Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008991.1 Hibiscus syriacus cultivar Beakdansim tig00112358_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: 64580
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3714 original size:85 final size:85
Alignment explanation
Indices: 3571--4137 Score: 652
Period size: 85 Copynumber: 6.7 Consensus size: 85
3561 GAACTATTGG
* * * * *
3571 CAGCATAACTCAAAGTGAGAAGGGCTATCTGTC-ACCAAAGTCCTTCGAGTTTGATTACACTCAA
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACC-AAGACCTTCGAGTTCGATTACACTCAA
* * *
3635 CTCAAAGGAATATTAAATTTA
65 CTCAAAGGCACATCAAATTTA
* * * *
3656 CAGCATAACTCAAGGCGGGAAAGGTTATATGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAAC
* *
3721 TCAAAGGCATATCGAATTTA
66 TCAAAGGCACATCAAATTTA
* * * * * * *
3741 CAACATAGCTCAAGGCGATAAGGGCTATATGTCAACAAAAGACCTTCAAGTTCGATTACACTCAA
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACACTCAA
*
3806 CTCAAAGGCACATCAAATTGA
65 CTCAAAGGCACATCAAATTTA
* * * * * * * *
3827 TAACATAGCTCAAGACGAGAAGGGTTATCTGTCAACCAAGGCCTTCTAGTTCGATTACACACAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAAC
*
3892 TCAAAGGCACATCAAATTCA
66 TCAAAGGCACATCAAATTTA
* * * * *
3912 CAGCGTAACTCAAGGCTAGAAGGGTTATCTGTCAACTAAGACCTTCGAGTTTGATTACACTTAAC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAAC
*
3977 TCAAAGGCACATTAAATTTA
66 TCAAAGGCACATCAAATTTA
* *
3997 CAGCATAACTCAAGGCGAGAAGGGTTATCTATCAACCAAGACCTTCGAGTCCGATTACA-TCCAA
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACT-CAA
*
4061 CTCAAAGGCATATCAAATTTA
65 CTCAAAGGCACATCAAATTTA
** * * * ** * *
4082 CAGCATAGTTTAAGGCTAAAAGGACTATCTGTCAACAAATACCTTCGAGTTCGATT
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATT
4138 CCATTAAGCT
Statistics
Matches: 409, Mismatches: 70, Indels: 6
0.84 0.14 0.01
Matches are distributed among these distances:
84 1 0.00
85 331 0.81
86 77 0.19
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (85 bp):
CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAAC
TCAAAGGCACATCAAATTTA
Found at i:4034 original size:170 final size:169
Alignment explanation
Indices: 3571--4137 Score: 722
Period size: 170 Copynumber: 3.3 Consensus size: 169
3561 GAACTATTGG
* * * *
3571 CAGCATAACTCAAAG-TGAGAAGGGCTATCTGTCACCAAAGTCCTTCGAGTTTGATTACACTCAA
1 CAGCATAACTCAAGGCT-AGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAA
* * * * *
3635 CTCAAAGGAATATTAAATTTACAGCATAACTCAAGGCGGGAAAGGTTATATGTCAACCAAGACCT
65 CTCAAAGGCACATTAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCT
*
3700 TCGAGTTCGATTACACTCAGCTCAAAGGCATATCGAATTTA
130 TCGAGTTCGATTACAC-CAGCTCAAAGGCATATCAAATTTA
* * * * * *
3741 CAACATAGCTCAAGGCGATAAGGGCTATATGTCAACAAAAGACCTTCAAGTTCGATTACACTCAA
1 CAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAA
* * * * * * *
3806 CTCAAAGGCACATCAAATTGATAACATAGCTCAAGACGAGAAGGGTTATCTGTCAACCAAGGCCT
65 CTCAAAGGCACATTAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCT
* * *
3871 TCTAGTTCGATTACACACAGCTCAAAGGCACATCAAATTCA
130 TCGAGTTCGATTACAC-CAGCTCAAAGGCATATCAAATTTA
* * * * *
3912 CAGCGTAACTCAAGGCTAGAAGGGTTATCTGTCAACTAAGACCTTCGAGTTTGATTACACTTAAC
1 CAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAAC
*
3977 TCAAAGGCACATTAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTATCAACCAAGACCTT
66 TCAAAGGCACATTAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTT
* *
4042 CGAGTCCGATTACATCCAACTCAAAGGCATATCAAATTTA
131 CGAGTTCGATTACA-CCAGCTCAAAGGCATATCAAATTTA
** * * * *
4082 CAGCATAGTTTAAGGCTAAAAGGACTATCTGTCAACAAATACCTTCGAGTTCGATT
1 CAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATT
4138 CCATTAAGCT
Statistics
Matches: 333, Mismatches: 61, Indels: 6
0.83 0.15 0.01
Matches are distributed among these distances:
170 189 0.57
171 144 0.43
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (169 bp):
CAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAAC
TCAAAGGCACATTAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTT
CGAGTTCGATTACACCAGCTCAAAGGCATATCAAATTTA
Found at i:4195 original size:85 final size:84
Alignment explanation
Indices: 3571--4205 Score: 536
Period size: 85 Copynumber: 7.5 Consensus size: 84
3561 GAACTATTGG
* * * * * * * *
3571 CAGCATAACTCAAAGTGAGAAGGGCTATCTGTCACCAAAGTCCTTCGAGTTTGATTACACTCAAC
1 CAGCATAACTTAAGGCGAGAAAGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACA-TTAAC
* *
3636 TCAAAGGAATATTAAATTTA
65 TCAAAGGCATATCAAATTTA
* * * * * * *
3656 CAGCATAACTCAAGGCGGGAAAGGTTATATGTCAACCAAGACCTTCGAGTTCGATTACACTCAGC
1 CAGCATAACTTAAGGCGAGAAAGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACA-TTAAC
*
3721 TCAAAGGCATATCGAATTTA
65 TCAAAGGCATATCAAATTTA
* * * * * * * *
3741 CAACATAGCTCAAGGCGATAAGGGCTATATGTCAACAAAAGACCTTCAAGTTCGATTACACTCAA
1 CAGCATAACTTAAGGCGAGAAAGGCTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACA-TTAA
* *
3806 CTCAAAGGCACATCAAATTGA
64 CTCAAAGGCATATCAAATTTA
* * * * * * * * * * *
3827 TAACATAGCTCAAGACGAGAAGGGTTATCTGTCAACCAAGGCCTTCTAGTTCGATTACA-CACAG
1 CAGCATAACTTAAGGCGAGAAAGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTA-A-
* *
3891 CTCAAAGGCACATCAAATTCA
64 CTCAAAGGCATATCAAATTTA
* * * * * * *
3912 CAGCGTAACTCAAGGCTAGAAGGGTTATCTGTCAACTAAGACCTTCGAGTTTGATTACACTTAAC
1 CAGCATAACTTAAGGCGAGAAAGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACA-TTAAC
* *
3977 TCAAAGGCACATTAAATTTA
65 TCAAAGGCATATCAAATTTA
* * * * * * *
3997 CAGCATAACTCAAGGCGAGAAGGGTTATCTATCAACCAAGACCTTCGAGTCCGATTACATCCAAC
1 CAGCATAACTTAAGGCGAGAAAGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACAT-TAAC
4062 TCAAAGGCATATCAAATTTA
65 TCAAAGGCATATCAAATTTA
** * * *
4082 CAGCATAGTTTAAGGCTA-AAAGGACTATCTGTCAACAAATACCTTCGAGTTCGATTCCATTAAG
1 CAGCATAACTTAAGGCGAGAAAGG-CTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTAA-
* * * *
4146 CTCTAGGGCATGTCAAATTCA
64 CTCAAAGGCATATCAAATTTA
* * * *
4167 TAGCATAACTTAAGTCGAGAAAAGCTATCTTTCAACAAA
1 CAGCATAACTTAAGGCGAGAAAGGCTATCTGTCAACAAA
4206 AACTGTCAAG
Statistics
Matches: 461, Mismatches: 80, Indels: 18
0.82 0.14 0.03
Matches are distributed among these distances:
83 2 0.00
84 8 0.02
85 371 0.80
86 79 0.17
87 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (84 bp):
CAGCATAACTTAAGGCGAGAAAGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTAACT
CAAAGGCATATCAAATTTA
Found at i:4220 original size:255 final size:256
Alignment explanation
Indices: 3590--4222 Score: 617
Period size: 256 Copynumber: 2.5 Consensus size: 256
3580 TCAAAGTGAG
* * * * * * * * * *
3590 AAGGGCTATCTGTCACCAAAGTCCTTCGAGTTTGATTACACTCAACTCAAAGGAATATTAAATTT
1 AAGGACTATCTGTCAACAAAGACCTTCGAGTTCGATTACACACAGCTCAAAGGCACATCAAATTC
* * * * * * * * * *
3655 ACAGCATAACTCAAGGCGGGAAAGGTTATATGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
66 ACAGCATAACTCAAGGCGAGAAAAGCTATCTGTCAACTAAAAACTTCAAGTTTGATTACACTCAA
* * * * *
3720 CTCAAAGGCATATCGAATTTACAACATAGCTCAAGGCGATAAGGGCTATATGTCAACAAAAGACC
131 CTCAAAGGCACATCAAATTTACAACATAACTCAAGGCGAGAAGGGCTATATATCAACAAAAGACC
* * *
3785 TTCAAGTTCGATTACACTCAACTCAAAGGCACATCAAATTGATAACATAGCTCAAGACGAG
196 TTCAAGTCCGATTACACTCAACTCAAAGGCACATCAAATTGACAACATAGCTCAAGACGAA
** * * *
3846 AAGGGTTATCTGTCAACCAAGGCCTTCTAGTTCGATTACACACAGCTCAAAGGCACATCAAATTC
1 AAGGACTATCTGTCAACAAAGACCTTCGAGTTCGATTACACACAGCTCAAAGGCACATCAAATTC
* * ** * * * * *
3911 ACAGCGTAACTCAAGGCTAGAAGGGTTATCTGTCAACTAAGACCTTCGAGTTTGATTACACTTAA
66 ACAGCATAACTCAAGGCGAGAAAAGCTATCTGTCAACTAAAAACTTCAAGTTTGATTACACTCAA
* * * * *
3976 CTCAAAGGCACATTAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTATCAAC-CAAGACC
131 CTCAAAGGCACATCAAATTTACAACATAACTCAAGGCGAGAAGGGCTATATATCAACAAAAGACC
* * * * * * * *
4040 TTCGAGTCCGATTACA-TCCAACTCAAAGGCATATCAAATTTACAGCATAGTTTAAGGCTAA
196 TTCAAGTCCGATTACACT-CAACTCAAAGGCACATCAAATTGACAACATAGCTCAAGACGAA
* * * * * **
4101 AAGGACTATCTGTCAACAAATACCTTCGAGTTCGATTCCATTA-AGCTCTAGGGCATGTCAAATT
1 AAGGACTATCTGTCAACAAAGACCTTCGAGTTCGATTACA-CACAGCTCAAAGGCACATCAAATT
* * * *
4165 CATAGCATAACTTAAGTCGAGAAAAGCTATCTTTCAAC-AAAAACTGTCAAGTTTGATT
65 CACAGCATAACTCAAGGCGAGAAAAGCTATCTGTCAACTAAAAACT-TCAAGTTTGATT
4223 TCATTCATCT
Statistics
Matches: 308, Mismatches: 66, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
254 6 0.02
255 144 0.47
256 158 0.51
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (256 bp):
AAGGACTATCTGTCAACAAAGACCTTCGAGTTCGATTACACACAGCTCAAAGGCACATCAAATTC
ACAGCATAACTCAAGGCGAGAAAAGCTATCTGTCAACTAAAAACTTCAAGTTTGATTACACTCAA
CTCAAAGGCACATCAAATTTACAACATAACTCAAGGCGAGAAGGGCTATATATCAACAAAAGACC
TTCAAGTCCGATTACACTCAACTCAAAGGCACATCAAATTGACAACATAGCTCAAGACGAA
Found at i:6168 original size:28 final size:28
Alignment explanation
Indices: 6136--6189 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
6126 ATGTATTCCT
6136 TTTATGATTATGTTCCAACAAAGCAACA
1 TTTATGATTATGTTCCAACAAAGCAACA
6164 TTTATGATTATGTTCCAACAAAGCAA
1 TTTATGATTATGTTCCAACAAAGCAA
6190 TAATTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (28 bp):
TTTATGATTATGTTCCAACAAAGCAACA
Found at i:6196 original size:28 final size:28
Alignment explanation
Indices: 6137--6196 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
6127 TGTATTCCTT
*
6137 TTATGATTATGTTCCAACAAAGCAACAT
1 TTATGATTATGTTCCAACAAAGCAACAA
*
6165 TTATGATTATGTTCCAACAAAGCAATAA
1 TTATGATTATGTTCCAACAAAGCAACAA
6193 TTAT
1 TTAT
6197 TTTTTCTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (28 bp):
TTATGATTATGTTCCAACAAAGCAACAA
Found at i:6236 original size:4 final size:4
Alignment explanation
Indices: 6223--6264 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
6213 AATTAACATT
* *
6223 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTTG TTTA TTGA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
6265 CCTTTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:6346 original size:15 final size:16
Alignment explanation
Indices: 6316--6350 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
6306 TTTCACCCTC
6316 TTTTATTTAGTATTTA
1 TTTTATTTAGTATTTA
*
6332 TTTTATTT-TTATTTA
1 TTTTATTTAGTATTTA
6347 TTTT
1 TTTT
6351 CCCCTTTTGA
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:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATTTAGTATTTA
Found at i:11081 original size:35 final size:35
Alignment explanation
Indices: 11042--11109 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
11032 TCATATTCAA
*
11042 AATTCCAAAACA-TTTCAATTACATTCTATACCCCG
1 AATTCCAAAACACTTT-AATTACATTCTAAACCCCG
*
11077 AATTCCAAAATACTTTAATTACATTCTAAACCC
1 AATTCCAAAACACTTTAATTACATTCTAAACCC
11110 TAAATCAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.40, C:0.26, G:0.01, T:0.32
Consensus pattern (35 bp):
AATTCCAAAACACTTTAATTACATTCTAAACCCCG
Found at i:11781 original size:11 final size:11
Alignment explanation
Indices: 11745--11771 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
11735 TAAATCCTAT
11745 TAATTTGATTC
1 TAATTTGATTC
11756 TAATTTGATTC
1 TAATTTGATTC
11767 TAATT
1 TAATT
11772 CTAATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (11 bp):
TAATTTGATTC
Found at i:18432 original size:14 final size:14
Alignment explanation
Indices: 18413--18463 Score: 102
Period size: 14 Copynumber: 3.6 Consensus size: 14
18403 ATATTTACCG
18413 CTTACTCAATTCCT
1 CTTACTCAATTCCT
18427 CTTACTCAATTCCT
1 CTTACTCAATTCCT
18441 CTTACTCAATTCCT
1 CTTACTCAATTCCT
18455 CTTACTCAA
1 CTTACTCAA
18464 ATCATCAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTACTCAATTCCT
Found at i:19599 original size:45 final size:46
Alignment explanation
Indices: 19521--19708 Score: 240
Period size: 45 Copynumber: 4.1 Consensus size: 46
19511 GCATATCCAA
19521 TATTTTACC-ATATACTTACCATTT-ATTCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCT
* * * * *
19565 TATTCTAACAATATACTTACCATTT-GTTCTATAAGCTCATAAGCT
1 TATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCT
* *
19610 TATTTTACCAAAATAC-TATCCATTTAATACCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTA-CCATTTAATTCCATAAGCTCGTAAGCT
* *
19656 TATTTTACCAATATATACTTACCATTTAATCCCATAAGCTCGTACGCT
1 TATTTTACC-A-ATATACTTACCATTTAATTCCATAAGCTCGTAAGCT
19704 TATTT
1 TATTT
19709 GCATGCTTAC
Statistics
Matches: 123, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
44 9 0.07
45 51 0.41
46 25 0.20
47 1 0.01
48 35 0.28
49 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.39
Consensus pattern (46 bp):
TATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCT
Found at i:23781 original size:10 final size:9
Alignment explanation
Indices: 23755--23814 Score: 57
Period size: 9 Copynumber: 6.1 Consensus size: 9
23745 TTTAGTCTCA
23755 TTTTTTTCT
1 TTTTTTTCT
*
23764 TTCTTTTCT
1 TTTTTTTCT
23773 TTTTCTTTCTT
1 TTTT-TTTC-T
*
23784 TTTCTTTTTT
1 TTT-TTTTCT
23794 TTTCTGTTTCT
1 TTT-T-TTTCT
23805 TTTTTTTCT
1 TTTTTTTCT
23814 T
1 T
23815 ATAAAATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 17 0.40
10 11 0.26
11 14 0.33
12 1 0.02
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:23786 original size:16 final size:16
Alignment explanation
Indices: 23757--23814 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
23747 TAGTCTCATT
23757 TTTTTCTTTC-TTTTC
1 TTTTTCTTTCTTTTTC
23772 TTTTTCTTTCTTTTTC
1 TTTTTCTTTCTTTTTC
* *
23788 TTTTTTTTTCTGTTTC
1 TTTTTCTTTCTTTTTC
23804 TTTTT-TTTCTT
1 TTTTTCTTTCTT
23815 ATAAAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
15 15 0.38
16 24 0.62
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTTTCTTTCTTTTTC
Found at i:26674 original size:46 final size:45
Alignment explanation
Indices: 26537--26722 Score: 257
Period size: 46 Copynumber: 4.1 Consensus size: 45
26527 GCATATCCAA
*
26537 TATTTTACC-ATATACTTACCATTTATGCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTATACCATAAGCTCGTAAGCT
* * * *
26581 TATTCTAACAATATACTTACCATTTGTTCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTATACCATAAGCTCGTAAGCT
* * *
26626 TATTTTACCAAAATACTTATCATTTAATACCATAAGCTCATAAGCT
1 TATTTTACCAATATACTTACCATTT-ATACCATAAGCTCGTAAGCT
* *
26672 TATTTTACCAATATACTTATCATTTAGTCCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTA-TACCATAAGCTCGTAAGCT
26718 TATTT
1 TATTT
26723 GCATGCTTAC
Statistics
Matches: 125, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
44 7 0.06
45 55 0.44
46 63 0.50
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (45 bp):
TATTTTACCAATATACTTACCATTTATACCATAAGCTCGTAAGCT
Found at i:26690 original size:91 final size:90
Alignment explanation
Indices: 26537--26722 Score: 275
Period size: 91 Copynumber: 2.1 Consensus size: 90
26527 GCATATCCAA
* * *
26537 TATTTTACCATATACTTACCATTTATGCCATAAGCTCGTAAGCTTATTCTAACAATATACTTACC
1 TATTTTACCAAATACTTACCATTTATACCATAAGCTCATAAGCTTATTCTAACAATATACTTACC
*
26602 ATTT-GTTCCATAAGCTCGTAAGCT
66 ATTTAGTCCCATAAGCTCGTAAGCT
* * *
26626 TATTTTACCAAAATACTTATCATTTAATACCATAAGCTCATAAGCTTATTTTACCAATATACTTA
1 TATTTTACC-AAATACTTACCATTT-ATACCATAAGCTCATAAGCTTATTCTAACAATATACTTA
*
26691 TCATTTAGTCCCATAAGCTCGTAAGCT
64 CCATTTAGTCCCATAAGCTCGTAAGCT
26718 TATTT
1 TATTT
26723 GCATGCTTAC
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
89 9 0.10
90 13 0.15
91 40 0.47
92 24 0.28
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (90 bp):
TATTTTACCAAATACTTACCATTTATACCATAAGCTCATAAGCTTATTCTAACAATATACTTACC
ATTTAGTCCCATAAGCTCGTAAGCT
Found at i:26854 original size:40 final size:40
Alignment explanation
Indices: 26810--26902 Score: 168
Period size: 40 Copynumber: 2.3 Consensus size: 40
26800 ATTTCATCGA
* *
26810 AGTGCTGAGGTCGAGCATTGGTCACCTAATAATGCACCGT
1 AGTGCCGAGGTCGAGCATTGCTCACCTAATAATGCACCGT
26850 AGTGCCGAGGTCGAGCATTGCTCACCTAATAATGCACCGT
1 AGTGCCGAGGTCGAGCATTGCTCACCTAATAATGCACCGT
26890 AGTGCCGAGGTCG
1 AGTGCCGAGGTCG
26903 GGTTTTACCC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
AGTGCCGAGGTCGAGCATTGCTCACCTAATAATGCACCGT
Found at i:26916 original size:40 final size:40
Alignment explanation
Indices: 26810--26918 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 40
26800 ATTTCATCGA
* ***
26810 AGTGCTGAGGTCGAGCATTGGTCACCTAATAATGCACCGT
1 AGTGCCGAGGTCGAGCATTACCCACCTAATAATGCACCGT
* *
26850 AGTGCCGAGGTCGAGCATTGCTCACCTAATAATGCACCGT
1 AGTGCCGAGGTCGAGCATTACCCACCTAATAATGCACCGT
* **
26890 AGTGCCGAGGTCGGGTTTTACCCACCTAA
1 AGTGCCGAGGTCGAGCATTACCCACCTAA
26919 CTTGTACTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.24, C:0.26, G:0.27, T:0.24
Consensus pattern (40 bp):
AGTGCCGAGGTCGAGCATTACCCACCTAATAATGCACCGT
Found at i:28395 original size:29 final size:29
Alignment explanation
Indices: 28363--28495 Score: 126
Period size: 29 Copynumber: 4.6 Consensus size: 29
28353 TAAATTAATT
* *
28363 TTTTTATAAATTACATTTAAGGACAAAGA
1 TTTTTATAAATTACAATTAAGGACAAATA
* * *
28392 TTTTTATAAACTACAATAAAGGACAAATC
1 TTTTTATAAATTACAATTAAGGACAAATA
* * * *
28421 TTTTTATAATTTA-AAATAGAGAACAAATT
1 TTTTTATAAATTACAATTA-AGGACAAATA
* *
28450 TTTTTATAAATTACAA-TAATGACATATA
1 TTTTTATAAATTACAATTAAGGACAAATA
*
28478 CTTTTTACAAATTACAAT
1 -TTTTTATAAATTACAAT
28496 AACAACTCAT
Statistics
Matches: 83, Mismatches: 17, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
28 9 0.11
29 72 0.87
30 2 0.02
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (29 bp):
TTTTTATAAATTACAATTAAGGACAAATA
Found at i:28425 original size:58 final size:59
Alignment explanation
Indices: 28363--28494 Score: 144
Period size: 58 Copynumber: 2.3 Consensus size: 59
28353 TAAATTAATT
** *
28363 TTTTTATAAATTACATTTA-AGGACAAAGATTTTTATAAACTACAATAAAGGACAAAT-C
1 TTTTTATAAATTACAAATAGAGAACAAAGATTTTTATAAACTACAAT-AAGGACAAATAC
* ** * * *
28421 TTTTTATAATTTA-AAATAGAGAACAAATTTTTTTATAAATTACAATAATGACATATAC
1 TTTTTATAAATTACAAATAGAGAACAAAGATTTTTATAAACTACAATAAGGACAAATAC
*
28479 TTTTTACAAATTACAA
1 TTTTTATAAATTACAA
28495 TAACAACTCA
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
57 11 0.18
58 47 0.78
59 2 0.03
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (59 bp):
TTTTTATAAATTACAAATAGAGAACAAAGATTTTTATAAACTACAATAAGGACAAATAC
Found at i:28519 original size:28 final size:28
Alignment explanation
Indices: 28450--28543 Score: 118
Period size: 28 Copynumber: 3.3 Consensus size: 28
28440 AGAACAAATT
* ** *
28450 TTTTTATAAATTACAATAATGACATATA
1 TTTTTACAAATTACAATAACAACCTATA
28478 CTTTTTACAAATTACAATAACAA-CTCATA
1 -TTTTTACAAATTACAATAACAACCT-ATA
*
28507 TTTTTACATATTACAATAACAACCTATA
1 TTTTTACAAATTACAATAACAACCTATA
28535 TTTTTACAA
1 TTTTTACAA
28544 TCACTACATT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 33 0.58
29 24 0.42
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.40
Consensus pattern (28 bp):
TTTTTACAAATTACAATAACAACCTATA
Found at i:31989 original size:30 final size:30
Alignment explanation
Indices: 31951--32009 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
31941 GTTGACATTT
31951 TTATTTTT-AGGTTGTTGGTATTAT-AAATG
1 TTATTTTTAAGGTTGTTGG-ATTATGAAATG
*
31980 TTATGTTTTAAGTTTGTTGGATTATGAAAT
1 TTAT-TTTTAAGGTTGTTGGATTATGAAAT
32010 TGATAATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 4 0.15
30 9 0.35
31 13 0.50
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.54
Consensus pattern (30 bp):
TTATTTTTAAGGTTGTTGGATTATGAAATG
Found at i:33680 original size:29 final size:29
Alignment explanation
Indices: 33645--33726 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
33635 AAACTAAATT
*
33645 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
33674 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
33703 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
33727 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:38447 original size:29 final size:29
Alignment explanation
Indices: 38412--38493 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
38402 AAACTAAATT
*
38412 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
38441 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
38470 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
38494 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:47814 original size:27 final size:27
Alignment explanation
Indices: 47754--47815 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
47744 TCTTATTGTT
* *
47754 CTAATTTTTTAAGTTATAAAATGAATA
1 CTAATTTTTTAAGTTATAAAATAAACA
*
47781 CTAATTTTTTTA-TTATAAAATAAACA
1 CTAATTTTTTAAGTTATAAAATAAACA
*
47807 TTACATTTT
1 CTA-ATTTT
47816 AGTTGTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (27 bp):
CTAATTTTTTAAGTTATAAAATAAACA
Found at i:48838 original size:44 final size:44
Alignment explanation
Indices: 48707--48839 Score: 248
Period size: 44 Copynumber: 3.0 Consensus size: 44
48697 AATCATCACT
*
48707 GAACTTTAATTTCTCTCATATTTCACTCACTATACTTTAAATCT
1 GAACTTTAATTTCTCTCATATTTCACTCACTATACTTTAAATCC
*
48751 GAACTTTAATTTCTCTCATATTTCACTCACTATACCTTAAATCC
1 GAACTTTAATTTCTCTCATATTTCACTCACTATACTTTAAATCC
48795 GAACTTTAATTTCTCTCATATTTCACTCACTATACTTTAAATCC
1 GAACTTTAATTTCTCTCATATTTCACTCACTATACTTTAAATCC
48839 G
1 G
48840 TTCAATTTCC
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 86 1.00
ACGTcount: A:0.29, C:0.25, G:0.03, T:0.43
Consensus pattern (44 bp):
GAACTTTAATTTCTCTCATATTTCACTCACTATACTTTAAATCC
Found at i:49970 original size:20 final size:21
Alignment explanation
Indices: 49920--49978 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 21
49910 CCAAAAGATA
*
49920 AAAAACATATCACAAAGGCAG
1 AAAAACATGTCACAAAGGCAG
*
49941 ATATAAACATGTCATAAAGGCAG
1 A-A-AAACATGTCACAAAGGCAG
*
49964 -AAAACATGTTACAAA
1 AAAAACATGTCACAAA
49979 AATATAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 12 0.38
21 2 0.06
22 1 0.03
23 17 0.53
ACGTcount: A:0.54, C:0.15, G:0.14, T:0.17
Consensus pattern (21 bp):
AAAAACATGTCACAAAGGCAG
Found at i:55556 original size:23 final size:22
Alignment explanation
Indices: 55530--55588 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
55520 CGTAATCTAC
*
55530 CAAAAGGCAAAGAAAACGTGTCA
1 CAAAAGGCAGAGAAAACGTG-CA
55553 C-AAAGGCAGAGATAAACGTGCA
1 CAAAAGGCAGAGA-AAACGTGCA
55575 -ATAAAGGCAGAGAA
1 CA-AAAGGCAGAGAA
55589 CATGTTACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 13 0.41
23 19 0.59
ACGTcount: A:0.51, C:0.15, G:0.25, T:0.08
Consensus pattern (22 bp):
CAAAAGGCAGAGAAAACGTGCA
Found at i:56523 original size:32 final size:33
Alignment explanation
Indices: 56479--56595 Score: 107
Period size: 32 Copynumber: 3.4 Consensus size: 33
56469 TTTAAATGGG
56479 TTTTAGTATTTTAATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTTAATTAAGTTTTAGGATATTAT
**
56512 TTTTA-TATTTT-ATCTTTGTTTTAGGTATTTAGTTTAAATT
1 TTTTAGTATTTTAAT-TAAGTTTTAGG-A--TA--TT--A-T
56552 TTTTAGTATTTTAATTAAGTTTTAGGATATTA-
1 TTTTAGTATTTTAATTAAGTTTTAGGATATTAT
56584 TTTTA-TATTTTA
1 TTTTAGTATTTTA
56596 TCTTTATTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 24
0.71 0.04 0.25
Matches are distributed among these distances:
31 9 0.13
32 20 0.29
33 6 0.09
34 1 0.01
35 2 0.03
36 2 0.03
37 2 0.03
38 2 0.03
39 1 0.01
40 7 0.10
41 15 0.22
42 2 0.03
ACGTcount: A:0.27, C:0.01, G:0.10, T:0.62
Consensus pattern (33 bp):
TTTTAGTATTTTAATTAAGTTTTAGGATATTAT
Found at i:56571 original size:73 final size:73
Alignment explanation
Indices: 56461--56643 Score: 278
Period size: 73 Copynumber: 2.5 Consensus size: 73
56451 TTTTATCTTT
*
56461 GTATTTAGTTTAAATGGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTATC
1 GTATTTAGTTTAAAT-GTTTTTAGTATTTTAATTAAGTTTTAGGATATTA-TTTTATATTTTATC
* *
56526 TTTGTTTTAG
64 TTTATTTTAA
56536 GTATTTAGTTTAAAT-TTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTATATTTTATCTT
1 GTATTTAGTTTAAATGTTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTATATTTTATCTT
56600 TATTTTAA
66 TATTTTAA
* *
56608 GTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTA
1 GTA-TTTAGTTTAAAT-GTTTTTAGTATTTTAATTA
56644 GGATTTAAGA
Statistics
Matches: 100, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
72 25 0.25
73 44 0.44
75 31 0.31
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.59
Consensus pattern (73 bp):
GTATTTAGTTTAAATGTTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTATATTTTATCTT
TATTTTAA
Found at i:58647 original size:21 final size:21
Alignment explanation
Indices: 58608--58648 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
58598 TGCATTCGAT
*
58608 ACTGTTCACGATATGTTCATC
1 ACTGTTCACGATATATTCATC
58629 ACTGTTCACG-TACTATTCAT
1 ACTGTTCACGATA-TATTCAT
58649 AAAATTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (21 bp):
ACTGTTCACGATATATTCATC
Found at i:60577 original size:16 final size:16
Alignment explanation
Indices: 60553--60598 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
60543 AATCTCTTTA
*
60553 ATTTGTTTATTTAATT
1 ATTTTTTTATTTAATT
60569 ATTTTTTTATTTAATT
1 ATTTTTTTATTTAATT
*
60585 CTTATCTTTTATTT
1 ATT-T-TTTTATTT
60599 TAAAAACAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 17 0.65
17 1 0.04
18 8 0.31
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (16 bp):
ATTTTTTTATTTAATT
Done.