Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008150.1 Corchorus capsularis cultivar CVL-1 contig08171, 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: 47808
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3483 original size:28 final size:28
Alignment explanation
Indices: 3451--3523 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
3441 GTAGATTAAG
*
3451 AATGACCAAAATACCCCCTAAATGCAAA
1 AATGACCAAAATGCCCCCTAAATGCAAA
* **
3479 AATGACCAAAATGCCCCCTAGATGTGAA
1 AATGACCAAAATGCCCCCTAAATGCAAA
3507 AATGACCAAAATGCCCC
1 AATGACCAAAATGCCCC
3524 TGGATGACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15
Consensus pattern (28 bp):
AATGACCAAAATGCCCCCTAAATGCAAA
Found at i:6484 original size:12 final size:12
Alignment explanation
Indices: 6462--6619 Score: 172
Period size: 12 Copynumber: 13.2 Consensus size: 12
6452 CTCCAGATCC
*
6462 AGTTGATGAAAG
1 AGTTGAAGAAAG
*
6474 GGTTGAAGAAAG
1 AGTTGAAGAAAG
* *
6486 GGTTCAAGAAAG
1 AGTTGAAGAAAG
*
6498 AGTTCAAGAAAG
1 AGTTGAAGAAAG
6510 AGTTGAAGAAAG
1 AGTTGAAGAAAG
* * *
6522 GGTTCAAGAAAC
1 AGTTGAAGAAAG
6534 AGTTGAAGAAAG
1 AGTTGAAGAAAG
* *
6546 AGTTCAAGAAAC
1 AGTTGAAGAAAG
*
6558 TGTTGAAGAAAG
1 AGTTGAAGAAAG
6570 AGTTGAAGAAAG
1 AGTTGAAGAAAG
*
6582 ATTTGAAGAAAG
1 AGTTGAAGAAAG
* *
6594 GGTTGAAGAAAT
1 AGTTGAAGAAAG
* *
6606 AGCTGCAGAAAG
1 AGTTGAAGAAAG
6618 AG
1 AG
6620 ATGGTGAAGA
Statistics
Matches: 121, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 121 1.00
ACGTcount: A:0.46, C:0.05, G:0.31, T:0.18
Consensus pattern (12 bp):
AGTTGAAGAAAG
Found at i:6516 original size:36 final size:36
Alignment explanation
Indices: 6462--6619 Score: 199
Period size: 36 Copynumber: 4.4 Consensus size: 36
6452 CTCCAGATCC
* *
6462 AGTTGATGAAAGGGTTGAAGAAAGGGTTCAAGAAAG
1 AGTTGAAGAAAGAGTTGAAGAAAGGGTTCAAGAAAG
* *
6498 AGTTCAAGAAAGAGTTGAAGAAAGGGTTCAAGAAAC
1 AGTTGAAGAAAGAGTTGAAGAAAGGGTTCAAGAAAG
* ** *
6534 AGTTGAAGAAAGAGTTCAAGAAACTGTTGAAGAAAG
1 AGTTGAAGAAAGAGTTGAAGAAAGGGTTCAAGAAAG
* * *
6570 AGTTGAAGAAAGATTTGAAGAAAGGGTTGAAGAAAT
1 AGTTGAAGAAAGAGTTGAAGAAAGGGTTCAAGAAAG
* *
6606 AGCTGCAGAAAGAG
1 AGTTGAAGAAAGAG
6620 ATGGTGAAGA
Statistics
Matches: 104, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 104 1.00
ACGTcount: A:0.46, C:0.05, G:0.31, T:0.18
Consensus pattern (36 bp):
AGTTGAAGAAAGAGTTGAAGAAAGGGTTCAAGAAAG
Found at i:10796 original size:35 final size:34
Alignment explanation
Indices: 10732--10980 Score: 225
Period size: 35 Copynumber: 7.0 Consensus size: 34
10722 ATCAGTAATA
10732 AGTAACTTAATTCAGGGTAATTAAGTAAGTTAGTAAGT
1 AGTAACTTAATTCAGGGTAA-T---TAAGTTAGTAAGT
* *
10770 CAGTAGCTTAATTCAGGGTAATTAAG-TAGTTCAGT
1 -AGTAACTTAATTCAGGGTAATTAAGTTAG-TAAGT
* *
10805 AAGTAACTTAATTCAGGGTAATTAAGTGAGTCAGT
1 -AGTAACTTAATTCAGGGTAATTAAGTTAGTAAGT
* * * *
10840 AATCAACTTAATTCAGGGTAATTAAGTAATTCAGT
1 AGT-AACTTAATTCAGGGTAATTAAGTTAGTAAGT
* * * *
10875 AATCAACTTAATTCAGGGTAATTGAGTAAGTTAGT
1 AGT-AACTTAATTCAGGGTAATTAAGTTAGTAAGT
*
10910 AATCAACCTTAATTCAGGGTAATTAAG-TAGTTCAA-T
1 AGT-AA-CTTAATTCAGGGTAATTAAGTTAG-T-AAGT
10946 AAGTAACTTAATTCAGGGTAATTAAGTTTAGTAAG
1 -AGTAACTTAATTCAGGGTAATTAAG-TTAGTAAG
10981 AAGCAGAGAT
Statistics
Matches: 185, Mismatches: 15, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
34 5 0.03
35 128 0.69
36 26 0.14
37 6 0.03
38 1 0.01
39 19 0.10
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (34 bp):
AGTAACTTAATTCAGGGTAATTAAGTTAGTAAGT
Found at i:10859 original size:70 final size:71
Alignment explanation
Indices: 10730--10972 Score: 382
Period size: 70 Copynumber: 3.4 Consensus size: 71
10720 GAATCAGTAA
*
10730 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTTAGTAAGTCAGTAGCTTAATTCAGGGTAATTAA
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTTAGTAA-TCA--ACCTTAATTCAGGGTAATTAA
10795 GTAGTTCAG
63 GTAGTTCAG
* *
10804 TAAGTAACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAA-CTTAATTCAGGGTAATTAAGTA
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTTAGTAATCAACCTTAATTCAGGGTAATTAAGTA
*
10868 ATTCAG
66 GTTCAG
*
10874 TAA-TCAACTTAATTCAGGGTAATTGAGTAAGTTAGTAATCAACCTTAATTCAGGGTAATTAAGT
1 TAAGT-AACTTAATTCAGGGTAATTAAGTAAGTTAGTAATCAACCTTAATTCAGGGTAATTAAGT
*
10938 AGTTCAA
65 AGTTCAG
10945 TAAGTAACTTAATTCAGGGTAATTAAGT
1 TAAGTAACTTAATTCAGGGTAATTAAGT
10973 TTAGTAAGAA
Statistics
Matches: 157, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
69 1 0.01
70 64 0.41
71 52 0.33
72 1 0.01
73 3 0.02
74 36 0.23
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (71 bp):
TAAGTAACTTAATTCAGGGTAATTAAGTAAGTTAGTAATCAACCTTAATTCAGGGTAATTAAGTA
GTTCAG
Found at i:10888 original size:17 final size:17
Alignment explanation
Indices: 10835--10890 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
10825 ATTAAGTGAG
10835 TCAGTAATCAACTTAAT
1 TCAGTAATCAACTTAAT
* *
10852 TCAGGGTAATTAA-GTAAT
1 TCA--GTAATCAACTTAAT
10870 TCAGTAATCAACTTAAT
1 TCAGTAATCAACTTAAT
10887 TCAG
1 TCAG
10891 GGTAATTGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
16 7 0.22
17 11 0.34
18 7 0.22
19 7 0.22
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (17 bp):
TCAGTAATCAACTTAAT
Found at i:15720 original size:24 final size:24
Alignment explanation
Indices: 15686--15759 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
15676 ATACATTTAA
15686 CAGAAACATAGCATGCCTAAAACT
1 CAGAAACATAGCATGCCTAAAACT
*
15710 CGGAAACATAGCATGCCTAAAACT
1 CAGAAACATAGCATGCCTAAAACT
* * *
15734 CAAAAACAGAGCAAGCCTAAAA-T
1 CAGAAACATAGCATGCCTAAAACT
15757 CAG
1 CAG
15760 GGCAATGCCT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.47, C:0.24, G:0.15, T:0.14
Consensus pattern (24 bp):
CAGAAACATAGCATGCCTAAAACT
Found at i:16371 original size:3 final size:3
Alignment explanation
Indices: 16363--16408 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
16353 CCTTTCCTGG
* * *
16363 AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA GGA AGA ACA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
16409 AAACCCTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:21192 original size:19 final size:19
Alignment explanation
Indices: 21168--21206 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
21158 ATATCACGTT
21168 TAATTTTGCTTTTAACATA
1 TAATTTTGCTTTTAACATA
*
21187 TAATTTTGCTTTTAATATA
1 TAATTTTGCTTTTAACATA
21206 T
1 T
21207 CATGCTCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (19 bp):
TAATTTTGCTTTTAACATA
Found at i:23058 original size:53 final size:53
Alignment explanation
Indices: 22997--23099 Score: 163
Period size: 53 Copynumber: 1.9 Consensus size: 53
22987 TGTTTGAATG
* * *
22997 TTTTGAAAACTTGATGGGAACTTTCCCATTTCGA-AAAGACCTAAATTGAACAT
1 TTTTGAAAACTTAAAGGGAACTTTCCCACTTCGAGAAA-ACCTAAATTGAACAT
23050 TTTTGAAAACTTAAAGGGAACTTTCCCACTTCGAGAAAACCTAAATTGAA
1 TTTTGAAAACTTAAAGGGAACTTTCCCACTTCGAGAAAACCTAAATTGAA
23100 TACATTGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
53 43 0.93
54 3 0.07
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (53 bp):
TTTTGAAAACTTAAAGGGAACTTTCCCACTTCGAGAAAACCTAAATTGAACAT
Found at i:30818 original size:53 final size:52
Alignment explanation
Indices: 30756--30872 Score: 164
Period size: 53 Copynumber: 2.2 Consensus size: 52
30746 TGTTTGAATG
* * *
30756 TTTTGAAAACTTGATGGGAACTTTCCCATTTCGA-AAAGACCTAAATTGAACA
1 TTTTGAAAACTTAAAGGGAACTTTCCCACTTCGAGAAA-ACCTAAATTGAACA
*
30808 TTTTTGAAAACTTAAAGGGAACTTTCCCACTTCGAGAAAACCTAAATTGAATA
1 -TTTTGAAAACTTAAAGGGAACTTTCCCACTTCGAGAAAACCTAAATTGAACA
*
30861 CTTTGAAAACTT
1 TTTTGAAAACTT
30873 TGAATGAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
52 11 0.19
53 44 0.76
54 3 0.05
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (52 bp):
TTTTGAAAACTTAAAGGGAACTTTCCCACTTCGAGAAAACCTAAATTGAACA
Found at i:36470 original size:40 final size:39
Alignment explanation
Indices: 36350--36473 Score: 142
Period size: 41 Copynumber: 3.1 Consensus size: 39
36340 CTCAGTTTGC
* *
36350 GTGTTGTTTAGTTTTCCTGTTTTGCCTTTCCTCACCGGAAG
1 GTGTTGTTTAG-TTTCCCGTTTTGCCCTTCC-CACCGGAAG
* *
36391 GTGTTGTTTGGATTTCCCGTTTTGACCTTCCCCACCGGAAG
1 GTGTTGTTTAG-TTTCCCGTTTTGCCCTT-CCCACCGGAAG
*
36432 GTGTTGTTTAGTTTCCCAG-TTTGCCCTTCCCAGTCGGAAG
1 GTGTTGTTTAGTTTCCC-GTTTTGCCCTTCCCA-CCGGAAG
36472 GT
1 GT
36474 CCCTGTTTTC
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
39 4 0.06
40 22 0.31
41 44 0.61
42 2 0.03
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.40
Consensus pattern (39 bp):
GTGTTGTTTAGTTTCCCGTTTTGCCCTTCCCACCGGAAG
Found at i:36664 original size:50 final size:50
Alignment explanation
Indices: 36455--36873 Score: 563
Period size: 50 Copynumber: 8.6 Consensus size: 50
36445 TCCCAGTTTG
* * *
36455 CCCTTCCCAGTCGGAAGGTCCCTGTTTTCTTTGTTT-ATT-CCAAAATGC
1 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
*
36503 CCCTTTCCGGTCGGAAGGTCCC----TT-TTT-TTTGTTTCCCAAAATGC
1 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
* * *
36547 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTT-ATTCCAAAAATAC
1 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
36596 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
1 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
* * *
36646 CCCTTCCCGATCAGAAGGTCCCTGTTTTCTTTATTTGTTTCCTAAAATGC
1 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
* * * **
36696 CTCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTT-ATTCAAAAAATGC
1 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
* *
36745 CCTTTCCCGGTCAGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
1 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
* * *
36795 CCCTTCTCGGTCAGAAGGTCCCTGTTTTCTTTATTTGCTTCCCAAAATGC
1 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
* *
36845 CCCTTCCCAGTCGGAAGGT-CCAGTTTTCT
1 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCT
36874 CTTCACATTT
Statistics
Matches: 327, Mismatches: 34, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.01
43 5 0.02
44 32 0.10
48 22 0.07
49 100 0.31
50 165 0.50
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.38
Consensus pattern (50 bp):
CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
Found at i:36667 original size:99 final size:99
Alignment explanation
Indices: 36455--36873 Score: 538
Period size: 99 Copynumber: 4.3 Consensus size: 99
36445 TCCCAGTTTG
* *
36455 CCCTTCCC-AGTCGGAAGGTCCCTGTTTTCTTTGTTT-ATTCCAAAATGCCCCTTTCCGGTCGGA
1 CCCTTCCCGA-TCGGAAGGTCCCTGTTTTCTTTATTTGATTCCAAAATGCCCCTTCCCGGTCGGA
36518 AGGTCCC----TT-TTT-TTTGTTTCCCAAAATGC
65 AGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
* *
36547 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTT-ATTCCAAAAATACCCCTTCCCGGTCGGA
1 CCCTTCCCGATCGGAAGGTCCCTGTTTTCTTTATTTGATTCC-AAAATGCCCCTTCCCGGTCGGA
36611 AGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
65 AGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
* * *
36646 CCCTTCCCGATCAGAAGGTCCCTGTTTTCTTTATTTGTTTCCTAAAATGCCTCTTCCCGGTCGGA
1 CCCTTCCCGATCGGAAGGTCCCTGTTTTCTTTATTTGATTCC-AAAATGCCCCTTCCCGGTCGGA
* * **
36711 AGGTCCCTGTTTTCTTTGTTT-ATTCAAAAAATGC
65 AGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
* * * * * *
36745 CCTTTCCCGGTCAGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCTCGGTCAGA
1 CCCTTCCCGATCGGAAGGTCCCTGTTTTCTTTATTTGATT-CCAAAATGCCCCTTCCCGGTCGGA
*
36810 AGGTCCCTGTTTTCTTTATTTGCTTCCCAAAATGC
65 AGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
*
36845 CCCTTCCC-AGTCGGAAGGT-CCAGTTTTCT
1 CCCTTCCCGA-TCGGAAGGTCCCTGTTTTCT
36874 CTTCACATTT
Statistics
Matches: 288, Mismatches: 27, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
92 38 0.13
93 27 0.09
97 2 0.01
98 3 0.01
99 147 0.51
100 71 0.25
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.38
Consensus pattern (99 bp):
CCCTTCCCGATCGGAAGGTCCCTGTTTTCTTTATTTGATTCCAAAATGCCCCTTCCCGGTCGGAA
GGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGC
Found at i:36717 original size:149 final size:149
Alignment explanation
Indices: 36455--36873 Score: 622
Period size: 149 Copynumber: 2.9 Consensus size: 149
36445 TCCCAGTTTG
* * * * *
36455 CCCTTCCCAGTCGGAAGGTCCCTGTTTTCTTTGTTT-ATT-CCAAAATGCCCCTTTCCGGTCGGA
1 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCAGA
36518 AGGTCCC----TT-TTT-TTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCT
66 AGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCT
*
36577 TTATTTATTCCAAAAATAC
131 TTATTTATTCAAAAAATAC
*
36596 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGATCAGA
1 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCAGA
* *
36661 AGGTCCCTGTTTTCTTTATTTGTTTCCTAAAATGCCTCTTCCCGGTCGGAAGGTCCCTGTTTTCT
66 AGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCT
* *
36726 TTGTTTATTCAAAAAATGC
131 TTATTTATTCAAAAAATAC
* * *
36745 CCTTTCCCGGTCAGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCTCGGTCAGA
1 CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCAGA
* * *
36810 AGGTCCCTGTTTTCTTTATTTGCTTCCCAAAATGCCCCTTCCCAGTCGGAAGGT-CCAGTTTTCT
66 AGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCT
36874 CTTCACATTT
Statistics
Matches: 250, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
141 34 0.14
142 2 0.01
143 28 0.11
147 2 0.01
148 12 0.05
149 172 0.69
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.38
Consensus pattern (149 bp):
CCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCAGA
AGGTCCCTGTTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCT
TTATTTATTCAAAAAATAC
Found at i:40663 original size:36 final size:37
Alignment explanation
Indices: 40569--40663 Score: 104
Period size: 37 Copynumber: 2.6 Consensus size: 37
40559 CACAAAGATC
* ** *
40569 AACAATCGACCACGAACTGGTCTCTTTTCAAGCTTCA
1 AACAATTGACCACGAACTGGTCTCTTCCCAAACTTCA
*
40606 AACAGTTGACCAC-ATACTGGTCTCTTCCCAAAC-TCA
1 AACAATTGACCACGA-ACTGGTCTCTTCCCAAACTTCA
* *
40642 AACAATTGGCCACGAATTGGTC
1 AACAATTGACCACGAACTGGTC
40664 ACCTTTCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
36 21 0.44
37 27 0.56
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (37 bp):
AACAATTGACCACGAACTGGTCTCTTCCCAAACTTCA
Found at i:40895 original size:39 final size:38
Alignment explanation
Indices: 40848--40934 Score: 120
Period size: 39 Copynumber: 2.3 Consensus size: 38
40838 GAAGTCATCG
*
40848 AAGTTGACTGGAAACAAGTCACCATTCAACAATCATCAA
1 AAGTTGACTGGAAACAAGTCACCATTCAACAATAATC-A
* * * *
40887 AAGTTGACTGGAAACAGGTCATCTTTCAGCAATAATCA
1 AAGTTGACTGGAAACAAGTCACCATTCAACAATAATCA
40925 AAGTTGACTG
1 AAGTTGACTG
40935 AAAAAAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 11 0.26
39 32 0.74
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (38 bp):
AAGTTGACTGGAAACAAGTCACCATTCAACAATAATCA
Found at i:44515 original size:6 final size:6
Alignment explanation
Indices: 44506--44538 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
44496 AAAGCAAAGC
44506 AAATCT AAATCT AAATCT AAATCT AAATC- AAAT
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAAT
44539 TAATAAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:44554 original size:13 final size:13
Alignment explanation
Indices: 44538--44562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44528 CTAAATCAAA
44538 TTAATAAAGCAAT
1 TTAATAAAGCAAT
44551 TTAATAAAGCAA
1 TTAATAAAGCAA
44563 ACAATAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (13 bp):
TTAATAAAGCAAT
Done.