTCAAAAAAT
4529962 TTTAAATAATTTTTTATATTTTTA-TTACA
1 TTTAAATAATTTTTT-TATTTTTAGTTACA
* * **
4529991 TTT-AATCAAATTTTTTTACTTTTATTTTGA
1 TTTAAAT--AATTTTTTTATTTTTAGTTACA
* *
4530021 CTCAAATAATTTTTTTTTATTTTTAGTTACA
1 TTTAAATAA--TTTTTTTATTTTTAGTTACA
4530052 T
1 T
4530053 AAACACTTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
28 3 0.07
29 12 0.26
30 12 0.26
31 19 0.41
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTAAATAATTTTTTTATTTTTAGTTACA
Found at i:4533583 original size:74 final size:73
Alignment explanation
Indices: 4533458--4533678 Score: 327
Period size: 74 Copynumber: 3.0 Consensus size: 73
4533448 CCAAAACATC
* * * *
4533458 TCCTGCTGCGGCATGTGCGAACTGGCAACATATTAAAGAAGCGAGCATAAGCGATAGCGTTAACA
1 TCCTGCTGCAGCAGGTGGGAACTGGCAACAAATTAAAGAAGCGAGCATAAGCGATAGCGTTAACA
4533523 TAGTCATT
66 TAGTCATT
*
4533531 TCCTGCTGCAGCAGGTGGGAACTGGCAACAAAATTAAAGAAGCGAGCATAAGCGATGGCGTTAAC
1 TCCTGCTGCAGCAGGTGGGAACTGGCAAC-AAATTAAAGAAGCGAGCATAAGCGATAGCGTTAAC
*
4533596 ATTCG-CATT
65 A-TAGTCATT
* * *
4533605 TCCTGCTGCAGCAGGTGGGAACTGGCAACAAATTAAAGAAGCAAGTATAAGCCATAGCGTTAACA
1 TCCTGCTGCAGCAGGTGGGAACTGGCAACAAATTAAAGAAGCGAGCATAAGCGATAGCGTTAACA
*
4533670 TACTCATT
66 TAGTCATT
4533678 T
1 T
4533679 GATTGATTGG
Statistics
Matches: 133, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
72 1 0.01
73 63 0.47
74 67 0.50
75 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (73 bp):
TCCTGCTGCAGCAGGTGGGAACTGGCAACAAATTAAAGAAGCGAGCATAAGCGATAGCGTTAACA
TAGTCATT
Found at i:4539847 original size:16 final size:16
Alignment explanation
Indices: 4539826--4539864 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
4539816 GTCACCTTTA
*
4539826 ATGATGTGGCATTGAG
1 ATGATGAGGCATTGAG
4539842 ATGATGAGGCATTGAG
1 ATGATGAGGCATTGAG
4539858 ATGATGA
1 ATGATGA
4539865 CGTGACAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.36, T:0.28
Consensus pattern (16 bp):
ATGATGAGGCATTGAG
Found at i:4540578 original size:107 final size:107
Alignment explanation
Indices: 4540380--4540588 Score: 271
Period size: 107 Copynumber: 1.9 Consensus size: 107
4540370 TAAAATGACT
* * *
4540380 AAATATGTTGATTTGATTACAAATTTTACAATTTACAAATATACATTTTTTGAAAATTATTCAAC
1 AAATATATTGATTTGATTACAAATTTCACAATTTACAAATACACATTTTTTG-AAATTATTCAAC
*
4540445 TCTTACCCAATTTACTTTTTATTTAAAATTGCTCAAATTAGCA
65 TCTTACCCAATTTACTTTTTATTTAAAATTACTCAAATTAGCA
* * * *
4540488 AAATATATTGATTT-AGTTATAACTTTCACAATTTACAACTACATATTCTTTTG-AATTATTCAA
1 AAATATATTGATTTGA-TTACAAATTTCACAATTTACAAATACACATT-TTTTGAAATTATTCAA
* *
4540551 CTCTTACCTAATTTA-TCTTTTATTTAAATTTACTCAAA
64 CTCTTACCCAATTTACT-TTTTATTTAAAATTACTCAAA
4540589 ATTTCTTATA
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
106 1 0.01
107 44 0.50
108 38 0.43
109 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.45
Consensus pattern (107 bp):
AAATATATTGATTTGATTACAAATTTCACAATTTACAAATACACATTTTTTGAAATTATTCAACT
CTTACCCAATTTACTTTTTATTTAAAATTACTCAAATTAGCA
Found at i:4543014 original size:20 final size:20
Alignment explanation
Indices: 4542989--4543026 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4542979 ATAAGATTTC
4542989 TATCAATACATTTAAGAATG
1 TATCAATACATTTAAGAATG
*
4543009 TATCAATAGATTTAAGAA
1 TATCAATACATTTAAGAA
4543027 ATGATACATT
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:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (20 bp):
TATCAATACATTTAAGAATG
Found at i:4543035 original size:36 final size:35
Alignment explanation
Indices: 4542994--4543101 Score: 98
Period size: 40 Copynumber: 3.0 Consensus size: 35
4542984 ATTTCTATCA
4542994 ATACATT-TAAGAATGTATCAATAGATTTAAGAAATG
1 ATACATTGTAA-AATGTATCAATAGATTTAAGAAA-G
* *
4543030 ATACATTTTGTGAAACATGTATCGATAGA-TCAAG--AG
1 ATACA--TTGT-AAA-ATGTATCAATAGATTTAAGAAAG
*
4543066 ATACATTGTAAAAAGGTATCAATAGATTTAAGAAAG
1 ATACATTGT-AAAATGTATCAATAGATTTAAGAAAG
4543102 GGTACATTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
33 11 0.19
34 11 0.19
36 13 0.22
37 1 0.02
38 2 0.03
39 6 0.10
40 14 0.24
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (35 bp):
ATACATTGTAAAATGTATCAATAGATTTAAGAAAG
Found at i:4543058 original size:40 final size:39
Alignment explanation
Indices: 4543006--4543134 Score: 126
Period size: 40 Copynumber: 3.4 Consensus size: 39
4542996 ACATTTAAGA
4543006 ATGTATCAATAGATTTAAGAAATGATACATTTTGTGAAAC
1 ATGTATCAATAGATTTAAGAAA-GATACATTTTGTGAAAC
* * *
4543046 ATGTATCGATAGA-TCAAG--AGATACA--TTGT-AAAA
1 ATGTATCAATAGATTTAAGAAAGATACATTTTGTGAAAC
* *
4543079 AGGTATCAATAGATTTAAGAAAGGGTACATTTTGTGAAAC
1 ATGTATCAATAGATTTAAGAAA-GATACATTTTGTGAAAC
* **
4543119 ACGTATTGATAGATTT
1 ATGTATCAATAGATTT
4543135 CTCCAATCTA
Statistics
Matches: 71, Mismatches: 11, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
33 14 0.20
34 8 0.11
36 7 0.10
37 6 0.08
39 8 0.11
40 28 0.39
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.33
Consensus pattern (39 bp):
ATGTATCAATAGATTTAAGAAAGATACATTTTGTGAAAC
Found at i:4543130 original size:73 final size:72
Alignment explanation
Indices: 4542994--4543132 Score: 215
Period size: 73 Copynumber: 1.9 Consensus size: 72
4542984 ATTTCTATCA
* * * *
4542994 ATACATTTAAGAATGTATCAATAGATTTAAGAAATGATACATTTTGTGAAACATGTATCGATAGA
1 ATACATTTAAAAAGGTATCAATAGATTTAAGAAAGGATACATTTTGTGAAACACGTATCGATAGA
4543059 TCAAGAG
66 TCAAGAG
* *
4543066 ATACATTGTAAAAAGGTATCAATAGATTTAAGAAAGGGTACATTTTGTGAAACACGTATTGATAG
1 ATACATT-TAAAAAGGTATCAATAGATTTAAGAAAGGATACATTTTGTGAAACACGTATCGATAG
4543131 AT
65 AT
4543133 TTCTCCAATC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 7 0.12
73 53 0.88
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (72 bp):
ATACATTTAAAAAGGTATCAATAGATTTAAGAAAGGATACATTTTGTGAAACACGTATCGATAGA
TCAAGAG
Found at i:4543400 original size:14 final size:14
Alignment explanation
Indices: 4543356--4543407 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
4543346 AAATAAAAAC
*
4543356 ATTTATATTTAAAGT
1 ATTTATA-TAAAAGT
*
4543371 ATATATACTAAAAGT
1 ATTTATA-TAAAAGT
*
4543386 ATTTATATAATAGT
1 ATTTATATAAAAGT
*
4543400 AATTATAT
1 ATTTATAT
4543408 TTTTTAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
14 13 0.42
15 18 0.58
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (14 bp):
ATTTATATAAAAGT
Found at i:4547604 original size:33 final size:33
Alignment explanation
Indices: 4547540--4547606 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
4547530 TTTTAACTTT
* *
4547540 AAATATATTTTAAAGTATTAAAATATTAATATA
1 AAATATATTTTAAACTATTAAAATATAAATATA
**
4547573 AAATATA-TTTAAACTATTTTAATAATAAATATA
1 AAATATATTTTAAACTATTAAAAT-ATAAATATA
4547606 A
1 A
4547607 TTTATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (33 bp):
AAATATATTTTAAACTATTAAAATATAAATATA
Found at i:4548168 original size:18 final size:18
Alignment explanation
Indices: 4548145--4548180 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4548135 GTCCATTAAG
4548145 AAAAAGAGACAAAA-AAAA
1 AAAAAGAGA-AAAAGAAAA
4548163 AAAAAGAGAAAAAGAAAA
1 AAAAAGAGAAAAAGAAAA
4548181 CTCAGTTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAGAGAAAAAGAAAA
Found at i:4561340 original size:10 final size:10
Alignment explanation
Indices: 4561325--4561351 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
4561315 GTCCAATAGT
4561325 TATATATACA
1 TATATATACA
4561335 TATATATACA
1 TATATATACA
4561345 TATATAT
1 TATATAT
4561352 CATCCTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (10 bp):
TATATATACA
Found at i:4573012 original size:13 final size:13
Alignment explanation
Indices: 4572994--4573019 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4572984 CTGTATTATG
4572994 ATAAAAATTTGTA
1 ATAAAAATTTGTA
4573007 ATAAAAATTTGTA
1 ATAAAAATTTGTA
4573020 TTTACTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
ATAAAAATTTGTA
Found at i:4577130 original size:20 final size:18
Alignment explanation
Indices: 4577074--4577120 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
4577064 ATATGTTGAA
* *
4577074 AATAATTAT-TAATAATT
1 AATAATTTTATAATAAAT
4577091 AA-ATATTTTATAATAAAT
1 AATA-ATTTTATAATAAAT
4577109 AATAATTTTATA
1 AATAATTTTATA
4577121 TAGTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 1 0.04
17 6 0.24
18 17 0.68
19 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAATTTTATAATAAAT
Found at i:4577371 original size:28 final size:28
Alignment explanation
Indices: 4577331--4577396 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
4577321 ATTTAAATTT
*
4577331 AAAATACTAAAT-ATTAAATTATAATGTAC
1 AAAATA-TAAATAATTAAA-TATAATATAC
*
4577360 AAAATATAAATAATTAAATATGATATAC
1 AAAATATAAATAATTAAATATAATATAC
4577388 AAAAT-TAAA
1 AAAATATAAA
4577397 AAAAATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 4 0.12
28 18 0.53
29 12 0.35
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAATATAAATAATTAAATATAATATAC
Found at i:4577403 original size:29 final size:29
Alignment explanation
Indices: 4577343--4577404 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
4577333 AATACTAAAT
* * *
4577343 ATTAAATTATAATGTACAAAATATAAATA
1 ATTAAATTATAATATACAAAATAAAAAAA
*
4577372 ATTAAA-TATGATATACAAAATTAAAAAAA
1 ATTAAATTATAATATACAAAA-TAAAAAAA
4577401 ATTA
1 ATTA
4577405 TATAATTAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (29 bp):
ATTAAATTATAATATACAAAATAAAAAAA
Found at i:4586109 original size:2 final size:2
Alignment explanation
Indices: 4586102--4586146 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4586092 CAAAGGGTTT
*
4586102 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4586144 TA T
1 TA T
4586147 GGTAAAGCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4586838 original size:14 final size:11
Alignment explanation
Indices: 4586808--4586837 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4586798 TGTTAATTTG
4586808 TTAACAACCAT
1 TTAACAACCAT
4586819 TTAACAACCAT
1 TTAACAACCAT
*
4586830 TTATCAAC
1 TTAACAAC
4586838 ACAAATGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (11 bp):
TTAACAACCAT
Found at i:4597197 original size:3 final size:3
Alignment explanation
Indices: 4597191--4597248 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
4597181 TTCTCCTCCG
* * * * ** *
4597191 ACC ACC ATC ACC ACC ACC ACC ACC ACA ACC ACC ACA ATC ACC ATT ACA
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
4597239 ACC ACC ACC A
1 ACC ACC ACC A
4597249 TAACCAACAG
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.40, C:0.53, G:0.00, T:0.07
Consensus pattern (3 bp):
ACC
Found at i:4597254 original size:21 final size:21
Alignment explanation
Indices: 4597215--4597254 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4597205 CACCACCACC
*
4597215 ACAACCACCACAATCACCATT
1 ACAACCACCACAATAACCATT
*
4597236 ACAACCACCACCATAACCA
1 ACAACCACCACAATAACCA
4597255 ACAGCAATTC
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:0.45, C:0.45, G:0.00, T:0.10
Consensus pattern (21 bp):
ACAACCACCACAATAACCATT
Found at i:4616291 original size:280 final size:280
Alignment explanation
Indices: 4615783--4616343 Score: 1056
Period size: 280 Copynumber: 2.0 Consensus size: 280
4615773 ATGAAAATAA
*
4615783 AAAATCAAAGTTTTTCCACAAGTTCAGTTACCTAATCTGCTGTGTATGGGGGTATGGCTTTCTGC
1 AAAATCAAAGTTTTTCCACAAGTTCAGTTACCTAATCTGCTGTGTAAGGGGGTATGGCTTTCTGC
4615848 AACATACTACTACTAGGAAAGTCTAATCCCCTTTTTAATTGCCTCTTTTTTTCCTTTTCTTCAGT
66 AACATACTACTACTAGGAAAGTCTAATCCCCTTTTTAATTGCCTCTTTTTTTCCTTTTCTTCAGT
*
4615913 AATGTTTCACCTTTTGCTTTTAATAATAGTTTGATTCAAGTTTTCCTAACTAACATAAGCAAATC
131 AATGTTTCACCTTTTCCTTTTAATAATAGTTTGATTCAAGTTTTCCTAACTAACATAAGCAAATC
4615978 AAAATGCTGAAATAATTCCTGGAAACAAAACAAACACACTATTTGATTAAATAAAATTACAAATA
196 AAAATGCTGAAATAATTCCTGGAAACAAAACAAACACACTA-TTGATTAAATAAAATTACAAATA
4616043 ATTAATCTAAAATACGACATC
260 ATTAATCTAAAATACGACATC
4616064 AAAATCAAAG-TTTTCCACAAGTTCAGTTACCTAATCTGCTGTGTAAGGGGGTATGGCTTTCTGC
1 AAAATCAAAGTTTTTCCACAAGTTCAGTTACCTAATCTGCTGTGTAAGGGGGTATGGCTTTCTGC
4616128 AACATACTACTACTAGGAAAGTCTAATCCCCTTTTTAATTGCCTCTTTTTTTCCTTTTCTTCAGT
66 AACATACTACTACTAGGAAAGTCTAATCCCCTTTTTAATTGCCTCTTTTTTTCCTTTTCTTCAGT
4616193 AATGTTTTCACCTTTTCCTTTTAATAATAGTTTGATTCAAGTTTTTCCTAACTAACAT-AGCAAA
131 AATG-TTTCACCTTTTCCTTTTAATAATAGTTTGATTCAAG-TTTTCCTAACTAACATAAGCAAA
4616257 TCAAAATGCTGAAATAATTCCTGGAAAC-AAACAAACACACTATTGATTAAATAAAATTACAAAT
194 TCAAAATGCTGAAATAATTCCTGGAAACAAAACAAACACACTATTGATTAAATAAAATTACAAAT
4616321 AATTAATCTAAAATACGACATC
259 AATTAATCTAAAATACGACATC
4616343 A
1 A
4616344 TTACCTTGAA
Statistics
Matches: 276, Mismatches: 2, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
279 45 0.16
280 136 0.49
281 79 0.29
282 16 0.06
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.36
Consensus pattern (280 bp):
AAAATCAAAGTTTTTCCACAAGTTCAGTTACCTAATCTGCTGTGTAAGGGGGTATGGCTTTCTGC
AACATACTACTACTAGGAAAGTCTAATCCCCTTTTTAATTGCCTCTTTTTTTCCTTTTCTTCAGT
AATGTTTCACCTTTTCCTTTTAATAATAGTTTGATTCAAGTTTTCCTAACTAACATAAGCAAATC
AAAATGCTGAAATAATTCCTGGAAACAAAACAAACACACTATTGATTAAATAAAATTACAAATAA
TTAATCTAAAATACGACATC
Found at i:4617186 original size:50 final size:55
Alignment explanation
Indices: 4617110--4617228 Score: 135
Period size: 55 Copynumber: 2.2 Consensus size: 55
4617100 GATCTATTTT
* *
4617110 TTTTAATTTAAAATTTATTATGAAATT-TTT-AT-AAA-AATTA-AT-AATTTTAAA
1 TTTTAA-TTAAAATTGATTATGAAATTATTTAATAAAATAATTATATAAATGTT-AA
*
4617161 TTTTAATTAAAATTGCTTGAT-AAATTATTTAATAAAATAATTATATAAATGTTAA
1 TTTTAATTAAAATTGATT-ATGAAATTATTTAATAAAATAATTATATAAATGTTAA
4617216 TTTTAATTAAAAT
1 TTTTAATTAAAAT
4617229 ATCATAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
50 15 0.26
51 11 0.19
52 2 0.03
53 3 0.05
54 5 0.09
55 17 0.29
56 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (55 bp):
TTTTAATTAAAATTGATTATGAAATTATTTAATAAAATAATTATATAAATGTTAA
Found at i:4618238 original size:19 final size:19
Alignment explanation
Indices: 4618214--4618251 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
4618204 TAAATATTTT
4618214 TATTTATTATAT-ATTTAAA
1 TATTTATT-TATCATTTAAA
4618233 TATTTATTTATCATTTAAA
1 TATTTATTTATCATTTAAA
4618252 ATCATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTATTTATCATTTAAA
Done.