Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 19 of 322
Found at i:5334647 original size:22 final size:22
Alignment explanation
Indices: 5334617--5334668 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
5334607 ATATAAAAAG
5334617 ATATATATAGACATAAACTAAA
1 ATATATATAGACATAAACTAAA
* * * *
5334639 ATATGTATATATATAAATTAAA
1 ATATATATAGACATAAACTAAA
5334661 A-ATATATA
1 ATATATATA
5334669 AAGTATATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATATATAGACATAAACTAAA
Found at i:5334894 original size:3 final size:3
Alignment explanation
Indices: 5334886--5334917 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5334876 AATAAGTAGG
5334886 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5334918 GGACTAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5336876 original size:21 final size:21
Alignment explanation
Indices: 5336852--5336894 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5336842 GAGGTGCCTA
*
5336852 TGGGCTGGACCGGGTTTGGGT
1 TGGGCCGGACCGGGTTTGGGT
5336873 TGGGCCGGACCGGGTTTGGGT
1 TGGGCCGGACCGGGTTTGGGT
5336894 T
1 T
5336895 TGGGTTGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.51, T:0.28
Consensus pattern (21 bp):
TGGGCCGGACCGGGTTTGGGT
Found at i:5339377 original size:18 final size:19
Alignment explanation
Indices: 5339340--5339377 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5339330 CATTGGTTTC
* *
5339340 AACTTCCTCTTTGTTCTCA
1 AACTTCCTCTTCGTTATCA
5339359 AACTT-CTCTTCGTTATCA
1 AACTTCCTCTTCGTTATCA
5339377 A
1 A
5339378 CCCTAATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.21, C:0.29, G:0.05, T:0.45
Consensus pattern (19 bp):
AACTTCCTCTTCGTTATCA
Found at i:5341841 original size:16 final size:16
Alignment explanation
Indices: 5341815--5341847 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5341805 AAATCAAATT
5341815 TAAAAATTTTTAGAAAA
1 TAAAAATTTTTA-AAAA
5341832 TAAAAA-TTTTAAAAA
1 TAAAAATTTTTAAAAA
5341847 T
1 T
5341848 TTATTTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TAAAAATTTTTAAAAA
Found at i:5343146 original size:3 final size:3
Alignment explanation
Indices: 5343138--5343166 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5343128 TTTTATCACT
5343138 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5343167 TGAAATATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5348296 original size:36 final size:36
Alignment explanation
Indices: 5348249--5348321 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
5348239 AGACTTGGAA
5348249 CTCCCTCCTGAGGTAGAGACACCAAGGGTTAATGCT
1 CTCCCTCCTGAGGTAGAGACACCAAGGGTTAATGCT
5348285 CTCCCTCCTGAGGTAGAGACACCAAGGGTTAATGCT
1 CTCCCTCCTGAGGTAGAGACACCAAGGGTTAATGCT
5348321 C
1 C
5348322 GTTCTTCTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.22
Consensus pattern (36 bp):
CTCCCTCCTGAGGTAGAGACACCAAGGGTTAATGCT
Found at i:5354272 original size:15 final size:15
Alignment explanation
Indices: 5354251--5354282 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
5354241 ATAAATGAAA
5354251 AATATATA-T-AATT
1 AATATATATTAAATT
5354264 AATATATATTAAATT
1 AATATATATTAAATT
5354279 AATA
1 AATA
5354283 ATAATACGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATATATTAAATT
Found at i:5354736 original size:22 final size:22
Alignment explanation
Indices: 5354694--5354736 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5354684 AAAAATCTAA
*
5354694 CCATAAATCATAACCCCTAAAC
1 CCATAAATCATAAACCCTAAAC
*
5354716 CCAT-AATCCATAAACCTTAAA
1 CCATAAAT-CATAAACCCTAAA
5354737 ATAGTAACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.21
Consensus pattern (22 bp):
CCATAAATCATAAACCCTAAAC
Found at i:5355149 original size:41 final size:41
Alignment explanation
Indices: 5355104--5355364 Score: 391
Period size: 41 Copynumber: 6.4 Consensus size: 41
5355094 GGCGCCTTTC
*
5355104 CAAAAACGCCGCTAAAGACCCAAGAATTAGCGGCGCTTCTT
1 CAAAAACGCCGCTAAAGACCCAAGCATTAGCGGCGCTTCTT
* ** *
5355145 CAAAAGCGCCGCTAAAGACGTAAGCATTAGCGGTGCTTCTT
1 CAAAAACGCCGCTAAAGACCCAAGCATTAGCGGCGCTTCTT
**
5355186 CAAAAGTGCCGCTAAAGACCCAAGCATTAGCGGCGCTTCTT
1 CAAAAACGCCGCTAAAGACCCAAGCATTAGCGGCGCTTCTT
* *
5355227 CAAAAGCGCCGCTAAAGACCCAAGCATTAGCGGCGCCTCTT
1 CAAAAACGCCGCTAAAGACCCAAGCATTAGCGGCGCTTCTT
* *
5355268 CAGAAACGCCGCAAAAGA-CCAAGCATTAGCGGCGCTTCTT
1 CAAAAACGCCGCTAAAGACCCAAGCATTAGCGGCGCTTCTT
*
5355308 CAAAAACGCCGCTAAAG-CCCTGAGCATTAGCGGCGCTTCTT
1 CAAAAACGCCGCTAAAGACCC-AAGCATTAGCGGCGCTTCTT
5355349 CAAAAACGCCGCTAAA
1 CAAAAACGCCGCTAAA
5355365 ATCCCAAAAA
Statistics
Matches: 200, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
40 38 0.19
41 162 0.81
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.17
Consensus pattern (41 bp):
CAAAAACGCCGCTAAAGACCCAAGCATTAGCGGCGCTTCTT
Found at i:5355371 original size:122 final size:123
Alignment explanation
Indices: 5355104--5355364 Score: 402
Period size: 122 Copynumber: 2.1 Consensus size: 123
5355094 GGCGCCTTTC
* * *
5355104 CAAAAACGCCGCTAAAGACCCAAGAATTAGCGGCGCTTCTTCAAAAGCGCCGCTAAAGACGTAAG
1 CAAAAACGCCGCTAAAGACCCAAGAATTAGCGGCGCCTCTTCAAAAGCGCCGCAAAAGACGCAAG
* **
5355169 CATTAGCGGTGCTTCTTCAAAAGTGCCGCTAAAGACCCAAGCATTAGCGGCGCTTCTT
66 CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCAAGCATTAGCGGCGCTTCTT
* *
5355227 CAAAAGCGCCGCTAAAGACCCAAGCATTAGCGGCGCCTCTTCAGAAA-CGCCGCAAAAGAC-CAA
1 CAAAAACGCCGCTAAAGACCCAAGAATTAGCGGCGCCTCTTCA-AAAGCGCCGCAAAAGACGCAA
*
5355290 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAG-CCCTGAGCATTAGCGGCGCTTCTT
65 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCC-AAGCATTAGCGGCGCTTCTT
5355349 CAAAAACGCCGCTAAA
1 CAAAAACGCCGCTAAA
5355365 ATCCCAAAAA
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
121 3 0.02
122 68 0.54
123 52 0.41
124 3 0.02
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.17
Consensus pattern (123 bp):
CAAAAACGCCGCTAAAGACCCAAGAATTAGCGGCGCCTCTTCAAAAGCGCCGCAAAAGACGCAAG
CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCAAGCATTAGCGGCGCTTCTT
Found at i:5355449 original size:39 final size:39
Alignment explanation
Indices: 5355401--5355552 Score: 121
Period size: 40 Copynumber: 3.8 Consensus size: 39
5355391 TGGGCTTAGG
* *
5355401 TTTTT-GCGGCGCTTTTTGGAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCGCTTTTTAGAAAACGCCGCTAATGCTGA
* * *
5355439 TTTTTAGCGGC-ATTTTTAGAAAAGCGCCGCGAATACTTGA
1 TTTTTAGCGGCGCTTTTTAGAAAA-CGCCGCTAATGC-TGA
* * * *
5355479 TCTTTAGCAGCGCTTTTCTAG-AAGCGCCGCTAATGATTGA
1 TTTTTAGCGGCGCTTTT-TAGAAAACGCCGCTAATG-CTGA
* * **
5355519 TTTTTAGCGGTGTTTTTTATCCAAACGCCGCTAA
1 TTTTTAGCGGCGCTTTTTA-GAAAACGCCGCTAA
5355553 AAGTCTGTTT
Statistics
Matches: 88, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
38 15 0.17
39 17 0.19
40 36 0.41
41 17 0.19
42 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (39 bp):
TTTTTAGCGGCGCTTTTTAGAAAACGCCGCTAATGCTGA
Found at i:5368878 original size:45 final size:45
Alignment explanation
Indices: 5368814--5368914 Score: 159
Period size: 45 Copynumber: 2.2 Consensus size: 45
5368804 GTAACGGTAG
* *
5368814 CAGTAACAGTAACAGTATTCAACACACAAAGT-GCTGAATCTGTAA
1 CAGTAACAGTAACAGTATTCAACACACAAAGTATC-GAATCAGTAA
*
5368859 CAGTAACAGTAACAGTATTCGACACACAAAGTATCGAATCAGTAA
1 CAGTAACAGTAACAGTATTCAACACACAAAGTATCGAATCAGTAA
5368904 CAGTAACAGTA
1 CAGTAACAGTA
5368915 GTCGGCACAT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
45 51 0.98
46 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.21
Consensus pattern (45 bp):
CAGTAACAGTAACAGTATTCAACACACAAAGTATCGAATCAGTAA
Found at i:5370426 original size:16 final size:17
Alignment explanation
Indices: 5370394--5370426 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5370384 CAATTAACCC
5370394 CTCAATTAATCTAATTTT
1 CTCAATTAA-CTAATTTT
5370412 CTCAATTAA-TAATTT
1 CTCAATTAACTAATTT
5370427 ACCTAGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
CTCAATTAACTAATTTT
Found at i:5371080 original size:16 final size:17
Alignment explanation
Indices: 5371048--5371080 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5371038 CAATTAACCC
5371048 CTCAATTAATCTAATTTT
1 CTCAATTAA-CTAATTTT
5371066 CTCAATTAA-TAATTT
1 CTCAATTAACTAATTT
5371081 ACCTAGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
CTCAATTAACTAATTTT
Found at i:5371224 original size:654 final size:654
Alignment explanation
Indices: 5369969--5371279 Score: 2568
Period size: 654 Copynumber: 2.0 Consensus size: 654
5369959 ACCACTCTTC
*
5369969 ACTAAAAATGAATTGTCTAATTGTACAAATTCGGATGATGTTTCCGTTTGTTTCCTTTGAAAATA
1 ACTAAAAATGAACTGTCTAATTGTACAAATTCGGATGATGTTTCCGTTTGTTTCCTTTGAAAATA
5370034 GACTCATCAAGGATTCTAAGAATATAAATTATAACTCATAATTATTTTTTTACAATTTTTAACAA
66 GACTCATCAAGGATTCTAAGAATATAAATTATAACTCATAATTATTTTTTTACAATTTTTAACAA
5370099 TTTTCCAAAGTCAGAACAGGGGAACCCGAAATCATTCTGACATTATCTCACAAAATTTAATATAT
131 TTTTCCAAAGTCAGAACAGGGGAACCCGAAATCATTCTGACATTATCTCACAAAATTTAATATAT
5370164 CTCATGATTTAAAATTCTATTGCTTACACCGTTTCTTCTATGAGAAACTAGACTCAATAAGATTT
196 CTCATGATTTAAAATTCTATTGCTTACACCGTTTCTTCTATGAGAAACTAGACTCAATAAGATTT
*
5370229 AATTTCATATTTTATTCACCCTCTAATTCAATTCCCATAATTTTTGGTGATTTTTAAAAGTTACA
261 AATTTCATATTTTATTCACCCTCTAATTCAATTCCCACAATTTTTGGTGATTTTTAAAAGTTACA
5370294 CTACTGCTGCTGCCAAAAACTGCTTTAGTGCAAAATGTTGATTTCCATTTTGCCCCCAAATTTCA
326 CTACTGCTGCTGCCAAAAACTGCTTTAGTGCAAAATGTTGATTTCCATTTTGCCCCCAAATTTCA
*
5370359 CAGTTTATGCAATTCGGTTCTTTCTCAATTAACCCCTCAATTAATCTAATTTTCTCAATTAATAA
391 CAGTTTATGCAATTCGGTCCTTTCTCAATTAACCCCTCAATTAATCTAATTTTCTCAATTAATAA
5370424 TTTACCTAGACATTATAAGTTATTTCACAACTATTGAAATTCAGAATTTTCACATATAACCCTAA
456 TTTACCTAGACATTATAAGTTATTTCACAACTATTGAAATTCAGAATTTTCACATATAACCCTAA
5370489 CTTCAAACTCTTTTACTATTAGGTCTCAAACATTCACTTTCTATTCATTTCTCTCAATAAAACCA
521 CTTCAAACTCTTTTACTATTAGGTCTCAAACATTCACTTTCTATTCATTTCTCTCAATAAAACCA
5370554 GTATATGAAAAATTTAAAGCTCTAATTCCATGCTAAATCATCATATACTTCCAGCATGCATTCAT
586 GTATATGAAAAATTTAAAGCTCTAATTCCATGCTAAATCATCATATACTTCCAGCATGCATTCAT
5370619 AGCA
651 AGCA
5370623 ACTAAAAATGAACTGTCTAATTGTACAAATTCGGATGATGTTTCCGTTTGTTTCCTTTGAAAATA
1 ACTAAAAATGAACTGTCTAATTGTACAAATTCGGATGATGTTTCCGTTTGTTTCCTTTGAAAATA
5370688 GACTCATCAAGGATTCTAAGAATATAAATTATAACTCATAATTATTTTTTTACAATTTTTAACAA
66 GACTCATCAAGGATTCTAAGAATATAAATTATAACTCATAATTATTTTTTTACAATTTTTAACAA
5370753 TTTTCCAAAGTCAGAACAGGGGAACCCGAAATCATTCTGACATTATCTCACAAAATTTAATATAT
131 TTTTCCAAAGTCAGAACAGGGGAACCCGAAATCATTCTGACATTATCTCACAAAATTTAATATAT
*
5370818 CTCATGATTTAAAATTCTATTGCTTACACCGTTTCTTCTATGAGAAACTAGACTCAATAAGCTTT
196 CTCATGATTTAAAATTCTATTGCTTACACCGTTTCTTCTATGAGAAACTAGACTCAATAAGATTT
5370883 AATTTCATATTTTATTCACCCTCTAATTCAATTCCCACAATTTTTGGTGATTTTTAAAAGTTACA
261 AATTTCATATTTTATTCACCCTCTAATTCAATTCCCACAATTTTTGGTGATTTTTAAAAGTTACA
*
5370948 CTACTGCTGCTGCCCAAAACTGCTTTAGTGCAAAATGTTGATTTCCATTTTGCCCCCAAATTTCA
326 CTACTGCTGCTGCCAAAAACTGCTTTAGTGCAAAATGTTGATTTCCATTTTGCCCCCAAATTTCA
5371013 CAGTTTATGCAATTCGGTCCTTTCTCAATTAACCCCTCAATTAATCTAATTTTCTCAATTAATAA
391 CAGTTTATGCAATTCGGTCCTTTCTCAATTAACCCCTCAATTAATCTAATTTTCTCAATTAATAA
5371078 TTTACCTAGACATTATAAGTTATTTCACAACTATTGAAATTCAGAATTTTCACATATAACCCTAA
456 TTTACCTAGACATTATAAGTTATTTCACAACTATTGAAATTCAGAATTTTCACATATAACCCTAA
5371143 CTTCAAACTCTTTTACTATTAGGTCTCAAACATTCACTTTCTATTCATTTCTCTCAATAAAACCA
521 CTTCAAACTCTTTTACTATTAGGTCTCAAACATTCACTTTCTATTCATTTCTCTCAATAAAACCA
*
5371208 GTATATGAACAATTTAAAGCTCTAATTCCATGCTAAATCATCATATACTTCCAGCATGCATTCAT
586 GTATATGAAAAATTTAAAGCTCTAATTCCATGCTAAATCATCATATACTTCCAGCATGCATTCAT
5371273 AGCA
651 AGCA
5371277 ACT
1 ACT
5371280 TTCAACTTCT
Statistics
Matches: 651, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
654 651 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.38
Consensus pattern (654 bp):
ACTAAAAATGAACTGTCTAATTGTACAAATTCGGATGATGTTTCCGTTTGTTTCCTTTGAAAATA
GACTCATCAAGGATTCTAAGAATATAAATTATAACTCATAATTATTTTTTTACAATTTTTAACAA
TTTTCCAAAGTCAGAACAGGGGAACCCGAAATCATTCTGACATTATCTCACAAAATTTAATATAT
CTCATGATTTAAAATTCTATTGCTTACACCGTTTCTTCTATGAGAAACTAGACTCAATAAGATTT
AATTTCATATTTTATTCACCCTCTAATTCAATTCCCACAATTTTTGGTGATTTTTAAAAGTTACA
CTACTGCTGCTGCCAAAAACTGCTTTAGTGCAAAATGTTGATTTCCATTTTGCCCCCAAATTTCA
CAGTTTATGCAATTCGGTCCTTTCTCAATTAACCCCTCAATTAATCTAATTTTCTCAATTAATAA
TTTACCTAGACATTATAAGTTATTTCACAACTATTGAAATTCAGAATTTTCACATATAACCCTAA
CTTCAAACTCTTTTACTATTAGGTCTCAAACATTCACTTTCTATTCATTTCTCTCAATAAAACCA
GTATATGAAAAATTTAAAGCTCTAATTCCATGCTAAATCATCATATACTTCCAGCATGCATTCAT
AGCA
Found at i:5371723 original size:21 final size:21
Alignment explanation
Indices: 5371694--5371735 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5371684 CTTTTTGTTC
* *
5371694 AATTAATTATCGGAACTTTAA
1 AATTAATTAACGAAACTTTAA
*
5371715 AATTTATTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
5371736 TACTAACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:5372211 original size:18 final size:18
Alignment explanation
Indices: 5372184--5372223 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
5372174 TAATTAATTT
5372184 TAATTTTTATA-TAAAAA
1 TAATTTTTATACTAAAAA
*
5372201 TAATATTTTATACTTAAAA
1 TAAT-TTTTATACTAAAAA
5372220 TAAT
1 TAAT
5372224 GAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
19 9 0.45
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTTTTATACTAAAAA
Found at i:5373506 original size:24 final size:24
Alignment explanation
Indices: 5373474--5373530 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
5373464 TTTTATCAAT
* * *
5373474 TTTAAGGGTTAAACTATAATTTTC
1 TTTAGGGGTGAAACTAGAATTTTC
* *
5373498 TTTAGGGGTGAAGCTAGAATTTTT
1 TTTAGGGGTGAAACTAGAATTTTC
5373522 TTTAGGGGT
1 TTTAGGGGT
5373531 AAAATTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.05, G:0.25, T:0.44
Consensus pattern (24 bp):
TTTAGGGGTGAAACTAGAATTTTC
Found at i:5374164 original size:23 final size:23
Alignment explanation
Indices: 5374138--5374229 Score: 64
Period size: 23 Copynumber: 3.9 Consensus size: 23
5374128 TTAATGATAT
5374138 TAAAAATAAATAATATAAAATTA
1 TAAAAATAAATAATATAAAATTA
* * * *
5374161 TAAAATTAGAT-TTGTAAAAATATA
1 TAAAAATAAATAATAT-AAAAT-TA
5374185 TAAATATTATAAATAATATAAAA-TA
1 TAAA-A--ATAAATAATATAAAATTA
*
5374210 TATTAAATAAATAA-ATAAAA
1 TA-AAAATAAATAATATAAAA
5374230 ATAACATGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
22 8 0.15
23 22 0.42
24 6 0.11
25 6 0.11
26 1 0.02
27 8 0.15
28 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
TAAAAATAAATAATATAAAATTA
Found at i:5374197 original size:9 final size:8
Alignment explanation
Indices: 5374178--5374226 Score: 53
Period size: 9 Copynumber: 5.6 Consensus size: 8
5374168 AGATTTGTAA
5374178 AAATATAT
1 AAATATAT
5374186 AAATATTAT
1 AAATA-TAT
5374195 AAATAATAT
1 AAAT-ATAT
5374204 AAAATATATT
1 -AAATATA-T
*
5374214 AAATAAAT
1 AAATATAT
5374222 AAATA
1 AAATA
5374227 AAAATAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
8 11 0.31
9 19 0.53
10 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATATAT
Found at i:5374208 original size:19 final size:19
Alignment explanation
Indices: 5374175--5374224 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
5374165 ATTAGATTTG
5374175 TAAA-AATATATAAATAT-T
1 TAAATAATATA-AAATATAT
5374193 ATAAATAATATAAAATATAT
1 -TAAATAATATAAAATATAT
5374213 TAAATAA-ATAAA
1 TAAATAATATAAA
5374225 TAAAAATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.17
19 17 0.59
20 7 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAATAATATAAAATATAT
Found at i:5374209 original size:27 final size:27
Alignment explanation
Indices: 5374143--5374227 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
5374133 GATATTAAAA
5374143 ATAAATAATATAAAAT-TATAAA-ATT
1 ATAAATAATATAAAATATATAAATATT
* * **
5374168 A-GATTTGTA-AAAATATATAAATATT
1 ATAAATAATATAAAATATATAAATATT
*
5374193 ATAAATAATATAAAATATATTAAATA-A
1 ATAAATAATATAAAATATA-TAAATATT
5374220 ATAAATAA
1 ATAAATAA
5374228 AAATAACATG
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
23 5 0.11
24 10 0.22
25 5 0.11
26 4 0.09
27 16 0.35
28 6 0.13
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
ATAAATAATATAAAATATATAAATATT
Found at i:5390378 original size:19 final size:19
Alignment explanation
Indices: 5390348--5390422 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
5390338 AATCATATCT
* *
5390348 TCTAATATTGCATACCATA
1 TCTAAGATTGCATATCATA
*
5390367 TCCAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
5390388 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5390407 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
5390423 CTTGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 33 0.66
21 17 0.34
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:5405103 original size:15 final size:15
Alignment explanation
Indices: 5405054--5405109 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
5405044 TATAATATCA
* *
5405054 AATTTAATCTTTAAT
1 AATTTAATTTTTTAT
5405069 -ATTTACATTTTTTAT
1 AATTTA-ATTTTTTAT
5405084 CAATTTAATTTTTTAT
1 -AATTTAATTTTTTAT
*
5405100 AATTAAATTT
1 AATTTAATTT
5405110 AATCTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 5 0.14
15 16 0.46
16 9 0.26
17 5 0.14
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTAATTTTTTAT
Found at i:5405760 original size:16 final size:16
Alignment explanation
Indices: 5405736--5405789 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
5405726 TTTGGTTCGC
*
5405736 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
5405752 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
* *
5405768 TGTAATGGAATAGATG
1 TGTAATGGATTAGAGG
5405784 TGTAAT
1 TGTAAT
5405790 AGCAAATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.35
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:5405834 original size:45 final size:44
Alignment explanation
Indices: 5405768--5405858 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
5405758 GGATTAGAGG
* *
5405768 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
5405813 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
5405857 TG
1 TG
5405859 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:5406040 original size:16 final size:16
Alignment explanation
Indices: 5406003--5406044 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5405993 TTAATCATAT
*
5406003 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
5406019 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5406034 TTAAAATATAT
1 TTAAAATATAT
5406045 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:5406051 original size:14 final size:15
Alignment explanation
Indices: 5406012--5406053 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5406002 TTTAAACATA
*
5406012 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5406027 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5406041 A-TATAATTTAATA
1 ATTATAATTAAATA
5406054 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5406150 original size:120 final size:120
Alignment explanation
Indices: 5406006--5406347 Score: 657
Period size: 120 Copynumber: 2.9 Consensus size: 120
5405996 ATCATATTTA
5406006 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
5406071 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
5406126 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
5406191 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* *
5406246 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAATATTATTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
5406311 TATTCTTATATGAATTTACTCAAATCATAATATATGA
66 TATTCTTATATGAATTTACTCAAATCATAATATATGA
5406348 CTGTTATTGC
Statistics
Matches: 218, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 218 1.00
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:5406171 original size:14 final size:15
Alignment explanation
Indices: 5406122--5406173 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
5406112 ATAAAATATA
5406122 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
5406137 TATTAAATATATTAT
1 AATTAAATATATTAT
5406152 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
5406165 AATTTAATA
1 AATTAAATA
5406174 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:5406270 original size:15 final size:15
Alignment explanation
Indices: 5406242--5406300 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
5406232 ATAAAATATA
5406242 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
5406257 TATTAAATATATTAT
1 AATTAAATATATTAT
5406272 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
5406285 AATTTAATAATATTAT
1 AATTAAAT-ATATTAT
5406301 TAATAATCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 9 0.24
14 6 0.16
15 19 0.51
16 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:5406300 original size:44 final size:43
Alignment explanation
Indices: 5406219--5406303 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
5406209 CTCAAATCAT
* *
5406219 AATATATGATACTATAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATATAAAATATAAATTAAAATAATTATTATTA
* *
5406262 AATATATTATAAT-TAAAATATATAATT-TAATAA-TATTATTA
1 AATATATGATAATATAAAATATA-AATTAAAATAATTATTATTA
5406303 A
1 A
5406304 TAATCAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
41 9 0.24
42 13 0.35
43 15 0.41
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (43 bp):
AATATATGATAATATAAAATATAAATTAAAATAATTATTATTA
Found at i:5417815 original size:21 final size:22
Alignment explanation
Indices: 5417786--5417832 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
5417776 CAGAAGGAGT
*
5417786 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
5417808 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
5417829 GAGT
1 GAGT
5417833 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:5423456 original size:13 final size:13
Alignment explanation
Indices: 5423438--5423465 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5423428 TTATGGTTAT
5423438 TATTATAAAAAAA
1 TATTATAAAAAAA
5423451 TATTATAAAAAAA
1 TATTATAAAAAAA
5423464 TA
1 TA
5423466 ATAAAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TATTATAAAAAAA
Found at i:5423865 original size:14 final size:14
Alignment explanation
Indices: 5423846--5423873 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5423836 AATTATATTT
5423846 ATATTTTGAATTAA
1 ATATTTTGAATTAA
5423860 ATATTTTGAATTAA
1 ATATTTTGAATTAA
5423874 GTTTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATATTTTGAATTAA
Found at i:5425510 original size:27 final size:25
Alignment explanation
Indices: 5425458--5425510 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
5425448 TAATGTATTC
* *
5425458 AAATAATGAATTAATAATATTTTAA
1 AAATAATGAATGAATAATATTATAA
*
5425483 AAATAGATGAATGGAATTATATTATAA
1 AAATA-ATGAAT-GAATAATATTATAA
5425510 A
1 A
5425511 TTAAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 6 0.26
27 12 0.52
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (25 bp):
AAATAATGAATGAATAATATTATAA
Found at i:5427300 original size:14 final size:15
Alignment explanation
Indices: 5427281--5427309 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5427271 GATCGCCCTA
5427281 TATTTTTTT-TTTTG
1 TATTTTTTTCTTTTG
5427295 TATTTTTTTCTTTTG
1 TATTTTTTTCTTTTG
5427310 ATGTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (15 bp):
TATTTTTTTCTTTTG
Found at i:5427303 original size:15 final size:17
Alignment explanation
Indices: 5427283--5427319 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5427273 TCGCCCTATA
5427283 TTTTTT-TTTT-TGTAT
1 TTTTTTCTTTTATGTAT
5427298 TTTTTTCTTTTGATGTAT
1 TTTTTTCTTTT-ATGTAT
5427316 TTTT
1 TTTT
5427320 AAAAATAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 4 0.21
18 9 0.47
ACGTcount: A:0.08, C:0.03, G:0.08, T:0.81
Consensus pattern (17 bp):
TTTTTTCTTTTATGTAT
Found at i:5439692 original size:35 final size:35
Alignment explanation
Indices: 5439653--5439722 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
5439643 CAGCTAATGA
*
5439653 AATGCTTGGT-TACTTGCATGTTACAGCTGTGTTGC
1 AATGCTTGGTAT-CTTGCATGCTACAGCTGTGTTGC
* *
5439688 AATGCTTGGTATCTTGCATGCTGCTGCTGTGTTGC
1 AATGCTTGGTATCTTGCATGCTACAGCTGTGTTGC
5439723 CACCATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.14, C:0.19, G:0.27, T:0.40
Consensus pattern (35 bp):
AATGCTTGGTATCTTGCATGCTACAGCTGTGTTGC
Found at i:5440870 original size:21 final size:21
Alignment explanation
Indices: 5440844--5440899 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
5440834 AACAGCGGTG
*
5440844 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
5440865 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
5440886 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
5440900 AACAATTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:5443117 original size:15 final size:15
Alignment explanation
Indices: 5443097--5443139 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
5443087 TATATATATA
5443097 TATTCCATTCCATAC
1 TATTCCATTCCATAC
5443112 TATTCCATGT-CATAC
1 TATTCCAT-TCCATAC
*
5443127 CATTCCATTCCAT
1 TATTCCATTCCAT
5443140 TTTATCAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.40
Consensus pattern (15 bp):
TATTCCATTCCATAC
Found at i:5444222 original size:51 final size:50
Alignment explanation
Indices: 5444038--5444487 Score: 388
Period size: 51 Copynumber: 8.9 Consensus size: 50
5444028 ACTATTATCA
* * * *
5444038 TTCGATACACGTAGTAGCCTTCACATAGTACTACATACGTGATC-AATTT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* *
5444087 TTACGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTT
1 TT-CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* * * *
5444137 TTACGGTTCACGTAGTAGCCTTCACATAGAACTACATACGTGACTAAAGCTT
1 TT-CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TT
* * * *
5444189 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCA-TT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTT
** * * *
5444239 TATCAATTCACGTAGTAGCCTTCACAAAGTACTACACGCGTGACCAAAGTT
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
** * * * * *
5444290 TCTCGGTACATATTGTAGCCTTCACTTAGTACTACGCATGTGACCATTA-TT
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTT
* * * * *
5444341 TACCGATTCACGTAGTAGCCTTTACACAGTACTACACACGTGACCAAAGCTT
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TT
* * * * * ***
5444393 CTCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCTTTCG-T
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAAGTT
* * * *
5444443 TCCAGTACACGTAGTAGCCTACACATAGTACTACACACGAGACCA
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA
5444488 TCACTTTCAC
Statistics
Matches: 317, Mismatches: 74, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
49 2 0.01
50 125 0.39
51 181 0.57
52 9 0.03
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (50 bp):
TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
Found at i:5444273 original size:102 final size:101
Alignment explanation
Indices: 5444040--5444487 Score: 510
Period size: 102 Copynumber: 4.4 Consensus size: 101
5444030 TATTATCATT
* * * * * *
5444040 CGATACACGTAGTAGCCTTCACATAGTACTACATACGTGATC-AA-TTTTTACGGTTCACGTAGT
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAGT
* * * ***
5444103 AGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
65 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * *
5444140 CGGTTCACGTAGTAGCCTTCACATAGAACTACATACGTGACTAAAGCTTTTCGGTACACATAGTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTA
5444205 GCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 GCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * * *
5444241 TCAATTCACGTAGTAGCCTTCACAAAGTACTACACGCGTGACCAAAG-TTTCTCGGTACATATTG
1 -CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTT-TCGGTACACATAG
* *
5444305 TAGCCTTCACTTAGTACTACGCATGTGACCATTATTTA
64 TAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * *
5444343 CCGATTCACGTAGTAGCCTTTACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGT
1 -CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
* *
5444408 AGCCTTCACTTAGTACTACACATGTGACCTTTC-GTT-
65 AGCCTTCACTTAGTACTACACATGTGACC-ATCATTTA
* * * *
5444444 CCAGTACACGTAGTAGCCTACACATAGTACTACACACGAGACCA
1 CGA-TTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCA
5444488 TCACTTTCAC
Statistics
Matches: 299, Mismatches: 42, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
100 39 0.13
101 82 0.27
102 175 0.59
103 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (101 bp):
CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTA
GCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:5453279 original size:21 final size:22
Alignment explanation
Indices: 5453229--5453279 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
5453219 ATATATATAT
* *
5453229 ATATTAATTATTTTTTTAAGAA
1 ATATTATTTATTTTTGTAAGAA
* *
5453251 A-ATAATTTCTTTTTGTAA-AA
1 ATATTATTTATTTTTGTAAGAA
5453271 ATATTATTT
1 ATATTATTT
5453280 TTATTTCCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 3 0.13
21 19 0.83
22 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
ATATTATTTATTTTTGTAAGAA
Found at i:5453710 original size:24 final size:26
Alignment explanation
Indices: 5453679--5453747 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
5453669 ATTATATATT
5453679 AAATATATTTTTTAATTTTTAATCAA
1 AAATATATTTTTTAATTTTTAATCAA
*
5453705 AAATATATTTTTTTATTTTTAATCAA
1 AAATATATTTTTTAATTTTTAATCAA
* *
5453731 ATATATA-TATTTAATTT
1 AAATATATTTTTTAATTT
5453748 ATATTTAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 8 0.21
26 31 0.79
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (26 bp):
AAATATATTTTTTAATTTTTAATCAA
Found at i:5456129 original size:41 final size:41
Alignment explanation
Indices: 5456072--5456154 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
5456062 GACAAACAGC
5456072 CACTGTCGGAAAGAACAGATATCATAAGTGCTAAAAGTCAG
1 CACTGTCGGAAAGAACAGATATCATAAGTGCTAAAAGTCAG
*
5456113 CACTGTCGGGAAGAACAGATATCATAAGTGCTAAAAGTCAG
1 CACTGTCGGAAAGAACAGATATCATAAGTGCTAAAAGTCAG
5456154 C
1 C
5456155 TTTGGAGGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
CACTGTCGGAAAGAACAGATATCATAAGTGCTAAAAGTCAG
Found at i:5457550 original size:20 final size:20
Alignment explanation
Indices: 5457527--5457568 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5457517 GTTATAAGTA
*
5457527 AAAAAT-TATTATAAATAATT
1 AAAAATCTAATATAAA-AATT
5457547 -AAAATCTAATATAAAAATT
1 AAAAATCTAATATAAAAATT
5457566 AAA
1 AAA
5457569 TTTATTTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATCTAATATAAAAATT
Found at i:5459455 original size:13 final size:13
Alignment explanation
Indices: 5459439--5459504 Score: 89
Period size: 13 Copynumber: 5.1 Consensus size: 13
5459429 TTTAAACTAA
5459439 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
5459452 ACTTCTCAAAAAC
1 ACTTTTCAAAAGC
*
5459465 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
5459478 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
5459491 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
5459504 A
1 A
5459505 ATAAATAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
12 4 0.09
13 38 0.83
14 4 0.09
ACGTcount: A:0.39, C:0.27, G:0.05, T:0.29
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:5462630 original size:42 final size:41
Alignment explanation
Indices: 5462578--5462786 Score: 287
Period size: 42 Copynumber: 5.0 Consensus size: 41
5462568 CGCTTACAGA
5462578 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
1 AAAAAACGCCGCTAAA-ATCATGTTCTTTAGCGGCGCTTAGG
*
5462620 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGGG
1 AAAAAACGCCGCTAAA-ATCATGTTCTTTAGCGGCGCTTAGG
*
5462662 AAAAAATGCCGCTAAAAATCATGTTCTTTAGCGGCGCTTAGG
1 AAAAAACGCCGCT-AAAATCATGTTCTTTAGCGGCGCTTAGG
* *
5462704 AAGAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTT-GG
1 AA-AAAACGCCGCTAAAA-TCATGTTCTTTAGCGGCGCTTAGG
*
5462746 TCAAAAACGCCGCTAAAAGT-AGTGTTCTTTAGCGGCGCTTA
1 -AAAAAACGCCGCTAAAA-TCA-TGTTCTTTAGCGGCGCTTA
5462787 TTTCACAAAC
Statistics
Matches: 153, Mismatches: 8, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
41 1 0.01
42 119 0.78
43 33 0.22
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAATCATGTTCTTTAGCGGCGCTTAGG
Found at i:5462737 original size:85 final size:84
Alignment explanation
Indices: 5462578--5462786 Score: 314
Period size: 85 Copynumber: 2.5 Consensus size: 84
5462568 CGCTTACAGA
* *
5462578 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATG
1 AAAAAACGCCGCTAAAAATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATAATG
*
5462643 TTCTTTAGCGGCGCTTGGG
66 TTCTATAGCGGCGCTTGGG
*
5462662 AAAAAATGCCGCTAAAAATCATGTTCTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAA-AGTAA
1 AAAAAACGCCGCTAAAAATCATGTTCTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAGA-TAA
*
5462726 TGTTCTATAGCGGCGCTTGGT
64 TGTTCTATAGCGGCGCTTGGG
* *
5462747 CAAAAACGCCGCTAAAAGT-AGTGTTCTTTAGCGGCGCTTA
1 AAAAAACGCCGCTAAAAATCA-TGTTCTTTAGCGGCGCTTA
5462787 TTTCACAAAC
Statistics
Matches: 114, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
84 44 0.39
85 70 0.61
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (84 bp):
AAAAAACGCCGCTAAAAATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATAATG
TTCTATAGCGGCGCTTGGG
Found at i:5463241 original size:21 final size:21
Alignment explanation
Indices: 5463217--5463267 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
5463207 TTCTTTTGAA
*
5463217 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
* *
5463238 CCTCCGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
5463259 CCTCTGCTT
1 CCTCTGCTT
5463268 TAAGTTGTAG
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:0.02, C:0.49, G:0.18, T:0.31
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:5469475 original size:26 final size:26
Alignment explanation
Indices: 5469439--5469492 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
5469429 TCAATATTTT
5469439 TTTGTACTCACTGTGTTAAAAAAATG
1 TTTGTACTCACTGTGTTAAAAAAATG
5469465 TTTGTACTCACTGTGTTAAAAAAATG
1 TTTGTACTCACTGTGTTAAAAAAATG
5469491 TT
1 TT
5469493 CACTTTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (26 bp):
TTTGTACTCACTGTGTTAAAAAAATG
Found at i:5472118 original size:9 final size:9
Alignment explanation
Indices: 5472101--5472355 Score: 187
Period size: 9 Copynumber: 29.4 Consensus size: 9
5472091 TATGTATTAA
*
5472101 GTAAATTAT
1 GTAAGTTAT
5472110 GTAAGTTAT
1 GTAAGTTAT
*
5472119 GTACGTGTA-
1 GTAAGT-TAT
5472128 -TAAGTTAT
1 GTAAGTTAT
5472136 GTAAGTTAT
1 GTAAGTTAT
*
5472145 GT-A-TTAA
1 GTAAGTTAT
*
5472152 GTAAGCTAT
1 GTAAGTTAT
* *
5472161 TTAAGTTGT
1 GTAAGTTAT
5472170 GT-A-TTAT
1 GTAAGTTAT
5472177 GTAAGTTAT
1 GTAAGTTAT
5472186 GTAAGTTAT
1 GTAAGTTAT
** *
5472195 CAAAGTAAT
1 GTAAGTTAT
*
5472204 GTATGTTAT
1 GTAAGTTAT
*
5472213 GTAA-AT-T
1 GTAAGTTAT
5472220 GTAAGTTAT
1 GTAAGTTAT
*
5472229 -TATGTATTAT
1 GTAAG--TTAT
*
5472239 GTAGGTTAT
1 GTAAGTTAT
5472248 GTAAGTTAT
1 GTAAGTTAT
5472257 GTAAGTTAT
1 GTAAGTTAT
*
5472266 GTAAGTTTT
1 GTAAGTTAT
*
5472275 GT-A-TTAC
1 GTAAGTTAT
*
5472282 GTAAGTTGT
1 GTAAGTTAT
5472291 GTAAGTTAT
1 GTAAGTTAT
* *
5472300 GTATGCTAT
1 GTAAGTTAT
5472309 GTAAGTTAT
1 GTAAGTTAT
5472318 GT-A-TTAT
1 GTAAGTTAT
5472325 GTAAGTT-T
1 GTAAGTTAT
**
5472333 AACAAGTTAT
1 -GTAAGTTAT
*
5472343 GTAAGTAAT
1 GTAAGTTAT
5472352 GTAA
1 GTAA
5472356 TATATACTTA
Statistics
Matches: 189, Mismatches: 39, Indels: 36
0.72 0.15 0.14
Matches are distributed among these distances:
7 27 0.14
8 18 0.10
9 134 0.71
10 7 0.04
11 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.44
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:5472121 original size:25 final size:25
Alignment explanation
Indices: 5472090--5472354 Score: 166
Period size: 25 Copynumber: 10.3 Consensus size: 25
5472080 TGATATATAT
*
5472090 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
5472115 TTATGTACGTGT-A-TAAGTTATGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
* *
5472141 TTATGTATTAAGTAAGCTATTTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
* *
5472166 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
** * * *
5472191 TTATCAAAGTAATGTATGTTATGTAAAT
1 TTAT-GTATTAA-GTAAGTTATGT-AAG
* * *
5472219 TGTAAGTTATTATGT-A-TTATGTAGG
1 T-TATG-TATTAAGTAAGTTATGTAAG
*
5472244 TTATGTAAGTTATGTAAGTTATGTAAG
1 TTATGT-A-TTAAGTAAGTTATGTAAG
* * *
5472271 TTTTGTATTACGTAAGTTGTGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
*
5472296 TTATGTATGCTATGTAAGTTATGT-A-
1 TTATGTAT--TAAGTAAGTTATGTAAG
*
5472321 TTATGTAAGTTTAA-CAAGTTATGTAAG
1 TTATGT-A--TTAAGTAAGTTATGTAAG
*
5472348 TAATGTA
1 TTATGTA
5472355 ATATATACTT
Statistics
Matches: 186, Mismatches: 33, Indels: 41
0.72 0.13 0.16
Matches are distributed among these distances:
23 2 0.01
24 6 0.03
25 88 0.47
26 36 0.19
27 42 0.23
28 7 0.04
29 5 0.03
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:5472190 original size:34 final size:34
Alignment explanation
Indices: 5472105--5472331 Score: 148
Period size: 34 Copynumber: 6.6 Consensus size: 34
5472095 TATTAAGTAA
*
5472105 ATTATGTAAGTTATGTACGTGTA--TAAGTTATGT
1 ATTATGTAAGTTATGTAAGT-TATTTAAGTTATGT
* * *
5472138 AAGTTATGT-A-TTAAGTAAGCTATTTAAGTTGTGT
1 -A-TTATGTAAGTTATGTAAGTTATTTAAGTTATGT
** *
5472172 ATTATGTAAGTTATGTAAGTTATCAAAGTAATGT
1 ATTATGTAAGTTATGTAAGTTATTTAAGTTATGT
* *
5472206 ATGTTATGTAA-AT-TGTAAGTTA-TTATGTATTATGT
1 A--TTATGTAAGTTATGTAAGTTATTTAAG--TTATGT
* *
5472241 AGGTTATGTAAGTTATGTAAGTTATGTAAGTTTTGT
1 A--TTATGTAAGTTATGTAAGTTATTTAAGTTATGT
* * * * *
5472277 ATTACGTAAGTTGTGTAAGTTATGTATGCTATGT
1 ATTATGTAAGTTATGTAAGTTATTTAAGTTATGT
5472311 AAGTTATGT-A-TTATGTAAGTT
1 -A-TTATGTAAGTTATGTAAGTT
5472332 TAACAAGTTA
Statistics
Matches: 152, Mismatches: 27, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
32 8 0.05
33 11 0.07
34 77 0.51
35 24 0.16
36 20 0.13
37 9 0.06
38 3 0.02
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (34 bp):
ATTATGTAAGTTATGTAAGTTATTTAAGTTATGT
Found at i:5472294 original size:43 final size:43
Alignment explanation
Indices: 5472105--5472355 Score: 194
Period size: 43 Copynumber: 5.8 Consensus size: 43
5472095 TATTAAGTAA
* *
5472105 ATTATGTAAGTTATGTACGTGTA--TAAGTTATGTAAGTTATGT
1 ATTACGTAAGTTATGTAAGT-TATGTAAGTTATGTAAGTTATGT
* * * *
5472147 ATTAAGTAAGCTATTTAAGTTGTGT-A-TTATGTAAGTTATGT
1 ATTACGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGT
* * * *
5472188 AAGTTATC-AAAGTAATGTATGTTATGTAA-AT-TGTAAGTTATTATGT
1 -A-TTA-CGTAAGTTATGTAAGTTATGTAAGTTATGTAAG---TTATGT
* * *
5472234 ATTATGTAGGTTATGTAAGTTATGTAAGTTATGTAAGTTTTGT
1 ATTACGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGT
* * *
5472277 ATTACGTAAGTTGTGTAAGTTATGTATGCTATGTAAGTTATGT
1 ATTACGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGT
* ** *
5472320 ATTATGTAAGTT-TAACAAGTTATGTAAGTAATGTAA
1 ATTACGTAAGTTAT-GTAAGTTATGTAAGTTATGTAA
5472356 TATATACTTA
Statistics
Matches: 164, Mismatches: 32, Indels: 25
0.74 0.14 0.11
Matches are distributed among these distances:
41 16 0.10
42 19 0.12
43 93 0.57
44 22 0.13
45 2 0.01
46 12 0.07
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (43 bp):
ATTACGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGT
Found at i:5472403 original size:13 final size:13
Alignment explanation
Indices: 5472382--5472447 Score: 89
Period size: 13 Copynumber: 5.1 Consensus size: 13
5472372 AGTAAGTAAT
5472382 ATATATTTAAGTA
1 ATATATTTAAGTA
*
5472395 ATGTATTTAAGTA
1 ATATATTTAAGTA
5472408 A-ATTATTTAAGTA
1 ATA-TATTTAAGTA
*
5472421 ATATATTCAAGTA
1 ATATATTTAAGTA
*
5472434 ATATATTAAAGTA
1 ATATATTTAAGTA
5472447 A
1 A
5472448 ATTTTAGTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
13 46 0.98
14 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (13 bp):
ATATATTTAAGTA
Found at i:5472417 original size:26 final size:27
Alignment explanation
Indices: 5472374--5472458 Score: 99
Period size: 26 Copynumber: 3.3 Consensus size: 27
5472364 TAAATTTTAG
*
5472374 TAAGTAATATATATTTAAGTAATGTATT
1 TAAGTAA-ATATATTTAAGTAATATATT
5472402 TAAGTAAAT-TATTTAAGTAATATATT
1 TAAGTAAATATATTTAAGTAATATATT
* *
5472428 CAAGT-AATATATTAAAGTAA-AT-TT
1 TAAGTAAATATATTTAAGTAATATATT
5472452 T-AGTAAA
1 TAAGTAAA
5472459 AAATATGTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
23 3 0.06
24 4 0.08
25 5 0.10
26 30 0.59
27 2 0.04
28 7 0.14
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.42
Consensus pattern (27 bp):
TAAGTAAATATATTTAAGTAATATATT
Found at i:5472746 original size:13 final size:13
Alignment explanation
Indices: 5472728--5472786 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
5472718 CAAATTTTAA
*
5472728 TAAGTAATGTATT
1 TAAGTAATATATT
5472741 TAAGTAA-ATTATT
1 TAAGTAATA-TATT
5472754 TAAGTAATATATT
1 TAAGTAATATATT
*
5472767 CAAGTAATATATT
1 TAAGTAATATATT
*
5472780 AAAGTAA
1 TAAGTAA
5472787 ATTTTAGTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
13 40 0.98
14 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:5472766 original size:26 final size:27
Alignment explanation
Indices: 5472728--5472797 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 27
5472718 CAAATTTTAA
*
5472728 TAAGTAATGTATTTAAGTAAAT-TATT
1 TAAGTAATATATTTAAGTAAATATATT
*
5472754 TAAGTAATATATTCAAGT-AATATATT
1 TAAGTAATATATTTAAGTAAATATATT
*
5472780 AAAGTAA-AT-TTT-AGTAAA
1 TAAGTAATATATTTAAGTAAA
5472798 AAATATGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 3 0.08
24 4 0.11
25 5 0.13
26 26 0.68
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.41
Consensus pattern (27 bp):
TAAGTAATATATTTAAGTAAATATATT
Found at i:5472859 original size:87 final size:86
Alignment explanation
Indices: 5472421--5472934 Score: 238
Period size: 86 Copynumber: 6.0 Consensus size: 86
5472411 TATTTAAGTA
* * *
5472421 ATATATTCAAGTAATATATTAAAGTAAATTTTAGTAAAAAATATGTTTTAGTAAGTAATGTAAGT
1 ATATATTTAAGTAATATATTAAAGTAAATTTTAG-AAAAAATATATTTTAATAAGTAATGTAAGT
*
5472486 CATGTAAAATATACTTAAAAAT
65 AATGTAAAATATACTTAAAAAT
* ** * * * * *
5472508 ATATATTTAAGTAATGTAAGATA-TCAATTTT--AAAAAAT-TATTACTTAACAA-TATATATTA
1 ATATATTTAAGTAATATATTAAAGTAAATTTTAGAAAAAATATATT--TTAATAAGTA-ATGTAA
* * * *
5472568 TTAATAAGTTAAAT-TAAATTCTAAAA-
63 GTAAT--GTAAAATAT-ACTT-AAAAAT
* * *
5472594 ATATATTTAA--AA-ATA-T-AA-TAAATATT-GAAATTATAATATATTTTAACAAGTTATGTAA
1 ATATATTTAAGTAATATATTAAAGTAAATTTTAGAAA--A-AATATATTTTAATAAGTAATGTAA
*
5472652 GTAATGTAATATATACTT--AAAT
63 GTAATGTAAAATATACTTAAAAAT
* * * * * *
5472674 -TTTA-GTAAGTAATATATATTTAAGTAATGTATTTA-AAATTTAAACAAATTTTAATAAGTAAT
1 ATATATTTAAGT-A-ATATATTAAAGTAA-AT-TTTAGAAA---AAATATATTTTAATAAGTAAT
** * **
5472736 GTATTTAA-GT-AAAT-TATTTAAGTA-
59 GTAAGTAATGTAAAATATACTTAAAAAT
* * *
5472760 ATATATTCAAGTAATATATTAAAGTAAATTTTAGTAAAAAATATGTTTTAGTAAGTAATGTAAGT
1 ATATATTTAAGTAATATATTAAAGTAAATTTTAG-AAAAAATATATTTTAATAAGTAATGTAAGT
*
5472825 CATGTAAAATATACTTAAAAAT
65 AATGTAAAATATACTTAAAAAT
* ** * * *
5472847 ATATATTTAAGTAATGTAAGATA-TCAATTTTA-AAAAATATATATATTAATAAGTCAAAT-TAA
1 ATATATTTAAGTAATATATTAAAGTAAATTTTAGAAAAA-ATATATTTTAATAAGT--AATGTAA
* *
5472909 --ATTGTAAAAATATATTTAAAAAT
63 GTAATGT-AAAATATACTTAAAAAT
5472932 ATA
1 ATA
5472935 ATAAATATTG
Statistics
Matches: 317, Mismatches: 69, Indels: 84
0.67 0.15 0.18
Matches are distributed among these distances:
78 3 0.01
79 6 0.02
81 8 0.03
82 15 0.05
83 37 0.12
84 45 0.14
85 48 0.15
86 70 0.22
87 51 0.16
88 31 0.10
89 3 0.01
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (86 bp):
ATATATTTAAGTAATATATTAAAGTAAATTTTAGAAAAAATATATTTTAATAAGTAATGTAAGTA
ATGTAAAATATACTTAAAAAT
Found at i:5472917 original size:36 final size:37
Alignment explanation
Indices: 5472840--5472923 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 37
5472830 AAAATATACT
* *
5472840 TAAAAATATATATTTAAGTAATGTAAGATATCAATTT
1 TAAAAATATATATTTAAGTAATGTAAGATATAAATTG
5472877 TAAAAAATATATATATTAA-TAA-GTCAA-AT-TAAATTG
1 T-AAAAATATATAT-TTAAGTAATGT-AAGATATAAATTG
5472913 TAAAAATATAT
1 TAAAAATATAT
5472924 TTAAAAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
35 10 0.24
36 6 0.14
37 5 0.12
38 17 0.40
39 4 0.10
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (37 bp):
TAAAAATATATATTTAAGTAATGTAAGATATAAATTG
Found at i:5473175 original size:16 final size:16
Alignment explanation
Indices: 5473154--5473189 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
5473144 ATTAATTGAA
*
5473154 ATAAAATTGAAAATTG
1 ATAAAATTGAAAATCG
5473170 ATAAAATTGAAAATCG
1 ATAAAATTGAAAATCG
5473186 ATAA
1 ATAA
5473190 TTATAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.28
Consensus pattern (16 bp):
ATAAAATTGAAAATCG
Found at i:5474697 original size:44 final size:44
Alignment explanation
Indices: 5474639--5474726 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
5474629 TTAAAACATT
* *
5474639 TTTGCGGCGTTTTAAGCAAAGCGCCACAAACTATAAGTCAAAAC
1 TTTGCGGCATTTTAAACAAAGCGCCACAAACTATAAGTCAAAAC
* *
5474683 TTTGCGGCATTTTAAACTAAGCGCCACTAACTATAAGTCAAAAC
1 TTTGCGGCATTTTAAACAAAGCGCCACAAACTATAAGTCAAAAC
5474727 GCAGTCGCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (44 bp):
TTTGCGGCATTTTAAACAAAGCGCCACAAACTATAAGTCAAAAC
Found at i:5475477 original size:21 final size:21
Alignment explanation
Indices: 5475453--5475498 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5475443 TCTAAACCTT
5475453 AAACCTCAAAAACC-AAACCCC
1 AAACC-CAAAAACCAAAACCCC
**
5475474 AAACCCAAACCCCAAAACCCC
1 AAACCCAAAAACCAAAACCCC
5475495 AAAC
1 AAAC
5475499 ACTAAAAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.52, C:0.46, G:0.00, T:0.02
Consensus pattern (21 bp):
AAACCCAAAAACCAAAACCCC
Found at i:5475491 original size:14 final size:14
Alignment explanation
Indices: 5475453--5475498 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
5475443 TCTAAACCTT
* *
5475453 AAACCTCAAAAACC
1 AAACCCCAAAACCC
5475467 AAACCCC-AAACCC
1 AAACCCCAAAACCC
5475480 AAACCCCAAAACCCC
1 AAACCCCAAAA-CCC
5475495 AAAC
1 AAAC
5475499 ACTAAAAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 12 0.43
14 9 0.32
15 7 0.25
ACGTcount: A:0.52, C:0.46, G:0.00, T:0.02
Consensus pattern (14 bp):
AAACCCCAAAACCC
Found at i:5475493 original size:8 final size:7
Alignment explanation
Indices: 5475465--5475498 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
5475455 ACCTCAAAAA
5475465 CCAAACC
1 CCAAACC
5475472 CCAAA-C
1 CCAAACC
5475478 CCAAACC
1 CCAAACC
5475485 CCAAAACC
1 CC-AAACC
5475493 CCAAAC
1 CCAAAC
5475499 ACTAAAAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (7 bp):
CCAAACC
Found at i:5475924 original size:19 final size:19
Alignment explanation
Indices: 5475892--5475928 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5475882 TCTAACCCAT
5475892 AACCCAAACCACTAACCCC
1 AACCCAAACCACTAACCCC
* *
5475911 AACCCTAACTACTAACCC
1 AACCCAAACCACTAACCC
5475929 TAAACCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.49, G:0.00, T:0.11
Consensus pattern (19 bp):
AACCCAAACCACTAACCCC
Found at i:5475988 original size:81 final size:81
Alignment explanation
Indices: 5475903--5476070 Score: 198
Period size: 81 Copynumber: 2.1 Consensus size: 81
5475893 ACCCAAACCA
* * *
5475903 CTAACCCCAA-CCCTAACTAC-TAACC-CTAAACCTTATTTAATACATAAATTAAAAAATATTAA
1 CTAACCCCAATCCCTAAC-ACTTAACCTCTAAACCATATTTAATA-A-AAATTAAAAAACACTAA
*
5475965 TTAATCAAAACCCTAAATC
63 TTAATCAAAACCCTAAAGC
* * * * *
5475984 CTAACCCGAATCCCTAACCCTTAACCTTTAAACCATATTTTATAAAAATTAAAACACACTAATTA
1 CTAACCCCAATCCCTAACACTTAACCTCTAAACCATATTTAATAAAAATTAAAAAACACTAATTA
*
5476049 ATCTAAACCCTAAAGC
66 ATCAAAACCCTAAAGC
5476065 CTAACC
1 CTAACC
5476071 TAACACTGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
81 47 0.64
82 13 0.18
83 14 0.19
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (81 bp):
CTAACCCCAATCCCTAACACTTAACCTCTAAACCATATTTAATAAAAATTAAAAAACACTAATTA
ATCAAAACCCTAAAGC
Found at i:5476782 original size:113 final size:113
Alignment explanation
Indices: 5476514--5477170 Score: 596
Period size: 113 Copynumber: 5.7 Consensus size: 113
5476504 TCGGGAAAAG
* * * ** * *
5476514 CGCCGCTAATACTATGC-TTCAGCGGCATTTTCCTGTGTGCGCCACTAATTCCAGTATACATCAA
1 CGCCGCTAATACTATACATT-AGCGGCGTTTTCC-ATAAGCGCCACTAATTCTAATATACATCAA
* * * * * * *
5476578 GAACTAAACGCTGTGTTTTCGTTAATAT-CTTTTGGCGGCGCTTAC-CAAAAA
64 G-ACCAAACTCTGCGTTTTGGTTAAGATAC-TTT-GCGGCGCTTTCGCACAAA
* * * ** * *
5476629 GCGTCGCAAATAGTA-AGCATTAGCGGCGTTTTGAAATAAGCGCCACTAACTCTAATATACGTCA
1 -CGCCGCTAATACTATA-CATTAGCGGCGTTTT-CCATAAGCGCCACTAATTCTAATATACATCA
*
5476693 AGGCCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTC-CACAAA
63 AGACCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTCGCACAAA
* * *
5476743 CGCCGCTACTACTATACTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTCAAG
1 CGCCGCTAATACTATACATTAGCGGCGTTTTCC-ATAAGCGCCACTAATTCTAATATACATCAAG
* * * *
5476808 ACCAAACTCCGCGTTTTGGTTAAGATATTTTGAGGCGCTTAC-CACCAAA
65 ACCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTCGCA-CAAA
* * * * * * * * *
5476857 CGCTGCTATTACTATGCTTTAGTGGCGTTTTCCTTAAACGCCACTAATTATAGTATACATCAAGA
1 CGCCGCTAATACTATACATTAGCGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCAAGA
* ** * *
5476922 CCAAAACGCTGCGTTTTGGTTAAGATTTTTTGCGGCG-TTTAGCGCTC-AG
66 CC-AAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTT--CGCACAAA
* *
5476971 CGCCGCTAATACTATACATTAGCGGCGTTTTCTTTATAAGCGCCACTAATTGTAATATACATCAA
1 CGCCGCTAATACTATACATTAGCGGCGTTTTC--CATAAGCGCCACTAATTCTAATATACATCAA
* * *
5477036 GACCAAACTCTGCGTTTTGGTTAACAT-CTTTTGCGGCGCTTTCGC-TAAG
64 GACCAAACTCTGCGTTTTGGTTAAGATAC-TTTGCGGCGCTTTCGCACAAA
* * * *
5477085 CGCCGCTAATACTATGCATTACCGGCGTTTGTTCGTAAGCGCCACTAATTCTAATATACATCAAG
1 CGCCGCTAATACTATACATTAGCGGCGTTT-TCCATAAGCGCCACTAATTCTAATATACATCAAG
* *
5477150 ACCAGAACGCTGCGTGTTGGT
65 ACCA-AACTCTGCGTTTTGGT
5477171 CTTGAGATTT
Statistics
Matches: 449, Mismatches: 74, Indels: 38
0.80 0.13 0.07
Matches are distributed among these distances:
113 156 0.35
114 154 0.34
115 56 0.12
116 81 0.18
117 2 0.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (113 bp):
CGCCGCTAATACTATACATTAGCGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCAAGA
CCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTCGCACAAA
Found at i:5476947 original size:114 final size:113
Alignment explanation
Indices: 5476514--5477170 Score: 640
Period size: 114 Copynumber: 5.7 Consensus size: 113
5476504 TCGGGAAAAG
* * ** * *
5476514 CGCCGCTAATACTATGC-TTCAGCGGCATTTTCCTGTGTGCGCCACTAATTCCAGTATACATCAA
1 CGCCGCTAATACTATGCATT-AGCGGCGTTTTCC-ATAAGCGCCACTAATTCTAATATACATCAA
* * * * * *
5476578 GAACTAAACGCTGTGTTTTCGTTAATATCTTTTGGCGGCGCTTACCA-AAAA
64 G-ACCAAACGCTGCGTTTTGGTTAAGATATTTT-GCGGCGCTTACCACCAAA
* * * * ** * *
5476629 GCGTCGCAAATAGTAAGCATTAGCGGCGTTTTGAAATAAGCGCCACTAACTCTAATATACGTCAA
1 -CGCCGCTAATACTATGCATTAGCGGCGTTTT-CCATAAGCGCCACTAATTCTAATATACATCAA
* * * *
5476694 GGCCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTCCA-CAAA
64 GACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTACCACCAAA
* * * *
5476743 CGCCGCTACTACTATACTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTCAAG
1 CGCCGCTAATACTATGCATTAGCGGCGTTTTCC-ATAAGCGCCACTAATTCTAATATACATCAAG
* * *
5476808 ACCAAACTCCGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAA
65 ACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTACCACCAAA
* * * * * * * *
5476857 CGCTGCTATTACTATGCTTTAGTGGCGTTTTCCTTAAACGCCACTAATTATAGTATACATCAAGA
1 CGCCGCTAATACTATGCATTAGCGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCAAGA
* * * * *
5476922 CCAAAACGCTGCGTTTTGGTTAAGATTTTTTGCGGCGTTTAGCGCTC-AG
66 CC-AAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTACCAC-CAAA
* * *
5476971 CGCCGCTAATACTATACATTAGCGGCGTTTTCTTTATAAGCGCCACTAATTGTAATATACATCAA
1 CGCCGCTAATACTATGCATTAGCGGCGTTTTC--CATAAGCGCCACTAATTCTAATATACATCAA
* * * * * * *
5477036 GACCAAACTCTGCGTTTTGGTTAACATCTTTTGCGGCGCTT-TCGCTAAG
64 GACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTACCACCAAA
* * *
5477085 CGCCGCTAATACTATGCATTACCGGCGTTTGTTCGTAAGCGCCACTAATTCTAATATACATCAAG
1 CGCCGCTAATACTATGCATTAGCGGCGTTT-TCCATAAGCGCCACTAATTCTAATATACATCAAG
*
5477150 ACCAGAACGCTGCGTGTTGGT
65 ACCA-AACGCTGCGTTTTGGT
5477171 CTTGAGATTT
Statistics
Matches: 449, Mismatches: 81, Indels: 24
0.81 0.15 0.04
Matches are distributed among these distances:
113 154 0.34
114 158 0.35
115 58 0.13
116 77 0.17
117 2 0.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (113 bp):
CGCCGCTAATACTATGCATTAGCGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCAAGA
CCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTACCACCAAA
Found at i:5477206 original size:229 final size:221
Alignment explanation
Indices: 5476514--5477209 Score: 660
Period size: 229 Copynumber: 3.0 Consensus size: 221
5476504 TCGGGAAAAG
* * * ** * *
5476514 CGCCGCTAATACTATGCTTCAGCGGCATTTTC-CTGTGTGCGCCACTAATTCCAGTATACATCAA
1 CGCCGCTAATACTATACTT-AGCGGCGTTTTCTCTATAAGCGCCACTAATTCTAATATACATCAA
* * * * * * * *
5476578 GAACTAAACGCTGTGTTTTCGTTAATATCTTTTGGCGGCGCTTACCAAAAAGCGTCGCAAATAGT
65 G-ACCAAACTCTGCGTTTTGGTTAACATCTTTT-GCGGCGCTTACC--AAAGCGCCGCTAATACT
* * * * * *
5476643 AAGCATTAGCGGCGTTTTGAAATAAGCGCCACTAACTCTAATATACGTCAAGGCCAAACTCTGCG
126 ATGCATTAGCGGCGTTTT-ACATAAGCGCCACTAATTCTAATATACATCAAGACCAAACGCTGCG
* *
5476708 TTTTGGTTAAGATACTTTGCGGCGCTTTCCA-CAAA
190 TTTTGGTTAAGAT--TTTGCGGCG-TTT-GAGTAAA
* * *
5476743 CGCCGCTACTACTATACTTTAGCGGCGTTTTC-CAATAAGCGCCACTAATTCTAATATACCTCAA
1 CGCCGCTAATACTATAC-TTAGCGGCGTTTTCTCTATAAGCGCCACTAATTCTAATATACATCAA
* * * * * * *
5476807 GACCAAACTCCGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAACGCTGCTATTACTAT
65 GACCAAACTCTGCGTTTTGGTTAACATCTTTTGCGGCGCTTACCA--AAGCGCCGCTAATACTAT
* * * * * * *
5476872 GCTTTAGTGGCGTTTTCCTTAAACGCCACTAATTATAGTATACATCAAGACCAAAACGCTGCGTT
128 GCATTAGCGGCGTTTTACATAAGCGCCACTAATTCTAATATACATCAAGACC-AAACGCTGCGTT
* * *
5476937 TTGGTTAAGATTTTTTGCGGCGTTTAGCGCTCAG
192 TTGGTTAAGA--TTTTGCGGCGTTT-GAG-TAAA
* *
5476971 CGCCGCTAATACTATACATTAGCGGCGTTTTCTTTATAAGCGCCACTAATTGTAATATACATCAA
1 CGCCGCTAATACTATAC-TTAGCGGCGTTTTCTCTATAAGCGCCACTAATTCTAATATACATCAA
* *
5477036 GACCAAACTCTGCGTTTTGGTTAACATCTTTTGCGGCGCTTTCGCTAAGCGCCGCTAATACTATG
65 GACCAAACTCTGCGTTTTGGTTAACATCTTTTGCGGCGCTTAC-CAAAGCGCCGCTAATACTATG
* * * *
5477101 CATTACCGGCGTTTGTTCGTAAGCGCCACTAATTCTAATATACATCAAGACCAGAACGCTGCGTG
129 CATTAGCGGCGTTT-TACATAAGCGCCACTAATTCTAATATACATCAAGACCA-AACGCTGCGTT
* *
5477166 TTGGTCTTGAGATTTTGTGGCGTTGTGTAGTAAA
192 TTGG--TTAAGATTTTGCGGCGTT-TG-AGTAAA
5477200 CGCCGCTAAT
1 CGCCGCTAAT
5477210 GATGTTCTTT
Statistics
Matches: 379, Mismatches: 72, Indels: 32
0.78 0.15 0.07
Matches are distributed among these distances:
225 1 0.00
226 30 0.08
227 66 0.17
228 83 0.22
229 189 0.50
230 5 0.01
231 5 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (221 bp):
CGCCGCTAATACTATACTTAGCGGCGTTTTCTCTATAAGCGCCACTAATTCTAATATACATCAAG
ACCAAACTCTGCGTTTTGGTTAACATCTTTTGCGGCGCTTACCAAAGCGCCGCTAATACTATGCA
TTAGCGGCGTTTTACATAAGCGCCACTAATTCTAATATACATCAAGACCAAACGCTGCGTTTTGG
TTAAGATTTTGCGGCGTTTGAGTAAA
Found at i:5477311 original size:40 final size:40
Alignment explanation
Indices: 5477266--5477391 Score: 117
Period size: 40 Copynumber: 3.1 Consensus size: 40
5477256 ACTTTTTGCT
*
5477266 GCGTTTTAAAAGAAGTGCCGCTAATGCTAGATCTTTAGCG
1 GCGTTTTAAAAGAAGCGCCGCTAATGCTAGATCTTTAGCG
******
5477306 GCGTTTTATTCTTTGCGCCGCTAATGCTAGATCTTTAGCG
1 GCGTTTTAAAAGAAGCGCCGCTAATGCTAGATCTTTAGCG
****** * *
5477346 GCGTTTTATTCTTTGCGCCGCTAATGCTCGATTTTTAGCG
1 GCGTTTTAAAAGAAGCGCCGCTAATGCTAGATCTTTAGCG
5477386 GCGTTT
1 GCGTTT
5477392 GTAATCCAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (40 bp):
GCGTTTTAAAAGAAGCGCCGCTAATGCTAGATCTTTAGCG
Found at i:5479050 original size:6 final size:6
Alignment explanation
Indices: 5479039--5479066 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5479029 TTCGGTGTGA
5479039 ATGTAT ATGTAT ATGTAT ATGTAT ATGT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGT
5479067 GTCTTTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:5481835 original size:42 final size:42
Alignment explanation
Indices: 5481776--5481856 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
5481766 TGAAAAGTTA
*
5481776 GAAGAGTGAATAGACTTGAAGATGAAAAGTTACACACATTAT
1 GAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACATTAT
*
5481818 GAAGAGTGAAGAGACTTGAATATGAAAAGTTACACACAT
1 GAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
5481857 GCATGAATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Consensus pattern (42 bp):
GAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACATTAT
Found at i:5486298 original size:23 final size:23
Alignment explanation
Indices: 5486272--5486385 Score: 128
Period size: 23 Copynumber: 5.1 Consensus size: 23
5486262 AAGTTAGAAG
5486272 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
*
5486295 AGTGAAGAGACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
* *
5486318 AGTGAATAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * * * *
5486341 AGT-TACACAC---ATTATGAAG
1 AGTGAAGAGACTTGAATATGAAA
5486360 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
5486383 AGT
1 AGT
5486386 TACACACATG
Statistics
Matches: 72, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
19 9 0.12
20 4 0.06
22 4 0.06
23 55 0.76
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.24
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:5486371 original size:42 final size:42
Alignment explanation
Indices: 5486268--5486394 Score: 155
Period size: 42 Copynumber: 2.9 Consensus size: 42
5486258 TGAAAAGTTA
* * * *
5486268 GAAGAGTGAAGAGACTTGAATATGAAAAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATATGAAAAGT-TACACAC---ATTAT
* * *
5486314 GAATAGTGAATAGACTTGAAGATGAAAAGTTACACACATTAT
1 GAAGAGTGAAGAGACTTGAATATGAAAAGTTACACACATTAT
5486356 GAAGAGTGAAGAGACTTGAATATGAAAAGTTACACACAT
1 GAAGAGTGAAGAGACTTGAATATGAAAAGTTACACACAT
5486395 GCATGAATAG
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
42 40 0.56
45 4 0.06
46 27 0.38
ACGTcount: A:0.46, C:0.08, G:0.24, T:0.23
Consensus pattern (42 bp):
GAAGAGTGAAGAGACTTGAATATGAAAAGTTACACACATTAT
Found at i:5496607 original size:61 final size:61
Alignment explanation
Indices: 5496512--5496634 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
5496502 TCTTAGAGGG
5496512 TAAGTTTTCTAGTTTGAGTACAACGGTGAAGTGGTTACTTGGTCAATGATTATGACTTAAA
1 TAAGTTTTCTAGTTTGAGTACAACGGTGAAGTGGTTACTTGGTCAATGATTATGACTTAAA
5496573 TAAGTTTTCTAGTTTGAGTACAACGGTGAAGTGGTTACTTGGTCAATGATTATGACTTAAA
1 TAAGTTTTCTAGTTTGAGTACAACGGTGAAGTGGTTACTTGGTCAATGATTATGACTTAAA
5496634 T
1 T
5496635 CACAACTTGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (61 bp):
TAAGTTTTCTAGTTTGAGTACAACGGTGAAGTGGTTACTTGGTCAATGATTATGACTTAAA
Found at i:5498611 original size:14 final size:13
Alignment explanation
Indices: 5498579--5498620 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
5498569 GATTTACTCC
*
5498579 TTTTATTTATCAT
1 TTTTCTTTATCAT
5498592 TTTTCTTTATCAT
1 TTTTCTTTATCAT
5498605 GTTTTC-TTA-CAT
1 -TTTTCTTTATCAT
5498617 TTTT
1 TTTT
5498621 TTAACTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 4 0.15
12 3 0.11
13 15 0.56
14 5 0.19
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTTCTTTATCAT
Found at i:5501580 original size:28 final size:28
Alignment explanation
Indices: 5501549--5501605 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
5501539 TACAAAAACA
*
5501549 AATAAAGTAATTAAAAG-TCATACTATAT
1 AATAAAGTAA-TAAAAGATAATACTATAT
5501577 AATAAAGTAATAAAAGATAATACTATAT
1 AATAAAGTAATAAAAGATAATACTATAT
5501605 A
1 A
5501606 TACATGTACG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (28 bp):
AATAAAGTAATAAAAGATAATACTATAT
Found at i:5503346 original size:42 final size:40
Alignment explanation
Indices: 5503243--5503524 Score: 302
Period size: 42 Copynumber: 6.9 Consensus size: 40
5503233 TGGTTTTTTT
*
5503243 TGTCTGCTCCACTGA-TGCTTAGGGAGATAAGAC-TGGATG
1 TGTCTGCTCCACT-ACTGCTTAGGGAGATAAGACTTGGTTG
*
5503282 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTT
1 TG-TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGTTG
* * *
5503325 TGTCTGCTCCGCTACTACTTAGGGAGATAAGACTT-GATG
1 TGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGTTG
* *
5503364 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTT
1 TG-TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGTTG
** * *
5503407 TGTCCACTCCGCTACTGCTTAGGGAGATAAGACTT-GATG
1 TGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGTTG
* * * *
5503446 CGATCTGCTCCATTATTGCTTAGGGAGATAAGATCTGTGGTTC
1 TG-TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGTTG
*
5503489 TGTCTGCTCCACTATTGCTTAGGGAGATAAGACTTG
1 TGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTG
5503525 CAACTTTTGA
Statistics
Matches: 203, Mismatches: 27, Indels: 25
0.80 0.11 0.10
Matches are distributed among these distances:
39 9 0.04
40 85 0.42
41 11 0.05
42 86 0.42
43 12 0.06
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (40 bp):
TGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGTTG
Found at i:5503346 original size:82 final size:82
Alignment explanation
Indices: 5503240--5503524 Score: 455
Period size: 82 Copynumber: 3.5 Consensus size: 82
5503230 GATTGGTTTT
* *
5503240 TTTTGTCTGCTCCACTGA-TGCTTAGGGAGATAAGACTGGATGTGATCTGCTCCACTACTGCTTA
1 TTTTGTCTGCTCCACT-ACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTA
5503304 GGGAGATAAGATCTGTGG
65 GGGAGATAAGATCTGTGG
* *
5503322 TTTTGTCTGCTCCGCTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG
1 TTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG
5503387 GGAGATAAGATCTGTGG
66 GGAGATAAGATCTGTGG
** * * *
5503404 TTTTGTCCACTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCATTATTGCTTAG
1 TTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG
5503469 GGAGATAAGATCTGTGG
66 GGAGATAAGATCTGTGG
* *
5503486 TTCTGTCTGCTCCACTATTGCTTAGGGAGATAAGACTTG
1 TTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTG
5503525 CAACTTTTGA
Statistics
Matches: 188, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
81 1 0.01
82 187 0.99
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (82 bp):
TTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG
GGAGATAAGATCTGTGG
Found at i:5503940 original size:72 final size:72
Alignment explanation
Indices: 5503704--5507332 Score: 3756
Period size: 72 Copynumber: 48.7 Consensus size: 72
5503694 ACATGTGAAC
* * *
5503704 TGAGGCTCAACTCACTTT-TCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCT
1 TGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAAATACCT
* *
5503768 CAGCGTGTCC
63 CAACGTGTCT
5503778 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAAATACCTCA
5503843 ACGTGTCT
65 ACGTGTCT
* *
5503851 TGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
*
5503916 TGTGTCT
66 CGTGTCT
* * * * *
5503923 CGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTCTTTCAAAAACATAATAATGAAAACAGAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT-TTT-GAAAACAGAA-ATTG-----A-AA
*** * * *
5503988 ATGGATAATACCTCGGT-G
57 ATACCTCA-ACGT--GTCT
* * * * *
5504006 TGACCTGAG-GCTCAACTCACCTT-TCGCAATATGAGTTGATTTTTTGAAAAACAGAAA-TCAAA
1 TGA---G-GCTC-AA-CTCA-TTTCTCGCAATATGAGTTGA-ATTTTG-AAAACAGAAATTGAAA
** * * * *
5504068 AGGCTTAATTGAAAATACCTCGGCG
57 A----TACCT---CA-ACGT-GTCT
* * * * * *
5504093 TGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAAT
1 TGAG-GCTCA-ACTC-A-T---TTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAAT
5504158 ACCTCAACGTGTCT
59 ACCTCAACGTGTCT
*
5504172 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5504237 CGTGTCT
66 CGTGTCT
*
5504244 TGAGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTTTTTTGAAAGACAGAAATTGAAAATA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-----TTTTGAAA-ACAGAAATTGAAAATA
* *
5504309 CCTCAGCATGTGAAC-
60 CCTCA--ACGTG-TCT
* ** *
5504324 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5504389 CGTGTCT
66 CGTGTCT
5504396 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5504461 CGTGTCT
66 CGTGTCT
5504468 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5504533 CGTGTCT
66 CGTGTCT
*
5504540 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5504605 CGTGTCT
66 CGTGTCT
*
5504612 TGAGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTTTTTTGAAAGACAGAAATTGAAAATA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-----TTTTGAAA-ACAGAAATTGAAAATA
* *
5504677 CCTCAGCATGTGAAC-
60 CCTCA--ACGTG-TCT
* ** *
5504692 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5504757 CGTGTCT
66 CGTGTCT
*
5504764 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5504829 CGTGTCT
66 CGTGTCT
*
5504836 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAGAAGCAGAAATTGAAAATACCTCA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGA-AAACAGAAATTGAAAATACCTCA
5504901 ACGTGTCT
65 ACGTGTCT
5504909 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5504974 CGTGTCT
66 CGTGTCT
5504981 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5505046 CGTGTCT
66 CGTGTCT
5505053 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5505118 CGTGTCT
66 CGTGTCT
*
5505125 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5505190 CGTGTCT
66 CGTGTCT
*
5505197 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5505262 CGTGTCT
66 CGTGTCT
*
5505269 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5505334 CGTGTCT
66 CGTGTCT
*
5505341 TGAGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTTTTTTGAAAGACAGAAATTGAAAATA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-----TTTTGAAA-ACAGAAATTGAAAATA
* *
5505406 CCTCAGCATGTGAAC-
60 CCTCA--ACGTG-TCT
* ** *
5505421 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5505486 CGTGTCT
66 CGTGTCT
5505493 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5505558 CGTGTCT
66 CGTGTCT
5505565 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5505630 CGTGTCT
66 CGTGTCT
5505637 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5505702 CGTGTCT
66 CGTGTCT
5505709 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5505774 CGTGTCT
66 CGTGTCT
*
5505781 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5505846 CGTGTCT
66 CGTGTCT
*
5505853 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5505918 CGTGTCT
66 CGTGTCT
** *
5505925 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGTTTTTTTTAACAACAGAAATT-AAAATTACCT
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTG-AATTTTGAA-AACAGAAATTGAAAA-TACCT
* *
5505989 CAGCGTGTCC
63 CAACGTGTCT
** * * *
5505999 TGAGGCTCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAAACAAAAATT-AAAAGGCTTAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAAA----TAC
* *
5506062 CTC-ACCTCTCGCAAT
61 CTCAACGTGT--C--T
* * *** ** * * *** * * *** * *
5506077 ATGA-G-TCAATTTAAAACATAAACTAAAAAT-ACCTTG--GCGTG--CACCGAGGCT-CAACTC
1 -TGAGGCTCAACTCATTTC-T---CGCAATATGA-GTTGAATTTTGAAAACAGAAATTGAAAAT-
** **
5506134 ACTTCTCGCAATATGAGT
59 AC--CT--CAACGTGTCT
*** * ** **** * * ** * * ** **
5506152 TGATTTTTGAAAACAGAAATTG-AAAAT-ACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGC
1 TGA-GGCTCAACTCATTTCTCGCAATATGAGTTGAA--T-T-TTGA----AAACAGAAAT-T-G-
* ** *
5506215 AATATGAGTTGAA--T-T-T
54 AAAAT-ACCTCAACGTGTCT
** ** * * * * * ** * *
5506231 TGAAAACAGAAATTGAAATTAC-CTCAACGTGTCTTGAGGCTCAACTCATTTCTCG-CAATATG-
1 TG-AGGC-TCAACT--CATTTCTCGCAA----T-ATGA-G-TTGA---ATTT-T-GAAAACA-GA
* ** * * * **
5506293 AGTTG--AAT-TTTGAGAAGCAGAAAT
49 AATTGAAAATACCTCA-ACG-TG-TCT
*** * * * *** * ** * ** *
5506317 TGAAAAT-ACCTCAACGTGTCTTG-AGGCTCAACT-CATTTCTCGCAATATGAGTTGAATTTTGA
1 TGAGGCTCAACTC-A--TTTCTCGCAATATGAGTTGAATTT-T-G-AA-A--A-CAGAA-ATTG-
* ** * ** **
5506379 AAACAGAAATTGAAAATACCT
54 AAA-A-TACCTCAACGTGTCT
** * * * * * ** * **
5506400 CAACGTGTCTTGAGGCTCAACTCATT-TCTCGCA-AT-ATGAGTTGAATTTTGAAAACAGAAATT
1 TGA-G-G-C-TCA-ACTC-A-T--TTCTCGC-AATATGA-G-TTGAATTTTGAAAA-CAGAAATT
5506462 GAAAATACCTCAACGTGTCT
53 GAAAATACCTCAACGTGTCT
* *
5506482 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAGCAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5506547 CGTGTCT
66 CGTGTCT
5506554 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5506619 CGTGTCT
66 CGTGTCT
*
5506626 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5506691 CGTGTCT
66 CGTGTCT
5506698 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5506763 CGTGTCT
66 CGTGTCT
*
5506770 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5506835 CGTGTCT
66 CGTGTCT
*
5506842 TGAGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTTTTTTGAAAGACAGAAATTGAAAATA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-----TTTTGAAA-ACAGAAATTGAAAATA
* *
5506907 CCTCAGCATGTGAAC-
60 CCTCA--ACGTG-TCT
* ** *
5506922 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5506987 CGTGTCT
66 CGTGTCT
5506994 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5507059 CGTGTCT
66 CGTGTCT
*
5507066 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5507131 CGTGTCT
66 CGTGTCT
*
5507138 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5507203 CGTGTCT
66 CGTGTCT
*
5507210 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
5507275 CGTGTCT
66 CGTGTCT
5507282 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTTG-AAACAGAAAT
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-TTTTGAAAACAGAAAT
5507333 AAAAGCATCA
Statistics
Matches: 3070, Mismatches: 302, Indels: 368
0.82 0.08 0.10
Matches are distributed among these distances:
71 6 0.00
72 2102 0.68
73 179 0.06
74 188 0.06
75 45 0.01
76 7 0.00
77 59 0.02
78 90 0.03
79 22 0.01
80 154 0.05
81 22 0.01
82 15 0.00
83 13 0.00
84 20 0.01
85 12 0.00
86 19 0.01
87 28 0.01
88 47 0.02
89 29 0.01
90 5 0.00
91 4 0.00
92 3 0.00
93 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (72 bp):
TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAA
CGTGTCT
Found at i:5504122 original size:89 final size:86
Alignment explanation
Indices: 5503891--5504150 Score: 285
Period size: 88 Copynumber: 3.0 Consensus size: 86
5503881 TTGAATTTTG
* * ** **
5503891 AAAACAGAAATTGAAATTACCTCAATGTGT-CTCGAGGCTCAACTCATTTCTCGCAATATGAGTT
1 AAAACAGAAATGGAAAATACCTCGGTGTGTCCT-GAGGCTCAACTCACCTCTCGCAATATGAGTT
* * * *
5503955 GATTCTTTCAAAAACATAATAATG
65 GATTTTTTGAAAAACA-GA-AATC
* * *
5503979 AAAACAGAAATGGATAATACCTCGGTGTGACCTGAGGCTCAACTCACCTTTCGCAATATGAGTTG
1 AAAACAGAAATGGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
5504044 ATTTTTTGAAAAACAGAAATC
66 ATTTTTTGAAAAACAGAAATC
** *
5504065 AAAAGGC-TTAATTGAAAATACCTCGGCGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAA--CAGAAATGGAAAATACCTC-G-GTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
5504129 GTTGA-TTTTTG-AAAACAGAAAT
62 GTTGATTTTTTGAAAAACAGAAAT
5504151 TGAAAATACC
Statistics
Matches: 148, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
86 7 0.05
87 25 0.17
88 74 0.50
89 42 0.28
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (86 bp):
AAAACAGAAATGGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTTGAAAAACAGAAATC
Found at i:5509535 original size:13 final size:13
Alignment explanation
Indices: 5509517--5509583 Score: 80
Period size: 13 Copynumber: 4.8 Consensus size: 13
5509507 TGGCATTTGA
5509517 TTTTTTTTTTGTT
1 TTTTTTTTTTGTT
*
5509530 TTTTTTTCTTGTCCT
1 TTTTTTTTTTGT--T
5509545 TTTTTCTTTTTGTT
1 TTTTT-TTTTTGTT
5509559 TTTTTTTTTTGTT
1 TTTTTTTTTTGTT
5509572 TTCTTTTCTTTT
1 TT-TTTT-TTTT
5509584 TCTTTTCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
13 21 0.45
14 10 0.21
15 10 0.21
16 6 0.13
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTGTT
Found at i:5509555 original size:29 final size:28
Alignment explanation
Indices: 5509517--5509589 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
5509507 TGGCATTTGA
5509517 TTTTT-TTTTTGTTTTTTTTTCTTGTCCT
1 TTTTTCTTTTTGTTTTTTTTTCTTGT-CT
* *
5509545 TTTTTCTTTTTGTTTTTTTTTTTTGTTT
1 TTTTTCTTTTTGTTTTTTTTTCTTGTCT
*
5509573 TCTTTTCTTTTTCTTTT
1 T-TTTTCTTTTTGTTTT
5509590 CATGACTGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 7 0.17
29 33 0.82
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (28 bp):
TTTTTCTTTTTGTTTTTTTTTCTTGTCT
Found at i:5511161 original size:165 final size:165
Alignment explanation
Indices: 5510889--5511216 Score: 568
Period size: 165 Copynumber: 2.0 Consensus size: 165
5510879 GCACTGTCAT
*
5510889 CTACTAAGATTAGTACAGAGCCTCGGTCATGGCCCATCATAGGCTTACGAGATCAATTCGAGGGA
1 CTACTAAGATTAGTACAGAGCCTCAGTCATGGCCCATCATAGGCTTACGAGATCAATTCGAGGGA
5510954 TTACATTTACTTATGCCTATGCGGAGGGACAAGTTAACTCACGAAAGCATAAGTCATATGTAACC
66 TTACATTTACTTATGCCTATGCGGAGGGACAAGTTAACTCACGAAAGCATAAGTCATATGTAACC
5511019 CGAAAGTATTCACTAGCCTGTGCGGAGGAACGAAA
131 CGAAAGTATTCACTAGCCTGTGCGGAGGAACGAAA
* * * *
5511054 CTACTAAGATTAGTATATAGCCTCAGTCATTGCCCATCATAGGCTTTCGAG-TCCAATTCGAGGG
1 CTACTAAGATTAGTACAGAGCCTCAGTCATGGCCCATCATAGGCTTACGAGAT-CAATTCGAGGG
* *
5511118 ATTACATTTACTTATGCTTATGTGGAGGGACAAGTTAACTCACGAAAGCATAAGTCATATGTAAC
65 ATTACATTTACTTATGCCTATGCGGAGGGACAAGTTAACTCACGAAAGCATAAGTCATATGTAAC
*
5511183 CCGAAAGTATTCACTAGCCTGTGCGGAGGGACGA
130 CCGAAAGTATTCACTAGCCTGTGCGGAGGAACGA
5511217 GTTAACTCAC
Statistics
Matches: 154, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
164 1 0.01
165 153 0.99
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (165 bp):
CTACTAAGATTAGTACAGAGCCTCAGTCATGGCCCATCATAGGCTTACGAGATCAATTCGAGGGA
TTACATTTACTTATGCCTATGCGGAGGGACAAGTTAACTCACGAAAGCATAAGTCATATGTAACC
CGAAAGTATTCACTAGCCTGTGCGGAGGAACGAAA
Found at i:5513178 original size:23 final size:23
Alignment explanation
Indices: 5513152--5513198 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5513142 CGGACGGCCA
* *
5513152 CCGGAGCCTCGCCGGTGCTGGCG
1 CCGGAGCCTCGCCGGCGCCGGCG
*
5513175 CCGGAGGCTCGCCGGCGCCGGCG
1 CCGGAGCCTCGCCGGCGCCGGCG
5513198 C
1 C
5513199 GGTGGCCGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.04, C:0.43, G:0.45, T:0.09
Consensus pattern (23 bp):
CCGGAGCCTCGCCGGCGCCGGCG
Found at i:5529053 original size:6 final size:6
Alignment explanation
Indices: 5529042--5529072 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
5529032 TTTATTTATT
5529042 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T
5529073 AATATAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:5537672 original size:31 final size:30
Alignment explanation
Indices: 5537623--5537680 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
5537613 TTACTCAAAA
* *
5537623 AATGAGTAAATTAATCCTTGTACGTTAAATC
1 AATGAGCAAACTAATCCTTGTA-GTTAAATC
* *
5537654 AATGAGCAAACTAGTCCTTTTAGTTAA
1 AATGAGCAAACTAATCCTTGTAGTTAA
5537681 CATTTTCATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 5 0.22
31 18 0.78
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (30 bp):
AATGAGCAAACTAATCCTTGTAGTTAAATC
Found at i:5540572 original size:4 final size:4
Alignment explanation
Indices: 5540563--5540595 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
5540553 GCAAAAAATG
5540563 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
5540596 ACTTGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:5541308 original size:26 final size:26
Alignment explanation
Indices: 5541275--5541327 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
5541265 TGAAAACTCG
5541275 TATTGTTTAAAATATTTC-TAATATAT
1 TATTGTTTAAAATATTTCATAA-ATAT
5541301 TATTGTTTAAAATATTTCATAAATAT
1 TATTGTTTAAAATATTTCATAAATAT
5541327 T
1 T
5541328 TTCAAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
TATTGTTTAAAATATTTCATAAATAT
Found at i:5562468 original size:16 final size:18
Alignment explanation
Indices: 5562447--5562482 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5562437 TTTTATGTGT
5562447 TATAAAT-TAA-ATAATA
1 TATAAATATAACATAATA
5562463 TATAAATATAACATAATA
1 TATAAATATAACATAATA
5562481 TA
1 TA
5562483 AAACATTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TATAAATATAACATAATA
Found at i:5565168 original size:16 final size:16
Alignment explanation
Indices: 5565147--5565180 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5565137 AAGGTATAAT
5565147 AAAATATTAAAAAATA
1 AAAATATTAAAAAATA
5565163 AAAATATTAAAAAATA
1 AAAATATTAAAAAATA
5565179 AA
1 AA
5565181 GACATATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATATTAAAAAATA
Found at i:5576230 original size:3 final size:3
Alignment explanation
Indices: 5576222--5576260 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
5576212 AAGACAAAAA
*
5576222 ATT ATT ATT ATT ATTT GTT ATT ATT -TT ATT ATT ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
5576261 TAGATATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.88
4 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:5576250 original size:24 final size:25
Alignment explanation
Indices: 5576223--5576270 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
5576213 AGACAAAAAA
*
5576223 TTATTATTATTATTT-GTTATTATT
1 TTATTATTATTATTTAGATATTATT
5576247 TTATTATTATTATTTAGATATTAT
1 TTATTATTATTATTTAGATATTAT
5576271 ATAACTCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
TTATTATTATTATTTAGATATTATT
Found at i:5576268 original size:14 final size:14
Alignment explanation
Indices: 5576226--5576270 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
5576216 CAAAAAATTA
5576226 TTATTATTATTT-G
1 TTATTATTATTTAG
5576239 TTATTA-T-TTTA-
1 TTATTATTATTTAG
5576250 TTATTATTATTTAG
1 TTATTATTATTTAG
*
5576264 ATATTAT
1 TTATTAT
5576271 ATAACTCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
11 9 0.33
12 2 0.07
13 10 0.37
14 6 0.22
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (14 bp):
TTATTATTATTTAG
Found at i:5576335 original size:12 final size:10
Alignment explanation
Indices: 5576308--5576367 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 10
5576298 TTTAAGTATA
5576308 AATATTTTTT
1 AATATTTTTT
5576318 AATATTTTTT
1 AATATTTTTT
**
5576328 AAT-TTATTAAA
1 AATATT-TT-TT
5576339 AATATTTATTTT
1 AATA-TT-TTTT
5576351 AATATTTTTT
1 AATATTTTTT
5576361 -ATATTTT
1 AATATTTT
5576368 GAAGTATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
9 9 0.21
10 19 0.45
11 5 0.12
12 4 0.10
13 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
AATATTTTTT
Found at i:5578901 original size:16 final size:18
Alignment explanation
Indices: 5578869--5578904 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5578859 TGTAATGTTT
5578869 TATATTATGTTATATTTA
1 TATATTATGTTATATTTA
5578887 TATATTAT-TTA-ATTTA
1 TATATTATGTTATATTTA
5578903 TA
1 TA
5578905 ACACATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATATTATGTTATATTTA
Found at i:5586990 original size:19 final size:18
Alignment explanation
Indices: 5586968--5587010 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
5586958 GCTTATTCTG
5586968 TTTTTGTAATTTTATAAT-A
1 TTTTTGT-ATTTT-TAATAA
*
5586987 TTTTTCTATTTTTAATAA
1 TTTTTGTATTTTTAATAA
5587005 TTTTTG
1 TTTTTG
5587011 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 11 0.52
19 6 0.29
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTTGTATTTTTAATAA
Found at i:5590731 original size:16 final size:16
Alignment explanation
Indices: 5590710--5590742 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5590700 TTCATAAATT
5590710 TTTATTTTTAATAATA
1 TTTATTTTTAATAATA
*
5590726 TTTATTTTTTATAATA
1 TTTATTTTTAATAATA
5590742 T
1 T
5590743 GAATATTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTTTAATAATA
Found at i:5592461 original size:22 final size:22
Alignment explanation
Indices: 5592416--5592461 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5592406 CTCTTTCTAA
* *
5592416 AAAAATTATAATTTAATCTCTT
1 AAAAATTATAATTTAATATATT
5592438 AAAAATTATAAATTT-ATATATT
1 AAAAATTAT-AATTTAATATATT
5592460 AA
1 AA
5592462 TATAATGACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAATTATAATTTAATATATT
Found at i:5593736 original size:12 final size:12
Alignment explanation
Indices: 5593716--5593745 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5593706 ATTTAAAAAT
5593716 TTAAAATTTTTA
1 TTAAAATTTTTA
*
5593728 TTAATATTTTTA
1 TTAAAATTTTTA
5593740 TTAAAA
1 TTAAAA
5593746 AAATAACAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTAAAATTTTTA
Found at i:5596089 original size:23 final size:23
Alignment explanation
Indices: 5596063--5596106 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5596053 AAAAAGTATA
5596063 AAAATTATAAAAAAAATATTTTT
1 AAAATTATAAAAAAAATATTTTT
* * *
5596086 AAAATTTTTAAAAAATTATTT
1 AAAATTATAAAAAAAATATTT
5596107 AATTGCTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAATTATAAAAAAAATATTTTT
Found at i:5600916 original size:26 final size:26
Alignment explanation
Indices: 5600861--5600917 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
5600851 TTTTTTTGTT
**
5600861 AATTTGGTAATTATATTTTAAAGTTA
1 AATTTGGTAATTATATTTTAAAGAAA
*
5600887 AATTTGGTAATTATTTTTTAAA-AAA
1 AATTTGGTAATTATATTTTAAAGAAA
5600912 GAATTT
1 -AATTT
5600918 TTTAAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (26 bp):
AATTTGGTAATTATATTTTAAAGAAA
Found at i:5600919 original size:15 final size:15
Alignment explanation
Indices: 5600899--5600928 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5600889 TTTGGTAATT
5600899 ATTTTTTAAAAAAGA
1 ATTTTTTAAAAAAGA
5600914 ATTTTTTAAAAAAGA
1 ATTTTTTAAAAAAGA
5600929 GTTGAATTTT
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:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (15 bp):
ATTTTTTAAAAAAGA
Found at i:5603479 original size:5 final size:5
Alignment explanation
Indices: 5603469--5603493 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5603459 ATTTAGAGCA
5603469 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
5603494 CCTTTACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:5622023 original size:31 final size:31
Alignment explanation
Indices: 5621988--5622049 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
5621978 CATGGATTTT
*
5621988 CTATTTTTCCAATTTTCTTTTT-TTATCGAAA
1 CTATTTTTCCAATTTTATTTTTGTT-TCGAAA
* *
5622019 CTATTTTTCGATTTTTATTTTTGTTTCGAAA
1 CTATTTTTCCAATTTTATTTTTGTTTCGAAA
5622050 TACTAGGGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.21, C:0.13, G:0.06, T:0.60
Consensus pattern (31 bp):
CTATTTTTCCAATTTTATTTTTGTTTCGAAA
Found at i:5622784 original size:21 final size:20
Alignment explanation
Indices: 5622758--5622801 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
5622748 AAAAATCAAT
*
5622758 AAAAATTATTAAATTTTAATA
1 AAAAATTATAAAATTTT-ATA
5622779 AAAAATTATAAAATTTTATA
1 AAAAATTATAAAATTTTATA
5622799 AAA
1 AAA
5622802 GACCCTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATTATAAAATTTTATA
Found at i:5623345 original size:89 final size:86
Alignment explanation
Indices: 5623179--5623347 Score: 232
Period size: 89 Copynumber: 1.9 Consensus size: 86
5623169 ACTAGGGATG
* * * * *
5623179 GTTCAAGTACCCAATTGAGTGTAAAAAAAGTAAGGGCTTAATTTTTTTTTGAAAAAATTTGAGGG
1 GTTCAAATACCCAATTGAGTGTAAAAAAAGTAAGAGCTTAATTTTTTCTTGAAAAAAATTGAGAG
5623244 TCTTTTTGATGCATTTTGAAA
66 TCTTTTTGATGCATTTTGAAA
*
5623265 GTTCAAATACCCAATTGAGTGTAAAACAAAAGTAA-AGTTTAATTGCTTTTCTTGAAAAAAATTG
1 GTTCAAATACCCAATTGAGTGT-AAA-AAAAGTAAGAGCTTAATT--TTTTCTTGAAAAAAATTG
*
5623329 AGAGTCTTTTTTATGCATT
62 AGAGTCTTTTTGATGCATT
5623348 GTAAAAATTG
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
86 21 0.29
87 10 0.14
88 8 0.11
89 33 0.46
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (86 bp):
GTTCAAATACCCAATTGAGTGTAAAAAAAGTAAGAGCTTAATTTTTTCTTGAAAAAAATTGAGAG
TCTTTTTGATGCATTTTGAAA
Found at i:5624744 original size:15 final size:16
Alignment explanation
Indices: 5624724--5624756 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
5624714 AATTAATTTT
5624724 TAAATAAATTT-TTAA
1 TAAATAAATTTGTTAA
5624739 TAAATAAATTTGTTAA
1 TAAATAAATTTGTTAA
5624755 TA
1 TA
5624757 TTAAACCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TAAATAAATTTGTTAA
Found at i:5634324 original size:29 final size:31
Alignment explanation
Indices: 5634273--5634339 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 31
5634263 AGTCTAATTA
5634273 AAAATTTTAAAAATTTTATGAG-AT-TAATG
1 AAAATTTTAAAAATTTTATGAGAATCTAATG
* *
5634302 AAAATTTTCAAAATTTTGA-GAGAATCTAATT
1 AAAATTTTAAAAATTTT-ATGAGAATCTAATG
5634333 AAAATTT
1 AAAATTT
5634340 AAAGAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 19 0.58
30 3 0.09
31 11 0.33
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.40
Consensus pattern (31 bp):
AAAATTTTAAAAATTTTATGAGAATCTAATG
Found at i:5635858 original size:42 final size:40
Alignment explanation
Indices: 5635763--5635881 Score: 125
Period size: 41 Copynumber: 2.9 Consensus size: 40
5635753 GGCCCGGCCA
* * *
5635763 ATATTTGATTAAAAATAAAAAAATAAATATTT--TTAATAT
1 ATATTTGATTAAAAAT-AAAAAATATATATTTAATAAAAAT
* *
5635802 ATAATTTGAATTAAAAGTCCAAAAATATATATTTAATAAAAAGT
1 AT-ATTTG-ATTAAAAAT-AAAAAATATATATTTAATAAAAA-T
5635846 ATATTTGATTAAAAATAAAAATATATATATTTAATA
1 ATATTTGATTAAAAATAAAAA-ATATATATTTAATA
5635882 TATAATCTGG
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
39 2 0.03
40 5 0.08
41 25 0.38
42 22 0.33
43 9 0.14
44 3 0.05
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (40 bp):
ATATTTGATTAAAAATAAAAAATATATATTTAATAAAAAT
Found at i:5649608 original size:55 final size:55
Alignment explanation
Indices: 5649543--5649649 Score: 205
Period size: 55 Copynumber: 1.9 Consensus size: 55
5649533 ATATGAGAGG
5649543 TCTGTAATCATCGGACCAAATCCTTAATTCTTTCTATGATTTTCTCTATCTTAAT
1 TCTGTAATCATCGGACCAAATCCTTAATTCTTTCTATGATTTTCTCTATCTTAAT
*
5649598 TCTGTAATCATCGGACCAAATCCTTAATTTTTTCTATGATTTTCTCTATCTT
1 TCTGTAATCATCGGACCAAATCCTTAATTCTTTCTATGATTTTCTCTATCTT
5649650 TAACCTGGTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.47
Consensus pattern (55 bp):
TCTGTAATCATCGGACCAAATCCTTAATTCTTTCTATGATTTTCTCTATCTTAAT
Found at i:5654151 original size:20 final size:18
Alignment explanation
Indices: 5654116--5654161 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 18
5654106 GATTCATTCA
5654116 ATTTTTTTATTTTTTATT
1 ATTTTTTTATTTTTTATT
5654134 ATTATTTTTATTTATTTATT
1 ATT-TTTTTATTT-TTTATT
5654154 ATTTTTTT
1 ATTTTTTT
5654162 TCTCTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.12
19 14 0.54
20 9 0.35
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
ATTTTTTTATTTTTTATT
Found at i:5654154 original size:17 final size:16
Alignment explanation
Indices: 5654128--5654159 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5654118 TTTTTTATTT
5654128 TTTATTATTATTTTTA
1 TTTATTATTATTTTTA
5654144 TTTATTTATTATTTTT
1 TTTA-TTATTATTTTT
5654160 TTTCTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTATTATTTTTA
Found at i:5654162 original size:20 final size:19
Alignment explanation
Indices: 5654117--5654162 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
5654107 ATTCATTCAA
5654117 TTTTTTTATTTTTTATTAT
1 TTTTTTTATTTTTTATTAT
*
5654136 TATTTTTATTTATTTATTAT
1 TTTTTTTATTT-TTTATTAT
5654156 TTTTTTT
1 TTTTTTT
5654163 CTCTTTTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTTATTTTTTATTAT
Found at i:5654347 original size:3 final size:3
Alignment explanation
Indices: 5654341--5654377 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
5654331 TACTACGCGG
5654341 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
5654378 TCTTATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5659178 original size:23 final size:23
Alignment explanation
Indices: 5659135--5659178 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5659125 AAATAAAAAA
* *
5659135 AGAAAAAAGAAAACTGCAAACAG
1 AGAAAAAAGAAAACAGAAAACAG
5659158 AGAACAAAAGAAAA-AGAAAAC
1 AGAA-AAAAGAAAACAGAAAAC
5659179 GAATAGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.70, C:0.11, G:0.16, T:0.02
Consensus pattern (23 bp):
AGAAAAAAGAAAACAGAAAACAG
Done.