Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020129.1 Corchorus olitorius cultivar O-4 contig20162, 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: 73967
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:894 original size:66 final size:66
Alignment explanation
Indices: 811--944 Score: 232
Period size: 66 Copynumber: 2.0 Consensus size: 66
801 CAAATAATGC
*
811 TACAGAATCTAGAATATCCTTCTATTTTATTCAATGCTTATAGATTTCAGCTTTAGGATTTTGCA
1 TACAGAATCTAGAATATCCTTCTATTTTATTCAATGCTCATAGATTTCAGCTTTAGGATTTTGCA
876 G
66 G
* * *
877 TACAGAATCTAGTATATCCTTCTATTTTATTCAGTTCTCATAGATTTCAGCTTTAGGATTTTGCA
1 TACAGAATCTAGAATATCCTTCTATTTTATTCAATGCTCATAGATTTCAGCTTTAGGATTTTGCA
942 G
66 G
943 TA
1 TA
945 AATTTTGGCT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (66 bp):
TACAGAATCTAGAATATCCTTCTATTTTATTCAATGCTCATAGATTTCAGCTTTAGGATTTTGCA
G
Found at i:16745 original size:27 final size:27
Alignment explanation
Indices: 16707--16760 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
16697 TATTGATTAT
16707 CAATCATTCAGAATACATATAGTTTTG
1 CAATCATTCAGAATACATATAGTTTTG
16734 CAATCATTCAGAATACATATAGTTTTG
1 CAATCATTCAGAATACATATAGTTTTG
16761 GTATGTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (27 bp):
CAATCATTCAGAATACATATAGTTTTG
Found at i:16781 original size:69 final size:69
Alignment explanation
Indices: 16666--16798 Score: 212
Period size: 69 Copynumber: 1.9 Consensus size: 69
16656 CCACACTACT
* * *
16666 AATCATTCAGAATACATATAGTTTTTGCACGTATTGATTATCAATCATTCAGAATACATATAGTT
1 AATCATTCAGAATACATATAGTTTTGGCACGTATTGATAATCAATCATTCAGAATACAGATAGTT
16731 TTGC
66 TTGC
* * *
16735 AATCATTCAGAATACATATAGTTTTGGTATGTATTGATAATTAATCATTCAGAATACAGATAGT
1 AATCATTCAGAATACATATAGTTTTGGCACGTATTGATAATCAATCATTCAGAATACAGATAGT
16799 AACCCCATGG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (69 bp):
AATCATTCAGAATACATATAGTTTTGGCACGTATTGATAATCAATCATTCAGAATACAGATAGTT
TTGC
Found at i:20509 original size:34 final size:34
Alignment explanation
Indices: 20398--20502 Score: 165
Period size: 35 Copynumber: 3.0 Consensus size: 34
20388 TAAATAGCAA
*
20398 GTAGCCATAGCTAGGATATCATCCAAAGACCAGGG
1 GTAGCCATAACTAGG-TATCATCCAAAGACCAGGG
*
20433 GTAGCCATAACTAGAGTATCATCCAAAGTCCAGGG
1 GTAGCCATAACTAG-GTATCATCCAAAGACCAGGG
*
20468 TTAGCCATAACTAGGTATCATCCAAAGACCAGGG
1 GTAGCCATAACTAGGTATCATCCAAAGACCAGGG
20502 G
1 G
20503 CCGCCATCAA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
34 19 0.30
35 44 0.69
36 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (34 bp):
GTAGCCATAACTAGGTATCATCCAAAGACCAGGG
Found at i:31945 original size:20 final size:20
Alignment explanation
Indices: 31920--31962 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
31910 TCTTTGCTTC
31920 TTTCCTTT-TCATTTTTCATT
1 TTTCCTTTCTC-TTTTTCATT
*
31940 TTTCCTTTCTCTTTTTCCTT
1 TTTCCTTTCTCTTTTTCATT
31960 TTT
1 TTT
31963 TTTCATTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTCCTTTCTCTTTTTCATT
Found at i:33025 original size:2 final size:2
Alignment explanation
Indices: 33018--33043 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33008 GCTATAGCTC
33018 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
33044 TTAAACGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39909 original size:26 final size:26
Alignment explanation
Indices: 39857--39905 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
39847 GCCCATATTT
39857 ATTTTTTAAAATAAAATAATAATTAA
1 ATTTTTTAAAATAAAATAATAATTAA
39883 ATTTTTTAATAA-AAAATAA-AATT
1 ATTTTTTAA-AATAAAATAATAATT
39906 TAAACATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 16 0.73
27 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTTTTTAAAATAAAATAATAATTAA
Found at i:40061 original size:29 final size:30
Alignment explanation
Indices: 40003--40063 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
39993 GTTCTAATTA
* *
40003 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
40033 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
40062 AT
1 AT
40064 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:47049 original size:15 final size:15
Alignment explanation
Indices: 47029--47064 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
47019 TGTATTAGGC
47029 CTGATCTGGTGTATT
1 CTGATCTGGTGTATT
47044 CTGATCTGGTGTATT
1 CTGATCTGGTGTATT
47059 CTGATC
1 CTGATC
47065 AATTCTACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.14, C:0.17, G:0.25, T:0.44
Consensus pattern (15 bp):
CTGATCTGGTGTATT
Found at i:52544 original size:20 final size:20
Alignment explanation
Indices: 52519--52559 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
52509 GAAAATAAAA
52519 GGCATTTGATTTACAAATTG
1 GGCATTTGATTTACAAATTG
*
52539 GGCATTTGATTTACAAGTTG
1 GGCATTTGATTTACAAATTG
52559 G
1 G
52560 TGCTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (20 bp):
GGCATTTGATTTACAAATTG
Found at i:58721 original size:50 final size:49
Alignment explanation
Indices: 58656--59124 Score: 319
Period size: 50 Copynumber: 9.5 Consensus size: 49
58646 TGAGTGTGGG
*
58656 GTAATAAGAATGTAATCTTTAAGCTAAAAGATGAAATTTTTGATTAATTT
1 GTAATAAAAATG-AATCTTTAAGCTAAAAGATGAAATTTTTGATTAATTT
* * * *
58706 ATGATAAAAATGTAATCTTTAAGCTAAAAGATGAGATTTTTGATTGATTT
1 GTAATAAAAATG-AATCTTTAAGCTAAAAGATGAAATTTTTGATTAATTT
* * * *
58756 ATGATAAAAATGTAATCTTTAAGC-------T-AAACTTTTGATTAATTA
1 GTAATAAAAATG-AATCTTTAAGCTAAAAGATGAAATTTTTGATTAATTT
** * *
58798 ACAATAAAAATGAAATCTTT-GGACTAAAAGAGTG-AATCTTTGATTAATTT
1 GTAATAAAAATG-AATCTTTAAG-CTAAAAGA-TGAAATTTTTGATTAATTT
** *
58848 GTAAATAAAAATGAGATCTTTGAA-CTAAAAGATTG-AATTTTAAAGTAATTT
1 GT-AATAAAAATGA-ATCTTT-AAGCTAAAAGA-TGAAATTTTTGATTAATTT
* * *
58899 GTGAATAAAAATGAGATCTTTAA-TTAAAAGATTAATTTTTTGATTAATTT
1 GT-AATAAAAATGA-ATCTTTAAGCTAAAAGATGAAATTTTTGATTAATTT
* * * * *
58949 GTAAATAAAAACGATATCTTTGAA-CTAAATGGT-AGAACTTTGGATTAATTT
1 GT-AATAAAAATGA-ATCTTT-AAGCTAAAAGATGA-AATTTTTGATTAATTT
*
59000 GTAAATAAAAATGAGAT-TTGAA-CTAAAAGATCG-AATTTTTGATTAATTT
1 GT-AATAAAAATGA-ATCTTTAAGCTAAAAGAT-GAAATTTTTGATTAATTT
* * * * *
59049 GTAATGAAAATGGAGTCTTTAGGCTAAAAAATTG-AATTTTTGGTTAATTT
1 GTAATAAAAAT-GAATCTTTAAGCTAAAAGA-TGAAATTTTTGATTAATTT
* *
59099 ATAATAAAGATGAAGTCTTTAAGCTA
1 GTAATAAAAATGAA-TCTTTAAGCTA
59125 GAAGGTTGAC
Statistics
Matches: 337, Mismatches: 58, Indels: 48
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.00
42 31 0.09
43 1 0.00
48 9 0.03
49 33 0.10
50 167 0.50
51 95 0.28
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.38
Consensus pattern (49 bp):
GTAATAAAAATGAATCTTTAAGCTAAAAGATGAAATTTTTGATTAATTT
Found at i:58861 original size:51 final size:50
Alignment explanation
Indices: 58800--59161 Score: 301
Period size: 51 Copynumber: 7.2 Consensus size: 50
58790 ATTAATTAAC
* *
58800 AATAAAAATGAAATCTTTGGACTAAAAGAGTGAATCTTTGATTAATTTGTA
1 AATAAAAATGAAATCTTTGAACTAAAAGA-TGAATTTTTGATTAATTTGTA
* ** * *
58851 AATAAAAATGAGATCTTTGAACTAAAAGATTGAATTTTAAAGTAATTTGTG
1 AATAAAAATGAAATCTTTGAACTAAAAGA-TGAATTTTTGATTAATTTGTA
* * *
58902 AATAAAAATGAGATCTTT-AATTAAAAGATTAATTTTTTGATTAATTTGTA
1 AATAAAAATGAAATCTTTGAACTAAAAGATGAA-TTTTTGATTAATTTGTA
* * * * * *
58952 AATAAAAACGATATCTTTGAACTAAATGGTAGAACTTTGGATTAATTTGTA
1 AATAAAAATGAAATCTTTGAACTAAAAGAT-GAATTTTTGATTAATTTGTA
*
59003 AATAAAAATGAGA--TTTGAACTAAAAGATCGAATTTTTGATTAATTTGT-
1 AATAAAAATGAAATCTTTGAACTAAAAGAT-GAATTTTTGATTAATTTGTA
* * * * * * *
59051 AATGAAAATGGAGTCTTT-AGGCTAAAAAATTGAATTTTTGGTTAATTTAT-
1 AATAAAAATGAAATCTTTGA-ACTAAAAGA-TGAATTTTTGATTAATTTGTA
* * * * * * *
59101 AATAAAGATGAAGTCTTT-AAGCTAGAAGGTTG-ACTTTTGATAAAATTG-A
1 AATAAAAATGAAATCTTTGAA-CTA-AAAGATGAATTTTTGATTAATTTGTA
59150 AATAAAAATGAA
1 AATAAAAATGAA
59162 GCCTTTAAGT
Statistics
Matches: 251, Mismatches: 50, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
48 9 0.04
49 56 0.22
50 86 0.34
51 98 0.39
52 2 0.01
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.36
Consensus pattern (50 bp):
AATAAAAATGAAATCTTTGAACTAAAAGATGAATTTTTGATTAATTTGTA
Found at i:58968 original size:101 final size:100
Alignment explanation
Indices: 58800--59052 Score: 319
Period size: 101 Copynumber: 2.5 Consensus size: 100
58790 ATTAATTAAC
* * * *
58800 AATAAAAATGAAATCTTTGGACTAAAAGAGTGAATCTTTGATTAATTTGTAAATAAAAATGAGAT
1 AATAAAAATGAGATCTTT-AACTAAAAGA-TGAATTTTTGATTAATTTGTAAATAAAAACGAGAT
* * *
58865 CTTTGAACTAAAAGATTGAATTTTAAAGTAATTTGTG
64 CTTTGAACTAAAAGATAGAACTTTAAAGTAATTTGTA
* * *
58902 AATAAAAATGAGATCTTTAATTAAAAGATTAATTTTTTGATTAATTTGTAAATAAAAACGATATC
1 AATAAAAATGAGATCTTTAACTAAAAGATGAA-TTTTTGATTAATTTGTAAATAAAAACGAGATC
* * ** *
58967 TTTGAACTAAATGGTAGAACTTTGGATTAATTTGTA
65 TTTGAACTAAAAGATAGAACTTTAAAGTAATTTGTA
*
59003 AATAAAAATGAGAT-TTGAACTAAAAGATCGAATTTTTGATTAATTTGTAA
1 AATAAAAATGAGATCTTTAACTAAAAGAT-GAATTTTTGATTAATTTGTAA
59053 TGAAAATGGA
Statistics
Matches: 131, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
100 33 0.25
101 81 0.62
102 17 0.13
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (100 bp):
AATAAAAATGAGATCTTTAACTAAAAGATGAATTTTTGATTAATTTGTAAATAAAAACGAGATCT
TTGAACTAAAAGATAGAACTTTAAAGTAATTTGTA
Found at i:59778 original size:49 final size:49
Alignment explanation
Indices: 59713--60099 Score: 589
Period size: 49 Copynumber: 7.9 Consensus size: 49
59703 TTGAAGTTCA
59713 TCTTTTTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTAAGTTTG
1 TCTTTTTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTAAGTTTG
* *
59762 TCTTTTTCCCAAATTGCCCTTCCCGGTCGGAAGGTGTTTTTTAAGTTTG
1 TCTTTTTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTAAGTTTG
* * *
59811 TCTTTTTCCCAAGTTGCCATTCCCAGTCAGAAGGTGTTGTTTAAGTTTG
1 TCTTTTTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTAAGTTTG
59860 TCTTTTTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTAAGTTTG
1 TCTTTTTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTAAGTTTG
* * *
59909 TCTTTTTCCCAAATTGCTCTTCCCGGTCGGAAGGTGTTTTTTAAGTTTG
1 TCTTTTTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTAAGTTTG
*
59958 TCTTTTTCCCAAGTTGCCCTTCCCAGTCGGAAGGTGTTGTTTAAGTTTG
1 TCTTTTTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTAAGTTTG
* * * * *
60007 TCTTTATCCCAAATTGCCCTTTCTAGTCGGAAGGTATTGTTCAAAG-TTG
1 TCTTTTTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTT-TAAGTTTG
* *
60056 TCTTTATTCCCAATTTGCCCTTTCCCA-CCGGAAGGTGTTGTTTA
1 TCTTT-TTCCCAAATTGCCC-TTCCCAGTCGGAAGGTGTTGTTTA
60100 CTTTTCGCTG
Statistics
Matches: 305, Mismatches: 30, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
49 273 0.90
50 28 0.09
51 4 0.01
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (49 bp):
TCTTTTTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTAAGTTTG
Found at i:60255 original size:41 final size:41
Alignment explanation
Indices: 60062--60548 Score: 646
Period size: 41 Copynumber: 12.0 Consensus size: 41
60052 GTTGTCTTTA
* *
60062 TTCCCAATTTGCCCTTTCCCACCGGAAGGTGTTGTTTACTT
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
* * * *
60103 TTCGCTGTTTTGCCCTTCCCCACCGGAAGGTGTTATTTACGT
1 TTCCCAG-TTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
*
60145 TT-CCAGTTTGCCCTTCCCCACCGAAAGGTGTTGTTTACTT
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
* * *
60185 TT-TCAGTTTGCCCTTCCCTACCGGAAGGTGTTGTTCACTT
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
* * * *
60225 TTCCCAATTCGCCTTTCCCCACCGGAAGGTGTTGTTCACTT
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
* * ** *
60266 TTCCCAATTTGCCCTTCCCTAATGAAAGGTGTTGTTTACTT
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
*
60307 TTCCCAGTTTGCCCTTCCCCA-GGGAAAGGTGTTGTTTACTT
1 TTCCCAGTTTGCCCTTCCCCACCGG-AAGGTGTTGTTTACTT
60348 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
**
60389 TTCCCAGTTTGCCCTTTGCCACCGGAAGGTGTTGTTTACTT
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
* * *
60430 TT-CCACTTTGCCCTTTCCCACCGGAAGGCGTTG-TT-C-T
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
*
60467 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTATTT
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
* * *
60508 TTCCTAGTTTGCCATTCCCAACCGGAAGGTGTTGTTTACTT
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
60549 ATCTTATTCC
Statistics
Matches: 393, Mismatches: 45, Indels: 16
0.87 0.10 0.04
Matches are distributed among these distances:
37 3 0.01
38 29 0.07
39 4 0.01
40 98 0.25
41 224 0.57
42 35 0.09
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (41 bp):
TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT
Found at i:64545 original size:27 final size:26
Alignment explanation
Indices: 64514--64573 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
64504 TAGACTCTGG
**
64514 ATTTTGAGTTTCGAACATGGCATGCAA
1 ATTTTGAGTTTCG-ACATGAAATGCAA
* *
64541 ATTTTGAGTTTTGAGATGAAATGCAA
1 ATTTTGAGTTTCGACATGAAATGCAA
64567 ATTTTGA
1 ATTTTGA
64574 ATTTTGACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 17 0.59
27 12 0.41
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (26 bp):
ATTTTGAGTTTCGACATGAAATGCAA
Found at i:64638 original size:43 final size:43
Alignment explanation
Indices: 64557--64638 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
64547 AGTTTTGAGA
* *
64557 TGAAATGCAAATTTTGAATTTTGACTTTTGAGGAATGAAATGC
1 TGAAATGCAAATTTTGAAATTTGACTTTTGAGCAATGAAATGC
** * *
64600 TGAAATGCAGGTTTTGAAATTTGATTTTTGAGCCATGAA
1 TGAAATGCAAATTTTGAAATTTGACTTTTGAGCAATGAA
64639 TTTTGAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (43 bp):
TGAAATGCAAATTTTGAAATTTGACTTTTGAGCAATGAAATGC
Found at i:64645 original size:7 final size:7
Alignment explanation
Indices: 64635--64680 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
64625 TTTTGAGCCA
64635 TGAATTT
1 TGAATTT
64642 TGAATTT
1 TGAATTT
*
64649 TGAGTTT
1 TGAATTT
*
64656 TGAGTTT
1 TGAATTT
*
64663 TGAGTTT
1 TGAATTT
64670 TGAATTT
1 TGAATTT
64677 TGAA
1 TGAA
64681 ATGCAAACAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (7 bp):
TGAATTT
Found at i:64656 original size:14 final size:14
Alignment explanation
Indices: 64639--64679 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
64629 GAGCCATGAA
64639 TTTTGAATTTTGAG
1 TTTTGAATTTTGAG
*
64653 TTTTGAGTTTTGAG
1 TTTTGAATTTTGAG
64667 TTTTGAATTTTGA
1 TTTTGAATTTTGA
64680 AATGCAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.59
Consensus pattern (14 bp):
TTTTGAATTTTGAG
Found at i:64670 original size:28 final size:28
Alignment explanation
Indices: 64610--64679 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
64600 TGAAATGCAG
* *
64610 GTTTTGAAATTTGATTTTTGAGCCATGA
1 GTTTTGAATTTTGAGTTTTGAGCCATGA
* ***
64638 ATTTTGAATTTTGAGTTTTGAGTTTTGA
1 GTTTTGAATTTTGAGTTTTGAGCCATGA
64666 GTTTTGAATTTTGA
1 GTTTTGAATTTTGA
64680 AATGCAAACA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.23, C:0.03, G:0.21, T:0.53
Consensus pattern (28 bp):
GTTTTGAATTTTGAGTTTTGAGCCATGA
Found at i:64854 original size:33 final size:33
Alignment explanation
Indices: 64812--64889 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
64802 AAAAACTGTG
* * *
64812 GATTTTGAACTTTGAGTTTTGATATGATATACA
1 GATTTTGAACTTTGAATTTTGAAATGAAATACA
*
64845 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATACA
* *
64878 AATTTTAAACTT
1 GATTTTGAACTT
64890 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATACA
Found at i:65050 original size:54 final size:54
Alignment explanation
Indices: 64952--65089 Score: 197
Period size: 54 Copynumber: 2.6 Consensus size: 54
64942 TTCTTAGAAT
* * *
64952 GACCGCACTTGGA-CAACTTAAGATAAACTTAGATCTTTGAAAACTTCTACGAAA
1 GACCACAC-TGGATCAACTTAAGATCAACTTAGATCTTTGAAAACTTCAACGAAA
* * * *
65006 GACCACACTGGGTCATCTTAAGATCAATTTAGATCTTTGAAAACTTCAATGAAA
1 GACCACACTGGATCAACTTAAGATCAACTTAGATCTTTGAAAACTTCAACGAAA
65060 GACCACACTGGATCAACTTAAGATCAACTT
1 GACCACACTGGATCAACTTAAGATCAACTT
65090 TCTAGAGAGA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 3 0.04
54 70 0.96
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (54 bp):
GACCACACTGGATCAACTTAAGATCAACTTAGATCTTTGAAAACTTCAACGAAA
Found at i:65141 original size:20 final size:18
Alignment explanation
Indices: 65121--65162 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
65111 CATTTTAAAC
*
65121 ACAAAACATGAATTTTGA
1 ACAAAAAATGAATTTTGA
* *
65139 ACAAGAAATGGATTTTGA
1 ACAAAAAATGAATTTTGA
65157 ACAAAA
1 ACAAAA
65163 TTTTGATAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (18 bp):
ACAAAAAATGAATTTTGA
Found at i:65242 original size:37 final size:37
Alignment explanation
Indices: 65200--65648 Score: 406
Period size: 37 Copynumber: 12.1 Consensus size: 37
65190 TTGAAGAGAC
* * *
65200 ACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAA
1 ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
* ** * * *
65237 ACCTAAACAGGAATTTTGAACAA-GATTTTGATGAGAC
1 ACCTAAACAGGGACCTTAAACAAGGA-TTTGATAAGAA
*
65274 ACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
* * * *
65311 ATCTAAACAGGGATCTTAAACAA-AATTTTTGACAAGAA
1 ACCTAAACAGGGACCTTAAACAAGGA--TTTGATAAGAA
* * **
65349 ACCTAAACAGGCACCTCAAGTAAGGATTTGATAAGAA
1 ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
* *
65386 ACCTAAACAGGGATCTTAAACAA-GATTTTGATAAGAC
1 ACCTAAACAGGGACCTTAAACAAGGA-TTTGATAAGAA
* * * *
65423 ACCTAAATAGGGACCTTAAATAAAGATTTAATAAGAA
1 ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
* * * * *
65460 ACCTAAACAGGAATCTTGAACAA-GATTTCGATGAGAC
1 ACCTAAACAGGGACCTTAAACAAGGATTT-GATAAGAA
* * * * *
65497 ACCTAAACAGGGATCTTGAACCA-GATTTCGATGAGAC
1 ACCTAAACAGGGACCTTAAACAAGGATTT-GATAAGAA
* * * *
65534 ACCTAAATAGGGACCTTAAATAAGGATTTGGTAAGAC
1 ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
* * *
65571 ACCTAAACAGGGACCTTAAATAAGAATTTAATAA-AA
1 ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
* *
65607 CACCTAAATAGGGACCTTAAACAAGGATTTGATAAGAC
1 -ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
65645 ACCT
1 ACCT
65649 TGATACGAAT
Statistics
Matches: 335, Mismatches: 66, Indels: 22
0.79 0.16 0.05
Matches are distributed among these distances:
36 11 0.03
37 286 0.85
38 37 0.11
39 1 0.00
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (37 bp):
ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
Found at i:65275 original size:74 final size:74
Alignment explanation
Indices: 65186--65648 Score: 531
Period size: 74 Copynumber: 6.2 Consensus size: 74
65176 CCTAAACTGG
* *
65186 GATTTTGA-AGAGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAA
1 GATTTTGATA-AGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGGA
* *
65250 TTTTGAACAA
65 TCTTAAACAA
* * *
65260 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAATCTAAACAGGGAT
1 GATTTTGATAAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGGAT
65325 CTTAAACAA
66 CTTAAACAA
* * * * * * *
65334 AATTTTTGACAAGAAACCTAAACAGGCACCTCAAGTAAGGATTTGATAAGAAACCTAAACAGGGA
1 GA-TTTTGATAAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGGA
65399 TCTTAAACAA
65 TCTTAAACAA
* * *
65409 GATTTTGATAAGACACCTAAATAGGGACCTTAAATAAAGATTTAATAAGAAACCTAAACAGGAAT
1 GATTTTGATAAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGGAT
*
65474 CTTGAACAA
66 CTTAAACAA
* * * * ** * * * *
65483 GATTTCGATGAGACACCTAAACAGGGATCTTGAACCA-GATTTCGATGAGACACCTAAATAGGGA
1 GATTTTGATAAGACACCTAAACAGGGACCTTAAATAAGGATTT-AATAAGAAACCTAAACAGGGA
* *
65547 CCTTAAATAA
65 TCTTAAACAA
* * *
65557 GGA-TTTGGTAAGACACCTAAACAGGGACCTTAAATAAGAATTTAATAA-AACACCTAAATAGGG
1 -GATTTTGATAAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAA-ACCTAAACAGGG
*
65620 ACCTTAAACAA
64 ATCTTAAACAA
65631 GGA-TTTGATAAGACACCT
1 -GATTTTGATAAGACACCT
65649 TGATACGAAT
Statistics
Matches: 329, Mismatches: 54, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
73 6 0.02
74 251 0.76
75 72 0.22
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (74 bp):
GATTTTGATAAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGGAT
CTTAAACAA
Found at i:65319 original size:111 final size:110
Alignment explanation
Indices: 65196--65648 Score: 480
Period size: 111 Copynumber: 4.1 Consensus size: 110
65186 GATTTTGAAG
* *
65196 AGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATTTTGAACAAG
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTGAACAAG
* *
65261 ATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
66 ATTTTGATAAGACACCTAAACAGGGACCTTAAACAA-GATTTGATA
* * * * * * * * * * *
65307 AGAAATCTAAACAGGGATCTTAAACAA-AATTTTTGACAAGAAACCTAAACAGGCA-CCTCAAGT
1 AGACACCTAAACAGGGACCTTAAATAAGGA--TTTAATAAGAAACCTAAACAGGAATCTTGAA-C
* *
65370 AAGGA-TTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGATA
63 AA-GATTTTGATAAGACACCTAAACAGGGACCTTAAACAAGA-TTTGATA
* *
65419 AGACACCTAAATAGGGACCTTAAATAAAGATTTAATAAGAAACCTAAACAGGAATCTTGAACAAG
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTGAACAAG
* * * * * *
65484 ATTTCGATGAGACACCTAAACAGGGATCTTGAACCAGATTTCGATG
66 ATTTTGATAAGACACCTAAACAGGGACCTTAAACAAGATTT-GATA
* ** * * * * *
65530 AGACACCTAAATAGGGACCTTAAATAAGGATTTGGTAAGACACCTAAACAGGGACCTTAAATAAG
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTGAACAAG
* * * *
65595 AATTTAATAAAACACCTAAATAGGGACCTTAAACAAGGATTTGATA
66 ATTTTGATAAGACACCTAAACAGGGACCTTAAACAA-GATTTGATA
65641 AGACACCT
1 AGACACCT
65649 TGATACGAAT
Statistics
Matches: 279, Mismatches: 53, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
110 6 0.02
111 179 0.64
112 91 0.33
113 3 0.01
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (110 bp):
AGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTGAACAAG
ATTTTGATAAGACACCTAAACAGGGACCTTAAACAAGATTTGATA
Found at i:65383 original size:149 final size:149
Alignment explanation
Indices: 65200--65630 Score: 467
Period size: 149 Copynumber: 2.9 Consensus size: 149
65190 TTGAAGAGAC
* * * *
65200 ACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATTTTGAACAAGATTT
1 ACCTAAACAGGCACCTCAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTAAACAAGATTT
* * * * *
65265 TGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAATCTAAACAGGGATCTTAA
66 TGATAAGACACCTAAACAGGGACCTTAAATAAAGATTTAATAAGAAACCTAAACAGGAATCTTAA
65330 ACAAAATTTTTGACAAGAA
131 ACAAAATTTTTGACAAGAA
* * *
65349 ACCTAAACAGGCACCTCAAGTAAGGATTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTT
1 ACCTAAACAGGCACCTCAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTAAACAAGATTT
* *
65414 TGATAAGACACCTAAATAGGGACCTTAAATAAAGATTTAATAAGAAACCTAAACAGGAATCTTGA
66 TGATAAGACACCTAAACAGGGACCTTAAATAAAGATTTAATAAGAAACCTAAACAGGAATCTTAA
* * ** *
65479 ACAAGA-TTTCGATGAGAC
131 ACAAAATTTTTGACAAGAA
* * ** ** * * * * * * *
65497 ACCTAAACAGGGATCTTGAACCA-GATTTCGATGAGACACCTAAATAGGGACCTTAAATAAGGA-
1 ACCTAAACAGGCACCTCAAATAAGGATTT-AATAAGAAACCTAAACAGGAATCTTAAACAA-GAT
* * * *
65560 TTTGGTAAGACACCTAAACAGGGACCTTAAAT-AAGAATTTAATAA-AACACCTAAATAGGGACC
64 TTTGATAAGACACCTAAACAGGGACCTTAAATAAAG-ATTTAATAAGAA-ACCTAAACAGGAATC
65623 TTAAACAA
127 TTAAACAA
65631 GGATTTGATA
Statistics
Matches: 241, Mismatches: 37, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
147 10 0.04
148 108 0.45
149 123 0.51
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.23
Consensus pattern (149 bp):
ACCTAAACAGGCACCTCAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTAAACAAGATTT
TGATAAGACACCTAAACAGGGACCTTAAATAAAGATTTAATAAGAAACCTAAACAGGAATCTTAA
ACAAAATTTTTGACAAGAA
Found at i:68351 original size:15 final size:16
Alignment explanation
Indices: 68318--68357 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
68308 TTACTTTCCT
68318 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
68334 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
68349 TTGCTTTCT
1 TTGTTTTCT
68358 TTCAACCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:68808 original size:29 final size:30
Alignment explanation
Indices: 68765--68837 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
68755 TGCGTTTTTG
**
68765 AAAAAAAAAAGTTTTGAGTTT-TGCGTCAT
1 AAAAAAAAATTTTTTGAGTTTCTGCGTCAT
**
68794 AAAAAAAAATTTTTTTTGTTTCTGCGTCAT
1 AAAAAAAAATTTTTTGAGTTTCTGCGTCAT
*
68824 -AAAAAATATTTTTT
1 AAAAAAAAATTTTTT
68838 CTTTTATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 30 0.79
30 8 0.21
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (30 bp):
AAAAAAAAATTTTTTGAGTTTCTGCGTCAT
Done.