Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 162 of 187
Found at i:47852998 original size:18 final size:19
Alignment explanation
Indices: 47852949--47853006 Score: 75
Period size: 18 Copynumber: 3.1 Consensus size: 19
47852939 CACGTAAAAC
47852949 TTTTA-ATACATCTAACAT
1 TTTTACATACATCTAACAT
* *
47852967 TTATTTCCTACATCTAAC-T
1 TT-TTACATACATCTAACAT
47852986 TTTTACATACATCTAACAT
1 TTTTACATACATCTAACAT
47853005 TT
1 TT
47853007 ATTTCAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 15 0.45
19 8 0.24
20 10 0.30
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTACATACATCTAACAT
Found at i:47853107 original size:52 final size:52
Alignment explanation
Indices: 47853038--47853481 Score: 816
Period size: 52 Copynumber: 8.5 Consensus size: 52
47853028 CTAAAACTTT
* * *
47853038 TTTTTTTCATTCAATCTCATTTGTTTCAATTTTTTTTCCTACATATAATACC
1 TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
47853090 TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
1 TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
47853142 TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
1 TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
47853194 TTTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
1 -TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
47853247 TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
1 TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
47853299 TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
1 TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
*
47853351 TATTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
1 TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
*
47853403 TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACTTT
1 TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATAC--C
47853457 TTTTTTTCATTCAATCTCATTTATT
1 TTTTTTTCATTCAATCTCATTTATT
47853482 ACATCTAATT
Statistics
Matches: 383, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
52 306 0.80
53 52 0.14
54 25 0.07
ACGTcount: A:0.26, C:0.19, G:0.02, T:0.53
Consensus pattern (52 bp):
TTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTACATATAATACC
Found at i:47853198 original size:157 final size:157
Alignment explanation
Indices: 47853002--47853481 Score: 822
Period size: 157 Copynumber: 3.1 Consensus size: 157
47852992 ATACATCTAA
** * * *
47853002 CATTTATTTCAACA-G-TTTTCCTACACCTAAAACTTTTTTTTTTCATTCAATCTCATTTGTTTC
1 CATTTATTTCAA-ATGTTTTTCCTACATATAATAC-CTTTTTTTTCATTCAATCTCATTTATTTC
* *
47853065 AATTTTTTTTCCTACATATAATACCTTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCT
64 AAATGTTTTTCCTACATATAATACCTTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCT
47853130 ACATATAATACCTTTTTTTCATTCAATCT
129 ACATATAATACCTTTTTTTCATTCAATCT
47853159 CATTTATTTCAAATGTTTTTCCTACATATAATACCTTTTTTTTCATTCAATCTCATTTATTTCAA
1 CATTTATTTCAAATGTTTTTCCTACATATAATACCTTTTTTTTCATTCAATCTCATTTATTTCAA
47853224 ATGTTTTTCCTACATATAATACCTTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTAC
66 ATGTTTTTCCTACATATAATACCTTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTAC
47853289 ATATAATACCTTTTTTTCATTCAATCT
131 ATATAATACCTTTTTTTCATTCAATCT
*
47853316 CATTTATTTCAAATGTTTTTCCTACATATAATACC-TATTTTTCATTCAATCTCATTTATTTCAA
1 CATTTATTTCAAATGTTTTTCCTACATATAATACCTTTTTTTTCATTCAATCTCATTTATTTCAA
47853380 ATGTTTTTCCTACATATAATACCTTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTAC
66 ATGTTTTTCCTACATATAATACCTTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTAC
*
47853445 ATATAATACTTTTTTTTTTCATTCAATCT
131 ATATAATAC--CTTTTTTTCATTCAATCT
47853474 CATTTATT
1 CATTTATT
47853482 ACATCTAATT
Statistics
Matches: 310, Mismatches: 9, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
156 103 0.33
157 167 0.54
158 40 0.13
ACGTcount: A:0.26, C:0.19, G:0.02, T:0.53
Consensus pattern (157 bp):
CATTTATTTCAAATGTTTTTCCTACATATAATACCTTTTTTTTCATTCAATCTCATTTATTTCAA
ATGTTTTTCCTACATATAATACCTTTTTTTCATTCAATCTCATTTATTTCAAATGTTTTTCCTAC
ATATAATACCTTTTTTTCATTCAATCT
Found at i:47853492 original size:14 final size:14
Alignment explanation
Indices: 47853470--47853509 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
47853460 TTTTCATTCA
*
47853470 ATCTCATTTATTAC
1 ATCTAATTTATTAC
47853484 ATCTAATTTATTAC
1 ATCTAATTTATTAC
47853498 ATCTAATTTATT
1 ATCTAATTTATT
47853510 TCCTACATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (14 bp):
ATCTAATTTATTAC
Found at i:47853562 original size:20 final size:19
Alignment explanation
Indices: 47853537--47853589 Score: 62
Period size: 14 Copynumber: 3.0 Consensus size: 19
47853527 ATGTTTTTAT
47853537 TACATCTAACATTTATTTC
1 TACATCTAACATTTATTTC
47853556 GTACATCT-A-A-TT-TTT-
1 -TACATCTAACATTTATTTC
47853571 TACATCTAACATTTATTTC
1 TACATCTAACATTTATTTC
47853590 AACTGTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
14 7 0.25
15 1 0.04
16 4 0.14
17 4 0.14
18 4 0.14
19 1 0.04
20 7 0.25
ACGTcount: A:0.30, C:0.19, G:0.02, T:0.49
Consensus pattern (19 bp):
TACATCTAACATTTATTTC
Found at i:47857163 original size:110 final size:107
Alignment explanation
Indices: 47856593--47857301 Score: 899
Period size: 106 Copynumber: 6.5 Consensus size: 107
47856583 TATATATGAT
47856593 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAAATTTTTATTTATTTTTTTCGTA-
1 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC----AAAATTTTT-TTTATTTTTTTCGTAT
* *
47856657 TTTTTTATTTGATTCTGACACAAAAAAAATATTAAATTTTTTTCCTTTGTACTG
61 TTTTTTATATGATTCTGACAC--GAAAAA-A--AAA-TTTTTT-CTTTGTACTG
* * *
47856711 TGTACTGGGTGCCGGCTATTGACAGGCCAGCTACCCTAAATTTTTTTTTTATTTTTTCGTATTTT
1 TGTACTGGGTGCCGGCCATTGACAGGCCAGC-ACCCAAAATTTTTTTTAT-TTTTTTCGTATTTT
*
47856776 TTTATATGATTCTGACACG-TAAAAAAA--TTTTCTTTGTACTG
64 TTTATATGATTCTGACACGAAAAAAAAATTTTTTCTTTGTACTG
* *
47856817 TGTACTGGGTGCCGGCCATTGACAGGCCAGCATCCTAAATTTTTTTT-TTTTTTTCGTATTTTTT
1 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTTTTCGTATTTTTT
47856881 TATATGATTCTGACACCG--AAAAAAA--TTTTCTTTGTACTG
66 TATATGATTCTGACA-CGAAAAAAAAATTTTTTCTTTGTACTG
* *
47856920 TGTACTGGGTGCCGGCCATTGACAGGCCAGCATCC-AAATTTTTTTT-TTTTATTCGTATTTTTT
1 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTTTTCGTATTTTTT
* **
47856983 TATCTGATTCTGACACGAAAAAAAAAAATTTTCTTTTGTACTG
66 TATATGATTCTGACACGAAAAAAAAATTTTTTC-TTTGTACTG
47857026 TGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CC-AAATTTTTTTTATTTTTTTCGTATTTTTT
1 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTTTTCGTATTTTTT
*
47857089 TATCTGATTCTGACACGAAAAAAAATAATTTTTTTTTCTTTGTACTG
66 TATATGATTCTGACACG-AAAAAAA-AA---TTTTTTCTTTGTACTG
* *
47857136 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTATTTTTTTTGTATTTTTT
1 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTTTTCGTATTTTTT
* *
47857201 TATTTGATTCTGACACGAAAAAAATAATAAATTTTT-TTTGTACTA
66 TATATGATTCTGACACGAAAAAAA-AAT---TTTTTCTTTGTACTG
*
47857246 TGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCAGAAATTTTTTTTTTGTTTTTT
1 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA-AAATTTTTTTTAT-TTTTTT
47857302 TTCTTTTTCG
Statistics
Matches: 550, Mismatches: 19, Indels: 51
0.89 0.03 0.08
Matches are distributed among these distances:
101 2 0.00
102 41 0.07
103 94 0.17
104 3 0.01
105 33 0.06
106 114 0.21
107 11 0.02
108 3 0.01
109 3 0.01
110 95 0.17
111 28 0.05
112 44 0.08
113 3 0.01
114 4 0.01
115 18 0.03
116 20 0.04
118 30 0.05
119 4 0.01
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (107 bp):
TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTTTTCGTATTTTTT
TATATGATTCTGACACGAAAAAAAAATTTTTTCTTTGTACTG
Found at i:47857190 original size:11 final size:11
Alignment explanation
Indices: 47857173--47857201 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
47857163 CAGCACCCAA
47857173 ATTTTTTTT-T
1 ATTTTTTTTGT
47857183 ATTTTTTTTGT
1 ATTTTTTTTGT
47857194 ATTTTTTT
1 ATTTTTTT
47857202 ATTTGATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.86
Consensus pattern (11 bp):
ATTTTTTTTGT
Found at i:47861303 original size:20 final size:20
Alignment explanation
Indices: 47861267--47861305 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
47861257 CGGCGCCAAT
47861267 TCTGTAAGTGTTCTAAAAAC
1 TCTGTAAGTGTTCTAAAAAC
*
47861287 TCTGATAAGT-TTTTAAAAA
1 TCTG-TAAGTGTTCTAAAAA
47861306 TATGAGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
TCTGTAAGTGTTCTAAAAAC
Found at i:47861895 original size:27 final size:28
Alignment explanation
Indices: 47861820--47861904 Score: 102
Period size: 30 Copynumber: 3.0 Consensus size: 28
47861810 AAAATATATT
*
47861820 AAATATATTATATATTTTTTATGTTTAAA
1 AAATATA-TATTTATTTTTTATGTTTAAA
*
47861849 ATATA-ATAGTTTAAATTTTTTATGTTTAAA
1 AAATATATA-TTT--ATTTTTTATGTTTAAA
47861879 AAATATATATTTA-TTTTTATGTTTAA
1 AAATATATATTTATTTTTTATGTTTAA
47861905 GTTTTTTACT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
27 15 0.31
28 4 0.08
29 4 0.08
30 23 0.47
31 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (28 bp):
AAATATATATTTATTTTTTATGTTTAAA
Found at i:47861912 original size:21 final size:21
Alignment explanation
Indices: 47861888--47861930 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
47861878 AAAATATATA
47861888 TTTA-TTTTTATGTTTAAGTTT
1 TTTACTTTTTA-GTTTAAGTTT
*
47861909 TTTACTTTTTAGTTTTAGTTT
1 TTTACTTTTTAGTTTAAGTTT
47861930 T
1 T
47861931 CATTTCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.72
Consensus pattern (21 bp):
TTTACTTTTTAGTTTAAGTTT
Found at i:47863746 original size:18 final size:17
Alignment explanation
Indices: 47863710--47863772 Score: 90
Period size: 17 Copynumber: 3.5 Consensus size: 17
47863700 TTCGCTCCTC
47863710 ATAGATTTTTTACTGTA
1 ATAGATTTTTTACTGTA
47863727 ATAGATTTTTTACTGCTA
1 ATAGATTTTTTACTG-TA
47863745 ATAGATTTTTATTCACTGTA
1 ATAGA-TTTT-TT-ACTGTA
47863765 ATAGATTT
1 ATAGATTT
47863773 CATTAATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
17 15 0.36
18 7 0.17
19 7 0.17
20 9 0.21
21 4 0.10
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (17 bp):
ATAGATTTTTTACTGTA
Found at i:47864455 original size:92 final size:92
Alignment explanation
Indices: 47864286--47864680 Score: 673
Period size: 92 Copynumber: 4.3 Consensus size: 92
47864276 TACAATTTTT
* *
47864286 AACCTATTTGTATATTTAATAAAATATGAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
1 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
*
47864351 TTAGACAGCAAGTATGCATTTTGTTTG
66 TTAAACAGCAAGTATGCATTTTGTTTG
* *
47864378 AACTTGTTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
1 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
*
47864443 TTAAACATCAAGTATGCATTTTGTTTG
66 TTAAACAGCAAGTATGCATTTTGTTTG
* *
47864470 AACCTATTCTTATATTTAATAAAATATAAACCTATTTGTATTAAAGTATGCATATAAGCTACAAT
1 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
*
47864535 TTAAATAGCAAGTATGCATTTTGTTTG
66 TTAAACAGCAAGTATGCATTTTGTTTG
*
47864562 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGTTACAAT
1 AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
* *
47864627 TTAGACAGCAAGTATGCATTTTGTTTT
66 TTAAACAGCAAGTATGCATTTTGTTTG
*
47864654 AACCTATTTGTATATTTAATAAAATAT
1 AACCTATTTTTATATTTAATAAAATAT
47864681 TTGTATATAT
Statistics
Matches: 284, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 284 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (92 bp):
AACCTATTTTTATATTTAATAAAATATAAACCTATTTGTATCAAAGTATGCATATAAGCTACAAT
TTAAACAGCAAGTATGCATTTTGTTTG
Found at i:47866845 original size:9 final size:9
Alignment explanation
Indices: 47866831--47866862 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
47866821 TTGCAAAAAG
47866831 GACGATGAC
1 GACGATGAC
47866840 GACGATGAC
1 GACGATGAC
47866849 GACGATGAC
1 GACGATGAC
47866858 GACGA
1 GACGA
47866863 GGTTTCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.34, C:0.22, G:0.34, T:0.09
Consensus pattern (9 bp):
GACGATGAC
Found at i:47867806 original size:16 final size:16
Alignment explanation
Indices: 47867785--47867826 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
47867775 AATAATTTGA
*
47867785 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
47867801 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
47867817 TAGTTTTAAT
1 TAATTTTAAT
47867827 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:47868812 original size:3 final size:3
Alignment explanation
Indices: 47868804--47868872 Score: 111
Period size: 3 Copynumber: 22.7 Consensus size: 3
47868794 TTAATATTCT
47868804 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
47868852 CTA TTA TTAA TTA CTA TTA TT
1 TTA TTA TT-A TTA TTA TTA TT
47868873 TAAATTTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:47873168 original size:12 final size:14
Alignment explanation
Indices: 47873116--47873172 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
47873106 ACGATAAACA
*
47873116 AATATAAAAATTAGT
1 AATATAATAA-TAGT
*
47873131 -ATGATAATAATAAT
1 AAT-ATAATAATAGT
47873145 AATATAATAATAGT
1 AATATAATAATAGT
47873159 AAT-T-ATAATAGT
1 AATATAATAATAGT
47873171 AA
1 AA
47873173 GAAAAGTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 10 0.27
13 1 0.03
14 18 0.49
15 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (14 bp):
AATATAATAATAGT
Found at i:47875269 original size:44 final size:43
Alignment explanation
Indices: 47875210--47875467 Score: 157
Period size: 44 Copynumber: 5.7 Consensus size: 43
47875200 TAGTGTCTCC
*
47875210 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCTAAATTTT
1 AATC-GCTCCACTGTAATCTCAGGGAGATAAGATCCTAAATTTT
* * *
47875254 AATTCGCTCCACTGTAACCTCAGGGAGATAGGATTATCAGCTTCAATCTGATGT
1 AA-TCGCTCCACTGTAATCTCAGGGAGATA--A-GATC--C-TAAAT-T--T-T
* * * * **
47875308 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTT
1 AATC-GCTCCACTGTAATC-TCAGGGAGATAAGATCCTAAATTTT
* * * * *
47875352 AACCCGCTCCACTGTAATTTCAGGGAGATAGGAT--TACTATCTTC
1 AA-TCGCTCCACTGTAATCTCAGGGAGATAAGATCCTA-AAT-TTT
*
47875396 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCT--ATTTT
1 AATC-GCTCCACTGTAATCTCAGGGAGATAAGATCCTAAATTTT
*
47875438 AATCCGCTCCACTGTAACCTCAGGGAGATA
1 AAT-CGCTCCACTGTAATCTCAGGGAGATA
47875468 GGATTATCAG
Statistics
Matches: 166, Mismatches: 27, Indels: 44
0.70 0.11 0.19
Matches are distributed among these distances:
42 29 0.17
43 7 0.04
44 80 0.48
45 4 0.02
46 2 0.01
47 4 0.02
48 3 0.02
49 2 0.01
50 4 0.02
51 4 0.02
52 1 0.01
53 4 0.02
54 22 0.13
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (43 bp):
AATCGCTCCACTGTAATCTCAGGGAGATAAGATCCTAAATTTT
Found at i:47875396 original size:98 final size:98
Alignment explanation
Indices: 47875221--47875401 Score: 258
Period size: 98 Copynumber: 1.8 Consensus size: 98
47875211 ATCTGCTCCG
* **
47875221 CTGTAATCTCAGGGAGATAAGATCCTAAATTTTAATTCGCTCCACTGTAACCTCAGGGAGATAGG
1 CTGTAATCTCAGAGAGATAAGATCCTAAATTTTAACCCGCTCCACTGTAACCTCAGGGAGATAGG
47875286 ATTATCAGCTTCAATCTGATGTGATCTACTCTA
66 ATTATCAGCTTCAATCTGATGTGATCTACTCTA
** **
47875319 CTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAACCCGCTCCACTGTAATTTCAGGGAGATAG
1 CTGTAATC-TCAGAGAGATAAGATCCTAAATTTTAACCCGCTCCACTGTAACCTCAGGGAGATAG
*
47875383 GATTA-CTATCTTCAATCTG
65 GATTATC-AGCTTCAATCTG
47875402 CTCCGCTGTA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
97 2 0.03
98 71 0.97
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (98 bp):
CTGTAATCTCAGAGAGATAAGATCCTAAATTTTAACCCGCTCCACTGTAACCTCAGGGAGATAGG
ATTATCAGCTTCAATCTGATGTGATCTACTCTA
Found at i:47875460 original size:42 final size:42
Alignment explanation
Indices: 47875318--47875467 Score: 165
Period size: 44 Copynumber: 3.5 Consensus size: 42
47875308 GATCTACTCT
* * *
47875318 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAACCCGCTCC
1 ACTGTAACCTCAGGGAGATAAGATCC--TATTTTAATCCGCTCC
** * * * *
47875362 ACTGTAATTTCAGGGAGATAGGATTACTATCTTCAATCTGCTCC
1 ACTGTAACCTCAGGGAGATAAGA-TCCTAT-TTTAATCCGCTCC
* *
47875406 GCTGTAATCTCAGGGAGATAAGATCCTATTTTAATCCGCTCC
1 ACTGTAACCTCAGGGAGATAAGATCCTATTTTAATCCGCTCC
47875448 ACTGTAACCTCAGGGAGATA
1 ACTGTAACCTCAGGGAGATA
47875468 GGATTATCAG
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
42 29 0.33
43 8 0.09
44 50 0.56
45 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (42 bp):
ACTGTAACCTCAGGGAGATAAGATCCTATTTTAATCCGCTCC
Found at i:47875466 original size:86 final size:87
Alignment explanation
Indices: 47875319--47875487 Score: 245
Period size: 86 Copynumber: 1.9 Consensus size: 87
47875309 ATCTACTCTA
**
47875319 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAACCCGCTCCACTGTAATTTCAGGGAGATAGG
1 CTGTAACTTCAGAGAGATAAGATCC-TTATTTTAACCCGCTCCACTGTAACCTCAGGGAGATAGG
*
47875384 ATTA-CTATCTTCAATCTGCTCCG
65 ATTATC-AGCTTCAATCTGCTCCG
* *
47875407 CTGTAA-TCTCAGGGAGATAAGATCC-TATTTTAATCCGCTCCACTGTAACCTCAGGGAGATAGG
1 CTGTAACT-TCAGAGAGATAAGATCCTTATTTTAACCCGCTCCACTGTAACCTCAGGGAGATAGG
47875470 ATTATCAGCTTCAATCTG
65 ATTATCAGCTTCAATCTG
47875488 ATGTGATCTA
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
86 50 0.68
87 2 0.03
88 22 0.30
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (87 bp):
CTGTAACTTCAGAGAGATAAGATCCTTATTTTAACCCGCTCCACTGTAACCTCAGGGAGATAGGA
TTATCAGCTTCAATCTGCTCCG
Found at i:47875486 original size:184 final size:185
Alignment explanation
Indices: 47875123--47875613 Score: 706
Period size: 184 Copynumber: 2.7 Consensus size: 185
47875113 TAACTGACAC
* ** * *
47875123 GATCTACTCTACTGTAACTTCAGAGAGATAATATCCTTTATTTTAATCTATTCTACTGAAATCTT
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAAT-TT
* * *
47875188 -AGGGGGATAGGA-TAGTGTCTCCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCTAAAT
65 CAGGGAGATAGGATTACTGTCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCT-AAT
*
47875251 TTTAATTCGCTCCACTGTAACCTCAGGGAGATAGGATTATCAGCTTCAATCTGATGT
129 TTTAATCCGCTCCACTGTAACCTCAGGGAGATAGGATTATCAGCTTCAATCTGATGT
* *
47875308 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAACCCGCTCCACTGTAATTTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATTTC
*
47875373 AGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCT-ATTT
66 AGGGAGATAGGATTACTGTCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCTAATTT
47875437 TAATCCGCTCCACTGTAACCTCAGGGAGATAGGATTATCAGCTTCAATCTGATGT
131 TAATCCGCTCCACTGTAACCTCAGGGAGATAGGATTATCAGCTTCAATCTGATGT
* * * * *
47875492 GATCTACTCTACTGTAACTTCAGAGAGATAAGAT-ATTGT-CTTGAATCTGCTCCGCTGTAATCT
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTT-TATTTTAATCTGCTCCACTGTAATTT
* * * * *
47875555 CAGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCACTATAACCTCAGGGAGATAAGATC
65 CAGGGAGATAGGAT-TACTGTCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC
47875614 TGAAATTCTT
Statistics
Matches: 277, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
183 71 0.26
184 96 0.35
185 66 0.24
186 44 0.16
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (185 bp):
GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATTTC
AGGGAGATAGGATTACTGTCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCTAATTT
TAATCCGCTCCACTGTAACCTCAGGGAGATAGGATTATCAGCTTCAATCTGATGT
Found at i:47875564 original size:43 final size:43
Alignment explanation
Indices: 47875493--47875612 Score: 134
Period size: 44 Copynumber: 2.7 Consensus size: 43
47875483 ATCTGATGTG
* * * * *
47875493 ATCTACTCTACTGTAACTTCAGAGAGATAAGATAT-TGTCTTGA
1 ATCTGCTCCACTGTAAC-TCAGGGAGATAAGATATCTGGCTTCA
* *
47875536 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCA
1 ATCTGCTCCACTGTAA-CTCAGGGAGATAAGATATCTGGCTTCA
*
47875580 ATCTGCTCCACTATAACCTCAGGGAGATAAGAT
1 ATCTGCTCCACTGTAA-CTCAGGGAGATAAGAT
47875613 CTGAAATTCT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
43 28 0.43
44 37 0.57
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (43 bp):
ATCTGCTCCACTGTAACTCAGGGAGATAAGATATCTGGCTTCA
Found at i:47875601 original size:44 final size:43
Alignment explanation
Indices: 47875506--47875614 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 43
47875496 TACTCTACTG
* * * * * * *
47875506 TAACTTCAGAGAGATAAGATATTGTCTTGAATCTGCTCCGCTG
1 TAACCTCAGGGAGATAAGATCTTGGCTTCAATCTGCTCCACTA
*
47875549 TAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTA
1 TAACCTCAGGGAGATAAGATCT-TGGCTTCAATCTGCTCCACTA
47875593 TAACCTCAGGGAGATAAGATCT
1 TAACCTCAGGGAGATAAGATCT
47875615 GAAATTCTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
43 18 0.32
44 38 0.68
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (43 bp):
TAACCTCAGGGAGATAAGATCTTGGCTTCAATCTGCTCCACTA
Found at i:47905768 original size:113 final size:113
Alignment explanation
Indices: 47905556--47906034 Score: 754
Period size: 113 Copynumber: 4.2 Consensus size: 113
47905546 GAAAATAAGC
* *
47905556 TTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCG
* * * *
47905621 TCGCAAAAAAACCTAAGTCCAACAACGCCATTTTCTGAGCTTTCGGGGA
66 CCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
* * *
47905670 TTTAGCGGC-ATTTTAAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGCTTTTGGAAAAGCG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCG
47905734 CCGCAAAAAATCCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
66 CCGCAAAAAA-CCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
*
47905783 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCG
*
47905848 CCGC-AAAAACCTAAGTCCAACGACGCCG-TTTCTGAGC-TTCGGGGA
66 CCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
* *
47905893 TTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTTAGGGCTTTAGCGGCGTTTTT-GAGAAAGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGA-AAAGC
47905957 GCCGCAAGAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
65 GCCGCAA-AAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
47906007 TTTAGCGGCGTTTTT-AGAAAAGCGCCGC
1 TTTAGCGGCGTTTTTAAG-AAAGCGCCGC
47906035 AAAAAATAAT
Statistics
Matches: 338, Mismatches: 19, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
109 1 0.00
110 72 0.21
111 10 0.03
112 46 0.14
113 114 0.34
114 95 0.28
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (113 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCG
CCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
Found at i:47905980 original size:224 final size:226
Alignment explanation
Indices: 47905556--47906034 Score: 790
Period size: 224 Copynumber: 2.1 Consensus size: 226
47905546 GAAAATAAGC
*
47905556 TTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCG
* *
47905621 TCGCAAAAAAACCTAAGTCCAACAACGCCATTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTAA
66 CCGC-AAAAAACCTAAGTCCAACAACGCCAGTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTAA
*
47905686 AAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGCTTTTGGAAAAGCGCCGCAAAAAATCCTAAG
130 AAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGCTTTTGGAAAAGCGCCGCAAAAAATCCTAAG
47905751 CCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
195 CCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
47905783 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCG
* *
47905848 CCGC-AAAAACCTAAGTCCAACGACGCC-GTTTCTGAGC-TTCGGGGATTTAGCGGCGTTTTTAA
66 CCGCAAAAAACCTAAGTCCAACAACGCCAGTTTCTGAGCTTTCGGGGATTTAGCGGC-ATTTTAA
* * *
47905910 GAAAGCGCCACTAATGCTTAGGGCTTTAGCGGCG-TTTTTGAGAAAGCGCCGCAAGAAAA-CCTA
130 AAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGCTTTTGGA-AAAGCGCCGCAA-AAAATCCTA
47905973 AGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
193 AGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
47906007 TTTAGCGGCGTTTTT-AGAAAAGCGCCGC
1 TTTAGCGGCGTTTTTAAG-AAAGCGCCGC
47906035 AAAAAATAAT
Statistics
Matches: 239, Mismatches: 9, Indels: 11
0.92 0.03 0.04
Matches are distributed among these distances:
223 25 0.10
224 121 0.51
225 26 0.11
227 67 0.28
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (226 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCG
CCGCAAAAAACCTAAGTCCAACAACGCCAGTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTAAA
AAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGCTTTTGGAAAAGCGCCGCAAAAAATCCTAAGC
CCAACGACGCCGTTTTCTGAGCTTTCGGGGA
Found at i:47906305 original size:15 final size:15
Alignment explanation
Indices: 47906285--47906315 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47906275 CATATTTTAA
47906285 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
47906300 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
47906315 G
1 G
47906316 ATTAGGGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.32
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:47906322 original size:14 final size:15
Alignment explanation
Indices: 47906288--47906331 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
47906278 ATTTTAAGGT
*
47906288 TTAGGGAGTATGGGT
1 TTAGGGAGTATGGGA
47906303 TTAGGGAGTAT-GGA
1 TTAGGGAGTATGGGA
47906317 TTAGGG-GT-TGGGA
1 TTAGGGAGTATGGGA
47906330 TT
1 TT
47906332 TAAGGTTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 1 0.04
13 7 0.26
14 8 0.30
15 11 0.41
ACGTcount: A:0.20, C:0.00, G:0.45, T:0.34
Consensus pattern (15 bp):
TTAGGGAGTATGGGA
Found at i:47906601 original size:14 final size:15
Alignment explanation
Indices: 47906575--47906607 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
47906565 AGGGAGTATA
47906575 TATGAATTTAGGGAT
1 TATGAATTTAGGGAT
47906590 TATGAA-TTAGGGAT
1 TATGAATTTAGGGAT
47906604 TATG
1 TATG
47906608 GTTTAAGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.39
Consensus pattern (15 bp):
TATGAATTTAGGGAT
Found at i:47906633 original size:21 final size:21
Alignment explanation
Indices: 47906599--47906676 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
47906589 TTATGAATTA
*
47906599 GGGA-TTATGGTTTAAGGGTT
1 GGGATTTAAGGTTTAAGGGTT
*
47906619 GGGATTTAAGGTTTAGGGGTT
1 GGGATTTAAGGTTTAAGGGTT
* * * *
47906640 -AGATGTTAGGGGTTAAGAGTT
1 GGGAT-TTAAGGTTTAAGGGTT
*
47906661 AGGAATTTAAGGTTTA
1 -GGGATTTAAGGTTTA
47906677 GGGATTCAGG
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
20 7 0.16
21 26 0.60
22 8 0.19
23 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (21 bp):
GGGATTTAAGGTTTAAGGGTT
Found at i:47906648 original size:14 final size:14
Alignment explanation
Indices: 47906631--47906663 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
47906621 GATTTAAGGT
47906631 TTAGGGGTT-AGATG
1 TTAGGGGTTAAGA-G
47906645 TTAGGGGTTAAGAG
1 TTAGGGGTTAAGAG
47906659 TTAGG
1 TTAGG
47906664 AATTTAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.33
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:47907163 original size:85 final size:83
Alignment explanation
Indices: 47907073--47907226 Score: 211
Period size: 85 Copynumber: 1.8 Consensus size: 83
47907063 AATTTTTAGC
* * * * *
47907073 ATAGCAAAATGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTT-ATGAAAAACG
1 ATAGCAAAACGACGTCATTCTATTCAAAATGAAA-AA-AATTTGCGGCGTTTTTCAT-AAAAACG
*
47907137 CCGCAAATAATAAAAACCAAA
63 CAGCAAATAATAAAAACCAAA
*
47907158 ATAGCAAAACGACGTCATTCTATTCAAAATGAAAAAAATTTGCGGTGTTTTTCATAAAAACGCAG
1 ATAGCAAAACGACGTCATTCTATTCAAAATGAAAAAAATTTGCGGCGTTTTTCATAAAAACGCAG
47907223 CAAA
66 CAAA
47907227 AGATAAGCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
83 27 0.44
84 4 0.07
85 30 0.49
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (83 bp):
ATAGCAAAACGACGTCATTCTATTCAAAATGAAAAAAATTTGCGGCGTTTTTCATAAAAACGCAG
CAAATAATAAAAACCAAA
Found at i:47907290 original size:20 final size:20
Alignment explanation
Indices: 47907255--47907292 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47907245 TTTTTATAGC
**
47907255 AAAAAATAAATCAATTTATA
1 AAAAAATAAAAAAATTTATA
47907275 AAAAAATAAAAAAATTTA
1 AAAAAATAAAAAAATTTA
47907293 GAATAGCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATAAAAAAATTTATA
Found at i:47907473 original size:141 final size:139
Alignment explanation
Indices: 47907181--47907734 Score: 721
Period size: 141 Copynumber: 4.1 Consensus size: 139
47907171 GTCATTCTAT
* *
47907181 TCAAAATGAAAAAAATTTGCGGTGTTTTTCATAAAAACGCAGCAAAAGATAAGCAATAGCGGCGT
1 TCAAAATGAAAAAAATTTGCGGCGTTTTTCATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGT
47907246 TTTTATAGCAAAAAATAAATCAATTTAT-AAAAAAATAAAAAA-ATTTAGAATAGCAAAACGGCG
66 TTTTATAGCAAAAAATAAATCAATTTATAAAAAAAATAAAAAATATTTAGAATAGCAAAACGGCG
47907309 TCGGTTTGC
131 TCGGTTTGC
* * * *
47907318 TCAAAATAAAAAAAATTTGTGACGTTTTTCATAAAAATGCCGCAAAAGATAAGCAATAGCGGCGT
1 TCAAAATGAAAAAAATTTGCGGCGTTTTTCATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGT
** *
47907383 TTTTACGCCGCAAAAAATAAATCAATTTATAAAAAAAATAAAAAATTTTTAGAATAGCAAAACGG
66 TTTTA--TAGCAAAAAATAAATCAATTTATAAAAAAAATAAAAAATATTTAGAATAGCAAAACGG
47907448 CGTCGGTTTGC
129 CGTCGGTTTGC
*
47907459 TCAAAATGAAAAAAATTTGTGGCGTTTTTCATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGT
1 TCAAAATGAAAAAAATTTGCGGCGTTTTTCATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGT
* * *
47907524 TTTTATAGCAAAAAATAAATCAATTTATTAAAAAAATAAAAAAAATTTAGAGTAGCAAAACGGCG
66 TTTTATAGCAAAAAATAAATCAATTTATAAAAAAAATAAAAAATATTTAGAATAGCAAAACGGCG
* *
47907589 TCGTTTTGT
131 TCGGTTTGC
* * *
47907598 TCAGAATG--AAAAATTTGCGGCATTTTT--T------------ATAGATAAGCAATAGCGGCGT
1 TCAAAATGAAAAAAATTTGCGGCGTTTTTCATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGT
* *
47907647 TTTTATAGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACG
66 TTTTATAGCAAAAAATAAATCAATTTAT--AAAA-AAAATAAAAAATATTTAGAATAGCAAAACG
* ** *
47907712 GTGTCATTTTGT
128 GCGTCGGTTTGC
47907724 TCAAAATGAAA
1 TCAAAATGAAA
47907735 TAGCGGCGTT
Statistics
Matches: 376, Mismatches: 32, Indels: 27
0.86 0.07 0.06
Matches are distributed among these distances:
123 48 0.13
125 3 0.01
126 43 0.11
128 1 0.00
135 1 0.00
137 81 0.22
139 89 0.24
140 14 0.04
141 96 0.26
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.28
Consensus pattern (139 bp):
TCAAAATGAAAAAAATTTGCGGCGTTTTTCATAAAAACGCCGCAAAAGATAAGCAATAGCGGCGT
TTTTATAGCAAAAAATAAATCAATTTATAAAAAAAATAAAAAATATTTAGAATAGCAAAACGGCG
TCGGTTTGC
Found at i:47907648 original size:123 final size:125
Alignment explanation
Indices: 47907505--47907734 Score: 369
Period size: 123 Copynumber: 1.8 Consensus size: 125
47907495 ACGCCGCAAA
*
47907505 AGATAAGCAATAGCGGCGTTTTTATAGCAAAAAATAAATCAATTTATTAAAAAA-ATAA-AAAAA
1 AGATAAGCAATAGCGGCGTTTTTATAGCAAAAAATAAATCAATTTA-TAAAAAATAAAATAAAAA
* *
47907568 A-TTTAG-AGTAGCAAAACGGCGTCGTTTTGTTCAGAATGAAAAATTTGCGGCATTTTTTAT
65 ATTTTAGCA-TAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAATTTGCGGCATTTTTTAT
47907628 AGATAAGCAATAGCGGCGTTTTTATAGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAA
1 AGATAAGCAATAGCGGCGTTTTTATAGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAA
*
47907693 TTTTTAGCATAGCAAAACGGTGTCATTTTGTTCAAAATGAAA
66 -TTTTAGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAA
47907735 TAGCGGCGTT
Statistics
Matches: 98, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
122 7 0.07
123 49 0.50
124 6 0.06
126 35 0.36
127 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.30
Consensus pattern (125 bp):
AGATAAGCAATAGCGGCGTTTTTATAGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAA
TTTTAGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAATTTGCGGCATTTTTTAT
Found at i:47907889 original size:132 final size:133
Alignment explanation
Indices: 47907749--47908012 Score: 435
Period size: 133 Copynumber: 2.0 Consensus size: 133
47907739 GGCGTTCTTA
*
47907749 AAAAAACGCCGCAAAAATAAATCAATTTAT-AAAAAAT-AAAAAAATTTAGAATAGCAAAACGGC
1 AAAAAACGCCGCAAAAAT-AATCAATTTATAAAAAAATAAAAAAAATTTAGAATAACAAAACGGC
* * *
47907812 GTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGTTT-TTATGAAAAACGCCGCAAAAGATAAGC
65 GTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGTTTGTCA-AAAAAACGCCGCAAAAGATAAGA
47907876 AATAT
129 AATAT
47907881 AAAAAACGCCGCAAAAATAATCAATTTATAAAAAAATAAAAAAAATTTAGAATAACAAAACGGCG
1 AAAAAACGCCGCAAAAATAATCAATTTATAAAAAAATAAAAAAAATTTAGAATAACAAAACGGCG
* *
47907946 TCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGTTTGTCAAAAAAACGCCGCTAAAGGTAAGAAA
66 TCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGTTTGTCAAAAAAACGCCGCAAAAGATAAGAAA
47908011 TA
131 TA
47908013 GCGGCGTTTT
Statistics
Matches: 123, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
131 11 0.09
132 25 0.20
133 85 0.69
134 2 0.02
ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23
Consensus pattern (133 bp):
AAAAAACGCCGCAAAAATAATCAATTTATAAAAAAATAAAAAAAATTTAGAATAACAAAACGGCG
TCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGTTTGTCAAAAAAACGCCGCAAAAGATAAGAAA
TAT
Found at i:47907910 original size:29 final size:30
Alignment explanation
Indices: 47907848--47907915 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 30
47907838 TTGCGGCGTT
*
47907848 TTTATGAAAAACGCCGCAAAAGATAAGCAA
1 TTTATAAAAAACGCCGCAAAAGATAAGCAA
*
47907878 --TATAAAAAACGCCGCAAAA-ATAATCAA
1 TTTATAAAAAACGCCGCAAAAGATAAGCAA
47907905 TTTATAAAAAA
1 TTTATAAAAAA
47907916 ATAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 7 0.21
28 18 0.53
29 9 0.26
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.19
Consensus pattern (30 bp):
TTTATAAAAAACGCCGCAAAAGATAAGCAA
Found at i:47911416 original size:18 final size:17
Alignment explanation
Indices: 47911393--47911425 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
47911383 GTTTATTTTA
47911393 AATTTTTTGTACATATT
1 AATTTTTTGTACATATT
47911410 AATTTTTTGTACATAT
1 AATTTTTTGTACATAT
47911426 AAAGTAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (17 bp):
AATTTTTTGTACATATT
Found at i:47912246 original size:42 final size:42
Alignment explanation
Indices: 47912195--47912374 Score: 238
Period size: 42 Copynumber: 4.3 Consensus size: 42
47912185 TTGTGATCTA
* * **
47912195 TAGCTGCGTTTATATTTAATCGCCGCTAAAGAACATGTTCTT
1 TAGCGGCGTTTATATTTAAGCGCCGCTAAAGAACATGACCTT
* * *
47912237 TAGCGGCGTTTTTATTCAAGCGCCGCTAAAGAACATGATCTT
1 TAGCGGCGTTTATATTTAAGCGCCGCTAAAGAACATGACCTT
*
47912279 TAGTGGCGTTTA-ATTTTAAAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTATA-TTT-AAGCGCCGCTAAAGAACATGACCTT
*
47912322 TAGCGGCGTTT-TTTTCTAAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTATATT-TAAGCGCCGCTAAAGAACATGACCTT
47912364 TAGCGGCGTTT
1 TAGCGGCGTTT
47912375 TTATCTGTAA
Statistics
Matches: 123, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
41 1 0.01
42 87 0.71
43 35 0.28
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (42 bp):
TAGCGGCGTTTATATTTAAGCGCCGCTAAAGAACATGACCTT
Found at i:47912333 original size:85 final size:85
Alignment explanation
Indices: 47912215--47912374 Score: 268
Period size: 85 Copynumber: 1.9 Consensus size: 85
47912205 TATATTTAAT
** *
47912215 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTATTC-AAGCGCCGCTAAAGAACATGATCTT
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTT-TTCTAAGCGCCGCTAAAGAACATGACCTT
*
47912279 TAGTGGCGTTTAATTTTAAAG
65 TAGCGGCGTTTAATTTTAAAG
47912300 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGACCTTT
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGACCTTT
47912365 AGCGGCGTTT
66 AGCGGCGTTT
47912375 TTATCTGTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
84 3 0.04
85 67 0.96
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (85 bp):
CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGACCTTT
AGCGGCGTTTAATTTTAAAG
Found at i:47912375 original size:42 final size:41
Alignment explanation
Indices: 47912215--47912376 Score: 243
Period size: 42 Copynumber: 3.9 Consensus size: 41
47912205 TATATTTAAT
**
47912215 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTATTCAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTT-TTCAAG
* * *
47912257 CGCCGCTAAAGAACATGATCTTTAGTGGCGTTTAATTTTAAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTT--TTTTCAAG
47912300 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTC-AAG
47912342 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTT
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTT
47912377 ATCTGTAAAC
Statistics
Matches: 111, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
41 4 0.04
42 69 0.62
43 36 0.32
44 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCAAG
Found at i:47916494 original size:17 final size:17
Alignment explanation
Indices: 47916472--47916715 Score: 80
Period size: 19 Copynumber: 13.5 Consensus size: 17
47916462 GATCCGATTG
47916472 AAACACGAGATTTTTTT
1 AAACACGAGATTTTTTT
* *
47916489 AAACACGAGAATTTTGT
1 AAACACGAGATTTTTTT
* * *
47916506 -AACACTATAATAATTTTTGA
1 AAACACGA-GAT--TTTTT-T
* * *
47916526 AAACATGA-AATTTTTG
1 AAACACGAGATTTTTTT
*
47916542 AAACATGAGAATTTTTTT
1 AAACACGAG-ATTTTTTT
* * *
47916560 GAAAACATGAAATTTTTTG
1 --AAACACGAGATTTTTTT
47916579 AAACACGAG-TTTTTTT
1 AAACACGAGATTTTTTT
* *
47916595 GAAAACGCGAAATTTTTTT
1 --AAACACGAGATTTTTTT
** *
47916614 TTACATGAGAATTTTTTT
1 AAACACGAG-ATTTTTTT
* * *
47916632 GAAAACACGAAAATTTTTA
1 --AAACACGAGATTTTTTT
* * *
47916651 AAACACGAACAATTTTTG
1 AAACACG-AGATTTTTTT
* *
47916669 AAAGAGCGAAAATTTTTTT
1 AAACA-CG-AGATTTTTTT
47916688 AAAACACGAGATTTTTTTT
1 -AAACACGAGA-TTTTTTT
47916707 GAAACACGA
1 -AAACACGA
47916716 AAATTTTTGA
Statistics
Matches: 168, Mismatches: 40, Indels: 36
0.69 0.16 0.15
Matches are distributed among these distances:
16 20 0.12
17 39 0.23
18 35 0.21
19 52 0.31
20 17 0.10
21 5 0.03
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.37
Consensus pattern (17 bp):
AAACACGAGATTTTTTT
Found at i:47916538 original size:36 final size:35
Alignment explanation
Indices: 47916518--47916648 Score: 104
Period size: 35 Copynumber: 3.6 Consensus size: 35
47916508 CACTATAATA
47916518 ATTTTTGAAAACATGAAATTTTTGAAACATGAGAAT
1 ATTTTTGAAAACATGAAA-TTTTGAAACATGAGAAT
* *
47916554 TTTTTTGAAAACATGAAATTTTTTGAAACACGAG--T
1 ATTTTTGAAAACATGAAA--TTTTGAAACATGAGAAT
* ** ***
47916589 TTTTTTGAAAACGCGAAATTTTTTTTTACATGAGAAT
1 ATTTTTGAAAACATGAAA--TTTTGAAACATGAGAAT
* *
47916626 TTTTTTGAAAACACGAAAATTTT
1 ATTTTTGAAAACATG-AAATTTT
47916649 TAAAACACGA
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
35 29 0.35
36 21 0.26
37 29 0.35
38 3 0.04
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (35 bp):
ATTTTTGAAAACATGAAATTTTGAAACATGAGAAT
Found at i:47916577 original size:37 final size:37
Alignment explanation
Indices: 47916469--47916727 Score: 209
Period size: 37 Copynumber: 7.2 Consensus size: 37
47916459 CGTGATCCGA
47916469 TTGAAACACGAG-ATTTTTTT--AAACACGAGAA--TT
1 TTGAAACACGAGAATTTTTTTGAAAACACGA-AATTTT
* * * * *
47916502 TTGTAACACTATAATAATTTTTGAAAACATGAAA-TTT
1 TTGAAACACGAGAAT-TTTTTTGAAAACACGAAATTTT
* *
47916539 TTGAAACATGAGAATTTTTTTGAAAACATGAAATTTT
1 TTGAAACACGAGAATTTTTTTGAAAACACGAAATTTT
*
47916576 TTGAAACACGAG--TTTTTTTGAAAACGCGAAATTTT
1 TTGAAACACGAGAATTTTTTTGAAAACACGAAATTTT
*** * *
47916611 TTTTTACATGAGAATTTTTTTGAAAACACGAAAATTT
1 TTGAAACACGAGAATTTTTTTGAAAACACGAAATTTT
* * *
47916648 TTAAAACACGA-ACA-ATTTTTGAAAGA-GCGAAAATTTTT
1 TTGAAACACGAGA-ATTTTTTTGAAA-ACACG-AAA-TTTT
* * *
47916686 TTAAAACACGAGATTTTTTTTG-AAACACGAAAATTT
1 TTGAAACACGAGAATTTTTTTGAAAACACGAAATTTT
47916722 TTGAAA
1 TTGAAA
47916728 AGAAGTATCG
Statistics
Matches: 180, Mismatches: 31, Indels: 27
0.76 0.13 0.11
Matches are distributed among these distances:
33 9 0.05
34 2 0.01
35 34 0.19
36 39 0.22
37 71 0.39
38 18 0.10
39 7 0.04
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGAAACACGAGAATTTTTTTGAAAACACGAAATTTT
Found at i:47916722 original size:17 final size:17
Alignment explanation
Indices: 47916469--47916727 Score: 117
Period size: 17 Copynumber: 14.4 Consensus size: 17
47916459 CGTGATCCGA
* *
47916469 TTGAAACACGAGATTTT
1 TTGAAACACGAAAATTT
* *
47916486 TTTAAACACGAGAA-TT
1 TTGAAACACGAAAATTT
* *
47916502 TTGTAACACTATAATAATTT
1 TTGAAACAC--GAA-AATTT
*
47916522 TTGAAAACATG-AAATTT
1 TTG-AAACACGAAAATTT
* *
47916539 TTGAAACATGAGAATTTTT
1 TTGAAACACGA-AA-ATTT
* *
47916558 TTGAAAACATGAAATTTT
1 TTG-AAACACGAAAATTT
***
47916576 TTGAAACACGAGTTTTT
1 TTGAAACACGAAAATTT
* *
47916593 TTGAAAACGCGAAATTTT
1 TTG-AAACACGAAAATTT
*** * *
47916611 TTTTTACATGAGAATTTTT
1 TTGAAACACGA-AA-ATTT
47916630 TTGAAAACACGAAAATTT
1 TTG-AAACACGAAAATTT
*
47916648 TTAAAACACGAACAATTT
1 TTGAAACACGAA-AATTT
*
47916666 TTGAAAGAGCGAAAATTTTT
1 TTGAAACA-CGAAAA--TTT
* **
47916686 TTAAAACACGAGATTTTTT
1 TTGAAACACGA-A-AATTT
47916705 TTGAAACACGAAAATTT
1 TTGAAACACGAAAATTT
47916722 TTGAAA
1 TTGAAA
47916728 AGAAGTATCG
Statistics
Matches: 187, Mismatches: 36, Indels: 38
0.72 0.14 0.15
Matches are distributed among these distances:
16 16 0.09
17 56 0.30
18 45 0.24
19 38 0.20
20 28 0.15
21 4 0.02
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (17 bp):
TTGAAACACGAAAATTT
Found at i:47917536 original size:13 final size:12
Alignment explanation
Indices: 47917471--47917532 Score: 65
Period size: 13 Copynumber: 5.1 Consensus size: 12
47917461 TGTGATATTA
47917471 TTTT-TTTTTCT
1 TTTTCTTTTTCT
*
47917482 TTTT-TCTTCTCT
1 TTTTCT-TTTTCT
47917494 TTTTCTTATTTCT
1 TTTTCTT-TTTCT
*
47917507 TTCTCTTTTTCT
1 TTTTCTTTTTCT
47917519 TCTTTCTTTTTCT
1 T-TTTCTTTTTCT
47917532 T
1 T
47917533 CTTTTTCTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
11 5 0.12
12 16 0.37
13 22 0.51
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:47917541 original size:6 final size:6
Alignment explanation
Indices: 47917471--47917532 Score: 65
Period size: 6 Copynumber: 10.2 Consensus size: 6
47917461 TGTGATATTA
* *
47917471 TTTT-T TTTTCT TTTT-T CTTCTCT TTTTCT TATTTCT TTCTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT -TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT
47917519 TCTTTCT TTTTCT T
1 T-TTTCT TTTTCT T
47917533 CTTTTTCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
5 5 0.10
6 30 0.62
7 13 0.27
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:47917542 original size:22 final size:21
Alignment explanation
Indices: 47917472--47917542 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 21
47917462 GTGATATTAT
*
47917472 TTTTTTTTCTTT-TTTCTTCTC
1 TTTTTCTTCTTTCTTT-TTCTC
*
47917493 TTTTTCTTATTTC--TTTCTC
1 TTTTTCTTCTTTCTTTTTCTC
47917512 TTTTTCTTCTTTCTTTTTCTTC
1 TTTTTCTTCTTTCTTTTTC-TC
47917534 TTTTTCTTC
1 TTTTTCTTC
47917543 CTTGCGCAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 17 0.40
20 1 0.02
21 14 0.33
22 11 0.26
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTCTTCTTTCTTTTTCTC
Found at i:47918186 original size:29 final size:30
Alignment explanation
Indices: 47918153--47918214 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
47918143 TCAAGATGCA
*
47918153 AATTTGGGAAAAG-TTAGGGGTTAAAATGT
1 AATTTGGGAAAAGTTTAGGGGCTAAAATGT
**
47918182 AATTTTTGAAAAGTTTAGGGGCTAAAATGT
1 AATTTGGGAAAAGTTTAGGGGCTAAAATGT
47918212 AAT
1 AAT
47918215 ATATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.34
Consensus pattern (30 bp):
AATTTGGGAAAAGTTTAGGGGCTAAAATGT
Found at i:47918418 original size:5 final size:5
Alignment explanation
Indices: 47918410--47918435 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
47918400 TATGATATAT
47918410 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
47918436 CATGAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:47918697 original size:75 final size:75
Alignment explanation
Indices: 47918594--47919493 Score: 1024
Period size: 75 Copynumber: 11.8 Consensus size: 75
47918584 CCTAGCGTAC
* * * * * *
47918594 GACCCGAGGCTCAACTCACCTCACGCATTATGAGTTGATTCTTGAAAAACAGGACTTGAAAATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATAC
*
47918659 CTCGGCATGC
66 CTCGGCATGT
* * * * * * *
47918669 GGCCCAAGGCTCAACTCACCTCTGGCATTATGAGTTGATATTTGGAAAACAGAAATTAAAGATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATAC
47918734 CTCGGCA--T
66 CTCGGCATGT
* * * *
47918742 GATCCGGGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAT
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTAAAAAT
*
47918807 ACCTCAGCA--T
64 ACCTCGGCATGT
* * * * *
47918817 GACCCAAGGCTCAACTCGCTTCTTGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAGATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATAC
**
47918882 CTCGATATGT
66 CTCGGCATGT
* * * *
47918892 GACTCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTAAAAAACAGAAATTAAAGATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATAC
*
47918957 CTCGGTATGT
66 CTCGGCATGT
*
47918967 GACCCGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAAACAGAAATTAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTG-AAAAACAGAAATT-AA
*
47919032 AAATACCTCGGCGTGT
60 AAATACCTCGGCATGT
* *
47919048 GACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT--AA-AA
*
47919113 ATACCTCGACATGT
62 ATACCTCGGCATGT
* * *** * *
47919127 G-TCAGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAAAAAAAACAAAAATTGAAAATAC
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATAC
* *
47919191 CTCAGCGTGT
66 CTCGGCATGT
* *
47919201 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATT-AAAAA
47919266 TACCTCGGCATGT
63 TACCTCGGCATGT
* * * **
47919279 AACCCGATGCTCAACTCACCTCTCGCAATATGAGTTGATTGTTTTTGAAAAAAATCAA--AAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAAACAGAAATTAAAAA
47919342 TACCTCGGCATGT
63 TACCTCGGCATGT
* * *
47919355 G-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAGGAATCTAAAAAAT
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAT-T-AAAAAT
*
47919419 ACCTCGGTATGT
64 ACCTCGGCATGT
* * *
47919431 GACCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAAACCGAAATTGAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAATTAAAAA
47919494 GTATTTCTTG
Statistics
Matches: 704, Mismatches: 97, Indels: 47
0.83 0.11 0.06
Matches are distributed among these distances:
72 14 0.02
73 62 0.09
74 14 0.02
75 293 0.42
76 50 0.07
77 64 0.09
78 108 0.15
79 35 0.05
80 13 0.02
81 51 0.07
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (75 bp):
GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATAC
CTCGGCATGT
Found at i:47918869 original size:148 final size:145
Alignment explanation
Indices: 47918597--47919493 Score: 904
Period size: 148 Copynumber: 5.9 Consensus size: 145
47918587 AGCGTACGAC
* * * * * *
47918597 CCGAGGCTCAACTCACCTCACGCATTATGAGTTGATTCTTGAAAAACAGGACTT-GAAAATACCT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAATACCT
* * * * *
47918661 CGGCATGCGGCCCAAGGCTCAACTCACCTCTGGCATTATGAGTTGATATTTGGAAAACAGAAATT
66 CGGCAT--GACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
47918726 AAAGATACCTCGGCATGAT
129 AAA-ATACCTCGGCATG-T
* * *
47918745 CCGGGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATT-GAAAATAC
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTAAAAAATAC
* * * *
47918809 CTCAGCATGACCCAAGGCTCAACTCGCTTCTTGCAATATGAGTTGATTTTTGAAAAACAGAAATT
64 CTCGGCATGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
**
47918874 AAAGATACCTCGATATGT
129 AAA-ATACCTCGGCATGT
* * *
47918892 GACTCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTAAAAAACAGAAATT-AAAGATA
1 --C-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAATA
* * *
47918956 CCTCGGTATGTGACCCGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAAA
63 CCTCGGCA--TGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTG-AAAAA
*
47919021 CAGAAATTAAAAAATACCTCGGCGTGT
121 CAGAAATT--AAAATACCTCGGCATGT
*
47919048 GACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAA
1 --C-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT-AAA-AA
* *** *** *
47919113 ATACCTCGACATGTGTCAGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAAAAAAAACAA
60 ATACCTCGGCATGACCCA-AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAG
* *
47919178 AAATTGAAAATACCTCAGCGTGT
124 AAATT-AAAATACCTCGGCATGT
* *
47919201 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAAA
1 ---CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTAAAAAA
* *
47919266 TACCTCGGCATGTAACCCGATGCTCAACTCACCTCTCGCAATATGAGTTGATTGTTTTTGAAAAA
61 TACCTCGGCATG--ACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAAA
* *
47919331 AATCAAA--AAAATACCTCGGCATGTGT
121 CA-GAAATTAAAATACCTCGGCA--TGT
* *
47919357 CCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAGGAATCTAAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAT-TAAAAAATACC
* * * *
47919422 TCGGTATGTGACCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAAACCGAAA
65 TCGGCA--TGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAA
47919487 TTGAAAA
127 TT-AAAA
47919494 GTATTTCTTG
Statistics
Matches: 638, Mismatches: 74, Indels: 70
0.82 0.09 0.09
Matches are distributed among these distances:
147 1 0.00
148 127 0.20
149 10 0.02
150 101 0.16
151 16 0.03
152 69 0.11
153 116 0.18
154 36 0.06
155 33 0.05
156 75 0.12
157 8 0.01
158 3 0.00
159 33 0.05
160 10 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (145 bp):
CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAATACCT
CGGCATGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
AATACCTCGGCATGT
Found at i:47920416 original size:16 final size:17
Alignment explanation
Indices: 47920390--47920422 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
47920380 CCTAATCTTT
47920390 TTTTGTTTTTGTTTTTA
1 TTTTGTTTTTGTTTTTA
47920407 TTTT-TTTTTGTTTTTA
1 TTTTGTTTTTGTTTTTA
47920423 GGCATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.06, C:0.00, G:0.09, T:0.85
Consensus pattern (17 bp):
TTTTGTTTTTGTTTTTA
Found at i:47923502 original size:36 final size:36
Alignment explanation
Indices: 47923455--47923526 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
47923445 GTCATCCATC
47923455 GACAATCATTTTGTACCCTGCCAAGGGACCAGTCGG
1 GACAATCATTTTGTACCCTGCCAAGGGACCAGTCGG
47923491 GACAATCATTTTGTACCCTGCCAAGGGACCAGTCGG
1 GACAATCATTTTGTACCCTGCCAAGGGACCAGTCGG
47923527 TTCTATCCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (36 bp):
GACAATCATTTTGTACCCTGCCAAGGGACCAGTCGG
Found at i:47924696 original size:29 final size:29
Alignment explanation
Indices: 47924627--47924686 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
47924617 TGATTTTAAG
47924627 TCAAATTTTTTTATGTTTTCTTATTTTGT
1 TCAAATTTTTTTATGTTTTCTTATTTTGT
47924656 TCAAATTTTTTTATGTTTTCTTATTTTGT
1 TCAAATTTTTTTATGTTTTCTTATTTTGT
47924685 TC
1 TC
47924687 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.17, C:0.08, G:0.07, T:0.68
Consensus pattern (29 bp):
TCAAATTTTTTTATGTTTTCTTATTTTGT
Found at i:47929790 original size:16 final size:17
Alignment explanation
Indices: 47929759--47929791 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
47929749 AAATTTTTTA
47929759 AAAATATTAATTTAATAT
1 AAAATATT-ATTTAATAT
47929777 AAAATATT-TTTAATA
1 AAAATATTATTTAATA
47929792 CTATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATATTATTTAATAT
Found at i:47929981 original size:24 final size:23
Alignment explanation
Indices: 47929930--47929983 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
47929920 CTTTAAATCA
* *
47929930 ATATACTAAATTAGTATATTACT
1 ATATACTAAAATAGTATATTAAT
47929953 A-ATACATAAAATAGTA-ATATAAT
1 ATATAC-TAAAATAGTATAT-TAAT
47929976 ATATACTA
1 ATATACTA
47929984 GGATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 6 0.23
23 16 0.62
24 4 0.15
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (23 bp):
ATATACTAAAATAGTATATTAAT
Found at i:47930463 original size:16 final size:17
Alignment explanation
Indices: 47930444--47930476 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
47930434 TATATAATGT
47930444 ACTACTATTAT-ATATA
1 ACTACTATTATAATATA
*
47930460 ACTATTATTATAATATA
1 ACTACTATTATAATATA
47930477 TATAAGGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
ACTACTATTATAATATA
Found at i:47931126 original size:9 final size:9
Alignment explanation
Indices: 47931109--47931145 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
47931099 TGAGTTTTCG
47931109 AATTCGAAT
1 AATTCGAAT
*
47931118 AACTCGAAT
1 AATTCGAAT
47931127 AATTCGAAT
1 AATTCGAAT
47931136 AATTCGAAT
1 AATTCGAAT
47931145 A
1 A
47931146 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:47931222 original size:21 final size:21
Alignment explanation
Indices: 47931181--47931223 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
47931171 ACCCCAAACT
* *
47931181 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTATTCC
47931202 CTCAAAAC-TTTTACTCATTCC
1 CTCAAAACTTTTTACT-ATTCC
47931223 C
1 C
47931224 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTATTCC
Found at i:47931377 original size:19 final size:21
Alignment explanation
Indices: 47931333--47931377 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
47931323 CAAAATTTTA
*
47931333 CTCCCAAAACCTTTTATTTTC
1 CTCCCAAAACCTTTTATTTCC
*
47931354 C-CCCAAAA-TTTTTA-TTCC
1 CTCCCAAAACCTTTTATTTCC
47931372 CTCCCA
1 CTCCCA
47931378 CTTTTCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 4 0.19
19 9 0.43
20 7 0.33
21 1 0.05
ACGTcount: A:0.24, C:0.38, G:0.00, T:0.38
Consensus pattern (21 bp):
CTCCCAAAACCTTTTATTTCC
Found at i:47931383 original size:30 final size:31
Alignment explanation
Indices: 47931349--47931408 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
47931339 AAACCTTTTA
*
47931349 TTTTCCCCCAAAATTTTTA-TTCCCTCCCAC
1 TTTTCCCCCAAAACTTTTATTTCCCTCCCAC
* *
47931379 TTTTCCCCTAAAACTTTTATTTCCTTCCCA
1 TTTTCCCCCAAAACTTTTATTTCCCTCCCA
47931409 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTATTTCCCTCCCAC
Found at i:47932706 original size:20 final size:20
Alignment explanation
Indices: 47932681--47932721 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
47932671 AAATTTTTTT
47932681 AAAGGTAAATTCATTAATTG
1 AAAGGTAAATTCATTAATTG
47932701 AAAGGTAAATTCATTAATTG
1 AAAGGTAAATTCATTAATTG
47932721 A
1 A
47932722 TTCAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (20 bp):
AAAGGTAAATTCATTAATTG
Found at i:47934322 original size:13 final size:14
Alignment explanation
Indices: 47934306--47934347 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
47934296 TTTCAATTTT
47934306 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
47934319 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
47934334 ATTTTAAATAATAT
1 ATTTT-AATAATAT
47934348 TCTTCACGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:47934332 original size:16 final size:16
Alignment explanation
Indices: 47934310--47934346 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
47934300 AATTTTATTT
47934310 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
47934327 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
47934342 TAATA
1 TAATA
47934347 TTCTTCACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:47935496 original size:31 final size:31
Alignment explanation
Indices: 47935470--47935564 Score: 154
Period size: 31 Copynumber: 3.1 Consensus size: 31
47935460 GTGACCTTGC
47935470 AACCACTGCCAATAGGAACTCTTGACCGCGT
1 AACCACTGCCAATAGGAACTCTTGACCGCGT
47935501 AACCACTGCCAATAGGAACTCTTGACCGCGT
1 AACCACTGCCAATAGGAACTCTTGACCGCGT
* ** *
47935532 AACCACTACCAATAAAAACTCTTAACCGCGT
1 AACCACTGCCAATAGGAACTCTTGACCGCGT
47935563 AA
1 AA
47935565 TTAATACCCT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.35, C:0.32, G:0.15, T:0.19
Consensus pattern (31 bp):
AACCACTGCCAATAGGAACTCTTGACCGCGT
Found at i:47936963 original size:5 final size:5
Alignment explanation
Indices: 47936953--47937003 Score: 102
Period size: 5 Copynumber: 10.2 Consensus size: 5
47936943 ATTAATATAC
47936953 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
47937003 G
1 G
47937004 TGTTAGAGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39
Consensus pattern (5 bp):
GATAT
Found at i:47937115 original size:24 final size:24
Alignment explanation
Indices: 47937081--47937132 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
47937071 TTTCTAGAAG
*
47937081 ATTTAGCATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGAATAATAT
* *
47937105 ATTTAGTATTTATTAGAATAATAT
1 ATTTAGCATTTATGAGAATAATAT
47937129 ATTT
1 ATTT
47937133 TACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGAATAATAT
Found at i:47937143 original size:24 final size:23
Alignment explanation
Indices: 47937088--47937147 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
47937078 AAGATTTAGC
* *
47937088 ATTTATGAGTATAATATATTTAGT
1 ATTTATTAGAATAATATATTTA-T
47937112 ATTTATTAGAATAATATATTT-T
1 ATTTATTAGAATAATATATTTAT
47937134 ACTTTGATTAGAAT
1 A-TTT-ATTAGAAT
47937148 TAGGTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 2 0.06
23 3 0.09
24 27 0.84
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (23 bp):
ATTTATTAGAATAATATATTTAT
Found at i:47941489 original size:24 final size:24
Alignment explanation
Indices: 47941426--47941477 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
47941416 TTTCTAGAAG
* * *
47941426 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
47941450 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
47941474 ATTT
1 ATTT
47941478 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:47941831 original size:17 final size:18
Alignment explanation
Indices: 47941809--47941855 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
47941799 TCATTGATGC
47941809 ATATATATAAACTAT-TA
1 ATATATATAAACTATATA
* *
47941826 ATATATTATATACTATATG
1 ATATA-TATAAACTATATA
47941845 ATATGATATAA
1 ATAT-ATATAA
47941856 CATTATAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 5 0.21
18 9 0.38
19 9 0.38
20 1 0.04
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (18 bp):
ATATATATAAACTATATA
Found at i:47943983 original size:18 final size:18
Alignment explanation
Indices: 47943952--47943999 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
47943942 TGTCACTCGT
*
47943952 TTTCAAAACATTATTC-A
1 TTTCAAAACGTTATTCAA
*
47943969 TTTACAAATCGTTATTCAA
1 TTT-CAAAACGTTATTCAA
47943988 TTTCAAAACGTT
1 TTTCAAAACGTT
47944000 TTCTTATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (18 bp):
TTTCAAAACGTTATTCAA
Found at i:47945780 original size:26 final size:26
Alignment explanation
Indices: 47945744--47945797 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
47945734 ATAACACCAT
47945744 AATCAGTCTTATCTCGTGATTAATCA
1 AATCAGTCTTATCTCGTGATTAATCA
47945770 AATCAGTCTTATCTCGTGATTAATCA
1 AATCAGTCTTATCTCGTGATTAATCA
47945796 AA
1 AA
47945798 GTCTCGAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (26 bp):
AATCAGTCTTATCTCGTGATTAATCA
Found at i:47948236 original size:24 final size:25
Alignment explanation
Indices: 47948209--47948255 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
47948199 TTCAAATACA
*
47948209 CTCAAAACATT-AAAATAAATGTTT
1 CTCAAAAAATTGAAAATAAATGTTT
*
47948233 CTCAAAAAATTGAAAATACATGT
1 CTCAAAAAATTGAAAATAAATGT
47948256 AAAAAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (25 bp):
CTCAAAAAATTGAAAATAAATGTTT
Found at i:47948532 original size:13 final size:14
Alignment explanation
Indices: 47948514--47948542 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
47948504 TTACTTTTTG
47948514 TTCAAGCCTAT-TT
1 TTCAAGCCTATATT
47948527 TTCAAGCCTATATT
1 TTCAAGCCTATATT
47948541 TT
1 TT
47948543 TATCCAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (14 bp):
TTCAAGCCTATATT
Found at i:47955767 original size:26 final size:25
Alignment explanation
Indices: 47955746--47955795 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
47955736 GTTATAAATT
*
47955746 TTTTTTATTTATCAAAA-ATATATAA
1 TTTTTTATTTACCAAAATATATA-AA
47955771 TTTTTTATTTACCAAAATATATAAA
1 TTTTTTATTTACCAAAATATATAAA
47955796 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTTTATTTACCAAAATATATAAA
Found at i:47955787 original size:24 final size:25
Alignment explanation
Indices: 47955746--47955794 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
47955736 GTTATAAATT
47955746 TTTTTTATTTATCAAAAATATATAA
1 TTTTTTATTTATCAAAAATATATAA
*
47955771 TTTTTTATTTA-CCAAAATATATAA
1 TTTTTTATTTATCAAAAATATATAA
47955795 AAAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTTTTATTTATCAAAAATATATAA
Found at i:47955888 original size:27 final size:27
Alignment explanation
Indices: 47955858--47955923 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
47955848 ACGCCAATGG
*
47955858 CATTGGTGGCACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
* **
47955885 CATTGGCGGCACCAATGGTGCCAATGC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
47955912 CATTGGCGGCAC
1 CATTGGCGGCAC
47955924 TATTCGTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.17
Consensus pattern (27 bp):
CATTGGCGGCACCAAAGGTGCCAAAAC
Found at i:47956029 original size:10 final size:11
Alignment explanation
Indices: 47956008--47956043 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
47955998 GTTGCTGCGG
47956008 AAAAGAAGAGA
1 AAAAGAAGAGA
47956019 AAAAGAA-AGA
1 AAAAGAAGAGA
47956029 AAAAGAAGAGA
1 AAAAGAAGAGA
47956040 AAAA
1 AAAA
47956044 AATGTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:47956106 original size:19 final size:21
Alignment explanation
Indices: 47956070--47956108 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
47956060 AATAATTGAT
*
47956070 TATATTGTTGTTATTATTTTA
1 TATATTGTTGTTAATATTTTA
47956091 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
47956109 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTA
Found at i:47956180 original size:3 final size:3
Alignment explanation
Indices: 47956174--47956247 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
47956164 ATTATTATTA
47956174 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
47956222 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
47956248 AGTATTAAGA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:47959231 original size:18 final size:18
Alignment explanation
Indices: 47959208--47959369 Score: 84
Period size: 18 Copynumber: 8.6 Consensus size: 18
47959198 CCTTCCCTCT
47959208 TCTTCTTCTTTTTTTTTC
1 TCTTCTTCTTTTTTTTTC
*
47959226 TCTTCTCCTTTCCTTTTCTT-
1 TCTTCTTCTTT--TTTT-TTC
*
47959246 TCCTTCTTTCTTTCTTTTT-
1 T-CTTC-TTCTTTTTTTTTC
*
47959265 TCTTC-TCTTTTCCTTTTC
1 TCTTCTTCTTTT-TTTTTC
47959283 TTCTTCTTTCTTTCTTTTTTTC
1 -TCTTC-TTC-TT-TTTTTTTC
* **
47959305 TCTTCTCCTTTCCTTTTC
1 TCTTCTTCTTTTTTTTTC
*
47959323 T-TTCCTTCTTTTTCTTTC
1 TCTT-CTTCTTTTTTTTTC
* *
47959341 T-TTCCTCTCTTTTCTTTC
1 TCTTCTTCT-TTTTTTTTC
47959359 T-TTCTTTCTTT
1 TCTTC-TTCTTT
47959370 CTTTCCCTCT
Statistics
Matches: 114, Mismatches: 15, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
16 5 0.04
17 10 0.09
18 49 0.43
19 13 0.11
20 10 0.09
21 13 0.11
22 12 0.11
23 2 0.02
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTCTTCTTTTTTTTTC
Found at i:47959235 original size:34 final size:37
Alignment explanation
Indices: 47959186--47959335 Score: 132
Period size: 39 Copynumber: 4.1 Consensus size: 37
47959176 AAAATTTACC
47959186 TTTTTTTTC-C-T-TCCTTCCCTCTTC-TT-CTTC-T
1 TTTTTTTTCTCTTCTCCTTCCCTCTTCTTTCCTTCTT
* *
47959217 TTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTT
1 TTTTTTTTCTCTTCTCCTTCCCTCTTCTTTCCTTCTT
* * * * *
47959254 TCTTTCTTTTTTCTTCTCTTTTCCTTTTCTTCTTCTTTCTT
1 T-TTT-TTTTCTCTTCTCCTTCCCTCTTC-T-TTCCTTCTT
* *
47959295 TCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTT
1 T-TTTTTTTCTCTTCTCCTTCCCTCTTCTTTCCTTCTT
47959333 TTT
1 TTT
47959336 CTTTCTTTCC
Statistics
Matches: 101, Mismatches: 8, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
31 9 0.09
32 1 0.01
33 1 0.01
34 11 0.11
35 2 0.02
36 4 0.04
37 4 0.04
38 12 0.12
39 22 0.22
40 22 0.22
41 13 0.13
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (37 bp):
TTTTTTTTCTCTTCTCCTTCCCTCTTCTTTCCTTCTT
Found at i:47959256 original size:4 final size:4
Alignment explanation
Indices: 47959240--47959374 Score: 102
Period size: 4 Copynumber: 33.0 Consensus size: 4
47959230 CTCCTTTCCT
*
47959240 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTC TTTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTT-C TTTC T-TTC
* * *
47959286 -TTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCC TTTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC TTTC
*
47959333 TTTC TTTC TTTCC TCTC TTTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTT-C TTTC -TTTC TTTC TTTC TTTC TTTC TTTC
47959375 CCTCTCCTTC
Statistics
Matches: 107, Mismatches: 9, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
3 13 0.12
4 71 0.66
5 17 0.16
6 6 0.06
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:47959292 original size:45 final size:43
Alignment explanation
Indices: 47959213--47959361 Score: 155
Period size: 44 Copynumber: 3.4 Consensus size: 43
47959203 CCTCTTCTTC
* * *
47959213 TTCTTTTTTTTTCTCTTCTCCTTTCCTT-TTCTTTCCTTCTTTCT
1 TTCTTTTTTCTTCTCTTTTCCTTTTCTTCTTCTTT--TTCTTTCT
47959257 TTCTTTTTTCTTCTCTTTTCCTTTTCTTCTTC--TTTCTTTCT
1 TTCTTTTTTCTTCTCTTTTCCTTTTCTTCTTCTTTTTCTTTCT
* *
47959298 TT-TTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCT
1 TTCTTTTTTCTTCTCTTTTCCTTTTC-TT-CTTCTTTTTCTTTCT
47959342 TTCCTCTCTTTTCTT-TCTTT
1 TT-CT-T-TTTTCTTCTCTTT
47959362 CTTTCTTTCT
Statistics
Matches: 89, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
40 21 0.24
41 12 0.13
42 4 0.04
43 1 0.01
44 36 0.40
45 3 0.03
46 1 0.01
47 5 0.06
48 6 0.07
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (43 bp):
TTCTTTTTTCTTCTCTTTTCCTTTTCTTCTTCTTTTTCTTTCT
Found at i:47959311 original size:79 final size:76
Alignment explanation
Indices: 47959205--47959373 Score: 251
Period size: 79 Copynumber: 2.2 Consensus size: 76
47959195 CTTCCTTCCC
47959205 TCTTCTTC-TTC-TT-TTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTT-TTT
1 TCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTC-TT-TTTCTTTCTTT
*
47959266 CTTCTCTTTTCCTTT
64 CCTCTCTTTT-C-TT
47959281 TCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
47959346 TCTCTTTTCTT
66 TCTCTTTTCTT
47959357 TC-T-TTCTTTCTTTCTTT
1 TCTTCTTCTTTCTTTCTTT
47959374 CCCTCTCCTT
Statistics
Matches: 88, Mismatches: 1, Indels: 10
0.89 0.01 0.10
Matches are distributed among these distances:
74 14 0.16
75 1 0.01
76 12 0.14
77 11 0.12
78 16 0.18
79 34 0.39
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (76 bp):
TCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
TCTCTTTTCTT
Found at i:47959320 original size:40 final size:40
Alignment explanation
Indices: 47959205--47959373 Score: 177
Period size: 40 Copynumber: 4.5 Consensus size: 40
47959195 CTTCCTTCCC
47959205 TCTTCTTC-TTC-TT-TTTTTTTCTCTTCTCCTTTCCTTT
1 TCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTT
*
47959242 TCTTTCCTTCTTTCTTTC--TTTTT-TCTTCTCTTTTCCTTT
1 TC-TT-CTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTT
47959281 TCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTT
1 TCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTT
* *
47959321 TCTTTCCTTC-TT-TTTCTTTCTTTC-C-TCT-CTTTTC-TT
1 TC-TT-CTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTT
47959357 TC-T-TTCTTTCTTTCTTT
1 TCTTCTTCTTTCTTTCTTT
47959374 CCCTCTCCTT
Statistics
Matches: 116, Mismatches: 4, Indels: 27
0.79 0.03 0.18
Matches are distributed among these distances:
32 3 0.03
33 2 0.02
34 8 0.07
36 4 0.03
37 19 0.16
38 7 0.06
39 27 0.23
40 36 0.31
41 6 0.05
42 4 0.03
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (40 bp):
TCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTT
Found at i:47959548 original size:27 final size:29
Alignment explanation
Indices: 47959518--47959587 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
47959508 GTTATTTTTT
47959518 TATATATTTTGGTAAAT-AAAAAAA-TTA
1 TATATATTTTGGTAAATAAAAAAAAGTTA
*
47959545 TATATTTTTTGGTAAATAAAAAAAAGTTA
1 TATATATTTTGGTAAATAAAAAAAAGTTA
*
47959574 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
47959588 TTTTTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.42
28 17 0.45
29 5 0.13
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.41
Consensus pattern (29 bp):
TATATATTTTGGTAAATAAAAAAAAGTTA
Found at i:47967202 original size:17 final size:18
Alignment explanation
Indices: 47967182--47967216 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
47967172 TAATTGCATA
*
47967182 AAAGGATTAAA-TTGAAT
1 AAAGGATAAAAGTTGAAT
47967199 AAAGGATAAAAGTTGAAT
1 AAAGGATAAAAGTTGAAT
47967217 TATAGATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (18 bp):
AAAGGATAAAAGTTGAAT
Found at i:47968680 original size:33 final size:33
Alignment explanation
Indices: 47968638--47968701 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
47968628 CGACCAAGTT
47968638 GGAGGTGAAGCAGATAGCAAATAGAATGCTGCA
1 GGAGGTGAAGCAGATAGCAAATAGAATGCTGCA
47968671 GGAGGTGAAGCAGATAGCAAATAGAATGCTG
1 GGAGGTGAAGCAGATAGCAAATAGAATGCTG
47968702 AAATCGAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.39, C:0.11, G:0.34, T:0.16
Consensus pattern (33 bp):
GGAGGTGAAGCAGATAGCAAATAGAATGCTGCA
Found at i:47969040 original size:33 final size:33
Alignment explanation
Indices: 47969003--47969065 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
47968993 CTTCGATTTT
47969003 AGCATTCTATTTGCTATCTGCTTCACCTCCTGC
1 AGCATTCTATTTGCTATCTGCTTCACCTCCTGC
47969036 AGCATTCTATTTGCTATCTGCTTCACCTCC
1 AGCATTCTATTTGCTATCTGCTTCACCTCC
47969066 AACTTGGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.16, C:0.33, G:0.11, T:0.40
Consensus pattern (33 bp):
AGCATTCTATTTGCTATCTGCTTCACCTCCTGC
Found at i:47977123 original size:8 final size:8
Alignment explanation
Indices: 47977112--47977136 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
47977102 ATTAATTTAT
47977112 TTTTATTA
1 TTTTATTA
47977120 TTTTATTA
1 TTTTATTA
47977128 TTTTATTA
1 TTTTATTA
47977136 T
1 T
47977137 ATTTTGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTATTA
Found at i:47977357 original size:13 final size:13
Alignment explanation
Indices: 47977339--47977374 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
47977329 ATCCGGCCCG
47977339 TATTATATTTTTA
1 TATTATATTTTTA
47977352 TATTAT-TTTTTA
1 TATTATATTTTTA
47977364 TA-TA-ATTTTTA
1 TATTATATTTTTA
47977375 AAAATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.36
12 8 0.36
13 6 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTATATTTTTA
Found at i:47977363 original size:12 final size:12
Alignment explanation
Indices: 47977339--47977373 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
47977329 ATCCGGCCCG
47977339 TATTATATTTTTA
1 TATTAT-TTTTTA
47977352 TATTATTTTTTA
1 TATTATTTTTTA
*
47977364 TATAATTTTT
1 TATTATTTTT
47977374 AAAAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:47981890 original size:3 final size:3
Alignment explanation
Indices: 47981882--47981918 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
47981872 CTCATTCTAT
47981882 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
47981919 ACATGTCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:47983662 original size:20 final size:20
Alignment explanation
Indices: 47983621--47983664 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
47983611 ACACTTCGAA
**
47983621 TTTTAAAATTTATTTTTTAT
1 TTTTAAAATTTATTTTAAAT
47983641 TTTTGAAAA-TTATTTTAAAT
1 TTTT-AAAATTTATTTTAAAT
47983661 TTTT
1 TTTT
47983665 TTTTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTAAAATTTATTTTAAAT
Found at i:47987237 original size:18 final size:17
Alignment explanation
Indices: 47987210--47987253 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
47987200 TTTTATGAAC
*
47987210 TTTTT-TTTTTGAAAT-
1 TTTTTATTTTTTAAATA
47987225 TTGTTTATTTTTTAAATA
1 TT-TTTATTTTTTAAATA
47987243 TTTTTATTTTT
1 TTTTTATTTTT
47987254 ATTTTTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 3 0.12
17 18 0.72
18 2 0.08
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (17 bp):
TTTTTATTTTTTAAATA
Found at i:47987711 original size:2 final size:2
Alignment explanation
Indices: 47987704--47987756 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
47987694 AATATTATTC
47987704 CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
47987745 CT CT CT CT CT CT
1 CT CT CT CT CT CT
47987757 ATATATATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:47987761 original size:2 final size:2
Alignment explanation
Indices: 47987756--47987786 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
47987746 TCTCTCTCTC
47987756 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47987787 CCAATGTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48000252 original size:75 final size:75
Alignment explanation
Indices: 48000129--48000293 Score: 285
Period size: 75 Copynumber: 2.2 Consensus size: 75
48000119 TTTTCTGCTT
* *
48000129 CTTTCATGCATGTTGGTTCACGGGTCCATTATTTCTTTGCTCTACTACATGCAAACAAAACACTA
1 CTTTCATGCATGCTGGTTCAAGGGTCCATTATTTCTTTGCTCTACTACATGCAAACAAAACACTA
48000194 CATTTTCCTG
66 CATTTTCCTG
* * *
48000204 CTTTCATGTATGCTGGTTCAAGGGTTCATTATTTCTTTGCTCTGCTACATGCAAACAAAACACTA
1 CTTTCATGCATGCTGGTTCAAGGGTCCATTATTTCTTTGCTCTACTACATGCAAACAAAACACTA
48000269 CATTTTCCTG
66 CATTTTCCTG
48000279 CTTTCATGCATGCTG
1 CTTTCATGCATGCTG
48000294 CCACGGGTTC
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 84 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (75 bp):
CTTTCATGCATGCTGGTTCAAGGGTCCATTATTTCTTTGCTCTACTACATGCAAACAAAACACTA
CATTTTCCTG
Found at i:48004699 original size:16 final size:16
Alignment explanation
Indices: 48004678--48004709 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48004668 AAATGTCAAT
48004678 TTGAAAATGTTAAAAA
1 TTGAAAATGTTAAAAA
48004694 TTGAAAATGTTAAAAA
1 TTGAAAATGTTAAAAA
48004710 AAACTAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (16 bp):
TTGAAAATGTTAAAAA
Found at i:48005046 original size:16 final size:16
Alignment explanation
Indices: 48005025--48005065 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
48005015 ATATTTGATA
48005025 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
48005041 TAATTTCAATAACAAT
1 TAATTTTAATAACAAT
*
48005057 TAGTTTTAA
1 TAATTTTAA
48005066 GTAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:48005950 original size:43 final size:43
Alignment explanation
Indices: 48005897--48006159 Score: 350
Period size: 43 Copynumber: 6.2 Consensus size: 43
48005887 TTTTAGAAAT
* * *
48005897 AAACGCCGCTATAGATCATGACCTTTAGTGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
48005940 AAACCCCGCTATAGATCAGGACCTTTAGCGGCGCTTTT-GCAT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
*
48005982 AAACGCCGCTATAGGTCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
48006025 AAACGCCGCTATAGATCAAGACCTTTAACGGCTCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
48006068 AAACGCCGCTATAGCTCGAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * * *
48006111 AAACGTCGCTATAGAACAA-ACCTTTAGCGACGCTTCTCGCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
48006153 AAACGCC
1 AAACGCC
48006160 ACTAAAAACA
Statistics
Matches: 193, Mismatches: 26, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
42 62 0.32
43 131 0.68
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:48006038 original size:85 final size:85
Alignment explanation
Indices: 48005877--48006159 Score: 343
Period size: 85 Copynumber: 3.3 Consensus size: 85
48005867 GCCGCAAACG
* * * * *
48005877 TTAGCGGCGTTTTTAGAAATAAACGCCGCTATAGATCATGACCTTTAGTGGCGCTTTTTCCACAA
1 TTAGCGGCGCTTTTAG-CATAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAA
*
48005942 ACCCCGCTATAGATCAGGACCT
65 ACGCCGCTATAGATCA-GACCT
*
48005964 TTAGCGGCGCTTTT-GCATAAACGCCGCTATAGGTCAAGACCTTTAGCGGCGCTTTTCCCACAAA
1 TTAGCGGCGCTTTTAGCATAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAA
48006028 CGCCGCTATAGATCAAGACCT
66 CGCCGCTATAGATC-AGACCT
* * ** * * *
48006049 TTAACGGCTCTTTTCCCACAAACGCCGCTATAGCTCGAGACCTTTAGCGGCGCTTTTCCCACAAA
1 TTAGCGGCGCTTTTAGCATAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAA
* * *
48006114 CGTCGCTATAGAACAAACCT
66 CGCCGCTATAGATCAGACCT
* * * *
48006134 TTAGCGACGCTTCTCGCAAAAACGCC
1 TTAGCGGCGCTTTTAGCATAAACGCC
48006160 ACTAAAAACA
Statistics
Matches: 172, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
85 99 0.58
86 60 0.35
87 13 0.08
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (85 bp):
TTAGCGGCGCTTTTAGCATAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAA
CGCCGCTATAGATCAGACCT
Found at i:48006134 original size:128 final size:128
Alignment explanation
Indices: 48005897--48006159 Score: 350
Period size: 128 Copynumber: 2.1 Consensus size: 128
48005887 TTTTAGAAAT
* ** *
48005897 AAACGCCGCTATAGATCATGACCTTTAGTGGCGCTTTTTCCACAAACCCCGCTATAGATCAGGAC
1 AAACGCCGCTATAGATCAAGACCTTTAACGGCGCTTTTCCCACAAACCCCGCTATAGATCAGGAC
* * ** * * *
48005962 CTTTAGCGGCGCTTTTGCATAAACGCCGCTATAGGTCAAGACCTTTAGCGGCGCTTTTCCCAC
66 CTTTAGCGGCGCTTTTCCACAAACGCCGCTATAGAACAAGACCTTTAGCGACGCTTCTCCCAA
* * *
48006025 AAACGCCGCTATAGATCAAGACCTTTAACGGCTCTTTTCCCACAAACGCCGCTATAGCTC-GAGA
1 AAACGCCGCTATAGATCAAGACCTTTAACGGCGCTTTTCCCACAAACCCCGCTATAGATCAG-GA
* *
48006089 CCTTTAGCGGCGCTTTTCCCACAAACGTCGCTATAGAACAA-ACCTTTAGCGACGCTTCTCGCAA
65 CCTTTAGCGGCGCTTTT-CCACAAACGCCGCTATAGAACAAGACCTTTAGCGACGCTTCTCCCAA
48006153 AAACGCC
1 AAACGCC
48006160 ACTAAAAACA
Statistics
Matches: 117, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
127 1 0.01
128 98 0.84
129 18 0.15
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (128 bp):
AAACGCCGCTATAGATCAAGACCTTTAACGGCGCTTTTCCCACAAACCCCGCTATAGATCAGGAC
CTTTAGCGGCGCTTTTCCACAAACGCCGCTATAGAACAAGACCTTTAGCGACGCTTCTCCCAA
Found at i:48012981 original size:19 final size:19
Alignment explanation
Indices: 48012957--48013005 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 19
48012947 TAAAATTATA
48012957 ATTTTTAGTTTTTGTATTTC
1 ATTTTTA-TTTTTGTATTTC
48012977 ATTTTTATTTTTGTATTTC
1 ATTTTTATTTTTGTATTTC
48012996 ATTTTTATTT
1 ATTTTTATTT
48013006 GTTATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (19 bp):
ATTTTTATTTTTGTATTTC
Found at i:48013368 original size:7 final size:7
Alignment explanation
Indices: 48013358--48013453 Score: 50
Period size: 7 Copynumber: 13.4 Consensus size: 7
48013348 ATCTAAAACT
48013358 TAAACCC
1 TAAACCC
48013365 TAAACCC
1 TAAACCC
** *
48013372 TTATTCCT
1 -TAAACCC
48013380 TAAACCC
1 TAAACCC
***
48013387 TAAATTA
1 TAAACCC
* *
48013394 TAAAACA
1 TAAACCC
48013401 TAAATCCC
1 TAAA-CCC
*
48013409 TAACCCC
1 TAAACCC
*
48013416 TAACCCC
1 TAAACCC
*
48013423 TAACCCC
1 TAAACCC
48013430 T-AACCC
1 TAAACCC
*
48013436 TTAACCC
1 TAAACCC
48013443 TTAAACCC
1 -TAAACCC
48013451 TAA
1 TAA
48013454 CCTTTAAACC
Statistics
Matches: 69, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
6 5 0.07
7 50 0.72
8 14 0.20
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAACCC
Found at i:48013423 original size:14 final size:14
Alignment explanation
Indices: 48013406--48013455 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
48013396 AAACATAAAT
48013406 CCCTAACCCCTAAC
1 CCCTAACCCCTAAC
48013420 CCCTAACCCCTAAC
1 CCCTAACCCCTAAC
* * *
48013434 CCTTAACCCTTAAA
1 CCCTAACCCCTAAC
48013448 CCCTAACC
1 CCCTAACC
48013456 TTTAAACCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.30, C:0.52, G:0.00, T:0.18
Consensus pattern (14 bp):
CCCTAACCCCTAAC
Found at i:48013451 original size:8 final size:7
Alignment explanation
Indices: 48013409--48013460 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
48013399 CATAAATCCC
*
48013409 TAACCCC
1 TAACCCT
*
48013416 TAACCCC
1 TAACCCT
*
48013423 TAACCCC
1 TAACCCT
48013430 TAACCCT
1 TAACCCT
48013437 TAACCCT
1 TAACCCT
48013444 TAAACCC-
1 T-AACCCT
*
48013451 TAACCTT
1 TAACCCT
48013458 TAA
1 TAA
48013461 ACCATAAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 4 0.10
7 32 0.78
8 5 0.12
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (7 bp):
TAACCCT
Found at i:48013460 original size:21 final size:21
Alignment explanation
Indices: 48013356--48013460 Score: 77
Period size: 21 Copynumber: 4.9 Consensus size: 21
48013346 TAATCTAAAA
**
48013356 CTTAAACCCTAAACCCTTATTC
1 CTTAAACCCT-AACCCTTAACC
** **
48013378 CTTAAACCCTAA-ATTATAAAA
1 CTTAAACCCTAACCCT-TAACC
* *
48013399 CATAAATCCCTAACCCCTAACC
1 CTTAAA-CCCTAACCCTTAACC
* *
48013421 CCTAACCCCTAACCCTTAACC
1 CTTAAACCCTAACCCTTAACC
*
48013442 CTTAAACCCTAACCTTTAA
1 CTTAAACCCTAACCCTTAA
48013461 ACCATAAATC
Statistics
Matches: 63, Mismatches: 17, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.62
22 23 0.37
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (21 bp):
CTTAAACCCTAACCCTTAACC
Found at i:48013475 original size:14 final size:14
Alignment explanation
Indices: 48013458--48013493 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
48013448 CCCTAACCTT
48013458 TAAACCATAAATCA-
1 TAAACCAT-AATCAC
48013472 TAAACCATAATCAC
1 TAAACCATAATCAC
48013486 TAAACCAT
1 TAAACCAT
48013494 CAGAGTAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCATAATCAC
Found at i:48014565 original size:40 final size:40
Alignment explanation
Indices: 48014490--48014769 Score: 251
Period size: 41 Copynumber: 6.9 Consensus size: 40
48014480 TTAAATCCCT
* * * ***
48014490 GAGCATTAGTGGCGCTT-TTTAGAAAACGCCGCTAAAAATA
1 GAGCATTAGCGGCGCTTCCTCA-AAAACGCCGCTAAAGCCA
** *
48014530 GAGCATTAGCGGCGCTTCCTCAAAAATACCACTAAAGCCA
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCA
*
48014570 CGAGCATTAGCGGCGCTTCCTCAAAAACGTCGCTAAAGCCCCA
1 -GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAG--CCA
*
48014613 -AGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCC
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCA
* * * *
48014652 GAGCATTAGCGGCGCCTCCTCAAAAACGCCTCTAAATCCCC
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAA-GCCA
* * * ** *
48014693 GAGCATTAGCGGAGCCTT-CACAGAAACGCCGCTGTAGCCCT
1 GAGCATTAGCGGCG-CTTCCTCAAAAACGCCGCTAAAG-CCA
* ** *
48014734 GAGCATTAGCGACGCTTTATTAAAAACGCCGCTAAA
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAA
48014770 TCCCCAAAAG
Statistics
Matches: 196, Mismatches: 35, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
39 2 0.01
40 64 0.33
41 125 0.64
42 2 0.01
43 3 0.02
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (40 bp):
GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCA
Found at i:48014582 original size:41 final size:41
Alignment explanation
Indices: 48014530--48014774 Score: 287
Period size: 41 Copynumber: 6.0 Consensus size: 41
48014520 GCTAAAAATA
** * *
48014530 GAGCATTAGCGGCGCTTCCTCAAAAATACCACTAAAGCCAC
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCC
*
48014571 GAGCATTAGCGGCGCTTCCTCAAAAACGTCGCTAAAGCCCC
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCC
*
48014612 AAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAG-CCC
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCC
* * *
48014652 GAGCATTAGCGGCGCCTCCTCAAAAACGCCTCTAAATCCCC
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCC
* * * ** *
48014693 GAGCATTAGCGGAGCCTT-CACAGAAACGCCGCTGTAGCCCT
1 GAGCATTAGCGGCG-CTTCCTCAAAAACGCCGCTAAAGCCCC
* ** * *
48014734 GAGCATTAGCGACGCTTTATTAAAAACGCCGCTAAATCCCC
1 GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCC
48014775 AAAAGCATAG
Statistics
Matches: 171, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
40 39 0.23
41 130 0.76
42 2 0.01
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.18
Consensus pattern (41 bp):
GAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCC
Found at i:48014720 original size:122 final size:122
Alignment explanation
Indices: 48014512--48014769 Score: 302
Period size: 122 Copynumber: 2.1 Consensus size: 122
48014502 CGCTTTTTAG
* * *
48014512 AAAACGCCGCTAAAAATAGAGCATTAGCGGCGCTTCCTCAAAAATACCACTAAAGCCACGAGCAT
1 AAAACGCCGCTAAAAACAGAGCATTAGCGGCGCCTCCTCAAAAACACCACTAAAGCCACGAGCAT
* * * * *
48014577 TAGCGGCGCTTCCTCAAAAACGTCGCTAAAGCCCCAAGCATTAGCGGCGCTTCCTCA
66 TAGCGGAGCTTCCACAAAAACGCCGCTAAAGCCCCAAGCATTAGCGACGCTTCATCA
** * * * * *
48014634 AAAACGCCGCTAAAGCCCGAGCATTAGCGGCGCCTCCTCAAAAACGCCTCTAAATCCCCGAGCAT
1 AAAACGCCGCTAAAAACAGAGCATTAGCGGCGCCTCCTCAAAAACACCACTAAAGCCACGAGCAT
* ** ** * *
48014699 TAGCGGAGCCTT-CACAGAAACGCCGCTGTAGCCCTGAGCATTAGCGACGCTTTATTA
66 TAGCGGAG-CTTCCACAAAAACGCCGCTAAAGCCCCAAGCATTAGCGACGCTTCATCA
48014756 AAAACGCCGCTAAA
1 AAAACGCCGCTAAA
48014770 TCCCCAAAAG
Statistics
Matches: 113, Mismatches: 22, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
122 110 0.97
123 3 0.03
ACGTcount: A:0.31, C:0.32, G:0.20, T:0.17
Consensus pattern (122 bp):
AAAACGCCGCTAAAAACAGAGCATTAGCGGCGCCTCCTCAAAAACACCACTAAAGCCACGAGCAT
TAGCGGAGCTTCCACAAAAACGCCGCTAAAGCCCCAAGCATTAGCGACGCTTCATCA
Found at i:48015615 original size:13 final size:13
Alignment explanation
Indices: 48015582--48015606 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48015572 CAACCTCAAT
48015582 GTTAAACACTAGG
1 GTTAAACACTAGG
48015595 GTTAAACACTAG
1 GTTAAACACTAG
48015607 AGGTGAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (13 bp):
GTTAAACACTAGG
Found at i:48016915 original size:6 final size:6
Alignment explanation
Indices: 48016891--48016935 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
48016881 TTAAAATTTG
*
48016891 TTTATT TTT-TT AATTATT TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT -TTTATT TTTATT TTTATT TTTATT TTTATT TTT
48016936 TTATGAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 2 0.06
6 31 0.89
7 2 0.06
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:48017367 original size:2 final size:2
Alignment explanation
Indices: 48017360--48017412 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
48017350 ATATCATTCC
48017360 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48017402 TA TA TA TA TA T
1 TA TA TA TA TA T
48017413 GTTATAGCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48017759 original size:19 final size:20
Alignment explanation
Indices: 48017721--48017760 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
48017711 TATTAATAAC
*
48017721 ATTTATCAAATTAAATTTAT
1 ATTTATCAAATTAAAATTAT
*
48017741 ATTTTTCAAA-TAAAATTAT
1 ATTTATCAAATTAAAATTAT
48017760 A
1 A
48017761 GTTAATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTATCAAATTAAAATTAT
Found at i:48022403 original size:88 final size:88
Alignment explanation
Indices: 48022254--48023210 Score: 1428
Period size: 88 Copynumber: 10.9 Consensus size: 88
48022244 GCAAGGCATA
* * * ** * **
48022254 CTGCTTCGTTGTCAATGTAAGAAGGCAAGATCTGCTATCTTTGACCAGCTCCA-CTACAACCGAG
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAACCGAG
* *
48022318 AGAGGTAAGGTTTGTGTCTTTGAC
65 AGAGGCAAGGTTTGTGTCTTCGAC
*
48022342 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
48022407 GAGGCAAGGTTTGTGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
* * * * * *
48022430 CTGCTTCACTGTCAATACAGGAAGGTAAGATATGTTGTCTTCAACCAGCTCCA-CTACAACTGAG
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAACCGAG
*
48022494 AGAGGCAAGGTTTGTGTCTTTGAC
65 AGAGGCAAGGTTTGTGTCTTCGAC
* * * **
48022518 CTACTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTTTTCAACCAGCTCC-GCTACAATTGAG
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAACCGAG
*
48022582 AGAGGCAAGGTTTGTGTCTTTGAC
65 AGAGGCAAGGTTTGTGTCTTCGAC
48022606 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATC--TTGTCTTCAACCAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
48022669 GAGGCAAGGTTTGTGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
* *
48022692 CTGCTTCGCTGTCAATACAGGAAGGCAAGATCTTTTGTTTTCAACCAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
48022757 GAGGCAAGGTTTGTGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
* *
48022780 CTGCTTCGCTGTCAATACAGGAAGGCAAGATCTTTTGTTTTCAACCAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
48022845 GAGGCAAGGTTTGTGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
* *
48022868 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTTTTCAACTAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
48022933 GAGGCAAGGTTTGTGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
*
48022956 CTACTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
48023021 GAGGCAAGGTTTGTGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
* *
48023044 CTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCATAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
*
48023109 GAGGCAAGGCTTTGT-T-TTCGAT
66 GAGGCAAGG-TTTGTGTCTTCGAC
* * * * * *
48023131 ATGCTTCGTTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCA-CTACAACCGAT
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAACCGA-
48023195 G-GAGGCAAGGCTTTGT
64 GAGAGGCAAGG-TTTGT
48023211 TTTCGATCTT
Statistics
Matches: 810, Mismatches: 50, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
86 79 0.10
87 77 0.10
88 648 0.80
89 6 0.01
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (88 bp):
CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
GAGGCAAGGTTTGTGTCTTCGAC
Found at i:48024884 original size:20 final size:19
Alignment explanation
Indices: 48024861--48024901 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
48024851 TCATCTAGAT
48024861 TTCTCTTTTT-TCATTCTTCA
1 TTCT-TTTTTCTCATT-TTCA
48024881 TTCTTTTTTCTCATTTTCA
1 TTCTTTTTTCTCATTTTCA
48024900 TT
1 TT
48024902 TTGATCTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.68
Consensus pattern (19 bp):
TTCTTTTTTCTCATTTTCA
Found at i:48024936 original size:15 final size:14
Alignment explanation
Indices: 48024912--48024980 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
48024902 TTGATCTTGA
48024912 TTTTGATTTTTTTTCT
1 TTTTG-TTTTTTTT-T
48024928 TTTTG--TTTTTTT
1 TTTTGTTTTTTTTT
* *
48024940 TTTTATTTTTTTAT
1 TTTTGTTTTTTTTT
*
48024954 TTTTGTTTTTTTTA
1 TTTTGTTTTTTTTT
48024968 TTTTGATTTTTTT
1 TTTTG-TTTTTTT
48024981 GCATTTTCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
12 5 0.11
13 6 0.13
14 22 0.49
15 7 0.16
16 5 0.11
ACGTcount: A:0.07, C:0.01, G:0.06, T:0.86
Consensus pattern (14 bp):
TTTTGTTTTTTTTT
Done.