Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015457.1 Corchorus capsularis cultivar CVL-1 contig15478, 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: 3319
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Found at i:80 original size:1 final size:1
Alignment explanation
Indices: 76--108 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
66 TTTGAGTTTG
*
76 TTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
109 GCCACCAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:938 original size:19 final size:17
Alignment explanation
Indices: 899--958 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
889 TGGACAAAAG
*
899 TATTATTTTATAGTGAT
1 TATTATTTTATAGAGAT
916 TATTAATTTTATAGAG--
1 TATT-ATTTTATAGAGAT
932 TATTATTGTATATAGAGAT
1 TATTATT-T-TATAGAGAT
951 TATATATT
1 TAT-TATT
959 GTACACTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
15 3 0.08
16 5 0.14
17 11 0.31
18 10 0.28
19 3 0.08
20 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (17 bp):
TATTATTTTATAGAGAT
Found at i:1765 original size:114 final size:114
Alignment explanation
Indices: 1237--3319 Score: 2878
Period size: 114 Copynumber: 17.8 Consensus size: 114
1227 CGTCAGACGT
1237 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
* ** *
1302 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACGC
66 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAATACGC
*
1351 CGCTAAATGGAGGCGTCTAAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
*
1416 TTGGGTAAAAATGTGAAGGCTAAAAGATAGCGGCGGCGTCTGGGGTCAAGACGC
66 TTGGGTAAAAA--TGAAGGCTAAAAGATA---GCGGCGTCTGGGGTCAATACGC
1470 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
*
1535 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGGCGTCTTGGGG-CAAAACGC
66 TTGGGTAAAAATGAAGGCTAAAAGATA---GCGGCGTC-TGGGGTCAATACGC
1587 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
*
1652 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAAAACGC
66 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAATACGC
1701 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
* *
1766 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAAAACAC
66 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAATACGC
* * * *
1815 CGCTAAATGGAGGCATCTGAACCTTATGACGCTGCGATCTTTAATTTTTCTCCAAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
** ** *
1880 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTCGCCCCATACGC
66 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAATACGC
* ** * *
1929 CGCTAAATGGAGGCGTCTAAACCGCAAAACGCCGCGATCTTTAA-TTTTCTCCAAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
** * *
1993 TTGGGTCAAATTGTGAAGGCTAAAAGATAGCGGCGTCATAAACGCTGTTGGGTCTAGACGC
66 TTGGGT-AAA-AATGAAGGCTAAAAGATAGCGGCG---T-----CTG--GGGTCAATACGC
*
2054 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCTGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
* ** *
2119 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACGC
66 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAATACGC
2168 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
* ** *
2233 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACGC
66 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAATACGC
* * * *
2282 CGCTAAATGGAGGCGTCTAAACCTTATGACGCTGCGATCTTTAATTTTTCTCCAAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
* ** *
2347 TTGGGTAAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACGC
66 TTGGGT-AAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAATACGC
*
2397 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCAATCTTTAATTTTTCTCCGAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
* * *
2462 TTGGGTAAAATTGAAGGCTAAAAGATAGCGGTGTCTGGCGTC-ATGACGC
66 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAAT-ACGC
*
2511 CGCTAAATGGAGGCGTCTGAACCATAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
*
2576 TTGGGTAAAAATGAAGGCTAAAAGATAGTGGCGGCGTCTGGGGTCAAAACGC
66 TTGGGTAAAAATGAAGGCTAAAAGATA---GCGGCGTCTGGGGTCAATACGC
* * ** *
2628 CGCTAAATGGAGGCGTCTGAACTTTATGACGCTACGATCTTTAATTTTTCTCCAAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
* ** *
2693 TTGGGTAAAAAGTGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACGC
66 TTGGGTAAAAA-TGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAATACGC
*
2743 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
** * ****
2808 TTGGGTCAAATTGTGAAGGCAAAAAGATAGCGGCGTCATAAACGCGGTTGGGTTTCGACGC
66 TTGGGT-AAA-AATGAAGGCTAAAAGATAGCGGCGTC-T-------G--GGGTCAATACGC
*
2869 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAACGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
* * *
2934 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCATAAACGCGGTTTGGTCTAGACGA
66 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTC-T------GG---GGTCAATACGC
* *
2993 TGCTAAATGGAGGCGTCTGAACCCCTTAAGACGCCGCAATCTTTAATTTTTCTCCGAGGAAGGCA
1 CGCTAAATGGAGGCGTCTGAA--CCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCA
3058 AATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTC-ATGACGC
64 AATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAAT-ACGC
*
3109 CGCTAAATGGAGGTGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
* ** *
3174 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACGC
66 TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAATACGC
* ** * *
3223 CGCTAAATGGAGGCGTCTAAACCACAAAACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAA
1 CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
**
3288 TTGGGTCAAATTGTGAAGGCTAAAAGATAGCG
66 TTGGGT-AAA-AATGAAGGCTAAAAGATAGCG
Statistics
Matches: 1795, Mismatches: 126, Indels: 94
0.89 0.06 0.05
Matches are distributed among these distances:
113 33 0.02
114 809 0.45
115 221 0.12
116 89 0.05
117 214 0.12
118 23 0.01
119 94 0.05
121 2 0.00
123 5 0.00
124 75 0.04
125 53 0.03
126 177 0.10
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (114 bp):
CGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAA
TTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAATACGC
Found at i:1931 original size:228 final size:228
Alignment explanation
Indices: 1004--3319 Score: 3022
Period size: 228 Copynumber: 9.9 Consensus size: 228
994 ATACACTTAT
*
1004 CCGCTAAATGGAGACGTCAT-AACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCA
1 CCGCTAAATGGAGGCGTC-TGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCA
** **
1068 AATTGGGTCAAATTGTGAAGGCTAAAAGATAGCGGCGTCATAAACGCGGTTGAGTTTAGACGCCG
65 AATTGGGT-AAA-AATGAAGGCTAAAAGATAGCGGCGTC-T------GG--G-GTCCAGACGCCG
* *
1133 CTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAACGAAGGCAATTT
118 CTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATT
* *
1198 GGGTAAAAATGAAGTCTAAAAGATAGCGGCG---T-----CAGACG
183 GGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACG
*
1236 TCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
* ** *
1301 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCG
66 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCCAGACGCCGCTAAATGGAGGCG
* *
1366 TCTAAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAATGTG
131 TCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTAAAAA--TG
* ** * *
1431 AAGGCTAAAAGATAGCGGCGGCGTCTGGGGTCAAGACG
194 AAGGCTAAAAGATA---GCGGCGTCTTGGCCCCATACG
1469 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
* *
1534 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGGCGTCTTGGGG-CAAAACGCCGCTAAATGGA
66 ATTGGGTAAAAATGAAGGCTAAAAGATA---GCGGCGTC-TGGGGTCCAGACGCCGCTAAATGGA
*
1598 GGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAA
127 GGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTAAAAA
* ** * *
1663 TGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAAAACG
192 TGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACG
1700 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
* * * *
1765 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAAAACACCGCTAAATGGAGGCA
66 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCCAGACGCCGCTAAATGGAGGCG
* *
1830 TCTGAACCTTATGACGCTGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTAAAAATGAA
131 TCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTAAAAATGAA
*
1895 GGCTAAAAGATAGCGGCGTCTTCGCCCCATACG
196 GGCTAAAAGATAGCGGCGTCTTGGCCCCATACG
* ** * *
1928 CCGCTAAATGGAGGCGTCTAAACCGCAAAACGCCGCGATCTTTAA-TTTTCTCCAAGGAAGGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
** *
1992 ATTGGGTCAAATTGTGAAGGCTAAAAGATAGCGGCGTCATAAACGCTGTTGGGTCTAGACGCCGC
66 ATTGGGT-AAA-AATGAAGGCTAAAAGATAGCGGCG---T-----CTG--GGGTCCAGACGCCGC
* *
2057 TAAATGGAGGCGTCTGAACCTTAAGACGCTGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTG
119 TAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTG
2122 GGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACG
184 GGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACG
2167 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
* ** *
2232 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCG
66 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCCAGACGCCGCTAAATGGAGGCG
* * *
2297 TCTAAACCTTATGACGCTGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTAAAAAATGA
131 TCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGT-AAAAATGA
2362 AGGCTAAAAGATAGCGGCGTCTTGGCCCCATACG
195 AGGCTAAAAGATAGCGGCGTCTTGGCCCCATACG
*
2396 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCAATCTTTAATTTTTCTCCGAGGAAGGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
* * *
2461 ATTGGGTAAAATTGAAGGCTAAAAGATAGCGGTGTCTGGCGT-CATGACGCCGCTAAATGGAGGC
66 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCCA-GACGCCGCTAAATGGAGGC
* *
2525 GTCTGAACCATAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAATGA
130 GTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTAAAAATGA
* ** * *
2590 AGGCTAAAAGATAGTGGCGGCGTCTGGGGTCAAAACG
195 AGGCTAAAAGATA---GCGGCGTCTTGGCCCCATACG
* * ** *
2627 CCGCTAAATGGAGGCGTCTGAACTTTATGACGCTACGATCTTTAATTTTTCTCCAAGGAAGGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
* ** *
2692 ATTGGGTAAAAAGTGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGC
66 ATTGGGTAAAAA-TGAAGGCTAAAAGATAGCGGCGTCTGGGGTCCAGACGCCGCTAAATGGAGGC
**
2757 GTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTCAAATTGT
130 GTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGT-AAA-AAT
* *** *
2822 GAAGGCAAAAAGATAGCGGCGTCATAAACGCGGTTGGGTTTC-GACG
193 GAAGGCTAAAAGATAGCGGCG---T-----C--TT-GGCCCCATACG
*
2868 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAACGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
* **
2933 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCATAAACGCGGTTTGGTCTAGACGATGCTA
66 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTC-T------GG---GGTCCAGACGCCGCTA
* *
2998 AATGGAGGCGTCTGAACCCCTTAAGACGCCGCAATCTTTAATTTTTCTCCGAGGAAGGCAAATTG
121 AATGGAGGCGTCTGAA--CCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTG
***
3063 GGTAAAAATGAAGGCTAAAAGATAGCGGCGTC-TGGGGTCATGACG
184 GGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCAT-ACG
*
3108 CCGCTAAATGGAGGTGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
* ** *
3173 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCG
66 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCCAGACGCCGCTAAATGGAGGCG
* ** * **
3238 TCTAAACCACAAAACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTCAAATTGTG
131 TCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGT-AAA-AATG
3303 AAGGCTAAAAGATAGCG
194 AAGGCTAAAAGATAGCG
Statistics
Matches: 1873, Mismatches: 143, Indels: 138
0.87 0.07 0.06
Matches are distributed among these distances:
220 77 0.04
221 1 0.00
222 15 0.01
223 1 0.00
225 6 0.00
227 30 0.02
228 306 0.16
229 238 0.13
230 70 0.04
231 209 0.11
232 167 0.09
233 103 0.05
234 32 0.02
235 1 0.00
236 89 0.05
237 6 0.00
238 26 0.01
239 165 0.09
240 151 0.08
241 76 0.04
242 4 0.00
247 2 0.00
250 47 0.03
251 3 0.00
252 48 0.03
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (228 bp):
CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCCAGACGCCGCTAAATGGAGGCG
TCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTAAAAATGAA
GGCTAAAAGATAGCGGCGTCTTGGCCCCATACG
Found at i:2226 original size:467 final size:467
Alignment explanation
Indices: 1004--3319 Score: 3364
Period size: 467 Copynumber: 5.0 Consensus size: 467
994 ATACACTTAT
*
1004 CCGCTAAATGGAGACGTCAT-AACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCA
1 CCGCTAAATGGAGGCGTC-TGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCA
* * * *
1068 AATTGGGTCAAATTGTGAAGGCTAAAAGATAGCGGCGTCATAAACGCGGTTGAGTTTAGACGCCG
65 AATTGGGT-AAA-TATGAAGGCTAAAAGATAGCGGCGTCATAAACGCTGTTGGGTCTAGACGCCG
* * *
1133 CTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAACGAAGGCAATTT
128 CTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATT
* * *
1198 GGGTAAAAATGAAGTCTAAAAGATAGC-G-G-C----GT-CAGACGTCGCTAAATGGAGGCGTCT
193 GGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGGTCCAAACGCCGCTAAATGGAGGCGTCT
1255 GAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAATGAAGGC
258 GAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAATGAAGGC
1320 TAAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCGTCTAAACCTTAAGACGCCG
323 TAAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCGTCTAAACCTTAAGACGCCG
*
1385 CGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGT-AAAAATGTGAAGGCTAAAAGATAGCGG
388 CGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTCAAAAA--TGAAGGCTAAAAGATA---G
** ** * *
1449 CGGCGTCTGGGGTCAAGACG
448 CGGCGTCTTCGCCCCATACG
1469 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
* * * * * *
1534 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCG------GCG-TCTTGGGGCAAAACGCCGCTA
66 ATTGGGTAAATATGAAGGCTAAAAGATAGCGGCGTCATAAACGCTGTTGGGTCTAGACGCCGCTA
1592 AATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGG
131 AATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGG
* *
1657 TAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGTCAAAACGCCGCTAAATGGAGGCGTCTGAA
196 TAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGGTCCAAACGCCGCTAAATGGAGGCGTCTGAA
1722 CCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAATGAAGGCTAA
261 CCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAATGAAGGCTAA
* ** * * * * * * *
1787 AAGATAGCGGCGTCTGGGGTCAAAACACCGCTAAATGGAGGCATCTGAACCTTATGACGCTGCGA
326 AAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCGTCTAAACCTTAAGACGCCGCGA
1852 TCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGT-AAAAATGAAGGCTAAAAGATAGCGGCGTCT
391 TCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTCAAAAATGAAGGCTAAAAGATAGCGGCGTCT
1916 TCGCCCCATACG
456 TCGCCCCATACG
* ** * *
1928 CCGCTAAATGGAGGCGTCTAAACCGCAAAACGCCGCGATCTTTAA-TTTTCTCCAAGGAAGGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
*
1992 ATTGGGTCAAATTGTGAAGGCTAAAAGATAGCGGCGTCATAAACGCTGTTGGGTCTAGACGCCGC
66 ATTGGGT-AAA-TATGAAGGCTAAAAGATAGCGGCGTCATAAACGCTGTTGGGTCTAGACGCCGC
*
2057 TAAATGGAGGCGTCTGAACCTTAAGACGCTGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTG
129 TAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTG
** *
2122 GGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCGTCTG
194 GGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGGTCCAAACGCCGCTAAATGGAGGCGTCTG
2187 AACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAATGAAGGCT
259 AACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAATGAAGGCT
* *
2252 AAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCGTCTAAACCTTATGACGCTGC
324 AAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCGTCTAAACCTTAAGACGCCGC
*
2317 GATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTAAAAAATGAAGGCTAAAAGATAGCGGCGT
389 GATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTCAAAAATGAAGGCTAAAAGATAGCGGCGT
*
2382 CTTGGCCCCATACG
454 CTTCGCCCCATACG
*
2396 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCAATCTTTAATTTTTCTCCGAGGAAGGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
* *
2461 ATTGGGTAAA-ATTGAAGGCTAAAAGATAGC-G-GT-GT-----CTG--GCGTC-ATGACGCCGC
66 ATTGGGTAAATA-TGAAGGCTAAAAGATAGCGGCGTCATAAACGCTGTTGGGTCTA-GACGCCGC
*
2514 TAAATGGAGGCGTCTGAACCATAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTG
129 TAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTG
* *
2579 GGTAAAAATGAAGGCTAAAAGATAGTGGCGGCGTCTGGGGTCAAAACGCCGCTAAATGGAGGCGT
194 GGTAAAAATGAAGGCTAAAAGATA---GCGGCGTCTTGGGTCCAAACGCCGCTAAATGGAGGCGT
* * ** *
2644 CTGAACTTTATGACGCTACGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTAAAAAGTGAA
256 CTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAA-TGAA
*
2709 GGCTAAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCGTCTGAACCTTAAGACG
320 GGCTAAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCGTCTAAACCTTAAGACG
** *
2774 CCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTCAAATTGTGAAGGCAAAAAGATAGC
385 CCGCGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTCAAA-AATGAAGGCTAAAAGATAGC
* ****
2839 GGCGTCATAAACGCGGTTGGGTTTCGACG
449 GGCGTC-T--TCGC-----CCCAT--ACG
*
2868 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAACGCAA
1 CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
* * * **
2933 ATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCATAAACGCGGTTTGGTCTAGACGATGCTA
66 ATTGGGTAAATATGAAGGCTAAAAGATAGCGGCGTCATAAACGCTGTTGGGTCTAGACGCCGCTA
*
2998 AATGGAGGCGTCTGAACCCCTTAAGACGCCGCAATCTTTAATTTTTCTCCGAGGAAGGCAAATTG
131 AATGGAGGCGTCTGAA--CCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTG
* * *
3063 GGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTGGGGT-CATGACGCCGCTAAATGGAGGTGTCT
194 GGTAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGGTCCA-AACGCCGCTAAATGGAGGCGTCT
3127 GAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAATGAAGGC
258 GAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAATGAAGGC
** *
3192 TAAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCGTCTAAACCACAAAACGCCG
323 TAAAAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCGTCTAAACCTTAAGACGCCG
**
3257 CGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTCAAATTGTGAAGGCTAAAAGATAGCG
388 CGATCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTCAAA-AATGAAGGCTAAAAGATAGCG
Statistics
Matches: 1680, Mismatches: 119, Indels: 89
0.89 0.06 0.05
Matches are distributed among these distances:
456 100 0.06
457 102 0.06
458 26 0.02
459 63 0.04
460 110 0.07
461 109 0.06
462 39 0.02
463 25 0.01
464 188 0.11
465 73 0.04
466 3 0.00
467 315 0.19
468 84 0.05
469 25 0.01
470 1 0.00
472 94 0.06
473 2 0.00
474 2 0.00
475 1 0.00
480 133 0.08
481 88 0.05
482 27 0.02
483 1 0.00
484 69 0.04
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (467 bp):
CCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAA
ATTGGGTAAATATGAAGGCTAAAAGATAGCGGCGTCATAAACGCTGTTGGGTCTAGACGCCGCTA
AATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGG
TAAAAATGAAGGCTAAAAGATAGCGGCGTCTTGGGTCCAAACGCCGCTAAATGGAGGCGTCTGAA
CCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGGCAAATTGGGTAAAAATGAAGGCTAA
AAGATAGCGGCGTCTTGGCCCCATACGCCGCTAAATGGAGGCGTCTAAACCTTAAGACGCCGCGA
TCTTTAATTTTTCTCCAAGGAAGGCAAATTGGGTCAAAAATGAAGGCTAAAAGATAGCGGCGTCT
TCGCCCCATACG
Found at i:3020 original size:126 final size:123
Alignment explanation
Indices: 2739--3319 Score: 743
Period size: 126 Copynumber: 4.8 Consensus size: 123
2729 TTGGCCCCAT
*
2739 ACGCCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCAAGGAAGG
1 ACGCCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGG
** * * *
2804 CAAATTGGGTCAAATTGTGAAGGCAAAAAGATAGCGGCGTCATAAACGCGGTTGGGTTTCG
66 CAAATTGGGT-AAA-AATGAAGGCTAAAAGATAGCGGCGTCATAAACGCGGTT-GGTCTAG
*
2865 ACGCCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAACG
1 ACGCCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGG
2930 CAAATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCATAAACGCGGTTTGGTCTAG
66 CAAATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCATAAACGCGG-TTGGTCTAG
** *
2989 ACGATGCTAAATGGAGGCGTCTGAACCCCTTAAGACGCCGCAATCTTTAATTTTTCTCCGAGGAA
1 ACGCCGCTAAATGGAGGCGTCTGAA--CCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAA
3054 GGCAAATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTC-T------GG--GGTC-ATG
64 GGCAAATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCATAAACGCGGTTGGTCTA-G
*
3105 ACGCCGCTAAATGGAGGTGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGG
1 ACGCCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGG
* * *
3170 CAAATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCG---T-----C--TTGGCCCCAT
66 CAAATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCATAAACGCGGTTGG-TCTAG
* ** * *
3219 ACGCCGCTAAATGGAGGCGTCTAAACCACAAAACGCCGCGATCTTTAATTTTTCTCCAAGGAAGG
1 ACGCCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGG
**
3284 CAAATTGGGTCAAATTGTGAAGGCTAAAAGATAGCG
66 CAAATTGGGT-AAA-AATGAAGGCTAAAAGATAGCG
Statistics
Matches: 419, Mismatches: 25, Indels: 32
0.88 0.05 0.07
Matches are distributed among these distances:
112 1 0.00
113 2 0.00
114 146 0.35
115 5 0.01
116 46 0.11
119 2 0.00
124 61 0.15
125 6 0.01
126 150 0.36
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (123 bp):
ACGCCGCTAAATGGAGGCGTCTGAACCTTAAGACGCCGCGATCTTTAATTTTTCTCCGAGGAAGG
CAAATTGGGTAAAAATGAAGGCTAAAAGATAGCGGCGTCATAAACGCGGTTGGTCTAG
Done.