Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011646.1 Corchorus capsularis cultivar CVL-1 contig11667, 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: 36188
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1017 original size:15 final size:15
Alignment explanation
Indices: 993--1023 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
983 TCGTCACTTT
*
993 AATATGAAAATAATA
1 AATATAAAAATAATA
1008 AATATAAAAATAATA
1 AATATAAAAATAATA
1023 A
1 A
1024 TAAGTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AATATAAAAATAATA
Found at i:1747 original size:9 final size:9
Alignment explanation
Indices: 1733--1764 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
1723 GGTCATTCAA
1733 TTATTTTTT
1 TTATTTTTT
1742 TTATTTTTT
1 TTATTTTTT
1751 TTAATTTTTT
1 TT-ATTTTTT
1761 TTAT
1 TTAT
1765 CTCATCCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTATTTTTT
Found at i:1751 original size:10 final size:10
Alignment explanation
Indices: 1735--1763 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1725 TCATTCAATT
1735 ATTTTTTTT-
1 ATTTTTTTTA
1744 ATTTTTTTTA
1 ATTTTTTTTA
1754 ATTTTTTTTA
1 ATTTTTTTTA
1764 TCTCATCCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:13763 original size:29 final size:28
Alignment explanation
Indices: 13669--13767 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 28
13659 CAAAATGCTA
*
13669 AAATAAGGGCCGATCTTTTAATTTGGCC
1 AAATAAGGGCCGATCTTTTAAATTGGCC
* * * *
13697 AAATAAGAGCCTAACGTTATTGAAAAT-GCTC
1 AAATAAGGGCCGATC-TT-TT-AAATTGGC-C
*
13728 AAATAAGGGCCCGATCTTTTAACTTGGCC
1 AAATAAGGG-CCGATCTTTTAAATTGGCC
13757 AAATAAGGGCC
1 AAATAAGGGCC
13768 TAACATTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
28 14 0.25
29 15 0.27
30 8 0.15
31 14 0.25
32 4 0.07
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Consensus pattern (28 bp):
AAATAAGGGCCGATCTTTTAAATTGGCC
Found at i:13769 original size:60 final size:60
Alignment explanation
Indices: 13637--13798 Score: 231
Period size: 60 Copynumber: 2.7 Consensus size: 60
13627 GCTAATTGCT
* *
13637 CAAATAAGGGCCTAACG-T-TTGCCAAAATGCTAAAATAAGGG-CCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATTG--AAAATGCTCAAATAAGGGCCCGATCTTTTAACTTGGC
*
13696 CAAATAAGAGCCTAACGTTATTGAAAATGCTCAAATAAGGGCCCGATCTTTTAACTTGGC
1 CAAATAAGGGCCTAACGTTATTGAAAATGCTCAAATAAGGGCCCGATCTTTTAACTTGGC
* * *
13756 CAAATAAGGGCCTAACATTATCGAAAATACTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATTGAAAATGCTCAAATAAGGGCC
13799 TGGTGTCAGT
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
59 33 0.35
60 57 0.61
61 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATTGAAAATGCTCAAATAAGGGCCCGATCTTTTAACTTGGC
Found at i:13864 original size:31 final size:30
Alignment explanation
Indices: 13829--13994 Score: 121
Period size: 31 Copynumber: 5.5 Consensus size: 30
13819 CGTGAGACAT
13829 GCCCTTATTTGAGCATTTTGGAAAACGTTAG
1 GCCCTTATTTGAGCATTTT-GAAAACGTTAG
** * *
13860 GCCCTTATTTG-GCCAAATTCAAAGATG-T-G
1 GCCCTTATTTGAG-CATTTTGAAA-ACGTTAG
*
13889 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTT-GAAAACGTTAG
** *
13920 GCCCTTATTTG-GCCAAATTCAAAGATCG---G
1 GCCCTTATTTGAG-CATTTTGAAA-A-CGTTAG
*
13949 GTCCTTATTTGAGCATTTTGACAAACGTTAG
1 GCCCTTATTTGAGCATTTTGA-AAACGTTAG
*
13980 GCTCTTATTTGAGCA
1 GCCCTTATTTGAGCA
13995 ATTAACCAAA
Statistics
Matches: 102, Mismatches: 19, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
28 2 0.02
29 35 0.34
30 15 0.15
31 48 0.47
32 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (30 bp):
GCCCTTATTTGAGCATTTTGAAAACGTTAG
Found at i:13898 original size:29 final size:29
Alignment explanation
Indices: 13859--13959 Score: 93
Period size: 29 Copynumber: 3.4 Consensus size: 29
13849 GAAAACGTTA
13859 GGCCCTTATTTGGCCAAATTCAAAGATGT
1 GGCCCTTATTTGGCCAAATTCAAAGATGT
**
13888 GGCCCTTATTTGAG-CATTTTGGCAAACG-T-T
1 GGCCCTTATTTG-GCCAAATT--CAAA-GATGT
13918 AGGCCCTTATTTGGCCAAATTCAAAGATCG-
1 -GGCCCTTATTTGGCCAAATTCAAAGAT-GT
*
13948 GGTCCTTATTTG
1 GGCCCTTATTTG
13960 AGCATTTTGA
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
28 1 0.02
29 32 0.55
30 3 0.05
31 21 0.36
32 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.34
Consensus pattern (29 bp):
GGCCCTTATTTGGCCAAATTCAAAGATGT
Found at i:13902 original size:60 final size:60
Alignment explanation
Indices: 13829--13990 Score: 265
Period size: 60 Copynumber: 2.7 Consensus size: 60
13819 CGTGAGACAT
13829 GCCCTTATTTGAGCATTTTGGAAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGAT-GTG
1 GCCCTTATTTGAGCATTTTGGAAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATCG-G
*
13889 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATCGG
1 GCCCTTATTTGAGCATTTTGGAAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATCGG
* *
13949 GTCCTTATTTGAGCATTTT-GACAAACGTTAGGCTCTTATTTG
1 GCCCTTATTTGAGCATTTTGGA-AAACGTTAGGCCCTTATTTG
13991 AGCAATTAAC
Statistics
Matches: 96, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
59 1 0.01
60 94 0.98
61 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGAAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATCGG
Found at i:15797 original size:66 final size:66
Alignment explanation
Indices: 15691--15824 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 66
15681 CTATCTCCAA
*
15691 AAGCAAGCCTTGGAAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGTGAAATGAC
1 AAGCAAGCCTTGGAAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGAC
15756 C
66 C
* *
15757 AAGCAAGCCTTGGTAGGGATCTTTTAGTAATTTCACTACTCTATTAAAGTCAATTGAGAAATGAC
1 AAGCAAGCCTTGGAAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGAC
15822 C
66 C
15823 AA
1 AA
15825 AAAGTCTAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (66 bp):
AAGCAAGCCTTGGAAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGAC
C
Found at i:21760 original size:12 final size:12
Alignment explanation
Indices: 21743--21769 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21733 TATAAAAAAT
21743 ATAAAAATAAAG
1 ATAAAAATAAAG
21755 ATAAAAATAAAG
1 ATAAAAATAAAG
21767 ATA
1 ATA
21770 TATATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (12 bp):
ATAAAAATAAAG
Found at i:23636 original size:442 final size:440
Alignment explanation
Indices: 22763--23691 Score: 1113
Period size: 442 Copynumber: 2.1 Consensus size: 440
22753 TGGGTCCCAT
* *
22763 TCTCAATAAACAAATATTTTTTTGTTGGATTATTTATCAAATGATCCATATACTTTTATGCTTTT
1 TCTCCATAAACAAATATTTTTTTGCTGGATTATTTATCAAATGATCCATATACTTTTATGCTTTT
* * * *
22828 TGCTATTTAGTCCCCCACAAGTTCTGGGTTGAACGATTGAACGTTTCGGCTTTAATTCTTATATT
66 TGCTATTTAATCCCCCACAAATTCTGGGTTGAACGATTGAACATTTCAGCTTTAATTCTTATATT
* *
22893 TTTTATTTTGTTTGTCCAATCAAGGTGATTCAAGTGTCTATTAAAAGGTTATTCCATGATCTACA
131 TTTTATTTTGTTTGTCCAATCAAGATGATTCAAGTGTCTATTAAAAGGTGATTCCATGATCTACA
* * * * *
22958 ACTTTCATGAAGGACTCAGAAGCCAATTTTAATGTTTTTTTATTCTAAAAAATGCTTCTGAAATA
196 ACTTTCATGAAGGACTCAAAAGCCAATTTCAATG-TATTTCATTCTAAAAAATGCTTCCGAAATA
* ** * ** * *
23023 TTGTGGTCTCGATTGCCGGTCTCTCTAATATTGTATAATTTTCGGTCCATTTGTCCGATTGAGAT
260 TTGTGGTCTCGATTGCCGGTCTATCTAATATCATATAATTTTCGATCCACATGTCCGATTAAGAC
* *** * * *
23088 TGTTCAAGTGTTGGTTAAAAGGTTATTGTGTGATCTACGACTTTCGCTAAGGACCTGAAAGCTGA
325 TGTTCAAGTGTCGGTTAAAAGGTTATTGCAAGATCTACAACTTTCACTAAGGACCTAAAAGCTGA
* * * *
23153 ATTTGATTAATGAGTTTCGTGGAGGGTTCGAGAGAGAATTTTTATGTTTGG
390 ATTTGATTAACGAGCTTCATGGAGGGTTCAAGAGAGAATTTTTATGTTTGG
*
23204 TCTCCATAAACAAATATTTTTTTTGCTGGATTATTTATTAAATGATCC-TCATACTTTTATG-TT
1 TCTCCATAAACAAATA-TTTTTTTGCTGGATTATTTATCAAATGATCCAT-ATACTTTTATGCTT
* * * *
23267 TTATGCTATTTAATCCCTCACAAATTCTGGGTTGGACGATTTAACATTTCAGCTTTAATTCTTTT
64 TT-TGCTATTTAATCCCCCACAAATTCTGGGTTGAACGATTGAACATTTCAGCTTTAATTCTTAT
* * * *
23332 ATGTTTTT-TGTTATGTTTGTCCGATTAAGATGATTCAAGTGTTTATTAAAAGGTGATTTCATGA
128 AT-TTTTTAT-TT-TGTTTGTCCAATCAAGATGATTCAAGTGTCTATTAAAAGGTGATTCCATGA
* ** *
23396 TCTACAACTTTCATTAAGTTCTCAAAAGCCAATTTCGA-G-ATTTCAGTTCTAAAAAATGCTTCC
190 TCTACAACTTTCATGAAGGACTCAAAAGCCAATTTCAATGTATTTCA-TTCTAAAAAATGCTTCC
* * * * * * * *
23459 G-AATTTTGGTGGTTTCGATTGCCGGTTTATTTAATATCATGTGATTTTCGATTCACATGTCTGA
254 GAAATATT-GTGGTCTCGATTGCCGGTCTATCTAATATCATATAATTTTCGATCCACATGTCCGA
* * *
23523 TTAA-AGCTGTTTAAGTGTCGGTTAAAAGGTTATTGCAAGATCTACAACTTTCATTAA-GAGTCT
318 TTAAGA-CTGTTCAAGTGTCGGTTAAAAGGTTATTGCAAGATCTACAACTTTCACTAAGGA-CCT
* * *
23586 AAAAGCTGAATTTGATCT-ACGAGCTTCATGGATGGTTCAAGAGGGAATTTTTATGTTTTG
381 AAAAGCTGAATTTGAT-TAACGAGCTTCATGGAGGGTTCAAGAGAGAATTTTTATGTTTGG
*
23646 TCTCCATAAACTATAATCA-TTTTTTGCTGGATTATTTATCGAATGA
1 TCTCCATAAAC-A-AAT-ATTTTTTTGCTGGATTATTTATCAAATGA
23692 CCCCCTATAT
Statistics
Matches: 413, Mismatches: 61, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
441 32 0.08
442 265 0.64
443 35 0.08
444 80 0.19
445 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (440 bp):
TCTCCATAAACAAATATTTTTTTGCTGGATTATTTATCAAATGATCCATATACTTTTATGCTTTT
TGCTATTTAATCCCCCACAAATTCTGGGTTGAACGATTGAACATTTCAGCTTTAATTCTTATATT
TTTTATTTTGTTTGTCCAATCAAGATGATTCAAGTGTCTATTAAAAGGTGATTCCATGATCTACA
ACTTTCATGAAGGACTCAAAAGCCAATTTCAATGTATTTCATTCTAAAAAATGCTTCCGAAATAT
TGTGGTCTCGATTGCCGGTCTATCTAATATCATATAATTTTCGATCCACATGTCCGATTAAGACT
GTTCAAGTGTCGGTTAAAAGGTTATTGCAAGATCTACAACTTTCACTAAGGACCTAAAAGCTGAA
TTTGATTAACGAGCTTCATGGAGGGTTCAAGAGAGAATTTTTATGTTTGG
Found at i:24305 original size:117 final size:116
Alignment explanation
Indices: 24156--24387 Score: 360
Period size: 117 Copynumber: 2.0 Consensus size: 116
24146 GGTTTTATGT
*
24156 TAATTTCTTTTGATAATTTAAGTTATTTATATTTACAAA-TCAATTTTAAAATTAAAATTAAGGC
1 TAATTTCTTTTGATAATTCAAGTTATTTATATTTACAAAGT-AATTTTAAAATTAAAATTAAGGC
*
24220 AATAAAAATAATTATAGATTTGTACATGTAAAACAATGAAAAAAAGGATTGAA
65 AATAAAAATAATTATAGATTTATACATGTAAAACAATG-AAAAAAGGATTGAA
*
24273 TAATTT-TTGTTGATAATTCAAGTTATTTATATTTACAAAGTAATTTTAAAATTAAAATTAAGGT
1 TAATTTCTT-TTGATAATTCAAGTTATTTATATTTACAAAGTAATTTTAAAATTAAAATTAAGGC
* * * *
24337 AATGAAAATAATTATAGATTTATCCATGTAAAAGAATGAAAAAGGGATTGA
65 AATAAAAATAATTATAGATTTATACATGTAAAACAATGAAAAAAGGATTGA
24388 TTTTGTTAGC
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
116 14 0.13
117 91 0.86
118 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (116 bp):
TAATTTCTTTTGATAATTCAAGTTATTTATATTTACAAAGTAATTTTAAAATTAAAATTAAGGCA
ATAAAAATAATTATAGATTTATACATGTAAAACAATGAAAAAAGGATTGAA
Found at i:27014 original size:265 final size:268
Alignment explanation
Indices: 26593--27125 Score: 901
Period size: 265 Copynumber: 2.0 Consensus size: 268
26583 CAAGAATATA
*
26593 TGCTTTGGAAATAGATTTTTCTACCATTAACTATTATATATCTCTCTCATCTAATCTAGAAGTGA
1 TGCTTTGGAAATAGATTTTCCTACCATTAACTATTATATATCTCTCTCATCTAATCTAGAAGTGA
*
26658 AGATGAAACCAACTATATCTCAATTTTATGTTCTCAAGGCTATAGAACAACTGCAGCAAGAATTG
66 AGATGAAACCAACTATATCTCAATTTTATGTTCTCAAGGCTATAGAACAACAGCAGCAAGAATTG
* * * * *
26723 GACACTGCCCTAGCTTGGTGGTCTTCATCTTTATTAGGTAATTCATCAATCTTTTTCCCCTTATG
131 GACACTGCCCTAACTTGATAGTCTTCATCTTTATCAGGTAATTCATCAATCTTTTTCCCCTTACG
* *
26788 TTTGTAAATGATTTTTTAGTCCAACTAGAAGTAGTTCAGCA-TTTTTCGCTGTTTAAATCTAAGA
196 TTTGTAAATGATTTTTCAATCCAACTAGAAGTAGTTCAGCATTTTTTCGCTGTTTAAATCTAAGA
26852 TTTCTGAG
261 TTTCTGAG
* * *
26860 TGCTTTGGAAATAGATTTTCCTGCCATTCACTA-T-TATATCTCTCTCATCTAATCTAGCAGTGA
1 TGCTTTGGAAATAGATTTTCCTACCATTAACTATTATATATCTCTCTCATCTAATCTAGAAGTGA
*
26923 AGATGGAACCAACTATATCTCAATTTTATGTTCTCAAGGCTATAGAACAACAGCAGCAAGAATTG
66 AGATGAAACCAACTATATCTCAATTTTATGTTCTCAAGGCTATAGAACAACAGCAGCAAGAATTG
* *
26988 GACACTGCCTTAATTTGATAGTCTTCATCTTTATCAGGTAATTCATCAATCTTTTTCCCCTTACG
131 GACACTGCCCTAACTTGATAGTCTTCATCTTTATCAGGTAATTCATCAATCTTTTTCCCCTTACG
*
27053 TTTGTTAATGATTTTTCAATCCAACTAGAAGTAGTTCAGCATTTTTTCGCTGTTTAAATCTAAGA
196 TTTGTAAATGATTTTTCAATCCAACTAGAAGTAGTTCAGCATTTTTTCGCTGTTTAAATCTAAGA
27118 TTTCTGAG
261 TTTCTGAG
27126 CAGACTTATA
Statistics
Matches: 249, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
265 187 0.75
266 32 0.13
267 30 0.12
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (268 bp):
TGCTTTGGAAATAGATTTTCCTACCATTAACTATTATATATCTCTCTCATCTAATCTAGAAGTGA
AGATGAAACCAACTATATCTCAATTTTATGTTCTCAAGGCTATAGAACAACAGCAGCAAGAATTG
GACACTGCCCTAACTTGATAGTCTTCATCTTTATCAGGTAATTCATCAATCTTTTTCCCCTTACG
TTTGTAAATGATTTTTCAATCCAACTAGAAGTAGTTCAGCATTTTTTCGCTGTTTAAATCTAAGA
TTTCTGAG
Found at i:27207 original size:29 final size:29
Alignment explanation
Indices: 27165--27222 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
27155 ATATATAGGA
27165 ACTATCAGATCTCTCTTTGAAGCAAACCT
1 ACTATCAGATCTCTCTTTGAAGCAAACCT
27194 ACTATCAGATCTCTCTTTGAAGCAAACCT
1 ACTATCAGATCTCTCTTTGAAGCAAACCT
27223 TGCCATCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (29 bp):
ACTATCAGATCTCTCTTTGAAGCAAACCT
Found at i:29788 original size:26 final size:28
Alignment explanation
Indices: 29759--29814 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
29749 GCTGCGAAGC
29759 TTCGCAGCGA-G-CTAGACTCTAGTATA
1 TTCGCAGCGAGGTCTAGACTCTAGTATA
29785 TTCGCAGCGAGGTCTAGACTCTAGTATA
1 TTCGCAGCGAGGTCTAGACTCTAGTATA
29813 TT
1 TT
29815 GGCATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 10 0.36
27 1 0.04
28 17 0.61
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (28 bp):
TTCGCAGCGAGGTCTAGACTCTAGTATA
Found at i:29973 original size:69 final size:69
Alignment explanation
Indices: 29862--30004 Score: 250
Period size: 69 Copynumber: 2.1 Consensus size: 69
29852 ACTGTCACTT
* *
29862 TGTCCCCAATTTTTTTATTTTGACCAAAATGCACCCTAAAGTTTTATTTTTGTGCCACCTTGCAC
1 TGTCCCCAACTTTTTTATTTTGACAAAAATGCACCCTAAAGTTTTATTTTTGTGCCACCTTGCAC
29927 CCTC
66 CCTC
* *
29931 TGTCCCCAACTTTTTTATTTTGACAAAAATGCACCCTAAAGTTTTATTTTTGTGTCACTTTGCAC
1 TGTCCCCAACTTTTTTATTTTGACAAAAATGCACCCTAAAGTTTTATTTTTGTGCCACCTTGCAC
29996 CCTC
66 CCTC
30000 TGTCC
1 TGTCC
30005 GGTAGGACAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.41
Consensus pattern (69 bp):
TGTCCCCAACTTTTTTATTTTGACAAAAATGCACCCTAAAGTTTTATTTTTGTGCCACCTTGCAC
CCTC
Found at i:30158 original size:31 final size:31
Alignment explanation
Indices: 30089--30251 Score: 155
Period size: 31 Copynumber: 5.5 Consensus size: 31
30079 TTCTTTTGTG
* * **
30089 CACGTGGCATGCCACGTGCCATTTTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
30120 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * *
30151 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
30182 CA--T-G--TGGCAC--G--ACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* *
30204 CATGTGGCATGCCACATGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
30235 CACGTGGCGTGCCACGT
1 CACGTGGCATGCCACGT
30252 TGGACACCGT
Statistics
Matches: 108, Mismatches: 15, Indels: 18
0.77 0.11 0.13
Matches are distributed among these distances:
22 13 0.12
24 2 0.02
25 1 0.01
26 4 0.04
27 5 0.05
28 1 0.01
29 2 0.02
31 80 0.74
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:30199 original size:22 final size:22
Alignment explanation
Indices: 30171--30212 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
30161 GACATGTGTC
30171 ACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACATGTGGCACG
30193 ACTTTTTGGTACATGTGGCA
1 ACTTTTTGGTACATGTGGCA
30213 TGCCACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (22 bp):
ACTTTTTGGTACATGTGGCACG
Found at i:30202 original size:53 final size:53
Alignment explanation
Indices: 30140--30242 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
30130 GCCACGTGTC
* ** *
30140 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCATGACACATGTCACTTTTTGGTACACGTGGCACG
* *
30193 ACTTTTTGGTACATGTGGCATGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCATGACACATGTCACTTTTTGGTACACGTGGC
30243 GTGCCACGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCATGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:32041 original size:15 final size:15
Alignment explanation
Indices: 32023--32053 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32013 TTTAAGTTTC
32023 AGGGACTTAATTGAA
1 AGGGACTTAATTGAA
*
32038 AGGGACTTATTTGAA
1 AGGGACTTAATTGAA
32053 A
1 A
32054 AGAAAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (15 bp):
AGGGACTTAATTGAA
Found at i:36121 original size:17 final size:17
Alignment explanation
Indices: 36096--36135 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
36086 AACTAAGTAG
36096 ACTAAGATAACTAACAT
1 ACTAAGATAACTAACAT
*
36113 ACTAGGATAACTAACAT
1 ACTAAGATAACTAACAT
*
36130 ATTAAG
1 ACTAAG
36136 CATTGACCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (17 bp):
ACTAAGATAACTAACAT
Done.