Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 170 of 199
Found at i:49693052 original size:13 final size:15
Alignment explanation
Indices: 49693034--49693066 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
49693024 CTGGATTTGG
49693034 TACAAGG-TAGC-AT
1 TACAAGGCTAGCTAT
49693047 TACAAGGCTAGCTAT
1 TACAAGGCTAGCTAT
49693062 TACAA
1 TACAA
49693067 CAAATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 4 0.22
15 7 0.39
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (15 bp):
TACAAGGCTAGCTAT
Found at i:49700708 original size:21 final size:24
Alignment explanation
Indices: 49700664--49700709 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 24
49700654 GCCTACCCCA
49700664 TTCTAGTTAAAGTAGAATAGTATT
1 TTCTAGTTAAAGTAGAATAGTATT
*
49700688 TTCTA-TTAAA-TA-AATATTATT
1 TTCTAGTTAAAGTAGAATAGTATT
49700709 T
1 T
49700710 GTGTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 2 0.10
23 5 0.24
24 5 0.24
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (24 bp):
TTCTAGTTAAAGTAGAATAGTATT
Found at i:49708222 original size:25 final size:25
Alignment explanation
Indices: 49708194--49708243 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
49708184 CCCGAGCTGT
* *
49708194 ATATCGAGAAGCTCTTGCGAGCCAA
1 ATATCGAGAAGCTCATGAGAGCCAA
49708219 ATATCGAGAAGCTCATGAGAGCCAA
1 ATATCGAGAAGCTCATGAGAGCCAA
49708244 GCATCAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (25 bp):
ATATCGAGAAGCTCATGAGAGCCAA
Found at i:49708456 original size:15 final size:14
Alignment explanation
Indices: 49708423--49708456 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
49708413 ATCACATACA
*
49708423 ACAATATTTAATTT
1 ACAATATTTAATAT
49708437 ACAATATTTAAATAT
1 ACAATATTT-AATAT
49708452 ACAAT
1 ACAAT
49708457 TTAGTTACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (14 bp):
ACAATATTTAATAT
Found at i:49710688 original size:19 final size:20
Alignment explanation
Indices: 49710651--49710689 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
49710641 AAGAGCAAAG
*
49710651 AGTTTAGAAAATCTCAAAAA
1 AGTTTAGAAAATCACAAAAA
*
49710671 AGTTTA-AAAATCAGAAAAA
1 AGTTTAGAAAATCACAAAAA
49710690 TATAGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.23
Consensus pattern (20 bp):
AGTTTAGAAAATCACAAAAA
Found at i:49711222 original size:18 final size:17
Alignment explanation
Indices: 49711201--49711243 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
49711191 TAAATTTAAT
49711201 TATTTTTAATAATTATTA
1 TATTTTTAATAATT-TTA
49711219 TATTTTCT-ATAATTTTA
1 TATTTT-TAATAATTTTA
49711236 -ATTTTTAA
1 TATTTTTAA
49711244 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 6 0.26
17 3 0.13
18 12 0.52
19 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTTTAATAATTTTA
Found at i:49711316 original size:12 final size:13
Alignment explanation
Indices: 49711293--49711331 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 13
49711283 TGTTTTGTAA
49711293 TTTTTATAAATTT
1 TTTTTATAAATTT
49711306 TTTTTAT-AATTT
1 TTTTTATAAATTT
49711318 TTTTGTGATAAATT
1 TTTT-T-ATAAATT
49711332 GGAGATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.39
13 8 0.35
14 2 0.09
15 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (13 bp):
TTTTTATAAATTT
Found at i:49712986 original size:4 final size:4
Alignment explanation
Indices: 49712977--49713003 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
49712967 TTTACCCTTT
49712977 AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AAT
49713004 TCAAGTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:49727016 original size:31 final size:33
Alignment explanation
Indices: 49726981--49727046 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 33
49726971 TTCCATTCCT
49726981 TTCTCATCTTCACAACTTTC-TTT-CCATTTTC
1 TTCTCATCTTCACAACTTTCATTTACCATTTTC
* * * *
49727012 TTCTCATTTTCTCCACTTTCATTTACTATTTTC
1 TTCTCATCTTCACAACTTTCATTTACCATTTTC
49727045 TT
1 TT
49727047 GCTTCTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 17 0.59
32 3 0.10
33 9 0.31
ACGTcount: A:0.15, C:0.29, G:0.00, T:0.56
Consensus pattern (33 bp):
TTCTCATCTTCACAACTTTCATTTACCATTTTC
Found at i:49729531 original size:19 final size:17
Alignment explanation
Indices: 49729505--49729558 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
49729495 AAAGCTGTAT
49729505 ACAATTAGAACTCTAAG
1 ACAATTAGAACTCTAAG
* *
49729522 ACATAATTAGAAGCTGT-AT
1 AC--AATTAGAA-CTCTAAG
49729541 ACAATTAGAACTCTAAG
1 ACAATTAGAACTCTAAG
49729558 A
1 A
49729559 TTAAATAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
16 3 0.10
17 12 0.41
19 11 0.38
20 3 0.10
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (17 bp):
ACAATTAGAACTCTAAG
Found at i:49729536 original size:36 final size:36
Alignment explanation
Indices: 49729488--49729558 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
49729478 ATCAAAGGCT
49729488 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
*
49729524 ATAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGA
49729559 TTAAATAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (36 bp):
ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:49729548 original size:17 final size:17
Alignment explanation
Indices: 49729490--49729550 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
49729480 CAAAGGCTAT
*
49729490 AATTAAAAGCTGTATAC
1 AATTAGAAGCTGTATAC
* *
49729507 AATTAGAA-CTCTAAGAC
1 AATTAGAAGCTGT-ATAC
49729524 ATAATTAGAAGCTGTATAC
1 --AATTAGAAGCTGTATAC
49729543 AATTAGAA
1 AATTAGAA
49729551 CTCTAAGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.09
17 18 0.51
19 11 0.31
20 3 0.09
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (17 bp):
AATTAGAAGCTGTATAC
Found at i:49734793 original size:19 final size:17
Alignment explanation
Indices: 49734767--49734820 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
49734757 AAAGCTGTAT
49734767 ACAATTAGAACTCTAAG
1 ACAATTAGAACTCTAAG
* *
49734784 ACATAATTAGAAGCTGT-AT
1 AC--AATTAGAA-CTCTAAG
49734803 ACAATTAGAACTCTAAG
1 ACAATTAGAACTCTAAG
49734820 A
1 A
49734821 TTAAATAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
16 3 0.10
17 12 0.41
19 11 0.38
20 3 0.10
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (17 bp):
ACAATTAGAACTCTAAG
Found at i:49734798 original size:36 final size:36
Alignment explanation
Indices: 49734750--49734820 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
49734740 ATCAAAGGCT
49734750 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
*
49734786 ATAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGA
49734821 TTAAATAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (36 bp):
ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:49734810 original size:17 final size:17
Alignment explanation
Indices: 49734752--49734812 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
49734742 CAAAGGCTAT
*
49734752 AATTAAAAGCTGTATAC
1 AATTAGAAGCTGTATAC
* *
49734769 AATTAGAA-CTCTAAGAC
1 AATTAGAAGCTGT-ATAC
49734786 ATAATTAGAAGCTGTATAC
1 --AATTAGAAGCTGTATAC
49734805 AATTAGAA
1 AATTAGAA
49734813 CTCTAAGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.09
17 18 0.51
19 11 0.31
20 3 0.09
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (17 bp):
AATTAGAAGCTGTATAC
Found at i:49736730 original size:15 final size:15
Alignment explanation
Indices: 49736698--49736731 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
49736688 TTAATAAAAA
*
49736698 TTTAACCATTTTATT
1 TTTAAACATTTTATT
49736713 TTTAAACATATTTATT
1 TTTAAACAT-TTTATT
49736729 TTT
1 TTT
49736732 TTTGAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAAACATTTTATT
Found at i:49736828 original size:49 final size:49
Alignment explanation
Indices: 49736756--49736852 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
49736746 AAAATTTAAC
* *
49736756 TAAATTTGTTAATTTTGTTTTCAATTTATATATATACTCTTTGTTTTTG
1 TAAATTTGTTAATTTTATTTTCAATTTATATATATACTCTTCGTTTTTG
*
49736805 TAAATTTGTTATTTTTATTTTCAATTTATATATATACTCTTCGTTTTT
1 TAAATTTGTTAATTTTATTTTCAATTTATATATATACTCTTCGTTTTT
49736853 CAATTTATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.25, C:0.07, G:0.06, T:0.62
Consensus pattern (49 bp):
TAAATTTGTTAATTTTATTTTCAATTTATATATATACTCTTCGTTTTTG
Found at i:49741110 original size:2 final size:2
Alignment explanation
Indices: 49741103--49741132 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49741093 TTAGGATGTG
49741103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49741133 TGGAGTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49742758 original size:20 final size:20
Alignment explanation
Indices: 49742733--49742772 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
49742723 CGTAAAATGA
*
49742733 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
49742753 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
49742773 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:49742762 original size:34 final size:35
Alignment explanation
Indices: 49742718--49742784 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
49742708 GAGTAAAATA
*
49742718 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
49742752 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
49742785 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:49742788 original size:14 final size:15
Alignment explanation
Indices: 49742712--49742788 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
49742702 CTGTTTGAGT
* *
49742712 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
49742726 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
49742740 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
49742760 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
49742775 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
49742789 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:49742902 original size:20 final size:19
Alignment explanation
Indices: 49742877--49742923 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
49742867 ACATATATTA
49742877 ATATATATTAATAAATTTTT
1 ATATATATTAAT-AATTTTT
* *
49742897 ATATAT-TAAATTATTTTT
1 ATATATATTAATAATTTTT
*
49742915 ACATATATT
1 ATATATATT
49742924 GCAATGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 11 0.50
19 5 0.23
20 6 0.27
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATATATTAATAATTTTT
Found at i:49745017 original size:8 final size:8
Alignment explanation
Indices: 49744970--49745022 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
49744960 ACATTATCTG
49744970 AAAA-TTT
1 AAAATTTT
*
49744977 AAAAATTT
1 AAAATTTT
*
49744985 ATAATTTAT
1 AAAATTT-T
*
49744994 ATAATTTT
1 AAAATTTT
49745002 AAAATTTT
1 AAAATTTT
49745010 AAAATTTT
1 AAAATTTT
*
49745018 CAAAT
1 AAAAT
49745023 GATGATTCGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
7 4 0.10
8 28 0.70
9 8 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (8 bp):
AAAATTTT
Found at i:49748670 original size:24 final size:24
Alignment explanation
Indices: 49748622--49748671 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
49748612 TTATTTGTGC
*
49748622 TATTTTATTTTTTTAGTTTAATAT
1 TATTTTATTTTATTAGTTTAATAT
*
49748646 TATTTTA-TTTATTAGTATTAGTAT
1 TATTTTATTTTATTAGT-TTAATAT
49748670 TA
1 TA
49748672 GTATTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (24 bp):
TATTTTATTTTATTAGTTTAATAT
Found at i:49748692 original size:24 final size:24
Alignment explanation
Indices: 49748654--49748711 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
49748644 ATTATTTTAT
* * * *
49748654 TTATTAGTATTAGTATTAGTATTA
1 TTATTATTATGAGTACTAGTACTA
* *
49748678 TTATTGTTATGAGTACTATTACTA
1 TTATTATTATGAGTACTAGTACTA
49748702 TTATTATTAT
1 TTATTATTAT
49748712 TGGTTTTATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.55
Consensus pattern (24 bp):
TTATTATTATGAGTACTAGTACTA
Found at i:49748724 original size:3 final size:3
Alignment explanation
Indices: 49748643--49748712 Score: 52
Period size: 3 Copynumber: 23.3 Consensus size: 3
49748633 TTTAGTTTAA
* * * *
49748643 TAT TAT T-T TATT TAT TAG TAT TAG TAT TAG TAT TAT TAT TGT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
49748688 GAG TAC TAT TAC TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
49748713 GGTTTTATTA
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:49753814 original size:25 final size:26
Alignment explanation
Indices: 49753769--49753826 Score: 100
Period size: 25 Copynumber: 2.3 Consensus size: 26
49753759 TATTTTCTCG
*
49753769 AAATTTTACCAAGGGTAAAATTGTCA
1 AAATTTTACCAAGGGTAAAATCGTCA
49753795 AAATTTTACC-AGGGTAAAATCGTCA
1 AAATTTTACCAAGGGTAAAATCGTCA
49753820 AAATTTT
1 AAATTTT
49753827 GTTGGGGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 21 0.68
26 10 0.32
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (26 bp):
AAATTTTACCAAGGGTAAAATCGTCA
Found at i:49768343 original size:16 final size:16
Alignment explanation
Indices: 49768309--49768343 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49768299 CCTTTTAATG
*
49768309 AAATGCCATGAAGTTA
1 AAATGCCATGAAGTCA
*
49768325 AAATGCCATGCAGTCA
1 AAATGCCATGAAGTCA
49768341 AAA
1 AAA
49768344 CAAAACAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (16 bp):
AAATGCCATGAAGTCA
Found at i:49769540 original size:20 final size:21
Alignment explanation
Indices: 49769497--49769541 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
49769487 GTATGGTGTT
*
49769497 AATATGCATAATGGAATAGTA
1 AATATGCATAATGGAATAGAA
49769518 AATATG-ATAATGTGAATA-AA
1 AATATGCATAATG-GAATAGAA
49769538 AATA
1 AATA
49769542 ATATGAGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.53, C:0.02, G:0.16, T:0.29
Consensus pattern (21 bp):
AATATGCATAATGGAATAGAA
Found at i:49771871 original size:46 final size:46
Alignment explanation
Indices: 49771806--49771893 Score: 158
Period size: 46 Copynumber: 1.9 Consensus size: 46
49771796 TCGAAAAATT
49771806 ATTAATTTTGGTAAGTTTTGTAGGTTGGACCCATTTTGATTTCATA
1 ATTAATTTTGGTAAGTTTTGTAGGTTGGACCCATTTTGATTTCATA
* *
49771852 ATTAATTTTGGTAAGTTTTGTATGTTGGACTCATTTTGATTT
1 ATTAATTTTGGTAAGTTTTGTAGGTTGGACCCATTTTGATTT
49771894 AATACTACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.23, C:0.07, G:0.19, T:0.51
Consensus pattern (46 bp):
ATTAATTTTGGTAAGTTTTGTAGGTTGGACCCATTTTGATTTCATA
Found at i:49773790 original size:15 final size:15
Alignment explanation
Indices: 49773770--49773799 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
49773760 ATTTACTTTT
49773770 ATATAAAAAATAATA
1 ATATAAAAAATAATA
49773785 ATATAAAAAATAATA
1 ATATAAAAAATAATA
49773800 TGGGCGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
ATATAAAAAATAATA
Found at i:49781641 original size:11 final size:13
Alignment explanation
Indices: 49781616--49781647 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
49781606 ATTTTAGTTT
49781616 AATTAAAATTATA
1 AATTAAAATTATA
49781629 AA-TAAAA-TATA
1 AATTAAAATTATA
49781640 AATTAAAA
1 AATTAAAA
49781648 AGGAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 10 0.56
13 2 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATTAAAATTATA
Found at i:49783793 original size:53 final size:54
Alignment explanation
Indices: 49783695--49784067 Score: 150
Period size: 53 Copynumber: 6.8 Consensus size: 54
49783685 TTTTTTTAAC
* * * *
49783695 ACACTAAAATTTTTTAAAACACGAGAATTTTAGAGACACGAAAA-TTCTTAAAA
1 ACACGAAAATTTTTGAAAACACGACAATTTTAGAAACACGAAAATTTCTTAAAA
* * * *
49783748 ACACGAAAATTTTTGAAAACACGACAATTTT-GAAATAGGAGAAATTTTTTGAAA
1 ACACGAAAATTTTTGAAAACACGACAATTTTAGAAACACGA-AAATTTCTTAAAA
* * * *
49783802 ACACGAAATTTTTTTGAAAAAACCGGA-AATTTTTTTAAAAAAACACGAAAATTT-TT-GAA
1 ACACGAAA-ATTTTTGAAAACA-C-GACAA---TTTT--AGAAACACGAAAATTTCTTAAAA
* * * * * *
49783861 ACAC-AGAAGTTTTTAGAAAACACGAAAAATTTCTTTG-ATCATCG-GAATTT-TTGAAA
1 ACACGA-AAATTTTT-GAAAACACG-ACAA-TT-TTAGAAACA-CGAAAATTTCTTAAAA
* ** **
49783917 ACACGAAAATTTTTTG-AAACACGA-AAGTTTTAAAAAACACGAGTA-TT-TTCGAA
1 ACACGAAAA-TTTTTGAAAACACGACAA-TTTT-AGAAACACGAAAATTTCTTAAAA
* * * *
49783970 ACACCAAAATTTTTGAAAACACGGA-AATTTTTA-AAACAC-ATGAATTTTTTGAAA
1 ACACGAAAATTTTTGAAAACAC-GACAA-TTTTAGAAACACGA-AAATTTCTTAAAA
* ** *
49784024 ACATGAAAA-TTTTGAAAACACGAGGATTTTTGAAAACACGAAAA
1 ACACGAAAATTTTTGAAAACACGACAATTTTAG-AAACACGAAAA
49784068 AAAAATTTTA
Statistics
Matches: 249, Mismatches: 39, Indels: 63
0.71 0.11 0.18
Matches are distributed among these distances:
51 1 0.00
52 28 0.11
53 73 0.29
54 48 0.19
55 29 0.12
56 14 0.06
57 12 0.05
58 10 0.04
59 20 0.08
60 2 0.01
61 6 0.02
62 6 0.02
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (54 bp):
ACACGAAAATTTTTGAAAACACGACAATTTTAGAAACACGAAAATTTCTTAAAA
Found at i:49783823 original size:21 final size:20
Alignment explanation
Indices: 49783744--49783861 Score: 90
Period size: 21 Copynumber: 6.1 Consensus size: 20
49783734 GAAAATTCTT
*
49783744 AAAAACACGAAAATTTTTG-
1 AAAAACACGAAATTTTTTGA
49783763 -AAAACACGACAA--TTTTGA
1 AAAAACACGA-AATTTTTTGA
* **
49783781 AATAGGA-GAAATTTTTTG-
1 AAAAACACGAAATTTTTTGA
49783799 -AAAACACGAAATTTTTTTGA
1 AAAAACACGAAA-TTTTTTGA
*
49783819 AAAAAC-CGGAAATTTTTTTAA
1 AAAAACAC-GAAA-TTTTTTGA
*
49783840 AAAAACACGAAAATTTTTGA
1 AAAAACACGAAATTTTTTGA
49783860 AA
1 AA
49783862 CACAGAAGTT
Statistics
Matches: 79, Mismatches: 9, Indels: 21
0.72 0.08 0.19
Matches are distributed among these distances:
17 10 0.13
18 15 0.19
19 17 0.22
20 9 0.11
21 27 0.34
22 1 0.01
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (20 bp):
AAAAACACGAAATTTTTTGA
Found at i:49784117 original size:25 final size:24
Alignment explanation
Indices: 49784089--49784135 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
49784079 AACCCAAAAA
49784089 TTTTT-AAAACACGAGAAATTTTTT
1 TTTTTGAAAACACGA-AAATTTTTT
*
49784113 TTTTTGAAAACATGAAAATTTTT
1 TTTTTGAAAACACGAAAATTTTT
49784136 GAAACACCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (24 bp):
TTTTTGAAAACACGAAAATTTTTT
Found at i:49784230 original size:19 final size:18
Alignment explanation
Indices: 49783695--49784229 Score: 316
Period size: 18 Copynumber: 29.1 Consensus size: 18
49783685 TTTTTTTAAC
* *
49783695 ACACTAAAATTTTTTAAA
1 ACACGAAAATTTTTGAAA
* * *
49783713 ACACGAGAATTTTAG-AG
1 ACACGAAAATTTTTGAAA
* *
49783730 ACACGAAAATTCTTAAAA
1 ACACGAAAATTTTTGAAA
49783748 ACACGAAAATTTTTGAAA
1 ACACGAAAATTTTTGAAA
*
49783766 ACACGACAA-TTTTGAAA
1 ACACGAAAATTTTTGAAA
* *
49783783 TAGGA-GAAATTTTTTGAAA
1 -A-CACGAAAATTTTTGAAA
*
49783802 ACACGAAATTTTTTTGAAA
1 ACACGAAA-ATTTTTGAAA
* * *
49783821 AAACCGGAAATTTTTTTAAAAAA
1 ACA-C-GAAA-ATTTTT--GAAA
49783844 ACACGAAAATTTTTG-AA
1 ACACGAAAATTTTTGAAA
*
49783861 ACAC-AGAAGTTTTTAGAAA
1 ACACGA-AAATTTTT-GAAA
49783880 ACACGAAAAATTTCTTTG--A
1 ACACG-AAAA-TT-TTTGAAA
* *
49783899 TCATCG-GAATTTTTGAAA
1 ACA-CGAAAATTTTTGAAA
49783917 ACACGAAAATTTTTTG-AA
1 ACACGAAAA-TTTTTGAAA
* **
49783935 ACACGAAAGTTTTAAAAA
1 ACACGAAAATTTTTGAAA
** *
49783953 ACACGAGTATTTTCG-AA
1 ACACGAAAATTTTTGAAA
*
49783970 ACACCAAAATTTTTGAAA
1 ACACGAAAATTTTTGAAA
*
49783988 ACACGGAAATTTTT-AAA
1 ACACGAAAATTTTTGAAA
*
49784005 ACAC-ATGAATTTTTTGAAA
1 ACACGA--AAATTTTTGAAA
*
49784024 ACATGAAAA-TTTTGAAA
1 ACACGAAAATTTTTGAAA
**
49784041 ACACGAGGATTTTTGAAA
1 ACACGAAAATTTTTGAAA
*
49784059 ACACGAAAAAAAAATTTT-AAA
1 ACACG----AAAATTTTTGAAA
* *
49784080 ACCCAAAAATTTTT-AAA
1 ACACGAAAATTTTTGAAA
49784097 ACACGAGAAATTTTTTTTTTTGAAA
1 ACACGA-AAA------TTTTTGAAA
*
49784122 ACATGAAAATTTTTG-AA
1 ACACGAAAATTTTTGAAA
*
49784139 ACACCG-AAA-TCTTGAAA
1 ACA-CGAAAATTTTTGAAA
*
49784156 ACACGAAGATTTTTGAAA
1 ACACGAAAATTTTTGAAA
*
49784174 ACACGAAGATTTTTTG-AA
1 ACACGAA-AATTTTTGAAA
*
49784192 ACACGAGAATTTTTTGAAA
1 ACACGA-AAATTTTTGAAA
*
49784211 ACACGAAAAATTTTGAAA
1 ACACGAAAATTTTTGAAA
49784229 A
1 A
49784230 ATAGAAATTT
Statistics
Matches: 403, Mismatches: 66, Indels: 96
0.71 0.12 0.17
Matches are distributed among these distances:
16 11 0.03
17 106 0.26
18 162 0.40
19 57 0.14
20 11 0.03
21 25 0.06
22 10 0.02
23 5 0.01
24 8 0.02
25 8 0.02
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (18 bp):
ACACGAAAATTTTTGAAA
Found at i:49784247 original size:23 final size:24
Alignment explanation
Indices: 49784221--49784265 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
49784211 ACACGAAAAA
49784221 TTTTGAAAA-AT-AGAAATTTTGTT
1 TTTTGAAAACATGAG-AATTTTGTT
*
49784244 TTTTTAAAACATGAGAATTTTG
1 TTTTGAAAACATGAGAATTTTG
49784266 AAAAACGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 9 0.47
25 2 0.11
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (24 bp):
TTTTGAAAACATGAGAATTTTGTT
Found at i:49784497 original size:21 final size:20
Alignment explanation
Indices: 49784473--49784517 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
49784463 GAACGCGAAT
49784473 ATTTTTTGAA-ACACGAGAAA
1 ATTTTTTGAAGACACGA-AAA
*
49784493 AATTTTTGAAGACACGAAAA
1 ATTTTTTGAAGACACGAAAA
49784513 ATTTT
1 ATTTT
49784518 GAAAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.33
Consensus pattern (20 bp):
ATTTTTTGAAGACACGAAAA
Found at i:49784498 original size:20 final size:18
Alignment explanation
Indices: 49784456--49784521 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 18
49784446 TTGCCTTATT
* * *
49784456 TTTTTGAGAACGCGAATAT
1 TTTTTGA-AACACGAAAAA
49784475 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACAC--GAAAAA
49784495 TTTTTGAAGACACGAAAAA
1 TTTTTGAA-ACACGAAAAA
49784514 -TTTTGAAA
1 TTTTTGAAA
49784522 ATTATAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.02
18 11 0.27
19 13 0.32
20 12 0.29
21 4 0.10
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (18 bp):
TTTTTGAAACACGAAAAA
Found at i:49784691 original size:5 final size:5
Alignment explanation
Indices: 49784681--49784708 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
49784671 AAAGTATTTA
49784681 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
49784709 AATATAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:49784899 original size:20 final size:20
Alignment explanation
Indices: 49784874--49784938 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 20
49784864 TTATTTTTTA
*
49784874 TTTTTTTCTCTTTTTTCCTC
1 TTTTTTTCTTTTTTTTCCTC
*
49784894 TTTTTTTCTTTTTCTTTTTCTC
1 TTTTTTTC-TTTT-TTTTCCTC
49784916 TCTTTTTTCTTTTTTTTCTCTC
1 T-TTTTTTCTTTTTTTTC-CTC
49784938 T
1 T
49784939 GCTGGGCTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
20 8 0.21
21 7 0.18
22 16 0.42
23 7 0.18
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTTCTTTTTTTTCCTC
Found at i:49784900 original size:23 final size:23
Alignment explanation
Indices: 49784874--49784928 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
49784864 TTATTTTTTA
49784874 TTTTTTTCTCTTTTT-TCCTCTTT
1 TTTTTTTCTCTTTTTCT-CTCTTT
*
49784897 TTTTCTTTTTCTTTTTCTCTCTTT
1 TTTT-TTTCTCTTTTTCTCTCTTT
49784921 TTTCTTTT
1 TTT-TTTT
49784929 TTTTCTCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.14
24 22 0.79
25 2 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTTCTCTTTTTCTCTCTTT
Found at i:49784930 original size:24 final size:25
Alignment explanation
Indices: 49784868--49784936 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
49784858 CCCTTTTTAT
*
49784868 TTTTTATTTTTTTCTCTTTTTTCCTC
1 TTTTT-TTTTTTTCTCTTTTCTCCTC
*
49784894 TTTTTTTCTTTTTCT-TTTTCTCTCTT
1 TTTTTTT-TTTTTCTCTTTTCTC-CTC
49784920 TTTTCTTTTTTTTCTCT
1 TTTT-TTTTTTTTCTCT
49784937 CTGCTGGGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 8 0.22
26 25 0.68
27 4 0.11
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTTTTTTTTTTCTCTTTTCTCCTC
Found at i:49784930 original size:32 final size:34
Alignment explanation
Indices: 49784860--49784934 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
49784850 ATTGAACCCC
* *
49784860 CTTTTTAT-TTTTTATTTTTTTCTCTTTTTTCCT
1 CTTTTTTTCTTTTTATTTTTCTCTCTTTTTTCCT
*
49784893 CTTTTTTTCTTTTTCTTTTTCTCTCTTTTTT-CT
1 CTTTTTTTCTTTTTATTTTTCTCTCTTTTTTCCT
49784926 -TTTTTTTCT
1 CTTTTTTTCT
49784935 CTCTGCTGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 9 0.24
33 9 0.24
34 20 0.53
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (34 bp):
CTTTTTTTCTTTTTATTTTTCTCTCTTTTTTCCT
Found at i:49785214 original size:3 final size:3
Alignment explanation
Indices: 49785208--49785234 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
49785198 GTTTTTTTCT
49785208 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
49785235 AAGCCCTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:49785596 original size:30 final size:30
Alignment explanation
Indices: 49785562--49785730 Score: 137
Period size: 30 Copynumber: 5.7 Consensus size: 30
49785552 TAAATGCAGA
*
49785562 AAAGTTTTGGGGCCAAAATGTAATTTTGAG
1 AAAGTTTTGGGGTCAAAATGTAATTTTGAG
* * *
49785592 AAAGTTTAGGGGTTAAAATGTAATTTTGAT
1 AAAGTTTTGGGGTCAAAATGTAATTTTGAG
*** *
49785622 AAA-TTTTCAATGTCAAAATGTAATTTAGA-
1 AAAGTTTT-GGGGTCAAAATGTAATTTTGAG
* * ** *
49785651 AAAGTTTAGGGCTTGAAATGTAATTTTGAA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGAG
* *
49785681 AAAATTTAGGGGTCAAAATGTAATTTT-AG
1 AAAGTTTTGGGGTCAAAATGTAATTTTGAG
* **
49785710 AAAAATTCAGGGGTCAAAATG
1 -AAAGTTTTGGGGTCAAAATG
49785731 CAAAATTTTA
Statistics
Matches: 111, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
29 21 0.19
30 90 0.81
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTGAG
Found at i:49785670 original size:59 final size:59
Alignment explanation
Indices: 49785575--49785713 Score: 181
Period size: 59 Copynumber: 2.3 Consensus size: 59
49785565 GTTTTGGGGC
* * * * *
49785575 CAAAATGTAATTTTGAGAAAGTTTAGGGGTTAAAATGTAATTTTGATAAATTTTCA-ATGT
1 CAAAATGTAATTTAGA-AAAGTTTAGGGCTTAAAATGTAATTTTGAAAAAATTT-AGAGGT
* *
49785635 CAAAATGTAATTTAGAAAAGTTTAGGGCTTGAAATGTAATTTTGAAAAAATTTAGGGGT
1 CAAAATGTAATTTAGAAAAGTTTAGGGCTTAAAATGTAATTTTGAAAAAATTTAGAGGT
49785694 CAAAATGTAATTTTAGAAAA
1 CAAAATGTAA-TTTAGAAAA
49785714 ATTCAGGGGT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
58 1 0.01
59 45 0.64
60 24 0.34
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.36
Consensus pattern (59 bp):
CAAAATGTAATTTAGAAAAGTTTAGGGCTTAAAATGTAATTTTGAAAAAATTTAGAGGT
Found at i:49785744 original size:30 final size:29
Alignment explanation
Indices: 49785666--49785745 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 29
49785656 TTAGGGCTTG
* *
49785666 AAATGTAATTTTGAAAAAATTTAGGGGTCA
1 AAATGAAATTTT-AAAAAATTCAGGGGTCA
*
49785696 AAATGTAATTTTAGAAAAATTCAGGGGTCA
1 AAATGAAATTTTA-AAAAATTCAGGGGTCA
49785726 AAATGCAAAATTTTAAAAAA
1 AAATG--AAATTTTAAAAAA
49785746 AATTTTAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
29 1 0.02
30 32 0.71
31 5 0.11
32 7 0.16
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (29 bp):
AAATGAAATTTTAAAAAATTCAGGGGTCA
Found at i:49786174 original size:74 final size:74
Alignment explanation
Indices: 49785920--49786345 Score: 663
Period size: 74 Copynumber: 5.6 Consensus size: 74
49785910 CGGCGTATGG
* * *
49785920 CCCGAGGCTCAACTCACCTCTAGCATTATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAAGA
1 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGA---TTTTTGAAAAACAAAAATTGAAAA-A
* *
49785985 TACCTCGGCATGTGG
62 TACCTCAGC--GTGA
* * * * *
49786000 CCCGAGGCTCAACTCACCTCTCGTAATATAAGTTGATTTTTGAAAAATAGAAACTTAAAAAATAC
1 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACA-AAAATTGAAAAATAC
49786065 CTCAGCGTGA
65 CTCAGCGTGA
49786075 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAAAAATTGAAAAATACC
1 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAAAAATTGAAAAATACC
49786140 TCAGCGTGA
66 TCAGCGTGA
*
49786149 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAACAAACAAAAATTAAAAAATA
1 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTG-AA-AAACAAAAATTGAAAAATA
49786214 CCTCAGCGTGA
64 CCTCAGCGTGA
49786225 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAAAAATTGAAAAATACC
1 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAAAAATTGAAAAATACC
*
49786290 TCAGCATGA
66 TCAGCGTGA
49786299 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAA
1 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAA
49786346 AGACAGAAAT
Statistics
Matches: 325, Mismatches: 18, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
74 140 0.43
75 53 0.16
76 71 0.22
77 21 0.06
78 8 0.02
80 32 0.10
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (74 bp):
CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAAAAATTGAAAAATACC
TCAGCGTGA
Found at i:49786248 original size:150 final size:150
Alignment explanation
Indices: 49785920--49786362 Score: 692
Period size: 150 Copynumber: 2.9 Consensus size: 150
49785910 CGGCGTATGG
* * *
49785920 CCCGAGGCTCAACTCACCTCTAGCATTATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAAGA
1 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGA---TTTTTGAAAAACAAAAATTGAAAA-A
* * * * *
49785985 TACCTCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTAATATAAGTTGATTTTTGAAAAATA-
62 TACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAGAC
* *
49786049 GAAACTTAAAAAATACCTCAGCGTGA
125 AAAAATTAAAAAATACCTCAGCGTGA
49786075 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAAAAATTGAAAAATACC
1 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAAAAATTGAAAAATACC
49786140 TCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAACAA-ACAAAAA
66 TCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAA-AAGACAAAAA
49786204 TTAAAAAATACCTCAGCGTGA
130 TTAAAAAATACCTCAGCGTGA
49786225 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAAAAATTGAAAAATACC
1 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAAAAATTGAAAAATACC
* *
49786290 TCAGCATGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAGACAGAAA
66 TCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTG-AAAAAGACAAAAA
49786355 TTAAAAAA
130 TTAAAAAA
49786363 ATATTTCTTA
Statistics
Matches: 273, Mismatches: 11, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
149 47 0.17
150 143 0.52
151 26 0.10
152 23 0.08
155 34 0.12
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (150 bp):
CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAAAAATTGAAAAATACC
TCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAGACAAAAAT
TAAAAAATACCTCAGCGTGA
Found at i:49787237 original size:23 final size:23
Alignment explanation
Indices: 49787211--49787256 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
49787201 TGATTTTTCT
*
49787211 TTTTATTTTCTT-TGTTTTTTTTA
1 TTTTATTTT-TTGTCTTTTTTTTA
*
49787234 TTTTGTTTTTTGTCTTTTTTTTA
1 TTTTATTTTTTGTCTTTTTTTTA
49787257 GACATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.07, C:0.04, G:0.07, T:0.83
Consensus pattern (23 bp):
TTTTATTTTTTGTCTTTTTTTTA
Found at i:49796036 original size:53 final size:53
Alignment explanation
Indices: 49795970--49796094 Score: 153
Period size: 53 Copynumber: 2.4 Consensus size: 53
49795960 TTTTTTGAAC
* * * *
49795970 ACACTAAAATTTTTTAAAACACGAGAATTTTAGAGACACGAAAA-TTCTTAAAA
1 ACACGAAATTTTTTTAAAACACGACAATTTT-GAAACACGAAAATTTCTTAAAA
* * * * *
49796023 ACATGAAATTTTTTGAAAACACGACAATTTTGAAACAGGAAAATTTTTTGAAA
1 ACACGAAATTTTTTTAAAACACGACAATTTTGAAACACGAAAATTTCTTAAAA
49796076 ACACGAAATTTTTTTAAAA
1 ACACGAAATTTTTTTAAAA
49796095 AAACTGGATT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
52 10 0.17
53 50 0.83
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.31
Consensus pattern (53 bp):
ACACGAAATTTTTTTAAAACACGACAATTTTGAAACACGAAAATTTCTTAAAA
Found at i:49796096 original size:20 final size:20
Alignment explanation
Indices: 49796055--49796130 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 20
49796045 GACAATTTTG
* * *
49796055 AAACAGGAAAATTTTTT-GA
1 AAACACGAAATTTTTTTAAA
49796074 AAACACGAAATTTTTTTAAA
1 AAACACGAAATTTTTTTAAA
* *
49796094 AAA-ACTGGATTTTTTTTAAAA
1 AAACAC-GAAATTTTTTT-AAA
49796115 AAACACGAAAATTTTT
1 AAACACG-AAATTTTT
49796131 GAAACAAAGC
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 17 0.38
20 13 0.29
21 7 0.16
22 8 0.18
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (20 bp):
AAACACGAAATTTTTTTAAA
Found at i:49796163 original size:37 final size:36
Alignment explanation
Indices: 49796114--49796210 Score: 99
Period size: 37 Copynumber: 2.7 Consensus size: 36
49796104 TTTTTTTAAA
*
49796114 AAAACACG-AAAATTTTTGAAACAAAGCAGTTTTTAG
1 AAAACACGAAAAATTTTTGAAACAAAGCAATTTTT-G
* ** *
49796150 AAAACACGAAAAATTTCTTTG-ATCATCGGAATTTTTG
1 AAAACACGAAAAA-TT-TTTGAAACAAAGCAATTTTTG
*
49796187 AAAACACGAAAATTTTTTGAAACA
1 AAAACACGAAAAATTTTTGAAACA
49796211 CGAAAGTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
35 4 0.08
36 13 0.26
37 17 0.34
38 12 0.24
39 4 0.08
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (36 bp):
AAAACACGAAAAATTTTTGAAACAAAGCAATTTTTG
Found at i:49796227 original size:36 final size:36
Alignment explanation
Indices: 49795970--49796515 Score: 140
Period size: 35 Copynumber: 15.1 Consensus size: 36
49795960 TTTTTTGAAC
* * * * *
49795970 ACACTAAAATTTTTTAAAACACGAGAATTTT-AGAG
1 ACACGAAAATTTTTTGAAACACGAAAATTTTAAAAA
* ** * * **
49796005 ACACGAAAATTCTTAAAAACATGAAATTTTTTGAAA
1 ACACGAAAATTTTTTGAAACACGAAAATTTTAAAAA
* * **
49796041 ACACGACAA--TTTTGAAACAGGAAAATTTTTTGAAA
1 ACACGAAAATTTTTTGAAACACGAAAA-TTTTAAAAA
* * * ***
49796076 ACACGAAATTTTTTTAAAAAAACTGGATTTTTTTTAAAAAA
1 ACACGAAAATTTTTT-GAAACAC--GA-AAATTTT-AAAAA
* * ** *
49796117 ACACGAAAA-TTTTTGAAACAAAGCAGTTTTTAGAAA
1 ACACGAAAATTTTTTGAAAC-ACGAAAATTTTAAAAA
* * **
49796153 ACACGAAAAATTTCTTTG-ATCATCG-GAATTTTTGAAA
1 ACACG-AAAATTT-TTTGAAACA-CGAAAATTTTAAAAA
*
49796190 ACACGAAAATTTTTTGAAACACGAAAGTTTTAAAAA
1 ACACGAAAATTTTTTGAAACACGAAAATTTTAAAAA
* ** * *
49796226 ACACTAGTA-TTTTCGAAACACGAAAATTTT-TAAA
1 ACACGAAAATTTTTTGAAACACGAAAATTTTAAAAA
** * *
49796260 ACACGGGAATTTTTTGAAAACATGAAAATTTT-GAAA
1 ACACGAAAATTTTTTG-AAACACGAAAATTTTAAAAA
* ** * ***
49796296 ACATGAGGA-TTTTTGAAAACAC-AAATTTTTTTTTAA
1 ACACGAAAATTTTTTG-AAACACGAAA-ATTTTAAAAA
* ** **
49796332 A-ACGCAAAAATTTTT-AAACACGAATTTTTTTTTTTTGAAA
1 ACACG-AAAATTTTTTGAAACACGAA-----AATTTTAAAAA
* * *
49796372 ACAGGAAAA-TTTTTGAAACACCG-AAATCTT-GAAA
1 ACACGAAAATTTTTTGAAACA-CGAAAATTTTAAAAA
* * ***
49796406 ACACGAAGA-TTTTTGAAAACACGAAGATTTTTTGAA
1 ACACGAAAATTTTTTG-AAACACGAAAATTTTAAAAA
* *
49796442 ACACGAGAATTTTTTGAAAACACGAAAAATTTTGAAAA
1 ACACGAAAATTTTTTG-AAACACG-AAAATTTTAAAAA
* * * * *
49796480 ATA-G-AATTTTTTTTAAACATGAAAATTTTGAAAA
1 ACACGAAAATTTTTTGAAACACGAAAATTTTAAAAA
49796514 AC
1 AC
49796516 GAAATCTTTT
Statistics
Matches: 384, Mismatches: 91, Indels: 73
0.70 0.17 0.13
Matches are distributed among these distances:
34 56 0.15
35 114 0.30
36 88 0.23
37 47 0.12
38 21 0.05
39 12 0.03
40 31 0.08
41 15 0.04
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (36 bp):
ACACGAAAATTTTTTGAAACACGAAAATTTTAAAAA
Found at i:49796291 original size:17 final size:18
Alignment explanation
Indices: 49796271--49796316 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
49796261 CACGGGAATT
49796271 TTTTGAAAACATGA-AAA
1 TTTTGAAAACATGAGAAA
* *
49796288 TTTTGAAAACATGAGGAT
1 TTTTGAAAACATGAGAAA
49796306 TTTTGAAAACA
1 TTTTGAAAACA
49796317 CAAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.33
Consensus pattern (18 bp):
TTTTGAAAACATGAGAAA
Found at i:49796480 original size:19 final size:18
Alignment explanation
Indices: 49795961--49796479 Score: 250
Period size: 18 Copynumber: 28.6 Consensus size: 18
49795951 TGAAACATTT
* *
49795961 TTTTTGAACACACTAAAA
1 TTTTTGAAAACACGAAAA
* *
49795979 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* *
49795997 TTTTAG-AGACACGAAAA
1 TTTTTGAAAACACGAAAA
* * * *
49796014 TTCTTAAAAACATGAAAT
1 TTTTTGAAAACACGAAAA
*
49796032 TTTTTGAAAACACGACAA
1 TTTTTGAAAACACGAAAA
*
49796050 -TTTTG-AAACAGGAAAA
1 TTTTTGAAAACACGAAAA
*
49796066 TTTTTTGAAAACACGAAATT
1 -TTTTTGAAAACACGAAA-A
* * ***
49796086 TTTTTAAAAAAACTGGATTT
1 TTTTTGAAAACAC--GAAAA
*
49796106 TTTTTAAAAAAACACGAAAA
1 TTTTT--GAAAACACGAAAA
*
49796126 TTTTTG-AAACA--AAGCAG
1 TTTTTGAAAACACGAA--AA
49796143 TTTTTAGAAAACACGAAAAA
1 TTTTT-GAAAACACG-AAAA
* *
49796163 TTTCTTTG--ATCATCG-GAA
1 -TT-TTTGAAAACA-CGAAAA
49796181 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
49796199 TTTTTTG-AAACACGAAAG
1 -TTTTTGAAAACACGAAAA
** * **
49796217 TTTTAAAAAACACTAGTA
1 TTTTTGAAAACACGAAAA
*
49796235 TTTTCG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
49796252 TTTTT-AAAACACGGGAAT
1 TTTTTGAAAACAC-GAAAA
*
49796270 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
* **
49796288 -TTTTGAAAACATGAGGA
1 TTTTTGAAAACACGAAAA
*
49796305 TTTTTGAAAACAC-AAATTT
1 TTTTTGAAAACACGAAA--A
* * *
49796324 TTTTTTAAAACGCAAAAA
1 TTTTTGAAAACACGAAAA
**
49796342 TTTTT--AAACACGAATTTTTTT
1 TTTTTGAAAACACGAA-----AA
*
49796363 TTTTTGAAAACAGGAAAA
1 TTTTTGAAAACACGAAAA
49796381 TTTTTG-AAACACCG-AAA
1 TTTTTGAAAACA-CGAAAA
* *
49796398 -TCTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
*
49796415 TTTTTGAAAACACGAAGAT
1 TTTTTGAAAACACGAA-AA
*
49796434 TTTTTG-AAACACGAGAAT
1 TTTTTGAAAACACGA-AAA
49796452 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
49796470 ATTTTGAAAA
1 TTTTTGAAAA
49796480 ATAGAATTTT
Statistics
Matches: 376, Mismatches: 80, Indels: 90
0.69 0.15 0.16
Matches are distributed among these distances:
15 2 0.01
16 26 0.07
17 85 0.23
18 148 0.39
19 66 0.18
20 19 0.05
21 10 0.03
22 12 0.03
23 8 0.02
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:49796526 original size:18 final size:17
Alignment explanation
Indices: 49796362--49796526 Score: 95
Period size: 18 Copynumber: 9.4 Consensus size: 17
49796352 CGAATTTTTT
*
49796362 TTTTTTGAAAACAGGAAA
1 TTTTTTGAAAA-ACGAAA
* *
49796380 ATTTTTGAAACACCGAAA
1 TTTTTTGAAA-AACGAAA
*
49796398 --TCTTGAAAACACGAAGA
1 TTTTTTGAAAA-ACGAA-A
49796415 -TTTTTGAAAACACGAAGA
1 TTTTTTGAAAA-ACGAA-A
*
49796433 TTTTTTGAAACACGAGAA
1 TTTTTTGAAAAACGA-AA
49796451 TTTTTTGAAAACACGAAA
1 TTTTTTGAAAA-ACGAAA
** * *
49796469 AATTTTGAAAAATAGAAT
1 TTTTTTGAAAAA-CGAAA
* * *
49796487 TTTTTTTAAACATGAAA
1 TTTTTTGAAAAACGAAA
*
49796504 -ATTTTGAAAAACGAAA
1 TTTTTTGAAAAACGAAA
49796520 TCTTTTT
1 T-TTTTT
49796527 TATTTTTATT
Statistics
Matches: 114, Mismatches: 23, Indels: 20
0.73 0.15 0.13
Matches are distributed among these distances:
15 1 0.01
16 23 0.20
17 5 0.04
18 70 0.61
19 15 0.13
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (17 bp):
TTTTTTGAAAAACGAAA
Found at i:49796526 original size:35 final size:36
Alignment explanation
Indices: 49796415--49796528 Score: 117
Period size: 35 Copynumber: 3.2 Consensus size: 36
49796405 AACACGAAGA
* ** *
49796415 TTTTTGAAAACACGAAGATTTTTTGAAACACGAGAAT
1 TTTTTTAAAACACGAA-AAATTTTGAAAAACGAGAAT
* *
49796452 TTTTTGAAAACACGAAAAATTTTGAAAAA-TAGAAT
1 TTTTTTAAAACACGAAAAATTTTGAAAAACGAGAAT
* *
49796487 TTTTTTTAAACATG-AAAATTTTGAAAAACGA-AAT
1 TTTTTTAAAACACGAAAAATTTTGAAAAACGAGAAT
49796521 CTTTTTTA
1 -TTTTTTA
49796529 TTTTTATTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
34 17 0.26
35 23 0.35
36 10 0.15
37 16 0.24
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (36 bp):
TTTTTTAAAACACGAAAAATTTTGAAAAACGAGAAT
Found at i:49796723 original size:19 final size:20
Alignment explanation
Indices: 49796699--49796761 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
49796689 GTTGCCTTAT
* *
49796699 TTTTTTGAAA-ACGCGAATA
1 TTTTTTGAAACACGAGAAAA
49796718 TTTTTTGAAACACGAGAAAA
1 TTTTTTGAAACACGAGAAAA
*
49796738 ATTTTTGAAGACACGA-AAAA
1 TTTTTTGAA-ACACGAGAAAA
49796758 TTTT
1 TTTT
49796762 GAAAAATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 10 0.26
20 22 0.58
21 6 0.16
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (20 bp):
TTTTTTGAAACACGAGAAAA
Found at i:49796742 original size:20 final size:19
Alignment explanation
Indices: 49796700--49796765 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
49796690 TTGCCTTATT
* *
49796700 TTTTTGAAA-ACGCGAATAT
1 TTTTTGAAACACG-GAAAAA
49796719 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACACG-GAAAAA
49796739 TTTTTGAAGACAC-GAAAAA
1 TTTTTGAA-ACACGGAAAAA
49796758 -TTTTGAAA
1 TTTTTGAAA
49796766 AATATAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.02
18 7 0.17
19 15 0.36
20 15 0.36
21 4 0.10
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (19 bp):
TTTTTGAAACACGGAAAAA
Found at i:49797132 original size:24 final size:26
Alignment explanation
Indices: 49797093--49797163 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 26
49797083 AATTGAACCC
*
49797093 TCTTTTTTTAT-T-TTTTATT-TT-T
1 TCTTTTTTTCTCTCTTTTATTCTTAT
*
49797115 TCTCTTTTTTC-CTCTTTTTTTCTTAT
1 TCT-TTTTTTCTCTCTTTTATTCTTAT
49797141 TCTTTTTTTCTCTCTTTT-TTCTT
1 TCTTTTTTTCTCTCTTTTATTCTT
49797164 TTTTTTCTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 3 0.07
23 7 0.17
24 6 0.15
25 14 0.34
26 11 0.27
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (26 bp):
TCTTTTTTTCTCTCTTTTATTCTTAT
Found at i:49797132 original size:26 final size:25
Alignment explanation
Indices: 49797103--49797167 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 25
49797093 TCTTTTTTTA
49797103 TTTTTTATTTTTTCTCTTTTTTC-CTC
1 TTTTTT-TTTTTTCT-TTTTTTCTCTC
*
49797129 TTTTTTTCTTATTCTTTTTTTCTCTC
1 TTTTTTT-TTTTTCTTTTTTTCTCTC
49797155 TTTTTTCTTTTTT
1 TTTTTT-TTTTTT
49797168 TTCTCTCTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 8 0.24
26 25 0.74
27 1 0.03
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTTTTTTTTTTCTTTTTTTCTCTC
Found at i:49797134 original size:34 final size:36
Alignment explanation
Indices: 49797091--49797169 Score: 105
Period size: 34 Copynumber: 2.3 Consensus size: 36
49797081 CAAATTGAAC
49797091 CCTCTTTTTTTATT-TT-TTATTTTT-TCTCTTTTTT
1 CCTCTTTTTTTATTATTCTT-TTTTTCTCTCTTTTTT
*
49797125 CCTCTTTTTTTCTTATTCTTTTTTTCTCTCTTTTTT
1 CCTCTTTTTTTATTATTCTTTTTTTCTCTCTTTTTT
49797161 -CT-TTTTTTT
1 CCTCTTTTTTT
49797170 CTCTCTGCTG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
34 20 0.49
35 9 0.22
36 12 0.29
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (36 bp):
CCTCTTTTTTTATTATTCTTTTTTTCTCTCTTTTTT
Found at i:49797160 original size:25 final size:24
Alignment explanation
Indices: 49797117--49797163 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
49797107 TTATTTTTTC
49797117 TCTTTTTTCCTCTTTTTTTCTTAT
1 TCTTTTTTCCTCTTTTTTTCTTAT
*
49797141 TCTTTTTTTCTCTCTTTTTTCTT
1 TCTTTTTTCCTCT-TTTTTTCTT
49797164 TTTTTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (24 bp):
TCTTTTTTCCTCTTTTTTTCTTAT
Found at i:49797170 original size:34 final size:37
Alignment explanation
Indices: 49797095--49797171 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 37
49797085 TTGAACCCTC
* *
49797095 TTTTT-TTATTTTTTATTTTTTCTCTTTTTTCCTCTT
1 TTTTTCTTATTCTTTATTTTCTCTCTTTTTTCCTCTT
49797131 TTTTTCTTATTCTTT-TTTTCTCTCTTTTTT-CT-TT
1 TTTTTCTTATTCTTTATTTTCTCTCTTTTTTCCTCTT
49797165 TTTTTCT
1 TTTTTCT
49797172 CTCTGCTGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 9 0.24
35 2 0.05
36 19 0.50
37 8 0.21
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.81
Consensus pattern (37 bp):
TTTTTCTTATTCTTTATTTTCTCTCTTTTTTCCTCTT
Found at i:49797226 original size:24 final size:22
Alignment explanation
Indices: 49797197--49797257 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
49797187 GCGCGCGGGC
*
49797197 CTGGGCTGCTGGTTTTGGGCTGCG
1 CTGGGCTGCTGGTGTTGGGCT--G
*
49797221 CTGGGCTTG-TGCTGTTGGGCTG
1 CTGGGC-TGCTGGTGTTGGGCTG
49797243 CTGTGGCTGCTGGTG
1 CTG-GGCTGCTGGTG
49797258 GGTCAGCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 6 0.19
23 7 0.23
24 16 0.52
25 2 0.06
ACGTcount: A:0.00, C:0.20, G:0.46, T:0.34
Consensus pattern (22 bp):
CTGGGCTGCTGGTGTTGGGCTG
Found at i:49797340 original size:14 final size:14
Alignment explanation
Indices: 49797323--49797349 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49797313 GCCTTTTTAT
49797323 TTGTTTTTTTTTTG
1 TTGTTTTTTTTTTG
49797337 TTGTTTTTTTTTT
1 TTGTTTTTTTTTT
49797350 AAATCAATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (14 bp):
TTGTTTTTTTTTTG
Found at i:49797469 original size:3 final size:3
Alignment explanation
Indices: 49797463--49797514 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
49797453 TTTTCTTTTT
*
49797463 TTC TTC TTC TTTC TTC TTC TT- TTCC TTC TTC TTC TTC TTC GTC TTC
1 TTC TTC TTC -TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC
49797509 TTC TTC
1 TTC TTC
49797515 AAGCCCTAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 37 0.84
4 5 0.11
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:49797475 original size:18 final size:18
Alignment explanation
Indices: 49797454--49797513 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 18
49797444 TTTGGTTTTT
49797454 TTTCTTTTTTTCTTCTTC
1 TTTCTTTTTTTCTTCTTC
49797472 TTTCTTCTTCTTTTCCTTCTTC
1 TTTC-T-TT-TTTT-CTTCTTC
**
49797494 -TTCTTCTTCGTCTTCTTC
1 TTTCTT-TTTTTCTTCTTC
49797512 TT
1 TT
49797514 CAAGCCCTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
18 11 0.32
19 5 0.15
20 4 0.12
21 7 0.21
22 7 0.21
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTCTTTTTTTCTTCTTC
Found at i:49797892 original size:30 final size:30
Alignment explanation
Indices: 49797858--49798003 Score: 172
Period size: 30 Copynumber: 4.9 Consensus size: 30
49797848 CCGAAACGTG
*
49797858 ATTTTGAGGAAGTTTAGGGGTCAAAATGTA
1 ATTTTGAGAAAGTTTAGGGGTCAAAATGTA
* * *
49797888 ATTTTGAGAAAGTTTCGAGGTTAAAATGTA
1 ATTTTGAGAAAGTTTAGGGGTCAAAATGTA
* * *
49797918 ATTTAGA-AAAGTTTA-GGGTTAAAACGTA
1 ATTTTGAGAAAGTTTAGGGGTCAAAATGTA
*
49797946 ATTTTGAGAAAATTTAGGGGTCAAAATGTA
1 ATTTTGAGAAAGTTTAGGGGTCAAAATGTA
* *
49797976 AATTT-AGAAAAATTTAGGGGTCAAAATG
1 ATTTTGAG-AAAGTTTAGGGGTCAAAATG
49798004 CAAAATTTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
28 17 0.17
29 16 0.16
30 67 0.67
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (30 bp):
ATTTTGAGAAAGTTTAGGGGTCAAAATGTA
Found at i:49797932 original size:59 final size:60
Alignment explanation
Indices: 49797867--49798003 Score: 197
Period size: 58 Copynumber: 2.3 Consensus size: 60
49797857 GATTTTGAGG
* * *
49797867 AAGTTTAGGGGTCAAAATGTAATTTTGAGAAAGTTTCGAGGTTAAAATGT-AATTTAGAA
1 AAGTTTAGGGGTCAAAATGTAATTTTGAGAAAATTTAGAGGTCAAAATGTAAATTTAGAA
* * *
49797926 AAGTTTA-GGGTTAAAACGTAATTTTGAGAAAATTTAGGGGTCAAAATGTAAATTTAGAA
1 AAGTTTAGGGGTCAAAATGTAATTTTGAGAAAATTTAGAGGTCAAAATGTAAATTTAGAA
*
49797985 AAATTTAGGGGTCAAAATG
1 AAGTTTAGGGGTCAAAATG
49798004 CAAAATTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
58 36 0.54
59 22 0.33
60 9 0.13
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (60 bp):
AAGTTTAGGGGTCAAAATGTAATTTTGAGAAAATTTAGAGGTCAAAATGTAAATTTAGAA
Found at i:49800507 original size:4 final size:4
Alignment explanation
Indices: 49800498--49800569 Score: 51
Period size: 4 Copynumber: 17.8 Consensus size: 4
49800488 AATACAAGAA
* *
49800498 AAAT AAAT AAAT AAAT AAAT GTAA- GAAT AAAT AAAT AAAT AAGA- ACAA-
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AA-AT A-AAT
* *
49800546 AAAG GAAT AAAT AAAT AAAAT AAA
1 AAAT AAAT AAAT AAAT -AAAT AAA
49800570 CTTGAAATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
3 4 0.07
4 44 0.79
5 8 0.14
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:49814110 original size:57 final size:57
Alignment explanation
Indices: 49814022--49814176 Score: 292
Period size: 57 Copynumber: 2.7 Consensus size: 57
49814012 CGCAGCGGCC
49814022 CCATAGCCATGGCCGCCTTCGTGATGAACTTCTCCCTTGTGCTCAGCGGCGCCATAA
1 CCATAGCCATGGCCGCCTTCGTGATGAACTTCTCCCTTGTGCTCAGCGGCGCCATAA
49814079 CCATAGCCATGGCCGCCTTCGTGATGAACTTCTCCCTTGTGCTCAGCGGCGCCATAA
1 CCATAGCCATGGCCGCCTTCGTGATGAACTTCTCCCTTGTGCTCAGCGGCGCCATAA
* *
49814136 CCATGGCCATGGCCGCCTTCGTGATGAGCTTCTCCCTTGTG
1 CCATAGCCATGGCCGCCTTCGTGATGAACTTCTCCCTTGTG
49814177 TTTCTCTTCT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 96 1.00
ACGTcount: A:0.15, C:0.35, G:0.24, T:0.26
Consensus pattern (57 bp):
CCATAGCCATGGCCGCCTTCGTGATGAACTTCTCCCTTGTGCTCAGCGGCGCCATAA
Found at i:49815649 original size:14 final size:15
Alignment explanation
Indices: 49815625--49815669 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
49815615 TTTTACGGTT
49815625 TTATTATAAAAATAA
1 TTATTATAAAAATAA
* *
49815640 -TATTAGAAAACTAA
1 TTATTATAAAAATAA
49815654 TTAATTATAAAAATAA
1 TT-ATTATAAAAATAA
49815670 GGTGAGAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 12 0.50
15 1 0.04
16 11 0.46
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
TTATTATAAAAATAA
Found at i:49815684 original size:29 final size:30
Alignment explanation
Indices: 49815627--49815694 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
49815617 TTACGGTTTT
* * *
49815627 ATTATAAAAATAATATTAGAAAACTAATTA
1 ATTATAAAAATAAGATGAGAAAACAAATTA
*
49815657 ATTATAAAAATAAGGTGAG-AAACAAATTA
1 ATTATAAAAATAAGATGAGAAAACAAATTA
49815686 ATTATAAAA
1 ATTATAAAA
49815695 TTAGAGTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.29
Consensus pattern (30 bp):
ATTATAAAAATAAGATGAGAAAACAAATTA
Found at i:49817438 original size:18 final size:19
Alignment explanation
Indices: 49817378--49817438 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 19
49817368 AAAATTTCAG
* * * *
49817378 AAAAAAATATAAAAAAGGA
1 AAAAAATTATCAAAAATGT
49817397 AAAAAATTATCAAAAATGT
1 AAAAAATTATCAAAAATGT
* *
49817416 -AAAAATTATTAAATAT-T
1 AAAAAATTATCAAAAATGT
49817433 AAAAAA
1 AAAAAA
49817439 ATATGACAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
17 1 0.03
18 19 0.54
19 15 0.43
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAAAATTATCAAAAATGT
Found at i:49817474 original size:9 final size:9
Alignment explanation
Indices: 49817398--49817608 Score: 60
Period size: 9 Copynumber: 22.6 Consensus size: 9
49817388 AAAAAAGGAA
49817398 AAAAATTAT
1 AAAAATTAT
*
49817407 CAAAAA-TGT
1 -AAAAATTAT
49817416 AAAAATTATT
1 AAAAATTA-T
*
49817426 AAATATTA-
1 AAAAATTAT
*
49817434 AAAAAATAT
1 AAAAATTAT
* *
49817443 GACAATTGAT
1 AAAAATT-AT
* *
49817453 ATAAACT-T
1 AAAAATTAT
49817461 AAAAATTAT
1 AAAAATTAT
49817470 AAAAATTAT
1 AAAAATTAT
49817479 -AAAATTAATT
1 AAAAATT-A-T
49817489 AAACAGATT-T
1 AAA-A-ATTAT
*
49817499 AAAATTTTAT
1 AAAA-ATTAT
49817509 AAACACA-TATT
1 AAA-A-ATTA-T
*
49817520 AAAATTCTAT
1 AAAAAT-TAT
* *
49817530 AAAAGTCAT
1 AAAAATTAT
49817539 AAAAATTAT
1 AAAAATTAT
*
49817548 AAATA-TAT
1 AAAAATTAT
**
49817556 ATGAATTAT
1 AAAAATTAT
* *
49817565 TAAAAGTA-
1 AAAAATTAT
49817573 ATAAAATTGAT
1 A-AAAATT-AT
* *
49817584 ATAAACTTTT
1 A-AAAATTAT
49817594 AAAAATTATT
1 AAAAATTA-T
49817604 AAAAA
1 AAAAA
49817609 ATCATTAAAA
Statistics
Matches: 144, Mismatches: 37, Indels: 40
0.65 0.17 0.18
Matches are distributed among these distances:
8 28 0.19
9 51 0.35
10 45 0.31
11 16 0.11
12 1 0.01
13 3 0.02
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:49817511 original size:20 final size:21
Alignment explanation
Indices: 49817488--49817532 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
49817478 TAAAATTAAT
* *
49817488 TAAACAGAT-TTAAAATTTTA
1 TAAACACATATTAAAATTCTA
49817508 TAAACACATATTAAAATTCTA
1 TAAACACATATTAAAATTCTA
49817529 TAAA
1 TAAA
49817533 AGTCATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAACACATATTAAAATTCTA
Found at i:49824446 original size:6 final size:6
Alignment explanation
Indices: 49824435--49824461 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
49824425 GAAATTCAAT
49824435 ATTTTA ATTTTA ATTTTA ATTTTA ATT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATT
49824462 AAAAACGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:49828970 original size:14 final size:14
Alignment explanation
Indices: 49828947--49828984 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
49828937 CTTTGAATGG
*
49828947 CATATTGGTTAGAA
1 CATATAGGTTAGAA
49828961 CATATAGGTTAGAA
1 CATATAGGTTAGAA
49828975 CATATAGGTT
1 CATATAGGTT
49828985 GGTTGAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (14 bp):
CATATAGGTTAGAA
Found at i:49833233 original size:20 final size:21
Alignment explanation
Indices: 49833193--49833233 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
49833183 GCTAAGATTT
49833193 TAAAATATATAAATATTATTA
1 TAAAATATATAAATATTATTA
* *
49833214 TAAAATA-ATATATTTTATTA
1 TAAAATATATAAATATTATTA
49833234 CTTTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAATATATAAATATTATTA
Found at i:49839725 original size:22 final size:22
Alignment explanation
Indices: 49839697--49839744 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
49839687 CTCTCTAATC
49839697 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
49839719 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
49839741 CTCT
1 CTCT
49839745 GAAACCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.42
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:49839775 original size:51 final size:51
Alignment explanation
Indices: 49839719--49839831 Score: 174
Period size: 51 Copynumber: 2.2 Consensus size: 51
49839709 TTCCAAAATT
* *
49839719 CTCTCAATTTCCTTCC-AAAATTCTCTGAAACCCATATTTAATTTCAATTTC
1 CTCTCAATTTCC-TCCGAAAATTCTCTCAAACCCATATTTAAATTCAATTTC
*
49839770 CTCTCAATTTCCTCCGAAAATTCTCTCAAATCCATATTTAAATTCAATTTC
1 CTCTCAATTTCCTCCGAAAATTCTCTCAAACCCATATTTAAATTCAATTTC
*
49839821 CCCTCAATTTC
1 CTCTCAATTTC
49839832 ATTTTTTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
50 3 0.05
51 54 0.95
ACGTcount: A:0.29, C:0.29, G:0.02, T:0.40
Consensus pattern (51 bp):
CTCTCAATTTCCTCCGAAAATTCTCTCAAACCCATATTTAAATTCAATTTC
Found at i:49839867 original size:30 final size:30
Alignment explanation
Indices: 49839833--49839895 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
49839823 CTCAATTTCA
*
49839833 TTTTTTAAAATAATTTTATATTTTTTATAT
1 TTTTTTAAAATAATTTTAAATTTTTTATAT
49839863 TTTTTTAAAATAATTTTAAATTTTTTATAT
1 TTTTTTAAAATAATTTTAAATTTTTTATAT
49839893 TTT
1 TTT
49839896 CATCAATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (30 bp):
TTTTTTAAAATAATTTTAAATTTTTTATAT
Found at i:49840988 original size:7 final size:7
Alignment explanation
Indices: 49840976--49841000 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49840966 AGTCAATTGA
49840976 TATTTAG
1 TATTTAG
49840983 TATTTAG
1 TATTTAG
49840990 TATTTAG
1 TATTTAG
49840997 TATT
1 TATT
49841001 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:49842246 original size:25 final size:25
Alignment explanation
Indices: 49842217--49842398 Score: 75
Period size: 25 Copynumber: 7.6 Consensus size: 25
49842207 TTTAAATTTA
49842217 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* ** *
49842242 TTATTTGATATAATAGGCATAGAAAT
1 TTATTTGATGTAATA-AAATAGAAGT
* * **
49842268 TTTTTTGA-GT--T--ATTTTAA-T
1 TTATTTGATGTAATAAAATAGAAGT
49842287 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
* * ** *
49842313 TTATTTGTTATAATAGGCATAGAAAT
1 TTATTTGATGTAATA-AAATAGAAGT
* **
49842339 TT-TTTCGA-GT--T--ATTTTAA-T
1 TTATTT-GATGTAATAAAATAGAAGT
49842358 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
*
49842384 TTATTTGATATAATA
1 TTATTTGATGTAATA
49842399 GGCATAGAAT
Statistics
Matches: 110, Mismatches: 29, Indels: 36
0.63 0.17 0.21
Matches are distributed among these distances:
19 2 0.02
20 17 0.15
21 7 0.06
23 4 0.04
25 54 0.49
26 26 0.24
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:49842302 original size:71 final size:71
Alignment explanation
Indices: 49842215--49842414 Score: 375
Period size: 71 Copynumber: 2.8 Consensus size: 71
49842205 TATTTAAATT
49842215 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATATAATAGGCATAGAAATTTTTTTGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATATAATAGGCATAGAAATTTTTTTGAGTTA
49842280 TTTTAA
66 TTTTAA
* *
49842286 TATTATTTGATGTAATAAAATAGAAGTTTATTTGTTATAATAGGCATAGAAATTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATATAATAGGCATAGAAATTTTTTTGAGTTA
49842351 TTTTAA
66 TTTTAA
49842357 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATATAATAGGCATAG-AATTTTTTT
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATATAATAGGCATAGAAATTTTTTT
49842415 CGAGGTAATT
Statistics
Matches: 125, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 8 0.06
71 117 0.94
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.47
Consensus pattern (71 bp):
TATTATTTGATGTAATAAAATAGAAGTTTATTTGATATAATAGGCATAGAAATTTTTTTGAGTTA
TTTTAA
Found at i:49842462 original size:29 final size:29
Alignment explanation
Indices: 49842420--49842690 Score: 427
Period size: 29 Copynumber: 9.2 Consensus size: 29
49842410 TTTTTCGAGG
49842420 TAATTAAAAACCCTAACCCTAACCTAACT
1 TAATTAAAAACCCTAACCCTAACCTAACT
* *
49842449 TAATTAAAAACCCTAACCCTAAACTAATT
1 TAATTAAAAACCCTAACCCTAACCTAACT
49842478 TAATTAAAAACCCTAACCCTAACCCTAACCTAACT
1 TAATT--AAA----AACCCTAACCCTAACCTAACT
49842513 TAATTAAAAACCCTAACCCTAACCTAACT
1 TAATTAAAAACCCTAACCCTAACCTAACT
*
49842542 TAATTAAAAACCCTAACCCTAACCTAATT
1 TAATTAAAAACCCTAACCCTAACCTAACT
49842571 TAATTAAAAACCCTAACCCTAACCTAACT
1 TAATTAAAAACCCTAACCCTAACCTAACT
* *
49842600 TAATTAAAAACCCTAACCCTAAACTAATT
1 TAATTAAAAACCCTAACCCTAACCTAACT
*
49842629 TAATTAAAAA-CCTAACCCTAAACTAACT
1 TAATTAAAAACCCTAACCCTAACCTAACT
49842657 TAATTAAAAACCCTAACCCTAACCTAACT
1 TAATTAAAAACCCTAACCCTAACCTAACT
49842686 TAATT
1 TAATT
49842691 TTACTAACCA
Statistics
Matches: 225, Mismatches: 10, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
28 27 0.12
29 168 0.75
31 3 0.01
33 3 0.01
35 24 0.11
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (29 bp):
TAATTAAAAACCCTAACCCTAACCTAACT
Found at i:49842529 original size:64 final size:63
Alignment explanation
Indices: 49842428--49842684 Score: 383
Period size: 64 Copynumber: 4.2 Consensus size: 63
49842418 GGTAATTAAA
*
49842428 AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCT
1 AACCCTAA-CCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAATTAAAAACCCT
*
49842492 AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCT
1 AACCCTAA-CCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAATTAAAAACCCT
*
49842556 AACCCTAACCTAA--T---TTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCT
1 AACCCTAACCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAATTAAAAACCCT
*
49842614 AACCCT-A---AA-CTAATTTAATTAAAAA-CCTAACCCTAAACTAACTTAATTAAAAACCCT
1 AACCCTAACCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAATTAAAAACCCT
49842671 AACCCTAACCTAAC
1 AACCCTAACCTAAC
49842685 TTAATTTTAC
Statistics
Matches: 181, Mismatches: 3, Indels: 20
0.89 0.01 0.10
Matches are distributed among these distances:
54 2 0.01
55 1 0.01
57 38 0.21
58 62 0.34
61 3 0.02
63 5 0.03
64 70 0.39
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (63 bp):
AACCCTAACCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAATTAAAAACCCT
Found at i:49842579 original size:93 final size:93
Alignment explanation
Indices: 49842420--49842684 Score: 438
Period size: 93 Copynumber: 2.9 Consensus size: 93
49842410 TTTTTCGAGG
49842420 TAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAA
1 TAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAA
49842485 AAACCCTAACCCTAACCCTAACCTAACT
66 AAACCCTAACCCTAACCCTAACCTAACT
*
49842513 TAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATT--
1 TAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAA
49842576 AAA----AACCCTAACCCTAACCTAACT
66 AAACCCTAACCCTAACCCTAACCTAACT
* * *
49842600 TAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAA-CCTAACCCTAAACTAACTTAATTAA
1 TAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAA
49842664 AAACCCTAACCCTAA-CCTAAC
66 AAACCCTAACCCTAACCCTAAC
49842685 TTAATTTTAC
Statistics
Matches: 161, Mismatches: 5, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
86 21 0.13
87 58 0.36
88 3 0.02
91 9 0.06
92 8 0.05
93 62 0.39
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (93 bp):
TAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAA
AAACCCTAACCCTAACCCTAACCTAACT
Found at i:49842746 original size:55 final size:55
Alignment explanation
Indices: 49842686--49842849 Score: 285
Period size: 55 Copynumber: 3.0 Consensus size: 55
49842676 TAACCTAACT
49842686 TAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGA
1 TAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGA
*
49842741 TAATTTTACTAACCATTAACACAATTTTTAGACTTAATAATTTTACATAATTTGA
1 TAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGA
*
49842796 TAATTTTACTAACCATTAACAAAATTTTTCTGG-CTTAATAATTTTACATAATTT
1 TAATTTTACTAACCATTAACACAA-TTTT-TGGACTTAATAATTTTACATAATTT
49842850 TACATAATGT
Statistics
Matches: 104, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
55 77 0.74
56 25 0.24
57 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (55 bp):
TAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGA
Found at i:49842848 original size:10 final size:10
Alignment explanation
Indices: 49842833--49842857 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49842823 TTCTGGCTTA
49842833 ATAATTTTAC
1 ATAATTTTAC
49842843 ATAATTTTAC
1 ATAATTTTAC
49842853 ATAAT
1 ATAAT
49842858 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:49846251 original size:125 final size:126
Alignment explanation
Indices: 49845968--49846322 Score: 570
Period size: 125 Copynumber: 2.8 Consensus size: 126
49845958 CCCAAACTTG
* *
49845968 CTACTGTAGCAAAATCGCGTCCACGAGGGTGCGATTTCACAATTTTTTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAA-TTTCTTCTCAAATAGCATCCTG
* *
49846033 GTAGAAGCGATTTTATACTATTTACTCAGAAACGTTAACAAAAAAATTATTTCTTACATGAC
65 GTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACAAAAAAATTATTTCTTACATGAC
* * * *
49846095 CTACTGTAGCAAAATCGCGTCTACGAGGGCGCGATTTCATAATTTCTTCTCAAATAACATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
** *
49846160 TAGAAGTAATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACAAAAAAATTATTTCTTACATGAC
49846220 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
49846285 TAGAAGCGATTTTATACAATTTGAC-CAGAAACGTCAAC
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACGTCAAC
49846323 TCGAAATAAT
Statistics
Matches: 208, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
125 115 0.55
126 54 0.26
127 39 0.19
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (126 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACAAAAAAATTATTTCTTACATGAC
Found at i:49856999 original size:2 final size:2
Alignment explanation
Indices: 49856992--49857020 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49856982 TTTAACCCAA
49856992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49857021 GTACTAAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49857310 original size:24 final size:24
Alignment explanation
Indices: 49857283--49857356 Score: 148
Period size: 24 Copynumber: 3.1 Consensus size: 24
49857273 ATAACATAAC
49857283 CATTCACCAAGTTAGCCATGTATA
1 CATTCACCAAGTTAGCCATGTATA
49857307 CATTCACCAAGTTAGCCATGTATA
1 CATTCACCAAGTTAGCCATGTATA
49857331 CATTCACCAAGTTAGCCATGTATA
1 CATTCACCAAGTTAGCCATGTATA
49857355 CA
1 CA
49857357 CATAAAAATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (24 bp):
CATTCACCAAGTTAGCCATGTATA
Found at i:49857679 original size:25 final size:24
Alignment explanation
Indices: 49857622--49857719 Score: 99
Period size: 25 Copynumber: 4.0 Consensus size: 24
49857612 TACGAGCCAT
* * *
49857622 AATCGGTAAACTCCTTCGAGCTGA
1 AATCGGTAAGCTCATACGAGCTGA
*
49857646 AATATGGTAAGCTCATACGAGCTGA
1 AAT-CGGTAAGCTCATACGAGCTGA
*
49857671 GAATCGGTAAGCTC-TCACGAGCTACA
1 -AATCGGTAAGCTCAT-ACGAGCT-GA
*
49857697 AATCGGTAAGCTCATACAAGCTG
1 AATCGGTAAGCTCATACGAGCTG
49857720 TGGTGACTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
24 4 0.07
25 52 0.85
26 5 0.08
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (24 bp):
AATCGGTAAGCTCATACGAGCTGA
Found at i:49863532 original size:248 final size:250
Alignment explanation
Indices: 49863095--49863584 Score: 844
Period size: 248 Copynumber: 2.0 Consensus size: 250
49863085 GACAAGAAGG
* * *
49863095 ATGAATAAGGAGAATATAACTGTCTTTTAAAGTTCGTCTGAAGTTAATGAACCTTGCATGGTTGG
1 ATGAATAAGAAGAATATAACTGTCTTTTAAAGTTCGTCTGAAGTTAATGAACCTTGCATGATTGA
*
49863160 AATAGAAGAAAAAGAAAGAGTTTCAGTAAAATAGACCATTGAGGTGTTACTGTTATTTGGTTTGT
66 AATAGAAGAAAAAGAAAGAGTTTCAGTAAAATAGACCATTGAGGTGTTACTGTTATTTGGTTTAT
49863225 TGGAAGGCATTCTTTTAATCAAGGCCATCTTTCTTATTTTCTTTATTGGTGCTAAT-G-G-TGTT
131 TGGAAGGCATTCTTTTAATCAAGGCCATCTTTCTTATTTTCTTTATTGGTGCTAATGGTGATGTT
49863287 ACAAAAAGTAACTAGATGATGGAAAAGCTGCATTTGTTTTTAAGAACGTCTCTTA
196 ACAAAAAGTAACTAGATGATGGAAAAGCTGCATTTGTTTTTAAGAACGTCTCTTA
* *
49863342 ATGAATAAGAAGAATGTAACTGTCTTTTAAAGTTCTTCTGAAGTTAATGAACCTTGCATGATTGA
1 ATGAATAAGAAGAATATAACTGTCTTTTAAAGTTCGTCTGAAGTTAATGAACCTTGCATGATTGA
*
49863407 AATAGAAGAAGAAA-AAAGGAGTTTCAGTAAAATAGACCATTGAGGTGTTACTGTTTTTTGGTTT
66 AATAGAAGAA-AAAGAAA-GAGTTTCAGTAAAATAGACCATTGAGGTGTTACTGTTATTTGGTTT
*
49863471 ATTGGAAGGCATTCTTTTAATCAAGGTCATCTTTCTTATTTTCTTTATTGGTGCTAATGGTGATG
129 ATTGGAAGGCATTCTTTTAATCAAGGCCATCTTTCTTATTTTCTTTATTGGTGCTAATGGTGATG
* *
49863536 TTACAAATAGTAACTAGATGATGGTAAAGCTGCATTTGTTTTTAAGAAC
194 TTACAAAAAGTAACTAGATGATGGAAAAGCTGCATTTGTTTTTAAGAAC
49863585 ATTATTATGT
Statistics
Matches: 228, Mismatches: 10, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
247 73 0.32
248 104 0.46
249 1 0.00
250 1 0.00
251 49 0.21
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (250 bp):
ATGAATAAGAAGAATATAACTGTCTTTTAAAGTTCGTCTGAAGTTAATGAACCTTGCATGATTGA
AATAGAAGAAAAAGAAAGAGTTTCAGTAAAATAGACCATTGAGGTGTTACTGTTATTTGGTTTAT
TGGAAGGCATTCTTTTAATCAAGGCCATCTTTCTTATTTTCTTTATTGGTGCTAATGGTGATGTT
ACAAAAAGTAACTAGATGATGGAAAAGCTGCATTTGTTTTTAAGAACGTCTCTTA
Found at i:49864017 original size:31 final size:31
Alignment explanation
Indices: 49863979--49864040 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
49863969 TTCCACTGTA
*
49863979 ACTGCATGCTAAGATATAGATTGAAGTGTTT
1 ACTGCATGCTAAGATATAGAATGAAGTGTTT
49864010 ACTGCATGCTAAGATATAGAATGAAGTGTTT
1 ACTGCATGCTAAGATATAGAATGAAGTGTTT
49864041 GCCTGGTGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.34
Consensus pattern (31 bp):
ACTGCATGCTAAGATATAGAATGAAGTGTTT
Found at i:49871179 original size:9 final size:9
Alignment explanation
Indices: 49871144--49871183 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
49871134 AAATAATCAG
49871144 AAAAATATT
1 AAAAATATT
*
49871153 AAATAT-TT
1 AAAAATATT
49871161 AAAAAGTATT
1 AAAAA-TATT
49871171 AAAAATATT
1 AAAAATATT
49871180 AAAA
1 AAAA
49871184 TTGATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 6 0.22
9 14 0.52
10 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAAATATT
Found at i:49871472 original size:18 final size:17
Alignment explanation
Indices: 49871445--49871480 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
49871435 TAGGCCATTG
*
49871445 ATTTTCCAGTTCGATTA
1 ATTTTCCAGTTCAATTA
49871462 ATTTGTCCAGTTCAATTA
1 ATTT-TCCAGTTCAATTA
49871480 A
1 A
49871481 ATAAAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (17 bp):
ATTTTCCAGTTCAATTA
Found at i:49871672 original size:20 final size:20
Alignment explanation
Indices: 49871649--49871726 Score: 88
Period size: 21 Copynumber: 3.9 Consensus size: 20
49871639 AGTTCATATC
*
49871649 AATTTTAATATTTTTTATAG
1 AATTTTAATATTTTTTATAA
*
49871669 AATTTTAATACATTTTTATAA
1 AATTTTAATA-TTTTTTATAA
* *
49871690 AATTTTAAATATGTTTTAT-T
1 AATTTT-AATATTTTTTATAA
49871710 AATTTT-ATATTTTTTAT
1 AATTTTAATATTTTTTAT
49871727 GATTTATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
18 10 0.20
20 16 0.32
21 20 0.40
22 4 0.08
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (20 bp):
AATTTTAATATTTTTTATAA
Found at i:49871771 original size:21 final size:19
Alignment explanation
Indices: 49871728--49871771 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
49871718 ATTTTTTATG
* *
49871728 ATTTATTAAAATTTATTAG
1 ATTTATTAAAATTTATAAA
49871747 ATTTATTATAATATTTATAAA
1 ATTTATTA-AA-ATTTATAAA
49871768 ATTT
1 ATTT
49871772 TCAAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 2 0.10
21 11 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
ATTTATTAAAATTTATAAA
Found at i:49871797 original size:18 final size:17
Alignment explanation
Indices: 49871755--49871818 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
49871745 AGATTTATTA
49871755 TAATATTTATAAAATTT
1 TAATATTTATAAAATTT
*
49871772 TCAA-ATTTATATCAATTT
1 T-AATATTTATA-AAATTT
*
49871790 TAATATTT-TAATATTT
1 TAATATTTATAAAATTT
49871806 AATAATATTTATA
1 --TAATATTTATA
49871819 TCTTTTATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
16 4 0.11
17 12 0.32
18 20 0.53
19 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATATTTATAAAATTT
Found at i:49871813 original size:10 final size:9
Alignment explanation
Indices: 49871752--49871818 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 9
49871742 ATTAGATTTA
49871752 TTATAATAT
1 TTATAATAT
*
49871761 TTATAAAAT
1 TTATAATAT
49871770 TT-TCAA-AT
1 TTAT-AATAT
49871778 TTAT-ATCAAT
1 TTATAAT--AT
49871788 TT-TAATAT
1 TTATAATAT
49871796 TT-TAATAT
1 TTATAATAT
49871804 TTAATAATAT
1 TT-ATAATAT
49871814 TTATA
1 TTATA
49871819 TCTTTTATGA
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
7 1 0.02
8 17 0.35
9 17 0.35
10 14 0.29
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (9 bp):
TTATAATAT
Found at i:49871815 original size:26 final size:28
Alignment explanation
Indices: 49871728--49871818 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 28
49871718 ATTTTTTATG
* *
49871728 ATTTATTAAAATTTATTAGATTTATTATAAT
1 ATTTA-TAAAATTT-TCAAATTTA-TATAAT
*
49871759 ATTTATAAAATTTTCAAATTTATATCA-
1 ATTTATAAAATTTTCAAATTTATATAAT
*
49871786 ATTT-TAATATTTT-AATATTTA-ATAAT
1 ATTTATAAAATTTTCAA-ATTTATATAAT
49871812 ATTTATA
1 ATTTATA
49871819 TCTTTTATGA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
25 5 0.10
26 17 0.33
27 6 0.12
28 4 0.08
29 7 0.13
30 8 0.15
31 5 0.10
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (28 bp):
ATTTATAAAATTTTCAAATTTATATAAT
Found at i:49871991 original size:19 final size:19
Alignment explanation
Indices: 49871964--49872001 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
49871954 TTTAATTGAT
*
49871964 TATTTAATATAAATATAAA
1 TATTAAATATAAATATAAA
*
49871983 TATTAAATATTAATATAAA
1 TATTAAATATAAATATAAA
49872002 ATTTATTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATTAAATATAAATATAAA
Found at i:49889209 original size:44 final size:43
Alignment explanation
Indices: 49889095--49889274 Score: 261
Period size: 43 Copynumber: 4.2 Consensus size: 43
49889085 GGCCTATAGT
* * *
49889095 GGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCATGGTCTTTAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCATGGTCTTTAGC
* *
49889138 GGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCATGGTCTTTAGCC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCATGGTCTTTAG-C
** * **
49889182 GGTATTTGTGGGAAGAGCGCCATTAAAGGCCATGGTCTTTAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCATGGTCTTTAGC
49889225 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCATGGTCTTTAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCATGGTCTTTAGC
49889268 GGCGTTT
1 GGCGTTT
49889275 ATTTCTGAAA
Statistics
Matches: 121, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
43 85 0.70
44 36 0.30
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.27
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCATGGTCTTTAGC
Found at i:49889296 original size:87 final size:86
Alignment explanation
Indices: 49889107--49889296 Score: 249
Period size: 87 Copynumber: 2.2 Consensus size: 86
49889097 CGTTTGTGGT
* * *
49889107 AGAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCATG
1 AGAA-CGCCGCTAAAGGCCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCATG
*
49889172 GTCTTTAGCCGGTATTTGTGGGA
65 GTCTTTAGCCGGTATTTCT-GGA
* **
49889195 AGAGCGCCATTAAAGGCCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCATGG
1 AGAACGCCGCTAAAGGCCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCATGG
*
49889260 TCTTTAGCGGCGTTTATTTCT-GA
66 TCTTTAGC--CG-GTATTTCTGGA
49889283 A-AACGCCGCTAAAG
1 AGAACGCCGCTAAAG
49889297 TTAGCGACGC
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
87 74 0.84
88 6 0.07
89 2 0.02
90 6 0.07
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (86 bp):
AGAACGCCGCTAAAGGCCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCATGG
TCTTTAGCCGGTATTTCTGGA
Found at i:49892088 original size:28 final size:28
Alignment explanation
Indices: 49892052--49892121 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
49892042 AATAAAAAAA
*
49892052 TTACCAAAATGT-TATACATTTTTTTTAT
1 TTACCAAAATATATATA-ATTTTTTTTAT
49892080 TTACCAAAATATATATAATTTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTTAT
49892108 TTACCAAAATATAT
1 TTACCAAAATATAT
49892122 CAAAAAAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 36 0.90
29 4 0.10
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (28 bp):
TTACCAAAATATATATAATTTTTTTTAT
Found at i:49892210 original size:27 final size:26
Alignment explanation
Indices: 49892170--49892247 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 26
49892160 TCCCTGGGTG
49892170 AAGGGAACACTGTTGGCGGCACCAAAC
1 AAGGGAAC-CTGTTGGCGGCACCAAAC
49892197 AAGGGAACCTTGTTGGCGGCACCAAAC
1 AAGGGAACC-TGTTGGCGGCACCAAAC
*
49892224 AA-GGATTCCCTGTTGGCGGCACCA
1 AAGGGA--ACCTGTTGGCGGCACCA
49892248 CTCGTGTTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
26 4 0.09
27 41 0.87
28 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.29, T:0.15
Consensus pattern (26 bp):
AAGGGAACCTGTTGGCGGCACCAAAC
Found at i:49892637 original size:3 final size:3
Alignment explanation
Indices: 49892629--49892684 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
49892619 AATTTTATAG
49892629 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
49892677 TAT TAT TA
1 TAT TAT TA
49892685 AGATGTTACT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:49892794 original size:12 final size:12
Alignment explanation
Indices: 49892629--49892794 Score: 79
Period size: 12 Copynumber: 13.6 Consensus size: 12
49892619 AATTTTATAG
*
49892629 TATTATTATTAT
1 TATTATTAATAT
*
49892641 TATTATTATTAT
1 TATTATTAATAT
*
49892653 TATTATTATTAT
1 TATTATTAATAT
*
49892665 TATTATTATTAT
1 TATTATTAATAT
*
49892677 TATTATTAAGA-
1 TATTATTAATAT
* *
49892688 TGTTACTTAGTAT
1 TATTA-TTAATAT
* *
49892701 TATTGTTAGTA-
1 TATTATTAATAT
* ** *
49892712 AAAAATTAGTAT
1 TATTATTAATAT
*
49892724 TATT-TTTATAGT
1 TATTATTAATA-T
49892736 TAGTTATTAATAAT
1 TA-TTATTAAT-AT
*
49892750 T-TTAGTTAGTAT
1 TATTA-TTAATAT
* *
49892762 TATTTTGTATATAA
1 TATTAT-TA-ATAT
*
49892776 AATTATTAATAT
1 TATTATTAATAT
49892788 TATTATT
1 TATTATT
49892795 GTGTTAGTTA
Statistics
Matches: 118, Mismatches: 25, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
11 15 0.13
12 75 0.64
13 15 0.13
14 12 0.10
15 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.57
Consensus pattern (12 bp):
TATTATTAATAT
Found at i:49897271 original size:27 final size:27
Alignment explanation
Indices: 49897233--49897310 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
49897223 ATAACACGAG
49897233 TGGTGCCGCCAACAGGGAAT-CCTTGTT
1 TGGTGCCGCCAACAGGG-ATCCCTTGTT
* *
49897260 TGGTGCCGCCAACAAGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGATCCCTTGTT
* *
49897287 TGGTGCCGCCAACAGTGTTCCCTT
1 TGGTGCCGCCAACAGGGATCCCTT
49897311 CACCCAGGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.15, C:0.29, G:0.27, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGATCCCTTGTT
Found at i:49897391 original size:27 final size:28
Alignment explanation
Indices: 49897356--49897425 Score: 108
Period size: 27 Copynumber: 2.5 Consensus size: 28
49897346 TCTGTTTTTT
49897356 TATATATTTTGGTAAATAAAAAAAT-TA
1 TATATATTTTGGTAAATAAAAAAATGTA
49897383 TATATATTTTGGTAAATAAAAAAATGTA
1 TATATATTTTGGTAAATAAAAAAATGTA
*
49897411 TA-ACATTTTTGGTAA
1 TATATA-TTTTGGTAA
49897426 TTTTTATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 27 0.68
28 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.41
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAATGTA
Found at i:49898055 original size:5 final size:5
Alignment explanation
Indices: 49898045--49898070 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
49898035 CAGCGAAACC
49898045 TTACA TTACA TTACA TTACA TTACA T
1 TTACA TTACA TTACA TTACA TTACA T
49898071 GTTAGTGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (5 bp):
TTACA
Found at i:49904644 original size:28 final size:29
Alignment explanation
Indices: 49904604--49904659 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
49904594 GCCTATTCCC
49904604 TTGCCGTTTAAGACAG-TTCCATATGATG
1 TTGCCGTTTAAGACAGTTTCCATATGATG
*
49904632 TTGCCGTTTAAGATAGTTTCCATATGAT
1 TTGCCGTTTAAGACAGTTTCCATATGAT
49904660 TTATGGGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (29 bp):
TTGCCGTTTAAGACAGTTTCCATATGATG
Found at i:49908246 original size:15 final size:15
Alignment explanation
Indices: 49908207--49908237 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49908197 GCTATTTTTT
*
49908207 TATTTTTTATTATTA
1 TATTATTTATTATTA
49908222 TATTATTTATTATTA
1 TATTATTTATTATTA
49908237 T
1 T
49908238 GGTTATTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTATTTATTATTA
Found at i:49915105 original size:50 final size:50
Alignment explanation
Indices: 49914994--49915290 Score: 274
Period size: 50 Copynumber: 5.8 Consensus size: 50
49914984 ATTTGGGTAA
* *
49914994 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA---AG---ATG
* * *
49915050 AGAGGTCCCATGTAAGATCATGTCTGGGACATAGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* *
49915100 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* * ** * * *
49915150 AGAGGTCCCCTGTAAGATCATGTCTATGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** * * * **
49915200 AGAACTCCCACGTAAGACCATATCTGGGATATGGCATTGGCAGTACAG--G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-AGATG
* ** * * *
49915249 AAACATCCAATGTAAGACCATGTCTGAGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
49915291 TGTTATTATC
Statistics
Matches: 200, Mismatches: 40, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
49 34 0.17
50 123 0.62
51 1 0.00
53 2 0.01
56 40 0.20
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Found at i:49915181 original size:100 final size:103
Alignment explanation
Indices: 49914994--49915241 Score: 306
Period size: 100 Copynumber: 2.4 Consensus size: 103
49914984 ATTTGGGTAA
*
49914994 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA-CGAG--TATGAGAGGTCCC
* * *
49915059 ATGTAAGATCATGTCTGGGACATAGCGTTGGCACCAAGATG
63 ATGTAAGATCATGTCTAGGACATAGCATGGGCACCAAGATG
* * *
49915100 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCA-C-CGAG-ATGAGAGGTCCCCTG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGTATGAGAGGTCCCATG
* * * *
49915162 TAAGATCATGTCTATGACATGGCATGGGCACCGATATG
66 TAAGATCATGTCTAGGACATAGCATGGGCACCAAGATG
* * *
49915200 AGA-ACTCCCACGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
49915242 GTACAGGAAA
Statistics
Matches: 125, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
100 81 0.65
103 3 0.02
105 1 0.01
106 40 0.32
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGTATGAGAGGTCCCATG
TAAGATCATGTCTAGGACATAGCATGGGCACCAAGATG
Done.