Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023058.1 Corchorus olitorius cultivar O-4 contig23091, 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: 65480
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:11469 original size:15 final size:16
Alignment explanation
Indices: 11445--11484 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
11435 AGAGGTTGAA
*
11445 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
11460 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
11476 AGAAAACAA
1 AGAAAACAA
11485 AGCGAAGTAA
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:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:13730 original size:194 final size:194
Alignment explanation
Indices: 13391--13774 Score: 646
Period size: 194 Copynumber: 2.0 Consensus size: 194
13381 CATATGTGTA
*
13391 ACGATCATCCCTTTGTGGGGATGAGCCATGAATCCCACATCAGCTGTGTGCTAGAGTTGGTCTTG
1 ACGATCATCCCTTTGTGGGGATGAGCCATGAATCCCACATCAGCTGTGTACTAGAGTTGGTCTTG
* *
13456 GGATATAAGTGTTCACACCACTTGAACTTGTGAGGCGCCTTTTGTAGACAAAACCGTGAGGCCTA
66 GGATATAAGTGTTCACAACACTTGAACTTGTGAGGCGCCTTTTGTAGACAAAACCGTGAGGCCCA
*
13521 TTGGGTCCAAATCCAATGGGTCAAAGCGGACAATGA-CTCACAAGTTGGTGTGGACCGTGATGTC
131 TTGGGTCCAAATCCAATGGGTCAAAGCGGACAAT-ACCTCACAAGTTGGTATGGACCGTGATGTC
* *
13585 ACGATCATCCCTTTGTGGGGATGAGCCATGAATCCCACATCGGTTGTGTACTAGAGTTGGTCTTG
1 ACGATCATCCCTTTGTGGGGATGAGCCATGAATCCCACATCAGCTGTGTACTAGAGTTGGTCTTG
* * *
13650 GGATATAAGTGTTCACAACACTTGAACTTGTGAGGTGCCTTTTGTGGATAAAACCGTGAGGCCCA
66 GGATATAAGTGTTCACAACACTTGAACTTGTGAGGCGCCTTTTGTAGACAAAACCGTGAGGCCCA
*
13715 TTGGG-CCGGAATCCAATGGGTCAAAGCGGACAATACCTCACAAGTTGGTATGGACCGTGA
131 TTGGGTCC-AAATCCAATGGGTCAAAGCGGACAATACCTCACAAGTTGGTATGGACCGTGA
13775 CAATATGTGT
Statistics
Matches: 178, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
193 3 0.02
194 175 0.98
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (194 bp):
ACGATCATCCCTTTGTGGGGATGAGCCATGAATCCCACATCAGCTGTGTACTAGAGTTGGTCTTG
GGATATAAGTGTTCACAACACTTGAACTTGTGAGGCGCCTTTTGTAGACAAAACCGTGAGGCCCA
TTGGGTCCAAATCCAATGGGTCAAAGCGGACAATACCTCACAAGTTGGTATGGACCGTGATGTC
Found at i:13787 original size:2 final size:2
Alignment explanation
Indices: 13780--13838 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
13770 CGTGACAATA
13780 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
13822 TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG T
13839 ATAACATCTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:14852 original size:70 final size:70
Alignment explanation
Indices: 14761--14901 Score: 178
Period size: 70 Copynumber: 2.0 Consensus size: 70
14751 TGAACATTGC
* * * * *
14761 TCTGAATCATTCATGTAAAAGACT-AAGCATTAG-TTCCTGTCAAAATAATTGGAATTTGATCTG
1 TCTGAATCACTCATATAAAAGA-TAAAGCATCAGTTTCCTGTCAAAATAATTAGAATTTGATCAG
14824 ACATCTT
65 ACA-CTT
* * *
14831 TCTGAATCACTCATATCAAAGATAAAGTATCAGTTTTCTGTCAAAATAATTAGAATTTGATCAGA
1 TCTGAATCACTCATATAAAAGATAAAGCATCAGTTTCCTGTCAAAATAATTAGAATTTGATCAGA
14896 CACTT
66 CACTT
14901 T
1 T
14902 ACTAGCAGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
69 1 0.02
70 30 0.49
71 30 0.49
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (70 bp):
TCTGAATCACTCATATAAAAGATAAAGCATCAGTTTCCTGTCAAAATAATTAGAATTTGATCAGA
CACTT
Found at i:16198 original size:24 final size:24
Alignment explanation
Indices: 16170--16218 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
16160 AGTATTGTTG
*
16170 TGTTTGCGAATCATGGTTATTGAT
1 TGTTTGCGAATCATGATTATTGAT
16194 TGTTTGCGAATCATGATTATTGAT
1 TGTTTGCGAATCATGATTATTGAT
16218 T
1 T
16219 TTGTTGTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (24 bp):
TGTTTGCGAATCATGATTATTGAT
Found at i:17012 original size:151 final size:150
Alignment explanation
Indices: 16755--17036 Score: 387
Period size: 151 Copynumber: 1.9 Consensus size: 150
16745 TGGTCACTCA
* * *
16755 TGGTTTAGCTAGAAAAGAAGATTTCAGTAATGGTCAGATTAATTGATATAGTGCATTTTATTGAC
1 TGGTTTAGCTAGAAAAGAAGATTTCAGTAATGGTCAGATTAATTGATATACTGCATTTTAGTAAC
* *
16820 ACTTAGATATCTTTGCTGTTTCATTTTCTTCATGCATGTCATTGACATTTGTGTTTTCCCATTGA
66 ACTTAGATATCTTTGCTGTTTCACTTTCTACATGCATGTCATTGACATTTGTGTTTT-CCATTGA
16885 ATGACACAAACTGATCACTTT
130 ATGACACAAACTGATCACTTT
* *
16906 TGGTTTAGGTAGAGAAGAAGATTAAT-A-TAATGGTCAGATTAATTGAT-T-CTGCACATTTTAG
1 TGGTTTAGCTAGAAAAGAAGATT--TCAGTAATGGTCAGATTAATTGATATACTG--CATTTTAG
*
16967 TAACACTTAGATATCTTTGTTGTTTCAACTTTC-ACAAT-CATGTCATTGACATTTGTGTTTTCC
62 TAACACTTAGATATCTTTGCTGTTTC-ACTTTCTAC-ATGCATGTCATTGACATTTGTGTTTTCC
17030 ATTGAAT
125 ATTGAAT
17037 CATTTTGGTG
Statistics
Matches: 117, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
149 2 0.02
150 10 0.09
151 96 0.82
152 8 0.07
153 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (150 bp):
TGGTTTAGCTAGAAAAGAAGATTTCAGTAATGGTCAGATTAATTGATATACTGCATTTTAGTAAC
ACTTAGATATCTTTGCTGTTTCACTTTCTACATGCATGTCATTGACATTTGTGTTTTCCATTGAA
TGACACAAACTGATCACTTT
Found at i:18313 original size:3 final size:3
Alignment explanation
Indices: 18305--18332 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
18295 AACTAACATT
18305 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
18333 TAATTTCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:18960 original size:353 final size:351
Alignment explanation
Indices: 18458--19131 Score: 980
Period size: 354 Copynumber: 1.9 Consensus size: 351
18448 TCACGTTCGA
* * ** * *
18458 GTTTTTGGTTTATGATTGGAACTGATTAATTTCAATTCTAACGTGAAATTTTATCTTATGTAGCA
1 GTTTTTGATTTATGATTAGAACCAAGTAATTTCAATTCTAACGTAAAATTTTATCTTATGTAGCA
* *
18523 ATTAAGTTAAATGGAAAAAAATATTGTTAGAATTCTAATGTTTATTCAAATAATTATCTAATGGA
66 ATTAAATTAAATGGAAAAAAATATTGTTAGAAATCTAATGTTTATTCAAATAATTATCTAATGGA
*
18588 AAAAGTAAATAGAGTTTTACTTTG-TTATAATTCAATGTTCTAAATATTATTTAAAAATA-T-TA
131 AAAAGAAAATAGAGTTTTACTTTGATTATAATTCAATGTTCTAAATATTATTTAAAAATATTGTA
* * * *
18650 TTTGGAATT-TCAAATATATAATAATATATATTAGTTTTTTTTCCAAACCAATCAACGTTGGACA
196 TTTGGAATTCT-AAATATATAATAATATATATT-G-GTTTTCTCCAAACCAACCAACGTCGGACA
* * * *
18714 AATGTCAGCATGAGAAGAGTCAAATATTGAGCATATAGCAGTTTGAGGATAACTTTAATAGTAAC
258 AATATCAGCATGAGAAGAGCCAAATATTGAGCATACAACAGTTTGAGGATAACTTTAATAGTAAC
18779 TAGATATTTTTCCCAACCATTTGTGTCGG
323 TAGATATTTTTCCCAACCATTTGTGTCGG
18808 GTTTTTCGATTTATGATTAGAACCAAGTAATTTCAATTCTAA-GTAAAATTTTATCTTATGTAAT
1 GTTTTT-GATTTATGATTAGAACCAAGTAATTTCAATTCTAACGTAAAATTTTATCTTATGT-A-
** * **
18872 CGCAATTAAATTAAATGGAAGGAAATATTGTTAGAAATCTAATGTTTATTCAAATAATTATTTGC
63 -GCAATTAAATTAAATGGAAAAAAATATTGTTAGAAATCTAATGTTTATTCAAATAATTATCTAA
* * *
18937 TGGAAGAAGAAAATTGAGTTTTACTTTGATTATAATTCAATGTTCTAAATATTATTTATAAATAT
127 TGGAAAAAGAAAATAGAGTTTTACTTTGATTATAATTCAATGTTCTAAATATTATTTAAAAATAT
* *
19002 TGTATTTGGAATTCTAAATATATAATACTATATATTGGTTTTCTCCCAACCAACCAACGTCGGAC
192 TGTATTTGGAATTCTAAATATATAATAATATATATTGGTTTTCTCCAAACCAACCAACGTCGGAC
* * *
19067 AAATATCAGCATGTGAGGAGCCAAATATTGAGCATACAACAGTTTGGGGATAACTTTAATAGTAA
257 AAATATCAGCATGAGAAGAGCCAAATATTGAGCATACAACAGTTTGAGGATAACTTTAATAGTAA
19132 GGTATAGATA
Statistics
Matches: 286, Mismatches: 30, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
350 24 0.08
351 31 0.11
353 82 0.29
354 115 0.40
355 2 0.01
356 31 0.11
357 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.38
Consensus pattern (351 bp):
GTTTTTGATTTATGATTAGAACCAAGTAATTTCAATTCTAACGTAAAATTTTATCTTATGTAGCA
ATTAAATTAAATGGAAAAAAATATTGTTAGAAATCTAATGTTTATTCAAATAATTATCTAATGGA
AAAAGAAAATAGAGTTTTACTTTGATTATAATTCAATGTTCTAAATATTATTTAAAAATATTGTA
TTTGGAATTCTAAATATATAATAATATATATTGGTTTTCTCCAAACCAACCAACGTCGGACAAAT
ATCAGCATGAGAAGAGCCAAATATTGAGCATACAACAGTTTGAGGATAACTTTAATAGTAACTAG
ATATTTTTCCCAACCATTTGTGTCGG
Found at i:24475 original size:78 final size:78
Alignment explanation
Indices: 24383--24811 Score: 592
Period size: 78 Copynumber: 5.5 Consensus size: 78
24373 CAGCTGTTGT
* * * * *
24383 GATGAGACAGTCTCAATGGAGACGATTGTTTCACTTATTTCTACACGAGGACACCAATGTTGGTG
1 GATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATTTCTATACGAGGACACCAATGTTGGTG
* *
24448 TTCGACCGTTTGT
66 TTCGGCCGTTTGC
* * * ** *
24461 GATGAAACGATCTCAACGGAGACGATTGTTTTGTTTATTTTTATAC-AGGAACACCAATGTTGGT
1 GATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATTTCTATACGAGG-ACACCAATGTTGGT
* *
24525 GTTCGGCTGTTTGT
65 GTTCGGCCGTTTGC
* * * *
24539 GATGAAGCGGTCTCAATGGAGACGACCGTTTCATTTATTTCTGTACGGGGACACCAATGTTGGTG
1 GATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATTTCTATACGAGGACACCAATGTTGGTG
24604 TTCGGCCGTTTGC
66 TTCGGCCGTTTGC
* *
24617 GATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATTTCTGTAC-AGGGACACCAATGTTAGT
1 GATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATTTCTATACGA-GGACACCAATGTTGGT
24681 GTTCGGCCGTTTGC
65 GTTCGGCCGTTTGC
* *
24695 GATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATTTCTGTACGGGGACACCAATGTTGGTG
1 GATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATTTCTATACGAGGACACCAATGTTGGTG
*
24760 TTCGGTCGTTTGC
66 TTCGGCCGTTTGC
* *
24773 GATGAAGCGGTCTCAATGAAGACGATCGTTTCATTTATT
1 GATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATT
24812 CAAAATATTT
Statistics
Matches: 315, Mismatches: 32, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
77 3 0.01
78 310 0.98
79 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (78 bp):
GATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATTTCTATACGAGGACACCAATGTTGGTG
TTCGGCCGTTTGC
Found at i:24595 original size:156 final size:156
Alignment explanation
Indices: 24323--24803 Score: 651
Period size: 156 Copynumber: 3.1 Consensus size: 156
24313 CGGGCTGTTG
* * * * ** * *
24323 GGAGACGTTCGTTTTGTTTATGTTTATACAGGGATACTACCGTTGGTATTCAGCTG-TTGTGATG
1 GGAGACGATCGTTTTGTTTATTTTTATACAGGGACACCAATGTTGGTGTTCGGCTGTTTGTGATG
* * * ** *
24387 -AGACAGTCTCAATGGAGACGATTGTTTCACTTATTTCTACACGAGGACACCAATGTTGGTGTTC
66 AAG-CGGTCTCAATGGAGACGATCGTTTCATTTATTTCTGTACGGGGACACCAATGTTGGTGTTC
* * * *
24451 GACCGTTTGTGATGAAACGATCTCAAC
130 GGCCGTTTGCGATGAAACGGTCTCAAT
* *
24478 GGAGACGATTGTTTTGTTTATTTTTATACAGGAACACCAATGTTGGTGTTCGGCTGTTTGTGATG
1 GGAGACGATCGTTTTGTTTATTTTTATACAGGGACACCAATGTTGGTGTTCGGCTGTTTGTGATG
*
24543 AAGCGGTCTCAATGGAGACGACCGTTTCATTTATTTCTGTACGGGGACACCAATGTTGGTGTTCG
66 AAGCGGTCTCAATGGAGACGATCGTTTCATTTATTTCTGTACGGGGACACCAATGTTGGTGTTCG
24608 GCCGTTTGCGATGAAACGGTCTCAAT
131 GCCGTTTGCGATGAAACGGTCTCAAT
** * * * * *
24634 GGAGACGATCGTTTCATTTATTTCTGTACAGGGACACCAATGTTAGTGTTCGGCCGTTTGCGATG
1 GGAGACGATCGTTTTGTTTATTTTTATACAGGGACACCAATGTTGGTGTTCGGCTGTTTGTGATG
*
24699 AAACGGTCTCAATGGAGACGATCGTTTCATTTATTTCTGTACGGGGACACCAATGTTGGTGTTCG
66 AAGCGGTCTCAATGGAGACGATCGTTTCATTTATTTCTGTACGGGGACACCAATGTTGGTGTTCG
* *
24764 GTCGTTTGCGATGAAGCGGTCTCAAT
131 GCCGTTTGCGATGAAACGGTCTCAAT
*
24790 GAAGACGATCGTTT
1 GGAGACGATCGTTT
24804 CATTTATTCA
Statistics
Matches: 289, Mismatches: 35, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
155 46 0.16
156 241 0.83
157 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (156 bp):
GGAGACGATCGTTTTGTTTATTTTTATACAGGGACACCAATGTTGGTGTTCGGCTGTTTGTGATG
AAGCGGTCTCAATGGAGACGATCGTTTCATTTATTTCTGTACGGGGACACCAATGTTGGTGTTCG
GCCGTTTGCGATGAAACGGTCTCAAT
Found at i:29411 original size:2 final size:2
Alignment explanation
Indices: 29404--29443 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29394 TCACTCTTGT
29404 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29444 AACATATCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32724 original size:31 final size:29
Alignment explanation
Indices: 32689--32746 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
32679 TAGGGTGAAG
*
32689 AAGAATGAAGAGAAAAAAGAAGGAAAAAAGA
1 AAGAAAGAAGAGAAAAAAG--GGAAAAAAGA
*
32720 AAGAAAGAAGAGAACAAAGGGAAAAAA
1 AAGAAAGAAGAGAAAAAAGGGAAAAAA
32747 AAGACGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
31 17 0.68
ACGTcount: A:0.71, C:0.02, G:0.26, T:0.02
Consensus pattern (29 bp):
AAGAAAGAAGAGAAAAAAGGGAAAAAAGA
Found at i:33232 original size:66 final size:67
Alignment explanation
Indices: 33098--33232 Score: 173
Period size: 66 Copynumber: 2.0 Consensus size: 67
33088 GATTGGTTCG
* *
33098 TTCAATAATTTATAATTATACATAGTCGAACATAATTGATGTGGGAGACATTTTGTGCAAATGAT
1 TTCAACAATTTATAATTATACATAGTCGAAC---A-GGATGTGGGAGACATTTTGTGCAAATGAT
33163 AGGCCT
62 AGGCCT
* ***
33169 TTCAACAATTTATAATTATGCATAGTCGAAC-GGATGTGGGAGTTTTTTTGTGCAAATGATAGGC
1 TTCAACAATTTATAATTATACATAGTCGAACAGGATGTGGGAGACATTTTGTGCAAATGATAGGC
33233 ATGACTCGGC
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
66 29 0.50
71 29 0.50
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.36
Consensus pattern (67 bp):
TTCAACAATTTATAATTATACATAGTCGAACAGGATGTGGGAGACATTTTGTGCAAATGATAGGC
CT
Found at i:34748 original size:18 final size:18
Alignment explanation
Indices: 34725--34772 Score: 78
Period size: 20 Copynumber: 2.6 Consensus size: 18
34715 ATTTGTTGTT
34725 TTATTCAAATATCCGTAA
1 TTATTCAAATATCCGTAA
34743 TTATTCACAAATATCCGTAA
1 TTATT--CAAATATCCGTAA
34763 TTATTCAAAT
1 TTATTCAAAT
34773 TAAATTAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.36
20 18 0.64
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (18 bp):
TTATTCAAATATCCGTAA
Found at i:34753 original size:20 final size:20
Alignment explanation
Indices: 34730--34769 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
34720 TTGTTTTATT
34730 CAAATATCCGTAATTATTCA
1 CAAATATCCGTAATTATTCA
34750 CAAATATCCGTAATTATTCA
1 CAAATATCCGTAATTATTCA
34770 AATTAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (20 bp):
CAAATATCCGTAATTATTCA
Found at i:38605 original size:2 final size:2
Alignment explanation
Indices: 38598--38631 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38588 CTATATGAGT
38598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38632 CACGAGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42514 original size:42 final size:42
Alignment explanation
Indices: 42467--42554 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
42457 TAAACAAACA
*
42467 GAATGGTGGTGAAAAGGAATTTGTATAGGATTATTTATTTAG
1 GAATGGTGGTGAAAAGGAATTTGTATAGGATTATTTATATAG
42509 GAATGGTGGTGAAAAGGAATTTGTATAGGATTATTTATATAG
1 GAATGGTGGTGAAAAGGAATTTGTATAGGATTATTTATATAG
42551 GAAT
1 GAAT
42555 TTGTATAGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.36
Consensus pattern (42 bp):
GAATGGTGGTGAAAAGGAATTTGTATAGGATTATTTATATAG
Found at i:42556 original size:12 final size:12
Alignment explanation
Indices: 42523--42563 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
42513 GGTGGTGAAA
42523 AGGAATTTGTAT
1 AGGAATTTGTAT
*
42535 AGGATTATTTATAT
1 AGGA--ATTTGTAT
42549 AGGAATTTGTAT
1 AGGAATTTGTAT
42561 AGG
1 AGG
42564 TTATCGATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 14 0.56
14 11 0.44
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (12 bp):
AGGAATTTGTAT
Found at i:45424 original size:24 final size:25
Alignment explanation
Indices: 45392--45443 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
45382 GATAATACAA
45392 TCACAATGGCCAACTTGAAATCT-T
1 TCACAATGGCCAACTTGAAATCTCT
* *
45416 TCACAATGGCCTATTTGAAATCTCT
1 TCACAATGGCCAACTTGAAATCTCT
45441 TCA
1 TCA
45444 GTCTTCTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.33
Consensus pattern (25 bp):
TCACAATGGCCAACTTGAAATCTCT
Found at i:45767 original size:11 final size:11
Alignment explanation
Indices: 45736--45778 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
45726 ATGAATTTTC
*
45736 GCTCTGATTTG
1 GCTCTGATTCG
*
45747 GCTCTAATTCG
1 GCTCTGATTCG
*
45758 GATCTGATTCG
1 GCTCTGATTCG
45769 GCTCTGATTC
1 GCTCTGATTC
45779 CAATTCCTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (11 bp):
GCTCTGATTCG
Found at i:46969 original size:24 final size:25
Alignment explanation
Indices: 46932--46979 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
46922 ATACAGTCAG
46932 AATGGCCAACTTGAAATCT-TTCAC
1 AATGGCCAACTTGAAATCTCTTCAC
* *
46956 AATGGCCTATTTGAAATCTCTTCA
1 AATGGCCAACTTGAAATCTCTTCA
46980 AGCTTCTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (25 bp):
AATGGCCAACTTGAAATCTCTTCAC
Found at i:50145 original size:80 final size:80
Alignment explanation
Indices: 50041--50195 Score: 283
Period size: 80 Copynumber: 1.9 Consensus size: 80
50031 AAATATTGGG
*
50041 TTTTCAAATTTCTTAAGAATGTGGAGAGGGATTTTTGGAGGGCCCAAAACCTCTCTCCAAAATCC
1 TTTTCAAATTTCTTAAAAATGTGGAGAGGGATTTTTGGAGGGCCCAAAACCTCTCTCCAAAATCC
50106 TTCTCATATGGTATT
66 TTCTCATATGGTATT
* *
50121 TTTTCAAATTTCTTAAAAATGTGGAGAGGGATTTTTGGAGGGCCCAAAACCTCTCTCCGAAATTC
1 TTTTCAAATTTCTTAAAAATGTGGAGAGGGATTTTTGGAGGGCCCAAAACCTCTCTCCAAAATCC
50186 TTCTCATATG
66 TTCTCATATG
50196 CCTATAGATG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (80 bp):
TTTTCAAATTTCTTAAAAATGTGGAGAGGGATTTTTGGAGGGCCCAAAACCTCTCTCCAAAATCC
TTCTCATATGGTATT
Found at i:50378 original size:9 final size:9
Alignment explanation
Indices: 50364--50411 Score: 96
Period size: 9 Copynumber: 5.3 Consensus size: 9
50354 TATAAAGAGA
50364 GATGACTTT
1 GATGACTTT
50373 GATGACTTT
1 GATGACTTT
50382 GATGACTTT
1 GATGACTTT
50391 GATGACTTT
1 GATGACTTT
50400 GATGACTTT
1 GATGACTTT
50409 GAT
1 GAT
50412 CTTTCTATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (9 bp):
GATGACTTT
Found at i:53230 original size:16 final size:16
Alignment explanation
Indices: 53205--53237 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53195 TAACAAAATA
*
53205 AACTACCTAATGTTAC
1 AACTAACTAATGTTAC
53221 AACTAACTAATGTTAC
1 AACTAACTAATGTTAC
53237 A
1 A
53238 TCAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (16 bp):
AACTAACTAATGTTAC
Found at i:65454 original size:13 final size:12
Alignment explanation
Indices: 65432--65475 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
65422 TTCTTTCAAC
65432 TTCTTTTTTTCT
1 TTCTTTTTTTCT
65444 TTCTGTTTTTTC-
1 TTCT-TTTTTTCT
*
65456 TTCTTTTTCTCT
1 TTCTTTTTTTCT
65468 GTTCTTTT
1 -TTCTTTT
65476 GTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 6 0.21
12 8 0.29
13 14 0.50
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (12 bp):
TTCTTTTTTTCT
Done.