Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001850.1 Hibiscus syriacus cultivar Beakdansim tig00003746_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: 52702
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:12012 original size:16 final size:17
Alignment explanation
Indices: 11967--12014 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
11957 TTTTTAGGTG
* *
11967 TTTCAGTATATATTTTA
1 TTTCAGAATATTTTTTA
11984 TTTCAGAAT-TTTTTTA
1 TTTCAGAATATTTTTTA
*
12000 TTTTA-AATATTTTTT
1 TTTCAGAATATTTTTT
12015 CTCGTTTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 3 0.11
16 16 0.59
17 8 0.30
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTCAGAATATTTTTTA
Found at i:15113 original size:12 final size:11
Alignment explanation
Indices: 15089--15131 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
15079 TTATTTTAAA
*
15089 TTTATATACTT
1 TTTATATAATT
15100 TTTAATATAATT
1 TTT-ATATAATT
*
15112 TTTGTATAATT
1 TTTATATAATT
*
15123 TTTTTATAA
1 TTTATATAA
15132 AATTTAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (11 bp):
TTTATATAATT
Found at i:17835 original size:17 final size:19
Alignment explanation
Indices: 17792--17836 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
17782 CCAATTTACT
17792 TAAAATATATGAAAATTTA
1 TAAAATATATGAAAATTTA
*
17811 TAATATATAT-AATAA-TTA
1 TAAAATATATGAA-AATTTA
17829 -AAAATATA
1 TAAAATATA
17837 AAAATATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.30
18 5 0.22
19 11 0.48
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TAAAATATATGAAAATTTA
Found at i:21628 original size:21 final size:21
Alignment explanation
Indices: 21564--21632 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
21554 GTGCGGCGGT
* * *
21564 GGACGGTGGTCGAAAGACGGC
1 GGACGATGGTCGGAGGACGGC
* * *
21585 GAACGGTGGTTGGAGGACGGC
1 GGACGATGGTCGGAGGACGGC
21606 GGACGATGGTCGGAGGACGGC
1 GGACGATGGTCGGAGGACGGC
21627 GGACGA
1 GGACGA
21633 CAAGCGACTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.22, C:0.17, G:0.51, T:0.10
Consensus pattern (21 bp):
GGACGATGGTCGGAGGACGGC
Found at i:26149 original size:48 final size:48
Alignment explanation
Indices: 26097--26192 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
26087 CTAATATACA
* *
26097 GTTAAGAAAAAACGTTACCGAAAATATTATTATTTTTTTACTAAAAAT
1 GTTAAGAAAAAACGCTACCGAAAATATTATTATTTTTTTACAAAAAAT
* **** *
26145 GTTAATATTGGACGCTACCTAAAATATTATTATTTTTTTACAAAAAAT
1 GTTAAGAAAAAACGCTACCGAAAATATTATTATTTTTTTACAAAAAAT
26193 TAAGTAGCGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (48 bp):
GTTAAGAAAAAACGCTACCGAAAATATTATTATTTTTTTACAAAAAAT
Found at i:26344 original size:79 final size:79
Alignment explanation
Indices: 26191--26343 Score: 200
Period size: 78 Copynumber: 1.9 Consensus size: 79
26181 TTTACAAAAA
* * * *
26191 ATTAAGTAGCGAAATTAATATTTTCGGTGAAAAAAAATAATATTTTAAGTAGCACTTTACCGAAA
1 ATTAAGTAGCGAAATTAACATTTCCGGTGAAAAAAAATAATATTTTAAGTAACACTTTACCAAAA
*
26256 ATGTTAAAAACTCC
66 ATATTAAAAACTCC
* * * ** *
26270 ATTAAGTAGCGAAATTAACATTTCCGGT-AAGAAAAATAATGTTTTAGGTAACGTTTTATCAAAA
1 ATTAAGTAGCGAAATTAACATTTCCGGTGAAAAAAAATAATATTTTAAGTAACACTTTACCAAAA
26334 ATATTAAAAA
66 ATATTAAAAA
26344 AATATTAACA
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
78 37 0.59
79 26 0.41
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (79 bp):
ATTAAGTAGCGAAATTAACATTTCCGGTGAAAAAAAATAATATTTTAAGTAACACTTTACCAAAA
ATATTAAAAACTCC
Found at i:33774 original size:580 final size:580
Alignment explanation
Indices: 32674--33834 Score: 2229
Period size: 580 Copynumber: 2.0 Consensus size: 580
32664 CAGAACATGG
32674 ATATGATTTGGCAATAAGAAAACATACATGTAATATTTTCCCCAATAACTGTTTCCTTTTTCTTC
1 ATATGATTTGGCAATAAGAAAACATACATGTAATATTTTCCCCAATAACTGTTTCCTTTTTCTTC
32739 CCTTATTAACAACTATAATAAGCCAAAAACTGATAAATCTCAGATTTCACTTCACGTATAAACTA
66 CCTTATTAACAACTATAATAAGCCAAAAACTGATAAATCTCAGATTTCACTTCACGTATAAACTA
32804 AAACAAAGAGAATTGCTTCATATTCCCTAGCCCTAGTCTTGGATTCATGTCATACCTTTCAAACC
131 AAACAAAGAGAATTGCTTCATATTCCCTAGCCCTAGTCTTGGATTCATGTCATACCTTTCAAACC
32869 ACGACTCCTGCAATATTTCATTTACATAAAAGAAAATCTCATTTGTTAAACAGTAAGATTTATAT
196 ACGACTCCTGCAATATTTCATTTACATAAAAGAAAATCTCATTTGTTAAACAGTAAGATTTATAT
*
32934 TCTTCAAAGGGTATCGCCTAATTTAACTACATCTATATTTCAATTCTTATTTCCTATTTAATTCA
261 TCTTCAAAGGGTATCGCCTAATTTAACTACATCTATACTTCAATTCTTATTTCCTATTTAATTCA
32999 GTAACAGTTATAAAAGCTGCAAAAAAAATTCCAAGTAACATTCATTTTCCCAGACAAAGAGATAA
326 GTAACAGTTATAAAAGCTGCAAAAAAAATTCCAAGTAACATTCATTTTCCCAGACAAAGAGATAA
33064 GGCATCTCGACAAAATGGCATCTCGATACAAACAATAATGTCCAAAACAAATTCTTATGGAATTA
391 GGCATCTCGACAAAATGGCATCTCGATACAAACAATAATGTCCAAAACAAATTCTTATGGAATTA
33129 AAAAAGTTGAAAACCCTATGTATATGAAAAAACAGAAATTTTCTTCTGTGTTATACGGAATCATT
456 AAAAAGTTGAAAACCCTATGTATATGAAAAAACAGAAATTTTCTTCTGTGTTATACGGAATCATT
33194 TTTGGGAAGCTTTCAAGTCAAATCCTAAAGAATTTATTTGTACTTATAGGAATGTGTGGT
521 TTTGGGAAGCTTTCAAGTCAAATCCTAAAGAATTTATTTGTACTTATAGGAATGTGTGGT
*
33254 ATATGATTTGGCAATAAGAAAACATACATGTAATATTTTCTCCAATAACTGTTTCCTTTTTCTTC
1 ATATGATTTGGCAATAAGAAAACATACATGTAATATTTTCCCCAATAACTGTTTCCTTTTTCTTC
33319 CCTTATTAACAACTATAATAAGCCAAAAACTGATAAATCTCAGATTTCACTTCACGTATAAACTA
66 CCTTATTAACAACTATAATAAGCCAAAAACTGATAAATCTCAGATTTCACTTCACGTATAAACTA
*
33384 AAACAAAGAGAATTGCTTCGTATTCCCTAGCCCTAGTCTTGGATTCATGTCATACCTTTCAAACC
131 AAACAAAGAGAATTGCTTCATATTCCCTAGCCCTAGTCTTGGATTCATGTCATACCTTTCAAACC
33449 ACGACTCCTGCAATATTTCATTTACATAAAAGAAAATC-CAATTTGTTAAACAGTAAGATTTATA
196 ACGACTCCTGCAATATTTCATTTACATAAAAGAAAATCTC-ATTTGTTAAACAGTAAGATTTATA
33513 TTCTTCAAAGGGTATCGCCTAATTTAACTACATCTATACTTCAATTCTTATTTCCTATTTAATTC
260 TTCTTCAAAGGGTATCGCCTAATTTAACTACATCTATACTTCAATTCTTATTTCCTATTTAATTC
33578 AGTAACAGTTATAAAAGCTGCAAAAAAAATTCCAAGTAACATTCATTTTCCCAGACAAAGAGATA
325 AGTAACAGTTATAAAAGCTGCAAAAAAAATTCCAAGTAACATTCATTTTCCCAGACAAAGAGATA
*
33643 AGGCATCTCGACAAAATGGCATCTCGATACAAACAATAATGTCCAAAATAAATTCTTATGGAATT
390 AGGCATCTCGACAAAATGGCATCTCGATACAAACAATAATGTCCAAAACAAATTCTTATGGAATT
*
33708 AAAAAAGTTGAAAACCCTATGTATATGAAAAAACATAAATTTTCTTCTAAGTG-T-TACGGAATC
455 AAAAAAGTTGAAAACCCTATGTATATGAAAAAACAGAAATTTTCTTCT--GTGTTATACGGAATC
33771 ATTTTTGGGAAGCTTTCAAGTCAAATCCTAAAGAATTTATTTGTACTTATAGGAATGTGTGGT
518 ATTTTTGGGAAGCTTTCAAGTCAAATCCTAAAGAATTTATTTGTACTTATAGGAATGTGTGGT
33834 A
1 A
33835 ATCAATTTTG
Statistics
Matches: 573, Mismatches: 5, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
579 1 0.00
580 568 0.99
581 1 0.00
582 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (580 bp):
ATATGATTTGGCAATAAGAAAACATACATGTAATATTTTCCCCAATAACTGTTTCCTTTTTCTTC
CCTTATTAACAACTATAATAAGCCAAAAACTGATAAATCTCAGATTTCACTTCACGTATAAACTA
AAACAAAGAGAATTGCTTCATATTCCCTAGCCCTAGTCTTGGATTCATGTCATACCTTTCAAACC
ACGACTCCTGCAATATTTCATTTACATAAAAGAAAATCTCATTTGTTAAACAGTAAGATTTATAT
TCTTCAAAGGGTATCGCCTAATTTAACTACATCTATACTTCAATTCTTATTTCCTATTTAATTCA
GTAACAGTTATAAAAGCTGCAAAAAAAATTCCAAGTAACATTCATTTTCCCAGACAAAGAGATAA
GGCATCTCGACAAAATGGCATCTCGATACAAACAATAATGTCCAAAACAAATTCTTATGGAATTA
AAAAAGTTGAAAACCCTATGTATATGAAAAAACAGAAATTTTCTTCTGTGTTATACGGAATCATT
TTTGGGAAGCTTTCAAGTCAAATCCTAAAGAATTTATTTGTACTTATAGGAATGTGTGGT
Found at i:34304 original size:233 final size:231
Alignment explanation
Indices: 33897--34325 Score: 562
Period size: 233 Copynumber: 1.8 Consensus size: 231
33887 ATAGATATGC
* * *
33897 TATAACACGTGTAATCATCTTGTTGATTGGAATTTACAACTTTGTAAACTTAGCAATTAGTGCAT
1 TATAACACGTGTAATCATCATGTTGATTGGAATTTACAACTTTGGAAACTTAGCAATGAGTGCAT
* *
33962 CTTTAATAACTAAAACAAGCTCTGCTAGAATTTAATCTTATTCACCTTCCTAAACAAGAAAAAAT
66 CTTTAATAACTAAAACAAGCTCTGCTAGAATTTAATCTTATTCACCTTCCAAAACAAG--AAAAC
* * * *
34027 AGATCCAAACCAGTTTACATGTAACTAAAATAGGATTGTTTGTAACCTTTTACTTGATGAGGCCT
129 AGATCCAAACCAGTTTACATATAAATAAAATAGGATTGTTTGTAACCGTTTACTTGATGAAGCCT
34092 ACAGTCATTAGCCAGGATAATGGAAAATCCAGAGATAG
194 ACAGTCATTAGCCAGGATAATGGAAAATCCAGAGATAG
* *
34130 TATAACACTCGTGTAAT-AGTCATGTTGATTGGAAATTT-CAACTTTGGAGACTTGGCAATGAGT
1 TATAACA--CGTGTAATCA-TCATGTTGATTGG-AATTTACAACTTTGGAAACTTAGCAATGAGT
** * *
34193 GTGT-TTCTAATAACTATAACAAGAC-CTTGCTAGAATTTAATCTTATTGACCTTCCAAAACAAG
62 GCATCTT-TAATAACTAAAACAAG-CTC-TGCTAGAATTTAATCTTATTCACCTTCCAAAACAAG
* * * * *
34256 -AAACAGATCCAAATCAGTTTATATATAAATGAAATTGGATTGTTTGTAACCGTTTACTTGTTGA
124 AAAACAGATCCAAACCAGTTTACATATAAATAAAATAGGATTGTTTGTAACCGTTTACTTGATGA
34320 AGCCTA
189 AGCCTA
34326 AAAAAGTAGT
Statistics
Matches: 169, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
233 67 0.40
234 3 0.02
235 59 0.35
236 40 0.24
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (231 bp):
TATAACACGTGTAATCATCATGTTGATTGGAATTTACAACTTTGGAAACTTAGCAATGAGTGCAT
CTTTAATAACTAAAACAAGCTCTGCTAGAATTTAATCTTATTCACCTTCCAAAACAAGAAAACAG
ATCCAAACCAGTTTACATATAAATAAAATAGGATTGTTTGTAACCGTTTACTTGATGAAGCCTAC
AGTCATTAGCCAGGATAATGGAAAATCCAGAGATAG
Found at i:46687 original size:17 final size:17
Alignment explanation
Indices: 46665--46698 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46655 AAAAGTGATA
*
46665 ATTAGAGTATCAAACGT
1 ATTAGAGTAGCAAACGT
46682 ATTAGAGTAGCAAACGT
1 ATTAGAGTAGCAAACGT
46699 GTAATTTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (17 bp):
ATTAGAGTAGCAAACGT
Found at i:46906 original size:20 final size:20
Alignment explanation
Indices: 46862--47072 Score: 146
Period size: 20 Copynumber: 10.4 Consensus size: 20
46852 AATGACCAAC
**
46862 AAAATCGCAACGCGA-TATC
1 AAAATCGCAACGCGATTAAG
*
46881 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
46901 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
46921 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
* ***
46941 AAAATCTCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
46962 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
46983 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
47004 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
47025 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
47047 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
47065 AAAATCGC
1 AAAATCGC
47073 TAAGAAAATC
Statistics
Matches: 150, Mismatches: 28, Indels: 27
0.73 0.14 0.13
Matches are distributed among these distances:
18 4 0.03
19 15 0.10
20 90 0.60
21 13 0.09
22 28 0.19
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:46994 original size:42 final size:42
Alignment explanation
Indices: 46938--47072 Score: 211
Period size: 42 Copynumber: 3.3 Consensus size: 42
46928 CAACGGTCAA
*
46938 AAGAAAATCTCAACGCGATATTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
* *
46980 AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
* *
47022 CAGAAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
47062 AAGAAAATCGC
1 AAGAAAATCGC
47073 TAAGAAAATC
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
40 31 0.36
42 54 0.64
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
Found at i:47060 original size:40 final size:40
Alignment explanation
Indices: 46862--47072 Score: 207
Period size: 42 Copynumber: 5.2 Consensus size: 40
46852 AATGACCAAC
*
46862 AAAATCGCAACGCGATAT-CAA-AATCGCAACGCGATTTAG
1 AAAATCGCAACGCGAT-TCCAAGAATCGCAACGCGATTAAG
* **** *
46901 AAAATCGCAACGTTGAAAAGAA-AATCGCAACG-G-TCAAAAG
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACGCGAT--TAAG
* *
46941 AAAATCTCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTAAG
* * *
46983 AGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAG
47025 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
47065 AAAATCGC
1 AAAATCGC
47073 TAAGAAAATC
Statistics
Matches: 141, Mismatches: 20, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
38 1 0.01
39 14 0.10
40 59 0.42
41 3 0.02
42 62 0.44
43 1 0.01
44 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
Found at i:47188 original size:6 final size:6
Alignment explanation
Indices: 47177--47227 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
47167 GACACGTATT
47177 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
47225 ACC
1 ACC
47228 CAACCCGACC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:47757 original size:6 final size:6
Alignment explanation
Indices: 47726--47791 Score: 104
Period size: 6 Copynumber: 11.7 Consensus size: 6
47716 CGCCGTCTCG
47726 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
47770 GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTC
47792 ATACGTGTCT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.33
6 40 0.67
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:47941 original size:20 final size:21
Alignment explanation
Indices: 47894--48013 Score: 156
Period size: 22 Copynumber: 5.7 Consensus size: 21
47884 TCATTTTCTG
47894 AATCGCGTTGCGATTCTTGGAA
1 AATCGCGTTGCGATTCTTGG-A
47916 AATCGCGTTGCGATTCTTGG-
1 AATCGCGTTGCGATTCTTGGA
*
47936 AATCGCGTTGTGATTCTTGGA
1 AATCGCGTTGCGATTCTTGGA
*
47957 AGATCGCGTTGCGATT-TTATG-
1 A-ATCGCGTTGCGATTCTT-GGA
*
47978 AATCGCATTGCGATTCTTGGA
1 AATCGCGTTGCGATTCTTGGA
47999 AGATCGCGTTGCGAT
1 A-ATCGCGTTGCGAT
48014 CTTCTTTTCA
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
20 33 0.38
21 7 0.08
22 46 0.53
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.34
Consensus pattern (21 bp):
AATCGCGTTGCGATTCTTGGA
Found at i:47952 original size:42 final size:42
Alignment explanation
Indices: 47893--48013 Score: 190
Period size: 42 Copynumber: 2.9 Consensus size: 42
47883 CTCATTTTCT
*
47893 GAATCGCGTTGCGATTCTTGGAAAATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTAG
* *
47935 GAATCGCGTTGTGATTCTTGGAAGATCGCGTTGCGATTTTAT
1 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTAG
*
47977 GAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGAT
1 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAT
48014 CTTCTTTTCA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 2 0.03
42 71 0.97
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (42 bp):
GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTAG
Found at i:48031 original size:42 final size:41
Alignment explanation
Indices: 47899--48031 Score: 128
Period size: 42 Copynumber: 3.2 Consensus size: 41
47889 TTCTGAATCG
* ** *
47899 CGTTGCGATTCTTGGAAAATCGCGTTGCGATTCTTGGAATC-G
1 CGTTGCGATTCTTGGAAGATCGCGTTGCGA-TCTT-TTATCAA
* *
47941 CGTTGTGATTCTTGGAAGATCGCGTTGCGA--TTTTATGAA
1 CGTTGCGATTCTTGGAAGATCGCGTTGCGATCTTTTATCAA
*
47980 TCGCATTGCGATTCTTGGAAGATCGCGTTGCGATCTTCTTTTCAA
1 -CG--TTGCGATTCTTGGAAGATCGCGTTGCGATCTT-TTATCAA
48025 CGTTGCG
1 CGTTGCG
48032 CTTTTCTAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 2 0.03
42 60 0.80
44 4 0.05
45 5 0.07
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (41 bp):
CGTTGCGATTCTTGGAAGATCGCGTTGCGATCTTTTATCAA
Found at i:48048 original size:20 final size:19
Alignment explanation
Indices: 48025--48076 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
48015 TTCTTTTCAA
* *
48025 CGTTGCGCTTTTCTAAATCG
1 CGTTGCGATTTT-GAAATCG
* *
48045 CGTTGCGGTTTTGATATCG
1 CGTTGCGATTTTGAAATCG
48064 CGTTGCGATTTTG
1 CGTTGCGATTTTG
48077 TTGGTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.12, C:0.19, G:0.27, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:48660 original size:15 final size:16
Alignment explanation
Indices: 48640--48742 Score: 57
Period size: 15 Copynumber: 7.0 Consensus size: 16
48630 CCGGATATAT
48640 ATATATTTAA-ATTAA
1 ATATATTTAATATTAA
*
48655 ATATA-TAAATATTAA
1 ATATATTTAATATTAA
48670 ATATATTT--T-TT--
1 ATATATTTAATATTAA
48681 -TA-ATTTAA-ATTAA
1 ATATATTTAATATTAA
* *
48694 ATTTA-TTAATATTAT
1 ATATATTTAATATTAA
*
48709 ATATATATATATATATAA
1 ATATATTTA-ATAT-TAA
* *
48727 TTATTTTTAATATTAA
1 ATATATTTAATATTAA
48743 TCGGGCCGGG
Statistics
Matches: 65, Mismatches: 10, Indels: 25
0.65 0.10 0.25
Matches are distributed among these distances:
9 4 0.06
10 2 0.03
11 2 0.03
13 2 0.03
14 9 0.14
15 24 0.37
16 6 0.09
17 8 0.12
18 8 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATATTTAATATTAA
Found at i:50265 original size:21 final size:21
Alignment explanation
Indices: 50239--50329 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
50229 GTTTATAGAT
* *
50239 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
50260 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
50281 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
50301 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
50322 TCGCAATG
1 TCGCAATG
50330 TGAATATGTA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.28
21 44 0.72
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:50305 original size:20 final size:20
Alignment explanation
Indices: 50280--50352 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
50270 AACTTGGACT
50280 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
50300 ATCGCAATGCGAACT-TGGACT
1 ATCGCAATGCGAA-TATGTA-A
*
50321 ATCGCAATGTGAATATGTAA
1 ATCGCAATGCGAATATGTAA
50341 ATCGCAATGCGA
1 ATCGCAATGCGA
50353 TAATCGACTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:50367 original size:21 final size:20
Alignment explanation
Indices: 50239--50367 Score: 93
Period size: 21 Copynumber: 6.2 Consensus size: 20
50229 GTTTATAGAT
* *
50239 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACAT-GACTA
*
50260 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACAT-GACTA
* *
50281 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAACATG-ACTA
*
50301 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACAT-GACTA
* * *
50322 TCGCAATGTGAATATGTA-AA
1 TCGCAATGCGAACATG-ACTA
50342 TCGCAATGCGATA-ATCGACTA
1 TCGCAATGCGA-ACAT-GACTA
50363 TCGCA
1 TCGCA
50368 TTGAGTCCAA
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
20 31 0.36
21 56 0.64
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAACATGACTA
Found at i:50367 original size:41 final size:41
Alignment explanation
Indices: 50259--50352 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
50249 AACTTCGACT
50259 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
*
50300 ATCGCAATGCGAACTTGGACTATCGCAATGTGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
50341 ATCGCAATGCGA
1 ATCGCAATGCGA
50353 TAATCGACTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (41 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
Found at i:51155 original size:21 final size:21
Alignment explanation
Indices: 51129--51283 Score: 103
Period size: 21 Copynumber: 7.5 Consensus size: 21
51119 TTGGACTCAA
*
51129 TGCGATAGTCGACTATCGCAT
1 TGCGATAGTCAACTATCGCAT
*
51150 TGCGAT--T-TACATATTCGCAT
1 TGCGATAGTCAAC-TA-TCGCAT
*
51170 TGCGATAGTCCAAGT-TCGCAT
1 TGCGATAGT-CAACTATCGCAT
*
51191 TGCGATAGTCGACTATCGCAT
1 TGCGATAGTCAACTATCGCAT
*
51212 TGCGAT--T-TACATATTCGCAT
1 TGCGATAGTCAAC-TA-TCGCAT
* * *
51232 TGTGATAGTCCAAGT-TCGTAT
1 TGCGATAGT-CAACTATCGCAT
*
51253 TGCGATAGTCCAAGT-TCGCAT
1 TGCGATAGT-CAACTATCGCAT
51274 TGCGATAGTC
1 TGCGATAGTC
51284 GAAGTTCGCG
Statistics
Matches: 109, Mismatches: 12, Indels: 27
0.74 0.08 0.18
Matches are distributed among these distances:
18 4 0.04
19 6 0.06
20 27 0.25
21 66 0.61
22 2 0.02
23 2 0.02
24 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (21 bp):
TGCGATAGTCAACTATCGCAT
Found at i:51204 original size:62 final size:62
Alignment explanation
Indices: 51129--51279 Score: 250
Period size: 62 Copynumber: 2.4 Consensus size: 62
51119 TTGGACTCAA
51129 TGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCAT
* *
51191 TGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGTGATAGTCCAAGTTCGTAT
1 TGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCAT
* *
51253 TGCGATAGTCCAAGT-TCGCATTGCGAT
1 TGCGATAGT-CGACTATCGCATTGCGAT
51280 AGTCGAAGTT
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
62 81 0.96
63 3 0.04
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (62 bp):
TGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCAT
Found at i:51288 original size:21 final size:21
Alignment explanation
Indices: 51163--51299 Score: 163
Period size: 21 Copynumber: 6.6 Consensus size: 21
51153 GATTTACATA
51163 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
51184 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
51204 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
*
51225 TTCGCATTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
51246 TTCGTATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
51267 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
51288 TTCGCGTTGCGA
1 TTCGCATTGCGA
51300 ATCTAGAAAC
Statistics
Matches: 99, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
20 16 0.16
21 82 0.83
22 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Done.