Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020140.1 Corchorus olitorius cultivar O-4 contig20173, 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: 72040
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:4611 original size:21 final size:22
Alignment explanation
Indices: 4585--4641 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
4575 GCAAAGCATT
4585 TGGCCGGTAGTGGCACGGTG-A
1 TGGCCGGTAGTGGCACGGTGAA
* **
4606 TGGCCGGTGGTGGCTTGGTGAA
1 TGGCCGGTAGTGGCACGGTGAA
*
4628 TAGCCGGTAGTGGC
1 TGGCCGGTAGTGGC
4642 CTGGTGTGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.12, C:0.18, G:0.47, T:0.23
Consensus pattern (22 bp):
TGGCCGGTAGTGGCACGGTGAA
Found at i:4640 original size:22 final size:21
Alignment explanation
Indices: 4587--4647 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 21
4577 AAAGCATTTG
* *
4587 GCCGGTAGTGGCACGGTGATG
1 GCCGGTAGTGGCATGGTGATA
* *
4608 GCCGGTGGTGGCTTGGTGAATA
1 GCCGGTAGTGGCATGGTG-ATA
*
4630 GCCGGTAGTGGCCTGGTG
1 GCCGGTAGTGGCATGGTG
4648 TGGCGCGGCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 15 0.45
22 18 0.55
ACGTcount: A:0.11, C:0.18, G:0.48, T:0.23
Consensus pattern (21 bp):
GCCGGTAGTGGCATGGTGATA
Found at i:16964 original size:16 final size:18
Alignment explanation
Indices: 16933--16965 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
16923 AACAAACAAT
16933 GAGGAGAATCTTGCAAAA
1 GAGGAGAATCTTGCAAAA
16951 GAGG-GAAT-TTGCAAA
1 GAGGAGAATCTTGCAAA
16966 TTCTTGGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.42, C:0.09, G:0.30, T:0.18
Consensus pattern (18 bp):
GAGGAGAATCTTGCAAAA
Found at i:31909 original size:9 final size:9
Alignment explanation
Indices: 31897--31927 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
31887 GGGCTCAAAC
31897 GGGCCTGAT
1 GGGCCTGAT
31906 GGGCCTGAT
1 GGGCCTGAT
31915 GGGCCTGAT
1 GGGCCTGAT
31924 GGGC
1 GGGC
31928 TGAAATCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.10, C:0.23, G:0.48, T:0.19
Consensus pattern (9 bp):
GGGCCTGAT
Found at i:33933 original size:29 final size:29
Alignment explanation
Indices: 33901--33969 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
33891 CCTAAATAAC
* * *
33901 ATATATGCAGCAAACAAATCCCAATCACA
1 ATATATACAACAAACAAATCCCAAGCACA
*
33930 ATATGTACAACAAACAAATCCCAAGCACA
1 ATATATACAACAAACAAATCCCAAGCACA
33959 ATATATACAAC
1 ATATATACAAC
33970 CATGATAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.51, C:0.26, G:0.06, T:0.17
Consensus pattern (29 bp):
ATATATACAACAAACAAATCCCAAGCACA
Found at i:38811 original size:15 final size:16
Alignment explanation
Indices: 38793--38829 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
38783 GTTGTTTTTA
38793 TTTCTTTA-ATAGTGT
1 TTTCTTTATATAGTGT
*
38808 TTTCTTTATATATTGT
1 TTTCTTTATATAGTGT
38824 TTTCTT
1 TTTCTT
38830 GTAGTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (16 bp):
TTTCTTTATATAGTGT
Found at i:42205 original size:66 final size:66
Alignment explanation
Indices: 42029--42205 Score: 250
Period size: 65 Copynumber: 2.7 Consensus size: 66
42019 CTGGGGAAAT
* * * * *
42029 TGCAGAGGGGCCAACCACTGGGGGTTTTACGGCACACGACCTGATTGAACGTCTCGTCGGGGAGA
1 TGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCACCTGATTGAACGTCTCGCCGGGGAGA
42094 C
66 C
* * *
42095 TGCA-GGGGGCCAAGCACTGGGGGTCTTACGCCGCATCACCTGATTGAACGTC-CTGCCGGGGAG
1 TGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCACCTGATTGAACGTCTC-GCCGGGGAG
42158 AC
65 AC
*
42160 TGCAGGGGGGCCAACCACTAGGGGTCTTACGGCGCACCACCTGATT
1 TGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCACCTGATT
42206 TAACATTCCG
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
64 1 0.01
65 55 0.57
66 41 0.42
ACGTcount: A:0.20, C:0.28, G:0.34, T:0.18
Consensus pattern (66 bp):
TGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCACCTGATTGAACGTCTCGCCGGGGAGA
C
Found at i:42222 original size:66 final size:65
Alignment explanation
Indices: 42018--42226 Score: 251
Period size: 66 Copynumber: 3.2 Consensus size: 65
42008 TGTTTGTTCT
* * * * * *
42018 GCTGGGGAAATTGCAGAGGGGCCAACCACTGGGGGTTTTACGGCACACGACCTGATTGAACGTCT
1 GCTGGGGAGACTGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCACCTGATTGAACGTC-
42083 C
65 C
* * *
42084 G-TCGGGGAGACTGCA-GGGGGCCAAGCACTGGGGGTCTTACGCCGCATCACCTGATTGAACGTC
1 GCT-GGGGAGACTGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCACCTGATTGAACGTC
42147 C
65 C
* * * *
42148 TGCCGGGGAGACTGCAGGGGGGCCAACCACTAGGGGTCTTACGGCGCACCACCTGATTTAACATT
1 -GCTGGGGAGACTGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCACCTGATTGAAC-GT
42213 CC
64 CC
42215 GCTGGGGAGACT
1 GCTGGGGAGACT
42227 TGATTGAGCT
Statistics
Matches: 121, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
64 1 0.01
65 55 0.45
66 62 0.51
67 3 0.02
ACGTcount: A:0.21, C:0.27, G:0.34, T:0.18
Consensus pattern (65 bp):
GCTGGGGAGACTGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCACCTGATTGAACGTCC
Found at i:47297 original size:21 final size:22
Alignment explanation
Indices: 47252--47303 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
47242 CCACTACCAA
* *
47252 GCCACAACCGGCCATTCACCGT
1 GCCACCACCGGCCATGCACCGT
47274 GCCACCACCGGCCATGCA-CGT
1 GCCACCACCGGCCATGCACCGT
*
47295 GCCATCACC
1 GCCACCACC
47304 ATTCCAAGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.21, C:0.48, G:0.19, T:0.12
Consensus pattern (22 bp):
GCCACCACCGGCCATGCACCGT
Found at i:48014 original size:4 final size:4
Alignment explanation
Indices: 48005--48029 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
47995 AATGTTTTAT
48005 TTGA TTGA TTGA TTGA TTGA TTGA T
1 TTGA TTGA TTGA TTGA TTGA TTGA T
48030 AGCATGCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TTGA
Found at i:50628 original size:15 final size:15
Alignment explanation
Indices: 50610--50638 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
50600 GTTTCTAGTA
50610 TAATTGTTTTCTTTT
1 TAATTGTTTTCTTTT
50625 TAATTGTTTTCTTT
1 TAATTGTTTTCTTT
50639 CAACCTCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TAATTGTTTTCTTTT
Found at i:50995 original size:66 final size:65
Alignment explanation
Indices: 50810--51040 Score: 356
Period size: 65 Copynumber: 3.5 Consensus size: 65
50800 TGCAATCGGT
50810 CCAACCACTGGGGTCTTACGGCACACCACCTGATTGAA-GATCCCGCCGGGGAGACTGCAGGGTG
1 CCAACCACTGGGGTCTTACGGCACACCACCTGATTGAACG-TCCCGCCGGGGAGACTGCAGGGTG
50874 G
65 G
* * *
50875 CCAACCACTGAGGTTTTACGGCACACGACCTGATTGAACGTCCCGCCGGGGAGACTGCAGGGTGG
1 CCAACCACTGGGGTCTTACGGCACACCACCTGATTGAACGTCCCGCCGGGGAGACTGCAGGGTGG
** * *
50940 CCAACCACTAGGGGTCTTACGGTGCACCACCTGATTGAACGTCCCGCCGGGGAGACTGTAGGGGG
1 CCAACCACT-GGGGTCTTACGGCACACCACCTGATTGAACGTCCCGCCGGGGAGACTGCAGGGTG
51005 G
65 G
* *
51006 CCAACCACTTGGGTCTTACGGCGCACCACCTGATT
1 CCAACCACTGGGGTCTTACGGCACACCACCTGATT
51041 CCACCGAGGC
Statistics
Matches: 152, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
65 93 0.61
66 59 0.39
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.17
Consensus pattern (65 bp):
CCAACCACTGGGGTCTTACGGCACACCACCTGATTGAACGTCCCGCCGGGGAGACTGCAGGGTGG
Found at i:52333 original size:38 final size:38
Alignment explanation
Indices: 52282--52706 Score: 294
Period size: 38 Copynumber: 10.6 Consensus size: 38
52272 TTAGCTTTAC
* * *
52282 CGAGGCTTGCCTCAAGGGGACTTACAGTGCATGGTTGT
1 CGAGGCCTGCCTCAAGGGGACTTACAGCGCACGGTTGT
* * * ***
52320 CGAGGCCTGCCTCAACGGGACTTACGGCACACGACCGT
1 CGAGGCCTGCCTCAAGGGGACTTACAGCGCACGGTTGT
* * *
52358 CGAGGCCTGCCTCAAAGGGACTTACGGCGCACGACTTGATTCT
1 CGAGGCCTGCCTCAAGGGGACTTACAGCGCACG----G-TTGT
* * * *
52401 ACCGAGGCTTGCCTCAAGGGGACTTACAGCACACGGCTGC
1 --CGAGGCCTGCCTCAAGGGGACTTACAGCGCACGGTTGT
* *
52441 CGATGCCTGCCTCAAGGGGACTTATAGCGCACGGTTGT
1 CGAGGCCTGCCTCAAGGGGACTTACAGCGCACGGTTGT
* *
52479 CGAGGTCTGCCTCAAGGGGACTTACGGCGCACGACGCAATAT-T
1 CGAGGCCTGCCTCAAGGGGACTTACAGCGCACG--G---T-TGT
* * * * *
52522 ACCGAGGCATGCTTCTAGGGGACTTACAACGCACGGCTGT
1 --CGAGGCCTGCCTCAAGGGGACTTACAGCGCACGGTTGT
**
52562 CGAGGCCTGCCTCAAGGGGACTTATGGCGCACGACGTAATGTT
1 CGAGGCCTGCCTCAAGGGGACTTACAGCGCACG--GT--TG-T
* * * *
52605 ACCGAGGCATGCCTCAAGAGGACTTACAGCACACGGCTGT
1 --CGAGGCCTGCCTCAAGGGGACTTACAGCGCACGGTTGT
* * * ***
52645 CGAGACCAGCCTCAAGGGGACTTACGGCGCACGACCGT
1 CGAGGCCTGCCTCAAGGGGACTTACAGCGCACGGTTGT
* *
52683 CGAGGCCTGCTTCAAAGGGACTTA
1 CGAGGCCTGCCTCAAGGGGACTTA
52707 TGGTGCACAA
Statistics
Matches: 300, Mismatches: 64, Indels: 46
0.73 0.16 0.11
Matches are distributed among these distances:
38 198 0.66
39 1 0.00
40 5 0.02
41 3 0.01
42 2 0.01
43 6 0.02
44 1 0.00
45 84 0.28
ACGTcount: A:0.22, C:0.29, G:0.30, T:0.19
Consensus pattern (38 bp):
CGAGGCCTGCCTCAAGGGGACTTACAGCGCACGGTTGT
Found at i:52348 original size:83 final size:79
Alignment explanation
Indices: 52198--52678 Score: 361
Period size: 83 Copynumber: 5.9 Consensus size: 79
52188 CTTGGTTTTG
* * * * * *
52198 CCGAGGCCTGCCTCAAGGGGACTTAC-GCCGCAC-ATCCGTCGGGGCCTGCCTCAAGGGGTCTTT
1 CCGAGGCATGCCTCAAGGGGACTTACAG-CGCACGGT-TGTCGAGGCCTGCCTCAAGGGGACTTA
*
52261 CGGCACAGGATTTAGCTTTA
64 CGGCACACGA---A-CTTTA
* * * *
52281 CCGAGGCTTGCCTCAAGGGGACTTACAGTGCATGGTTGTCGAGGCCTGCCTCAACGGGACTTACG
1 CCGAGGCATGCCTCAAGGGGACTTACAGCGCACGGTTGTCGAGGCCTGCCTCAAGGGGACTTACG
**
52346 GCACACG-ACCGT-
66 GCACACGAACTTTA
* * * * *
52358 -CGAGGCCTGCCTCAAAGGGACTTACGGCGCACGACTTGATTCTACCGAGGCTTGCCTCAAGGGG
1 CCGAGGCATGCCTCAAGGGGACTTACAGCGCACG----G-TTGT--CGAGGCCTGCCTCAAGGGG
* * *
52422 ACTTACAGCACACG-GC--TG
59 ACTTACGGCACACGAACTTTA
* * * *
52440 CCGATGCCTGCCTCAAGGGGACTTATAGCGCACGGTTGTCGAGGTCTGCCTCAAGGGGACTTACG
1 CCGAGGCATGCCTCAAGGGGACTTACAGCGCACGGTTGTCGAGGCCTGCCTCAAGGGGACTTAC-
52505 GCGCACGACGCAA-TATTA
65 G-GCAC-ACG-AACT-TTA
* * * * *
52523 CCGAGGCATGCTTCTAGGGGACTTACAACGCACGGCTGTCGAGGCCTGCCTCAAGGGGACTTATG
1 CCGAGGCATGCCTCAAGGGGACTTACAGCGCACGGTTGTCGAGGCCTGCCTCAAGGGGACTTA-C
52588 GCGCACGACGTAA-TGTTA
65 G-GCAC-ACG-AACT-TTA
* * * * *
52606 CCGAGGCATGCCTCAAGAGGACTTACAGCACACGGCTGTCGAGACCAGCCTCAAGGGGACTTACG
1 CCGAGGCATGCCTCAAGGGGACTTACAGCGCACGGTTGTCGAGGCCTGCCTCAAGGGGACTTACG
*
52671 GCGCACGA
66 GCACACGA
52679 CCGTCGAGGC
Statistics
Matches: 326, Mismatches: 52, Indels: 44
0.77 0.12 0.10
Matches are distributed among these distances:
76 51 0.16
78 9 0.03
79 6 0.02
80 4 0.01
81 7 0.02
82 1 0.00
83 246 0.75
84 2 0.01
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.19
Consensus pattern (79 bp):
CCGAGGCATGCCTCAAGGGGACTTACAGCGCACGGTTGTCGAGGCCTGCCTCAAGGGGACTTACG
GCACACGAACTTTA
Found at i:52413 original size:121 final size:120
Alignment explanation
Indices: 52199--52596 Score: 474
Period size: 121 Copynumber: 3.3 Consensus size: 120
52189 TTGGTTTTGC
* * * *
52199 CGAGGCCTGCCTCAAGGGGACTTACGCCGCAC-ATCCGTCGGGGCCTGCCTCAAGGGGTCTTTCG
1 CGAGGCCTGCCTCAAGGGGACTTACGGCGCACGA-CCGTCGAGGCCTGCCTCAAGGGGACTTACG
* * * * * * *
52263 GCACAGGATTTAGCTTTACCGAGGCTTGCCTCAAGGGGACTTACAGTGCATGGTTGT
65 GCGCACGACTT-GATTTACCGAGGCTTGCCTCAAGGGGACTTACAGCGCACGGCTGT
* * *
52320 CGAGGCCTGCCTCAACGGGACTTACGGCACACGACCGTCGAGGCCTGCCTCAAAGGGACTTACGG
1 CGAGGCCTGCCTCAAGGGGACTTACGGCGCACGACCGTCGAGGCCTGCCTCAAGGGGACTTACGG
* *
52385 CGCACGACTTGATTCTACCGAGGCTTGCCTCAAGGGGACTTACAGCACACGGCTGC
66 CGCACGACTTGATT-TACCGAGGCTTGCCTCAAGGGGACTTACAGCGCACGGCTGT
* ** *** *
52441 CGATGCCTGCCTCAAGGGGACTTATAGCGCACGGTTGTCGAGGTCTGCCTCAAGGGGACTTACGG
1 CGAGGCCTGCCTCAAGGGGACTTACGGCGCACGACCGTCGAGGCCTGCCTCAAGGGGACTTACGG
*** * * * *
52506 CGCACGACGCAATATTACCGAGGCATGCTTCTAGGGGACTTACAACGCACGGCTGT
66 CGCACGACTTGAT-TTACCGAGGCTTGCCTCAAGGGGACTTACAGCGCACGGCTGT
*
52562 CGAGGCCTGCCTCAAGGGGACTTATGGCGCACGAC
1 CGAGGCCTGCCTCAAGGGGACTTACGGCGCACGAC
52597 GTAATGTTAC
Statistics
Matches: 235, Mismatches: 39, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
120 3 0.01
121 230 0.98
122 2 0.01
ACGTcount: A:0.20, C:0.30, G:0.31, T:0.20
Consensus pattern (120 bp):
CGAGGCCTGCCTCAAGGGGACTTACGGCGCACGACCGTCGAGGCCTGCCTCAAGGGGACTTACGG
CGCACGACTTGATTTACCGAGGCTTGCCTCAAGGGGACTTACAGCGCACGGCTGT
Found at i:52663 original size:121 final size:124
Alignment explanation
Indices: 52289--52761 Score: 390
Period size: 121 Copynumber: 3.9 Consensus size: 124
52279 TACCGAGGCT
* * * * *
52289 TGCCTCAAGGGGACTTACAGTGCATGGTTGTCGAGGCCTGCCTCAACGGGACTTA-CG-GCAC-A
1 TGCCTCAAGGGGACTTACAGCGCACGGCTGTCGAGGCCTGCCTCAAGGGGACTTATGGCGCACGA
** * * * * ** * *
52351 CG-ACCG-T--CGAGGCCTGCCTCAAAGGGACTTACGGCGCACGACTTGATTCTACCGAGGCT
66 CGTAATGTTACCGAGGCATGCCTCAAGGGGACTTACAGCGCACGGC---ATAGTA-CGAGCCA
* * * *
52410 TGCCTCAAGGGGACTTACAGCACACGGCTGCCGATGCCTGCCTCAAGGGGACTTATAGCGCACG-
1 TGCCTCAAGGGGACTTACAGCGCACGGCTGTCGAGGCCTGCCTCAAGGGGACTTATGGCGCACGA
* * *
52474 -GT--TG-T--CGAGGTC-TGCCTCAAGGGGACTTACGGCGCACGACGCAATATTACCGAGGCA
66 CGTAATGTTACCGAGG-CATGCCTCAAGGGGACTTACAGCGCACG--GC-ATAGTA-CGAGCCA
* * *
52531 TGCTTCTAGGGGACTTACAACGCACGGCTGTCGAGGCCTGCCTCAAGGGGACTTATGGCGCACGA
1 TGCCTCAAGGGGACTTACAGCGCACGGCTGTCGAGGCCTGCCTCAAGGGGACTTATGGCGCACGA
* *
52596 CGTAATGTTACCGAGGCATGCCTCAAGAGGACTTACAGCACACGGC-T-GT-CGAGACCA
66 CGTAATGTTACCGAGGCATGCCTCAAGGGGACTTACAGCGCACGGCATAGTACGAG-CCA
* * * * * * *
52653 -GCCTCAAGGGGACTTACGGCGCACGACCGTCGAGGCCTGCTTCAAAGGGACTTATGGTGCACAA
1 TGCCTCAAGGGGACTTACAGCGCACGGCTGTCGAGGCCTGCCTCAAGGGGACTTATGGCGCACGA
** *
52717 CACAATGTTACTGAGGCATGCCTCAAGGGGACTTACAGCGCACGG
66 CGTAATGTTACCGAGGCATGCCTCAAGGGGACTTACAGCGCACGG
52762 TTTTGCTTCG
Statistics
Matches: 294, Mismatches: 42, Indels: 32
0.80 0.11 0.09
Matches are distributed among these distances:
121 246 0.84
122 5 0.02
123 8 0.03
124 1 0.00
125 2 0.01
126 3 0.01
127 1 0.00
128 28 0.10
ACGTcount: A:0.23, C:0.29, G:0.30, T:0.19
Consensus pattern (124 bp):
TGCCTCAAGGGGACTTACAGCGCACGGCTGTCGAGGCCTGCCTCAAGGGGACTTATGGCGCACGA
CGTAATGTTACCGAGGCATGCCTCAAGGGGACTTACAGCGCACGGCATAGTACGAGCCA
Found at i:52761 original size:204 final size:204
Alignment explanation
Indices: 52320--52761 Score: 573
Period size: 204 Copynumber: 2.2 Consensus size: 204
52310 GCATGGTTGT
* * * * *
52320 CGAGGCCTGCCTCAACGGGACTTACGGCACACGACCGTCGAGGCCTGCCTCAAAGGGACTTACGG
1 CGAGGCATGCCTCAAGGGGACTTACAGCGCACGGCCGTCGAGGCCTGCCTCAAAGGGACTTACGG
* * * * *
52385 CGCACGACTTGATTCTACCGAGGCTTGCCTCAAGGGGACTTACAGCACACGGCTGCCGATGCCTG
66 CGCACGACGTAATTCTACCGAGGCATGCCTCAAGAGGACTTACAGCACACGGCTGCCGATGCCAG
* *** * * * *
52450 CCTCAAGGGGACTTATAGCGCACGGTTGTCGAGGTCTGCCTCAAGGGGACTTACGGCGCACGACG
131 CCTCAAGGGGACTTACAGCGCACGACCGTCGAGGCCTGCCTCAAAGGGACTTACGGCGCACAACA
52515 CAATATTAC
196 CAATATTAC
* * * * * *
52524 CGAGGCATGCTTCTAGGGGACTTACAACGCACGGCTGTCGAGGCCTGCCTCAAGGGGACTTATGG
1 CGAGGCATGCCTCAAGGGGACTTACAGCGCACGGCCGTCGAGGCCTGCCTCAAAGGGACTTACGG
*
52589 CGCACGACGTAATGT-TACCGAGGCATGCCTCAAGAGGACTTACAGCACACGGCTGTCGA-GACC
66 CGCACGACGTAAT-TCTACCGAGGCATGCCTCAAGAGGACTTACAGCACACGGCTGCCGATG-CC
* * * *
52652 AGCCTCAAGGGGACTTACGGCGCACGACCGTCGAGGCCTGCTTCAAAGGGACTTATGGTGCACAA
129 AGCCTCAAGGGGACTTACAGCGCACGACCGTCGAGGCCTGCCTCAAAGGGACTTACGGCGCACAA
*
52717 CACAATGTTAC
194 CACAATATTAC
*
52728 TGAGGCATGCCTCAAGGGGACTTACAGCGCACGG
1 CGAGGCATGCCTCAAGGGGACTTACAGCGCACGG
52762 TTTTGCTTCG
Statistics
Matches: 202, Mismatches: 34, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
203 1 0.00
204 200 0.99
205 1 0.00
ACGTcount: A:0.23, C:0.29, G:0.30, T:0.18
Consensus pattern (204 bp):
CGAGGCATGCCTCAAGGGGACTTACAGCGCACGGCCGTCGAGGCCTGCCTCAAAGGGACTTACGG
CGCACGACGTAATTCTACCGAGGCATGCCTCAAGAGGACTTACAGCACACGGCTGCCGATGCCAG
CCTCAAGGGGACTTACAGCGCACGACCGTCGAGGCCTGCCTCAAAGGGACTTACGGCGCACAACA
CAATATTAC
Found at i:53198 original size:56 final size:57
Alignment explanation
Indices: 53136--53289 Score: 195
Period size: 56 Copynumber: 2.7 Consensus size: 57
53126 GGCGTTGGCG
* * * *
53136 CGCGCTACTTCTTTTAGAGTTCTGCAACATGGTGAGTGTCGCATGAGGCGTTTGGG-
1 CGCGCTACTTCTTTCAGAGTTCTGCCACATGGGGAGTGCCGCATGAGGCGTTTGGGA
* * ** *
53192 TGCGCTACTTCTTTCAGAATTCTGCCACATGGGGTTTGCCGCCTGAGGCGTTTGGGA
1 CGCGCTACTTCTTTCAGAGTTCTGCCACATGGGGAGTGCCGCATGAGGCGTTTGGGA
*
53249 CACGCTA-TTCCTTTCAGAGTTCTGCCACATGGGGAGTGCCG
1 CGCGCTACTT-CTTTCAGAGTTCTGCCACATGGGGAGTGCCG
53290 TAGAGTTCTG
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
56 49 0.60
57 33 0.40
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.31
Consensus pattern (57 bp):
CGCGCTACTTCTTTCAGAGTTCTGCCACATGGGGAGTGCCGCATGAGGCGTTTGGGA
Found at i:53403 original size:141 final size:140
Alignment explanation
Indices: 53150--53425 Score: 342
Period size: 141 Copynumber: 2.0 Consensus size: 140
53140 CTACTTCTTT
* *
53150 TAGAGTTCTGCAACATGGTGAGTGTCGCATGAGGCGTTTGGGTGCGCTACTTCTTTCAGAATTCT
1 TAGAGTTCTGCAACATGGTGAGTGTCGCATGAGACGTTTGGGTGCGCTACTTCTTTCAGAATTCC
* * ** ** * *
53215 GCCACATGGGGTTTGCCGCCTGAGGCGTTTGGGACACGCTATTCCTTTCAGAGTTCTGCCACATG
66 GCCACACGAGGAGTGCCGCAAGAGGAGTTTGGGACACGCTATTCCTTTCAAAGTTCTGCCACATG
53280 GGGAGTGCCG
131 GGGAGTGCCG
* * *
53290 TAGAGTTCTGCCACAT-GTGGAGTGTCGCATGAGATGTTTGGG-GCGTGCTATTTCTTTCA-AAG
1 TAGAGTTCTGCAACATGGT-GAGTGTCGCATGAGACGTTTGGGTGC--GCTACTTCTTTCAGAA-
* ** *
53352 TTCCGCCACACGAGGAGTGCCGCAAGAGGAGTTTGGGGCGTGCTATTCCTTTCAAAGTTTTGCCA
62 TTCCGCCACACGAGGAGTGCCGCAAGAGGAGTTTGGGACACGCTATTCCTTTCAAAGTTCTGCCA
53417 CATGGGGAG
127 CATGGGGAG
53426 CGTCGCATGA
Statistics
Matches: 115, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
139 4 0.03
140 38 0.33
141 73 0.63
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (140 bp):
TAGAGTTCTGCAACATGGTGAGTGTCGCATGAGACGTTTGGGTGCGCTACTTCTTTCAGAATTCC
GCCACACGAGGAGTGCCGCAAGAGGAGTTTGGGACACGCTATTCCTTTCAAAGTTCTGCCACATG
GGGAGTGCCG
Found at i:53417 original size:57 final size:57
Alignment explanation
Indices: 53293--53418 Score: 173
Period size: 57 Copynumber: 2.2 Consensus size: 57
53283 AGTGCCGTAG
* * * * *
53293 AGTTCTGCCACATGTGGAGTGTCGCATGAGATGTTTGGGGCGTGCTATTTCTTTCAA
1 AGTTCTGCCACACGAGGAGTGCCGCAAGAGATGTTTGGGGCGTGCTATTCCTTTCAA
*
53350 AGTTCCGCCACACGAGGAGTGCCGCAAGAGGA-GTTTGGGGCGTGCTATTCCTTTCAA
1 AGTTCTGCCACACGAGGAGTGCCGCAAGA-GATGTTTGGGGCGTGCTATTCCTTTCAA
*
53407 AGTTTTGCCACA
1 AGTTCTGCCACA
53419 TGGGGAGCGT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 58 0.97
58 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.29
Consensus pattern (57 bp):
AGTTCTGCCACACGAGGAGTGCCGCAAGAGATGTTTGGGGCGTGCTATTCCTTTCAA
Found at i:59922 original size:15 final size:16
Alignment explanation
Indices: 59902--59933 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
59892 GCTTCATATT
59902 TCAAAAT-TTTAAATA
1 TCAAAATCTTTAAATA
59917 TCAAAATCTTTAAATA
1 TCAAAATCTTTAAATA
59933 T
1 T
59934 ATATGTAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
TCAAAATCTTTAAATA
Found at i:65054 original size:69 final size:69
Alignment explanation
Indices: 64977--65110 Score: 223
Period size: 69 Copynumber: 1.9 Consensus size: 69
64967 TTTTGCTTGA
** * *
64977 AATGCATTGTCTTTATATGCAATTTTAGCATTTGGATGTAATTAATGGTGTTCCTACCATTTTTT
1 AATGCATTGTCTTTATATGCAATTTTAGCATTCAGATGTAATTAATGGTGCTCCCACCATTTTTT
65042 CTTT
66 CTTT
*
65046 AATGCATTGTCTTTATATGTAATTTTAGCATTCAGATGTAATTAATGGTGCTCCCACCATTTTTT
1 AATGCATTGTCTTTATATGCAATTTTAGCATTCAGATGTAATTAATGGTGCTCCCACCATTTTTT
65111 TCCTTAGTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (69 bp):
AATGCATTGTCTTTATATGCAATTTTAGCATTCAGATGTAATTAATGGTGCTCCCACCATTTTTT
CTTT
Found at i:70864 original size:215 final size:215
Alignment explanation
Indices: 70489--71029 Score: 974
Period size: 215 Copynumber: 2.5 Consensus size: 215
70479 GTTATAATCG
70489 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCTTTTCATGCATATAAGGCAC
1 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCTTTTCATGCATATAAGGCAC
*
70554 TCAGTCATGTCAAACATAACCAATGTGGGATATTACCACTCTAACACGCCCCCTCATGTGTAGCC
66 TCAGTCATGTCAAACATAACCAATGTGGGATATTACCACTCTAACACGCCCCCTCACGTGTAGCC
* * * *
70619 CGGGACAACACCGAAATAGAACGGGCCTACACGTGGACACAACCGGGTCTGGGGCGCAACAAGAC
131 CGGGACAACACCGAAACAGAACGAGCCTACACGTGGACACAACAGAGTCTGGGGCGCAACAAGAC
*
70684 AGACCTGAGCTCTGATACCA
196 AGACCTAAGCTCTGATACCA
** *
70704 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCCCTTCATGTATATAAGGCAC
1 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCTTTTCATGCATATAAGGCAC
*
70769 TCAGTCATGTCAAACATAACCAATGTGGGATATTACCACTCTAACACGCCCCCTCACGTGTAGTC
66 TCAGTCATGTCAAACATAACCAATGTGGGATATTACCACTCTAACACGCCCCCTCACGTGTAGCC
* *
70834 CGGGACAACACCGAAACAGAATGAGCCTACACGTGGACACAACAGAGTCTGGGGCGCAACAGGAC
131 CGGGACAACACCGAAACAGAACGAGCCTACACGTGGACACAACAGAGTCTGGGGCGCAACAAGAC
70899 AGACCTAAGCTCTGATACCA
196 AGACCTAAGCTCTGATACCA
70919 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCTTTTCATGCATATAAGGCAC
1 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCTTTTCATGCATATAAGGCAC
70984 TCAGTCATGTCAAACATAACCAATGTGGGATATTACCACTCTAACA
66 TCAGTCATGTCAAACATAACCAATGTGGGATATTACCACTCTAACA
71030 AATCACAAGA
Statistics
Matches: 311, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
215 311 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (215 bp):
TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCTTTTCATGCATATAAGGCAC
TCAGTCATGTCAAACATAACCAATGTGGGATATTACCACTCTAACACGCCCCCTCACGTGTAGCC
CGGGACAACACCGAAACAGAACGAGCCTACACGTGGACACAACAGAGTCTGGGGCGCAACAAGAC
AGACCTAAGCTCTGATACCA
Found at i:71980 original size:2 final size:2
Alignment explanation
Indices: 71973--72038 Score: 114
Period size: 2 Copynumber: 32.0 Consensus size: 2
71963 AAAAGAAGGC
71973 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
72015 AG CAG AG AG AG AG AG AG AG TAG AG
1 AG -AG AG AG AG AG AG AG AG -AG AG
72039 TA
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 58 0.94
3 4 0.06
ACGTcount: A:0.48, C:0.02, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Done.