Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008078.1 Hibiscus syriacus cultivar Beakdansim tig00110580_pilon, whole genome shotgun sequence
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: 1434613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:431485 original size:30 final size:30
Alignment explanation
Indices: 431450--431506 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
431440 CGGTGGTCAC
* *
431450 TAATAAATAGCACAATAAATCATAAAGACA
1 TAATAAATAGAACAATAAATAATAAAGACA
* *
431480 TAATAAATGGAACAGTAAATAATAAAG
1 TAATAAATAGAACAATAAATAATAAAG
431507 GTGGATTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.21
Consensus pattern (30 bp):
TAATAAATAGAACAATAAATAATAAAGACA
Found at i:433771 original size:37 final size:37
Alignment explanation
Indices: 433676--433780 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
433666 CATTTTCGTC
*
433676 CTACTATGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * * *
433713 TTGCTAGGATTCAAACCCCTAAAAATAGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
433750 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAAGATTCAAACTCCTAAAAATAGGAT
433781 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:434173 original size:18 final size:17
Alignment explanation
Indices: 434134--434176 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
434124 ATTATATGGA
434134 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
434150 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
434168 TATTATTAT
1 TATTATTAT
434177 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:434480 original size:21 final size:20
Alignment explanation
Indices: 434421--434489 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
434411 TCTTATAACT
* *
434421 TTATATTTATATTATTTTTTA
1 TTAT-TTTATATTATTATTCA
* *
434442 TTATTTTCATTTTTTTATTCA
1 TTATTTT-ATATTATTATTCA
434463 TTATTATTATATTATTATT-A
1 TTATT-TTATATTATTATTCA
434483 TT-TTTTA
1 TTATTTTA
434490 AAAAAACCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
18 3 0.08
19 2 0.05
20 6 0.15
21 27 0.68
22 2 0.05
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTTTATATTATTATTCA
Found at i:439066 original size:183 final size:183
Alignment explanation
Indices: 438758--439282 Score: 944
Period size: 183 Copynumber: 2.9 Consensus size: 183
438748 ATTAAATCCG
*
438758 TAAAGCTGAGTTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
438823 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
438888 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
438941 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
439006 ATAGATTATGTTCAAACTATGACACTGCTCGGACAGTTGGCAATTTGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
439071 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
439124 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
439189 ATAGATTACATTCAAA-TCATGACATTGCTCAGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
* *
439253 TTTGTCAGGTCAAAGAATTTGTGATGAGAT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGAT
439283 AAGTTAAACC
Statistics
Matches: 328, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
182 1 0.00
183 327 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:440471 original size:36 final size:34
Alignment explanation
Indices: 440426--440529 Score: 102
Period size: 36 Copynumber: 2.9 Consensus size: 34
440416 ATGCAGATGA
440426 TTATCTCACTCAAATTTGTTTTTCTTAAAACATACT
1 TTATCTCACTCAAA-TTGTTTTTCTTAAAACATA-T
* * * *
440462 TTGTCTCACTTGAGACTGTTTTTCTTGAAAGA-ATAT
1 TTATCTCAC-TCAAATTGTTTTTCTT-AAA-ACATAT
*
440498 TTATTTCACTCAAGATTGTTTTTCTTAAAACA
1 TTATCTCACTCAA-ATTGTTTTTCTTAAAACA
440530 AGATTTGTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
34 1 0.02
35 6 0.11
36 37 0.69
37 9 0.17
38 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (34 bp):
TTATCTCACTCAAATTGTTTTTCTTAAAACATAT
Found at i:440518 original size:72 final size:75
Alignment explanation
Indices: 440426--440587 Score: 199
Period size: 72 Copynumber: 2.2 Consensus size: 75
440416 ATGCAGATGA
* * * * *
440426 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTT
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
*
440488 GAAAGAA-TAT
65 GAAAGAAGCAT
*
440498 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCG
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCG
440562 AAAGAAGGCAT
66 AAAGAA-GCAT
440573 TTCATTTCACTCAAG
1 TT-ATTTCACTCAAG
440588 GCTATTTTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
71 1 0.01
72 50 0.65
73 10 0.13
75 4 0.05
76 12 0.16
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (75 bp):
TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCG
AAAGAAGCAT
Found at i:440555 original size:36 final size:35
Alignment explanation
Indices: 440442--440555 Score: 111
Period size: 36 Copynumber: 3.2 Consensus size: 35
440432 CACTCAAATT
*
440442 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-AATTTGTCTCACTTGAGAC
* * * * ** *
440478 TGTTTTTCTTGAAAGAATATTTATTTCACTCAAGAT
1 TGTTTTTCTTAAAACAA-ATTTGTCTCACTTGAGAC
*
440514 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAACAA-ATTTGTCTCACTTGAGAC
*
440550 CGTTTT
1 TGTTTT
440556 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 18, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
35 1 0.02
36 58 0.98
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (35 bp):
TGTTTTTCTTAAAACAAATTTGTCTCACTTGAGAC
Found at i:440780 original size:104 final size:104
Alignment explanation
Indices: 440672--440989 Score: 489
Period size: 104 Copynumber: 3.1 Consensus size: 104
440662 ACAGTTTCTC
* * *
440672 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCACCTGAGATATTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCACTTGAGATAGTTTCCCTCGAAACAGAAAAT
440737 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* *
440776 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCACTTGAGATAGTTTCCCTCGAAACAGAAAAT
*
440841 TTTGTCTCCCTTGAGACAGCTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
440880 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCACTTGAGATAGTTTCCCTCGAAACAGAAAAT
* * ** *
440942 TTTGTCTCTCTTAAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
440981 TTGAAAACA
1 TTGAAAACA
440990 ATTTAACGAA
Statistics
Matches: 198, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
101 45 0.23
103 1 0.01
104 152 0.77
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCACTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:440936 original size:36 final size:36
Alignment explanation
Indices: 440889--440964 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
440879 ATTGAAAACA
* * *
440889 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCGCTTAAGACAG
* *
440925 TTTCCCTTGAAACGAATTTTGTCTCTCTTAAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCGCTTAAGACAG
440961 TTTC
1 TTTC
440965 TCTCCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCGCTTAAGACAG
Found at i:441361 original size:105 final size:105
Alignment explanation
Indices: 441164--441467 Score: 491
Period size: 105 Copynumber: 2.9 Consensus size: 105
441154 ATATCGTGAC
* * * * * *
441164 ACTCGAGACAACACAAGTTCAACTTCACAACAAAGGGACAGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
441229 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
* *
441270 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTTCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
441335 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
* *
441375 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
441440 ATCTCAGAGCCAATTTCAACTTCACAAT
66 ATTTCAGAGCCAATTTCAACTTCACAAT
441468 CACGACGAAG
Statistics
Matches: 183, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
105 138 0.75
106 45 0.25
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
Found at i:441474 original size:68 final size:68
Alignment explanation
Indices: 441399--441534 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
441389 AAGTTCAACT
441399 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
1 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
441464 CAA
66 CAA
* *
441467 TCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGAGCCAATTTTAACTTCA
1 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
441532 CAA
66 CAA
441535 CGAAGGATAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (68 bp):
TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
CAA
Found at i:441493 original size:173 final size:169
Alignment explanation
Indices: 441294--441634 Score: 556
Period size: 173 Copynumber: 2.0 Consensus size: 169
441284 AAGTTCAACT
* * * *
441294 TCACGATGAAGGGACCGCTTCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCA
1 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
* * *
441359 CAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT
66 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAA-GGACCACTGCTTGT
441424 CAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAA
130 ---CAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAA
* *
441467 TCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGAGCCAATTTTAACTTCA
1 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
441532 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGACCACTGCTTGTC
66 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGACCACTGCTTGTC
*
441597 AACAACTTCCCAATCTCAGAGTCAATTTCAACTTCACA
131 AACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACA
441635 GCGAAGGATA
Statistics
Matches: 158, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
169 38 0.24
172 13 0.08
173 107 0.68
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.23
Consensus pattern (169 bp):
TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGACCACTGCTTGTC
AACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAA
Found at i:441593 original size:104 final size:104
Alignment explanation
Indices: 441468--441756 Score: 374
Period size: 101 Copynumber: 2.8 Consensus size: 104
441458 ACTTCACAAT
*
441468 CACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGAGCCAATTTTAACTTCAC
1 CACGACGAAGGGACCGCTGCTTGTCAA-AACAACTTCCCAATCTCAGAGCCAATTTCAACTTCAC
*
441533 AACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTC
65 AACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTC
* *
441573 CACGACGAA-GGACCACTGCTTGTC--AACAACTTCCCAATCTCAGAGTCAATTTCAACTTCACA
1 CACGACGAAGGGACCGCTGCTTGTCAAAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACA
* * *
441635 GCGAAGGATA-TGGACTCGAGACAACACAAGTTCAACTT
66 ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTC
* * * * **
441673 CACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGTTC-CAGAGCCAATTTCAACTTCA
1 CACGACGAAGGGACCGCTGCTTGTC-A-AAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
*
441737 CGAC-AGAGGATATTGGACTC
64 CAACGA-AGGATATTGGACTC
441757 AGAACAATGC
Statistics
Matches: 160, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
100 33 0.21
101 57 0.36
103 1 0.01
104 41 0.26
105 28 0.17
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (104 bp):
CACGACGAAGGGACCGCTGCTTGTCAAAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACA
ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTC
Found at i:442389 original size:37 final size:37
Alignment explanation
Indices: 442294--442398 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
442284 CATTTTCGTC
442294 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
442331 TTGCTAGGATTCAAACCCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
442368 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
442399 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:442792 original size:18 final size:18
Alignment explanation
Indices: 442751--442793 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
442741 ATTATATGGA
442751 TATT-TTATTCATTTAAT
1 TATTATTATTCATTTAAT
442768 T-TTATTATTCATGTT-AT
1 TATTATTATTCAT-TTAAT
442785 TATTATTAT
1 TATTATTAT
442794 ATGTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.09
17 12 0.52
18 9 0.39
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (18 bp):
TATTATTATTCATTTAAT
Found at i:444037 original size:104 final size:104
Alignment explanation
Indices: 443857--444135 Score: 438
Period size: 104 Copynumber: 2.7 Consensus size: 104
443847 GGAGTGATCA
*
443857 AGATATTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
1 AGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
443922 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCTTG
66 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTG
*
443961 AGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACATAAACA
1 AGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
444026 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTG
66 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTG
* * * ** *
444065 AGATAGTTTCCCTTGAAAC-G--AATTTTGTCTCTCTTAAGACAGTTTCTCTCCAAACATAAACT
1 AGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
444127 TTGAAAACA
66 TTGAAAACA
444136 ATTTAACGAA
Statistics
Matches: 163, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
101 45 0.28
103 1 0.01
104 117 0.72
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (104 bp):
AGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTG
Found at i:444082 original size:36 final size:36
Alignment explanation
Indices: 444035--444110 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
444025 ATTGAAAACA
* * *
444035 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCGCTTAAGACAG
* *
444071 TTTCCCTTGAAACGAATTTTGTCTCTCTTAAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCGCTTAAGACAG
444107 TTTC
1 TTTC
444111 TCTCCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCGCTTAAGACAG
Found at i:444507 original size:105 final size:105
Alignment explanation
Indices: 444310--444613 Score: 491
Period size: 105 Copynumber: 2.9 Consensus size: 105
444300 ATATCGTGAC
* * * * * *
444310 ACTCGAGACAACACAAGTTCAACTTCACAACAAAGGGACAGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
444375 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
* *
444416 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTTCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
444481 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
* *
444521 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
444586 ATCTCAGAGCCAATTTCAACTTCACAAT
66 ATTTCAGAGCCAATTTCAACTTCACAAT
444614 CACGACGAAG
Statistics
Matches: 183, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
105 138 0.75
106 45 0.25
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
Found at i:444620 original size:68 final size:68
Alignment explanation
Indices: 444545--444680 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
444535 AAGTTCAACT
444545 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
1 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
444610 CAA
66 CAA
* *
444613 TCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGAGCCAATTTTAACTTCA
1 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
444678 CAA
66 CAA
444681 CGAAGGATAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (68 bp):
TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
CAA
Found at i:444639 original size:173 final size:170
Alignment explanation
Indices: 444440--444781 Score: 567
Period size: 173 Copynumber: 2.0 Consensus size: 170
444430 AAGTTCAACT
* * * *
444440 TCACGATGAAGGGACCGCTTCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCA
1 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
* * *
444505 CAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT
66 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCACTGCTTGT
444570 CAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAA
131 ---CAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAA
* *
444613 TCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGAGCCAATTTTAACTTCA
1 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
444678 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCACTGCTTGT
66 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCACTGCTTGT
*
444743 CAACAACTTCCCAATCTCAGAGTCAATTTCAACTTCACA
131 CAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACA
444782 GCGAAGGATA
Statistics
Matches: 159, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
170 38 0.24
173 121 0.76
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.23
Consensus pattern (170 bp):
TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCACTGCTTGT
CAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAA
Found at i:444901 original size:106 final size:103
Alignment explanation
Indices: 444613--444905 Score: 378
Period size: 102 Copynumber: 2.8 Consensus size: 103
444603 AACTTCACAA
* *
444613 TCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGAGCCAATTTTAACTTCA
1 TCACGACGAAGGGACCGCTGCTTGTCAACAACAA-TTCCCAATCTCAGAGCCAATTTCAACTTCA
*
444678 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
65 C-ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACT
* * *
444718 CCACGACGAAGGGACCACTGCTTGTCAACAAC--TTCCCAATCTCAGAGTCAATTTCAACTTCAC
1 TCACGACGAAGGGACCGCTGCTTGTCAACAACAATTCCCAATCTCAGAGCCAATTTCAACTTCAC
*
444781 AGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
66 A-CGAAGGATATTGGACTCCAGACAACACAAGTTCAACT
* * * **
444820 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGT-TCCAGAGCCAATTTCAACTT
1 TCACGACGAAGGGACCGCTGCTTGTCAAC-AACAA-TTCCCAATCT-CAGAGCCAATTTCAACTT
444884 CACGAC-AGAGGATATTGGACTC
63 CAC-ACGA-AGGATATTGGACTC
444906 AGAACAATGC
Statistics
Matches: 165, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
101 1 0.01
102 88 0.53
103 3 0.02
105 31 0.19
106 41 0.25
107 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (103 bp):
TCACGACGAAGGGACCGCTGCTTGTCAACAACAATTCCCAATCTCAGAGCCAATTTCAACTTCAC
ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACT
Found at i:445543 original size:37 final size:37
Alignment explanation
Indices: 445448--445552 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
445438 CATTTTCGTC
445448 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
445485 TTGCTAGGATTCAAACCCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
445522 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
445553 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:445929 original size:15 final size:16
Alignment explanation
Indices: 445911--445940 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
445901 TATATGGATA
445911 TTTTATTCAT-TTATT
1 TTTTATTCATGTTATT
445926 TTTTATTCATGTTAT
1 TTTTATTCATGTTAT
445941 ATTATATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTATTCATGTTATT
Found at i:447865 original size:27 final size:26
Alignment explanation
Indices: 447819--447870 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
447809 AGACTTTTTA
*
447819 TTATAATTAAAATATTATTATTATTT
1 TTATAATTAAAAAATTATTATTATTT
*
447845 TTATATTTAAAAAAATTATTATTATT
1 TTATAATT-AAAAAATTATTATTATT
447871 ATATTGTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATAATTAAAAAATTATTATTATTT
Found at i:448505 original size:39 final size:39
Alignment explanation
Indices: 448451--448528 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
448441 TAAGTTTAAT
448451 TTTTAATCAAGAATTCATGCTGCTTCTTTATATTTTCTC
1 TTTTAATCAAGAATTCATGCTGCTTCTTTATATTTTCTC
448490 TTTTAATCAAGAATTCATGCTGCTTCTTTATATTTTCTC
1 TTTTAATCAAGAATTCATGCTGCTTCTTTATATTTTCTC
448529 CTTGGGTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.18, G:0.08, T:0.51
Consensus pattern (39 bp):
TTTTAATCAAGAATTCATGCTGCTTCTTTATATTTTCTC
Found at i:453964 original size:2 final size:2
Alignment explanation
Indices: 453957--453993 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
453947 TCTTTGACGA
453957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
453994 AACGATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:454877 original size:5 final size:5
Alignment explanation
Indices: 454867--454899 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
454857 ATTTACAATT
454867 ATTTG ATTTG ATTTG ATTTG ATTTG ATTTG ATT
1 ATTTG ATTTG ATTTG ATTTG ATTTG ATTTG ATT
454900 CACTAGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (5 bp):
ATTTG
Found at i:462811 original size:46 final size:45
Alignment explanation
Indices: 462691--462834 Score: 216
Period size: 45 Copynumber: 3.2 Consensus size: 45
462681 AAAAGATGCA
* * *
462691 AAATTTATGGGAAATTAGATGCTCAAACTTGATACTCAAATTATG
1 AAATTTATGGGGAATTAGATGCTCAAACTTTATACTAAAATTATG
* * *
462736 AAATTTATGGAGAATTAGATGCACAAACTTTATACTAAAATAATG
1 AAATTTATGGGGAATTAGATGCTCAAACTTTATACTAAAATTATG
*
462781 AAATTTATGGGGGAATTAGATGCTCAAACTTTATATTAAAATTATG
1 AAATTTAT-GGGGAATTAGATGCTCAAACTTTATACTAAAATTATG
462827 AAATTTAT
1 AAATTTAT
462835 TTATAAATAA
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
45 47 0.53
46 41 0.47
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (45 bp):
AAATTTATGGGGAATTAGATGCTCAAACTTTATACTAAAATTATG
Found at i:465881 original size:18 final size:18
Alignment explanation
Indices: 465858--465894 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
465848 GATACAAATA
* *
465858 ACTCCAATTATGAATATG
1 ACTCCAATGATGAAGATG
465876 ACTCCAATGATGAAGATG
1 ACTCCAATGATGAAGATG
465894 A
1 A
465895 AGTAGCCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (18 bp):
ACTCCAATGATGAAGATG
Found at i:469950 original size:149 final size:149
Alignment explanation
Indices: 469773--470058 Score: 554
Period size: 149 Copynumber: 1.9 Consensus size: 149
469763 TTCAGGATAT
469773 ATATATATATATTATGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
1 ATATATATATATTATGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
469838 GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA
66 GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA
469903 TTCTACGCGGTCCTTTGGG
131 TTCTACGCGGTCCTTTGGG
* *
469922 ATATATATATATTCTGTGGAACATGTGTGAAGTCTTTTAAGACACATACTTGATCCCTAGTATAT
1 ATATATATATATTATGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
469987 GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA
66 GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA
470052 TTCTACG
131 TTCTACG
470059 TGCACTTCGG
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 135 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.37
Consensus pattern (149 bp):
ATATATATATATTATGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA
TTCTACGCGGTCCTTTGGG
Found at i:470080 original size:22 final size:22
Alignment explanation
Indices: 470038--470080 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
470028 TTATTATATG
**
470038 GCACTACGGTGCAATTCTACGT
1 GCACTACGGTGCAATGATACGT
*
470060 GCACTTCGGTGCAATGATACG
1 GCACTACGGTGCAATGATACG
470081 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GCACTACGGTGCAATGATACGT
Found at i:470297 original size:18 final size:16
Alignment explanation
Indices: 470274--470315 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
470264 AAATAATTCG
470274 ATGATAATGATAGATAT
1 ATGATAATGA-AGATAT
*
470291 AATGATAAT-AATATAT
1 -ATGATAATGAAGATAT
470307 ATGATAATG
1 ATGATAATG
470316 CTAAGAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
16 5 0.23
17 1 0.05
18 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (16 bp):
ATGATAATGAAGATAT
Found at i:473590 original size:64 final size:65
Alignment explanation
Indices: 473522--473682 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 65
473512 TTATTTGAAG
* **
473522 GTGCATCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-AT
1 GTGCATCGATGCATAGGTAATGCATCGATGCATCTC-AGTAATAATA-AAACATCGAATGCATAT
473584 TA
64 TA
* * *
473586 GTGCATCGATGCATAAGG-CATGCATCGATGCATCTCAGTAATAATACAACATCGAATGCATTTT
1 GTGCATCGATGCAT-AGGTAATGCATCGATGCATCTCAGTAATAATAAAACATCGAATGCATATT
473650 A
65 A
* *
473651 -TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGTAATGCATCGATGCAT
473683 ACCTTCATTA
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
63 1 0.01
64 69 0.84
65 12 0.15
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (65 bp):
GTGCATCGATGCATAGGTAATGCATCGATGCATCTCAGTAATAATAAAACATCGAATGCATATTA
Found at i:475307 original size:149 final size:149
Alignment explanation
Indices: 475055--475340 Score: 536
Period size: 149 Copynumber: 1.9 Consensus size: 149
475045 CAGGATATAT
* *
475055 ATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGGCACATACTTGATCCCTAGTATAT
1 ATATATATATATTATGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
*
475120 GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA
66 GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGAACTACGGTGCAA
475185 TTCTACGCGGTCCTTCGGG
131 TTCTACGCGGTCCTTCGGG
*
475204 ATATATATATATTATGTGGAACATGTGTGAAGTCTTTTAAGACACATACTTGATCCCTAGTATAT
1 ATATATATATATTATGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
475269 GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGAACTACGGTGCAA
66 GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGAACTACGGTGCAA
475334 TTCTACG
131 TTCTACG
475341 TGCACTTCGG
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 133 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (149 bp):
ATATATATATATTATGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
GTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGAACTACGGTGCAA
TTCTACGCGGTCCTTCGGG
Found at i:478769 original size:3 final size:3
Alignment explanation
Indices: 478761--478828 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
478751 AGCATTAGCC
478761 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
478809 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
478829 TCCTTCTGGC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:488687 original size:21 final size:20
Alignment explanation
Indices: 488648--488685 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
488638 AGAATGTCCA
488648 GGGGGTATCGATTCCCCCTG
1 GGGGGTATCGATTCCCCCTG
488668 GGGGGTATCGATTCCCCC
1 GGGGGTATCGATTCCCCC
488686 CTAAATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTG
Found at i:489048 original size:14 final size:15
Alignment explanation
Indices: 489031--489059 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
489021 TACATGATAT
489031 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
489045 GCATAAAACATAAGA
1 GCATAAAACATAAGA
489060 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:512405 original size:18 final size:18
Alignment explanation
Indices: 512382--512448 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
512372 AGGGATTATC
512382 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
512400 AGTGGTTCTTCGGAATAATT
1 AGTGGTCCTTCGGGA-CA-T
*
512420 AGTGGTCTTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
512438 AGGGGTCCTTC
1 AGTGGTCCTTC
512449 AGGATAAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
18 23 0.61
19 2 0.05
20 13 0.34
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.33
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:519280 original size:38 final size:38
Alignment explanation
Indices: 519224--519297 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
519214 AGGGATTATC
*
519224 AGTGGTCCTTCGGAACATAGTGGTTCTTCGGAACAATT
1 AGTGGTCCTTCGGAACATAGTGGTCCTTCGGAACAATT
* *
519262 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGAACATAGTGGTCCTTCGGAACAA
519298 ATATTCAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (38 bp):
AGTGGTCCTTCGGAACATAGTGGTCCTTCGGAACAATT
Found at i:519296 original size:18 final size:18
Alignment explanation
Indices: 519224--519292 Score: 102
Period size: 18 Copynumber: 3.7 Consensus size: 18
519214 AGGGATTATC
519224 AGTGGTCCTTCGGAACAT
1 AGTGGTCCTTCGGAACAT
*
519242 AGTGGTTCTTCGGAACAATT
1 AGTGGTCCTTCGGAAC-A-T
*
519262 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACAT
519280 AGTGGTCCTTCGG
1 AGTGGTCCTTCGG
519293 GACAAATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
18 29 0.63
19 2 0.04
20 15 0.33
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGAACAT
Found at i:526953 original size:19 final size:20
Alignment explanation
Indices: 526929--526975 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
526919 TGTTTTTATA
* *
526929 AATAGTGCT-ATATTGTATG
1 AATAGTACTGATACTGTATG
*
526948 AATAGTACTGATACTGTGTG
1 AATAGTACTGATACTGTATG
526968 AATAGTAC
1 AATAGTAC
526976 CAATATTGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (20 bp):
AATAGTACTGATACTGTATG
Found at i:526971 original size:20 final size:20
Alignment explanation
Indices: 526946--526989 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
526936 CTATATTGTA
**
526946 TGAATAGTACTGATACTGTG
1 TGAATAGTACCAATACTGTG
*
526966 TGAATAGTACCAATATTGTG
1 TGAATAGTACCAATACTGTG
526986 TGAA
1 TGAA
526990 CATTAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (20 bp):
TGAATAGTACCAATACTGTG
Found at i:529125 original size:23 final size:23
Alignment explanation
Indices: 529091--529154 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
529081 ATGACCAAAC
529091 AAAAAAA-GTGTCATAAAGAC-A
1 AAAAAAATGTGTCATAAAGACAA
* * *
529112 GAGAAAATGATGTCAAAAAGACAA
1 AAAAAAATG-TGTCATAAAGACAA
529136 AAAAAAATGTGTCATAAAG
1 AAAAAAATGTGTCATAAAG
529155 GTATAATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 5 0.15
22 1 0.03
23 20 0.59
24 8 0.24
ACGTcount: A:0.59, C:0.08, G:0.17, T:0.16
Consensus pattern (23 bp):
AAAAAAATGTGTCATAAAGACAA
Found at i:531211 original size:3 final size:3
Alignment explanation
Indices: 531203--531244 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
531193 TAACGTACCA
531203 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
531245 TATTTATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:544411 original size:20 final size:20
Alignment explanation
Indices: 544373--544412 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
544363 ATTTGGTAAT
* **
544373 TTTAAAAAATTTATTTAAAA
1 TTTAAAAAATATACATAAAA
544393 TTTAAAAAATATACATAAAA
1 TTTAAAAAATATACATAAAA
544413 AAACAAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAAAAAATATACATAAAA
Found at i:546279 original size:20 final size:21
Alignment explanation
Indices: 546254--546296 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
546244 GTTATTGTCG
* *
546254 GGCGTTGGAAGA-GTGGGAAA
1 GGCGTTGCAAGATATGGGAAA
546274 GGCGTTGCAAGATATGGGAAA
1 GGCGTTGCAAGATATGGGAAA
546295 GG
1 GG
546297 GAGATGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.30, C:0.07, G:0.47, T:0.16
Consensus pattern (21 bp):
GGCGTTGCAAGATATGGGAAA
Found at i:550130 original size:103 final size:103
Alignment explanation
Indices: 549993--550349 Score: 518
Period size: 103 Copynumber: 3.5 Consensus size: 103
549983 GTTAACATAC
* ** *
549993 AAAAGATGTTTTCTTTGAAATGGTTGTCTATTTGTTTGTGTAGGATTTAGATTTCGTATTTTACT
1 AAAAGATCTTTTCTTTGAAATTATTGTCTATTTGTTTGTGTAGGATTTAGATTTCATATTTTACT
* *
550058 GAAACTCGTAGGGAGGCTTCTCATGTGAAGAAAGACTG
66 GAAACTCATAGGGAGGCTTCTCGTGTGAAGAAAGACTG
* *
550096 AAAGGATCTTTTCTTTGAAATTATTGTCTATTTGTTTGTGTAGGATTTAGATTTCATATTTTCCT
1 AAAAGATCTTTTCTTTGAAATTATTGTCTATTTGTTTGTGTAGGATTTAGATTTCATATTTTACT
*
550161 GAAACTCATAGGGAGACTTCTCGTGTGAAGAAAGACTG
66 GAAACTCATAGGGAGGCTTCTCGTGTGAAGAAAGACTG
* * * * * * *
550199 AAATGATCTTTTCTTTGTAATAATTGTCCATTTGTTTGTGTAAGTTTTAGATGTCATATTTTACT
1 AAAAGATCTTTTCTTTGAAATTATTGTCTATTTGTTTGTGTAGGATTTAGATTTCATATTTTACT
* * * *
550264 TAAACTCTTAGGGAGGCTTCTCGCGTGAAGAAAGTCTG
66 GAAACTCATAGGGAGGCTTCTCGTGTGAAGAAAGACTG
550302 AAAAGATCTTTTCTTTGAAA-TAGTTGTCTATTTGTTTGTGTAGGATTT
1 AAAAGATCTTTTCTTTGAAATTA-TTGTCTATTTGTTTGTGTAGGATTT
550350 TATGAGCTTG
Statistics
Matches: 225, Mismatches: 28, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
102 1 0.00
103 224 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (103 bp):
AAAAGATCTTTTCTTTGAAATTATTGTCTATTTGTTTGTGTAGGATTTAGATTTCATATTTTACT
GAAACTCATAGGGAGGCTTCTCGTGTGAAGAAAGACTG
Found at i:567303 original size:27 final size:28
Alignment explanation
Indices: 567246--567303 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
567236 AGAGGTGCAC
567246 AAAAAATCCGAATATCCGATTTTGGGTAA
1 AAAAAATCCGAATATCCGATTTTGGG-AA
*
567275 AAAATATCCGAA-A-CCGGATTTT-GGAA
1 AAAAAATCCGAATATCC-GATTTTGGGAA
567301 AAA
1 AAA
567304 TCGGTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.19
27 4 0.15
28 7 0.26
29 11 0.41
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGATTTTGGGAA
Found at i:567451 original size:16 final size:17
Alignment explanation
Indices: 567420--567493 Score: 76
Period size: 17 Copynumber: 4.0 Consensus size: 17
567410 TCAAACCGGA
567420 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
*
567437 TAAAAAACTGGTTTTTT
1 TAAAAAACCGGTTTTTT
567454 ATCCGAAAAAATCCGGTTTTTTT
1 -T---AAAAAA-CCGG-TTTTTT
*
567477 TTAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
567494 GCAAACCGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
17 22 0.46
18 5 0.10
19 5 0.10
21 6 0.12
22 4 0.08
23 6 0.12
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (17 bp):
TAAAAAACCGGTTTTTT
Found at i:577046 original size:21 final size:21
Alignment explanation
Indices: 577021--577060 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
577011 AACTATTCAT
577021 TTAAAAAGATAA-AAATATTAA
1 TTAAAAA-ATAATAAATATTAA
*
577042 TTAAATAATAATAAATATT
1 TTAAAAAATAATAAATATT
577061 TTATGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
TTAAAAAATAATAAATATTAA
Found at i:577711 original size:18 final size:18
Alignment explanation
Indices: 577688--577724 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
577678 TTAAAACACA
577688 AGAGGGTTAAAATAACCC
1 AGAGGGTTAAAATAACCC
577706 AGAGGGTTAAAATAACCC
1 AGAGGGTTAAAATAACCC
577724 A
1 A
577725 AAAGCTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (18 bp):
AGAGGGTTAAAATAACCC
Found at i:577894 original size:23 final size:23
Alignment explanation
Indices: 577850--577894 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
577840 AGATTGAATA
*
577850 TAAATAATAAAATATAACATAAT
1 TAAATAATAAAATATAAAATAAT
* * *
577873 TAAATTATAAGATTTAAAATAA
1 TAAATAATAAAATATAAAATAA
577895 ATGGGACTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAATAATAAAATATAAAATAAT
Found at i:578504 original size:26 final size:25
Alignment explanation
Indices: 578470--578520 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 25
578460 TGACTTAAGA
578470 TTTGATTTTGAATTGATTATTTAGT
1 TTTGATTTTGAATTGATTATTTAGT
578495 TTTGATTTTTGAATTGATTATTTAGT
1 TTTGA-TTTTGAATTGATTATTTAGT
578521 CTGGTGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.61
Consensus pattern (25 bp):
TTTGATTTTGAATTGATTATTTAGT
Found at i:579336 original size:37 final size:39
Alignment explanation
Indices: 579281--579501 Score: 285
Period size: 39 Copynumber: 5.7 Consensus size: 39
579271 TAGTATATAT
*
579281 ATATATATATTAATATATAGTTTTT-ATAAACGTTTTAAAA
1 ATATATATA-TAATATATAGTTTTTGA-AAACATTTTAAAA
579321 ATATATATATAATATATAGTTTTTGAAAACATTTT-AAA
1 ATATATATATAATATATAGTTTTTGAAAACATTTTAAAA
579359 A-ATATATATAATATATAGTTTTTGAAAACATTTTGAAAA
1 ATATATATATAATATATAGTTTTTGAAAACATTTT-AAAA
* *
579398 A-ATATATATAATATATAGTTTTTGAAAATATTTT-GAA
1 ATATATATATAATATATAGTTTTTGAAAACATTTTAAAA
* * * *
579435 A-ATATATATAATATATGGTTTTTAAAAATATTTTAAAT
1 ATATATATATAATATATAGTTTTTGAAAACATTTTAAAA
*
579473 ATATATATAT-ATATTATAGTTTTTAAAAA
1 ATATATATATAATA-TATAGTTTTTGAAAA
579502 ATATATATAT
Statistics
Matches: 167, Mismatches: 8, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
37 67 0.40
38 9 0.05
39 81 0.49
40 10 0.06
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (39 bp):
ATATATATATAATATATAGTTTTTGAAAACATTTTAAAA
Found at i:579343 original size:39 final size:38
Alignment explanation
Indices: 579283--579501 Score: 284
Period size: 37 Copynumber: 5.7 Consensus size: 38
579273 GTATATATAT
*
579283 ATATATATTAATATATAGTTTTT-ATAAACGTTTTAAAAA
1 ATATATA-TAATATATAGTTTTTGA-AAACATTTTAAAAA
579322 TATATATATAATATATAGTTTTTGAAAACATTTT-AAAA
1 -ATATATATAATATATAGTTTTTGAAAACATTTTAAAAA
579360 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTT-AAAAA
* *
579399 ATATATATAATATATAGTTTTTGAAAATATTTT-GAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTAAAAA
* * * *
579436 ATATATATAATATATGGTTTTTAAAAATATTTT-AAAT
1 ATATATATAATATATAGTTTTTGAAAACATTTTAAAAA
*
579473 ATATATATATATATTATAGTTTTTAAAAA
1 ATATATATA-ATA-TATAGTTTTTGAAAA
579502 ATATATATAT
Statistics
Matches: 166, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
37 78 0.47
38 7 0.04
39 73 0.44
40 8 0.05
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (38 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTAAAAA
Found at i:579403 original size:76 final size:74
Alignment explanation
Indices: 579283--579501 Score: 296
Period size: 76 Copynumber: 2.9 Consensus size: 74
579273 GTATATATAT
*
579283 ATATATATTAATATATAGTTTTTATAAACGTTTTAAAAATATATATATAATATATAGTTTTTGAA
1 ATATATA-TAATATATAGTTTTTA-AAACATTTTAAAAA-ATATATATAATATATAGTTTTTGAA
579348 AACATTTTAAAA
63 AACATTTTAAAA
579360 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAAAATATATATAATATATAGTTTTTGAAA
1 ATATATATAATATATAGTTTTT-AAAACATTTT-AAAAAATATATATAATATATAGTTTTTGAAA
* *
579425 ATATTTTGAAA
64 ACATTTTAAAA
* * * *
579436 ATATATATAATATATGGTTTTTAAAA-ATATTTTAAATATATATATATATATTATAGTTTTTAAA
1 ATATATATAATATATAGTTTTTAAAACAT-TTTAAAAAATATATATA-ATA-TATAGTTTTTGAA
579500 AA
63 AA
579502 ATATATATAT
Statistics
Matches: 130, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
74 14 0.11
75 10 0.08
76 93 0.72
77 13 0.10
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (74 bp):
ATATATATAATATATAGTTTTTAAAACATTTTAAAAAATATATATAATATATAGTTTTTGAAAAC
ATTTTAAAA
Found at i:579517 original size:39 final size:40
Alignment explanation
Indices: 579277--579525 Score: 209
Period size: 37 Copynumber: 6.5 Consensus size: 40
579267 TATTTAGTAT
* ** *
579277 ATATATATATATATTAATATATAGTTTTTATAAACGTTTTAA
1 ATATATATATATA-T-ATATATAGTTTTTAAAAATATTATAA
* * * *
579319 AAATATATATATA-ATATATAGTTTTTGAAAACATTTTAA
1 ATATATATATATATATATATAGTTTTTAAAAATATTATAA
* * *
579358 A-A-ATATATATA-ATATATAGTTTTTGAAAACATTTTGAA
1 ATATATATATATATATATATAGTTTTTAAAAATATTAT-AA
* * * *
579396 A-AAATATATATA-ATATATAGTTTTTGAAAATATTTTGA
1 ATATATATATATATATATATAGTTTTTAAAAATATTATAA
* *
579434 A-A-ATATATATA-ATATATGGTTTTTAAAAATATTTTAA
1 ATATATATATATATATATATAGTTTTTAAAAATATTATAA
*
579471 ATATATATATATATAT-TATAGTTTTTAAAAA-A-TATAT
1 ATATATATATATATATATATAGTTTTTAAAAATATTATAA
*
579508 ATATTTATATAT-TATATA
1 ATATATATATATATATATA
579526 GTATTATATT
Statistics
Matches: 188, Mismatches: 13, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
36 3 0.02
37 82 0.44
38 10 0.05
39 79 0.42
40 2 0.01
42 12 0.06
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (40 bp):
ATATATATATATATATATATAGTTTTTAAAAATATTATAA
Found at i:579517 original size:76 final size:75
Alignment explanation
Indices: 579274--579525 Score: 269
Period size: 76 Copynumber: 3.3 Consensus size: 75
579264 TTTTATTTAG
* * *
579274 TATATATATATATATATTAATATATAGTTTTTATAAACGTTTTAAAAATATATATATAATATATA
1 TATATATAAATATATA-TAATATATAGTTTTTAAAAACATTTT-AAAATATATATATAATATATA
*
579339 GTTTTTGAAAACA
64 GTTTTT-AAAAAA
* * * *
579352 T-TTTAAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAAAATATATATAATATATAG
1 TATATATAAATATATATAATATATAGTTTTTAAAAACATTTT-AAAATATATATATAATATATAG
*
579416 TTTTT-GAAAA
65 TTTTTAAAAAA
* * *
579426 TAT-TTTGAAAATATATATAATATATGGTTTTTAAAAATATTTT-AAATATATATATATATATTA
1 TATATAT--AAATATATATAATATATAGTTTTTAAAAACATTTTAAAATATATATATA-ATA-TA
579489 TAGTTTTTAAAAAA
62 TAGTTTTTAAAAAA
** *
579503 TATATATATTTATATATTATATA
1 TATATATAAATATATATAATATA
579526 GTATTATATT
Statistics
Matches: 146, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
74 17 0.12
75 4 0.03
76 104 0.71
77 18 0.12
78 3 0.02
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (75 bp):
TATATATAAATATATATAATATATAGTTTTTAAAAACATTTTAAAATATATATATAATATATAGT
TTTTAAAAAA
Found at i:585277 original size:20 final size:20
Alignment explanation
Indices: 585240--585278 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
585230 AGATTGAGTG
* * *
585240 GATTTTGATGTTGTTTGCAT
1 GATTTTAATGATGCTTGCAT
585260 GATTTTAATGATGCTTGCA
1 GATTTTAATGATGCTTGCA
585279 AGTTTAGAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.49
Consensus pattern (20 bp):
GATTTTAATGATGCTTGCAT
Found at i:585516 original size:20 final size:20
Alignment explanation
Indices: 585435--585516 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
585425 CCAGAACCCC
* *
585435 ATGGGGGTATCGATTCCCCT
1 ATGGGGGAATCGATTCCCTT
* * *
585455 GTGGGGGAATTGGTTCCCCTT
1 ATGGGGGAATCGATT-CCCTT
* *
585476 CAAAGGGGGAATCGGTTCCCTT
1 --ATGGGGGAATCGATTCCCTT
*
585498 ATGGGGGTATCGATTCCCT
1 ATGGGGGAATCGATTCCCT
585517 CTGCACCAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
20 27 0.56
21 4 0.08
22 5 0.10
23 12 0.25
ACGTcount: A:0.16, C:0.22, G:0.33, T:0.29
Consensus pattern (20 bp):
ATGGGGGAATCGATTCCCTT
Found at i:589354 original size:22 final size:21
Alignment explanation
Indices: 589312--589351 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
589302 GAGTTTATTT
*
589312 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
589333 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
589352 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:592440 original size:31 final size:31
Alignment explanation
Indices: 592402--592496 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
592392 GAACCTCGGC
* *
592402 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
592433 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
592464 TACTGTCCATATGTCTCTAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
592495 AA
1 AA
592497 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:592662 original size:17 final size:19
Alignment explanation
Indices: 592630--592665 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
592620 CATATATCTC
592630 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
592649 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
592666 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:593260 original size:64 final size:65
Alignment explanation
Indices: 593149--593317 Score: 191
Period size: 64 Copynumber: 2.6 Consensus size: 65
593139 TCTTTCAATG
* * * * *
593149 AAGGTATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TTTATTTA
1 AAGGAATGCATCGATGCATTAGC-TATGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTT-
593212 AA
64 AA
* * *
593214 AAGG-ATGCATCGATGCATTAGCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTTCTTTTA
1 AAGGAATGCATCGATGCATTAGCTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTAA
*
593278 AAGGAATGCATCGATGCACTTATGAATATGCATCGATGCA
1 AAGGAATGCATCGATGCA-TTA-G-CTATGCATCGATGCA
593318 CCTTGTCCAG
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
64 48 0.53
65 24 0.27
66 3 0.03
67 1 0.01
68 14 0.16
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (65 bp):
AAGGAATGCATCGATGCATTAGCTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTAA
Found at i:596622 original size:31 final size:31
Alignment explanation
Indices: 596584--596678 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
596574 GAACCTCGGC
* *
596584 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
596615 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
596646 TACTGTCCATATGTCTCTAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
596677 AA
1 AA
596679 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:596844 original size:17 final size:19
Alignment explanation
Indices: 596812--596847 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
596802 CATATATCTC
596812 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
596831 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
596848 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:597442 original size:64 final size:67
Alignment explanation
Indices: 597330--597479 Score: 186
Period size: 64 Copynumber: 2.3 Consensus size: 67
597320 CTCTTTCAAT
* * *
597330 GAAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TTT-ATTT
1 GAAGG-ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTCATTT
597393 AAA
65 AAA
* * *
597396 -AAGGATGCATCGATGCATTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTTCTTTT
1 GAAGGATGCATCGATGCACTA-CTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTCATTT
597459 AAA
65 AAA
597462 GAA--ATGCATCGATGCACT
1 GAAGGATGCATCGATGCACT
597480 TATGAATGTG
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
64 43 0.59
65 22 0.30
66 6 0.08
67 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (67 bp):
GAAGGATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTCATTTA
AA
Found at i:598648 original size:18 final size:18
Alignment explanation
Indices: 598625--598679 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
598615 AAGGATTATC
598625 AGTGGTCATTCGGGACAA
1 AGTGGTCATTCGGGACAA
*
598643 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAA
*
598661 TGTGGTCATTCGGGACAA
1 AGTGGTCATTCGGGACAA
598679 A
1 A
598680 TATTCAGTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.25
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAA
Found at i:599490 original size:21 final size:21
Alignment explanation
Indices: 599430--599484 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
599420 AGTCGTACAT
599430 AGCCG-TTGGGGATGTTTTGG
1 AGCCGTTTGGGGATGTTTTGG
599450 AGCCGTTTGGGGATGTTTTGG
1 AGCCGTTTGGGGATGTTTTGG
599471 AGCCGTTTGGGGAT
1 AGCCGTTTGGGGAT
599485 AATTTGTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 5 0.15
21 29 0.85
ACGTcount: A:0.11, C:0.11, G:0.44, T:0.35
Consensus pattern (21 bp):
AGCCGTTTGGGGATGTTTTGG
Found at i:599546 original size:21 final size:21
Alignment explanation
Indices: 599520--599560 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
599510 CACAATAGGG
*
599520 GGTATCGGTACCCCTTCATAT
1 GGTATCGATACCCCTTCATAT
*
599541 GGTATCGATACTCCTTCATA
1 GGTATCGATACCCCTTCATA
599561 AAATTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (21 bp):
GGTATCGATACCCCTTCATAT
Found at i:599614 original size:18 final size:18
Alignment explanation
Indices: 599591--599625 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
599581 GTTGCAGCCA
*
599591 GGGGGTATCGATACCATG
1 GGGGGTATAGATACCATG
599609 GGGGGTATAGATACCAT
1 GGGGGTATAGATACCAT
599626 CCGAGCAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.14, G:0.37, T:0.23
Consensus pattern (18 bp):
GGGGGTATAGATACCATG
Found at i:599953 original size:21 final size:20
Alignment explanation
Indices: 599925--599980 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 20
599915 TGTTTAACAA
599925 AAAAGATACCAATTGTTAAC
1 AAAAGATACCAATTGTTAAC
* *
599945 AAAAGGATATCAATTATT-A-
1 AAAA-GATACCAATTGTTAAC
599964 AAAAGATACCAATTGTT
1 AAAAGATACCAATTGTT
599981 GGAAAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 11 0.35
19 4 0.13
20 5 0.16
21 11 0.35
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (20 bp):
AAAAGATACCAATTGTTAAC
Found at i:599971 original size:18 final size:19
Alignment explanation
Indices: 599923--599977 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
599913 AATGTTTAAC
*
599923 AAAAAAGATACCAATTGTT
1 AAAAAAGATACCAATTATT
*
599942 AACAAAAGGATATCAATTATT
1 AA-AAAA-GATACCAATTATT
599963 -AAAAAGATACCAATT
1 AAAAAAGATACCAATT
599978 GTTGGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 9 0.29
19 6 0.19
20 5 0.16
21 11 0.35
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (19 bp):
AAAAAAGATACCAATTATT
Found at i:601136 original size:19 final size:21
Alignment explanation
Indices: 601089--601136 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
601079 TCTAAATCCT
*
601089 TTTTCAAAATTTCATTTTGGC
1 TTTTCAAAATCTCATTTTGGC
*
601110 TTTT-AAAATCT-ATTTTTG-
1 TTTTCAAAATCTCATTTTGGC
601128 TTTTCAAAA
1 TTTTCAAAA
601137 GAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 6 0.25
21 4 0.17
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTTCAAAATCTCATTTTGGC
Found at i:611530 original size:14 final size:15
Alignment explanation
Indices: 611507--611555 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
611497 AATATGATAA
611507 TTTTATAATAATTGT
1 TTTTATAATAATTGT
611522 TTTTA-AAT-A-TGAT
1 TTTTATAATAATTG-T
611535 AATTTTATAATAATTGT
1 --TTTTATAATAATTGT
611552 TTTT
1 TTTT
611556 TACAAGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 2 0.07
13 2 0.07
14 3 0.11
15 14 0.50
16 3 0.11
17 2 0.07
18 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
TTTTATAATAATTGT
Found at i:611532 original size:30 final size:30
Alignment explanation
Indices: 611496--611555 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
611486 TTGTTTAAAG
611496 AAATATGATAATTTTATAATAATTGTTTTT
1 AAATATGATAATTTTATAATAATTGTTTTT
611526 AAATATGATAATTTTATAATAATTGTTTTT
1 AAATATGATAATTTTATAATAATTGTTTTT
611556 TACAAGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (30 bp):
AAATATGATAATTTTATAATAATTGTTTTT
Found at i:611546 original size:16 final size:16
Alignment explanation
Indices: 611497--611546 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
611487 TGTTTAAAGA
611497 AATATGATAATTTTAT
1 AATATGATAATTTTAT
611513 AATAATTG-T--TTTTA-
1 AAT-A-TGATAATTTTAT
611527 AATATGATAATTTTAT
1 AATATGATAATTTTAT
611543 AATA
1 AATA
611547 ATTGTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 2 0.07
13 2 0.07
14 3 0.11
15 10 0.36
16 7 0.25
17 2 0.07
18 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
AATATGATAATTTTAT
Found at i:611571 original size:30 final size:29
Alignment explanation
Indices: 611503--611580 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
611493 AAGAAATATG
611503 ATAATTTTATAATAATTG-TTTTTAAATA
1 ATAATTTTATAATAATTGTTTTTTAAATA
*
611531 TGATAATTTTATAATAATTGTTTTTTACA-A
1 --ATAATTTTATAATAATTGTTTTTTAAATA
* * *
611561 GTATTTTTTTAATAATTGTT
1 ATAATTTTATAATAATTGTT
611581 AAAATTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 17 0.40
30 19 0.44
31 7 0.16
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.56
Consensus pattern (29 bp):
ATAATTTTATAATAATTGTTTTTTAAATA
Found at i:612023 original size:13 final size:13
Alignment explanation
Indices: 612005--612029 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
611995 TTAAAAGTAT
612005 CAATATTTAATAA
1 CAATATTTAATAA
612018 CAATATTTAATA
1 CAATATTTAATA
612030 CGTACTCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
CAATATTTAATAA
Found at i:614587 original size:63 final size:64
Alignment explanation
Indices: 614504--614626 Score: 187
Period size: 63 Copynumber: 1.9 Consensus size: 64
614494 TCCAACTATT
* * *
614504 TTAAAAAAATATATATTTCTAACGTTATATTTTGATTTCATTTT-GATCACTCACTGTTAAAAAA
1 TTAAAAAAAAATATATTTCTAACGCTATATTTTGATTTCATTTTAG-TCACTCACTATTAAAAAA
*
614568 TTAAAAAAAAAT-TATTTCTAACGCTATATTTTGATTTTATTTTAGTCACTCACTATTAA
1 TTAAAAAAAAATATATTTCTAACGCTATATTTTGATTTCATTTTAGTCACTCACTATTAA
614627 TCAAAATAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
63 42 0.78
64 12 0.22
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (64 bp):
TTAAAAAAAAATATATTTCTAACGCTATATTTTGATTTCATTTTAGTCACTCACTATTAAAAAA
Found at i:624004 original size:2 final size:2
Alignment explanation
Indices: 623997--624053 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
623987 AGTATAATAA
623997 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
624039 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
624054 CTAATCGAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:625274 original size:26 final size:25
Alignment explanation
Indices: 625245--625298 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
625235 TGAAGTATGA
625245 TATATATATAATAAACATTTATACAT
1 TATATATATAATAAACATTTATAC-T
* * *
625271 TATATATATTATATATATTTATACT
1 TATATATATAATAAACATTTATACT
625296 TAT
1 TAT
625299 GAGTGTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (25 bp):
TATATATATAATAAACATTTATACT
Found at i:625484 original size:196 final size:195
Alignment explanation
Indices: 625130--625489 Score: 501
Period size: 196 Copynumber: 1.8 Consensus size: 195
625120 TTATGTGATT
* *
625130 TATAGGGTTTGAAATAAATACAAAAATATAAATAAGTATGGGTCAATTTTAGATACAAATATAAT
1 TATAGAGTTTGAAATAAATACAAAAATATAAATAAGTATGAGTCAATTTTAGATACAAATATAAT
* * *
625195 TTTAAGGACTCAATTAAATAAATATAAAAATATGAATAAATGAAGTATGATATATATATAATAAA
66 TTTAAGGACTCAATTAAACAAATATAAAAATATGAATAAAGGAAGTATGATATATACATAAT-AA
** * * *
625260 CATTTATACATTATATATATTATATATATTTATACTTATGAGTGTATATATAATAAACATTATAT
130 CAAGTATACATTATATACATAATATATATATATACTTATGAGTGTATATATAATAAACATTATAT
625325 A
195 A
***
625326 TATAGAGTTTGAAATAAATACAAAAATATAAATAAGTATGAGTCAATTTTAGATGTTAATATAAT
1 TATAGAGTTTGAAATAAATACAAAAATATAAATAAGTATGAGTCAATTTTAGATACAAATATAAT
* *
625391 TTTAAGGACTCAATTAAACAAATATAAAATTAT-AGATAAAGGAAGTATGGTATATACATACAT-
66 TTTAAGGACTCAATTAAACAAATATAAAAATATGA-ATAAAGGAAGTATGATATATACATA-ATA
* *
625454 ACAAGTAT-GATATATGTACATAAGTATATATATATA
129 ACAAGTATACAT-TATATACATAA-TATATATATATA
625490 TATATATTAT
Statistics
Matches: 143, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
194 2 0.01
195 15 0.10
196 124 0.87
197 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.36
Consensus pattern (195 bp):
TATAGAGTTTGAAATAAATACAAAAATATAAATAAGTATGAGTCAATTTTAGATACAAATATAAT
TTTAAGGACTCAATTAAACAAATATAAAAATATGAATAAAGGAAGTATGATATATACATAATAAC
AAGTATACATTATATACATAATATATATATATACTTATGAGTGTATATATAATAAACATTATATA
Found at i:629385 original size:2 final size:2
Alignment explanation
Indices: 629378--629411 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
629368 TCACTCCATT
629378 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
629412 AAAGCTTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:629833 original size:2 final size:2
Alignment explanation
Indices: 629828--629882 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
629818 GTGATAATTG
629828 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
629870 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
629883 GAATTAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:630091 original size:21 final size:20
Alignment explanation
Indices: 630061--630104 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
630051 AATAGTGTTT
*
630061 TTAATATATTTTTATTTCTTA
1 TTAATATATTTTT-TTTATTA
*
630082 TTAATTTATTTTTTTTATTA
1 TTAATATATTTTTTTTATTA
630102 TTA
1 TTA
630105 GTAACTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTAATATATTTTTTTTATTA
Found at i:630113 original size:24 final size:24
Alignment explanation
Indices: 630060--630120 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
630050 TAATAGTGTT
* *
630060 TTTAATATATTTTTATTTCTTATTAA
1 TTTAAT-T-TTTTTATTTATTAGTAA
*
630086 TTTATTTTTTTTA-TTATTAGTAA
1 TTTAATTTTTTTATTTATTAGTAA
630109 CTTTAATTTTTT
1 -TTTAATTTTTT
630121 GAATATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 8 0.27
24 16 0.53
25 1 0.03
26 5 0.17
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTAATTTTTTTATTTATTAGTAA
Found at i:630519 original size:17 final size:17
Alignment explanation
Indices: 630497--630530 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
630487 ATCTTATATC
630497 TCACTGTCAAGCAATCT
1 TCACTGTCAAGCAATCT
630514 TCACTGTCAAGCAATCT
1 TCACTGTCAAGCAATCT
630531 AGCTCGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
TCACTGTCAAGCAATCT
Found at i:633476 original size:48 final size:48
Alignment explanation
Indices: 633360--633490 Score: 149
Period size: 48 Copynumber: 2.7 Consensus size: 48
633350 ACTGGCACCA
* * ** * *
633360 CATCACCTTGTTCACTAAGCTCCACATGATTTTGTTCACTGTACTCTC
1 CATCACCTTGTACACTGAGCTCTTCATTATTTTGTTCACGGTACTCTC
*
633408 CATCACCTTGTACACTGAGCTGTTCATTATTTTGTTCACCGGT-CTCTC
1 CATCACCTTGTACACTGAGCTCTTCATTATTTTGTTCA-CGGTACTCTC
* *
633456 CATCACCTTGTCCA-TCGAGCTCTTCATTATATTGT
1 CATCACCTTGTACACT-GAGCTCTTCATTATTTTGT
633491 CCACTGGGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
47 1 0.01
48 67 0.94
49 3 0.04
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (48 bp):
CATCACCTTGTACACTGAGCTCTTCATTATTTTGTTCACGGTACTCTC
Found at i:637813 original size:15 final size:16
Alignment explanation
Indices: 637785--637814 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
637775 GAAATTAGGT
637785 GTTTTCCATTATTTTG
1 GTTTTCCATTATTTTG
637801 GTTTTCC-TTATTTT
1 GTTTTCCATTATTTT
637815 AAAAGTCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.13, G:0.10, T:0.67
Consensus pattern (16 bp):
GTTTTCCATTATTTTG
Found at i:640406 original size:23 final size:23
Alignment explanation
Indices: 640380--640427 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
640370 ATAAAGTACA
*
640380 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
640403 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
640426 AT
1 AT
640428 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:641176 original size:18 final size:18
Alignment explanation
Indices: 641153--641189 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
641143 CGAAATATAT
641153 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
641171 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
641189 A
1 A
641190 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:641419 original size:23 final size:23
Alignment explanation
Indices: 641393--641457 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
641383 ATGCGAGATA
641393 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
641416 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
641439 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
641458 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:641852 original size:23 final size:23
Alignment explanation
Indices: 641815--641886 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
641805 ACACTTTACA
*
641815 ATAAACCATTACCTATTACATTAT
1 ATAAACGA-TACCTATTACATTAT
641839 ATAAACGATACCTATTACATTAT
1 ATAAACGATACCTATTACATTAT
** * *
641862 ATAAGGGCTACCTATTACATCAT
1 ATAAACGATACCTATTACATTAT
641885 AT
1 AT
641887 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 36 0.84
24 7 0.16
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
ATAAACGATACCTATTACATTAT
Found at i:642259 original size:429 final size:430
Alignment explanation
Indices: 641395--642842 Score: 2807
Period size: 429 Copynumber: 3.4 Consensus size: 430
641385 GCGAGATAGA
641395 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
641460 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
641524 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
641589 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTG-TTTTATATTTTATAAAATATTATTTAGAATTTTT
641654 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
260 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
641719 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
325 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
*
641784 ACACTTTTATAAAAAGGATAGACACTTTACAATA-AACCAT
390 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
641824 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
641889 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
641954 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
642019 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTATATTTTATAAAATATTA-TTAGAATTTTTA
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTATATTTTATAAAATATTATTTAGAATTTTTA
*
642083 ATTTAATAATAATATATACTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
261 ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
*
642148 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGA
326 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
642213 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
642253 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATG-
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
*
642317 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
642382 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
642447 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTATATTTTATAAAATATTATTTAGAATTTTTA
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTATATTTTATAAAATATTATTTAGAATTTTTA
642512 ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
261 ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
642577 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
326 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
642642 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
642682 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
*
642747 TTACCTATTTTATTGAAAGTGTCCATAC-TTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
642811 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
642843 ACTGCGAATT
Statistics
Matches: 1009, Mismatches: 6, Indels: 8
0.99 0.01 0.01
Matches are distributed among these distances:
428 354 0.35
429 518 0.51
430 137 0.14
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (430 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
ATTTCATTTGCACAAAAAATTATTTGATTGTTTTATATTTTATAAAATATTATTTAGAATTTTTA
ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
Found at i:642268 original size:21 final size:22
Alignment explanation
Indices: 642243--642294 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
642233 ACACTTTACA
*
642243 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
642266 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
642289 ATATAA
1 ATATAA
642295 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:642279 original size:23 final size:23
Alignment explanation
Indices: 642253--642315 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
642243 ATATAACCAC
642253 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
642276 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
642299 TACCTATTACATCATAT
1 TACCTATTACATTATAT
642316 GTTACCTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:642500 original size:30 final size:29
Alignment explanation
Indices: 642460--642526 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
642450 TCATTTGCAC
* * *
642460 AAAAAATTATTT-GATTGTTTTATATTTTAT
1 AAAATATTATTTAGAAT-TTTTA-ATTTAAT
642490 AAAATATTATTTAGAATTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTAATTTAAT
642519 AATAATAT
1 AA-AATAT
642527 ATACCGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 21 0.66
31 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTAGAATTTTTAATTTAAT
Found at i:642697 original size:21 final size:22
Alignment explanation
Indices: 642672--642723 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
642662 ACACTTTACA
*
642672 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
642695 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
642718 ATATAA
1 ATATAA
642724 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:642708 original size:23 final size:23
Alignment explanation
Indices: 642682--642744 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
642672 ATATAACCAC
642682 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
642705 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
642728 TACCTATTACATCATAT
1 TACCTATTACATTATAT
642745 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:645004 original size:3 final size:3
Alignment explanation
Indices: 644996--645070 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
644986 ACTTGTTTGG
* * * **
644996 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
645044 AGC TTC ATC GTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
645071 GTCACCTTCA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.25, C:0.35, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:645033 original size:30 final size:29
Alignment explanation
Indices: 644997--645086 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 29
644987 CTTGTTTGGA
* *
644997 TCATCATCTTCATCATCATCATCATCATCG
1 TCATCATCTTCATCATC-TCACCTTCATCG
* *
645027 TCATCATCTTCATC-GC-CAGCTTCATCG
1 TCATCATCTTCATCATCTCACCTTCATCG
*
645054 TCATCATCATCATCATCGTCACCTTCATCG
1 TCATCATCTTCATCATC-TCACCTTCATCG
645084 TCA
1 TCA
645087 GCTTCATCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
27 22 0.43
28 1 0.02
29 1 0.02
30 27 0.53
ACGTcount: A:0.23, C:0.36, G:0.07, T:0.34
Consensus pattern (29 bp):
TCATCATCTTCATCATCTCACCTTCATCG
Found at i:645063 original size:42 final size:42
Alignment explanation
Indices: 645004--645094 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
644994 GGATCATCAT
* *
645004 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCACCTTCATCGCCAG
* * *
645046 CTTCATCGTCATCATCATCATCATCGTCACCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCACCTTCATCGCCAG
645088 CTTCATC
1 CTTCATC
645095 TTCTGCGACC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.36, G:0.08, T:0.34
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCACCTTCATCGCCAG
Found at i:646897 original size:199 final size:199
Alignment explanation
Indices: 646557--647980 Score: 2659
Period size: 199 Copynumber: 7.1 Consensus size: 199
646547 TTTAAATTAG
* *
646557 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
646622 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
646687 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
646752 AAAA
196 AAAA
* *
646756 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
646821 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
646886 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
646951 AAAA
196 AAAA
*
646955 TATCGAAACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
647020 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
647085 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
647150 AAAA
196 AAAA
647154 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
647219 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
647284 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
647349 AAAA
196 AAAA
647353 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
647418 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
647483 CGACACTTTTTATATATGGATTGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG-AAA
647548 AAAAA
195 AAAAA
647553 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
647618 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
647683 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
647748 AAAA
196 AAAA
647752 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
647817 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
647882 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAA
647947 AAAAA
195 AAAAA
*
647952 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
647981 TGACCCTTAA
Statistics
Matches: 1195, Mismatches: 28, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
199 912 0.76
200 283 0.24
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAA
Found at i:648088 original size:19 final size:19
Alignment explanation
Indices: 648066--648104 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
648056 ACATAAAAAA
648066 ATAAATCGTATACAAAATT
1 ATAAATCGTATACAAAATT
*
648085 ATAAATCTTATACAAAATT
1 ATAAATCGTATACAAAATT
648104 A
1 A
648105 ACTCGACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAAATCGTATACAAAATT
Found at i:649925 original size:33 final size:33
Alignment explanation
Indices: 649888--649953 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
649878 CATCTTAATA
* *
649888 TCACCCCTTAACATCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
649921 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
649954 CCATCTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.24, C:0.44, G:0.02, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:652096 original size:24 final size:24
Alignment explanation
Indices: 652059--652111 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
652049 CCGTTCTATC
652059 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
652083 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
652107 TATTT
1 TATTT
652112 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:652302 original size:20 final size:19
Alignment explanation
Indices: 652256--652302 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
652246 TCCGGTATCA
*
652256 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
652275 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
652296 TTTTACC
1 TTTTACC
652303 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:652450 original size:20 final size:20
Alignment explanation
Indices: 652424--652469 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
652414 CACTTTTAAA
652424 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
652443 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
652464 TTTACC
1 TTTACC
652470 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:654921 original size:26 final size:27
Alignment explanation
Indices: 654892--655016 Score: 100
Period size: 26 Copynumber: 4.6 Consensus size: 27
654882 CATTCAAAAC
654892 AACAACATGATCCAAA-AACAGCTCCA
1 AACAACATGATCCAAACAACAGCTCCA
* *
654918 AACAACA-GCTCCAAACAACAACTCCA
1 AACAACATGATCCAAACAACAGCTCCA
* * *
654944 AACAGCA-GCTCCAAACAAAAGCAATTCCAA
1 AACAACATGATCCAAACAACAGC---TCC-A
654974 ATAGCAACATGATCTC--A-AACAGCTCCA
1 A-A-CAACATGATC-CAAACAACAGCTCCA
655001 AACAACATGATCCAAA
1 AACAACATGATCCAAA
655017 GTTCACTGCA
Statistics
Matches: 80, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
24 1 0.01
25 17 0.21
26 37 0.46
27 2 0.03
28 3 0.04
29 3 0.04
30 2 0.03
31 6 0.08
32 5 0.06
33 3 0.04
34 1 0.01
ACGTcount: A:0.49, C:0.31, G:0.08, T:0.12
Consensus pattern (27 bp):
AACAACATGATCCAAACAACAGCTCCA
Found at i:654924 original size:13 final size:13
Alignment explanation
Indices: 654892--654961 Score: 97
Period size: 13 Copynumber: 5.4 Consensus size: 13
654882 CATTCAAAAC
*
654892 AACAACATGATCCA
1 AACAACA-GCTCCA
654906 AA-AACAGCTCCA
1 AACAACAGCTCCA
654918 AACAACAGCTCCA
1 AACAACAGCTCCA
*
654931 AACAACAACTCCA
1 AACAACAGCTCCA
*
654944 AACAGCAGCTCCA
1 AACAACAGCTCCA
654957 AACAA
1 AACAA
654962 AAGCAATTCC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
12 7 0.14
13 41 0.82
14 2 0.04
ACGTcount: A:0.50, C:0.34, G:0.07, T:0.09
Consensus pattern (13 bp):
AACAACAGCTCCA
Found at i:654935 original size:39 final size:39
Alignment explanation
Indices: 654892--655016 Score: 105
Period size: 39 Copynumber: 3.1 Consensus size: 39
654882 CATTCAAAAC
654892 AACAACATGATCCAAAAACAGCTCCAAACAACAGCTCCA
1 AACAACATGATCCAAAAACAGCTCCAAACAACAGCTCCA
* *
654931 AACAACA--ACTCCAAACAGCAGCTCCAAACAAAAGCAATTCCAA
1 AACAACATGA-TCCAAA-AACAGCTCCAAACAACAGC---TCC-A
*
654974 ATAGCAACATGATCTC--AAACAGCTCCAAACAACATGATCCA
1 A-A-CAACATGATC-CAAAAACAGCTCCAAACAACA-GCTCCA
655015 AA
1 AA
655017 GTTCACTGCA
Statistics
Matches: 69, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
37 1 0.01
38 6 0.09
39 24 0.35
40 1 0.01
41 2 0.03
42 6 0.09
43 2 0.03
44 16 0.23
45 7 0.10
46 2 0.03
47 2 0.03
ACGTcount: A:0.49, C:0.31, G:0.08, T:0.12
Consensus pattern (39 bp):
AACAACATGATCCAAAAACAGCTCCAAACAACAGCTCCA
Found at i:658903 original size:24 final size:23
Alignment explanation
Indices: 658879--658964 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
658869 TCGTATAAAT
*
658879 TTGCACAGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
658902 TTTGTC-CCGAA-TGATCGCGTAGAA
1 -TTG-CACCGAAGTG-CCACGTAGAA
*
658926 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
658949 TTGCACCGTAA-TGCCA
1 TTGCACCG-AAGTGCCA
658965 TATAATATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
22 1 0.02
23 29 0.58
24 19 0.38
25 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:659314 original size:25 final size:25
Alignment explanation
Indices: 659284--659342 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
659274 AATGCATATG
** *
659284 ATATGAATTCTGGTCATGTATCATA
1 ATATGAATTCTCATCATGTATCAAA
* *
659309 ATATGAAATGTCATCATGTATCAAA
1 ATATGAATTCTCATCATGTATCAAA
659334 ATATTGAAT
1 ATA-TGAAT
659343 CTAGACTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (25 bp):
ATATGAATTCTCATCATGTATCAAA
Found at i:666040 original size:24 final size:24
Alignment explanation
Indices: 666013--666087 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
666003 ATCTCGTATA
666013 AATTTGCATCGAAGTGCCACGTAG
1 AATTTGCATCGAAGTGCCACGTAG
*
666037 AATTTG--TCCAGAAG-GACCGCGTAG
1 AATTTGCAT-C-GAAGTG-CCACGTAG
* *
666061 AA-ATGCACCGAAGTGCCACGTAG
1 AATTTGCATCGAAGTGCCACGTAG
666084 AATT
1 AATT
666088 GCACCGTAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
22 1 0.03
23 17 0.44
24 21 0.54
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.21
Consensus pattern (24 bp):
AATTTGCATCGAAGTGCCACGTAG
Found at i:666082 original size:23 final size:23
Alignment explanation
Indices: 666016--666098 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 23
666006 TCGTATAAAT
*
666016 TTGCATCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
666039 TTTGTC-CAGAAG-GACCGCGTAGAA
1 -TTG-CACCGAAGTG-CCACGTAGAA
*
666063 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
666086 TTGCACCGTAGTG
1 TTGCACCGAAGTG
666099 TCATATAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
22 1 0.02
23 28 0.60
24 17 0.36
25 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:666449 original size:25 final size:25
Alignment explanation
Indices: 666419--666481 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
666409 AATGCATATG
*
666419 ATATGAATTCTAGTCATGTATCATA
1 ATATGAATTCTAGTCATGTATCAAA
666444 ATATGAAATGTC-A-TCATGTATCAAA
1 ATATG-AAT-TCTAGTCATGTATCAAA
666469 ATATTGAA-TCTAG
1 ATA-TGAATTCTAG
666482 ATTTATCACA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
23 2 0.06
24 1 0.03
25 21 0.66
26 6 0.19
27 2 0.06
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (25 bp):
ATATGAATTCTAGTCATGTATCAAA
Found at i:670124 original size:7 final size:7
Alignment explanation
Indices: 670112--670150 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
670102 AAATTTGTTA
670112 AAATTAT
1 AAATTAT
670119 AAATTAT
1 AAATTAT
* *
670126 AAAAATAA
1 -AAATTAT
670134 AAATTAT
1 AAATTAT
670141 AAATTAT
1 AAATTAT
670148 AAA
1 AAA
670151 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 22 0.81
8 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
AAATTAT
Found at i:670137 original size:15 final size:16
Alignment explanation
Indices: 670119--670153 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
670109 TTAAAATTAT
670119 AAATTATAAA-AATAA
1 AAATTATAAATAATAA
*
670134 AAATTATAAATTATAA
1 AAATTATAAATAATAA
670150 AAAT
1 AAAT
670154 AAAAAATTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTATAAATAATAA
Done.