Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 281 of 332
Found at i:93919790 original size:29 final size:29
Alignment explanation
Indices: 93919758--93919814 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
93919748 TTTTAATCCT
*
93919758 TTTTAAATTTTTTATATATAATTTATTTA
1 TTTTAAATATTTTATATATAATTTATTTA
*
93919787 TTTTAAATATTTTATATATTATTTATTT
1 TTTTAAATATTTTATATATAATTTATTT
93919815 TTACTATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
TTTTAAATATTTTATATATAATTTATTTA
Found at i:93919861 original size:3 final size:3
Alignment explanation
Indices: 93919846--93919941 Score: 58
Period size: 3 Copynumber: 31.0 Consensus size: 3
93919836 TGTAAAAAAA
*
93919846 TAT TA- TAT ATAT TAT TTT TAT TA- TAT ATAT TAT TCAT TA- TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT -TAT TAT T-AT TAT TAT TAT
* *
93919891 T-T TTT TAT T-T TTT TAT ATATT TAT TATT TAT TATT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT -TA-T TAT TA-T TAT TA-T TAT TA-T TAT
93919936 TAT TAT
1 TAT TAT
93919942 GTATAATTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 26
0.72 0.04 0.25
Matches are distributed among these distances:
2 10 0.13
3 43 0.57
4 22 0.29
5 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:93919888 original size:39 final size:36
Alignment explanation
Indices: 93919845--93919946 Score: 120
Period size: 35 Copynumber: 2.8 Consensus size: 36
93919835 ATGTAAAAAA
93919845 ATATTATATATATTATTTTTATTATATATATTATTCATT
1 ATATTAT-T-TATTATTTTTATTATATATATTATT-ATT
*
93919884 ATATTATTTTTTTATTTTT-TTATATAT-TTATTATT
1 ATATTA-TTTATTATTTTTATTATATATATTATTATT
*
93919919 -TATTATTTATTATTTATTATTATGTATA
1 ATATTATTTATTATTT-TTATTATATATA
93919947 ATTTTAAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
33 9 0.16
34 7 0.12
35 10 0.18
36 5 0.09
37 8 0.14
38 9 0.16
39 7 0.12
40 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (36 bp):
ATATTATTTATTATTTTTATTATATATATTATTATT
Found at i:93919901 original size:7 final size:7
Alignment explanation
Indices: 93919857--93919939 Score: 79
Period size: 7 Copynumber: 12.1 Consensus size: 7
93919847 ATTATATATA
93919857 TTATT-T
1 TTATTAT
93919863 TTATTAT
1 TTATTAT
93919870 ATATATTAT
1 -T-TATTAT
*
93919879 TCATTAT
1 TTATTAT
93919886 ATTATT-T
1 -TTATTAT
93919893 TT-TTA-
1 TTATTAT
93919898 TT-TT-T
1 TTATTAT
93919903 TTATATAT
1 TTAT-TAT
93919911 TTATTAT
1 TTATTAT
93919918 TTATTAT
1 TTATTAT
93919925 TTATTAT
1 TTATTAT
93919932 TTATTAT
1 TTATTAT
93919939 T
1 T
93919940 ATGTATAATT
Statistics
Matches: 66, Mismatches: 2, Indels: 17
0.78 0.02 0.20
Matches are distributed among these distances:
5 8 0.12
6 8 0.12
7 33 0.50
8 11 0.17
9 6 0.09
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATTAT
Found at i:93919921 original size:4 final size:4
Alignment explanation
Indices: 93919882--93919936 Score: 53
Period size: 4 Copynumber: 14.2 Consensus size: 4
93919872 ATATTATTCA
* * *
93919882 TTAT ATTAT TTTT TTAT TTTT TTAT ATAT TTA- TTAT TTA- TTAT TTA-
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
93919928 TTAT TTAT T
1 TTAT TTAT T
93919937 ATTATGTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
3 9 0.22
4 28 0.68
5 4 0.10
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:93919974 original size:21 final size:21
Alignment explanation
Indices: 93919950--93920011 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
93919940 ATGTATAATT
*
93919950 TTAAAAATTTATAAATTATTA
1 TTAAAAATTTATATATTATTA
* *
93919971 TTAAATAA-TCATATATCATTA
1 TTAAA-AATTTATATATTATTA
*
93919992 TTAAATATTTAGTATATTAT
1 TTAAAAATTTA-TATATTAT
93920012 ATAATATTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.03
21 22 0.69
22 9 0.28
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAAAAATTTATATATTATTA
Found at i:93920287 original size:19 final size:19
Alignment explanation
Indices: 93920250--93920288 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
93920240 TAATTTGTTG
*
93920250 ATTTATTTTCGTATTTTTT
1 ATTTATTTTAGTATTTTTT
93920269 ATTTA-TTTAGTATTGTTTT
1 ATTTATTTTAGTATT-TTTT
93920288 A
1 A
93920289 GTGTGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.69
Consensus pattern (19 bp):
ATTTATTTTAGTATTTTTT
Found at i:93921373 original size:17 final size:16
Alignment explanation
Indices: 93921343--93921376 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
93921333 AGAAATACAA
93921343 ATTAACAAAATTATAC
1 ATTAACAAAATTATAC
*
93921359 ATTATACAAACTTATAC
1 ATTA-ACAAAATTATAC
93921376 A
1 A
93921377 AACATAGCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTAACAAAATTATAC
Found at i:93922176 original size:27 final size:28
Alignment explanation
Indices: 93922131--93922224 Score: 126
Period size: 30 Copynumber: 3.5 Consensus size: 28
93922121 AACCATCAAC
*
93922131 TGAAAAAATAAAA-T-T-CAGAACAAAT
1 TGAAAAAACAAAATTATCCAGAACAAAT
93922156 TGAAAAAA-AAAATTATCCAGAACAAAT
1 TGAAAAAACAAAATTATCCAGAACAAAT
93922183 TGAAAAAAAACAAAATTATCCAGAACAAAT
1 TG--AAAAAACAAAATTATCCAGAACAAAT
93922213 TGAAAAAA-AAAA
1 TGAAAAAACAAAA
93922225 CAAAATTAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
24 4 0.06
25 9 0.14
26 1 0.02
27 16 0.25
28 6 0.10
29 6 0.10
30 21 0.33
ACGTcount: A:0.66, C:0.10, G:0.07, T:0.17
Consensus pattern (28 bp):
TGAAAAAACAAAATTATCCAGAACAAAT
Found at i:93922226 original size:32 final size:30
Alignment explanation
Indices: 93922146--93922232 Score: 135
Period size: 30 Copynumber: 2.9 Consensus size: 30
93922136 AAATAAAATT
93922146 CAGAACAAATTG--AAAAAA-AAAATTATC
1 CAGAACAAATTGAAAAAAAACAAAATTATC
93922173 CAGAACAAATTGAAAAAAAACAAAATTATC
1 CAGAACAAATTGAAAAAAAACAAAATTATC
93922203 CAGAACAAATTGAAAAAAAAAACAAAATTA
1 CAGAACAAATTG--AAAAAAAACAAAATTA
93922233 AGGAAAACAT
Statistics
Matches: 55, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
27 12 0.22
29 6 0.11
30 21 0.38
32 16 0.29
ACGTcount: A:0.66, C:0.11, G:0.07, T:0.16
Consensus pattern (30 bp):
CAGAACAAATTGAAAAAAAACAAAATTATC
Found at i:93923239 original size:16 final size:17
Alignment explanation
Indices: 93923218--93923258 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
93923208 TTACTTTTAG
93923218 ATAAAATCAAAATA-AA
1 ATAAAATCAAAATATAA
* *
93923234 ATAAAAACAAAATATAC
1 ATAAAATCAAAATATAA
93923251 ATAAAATC
1 ATAAAATC
93923259 CACTACTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (17 bp):
ATAAAATCAAAATATAA
Found at i:93923334 original size:15 final size:15
Alignment explanation
Indices: 93923316--93923348 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
93923306 TCTATCTTCT
*
93923316 TTTTTTTAAAAGAAA
1 TTTTTCTAAAAGAAA
93923331 TTTTTCTAAAAGAAA
1 TTTTTCTAAAAGAAA
93923346 TTT
1 TTT
93923349 GGAGGGTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (15 bp):
TTTTTCTAAAAGAAA
Found at i:93923473 original size:23 final size:24
Alignment explanation
Indices: 93923443--93923505 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
93923433 TTATATTTAA
93923443 TAATTAAAATAATTAATTATA-AT
1 TAATTAAAATAATTAATTATATAT
*
93923466 TAATTAAAATAATTAA-AATATAT
1 TAATTAAAATAATTAATTATATAT
*
93923489 T-ATTTAAA-AATTAATTA
1 TAATTAAAATAATTAATTA
93923506 AAAATCAGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 6 0.17
22 10 0.29
23 19 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATTAAAATAATTAATTATATAT
Found at i:93923508 original size:10 final size:10
Alignment explanation
Indices: 93923453--93923508 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 10
93923443 TAATTAAAAT
*
93923453 AATTAATTAT
1 AATTAATTAA
93923463 AATTAATTAA
1 AATTAATTAA
93923473 AA-TAATTAA
1 AATTAATTAA
93923482 AATATATTATTTAAA
1 AAT-TA--A-TT-AA
93923497 AATTAATTAA
1 AATTAATTAA
93923507 AA
1 AA
93923509 ATCAGACACG
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
9 9 0.23
10 15 0.38
11 4 0.10
12 1 0.03
13 1 0.03
14 4 0.10
15 5 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATTAATTAA
Found at i:93930103 original size:20 final size:19
Alignment explanation
Indices: 93930065--93930106 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
93930055 TTATTTTTAC
93930065 TATAAATATTATGTATATA
1 TATAAATATTATGTATATA
93930084 TATAAATGATTTAT-TATATA
1 TATAAAT-A-TTATGTATATA
93930104 TAT
1 TAT
93930107 TATTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 10 0.48
21 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
TATAAATATTATGTATATA
Found at i:93930184 original size:20 final size:22
Alignment explanation
Indices: 93930169--93930222 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
93930159 ATATTTTTTA
93930169 ATATATTATATCATTTTACTAT
1 ATATATTATATCATTTTACTAT
* *
93930191 ATATATTAT-TCATTATATTAT
1 ATATATTATATCATTTTACTAT
* *
93930212 TTTTATTATAT
1 ATATATTATAT
93930223 TTTATATTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATATTATATCATTTTACTAT
Found at i:93930219 original size:14 final size:14
Alignment explanation
Indices: 93930172--93930223 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
93930162 TTTTTTAATA
*
93930172 TATTATATCA-TTT
1 TATTATATTATTTT
*
93930185 TACTATATATATTATT
1 TATTATAT-TATT-TT
*
93930201 CATTATATTATTTT
1 TATTATATTATTTT
93930215 TATTATATT
1 TATTATATT
93930224 TTATATTACT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.23
14 11 0.35
15 5 0.16
16 8 0.26
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATATTATTTT
Found at i:93930245 original size:33 final size:35
Alignment explanation
Indices: 93930192--93930261 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 35
93930182 TTTTACTATA
* *
93930192 TATATTATTCATTATATTATTTTTAT-TAT-ATTT
1 TATATTATTCAATATATTATTATTATGTATAATTT
93930225 TATATTACTTCAATAT-TTATTATTATGTATAATTT
1 TATATTA-TTCAATATATTATTATTATGTATAATTT
93930260 TA
1 TA
93930262 AAAATTTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 16 0.50
34 10 0.31
35 6 0.19
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (35 bp):
TATATTATTCAATATATTATTATTATGTATAATTT
Found at i:93934482 original size:29 final size:27
Alignment explanation
Indices: 93934450--93934523 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
93934440 CTTTAATTTG
* *
93934450 TATACCATATATATATTAGTGGTGTTATA
1 TATA-CATATATATATTAGAGGTGGTA-A
* *
93934479 TATA-ATATATAAATAATGGAGGTGGTAA
1 TATACATATAT--ATATTAGAGGTGGTAA
93934507 TATACATATATATATTA
1 TATACATATATATATTA
93934524 TATATAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
27 10 0.28
28 5 0.14
29 21 0.58
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.41
Consensus pattern (27 bp):
TATACATATATATATTAGAGGTGGTAA
Found at i:93934628 original size:28 final size:29
Alignment explanation
Indices: 93934581--93934650 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
93934571 TGATTATTCA
*
93934581 TATATTATATATATGCATGG-CTTTG-TTT
1 TATA-TATATATATGCATGGACTTTGATGT
*
93934609 TATATAATATATAT-CAATGGATTTTGATGT
1 TATAT-ATATATATGC-ATGGACTTTGATGT
93934639 TATATATATATA
1 TATATATATATA
93934651 ATACAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 2 0.06
28 16 0.44
29 11 0.31
30 7 0.19
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.50
Consensus pattern (29 bp):
TATATATATATATGCATGGACTTTGATGT
Found at i:93934725 original size:77 final size:76
Alignment explanation
Indices: 93934580--93934728 Score: 178
Period size: 77 Copynumber: 1.9 Consensus size: 76
93934570 GTGATTATTC
* * * *
93934580 ATATATTATATATATGCATGGCTTTGTTTTATATAATATATATCAATGGATTTTGATGTTATATA
1 ATATATTATATATATGCATGGCTTTATTGTATACAATATATATCAATGGATTATGATGTTATATA
93934645 TATATAATACA
66 TATATAATACA
* * *
93934656 ATATATATATATATATGCATGG-TTCTATTGTATACAATATATAAT-TATGGA-TATGGTTTTAT
1 ATATAT-TATATATATGCATGGCTT-TATTGTATACAATATAT-ATCAATGGATTATGATGTTAT
93934718 ATAATATATAA
63 AT-ATATATAA
93934729 GTTTATGAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
76 18 0.29
77 42 0.68
78 2 0.03
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (76 bp):
ATATATTATATATATGCATGGCTTTATTGTATACAATATATATCAATGGATTATGATGTTATATA
TATATAATACA
Found at i:93935055 original size:17 final size:18
Alignment explanation
Indices: 93935035--93935085 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
93935025 TTGTGTATTG
*
93935035 TGTTATATT-GTGACCTA
1 TGTTATATTGGTGAACTA
*
93935052 TGTTA-ATTGGTGAATTA
1 TGTTATATTGGTGAACTA
93935069 TGTTAT-TATGGTGAACT
1 TGTTATAT-TGGTGAACT
93935086 GTATTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 3 0.11
17 17 0.61
18 8 0.29
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (18 bp):
TGTTATATTGGTGAACTA
Found at i:93941322 original size:42 final size:42
Alignment explanation
Indices: 93941275--93941361 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
93941265 CACCTTTTGT
* *
93941275 TACAAGGTAATGCCATTCGGGCTAAAGAATGCAGGGGCAACA
1 TACAAGGTAATGCCATTCAGGCTAAAAAATGCAGGGGCAACA
*
93941317 TACAAGGTAATGCCCTTCAGGCTAAAAAATGCAGGGGCAACA
1 TACAAGGTAATGCCATTCAGGCTAAAAAATGCAGGGGCAACA
93941359 TAC
1 TAC
93941362 CAAAGTGCTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (42 bp):
TACAAGGTAATGCCATTCAGGCTAAAAAATGCAGGGGCAACA
Found at i:93945065 original size:44 final size:44
Alignment explanation
Indices: 93944982--93946277 Score: 1373
Period size: 44 Copynumber: 29.5 Consensus size: 44
93944972 TCACCAATAG
* * * * *
93944982 CAGATTTGACGTCTCTGTATTGTCAGAGAACAGACCGAAAATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
93945026 CAAATTTGGCGTCTCTGTATTGACAAAGAGCAGATCGAAAATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * ** **
93945070 AAAATTTAGCGTCTTTGTATTGACAGAGAATAGATCGAACTTAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * *
93945114 CAAATTTGGCATCTTTGTATTGAAAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
93945158 CAGATTTGGCGTCTTTGTATTGATAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* *
93945202 CAGATTTGGTGTCTCTGTATTGACAGGGAGCAGATCGAAGATGAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGAT-AA
* * *
93945247 -AAATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCGAAGATAGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATA-A
* * * ** * * *
93945291 C-GATTTGACATCTCTATATTGTTAGAGAACAGATTGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * *
93945334 CAGATTTGGCGTCTCT-TATTGTCAGAGAGTAGATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * *
93945377 CAGATTTGACATTTCTGTATTGGCAAAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * *
93945421 CAGATTTGGTGTTTCTGTATTGGCAGAAAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * * *
93945465 CAGATTTGACATTTCTGTATTGATAGAGAGCAGATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* *
93945509 CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATC-AGAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGA-AGATAA
*
93945553 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
*
93945597 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * **
93945641 CAGATTTGGCGTCTCTATATTGACAGAGAGCAAATCGAATATGG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * * *
93945685 TAGATTTGGCATTTCTGTATTGATAGAGAGCGGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * * *
93945729 TAGATTTAGTGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGC
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATA-A
* * ** * *
93945774 CA-ATTTGACATCTCTGTATTTTCAGAGAGCAGATCGAATATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
93945817 TAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * * *
93945861 TAGATTTGGCATTTCTGTATTGGCAGAGAGTAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* *
93945905 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * *
93945949 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATTGGAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
93945993 CAGATTTGGTGTCTCTATATTGACAGAAAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
93946037 CAGATTTGTCATCTCTGTATTGACAAAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
93946081 CAGATTTGTCGTCT-TGTTATTGACAAAGAGTAGATCGAAGATAA
1 CAGATTTGGCGTCTCTG-TATTGACAGAGAGCAGATCGAAGATAA
* * * * * *
93946125 TAGATTTGGCGTCTCTGTATTAATAGAGGGCAGATTGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * *
93946169 TATATTTGGTGTCTCTGTATTGACAGAGAGAAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
93946213 CAGATTTGGTGTCTCTGTATTGACAAAG-GACAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAG-CAGATCGAAGATAA
* * *
93946257 CAGATTCGGCTTCTCCGTATT
1 CAGATTTGGCGTCTCTGTATT
93946278 AGGCAAGGAG
Statistics
Matches: 1065, Mismatches: 175, Indels: 24
0.84 0.14 0.02
Matches are distributed among these distances:
43 42 0.04
44 1018 0.96
45 5 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
Found at i:93947781 original size:20 final size:19
Alignment explanation
Indices: 93947743--93947785 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
93947733 TTATTTTTAC
93947743 TATAAATATTATGTATATA
1 TATAAATATTATGTATATA
93947762 TATAAATGATTTAT-TATATA
1 TATAAAT-A-TTATGTATATA
93947782 TATA
1 TATA
93947786 TTATTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.32
20 11 0.50
21 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
TATAAATATTATGTATATA
Found at i:93947864 original size:20 final size:22
Alignment explanation
Indices: 93947835--93947902 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 22
93947825 TATGTTTTAT
93947835 TTATAT-ATTTTA-TA-ATATA
1 TTATATCATTTTACTATATATA
93947854 TTATATCATTTTACTATATATA
1 TTATATCATTTTACTATATATA
* * * *
93947876 TTAT-TCATTATATTATTTTTA
1 TTATATCATTTTACTATATATA
93947897 TTATAT
1 TTATAT
93947903 TTTATATTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 6 0.15
20 6 0.15
21 19 0.46
22 10 0.24
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATATCATTTTACTATATATA
Found at i:93947925 original size:33 final size:35
Alignment explanation
Indices: 93947872--93947941 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 35
93947862 TTTTACTATA
* *
93947872 TATATTATTCATTATATTATTTTTAT-TAT-ATTT
1 TATATTATTCAATATATTATTATTATGTATAATTT
93947905 TATATTACTTCAATAT-TTATTATTATGTATAATTT
1 TATATTA-TTCAATATATTATTATTATGTATAATTT
93947940 TA
1 TA
93947942 AAAATTTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 16 0.50
34 10 0.31
35 6 0.19
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (35 bp):
TATATTATTCAATATATTATTATTATGTATAATTT
Found at i:93952154 original size:29 final size:29
Alignment explanation
Indices: 93952122--93952195 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
93952112 ACATGAGCTG
*
93952122 TATACCATATATATATTAGTGGTGTT-AT-A
1 TATA-CATATATATATTAG-GGAGTTGATAA
* * *
93952151 TATA-ATATATAAATAAGGGAGTTGGTAA
1 TATACATATATATATTAGGGAGTTGATAA
93952179 TATACATATATATATTA
1 TATACATATATATATTA
93952196 TATATATAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
26 5 0.14
27 12 0.33
28 5 0.14
29 14 0.39
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.41
Consensus pattern (29 bp):
TATACATATATATATTAGGGAGTTGATAA
Found at i:93952697 original size:17 final size:18
Alignment explanation
Indices: 93952677--93952727 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
93952667 TTGTGTATTG
*
93952677 TGTTATATT-GTGACCTA
1 TGTTATATTGGTGAACTA
*
93952694 TGTTA-ATTGGTGAATTA
1 TGTTATATTGGTGAACTA
93952711 TGTTAT-TATGGTGAACT
1 TGTTATAT-TGGTGAACT
93952728 GTATTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 3 0.11
17 17 0.61
18 8 0.29
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (18 bp):
TGTTATATTGGTGAACTA
Found at i:93956813 original size:14 final size:15
Alignment explanation
Indices: 93956794--93956823 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
93956784 GTTTATTATA
93956794 TGTG-AAGTATCATG
1 TGTGAAAGTATCATG
93956808 TGTGAAAGTATCATG
1 TGTGAAAGTATCATG
93956823 T
1 T
93956824 CTTAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.37
Consensus pattern (15 bp):
TGTGAAAGTATCATG
Found at i:93964376 original size:28 final size:32
Alignment explanation
Indices: 93964321--93964399 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 32
93964311 TGTACGTGGG
* *
93964321 TGATTATATATATATTATATATGCATGG-CTT
1 TGATTATATATATAATATATATGAATGGACTT
* *
93964352 T-ATT-T-TATATAATATATATTAATGGATTT
1 TGATTATATATATAATATATATGAATGGACTT
93964381 TGATTATATATATAATATA
1 TGATTATATATATAATATA
93964400 ATGTATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 17 0.43
29 4 0.10
30 6 0.15
31 2 0.05
32 11 0.28
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.51
Consensus pattern (32 bp):
TGATTATATATATAATATATATGAATGGACTT
Found at i:93966257 original size:21 final size:21
Alignment explanation
Indices: 93966231--93966302 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
93966221 AAATTATGTA
93966231 ATCTGAACTCATTGAGTTGTG
1 ATCTGAACTCATTGAGTTGTG
** *
93966252 ATCTGAGTTCA-TGATATATGTG
1 ATCTGAACTCATTGA-GT-TGTG
*
93966274 ACATCCGAACTCATTGAGTTGTG
1 --ATCTGAACTCATTGAGTTGTG
*
93966297 GTCTGA
1 ATCTGA
93966303 GTTCGTGATA
Statistics
Matches: 37, Mismatches: 9, Indels: 10
0.66 0.16 0.18
Matches are distributed among these distances:
20 3 0.08
21 14 0.38
22 4 0.11
23 4 0.11
24 9 0.24
25 3 0.08
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (21 bp):
ATCTGAACTCATTGAGTTGTG
Found at i:93966287 original size:45 final size:45
Alignment explanation
Indices: 93966235--93966321 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
93966225 TATGTAATCT
93966235 GAACTCATTGAGTTGTGATCTGAGTTCATGATATATGTGACATCC
1 GAACTCATTGAGTTGTGATCTGAGTTCATGATATATGTGACATCC
* *
93966280 GAACTCATTGAGTTGTGGTCTGAGTTCGTGATATATGTGACA
1 GAACTCATTGAGTTGTGATCTGAGTTCATGATATATGTGACA
93966322 CATGTTTTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (45 bp):
GAACTCATTGAGTTGTGATCTGAGTTCATGATATATGTGACATCC
Found at i:93970562 original size:27 final size:27
Alignment explanation
Indices: 93970509--93970564 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
93970499 ATCTCATAGA
*
93970509 GGCATATCAGTCATTTTACTATGTAGG
1 GGCATATCAGTCATTTTACAATGTAGG
*
93970536 GGCATTTCAGTCATTTTATCAAT-TAGG
1 GGCATATCAGTCATTTTA-CAATGTAGG
93970563 GG
1 GG
93970565 GTCTAGGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (27 bp):
GGCATATCAGTCATTTTACAATGTAGG
Found at i:93983965 original size:56 final size:55
Alignment explanation
Indices: 93983842--93983971 Score: 129
Period size: 56 Copynumber: 2.4 Consensus size: 55
93983832 GGGTCATGTG
* * * * *
93983842 AAATTACCGAAATACT-TTTAATTTGTAAAATTACCAAAATACCCCTGATTTACA
1 AAATTACTGAAATACTCTTGAATTTCTAAAATTACAAAAATACCACTGATTTACA
* * * * *
93983896 AAATTA-TAAAAATACTCTTGACTTTCTAAAAATTATAAAAATACCATTGGTTTACA
1 AAATTACT-GAAATACTCTTGAATTTCT-AAAATTACAAAAATACCACTGATTTACA
*
93983952 AAATTACTGAAATACCCTTG
1 AAATTACTGAAATACTCTTG
93983972 GTTTGTAGAT
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
54 13 0.22
55 7 0.12
56 39 0.65
57 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (55 bp):
AAATTACTGAAATACTCTTGAATTTCTAAAATTACAAAAATACCACTGATTTACA
Found at i:93984071 original size:27 final size:27
Alignment explanation
Indices: 93983997--93984093 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 27
93983987 AAAACACCAT
* **
93983997 TGTAGGGTGAAATGACTAAAATACCCC
1 TGTAGGGTAAAATGACTGTAATACCCC
* * * *
93984024 TATTA-GGTAAAAAGACCGTAA-AGCCCT
1 T-GTAGGGTAAAATGACTGTAATA-CCCC
*
93984051 TGTAGGGTAAAGTGACTGTAATACCCC
1 TGTAGGGTAAAATGACTGTAATACCCC
*
93984078 TGTATGGTAAAATGAC
1 TGTAGGGTAAAATGAC
93984094 GAATACGCCC
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
26 3 0.06
27 46 0.88
28 3 0.06
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (27 bp):
TGTAGGGTAAAATGACTGTAATACCCC
Found at i:93984108 original size:25 final size:27
Alignment explanation
Indices: 93983997--93984108 Score: 72
Period size: 27 Copynumber: 4.2 Consensus size: 27
93983987 AAAACACCAT
* * **
93983997 TGTAGGGTGAAATGACTAAAATACCCC
1 TGTATGGTAAAATGACTGTAATACCCC
* * * *
93984024 TAT-TAGGTAAAAAGACCGTAA-AGCCCT
1 TGTAT-GGTAAAATGACTGTAATA-CCCC
* *
93984051 TGTAGGGTAAAGTGACTGTAATACCCC
1 TGTATGGTAAAATGACTGTAATACCCC
93984078 TGTATGGTAAAATGAC-G-AATACGCCC
1 TGTATGGTAAAATGACTGTAATAC-CCC
93984104 T-TATG
1 TGTATG
93984109 TTCCGTATGA
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
25 9 0.14
26 6 0.09
27 48 0.75
28 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (27 bp):
TGTATGGTAAAATGACTGTAATACCCC
Found at i:93984860 original size:16 final size:16
Alignment explanation
Indices: 93984839--93984870 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
93984829 TTCAAATATG
*
93984839 ACATGACATTTTGCAT
1 ACATGACATGTTGCAT
93984855 ACATGACATGTTGCAT
1 ACATGACATGTTGCAT
93984871 GGGTTGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (16 bp):
ACATGACATGTTGCAT
Found at i:93984939 original size:25 final size:24
Alignment explanation
Indices: 93984901--93985007 Score: 135
Period size: 25 Copynumber: 4.4 Consensus size: 24
93984891 AGGAAGTGCT
*
93984901 AAAAGGGCTATGCCCCAGTTTATC
1 AAAAGGGCTTTGCCCCAGTTTATC
* *
93984925 GAAAAGGGCTTTGCCCTAGTTTACC
1 -AAAAGGGCTTTGCCCCAGTTTATC
93984950 AAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTATC
* *
93984975 AAAAGGGATTTGCCCCAG-TTATT
1 AAAAGGGCTTTGCCCCAGTTTATC
93984998 AAAAGAGGCT
1 AAAAG-GGCT
93985008 AGGCCTCCAG
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
23 9 0.12
24 20 0.28
25 43 0.60
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATC
Found at i:93984986 original size:24 final size:25
Alignment explanation
Indices: 93984901--93984994 Score: 136
Period size: 25 Copynumber: 3.8 Consensus size: 25
93984891 AGGAAGTGCT
* *
93984901 AAAAGGGCTATGCCCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
* *
93984926 AAAAGGGCTTTGCCCTAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
93984951 AAAAGGGCTTTGCCCCAGTTTATC-
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
93984975 AAAAGGGATTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
93984995 ATTAAAAGAG
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
24 19 0.31
25 43 0.69
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:93985248 original size:31 final size:31
Alignment explanation
Indices: 93985213--93985384 Score: 240
Period size: 31 Copynumber: 5.5 Consensus size: 31
93985203 CATTTACAGT
93985213 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
* *
93985244 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
93985275 AAAGGCTTCGGCCCAGA-GATATGATTTATGA
1 AAAGGCTTCGGCCCA-ATGATATGATTTATGA
* * * *
93985306 TAAGGCTTCGGCCCAGTGATATGTTTTGTGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
*
93985337 TAAA-GCTTCGGCCCAGTGATATGATTTATGA
1 -AAAGGCTTCGGCCCAATGATATGATTTATGA
*
93985368 AAAGGCTTTGGCCCAAT
1 AAAGGCTTCGGCCCAAT
93985385 AACCGTTAAA
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
30 3 0.02
31 119 0.96
32 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATGATATGATTTATGA
Found at i:93985373 original size:93 final size:93
Alignment explanation
Indices: 93985214--93985382 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 93
93985204 ATTTACAGTA
*
93985214 AAGGCTTCGGCCCAATGATATGATTTATGAAAAGGCTTCGGCCTAGTGATATGATTTATGAAAAG
1 AAGGCTTCGGCCCAATGATATGATTTATGAAAAGGCTTCGGCCCAGTGATATGATTTATGAAAAG
93985279 GCTTCGGCCCAGAGATATGATTTATGAT
66 GCTTCGGCCCAGAGATATGATTTATGAT
* * *
93985307 AAGGCTTCGGCCCAGTGATATGTTTTGTGATAAA-GCTTCGGCCCAGTGATATGATTTATGAAAA
1 AAGGCTTCGGCCCAATGATATGATTTATGA-AAAGGCTTCGGCCCAGTGATATGATTTATGAAAA
*
93985371 GGCTTTGGCCCA
65 GGCTTCGGCCCA
93985383 ATAACCGTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
93 67 0.96
94 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (93 bp):
AAGGCTTCGGCCCAATGATATGATTTATGAAAAGGCTTCGGCCCAGTGATATGATTTATGAAAAG
GCTTCGGCCCAGAGATATGATTTATGAT
Found at i:93988447 original size:31 final size:31
Alignment explanation
Indices: 93988412--93988476 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
93988402 GTATGACTTA
*
93988412 GAGGTGGCCCCTCTCTTCTAGAACTTTTCTG
1 GAGGTGGCCCCTCTCCTCTAGAACTTTTCTG
93988443 GAGGTGGCCCCTCTCCTCTAGAACTTTTCTG
1 GAGGTGGCCCCTCTCCTCTAGAACTTTTCTG
93988474 GAG
1 GAG
93988477 TACAAAACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.14, C:0.29, G:0.25, T:0.32
Consensus pattern (31 bp):
GAGGTGGCCCCTCTCCTCTAGAACTTTTCTG
Found at i:93989200 original size:13 final size:13
Alignment explanation
Indices: 93989182--93989210 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
93989172 TCTAGTTTAA
93989182 TTAGTTAATTAGT
1 TTAGTTAATTAGT
93989195 TTAGTTAATTAGT
1 TTAGTTAATTAGT
93989208 TTA
1 TTA
93989211 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:93992737 original size:23 final size:23
Alignment explanation
Indices: 93992711--93992757 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
93992701 CATTCTATTG
*
93992711 TCATACCCATGCCATTACTATGC
1 TCATACCCATGCCATTACCATGC
* * *
93992734 TCATTCTCATGCTATTACCATGC
1 TCATACCCATGCCATTACCATGC
93992757 T
1 T
93992758 AATGTCACGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (23 bp):
TCATACCCATGCCATTACCATGC
Found at i:93995014 original size:67 final size:64
Alignment explanation
Indices: 93994885--93995056 Score: 168
Period size: 64 Copynumber: 2.7 Consensus size: 64
93994875 TCTCTTTTAC
* * * * * * * *
93994885 ACATGGTGAACACTTAGTACCACCCATGTGACCTAGC--CAGTTTATCTCGTAGCTCTCTTGTCT
1 ACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACA-TATATCCCTTAGCTCTATTGTCT
* * * *
93994948 CCATGGTGTCCTTCACCTAGAACCACGCATGCGACCTAGCTACATATATCCCTTAGCTCTATTGT
1 ACATGGTG---TACACATAGAACCACCCATGCGACCTAGCTACATATATCCCTTAGCTCTATTGT
93995013 CT
63 CT
* *
93995015 ACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACAT
1 ACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACAT
93995057 CATAATGTCT
Statistics
Matches: 87, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
63 7 0.08
64 29 0.33
66 23 0.26
67 26 0.30
68 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.29
Consensus pattern (64 bp):
ACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACATATATCCCTTAGCTCTATTGTCT
Found at i:93997235 original size:6 final size:6
Alignment explanation
Indices: 93997226--93997305 Score: 101
Period size: 6 Copynumber: 13.7 Consensus size: 6
93997216 GATGATGATG
93997226 TTTAAT TTT-AT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTT-AT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
* * * * *
93997272 TTTCAT TTTTAT TTTCAT TTTTAT TTTTAT TTTA
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTA
93997306 TGTTTTTATT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
5 10 0.15
6 58 0.85
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTAAT
Found at i:93997662 original size:11 final size:11
Alignment explanation
Indices: 93997646--93997673 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
93997636 ACCAAGAGTC
93997646 AAAAGGAGCCA
1 AAAAGGAGCCA
93997657 AAAAGGAGCCA
1 AAAAGGAGCCA
93997668 AAAAGG
1 AAAAGG
93997674 GACAAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.14, G:0.29, T:0.00
Consensus pattern (11 bp):
AAAAGGAGCCA
Found at i:94013530 original size:42 final size:42
Alignment explanation
Indices: 94013469--94013589 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
94013459 GGAAAGCTCG
** * *
94013469 TACAATGCCAACATCCCAAACGTGGTCTTACATGTAATCAAA
1 TACAATGCCAATGTCCCAAAAGTGGTCTTACATGAAATCAAA
* **
94013511 TATCAATGCCACTGT-CCAAATAG-GGTCTTACACAAAATCAAA
1 TA-CAATGCCAATGTCCCAAA-AGTGGTCTTACATGAAATCAAA
* * *
94013553 TACGATGCCAATGTCCCAGATGTGGTCTTACATGAAA
1 TACAATGCCAATGTCCCAAAAGTGGTCTTACATGAAA
94013590 ATAACAAATC
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
41 11 0.18
42 41 0.66
43 10 0.16
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (42 bp):
TACAATGCCAATGTCCCAAAAGTGGTCTTACATGAAATCAAA
Found at i:94013607 original size:44 final size:42
Alignment explanation
Indices: 94013473--94013626 Score: 116
Period size: 42 Copynumber: 3.6 Consensus size: 42
94013463 AGCTCGTACA
* * * *** *
94013473 ATGCCAACATCCCAAACGTGGTCTTACATGTAATCAAATATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACAAAATCAAATA-CG
* * *
94013516 ATGCC-ACTGT-CCAAATAGGGTCTTACACAAAATCAAATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACAAAATCAAATACG
* ** *
94013557 ATGCCAATGTCCCAGATGTGGTCTTACATGAAAATAACAAAT-CG
1 ATGCCAACGTCCCAGACATGGTCTTACA-CAAAAT--CAAATACG
94013601 ATGCCAACGTCCCAGACATGGTCTTA
1 ATGCCAACGTCCCAGACATGGTCTTA
94013627 ATTGATAACA
Statistics
Matches: 89, Mismatches: 16, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
41 8 0.09
42 40 0.45
43 11 0.12
44 25 0.28
45 5 0.06
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACAAAATCAAATACG
Found at i:94017977 original size:14 final size:15
Alignment explanation
Indices: 94017950--94017979 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
94017940 AAGACTTAAG
94017950 GATTAATGCACAAAA
1 GATTAATGCACAAAA
94017965 GATTAAT-CACAAAA
1 GATTAATGCACAAAA
94017979 G
1 G
94017980 GTTATGTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (15 bp):
GATTAATGCACAAAA
Found at i:94025151 original size:13 final size:14
Alignment explanation
Indices: 94025122--94025156 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
94025112 AAATAATTAT
94025122 AATATTTAATTTAAA
1 AATA-TTAATTTAAA
94025137 AATATTAATTTAAA
1 AATATTAATTTAAA
94025151 AA-ATTA
1 AATATTA
94025157 CATATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.20
14 12 0.60
15 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATTAATTTAAA
Found at i:94025200 original size:17 final size:17
Alignment explanation
Indices: 94025168--94025207 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
94025158 ATATAATTTT
*
94025168 TTTAATAATTATTATACA
1 TTTAATAATAATTATA-A
94025186 TTTAA-AATAATTATAA
1 TTTAATAATAATTATAA
94025202 TTTAAT
1 TTTAAT
94025208 TTAAATTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAATAATAATTATAA
Found at i:94025213 original size:20 final size:20
Alignment explanation
Indices: 94025112--94025213 Score: 51
Period size: 20 Copynumber: 5.2 Consensus size: 20
94025102 TCACATTTTA
94025112 AAATAATTATAATATTTAATTT
1 AAATAATTAT-A-ATTTAATTT
*
94025134 AAA-AA-TATTAATTTAA--A
1 AAATAATTA-TAATTTAATTT
94025151 AAATTACA-TATAATTT--TTT
1 AAA-TA-ATTATAATTTAATTT
* *
94025170 TAATAATTAT--TATACATTT
1 AAATAATTATAATTTA-ATTT
94025189 AAAATAATTATAATTTAATTT
1 -AAATAATTATAATTTAATTT
94025210 AAAT
1 AAAT
94025214 TGTGATAGTA
Statistics
Matches: 61, Mismatches: 6, Indels: 28
0.64 0.06 0.29
Matches are distributed among these distances:
16 2 0.03
17 4 0.07
18 5 0.08
19 18 0.30
20 19 0.31
21 7 0.11
22 6 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATAATTATAATTTAATTT
Found at i:94026682 original size:3 final size:3
Alignment explanation
Indices: 94026674--94026706 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
94026664 TTATCTGATT
94026674 TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TT
94026707 CATATAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:94041800 original size:25 final size:24
Alignment explanation
Indices: 94041771--94041826 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
94041761 ATTTTTATTA
* *
94041771 AATTTTAATATG-ATTATTATGAAT
1 AATTTTAATA-GAAATATTATAAAT
94041795 ATATTTTAATAGAAATATTATAAAT
1 A-ATTTTAATAGAAATATTATAAAT
94041820 AATTTTA
1 AATTTTA
94041827 TCATATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (24 bp):
AATTTTAATAGAAATATTATAAAT
Found at i:94051337 original size:30 final size:30
Alignment explanation
Indices: 94051303--94051377 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
94051293 CTTTATTGGA
94051303 AATTATTTTAAAATTATAATTTATAATTAT
1 AATTATTTTAAAATTATAATTTATAATTAT
* **
94051333 AATTATTCT-ATGTTATTAATTTATAATTAT
1 AATTATTTTAAAATTA-TAATTTATAATTAT
94051363 --TTATTTTAAAATTAT
1 AATTATTTTAAAATTAT
94051378 TGATATATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 7 0.19
29 8 0.22
30 22 0.59
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (30 bp):
AATTATTTTAAAATTATAATTTATAATTAT
Found at i:94052417 original size:19 final size:19
Alignment explanation
Indices: 94052393--94052431 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
94052383 TTGATAAAAA
94052393 TTCATTTGTGAGATTTCTT
1 TTCATTTGTGAGATTTCTT
94052412 TTCATTTGTGAGATTTCTT
1 TTCATTTGTGAGATTTCTT
94052431 T
1 T
94052432 CTCTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.59
Consensus pattern (19 bp):
TTCATTTGTGAGATTTCTT
Found at i:94060236 original size:27 final size:27
Alignment explanation
Indices: 94060205--94060377 Score: 233
Period size: 27 Copynumber: 6.4 Consensus size: 27
94060195 GGGCATAATC
* * *
94060205 GTCATTTTACCATAC-AGGGATATTATG
1 GTCATTTTACCCTACAAGGG-CATTACG
* *
94060232 GTCATTTTATCCTAC-AGGGACATTACT
1 GTCATTTTACCCTACAAGGG-CATTACG
*
94060259 GTCATTTTACCCTACAAGGGTATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
* *
94060286 GTCATTTTATCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
94060313 GTCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
*
94060340 GTCATTTTACCCTACAAGGGTATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
94060367 GTCATTTTACC
1 GTCATTTTACC
94060378 TATTTTGGGG
Statistics
Matches: 131, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
27 127 0.97
28 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTACAAGGGCATTACG
Found at i:94060328 original size:81 final size:80
Alignment explanation
Indices: 94060205--94060379 Score: 271
Period size: 81 Copynumber: 2.2 Consensus size: 80
94060195 GGGCATAATC
* * * *
94060205 GTCATTTTACCATACAGGGATATTATGGTCATTTTATCCTAC-AGGGACATTACTGTCATTTTAC
1 GTCATTTTACC-TACAGGGACATTACGGTCATTTTACCCTACAAGGG-CATTACGGTCATTTTAC
94060269 CCTACAAGGGTATTACG
64 CCTACAAGGGTATTACG
*
94060286 GTCATTTTATCCTACAGGGGCATTACGGTCATTTTACCCTACAAGGGCATTACGGTCATTTTACC
1 GTCATTTTA-CCTACAGGGACATTACGGTCATTTTACCCTACAAGGGCATTACGGTCATTTTACC
94060351 CTACAAGGGTATTACG
65 CTACAAGGGTATTACG
94060367 GTCATTTTACCTA
1 GTCATTTTACCTA
94060380 TTTTGGGGTT
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
80 4 0.05
81 77 0.89
82 6 0.07
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (80 bp):
GTCATTTTACCTACAGGGACATTACGGTCATTTTACCCTACAAGGGCATTACGGTCATTTTACCC
TACAAGGGTATTACG
Found at i:94071953 original size:96 final size:96
Alignment explanation
Indices: 94071756--94072026 Score: 314
Period size: 96 Copynumber: 2.8 Consensus size: 96
94071746 TGAATTACCA
* * * * * *
94071756 ATGCTATGTTCCAAACACGATCTTACACTGGCTC-ACATGTCGAGGCCGATGCCATGTCCC-AAC
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTA-ATATCGTGGCCGATGCCATGTCCCAAAC
* * **
94071819 ACGGTCTTACACTAGCTCTCGTCTCAATGCCG
65 ATGGTCTTACACTAGCTCTCATAACAATGCCG
* * * *
94071851 ATGCCATGTCCCAGACATGGTCTTACATTGGCTCTGATAAT-GTGGTCGATGCCATGTCCCAAAC
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTAAT-ATCGTGGCCGATGCCATGTCCCAAAC
* *
94071915 ATGGTCTTACACTGGCTCTCATAACATTGCCG
65 ATGGTCTTACACTAGCTCTCATAACAATGCCG
* ** * *
94071947 ATGCCATGTTCCAAACATGGTCTTATGCTGGCTCTAATATCGTGGCCGACGCCATGTCCCAGACA
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTAATATCGTGGCCGATGCCATGTCCCAAACA
94072012 TGGTCTTACACTAGC
66 TGGTCTTACACTAGC
94072027 GCACATATCA
Statistics
Matches: 146, Mismatches: 26, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
95 49 0.34
96 97 0.66
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (96 bp):
ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTAATATCGTGGCCGATGCCATGTCCCAAACA
TGGTCTTACACTAGCTCTCATAACAATGCCG
Found at i:94072035 original size:48 final size:48
Alignment explanation
Indices: 94071756--94072035 Score: 253
Period size: 48 Copynumber: 5.9 Consensus size: 48
94071746 TGAATTACCA
* * * * * *
94071756 ATGCTATGTTCCAAACACGATCTTACACTGGCTCACATGTCGAGGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCGTGGCCG
* * * * * *
94071804 ATGCCATGTCCC-AACACGGTCTTACACTAGCTCTCGTCTCAAT-GCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATC-GTGGCCG
* * ** *
94071851 ATGCCATGTCCCAGACATGGTCTTACATTGGCTCTGATAAT-GTGGTCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACAT-ATCGTGGCCG
* * * *
94071899 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAACATTGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCGTGGCCG
* **
94071947 ATGCCATGTTCCAAACATGGTCTTATGCTGGCTCTA-ATATCGTGGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTC-ACATATCGTGGCCG
* * * *
94071995 ACGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATC
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATC
94072036 ACCCAAATGT
Statistics
Matches: 186, Mismatches: 39, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
47 42 0.23
48 143 0.77
49 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCGTGGCCG
Found at i:94075070 original size:25 final size:24
Alignment explanation
Indices: 94075037--94075129 Score: 109
Period size: 25 Copynumber: 3.8 Consensus size: 24
94075027 GGCTCTTTGT
94075037 GAGCTTCCTGAATAATGGCTATCTG
1 GAGCTTCCTG-ATAATGGCTATCTG
*
94075062 GAGCTTCCTGAT-ATGGCTCA-CTT
1 GAGCTTCCTGATAATGGCT-ATCTG
* *
94075085 GAACTTCCTGATATATGGCTATCAG
1 GAGCTTCCTGATA-ATGGCTATCTG
94075110 GAGCTTCCTGATTAATGGCT
1 GAGCTTCCTGA-TAATGGCT
94075130 CTTCAGAGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
23 19 0.33
24 4 0.07
25 33 0.57
26 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (24 bp):
GAGCTTCCTGATAATGGCTATCTG
Found at i:94075138 original size:25 final size:25
Alignment explanation
Indices: 94074994--94075144 Score: 75
Period size: 25 Copynumber: 6.0 Consensus size: 25
94074984 GAGTTTCTCT
* *
94074994 ATTATATGGCTCTTCGTGAGCTTCCCG
1 ATTA-ATGGCTCTTC-AGAGCTTCCTG
**
94075021 -TTAATTGGCTCTTTGTGAGCTTCCTG
1 ATTAA-TGGCTC-TTCAGAGCTTCCTG
* * *
94075047 AATAATGGCT-ATCTGGAGCTTCCTG
1 ATTAATGGCTCTTC-AGAGCTTCCTG
*
94075072 A-T-ATGGCTCACTT--GAACTTCCTG
1 ATTAATGGCT--CTTCAGAGCTTCCTG
*
94075095 A-TATATGGCT-ATCAGGAGCTTCCTG
1 ATTA-ATGGCTCTTCA-GAGCTTCCTG
*
94075120 ATTAATGGCTCTTCAGAGCTACCTG
1 ATTAATGGCTCTTCAGAGCTTCCTG
94075145 TTATAGGCTC
Statistics
Matches: 98, Mismatches: 12, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
22 1 0.01
23 17 0.17
24 2 0.02
25 43 0.44
26 30 0.31
27 5 0.05
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (25 bp):
ATTAATGGCTCTTCAGAGCTTCCTG
Found at i:94083192 original size:12 final size:14
Alignment explanation
Indices: 94083162--94083193 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
94083152 AACAAAAGAA
94083162 AAAAATTAGAATAT
1 AAAAATTAGAATAT
94083176 AAAAATTA-AAT-T
1 AAAAATTAGAATAT
94083188 AAAAAT
1 AAAAAT
94083194 AAAAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (14 bp):
AAAAATTAGAATAT
Found at i:94083204 original size:20 final size:18
Alignment explanation
Indices: 94083164--94083218 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 18
94083154 CAAAAGAAAA
*
94083164 AAATTAGAATATAAAAATT
1 AAATTA-AAAATAAAAATT
94083183 AAATTAAAAATAAAAATTTT
1 AAATTAAAAATAAAAA--TT
*
94083203 AAAATAAAAATAAAAA
1 AAATTAAAAATAAAAA
94083219 ATGGTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 9 0.28
19 6 0.19
20 17 0.53
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATTAAAAATAAAAATT
Found at i:94083228 original size:21 final size:19
Alignment explanation
Indices: 94083181--94083228 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
94083171 AATATAAAAA
*
94083181 TTAAATTAAAAATAAAAATT
1 TTAAA-TAAAAATAAAAATG
94083201 TTAAAATAAAAATAAAAAATGG
1 TT-AAATAAAAAT-AAAAAT-G
94083223 TTAAAT
1 TTAAAT
94083229 TAATAGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 9 0.38
21 13 0.54
22 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
TTAAATAAAAATAAAAATG
Found at i:94083585 original size:31 final size:31
Alignment explanation
Indices: 94083547--94083609 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
94083537 CAGGAAAGAA
*
94083547 TTCACCTAGATTTCATCTGTCATTATCAATC
1 TTCACCTAGATTTCATCTATCATTATCAATC
*
94083578 TTCACCTAGATTTCATCTATTATTATCAATC
1 TTCACCTAGATTTCATCTATCATTATCAATC
94083609 T
1 T
94083610 AAATTATGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (31 bp):
TTCACCTAGATTTCATCTATCATTATCAATC
Found at i:94102292 original size:6 final size:5
Alignment explanation
Indices: 94102264--94102355 Score: 66
Period size: 5 Copynumber: 17.6 Consensus size: 5
94102254 ATGTCGTTCG
* *
94102264 AAATA AAAT- -AATA AAATTG AAATGA AAATAA AAATCA AAAGAA AAATA
1 AAATA AAATA AAATA AAA-TA AAAT-A AAAT-A AAAT-A AAA-TA AAATA
94102312 AAA-A TAAATA AAATA AAATA AAATAA AAATA AGAAT- AAATA AAA
1 AAATA -AAATA AAATA AAATA AAAT-A AAATA A-AATA AAATA AAA
94102356 AAATAGGAGG
Statistics
Matches: 71, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
3 3 0.04
4 4 0.06
5 34 0.48
6 30 0.42
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:94102343 original size:49 final size:49
Alignment explanation
Indices: 94102264--94102360 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 49
94102254 ATGTCGTTCG
* * * *
94102264 AAATAAAATAATAAAATTGAAATGAAAATAAAAATCAAA-AGAAAAATAA
1 AAATAAAAAAATAAAATTAAAATAAAAATAAAAAT-AAATAAAAAAATAA
*
94102313 AAATAAATAAAATAAAA-TAAAATAAAAATAAGAATAAATAAAAAAATA
1 AAATAAA-AAAATAAAATTAAAATAAAAATAAAAATAAATAAAAAAATA
94102361 GGAGGATTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 3 0.07
49 30 0.73
50 8 0.20
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (49 bp):
AAATAAAAAAATAAAATTAAAATAAAAATAAAAATAAATAAAAAAATAA
Found at i:94108787 original size:27 final size:27
Alignment explanation
Indices: 94108757--94108935 Score: 241
Period size: 27 Copynumber: 6.6 Consensus size: 27
94108747 TTAGTTTACC
* *
94108757 AAATTATCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * * *
94108784 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
94108811 AAATTACCAAAATACCCCTATTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
94108838 TAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
94108865 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* *
94108892 AAATTACCAAAATACTCCTAATTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
**
94108919 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
94108936 TCGACCTGTA
Statistics
Matches: 133, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 133 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAGTTTGTA
Found at i:94108945 original size:27 final size:27
Alignment explanation
Indices: 94108915--94109006 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
94108905 ACTCCTAATT
94108915 TGTAAAATTACTGAAATACCCTCGACC
1 TGTAAAATTACTGAAATACCCTCGACC
*
94108942 TGTAAAATTATTGAAATACCCTCGACC
1 TGTAAAATTACTGAAATACCCTCGACC
* * * *
94108969 TGTAAAATTATTGAAATATCCTCAACT
1 TGTAAAATTACTGAAATACCCTCGACC
94108996 TGTAAAATTAC
1 TGTAAAATTAC
94109007 CAAAGTACCC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (27 bp):
TGTAAAATTACTGAAATACCCTCGACC
Found at i:94108946 original size:54 final size:52
Alignment explanation
Indices: 94108779--94109016 Score: 165
Period size: 54 Copynumber: 4.4 Consensus size: 52
94108769 TACCCCTGGT
* ** * ** **
94108779 TTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCC-CTATT
1 TTGTAAAATTACCAAAATACCC-TAATTTGTAAAATTA-TGAAATACCCTC-AAC
* * * **
94108833 TTGTATAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAAATACCC-CTAGT
1 TTGTAAAATTACCAAAATA-CCCTAATTTGTAAAATTAT-GAAATACCCTC-AAC
*
94108887 TTGTAAAATTACCAAAATACTCCTAATTTGTAAAATTACTGAAATACCCTCGAC
1 TTGTAAAATTACCAAAATAC-CCTAATTTGTAAAATTA-TGAAATACCCTCAAC
* *** * ** *
94108941 CTGTAAAATTATTGAAATACCCTCGACCTGTAAAATTATTGAAATATCCTCAAC
1 TTGTAAAATTACCAAAATACCCT-AATTTGTAAAATTA-TGAAATACCCTCAAC
*
94108995 TTGTAAAATTACCAAAGTACCC
1 TTGTAAAATTACCAAAATACCC
94109017 CCGATTTATA
Statistics
Matches: 151, Mismatches: 27, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
53 4 0.03
54 142 0.94
55 5 0.03
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (52 bp):
TTGTAAAATTACCAAAATACCCTAATTTGTAAAATTATGAAATACCCTCAAC
Found at i:94108946 original size:81 final size:81
Alignment explanation
Indices: 94108757--94108962 Score: 220
Period size: 81 Copynumber: 2.5 Consensus size: 81
94108747 TTAGTTTACC
* ** * *
94108757 AAATTATCAAAATACCCCTG-GTTTGTAAAATTA-CTAAAATACCCTTGGTTTATAAAATTACCA
1 AAATTACCAAAATACCCC-GAGCCTGTAAAATTATC-AAAATACCCCTAGTTTATAAAATTACCA
*
94108820 AAATACCCCTATTTTGTA
64 AAATACCCCTAATTTGTA
* * ** *
94108838 TAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAA
1 AAATTACCAAAATACCCCGAGCCTGTAAAATTATCAAAATACCCCTAGTTTATAAAATTACCAAA
*
94108903 ATACTCCTAATTTGTA
66 ATACCCCTAATTTGTA
** **
94108919 AAATTACTGAAATACCCTCGA-CCTGTAAAATTATTGAAATACCC
1 AAATTACCAAAATACCC-CGAGCCTGTAAAATTATCAAAATACCC
94108963 TCGACCTGTA
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
81 103 0.97
82 3 0.03
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (81 bp):
AAATTACCAAAATACCCCGAGCCTGTAAAATTATCAAAATACCCCTAGTTTATAAAATTACCAAA
ATACCCCTAATTTGTA
Found at i:94108973 original size:81 final size:81
Alignment explanation
Indices: 94108809--94109017 Score: 208
Period size: 81 Copynumber: 2.6 Consensus size: 81
94108799 CCTTGGTTTA
* * * * **
94108809 TAAAATTACCAAAATACCCCTATTTTGTATAATTACCAAAATACCCCTAGTTTGTAAAATTATCA
1 TAAAATTACCAAAATACTCCTAATTTGTAAAATTACCAAAATACCCCGAGCCTGTAAAATTATCA
* **
94108874 AAATACCCCTAGTTTG
66 AAATACCCCGAGCCTG
** *
94108890 TAAAATTACCAAAATACTCCTAATTTGTAAAATTACTGAAATACCCTCGA-CCTGTAAAATTATT
1 TAAAATTACCAAAATACTCCTAATTTGTAAAATTACCAAAATACCC-CGAGCCTGTAAAATTATC
*
94108954 GAAATACCCTCGA-CCTG
65 AAAATACCC-CGAGCCTG
*** * *
94108971 TAAAATTATTGAAATA-TCCTCAACTTGTAAAATTACCAAAGTACCCC
1 TAAAATTACCAAAATACTCCT-AATTTGTAAAATTACCAAAATACCCC
94109018 CGATTTATAG
Statistics
Matches: 105, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
80 5 0.05
81 96 0.91
82 4 0.04
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (81 bp):
TAAAATTACCAAAATACTCCTAATTTGTAAAATTACCAAAATACCCCGAGCCTGTAAAATTATCA
AAATACCCCGAGCCTG
Found at i:94109042 original size:27 final size:27
Alignment explanation
Indices: 94108998--94109195 Score: 216
Period size: 27 Copynumber: 7.3 Consensus size: 27
94108988 CCTCAACTTG
*** *
94108998 TAAAATTACCAAAGTACCCCCGATTTA
1 TAAAATTACCATTTTACCCTCGATTTA
* *
94109025 TAGAATTACCATTTTACCCTTGATTTA
1 TAAAATTACCATTTTACCCTCGATTTA
* *
94109052 CAAAATTACCATTTTACCCTCAATTTA
1 TAAAATTACCATTTTACCCTCGATTTA
* * * *
94109079 CAAAATTACCGTTTTACCCTCAATTAA
1 TAAAATTACCATTTTACCCTCGATTTA
*
94109106 TAAAATTACCGTTTTACCCTCGATTTA
1 TAAAATTACCATTTTACCCTCGATTTA
* * *
94109133 TAGAATTATCGTTTTACCCTCGATTTA
1 TAAAATTACCATTTTACCCTCGATTTA
* * *
94109160 TAGAATTACCATTTTACACTCAATTTA
1 TAAAATTACCATTTTACCCTCGATTTA
*
94109187 CAAAATTAC
1 TAAAATTAC
94109196 TGAAATACCC
Statistics
Matches: 148, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (27 bp):
TAAAATTACCATTTTACCCTCGATTTA
Found at i:94109220 original size:27 final size:27
Alignment explanation
Indices: 94109190--94109384 Score: 230
Period size: 27 Copynumber: 7.3 Consensus size: 27
94109180 CAATTTACAA
*
94109190 AATTACTGAAATACCCATGTAAGGTAG
1 AATTACCGAAATACCCATGTAAGGTAG
94109217 AATTACCGAAATACCCATGTAAGGTAG
1 AATTACCGAAATACCCATGTAAGGTAG
94109244 AATTACCGAAATACCCATGTAAGGTAG
1 AATTACCGAAATACCCATGTAAGGTAG
* *
94109271 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCATGTAAGGTAG
* * * *
94109298 AATTACCAAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCATGTAAGGTAG
** * * *
94109325 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCATGTAAGGTAG
* * * * *
94109352 AATTACAGAGATA-CCTTGTGAGGTAA
1 AATTACCGAAATACCCATGTAAGGTAG
94109378 AATTACC
1 AATTACC
94109385 ATTTTGCCCC
Statistics
Matches: 151, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 14 0.09
27 137 0.91
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCATGTAAGGTAG
Found at i:94109862 original size:22 final size:22
Alignment explanation
Indices: 94109810--94109874 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
94109800 TTAAAGCATT
* *
94109810 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
94109832 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
94109854 CTGATTATGGTTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
94109875 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:94110072 original size:26 final size:27
Alignment explanation
Indices: 94110033--94110106 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
94110023 TTTCTGTTAA
* * *
94110033 GTGGCTTTGCCACATTATCTGT-TCTG
1 GTGGCTCTGTCACAATATCTGTATCTG
94110059 GTGGCTCTGTCACAATATCTGTATCTG
1 GTGGCTCTGTCACAATATCTGTATCTG
*
94110086 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGTCACAATATCTG
94110107 ATAACTGAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 19 0.44
27 24 0.56
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.38
Consensus pattern (27 bp):
GTGGCTCTGTCACAATATCTGTATCTG
Found at i:94110283 original size:6 final size:6
Alignment explanation
Indices: 94110272--94110362 Score: 71
Period size: 6 Copynumber: 14.8 Consensus size: 6
94110262 TTACCTAATG
* * *
94110272 CTGATT CTGATT TTGATT CTG-TT ACCTGATA CTGATT CCGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT CTGATT
* *
94110321 CTG-TCAC CTAATT CTGATT CTGATT CTGATT CT-AGTT CTGAT
1 CTGAT--T CTGATT CTGATT CTGATT CTGATT CTGA-TT CTGAT
94110363 AATGTTTCTT
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
5 4 0.06
6 55 0.82
7 6 0.09
8 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (6 bp):
CTGATT
Found at i:94110288 original size:31 final size:31
Alignment explanation
Indices: 94110254--94110353 Score: 146
Period size: 31 Copynumber: 3.2 Consensus size: 31
94110244 TTTTGATTTT
* *
94110254 TGATTCTGTTACCTAATGCTGATTCTGATTT
1 TGATTCTGTTACCTAATACTGATTCTGATTC
* *
94110285 TGATTCTGTTACCTGATACTGATTCCGATTC
1 TGATTCTGTTACCTAATACTGATTCTGATTC
* *
94110316 TGATTCTGTCACCTAATTCTGATTCTGATTC
1 TGATTCTGTTACCTAATACTGATTCTGATTC
94110347 TGATTCT
1 TGATTCT
94110354 AGTTCTGATA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (31 bp):
TGATTCTGTTACCTAATACTGATTCTGATTC
Found at i:94112320 original size:27 final size:27
Alignment explanation
Indices: 94112290--94112468 Score: 268
Period size: 27 Copynumber: 6.6 Consensus size: 27
94112280 TTAGTTTACC
*
94112290 AAATTATCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
94112317 AAATTACCAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
94112344 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
94112371 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
94112398 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
94112425 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
**
94112452 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
94112469 TCGACCTGTA
Statistics
Matches: 137, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 137 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:94112465 original size:54 final size:54
Alignment explanation
Indices: 94112290--94112566 Score: 258
Period size: 54 Copynumber: 5.1 Consensus size: 54
94112280 TTAGTTTACC
* * * *
94112290 AAATTA-TCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
1 AAATTACT-AAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTA
* *
94112344 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTA
*
94112398 AAATTA-TCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTG
1 AAATTACT-AAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTA
* * ** *** **
94112452 AAATTACTGAAATA-CCCTCGACCTGTAAAATTATTGAAATA-CCCTCGACCTGTA
1 AAATTACTAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCCT-GATTTGTA
* * ** * * *
94112506 AAATTATTGAAATA-CCCTCAACTTGTAAAATTACCAAAGTACCCCCGATTTATA
1 AAATTACTAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCCTGATTTGTA
*
94112560 GAATTAC
1 AAATTAC
94112567 CATTTTACCC
Statistics
Matches: 185, Mismatches: 31, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
53 9 0.05
54 172 0.93
55 4 0.02
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (54 bp):
AAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTA
Found at i:94112575 original size:27 final size:27
Alignment explanation
Indices: 94112545--94112728 Score: 251
Period size: 27 Copynumber: 6.8 Consensus size: 27
94112535 ATTACCAAAG
* * *
94112545 TACCCCCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACCATTT
94112572 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACCATTT
**
94112599 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACCATTT
* * * *
94112626 TACCCTCGATTAATAAAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCATTT
* *
94112653 TACCCTCGATTTACAGAATTATCATTT
1 TACCCTCGATTTACAAAATTACCATTT
* *
94112680 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACCATTT
94112707 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAAAATTAC
94112729 TAAAATACCC
Statistics
Matches: 140, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 140 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCATTT
Found at i:94112737 original size:27 final size:27
Alignment explanation
Indices: 94112290--94112738 Score: 233
Period size: 27 Copynumber: 16.6 Consensus size: 27
94112280 TTAGTTTACC
* * *
94112290 AAATTATCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTATA
* *
94112317 AAATTACCAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* *
94112344 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTATA
* *
94112371 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTATA
* * *
94112398 AAATTATCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTATA
* *
94112425 AAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACCAAAATACCCTC-GATTTATA
** ** *
94112452 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTCGATTTATA
*** ** *
94112479 AAATTATTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTCGATTTATA
*** * * *
94112506 AAATTATTGAAATACCCTCAACTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* *
94112533 AAATTACCAAAGTACCCCCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* *** *
94112560 GAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
*** *
94112587 AAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
***** *
94112614 AAATTACTGTTTTACCCTCGATTAATA
1 AAATTACCAAAATACCCTCGATTTATA
* **** *
94112641 AAATTATCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* * ***
94112668 GAATTATCATTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* *** *
94112695 GAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
*
94112722 AAATTACTAAAATACCC
1 AAATTACCAAAATACCC
94112739 ATGTAAGGTA
Statistics
Matches: 360, Mismatches: 56, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
27 358 0.99
28 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTATA
Found at i:94112753 original size:27 final size:27
Alignment explanation
Indices: 94112723--94112890 Score: 219
Period size: 27 Copynumber: 6.2 Consensus size: 27
94112713 CGATTTACAA
* * *
94112723 AATTACTAAAATACCCATGTAAGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* * *
94112750 AATTACCGAAATACCCATGTAAGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* * *
94112777 AATTACCGAAATACCCTTATAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
**
94112804 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
94112831 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* *
94112858 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCAAAATACCCCTGTAGGGTAG
94112885 AATTAC
1 AATTAC
94112891 AGAGATACCT
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 129 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGTAGGGTAG
Found at i:94112881 original size:81 final size:81
Alignment explanation
Indices: 94112723--94112918 Score: 241
Period size: 81 Copynumber: 2.4 Consensus size: 81
94112713 CGATTTACAA
* * *
94112723 AATTACTAAAATACCCATGTAAGGTAGAATTACCGAAATACCCATGTAAGGTAGAATTACCGAAA
1 AATTACTGAAATACCCATGTAAGGTAGAATTACCAAAATACCCATGTAAGGTAGAATTACCAAAA
*
94112788 TACCCTTATAGGGTAG
66 TACCCCTATAGGGTAG
* * * * *
94112804 AATTACTGAAATACCCCTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACTAAAA
1 AATTACTGAAATACCCATGTAAGGTAGAATTACCAAAATACCCATGTAAGGTAGAATTACCAAAA
* *
94112869 TACCCCTGTAGGGTGG
66 TACCCCTATAGGGTAG
* * * * *
94112885 AATTACAGAGATA-CCTTGTGAGGTAAAATTACCA
1 AATTACTGAAATACCCATGTAAGGTAGAATTACCA
94112919 TTTTACCCCT
Statistics
Matches: 98, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
80 17 0.17
81 81 0.83
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (81 bp):
AATTACTGAAATACCCATGTAAGGTAGAATTACCAAAATACCCATGTAAGGTAGAATTACCAAAA
TACCCCTATAGGGTAG
Found at i:94113395 original size:22 final size:22
Alignment explanation
Indices: 94113343--94113396 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
94113333 TTAAAGCATT
** *
94113343 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCAGTGCCAAC
*
94113365 CT-ACATATGGCTCAGTGCCAAC
1 CTGA-TTATGGCTCAGTGCCAAC
94113387 CTGATTATGG
1 CTGATTATGG
94113397 TTGTGTGCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (22 bp):
CTGATTATGGCTCAGTGCCAAC
Found at i:94113626 original size:27 final size:27
Alignment explanation
Indices: 94113588--94113639 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
94113578 CATTATCTAT
*
94113588 TCTGGTGGCTCTGTCACAATATCTGTA
1 TCTGGTGACTCTGTCACAATATCTGTA
94113615 TCTGGTGACTCTGTCACAATATCTG
1 TCTGGTGACTCTGTCACAATATCTG
94113640 ATAACTGAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (27 bp):
TCTGGTGACTCTGTCACAATATCTGTA
Found at i:94113816 original size:6 final size:6
Alignment explanation
Indices: 94113805--94113895 Score: 71
Period size: 6 Copynumber: 14.8 Consensus size: 6
94113795 TTACCTAATA
* *
94113805 CTGATT CTGATT TTGATT CTG-TT ACCTGATA CTGATT CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT CTGATT
* * *
94113854 TTG-TCAC CTAATT CTGATT CTGATT CTGATT CT-AGTT CTGAT
1 CTGAT--T CTGATT CTGATT CTGATT CTGATT CTGA-TT CTGAT
94113896 AATGTTTCTT
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
5 4 0.06
6 56 0.84
7 5 0.07
8 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (6 bp):
CTGATT
Found at i:94113821 original size:31 final size:31
Alignment explanation
Indices: 94113787--94113886 Score: 155
Period size: 31 Copynumber: 3.2 Consensus size: 31
94113777 TTTTGATTTT
*
94113787 TGATTCTGTTACCTAATACTGATTCTGATTT
1 TGATTCTGTTACCTAATACTGATTCTGATTC
*
94113818 TGATTCTGTTACCTGATACTGATTCTGATTC
1 TGATTCTGTTACCTAATACTGATTCTGATTC
* * *
94113849 TGATTTTGTCACCTAATTCTGATTCTGATTC
1 TGATTCTGTTACCTAATACTGATTCTGATTC
94113880 TGATTCT
1 TGATTCT
94113887 AGTTCTGATA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (31 bp):
TGATTCTGTTACCTAATACTGATTCTGATTC
Found at i:94118323 original size:10 final size:11
Alignment explanation
Indices: 94118298--94118322 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
94118288 GTTTTGTCCC
94118298 TTTTGGCTCAT
1 TTTTGGCTCAT
94118309 TTTTGGCTCAT
1 TTTTGGCTCAT
94118320 TTT
1 TTT
94118323 GACTCCGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTTGGCTCAT
Found at i:94123317 original size:28 final size:27
Alignment explanation
Indices: 94123273--94123381 Score: 112
Period size: 28 Copynumber: 3.9 Consensus size: 27
94123263 CTGTACAATC
* *
94123273 GATGTCTT-GCACGCTAAGTGCTATACCG
1 GATGT-TTCGCACACTAAGTGCCAT-CCG
*
94123301 GATGTTTCGCACACTAAGTGCCATCCTC
1 GATGTTTCGCACACTAAGTGCCATCC-G
** *
94123329 GATACTTCGCACACTAAGTGCCATTTCG
1 GATGTTTCGCACACTAAGTGCCA-TCCG
*
94123357 GATGTTTCGCACACTAAGTGTCATC
1 GATGTTTCGCACACTAAGTGCCATC
94123382 ATCAATACTT
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
27 5 0.07
28 60 0.90
29 2 0.03
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (27 bp):
GATGTTTCGCACACTAAGTGCCATCCG
Found at i:94123359 original size:56 final size:56
Alignment explanation
Indices: 94123281--94123460 Score: 231
Period size: 56 Copynumber: 3.2 Consensus size: 56
94123271 TCGATGTCTT
* * ** *
94123281 GCACGCTAAGTGCTATACCGGATGTTTCGCACACTAAGTGCCATCCTCGATACTTC
1 GCACACTAAGTGCCATTTCGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTC
* *
94123337 GCACACTAAGTGCCATTTCGGATGTTTCGCACACTAAGTGTCATCATCAATACTTC
1 GCACACTAAGTGCCATTTCGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTC
** * *
94123393 ATACACT--GTGTCATTTCGAATGTCTT-GCACACTAAGTGCCATCCTCAATACTTC
1 GCACACTAAGTGCCATTTCGGATGT-TTCGCACACTAAGTGCCATCCTCAATACTTC
94123447 GCACACTAAGTGCC
1 GCACACTAAGTGCC
94123461 GTTCGTTTGG
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
54 45 0.43
55 2 0.02
56 58 0.55
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (56 bp):
GCACACTAAGTGCCATTTCGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTC
Found at i:94123441 original size:54 final size:55
Alignment explanation
Indices: 94123302--94123460 Score: 205
Period size: 54 Copynumber: 2.9 Consensus size: 55
94123292 GCTATACCGG
* * *
94123302 ATGTTTCGCACACTAAGTGCCATCCTCGATACTTCGCACACTAAGTGCCATTTCGG
1 ATGTTTCGCACACTAAGTGCCATCCTCAATACTTCACACACT-AGTGCCATTTCGA
* * * *
94123358 ATGTTTCGCACACTAAGTGTCATCATCAATACTTCATACACT-GTGTCATTTCGA
1 ATGTTTCGCACACTAAGTGCCATCCTCAATACTTCACACACTAGTGCCATTTCGA
*
94123412 ATGTCTT-GCACACTAAGTGCCATCCTCAATACTTCGCACACTAAGTGCC
1 ATGT-TTCGCACACTAAGTGCCATCCTCAATACTTCACACACT-AGTGCC
94123461 GTTCGTTTGG
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
54 45 0.51
55 2 0.02
56 41 0.47
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (55 bp):
ATGTTTCGCACACTAAGTGCCATCCTCAATACTTCACACACTAGTGCCATTTCGA
Found at i:94123459 original size:28 final size:28
Alignment explanation
Indices: 94123306--94123460 Score: 140
Period size: 28 Copynumber: 5.6 Consensus size: 28
94123296 TACCGGATGT
*
94123306 TTCGCACACTAAGTGCCATCCTCGATAC
1 TTCGCACACTAAGTGCCATCCTCAATAC
* * **
94123334 TTCGCACACTAAGTGCCAT-TTCGGATGT
1 TTCGCACACTAAGTGCCATCCTC-AATAC
* *
94123362 TTCGCACACTAAGTGTCATCATCAATAC
1 TTCGCACACTAAGTGCCATCCTCAATAC
** * * *
94123390 TTCATACACT--GTGTCAT-TTCGAATGTC
1 TTCGCACACTAAGTGCCATCCTC-AAT-AC
94123417 TT-GCACACTAAGTGCCATCCTCAATAC
1 TTCGCACACTAAGTGCCATCCTCAATAC
94123444 TTCGCACACTAAGTGCC
1 TTCGCACACTAAGTGCC
94123461 GTTCGTTTGG
Statistics
Matches: 102, Mismatches: 17, Indels: 16
0.76 0.13 0.12
Matches are distributed among these distances:
25 2 0.02
26 15 0.15
27 8 0.08
28 73 0.72
29 4 0.04
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (28 bp):
TTCGCACACTAAGTGCCATCCTCAATAC
Found at i:94134541 original size:28 final size:28
Alignment explanation
Indices: 94134501--94134558 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
94134491 TTGTTGTTAG
94134501 AGAAAGATGCAGAGTTCAATTTTAACAA
1 AGAAAGATGCAGAGTTCAATTTTAACAA
*
94134529 AGAAAGATGCAGAGTTCGATTTTAACAA
1 AGAAAGATGCAGAGTTCAATTTTAACAA
94134557 AG
1 AG
94134559 CTTGTTTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (28 bp):
AGAAAGATGCAGAGTTCAATTTTAACAA
Found at i:94144419 original size:18 final size:18
Alignment explanation
Indices: 94144396--94144432 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
94144386 TATGACACTA
94144396 ATTTTGTAAAAACTTTGT
1 ATTTTGTAAAAACTTTGT
*
94144414 ATTTTGTAAAAATTTTGT
1 ATTTTGTAAAAACTTTGT
94144432 A
1 A
94144433 AAAAGTGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
ATTTTGTAAAAACTTTGT
Found at i:94147350 original size:28 final size:28
Alignment explanation
Indices: 94147305--94147437 Score: 178
Period size: 28 Copynumber: 4.8 Consensus size: 28
94147295 GGCTATGTAC
* *
94147305 GGCACTTAGCGTGTGAGACATTGATTAT
1 GGCACTTAGTGTGCGAGACATTGATTAT
*
94147333 GGCACTTAGTGTGCGAGATATTGATTAT
1 GGCACTTAGTGTGCGAGACATTGATTAT
* * *
94147361 GGCACTTAGTGTGTGAGGCATTGATTGT
1 GGCACTTAGTGTGCGAGACATTGATTAT
*
94147389 GGCACTTAGTGTGCCATG-CATTGATTAT
1 GGCACTTAGTGTGCGA-GACATTGATTAT
*
94147417 GGAACTTAGTGTGCGAGACAT
1 GGCACTTAGTGTGCGAGACAT
94147438 CAAGTATGCG
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.01
28 89 0.98
29 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (28 bp):
GGCACTTAGTGTGCGAGACATTGATTAT
Found at i:94152076 original size:13 final size:13
Alignment explanation
Indices: 94152058--94152087 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
94152048 AAAAATGGAT
94152058 AGAAAATGAAGAG
1 AGAAAATGAAGAG
*
94152071 AGAAAATTAAGAG
1 AGAAAATGAAGAG
94152084 AGAA
1 AGAA
94152088 GAGAATAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.27, T:0.10
Consensus pattern (13 bp):
AGAAAATGAAGAG
Found at i:94163311 original size:79 final size:80
Alignment explanation
Indices: 94163213--94163474 Score: 372
Period size: 79 Copynumber: 3.3 Consensus size: 80
94163203 TACTCGTTCA
* * **
94163213 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGACCTTAGTCCGG
94163276 ATTTAGTGACTCGCACC
64 ATTTAGTGACTCGCACC
*
94163293 AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGACCTTAGTCCGGAT
94163357 TTAGTGACTCGCACC
66 TTAGTGACTCGCACC
*
94163372 AATGCCTTC-GGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGACCTTAGTCCGAAT
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGACCTTAGTCCGGAT
* * *
94163436 ATAGTCACTTAGCA-C
66 TTAGTGAC-TCGCACC
*
94163451 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
94163475 CATCATTCGA
Statistics
Matches: 167, Mismatches: 10, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
78 5 0.03
79 131 0.78
80 31 0.19
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGACCTTAGTCCGGAT
TTAGTGACTCGCACC
Found at i:94163327 original size:39 final size:39
Alignment explanation
Indices: 94163211--94163474 Score: 291
Period size: 40 Copynumber: 6.6 Consensus size: 39
94163201 GCTACTCGTT
* *
94163211 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCA
* * *
94163251 CAAATGCCTTCGGGACTTAACCCGGATTTAGTGACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
*
94163291 CCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
* * * *
94163330 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTGACTCGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGAATTAGTAACTCGCA
* *
94163370 CCAATGCCTTCGGACTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
* * * *
94163409 CAAATGCCTTCGGACCTTAGTCC-GAATATAGTCACTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGAAT-TAGTAAC-TCGCA
94163450 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
94163475 CATCATTCGA
Statistics
Matches: 193, Mismatches: 24, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
39 72 0.37
40 109 0.56
41 12 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
Found at i:94163428 original size:119 final size:121
Alignment explanation
Indices: 94163211--94163474 Score: 344
Period size: 119 Copynumber: 2.2 Consensus size: 121
94163201 GCTACTCGTT
*
94163211 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* * * * *
94163275 GATTTAGTGACTCGCACCAATGCCTTCGGGCTTAGCCCGGAAT-TAGTAAC-TCGCA
66 GAATTAGTAACTCGCACAAATGCCTTCGGCCTTAGCCC-GAATATAGTAACTTAGCA
* * * *
94163330 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTGACTCGCACCAATGCCTTC-GGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
* *
94163392 GGAATTAGTAACTCGCACAAATGCCTTCGGACCTTAGTCCGAATATAGTCACTTAGCA
65 GGAATTAGTAACTCGCACAAATGCCTTCGG-CCTTAGCCCGAATATAGTAACTTAGCA
94163450 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
94163475 CATCATTCGA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
118 44 0.35
119 69 0.55
120 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (121 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
GAATTAGTAACTCGCACAAATGCCTTCGGCCTTAGCCCGAATATAGTAACTTAGCA
Found at i:94171451 original size:39 final size:39
Alignment explanation
Indices: 94171375--94171637 Score: 296
Period size: 39 Copynumber: 6.6 Consensus size: 39
94171365 GCTACTCGTT
*
94171375 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCA
* *
94171415 CAAATGCCTTCGGACTTAACCCGGATTTAGTGACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
94171454 CCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
94171493 AAAATGCCTTCGGATCTTAGTCCGAATTTAGTGACTCGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * *
94171533 CCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
94171572 CAAATGCCTTCGGATCTTAGTCCAGATATAGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
94171613 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
94171638 CATCATTCGA
Statistics
Matches: 186, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
39 100 0.54
40 75 0.40
41 11 0.06
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:94171528 original size:79 final size:80
Alignment explanation
Indices: 94171377--94171637 Score: 363
Period size: 79 Copynumber: 3.3 Consensus size: 80
94171367 TACTCGTTCA
* * ** *
94171377 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGA-CTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGAA
94171440 TTTAGTGACTCGCACC
65 TTTAGTGACTCGCACC
*
94171456 AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCAAAAATGCCTTCGGATCTTAGTCCGAAT
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGAAT
94171520 TTAGTGACTCGCACC
66 TTAGTGACTCGCACC
94171535 AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCC-AGA
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGA-A
* * *
94171598 TATAGTCACTTAGCA-C
65 TTTAGTGAC-TCGCACC
*
94171614 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
94171638 CATCATTCGA
Statistics
Matches: 166, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
78 35 0.21
79 116 0.70
80 15 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGAAT
TTAGTGACTCGCACC
Found at i:94176494 original size:18 final size:19
Alignment explanation
Indices: 94176466--94176505 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
94176456 TATTACAAAA
94176466 TTAATTAAAATTCATTATG
1 TTAATTAAAATTCATTATG
94176485 TTAA-TAAAATTCATTATG
1 TTAATTAAAATTCATTATG
94176503 TTA
1 TTA
94176506 GTAATTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (19 bp):
TTAATTAAAATTCATTATG
Found at i:94182144 original size:20 final size:20
Alignment explanation
Indices: 94182105--94182144 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
94182095 TCTTTCTTTA
94182105 ACAGCTTTTAAATCTTCCTTG
1 ACAGCTTTTAAA-CTTCCTTG
94182126 ACAGCTTTTACAA-TTCCTT
1 ACAGCTTTTA-AACTTCCTT
94182145 TATCTTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 10 0.56
22 2 0.11
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.42
Consensus pattern (20 bp):
ACAGCTTTTAAACTTCCTTG
Found at i:94186004 original size:29 final size:28
Alignment explanation
Indices: 94185972--94186050 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
94185962 AAAAACTTAA
*
94185972 AAATTGTAAAAAAATTATAAAATATATAG
1 AAATTATAAAAAAATTATAAAAT-TATAG
* * *
94186001 AAA-TATAGAAAAATTATAAAATTTTAT
1 AAATTATAAAAAAATTATAAAATTATAG
*
94186028 AAATTCATAAGAAAATTATAAAA
1 AAATT-ATAAAAAAATTATAAAA
94186051 AAATGTAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
27 6 0.14
28 18 0.43
29 18 0.43
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (28 bp):
AAATTATAAAAAAATTATAAAATTATAG
Found at i:94186051 original size:38 final size:38
Alignment explanation
Indices: 94186004--94186093 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 38
94185994 TATATAGAAA
* *
94186004 TATAGAAAAATTATAAA-ATTTTATAAATTCATAAGAAAAT
1 TATA-AAAAATTATAAAGAATATA-AAATTCATAA-AAAAT
* * *
94186044 TATAAAAAAATGTAAAGAATATAAAATTCGTAAAAAAT
1 TATAAAAAATTATAAAGAATATAAAATTCATAAAAAAT
94186082 TAT-AAAAATTAT
1 TATAAAAAATTAT
94186094 TGTACCAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
37 7 0.17
38 8 0.19
39 19 0.45
40 8 0.19
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (38 bp):
TATAAAAAATTATAAAGAATATAAAATTCATAAAAAAT
Found at i:94186085 original size:19 final size:19
Alignment explanation
Indices: 94186018--94186088 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
94186008 GAAAAATTAT
* *
94186018 AAAATTTTATAAATTCATAA
1 AAAATTATA-AAATTCGTAA
*
94186038 GAAAATTATAAAAAAAT-GTAA
1 -AAAATTAT--AAAATTCGTAA
*
94186059 AGAA-TATAAAATTCGTAA
1 AAAATTATAAAATTCGTAA
94186077 AAAATTATAAAA
1 AAAATTATAAAA
94186089 ATTATTGTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
17 5 0.12
18 7 0.17
19 10 0.25
20 3 0.08
21 10 0.25
22 4 0.10
23 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.30
Consensus pattern (19 bp):
AAAATTATAAAATTCGTAA
Found at i:94186087 original size:10 final size:10
Alignment explanation
Indices: 94185928--94186093 Score: 61
Period size: 9 Copynumber: 17.2 Consensus size: 10
94185918 GTGGTAAAAA
*
94185928 ATAAAAAATA
1 ATAAAAAATT
*
94185938 AT-AAAATTT
1 ATAAAAAATT
94185947 ATAAAAAATAAT
1 ATAAAAAAT--T
* *
94185959 TTAAAAAACT
1 ATAAAAAATT
94185969 -T-AAAAATT
1 ATAAAAAATT
*
94185977 GTAAAAAAATT
1 AT-AAAAAATT
*
94185988 ATAAAATA-T
1 ATAAAAAATT
*
94185997 AT-AGAAA-T
1 ATAAAAAATT
94186005 ATAGAAAAATT
1 ATA-AAAAATT
94186016 AT--AAAATT
1 ATAAAAAATT
* *
94186024 -TTATAAATT
1 ATAAAAAATT
94186033 CATAAGAAAATT
1 -ATAA-AAAATT
*
94186045 ATAAAAAAAT
1 ATAAAAAATT
* *
94186055 GTAAAGAA-T
1 ATAAAAAATT
94186064 AT--AAAATT
1 ATAAAAAATT
*
94186072 CGTAAAAAATT
1 -ATAAAAAATT
94186083 AT-AAAAATT
1 ATAAAAAATT
94186092 AT
1 AT
94186094 TGTACCAAAA
Statistics
Matches: 117, Mismatches: 21, Indels: 37
0.67 0.12 0.21
Matches are distributed among these distances:
7 4 0.03
8 19 0.16
9 29 0.25
10 29 0.25
11 23 0.20
12 13 0.11
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:94186284 original size:20 final size:19
Alignment explanation
Indices: 94186259--94186317 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
94186249 TTAAAGGGCC
94186259 TTTTTTATACATTTTATAAT
1 TTTTTTATA-ATTTTATAAT
**
94186279 TTTTTTATGAAAGTTATAATT
1 TTTTTTAT-AATTTTATAA-T
94186300 TTTTTTATAATTTT-TAAT
1 TTTTTTATAATTTTATAAT
94186318 AAAATTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 1 0.03
19 3 0.09
20 19 0.58
21 10 0.30
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTTATAATTTTATAAT
Found at i:94186662 original size:87 final size:86
Alignment explanation
Indices: 94186484--94186713 Score: 189
Period size: 87 Copynumber: 2.6 Consensus size: 86
94186474 TCAAAGGGCC
* * *
94186484 TTTTTGATGTATTTTGACAGTTCAAGTACCCAATTGAATATAAAAAAAAAGTAATGAACTTAATT
1 TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTGAATATAAAAAAAAAGTAATGAACTTAATT
*** *
94186549 TTTTTTTTTAAGTTTGAGGGA
66 TTTTTTAAAAAGTTTAAGGGA
* * * * *
94186570 CTTTTTTATGCATTTTGAAAGTTCAAGTAGCCAATTGAGTGT-AAAAAAAATTAATG-GCTTAAT
1 -TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTGAATATAAAAAAAAAGTAATGAACTTAAT
94186633 TGCTTGTTTTGAAAAAGTTTAAGGG-
65 T--TT-TTTT-AAAAAGTTTAAGGGA
* * * * *
94186658 TTTTTTTTGACATATTTTGAAAGTTTAAATACTCAATT-AAGTACAAAATAAAAAGT
1 TTTTTTATG-C--ATTTTGAAAGTTCAAGTACCCAATTGAA-TATAAAA-AAAAAGT
94186714 GATTAATTGC
Statistics
Matches: 112, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
85 7 0.06
86 13 0.12
87 45 0.40
88 5 0.04
89 11 0.10
90 22 0.20
91 3 0.03
92 6 0.05
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.40
Consensus pattern (86 bp):
TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTGAATATAAAAAAAAAGTAATGAACTTAATT
TTTTTTAAAAAGTTTAAGGGA
Found at i:94187302 original size:12 final size:12
Alignment explanation
Indices: 94187285--94187310 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
94187275 TCAAGAAAAC
94187285 AACAACAACAAT
1 AACAACAACAAT
94187297 AACAACAACAAT
1 AACAACAACAAT
94187309 AA
1 AA
94187311 TAGTAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.23, G:0.00, T:0.08
Consensus pattern (12 bp):
AACAACAACAAT
Found at i:94189931 original size:21 final size:21
Alignment explanation
Indices: 94189890--94190034 Score: 62
Period size: 21 Copynumber: 7.0 Consensus size: 21
94189880 AATAAAGTAG
*
94189890 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
94189911 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
*
94189932 AAATTCATATAATAATATTTA-A-T
1 --ATT-ATAT-ATTATATTTATAGT
* *
94189955 ATTA-AGA--AT-TTTATTA-A
1 ATTATATATTATATTTA-TAGT
*
94189972 ATTATAT-TTAATAATTAT--T
1 ATTATATATT-ATATTTATAGT
* *
94189991 ATTTTAAATTATATTTTATAGT
1 ATTATATATTATA-TTTATAGT
94190013 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
94190034 A
1 A
94190035 AATTCATATA
Statistics
Matches: 94, Mismatches: 12, Indels: 36
0.66 0.08 0.25
Matches are distributed among these distances:
15 4 0.04
16 2 0.02
17 5 0.05
18 2 0.02
19 9 0.10
20 10 0.11
21 27 0.29
22 17 0.18
23 5 0.05
24 9 0.10
25 4 0.04
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:94190004 original size:26 final size:26
Alignment explanation
Indices: 94189968--94190119 Score: 90
Period size: 26 Copynumber: 6.0 Consensus size: 26
94189958 AAGAATTTTA
94189968 TTAAATTATATTTAATAATTATTATT
1 TTAAATTATATTTAATAATTATTATT
*
94189994 TTAAATTATATTT--T-A-TAGTATT
1 TTAAATTATATTTAATAATTATTATT
* * * *
94190016 ATATATTATGATTTTAGTAAATTCA-TATA
1 TTAAATTAT-A-TTTAAT-AATT-ATTATT
* *
94190045 GTAATATT-TAATATTAAGAATT-TTA--
1 TTAA-ATTAT-AT-TTAATAATTATTATT
*
94190070 TTAAATTATATTTAATAATAATTATT
1 TTAAATTATATTTAATAATTATTATT
*
94190096 TTAAATTATATTTTAT-ATTATTAT
1 TTAAATTATATTTAATAATTATTAT
94190120 ATATTATGAT
Statistics
Matches: 97, Mismatches: 14, Indels: 31
0.68 0.10 0.22
Matches are distributed among these distances:
22 13 0.13
23 9 0.09
24 12 0.12
25 11 0.11
26 29 0.30
27 2 0.02
28 6 0.06
29 11 0.11
30 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (26 bp):
TTAAATTATATTTAATAATTATTATT
Found at i:94190139 original size:38 final size:38
Alignment explanation
Indices: 94190097--94190262 Score: 103
Period size: 38 Copynumber: 4.3 Consensus size: 38
94190087 ATAATTATTT
94190097 TAAATTATATTTTATATTATTATATATTATGATTTTAG
1 TAAATTATATTTTATATTATTATATATTATGATTTTAG
* * * *
94190135 TAAATTCATA--TAAGAATATT-TAATATTAAGAATTTTA-
1 TAAATT-ATATTTTATATTATTAT-ATATTATG-ATTTTAG
* **
94190172 TAAATTATATATTT-T-TTAAATTATAT-TTAATAATAATTATTT
1 TAAATTATAT-TTTATATT--ATTATATATT-ATGAT--TT-TAG
* *
94190214 TAAATTAAATTTTATAGTATTATATATTATGATTTTAG
1 TAAATTATATTTTATATTATTATATATTATGATTTTAG
94190252 TAAATTCATAT
1 TAAATT-ATAT
94190263 AAGAATATTT
Statistics
Matches: 94, Mismatches: 16, Indels: 35
0.65 0.11 0.24
Matches are distributed among these distances:
36 4 0.04
37 21 0.22
38 23 0.24
39 15 0.16
40 3 0.03
41 15 0.16
42 12 0.13
43 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (38 bp):
TAAATTATATTTTATATTATTATATATTATGATTTTAG
Found at i:94190185 original size:16 final size:16
Alignment explanation
Indices: 94190166--94190197 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
94190156 AATATTAAGA
94190166 ATTTTATAAATTATAT
1 ATTTTATAAATTATAT
*
94190182 ATTTTTTAAATTATAT
1 ATTTTATAAATTATAT
94190198 TTAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTATAAATTATAT
Found at i:94190191 original size:117 final size:119
Alignment explanation
Indices: 94190064--94190337 Score: 498
Period size: 117 Copynumber: 2.3 Consensus size: 119
94190054 AATATTAAGA
* *
94190064 ATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATATTATTATATATTATGA
1 ATTTTATTAAATTATATTTAATAATAATTATTTTAAATTAAATTTTATAGTATTATATATTATGA
94190129 TTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTA-TAAATTATAT
66 TTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
94190182 ATTTT-TTAAATTATATTTAATAATAATTATTTTAAATTAAATTTTATAGTATTATATATTATGA
1 ATTTTATTAAATTATATTTAATAATAATTATTTTAAATTAAATTTTATAGTATTATATATTATGA
94190246 TTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
66 TTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
*
94190300 ATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
1 A-TTTTATTAAATTATATTTAATAATAATTATTTTAAA
94190338 ATATGATTAA
Statistics
Matches: 150, Mismatches: 3, Indels: 4
0.96 0.02 0.03
Matches are distributed among these distances:
117 100 0.67
118 16 0.11
119 4 0.03
120 30 0.20
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (119 bp):
ATTTTATTAAATTATATTTAATAATAATTATTTTAAATTAAATTTTATAGTATTATATATTATGA
TTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
Found at i:94190201 original size:102 final size:104
Alignment explanation
Indices: 94189897--94190319 Score: 558
Period size: 102 Copynumber: 4.0 Consensus size: 104
94189887 TAGATTATAT
*
94189897 ATTAT-TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAATAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
*
94189961 AATTTTATTAAA-T-TATATTTAAT-AATTATTATTTTAA
66 AATTTTATTAAATTATATATTTATTAAATTA-TATTTTAA
94189998 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATAT-AGTAATATTTAATATTAA
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAG-AATATTTAATATTAA
* *
94190062 GAATTTTATTAAA-T-TATATTTAAT-AATAATTATTTTAA
65 GAATTTTATTAAATTATATATTTATTAAATTA-TATTTTAA
*
94190100 ATTATATTTTATATTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
94190165 AATTTTA-TAAATTATATATTTTTTAAATTATATTTAATAATAATTATTTTAA
66 AATTTTATTAAATTATATA---TTT--A-T-TA---AAT--T-A-TATTTTAA
*
94190217 ATTAAATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
94190282 AATTTTATTAAATTATATATTTTTATTAAATTATATTT
66 AATTTTATTAAATTATATA--TTTATTAAATTATATTT
94190320 AATAATAATT
Statistics
Matches: 295, Mismatches: 7, Indels: 35
0.88 0.02 0.10
Matches are distributed among these distances:
101 10 0.03
102 161 0.55
103 6 0.02
106 8 0.03
107 1 0.00
108 2 0.01
110 4 0.01
113 2 0.01
114 4 0.01
115 1 0.00
117 85 0.29
118 11 0.04
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (104 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
AATTTTATTAAATTATATATTTATTAAATTATATTTTAA
Done.