Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 62
Found at i:3226005 original size:29 final size:29
Alignment explanation
Indices: 3225971--3226042 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
3225961 CATATTATGA
** *
3225971 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAACGTAT
*
3226000 TACATGACATGAATTCATATTATACGTAT
1 TACATGACATGAATTCATATTAAACGTAT
3226029 TACATGACATGAAT
1 TACATGACATGAAT
3226043 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAACGTAT
Found at i:3226098 original size:30 final size:29
Alignment explanation
Indices: 3226055--3226132 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
3226045 GCAGAAAAGT
*
3226055 TATATGCACTATGTGATAAAGGTATGTAAA
1 TATATGC-CTATGTGATAAAGGTATGGAAA
* *
3226085 TGATATGCCTATGTGTTAAAGTTATGGAAA
1 T-ATATGCCTATGTGATAAAGGTATGGAAA
* *
3226115 TACTATGTCTACGTGATA
1 TA-TATGCCTATGTGATA
3226133 TGAACTACGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (29 bp):
TATATGCCTATGTGATAAAGGTATGGAAA
Found at i:3226409 original size:22 final size:22
Alignment explanation
Indices: 3226335--3226401 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
3226325 TTATGGACAT
3226335 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
3226357 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
3226379 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
3226401 A
1 A
3226402 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:3232468 original size:21 final size:21
Alignment explanation
Indices: 3232442--3232484 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3232432 TTTCTGGGTT
* *
3232442 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
3232463 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
3232484 A
1 A
3232485 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:3232603 original size:69 final size:69
Alignment explanation
Indices: 3232464--3232618 Score: 215
Period size: 69 Copynumber: 2.2 Consensus size: 69
3232454 ACCCATTCAA
* * *
3232464 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCAAG
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCAAG
3232529 GGGG
66 GGGG
* * *
3232533 GGGGAACCGATACCCCCTCATCGTATAA-GAAATTCCAGAATGCTATAGGGGAACCGATACCCC-
1 GGGGAACCGATACCCCCTCAACG-A-AATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCA
3232596 AGGGGG
64 AGGGGG
*
3232602 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
3232619 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
69 43 0.56
70 32 0.42
71 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.15
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCAAG
GGGG
Found at i:3232955 original size:29 final size:29
Alignment explanation
Indices: 3232921--3232992 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
3232911 CATATTATGA
** *
3232921 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAACGTAT
*
3232950 TACATGACATGAATTCATATTATACGTAT
1 TACATGACATGAATTCATATTAAACGTAT
3232979 TACATGACATGAAT
1 TACATGACATGAAT
3232993 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAACGTAT
Found at i:3233049 original size:30 final size:29
Alignment explanation
Indices: 3233006--3233083 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
3232996 CAGAAAAAGT
*
3233006 TATATGCACTATGTGATAAAGGTATGTAAA
1 TATATGC-CTATGTGATAAAGGTATGGAAA
* *
3233036 TGATATGCCTATGTGTTAAAGTTATGGAAA
1 T-ATATGCCTATGTGATAAAGGTATGGAAA
* *
3233066 TACTATGTCTACGTGATA
1 TA-TATGCCTATGTGATA
3233084 TGAACTACGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (29 bp):
TATATGCCTATGTGATAAAGGTATGGAAA
Found at i:3233360 original size:22 final size:22
Alignment explanation
Indices: 3233286--3233352 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
3233276 TTATGGACAT
3233286 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
3233308 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
3233330 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
3233352 A
1 A
3233353 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:3237891 original size:17 final size:19
Alignment explanation
Indices: 3237852--3237898 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
3237842 AATAGCCTGG
3237852 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
3237871 TGCATCGGTGCAT-GA-AA
1 TGCATCGATGCATGGAGAA
3237888 TGCATTCGATG
1 TGCA-TCGATG
3237899 TTCAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 12 0.48
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:3240616 original size:24 final size:23
Alignment explanation
Indices: 3240544--3240624 Score: 87
Period size: 24 Copynumber: 3.6 Consensus size: 23
3240534 GAATGGTCTT
* *
3240544 ATGCATCGATGCATATTCAAGGC
1 ATGCATCGATGCACATTCAAGGG
* *
3240567 ATGCATCGGTG--CA-TCATGCGG
1 ATGCATCGATGCACATTCAAG-GG
3240588 ATGCATCGATGCACATTCAAAGGG
1 ATGCATCGATGCACATTC-AAGGG
3240612 ATGCATCGATGCA
1 ATGCATCGATGCA
3240625 TTGTTAAGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 12 0.26
23 12 0.26
24 17 0.36
25 2 0.04
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (23 bp):
ATGCATCGATGCACATTCAAGGG
Found at i:3241579 original size:27 final size:27
Alignment explanation
Indices: 3241549--3241601 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
3241539 TAAAGCAATG
3241549 AGCCAATCATGGATCTATATAATTTAT
1 AGCCAATCATGGATCTATATAATTTAT
3241576 AGCCAATCATGGATCTATATAATTTA
1 AGCCAATCATGGATCTATATAATTTA
3241602 ACATCTACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (27 bp):
AGCCAATCATGGATCTATATAATTTAT
Found at i:3244713 original size:17 final size:19
Alignment explanation
Indices: 3244674--3244720 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
3244664 AATAGCCTGG
3244674 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
3244693 TGCATCGGTGCAT-GA-AA
1 TGCATCGATGCATGGAGAA
3244710 TGCATTCGATG
1 TGCA-TCGATG
3244721 TTCAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 12 0.48
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:3244740 original size:64 final size:63
Alignment explanation
Indices: 3244627--3244771 Score: 179
Period size: 64 Copynumber: 2.3 Consensus size: 63
3244617 GTGCACTAAG
* * * *
3244627 GATGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGA-
1 GATGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAATA-CATGGTGCATCGATGCATGGAC
3244690 GAATGCATCGGTGCATGAAATGCATTCGATG-TTCAATTAAAT-CATAGGTGCATCGATGCATGG
1 G-ATGCATCGGTGCATGAAATGCATTCGATGTTTCAA--AAATACAT-GGTGCATCGATGCATGG
3244753 AC
62 AC
3244755 TGATGCATCGGTGCATG
1 -GATGCATCGGTGCATG
3244772 CCTTTGAAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
63 7 0.10
64 45 0.62
65 19 0.26
66 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (63 bp):
GATGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAATACATGGTGCATCGATGCATGGAC
Found at i:3244958 original size:12 final size:12
Alignment explanation
Indices: 3244941--3244976 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
3244931 ATCGAATATA
3244941 ATTTGTAAAATC
1 ATTTGTAAAATC
3244953 ATTTGTAAAATC
1 ATTTGTAAAATC
3244965 ATTTGTAAAATC
1 ATTTGTAAAATC
3244977 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
ATTTGTAAAATC
Found at i:3254756 original size:30 final size:30
Alignment explanation
Indices: 3254720--3254970 Score: 172
Period size: 30 Copynumber: 8.5 Consensus size: 30
3254710 GGGAGCTGGC
*** *
3254720 GGTGACTTGTATGTGTATGGAGGTGGTGGA
1 GGTGACTTGTATACATATGGAGGTGGAGGA
** * * * *
3254750 GGTGACTCATAAACGTATGGAGGAGGTGGA
1 GGTGACTTGTATACATATGGAGGTGGAGGA
* * * * *
3254780 GGTGACTTATAAACGTACGGAGGCGGAGGA
1 GGTGACTTGTATACATATGGAGGTGGAGGA
3254810 GGTGACTTGTATACATATGGA---GGAGGA
1 GGTGACTTGTATACATATGGAGGTGGAGGA
* * **
3254837 GGTGATTTGTACT-TATACAGAGGTGGAGGA
1 GGTGACTTGTA-TACATATGGAGGTGGAGGA
* * * *
3254867 GGTGATTTGTATACGTATGGAGGTGGTGGT
1 GGTGACTTGTATACATATGGAGGTGGAGGA
* *
3254897 GGTGACTTGTACT-CATATGGAGGAGGATGA
1 GGTGACTTGTA-TACATATGGAGGTGGAGGA
* * *
3254927 GGTGATTTGTACT-TATAAGGAGGTGGAGGA
1 GGTGACTTGTA-TACATATGGAGGTGGAGGA
*
3254957 GGTGGCTTGTATAC
1 GGTGACTTGTATAC
3254971 GTACGGAAGT
Statistics
Matches: 176, Mismatches: 38, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
27 21 0.12
28 1 0.01
29 2 0.01
30 151 0.86
31 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.40, T:0.28
Consensus pattern (30 bp):
GGTGACTTGTATACATATGGAGGTGGAGGA
Found at i:3254841 original size:57 final size:57
Alignment explanation
Indices: 3254771--3254889 Score: 139
Period size: 57 Copynumber: 2.1 Consensus size: 57
3254761 AACGTATGGA
* * *
3254771 GGAGGTGGAGGTGACTTATAAACGTACGGAGGCGGAGGAGGTGACTTGTATACATAT
1 GGAGGAGGAGGTGACTTATAAACATACAGAGGCGGAGGAGGTGACTTGTATACATAT
* * *** * * *
3254828 GGAGGAGGAGGTGATTTGTACTTATACAGAGGTGGAGGAGGTGATTTGTATACGTAT
1 GGAGGAGGAGGTGACTTATAAACATACAGAGGCGGAGGAGGTGACTTGTATACATAT
3254885 GGAGG
1 GGAGG
3254890 TGGTGGTGGT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.27, C:0.08, G:0.40, T:0.25
Consensus pattern (57 bp):
GGAGGAGGAGGTGACTTATAAACATACAGAGGCGGAGGAGGTGACTTGTATACATAT
Found at i:3254949 original size:117 final size:117
Alignment explanation
Indices: 3254739--3254955 Score: 256
Period size: 117 Copynumber: 1.9 Consensus size: 117
3254729 TATGTGTATG
* * *
3254739 GAGGTGGTGGAGGTGACTCATAAACGTATGGAGGAGGTGGAGGTGACTTATAAACGTACGGAGGC
1 GAGGTGGAGGAGGTGACTCATAAACGTATGGAGGAGGTGGAGGTGACTTATAAACATACGGAGGA
*
3254804 GGAGGAGGTGACTTGTATACATATGGAGGAGGAGGTGATTTGTACTTATACA
66 GGAGGAGGTGACTTGTATACATAAGGAGGAGGAGGTGATTTGTACTTATACA
* ** * * * * ** *
3254856 GAGGTGGAGGAGGTGATTTGTATACGTATGGAGGTGGTGGTGGTGACTTGTACTCATATGGAGGA
1 GAGGTGGAGGAGGTGACTCATAAACGTATGGAGGAGGTGGAGGTGACTTATAAACATACGGAGGA
* * * *
3254921 GGATGAGGTGATTTGTACT-TATAAGGAGGTGGAGG
66 GGAGGAGGTGACTTGTA-TACATAAGGAGGAGGAGG
3254956 AGGTGGCTTG
Statistics
Matches: 81, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
117 80 0.99
118 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.41, T:0.26
Consensus pattern (117 bp):
GAGGTGGAGGAGGTGACTCATAAACGTATGGAGGAGGTGGAGGTGACTTATAAACATACGGAGGA
GGAGGAGGTGACTTGTATACATAAGGAGGAGGAGGTGATTTGTACTTATACA
Found at i:3254983 original size:87 final size:87
Alignment explanation
Indices: 3254777--3255011 Score: 282
Period size: 87 Copynumber: 2.7 Consensus size: 87
3254767 TGGAGGAGGT
* * * * *
3254777 GGAGGTGACTTATAAACGTACGGAGGCGGAGGAGGTGACTTGTA-TACATATGGAGGA-G-GAGG
1 GGAGGTGACTTGTATACGTACGGA-G-AGTGGTGGTGACTTGTACT-CATATGGAGGAGGAGAGG
3254839 TGATTTGTACTTATACAGAGGTGGA
63 TGATTTGTACTTATACAGAGGTGGA
* * *
3254864 GGAGGTGATTTGTATACGTATGGAGGTGGTGGTGGTGACTTGTACTCATATGGAGGAGGATGAGG
1 GGAGGTGACTTGTATACGTACGGA-G-AGTGGTGGTGACTTGTACTCATATGGAGGAGGA-GAGG
3254929 TGATTTGTACTTATA-AGGAGGTGGA
63 TGATTTGTACTTATACA-GAGGTGGA
* *
3254954 GGAGGTGGCTTGTATACGTACGGA-AGTGGTGGTGACTTATACTCATATGGAGGAGGAG
1 GGAGGTGACTTGTATACGTACGGAGAGTGGTGGTGACTTGTACTCATATGGAGGAGGAG
3255012 GAGGAGGTGT
Statistics
Matches: 131, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
86 1 0.01
87 79 0.60
88 2 0.02
89 1 0.01
90 48 0.37
ACGTcount: A:0.26, C:0.08, G:0.39, T:0.27
Consensus pattern (87 bp):
GGAGGTGACTTGTATACGTACGGAGAGTGGTGGTGACTTGTACTCATATGGAGGAGGAGAGGTGA
TTTGTACTTATACAGAGGTGGA
Found at i:3255020 original size:90 final size:88
Alignment explanation
Indices: 3254828--3255015 Score: 281
Period size: 90 Copynumber: 2.1 Consensus size: 88
3254818 GTATACATAT
* * *
3254828 GGAGGAGGAGGTGATTTGTACTTATACAGAGGTGGAGGAGGTGATTTGTATACGTATGGAGGTGG
1 GGAGGAGGAGGTGATTTGTACTTATACAGAGGTGGAGGAGGTGACTTGTATACGTACGGA-G-AG
*
3254893 TGGTGGTGACTTGTACTCATATGGA
64 TGGTGGTGACTTATACTCATATGGA
* *
3254918 GGAGGATGAGGTGATTTGTACTTATA-AGGAGGTGGAGGAGGTGGCTTGTATACGTACGGA-AGT
1 GGAGGAGGAGGTGATTTGTACTTATACA-GAGGTGGAGGAGGTGACTTGTATACGTACGGAGAGT
3254981 GGTGGTGACTTATACTCATATGGA
65 GGTGGTGACTTATACTCATATGGA
3255005 GGAGGAGGAGG
1 GGAGGAGGAGG
3255016 AGGTGTTGGC
Statistics
Matches: 90, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
87 35 0.39
89 1 0.01
90 54 0.60
ACGTcount: A:0.24, C:0.07, G:0.41, T:0.28
Consensus pattern (88 bp):
GGAGGAGGAGGTGATTTGTACTTATACAGAGGTGGAGGAGGTGACTTGTATACGTACGGAGAGTG
GTGGTGACTTATACTCATATGGA
Found at i:3255230 original size:78 final size:78
Alignment explanation
Indices: 3255100--3255257 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 78
3255090 AAGGAGAAGA
* *
3255100 TGAGTAGTACTCAGGAGATGGTGGAGACTCATATTCGTATGGTGCAGGTGCAGGTGATGCATAGT
1 TGAGTAGTACTCAGGAGATGGTGGAGACTCATATTCATATGGTGCAGATGCAGGTGATGCATAGT
*
3255165 AGTACGGTGGTGG
66 AGTACGGAGGTGG
*
3255178 TGAGTAGTACTCAGGAGATGGTGGAGACTCATATTCATATGGTGCATATGCAGGTGATGCATAGT
1 TGAGTAGTACTCAGGAGATGGTGGAGACTCATATTCATATGGTGCAGATGCAGGTGATGCATAGT
3255243 AGTACGGAGGTGG
66 AGTACGGAGGTGG
3255256 TG
1 TG
3255258 GTGGATGAGG
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.25, C:0.11, G:0.37, T:0.27
Consensus pattern (78 bp):
TGAGTAGTACTCAGGAGATGGTGGAGACTCATATTCATATGGTGCAGATGCAGGTGATGCATAGT
AGTACGGAGGTGG
Found at i:3255566 original size:11 final size:12
Alignment explanation
Indices: 3255550--3255578 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3255540 TGATAATAGT
3255550 AATTTT-AAATG
1 AATTTTAAAATG
3255561 AATTTTAAAATG
1 AATTTTAAAATG
3255573 AATTTT
1 AATTTT
3255579 TTTGCTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
AATTTTAAAATG
Found at i:3264599 original size:33 final size:33
Alignment explanation
Indices: 3264562--3264628 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
3264552 TAGAAAACTG
3264562 ATAATCTATAAAACACATAAAGTTAGCAGTAAC
1 ATAATCTATAAAACACATAAAGTTAGCAGTAAC
3264595 ATAATCTATAAAACACATAAAGTTAGCAGTAAC
1 ATAATCTATAAAACACATAAAGTTAGCAGTAAC
3264628 A
1 A
3264629 CAAGTAGCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (33 bp):
ATAATCTATAAAACACATAAAGTTAGCAGTAAC
Found at i:3282208 original size:47 final size:47
Alignment explanation
Indices: 3282139--3282234 Score: 158
Period size: 47 Copynumber: 2.0 Consensus size: 47
3282129 TGTAGAAATC
*
3282139 GCAGGCTTCAGGAATCATAGATACTTGGTAAGCCATGGA-AGATCCTT
1 GCAGGCTTCAGAAATCATAGATACTTGGTAAGCCAT-GACAGATCCTT
*
3282186 GCAGGCTTCAGAAATCATAGATACTTGGTAAGCTATGACAGATCCTT
1 GCAGGCTTCAGAAATCATAGATACTTGGTAAGCCATGACAGATCCTT
3282233 GC
1 GC
3282235 TGTCTTTCAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 2 0.04
47 44 0.96
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (47 bp):
GCAGGCTTCAGAAATCATAGATACTTGGTAAGCCATGACAGATCCTT
Found at i:3283475 original size:20 final size:20
Alignment explanation
Indices: 3283439--3283476 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3283429 ACAATGTTTT
* *
3283439 AAAACCTTCTATGATGTTCC
1 AAAACCTTCCATAATGTTCC
3283459 AAAACCTTCCATAATGTT
1 AAAACCTTCCATAATGTT
3283477 TCAGAACACT
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:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (20 bp):
AAAACCTTCCATAATGTTCC
Found at i:3283548 original size:20 final size:20
Alignment explanation
Indices: 3283525--3283576 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3283515 TTCCGAAGTA
3283525 TTCTAGAACTTTCCATAAG-G
1 TTCTAGAACTTTCCAT-AGTG
* * *
3283545 TTCTAGATCTTTCTATTGTG
1 TTCTAGAACTTTCCATAGTG
3283565 TTCTAGAACTTT
1 TTCTAGAACTTT
3283577 TCGTTATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.46
Consensus pattern (20 bp):
TTCTAGAACTTTCCATAGTG
Found at i:3291395 original size:15 final size:15
Alignment explanation
Indices: 3291375--3291423 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
3291365 TGAAAATAAA
3291375 AAATTTTATATTCTT
1 AAATTTTATATTCTT
* *
3291390 AAATTTT-TAAT-AT
1 AAATTTTATATTCTT
3291403 -AATTTTATATTCTT
1 AAATTTTATATTCTT
*
3291417 ACATTTT
1 AAATTTT
3291424 TAATAAATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 4 0.15
15 12 0.46
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
AAATTTTATATTCTT
Found at i:3291409 original size:27 final size:26
Alignment explanation
Indices: 3291375--3291437 Score: 99
Period size: 27 Copynumber: 2.4 Consensus size: 26
3291365 TGAAAATAAA
3291375 AAATTTTATATTCTTAAATTTTTAAT
1 AAATTTTATATTCTTAAATTTTTAAT
*
3291401 ATAATTTTATATTCTTACATTTTTAAT
1 A-AATTTTATATTCTTAAATTTTTAAT
*
3291428 AAATTGTATA
1 AAATTTTATA
3291438 GAAAATGACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (26 bp):
AAATTTTATATTCTTAAATTTTTAAT
Found at i:3293507 original size:20 final size:21
Alignment explanation
Indices: 3293472--3293524 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
3293462 ATAATATTTA
3293472 TTTTAATATATAAAATAAATT
1 TTTTAATATATAAAATAAATT
* *
3293493 TTTTAATAT-TTAAATAAAAT
1 TTTTAATATATAAAATAAATT
* *
3293513 ATATAATATATA
1 TTTTAATATATA
3293525 CTAAAGTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTTAATATATAAAATAAATT
Found at i:3296129 original size:41 final size:40
Alignment explanation
Indices: 3296084--3296231 Score: 133
Period size: 41 Copynumber: 3.6 Consensus size: 40
3296074 TAAACAATAA
*
3296084 CGGCGTTTATAGTAAAACGCCGCAATATAGTAG-ACATTTAG
1 CGGCGTTTATAGTAAAACGCCGCAATATAGT-GTA-ATATAG
*
3296125 CGGCGTTTTTAGCTAAAAACGCCGCAATATAGTGTAATATAG
1 CGGCGTTTATAG-T-AAAACGCCGCAATATAGTGTAATATAG
* * * * *
3296167 CGACGCTTATTGTATAAACGCCGCAAAAATA-TGTGATATAG
1 CGGCGTTTATAGTA-AAACGCCGC-AATATAGTGTAATATAG
*
3296208 TGGCGTTT-T-GTAAAAACGCCGCAA
1 CGGCGTTTATAGT-AAAACGCCGCAA
3296232 AATGTTAAAT
Statistics
Matches: 90, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
38 2 0.02
39 11 0.12
40 3 0.03
41 35 0.39
42 20 0.22
43 19 0.21
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (40 bp):
CGGCGTTTATAGTAAAACGCCGCAATATAGTGTAATATAG
Found at i:3297325 original size:57 final size:57
Alignment explanation
Indices: 3297258--3297445 Score: 367
Period size: 57 Copynumber: 3.3 Consensus size: 57
3297248 GTGAAGACTG
*
3297258 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTTTTAAGTAGT
1 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
3297315 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
1 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
3297372 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
1 TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
3297429 TTTATGCATAAGTACTT
1 TTTATGCATAAGTACTT
3297446 CTGTTTTAAT
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 130 1.00
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (57 bp):
TTTATGCATAAGTACTTTAATGTTTCTAAATTATAATGTATTTTGTTGTTAAGTAGT
Found at i:3297808 original size:43 final size:43
Alignment explanation
Indices: 3297708--3297824 Score: 138
Period size: 43 Copynumber: 2.8 Consensus size: 43
3297698 ATATTTATAT
*
3297708 TTTAGTGGCGTTT-GTATGAAAACGCCGCTACGTCCTTTCCTAC
1 TTTAGTGGCGTTTCGTATGAAAACGCCGCTAAGTCC-TTCCTAC
*
3297751 TTTAGTGGCG-TTCGTATGAAAACGCCGCTATAG-CC-TCGTAC
1 TTTAGTGGCGTTTCGTATGAAAACGCCGCTA-AGTCCTTCCTAC
*
3297792 TTTAGTGGCGTTTTCGTA-G-AAACGCCGCAAAGT
1 TTTAGTGGCG-TTTCGTATGAAAACGCCGCTAAGT
3297825 ATTAGTAATT
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
40 2 0.03
41 25 0.38
42 3 0.05
43 35 0.53
44 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (43 bp):
TTTAGTGGCGTTTCGTATGAAAACGCCGCTAAGTCCTTCCTAC
Found at i:3298207 original size:43 final size:43
Alignment explanation
Indices: 3298131--3298254 Score: 113
Period size: 43 Copynumber: 2.9 Consensus size: 43
3298121 AGACGCCGCC
* * * * *
3298131 AAATCAAACACATATTGCGGCGTTAAAGCTAAAAATGCCGCTAA
1 AAATC-AACACATATTGCGGCGTTTATGATAAAAACGCCACTAA
** * * *
3298175 ACCTTAACACTTATTGCGGCGTTTGTGATAAAAACGCCACTAA
1 AAATCAACACATATTGCGGCGTTTATGATAAAAACGCCACTAA
* * * *
3298218 AAATCAACACCTACTGCGGCGTTTCTGAGAAAAACGC
1 AAATCAACACATATTGCGGCGTTTATGATAAAAACGC
3298255 TGCTATAAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
43 61 0.97
44 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (43 bp):
AAATCAACACATATTGCGGCGTTTATGATAAAAACGCCACTAA
Found at i:3298265 original size:43 final size:44
Alignment explanation
Indices: 3298180--3298284 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
3298170 GCTAAACCTT
* * * *
3298180 AACACTTATTGCGGCGTTTGTGATAAAAACGCCACTAAAAATC-
1 AACACCTACTGCGGCGTTTCTGAGAAAAACGCCACTAAAAATCG
** *
3298223 AACACCTACTGCGGCGTTTCTGAGAAAAACGCTGCTATAAATCG
1 AACACCTACTGCGGCGTTTCTGAGAAAAACGCCACTAAAAATCG
*
3298267 AA-ACCTACTGTGGCGTTT
1 AACACCTACTGCGGCGTTT
3298285 GTCTTCCAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 51 0.96
44 2 0.04
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (44 bp):
AACACCTACTGCGGCGTTTCTGAGAAAAACGCCACTAAAAATCG
Found at i:3298325 original size:43 final size:43
Alignment explanation
Indices: 3298278--3298413 Score: 211
Period size: 43 Copynumber: 3.2 Consensus size: 43
3298268 AACCTACTGT
*
3298278 GGCGTTTGTCTTCCAAATGCCGCTAAATATCAACATCTATTGC
1 GGCGTTTGTCTTCCAAACGCCGCTAAATATCAACATCTATTGC
**
3298321 GGCGTTTGTCTTCCAAACGCCGCTAAATATCAACATCTATTAT
1 GGCGTTTGTCTTCCAAACGCCGCTAAATATCAACATCTATTGC
* *
3298364 GGCATTTGTCTAT-CAAACGCCGCTAAATATCAACACCTATTGC
1 GGCGTTTGTCT-TCCAAACGCCGCTAAATATCAACATCTATTGC
3298407 GGCGTTT
1 GGCGTTT
3298414 TTTCTTGAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 83 0.99
44 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (43 bp):
GGCGTTTGTCTTCCAAACGCCGCTAAATATCAACATCTATTGC
Found at i:3298339 original size:86 final size:86
Alignment explanation
Indices: 3298206--3298413 Score: 224
Period size: 86 Copynumber: 2.4 Consensus size: 86
3298196 TTTGTGATAA
* * * * ***** *
3298206 AAACGCCACTAAAAATCAACACCTACTGCGGCGTTTCTGAGAAAAACGCTGCTATAA-ATCGAA-
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTA-AATATC-AAC
* *
3298269 ACCTACTGTGGCGTTTGTCT-TCC
64 ACCTACTATGGCATTTGTCTAT-C
* * *
3298292 AAATGCCGCTAAATATCAACATCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATCAACAT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATCAACAC
*
3298357 CTATTATGGCATTTGTCTATC
66 CTACTATGGCATTTGTCTATC
3298378 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
3298414 TTTCTTGAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
85 4 0.04
86 96 0.95
87 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (86 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTTCCAAACGCCGCTAAATATCAACAC
CTACTATGGCATTTGTCTATC
Found at i:3299633 original size:20 final size:20
Alignment explanation
Indices: 3299608--3299647 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3299598 GAGGTCTTGA
3299608 GTTCGACTCTCAACGACAGC
1 GTTCGACTCTCAACGACAGC
3299628 GTTCGACTCTCAACGACAGC
1 GTTCGACTCTCAACGACAGC
3299648 AGTGTTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.35, G:0.20, T:0.20
Consensus pattern (20 bp):
GTTCGACTCTCAACGACAGC
Found at i:3300274 original size:18 final size:19
Alignment explanation
Indices: 3300251--3300300 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
3300241 ACCAATATTT
3300251 TTTTTTTATTTTTTTTAC-
1 TTTTTTTATTTTTTTTACA
* **
3300269 TTTTTTTAATAATTTTACA
1 TTTTTTTATTTTTTTTACA
3300288 TTTTTTTATTTTT
1 TTTTTTTATTTTT
3300301 ATAAATGTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTTATTTTTTTTACA
Found at i:3312717 original size:15 final size:15
Alignment explanation
Indices: 3312697--3312725 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3312687 TTTTATTAAT
3312697 TCTCGTGGTAAGATC
1 TCTCGTGGTAAGATC
3312712 TCTCGTGGTAAGAT
1 TCTCGTGGTAAGAT
3312726 TTAATTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (15 bp):
TCTCGTGGTAAGATC
Found at i:3323538 original size:42 final size:42
Alignment explanation
Indices: 3323476--3323568 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
3323466 ACTTAATAAG
* * *
3323476 TCCTTCGGGCTATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTAGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
*
3323518 TCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTAGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
3323560 TCCTTAGGG
1 TCCTTAGGG
3323569 TAATTTGTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (42 bp):
TCCTTAGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
Found at i:3323659 original size:22 final size:22
Alignment explanation
Indices: 3323628--3323703 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
3323618 TGTCATTAGT
* *
3323628 AAGTCTTTCGAGCATGATGATG
1 AAGTCCTTCGAGCATGATGATC
* *
3323650 AAGTCCTTCGGGCCATCA-G--C
1 AAGTCCTTCGAG-CATGATGATC
* * *
3323670 AAGTCTTTCAAGCATGATGATT
1 AAGTCCTTCGAGCATGATGATC
3323692 AAGTCCTTCGAG
1 AAGTCCTTCGAG
3323704 AAATTTGTAA
Statistics
Matches: 39, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
19 4 0.10
20 10 0.26
22 21 0.54
23 4 0.10
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (22 bp):
AAGTCCTTCGAGCATGATGATC
Found at i:3323781 original size:22 final size:21
Alignment explanation
Indices: 3323749--3323823 Score: 55
Period size: 22 Copynumber: 3.5 Consensus size: 21
3323739 AACCCATCAG
*
3323749 TAAGTCTTTCGAGCATGATGA
1 TAAGTCCTTCGAGCATGATGA
* *
3323770 TGAAGTCCTTCGGGCCATCA-G-
1 T-AAGTCCTTCGAG-CATGATGA
* *
3323791 TAAGTCTTTTGAGCATGATGA
1 TAAGTCCTTCGAGCATGATGA
*
3323812 TTAAATCCTTCG
1 -TAAGTCCTTCG
3323824 GGTAATTTGT
Statistics
Matches: 39, Mismatches: 10, Indels: 9
0.67 0.17 0.16
Matches are distributed among these distances:
19 4 0.10
20 10 0.26
21 2 0.05
22 19 0.49
23 4 0.10
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (21 bp):
TAAGTCCTTCGAGCATGATGA
Found at i:3323789 original size:42 final size:42
Alignment explanation
Indices: 3323742--3323825 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
3323732 TGAAACAAAC
*
3323742 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* *
3323784 CCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
3323826 TAATTTGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (42 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
Found at i:3323836 original size:42 final size:42
Alignment explanation
Indices: 3323625--3323825 Score: 137
Period size: 42 Copynumber: 4.9 Consensus size: 42
3323615 AAGTGTCATT
* *
3323625 AGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATC
1 AGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCAATC
* * * * * * *
3323667 AGCAAGTCTTTCAAGCATGATGATTAAGTCCTTCGAGAAATT
1 AGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCAATC
* * * * *** *
3323709 TGTAAG-CCTTC-ACGGAAGA-GTAGTGAAA-CAAAC---CCATC
1 AGTAAGTCTTTCGA-GCATGATG-A-TGAAATCCTTCGGGCAATC
* *
3323747 AGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATC
1 AGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCAATC
* *
3323789 AGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGG
1 AGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
3323826 TAATTTGTAA
Statistics
Matches: 118, Mismatches: 31, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
38 11 0.09
39 11 0.09
40 4 0.03
41 11 0.09
42 81 0.69
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (42 bp):
AGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCAATC
Found at i:3323842 original size:122 final size:122
Alignment explanation
Indices: 3323487--3323901 Score: 533
Period size: 122 Copynumber: 3.3 Consensus size: 122
3323477 CCTTCGGGCT
* * * *
3323487 ATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGA
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
*
3323552 TGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGTGAACCCATAAGTAA
66 TGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACGGAAGAGTAGTG-A---AA--C---A--AA
**
3323617 GTGTC
120 --CCC
* * * *
3323622 ATTAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGCAAGTCTTTCAAGCATGA
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * *
3323687 TGATTAAGTCCTTCGAGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAACAAACCC
66 TGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAACAAACCC
* *
3323744 ATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGA
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * *
3323809 TGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
66 TGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAACAAACCC
*
3323866 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTT
3323902 TGGGTAATTT
Statistics
Matches: 254, Mismatches: 26, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
122 147 0.58
124 2 0.01
126 1 0.00
129 1 0.00
131 2 0.01
134 1 0.00
135 100 0.39
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (122 bp):
ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
TGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAACAAACCC
Found at i:3323885 original size:80 final size:80
Alignment explanation
Indices: 3323784--3323996 Score: 381
Period size: 80 Copynumber: 2.7 Consensus size: 80
3323774 GTCCTTCGGG
*
3323784 CCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
3323849 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAT
* *
3323864 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTAATTTGTAAGCCTTCACCGATG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
3323929 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAT
* *
3323944 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTTGTAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAG
3323997 TCTTTCGAGC
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 127 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
AGTAGTGAAGCAAAT
Found at i:3324489 original size:53 final size:53
Alignment explanation
Indices: 3324409--3324788 Score: 537
Period size: 53 Copynumber: 7.2 Consensus size: 53
3324399 GAATCACACT
* * *
3324409 AGAAGATTGTTCAAGTTCTACTCCCTGAATCAAGAGGGAGCGAACCCGTAGGC
1 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
3324462 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
1 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * * *
3324515 AGAAGACTGTTTGAGTTCTACTCCCTAAAGCAAGAGGGAACGAACCTGTAGGC
1 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
*
3324568 AGAAGATTATTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
1 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * * *
3324621 AGAAGACTGTTTGAGTTCTACTCCCTAAAGCAAAAGGGAGCGAACCCGTAGGT
1 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* *
3324674 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGGGAACCCATAGGC
1 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
** * * *
3324727 AGAAGGCTATTCGAGTTCTACTCCCTAAAGCAAGAGGAAGCGAACCCGCTAGTC
1 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGGC
3324781 -GAAGATTA
1 AGAAGATTA
3324789 CTCAAAGAAG
Statistics
Matches: 286, Mismatches: 40, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 282 0.99
54 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (53 bp):
AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
Found at i:3338993 original size:4 final size:4
Alignment explanation
Indices: 3338984--3339146 Score: 326
Period size: 4 Copynumber: 40.8 Consensus size: 4
3338974 TTTGGTCAGT
3338984 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3339032 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3339080 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3339128 ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATA
3339147 TACATATGTA
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 159 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:3342512 original size:21 final size:21
Alignment explanation
Indices: 3342470--3342512 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3342460 GAACTGTCAT
* * *
3342470 GTCAACATTGTGGATTCTCAC
1 GTCAACATCGTGAATTCGCAC
*
3342491 GTCAACATCGTGAATTGGCAC
1 GTCAACATCGTGAATTCGCAC
3342512 G
1 G
3342513 CCAGTACTGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
GTCAACATCGTGAATTCGCAC
Found at i:3343152 original size:19 final size:19
Alignment explanation
Indices: 3343128--3343171 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3343118 TTGGTTGGGG
**
3343128 GAATGTGAGATTCTTCCGA
1 GAATGTGAGATTCCCCCGA
3343147 GAATGTGAGATTCCCCCGA
1 GAATGTGAGATTCCCCCGA
3343166 GAATGT
1 GAATGT
3343172 AATCCACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (19 bp):
GAATGTGAGATTCCCCCGA
Found at i:3344283 original size:23 final size:23
Alignment explanation
Indices: 3344256--3344302 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3344246 AAAACCTAAG
3344256 TTCATCCCTAATCCTCTTCAAGT
1 TTCATCCCTAATCCTCTTCAAGT
3344279 TTCATCCCTAATCCTCTTCAAGT
1 TTCATCCCTAATCCTCTTCAAGT
3344302 T
1 T
3344303 CCTTTTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.34, G:0.04, T:0.40
Consensus pattern (23 bp):
TTCATCCCTAATCCTCTTCAAGT
Found at i:3346058 original size:39 final size:39
Alignment explanation
Indices: 3346013--3346091 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
3346003 TTTAAAAATT
3346013 CAATTTGAACTACTTACCTTTGATTGATTGAAATTACCC
1 CAATTTGAACTACTTACCTTTGATTGATTGAAATTACCC
3346052 CAATTTGAACTACTTACCTTTGATTGATTGAAATTACCC
1 CAATTTGAACTACTTACCTTTGATTGATTGAAATTACCC
3346091 C
1 C
3346092 TCCGATCGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (39 bp):
CAATTTGAACTACTTACCTTTGATTGATTGAAATTACCC
Found at i:3349553 original size:19 final size:20
Alignment explanation
Indices: 3349526--3349583 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
3349516 CGTTTGAACA
*
3349526 AGGGAGAATCGGTA-CCCCT
1 AGGGGGAATCGGTATCCCCT
3349545 AGGGGGAATCGGTATCCCCTT
1 AGGGGGAATCGGTATCCCC-T
*
3349566 GGGGGGAAATCGGT-TCCC
1 AGGGGG-AATCGGTATCCC
3349584 TCTGAGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.38
20 4 0.12
21 10 0.29
22 7 0.21
ACGTcount: A:0.21, C:0.24, G:0.36, T:0.19
Consensus pattern (20 bp):
AGGGGGAATCGGTATCCCCT
Found at i:3349583 original size:21 final size:20
Alignment explanation
Indices: 3349527--3349583 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
3349517 GTTTGAACAA
*
3349527 GGGAGAATCGGTACCCCTAGG
1 GGGA-AATCGGTTCCCCTAGG
*
3349548 GGG-AATCGGTATCCCCTTGGG
1 GGGAAATCGGT-TCCCC-TAGG
3349569 GGGAAATCGGTTCCC
1 GGGAAATCGGTTCCC
3349584 TCTGAGCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 13 0.42
22 7 0.23
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.19
Consensus pattern (20 bp):
GGGAAATCGGTTCCCCTAGG
Found at i:3350234 original size:17 final size:17
Alignment explanation
Indices: 3350209--3350242 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3350199 CAAACAAATT
*
3350209 CAAAGTCAAACAATCCA
1 CAAAATCAAACAATCCA
*
3350226 CAAAATCAAACATTCCA
1 CAAAATCAAACAATCCA
3350243 AAATATTCAA
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:0.53, C:0.29, G:0.03, T:0.15
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:3352193 original size:19 final size:19
Alignment explanation
Indices: 3352165--3352201 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3352155 AGAACCCTTA
*
3352165 GGGGGTATCGATTCCCCTG
1 GGGGGAATCGATTCCCCTG
*
3352184 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
3352202 TCAAGGGGGT
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:0.11, C:0.27, G:0.38, T:0.24
Consensus pattern (19 bp):
GGGGGAATCGATTCCCCTG
Found at i:3355969 original size:22 final size:21
Alignment explanation
Indices: 3355927--3355966 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3355917 GAATTTATTC
*
3355927 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
3355948 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3355967 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:3365919 original size:2 final size:2
Alignment explanation
Indices: 3365830--3365903 Score: 127
Period size: 2 Copynumber: 38.5 Consensus size: 2
3365820 TATTTTTGGT
3365830 TA TA TA T- TA TA TA TA TA TA -A 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
3365870 TA TA TA TA TA TA TA -A 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 T
3365904 GTCAACATGA
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 66 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3365919 original size:29 final size:27
Alignment explanation
Indices: 3365830--3365903 Score: 123
Period size: 27 Copynumber: 2.7 Consensus size: 27
3365820 TATTTTTGGT
3365830 TATATAT-TATATATATATAATATATATA
1 TATATATATATATATATAT-ATATATA-A
3365858 TATATATATATATATATATATATATAA
1 TATATATATATATATATATATATATAA
3365885 TATATATATATATATATAT
1 TATATATATATATATATAT
3365904 GTCAACATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
27 20 0.44
28 14 0.31
29 11 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATATATATATATATATATATATATAA
Found at i:3369608 original size:21 final size:21
Alignment explanation
Indices: 3369582--3369650 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
3369572 CGGTGGCATA
3369582 TGAAATGGTTGCGATGCCATC
1 TGAAATGGTTGCGATGCCATC
* *
3369603 TGAAATGGTTGTGATTCCATC
1 TGAAATGGTTGCGATGCCATC
* *
3369624 TGAAACGATTGCGATGCCATC
1 TGAAATGGTTGCGATGCCATC
3369645 TGAAAT
1 TGAAAT
3369651 AGAAGTGGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (21 bp):
TGAAATGGTTGCGATGCCATC
Found at i:3371296 original size:39 final size:37
Alignment explanation
Indices: 3371210--3371299 Score: 94
Period size: 39 Copynumber: 2.4 Consensus size: 37
3371200 AATCATTCCC
* * *
3371210 CTAATT-AAATAAATAATATATAAATTAAAATTTAAA
1 CTAATTAAAATAAATAATAAATAAATAAAAATTCAAA
3371246 CTAATACTAAAATAAATAAATAAATAAATAAAACATTCACAA
1 CTAAT--TAAAATAAAT-AATAAATAAATAAAA-ATTCA-AA
3371288 -TAATTAAAATAA
1 CTAATTAAAATAA
3371300 TACAATTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
36 5 0.11
38 1 0.02
39 16 0.36
40 13 0.29
41 8 0.18
42 2 0.04
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (37 bp):
CTAATTAAAATAAATAATAAATAAATAAAAATTCAAA
Found at i:3371832 original size:16 final size:17
Alignment explanation
Indices: 3371811--3371848 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3371801 ATGGCGTGAT
3371811 CGGTTAAAAAATT-GAC
1 CGGTTAAAAAATTAGAC
*
3371827 CGGTT-AAAATTTAGAC
1 CGGTTAAAAAATTAGAC
3371843 CGGTTA
1 CGGTTA
3371849 TGTTATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (17 bp):
CGGTTAAAAAATTAGAC
Found at i:3373651 original size:182 final size:182
Alignment explanation
Indices: 3372783--3373638 Score: 1079
Period size: 182 Copynumber: 4.7 Consensus size: 182
3372773 GACTTTTTAG
* * * *
3372783 TTTAATTTCATAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATTCGGTATCGT
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACAC-TTCAACATATCCGGTAACGT
* *
3372848 TTTA-CTGGTTTTGTCAATTTTGGGACATGTTTTATCATATTTTTACCTGTTATATTGTTGTGGA
65 TTTATCTGGTTTTGTC-ATTTTGGGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
*
3372912 TCGATAT-TTTTT-TAAAGTATCGACACTTTATAGGCGCTATAACTTATTCTCT
129 TCGATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
* * *
3372964 TTTAAATTCAGAAAGTTTCGATACCTATATTAAATTATCGACACTTTCAATATATCCGGTAACGT
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACAC-TTCAACATATCCGGTAACGT
* * * *
3373029 TTTA-CTGGTTTTATCAATTTTGAGACATGTTTTATTATATTTTTACCTGTTATATTGTTATGGA
65 TTTATCTGGTTTTGTC-ATTTTGGGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
* * * * * * *
3373093 TCGATACATTTTCATAAAGTGTCGACACTTTTTAAGCGCAATAACTTTTTCTCT
129 TCGATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
* *
3373147 TTTAAATTCAGAAAGTATCGATACTTATATTAAATTATCGACACTTTTAACATATCCGGTAA--T
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACAC-TTCAACATATCCGGTAACGT
* * * *
3373210 TTTTTCAT-GTTTTGTCATTTTTAGGACCTGTTTTATCATATTTTTACCTGTTATATTGGTAAGG
65 TTTATC-TGGTTTTGTCA-TTTTGGGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGG
* *
3373274 ATCGATATATTTTCATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCT
128 ATCGATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
* * *
3373329 TTTAAATTCAGAAAGTGTCGATACTAATATTAAATTATCGACACTTTCAATATATCCAGTAAC-T
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACAC-TTCAACATATCCGGTAACGT
* * ** * *
3373393 TTT-TCCT-GTTTTGTCATTTTTGAGATCAATTTTATCATATTTTTATCTGTTATATTGTTGTGG
65 TTTAT-CTGGTTTTGTCA-TTTTGGGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGG
* *
3373456 ATCGATATATTTTTTTAAAGTATCGACACTTTATAGGCACTATAACTTCTTCTCT
128 ATCGATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
* * *
3373511 TTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCAACAC-TCGACACATATCCGGTAGCG
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTC-A-ACATATCCGGTAACG
* * * * * *
3373575 TTTTATC-GGTTTTGTCATTTTGGGACCGGTTTTGTCATATTTGTACCTATAATATTGCTATGGA
64 TTTTATCTGGTTTTGTCATTTTGGGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
3373639 GCAATCTATT
Statistics
Matches: 593, Mismatches: 70, Indels: 23
0.86 0.10 0.03
Matches are distributed among these distances:
180 2 0.00
181 130 0.22
182 347 0.59
183 113 0.19
184 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.45
Consensus pattern (182 bp):
TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTCAACATATCCGGTAACGTT
TTATCTGGTTTTGTCATTTTGGGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGGATC
GATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
Found at i:3379301 original size:74 final size:74
Alignment explanation
Indices: 3379218--3379364 Score: 217
Period size: 74 Copynumber: 2.0 Consensus size: 74
3379208 AAATAATCGC
** *
3379218 TTTGATTTTT-TTCTTTTAAATGTTTTAATTTAAATA-TTTATTGTAAGACAAAAATTTTCTTTT
1 TTTGATTTTTATTCTTTTAAATGTTTTAATCCAAATATTTTATTGCAAG--AAAAATTTTCTTTT
3379281 AAACATTTTAA
64 AAACATTTTAA
*
3379292 TTTGATTTTTATTCTTTTAAATTTTTTAATCCAAATATTTTATTGCAAGAAAAATTTTCTTTTAA
1 TTTGATTTTTATTCTTTTAAATGTTTTAATCCAAATATTTTATTGCAAGAAAAATTTTCTTTTAA
*
3379357 GCATTTTA
66 ACATTTTA
3379365 GTCCCTAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
74 33 0.50
75 23 0.35
76 10 0.15
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (74 bp):
TTTGATTTTTATTCTTTTAAATGTTTTAATCCAAATATTTTATTGCAAGAAAAATTTTCTTTTAA
ACATTTTAA
Found at i:3384027 original size:25 final size:25
Alignment explanation
Indices: 3383999--3384079 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
3383989 AATATAACAC
3383999 TAACTCTTAGAAAGTTAGATAAAGA
1 TAACTCTTAGAAAGTTAGATAAAGA
* * * *
3384024 TAACTACTAAG-TAGTTTAGCTTAA-A
1 TAACT-CTTAGAAAG-TTAGATAAAGA
*
3384049 TCAACTCTTAGAAAGTTAGATAAGGA
1 T-AACTCTTAGAAAGTTAGATAAAGA
3384075 TAACT
1 TAACT
3384080 ATTAAGTAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
25 23 0.55
26 19 0.45
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (25 bp):
TAACTCTTAGAAAGTTAGATAAAGA
Found at i:3384062 original size:51 final size:51
Alignment explanation
Indices: 3384000--3384100 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
3383990 ATATAACACT
3384000 AACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGCTTAAATC
1 AACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGCTTAAATC
* * *
3384051 AACTCTTAGAAAGTTAGATAAGGATAACTATTAAGTAGTTTAGTTTAAAT
1 AACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGCTTAAAT
3384101 TAAATACTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.34
Consensus pattern (51 bp):
AACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGCTTAAATC
Found at i:3384090 original size:25 final size:24
Alignment explanation
Indices: 3384011--3384090 Score: 56
Period size: 25 Copynumber: 3.2 Consensus size: 24
3384001 ACTCTTAGAA
*
3384011 AGTTAGATAAAGATAACTACTAAGT
1 AGTTAGAT-AAGATAACTATTAAGT
* * *
3384036 AGTTTAGCTTAA-ATCAACTCTT-AGAA
1 AG-TTAG-ATAAGAT-AACTATTAAG-T
3384062 AGTTAGATAAGGATAACTATTAAGT
1 AGTTAGATAA-GATAACTATTAAGT
3384087 AGTT
1 AGTT
3384091 TAGTTTAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 3 0.07
25 20 0.49
26 17 0.41
27 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (24 bp):
AGTTAGATAAGATAACTATTAAGT
Found at i:3388893 original size:51 final size:51
Alignment explanation
Indices: 3388767--3388907 Score: 178
Period size: 51 Copynumber: 2.8 Consensus size: 51
3388757 GGTTATGCGA
* * * * *
3388767 TAGATAAGGATAATTAATT-AGTATTTTAATATAACACTAACTCTTAGAAAGT
1 TAGATAAGGATAACT-ATTAAGTAGTTTAGTTTAA-ATTAACTCTTAGAAAGT
* *
3388819 TAGA-AAAGATAACTACTAAGTAGTTTAGTTTAAATTAACTCTTAGAAAGT
1 TAGATAAGGATAACTATTAAGTAGTTTAGTTTAAATTAACTCTTAGAAAGT
*
3388869 TCGATAAGGATAACTATTAAGTAGTTTAGTTTAAATTAA
1 TAGATAAGGATAACTATTAAGTAGTTTAGTTTAAATTAA
3388908 ATACTTGTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
50 21 0.27
51 52 0.68
52 4 0.05
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.36
Consensus pattern (51 bp):
TAGATAAGGATAACTATTAAGTAGTTTAGTTTAAATTAACTCTTAGAAAGT
Found at i:3399263 original size:32 final size:32
Alignment explanation
Indices: 3399176--3399256 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
3399166 ATTCACTATA
* *
3399176 TACATAAATAATGATATGATATATGTTATGTG
1 TACATAAATGATGATGTGATATATGTTATGTG
*
3399208 TACATAAATGATGGTGTGATATATGTTAT-TCG
1 TACATAAATGATGATGTGATATATGTTATGT-G
* *
3399240 TGCATAAGTGATGATGT
1 TACATAAATGATGATGT
3399257 ATTATATATC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 1 0.02
32 41 0.98
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (32 bp):
TACATAAATGATGATGTGATATATGTTATGTG
Found at i:3400182 original size:16 final size:17
Alignment explanation
Indices: 3400118--3400194 Score: 72
Period size: 16 Copynumber: 4.8 Consensus size: 17
3400108 ATCTAATTGG
*
3400118 ACCCGAATCGAAAA-CA
1 ACCCGAATCGAAAATTA
* *
3400134 ATCCGAACCGAAAA-TA
1 ACCCGAATCGAAAATTA
*
3400150 ACCCGAATC-AAATTTA
1 ACCCGAATCGAAAATTA
3400166 ACCCG-ATCGAAAATTA
1 ACCCGAATCGAAAATTA
* *
3400182 ATCAGAATCGAAA
1 ACCCGAATCGAAA
3400195 GCAATCTGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
15 6 0.12
16 36 0.73
17 7 0.14
ACGTcount: A:0.48, C:0.25, G:0.12, T:0.16
Consensus pattern (17 bp):
ACCCGAATCGAAAATTA
Found at i:3401027 original size:30 final size:31
Alignment explanation
Indices: 3400961--3401027 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
3400951 ATACTTATAG
*
3400961 ATTAATTTTCATAAATTTTATATTTGTATGT
1 ATTAATTTTCATAAATTTTATATTTGCATGT
**
3400992 A-TAATTTTCAT-TTTTTTATATATT-CATGT
1 ATTAATTTTCATAAATTTTATAT-TTGCATGT
3401021 ATTAATT
1 ATTAATT
3401028 ATTGTGTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 13 0.42
30 17 0.55
31 1 0.03
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (31 bp):
ATTAATTTTCATAAATTTTATATTTGCATGT
Found at i:3402118 original size:24 final size:24
Alignment explanation
Indices: 3402086--3402142 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
3402076 TCAATATTAT
3402086 TTTATTTTTATAAAATAAATATCA
1 TTTATTTTTATAAAATAAATATCA
3402110 TTTATTTTTATAAAATAAATATCA
1 TTTATTTTTATAAAATAAATATCA
3402134 TTTATTTTT
1 TTTATTTTT
3402143 GCACAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTATTTTTATAAAATAAATATCA
Found at i:3402150 original size:25 final size:24
Alignment explanation
Indices: 3402086--3402151 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
3402076 TCAATATTAT
*
3402086 TTTATTTTTATAAAATAAATATCA
1 TTTATTTTTACAAAATAAATATCA
*
3402110 TTTATTTTTATAAAATAAATATCA
1 TTTATTTTTACAAAATAAATATCA
*
3402134 TTTATTTTTGCACAAATA
1 TTTATTTTTACA-AAATA
3402152 TTAGTTGAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 34 0.87
25 5 0.13
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTATTTTTACAAAATAAATATCA
Found at i:3403036 original size:20 final size:20
Alignment explanation
Indices: 3403011--3403055 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
3403001 TTATTCGGAA
* *
3403011 AAAAATCTGGTCTGGGGTTT
1 AAAAATCCGGTCTGAGGTTT
3403031 AAAAATCCGGTCTGAGGTTT
1 AAAAATCCGGTCTGAGGTTT
3403051 AAAAA
1 AAAAA
3403056 ATTGTATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (20 bp):
AAAAATCCGGTCTGAGGTTT
Found at i:3403229 original size:21 final size:21
Alignment explanation
Indices: 3403203--3403257 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
3403193 AGTGAAAAAA
*
3403203 CCGGATCGATTTTTATCCGAT
1 CCGGATCGATTTGTATCCGAT
*
3403224 CCGGATCGGTTTGTATCCGAT
1 CCGGATCGATTTGTATCCGAT
3403245 CCGGATCGGATTT
1 CCGGATC-GATTT
3403258 AAATCCGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (21 bp):
CCGGATCGATTTGTATCCGAT
Found at i:3403627 original size:22 final size:21
Alignment explanation
Indices: 3403585--3403637 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3403575 ATTCTGACTA
3403585 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
3403606 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGA-TTTCCCAAAT
*
3403627 TCGCAATGCGA
1 TCGCATTGCGA
3403638 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:3403648 original size:20 final size:20
Alignment explanation
Indices: 3403623--3403772 Score: 171
Period size: 20 Copynumber: 7.5 Consensus size: 20
3403613 GCGATTTTCC
*
3403623 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGATTACG
3403643 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
*
3403663 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCG-ATTACG
* *
3403684 AAAATCGCAATGCTATTACG
1 TAAATCGCAATGCGATTACG
*
3403704 TAAATCGCAATACGATTACG
1 TAAATCGCAATGCGATTACG
* *
3403724 T-ATTCGCATTGCGATTTACG
1 TAAATCGCAATGCGA-TTACG
*
3403744 T-AATCGCATTGCGATTTA-G
1 TAAATCGCAATGCGA-TTACG
*
3403763 TAAATTGCAA
1 TAAATCGCAA
3403773 CGAGATTCTG
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
19 12 0.11
20 84 0.74
21 17 0.15
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (20 bp):
TAAATCGCAATGCGATTACG
Found at i:3403657 original size:41 final size:40
Alignment explanation
Indices: 3403623--3403757 Score: 166
Period size: 41 Copynumber: 3.4 Consensus size: 40
3403613 GCGATTTTCC
3403623 TAAATCGCAATGCGAATACGTAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGAATACGTAAATCGCAATGCGATTACG
* * *
3403663 TAAATCGCAATGCGAATTAGGAAAATCGCAATGCTATTACG
1 TAAATCGCAATGCGAA-TACGTAAATCGCAATGCGATTACG
* * * *
3403704 TAAATCGCAATACGATTACGT-ATTCGCATTGCGATTTACG
1 TAAATCGCAATGCGAATACGTAAATCGCAATGCGA-TTACG
*
3403744 T-AATCGCATTGCGA
1 TAAATCGCAATGCGA
3403758 TTTAGTAAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 21 0.26
40 25 0.31
41 35 0.43
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (40 bp):
TAAATCGCAATGCGAATACGTAAATCGCAATGCGATTACG
Found at i:3404677 original size:24 final size:24
Alignment explanation
Indices: 3404629--3404679 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3404619 TTCGAAATTC
* *
3404629 GATCTTGGTCAATACCCGGACTTT
1 GATCTTGGTCAATAACCAGACTTT
* *
3404653 GATCTTGGTCAATAATCAGATTTT
1 GATCTTGGTCAATAACCAGACTTT
3404677 GAT
1 GAT
3404680 GATTTTTCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (24 bp):
GATCTTGGTCAATAACCAGACTTT
Found at i:3406459 original size:24 final size:24
Alignment explanation
Indices: 3406392--3406451 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
3406382 CTGAAAAATC
3406392 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
3406416 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
3406440 ATCAAATTTCGA
1 ATCAAAATTCGA
3406452 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:3406741 original size:19 final size:20
Alignment explanation
Indices: 3406699--3406753 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
3406689 CAATCATCTT
*
3406699 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGCGGA
*
3406719 AATGACTATCGCAATGC-GA
1 AATGACTATCGCAACGCGGA
**
3406738 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
3406754 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGGA
Found at i:3406996 original size:274 final size:274
Alignment explanation
Indices: 3406501--3407039 Score: 997
Period size: 274 Copynumber: 2.0 Consensus size: 274
3406491 CGGCTTCACC
*
3406501 TTTTGGGACTGTTAACTTAGATGATTTTTAAATTCAAACGTTGTATTATGTGGATTTTATGTGTT
1 TTTTGGGACTGTTAACTTAGATGATTTTTAAATACAAACGTTGTATTATGTGGATTTTATGTGTT
* *
3406566 AACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAAATTGCTATGATCTGTT
66 AACTTTTAACATTTTCAGTTAGGCATGTATTAGCAACTTGAGTTTGAAAATTGCTATGATATGTT
*
3406631 TAGTTGTTATCACTTATTAGGCATTCATTTGAATATCGCAACACGGAAATGACGTTCGCAATCAT
131 CAGTTGTTATCACTTATTAGGCATTCATTTGAATATCGCAACACGGAAATGACGTTCGCAATCAT
*
3406696 CTTAATGTCTATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAGAAT
196 CTTAATGTCTATCGCAACGCGGAAATGACTATCGCAATGCAAAATGAAAATCGCAACGAGAGAAT
3406761 CGCAACTTTTAACA
261 CGCAACTTTTAACA
*
3406775 TTTTGGGACTGTTAACTTAGGTGATTTTTAAATACAAACGTTGTATTATGTGGATTTTATGTGTT
1 TTTTGGGACTGTTAACTTAGATGATTTTTAAATACAAACGTTGTATTATGTGGATTTTATGTGTT
*
3406840 ACCTTTTAACATTTTCAGTTAGGCATGTATTAGCAACTTGAGTTTGAAAATTGCTATGATATGTT
66 AACTTTTAACATTTTCAGTTAGGCATGTATTAGCAACTTGAGTTTGAAAATTGCTATGATATGTT
*
3406905 CAGTTGTTATCACTTATTAGGCATTCATTTGACTATCGCAACACGGAAATGACGTTCGCAATCAT
131 CAGTTGTTATCACTTATTAGGCATTCATTTGAATATCGCAACACGGAAATGACGTTCGCAATCAT
*
3406970 CTTAATGTCTATCGCAACGTGGAAATGACTATCGCAATGCAAAATGAAAATCGCAACGAGAGAAT
196 CTTAATGTCTATCGCAACGCGGAAATGACTATCGCAATGCAAAATGAAAATCGCAACGAGAGAAT
3407035 CGCAA
261 CGCAA
3407040 TGCGAAATGA
Statistics
Matches: 256, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
274 256 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (274 bp):
TTTTGGGACTGTTAACTTAGATGATTTTTAAATACAAACGTTGTATTATGTGGATTTTATGTGTT
AACTTTTAACATTTTCAGTTAGGCATGTATTAGCAACTTGAGTTTGAAAATTGCTATGATATGTT
CAGTTGTTATCACTTATTAGGCATTCATTTGAATATCGCAACACGGAAATGACGTTCGCAATCAT
CTTAATGTCTATCGCAACGCGGAAATGACTATCGCAATGCAAAATGAAAATCGCAACGAGAGAAT
CGCAACTTTTAACA
Found at i:3407042 original size:33 final size:33
Alignment explanation
Indices: 3407000--3407093 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
3406990 GGAAATGACT
*
3407000 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3407033 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3407066 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3407094 CGAATTTAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3407096 original size:19 final size:18
Alignment explanation
Indices: 3407000--3407097 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 18
3406990 GGAAATGACT
*
3407000 ATCGCAATGCAAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
3407019 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
3407033 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
3407052 ATCGCAA-CG-AGTG--A
1 ATCGCAAGCGAAATGAAA
3407066 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
3407085 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
3407098 TTTAGTTTCG
Statistics
Matches: 63, Mismatches: 5, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
14 16 0.25
15 3 0.05
16 7 0.11
17 6 0.10
18 3 0.05
19 28 0.44
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:3407115 original size:19 final size:19
Alignment explanation
Indices: 3407093--3407167 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
3407083 AAATCGCAAC
3407093 GCGAATTT-AGTTTCGCGTT
1 GCGAATTTCA-TTTCGCGTT
*
3407112 GCG-ATTT--TGTCG--TT
1 GCGAATTTCATTTCGCGTT
*
3407126 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
* *
3407145 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCGTT
3407164 GCGA
1 GCGA
3407168 TAGTCATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
14 5 0.11
15 3 0.06
16 4 0.09
17 4 0.09
18 4 0.09
19 27 0.57
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.44
Consensus pattern (19 bp):
GCGAATTTCATTTCGCGTT
Found at i:3407168 original size:19 final size:19
Alignment explanation
Indices: 3407124--3407168 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
3407114 GATTTTGTCG
*
3407124 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3407143 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3407162 TTGCGAT
1 TTGCGAT
3407169 AGTCATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3407174 original size:19 final size:19
Alignment explanation
Indices: 3407133--3407176 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3407123 GTTGCGATTT
* **
3407133 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTGCGATAG
3407152 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
3407171 TCATTT
1 TCATTT
3407177 TTGCCTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:3407294 original size:14 final size:14
Alignment explanation
Indices: 3407275--3407311 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3407265 CATCAATTAA
3407275 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3407289 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3407303 ACAAATCAA
1 ACAAATCAA
3407312 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:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3409244 original size:19 final size:19
Alignment explanation
Indices: 3409180--3409306 Score: 120
Period size: 19 Copynumber: 6.8 Consensus size: 19
3409170 TCTGGAACTT
*
3409180 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
** *
3409201 ACTATCGCAACGAGAGAATG
1 AAAATCGCAACGCGA-AATG
*
3409221 AAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGAAATG
3409240 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
3409259 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* * *
3409273 AGAATCGCAATGTGAAATG
1 AAAATCGCAACGCGAAATG
3409292 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
3409307 TTATAGTTTC
Statistics
Matches: 87, Mismatches: 13, Indels: 14
0.76 0.11 0.12
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 1 0.01
17 2 0.02
18 1 0.01
19 45 0.52
20 16 0.18
21 11 0.13
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:3409279 original size:33 final size:35
Alignment explanation
Indices: 3409204--3409303 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 35
3409194 AAAAATGACT
3409204 ATCGCAACGAGAGAATGAAAATCGCAACGCGAAACGAAA
1 ATCGCAACGAGA-AATGAAAATCGCAA--CG-AACGAAA
* *
3409243 ATCGCAACGCGAAATGAAAATCGCAACG-A-GAGA
1 ATCGCAACGAGAAATGAAAATCGCAACGAACGAAA
* *
3409276 ATCGCAATGTGAAATGAAAATCGCAACG
1 ATCGCAACGAGAAATGAAAATCGCAACG
3409304 CGATTATAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
33 29 0.51
34 1 0.02
36 2 0.04
38 14 0.25
39 11 0.19
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (35 bp):
ATCGCAACGAGAAATGAAAATCGCAACGAACGAAA
Found at i:3409337 original size:20 final size:20
Alignment explanation
Indices: 3409312--3409349 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3409302 CGCGATTATA
3409312 GTTTCGCATTGCGATTTTTG
1 GTTTCGCATTGCGATTTTTG
*
3409332 GTTTCGCGTTGCGATTTT
1 GTTTCGCATTGCGATTTT
3409350 GTCGTTGCGA
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:0.08, C:0.16, G:0.26, T:0.50
Consensus pattern (20 bp):
GTTTCGCATTGCGATTTTTG
Found at i:3409388 original size:19 final size:19
Alignment explanation
Indices: 3409352--3409388 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3409342 GCGATTTTGT
* *
3409352 CGTTGCGATTTTCGTTTCG
1 CGTTGCGATTTCCATTTCG
3409371 CGTTGCGATTTCCATTTC
1 CGTTGCGATTTCCATTTC
3409389 AACCAAAAGA
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:0.08, C:0.24, G:0.22, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTCCATTTCG
Found at i:3409596 original size:94 final size:94
Alignment explanation
Indices: 3409479--3409852 Score: 573
Period size: 94 Copynumber: 4.1 Consensus size: 94
3409469 ATGGATTGCA
* *
3409479 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
3409543 TTAGCAGAATTGGCAGTAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
3409572 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
3409637 TTAGCAGAATTGACAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
3409666 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAGCTTTACAGTGTTAAAGAATACACAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
3409731 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
3409760 TTAC-TTCAACCAAAAGACAACA-AAAGACAAATACTAACTTCACAATGTT----AATAAACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
3409819 TTAGCAGTATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
3409848 TTACT
1 TTACT
3409853 AAGTAATCTA
Statistics
Matches: 262, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
88 40 0.15
92 24 0.09
93 21 0.08
94 177 0.68
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3411595 original size:19 final size:19
Alignment explanation
Indices: 3411545--3411656 Score: 126
Period size: 19 Copynumber: 6.1 Consensus size: 19
3411535 TCTTTTGGTT
* *
3411545 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGC
3411564 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
3411584 GAAATAAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
3411601 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3411617 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3411636 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3411655 GA
1 GA
3411657 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 46 0.59
20 17 0.22
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3411702 original size:21 final size:20
Alignment explanation
Indices: 3411679--3411754 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
3411669 GTTGCGATTC
3411679 TCTTGTTGCGATTTTCATTT
1 TCTTGTTGCGATTTTCATTT
* **
3411699 CTCTCGTTGCGATAGTCATTT
1 -TCTTGTTGCGATTTTCATTT
*
3411720 TCGTGTTGCGATTTTCATTT
1 TCTTGTTGCGATTTTCATTT
3411740 T-TATGTTGCGATTTT
1 TCT-TGTTGCGATTTT
3411755 AAGTTTAGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 29 0.63
21 17 0.37
ACGTcount: A:0.12, C:0.16, G:0.18, T:0.54
Consensus pattern (20 bp):
TCTTGTTGCGATTTTCATTT
Found at i:3412328 original size:20 final size:20
Alignment explanation
Indices: 3412305--3412398 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
3412295 CGATAGTCAG
3412305 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
3412325 ATTCGCGTTGCGATTTTCTT
1 ATTCGCATTGCGATTTACGT
3412345 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* * *
3412366 AATCGCGTTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
3412386 ATTCGCTTTGCGA
1 ATTCGCATTGCGA
3412399 ATTAGGAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 44 0.72
21 17 0.28
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:3412352 original size:41 final size:40
Alignment explanation
Indices: 3412305--3412398 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
3412295 CGATAGTCAG
* * * *
3412305 ATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCTT
1 ATTCGCATTGCGATTTACGTAATCGCGTTACGATTTACGT
3412345 AATTCGCATTGCGATTTACGTAATCGCGTTACGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCGTTACGATTTACGT
*
3412386 ATTCGCTTTGCGA
1 ATTCGCATTGCGA
3412399 ATTAGGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 12 0.25
41 36 0.75
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCGTTACGATTTACGT
Found at i:3412419 original size:21 final size:21
Alignment explanation
Indices: 3412395--3412435 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3412385 TATTCGCTTT
3412395 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
3412416 GCGAATTTGGGAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
3412436 TACGATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:3415107 original size:20 final size:19
Alignment explanation
Indices: 3415079--3415120 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
3415069 TTTAAAAAAA
3415079 ATAACAAAAGCTTAATTTATTT
1 ATAA-AAAA-CTTAATTT-TTT
3415101 ATAAAAAACTTAATTTTTT
1 ATAAAAAACTTAATTTTTT
3415120 A
1 A
3415121 CTGAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 8 0.40
21 4 0.20
22 4 0.20
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (19 bp):
ATAAAAAACTTAATTTTTT
Found at i:3415757 original size:29 final size:28
Alignment explanation
Indices: 3415724--3415797 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 28
3415714 TTAAGCCCTC
*
3415724 AAAATTT-AATTACTTTTAACTTAAGTATT
1 AAAATTTGAATTA--TTTAACTTAAATATT
3415753 AAAATTTTGAATTATTTAACTTAAATATT
1 AAAA-TTTGAATTATTTAACTTAAATATT
3415782 AAAATTTTGAATTATT
1 AAAA-TTTGAATTATT
3415798 CTTATTTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 34 0.81
30 3 0.07
31 5 0.12
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (28 bp):
AAAATTTGAATTATTTAACTTAAATATT
Found at i:3415797 original size:16 final size:16
Alignment explanation
Indices: 3415749--3415797 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
3415739 TTAACTTAAG
3415749 TATTAAAATTTTGAAT
1 TATTAAAATTTTGAAT
* * *
3415765 TATT-TAA-CTT-AAA
1 TATTAAAATTTTGAAT
3415778 TATTAAAATTTTGAAT
1 TATTAAAATTTTGAAT
3415794 TATT
1 TATT
3415798 CTTATTTTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
13 6 0.25
14 4 0.17
15 4 0.17
16 10 0.42
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (16 bp):
TATTAAAATTTTGAAT
Found at i:3424135 original size:21 final size:21
Alignment explanation
Indices: 3424109--3424155 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
3424099 CTCATAAACA
3424109 TGCATTCCTTACATGAATGCT
1 TGCATTCCTTACATGAATGCT
3424130 TGCATTCCTTACATGAATGCT
1 TGCATTCCTTACATGAATGCT
3424151 TGCAT
1 TGCAT
3424156 ACACATATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TGCATTCCTTACATGAATGCT
Found at i:3451258 original size:48 final size:48
Alignment explanation
Indices: 3451192--3451317 Score: 207
Period size: 48 Copynumber: 2.6 Consensus size: 48
3451182 GTATTAATAT
3451192 AATGGTATTGATGCCATTCGAGGAGTATTGGTACTGTTCATCTGATACC
1 AATGG-ATTGATGCCATTCGAGGAGTATTGGTACTGTTCATCTGATACC
* *
3451241 AATGGATCGATGTCATTCGAGGAGTATTGGTACTGTTCATCTGATACC
1 AATGGATTGATGCCATTCGAGGAGTATTGGTACTGTTCATCTGATACC
* *
3451289 AATGTATTGATGCCTTTCGAGGAGTATTG
1 AATGGATTGATGCCATTCGAGGAGTATTG
3451318 AAGCAGGCAT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
48 66 0.93
49 5 0.07
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (48 bp):
AATGGATTGATGCCATTCGAGGAGTATTGGTACTGTTCATCTGATACC
Found at i:3454062 original size:20 final size:20
Alignment explanation
Indices: 3454024--3454062 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3454014 ATTTCACCAC
**
3454024 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGAACCTAA
*
3454044 ATGCATCTATATGAACCTA
1 ATGCAACTATATGAACCTA
3454063 TATGAGCTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (20 bp):
ATGCAACTATATGAACCTAA
Found at i:3459239 original size:21 final size:21
Alignment explanation
Indices: 3459188--3459240 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
3459178 ATTATTACTA
3459188 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
3459209 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
3459230 TCGCAATGCGA
1 TCGCAATGCGA
3459241 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:3459277 original size:21 final size:20
Alignment explanation
Indices: 3459230--3459278 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3459220 TTTTCCCAAT
*
3459230 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
3459250 TCACAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
3459271 TCGCAATG
1 TCGCAATG
3459279 AGATACTGAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:3459295 original size:20 final size:20
Alignment explanation
Indices: 3459270--3459384 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
3459260 AATTTGGAAA
* *
3459270 ATCGCAATGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
3459290 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
3459311 ATCGCAACGCGATACTGAAT
1 ATCGCAACGCGATACTGACT
* *
3459331 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
3459351 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
3459371 TTCGCAACGAGATA
1 ATCGCAACGCGATA
3459385 ATACATAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.77
21 15 0.19
22 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3459312 original size:41 final size:41
Alignment explanation
Indices: 3459267--3459404 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
3459257 GCGAATTTGG
* * *
3459267 AAAATCGCAATGAGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
3459308 AAAATCGCAACGCGATACTGAATTTCGCAACGCGATACTTAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATAC
** *
3459350 --TTTCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
3459389 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
3459405 TTTCAAAGTG
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.38
41 44 0.54
42 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:3459599 original size:22 final size:22
Alignment explanation
Indices: 3459571--3459614 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3459561 CACTCTCTCA
*
3459571 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
3459593 CCCATCTCCGAAGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
3459615 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.43, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGAAGAAATCCGTC
Found at i:3459912 original size:20 final size:20
Alignment explanation
Indices: 3459863--3459921 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3459853 TTTATTCTCT
* **
3459863 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
3459883 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
3459903 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
3459922 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:3460113 original size:25 final size:24
Alignment explanation
Indices: 3460059--3460113 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
3460049 TGTTTATTAT
* *
3460059 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
3460083 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
3460109 TGTTT
1 TGTTT
3460114 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:3461264 original size:18 final size:18
Alignment explanation
Indices: 3461243--3461290 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
3461233 TCCACTTCGG
3461243 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
3461261 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3461279 GAGCCATCACCT
1 GAGCCATCACCT
3461291 GATCGACCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3461869 original size:14 final size:14
Alignment explanation
Indices: 3461850--3461908 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
3461840 TTTCATTTCG
3461850 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3461864 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
3461881 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
3461897 CGTTGCGATTTT
1 CGTTGCGATTTT
3461909 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3461876 original size:33 final size:33
Alignment explanation
Indices: 3461834--3461919 Score: 163
Period size: 33 Copynumber: 2.6 Consensus size: 33
3461824 GCTATCGCAA
*
3461834 TGCGATTTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
3461867 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
3461900 TGCGATTTTCATTTCGCATT
1 TGCGATTTTCATTTCGCATT
3461920 TTGATAGCCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.49
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
Found at i:3461947 original size:20 final size:20
Alignment explanation
Indices: 3461922--3461983 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
3461912 TTCGCATTTT
3461922 GATAGCCATTTCCGCGTTGC
1 GATAGCCATTTCCGCGTTGC
*
3461942 GATAGCTATTTCCGCGTTGC
1 GATAGCCATTTCCGCGTTGC
* *
3461962 GATAGTCATTTTCGCGTTGC
1 GATAGCCATTTCCGCGTTGC
3461982 GA
1 GA
3461984 AAGTAAACTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (20 bp):
GATAGCCATTTCCGCGTTGC
Found at i:3462383 original size:21 final size:20
Alignment explanation
Indices: 3462331--3462386 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
3462321 GACTCACCTG
*
3462331 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGGCCCCT
* **
3462351 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGGCCCCT
3462372 ATCATCCCTCAAGAG
1 -TCATCCCTCAAGAG
3462387 TCTCCCCCCA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGGCCCCT
Found at i:3462407 original size:42 final size:42
Alignment explanation
Indices: 3462331--3462419 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
3462321 GACTCACCTG
* *
3462331 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* * *
3462373 TCATCCCTCAAGAGTCTCCC-CCCACCGTTTAAGAGGCCACTG
1 TCATCCCTCAAGAGTC-CCCTCCAACCGTTCAAGAGGCCACTA
3462415 TCATC
1 TCATC
3462420 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
42 38 0.93
43 3 0.07
ACGTcount: A:0.22, C:0.40, G:0.15, T:0.22
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:3463861 original size:14 final size:14
Alignment explanation
Indices: 3463827--3463865 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3463817 TTGATTGTTT
3463827 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
3463841 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
3463855 TGTTGATTTGT
1 AATTGATTTGT
3463866 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:3464027 original size:19 final size:19
Alignment explanation
Indices: 3463982--3464049 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
3463972 ATCGCAACGA
*
3463982 GAAAATCACAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3464001 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3464020 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
3464034 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
3464050 TTTTCATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 29 0.64
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:3464098 original size:20 final size:20
Alignment explanation
Indices: 3464068--3464143 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
3464058 TCGCATTGCG
*
3464068 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
3464088 ATTTTTGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
3464108 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
*
3464128 ATTTTCACGTTGCGAT
1 ATTTTCGCGTTGCGAT
3464144 TTCCCCGTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:3464715 original size:20 final size:20
Alignment explanation
Indices: 3464694--3464781 Score: 149
Period size: 20 Copynumber: 4.4 Consensus size: 20
3464684 TGTATTATCT
* *
3464694 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
3464714 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
3464734 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
3464754 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
3464774 CGTTGCGA
1 CGTTGCGA
3464782 TTTTGTATTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Done.