Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011223.1 Corchorus capsularis cultivar CVL-1 contig11244, 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: 62897
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2443 original size:23 final size:23
Alignment explanation
Indices: 2413--2459 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2403 TGGAGGAAGA
* *
2413 GGGTTAGTGGTGACTGTTTTGAT
1 GGGTTAGTAGTGAATGTTTTGAT
2436 GGGTTAGTAGTGAATGTTTTGAT
1 GGGTTAGTAGTGAATGTTTTGAT
2459 G
1 G
2460 CAATTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.38, T:0.43
Consensus pattern (23 bp):
GGGTTAGTAGTGAATGTTTTGAT
Found at i:15936 original size:20 final size:21
Alignment explanation
Indices: 15902--15942 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
15892 CCCCCCAATT
15902 TTTGTTTTCTAATTTGGCCCC
1 TTTGTTTTCTAATTTGGCCCC
*
15923 TTTGTTTT-TAATTTGTCCCC
1 TTTGTTTTCTAATTTGGCCCC
15943 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.10, C:0.22, G:0.12, T:0.56
Consensus pattern (21 bp):
TTTGTTTTCTAATTTGGCCCC
Found at i:19187 original size:13 final size:13
Alignment explanation
Indices: 19169--19193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19159 ACGAAAAATT
19169 CAGAAGTGCTTTC
1 CAGAAGTGCTTTC
19182 CAGAAGTGCTTT
1 CAGAAGTGCTTT
19194 TCAGTTGTTT
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
CAGAAGTGCTTTC
Found at i:20530 original size:36 final size:36
Alignment explanation
Indices: 20490--20611 Score: 108
Period size: 36 Copynumber: 3.4 Consensus size: 36
20480 GGAGCCATAT
*
20490 AAGTACAAGTCTCCTCCTCCTCCAACCCCAGTTTAC
1 AAGTACAAATCTCCTCCTCCTCCAACCCCAGTTTAC
* **
20526 AAGTACAAATCACCTCCTCCTCCTAAAGAGCCA---TAC
1 AAGTACAAATCTCCTCCTCCTCC--AA-CCCCAGTTTAC
* * *
20562 AAGTACAAGTCTCCTCCACCTCC-ACCTCCAGTTTAT
1 AAGTACAAATCTCCTCCTCCTCCAACC-CCAGTTTAC
*
20598 AAGTATAAATCTCC
1 AAGTACAAATCTCC
20612 ACCACCACCA
Statistics
Matches: 67, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
33 4 0.06
36 58 0.87
38 2 0.03
39 3 0.04
ACGTcount: A:0.30, C:0.37, G:0.08, T:0.25
Consensus pattern (36 bp):
AAGTACAAATCTCCTCCTCCTCCAACCCCAGTTTAC
Found at i:20569 original size:72 final size:71
Alignment explanation
Indices: 20389--20969 Score: 263
Period size: 72 Copynumber: 8.1 Consensus size: 71
20379 TCATCTCCTC
* * * * * * * *
20389 CACCTCCACCTCCT-AAGAAACCATACAAGTATAAATCTCCACCACCACCACCTCTAGTCTACAA
1 CACCTCCTCCTCCTAAAG-AGCCATACAAGTACAAGTCTCCTCCACCTCCACC-CCAGTTTACAA
* *
20453 ATACAAGT
64 GTACAAAT
* * * * *
20461 CCCCTCCACCACCTCCTAAGGAGCCATATAAGTACAAGTCTCCTCCTCCTCCAACCCCAGTTTAC
1 CACCT---CCTCCTCCTAAAGAGCCATACAAGTACAAGTCTCCTCCACCTCC-ACCCCAGTTTAC
20526 AAGTACAAAT
62 AAGTACAAAT
*
20536 CACCTCCTCCTCCTAAAGAGCCATACAAGTACAAGTCTCCTCCACCTCCACCTCCAGTTTATAAG
1 CACCTCCTCCTCCTAAAGAGCCATACAAGTACAAGTCTCCTCCACCTCCACC-CCAGTTTACAAG
*
20601 TATAAATCT
65 TACAAA--T
* *** *** * * *
20610 CCACCACCACCAGTGCATTCTCCCCCACCTCCATACAAGTACAAGTCTCCCCCACCACCACCCCC
1 ----CACCTCC--T-C---CTCCTAAAGAGCCATACAAGTACAAGTCTCCTCCACCTCCACCCCA
*
20675 GTTTACAAGTACAAGT
56 GTTTACAAGTACAAAT
* * * *
20691 CCCCTCCCCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCT---CCT-C-CCCCACTCTACAA
1 CACCT--CCTCCTCCTAAAGAGCCATACAAGTACAAGTCTCCTCCACCTCCACCCCAGTTTACAA
* *
20751 GTATAAGT
64 GTACAAAT
* * * * * *
20759 CACCACCACCACC---A-A--C--AC-ATTACAAGT-ACCACCACCT-----CCAGTTTACAAGT
1 CACCTCCTCCTCCTAAAGAGCCATACAAGTACAAGTCTCCTCCACCTCCACCCCAGTTTACAAGT
*
20809 ACAAGT
66 ACAAAT
* * *
20815 CTCCTCCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCC-CCACCACC-CCTCCAGTTTACAAG
1 CACCTCCTCCTCCTAAAGAGCCATACAAGTACAAGTCTCCTCCACCTCCACC-CCAGTTTACAAG
*
20878 TACAAGTCTCCT
65 TACAA-----AT
* * * * * *
20890 CCTCCTCCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCCCCACCACCCCCTCCAGTCTACAA
1 -CACCTCCTCCTCCTAAAGAGCCATACAAGTACAAGTCTCCTCCACCTCCACC-CCAGTTTACAA
*
20955 GTACAAGT
64 GTACAAAT
*
20963 CTCCTCC
1 CACCTCC
20970 ACCACCACCA
Statistics
Matches: 393, Mismatches: 70, Indels: 92
0.71 0.13 0.17
Matches are distributed among these distances:
56 27 0.07
57 8 0.02
58 2 0.01
59 3 0.01
60 2 0.01
62 2 0.01
64 2 0.01
65 13 0.03
66 8 0.02
68 20 0.05
69 1 0.00
70 19 0.05
71 3 0.01
72 67 0.17
73 25 0.06
74 1 0.00
75 53 0.13
76 46 0.12
77 12 0.03
78 25 0.06
79 2 0.01
80 1 0.00
81 2 0.01
83 14 0.04
84 35 0.09
ACGTcount: A:0.29, C:0.41, G:0.09, T:0.21
Consensus pattern (71 bp):
CACCTCCTCCTCCTAAAGAGCCATACAAGTACAAGTCTCCTCCACCTCCACCCCAGTTTACAAGT
ACAAAT
Found at i:20926 original size:76 final size:77
Alignment explanation
Indices: 20786--20969 Score: 292
Period size: 76 Copynumber: 2.5 Consensus size: 77
20776 CATTACAAGT
20786 ACCACCACCTCCAGTTTACAAGTACAAG-----T-CTCCTCCTCCTCCTAAGGAGCCATACAAGT
1 ACCACC-CCTCCAGTTTACAAGTACAAGTCTCCTCCTCCTCCTCCTCCTAAGGAGCCATACAAGT
20845 ACAAGTCT-CCCC
65 ACAAGTCTCCCCC
20857 ACCACCCCTCCAGTTTACAAGTACAAGTCTCCTCCTCCTCCTCCTCCTAAGGAGCCATACAAGTA
1 ACCACCCCTCCAGTTTACAAGTACAAGTCTCCTCCTCCTCCTCCTCCTAAGGAGCCATACAAGTA
20922 CAAGTCTCCCCC
66 CAAGTCTCCCCC
*
20934 ACCACCCCCTCCAGTCTACAAGTACAAGTCTCCTCC
1 ACCA-CCCCTCCAGTTTACAAGTACAAGTCTCCTCC
20970 ACCACCACCA
Statistics
Matches: 104, Mismatches: 1, Indels: 9
0.91 0.01 0.08
Matches are distributed among these distances:
70 21 0.20
71 6 0.06
75 1 0.01
76 38 0.37
77 8 0.08
78 30 0.29
ACGTcount: A:0.26, C:0.42, G:0.10, T:0.21
Consensus pattern (77 bp):
ACCACCCCTCCAGTTTACAAGTACAAGTCTCCTCCTCCTCCTCCTCCTAAGGAGCCATACAAGTA
CAAGTCTCCCCC
Found at i:20945 original size:42 final size:36
Alignment explanation
Indices: 20833--20975 Score: 146
Period size: 36 Copynumber: 3.8 Consensus size: 36
20823 CCTCCTAAGG
20833 AGCCATACAAGTACAAGTCTCC-CCACCA-CCCCTCC
1 AGCC-TACAAGTACAAGTCTCCTCCACCACCCCCTCC
** * * *
20868 AGTTTACAAGTACAAGTCTCCTCCTCCTCCTCCTCC
1 AGCCTACAAGTACAAGTCTCCTCCACCACCCCCTCC
*
20904 TAAGGAGCCATACAAGTACAAGTCTCCCCCACCACCCCCTCC
1 -----AGCC-TACAAGTACAAGTCTCCTCCACCACCCCCTCC
*
20946 AGTCTACAAGTACAAGTCTCCTCCACCACC
1 AGCCTACAAGTACAAGTCTCCTCCACCACC
20976 ACCACCTCAC
Statistics
Matches: 87, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
34 17 0.20
35 6 0.07
36 31 0.36
37 3 0.03
41 2 0.02
42 28 0.32
ACGTcount: A:0.27, C:0.44, G:0.10, T:0.20
Consensus pattern (36 bp):
AGCCTACAAGTACAAGTCTCCTCCACCACCCCCTCC
Found at i:20993 original size:42 final size:36
Alignment explanation
Indices: 20786--20978 Score: 142
Period size: 36 Copynumber: 5.2 Consensus size: 36
20776 CATTACAAGT
* *
20786 ACCACCACCTCCAGTTTACAAGTACAAGTCTCCTCC
1 ACCACCACCTCCAGTCTACAAGTACAAGTCTCCCCC
* * *** *
20822 TCCTCCTA--AGGAGCCATACAAGTACAAGTCT-CCCC
1 ACCACC-ACCTCCAGTC-TACAAGTACAAGTCTCCCCC
* *
20857 ACCACC-CCTCCAGTTTACAAGTACAAGTCTCCTCC
1 ACCACCACCTCCAGTCTACAAGTACAAGTCTCCCCC
* * * *
20892 TCCTCCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCCCC
1 ACCACCACCTCC-----AGTC-TACAAGTACAAGTCTCCCCC
* *
20934 ACCACCCCCTCCAGTCTACAAGTACAAGTCTCCTCC
1 ACCACCACCTCCAGTCTACAAGTACAAGTCTCCCCC
20970 ACCACCACC
1 ACCACCACC
20979 ACCTCACTAT
Statistics
Matches: 118, Mismatches: 27, Indels: 24
0.70 0.16 0.14
Matches are distributed among these distances:
34 15 0.13
35 18 0.15
36 51 0.43
37 4 0.03
41 2 0.02
42 28 0.24
ACGTcount: A:0.26, C:0.44, G:0.10, T:0.20
Consensus pattern (36 bp):
ACCACCACCTCCAGTCTACAAGTACAAGTCTCCCCC
Found at i:23436 original size:21 final size:22
Alignment explanation
Indices: 23400--23444 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 22
23390 ATATTGTCAT
23400 TCAATTCATTTTTTTTAACTAAA
1 TCAATTCA-TTTTTTTAACTAAA
23423 TCAATTCA-TTTTTTAACTAAA
1 TCAATTCATTTTTTTAACTAAA
23444 T
1 T
23445 TATTGTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 14 0.64
23 8 0.36
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (22 bp):
TCAATTCATTTTTTTAACTAAA
Found at i:23499 original size:19 final size:20
Alignment explanation
Indices: 23467--23508 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
23457 TTAGGTCGGT
*
23467 TTAGTTTTTGGCACACTTAA
1 TTAGTTTTTAGCACACTTAA
23487 TTAG-TTTTAGCACACTTAA
1 TTAGTTTTTAGCACACTTAA
23506 TTA
1 TTA
23509 TTGCTTGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (20 bp):
TTAGTTTTTAGCACACTTAA
Found at i:24117 original size:19 final size:19
Alignment explanation
Indices: 24095--24133 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
24085 GTTTTCTTTG
24095 TAATTTATTTGTTTGTGTA
1 TAATTTATTTGTTTGTGTA
24114 TAATTTATTTGTTTGTGTA
1 TAATTTATTTGTTTGTGTA
24133 T
1 T
24134 TTAGTATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (19 bp):
TAATTTATTTGTTTGTGTA
Found at i:27655 original size:24 final size:24
Alignment explanation
Indices: 27620--27666 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27610 GCTACAAAAC
*
27620 AGCAAAATAGAACATAA-TTATAAT
1 AGCAAAAGAGAACA-AACTTATAAT
27644 AGCAAAAGAGAACAAACTTATAA
1 AGCAAAAGAGAACAAACTTATAA
27667 CATAACATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.19
Consensus pattern (24 bp):
AGCAAAAGAGAACAAACTTATAAT
Found at i:27909 original size:45 final size:45
Alignment explanation
Indices: 27845--27936 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
27835 CATGTTGCAA
* * *
27845 GAAAGTTATTCGAATGTAACTTTTACAAACAGAAAGTTAAATGGT
1 GAAAGTTATTCAAATGTAACTTTTACAAACAAAAAGTTAAAGGGT
27890 GAAAGTTATTCAAATGTAACTTTTACAAACAAAAAGTTAAAGGGT
1 GAAAGTTATTCAAATGTAACTTTTACAAACAAAAAGTTAAAGGGT
27935 GA
1 GA
27937 TCAATCATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (45 bp):
GAAAGTTATTCAAATGTAACTTTTACAAACAAAAAGTTAAAGGGT
Found at i:29047 original size:17 final size:17
Alignment explanation
Indices: 29018--29050 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29008 ATTTAGGTTA
29018 AAATTTTAGTATATATC
1 AAATTTTAGTATATATC
29035 AAATATTTA-TATATAT
1 AAAT-TTTAGTATATAT
29051 ATATATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (17 bp):
AAATTTTAGTATATATC
Found at i:31000 original size:15 final size:15
Alignment explanation
Indices: 30977--31027 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
30967 CCAAAAATGA
30977 AAAAACTCAAACCCG
1 AAAAACTCAAACCCG
* *
30992 AAAATCTCAAACCTG
1 AAAAACTCAAACCCG
* *
31007 AAAAAACCCAAACCCC
1 -AAAAACTCAAACCCG
31023 AAAAA
1 AAAAA
31028 AGCCGAACTC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.57, C:0.31, G:0.04, T:0.08
Consensus pattern (15 bp):
AAAAACTCAAACCCG
Found at i:39059 original size:21 final size:21
Alignment explanation
Indices: 39033--39082 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
39023 GAAGAGGAAA
** *
39033 AAGAAGAAAGTGAGGACGAGG
1 AAGAAGAAAGTGAAAAAGAGG
*
39054 AAGAAGGAAGTGAAAAAGAGG
1 AAGAAGAAAGTGAAAAAGAGG
39075 AAGAAGAA
1 AAGAAGAA
39083 GGACCTGCTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.38, T:0.04
Consensus pattern (21 bp):
AAGAAGAAAGTGAAAAAGAGG
Found at i:43731 original size:27 final size:26
Alignment explanation
Indices: 43651--43743 Score: 98
Period size: 27 Copynumber: 3.5 Consensus size: 26
43641 CCTTCAATTT
* * *
43651 ATTTTGTTCATTTTCGGCACCAGAGGC
1 ATTTTGGTCATTTTC-ACACCAGGGGC
* * *
43678 ATTTCGGTCAGTTGCAC-CCAGGGGC
1 ATTTTGGTCATTTTCACACCAGGGGC
43703 ATTTTGGTCATTTTCACATCCAGGGGC
1 ATTTTGGTCATTTTCACA-CCAGGGGC
*
43730 ATTTAGGTCATTTT
1 ATTTTGGTCATTTT
43744 GGCATTTAGG
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
25 21 0.39
26 1 0.02
27 32 0.59
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.37
Consensus pattern (26 bp):
ATTTTGGTCATTTTCACACCAGGGGC
Found at i:43755 original size:27 final size:27
Alignment explanation
Indices: 43670--43743 Score: 89
Period size: 25 Copynumber: 2.8 Consensus size: 27
43660 ATTTTCGGCA
* * * *
43670 CCAGAGGCATTTCGGTCAGTTGCAC--
1 CCAGGGGCATTTAGGTCATTTTCACAT
*
43695 CCAGGGGCATTTTGGTCATTTTCACAT
1 CCAGGGGCATTTAGGTCATTTTCACAT
43722 CCAGGGGCATTTAGGTCATTTT
1 CCAGGGGCATTTAGGTCATTTT
43744 GGCATTTAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
25 21 0.50
27 21 0.50
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (27 bp):
CCAGGGGCATTTAGGTCATTTTCACAT
Found at i:47797 original size:55 final size:55
Alignment explanation
Indices: 47737--48475 Score: 1077
Period size: 55 Copynumber: 13.6 Consensus size: 55
47727 AAAAAGGGAC
* * * *
47737 AATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGTC
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
*
47792 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATTAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
* * * * *
47847 AATCAATAATTAATTGAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
*
47902 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTGATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
*
47957 AATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
*
48012 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTC
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
* * * * *
48067 AATCAGTAATTAAGTAAAAAGAGATTAATAAGAGTTAAGGTAATAATAATCAGTC
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
*
48122 AATCAGTAATTAAGTAAAAAGAGATTAATCAGGGTCAAAGTAATAGTAATCAGTAA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT-A
* *
48178 AATCAGTAATTAAGTAAAAAGAGGTTAATTAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
*
48233 AATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT-A
* *
48289 AATCAGTAATTAAGTAAAAAGAGGTTAATTAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
* ** *
48344 AATCAGTAAATT--G-----ATA-ATT-A--AGAACCAATGTAATAGTAATCAGTA
1 AATCAGT-AATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
*
48389 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
* * * *
48444 AATCAGTAATCAGGTAAAAAGATAGTAATCAG
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAG
48476 TAAATTGAGT
Statistics
Matches: 617, Mismatches: 53, Indels: 28
0.88 0.08 0.04
Matches are distributed among these distances:
44 4 0.01
45 29 0.05
46 1 0.00
47 1 0.00
48 2 0.00
49 2 0.00
51 2 0.00
52 3 0.00
53 1 0.00
54 1 0.00
55 464 0.75
56 107 0.17
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.26
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
Found at i:47997 original size:26 final size:25
Alignment explanation
Indices: 47913--48054 Score: 74
Period size: 26 Copynumber: 5.2 Consensus size: 25
47903 ATCAGTAATT
47913 AAGTAAAAAGAGATTAATCAGAGTCA
1 AAGT-AAAAGAGATTAATCAGAGTCA
* * * *
47939 AAGTAATAGTGATCAGTAAATCAGTAAT-T
1 AAGTAAAAGAGAT---T-AATCAG-AGTCA
47968 AAGTGAAAAGAGATTAATCAGAGTCA
1 AAGT-AAAAGAGATTAATCAGAGTCA
* * *
47994 AAGTAATAGTA-ATCAGTAAATCAGTAAT-T
1 AAGTAAAAG-AGAT---T-AATCAG-AGTCA
48023 AAGTAAAAAGAGATTAATCAGAGTCA
1 AAGT-AAAAGAGATTAATCAGAGTCA
48049 AAGTAA
1 AAGTAA
48055 TAGTAATCAG
Statistics
Matches: 86, Mismatches: 14, Indels: 33
0.65 0.11 0.25
Matches are distributed among these distances:
25 19 0.22
26 25 0.29
27 2 0.02
28 2 0.02
29 21 0.24
30 17 0.20
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.24
Consensus pattern (25 bp):
AAGTAAAAGAGATTAATCAGAGTCA
Found at i:48488 original size:16 final size:15
Alignment explanation
Indices: 48433--48494 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 15
48423 TCAAGGTAAT
*
48433 AGTAATCAGTAAATC
1 AGTAATCAGTAAATG
*
48448 AGTAATCAGGTAAAAAG
1 AGTAATCA-GT-AAATG
48465 ATAGTAATCAGTAAATTG
1 --AGTAATCAGTAAA-TG
48483 AGTAATCAGTAA
1 AGTAATCAGTAA
48495 TTAAAGAGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 8 0.21
16 14 0.36
17 6 0.15
18 3 0.08
19 8 0.21
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (15 bp):
AGTAATCAGTAAATG
Found at i:49776 original size:7 final size:7
Alignment explanation
Indices: 49764--49796 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
49754 TTGATGAAAA
49764 ATGCTTT
1 ATGCTTT
49771 ATGCTTT
1 ATGCTTT
49778 ATGCTTT
1 ATGCTTT
*
49785 ATGCTTA
1 ATGCTTT
49792 ATGCT
1 ATGCT
49797 AAACTGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (7 bp):
ATGCTTT
Found at i:52027 original size:20 final size:20
Alignment explanation
Indices: 51988--52027 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
51978 TGTTTTTATA
* *
51988 GCTATTTTTATATATTTTTT
1 GCTACTTTTATATATGTTTT
*
52008 GCTACTTTTATATGTGTTTT
1 GCTACTTTTATATATGTTTT
52028 TACCCTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.65
Consensus pattern (20 bp):
GCTACTTTTATATATGTTTT
Found at i:52201 original size:11 final size:10
Alignment explanation
Indices: 52183--52216 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
52173 GAAGTTCGTG
52183 TTTTGAAGAT
1 TTTTGAAGAT
52193 TTCTTGAAGAT
1 TT-TTGAAGAT
52204 ATTTTGAAGAT
1 -TTTTGAAGAT
52215 TT
1 TT
52217 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:59796 original size:26 final size:26
Alignment explanation
Indices: 59760--59811 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
59750 GATGTTCTCA
59760 TGTTTTGTGTTTGGTTGAGAGGAGGG
1 TGTTTTGTGTTTGGTTGAGAGGAGGG
59786 TGTTTTGTGTTTGGTTGAGAGGAGGG
1 TGTTTTGTGTTTGGTTGAGAGGAGGG
59812 GTTAGGAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.46, T:0.42
Consensus pattern (26 bp):
TGTTTTGTGTTTGGTTGAGAGGAGGG
Found at i:60522 original size:2 final size:2
Alignment explanation
Indices: 60515--60562 Score: 50
Period size: 2 Copynumber: 25.5 Consensus size: 2
60505 ACCGACCGAT
*
60515 TA TA TA TA TA TA TA TA TA TA T- TA T- TGA -A TA TA TT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
60554 TA TA TA TA T
1 TA TA TA TA T
60563 TATTAAGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
1 4 0.10
2 35 0.90
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:62667 original size:434 final size:433
Alignment explanation
Indices: 61943--62840 Score: 1139
Period size: 434 Copynumber: 2.1 Consensus size: 433
61933 GCTTTAGGGT
* * *
61943 TTTTTTTTCCTATTTG-CCTGATTAAGGTGATTCAGGTGTCTATTAAAAGGTAATTTTATAATTT
1 TTTTTTTT-CTATTTGTCC-GATTAAGGTGATTCAGGTGTCGATTAAAAGGTAATTTCATAATCT
* * **
62007 ACAACTTTCATGAAAAGACTTAAAAGCCAATTTTATGTTTCAATTAAAAAAATACTTCTGAAATT
64 ACAACTTTAATGAAAAGACTCAAAAGCCAATTTTACATTTCAATTAAAAAAATACTTC-GAAATT
* * ** * *
62072 TGATGATTTTGATTGCCGATCTATTTAATATCATATTATTTTCTATCGACATGTCCGATTAATGT
128 TGATGATTTTGATTGCCGATCTATTTAATACCATATAATTTTAGATCCACATGTCCGATTAAAGT
* *
62137 TTCTCAAGTGTCGGTTAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCCAAAAGCTAA
193 TTCTCAAGTATCGGTTAAAAGGTTATTACATGATCTACGACTTTCATGAAGGACCCAAAAGCTAA
* * *
62202 ATTTGATCTACGAGTTTCATTAAGTGTTCAAAAGAGAATTTTTATGTTCT-AAGATCTCCATCAA
258 ATTTGATCTACAAGTTTCATGAAGGGTTCAAAAGAGAATTTTTATGTT-TGAAGATCTCCATCAA
* * *
62266 GAAACATTTTTTTTATTTTG-ATTATTTATGAAATGACCCTC-ATAT-TTTTCTACTTTATACTA
322 GAAACA-TTTTATTA-TTTGAATTATTTATCAAATGACCCACAATATATTTTCTACTTTATACTA
* * *
62328 CTTAGTCCTTTACTAATTCTATCTTAATCGATTTAACGTTTAAATTTTA
385 CTTAATCCTTTACAAATTCTATCTTAATCGATTTAACGCTTAAATTTTA
* *
62377 TTTTTTTTCTATTTGTCCGATTAAGGTGATTCAGGTGTCGATTAAAAGGTAATTTCATGATCTCC
1 TTTTTTTTCTATTTGTCCGATTAAGGTGATTCAGGTGTCGATTAAAAGGTAATTTCATAATCTAC
*
62442 AACTTTAATGAAAA-ACTCAAAAGCCAATTTTAACATTTCAATTTGAAGAAAAATGCTTC-AAAT
66 AACTTTAATGAAAAGACTCAAAAGCCAATTTT-ACATTTCAA-TT-AA-AAAAATACTTCGAAAT
* **
62505 TT-AGTGATTTTGATTGCCGGTCTATTTAATACCATATAATTTTAGATCCACATGTTTGATTAAA
127 TTGA-TGATTTTGATTGCCGATCTATTTAATACCATATAATTTTAGATCCACATGTCCGATTAAA
* * * * * *
62569 GTTAT-TTAAGTATCGGTTAAAAGGTTATTACGTGATCTACGACTTTCATGAAGTACTCGAAAGT
191 GTT-TCTCAAGTATCGGTTAAAAGGTTATTACATGATCTACGACTTTCATGAAGGACCCAAAAGC
* * * * *
62633 TAAATTTGATTTGCAAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTGAAGGTCTCTATC
255 TAAATTTGATCTACAAGTTTCATGAAGGGTTCAAAAGAGAATTTTTATGTTTGAAGATCTCCATC
*
62698 AAGCAACATTTTATTATTTGAATTATTTATCAAATGACCCACATATATACTTTTCTACTTTATAC
320 AAGAAACATTTTATTATTTGAATTATTTATCAAATGACCCACA-ATATA-TTTTCTACTTTATAC
* * * * * *
62763 TATTTAATTCTTTACAAATTCTATTTTACTCGATTTAACGCTTCAATTTTT
383 TACTTAATCCTTTACAAATTCTATCTTAATCGATTTAACGCTTAAATTTTA
* *
62814 TTTCTTTGTTCTATTTATCCAATTAAG
1 TTT-TTT-TTCTATTTGTCCGATTAAG
62841 ATAATTCATG
Statistics
Matches: 399, Mismatches: 50, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
432 20 0.05
433 97 0.24
434 185 0.46
435 7 0.02
436 10 0.03
437 60 0.15
438 3 0.01
439 17 0.04
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (433 bp):
TTTTTTTTCTATTTGTCCGATTAAGGTGATTCAGGTGTCGATTAAAAGGTAATTTCATAATCTAC
AACTTTAATGAAAAGACTCAAAAGCCAATTTTACATTTCAATTAAAAAAATACTTCGAAATTTGA
TGATTTTGATTGCCGATCTATTTAATACCATATAATTTTAGATCCACATGTCCGATTAAAGTTTC
TCAAGTATCGGTTAAAAGGTTATTACATGATCTACGACTTTCATGAAGGACCCAAAAGCTAAATT
TGATCTACAAGTTTCATGAAGGGTTCAAAAGAGAATTTTTATGTTTGAAGATCTCCATCAAGAAA
CATTTTATTATTTGAATTATTTATCAAATGACCCACAATATATTTTCTACTTTATACTACTTAAT
CCTTTACAAATTCTATCTTAATCGATTTAACGCTTAAATTTTA
Done.