Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 153 of 279
Found at i:49919719 original size:15 final size:15
Alignment explanation
Indices: 49919699--49919736 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
49919689 CATAAAATTG
49919699 ATTATTTTTAGTATT
1 ATTATTTTTAGTATT
*
49919714 ATTATTTTTATTATT
1 ATTATTTTTAGTATT
*
49919729 ACTATTTT
1 ATTATTTT
49919737 ATTATACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (15 bp):
ATTATTTTTAGTATT
Found at i:49919789 original size:16 final size:17
Alignment explanation
Indices: 49919759--49919790 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49919749 TGTTAATAGT
49919759 TAATATTATTTTATTAC
1 TAATATTATTTTATTAC
49919776 TAATATTA-TTTATTA
1 TAATATTATTTTATTA
49919791 TATTCTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATATTATTTTATTAC
Found at i:49941840 original size:3 final size:3
Alignment explanation
Indices: 49941832--49941860 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
49941822 CTGTGAGAAC
49941832 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
49941861 AAAAAGCAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:49957886 original size:53 final size:53
Alignment explanation
Indices: 49957745--49957879 Score: 211
Period size: 53 Copynumber: 2.6 Consensus size: 53
49957735 GACGAAAAAT
* *
49957745 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
*
49957797 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
*
49957850 ATGTGATAATGTGATTCCGTATAAGACCAT
1 ATGTGATAATGTGACTCCGTATAAGACCAT
49957880 GTCTGGGATA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
51 4 0.05
52 10 0.13
53 63 0.82
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
Found at i:49957901 original size:53 final size:54
Alignment explanation
Indices: 49957745--49957910 Score: 182
Period size: 53 Copynumber: 3.1 Consensus size: 54
49957735 GACGAAAAAT
* * *
49957745 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGG--TGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGATACGGCATCGGTATG-A
* *
49957797 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTAT-A
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGATACGGCATCGGTATGA
* * *
49957850 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATACGGCTTTGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGATACGGCATCGGTATGA
49957904 TATGTGA
1 -ATGTGA
49957911 ACCGTGTAAG
Statistics
Matches: 101, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 78 0.77
54 1 0.01
55 7 0.07
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (54 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGATACGGCATCGGTATGA
Found at i:49965419 original size:53 final size:53
Alignment explanation
Indices: 49965263--49965428 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
49965253 GACGAAAAAT
* **
49965263 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
49965315 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
49965368 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
49965422 TATGTGA
1 -ATGTGA
49965429 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:49982087 original size:14 final size:14
Alignment explanation
Indices: 49982068--49982096 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
49982058 TCTATTAAAA
49982068 AGAAAAAAGGACTT
1 AGAAAAAAGGACTT
49982082 AGAAAAAAGGACTT
1 AGAAAAAAGGACTT
49982096 A
1 A
49982097 CTTAGAGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
AGAAAAAAGGACTT
Found at i:49982524 original size:2 final size:2
Alignment explanation
Indices: 49982517--49982543 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49982507 ACTTTAATAA
49982517 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
49982544 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:49994543 original size:36 final size:36
Alignment explanation
Indices: 49994503--49994595 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 36
49994493 TGGAATCAGA
* *
49994503 CGGAGGCGGAGGAGGAGATGGAGTCCCGGAATTCCT
1 CGGAGGCGGAGGAGGAGATGGAGTACCGGAACTCCT
* * * *
49994539 CGGAGGCGGTGGTGGAGATGCAGTACCGGGACTCCT
1 CGGAGGCGGAGGAGGAGATGGAGTACCGGAACTCCT
* * *
49994575 CGGTGGCGGCGGCGGAGATGG
1 CGGAGGCGGAGGAGGAGATGG
49994596 TGTTGATGAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.17, C:0.20, G:0.48, T:0.14
Consensus pattern (36 bp):
CGGAGGCGGAGGAGGAGATGGAGTACCGGAACTCCT
Found at i:49994755 original size:24 final size:24
Alignment explanation
Indices: 49994690--49994755 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 24
49994680 GGATGAAGGC
* *
49994690 GGAGGTGATGAGGTGGAAGGAGGA
1 GGAGGTGATGGGGTAGAAGGAGGA
*
49994714 GGAGGGGATGGAGTGGTAGAAGGAGGA
1 GGAGGTGAT-G-G-GGTAGAAGGAGGA
*
49994741 GGAGCTGATGGGGTA
1 GGAGGTGATGGGGTA
49994756 ACGGGTGGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
24 12 0.35
25 2 0.06
26 1 0.03
27 19 0.56
ACGTcount: A:0.27, C:0.02, G:0.58, T:0.14
Consensus pattern (24 bp):
GGAGGTGATGGGGTAGAAGGAGGA
Found at i:50011001 original size:18 final size:17
Alignment explanation
Indices: 50010969--50011002 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
50010959 CAGGCTACAC
*
50010969 AAAAAGGAAAAAAAGAA
1 AAAAAGAAAAAAAAGAA
50010986 AAAAAGAAAAAGAAAGA
1 AAAAAGAAAAA-AAAGA
50011003 TCGCTAACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAAGAA
Found at i:50016115 original size:23 final size:23
Alignment explanation
Indices: 50016042--50016115 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
50016032 CAACAAAATG
* * *
50016042 ACACCTATAACACCACCAAACCA
1 ACACCTATTACAACACCAAAACA
** * **
50016065 GTAGCTATTACAACACCATGACA
1 ACACCTATTACAACACCAAAACA
*
50016088 GCACCTATTACAACACCAAAACA
1 ACACCTATTACAACACCAAAACA
50016111 ACACC
1 ACACC
50016116 CATAACAGCA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.45, C:0.36, G:0.05, T:0.14
Consensus pattern (23 bp):
ACACCTATTACAACACCAAAACA
Found at i:50017276 original size:61 final size:61
Alignment explanation
Indices: 50017181--50017296 Score: 196
Period size: 61 Copynumber: 1.9 Consensus size: 61
50017171 GCCAAATGAC
* *
50017181 AAGAAGCATCAATAGATATACAAAGAGTGACTGATACTTGAAAAATAACTACACATGGTAT
1 AAGAAGCATCAATACATATACAAAGAGTGACTGATACCTGAAAAATAACTACACATGGTAT
* *
50017242 AAGAAGCATCAATACATATACAAAGAGTGACTGATACCTGACAAATAATTACACA
1 AAGAAGCATCAATACATATACAAAGAGTGACTGATACCTGAAAAATAACTACACA
50017297 CTGATTTTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.22
Consensus pattern (61 bp):
AAGAAGCATCAATACATATACAAAGAGTGACTGATACCTGAAAAATAACTACACATGGTAT
Found at i:50019472 original size:33 final size:32
Alignment explanation
Indices: 50019435--50019512 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
50019425 TGGCCCTGCC
* *
50019435 ATGGTCTTACACTCGT-AGTGCCATAACCCAGTT
1 ATGGTCTTACA-TCATGA-TGCCATAACCCAGCT
*
50019468 ATGGTCTTATCATCATGATGCCATAGCCCAGCT
1 ATGGTCTTA-CATCATGATGCCATAACCCAGCT
50019501 ATGGTCTTACAT
1 ATGGTCTTACAT
50019513 GAATATTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
32 3 0.08
33 34 0.85
34 3 0.08
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (32 bp):
ATGGTCTTACATCATGATGCCATAACCCAGCT
Found at i:50019560 original size:103 final size:97
Alignment explanation
Indices: 50019384--50019647 Score: 249
Period size: 103 Copynumber: 2.6 Consensus size: 97
50019374 ATCGTTTACT
* * * * **
50019384 TGATGCCATAGTCCAACTATAGTCTTACACGAATATTGCCATGGCCCTGCCATGGTCTTACACTC
1 TGATGCCATAGCCCAGCTATGGTCTTACATGAATATTGCCATGGCCCAACCATGGTCTTACACTC
** *
50019449 GTAGTGCCATAACCCAGTTATGGTCTTATCATC
66 ACAATGCCATAACCCAGTTATGGTCTTATCA-C
*
50019482 ATGATGCCATAGCCCAGCTATGGTCTTACATGAATATTTATTGCCATGGTCCAACCATGGTCTTA
1 -TGATGCCATAGCCCAGCTATGGTCTTACATG-A-A--TATTGCCATGGCCCAACCATGGTCTTA
** * *
50019547 CGTTCACAATGCCATAACTCAGTTATGGTCTTTTCAC
61 CACTCACAATGCCATAACCCAGTTATGGTCTTATCAC
* * * * * * *
50019584 TGAAATGCCATAACCCAGGTATGGTCTTACATTTAAACATTGCCATGGTCTAAACATGGTCTTA
1 TG--ATGCCATAGCCCAGCTATGGTCTTACA--TGAATATTGCCATGGCCCAACCATGGTCTTA
50019648 TCCGTCAATT
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
99 27 0.20
100 1 0.01
101 27 0.20
102 1 0.01
103 79 0.58
104 1 0.01
105 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (97 bp):
TGATGCCATAGCCCAGCTATGGTCTTACATGAATATTGCCATGGCCCAACCATGGTCTTACACTC
ACAATGCCATAACCCAGTTATGGTCTTATCAC
Found at i:50019575 original size:33 final size:33
Alignment explanation
Indices: 50019538--50019613 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
50019528 TGGTCCAACC
* *
50019538 ATGGTCTTACGTTCAC-AATGCCATAACTCAGTT
1 ATGGTCTTAC-TTCACAAATGCCATAACCCAGGT
50019571 ATGGTCTT--TTCACTGAAATGCCATAACCCAGGT
1 ATGGTCTTACTTCAC--AAATGCCATAACCCAGGT
50019604 ATGGTCTTAC
1 ATGGTCTTAC
50019614 ATTTAAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
30 5 0.14
33 31 0.86
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (33 bp):
ATGGTCTTACTTCACAAATGCCATAACCCAGGT
Found at i:50031053 original size:22 final size:22
Alignment explanation
Indices: 50031023--50031091 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 22
50031013 CTCTTCATAA
50031023 TTTTAATA-TTTAATATTTAATT
1 TTTTAATATTTTAA-ATTTAATT
*
50031045 TTTTTATATTTTAAATTTAACTT
1 TTTTAATATTTTAAATTTAA-TT
50031068 TAGCTATTAATATTTTAAAATTTA
1 T---T-TTAATATTTT-AAATTTA
50031092 TTAATGTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 13 0.34
23 8 0.21
26 1 0.03
27 9 0.24
28 7 0.18
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (22 bp):
TTTTAATATTTTAAATTTAATT
Found at i:50043239 original size:78 final size:78
Alignment explanation
Indices: 50043110--50044045 Score: 1872
Period size: 78 Copynumber: 12.0 Consensus size: 78
50043100 TCCTCCTTCC
50043110 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
1 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
50043175 GCATTAGTAAGGA
66 GCATTAGTAAGGA
50043188 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
1 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
50043253 GCATTAGTAAGGA
66 GCATTAGTAAGGA
50043266 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
1 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
50043331 GCATTAGTAAGGA
66 GCATTAGTAAGGA
50043344 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
1 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
50043409 GCATTAGTAAGGA
66 GCATTAGTAAGGA
50043422 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
1 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
50043487 GCATTAGTAAGGA
66 GCATTAGTAAGGA
50043500 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
1 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
50043565 GCATTAGTAAGGA
66 GCATTAGTAAGGA
50043578 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
1 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
50043643 GCATTAGTAAGGA
66 GCATTAGTAAGGA
50043656 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
1 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
50043721 GCATTAGTAAGGA
66 GCATTAGTAAGGA
50043734 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
1 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
50043799 GCATTAGTAAGGA
66 GCATTAGTAAGGA
50043812 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
1 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
50043877 GCATTAGTAAGGA
66 GCATTAGTAAGGA
50043890 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
1 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
50043955 GCATTAGTAAGGA
66 GCATTAGTAAGGA
50043968 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
1 CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
50044033 GCATTAGTAAGGA
66 GCATTAGTAAGGA
50044046 TTAGTAAATA
Statistics
Matches: 858, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 858 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (78 bp):
CATCTCTCTCTAGCCACGGCTAAACCCTAACGAAATGTTCTCGTTTCAATGGCTTATATTTTATG
GCATTAGTAAGGA
Found at i:50049272 original size:58 final size:58
Alignment explanation
Indices: 50049182--50049291 Score: 202
Period size: 58 Copynumber: 1.9 Consensus size: 58
50049172 TTCTATGTTG
50049182 TTTTCTCGACATCTAGCCATAGCTTTAAAACTAGGCTTCGAAATGTTTTTTTTTTTTT
1 TTTTCTCGACATCTAGCCATAGCTTTAAAACTAGGCTTCGAAATGTTTTTTTTTTTTT
**
50049240 TTTTCTCGACATCTAGCTGTAGCTTTAAAACTAGGCTTCGAAATGTTTTTTT
1 TTTTCTCGACATCTAGCCATAGCTTTAAAACTAGGCTTCGAAATGTTTTTTT
50049292 GAAAATTTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (58 bp):
TTTTCTCGACATCTAGCCATAGCTTTAAAACTAGGCTTCGAAATGTTTTTTTTTTTTT
Found at i:50055057 original size:173 final size:173
Alignment explanation
Indices: 50054845--50055190 Score: 611
Period size: 173 Copynumber: 2.0 Consensus size: 173
50054835 TACCGATTTT
*
50054845 GGGCGTTACGAAGGTGCTAATCCTTCCTCCTACGTAATTGATTCCCGAACATGTTTTCTTAACAT
1 GGGCGTTACGAAGGTGCTAATCCTTCATCCTACGTAATTGATTCCCGAACATGTTTTCTTAACAT
* *
50054910 TCGTAGACCAAAATGCTTTATAAGGTGACCCAATTACACCTCAAAAAGAATTGGTGGCGACTCCA
66 TCGTAGACCAAAATGCTTTATAAGGTGACCCAATTACACATCAAAAAAAATTGGTGGCGACTCCA
50054975 TCCATGTTTTTAAAGTCGATCCACGTTTTAAAATTAAAAATGG
131 TCCATGTTTTTAAAGTCGATCCACGTTTTAAAATTAAAAATGG
* * * *
50055018 GGGCGTTACGAGGGTGCTAATCCTTCATCGTATGTAATTGATTCCCGAACCTGTTTTCTTAACAT
1 GGGCGTTACGAAGGTGCTAATCCTTCATCCTACGTAATTGATTCCCGAACATGTTTTCTTAACAT
* *
50055083 TCGTAGACCAAAATGCTTTATAAGGTGACCCAATTGCACATCAAAAAAAATTGGTGGCGACTTCA
66 TCGTAGACCAAAATGCTTTATAAGGTGACCCAATTACACATCAAAAAAAATTGGTGGCGACTCCA
50055148 TCCATGTTTTTAAAGTCGATCCACGTTTTAAAATTAAAAATGG
131 TCCATGTTTTTAAAGTCGATCCACGTTTTAAAATTAAAAATGG
50055191 TTTCGACAGC
Statistics
Matches: 164, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
173 164 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (173 bp):
GGGCGTTACGAAGGTGCTAATCCTTCATCCTACGTAATTGATTCCCGAACATGTTTTCTTAACAT
TCGTAGACCAAAATGCTTTATAAGGTGACCCAATTACACATCAAAAAAAATTGGTGGCGACTCCA
TCCATGTTTTTAAAGTCGATCCACGTTTTAAAATTAAAAATGG
Found at i:50058248 original size:21 final size:21
Alignment explanation
Indices: 50058218--50058262 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
50058208 GAATGATCAA
*
50058218 ATGCTAGAGTCCCAGAAAAAC
1 ATGCTAGAGTCACAGAAAAAC
* *
50058239 ATGCTGGAGTCACAGAACAAC
1 ATGCTAGAGTCACAGAAAAAC
50058260 ATG
1 ATG
50058263 ATGAGCCAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (21 bp):
ATGCTAGAGTCACAGAAAAAC
Found at i:50066075 original size:45 final size:45
Alignment explanation
Indices: 50066024--50066509 Score: 174
Period size: 45 Copynumber: 10.8 Consensus size: 45
50066014 TATCATCAGC
* *
50066024 CTTATCTTCACTGAGCAGGAGTGGAGCAGGTTAAACATACTCGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATTAAATATACTCGAT
* * * * * ****
50066069 CTTATCTTCATTGAGCAGGAGTGAAGCAGATCAAGTTTTGGAGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATTAAATATACTCG-AT
* * ** * *
50066115 CTTATCTCCAC-GTACCAGCGA-TGGAGCAGATTCCA-AT-CATCAAC
1 CTTATCTTCACTG-AGCAG-GAGTGGAGCAGATTAAATATAC-TCGAT
**
50066159 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATAC-CAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATTAAATATACTC-GAT
* * * ** * ****
50066204 CTTATCTTCATTGAGCAAGAGTGAAGCAGATCGAATTTTGGAGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATTAAATATACTCG-AT
* * * * ** * *
50066250 CTTGTCTCCAC-GTACCGACGA-TGGAGCAGATTCCA-AT-CATCAAC
1 CTTATCTTCACTG-AGC-AGGAGTGGAGCAGATTAAATATAC-TCGAT
**
50066294 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATAC-CAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATTAAATATACTC-GAT
* * * ** * ****
50066339 CTTATCTTCATTGAGCAGGAGTGAAGTAGATCGAATTTTGGAGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATTAAATATACTCG-AT
* * ** * *
50066385 CTTATCTCCAC-GTACCAGCGA-TGGAGCAGATTCCA-AT-CATCAAC
1 CTTATCTTCACTG-AGCAG-GAGTGGAGCAGATTAAATATAC-TCGAT
* **
50066429 CTTATCTTCACTGAGCAGGAGTGGAGTAGGCTAAATATAC-CAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATTAAATATACTC-GAT
* * * *
50066474 CTTATCTTCATTGAGCAAGAGTGAAGCAGATCAAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGATTAAAT
50066510 TTTGGAGAAT
Statistics
Matches: 302, Mismatches: 110, Indels: 58
0.64 0.23 0.12
Matches are distributed among these distances:
43 7 0.02
44 74 0.25
45 141 0.47
46 73 0.24
47 7 0.02
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (45 bp):
CTTATCTTCACTGAGCAGGAGTGGAGCAGATTAAATATACTCGAT
Found at i:50066258 original size:135 final size:135
Alignment explanation
Indices: 50066015--50066664 Score: 1011
Period size: 135 Copynumber: 4.8 Consensus size: 135
50066005 AAAGACAGAT
* * *
50066015 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGTTAAACATACTC-GATCTTATCTTCA
1 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATAC-CAGATCTTATCTTCA
*
50066079 TTGAGCAGGAGTGAAGCAGATC-AAGTTTTGGAGAATCTTATCTCCACGTACCAGCGATGGAGCA
65 TTGAGCAAGAGTGAAGCAGATCGAA-TTTTGGAGAATCTTATCTCCACGTACCAGCGATGGAGCA
50066143 GATTCCA
129 GATTCCA
50066150 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
1 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
*
50066215 TGAGCAAGAGTGAAGCAGATCGAATTTTGGAGAATCTTGTCTCCACGTACC-GACGATGGAGCAG
66 TGAGCAAGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCAG-CGATGGAGCAG
50066279 ATTCCA
130 ATTCCA
50066285 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
1 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
* *
50066350 TGAGCAGGAGTGAAGTAGATCGAATTTTGGAGAATCTTATCTCCACGTACCAGCGATGGAGCAGA
66 TGAGCAAGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCAGCGATGGAGCAGA
50066415 TTCCA
131 TTCCA
*
50066420 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGTAGGCTAAATATACCAGATCTTATCTTCAT
1 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
* * ** *
50066485 TGAGCAAGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCGATTAAACAGA
66 TGAGCAAGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCAGCGATGGAGCAGA
50066550 TTCCA
131 TTCCA
* * * * **
50066555 ATCATCAGCTTTATCTTCACTGAGTAGGAGTGGAGCAGGCTAAATATACCAGGTCTTATCTTCGC
1 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
* * * * * *
50066620 TGAGCAGGAG-CAGAGCAGACCAAATTTCGGTGAATCTTATCTCCA
66 TGAGCAAGAGTGA-AGCAGATCGAATTTTGGAGAATCTTATCTCCA
50066665 TGGATTGAAA
Statistics
Matches: 482, Mismatches: 28, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
134 3 0.01
135 476 0.99
136 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (135 bp):
ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
TGAGCAAGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCAGCGATGGAGCAGA
TTCCA
Found at i:50069370 original size:47 final size:49
Alignment explanation
Indices: 50069252--50069616 Score: 382
Period size: 46 Copynumber: 7.8 Consensus size: 49
50069242 TGTAACCCGC
* * * *
50069252 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGG--G-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
50069298 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
50069348 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
50069391 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
50069441 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
50069484 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
50069534 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
50069577 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
50069617 TCAACCATCC
Statistics
Matches: 267, Mismatches: 22, Indels: 57
0.77 0.06 0.16
Matches are distributed among these distances:
42 6 0.02
43 12 0.04
44 6 0.02
45 6 0.02
46 120 0.45
47 87 0.33
48 7 0.03
49 6 0.02
50 11 0.04
51 6 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:50069388 original size:93 final size:93
Alignment explanation
Indices: 50069259--50069616 Score: 680
Period size: 93 Copynumber: 3.8 Consensus size: 93
50069249 CGCCCATAAG
* * * *
50069259 CGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
50069324 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
50069352 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
50069417 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
50069445 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
50069510 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
50069538 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
50069603 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
50069617 TCAACCATCC
Statistics
Matches: 261, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 261 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:50069632 original size:46 final size:45
Alignment explanation
Indices: 50069303--50069625 Score: 256
Period size: 47 Copynumber: 7.0 Consensus size: 45
50069293 CGCATCCATA
50069303 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCTC
* * * *
50069351 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--TA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTC
50069396 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCTC
* * * *
50069444 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--TA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTC
50069489 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCTC
* * * *
50069537 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--TA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTC
50069582 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCATC
50069626 CTAGTGACAT
Statistics
Matches: 222, Mismatches: 24, Indels: 60
0.73 0.08 0.20
Matches are distributed among these distances:
43 2 0.01
44 16 0.07
45 6 0.03
46 88 0.40
47 90 0.41
48 5 0.02
49 12 0.05
50 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTC
Found at i:50071351 original size:68 final size:67
Alignment explanation
Indices: 50071279--50071428 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
50071269 CATCATGTGT
* * * *
50071279 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
50071341 ATGTAG
62 ATGTAG
** * *
50071347 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
50071412 AG
66 AG
50071414 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
50071429 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:50071384 original size:64 final size:64
Alignment explanation
Indices: 50071303--50071486 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
50071293 AGACATTATG
* *
50071303 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
50071367 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
50071432 AA
63 AA
* * * *
50071434 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
50071487 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:50074833 original size:17 final size:17
Alignment explanation
Indices: 50074811--50074854 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
50074801 GTTATATTAT
50074811 TATTTTTTACTAATAAG
1 TATTTTTTACTAATAAG
* *
50074828 TATTTTTATACTATTTAG
1 TATTTTT-TACTAATAAG
*
50074846 TTTTTTTTA
1 TATTTTTTA
50074855 GGCTCATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (17 bp):
TATTTTTTACTAATAAG
Found at i:50075210 original size:63 final size:63
Alignment explanation
Indices: 50075111--50075235 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 63
50075101 CCGGAGTCAA
50075111 GCAGGAGACATTACAAAACTTATCTTAGCACTTAAACAGTTTTCGTAGTAAACTATCCATCTG
1 GCAGGAGACATTACAAAACTTATCTTAGCACTTAAACAGTTTTCGTAGTAAACTATCCATCTG
*
50075174 GCAGGAGACATTACAAAACTTATCTTAGCACTTAAACAGTTTTCGTAGTAAATTATCCATCT
1 GCAGGAGACATTACAAAACTTATCTTAGCACTTAAACAGTTTTCGTAGTAAACTATCCATCT
50075236 ACGTCACGGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (63 bp):
GCAGGAGACATTACAAAACTTATCTTAGCACTTAAACAGTTTTCGTAGTAAACTATCCATCTG
Found at i:50077231 original size:79 final size:81
Alignment explanation
Indices: 50077063--50077247 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
50077053 GCTACTCGTT
* *
50077063 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* *
50077127 GATTTAGTAACTCGCAC
65 GATATAGTAACTAGCAC
* * **
50077144 CAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* **
50077206 GATATGGTCATTTAGCA-
65 GATATAGT-AACTAGCAC
50077223 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
50077248 CATCATTCGA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 56 0.64
80 26 0.30
81 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTAGCAC
Found at i:50077247 original size:40 final size:40
Alignment explanation
Indices: 50077044--50077247 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
50077034 CGGAATTTAA
** *
50077044 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
50077084 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
50077124 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
50077163 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* ** *
50077203 CCGGATATGGTCATTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGT-AACTCGCACAAATGCCTTCGGGACTTAGC
50077243 CCGGA
1 CCGGA
50077248 CATCATTCGA
Statistics
Matches: 140, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 92 0.66
41 14 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:50093275 original size:19 final size:18
Alignment explanation
Indices: 50093253--50093295 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
50093243 AATTACAAAA
*
50093253 AAAAATCAAAATAATTTTT
1 AAAAATCAAAAT-ATTTAT
* *
50093272 AAAATTCAACATATTTAT
1 AAAAATCAAAATATTTAT
50093290 AAAAAT
1 AAAAAT
50093296 TTTAAACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATCAAAATATTTAT
Found at i:50094669 original size:23 final size:23
Alignment explanation
Indices: 50094587--50094673 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
50094577 CCTGATCAGT
*
50094587 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
50094609 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
50094629 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
50094652 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
50094674 TCAGTAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:50110676 original size:18 final size:18
Alignment explanation
Indices: 50110653--50110687 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
50110643 TAAATTACTT
50110653 TGATAATAAATTCTAATC
1 TGATAATAAATTCTAATC
50110671 TGATAATAAATTCTAAT
1 TGATAATAAATTCTAAT
50110688 TAATTAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (18 bp):
TGATAATAAATTCTAATC
Found at i:50110695 original size:18 final size:18
Alignment explanation
Indices: 50110655--50110691 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
50110645 AATTACTTTG
*
50110655 ATAATAAATTCTAATCTG
1 ATAATAAATTCTAATCTA
50110673 ATAATAAATTCTAAT-TA
1 ATAATAAATTCTAATCTA
50110690 AT
1 AT
50110692 TAATTGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (18 bp):
ATAATAAATTCTAATCTA
Found at i:50114628 original size:17 final size:17
Alignment explanation
Indices: 50114596--50114629 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
50114586 TCTTCTTCTC
* *
50114596 CCTTTAATTTTGGGATT
1 CCTTTAATTATAGGATT
50114613 CCTTTAATTATAGGATT
1 CCTTTAATTATAGGATT
50114630 TTATGCAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (17 bp):
CCTTTAATTATAGGATT
Found at i:50115352 original size:11 final size:11
Alignment explanation
Indices: 50115336--50115360 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
50115326 TCTTTTTTAA
50115336 AAAAAAAAAAG
1 AAAAAAAAAAG
50115347 AAAAAAAAAAG
1 AAAAAAAAAAG
50115358 AAA
1 AAA
50115361 GAGAGAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:50116921 original size:18 final size:19
Alignment explanation
Indices: 50116898--50116936 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
50116888 TACAAATACA
*
50116898 AACATT-ACATAATTATTT
1 AACATTCACATAATGATTT
*
50116916 AACATTCACATCATGATTT
1 AACATTCACATAATGATTT
50116935 AA
1 AA
50116937 TCATATCGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (19 bp):
AACATTCACATAATGATTT
Found at i:50117627 original size:22 final size:22
Alignment explanation
Indices: 50117602--50117654 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
50117592 GAGAGTACGG
* *
50117602 ATGTGCTAAACAGATAGCAC-A
1 ATGTGCTAAACAAAGAGCACTA
50117623 TATGTGCTAAACAAAGAGCACTA
1 -ATGTGCTAAACAAAGAGCACTA
50117646 ATGTGCTAA
1 ATGTGCTAA
50117655 TAATCAGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.23
Consensus pattern (22 bp):
ATGTGCTAAACAAAGAGCACTA
Found at i:50132484 original size:21 final size:21
Alignment explanation
Indices: 50132458--50132498 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
50132448 TTTCTCTTTC
50132458 AAATTTTATTTTTTTAATTAT
1 AAATTTTATTTTTTTAATTAT
50132479 AAATTTTATTTTTTTAATTA
1 AAATTTTATTTTTTTAATTA
50132499 CAAGAGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
AAATTTTATTTTTTTAATTAT
Found at i:50133664 original size:15 final size:15
Alignment explanation
Indices: 50133644--50133700 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
50133634 CGATGAATTT
50133644 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
50133659 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
50133674 ATTGAATTTATATTG
1 ATTGAATTTATATTG
50133689 ATTGAA-TTATAT
1 ATTGAATTTATAT
50133701 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:50134102 original size:23 final size:23
Alignment explanation
Indices: 50134072--50134139 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
50134062 GGCTTTATCG
50134072 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
* ** *
50134095 ATCAGGCACCTCGTGTGTTGT-T
1 ATCAGGCACTTTATGTGTCGTAT
*
50134117 -TTAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
50134139 A
1 A
50134140 CTGATCAGAT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
21 15 0.44
22 2 0.06
23 17 0.50
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:50137429 original size:16 final size:16
Alignment explanation
Indices: 50137408--50137440 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
50137398 CATGTGGTAA
*
50137408 AAAAATTATAAAAAAT
1 AAAAATTAGAAAAAAT
50137424 AAAAATTAGAAAAAAT
1 AAAAATTAGAAAAAAT
50137440 A
1 A
50137441 TTTAAATTTT
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:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAAATTAGAAAAAAT
Found at i:50137482 original size:11 final size:10
Alignment explanation
Indices: 50137464--50137510 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 10
50137454 AAAAATTAGG
50137464 AAAAAAATAT
1 AAAAAAATAT
50137474 AAAAGAAATAT
1 AAAA-AAATAT
* *
50137485 AAAAAATTGT
1 AAAAAAATAT
50137495 AAAAAATATAT
1 AAAAAA-ATAT
50137506 AAAAA
1 AAAAA
50137511 GACATCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 14 0.45
11 17 0.55
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (10 bp):
AAAAAAATAT
Found at i:50137490 original size:21 final size:21
Alignment explanation
Indices: 50137464--50137510 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
50137454 AAAAATTAGG
50137464 AAAAAAATATAAAAGAA-ATAT
1 AAAAAAATATAAAA-AATATAT
* *
50137485 AAAAAATTGTAAAAAATATAT
1 AAAAAAATATAAAAAATATAT
50137506 AAAAA
1 AAAAA
50137511 GACATCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAAATATAAAAAATATAT
Found at i:50137874 original size:26 final size:26
Alignment explanation
Indices: 50137836--50137885 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
50137826 TTTTATTAGA
50137836 ATTTAATAATTTTTACAATTTTTATT
1 ATTTAATAATTTTTACAATTTTTATT
* * * *
50137862 ATTTATTATTTTTTATATTTTTTA
1 ATTTAATAATTTTTACAATTTTTA
50137886 CCACATGTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (26 bp):
ATTTAATAATTTTTACAATTTTTATT
Found at i:50138920 original size:16 final size:17
Alignment explanation
Indices: 50138897--50138932 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
50138887 GGAAACGAGA
*
50138897 ATTTTTAAATATTTAAT
1 ATTTTAAAATATTTAAT
50138914 ATTTTAAAAATATTTAAT
1 ATTTT-AAAATATTTAAT
50138932 A
1 A
50138933 ATTATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTAAAATATTTAAT
Found at i:50139181 original size:14 final size:13
Alignment explanation
Indices: 50139136--50139179 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 13
50139126 TTATATTAAT
50139136 AATATTAAAAATA
1 AATATTAAAAATA
50139149 AA-A-TAAAAATA
1 AATATTAAAAATA
*
50139160 ATATTTTAAAAATA
1 A-ATATTAAAAATA
50139174 AATATT
1 AATATT
50139180 TATTTTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 9 0.35
12 2 0.08
13 6 0.23
14 9 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AATATTAAAAATA
Found at i:50148482 original size:15 final size:15
Alignment explanation
Indices: 50148450--50148491 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
50148440 TTTTCCATAT
* *
50148450 TTAATTTCTCAACAC
1 TTAATTTTTCAGCAC
*
50148465 TTATTTTTTCAGCAC
1 TTAATTTTTCAGCAC
50148480 TTAATTTTTCAG
1 TTAATTTTTCAG
50148492 TTTATCAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.50
Consensus pattern (15 bp):
TTAATTTTTCAGCAC
Found at i:50150853 original size:18 final size:18
Alignment explanation
Indices: 50150830--50150867 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
50150820 TATCTGAAAC
50150830 TTAATTTTGAATATGATA
1 TTAATTTTGAATATGATA
50150848 TTAATTTTGAATATGATA
1 TTAATTTTGAATATGATA
50150866 TT
1 TT
50150868 CCTATTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
TTAATTTTGAATATGATA
Found at i:50167873 original size:14 final size:12
Alignment explanation
Indices: 50167845--50167905 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 12
50167835 AATATACATA
50167845 AATTTTATATTT
1 AATTTTATATTT
50167857 AATTTATATATTTT
1 AATTT-TATA-TTT
*
50167871 AATTTCTA-ATAT
1 AATTT-TATATTT
*
50167883 AATTTTATCTTT
1 AATTTTATATTT
50167895 ATAGTTTTATA
1 A-A-TTTTATA
50167906 ATGTTATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
11 2 0.05
12 15 0.38
13 6 0.15
14 16 0.41
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (12 bp):
AATTTTATATTT
Found at i:50167875 original size:26 final size:26
Alignment explanation
Indices: 50167845--50167905 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
50167835 AATATACATA
*
50167845 AATTTTATATTTAATTTATATATTT-T
1 AATTTTATATATAATTT-TATATTTAT
*
50167871 AATTTCTA-ATATAATTTTATCTTTAT
1 AATTT-TATATATAATTTTATATTTAT
*
50167897 AGTTTTATA
1 AATTTTATA
50167906 ATGTTATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 8 0.28
26 19 0.66
27 2 0.07
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (26 bp):
AATTTTATATATAATTTTATATTTAT
Found at i:50174673 original size:39 final size:40
Alignment explanation
Indices: 50174630--50174738 Score: 107
Period size: 38 Copynumber: 2.8 Consensus size: 40
50174620 GATAGTTTGT
*
50174630 AGTAATAGTTGACACCCAGTGTCTCATCG-GCCTAGCCGA
1 AGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGCCGA
** ** * *
50174669 AGTAA-AGTTGGTACCCAGTACCTCATCGAATCTATCCGA
1 AGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGCCGA
*
50174708 AGAAATA-TAGTGACACCCAGTGTCTCATCGA
1 AGTAATAGT--TGACACCCAGTGTCTCATCGA
50174739 CTCGAGGTCG
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
38 19 0.35
39 17 0.31
40 1 0.02
41 17 0.31
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (40 bp):
AGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGCCGA
Found at i:50176209 original size:39 final size:39
Alignment explanation
Indices: 50176139--50176276 Score: 120
Period size: 39 Copynumber: 3.5 Consensus size: 39
50176129 CACACCAATA
* *
50176139 TGACACCCAGTGCCTCATC-GTATAGTTCGAAGTAATAGT
1 TGACACCCAGTGCCTCATCGGTCTAG-CCGAAGTAATAGT
* *
50176178 TGACACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGT
1 TGACACCCAGTGCCTCATCGGTCTAGCCGAAGTAATAGT
** * * * *
50176216 TGGTACCCAGTACCTCATCGAATCTATCCGAAGAAATA-T
1 TGACACCCAGTGCCTCATCG-GTCTAGCCGAAGTAATAGT
*
50176255 AGTGACACCCAGTGTCTCATCG
1 --TGACACCCAGTGCCTCATCG
50176277 ACTCGAGGTC
Statistics
Matches: 78, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
38 19 0.24
39 38 0.49
40 5 0.06
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (39 bp):
TGACACCCAGTGCCTCATCGGTCTAGCCGAAGTAATAGT
Found at i:50177855 original size:5 final size:5
Alignment explanation
Indices: 50177845--50177907 Score: 126
Period size: 5 Copynumber: 12.6 Consensus size: 5
50177835 TTTATATATA
50177845 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
50177895 ATAAT ATAAT ATA
1 ATAAT ATAAT ATA
50177908 CTTAATTATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 58 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:50184077 original size:38 final size:39
Alignment explanation
Indices: 50183993--50184086 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
50183983 ACCAATATGG
*
50183993 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
50184032 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* *
50184070 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
50184087 AATCTATCCG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
38 19 0.40
39 25 0.53
40 3 0.06
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:50189843 original size:20 final size:21
Alignment explanation
Indices: 50189805--50189844 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
50189795 CATTTAATTA
*
50189805 ATTTTTTAAAATTTTAAAAAT
1 ATTTTTTAAAATTTAAAAAAT
50189826 ATTTTTTAAAA-TTAAAAAA
1 ATTTTTTAAAATTTAAAAAA
50189845 CATTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTTTTAAAATTTAAAAAAT
Found at i:50203167 original size:21 final size:22
Alignment explanation
Indices: 50203128--50203174 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
50203118 TAGTAAGAAT
*
50203128 AAAAATGTTTTCTAAAATT-TA
1 AAAAATGTTTGCTAAAATTGTA
* *
50203149 AAAAATGTTTGGTATAATTGTA
1 AAAAATGTTTGCTAAAATTGTA
50203171 AAAA
1 AAAA
50203175 TAATAATGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (22 bp):
AAAAATGTTTGCTAAAATTGTA
Found at i:50206357 original size:21 final size:23
Alignment explanation
Indices: 50206306--50206357 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
50206296 GGGGGCCAAA
50206306 ATTAAATTATAACTTTTATAATAG
1 ATTAAA-TATAACTTTTATAATAG
*
50206330 -TAAAAATATAA-TTTT-TAATAG
1 AT-TAAATATAACTTTTATAATAG
50206351 ATTAAAT
1 ATTAAAT
50206358 CAAAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
21 10 0.42
22 5 0.21
23 6 0.25
24 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
ATTAAATATAACTTTTATAATAG
Found at i:50229248 original size:14 final size:14
Alignment explanation
Indices: 50229229--50229265 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
50229219 TTTTTTAATA
50229229 TTATATTAATTTTT
1 TTATATTAATTTTT
*
50229243 TTATATAAATTTTT
1 TTATATTAATTTTT
50229257 TTAATATTA
1 TT-ATATTA
50229266 GCAAAATCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATATTAATTTTT
Found at i:50229690 original size:23 final size:22
Alignment explanation
Indices: 50229664--50229707 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
50229654 CACTCGAAAT
50229664 CATTATA-AACTTAATTTTATATC
1 CATTATATAA-TT-ATTTTATATC
*
50229687 CATTTTATAATTATTTTATAT
1 CATTATATAATTATTTTATAT
50229708 ATTAGAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 8 0.42
24 2 0.11
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (22 bp):
CATTATATAATTATTTTATATC
Found at i:50230376 original size:20 final size:20
Alignment explanation
Indices: 50230353--50230390 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
50230343 TAAATTTTCA
50230353 ATTTAATTATT-AAATTTAGT
1 ATTT-ATTATTAAAATTTAGT
*
50230373 ATTTTTTATTAAAATTTA
1 ATTTATTATTAAAATTTA
50230391 TCAACTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTTATTATTAAAATTTAGT
Found at i:50235811 original size:42 final size:42
Alignment explanation
Indices: 50235748--50235830 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
50235738 GCCTGAACCG
*
50235748 TGAAGGGTGGGTAAAAGCTAAGAAGCTCCTAAAATGGCCAAA
1 TGAAGGGTGGGTAAAAGCTAAGAAGCTCCCAAAATGGCCAAA
50235790 TGAAGGGTGGGTAGAAA-CTAAGAAGCTCCCAAAATGGCCAA
1 TGAAGGGTGGGTA-AAAGCTAAGAAGCTCCCAAAATGGCCAA
50235831 GTAAACCAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 36 0.92
43 3 0.08
ACGTcount: A:0.40, C:0.16, G:0.29, T:0.16
Consensus pattern (42 bp):
TGAAGGGTGGGTAAAAGCTAAGAAGCTCCCAAAATGGCCAAA
Found at i:50241470 original size:52 final size:52
Alignment explanation
Indices: 50241372--50241523 Score: 153
Period size: 52 Copynumber: 2.9 Consensus size: 52
50241362 CAGAAAAGAT
** * * *
50241372 GTGATATGTGCACCCGCATAAGACCATAGCTGGGCTATGGTATCGGTGCAAC
1 GTGATATGTGTTCCCGTATAAGACCATAACTGGGCTATGGCATCGGTGCAAC
* * ** *
50241424 GTGATATGTGTTCCCGTATAAGACCATAATTGGGCTATGGCGTCGGTGTGAT
1 GTGATATGTGTTCCCGTATAAGACCATAACTGGGCTATGGCATCGGTGCAAC
* * **
50241476 GTGATAATGTGATT-TCGTATAAGACCATATCTGGAATATGGCATCGGT
1 GTGAT-ATGTG-TTCCCGTATAAGACCATAACTGGGCTATGGCATCGGT
50241524 ATTATATGTG
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
52 47 0.57
53 33 0.40
54 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (52 bp):
GTGATATGTGTTCCCGTATAAGACCATAACTGGGCTATGGCATCGGTGCAAC
Found at i:50245285 original size:18 final size:18
Alignment explanation
Indices: 50245264--50245314 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
50245254 TAAAAGTCAG
*
50245264 TTATTCAGTAACGATAAA
1 TTATTCAGTAACAATAAA
* *
50245282 TTATTCAGTAATAATCAA
1 TTATTCAGTAACAATAAA
*
50245300 TTATTTAGTAACAAT
1 TTATTCAGTAACAAT
50245315 TTTTTTACGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (18 bp):
TTATTCAGTAACAATAAA
Found at i:50246598 original size:13 final size:13
Alignment explanation
Indices: 50246580--50246609 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
50246570 TTTCTTTTCT
50246580 TTTCTTTTTCTCC
1 TTTCTTTTTCTCC
*
50246593 TTTCTTTTTTTCC
1 TTTCTTTTTCTCC
50246606 TTTC
1 TTTC
50246610 CCGTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTCTTTTTCTCC
Found at i:50246826 original size:15 final size:16
Alignment explanation
Indices: 50246806--50246838 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
50246796 TCTCAAATTG
*
50246806 TAATTAT-TTAATTAA
1 TAATTATCTTAATAAA
50246821 TAATTATCTTAATAAA
1 TAATTATCTTAATAAA
50246837 TA
1 TA
50246839 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTATCTTAATAAA
Found at i:50247043 original size:31 final size:30
Alignment explanation
Indices: 50246964--50247044 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 30
50246954 AATTTATTTC
*
50246964 ATAATATAATATCAATTTAATA-AAAATAATA
1 ATAATA-AATAT-AATTTAATATAAAACAATA
* *
50246995 TTAATAAATATAA---AATATAAAACCATA
1 ATAATAAATATAATTTAATATAAAACAATA
50247022 ATAATAAATAATAATTTAATATA
1 ATAATAAAT-ATAATTTAATATA
50247045 CATTATGCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
26 4 0.10
27 15 0.37
28 4 0.10
29 2 0.05
30 5 0.12
31 11 0.27
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (30 bp):
ATAATAAATATAATTTAATATAAAACAATA
Found at i:50250917 original size:42 final size:42
Alignment explanation
Indices: 50250853--50250979 Score: 143
Period size: 42 Copynumber: 3.0 Consensus size: 42
50250843 CTTCGTTTTC
** ** *
50250853 TCGATGCCATAGTTCAATTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
* *
50250896 T-GATGCCATAGCCCAGCTATGGTCGTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
*
50250937 TCGATGCTATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
50250978 TC
1 TC
50250980 TCACTGATGC
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 10 0.14
42 60 0.83
43 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:50251041 original size:47 final size:48
Alignment explanation
Indices: 50250936--50251063 Score: 156
Period size: 47 Copynumber: 2.7 Consensus size: 48
50250926 ATATTCATAT
* * * * *
50250936 ATCGATGCTATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 ATCGATGCCATATCCCAGATATGGTCTTATACGAATCACATATATCAC
*
50250984 -T-GATGCCATATCCCAGATATGGTCTTATAC-AGT-AGCATATATCAC
1 ATCGATGCCATATCCCAGATATGGTCTTATACGAATCA-CATATATCAC
*
50251029 ATCGATGCCATATCCCATATATGGTCTTATACGAA
1 ATCGATGCCATATCCCAGATATGGTCTTATACGAA
50251064 AATCACTTGT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
44 1 0.01
45 11 0.16
46 26 0.38
47 29 0.43
48 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (48 bp):
ATCGATGCCATATCCCAGATATGGTCTTATACGAATCACATATATCAC
Found at i:50251121 original size:31 final size:31
Alignment explanation
Indices: 50251086--50251265 Score: 263
Period size: 31 Copynumber: 5.8 Consensus size: 31
50251076 CTTGTCACTT
* *
50251086 GTAGCCGAAGCTACCACTATTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
50251117 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
50251148 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
50251179 GTAGTCGGAA-CTACCACTTTTCACTGATCAG
1 GTAG-CCGAAGCTACCACTTTTCACTGATCAG
*
50251210 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
**
50251241 GTAGCTAAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
50251266 TGTCATTTGT
Statistics
Matches: 137, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
30 4 0.03
31 130 0.95
32 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:50258754 original size:25 final size:24
Alignment explanation
Indices: 50258726--50258804 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 24
50258716 TGGTTATACG
50258726 AGCTGTGAATCGGTATGCTTACTCA-
1 AGCTGT-AATCGGTATGCTT-CTCAC
*
50258751 AGCTATAGATCGGTATGC-TCTCAC
1 AGCTGTA-ATCGGTATGCTTCTCAC
50258775 GAGCTGTAAATCGGTATGC-TCTCAC
1 -AGCTGT-AATCGGTATGCTTCTCAC
50258800 GAGCT
1 -AGCT
50258805 ATGGTTCAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.08
24 2 0.04
25 41 0.85
26 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (24 bp):
AGCTGTAATCGGTATGCTTCTCAC
Found at i:50260234 original size:30 final size:31
Alignment explanation
Indices: 50260158--50260242 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 31
50260148 TATAATAATA
** *
50260158 TTAA-TTCATTTTAGTTATACACATAAAACT
1 TTAATTTCATTTTAAATGTACACATAAAACT
* *
50260188 TTAATTTCATTTTAAATGTATACATGAAACT
1 TTAATTTCATTTTAAATGTACACATAAAACT
* *
50260219 TTAGTTTGA-TTTAAATGTACACAT
1 TTAATTTCATTTTAAATGTACACAT
50260243 TTAAAGGAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 18 0.39
31 28 0.61
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.45
Consensus pattern (31 bp):
TTAATTTCATTTTAAATGTACACATAAAACT
Found at i:50275106 original size:11 final size:11
Alignment explanation
Indices: 50275090--50275114 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
50275080 GAAAAGAAAC
50275090 AAAATAAAATA
1 AAAATAAAATA
50275101 AAAATAAAATA
1 AAAATAAAATA
50275112 AAA
1 AAA
50275115 TAATTAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:50282446 original size:13 final size:13
Alignment explanation
Indices: 50282428--50282460 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
50282418 ACGCCTTCTT
*
50282428 TTCCCCTTTCCTC
1 TTCCCCTTTCCCC
50282441 TTCCCC-TTCCCC
1 TTCCCCTTTCCCC
50282453 TTCCCCTT
1 TTCCCCTT
50282461 GGGTTGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (13 bp):
TTCCCCTTTCCCC
Found at i:50285180 original size:14 final size:14
Alignment explanation
Indices: 50285127--50285182 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
50285117 CATCCAAACA
*
50285127 CCAGAAAATATTTT
1 CCAGAAAACATTTT
*
50285141 -CAGTAAATCATTTT
1 CCAG-AAAACATTTT
*
50285155 CCAGAAATCATTTT
1 CCAGAAAACATTTT
50285169 CC-GAAAAACATTTT
1 CCAG-AAAACATTTT
50285183 ACTGGCAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 4 0.11
14 29 0.81
15 3 0.08
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (14 bp):
CCAGAAAACATTTT
Found at i:50285180 original size:28 final size:28
Alignment explanation
Indices: 50285127--50285182 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
50285117 CATCCAAACA
* *
50285127 CCAGAAAATATTTTCAGTAAATCATTTT
1 CCAGAAAATATTTTCAGAAAAACATTTT
*
50285155 CCAG-AAATCATTTTCCGAAAAACATTTT
1 CCAGAAAAT-ATTTTCAGAAAAACATTTT
50285183 ACTGGCAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (28 bp):
CCAGAAAATATTTTCAGAAAAACATTTT
Found at i:50285238 original size:13 final size:13
Alignment explanation
Indices: 50285220--50285245 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50285210 TTTTTTCGAA
50285220 GGGGCAACACGGT
1 GGGGCAACACGGT
50285233 GGGGCAACACGGT
1 GGGGCAACACGGT
50285246 AAAACATGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.46, T:0.08
Consensus pattern (13 bp):
GGGGCAACACGGT
Found at i:50286427 original size:422 final size:415
Alignment explanation
Indices: 50285234--50286537 Score: 1168
Period size: 422 Copynumber: 3.1 Consensus size: 415
50285224 CAACACGGTG
* * * * *
50285234 GGGCAACACGGTAAAACATGCATTGTTAGTTTCCTAAAAAAAAGCAACTGACCAGATTTTTCACA
1 GGGCAAAACGGTAAAACA-GCAGTGTTAGTTTCTTAAAAAAATGCAACTTACCAGATTTTTCACA
* * * *
50285299 ATAGTTAGAGGATTTTCCACAACTGAAAATATTTTAAAAAAAA--AAGAAAAAACCAAAAAAATT
65 ACAGTTAGA-GATTTTCCGCAATTGAAAATATTTTAAAAAAAATTAA-AAAAAAAC-AAAAAATT
* * ** * * *
50285362 ATCCAAAAAGAAACACACATGGTACGTGTCGTAGACATGTGTTAAGACGGACATGGACACGCCAT
127 TTCCAAAAAGAAACACGCGCGGTACGTGTCGTAGACACGTGTTAAGACGGAAATAGACACG--A-
* * * * * *
50285427 ACCAAGTCTGAGCGGCGATTTGTATACCCGAGTAAAGAAGGTGAAACACAATTGATATTGCACTT
189 A-CTAGTC-GAGCGGCGATTCGTACACACGAATAAAGAAGGTGAAACACAATTGATATTGCTCTT
* * ** *
50285492 CTCGAAAGAAATCATAAAACAAAGCAAAAAAAATGTAGTTGAAAATTTGA-TTGAAAATTGTTAA
252 CTCGAAAGAAATCATAAAACAAAGC--AGAAAATGTAGTAGAAAATTTGACTAAAAAATTGCTAA
* * * * * *
50285556 AAAGAAATCAGATGAGAGAAAAGGAGAATGAGATAAAGATTGATGTTTGGTTGTTATGTAAACA-
315 AAAGAAAACAGACGAAAGAAAAGGAGAATGAGAGAAAGATTGTTGTTTGCTTGTTATGTAAA-AT
* * * *
50285620 GAGAAAAATGACCTGCTATTTATATTGTTTTCTAAAA
379 GAGGAAAATGACCCGCTATTTATACTATTTTCTAAAA
* * * * * **
50285657 GGGCAAAATGGTTAAATA-TAGTGTTAGTTTCTTCAAAAAATGCAA-TTGACCAGATTTTTTTGC
1 GGGCAAAACGGTAAAACAGCAGTGTTAGTTTCTTAAAAAAATGCAACTT-ACCAGA-TTTTTCAC
* * * *
50285720 AACAATCAGAGAATTTTCCGCAATTGAAAATATTTTTAAAATAATTTAAAAAAGAAA-AACATAA
64 AACAGTTAGAG-ATTTTCCGCAATTGAAAATA-TTTTAAAAAAAATTAAAAAA-AAACAA-A-AA
* * * * * * *
50285784 ATTTTATCCAAAAGGAAACACGTGCGGTACGTGTTGTAGATACATGTTAACATGGAAATAG--AC
124 A-TTT-TCCAAAAAGAAACACGCGCGGTACGTGTCGTAGACACGTGTTAAGACGGAAATAGACAC
* ** *** * * *
50285847 ---CTAGTCGGGCGGCGGCTCGTACACTTAAATAAAAAAGGTGGAACACAATTGATATTACTCTT
187 GAACTAGTCGAGCGGCGATTCGTACACACGAATAAAGAAGGTGAAACACAATTGATATTGCTCTT
* * * * * * * *
50285909 CTCGAAAGGAATCATAAAACAAAACAGAAATTGTAGTAAAAAAATTGACTGAAAAACTACTAAAA
252 CTCGAAAGAAATCATAAAACAAAGCAGAAAATGTAGTAGAAAATTTGACTAAAAAATTGCTAAAA
*
50285974 ATAAAACAGACGAAAGAAAAGGAGAATGAGAGAAAGATTGTTGTTTGCTTGTTATGTAAAATGAG
317 AGAAAACAGACGAAAGAAAAGGAGAATGAGAGAAAGATTGTTGTTTGCTTGTTATGTAAAATGAG
* *
50286039 GAAAATGACCCGCTATTTATGCTATTTTC-CAAA
382 GAAAATGACCCGCTATTTATACTATTTTCTAAAA
* * * * * * *
50286072 GGAGTAAAACGGTAAAACACGCAGTGTCAGTTTCTTTAAACAATGAAACTTATCAGATTTTCCAC
1 GG-GCAAAACGGTAAAACA-GCAGTGTTAGTTTCTTAAAAAAATGCAACTTACCAGATTTTTCAC
* *
50286137 AACAGTTAGATGATTTTCTGTAATTGAAAATATTTTGAAAAAAAAGTTGAAAAAAAAACAGAAAA
64 AACAGTTAGA-GATTTTCCGCAATTGAAAATATTTT-AAAAAAAA-TT-AAAAAAAAACA-AAAA
* * * ** *
50286202 ATTTTCTAAAAAGAAACACGCGGGGTACCTGTCAAAGACACGTGTTAAGACGGAAACAGACACGA
124 ATTTTCCAAAAAGAAACACGCGCGGTACGTGTCGTAGACACGTGTTAAGACGGAAATAGACACGA
* * * * *
50286267 ACTAGGTCAAGTGGCGATTCGTACACACGAATAAAGAAGGTGAAACACAATTGATAATGTTTTTC
189 ACTA-GTCGAGCGGCGATTCGTACACACGAATAAAGAAGGTGAAACACAATTGATATTGCTCTTC
* * *
50286332 TCGAAAGAAATTGA-AAAACAAAGCAGAAAATGTAGTCGAAAATTTGACTAAAAAATTGGTAAAA
253 TCGAAAGAAA-TCATAAAACAAAGCAGAAAATGTAGTAGAAAATTTGACTAAAAAATTGCTAAAA
* * * * *
50286396 AGAAAACAGACAAAAGAAAAAGAGCATGAGAGACAA-ATTGTTGTTTGTTTGTTATGTAAAATTA
317 AGAAAACAGACGAAAGAAAAGGAGAATGAGAGA-AAGATTGTTGTTTGCTTGTTATGTAAAATGA
*** *
50286460 GGAAAATGACTTACTATTTATA-T-TGTTTCTTGAAA
381 GGAAAATGACCCGCTATTTATACTAT-TTTC-TAAAA
** *
50286495 GGGCAAAGTGGTAAAACA-CACCGTGTTAGTCTTCTAAAAAAAA
1 GGGCAAAACGGTAAAACAGCA--GTGTTAGT-TTCTTAAAAAAA
50286538 ATACAAGTGA
Statistics
Matches: 696, Mismatches: 148, Indels: 74
0.76 0.16 0.08
Matches are distributed among these distances:
415 24 0.03
416 149 0.21
417 106 0.15
418 43 0.06
419 10 0.01
420 5 0.01
421 37 0.05
422 220 0.32
423 44 0.06
424 5 0.01
425 9 0.01
426 2 0.00
427 42 0.06
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (415 bp):
GGGCAAAACGGTAAAACAGCAGTGTTAGTTTCTTAAAAAAATGCAACTTACCAGATTTTTCACAA
CAGTTAGAGATTTTCCGCAATTGAAAATATTTTAAAAAAAATTAAAAAAAAACAAAAAATTTTCC
AAAAAGAAACACGCGCGGTACGTGTCGTAGACACGTGTTAAGACGGAAATAGACACGAACTAGTC
GAGCGGCGATTCGTACACACGAATAAAGAAGGTGAAACACAATTGATATTGCTCTTCTCGAAAGA
AATCATAAAACAAAGCAGAAAATGTAGTAGAAAATTTGACTAAAAAATTGCTAAAAAGAAAACAG
ACGAAAGAAAAGGAGAATGAGAGAAAGATTGTTGTTTGCTTGTTATGTAAAATGAGGAAAATGAC
CCGCTATTTATACTATTTTCTAAAA
Found at i:50292989 original size:15 final size:13
Alignment explanation
Indices: 50292955--50293009 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
50292945 GCTCGCACCT
50292955 AAGGGTTCGCACA
1 AAGGGTTCGCACA
*
50292968 AAGGGTTTGCACA
1 AAGGGTTCGCACA
*
50292981 AGTAGGGTTCGCACTT
1 A--AGGGTTCGCAC-A
*
50292997 AGGGGTTCGCACA
1 AAGGGTTCGCACA
50293010 TACAAAGTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 13 0.38
14 10 0.29
15 10 0.29
16 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.22
Consensus pattern (13 bp):
AAGGGTTCGCACA
Found at i:50293450 original size:26 final size:26
Alignment explanation
Indices: 50293397--50293450 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
50293387 GCCTTGCTCT
* **
50293397 TAGGTTTACACACAAGGGCTCATGCA
1 TAGGCTTACACACAAGGGCTCACACA
*
50293423 TAGGCTTACACACAAGGGCTCGCACA
1 TAGGCTTACACACAAGGGCTCACACA
50293449 TA
1 TA
50293451 AGTACGTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.20
Consensus pattern (26 bp):
TAGGCTTACACACAAGGGCTCACACA
Found at i:50296877 original size:9 final size:9
Alignment explanation
Indices: 50296860--50296896 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
50296850 TGAGTTTTCA
50296860 AATTCGAAT
1 AATTCGAAT
*
50296869 AACTCGAAT
1 AATTCGAAT
50296878 AATTCGAAT
1 AATTCGAAT
50296887 AATTCGAAT
1 AATTCGAAT
50296896 A
1 A
50296897 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:50297469 original size:37 final size:37
Alignment explanation
Indices: 50297421--50297497 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
50297411 TAAATTTCAC
*
50297421 ATTTTATATTATTTTTATTATTGAATTGTTTAGTCAT
1 ATTTTATATTATTTATATTATTGAATTGTTTAGTCAT
50297458 ATTTTATATTATTTATATTATTGAATTGTTTAGTCAT
1 ATTTTATATTATTTATATTATTGAATTGTTTAGTCAT
50297495 ATT
1 ATT
50297498 GAATATTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (37 bp):
ATTTTATATTATTTATATTATTGAATTGTTTAGTCAT
Found at i:50297499 original size:18 final size:18
Alignment explanation
Indices: 50297439--50297501 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
50297429 TTATTTTTAT
50297439 TATTGAATTGTTTAGTCA
1 TATTGAATTGTTTAGTCA
* *
50297457 TATTTTATATTATTTA-T-A
1 TA-TTGA-ATTGTTTAGTCA
50297475 TTATTGAATTGTTTAGTCA
1 -TATTGAATTGTTTAGTCA
50297494 TATTGAAT
1 TATTGAAT
50297502 ATTTATATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
17 7 0.19
18 15 0.42
19 7 0.19
20 7 0.19
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (18 bp):
TATTGAATTGTTTAGTCA
Found at i:50297521 original size:37 final size:37
Alignment explanation
Indices: 50297421--50297511 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
50297411 TAAATTTCAC
* *
50297421 ATTTTATATTATTTTTATTATTGAATTGTTTAGTCAT
1 ATTTGATATTATTTATATTATTGAATTGTTTAGTCAT
*
50297458 ATTTTATATTATTTATATTATTGAATTGTTTAGTCAT
1 ATTTGATATTATTTATATTATTGAATTGTTTAGTCAT
50297495 A-TTGA-A-TATTTATATTA
1 ATTTGATATTATTTATATTA
50297512 AAATTGAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
34 11 0.21
35 1 0.02
36 3 0.06
37 37 0.71
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (37 bp):
ATTTGATATTATTTATATTATTGAATTGTTTAGTCAT
Found at i:50297968 original size:5 final size:5
Alignment explanation
Indices: 50297955--50297985 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
50297945 CTCGAAAATT
*
50297955 TTCGT TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
50297986 CGAATGCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.45
Consensus pattern (5 bp):
TTCGA
Found at i:50301688 original size:75 final size:75
Alignment explanation
Indices: 50301582--50301846 Score: 284
Period size: 75 Copynumber: 3.5 Consensus size: 75
50301572 CAGTGCTAGA
* * * *
50301582 CACACCCTCTATATCTGTCGGTTTATCCGACTAGTGCTGGGCTCAA-TCTTCGTTAGTTTATCTG
1 CACACCAT-TATATTTGTCGGTTTATCCGACTAGCGCTGGGCTCAACT-TTCGTCAGTTTATCTG
*
50301646 GCTAGTGTAGGG
64 ACTAGTGTAGGG
* * * * *
50301658 CACACCATTATATTTGTCGGTTTATTCGACTAGCGCTTGGCGCAACTTTCGTCAATTTATCTAAC
1 CACACCATTATATTTGTCGGTTTATCCGACTAGCGCTGGGCTCAACTTTCGTCAGTTTATCTGAC
* *
50301723 TAGTGCAGAG
66 TAGTGTAGGG
* * *
50301733 CACACCATTATATTTGTCGGTTTATCCGACTAGCACTGGGCAT-AACTTTCATCAGTTTATGTGA
1 CACACCATTATATTTGTCGGTTTATCCGACTAGCGCTGGGC-TCAACTTTCGTCAGTTTATCTGA
*
50301797 CTAGTGTTGGG
65 CTAGTGTAGGG
* * * * **
50301808 CACATCATTATAATTGCCAG-TTATCTAACTAGCGCTGGG
1 CACACCATTATATTTGTCGGTTTATCCGACTAGCGCTGGG
50301847 TGAAAAACTT
Statistics
Matches: 157, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
74 16 0.10
75 133 0.85
76 8 0.05
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (75 bp):
CACACCATTATATTTGTCGGTTTATCCGACTAGCGCTGGGCTCAACTTTCGTCAGTTTATCTGAC
TAGTGTAGGG
Found at i:50302779 original size:9 final size:9
Alignment explanation
Indices: 50302765--50302790 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
50302755 TGTGTCCCCT
50302765 ATTTTCAAA
1 ATTTTCAAA
50302774 ATTTTCAAA
1 ATTTTCAAA
50302783 ATTTTCAA
1 ATTTTCAA
50302791 CTTTTACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (9 bp):
ATTTTCAAA
Found at i:50303606 original size:16 final size:16
Alignment explanation
Indices: 50303585--50303618 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
50303575 CAGTTTTCTC
50303585 TATTTTTA-AATATTTT
1 TATTTTTATAA-ATTTT
50303601 TATTTTTATAAATTTT
1 TATTTTTATAAATTTT
50303617 TA
1 TA
50303619 GTAATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTTATAAATTTT
Found at i:50305553 original size:31 final size:31
Alignment explanation
Indices: 50305516--50305613 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
50305506 GAAATCAACA
*
50305516 AATTTAACTCTTAATATTTACAAAATTTATT
1 AATTTAACTCTTAATATTTAAAAAATTTATT
* * *
50305547 ATTTTAA-T-TTAA-ATTATAAAAAAATTAATA
1 AATTTAACTCTTAATATT-T-AAAAAATTTATT
* ** *
50305577 AATTTAACCCTCGATATTTATAAAATTTATT
1 AATTTAACTCTTAATATTTAAAAAATTTATT
50305608 AATTTA
1 AATTTA
50305614 GTTCTCATTC
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
28 3 0.06
29 5 0.10
30 16 0.31
31 21 0.41
32 3 0.06
33 3 0.06
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (31 bp):
AATTTAACTCTTAATATTTAAAAAATTTATT
Found at i:50311021 original size:41 final size:41
Alignment explanation
Indices: 50310964--50311067 Score: 172
Period size: 41 Copynumber: 2.5 Consensus size: 41
50310954 TTTAAAATAT
* *
50310964 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAAA
1 TCACCGGCACTTAGCCTGCTAGGTTCATAACCTGATTCAAA
* *
50311005 TCACCGGCACTTAGCCTGCTAGGTTCATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTCATAACCTGATTCAAA
50311046 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
50311068 ACTTAAAGTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTCATAACCTGATTCAAA
Found at i:50311091 original size:41 final size:40
Alignment explanation
Indices: 50310962--50311097 Score: 134
Period size: 41 Copynumber: 3.3 Consensus size: 40
50310952 AATTTAAAAT
* *
50310962 ATTCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCA
1 ATTCACCGGCACTTAGCCTGCTA-GCTTATAACCTGATTCA
* * *
50311003 AATCACCGGCACTTAGCCTGCTAGGTTCATAACCTGGTTCA
1 ATTCACCGGCACTTAGCCTGCTAGCTT-ATAACCTGATTCA
*
50311044 GA-TCACCGGCACTTAGCCTGCTAGACTTA-AAGTCTGAATT-A
1 -ATTCACCGGCACTTAGCCTGCTAG-CTTATAA-CCTG-ATTCA
*
50311085 ATTCACCAGCACT
1 ATTCACCGGCACT
50311098 ACATCTGCTA
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
40 6 0.07
41 70 0.86
42 5 0.06
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.27
Consensus pattern (40 bp):
ATTCACCGGCACTTAGCCTGCTAGCTTATAACCTGATTCA
Found at i:50317698 original size:16 final size:17
Alignment explanation
Indices: 50317674--50317717 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
50317664 TTTACTTCTT
50317674 AAAAA-TTAAAAA-TAA
1 AAAAATTTAAAAACTAA
50317689 AAAAATTTAAAAACTAA
1 AAAAATTTAAAAACTAA
*
50317706 AAATATTTAAAA
1 AAAAATTTAAAA
50317718 GTTCATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 5 0.19
16 7 0.27
17 14 0.54
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAAATTTAAAAACTAA
Found at i:50318382 original size:20 final size:20
Alignment explanation
Indices: 50318340--50318388 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
50318330 CCCCACTTAA
* *
50318340 ATTGTTTTATTTATAAGATT
1 ATTGTTTTATTTATAAAAAT
50318360 ATTGTTTTATTTATAAAAAT
1 ATTGTTTTATTTATAAAAAT
*
50318380 ATTATTTTA
1 ATTGTTTTA
50318389 ATAATTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (20 bp):
ATTGTTTTATTTATAAAAAT
Found at i:50324966 original size:84 final size:83
Alignment explanation
Indices: 50324829--50324994 Score: 296
Period size: 84 Copynumber: 2.0 Consensus size: 83
50324819 AGCCAAAAAT
* *
50324829 AAAACAGCACAAAGAAAACTCATTTTTTTTACATATTCGAGCTAGGTCCGGACCGAAAAAGCCTT
1 AAAACAGCACAAAGAAAACTAATTTTTTTTACATATTCGAGCCAGGTCCGGACCGAAAAAGCCTT
50324894 ACCCGAGGCCCGATTCAA
66 ACCCGAGGCCCGATTCAA
*
50324912 AAAACAGCACAAAGAAAACTGAATTTTTTTTACATATTCGGGCCAGGTCCGGACCGAAAAAGCCT
1 AAAACAGCACAAAGAAAACT-AATTTTTTTTACATATTCGAGCCAGGTCCGGACCGAAAAAGCCT
50324977 TACCCGAGGCCCGATTCA
65 TACCCGAGGCCCGATTCA
50324995 TTTTTTAAAC
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 20 0.25
84 59 0.75
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (83 bp):
AAAACAGCACAAAGAAAACTAATTTTTTTTACATATTCGAGCCAGGTCCGGACCGAAAAAGCCTT
ACCCGAGGCCCGATTCAA
Found at i:50325139 original size:91 final size:89
Alignment explanation
Indices: 50325010--50325177 Score: 250
Period size: 91 Copynumber: 1.9 Consensus size: 89
50325000 TAAACTATTC
*
50325010 TTTTTTTTCCCAAATCTATTGTTTGGACTTATAGTTTTACCCAAACCTT-TCCACTTTTTGAACG
1 TTTTTTTTCCCAAATCTATTGTTTGGACCTATAGTTTTACCCAAACCTTCT-CACTTTTTGAAC-
*
50325074 GCCCATCTCGACCCAACTGATCTTTT
64 GACCATCTCGACCCAACTGATCTTTT
* *
50325100 TTTTTTTTGCCCAAATCTATT-TTTGGGACCTATATTTTTACCCAAATCTTCTCACTTTTTGAAC
1 TTTTTTTT-CCCAAATCTATTGTTT-GGACCTATAGTTTTACCCAAACCTTCTCACTTTTTGAAC
50325164 GACCATCTCGACCC
64 GACCATCTCGACCC
50325178 GTTTTTTCCC
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
90 24 0.34
91 46 0.65
92 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.42
Consensus pattern (89 bp):
TTTTTTTTCCCAAATCTATTGTTTGGACCTATAGTTTTACCCAAACCTTCTCACTTTTTGAACGA
CCATCTCGACCCAACTGATCTTTT
Found at i:50325215 original size:76 final size:78
Alignment explanation
Indices: 50325102--50325254 Score: 224
Period size: 76 Copynumber: 2.0 Consensus size: 78
50325092 GATCTTTTTT
* *
50325102 TTTTTTGCCCAAATCTATTTTTGGGACCTATATTTTTACCCAAATC-TTCTCACTTTTTGAAC-G
1 TTTTTTGCCCAAATCTATTTTTGGGACCTATAGTTTTACCCAAACCTTTC-CACTTTTTGAACGG
50325165 ACCATCTCGACCCG
65 ACCATCTCGACCCG
*
50325179 TTTTTT-CCCAAATCTATTGTTT-GGACTTATAGTTTTACCCAAACCTTTCCACTTTTTGAACGG
1 TTTTTTGCCCAAATCTATT-TTTGGGACCTATAGTTTTACCCAAACCTTTCCACTTTTTGAACGG
*
50325242 CCCATCTCGACCC
65 ACCATCTCGACCC
50325255 ATGAGCAGGT
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
76 44 0.64
77 25 0.36
ACGTcount: A:0.22, C:0.28, G:0.10, T:0.40
Consensus pattern (78 bp):
TTTTTTGCCCAAATCTATTTTTGGGACCTATAGTTTTACCCAAACCTTTCCACTTTTTGAACGGA
CCATCTCGACCCG
Found at i:50331950 original size:2 final size:2
Alignment explanation
Indices: 50331943--50331974 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
50331933 CTTAGGGTAA
50331943 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
50331975 GACATCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:50338620 original size:26 final size:26
Alignment explanation
Indices: 50338564--50338633 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
50338554 AATGTAATAT
* * * * *
50338564 GTATTGAATGAACGAAAACTGTACTAG
1 GTATTGAAAGAATG-AAACTGCACCAA
50338591 GTATTGAAAGAATGAAACTGCACCAA
1 GTATTGAAAGAATGAAACTGCACCAA
*
50338617 GTATTCAAAGAATGAAA
1 GTATTGAAAGAATGAAA
50338634 ATGTATTGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 25 0.68
27 12 0.32
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (26 bp):
GTATTGAAAGAATGAAACTGCACCAA
Found at i:50343742 original size:27 final size:26
Alignment explanation
Indices: 50343712--50343768 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
50343702 GTGAATTTAA
* *
50343712 TGTAATATGTATTGAATGAACGAAAAC
1 TGTAATAGGTATTGAAAGAACG-AAAC
* *
50343739 TGTACTAGGTATTGAAAGAATGAAAC
1 TGTAATAGGTATTGAAAGAACGAAAC
50343765 TGTA
1 TGTA
50343769 CTAAAGGTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (26 bp):
TGTAATAGGTATTGAAAGAACGAAAC
Found at i:50343771 original size:26 final size:27
Alignment explanation
Indices: 50343720--50343771 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
50343710 AATGTAATAT
*
50343720 GTATTGAATGAACGAAAACTGTACTAG
1 GTATTGAAAGAACGAAAACTGTACTAG
*
50343747 GTATTGAAAGAATG-AAACTGTACTA
1 GTATTGAAAGAACGAAAACTGTACTA
50343772 AAGGTGGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (27 bp):
GTATTGAAAGAACGAAAACTGTACTAG
Found at i:50347256 original size:3 final size:3
Alignment explanation
Indices: 50347248--50347277 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
50347238 CAGCAAACAT
50347248 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
50347278 AAGCTTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:50347788 original size:27 final size:28
Alignment explanation
Indices: 50347742--50347798 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
50347732 AAATGAATGG
*
50347742 AATAATTAGTTCTAATTATTA-AATATA
1 AATAATTAGTTCTAACTATTACAATATA
* *
50347769 AATAATTAGTTCTAGCTATTACACTATA
1 AATAATTAGTTCTAACTATTACAATATA
50347797 AA
1 AA
50347799 AAAGAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (28 bp):
AATAATTAGTTCTAACTATTACAATATA
Found at i:50348293 original size:18 final size:18
Alignment explanation
Indices: 50348266--50348308 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
50348256 CGCATAAAAA
* *
50348266 GAAAGCAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
*
50348284 GAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
50348302 GAAAGAA
1 GAAAGAA
50348309 GGGGNTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:50348322 original size:3 final size:3
Alignment explanation
Indices: 50348314--50348480 Score: 334
Period size: 3 Copynumber: 55.7 Consensus size: 3
50348304 AAGAAGGGGN
50348314 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
50348362 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
50348410 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
50348458 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
50348481 GTGATAATTA
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 164 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:50357234 original size:80 final size:81
Alignment explanation
Indices: 50357131--50357292 Score: 272
Period size: 80 Copynumber: 2.0 Consensus size: 81
50357121 GTTTTATGAT
* * *
50357131 TTTATTTACATGGAAAATAAAATATTAAACTAGGGGTTGTCATGTGTCACTATCTAATTCTTAAT
1 TTTATTTACAAGAAAAATAAAATATTAAACTAGGGGTTGCCATGTGTCACTATCTAATTCTTAAT
50357196 TGA-TTTTTTTGTTAA
66 TGATTTTTTTTGTTAA
* *
50357211 TTTATTTACAAGAAAAATGAAATATTAAACTAGGGGTTGCCATGTGTCACTATCTGATTCTTAAT
1 TTTATTTACAAGAAAAATAAAATATTAAACTAGGGGTTGCCATGTGTCACTATCTAATTCTTAAT
50357276 TGATTTTTTTTGTTAA
66 TGATTTTTTTTGTTAA
50357292 T
1 T
50357293 GTAAGAGCTC
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 63 0.83
81 13 0.17
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.44
Consensus pattern (81 bp):
TTTATTTACAAGAAAAATAAAATATTAAACTAGGGGTTGCCATGTGTCACTATCTAATTCTTAAT
TGATTTTTTTTGTTAA
Found at i:50360147 original size:27 final size:27
Alignment explanation
Indices: 50360115--50360170 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
50360105 CTACCATCTA
50360115 TTAGAACTGTTGACTTAACTACTTTTT
1 TTAGAACTGTTGACTTAACTACTTTTT
50360142 TTAGAACTGTTGACTTAACTACTTTTT
1 TTAGAACTGTTGACTTAACTACTTTTT
50360169 TT
1 TT
50360171 TTCTCCTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (27 bp):
TTAGAACTGTTGACTTAACTACTTTTT
Found at i:50363257 original size:18 final size:18
Alignment explanation
Indices: 50363234--50363269 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
50363224 CCAACACCTT
*
50363234 CACCCTCATTACACTCCC
1 CACCCTCATTACAATCCC
50363252 CACCCTCATTACAATCCC
1 CACCCTCATTACAATCCC
50363270 TACCAGCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.53, G:0.00, T:0.22
Consensus pattern (18 bp):
CACCCTCATTACAATCCC
Found at i:50374090 original size:43 final size:42
Alignment explanation
Indices: 50374028--50374152 Score: 126
Period size: 43 Copynumber: 2.9 Consensus size: 42
50374018 TGACTCCGAT
* *
50374028 ATGTGTTTTCGTGTAAGACCACATCTGGGACGTCGGCATCGAC
1 ATGTGTTTACGTGTAAGACCACGTCTGGGACGT-GGCATCGAC
* * **
50374071 CTGTGTTTACGTGTAAGACC-CTGTCTAGGACAGTGGCATCGGT
1 ATGTGTTTACGTGTAAGACCAC-GTCTGGGAC-GTGGCATCGAC
* * *
50374114 ATGTGATTACATGTAAGACCACGTTTGGGACGTTGGCAT
1 ATGTGTTTACGTGTAAGACCACGTCTGGGACG-TGGCAT
50374153 TGTACGAGCT
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
42 2 0.03
43 62 0.93
44 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (42 bp):
ATGTGTTTACGTGTAAGACCACGTCTGGGACGTGGCATCGAC
Found at i:50381124 original size:489 final size:489
Alignment explanation
Indices: 50380206--50381182 Score: 1900
Period size: 489 Copynumber: 2.0 Consensus size: 489
50380196 AGATACACGG
*
50380206 GGTCGATTTGGTTAAAGAGAGTGAACAAAAAGTGAAAGTGATTCGGGACAGTCTGAAAAAGCATC
1 GGTCGATTTGGTTAAAGAGACTGAACAAAAAGTGAAAGTGATTCGGGACAGTCTGAAAAAGCATC
50380271 GGATCGTCAGAAATCCTATGCGGATTTGAAAAGAAAGGATATAGAATTTCAGATCGGGAACAAAG
66 GGATCGTCAGAAATCCTATGCGGATTTGAAAAGAAAGGATATAGAATTTCAGATCGGGAACAAAG
*
50380336 TGTTTTTGAAAGTCTCACCGTGGAAGAAAATACTTAAATTTGGTCGCAAAGGTAAATTAAGTCCG
131 TGTTTTTGAAAGTCTCACCGTGGAAGAAAATACTCAAATTTGGTCGCAAAGGTAAATTAAGTCCG
*
50380401 AGATTCATTGGACCGTATGAGATTATAAAGCGTATCGGGCTGGTTGCATATAAATTGTTGTTGCC
196 AGATTCATTGGACCGTATGAGATTATAAAGCGTATCGGGCTGGTTGCATATAAATTGTTGCTGCC
50380466 ATCTGAGTTAGAAAAGATTCACAATGTATTCCACGTTTCGATGCTTTGTAGATACAGATCCGATC
261 ATCTGAGTTAGAAAAGATTCACAATGTATTCCACGTTTCGATGCTTTGTAGATACAGATCCGATC
50380531 CTTCACATGTGATTAGTCCGACAGAGATTGAAATTAACTCTAATATGTCATATGAAGAAGAACCG
326 CTTCACATGTGATTAGTCCGACAGAGATTGAAATTAACTCTAATATGTCATATGAAGAAGAACCG
50380596 ATTAGCATTCTGGCTCGTGAGATCGAAGAATTACGAAATAAGAAAATTTTGTCAGTTAAAGTATT
391 ATTAGCATTCTGGCTCGTGAGATCGAAGAATTACGAAATAAGAAAATTTTGTCAGTTAAAGTATT
50380661 GTGACATAAACACAGAGTTGAAGAAGCAACTTGA
456 GTGACATAAACACAGAGTTGAAGAAGCAACTTGA
50380695 GGTCGATTTGGTTAAAGAGACTGAACAAAAAGTGAAAGTGATTCGGGACAGTCTGAAAAAGCATC
1 GGTCGATTTGGTTAAAGAGACTGAACAAAAAGTGAAAGTGATTCGGGACAGTCTGAAAAAGCATC
*
50380760 GGATCGTCAGAAATCTTATGCGGATTTGAAAAGAAAGGATATAGAATTTCAGATCGGGAACAAAG
66 GGATCGTCAGAAATCCTATGCGGATTTGAAAAGAAAGGATATAGAATTTCAGATCGGGAACAAAG
50380825 TGTTTTTGAAAGTCTCACCGTGGAAGAAAATACTCAAATTTGGTCGCAAAGGTAAATTAAGTCCG
131 TGTTTTTGAAAGTCTCACCGTGGAAGAAAATACTCAAATTTGGTCGCAAAGGTAAATTAAGTCCG
50380890 AGATTCATTGGACCGTATGAGATTATAAAGCGTATCGGGCTGGTTGCATATAAATTGTTGCTGCC
196 AGATTCATTGGACCGTATGAGATTATAAAGCGTATCGGGCTGGTTGCATATAAATTGTTGCTGCC
*
50380955 ATCTGAGTTAGAAAAGATTCACAATGTATTCCATGTTTCGATGCTTTGTAGATACAGATCCGATC
261 ATCTGAGTTAGAAAAGATTCACAATGTATTCCACGTTTCGATGCTTTGTAGATACAGATCCGATC
50381020 CTTCACATGTGATTAGTCCGACAGAGATTGAAATTAACTCTAATATGTCATATGAAGAAGAACCG
326 CTTCACATGTGATTAGTCCGACAGAGATTGAAATTAACTCTAATATGTCATATGAAGAAGAACCG
50381085 ATTAGCATTCTGGCTCGTGAGATCGAAGAATTACGAAATAAGAAAATTTTGTCAGTTAAAGTATT
391 ATTAGCATTCTGGCTCGTGAGATCGAAGAATTACGAAATAAGAAAATTTTGTCAGTTAAAGTATT
*
50381150 GTGACATAAACACGGAGTTGAAGAAGCAACTTG
456 GTGACATAAACACAGAGTTGAAGAAGCAACTTG
50381183 GGAGTTAGAA
Statistics
Matches: 482, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
489 482 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (489 bp):
GGTCGATTTGGTTAAAGAGACTGAACAAAAAGTGAAAGTGATTCGGGACAGTCTGAAAAAGCATC
GGATCGTCAGAAATCCTATGCGGATTTGAAAAGAAAGGATATAGAATTTCAGATCGGGAACAAAG
TGTTTTTGAAAGTCTCACCGTGGAAGAAAATACTCAAATTTGGTCGCAAAGGTAAATTAAGTCCG
AGATTCATTGGACCGTATGAGATTATAAAGCGTATCGGGCTGGTTGCATATAAATTGTTGCTGCC
ATCTGAGTTAGAAAAGATTCACAATGTATTCCACGTTTCGATGCTTTGTAGATACAGATCCGATC
CTTCACATGTGATTAGTCCGACAGAGATTGAAATTAACTCTAATATGTCATATGAAGAAGAACCG
ATTAGCATTCTGGCTCGTGAGATCGAAGAATTACGAAATAAGAAAATTTTGTCAGTTAAAGTATT
GTGACATAAACACAGAGTTGAAGAAGCAACTTGA
Found at i:50385977 original size:21 final size:19
Alignment explanation
Indices: 50385951--50385989 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
50385941 TCAACCATTC
50385951 AAAACACAATCAAATACAATT
1 AAAACA-AATCAAA-ACAATT
*
50385972 AAAACATATCAAAACAAT
1 AAAACAAATCAAAACAAT
50385990 AATCCTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAACAAATCAAAACAATT
Found at i:50386526 original size:21 final size:20
Alignment explanation
Indices: 50386502--50386552 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
50386492 ATTCATAACA
*
50386502 TATTCAATTCTCATCACTTGC
1 TATTCAAATCTCAT-ACTTGC
50386523 TATTTCAAATCTCATACTTGC
1 TA-TTCAAATCTCATACTTGC
*
50386544 TATACAAAT
1 TATTCAAAT
50386553 AGCTTTCCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 6 0.22
21 10 0.37
22 11 0.41
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (20 bp):
TATTCAAATCTCATACTTGC
Found at i:50386529 original size:22 final size:21
Alignment explanation
Indices: 50386504--50386546 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
50386494 TCATAACATA
*
50386504 TTCAATTCTCATCACTTGCTAT
1 TTCAAATCTCAT-ACTTGCTAT
50386526 TTCAAATCTCATACTTGCTAT
1 TTCAAATCTCATACTTGCTAT
50386547 ACAAATAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (21 bp):
TTCAAATCTCATACTTGCTAT
Found at i:50386833 original size:41 final size:40
Alignment explanation
Indices: 50386737--50386843 Score: 123
Period size: 37 Copynumber: 2.7 Consensus size: 40
50386727 AGATAATTCC
* *
50386737 AAGTAATAAATTGAAACCCAGTGTCTCATCAGCTAAACCG
1 AAGTAATAAATTGACACCCAGTGTCTCATCAACTAAACCG
* * *
50386777 -A--AATAAATTGGCACCCAGTG-CGTCATCGAATTAATCCG
1 AAGTAATAAATTGACACCCAGTGTC-TCATC-AACTAAACCG
50386815 AAGTAATAAATTGACACCCAGTGTCTCAT
1 AAGTAATAAATTGACACCCAGTGTCTCAT
50386844 TGACTCGAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
36 1 0.02
37 22 0.40
38 7 0.13
39 2 0.04
41 22 0.40
42 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (40 bp):
AAGTAATAAATTGACACCCAGTGTCTCATCAACTAAACCG
Found at i:50387729 original size:20 final size:21
Alignment explanation
Indices: 50387704--50387759 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
50387694 TTTTCTCCTT
50387704 CTTTCTTTCTCTTTTTTT-TC
1 CTTTCTTTCTCTTTTTTTCTC
*
50387724 CTTTCTCTC-CTTCTTTTTCTC
1 CTTTCTTTCTCTT-TTTTTCTC
*
50387745 CTTCTTTTTCTCTTT
1 CTT-TCTTTCTCTTT
50387760 CTTAATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 3 0.10
20 13 0.45
21 5 0.17
22 5 0.17
23 3 0.10
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
CTTTCTTTCTCTTTTTTTCTC
Found at i:50387734 original size:32 final size:32
Alignment explanation
Indices: 50387693--50387761 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
50387683 GAAACCCTAA
*
50387693 CTTT-TCTCCTTCTTTCTT-TCTCTTTTTTTTC-
1 CTTTCTCTCCTTCTTT-TTCTC-CTTCTTTTTCT
50387724 CTTTCTCTCCTTCTTTTTCTCCTTCTTTTTCT
1 CTTTCTCTCCTTCTTTTTCTCCTTCTTTTTCT
50387756 CTTTCT
1 CTTTCT
50387762 TAATTATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
31 15 0.44
32 19 0.56
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (32 bp):
CTTTCTCTCCTTCTTTTTCTCCTTCTTTTTCT
Found at i:50387744 original size:12 final size:12
Alignment explanation
Indices: 50387724--50387762 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
50387714 CTTTTTTTTC
*
50387724 CTTTCTCTCCTT
1 CTTTTTCTCCTT
50387736 CTTTTTCTCCTT
1 CTTTTTCTCCTT
*
50387748 CTTTTTCTCTTT
1 CTTTTTCTCCTT
50387760 CTT
1 CTT
50387763 AATTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
CTTTTTCTCCTT
Found at i:50387751 original size:24 final size:24
Alignment explanation
Indices: 50387694--50387762 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
50387684 AAACCCTAAC
*
50387694 TTTTCTCCTTCTTTCT-TTC-TCT
1 TTTTCTCCTTCTTTCTCTCCTTCT
50387716 TTTT-T--TTCCTTTCTCTCCTTCT
1 TTTTCTCCTT-CTTTCTCTCCTTCT
* *
50387738 TTTTCTCCTTCTTTTTCTCTTTCT
1 TTTTCTCCTTCTTTCTCTCCTTCT
50387762 T
1 T
50387763 AATTATTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
19 2 0.05
20 6 0.16
21 3 0.08
22 11 0.29
23 1 0.03
24 13 0.34
25 2 0.05
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTCTCCTTCTTTCTCTCCTTCT
Found at i:50389930 original size:25 final size:25
Alignment explanation
Indices: 50389902--50389970 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 25
50389892 GGCAATATGA
50389902 GGAAGCTCCGAAGAGCCGTTAATCG
1 GGAAGCTCCGAAGAGCCGTTAATCG
* *
50389927 GGAAGCTCATGAAAGAGCCTTTAATCG
1 GGAAGCTC-CG-AAGAGCCGTTAATCG
* *
50389954 GAAAACTCCGAAGAGCC
1 GGAAGCTCCGAAGAGCC
50389971 ATATATATGG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 15 0.41
26 2 0.05
27 20 0.54
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.16
Consensus pattern (25 bp):
GGAAGCTCCGAAGAGCCGTTAATCG
Done.