Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 163 of 190
Found at i:47601523 original size:20 final size:20
Alignment explanation
Indices: 47601476--47601523 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
47601466 AATGTGCTAC
*
47601476 ATTTGAAAAAGAAAATTTTG
1 ATTTGAAGAAGAAAATTTTG
47601496 ATTTGAAGAAGAAAATTTTG
1 ATTTGAAGAAGAAAATTTTG
*
47601516 GTTTGAAG
1 ATTTGAAG
47601524 TTAAAACTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (20 bp):
ATTTGAAGAAGAAAATTTTG
Found at i:47601811 original size:23 final size:23
Alignment explanation
Indices: 47601755--47601811 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
47601745 TTGTATATTA
47601755 TTTT-AAATTTTAAATTATAAAT
1 TTTTAAAATTTTAAATTATAAAT
* *
47601777 TTTTAAAA-TTTACATT-TATAT
1 TTTTAAAATTTTAAATTATAAAT
47601798 GTTTTAAAATTTTA
1 -TTTTAAAATTTTA
47601812 TTTAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.13
22 19 0.63
23 7 0.23
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTTAAAATTTTAAATTATAAAT
Found at i:47608227 original size:2 final size:2
Alignment explanation
Indices: 47608222--47608249 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
47608212 TAAAAAGACG
47608222 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47608250 AAAGTTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47608397 original size:33 final size:33
Alignment explanation
Indices: 47608321--47608400 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
47608311 TAGGTATGTT
* * **
47608321 TATATGTATATATATTACAAAAAAAAGTATTTG
1 TATATATATATATATTACAAAAAAAAATATACG
*
47608354 TACA-AGTATATATATTA-AATAAAAAAATATACG
1 TATATA-TATATATATTACAA-AAAAAAATATACG
47608387 TATATATATATATA
1 TATATATATATATA
47608401 AGCAATAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
32 2 0.05
33 35 0.92
34 1 0.03
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.38
Consensus pattern (33 bp):
TATATATATATATATTACAAAAAAAAATATACG
Found at i:47608412 original size:3 final size:3
Alignment explanation
Indices: 47608404--47608443 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
47608394 ATATATAAGC
47608404 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
47608444 TGAAATTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:47609081 original size:17 final size:16
Alignment explanation
Indices: 47609059--47609092 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
47609049 ATACGTTGTT
47609059 TAAAAATAAAATAAAAA
1 TAAAAATAAAA-AAAAA
*
47609076 TAAAAATATAAAAAAA
1 TAAAAATAAAAAAAAA
47609092 T
1 T
47609093 CGATTGCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAAATAAAAAAAAA
Found at i:47621359 original size:14 final size:14
Alignment explanation
Indices: 47621340--47621372 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
47621330 CCTTGTTTGG
47621340 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
47621354 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
47621368 TTTGG
1 TTTGG
47621373 TTTTGGGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.33
Consensus pattern (14 bp):
TTTGGGCCACTGAA
Found at i:47628369 original size:22 final size:21
Alignment explanation
Indices: 47628325--47628365 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47628315 ATGTCATTAG
*
47628325 GGTTTAAACAAAAAAGGAAAT
1 GGTTCAAACAAAAAAGGAAAT
*
47628346 GGTTCAAACGAAAAAGGAAA
1 GGTTCAAACAAAAAAGGAAA
47628366 ATGGGTGTGT
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:0.56, C:0.07, G:0.22, T:0.15
Consensus pattern (21 bp):
GGTTCAAACAAAAAAGGAAAT
Found at i:47628828 original size:17 final size:17
Alignment explanation
Indices: 47628799--47628949 Score: 87
Period size: 17 Copynumber: 8.8 Consensus size: 17
47628789 AACACGAAAA
47628799 AATTTTA-AAACACGAG
1 AATTTTAGAAACACGAG
*
47628815 AATTTTAGAAACACGAA
1 AATTTTAGAAACACGAG
47628832 AATTCTTA-AAACACGA-
1 AATT-TTAGAAACACGAG
* *
47628848 ATTTTTTTTGAAAACACG-G
1 A--ATTTTAG-AAACACGAG
* *
47628867 AAATTTTTGAAATACGAG
1 -AATTTTAGAAACACGAG
* *
47628885 AATTTTAAAAACATGA-
1 AATTTTAGAAACACGAG
* *
47628901 AAATTTACAAAACACGAG
1 AATTTTA-GAAACACGAG
* * *
47628919 AATTTTTAAAAATACGAA
1 AA-TTTTAGAAACACGAG
*
47628937 AATTTTTGAAACA
1 AATTTTAGAAACA
47628950 ATAGATTTTT
Statistics
Matches: 106, Mismatches: 17, Indels: 23
0.73 0.12 0.16
Matches are distributed among these distances:
16 14 0.13
17 56 0.53
18 24 0.23
19 11 0.10
20 1 0.01
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (17 bp):
AATTTTAGAAACACGAG
Found at i:47628846 original size:34 final size:33
Alignment explanation
Indices: 47628781--47628942 Score: 146
Period size: 34 Copynumber: 4.6 Consensus size: 33
47628771 CAATTATTTT
47628781 TTTTGAAAAACACGAAAAAATTTTAAAACACGAGAA
1 TTTT-AAAAACACG--AAAATTTTAAAACACGAGAA
* *
47628817 TTTTAGAAACACGAAAATTCTTAAAACACGA-ATTTT
1 TTTTAAAAACACGAAAATT-TTAAAACACGAGA---A
* * * *
47628853 TTTTGAAAACACGGAAATTTTTGAAATACGAGAA
1 TTTTAAAAACAC-GAAAATTTTAAAACACGAGAA
* *
47628887 TTTTAAAAACATGAAAATTTACAAAACACGAGAA
1 TTTTAAAAACACGAAAATTT-TAAAACACGAGAA
*
47628921 TTTTTAAAAATACGAAAATTTT
1 -TTTTAAAAACACGAAAATTTT
47628943 TGAAACAATA
Statistics
Matches: 101, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
33 14 0.14
34 31 0.31
35 26 0.26
36 23 0.23
37 7 0.07
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.30
Consensus pattern (33 bp):
TTTTAAAAACACGAAAATTTTAAAACACGAGAA
Found at i:47628871 original size:36 final size:36
Alignment explanation
Indices: 47628776--47628971 Score: 115
Period size: 35 Copynumber: 5.5 Consensus size: 36
47628766 CGAAACAATT
47628776 ATTTTTTTTGAAAAACACGAAAAAATTTTAAAACACGAG
1 ATTTTTTTTG-AAAACACG--AAAATTTTAAAACACGAG
* *
47628815 A--ATTTTAG-AAACACGAAAATTCTTAAAACACGA-
1 ATTTTTTTTGAAAACACGAAAATT-TTAAAACACGAG
* * *
47628848 ATTTTTTTTGAAAACACGGAAATTTTTGAAATACGAG
1 ATTTTTTTTGAAAACAC-GAAAATTTTAAAACACGAG
* * * *
47628885 A---ATTTTAAAAACATGAAAATTTACAAAACACGAG
1 ATTTTTTTTGAAAACACGAAAATTT-TAAAACACGAG
* * * * **
47628919 A--ATTTTTAAAAATACGAAAATTTTTGAAACAATAG
1 ATTTTTTTTGAAAACACGAAAA-TTTTAAAACACGAG
*
47628954 ATTTTTTTT-ATAACACGA
1 ATTTTTTTTGAAAACACGA
47628972 GGATTTTTTT
Statistics
Matches: 122, Mismatches: 24, Indels: 25
0.71 0.14 0.15
Matches are distributed among these distances:
33 14 0.11
34 30 0.25
35 35 0.29
36 25 0.20
37 17 0.14
39 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (36 bp):
ATTTTTTTTGAAAACACGAAAATTTTAAAACACGAG
Found at i:47628903 original size:70 final size:71
Alignment explanation
Indices: 47628776--47628949 Score: 203
Period size: 70 Copynumber: 2.5 Consensus size: 71
47628766 CGAAACAATT
* * * *
47628776 ATTTTTTTTGAAAAACACGAAAAAATTTTAAAACACGAGAATTTTAGAAACACGAAAATTCT-TA
1 ATTTTTTTTG-AAAACACG-AAAATTTTTGAAACACGAGAATTTTAAAAACACGAAAATT-TACA
47628840 AAACACGA-
63 AAACACGAG
* * *
47628848 ATTTTTTTTGAAAACACGGAAATTTTTGAAATACGAGAATTTTAAAAACATGAAAATTTACAAAA
1 ATTTTTTTTGAAAACACGAAAATTTTTGAAACACGAGAATTTTAAAAACACGAAAATTTACAAAA
47628913 CACGAG
66 CACGAG
* * *
47628919 A--ATTTTTAAAAATACGAAAATTTTTGAAACA
1 ATTTTTTTTGAAAACACGAAAATTTTTGAAACA
47628950 ATAGATTTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
69 26 0.30
70 43 0.49
71 9 0.10
72 10 0.11
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.30
Consensus pattern (71 bp):
ATTTTTTTTGAAAACACGAAAATTTTTGAAACACGAGAATTTTAAAAACACGAAAATTTACAAAA
CACGAG
Found at i:47629052 original size:17 final size:17
Alignment explanation
Indices: 47629030--47629068 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
47629020 TTAATAGGAG
47629030 AATTTAAAAAAAACGAA
1 AATTTAAAAAAAACGAA
* *
47629047 AATTTACAAAACACGAA
1 AATTTAAAAAAAACGAA
47629064 AATTT
1 AATTT
47629069 TTGAAAAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (17 bp):
AATTTAAAAAAAACGAA
Found at i:47629093 original size:16 final size:17
Alignment explanation
Indices: 47629038--47629092 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
47629028 AGAATTTAAA
**
47629038 AAAAACGAAAA-TTTAC
1 AAAAACGAAAATTTTTG
47629054 AAAACACGAAAATTTTTG
1 AAAA-ACGAAAATTTTTG
*
47629072 AAAAACGATAATTTTTG
1 AAAAACGAAAATTTTTG
47629089 AAAA
1 AAAA
47629093 CACAAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.12
17 23 0.68
18 7 0.21
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.25
Consensus pattern (17 bp):
AAAAACGAAAATTTTTG
Found at i:47629489 original size:23 final size:23
Alignment explanation
Indices: 47629463--47629512 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
47629453 ACTCGGACTT
*
47629463 TTTCTTTTTTGCTTT-TTTTTTTC
1 TTTCTCTTTTG-TTTCTTTTTTTC
47629486 TTTCTCTTTTGTTTGCTTTTTTTC
1 TTTCTCTTTTGTTT-CTTTTTTTC
47629510 TTT
1 TTT
47629513 TTTCCTTCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 3 0.12
23 10 0.42
24 11 0.46
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (23 bp):
TTTCTCTTTTGTTTCTTTTTTTC
Found at i:47629580 original size:24 final size:24
Alignment explanation
Indices: 47629543--47629596 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
47629533 CTGGTGGGCT
* **
47629543 GCCTGTTGGGCTGGTGTGCGC-GG
1 GCCTGCTGGGCTGGCCTGCGCTGG
47629566 GCCTGCTGGTGCTGGCCTGCGCTGG
1 GCCTGCTGG-GCTGGCCTGCGCTGG
47629591 GCCTGC
1 GCCTGC
47629597 GCTGTTGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 8 0.31
24 10 0.38
25 8 0.31
ACGTcount: A:0.00, C:0.30, G:0.46, T:0.24
Consensus pattern (24 bp):
GCCTGCTGGGCTGGCCTGCGCTGG
Found at i:47629609 original size:24 final size:24
Alignment explanation
Indices: 47629552--47629609 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
47629542 TGCCTGTTGG
* *
47629552 GCTGGTGTGCGCGGGCCTGCTGGT
1 GCTGGTCTGCGCGGGCCTGCTGCT
*
47629576 GCTGGCCTGCGCTGGGCCTGC-GCT
1 GCTGGTCTGCGC-GGGCCTGCTGCT
*
47629600 GTTGGTCTGC
1 GCTGGTCTGC
47629610 TGTGGTTGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.00, C:0.29, G:0.45, T:0.26
Consensus pattern (24 bp):
GCTGGTCTGCGCGGGCCTGCTGCT
Found at i:47629713 original size:12 final size:12
Alignment explanation
Indices: 47629698--47629730 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
47629688 TTGGGCTGTT
47629698 TTTTTGTTTTGA
1 TTTTTGTTTTGA
*
47629710 TTTTTGTTTTGC
1 TTTTTGTTTTGA
47629722 TTTTT-TTTT
1 TTTTTGTTTT
47629731 AAAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.82
Consensus pattern (12 bp):
TTTTTGTTTTGA
Found at i:47629860 original size:26 final size:25
Alignment explanation
Indices: 47629823--47629884 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
47629813 ATCCGAATAT
* *
47629823 TTTCATTT-TTTTGTTTTTTGTTTTC
1 TTTCTTTTCTTTTGTTTTTT-CTTTC
47629848 TTTCTTTTCTTTTTGTTTTTTCTTTC
1 TTTCTTTTC-TTTTGTTTTTTCTTTC
47629874 -TTCTTCTTCTT
1 TTTCTT-TTCTT
47629885 CTTCTTCTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 14 0.44
26 7 0.22
27 11 0.34
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.79
Consensus pattern (25 bp):
TTTCTTTTCTTTTGTTTTTTCTTTC
Found at i:47629861 original size:22 final size:23
Alignment explanation
Indices: 47629843--47629905 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
47629833 TTGTTTTTTG
47629843 TTTTCTTTCTT-TTCTTTTTGTT
1 TTTTCTTTCTTCTTCTTTTTGTT
* *
47629865 TTTTCTTTCTTCTTCTTCTTCTT
1 TTTTCTTTCTTCTTCTTTTTGTT
47629888 CTTCTTC-TTCTTCTTCTT
1 -TT-TTCTTTCTTCTTCTT
47629906 CTGGAGGCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.31
23 9 0.25
24 13 0.36
25 3 0.08
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTCTTTCTTCTTCTTTTTGTT
Found at i:47629862 original size:20 final size:22
Alignment explanation
Indices: 47629837--47629902 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
47629827 ATTTTTTTGT
47629837 TTTTTG-TTTTCTTTCTT-TTC
1 TTTTTGTTTTTCTTTCTTCTTC
47629857 TTTTTGTTTTTTCTTTCTTCTTC
1 TTTTTG-TTTTTCTTTCTTCTTC
* * *
47629880 TTCTTCTTCTTC-TTCTTCTTC
1 TTTTTGTTTTTCTTTCTTCTTC
47629901 TT
1 TT
47629903 CTTCTGGAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
20 6 0.15
21 11 0.28
22 16 0.40
23 7 0.17
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (22 bp):
TTTTTGTTTTTCTTTCTTCTTC
Found at i:47629879 original size:3 final size:3
Alignment explanation
Indices: 47629871--47629907 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
47629861 TGTTTTTTCT
47629871 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
47629908 GGAGGCCCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:47630358 original size:30 final size:29
Alignment explanation
Indices: 47630248--47630403 Score: 156
Period size: 29 Copynumber: 5.2 Consensus size: 29
47630238 GGCCCAAGTA
*
47630248 TAATTTTAGGAAAATTTAGGAGTCAAAATG
1 TAATTTTA-GAAAATTTAGGGGTCAAAATG
* * * *
47630278 CAATTTCA-AATAGTTTATGGGTCAAAATG
1 TAATTTTAGAA-AATTTAGGGGTCAAAATG
*
47630307 TAA-TTTAGAAAAAGTTTTAGGGGTCAAAATA
1 TAATTTTAG-AAAA--TTTAGGGGTCAAAATG
47630338 TAATTTTAGGAAAATTTAGGGGTCAAAATG
1 TAATTTTA-GAAAATTTAGGGGTCAAAATG
* *
47630368 CAATTTTA-AAATTTTTAGGGGTCAAAATG
1 TAATTTTAGAAA-ATTTAGGGGTCAAAATG
47630397 TAATTTT
1 TAATTTT
47630404 TATTTTTTGT
Statistics
Matches: 104, Mismatches: 14, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
28 8 0.08
29 40 0.38
30 30 0.29
31 17 0.16
32 8 0.08
33 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (29 bp):
TAATTTTAGAAAATTTAGGGGTCAAAATG
Found at i:47633137 original size:24 final size:23
Alignment explanation
Indices: 47633110--47633154 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
47633100 CCATGATTGC
*
47633110 ATATTAAAATAATTATTTAAAAAT
1 ATATTAAAATAA-AATTTAAAAAT
*
47633134 ATATTTAAATAAAATTTAAAA
1 ATATTAAAATAAAATTTAAAA
47633155 GTTTGTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATATTAAAATAAAATTTAAAAAT
Found at i:47633138 original size:12 final size:13
Alignment explanation
Indices: 47633110--47633153 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 13
47633100 CCATGATTGC
*
47633110 ATATTAAAATAAT
1 ATATTTAAATAAT
47633123 -TATTTAAA-AAT
1 ATATTTAAATAAT
47633134 ATATTTAAATAA-
1 ATATTTAAATAAT
47633146 A-ATTTAAA
1 ATATTTAAA
47633154 AGTTTGTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 10 0.36
12 16 0.57
13 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTTAAATAAT
Found at i:47643100 original size:24 final size:25
Alignment explanation
Indices: 47643072--47643118 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
47643062 TAGTATTTTA
*
47643072 ATTTACTTTTAC-TAAATATAAATT
1 ATTTACTTTTACATAAAAATAAATT
*
47643096 ATTTATTTTTACATAAAAATAAA
1 ATTTACTTTTACATAAAAATAAA
47643119 ATAAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTTACTTTTACATAAAAATAAATT
Found at i:47645475 original size:13 final size:13
Alignment explanation
Indices: 47645457--47645482 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47645447 TTGGATCTGT
47645457 ACCAAAACAATCA
1 ACCAAAACAATCA
47645470 ACCAAAACAATCA
1 ACCAAAACAATCA
47645483 TAAAACATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
ACCAAAACAATCA
Found at i:47649630 original size:7 final size:7
Alignment explanation
Indices: 47649615--47649653 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
47649605 ACCCAACAAT
*
47649615 AACCTTA
1 AACCCTA
47649622 AACCCTA
1 AACCCTA
*
47649629 AACCTTA
1 AACCCTA
47649636 AACCCTAA
1 AACCCT-A
47649644 AACCCTA
1 AACCCTA
47649651 AAC
1 AAC
47649654 AAAAGAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (7 bp):
AACCCTA
Found at i:47649632 original size:14 final size:14
Alignment explanation
Indices: 47649615--47649644 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
47649605 ACCCAACAAT
47649615 AACCTTAAACCCTA
1 AACCTTAAACCCTA
47649629 AACCTTAAACCCTA
1 AACCTTAAACCCTA
47649643 AA
1 AA
47649645 ACCCTAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
AACCTTAAACCCTA
Found at i:47670764 original size:22 final size:22
Alignment explanation
Indices: 47670721--47670769 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
47670711 TGATGTGAAT
47670721 GTAATATAATATGAAATATCTG
1 GTAATATAATATGAAATATCTG
* * *
47670743 TTAATTTAATATGTAAA-CTCTG
1 GTAATATAATATG-AAATATCTG
47670765 GTAAT
1 GTAAT
47670770 GCTCCGTAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (22 bp):
GTAATATAATATGAAATATCTG
Found at i:47672717 original size:2 final size:2
Alignment explanation
Indices: 47672710--47672739 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47672700 AGCAAAACAT
47672710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47672740 GATTGAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47674015 original size:15 final size:16
Alignment explanation
Indices: 47673982--47674024 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
47673972 TGATAAACTG
* *
47673982 AAAAATTAACTGTTGA
1 AAAAATTAAGTATTGA
47673998 AAAAATTAAGTATT-A
1 AAAAATTAAGTATTGA
*
47674013 AAAAGTTAAGTA
1 AAAAATTAAGTA
47674025 GTTTTAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (16 bp):
AAAAATTAAGTATTGA
Found at i:47682613 original size:66 final size:66
Alignment explanation
Indices: 47682530--47682676 Score: 208
Period size: 66 Copynumber: 2.2 Consensus size: 66
47682520 GAGGCAACAT
47682530 CGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTGAAAGTAGATGCAG
1 CGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-AGCAACTGAAAGTAGATGCAG
47682593 CAG
64 CAG
* * * *
47682596 CGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTTAAAGTAGATGCGGCA
1 CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTGAAAGTAGATGCAGCA
47682661 G
66 G
* *
47682662 CAAGAGAAGCAGAGG
1 CGAGAGAAGCTGAGG
47682677 CGGCAGCGAG
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
65 1 0.01
66 68 0.93
67 4 0.05
ACGTcount: A:0.40, C:0.17, G:0.29, T:0.14
Consensus pattern (66 bp):
CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTGAAAGTAGATGCAGCA
G
Found at i:47682681 original size:21 final size:21
Alignment explanation
Indices: 47682655--47682759 Score: 106
Period size: 21 Copynumber: 5.0 Consensus size: 21
47682645 TAAAGTAGAT
*
47682655 GCGGCAGCAAGAGAAGCAGAG
1 GCGGCAGCGAGAGAAGCAGAG
* *
47682676 GCGGCAGCGAGAGAAGTACAG
1 GCGGCAGCGAGAGAAGCAGAG
47682697 G-GTGCAGCGA-AGGAAGCAGAG
1 GCG-GCAGCGAGA-GAAGCAGAG
*** *
47682718 GCTAAAGCGAGGGAAGCAGAG
1 GCGGCAGCGAGAGAAGCAGAG
*
47682739 GCTGCAGCGAGAGAAGCAGAG
1 GCGGCAGCGAGAGAAGCAGAG
47682760 CAGCGTCAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 66 0.97
ACGTcount: A:0.35, C:0.17, G:0.44, T:0.04
Consensus pattern (21 bp):
GCGGCAGCGAGAGAAGCAGAG
Found at i:47683158 original size:43 final size:43
Alignment explanation
Indices: 47683111--47683383 Score: 282
Period size: 43 Copynumber: 6.3 Consensus size: 43
47683101 AAGTGTTGGC
* * *
47683111 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
47683154 CTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
47683197 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * * * *
47683240 CTTTAGTGGCGTTTGTGATCGAAGCACCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * ** *
47683283 CTATT-GCAGCGTTTGAGGGGAAAGCGCCGCTAAAGAAT-AGGTT
1 CT-TTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAG-ATCAGGGT
* * *
47683326 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
47683369 CTATTA-CGGCGTTTG
1 CT-TTAGCGGCGTTTG
47683384 AGAGAAAAAT
Statistics
Matches: 184, Mismatches: 41, Indels: 10
0.78 0.17 0.04
Matches are distributed among these distances:
42 4 0.02
43 173 0.94
44 7 0.04
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
Found at i:47683307 original size:129 final size:129
Alignment explanation
Indices: 47683111--47683362 Score: 314
Period size: 129 Copynumber: 2.0 Consensus size: 129
47683101 AAGTGTTGGC
* * * * *
47683111 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAA
1 CTTTAGTGGCGTTTGTGATCAAAGCACCGCTAAAGATAAGGGTCTTTAGCAGCGTTTGAGGAAAA
*
47683176 AGCGCCACTAAAG-ATCATGG-TCTTTAGCGGCGTTTGTGG-GGAAAGCGCCGCTAAAGATTAGG
66 AGCGCCACTAAAGAAT-A-GGTTCTTTAGCGGCGTTTGTGGTCG-AAGCGCCGCTAAAGATTAGG
47683238 TT
128 TT
* * * **
47683240 CTTTAGTGGCGTTTGTGATCGAAGCACCGCTATAGATCAGGGTCTATT-GCAGCGTTTGAGGGGA
1 CTTTAGTGGCGTTTGTGATCAAAGCACCGCTAAAGATAAGGGTCT-TTAGCAGCGTTTGAGGAAA
* * *
47683304 AAGCGCCGCTAAAGAATAGGTTCTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGAT
65 AAGCGCCACTAAAGAATAGGTTCTTTAGCGGCGTTTGTGGTCGAAGCGCCGCTAAAGAT
47683363 CAGGGTCTAT
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
128 2 0.02
129 98 0.93
130 5 0.05
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (129 bp):
CTTTAGTGGCGTTTGTGATCAAAGCACCGCTAAAGATAAGGGTCTTTAGCAGCGTTTGAGGAAAA
AGCGCCACTAAAGAATAGGTTCTTTAGCGGCGTTTGTGGTCGAAGCGCCGCTAAAGATTAGGTT
Found at i:47683404 original size:86 final size:86
Alignment explanation
Indices: 47683131--47683385 Score: 352
Period size: 86 Copynumber: 3.0 Consensus size: 86
47683121 GTTTTTGGTC
* * *** * * *
47683131 AAAGCGCCGCTAAAG-ATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATG
1 AAAGCGCCGCTAAAGAAT-AGGTTCTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGG
*
47683195 GTCT-TTAGCGGCGTTTGTGGGG
65 GTCTATTA-CGGCGTTTGAGGGG
* * *
47683217 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGATCGAAGCACCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGAATAGGTTCTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGG
* *
47683282 TCTATTGCAGCGTTTGAGGGG
66 TCTATTACGGCGTTTGAGGGG
47683303 AAAGCGCCGCTAAAGAATAGGTTCTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGAATAGGTTCTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGG
47683368 TCTATTACGGCGTTTGAG
66 TCTATTACGGCGTTTGAG
47683386 AGAAAAATGC
Statistics
Matches: 148, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
86 145 0.98
87 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (86 bp):
AAAGCGCCGCTAAAGAATAGGTTCTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGG
TCTATTACGGCGTTTGAGGGG
Found at i:47683415 original size:86 final size:86
Alignment explanation
Indices: 47683221--47683422 Score: 233
Period size: 86 Copynumber: 2.3 Consensus size: 86
47683211 GTGGGGAAAG
* ** *
47683221 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGATCGAAGCACCGCTATAGATCAGGGTCTA
1 CGCCGCGAAAGAACAGGATCTTTAGTGGCGTTTGTGATCGAAGCACCGCTATAGATCAGGGTCTA
* * * *
47683286 TTGCAGCGTTTGAGGGGAAAG
66 TTACAGCGTTTGAGAGAAAAA
* * * * *
47683307 CGCCGCTAAAGAATAGGTTCTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGGTCTA
1 CGCCGCGAAAGAACAGGATCTTTAGTGGCGTTTGTGATCGAAGCACCGCTATAGATCAGGGTCTA
*
47683372 TTACGGCGTTTGAGAGAAAAA
66 TTACAGCGTTTGAGAGAAAAA
* * ** *
47683393 TGCCGCGAAAGACCCTGATCTTTAGCGGCG
1 CGCCGCGAAAGAACAGGATCTTTAGTGGCG
47683423 CTTCTCCCAA
Statistics
Matches: 100, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 100 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (86 bp):
CGCCGCGAAAGAACAGGATCTTTAGTGGCGTTTGTGATCGAAGCACCGCTATAGATCAGGGTCTA
TTACAGCGTTTGAGAGAAAAA
Found at i:47683435 original size:43 final size:43
Alignment explanation
Indices: 47683388--47683469 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
47683378 CGTTTGAGAG
*
47683388 AAAAATGCCGCGAAAGACCCTGATCTTTAGCGGCGCTTCTCCC
1 AAAAATGCCGCGAAAGACCATGATCTTTAGCGGCGCTTCTCCC
* * * *
47683431 AAAAATGTCGCTAAAGATCATGGTCTTTAGCGGCGCTTC
1 AAAAATGCCGCGAAAGACCATGATCTTTAGCGGCGCTTC
47683470 CACTAAAGCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (43 bp):
AAAAATGCCGCGAAAGACCATGATCTTTAGCGGCGCTTCTCCC
Found at i:47684181 original size:25 final size:26
Alignment explanation
Indices: 47684123--47684183 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
47684113 TACCCCCAAC
* *
47684123 AAAATTTTGATGATTTTACCCTTGGT
1 AAAATTTTGACGATTTTACCCTTAGT
*
47684149 AAAATTTTGACGATTTTTCCC-TAGT
1 AAAATTTTGACGATTTTACCCTTAGT
47684174 AAAATTTTGA
1 AAAATTTTGA
47684184 GAAAATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 13 0.41
26 19 0.59
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (26 bp):
AAAATTTTGACGATTTTACCCTTAGT
Found at i:47684458 original size:16 final size:16
Alignment explanation
Indices: 47684437--47684487 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
47684427 TCATTTCTCT
47684437 TTTTTTATTC-ATTCGA
1 TTTTTTATTCTATTC-A
*
47684453 TTTTTTTTTCTATTCA
1 TTTTTTATTCTATTCA
47684469 TTTTATTCATTTCTATTCA
1 TTTT-TT-A-TTCTATTCA
47684488 AAACAAGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 14 0.48
17 6 0.21
19 9 0.31
ACGTcount: A:0.18, C:0.14, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTTTATTCTATTCA
Found at i:47684458 original size:17 final size:16
Alignment explanation
Indices: 47684436--47684487 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 16
47684426 CTCATTTCTC
47684436 TTTTTTTATTC-ATTCGA
1 TTTTTTT-TTCTATTC-A
47684453 TTTTTTTTTCTATTCA
1 TTTTTTTTTCTATTCA
47684469 TTTTATTCATTTCTATTCA
1 TTTT-TT--TTTCTATTCA
47684488 AAACAAGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.26
17 13 0.42
19 10 0.32
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTTTTTTCTATTCA
Found at i:47684477 original size:9 final size:10
Alignment explanation
Indices: 47684459--47684487 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
47684449 TCGATTTTTT
47684459 TTTCTATTCA
1 TTTCTATTCA
47684469 TTT-TATTCA
1 TTTCTATTCA
47684478 TTTCTATTCA
1 TTTCTATTCA
47684488 AAACAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:47686524 original size:19 final size:20
Alignment explanation
Indices: 47686487--47686538 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
47686477 AGGTCGCTCC
47686487 TACTTTAATTTTATTTATAT-
1 TACTTTAATTTT-TTTATATA
47686507 TACTTTAATTTTTTTATATA
1 TACTTTAATTTTTTTATATA
*
47686527 TA-ATTAATTTTT
1 TACTTTAATTTTT
47686539 ATGATTCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (20 bp):
TACTTTAATTTTTTTATATA
Found at i:47688049 original size:22 final size:22
Alignment explanation
Indices: 47688001--47688049 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
47687991 ATTTGAAATT
*
47688001 TAATTTTTATTTTAATTTGATA
1 TAATTTTTATTTTAATTTCATA
* *
47688023 TAATTTATTTTTTTATTTTCATA
1 TAATTT-TTATTTTAATTTCATA
47688046 -AATT
1 TAATT
47688050 AGTCCGGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TAATTTTTATTTTAATTTCATA
Found at i:47688733 original size:21 final size:22
Alignment explanation
Indices: 47688709--47688750 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
47688699 ATCTAAATTT
47688709 TTAAATT-TAAAAAATAAAAAA
1 TTAAATTCTAAAAAATAAAAAA
**
47688730 TTAAATTCTTGAAAATAAAAA
1 TTAAATTCTAAAAAATAAAAA
47688751 TGAGTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAAATTCTAAAAAATAAAAAA
Found at i:47694207 original size:2 final size:2
Alignment explanation
Indices: 47694200--47694238 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
47694190 TTCTTTAAGT
47694200 TA 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 TA T
47694239 TCAAAACTCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47696534 original size:91 final size:92
Alignment explanation
Indices: 47696393--47696563 Score: 245
Period size: 91 Copynumber: 1.8 Consensus size: 92
47696383 TCGCACTTGA
* * * *
47696393 TATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTTTAATCTCACATTGACTA
1 TATAAATAAGTGACAATTTC-T-ACTATTTTCATTAAAAAGTTAATTTTAATCCCACATTAACTA
* *
47696458 GAGAACATTCTCATATCTCACATTGACCT
64 GAGAAAACTCTCATATCTCACATTGACCT
* *
47696487 TATAAATAAGTGACAATTTC-ACTATTTTCATTAAAAATTTAATTTTAATCCCACATTAACTAGG
1 TATAAATAAGTGACAATTTCTACTATTTTCATTAAAAAGTTAATTTTAATCCCACATTAACTAGA
47696551 GAAAACTCTCATA
66 GAAAACTCTCATA
47696564 GCTCTCTTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
91 50 0.72
94 19 0.28
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (92 bp):
TATAAATAAGTGACAATTTCTACTATTTTCATTAAAAAGTTAATTTTAATCCCACATTAACTAGA
GAAAACTCTCATATCTCACATTGACCT
Found at i:47696629 original size:69 final size:68
Alignment explanation
Indices: 47696504--47696635 Score: 174
Period size: 69 Copynumber: 1.9 Consensus size: 68
47696494 AAGTGACAAT
* *
47696504 TTCACTATTTTCATTAAAAATTTAATTTTAATCCCACATTAACTAGGGAAAACTCTCATAGCTCT
1 TTCACTATTTTCATTAAAAAGTTAATTTTAATCCCACATTAACTAGAGAAAACTCTCAT-GCTCT
47696569 CTTC
65 CTTC
* * * ** **
47696573 TTCACTATTTTCATTAAAACGTTAATTTTAATCCTATATTAGTTAGAGAACTCTCTCATGCTC
1 TTCACTATTTTCATTAAAAAGTTAATTTTAATCCCACATTAACTAGAGAAAACTCTCATGCTC
47696636 ATACTTACAC
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
68 4 0.07
69 50 0.93
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (68 bp):
TTCACTATTTTCATTAAAAAGTTAATTTTAATCCCACATTAACTAGAGAAAACTCTCATGCTCTC
TTC
Found at i:47696801 original size:67 final size:65
Alignment explanation
Indices: 47696716--47696839 Score: 196
Period size: 67 Copynumber: 1.9 Consensus size: 65
47696706 ATATTAGTAT
*
47696716 ATGCACTTAAATTGTAGTATGTATAAATATTATATATATAAATATGTGAATTAATTAAATCTTTA
1 ATGCACTTAAATTATAGTATGTATAAATATTATATATAT-AATA--TGAATTAATTAAATCTTTA
47696781 TAC
63 TAC
*
47696784 ATGCAC-TAAATTATAGTATGTGTAAATATTATATATATAATATGAATTAATTAAAT
1 ATGCACTTAAATTATAGTATGTATAAATATTATATATATAATATGAATTAATTAAAT
47696840 ATATTTTTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
64 14 0.26
66 4 0.07
67 30 0.56
68 6 0.11
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (65 bp):
ATGCACTTAAATTATAGTATGTATAAATATTATATATATAATATGAATTAATTAAATCTTTATAC
Found at i:47697128 original size:19 final size:20
Alignment explanation
Indices: 47697106--47697145 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
47697096 GTTTTTATAA
47697106 TAAAAT-TATCATTTATTTT
1 TAAAATGTATCATTTATTTT
**
47697125 TAAAATGTATTTTTTATTTT
1 TAAAATGTATCATTTATTTT
47697145 T
1 T
47697146 TTTATTTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TAAAATGTATCATTTATTTT
Found at i:47699198 original size:8 final size:8
Alignment explanation
Indices: 47699185--47699210 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
47699175 GGGATTTCCT
47699185 TTTTCTTC
1 TTTTCTTC
47699193 TTTTCTTC
1 TTTTCTTC
47699201 TTTTCTTC
1 TTTTCTTC
47699209 TT
1 TT
47699211 ATTGTCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCTTC
Found at i:47704259 original size:15 final size:15
Alignment explanation
Indices: 47704230--47704272 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
47704220 TTCTGGGCAA
47704230 CCAAA-CAACCCAAC
1 CCAAACCAACCCAAC
* *
47704244 CCAATCCAACCGAAC
1 CCAAACCAACCCAAC
*
47704259 CCAAACCAAACCAA
1 CCAAACCAACCCAA
47704273 AATTCCCAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.49, C:0.47, G:0.02, T:0.02
Consensus pattern (15 bp):
CCAAACCAACCCAAC
Found at i:47704945 original size:21 final size:22
Alignment explanation
Indices: 47704906--47704946 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
47704896 TATTTTTTAT
*
47704906 TTTTAAGAATTTAATTTTAAAA
1 TTTTAAGAATTTAAGTTTAAAA
*
47704928 TTTTAA-AATTTAGGTTTAA
1 TTTTAAGAATTTAAGTTTAA
47704947 TGGTTAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTTAAGAATTTAAGTTTAAAA
Found at i:47706905 original size:18 final size:17
Alignment explanation
Indices: 47706884--47706917 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
47706874 GAGAGAAAAT
47706884 ATTTTATGTTAAAAGTTA
1 ATTTT-TGTTAAAAGTTA
*
47706902 ATTTTTTTTAAAAGTT
1 ATTTTTGTTAAAAGTT
47706918 CACTCAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (17 bp):
ATTTTTGTTAAAAGTTA
Found at i:47707582 original size:16 final size:16
Alignment explanation
Indices: 47707561--47707605 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
47707551 GTTTGGTTCA
47707561 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
47707577 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
47707593 TTGTAATGGAATA
1 CTGTAATGGAATA
47707606 ATGATGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:47707613 original size:16 final size:16
Alignment explanation
Indices: 47707562--47707615 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
47707552 TTTGGTTCAC
*
47707562 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGA
* *
47707578 TGTAATTGAATAGAGT
1 TGTAATGGAATAGAGA
47707594 TGTAATGGAATA-ATGA
1 TGTAATGGAATAGA-GA
47707610 TGTAAT
1 TGTAAT
47707616 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 1 0.03
16 32 0.97
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGA
Found at i:47724536 original size:16 final size:17
Alignment explanation
Indices: 47724500--47724536 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
47724490 AATTTTATTT
*
47724500 TAATAGTAAGTTTTAAA
1 TAATAATAAGTTTTAAA
47724517 -AATAATAA-TTTTAAA
1 TAATAATAAGTTTTAAA
47724532 TAATA
1 TAATA
47724537 TTATTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TAATAATAAGTTTTAAA
Found at i:47728039 original size:5 final size:5
Alignment explanation
Indices: 47728029--47728055 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
47728019 AAGCATGAAG
47728029 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
47728056 ATCTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:47728062 original size:15 final size:15
Alignment explanation
Indices: 47728029--47728062 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
47728019 AAGCATGAAG
*
47728029 TTTTATTTTATTTTA
1 TTTTATTTTATTATA
*
47728044 TTTTATTTTATTATC
1 TTTTATTTTATTATA
47728059 TTTT
1 TTTT
47728063 TTACAGGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATTTTATTATA
Found at i:47730482 original size:19 final size:19
Alignment explanation
Indices: 47730443--47730493 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 19
47730433 AAAATTTAGA
47730443 AAAATATAAAAATTATATTT
1 AAAAT-TAAAAATTATATTT
47730463 AAAATTATAAAATT-TATTT
1 AAAATTA-AAAATTATATTT
47730482 AAAATTAAAAAT
1 AAAATTAAAAAT
47730494 AGCTAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.17
19 14 0.47
20 11 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTAAAAATTATATTT
Found at i:47733677 original size:2 final size:2
Alignment explanation
Indices: 47733670--47733696 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47733660 ACAAATTTCA
47733670 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
47733697 AACTTGAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47734317 original size:22 final size:21
Alignment explanation
Indices: 47734292--47734345 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
47734282 TTAAATTTTG
47734292 AAATCTAAAAAATAAAAGAATT
1 AAATCTAAAAAATAAAAGAA-T
*
47734314 AAAT-TCAATAAAATAAAAGCAT
1 AAATCT-AA-AAAATAAAAGAAT
47734336 AAATACTAAA
1 AAAT-CTAAA
47734346 TTATTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
21 1 0.04
22 12 0.44
23 13 0.48
24 1 0.04
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (21 bp):
AAATCTAAAAAATAAAAGAAT
Found at i:47747374 original size:2 final size:2
Alignment explanation
Indices: 47747369--47747408 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
47747359 TTTCTCTCTT
47747369 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47747409 ATAATATTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47747425 original size:3 final size:3
Alignment explanation
Indices: 47747413--47747490 Score: 72
Period size: 3 Copynumber: 26.0 Consensus size: 3
47747403 TATATAATAA
* * *
47747413 TAT TACT TAT TAT TAT TAT TATT TAG T-T TAG TAA TAT TAT TAT T-T
1 TAT TA-T TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
*
47747458 TATT TAT TCT T-T TAT TAT TAT TAT TAT TAT TAT
1 TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
47747491 ATATNNNNNN
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
2 5 0.08
3 49 0.78
4 9 0.14
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:47748552 original size:22 final size:22
Alignment explanation
Indices: 47748496--47748559 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
47748486 GGGCCGAAAT
47748496 TTAATTATAATTTTATCATATA
1 TTAATTATAATTTTATCATATA
* * *
47748518 TCAAAATATAATTTTAT-ATGTA
1 T-TAATTATAATTTTATCATATA
*
47748540 TTAATTTATAATTTCATCAT
1 TTAA-TTATAATTTTATCAT
47748560 TTTTTAAGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
21 2 0.06
22 16 0.48
23 15 0.45
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (22 bp):
TTAATTATAATTTTATCATATA
Found at i:47748659 original size:76 final size:76
Alignment explanation
Indices: 47748579--47748720 Score: 196
Period size: 76 Copynumber: 1.9 Consensus size: 76
47748569 GGCTAAACAA
* * ** *
47748579 AAAAAAATTAGGGG-GTTAAAATGTAATTTTTCTATATATTAATTTATAATTTCTTTATCTATAA
1 AAAAAAATT-GGGGACTCAAAATGTAATTTCACTATATATTAATTTATAATTTCTCTATCTATAA
47748643 GAGGATTGAATT
65 GAGGATTGAATT
* * *
47748655 AAAAAAATTGGGGACTCAAAGTGTAATTTCACTATATATTAATTTATAGTTTCTCTATTTATAAG
1 AAAAAAATTGGGGACTCAAAATGTAATTTCACTATATATTAATTTATAATTTCTCTATCTATAAG
47748720 A
66 A
47748721 AAACTCAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 4 0.07
76 53 0.93
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (76 bp):
AAAAAAATTGGGGACTCAAAATGTAATTTCACTATATATTAATTTATAATTTCTCTATCTATAAG
AGGATTGAATT
Found at i:47750740 original size:13 final size:13
Alignment explanation
Indices: 47750722--47750751 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
47750712 GATAATAGAA
47750722 CATATAGAATACC
1 CATATAGAATACC
47750735 CATATAGAATACC
1 CATATAGAATACC
47750748 CATA
1 CATA
47750752 AGAGATCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (13 bp):
CATATAGAATACC
Found at i:47754269 original size:25 final size:25
Alignment explanation
Indices: 47754224--47754272 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
47754214 ATATAGTTTT
*
47754224 TATATTAATTATAAATGTTATAATA
1 TATATTAATTATAAATATTATAATA
47754249 TATATTATATTAT-AATATTATAAT
1 TATATTA-ATTATAAATATTATAAT
47754273 TAAACAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TATATTAATTATAAATATTATAATA
Found at i:47754437 original size:17 final size:18
Alignment explanation
Indices: 47754404--47754437 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47754394 GTATGTTTGG
*
47754404 TTTCGGTTTTTGATGATT
1 TTTCCGTTTTTGATGATT
47754422 TTTCCGTTTTTG-TGAT
1 TTTCCGTTTTTGATGAT
47754438 CGTTGCTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.09, C:0.09, G:0.21, T:0.62
Consensus pattern (18 bp):
TTTCCGTTTTTGATGATT
Found at i:47755754 original size:12 final size:12
Alignment explanation
Indices: 47755737--47755774 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
47755727 TATTGAGCTG
47755737 GAATTGATGTTT
1 GAATTGATGTTT
* *
47755749 GAATTGA-GCTG
1 GAATTGATGTTT
47755760 GAATTGATGTTT
1 GAATTGATGTTT
47755772 GAA
1 GAA
47755775 CTTTATATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.39
Consensus pattern (12 bp):
GAATTGATGTTT
Found at i:47755755 original size:23 final size:23
Alignment explanation
Indices: 47755728--47755774 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
47755718 GTATGAAATT
47755728 ATTGAGCTGGAATTGATGTTTGA
1 ATTGAGCTGGAATTGATGTTTGA
47755751 ATTGAGCTGGAATTGATGTTTGA
1 ATTGAGCTGGAATTGATGTTTGA
47755774 A
1 A
47755775 CTTTATATTA
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:0.28, C:0.04, G:0.30, T:0.38
Consensus pattern (23 bp):
ATTGAGCTGGAATTGATGTTTGA
Found at i:47755765 original size:11 final size:11
Alignment explanation
Indices: 47755728--47755766 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
47755718 GTATGAAATT
47755728 ATTGAGCTGGA
1 ATTGAGCTGGA
* *
47755739 ATTGATGTTTGA
1 ATTGA-GCTGGA
47755751 ATTGAGCTGGA
1 ATTGAGCTGGA
47755762 ATTGA
1 ATTGA
47755767 TGTTTGAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.28, C:0.05, G:0.31, T:0.36
Consensus pattern (11 bp):
ATTGAGCTGGA
Found at i:47755973 original size:41 final size:41
Alignment explanation
Indices: 47755922--47756043 Score: 111
Period size: 41 Copynumber: 3.0 Consensus size: 41
47755912 TATTGCCAGT
* * * *
47755922 GAAATAATTCAGATTTTATGTCTAGCAGGCTTTATGCCGGA
1 GAAATAATTCAGACTATACGTCTAGCAGGCTTAATGCCGGA
* * *
47755963 GAAATTATTCAGACTATACGTCTAGCAGGCTTAATGCTGGT
1 GAAATAATTCAGACTATACGTCTAGCAGGCTTAATGCCGGA
* * * * * *
47756004 GATACATTTC-GAACTATAAGTCTAGCAGGCTAAAAGCCGG
1 GAAATAATTCAG-ACTATACGTCTAGCAGGCTTAATGCCGG
47756044 TGTACCGAAT
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
40 1 0.02
41 64 0.98
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (41 bp):
GAAATAATTCAGACTATACGTCTAGCAGGCTTAATGCCGGA
Found at i:47756247 original size:13 final size:13
Alignment explanation
Indices: 47756231--47756255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47756221 ATATTAAATA
47756231 TATATGCATTTGG
1 TATATGCATTTGG
47756244 TATATGCATTTG
1 TATATGCATTTG
47756256 ATAAGCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
TATATGCATTTGG
Found at i:47763371 original size:256 final size:256
Alignment explanation
Indices: 47762916--47763427 Score: 988
Period size: 256 Copynumber: 2.0 Consensus size: 256
47762906 TTCAAGAAAC
47762916 AACTCAACTCTTCAATGACAAAAGTTATAGAGTTTGACAGTTTTACGAATTGGTCATCAGGTTAG
1 AACTCAACTCTTCAATGACAAAAGTTATAGAGTTTGACAGTTTTACGAATTGGTCATCAGGTTAG
*
47762981 CCAGATTAAGCTAATACGAGCTCAAAAACATAAAAATTACTAAAAACAGGCTAAATTTCACTTAC
66 CCAGATTAAGCTAATACGAGCTCAAAAACATAAAAATTACTAAAAACAAGCTAAATTTCACTTAC
47763046 CAAAAGGAGATTAAAGCTTGACAGAAGCTTTCCCAACCCTAACAATGGCTATTTGGATTTTCTTC
131 CAAAAGGAGATTAAAGCTTGACAGAAGCTTTCCCAACCCTAACAATGGCTATTTGGATTTTCTTC
47763111 CATGAAGAAGAAAAGAAAATGTTCATATTATCATTTAATTTCTTTAATTTTAACTTAAATT
196 CATGAAGAAGAAAAGAAAATGTTCATATTATCATTTAATTTCTTTAATTTTAACTTAAATT
* *
47763172 AACTCAACTCTTCAATGACAAAAGTTATAGCGTTTGATAGTTTTACGAATTGGTCATCAGGTTAG
1 AACTCAACTCTTCAATGACAAAAGTTATAGAGTTTGACAGTTTTACGAATTGGTCATCAGGTTAG
*
47763237 CTAGATTAAGCTAATACGAGCTCAAAAACATAAAAATTACTAAAAACAAGCTAAATTTCACTTAC
66 CCAGATTAAGCTAATACGAGCTCAAAAACATAAAAATTACTAAAAACAAGCTAAATTTCACTTAC
47763302 CAAAAGGAGATTAAAGCTTGACAGAAGCTTTCCCAACCCTAACAATGGCTATTTGGATTTTCTTC
131 CAAAAGGAGATTAAAGCTTGACAGAAGCTTTCCCAACCCTAACAATGGCTATTTGGATTTTCTTC
47763367 CATGAAGAAGAAAAGAAAATGTTCATATTATCATTTAATTTCTTTAATTTTAACTTAAATT
196 CATGAAGAAGAAAAGAAAATGTTCATATTATCATTTAATTTCTTTAATTTTAACTTAAATT
47763428 TTAACTATTT
Statistics
Matches: 252, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
256 252 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (256 bp):
AACTCAACTCTTCAATGACAAAAGTTATAGAGTTTGACAGTTTTACGAATTGGTCATCAGGTTAG
CCAGATTAAGCTAATACGAGCTCAAAAACATAAAAATTACTAAAAACAAGCTAAATTTCACTTAC
CAAAAGGAGATTAAAGCTTGACAGAAGCTTTCCCAACCCTAACAATGGCTATTTGGATTTTCTTC
CATGAAGAAGAAAAGAAAATGTTCATATTATCATTTAATTTCTTTAATTTTAACTTAAATT
Found at i:47770120 original size:47 final size:46
Alignment explanation
Indices: 47770022--47770124 Score: 111
Period size: 46 Copynumber: 2.2 Consensus size: 46
47770012 CAATAAAGTC
* * *
47770022 CATGAACTAATAAAAATATATTTTTTAAAAATAAGTACACAATGTAT
1 CATGAAC-AATAAAAATATATTTTTTAAAAATAAATAAAAAATGTAT
* * *
47770069 -ATGAACATTAAAATTATATTTATTTTAAAATAAATCAAAAAATG-AT
1 CATGAACAATAAAAATATATTT-TTTAAAAATAAAT-AAAAAATGTAT
47770115 CATGAACAAT
1 CATGAACAAT
47770125 TTATATCATA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
45 13 0.28
46 19 0.41
47 14 0.30
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (46 bp):
CATGAACAATAAAAATATATTTTTTAAAAATAAATAAAAAATGTAT
Found at i:47771315 original size:20 final size:21
Alignment explanation
Indices: 47771274--47771316 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
47771264 CTTTTTTTAT
*
47771274 AAAATAAATTAAATATTATTA
1 AAAATAAATTAAATAATATTA
*
47771295 AAAAT-AATTAAATAATGTTA
1 AAAATAAATTAAATAATATTA
47771315 AA
1 AA
47771317 TTCAAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAATAAATTAAATAATATTA
Found at i:47776371 original size:73 final size:71
Alignment explanation
Indices: 47776292--47776484 Score: 262
Period size: 71 Copynumber: 2.7 Consensus size: 71
47776282 ACAAGGTTTG
* ** *
47776292 AACCTAAGATCTCTATCCTGGAAATCAG-TTTAACTCTCTGTCATCCTCTAACCCATGAACTTCC
1 AACCTAATATCTCTAAACTGGAAAT-AGATTTAA--CTCTGTCATACTCTAACCCATGAACTTCC
47776356 CAGGGTCTA
63 CAGGGTCTA
* *
47776365 AACCTAATATCTCTAAATTGGAAATGGATTTAACTCTGTCATACTCTAACCCATGAACTTCCCAG
1 AACCTAATATCTCTAAACTGGAAATAGATTTAACTCTGTCATACTCTAACCCATGAACTTCCCAG
*
47776430 GGTCTC
66 GGTCTA
* * *
47776436 AACCTAATATCTCTAAATTGGAAATTGATTTAACTCTGTCATTCTCTAA
1 AACCTAATATCTCTAAACTGGAAATAGATTTAACTCTGTCATACTCTAA
47776485 ATTATGTACT
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
71 83 0.75
72 1 0.01
73 26 0.24
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (71 bp):
AACCTAATATCTCTAAACTGGAAATAGATTTAACTCTGTCATACTCTAACCCATGAACTTCCCAG
GGTCTA
Found at i:47776497 original size:71 final size:71
Alignment explanation
Indices: 47776327--47776484 Score: 280
Period size: 71 Copynumber: 2.2 Consensus size: 71
47776317 CAGTTTAACT
*
47776327 CTCTGTCATCCTCTAACCCATGAACTTCCCAGGGTCTAAACCTAATATCTCTAAATTGGAAATGG
1 CTCTGTCATACTCTAACCCATGAACTTCCCAGGGTCTAAACCTAATATCTCTAAATTGGAAATGG
47776392 ATTTAA
66 ATTTAA
* *
47776398 CTCTGTCATACTCTAACCCATGAACTTCCCAGGGTCTCAACCTAATATCTCTAAATTGGAAATTG
1 CTCTGTCATACTCTAACCCATGAACTTCCCAGGGTCTAAACCTAATATCTCTAAATTGGAAATGG
47776463 ATTTAA
66 ATTTAA
*
47776469 CTCTGTCATTCTCTAA
1 CTCTGTCATACTCTAA
47776485 ATTATGTACT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 83 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (71 bp):
CTCTGTCATACTCTAACCCATGAACTTCCCAGGGTCTAAACCTAATATCTCTAAATTGGAAATGG
ATTTAA
Found at i:47779894 original size:36 final size:37
Alignment explanation
Indices: 47779834--47779908 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 37
47779824 TTTAAGTTTG
*
47779834 TTTATATTATTATTTAAATTTTTTA-AAAATATTTAT
1 TTTATATTATTATTTAAATATTTTATAAAATATTTAT
* * *
47779870 TTTATTTTATTATTT-AATAATTTTATATAATTTTTAT
1 TTTATATTATTATTTAAAT-ATTTTATAAAATATTTAT
47779907 TT
1 TT
47779909 ATTGAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 3 0.09
36 19 0.58
37 11 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (37 bp):
TTTATATTATTATTTAAATATTTTATAAAATATTTAT
Found at i:47779904 original size:27 final size:26
Alignment explanation
Indices: 47779874--47779924 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
47779864 ATTTATTTTA
*
47779874 TTTTA-TTATTTAATAATTTTATATAAT
1 TTTTATTTATTGAA-AATTTT-TATAAT
47779901 TTTTATTTATTGAAAATTTTTATA
1 TTTTATTTATTGAAAATTTTTATA
47779925 CAGTCATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 4 0.18
27 11 0.50
28 7 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTATTTATTGAAAATTTTTATAAT
Found at i:47784076 original size:15 final size:15
Alignment explanation
Indices: 47784056--47784086 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47784046 TTTAGTGTAA
47784056 AAATATTTTAATCAT
1 AAATATTTTAATCAT
47784071 AAATATTTTAATCAT
1 AAATATTTTAATCAT
47784086 A
1 A
47784087 CTCTTGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATATTTTAATCAT
Found at i:47784600 original size:17 final size:17
Alignment explanation
Indices: 47784580--47784616 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
47784570 ATTTTTTGAA
47784580 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
*
47784597 TTAGTGAATTTTGTGAT
1 TTAGTGAATTCTGTGAT
47784614 TTA
1 TTA
47784617 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:47785355 original size:46 final size:45
Alignment explanation
Indices: 47785288--47785418 Score: 190
Period size: 46 Copynumber: 2.8 Consensus size: 45
47785278 TAAGGGATAC
* *
47785288 GTAGGTATGATGTTTTAGTGAAGAAAGCCATACTGAGTTGTGAAAA
1 GTAGGTATGGTGTTTCAGTGAAGAAA-CCATACTGAGTTGTGAAAA
*
47785334 GTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAGTTGTGAAAA
1 GTAGGTATGGTGTTTCAGTGAAG-AAACCATACTGAGTTGTGAAAA
* *
47785380 GTAGGTATGGTATTTCAATGAAGGAAACCATACTGAGTT
1 GTAGGTATGGTGTTTCAGTGAA-GAAACCATACTGAGTT
47785419 ATAGCATTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
46 73 0.95
47 4 0.05
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.31
Consensus pattern (45 bp):
GTAGGTATGGTGTTTCAGTGAAGAAACCATACTGAGTTGTGAAAA
Found at i:47792881 original size:21 final size:21
Alignment explanation
Indices: 47792857--47792911 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
47792847 AACAGCGGTG
*
47792857 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
47792878 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
47792899 GCGGTGAGATTAG
1 GCGGTGAGATTAG
47792912 AAATAATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.09, G:0.40, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:47796999 original size:14 final size:14
Alignment explanation
Indices: 47796980--47797020 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
47796970 CTTTTGTTTT
47796980 ATATATATAATATA
1 ATATATATAATATA
47796994 ATATAT-TAATAATA
1 ATATATATAAT-ATA
47797008 ATATA-ATAATATA
1 ATATATATAATATA
47797021 TATTAACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.28
14 18 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATAATATA
Found at i:47797021 original size:24 final size:24
Alignment explanation
Indices: 47796984--47797035 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
47796974 TGTTTTATAT
47796984 ATATAATATAATATATTAA-TAATA
1 ATATAATATAATATATTAACTAA-A
47797008 ATATAATA-ATATATATTAACTAAA
1 ATATAATATA-ATATATTAACTAAA
47797032 ATAT
1 ATAT
47797036 CTTTAACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 1 0.04
24 22 0.85
25 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATAATATAATATATTAACTAAA
Found at i:47797035 original size:14 final size:13
Alignment explanation
Indices: 47796980--47797035 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
47796970 CTTTTGTTTT
*
47796980 ATATATATAATATA
1 ATATAT-TAATAAA
*
47796994 ATATATTAATAAT
1 ATATATTAATAAA
*
47797007 A-ATA-TAATAAT
1 ATATATTAATAAA
47797018 ATATATTAACTAAA
1 ATATATTAA-TAAA
47797032 ATAT
1 ATAT
47797036 CTTTAACATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 8 0.22
12 6 0.17
13 9 0.25
14 13 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATATTAATAAA
Found at i:47799926 original size:42 final size:42
Alignment explanation
Indices: 47799859--47800020 Score: 175
Period size: 42 Copynumber: 3.9 Consensus size: 42
47799849 TCTCATGAGC
* * * * *
47799859 TTCAG-TCAACTCATATGAGTTTCAGTTTGACCCTTCTGGGT
1 TTCAGTTCAGCTCTTATGAGCTTCAGTTTAACCCTTATGGGT
* *
47799900 TTCAGTTCAGCTCTTGTGAGCTTCAGTTTAACCCTAATGGGT
1 TTCAGTTCAGCTCTTATGAGCTTCAGTTTAACCCTTATGGGT
* * * * *
47799942 TTCAGTTTAGCTATTTTGAGCTTCAGATTAACCCTTATAGGTT
1 TTCAGTTCAGCTCTTATGAGCTTCAGTTTAACCCTTAT-GGGT
* *
47799985 TTC-GTTCAGCTCCTATGAGCTTCTGTTTAACCCTTA
1 TTCAGTTCAGCTCTTATGAGCTTCAGTTTAACCCTTA
47800021 CAGGTTTCCC
Statistics
Matches: 100, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
41 5 0.05
42 89 0.89
43 6 0.06
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.41
Consensus pattern (42 bp):
TTCAGTTCAGCTCTTATGAGCTTCAGTTTAACCCTTATGGGT
Found at i:47808064 original size:45 final size:45
Alignment explanation
Indices: 47808013--47808104 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
47808003 AGGATATCTT
47808013 TATCTGTTAATATAAAACATACATAAATTCTCAATATATATGTTC
1 TATCTGTTAATATAAAACATACATAAATTCTCAATATATATGTTC
47808058 TATCTGTTAATATAAAACATACATAAATTCTCAATATATATGTTC
1 TATCTGTTAATATAAAACATACATAAATTCTCAATATATATGTTC
47808103 TA
1 TA
47808105 CTTCTTACAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (45 bp):
TATCTGTTAATATAAAACATACATAAATTCTCAATATATATGTTC
Found at i:47809640 original size:20 final size:20
Alignment explanation
Indices: 47809582--47809650 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
47809572 TTTTATTTAT
*
47809582 AATTTAAATTAATAAAATTA
1 AATTTTAATTAATAAAATTA
** *
47809602 GTTTTATAACTT-TTAAAATTA
1 AATTT-TAA-TTAATAAAATTA
47809623 AATTTTAATTAATAAAA-TA
1 AATTTTAATTAATAAAATTA
47809642 AATTTTAAT
1 AATTTTAAT
47809651 GTAGGATCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
19 13 0.33
20 11 0.28
21 13 0.33
22 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (20 bp):
AATTTTAATTAATAAAATTA
Found at i:47811746 original size:27 final size:26
Alignment explanation
Indices: 47811716--47811770 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
47811706 ATATTTAATA
*
47811716 AAAAAATGTTATT-TTTATTAAATTTTT
1 AAAAAATGATATTATTT-TT-AATTTTT
*
47811743 AAAAATTGATATTATTTTTAATTTTT
1 AAAAAATGATATTATTTTTAATTTTT
47811769 AA
1 AA
47811771 TTATAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.36
27 13 0.52
28 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
AAAAAATGATATTATTTTTAATTTTT
Found at i:47816539 original size:48 final size:48
Alignment explanation
Indices: 47816468--47816565 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
47816458 ATATGAATTG
*
47816468 ATGGACCCGGATTTGTACACTTAGGTGTACCCCTGAACATCCATCGAA
1 ATGGACCCGGATTTGTACACTTAGGTGTACCCCTGAAAATCCATCGAA
47816516 ATGGACCCGGATTTGTACACTTAGGTGTACCCCTGAAAATCCATCGAA
1 ATGGACCCGGATTTGTACACTTAGGTGTACCCCTGAAAATCCATCGAA
47816564 AT
1 AT
47816566 TCCAAGTAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (48 bp):
ATGGACCCGGATTTGTACACTTAGGTGTACCCCTGAAAATCCATCGAA
Found at i:47817620 original size:31 final size:31
Alignment explanation
Indices: 47817561--47817625 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 31
47817551 GGCAAATTAC
47817561 AAGAGTAATTGAATCCTATGAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAT-AAAAACTCTTTA
47817593 AAGAGTAATTGAATCCTA-ATAAAACTCTTTA
1 AAGAGTAATTGAATCCTATA-AAAACTCTTTA
47817624 AA
1 AA
47817626 ATTATCTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 1 0.03
31 13 0.41
32 18 0.56
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTATAAAAACTCTTTA
Found at i:47818566 original size:42 final size:41
Alignment explanation
Indices: 47818507--47818609 Score: 152
Period size: 42 Copynumber: 2.5 Consensus size: 41
47818497 CGGCTATACG
* *
47818507 AACGGCACTAAGTGTGCGAAACTAAAATGACGATGTTGAAT
1 AACGGCACTAAGTGTGCGAAACTAAAATGACAACGTTGAAT
* *
47818548 AACAGGCACTAAGTGTGCGAAATTGAAATGACAACGTTGAAT
1 AAC-GGCACTAAGTGTGCGAAACTAAAATGACAACGTTGAAT
47818590 AACGAGCACTAAGTGTGCGA
1 AACG-GCACTAAGTGTGCGA
47818610 TACCGAGAGC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
41 4 0.07
42 52 0.93
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (41 bp):
AACGGCACTAAGTGTGCGAAACTAAAATGACAACGTTGAAT
Found at i:47820762 original size:33 final size:32
Alignment explanation
Indices: 47820720--47820791 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
47820710 AAATGAGTAC
*
47820720 ATTTGTATTATTTATATA-TAATTAGTAAAAAGAT
1 ATTT-TATTATTCAT-TACTAATTAGT-AAAAGAT
47820754 ATTTTATTATTCATTACTAATTAGTAAAAGAT
1 ATTTTATTATTCATTACTAATTAGTAAAAGAT
47820786 -TTTTAT
1 ATTTTAT
47820792 ATGATAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 6 0.17
32 9 0.25
33 17 0.47
34 4 0.11
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (32 bp):
ATTTTATTATTCATTACTAATTAGTAAAAGAT
Found at i:47820900 original size:18 final size:19
Alignment explanation
Indices: 47820877--47820944 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 19
47820867 TGTAATATTT
*
47820877 ATATTTGTTATTA-AATAG
1 ATATTTATTATTATAATAG
47820895 ATATTTATTATTATAATA-
1 ATATTTATTATTATAATAG
* *
47820913 AT-TATTATTGTT-TAATTG
1 ATAT-TTATTATTATAATAG
47820931 ATATTATATTATTA
1 ATATT-TATTATTA
47820945 GATTAATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
17 5 0.12
18 24 0.60
19 11 0.28
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
ATATTTATTATTATAATAG
Found at i:47821121 original size:26 final size:25
Alignment explanation
Indices: 47821098--47821154 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
47821088 AGAAAGAAGC
* *
47821098 AGAATAGAAACGAAACAGGGAGAAAA
1 AGAA-AGAAAAGAAAAAGGGAGAAAA
47821124 AGAAAGAAAAGAAAAAGGGA-AAGAA
1 AGAAAGAAAAGAAAAAGGGAGAA-AA
47821149 AGAAAG
1 AGAAAG
47821155 GAGAAATAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 22 0.79
26 4 0.14
ACGTcount: A:0.67, C:0.04, G:0.28, T:0.02
Consensus pattern (25 bp):
AGAAAGAAAAGAAAAAGGGAGAAAA
Found at i:47821340 original size:29 final size:29
Alignment explanation
Indices: 47821299--47821356 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
47821289 TTTTTTAGTA
47821299 GGGTTCATGTTGAATA-AATGATTGAATTAG
1 GGGTTCATGTTG-ATAGAATGATTG-ATTAG
* *
47821329 GGGTTTAT-TTGATAGAATTATTGATTAG
1 GGGTTCATGTTGATAGAATGATTGATTAG
47821357 AATTGATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.32
29 10 0.40
30 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.41
Consensus pattern (29 bp):
GGGTTCATGTTGATAGAATGATTGATTAG
Found at i:47822016 original size:2 final size:2
Alignment explanation
Indices: 47822009--47822035 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47821999 TAATTCATTT
47822009 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 T
47822036 CAAAATACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47822554 original size:22 final size:22
Alignment explanation
Indices: 47822491--47822571 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 22
47822481 TGCACTAATG
*
47822491 AACAGAGAGCACTAAAGTGC-A
1 AACAGAGAGCACTGAAGTGCTA
* *
47822512 ATACAGAGAGCACAGATGTGCTA
1 A-ACAGAGAGCACTGAAGTGCTA
* *
47822535 AACAGAGAGCATTGACGTGCTAA
1 AACAGAGAGCACTGAAGTGCT-A
47822558 TAATCAGAGAGCAC
1 -AA-CAGAGAGCAC
47822572 CAACGTGCTA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
21 1 0.02
22 33 0.69
23 3 0.06
24 2 0.04
25 9 0.19
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.15
Consensus pattern (22 bp):
AACAGAGAGCACTGAAGTGCTA
Found at i:47822568 original size:25 final size:25
Alignment explanation
Indices: 47822485--47822619 Score: 115
Period size: 25 Copynumber: 5.6 Consensus size: 25
47822475 TTGATATGCA
* *
47822485 CTAATGAA-CAGAGAGCACTAAAGTG
1 CTAAT-AATCAGAGAGCACCAACGTG
*
47822510 C-AAT-A-CAGAGAGCA-CAGATGTG
1 CTAATAATCAGAGAGCACCA-ACGTG
***
47822532 CT-A-AA-CAGAGAGCATTGACGTG
1 CTAATAATCAGAGAGCACCAACGTG
47822554 CTAATAATCAGAGAGCACCAACGTG
1 CTAATAATCAGAGAGCACCAACGTG
* * *
47822579 CTAGTAGTCAGAGAGCACCAATGTG
1 CTAATAATCAGAGAGCACCAACGTG
47822604 CTAATAATCAGAGAGC
1 CTAATAATCAGAGAGC
47822620 GCGCTAAAGT
Statistics
Matches: 90, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
21 1 0.01
22 32 0.36
23 1 0.01
24 5 0.06
25 51 0.57
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.17
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACCAACGTG
Found at i:47825625 original size:9 final size:9
Alignment explanation
Indices: 47825611--47825695 Score: 107
Period size: 9 Copynumber: 9.4 Consensus size: 9
47825601 GTAGTGATTC
*
47825611 AATTTGGTT
1 AATTCGGTT
*
47825620 AATTTGGTT
1 AATTCGGTT
*
47825629 AATTCGGGT
1 AATTCGGTT
*
47825638 AATTCGGGT
1 AATTCGGTT
*
47825647 AATTCGGGT
1 AATTCGGTT
47825656 AATTCGGTT
1 AATTCGGTT
* *
47825665 AATTTGGGT
1 AATTCGGTT
47825674 AATTCGGTT
1 AATTCGGTT
47825683 AATTCGGTT
1 AATTCGGTT
47825692 AATT
1 AATT
47825696 TTTAACCAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 69 1.00
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:47825640 original size:18 final size:18
Alignment explanation
Indices: 47825619--47825695 Score: 118
Period size: 18 Copynumber: 4.3 Consensus size: 18
47825609 TCAATTTGGT
*
47825619 TAATTTGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
*
47825637 TAATTCGGGTAATTCGGG
1 TAATTCGGTTAATTCGGG
*
47825655 TAATTCGGTTAATTTGGG
1 TAATTCGGTTAATTCGGG
*
47825673 TAATTCGGTTAATTCGGT
1 TAATTCGGTTAATTCGGG
47825691 TAATT
1 TAATT
47825696 TTTAACCAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.23, C:0.08, G:0.26, T:0.43
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGG
Found at i:47825696 original size:27 final size:27
Alignment explanation
Indices: 47825611--47825696 Score: 127
Period size: 27 Copynumber: 3.2 Consensus size: 27
47825601 GTAGTGATTC
* * *
47825611 AATTTGGTTAATTTGGTTAATTCGGGT
1 AATTTGGGTAATTCGGTTAATTCGGTT
* *
47825638 AATTCGGGTAATTCGGGTAATTCGGTT
1 AATTTGGGTAATTCGGTTAATTCGGTT
47825665 AATTTGGGTAATTCGGTTAATTCGGTT
1 AATTTGGGTAATTCGGTTAATTCGGTT
47825692 AATTT
1 AATTT
47825697 TTAACCAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.23, C:0.07, G:0.26, T:0.44
Consensus pattern (27 bp):
AATTTGGGTAATTCGGTTAATTCGGTT
Found at i:47831426 original size:20 final size:20
Alignment explanation
Indices: 47831398--47831461 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
47831388 GCATTATTTA
*
47831398 TTTAAGGTTTAGGATTCAAG
1 TTTAGGGTTTAGGATTCAAG
* *
47831418 TTTAGGGTTTAGGACTCTAG
1 TTTAGGGTTTAGGATTCAAG
* *
47831438 TTTGGGGTTTAAGG-TTTAAG
1 TTTAGGGTTT-AGGATTCAAG
47831458 TTTA
1 TTTA
47831462 AGATTTGAGC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.91
21 3 0.09
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.44
Consensus pattern (20 bp):
TTTAGGGTTTAGGATTCAAG
Found at i:47832797 original size:12 final size:13
Alignment explanation
Indices: 47832780--47832808 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
47832770 TTTAAAATTT
47832780 TTAAA-TAAAAAA
1 TTAAATTAAAAAA
47832792 TTAAATTAAAAAA
1 TTAAATTAAAAAA
47832805 TTAA
1 TTAA
47832809 TACATGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAATTAAAAAA
Found at i:47840813 original size:25 final size:23
Alignment explanation
Indices: 47840756--47840825 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 23
47840746 CCCATTATGA
*
47840756 CTCTTTGTGAGCTTTCCGATTAAAGG
1 CTCTTTGTGAGCTTCCCG-TT--AGG
47840782 CTCTTTGTGAGCTTCCCGTTAGTG
1 CTCTTTGTGAGCTTCCCGTTAG-G
* *
47840806 CTCGTT-TGAACTTCCCGTTA
1 CTCTTTGTGAGCTTCCCGTTA
47840826 TATGGCTATC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
23 15 0.38
24 6 0.15
25 2 0.05
26 17 0.43
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.40
Consensus pattern (23 bp):
CTCTTTGTGAGCTTCCCGTTAGG
Found at i:47844797 original size:9 final size:9
Alignment explanation
Indices: 47844783--47844827 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
47844773 CATTTAAATA
47844783 AATAATTAT
1 AATAATTAT
47844792 AATAATTAT
1 AATAATTAT
47844801 AATAATTAT
1 AATAATTAT
47844810 -ATACA-TAT
1 AATA-ATTAT
*
47844818 AATACTTAT
1 AATAATTAT
47844827 A
1 A
47844828 TATATCTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (9 bp):
AATAATTAT
Found at i:47851679 original size:66 final size:66
Alignment explanation
Indices: 47851573--47851698 Score: 252
Period size: 66 Copynumber: 1.9 Consensus size: 66
47851563 CATTTCAAAG
47851573 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
47851638 T
66 T
47851639 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
47851699 TAATATAAAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.26, C:0.37, G:0.18, T:0.18
Consensus pattern (66 bp):
AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
T
Found at i:47851913 original size:57 final size:57
Alignment explanation
Indices: 47851825--47851933 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 57
47851815 AATTCGGATT
* *
47851825 ACCCGTCCGGGCTAAATCAATTTTCCACATATTATTCGGGAGGGCTATATCAAGATC
1 ACCCGTCCAGGCTAAATCAATTTTCCACATATTATTCGGGAGGGATATATCAAGATC
* * *
47851882 ACCCGTCCAGGCTAGATC-TTTTTCACACATATTCTTCGGGAGGGATATATCA
1 ACCCGTCCAGGCTAAATCAATTTTC-CACATATTATTCGGGAGGGATATATCA
47851934 GGATAGGATC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
56 5 0.11
57 41 0.89
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (57 bp):
ACCCGTCCAGGCTAAATCAATTTTCCACATATTATTCGGGAGGGATATATCAAGATC
Found at i:47855341 original size:16 final size:16
Alignment explanation
Indices: 47855317--47855354 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
47855307 ACTTGTATAT
*
47855317 AACTGATTCTGCTAAC
1 AACTAATTCTGCTAAC
47855333 AACTAATTCTGCTAAC
1 AACTAATTCTGCTAAC
*
47855349 TACTAA
1 AACTAA
47855355 CTGTCTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.32
Consensus pattern (16 bp):
AACTAATTCTGCTAAC
Found at i:47856422 original size:22 final size:22
Alignment explanation
Indices: 47856384--47856425 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
47856374 TTAAAAAATA
47856384 TATTTTAAAAATGATTTTATGT
1 TATTTTAAAAATGATTTTATGT
*
47856406 TATTTATAAATAT-ATTTTAT
1 TATTT-TAAAAATGATTTTAT
47856426 TTAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TATTTTAAAAATGATTTTATGT
Found at i:47856585 original size:27 final size:27
Alignment explanation
Indices: 47856555--47856613 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
47856545 AATTTTAAAA
*
47856555 ATTTAAATATAAAAG-AAAATTTTTATT
1 ATTTAAATA-AAAAGTAAAATTATTATT
*
47856582 ATTTAATTAAAAAGTAAAATTATTATT
1 ATTTAAATAAAAAGTAAAATTATTATT
*
47856609 TTTTA
1 ATTTA
47856614 GTAATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
ATTTAAATAAAAAGTAAAATTATTATT
Found at i:47858499 original size:46 final size:46
Alignment explanation
Indices: 47858426--47858612 Score: 236
Period size: 46 Copynumber: 4.1 Consensus size: 46
47858416 ACAAGGCTAT
* *
47858426 AACTCAGTATGATTTTCTTCACGGAAATACCCTACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
* *
47858472 GACTCAGTATGGTTTTCTTTATC-GAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCA-CGGAAATACCATACCTACTTTTCAC
* * ** *
47858518 AACTCAGTATGGTTTTTTTTACCAAAATACCATACATACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
* *
47858564 AACTTAGTATGGTTTTCTTCACTGG-AATACCATACCTACGTTTCA-
1 AACTCAGTATGGTTTTCTTCAC-GGAAATACCATACCTACTTTTCAC
47858609 AACT
1 AACT
47858613 TTGCCATGGA
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
45 5 0.04
46 117 0.95
47 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
Found at i:47859379 original size:17 final size:17
Alignment explanation
Indices: 47859357--47859404 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
47859347 AAATTCTTTT
47859357 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
* *
47859374 TAAATCACAAAATCCAC
1 TAAATCACAAAATTCAA
*
47859391 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
47859405 TTCTAAATCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:47860635 original size:31 final size:30
Alignment explanation
Indices: 47860599--47860671 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
47860589 GTTTGAGTTA
*
47860599 GGACTAAAATTTCAA-AATTCGAAATGTACAT
1 GGACT-AAATTT-AACAATTCGAAAAGTACAT
47860630 GGACTAAATTTAACCAATTCGAAAAGTACAT
1 GGACTAAATTTAA-CAATTCGAAAAGTACAT
* *
47860661 GAATTAAATTT
1 GGACTAAATTT
47860672 GATCAAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 2 0.05
30 6 0.16
31 29 0.78
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (30 bp):
GGACTAAATTTAACAATTCGAAAAGTACAT
Found at i:47867547 original size:12 final size:13
Alignment explanation
Indices: 47867530--47867567 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
47867520 CAAAAAGCAT
47867530 TATTTTTTCTT-A
1 TATTTTTTCTTCA
*
47867542 TATTTTTTTTTCA
1 TATTTTTTCTTCA
47867555 T-TTTTTTCTTCA
1 TATTTTTTCTTCA
47867567 T
1 T
47867568 GTAAAACCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 21 0.91
13 2 0.09
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTTTCTTCA
Found at i:47870553 original size:13 final size:13
Alignment explanation
Indices: 47870535--47870563 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
47870525 TTCCTCAAGG
47870535 AATGTCTACTCGA
1 AATGTCTACTCGA
47870548 AATGTCTACTCGA
1 AATGTCTACTCGA
47870561 AAT
1 AAT
47870564 CATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (13 bp):
AATGTCTACTCGA
Done.