Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007841.1 Hibiscus syriacus cultivar Beakdansim tig00110195_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: 1873963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:487673 original size:14 final size:14
Alignment explanation
Indices: 487654--487707 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
487644 CGAAATGGCT
487654 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
487668 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
487687 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
487701 ATTGCAA
1 ATCGCAA
487708 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 17 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:487700 original size:19 final size:19
Alignment explanation
Indices: 487664--487700 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
487654 ATCGCAACGA
* *
487664 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
487683 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
487701 ATTGCAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:487725 original size:33 final size:33
Alignment explanation
Indices: 487635--487712 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
487625 AAAACAGACT
* ***
487635 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
487668 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
487701 ATTGCAATGCGA
1 ATCGCAATGCGA
487713 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:487756 original size:20 final size:20
Alignment explanation
Indices: 487731--487768 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
487721 TCGCATTGCG
*
487731 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
487751 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
487769 TCAAATGAAT
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:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:488847 original size:24 final size:24
Alignment explanation
Indices: 488820--488866 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
488810 AGTCAGTATT
*
488820 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACC
*
488844 CGAACTTTGATATTGGTCAATAC
1 CGAAATTTGATATTGGTCAATAC
488867 ACGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACC
Found at i:488876 original size:24 final size:24
Alignment explanation
Indices: 488820--488878 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
488810 AGTCAGTATT
* * *
488820 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATATTGGTCAATACA
488844 CGAACTTTGATATTGGTCAATACA
1 CGAACTTTGATATTGGTCAATACA
* *
488868 CGGATTTTGAT
1 CGAACTTTGAT
488879 GATGTTTCAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAACTTTGATATTGGTCAATACA
Found at i:489070 original size:12 final size:12
Alignment explanation
Indices: 489053--489077 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
489043 ATATAATCCT
489053 GAAGAAGAAAAA
1 GAAGAAGAAAAA
489065 GAAGAAGAAAAA
1 GAAGAAGAAAAA
489077 G
1 G
489078 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:490328 original size:64 final size:63
Alignment explanation
Indices: 490244--490469 Score: 237
Period size: 64 Copynumber: 3.5 Consensus size: 63
490234 TTGAAGGTGT
* *
490244 ATCGATGCATAGGTAGTGCATCGATGCA-CTCTTTTAAAATACAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTT-AAATACAAACATCGAATGCAATTA-TGC
* ** * * *
490308 ATCGATGCATAAGTCA-TGCATTGATGCATCCCAGTGATAATAC-TACATCGAATGTAATTCATG
1 ATCGATGCATAAGT-AGTGCATCGATGCATCCCTTTTA-AATACAAACATCGAATGCAATT-ATG
490371 C
63 C
* *
490372 ATCGATGCATAAGTAGTGCATCGATGCATCCCGTTATT-AAT-GAAACATCGAATGCATTTTATG
1 ATCGATGCATAAGTAGTGCATCGATGCATCCC-TT-TTAAATACAAACATCGAATGCA-ATTATG
490435 C
63 C
* *
490436 ATCGATGCACAAGTAGTGCATCGATGCATACCTT
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTT
490470 CATTAAAAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 19
0.78 0.10 0.11
Matches are distributed among these distances:
63 3 0.02
64 119 0.88
65 12 0.09
66 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (63 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTTAAATACAAACATCGAATGCAATTATGC
Found at i:491194 original size:30 final size:30
Alignment explanation
Indices: 491143--491206 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
491133 AAGGAACATA
* *
491143 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* *
491173 TGGATAGTTACC-AGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGA-GGATCTTTATAACCTC
491203 TGGA
1 TGGA
491207 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:494480 original size:64 final size:63
Alignment explanation
Indices: 494396--494621 Score: 237
Period size: 64 Copynumber: 3.5 Consensus size: 63
494386 TTGAAGGTGT
* *
494396 ATCGATGCATAGGTAGTGCATCGATGCA-CTCTTTTAAAATACAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTT-AAATACAAACATCGAATGCAATTA-TGC
* ** * * *
494460 ATCGATGCATAAGTCA-TGCATTGATGCATCCCAGTGATAATAC-TACATCGAATGTAATTCATG
1 ATCGATGCATAAGT-AGTGCATCGATGCATCCCTTTTA-AATACAAACATCGAATGCAATT-ATG
494523 C
63 C
* *
494524 ATCGATGCATAAGTAGTGCATCGATGCATCCCGTTATT-AAT-GAAACATCGAATGCATTTTATG
1 ATCGATGCATAAGTAGTGCATCGATGCATCCC-TT-TTAAATACAAACATCGAATGCA-ATTATG
494587 C
63 C
* *
494588 ATCGATGCACAAGTAGTGCATCGATGCATACCTT
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTT
494622 CATTAAAAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 19
0.78 0.10 0.11
Matches are distributed among these distances:
63 3 0.02
64 119 0.88
65 12 0.09
66 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (63 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTTAAATACAAACATCGAATGCAATTATGC
Found at i:495346 original size:30 final size:30
Alignment explanation
Indices: 495295--495358 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
495285 AAGAAACATA
* *
495295 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* *
495325 TGGATAGTTACC-AGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGA-GGATCTTTATAACCTC
495355 TGGA
1 TGGA
495359 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:497940 original size:19 final size:19
Alignment explanation
Indices: 497918--498048 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
497908 GGAAATTACT
497918 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
497937 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
497951 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
497970 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
497984 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
498003 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
498017 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
498036 ATCGCAACGCGAA
1 ATCGCAATGCGAA
498049 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:497960 original size:33 final size:33
Alignment explanation
Indices: 497918--498044 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
497908 GGAAATTACT
497918 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
497951 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
497983 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
498017 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
498045 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:498025 original size:66 final size:66
Alignment explanation
Indices: 497919--498051 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
497909 GAAATTACTA
*
497919 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
497984 T
66 T
*
497985 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
498050 T
66 T
498051 T
1 T
498052 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:498066 original size:19 final size:20
Alignment explanation
Indices: 498044--498086 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
498034 AAATCGCAAC
498044 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
498063 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
498083 GCGA
1 GCGA
498087 TTCCCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:498246 original size:14 final size:14
Alignment explanation
Indices: 498227--498263 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
498217 CATCAATTAA
498227 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
498241 ACAAATCACCTTTT
1 ACAAATCAACTTTT
498255 ACAAATCAA
1 ACAAATCAA
498264 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:501612 original size:20 final size:20
Alignment explanation
Indices: 501583--501645 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
501573 TTTTGGTTGA
501583 AATGAAAATCGCAACGAGAT
1 AATGAAAATCGCAACGAGAT
* *
501603 AATGAGAATCGCAACGCGGA-
1 AATGAAAATCGCAACG-AGAT
**
501623 AATGACTATCGCAACGAGAT
1 AATGAAAATCGCAACGAGAT
501643 AAT
1 AAT
501646 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.16
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAT
Found at i:501698 original size:19 final size:19
Alignment explanation
Indices: 501581--501765 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
501571 TCTTTTGGTT
*
501581 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
501600 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
501620 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
501638 G--A-GATAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
501654 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
501672 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
501687 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
501707 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
501726 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
501745 GAAATAAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
501764 GA
1 GA
501766 TTTTTGTTTC
Statistics
Matches: 137, Mismatches: 16, Indels: 26
0.77 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 61 0.45
20 45 0.33
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:501719 original size:39 final size:38
Alignment explanation
Indices: 501581--501765 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
501571 TCTTTTGGTT
* * *
501581 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATAAAAATCGCAACGC
** *
501620 GGAAATGACTATCGCAA--CGAGAT---AATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATAAAAATCGCAACGC
** * * *
501654 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATAAAAATCGCAACGC
501687 GAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATAAAAATCGCAACGC
*
501726 GAAATGAAAATCGCAACGCGAAATAAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATAAAAATCGCAACGC
501764 GA
1 GA
501766 TTTTTGTTTC
Statistics
Matches: 124, Mismatches: 11, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
31 1 0.01
33 39 0.31
34 13 0.10
35 1 0.01
37 2 0.02
38 26 0.21
39 28 0.23
40 14 0.11
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATAAAAATCGCAACGC
Found at i:501797 original size:19 final size:19
Alignment explanation
Indices: 501761--501805 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
501751 AAAATCGCAA
*
501761 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
501780 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
501799 TGCGATT
1 TGCGATT
501806 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:502379 original size:20 final size:20
Alignment explanation
Indices: 502354--502406 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
502344 GCGCTATGTA
502354 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
502374 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
502394 TATCTCGTTGCGA
1 AATCGCGTTGCGA
502407 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:502467 original size:41 final size:41
Alignment explanation
Indices: 502375--502469 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
502365 GAAAGTCAGA
* * * * ** *
502375 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
502416 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
502458 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
502470 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:502559 original size:21 final size:21
Alignment explanation
Indices: 502519--502559 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
502509 ATTGTATACC
**
502519 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
502540 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
502560 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:503030 original size:15 final size:15
Alignment explanation
Indices: 502985--503031 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
502975 TAAGTGGTAC
502985 AAATATTAATAAAAT
1 AAATATTAATAAAAT
*
503000 AAATAATT--TCATAAT
1 AAAT-ATTAAT-AAAAT
503015 AAATATTAATAAAAT
1 AAATATTAATAAAAT
503030 AA
1 AA
503032 GTTATATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 4 0.15
15 18 0.69
16 4 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATATTAATAAAAT
Found at i:503235 original size:3 final size:3
Alignment explanation
Indices: 503227--503286 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
503217 TATTGTATAC
503227 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
503275 ATA ATA ACA ATA
1 ATA ATA ATA ATA
503287 GTCAGGACAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:503976 original size:26 final size:24
Alignment explanation
Indices: 503910--503979 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 24
503900 TATTTAATGG
*
503910 TAGATATTATAAAAGAA-TATTTTT
1 TAGATA-TATAAAAGAAGTTTTTTT
*
503934 TAGAAGATATAAAAGAAGTTTTTTAT
1 TAG-ATATATAAAAGAAGTTTTTT-T
503960 TAAGATATATAAAAGAAGTT
1 T-AGATATATAAAAGAAGTT
503980 ATATAATCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.33
25 7 0.18
26 17 0.44
27 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.39
Consensus pattern (24 bp):
TAGATATATAAAAGAAGTTTTTTT
Found at i:504614 original size:17 final size:17
Alignment explanation
Indices: 504594--504627 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
504584 AATTTGTATC
504594 AGATTTTAATTAATTTT
1 AGATTTTAATTAATTTT
504611 AGATTTTAATTAATTTT
1 AGATTTTAATTAATTTT
504628 TATTTAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
AGATTTTAATTAATTTT
Found at i:505014 original size:12 final size:10
Alignment explanation
Indices: 504982--505011 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
504972 GTTTCCATGG
*
504982 CTCTCCATTT
1 CTCTCCCTTT
504992 CTCTCCCTTT
1 CTCTCCCTTT
505002 CTCTCCCTTT
1 CTCTCCCTTT
505012 TTCCCCCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (10 bp):
CTCTCCCTTT
Found at i:511731 original size:26 final size:26
Alignment explanation
Indices: 511695--511746 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
511685 CTTTTTATCA
*
511695 AAATAACTCATGTTGGATGAAAACCG
1 AAATAACTCATGTTGAATGAAAACCG
*
511721 AAATAACTCATGTTGAATTAAAACCG
1 AAATAACTCATGTTGAATGAAAACCG
511747 TTAGTTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (26 bp):
AAATAACTCATGTTGAATGAAAACCG
Found at i:518564 original size:16 final size:16
Alignment explanation
Indices: 518543--518576 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
518533 TTACTATTCA
*
518543 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
518559 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
518575 CG
1 CG
518577 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:519344 original size:15 final size:16
Alignment explanation
Indices: 519326--519358 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
519316 GTGGCAGATC
519326 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
519341 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
519357 AA
1 AA
519359 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:531012 original size:3 final size:3
Alignment explanation
Indices: 531004--531055 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
530994 CAAACATCTA
531004 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
531051 TTC TT
1 TTC TT
531056 TTAATTTTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:549713 original size:28 final size:28
Alignment explanation
Indices: 549681--549736 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
549671 AGAAAATCTG
549681 TCCTAGAAAAGAAATAACAAACAATTCT
1 TCCTAGAAAAGAAATAACAAACAATTCT
*
549709 TCCTAGAAAAGAAATAGCAAACAATTCT
1 TCCTAGAAAAGAAATAACAAACAATTCT
549737 AGTAACATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21
Consensus pattern (28 bp):
TCCTAGAAAAGAAATAACAAACAATTCT
Found at i:554975 original size:18 final size:18
Alignment explanation
Indices: 554952--554987 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
554942 GGTACAATGT
554952 TTGACGAGTTATTCATGA
1 TTGACGAGTTATTCATGA
554970 TTGACGAGTTATTCATGA
1 TTGACGAGTTATTCATGA
554988 ATTACTTATA
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:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (18 bp):
TTGACGAGTTATTCATGA
Found at i:567558 original size:26 final size:25
Alignment explanation
Indices: 567515--567563 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
567505 AAGTTATATT
567515 AAAATTTTAAAAAATATAAAATTAC
1 AAAATTTTAAAAAATATAAAATTAC
* *
567540 AAAATTTTTAAGAAGTATAAAATT
1 AAAA-TTTTAAAAAATATAAAATT
567564 TGATTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
AAAATTTTAAAAAATATAAAATTAC
Found at i:568481 original size:13 final size:13
Alignment explanation
Indices: 568463--568489 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
568453 TATTTATAGA
568463 ATTAAATTTAAAT
1 ATTAAATTTAAAT
568476 ATTAAATTTAAAT
1 ATTAAATTTAAAT
568489 A
1 A
568490 ACATCTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAATTTAAAT
Found at i:568824 original size:13 final size:13
Alignment explanation
Indices: 568803--568836 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
568793 TCATAAAAAA
*
568803 AAATTTGTGGGAT
1 AAATGTGTGGGAT
568816 AAATGTGTGGGAT
1 AAATGTGTGGGAT
568829 AAATGTGT
1 AAATGTGT
568837 ATAATGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (13 bp):
AAATGTGTGGGAT
Found at i:569317 original size:2 final size:2
Alignment explanation
Indices: 569310--569343 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
569300 ATTACATGCA
569310 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
569344 CGATGACTAA
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:571088 original size:3 final size:3
Alignment explanation
Indices: 571082--571127 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
571072 GACCACGACG
* *
571082 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATT ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
571128 ATGATACATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:571263 original size:18 final size:19
Alignment explanation
Indices: 571240--571286 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
571230 CGACCGTCGA
571240 TATTTTTTAT-TATCAT-TT
1 TATTTTTTATATA-CATCTT
571258 TATTTTCTTATATCACATCTT
1 TATTTT-TTATAT-ACATCTT
571279 TATTTTTT
1 TATTTTTT
571287 TATTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.24
19 4 0.16
20 6 0.24
21 9 0.36
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTTTTATATACATCTT
Found at i:571945 original size:3 final size:3
Alignment explanation
Indices: 571937--571963 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
571927 AATGACTTCT
571937 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
571964 TTTTTAAATT
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):
ATA
Found at i:572889 original size:20 final size:20
Alignment explanation
Indices: 572852--572889 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
572842 ACATAATAAT
*
572852 AAATTAATATATTTGTAAAA
1 AAATTAATATATTAGTAAAA
572872 AAATT-ATATATTAAGTAA
1 AAATTAATATATT-AGTAA
572890 TAACTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
AAATTAATATATTAGTAAAA
Found at i:579857 original size:3 final size:3
Alignment explanation
Indices: 579849--579874 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
579839 GTAAAATATG
579849 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
579875 GGGAAACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:591865 original size:51 final size:50
Alignment explanation
Indices: 591724--591877 Score: 195
Period size: 51 Copynumber: 3.0 Consensus size: 50
591714 AAAAATGACC
** * *
591724 TTTAGCGATGAAGGAAAAGATATAGCCTC-AAAAATAAAATAAAAAAACG-T
1 TTTAGCGATGAAGGAAAAGATATAGCGGCGAAAAAT-AAA-AGAAAAATGTT
*
591774 TTTAGCGATGAAGGAAAAGATACAGCGGCGAAAAATAAAAGAAAATATGTT
1 TTTAGCGATGAAGGAAAAGATATAGCGGCGAAAAATAAAAGAAAA-ATGTT
* *
591825 TTTAGCGACGAAGGAAAAGATATAGCGGCGAACAATAAAAGAAGAAATGTT
1 TTTAGCGATGAAGGAAAAGATATAGCGGCGAAAAATAAAAGAA-AAATGTT
591876 TT
1 TT
591878 ACCGACGGAA
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
49 5 0.05
50 31 0.34
51 54 0.59
52 2 0.02
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.20
Consensus pattern (50 bp):
TTTAGCGATGAAGGAAAAGATATAGCGGCGAAAAATAAAAGAAAAATGTT
Found at i:595481 original size:164 final size:165
Alignment explanation
Indices: 595210--595540 Score: 655
Period size: 164 Copynumber: 2.0 Consensus size: 165
595200 ATGGCTCAGC
595210 TGATTTTGATTCTATTGATGAAAATTAAGACTTGGATTCATCTCGACTTTACTTAATTACCCATT
1 TGATTTTGATTCTATTGATGAAAATTAAGACTTGGATTCATCTCGACTTTACTTAATTACCCATT
595275 AATTAGCTTATTTTAGTGCAAATTTGTTGTCTTGTCTTGTCAGAACA-TCATGTGCTTCCATGGA
66 AATTAGCTTATTTTAGTGCAAATTTGTTGTCTTGTCTTGTCAGAACATTCATGTGCTTCCATGGA
595339 AGTTCGAGTTACTTAATGGTATTGTATTGGACTTT
131 AGTTCGAGTTACTTAATGGTATTGTATTGGACTTT
595374 TGATTTTGATTCTATTGATGAAAATTAAGACTTGGATTCATCTCGACTTTACTTAATTACCCATT
1 TGATTTTGATTCTATTGATGAAAATTAAGACTTGGATTCATCTCGACTTTACTTAATTACCCATT
595439 AATTAGCTTATTTTAGTGCAAATTTGTTGTCTTGTCTTGTCAGAACATTCATGTGCTTCCATGGA
66 AATTAGCTTATTTTAGTGCAAATTTGTTGTCTTGTCTTGTCAGAACATTCATGTGCTTCCATGGA
595504 AGTTCGAGTTACTTAATGGTATTGTATTGGACTTT
131 AGTTCGAGTTACTTAATGGTATTGTATTGGACTTT
595539 TG
1 TG
595541 GCTCATCTGT
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
164 112 0.67
165 54 0.33
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (165 bp):
TGATTTTGATTCTATTGATGAAAATTAAGACTTGGATTCATCTCGACTTTACTTAATTACCCATT
AATTAGCTTATTTTAGTGCAAATTTGTTGTCTTGTCTTGTCAGAACATTCATGTGCTTCCATGGA
AGTTCGAGTTACTTAATGGTATTGTATTGGACTTT
Found at i:601388 original size:4 final size:4
Alignment explanation
Indices: 601379--601404 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
601369 CTGCATTATC
601379 AACA AACA AACA AACA AACA AACA AA
1 AACA AACA AACA AACA AACA AACA AA
601405 AAAAGTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:603907 original size:21 final size:21
Alignment explanation
Indices: 603881--603925 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
603871 GATTTCTGGG
* *
603881 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
603902 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
603923 CAA
1 CAA
603926 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:605625 original size:13 final size:13
Alignment explanation
Indices: 605607--605669 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
605597 TTATATGGCA
605607 CTACGGTGCAATT
1 CTACGGTGCAATT
605620 CTACGG-GC-A--
1 CTACGGTGCAATT
*
605629 CTTCGGTGCAATT
1 CTACGGTGCAATT
605642 CTACGG-GC-A--
1 CTACGGTGCAATT
*
605651 CTTCGGTGCAATT
1 CTACGGTGCAATT
605664 CTACGG
1 CTACGG
605670 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:605635 original size:22 final size:22
Alignment explanation
Indices: 605603--605683 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
605593 ATCATTATAT
*
605603 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
605625 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
605647 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
605670 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
605684 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:611374 original size:2 final size:2
Alignment explanation
Indices: 611367--611403 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
611357 ATCCCTAGTT
611367 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
611404 GGGAAATCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:617336 original size:2 final size:2
Alignment explanation
Indices: 617329--617361 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
617319 ATAAATTTTA
617329 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
617362 ATTTATTTTA
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:623053 original size:17 final size:16
Alignment explanation
Indices: 623020--623056 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
623010 TAGAGAAATG
*
623020 ATTATTTTATTTTTAT
1 ATTATTTTATTTATAT
623036 ATTATTTGTATTTATAT
1 ATTATTT-TATTTATAT
623053 ATTA
1 ATTA
623057 ATAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTATTTTATTTATAT
Found at i:625269 original size:2 final size:2
Alignment explanation
Indices: 625262--625292 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
625252 TTTTTAAAAC
625262 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 A
625293 CACCCCCATC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:625399 original size:35 final size:35
Alignment explanation
Indices: 625356--625422 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
625346 CGTCACGTCC
*
625356 AGTAAGGCCCTGAGCACACAGTCGAGGAACCTGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTGTA
625391 AGTAAGGCCCTGAGCACACAGCCGAGGAACCT
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCT
625423 CCAAGTAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.12
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCTGTA
Found at i:625429 original size:35 final size:35
Alignment explanation
Indices: 625356--625430 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
625346 CGTCACGTCC
* **
625356 AGTAAGGCCCTGAGCACACAGTCGAGGAACCTGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
625391 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
625426 AGTAA
1 AGTAA
625431 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.28, G:0.27, T:0.12
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
Found at i:625535 original size:24 final size:24
Alignment explanation
Indices: 625508--625591 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
625498 CATAATTCAA
625508 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* * *
625532 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
625556 GTCAA-TATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
*
625579 GTCAGGTATCATA
1 GTCAAGTATCATA
625592 ACATAATTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
23 20 0.38
24 32 0.62
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:626770 original size:18 final size:18
Alignment explanation
Indices: 626749--626783 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
626739 TTTTTCCTCC
* *
626749 ATCCAGTCTTATTATTTA
1 ATCCAATCTTATCATTTA
626767 ATCCAATCTTATCATTT
1 ATCCAATCTTATCATTT
626784 CCTTCAGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.49
Consensus pattern (18 bp):
ATCCAATCTTATCATTTA
Found at i:628116 original size:13 final size:13
Alignment explanation
Indices: 628098--628140 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
628088 GCCGGTCAAC
*
628098 GGTCAACGGGTTG
1 GGTCAACGGGTCG
*
628111 GGTCAACAGGTCG
1 GGTCAACGGGTCG
*
628124 GGTAAACGGGTCG
1 GGTCAACGGGTCG
628137 GGTC
1 GGTC
628141 GGGTTATGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.44, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:632371 original size:17 final size:17
Alignment explanation
Indices: 632338--632371 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
632328 ATTTTAAATG
**
632338 ATAAAAATATATTATTA
1 ATAAAAATATAAAATTA
632355 ATAAAAATATAAAATTA
1 ATAAAAATATAAAATTA
632372 TTGTAATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAAAATATAAAATTA
Found at i:634872 original size:20 final size:18
Alignment explanation
Indices: 634847--634886 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
634837 AACAATACGA
634847 TATATTTATCATATAATAAT
1 TATATTT-TCATATAA-AAT
*
634867 TATATTTTCATGTAAAAT
1 TATATTTTCATATAAAAT
634885 TA
1 TA
634887 ATAAATAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 7 0.37
20 7 0.37
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (18 bp):
TATATTTTCATATAAAAT
Found at i:636016 original size:137 final size:134
Alignment explanation
Indices: 635850--636399 Score: 599
Period size: 137 Copynumber: 4.1 Consensus size: 134
635840 AATTCTAAAC
*
635850 AAATAATATTTTATAATCACCTTAAACTACTCAAAATAAATAAATAAATTTAGCATATTCATTAT
1 AAATTATATTTTATAATCACCTTAAACTACTCAAAATAAATAAATAAATTTAGCATATTCATTAT
*
635915 AAAAAAGTATATTTGACTTCTTGTGAAAGGTTGATGATCAAATTTAACTTTTAAAAAGGGTTAAA
66 GAAAAAGTATATTTGACTTCTTGTGAAAGG-T--TGATCAAATTTAACTTTTAAAAAGGGTTAAA
635980 TTGATAA
128 TTGATAA
635987 AAATTATATTTTATAATCACCTTAAACTACTCAAAATAAATAAATAAATTTAGCATATTCATTAT
1 AAATTATATTTTATAATCACCTTAAACTACTCAAAATAAATAAATAAATTTAGCATATTCATTAT
*
636052 GAAAAAGTATATTTGACTTCTTGTGAAAGGTTGATCAAATTTAACTTTTACAAAGGGTTAAATTG
66 GAAAAAGTATATTTGACTTCTTGTGAAAGGTTGATCAAATTTAACTTTTAAAAAGGGTTAAATTG
636117 AT-A
131 ATAA
**** * * * * * *
636120 AAA-TATAAACGCATAA-GA-C-TAAATTTA-TCATTAGTCGAAATATAT-AA-TT-GTA-ATT-
1 AAATTAT-ATTTTATAATCACCTTAAA-CTACTCA-AAAT--AAATAAATAAATTTAGCATATTC
* * * * * * * *
636175 ATTATTG---TA-TATATTTTAATTTTTTTAAAATGAATAATGATAAATTTAATTCTCATACTTT
61 ATTA-TGAAAAAGTATATTTGACTTCTTGTGAAA-G-GT--TGAT-CA---AATT-T-A-ACTTT
636236 TAAAAAGGGTTAAATTGATAA
114 TAAAAAGGGTTAAATTGATAA
*
636257 AAATAATATTTTATAATCACCTTAAACTACTCAAAATAAATAAATAAATTTAGCATATTCATTAT
1 AAATTATATTTTATAATCACCTTAAACTACTCAAAATAAATAAATAAATTTAGCATATTCATTAT
*
636322 GAAAAAGTATATTTGACTTCTTGTGAAAGGTTGATCAAATTTAACTTTTACAAAGGGTTAAATTG
66 GAAAAAGTATATTTGACTTCTTGTGAAAGGTTGATCAAATTTAACTTTTAAAAAGGGTTAAATTG
636387 ATAA
131 ATAA
636391 AAATATATA
1 AAAT-TATA
636400 AACGCATAAG
Statistics
Matches: 337, Mismatches: 43, Indels: 68
0.75 0.10 0.15
Matches are distributed among these distances:
125 16 0.05
126 2 0.01
127 1 0.00
128 4 0.01
129 9 0.03
130 10 0.03
131 7 0.02
132 6 0.02
133 20 0.06
134 65 0.19
135 5 0.01
136 25 0.07
137 113 0.34
138 5 0.01
139 7 0.02
140 10 0.03
141 9 0.03
142 4 0.01
143 1 0.00
144 2 0.01
145 16 0.05
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.38
Consensus pattern (134 bp):
AAATTATATTTTATAATCACCTTAAACTACTCAAAATAAATAAATAAATTTAGCATATTCATTAT
GAAAAAGTATATTTGACTTCTTGTGAAAGGTTGATCAAATTTAACTTTTAAAAAGGGTTAAATTG
ATAA
Found at i:639887 original size:4 final size:4
Alignment explanation
Indices: 639878--639907 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
639868 GCATTCACAC
*
639878 TATG TATG TATG TATA TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
639908 CGAAGGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:640757 original size:60 final size:59
Alignment explanation
Indices: 640671--640784 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
640661 GGGGGTATTA
* * * *
640671 TTGGAATGTTCAAAAGTTTGGGGACTAATTTAAAATAAGGGTCATAGTTTGAGGATAAAT
1 TTGGAATGTTCAAAAGTTTAGAGACTAATTTAAAATAAGAGTCATAATTT-AGGATAAAT
* * * *
640731 TTGGAATGTTCAAAATTTTATAGACTAATTTAGAATGAGAGTCATAATTTAGGA
1 TTGGAATGTTCAAAAGTTTAGAGACTAATTTAAAATAAGAGTCATAATTTAGGA
640785 ATGTATGTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
59 4 0.09
60 42 0.91
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (59 bp):
TTGGAATGTTCAAAAGTTTAGAGACTAATTTAAAATAAGAGTCATAATTTAGGATAAAT
Found at i:650487 original size:2 final size:2
Alignment explanation
Indices: 650480--650516 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
650470 TTAGTTAAGT
650480 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
650517 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:650521 original size:2 final size:2
Alignment explanation
Indices: 650516--650546 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
650506 TCTCTCTCTC
650516 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
650547 GTGTGTGGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:654642 original size:38 final size:38
Alignment explanation
Indices: 654600--654672 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
654590 GTTCGACACT
654600 AACAAAGAATGCTTCTGCCGTGTTGGACCCTTCACAAC
1 AACAAAGAATGCTTCTGCCGTGTTGGACCCTTCACAAC
654638 AACAAAGAATGCTTCTGCCGTGTTGGACCCTTCAC
1 AACAAAGAATGCTTCTGCCGTGTTGGACCCTTCAC
654673 CCTTCCATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (38 bp):
AACAAAGAATGCTTCTGCCGTGTTGGACCCTTCACAAC
Found at i:654999 original size:44 final size:44
Alignment explanation
Indices: 654936--655025 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
654926 GTTAAATCGT
*
654936 ATGGGAATTATTGTTGATAGTTCTTGTATATTGTGTGGTTTAGC
1 ATGGGAATTATTGTTGATAGTTCTTGTATATTGTGTGATTTAGC
* *
654980 ATGGGGATTATTGTTGATAGTTCTTGTATATTGTGTGATTTGGC
1 ATGGGAATTATTGTTGATAGTTCTTGTATATTGTGTGATTTAGC
655024 AT
1 AT
655026 AAATTCATGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.20, C:0.04, G:0.28, T:0.48
Consensus pattern (44 bp):
ATGGGAATTATTGTTGATAGTTCTTGTATATTGTGTGATTTAGC
Found at i:657770 original size:3 final size:3
Alignment explanation
Indices: 657762--657809 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
657752 AGATTACACA
* *
657762 ATG ATG ATG AAG ATG ATG ATG ATG AAG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
657810 GGGATCTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:657782 original size:15 final size:15
Alignment explanation
Indices: 657762--657809 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
657752 AGATTACACA
657762 ATGATGATGAAGATG
1 ATGATGATGAAGATG
657777 ATGATGATGAAGATG
1 ATGATGATGAAGATG
*
657792 ATGATGATGATGATG
1 ATGATGATGAAGATG
657807 ATG
1 ATG
657810 GGGATCTCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (15 bp):
ATGATGATGAAGATG
Found at i:658138 original size:7 final size:7
Alignment explanation
Indices: 658126--658150 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
658116 TGAGCCAATA
658126 TATATAT
1 TATATAT
658133 TATATAT
1 TATATAT
658140 TATATAT
1 TATATAT
658147 TATA
1 TATA
658151 ATAAGATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:658317 original size:30 final size:31
Alignment explanation
Indices: 658257--658331 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
658247 ATGTTTTATC
*
658257 CGTTATATTTTTAGATGTCTAATATTTTTTA
1 CGTTATACTTTTAGATGTCTAATATTTTTTA
*
658288 CGTTATACTTTTAGATGTCTAA-CTTTTTTA
1 CGTTATACTTTTAGATGTCTAATATTTTTTA
*
658318 TGTTATACTTTTAG
1 CGTTATACTTTTAG
658332 GTGTGTGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 20 0.49
31 21 0.51
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.56
Consensus pattern (31 bp):
CGTTATACTTTTAGATGTCTAATATTTTTTA
Found at i:658320 original size:15 final size:15
Alignment explanation
Indices: 658281--658329 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
658271 ATGTCTAATA
*
658281 TTTTTTACGTTATAC
1 TTTTTTATGTTATAC
**
658296 TTTTAGATGTCTA-AC
1 TTTTTTATGT-TATAC
658311 TTTTTTATGTTATAC
1 TTTTTTATGTTATAC
658326 TTTT
1 TTTT
658330 AGGTGTGTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 2 0.07
15 23 0.85
16 2 0.07
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.61
Consensus pattern (15 bp):
TTTTTTATGTTATAC
Found at i:664287 original size:51 final size:49
Alignment explanation
Indices: 664227--664359 Score: 137
Period size: 49 Copynumber: 2.6 Consensus size: 49
664217 CACCTGTAGC
* * *
664227 AGTAAAGCGCGCTCCCTGAATCGCGCTATATGCTGATTTGGCG-T-CACGTGG
1 AGTATAGCGCGC-CCCTG-ATCGCGCTATACGCTGA-CTGG-GTTACACGTGG
*
664278 AGTATAGCGC-CCCCTGTACCGCGCTATACGCTGACTGGGTTACACGTGG
1 AGTATAGCGCGCCCCTG-ATCGCGCTATACGCTGACTGGGTTACACGTGG
*
664327 GGTATAGCGCGACCCCTGATCCGCGCTATACGC
1 AGTATAGCGCG-CCCCTGAT-CGCGCTATACGC
664360 CACGTAGGGG
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
47 1 0.01
48 4 0.06
49 36 0.51
50 2 0.03
51 27 0.39
ACGTcount: A:0.19, C:0.30, G:0.29, T:0.23
Consensus pattern (49 bp):
AGTATAGCGCGCCCCTGATCGCGCTATACGCTGACTGGGTTACACGTGG
Found at i:665419 original size:17 final size:18
Alignment explanation
Indices: 665376--665416 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
665366 GAATTATATT
665376 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
665393 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
665411 ATTAAA
1 AGTAAA
665417 TACATATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:665685 original size:50 final size:50
Alignment explanation
Indices: 665631--665772 Score: 196
Period size: 50 Copynumber: 2.8 Consensus size: 50
665621 TTGCGCGGAT
* * *
665631 CAGGGAGCGCGCTATACCTACGTAGCGCCAAATCA-CTGTATATCACGGGA
1 CAGGGGGCGCGCTATACCCACGTAACGCCAAATCAGC-GTATATCACGGGA
* * *
665681 CAGGGGGTGCGCTATACCCACGTAACTCCAAATCAGCGTATATCACGGGG
1 CAGGGGGCGCGCTATACCCACGTAACGCCAAATCAGCGTATATCACGGGA
* *
665731 CAGGGGGCGCGCTATACCCACGTGACGTCAAATCAGCGTATA
1 CAGGGGGCGCGCTATACCCACGTAACGCCAAATCAGCGTATA
665773 GCGCAATTCA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 80 0.99
51 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (50 bp):
CAGGGGGCGCGCTATACCCACGTAACGCCAAATCAGCGTATATCACGGGA
Found at i:665785 original size:50 final size:50
Alignment explanation
Indices: 665631--665789 Score: 144
Period size: 50 Copynumber: 3.2 Consensus size: 50
665621 TTGCGCGGAT
* * * * * *
665631 CAGGGAGCGCGCTATACCTACGTAGCGCCAAATCA-CTGTATATCAC-GGG
1 CAGGGGGCGCGCTATACCCACGTAACTCCAAATCAGC-GTATAGCACAAGG
* * **
665680 ACAGGGGGTGCGCTATACCCACGTAACTCCAAATCAGCGTATATCACGGGG
1 -CAGGGGGCGCGCTATACCCACGTAACTCCAAATCAGCGTATAGCACAAGG
* * **
665731 CAGGGGGCGCGCTATACCCACGTGACGT-CAAATCAGCGTATAGCGCAATT
1 CAGGGGGCGCGCTATACCCACGTAAC-TCCAAATCAGCGTATAGCACAAGG
665781 CAGGGGGCG
1 CAGGGGGCG
665790 TACTTTACTG
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
50 88 0.95
51 5 0.05
ACGTcount: A:0.26, C:0.28, G:0.30, T:0.17
Consensus pattern (50 bp):
CAGGGGGCGCGCTATACCCACGTAACTCCAAATCAGCGTATAGCACAAGG
Found at i:666940 original size:8 final size:8
Alignment explanation
Indices: 666927--666967 Score: 82
Period size: 8 Copynumber: 5.1 Consensus size: 8
666917 GATACTACTG
666927 TTTAATAT
1 TTTAATAT
666935 TTTAATAT
1 TTTAATAT
666943 TTTAATAT
1 TTTAATAT
666951 TTTAATAT
1 TTTAATAT
666959 TTTAATAT
1 TTTAATAT
666967 T
1 T
666968 ATTCATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTAATAT
Found at i:677148 original size:22 final size:21
Alignment explanation
Indices: 677100--677145 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
677090 TAAATTATTT
677100 ATTTAATGATAAATCTTAAAA
1 ATTTAATGATAAATCTTAAAA
677121 ATTTAATGATAAATCTTAAAA
1 ATTTAATGATAAATCTTAAAA
677142 ATTT
1 ATTT
677146 TAAAAGTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (21 bp):
ATTTAATGATAAATCTTAAAA
Found at i:704078 original size:31 final size:31
Alignment explanation
Indices: 704008--704070 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
703998 TACGTCGGGA
* * *
704008 ACCATATTACAAACGGACTAAATGTTGAGGG
1 ACCATATTGCAAACAGACTAAATATTGAGGG
*
704039 ACCATATTGCAAACAGACTAAATATTGGGGG
1 ACCATATTGCAAACAGACTAAATATTGAGGG
704070 A
1 A
704071 TTATATTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (31 bp):
ACCATATTGCAAACAGACTAAATATTGAGGG
Found at i:705833 original size:31 final size:30
Alignment explanation
Indices: 705794--705856 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
705784 TACAATATAA
* *
705794 TCCCCAACATTTAGTCTGTTTGTAATATGG
1 TCCCCAACATTTAGTCCGTTTGCAATATGG
705824 TCCCTCAACATTTAGTCCGTTTGCAATATGG
1 TCCC-CAACATTTAGTCCGTTTGCAATATGG
705855 TC
1 TC
705857 TCCGACGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (30 bp):
TCCCCAACATTTAGTCCGTTTGCAATATGG
Found at i:706844 original size:56 final size:57
Alignment explanation
Indices: 706744--706862 Score: 186
Period size: 56 Copynumber: 2.1 Consensus size: 57
706734 TTGGAATTTT
* *
706744 CCATCTTCATATATACACCTTTCTCCATGCACTTCTTTCAACCACTAAATATTCGTA
1 CCATCTCCATATATACACCTCTCTCCATGCACTTCTTTCAACCACTAAATATTCGTA
* * *
706801 CCATCTCCATATATACACCTCTC-CCATGCATTTCTTTCTACCACTAAATATTTGTA
1 CCATCTCCATATATACACCTCTCTCCATGCACTTCTTTCAACCACTAAATATTCGTA
706857 CCATCT
1 CCATCT
706863 TTCCTTTGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
56 36 0.63
57 21 0.37
ACGTcount: A:0.27, C:0.33, G:0.03, T:0.37
Consensus pattern (57 bp):
CCATCTCCATATATACACCTCTCTCCATGCACTTCTTTCAACCACTAAATATTCGTA
Found at i:707302 original size:26 final size:26
Alignment explanation
Indices: 707272--707324 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
707262 GAAACATTAT
707272 AGTGATCATCTCTAAATACGTATAAG
1 AGTGATCATCTCTAAATACGTATAAG
707298 AGTGATCATCTCTAAATACGTATAAG
1 AGTGATCATCTCTAAATACGTATAAG
707324 A
1 A
707325 TAATTATATT
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:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (26 bp):
AGTGATCATCTCTAAATACGTATAAG
Found at i:717437 original size:3 final size:3
Alignment explanation
Indices: 717429--717491 Score: 94
Period size: 3 Copynumber: 21.3 Consensus size: 3
717419 ATATTTTATT
*
717429 TAA TAA TAA TAA T-A TAA T-A TAAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
717473 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
717492 TTTAAAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.07
3 49 0.89
4 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:718829 original size:12 final size:12
Alignment explanation
Indices: 718814--718838 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
718804 TCAACTTTTT
718814 CCACAACTTCAG
1 CCACAACTTCAG
718826 CCACAACTTCAG
1 CCACAACTTCAG
718838 C
1 C
718839 ATCATTGTCT
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:0.32, C:0.44, G:0.08, T:0.16
Consensus pattern (12 bp):
CCACAACTTCAG
Found at i:720005 original size:48 final size:48
Alignment explanation
Indices: 719806--719989 Score: 296
Period size: 48 Copynumber: 3.8 Consensus size: 48
719796 TTTCCTTCTA
* **
719806 TCCAAACAATTCCCAGCAAGCTCACTTTTTCCCAGACTCTCACCATCG
1 TCCAAACAATTCCCAGCAAGCTCACTTTTTCCCAGATTCTCGGCATCG
*
719854 TCTAAACAATTCCCAGCAAGCTCACTTTTTCCCAGATTCTCGGCATCG
1 TCCAAACAATTCCCAGCAAGCTCACTTTTTCCCAGATTCTCGGCATCG
* *
719902 TTCAAACAATTCCCGGCAAGCTCACTTTTTCCCAGATTCTCGGCATCG
1 TCCAAACAATTCCCAGCAAGCTCACTTTTTCCCAGATTCTCGGCATCG
* *
719950 TCCAAACAATTCCCAGAAACCTCACTTTTTCCCAGATTCT
1 TCCAAACAATTCCCAGCAAGCTCACTTTTTCCCAGATTCT
719990 GATCATCATC
Statistics
Matches: 125, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 125 1.00
ACGTcount: A:0.26, C:0.35, G:0.10, T:0.28
Consensus pattern (48 bp):
TCCAAACAATTCCCAGCAAGCTCACTTTTTCCCAGATTCTCGGCATCG
Found at i:722880 original size:20 final size:20
Alignment explanation
Indices: 722855--722899 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
722845 AATAGAAAGG
*
722855 AAAAAATCCAAATTAATT-TT
1 AAAAAATCCAAA-AAATTATT
*
722875 AAAAAATTCAAAAAATTATT
1 AAAAAATCCAAAAAATTATT
722895 AAAAA
1 AAAAA
722900 TTAATTCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAATCCAAAAAATTATT
Found at i:732362 original size:24 final size:24
Alignment explanation
Indices: 732329--732399 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 24
732319 TACATGACCT
* * *
732329 GAATTTTGTTCTGATTTCTGATCC
1 GAATTCTGTTATGATTTCTGATAC
* * * *
732353 GGATTCTGTTATGATATCTGTTAT
1 GAATTCTGTTATGATTTCTGATAC
*
732377 GAATTCTGTTTTGATTTCTGATA
1 GAATTCTGTTATGATTTCTGATA
732400 TCTCCGTTTA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.51
Consensus pattern (24 bp):
GAATTCTGTTATGATTTCTGATAC
Found at i:733272 original size:54 final size:55
Alignment explanation
Indices: 733214--733333 Score: 190
Period size: 54 Copynumber: 2.2 Consensus size: 55
733204 TGCTAAATGT
* *
733214 TGTTGCTTTT-TACAAAATAATTGTTAGTTTTTTCTTTTAAATTTTTCTAAACAC
1 TGTTGCTTTTATACAAAATAATTGTTAATTTTTTCTTTTAAATTTTGCTAAACAC
*
733268 TGTTG-TTTTATACAAAATAATTGTTAATTTTTTCTTTTAAATTTTGCTAAACGC
1 TGTTGCTTTTATACAAAATAATTGTTAATTTTTTCTTTTAAATTTTGCTAAACAC
*
733322 TGCTGCTTTTAT
1 TGTTGCTTTTAT
733334 TATTCGATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
53 4 0.07
54 50 0.83
55 6 0.10
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (55 bp):
TGTTGCTTTTATACAAAATAATTGTTAATTTTTTCTTTTAAATTTTGCTAAACAC
Found at i:740869 original size:19 final size:21
Alignment explanation
Indices: 740830--740872 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
740820 TAAAAAAATA
*
740830 TAAAATACTTATTAAATTTAT
1 TAAAATACTTATTAAAATTAT
740851 TAAAATA-TTA-TAAAATTAT
1 TAAAATACTTATTAAAATTAT
740870 TAA
1 TAA
740873 TAAATTTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 3 0.14
21 7 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATACTTATTAAAATTAT
Found at i:740913 original size:31 final size:32
Alignment explanation
Indices: 740828--740913 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 32
740818 TTTAAAAAAA
* *
740828 TATAAAATACTTATTAAATTTAT-TAAAATAT
1 TATAAAATAATTATTAAATTTATCTAAAATAC
* *
740859 TATAAAATTATTAATAAATTTATCT-AAATAC
1 TATAAAATAATTATTAAATTTATCTAAAATAC
* *
740890 TATACAATAATTATTATATTTATC
1 TATAAAATAATTATTAAATTTATC
740914 GAATTTTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 45 0.98
32 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (32 bp):
TATAAAATAATTATTAAATTTATCTAAAATAC
Found at i:749107 original size:21 final size:21
Alignment explanation
Indices: 749058--749103 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
749048 ATATTGTTGT
749058 TAAAATATACTTTTAAGAAGA
1 TAAAATATACTTTTAAGAAGA
*
749079 TAAAATAT-CATTTTAA-AAGT
1 TAAAATATAC-TTTTAAGAAGA
749099 TAAAA
1 TAAAA
749104 ATATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (21 bp):
TAAAATATACTTTTAAGAAGA
Found at i:751023 original size:19 final size:19
Alignment explanation
Indices: 750999--751037 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
750989 CAAAGTGAAA
*
750999 CGTTGAGGTTCAAAATGCT
1 CGTTGAGATTCAAAATGCT
751018 CGTTGAGATTCAAAATGCT
1 CGTTGAGATTCAAAATGCT
751037 C
1 C
751038 CAAAAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (19 bp):
CGTTGAGATTCAAAATGCT
Found at i:755110 original size:388 final size:388
Alignment explanation
Indices: 754394--755174 Score: 1445
Period size: 388 Copynumber: 2.0 Consensus size: 388
754384 AATAATATGG
*
754394 GGATCCCTTAATAGATCATCGAGTAGAAGCCATTAAGAACACATTTCATAGGAAGTATTCATAAT
1 GGATCCCTTAATAGATCATCGAGTAGAAGCCATGAAGAACACATTTCATAGGAAGTATTCATAAT
*
754459 ATCACGTTTCATGAGGTCGAATAGGATGTCTAGTGTGTTCCATCAGTACGATAAAATCATAATAA
66 ATCACGTTTCACGAGGTCGAATAGGATGTCTAGTGTGTTCCATCAGTACGATAAAATCATAATAA
754524 GTACACTAATCAAATGATAGTTCAGTAAATCCCATAAACCATACTGTAGTGGAGCTTTCTAAACT
131 GTACACTAATCAAATGATAGTTCAGTAAATCCCATAAACCATACTGTAGTGGAGCTTTCTAAACT
754589 CGTATTTTAAAACCATCGTATAAATAATTAACCTAAGGGAACATCTTAGAGCCTGAGAGCCTACC
196 CGTATTTTAAAACCATCGTATAAATAATTAACCTAAGGGAACATCTTAGAGCCTGAGAGCCTACC
* *
754654 CAAGAAAGTTCGGGGCCACGAGGCCTACCTAAGAACACATCTTATAACCGCGGTGCCTACCCGAG
261 CAAGAAAGTTCGGGGCCACGAGGCCTACATAAGAACACATCTTATAACCGCGGTGCCTACCAGAG
*
754719 AATGATCTCAGGGCCGCAAAGCCTACCTAAGAGTCACATTAGGTCCATAAAAATTTTCCAGCT
326 AATGATCTCAAGGCCGCAAAGCCTACCTAAGAGTCACATTAGGTCCATAAAAATTTTCCAGCT
754782 GGATCCCTTAATAGATCATCGAGTAGAAGCCATGAAGAACACATTTCATAGGAAGTATTCATAAT
1 GGATCCCTTAATAGATCATCGAGTAGAAGCCATGAAGAACACATTTCATAGGAAGTATTCATAAT
754847 ATCACGTTTCACGAGGTCGAATAGGATGTCTAGTGTGTTCCATCAGTACGATAAAATCATAATAA
66 ATCACGTTTCACGAGGTCGAATAGGATGTCTAGTGTGTTCCATCAGTACGATAAAATCATAATAA
* *
754912 GTACTCTAATCAAATGATAGTTCAGTAAATCCCATAAACCATACTGTAGTGGAGCTTTTTAAACT
131 GTACACTAATCAAATGATAGTTCAGTAAATCCCATAAACCATACTGTAGTGGAGCTTTCTAAACT
* *
754977 CGTATTTTAAAACCATCGTATAAATAGTTAACCTAAGGGAACATCTTAGGGCCTGAGAGCCTACC
196 CGTATTTTAAAACCATCGTATAAATAATTAACCTAAGGGAACATCTTAGAGCCTGAGAGCCTACC
**
755042 CAAGAAAGTTCGGGGCCACGAGGCCTACATAAGAACACATCTTATGGCCGCGGTGCCTACCAGAG
261 CAAGAAAGTTCGGGGCCACGAGGCCTACATAAGAACACATCTTATAACCGCGGTGCCTACCAGAG
*
755107 AATGATCTCAAGGCCGCAGAGCCTACCTAAGAGTCACATTAGGTCCATAAAAATTTTCCAGCT
326 AATGATCTCAAGGCCGCAAAGCCTACCTAAGAGTCACATTAGGTCCATAAAAATTTTCCAGCT
*
755170 TGATC
1 GGATC
755175 AGAGCTGTAC
Statistics
Matches: 380, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
388 380 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (388 bp):
GGATCCCTTAATAGATCATCGAGTAGAAGCCATGAAGAACACATTTCATAGGAAGTATTCATAAT
ATCACGTTTCACGAGGTCGAATAGGATGTCTAGTGTGTTCCATCAGTACGATAAAATCATAATAA
GTACACTAATCAAATGATAGTTCAGTAAATCCCATAAACCATACTGTAGTGGAGCTTTCTAAACT
CGTATTTTAAAACCATCGTATAAATAATTAACCTAAGGGAACATCTTAGAGCCTGAGAGCCTACC
CAAGAAAGTTCGGGGCCACGAGGCCTACATAAGAACACATCTTATAACCGCGGTGCCTACCAGAG
AATGATCTCAAGGCCGCAAAGCCTACCTAAGAGTCACATTAGGTCCATAAAAATTTTCCAGCT
Found at i:764479 original size:171 final size:172
Alignment explanation
Indices: 764163--764502 Score: 493
Period size: 171 Copynumber: 2.0 Consensus size: 172
764153 AATATTTTAC
* * *
764163 TAAAAAGGAGATATAACAATACTTAACCACCAACAAACTAATCAAAAAACAAATATCATGAGGGT
1 TAAAAAAGAGATATAACAATACTTAACCACCAACAAACCAATCAAAAAACAAATATCATGAGGAT
* * * * *
764228 TTTTGTGCGAGCACCAACACGATCACAGAGATATGCGAAAAACGTACCAAAAGCCATAAGGAACG
66 TTTTATGCGAGCACCAACACGATCACAAAGATATGCGAAAAACGTACAAAAAACCATAAGAAACG
*
764293 TGCCACAATAGTAAAGA-AAAAGCATGACACAATAGTAATAT
131 TGCCACAAGAGTAAAGAGAAAAGCATGACACAATAGTAATAT
* * * * * *
764334 TAAAAAAGAGATCTAACAATACTTAACTACCGATAAACCAATTAAAAAATAAATATCATGAGGAT
1 TAAAAAAGAGATATAACAATACTTAACCACCAACAAACCAATCAAAAAACAAATATCATGAGGAT
* * *
764399 TTTTATGTGAGCACCAACACGATCGCAAAGGTATGCGAAAAACGTACAAAAAACCATAAGAAACG
66 TTTTATGCGAGCACCAACACGATCACAAAGATATGCGAAAAACGTACAAAAAACCATAAGAAACG
* *
764464 TGTCACAAGAGTAAAGAGAAAAGTATGACACAATAGTAA
131 TGCCACAAGAGTAAAGAGAAAAGCATGACACAATAGTAA
764503 AGAAATATGT
Statistics
Matches: 148, Mismatches: 20, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
171 128 0.86
172 20 0.14
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.19
Consensus pattern (172 bp):
TAAAAAAGAGATATAACAATACTTAACCACCAACAAACCAATCAAAAAACAAATATCATGAGGAT
TTTTATGCGAGCACCAACACGATCACAAAGATATGCGAAAAACGTACAAAAAACCATAAGAAACG
TGCCACAAGAGTAAAGAGAAAAGCATGACACAATAGTAATAT
Found at i:773858 original size:11 final size:11
Alignment explanation
Indices: 773828--773859 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
773818 TATAAAAAAA
773828 ATTAATATATT
1 ATTAATATATT
773839 A-T-ATATATT
1 ATTAATATATT
773848 ATTAATATATT
1 ATTAATATATT
773859 A
1 A
773860 GAGTGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.42
10 2 0.11
11 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTAATATATT
Found at i:789429 original size:17 final size:17
Alignment explanation
Indices: 789407--789460 Score: 108
Period size: 17 Copynumber: 3.2 Consensus size: 17
789397 CGGGTGTAAG
789407 TGTGTCATACATGGGAA
1 TGTGTCATACATGGGAA
789424 TGTGTCATACATGGGAA
1 TGTGTCATACATGGGAA
789441 TGTGTCATACATGGGAA
1 TGTGTCATACATGGGAA
789458 TGT
1 TGT
789461 ATCAGACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.31
Consensus pattern (17 bp):
TGTGTCATACATGGGAA
Found at i:795002 original size:121 final size:121
Alignment explanation
Indices: 794787--795011 Score: 299
Period size: 121 Copynumber: 1.9 Consensus size: 121
794777 CAAATATGTT
* * * * * * *
794787 GAGGTCCATTTCATATAGACAGGTTAGAAGTAGGCAGTTCGTATTTGTTCAGGTCCATTGAAACA
1 GAGGTACATCTCATATAGACAGGTTAGAAGTAGCCAATTCGTATCTGTTCAGATCCATAGAAACA
* * *
794852 TAAAATCTATTCTCTTCCATTTTCAGCTCATAGAAATGATCATTTATTGCCTCGTC
66 TAAAATCTACTCTCTTCAATTCTCAGCTCATAGAAATGATCATTTATTGCCTCGTC
* *
794908 GAGGTACATCTCATATGGACATGTTCA-AAGTAGCCAATTCGTATCTGTTCAGATCCATAGAAAC
1 GAGGTACATCTCATATAGACAGGTT-AGAAGTAGCCAATTCGTATCTGTTCAGATCCATAGAAAC
* * *
794972 ATGAGATCTACTCTCTTCAATTCTCTGCTCATAGAAATGA
65 ATAAAATCTACTCTCTTCAATTCTCAGCTCATAGAAATGA
795012 ACGTTTAGCT
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
121 87 0.99
122 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (121 bp):
GAGGTACATCTCATATAGACAGGTTAGAAGTAGCCAATTCGTATCTGTTCAGATCCATAGAAACA
TAAAATCTACTCTCTTCAATTCTCAGCTCATAGAAATGATCATTTATTGCCTCGTC
Found at i:795438 original size:32 final size:32
Alignment explanation
Indices: 795402--795467 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
795392 GAGTGAAATG
795402 AATTCAAATATATTAGCTCTCTGATTTTTATA
1 AATTCAAATATATTAGCTCTCTGATTTTTATA
795434 AATTCAAATATATTAGCTCTCTGATTTTTATA
1 AATTCAAATATATTAGCTCTCTGATTTTTATA
795466 AA
1 AA
795468 CCTAAAATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (32 bp):
AATTCAAATATATTAGCTCTCTGATTTTTATA
Found at i:797219 original size:21 final size:21
Alignment explanation
Indices: 797194--797234 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
797184 CATATGAAAT
797194 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
797215 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
797235 AACCCTCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:802444 original size:2 final size:2
Alignment explanation
Indices: 802437--802470 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
802427 TTTCTAAAAC
802437 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
802471 TAAAAATTAA
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:804448 original size:41 final size:41
Alignment explanation
Indices: 804403--804572 Score: 102
Period size: 42 Copynumber: 4.1 Consensus size: 41
804393 TATTGTGGCA
804403 TTTTTTAATAAAAGCCGCAACATATTAGT-ACTTTAGCGGCG
1 TTTTTTAATAAAAGCCGCAA-ATATTAGTAACTTTAGCGGCG
* * * *
804444 -TTTTT-ATACAAATGCCAC-AATA-TGGTTCACCTATAGCGGCG
1 TTTTTTAATA-AAA-GCCGCAAATATTAG-T-AACTTTAGCGGCG
* * *
804485 TTTTTTAATAAACGCCGCAAAAAATTA-TAACTTTAGCGGTG
1 TTTTTTAATAAAAGCCGC-AAATATTAGTAACTTTAGCGGCG
* * * * * *
804526 TTTTGGTAACAAACGCCGCAAATGAATCGT-ACTTTAGTGGCG
1 TTTT-TTAATAAAAGCCGCAAAT-ATTAGTAACTTTAGCGGCG
804568 TTTTT
1 TTTTT
804573 ACAAAAACGC
Statistics
Matches: 97, Mismatches: 19, Indels: 26
0.68 0.13 0.18
Matches are distributed among these distances:
38 2 0.02
39 7 0.07
40 9 0.09
41 35 0.36
42 36 0.37
43 7 0.07
44 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (41 bp):
TTTTTTAATAAAAGCCGCAAATATTAGTAACTTTAGCGGCG
Found at i:804792 original size:14 final size:14
Alignment explanation
Indices: 804773--804801 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
804763 GTCTACTTTC
804773 TGCCGTTTACAACT
1 TGCCGTTTACAACT
804787 TGCCGTTTACAACT
1 TGCCGTTTACAACT
804801 T
1 T
804802 ACCCACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.38
Consensus pattern (14 bp):
TGCCGTTTACAACT
Found at i:807602 original size:42 final size:42
Alignment explanation
Indices: 807512--807931 Score: 445
Period size: 43 Copynumber: 9.9 Consensus size: 42
807502 GTTTGTATAT
* * * * * *
807512 AAAACGTCGCTATATATCTGACCTTTTGTGACGTTTTTTCTAAA
1 AAAACGCCGCTATATATCTAACCTTTTGCGGCGTTTGTTC--CA
*
807556 AAAACGCCGCTATATATCTAACCTATTGCGGCGTTTGTTCCA
1 AAAACGCCGCTATATATCTAACCTTTTGCGGCGTTTGTTCCA
* * * *
807598 AAAACGCCGCTATAGATACCAACCTTTTGCGGTGTTTGTAT-AA
1 AAAACGCCGCTATATAT-CTAACCTTTTGCGGCGTTTGT-TCCA
* *
807641 AAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAA
1 AAAACGCCGCTATATATCTAACCTTTTGCGGCGTTTGTTCC-A
* * *
807684 AAAATGCCGCTATCTATCTAACCTATTGCGGCGTTTGTTCCA
1 AAAACGCCGCTATATATCTAACCTTTTGCGGCGTTTGTTCCA
* * *
807726 AAAACGCCGCTATCTATCTGACCTATTGCGGCGTTTGTTCCAA
1 AAAACGCCGCTATATATCTAACCTTTTGCGGCGTTTGTTCC-A
* * * *
807769 AAAACGCCGC--TATATGTGACCTATTGCTGCGTTTGTTCCA
1 AAAACGCCGCTATATATCTAACCTTTTGCGGCGTTTGTTCCA
* *
807809 AAAACGCCGCTATAGATATC-AACCTTTTGCGACGTTAGTTCCA
1 AAAACGCCGCTAT--ATATCTAACCTTTTGCGGCGTTTGTTCCA
**
807852 AAAACGCCTATATAGATATC-AACCTTTTGCGGCGTTTGTTCCA
1 AAAACGCCGCTAT--ATATCTAACCTTTTGCGGCGTTTGTTCCA
* *
807895 AAAATGCCGCTATAGATCTCAACCTTTTGCGGCGTTT
1 AAAACGCCGCTATATATCT-AACCTTTTGCGGCGTTT
807932 TTGGTTCTCA
Statistics
Matches: 325, Mismatches: 40, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
40 11 0.03
41 31 0.10
42 76 0.23
43 168 0.52
44 39 0.12
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (42 bp):
AAAACGCCGCTATATATCTAACCTTTTGCGGCGTTTGTTCCA
Found at i:807675 original size:85 final size:85
Alignment explanation
Indices: 807555--807931 Score: 442
Period size: 85 Copynumber: 4.4 Consensus size: 85
807545 TTTTTTCTAA
* *
807555 AAAAACGCCGCTATATATCTAACCTATTGCGGCGTTTGTTCC-AAAAACGCCGCTATAGATACCA
1 AAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAAACGCCGCTATAGAT-CCA
* * *
807619 ACCTTTTGCGGTGTTTGTAT-A
65 ACCTATTGCGGCGTTTGT-TCC
* * ** *
807640 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAAATGCCGCTATCTATCTAA
1 AAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAAACGCCGCTATAGATCCAA
807705 CCTATTGCGGCGTTTGTTCC
66 CCTATTGCGGCGTTTGTTCC
** * * *
807725 AAAAACGCCGCTATCTATCTGACCTATTGCGGCGTTTGTTCCAAAAAACGCCGCTATATG-T--G
1 AAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAAACGCCGCTATA-GATCCA
*
807787 ACCTATTGCTGCGTTTGTTCC
65 ACCTATTGCGGCGTTTGTTCC
* * * ** *
807808 AAAAACGCCGCTATAGATATCAACCTTTTGCGACGTTAGTTCC-AAAAACGCCTATATAGATATC
1 AAAAACGCCGCTATAGATCT-AACCTTTTGCGGCGTTTGTTCCAAAAAACGCCGCTATAGAT-CC
*
807872 AACCTTTTGCGGCGTTTGTTCC
64 AACCTATTGCGGCGTTTGTTCC
*
807894 AAAAATGCCGCTATAGATCTCAACCTTTTGCGGCGTTT
1 AAAAACGCCGCTATAGATCT-AACCTTTTGCGGCGTTT
807932 TTGGTTCTCA
Statistics
Matches: 250, Mismatches: 34, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
82 1 0.00
83 51 0.20
84 19 0.08
85 111 0.44
86 68 0.27
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (85 bp):
AAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAAACGCCGCTATAGATCCAA
CCTATTGCGGCGTTTGTTCC
Found at i:814789 original size:168 final size:169
Alignment explanation
Indices: 814478--814818 Score: 666
Period size: 168 Copynumber: 2.0 Consensus size: 169
814468 CTTCCCCATA
814478 AAATGCCTTATAAGACTTGATTTAATATTAGAAAGGACTTATTATTTTAAAATGTTAGTTATTGT
1 AAATGCCTTATAAGACTTGATTTAATATTAGAAAGGACTTATTATTTTAAAATGTTAGTTATTGT
814543 GTAAATTAAATTACTGCTCTGCCTACACGAGAATGGTCGGTTCAATTTTTATTTAAAGAGATCTT
66 GTAAATTAAATTACTGCTCTGCCTACACGAGAATGGTCGGTTCAATTTTTATTTAAAGAGATCTT
814608 GGGTCTAAAAAAAATTATTTTTTTTTAA-TTTTTTTAGT
131 GGGTCTAAAAAAAATTATTTTTTTTTAATTTTTTTTAGT
814646 AAATGCCTTATAAGACTTGATTTAATATTAGAAAGGACTTATTATTTTAAAATGTTAGTTATTGT
1 AAATGCCTTATAAGACTTGATTTAATATTAGAAAGGACTTATTATTTTAAAATGTTAGTTATTGT
814711 GTAAATTAAATTACTGCTCTGCCTACAACGAGAATGGTCGGTTCAATTTTTATTTAAAGAGATCT
66 GTAAATTAAATTACTGCTCTGCCTAC-ACGAGAATGGTCGGTTCAATTTTTATTTAAAGAGATCT
814776 TGGGTCTAAAAAAAATTATTTTTTTTTAATTTTTTTTAGT
130 TGGGTCTAAAAAAAATTATTTTTTTTTAATTTTTTTTAGT
814816 AAA
1 AAA
814819 ATACACAAAT
Statistics
Matches: 171, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
168 91 0.53
169 67 0.39
170 13 0.08
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (169 bp):
AAATGCCTTATAAGACTTGATTTAATATTAGAAAGGACTTATTATTTTAAAATGTTAGTTATTGT
GTAAATTAAATTACTGCTCTGCCTACACGAGAATGGTCGGTTCAATTTTTATTTAAAGAGATCTT
GGGTCTAAAAAAAATTATTTTTTTTTAATTTTTTTTAGT
Found at i:822575 original size:24 final size:25
Alignment explanation
Indices: 822517--822578 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 25
822507 GAGTGATTCT
822517 AAAGTCTAATTTACCCTGTTTTTAA
1 AAAGTCTAATTTACCCTGTTTTTAA
*
822542 AAAGTGTAATTTACCCTAG-TTTT-A
1 AAAGTCTAATTTACCCT-GTTTTTAA
822566 AAAGTCTAATTTA
1 AAAGTCTAATTTA
822579 ACAAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 13 0.38
25 20 0.59
26 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (25 bp):
AAAGTCTAATTTACCCTGTTTTTAA
Found at i:824369 original size:30 final size:29
Alignment explanation
Indices: 824333--824419 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 29
824323 TTTTGCAACT
*
824333 ATTTGATAAAATTTAATTATATTTTTAATA
1 ATTTGATAAAATTTAATTA-ATTATTAATA
824363 ATTTGAT-AAATTTAA-TAATTATTAATA
1 ATTTGATAAAATTTAATTAATTATTAATA
* *
824390 ATATT-TTAAAATTTAA-TAATTA-AAATA
1 AT-TTGATAAAATTTAATTAATTATTAATA
824417 ATT
1 ATT
824420 ATTTGAACAT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
26 1 0.02
27 18 0.35
28 18 0.35
29 8 0.15
30 7 0.13
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
ATTTGATAAAATTTAATTAATTATTAATA
Found at i:824409 original size:28 final size:26
Alignment explanation
Indices: 824339--824419 Score: 83
Period size: 28 Copynumber: 3.0 Consensus size: 26
824329 AACTATTTGA
*
824339 TAAAATTTAATTATATTTTTAATAATTT
1 TAAAATTTAA-TA-ATTATTAATAATTT
*
824367 GATAAATTTAATAATTATTAATAATATTT
1 TA-AAATTTAATAATTATTAAT-A-ATTT
*
824396 TAAAATTTAATAATTA-AAATAATT
1 TAAAATTTAATAATTATTAATAATT
824420 ATTTGAACAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
25 3 0.07
26 1 0.02
27 11 0.24
28 18 0.39
29 13 0.28
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
TAAAATTTAATAATTATTAATAATTT
Found at i:824417 original size:37 final size:39
Alignment explanation
Indices: 824345--824422 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 39
824335 TTGATAAAAT
* * *
824345 TTAATTATATTTTTAATAATTTGATAAATTTAATAATTA
1 TTAATAATATTTTTAATAATTTAATAAATTAAATAATTA
824384 TTAATAATA-TTTTAA-AATTTAAT-AATTAAAATAATTA
1 TTAATAATATTTTTAATAATTTAATAAATT-AAATAATTA
824421 TT
1 TT
824423 TGAACATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 4 0.11
37 17 0.49
38 6 0.17
39 8 0.23
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (39 bp):
TTAATAATATTTTTAATAATTTAATAAATTAAATAATTA
Found at i:830276 original size:6 final size:6
Alignment explanation
Indices: 830265--830316 Score: 79
Period size: 6 Copynumber: 8.7 Consensus size: 6
830255 AAGAGTCATA
*
830265 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGAG AGAA-A AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAG-G AGAAGG AGAAGG
830313 AGAA
1 AGAA
830317 AAAAGAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 4 0.10
6 33 0.79
7 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:830324 original size:9 final size:9
Alignment explanation
Indices: 830300--830333 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
830290 GAAGGAGAAG
830300 AGAGAAAAGA
1 AGAGAAAA-A
830310 AGGAGAAAAA
1 A-GAGAAAAA
830320 AGAGAAAAA
1 AGAGAAAAA
830329 AGAGA
1 AGAGA
830334 GAGATGGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.57
10 3 0.13
11 7 0.30
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (9 bp):
AGAGAAAAA
Found at i:837339 original size:24 final size:24
Alignment explanation
Indices: 837292--837339 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
837282 GTGGGGGAGG
*
837292 AAAAAGAAAAAAAAGGACTTGGAAA
1 AAAAAGAAAAAAAAAGAC-TGGAAA
837317 AAAAGAGAAAAAAAAAGAC-GGAA
1 AAAA-AGAAAAAAAAAGACTGGAA
837340 GACAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 4 0.19
26 13 0.62
ACGTcount: A:0.71, C:0.04, G:0.21, T:0.04
Consensus pattern (24 bp):
AAAAAGAAAAAAAAAGACTGGAAA
Found at i:839540 original size:45 final size:45
Alignment explanation
Indices: 839483--839669 Score: 252
Period size: 45 Copynumber: 4.2 Consensus size: 45
839473 CTTCCTCTGT
* *
839483 GATGCATT-CCATCAGCAGATCTTGACCTTGACCGCTTTCTATCCC
1 GATGC-TTGCCATCAGCAGATCTTGACCTCGACCGCCTTCTATCCC
* *
839528 GATGCTTGCCATCAGCAGATCTTGAACAT-GACCGCTTTCTATCCC
1 GATGCTTGCCATCAGCAGATCTTG-ACCTCGACCGCCTTCTATCCC
* *
839573 GATGCTTGCCATCAGCAGATCTTGACCTCAACCGCCTTCTATCTC
1 GATGCTTGCCATCAGCAGATCTTGACCTCGACCGCCTTCTATCCC
* * * *
839618 GATGCTTGCCATCAGCAGATCTTGATCTCGAACACCTTCTATCTC
1 GATGCTTGCCATCAGCAGATCTTGACCTCGACCGCCTTCTATCCC
839663 GATGCTT
1 GATGCTT
839670 AGAATTCTTA
Statistics
Matches: 130, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
44 5 0.04
45 122 0.94
46 3 0.02
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.30
Consensus pattern (45 bp):
GATGCTTGCCATCAGCAGATCTTGACCTCGACCGCCTTCTATCCC
Found at i:840448 original size:42 final size:42
Alignment explanation
Indices: 840390--840510 Score: 136
Period size: 42 Copynumber: 2.9 Consensus size: 42
840380 CTCTTCGTCT
* * * *
840390 ATAACTGATTGATGATCTTGATTTGGACCTTGACCTTCCCCT
1 ATAACTAATTGGTGATCTTGATTTGGATCTTGACCTTCCCCG
* * *
840432 ATAAAC-AATTGGTGATCTTGACTTGGATCTTGATCTTCTCCG
1 AT-AACTAATTGGTGATCTTGATTTGGATCTTGACCTTCCCCG
** *
840474 ATAACTAAGGGGTGATTTTGATTTGGATCTTGACCTT
1 ATAACTAATTGGTGATCTTGATTTGGATCTTGACCTT
840511 GCACGGGAAG
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 3 0.05
42 59 0.91
43 3 0.05
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (42 bp):
ATAACTAATTGGTGATCTTGATTTGGATCTTGACCTTCCCCG
Found at i:849304 original size:30 final size:30
Alignment explanation
Indices: 849265--849329 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
849255 TGCCGCACAC
*
849265 GAGAGATGGAACGATGTTTGTAGGGTGGAG
1 GAGAAATGGAACGATGTTTGTAGGGTGGAG
849295 GAGAAATGGAACGATGTTTGTAGGGTGGAG
1 GAGAAATGGAACGATGTTTGTAGGGTGGAG
849325 GAGAA
1 GAGAA
849330 CCAACTGTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.31, C:0.03, G:0.45, T:0.22
Consensus pattern (30 bp):
GAGAAATGGAACGATGTTTGTAGGGTGGAG
Found at i:855671 original size:42 final size:42
Alignment explanation
Indices: 855620--855827 Score: 272
Period size: 42 Copynumber: 5.2 Consensus size: 42
855610 ATAAACAAGT
* *
855620 AAATAAATAACATCATAACACCATTAAGTCTCAACAAGTCTA
1 AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCTA
*
855662 AAATAAATAACACCATAACACCATTAAGTCTTAATAAGTCTA
1 AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCTA
855704 AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCT-
1 AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCTA
* * *
855745 --A-AAA-AA-A--ATAACATCATTAAATCTCAATAAGTTTA
1 AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCTA
* * *
855780 AAATAAACAACACCATAACACTAATAAGTCTCAATAAGTCT-
1 AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCTA
855821 AAATAAA
1 AAATAAA
855828 ATCAACATCA
Statistics
Matches: 146, Mismatches: 12, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
34 24 0.16
36 1 0.01
37 3 0.02
38 6 0.04
39 3 0.02
40 1 0.01
41 7 0.05
42 101 0.69
ACGTcount: A:0.52, C:0.19, G:0.04, T:0.25
Consensus pattern (42 bp):
AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCTA
Found at i:855756 original size:76 final size:76
Alignment explanation
Indices: 855676--855834 Score: 237
Period size: 76 Copynumber: 2.1 Consensus size: 76
855666 AAATAACACC
* * * *
855676 ATAACACCATTAAGTCTTAATAAGTCTAAAATAAATAACACCATAACACCATTAAGTCTCAATAA
1 ATAACACCATTAAATCTCAATAAGTCTAAAATAAACAACACCATAACACCAATAAGTCTCAATAA
855741 GTCTAAAAAAA
66 GTCTAAAAAAA
* * *
855752 ATAACATCATTAAATCTCAATAAGTTTAAAATAAACAACACCATAACACTAATAAGTCTCAATAA
1 ATAACACCATTAAATCTCAATAAGTCTAAAATAAACAACACCATAACACCAATAAGTCTCAATAA
*
855817 GTCTAAATAAA
66 GTCTAAAAAAA
855828 ATCAACA
1 AT-AACA
855835 TCAATAATAT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
76 70 0.95
77 4 0.05
ACGTcount: A:0.52, C:0.18, G:0.04, T:0.25
Consensus pattern (76 bp):
ATAACACCATTAAATCTCAATAAGTCTAAAATAAACAACACCATAACACCAATAAGTCTCAATAA
GTCTAAAAAAA
Found at i:859999 original size:287 final size:288
Alignment explanation
Indices: 859559--860088 Score: 757
Period size: 287 Copynumber: 1.8 Consensus size: 288
859549 TCTCAGTGAC
*
859559 CATTTTCCAACAGAAATCCTCTTATTGCCAAACATTCAAAGCATCAACATTTCAAGCAATTACGA
1 CATTTTCCAACAGAAATCCTCTTATTGCCAAACATTCAAAGCATCAACATTTCAAGCAATGACGA
* * * *
859624 TTTAGTGGGTCAATTGCCAGAATTTCCATCAAACAATGCTTTGAGGAGTTTGTCACTTTATGATA
66 TTTAGTGGGTCAATTACCAGAATTTCCATCAAACAATGCTTTAAGAAGTTTATCACTTTATGATA
* *
859689 CAAATTTCAGTGGAAAACTGCCTGAATCAATAGGTAACCTTAAT-TTCCTGAGGGATTTAATTCT
131 CAAATTTCAGTGGAAAACTGCCTGAATCAATAGGGAACCTT-ATGTTCCTGAGGGATTTAACTCT
* *
859753 TGATGATTG-TAACTTTCTTGGATCCATTCCATCTTCAATTGCAAGTCTTGGTCTTCTGGTGAAC
195 TGATGATTGTTAACTTT-TTGGATCCATTCCATCGTCAATTGCAAATCTTGGTCTTCTGGTGAAC
859817 CTGCATCAAGCACGTAATAATTTCAGTGGG
259 CTGCATCAAGCACGTAATAATTTCAGTGGG
* * ** *
859847 CATTTTCCACCAGAAATTCTCTTATTGCCAAGA-ATTCAAAGCATTGACATTTCAA-CAATGACT
1 CATTTTCCAACAGAAATCCTCTTATTGCCAA-ACATTCAAAGCATCAACATTTCAAGCAATGACG
* * * *
859910 ATCTTA-TGGGTCAGTTACCAGAATTTTCATCAAACAATGCTTTAAGAAGTTTATCGCTTTCTGG
65 AT-TTAGTGGGTCAATTACCAGAATTTCCATCAAACAATGCTTTAAGAAGTTTATCACTTTAT-G
* * *
859974 A-ACAAATTTCAGTGGAAAACTGCCTGAATCAATTGGGAAGCTTATGTTCTTGAGGGATTTAACT
128 ATACAAATTTCAGTGGAAAACTGCCTGAATCAATAGGGAACCTTATGTTCCTGAGGGATTTAACT
* * *
860038 CTTTATGATTGTTATCTTTTTGGATCCATTCCATGGTCAATTGCAAATCTT
193 CTTGATGATTGTTAACTTTTTGGATCCATTCCATCGTCAATTGCAAATCTT
860089 ACTCACCTGG
Statistics
Matches: 213, Mismatches: 24, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
286 2 0.01
287 150 0.70
288 60 0.28
289 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (288 bp):
CATTTTCCAACAGAAATCCTCTTATTGCCAAACATTCAAAGCATCAACATTTCAAGCAATGACGA
TTTAGTGGGTCAATTACCAGAATTTCCATCAAACAATGCTTTAAGAAGTTTATCACTTTATGATA
CAAATTTCAGTGGAAAACTGCCTGAATCAATAGGGAACCTTATGTTCCTGAGGGATTTAACTCTT
GATGATTGTTAACTTTTTGGATCCATTCCATCGTCAATTGCAAATCTTGGTCTTCTGGTGAACCT
GCATCAAGCACGTAATAATTTCAGTGGG
Found at i:866530 original size:23 final size:21
Alignment explanation
Indices: 866477--866530 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
866467 TGGGTACTTA
866477 ACCAAAAAAAAAATCAAACAT
1 ACCAAAAAAAAAATCAAACAT
866498 --CAAATGAAAAAAATTCAAAACAT
1 ACCAAA--AAAAAAA-TC-AAACAT
866521 ACCAAAAAAA
1 ACCAAAAAAA
866531 TTGAATCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
19 4 0.15
21 7 0.26
22 2 0.07
23 10 0.37
25 4 0.15
ACGTcount: A:0.70, C:0.17, G:0.02, T:0.11
Consensus pattern (21 bp):
ACCAAAAAAAAAATCAAACAT
Found at i:873636 original size:60 final size:60
Alignment explanation
Indices: 873551--873792 Score: 262
Period size: 60 Copynumber: 4.1 Consensus size: 60
873541 TGCATCATAT
* * * * * *
873551 ATCCCTAAAC--T-ACCCTCATTTTAAATTGGTCTTTAAAGTTTTAAATATTCTAATTTC
1 ATCCCTAAACTATGACCCTCATTCTAAATTAGTCCTTAAAGATTTGAACATTCTAATTTC
* * * *
873608 ATTCCTAAATTATGACTCTCATTCTAAATTAGCCCTT-AAGCATTTGAACATTCTAATTTC
1 ATCCCTAAACTATGACCCTCATTCTAAATTAGTCCTTAAAG-ATTTGAACATTCTAATTTC
* *
873668 ATCCCTAAACTATGACCCTCATTCTAAATTAGTCCTTAAACATTTGAACATCCTAATTTC
1 ATCCCTAAACTATGACCCTCATTCTAAATTAGTCCTTAAAGATTTGAACATTCTAATTTC
* * ** *
873728 ATCCCTAAACTATGACCCTCTTTCTAAGTTAGTCCCCAAA-ATTTTGAATATT-TCAATTTC
1 ATCCCTAAACTATGACCCTCATTCTAAATTAGTCCTTAAAGA-TTTGAACATTCT-AATTTC
873788 ATCCC
1 ATCCC
873793 CAATTTCATC
Statistics
Matches: 156, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
57 8 0.05
59 6 0.04
60 140 0.90
61 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (60 bp):
ATCCCTAAACTATGACCCTCATTCTAAATTAGTCCTTAAAGATTTGAACATTCTAATTTC
Done.