Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 11 of 230
Found at i:3048802 original size:107 final size:106
Alignment explanation
Indices: 3048617--3048831 Score: 290
Period size: 107 Copynumber: 2.0 Consensus size: 106
3048607 AAACCCATAC
* * * * * *
3048617 TTTGAAGTTTTAAGAGGATATTTGGCCATTTGGTTCAACGAGAAATTGAAAACTAGCACATTAGG
1 TTTGAACTTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
*
3048682 GCACGTTTTCTCGAATTTT-CAAACGCAAAATATCGCTTTAT
66 GCACGTTTTCTCG-ATTTTCCAAACGCAAAATATCGCCTTAT
* * *
3048723 TTTGAACTTTTAAAAGGATATTTTAGCTATTTGG-TCGAACGAAAAATCGAAACCCAGCACGTTA
1 TTTGAACTTTTAAAAGGATA-TTTAGCCATTTGGTTC-AACGAAAAATCGAAAACCAGCACATTA
*
3048787 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATTGCCTTAT
64 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATCGCCTTAT
3048830 TT
1 TT
3048832 AGAAAAATTT
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
106 25 0.26
107 70 0.74
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (106 bp):
TTTGAACTTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
GCACGTTTTCTCGATTTTCCAAACGCAAAATATCGCCTTAT
Found at i:3049224 original size:21 final size:21
Alignment explanation
Indices: 3049185--3049243 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
3049175 TATAAAAAAT
3049185 ATGATTAACAAAT-ATAACCC
1 ATGATTAACAAATAATAACCC
3049205 ATGATTAACAAATAATAACCC
1 ATGATTAACAAATAATAACCC
3049226 ATGATTAACAAATAATAA
1 ATGATTAACAAATAATAA
3049244 ATCATACTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.25
Consensus pattern (21 bp):
ATGATTAACAAATAATAACCC
Found at i:3049659 original size:159 final size:152
Alignment explanation
Indices: 3049325--3049767 Score: 409
Period size: 159 Copynumber: 2.8 Consensus size: 152
3049315 GCAAGTTCAA
* * * * * *
3049325 AAAAAATTTAGTAAAAACTCTTATTTCGGTCATTTATTCGTACTATTTTCCCGAATTTTATTACT
1 AAAAAATTTAGTAAAAACTCTTA-TTCGGCCCTTTGTTCGTATTATTTTCTCGAATTTTATTACC
* * * *
3049390 TTCAATAAAAATAAATTACTTTC-ATTTTATATTATTTTACATTATTTTATTACATTATGTTTGA
65 TTCAATAAAAATATATTATTTTCTA-TTT-TATTATTTTACATTATTTTAGTACATTATGTTTAA
* *
3049454 AGTGTATTAATTTAGTGTGTTTTTT
128 AGTGTATTAATTTAGTCTGATTTTT
** * * * *
3049479 AAATAAATTTTTTTAAAAAAAACCCTTATTCCTGCCCTTTGCTCGTATTACTTTCTCGAATTTTA
1 AAA-AAA----TTTAGTAAAAACTCTTATT-CGGCCCTTTGTTCGTATTATTTTCTCGAATTTTA
* * *
3049544 TTACCTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGT
60 TTACCTTCAATAAAAATATATTATTTTC-TATTTTATTATTTTACATTATTTTAGTACATTATGT
* *
3049609 TTAAAATATTTGTATTAA-TTATTTCTGAATTTTT
124 TT--AA-A-GTGTATTAATTTA-GTCTG-ATTTTT
*
3049643 AAAAAATTTAGTAAAAAACTCTTACTTCGGCCCTTTGTTCGTATT-TTTTCTCCGCATTTTATTA
1 AAAAAATTTAGT-AAAAACTCTTA-TTCGGCCCTTTGTTCGTATTATTTTCT-CGAATTTTATTA
3049707 -CTT---TAAAAAGTATCA-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTAT-TT
63 CCTTCAATAAAAA-TAT-ATTATTTTCT-ATTTTATTATTTTACATTATTTTAGTACATTATGTT
3049766 TA
125 TA
3049768 TTACTTTAAA
Statistics
Matches: 236, Mismatches: 33, Indels: 40
0.76 0.11 0.13
Matches are distributed among these distances:
154 4 0.02
155 3 0.01
156 10 0.04
157 40 0.17
158 3 0.01
159 106 0.45
160 40 0.17
161 4 0.02
162 4 0.02
163 14 0.06
164 8 0.03
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.51
Consensus pattern (152 bp):
AAAAAATTTAGTAAAAACTCTTATTCGGCCCTTTGTTCGTATTATTTTCTCGAATTTTATTACCT
TCAATAAAAATATATTATTTTCTATTTTATTATTTTACATTATTTTAGTACATTATGTTTAAAGT
GTATTAATTTAGTCTGATTTTT
Found at i:3049750 original size:13 final size:13
Alignment explanation
Indices: 3049743--3049767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3049733 TTTATTATTT
3049743 TACATTATTTTAG
1 TACATTATTTTAG
3049756 TACATTATTTTA
1 TACATTATTTTA
3049768 TTACTTTAAA
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:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TACATTATTTTAG
Found at i:3051417 original size:49 final size:49
Alignment explanation
Indices: 3051364--3051491 Score: 139
Period size: 49 Copynumber: 2.6 Consensus size: 49
3051354 AGTCCAACCG
* ** *
3051364 TGGTCTTACACATAATCAGTTATCACATACCGATGCAATAGCCCAGCTA
1 TGGTCTTACACAGAATCACATATCACATACCGATGCAATAGCCCAGATA
* * * * *
3051413 TGGTCTTATACGGAATCACATATCACTTACCGATGCCATATCCCAGATA
1 TGGTCTTACACAGAATCACATATCACATACCGATGCAATAGCCCAGATA
* *
3051462 TGGTCTTATATAGAAATCACATAATCACAT
1 TGGTCTTACACAG-AATCACAT-ATCACAT
3051492 TTTCACATGT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 51 0.78
50 8 0.12
51 6 0.09
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (49 bp):
TGGTCTTACACAGAATCACATATCACATACCGATGCAATAGCCCAGATA
Found at i:3053287 original size:41 final size:41
Alignment explanation
Indices: 3053203--3053400 Score: 315
Period size: 41 Copynumber: 4.8 Consensus size: 41
3053193 TTGTATATAA
* ** * * *
3053203 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* * *
3053244 CACCAGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
3053285 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
3053326 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
3053367 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGA
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGA
3053401 ACTTACAAAA
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 145 1.00
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:3056535 original size:16 final size:18
Alignment explanation
Indices: 3056510--3056611 Score: 59
Period size: 18 Copynumber: 5.6 Consensus size: 18
3056500 TCCTTCCCAC
3056510 TTCTTCTTCTTCTTT-CTT
1 TTCTT-TTCTTCTTTCCTT
3056528 TT-TTTTCTTCTCCGTTCCTT
1 TTCTTTTCTTCT---TTCCTT
*
3056548 TTCTTTTCTTCTTT-TTT
1 TTCTTTTCTTCTTTCCTT
** * *
3056565 CTTCTCCTCTCCTCTCCTT
1 -TTCTTTTCTTCTTTCCTT
* *
3056584 TCCTTTTCTTTCTTTTC-T
1 TTCTTTTC-TTCTTTCCTT
3056602 TTCTTTTCTT
1 TTCTTTTCTT
3056612 TATTTCTTTC
Statistics
Matches: 63, Mismatches: 13, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
16 7 0.11
17 6 0.10
18 27 0.43
19 9 0.14
20 5 0.08
21 9 0.14
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (18 bp):
TTCTTTTCTTCTTTCCTT
Found at i:3056566 original size:31 final size:29
Alignment explanation
Indices: 3056522--3056633 Score: 102
Period size: 31 Copynumber: 3.7 Consensus size: 29
3056512 CTTCTTCTTC
3056522 TTTCTTTTTTTTCTTCTCCGTTCCTTTTCT
1 TTTCTTTTTTTTCTTCTCC-TTCCTTTTCT
* *
3056552 TTTCTTCTTTTTTCTTCTCCTCTCCTCTCCT
1 TTTCTT-TTTTTTCTTCTCCT-TCCTTTTCT
* * * *
3056583 TTCCTTTTCTTTCTT-TTCTTTCTTTTCT
1 TTTCTTTTTTTTCTTCTCCTTCCTTTTCT
3056611 TTAT-TTCTTTCTTTCTTCTCCTT
1 TT-TCTT-TTT-TTTCTTCTCCTT
3056634 TCCCTCTCCT
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
28 10 0.15
29 5 0.08
30 21 0.32
31 29 0.45
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (29 bp):
TTTCTTTTTTTTCTTCTCCTTCCTTTTCT
Found at i:3056583 original size:36 final size:36
Alignment explanation
Indices: 3056510--3056599 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 36
3056500 TCCTTCCCAC
* * *
3056510 TTCTTCTTCTTCTTTCTTTTTTTTCTTCTCCGTTCCTT
1 TTCTT-TTCTTCTTT-TTTCTTCTCCTCTCCGTTCCTT
3056548 TTCTTTTCTTCTTTTTTCTTCTCCTCTCC-TCTCCTT
1 TTCTTTTCTTCTTTTTTCTTCTCCTCTCCGT-TCCTT
*
3056584 TCCTTTTCTTTCTTTT
1 TTCTTTTC-TTCTTTT
3056600 CTTTCTTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 1 0.02
36 24 0.52
37 16 0.35
38 5 0.11
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (36 bp):
TTCTTTTCTTCTTTTTTCTTCTCCTCTCCGTTCCTT
Found at i:3056597 original size:4 final size:4
Alignment explanation
Indices: 3056588--3056627 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
3056578 CTCCTTTCCT
*
3056588 TTTC TTTC TTTTC TTTC TTTTC TTTA TTTC TTTC TTTC TT
1 TTTC TTTC -TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TT
3056628 CTCCTTTCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 24 0.75
5 8 0.25
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:3056909 original size:9 final size:9
Alignment explanation
Indices: 3056895--3056964 Score: 86
Period size: 9 Copynumber: 7.6 Consensus size: 9
3056885 TTTGGTTAAA
3056895 AATTACCCG
1 AATTACCCG
*
3056904 AATTACCCA
1 AATTACCCG
3056913 AATTACCCG
1 AATTACCCG
*
3056922 ACTTACCCG
1 AATTACCCG
*
3056931 ACTTACCCG
1 AATTACCCG
*
3056940 AAAATTACCCA
1 --AATTACCCG
3056951 AATTACCCG
1 AATTACCCG
3056960 AATTA
1 AATTA
3056965 AATCACTACA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
9 46 0.87
11 7 0.13
ACGTcount: A:0.37, C:0.33, G:0.07, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:3056917 original size:18 final size:18
Alignment explanation
Indices: 3056894--3056964 Score: 97
Period size: 18 Copynumber: 3.8 Consensus size: 18
3056884 TTTTGGTTAA
3056894 AAATTACCCGAATTACCC
1 AAATTACCCGAATTACCC
*
3056912 AAATTACCCGACTTACCC
1 AAATTACCCGAATTACCC
* *
3056930 GACTTACCCGAAAATTACCC
1 AAATTACCCG--AATTACCC
3056950 AAATTACCCGAATTA
1 AAATTACCCGAATTA
3056965 AATCACTACA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.67
20 15 0.33
ACGTcount: A:0.38, C:0.32, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATTACCCGAATTACCC
Found at i:3057030 original size:17 final size:17
Alignment explanation
Indices: 3056971--3057030 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
3056961 ATTAAATCAC
3056971 TACATAATTAAAAGC-AT
1 TACATAATTAAAA-CTAT
* * *
3056988 TACATAAATCTTTAAATTAC
1 TACAT-AA--TTAAAACTAT
3057008 TACATAATTAAAACTAT
1 TACATAATTAAAACTAT
3057025 TACATA
1 TACATA
3057031 CGTCTTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 18 0.55
18 2 0.06
19 2 0.06
20 11 0.33
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAACTAT
Found at i:3057067 original size:17 final size:17
Alignment explanation
Indices: 3057045--3057107 Score: 63
Period size: 17 Copynumber: 3.4 Consensus size: 17
3057035 TTTGAATCAC
3057045 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
* *
3057062 TACATAAGTCTTGAATTAACAC
1 TACATAA---TT-AA-AAACAT
3057084 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
3057101 TACATAA
1 TACATAA
3057108 GTCTTGAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
17 18 0.49
18 2 0.05
19 2 0.05
20 2 0.05
21 2 0.05
22 11 0.30
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.30
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:3057087 original size:22 final size:22
Alignment explanation
Indices: 3057057--3057122 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
3057047 CATAATTAAA
*
3057057 AACATTACATAAGTCTTGAATT
1 AACACTACATAAGTCTTGAATT
*
3057079 AACACTACATAA---TT-AA-A
1 AACACTACATAAGTCTTGAATT
*
3057096 AACATTACATAAGTCTTGAATT
1 AACACTACATAAGTCTTGAATT
3057118 AACAC
1 AACAC
3057123 ATAATTGACA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
17 11 0.32
18 2 0.06
19 2 0.06
20 2 0.06
21 2 0.06
22 15 0.44
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (22 bp):
AACACTACATAAGTCTTGAATT
Found at i:3057094 original size:39 final size:40
Alignment explanation
Indices: 3056959--3057122 Score: 202
Period size: 37 Copynumber: 4.2 Consensus size: 40
3056949 CAAATTACCC
* *
3056959 GAATTAAATCACTACATAATTAAAAGCATTACATAAATCTTT
1 GAATT-AA-CACTACATAATTAAAAACATTACATAAGTCTTT
* *
3057001 AAATT---ACTACATAATT-AAAACTATTACATACGTCTTT
1 GAATTAACACTACATAATTAAAAAC-ATTACATAAGTCTTT
3057038 GAA-T--CACTACATAATTAAAAACATTACATAAGTC-TT
1 GAATTAACACTACATAATTAAAAACATTACATAAGTCTTT
3057074 GAATTAACACTACATAATTAAAAACATTACATAAGTC-TT
1 GAATTAACACTACATAATTAAAAACATTACATAAGTCTTT
3057113 GAATTAACAC
1 GAATTAACAC
3057123 ATAATTGACA
Statistics
Matches: 110, Mismatches: 6, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
36 10 0.09
37 49 0.45
38 5 0.05
39 42 0.38
42 4 0.04
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (40 bp):
GAATTAACACTACATAATTAAAAACATTACATAAGTCTTT
Found at i:3059939 original size:16 final size:16
Alignment explanation
Indices: 3059918--3059973 Score: 96
Period size: 17 Copynumber: 3.5 Consensus size: 16
3059908 TGGCCTTGAT
3059918 ATTATAATGATGAAAA
1 ATTATAATGATGAAAA
3059934 ATTATAATGATGAAAAA
1 ATTATAATGATG-AAAA
3059951 ATTATAATGATG-AAA
1 ATTATAATGATGAAAA
3059966 ATTATAAT
1 ATTATAAT
3059974 ATTAGTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 11 0.28
16 12 0.31
17 16 0.41
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (16 bp):
ATTATAATGATGAAAA
Found at i:3060199 original size:16 final size:15
Alignment explanation
Indices: 3060163--3060195 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3060153 ATGTGTAAAG
3060163 AAATTTGTAAGTAAT
1 AAATTTGTAAGTAAT
3060178 AAATTTGTAAGTAAT
1 AAATTTGTAAGTAAT
3060193 AAA
1 AAA
3060196 ATTTTACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (15 bp):
AAATTTGTAAGTAAT
Found at i:3060267 original size:42 final size:43
Alignment explanation
Indices: 3060178--3060272 Score: 140
Period size: 42 Copynumber: 2.2 Consensus size: 43
3060168 TGTAAGTAAT
3060178 AAATTTGTAAGTAATAAAATTTTACTTACACTGGATGTGTAAAG
1 AAATTTGTAAGTAATAAAATTTTAC-TACACTGGATGTGTAAAG
**
3060222 AAATTTGTAAGTAAT-AAATTTATA-TATGCTGGATGTGTAAAG
1 AAATTTGTAAGTAATAAAATTT-TACTACACTGGATGTGTAAAG
3060264 AAATTTGTA
1 AAATTTGTA
3060273 CACTGGATGT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
42 25 0.52
43 6 0.12
44 17 0.35
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.38
Consensus pattern (43 bp):
AAATTTGTAAGTAATAAAATTTTACTACACTGGATGTGTAAAG
Found at i:3060280 original size:25 final size:25
Alignment explanation
Indices: 3060250--3060297 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
3060240 TTTATATATG
3060250 CTGGATGTGTAAAGAAATTTGTACA
1 CTGGATGTGTAAAGAAATTTGTACA
3060275 CTGGATGTGTAAAGAAATTTGTA
1 CTGGATGTGTAAAGAAATTTGTA
3060298 AGTAATAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.33
Consensus pattern (25 bp):
CTGGATGTGTAAAGAAATTTGTACA
Found at i:3062028 original size:14 final size:15
Alignment explanation
Indices: 3061996--3062029 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3061986 TATGTCTAAG
*
3061996 TTTTATTGTTTTTAT
1 TTTTATTGTATTTAT
3062011 TTTTATT-TATTTAT
1 TTTTATTGTATTTAT
3062025 TTTTA
1 TTTTA
3062030 AGGTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTATTGTATTTAT
Found at i:3062046 original size:37 final size:36
Alignment explanation
Indices: 3061945--3062047 Score: 95
Period size: 38 Copynumber: 2.8 Consensus size: 36
3061935 GATTTGAGCT
*
3061945 TTTATTTTTAAGGTGATATTTGTTTGATTTTTTCTTA
1 TTTATTTTTAAGGTGATATTT-TTTTATTTTTTCTTA
**
3061982 TTT-TTATGTCTAA-GTTTTATTGTTTTTATTTTTAT-TTA
1 TTTATT-T-T-TAAGGTGATATT-TTTTTATTTTT-TCTTA
3062020 TTTATTTTTAAGGTGATATTTATTTTAT
1 TTTATTTTTAAGGTGATATTT-TTTTAT
3062048 CTACAATAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
36 6 0.11
37 17 0.32
38 23 0.43
39 7 0.13
ACGTcount: A:0.20, C:0.02, G:0.11, T:0.67
Consensus pattern (36 bp):
TTTATTTTTAAGGTGATATTTTTTTATTTTTTCTTA
Found at i:3066080 original size:19 final size:19
Alignment explanation
Indices: 3066056--3066092 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3066046 AGTCTCTTTC
3066056 CAGGGATAGTAAAACACGG
1 CAGGGATAGTAAAACACGG
3066075 CAGGGATAGTAAAACACG
1 CAGGGATAGTAAAACACG
3066093 AATATTGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.16, G:0.30, T:0.11
Consensus pattern (19 bp):
CAGGGATAGTAAAACACGG
Found at i:3073668 original size:58 final size:57
Alignment explanation
Indices: 3073551--3073672 Score: 147
Period size: 58 Copynumber: 2.1 Consensus size: 57
3073541 CAAGCATGTG
* *
3073551 TATATAAAAATTAAAAATATGTATAAAAGATATATATATATAAGATTTATTAAATATA
1 TATATAAAAATAAAAAATATGTATAAAAGATATATATATATAAGA-GTATTAAATATA
* * *
3073609 TATATGAAAATAAAAAATGTGTATATAAAGATATATAAATAATATAAG-GTATAAAATATA
1 TATATAAAAATAAAAAATATGTATA-AAAGATATAT--AT-ATATAAGAGTATTAAATATA
3073669 TATA
1 TATA
3073673 CCTCTTTTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
58 22 0.40
59 10 0.18
60 14 0.25
61 2 0.04
62 7 0.13
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (57 bp):
TATATAAAAATAAAAAATATGTATAAAAGATATATATATATAAGAGTATTAAATATA
Found at i:3073671 original size:18 final size:19
Alignment explanation
Indices: 3073584--3073672 Score: 56
Period size: 18 Copynumber: 4.5 Consensus size: 19
3073574 TAAAAGATAT
*
3073584 ATATATATAAGATTTATTAA
1 ATATATATAAGATATA-TAA
* * *
3073604 ATATATATATGAAAATAAAAA
1 ATATATATAAG-ATAT-ATAA
*
3073625 ATGTGTATATAAAGATATATAA
1 A--TATATAT-AAGATATATAA
*
3073647 ATA-ATATAAGGTATA-AA
1 ATATATATAAGATATATAA
3073664 ATATATATA
1 ATATATATA
3073673 CCTCTTTTCA
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
17 5 0.09
18 12 0.23
19 4 0.08
20 11 0.21
21 5 0.09
22 5 0.09
23 9 0.17
24 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (19 bp):
ATATATATAAGATATATAA
Found at i:3077276 original size:6 final size:7
Alignment explanation
Indices: 3077251--3077275 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3077241 ATAATAAATA
3077251 TTTTTAT
1 TTTTTAT
3077258 TTTTTAT
1 TTTTTAT
3077265 TTTTTAT
1 TTTTTAT
3077272 TTTT
1 TTTT
3077276 AAAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:3077548 original size:30 final size:32
Alignment explanation
Indices: 3077495--3077559 Score: 107
Period size: 30 Copynumber: 2.1 Consensus size: 32
3077485 ATTTTACTAA
3077495 ATTCAAATTAATTACTGTCATTTTTAAATTAT
1 ATTCAAATTAATTACTGTCATTTTTAAATTAT
*
3077527 ATTCAAATTAATTAC-GT-ATTTTTTAATTAT
1 ATTCAAATTAATTACTGTCATTTTTAAATTAT
3077557 ATT
1 ATT
3077560 GCCCCCAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 15 0.47
31 2 0.06
32 15 0.47
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (32 bp):
ATTCAAATTAATTACTGTCATTTTTAAATTAT
Found at i:3082011 original size:18 final size:19
Alignment explanation
Indices: 3081974--3082011 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3081964 ATATTCACTA
*
3081974 AAAAAAATATTATTCCAAC
1 AAAAAAATATTATTCAAAC
*
3081993 AAAAAAAT-TTATTTAAAC
1 AAAAAAATATTATTCAAAC
3082011 A
1 A
3082012 TGGTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAAATATTATTCAAAC
Found at i:3083876 original size:50 final size:50
Alignment explanation
Indices: 3083801--3083901 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
3083791 GTCTGGAACA
3083801 GGACTGAAATCCGGTAACTCTGAATAATTTGATCGCTTGGCAAAGAAGGC
1 GGACTGAAATCCGGTAACTCTGAATAATTTGATCGCTTGGCAAAGAAGGC
* *
3083851 GGACTGAAATCGGGTAACTCTGAATAATTTGATCGCTTGGCAACGAAGGC
1 GGACTGAAATCCGGTAACTCTGAATAATTTGATCGCTTGGCAAAGAAGGC
3083901 G
1 G
3083902 CTGTTGCTAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.24
Consensus pattern (50 bp):
GGACTGAAATCCGGTAACTCTGAATAATTTGATCGCTTGGCAAAGAAGGC
Found at i:3089346 original size:501 final size:502
Alignment explanation
Indices: 3088305--3089360 Score: 1864
Period size: 501 Copynumber: 2.1 Consensus size: 502
3088295 TAATCCTACA
* ** *
3088305 ATATTGATGCCCTAAATGAAGGTTAGAGCCCCCCTTCACATCATAATTATTTCTATCCTTGGAAA
1 ATATTGTTGCCCTAAATGAAGGTTAGAG-CCCCCTTCACATGGTAATTATTTCTATCATTGGAAA
* * *
3088370 GTGACTGGTTATGCATTTTCCAATGCTGCTTGTCATTGTATTTGGTTTGCTCTAAATGAAGGTTA
65 GTGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTA
* * *
3088435 GTGCTATCATAATTATTCCTATCCTTGTAAATTGACTTATTTTTCATTTGCGCGTACTGCTTGTC
130 GTGCCATCATAATTATTCCTATCCTTGTAAATTGACTGATTTTTCATTTGCGCGTAATGCTTGTC
* * *
3088500 TTTGCGTTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACATCCTGTATAT
195 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACATCCTGTATAA
*
3088565 AACTTGAGTAATGCTAAGGTACAAAGAAGTCTGAGTGGTTGTGTGAAAATGTCTTCCTTTTTCCA
260 AACTTGAGTAATGCTAAGGTACAAAGAAGTCTGAGTCGTTGTGTGAAAATGTCTTCCTTTTTCCA
*
3088630 AGATGAATGAGTGGACTCAGTTTTGTTAGGACTATATGTCATGCTCTTCTTGTTGTTTTGAATGG
325 AGATGAATGAGTGGACTCAGTTTTGTCAGGACTATATGTCATGCTCTTCTTGTTGTTTTGAATGG
3088695 GTACGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTT
390 GTACGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTT
3088760 TAACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAC
455 TAACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAC
3088808 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTCTATCATTGGAAAG
1 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTCTATCATTGGAAAG
* *
3088873 TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAATGTTGG
66 TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTAG
3088938 TGCCATCATAATTATTCCTATCCTTGTAAATTGACTGATTTTTCATTTGC-CAGTAATGCTTGTC
131 TGCCATCATAATTATTCCTATCCTTGTAAATTGACTGATTTTTCATTTGCGC-GTAATGCTTGTC
*
3089002 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTTCCTGTATAA
195 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACATCCTGTATAA
*
3089067 AACTTGAGTAATGCTAAGGTACAAAGAAGTC-GAGTCGTTGTGTGAAAATGTGTTCCTTTTTCCA
260 AACTTGAGTAATGCTAAGGTACAAAGAAGTCTGAGTCGTTGTGTGAAAATGTCTTCCTTTTTCCA
* *
3089131 AGATGAATGAGTGGACTCAGTTTTGTCAGGACTATGTGTCGTGCTCTTCTTGTTGTTTTGAATGG
325 AGATGAATGAGTGGACTCAGTTTTGTCAGGACTATATGTCATGCTCTTCTTGTTGTTTTGAATGG
* *
3089196 GTACGAGGCTCCTAGCACCTTTAGGGAACTGGAGCTGAAGTTCGTTAGCTTTGGGCAGAGAATTT
390 GTACGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTT
*
3089261 TAACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAT
455 TAACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAC
3089309 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTC
1 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTC
3089361 CATCCTTGAA
Statistics
Matches: 528, Mismatches: 24, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
501 256 0.48
502 245 0.46
503 27 0.05
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (502 bp):
ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTCTATCATTGGAAAG
TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTAG
TGCCATCATAATTATTCCTATCCTTGTAAATTGACTGATTTTTCATTTGCGCGTAATGCTTGTCA
TTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACATCCTGTATAAA
ACTTGAGTAATGCTAAGGTACAAAGAAGTCTGAGTCGTTGTGTGAAAATGTCTTCCTTTTTCCAA
GATGAATGAGTGGACTCAGTTTTGTCAGGACTATATGTCATGCTCTTCTTGTTGTTTTGAATGGG
TACGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTTT
AACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAC
Found at i:3095947 original size:4 final size:4
Alignment explanation
Indices: 3095938--3095971 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
3095928 AAGTTTTATT
3095938 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
3095972 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:3095979 original size:22 final size:22
Alignment explanation
Indices: 3095921--3095980 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
3095911 AAGTGGCCCA
*
3095921 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
3095945 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
3095966 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
3095981 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:3099754 original size:4 final size:4
Alignment explanation
Indices: 3099745--3099778 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
3099735 AAGTTTTATT
3099745 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
3099779 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:3099786 original size:22 final size:22
Alignment explanation
Indices: 3099728--3099787 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
3099718 AAGTGGCCCA
*
3099728 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
3099752 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
3099773 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
3099788 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:3101707 original size:4 final size:4
Alignment explanation
Indices: 3101698--3101722 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3101688 GGTCCTTGTA
3101698 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
3101723 GAGAGCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:3104946 original size:21 final size:22
Alignment explanation
Indices: 3104917--3104963 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
3104907 CAGAAGGAGT
*
3104917 GAGTAGTACTTCACAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
*
3104939 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
3104960 GAGT
1 GAGT
3104964 TTGAGCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCACAGCAGGTG
Found at i:3107280 original size:21 final size:20
Alignment explanation
Indices: 3107254--3107303 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
3107244 TTTTTACTTT
* *
3107254 TAAAAAATATATAATATGAAA
1 TAAAAAAAAT-TAAAATGAAA
3107275 TAAAAAGAAATTAAAATGAAA
1 TAAAAA-AAATTAAAATGAAA
3107296 -AAAAAAAA
1 TAAAAAAAA
3107304 GAAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 3 0.12
20 5 0.19
21 15 0.58
22 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (20 bp):
TAAAAAAAATTAAAATGAAA
Found at i:3108124 original size:21 final size:21
Alignment explanation
Indices: 3108100--3108143 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3108090 TTTTAAAATG
*
3108100 AAAATATTTAAAT-TTAACTAT
1 AAAATATATAAATATTAA-TAT
3108121 AAAATATATAAATATTAATAT
1 AAAATATATAAATATTAATAT
3108142 AA
1 AA
3108144 TTTTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAATATATAAATATTAATAT
Found at i:3111065 original size:58 final size:57
Alignment explanation
Indices: 3110948--3111069 Score: 147
Period size: 58 Copynumber: 2.1 Consensus size: 57
3110938 CAAGCATGTG
* *
3110948 TATATAAAAATTAAAAATATGTATAAAAGATATATATATATAAGATTTATTAAATATA
1 TATATAAAAATAAAAAATATGTATAAAAGATATATATATATAAGA-GTATTAAATATA
* * *
3111006 TATATGAAAATAAAAAATGTGTATATAAAGATATATAAATAATATAAG-GTATAAAATATA
1 TATATAAAAATAAAAAATATGTATA-AAAGATATAT--AT-ATATAAGAGTATTAAATATA
3111066 TATA
1 TATA
3111070 ATATATATTA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
58 22 0.40
59 10 0.18
60 14 0.25
61 2 0.04
62 7 0.13
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (57 bp):
TATATAAAAATAAAAAATATGTATAAAAGATATATATATATAAGAGTATTAAATATA
Found at i:3111068 original size:18 final size:19
Alignment explanation
Indices: 3110981--3111077 Score: 63
Period size: 18 Copynumber: 4.9 Consensus size: 19
3110971 TAAAAGATAT
*
3110981 ATATATATAAGATTTATTAA
1 ATATATATAAGATATA-TAA
* * *
3111001 ATATATATATGAAAATAAAAA
1 ATATATATAAG-ATAT-ATAA
*
3111022 ATGTGTATATAAAGATATATAA
1 A--TATATAT-AAGATATATAA
*
3111044 ATA-ATATAAGGTATA-AA
1 ATATATATAAGATATATAA
*
3111061 ATATATATAATATATAT
1 ATATATATAAGATATAT
3111078 TAGAAAAGTA
Statistics
Matches: 58, Mismatches: 12, Indels: 15
0.68 0.14 0.18
Matches are distributed among these distances:
17 5 0.09
18 17 0.29
19 4 0.07
20 11 0.19
21 5 0.09
22 5 0.09
23 9 0.16
24 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (19 bp):
ATATATATAAGATATATAA
Found at i:3111283 original size:30 final size:28
Alignment explanation
Indices: 3111209--3111283 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 28
3111199 ATAATTATAA
3111209 ATAAAA-ATGCATGTATATATATAGATT
1 ATAAAATATGCATGTATATATATAGATT
* *
3111236 ATAAAATATAGGTATGTATATATATATATGTT
1 ATAAAATAT--GCATGTATATATATAGA--TT
*
3111268 TTAAAATATGCATGTA
1 ATAAAATATGCATGTA
3111284 AAAAAAACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 6 0.15
28 2 0.05
30 21 0.54
32 10 0.26
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (28 bp):
ATAAAATATGCATGTATATATATAGATT
Found at i:3113559 original size:6 final size:6
Alignment explanation
Indices: 3113543--3113589 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
3113533 GCCCCTCCAT
*
3113543 TTTTCA TTTTTCA TTTTCA TTTTCA TTTTCA TTTTTA TTTTCA TTTT
1 TTTTCA -TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
3113590 TTTTACTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
6 32 0.84
7 6 0.16
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTCA
Found at i:3114420 original size:12 final size:11
Alignment explanation
Indices: 3114399--3114444 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
3114389 ATTTTTCTTC
*
3114399 TTTTTCTTTTA
1 TTTTTTTTTTA
3114410 TTTTTTATTTTAA
1 TTTTTT-TTTT-A
3114423 TTTTTCTTTTTA
1 TTTTT-TTTTTA
3114435 TTTTTTTTTT
1 TTTTTTTTTT
3114445 GCTTTTGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 10 0.32
12 10 0.32
13 10 0.32
14 1 0.03
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:3114426 original size:18 final size:18
Alignment explanation
Indices: 3114405--3114476 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
3114395 CTTCTTTTTC
3114405 TTTTATTTTTTATTTTAA
1 TTTTATTTTTTATTTTAA
**
3114423 TTTT-TCTTTTTATTTTTT
1 TTTTAT-TTTTTATTTTAA
** * *
3114441 TTTTGCTTTTGATTTTGA
1 TTTTATTTTTTATTTTAA
3114459 TTTTGATTTTTTGATTTT
1 TTTT-ATTTTTT-ATTTT
3114477 TTTTGAATTG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
17 1 0.02
18 31 0.76
19 4 0.10
20 5 0.12
ACGTcount: A:0.12, C:0.03, G:0.07, T:0.78
Consensus pattern (18 bp):
TTTTATTTTTTATTTTAA
Found at i:3114427 original size:24 final size:24
Alignment explanation
Indices: 3114399--3114444 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
3114389 ATTTTTCTTC
3114399 TTTTTC-TTTTATTTTTTATTTTAA
1 TTTTTCTTTTTATTTTTT-TTTTAA
3114423 TTTTTCTTTTTATTTTTTTTTT
1 TTTTTCTTTTTATTTTTTTTTT
3114445 GCTTTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (24 bp):
TTTTTCTTTTTATTTTTTTTTTAA
Found at i:3114450 original size:12 final size:12
Alignment explanation
Indices: 3114399--3114480 Score: 69
Period size: 12 Copynumber: 6.7 Consensus size: 12
3114389 ATTTTTCTTC
*
3114399 TTTTTCTTTT-A
1 TTTTTTTTTTGA
*
3114410 TTTTTTATTTTAA
1 TTTTTT-TTTTGA
3114423 TTTTTCTTTTT-A
1 TTTTT-TTTTTGA
*
3114435 TTTTTTTTTTGC
1 TTTTTTTTTTGA
**
3114447 TTTTGATTTTGA
1 TTTTTTTTTTGA
3114459 TTTTGATTTTTTGA
1 TTTT--TTTTTTGA
3114473 TTTTTTTT
1 TTTTTTTT
3114481 GAATTGGATC
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
11 10 0.17
12 27 0.47
13 10 0.17
14 11 0.19
ACGTcount: A:0.11, C:0.04, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTTGA
Found at i:3119495 original size:60 final size:60
Alignment explanation
Indices: 3119431--3119554 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 60
3119421 CAAGCATGTG
* * * *
3119431 TATATAAAAATTAAAAATATGTATA-AAAGATATATATAT-ATATAAGATTTATTAAATATA
1 TATATAAAAATAAAAAATATGTATATAAAGATATATAAATAATATAAG--GTATAAAATATA
* *
3119491 TATATGAAAATAAAAAATGTGTATATAAAGATATATAAATAATATAAGGTATAAAATATA
1 TATATAAAAATAAAAAATATGTATATAAAGATATATAAATAATATAAGGTATAAAATATA
3119551 TATA
1 TATA
3119555 ATATATATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 36 0.64
61 13 0.23
62 7 0.12
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (60 bp):
TATATAAAAATAAAAAATATGTATATAAAGATATATAAATAATATAAGGTATAAAATATA
Found at i:3119553 original size:18 final size:19
Alignment explanation
Indices: 3119445--3119562 Score: 69
Period size: 18 Copynumber: 6.0 Consensus size: 19
3119435 TAAAAATTAA
* * *
3119445 AAATATGTATAAAAGATAT
1 AAATATATATAAGATATAT
* *
3119464 ATATATATATAAGATTTATT
1 AAATATATATAAGATATA-T
* * *
3119484 AAATATATATATGAAAATAAA
1 AAATATATATAAG-ATAT-AT
*
3119505 AAATGTGTATATAAAGATATAT
1 AAA--TATATAT-AAGATATAT
*
3119527 AAATA-ATATAAGGTATA-
1 AAATATATATAAGATATAT
*
3119544 AAATATATATAATATATAT
1 AAATATATATAAGATATAT
3119563 TAGAAAAGTA
Statistics
Matches: 73, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
17 5 0.07
18 17 0.23
19 17 0.23
20 13 0.18
21 5 0.07
22 5 0.07
23 9 0.12
24 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (19 bp):
AAATATATATAAGATATAT
Found at i:3122048 original size:6 final size:7
Alignment explanation
Indices: 3122029--3122062 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
3122019 TTAGCCTCTC
3122029 CATTTTT
1 CATTTTT
3122036 CATTTTT
1 CATTTTT
3122043 CATTTTT
1 CATTTTT
3122050 CA-TTTT
1 CATTTTT
3122056 CATTTTT
1 CATTTTT
3122063 TTGACTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:3122063 original size:14 final size:14
Alignment explanation
Indices: 3122029--3122062 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
3122019 TTAGCCTCTC
3122029 CATTTTTCATTTTT
1 CATTTTTCATTTTT
3122043 CATTTTTCA-TTTT
1 CATTTTTCATTTTT
3122056 CATTTTT
1 CATTTTT
3122063 TTGACTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:3122879 original size:6 final size:6
Alignment explanation
Indices: 3122868--3122915 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
3122858 CTCATTTTTC
**
3122868 TTCTTT TTCTTT TAT-TTT TTCTTT TAATTT TTCTTT TTCTTT TT-TTT
1 TTCTTT TTCTTT T-TCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
3122915 T
1 T
3122916 CTGCTTTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 5 0.14
6 30 0.83
7 1 0.03
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.83
Consensus pattern (6 bp):
TTCTTT
Found at i:3122891 original size:18 final size:16
Alignment explanation
Indices: 3122862--3122915 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 16
3122852 TGACCTCTCA
*
3122862 TTTTTCTTCTTTTTCTT
1 TTTTTTTTCTTTTT-TT
3122879 TTATTTTTTCTTTTAATTT
1 TT-TTTTTTCTTTT--TTT
*
3122898 TTCTTTTTCTTTTTTT
1 TTTTTTTTCTTTTTTT
3122914 TT
1 TT
3122916 CTGCTTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
18 20 0.62
19 4 0.12
20 1 0.03
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTTCTTTTTTT
Found at i:3122910 original size:24 final size:23
Alignment explanation
Indices: 3122871--3122915 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
3122861 ATTTTTCTTC
3122871 TTTTTCTTTTATTTTTTCTTTTAA
1 TTTTTCTTTTATTTTTT-TTTTAA
3122895 TTTTTCTTTT-TCTTTTTTTTT
1 TTTTTCTTTTAT-TTTTTTTTT
3122916 CTGCTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTCTTTTATTTTTTTTTTAA
Found at i:3126880 original size:12 final size:12
Alignment explanation
Indices: 3126865--3126889 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3126855 TGATGAAAAC
3126865 ATAAATAAAGAA
1 ATAAATAAAGAA
3126877 ATAAATAAAGAA
1 ATAAATAAAGAA
3126889 A
1 A
3126890 GGAATAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
ATAAATAAAGAA
Found at i:3127103 original size:3 final size:3
Alignment explanation
Indices: 3127097--3127153 Score: 53
Period size: 3 Copynumber: 18.3 Consensus size: 3
3127087 CAACAACAAC
* * *
3127097 AAT AAT AAT AAT AAT AAC AAC AAT -AT AAT AAT AAT ACT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
3127142 AAGGT AAT AAT A
1 AA--T AAT AAT A
3127154 GTGCAATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 2 0.04
3 39 0.85
4 2 0.04
5 3 0.07
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:3127117 original size:21 final size:21
Alignment explanation
Indices: 3127091--3127153 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
3127081 TATCAACAAC
3127091 AACAACAATAATAATAATAAT
1 AACAACAATAATAATAATAAT
3127112 AACAACAAT-ATAATAATAAT
1 AACAACAATAATAATAATAAT
*
3127132 -ACTA-AATAATAAGGTAATAAT
1 AACAACAATAATAA--TAATAAT
3127153 A
1 A
3127154 GTGCAATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 3 0.08
19 7 0.19
20 11 0.30
21 16 0.43
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.25
Consensus pattern (21 bp):
AACAACAATAATAATAATAAT
Found at i:3128413 original size:8 final size:8
Alignment explanation
Indices: 3128400--3128440 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
3128390 TATTTTATGC
3128400 ATTTTTAT
1 ATTTTTAT
3128408 ATTTTTAT
1 ATTTTTAT
*
3128416 ATTTTTGT
1 ATTTTTAT
3128424 A--TTTAT
1 ATTTTTAT
3128430 ATTTTTA-
1 ATTTTTAT
3128437 ATTT
1 ATTT
3128441 AATTCAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
6 5 0.17
7 4 0.14
8 20 0.69
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (8 bp):
ATTTTTAT
Found at i:3128452 original size:17 final size:17
Alignment explanation
Indices: 3128430--3128463 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3128420 TTGTATTTAT
3128430 ATTTTTAATTTAATTCA
1 ATTTTTAATTTAATTCA
* *
3128447 ATTTTTATTTTATTTCA
1 ATTTTTAATTTAATTCA
3128464 CTTTAAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTAATTTAATTCA
Found at i:3128612 original size:18 final size:19
Alignment explanation
Indices: 3128591--3128673 Score: 77
Period size: 18 Copynumber: 4.5 Consensus size: 19
3128581 ATAAAAAATA
3128591 TTCAAAAAAATT-CGTGTT
1 TTCAAAAAAATTCCGTGTT
3128609 TTCAAAAAAAATTCCG-GTGT
1 TTC-AAAAAAATTCCGTGT-T
* * *
3128629 TTC-AAAAATTTTCATGTT
1 TTCAAAAAAATTCCGTGTT
3128647 TTC--AAAAATTCCCGTGTT
1 TTCAAAAAAATT-CCGTGTT
3128665 TTCAAAAAA
1 TTCAAAAAA
3128674 TTTCTATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
17 6 0.12
18 23 0.44
19 13 0.25
20 10 0.19
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (19 bp):
TTCAAAAAAATTCCGTGTT
Found at i:3128617 original size:20 final size:20
Alignment explanation
Indices: 3128594--3128636 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3128584 AAAAATATTC
3128594 AAAAAAATT-C-GTGTTTTCA
1 AAAAAAATTCCGGTG-TTTCA
3128613 AAAAAAATTCCGGTGTTTCA
1 AAAAAAATTCCGGTGTTTCA
3128633 AAAA
1 AAAA
3128637 TTTTCATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 10 0.45
21 3 0.14
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (20 bp):
AAAAAAATTCCGGTGTTTCA
Found at i:3128684 original size:18 final size:18
Alignment explanation
Indices: 3128591--3128689 Score: 76
Period size: 19 Copynumber: 5.4 Consensus size: 18
3128581 ATAAAAAATA
* *
3128591 TTCAAAAAAATTCGTGTT
1 TTCAAAAAATTTCATGTT
* **
3128609 TTCAAAAAAAATTCCGGTGT
1 TTC-AAAAAATTTCATGT-T
*
3128629 TTCAAAAATTTTCATGTT
1 TTCAAAAAATTTCATGTT
* *
3128647 TTC-AAAAATTCCCGTGTT
1 TTCAAAAAATT-TCATGTT
3128665 TTCAAAAAATTTCTAT-TT
1 TTCAAAAAATTTC-ATGTT
3128683 TTCAAAA
1 TTCAAAA
3128690 TTTTTATTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
17 6 0.09
18 25 0.38
19 30 0.46
20 4 0.06
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.40
Consensus pattern (18 bp):
TTCAAAAAATTTCATGTT
Found at i:3128691 original size:35 final size:35
Alignment explanation
Indices: 3128591--3128689 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 35
3128581 ATAAAAAATA
* * *
3128591 TTCAAAAAAATTCGTGTTTTCAAAAAAAATTCCGGTGT
1 TTCAAAAAATTTCATGTTTTC---AAAAATTCCCGTGT
*
3128629 TTCAAAAATTTTCATGTTTTCAAAAATTCCCGTGTT
1 TTCAAAAAATTTCATGTTTTCAAAAATTCCCGTG-T
3128665 TTCAAAAAATTTCTAT-TTTTCAAAA
1 TTCAAAAAATTTC-ATGTTTTCAAAA
3128690 TTTTTATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
35 12 0.22
36 22 0.41
37 2 0.04
38 18 0.33
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.40
Consensus pattern (35 bp):
TTCAAAAAATTTCATGTTTTCAAAAATTCCCGTGT
Found at i:3128701 original size:17 final size:16
Alignment explanation
Indices: 3128670--3128700 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3128660 GTGTTTTCAA
3128670 AAAATTTCTATTTTTC
1 AAAATTTCTATTTTTC
*
3128686 AAAATTTTTATTTTT
1 AAAATTTCTATTTTT
3128701 TTATTTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
AAAATTTCTATTTTTC
Found at i:3149031 original size:25 final size:23
Alignment explanation
Indices: 3149003--3149059 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
3148993 AAATATATTC
3149003 ATTTCTTAAAAATATAAAATAAAAT
1 ATTTC-TAAAAA-ATAAAATAAAAT
* * *
3149028 ATTTCTACAAAATCAATTAAAAT
1 ATTTCTAAAAAATAAAATAAAAT
3149051 ATTT-TAAAA
1 ATTTCTAAAA
3149060 TTGGGTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 4 0.14
23 14 0.50
24 5 0.18
25 5 0.18
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTTCTAAAAAATAAAATAAAAT
Found at i:3149512 original size:25 final size:25
Alignment explanation
Indices: 3149484--3149531 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3149474 AAAAGGAATC
3149484 TTTATGTTTGT-TTAATAATTATTTT
1 TTTA-GTTTGTCTTAATAATTATTTT
* *
3149509 TTTAGTTTTTCTTAATTATTATT
1 TTTAGTTTGTCTTAATAATTATT
3149532 ATTCTTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (25 bp):
TTTAGTTTGTCTTAATAATTATTTT
Found at i:3152789 original size:126 final size:126
Alignment explanation
Indices: 3152636--3152896 Score: 375
Period size: 126 Copynumber: 2.1 Consensus size: 126
3152626 TCCATGAAAC
*
3152636 TAAAAATAGATGTTGTAATGAACTT-AAATTAACAAATAATTAGATCTAAATTTAAAATCTGAAA
1 TAAAAATAGACGTTGTAATGAACTTAAAATTAACAAATAATTAGATCTAAATTTAAAAT-TGAAA
* * *
3152700 AATAAAGGGAATAGATTTCAAATTTATGAAAAAATACCGAAACTTATTG-CATATCTTAATCAT
65 AATAAAGGGAATAAATTTCAAATTTATAAAAAAATA-CAAAACTTA-TGACATATCTTAATCAT
* * *
3152763 TAAAAATAGACG-TGTAATGAACTTAAAATTAACAAATAATTAGATCTGAATTTTAAATTTAAAA
1 TAAAAATAGACGTTGTAATGAACTTAAAATTAACAAATAATTAGATCTAAATTTAAAATTGAAAA
* * *
3152827 ATAAAGGGACTAAATTTTAAATTTATAAAAAAATACAAAACTTATGACATTTCTTAATCAT
66 ATAAAGGGAATAAATTTCAAATTTATAAAAAAATACAAAACTTATGACATATCTTAATCAT
3152888 TAAATAATA
1 TAAA-AATA
3152897 ATTGAAACTA
Statistics
Matches: 121, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
124 2 0.02
125 25 0.21
126 52 0.43
127 42 0.35
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (126 bp):
TAAAAATAGACGTTGTAATGAACTTAAAATTAACAAATAATTAGATCTAAATTTAAAATTGAAAA
ATAAAGGGAATAAATTTCAAATTTATAAAAAAATACAAAACTTATGACATATCTTAATCAT
Found at i:3153866 original size:4 final size:4
Alignment explanation
Indices: 3153857--3153883 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3153847 TGTTATGACA
3153857 ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACA
3153884 GAGAAACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:3157052 original size:2 final size:2
Alignment explanation
Indices: 3157045--3157074 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3157035 GCATAAGTGG
3157045 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3157075 TATATATACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3157426 original size:18 final size:17
Alignment explanation
Indices: 3157399--3157445 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
3157389 TCGGCTTATA
*
3157399 GACATCTTATATAAATTT
1 GACATATTATAT-AATTT
3157417 GACATATTAT-T-ATTT
1 GACATATTATATAATTT
3157432 GACATAATTATATA
1 GACAT-ATTATATA
3157446 TTTTATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 9 0.36
16 5 0.20
17 2 0.08
18 9 0.36
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
GACATATTATATAATTT
Found at i:3157433 original size:15 final size:17
Alignment explanation
Indices: 3157408--3157448 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
3157398 AGACATCTTA
*
3157408 TATAAATTTGACAT-AT
1 TATATATTTGACATAAT
3157424 TAT-TATTTGACATAAT
1 TATATATTTGACATAAT
3157440 TATATATTT
1 TATATATTT
3157449 TATTATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 9 0.41
16 8 0.36
17 5 0.23
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (17 bp):
TATATATTTGACATAAT
Found at i:3160302 original size:24 final size:22
Alignment explanation
Indices: 3160252--3160302 Score: 52
Period size: 24 Copynumber: 2.2 Consensus size: 22
3160242 TGCAGAAACT
3160252 AATA-CTAGAATTTAACCTAAA
1 AATATCTAGAATTTAACCTAAA
3160273 ATATATCTA-AATTTGAACCCTAATA
1 A-ATATCTAGAATTT-AA-CCTAA-A
3160298 AATAT
1 AATAT
3160303 GAAAATAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
21 1 0.04
22 8 0.32
23 5 0.20
24 9 0.36
25 2 0.08
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (22 bp):
AATATCTAGAATTTAACCTAAA
Found at i:3166806 original size:22 final size:23
Alignment explanation
Indices: 3166778--3166828 Score: 95
Period size: 22 Copynumber: 2.3 Consensus size: 23
3166768 TGAGTTGGTG
3166778 TCACAAATCAATTCGACACT-AC
1 TCACAAATCAATTCGACACTAAC
3166800 TCACAAATCAATTCGACACTAAC
1 TCACAAATCAATTCGACACTAAC
3166823 TCACAA
1 TCACAA
3166829 TTGATGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.43, C:0.31, G:0.04, T:0.22
Consensus pattern (23 bp):
TCACAAATCAATTCGACACTAAC
Found at i:3168123 original size:40 final size:40
Alignment explanation
Indices: 3168078--3168157 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
3168068 ATTTTTAAAA
* *
3168078 TTCATAATATTT-TTTCTTGTAGGTAACTGTCGATAAGATT
1 TTCATAATATTTCTTT-TTGTACGTAACTATCGATAAGATT
*
3168118 TTCATAATATTTCTTTTTGTACGTAATTATCGATAAGATT
1 TTCATAATATTTCTTTTTGTACGTAACTATCGATAAGATT
3168158 AAAAATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 33 0.92
41 3 0.08
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (40 bp):
TTCATAATATTTCTTTTTGTACGTAACTATCGATAAGATT
Found at i:3169423 original size:20 final size:21
Alignment explanation
Indices: 3169387--3169436 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3169377 AATGATTTTT
3169387 TTTTTAA-ATTTTAATATA-A
1 TTTTTAATATTTTAATATATA
*
3169406 TATTTTAATATTTT-ATATTTA
1 T-TTTTAATATTTTAATATATA
3169427 TTTTTAATAT
1 TTTTTAATAT
3169437 GATTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.04
20 19 0.70
21 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTAATATTTTAATATATA
Found at i:3170025 original size:21 final size:20
Alignment explanation
Indices: 3169979--3170028 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
3169969 TCCGTTTTTC
*
3169979 TATAATTGACATTTTAACAA
1 TATAATTGTCATTTTAACAA
* **
3169999 TTTAATTGTCATATTTATTAA
1 TATAATTGTCAT-TTTAACAA
3170020 TATAATTGT
1 TATAATTGT
3170029 ATTCGTTATG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (20 bp):
TATAATTGTCATTTTAACAA
Found at i:3170525 original size:23 final size:22
Alignment explanation
Indices: 3170483--3170527 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3170473 AATTTTACCA
*
3170483 AACTTTCAAAATTTGCAAGAGT
1 AACTTTCAAAATTTGAAAGAGT
3170505 AACTTTCGAAAATGTT-AAAGAGT
1 AACTTTC-AAAAT-TTGAAAGAGT
3170528 GATAGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 11 0.55
24 2 0.10
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (22 bp):
AACTTTCAAAATTTGAAAGAGT
Found at i:3171245 original size:67 final size:69
Alignment explanation
Indices: 3171174--3171313 Score: 214
Period size: 71 Copynumber: 2.0 Consensus size: 69
3171164 TTTTTTATTT
3171174 TATCTTTTCATTATTTAATTGAGTTT-GTTT-TATATCTA-TAATTTTATATTTTACATTGTTTT
1 TATCTTTTCATTATTTAATTGAGTTTAGTTTATATATCTACTAATTTTATATTTTACATTGTTTT
3171236 TACGA
66 TAC-A
* * *
3171241 TATCTTTTTATTATTTAATTGAGTTTATTTTATATATGTACGTAATTTTATATTTTACATTGTTT
1 TATCTTTTCATTATTTAATTGAGTTTAGTTTATATATCTAC-TAATTTTATATTTTACATTGTTT
3171306 TTACA
65 TTACA
3171311 TAT
1 TAT
3171314 ATTAAAAATA
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
67 25 0.38
68 3 0.05
69 7 0.11
70 4 0.06
71 27 0.41
ACGTcount: A:0.26, C:0.06, G:0.07, T:0.60
Consensus pattern (69 bp):
TATCTTTTCATTATTTAATTGAGTTTAGTTTATATATCTACTAATTTTATATTTTACATTGTTTT
TACA
Found at i:3171344 original size:71 final size:71
Alignment explanation
Indices: 3171212--3171344 Score: 160
Period size: 71 Copynumber: 1.9 Consensus size: 71
3171202 TTTATATCTA
* *** * * * *
3171212 TAATTTTATATTTTACATTGTTTTTACGATATCTTTTTATTATTTAATTGAGTTTATTTTATATA
1 TAATTTTATATTTTACATTGTTTTTACGATATATTAAAAATATTTAATTAAATTTAATTTATATA
3171277 TGTACG
66 TGTACG
**
3171283 TAATTTTATATTTTACATTGTTTTTAC-ATATATTAAAAATATTTTGTTAAATTTAGATTTAT
1 TAATTTTATATTTTACATTGTTTTTACGATATATTAAAAATATTTAATTAAATTTA-ATTTAT
3171345 TGCAACGTCA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
70 19 0.37
71 32 0.63
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.58
Consensus pattern (71 bp):
TAATTTTATATTTTACATTGTTTTTACGATATATTAAAAATATTTAATTAAATTTAATTTATATA
TGTACG
Found at i:3171592 original size:15 final size:15
Alignment explanation
Indices: 3171572--3171623 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
3171562 AAGACAAAAC
3171572 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
3171587 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
3171606 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
3171621 ATT
1 ATT
3171624 AATATTGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:3171686 original size:16 final size:16
Alignment explanation
Indices: 3171655--3171691 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
3171645 ATGTGAATAA
3171655 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
3171671 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
3171687 TATTA
1 TATTA
3171692 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:3171715 original size:18 final size:18
Alignment explanation
Indices: 3171677--3171712 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3171667 TTATTATTTT
*
3171677 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
3171695 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
3171713 TAATGTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:3171733 original size:9 final size:9
Alignment explanation
Indices: 3171719--3171759 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
3171709 TAAATAATGT
3171719 ATTATATTA
1 ATTATATTA
3171728 ATTATATTA
1 ATTATATTA
3171737 ATTATATTA
1 ATTATATTA
*
3171746 A-TA-ATTT
1 ATTATATTA
3171753 ATTATAT
1 ATTATAT
3171760 GACAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 4 0.14
8 4 0.14
9 21 0.72
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTATATTA
Found at i:3171742 original size:18 final size:16
Alignment explanation
Indices: 3171705--3171759 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 16
3171695 TAAAATTTAA
3171705 ATATTAAATAATGT-ATT
1 ATATT-AATAAT-TAATT
3171722 ATATTAATTATATTAATT
1 ATATTAA-TA-ATTAATT
*
3171740 ATATTAATAATTTATT
1 ATATTAATAATTAATT
3171756 ATAT
1 ATAT
3171760 GACAATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
16 12 0.35
17 10 0.29
18 12 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATATTAATAATTAATT
Found at i:3171806 original size:38 final size:40
Alignment explanation
Indices: 3171763--3171849 Score: 94
Period size: 38 Copynumber: 2.3 Consensus size: 40
3171753 ATTATATGAC
3171763 AATATAAATAATTAAATATGT-AT-TTT-AATATTATTAAA
1 AATATAAATAATTAAATAT-TAATATTTAAATATTATTAAA
** *
3171801 AATAT-AAT-ATTTTATATTAATATTTAAATATTTTTAAA
1 AATATAAATAATTAAATATTAATATTTAAATATTATTAAA
*
3171839 AATAAAAATAA
1 AATATAAATAA
3171850 AATTTATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
35 1 0.03
36 9 0.22
37 6 0.15
38 20 0.50
39 3 0.08
40 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (40 bp):
AATATAAATAATTAAATATTAATATTTAAATATTATTAAA
Found at i:3178536 original size:30 final size:31
Alignment explanation
Indices: 3178502--3178570 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
3178492 TTACCCAAGA
* **
3178502 GTAAATACT-AAAAAATTGAGGGGTTAA-AGT
1 GTAAATA-TGAAAAAATTGAAGGACTAATAGT
*
3178532 GTAAATATGAAAAAGTTGAAGGACTAATAGT
1 GTAAATATGAAAAAATTGAAGGACTAATAGT
3178563 GTAAATAT
1 GTAAATAT
3178571 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 1 0.03
30 21 0.64
31 11 0.33
ACGTcount: A:0.48, C:0.03, G:0.22, T:0.28
Consensus pattern (31 bp):
GTAAATATGAAAAAATTGAAGGACTAATAGT
Found at i:3181955 original size:14 final size:14
Alignment explanation
Indices: 3181936--3181966 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3181926 ATCCAAACAA
3181936 TAACAACAAAATAG
1 TAACAACAAAATAG
*
3181950 TAACAACATAATAG
1 TAACAACAAAATAG
3181964 TAA
1 TAA
3181967 AATGACAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (14 bp):
TAACAACAAAATAG
Found at i:3183734 original size:30 final size:30
Alignment explanation
Indices: 3183698--3183759 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
3183688 TAATAAGTGA
3183698 TTACCAATTTAGGGTCTTATTAAATGGAAC
1 TTACCAATTTAGGGTCTTATTAAATGGAAC
3183728 TTACCAATTTAGGGTCTTATTAAATGGAAC
1 TTACCAATTTAGGGTCTTATTAAATGGAAC
3183758 TT
1 TT
3183760 GATCTTGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (30 bp):
TTACCAATTTAGGGTCTTATTAAATGGAAC
Found at i:3194621 original size:47 final size:49
Alignment explanation
Indices: 3194568--3194672 Score: 180
Period size: 47 Copynumber: 2.2 Consensus size: 49
3194558 TAAAAATAAT
3194568 CTTTTTTTTAA-GTGGATAACATATTTAGAGTTTTTATTTATTGGGTCA
1 CTTTTTTTTAAGGTGGATAACATATTTAGAGTTTTTATTTATTGGGTCA
3194616 --TTTTTTTAAGGTGGATAACATATTTAGAGTTTTTATTTATTGGGTCA
1 CTTTTTTTTAAGGTGGATAACATATTTAGAGTTTTTATTTATTGGGTCA
*
3194663 CTTTCTTTTA
1 CTTTTTTTTA
3194673 TTTGAAGTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
46 9 0.17
47 37 0.70
49 7 0.13
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.53
Consensus pattern (49 bp):
CTTTTTTTTAAGGTGGATAACATATTTAGAGTTTTTATTTATTGGGTCA
Found at i:3197367 original size:9 final size:9
Alignment explanation
Indices: 3197350--3197386 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
3197340 TAAGTTTTCG
3197350 AATTCGAAT
1 AATTCGAAT
*
3197359 AACTCGAAT
1 AATTCGAAT
3197368 AATTCGAAT
1 AATTCGAAT
3197377 AATTCGAAT
1 AATTCGAAT
3197386 A
1 A
3197387 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:3197507 original size:30 final size:30
Alignment explanation
Indices: 3197445--3197507 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
3197435 ACTTTTCTCT
*
3197445 CAAAACTTTTACTCCTTCCCACTTTCCCCC
1 CAAAACTTTTACTCCCTCCCACTTTCCCCC
3197475 CAAAACTTTTACTCCCCTCCC-C-TTCCCTCC
1 CAAAACTTTTACT-CCCTCCCACTTTCCC-CC
3197505 CAA
1 CAA
3197508 CCCCCCAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 5 0.17
30 19 0.63
31 6 0.20
ACGTcount: A:0.21, C:0.49, G:0.00, T:0.30
Consensus pattern (30 bp):
CAAAACTTTTACTCCCTCCCACTTTCCCCC
Found at i:3197639 original size:30 final size:31
Alignment explanation
Indices: 3197605--3197664 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
3197595 AAACCTTTTA
*
3197605 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
3197635 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
3197665 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:3205656 original size:86 final size:88
Alignment explanation
Indices: 3205554--3205895 Score: 392
Period size: 88 Copynumber: 3.9 Consensus size: 88
3205544 TGTAACCTTT
* ** * * *
3205554 AACCAGCTCCAAT-GCAACCGATGGAGGCAAGGCTTTGT-T-TTTGATCTGCTTTGCTGTTAATG
1 AACCAGCTCC-ATCACAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATG
* * *
3205616 CAAGAAGGCAAGATCTGCT-TCTTT
64 CAGGAAGGCAAGATCTGTTGTCTTC
* * * ** * * *
3205640 AACTAGCTCCA-CTGCAATCGATGGACGCAAGGCTTTGT-T-TTCAATCTGCTTCGCTGTTAATG
1 AACCAGCTCCATC-ACAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATG
* *
3205702 TAGGAAGGCAAGATCTTTTGTCTTC
64 CAGGAAGGCAAGATCTGTTGTCTTC
* *
3205727 AACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
*
3205792 GGAAGGCAAGATCTTTTGTCTTC
66 GGAAGGCAAGATCTGTTGTCTTC
*
3205815 AACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
3205880 GGAAGGCAAGATCTGT
66 GGAAGGCAAGATCTGT
3205896 AACTTCATTG
Statistics
Matches: 228, Mismatches: 22, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
85 1 0.00
86 73 0.32
87 28 0.12
88 126 0.55
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (88 bp):
AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
GGAAGGCAAGATCTGTTGTCTTC
Found at i:3205728 original size:45 final size:45
Alignment explanation
Indices: 3205673--3205893 Score: 139
Period size: 44 Copynumber: 5.0 Consensus size: 45
3205663 GACGCAAGGC
* *
3205673 TTTGTTTTCAATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCT
1 TTTGTCTTCAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
* * ** ** * * * *
3205718 TTTGTCTTCAACCAGC-TCTATCACAACCGAAAG-AGGCAAGGT-T
1 TTTGTCTTCAATCTGCTTCGCTGTCAA-TGTAGGAAGGCAAGATCT
* *
3205761 TGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 TTTGTCTTCAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
* * ** ** * * * *
3205806 TTTGTCTTCAACCAGC-TCTATCACAACCGAAAG-AGGCAAGGT-T
1 TTTGTCTTCAATCTGCTTCGCTGTCAA-TGTAGGAAGGCAAGATCT
* * *
3205849 TGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 TTTGTCTTCAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
3205894 GTAACTTCAT
Statistics
Matches: 120, Mismatches: 48, Indels: 16
0.65 0.26 0.09
Matches are distributed among these distances:
43 32 0.27
44 55 0.46
45 33 0.28
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (45 bp):
TTTGTCTTCAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
Found at i:3205790 original size:88 final size:88
Alignment explanation
Indices: 3205666--3205893 Score: 406
Period size: 88 Copynumber: 2.6 Consensus size: 88
3205656 ATCGATGGAC
* *
3205666 GCAAGGCTTTGT-T-TTCAATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTTCAA
1 GCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAA
3205729 CCAGCTCTATCACAACCGAAAGAG
65 CCAGCTCTATCACAACCGAAAGAG
3205753 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
3205818 CAGCTCTATCACAACCGAAAGAG
66 CAGCTCTATCACAACCGAAAGAG
*
3205841 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
3205894 GTAACTTCAT
Statistics
Matches: 136, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
86 5 0.04
87 7 0.05
88 124 0.91
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (88 bp):
GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
CAGCTCTATCACAACCGAAAGAG
Found at i:3208145 original size:16 final size:17
Alignment explanation
Indices: 3208120--3208153 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3208110 TTGATCTTGA
*
3208120 TTTTGATTTTTTCTTCT
1 TTTTGATTTTTTATTCT
3208137 TTTTG-TTTTTTATTCT
1 TTTTGATTTTTTATTCT
3208153 T
1 T
3208154 AAGCCTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTGATTTTTTATTCT
Found at i:3210661 original size:19 final size:20
Alignment explanation
Indices: 3210632--3210680 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
3210622 CACTTCGTGA
* *
3210632 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAGATGCATG
*
3210651 CAATGTAATGCAGATGCATG
1 AAATGTAATGCAGATGCATG
3210671 AAATG-AATGC
1 AAATGTAATGC
3210681 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAGATGCATG
Found at i:3214492 original size:21 final size:22
Alignment explanation
Indices: 3214450--3214498 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
3214440 TAAAAAGTTG
*
3214450 TTTTTATTTTAAATTTTAATTA
1 TTTTTATTTTAAATATTAATTA
*
3214472 TTTTTATTTTAAA-ATTGATTA
1 TTTTTATTTTAAATATTAATTA
3214493 TTTTTA
1 TTTTTA
3214499 ATAATTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTATTTTAAATATTAATTA
Found at i:3214493 original size:15 final size:15
Alignment explanation
Indices: 3214462--3214512 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
3214452 TTTATTTTAA
* *
3214462 ATTTTAATTATTTTT
1 ATTTTAATAATTATT
3214477 ATTTTAA-AATTGATT
1 ATTTTAATAATT-ATT
3214492 ATTTTTAATAATTATT
1 A-TTTTAATAATTATT
3214508 ATTTT
1 ATTTT
3214513 TAACTCACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 3 0.10
15 14 0.45
16 10 0.32
17 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
ATTTTAATAATTATT
Found at i:3214499 original size:16 final size:16
Alignment explanation
Indices: 3214463--3214515 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
3214453 TTATTTTAAA
* *
3214463 TTTTAATTATTTTTA-
1 TTTTAATAATTATTAT
3214478 TTTTAA-AATTGATTAT
1 TTTTAATAATT-ATTAT
3214494 TTTTAATAATTATTAT
1 TTTTAATAATTATTAT
3214510 TTTTAA
1 TTTTAA
3214516 CTCACATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
14 3 0.09
15 9 0.27
16 17 0.52
17 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTTAATAATTATTAT
Found at i:3220683 original size:5 final size:5
Alignment explanation
Indices: 3220673--3220699 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3220663 TCATATGTCT
3220673 ATAAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA AT
3220700 TACAACACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:3220743 original size:17 final size:19
Alignment explanation
Indices: 3220708--3220744 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3220698 ATTACAACAC
3220708 TATAATATTTAATACAAAT
1 TATAATATTTAATACAAAT
3220727 TATAAT-TTTAATA-AAAT
1 TATAATATTTAATACAAAT
3220744 T
1 T
3220745 TACTTTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 7 0.39
19 6 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TATAATATTTAATACAAAT
Found at i:3222031 original size:83 final size:83
Alignment explanation
Indices: 3221890--3222057 Score: 291
Period size: 83 Copynumber: 2.0 Consensus size: 83
3221880 CCACGTATAA
* * *
3221890 GAAAGAAGAAGAGGGATAGGGGGGGGAGAAAGACAAGTGGCATAGGTTTAGTGGAATTAGGTAGC
1 GAAAGAAGAAGAGGGATAAGGGGAGGAGAAAGACAAGTGGCATAGGTTTAGTGAAATTAGGTAGC
3221955 TGTTATCGTTAAAGTGAT
66 TGTTATCGTTAAAGTGAT
* *
3221973 GAAAGAAGAAGAGGGATAAGGGGAGGAGAAAGGCAAGTGGCATGGGTTTAGTGAAATTAGGTAGC
1 GAAAGAAGAAGAGGGATAAGGGGAGGAGAAAGACAAGTGGCATAGGTTTAGTGAAATTAGGTAGC
3222038 TGTTATCGTTAAAGTGAT
66 TGTTATCGTTAAAGTGAT
3222056 GA
1 GA
3222058 TGTGAAATAT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.36, C:0.05, G:0.38, T:0.21
Consensus pattern (83 bp):
GAAAGAAGAAGAGGGATAAGGGGAGGAGAAAGACAAGTGGCATAGGTTTAGTGAAATTAGGTAGC
TGTTATCGTTAAAGTGAT
Found at i:3235277 original size:26 final size:26
Alignment explanation
Indices: 3235222--3235283 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
3235212 AATACAAGTG
3235222 AAAATGATT-ATATAATAAATTTATT
1 AAAATGATTAATATAATAAATTTATT
*
3235247 AAAATAATTAATATAA-AAATTTGATT
1 AAAATGATTAATATAATAAATTT-ATT
*
3235273 GAAATGATTAA
1 AAAATGATTAA
3235284 GTTGAAAGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (26 bp):
AAAATGATTAATATAATAAATTTATT
Found at i:3236795 original size:6 final size:6
Alignment explanation
Indices: 3236784--3236824 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
3236774 CACCCTCTCT
*
3236784 CGAAGA CGAAGA -AAAGA CGAAGA CGAAGA CGAAGA CGAAGA
1 CGAAGA CGAAGA CGAAGA CGAAGA CGAAGA CGAAGA CGAAGA
3236825 GCCCTTTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.54, C:0.15, G:0.32, T:0.00
Consensus pattern (6 bp):
CGAAGA
Found at i:3251438 original size:17 final size:17
Alignment explanation
Indices: 3251416--3251455 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3251406 AATAATATAG
3251416 TAATAATTAAAAATAA-A
1 TAATAA-TAAAAATAACA
*
3251433 TAATAATAATAATAACA
1 TAATAATAAAAATAACA
3251450 TAATAA
1 TAATAA
3251456 AAATAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TAATAATAAAAATAACA
Found at i:3251460 original size:17 final size:16
Alignment explanation
Indices: 3251427--3251461 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3251417 AATAATTAAA
*
3251427 AATAAATAATAATAAT
1 AATAAATAATAAAAAT
3251443 AATAACATAATAAAAAT
1 AATAA-ATAATAAAAAT
3251460 AA
1 AA
3251462 AAAAACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAATAATAAAAAT
Found at i:3253271 original size:21 final size:21
Alignment explanation
Indices: 3253247--3253286 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3253237 ACTTCTCTAA
*
3253247 AGTTAAAAGTCAAAACTATTC
1 AGTTAAAAGACAAAACTATTC
*
3253268 AGTTTAAAGACAAAACTAT
1 AGTTAAAAGACAAAACTAT
3253287 ATTATTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (21 bp):
AGTTAAAAGACAAAACTATTC
Found at i:3256651 original size:28 final size:28
Alignment explanation
Indices: 3256594--3256653 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
3256584 GATTTCCCGG
*
3256594 AAAATGGACCATTCCGATAAATAATCAA
1 AAAATGGACCATTCCGATAAATAATAAA
* * *
3256622 AAAATCGGCCCATTTCGATAAAT-TTAAA
1 AAAAT-GGACCATTCCGATAAATAATAAA
3256650 AAAA
1 AAAA
3256654 AGGCTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (28 bp):
AAAATGGACCATTCCGATAAATAATAAA
Found at i:3263939 original size:25 final size:26
Alignment explanation
Indices: 3263898--3263970 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 26
3263888 AAAAAGTTTC
*
3263898 AAATAAACAATATATAAAAAAACTTA
1 AAATAAATAATATATAAAAAAACTTA
* * **
3263924 AAATGAATAATA-ATAAAACAGTTTA
1 AAATAAATAATATATAAAAAAACTTA
*
3263949 AAATAAATAATATATATAAAAA
1 AAATAAATAATATATAAAAAAA
3263971 TAACATATAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
25 21 0.57
26 16 0.43
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (26 bp):
AAATAAATAATATATAAAAAAACTTA
Found at i:3264055 original size:26 final size:24
Alignment explanation
Indices: 3263988--3264101 Score: 103
Period size: 26 Copynumber: 4.8 Consensus size: 24
3263978 TAAAACATTT
* *
3263988 TTTAAA-ACAATAATGTATA-AAAA
1 TTTAAATA-AATAATATATATAAAG
*
3264011 TTTAAA-AGATAATATATATAATAG
1 TTTAAATAAATAATATATATAA-AG
3264035 TTTAAAATAAATAATATATAT-AA-
1 TTT-AAATAAATAATATATATAAAG
* *
3264058 TTTAAATAAATAATATGTAAAACAG
1 TTTAAATAAATAATATATATAA-AG
3264083 TTTGAAATAAATAATATAT
1 TTT-AAATAAATAATATAT
3264102 GAAAGAAACT
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
22 24 0.32
23 13 0.17
24 6 0.08
25 7 0.09
26 26 0.34
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (24 bp):
TTTAAATAAATAATATATATAAAG
Found at i:3264085 original size:48 final size:47
Alignment explanation
Indices: 3263929--3264101 Score: 164
Period size: 48 Copynumber: 3.8 Consensus size: 47
3263919 ACTTAAAATG
3263929 AATAATA-ATAAAACAGTTTAAAATAAAT-A-ATATAT-A--T-AAA
1 AATAATATATAAAACAGTTTAAAATAAATAATATATATAATTTAAAA
* * * * *
3263969 AATAACATATAAAACATTTTTTAAAA-CAATAATGTATAAAAATTTAAAA
1 AATAATATATAAAACA--GTTTAAAATAAATAATATAT-ATAATTTAAAA
* * *
3264018 GATAATATATATAATAGTTTAAAATAAATAATATATATAATTTAAATA
1 AATAATATATAAAACAGTTTAAAATAAATAATATATATAATTTAAA-A
* *
3264066 AATAATATGTAAAACAGTTTGAAATAAATAATATAT
1 AATAATATATAAAACAGTTTAAAATAAATAATATAT
3264102 GAAAGAAACT
Statistics
Matches: 103, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
40 6 0.06
41 8 0.08
42 3 0.03
43 8 0.08
44 3 0.03
45 1 0.01
46 1 0.01
47 16 0.16
48 42 0.41
49 15 0.15
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (47 bp):
AATAATATATAAAACAGTTTAAAATAAATAATATATATAATTTAAAA
Found at i:3269422 original size:41 final size:39
Alignment explanation
Indices: 3269294--3269433 Score: 115
Period size: 40 Copynumber: 3.6 Consensus size: 39
3269284 ACACACTAGT
* * *
3269294 TTGATACCCAGTACCTCATCGGA-TAATTCGAAGTAATAA
1 TTGACACCCAGTGCCTCATCGAATTAA-TCGAAGTAATAA
* * ** * *
3269333 GTTGACACTCAGTGTCTCATCGGCTAAATTGAAGT-A-AA
1 -TTGACACCCAGTGCCTCATCGAATTAATCGAAGTAATAA
*
3269371 TTGGCACCCAGTGCCTCATCGAATTAATCCGAAGTAATAGA
1 TTGACACCCAGTGCCTCATCGAATTAAT-CGAAGTAATA-A
* *
3269412 TTGACACCCAGTGTCGCATCGA
1 TTGACACCCAGTGCCTCATCGA
3269434 CTCGAAGACG
Statistics
Matches: 78, Mismatches: 17, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
37 22 0.28
38 7 0.09
39 2 0.03
40 25 0.32
41 22 0.28
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (39 bp):
TTGACACCCAGTGCCTCATCGAATTAATCGAAGTAATAA
Found at i:3269871 original size:15 final size:15
Alignment explanation
Indices: 3269851--3269879 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3269841 TTCTTTCTCC
3269851 TTTTCTTTCTTTTTT
1 TTTTCTTTCTTTTTT
3269866 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
3269880 CCCTTCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTCTTTCTTTTTT
Found at i:3300406 original size:42 final size:43
Alignment explanation
Indices: 3300354--3300446 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 43
3300344 GCTTTGGAAG
3300354 AAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTT-GTTCA
1 AAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAGTTCA
* * * * *
3300396 AAAACGCCGCTAACAGTAGTGTTCTTTAGTGGCGCTTATTTCA
1 AAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAGTTCA
*
3300439 CAAACGCC
1 AAAACGCC
3300447 ACTATTTGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 33 0.75
43 11 0.25
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (43 bp):
AAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAGTTCA
Found at i:3300906 original size:21 final size:21
Alignment explanation
Indices: 3300882--3300950 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
3300872 ACTTCTATCG
*
3300882 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
3300903 CTGCTTCTCTTGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
3300924 CTGCTTCTCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
3300945 CTGCTT
1 CTGCTT
3300951 TAAGTTGTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.01, C:0.41, G:0.20, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:3306436 original size:7 final size:7
Alignment explanation
Indices: 3306426--3306471 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
3306416 TGATATATTT
3306426 TTATGTA
1 TTATGTA
3306433 TTATGTAA
1 TTATGT-A
3306441 GTTATGTAA
1 -TTATGT-A
3306450 GTTATGTA
1 -TTATGTA
3306458 TTATGTA
1 TTATGTA
3306465 TTATGTA
1 TTATGTA
3306472 AGTACTGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 20 0.54
8 2 0.05
9 15 0.41
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (7 bp):
TTATGTA
Found at i:3306447 original size:9 final size:9
Alignment explanation
Indices: 3306433--3307395 Score: 616
Period size: 9 Copynumber: 107.7 Consensus size: 9
3306423 TTTTTATGTA
3306433 TTATGTAAG
1 TTATGTAAG
3306442 TTATGTAAG
1 TTATGTAAG
3306451 TTATGT-A-
1 TTATGTAAG
3306458 TTATGT-A-
1 TTATGTAAG
3306465 TTATGTAAG
1 TTATGTAAG
3306474 -TACTGTAAG
1 TTA-TGTAAG
*
3306483 TAATGTAAG
1 TTATGTAAG
3306492 TTATGTAAG
1 TTATGTAAG
* *
3306501 TTATTTAAT
1 TTATGTAAG
*
3306510 TTATGCAAG
1 TTATGTAAG
3306519 TTTATGTAAG
1 -TTATGTAAG
3306529 TTATGTAAG
1 TTATGTAAG
*
3306538 TTAAT-TAAT
1 TT-ATGTAAG
*
3306547 TTATGCAAG
1 TTATGTAAG
3306556 TTTATGTAAG
1 -TTATGTAAG
3306566 TTATGTAAG
1 TTATGTAAG
*
3306575 TTACT-TAAT
1 TTA-TGTAAG
3306584 TTATGTAAG
1 TTATGTAAG
3306593 TTATGTAAG
1 TTATGTAAG
* *
3306602 TTATTTAAT
1 TTATGTAAG
3306611 TTATGTAAG
1 TTATGTAAG
3306620 TTATGTAAG
1 TTATGTAAG
* *
3306629 TTATTTAAT
1 TTATGTAAG
*
3306638 TTATGTAGG
1 TTATGTAAG
3306647 TTATGTAAG
1 TTATGTAAG
*
3306656 TTACT-TAAT
1 TTA-TGTAAG
3306665 TTATGTAAG
1 TTATGTAAG
3306674 TTATGTAAG
1 TTATGTAAG
* *
3306683 TTATTTAAT
1 TTATGTAAG
*
3306692 TTATGTAGG
1 TTATGTAAG
3306701 TTATGTAAG
1 TTATGTAAG
* *
3306710 TTATTTAAT
1 TTATGTAAG
*
3306719 TTATGCAAG
1 TTATGTAAG
3306728 TTTATGTAAG
1 -TTATGTAAG
*
3306738 TTACT-TAAT
1 TTA-TGTAAG
3306747 TTATGTAAG
1 TTATGTAAG
3306756 TTATGTAAG
1 TTATGTAAG
* *
3306765 TTATTTAAT
1 TTATGTAAG
*
3306774 TTATGTAGG
1 TTATGTAAG
3306783 TTATGTAAG
1 TTATGTAAG
*
3306792 TTACT-TAAT
1 TTA-TGTAAG
3306801 TTATGTAAG
1 TTATGTAAG
3306810 TTATGTAAG
1 TTATGTAAG
* *
3306819 TTATTTAAT
1 TTATGTAAG
*
3306828 TTACT-CAAG
1 TTA-TGTAAG
3306837 TTTATGTAAG
1 -TTATGTAAG
3306847 TTATGTAAG
1 TTATGTAAG
*
3306856 TTACT-TAAT
1 TTA-TGTAAG
3306865 TTATGTAAG
1 TTATGTAAG
3306874 TTATGTAAG
1 TTATGTAAG
* *
3306883 TTATTTAAT
1 TTATGTAAG
3306892 TTATGTAAG
1 TTATGTAAG
3306901 TTATGTAAG
1 TTATGTAAG
* *
3306910 TTATTTAAT
1 TTATGTAAG
*
3306919 TTATGTAGG
1 TTATGTAAG
3306928 TTATGTAAG
1 TTATGTAAG
*
3306937 TTACT-TAAT
1 TTA-TGTAAG
3306946 TTATGTAAG
1 TTATGTAAG
*
3306955 TTAT-TATG
1 TTATGTAAG
*
3306963 TTAT-TATG
1 TTATGTAAG
*
3306971 TTATTATATAAG
1 ---TTATGTAAG
*
3306983 TTATTTAAG
1 TTATGTAAG
*
3306992 TTAT-TATG
1 TTATGTAAG
3307000 TTAT-TATA-
1 TTATGTA-AG
* *
3307008 TAAAGT-A-
1 TTATGTAAG
*
3307015 TTATGTAAT
1 TTATGTAAG
*
3307024 TTAT-TATG
1 TTATGTAAG
3307032 TTAT-T-A-
1 TTATGTAAG
3307038 -TATGTAAG
1 TTATGTAAG
3307046 TTATGTAAG
1 TTATGTAAG
*
3307055 TTA--TAAA
1 TTATGTAAG
3307062 TTATGTAAG
1 TTATGTAAG
*
3307071 TTATGCAAG
1 TTATGTAAG
*
3307080 CTTATATACAAG
1 -TTATGT--AAG
3307092 TTATGT-A-
1 TTATGTAAG
*
3307099 TTATAACATAAAG
1 TTAT---GT-AAG
*
3307112 TATTATGTAAT
1 --TTATGTAAG
*
3307123 TTATGT-TG
1 TTATGTAAG
3307131 TTAT-T-A-
1 TTATGTAAG
*
3307137 -TATATAAG
1 TTATGTAAG
3307145 TTATGT-AG
1 TTATGTAAG
3307153 ATTATGTAAG
1 -TTATGTAAG
3307163 TTATGTAAG
1 TTATGTAAG
*
3307172 TTAAT-TAAT
1 TT-ATGTAAG
*
3307181 TTATGCAAG
1 TTATGTAAG
3307190 TTTATGTAAG
1 -TTATGTAAG
3307200 TTATGTAAG
1 TTATGTAAG
* *
3307209 TTATTTAAT
1 TTATGTAAG
*
3307218 TTATGTGAG
1 TTATGTAAG
* *
3307227 TTTCTATATATG
1 --T-TATGTAAG
*
3307239 TT-TATATA-
1 TTATGTA-AG
3307247 TTATGTAAG
1 TTATGTAAG
*
3307256 TTATGTACG
1 TTATGTAAG
3307265 TGTA--TAAG
1 T-TATGTAAG
3307273 TTATGT-A-
1 TTATGTAAG
*
3307280 TTAAGTAAG
1 TTATGTAAG
*
3307289 CTATGTAAG
1 TTATGTAAG
*
3307298 TTGTGT-A-
1 TTATGTAAG
3307305 TTATGTAAG
1 TTATGTAAG
*
3307314 TTGTGTCAA-
1 TTATGT-AAG
* *
3307323 ATATTTAAG
1 TTATGTAAG
3307332 TTATGTAAG
1 TTATGTAAG
*
3307341 TTTTTTGT-A-
1 --TTATGTAAG
3307350 TTATGTAAG
1 TTATGTAAG
*
3307359 TTATGTTATG
1 TTATG-TAAG
3307369 TTATTACGTAAG
1 TTA-T--GTAAG
*
3307381 TTATGCAAG
1 TTATGTAAG
3307390 TTATGT
1 TTATGT
3307396 TTATAACGAG
Statistics
Matches: 747, Mismatches: 126, Indels: 162
0.72 0.12 0.16
Matches are distributed among these distances:
5 6 0.01
6 2 0.00
7 48 0.06
8 69 0.09
9 510 0.68
10 69 0.09
11 19 0.03
12 19 0.03
13 1 0.00
15 4 0.01
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:3306967 original size:8 final size:8
Alignment explanation
Indices: 3306954--3307006 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 8
3306944 ATTTATGTAA
3306954 GTTATTAT
1 GTTATTAT
3306962 GTTATTAT
1 GTTATTAT
3306970 GTTATTATAT
1 GTTA-T-TAT
*
3306980 AAGTTATTTAA
1 --GTTA-TTAT
3306991 GTTATTAT
1 GTTATTAT
3306999 GTTATTAT
1 GTTATTAT
3307007 ATAAAGTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 23 0.59
9 5 0.13
10 3 0.08
11 2 0.05
12 6 0.15
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.58
Consensus pattern (8 bp):
GTTATTAT
Found at i:3306971 original size:20 final size:20
Alignment explanation
Indices: 3306946--3307058 Score: 76
Period size: 20 Copynumber: 5.7 Consensus size: 20
3306936 GTTACTTAAT
3306946 TTATGTAAGTTATTATGTTA
1 TTATGTAAGTTATTATGTTA
* *
3306966 TTATGTTA-TTATATAAGTTA
1 TTATGTAAGTTAT-TATGTTA
3306986 -T-T-TAAGTTATTATGTTA
1 TTATGTAAGTTATTATGTTA
* *
3307003 TTATATAAAG-TATTATGTAA
1 TTATGT-AAGTTATTATGTTA
* *
3307023 TTTAT-TATGTTATTATATGTAA
1 -TTATGTAAGTTA-T-TATGTTA
3307045 GTTATGTAAGTTAT
1 -TTATGTAAGTTAT
3307059 AAATTATGTA
Statistics
Matches: 74, Mismatches: 8, Indels: 20
0.73 0.08 0.20
Matches are distributed among these distances:
17 8 0.11
18 6 0.08
19 8 0.11
20 26 0.35
21 8 0.11
22 12 0.16
23 6 0.08
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (20 bp):
TTATGTAAGTTATTATGTTA
Found at i:3307044 original size:22 final size:23
Alignment explanation
Indices: 3306962--3307084 Score: 68
Period size: 20 Copynumber: 5.6 Consensus size: 23
3306952 AAGTTATTAT
*
3306962 GTTAT-TATGTTATTATA--TAA
1 GTTATGTAAGTTATTATATGTAA
* *
3306982 GTTATTTAAGTTA-T-TATGTTA
1 GTTATGTAAGTTATTATATGTAA
*
3307003 -TTATATAAAG-TA-T-TATGTAA
1 GTTATGT-AAGTTATTATATGTAA
* *
3307023 TTTAT-TATGTTATTATATGTAA
1 GTTATGTAAGTTATTATATGTAA
*
3307045 GTTATGTAAGTTATAAATTATGTAA
1 GTTATGTAAGTTAT-TA-TATGTAA
*
3307070 GTTATGCAAGCTTAT
1 GTTATGTAAG-TTAT
3307085 ATACAAGTTA
Statistics
Matches: 82, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
19 4 0.05
20 23 0.28
21 16 0.20
22 11 0.13
23 7 0.09
24 1 0.01
25 16 0.20
26 4 0.05
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (23 bp):
GTTATGTAAGTTATTATATGTAA
Done.