Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021171.1 Corchorus olitorius cultivar O-4 contig21204, 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: 72291
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:2109 original size:61 final size:60
Alignment explanation
Indices: 2003--2225 Score: 268
Period size: 61 Copynumber: 3.6 Consensus size: 60
1993 AATATCATTC
* * * * *
2003 AGGAACTGTCTTCAGAACCCATTTTCGTGAAATGCCTTCAGATTCACTCTCAAATACCTTTT
1 AGGAAATGTCTTCA-AATCCA-TTTCGTGAACTGTCTTCATATTCACTCTCAAATACCTTTT
* *
2065 AGGAAATGTCTTCATATCCATTTCGGTGAACTGTCTTCATATTCACTCTCAAATTCGC-TTT
1 AGGAAATGTCTTCAAATCCATTTC-GTGAACTGTCTTCATATTCACTCTCAAATAC-CTTTT
* * * * *
2126 AGGAAATGTCTACAGATCCATCTCCGTGAACTGTCTTCATTTTCACTCTTAAATACCTTTT
1 AGGAAATGTCTTCAAATCCAT-TTCGTGAACTGTCTTCATATTCACTCTCAAATACCTTTT
*
2187 AGGAAATGTCTTCAAATCCATCTTTGTGAACTGTCTTCA
1 AGGAAATGTCTTCAAATCCAT-TTCGTGAACTGTCTTCA
2226 GATCCATATT
Statistics
Matches: 140, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
60 5 0.04
61 119 0.85
62 16 0.11
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (60 bp):
AGGAAATGTCTTCAAATCCATTTCGTGAACTGTCTTCATATTCACTCTCAAATACCTTTT
Found at i:2221 original size:25 final size:25
Alignment explanation
Indices: 2193--2250 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
2183 TTTTAGGAAA
* *
2193 TGTCTTCAAATCCATCTTTGTGAAC
1 TGTCTTCAAATCCATATTCGTGAAC
*
2218 TGTCTTCAGATCCATATTCGTGAAC
1 TGTCTTCAAATCCATATTCGTGAAC
*
2243 CGTCTTCA
1 TGTCTTCA
2251 TATTCACTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (25 bp):
TGTCTTCAAATCCATATTCGTGAAC
Found at i:22976 original size:13 final size:13
Alignment explanation
Indices: 22958--22982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22948 TACTTGAGAA
22958 GTTTTTTTTTTTG
1 GTTTTTTTTTTTG
22971 GTTTTTTTTTTT
1 GTTTTTTTTTTT
22983 TCTGTTTCTT
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
GTTTTTTTTTTTG
Found at i:30742 original size:68 final size:68
Alignment explanation
Indices: 30634--31083 Score: 313
Period size: 68 Copynumber: 6.7 Consensus size: 68
30624 AAGTAAAGTT
* * *
30634 TTATTTTCTCTTTCC-AGAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAG
1 TTATTTT-TCTTTCCAAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCATTTTGCATTTAAG
30697 TTTA
65 TTTA
* * * * *
30701 TTATTTTCTCTTTTCAAAAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCATTCAAG
1 TTATTTT-TCTTTCCAAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCATTTTGCATTTAAG
30766 TTTA
65 TTTA
* * * * * ** * * *
30770 GTA-TTTTCGTTCCCAGAGATACCCTTTCGGTTGAAGGGTCAGTTTCGTCTTTTTGTA-TTCAG-
1 TTATTTTTCTTTCCAAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCATTTTGCATTTAAGT
30832 TT-
66 TTA
** * * * *
30834 TTAGTTTTGATTTCC-AAAAGTACCCTTTCGGTGAAAAGGTCAGTTTCATCAGGTTGTTGCATTT
1 TTA-TTTTTCTTTCCAAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCA--TT-TTGCATTT
*
30898 AAGTCTA
62 AAGTTTA
* * * * *
30905 GTA--TTTCTTTCCAAAGAATACCCTTTCGGTCAAGGGGTCA-ATTCTGTCATTCTTGCACTTAA
1 TTATTTTTCTTTCCAAAAAATACCCTTTCGGTCAAAGGGTCAGTTTC-GTCATT-TTGCATTTAA
30967 GTTTA
64 GTTTA
* ** * * * *
30972 --CTTTTGATTTCCAAAAAAATACCCTTCCGGTCAAAGGGTCAGTTTCAT-ATTTTTCACATCTA
1 TTATTTTTCTTTCC-AAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCA-TTTT-GCATTTA
*
31034 AGTTCA
63 AGTTTA
* *
31040 --ATTTTGT-TTTCC-AAAAATACCCTTTCGGTCGAAGGATCAGTTTC
1 TTATTTT-TCTTTCCAAAAAATACCCTTTCGGTCAAAGGGTCAGTTTC
31084 ATATTTTTCA
Statistics
Matches: 299, Mismatches: 65, Indels: 39
0.74 0.16 0.10
Matches are distributed among these distances:
64 2 0.01
65 30 0.10
66 39 0.13
67 82 0.27
68 93 0.31
69 50 0.17
70 1 0.00
71 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (68 bp):
TTATTTTTCTTTCCAAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCATTTTGCATTTAAGT
TTA
Found at i:30894 original size:135 final size:130
Alignment explanation
Indices: 30642--31019 Score: 350
Period size: 135 Copynumber: 2.8 Consensus size: 130
30632 TTTTATTTTC
* * * * *
30642 TCTTTCCAGAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTATTATT
1 TCTTCCCAGAGATACCCTTTCGGTTGAAGGGTCA-TTTCGTCTTTTTGCACTTAAG-TT-TTACT
** * * ** * *
30706 TTCTCTTTTCAAAAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCATTCAAGTTTAG
63 TT-TGATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATCTTGTTGCATTCAAGTCTAG
30771 TATTT
127 TA-TT
* * *
30776 TCGTTCCCAGAGATACCCTTTCGGTTGAAGGGTCAGTTTCGTCTTTTTGTA-TTCAGTTTTAGTT
1 TC-TTCCCAGAGATACCCTTTCGGTTGAAGGGTCA-TTTCGTCTTTTTGCACTTAAGTTTTACTT
* * * *
30840 TTGATTTCCAAAAGTACCCTTTCGGTGAAAAGGTCAGTTTCATCAGGTTGTTGCATTTAAGTCTA
64 TTGATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATC---TTGTTGCATTCAAGTCTA
30905 GTATT
126 GTATT
* * * * *
30910 TCTTTCCAAAGAATACCCTTTCGG-TCAAGGGGTCAATTCTGTCATTCTTGCACTTAAG-TTTAC
1 TCTTCCCAGAG-ATACCCTTTCGGTTGAA-GGGTCATTTC-GTC-TTTTTGCACTTAAGTTTTAC
*
30973 TTTTGATTTCCAAAAAAATACCCTTCCGGTCAAAGGGTCAGTTTCAT
62 TTTTGATTTCC--AAAAATACCCTTTCGGTCAAAGGGTCAGTTTCAT
31020 ATTTTTCACA
Statistics
Matches: 201, Mismatches: 31, Indels: 21
0.79 0.12 0.08
Matches are distributed among these distances:
132 34 0.17
133 19 0.09
134 29 0.14
135 79 0.39
136 10 0.05
137 30 0.15
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.41
Consensus pattern (130 bp):
TCTTCCCAGAGATACCCTTTCGGTTGAAGGGTCATTTCGTCTTTTTGCACTTAAGTTTTACTTTT
GATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATCTTGTTGCATTCAAGTCTAGTATT
Found at i:31036 original size:135 final size:130
Alignment explanation
Indices: 30642--31074 Score: 348
Period size: 135 Copynumber: 3.2 Consensus size: 130
30632 TTTTATTTTC
* *
30642 TCTTTCCAGA-AATACCCTTTCGGTCGAA-GGGTCATTTTCGTCTT-TTGCATTTAAGTTTATTA
1 TCTTTCCAAAGAATACCCTTTCGGTC-AAGGGGTCAATTTCGTCTTCTTGCA-TTAAG-TT-TTA
** * * ** *
30704 -TTTTCTCTTTTCAAAAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCATTCAAGTT
62 CTTTT-GATTTCCAAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTGCATT-AAG-T
30768 TAGTATTT
124 TAGTA-TT
* * * * * * * *
30776 TCGTTCC-CAGAGATACCCTTTCGGTTGAA-GGGTCAGTTTCGTCTTTTTGTATTCAGTTTTAGT
1 TCTTTCCAAAGA-ATACCCTTTCGG-TCAAGGGGTCAATTTCGTCTTCTTGCATTAAGTTTTACT
* * * *
30839 TTTGATTTCC-AAAAGTACCCTTTCGGTGAAAAGGTCAGTTTCATCAGGTTGTTGCATTTAAGTC
64 TTTGATTTCCAAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCAT-A--TTTTTGCA-TTAAGT-
30903 TAGTATT
124 TAGTATT
30910 TCTTTCCAAAGAATACCCTTTCGGTCAAGGGGTCAA-TTCTGTCATTCTTGCACTTAAG-TTTAC
1 TCTTTCCAAAGAATACCCTTTCGGTCAAGGGGTCAATTTC-GTC-TTCTTGCA-TTAAGTTTTAC
* *
30973 TTTTGATTTCCAAAAAAATACCCTTCCGGTCAAAGGGTCAGTTTCATATTTTTCACATCTAAGTT
63 TTTTGATTTCC-AAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTT-GCAT-TAAGTT
*
31038 CAAT-TT
125 -AGTATT
*
31044 TGTTTTCCAAA-AATACCCTTTCGGTCGAAGG
1 T-CTTTCCAAAGAATACCCTTTCGGTC-AAGG
31075 ATCAGTTTCA
Statistics
Matches: 244, Mismatches: 33, Indels: 43
0.76 0.10 0.13
Matches are distributed among these distances:
132 28 0.11
133 14 0.06
134 67 0.27
135 93 0.38
136 12 0.05
137 30 0.12
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (130 bp):
TCTTTCCAAAGAATACCCTTTCGGTCAAGGGGTCAATTTCGTCTTCTTGCATTAAGTTTTACTTT
TGATTTCCAAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTGCATTAAGTTAGTATT
Found at i:31069 original size:66 final size:66
Alignment explanation
Indices: 30644--31427 Score: 460
Period size: 66 Copynumber: 11.8 Consensus size: 66
30634 TTATTTTCTC
* * * * * * * *
30644 TTTCCAGAAATACCCTTTCGGTCGAAGGGTCATTTTCGT-CTTTT-GCATTTAAGTTTATTATTT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTCACATCTAAG--T-TTAGTT
*
30707 TCTCT
63 T-TGT
* * ** * *
30712 TTTCAAAAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTT-GCAT-TCAAGTTTAGTATT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTCACATCT-AAGTTTAGT-TT
30775 T-T
64 TGT
* * * ** * * ** *
30777 CGTTCCCAGAGATACCCTTTCGGTTGAAGGGTCAGTTTCGTCTTTTT-GTAT-TCAGTTTTAGTT
1 --TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTCACATCTAAG-TTTAGTT
*
30840 TTGA
63 TTGT
* * * * * * *
30844 TTTCCAAAAGTACCCTTTCGGTGAAAAGGTCAGTTTCATCAGGTTGTT-GCATTTAAGTCTAGTA
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCAT-A--TTTTTCACATCTAAGTTTAGT-
*
30908 TTT-C
62 TTTGT
* * * * *
30912 TTTCCAAAGAATACCCTTTCGGTCAAGGGGTCAATTCTGTCAT-TCTTGCAC-T-TAAGTTTACT
1 TTTCCAAA-AATACCCTTTCGGTCAAAGGGTC-AGT-T-TCATATTTTTCACATCTAAGTTTAGT
*
30974 TTTGA
62 TTTGT
* * *
30979 TTTCCAAAAAAATACCCTTCCGGTCAAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTT
1 TTTCC--AAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTCACATCTAAGTTTAGTTT
31044 TGT
64 TGT
* * *
31047 TTTCCAAAAATACCCTTTCGGTCGAAGGATCAGTTTCATATTTTTCACATCT-AGGTTAGGTTTT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTCACATCTAAGTTTA-GTTTT
31111 GT
65 GT
** ** *
31113 TTTCCCCAAATACCCTTTCGGTTGAAGGGTCAGTTTCATATTTTTCACATCT-AGGTTAGGTTTT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTCACATCTAAGTTTA-GTTTT
31177 GT
65 GT
* * * * * *
31179 TTTCCCAAAATTCCATTTTGGTCGAAGGGTCAGTTTCATATTTTTCACATCT-AGGTTAGGTTTT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTCACATCTAAGTTTA-GTTTT
31243 GT
65 GT
* * * * ** *
31245 TCTCCTAATATACCCTTTCGGTCGAAA-GGTCAGTTTCGT-TTTTTTGCATCTAAGTTTAGCTTT
1 TTTCCAAAAATACCCTTTCGGTC-AAAGGGTCAGTTTCATATTTTTCACATCTAAGTTTAGTTTT
31308 GT
65 GT
* * * * * * * * * * *
31310 CTTCCAAAAATGATCC-TTCAGTGAAAGGTTCAGTTTCTTCA-TTTTCGCATTTGAGTTTACTTA
1 TTTCCAAAAAT-ACCCTTTCGGTCAAAGGGTCAGTTTCAT-ATTTTTCACATCTAAGTTTAGTTT
***
31373 CAA
64 TGT
* * *
31376 TTTCCAAAAATGCCCTTTCGGTCAAAGGGTC--TGTCATA-TTTTCACATTTAAG
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTCACATCTAAG
31428 GGAATAAAAG
Statistics
Matches: 577, Mismatches: 108, Indels: 67
0.77 0.14 0.09
Matches are distributed among these distances:
63 13 0.02
64 7 0.01
65 80 0.14
66 267 0.46
67 68 0.12
68 95 0.16
69 40 0.07
70 2 0.00
71 1 0.00
72 4 0.01
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.42
Consensus pattern (66 bp):
TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATATTTTTCACATCTAAGTTTAGTTTTG
T
Found at i:42050 original size:6 final size:6
Alignment explanation
Indices: 42039--42079 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
42029 AGTGCAAATC
*
42039 AAAAAG AAAAAG AAATAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
42080 TAATACACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:43060 original size:18 final size:19
Alignment explanation
Indices: 43037--43073 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
43027 CACCCTAGCC
43037 CTAAAACTAGAAGA-AAAA
1 CTAAAACTAGAAGAGAAAA
43055 CTAAAACTAGAAGAGAAAA
1 CTAAAACTAGAAGAGAAAA
43074 AGAAGAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.65, C:0.11, G:0.14, T:0.11
Consensus pattern (19 bp):
CTAAAACTAGAAGAGAAAA
Found at i:45035 original size:48 final size:48
Alignment explanation
Indices: 44980--45076 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
44970 CATTGTTTTT
44980 GGGCTCTCCATTTTTGTTTGGGCCTGAAAGAGAATTTTGAGATAACAA
1 GGGCTCTCCATTTTTGTTTGGGCCTGAAAGAGAATTTTGAGATAACAA
45028 GGGCTCTCCATTTTTGTTTGGGCCTGAAAGAGAATTTTGAGATAACAA
1 GGGCTCTCCATTTTTGTTTGGGCCTGAAAGAGAATTTTGAGATAACAA
45076 G
1 G
45077 ACCCAACGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (48 bp):
GGGCTCTCCATTTTTGTTTGGGCCTGAAAGAGAATTTTGAGATAACAA
Found at i:45361 original size:19 final size:19
Alignment explanation
Indices: 45337--45376 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
45327 ACTTTAAGCT
*
45337 TTAATTTGGATTAAGCCCA
1 TTAATTTGGATCAAGCCCA
45356 TTAATTTGGATCAAGCCCA
1 TTAATTTGGATCAAGCCCA
45375 TT
1 TT
45377 TCCTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (19 bp):
TTAATTTGGATCAAGCCCA
Found at i:48011 original size:41 final size:42
Alignment explanation
Indices: 47951--48247 Score: 241
Period size: 41 Copynumber: 7.0 Consensus size: 42
47941 CTTTGCCATA
* * *
47951 TAGAAATTGCCCTTGTGTTATAATTGTGTTT-AGGGACTTTAG
1 TAGAGATTGCCCCTGTGTTATAAATGTGTTTGA-GGACTTTAG
* * *
47993 TATAGA-TGGCTCTGTGTTATAAATGTGTTTGAGGACTTTTAG
1 TAGAGATTGCCCCTGTGTTATAAATGTGTTTGAGGAC-TTTAG
* *
48035 -AGAGGATTGCCCCTATGTTATAATTGTGTTTGAGGACTTT-G
1 TAGA-GATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG
* * * * *
48076 ATATAGA-TGTCTCTATGTTATAAATCTGTTTGAGGACTTTA-
1 -TAGAGATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG
** * *
48117 TAAAGAGAATTGCCCCTGTGTTGGAAATGTGCTTTG-GGGCTTTGG
1 T--AGAG-ATTGCCCCTGTGTTATAAATGTG-TTTGAGGACTTTAG
* * **
48162 TATAGA-TGTCTTTGTGTTATAAATGTGTTTGAGGACTTTAG
1 TAGAGATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG
* *
48203 AAAGAGAATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTAG
1 -TAGAG-ATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG
48247 T
1 T
48248 TATTTAGTAA
Statistics
Matches: 198, Mismatches: 40, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
40 5 0.03
41 79 0.40
42 24 0.12
43 33 0.17
44 52 0.26
45 5 0.03
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (42 bp):
TAGAGATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG
Found at i:48171 original size:85 final size:84
Alignment explanation
Indices: 47955--48244 Score: 393
Period size: 85 Copynumber: 3.4 Consensus size: 84
47945 GCCATATAGA
* * * *
47955 AATTGCCCTTGTGTTATAATTGTGTTTAGGGACTTTAGTATAGATGGCTCTGTGTTATAAATGTG
1 AATTGCCCCTGTGTTATAAATGTGTTT-GGGACTTTGGTATAGATGTCTCTGTGTTATAAATGTG
*
48020 TTTGAGGACTTT-TAGAGAG
65 TTTGAGGACTTTATAAAGAG
* * * * * *
48039 GATTGCCCCTATGTTATAATTGTGTTTGAGGACTTTGATATAGATGTCTCTATGTTATAAATCTG
1 AATTGCCCCTGTGTTATAAATGTGTTTG-GGACTTTGGTATAGATGTCTCTGTGTTATAAATGTG
48104 TTTGAGGACTTTATAAAGAG
65 TTTGAGGACTTTATAAAGAG
** * *
48124 AATTGCCCCTGTGTTGGAAATGTGCTTTGGGGCTTTGGTATAGATGTCTTTGTGTTATAAATGTG
1 AATTGCCCCTGTGTTATAAATGTG-TTTGGGACTTTGGTATAGATGTCTCTGTGTTATAAATGTG
*
48189 TTTGAGGACTTTAGAAAGAG
65 TTTGAGGACTTTATAAAGAG
48209 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTT
1 AATTGCCCCTGTGTTATAAATGTGTTT-GGGACTTT
48245 AGTTATTTAG
Statistics
Matches: 179, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
83 1 0.01
84 70 0.39
85 104 0.58
86 4 0.02
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.41
Consensus pattern (84 bp):
AATTGCCCCTGTGTTATAAATGTGTTTGGGACTTTGGTATAGATGTCTCTGTGTTATAAATGTGT
TTGAGGACTTTATAAAGAG
Found at i:55326 original size:21 final size:21
Alignment explanation
Indices: 55302--55352 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
55292 AGGTGATGGC
55302 GCCTCCTACCTCCCAGGAGAT
1 GCCTCCTACCTCCCAGGAGAT
*
55323 GCCTCCTACCTCCTAGGAGAT
1 GCCTCCTACCTCCCAGGAGAT
55344 GCCTCCTAC
1 GCCTCCTAC
55353 AAGTAGAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.43, G:0.18, T:0.22
Consensus pattern (21 bp):
GCCTCCTACCTCCCAGGAGAT
Found at i:55384 original size:21 final size:21
Alignment explanation
Indices: 55301--55386 Score: 70
Period size: 21 Copynumber: 4.1 Consensus size: 21
55291 AAGGTGATGG
*
55301 CGCCTCCTACCTCCCAGGAGA
1 CGCCTCCTACCTCACAGGAGA
*
55322 TGCCTCCTACCTC-CTAGGAGA
1 CGCCTCCTACCTCAC-AGGAGA
* * *
55343 TGCCTCCTA-C-AAGTAGAGAGA
1 CGCCTCCTACCTCA-CAG-GAGA
*
55364 CGCCTCCTATCTCACAGGAGA
1 CGCCTCCTACCTCACAGGAGA
55385 CG
1 CG
55387 TCACTTGCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
20 4 0.08
21 45 0.85
22 3 0.06
23 1 0.02
ACGTcount: A:0.23, C:0.37, G:0.21, T:0.19
Consensus pattern (21 bp):
CGCCTCCTACCTCACAGGAGA
Found at i:71767 original size:31 final size:31
Alignment explanation
Indices: 71732--71798 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
71722 TATACATTAC
*
71732 AATAGACTAAACCCATATAAGAAATTGAACA
1 AATAGACTAAACCCAAATAAGAAATTGAACA
71763 AATAGACTAAACCCAAATAAGAAATTGAACA
1 AATAGACTAAACCCAAATAAGAAATTGAACA
71794 AATAG
1 AATAG
71799 GTTAAATCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.57, C:0.15, G:0.10, T:0.18
Consensus pattern (31 bp):
AATAGACTAAACCCAAATAAGAAATTGAACA
Done.