Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 67 of 141
Found at i:19674325 original size:27 final size:28
Alignment explanation
Indices: 19674282--19674337 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
19674272 GTAATGTAAT
19674282 AATTTTAAGTAAGTAATATATTTAAGTA
1 AATTTTAAGTAAGTAATATATTTAAGTA
* *
19674310 AATTTT-AGTAATTAATATATTTACGTA
1 AATTTTAAGTAAGTAATATATTTAAGTA
19674337 A
1 A
19674338 TGTAAGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (28 bp):
AATTTTAAGTAAGTAATATATTTAAGTA
Found at i:19674404 original size:11 final size:11
Alignment explanation
Indices: 19674373--19674405 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
19674363 ATATATTAAT
19674373 AATTCATTGAC
1 AATTCATTGAC
19674384 -ATTCATTGAC
1 AATTCATTGAC
*
19674394 AATTCACTGAC
1 AATTCATTGAC
19674405 A
1 A
19674406 GTCAATCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (11 bp):
AATTCATTGAC
Found at i:19675482 original size:12 final size:12
Alignment explanation
Indices: 19675461--19675491 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19675451 AAATATCGCT
*
19675461 AAACAGACTAGA
1 AAACAAACTAGA
19675473 AAACAAACTAGA
1 AAACAAACTAGA
19675485 AAACAAA
1 AAACAAA
19675492 ACCCAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.16, G:0.10, T:0.06
Consensus pattern (12 bp):
AAACAAACTAGA
Found at i:19675985 original size:157 final size:157
Alignment explanation
Indices: 19675699--19676010 Score: 597
Period size: 157 Copynumber: 2.0 Consensus size: 157
19675689 CTTCATTATT
19675699 ATTTTGAGATTCAATTTACCTAGATTTTCCCTTTTGTGTCCTGCACTTAAAAAAGCCACTAACAA
1 ATTTTGAGATTCAATTTACCTAGATTTTCCCTTTTGTGTCCTGCACTTAAAAAAGCCACTAACAA
*
19675764 ACCCATCATTTTGCAACATATGCTAAGAAACAGTTTTCAATAAACATGAAATGATGATATTTTCT
66 ACCCATCATTTTGCAACATATGCTAAGAAACAGTTCTCAATAAACATGAAATGATGATATTTTCT
*
19675829 GCTGCAGATTAGCTAGAGGAATGGTGA
131 GCTGCAGATTAGCTAGACGAATGGTGA
*
19675856 ATTTTGAGATTCAATTTAGCTAGATTTTCCCTTTTGTGTCCTGCACTTAAAAAAGCCACTAACAA
1 ATTTTGAGATTCAATTTACCTAGATTTTCCCTTTTGTGTCCTGCACTTAAAAAAGCCACTAACAA
19675921 ACCCATCATTTTGCAACATATGCTAAGAAACAGTTCTCAATAAACATGAAATGATGATATTTTCT
66 ACCCATCATTTTGCAACATATGCTAAGAAACAGTTCTCAATAAACATGAAATGATGATATTTTCT
19675986 GCTGCAGATTAGCTAGACGAATGGT
131 GCTGCAGATTAGCTAGACGAATGGT
19676011 CAAAGACATT
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 152 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (157 bp):
ATTTTGAGATTCAATTTACCTAGATTTTCCCTTTTGTGTCCTGCACTTAAAAAAGCCACTAACAA
ACCCATCATTTTGCAACATATGCTAAGAAACAGTTCTCAATAAACATGAAATGATGATATTTTCT
GCTGCAGATTAGCTAGACGAATGGTGA
Found at i:19676082 original size:16 final size:16
Alignment explanation
Indices: 19676063--19676123 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
19676053 AAATTTGAGT
19676063 ATACCAAAATAATTAG
1 ATACCAAAATAATTAG
** *
19676079 ATACCAAAATAAGAATT
1 ATACCAAAATAATTA-G
19676096 ATACCAAAATAATTAG
1 ATACCAAAATAATTAG
19676112 ATACCAAAATAA
1 ATACCAAAATAA
19676124 GAAAACAGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 25 0.66
17 13 0.34
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.23
Consensus pattern (16 bp):
ATACCAAAATAATTAG
Found at i:19676102 original size:33 final size:33
Alignment explanation
Indices: 19676062--19676126 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
19676052 GAAATTTGAG
19676062 TATACCAAAATAATTAGATACCAAAATAAGAAT
1 TATACCAAAATAATTAGATACCAAAATAAGAAT
19676095 TATACCAAAATAATTAGATACCAAAATAAGAA
1 TATACCAAAATAATTAGATACCAAAATAAGAA
19676127 AACAGGTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.23
Consensus pattern (33 bp):
TATACCAAAATAATTAGATACCAAAATAAGAAT
Found at i:19676482 original size:14 final size:14
Alignment explanation
Indices: 19676445--19676483 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
19676435 CTCCTCTGAT
*
19676445 TTTTTTTCTTTGTA
1 TTTTTTTCTTTCTA
**
19676459 TTTTGGTCTTTCTA
1 TTTTTTTCTTTCTA
19676473 TTTTTTTCTTT
1 TTTTTTTCTTT
19676484 TCCTTTCGAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.05, C:0.10, G:0.08, T:0.77
Consensus pattern (14 bp):
TTTTTTTCTTTCTA
Found at i:19677858 original size:72 final size:72
Alignment explanation
Indices: 19677772--19677909 Score: 267
Period size: 72 Copynumber: 1.9 Consensus size: 72
19677762 CTTAAACCAT
19677772 AATCCCTAAATCCATACCCCCTAAACCTTAAAATAATAACTCCTAACCCGGTCTTAAATCTTAAA
1 AATCCCTAAATCCATACCCCCTAAACCTTAAAATAATAACTCCTAACCCGGTCTTAAATCTTAAA
19677837 TCCCAAG
66 TCCCAAG
*
19677844 AATCCCTAAATCCATACCCCCTAAACCTTAAAATAATAACTCCTAACCCGGTCTTAAATTTTAAA
1 AATCCCTAAATCCATACCCCCTAAACCTTAAAATAATAACTCCTAACCCGGTCTTAAATCTTAAA
19677909 T
66 T
19677910 TAATCATATA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.39, C:0.30, G:0.04, T:0.27
Consensus pattern (72 bp):
AATCCCTAAATCCATACCCCCTAAACCTTAAAATAATAACTCCTAACCCGGTCTTAAATCTTAAA
TCCCAAG
Found at i:19677941 original size:72 final size:71
Alignment explanation
Indices: 19677772--19677941 Score: 200
Period size: 72 Copynumber: 2.4 Consensus size: 71
19677762 CTTAAACCAT
* **
19677772 AATCCCTAAATCCATACCCCCTAAACCTTAAAATAATAACTCCTAACCCGGTCTTAAATCTTAAA
1 AATCCCTAAATCCAAAAACCCTAAACCTTAAAATAATAACTCCTAACCCGGTCTTAAATCTTAAA
*
19677837 TCCCAAG
66 T-CCAAC
* ** *
19677844 AATCCCTAAATCCATACCCCCTAAACCTTAAAATAATAACTCCTAACCCGGTCTTAAATTTTAAA
1 AATCCCTAAATCCAAAAACCCTAAACCTTAAAATAATAACTCCTAACCCGGTCTTAAATCTTAAA
*
19677909 T-TAATC
66 TCCAA-C
*
19677915 ATATACCCTAAA-CCAAAAACCTTAAAC
1 A-AT-CCCTAAATCCAAAAACCCTAAAC
19677942 AAATTTATTA
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
70 2 0.02
71 1 0.01
72 78 0.89
73 7 0.08
ACGTcount: A:0.41, C:0.30, G:0.03, T:0.26
Consensus pattern (71 bp):
AATCCCTAAATCCAAAAACCCTAAACCTTAAAATAATAACTCCTAACCCGGTCTTAAATCTTAAA
TCCAAC
Found at i:19678557 original size:42 final size:42
Alignment explanation
Indices: 19678466--19678586 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 42
19678456 GATAAAATGT
* * * **
19678466 CATTAGCGGCACTTTTCCATAAAACGCCGCTAAATACCTCAG
1 CATTAGCGGCGCTTTTCCAAAAAACGCCGCTAAAGACCAAAG
* *
19678508 CACTAGCGGCGCTTTTCCAAAAAACGCCGCTAAAGGCCAAAG
1 CATTAGCGGCGCTTTTCCAAAAAACGCCGCTAAAGACCAAAG
19678550 CATTAGCGGCGCTTATT--AAAAAACGCCGCTAAAGACC
1 CATTAGCGGCGCTT-TTCCAAAAAACGCCGCTAAAGACC
19678587 CGAAAGTAGG
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 19 0.28
42 48 0.70
43 2 0.03
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.19
Consensus pattern (42 bp):
CATTAGCGGCGCTTTTCCAAAAAACGCCGCTAAAGACCAAAG
Found at i:19678662 original size:39 final size:38
Alignment explanation
Indices: 19678617--19678731 Score: 140
Period size: 40 Copynumber: 2.9 Consensus size: 38
19678607 TTTGCTTTGG
* * *
19678617 CTTTTTTGCGGCGTTTTTATTAAAACCGCCGCTAATGGTT
1 CTTTTTAGCGGCG-TTTTATTAAAA-CGCCGCTAATGCTC
*
19678657 CTTTTTAGCGGCGTGTTATTTAAAACGCCGCTAATGCTC
1 CTTTTTAGCGGCGTTTTA-TTAAAACGCCGCTAATGCTC
*
19678696 CTATTTTAGCGGCGTTTTCTTAAAAACGCCGCTAAT
1 CT-TTTTAGCGGCGTTTTATT-AAAACGCCGCTAAT
19678732 TCTCGATTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
39 20 0.30
40 46 0.70
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (38 bp):
CTTTTTAGCGGCGTTTTATTAAAACGCCGCTAATGCTC
Found at i:19678749 original size:40 final size:38
Alignment explanation
Indices: 19678617--19678771 Score: 132
Period size: 40 Copynumber: 3.9 Consensus size: 38
19678607 TTTGCTTTGG
* *
19678617 CTTTTTTGCGGCGTTTTTATTAAAACCGCCGCTAATGGT-T
1 CTTTTTAGCGGCG-TTTTATTAAAAACGCCGCTAAT--TCT
* * *
19678657 CTTTTTAGCGGCGTGTTATTTAAAACGCCGCTAATGCT
1 CTTTTTAGCGGCGTTTTATTAAAAACGCCGCTAATTCT
*
19678695 CCTATTTTAGCGGCGTTTTCTTAAAAACGCCGCTAATTCT
1 -CT-TTTTAGCGGCGTTTTATTAAAAACGCCGCTAATTCT
** * * *
19678735 CGATTTTTTCCGGCGTTTTTTGTTAAAACGCCACTAA
1 C--TTTTTAGCGGCGTTTTAT-TAAAAACGCCGCTAA
19678772 AGGTGCCGCT
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
38 1 0.01
39 22 0.23
40 58 0.61
41 14 0.15
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (38 bp):
CTTTTTAGCGGCGTTTTATTAAAAACGCCGCTAATTCT
Found at i:19681775 original size:42 final size:42
Alignment explanation
Indices: 19681724--19682265 Score: 1039
Period size: 42 Copynumber: 12.9 Consensus size: 42
19681714 GTTTACAAAC
* *
19681724 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
19681766 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
19681808 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
19681850 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
19681892 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
19681934 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
* *
19681976 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
19682018 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
19682060 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
19682102 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
19682144 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
19682186 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
*
19682228 AAAAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCTT
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
19682266 TTATACAAAA
Statistics
Matches: 493, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 493 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
Found at i:19682356 original size:14 final size:14
Alignment explanation
Indices: 19682333--19682366 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
19682323 GCCCTCCTGT
*
19682333 AGCAAAATTTCAAA
1 AGCAACATTTCAAA
19682347 AGCAACATTTCAAA
1 AGCAACATTTCAAA
19682361 AGCAAC
1 AGCAAC
19682367 CAATAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.18
Consensus pattern (14 bp):
AGCAACATTTCAAA
Found at i:19682658 original size:21 final size:21
Alignment explanation
Indices: 19682590--19682660 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
19682580 TTTTGCTCTG
* *
19682590 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
19682611 CTCCGCTTCCCTCGCTGCAGT
1 CTCTGCTTCCCTCGCTGCAGC
* * *
19682632 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
19682653 CTCTGCTT
1 CTCTGCTT
19682661 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.45, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:19688126 original size:150 final size:150
Alignment explanation
Indices: 19687855--19688154 Score: 591
Period size: 150 Copynumber: 2.0 Consensus size: 150
19687845 CCATGAAATA
*
19687855 ACCATTGTTTATAACCCCGAACAAACCCATCAACAATTAGATGCTCGTATACAACTTCACGATAA
1 ACCATTGTTTATAACCCCGAACAAACCCATCAACAATTAAATGCTCGTATACAACTTCACGATAA
19687920 TGCCAGTTTATGTTGACACACTTCTTACACGGGCAAAGAATCATGTTCTCTTGGCTTGCATATTG
66 TGCCAGTTTATGTTGACACACTTCTTACACGGGCAAAGAATCATGTTCTCTTGGCTTGCATATTG
19687985 AAATGCAAAATTTAGAAAAG
131 AAATGCAAAATTTAGAAAAG
19688005 ACCATTGTTTATAACCCCGAACAAACCCATCAACAATTAAATGCTCGTATACAACTTCACGATAA
1 ACCATTGTTTATAACCCCGAACAAACCCATCAACAATTAAATGCTCGTATACAACTTCACGATAA
19688070 TGCCAGTTTATGTTGACACACTTCTTACACGGGCAAAGAATCATGTTCTCTTGGCTTGCATATTG
66 TGCCAGTTTATGTTGACACACTTCTTACACGGGCAAAGAATCATGTTCTCTTGGCTTGCATATTG
19688135 AAATGCAAAATTTAGAAAAG
131 AAATGCAAAATTTAGAAAAG
19688155 TCTGTACTCC
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 149 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (150 bp):
ACCATTGTTTATAACCCCGAACAAACCCATCAACAATTAAATGCTCGTATACAACTTCACGATAA
TGCCAGTTTATGTTGACACACTTCTTACACGGGCAAAGAATCATGTTCTCTTGGCTTGCATATTG
AAATGCAAAATTTAGAAAAG
Found at i:19688306 original size:11 final size:9
Alignment explanation
Indices: 19688258--19688747 Score: 96
Period size: 7 Copynumber: 57.0 Consensus size: 9
19688248 AATTGCAATG
19688258 GTAAGTTAT
1 GTAAGTTAT
19688267 GTAAGTTAT
1 GTAAGTTAT
19688276 GTAAGTTAAAT
1 GTAAGTT--AT
19688287 GT-A-TTAT
1 GTAAGTTAT
19688294 GTAAGTTAAAT
1 GTAAGTT--AT
19688305 GTAAG-T-T
1 GTAAGTTAT
19688312 GTAAGTTAT
1 GTAAGTTAT
*
19688321 -TATGTATTAT
1 GTAAG--TTAT
19688331 GTAAG-T-T
1 GTAAGTTAT
19688338 GTAAGTTAAAT
1 GTAAGTT--AT
*
19688349 GT-A-TTGT
1 GTAAGTTAT
19688356 GTAAG-T-T
1 GTAAGTTAT
19688363 GTAAGTTAAAT
1 GTAAGTT--AT
19688374 GT-A-TTAT
1 GTAAGTTAT
19688381 GTAAG-T-T
1 GTAAGTTAT
19688388 GTAAGTTATT
1 GTAAGTTA-T
*
19688398 ATTAAG-T-T
1 -GTAAGTTAT
19688406 GTAAGTTAAAT
1 GTAAGTT--AT
19688417 GT-A-TTAT
1 GTAAGTTAT
19688424 GTAAG-T-T
1 GTAAGTTAT
19688431 GTAAGTTAT
1 GTAAGTTAT
*
19688440 -TATGTATTAT
1 GTAAG--TTAT
19688450 GTAAG-T-T
1 GTAAGTTAT
19688457 GTAAGTTAAAT
1 GTAAGTT--AT
19688468 GT-A-TTAT
1 GTAAGTTAT
19688475 GTAAG-T-T
1 GTAAGTTAT
19688482 GTAAGTTAT
1 GTAAGTTAT
*
19688491 -TATGTATTAT
1 GTAAG--TTAT
19688501 GTAAG-T-T
1 GTAAGTTAT
19688508 GTAAGTTAAAT
1 GTAAGTT--AT
19688519 GT-A-TTAT
1 GTAAGTTAT
19688526 GTAAG-T-T
1 GTAAGTTAT
19688533 GTAAGTTAT
1 GTAAGTTAT
*
19688542 -TATGTATTAT
1 GTAAG--TTAT
19688552 GTAAG-T-T
1 GTAAGTTAT
19688559 GTAAGTTAAAT
1 GTAAGTT--AT
19688570 GT-A-TTAT
1 GTAAGTTAT
19688577 GTAAG-T-T
1 GTAAGTTAT
19688584 GTAAGTTAT
1 GTAAGTTAT
*
19688593 -TATGTATTAT
1 GTAAG--TTAT
19688603 GTAAG-T-T
1 GTAAGTTAT
19688610 GTAAGTTAAAT
1 GTAAGTT--AT
19688621 GT-A-TTAAT
1 GTAAGTT-AT
19688629 GT-A-TTAT
1 GTAAGTTAT
* *
19688636 GTCAGTCAAAT
1 GTAAGT--TAT
19688647 GT-A-TTAT
1 GTAAGTTAT
19688654 GTAAG-T-T
1 GTAAGTTAT
19688661 GTAAGTTAAAT
1 GTAAGTT--AT
19688672 GT-A-TTAT
1 GTAAGTTAT
19688679 GTAAG-T-T
1 GTAAGTTAT
19688686 GTAAGTTAT
1 GTAAGTTAT
*
19688695 -TATGTATTAT
1 GTAAG--TTAT
*
19688705 GTAAGTAAT
1 GTAAGTTAT
19688714 GTAAGTTAAAT
1 GTAAGTT--AT
19688725 GT-A-TTAT
1 GTAAGTTAT
19688732 GTAAG-T-T
1 GTAAGTTAT
19688739 GTAAGTTAT
1 GTAAGTTAT
19688748 TATGTATTAT
Statistics
Matches: 364, Mismatches: 19, Indels: 196
0.63 0.03 0.34
Matches are distributed among these distances:
7 137 0.38
8 68 0.19
9 56 0.15
10 38 0.10
11 65 0.18
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:19688370 original size:51 final size:51
Alignment explanation
Indices: 19688303--19688757 Score: 725
Period size: 51 Copynumber: 9.0 Consensus size: 51
19688293 TGTAAGTTAA
* *
19688303 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
*
19688354 GTGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAG------T-TATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
19688398 AT-TAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
19688448 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
19688499 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
19688550 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
* * * *
19688601 ATGTAAGTTGTAAGTTAAATGTATTAATGT-ATTATGTCAGTCA-AATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATT-ATGTAAGT-TGTAAGTTATTATGTATT
19688652 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
19688703 ATGTAAGTAATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGT--TGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
19688756 AT
1 AT
19688758 TTAATAAAAT
Statistics
Matches: 379, Mismatches: 11, Indels: 26
0.91 0.03 0.06
Matches are distributed among these distances:
43 36 0.09
44 5 0.01
45 1 0.00
49 1 0.00
50 38 0.10
51 242 0.64
52 11 0.03
53 45 0.12
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.46
Consensus pattern (51 bp):
ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
Found at i:19688697 original size:19 final size:19
Alignment explanation
Indices: 19688673--19688753 Score: 84
Period size: 19 Copynumber: 4.5 Consensus size: 19
19688663 AAGTTAAATG
19688673 TATTATGTAAGTTGTAAGT
1 TATTATGTAAGTTGTAAGT
*
19688692 TATTATGT-ATTATGTAAG-
1 TATTATGTAAGT-TGTAAGT
*
19688710 TA--ATGTAAG-T-TAAAT
1 TATTATGTAAGTTGTAAGT
19688725 GTATTATGTAAGTTGTAAGT
1 -TATTATGTAAGTTGTAAGT
19688745 TATTATGTA
1 TATTATGTA
19688754 TTATTTAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
14 3 0.06
15 1 0.02
16 6 0.12
17 1 0.02
18 11 0.22
19 24 0.48
20 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.47
Consensus pattern (19 bp):
TATTATGTAAGTTGTAAGT
Found at i:19689035 original size:13 final size:13
Alignment explanation
Indices: 19689017--19689061 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
19689007 ATTTATAATT
19689017 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
19689030 ATTTAAGTAACAT
1 ATTTAAGTAATAA
19689043 ATTTAAGTAATAA
1 ATTTAAGTAATAA
19689056 ATTTAA
1 ATTTAA
19689062 ACAAATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (13 bp):
ATTTAAGTAATAA
Found at i:19689069 original size:23 final size:25
Alignment explanation
Indices: 19689017--19689075 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
19689007 ATTTATAATT
*
19689017 ATTTAAGTAATAAATTTAAGTAACAT
1 ATTTAAGTAATAAATTTAAG-AACAA
19689043 ATTTAAGTAATAAATTT-A-AACAA
1 ATTTAAGTAATAAATTTAAGAACAA
*
19689066 ATTTTAGTAA
1 ATTTAAGTAA
19689076 GTAATGTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 13 0.42
25 1 0.03
26 17 0.55
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (25 bp):
ATTTAAGTAATAAATTTAAGAACAA
Found at i:19689088 original size:17 final size:17
Alignment explanation
Indices: 19689066--19689109 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
19689056 ATTTAAACAA
19689066 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
19689083 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
19689100 ATTTTAGTAA
1 ATTTTAGTAA
19689110 TAAATTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (17 bp):
ATTTTAGTAAGTAATGT
Found at i:19689116 original size:13 final size:13
Alignment explanation
Indices: 19689017--19689116 Score: 53
Period size: 13 Copynumber: 7.3 Consensus size: 13
19689007 ATTTATAATT
*
19689017 ATTTAAGTAATAA
1 ATTTTAGTAATAA
* * *
19689030 ATTTAAGTAACAT
1 ATTTTAGTAATAA
*
19689043 ATTTAAGTAATAA
1 ATTTTAGTAATAA
*
19689056 A-TTTA--AACAA
1 ATTTTAGTAATAA
19689066 ATTTTAGTAAGTAA
1 ATTTTAGTAA-TAA
19689080 TGTATTTTAGTAAGTAA
1 ---ATTTTAGTAA-TAA
19689097 TGTATTTTAGTAATAA
1 ---ATTTTAGTAATAA
19689113 ATTT
1 ATTT
19689117 AACATTCAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
10 5 0.07
11 4 0.05
12 3 0.04
13 29 0.40
14 2 0.03
16 3 0.04
17 27 0.37
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (13 bp):
ATTTTAGTAATAA
Found at i:19691245 original size:45 final size:45
Alignment explanation
Indices: 19691181--19691270 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
19691171 CGTTACACTG
19691181 ATAATGAAAGCATCTCAAATAAATAAAGCA-GCAGTTCTGTACCTT
1 ATAATGAAAGCATCTCAAATAAATAAAGCATG-AGTTCTGTACCTT
19691226 ATAATGAAAGCATCTCAAATAAATAAAGCATGAGTTCTGTACCTT
1 ATAATGAAAGCATCTCAAATAAATAAAGCATGAGTTCTGTACCTT
19691271 CAGTTGGATG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 43 0.98
46 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (45 bp):
ATAATGAAAGCATCTCAAATAAATAAAGCATGAGTTCTGTACCTT
Found at i:19692477 original size:23 final size:24
Alignment explanation
Indices: 19692451--19692501 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
19692441 TAATTTAAAT
19692451 ATTATCAA-TATTTAAAATTATT-A
1 ATTATCAATTATTT-AAATTATTCA
* *
19692474 ATTATTAATTATTTATATTATTCA
1 ATTATCAATTATTTAAATTATTCA
19692498 ATTA
1 ATTA
19692502 ATGTATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTATCAATTATTTAAATTATTCA
Found at i:19692485 original size:14 final size:17
Alignment explanation
Indices: 19692466--19692501 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
19692456 CAATATTTAA
19692466 AATTA-TTA-ATTATT-
1 AATTATTTATATTATTC
19692480 AATTATTTATATTATTC
1 AATTATTTATATTATTC
19692497 AATTA
1 AATTA
19692502 ATGTATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.26
15 3 0.16
16 6 0.32
17 5 0.26
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTATTTATATTATTC
Found at i:19693757 original size:190 final size:190
Alignment explanation
Indices: 19693434--19693794 Score: 616
Period size: 190 Copynumber: 1.9 Consensus size: 190
19693424 GCGTTTTTCA
19693434 ATAAGCGCCACTAATTCTAATATACATCAATACCAAACTCTGCGTTTTGGTGTGCATATCTTGCG
1 ATAAGCGCCACTAATTCTAATATACATCAATACCAAACTCTGCGTTTTGGTGTGCATATCTTGCG
* *
19693499 GCGCTTAACGTTAAGTGCCGCTAATACTGTTATGTAGCGGCGTTTTATTGTAAACGCCACTAATT
66 GCGCTTAACGTAAAGCGCCGCTAATACTGTTATGTAGCGGCGTTTTATTGTAAACGCCACTAATT
*
19693564 ATAGTATACATCAAGACCAAAACGTTGAGTTTTAGTTAAGAAATATAGCGGCGCTTTATC
131 ATAGTATACATCAAGACCAAAACGCTGAGTTTTAGTTAAGAAATATAGCGGCGCTTTATC
*
19693624 ATAAGCGCCACTAATTCTAATATACCTCAATACCAAACTCTGCGTTTTGGTGTGCATATCTTGCG
1 ATAAGCGCCACTAATTCTAATATACATCAATACCAAACTCTGCGTTTTGGTGTGCATATCTTGCG
* *
19693689 GCGCTTAAC-TGAAAGCGCCGCTAATACTGTTATTTAGCGGCGTTTTATTGTAAGCGCCACTAAT
66 GCGCTTAACGT-AAAGCGCCGCTAATACTGTTATGTAGCGGCGTTTTATTGTAAACGCCACTAAT
* * * *
19693753 TATAGTATACATCGATACCAAAACGCTGCGTTTTGGTTAAGA
130 TATAGTATACATCAAGACCAAAACGCTGAGTTTTAGTTAAGA
19693795 TTTTTGCGGC
Statistics
Matches: 160, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
189 1 0.01
190 159 0.99
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (190 bp):
ATAAGCGCCACTAATTCTAATATACATCAATACCAAACTCTGCGTTTTGGTGTGCATATCTTGCG
GCGCTTAACGTAAAGCGCCGCTAATACTGTTATGTAGCGGCGTTTTATTGTAAACGCCACTAATT
ATAGTATACATCAAGACCAAAACGCTGAGTTTTAGTTAAGAAATATAGCGGCGCTTTATC
Found at i:19693874 original size:113 final size:112
Alignment explanation
Indices: 19693609--19693941 Score: 352
Period size: 114 Copynumber: 2.9 Consensus size: 112
19693599 TTAAGAAATA
* * * * *
19693609 TAGCGGCGCTTTATCATAAGCGCCACTAATTCTAATATACCTCAATACC-AAACTCTGCGTTTTG
1 TAGCGGCGTTTTATCATAAGCGCCACTAATTATAGTATACATCAATACCAAAACGCTGCGTTTTG
* **
19693673 GTGT-GCATATCTTGCGGCGCTTAACTGAAAGCGCCGCTAATACTGTTATT
66 GT-TAG-AT-TTTTGCGGCGCTTAACACAAAGCGCCGCTAATAC-GTTATT
** *
19693723 TAGCGGCGTTTTATTGTAAGCGCCACTAATTATAGTATACATCGATACCAAAACGCTGCGTTTTG
1 TAGCGGCGTTTTATCATAAGCGCCACTAATTATAGTATACATCAATACCAAAACGCTGCGTTTTG
** * *
19693788 GTTAAGATTTTTGCGGCGCTTCCCACAATGCGCCGCTATTAC-TTACTT
66 GTT-AGATTTTTGCGGCGCTTAACACAAAGCGCCGCTAATACGTTA-TT
* * * *
19693836 TAGCGGCGTTTTATCATAATCGCCACTAATTATTGTATACATCAATACAAAAACGATGCGTTTTG
1 TAGCGGCGTTTTATCATAAGCGCCACTAATTATAGTATACATCAATACCAAAACGCTGCGTTTTG
* *
19693901 GTCTTGAGA-TTTTGCGGCGCATAAC-CAAAAACGCCGCTAAT
66 G--TT-AGATTTTTGCGGCGCTTAACAC-AAAGCGCCGCTAAT
19693942 TATGTTCTTT
Statistics
Matches: 183, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
112 3 0.02
113 62 0.34
114 94 0.51
115 23 0.13
116 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (112 bp):
TAGCGGCGTTTTATCATAAGCGCCACTAATTATAGTATACATCAATACCAAAACGCTGCGTTTTG
GTTAGATTTTTGCGGCGCTTAACACAAAGCGCCGCTAATACGTTATT
Found at i:19696179 original size:24 final size:23
Alignment explanation
Indices: 19696148--19696193 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
19696138 TATTCACACG
19696148 TATTCTTA-CTTAATTTCAAATGC
1 TATTCTTACCTTAATTT-AAATGC
*
19696171 TATTACTTACCTTACTTTAAATG
1 TATT-CTTACCTTAATTTAAATG
19696194 TCCCATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 9 0.45
25 7 0.35
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.48
Consensus pattern (23 bp):
TATTCTTACCTTAATTTAAATGC
Found at i:19696900 original size:3 final size:3
Alignment explanation
Indices: 19696892--19696938 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
19696882 TTTTTACTTT
19696892 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19696939 TAAATATCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19701953 original size:27 final size:27
Alignment explanation
Indices: 19701923--19702046 Score: 149
Period size: 27 Copynumber: 4.6 Consensus size: 27
19701913 TCATCTCCTA
** *
19701923 GGGGTATAACAGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
19701950 GGGGTATTTCGGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
19701977 GAGGTATTTCAGTCATTCTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
19702004 GTGGTATTTCGGTCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
19702031 GAGGTATTTCGGTCAT
1 GGGGTATTTCAGTCAT
19702047 AACAATGTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 85 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.40
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:19702038 original size:54 final size:54
Alignment explanation
Indices: 19701932--19702046 Score: 185
Period size: 54 Copynumber: 2.1 Consensus size: 54
19701922 AGGGGTATAA
* * *
19701932 CAGTCATTTTACCTTATGGGGGTATTTCGGTCATTTTACCCTATGGAGGTATTT
1 CAGTCATTCTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGAGGTATTT
*
19701986 CAGTCATTCTACCCTATGGTGGTATTTCGGTCATTTTACCCTATAGAGGTATTT
1 CAGTCATTCTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGAGGTATTT
*
19702040 CGGTCAT
1 CAGTCAT
19702047 AACAATGTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (54 bp):
CAGTCATTCTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGAGGTATTT
Found at i:19702976 original size:14 final size:15
Alignment explanation
Indices: 19702957--19702996 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
19702947 TCGACGTGAT
19702957 TTTTAGTTTTA-GAC
1 TTTTAGTTTTAGGAC
*
19702971 TTTTAGTTTTAGGAT
1 TTTTAGTTTTAGGAC
*
19702986 TTTTATTTTTA
1 TTTTAGTTTTA
19702997 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (15 bp):
TTTTAGTTTTAGGAC
Found at i:19703248 original size:28 final size:28
Alignment explanation
Indices: 19703214--19703278 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
19703204 CCAGAAAATT
19703214 ATTAACTGACCCCAACTGAATTAATTCG
1 ATTAACTGACCCCAACTGAATTAATTCG
* *
19703242 GTTAACTGACCCCAACTGATTTAATTCG
1 ATTAACTGACCCCAACTGAATTAATTCG
19703270 ATTAACTGA
1 ATTAACTGA
19703279 TTAATCTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (28 bp):
ATTAACTGACCCCAACTGAATTAATTCG
Found at i:19709303 original size:24 final size:23
Alignment explanation
Indices: 19709276--19709361 Score: 61
Period size: 24 Copynumber: 3.6 Consensus size: 23
19709266 TTATGTGCAT
19709276 GTATGTATTATAAAGTATATAAA
1 GTATGTATTATAAAGTATATAAA
*
19709299 GGTATATA-TATACAAGGGTATATAAA
1 -GTATGTATTATA-AA--GTATATAAA
* *
19709325 -TAAGTAAGATATAAAGTATAT-AA
1 GTATGT-A-TTATAAAGTATATAAA
*
19709348 GTATGTATTTTAAA
1 GTATGTATTATAAA
19709362 AATATATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
22 5 0.10
23 7 0.14
24 21 0.43
25 1 0.02
26 11 0.22
27 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.15, T:0.36
Consensus pattern (23 bp):
GTATGTATTATAAAGTATATAAA
Found at i:19711390 original size:87 final size:87
Alignment explanation
Indices: 19711280--19711441 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
19711270 AGACTTGATG
* * * * *
19711280 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAACT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTC-TGACTTCAATCCGCTCCACTGTAACC
19711344 TCAGGGAGATAGGATAGCGTCTT
65 TCAGGGAGATAGGATAGCGTCTT
* * * * *
19711367 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
19711432 CAGGGAGATA
66 CAGGGAGATA
19711442 AGATCTGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 63 0.98
88 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (87 bp):
CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
CAGGGAGATAGGATAGCGTCTT
Found at i:19711624 original size:214 final size:214
Alignment explanation
Indices: 19711241--19711708 Score: 672
Period size: 214 Copynumber: 2.2 Consensus size: 214
19711231 GTTATTTTCA
* * * * *
19711241 GTCTATTCCACTGCATCTTCAGGGAAATAAGACTTGATGCGATCTACTCTGCTGTAACCTCAGAG
1 GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
* *
19711306 AGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGCGTCTTCGAT
66 AGATAAGATCC----TTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGCATCTTCGAT
19711371 CTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGG
127 CTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGG
19711436 GAGATAAGATCTGAAATTCTCCG
192 GAGATAAGATCTGAAATTCTCCG
* * * * **
19711459 GTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGATGTGATTTTCTCTACTGTAATTTCAGAG
1 GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
* *
19711524 AGATAAGATCC-TTTAATCCGCTCCATTGTAA-TCTCAAGGAGATAGGATTA-CTATCTTTGATC
66 AGATAAGATCCTTTTAATCCGCTCCACTGTAACT-TCAAGGAGATAGGA-TAGC-ATCTTCGATC
19711586 TGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGG
128 TGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGG
**
19711651 AGATAAGATCTGAAATTCTTTG
193 AGATAAGATCTGAAATTCTCCG
* * *
19711673 GTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG
1 GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTG
19711709 TATAATAAAC
Statistics
Matches: 226, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
212 1 0.00
213 33 0.15
214 127 0.56
218 65 0.29
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (214 bp):
GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
AGATAAGATCCTTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGCATCTTCGATCTGC
TCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGA
TAAGATCTGAAATTCTCCG
Found at i:19711700 original size:46 final size:44
Alignment explanation
Indices: 19711292--19711704 Score: 248
Period size: 44 Copynumber: 9.5 Consensus size: 44
19711282 ATCTACTCTG
* * * * * *
19711292 CTGTAACCTCAGAGAGATAAGATCCTTTAT-TTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGAT-CTATGTCTTTGATCTGCTCCA
* * * *
19711336 CTGTAA-CTTCAGGGAGATAGGA--TAGCGTCTTCGATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGATCTA-TGTCTTTGATCTGCTCCA
* * **
19711379 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCTATGTCTTTGATCTGCTCCA
* ** * *
19711423 CTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTCCGGTCTACTCCA
1 CTGTAATCTCAGGGAGATAAGATCT---ATGTCTTTGATCTGCTCCA
* * * *
19711469 CTGTAACCTCAGGGAAATAAGACCTGATGTGATTT--TCT-CT--A
1 CTGTAATCTCAGGGAGATAAGATCT-ATGT-CTTTGATCTGCTCCA
* * * *
19711510 CTGTAATTTCAGAGAGATAAGATC-----CTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCTATGTCTTTGATCTGCTCCA
* * * * *
19711549 TTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATCTA-TGTCTTTGATCTGCTCCA
* * **
19711593 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCTATGTCTTTGATCTGCTCCA
* * *
19711637 CTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTTGGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCT---ATGTCTTTGATCTGCTCCA
19711683 CTGTAATCTCAGGGAGATAAGA
1 CTGTAATCTCAGGGAGATAAGA
19711705 CCTGTATAAT
Statistics
Matches: 283, Mismatches: 60, Indels: 50
0.72 0.15 0.13
Matches are distributed among these distances:
34 3 0.01
36 2 0.01
37 2 0.01
39 19 0.07
41 21 0.07
42 1 0.00
43 32 0.11
44 131 0.46
45 3 0.01
46 67 0.24
47 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
CTGTAATCTCAGGGAGATAAGATCTATGTCTTTGATCTGCTCCA
Found at i:19713371 original size:67 final size:67
Alignment explanation
Indices: 19713260--19713393 Score: 232
Period size: 67 Copynumber: 2.0 Consensus size: 67
19713250 TGAATAGCTC
**
19713260 TTAGCCTCTTTTCCTCTATTAGGTTCAACTGATCGTACCGAGATTGGATCCAATCGGCTTTACCC
1 TTAGCCTCTTTTCCTCTATTAGGTTCAACTGATCGTACAAAGATTGGATCCAATCGGCTTTACCC
19713325 AA
66 AA
* *
19713327 TTAGCCTCTTTTCTTCTATTAGGTTCAACTGATCGTACAAAGATTGGATCCAATCGGCTTTATCC
1 TTAGCCTCTTTTCCTCTATTAGGTTCAACTGATCGTACAAAGATTGGATCCAATCGGCTTTACCC
19713392 AA
66 AA
19713394 CTGTAGCTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.36
Consensus pattern (67 bp):
TTAGCCTCTTTTCCTCTATTAGGTTCAACTGATCGTACAAAGATTGGATCCAATCGGCTTTACCC
AA
Found at i:19718620 original size:31 final size:31
Alignment explanation
Indices: 19718582--19718644 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
19718572 AATGGAGTTT
19718582 TTACTTCAGCAATGTCAGTCTTGACTTCTTC
1 TTACTTCAGCAATGTCAGTCTTGACTTCTTC
19718613 TTACTTCAGCAATGTCAGTCTTGACTTCTTC
1 TTACTTCAGCAATGTCAGTCTTGACTTCTTC
19718644 T
1 T
19718645 CCCGTACCTT
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:0.19, C:0.25, G:0.13, T:0.43
Consensus pattern (31 bp):
TTACTTCAGCAATGTCAGTCTTGACTTCTTC
Found at i:19726604 original size:43 final size:43
Alignment explanation
Indices: 19726537--19726623 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
19726527 TGGCCAGAGA
* *
19726537 GAAAACGTTTCCTGCAAGAGGCGTTTTCATCTAACATGTTAGT
1 GAAAACGCTTCCTGCAAGACGCGTTTTCATCTAACATGTTAGT
* * * *
19726580 GAAAACGCTTCCTGTAGGACGCGTTTTCCTCTAAGATGTTAGT
1 GAAAACGCTTCCTGCAAGACGCGTTTTCATCTAACATGTTAGT
19726623 G
1 G
19726624 GAAATGCATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (43 bp):
GAAAACGCTTCCTGCAAGACGCGTTTTCATCTAACATGTTAGT
Found at i:19726650 original size:43 final size:43
Alignment explanation
Indices: 19726537--19726650 Score: 106
Period size: 43 Copynumber: 2.7 Consensus size: 43
19726527 TGGCCAGAGA
* * * *
19726537 GAAAACGTTTCCTGCAAGAGGCGTTTTCATCTAACATGTTAGT
1 GAAAACGCTTCCTGCAGGACGCATTTTCATCTAACATGTTAGT
* * * *
19726580 GAAAACGCTTCCTGTAGGACGCGTTTTCCTCTAAGATGTTAGT
1 GAAAACGCTTCCTGCAGGACGCATTTTCATCTAACATGTTAGT
* *
19726623 GGAAATGCATT-CTGCAGGGA-GCATTTTC
1 GAAAACGC-TTCCTGCA-GGACGCATTTTC
19726651 TCTTTGGCCA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 54 0.92
44 5 0.08
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
GAAAACGCTTCCTGCAGGACGCATTTTCATCTAACATGTTAGT
Found at i:19729326 original size:20 final size:20
Alignment explanation
Indices: 19729301--19729340 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19729291 TATTTTGCAT
19729301 GCATAGCAAAATTATGACAA
1 GCATAGCAAAATTATGACAA
*
19729321 GCATAGCAAAATTGTGACAA
1 GCATAGCAAAATTATGACAA
19729341 ACAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.20
Consensus pattern (20 bp):
GCATAGCAAAATTATGACAA
Found at i:19731584 original size:19 final size:19
Alignment explanation
Indices: 19731560--19731597 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19731550 TTTTTCTAAC
19731560 ACGTTGTGCATAGAATTGG
1 ACGTTGTGCATAGAATTGG
19731579 ACGTTGTGCATAGAATTGG
1 ACGTTGTGCATAGAATTGG
19731598 TTTCCTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.32
Consensus pattern (19 bp):
ACGTTGTGCATAGAATTGG
Found at i:19740264 original size:20 final size:20
Alignment explanation
Indices: 19740239--19740307 Score: 84
Period size: 20 Copynumber: 3.2 Consensus size: 20
19740229 TAATACCTAC
19740239 ATTCGAATATATATATACAT
1 ATTCGAATATATATATACAT
*
19740259 ATTCGAATACATAGCTAATACAT
1 ATTCGAATATATA--T-ATACAT
19740282 ACATTCGAATATATATATACAT
1 --ATTCGAATATATATATACAT
19740304 ATTC
1 ATTC
19740308 ATCATATACA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 16 0.38
22 7 0.17
23 7 0.17
25 12 0.29
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.36
Consensus pattern (20 bp):
ATTCGAATATATATATACAT
Found at i:19740271 original size:45 final size:45
Alignment explanation
Indices: 19740220--19740307 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
19740210 TTATACCTGG
*
19740220 ATACATAGCTAATACCTACATTCGAATATATATATACATATTCGA
1 ATACATAGCTAATACATACATTCGAATATATATATACATATTCGA
19740265 ATACATAGCTAATACATACATTCGAATATATATATACATATTC
1 ATACATAGCTAATACATACATTCGAATATATATATACATATTC
19740308 ATCATATACA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (45 bp):
ATACATAGCTAATACATACATTCGAATATATATATACATATTCGA
Found at i:19740290 original size:25 final size:25
Alignment explanation
Indices: 19740220--19740292 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
19740210 TTATACCTGG
*
19740220 ATACATAGCTAATACCTACATTCGA
1 ATACATAGCTAATACATACATTCGA
*
19740245 ATATATA--T-ATACAT--ATTCGA
1 ATACATAGCTAATACATACATTCGA
19740265 ATACATAGCTAATACATACATTCGA
1 ATACATAGCTAATACATACATTCGA
19740290 ATA
1 ATA
19740293 TATATATACA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 12 0.30
22 6 0.15
23 7 0.17
25 15 0.38
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.32
Consensus pattern (25 bp):
ATACATAGCTAATACATACATTCGA
Found at i:19740758 original size:41 final size:41
Alignment explanation
Indices: 19740656--19740764 Score: 146
Period size: 41 Copynumber: 2.7 Consensus size: 41
19740646 ACCGGCTTTT
* * * * * *
19740656 AGCCTGCTAGACCTATAGTCCGAAATGTATCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGAATTATATCACCGGCATCA
*
19740697 AGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAATTATATCACCGGCATCA
*
19740738 AGCCTGCTAGACGTAAAGTCTGTATTA
1 AGCCTGCTAGACGTAAAGTCTGAATTA
19740765 CATTCGATCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAATTATATCACCGGCATCA
Found at i:19744370 original size:22 final size:22
Alignment explanation
Indices: 19744305--19744362 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
19744295 TAAGCTTGCT
*
19744305 AGGCACAAAGCCTGAATAACAC
1 AGGCACAAAGCCTAAATAACAC
* *
19744327 AGGTACAAAGACTAAATAACAC
1 AGGCACAAAGCCTAAATAACAC
*
19744349 CGGCACAAAGCCTA
1 AGGCACAAAGCCTA
19744363 CTAGACACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.10
Consensus pattern (22 bp):
AGGCACAAAGCCTAAATAACAC
Found at i:19744383 original size:38 final size:38
Alignment explanation
Indices: 19744331--19744461 Score: 172
Period size: 38 Copynumber: 3.4 Consensus size: 38
19744321 TAACACAGGT
* * * *
19744331 ACAAAGACTAAATAACACCGGCACAAAGCCTACTAGAC
1 ACAAAGCCTGAATAACACCGGCACAAAGCCTGCTAGGC
*** *
19744369 ACAAAGCCTGAATAACACTACCACAAAGCCTGTTAGGC
1 ACAAAGCCTGAATAACACCGGCACAAAGCCTGCTAGGC
*
19744407 ACAAAGCCTGAATAACACCGGCACGAAGCCTGCTAGGC
1 ACAAAGCCTGAATAACACCGGCACAAAGCCTGCTAGGC
*
19744445 ATAAAGCCTGAATAACA
1 ACAAAGCCTGAATAACA
19744462 ATATAATTCA
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 79 1.00
ACGTcount: A:0.42, C:0.28, G:0.17, T:0.13
Consensus pattern (38 bp):
ACAAAGCCTGAATAACACCGGCACAAAGCCTGCTAGGC
Found at i:19757867 original size:28 final size:28
Alignment explanation
Indices: 19757808--19757870 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
19757798 TTAGAAAAAT
* **
19757808 TAAAAAATTCTAAATAAATAAATATTGT
1 TAAAAAATTCTAAATAAATAAATAATAC
*
19757836 TAAAAAATTCT-AATATATAAATAAATAC
1 TAAAAAATTCTAAATAAATAAAT-AATAC
19757864 TAAAAAA
1 TAAAAAA
19757871 ATATTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 10 0.33
28 20 0.67
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (28 bp):
TAAAAAATTCTAAATAAATAAATAATAC
Found at i:19761111 original size:29 final size:29
Alignment explanation
Indices: 19761065--19761128 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
19761055 TGTTGACGCT
* *
19761065 ACACGGCCATGTGTTGGACCGTGTGAGAC
1 ACACGGCCATATGCTGGACCGTGTGAGAC
*
19761094 ACACGGCCGTATGCTGGACCGTGTGAGAC
1 ACACGGCCATATGCTGGACCGTGTGAGAC
19761123 ACACGG
1 ACACGG
19761129 GCGTGTGAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.34, T:0.17
Consensus pattern (29 bp):
ACACGGCCATATGCTGGACCGTGTGAGAC
Found at i:19764923 original size:9 final size:9
Alignment explanation
Indices: 19764909--19764939 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19764899 GTTAAACGAA
19764909 TCGAGTTAT
1 TCGAGTTAT
*
19764918 TCGAGTTAA
1 TCGAGTTAT
19764927 TCGAGTTAT
1 TCGAGTTAT
19764936 TCGA
1 TCGA
19764940 ATCAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:19765276 original size:30 final size:30
Alignment explanation
Indices: 19765223--19765281 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
19765213 AAACCTTTTA
*
19765223 TTTTCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCAAAACTTTTACTCCCTTCCCAC
*
19765252 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCC-AAAACTTTTACTCCCTTCCCA
19765282 TCTCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 13 0.50
31 5 0.19
ACGTcount: A:0.20, C:0.39, G:0.00, T:0.41
Consensus pattern (30 bp):
TTTTCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:19765950 original size:5 final size:5
Alignment explanation
Indices: 19765940--19765975 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
19765930 GAACAGATAT
19765940 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
19765976 ATTCCATCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:19766899 original size:20 final size:20
Alignment explanation
Indices: 19766874--19766970 Score: 67
Period size: 20 Copynumber: 4.8 Consensus size: 20
19766864 TTTTCAAAAA
*
19766874 TAATATTATTTTAATAGATT
1 TAATATTAATTTAATAGATT
*
19766894 TAATATTAAATT-A-A-ATT
1 TAATATTAATTTAATAGATT
* *
19766911 TAATACTTATCTTATACATAAATAT
1 TAATA-TTA-ATT-TA-ATAGAT-T
*
19766936 T-CTATTAATTTAATAGATT
1 TAATATTAATTTAATAGATT
19766955 TAATATTAAATTTAAT
1 TAATATT-AATTTAAT
19766971 CTAATAATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
17 8 0.14
18 4 0.07
19 4 0.07
20 20 0.34
21 10 0.17
22 3 0.05
23 4 0.07
24 4 0.07
25 2 0.03
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (20 bp):
TAATATTAATTTAATAGATT
Found at i:19767012 original size:49 final size:49
Alignment explanation
Indices: 19766902--19767020 Score: 120
Period size: 49 Copynumber: 2.4 Consensus size: 49
19766892 TTTAATATTA
* * *
19766902 AATTAAAT-TTAATACTT-ATCTTATACATAAATATTCTATTAATTTAAT
1 AATTAAATATTAA-ATTTAATCTAATACATAAATATTATATTAATTTAAT
* *
19766950 AGATTTAATATTAAATTTAATCTAATA-ATAAGTATTATATTAATTTAAT
1 A-ATTAAATATTAAATTTAATCTAATACATAAATATTATATTAATTTAAT
*
19766999 -ATTAAAGTGATTAAGTTTAATC
1 AATTAAA-T-ATTAAATTTAATC
19767021 ATAGCTAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
47 5 0.08
48 2 0.03
49 41 0.69
50 11 0.19
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (49 bp):
AATTAAATATTAAATTTAATCTAATACATAAATATTATATTAATTTAAT
Found at i:19777732 original size:14 final size:15
Alignment explanation
Indices: 19777707--19777737 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
19777697 TTTATCCTTT
19777707 TTTTTATATGAACAA
1 TTTTTATATGAACAA
19777722 TTTTTAT-TGAACAA
1 TTTTTATATGAACAA
19777736 TT
1 TT
19777738 ATGTATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (15 bp):
TTTTTATATGAACAA
Found at i:19795358 original size:20 final size:20
Alignment explanation
Indices: 19795333--19795387 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
19795323 TGTGGTTCAA
*
19795333 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
19795353 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
19795373 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
19795388 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:19795770 original size:45 final size:45
Alignment explanation
Indices: 19795720--19795913 Score: 289
Period size: 45 Copynumber: 4.3 Consensus size: 45
19795710 GAACGGCATG
*
19795720 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTTATGGAAC
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* *
19795765 AAATTAAGGAAGCACTTGACCAACATCATGCATAATTCATGGAAG
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * *
19795810 AATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAG
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * * *
19795855 AATTTAAGGAAGCATTTGGCCAACATCATGCATAATTTAAGGAAC
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
*
19795900 AAATTGAGGAAGCA
1 AAATTAAGGAAGCA
19795914 CCATGGCCGA
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 136 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (45 bp):
AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
Found at i:19798361 original size:45 final size:45
Alignment explanation
Indices: 19798297--19798439 Score: 232
Period size: 45 Copynumber: 3.2 Consensus size: 45
19798287 CCTGAAATTA
19798297 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
19798342 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * * *
19798387 AGGAAGCATTTGGCCAACATCATGCATAATTTAAGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
19798432 AGGAAGCA
1 AGGAAGCA
19798440 CCATGGCCGA
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 91 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.24
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:19813485 original size:2 final size:2
Alignment explanation
Indices: 19813480--19813536 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
19813470 GTGTGATATA
19813480 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
19813522 TA TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
19813537 TCAAATTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:19825909 original size:17 final size:17
Alignment explanation
Indices: 19825883--19825915 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19825873 CATCCATGCA
*
19825883 AACTGTGAGCTCACTAG
1 AACTGAGAGCTCACTAG
19825900 AACTGAGAGCTCACTA
1 AACTGAGAGCTCACTA
19825916 ATATTGCGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (17 bp):
AACTGAGAGCTCACTAG
Found at i:19829489 original size:17 final size:17
Alignment explanation
Indices: 19829432--19829491 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
19829422 TATGAACTGC
*
19829432 GAGCTCACCAAA-TATGC
1 GAGCTCACCAAACT-TGA
*
19829449 GAGCTCACCAAGACTTTA
1 GAGCTCACCAA-ACTTGA
*
19829467 -ACCTCACCAAACTTGA
1 GAGCTCACCAAACTTGA
19829483 GAGCTCACC
1 GAGCTCACC
19829492 TATGAGTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 5 0.14
17 27 0.77
18 2 0.06
19 1 0.03
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.18
Consensus pattern (17 bp):
GAGCTCACCAAACTTGA
Found at i:19839393 original size:22 final size:23
Alignment explanation
Indices: 19839368--19839412 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
19839358 ACCACAAATT
19839368 CTTTATTTAAAA-TGTAAATAAG
1 CTTTATTTAAAATTGTAAATAAG
*
19839390 CTTTATTTAAAATTGTGAATAAG
1 CTTTATTTAAAATTGTAAATAAG
19839413 AAAGACTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.42
Consensus pattern (23 bp):
CTTTATTTAAAATTGTAAATAAG
Found at i:19844647 original size:28 final size:29
Alignment explanation
Indices: 19844615--19844673 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
19844605 TTAAAAAATG
* *
19844615 ACAAGAATAAG-AAAATGCAGAAAAATTA
1 ACAAGAACAAGAAAAAAGCAGAAAAATTA
* *
19844643 ACAAGAACCAGAAAAAAGTAGAAAAATTA
1 ACAAGAACAAGAAAAAAGCAGAAAAATTA
19844672 AC
1 AC
19844674 CCTACAGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.64, C:0.10, G:0.14, T:0.12
Consensus pattern (29 bp):
ACAAGAACAAGAAAAAAGCAGAAAAATTA
Found at i:19857728 original size:9 final size:8
Alignment explanation
Indices: 19857711--19857765 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
19857701 TTAAATATAC
19857711 TTTATATT
1 TTTATATT
19857719 TTTATCATT
1 TTTAT-ATT
*
19857728 TTAATATTTT
1 TT--TATATT
*
19857738 TTTATACT
1 TTTATATT
19857746 TTTATATT
1 TTTATATT
*
19857754 TTTAAATT
1 TTTATATT
19857762 TTTA
1 TTTA
19857766 ATAAATTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 27 0.69
9 5 0.13
10 4 0.10
11 3 0.08
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTATATT
Found at i:19857739 original size:19 final size:18
Alignment explanation
Indices: 19857706--19857756 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
19857696 AATTTTTAAA
19857706 TATAC-TTTATA--TTTT
1 TATACTTTTATATTTTTT
19857721 TAT-CATTTTAATATTTTTT
1 TATAC-TTTT-ATATTTTTT
19857740 TATACTTTTATATTTTT
1 TATACTTTTATATTTTT
19857757 AAATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.03
15 3 0.10
16 3 0.10
17 3 0.10
18 8 0.27
19 11 0.37
20 1 0.03
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TATACTTTTATATTTTTT
Found at i:19857741 original size:27 final size:26
Alignment explanation
Indices: 19857697--19857764 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
19857687 ATTTTATATA
** *
19857697 ATTTTTAAATATACTTTATATTTTTAT
1 ATTTTTAAAT-TTTTTTATACTTTTAT
**
19857724 CATTTTAATATTTTTTTATACTTTTAT
1 ATTTTTAA-ATTTTTTTATACTTTTAT
19857751 ATTTTTAAATTTTT
1 ATTTTTAAATTTTT
19857765 AATAAATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
26 6 0.18
27 25 0.76
28 2 0.06
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.66
Consensus pattern (26 bp):
ATTTTTAAATTTTTTTATACTTTTAT
Found at i:19857885 original size:29 final size:28
Alignment explanation
Indices: 19857813--19857907 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 28
19857803 TTTATAATTC
19857813 TTTTAT-ATTTTTCATAATATATTAATAATA
1 TTTTATAATTTTTCAT-A-AT-TTAATAATA
**
19857843 TTTTATAACATTTCATGAATTTAATACAT-
1 TTTTATAATTTTTCAT-AATTTAATA-ATA
*
19857872 TTTTATAATTTTTCTATAATTT-CTAA-A
1 TTTTATAATTTTTC-ATAATTTAATAATA
19857899 TTTTATAAT
1 TTTTATAAT
19857908 ATGTTTTATA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
27 10 0.18
28 2 0.04
29 23 0.42
30 12 0.22
31 8 0.15
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (28 bp):
TTTTATAATTTTTCATAATTTAATAATA
Found at i:19857968 original size:33 final size:31
Alignment explanation
Indices: 19857891--19857982 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 31
19857881 TTTTCTATAA
* * *
19857891 TTTCTAAATTTTATAATATGTTTTATATTTTT
1 TTTCTAAGTTTCATAATAT-TTTAATATTTTT
*
19857923 TTTCATATGTTTCATAATATATTTAATAATTTTT
1 TTTC-TAAGTTTCATAATAT-TTTAAT-ATTTTT
19857957 TTTCTAAGTTTCCTATAATATTTTAA
1 TTTCTAAGTTT-C-ATAATATTTTAA
19857983 CAAATTTAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
32 4 0.08
33 23 0.46
34 16 0.32
35 7 0.14
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (31 bp):
TTTCTAAGTTTCATAATATTTTAATATTTTT
Found at i:19857989 original size:35 final size:34
Alignment explanation
Indices: 19857917--19857989 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
19857907 TATGTTTTAT
* *
19857917 ATTTTTTTTCATATGTTTCATAATATATTTAATA
1 ATTTTTTTTCATAAGTTTCATAATATATTTAAAA
19857951 ATTTTTTTTC-TAAGTTTCCTATAATAT-TTTAACAA
1 ATTTTTTTTCATAAGTTT-C-ATAATATATTTAA-AA
19857986 ATTT
1 ATTT
19857990 AGGCTTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 6 0.18
34 16 0.47
35 12 0.35
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (34 bp):
ATTTTTTTTCATAAGTTTCATAATATATTTAAAA
Found at i:19865269 original size:11 final size:12
Alignment explanation
Indices: 19865240--19865281 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
19865230 AAAACTAAAA
*
19865240 AATAATAACTAT
1 AATAAAAACTAT
*
19865252 AAT-AAAACTTT
1 AATAAAAACTAT
19865263 AA-AAAAACTAT
1 AATAAAAACTAT
19865274 AATAAAAA
1 AATAAAAA
19865282 AAACACTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAAAAACTAT
Found at i:19865553 original size:21 final size:21
Alignment explanation
Indices: 19865512--19865554 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
19865502 ACCCCAAACT
* *
19865512 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
19865533 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
19865554 C
1 C
19865555 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:19866950 original size:153 final size:154
Alignment explanation
Indices: 19866663--19866955 Score: 489
Period size: 154 Copynumber: 1.9 Consensus size: 154
19866653 GCTCTCCAAC
* * **
19866663 TTTTTAAAAATAGCAGTATTTCTTTAGTTTTTATATAGATGACGCCATTCTACATGGCTCCATTA
1 TTTTTAAAAATAGCAGTATTTCTCTAGTATTTATATAGATGACGCCATTCTACATGGCTCCACCA
*
19866728 AAAAAAGAAATTTTTTTATTGGGTTTCTTGATGTGGCATGTTGGTGGTGCCAAACTCTTTGGCTC
66 AAAAAAGAAATTTTTTTATTGGGTTTCTTGATGTGGCATGTTGGTGGTGCCAAACTCTATGGCTC
19866793 CACCAATTTTTACCTGAAATAATT
131 CACCAATTTTTACCTGAAATAATT
*
19866817 TTTTTAAAAATAGCAGTATTTCTCTAGTATTTATATAGGTGACGCCATTCTACATGGCTCCACCA
1 TTTTTAAAAATAGCAGTATTTCTCTAGTATTTATATAGATGACGCCATTCTACATGGCTCCACCA
* * * *
19866882 AAAAAA-TAATTTTTTTATTGGGTTTGTTGATGTGGGATGTTGGTGGTGCCAAATTCTATGGCTC
66 AAAAAAGAAATTTTTTTATTGGGTTTCTTGATGTGGCATGTTGGTGGTGCCAAACTCTATGGCTC
19866946 CACCAATTTT
131 CACCAATTTT
19866956 CACTATAGAT
Statistics
Matches: 129, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
153 63 0.49
154 66 0.51
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (154 bp):
TTTTTAAAAATAGCAGTATTTCTCTAGTATTTATATAGATGACGCCATTCTACATGGCTCCACCA
AAAAAAGAAATTTTTTTATTGGGTTTCTTGATGTGGCATGTTGGTGGTGCCAAACTCTATGGCTC
CACCAATTTTTACCTGAAATAATT
Found at i:19877337 original size:28 final size:29
Alignment explanation
Indices: 19877289--19877354 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
19877279 CTGCTCTTAT
* *
19877289 TAAAAATTAGAAAAATTATTAAATTTTAA
1 TAAAAATTAGAAAAATAATTAAAATTTAA
*
19877318 TAAAAA-TATGAAAAA-AATTAAAATTTAT
1 TAAAAATTA-GAAAAATAATTAAAATTTAA
19877346 TAAAAATTA
1 TAAAAATTA
19877355 TAATTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (29 bp):
TAAAAATTAGAAAAATAATTAAAATTTAA
Found at i:19877347 original size:10 final size:10
Alignment explanation
Indices: 19877285--19877355 Score: 58
Period size: 10 Copynumber: 7.4 Consensus size: 10
19877275 AGTCCTGCTC
19877285 TTATTAAAAA
1 TTATTAAAAA
*
19877295 TTA-GAAAAA
1 TTATTAAAAA
**
19877304 TTATTAAATT
1 TTATTAAAAA
*
19877314 TTAATAAAAA
1 TTATTAAAAA
*
19877324 -TATGAAAAA
1 TTATTAAAAA
* *
19877333 -AATTAAAAT
1 TTATTAAAAA
19877342 TTATTAAAAA
1 TTATTAAAAA
19877352 TTAT
1 TTAT
19877356 AATTTTTTTT
Statistics
Matches: 45, Mismatches: 14, Indels: 4
0.71 0.22 0.06
Matches are distributed among these distances:
9 21 0.47
10 24 0.53
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (10 bp):
TTATTAAAAA
Found at i:19877579 original size:10 final size:10
Alignment explanation
Indices: 19877560--19877596 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
19877550 TTTTGGAACG
19877560 ATAA-TTTTT
1 ATAATTTTTT
19877569 ATAATTTTTT
1 ATAATTTTTT
*
19877579 ATATTTTTTT
1 ATAATTTTTT
19877589 ATAATTTT
1 ATAATTTT
19877597 CTTACAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 4 0.16
10 21 0.84
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:19877661 original size:18 final size:18
Alignment explanation
Indices: 19877640--19877709 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
19877630 TTTCCATATA
19877640 TTTTATATTTTTTACGAT
1 TTTTATATTTTTTACGAT
*** *
19877658 TTTTATAAAATTTACAATTTT
1 TTTTATATTTTTTACGA---T
*
19877679 TTTTATATTTTTTACGGT
1 TTTTATATTTTTTACGAT
19877697 TTTTATATTTTTT
1 TTTTATATTTTTT
19877710 TTCTAATTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 27 0.68
21 13 0.32
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTTATATTTTTTACGAT
Found at i:19877898 original size:89 final size:90
Alignment explanation
Indices: 19877805--19878010 Score: 229
Period size: 89 Copynumber: 2.3 Consensus size: 90
19877795 AATTTTTAAT
* ** *
19877805 AAAAGCAGGGGTTTAATTGCTTTTTTTGAAAAAGCTTGA-GAGTTTTTTTGATGCATTTT-AAAA
1 AAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAAGCTTGACG-GCCTTTTTGATACATTTTGAAAA
* * *
19877868 GTTCAAGTACCCGATTGGGTGC-AAAA
65 -TTCAAGTACCCAAATGAGTGCAAAAA
* * * *
19877894 AAAAGTAGGGGCTTAATTGCTTTTTCTGAAAATGTTTGACGGCCTTTTTGATACATTTTGAAAAT
1 AAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAAGCTTGACGGCCTTTTTGATACATTTTGAAAAT
* *
19877959 TTAAGTACCTAAATGAGTGCAAAAA
66 TCAAGTACCCAAATGAGTGCAAAAA
* * *
19877984 AAAATCAAGGGCTTAATTGGTTTTTTT
1 AAAAGCAGGGGCTTAATTGCTTTTTTT
19878011 TTTTAAATGG
Statistics
Matches: 96, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
89 65 0.68
90 31 0.32
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (90 bp):
AAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAAGCTTGACGGCCTTTTTGATACATTTTGAAAAT
TCAAGTACCCAAATGAGTGCAAAAA
Found at i:19878767 original size:21 final size:21
Alignment explanation
Indices: 19878741--19878791 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
19878731 AGCGGTGGCG
*
19878741 GTGAGATTAGTTACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
* *
19878762 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCA
19878783 GTGAGATTA
1 GTGAGATTA
19878792 AAAACAATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.33, T:0.31
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:19881882 original size:19 final size:18
Alignment explanation
Indices: 19881832--19881871 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
19881822 ATAAAATTAT
19881832 ATTTT-TATAATTTTAAC
1 ATTTTCTATAATTTTAAC
*
19881849 ATTTTCTATAATTTTAAT
1 ATTTTCTATAATTTTAAC
19881867 ATTTT
1 ATTTT
19881872 ATTTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTCTATAATTTTAAC
Found at i:19883025 original size:12 final size:12
Alignment explanation
Indices: 19883010--19883039 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19883000 AAACATAATT
19883010 AATAAATTACTA
1 AATAAATTACTA
*
19883022 AATAAATTATTA
1 AATAAATTACTA
19883034 AATAAA
1 AATAAA
19883040 ATATAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAAATTACTA
Found at i:19883639 original size:43 final size:43
Alignment explanation
Indices: 19883577--19883723 Score: 258
Period size: 43 Copynumber: 3.4 Consensus size: 43
19883567 CCTTGGATAA
*
19883577 GAGTTGTTCCCAAATAATGGTTATTTTGACTTACTCTAAACGT
1 GAGTTGTTCCCAAATAATGGTTATTTTGACTTATTCTAAACGT
*
19883620 AAGTTGTTCCCAAATAATGGTTATTTTGACTTATTCTAAACGT
1 GAGTTGTTCCCAAATAATGGTTATTTTGACTTATTCTAAACGT
19883663 GAGTTGTTCCCAAATAATGGTTATTTTGACTTATTCTAAACGT
1 GAGTTGTTCCCAAATAATGGTTATTTTGACTTATTCTAAACGT
*
19883706 GAGTTGTTCTCAATATAA
1 GAGTTGTTCCCAA-ATAA
19883724 AGGTCGAACA
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
43 95 0.96
44 4 0.04
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (43 bp):
GAGTTGTTCCCAAATAATGGTTATTTTGACTTATTCTAAACGT
Found at i:19885166 original size:16 final size:16
Alignment explanation
Indices: 19885113--19885172 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
19885103 ACTAAAACTT
19885113 TATTCTGAAC-ATAGC
1 TATTCTGAACAATAGC
* *
19885128 TATTCTCGAACAACAGT
1 TATTCT-GAACAATAGC
* *
19885145 TGTTCTGAACAATAAC
1 TATTCTGAACAATAGC
*
19885161 TATTCTAAACAA
1 TATTCTGAACAA
19885173 GAGTTATTAC
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 6 0.17
16 21 0.60
17 8 0.23
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (16 bp):
TATTCTGAACAATAGC
Found at i:19885172 original size:32 final size:32
Alignment explanation
Indices: 19885115--19885177 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
19885105 TAAAACTTTA
* *
19885115 TTCTGAACATAGCTATTCTCGAACAACAGTTG
1 TTCTGAACATAACTATTCTCAAACAACAGTTG
*
19885147 TTCTGAACAATAACTATTCT-AAACAAGAGTT
1 TTCTGAAC-ATAACTATTCTCAAACAACAGTT
19885178 ATTACTCCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTCTGAACATAACTATTCTCAAACAACAGTTG
Found at i:19887125 original size:19 final size:21
Alignment explanation
Indices: 19887093--19887137 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
19887083 TAAAAATATT
* *
19887093 AAATTTTAATAAAAA-ATTAA
1 AAATTTGAATAAAAATATAAA
19887113 AAATTTGAA-AAAAATATAAA
1 AAATTTGAATAAAAATATAAA
19887133 AAATT
1 AAATT
19887138 GTAAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AAATTTGAATAAAAATATAAA
Found at i:19887143 original size:19 final size:18
Alignment explanation
Indices: 19887102--19887149 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
19887092 TAAATTTTAA
*
19887102 TAAAAAATTAAAAATTTG
1 TAAAAAATTAAAAAATTG
*
19887120 AAAAAAATATAAAAAATTG
1 TAAAAAAT-TAAAAAATTG
19887139 TAAAATAATTA
1 TAAAA-AATTA
19887150 TAATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 7 0.28
19 15 0.60
20 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
TAAAAAATTAAAAAATTG
Found at i:19887219 original size:10 final size:10
Alignment explanation
Indices: 19887206--19887254 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
19887196 TATTAAAAAA
19887206 TTATAATTTT
1 TTATAATTTT
19887216 TTATAA-TTT
1 TTATAATTTT
***
19887225 TTATTGGTTT
1 TTATAATTTT
19887235 TTAT--TTTT
1 TTATAATTTT
19887243 TTATAATTTT
1 TTATAATTTT
19887253 TT
1 TT
19887255 GTCACATGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 7 0.21
9 7 0.21
10 19 0.58
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (10 bp):
TTATAATTTT
Found at i:19887547 original size:85 final size:85
Alignment explanation
Indices: 19887359--19887595 Score: 268
Period size: 85 Copynumber: 2.8 Consensus size: 85
19887349 CAAAGTACTC
* * * *
19887359 TTTTGATGCACTTTGACAGTTCAAGTGCCCAATTGAGTGCAAAAAAAATGACTTAATTGCTTTTT
1 TTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAATGACTTAATGGCTTTTT
* *
19887424 TTGAAAAAAAGTTTGAGAGTCT
65 TTG-AAAAAAGTTTAAGAGCCT
* * *
19887446 TTTTTATGCATTTTGAAAGTTCAAGCACCTAATTGAGTG-AAAAAAATGAGCTTAATGGCTTTTA
1 TTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAATGA-CTTAATGGCTTTT-
19887510 TTTG-AAAAAGCTTTAAG-GCCT
64 TTTGAAAAAAG-TTTAAGAGCCT
* * * *
19887531 TTTTGATACATTTTGAAAATTCAAGTACCCAATTGAGTGTAAAAAAA--ACTTAATTGCTCTTTT
1 TTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAATGACTTAATGGCT-TTTT
19887594 TT
65 TT
19887596 TTTAAAGAAT
Statistics
Matches: 130, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
83 12 0.09
84 4 0.03
85 53 0.41
86 24 0.18
87 37 0.28
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (85 bp):
TTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAATGACTTAATGGCTTTTTT
TGAAAAAAGTTTAAGAGCCT
Found at i:19888185 original size:28 final size:28
Alignment explanation
Indices: 19888144--19888273 Score: 99
Period size: 28 Copynumber: 4.6 Consensus size: 28
19888134 ATAAACATCA
*
19888144 ATAAAAATTATTAAAATTTAAT-AAAATT
1 ATAAAAAAT-TTAAAATTTAATAAAAATT
* * *
19888172 ATAACAATATTTAAATTTTATTAAAAATT
1 ATAA-AAAATTTAAAATTTAATAAAAATT
* *
19888201 A-GAAAAATATAAAAATTGTAA-AAAAA-T
1 ATAAAAAAT-TTAAAATT-TAATAAAAATT
*
19888228 ATAAAAAAGTGTAAAATGTT-ATAAAAATT
1 ATAAAAAA-TTTAAAAT-TTAATAAAAATT
19888257 ATAAAAAATTATAAAAT
1 ATAAAAAATT-TAAAAT
19888274 GCATCAAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
27 7 0.09
28 43 0.54
29 29 0.37
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.34
Consensus pattern (28 bp):
ATAAAAAATTTAAAATTTAATAAAAATT
Found at i:19888227 original size:19 final size:19
Alignment explanation
Indices: 19888203--19888272 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
19888193 TAAAAATTAG
19888203 AAAAATATAAAAATTGTAA
1 AAAAATATAAAAATTGTAA
*
19888222 AAAAATATAAAAAAGTGTAA
1 AAAAATAT-AAAAATTGTAA
*** *
19888242 AATGTTATAAAAATTATAA
1 AAAAATATAAAAATTGTAA
*
19888261 AAAATTATAAAA
1 AAAAATATAAAA
19888273 TGCATCAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 27 0.64
20 15 0.36
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (19 bp):
AAAAATATAAAAATTGTAA
Found at i:19888233 original size:9 final size:9
Alignment explanation
Indices: 19888194--19888272 Score: 52
Period size: 10 Copynumber: 8.3 Consensus size: 9
19888184 AAATTTTATT
19888194 AAAAAT-TA
1 AAAAATATA
19888202 GAAAAATATA
1 -AAAAATATA
* *
19888212 AAAATTGTAA
1 AAAAATAT-A
19888222 AAAAATATA
1 AAAAATATA
*
19888231 AAAAAGTGTA
1 AAAAA-TATA
**
19888241 AAATGTTATA
1 AAA-AATATA
*
19888251 AAAATTATA
1 AAAAATATA
19888260 AAAAATTATA
1 AAAAA-TATA
19888270 AAA
1 AAA
19888273 TGCATCAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
9 27 0.49
10 28 0.51
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (9 bp):
AAAAATATA
Found at i:19888274 original size:29 final size:27
Alignment explanation
Indices: 19888146--19888273 Score: 100
Period size: 29 Copynumber: 4.5 Consensus size: 27
19888136 AAACATCAAT
19888146 AAAAATTATTAAAATTTAATAAAATTATA
1 AAAAATTA-TAAAATTTAA-AAAATTATA
* * *
19888175 ACAATATT-TAAATTTTATTAAAAATTA-G
1 A-AAAATTATAAAATTTA--AAAAATTATA
*
19888203 AAAAA-TATAAAAATTGTAAAAAAATATA
1 AAAAATTAT-AAAATT-TAAAAAATTATA
* *
19888231 AAAAAGTGTAAAATGTTATAAAAATTATA
1 AAAAATTATAAAAT-TTA-AAAAATTATA
19888260 AAAAATTATAAAAT
1 AAAAATTATAAAAT
19888274 GCATCAAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
26 1 0.01
27 11 0.14
28 26 0.33
29 34 0.44
30 6 0.08
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.34
Consensus pattern (27 bp):
AAAAATTATAAAATTTAAAAAATTATA
Found at i:19888282 original size:29 final size:29
Alignment explanation
Indices: 19888221--19888283 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
19888211 AAAAATTGTA
* *
19888221 AAAAAATATAAAAAAGTGTAAAATGTTAT
1 AAAAAATATAAAAAAGTATAAAATGTCAT
* *
19888250 AAAAATTATAAAAAATTATAAAATG-CAT
1 AAAAAATATAAAAAAGTATAAAATGTCAT
*
19888278 CAAAAA
1 AAAAAA
19888284 GGTCCTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.25
Consensus pattern (29 bp):
AAAAAATATAAAAAAGTATAAAATGTCAT
Found at i:19888466 original size:20 final size:19
Alignment explanation
Indices: 19888441--19888497 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
19888431 GCATGATAAT
19888441 TTTTATAGTTTTTTTATGAA
1 TTTTATA-TTTTTTTATGAA
* *
19888461 TTTTATATTTCTTTAT-AT
1 TTTTATATTTTTTTATGAA
*
19888479 TTTTATAATTTTCTTATGA
1 TTTTAT-ATTTTTTTATGA
19888498 CTATAAAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 7 0.23
19 16 0.52
20 8 0.26
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTATATTTTTTTATGAA
Found at i:19896426 original size:16 final size:18
Alignment explanation
Indices: 19896385--19896419 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19896375 AATGGTACAA
19896385 AATAACTTTTATTATTTTG
1 AATAA-TTTTATTATTTTG
19896404 AATAATTTTATT-TTTT
1 AATAATTTTATTATTTT
19896420 ATTAATTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
AATAATTTTATTATTTTG
Found at i:19896524 original size:24 final size:23
Alignment explanation
Indices: 19896480--19896524 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
19896470 CTTATTTATT
** *
19896480 ATTTGATTTTTTTATATTATAAC
1 ATTTGATTTTTAAATAATATAAC
19896503 ATTTGGATTTTTAAATAATATA
1 ATTT-GATTTTTAAATAATATA
19896525 TTTTTAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (23 bp):
ATTTGATTTTTAAATAATATAAC
Found at i:19896888 original size:22 final size:23
Alignment explanation
Indices: 19896854--19896901 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
19896844 GTTTATTAAT
*
19896854 ATTTAATTTAAAATTTAAAATTA
1 ATTTAATTCAAAATTTAAAATTA
*
19896877 ATTTAA-TCAAAATTTATAATTA
1 ATTTAATTCAAAATTTAAAATTA
19896899 ATT
1 ATT
19896902 AACAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAATTCAAAATTTAAAATTA
Found at i:19902985 original size:25 final size:25
Alignment explanation
Indices: 19902939--19902991 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
19902929 TGATTAATGA
** * *
19902939 TTTAATTTTGTTTTAAATTTTTTAT
1 TTTAATTTCATTTTAAAGTTTTAAT
*
19902964 TTTAATTTCATTTTAACGTTTTAAT
1 TTTAATTTCATTTTAAAGTTTTAAT
19902989 TTT
1 TTT
19902992 CTCTAATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTAATTTCATTTTAAAGTTTTAAT
Found at i:19909925 original size:51 final size:51
Alignment explanation
Indices: 19909862--19910209 Score: 323
Period size: 51 Copynumber: 6.9 Consensus size: 51
19909852 CGAGAAGCTT
* *
19909862 TGGTCACGTGTGTAGTATTGTGTGAAGGCTACTACGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* * * ** * * * * *
19909913 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA-ATAA
* * *
19909964 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* * * * *
19910015 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGA-AAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAA--TAA
* * * *
19910066 TAGTCACATATGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAA-ACT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-A
* * * * *
19910116 TGATCACGTGTATAGTACTATGTGAAGGTTATTACGTGAACCG-TAAA-AA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* *
19910165 TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 -TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
19910210 ATGATAATAG
Statistics
Matches: 238, Mismatches: 50, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
50 83 0.35
51 153 0.64
52 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (51 bp):
TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
Found at i:19910023 original size:102 final size:102
Alignment explanation
Indices: 19909844--19910209 Score: 461
Period size: 102 Copynumber: 3.6 Consensus size: 102
19909834 TTTTGGACTG
* *
19909844 ATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTATTGTGTGAAGGCTACTACGTGAATCGATAA
1 ATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA
*
19909909 ATAATGGTCACATGTGTAGTACTAAGTGAAGGCTACA
66 ATAATGGTCACATGTGTAGTACTAAGTGAAGGCTACT
* * *
19909946 ATATGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAA
1 ATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA
*
19910011 ATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACT
66 ATAATGGTCACATGTGTAGTACTAAGTGAAGGCTACT
* * * * *
19910048 ATGTGTATCGAAAAGCTTTAGTCACATATGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAA
1 ATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA
* * * * * * *
19910112 A-ACTTGATCACGTGTATAGTACTATGTGAAGGTTATT
66 ATA-ATGGTCACATGTGTAGTACTAAGTGAAGGCTACT
* * ** * *
19910149 ACGTGAACCGTA-AA-AATTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 ATGTGTACCG-AGAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
19910210 ATGATAATAG
Statistics
Matches: 230, Mismatches: 31, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
100 39 0.17
101 40 0.17
102 151 0.66
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (102 bp):
ATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA
ATAATGGTCACATGTGTAGTACTAAGTGAAGGCTACT
Found at i:19913221 original size:27 final size:27
Alignment explanation
Indices: 19913179--19913257 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
19913169 TATACTAGGT
*
19913179 GTGCCACCTATTAGATAGGCACCAC-C
1 GTGCCACCTATCAGATAGGCACCACTC
***
19913205 AGTGCCACCTATCAGATAGGGGTCACTC
1 -GTGCCACCTATCAGATAGGCACCACTC
*
19913233 GTGCCGCCTATCAGATAGGCACCAC
1 GTGCCACCTATCAGATAGGCACCAC
19913258 ACTCCCTTCG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 42 0.98
28 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.19
Consensus pattern (27 bp):
GTGCCACCTATCAGATAGGCACCACTC
Found at i:19913341 original size:3 final size:3
Alignment explanation
Indices: 19913335--19913361 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
19913325 CCACTACTAA
19913335 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
19913362 TAAAGTGTAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19917970 original size:7 final size:7
Alignment explanation
Indices: 19917958--19917986 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
19917948 AGAGGTTTCC
19917958 CTTTTTT
1 CTTTTTT
19917965 CTTTTTT
1 CTTTTTT
19917972 -TTTTTT
1 CTTTTTT
19917978 CTTTTTT
1 CTTTTTT
19917985 CT
1 CT
19917987 CGTTTTTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
CTTTTTT
Found at i:19917977 original size:13 final size:13
Alignment explanation
Indices: 19917959--19917984 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19917949 GAGGTTTCCC
19917959 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
19917972 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
19917985 CTCGTTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:19925050 original size:24 final size:24
Alignment explanation
Indices: 19925018--19925066 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
19925008 ATGGGTAAGA
19925018 CTTTCATCCTACGACTACAAATGT
1 CTTTCATCCTACGACTACAAATGT
19925042 CTTTCATCCTACGACTACAAATGT
1 CTTTCATCCTACGACTACAAATGT
19925066 C
1 C
19925067 AATGTACTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.33
Consensus pattern (24 bp):
CTTTCATCCTACGACTACAAATGT
Found at i:19925270 original size:16 final size:16
Alignment explanation
Indices: 19925249--19925279 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19925239 TTCACTATTA
*
19925249 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
19925265 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
19925280 GCATGCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:19926400 original size:14 final size:15
Alignment explanation
Indices: 19926381--19926409 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19926371 GAATTTTCTT
19926381 GAAAAATT-ATTTTG
1 GAAAAATTAATTTTG
19926395 GAAAAATTAATTTTG
1 GAAAAATTAATTTTG
19926410 ATGAAGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
GAAAAATTAATTTTG
Found at i:19926934 original size:32 final size:33
Alignment explanation
Indices: 19926867--19926938 Score: 78
Period size: 32 Copynumber: 2.2 Consensus size: 33
19926857 TTAATAGTTT
***
19926867 AATATTAAATTTAATTTAATATTTATCTTGATA
1 AATATTAAATTTAATTTAATATTTAAAGTGATA
*
19926900 AATATTATA-TTAATTTAATA-TTAAAGTGATTA
1 AATATTAAATTTAATTTAATATTTAAAGTGA-TA
19926932 AAT-TTAA
1 AATATTAA
19926939 TCATAGTTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
31 9 0.27
32 16 0.48
33 8 0.24
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (33 bp):
AATATTAAATTTAATTTAATATTTAAAGTGATA
Found at i:19929693 original size:8 final size:8
Alignment explanation
Indices: 19929680--19929711 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
19929670 TGTTAAACAG
19929680 ATTGTTTT
1 ATTGTTTT
19929688 ATTGTTTT
1 ATTGTTTT
19929696 ATTGTTTT
1 ATTGTTTT
*
19929704 ATGGTTTT
1 ATTGTTTT
19929712 GGTGATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (8 bp):
ATTGTTTT
Found at i:19931764 original size:59 final size:59
Alignment explanation
Indices: 19931699--19931886 Score: 150
Period size: 59 Copynumber: 3.2 Consensus size: 59
19931689 ATTTTATTAA
19931699 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
* * ** * * * ** * * * *
19931758 ATCATATATTATGATTTTAGTA-AATTCATA-TAAGAATATTGATTATTAGAATTTTATTA-A
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCA-AATTA-TATTTTA-TAGT
* * * *
19931818 ATTATATATTTTAATTAAAATATATTTAATAATT-ATTATTTTAATTTATATTTTACAGT
1 ATCATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTCAAATTATATTTTATAGT
19931877 ATCATATATT
1 ATCATATATT
19931887 ATGATTTGAG
Statistics
Matches: 91, Mismatches: 30, Indels: 16
0.66 0.22 0.12
Matches are distributed among these distances:
57 5 0.05
58 10 0.11
59 36 0.40
60 25 0.27
61 10 0.11
62 4 0.04
63 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (59 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
Found at i:19931813 original size:119 final size:120
Alignment explanation
Indices: 19931688--19931976 Score: 492
Period size: 119 Copynumber: 2.4 Consensus size: 120
19931678 AATTATTTTA
*
19931688 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTT
* * *
19931753 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATT-AG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
19931807 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATT-ATTATTTTAATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTCAAATTATATTT
19931871 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
19931927 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTAT
19931977 GTTTAAATAT
Statistics
Matches: 160, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
119 109 0.68
120 51 0.32
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:19931834 original size:18 final size:18
Alignment explanation
Indices: 19931808--19931863 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 18
19931798 GATTATTAGA
19931808 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
19931825 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
19931841 A-TTTAA-T-AATTAT-T
1 ATTTTAATTAAATTATAT
19931855 ATTTTAATT
1 ATTTTAATT
19931864 TATATTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.06
14 3 0.09
15 12 0.35
16 6 0.18
17 5 0.15
18 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:19931944 original size:59 final size:58
Alignment explanation
Indices: 19931762--19931944 Score: 146
Period size: 56 Copynumber: 3.1 Consensus size: 58
19931752 TATAGTATCA
*
19931762 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATT-AGAATTTTATTAAAT
1 TATATTATGATTTAAGTAAATTCATATAAGAATATT-ATTATTAAGAATTTTATTAAAT
* * * * * *
19931820 TATA-TAT--TTTAATTAAAATAT-ATTTAATAATTATTATT-TTAATTTATATTTTA-CAGTAT
1 TATATTATGATTTAAGT-AAAT-TCATATAAGAA-TATTATTATTAA--GA-ATTTTATTA-AAT
*
19931879 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTAAGTAAATTCATATAAGAATATT-ATTATTAAGAATTTTATTAAAT
19931940 TATAT
1 TATAT
19931945 ATTTTAATTA
Statistics
Matches: 94, Mismatches: 14, Indels: 33
0.67 0.10 0.23
Matches are distributed among these distances:
55 7 0.07
56 15 0.16
57 8 0.09
58 6 0.06
59 13 0.14
61 12 0.13
62 10 0.11
63 14 0.15
64 9 0.10
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (58 bp):
TATATTATGATTTAAGTAAATTCATATAAGAATATTATTATTAAGAATTTTATTAAAT
Found at i:19931956 original size:18 final size:17
Alignment explanation
Indices: 19931928--19931962 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19931918 ATTATTAAGA
*
19931928 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
19931945 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
19931963 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:19932070 original size:147 final size:149
Alignment explanation
Indices: 19931916--19932190 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 149
19931906 ATAAGAATAT
*
19931916 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
19931981 AAATATGAGTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGAGTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
19932044 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
19932063 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
* *
19932128 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGAGTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
19932191 CAATAATCAT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
147 90 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGAGTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:19932103 original size:18 final size:17
Alignment explanation
Indices: 19932075--19932109 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19932065 ATTATTAAGA
*
19932075 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
19932092 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
19932110 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:19932320 original size:44 final size:45
Alignment explanation
Indices: 19932271--19932365 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
19932261 TTACACCTCT
* * *
19932271 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCTTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
** *
19932315 ATTACATTCAACCAAACAGTTGATTTGCTATTACACATCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
19932360 ATTACA
1 ATTACA
19932366 CCTCTAATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
Found at i:19932365 original size:16 final size:16
Alignment explanation
Indices: 19932346--19932413 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
19932336 GATTTGCTAT
* *
19932346 TACACATCTATTCCAT
1 TACACATCTAATCCAA
*
19932362 TACACCTCTAATCCAA
1 TACACATCTAATCCAA
19932378 TACACATCTAATCCAA
1 TACACATCTAATCCAA
*
19932394 TACACCTCTAATCCAA
1 TACACATCTAATCCAA
19932410 TACA
1 TACA
19932414 GCGAACCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACATCTAATCCAA
Done.