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 14 of 332
Found at i:4082467 original size:3 final size:3
Alignment explanation
Indices: 4082459--4082824 Score: 112
Period size: 3 Copynumber: 122.3 Consensus size: 3
4082449 ATTTAATATA
* * * *
4082459 TAT TAT TAT TAC TAT CAT TAT T-T TAC TAT TAT T-T AGAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
* * * * *
4082503 TAT TAT TA- TAT TAC TGT TAC T-T TAC TAT T-T AAT ATAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
* * * * *
4082546 TACCT TTT TAT TAT TAT TAC TAC TAT T-G TAT TAT TAC TAT TAT TA-
1 TA--T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
4082591 TAT T-T TCAT CTA- TATT TAT T-T TCT TAT TATT TAT CTAGT TTT TATT
1 TAT TAT T-AT -TAT TA-T TAT TAT TAT TAT TA-T TAT -TA-T TAT TA-T
* *
4082637 TAT CTAT T-T GTAT T-T TGT TAT TAT TA- TAT T-T TAGG TAT TA- TAT
1 TAT -TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * * **
4082680 CT-T TAT T-T ATATT TAT GTAT TAA TAT CAT TATT TAC TAT TGC TA-
1 -TAT TAT TAT -TA-T TAT -TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* *
4082724 TAT T-T T-T TA- TAT TAT TAT TAT TAT CAT TAC TAT TA- TACT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* * * *
4082765 TAT TAC TAC TAC TACGG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TA--T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4082812 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
4082825 TACTTATTTT
Statistics
Matches: 271, Mismatches: 48, Indels: 88
0.67 0.12 0.22
Matches are distributed among these distances:
2 39 0.14
3 193 0.71
4 32 0.12
5 7 0.03
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:4082491 original size:29 final size:29
Alignment explanation
Indices: 4082445--4082591 Score: 73
Period size: 32 Copynumber: 4.7 Consensus size: 29
4082435 TATTAAATTA
* *
4082445 ATTAATTTAATATATATTATTATTACTATC
1 ATTATTTTACTAT-TATTATTATTACTATC
* *
4082475 ATTATTTTACTATTATTTAGATTATTATTATT
1 ATTATTTTACTATTA-TT--ATTATTACTATC
* * * *
4082507 ATTATATTACTGTTACTTTACTATTTAATAT-
1 ATTATTTTACTATTA--TTATTA-TTACTATC
*
4082538 ATTATTATTACCTTTTTATTATTATTACTA-C
1 ATTATT-TTA-C-TATTATTATTATTACTATC
4082569 TATTGTATTATTACTATTATTAT
1 -A-T-TATT-TTACTATTATTAT
4082592 ATTTTCATCT
Statistics
Matches: 92, Mismatches: 13, Indels: 22
0.72 0.10 0.17
Matches are distributed among these distances:
29 2 0.02
30 13 0.14
31 13 0.14
32 46 0.50
33 6 0.07
34 12 0.13
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (29 bp):
ATTATTTTACTATTATTATTATTACTATC
Found at i:4082511 original size:32 final size:33
Alignment explanation
Indices: 4082463--4082526 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
4082453 AATATATATT
*
4082463 ATTATTACTATCATTATTTTACTATTA-TTTAG
1 ATTATTACTATCATTATATTACTATTACTTTAG
* * *
4082495 ATTATTATTATTATTATATTACTGTTACTTTA
1 ATTATTACTATCATTATATTACTATTACTTTA
4082527 CTATTTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (33 bp):
ATTATTACTATCATTATATTACTATTACTTTAG
Found at i:4082562 original size:20 final size:20
Alignment explanation
Indices: 4082459--4082587 Score: 65
Period size: 20 Copynumber: 6.5 Consensus size: 20
4082449 ATTTAATATA
*
4082459 TATTATTATTACTA-T-CAT
1 TATTATTATTACTATTGTAT
* *
4082477 TATT-TTACTATTATT-TA-
1 TATTATTATTACTATTGTAT
* * *
4082494 GATTATTATTATTATTATAT
1 TATTATTATTACTATTGTAT
* *
4082514 TACTGTTACTTTACTATT-TAAT
1 TATTATTA--TTACTATTGT-AT
*
4082536 ATATTATTATTACCT-TTTTAT
1 -TATTATTATTA-CTATTGTAT
*
4082557 TATTATTACTACTATTGTAT
1 TATTATTATTACTATTGTAT
*
4082577 TATTACTATTA
1 TATTATTATTA
4082588 TTATATTTTC
Statistics
Matches: 85, Mismatches: 15, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
17 10 0.12
18 16 0.19
19 4 0.05
20 29 0.34
21 8 0.09
22 12 0.14
23 6 0.07
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTATTATTACTATTGTAT
Found at i:4082577 original size:17 final size:17
Alignment explanation
Indices: 4082557--4082594 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4082547 ACCTTTTTAT
*
4082557 TATTATTACTACTATTG
1 TATTATTACTACTATTA
*
4082574 TATTATTACTATTATTA
1 TATTATTACTACTATTA
4082591 TATT
1 TATT
4082595 TTCATCTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (17 bp):
TATTATTACTACTATTA
Found at i:4082685 original size:25 final size:26
Alignment explanation
Indices: 4082656--4082719 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
4082646 GTATTTTGTT
4082656 ATTA-TTATATTTTAGGTATT-ATATC
1 ATTATTTATA-TTTAGGTATTAATATC
* *
4082681 TTTATTTATATTTATGTATTAATATC
1 ATTATTTATATTTAGGTATTAATATC
4082707 ATTATTTACTATT
1 ATTATTTA-TATT
4082720 GCTATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 12 0.36
26 17 0.52
27 4 0.12
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (26 bp):
ATTATTTATATTTAGGTATTAATATC
Found at i:4082871 original size:26 final size:27
Alignment explanation
Indices: 4082791--4082892 Score: 73
Period size: 26 Copynumber: 3.6 Consensus size: 27
4082781 GTATTATTAT
* * *
4082791 TATTATTATTATTATTATTATTATTATTAT
1 TATTTTTATTTTTATT-TTATT-TTATT-C
4082821 TATTTACTTATTTTT-TGTTTATTTTATTC
1 TATTT--TTATTTTTAT-TTTATTTTATTC
*
4082850 TATTTTTATTTTTATTTT-TTTTCTTC
1 TATTTTTATTTTTATTTTATTTTATTC
* *
4082876 TCTTTTTCTTTCTTATT
1 TATTTTTATTT-TTATT
4082893 GATTTGTTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
26 16 0.26
27 16 0.26
28 1 0.02
29 5 0.08
30 9 0.15
31 6 0.10
32 8 0.13
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.74
Consensus pattern (27 bp):
TATTTTTATTTTTATTTTATTTTATTC
Found at i:4082886 original size:6 final size:6
Alignment explanation
Indices: 4082784--4082868 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
4082774 TACTACGGTA
* * * * * *
4082784 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTT ACTTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT --TTATTT
* *
4082834 TT-TGT TTA-TT TTA-TT CTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TT
4082869 TTTCTTCTCT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
5 12 0.17
6 52 0.74
8 6 0.09
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.73
Consensus pattern (6 bp):
TTATTT
Found at i:4085254 original size:19 final size:19
Alignment explanation
Indices: 4085230--4085284 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
4085220 CATTAAATCG
4085230 TGACTTGATCTTGAATAGT
1 TGACTTGATCTTGAATAGT
*
4085249 TGACTT-A-----AATCG-
1 TGACTTGATCTTGAATAGT
4085261 TGACTTGATCTTGAATAGT
1 TGACTTGATCTTGAATAGT
4085280 TGACT
1 TGACT
4085285 ATGTTATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 14
0.63 0.05 0.33
Matches are distributed among these distances:
12 6 0.22
13 5 0.19
18 5 0.19
19 11 0.41
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (19 bp):
TGACTTGATCTTGAATAGT
Found at i:4085260 original size:31 final size:31
Alignment explanation
Indices: 4085222--4085284 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4085212 ATTTTCGACA
4085222 TTAAATCGTGACTTGATCTTGAATAGTTGAC
1 TTAAATCGTGACTTGATCTTGAATAGTTGAC
4085253 TTAAATCGTGACTTGATCTTGAATAGTTGAC
1 TTAAATCGTGACTTGATCTTGAATAGTTGAC
4085284 T
1 T
4085285 ATGTTATGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.40
Consensus pattern (31 bp):
TTAAATCGTGACTTGATCTTGAATAGTTGAC
Found at i:4106692 original size:35 final size:33
Alignment explanation
Indices: 4106628--4106705 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 33
4106618 ACAATAATAA
* *
4106628 ATATTTTATAAAATAATTTGATATTAATATTTAT
1 ATATTTTATAAAATAATTTAATATAAATA-TTAT
*
4106662 ATATTTTATAAATTAAATTTAA-ATAAAATATTAT
1 ATATTTTATAAAAT-AATTTAATAT-AAATATTAT
4106696 -TATTTT-TAAA
1 ATATTTTATAAA
4106706 CAATAGTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
32 4 0.10
33 6 0.15
34 19 0.49
35 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (33 bp):
ATATTTTATAAAATAATTTAATATAAATATTAT
Found at i:4118937 original size:92 final size:95
Alignment explanation
Indices: 4118814--4119034 Score: 269
Period size: 92 Copynumber: 2.3 Consensus size: 95
4118804 ACATTATGAG
* * *
4118814 AGCCAGTATAAGACCATGTCTGGGACATGGCATTGGCATTGATACTAGA-GT-T-AGTGTAAGA-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CG-TA-TAGAGGTGTCAGTGTAAGAC
4118875 CATGTCT-GAGACAT-GCATCGGCTAC-GAGATGT
63 CATGTCTAG-GACATGGCATCGGC-ACGGAGATGT
*
4118907 -GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTCAGTGTAAGACCAT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTCAGTGTAAGACCAT
4118971 GTCTAGGACATGGCATCGGCACGGAGATGT
66 GTCTAGGACATGGCATCGGCACGGAGATGT
*
4119001 GAAAGCCAATGTAAGACCATGTCTGGGACATGGC
1 ---AGCCAGTGTAAGACCATGTCTGGGACATGGC
4119035 GTTAACCTCG
Statistics
Matches: 111, Mismatches: 6, Indels: 17
0.83 0.04 0.13
Matches are distributed among these distances:
89 4 0.04
90 4 0.04
91 2 0.02
92 43 0.39
93 14 0.13
94 16 0.14
98 28 0.25
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (95 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTCAGTGTAAGACCAT
GTCTAGGACATGGCATCGGCACGGAGATGT
Found at i:4118966 original size:48 final size:48
Alignment explanation
Indices: 4118817--4119034 Score: 209
Period size: 48 Copynumber: 4.6 Consensus size: 48
4118807 TTATGAGAGC
* * *
4118817 CAGTATAAGACCATGTCTGGGACATGGCATTGGCATTGATACTAGA-GT-T
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CG-TA-TAGAGGTGT
* *
4118866 -AGTGTAAGA-CATGTCTGAGACAT-GCATCGGCTACG---AGATGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGTATAGAGGTGT
4118909 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
* * * * ** *
4118957 CAGTGTAAGACCATGTCTAGGACATGGCATCGGCACGGAGATGTGAAAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATA-GAG-GTGT
*
4119007 CAATGTAAGACCATGTCTGGGACATGGC
1 CAGTGTAAGACCATGTCTGGGACATGGC
4119035 GTTAACCTCG
Statistics
Matches: 143, Mismatches: 15, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
41 3 0.02
42 2 0.01
43 1 0.01
44 9 0.06
45 16 0.11
46 16 0.11
47 14 0.10
48 53 0.37
49 2 0.01
50 27 0.19
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.23
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
Found at i:4130384 original size:15 final size:16
Alignment explanation
Indices: 4130364--4130393 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4130354 GGGTTAATGA
4130364 TAAATTAAA-TAAAAT
1 TAAATTAAATTAAAAT
4130379 TAAATTAAATTAAAA
1 TAAATTAAATTAAAA
4130394 ATATTCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAATTAAATTAAAAT
Found at i:4131420 original size:6 final size:6
Alignment explanation
Indices: 4131409--4131439 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
4131399 CCAGAACAAC
4131409 AAGAAA AAGAAA AAGAAA AAGAAA AA-AAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AA
4131440 CACTGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:4152221 original size:16 final size:16
Alignment explanation
Indices: 4152197--4152234 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4152187 ACATTCATAA
4152197 TTATAAAA-TACATTAT
1 TTATAAAATTA-ATTAT
*
4152213 TTATTAAATTAATTAT
1 TTATAAAATTAATTAT
4152229 TTATAA
1 TTATAA
4152235 CAACACATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATAAAATTAATTAT
Found at i:4156914 original size:18 final size:18
Alignment explanation
Indices: 4156891--4156930 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
4156881 TATTATTTTA
*
4156891 AAAAATA-TATAATACATC
1 AAAAATACTA-AAAACATC
4156909 AAAAATACTAAAAACATC
1 AAAAATACTAAAAACATC
4156927 AAAA
1 AAAA
4156931 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATACTAAAAACATC
Found at i:4157056 original size:29 final size:30
Alignment explanation
Indices: 4157014--4157073 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
4157004 CTTAACAGGT
*
4157014 AAATGCCTCTAAAATAATAA-AAATTTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
*
4157043 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
4157073 A
1 A
4157074 TGAAAATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:4163627 original size:11 final size:11
Alignment explanation
Indices: 4163613--4163651 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
4163603 GAAGCTCACC
4163613 AGAAAAAAAAA
1 AGAAAAAAAAA
*
4163624 AGAAAAAAGAA
1 AGAAAAAAAAA
*
4163635 AG-AAAACAAA
1 AGAAAAAAAAA
4163645 AGAAAAA
1 AGAAAAA
4163652 GGACAACCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:4163631 original size:10 final size:10
Alignment explanation
Indices: 4163616--4163651 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
4163606 GCTCACCAGA
4163616 AAAAAAAAAG
1 AAAAAAAAAG
4163626 AAAAAAGAAAG
1 AAAAAA-AAAG
*
4163637 AAAACAAAAG
1 AAAAAAAAAG
4163647 AAAAA
1 AAAAA
4163652 GGACAACCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:4167366 original size:20 final size:20
Alignment explanation
Indices: 4167320--4167366 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
4167310 TATTTAAATT
*
4167320 AAATTTAATGTAAATTATCA
1 AAATTTAATGAAAATTATCA
* *
4167340 TATTTTAATGAAATATTA-CA
1 AAATTTAATGAAA-ATTATCA
4167360 AAATTTA
1 AAATTTA
4167367 TGACAAAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (20 bp):
AAATTTAATGAAAATTATCA
Found at i:4181874 original size:12 final size:12
Alignment explanation
Indices: 4181859--4181885 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4181849 TTATTTGTTT
4181859 TTTGTTTTAATA
1 TTTGTTTTAATA
4181871 TTTGTTTTAATA
1 TTTGTTTTAATA
4181883 TTT
1 TTT
4181886 TTAGATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTGTTTTAATA
Found at i:4183819 original size:4 final size:4
Alignment explanation
Indices: 4183810--4183835 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4183800 TGTGTTGTTA
4183810 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
4183836 CCTATGACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:4194478 original size:20 final size:22
Alignment explanation
Indices: 4194453--4194495 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4194443 ATTGTCCAAA
*
4194453 TTAATTT-TTTA-TGTATAATT
1 TTAATTTGTTTATTGAATAATT
4194473 TTAATTTGTTTATTGAATAATT
1 TTAATTTGTTTATTGAATAATT
4194495 T
1 T
4194496 CATTATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 4 0.20
22 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
TTAATTTGTTTATTGAATAATT
Found at i:4195466 original size:16 final size:17
Alignment explanation
Indices: 4195437--4195468 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4195427 GAGAAATATA
4195437 AATAGAATAGAAAGAGC
1 AATAGAATAGAAAGAGC
4195454 AATAGAA-AGAAAGAG
1 AATAGAATAGAAAGAG
4195469 GAAGGCGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.62, C:0.03, G:0.25, T:0.09
Consensus pattern (17 bp):
AATAGAATAGAAAGAGC
Found at i:4205519 original size:2 final size:2
Alignment explanation
Indices: 4205512--4205541 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
4205502 TGATTCGAAT
4205512 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
4205542 GATTGAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4206285 original size:19 final size:20
Alignment explanation
Indices: 4206256--4206307 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
4206246 AAAATATAAT
4206256 TTTTGGAATTTTT-ATAAA-TA
1 TTTT-GAATTTTTGA-AAATTA
4206276 TTTTGAATTTTTGAAAATTA
1 TTTTGAATTTTTGAAAATTA
4206296 TTTTGAATTTTT
1 TTTTGAATTTTT
4206308 TTTATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (20 bp):
TTTTGAATTTTTGAAAATTA
Found at i:4206287 original size:20 final size:20
Alignment explanation
Indices: 4206242--4206308 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
4206232 TTTATATATA
4206242 TTTTAAAATATAATTTTTGGAA-T
1 TTTTAAAAT-T-A-TTTT-GAATT
4206265 TTTTATAAA-TATTTTGAATT
1 TTTTA-AAATTATTTTGAATT
*
4206285 TTTGAAAATTATTTTGAATT
1 TTTTAAAATTATTTTGAATT
4206305 TTTT
1 TTTT
4206309 TTATAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 6 0.15
20 23 0.59
21 1 0.03
22 1 0.03
23 5 0.13
24 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.58
Consensus pattern (20 bp):
TTTTAAAATTATTTTGAATT
Found at i:4206319 original size:20 final size:20
Alignment explanation
Indices: 4206250--4206320 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
4206240 TATTTTAAAA
*
4206250 TATAAT-TTTTGGAATTTTTA
1 TATAATATTTT-GAATTTTTT
4206270 TA-AATATTTTGAA-TTTTT
1 TATAATATTTTGAATTTTTT
* *
4206288 GAAAATTATTTTGAATTTTTTT
1 TATAA-TATTTTGAA-TTTTTT
4206310 TATAAT-TTTTG
1 TATAATATTTTG
4206321 TTGAGAGACT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 5 0.12
19 8 0.19
20 20 0.48
21 1 0.02
22 8 0.19
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (20 bp):
TATAATATTTTGAATTTTTT
Found at i:4207171 original size:18 final size:18
Alignment explanation
Indices: 4207145--4207180 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4207135 AAAATTGTAA
4207145 TAAAAATATTTATAAAAT
1 TAAAAATATTTATAAAAT
*
4207163 TAAATATATTTATAAAAT
1 TAAAAATATTTATAAAAT
4207181 CTTATAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAAATATTTATAAAAT
Found at i:4208972 original size:26 final size:26
Alignment explanation
Indices: 4208924--4208977 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
4208914 TTGATTGCAG
* *
4208924 TAGTTGATTTGATCAATTGATTCTAT
1 TAGTTGATTTGATCAACTAATTCTAT
* *
4208950 TAGTTTATTTGATGAACTAATTCTAT
1 TAGTTGATTTGATCAACTAATTCTAT
4208976 TA
1 TA
4208978 ATTGTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (26 bp):
TAGTTGATTTGATCAACTAATTCTAT
Found at i:4218349 original size:9 final size:9
Alignment explanation
Indices: 4218335--4218399 Score: 103
Period size: 9 Copynumber: 7.2 Consensus size: 9
4218325 TTTGGTTAAA
4218335 AATTACCCG
1 AATTACCCG
4218344 AATTACCCG
1 AATTACCCG
4218353 AATTACCCG
1 AATTACCCG
*
4218362 AATTACCCA
1 AATTACCCG
4218371 AATTACCCG
1 AATTACCCG
*
4218380 AATTAACCG
1 AATTACCCG
*
4218389 AATTAACCG
1 AATTACCCG
4218398 AA
1 AA
4218400 AAATACCCGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.40, C:0.29, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:4218374 original size:27 final size:27
Alignment explanation
Indices: 4218335--4218412 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
4218325 TTTGGTTAAA
* *
4218335 AATTACCCGAATTACCCGAATTACCCG
1 AATTACCCAAATTACCCGAATTAACCG
4218362 AATTACCCAAATTACCCGAATTAACCG
1 AATTACCCAAATTACCCGAATTAACCG
* *
4218389 AATTAACCGAAAAATACCCGAATT
1 AATT-ACC-CAAATTACCCGAATT
4218413 TTTTTTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 29 0.64
28 3 0.07
29 13 0.29
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.22
Consensus pattern (27 bp):
AATTACCCAAATTACCCGAATTAACCG
Found at i:4218948 original size:5 final size:5
Alignment explanation
Indices: 4218938--4218989 Score: 104
Period size: 5 Copynumber: 10.4 Consensus size: 5
4218928 ATGGGGGTAA
4218938 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
4218988 GA
1 GA
4218990 AATGTGCTAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
GATAT
Found at i:4226138 original size:31 final size:31
Alignment explanation
Indices: 4226102--4226164 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
4226092 TAAATTTTGG
* **
4226102 ATTAATT-GAAATAAATTATTTTATTTTTTTA
1 ATTAATTCG-AATAAATAATTAAATTTTTTTA
4226133 ATTAATTCGAATAAATAATTAAATTTTTTTA
1 ATTAATTCGAATAAATAATTAAATTTTTTTA
4226164 A
1 A
4226165 GGTGAGTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTAATTCGAATAAATAATTAAATTTTTTTA
Found at i:4228987 original size:179 final size:177
Alignment explanation
Indices: 4228677--4229005 Score: 464
Period size: 179 Copynumber: 1.8 Consensus size: 177
4228667 ACATGACCAT
* * *
4228677 CAGGAACAGTGAGCGGCAGCAACGGAAAGTTCACATCAAAGATAAATGAAATCCATATACGGTAA
1 CAGGAACAGTGAGCGGCAGCAACGGAAAGTTAACATCAAAGAAAAATGAAATCCATATACGCTAA
** *
4228742 GTATAATCATAATTAAAAATGAAATCCAAATATGCTTTTTCAAATGACCAAACCTTAATAAAAGG
66 GTATAATCATAATTAAAAATGAAATCCAAATACACTTTTTCAAATGACCAAACCTCAATAAAAGG
*
4228807 GAAAAAGATTTAATC-TAAATCCAATTAATCTTAAATTGGAAGTGCAA
131 GAAAAA-AGTTAATCTTAAATCCAATTAATCTTAAATTGGAAGTGCAA
* *
4228854 CAGGAACAGTGAGAGCGGCAGCAACAGG-AAGTTAATATCAAAGAAAAATGAAATCCATATATGC
1 CAGGAACAGT--GAGCGGCAGCAAC-GGAAAGTTAACATCAAAGAAAAATGAAATCCATATACGC
* * ** ** *
4228918 TGAGTATAATCATAATTAAAACTGAAATCCGTATACACTTTTTTGAATGACCAAACCTCACTAAA
63 TAAGTATAATCATAATTAAAAATGAAATCCAAATACACTTTTTCAAATGACCAAACCTCAATAAA
4228983 AGGGAAAAAAGTTAATCTTAAAT
128 AGGGAAAAAAGTTAATCTTAAAT
4229006 TAAGATGTAG
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
177 10 0.08
178 7 0.05
179 113 0.86
180 2 0.02
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (177 bp):
CAGGAACAGTGAGCGGCAGCAACGGAAAGTTAACATCAAAGAAAAATGAAATCCATATACGCTAA
GTATAATCATAATTAAAAATGAAATCCAAATACACTTTTTCAAATGACCAAACCTCAATAAAAGG
GAAAAAAGTTAATCTTAAATCCAATTAATCTTAAATTGGAAGTGCAA
Found at i:4230604 original size:144 final size:143
Alignment explanation
Indices: 4230338--4230608 Score: 317
Period size: 144 Copynumber: 1.9 Consensus size: 143
4230328 CTCGGATGTA
* ** * * * *
4230338 GTTCTTCATCTTAGTTTCCTTGAGTAAATCTTTCTCTTTGATTAAACCACGCACCAAATTAGTAT
1 GTTCTTCATCTCAACTTCCTTGAGTAAATCTTTATCTTTAATTAAACCACACACCAAATTAGCAT
* * * *** * * * **
4230403 TACAGTCTCCTTTTTGGCACTTGTGATGGCGGATAACAATCATTCACACGGTATTAGAAGGTATT
66 CAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCATTCACACGACATTAGAAGGTATT
4230468 ACTCTGAATTGTT
131 ACTCTGAATTGTT
* * *
4230481 GTTCTTCATCTCAACTTCCTTGAGTAATTTCTTTATCTTTAATTAAACCGCACACCAAATTGGCA
1 GTTCTTCATCTCAACTTCCTTGAGTAA-ATCTTTATCTTTAATTAAACCACACACCAAATTAGCA
* * *
4230546 TCAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCCTTCACATGACCTTAGAAGGT
65 TCAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCATTCACACGACATTAGAAGGT
4230609 TGGAAGAGTT
Statistics
Matches: 103, Mismatches: 24, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
143 24 0.23
144 79 0.77
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (143 bp):
GTTCTTCATCTCAACTTCCTTGAGTAAATCTTTATCTTTAATTAAACCACACACCAAATTAGCAT
CAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCATTCACACGACATTAGAAGGTATT
ACTCTGAATTGTT
Found at i:4238553 original size:14 final size:14
Alignment explanation
Indices: 4238536--4238573 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
4238526 GCTTTTGTCA
4238536 ATGCACTTTTCTTG
1 ATGCACTTTTCTTG
4238550 ATGCACTTTTCTTG
1 ATGCACTTTTCTTG
4238564 ATGCACTTTT
1 ATGCACTTTT
4238574 TAAAATTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.50
Consensus pattern (14 bp):
ATGCACTTTTCTTG
Found at i:4241953 original size:20 final size:22
Alignment explanation
Indices: 4241909--4241954 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
4241899 CTTTAGTATC
* *
4241909 ATTTTTATTTGTTTTAATATTT
1 ATTTTTATGTGTTTTAATATAT
4241931 ATTTTTATGT-TTTTAA-ATAT
1 ATTTTTATGTGTTTTAATATAT
4241951 ATTT
1 ATTT
4241955 GATTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 6 0.27
22 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (22 bp):
ATTTTTATGTGTTTTAATATAT
Found at i:4241971 original size:26 final size:24
Alignment explanation
Indices: 4241925--4241984 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
4241915 ATTTGTTTTA
*
4241925 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
4241949 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
4241975 TTTTTTATTT
1 ATATTTATTT
4241985 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:4242104 original size:41 final size:41
Alignment explanation
Indices: 4242047--4242138 Score: 184
Period size: 41 Copynumber: 2.2 Consensus size: 41
4242037 AATTTTATTT
4242047 CGGGCCGGGCTTGGACAAAATTTTAGGCCCATATTTCAGGC
1 CGGGCCGGGCTTGGACAAAATTTTAGGCCCATATTTCAGGC
4242088 CGGGCCGGGCTTGGACAAAATTTTAGGCCCATATTTCAGGC
1 CGGGCCGGGCTTGGACAAAATTTTAGGCCCATATTTCAGGC
4242129 CGGGCCGGGC
1 CGGGCCGGGC
4242139 CCGGGCCTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.22
Consensus pattern (41 bp):
CGGGCCGGGCTTGGACAAAATTTTAGGCCCATATTTCAGGC
Found at i:4242307 original size:54 final size:53
Alignment explanation
Indices: 4242228--4242397 Score: 200
Period size: 54 Copynumber: 3.2 Consensus size: 53
4242218 CCATGGCAAC
* *
4242228 AAGTGATAAGTGATATCCGTATAAGACCATAGCTAGGCTATGGCATCGGAAAA
1 AAGTGATAAGCGATATCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAA
* * * **
4242281 CAAGTGATAAGCGATATCAGTATAAGACCATAACTGGGCTATGGCTTCGGATTA
1 -AAGTGATAAGCGATATCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAA
* * * *
4242335 AAGTGAT-A-CAAGTGATCCGTATAAGACCATAGTTGGGCTATGGAATCGGAGAA
1 AAGTGATAAGCGA-T-ATCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAA
4242388 AAGTGATAAG
1 AAGTGATAAG
4242398 TGCTCCCGTG
Statistics
Matches: 97, Mismatches: 15, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
51 2 0.02
52 2 0.02
53 46 0.47
54 47 0.48
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (53 bp):
AAGTGATAAGCGATATCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAA
Found at i:4242362 original size:53 final size:51
Alignment explanation
Indices: 4242228--4242417 Score: 200
Period size: 53 Copynumber: 3.6 Consensus size: 51
4242218 CCATGGCAAC
*
4242228 AAGTGATAAGTGATATCCGTATAAGACCATAGCTAGGCTATGGCATCGGAAAA
1 AAGTGATAAGTG--ATCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAA
* * * * **
4242281 CAAGTGATAAGCGATATCAGTATAAGACCATAACTGGGCTATGGCTTCGGATTA
1 -AAGTGATAAGTG--ATCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAA
* * *
4242335 AAGTGATACAAGTGATCCGTATAAGACCATAGTTGGGCTATGGAATCGGAGAA
1 AAGTGAT--AAGTGATCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAA
* *
4242388 AAGTGATAAGTGCTCCCGTGTAAGACCATA
1 AAGTGATAAGTGAT-CCGTATAAGACCATA
4242418 TCGGGATATG
Statistics
Matches: 116, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
51 6 0.05
52 14 0.12
53 46 0.40
54 46 0.40
55 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (51 bp):
AAGTGATAAGTGATCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAA
Found at i:4242432 original size:51 final size:52
Alignment explanation
Indices: 4242228--4242433 Score: 145
Period size: 54 Copynumber: 3.9 Consensus size: 52
4242218 CCATGGCAAC
* * * *
4242228 AAGTGAT-AAGTGATATCCGTATAAGACCATAG-CTAGGCTATGGCATCGGAAAA
1 AAGTGATAAAGTG--ATCCGTATAAGACCATAGTC-GGGATATGGAATCGGAGAA
* * * * ** **
4242281 CAAGTGAT-AAGCGATATCAGTATAAGACCATA-ACTGGGCTATGGCTTCGGATTA
1 -AAGTGATAAAGTG--ATCCGTATAAGACCATAGTC-GGGATATGGAATCGGAGAA
* *
4242335 AAGTGATACAAGTGATCCGTATAAGACCATAGTTGGGCTATGGAATCGGAGAA
1 AAGTGATA-AAGTGATCCGTATAAGACCATAGTCGGGATATGGAATCGGAGAA
* *
4242388 AAGTGAT-AAGTGCTCCCGTGTAAGACCATA-TCGGGATATGGAATCG
1 AAGTGATAAAGTGAT-CCGTATAAGACCATAGTCGGGATATGGAATCG
4242434 ATATGATATA
Statistics
Matches: 129, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
51 20 0.16
52 14 0.11
53 45 0.35
54 46 0.36
55 4 0.03
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (52 bp):
AAGTGATAAAGTGATCCGTATAAGACCATAGTCGGGATATGGAATCGGAGAA
Found at i:4253954 original size:25 final size:24
Alignment explanation
Indices: 4253918--4253966 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
4253908 GAAAAGTAAC
*
4253918 TTATAAATATATTTTATTTATTTTT
1 TTATAAATATATTTTAGTT-TTTTT
4253943 TTATGAAA-ATATTTTAGTTTTTTT
1 TTAT-AAATATATTTTAGTTTTTTT
4253967 AATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 14 0.64
26 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TTATAAATATATTTTAGTTTTTTT
Found at i:4257363 original size:19 final size:17
Alignment explanation
Indices: 4257339--4257373 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
4257329 TATTATATGA
4257339 TGAATTGATGAATTGATGT
1 TGAATTGA-GAA-TGATGT
4257358 TGAATTGAGAATGATG
1 TGAATTGAGAATGATG
4257374 GAATGTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (17 bp):
TGAATTGAGAATGATGT
Found at i:4260414 original size:34 final size:35
Alignment explanation
Indices: 4260356--4260422 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
4260346 CAAACACCAG
4260356 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
4260391 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
4260423 CATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:4260674 original size:17 final size:17
Alignment explanation
Indices: 4260654--4260693 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
4260644 ATATAAATGT
4260654 GATTTGGCTATAAGGTA
1 GATTTGGCTATAAGGTA
4260671 GATTTGGCTATAAGGTA
1 GATTTGGCTATAAGGTA
4260688 GATTTG
1 GATTTG
4260694 ATATGAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.28, C:0.05, G:0.30, T:0.38
Consensus pattern (17 bp):
GATTTGGCTATAAGGTA
Found at i:4264456 original size:17 final size:16
Alignment explanation
Indices: 4264428--4264459 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
4264418 TCACTCTAAT
4264428 ATTAAATTAATATTAG
1 ATTAAATTAATATTAG
4264444 ATTAAATTTAATATTA
1 ATTAAA-TTAATATTA
4264460 AATGTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTAAATTAATATTAG
Found at i:4272094 original size:3 final size:3
Alignment explanation
Indices: 4272086--4272127 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
4272076 CCGTCATGGA
* * *
4272086 GAT GAT GAT GGT GAT AAT GAT GAT GTT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
4272128 TGGTTCAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (3 bp):
GAT
Found at i:4277014 original size:25 final size:24
Alignment explanation
Indices: 4276986--4277051 Score: 80
Period size: 23 Copynumber: 2.7 Consensus size: 24
4276976 TTTGAAATGC
*
4276986 ATATTTGAAATGTTTTATAATATAT
1 ATATTTGAAATATTTT-TAATATAT
*
4277011 ATATTTTAAA-ATTTTTAATATAT
1 ATATTTGAAATATTTTTAATATAT
*
4277034 ATTTTTGAAATTATTTTT
1 ATATTTGAAA-TATTTTT
4277052 TAAAATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 16 0.46
24 4 0.11
25 15 0.43
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (24 bp):
ATATTTGAAATATTTTTAATATAT
Found at i:4277039 original size:13 final size:13
Alignment explanation
Indices: 4277021--4277127 Score: 63
Period size: 13 Copynumber: 8.8 Consensus size: 13
4277011 ATATTTTAAA
4277021 ATTTTTAATATAT
1 ATTTTTAATATAT
4277034 ATTTTTGAA-AT-T
1 ATTTTT-AATATAT
*
4277046 ATTTTT--TA-AA
1 ATTTTTAATATAT
*
4277056 ATTTTAAATAT-T
1 ATTTTTAATATAT
*
4277068 ATTTTT--TA-AA
1 ATTTTTAATATAT
*
4277078 ATTTTAAATATAT
1 ATTTTTAATATAT
*
4277091 -TTTTTAAAATTTAT
1 ATTTTT--AATATAT
*
4277105 ATGTTTAATATAT
1 ATTTTTAATATAT
4277118 ATTTTTAATA
1 ATTTTTAATA
4277128 GGTAAAGACA
Statistics
Matches: 69, Mismatches: 12, Indels: 26
0.64 0.11 0.24
Matches are distributed among these distances:
10 13 0.19
12 20 0.29
13 24 0.35
14 8 0.12
15 4 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
ATTTTTAATATAT
Found at i:4277059 original size:22 final size:20
Alignment explanation
Indices: 4277036--4277102 Score: 98
Period size: 21 Copynumber: 3.1 Consensus size: 20
4277026 TAATATATAT
4277036 TTTTGAAATTATTTTTTAAAA
1 TTTT-AAATTATTTTTTAAAA
4277057 TTTTAAATATTATTTTTTAAAA
1 TTTT-AA-ATTATTTTTTAAAA
4277079 TTTTAAATATATTTTTTAAAA
1 TTTTAAAT-TATTTTTTAAAA
4277100 TTT
1 TTT
4277103 ATATGTTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
20 2 0.05
21 23 0.53
22 18 0.42
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (20 bp):
TTTTAAATTATTTTTTAAAA
Found at i:4277072 original size:21 final size:22
Alignment explanation
Indices: 4277043--4277102 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
4277033 TATTTTTGAA
4277043 ATTATTTTTTAAAATTTTAAAT
1 ATTATTTTTTAAAATTTTAAAT
4277065 ATTATTTTTTAAAATTTTAAAT
1 ATTATTTTTTAAAATTTTAAAT
4277087 A-TATTTTTTAAAATTT
1 ATTATTTTTTAAAATTT
4277103 ATATGTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 15 0.39
22 23 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTATTTTTTAAAATTTTAAAT
Found at i:4277074 original size:35 final size:35
Alignment explanation
Indices: 4277014--4277080 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
4277004 AATATATATA
* *
4277014 TTTTAAAATTTTTAATATATATTTTTGAAATTATT
1 TTTTAAAATTTTAAATATATATTTTTAAAATTATT
4277049 TTTTAAAATTTTAAATAT-TATTTTTTAAAATT
1 TTTTAAAATTTTAAATATATA-TTTTTAAAATT
4277081 TTAAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 2 0.07
35 27 0.93
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (35 bp):
TTTTAAAATTTTAAATATATATTTTTAAAATTATT
Found at i:4277294 original size:12 final size:11
Alignment explanation
Indices: 4277226--4277295 Score: 55
Period size: 9 Copynumber: 6.7 Consensus size: 11
4277216 AATTTTAAAA
4277226 TTTTAATATA-
1 TTTTAATATAT
4277236 -TTTAATATAT
1 TTTTAATATAT
*
4277246 TTTTAAAAATAT
1 TTTT-AATATAT
4277258 ATTTTAA-A-A-
1 -TTTTAATATAT
4277267 TTTTAATATA-
1 TTTTAATATAT
4277277 -TTTAATATATT
1 TTTTAATATA-T
4277288 TTTTAATA
1 TTTTAATA
4277296 GGAAAAGAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
8 6 0.12
9 19 0.38
10 2 0.04
11 4 0.08
12 15 0.30
13 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:4277368 original size:16 final size:17
Alignment explanation
Indices: 4277314--4277383 Score: 70
Period size: 17 Copynumber: 4.0 Consensus size: 17
4277304 GAAAAAATAT
*
4277314 TTTTTAATATATTTAAAA
1 TTTTAAATATA-TTAAAA
*
4277332 TTTTAAA-AAACTTAAAAA
1 TTTTAAATATA-TT-AAAA
*
4277350 ATTTAAATATATTAAAA
1 TTTTAAATATATTAAAA
*
4277367 TTTTAAATATGTTAAAA
1 TTTTAAATATATTAAAA
4277384 GAAAATGTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
17 23 0.53
18 18 0.42
19 2 0.05
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTTAAATATATTAAAA
Found at i:4277961 original size:23 final size:24
Alignment explanation
Indices: 4277920--4277970 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
4277910 CATATCTTTA
*
4277920 AAAATAATATATTTTAAATAATT-T
1 AAAATAATATATTTCAAAT-ATTAT
*
4277944 AAAATCATA-ATTTCAAATATTAT
1 AAAATAATATATTTCAAATATTAT
4277967 AAAA
1 AAAA
4277971 CAAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 3 0.12
23 13 0.54
24 8 0.33
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATAATATATTTCAAATATTAT
Found at i:4278000 original size:20 final size:20
Alignment explanation
Indices: 4277975--4278014 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4277965 ATAAAACAAA
*
4277975 TTAAAAAAAATATTTAAAAT
1 TTAAAAAAAACATTTAAAAT
* *
4277995 TTAAAATATACATTTAAAAT
1 TTAAAAAAAACATTTAAAAT
4278015 ATTATAAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAAAAAAACATTTAAAAT
Found at i:4278091 original size:21 final size:20
Alignment explanation
Indices: 4278065--4278169 Score: 81
Period size: 21 Copynumber: 5.2 Consensus size: 20
4278055 CAATATTTAA
*
4278065 ATATTTTATATTATTAAAAAT
1 ATATTTAATATT-TTAAAAAT
*
4278086 ATATTTAATATTTAAAAAAT
1 ATATTTAATATTTTAAAAAT
* *
4278106 AATATTTAAAATTTTAAAAAA
1 -ATATTTAATATTTTAAAAAT
* * *
4278127 ATAATTTAA-A--ATATATAT
1 AT-ATTTAATATTTTAAAAAT
*
4278145 ATATTTAAAATTTTAAAAAAT
1 ATATTTAATATTTT-AAAAAT
4278166 ATAT
1 ATAT
4278170 ATTATAAAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
17 6 0.09
18 7 0.11
20 11 0.17
21 42 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTTAATATTTTAAAAAT
Found at i:4278160 original size:25 final size:24
Alignment explanation
Indices: 4278131--4278178 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
4278121 AAAAAAATAA
4278131 TTTAAAATATATATATATT-TAAAAT
1 TTTAAAA-A-ATATATATTATAAAAT
4278156 TTTAAAAAATATATATTATAAAA
1 TTTAAAAAATATATATTATAAAA
4278179 CATTTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 6 0.27
25 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TTTAAAAAATATATATTATAAAAT
Found at i:4278247 original size:9 final size:9
Alignment explanation
Indices: 4278229--4278282 Score: 58
Period size: 9 Copynumber: 6.0 Consensus size: 9
4278219 AAATAAGGAT
4278229 AAAG-AAAA
1 AAAGTAAAA
4278237 AAAGTAAAAAA
1 AAAGT--AAAA
4278248 AAAGTAAAA
1 AAAGTAAAA
**
4278257 AACTTAAAA
1 AAAGTAAAA
4278266 AAAGTAAAA
1 AAAGTAAAA
4278275 AAAG-AAAA
1 AAAGTAAAA
4278283 GAAAAAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 8 0.21
9 22 0.56
11 9 0.23
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (9 bp):
AAAGTAAAA
Found at i:4278277 original size:11 final size:11
Alignment explanation
Indices: 4278233--4278258 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4278223 AAGGATAAAG
4278233 AAAAAAAGTAA
1 AAAAAAAGTAA
4278244 AAAAAAAGTAA
1 AAAAAAAGTAA
4278255 AAAA
1 AAAA
4278259 CTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAAAGTAA
Found at i:4278302 original size:13 final size:14
Alignment explanation
Indices: 4278265--4278294 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4278255 AAAACTTAAA
*
4278265 AAAAGTAAAAAAAG
1 AAAAGAAAAAAAAG
4278279 AAAAGAAAAAAAAG
1 AAAAGAAAAAAAAG
4278293 AA
1 AA
4278295 GGATAAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:4280623 original size:25 final size:25
Alignment explanation
Indices: 4280595--4280658 Score: 96
Period size: 24 Copynumber: 2.6 Consensus size: 25
4280585 GAGAAATAAT
*
4280595 TTTCCAGTTAAACTCTGTTTATTTG
1 TTTCCAATTAAACTCTGTTTATTTG
4280620 TTT-CAATTAAACTCTGTTTATTTG
1 TTTCCAATTAAACTCTGTTTATTTG
*
4280644 TTT-CAATCAAACTCT
1 TTTCCAATTAAACTCT
4280659 AATTAGTCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
24 34 0.92
25 3 0.08
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (25 bp):
TTTCCAATTAAACTCTGTTTATTTG
Found at i:4280629 original size:24 final size:24
Alignment explanation
Indices: 4280602--4280658 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
4280592 AATTTTCCAG
4280602 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
4280626 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
4280650 TCAAACTCT
1 TTAAACTCT
4280659 AATTAGTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Found at i:4283806 original size:127 final size:126
Alignment explanation
Indices: 4283592--4284053 Score: 547
Period size: 127 Copynumber: 3.6 Consensus size: 126
4283582 TATCGAATTT
* * * * *
4283592 CCAAATACGAAACATTGCCTCATTTTAATTTGAGAAAACATGGATGAAACTTCAAAAGGATATTC
1 CCAAATACGAAATATTGCCTCATTTTAATTTAAAAAAACATGGACGAAATTTCAAAAGGATATTC
* * * *
4283657 TGTATTTTAG-TCGGATGAAAAATTGAAGCCCAGCATGATTGGGCACGACTCCCCAAACTCC
66 CGTATTTTAGCT-GAATGGAAAATTGAAGCCCAGCACGATTGGGCACGACTCCCCAAACTCC
* *
4283718 CCAAATACGAAATATTGCCTCATTTTAATTTAAAAAAAACGTGGACGAAATTTCTAAAGGATATT
1 CCAAATACGAAATATTGCCTCATTTTAATTT-AAAAAAACATGGACGAAATTTCAAAAGGATATT
* * * *
4283783 CCGTATTTTAGCTAAATGGAAAATTAAAACCCAGCACGATTGGGCACGACTCTCCAAACTCC
65 CCGTATTTTAGCTGAATGGAAAATTGAAGCCCAGCACGATTGGGCACGACTCCCCAAACTCC
* * * *
4283845 CCAAATACGAAATATTGCCTCATTTTAATTTTTAAAAAACATAGACGAAGTTTCCAAAGGATATT
1 CCAAATACGAAATATTGCCTCATTTTAA-TTTAAAAAAACATGGACGAAATTTCAAAAGGATATT
* * *
4283910 CCGTATTTTAGCTGAATGGAAAATTGAAGCCCAACACGATTGGGCACGAC-CTCCCAACCT-T
65 CCGTATTTTAGCTGAATGGAAAATTGAAGCCCAGCACGATTGGGCACGACTC-CCCAAACTCC
* * *** *
4283971 CCAAACACGAAATATTGCCTCGTTTTAATTTTTTTTTTAAAA-ATGGACAAAATTTTC-AAAGGA
1 CCAAATACGAAATATTGCCTCATTTTAA----TTTAAAAAAACATGGACGAAA-TTTCAAAAGGA
*
4284034 TATTTCGTATTTTAGCTGAA
61 TATTCCGTATTTTAGCTGAA
4284054 CGAAAAAAAA
Statistics
Matches: 293, Mismatches: 35, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
126 57 0.19
127 187 0.64
128 36 0.12
129 13 0.04
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (126 bp):
CCAAATACGAAATATTGCCTCATTTTAATTTAAAAAAACATGGACGAAATTTCAAAAGGATATTC
CGTATTTTAGCTGAATGGAAAATTGAAGCCCAGCACGATTGGGCACGACTCCCCAAACTCC
Found at i:4296243 original size:20 final size:21
Alignment explanation
Indices: 4296218--4296261 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
4296208 TATAATTTTT
4296218 AATATTTTTTAAAATTT-TAA
1 AATATTTTTTAAAATTTCTAA
* *
4296238 AATATTTTTTGAATTTTCTAA
1 AATATTTTTTAAAATTTCTAA
4296259 AAT
1 AAT
4296262 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
AATATTTTTTAAAATTTCTAA
Found at i:4296263 original size:19 final size:19
Alignment explanation
Indices: 4296206--4296264 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
4296196 AGGAAAGAAA
* *
4296206 TTTATAATTTTTAATATTT
1 TTTAAAATTTTTAAAATTT
4296225 TTTAAAA-TTTTAAAATATT
1 TTTAAAATTTTTAAAAT-TT
**
4296244 TTTTGAATTTTCTAAAATTT
1 TTTAAAATTTT-TAAAATTT
4296264 T
1 T
4296265 AAAAATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 8 0.24
19 13 0.39
20 6 0.18
21 6 0.18
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTAAAATTTTTAAAATTT
Found at i:4296281 original size:29 final size:29
Alignment explanation
Indices: 4296221--4296283 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
4296211 AATTTTTAAT
* ** *
4296221 ATTTTTTAAAATTTTAAAATATTTTTTGA
1 ATTTTCTAAAATTTTAAAATATAATATGA
4296250 ATTTTCTAAAATTTTAAAAATATAATAT-A
1 ATTTTCTAAAATTTT-AAAATATAATATGA
4296279 ATTTT
1 ATTTT
4296284 AGGAATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (29 bp):
ATTTTCTAAAATTTTAAAATATAATATGA
Found at i:4296543 original size:22 final size:23
Alignment explanation
Indices: 4296495--4296544 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
4296485 TAAGATAATT
*
4296495 AAATTTGAAAAGATTTGACTTTC
1 AAATTTGAAAAGATTTGACTTTA
*
4296518 AAATTT-AAATGATTTGAAC-TTA
1 AAATTTGAAAAGATTTG-ACTTTA
4296540 AAATT
1 AAATT
4296545 ATTACAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (23 bp):
AAATTTGAAAAGATTTGACTTTA
Found at i:4299088 original size:21 final size:21
Alignment explanation
Indices: 4299064--4299420 Score: 294
Period size: 21 Copynumber: 16.7 Consensus size: 21
4299054 TAAATCACCA
* *
4299064 CCACTACCACCGGTCCACTCC
1 CCACCACCACCAGTCCACTCC
* * *
4299085 CCACCCCCACCAGTGCACTCA
1 CCACCACCACCAGTCCACTCC
* * *
4299106 CCACCCCCACCAGTCTTCTCACC
1 CCACCACCACCAGTC--CACTCC
*
4299129 ACCACCACCACCAGTCCACTCT
1 -CCACCACCACCAGTCCACTCC
* * *
4299151 CCACCCCCACCCGTTCACT-C
1 CCACCACCACCAGTCCACTCC
*
4299171 CCACC-CCACCAGTGCACTCC
1 CCACCACCACCAGTCCACTCC
* * *
4299191 CCACCCCCACCAGTCTTCTCACC
1 CCACCACCACCAGTC--CACTCC
4299214 ACCACCACCACCAGTCCACT-C
1 -CCACCACCACCAGTCCACTCC
*
4299235 CCACC-CCACCCGTCCACT-C
1 CCACCACCACCAGTCCACTCC
*
4299254 CCACCACCACCAGTCCACTCG
1 CCACCACCACCAGTCCACTCC
* *
4299275 CCACCCCCACCCA-TCCACTCA
1 CCACCACCA-CCAGTCCACTCC
* *
4299296 CCACCACCACCCGTCTACTCACC
1 CCACCACCACCAGTCCACT--CC
4299319 ACCACCACCACCAGTCCACTCC
1 -CCACCACCACCAGTCCACTCC
* *
4299341 CCACCACCACCACCCGTCTACTCA
1 CCACCACCACCA---GTCCACTCC
* * *
4299365 CCACCACCACCCGTCTACTCA
1 CCACCACCACCAGTCCACTCC
*
4299386 CCACCACCACCAGTCTACTCC
1 CCACCACCACCAGTCCACTCC
*
4299407 CCACCCCCACCAGT
1 CCACCACCACCAGT
4299421 ACAATCTCCA
Statistics
Matches: 276, Mismatches: 42, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
19 29 0.11
20 30 0.11
21 136 0.49
22 10 0.04
23 8 0.03
24 63 0.23
ACGTcount: A:0.22, C:0.60, G:0.06, T:0.12
Consensus pattern (21 bp):
CCACCACCACCAGTCCACTCC
Found at i:4299108 original size:45 final size:42
Alignment explanation
Indices: 4299070--4299420 Score: 327
Period size: 45 Copynumber: 8.2 Consensus size: 42
4299060 ACCACCACTA
* * *
4299070 CCACCGGTCCACTCCCCACCCCCACCAGTGCACTCACCACCC
1 CCACCAGTCCACTCCCCACCACCACCAGTCCACTCACCACCC
* * *
4299112 CCACCAGTCTTCTCACCACCACCACCACCAGTCCACTCTCCACCC
1 CCACCAGTC--CACTCC-CCACCACCACCAGTCCACTCACCACCC
* * * *
4299157 CCACCCGTTCACT-CCCACC-CCACCAGTGCACTCCCCACCC
1 CCACCAGTCCACTCCCCACCACCACCAGTCCACTCACCACCC
* *
4299197 CCACCAGTCTTCTCACCACCACCACCACCAGTCCACTC-CCA-CC
1 CCACCAGTC--CACTCC-CCACCACCACCAGTCCACTCACCACCC
* *
4299240 CCACCCGTCCACT-CCCACCACCACCAGTCCACTCGCCACCC
1 CCACCAGTCCACTCCCCACCACCACCAGTCCACTCACCACCC
* * *
4299281 CCACCCA-TCCACTCACCACCACCACCCGTCTACTCACCACCACC
1 CCA-CCAGTCCACTCCCCACCACCACCAGTCCACTCACCA-C-CC
* *
4299325 ACCACCAGTCCACTCCCCACCACCACCACCCGTCTACTCACCACCA
1 -CCACCAGTCCACTCCCCACCACCACCA---GTCCACTCACCACCC
* * * * *
4299371 CCACCCGTCTACTCACCACCACCACCAGTCTACTCCCCACCC
1 CCACCAGTCCACTCCCCACCACCACCAGTCCACTCACCACCC
4299413 CCACCAGT
1 CCACCAGT
4299421 ACAATCTCCA
Statistics
Matches: 256, Mismatches: 34, Indels: 38
0.78 0.10 0.12
Matches are distributed among these distances:
39 20 0.08
40 30 0.12
41 18 0.07
42 54 0.21
43 14 0.05
44 17 0.07
45 89 0.35
46 1 0.00
47 1 0.00
48 12 0.05
ACGTcount: A:0.22, C:0.60, G:0.06, T:0.12
Consensus pattern (42 bp):
CCACCAGTCCACTCCCCACCACCACCAGTCCACTCACCACCC
Found at i:4299395 original size:3 final size:3
Alignment explanation
Indices: 4299210--4299354 Score: 57
Period size: 3 Copynumber: 45.3 Consensus size: 3
4299200 CCAGTCTTCT
**
4299210 CAC CAC CAC CAC CAC CAGTC CAC TC-C CAC C-C CAC C-C GTC CAC TC-C
1 CAC CAC CAC CAC CAC CA--C CAC -CAC CAC CAC CAC CAC CAC CAC -CAC
* *
4299255 CAC CAC CAC CAGTC CAC TCGC CAC CCC CACC CATC CAC TCAC CAC CAC
1 CAC CAC CAC CA--C CAC -CAC CAC CAC CA-C CA-C CAC -CAC CAC CAC
** * *
4299303 CAC C-C GTC TAC TCAC CAC CAC CAC CAC CAGTC CAC TCCC CAC CAC CAC
1 CAC CAC CAC CAC -CAC CAC CAC CAC CAC CA--C CAC -CAC CAC CAC CAC
4299351 CAC C
1 CAC C
4299355 CGTCTACTCA
Statistics
Matches: 110, Mismatches: 14, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
2 6 0.05
3 78 0.71
4 17 0.15
5 9 0.08
ACGTcount: A:0.24, C:0.63, G:0.04, T:0.09
Consensus pattern (3 bp):
CAC
Found at i:4300628 original size:19 final size:19
Alignment explanation
Indices: 4300604--4300648 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
4300594 TCCTAAACTT
4300604 TTTTACTTTCCCT-AAAAA
1 TTTTACTTTCCCTCAAAAA
*
4300622 TTATTACTTTTCCTCAAAAA
1 TT-TTACTTTCCCTCAAAAA
4300642 TTTTACT
1 TTTTACT
4300649 CCTCCCTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTACTTTCCCTCAAAAA
Found at i:4303340 original size:21 final size:21
Alignment explanation
Indices: 4303316--4303387 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
4303306 TCCCTTCCTT
*
4303316 ACCACCACCCATCCAATCTCC
1 ACCACCACCCATCCAATCACC
* * *
4303337 ACCACCACCAATGCACTCACC
1 ACCACCACCCATCCAATCACC
* *
4303358 ACCACCACCCGTCCATTCACC
1 ACCACCACCCATCCAATCACC
4303379 ACCACCACC
1 ACCACCACC
4303388 ATCGGTTCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.29, C:0.57, G:0.03, T:0.11
Consensus pattern (21 bp):
ACCACCACCCATCCAATCACC
Found at i:4303381 original size:24 final size:24
Alignment explanation
Indices: 4303354--4303412 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
4303344 CCAATGCACT
4303354 CACCACCACCACCCG-TCCATTCAC
1 CACCACCACCACCCGTTCC-TTCAC
* *
4303378 CACCACCACCATCGGTTCCTTCAC
1 CACCACCACCACCCGTTCCTTCAC
*
4303402 CCCCACCACCA
1 CACCACCACCA
4303413 GTAAAATCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.24, C:0.58, G:0.05, T:0.14
Consensus pattern (24 bp):
CACCACCACCACCCGTTCCTTCAC
Found at i:4303402 original size:21 final size:21
Alignment explanation
Indices: 4303335--4303670 Score: 154
Period size: 21 Copynumber: 15.7 Consensus size: 21
4303325 CATCCAATCT
* *
4303335 CCACCACCACCAATGCAC-TCA
1 CCACCACCACCAGTAC-CTTCA
*
4303356 CCACCACCACCCGT-CCATTCA
1 CCACCACCACCAGTACC-TTCA
*
4303377 CCACCACCACCATCGGTTCCTTCA
1 CCACCACCACCA---GTACCTTCA
* *** *
4303401 CCCCCACCACCAGTAAAATCC
1 CCACCACCACCAGTACCTTCA
* *
4303422 CCACCCCCACCGGTACCTTCA
1 CCACCACCACCAGTACCTTCA
*
4303443 CCACCACCACCAGTTCCTTCA
1 CCACCACCACCAGTACCTTCA
* * *** *
4303464 CCCCCACCGCCAGTAAAATCT
1 CCACCACCACCAGTACCTTCA
* * * *
4303485 CCACCTCCACCGGTGCCCTCACCA
1 CCACCACCACCAGT-ACCT--TCA
*
4303509 CCACCACCACCAGTTCCTTCA
1 CCACCACCACCAGTACCTTCA
* * *** *
4303530 CCCCCACCCCCAGTAAAATCC
1 CCACCACCACCAGTACCTTCA
* * * *
4303551 CCACCTCCACCGGTGCCCTCA
1 CCACCACCACCAGTACCTTCA
*
4303572 CCACCACCACCAGTTCCTTCA
1 CCACCACCACCAGTACCTTCA
* * * *** *
4303593 CCCCCACCCCCAATAAAATCC
1 CCACCACCACCAGTACCTTCA
* * * *
4303614 CCACCTCCACCGGTGCCCTCA
1 CCACCACCACCAGTACCTTCA
* *
4303635 CCACCACCACCAGTTCTTTCA
1 CCACCACCACCAGTACCTTCA
*
4303656 CCCCCACCACCAGTA
1 CCACCACCACCAGTA
4303671 AAATCCCTAC
Statistics
Matches: 221, Mismatches: 85, Indels: 18
0.68 0.26 0.06
Matches are distributed among these distances:
19 1 0.00
20 1 0.00
21 184 0.83
23 3 0.01
24 30 0.14
25 2 0.01
ACGTcount: A:0.24, C:0.54, G:0.07, T:0.15
Consensus pattern (21 bp):
CCACCACCACCAGTACCTTCA
Found at i:4303449 original size:129 final size:126
Alignment explanation
Indices: 4303338--4303708 Score: 503
Period size: 129 Copynumber: 2.9 Consensus size: 126
4303328 CCAATCTCCA
** * * * *
4303338 CCACCACCAATGCACTCACCACCACCACCCGT-CCATTCACCACCACCACCATCGGTTCCTTCAC
1 CCACCACCAATAAAATCACCACCTCCACCGGTGCC-CTCACCACCACCACCA-C-GTTCCTTCAC
* * *
4303402 CCCCACCACCAGTAAAATCCCCACCCCCACCGGTACCTTCACCACCACCACCAGTTCCTTCACCC
63 CCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCTCACCACCACCACCAG-TCCTTCACCC
* * *
4303467 CCACCGCCAGTAAAATCTCCACCTCCACCGGTGCCCTCACCACCACCACCACCAGTTCCTTCACC
1 CCACCACCAATAAAATCACCACCTCCACCGGTGCCCTCACCACCACCACCA-C-GTTCCTTCACC
*
4303532 CCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCTCACCACCACCACCAGTTCCTTCACCC
64 CCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCTCACCACCACCACCAG-TCCTTCACCC
* * *
4303596 CCACCCCCAATAAAATCCCCACCTCCACCGGTGCCCTCACCACCACCACCA-GTTCTTTCACCCC
1 CCACCACCAATAAAATCACCACCTCCACCGGTGCCCTCACCACCACCACCACGTTCCTTCACCCC
* *
4303660 CACCACCAGTAAAATCCCTACCTCCACCGGTGCCCTCACCACCCCCACC
66 CACCACCAGTAAAATCCCCACCTCCACCGGTGCCCTCACCACCACCACC
4303709 TGTGCCATCT
Statistics
Matches: 219, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
126 58 0.26
129 159 0.73
130 2 0.01
ACGTcount: A:0.24, C:0.54, G:0.07, T:0.15
Consensus pattern (126 bp):
CCACCACCAATAAAATCACCACCTCCACCGGTGCCCTCACCACCACCACCACGTTCCTTCACCCC
CACCACCAGTAAAATCCCCACCTCCACCGGTGCCCTCACCACCACCACCAGTCCTTCACCC
Found at i:4303477 original size:63 final size:63
Alignment explanation
Indices: 4303378--4303770 Score: 520
Period size: 63 Copynumber: 6.2 Consensus size: 63
4303368 GTCCATTCAC
* * * * *
4303378 CACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCCCCACCGGTACCTT
1 CACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCT
* *
4303441 CACCACCACCACCAGTTCCTTCACCCCCACCGCCAGTAAAATCTCCACCTCCACCGGTGCCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCT
*
4303504 CACCACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCC
1 ---CACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCC
4303569 T
63 T
* *
4303570 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAATAAAATCCCCACCTCCACCGGTGCCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCT
* *
4303633 CACCACCACCACCAGTTCTTTCACCCCCACCACCAGTAAAATCCCTACCTCCACCGGTGCCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCT
* * * * * * ** * * *
4303696 CACCACCCCCACCTGTGCCATCTCCACCC-CCACCCGTCCACTCCCCACCCCCACCTGTGCCCT
1 CACCACCACCACCAGTTCCTTCACC-CCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCT
*
4303759 CTCCACC-CCACC
1 CACCACCACCACC
4303771 CGTCCATTCC
Statistics
Matches: 298, Mismatches: 28, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
62 5 0.02
63 229 0.77
64 3 0.01
66 61 0.20
ACGTcount: A:0.22, C:0.56, G:0.08, T:0.15
Consensus pattern (63 bp):
CACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCT
Found at i:4303512 original size:24 final size:24
Alignment explanation
Indices: 4303485--4303537 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
4303475 AGTAAAATCT
* *
4303485 CCACCTCCACCGGTGCCCTCACCA
1 CCACCACCACCAGTGCCCTCACCA
* * *
4303509 CCACCACCACCAGTTCCTTCACCC
1 CCACCACCACCAGTGCCCTCACCA
4303533 CCACC
1 CCACC
4303538 CCCAGTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.19, C:0.60, G:0.08, T:0.13
Consensus pattern (24 bp):
CCACCACCACCAGTGCCCTCACCA
Found at i:4303707 original size:21 final size:21
Alignment explanation
Indices: 4303698--4303976 Score: 203
Period size: 21 Copynumber: 13.5 Consensus size: 21
4303688 GGTGCCCTCA
*
4303698 CCACCCCCACCTGTGCCA-TCT
1 CCACCCCCACCCGT-CCACTCT
*
4303719 CCACCCCCACCCGTCCACTCC
1 CCACCCCCACCCGTCCACTCT
*
4303740 CCACCCCCACCTGTGCC-CTCT
1 CCACCCCCACCCGT-CCACTCT
* *
4303761 CCA-CCCCACCCGTCCATTCC
1 CCACCCCCACCCGTCCACTCT
**
4303781 CCACCCCCACCCGTCCGTTC-
1 CCACCCCCACCCGTCCACTCT
** *
4303801 CCA-CCCCACCTATCCTCTCT
1 CCACCCCCACCCGTCCACTCT
* * * *
4303821 CCACCCCCACCGGTGCGCTCA
1 CCACCCCCACCCGTCCACTCT
**
4303842 CCA-CCCCACCCGTCCTTTCT
1 CCACCCCCACCCGTCCACTCT
* * * *
4303862 CCACCCCCACCAGTGCGCTCA
1 CCACCCCCACCCGTCCACTCT
* *
4303883 CCACCCCCACCCATCCACTCC
1 CCACCCCCACCCGTCCACTCT
* * * *
4303904 CCA-CCCCACCAGTACATTCA
1 CCACCCCCACCCGTCCACTCT
* * *
4303924 CCACCACCACCCGTCTACTCA
1 CCACCCCCACCCGTCCACTCT
* *
4303945 CCACCTCCACCCGTCTACTCT
1 CCACCCCCACCCGTCCACTCT
*
4303966 CCACCACCACC
1 CCACCCCCACC
4303977 AGTAAAATCT
Statistics
Matches: 205, Mismatches: 45, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
19 14 0.07
20 53 0.26
21 136 0.66
22 2 0.01
ACGTcount: A:0.16, C:0.61, G:0.07, T:0.15
Consensus pattern (21 bp):
CCACCCCCACCCGTCCACTCT
Found at i:4303730 original size:129 final size:127
Alignment explanation
Indices: 4303377--4303708 Score: 531
Period size: 129 Copynumber: 2.6 Consensus size: 127
4303367 CGTCCATTCA
* * * * *
4303377 CCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCCCCACCGGTACCTTC
1 CCACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCTC
* * *
4303442 ACCACCACCACCAGTTCCTTCACCCCCACCGCCAGTAAAATCTCCACCTCCACCGGTGCCCT
66 ACCACCACCACCAGTTCCTTCACCCCCACCCCCAATAAAATCCCCACCTCCACCGGTGCCCT
*
4303504 CACCACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCC
1 --CCACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCC
4303569 TCACCACCACCACCAGTTCCTTCACCCCCACCCCCAATAAAATCCCCACCTCCACCGGTGCCCT
64 TCACCACCACCACCAGTTCCTTCACCCCCACCCCCAATAAAATCCCCACCTCCACCGGTGCCCT
* *
4303633 -CACCACCACCACCAGTTCTTTCACCCCCACCACCAGTAAAATCCCTACCTCCACCGGTGCCCTC
1 CCACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCTC
*
4303697 ACCACCCCCACC
66 ACCACCACCACC
4303709 TGTGCCATCT
Statistics
Matches: 190, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
126 72 0.38
129 118 0.62
ACGTcount: A:0.23, C:0.55, G:0.08, T:0.15
Consensus pattern (127 bp):
CCACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCTC
ACCACCACCACCAGTTCCTTCACCCCCACCCCCAATAAAATCCCCACCTCCACCGGTGCCCT
Found at i:4303911 original size:41 final size:41
Alignment explanation
Indices: 4303698--4303955 Score: 243
Period size: 41 Copynumber: 6.3 Consensus size: 41
4303688 GGTGCCCTCA
* *
4303698 CCACCCCCACCTGTGC-CATCTCCACCCCCACCCGTCCACTCC
1 CCACCCCCACCAGTGCGC-TCACCA-CCCCACCCGTCCACTCC
* * * *
4303740 CCACCCCCACCTGTGCCCTCTCCACCCCACCCGTCCATTCC
1 CCACCCCCACCAGTGCGCTCACCACCCCACCCGTCCACTCC
* * * ** * *
4303781 CCACCCCCACCCGTCCGTTC-CCACCCCACCTATCCTCTCT
1 CCACCCCCACCAGTGCGCTCACCACCCCACCCGTCCACTCC
* ** *
4303821 CCACCCCCACCGGTGCGCTCACCACCCCACCCGTCCTTTCT
1 CCACCCCCACCAGTGCGCTCACCACCCCACCCGTCCACTCC
*
4303862 CCACCCCCACCAGTGCGCTCACCACCCCCACCCATCCACTCC
1 CCACCCCCACCAGTGCGCTCACCA-CCCCACCCGTCCACTCC
* ** * *
4303904 CCA-CCCCACCAGTACATTCACCACCACCACCCGTCTACTCA
1 CCACCCCCACCAGTGCGCTCACCACC-CCACCCGTCCACTCC
*
4303945 CCACCTCCACC
1 CCACCCCCACC
4303956 CGTCTACTCT
Statistics
Matches: 183, Mismatches: 28, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
40 34 0.19
41 104 0.57
42 44 0.24
43 1 0.01
ACGTcount: A:0.16, C:0.62, G:0.07, T:0.15
Consensus pattern (41 bp):
CCACCCCCACCAGTGCGCTCACCACCCCACCCGTCCACTCC
Found at i:4303911 original size:62 final size:61
Alignment explanation
Indices: 4303674--4303976 Score: 240
Period size: 62 Copynumber: 4.9 Consensus size: 61
4303664 ACCAGTAAAA
* * * *
4303674 TCCCTACCTCCACCGGTGCCCTCACCACCCCCACCTGTGCCA-TCTCCACCCCCACCCGTCCACT
1 TCCC-ACCCCCACCAGTGCCCTCACCACCCCCACCCGT-CCACTCCCCA-CCCCACCCGTCCA-T
* * * * *
4303738 CCCCACCCCCACCTGTGCCCTCTCCA-CCCCACCCGTCCATTCCCCACCCCCACCCGTCCGT
1 TCCCACCCCCACCAGTGCCCTCACCACCCCCACCCGTCCACTCCCCA-CCCCACCCGTCCAT
* * * * * *
4303799 TCCCA-CCCCACCTA-T-CCTCTCTCCACCCCCACCGGTGCGCTCACCACCCCACCCGTCCTT
1 TCCCACCCCCACC-AGTGCC-CTCACCACCCCCACCCGTCCACTCCCCACCCCACCCGTCCAT
* * * *
4303859 TCTCCACCCCCACCAGTGCGCTCACCACCCCCACCCATCCACTCCCCACCCCACCAGTACAT
1 TC-CCACCCCCACCAGTGCCCTCACCACCCCCACCCGTCCACTCCCCACCCCACCCGTCCAT
* * * * * *
4303921 TCACCACCACCACCCGT-CTACTCACCACCTCCACCCGTCTACTCTCCACCACCACC
1 TC-CCACCCCCACCAGTGC-CCTCACCACCCCCACCCGTCCACTCCCCACC-CCACC
4303977 AGTAAAATCT
Statistics
Matches: 196, Mismatches: 33, Indels: 21
0.78 0.13 0.08
Matches are distributed among these distances:
59 2 0.01
60 30 0.15
61 28 0.14
62 108 0.55
63 25 0.13
64 3 0.02
ACGTcount: A:0.16, C:0.61, G:0.07, T:0.16
Consensus pattern (61 bp):
TCCCACCCCCACCAGTGCCCTCACCACCCCCACCCGTCCACTCCCCACCCCACCCGTCCAT
Found at i:4304817 original size:12 final size:13
Alignment explanation
Indices: 4304790--4304822 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4304780 TTAAAAAATT
*
4304790 ATAAGTTTTGTAA
1 ATAAATTTTGTAA
4304803 ATAAATTTT-TAA
1 ATAAATTTTGTAA
4304815 ATAAATTT
1 ATAAATTT
4304823 GTATAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (13 bp):
ATAAATTTTGTAA
Found at i:4305331 original size:190 final size:190
Alignment explanation
Indices: 4304991--4305437 Score: 523
Period size: 190 Copynumber: 2.4 Consensus size: 190
4304981 AAGTAATAAG
** * **
4304991 TAATGTACTACTATTATATATGTCTATTATTATAATATAGATTATAATAAAAGATATAGTTTTAC
1 TAATGTACTACTATTATATATAACTATTATTATAATATAAATTATAATAAAAGATATAGCATTAC
* * * *
4305056 ATGATATTATTATGTTTAATTATATATAAACTATTAATATATTATATAATATGATATAGCGTTAC
66 ATAATATTATAATGTTTAACTATATATAAACTATTAATATATTATATAATATGATATAACGTTAC
* *
4305121 ATTATATAATAGGAGGTTAACTTTCAAATGTACGAAAAATATAAAGACTTGGAGCATATT
131 ATAATATAATAAGAGGTTAACTTTCAAATGTACGAAAAATATAAAGACTTGGAGCATATT
* * * *
4305181 TAATGTACTACTATTATATATAACTATTATTA-AATTATAAATTATAATAAAGGGTATGGCATTG
1 TAATGTACTACTATTATATATAACTATTATTATAA-TATAAATTATAATAAAAGATATAGCATTA
* *
4305245 CATAATATTATAATGTTTAACTATATATAAACTATTAATATATTATATGATATGA-ATAACTTTA
65 CATAATATTATAATGTTTAACTATATATAAACTATTAATATATTATATAATATGATATAACGTTA
* * * * *
4305309 TATAATATAGTAAGATGGTTAACTTTCAAA-G---G---GAT-TTAA-A--T----CATATA
130 CATAATATAATAAGA-GGTTAACTTTCAAATGTACGAAAAATATAAAGACTTGGAGCATATT
* * *
4305356 TAATGTACTACTATTATATATAACGATTATTATAATATAGATTATAATAAAAGATATAGTATTAC
1 TAATGTACTACTATTATATATAACTATTATTATAATATAAATTATAATAAAAGATATAGCATTAC
*
4305421 ATGATATTATAATGTTT
66 ATAATATTATAATGTTT
4305438 GATCATTGAT
Statistics
Matches: 224, Mismatches: 30, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
175 76 0.34
176 2 0.01
179 1 0.00
181 1 0.00
182 3 0.01
183 2 0.01
186 1 0.00
189 21 0.09
190 117 0.52
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (190 bp):
TAATGTACTACTATTATATATAACTATTATTATAATATAAATTATAATAAAAGATATAGCATTAC
ATAATATTATAATGTTTAACTATATATAAACTATTAATATATTATATAATATGATATAACGTTAC
ATAATATAATAAGAGGTTAACTTTCAAATGTACGAAAAATATAAAGACTTGGAGCATATT
Found at i:4306852 original size:26 final size:26
Alignment explanation
Indices: 4306815--4306869 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
4306805 ACACACCGCA
*
4306815 GCTCTTCGTGAGCTTCCTGA-TATATG
1 GCTCTTCATGAGCTTCCTGATTA-ATG
4306841 GCTCTTCATGAGCTTCCTGATTAATG
1 GCTCTTCATGAGCTTCCTGATTAATG
4306867 GCT
1 GCT
4306870 TTTGGGAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (26 bp):
GCTCTTCATGAGCTTCCTGATTAATG
Found at i:4306929 original size:24 final size:24
Alignment explanation
Indices: 4306823--4306929 Score: 79
Period size: 24 Copynumber: 4.3 Consensus size: 24
4306813 CAGCTCTTCG
* *
4306823 TGAGCTTCCTGATATATGGCTCTTCA
1 TGAGCTTCCCGATAT-TGGCTCGT-A
* * ** *
4306849 TGAGCTTCCTGATTAATGGCTTTTG
1 TGAGCTTCCCGA-TATTGGCTCGTA
* * *
4306874 GGAGCTTCCCGTTATTGGCTCGCA
1 TGAGCTTCCCGATATTGGCTCGTA
* *
4306898 AGAACTTCCCGATATTGGCTCGTA
1 TGAGCTTCCCGATATTGGCTCGTA
4306922 TGAGCTTC
1 TGAGCTTC
4306930 TCGTTATATG
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
24 33 0.52
25 9 0.14
26 19 0.30
27 2 0.03
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (24 bp):
TGAGCTTCCCGATATTGGCTCGTA
Found at i:4309465 original size:146 final size:145
Alignment explanation
Indices: 4309226--4309519 Score: 489
Period size: 146 Copynumber: 2.0 Consensus size: 145
4309216 TGCCATTAAA
* * *
4309226 GATCTGAGTGTTTTATCTTGTGTTTTTCCCATCATGTTTTTATCCTATAACGCCCCAAATTTTGA
1 GATCCGAGTGTTTTATCTTGTATTTTTCCCATCATGTTGTTATCCTATAACGCCCCAAATTTTGA
* * * *
4309291 ACATTTGCTTGTTAAATTTTATCATTAAATGCATGTTTACTTTAGTGGTTTAGTGCTTTAATTGT
66 ACATTTACTTGTTAAATTTTATCATTAAATGCATGTTTACTTTAGTGGTGTAGTACCTTAATTGT
4309356 GTGTTTAAGATTAGG
131 GTGTTTAAGATTAGG
* *
4309371 GATCCGAGTGTTTTATCTTGTATTTTTTCCATCAATGTTGTTATCCTGTAACGCCCCAAATTTTG
1 GATCCGAGTGTTTTATCTTGTATTTTTCCCATC-ATGTTGTTATCCTATAACGCCCCAAATTTTG
*
4309436 AACATTTACTTGTTAAATTTTATCATTAAATTCATGTTTACTTTAGTGGTGTAGTACCTTAATTG
65 AACATTTACTTGTTAAATTTTATCATTAAATGCATGTTTACTTTAGTGGTGTAGTACCTTAATTG
4309501 TGTGTTTAAGATTAGG
130 TGTGTTTAAGATTAGG
4309517 GAT
1 GAT
4309520 TTAAGTCCCA
Statistics
Matches: 138, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
145 30 0.22
146 108 0.78
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (145 bp):
GATCCGAGTGTTTTATCTTGTATTTTTCCCATCATGTTGTTATCCTATAACGCCCCAAATTTTGA
ACATTTACTTGTTAAATTTTATCATTAAATGCATGTTTACTTTAGTGGTGTAGTACCTTAATTGT
GTGTTTAAGATTAGG
Found at i:4315328 original size:27 final size:27
Alignment explanation
Indices: 4315290--4315363 Score: 118
Period size: 26 Copynumber: 2.9 Consensus size: 27
4315280 TTAGCCCTTA
4315290 TGAGCTTCCCGATTATATGGCTCTTTG
1 TGAGCTTCCCGATTATATGGCTCTTTG
*
4315317 TGAGCTTCCCGATT-TAAGGCTCTTTG
1 TGAGCTTCCCGATTATATGGCTCTTTG
4315343 TGAGCTTCCCGA-TA-ATGGCTC
1 TGAGCTTCCCGATTATATGGCTC
4315364 GCTTGAACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.16
26 23 0.52
27 14 0.32
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TGAGCTTCCCGATTATATGGCTCTTTG
Found at i:4318478 original size:11 final size:11
Alignment explanation
Indices: 4318464--4318508 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
4318454 AGATAAATAT
4318464 TATTTTATTAA
1 TATTTTATTAA
*
4318475 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
4318488 TATTTTATTAT
1 TATTTTATTAA
4318499 TATTTTATTA
1 TATTTTATTA
4318509 GTATAAAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:4320673 original size:46 final size:46
Alignment explanation
Indices: 4320621--4320880 Score: 297
Period size: 46 Copynumber: 5.6 Consensus size: 46
4320611 GCTTTCTGAA
* *
4320621 ATGAAATGTGTAAGACCATGGTTGAGAGATATCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
4320667 ATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * *
4320713 ATGAAATGTGTAAAACCATGGTTGAAAGTTACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * *
4320759 ATGAAATGAATAAGACTATGGTTGAAAGATACCATGGCAACATGACG
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-T
** ** * * * *
4320806 GGGAAATGAATAAGATCGTGGTTGAAAGATACCATAGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
4320852 A-GAAAATGAGTAAGACCGTAGTTGAAAGA
1 ATG-AAATGTGTAAGACCATGGTTGAAAGA
4320881 CACTAAGGCA
Statistics
Matches: 186, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
45 1 0.01
46 146 0.78
47 39 0.21
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:4322184 original size:24 final size:24
Alignment explanation
Indices: 4322156--4322207 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
4322146 TTAGTAGGTC
* *
4322156 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
4322180 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
4322204 AAAT
1 AAAT
4322208 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:4326227 original size:26 final size:26
Alignment explanation
Indices: 4326198--4326255 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
4326188 TTTAAATCAA
4326198 ACTTTTTAAAAAAACTTTTCAAAAAC
1 ACTTTTTAAAAAAACTTTTCAAAAAC
* * **
4326224 ACTTTTTCACATCACTTTTCAAAAAC
1 ACTTTTTAAAAAAACTTTTCAAAAAC
4326250 ACTTTT
1 ACTTTT
4326256 AAGAAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.40
Consensus pattern (26 bp):
ACTTTTTAAAAAAACTTTTCAAAAAC
Found at i:4326252 original size:13 final size:13
Alignment explanation
Indices: 4326198--4326255 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
4326188 TTTAAATCAA
* *
4326198 ACTTTTTAAAAAA
1 ACTTTTCAAAAAC
4326211 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
* *
4326224 ACTTTTTC-ACATC
1 AC-TTTTCAAAAAC
4326237 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
4326250 ACTTTT
1 ACTTTT
4326256 AAGAAATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
12 5 0.14
13 27 0.73
14 5 0.14
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.40
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:4327361 original size:18 final size:17
Alignment explanation
Indices: 4327328--4327366 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
4327318 TTGTATAAAT
4327328 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
4327346 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
4327363 TGTG
1 TGTG
4327367 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:4327484 original size:8 final size:8
Alignment explanation
Indices: 4327471--4327499 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4327461 CACTAGAGAC
4327471 CAGTGTTA
1 CAGTGTTA
4327479 CAGTGTTA
1 CAGTGTTA
4327487 CAGTGTTA
1 CAGTGTTA
4327495 CAGTG
1 CAGTG
4327500 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:4327613 original size:23 final size:23
Alignment explanation
Indices: 4327586--4327661 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
4327576 AGTGTTATTG
4327586 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
4327609 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4327632 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4327655 ATCAGTG
1 ATCAGTG
4327662 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:4334707 original size:18 final size:17
Alignment explanation
Indices: 4334674--4334712 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
4334664 TTGTATAAAT
4334674 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
4334692 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
4334709 TGTG
1 TGTG
4334713 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:4334830 original size:8 final size:8
Alignment explanation
Indices: 4334817--4334845 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4334807 CACTAGAGAC
4334817 CAGTGTTA
1 CAGTGTTA
4334825 CAGTGTTA
1 CAGTGTTA
4334833 CAGTGTTA
1 CAGTGTTA
4334841 CAGTG
1 CAGTG
4334846 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:4334959 original size:23 final size:23
Alignment explanation
Indices: 4334932--4335007 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
4334922 AGTGTTATTG
4334932 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
4334955 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4334978 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4335001 ATCAGTG
1 ATCAGTG
4335008 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:4338149 original size:27 final size:27
Alignment explanation
Indices: 4338098--4338150 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
4338088 ACATGAATCG
4338098 ATTATTTAATTAGTAAACAAGTATAAA
1 ATTATTTAATTAGTAAACAAGTATAAA
4338125 ATTATTTAACTATA-TAAACAA-TATAA
1 ATTATTTAA-T-TAGTAAACAAGTATAA
4338151 TGGCTTTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 14 0.58
28 8 0.33
29 2 0.08
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (27 bp):
ATTATTTAATTAGTAAACAAGTATAAA
Found at i:4338577 original size:35 final size:37
Alignment explanation
Indices: 4338507--4338578 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 37
4338497 TATATATAAA
* *
4338507 ATTATATTATAATGAATAATAAATATAATTATTAATT
1 ATTAAATTATAATAAATAATAAATATAATTATTAATT
* *
4338544 ATTAAATTA-AATAAAT-ATAAATATATTTTTTAATT
1 ATTAAATTATAATAAATAATAAATATAATTATTAATT
4338579 GTAGCCTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 17 0.55
36 6 0.19
37 8 0.26
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTAAATTATAATAAATAATAAATATAATTATTAATT
Found at i:4356299 original size:20 final size:22
Alignment explanation
Indices: 4356274--4356315 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
4356264 ATAAATAAAA
4356274 AAATTAAAAT-AT-TAAATATT
1 AAATTAAAATAATATAAATATT
4356294 AAATTAAAATAATATAAATATT
1 AAATTAAAATAATATAAATATT
4356316 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 2 0.10
22 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTAAAATAATATAAATATT
Found at i:4363053 original size:17 final size:18
Alignment explanation
Indices: 4363025--4363058 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4363015 GGATTCCGAT
4363025 ATATTGTAAATTAAGATG
1 ATATTGTAAATTAAGATG
*
4363043 ATATT-TAAATTCAGAT
1 ATATTGTAAATTAAGAT
4363059 ATTATAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (18 bp):
ATATTGTAAATTAAGATG
Found at i:4363448 original size:241 final size:240
Alignment explanation
Indices: 4363002--4363690 Score: 822
Period size: 241 Copynumber: 2.9 Consensus size: 240
4362992 TGGATATTTG
* * * * *
4363002 ACTTGTATTTTGAGGATTCCGATATATTGTAAATTAAGATGATATTTAAATTCAGATATTATAAT
1 ACTTGCATTTTGAGGATT---AGATATTGTAGATT-AGATGATATTTAAATTCGGATATTCTAAT
* * **
4363067 TACTATCCCTAGCAAATTTAAAGTGAATATTAGTTCTTGAATATCCAAAATGGCTTGAACTAGCA
62 TACTATTCCTAGCAAATTTAAAGTGAATATTAGTTCTCGAATATCCAAAATGGCTTGAACTAATA
* * * * * *
4363132 ACGGCCCACCTAAAAATCCTAGACTCAAACTACTTGATCCCAAAACAACTCGAACACAAAATTGA
127 ATGACCCACTTAAAAATACTAGACTCAAACCACTTGAACCCAAAACAACTCGAACACAAAATTGA
* *
4363197 TTCAAACCCTTCTCCAAGTAGTGCAGATTTGAATATTTGCAAATATCTA
192 TCCAAACCCTTCTCCAAGTAGTGCAAATTTGAATATTTGCAAATATCTA
* *
4363246 ACTTGC-TTTTTAGGATTCAGATATTGTAGATTCAGATGATATTTAAATTCGGATTTTCTAATTA
1 ACTTGCATTTTGAGGATT-AGATATTGTAGATT-AGATGATATTTAAATTCGGATATTCTAATTA
* *
4363310 CTATTCCTAGCAAATTCAAAGTGAATATTAGTTCTCGCATATCCAAAATGGCTTGAACTAATAAT
64 CTATTCCTAGCAAATTTAAAGTGAATATTAGTTCTCGAATATCCAAAATGGCTTGAACTAATAAT
* *
4363375 GACCCACTTAAAAATACTTGACTCAAACCACATGAACCCAAAACAACTCGAACACAAAATTGATC
129 GACCCACTTAAAAATACTAGACTCAAACCACTTGAACCCAAAACAACTCGAACACAAAATTGATC
* * *
4363440 CAAACCCTTCTTCAAGTAGTGCAAATTTGAATATTTGCAAATTTTTA
194 CAAACCCTTCTCCAAGTAGTGCAAATTTGAATATTTGCAAATATCTA
* * * *
4363487 ACTTGCATTTTGAGGATTGGTTATTG--GA-T-G--G-TATTTAAATTTGAATATTCTAATTACT
1 ACTTGCATTTTGAGGATTAGATATTGTAGATTAGATGATATTTAAATTCGGATATTCTAATTACT
* * * * * ** * *
4363545 ATTTCTAGCATATTTGAAGTGGATATTAG-CCTTCGAATATCCAAAATAACTTGAATTTATAAT-
66 ATTCCTAGCAAATTTAAAGTGAATATTAGTTC-TCGAATATCCAAAATGGCTTGAACTAATAATG
* * * * * *
4363608 ATCCCACTTAAATATTCAAGACTCAAGCCACTTGAACCTAAAACAACTTGGAACACAAAATTGAT
130 A-CCCACTTAAAAATACTAGACTCAAACCACTTGAACCCAAAACAAC-TCGAACACAAAATTGAT
4363673 CCAAACCCTTCTCCAAGT
193 CCAAACCCTTCTCCAAGT
4363691 TTGCTTCTTA
Statistics
Matches: 387, Mismatches: 54, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
232 2 0.01
233 112 0.29
234 34 0.09
236 1 0.00
238 1 0.00
239 2 0.01
241 210 0.54
242 10 0.03
243 10 0.03
244 5 0.01
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (240 bp):
ACTTGCATTTTGAGGATTAGATATTGTAGATTAGATGATATTTAAATTCGGATATTCTAATTACT
ATTCCTAGCAAATTTAAAGTGAATATTAGTTCTCGAATATCCAAAATGGCTTGAACTAATAATGA
CCCACTTAAAAATACTAGACTCAAACCACTTGAACCCAAAACAACTCGAACACAAAATTGATCCA
AACCCTTCTCCAAGTAGTGCAAATTTGAATATTTGCAAATATCTA
Found at i:4368814 original size:37 final size:36
Alignment explanation
Indices: 4368743--4368832 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
4368733 ACATTATCAC
* *
4368743 TTTCATAGATGATT-T-TTGGATGACATGGAGCTAT
1 TTTCATAGATGATTGTATCGGAAGACATGGAGCTAT
*
4368777 TTTCATAGATGATTGTAGTCGGAAGACATGGATCTAT
1 TTTCATAGATGATTGTA-TCGGAAGACATGGAGCTAT
*
4368814 TTTCATAGATAATTGTATC
1 TTTCATAGATGATTGTATC
4368833 AACCCTATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 14 0.29
35 1 0.02
36 2 0.04
37 32 0.65
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (36 bp):
TTTCATAGATGATTGTATCGGAAGACATGGAGCTAT
Found at i:4369170 original size:21 final size:21
Alignment explanation
Indices: 4369144--4369186 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4369134 TTTAAGTTTG
4369144 TTTAAAAATGGATTACATGTA
1 TTTAAAAATGGATTACATGTA
4369165 TTTAAAAATGGATTACATGTA
1 TTTAAAAATGGATTACATGTA
4369186 T
1 T
4369187 GATTACTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.40
Consensus pattern (21 bp):
TTTAAAAATGGATTACATGTA
Found at i:4372609 original size:3 final size:3
Alignment explanation
Indices: 4372601--4372976 Score: 148
Period size: 3 Copynumber: 128.0 Consensus size: 3
4372591 TTAATTTTAA
* * *
4372601 TAT TAT TAT TCT TAT TAT TAG TAT TAT TAT TAA TAT TAAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
* * * * * * *
4372646 TTT TAT TAT TTT CTAT TTT TAC TAT TGT TAT TAT TAG CA- TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
4372691 TAT TCAT ATAT TAT TAT TTT CTATT TAT TAT TAT TAT TAT TGT TAA CA-
1 TAT T-AT -TAT TAT TAT TAT -TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* * *
4372739 TAT CAT TAT TAT TAT T-T TAT TAT CT-T CTA- TAT TTT TAT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TAT TAT
* * * * *
4372783 TGT TAT T-T CAT TAT TAT TAT ATGT TAC TAT TA- CAT TCAT CT-T T-T
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT T-AT -TAT TAT
* * * * * *
4372827 TAT T-T T-T TAT TAT TCT TTT TAT TAA TAA TAA TAT TAT TA- TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
4372872 TAC TAT TAT TTT TA- TAC TAT AAT TA- TAT T-T TCT T-T TAT GT-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * *
4372913 TAT CAT TAT TCT TAT TCT TAT T-T CT-T TA- TAT TAT T-T TCAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT T-AT TAT
4372956 TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
4372977 ACTTTCCTTT
Statistics
Matches: 279, Mismatches: 62, Indels: 64
0.69 0.15 0.16
Matches are distributed among these distances:
2 34 0.12
3 222 0.80
4 20 0.07
5 3 0.01
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:4372692 original size:14 final size:13
Alignment explanation
Indices: 4372673--4372749 Score: 50
Period size: 14 Copynumber: 5.7 Consensus size: 13
4372663 TTTACTATTG
4372673 TTATTATTAGCATA
1 TTATTATTA-CATA
*
4372687 TTATTATTCATATA
1 TTATTATT-ACATA
*
4372701 TTATTATTTTC-TA
1 TTATTA-TTACATA
*
4372714 TTTATTATTA-TTA
1 -TTATTATTACATA
*
4372727 TTATTGTTAACATA
1 TTATTATT-ACATA
*
4372741 TCATTATTA
1 TTATTATTA
4372750 TTATTTTATT
Statistics
Matches: 49, Mismatches: 8, Indels: 13
0.70 0.11 0.19
Matches are distributed among these distances:
12 7 0.14
13 8 0.16
14 31 0.63
15 3 0.06
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (13 bp):
TTATTATTACATA
Found at i:4372705 original size:17 final size:18
Alignment explanation
Indices: 4372685--4372728 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
4372675 ATTATTAGCA
4372685 TATTATTATTC-ATATAT
1 TATTATTATTCTATATAT
*
4372702 TATTATT-TTCTATTTAT
1 TATTATTATTCTATATAT
4372719 TATTATTATT
1 TATTATTATT
4372729 ATTGTTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 19 0.79
18 2 0.08
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTATTATTCTATATAT
Found at i:4372748 original size:54 final size:53
Alignment explanation
Indices: 4372615--4372781 Score: 175
Period size: 54 Copynumber: 3.2 Consensus size: 53
4372605 ATTATTCTTA
* * *
4372615 TTATTAGTATTATTATTAATAT-TAATT-TTATT-T-TTATTATTTTCTATTT
1 TTATTATTATTATTATTAACATATCATTATTATTATATTATTATTTTCTATTT
* * * *
4372664 TTACTATTGTTATTATTAGCATATTATTATTCA-TATATTATTATTTTCTATTT
1 TTATTATTATTATTATTAACATATCATTATT-ATTATATTATTATTTTCTATTT
* * * *
4372717 ATTATTATTATTATTGTTAACATATCATTATTATTATTTTATTATCTTCTATAT
1 -TTATTATTATTATTATTAACATATCATTATTATTATATTATTATTTTCTATTT
4372771 TT-TTATTATTA
1 TTATTATTATTA
4372782 GTGTTATTTC
Statistics
Matches: 97, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
49 17 0.18
50 4 0.04
51 3 0.03
52 11 0.11
53 19 0.20
54 43 0.44
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (53 bp):
TTATTATTATTATTATTAACATATCATTATTATTATATTATTATTTTCTATTT
Found at i:4372880 original size:17 final size:17
Alignment explanation
Indices: 4372858--4372902 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 17
4372848 TTAATAATAA
4372858 TATTATTATATTTTTAC
1 TATTATTATATTTTTAC
*
4372875 TATTA-T-T-TTTATAC
1 TATTATTATATTTTTAC
*
4372889 TATAATTATATTTT
1 TATTATTATATTTT
4372903 CTTTTATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 6
0.71 0.10 0.19
Matches are distributed among these distances:
14 10 0.45
15 2 0.09
16 2 0.09
17 8 0.36
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTATTATATTTTTAC
Found at i:4372935 original size:34 final size:35
Alignment explanation
Indices: 4372858--4372968 Score: 90
Period size: 34 Copynumber: 3.3 Consensus size: 35
4372848 TTAATAATAA
* * * *
4372858 TATTATTATATT-TTTACTATTATTTTTA-TACTAT
1 TATTATTATTTTCTTTA-TATTATTATCATTATTAT
* *
4372892 AATTA-TATTTTCTTT-TATGT-TTATCATTATTCT
1 TATTATTATTTTCTTTATAT-TATTATCATTATTAT
* *
4372925 TATTCTTA-TTTCTTTATATTATTTTCATTATTAT
1 TATTATTATTTTCTTTATATTATTATCATTATTAT
4372959 TATTATTATT
1 TATTATTATT
4372969 ATTATTATAC
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
32 7 0.12
33 21 0.36
34 30 0.51
35 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (35 bp):
TATTATTATTTTCTTTATATTATTATCATTATTAT
Found at i:4373241 original size:6 final size:6
Alignment explanation
Indices: 4373225--4373265 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
4373215 CTATTTAATA
4373225 TATTATT TATTTT TATTTT TATTTT TATTTCT TATTTT TAT
1 TATT-TT TATTTT TATTTT TATTTT TATTT-T TATTTT TAT
4373266 CTATTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 23 0.70
7 10 0.30
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:4373250 original size:13 final size:13
Alignment explanation
Indices: 4373225--4373265 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
4373215 CTATTTAATA
*
4373225 TATTATTTATTTT
1 TATTTTTTATTTT
4373238 TA-TTTTTATTTT
1 TATTTTTTATTTT
*
4373250 TATTTCTTATTTT
1 TATTTTTTATTTT
4373263 TAT
1 TAT
4373266 CTATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:4388101 original size:4 final size:4
Alignment explanation
Indices: 4388085--4388164 Score: 63
Period size: 4 Copynumber: 19.8 Consensus size: 4
4388075 TAAGTTAAAA
* *** * *
4388085 AAAG AAA- AAAG AAAG AAAG AAAG ATAG AAAG AGTT ACAG AGAG CAAACG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAA-G
**
4388134 TGAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
4388165 TAGAAAAGGG
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
3 3 0.05
4 52 0.88
5 3 0.05
6 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.25, T:0.05
Consensus pattern (4 bp):
AAAG
Found at i:4388990 original size:47 final size:47
Alignment explanation
Indices: 4388926--4389036 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
4388916 GACATTGAGT
*
4388926 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
4388973 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
4389020 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
4389037 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:4390531 original size:24 final size:24
Alignment explanation
Indices: 4390477--4390531 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
4390467 GTTGTTAATT
*
4390477 TATTACTTTATTTTAATATCTTTAT
1 TATTA-TTTATTTTAATATCTTTAG
*
4390502 TA-TATTTACTTTTTATAT-TTTAG
1 TATTATTTA-TTTTAATATCTTTAG
4390525 TATTATT
1 TATTATT
4390532 ATTATCATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.38
24 14 0.54
25 2 0.08
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (24 bp):
TATTATTTATTTTAATATCTTTAG
Done.