Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007915.1 Hibiscus syriacus cultivar Beakdansim tig00110318_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: 1667290
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:413926 original size:83 final size:83
Alignment explanation
Indices: 413797--414021 Score: 270
Period size: 83 Copynumber: 2.7 Consensus size: 83
413787 GAAGAGTTCT
* * * * * ** *
413797 GGTCGTCTAAGGGTGACATGGCTCCTACGTGATGAGGAGATTTGGTCTGTGGATGACATGGTTCC
1 GGTCATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAATGGATGACACGGTTCC
*
413862 TACGCGATGAGGATGGTT
66 TACGCGATGAGGATGGTA
* *
413880 GGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAATGGATGAGACGGTTCC
1 GGTCATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAATGGATGACACGGTTCC
*
413945 TACGTGATGAGGATGGTA
66 TACGCGATGAGGATGGTA
* * *
413963 GGTCATCTTTAGGGTTGATAAGGCGGTTCCTACGTGATGAGGAGGTCTGGTCAATGGAT
1 GGTCATC--TAGGGGTGA-CA--CGGCTCCTACGTGATGAGGAGGTCTGGTCAATGGAT
414022 TAATTTTATT
Statistics
Matches: 121, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
83 77 0.64
85 8 0.07
86 1 0.01
88 35 0.29
ACGTcount: A:0.20, C:0.15, G:0.36, T:0.28
Consensus pattern (83 bp):
GGTCATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAATGGATGACACGGTTCC
TACGCGATGAGGATGGTA
Found at i:413967 original size:40 final size:39
Alignment explanation
Indices: 413810--414021 Score: 136
Period size: 40 Copynumber: 5.0 Consensus size: 39
413800 CGTCTAAGGG
* * * **
413810 TGACATGGCTCCTACGTGATGAGGAGATTTGGTCTGTGGA
1 TGACACGGTTCCTACGTGATGAGGAG-GTTGGTCAATGGA
* * * * *
413850 TGACATGGTTCCTACGCGATGAGGATGGTTGGTTATCTAGGGG
1 TGACACGGTTCCTACGTGATGAGGA-GGTTGG---TCAATGGA
*
413893 TGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAATGGA
1 TGACACGGTTCCTACGTGATGAGGAGGT-TGGTCAATGGA
* * * *
413933 TGAGACGGTTCCTACGTGATGAGGATGGTAGGTCATCTTTAGGGT
1 TGACACGGTTCCTACGTGATGAGGA-GGTTGGTCA-----ATGGA
*
413978 TGATAAGGCGGTTCCTACGTGATGAGGAGGTCTGGTCAATGGA
1 TGA-CA--CGGTTCCTACGTGATGAGGAGGT-TGGTCAATGGA
414021 T
1 T
414022 TAATTTTATT
Statistics
Matches: 136, Mismatches: 21, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
40 60 0.44
41 4 0.03
42 3 0.02
43 34 0.25
45 6 0.04
46 1 0.01
47 3 0.02
48 25 0.18
ACGTcount: A:0.21, C:0.15, G:0.36, T:0.28
Consensus pattern (39 bp):
TGACACGGTTCCTACGTGATGAGGAGGTTGGTCAATGGA
Found at i:416781 original size:19 final size:20
Alignment explanation
Indices: 416759--416822 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 20
416749 AATATGATCT
416759 ATTTA-TTGAAATATAATTA
1 ATTTACTTGAAATATAATTA
*
416778 ATTTACTTCGAATTAATTAATTA
1 ATTTACTT-GAAAT-A-TAATTA
416801 ATTTACTTTG-AAT-TAATTA
1 ATTTAC-TTGAAATATAATTA
416820 ATT
1 ATT
416823 AAAGAAAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 14 0.37
20 2 0.05
21 4 0.11
22 3 0.08
23 13 0.34
24 2 0.05
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
ATTTACTTGAAATATAATTA
Found at i:416802 original size:23 final size:23
Alignment explanation
Indices: 416772--416824 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
416762 TATTGAAATA
416772 TAATTAATTTACTTCGAATTAAT
1 TAATTAATTTACTTCGAATTAAT
*
416795 TAATTAATTTACTTTGAATTAAT
1 TAATTAATTTACTTCGAATTAAT
416818 TAATTAA
1 TAATTAA
416825 AGAAAACCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (23 bp):
TAATTAATTTACTTCGAATTAAT
Found at i:417492 original size:29 final size:30
Alignment explanation
Indices: 417425--417492 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 30
417415 GAAAACATAC
*
417425 ATTTAAAGGACTAAAATAGAAAAAATAGAA
1 ATTTAAAGGACTAAAATAGAAAAAATAAAA
*
417455 CTTTAAAGGACTAAAATA-AAAAAATAAAA
1 ATTTAAAGGACTAAAATAGAAAAAATAAAA
*
417484 ATTTGAAGG
1 ATTTAAAGG
417493 GCTGAACCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.22
Consensus pattern (30 bp):
ATTTAAAGGACTAAAATAGAAAAAATAAAA
Found at i:418968 original size:3 final size:3
Alignment explanation
Indices: 418949--419011 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
418939 TAATATGTAT
* * * *
418949 TAA TAA TTA TAA TTAA TAA TAA TAG TAG TAA TAA -AA TAA TTA T-A
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
418993 CAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TA
419012 TTTTTGTAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
2 5 0.10
3 41 0.84
4 3 0.06
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:418981 original size:28 final size:29
Alignment explanation
Indices: 418939--419000 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
418929 CAAAACAATG
* * *
418939 TAATATGTATTAATAATTATAATTA-ATAA
1 TAATATGTAGTAATAA-AATAATTATACAA
418968 TAATA-GTAGTAATAAAATAATTATACAA
1 TAATATGTAGTAATAAAATAATTATACAA
418996 TAATA
1 TAATA
419001 ATAATATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.24
28 17 0.59
29 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (29 bp):
TAATATGTAGTAATAAAATAATTATACAA
Found at i:419608 original size:14 final size:14
Alignment explanation
Indices: 419589--419623 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
419579 GTTCTGCTTG
419589 CGCACGGGCGTGTA
1 CGCACGGGCGTGTA
*
419603 CGCACGGGTGTGTA
1 CGCACGGGCGTGTA
*
419617 CACACGG
1 CGCACGG
419624 AATGAAGCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.29, G:0.40, T:0.14
Consensus pattern (14 bp):
CGCACGGGCGTGTA
Found at i:420578 original size:110 final size:110
Alignment explanation
Indices: 420309--420578 Score: 362
Period size: 110 Copynumber: 2.5 Consensus size: 110
420299 TCCTTAGGCG
* * * * * *
420309 GATTGTGGAATTTCACATGCCAACTATGAACAAGCAACCCACTTGATAAAAGTTATTAAAGACAA
1 GATTGTGGAATTTCATATGCCAATTATGAACTAGCAACCCACTTGATAACAGTAATGAAAGACAA
* * * *
420374 ATGCACACGACAAGACCTAACTTAACAACAACATTTCCTAAGGAA
66 AGGCACACAACAAGACCTAAATTAACAAAAACATTTCCTAAGGAA
* * * * *
420419 GATTGTGGAATTTCATATACCATTTCTGAAGTAGCAACCCACTTGATAACGGTAATGAAAGACAA
1 GATTGTGGAATTTCATATGCCAATTATGAACTAGCAACCCACTTGATAACAGTAATGAAAGACAA
* *
420484 AGGCATACAACAAGACCTAAATTAACAAAAACATTTCCTGAA-GCA
66 AGGCACACAACAAGACCTAAATTAACAAAAACATTTCCT-AAGGAA
*
420529 GATTGTGGAATTTCATATGCCAGTTATGAACTAGCAACCCACTTGATAAC
1 GATTGTGGAATTTCATATGCCAATTATGAACTAGCAACCCACTTGATAAC
420579 CATAACAAAA
Statistics
Matches: 138, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
110 136 0.99
111 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.24
Consensus pattern (110 bp):
GATTGTGGAATTTCATATGCCAATTATGAACTAGCAACCCACTTGATAACAGTAATGAAAGACAA
AGGCACACAACAAGACCTAAATTAACAAAAACATTTCCTAAGGAA
Found at i:421006 original size:15 final size:15
Alignment explanation
Indices: 420986--421015 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
420976 TCATTACCCG
420986 ACAAAATCCTACTTT
1 ACAAAATCCTACTTT
421001 ACAAAATCCTACTTT
1 ACAAAATCCTACTTT
421016 TGTATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (15 bp):
ACAAAATCCTACTTT
Found at i:426789 original size:2 final size:2
Alignment explanation
Indices: 426782--426807 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
426772 AAATTGTTTA
426782 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
426808 CTTGACTATT
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:433662 original size:24 final size:24
Alignment explanation
Indices: 433630--433680 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
433620 CCTCTTTCTA
433630 TCAAAAAAAATTAAAGTGCCATTT
1 TCAAAAAAAATTAAAGTGCCATTT
433654 TCAAAAAAAATTAAAGTGCCATTT
1 TCAAAAAAAATTAAAGTGCCATTT
433678 TCA
1 TCA
433681 GCATACAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (24 bp):
TCAAAAAAAATTAAAGTGCCATTT
Found at i:441434 original size:3 final size:3
Alignment explanation
Indices: 441419--441449 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
441409 GCTTCACAAT
*
441419 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
441450 AACTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:444694 original size:10 final size:10
Alignment explanation
Indices: 444679--444764 Score: 64
Period size: 10 Copynumber: 8.1 Consensus size: 10
444669 TATTTAAATG
444679 ATAAACGAAC
1 ATAAACGAAC
444689 ATAAACGAAC
1 ATAAACGAAC
*
444699 GTAAACGAAC
1 ATAAACGAAC
* *
444709 ACAAACGAAATA
1 ATAAACG-AA-C
** *
444721 ATAAATAAAT
1 ATAAACGAAC
444731 ATAAACGAACAC
1 ATAAACG-A-AC
*
444743 AATAAGCGAAC
1 -ATAAACGAAC
444754 ATAAACGAAC
1 ATAAACGAAC
444764 A
1 A
444765 ACACAAACAC
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
10 39 0.67
11 7 0.12
12 6 0.10
13 6 0.10
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:445048 original size:14 final size:14
Alignment explanation
Indices: 445029--445064 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
445019 GCCCTCTGTT
445029 CGAACATAAATAAA
1 CGAACATAAATAAA
*
445043 CGAACATAAATGAA
1 CGAACATAAATAAA
445057 CGAACATA
1 CGAACATA
445065 TAATCGAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.58, C:0.17, G:0.11, T:0.14
Consensus pattern (14 bp):
CGAACATAAATAAA
Found at i:445586 original size:11 final size:11
Alignment explanation
Indices: 445570--445632 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
445560 AAAATTACAT
445570 TATTAAAAATA
1 TATTAAAAATA
445581 TATTAAAAATA
1 TATTAAAAATA
* * ***
445592 CACTATTGATA
1 TATTAAAAATA
445603 -ATTATAAAAT-
1 TATTA-AAAATA
445613 T-TTAAAAATA
1 TATTAAAAATA
445623 TATTAAAAAT
1 TATTAAAAAT
445633 TTTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:448977 original size:18 final size:18
Alignment explanation
Indices: 448954--448989 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
448944 TGAGTTCACG
448954 TGGGTGACGCACTGTCTC
1 TGGGTGACGCACTGTCTC
448972 TGGGTGACGCACTGTCTC
1 TGGGTGACGCACTGTCTC
448990 GGGCTTCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.28, G:0.33, T:0.28
Consensus pattern (18 bp):
TGGGTGACGCACTGTCTC
Found at i:449286 original size:24 final size:23
Alignment explanation
Indices: 449238--449292 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
449228 AGGTTCAAAT
* * *
449238 TCGAGTTCGAGTTCGAGCTTGAA
1 TCGAGCTCGAGTTCGAACTTCAA
449261 TCGAGCTCGAGTCTCGAACTTCAA
1 TCGAGCTCGAGT-TCGAACTTCAA
*
449285 TCAAGCTC
1 TCGAGCTC
449293 CTGAATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (23 bp):
TCGAGCTCGAGTTCGAACTTCAA
Found at i:456137 original size:331 final size:331
Alignment explanation
Indices: 455535--456197 Score: 1317
Period size: 331 Copynumber: 2.0 Consensus size: 331
455525 TAATATCATG
*
455535 AAAAAAAATTAGTGGCTCAATTATCATTTATGTTAAAATCATCATAATTTAACTAAGAATTAACG
1 AAAAAAAATTAGTGGCTCAATAATCATTTATGTTAAAATCATCATAATTTAACTAAGAATTAACG
455600 ATTGAGGATTAAATTTAACTAAAAATTAATATAAATTATTAAAACACTTGAAATGATAAGAGTTA
66 ATTGAGGATTAAATTTAACTAAAAATTAATATAAATTATTAAAACACTTGAAATGATAAGAGTTA
455665 ATTTATTATATTTAATCTGATTCGTAAAATATCTTTGATTATTTTTAAAGATTTCTTATAAGTAT
131 ATTTATTATATTTAATCTGATTCGTAAAATATCTTTGATTATTTTTAAAGATTTCTTATAAGTAT
455730 CAAAGTGATCTTAAAAATTAATTTTAAACCCACTAAAAATATTTATTAAAGGCTTAATGAAAAAA
196 CAAAGTGATCTTAAAAATTAATTTTAAACCCACTAAAAATATTTATTAAAGGCTTAATGAAAAAA
455795 ACAAGTGTCTAAAAGTATAAACTATATTCTTTATTCATTTAGGTGCTTAAAATATTTTTTTAAAG
261 ACAAGTGTCTAAAAGTATAAACTATATTCTTTATTCATTTAGGTGCTTAAAATATTTTTTTAAAG
455860 TACTTA
326 TACTTA
455866 AAAAAAAATTAGTGGCTCAATAATCATTTATGTTAAAATCATCATAATTTAACTAAGAATTAACG
1 AAAAAAAATTAGTGGCTCAATAATCATTTATGTTAAAATCATCATAATTTAACTAAGAATTAACG
455931 ATTGAGGATTAAATTTAACTAAAAATTAATATAAATTATTAAAACACTTGAAATGATAAGAGTTA
66 ATTGAGGATTAAATTTAACTAAAAATTAATATAAATTATTAAAACACTTGAAATGATAAGAGTTA
455996 ATTTATTATATTTAATCTGATTCGTAAAATATCTTTGATTATTTTTAAAGATTTCTTATAAGTAT
131 ATTTATTATATTTAATCTGATTCGTAAAATATCTTTGATTATTTTTAAAGATTTCTTATAAGTAT
456061 CAAAGTGATCTTAAAAATTAATTTTAAACCCACTAAAAATATTTATTAAAGGCTTAATGAAAAAA
196 CAAAGTGATCTTAAAAATTAATTTTAAACCCACTAAAAATATTTATTAAAGGCTTAATGAAAAAA
456126 ACAAGTGTCTAAAAGTATAAACTATATTCTTTATTCATTTAGGTGCTTAAAATATTTTTTTAAAG
261 ACAAGTGTCTAAAAGTATAAACTATATTCTTTATTCATTTAGGTGCTTAAAATATTTTTTTAAAG
456191 TACTTA
326 TACTTA
456197 A
1 A
456198 TATTTTCCAC
Statistics
Matches: 331, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
331 331 1.00
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (331 bp):
AAAAAAAATTAGTGGCTCAATAATCATTTATGTTAAAATCATCATAATTTAACTAAGAATTAACG
ATTGAGGATTAAATTTAACTAAAAATTAATATAAATTATTAAAACACTTGAAATGATAAGAGTTA
ATTTATTATATTTAATCTGATTCGTAAAATATCTTTGATTATTTTTAAAGATTTCTTATAAGTAT
CAAAGTGATCTTAAAAATTAATTTTAAACCCACTAAAAATATTTATTAAAGGCTTAATGAAAAAA
ACAAGTGTCTAAAAGTATAAACTATATTCTTTATTCATTTAGGTGCTTAAAATATTTTTTTAAAG
TACTTA
Found at i:460145 original size:33 final size:35
Alignment explanation
Indices: 460108--460172 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 35
460098 TTAAGTATAA
460108 ATATAAAAGATA-AATAA-ATAAATAAATTATTGT
1 ATATAAAAGATATAATAATATAAATAAATTATTGT
* * *
460141 ATATAGAAGATATAATAATTTACATAAATTAT
1 ATATAAAAGATATAATAATATAAATAAATTAT
460173 GTAAAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 11 0.41
34 5 0.19
35 11 0.41
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (35 bp):
ATATAAAAGATATAATAATATAAATAAATTATTGT
Found at i:460271 original size:15 final size:15
Alignment explanation
Indices: 460251--460281 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
460241 CAACAAATAG
460251 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
460266 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
460281 A
1 A
460282 TTTAGAATTT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:460573 original size:15 final size:15
Alignment explanation
Indices: 460553--460583 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
460543 CAACAAATAG
460553 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
460568 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
460583 A
1 A
460584 TTTAGAATTT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:460775 original size:20 final size:20
Alignment explanation
Indices: 460739--460776 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
460729 ATCCTATTCT
**
460739 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
460759 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
460777 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:469453 original size:22 final size:22
Alignment explanation
Indices: 469428--469473 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
469418 GATGATCATG
*
469428 GTTTATACCTGTTGCACTACAT
1 GTTTATACCTGTTGCACAACAT
469450 GTTTATACCTGTTGCACAACAT
1 GTTTATACCTGTTGCACAACAT
469472 GT
1 GT
469474 ATGAGGACCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (22 bp):
GTTTATACCTGTTGCACAACAT
Found at i:471027 original size:128 final size:129
Alignment explanation
Indices: 470797--471278 Score: 862
Period size: 128 Copynumber: 3.8 Consensus size: 129
470787 ACTATTCACA
*
470797 TGAAGGCGCGTTCCCGTGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
470862 TTATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
*
470925 TGAAGGCGCGTTCCCGGGGGAGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
470990 TTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
* *
471053 TGAAGGCGCATTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
471118 TTATGTGACTCATGTCCCTCGGGGACACT-GTTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
*
471181 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCGTTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
471246 TTATGTAACTCATGTCCCTCGGGGACACTAGAT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGAT
471279 GGATTGTGAA
Statistics
Matches: 338, Mismatches: 13, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
127 2 0.01
128 333 0.99
129 3 0.01
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (129 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:471678 original size:34 final size:33
Alignment explanation
Indices: 471640--471745 Score: 149
Period size: 34 Copynumber: 3.2 Consensus size: 33
471630 TAAGTTGAAA
* *
471640 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATAT-ATTTATAT
*
471674 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATA-TATTTATAT
* *
471708 TTTTATTTTAAATTTCGAATAATATATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATATTTATAT
471741 TTTAA
1 TTTAA
471746 AAACATTTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
33 12 0.18
34 52 0.80
35 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.56
Consensus pattern (33 bp):
TTTAATTTTAAATTTCGAATAATATATTTATAT
Found at i:472295 original size:21 final size:20
Alignment explanation
Indices: 472268--472358 Score: 103
Period size: 21 Copynumber: 4.3 Consensus size: 20
472258 GGTATAAAAC
*
472268 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
472288 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
472309 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
*
472330 CCCCGCGGGCTCA-GAATGTAA
1 -CCTGCGGGCT-AGGAATGTAA
472351 CCCTGCGG
1 -CCTGCGG
472359 AGATGACATA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.05
21 57 0.90
22 3 0.05
ACGTcount: A:0.20, C:0.29, G:0.34, T:0.18
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:472328 original size:42 final size:42
Alignment explanation
Indices: 472265--472358 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 42
472255 TATGGTATAA
* **
472265 AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCT-AGGAATGT
1 AACCCTGCGGGCTAGGAATGTAACCCCGCGGGCTCA-GAATGT
*
472307 AACCCTGCGGGCTCGGAATGTAACCCCGCGGGCTCAGAATGT
1 AACCCTGCGGGCTAGGAATGTAACCCCGCGGGCTCAGAATGT
472349 AACCCTGCGG
1 AACCCTGCGG
472359 AGATGACATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (42 bp):
AACCCTGCGGGCTAGGAATGTAACCCCGCGGGCTCAGAATGT
Found at i:474216 original size:35 final size:35
Alignment explanation
Indices: 474137--474223 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
474127 TAATAATTCT
* *
474137 AAATAAATAATAATTATATAAATATTATTTTAATAA
1 AAATAAATAATATTTACATAAATATTA-TTTAATAA
474173 AAA-AAATAATATTTACATAAATA-TA-TTAATATA
1 AAATAAATAATATTTACATAAATATTATTTAATA-A
474206 AAATATAATAACTATTTA
1 AAATA-AATAA-TATTTA
474224 AAAAAATACT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
32 6 0.13
33 4 0.09
34 3 0.07
35 23 0.51
36 9 0.20
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (35 bp):
AAATAAATAATATTTACATAAATATTATTTAATAA
Found at i:474241 original size:34 final size:34
Alignment explanation
Indices: 474169--474246 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
474159 TATTATTTTA
* * * *
474169 ATAAAAAAAATAATATTTACATAAATATATTAAT
1 ATAAAAATAATAATATTTACATAAAAATACTAAC
474203 ATAAAATATAATAACTATTTA-A-AAAAATACTAAC
1 ATAAAA-ATAATAA-TATTTACATAAAAATACTAAC
474237 ATAAAAATAA
1 ATAAAAATAA
474247 ATTTCTTACC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 4 0.11
34 21 0.55
35 7 0.18
36 6 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (34 bp):
ATAAAAATAATAATATTTACATAAAAATACTAAC
Found at i:481615 original size:24 final size:24
Alignment explanation
Indices: 481583--481641 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
481573 AAGAGTCTGA
481583 GAAGAAGGTTGCGGTTGATAAGGG
1 GAAGAAGGTTGCGGTTGATAAGGG
481607 GAAGAAGGTTGCGGTTGATAAGGG
1 GAAGAAGGTTGCGGTTGATAAGGG
*
481631 GAAAAAGGTTG
1 GAAGAAGGTTG
481642 ATATTCAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.32, C:0.03, G:0.44, T:0.20
Consensus pattern (24 bp):
GAAGAAGGTTGCGGTTGATAAGGG
Found at i:486654 original size:8 final size:8
Alignment explanation
Indices: 486641--486722 Score: 52
Period size: 7 Copynumber: 10.5 Consensus size: 8
486631 TTCGCCTGAA
486641 AAAAAATG
1 AAAAAATG
486649 AAAAAA-G
1 AAAAAATG
*
486656 -AAAAATA
1 AAAAAATG
486663 AAAAAAT-
1 AAAAAATG
486670 -AAAAA-G
1 AAAAAATG
486676 AAAAAA-G
1 AAAAAATG
*
486683 AAAAATTGAG
1 AAAAAAT--G
486693 AAAAAAATG
1 -AAAAAATG
486702 -AAAAATG
1 AAAAAATG
486709 ATGAAAAATG
1 A--AAAAATG
486719 AAAA
1 AAAA
486723 GGAAAAAAAG
Statistics
Matches: 60, Mismatches: 3, Indels: 22
0.71 0.04 0.26
Matches are distributed among these distances:
6 10 0.17
7 19 0.32
8 15 0.25
9 1 0.02
10 9 0.15
11 6 0.10
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:486658 original size:7 final size:7
Alignment explanation
Indices: 486641--486687 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
486631 TTCGCCTGAA
486641 AAAAAATG
1 AAAAAA-G
486649 AAAAAAG
1 AAAAAAG
486656 AAAAATA-
1 AAAAA-AG
486663 AAAAAA-
1 AAAAAAG
*
486669 TAAAAAG
1 AAAAAAG
486676 AAAAAAG
1 AAAAAAG
486683 AAAAA
1 AAAAA
486688 TTGAGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 6 0.17
7 22 0.63
8 7 0.20
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (7 bp):
AAAAAAG
Found at i:486687 original size:20 final size:20
Alignment explanation
Indices: 486640--486680 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
486630 TTTCGCCTGA
486640 AAAAAAATGAAAAAAGAAAAAT
1 AAAAAAAT--AAAAAGAAAAAT
486662 AAAAAAATAAAAAGAAAAA
1 AAAAAAATAAAAAGAAAAA
486681 AGAAAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (20 bp):
AAAAAAATAAAAAGAAAAAT
Found at i:486697 original size:18 final size:19
Alignment explanation
Indices: 486676--486716 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
486666 AAATAAAAAG
486676 AAAAAA-GAAAAATTGA-GA
1 AAAAAATGAAAAA-TGATGA
486694 AAAAAATGAAAAATGATGA
1 AAAAAATGAAAAATGATGA
486713 AAAA
1 AAAA
486717 TGAAAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (19 bp):
AAAAAATGAAAAATGATGA
Found at i:486706 original size:27 final size:26
Alignment explanation
Indices: 486639--486738 Score: 94
Period size: 27 Copynumber: 3.6 Consensus size: 26
486629 ATTTCGCCTG
486639 AAAAAAAATGAAAAAAGAAAAATAAA
1 AAAAAAAATGAAAAAAGAAAAATAAA
* **
486665 AAAATAAAAAGAAAAAAGAAAAATTGA
1 AAAA-AAAATGAAAAAAGAAAAATAAA
*
486692 GAAAAAAATGAAAAATGATGAAAAATGAAA
1 AAAAAAAATGAAAAA--A-GAAAAAT-AAA
486722 AGGAAAAAAA-GAAAAAA
1 A--AAAAAAATGAAAAAA
486739 ATAGAAAATG
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
26 14 0.24
27 22 0.37
28 1 0.02
29 8 0.14
30 1 0.02
31 6 0.10
32 7 0.12
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (26 bp):
AAAAAAAATGAAAAAAGAAAAATAAA
Found at i:486865 original size:45 final size:45
Alignment explanation
Indices: 486780--486865 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
486770 AAATTAAATA
** * *
486780 AAAGGAGGGTTCAAGATGAAAATTCGAAAATGGCGTCTTGAAACC
1 AAAGGAGGGTTCAAGATGAAAACCCGAAAAGGGCGACTTGAAACC
* *
486825 AAAGGA-GGTCTCAAGTTGAAAACCCGCAAAGGGCGACTTGA
1 AAAGGAGGGT-TCAAGATGAAAACCCGAAAAGGGCGACTTGA
486866 GTTTTGTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 3 0.09
45 31 0.91
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.17
Consensus pattern (45 bp):
AAAGGAGGGTTCAAGATGAAAACCCGAAAAGGGCGACTTGAAACC
Found at i:488181 original size:55 final size:54
Alignment explanation
Indices: 488098--488357 Score: 326
Period size: 55 Copynumber: 4.7 Consensus size: 54
488088 ATTTTATGAA
* *
488098 GATCGAGT-TCTATACTCTCTGATGGAATAGGGAGCAGACCTGTTTGTTGAAGATT
1 GATCGAGTCT-TATACTCCCTGAAGGAATAGGGAGCAGACC-GTTTGTTGAAGATT
* * * *
488153 GTTCGAGT-TCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATT
1 GATCGAGTCT-TATACTCCCTGAAGGAATAGGGAGCAGA-CCGTTTGTTGAAGATT
* * *
488208 GATCGAGTCTTATACTCTCTGAATGAATAGGGAGCAGACACATTTGTTGAAGATT
1 GATCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGAC-CGTTTGTTGAAGATT
* *
488263 GATCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCTGAAGATT
1 GATCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGAC-CGTTTGTTGAAGATT
* * *
488318 GGTCTAGTCTTATACTCCCTGAAGGGATAGGGAGCAGACC
1 GATCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACC
488358 CGTCATTCGA
Statistics
Matches: 183, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
54 2 0.01
55 178 0.97
56 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (54 bp):
GATCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACCGTTTGTTGAAGATT
Found at i:488372 original size:110 final size:110
Alignment explanation
Indices: 488098--488360 Score: 359
Period size: 110 Copynumber: 2.4 Consensus size: 110
488088 ATTTTATGAA
* * *
488098 GATCGAGT-TCTATACTCTCTGATGGAATAGGGAGCAGACCTGTTTGTTGAAGATTGTTCGAGTT
1 GATCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCAGACCCGTTTGTTGAAGATTGATCGAGTT
* * *
488162 CTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATT
65 CTATACTCCCTGAACGAATAGGGAGCAGACACGTTTACTGAAGATT
* * *
488208 GATCGAGTCTTATACTCTCTGAATGAATAGGGAGCAGACACATTTGTTGAAGATTGATCGAG-TC
1 GATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACCCGTTTGTTGAAGATTGATCGAGTTC
* *
488272 TTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCTGAAGATT
66 -TATACTCCCTGAACGAATAGGGAGCAGACACGTTTACTGAAGATT
* * * *
488318 GGTCTAGTCTTATACTCCCTGAAGGGATAGGGAGCAGACCCGT
1 GATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACCCGT
488361 CATTCGAAGA
Statistics
Matches: 133, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
109 2 0.02
110 130 0.98
111 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (110 bp):
GATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACCCGTTTGTTGAAGATTGATCGAGTTC
TATACTCCCTGAACGAATAGGGAGCAGACACGTTTACTGAAGATT
Found at i:499783 original size:18 final size:18
Alignment explanation
Indices: 499760--499817 Score: 116
Period size: 18 Copynumber: 3.2 Consensus size: 18
499750 GTTCTAGAAT
499760 GAATCTAGAATGAGTCTA
1 GAATCTAGAATGAGTCTA
499778 GAATCTAGAATGAGTCTA
1 GAATCTAGAATGAGTCTA
499796 GAATCTAGAATGAGTCTA
1 GAATCTAGAATGAGTCTA
499814 GAAT
1 GAAT
499818 GTTGAAGCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (18 bp):
GAATCTAGAATGAGTCTA
Found at i:499795 original size:11 final size:11
Alignment explanation
Indices: 499752--499818 Score: 69
Period size: 11 Copynumber: 6.8 Consensus size: 11
499742 AAGTAAACGT
*
499752 TCTAGAATGAA
1 TCTAGAATGAG
499763 TCTAGAATGAG
1 TCTAGAATGAG
499774 TCTAG-A--A-
1 TCTAGAATGAG
499781 TCTAGAATGAG
1 TCTAGAATGAG
499792 TCTAG-A--A-
1 TCTAGAATGAG
499799 TCTAGAATGAG
1 TCTAGAATGAG
499810 TCTAGAATG
1 TCTAGAATG
499819 TTGAAGCAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
7 10 0.21
8 4 0.09
10 4 0.09
11 29 0.62
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.28
Consensus pattern (11 bp):
TCTAGAATGAG
Found at i:506391 original size:20 final size:20
Alignment explanation
Indices: 506330--506389 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
506320 AAAGGAATAT
*
506330 ATAAAGTAAATAATAGTAATAA-
1 ATAAA-TAAATAA-AG-AAAAAG
*
506352 ATAAATAAATAAAGATAAAG
1 ATAAATAAATAAAGAAAAAG
506372 ATAAATAAA-AAAGAAAAA
1 ATAAATAAATAAAGAAAAA
506390 AGGATTTAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 11 0.32
20 11 0.32
21 7 0.21
22 5 0.15
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (20 bp):
ATAAATAAATAAAGAAAAAG
Found at i:506453 original size:12 final size:13
Alignment explanation
Indices: 506432--506460 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
506422 AAAGATAAAG
506432 ATAAAGTAAATAA
1 ATAAAGTAAATAA
506445 ATAAA-TAAATAA
1 ATAAAGTAAATAA
506457 ATAA
1 ATAA
506461 TTGAGAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
ATAAAGTAAATAA
Found at i:507194 original size:2 final size:2
Alignment explanation
Indices: 507187--507226 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
507177 AAAAATATTA
507187 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
507227 TCCTAAGGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:509035 original size:15 final size:15
Alignment explanation
Indices: 509004--509053 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
508994 AAATATCCAA
*
509004 TAAAATAAATATAAAT
1 TAAAAAAAAT-TAAAT
509020 TAAAAAAAATTAAAT
1 TAAAAAAAATTAAAT
**
509035 TATGAAAAATTAAAT
1 TAAAAAAAATTAAAT
509050 TAAA
1 TAAA
509054 TGAAATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 20 0.69
16 9 0.31
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
TAAAAAAAATTAAAT
Found at i:509059 original size:15 final size:15
Alignment explanation
Indices: 509006--509074 Score: 61
Period size: 15 Copynumber: 4.6 Consensus size: 15
508996 ATATCCAATA
509006 AAAT-AAATATAAATT
1 AAATAAAAT-TAAATT
*
509021 AAAAAAAATTAAATT
1 AAATAAAATTAAATT
*
509036 ATGA-AAAATTAAATT
1 A-AATAAAATTAAATT
* * *
509051 AAATGAAATAAAAAT
1 AAATAAAATTAAATT
509066 AAATAAAAT
1 AAATAAAAT
509075 GGGTTACCTC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
14 1 0.02
15 38 0.86
16 5 0.11
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAATAAAATTAAATT
Found at i:513375 original size:2 final size:2
Alignment explanation
Indices: 513368--513432 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
513358 CATTATCTTT
513368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
513410 TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
513433 CTATTTGTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:515687 original size:12 final size:14
Alignment explanation
Indices: 515670--515702 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
515660 TATCATCACT
515670 TTTGCATC-T-GTA
1 TTTGCATCTTCGTA
515682 TTTGCATCTTCGTA
1 TTTGCATCTTCGTA
515696 TTTGCAT
1 TTTGCAT
515703 AATGATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 1 0.05
14 10 0.53
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.52
Consensus pattern (14 bp):
TTTGCATCTTCGTA
Found at i:518679 original size:2 final size:2
Alignment explanation
Indices: 518667--518709 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
518657 TTTACCCAAC
518667 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
518707 AT A
1 AT A
518710 CAATAAAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:520337 original size:126 final size:125
Alignment explanation
Indices: 520112--520569 Score: 568
Period size: 126 Copynumber: 3.6 Consensus size: 125
520102 AAATCAAAAT
* * *
520112 CCCTTATATGGACAAGACTCATGAACAAATGAGCAGTGTCATCACCTGACCATATCTCCTCATTA
1 CCCTTAGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACCTGACCAGATCTCCTCATTA
* *
520177 TGTAGGAGCTGTGTCAACTCAAATAACCAGCCGTCCCCATCAGAGTGGAACCGTGTTATCA
66 TGTAGGAGCTGTGTCAACTCAGATAACCAGCCGT-CCCATCAAAGTGGAACCGTGTTATCA
*
520238 CCCTTGGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACCTGACCAGATCTCCTCATTA
1 CCCTTAGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACCTGACCAGATCTCCTCATTA
*
520303 TGTAGGAGCTGTGTCAACTCAGATAAACAGCCGTCCTCATCAAAGTGGAACCGTGTTATCA
66 TGTAGGAGCTGTGTCAACTCAGATAACCAGCCGTCC-CATCAAAGTGGAACCGTGTTATCA
* ** * * *
520364 CCCTTAGATGGTCAAGACTCATGAACGGATGAGCAGTGTCATCACATGATCATATCTCCTCATTA
1 CCCTTAGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACCTGACCAGATCTCCTCATTA
* * * * * * * *
520429 TGTAGGA-CACGTGTCAA-TCCTAGATAACCAAGAC-T--TATCATAGTATGAGCAGTTTTATCA
66 TGTAGGAGC-TGTGTCAACT-C-AGATAACC-AGCCGTCCCATCAAAGT-GGAACCGTGTTATCA
* * ** *
520489 CCCTTAGATGGCCAAGACTCATGAACAGATGAGCAGTGTCATCACTTGATTAGATCTCCACATTA
1 CCCTTAGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACCTGACCAGATCTCCTCATTA
520554 TGTAGGAG-TCGTGTCA
66 TGTAGGAGCT-GTGTCA
520570 CCCTTAGACG
Statistics
Matches: 294, Mismatches: 30, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
124 7 0.02
125 87 0.30
126 189 0.64
127 8 0.03
128 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (125 bp):
CCCTTAGATGGCCAAGACTCATGAACAAATGAGCAGTGTCATCACCTGACCAGATCTCCTCATTA
TGTAGGAGCTGTGTCAACTCAGATAACCAGCCGTCCCATCAAAGTGGAACCGTGTTATCA
Found at i:520776 original size:3 final size:3
Alignment explanation
Indices: 520762--520866 Score: 147
Period size: 3 Copynumber: 34.3 Consensus size: 3
520752 GGCTTTAAAA
* ** *
520762 ATT ATA ATT ATT ATT ATAT ATT ATT AAAC ATT ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT -ATT ATT ATT ATT ATT ATT ATT
*
520809 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
520857 ATT ATT ATT A
1 ATT ATT ATT A
520867 AATTTGTATT
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
3 86 0.96
4 4 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:521916 original size:11 final size:11
Alignment explanation
Indices: 521900--521934 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
521890 ATCGATTCCC
521900 CTGCTACAGTA
1 CTGCTACAGTA
521911 CTGCTACAGTA
1 CTGCTACAGTA
521922 CTGCTACAGTA
1 CTGCTACAGTA
521933 CT
1 CT
521935 TTCGTAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:522548 original size:23 final size:23
Alignment explanation
Indices: 522482--522567 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 23
522472 TCATATAAAT
522482 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
522505 TTTGTC-CCGAAG-GACCGCGTAGAGA
1 -TTG-CACCGAAGTG-CCACGTAGA-A
522530 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
522552 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
522568 TATAATATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
22 2 0.04
23 31 0.58
24 18 0.34
25 2 0.04
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:525648 original size:14 final size:14
Alignment explanation
Indices: 525629--525661 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
525619 AACCGACTCC
525629 CGAATCCATTTAAT
1 CGAATCCATTTAAT
525643 CGAATCCATTTAAT
1 CGAATCCATTTAAT
525657 CGAAT
1 CGAAT
525662 ATTTGGTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (14 bp):
CGAATCCATTTAAT
Found at i:528172 original size:37 final size:38
Alignment explanation
Indices: 528122--528211 Score: 128
Period size: 38 Copynumber: 2.4 Consensus size: 38
528112 TTTTGTTCGG
528122 GTCGGGTCGGG-TTTTTTAAGTGTGAAATTCAGGTCGA
1 GTCGGGTCGGGTTTTTTTAAGTGTGAAATTCAGGTCGA
* * * *
528159 GTCGGGTCTGGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGGTCGGGTTTTTTTAAGTGTGAAATTCAGGTCGA
528197 GTCGGGTTCGGGTTT
1 GTCGGG-TCGGGTTT
528212 AGGGTGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 10 0.22
38 29 0.63
39 7 0.15
ACGTcount: A:0.12, C:0.11, G:0.38, T:0.39
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGAAATTCAGGTCGA
Found at i:528683 original size:37 final size:38
Alignment explanation
Indices: 528641--528726 Score: 138
Period size: 38 Copynumber: 2.3 Consensus size: 38
528631 TTTATTTTGT
528641 TCGGGTCGGG-TTTTTTAAGTGTGATATTCAGGTCGAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGAG
* *
528678 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGAG
528716 TCGGGTTCGGG
1 TCGGG-TCGGG
528727 ATTAGGGTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 10 0.22
38 30 0.67
39 5 0.11
ACGTcount: A:0.12, C:0.12, G:0.40, T:0.37
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGAG
Found at i:529074 original size:518 final size:518
Alignment explanation
Indices: 528006--528991 Score: 1719
Period size: 518 Copynumber: 1.9 Consensus size: 518
527996 TATTTTTTTT
* * *
528006 CAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATTTTGGGTCGGGTCGGTCGGA
1 CAATTAAGTCACTATTTTAAATGAATAAAAATATTTTTTTATTATTTTGGGTCGGGTCGGTCAGA
528071 TTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTT
66 TTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTT---GTCGGGTCGGGTTT
*
528136 TTTAAGTGTGAAATTCAGGTCGAGTCGGGTCTGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCG
128 TTTAAGTGTGAAATTCAGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCG
* *
528201 GGTTCGGGTTTAGGGTGAAAAAAATCGGACCGACCCGAAAAATATATATAATTTTACCTTATATA
193 GGTTCGGGATTAGGGTGAAAAAAACCGGACCGACCCGAAAAATATATATAATTTTACCTTATATA
* *
528266 TTTAGGAATAATTACAATAATACCCCTCTATATATATTTTTTTTCAATTAAGTCAATGTTTTTTA
258 TTTAGGAATAATTACAATAATACCCCTATATATATAATTTTTTTCAATTAAGTCAATGTTTTTTA
528331 TTAAATAAAAATAATTTTTTTATTATTTTGTGTAGTGTCGGGTTTCTAATTCATATATTGAATAA
323 TTAAATAAAAATAATTTTTTTATTATTTTGTGTAGTGTCGGGTTTCTAATTCATATATTGAATAA
*
528396 AAATAGTTTTTGGTATATTTTTTGTAACTAATTAACATACTCCGATTGGAATGTATCGAAATATT
388 AAATAGTTTTTGGTATATTTTTGGTAACTAATTAACATACTCCGATTGGAATGTATCGAAATATT
* ** * *
528461 GCTCTATCTTTTTTTCAATTAAGTCACTTTAGGAATAATTATAATAATACTCCTCCATATATTTT
453 GCTATATCTTTTGGTCAATTAAGTAACTTTAGGAATAATGATAATAATACT-CT-CATATATTTT
**
528526 TTT
516 TAG
* *
528529 CAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATTTTGGGTCGGGTCGGTCAGA
1 CAATTAAGTCACTATTTTAAATGAATAAAAATATTTTTTTATTATTTTGGGTCGGGTCGGTCAGA
528594 TTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTG-T-TCGGGTCGGGTTTTTT
66 TTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTGTCGGGTCGGGTTTTTT
*
528657 AAGTGTGATATTCAGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGT
131 AAGTGTGAAATTCAGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGT
528722 TCGGGATTAGGGTGAAAAAAACCGGACCGACCCGAAAAATATATATAATTTTACCTTATATATTT
196 TCGGGATTAGGGTGAAAAAAACCGGACCGACCCGAAAAATATATATAATTTTACCTTATATATTT
528787 AGGAATAATTACAATAATACCCCTATATATATAATTTTTTTCAATTAAGTCAATG-TTTTTATTA
261 AGGAATAATTACAATAATACCCCTATATATATAATTTTTTTCAATTAAGTCAATGTTTTTTATTA
*
528851 AATAAAAATAATTTTTTTATTATTTTGTGTCGTGTCGGGTTTCTAATTCATATATTGAATAAAAA
326 AATAAAAATAATTTTTTTATTATTTTGTGTAGTGTCGGGTTTCTAATTCATATATTGAATAAAAA
528916 TAG-TTTTGGTATATTTTTGGTAACTAATTAACATACTCCGATTGGAATGTATCGAAATATTGCT
391 TAGTTTTTGGTATATTTTTGGTAACTAATTAACATACTCCGATTGGAATGTATCGAAATATTGCT
528980 ATATCTTTTGGT
456 ATATCTTTTGGT
528992 AACTTATTAA
Statistics
Matches: 451, Mismatches: 12, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
516 69 0.15
517 76 0.17
518 195 0.43
522 1 0.00
523 110 0.24
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (518 bp):
CAATTAAGTCACTATTTTAAATGAATAAAAATATTTTTTTATTATTTTGGGTCGGGTCGGTCAGA
TTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTGTCGGGTCGGGTTTTTT
AAGTGTGAAATTCAGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGT
TCGGGATTAGGGTGAAAAAAACCGGACCGACCCGAAAAATATATATAATTTTACCTTATATATTT
AGGAATAATTACAATAATACCCCTATATATATAATTTTTTTCAATTAAGTCAATGTTTTTTATTA
AATAAAAATAATTTTTTTATTATTTTGTGTAGTGTCGGGTTTCTAATTCATATATTGAATAAAAA
TAGTTTTTGGTATATTTTTGGTAACTAATTAACATACTCCGATTGGAATGTATCGAAATATTGCT
ATATCTTTTGGTCAATTAAGTAACTTTAGGAATAATGATAATAATACTCTCATATATTTTTAG
Found at i:529274 original size:17 final size:18
Alignment explanation
Indices: 529252--529298 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
529242 TATGGAATTG
*
529252 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
529269 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
529287 AATTCCAATTCC
1 GATTCCAATTCC
529299 CTCATAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.30, C:0.32, G:0.06, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:529445 original size:14 final size:14
Alignment explanation
Indices: 529426--529493 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
529416 AGATGAGAGA
*
529426 AAAAATGAATAGAT
1 AAAAATAAATAGAT
529440 AAAAAT-AATA-AT
1 AAAAATAAATAGAT
* *
529452 AGTAAATAAATAAAT
1 A-AAAATAAATAGAT
*
529467 AAATATAAATAGAT
1 AAAAATAAATAGAT
529481 AAATAAATAAATA
1 -AA-AAATAAATA
529494 AATAGAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
12 3 0.07
13 8 0.18
14 20 0.45
15 5 0.11
16 8 0.18
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (14 bp):
AAAAATAAATAGAT
Found at i:529463 original size:4 final size:4
Alignment explanation
Indices: 529454--529497 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
529444 ATAATAATAG
*
529454 TAAA TAAA TAAA TAAA T--A TAAA TAGA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
529498 GAAAAAAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
4 34 0.94
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:529490 original size:26 final size:25
Alignment explanation
Indices: 529449--529497 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
529439 TAAAAATAAT
529449 AATAGTAAATAAATAAATAAATATA
1 AATAGTAAATAAATAAATAAATATA
529474 AATAGATAAATAAATAAATAAATA
1 AATAG-TAAATAAATAAATAAATA
529498 GAAAAAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (25 bp):
AATAGTAAATAAATAAATAAATATA
Found at i:531772 original size:32 final size:31
Alignment explanation
Indices: 531683--531776 Score: 86
Period size: 31 Copynumber: 3.0 Consensus size: 31
531673 GATCCTTGGC
** * *
531683 AACTGTCCATGGGTTCCTTAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
531714 AACTGTCCATATG-TCTCG-AAATACATAGGTA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGTA
531745 ATTA-TGTCCATATGTTCCGTAGAACATAGGTA
1 A--ACTGTCCATATGTTCCGTAGAACATAGGTA
531777 TACCCTCGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
30 4 0.08
31 21 0.41
32 21 0.41
33 5 0.10
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:536472 original size:30 final size:30
Alignment explanation
Indices: 536436--536507 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
536426 CCCGAAGGAC
*
536436 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
*
536466 CTATCCAGAGGTCATAAAGATCCTTGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
536496 TTATCCATAGGT
1 CTATCCAGAGGT
536508 TCCGAAGAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:541887 original size:32 final size:32
Alignment explanation
Indices: 541781--541941 Score: 206
Period size: 32 Copynumber: 5.1 Consensus size: 32
541771 GCTCGTATAA
*
541781 TAAT-CTGTTCATATGTCCC-AAAGAACATAGG
1 TAATACTGTCCATATGTCCCGAAAG-ACATAGG
*
541812 TAA-ACTGTCAATATGTCCCG-AAGAACATAGG
1 TAATACTGTCCATATGTCCCGAAAG-ACATAGG
*
541843 TAA-ATTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
*
541874 TAATATTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
* **
541906 TAATACTATCCATATGTCCTAAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
541938 TAAT
1 TAAT
541942 CCCTCGACTC
Statistics
Matches: 118, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
31 55 0.47
32 63 0.53
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (32 bp):
TAATACTGTCCATATGTCCCGAAAGACATAGG
Found at i:541937 original size:64 final size:62
Alignment explanation
Indices: 541790--541941 Score: 191
Period size: 63 Copynumber: 2.4 Consensus size: 62
541780 ATAATCTGTT
* * *
541790 CATATGTCCCAAAGAACATAGGTAA-ACTGTCAATATGTCCCGAAGAACATAGGTAAATTGTC
1 CATATGTCCAAAAG-ACATAGGTAATACTGTCAATATGTCCCGAAGAACATAGGTAAACTATC
* * *
541852 CATATGTCCCGAAAGACATAGGTAATATTGTCCATATGTCCCGAA-AGACATAGGTAATACTATC
1 CATATGT-CCAAAAGACATAGGTAATACTGTCAATATGTCCCGAAGA-ACATAGGTAA-ACTATC
541916 CATATGTCCTAAAAGACATAGGTAAT
1 CATATGTCC-AAAAGACATAGGTAAT
541942 CCCTCGACTC
Statistics
Matches: 79, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
62 18 0.23
63 35 0.44
64 26 0.33
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (62 bp):
CATATGTCCAAAAGACATAGGTAATACTGTCAATATGTCCCGAAGAACATAGGTAAACTATC
Found at i:547412 original size:2 final size:2
Alignment explanation
Indices: 547405--547429 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
547395 GATATTAAGT
547405 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
547430 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:551929 original size:2 final size:2
Alignment explanation
Indices: 551922--551957 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
551912 GATTCATAAG
551922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
551958 ACCGAAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:554572 original size:18 final size:19
Alignment explanation
Indices: 554538--554574 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
554528 CACGTAATGT
554538 AAGATTACCAATGGGAATAA
1 AAGATTACC-ATGGGAATAA
554558 AAGATTACC-TGGGAATA
1 AAGATTACCATGGGAATA
554575 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (19 bp):
AAGATTACCATGGGAATAA
Found at i:554586 original size:15 final size:16
Alignment explanation
Indices: 554560--554589 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
554550 GGGAATAAAA
554560 GATTACCTGGGAATAG
1 GATTACCTGGGAATAG
554576 GATTA-CTGGGAATA
1 GATTACCTGGGAATA
554590 TTGTATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (16 bp):
GATTACCTGGGAATAG
Found at i:554798 original size:37 final size:37
Alignment explanation
Indices: 554725--554799 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
554715 GATGAAAAAT
* *
554725 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
554762 ATTTATATAATTTAT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTT-TCTTTAAAAAATTGAAAATCATAAA
554799 A
1 A
554800 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 18 0.55
39 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:555938 original size:27 final size:28
Alignment explanation
Indices: 555900--555963 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
555890 CTTTATTTTG
555900 TTCGGGTCGGG-TTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
555927 TTCGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
555955 TTCGGGTCG
1 TTCGGGTCG
555964 AGTTCGGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 11 0.31
28 25 0.69
ACGTcount: A:0.12, C:0.09, G:0.34, T:0.44
Consensus pattern (28 bp):
TTCGGGTCGGGTTTTTTTAAGTGTGATA
Found at i:556531 original size:38 final size:38
Alignment explanation
Indices: 556475--556553 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
556465 TCTGACATGT
* *
556475 CTGCGAACCAAACAGAATATGGAATTGGATTCCATTTC
1 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTC
556513 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTC
1 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTC
556551 CTG
1 CTG
556554 ACAGATTCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (38 bp):
CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTC
Found at i:556577 original size:18 final size:17
Alignment explanation
Indices: 556540--556590 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
556530 TATGGAATTG
*
556540 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
556557 GATTCCAATTCCTTCACA
1 GATTCCAATTCC-TCACA
*
556575 GATTCTAATTTCCTCA
1 GATTCCAA-TTCCTCA
556591 TAAACATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 12 0.40
18 14 0.47
19 4 0.13
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.35
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:558114 original size:16 final size:16
Alignment explanation
Indices: 558093--558124 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
558083 TTTTAGTTAT
558093 TCCTCGGCAAATCTTG
1 TCCTCGGCAAATCTTG
558109 TCCTCGGCAAATCTTG
1 TCCTCGGCAAATCTTG
558125 ACTGATCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (16 bp):
TCCTCGGCAAATCTTG
Found at i:564378 original size:67 final size:67
Alignment explanation
Indices: 564270--564403 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
564260 CAGCTAATCC
564270 GGACATAAACATTGTAAGTGAATTGCTGTTCGCTTAAATACTTGTGTAACATTCTAGCTCTTTCA
1 GGACATAAACATTGTAAGTGAATTGCTGTTCGCTTAAATACTTGTGTAACATTCTAGCTCTTTCA
564335 AT
66 AT
564337 GGACATAAACATTGTAAGTGAATTGCTGTTCGCTTAAATACTTGTGTAACATTCTAGCTCTTTCA
1 GGACATAAACATTGTAAGTGAATTGCTGTTCGCTTAAATACTTGTGTAACATTCTAGCTCTTTCA
564402 AT
66 AT
564404 AAATTTTGAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (67 bp):
GGACATAAACATTGTAAGTGAATTGCTGTTCGCTTAAATACTTGTGTAACATTCTAGCTCTTTCA
AT
Found at i:566925 original size:19 final size:20
Alignment explanation
Indices: 566883--566925 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
566873 AAACAAGAGA
*
566883 AATCAATAATTAAAATACACAT
1 AATCAATAATT--AATACAAAT
566905 AATCAATAATT-ATACAAAT
1 AATCAATAATTAATACAAAT
566924 AA
1 AA
566926 AGTAAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
22 11 0.55
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (20 bp):
AATCAATAATTAATACAAAT
Found at i:567387 original size:20 final size:20
Alignment explanation
Indices: 567364--567404 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
567354 TATTATTTAA
567364 AATTATGGCAAACTGCTGAG
1 AATTATGGCAAACTGCTGAG
*
567384 AATTATGGTAAACTGCTGAG
1 AATTATGGCAAACTGCTGAG
567404 A
1 A
567405 TAGTCCTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (20 bp):
AATTATGGCAAACTGCTGAG
Found at i:567479 original size:21 final size:23
Alignment explanation
Indices: 567454--567502 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
567444 TGATTATATA
567454 AAATTAT-AAAAT-AAT-CACATT
1 AAATTATAAAAATAAATCCACA-T
*
567475 AAATTTTAAAAATAAATCCACAT
1 AAATTATAAAAATAAATCCACAT
567498 AAATT
1 AAATT
567503 TCACACCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.25
22 5 0.21
23 9 0.38
24 4 0.17
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATTATAAAAATAAATCCACAT
Found at i:567486 original size:22 final size:23
Alignment explanation
Indices: 567461--567503 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
567451 ATAAAATTAT
567461 AAAAT-AAT-CACATTAAATTTTA
1 AAAATAAATCCACA-TAAATTTTA
567483 AAAATAAATCCACATAAATTT
1 AAAATAAATCCACATAAATTT
567504 CACACCAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAAATCCACATAAATTTTA
Found at i:568962 original size:20 final size:20
Alignment explanation
Indices: 568916--568982 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
568906 TAAAAAGACC
*
568916 AAAATATATTTTTAT-AGAAT
1 AAAAT-TATTTTTATAAGAAA
*
568936 AAGATTATTTATTATAA-AAA
1 AAAATTATTT-TTATAAGAAA
*
568956 ATAATTATTTTTATAAGAAA
1 AAAATTATTTTTATAAGAAA
568976 AAAATTA
1 AAAATTA
568983 ATCGTTTTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 11 0.28
20 27 0.69
21 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
AAAATTATTTTTATAAGAAA
Found at i:571823 original size:182 final size:182
Alignment explanation
Indices: 571553--572008 Score: 691
Period size: 182 Copynumber: 2.5 Consensus size: 182
571543 ATACATATTA
* * * * * * * *
571553 ATATAACAGGTAAAAATATGAAAAAACCGGTTAT-GAAAAGACAATACCGATAAAGTAATACCAG
1 ATATAACATGTAAAAATATGACAAAACCGG-TATCGAAATGATAAAACCGGTAAATTACTACCAG
* *
571617 ATATATTGAAAGTGTCGATACTTTAATATAAGTATTGACACTTTGTGAATTTAAAAGAGAAGTAG
65 ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAG
** * *
571682 TTTTAGCGTCTATATAGTGTCGATACTTTATAAAAATGTATCGATCCACAACG
130 TTTTAGCACCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCCACAACG
* *
571735 ATATAACATGTAAAAATATGACAAAACCAGTATCGAAATGATAAAACCGGTAAATTACTACCATA
1 ATATAACATGTAAAAATATGACAAAACCGGTATCGAAATGATAAAACCGGTAAATTACTACCAGA
571800 TATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGT
66 TATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGT
* *
571865 TTTAGCACCTATAAAGTTTCGATACTTTAAAAAAATGTATCGATCCACAATG
131 TTTAGCACCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCCACAACG
* * *
571917 ATATAACATGTAAAAATATAACAAAACCGGTATCGAAATGATAAACCCGGTAAATCT-CTACCGG
1 ATATAACATGTAAAAATATGACAAAACCGGTATCGAAATGATAAAACCGGTAAAT-TACTACCAG
571981 ATATATTGAAAGTGTCGATACTTTAATA
65 ATATATTGAAAGTGTCGATACTTTAATA
572009 AGTACGTGTA
Statistics
Matches: 249, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
181 3 0.01
182 245 0.98
183 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (182 bp):
ATATAACATGTAAAAATATGACAAAACCGGTATCGAAATGATAAAACCGGTAAATTACTACCAGA
TATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGT
TTTAGCACCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCCACAACG
Found at i:574212 original size:21 final size:21
Alignment explanation
Indices: 574188--574231 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
574178 AAGACAATCA
574188 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
574209 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
574230 AG
1 AG
574232 GCATAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.34, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:574333 original size:33 final size:33
Alignment explanation
Indices: 574280--574345 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
574270 AAATAGATGG
* *
574280 AGTGGTGAAAGACATAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGACATAGAGGTCTTAAGGGGTGA
*
574313 AGTGGTGAAAGA-AGTTGAGGTCTTAAGGGGTGA
1 AGTGGTGAAAGACA-TAGAGGTCTTAAGGGGTGA
574346 TCTTAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.30, C:0.03, G:0.44, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGACATAGAGGTCTTAAGGGGTGA
Found at i:574553 original size:18 final size:18
Alignment explanation
Indices: 574530--574565 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
574520 TGAAAAATAT
574530 GAAGAAGAAAAGAGGGAG
1 GAAGAAGAAAAGAGGGAG
*
574548 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGAGGGAG
574566 AAAATGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.03
Consensus pattern (18 bp):
GAAGAAGAAAAGAGGGAG
Found at i:575454 original size:4 final size:4
Alignment explanation
Indices: 575445--575469 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
575435 TAAGAGGTTG
575445 GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
575470 AAAGAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:576035 original size:19 final size:19
Alignment explanation
Indices: 576011--576059 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
576001 AATGTAGGGT
576011 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
576030 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
576049 TAATTTTGTAT
1 TAATTTTGTAT
576060 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:577367 original size:200 final size:199
Alignment explanation
Indices: 576409--577327 Score: 1211
Period size: 200 Copynumber: 4.6 Consensus size: 199
576399 GTAAGCATAT
* * * * * *
576409 GTGTCGAT-CTATTTATAGAAAGTATCGATCCCAGAAACATCGAAACCTACAAGTATAACGTAAT
1 GTGTCGATAC-ATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAAT
* * * *
576473 AGGTAACCTTTCAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACAACATG
65 AGGTAA-TTTTTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATG
576538 TATCGACACTTGTGGAGATTGTGTCGATACTTTTGGAACAGAATCAAATCCCAAAAAGGTGCACC
129 TATCGACACTTGTGGAGATTGTGTCGATACTTTTGGAACAGAATCAAATCCCAAAAAGGTGCACC
*
576603 CATATA
194 CATAAA
* *
576609 GTGTTGATACATTTTTAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * * *
576674 GGTAATTTTTCAATGTAAGCGATATAAATATACCGGTTTTATAAGAGAATAGGTCTACAACATCT
66 GGTAATTTTT-AATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
* * * * *
576739 ATCGACACTTGTGGAGATCGTGTCGATAGTTTTGGAATAGAATCAAATCCCGAAAAGGTACACCC
130 ATCGACACTTGTGGAGATTGTGTCGATACTTTTGGAACAGAATCAAATCCCAAAAAGGTGCACCC
*
576804 ATATA
195 ATAAA
*
576809 GTGTC-ATTACATTTTTAAAAAGTGTAGATCCCAGAAACATCGAAACCCATAAGTATAATGTAAT
1 GTGTCGA-TACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAAT
** **
576873 AGCCAATTTTTCAATGTAACTAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATG
65 AGGTAATTTTT-AATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATG
* ** ** * ** * *
576938 TATCGACACTTTTTAATTTTGTGTCGATA-TGTTTTGTCCAGAAT-AAATGCCAAAAAGGGTGAA
129 TATCGACACTTGTGGAGATTGTGTCGATACT-TTTGGAACAGAATCAAATCCCAAAAA-GGTGCA
**
577001 CGAATAAA
192 CCCATAAA
* * * *
577009 GTATCGGTACATTTTCAAAAAGTGTCGATCCCA-AATACATCGAAACCCATAATTATAATGTAAT
1 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAA-ACATCGAAACCCATAAGTATAATGTAAT
* * *
577073 ATGTAATTTTTAATGTAACCGATATAAATATACCGGTTTTATGAGAGAATAGGTCTACAAGATGT
65 AGGTAATTTTTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
*
577138 ATCGACACTTGTGGAGATCGTGTCGATACTTTTGGAACAGAATCAAATCCCAAAAAGGGTGCACC
130 ATCGACACTTGTGGAGATTGTGTCGATACTTTTGGAACAGAATCAAATCCCAAAAA-GGTGCACC
577203 CATAAA
194 CATAAA
* * *
577209 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAA-TCATAATTATAATGTAATA
1 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * * *
577273 GGTAATTTTGTAATATAACCGGTATAACTATACCGATTTTATGAGAAAATAGGTC
66 GGTAATTTT-TAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTC
577328 ATCATAAAGT
Statistics
Matches: 626, Mismatches: 82, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
199 125 0.20
200 498 0.80
201 3 0.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Consensus pattern (199 bp):
GTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
GGTAATTTTTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTA
TCGACACTTGTGGAGATTGTGTCGATACTTTTGGAACAGAATCAAATCCCAAAAAGGTGCACCCA
TAAA
Found at i:578864 original size:3 final size:3
Alignment explanation
Indices: 578856--578893 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
578846 CAAGCGGTCA
* *
578856 ATG ATG ATG AAG ATG AAG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
578894 CCAAACAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:580575 original size:200 final size:200
Alignment explanation
Indices: 580232--580992 Score: 1155
Period size: 200 Copynumber: 3.8 Consensus size: 200
580222 ATAACATGTA
* * * *
580232 TCGATACATTTTCAAAAAGTTTCGATCCCAAAAACATCGAAATCGATAATTATAATGTAATATGT
1 TCGATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
* * *
580297 AATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAATATATATT
66 AATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATC
* ** * *
580362 GACACATTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATACCAAAAAGGGTTAACGTATA
131 GACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGTCAAAAAGGGTAAACGAATA
580427 AAGTG
196 AAGTG
* *
580432 TCGATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGTT
1 TCGATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
* *
580497 AATTTTGTAATATAACCAGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATC
66 AATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATC
* * * *
580562 GACAGTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGTAAAAAAGGGTAAACGCACA
131 GACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGTCAAAAAGGGTAAACGAATA
580627 AAGTG
196 AAGTG
* ** *
580632 TCGATACATTTTCAAAAAGTGTCGATTCCAAAAATATCTTAACCGATAATTATAATGCAATAGGT
1 TCGATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
* *
580697 AATTTTGTAATACAACCGGTATAAATATACCGGTTTTATGATAGAATAGGTCTACAACATGTATC
66 AATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATC
* * *
580762 GACACTTTTTAATATTGTGTCGATACATTTTGTCCAGAATGGATGTCAAAAAGGGTGAACAAAAT
131 GACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGTCAAAAAGGGTAAAC-GAAT
580827 AAAGTG
195 AAAGTG
* * *
580833 TCGATACATTTTCAAAACGTGTCGA-TCCTAAAAACATCAAAACCCATAATTATAATGTAATAGG
1 TCGATACATTTTCAAAAAGTGTCGATTCC-AAAAACATCGAAACCGATAATTATAATGTAATAGG
* * * *
580897 TAATTTTGTAATATAACCGATTTAAATATACCGATTTTATGAGATAATAGGTCTACAACATGTAT
65 TAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTAT
* *
580962 CGATACTTTTTAATATTGTGTCAATACTTTT
130 CGACACTTTTTAATATTGTGTCGATACTTTT
580993 AAATAACTCG
Statistics
Matches: 510, Mismatches: 49, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
200 362 0.71
201 148 0.29
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (200 bp):
TCGATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
AATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATC
GACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGTCAAAAAGGGTAAACGAATA
AAGTG
Found at i:582589 original size:21 final size:21
Alignment explanation
Indices: 582565--582614 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
582555 CTTAGGGAAC
582565 CGATTCCCTATGAGGGGGTAT
1 CGATTCCCTATGAGGGGGTAT
582586 CGATTCCCTATGAGGGGGTAT
1 CGATTCCCTATGAGGGGGTAT
582607 CGATTCCC
1 CGATTCCC
582615 CCCACGCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (21 bp):
CGATTCCCTATGAGGGGGTAT
Found at i:584096 original size:23 final size:24
Alignment explanation
Indices: 584053--584097 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
584043 TTTGGTTTTC
*
584053 AAAATCCATTTTAGCTATTAAAAG
1 AAAATCCATTTTAACTATTAAAAG
584077 AAAAT-CATTTTCAACT-TTAAA
1 AAAATCCATTTT-AACTATTAAA
584098 TTTAGAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (24 bp):
AAAATCCATTTTAACTATTAAAAG
Found at i:585264 original size:106 final size:105
Alignment explanation
Indices: 585075--585298 Score: 394
Period size: 106 Copynumber: 2.1 Consensus size: 105
585065 GTGGTCGTTT
* *
585075 CTAGCCGTTGGGGATCAATTTCATGCAAAATAAAGCTACCTAGACCAAGGGGTATTAATACTCCT
1 CTAGCCGTTGGGGATCAATTTCATGCAAAATAAAGATACCTAGACCAAGGGGTATCAATACTCCT
585140 AAAGGGAGTATCGGTACCACCTTTATTTTATTTAAATCAA
66 AAAGGGAGTATCGGTACCACCTTTATTTTATTTAAATCAA
* * *
585180 CTAGTCGTTGGGGATCAATTTTCATGCAAAATAAAGATGCCTAGACCAAGGGGTATCGATACTCC
1 CTAGCCGTTGGGGATCAA-TTTCATGCAAAATAAAGATACCTAGACCAAGGGGTATCAATACTCC
585245 TAAAGGGAGTATCGGTACCACCTTTATTTTATTTAAATCAA
65 TAAAGGGAGTATCGGTACCACCTTTATTTTATTTAAATCAA
585286 CTAGCCGTTGGGG
1 CTAGCCGTTGGGG
585299 CCTTATGGTA
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
105 17 0.15
106 95 0.85
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (105 bp):
CTAGCCGTTGGGGATCAATTTCATGCAAAATAAAGATACCTAGACCAAGGGGTATCAATACTCCT
AAAGGGAGTATCGGTACCACCTTTATTTTATTTAAATCAA
Found at i:586656 original size:18 final size:18
Alignment explanation
Indices: 586635--586717 Score: 76
Period size: 18 Copynumber: 4.6 Consensus size: 18
586625 TCATTATCAA
* *
586635 TATCGTTATCATGATCTC
1 TATCATTATCAAGATCTC
* **
586653 TATCATTATCAACATCAA
1 TATCATTATCAAGATCTC
*
586671 TATCATTATCACGATCTC
1 TATCATTATCAAGATCTC
* * **
586689 TATTATTATCAACATCAA
1 TATCATTATCAAGATCTC
586707 TATCATTATCA
1 TATCATTATCA
586718 TGTAATACAT
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.40
Consensus pattern (18 bp):
TATCATTATCAAGATCTC
Found at i:586662 original size:6 final size:6
Alignment explanation
Indices: 586624--586718 Score: 50
Period size: 6 Copynumber: 15.8 Consensus size: 6
586614 CATAAATACC
* * * ** *
586624 ATCATT ATCAAT ATCGTT ATCATG ATC-TCT ATCATT ATCAAC ATCAAT
1 ATCATT ATCATT ATCATT ATCATT ATCAT-T ATCATT ATCATT ATCATT
** * ** *
586672 ATCATT ATCACG ATC-TCT ATTATT ATCAAC ATCAAT ATCATT ATCAT
1 ATCATT ATCATT ATCAT-T ATCATT ATCATT ATCATT ATCATT ATCAT
586719 GTAATACATT
Statistics
Matches: 65, Mismatches: 20, Indels: 8
0.70 0.22 0.09
Matches are distributed among these distances:
5 1 0.02
6 62 0.95
7 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (6 bp):
ATCATT
Found at i:586680 original size:36 final size:36
Alignment explanation
Indices: 586630--586719 Score: 153
Period size: 36 Copynumber: 2.5 Consensus size: 36
586620 TACCATCATT
*
586630 ATCAATATCGTTATCATGATCTCTATCATTATCAAC
1 ATCAATATCATTATCATGATCTCTATCATTATCAAC
* *
586666 ATCAATATCATTATCACGATCTCTATTATTATCAAC
1 ATCAATATCATTATCATGATCTCTATCATTATCAAC
586702 ATCAATATCATTATCATG
1 ATCAATATCATTATCATG
586720 TAATACATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.39
Consensus pattern (36 bp):
ATCAATATCATTATCATGATCTCTATCATTATCAAC
Found at i:586892 original size:30 final size:30
Alignment explanation
Indices: 586858--586920 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
586848 TTTATACTTT
* *
586858 TGATATCTTTTGTAGGCCCATGTACAATAC
1 TGATATCTTTTATAAGCCCATGTACAATAC
* *
586888 TGATATCTTTTATAAGCCCATGTATATTAC
1 TGATATCTTTTATAAGCCCATGTACAATAC
586918 TGA
1 TGA
586921 GAACTTAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (30 bp):
TGATATCTTTTATAAGCCCATGTACAATAC
Found at i:587085 original size:21 final size:21
Alignment explanation
Indices: 587050--587114 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
587040 ACCACTCCTT
* * *
587050 AAGAATCACATATATATTCCA
1 AAGAACCAAATATATGTTCCA
*
587071 AAGGACCAAATATATGTTCCA
1 AAGAACCAAATATATGTTCCA
**
587092 AAGAACCGCATATATGTTCCA
1 AAGAACCAAATATATGTTCCA
587113 AA
1 AA
587115 AGATTACATA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.25
Consensus pattern (21 bp):
AAGAACCAAATATATGTTCCA
Found at i:588367 original size:29 final size:30
Alignment explanation
Indices: 588335--588398 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
588325 ACTATTAGAT
* *
588335 AATTATAC-AATTATTCA-CAACTTTTCCAA
1 AATTAT-CGAATTAGTCACCAACTTTTCAAA
*
588364 AATTATCGAATTGGTCACCAACTTTTCAAA
1 AATTATCGAATTAGTCACCAACTTTTCAAA
588394 AATTA
1 AATTA
588399 CATAATGGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 13 0.43
30 16 0.53
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.36
Consensus pattern (30 bp):
AATTATCGAATTAGTCACCAACTTTTCAAA
Found at i:588407 original size:29 final size:30
Alignment explanation
Indices: 588352--588419 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
588342 CAATTATTCA
* *
588352 CAACTTTTCCAAAATTATCGAATTGGTCAC
1 CAACTTTTCAAAAATTATCGAAATGGTCAC
*
588382 CAACTTTTCAAAAATTA-C-ATAATGGTCCC
1 CAACTTTTCAAAAATTATCGA-AATGGTCAC
*
588411 CAAATTTTC
1 CAACTTTTC
588420 TAAGGCTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 16 0.48
30 16 0.48
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.34
Consensus pattern (30 bp):
CAACTTTTCAAAAATTATCGAAATGGTCAC
Found at i:589244 original size:30 final size:31
Alignment explanation
Indices: 589210--589274 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
589200 ATTGGTCCCT
* *
589210 AAACTTTTCAAAGT-TTATACTTTAGTCACC
1 AAACTTTTCAAAATCTTATAATTTAGTCACC
* *
589240 AAAC-TTTCAAAATCTTATAATTTGGTCACT
1 AAACTTTTCAAAATCTTATAATTTAGTCACC
589270 AAACT
1 AAACT
589275 AAATCCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.38
Consensus pattern (31 bp):
AAACTTTTCAAAATCTTATAATTTAGTCACC
Found at i:590369 original size:18 final size:19
Alignment explanation
Indices: 590346--590382 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
590336 AAATTTGTTC
*
590346 AAATAAT-TAATATAAAAT
1 AAATAATATAATAAAAAAT
590364 AAATAATATAATAAAAAAT
1 AAATAATATAATAAAAAAT
590383 TTTCTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATAATATAATAAAAAAT
Found at i:591902 original size:18 final size:18
Alignment explanation
Indices: 591861--591895 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
591851 AGTTAAAATA
591861 GTTTTTCTTTGTTCTTTG
1 GTTTTTCTTTGTTCTTTG
*
591879 GTTTTTTTTTGTTCTTT
1 GTTTTTCTTTGTTCTTT
591896 TTTTTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.14, T:0.77
Consensus pattern (18 bp):
GTTTTTCTTTGTTCTTTG
Found at i:595796 original size:3 final size:3
Alignment explanation
Indices: 595788--595814 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
595778 ATTCTGCTTC
595788 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
595815 AAAGTTTAAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:597573 original size:23 final size:23
Alignment explanation
Indices: 597547--597590 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
597537 CGGTGCCTCC
597547 TAGCCCCCTTAATTGACTTTCCT
1 TAGCCCCCTTAATTGACTTTCCT
*
597570 TAGCCCTCTTAATTGACTTTC
1 TAGCCCCCTTAATTGACTTTC
597591 AACAATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (23 bp):
TAGCCCCCTTAATTGACTTTCCT
Found at i:598545 original size:167 final size:167
Alignment explanation
Indices: 598269--598604 Score: 672
Period size: 167 Copynumber: 2.0 Consensus size: 167
598259 TCCCCTCTGA
598269 TTTCGTTGGCATTTACTCAAAATTACGTCAGCATTTCTTATTCCATGAAGTCTGACACTCCTGGC
1 TTTCGTTGGCATTTACTCAAAATTACGTCAGCATTTCTTATTCCATGAAGTCTGACACTCCTGGC
598334 ATTGAACCCTTGTCATTGGAGTTCTTTGTGCCACCATGCATCGATACTTTCTCACGGCAAAGTCC
66 ATTGAACCCTTGTCATTGGAGTTCTTTGTGCCACCATGCATCGATACTTTCTCACGGCAAAGTCC
598399 GATGCCCCTTCTTGCCTCCTCCCTTCTAACACGAAGG
131 GATGCCCCTTCTTGCCTCCTCCCTTCTAACACGAAGG
598436 TTTCGTTGGCATTTACTCAAAATTACGTCAGCATTTCTTATTCCATGAAGTCTGACACTCCTGGC
1 TTTCGTTGGCATTTACTCAAAATTACGTCAGCATTTCTTATTCCATGAAGTCTGACACTCCTGGC
598501 ATTGAACCCTTGTCATTGGAGTTCTTTGTGCCACCATGCATCGATACTTTCTCACGGCAAAGTCC
66 ATTGAACCCTTGTCATTGGAGTTCTTTGTGCCACCATGCATCGATACTTTCTCACGGCAAAGTCC
598566 GATGCCCCTTCTTGCCTCCTCCCTTCTAACACGAAGG
131 GATGCCCCTTCTTGCCTCCTCCCTTCTAACACGAAGG
598603 TT
1 TT
598605 GGAGCTCACT
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 169 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (167 bp):
TTTCGTTGGCATTTACTCAAAATTACGTCAGCATTTCTTATTCCATGAAGTCTGACACTCCTGGC
ATTGAACCCTTGTCATTGGAGTTCTTTGTGCCACCATGCATCGATACTTTCTCACGGCAAAGTCC
GATGCCCCTTCTTGCCTCCTCCCTTCTAACACGAAGG
Found at i:599840 original size:12 final size:12
Alignment explanation
Indices: 599823--599847 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
599813 ATTCCTGCTA
599823 CTTCTCTTTCTT
1 CTTCTCTTTCTT
599835 CTTCTCTTTCTT
1 CTTCTCTTTCTT
599847 C
1 C
599848 CATCCTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (12 bp):
CTTCTCTTTCTT
Found at i:605187 original size:19 final size:19
Alignment explanation
Indices: 605163--605224 Score: 106
Period size: 19 Copynumber: 3.3 Consensus size: 19
605153 ACCTATCTCT
*
605163 TAAAACCTAGATCTATGTA
1 TAAAACCTAGATCTAGGTA
*
605182 TAAAACCTAAATCTAGGTA
1 TAAAACCTAGATCTAGGTA
605201 TAAAACCTAGATCTAGGTA
1 TAAAACCTAGATCTAGGTA
605220 TAAAA
1 TAAAA
605225 TCAACATGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (19 bp):
TAAAACCTAGATCTAGGTA
Found at i:608685 original size:21 final size:21
Alignment explanation
Indices: 608660--608699 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
608650 TATATTACAT
*
608660 ATCATAAGATGTTAAATATAA
1 ATCATAAAATGTTAAATATAA
*
608681 ATCATAAAATTTTAAATAT
1 ATCATAAAATGTTAAATAT
608700 GTGATGGCTT
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:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATCATAAAATGTTAAATATAA
Found at i:608949 original size:26 final size:26
Alignment explanation
Indices: 608920--608972 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
608910 GGCGGTTAGG
608920 CTGACATAGTTAGCCGTCGCGCCCCT
1 CTGACATAGTTAGCCGTCGCGCCCCT
608946 CTGACATAGTTAGCCGTCGCGCCCCT
1 CTGACATAGTTAGCCGTCGCGCCCCT
608972 C
1 C
608973 CTTGCTCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.40, G:0.23, T:0.23
Consensus pattern (26 bp):
CTGACATAGTTAGCCGTCGCGCCCCT
Found at i:609799 original size:16 final size:15
Alignment explanation
Indices: 609778--609813 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
609768 CTTATAGTTT
609778 TATTTTTTTAAAAT-
1 TATTTTTTTAAAATA
609792 TATATTTTTTAAAATA
1 TAT-TTTTTTAAAATA
609808 TATTTT
1 TATTTT
609814 ATGGATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 14 0.70
16 3 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTTTTTAAAATA
Found at i:609801 original size:15 final size:15
Alignment explanation
Indices: 609777--609813 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
609767 CCTTATAGTT
609777 TTAT-TTTTTTAAAA
1 TTATATTTTTTAAAA
609791 TTATATTTTTTAAAA
1 TTATATTTTTTAAAA
609806 -TATATTTT
1 TTATATTTT
609814 ATGGATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTTTTTAAAA
Found at i:610385 original size:28 final size:31
Alignment explanation
Indices: 610328--610386 Score: 97
Period size: 28 Copynumber: 2.0 Consensus size: 31
610318 CAATTTAAGG
610328 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
610359 CAAAAT-G-TTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
610387 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 11 0.39
29 10 0.36
30 1 0.04
31 6 0.21
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:610492 original size:21 final size:20
Alignment explanation
Indices: 610466--610605 Score: 147
Period size: 21 Copynumber: 6.8 Consensus size: 20
610456 AGGGTGTCAA
*
610466 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCATGC
*
610487 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCATGC
* * *
610508 AGTGTATCCATGCATCCTTAC
1 AGTGCATCCATGCA-CCATGC
*
610529 AGTGCATCCATGCA-CTTGCAC
1 AGTGCATCCATGCACCATG--C
* *
610550 TAGTGCATCGATGCACCATAC
1 -AGTGCATCCATGCACCATGC
610571 AGTGCATCCATGCACCATGC
1 AGTGCATCCATGCACCATGC
610591 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
610606 TCAAACACCG
Statistics
Matches: 104, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
19 3 0.03
20 33 0.32
21 53 0.51
22 13 0.12
23 2 0.02
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.24
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGC
Found at i:610670 original size:21 final size:21
Alignment explanation
Indices: 610644--610688 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
610634 ATGCATCCTT
*
610644 CTGTGCATCGATGCATC-AAGG
1 CTGTGCATCCATGCA-CGAAGG
610665 CTGTGCATCCATGCACGAAGG
1 CTGTGCATCCATGCACGAAGG
610686 CTG
1 CTG
610689 CAACGACTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22
Consensus pattern (21 bp):
CTGTGCATCCATGCACGAAGG
Found at i:612188 original size:18 final size:19
Alignment explanation
Indices: 612155--612197 Score: 79
Period size: 18 Copynumber: 2.3 Consensus size: 19
612145 ATTATGTTAA
612155 TGTTATTTTTATAAATTTT
1 TGTTATTTTTATAAATTTT
612174 TGTTATTTTTA-AAATTTT
1 TGTTATTTTTATAAATTTT
612192 TGTTAT
1 TGTTAT
612198 GTTAATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (19 bp):
TGTTATTTTTATAAATTTT
Found at i:614115 original size:2 final size:2
Alignment explanation
Indices: 614108--614155 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
614098 GTTTTAACAC
614108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
614150 T- TA TA T
1 TA TA TA T
614156 TATGAAACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:615456 original size:19 final size:19
Alignment explanation
Indices: 615432--615469 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
615422 TTCCAAAATA
615432 CAAAATAGGTACCGATACT
1 CAAAATAGGTACCGATACT
615451 CAAAATAGGTACCGATACT
1 CAAAATAGGTACCGATACT
615470 ACTTTGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (19 bp):
CAAAATAGGTACCGATACT
Found at i:617934 original size:3 final size:3
Alignment explanation
Indices: 617926--617986 Score: 56
Period size: 3 Copynumber: 20.0 Consensus size: 3
617916 TGATTATTTA
*
617926 TTC TTC TTC CT- TTC TTC ATTC TTC TT- TTC TTTC TTC ATTC TTC TT-
1 TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC -TTC TTC -TTC TTC TTC
617971 TTC TTTC TTC TTC TTC
1 TTC -TTC TTC TTC TTC
617987 ATTTCTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
2 5 0.10
3 32 0.65
4 12 0.24
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:617959 original size:19 final size:19
Alignment explanation
Indices: 617925--617994 Score: 108
Period size: 19 Copynumber: 3.8 Consensus size: 19
617915 TTGATTATTT
*
617925 ATTCTTC-TTCCTTTCTTC
1 ATTCTTCTTTTCTTTCTTC
617943 ATTCTTCTTTTCTTTCTTC
1 ATTCTTCTTTTCTTTCTTC
617962 ATTCTTCTTTTCTTTCTTC
1 ATTCTTCTTTTCTTTCTTC
*
617981 -TTCTTCATTTCTTT
1 ATTCTTCTTTTCTTT
617995 TTTCCTTCTC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
18 20 0.41
19 29 0.59
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTCTTCTTTTCTTTCTTC
Found at i:617981 original size:15 final size:15
Alignment explanation
Indices: 617926--618021 Score: 60
Period size: 15 Copynumber: 6.5 Consensus size: 15
617916 TGATTATTTA
*
617926 TTCTTCTTCCTTTC-
1 TTCTTCTTCTTTTCT
617940 TTCATTCTTCTTTTCT
1 TTC-TTCTTCTTTTCT
*
617956 TTCTTCATTCTTCT-T
1 TTCTTC-TTCTTTTCT
617971 TTCTTTCTTCTTCTTC-
1 TTC-TTCTTCTT-TTCT
* *
617987 AT-TTCTT-TTTTCC
1 TTCTTCTTCTTTTCT
*
618000 TTCTCCTAT-TTTTCT
1 TTCTTCT-TCTTTTCT
618015 TTCTTCT
1 TTCTTCT
618022 CCCGGTGCCC
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
12 3 0.05
13 3 0.05
14 11 0.17
15 34 0.52
16 14 0.22
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (15 bp):
TTCTTCTTCTTTTCT
Done.