Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2298
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: 581295
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.21
Warning! 216560 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:501008 original size:126 final size:126
Alignment explanation
Indices: 500770--501016 Score: 309
Period size: 126 Copynumber: 2.0 Consensus size: 126
500760 AAGGAAAAGA
* * * *
500770 TGCCACGGAGTTGTGGACTTAAAAGGAATAAGATGCCACGGAGTTATGGACCTTGAAGGAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAAGAACAAGATGCCACGGAGTTATGAACCTTGAAGAAAAAGA
* *** * *
500835 TGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCTATAGAGTTGTGGACTTAACTAGG
66 TGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGACACCACAGAGTTGTGGACTTAACTAGG
* * * *
500896 TGCCACGGAGTTGTCGG-TTTAAAAAGAACAAGGTGCCATGGAGTTGTGAACCTTGAAGAAAAAG
1 TGCCACGGAGTTGT-GGACTTAAAAAGAACAAGATGCCACGGAGTTATGAACCTTGAAGAAAAAG
* * *
500960 ATGTCACAGAGTTGTGGGCTTT-AAAGAGAAAAAGACACCACGGGGTTGTGGACTTAA
65 ATGCCACAGAGTTGTGGGCTTTGAAA-AGAAAAAGACACCACAGAGTTGTGGACTTAA
501017 AAGGAACAAG
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
125 3 0.03
126 97 0.95
127 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.23
Consensus pattern (126 bp):
TGCCACGGAGTTGTGGACTTAAAAAGAACAAGATGCCACGGAGTTATGAACCTTGAAGAAAAAGA
TGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGACACCACAGAGTTGTGGACTTAACTAGG
Found at i:501035 original size:33 final size:32
Alignment explanation
Indices: 500445--501580 Score: 582
Period size: 33 Copynumber: 34.7 Consensus size: 32
500435 TTTAGAAGGG
*
500445 GGTGTCACGGAGTTGTGGACTTAAAA-G----
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAA
* * *
500472 GGTGCTATGGAGTTATGGACTTAAAAGGAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAA
* * * * *
500504 GATGCCATGGAGTTATGGGCTTCGAAAAGAAAAA
1 GGTGCCACGGAGTTGTGGACTT--AAAAGGAAAA
* ** *
500538 AGTGCCACGGAGTTGTGGACTTTCAAGAAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAA
* * * * *
500570 GATGCCACGAAGTTGTGGGCCCT-GAAGAGAAAA
1 GGTGCCACGGAGTTGT-GGACTTAAAAG-GAAAA
* *
500603 CAGTGCCAC-AAGGTTGTGGACTTAAAAGGAACAA
1 -GGTGCCACGGA-GTTGTGGACTTAAAAGGAA-AA
* ** * * *
500637 GATGTTACGGAGCTATGGACCTT-GAAGGAAAA
1 GGTGCCACGGAGTTGTGGA-CTTAAAAGGAAAA
* * * **
500669 GATGCCACGAAGTTGTGGGCTTTGAAGAGAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAG-GAAAA
*
500702 CAGTGCCACAGG-GTTGTGGACTTAAAAGGAATAA
1 -GGTGCCAC-GGAGTTGTGGACTTAAAAGGAA-AA
* * * *
500736 GATGCCTCGGAGTTATGGACCTT-GAAGGAAAA
1 GGTGCCACGGAGTTGTGGA-CTTAAAAGGAAAA
*
500768 GATGCCACGGAGTTGTGGACTTAAAAGGAATAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAA-AA
* * *
500801 GATGCCACGGAGTTATGGACCTT-GAAGGAAAA
1 GGTGCCACGGAGTTGTGGA-CTTAAAAGGAAAA
* * *
500833 GATGCCACGGAGTTGTGGGCTTTGAAAAGAAAAA
1 GGTGCCACGGAGTTGTGGAC-TT-AAAAGGAAAA
* ** **
500867 GGTGCTATAGAGTTGTGGACTT---A--ACTA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAA
* *
500894 GGTGCCACGGAGTTGTCGG-TTTAAAAAGAACAA
1 GGTGCCACGGAGTTGT-GGACTTAAAAGGAA-AA
* * * *
500927 GGTGCCATGGAGTTGTGAACCTT-GAAGAAAAA
1 GGTGCCACGGAGTTGTGGA-CTTAAAAGGAAAA
* * * * *
500959 GATGTCACAGAGTTGTGGGCTTTAAAGAGAAAAA
1 GGTGCCACGGAGTTGTGGAC-TTAAA-AGGAAAA
*** *
500993 GACACCACGGGGTTGTGGACTTAAAAGGAACAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAA-AA
* * * *
501026 GGTGTCACGGAGTTATAGACTTTAAAGGAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAA
* * * *
501058 GATGCCACGAAGTTGTGGGCTTTGAAAA-AAAAA
1 GGTGCCACGGAGTTGTGGAC-TT-AAAAGGAAAA
*
501091 GGTGCCACGGGGTTGTGTTGTGGACTTAAAAGGAACAA
1 GGTGCCAC---G--GAGTTGTGGACTTAAAAGGAA-AA
* * *
501129 GGTGCCATGGAGTTATGGACTTTGAAA-GAAAA
1 GGTGCCACGGAGTTGTGGAC-TTAAAAGGAAAA
* * * *
501161 GATGCCACAGAGTTGTGGGTCTTGAAAAGAAAAA
1 GGTGCCACGGAGTTGT-GGACTT-AAAAGGAAAA
*
501195 GATGCCACGGAGTTGTGGACTTAAAA-G----
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAA
501222 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAA
* ** * *
501254 GATGCCACAAAGTTGTGGGCTTTAAAAAGAAAAAA
1 GGTGCCACGGAGTTGTGGAC-TT-AAAAG-GAAAA
*
501289 GGTGCCACGGAGTTGTGGACTTAAAAAGAAGAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAA-AA
* * * * ** **
501322 GGTGCTATGGAATTGTAGACTTTGAAGGAAGT
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAA
* * *
501354 GGATGCCACGGAGTTGTGGGCTTTGAAGAGAAAAA
1 GG-TGCCACGGAGTTGTGGAC-TT-AAAAGGAAAA
* *
501389 GGTACCACAGG-GTTGTGGACTTAAAAAGAACAA
1 GGTGCCAC-GGAGTTGTGGACTTAAAAGGAA-AA
* * *
501422 GGTGCTACGGAGTTATGGACCTT-GAAGGAAAA
1 GGTGCCACGGAGTTGTGGA-CTTAAAAGGAAAA
* * * *
501454 GATGCCAAGG-GATTGTGGGCTTTAAAAAGAAAA
1 GGTGCCACGGAG-TTGTGGAC-TTAAAAGGAAAA
*
501487 GGTGCCACGGAGTTGTGTTGTGGATTTAAAAGGAACAA
1 GGTGCCACGGA-----GTTGTGGACTTAAAAGGAA-AA
** *
501525 GGTGCCACGGAGTTGTGGACTTTGAAGGAAAC
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAA
** *
501557 GGATGCCACTAAGTCGTGGACTTA
1 GG-TGCCACGGAGTTGTGGACTTA
501581 GAAAAAGGGT
Statistics
Matches: 837, Mismatches: 191, Indels: 156
0.71 0.16 0.13
Matches are distributed among these distances:
27 64 0.08
28 4 0.00
29 1 0.00
30 1 0.00
31 10 0.01
32 215 0.26
33 287 0.34
34 170 0.20
35 30 0.04
36 5 0.01
37 13 0.02
38 36 0.04
39 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.22
Consensus pattern (32 bp):
GGTGCCACGGAGTTGTGGACTTAAAAGGAAAA
Found at i:501228 original size:27 final size:27
Alignment explanation
Indices: 501197--501249 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
501187 AAGAAAAAGA
501197 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
501224 TGCCACGGAGTTGTGGACTTAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGG
501250 AAAAGATGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:501435 original size:67 final size:65
Alignment explanation
Indices: 501217--501503 Score: 208
Period size: 67 Copynumber: 4.3 Consensus size: 65
501207 TTGTGGACTT
* * ** *
501217 AAAAGGGTGCCACGGAGTTGTGGA-CTTAAAAGGAAAAGATGCCACAAAG-TTGTGGGCTTTAAA
1 AAAA-GGTGCCACGGAGTTGTGGACCTT-GAAGGAAAAGATACCA-AGGGATTGTGGACTTTAAA
501280 AAG
63 AAG
* * * * * * * * *
501283 AAAAAAGGTGCCACGGAGTTGTGGA-CTTAAAAAGAAGAAGGTGCTATGGAATTGTAGACTTT-G
1 --AAAAGGTGCCACGGAGTTGTGGACCTT-GAAGGAA-AAGATACCAAGGGATTGTGGACTTTAA
*
501346 AAGG
62 AAAG
** * * *
501350 AAGTGGATGCCACGGAGTTGTGGGCTTTGAAGAGAAAAAGGTACCACAGGG-TTGTGGAC-TTAA
1 AAAAGG-TGCCACGGAGTTGTGGACCTTGAAG-G-AAAAGATACCA-AGGGATTGTGGACTTTAA
501413 AAAG
62 AAAG
* * * *
501417 AACAAGGTGCTACGGAGTTATGGACCTTGAAGGAAAAGATGCCAAGGGATTGTGGGCTTTAAAAA
1 AA-AAGGTGCCACGGAGTTGTGGACCTTGAAGGAAAAGATACCAAGGGATTGTGGACTTTAAAAA
501482 G
65 G
501483 AAAAGGTGCCACGGAGTTGTG
1 AAAAGGTGCCACGGAGTTGTG
501504 TTGTGGATTT
Statistics
Matches: 173, Mismatches: 35, Indels: 25
0.74 0.15 0.11
Matches are distributed among these distances:
64 4 0.02
65 37 0.21
66 31 0.18
67 75 0.43
68 26 0.15
ACGTcount: A:0.35, C:0.11, G:0.32, T:0.21
Consensus pattern (65 bp):
AAAAGGTGCCACGGAGTTGTGGACCTTGAAGGAAAAGATACCAAGGGATTGTGGACTTTAAAAAG
Found at i:501606 original size:30 final size:30
Alignment explanation
Indices: 501523--501798 Score: 221
Period size: 33 Copynumber: 8.8 Consensus size: 30
501513 TAAAAGGAAC
* * *
501523 AAGG-TGCCACGGAGTTGTGGACTTTGAAGGA
1 AAGGATGCCACTGAGTCGTGGACTTAGAA--A
*
501554 AACGGATGCCACTAAGTCGTGGACTTAGAAA
1 AA-GGATGCCACTGAGTCGTGGACTTAGAAA
* * *
501585 AAGGGTGCCAATGAGTAGTGGACTTTTAAGAAA
1 AAGGATGCCACTGAGTCGTGGAC--TT-AGAAA
* * * *
501618 AAGGACGCCACTGAGTCCTGGAATTAAAAA
1 AAGGATGCCACTGAGTCGTGGACTTAGAAA
* *
501648 AAGGATACTACTGAGTCGTGGACTTTGAAGAAA
1 AAGGATGCCACTGAGTCGTGGAC-TT--AGAAA
* * * * *
501681 AAAGAAGCCACTAAGTTGTGGACTTTGAAA
1 AAGGATGCCACTGAGTCGTGGACTTAGAAA
*
501711 AAGGATGCCACTGAGTCGTGGACTTTTAAAAAA
1 AAGGATGCCACTGAGTCGTGGAC--TT-AGAAA
* **
501744 AAGGATGCCACTGAGTCGTAGACTTTTAAA
1 AAGGATGCCACTGAGTCGTGGACTTAGAAA
* *
501774 AATGATGCCACTGAGTAGTGGACTT
1 AAGGATGCCACTGAGTCGTGGACTT
501799 TTAGGAAAGG
Statistics
Matches: 194, Mismatches: 40, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
30 87 0.45
31 11 0.06
32 8 0.04
33 88 0.45
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (30 bp):
AAGGATGCCACTGAGTCGTGGACTTAGAAA
Found at i:501606 original size:63 final size:63
Alignment explanation
Indices: 501523--501799 Score: 304
Period size: 63 Copynumber: 4.4 Consensus size: 63
501513 TAAAAGGAAC
* * * *
501523 AAGG-TGCCACGGAGTTGTGGACTTTGAAGGAAACGGATGCCACTAAGTCGTGGACTTAGAAA
1 AAGGATGCCACTGAGTAGTGGACTTTGAAGAAAAAGGATGCCACTAAGTCGTGGACTTAGAAA
* * * * * * * *
501585 AAGGGTGCCAATGAGTAGTGGACTTTTAAGAAAAAGGACGCCACTGAGTCCTGGAATTAAAAA
1 AAGGATGCCACTGAGTAGTGGACTTTGAAGAAAAAGGATGCCACTAAGTCGTGGACTTAGAAA
* * * * * * *
501648 AAGGATACTACTGAGTCGTGGACTTTGAAGAAAAAAGAAGCCACTAAGTTGTGGACTTTGAAA
1 AAGGATGCCACTGAGTAGTGGACTTTGAAGAAAAAGGATGCCACTAAGTCGTGGACTTAGAAA
* * * * * **
501711 AAGGATGCCACTGAGTCGTGGACTTTTAAAAAAAAGGATGCCACTGAGTCGTAGACTTTTAAA
1 AAGGATGCCACTGAGTAGTGGACTTTGAAGAAAAAGGATGCCACTAAGTCGTGGACTTAGAAA
*
501774 AATGATGCCACTGAGTAGTGGACTTT
1 AAGGATGCCACTGAGTAGTGGACTTT
501800 TAGGAAAGGT
Statistics
Matches: 177, Mismatches: 37, Indels: 1
0.82 0.17 0.00
Matches are distributed among these distances:
62 4 0.02
63 173 0.98
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (63 bp):
AAGGATGCCACTGAGTAGTGGACTTTGAAGAAAAAGGATGCCACTAAGTCGTGGACTTAGAAA
Found at i:501633 original size:33 final size:33
Alignment explanation
Indices: 501523--501806 Score: 261
Period size: 30 Copynumber: 9.0 Consensus size: 33
501513 TAAAAGGAAC
* * * *
501523 AAGG-TGCCACGGAGTTGTGGACTTTGAAGGAA
1 AAGGATGCCACTGAGTCGTGGACTTTTAAGAAA
* *
501555 ACGGATGCCACTAAGTCGTGGAC--TT-AGAAA
1 AAGGATGCCACTGAGTCGTGGACTTTTAAGAAA
* * *
501585 AAGGGTGCCAATGAGTAGTGGACTTTTAAGAAA
1 AAGGATGCCACTGAGTCGTGGACTTTTAAGAAA
* * *
501618 AAGGACGCCACTGAGTCCTGGA--ATTAA-AAA
1 AAGGATGCCACTGAGTCGTGGACTTTTAAGAAA
* * *
501648 AAGGATACTACTGAGTCGTGGACTTTGAAGAAA
1 AAGGATGCCACTGAGTCGTGGACTTTTAAGAAA
* * * *
501681 AAAGAAGCCACTAAGTTGTGGAC-TTT--GAAA
1 AAGGATGCCACTGAGTCGTGGACTTTTAAGAAA
*
501711 AAGGATGCCACTGAGTCGTGGACTTTTAAAAAA
1 AAGGATGCCACTGAGTCGTGGACTTTTAAGAAA
*
501744 AAGGATGCCACTGAGTCGTAGACTTTT---AAA
1 AAGGATGCCACTGAGTCGTGGACTTTTAAGAAA
* * *
501774 AATGATGCCACTGAGTAGTGGACTTTTAGGAAA
1 AAGGATGCCACTGAGTCGTGGACTTTTAAGAAA
501807 GGTGTCATAG
Statistics
Matches: 200, Mismatches: 39, Indels: 25
0.76 0.15 0.09
Matches are distributed among these distances:
30 93 0.47
31 8 0.04
32 10 0.05
33 89 0.44
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.23
Consensus pattern (33 bp):
AAGGATGCCACTGAGTCGTGGACTTTTAAGAAA
Found at i:501692 original size:126 final size:126
Alignment explanation
Indices: 501534--501760 Score: 346
Period size: 126 Copynumber: 1.8 Consensus size: 126
501524 AGGTGCCACG
* * ** * *
501534 GAGTTGTGGACTTTGAAGGAAACGGATGCCACTAAGTCGTGGACTTAGAAAAAGGGTGCCAATGA
1 GAGTCGTGGACTTTGAAGAAAAAAGAAGCCACTAAGTCGTGGACTTAGAAAAAGGATGCCAATGA
*
501599 GTAGTGGACTTTTAAGAAAAAGGACGCCACTGAGTCCTGGAATTAAAAAAAGGATACTACT
66 GTAGTGGACTTTTAAAAAAAAGGACGCCACTGAGTCCTGGAATTAAAAAAAGGATACTACT
* * *
501660 GAGTCGTGGACTTTGAAGAAAAAAGAAGCCACTAAGTTGTGGACTTTGAAAAAGGATGCCACTGA
1 GAGTCGTGGACTTTGAAGAAAAAAGAAGCCACTAAGTCGTGGACTTAGAAAAAGGATGCCAATGA
* *
501725 GTCGTGGACTTTTAAAAAAAAGGATGCCACTGAGTC
66 GTAGTGGACTTTTAAAAAAAAGGACGCCACTGAGTC
501761 GTAGACTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
126 89 1.00
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (126 bp):
GAGTCGTGGACTTTGAAGAAAAAAGAAGCCACTAAGTCGTGGACTTAGAAAAAGGATGCCAATGA
GTAGTGGACTTTTAAAAAAAAGGACGCCACTGAGTCCTGGAATTAAAAAAAGGATACTACT
Found at i:501775 original size:126 final size:126
Alignment explanation
Indices: 501529--501799 Score: 344
Period size: 126 Copynumber: 2.2 Consensus size: 126
501519 GAACAAGGTG
* * * ** * *
501529 CCACGGAGTTGTGGACTTTGAAGGAAACGGATGCCACTAAGTCGTGGACTTAGAAAAAGGGTGCC
1 CCACTGAGTAGTGGACTTTGAAGAAAAAAGAAGCCACTAAGTCGTGGACTTAGAAAAAGGATGCC
* *
501594 AATGAGTAGTGGACTTTTAAGAAAAAGGACGCCACTGAGTCCTGGAATTAAAAAAAGGATA
66 AATGAGTAGTGGACTTTTAAAAAAAAGGACGCCACTGAGTCCTAGAATTAAAAAAAGGATA
* * * *
501655 CTACTGAGTCGTGGACTTTGAAGAAAAAAGAAGCCACTAAGTTGTGGACTTTGAAAAAGGATGCC
1 CCACTGAGTAGTGGACTTTGAAGAAAAAAGAAGCCACTAAGTCGTGGACTTAGAAAAAGGATGCC
* * * * * ** * *
501720 ACTGAGTCGTGGACTTTTAAAAAAAAGGATGCCACTGAGTCGTAGACTTTTAAAAATGATG
66 AATGAGTAGTGGACTTTTAAAAAAAAGGACGCCACTGAGTCCTAGAATTAAAAAAAGGATA
501781 CCACTGAGTAGTGGACTTT
1 CCACTGAGTAGTGGACTTT
501800 TAGGAAAGGT
Statistics
Matches: 122, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
126 122 1.00
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.24
Consensus pattern (126 bp):
CCACTGAGTAGTGGACTTTGAAGAAAAAAGAAGCCACTAAGTCGTGGACTTAGAAAAAGGATGCC
AATGAGTAGTGGACTTTTAAAAAAAAGGACGCCACTGAGTCCTAGAATTAAAAAAAGGATA
Found at i:506435 original size:70 final size:70
Alignment explanation
Indices: 506346--506483 Score: 213
Period size: 70 Copynumber: 2.0 Consensus size: 70
506336 GGAGGAATGG
** * *
506346 GGTTGGAGTGTCCCCGATGATGACAATTTAAGCGAGAATAATATTTGAATCTTGACAAGTTTAAA
1 GGTTGGAGCATCCCCGATGAAGACAATTTAAGCGAGAATAAGATTTGAATCTTGACAAGTTTAAA
506411 AGCGA
66 AGCGA
* * *
506416 GGTTGGAGCATCCCTGATGAAGGCAATTTAAGTGAGAATAAGATTTGAATCTTGACAAGTTTAAA
1 GGTTGGAGCATCCCCGATGAAGACAATTTAAGCGAGAATAAGATTTGAATCTTGACAAGTTTAAA
506481 AGC
66 AGC
506484 CCCTCAGAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (70 bp):
GGTTGGAGCATCCCCGATGAAGACAATTTAAGCGAGAATAAGATTTGAATCTTGACAAGTTTAAA
AGCGA
Found at i:508691 original size:20 final size:20
Alignment explanation
Indices: 508647--508763 Score: 164
Period size: 20 Copynumber: 5.8 Consensus size: 20
508637 AATTTTAACT
*
508647 AAATGTATCGACACATTGAAA
1 AAATGTATCGATACATTG-AA
508668 AAATGTATCGATACATTGAA
1 AAATGTATCGATACATTGAA
508688 AAATGTATCGATACATT-AA
1 AAATGTATCGATACATTGAA
* *
508707 AGAATGTATCGATACATTCAT
1 A-AATGTATCGATACATTGAA
* *
508728 ACATGTATCGATACATTAAA
1 AAATGTATCGATACATTGAA
508748 AAATGTATCGATACAT
1 AAATGTATCGATACAT
508764 CTTGGTACTT
Statistics
Matches: 88, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
19 3 0.03
20 66 0.75
21 19 0.22
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACATTGAA
Found at i:509669 original size:32 final size:32
Alignment explanation
Indices: 509633--510377 Score: 592
Period size: 32 Copynumber: 24.7 Consensus size: 32
509623 GGTGCCACTA
** *
509633 ACTTGTGTGAACTTTGAAAAGAGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* * * *
509665 ACTTGTGTGGACTTTGAAAAGAGTTACCA-CT
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* **
509696 AC-T-TGTGGGCTTTGAAAAGAG-TGCCACTA
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* * * *
509725 AC-T-TATGGGCTTTGAAA-G-GGTACCACTG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* *
509753 AC-T-TGTGGGCTTTGAAA-G-GGTGCCACTG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* * *
509781 AC-T-TGTGGGTTTTGAAA-G-GATGCCACTG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* * *
509809 ACTT-T-TGGGCTTTGAAAAGA-ATGCCACTG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* * *
509838 ACTT-T-TGGGCTTTGAAA-G-GGTGTCACTG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* * **
509866 AC-T-TATGGGCTTTGAAA-G-GATGCCATTG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* *
509894 AC-T-TGTGGGCTTTGAAATGTGTTGCCACCA
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* *
509924 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCA
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* * *
509956 ACTTGTGTGGGCTTTGAAATGGGTTCCCACCA
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
*
509988 ACTTGTGTGGGCTTTCAAATGAGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
*
510020 ACTTGTGTGGGCTTTGAAATGA--TGCCACTG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
*
510050 AC-T-TGTGGGCTTTGAAATGGGTTGCCACTC-
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCAC-CG
* *
510080 ACTTGTGTGGGCTTTGAAATGGGTTGCCACTG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
**
510112 ACTTGTGTGGGCTTTGAAATGA--TGCCACTA
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
*
510142 AC-T-TGTGGGCTTTGAAATGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* * * *
510172 ACTTGTGTGGGCTTTGCAATGGGTTGCCAACA
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* *
510204 ACTTGTGTGGGCTTTCAAATGAGTTGCCACCA
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* * * ** *
510236 ACTTGTTTGGGCTTGGAAATGGGTTGCTGCCA
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* *
510268 ACTTGTGTGGGCTTTCAAATGAGTTGCCATCG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
*
510300 ACTTGTGTGGGCTTTGAAATGA--TGCCACTG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
* * *
510330 AC-T-TGTGAGCTTTGAAA-G-GATGCCACTG
1 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
*
510358 AC-T-TGTGGGCTTTAAAATGA
1 ACTTGTGTGGGCTTTGAAATGA
510378 TGCCACTAAC
Statistics
Matches: 620, Mismatches: 68, Indels: 52
0.84 0.09 0.07
Matches are distributed among these distances:
27 4 0.01
28 190 0.31
29 67 0.11
30 51 0.08
31 6 0.01
32 302 0.49
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (32 bp):
ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
Found at i:510100 original size:92 final size:92
Alignment explanation
Indices: 509625--510377 Score: 712
Period size: 92 Copynumber: 8.3 Consensus size: 92
509615 TTAAAAAAGG
* ** * * *
509625 TGCCACTAACTTGTGTGAACTTTGAAAAGAGTTGCCACCGACTTGTGTGGACTTTGAAAAGAGTT
1 TGCCACTCACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGA--T
* * *
509690 ACCACT-ACTTGTGGGCTTTGAAAAGAG-
64 GCCACTGACTTGTGGGCTTTGAAATGGGT
* * * * * * *
509717 TGCCACTAAC-T-TATGGGCTTTGAAA-G-GGTACCACTGAC-T-TGTGGGCTTTGAAAGGGTGC
1 TGCCACTCACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGATGC
* *
509776 CACTGACTTGTGGGTTTTGAAA--GGA
66 CACTGACTTGTGGGCTTTGAAATGGGT
* * * * * * *
509801 TGCCACTGACTT-T-TGGGCTTTGAAAAGA-ATGCCACTGACTT-T-TGGGCTTTGAAAGGGTGT
1 TGCCACTCACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGATGC
* *
509861 CACTGACTTATGGGCTTTGAAA--GGA
66 CACTGACTTGTGGGCTTTGAAATGGGT
* * * * *
509886 TGCCATTGAC-T-TGTGGGCTTTGAAATGTGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTT
1 TGCCACTCACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAAT--GAT
**
509949 GCCACCAACTTGTGTGGGCTTTGAAATGGGT
64 GCCACTGAC-T-TGTGGGCTTTGAAATGGGT
* *
509980 TCCCAC-CAACTTGTGTGGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGATG
1 TGCCACTC-ACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGATG
510044 CCACTGACTTGTGGGCTTTGAAATGGGT
65 CCACTGACTTGTGGGCTTTGAAATGGGT
* *
510072 TGCCACTCACTTGTGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGATGC
1 TGCCACTCACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGATGC
*
510137 CACTAACTTGTGGGCTTTGAAATGGGT
66 CACTGACTTGTGGGCTTTGAAATGGGT
* * * * *
510164 TGCCAC-CGACTTGTGTGGGCTTTGCAATGGGTTGCCAACAACTTGTGTGGGCTTTCAAATGAGT
1 TGCCACTC-ACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGA--
** *
510228 TGCCACCAACTTGTTTGGGCTTGGAAATGGGT
63 TGCCACTGACTTG--TGGGCTTTGAAATGGGT
** * *
510260 TGCTGC-CAACTTGTGTGGGCTTTCAAATGAGTTGCCATCGACTTGTGTGGGCTTTGAAATGATG
1 TGCCACTC-ACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGATG
* *
510324 CCACTGACTTGTGAGCTTTGAAA--GGA
65 CCACTGACTTGTGGGCTTTGAAATGGGT
* *
510350 TGCCACTGAC-T-TGTGGGCTTTAAAATGA
1 TGCCACTCACTTGTGTGGGCTTTGAAATGA
510378 TGCCACTAAC
Statistics
Matches: 565, Mismatches: 70, Indels: 56
0.82 0.10 0.08
Matches are distributed among these distances:
83 1 0.00
84 29 0.05
85 90 0.16
86 26 0.05
87 2 0.00
88 37 0.07
89 2 0.00
90 27 0.05
91 3 0.01
92 192 0.34
93 2 0.00
94 40 0.07
95 1 0.00
96 113 0.20
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (92 bp):
TGCCACTCACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGATGC
CACTGACTTGTGGGCTTTGAAATGGGT
Found at i:510407 original size:28 final size:28
Alignment explanation
Indices: 509620--510881 Score: 540
Period size: 28 Copynumber: 43.4 Consensus size: 28
509610 TTCTTTTAAA
* *
509620 AAAGG-TGCCACTAACTTGTGTGAACTTTG
1 AAAGGTTGCCACTGACTTGTG-G-GCTTTG
*
509649 AAAAGAGTTGCCACCGACTTGTGTGGACTTTG
1 -AAAG-GTTGCCACTGACTTGTG-GG-CTTTG
*
509681 AAAAGAGTTACCACT-ACTTGTGGGCTTTG
1 -AAAG-GTTGCCACTGACTTGTGGGCTTTG
* *
509710 AAAAGAG-TGCCACTAACTTATGGGCTTTG
1 -AAAG-GTTGCCACTGACTTGTGGGCTTTG
* *
509739 AAAGGGTACCACTGACTTGTGGGCTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* *
509767 AAAGGGTGCCACTGACTTGTGGGTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* *
509795 AAAGGATGCCACTGACTTTTGGGCTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
** *
509823 AAAAGAATGCCACTGACTTTTGGGCTTTG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTG
* * *
509852 AAAGGGTGTCACTGACTTATGGGCTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* *
509880 AAAGGATGCCATTGACTTGTGGGCTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
**
509908 AAATGTGTTGCCACCAACTTGTGTGGGCTTTG
1 AAA-G-GTTGCCACTGAC-T-TGTGGGCTTTG
**
509940 AAATGGGTTGCCACCAACTTGTGTGGGCTTTG
1 AAA--GGTTGCCACTGAC-T-TGTGGGCTTTG
* ** *
509972 AAATGGGTTCCCACCAACTTGTGTGGGCTTTC
1 AAA--GGTTGCCACTGAC-T-TGTGGGCTTTG
*
510004 AAATGAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA-G-GTTGCCACTGAC-T-TGTGGGCTTTG
* *
510036 AAATGATGCCACTGACTTGTGGGCTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
*
510064 AAATGGGTTGCCACTCACTTGTGTGGGCTTTG
1 AAA--GGTTGCCACTGAC-T-TGTGGGCTTTG
510096 AAATGGGTTGCCACTGACTTGTGTGGGCTTTG
1 AAA--GGTTGCCACTGAC-T-TGTGGGCTTTG
* * *
510128 AAATGATGCCACTAACTTGTGGGCTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
*
510156 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA--GGTTGCCACTGAC-T-TGTGGGCTTTG
* * *
510188 CAATGGGTTGCCAAC-AACTTGTGTGGGCTTTC
1 -AA-AGGTTGCC-ACTGAC-T-TGTGGGCTTTG
** *
510220 AAATGAGTTGCCACCAACTTGTTTGGGCTTGG
1 AAA-G-GTTGCCACTGACTTG--TGGGCTTTG
** ** *
510252 AAATGGGTTGCTGCCAACTTGTGTGGGCTTTC
1 AAA--GGTTGCCACTGAC-T-TGTGGGCTTTG
510284 AAATGAGTTGCCA-TCGACTTGTGTGGGCTTTG
1 AAA-G-GTTGCCACT-GAC-T-TGTGGGCTTTG
* * *
510316 AAATGATGCCACTGACTTGTGAGCTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* *
510344 AAAGGATGCCACTGACTTGTGGGCTTTA
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * *
510372 AAATGATGCCACTAACTTGTGGGCTTTC
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * *
510400 AAAGGATGCTGCCACAGAGTTGTGGAC-TTA
1 AAAGG-T--TGCCACTGACTTGTGGGCTTTG
* * * * *
510430 AAAGGATGCCACGGAGTTGTGGAC-TTA
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * * * *
510457 AAAGGATGCCACAGAGTTAT-GGATTTA
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * * *
510484 AAAGGGTGCCA-TGGAGTGGTGGACTTTA
1 AAAGGTTGCCACT-GACTTGTGGGCTTTG
* * * * * *
510512 AAAGAG-TGTCACGGAGTTATGGACTTTA
1 AAAG-GTTGCCACTGACTTGTGGGCTTTG
** * * * * *
510540 AAAGGAAGCCACAGAGTTGTTGACTTTA
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * * *
510568 AAAGGATGCCACGGAGTTGTGGAC-TTA
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * * *
510595 AAAGGATGCCACGGA-GTGATGGACTTTA
1 AAAGGTTGCCACTGACTTG-TGGGCTTTG
* * * *
510623 AAAGGGTGCCACGGAGTTGTGGACTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * * *
510651 -AAGGATGCCACGGAGTTGTGGAC-TTA
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * * * *
510677 AAAGGATGCCACCGATTTGTAGACTTTA
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * ** *
510705 AAAGGGTGCCACGGAGTTGTGGATTTTA
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * * *
510733 AAAAGATGCCACAGAGTTGTGGACTTT-
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * * *
510760 AAAGGGTGCCACAGAGTTGTGGACTTTA
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * * *
510788 AAAGGGTGCCACGGAGTTGTGGACTTTA
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * *
510816 AAAGGGTGCCACGGAGTTGTGGACTTT-
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
* * * * *
510843 AAAGGATGCCACGGAGTTGTGGACTTTA
1 AAAGGTTGCCACTGACTTGTGGGCTTTG
*
510871 AAAGGGTGCCA
1 AAAGGTTGCCA
510882 TGGAGTTGAG
Statistics
Matches: 1053, Mismatches: 129, Indels: 102
0.82 0.10 0.08
Matches are distributed among these distances:
26 5 0.00
27 174 0.17
28 429 0.41
29 59 0.06
30 71 0.07
31 34 0.03
32 272 0.26
33 7 0.01
34 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTG
Found at i:510598 original size:83 final size:82
Alignment explanation
Indices: 510344--511169 Score: 988
Period size: 83 Copynumber: 10.0 Consensus size: 82
510334 GTGAGCTTTG
* * * * ** * * *
510344 AAAGGATGCCACTGACTTGTGGGCTTTAAAATGATGCCACTAACTTGTGGGCTTTCAAAGGATGC
1 AAAGG-TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGA---
*
510409 TGCCACAGAGTTGTGGACTTA
62 TGCCACGGAGTTGTGGACTTA
* * *
510430 AAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACAGAGTTATGGA-TTTAAAAGGGTGC
1 AAAGG-TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGC
* *
510493 CATGGAGTGGTGGACTTTA
65 CACGGAGTTGTGGAC-TTA
* * * * *
510512 AAAGAGTGTCACGGAGTTATGGACTTTAAAAGGAAGCCACAGAGTTGTTGACTTTAAAAGGATGC
1 AAAG-GTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGC
510577 CACGGAGTTGTGGACTTA
65 CACGGAGTTGTGGACTTA
* *
510595 AAAGGATGCCACGGAG-TGATGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-GAAGGATG
1 AAAGG-TGCCACGGAGTTG-TGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATG
510658 CCACGGAGTTGTGGACTTA
64 CCACGGAGTTGTGGACTTA
* * * * * *
510677 AAAGGATGCCACCGATTTGTAGACTTTAAAAGGGTGCCACGGAGTTGTGGATTTTAAAAAGATGC
1 AAAGG-TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGC
*
510742 CACAGAGTTGTGGACTTTA
65 CACGGAGTTGTGGAC-TTA
* * * *
510761 AAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCC
1 AAAGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCC
*
510826 ACGGAGTTGTGGACTTT
66 ACGGAGTTGTGGACTTA
* * *
510843 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCATGGAGTTGAGGACTTTAAAAGGATGC
1 AAAGG-TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGC
* *
510908 CATGGA-TTGGTGAACTTTA
65 CACGGAGTT-GTGGAC-TTA
* *
510927 AAAGGGTACCACGGAGTTGTGGACTTT-AAA-GAGTGCCACGGAGTTGTGGAC-TTAAAAGGATA
1 AAA-GGTGCCACGGAGTTGTGGACTTTAAAAGGA-TGCCACGGAGTTGTGGACTTTAAAAGGATG
510989 CCACGGAGTTGTGGACTTTA
64 CCACGGAGTTGTGGAC-TTA
* *
511009 AAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGATAC
1 AAA-GGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGC
511073 CACGGAGTTGTGGACTTTA
65 CACGGAGTTGTGGAC-TTA
*
511092 AAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGATGC
1 AAA-GGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGC
**
511156 CACAAAGTTGTGGA
65 CACGGAGTTGTGGA
511170 TTTTGAAAAG
Statistics
Matches: 659, Mismatches: 64, Indels: 37
0.87 0.08 0.05
Matches are distributed among these distances:
81 15 0.02
82 159 0.24
83 375 0.57
84 67 0.10
85 22 0.03
86 21 0.03
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.25
Consensus pattern (82 bp):
AAAGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCC
ACGGAGTTGTGGACTTA
Found at i:510760 original size:193 final size:194
Alignment explanation
Indices: 510322--511203 Score: 1068
Period size: 193 Copynumber: 4.5 Consensus size: 194
510312 TTTGAAATGA
* * * * * * * *
510322 TGCCACTGACTTGT-GAGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAATGATGCCACTA
1 TGCCACGGAGTTGTGGA-CTTTAAAAAGATGCCACAGAGTTGTGGACTTTAAAAGGATGCCAC-A
* * * * *
510386 -ACTTGTGGGCTTTCAAAGGATGCTGCCACAGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTG
64 GAGTTGTGGACTTTAAAAGGA---TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTG
* * * * * * * *
510449 TGGACTTAAAAGGATGCCACAGAGTTATGGATTTAAAAGGGTGCCATGGAGTGGTGGACTTTAAA
126 TGGACTTTAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTAGACTTTAAA
*
510514 AGAG
191 AGGG
* * * * * *
510518 TGTCACGGAGTTATGGACTTTAAAAGGAAGCCACAGAGTTGTTGACTTTAAAAGGATGCCACGGA
1 TGCCACGGAGTTGTGGACTTTAAAAAGATGCCACAGAGTTGTGGACTTTAAAAGGATGCCACAGA
510583 GTTGTGGAC-TTAAAAGGATGCCACGGAG-TGATGGACTTTAAAAGGGTGCCACGGAGTTGTGGA
66 GTTGTGGACTTTAAAAGGATGCCACGGAGTTG-TGGACTTTAAAAGGGTGCCACGGAGTTGTGGA
* * *
510646 CTTTGAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACCGATTTGTAGACTTTAAAAGGG
130 CTTTAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTAGACTTTAAAAGGG
* *
510711 TGCCACGGAGTTGTGGATTTTAAAAAGATGCCACAGAGTTGTGGACTTT-AAAGGGTGCCACAGA
1 TGCCACGGAGTTGTGGACTTTAAAAAGATGCCACAGAGTTGTGGACTTTAAAAGGATGCCACAGA
*
510775 GTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
66 GTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
* *
510840 TTTAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCATGGAGTTG-AGGACTTTAAAAGG
131 TTTAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTA-GACTTTAAAAGG
*
510904 A
194 G
* * * * * * *
510905 TGCCATGGA-TTGGTGAACTTTAAAAGGGTACCACGGAGTTGTGGACTTT-AAA-GAGTGCCACG
1 TGCCACGGAGTT-GTGGACTTTAAAAAGATGCCACAGAGTTGTGGACTTTAAAAGGA-TGCCACA
*
510967 GAGTTGTGGAC-TTAAAAGGATACCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGG
64 GAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGG
* * *
511031 ACTTTAAAAAGATGCCACGGAGTTGTGGACTTAAAAGGATACCACGGAGTTGTGGACTTTAAAAG
129 ACTTT-AAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTAGACTTTAAAAG
511096 GG
193 GG
* *
511098 TGCCACGGAGTTGTGGACTTTAAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACAAA
1 TGCCACGGAGTTGTGGACTTTAAAAAGATGCCACAGAGTTGTGGACTTTAAAAGGATGCCACAGA
* * * * *
511162 GTTGTGGATTTTGAAAAGAAATGCCACTGAATCGTGGACTTT
66 GTTGTGGACTTT-AAAAG-GATGCCACGGAGTTGTGGACTTT
511204 GAAGAGTCAT
Statistics
Matches: 594, Mismatches: 74, Indels: 36
0.84 0.11 0.05
Matches are distributed among these distances:
191 2 0.00
192 38 0.06
193 345 0.58
194 120 0.20
195 13 0.02
196 74 0.12
197 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.26
Consensus pattern (194 bp):
TGCCACGGAGTTGTGGACTTTAAAAAGATGCCACAGAGTTGTGGACTTTAAAAGGATGCCACAGA
GTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC
TTTAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTAGACTTTAAAAGGG
Found at i:510886 original size:28 final size:28
Alignment explanation
Indices: 510305--511203 Score: 1058
Period size: 28 Copynumber: 32.4 Consensus size: 28
510295 CATCGACTTG
* * * * *
510305 TGTGGGCTTTGAAATGATGCCACTGACT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* * *
510333 TGT-GAGCTTTGAAAGGATGCCACTGACT
1 TGTGGA-CTTTAAAAGGATGCCACGGAGT
* * ** *
510361 TGTGGGCTTTAAAATGATGCCACTAACT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* * *
510389 TGTGGGCTTTCAAAGGATGCTGCCACAGAGT
1 TGTGGACTTTAAAAGGA---TGCCACGGAGT
510420 TGTGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
510447 TGTGGAC-TTAAAAGGATGCCACAGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* * *
510474 TATGGA-TTTAAAAGGGTGCCATGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* *
510501 GGTGGACTTTAAAA-GAGTGTCACGGAGT
1 TGTGGACTTTAAAAGGA-TGCCACGGAGT
* * *
510529 TATGGACTTTAAAAGGAAGCCACAGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
510557 TGTTGACTTTAAAAGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
510585 TGTGGAC-TTAAAAGGATGCCACGGAG-
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
510611 TGATGGACTTTAAAAGGGTGCCACGGAGT
1 TG-TGGACTTTAAAAGGATGCCACGGAGT
*
510640 TGTGGACTTT-GAAGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* *
510667 TGTGGAC-TTAAAAGGATGCCACCGATT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* *
510694 TGTAGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* * *
510722 TGTGGATTTTAAAAAGATGCCACAGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* *
510750 TGTGGACTTT-AAAGGGTGCCACAGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
510777 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
510805 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
510833 TGTGGACTTT-AAAGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* *
510860 TGTGGACTTTAAAAGGGTGCCATGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* *
510888 TGAGGACTTTAAAAGGATGCCATGGA-T
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* * *
510915 TGGTGAACTTTAAAAGGGTACCACGGAGT
1 T-GTGGACTTTAAAAGGATGCCACGGAGT
510944 TGTGGACTTT-AAA-GAGTGCCACGGAGT
1 TGTGGACTTTAAAAGGA-TGCCACGGAGT
*
510971 TGTGGAC-TTAAAAGGATACCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
510998 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
511026 TGTGGACTTTAAAAAGATGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
511054 TGTGGAC-TTAAAAGGATACCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
511081 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
*
511109 TGTGGACTTTAAAAAGATGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
**
511137 TGTGGAC-TTAAAAGGATGCCACAAAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGT
* * * *
511164 TGTGGATTTTGAAAAGAAATGCCACTGAAT
1 TGTGGACTTT-AAAAG-GATGCCACGGAGT
*
511194 CGTGGACTTT
1 TGTGGACTTT
511204 GAAGAGTCAT
Statistics
Matches: 758, Mismatches: 87, Indels: 50
0.85 0.10 0.06
Matches are distributed among these distances:
26 7 0.01
27 271 0.36
28 429 0.57
29 12 0.02
30 25 0.03
31 14 0.02
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (28 bp):
TGTGGACTTTAAAAGGATGCCACGGAGT
Found at i:511165 original size:55 final size:56
Alignment explanation
Indices: 510305--511203 Score: 1058
Period size: 55 Copynumber: 16.2 Consensus size: 56
510295 CATCGACTTG
* * * * * * * *
510305 TGTGGGCTTTGAAATGATGCCACTGACTTGT-GAGCTTTGAAAGGATGCCACTGACT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGA-CTTTAAAAGGATGCCACGGAGT
* * ** * * * *
510361 TGTGGGCTTTAAAATGATGCCACTAACTTGTGGGCTTTCAAAGGATGCTGCCACAGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGA---TGCCACGGAGT
*
510420 TGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACAGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
* * * * *
510474 TATGGA-TTTAAAAGGGTGCCATGGAGTGGTGGACTTTAAAA-GAGTGTCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGA-TGCCACGGAGT
* * * *
510529 TATGGACTTTAAAAGGAAGCCACAGAGTTGTTGACTTTAAAAGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
*
510585 TGTGGAC-TTAAAAGGATGCCACGGAG-TGATGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTG-TGGACTTTAAAAGGATGCCACGGAGT
* * *
510640 TGTGGACTTT-GAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACCGATT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
* * * * *
510694 TGTAGACTTTAAAAGGGTGCCACGGAGTTGTGGATTTTAAAAAGATGCCACAGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
* * *
510750 TGTGGACTTT-AAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
*
510805 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
* * * *
510860 TGTGGACTTTAAAAGGGTGCCATGGAGTTGAGGACTTTAAAAGGATGCCATGGA-T
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
* * *
510915 TGGTGAACTTTAAAAGGGTACCACGGAGTTGTGGACTTT-AAA-GAGTGCCACGGAGT
1 T-GTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGA-TGCCACGGAGT
* *
510971 TGTGGAC-TTAAAAGGATACCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
* *
511026 TGTGGACTTTAAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGATACCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
* *
511081 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGATGCCACGGAGT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
** * * * *
511137 TGTGGAC-TTAAAAGGATGCCACAAAGTTGTGGATTTTGAAAAGAAATGCCACTGAAT
1 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTT-AAAAG-GATGCCACGGAGT
*
511194 CGTGGACTTT
1 TGTGGACTTT
511204 GAAGAGTCAT
Statistics
Matches: 739, Mismatches: 78, Indels: 50
0.85 0.09 0.06
Matches are distributed among these distances:
54 101 0.14
55 328 0.44
56 244 0.33
57 27 0.04
58 24 0.03
59 15 0.02
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (56 bp):
TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGT
Found at i:520892 original size:70 final size:70
Alignment explanation
Indices: 520810--520966 Score: 251
Period size: 70 Copynumber: 2.2 Consensus size: 70
520800 TCGGAGGAAT
**
520810 GGGGTTGGAGTATCCCCGATGATGACAATTTAAGCGAGAATAAGATTTGAATCTTGGTAAGTTTA
1 GGGGTTGGAGTATCCCCGATGATGACAATTTAAGCGAGAATAAGATTTGAATCTTGACAAGTTTA
520875 AAAAC
66 AAAAC
* **
520880 GGGGTTGGAGTATCCCTGATGATGGTAATTTAAGCGAGAATAAGATTTGAATCTTGACAAGTTTA
1 GGGGTTGGAGTATCCCCGATGATGACAATTTAAGCGAGAATAAGATTTGAATCTTGACAAGTTTA
*
520945 AAAGC
66 AAAAC
*
520950 GAGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
520967 TGGAGGAATG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 79 1.00
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (70 bp):
GGGGTTGGAGTATCCCCGATGATGACAATTTAAGCGAGAATAAGATTTGAATCTTGACAAGTTTA
AAAAC
Found at i:521931 original size:14 final size:14
Alignment explanation
Indices: 521912--522005 Score: 62
Period size: 14 Copynumber: 7.2 Consensus size: 14
521902 ATCACTGTTC
521912 ATCACTGTTCATGT
1 ATCACTGTTCATGT
*
521926 ATCACTATTC----
1 ATCACTGTTCATGT
521936 AT-ACTGTTCATGT
1 ATCACTGTTCATGT
**
521949 ATCACTGTGAATAGT
1 ATCACTGTTCAT-GT
*
521964 AT--C-GATACAT-T
1 ATCACTG-TTCATGT
*
521975 ATAACTGTTCATGT
1 ATCACTGTTCATGT
521989 ATCACTGTTCATGT
1 ATCACTGTTCATGT
522003 ATC
1 ATC
522006 GATACAGTGT
Statistics
Matches: 61, Mismatches: 8, Indels: 22
0.67 0.09 0.24
Matches are distributed among these distances:
9 6 0.10
10 2 0.03
11 3 0.05
12 1 0.02
13 11 0.18
14 34 0.56
15 4 0.07
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (14 bp):
ATCACTGTTCATGT
Found at i:521931 original size:24 final size:23
Alignment explanation
Indices: 521899--521956 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
521889 TACCCTTAAT
521899 TGTATCACTGTTCATCACTGTTCA
1 TGTATCACTGTTCAT-ACTGTTCA
*
521923 TGTATCACTATTCATACTGTTCA
1 TGTATCACTGTTCATACTGTTCA
521946 TGTATCACTGT
1 TGTATCACTGT
521957 GAATAGTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (23 bp):
TGTATCACTGTTCATACTGTTCA
Found at i:522535 original size:32 final size:34
Alignment explanation
Indices: 522494--522585 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 34
522484 CAAGTGATTG
522494 AGAGGTTCTATCTTAGCCTTAAAAGAT-A-GTGT
1 AGAGGTTCTATCTTAGCCTTAAAAGATAAGGTGT
522526 AGAGGTTCTATCTTAGCCTTTGTAAAAGATAGAGGTGT
1 AGAGGTTCTATCTTAGCC--T-TAAAAGATA-AGGTGT
* *
522564 A-AGGTTATACCTTAGCCTTAAA
1 AGAGGTTCTATCTTAGCCTTAAA
522586 GGTAAACAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
32 18 0.35
34 5 0.10
35 9 0.17
37 15 0.29
38 5 0.10
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.34
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCCTTAAAAGATAAGGTGT
Found at i:524140 original size:21 final size:21
Alignment explanation
Indices: 524116--524174 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
524106 TAATATTCTT
* *
524116 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
524137 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
** *
524158 GAGGAGAAAAGAAATGA
1 GAAAAGAAAATAAATGA
524175 GTTGCAAGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:525363 original size:13 final size:13
Alignment explanation
Indices: 525345--525370 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
525335 CAATTTTTTG
525345 TGTATCGATACAT
1 TGTATCGATACAT
525358 TGTATCGATACAT
1 TGTATCGATACAT
525371 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:525455 original size:20 final size:20
Alignment explanation
Indices: 525430--525502 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
525420 CAACTTTTTT
525430 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
525450 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
525471 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
525491 ATGTATCGATAC
1 ATGTATCGATAC
525503 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:525468 original size:41 final size:41
Alignment explanation
Indices: 525409--525502 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
525399 CTGCCAAGAA
*
525409 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
525450 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
525491 ATGTATCGATAC
1 ATGTATCGATAC
525503 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:525484 original size:21 final size:21
Alignment explanation
Indices: 525409--525484 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
525399 CTGCCAAGAA
* *
525409 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
525430 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
525450 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
525471 ATGTATCGATACAT
1 ATGTATCGATACAT
525485 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:526168 original size:21 final size:21
Alignment explanation
Indices: 526144--526185 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
526134 ATCTCCCCCT
526144 TAATCAAGTAATTCACAACAA
1 TAATCAAGTAATTCACAACAA
526165 TAATCAAGTAATTCACAACAA
1 TAATCAAGTAATTCACAACAA
526186 AAATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (21 bp):
TAATCAAGTAATTCACAACAA
Found at i:527991 original size:13 final size:13
Alignment explanation
Indices: 527973--528010 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
527963 ATAATCACCC
527973 TGTATCGATACAG
1 TGTATCGATACAG
*
527986 TGTATCGATACAT
1 TGTATCGATACAG
527999 TGTATCGATACA
1 TGTATCGATACA
528011 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:528024 original size:20 final size:20
Alignment explanation
Indices: 527999--528075 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
527989 ATCGATACAT
527999 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
528019 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
* *
528044 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAAA
528064 TGTATCGATACA
1 TGTATCGATACA
528076 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:530104 original size:15 final size:15
Alignment explanation
Indices: 530084--530114 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
530074 ATTTCGTTTG
*
530084 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
530099 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
530114 G
1 G
530115 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:534194 original size:13 final size:13
Alignment explanation
Indices: 534176--534201 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
534166 CAATTTTTTG
534176 TGTATCGATACAT
1 TGTATCGATACAT
534189 TGTATCGATACAT
1 TGTATCGATACAT
534202 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:534286 original size:20 final size:20
Alignment explanation
Indices: 534261--534333 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
534251 CAACTTTTTT
534261 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
534281 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
534302 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
534322 ATGTATCGATAC
1 ATGTATCGATAC
534334 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:534299 original size:41 final size:41
Alignment explanation
Indices: 534240--534333 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
534230 CTGCCAAGAA
*
534240 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
534281 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
534322 ATGTATCGATAC
1 ATGTATCGATAC
534334 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:534315 original size:21 final size:21
Alignment explanation
Indices: 534240--534315 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
534230 CTGCCAAGAA
* *
534240 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
534261 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
534281 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
534302 ATGTATCGATACAT
1 ATGTATCGATACAT
534316 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:537559 original size:13 final size:13
Alignment explanation
Indices: 537541--537567 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
537531 TCACTGTTCA
537541 TGTATCGATACAT
1 TGTATCGATACAT
537554 TGTATCGATACAT
1 TGTATCGATACAT
537567 T
1 T
537568 ATGAATAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:537638 original size:13 final size:13
Alignment explanation
Indices: 537616--537657 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
537606 TCACTGTTCA
*
537616 TGTATTGATACAT
1 TGTATCGATACAT
*
537629 TGTATCGATACAG
1 TGTATCGATACAT
*
537642 TGTATCGATGCAT
1 TGTATCGATACAT
537655 TGT
1 TGT
537658 GAATAGTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:539982 original size:20 final size:20
Alignment explanation
Indices: 539957--540082 Score: 74
Period size: 20 Copynumber: 5.8 Consensus size: 20
539947 TTTTAACTCG
539957 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
539977 ATGTATCGATACATCTGGGTAAAAA
1 ATGTATCGATACAT-T--G--AAAA
* *
540002 GACAGAATATATCGATATATT-AAAGA
1 -A-TG--T--ATCGATACATTGAAA-A
* * *
540028 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
540048 ATGTATCGATATATTGAAAA
1 ATGTATCGATACATTGAAAA
*
540068 ATGCATCGATACATT
1 ATGTATCGATACATT
540083 TGGGTACTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 26
0.68 0.10 0.22
Matches are distributed among these distances:
20 53 0.65
21 3 0.04
22 1 0.01
23 1 0.01
24 1 0.01
25 8 0.10
26 2 0.02
27 1 0.01
29 1 0.01
30 1 0.01
31 9 0.11
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:543010 original size:68 final size:69
Alignment explanation
Indices: 542920--543071 Score: 252
Period size: 69 Copynumber: 2.2 Consensus size: 69
542910 AGAGGAATGA
* *
542920 GGTTGGAGTATCCTCGACAATGATAA-TTGGACAAAATAAGACTTAAATTTCGATGAGTTTAAAA
1 GGTTGGAGTATCCCCGACAATGATAATTTAGACAAAATAAGACTTAAATTTCGATGAGTTTAAAA
542984 ACGG
66 ACGG
* * *
542988 GGTTGGAGTATCCCCGATAATGATAATTTAGACAAAATAAGATTTAAATTTCGATGAGTTTACAA
1 GGTTGGAGTATCCCCGACAATGATAATTTAGACAAAATAAGACTTAAATTTCGATGAGTTTAAAA
543053 ACGG
66 ACGG
543057 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
543072 TCGGAGAAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 24 0.31
69 54 0.69
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (69 bp):
GGTTGGAGTATCCCCGACAATGATAATTTAGACAAAATAAGACTTAAATTTCGATGAGTTTAAAA
ACGG
Found at i:543133 original size:97 final size:96
Alignment explanation
Indices: 542986--543168 Score: 235
Period size: 97 Copynumber: 1.9 Consensus size: 96
542976 GTTTAAAAAC
* * * *
542986 GGGGTTGGAGTATCCCCGATAATGATAATTTAGACAAAATAAGATTTAAATTTCGATGAGTTTAC
1 GGGGTAGGAGTATCCCCGATAATGACAATTTAGACAAAATAAGATTTAAATTTCGATAAATTTA-
* *
543051 AAA-CGGGGTTGGAGTATCCCCTCGGAGAAAT
65 AAAGCGGGGTTAGAGCATCCCCTCGGAGAAAT
* * * *
543082 GGGGTAGGAGTGTCCCTGATGATGACAATTTA-ACTAAAAATAAGATTTAAATTTTGATAAATTT
1 GGGGTAGGAGTATCCCCGATAATGACAATTTAGAC--AAAATAAGATTTAAATTTCGATAAATTT
543146 AAAAGCGGGGTTAGAGCATCCCC
64 AAAAGCGGGGTTAGAGCATCCCC
543169 GATAAACAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
95 2 0.03
96 30 0.41
97 42 0.57
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (96 bp):
GGGGTAGGAGTATCCCCGATAATGACAATTTAGACAAAATAAGATTTAAATTTCGATAAATTTAA
AAGCGGGGTTAGAGCATCCCCTCGGAGAAAT
Found at i:544952 original size:18 final size:19
Alignment explanation
Indices: 544929--544974 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
544919 TTTCTTTTAA
*
544929 TTTTTTATTAA-TTTGATT
1 TTTTTTATTAATTTTAATT
**
544947 TTTTTTAGAAATTTTAATT
1 TTTTTTATTAATTTTAATT
544966 TTTTTTATT
1 TTTTTTATT
544975 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (19 bp):
TTTTTTATTAATTTTAATT
Found at i:544985 original size:24 final size:26
Alignment explanation
Indices: 544957--545017 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 26
544947 TTTTTTAGAA
*
544957 ATTTTAATTTTTTTTATTTTA-AATT
1 ATTTTAATTTTTTTCATTTTATAATT
* * *
544982 -TTTTGATTGTTTTCATTTTATTATT
1 ATTTTAATTTTTTTCATTTTATAATT
545007 ATTTTAATTTT
1 ATTTTAATTTT
545018 ATATATAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 17 0.61
25 3 0.11
26 8 0.29
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (26 bp):
ATTTTAATTTTTTTCATTTTATAATT
Found at i:545019 original size:17 final size:16
Alignment explanation
Indices: 544923--545017 Score: 77
Period size: 16 Copynumber: 5.6 Consensus size: 16
544913 CCACTTTTTC
544923 TTTTAATTTTTTATTA
1 TTTTAATTTTTTATTA
* *
544939 ATTTGATTTTTT-TTAGAAA
1 TTTTAATTTTTTATT----A
544958 TTTTAATTTTTT-TTA
1 TTTTAATTTTTTATTA
*
544973 TTTTAAATTTTTTGATTG
1 TTTT-AATTTTTT-ATTA
*
544991 TTTTCATTTTATTATTA
1 TTTTAATTTT-TTATTA
545008 TTTTAATTTT
1 TTTTAATTTT
545018 ATATATAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
15 7 0.11
16 18 0.29
17 17 0.27
18 8 0.13
19 13 0.21
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTTAATTTTTTATTA
Found at i:546327 original size:62 final size:61
Alignment explanation
Indices: 546155--546359 Score: 288
Period size: 61 Copynumber: 3.3 Consensus size: 61
546145 TAGCCCTTGC
* * * *
546155 AGTCCTCAAAGAGCAGGACGCCTTTT-TTTTTCAAAGCGCACACGAGTTGGTGGCACCTT-T
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTCT
* *
546215 AGTCCTCAAAGAGTAGGACGCCTTTTTCCTTTTAAAGCTCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGACGCC-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCT
* * *
546278 AGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCT
546339 AGTCCTCAAAGAGCAGGACGC
1 AGTCCTCAAAGAGCAGGACGC
546360 TCTCTCCTTT
Statistics
Matches: 132, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
60 21 0.16
61 49 0.37
62 39 0.30
63 23 0.17
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (61 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCT
Found at i:546530 original size:61 final size:60
Alignment explanation
Indices: 546373--546634 Score: 295
Period size: 61 Copynumber: 4.4 Consensus size: 60
546363 CTCCTTTCGC
546373 CTTTT-AGTCCTCAAAGAGCAGGACG-C---CTTTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
546427 CTTTTCTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTCAAAGCCCACATAAGTTGGTGGCA
1 CTTTTC-AGTCCTCAAAGAGCAGGACG-CCTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
546489 TTTTTCAGTCCTCAAAGAGCAGGATG-CTTTCTCTTTGCAAAGCCCATACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCT-TTT-CAAAGCCCACACAAGTTGGTGGCA
* * * * * *
546550 CCTTCCAGTCTTCAAAGAACGGGACGCCTTTCTTTTTCAAAGCCCACACGAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTC-TTTTCAAAGCCCACACAAGTTGGTGGCA
* **
546611 CTTTTTAGTCCTCGTAGAGCAGGA
1 CTTTTCAGTCCTCAAAGAGCAGGA
546635 TACGTTCCAT
Statistics
Matches: 170, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
54 5 0.03
56 20 0.12
59 4 0.02
60 3 0.02
61 102 0.60
62 35 0.21
63 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (60 bp):
CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:546542 original size:217 final size:219
Alignment explanation
Indices: 546155--546576 Score: 570
Period size: 217 Copynumber: 1.9 Consensus size: 219
546145 TAGCCCTTGC
* *
546155 AGTCCTCAAAGAGCAGGACGCCTTTTTTTTTCAAAGCGCACACGAGTTGGTGGCACCTTTAGTCC
1 AGTCCTCAAAGAGCAGGACGCC----TTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCC
* * *
546220 TCAAAGAGTAGGACGCCTTTTTCCTTTTAAAGCTCACACAAGTTGGTGGCACTTTTCTAGTCCTC
62 TCAAAGAGCAGGACGCCTTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTC
* *
546285 AAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAA
127 AAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAA
*
546349 GAGCAGGACGCTCTCTCCTTTCGCCTTTT
191 GAACAGGACGCTCTCTCCTTTCGCCTTTT
*
546378 AGTCCTCAAAGAGCAGGACGCC-TTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCAAAGCCCACACAAGTTGGTGGCAC-CTT-TAGTCCTC
* * *
546441 AAAGAGCAGGACGTC-TTTTCCTTTCAAAGCCCACATAAGTTGGTGGCATTTTTC-AGTCCTCAA
64 AAAGAGCAGGACGCCTTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAA
* * *
546504 AGAGCAGGATG-C-TTTCTCTTTGCAAAGCCCATACAAGTTGGTGGCACCTTCCAGTCTTCAAAG
129 AGAGCAGGACGCCTTTTC-CTTT-CAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAG
*
546567 AACGGGACGC
192 AACAGGACGC
546577 CTTTCTTTTT
Statistics
Matches: 178, Mismatches: 16, Indels: 16
0.85 0.08 0.08
Matches are distributed among these distances:
215 4 0.02
216 5 0.03
217 82 0.46
218 44 0.25
219 21 0.12
223 22 0.12
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (219 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAA
AGAGCAGGACGCCTTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAG
AGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAACA
GGACGCTCTCTCCTTTCGCCTTTT
Found at i:546680 original size:47 final size:47
Alignment explanation
Indices: 546611--546815 Score: 192
Period size: 47 Copynumber: 4.5 Consensus size: 47
546601 GTTGGTGGCA
* ** *
546611 CTTTTTAGTCCTCGTAGAGCAGGATACGTTCCATTTCCTTATTTTCC
1 CTTTTTTGTCCTCAAAGAGCAGGACACGTTCCATTTCCTTATTTTCC
* * * *
546658 CTTTTTTGTCCTCAAAGAGCAGGACACATTTCATTTTCTT-CTTTCC
1 CTTTTTTGTCCTCAAAGAGCAGGACACGTTCCATTTCCTTATTTTCC
* * * * * *
546704 C-CTTTTGTCCTCAAAGAGTAGGACGCAGTT-TATTTTCC-TCTTCT-C
1 CTTTTTTGTCCTCAAAGAGCAGGACAC-GTTCCA-TTTCCTTATTTTCC
*
546749 C---TTTGTCCTCAAAGAGTAGGACACGTTCCATTTCCTTATTTTCC
1 CTTTTTTGTCCTCAAAGAGCAGGACACGTTCCATTTCCTTATTTTCC
*
546793 CCTTTTTGTCCTCAAAGAGCAGG
1 CTTTTTTGTCCTCAAAGAGCAGG
546816 GCGCACTTTA
Statistics
Matches: 128, Mismatches: 21, Indels: 18
0.77 0.13 0.11
Matches are distributed among these distances:
42 8 0.06
43 27 0.21
44 2 0.02
45 26 0.20
46 14 0.11
47 51 0.40
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (47 bp):
CTTTTTTGTCCTCAAAGAGCAGGACACGTTCCATTTCCTTATTTTCC
Found at i:546727 original size:45 final size:44
Alignment explanation
Indices: 546661--546881 Score: 202
Period size: 42 Copynumber: 5.0 Consensus size: 44
546651 ATTTTCCCTT
546661 TTTTGTCCTCAAAGAGCAGGACACATTTCATTTTCTTCTTTCCCC
1 TTTTGTCCTCAAAGAGCAGGACACATTT-ATTTTCTTCTTTCCCC
* * * *
546706 TTTTGTCCTCAAAGAGTAGGACGCAGTTTATTTTCCTC-TTCTCC
1 TTTTGTCCTCAAAGAGCAGGACACA-TTTATTTTCTTCTTTCCCC
* * * * *
546750 -TTTGTCCTCAAAGAGTAGGACACGTTCCATTTCCTTATTTTCCCC
1 TTTTGTCCTCAAAGAGCAGGACACATT-TATTTTCTT-CTTTCCCC
* *
546795 TTTTTGTCCTCAAAGAGCAGGGCGCACTTTATTTTCCTT-TTT---C
1 -TTTTGTCCTCAAAGAGCAGGACACA-TTTATTTT-CTTCTTTCCCC
* *
546838 TTTTGTCCTCAAAAAGCAGGACACATTTTATTTTCCTTTTTTCC
1 TTTTGTCCTCAAAGAGCAGGACACA-TTTATTTT-CTTCTTTCC
546882 TTTTCCTCGA
Statistics
Matches: 144, Mismatches: 21, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
42 36 0.25
43 32 0.22
44 5 0.03
45 36 0.25
46 6 0.04
47 24 0.17
48 5 0.03
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (44 bp):
TTTTGTCCTCAAAGAGCAGGACACATTTATTTTCTTCTTTCCCC
Found at i:546801 original size:135 final size:131
Alignment explanation
Indices: 546626--546900 Score: 367
Period size: 135 Copynumber: 2.1 Consensus size: 131
546616 TAGTCCTCGT
* *
546626 AGAGCAGGATACGTTCCATTTCCTTATTTTCCCTTTTTTGTCCTCAAAGAGCAGGACACA-TTTC
1 AGAGCAGGACACGTTCCATTTCCTTATTTTCCCCTTTTTGTCCTCAAAGAGCAGGACACACTTT-
* * *
546690 ATTTT-CTTCTTTCCCCTTTTGTCCTCAAAGAGTAGGACGCAGTTTATTTTCCTCTTCTCCTTTG
65 ATTTTCCTT-TTT---CTTTTGTCCTCAAAAAGCAGGACACAGTTTATTTTCCTCTTCTCCTTT-
546754 TCCTCAA
125 TCCTCAA
* * *
546761 AGAGTAGGACACGTTCCATTTCCTTATTTTCCCCTTTTTGTCCTCAAAGAGCAGGGCGCACTTTA
1 AGAGCAGGACACGTTCCATTTCCTTATTTTCCCCTTTTTGTCCTCAAAGAGCAGGACACACTTTA
* * *
546826 TTTTCCTTTTTCTTTTGTCCTCAAAAAGCAGGACACATTTTATTTTCCTTTTTTCCTTTTCCTCG
66 TTTTCCTTTTTCTTTTGTCCTCAAAAAGCAGGACACAGTTTATTTTCCTCTTCTCCTTTTCCTC-
546891 AA
130 AA
546893 A-AGCAGGA
1 AGAGCAGGA
546901 TGCACTCTTT
Statistics
Matches: 125, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
131 11 0.09
132 45 0.36
135 63 0.50
136 6 0.05
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.40
Consensus pattern (131 bp):
AGAGCAGGACACGTTCCATTTCCTTATTTTCCCCTTTTTGTCCTCAAAGAGCAGGACACACTTTA
TTTTCCTTTTTCTTTTGTCCTCAAAAAGCAGGACACAGTTTATTTTCCTCTTCTCCTTTTCCTCA
A
Found at i:546880 original size:89 final size:89
Alignment explanation
Indices: 546661--546881 Score: 304
Period size: 89 Copynumber: 2.5 Consensus size: 89
546651 ATTTTCCCTT
* *
546661 TTTTGTCCTCAAAGAGCAGGACACATTTCATTTT-CTTCTTTCCCCTTTTGTCCTCAAAGAGTAG
1 TTTTGTCCTCAAAGAGCAGGACACATTTCATTTTCCTTTTTTCCCCTTTTGTCCTCAAAGAGCAG
*
546725 GACGCAGTTTATTTTCCTCTTCTC
66 GACGCACTTTATTTTCCTCTTCTC
* * * *
546749 CTTTGTCCTCAAAGAGTAGGACACGTTCCA-TTTCCTTATTTTCCCCTTTTTGTCCTCAAAGAGC
1 TTTTGTCCTCAAAGAGCAGGACACATTTCATTTTCCTT-TTTTCCCC-TTTTGTCCTCAAAGAGC
* *
546813 AGGGCGCACTTTATTTTCCT-TTTTC
64 AGGACGCACTTTATTTTCCTCTTCTC
* *
546838 TTTTGTCCTCAAAAAGCAGGACACATTTTATTTTCCTTTTTTCC
1 TTTTGTCCTCAAAGAGCAGGACACATTTCATTTTCCTTTTTTCC
546882 TTTTCCTCGA
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
87 3 0.03
88 29 0.25
89 41 0.36
90 41 0.36
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (89 bp):
TTTTGTCCTCAAAGAGCAGGACACATTTCATTTTCCTTTTTTCCCCTTTTGTCCTCAAAGAGCAG
GACGCACTTTATTTTCCTCTTCTC
Found at i:546932 original size:35 final size:36
Alignment explanation
Indices: 546870--546986 Score: 120
Period size: 39 Copynumber: 3.2 Consensus size: 36
546860 ACATTTTATT
546870 TTCCTTTTTTC-CTTT-TCCTCGAA-AAGCAGGATGCAC
1 TTCCTTTTTTCACTTTGTCCTC-AAGAAGCAGGA--CAC
546906 -T-C-TTTTTCACTTTGTCCTCAAGAAGCAGGACAC
1 TTCCTTTTTTCACTTTGTCCTCAAGAAGCAGGACAC
*
546939 TTTCCTTTTCTTTCACTTTGTCTTCAAGAAGCAGGACAC
1 -TTCC-TTT-TTTCACTTTGTCCTCAAGAAGCAGGACAC
546978 TTTCCTTTT
1 -TTCCTTTT
546987 CTTTCTTCCT
Statistics
Matches: 71, Mismatches: 1, Indels: 17
0.80 0.01 0.19
Matches are distributed among these distances:
33 9 0.13
34 7 0.10
35 15 0.21
36 1 0.01
37 1 0.01
38 5 0.07
39 33 0.46
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (36 bp):
TTCCTTTTTTCACTTTGTCCTCAAGAAGCAGGACAC
Found at i:546966 original size:39 final size:39
Alignment explanation
Indices: 546910--547046 Score: 159
Period size: 39 Copynumber: 3.4 Consensus size: 39
546900 ATGCACTCTT
546910 TTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCTTTTC
1 TTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCTTTTC
*
546949 TTTCACTTTGTCTTCAAGAAGCAGGACACTTTCCTTTTC
1 TTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCTTTTC
* * * * * * *
546988 TTTCTTCCTTTGTCCTTAAGGAGCAAGACCCATTTCATTCTC
1 TTTC--ACTTTGTCCTCAAGAAGCAGGACAC-TTTCCTTTTC
547030 TTTTC-CTTTGTCCTCAA
1 -TTTCACTTTGTCCTCAA
547047 AAGTGGGACA
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
39 42 0.50
40 11 0.13
41 19 0.23
42 8 0.10
43 4 0.05
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.42
Consensus pattern (39 bp):
TTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCTTTTC
Found at i:547700 original size:49 final size:49
Alignment explanation
Indices: 547646--547808 Score: 153
Period size: 49 Copynumber: 3.7 Consensus size: 49
547636 TCAAAATTTA
*
547646 TATCGATACATTGTTCATTGCATCGATACATTTTGGGTTTACCCAAATG
1 TATCGATACATTGTTCATTGTATCGATACATTTTGGGTTTACCCAAATG
* *
547695 TATCGATACATTTTTCATTGTATCGATACA--TT--GTTT-----ATTG
1 TATCGATACATTGTTCATTGTATCGATACATTTTGGGTTTACCCAAATG
* *
547735 TATCGATACATTG-------TATCGATACATTCTGGGTTTACCCAGATG
1 TATCGATACATTGTTCATTGTATCGATACATTTTGGGTTTACCCAAATG
547777 TATCGATACATT-TTGCATTGTATCGATACATT
1 TATCGATACATTGTT-CATTGTATCGATACATT
547809 GCTCATTGTA
Statistics
Matches: 90, Mismatches: 7, Indels: 34
0.69 0.05 0.26
Matches are distributed among these distances:
33 10 0.11
35 1 0.01
37 4 0.04
40 15 0.17
42 14 0.16
45 4 0.04
47 2 0.02
49 40 0.44
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (49 bp):
TATCGATACATTGTTCATTGTATCGATACATTTTGGGTTTACCCAAATG
Found at i:547718 original size:20 final size:20
Alignment explanation
Indices: 547693--547868 Score: 125
Period size: 20 Copynumber: 8.7 Consensus size: 20
547683 TTTACCCAAA
547693 TGTATCGATACATTTTTCAT
1 TGTATCGATACATTTTTCAT
547713 TGTATCGATACATTGTTT-AT
1 TGTATCGATACATT-TTTCAT
547733 TGTATCGAT--A-----CAT
1 TGTATCGATACATTTTTCAT
*
547746 TGTATCGATACATTCTGGGTTTACCCAGA
1 TGTATCGATACA-T-T---TTT---CA-T
*
547775 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTTTCAT
**
547795 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTTTTCAT
* **
547815 TGTATCAATACATTACTCAT
1 TGTATCGATACATTTTTCAT
* *
547835 TGTATCGATACATTTTACAG
1 TGTATCGATACATTTTTCAT
547855 TGTATCGATACATT
1 TGTATCGATACATT
547869 CAGGCATTTT
Statistics
Matches: 125, Mismatches: 13, Indels: 36
0.72 0.07 0.21
Matches are distributed among these distances:
13 11 0.09
15 1 0.01
18 1 0.01
20 89 0.71
21 5 0.04
24 2 0.02
27 1 0.01
28 3 0.02
29 12 0.10
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTTTTCAT
Found at i:547728 original size:13 final size:13
Alignment explanation
Indices: 547710--547759 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
547700 ATACATTTTT
547710 CATTGTATCGATA
1 CATTGTATCGATA
547723 CATTGT-T---TA
1 CATTGTATCGATA
547732 --TTGTATCGATA
1 CATTGTATCGATA
547743 CATTGTATCGATA
1 CATTGTATCGATA
547756 CATT
1 CATT
547760 CTGGGTTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
7 4 0.13
8 1 0.03
9 2 0.06
11 2 0.06
12 1 0.03
13 21 0.68
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:547765 original size:82 final size:82
Alignment explanation
Indices: 547661--547828 Score: 273
Period size: 82 Copynumber: 2.0 Consensus size: 82
547651 ATACATTGTT
* *
547661 CATTGCATCGATACATTTTGGGTTTACCCAAATGTATCGATACATTTTTCATTGTATCGATACAT
1 CATTGCATCGATACATTCTGGGTTTACCCAAATGTATCGATACATTTTGCATTGTATCGATACAT
* * *
547726 TGTTTATTGTATCGATA
66 TGCTCATTGTATCAATA
* *
547743 CATTGTATCGATACATTCTGGGTTTACCCAGATGTATCGATACATTTTGCATTGTATCGATACAT
1 CATTGCATCGATACATTCTGGGTTTACCCAAATGTATCGATACATTTTGCATTGTATCGATACAT
547808 TGCTCATTGTATCAATA
66 TGCTCATTGTATCAATA
547825 CATT
1 CATT
547829 ACTCATTGTA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (82 bp):
CATTGCATCGATACATTCTGGGTTTACCCAAATGTATCGATACATTTTGCATTGTATCGATACAT
TGCTCATTGTATCAATA
Found at i:548747 original size:51 final size:51
Alignment explanation
Indices: 548658--548835 Score: 211
Period size: 51 Copynumber: 3.5 Consensus size: 51
548648 TAATTTCTAG
* * * *
548658 ATTTTTCAT-CTCGGGGATA-TCCAA-TCCCGGTTTCATTTCCAAAACATCA
1 ATTTTTCATAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACCA
* * *
548707 ATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACCC
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCA
* *
548758 ATTTTCCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAATACCGA
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACC-A
* *
548810 A-TTTTCACAATCGAGGATACTCCAAC
1 ATTTTTCATAATCGGGGATACTCCAAC
548836 CCCGTTATTT
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
49 8 0.07
50 9 0.08
51 91 0.83
52 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (51 bp):
ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCA
Found at i:549018 original size:78 final size:78
Alignment explanation
Indices: 548771--549196 Score: 481
Period size: 79 Copynumber: 5.5 Consensus size: 78
548761 TTCCATAATC
* * * * *
548771 GGGGATACTCCAACTCCGATTTTATTTCCAAAATACCGAATTTTCACAATCGAGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATC-AATTTTCATAATCGGGGATACTCCAAC
548836 CCCGTTA-TTTCTGA
65 CCCGTTATTTTC-GA
* *
548850 GGGGACACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCAT--T-GGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATCAA-TTTTCATAATCGGGGATACTCCAAC
* *
548912 CCCATTATTTTTGA
65 CCCGTTATTTTCGA
* * *
548926 GAGGATAC-CCAACCCCGACTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCC-AC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATCAATTT-TCATAATCGGGGATACTCCAAC
*
548989 CCCATTATTTTCGA
65 CCCGTTATTTTCGA
* * *
549003 GGGGATACTCCAACCCCGGA-TTTATTTCTAAAACATCAAATTTTTATAGTCGGGGATACTCCAA
1 GGGGATACTCCAACCCC-GATTTTATTTCTAAAATATC-AATTTTCATAATCGGGGATACTCCAA
* *
549067 CCCTGTTATTTCCGA
64 CCCCGTTATTTTCGA
* * * * * *
549082 GGAGATACTCCAATCCCGATTTTATTTCGAAATTATCGATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATC-AATTTTCATAATCGGGGATACTCCAAC
*
549147 CCCGTTATTTTCAA
65 CCCGTTATTTTCGA
* *
549161 GGGGATACTCCAACCCCG-TTATTATCTCCAAAATAT
1 GGGGATACTCCAACCCCGATT-TTATTTCTAAAATAT
549197 TAAATTGCTC
Statistics
Matches: 294, Mismatches: 41, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
74 3 0.01
75 31 0.11
76 27 0.09
77 27 0.09
78 57 0.19
79 149 0.51
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATATCAATTTTCATAATCGGGGATACTCCAACC
CCGTTATTTTCGA
Found at i:550321 original size:13 final size:13
Alignment explanation
Indices: 550303--550328 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
550293 GTGCATATAC
550303 TATAATTTTATCA
1 TATAATTTTATCA
550316 TATAATTTTATCA
1 TATAATTTTATCA
550329 ATCATATAAG
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TATAATTTTATCA
Found at i:550508 original size:18 final size:19
Alignment explanation
Indices: 550485--550521 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
550475 ATAAAATAGT
550485 TAATAATA-TTTTCATCAA
1 TAATAATATTTTTCATCAA
550503 TAATAATATTTTTCATCAA
1 TAATAATATTTTTCATCAA
550522 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATAATATTTTTCATCAA
Found at i:550531 original size:19 final size:19
Alignment explanation
Indices: 550489--550532 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
550479 AATAGTTAAT
*
550489 AATA-TTTTCATCAATAAT
1 AATATTTTTCATCAATAAA
550507 AATATTTTTCATCAA-AAA
1 AATATTTTTCATCAATAAA
550525 AATTATTT
1 AA-TATTT
550533 CTAACAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (19 bp):
AATATTTTTCATCAATAAA
Found at i:550899 original size:26 final size:27
Alignment explanation
Indices: 550842--550913 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 27
550832 AAAGAAGTAT
*
550842 ATAAAATATAAATAT-T-AAATATTAA
1 ATAAAATATAAATATATAAAAAATTAA
550867 ATAAAATATAAATATATAAAAAATT-A
1 ATAAAATATAAATATATAAAAAATTAA
* * *
550893 ATCAAATATAATTAAATAAAA
1 ATAAAATATAAATATATAAAA
550914 TGTAAATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
25 15 0.37
26 20 0.49
27 6 0.15
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (27 bp):
ATAAAATATAAATATATAAAAAATTAA
Found at i:550913 original size:41 final size:41
Alignment explanation
Indices: 550839--550940 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 41
550829 TCAAAAGAAG
* *
550839 TATATAAAATATAAATATTAA-AT-ATTAAATAAAATATAAA
1 TATATAAAAAATAAATA-AAATATAATTAAATAAAATATAAA
* * *
550879 TATATAAAAAATTAATCAAATATAATTAAATAAAATGTAAA
1 TATATAAAAAATAAATAAAATATAATTAAATAAAATATAAA
*
550920 TATATAATAAATAAATAAAAT
1 TATATAAAAAATAAATAAAAT
550941 TGTATGTCCA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
39 2 0.04
40 16 0.31
41 34 0.65
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (41 bp):
TATATAAAAAATAAATAAAATATAATTAAATAAAATATAAA
Found at i:550930 original size:18 final size:19
Alignment explanation
Indices: 550839--550930 Score: 82
Period size: 18 Copynumber: 4.6 Consensus size: 19
550829 TCAAAAGAAG
550839 TATATAAAATATAAATATTAAA
1 TATAT-AAATA-AAATA-TAAA
550861 TAT-TAAATAAAATATAAA
1 TATATAAATAAAATATAAA
*
550879 TATATAAA-AAATTAATCAAA
1 TATATAAATAAAAT-AT-AAA
*
550899 TATAATTAAATAAAATGTAAA
1 TAT-A-TAAATAAAATATAAA
550920 TATAT-AATAAA
1 TATATAAATAAA
550931 TAAATAAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
18 17 0.28
19 12 0.20
20 12 0.20
21 8 0.13
22 8 0.13
23 4 0.07
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (19 bp):
TATATAAATAAAATATAAA
Found at i:551032 original size:145 final size:145
Alignment explanation
Indices: 550873--551165 Score: 559
Period size: 145 Copynumber: 2.0 Consensus size: 145
550863 TTAAATAAAA
550873 TATAAATATATAAAAAATTAATCAAATATAATTAAATAAAATGTAAATATATAATAAATAAATAA
1 TATAAATATATAAAAAATTAATCAAATATAATTAAATAAAATGTAAATATATAATAAATAAATAA
* **
550938 AATTGTATGTCCAGAGTTGTATAAAAAATAAAAAAACATACATCACTATGGATGCGAAATAGTTA
66 AATTGTATGTCCAGAGTTGTATAAAAAATAAAAAAACATACATCACTATGGATGCGAAAGAGGGA
551003 ACGATGGAAGGTTGC
131 ACGATGGAAGGTTGC
551018 TATAAATATATAAAAAATTAATCAAATATAATTAAATAAAATGTAAATATATAATAAATAAATAA
1 TATAAATATATAAAAAATTAATCAAATATAATTAAATAAAATGTAAATATATAATAAATAAATAA
551083 AATTGTATGTCCAGAGTTGTATAAAAAATAAAAAAACATACATCACTATGGATGCGAAAGAGGGA
66 AATTGTATGTCCAGAGTTGTATAAAAAATAAAAAAACATACATCACTATGGATGCGAAAGAGGGA
551148 ACGATGGAAGGTTGC
131 ACGATGGAAGGTTGC
551163 TAT
1 TAT
551166 TGTTAGAACT
Statistics
Matches: 145, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.28
Consensus pattern (145 bp):
TATAAATATATAAAAAATTAATCAAATATAATTAAATAAAATGTAAATATATAATAAATAAATAA
AATTGTATGTCCAGAGTTGTATAAAAAATAAAAAAACATACATCACTATGGATGCGAAAGAGGGA
ACGATGGAAGGTTGC
Found at i:552369 original size:13 final size:13
Alignment explanation
Indices: 552351--552376 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
552341 TTATAGATTT
552351 ATTTTAATTTAAA
1 ATTTTAATTTAAA
552364 ATTTTAATTTAAA
1 ATTTTAATTTAAA
552377 CATAAAAAAC
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTTAATTTAAA
Found at i:553176 original size:20 final size:20
Alignment explanation
Indices: 553110--553178 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
553100 TAAAAGATTT
*
553110 ATTTAATTAAAAAATAAATTTA
1 ATTTAATTAAAAGATAAA--TA
* * * * *
553132 TTTTTTATTAAAAGTTTAATC
1 -ATTTAATTAAAAGATAAATA
553153 ATTTAATTAAAAGATAAATA
1 ATTTAATTAAAAGATAAATA
553173 ATTTAA
1 ATTTAA
553179 AAGTTTAATT
Statistics
Matches: 35, Mismatches: 11, Indels: 3
0.71 0.22 0.06
Matches are distributed among these distances:
20 21 0.60
21 1 0.03
23 13 0.37
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (20 bp):
ATTTAATTAAAAGATAAATA
Found at i:554631 original size:13 final size:16
Alignment explanation
Indices: 554612--554649 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 16
554602 TGCCTTTAGT
554612 TTTAAAATAA-ATT-A
1 TTTAAAATAAGATTAA
554626 -TTAAAATAAGATTAA
1 TTTAAAATAAGATTAA
554641 TTTAAAATA
1 TTTAAAATA
554650 TTTTATCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.43
14 3 0.14
15 1 0.05
16 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TTTAAAATAAGATTAA
Found at i:555273 original size:2 final size:2
Alignment explanation
Indices: 555266--555308 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
555256 GGCTATTTAC
555266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
555308 A
1 A
555309 CACAACACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:555415 original size:20 final size:20
Alignment explanation
Indices: 555390--555438 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
555380 TTTCTACGAG
555390 TTTATTAATAACCCTAATCT
1 TTTATTAATAACCCTAATCT
* *
555410 TTTATTAATAACCTTAATTT
1 TTTATTAATAACCCTAATCT
555430 TTTATTAAT
1 TTTATTAAT
555439 TTGAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATTAATAACCCTAATCT
Found at i:555485 original size:22 final size:22
Alignment explanation
Indices: 555460--555565 Score: 78
Period size: 22 Copynumber: 4.8 Consensus size: 22
555450 ATAATAATTT
555460 TAATAATATAAATAAATAATAA
1 TAATAATATAAATAAATAATAA
* *
555482 TAATTTAATAT--ATAATTAAGAA
1 TAA--TAATATAAATAAATAATAA
* *
555504 TAATAATATAAA-AATTAACATGA
1 TAATAATATAAATAAAT-A-ATAA
555527 TAATAATATAAATAAA-AATTAA
1 TAATAATATAAATAAATAA-TAA
* *
555549 TAACATTAT-AATAAATA
1 TAATAATATAAATAAATA
555566 TTAACCCTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
20 6 0.09
21 11 0.16
22 28 0.42
23 14 0.21
24 8 0.12
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATAATATAAATAAATAATAA
Found at i:555509 original size:31 final size:28
Alignment explanation
Indices: 555445--555511 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
555435 TAATTTGAAA
555445 AAATAATAATAATTTTAATAATATAAAT
1 AAATAATAATAATTTTAATAATATAAAT
*
555473 AAATAATAATAA-TTTAAT-ATATAATT
1 AAATAATAATAATTTTAATAATATAAAT
555499 AAGAATAATAATA
1 -A-AATAATAATA
555512 TAAAAATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 7 0.19
27 7 0.19
28 22 0.61
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (28 bp):
AAATAATAATAATTTTAATAATATAAAT
Found at i:555512 original size:20 final size:21
Alignment explanation
Indices: 555487--555538 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
555477 AATAATAATT
* *
555487 TAATATATAATTAAGA-ATAA
1 TAATATAAAATTAACAGATAA
555507 TAATATAAAAATTAACATGATAA
1 TAATAT-AAAATTAACA-GATAA
555530 TAATATAAA
1 TAATATAAA
555539 TAAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 6 0.22
21 8 0.30
22 3 0.11
23 10 0.37
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
TAATATAAAATTAACAGATAA
Found at i:555559 original size:27 final size:28
Alignment explanation
Indices: 555506--555566 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
555496 ATTAAGAATA
**
555506 ATAATATAAAAATTAACATGATAATAAT
1 ATAATATAAAAATTAACAACATAATAAT
* *
555534 ATAA-ATAAAAATTAATAACATTATAAT
1 ATAATATAAAAATTAACAACATAATAAT
555561 A-AATAT
1 ATAATAT
555567 TAACCCTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.07
27 22 0.79
28 4 0.14
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (28 bp):
ATAATATAAAAATTAACAACATAATAAT
Found at i:555578 original size:38 final size:37
Alignment explanation
Indices: 555535--555606 Score: 108
Period size: 38 Copynumber: 1.9 Consensus size: 37
555525 GATAATAATA
*
555535 TAAATAAAAATTAATAACATTATAATAAATATTAACCC
1 TAAATAAAAATTAATAACATTATAAAAAAT-TTAACCC
**
555573 TAAATAAAAATTAATATTATTATAAAAAATTTAA
1 TAAATAAAAATTAATAACATTATAAAAAATTTAA
555607 TAAATTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 4 0.13
38 27 0.87
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (37 bp):
TAAATAAAAATTAATAACATTATAAAAAATTTAACCC
Found at i:555613 original size:19 final size:19
Alignment explanation
Indices: 555578--555615 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
555568 AACCCTAAAT
*
555578 AAAAATTAATATTATTATA
1 AAAAATTAATATAATTATA
555597 AAAAATTTAATA-AATTATA
1 AAAAA-TTAATATAATTATA
555616 TTTAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTAATATAATTATA
Found at i:555836 original size:29 final size:29
Alignment explanation
Indices: 555789--555861 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
555779 CACTATACAT
* *
555789 TAATATTTTTATATTAAATTCTTTA-AAAAA
1 TAATATTTTAATA-AAAATT-TTTATAAAAA
*
555819 TAATATTTTAATAAAAATTTTTATATAAA
1 TAATATTTTAATAAAAATTTTTATAAAAA
**
555848 TCCTATTTTAATAA
1 TAATATTTTAATAA
555862 TTTATTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.11
29 21 0.57
30 12 0.32
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (29 bp):
TAATATTTTAATAAAAATTTTTATAAAAA
Found at i:557339 original size:20 final size:23
Alignment explanation
Indices: 557292--557341 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 23
557282 TATAAAATTA
557292 AAATTT-ATTTATTATTCATATT
1 AAATTTAATTTATTATTCATATT
*
557314 ACATTTAATTTA-TATT-AT-TT
1 AAATTTAATTTATTATTCATATT
557334 AAATTTAA
1 AAATTTAA
557342 ATTAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 9 0.36
21 2 0.08
22 9 0.36
23 5 0.20
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATTTAATTTATTATTCATATT
Found at i:557375 original size:17 final size:17
Alignment explanation
Indices: 557342--557399 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
557332 TTAAATTTAA
*
557342 ATTAAATA-ATATTATTT
1 ATTAAATATATA-AATTT
* *
557359 ATTAAATATCTGAATTT
1 ATTAAATATATAAATTT
557376 ATTAAATATATAAATTT
1 ATTAAATATATAAATTT
*
557393 AATAAAT
1 ATTAAAT
557400 TAATTTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 33 0.97
18 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTAAATATATAAATTT
Found at i:557505 original size:30 final size:28
Alignment explanation
Indices: 557461--557535 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 28
557451 TAATATAATT
* * *
557461 AATTAATTAAATTTTATAATTAATTTTAT
1 AATT-ATTATATTTTATAAATAATTTTAA
* *
557490 TATTATATATTATTTTAAAAATAATTTTAA
1 AATTAT-TA-TATTTTATAAATAATTTTAA
557520 AATTATTATATTTTAT
1 AATTATTATATTTTAT
557536 TACAATTGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 9 0.24
29 7 0.19
30 21 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTATTATATTTTATAAATAATTTTAA
Found at i:558100 original size:2 final size:2
Alignment explanation
Indices: 558093--558122 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
558083 CATGATATTG
558093 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
558123 GACAAGGTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:558567 original size:19 final size:19
Alignment explanation
Indices: 558543--558580 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
558533 TCAAAATCTC
558543 GCTTGATATTTGGAGGGAT
1 GCTTGATATTTGGAGGGAT
558562 GCTTGATATTTGGAGGGAT
1 GCTTGATATTTGGAGGGAT
558581 TTGGATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.37, T:0.37
Consensus pattern (19 bp):
GCTTGATATTTGGAGGGAT
Found at i:558819 original size:34 final size:35
Alignment explanation
Indices: 558776--558846 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 35
558766 GCAAAAAAAG
558776 ACAATTGTCCTAGATGGATAGCTTAAA-TTTTGGC
1 ACAATTGTCCTAGATGGATAGCTTAAATTTTTGGC
558810 ACAATTGTCCTAGATGGATAGCTTAAATTTTTGGC
1 ACAATTGTCCTAGATGGATAGCTTAAATTTTTGGC
558845 AC
1 AC
558847 GTAAATTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 27 0.75
35 9 0.25
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (35 bp):
ACAATTGTCCTAGATGGATAGCTTAAATTTTTGGC
Found at i:563524 original size:2 final size:2
Alignment explanation
Indices: 563519--563566 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
563509 TTAGTGTGTG
563519 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
563561 TA TA TA
1 TA TA TA
563567 AGATTGCATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:564124 original size:3 final size:3
Alignment explanation
Indices: 564116--564156 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
564106 TTGGAACCTC
564116 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
564157 GGTTCCCCCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:564686 original size:41 final size:41
Alignment explanation
Indices: 564566--564705 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 41
564556 TCCCTCAGTG
* *
564566 TAAAAACGCCGCTAATAATAAAAATTTAGCAGTGTTCACCA
1 TAAAAACGCCGCTAATAAGAAAAATTTAGCAGTGTTCATCA
* * * *
564607 TAAAAACGCTGCTAATAAGAAAAATTTAACGGGGTTCATCA
1 TAAAAACGCCGCTAATAAGAAAAATTTAGCAGTGTTCATCA
* * * * *
564648 TAAAAATGCCGTTTATAGGAAAAATTTAGCTGTGTTCAT-A
1 TAAAAACGCCGCTAATAAGAAAAATTTAGCAGTGTTCATCA
* *
564688 GTAAAAACGTCGTTAATA
1 -TAAAAACGCCGCTAATA
564706 TTAATGATTA
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 1 0.01
41 80 0.99
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (41 bp):
TAAAAACGCCGCTAATAAGAAAAATTTAGCAGTGTTCATCA
Found at i:566315 original size:27 final size:27
Alignment explanation
Indices: 566285--566337 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
566275 CCTTAGATGT
566285 TCTTTTATCTGTA-AAGTGATAATATCA
1 TCTTTTATCTGTACAA-TGATAATATCA
*
566312 TCTTTTTTCTGTACAATGATAATATC
1 TCTTTTATCTGTACAATGATAATATC
566338 GAAGTTTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.47
Consensus pattern (27 bp):
TCTTTTATCTGTACAATGATAATATCA
Found at i:567393 original size:25 final size:26
Alignment explanation
Indices: 567342--567399 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
567332 CAAAATCTAT
* *
567342 AATCTCAGATAAAGTTGAACTTTATC
1 AATCTTAGATAAAGTTAAACTTTATC
567368 AATCTTAGATAAAG-TAAACTTTATC
1 AATCTTAGATAAAGTTAAACTTTATC
567393 AATCTTA
1 AATCTTA
567400 TATCTATAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 17 0.57
26 13 0.43
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (26 bp):
AATCTTAGATAAAGTTAAACTTTATC
Found at i:568303 original size:20 final size:20
Alignment explanation
Indices: 568272--568346 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
568262 TTTTACCCAG
568272 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * * *
568292 ATATATCAATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
568312 ATGTATCGATATATTTTGCA
1 ATGTATCGATACATTTTTCA
568332 ATGTATCGATACATT
1 ATGTATCGATACATT
568347 ATATCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:572645 original size:20 final size:20
Alignment explanation
Indices: 572607--572647 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
572597 GGAAGGGCCA
*
572607 TTTTTTTTATTGATGTTCAT
1 TTTTTTTTATTGATATTCAT
* *
572627 TTTTTTTTCTTGCTATTCAT
1 TTTTTTTTATTGATATTCAT
572647 T
1 T
572648 CCCATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTTTTTTATTGATATTCAT
Done.