Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 121 of 182
Found at i:39037828 original size:21 final size:20
Alignment explanation
Indices: 39037799--39037840 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
39037789 TAGTCTTGAC
39037799 TTTTTCTTTCTTT-TCTTTTT
1 TTTTTCTTT-TTTCTCTTTTT
39037819 TTTTTCCTTTTTTCTCTTTTT
1 TTTTT-CTTTTTTCTCTTTTT
39037840 T
1 T
39037841 ATTAGGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTCTTTTTTCTCTTTTT
Found at i:39037831 original size:19 final size:21
Alignment explanation
Indices: 39037799--39037840 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
39037789 TAGTCTTGAC
*
39037799 TTTTTCTTTCTTTTCT-TTTT
1 TTTTTCCTTCTTTTCTCTTTT
39037819 TTTTTCCTT-TTTTCTCTTTT
1 TTTTTCCTTCTTTTCTCTTTT
39037839 TT
1 TT
39037841 ATTAGGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTCCTTCTTTTCTCTTTT
Found at i:39042270 original size:59 final size:59
Alignment explanation
Indices: 39042117--39042521 Score: 401
Period size: 59 Copynumber: 6.8 Consensus size: 59
39042107 AACAAACAGA
* *** * *
39042117 GTCAAAAATGTGATTTTTGGATGCTCGAGAGTAAAATGGTAATTTTTAG-AAGTTCGAGG
1 GTCAAAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGA-G
** * * * *
39042176 GT-AAAACGGTAATTTTTGGACACTT-TAGGGCAAAATGGTAATTTTTGGGAA-TTCGGG
1 GTCAAAAATGTAATTTTTGGACA-TTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGAG
* * * *
39042233 GACCAAAAATGTAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTTGAAAGTTCGAA
1 G-TCAAAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGAG
* * * * * * *
39042293 GTTAAAAATGTAATTCTTGGACATTCAAGGGTAAAATAGTAATTTTTGAAAATTTTGAG
1 GTCAAAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGAG
* *
39042352 GCCAAAAATGTAATTTTTGGACATGCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGAG
1 GTCAAAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGAG
* * * * *
39042411 GTCAAAAATGGAATTTTTGGAAATTTGAGGGTAAAAATGGTAATTTTTGGAAAGTTTGGG
1 GTCAAAAATGTAATTTTTGGACATTCGAGGGT-AAAATGGTAATTTTTGGAAAGTTCGAG
* *
39042471 GTCTAAAATAGTAATTTTTGGA-AGGTTCG-GGGTCAAAATGAT-ATTTTTGGA
1 GTCAAAAAT-GTAATTTTTGGACA--TTCGAGGGT-AAAATGGTAATTTTTGGA
39042522 TTTTCGAGGG
Statistics
Matches: 283, Mismatches: 53, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
57 2 0.01
58 40 0.14
59 168 0.59
60 48 0.17
61 22 0.08
62 3 0.01
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (59 bp):
GTCAAAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGAG
Found at i:39042612 original size:29 final size:29
Alignment explanation
Indices: 39042121--39042624 Score: 320
Period size: 29 Copynumber: 17.1 Consensus size: 29
39042111 AACAGAGTCA
* * * *
39042121 AAAAT-GTGATTTTTGGATGCTCGAGAGT
1 AAAATGGTAATTTTTGGAAGTTCGAGGGT
*
39042149 AAAATGGTAATTTTTAGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGTTCGAGGGT
* * * *
39042178 AAAACGGTAATTTTTGGACACTT-TAGGGC
1 AAAATGGTAATTTTTGGA-AGTTCGAGGGT
*
39042207 AAAATGGTAATTTTTGGGAA-TTCG-GGGACCA
1 AAAATGGTAATTTTT-GGAAGTTCGAGGG---T
*
39042238 AAAAT-GTAATTTTTGGACA-TTCGGGGGT
1 AAAATGGTAATTTTTGGA-AGTTCGAGGGT
* * *
39042266 AAAATGGTAATTTTTTGAAAGTTCGAAGTT
1 AAAATGGTAA-TTTTTGGAAGTTCGAGGGT
* *
39042296 AAAAAT-GTAATTCTTGGACA-TTCAAGGGT
1 -AAAATGGTAATTTTTGGA-AGTTCGAGGGT
* * * * **
39042325 AAAATAGTAATTTTTGAAAATTTTGAGGCCA
1 AAAATGGTAATTTTTG-GAAGTTCGAGG-GT
*
39042356 AAAAT-GTAATTTTTGGACA-TGCGAGGGT
1 AAAATGGTAATTTTTGGA-AGTTCGAGGGT
39042384 AAAATGGTAATTTTTGGAAAGTTCGA-GGT
1 AAAATGGTAATTTTTGG-AAGTTCGAGGGT
* *
39042413 CAAAAATGG-AATTTTTGGAAATTTGAGGGT
1 --AAAATGGTAATTTTTGGAAGTTCGAGGGT
*
39042443 AAAAATGGTAATTTTTGGAAAGTTTG-GGGTCT
1 -AAAATGGTAATTTTTGG-AAGTTCGAGGG--T
*
39042475 AAAATAGTAATTTTTGGAAGGTTCG-GGGT
1 AAAATGGTAATTTTTGGAA-GTTCGAGGGT
* **
39042504 CAAAATGAT-ATTTTTGGATTTTCGAGGGT
1 -AAAATGGTAATTTTTGGAAGTTCGAGGGT
* * ** *
39042533 AAAATAGTAATTTTTAGAAGTTTAAGGGC
1 AAAATGGTAATTTTTGGAAGTTCGAGGGT
** * *
39042562 AAAAAAGTGATTTTTTGTAAGTTCGAGGGT
1 AAAATGGT-AATTTTTGGAAGTTCGAGGGT
* *
39042592 AAAATGGTAA-TTTTGTGAAGTTTGGGGGT
1 AAAATGGTAATTTTTG-GAAGTTCGAGGGT
39042621 AAAA
1 AAAA
39042625 ATGTGATTTT
Statistics
Matches: 376, Mismatches: 65, Indels: 69
0.74 0.13 0.14
Matches are distributed among these distances:
28 40 0.11
29 168 0.45
30 113 0.30
31 54 0.14
32 1 0.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTCGAGGGT
Found at i:39042626 original size:30 final size:30
Alignment explanation
Indices: 39042149--39042680 Score: 223
Period size: 30 Copynumber: 18.0 Consensus size: 30
39042139 GCTCGAGAGT
* * *
39042149 AAAATGGTAATTTTTAGAAGTTCGAGGGT-
1 AAAATGGTAATTTTTGGAAGTTTGGGGGTA
* * * *
39042178 AAAACGGTAATTTTTGGACACTTT-AGGG-C
1 AAAATGGTAATTTTTGGA-AGTTTGGGGGTA
* **
39042207 AAAATGGTAATTTTTGGGAA-TTCGGGGACCA
1 AAAATGGTAATTTTT-GGAAGTTTGGGG-GTA
*
39042238 AAAAT-GTAATTTTTGGACA-TTCGGGGGT-
1 AAAATGGTAATTTTTGGA-AGTTTGGGGGTA
* * ** *
39042266 AAAATGGTAATTTTTTGAAAGTTCGAAGTTA
1 AAAATGGTAA-TTTTTGGAAGTTTGGGGGTA
* ***
39042297 AAAAT-GTAATTCTTGGACA-TTCAAGGGT-
1 AAAATGGTAATTTTTGGA-AGTTTGGGGGTA
* * * * **
39042325 AAAATAGTAATTTTTGAAAATTTTGAGGCCA
1 AAAATGGTAATTTTTG-GAAGTTTGGGGGTA
** *
39042356 AAAAT-GTAATTTTTGGACA-TGCGAGGGT-
1 AAAATGGTAATTTTTGGA-AGTTTGGGGGTA
* *
39042384 AAAATGGTAATTTTTGGAAAG-TTCGAGGTCA
1 AAAATGGTAATTTTTGG-AAGTTTGGGGGT-A
* *
39042415 AAAATGG-AATTTTTGGAAATTTGAGGGTA
1 AAAATGGTAATTTTTGGAAGTTTGGGGGTA
*
39042444 AAAATGGTAATTTTTGGAAAGTTT-GGGGTCT
1 AAAATGGTAATTTTTGG-AAGTTTGGGGGT-A
* * * *
39042475 AAAATAGTAATTTTTGGAAGGTTCGGGGTC
1 AAAATGGTAATTTTTGGAAGTTTGGGGGTA
* * *
39042505 AAAATGAT-ATTTTTGG-ATTTTCGAGGGT-
1 AAAATGGTAATTTTTGGAAGTTT-GGGGGTA
* * ** *
39042533 AAAATAGTAATTTTTAGAAGTTTAAGGGCA
1 AAAATGGTAATTTTTGGAAGTTTGGGGGTA
* * * * *
39042563 AAAA-AGTGATTTTTTGTAAGTTCGAGGGT-
1 AAAATGGT-AATTTTTGGAAGTTTGGGGGTA
39042592 AAAATGGTAA-TTTTGTGAAGTTTGGGGGTA
1 AAAATGGTAATTTTTG-GAAGTTTGGGGGTA
* * *
39042622 AAAAT-GTGA-TTTTGAAAAAGTTTGGGGGTC
1 AAAATGGTAATTTTTG--GAAGTTTGGGGGTA
* *
39042652 AAAAT-ATAATTTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGG-AAGTTTGGGGGT
39042681 CAAATCGTGA
Statistics
Matches: 388, Mismatches: 77, Indels: 75
0.72 0.14 0.14
Matches are distributed among these distances:
28 31 0.08
29 147 0.38
30 157 0.40
31 53 0.14
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAGTTTGGGGGTA
Found at i:39042643 original size:59 final size:58
Alignment explanation
Indices: 39042401--39042708 Score: 173
Period size: 59 Copynumber: 5.2 Consensus size: 58
39042391 TAATTTTTGG
* * * * **
39042401 AAAGTTCGA-GGTCAAAAATGGAATTTTTGGAAATTT-GAGGGTAAAAATGGTAATTTTTGG
1 AAAGTTCGAGGGT--AAAATGTAATTTTTAGAAGTTTAG-GGGTAAAAAT-GTGATTTTTAA
* * * * * *
39042461 AAAGTTTG-GGGTCTAAAATAGTAATTTTTGGAAGGTTCGGGGTCAAAATGAT-ATTTTT-G
1 AAAGTTCGAGGG--TAAAAT-GTAATTTTTAGAAGTTTAGGGGTAAAAATG-TGATTTTTAA
* ** * * * **
39042520 GATTTTCGAGGGTAAAATAGTAATTTTTAGAAGTTTAAGGGCAAAAAAGTGATTTTTTG
1 AAAGTTCGAGGGTAAAAT-GTAATTTTTAGAAGTTTAGGGGTAAAAATGTGATTTTTAA
* * *
39042579 TAAGTTCGAGGGTAAAATGGTAATTTTGT-GAAGTTTGGGGGTAAAAATGTGATTTTGAA
1 AAAGTTCGAGGGTAAAAT-GTAATTTT-TAGAAGTTTAGGGGTAAAAATGTGATTTTTAA
* * * * *
39042638 AAAGTTTGGGGGTCAAAATATAATTTTTGGAAAGTTTAGGGGT-CAAATCGTGATTTTTAA
1 AAAGTTCGAGGGT-AAAATGTAATTTTTAG-AAGTTTAGGGGTAAAAAT-GTGATTTTTAA
*
39042698 AAAATTC-AGGG
1 AAAGTTCGAGGG
39042709 ACCTTTTGGG
Statistics
Matches: 197, Mismatches: 37, Indels: 29
0.75 0.14 0.11
Matches are distributed among these distances:
57 1 0.01
58 37 0.19
59 77 0.39
60 56 0.28
61 24 0.12
62 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (58 bp):
AAAGTTCGAGGGTAAAATGTAATTTTTAGAAGTTTAGGGGTAAAAATGTGATTTTTAA
Found at i:39044533 original size:17 final size:17
Alignment explanation
Indices: 39044511--39044574 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
39044501 GTAGGACCTT
*
39044511 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAA
* * *
39044528 TAAATTCAAACTCAAAA
1 TAAATTTAAATTTAAAA
* *
39044545 TGAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
39044562 TAAATTAAAATTT
1 TAAATTTAAATTT
39044575 GGACTCAATT
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:39047742 original size:24 final size:24
Alignment explanation
Indices: 39047695--39047742 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
39047685 ACTATAACAT
* *
39047695 TCATTTCTATTTTCATTTTAATTC
1 TCATTTCTAATTTCATTTCAATTC
39047719 TCATTTC-AATTTCATTTCATATTC
1 TCATTTCTAATTTCATTTCA-ATTC
39047743 AAATCATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (24 bp):
TCATTTCTAATTTCATTTCAATTC
Found at i:39047743 original size:11 final size:11
Alignment explanation
Indices: 39047694--39047737 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
39047684 GACTATAACA
*
39047694 TTCATTTCTATT
1 TTCATTTC-AAT
*
39047706 TTCATTTTAAT
1 TTCATTTCAAT
39047717 TCTCATTTCAAT
1 T-TCATTTCAAT
39047729 TTCATTTCA
1 TTCATTTCA
39047738 TATTCAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.59
Consensus pattern (11 bp):
TTCATTTCAAT
Found at i:39054636 original size:21 final size:19
Alignment explanation
Indices: 39054583--39054638 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
39054573 TGTAACTTGG
*
39054583 ATGATATTGTGATATTATGT
1 ATGATA-TGTGATATGATGT
39054603 -TGATATG-GAATATAGATGT
1 ATGATATGTG-ATAT-GATGT
39054622 CATGATATGTGATATGA
1 -ATGATATGTGATATGA
39054639 ATATTAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
17 1 0.03
18 6 0.20
19 9 0.30
20 2 0.07
21 11 0.37
22 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (19 bp):
ATGATATGTGATATGATGT
Found at i:39060711 original size:38 final size:40
Alignment explanation
Indices: 39060647--39060734 Score: 114
Period size: 38 Copynumber: 2.3 Consensus size: 40
39060637 ATTATGATTT
39060647 TTATT-AATTCATATTTTAATAATAATTATAATAAAA-ATG
1 TTATTAAATT-ATATTTTAATAATAATTATAATAAAATATG
**
39060686 TTATTAAATTATA-TTTAATAATAATTATGTTAAAATATG
1 TTATTAAATTATATTTTAATAATAATTATAATAAAATATG
39060725 --ATTAAATTAT
1 TTATTAAATTAT
39060735 TTATTATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
37 10 0.22
38 20 0.44
39 11 0.24
40 4 0.09
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (40 bp):
TTATTAAATTATATTTTAATAATAATTATAATAAAATATG
Found at i:39060923 original size:16 final size:16
Alignment explanation
Indices: 39060902--39060941 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
39060892 CAAGAATGCT
39060902 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
*
39060918 ATTACATCTCTATTCC
1 ATTACAACTCTATTCC
39060934 ATTACAAC
1 ATTACAAC
39060942 CCAATTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:39067838 original size:4 final size:4
Alignment explanation
Indices: 39067829--39067853 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39067819 TTGAGAGAAG
39067829 AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA A
39067854 GAGAGAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:39067873 original size:17 final size:16
Alignment explanation
Indices: 39067821--39067883 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 16
39067811 TGGGGCTTTT
*
39067821 GAGAGAAGAAGAAAGAAA
1 GAGAGAA-AA-AAAGAGA
* *
39067839 GAAAGAAAGAAAGAAGA
1 GAGAGAAAAAAAG-AGA
39067856 GAGAGAATAAAAAGAGA
1 GAGAGAA-AAAAAGAGA
39067873 GAGAGAAAAAA
1 GAGAGAAAAAA
39067884 TAAAAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 8 0.21
17 19 0.50
18 11 0.29
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (16 bp):
GAGAGAAAAAAAGAGA
Found at i:39067877 original size:21 final size:22
Alignment explanation
Indices: 39067844--39067889 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
39067834 AGAAAGAAAG
* *
39067844 AAAGAAAGAAGAGAGAGAATAA
1 AAAGAAAGAAGAGAAAAAATAA
*
39067866 AAAGAGAG-AGAGAAAAAATAA
1 AAAGAAAGAAGAGAAAAAATAA
39067887 AAA
1 AAA
39067890 TAATTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (22 bp):
AAAGAAAGAAGAGAAAAAATAA
Found at i:39069934 original size:8 final size:8
Alignment explanation
Indices: 39069927--39069976 Score: 66
Period size: 8 Copynumber: 6.2 Consensus size: 8
39069917 TTTGAGAATT
*
39069927 TAACAATT
1 TAACAATG
39069935 TAACAATG
1 TAACAATG
*
39069943 TAATAATG
1 TAACAATG
39069951 TAACAATG
1 TAACAATG
39069959 TAACAATG
1 TAACAATG
39069967 TTAA-AATG
1 -TAACAATG
39069975 TA
1 TA
39069977 TACAGTGTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
7 2 0.05
8 33 0.87
9 3 0.08
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (8 bp):
TAACAATG
Found at i:39069962 original size:24 final size:24
Alignment explanation
Indices: 39069927--39069976 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
39069917 TTTGAGAATT
*
39069927 TAACAATTTAACAATG-TAATAATG
1 TAACAATGTAACAATGTTAA-AATG
39069951 TAACAATGTAACAATGTTAAAATG
1 TAACAATGTAACAATGTTAAAATG
39069975 TA
1 TA
39069977 TACAGTGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (24 bp):
TAACAATGTAACAATGTTAAAATG
Found at i:39070822 original size:27 final size:27
Alignment explanation
Indices: 39070787--39070840 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
39070777 TCGAGAGGGA
39070787 GGGGAGGAAGCTGTTCCAAAGGGAGAT
1 GGGGAGGAAGCTGTTCCAAAGGGAGAT
* *
39070814 GGGGAGGAAGTTGTTCTAAAGGGAGAT
1 GGGGAGGAAGCTGTTCCAAAGGGAGAT
39070841 AGTGATAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.44, T:0.19
Consensus pattern (27 bp):
GGGGAGGAAGCTGTTCCAAAGGGAGAT
Found at i:39074361 original size:21 final size:21
Alignment explanation
Indices: 39074337--39074402 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
39074327 GTAGAAAAAT
39074337 AACACATTCTAAGATAAACAA
1 AACACATTCTAAGATAAACAA
* * *
39074358 AACA-ATTCTTAACAATTAA-AT
1 AACACATTC-TAA-GATAAACAA
*
39074379 AAC-CATACTAAGATAAACAA
1 AACACATTCTAAGATAAACAA
39074399 AACA
1 AACA
39074403 GAACAATTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
19 4 0.12
20 11 0.33
21 14 0.42
22 4 0.12
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.21
Consensus pattern (21 bp):
AACACATTCTAAGATAAACAA
Found at i:39075522 original size:34 final size:36
Alignment explanation
Indices: 39075475--39075541 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
39075465 TAAAAATTTC
39075475 ATAATTTA-CTTTTT-TAATTTTACATATTTTTTTT
1 ATAATTTATCTTTTTCTAATTTTACATATTTTTTTT
* *
39075509 ATAATTTATTTTTTTCTAATTTTATATATTTTT
1 ATAATTTATCTTTTTCTAATTTTACATATTTTT
39075542 AAATTACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 8 0.28
35 5 0.17
36 16 0.55
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (36 bp):
ATAATTTATCTTTTTCTAATTTTACATATTTTTTTT
Found at i:39083986 original size:295 final size:297
Alignment explanation
Indices: 39083454--39083993 Score: 1012
Period size: 295 Copynumber: 1.8 Consensus size: 297
39083444 ATTTGGAACC
39083454 AAATCACAATGTCAATGTTACTCTAATTGGCAAGAACTGGACCCAAAATCACAGCATGACTAACA
1 AAATCACAATGTCAATGTTACTCTAATTGGCAAGAACTGGACCCAAAATCACAGCATGACTAACA
**
39083519 CTCAAAAAATGAAGGGGTTTAAGTTTTTAGAAAAAAAAGAAATTTATTTCTTTAATGTATAGTTC
66 CTCAAAAAATGAAGGGGTTTAAGTTTTTAGAAAAAAAAGAAATTTATTTCTTTAACCTATAGTTC
39083584 TATTTGATTTTTTTATTGTTATTGATATTAGTATTAAAGAAATATGACCCTTTTACTATAATTTG
131 TATTTGATTTTTTTATTGTTATTGATATTAGTATTAAAGAAATATGACCCTTTTACTATAATTTG
39083649 AAGATATATAACACTTTAATATCTTGCAGCAATGACTCGTTTGCCTTTAACTATTTGGAACCAAA
196 AAGATATATAACACTTTAATATCTTGCAGCAATGACTCGTTTGCCTTTAACTATTTGGAACCAAA
39083714 CCTATAGTGTAAGACAAAGGTATACATGGCTAACCCA
261 CCTATAGTGTAAGACAAAGGTATACATGGCTAACCCA
* *
39083751 AAATCACAATGTCAGTGTTACTCTAATTGGCAAGAACTGGACCCAAAATCACAGCATGACTGACA
1 AAATCACAATGTCAATGTTACTCTAATTGGCAAGAACTGGACCCAAAATCACAGCATGACTAACA
*
39083816 CTC-AAAAATGAGGGGGTTTAAGTTTTTAGAAAAAAAAGAAATTTATTTCTTT-ACCTATAGTTC
66 CTCAAAAAATGAAGGGGTTTAAGTTTTTAGAAAAAAAAGAAATTTATTTCTTTAACCTATAGTTC
39083879 TATTTGATTTTTTTATTGTTATTGATATTAGTATTAAAGAAATATGACCCTTTTACTATAATTTG
131 TATTTGATTTTTTTATTGTTATTGATATTAGTATTAAAGAAATATGACCCTTTTACTATAATTTG
*
39083944 AATATATATAACACTTTAATATCTTGCAGCAATGACTCGTTTGCCTTTAA
196 AAGATATATAACACTTTAATATCTTGCAGCAATGACTCGTTTGCCTTTAA
39083994 TAGTACAAAG
Statistics
Matches: 237, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
295 123 0.52
296 48 0.20
297 66 0.28
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (297 bp):
AAATCACAATGTCAATGTTACTCTAATTGGCAAGAACTGGACCCAAAATCACAGCATGACTAACA
CTCAAAAAATGAAGGGGTTTAAGTTTTTAGAAAAAAAAGAAATTTATTTCTTTAACCTATAGTTC
TATTTGATTTTTTTATTGTTATTGATATTAGTATTAAAGAAATATGACCCTTTTACTATAATTTG
AAGATATATAACACTTTAATATCTTGCAGCAATGACTCGTTTGCCTTTAACTATTTGGAACCAAA
CCTATAGTGTAAGACAAAGGTATACATGGCTAACCCA
Found at i:39087144 original size:16 final size:16
Alignment explanation
Indices: 39087123--39087173 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
39087113 TGAATTACTG
39087123 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
* * *
39087139 ATTACAGCTATATTTC
1 ATTACAACTCTATTCC
*
39087155 ATTACATCTCTATTCC
1 ATTACAACTCTATTCC
39087171 ATT
1 ATT
39087174 CCAGTGAACC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.02, T:0.43
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:39094162 original size:35 final size:35
Alignment explanation
Indices: 39094123--39094193 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
39094113 TAATTAACTA
** *
39094123 ACTAAATTGCATAATATATCTTATAAATTATTTAT
1 ACTAAATTAAATAATATATATTATAAATTATTTAT
* *
39094158 ACTAAATTAAATAATATTTATTATTAATTATTTAT
1 ACTAAATTAAATAATATATATTATAAATTATTTAT
39094193 A
1 A
39094194 TTTGGTTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (35 bp):
ACTAAATTAAATAATATATATTATAAATTATTTAT
Found at i:39097580 original size:20 final size:20
Alignment explanation
Indices: 39097555--39097599 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39097545 TACAAGGTTG
* *
39097555 TAAGAAATTTAGTAATCTTA
1 TAAGAAACTTAATAATCTTA
* *
39097575 TAAGAAGCTTAATAATTTTA
1 TAAGAAACTTAATAATCTTA
39097595 TAAGA
1 TAAGA
39097600 TATTCAAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (20 bp):
TAAGAAACTTAATAATCTTA
Found at i:39100458 original size:73 final size:72
Alignment explanation
Indices: 39100343--39100606 Score: 263
Period size: 73 Copynumber: 3.7 Consensus size: 72
39100333 TTCTTGGCGA
* * *
39100343 ACTATTTATGATGTCGTAGAATCTTTCAACTATGGTCATACACAATATAACCCTATGTTTATCGT
1 ACTATCTATGATGTCGTAGCATCTTTCAACTATGGTCTTACACAATATAACCCTATGTTTA-CGT
* *
39100408 CTTGATGG
65 CTCGACGG
* * * ** *
39100416 ACTATCTATGATGTTGTAGCATCTTTTAACTATGGTCTTACACAATATATCTTTATGTTTACCAT
1 ACTATCTATGATGTCGTAGCATCTTTCAACTATGGTCTTACACAATATAACCCTATGTTTA-CGT
*
39100481 CTCGGCGG
65 CTCGACGG
* * * * **
39100489 ATTATCTATGATGTCGTAGCTTCTTT---C-A-GCTCTTACATAATATAACCCCGTGTTTACTGT
1 ACTATCTATGATGTCGTAGCATCTTTCAACTATGGTCTTACACAATATAACCCTATGTTTAC-GT
*
39100549 CTCGACAG
65 CTCGACGG
* *
39100557 ACTATCTATGATGTCATAG--TCTTTCAATTATGGTCTTACACAATATAACC
1 ACTATCTATGATGTCGTAGCATCTTTCAACTATGGTCTTACACAATATAACC
39100607 TCGTGCTTAT
Statistics
Matches: 154, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
66 5 0.03
67 1 0.01
68 45 0.29
69 1 0.01
70 2 0.01
71 17 0.11
73 83 0.54
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (72 bp):
ACTATCTATGATGTCGTAGCATCTTTCAACTATGGTCTTACACAATATAACCCTATGTTTACGTC
TCGACGG
Found at i:39101854 original size:28 final size:28
Alignment explanation
Indices: 39101822--39101882 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
39101812 AAAATAGGAC
*
39101822 CTTTTAGA-TACTCGGGGGCAAAATGGTA
1 CTTTTAGACT-CTCAGGGGCAAAATGGTA
*
39101850 CTTTTAGACTCTTAGGGGCAAAATGGTA
1 CTTTTAGACTCTCAGGGGCAAAATGGTA
*
39101878 ATTTT
1 CTTTT
39101883 TTGAAGAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (28 bp):
CTTTTAGACTCTCAGGGGCAAAATGGTA
Found at i:39102075 original size:29 final size:29
Alignment explanation
Indices: 39102043--39102279 Score: 139
Period size: 29 Copynumber: 8.1 Consensus size: 29
39102033 AATCAGGATC
*
39102043 AAAAATGGGATTTTTGGACATTT-GGGGT-
1 AAAAATGGAATTTTTGGA-ATTTCGGGGTA
* * *
39102071 TAAAATGGTAATTTTGGGAGTTTCGGGGTA
1 AAAAATGG-AATTTTTGGAATTTCGGGGTA
*
39102101 AAAAATGGAATTTTTGGAAGTTCGGGGT-
1 AAAAATGGAATTTTTGGAATTTCGGGGTA
* * *
39102129 CAAAACGAAATGTTTT-GAAGTTT-GGGAG-A
1 AAAAATGGAAT-TTTTGGAA-TTTCGGG-GTA
** *
39102158 AAAAATATAATTTTTGGAAGTTTCGAGGTA
1 AAAAATGGAATTTTTGGAA-TTTCGGGGTA
* *
39102188 AAAAATAGAAATTTTGGAAGTTT-GAGGGT-
1 AAAAATGGAATTTTTGGAA-TTTCG-GGGTA
* * ** *
39102217 AAAAATGTAATTTTTAGAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGGAA-TTTCGGGGTA
* * *
39102247 AAAAATGGAAATTTTAGAAGTTTGGGGGTA
1 AAAAATGGAATTTTTGGAA-TTTCGGGGTA
39102277 AAA
1 AAA
39102280 TGTACTTTTT
Statistics
Matches: 166, Mismatches: 30, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
28 28 0.17
29 76 0.46
30 62 0.37
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAATTTCGGGGTA
Found at i:39102108 original size:30 final size:30
Alignment explanation
Indices: 39102043--39102279 Score: 170
Period size: 30 Copynumber: 8.1 Consensus size: 30
39102033 AATCAGGATC
* *
39102043 AAAAATGGGATTTTTGGACA-TTT-GGGGT-
1 AAAAATGGAAATTTTGGA-AGTTTCGGGGTA
* * *
39102071 TAAAATGGTAATTTTGGGAGTTTCGGGGTA
1 AAAAATGGAAATTTTGGAAGTTTCGGGGTA
*
39102101 AAAAATGGAATTTTTGGAAG-TTCGGGGT-
1 AAAAATGGAAATTTTGGAAGTTTCGGGGTA
* * *
39102129 CAAAA-CGAAATGTTTTGAAGTTT-GGGAG-A
1 AAAAATGGAAAT-TTTGGAAGTTTCGGG-GTA
** * *
39102158 AAAAATATAATTTTTGGAAGTTTCGAGGTA
1 AAAAATGGAAATTTTGGAAGTTTCGGGGTA
*
39102188 AAAAATAGAAATTTTGGAAGTTT-GAGGGT-
1 AAAAATGGAAATTTTGGAAGTTTCG-GGGTA
* * * ** *
39102217 AAAAATGTAATTTTTAGAAGTTTTAGGGTT
1 AAAAATGGAAATTTTGGAAGTTTCGGGGTA
* *
39102247 AAAAATGGAAATTTTAGAAGTTTGGGGGTA
1 AAAAATGGAAATTTTGGAAGTTTCGGGGTA
39102277 AAA
1 AAA
39102280 TGTACTTTTT
Statistics
Matches: 165, Mismatches: 31, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
27 5 0.03
28 31 0.19
29 55 0.33
30 74 0.45
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
AAAAATGGAAATTTTGGAAGTTTCGGGGTA
Found at i:39102222 original size:59 final size:58
Alignment explanation
Indices: 39102080--39102420 Score: 268
Period size: 58 Copynumber: 5.8 Consensus size: 58
39102070 TTAAAATGGT
* ** * *
39102080 AATTTTGGGAGTTTCG-GGGTAAAAA-ATGGAATTTTTGGAAG-TTCGGGGTCAAAA-CGA
1 AATTTTGGAAGTTT-GAGGGTAAAAATAT--AATTTTTGGAAGTTTTAGGGTAAAAATAGA
* * *
39102137 AATGTTTTGAAGTTTG-GGAGAAAAAATATAATTTTTGGAAG-TTTCGAGGTAAAAAATAGA
1 AAT-TTTGGAAGTTTGAGG-GTAAAAATATAATTTTTGGAAGTTTTAG-GGT-AAAAATAGA
* * *
39102197 AATTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTAGAAGTTTTAGGGTTAAAAATGGA
1 AATTTTGGAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTTTAGGG-TAAAAATAGA
* * * * * *
39102256 AATTTTAGAAGTTTGGGGGT-AAAATGTACTTTTTAGAAGTTTTAGGGTCAAAAAT-GT
1 AATTTTGGAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTTTAGGGT-AAAAATAGA
* * * * * * *
39102313 AATTTTCAGAAGTTTTAAGGATAAAATTGTAATTTTTGGAAGTTTTAGGGTTAAAATATA
1 AATTTT-GGAAG-TTTGAGGGTAAAAATATAATTTTTGGAAGTTTTAGGGTAAAAATAGA
* * *
39102373 ATTTTTGGAAGTTTTAGGGTCAAAATATAATTTTTGGATAG-TTTAGGG
1 AATTTTGGAAGTTTGAGGGTAAAAATATAATTTTTGGA-AGTTTTAGGG
39102421 ACCCTTAGGG
Statistics
Matches: 236, Mismatches: 33, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
57 29 0.12
58 84 0.36
59 81 0.34
60 42 0.18
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (58 bp):
AATTTTGGAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTTTAGGGTAAAAATAGA
Found at i:39102312 original size:30 final size:29
Alignment explanation
Indices: 39102158--39102420 Score: 246
Period size: 30 Copynumber: 9.0 Consensus size: 29
39102148 GTTTGGGAGA
* * *
39102158 AAAAATATAATTTTTGGAAG-TTTCGAGGT
1 AAAAATGTAATTTTTAGAAGTTTTAG-GGT
* * *
39102187 AAAAAATAG-AAATTTTGGAAGTTTGAGGGT
1 -AAAAAT-GTAATTTTTAGAAGTTTTAGGGT
39102217 AAAAATGTAATTTTTAGAAGTTTTAGGGTT
1 AAAAATGTAATTTTTAGAAGTTTTAGGG-T
* * **
39102247 AAAAATGGAAATTTTAGAAGTTTGGGGGT
1 AAAAATGTAATTTTTAGAAGTTTTAGGGT
*
39102276 -AAAATGTACTTTTTAGAAGTTTTAGGGT
1 AAAAATGTAATTTTTAGAAGTTTTAGGGT
* *
39102304 CAAAAATGTAATTTTCAGAAGTTTTAAGGAT
1 -AAAAATGTAATTTTTAGAAGTTTT-AGGGT
* *
39102335 AAAATTGTAATTTTTGGAAGTTTTAGGGT
1 AAAAATGTAATTTTTAGAAGTTTTAGGGT
* * *
39102364 TAAAATATAATTTTTGGAAGTTTTAGGGT
1 AAAAATGTAATTTTTAGAAGTTTTAGGGT
* * *
39102393 CAAAATATAATTTTTGGATAG-TTTAGGG
1 AAAAATGTAATTTTTAGA-AGTTTTAGGG
39102421 ACCCTTAGGG
Statistics
Matches: 198, Mismatches: 27, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
28 24 0.12
29 78 0.39
30 89 0.45
31 7 0.04
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (29 bp):
AAAAATGTAATTTTTAGAAGTTTTAGGGT
Found at i:39102417 original size:29 final size:28
Alignment explanation
Indices: 39102159--39102420 Score: 215
Period size: 29 Copynumber: 9.0 Consensus size: 28
39102149 TTTGGGAGAA
*
39102159 AAAATATAATTTTTGGAAG-TTTCGAGGT
1 AAAATATAATTTTTGGAAGTTTTAG-GGT
* * *
39102187 AAAAAATAGAAATTTTGGAAGTTTGAGGGT
1 --AAAATATAATTTTTGGAAGTTTTAGGGT
* *
39102217 AAAAATGTAATTTTTAGAAGTTTTAGGGTT
1 -AAAATATAATTTTTGGAAGTTTTAGGG-T
* * **
39102247 AAAA-ATGGAAATTTTAGAAGTTTGGGGGT
1 AAAATAT--AATTTTTGGAAGTTTTAGGGT
* * *
39102276 AAAATGTACTTTTTAGAAGTTTTAGGGT
1 AAAATATAATTTTTGGAAGTTTTAGGGT
* ** *
39102304 CAAAAATGTAATTTTCAGAAGTTTTAAGGAT
1 --AAAATATAATTTTTGGAAGTTTT-AGGGT
*
39102335 AAAATTGTAATTTTTGGAAGTTTTAGGGTT
1 AAAA-TATAATTTTTGGAAGTTTTAGGG-T
39102365 AAAATATAATTTTTGGAAGTTTTAGGGT
1 AAAATATAATTTTTGGAAGTTTTAGGGT
39102393 CAAAATATAATTTTTGGATAG-TTTAGGG
1 -AAAATATAATTTTTGGA-AGTTTTAGGG
39102421 ACCCTTAGGG
Statistics
Matches: 195, Mismatches: 25, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
28 19 0.10
29 85 0.44
30 84 0.43
31 7 0.04
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.39
Consensus pattern (28 bp):
AAAATATAATTTTTGGAAGTTTTAGGGT
Found at i:39103597 original size:13 final size:15
Alignment explanation
Indices: 39103581--39103645 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 15
39103571 CCTTATTTAA
39103581 TAATAACATT-TT-T
1 TAATAACATTATTAT
39103594 TAATAACATTATTAT
1 TAATAACATTATTAT
**
39103609 TAATAGTATTTATTAT
1 TAATAACA-TTATTAT
39103625 T-ATAA-ATAGTATTAT
1 TAATAACAT--TATTAT
39103640 TAATAA
1 TAATAA
39103646 TGTTAAAACC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
13 11 0.26
14 3 0.07
15 17 0.40
16 12 0.28
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (15 bp):
TAATAACATTATTAT
Found at i:39103625 original size:19 final size:18
Alignment explanation
Indices: 39103601--39103641 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
39103591 TTTTAATAAC
*
39103601 ATTATTATTAATAGTATTT
1 ATTATTATAAATAGTA-TT
39103620 ATTATTATAAATAGTATT
1 ATTATTATAAATAGTATT
39103638 ATTA
1 ATTA
39103642 ATAATGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
ATTATTATAAATAGTATT
Found at i:39104323 original size:12 final size:12
Alignment explanation
Indices: 39104308--39104339 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39104298 GGGCTTTGAC
39104308 TTGGACTTGTAA
1 TTGGACTTGTAA
*
39104320 TTGGACATGTAA
1 TTGGACTTGTAA
39104332 TTGGACTT
1 TTGGACTT
39104340 TGGACATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (12 bp):
TTGGACTTGTAA
Found at i:39104371 original size:17 final size:17
Alignment explanation
Indices: 39104349--39104410 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
39104339 TTGGACATTT
39104349 TATTAAATTTACAA-TAA
1 TATTAAATTTA-AATTAA
39104366 TATTAAATTTAAATTAA
1 TATTAAATTTAAATTAA
* *
39104383 -ATTAAAATTGAATTTAA
1 TATT-AAATTTAAATTAA
*
39104400 -AATAAATTTAA
1 TATTAAATTTAA
39104411 TATCAAAGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
16 12 0.31
17 27 0.69
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TATTAAATTTAAATTAA
Found at i:39104383 original size:11 final size:11
Alignment explanation
Indices: 39104367--39104410 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
39104357 TTACAATAAT
39104367 ATTAAATTTAA
1 ATTAAATTTAA
*
39104378 ATTAAATTAAA
1 ATTAAATTTAA
*
39104389 ATTGAATTTAA
1 ATTAAATTTAA
*
39104400 AATAAATTTAA
1 ATTAAATTTAA
39104411 TATCAAAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:39104784 original size:92 final size:92
Alignment explanation
Indices: 39104678--39105088 Score: 732
Period size: 92 Copynumber: 4.5 Consensus size: 92
39104668 GATGTCGAGC
* *
39104678 CTTCATCTTGCTCTTACGACAACTTCAGAGAGATAAATACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
39104743 CAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* *
39104770 CTTCATCTTACTCTTACTACAACTTTAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
39104835 CAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* * *
39104862 CTTCATGTTGCTCTTACTACAACTTCAGAGAGATAAAAACTTGCTATCCAACTTTACTACAACAT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
39104927 CAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* *
39104954 CTTCATCTTGGTTTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
39105019 CAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
*
39105046 CTTCATCTTGCTCTTACTACAAGTTCAGAGAGATAAAGACTTG
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTG
39105089 TTATTTTAAT
Statistics
Matches: 302, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 302 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (92 bp):
CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
CAAGAGGATAGGAATTGATGTTTGAAA
Found at i:39109959 original size:18 final size:17
Alignment explanation
Indices: 39109936--39109970 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39109926 GGGCTTTCCT
39109936 TATCTCTCTCTTCCTTTC
1 TATCTCTCTCTT-CTTTC
*
39109954 TATCTCTTTCTTCTTTC
1 TATCTCTCTCTTCTTTC
39109971 CTTTTCATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.06, C:0.34, G:0.00, T:0.60
Consensus pattern (17 bp):
TATCTCTCTCTTCTTTC
Found at i:39117016 original size:28 final size:28
Alignment explanation
Indices: 39116984--39117043 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
39116974 AAATAGGACC
* *
39116984 TTTTAGA-TACCCGGGGGTAAAATGGTAA
1 TTTTAGACT-CCCGAGGGCAAAATGGTAA
*
39117012 TTTTAGACTCTCGAGGGCAAAATGGTAA
1 TTTTAGACTCCCGAGGGCAAAATGGTAA
39117040 TTTT
1 TTTT
39117044 CAAAAGAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (28 bp):
TTTTAGACTCCCGAGGGCAAAATGGTAA
Found at i:39117103 original size:29 final size:29
Alignment explanation
Indices: 39117071--39117131 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
39117061 AAAATAGGAC
*
39117071 TTTTTGGA-TGCTCGAGGGTAAAATGGTAA
1 TTTTTGGACT-CTCGAGGGAAAAATGGTAA
*
39117100 -TTTTGGACTTTCGAGGGAAAAATGGTAA
1 TTTTTGGACTCTCGAGGGAAAAATGGTAA
39117128 TTTT
1 TTTT
39117132 GGGAAATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.38
Consensus pattern (29 bp):
TTTTTGGACTCTCGAGGGAAAAATGGTAA
Found at i:39117302 original size:29 final size:29
Alignment explanation
Indices: 39117249--39117568 Score: 237
Period size: 29 Copynumber: 11.0 Consensus size: 29
39117239 CGGTAATTTA
** *
39117249 GGGTCAAAAAT-GAAAATTTGGAAGTTCG
1 GGGTCAAAAATGGAATTTTTGGAAGTTTG
*
39117277 GGGTCAAAAATGGAATTTTTTGAAGTTTG
1 GGGTCAAAAATGGAATTTTTGGAAGTTTG
*
39117306 GGAG-CAAAAATGTAATTTTT-GAAGTTTCG
1 GG-GTCAAAAATGGAATTTTTGGAAGTTT-G
* * * *
39117335 AGGTTAAAAATGGAAATTTTGGAAGTTTA
1 GGGTCAAAAATGGAATTTTTGGAAGTTTG
* * *
39117364 AGGACAAAAATGTAATTTTTGGAAGTTTTG
1 GGGTCAAAAATGGAATTTTTGGAAG-TTTG
* *
39117394 GGGTTAAAAATGGAAATTTTGGAAGTTTG
1 GGGTCAAAAATGGAATTTTTGGAAGTTTG
* * *
39117423 GGTTTAAAAATGTAATTTTTGGAAGTTTG
1 GGGTCAAAAATGGAATTTTTGGAAGTTTG
* * *
39117452 AAGGTTAAAATAT--AATTTTTAGAAGTTTCG
1 -GGGTCAAAA-ATGGAATTTTTGGAAGTTT-G
* *
39117482 TGGTCAAAATAT--AATTTTTGGAAGTTTTA
1 GGGTCAAAA-ATGGAATTTTTGGAAG-TTTG
* * *
39117511 GGGTCAAAAATGTAA-TTTGGAGAAGTTCGG
1 GGGTCAAAAATGGAATTTTTG-GAAGTT-TG
39117541 GGGTCAAAATAT--AATTTTTGGATAGTTT
1 GGGTCAAAA-ATGGAATTTTTGGA-AGTTT
39117569 AGGGACCCCA
Statistics
Matches: 239, Mismatches: 36, Indels: 33
0.78 0.12 0.11
Matches are distributed among these distances:
28 21 0.09
29 149 0.62
30 65 0.27
31 4 0.02
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
GGGTCAAAAATGGAATTTTTGGAAGTTTG
Found at i:39117400 original size:59 final size:58
Alignment explanation
Indices: 39117265--39117522 Score: 267
Period size: 58 Copynumber: 4.4 Consensus size: 58
39117255 AAAATGAAAA
* * * *
39117265 TTTGGAAG-TTCGGGGTCAAAAATGGAATTTTTTGAAGTTTGGGAGCAAAAATGTAATT
1 TTTGGAAGTTTTGGGGTTAAAAATGGAAATTTTGGAAGTTTGGGA-CAAAAATGTAATT
* * *
39117323 TTT-GAAGTTTCGAGGTTAAAAATGGAAATTTTGGAAGTTTAAGGACAAAAATGTAATT
1 TTTGGAAGTTTTGGGGTTAAAAATGGAAATTTTGGAAGTTT-GGGACAAAAATGTAATT
**
39117381 TTTGGAAGTTTTGGGGTTAAAAATGGAAATTTTGGAAGTTTGGGTTTAAAAATGTAATT
1 TTTGGAAGTTTTGGGGTTAAAAATGGAAATTTTGGAAGTTTGGG-ACAAAAATGTAATT
* * * * *
39117440 TTTGGAAG-TTTGAAGGTTAAAATAT--AATTTTTAGAAGTTTCGTGGTC-AAAATATAATT
1 TTTGGAAGTTTTG-GGGTTAAAA-ATGGAAATTTTGGAAGTTT-G-GGACAAAAATGTAATT
* *
39117498 TTTGGAAGTTTTAGGGTCAAAAATG
1 TTTGGAAGTTTTGGGGTTAAAAATG
39117523 TAATTTGGAG
Statistics
Matches: 172, Mismatches: 18, Indels: 20
0.82 0.09 0.10
Matches are distributed among these distances:
57 6 0.03
58 91 0.53
59 71 0.41
60 4 0.02
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (58 bp):
TTTGGAAGTTTTGGGGTTAAAAATGGAAATTTTGGAAGTTTGGGACAAAAATGTAATT
Found at i:39117536 original size:88 final size:87
Alignment explanation
Indices: 39117252--39117568 Score: 251
Period size: 88 Copynumber: 3.6 Consensus size: 87
39117242 TAATTTAGGG
* * * *
39117252 TCAAAAATGAAAATTT-GGAAGTTCG-GGGTCAAAA-ATGGAATTTTTTGAAGTTT-GGGAG-CA
1 TCAAAAATGTAATTTTGGGAAGTTCGAAGGTCAAAATAT--AATTTTTGGAAGTTTCGGG-GTCA
* *
39117312 AAAATGTAATTTTTGAAGTTTCGAGGT
63 AAAATGAAATTTTGGAAGTTT-G-GGT
* * * * * *
39117339 T-AAAAATGGAAATTTT-GGAAGTT-TAAGGACAAAAATGTAATTTTTGGAAGTTTTGGGGTTAA
1 TCAAAAAT-GTAATTTTGGGAAGTTCGAAGGTC-AAAATATAATTTTTGGAAGTTTCGGGGTCAA
39117401 AAATGGAAATTTTGGAAGTTTGGGT
64 AAAT-GAAATTTTGGAAGTTTGGGT
* * * * * *
39117426 TTAAAAATGTAATTTTTGGAAGTTTGAAGGTTAAAATATAATTTTTAGAAGTTTCGTGGTCAAAA
1 TCAAAAATGTAATTTTGGGAAGTTCGAAGGTCAAAATATAATTTTTGGAAGTTTCGGGGTCAAAA
*
39117491 TAT-AATTTTTGGAAGTTTTAGGG-
66 -ATGAAATTTTGGAAG-TTT-GGGT
**
39117514 TCAAAAATGTAA-TTTGGAGAAGTTCGGGGGTCAAAATATAATTTTTGGATAGTTT
1 TCAAAAATGTAATTTTGG-GAAGTTCGAAGGTCAAAATATAATTTTTGGA-AGTTT
39117569 AGGGACCCCA
Statistics
Matches: 189, Mismatches: 26, Indels: 28
0.78 0.11 0.12
Matches are distributed among these distances:
86 6 0.03
87 59 0.31
88 95 0.50
89 29 0.15
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (87 bp):
TCAAAAATGTAATTTTGGGAAGTTCGAAGGTCAAAATATAATTTTTGGAAGTTTCGGGGTCAAAA
ATGAAATTTTGGAAGTTTGGGT
Found at i:39117536 original size:117 final size:116
Alignment explanation
Indices: 39117277--39117568 Score: 313
Period size: 117 Copynumber: 2.5 Consensus size: 116
39117267 TGGAAGTTCG
* * *
39117277 GGGTCAAAAATGGAATTTTTTGAAGTTTGGGAGCAAAAATGTAATTTTT-GAAGTTTCGAGGTTA
1 GGGTCAAAAAT-GAAATTTTGGAAGTTTGGGAGTAAAAATGTAATTTTTGGAAGTTTCGAGGTTA
* * *
39117341 AAAATGGAAATTTTGGAAGTTTAAGGACAAAAATGTAATTTTTGGAAGTTTTG
65 AAAAT-GAAATTTTAGAAGTTTAAGGACAAAAATATAATTTTTGGAAGTTTTA
* **
39117394 GGGTTAAAAATGGAAATTTTGGAAGTTTGGGTTTAAAAATGTAATTTTTGGAAGTTT-GAAGGTT
1 GGGTCAAAAAT-GAAATTTTGGAAGTTTGGGAGTAAAAATGTAATTTTTGGAAGTTTCG-AGGTT
* ** *
39117458 AAAATAT-AATTTTTAGAAGTTTCGTGGTC-AAAATATAATTTTTGGAAGTTTTA
64 AAAA-ATGAAATTTTAGAAGTTT-AAGGACAAAAATATAATTTTTGGAAGTTTTA
* * * * * *
39117511 GGGTCAAAAATGTAATTTGGAGAAGTTCGGGGGTCAAAATATAATTTTTGGATAGTTT
1 GGGTCAAAAATGAAATTTTG-GAAGTTTGGGAGTAAAAATGTAATTTTTGGA-AGTTT
39117569 AGGGACCCCA
Statistics
Matches: 148, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
116 7 0.05
117 115 0.78
118 24 0.16
119 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (116 bp):
GGGTCAAAAATGAAATTTTGGAAGTTTGGGAGTAAAAATGTAATTTTTGGAAGTTTCGAGGTTAA
AAATGAAATTTTAGAAGTTTAAGGACAAAAATATAATTTTTGGAAGTTTTA
Found at i:39117546 original size:59 final size:58
Alignment explanation
Indices: 39117370--39117572 Score: 205
Period size: 59 Copynumber: 3.5 Consensus size: 58
39117360 TTTAAGGACA
* * * * ** *
39117370 AAAATGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGAAATTTTG-GAAGTTTGGGTTTA
1 AAAATATAATTTTTGGAAGTTTTAGGG-TAAAAAT-GTAATTTTGAGAAGTTCGGGGGTC
* * * * * * *
39117429 AAAATGTAATTTTTGGAAGTTTGAAGGTTAAAATATAATTTTTAGAAGTTTC-GTGGTC
1 AAAATATAATTTTTGGAAGTTTTAGGGTAAAAATGTAATTTTGAGAAG-TTCGGGGGTC
*
39117487 AAAATATAATTTTTGGAAGTTTTAGGGTCAAAAATGTAATTTGGAGAAGTTCGGGGGTC
1 AAAATATAATTTTTGGAAGTTTTAGGGT-AAAAATGTAATTTTGAGAAGTTCGGGGGTC
39117546 AAAATATAATTTTTGGATAG-TTTAGGG
1 AAAATATAATTTTTGGA-AGTTTTAGGG
39117573 ACCCCATAGC
Statistics
Matches: 119, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
57 6 0.05
58 40 0.34
59 71 0.60
60 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (58 bp):
AAAATATAATTTTTGGAAGTTTTAGGGTAAAAATGTAATTTTGAGAAGTTCGGGGGTC
Found at i:39118568 original size:30 final size:29
Alignment explanation
Indices: 39118534--39118639 Score: 108
Period size: 29 Copynumber: 3.6 Consensus size: 29
39118524 AACTGTCCAT
* * *
39118534 AAATTATATTTTGACCTCCGAATTTCTCTA
1 AAATTATATTTTAACC-CCGAACTTCTCAA
* *
39118564 AAATTACATTTTTAACCCCAAAACTTCT-AA
1 AAATTATA-TTTTAACCCC-GAACTTCTCAA
39118594 AAATTATATTTTAACCCCGAAACTTC-CAA
1 AAATTATATTTTAACCCCG-AACTTCTCAA
39118623 AAATTATATTTTGAACC
1 AAATTATATTTT-AACC
39118640 TTAAAAATAC
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
29 30 0.47
30 21 0.33
31 13 0.20
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.37
Consensus pattern (29 bp):
AAATTATATTTTAACCCCGAACTTCTCAA
Found at i:39120699 original size:31 final size:29
Alignment explanation
Indices: 39120664--39120886 Score: 80
Period size: 31 Copynumber: 7.6 Consensus size: 29
39120654 GTTCGAGGGT
39120664 AAAATGGTAATTTTGGGGAAAATCAAGGTCA
1 AAAATGG-AATTTT-GGGAAAATCAAGGTCA
** ***
39120695 AAAATGGAATTTT--GAAAATTTAGGGGT
1 AAAATGGAATTTTGGGAAAATCAAGGTCA
*
39120722 AAAATGGTAATTTTTGGTG-AAATCAAGGTTA
1 AAAATGG-AA-TTTTGG-GAAAATCAAGGTCA
* * *** ***
39120753 AAAATGGGATTTT-GGAAAGTTTGGGGGT
1 AAAATGGAATTTTGGGAAAATCAAGGTCA
***
39120781 AAAATGGTAATTTTGGGTAAAATTGGGGTCA
1 AAAATGG-AATTTTGGG-AAAATCAAGGTCA
* * ** ***
39120812 AAAATAGAATTTT-GGAAAGTTTGAGGGGT
1 AAAATGGAATTTTGGGAAA-ATCAAGGTCA
* *
39120841 AAAATGGTAATTTTAGGTACAATCAAGGTC-
1 AAAATGG-AATTTT-GGGAAAATCAAGGTCA
39120871 AAAATGGAATTTTGGG
1 AAAATGGAATTTTGGG
39120887 GGTAAAATGG
Statistics
Matches: 140, Mismatches: 39, Indels: 29
0.67 0.19 0.14
Matches are distributed among these distances:
27 17 0.12
28 20 0.14
29 32 0.23
30 28 0.20
31 39 0.28
32 4 0.03
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (29 bp):
AAAATGGAATTTTGGGAAAATCAAGGTCA
Found at i:39120737 original size:59 final size:59
Alignment explanation
Indices: 39120660--39120885 Score: 296
Period size: 59 Copynumber: 3.8 Consensus size: 59
39120650 AAAAGTTCGA
*
39120660 GGGTAAAATGGTAATTTTGGGGAAAATCAAGGTCAAAAATGGAATTTT-GAAAATTTAG
1 GGGTAAAATGGTAATTTTGGGGAAAATCAAGGTCAAAAATGGAATTTTGGAAAGTTTAG
* * * *
39120718 GGGTAAAATGGTAATTTTTGGTG-AAATCAAGGTTAAAAATGGGATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAA-TTTTGGGGAAAATCAAGGTCAAAAATGGAATTTTGGAAAGTTTAG
* *** *
39120777 GGGTAAAATGGTAATTTTGGGTAAAATTGGGGTCAAAAATAGAATTTTGGAAAGTTTGAG
1 GGGTAAAATGGTAATTTTGGGGAAAATCAAGGTCAAAAATGGAATTTTGGAAAGTTT-AG
* * *
39120837 GGGTAAAATGGTAATTTTAGGTACAATCAAGGTC-AAAATGGAATTTTGG
1 GGGTAAAATGGTAATTTTGGGGAAAATCAAGGTCAAAAATGGAATTTTGG
39120886 GGGTAAAATG
Statistics
Matches: 144, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
58 43 0.30
59 71 0.49
60 30 0.21
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.31
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTGGGGAAAATCAAGGTCAAAAATGGAATTTTGGAAAGTTTAG
Found at i:39120811 original size:117 final size:118
Alignment explanation
Indices: 39120601--39120885 Score: 355
Period size: 117 Copynumber: 2.4 Consensus size: 118
39120591 TTGATACCCG
* ** **
39120601 GGGGCAAAATGGTAA-TTTTGGTTGAAAT-TGGGTCAAAATAGGGATTTTAAAAAGTTCGAGGGT
1 GGGGTAAAATGGTAATTTTTGG-TGAAATCAAGGTCAAAAT-GGGATTTTGGAAAGTTCGAGGGT
*
39120664 AAAATGGTAATTTTGGGGAAAATCAAGGTCAAAAATGGAATTTT-GAAAATTT-A
64 AAAATGGTAATTTTGGGGAAAATCAAGGTCAAAAATAGAATTTTGGAAAATTTGA
* * *
39120717 GGGGTAAAATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGGATTTTGGAAAGTTTGGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAAGG-TCAAAATGGGATTTTGGAAAGTTCGAGGGTA
* *** *
39120782 AAATGGTAATTTTGGGTAAAATTGGGGTCAAAAATAGAATTTTGGAAAGTTTGA
65 AAATGGTAATTTTGGGGAAAATCAAGGTCAAAAATAGAATTTTGGAAAATTTGA
* *
39120836 GGGGTAAAATGGTAATTTTAGGT-ACAATCAAGGTCAAAATGGAATTTTGG
1 GGGGTAAAATGGTAATTTTTGGTGA-AATCAAGGTCAAAATGGGATTTTGG
39120886 GGGTAAAATG
Statistics
Matches: 146, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
116 20 0.14
117 66 0.45
118 29 0.20
119 31 0.21
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (118 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCAAGGTCAAAATGGGATTTTGGAAAGTTCGAGGGTAA
AATGGTAATTTTGGGGAAAATCAAGGTCAAAAATAGAATTTTGGAAAATTTGA
Found at i:39120853 original size:30 final size:27
Alignment explanation
Indices: 39120695--39120962 Score: 110
Period size: 30 Copynumber: 9.5 Consensus size: 27
39120685 ATCAAGGTCA
*
39120695 AAAATGGAATTTTGAAAATTTAGGGGT
1 AAAATGGAATTTTGGAAATTTAGGGGT
* * *
39120722 AAAATGGTAATTTTTGGTGAAA-TCAAGGTT
1 AAAATGG-AA-TTTT-G-GAAATTTAGGGGT
* *
39120752 AAAAATGGGATTTTGGAAAGTTTGGGGGT
1 -AAAATGGAATTTTGGAAA-TTTAGGGGT
*
39120781 AAAATGGTAATTTTGGGTAAAATT-GGGGT
1 AAAATGG-AATTTT-GG-AAATTTAGGGGT
*
39120810 CAAAAATAGAATTTTGGAAAGTTTGAGGGGT
1 --AAAATGGAATTTTGGAAA-TTT-AGGGGT
* *
39120841 AAAATGGTAATTTTAGGTACAA-TCA-AGGT
1 AAAATGG-AATTTT-GG-A-AATTTAGGGGT
39120870 CAAAATGGAATTTT-G-------GGGGT
1 -AAAATGGAATTTTGGAAATTTAGGGGT
*
39120890 AAAATGGTAATTTTGGAAAGTTTTGGGGT
1 AAAATGG-AATTTTGGAAA-TTTAGGGGT
**
39120919 CAAAATCTAATTTTGGAAAAGTTTAGGGGT
1 -AAAATGGAATTTTGG-AAA-TTTAGGGGT
*
39120949 CAAAATGTAATTTT
1 -AAAATGGAATTTT
39120963 TAGAAAGTTT
Statistics
Matches: 187, Mismatches: 21, Indels: 63
0.69 0.08 0.23
Matches are distributed among these distances:
19 7 0.04
20 9 0.05
21 1 0.01
27 12 0.06
28 13 0.07
29 54 0.29
30 61 0.33
31 27 0.14
32 1 0.01
33 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAATTTAGGGGT
Found at i:39120970 original size:30 final size:30
Alignment explanation
Indices: 39120900--39121144 Score: 228
Period size: 30 Copynumber: 8.1 Consensus size: 30
39120890 AAAATGGTAA
* *
39120900 TTTTGGAAAGTTTTGGGGTCAAAATCTAA-
1 TTTTAGAAAGTTTTGGGGTCAAAATATAAT
* * *
39120929 TTTTGGAAAAGTTTAGGGGTCAAAATGTAAT
1 TTTTAG-AAAGTTTTGGGGTCAAAATATAAT
* *
39120960 TTTTAGAAAGTTTTGAGGTTAAAATATAAT
1 TTTTAGAAAGTTTTGGGGTCAAAATATAAT
* * * * *
39120990 TTTGAAAAAGTTTAGAGGTTAAAATATAAT
1 TTTTAGAAAGTTTTGGGGTCAAAATATAAT
*
39121020 TTTTAGAAAGTTTTGGGGTTAAAATATAAT
1 TTTTAGAAAGTTTTGGGGTCAAAATATAAT
** * * *
39121050 TTCAAAAAAG-TTTGGTGGTTAAAATGTAAT
1 TTTTAGAAAGTTTTGG-GGTCAAAATATAAT
39121080 TTTTA-AGAAGTTTTGGGGTCAAAAATATAA-
1 TTTTAGA-AAGTTTTGGGGTC-AAAATATAAT
* * *
39121110 TTTTGGAAAAGTTTAGGGGTCAAAATGTAAT
1 TTTTAG-AAAGTTTTGGGGTCAAAATATAAT
39121141 TTTT
1 TTTT
39121145 GAACAGTCCA
Statistics
Matches: 182, Mismatches: 25, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
29 12 0.07
30 135 0.74
31 34 0.19
32 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.39
Consensus pattern (30 bp):
TTTTAGAAAGTTTTGGGGTCAAAATATAAT
Found at i:39120971 original size:60 final size:60
Alignment explanation
Indices: 39120885--39121144 Score: 339
Period size: 60 Copynumber: 4.3 Consensus size: 60
39120875 TGGAATTTTG
* * *
39120885 GGGGT-AAAATGGTAA-TTTTGGAAAGTTTTGGGGTCAAAATCTAATTTTGGAAAAGTTTA
1 GGGGTCAAAAT-GTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGAAAAAGTTTA
* *
39120944 GGGGTCAAAATGTAATTTTTAGAAAGTTTTGAGGTTAAAATATAATTTTGAAAAAGTTTA
1 GGGGTCAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGAAAAAGTTTA
* * * * **
39121004 GAGGTTAAAATATAATTTTTAGAAAGTTTTGGGGTTAAAATATAATTTCAAAAAAGTTT-
1 GGGGTCAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGAAAAAGTTTA
* *
39121063 GGTGGTTAAAATGTAATTTTTA-AGAAGTTTTGGGGTCAAAAATATAATTTTGGAAAAGTTTA
1 GG-GGTCAAAATGTAATTTTTAGA-AAGTTTTGGGGTC-AAAATATAATTTTGAAAAAGTTTA
39121125 GGGGTCAAAATGTAATTTTT
1 GGGGTCAAAATGTAATTTTT
39121145 GAACAGTCCA
Statistics
Matches: 177, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
59 11 0.06
60 127 0.72
61 37 0.21
62 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (60 bp):
GGGGTCAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGAAAAAGTTTA
Found at i:39120993 original size:109 final size:109
Alignment explanation
Indices: 39120772--39120968 Score: 260
Period size: 109 Copynumber: 1.8 Consensus size: 109
39120762 TTTTGGAAAG
39120772 TTTGGGGGTAAAATGGTAATTTTGGGTAAAATTGGGGTCAAAAATAGAATTTTGGAAAGTTTGAG
1 TTTGGGGGTAAAATGGTAATTTTGGGTAAAATTGGGGTCAAAAATAGAATTTTGGAAAGTTTGAG
** *
39120837 GGGTAAAATGGTAATTTTAGGTACAATCAAGGTCAAAATGGAAT
66 GGGTAAAATGGTAATTTTAGAAACAATCAAGGTCAAAATAGAAT
* **
39120881 TTTGGGGGTAAAATGGTAATTTT-GG-AAAGTTTTGGGGTC-AAAATCTAATTTTGGAAAAGTTT
1 TTTGGGGGTAAAATGGTAATTTTGGGTAAA--ATTGGGGTCAAAAATAGAATTTTGG-AAAGTTT
39120943 -AGGGGTCAAAAT-GTAATTTTTAGAAA
63 GAGGGGT-AAAATGGTAA-TTTTAGAAA
39120969 GTTTTGAGGT
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
107 3 0.04
108 25 0.32
109 50 0.64
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.34
Consensus pattern (109 bp):
TTTGGGGGTAAAATGGTAATTTTGGGTAAAATTGGGGTCAAAAATAGAATTTTGGAAAGTTTGAG
GGGTAAAATGGTAATTTTAGAAACAATCAAGGTCAAAATAGAAT
Found at i:39121000 original size:90 final size:90
Alignment explanation
Indices: 39120897--39121144 Score: 311
Period size: 90 Copynumber: 2.8 Consensus size: 90
39120887 GGTAAAATGG
* *
39120897 TAATTTTG-GAAAGTTTTGGGGTCAAAATCTAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATT
1 TAATTTTGAAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATT
* *
39120961 TTTAGAAAGTTTTGAGGTTAAAATA
66 TTTAAAAAGTTTGGAGGTTAAAATA
* * * * * * *
39120986 TAATTTTGAAAAAGTTTAGAGGTTAAAATATAATTTT-TAGAAAGTTTTGGGGTTAAAATATAAT
1 TAATTTTGAAAAAGTTTTGGGGTCAAAATATAATTTTGGA-AAAGTTTAGGGGTCAAAATGTAAT
** * *
39121050 TTCAAAAAAGTTTGGTGGTTAAAATG
65 TTTTAAAAAGTTTGGAGGTTAAAATA
* *
39121076 TAATTTTTAAGAAGTTTTGGGGTCAAAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATGTAAT
1 TAATTTTGAAAAAGTTTTGGGGTC-AAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATGTAAT
39121141 TTTT
65 TTTT
39121145 GAACAGTCCA
Statistics
Matches: 129, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
89 9 0.07
90 83 0.64
91 36 0.28
92 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.39
Consensus pattern (90 bp):
TAATTTTGAAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATT
TTTAAAAAGTTTGGAGGTTAAAATA
Found at i:39122339 original size:12 final size:11
Alignment explanation
Indices: 39122324--39122382 Score: 54
Period size: 12 Copynumber: 5.5 Consensus size: 11
39122314 AATACTATCA
39122324 TTATTACTATAT
1 TTATTA-TATAT
*
39122336 TTATTAT-GA-
1 TTATTATATAT
39122345 TTATTAT-TA-
1 TTATTATATAT
*
39122354 TTAATATATAT
1 TTATTATATAT
39122365 TTATTACTATAT
1 TTATTA-TATAT
39122377 TTATTA
1 TTATTA
39122383 GATACATGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 14 0.35
10 3 0.08
11 6 0.15
12 17 0.43
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (11 bp):
TTATTATATAT
Found at i:39123008 original size:17 final size:17
Alignment explanation
Indices: 39122984--39123113 Score: 163
Period size: 17 Copynumber: 7.5 Consensus size: 17
39122974 TGGACATTTG
*
39122984 AATTTAAATTTATAATA
1 AATTTAAATTTAAAATA
*
39123001 ATTTTAAATTTGAAAATA
1 AATTTAAATTT-AAAATA
* *
39123019 AATTTAAACTTAAATTA
1 AATTTAAATTTAAAATA
39123036 AATTTAAATTTAAAAATA
1 AATTTAAATTT-AAAATA
39123054 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
39123071 AATTTAAATTTTAAAACA
1 AATTTAAA-TTTAAAATA
*
39123089 AATTT-AATCTTAAGATA
1 AATTTAAAT-TTAAAATA
39123106 AATTTAAA
1 AATTTAAA
39123114 ATGGGTTTGG
Statistics
Matches: 98, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
16 1 0.01
17 52 0.53
18 45 0.46
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:39123011 original size:29 final size:28
Alignment explanation
Indices: 39122979--39123049 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
39122969 TAATTTGGAC
*
39122979 ATTTGAATTTAAATTTATAA-TAATTTTAA
1 ATTTGAATTTAAATTTA-AACTAA-ATTAA
**
39123008 ATTTGAAAATAAATTTAAACTTAAATTAA
1 ATTTGAATTTAAATTTAAAC-TAAATTAA
*
39123037 ATTTAAATTTAAA
1 ATTTGAATTTAAA
39123050 AATAAATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.06
29 29 0.85
30 3 0.09
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (28 bp):
ATTTGAATTTAAATTTAAACTAAATTAA
Found at i:39123024 original size:35 final size:34
Alignment explanation
Indices: 39122984--39123113 Score: 163
Period size: 35 Copynumber: 3.7 Consensus size: 34
39122974 TGGACATTTG
* *
39122984 AATTTAAATTTATAATAATTTTAAATTTGAAAATA
1 AATTTAAATTTA-AATAAATTTAAATTTAAAAATA
*
39123019 AATTTAAACTTAAATTAAATTTAAATTTAAAAATA
1 AATTTAAATTTAAA-TAAATTTAAATTTAAAAATA
* *
39123054 AATTTAAATTTAAAATAAATTTAAATTTTAAAACA
1 AATTTAAATTT-AAATAAATTTAAATTTAAAAATA
39123089 AATTT-AATCTTAAGATAAATTTAAA
1 AATTTAAAT-TTAA-ATAAATTTAAA
39123114 ATGGGTTTGG
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
34 7 0.08
35 75 0.88
36 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (34 bp):
AATTTAAATTTAAATAAATTTAAATTTAAAAATA
Found at i:39123085 original size:7 final size:6
Alignment explanation
Indices: 39122979--39123081 Score: 90
Period size: 6 Copynumber: 17.7 Consensus size: 6
39122969 TAATTTGGAC
* * *
39122979 ATTTGA ATTTAA ATTTATA A--TAA TTTTAA ATTTGAA A-ATAA ATTTAA
1 ATTTAA ATTTAA ATTTA-A ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA
* ** *
39123026 ACTTAA A-TTAA ATTTAA ATTTAA AAATAA ATTTAA ATTTAA A-ATAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
39123072 ATTTAA ATTT
1 ATTTAA ATTT
39123082 TAAAACAAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
4 1 0.01
5 14 0.18
6 58 0.74
7 5 0.06
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:39123817 original size:92 final size:92
Alignment explanation
Indices: 39123701--39125218 Score: 2561
Period size: 92 Copynumber: 16.5 Consensus size: 92
39123691 GGTGTCGAAG
** * *
39123701 CTTCATCTTGCTCTTACTGCAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
* *
39123766 CAAGAGGATAAGAATTGACGTTTGAAG
66 CAAGAGGATAAGAATTGACATTTGAAA
* * *
39123793 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACAT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
* *
39123858 CAAGAGGATAAGAATTGACGTTTGAAG
66 CAAGAGGATAAGAATTGACATTTGAAA
* *
39123885 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATGAAGGTTCGTTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
* *
39123950 CAAGAGGATAAGAATTGACGTTTGAAG
66 CAAGAGGATAAGAATTGACATTTGAAA
* *
39123977 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATGAAGGTTCGTTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
* * * *
39124042 CAAGAGAATAAGAATTGACGTTCGAAG
66 CAAGAGGATAAGAATTGACATTTGAAA
* *
39124069 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATGAAGGTTCGTTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
* * * *
39124134 CAAGAGAATAAGAATTGACGTTCGAAG
66 CAAGAGGATAAGAATTGACATTTGAAA
* *
39124161 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATGAAGGTTCGTTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
* *
39124226 CAAGAGGATAAGAAATGACGTTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
* *
39124253 CTTCATCTTGTTCTTACTATAACTTCAGAGAAATAAAGGTTCATTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
39124318 CAAGAGGATAAGAATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
39124345 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
39124410 CAAGAGGATAAGAATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
** *
39124437 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTTGTTATCCAACTTTACTATATCTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
*
39124502 CAAGAGGATAAAAATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
* * *
39124529 CTTCATCTTGCTGTTACTGTAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACAATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
39124594 CAAGAGGATAAGAATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
*
39124621 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCATTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
39124686 CAAGAGGATAA-AATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
*
39124712 CTTCATCTTGCTCTTATTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
39124777 CAAGAGGATAAGAATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
* * *
39124804 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATATAGATTCATTATCCAACTTTACTGTAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
*
39124869 CAAGAGGATAAAAATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
*
39124896 CTTCATCTTGCTGTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
39124961 CAAGAGGATAAGAATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
39124988 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
39125053 CAAGAGGATAAGAATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
39125080 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
* * *
39125145 CAAAAGGATAAGAATTGACGTTTGAAG
66 CAAGAGGATAAGAATTGACATTTGAAA
* *
39125172 CTTCATCTTGCTCTTACTAAAACTTCAGAGAGATAAAGATTCATTAT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTAT
39125219 TTTTGATCTG
Statistics
Matches: 1372, Mismatches: 53, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
91 89 0.06
92 1283 0.94
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (92 bp):
CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCATTATCCAACTTTACTATAACTT
CAAGAGGATAAGAATTGACATTTGAAA
Found at i:39126608 original size:7 final size:8
Alignment explanation
Indices: 39126592--39126632 Score: 52
Period size: 7 Copynumber: 5.5 Consensus size: 8
39126582 TCTCCTTTTC
39126592 TTTT-TCT
1 TTTTCTCT
39126599 TTTTCT-T
1 TTTTCTCT
39126606 TTTTCTCT
1 TTTTCTCT
*
39126614 TTTT-TAT
1 TTTTCTCT
39126621 TTTTCTCT
1 TTTTCTCT
39126629 TTTT
1 TTTT
39126633 TTATTTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
7 17 0.59
8 12 0.41
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTCTCT
Found at i:39126610 original size:13 final size:14
Alignment explanation
Indices: 39126586--39126631 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 14
39126576 TCGACCTCTC
39126586 CTTTTC-TTTTTCT
1 CTTTTCTTTTTTCT
39126599 -TTTTCTTTTTTCT
1 CTTTTCTTTTTTCT
*
39126612 CTTTTTTATTTTTCT
1 CTTTTCT-TTTTTCT
39126627 CTTTT
1 CTTTT
39126632 TTTATTTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 5 0.17
13 7 0.24
14 5 0.17
15 12 0.41
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (14 bp):
CTTTTCTTTTTTCT
Found at i:39126616 original size:15 final size:15
Alignment explanation
Indices: 39126587--39126638 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
39126577 CGACCTCTCC
*
39126587 TTTTCTTTTTCT-TT
1 TTTTATTTTTCTCTT
*
39126601 TTCT-TTTTTCTCTT
1 TTTTATTTTTCTCTT
39126615 TTTTATTTTTCTCTTT
1 TTTTATTTTTCTC-TT
39126631 TTTTATTT
1 TTTTATTT
39126639 GTTTTTCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 7 0.21
14 8 0.24
15 8 0.24
16 10 0.30
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTATTTTTCTCTT
Found at i:39127441 original size:11 final size:10
Alignment explanation
Indices: 39127420--39127460 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
39127410 CGTCTTGCCC
39127420 TTTTT-TGTT
1 TTTTTATGTT
39127429 TTTTTACTGTT
1 TTTTTA-TGTT
*
39127440 TTTTT-TGCT
1 TTTTTATGTT
39127449 TTTTTATGTT
1 TTTTTATGTT
39127459 TT
1 TT
39127461 ATTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 13 0.48
10 5 0.19
11 9 0.33
ACGTcount: A:0.05, C:0.05, G:0.10, T:0.80
Consensus pattern (10 bp):
TTTTTATGTT
Found at i:39127445 original size:20 final size:19
Alignment explanation
Indices: 39127420--39127470 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
39127410 CGTCTTGCCC
39127420 TTTTTTGTTTTTTTACTGTT
1 TTTTTTGTTTTTTTA-TGTT
*
39127440 TTTTTTGCTTTTTTATGTT
1 TTTTTTGTTTTTTTATGTT
39127459 TTATTTT-TTTTT
1 TT-TTTTGTTTTT
39127471 GATAGCACGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.06, C:0.04, G:0.08, T:0.82
Consensus pattern (19 bp):
TTTTTTGTTTTTTTATGTT
Found at i:39132131 original size:29 final size:29
Alignment explanation
Indices: 39132094--39132384 Score: 167
Period size: 29 Copynumber: 9.9 Consensus size: 29
39132084 GGTTGAAATT
* * *
39132094 GGGTCAAAACGGGAATTTTGGAAAGTTTGA
1 GGGT-AAAATGGGAATTTTGGAAAATTCGA
* *
39132124 GGGTAAAATGGTAATTTTGAGAAAAATCGA
1 GGGTAAAATGGGAATTTTG-GAAAATTCGA
*
39132154 GGTTAAAAAT-GGAATTTT-GAAAATTCGA
1 GGGT-AAAATGGGAATTTTGGAAAATTCGA
* *
39132182 GGGTAAAATGGTAATTTTTGGTGAAATT--A
1 GGGTAAAATGGGAA-TTTTGG-AAAATTCGA
* * *
39132211 GGGTTAAAAATGGG-ATTTTAGAAAGTT-TA
1 GGG-T-AAAATGGGAATTTTGGAAAATTCGA
*
39132240 GGGGTAAAATGGTAATTTTGGGTAAAA-TC-A
1 -GGGTAAAATGGGAATTTT-GG-AAAATTCGA
* *
39132270 AGGTCAAAAAT-GGAATTTTGGAAAGTTCGA
1 GGGT--AAAATGGGAATTTTGGAAAATTCGA
*
39132300 GGGGTAAAATGGTAATTTTCGGTAAAA-TC-A
1 -GGGTAAAATGGGAATTTT-GG-AAAATTCGA
** *
39132330 GGGTCAAAAAT-GGAATTTTGGAAGTTTAG-
1 GGGT--AAAATGGGAATTTTGGAAAATTCGA
*
39132359 GGGTAAAATGGTAATTTTGGAAAATT
1 GGGTAAAATGGGAATTTTGGAAAATT
39132385 TTGGGGTCAA
Statistics
Matches: 203, Mismatches: 31, Indels: 56
0.70 0.11 0.19
Matches are distributed among these distances:
27 10 0.05
28 44 0.22
29 56 0.28
30 53 0.26
31 37 0.18
32 3 0.01
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (29 bp):
GGGTAAAATGGGAATTTTGGAAAATTCGA
Found at i:39132171 original size:59 final size:59
Alignment explanation
Indices: 39132077--39132435 Score: 373
Period size: 59 Copynumber: 6.1 Consensus size: 59
39132067 GGCAAAACGA
* * **
39132077 TAATTTTGGTTGAAAT-TGGGTCAAAACGGGAATTTTGGAAAGTTTGA-GGGTAAAATGG
1 TAATTTTGG-TAAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGGTAAAATGG
* * * *
39132135 TAATTTTGAGAAAAATC-GAGGTTAAAAATGGAATTTT-GAAAATTCGA-GGGTAAAATGG
1 TAATTTTG-GTAAAATCAG-GGTCAAAAATGGAATTTTGGAAAGTTTGAGGGGTAAAATGG
* * * * *
39132193 TAATTTTTGGTGAAATTAGGGTTAAAAATGGGATTTTAGAAAGTTT-AGGGGTAAAATGG
1 TAA-TTTTGGTAAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGGTAAAATGG
* *
39132252 TAATTTTGGGTAAAATCAAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGGTAAAATGG
1 TAATTTT-GGTAAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGGTAAAATGG
39132312 TAATTTTCGGTAAAATCAGGGTCAAAAATGGAATTTTGG-AAGTTT-AGGGGTAAAATGG
1 TAATTTT-GGTAAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGGTAAAATGG
** **
39132370 TAATTTTGG-AAAATTTTGGGGTC-AAAATCTAATTTTGGAAAAGTTT-AGGGGTTAAAAT-G
1 TAATTTTGGTAAAA--TCAGGGTCAAAAATGGAATTTTGG-AAAGTTTGAGGGG-TAAAATGG
39132429 TAATTTT
1 TAATTTT
39132436 TAGAAAGTTT
Statistics
Matches: 260, Mismatches: 27, Indels: 27
0.83 0.09 0.09
Matches are distributed among these distances:
56 4 0.02
57 15 0.06
58 88 0.34
59 97 0.37
60 56 0.22
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (59 bp):
TAATTTTGGTAAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGGTAAAATGG
Found at i:39132238 original size:117 final size:117
Alignment explanation
Indices: 39132080--39132382 Score: 400
Period size: 117 Copynumber: 2.6 Consensus size: 117
39132070 AAAACGATAA
* *
39132080 TTTTGGTTGAAATT-GGG-TCAAAACGGGAATTTTGGAAAGTTT-GAGGGTAAAATGGTAATTTT
1 TTTTGG-TGAAATTAGGGTTAAAAATGGG-ATTTT-GAAAGTTTAG-GGGTAAAATGGTAATTTT
* *
39132142 GAGAAAAATCGAGGTTAAAAATGGAATTTT-GAAAATTCGA-GGGTAAAATGGTAAT
62 G-GAAAAATCAAGGTCAAAAATGGAATTTTGGAAAATTCGAGGGGTAAAATGGTAAT
39132197 TTTTGGTGAAATTAGGGTTAAAAATGGGATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTGGG
1 TTTTGGTGAAATTAGGGTTAAAAATGGGATTTT-GAAAGTTTAGGGGTAAAATGGTAATTTT-GG
* *
39132262 TAAAATCAAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGGTAAAATGGTAAT
64 AAAAATCAAGGTCAAAAATGGAATTTTGGAAAATTCGAGGGGTAAAATGGTAAT
* * * * * *
39132316 TTTCGGTAAAATCAGGGTCAAAAATGGAATTTTGGAAGTTTAGGGGTAAAATGGTAATTTTGGAA
1 TTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGAAAGTTTAGGGGTAAAATGGTAATTTTGGAA
39132381 AA
66 AA
39132383 TTTTGGGGTC
Statistics
Matches: 166, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
116 7 0.04
117 70 0.42
118 46 0.28
119 43 0.26
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (117 bp):
TTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGAAAGTTTAGGGGTAAAATGGTAATTTTGGAA
AAATCAAGGTCAAAAATGGAATTTTGGAAAATTCGAGGGGTAAAATGGTAAT
Found at i:39132402 original size:29 final size:29
Alignment explanation
Indices: 39132343--39132553 Score: 212
Period size: 29 Copynumber: 7.2 Consensus size: 29
39132333 TCAAAAATGG
* * *
39132343 AATTTTGG-AAGTTTAGGGG-TAAAATGGT
1 AATTTTGGAAAATTTTGGGGTTAAAAT-AT
* *
39132371 AATTTTGGAAAATTTTGGGGTCAAAATCT
1 AATTTTGGAAAATTTTGGGGTTAAAATAT
* *
39132400 AATTTTGGAAAAGTTTAGGGGTTAAAATGT
1 AATTTTGGAAAA-TTTTGGGGTTAAAATAT
* *
39132430 AATTTTTAGAAAGTTTTGGGGTTAAAATAT
1 AA-TTTTGGAAAATTTTGGGGTTAAAATAT
* *
39132460 AATTTTGGAAAAGTTTAGGGTTAAAATAT
1 AATTTTGGAAAATTTTGGGGTTAAAATAT
* *
39132489 AATTTT-TAGAAATTTTAGGGTTAAAATAT
1 AATTTTGGA-AAATTTTGGGGTTAAAATAT
* * *
39132518 AATTTTGGAAAAGTTTAGTGGTTAAAATGT
1 AATTTTGGAAAA-TTTTGGGGTTAAAATAT
39132548 AATTTT
1 AATTTT
39132554 TAAGAAGTTT
Statistics
Matches: 154, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
28 9 0.06
29 79 0.51
30 58 0.38
31 8 0.05
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.40
Consensus pattern (29 bp):
AATTTTGGAAAATTTTGGGGTTAAAATAT
Found at i:39132421 original size:30 final size:30
Alignment explanation
Indices: 39132276--39132583 Score: 266
Period size: 30 Copynumber: 10.4 Consensus size: 30
39132266 ATCAAGGTCA
* *
39132276 AAAATGGAATTTTGG-AAAGTTCGAGGGG-T
1 AAAATGTAATTTTGGAAAAGTT-TAGGGGTT
* *
39132305 AAAATGGTAATTTTCGGTAAAA--TCA-GGGTCA
1 AAAAT-GTAATTTT-GG-AAAAGTTTAGGGGT-T
*
39132336 AAAATGGAATTTTGG--AAGTTTAGGGG-T
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* *
39132363 AAAATGGTAATTTTGGAAAA-TTTTGGGGTC
1 AAAAT-GTAATTTTGGAAAAGTTTAGGGGTT
*
39132393 AAAATCTAATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* *
39132423 AAAATGTAATTTT-TAGAAAGTTTTGGGGTT
1 AAAATGTAATTTTGGA-AAAGTTTAGGGGTT
*
39132453 AAAATATAATTTTGGAAAAGTTTA-GGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* * *
39132482 AAAATATAATTTT-TAGAAATTTTA-GGGTT
1 AAAATGTAATTTTGGA-AAAGTTTAGGGGTT
* *
39132511 AAAATATAATTTTGGAAAAGTTTAGTGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* * *
39132541 AAAATGTAATTTT-TAAGAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAA-AAGTTTAGGGGTT
39132571 AAAATGTAATTTT
1 AAAATGTAATTTT
39132584 TGAACAGTCC
Statistics
Matches: 231, Mismatches: 28, Indels: 39
0.78 0.09 0.13
Matches are distributed among these distances:
26 2 0.01
27 5 0.02
28 12 0.05
29 86 0.37
30 114 0.49
31 9 0.04
33 3 0.01
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGGTT
Found at i:39132492 original size:59 final size:59
Alignment explanation
Indices: 39132329--39132583 Score: 315
Period size: 60 Copynumber: 4.3 Consensus size: 59
39132319 CGGTAAAATC
* * *
39132329 AGGGTCAAAA-ATGGAATTTTGG--AAGTTTAGGGGTAAAATGGTAA-TTTTGGAAAATTTT
1 AGGGTCAAAATAT--AATTTTGGAAAAGTTTAGGGTTAAAAT-GTAATTTTTAGAAAGTTTT
* *
39132387 GGGGTCAAAATCTAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTTAGAAAGTTTT
1 AGGGTCAAAATATAATTTTGGAAAAGTTTA-GGGTTAAAATGTAATTTTTAGAAAGTTTT
* * *
39132447 GGGGTTAAAATATAATTTTGGAAAAGTTTAGGGTTAAAATATAATTTTTAGAAA-TTTT
1 AGGGTCAAAATATAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTTAGAAAGTTTT
* *
39132505 AGGGTTAAAATATAATTTTGGAAAAGTTTAGTGGTTAAAATGTAATTTTTA-AGAAGTTTA
1 AGGGTCAAAATATAATTTTGGAAAAGTTTAG-GGTTAAAATGTAATTTTTAGA-AAGTTTT
*
39132565 AGGGTCAAAATGTAATTTT
1 AGGGTCAAAATATAATTTT
39132584 TGAACAGTCC
Statistics
Matches: 176, Mismatches: 13, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
57 8 0.05
58 44 0.25
59 55 0.31
60 69 0.39
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (59 bp):
AGGGTCAAAATATAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTTAGAAAGTTTT
Found at i:39133681 original size:3 final size:3
Alignment explanation
Indices: 39133675--39133726 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
39133665 TTAAAAAAAA
* * * *
39133675 ATT ATT ATT ATT ACT ATC ATT ATT ACT A-T ATTT ATT ATG ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
39133720 ATT ATT A
1 ATT ATT A
39133727 ATACATATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:39133709 original size:12 final size:11
Alignment explanation
Indices: 39133680--39133752 Score: 57
Period size: 12 Copynumber: 6.7 Consensus size: 11
39133670 AAAAAATTAT
39133680 TATTATTACTA
1 TATTATTACTA
39133691 TCATTATTACTA
1 T-ATTATTACTA
39133703 TATTTATTA-T-
1 TA-TTATTACTA
*
39133713 GATTATTA-T-
1 TATTATTACTA
*
39133722 TATTAATAC-A
1 TATTATTACTA
39133732 TATTTATTACTA
1 TA-TTATTACTA
39133744 TATTTATTA
1 TA-TTATTA
39133753 GATACATGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
9 13 0.25
10 3 0.06
11 9 0.17
12 27 0.52
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (11 bp):
TATTATTACTA
Found at i:39134364 original size:6 final size:6
Alignment explanation
Indices: 39134350--39134434 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
39134340 TAATTTAGAC
* * *
39134350 ATTTGA ATTTAA ATTTATA A--TAA TTTTAA ATTTGAA A-ATAA ATTT-A
1 ATTTAA ATTTAA ATTTA-A ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA
*
39134396 ATCTTAA A-TTAA ATTTAA ATTTAA A-ATAA ATTTAA ATTT
1 AT-TTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
39134435 TTAAAACAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
4 1 0.02
5 17 0.27
6 38 0.60
7 7 0.11
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:39134379 original size:17 final size:17
Alignment explanation
Indices: 39134355--39134467 Score: 122
Period size: 17 Copynumber: 6.5 Consensus size: 17
39134345 TAGACATTTG
*
39134355 AATTTAAATTTATAATA
1 AATTTAAATTTAAAATA
*
39134372 ATTTTAAATTTGAAAATA
1 AATTTAAATTT-AAAATA
*
39134390 AATTT-AATCTTAAATTA
1 AATTTAAAT-TTAAAATA
39134407 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
39134424 AATTTAAATTTTTAAAACA
1 AATTTAAA--TTTAAAATA
*
39134443 AATTT-AATCTTAAGATA
1 AATTTAAAT-TTAAAATA
39134460 AATTTAAA
1 AATTTAAA
39134468 ATGAGTTTGG
Statistics
Matches: 81, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
16 1 0.01
17 49 0.60
18 18 0.22
19 13 0.16
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:39134413 original size:11 final size:11
Alignment explanation
Indices: 39134375--39134433 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
39134365 TATAATAATT
39134375 TTAAATTTGAAA
1 TTAAATTT-AAA
* *
39134387 ATAAATTTAATC
1 TTAAATTTAA-A
39134399 TTAAA-TTAAA
1 TTAAATTTAAA
39134409 TTTAAATTTAAA
1 -TTAAATTTAAA
*
39134421 ATAAATTTAAA
1 TTAAATTTAAA
39134432 TT
1 TT
39134434 TTTAAAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
11 22 0.58
12 16 0.42
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:39134452 original size:53 final size:52
Alignment explanation
Indices: 39134355--39134467 Score: 165
Period size: 53 Copynumber: 2.2 Consensus size: 52
39134345 TAGACATTTG
* * *
39134355 AATTTAAATTTATAATAATTTTAAATTTGAAAATAAATTTAATCTTAA-ATTA
1 AATTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAATCTTAAGA-TA
*
39134407 AATTTAAATTTAAAATAAATTTAAATTTTTAAAACAAATTTAATCTTAAGATA
1 AATTTAAATTTAAAATAAATTTAAA-TTTGAAAACAAATTTAATCTTAAGATA
39134460 AATTTAAA
1 AATTTAAA
39134468 ATGAGTTTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
52 23 0.42
53 31 0.56
54 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (52 bp):
AATTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAATCTTAAGATA
Found at i:39138679 original size:26 final size:27
Alignment explanation
Indices: 39138643--39138697 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
39138633 TTAAAGAAAA
39138643 AAGATGAGAAA-AAGTGGTAGTGGATG
1 AAGATGAGAAATAAGTGGTAGTGGATG
39138669 AAGATGAGAAATAAGTGGTAGTGGATG
1 AAGATGAGAAATAAGTGGTAGTGGATG
39138696 AA
1 AA
39138698 AAAGGAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (27 bp):
AAGATGAGAAATAAGTGGTAGTGGATG
Found at i:39138842 original size:30 final size:31
Alignment explanation
Indices: 39138775--39138847 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
39138765 GACAACAAGA
* * *
39138775 TGACTATTTTGTCACTTTTTGATAACTTTAG
1 TGACTGTTTTGTCACTTTTTGATAACTTGAC
*
39138806 TGACTGTTTTGTCACATTTTT-A-AAGTTGAC
1 TGACTGTTTTGTCAC-TTTTTGATAACTTGAC
39138836 TGACTGTTTTGT
1 TGACTGTTTTGT
39138848 TAAATGTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 17 0.46
31 15 0.41
32 5 0.14
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (31 bp):
TGACTGTTTTGTCACTTTTTGATAACTTGAC
Found at i:39141426 original size:28 final size:26
Alignment explanation
Indices: 39141364--39141426 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
39141354 TTTAATATAT
*
39141364 GTCGATTTTTTTAATTTGCCAAATAG
1 GTCGATTTTTTTAATTTGCAAAATAG
* *
39141390 G-CAATTTTTTTTAAATTTAGGAAAATAG
1 GTCGA-TTTTTTT-AATTT-GCAAAATAG
39141418 GTCGATTTT
1 GTCGATTTT
39141427 GGAGAGAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
25 2 0.07
26 8 0.28
27 5 0.17
28 12 0.41
29 2 0.07
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (26 bp):
GTCGATTTTTTTAATTTGCAAAATAG
Found at i:39143503 original size:16 final size:16
Alignment explanation
Indices: 39143484--39143525 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
39143474 CCGTTACATA
39143484 TATATTATATTTACTT
1 TATATTATATTTACTT
* *
39143500 TATATTTTATTTATTT
1 TATATTATATTTACTT
39143516 TATATTATAT
1 TATATTATAT
39143526 AATTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTATATTTACTT
Found at i:39156312 original size:50 final size:50
Alignment explanation
Indices: 39156258--39156364 Score: 160
Period size: 50 Copynumber: 2.1 Consensus size: 50
39156248 AAGAATAGTG
* * * *
39156258 GATTGAAGCTATAAAACCAAATCTTATATCCCTGAAGTTGCATTGGATCA
1 GATTGAAGCTACAAAACCAAATCCTATATCCCTAAAGTTGCAGTGGATCA
* *
39156308 GATTGAAGCTACAAAACCAAATCCTATATCCTTAAAGTTGCAGTGGATCC
1 GATTGAAGCTACAAAACCAAATCCTATATCCCTAAAGTTGCAGTGGATCA
39156358 GATTGAA
1 GATTGAA
39156365 ATTAGGAAGG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (50 bp):
GATTGAAGCTACAAAACCAAATCCTATATCCCTAAAGTTGCAGTGGATCA
Found at i:39156469 original size:51 final size:51
Alignment explanation
Indices: 39156364--39156471 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 51
39156354 ATCCGATTGA
* *
39156364 AATTAGGAAGGCAAATCCTTATCTCTCTGAGGTTGCAATAGAGAACAATGG
1 AATTACGAAGGCAAATCCTTATCTCTCTGAGGTTGCAATAGAGAACAATAG
* * * *
39156415 AATTACGAAGGCAAATCCTTCTCTCTCTTAGGTTGCAGTAGAGCAA-GATAG
1 AATTACGAAGGCAAATCCTTATCTCTCTGAGGTTGCAATAGAG-AACAATAG
39156466 AATTAC
1 AATTAC
39156472 AAAATCGAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
51 48 0.96
52 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (51 bp):
AATTACGAAGGCAAATCCTTATCTCTCTGAGGTTGCAATAGAGAACAATAG
Found at i:39156483 original size:51 final size:51
Alignment explanation
Indices: 39156374--39156484 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 51
39156364 AATTAGGAAG
* * *
39156374 GCAAATCCTTATCTCTCTGAGGTTGCAATAGAGAACAATGGAATTACGAAG
1 GCAAATCCTTATCTCTCTGAGGTTGCAATAGAGAACAATAGAATTACAAAA
* * * *
39156425 GCAAATCCTTCTCTCTCTTAGGTTGCAGTAGAGCAA-GATAGAATTACAAAA
1 GCAAATCCTTATCTCTCTGAGGTTGCAATAGAG-AACAATAGAATTACAAAA
* *
39156476 TCGAATCCT
1 GCAAATCCT
39156485 ATACCCCTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 48 0.96
52 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (51 bp):
GCAAATCCTTATCTCTCTGAGGTTGCAATAGAGAACAATAGAATTACAAAA
Found at i:39157389 original size:11 final size:10
Alignment explanation
Indices: 39157371--39157416 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
39157361 CATACATACA
39157371 TATTTATATT
1 TATTTATATT
39157381 TACTTTATATTT
1 TA-TTTATA-TT
39157393 TATTTAT-TT
1 TATTTATATT
39157402 TATATTATA-T
1 TAT-TTATATT
39157412 TATTT
1 TATTT
39157417 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
9 7 0.22
10 10 0.31
11 11 0.34
12 4 0.12
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTATATT
Found at i:39157418 original size:16 final size:16
Alignment explanation
Indices: 39157374--39157422 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
39157364 ACATACATAT
*
39157374 TTATATTTACTTTATA
1 TTATATTTATTTTATA
*
39157390 TTTTATTTATTTTATA
1 TTATATTTATTTTATA
*
39157406 TTATA-TTATTTTTTA
1 TTATATTTATTTTATA
39157421 TT
1 TT
39157423 TCAAAACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATATTTATTTTATA
Found at i:39160301 original size:21 final size:21
Alignment explanation
Indices: 39160277--39160347 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
39160267 TTTGTTTTAC
*
39160277 CGGTAGAAGTATGGGTTGTAT
1 CGGTAGAAGTATGAGTTGTAT
*
39160298 CGGTAGAACCTA-GAGTTGTAT
1 CGGTAGAA-GTATGAGTTGTAT
* * * *
39160319 CAGTAGAAGTCTGAGTTCTAC
1 CGGTAGAAGTATGAGTTGTAT
39160340 CGGTAGAA
1 CGGTAGAA
39160348 TTCTGAAGCT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.03
21 37 0.93
22 2 0.05
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (21 bp):
CGGTAGAAGTATGAGTTGTAT
Found at i:39161037 original size:22 final size:22
Alignment explanation
Indices: 39161012--39161055 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
39161002 TTAGTCATCC
39161012 TTAGTATA-TATATTAGCATTTT
1 TTAGTATAGTATATT-GCATTTT
* *
39161034 TTAGTTTAGTTTATTGCATTTT
1 TTAGTATAGTATATTGCATTTT
39161056 CTAACTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (22 bp):
TTAGTATAGTATATTGCATTTT
Found at i:39169941 original size:13 final size:14
Alignment explanation
Indices: 39169923--39169952 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39169913 GTCAACATAA
39169923 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
39169936 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
39169950 TCA
1 TCA
39169953 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:39172143 original size:17 final size:17
Alignment explanation
Indices: 39172107--39172141 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
39172097 TAACAAAAGT
39172107 AATGCAATGACAAATAA
1 AATGCAATGACAAATAA
39172124 AATGCAATGAC-AATAA
1 AATGCAATGACAAATAA
39172140 AA
1 AA
39172142 ATACAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.17
Consensus pattern (17 bp):
AATGCAATGACAAATAA
Found at i:39174260 original size:20 final size:21
Alignment explanation
Indices: 39174235--39174273 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39174225 GTAAGGAATT
39174235 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
39174255 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
39174274 TAGAAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:39192690 original size:24 final size:24
Alignment explanation
Indices: 39192643--39192695 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
39192633 ATTCGTAAGG
*
39192643 ATAAATGTAAAGTGGCTGACGAGC
1 ATAAATGTAAAGTGGCTCACGAGC
* *
39192667 CTAAATGTAAAGTGGCTCATGAGC
1 ATAAATGTAAAGTGGCTCACGAGC
39192691 ATAAA
1 ATAAA
39192696 AGTGGCTGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.23
Consensus pattern (24 bp):
ATAAATGTAAAGTGGCTCACGAGC
Found at i:39195233 original size:24 final size:24
Alignment explanation
Indices: 39195194--39195251 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
39195184 TATCTTCTTT
* *
39195194 ATCTTCACCTCGACCCTAATATTC
1 ATCTTCATCTCAACCCTAATATTC
** *
39195218 ATCTTCATCTCAACCCTCGTCTTC
1 ATCTTCATCTCAACCCTAATATTC
39195242 ATCTTCATCT
1 ATCTTCATCT
39195252 TCACACCTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.21, C:0.38, G:0.03, T:0.38
Consensus pattern (24 bp):
ATCTTCATCTCAACCCTAATATTC
Found at i:39195263 original size:24 final size:25
Alignment explanation
Indices: 39195215--39195275 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
39195205 GACCCTAATA
39195215 TTCATCTTCATC-TCAACCCTCGTC
1 TTCATCTTCATCTTCAACCCTCGTC
39195239 TTCATCTTCATCTTC-ACACCT-GTC
1 TTCATCTTCATCTTCAAC-CCTCGTC
* *
39195263 TTCGTCTCCATCT
1 TTCATCTTCATCT
39195276 AATTCTTCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.15, C:0.39, G:0.05, T:0.41
Consensus pattern (25 bp):
TTCATCTTCATCTTCAACCCTCGTC
Found at i:39201189 original size:15 final size:14
Alignment explanation
Indices: 39201149--39201190 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
39201139 GGGGGTTTTC
39201149 TATAAAAATAA-TA
1 TATAAAAATAATTA
*
39201162 TTTAAAAATTAATTAA
1 TATAAAAA-TAATT-A
39201178 TATAAAAATAATT
1 TATAAAAATAATT
39201191 GTTATAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 7 0.29
14 3 0.12
15 6 0.25
16 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TATAAAAATAATTA
Found at i:39201525 original size:15 final size:14
Alignment explanation
Indices: 39201505--39201552 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 14
39201495 TTGTTTCGGA
39201505 TTATATTCTAATTAT
1 TTATATT-TAATTAT
39201520 TTATATTTAAATTA-
1 TTATATTT-AATTAT
39201534 TTATATTTTAATTAT
1 TTATA-TTTAATTAT
39201549 TTAT
1 TTAT
39201553 GGTATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATATTTAATTAT
Found at i:39201704 original size:18 final size:18
Alignment explanation
Indices: 39201681--39201723 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39201671 TAATAAGATT
39201681 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
39201699 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
39201717 TTAATTA
1 TTAATTA
39201724 TACCTTGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:39202789 original size:31 final size:32
Alignment explanation
Indices: 39202730--39202791 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
39202720 AAATTTTAAA
*
39202730 TTAATAAAAATAAAATTATACTTTAATTTTTC
1 TTAATAAAAATAAAATTATAATTTAATTTTTC
39202762 TTAA-AAATAATAAAATT-TAATTTAATTTTT
1 TTAATAAA-AATAAAATTATAATTTAATTTTT
39202792 AAAAATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (32 bp):
TTAATAAAAATAAAATTATAATTTAATTTTTC
Found at i:39203614 original size:22 final size:21
Alignment explanation
Indices: 39203573--39203628 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
39203563 TTCTTTTTAT
39203573 TTATGATATTT-TTTCCCTTAAA
1 TTATGATATTTATTT-CCTT-AA
39203595 TTATGATATTTATGTT-CTTAA
1 TTATGATATTTAT-TTCCTTAA
39203616 TTAT-ATTATTTAT
1 TTATGA-TATTTAT
39203629 ACTTATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.03
21 13 0.42
22 14 0.45
23 1 0.03
24 2 0.06
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (21 bp):
TTATGATATTTATTTCCTTAA
Found at i:39207688 original size:47 final size:47
Alignment explanation
Indices: 39207635--39207725 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
39207625 GAATTGATGA
39207635 CTAATTGATGTACAATAAATAAATTGTACAAGCTACGAAAGTTATAG
1 CTAATTGATGTACAATAAATAAATTGTACAAGCTACGAAAGTTATAG
*
39207682 CTAATTGATGTACAGTAAATAAATTGTACAAGCTACGAAAGTTA
1 CTAATTGATGTACAATAAATAAATTGTACAAGCTACGAAAGTTA
39207726 ATTCCTATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (47 bp):
CTAATTGATGTACAATAAATAAATTGTACAAGCTACGAAAGTTATAG
Found at i:39208545 original size:13 final size:13
Alignment explanation
Indices: 39208529--39208554 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39208519 TTATGATTGG
39208529 ATAGTATGTATAT
1 ATAGTATGTATAT
39208542 ATAGTATGTATAT
1 ATAGTATGTATAT
39208555 GATGATATTA
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:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
ATAGTATGTATAT
Found at i:39216747 original size:24 final size:24
Alignment explanation
Indices: 39216714--39216791 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
39216704 ATTCGTAAGG
*
39216714 ATAAATGTAAAGTGGCTGACGAGC
1 ATAAACGTAAAGTGGCTGACGAGC
* * *
39216738 CTAAACGTAAAGTGGCTTATGAGC
1 ATAAACGTAAAGTGGCTGACGAGC
* *
39216762 ATAAACGTAAAGTGGCTGAGGAAC
1 ATAAACGTAAAGTGGCTGACGAGC
39216786 ATAAAC
1 ATAAAC
39216792 ATACATTAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.21
Consensus pattern (24 bp):
ATAAACGTAAAGTGGCTGACGAGC
Found at i:39222810 original size:15 final size:15
Alignment explanation
Indices: 39222764--39222811 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
39222754 GGGGGTTTTC
39222764 TATAAAAATAA-TAT
1 TATAAAAATAATTAT
* *
39222778 TA-AAAATTAATTAA
1 TATAAAAATAATTAT
*
39222792 TATAAAAATAATTGT
1 TATAAAAATAATTAT
39222807 TATAA
1 TATAA
39222812 TATCTATTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
13 7 0.26
14 6 0.22
15 14 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
TATAAAAATAATTAT
Found at i:39223168 original size:15 final size:14
Alignment explanation
Indices: 39223148--39223195 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
39223138 TTGTTTCGGA
39223148 TTATATTCTAATTAT
1 TTATATT-TAATTAT
39223163 TTATATTTAAATTA-
1 TTATATTT-AATTAT
*
39223177 TTATATTTTAACTAT
1 TTATA-TTTAATTAT
39223192 TTAT
1 TTAT
39223196 GGTATAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATATTTAATTAT
Found at i:39223192 original size:14 final size:14
Alignment explanation
Indices: 39223147--39223192 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
39223137 TTTGTTTCGG
*
39223147 ATTATATTCTAATT
1 ATTATATTTTAATT
*
39223161 ATTTATATTTAAATT
1 A-TTATATTTTAATT
*
39223176 ATTATATTTTAACT
1 ATTATATTTTAATT
39223190 ATT
1 ATT
39223193 TATGGTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATATTTTAATT
Found at i:39223348 original size:18 final size:18
Alignment explanation
Indices: 39223325--39223367 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39223315 TAATAAGATT
39223325 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
39223343 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
39223361 TTAATTA
1 TTAATTA
39223368 TACTTTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:39225252 original size:22 final size:21
Alignment explanation
Indices: 39225211--39225266 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
39225201 TTCTTTTTAT
39225211 TTATGATATTT-TTTCCCTTAAA
1 TTATGATATTTATTT-CCTT-AA
39225233 TTATGATATTTATGTT-CTTAA
1 TTATGATATTTAT-TTCCTTAA
39225254 TTAT-ATTATTTAT
1 TTATGA-TATTTAT
39225267 ACTTATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.03
21 13 0.42
22 14 0.45
23 1 0.03
24 2 0.06
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (21 bp):
TTATGATATTTATTTCCTTAA
Found at i:39230242 original size:18 final size:19
Alignment explanation
Indices: 39230209--39230251 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
39230199 CATCAAATGG
*
39230209 ATTAAATCGTAAAATATGA
1 ATTAAATCGGAAAATATGA
39230228 ATTAAAT-GGAAAATATGA
1 ATTAAATCGGAAAATATGA
39230246 A-TAAAT
1 ATTAAAT
39230252 ACATTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 11 0.48
19 7 0.30
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (19 bp):
ATTAAATCGGAAAATATGA
Found at i:39247768 original size:18 final size:18
Alignment explanation
Indices: 39247745--39247788 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
39247735 ATATACATTT
39247745 TTTCTTCTCTCAATTCTC
1 TTTCTTCTCTCAATTCTC
39247763 TTTCTTCTCTCAATTCTC
1 TTTCTTCTCTCAATTCTC
39247781 TTTCTTCT
1 TTTCTTCT
39247789 TCTGGTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.09, C:0.32, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTCTTCTCTCAATTCTC
Found at i:39248649 original size:51 final size:51
Alignment explanation
Indices: 39248588--39248689 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
39248578 ACACGGAAGT
* *
39248588 CATGTTACCATTTAAC-GAGTCAGTTATGGTTTTCGTACAACACTATAAACA
1 CATGTCACCATTTAACAG-GTCAGTTATGATTTTCGTACAACACTATAAACA
39248639 CATGTCACCATTTAACAGGTCAGTTATGATTTTCGTACAACACTATAAACA
1 CATGTCACCATTTAACAGGTCAGTTATGATTTTCGTACAACACTATAAACA
39248690 AAAAATGATC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 47 0.98
52 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (51 bp):
CATGTCACCATTTAACAGGTCAGTTATGATTTTCGTACAACACTATAAACA
Found at i:39251930 original size:18 final size:18
Alignment explanation
Indices: 39251907--39251945 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
39251897 AGCTATTGAG
39251907 AATATGTACTTATGCATA
1 AATATGTACTTATGCATA
39251925 AATATGTACTTATGCATA
1 AATATGTACTTATGCATA
39251943 AAT
1 AAT
39251946 CCTAACCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (18 bp):
AATATGTACTTATGCATA
Found at i:39254202 original size:21 final size:22
Alignment explanation
Indices: 39254178--39254225 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
39254168 TAAAAGTACC
39254178 TAAACAATTAAAAA-A-ATATTT
1 TAAA-AATTAAAAATATATATTT
39254199 TAAAAATTAAAAATATTATATTT
1 TAAAAATTAAAAATA-TATATTT
39254222 TAAA
1 TAAA
39254226 TAAAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.38
21 5 0.21
23 10 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAATTAAAAATATATATTT
Found at i:39256900 original size:55 final size:54
Alignment explanation
Indices: 39256788--39256948 Score: 171
Period size: 55 Copynumber: 2.9 Consensus size: 54
39256778 GCTATGTAAT
* * ** * *
39256788 AATCGATTTAAATATATAAACAATTGATT-AATAAGAAGTAGCATTTCAGCATAAC
1 AATCGATTTAAACATATAAA-AATTGATTCAA-AAGAAGCAATATTCCAACATAAC
* * *
39256843 AATCGATTTAAACATATAAATAATTAATTCAAAAGAAACAATATTCCAACATGAC
1 AATCGATTTAAACATATAAA-AATTGATTCAAAAGAAGCAATATTCCAACATAAC
** *
39256898 AATAAATTTAAGCATATGAAAAATTGATTCAAAAGAAGCAATATTCCAACA
1 AATCGATTTAAACATAT-AAAAATTGATTCAAAAGAAGCAATATTCCAACA
39256949 ATTAAGAAGA
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
55 84 0.94
56 5 0.06
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (54 bp):
AATCGATTTAAACATATAAAAATTGATTCAAAAGAAGCAATATTCCAACATAAC
Found at i:39257211 original size:6 final size:6
Alignment explanation
Indices: 39257195--39257224 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
39257185 AACTGTAACA
39257195 TCCATT T-CATT TCCATT TCCATT TCCATT T
1 TCCATT TCCATT TCCATT TCCATT TCCATT T
39257225 TCATATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.17, C:0.30, G:0.00, T:0.53
Consensus pattern (6 bp):
TCCATT
Found at i:39257217 original size:17 final size:17
Alignment explanation
Indices: 39257195--39257248 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
39257185 AACTGTAACA
*
39257195 TCCATTTCATTTCCATT
1 TCCATTTCATTTTCATT
*
39257212 TCCATTTCCATTTTCATA
1 TCCATTT-CATTTTCATT
39257230 T-CATTCTCATTTTCATT
1 TCCATT-TCATTTTCATT
39257247 TC
1 TC
39257249 ATATTCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 21 0.68
18 10 0.32
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.54
Consensus pattern (17 bp):
TCCATTTCATTTTCATT
Found at i:39257219 original size:12 final size:11
Alignment explanation
Indices: 39257195--39257250 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
39257185 AACTGTAACA
39257195 TCCATTTCATT
1 TCCATTTCATT
39257206 TCCATTTCCATT
1 TCCATTT-CATT
*
39257218 TCCATTTTCATA
1 TCCA-TTTCATT
39257230 T-CATTCTCATT
1 TCCATT-TCATT
*
39257241 TTCATTTCAT
1 TCCATTTCAT
39257251 ATTCAAATCA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 2 0.05
11 18 0.46
12 16 0.41
13 3 0.08
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.54
Consensus pattern (11 bp):
TCCATTTCATT
Found at i:39257234 original size:23 final size:23
Alignment explanation
Indices: 39257195--39257252 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
39257185 AACTGTAACA
*
39257195 TCCATTTCATTTCCATT-TCCATT
1 TCCATTTCATATCCATTCT-CATT
39257218 TCCATTTTCATAT-CATTCTCATT
1 TCCA-TTTCATATCCATTCTCATT
*
39257241 TTCATTTCATAT
1 TCCATTTCATAT
39257253 TCAAATCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 8 0.26
23 15 0.48
24 8 0.26
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (23 bp):
TCCATTTCATATCCATTCTCATT
Found at i:39257250 original size:17 final size:16
Alignment explanation
Indices: 39257197--39257255 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 16
39257187 CTGTAACATC
*
39257197 CATTTCATTTCCATTT
1 CATTTCATTTTCATTT
*
39257213 CCATTTCCATTTTCATAT
1 -CATTT-CATTTTCATTT
39257231 CATTCTCATTTTCATTT
1 CATT-TCATTTTCATTT
39257248 CATATTCA
1 CAT-TTCA
39257256 AATCATAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 25 0.69
18 11 0.31
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (16 bp):
CATTTCATTTTCATTT
Found at i:39258147 original size:26 final size:26
Alignment explanation
Indices: 39258107--39258158 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
39258097 TTTAATTTCT
* *
39258107 TCAAGAAT-ATTTTTTCTTTATTTTTA
1 TCAAGAATAAATTTTT-ATTATTTTTA
39258133 TCAAGAATAAATTTTTATTATTTTTA
1 TCAAGAATAAATTTTTATTATTTTTA
39258159 ATACTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.58
Consensus pattern (26 bp):
TCAAGAATAAATTTTTATTATTTTTA
Found at i:39268642 original size:30 final size:30
Alignment explanation
Indices: 39268576--39268689 Score: 97
Period size: 30 Copynumber: 3.8 Consensus size: 30
39268566 ATTTTGACCC
*
39268576 CAAACTTTTCAAAAATTATGTTTTAGCCTT
1 CAAACTTTTCAAAAATTATGTTTTAGCCCT
* * *
39268606 TAAACTTTTCAAAAATTATTTTTTGGCCCT
1 CAAACTTTTCAAAAATTATGTTTTAGCCCT
* ** * * *
39268636 CGAAC-TTTCTAAAAATTCAAATTTGA-TCAT
1 CAAACTTTTC-AAAAATT-ATGTTTTAGCCCT
*
39268666 CAAACTTTTTAAAAATTATGTTTT
1 CAAACTTTTCAAAAATTATGTTTT
39268690 TACCCTTAAC
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
29 8 0.12
30 49 0.77
31 7 0.11
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (30 bp):
CAAACTTTTCAAAAATTATGTTTTAGCCCT
Done.