Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1245
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: 25617
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:5242 original size:16 final size:16
Alignment explanation
Indices: 5217--5248 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5207 GATGAAAAGA
*
5217 ATTTTTTTATTATTTT
1 ATTTTGTTATTATTTT
5233 ATTTTGTTATTATTTT
1 ATTTTGTTATTATTTT
5249 TTATTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (16 bp):
ATTTTGTTATTATTTT
Found at i:6225 original size:31 final size:31
Alignment explanation
Indices: 6184--6272 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
6174 CTGCTGTGTT
*
6184 TGTGAAAGCTGGAAGAGGCTCGAGCTGCTA-
1 TGTGGAAGCTGGAAGAGGCTCGAGCTGCTAG
6214 TCGTGGAAGCTGGAAGAGGCTCGAGCTGCTAG
1 T-GTGGAAGCTGGAAGAGGCTCGAGCTGCTAG
* * *
6246 TGTGGAAGCTAGAAGAAGCTCAAGCTG
1 TGTGGAAGCTGGAAGAGGCTCGAGCTG
6273 TTGGTTTCGG
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
30 1 0.02
31 51 0.96
32 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.37, T:0.19
Consensus pattern (31 bp):
TGTGGAAGCTGGAAGAGGCTCGAGCTGCTAG
Found at i:6864 original size:31 final size:31
Alignment explanation
Indices: 6817--6880 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
6807 TTCTTTCTGT
*
6817 TTGCTTGTGTCCCCCATGATTGCATGCTACA
1 TTGCATGTGTCCCCCATGATTGCATGCTACA
*
6848 TTGCATGTGTCTCCCATGATTGCATGCTACA
1 TTGCATGTGTCCCCCATGATTGCATGCTACA
6879 TT
1 TT
6881 ACCTTGCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.38
Consensus pattern (31 bp):
TTGCATGTGTCCCCCATGATTGCATGCTACA
Found at i:7593 original size:42 final size:42
Alignment explanation
Indices: 7547--8954 Score: 981
Period size: 42 Copynumber: 33.6 Consensus size: 42
7537 TAGATGAGGC
* * * * *
7547 AGTCTTCAAGGTCAAAGCCGACAGGCAGACTGATGGTAGAAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * * * * *
7589 AGTCTCCAGGGTC-AAGATCGATAAGCAGGCTAAAGGTAGAAA
1 AGTCTTCAGGGTCAAAG-CCGACAGGCAGACTAAGGGAAGGAA
* ** * * * * * *
7631 AGTCTCCAGGGTCAAAGCTAACAAGTAGATTAAAGGTAGAAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* ** * * ** * *
7673 ATTCACCAAGGTC-CAGCCGATGGGTAGACTGAGGGAAGGAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * *
7714 AGTC-TCTAGGGTCAAAGCCGATAGGCAAACTAA-AGATAAGAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGA-AGGAA
* * *
7756 AGTC-TCTAAGGTAAAAGCCGACAGGCAGACTAAGGGAAGAAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * ***
7798 AGTCTCCAAGGTCAAAGCTGACAATTAGACTAAGGGAAGGAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
** * * * **
7840 AGTCCCCAGGATCAAAGCCGACAGGTAGACTGA-GGATAACAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGA-AGGAA
* * * * * *
7882 AGTCTCCAGGGTC-AAGACCGATAGGCAGGCTAAAGGTAGAAA
1 AGTCTTCAGGGTCAAAG-CCGACAGGCAGACTAAGGGAAGGAA
* * ** * * *
7924 AGTCTCCAAGGTCAAAGCTAACAGGCAAACTAAGGGTAGAAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* ** * * * *
7966 AGTC-TCTAAGGTCAAAGCTAACAGGAAAACTAAGGGCAGAAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * *
8008 AGTCTCCAAGGTC-CAGCCGAC-GAGTAGACTGAGGGAAGGAA
1 AGTCTTCAGGGTCAAAGCCGACAG-GCAGACTAAGGGAAGGAA
* * * *
8049 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGTAGGAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* *** * * * *
8091 AGTCTCCAGGGTCAAAGTTAATAAGTAGACTAAGGAAAGGAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * * **
8133 AATC-TCTAGGGTCAAAGCTGAAAGGAAGAGTAAGGGTTGGAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * *
8175 AGTCTTCAAGGTCAAAGCCGACAGGAAGATTAAGGGAAGGAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
*
8217 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * * *
8259 AGTCTCCAAGGTCAAAGCCGATAAGTAGACTAAGGGAAGAAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* *
8301 AGTC-TCTAGGGTCAAAGCCGACAAGCAGACTAAGGAAAGGAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
*
8343 AGTC-TCTAGGGTCAAAGCCGACAGGCAGACTAAGGGTAGGAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* *
8385 AGTC-TCTAGGGTCAAAGCCGACAGGCAGGCTAAGGGAAAGAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * *
8427 AGTC-TCTAGGGTCAAAGCAGACAAGTAGACTAAAGGAAGAAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * *
8469 AGTC-TCTAGGGTGAAAGTCGATAGGCAAACTAAGGGAAGGAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* *
8511 AGTC-TCAAGGGTCAAAGTCGACA-GTAGACTAAGGGAAGGAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * *
8552 AGTCTTAAAGGTCGAAGCTGACAGGAAGACTAAGGGAAGGAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * *
8594 AGTCTCCAAGGTCAAAGTCGACAGGCAGACTAAGGGTAGGAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * *
8636 AGTC-TCTAGGGTCAAAGCTGACACGTAGACTAAGGGAAGGAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * *
8678 AGTCTCCAGGGTCAAAGTCGATAGGTAGACTAAGGGAAGGAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
** * * *
8720 AGTC-TCTAGGGTCAAAGTGGATAGGCAGACTTAGGGAAGAAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* *
8762 AGTCTTCAGGGTGAAAGCCGACAGGTAGACTAAGGGAAGGAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * * * * *
8804 AGTCTCCAAGGTCAAAGCCGATAAGCAAACTAAGGAAAGGAA
1 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
* * ** * * ** * *
8846 AGT-TTCCAAGGTTAAAATCAATAGAAAAACTAAGAGAAGGAA
1 AGTCTT-CAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
** * * *
8888 AGTC-TCTAGGGTCAAAATCGATAGGAAGACTAAGGGAAGAAA
1 AGTCTTC-AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
*
8930 AGTC-TCTAGGGTGAAAGCCGACAGG
1 AGTCTTC-AGGGTCAAAGCCGACAGG
8955 AAAGTCTTTA
Statistics
Matches: 1109, Mismatches: 229, Indels: 56
0.80 0.16 0.04
Matches are distributed among these distances:
40 2 0.00
41 106 0.10
42 984 0.89
43 17 0.02
ACGTcount: A:0.39, C:0.16, G:0.29, T:0.15
Consensus pattern (42 bp):
AGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
Found at i:7644 original size:84 final size:84
Alignment explanation
Indices: 7556--8952 Score: 1162
Period size: 84 Copynumber: 16.7 Consensus size: 84
7546 CAGTCTTCAA
* * * * * * * *
7556 GGTCAAAGCCGACAGGCAGACTGATGGTAGAAAAGTCTCCAGGGTC-AAGATCGATAAGCAGGCT
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAG-CCGACAAGTAGACT
* * *
7620 AAAGGTAGAAAAGTCTCCAG
65 AAGGGAAGAAAAGTCTCTAG
** * * * * * * * * * * *** *
7640 GGTCAAAGCTAACAAGTAGATTAAAGGTAGAAAATTCACCAAGGTC-CAGCCGATGGGTAGACTG
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
*
7704 AGGGAAGGAAAGTCTCTAG
66 AGGGAAGAAAAGTCTCTAG
* * * * * * * * *
7723 GGTCAAAGCCGATAGGCAAACTAA-AGATAAGAAAGTCTCTAAGGTAAAAGCCGACAGGCAGACT
1 GGTCAAAGCCGACAGGCAGACTAAGGGA-AGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACT
* *
7787 AAGGGAAGAAAAGTCTCCAA
65 AAGGGAAGAAAAGTCTCTAG
* *** * * * *
7807 GGTCAAAGCTGACAATTAGACTAAGGGAAGGAAAGTCCCCAGGATCAAAGCCGACAGGTAGACTG
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
*
7872 A-GGATA-ACAAAGTCTCCAG
66 AGGGA-AGA-AAAGTCTCTAG
* * * * * * ** * * *
7891 GGTC-AAGACCGATAGGCAGGCTAAAGGTAGAAAAGTCTCCAAGGTCAAAGCTAACAGGCAAACT
1 GGTCAAAG-CCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACT
* *
7955 AAGGGTAGAAAAGTCTCTAA
65 AAGGGAAGAAAAGTCTCTAG
** * * * * * * * *
7975 GGTCAAAGCTAACAGGAAAACTAAGGGCAGAAAAGTCTCCAAGGTC-CAGCCGACGAGTAGACTG
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
* * *
8039 AGGGAAGGAAAGTCTCCAA
66 AGGGAAGAAAAGTCTCTAG
* * *** *
8058 GGTCAAAGCCGACAAGCAGACTAAGGGTAGGAAAGTCTCCAGGGTCAAAGTTAATAAGTAGACTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
*
8123 AGGAAAGGAAAA-TCTCTAG
66 AGGGAA-GAAAAGTCTCTAG
* * * * ** * * * * *
8142 GGTCAAAGCTGAAAGGAAGAGTAAGGGTTGGAAAGTCTTCAAGGTCAAAGCCGACAGGAAGATTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
* *
8207 AGGGAAGGAAAGTCTCCAG
66 AGGGAAGAAAAGTCTCTAG
* *
8226 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGATAAGTAGACTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
8291 AGGGAAGAAAAGTCTCTAG
66 AGGGAAGAAAAGTCTCTAG
* * * * *
8310 GGTCAAAGCCGACAAGCAGACTAAGGAAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
* *
8375 AGGGTAGGAAAGTCTCTAG
66 AGGGAAGAAAAGTCTCTAG
* * * *
8394 GGTCAAAGCCGACAGGCAGGCTAAGGGAAAGAAAGTCTCTAGGGTCAAAGCAGACAAGTAGACTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
*
8459 AAGGAAGAAAAGTCTCTAG
66 AGGGAAGAAAAGTCTCTAG
* * * * * *
8478 GGTGAAAGTCGATAGGCAAACTAAGGGAAGGAAAGTCTCAAGGGTCAAAGTCGAC-AGTAGACTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
* *
8542 AGGGAAGGAAAGTCT-TAAA
66 AGGGAAGAAAAGTCTCT-AG
* * * * * * *
8561 GGTCGAAGCTGACAGGAAGACTAAGGGAAGGAAAGTCTCCAAGGTCAAAGTCGACAGGCAGACTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
* *
8626 AGGGTAGGAAAGTCTCTAG
66 AGGGAAGAAAAGTCTCTAG
* * * * * *
8645 GGTCAAAGCTGACACGTAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGTCGATAGGTAGACTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
*
8710 AGGGAAGGAAAGTCTCTAG
66 AGGGAAGAAAAGTCTCTAG
** * * * * * *
8729 GGTCAAAGTGGATAGGCAGACTTAGGGAAGAAAAGTCTTCAGGGTGAAAGCCGACAGGTAGACTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
* * *
8794 AGGGAAGGAAAGTCTCCAA
66 AGGGAAGAAAAGTCTCTAG
* * * * * * * ** * *
8813 GGTCAAAGCCGATAAGCAAACTAAGGAAAGGAAAGTTTCCAAGGTTAAAATC-A-ATAGAAAAAC
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA-AG-TAGAC
* *
8876 TAAGAGAAGGAAAGTCTCTAG
64 TAAGGGAAGAAAAGTCTCTAG
** * * * * *
8897 GGTCAAAATCGATAGGAAGACTAAGGGAAGAAAAGTCTCTAGGGTGAAAGCCGACA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
8953 GGAAAGTCTT
Statistics
Matches: 1049, Mismatches: 245, Indels: 36
0.79 0.18 0.03
Matches are distributed among these distances:
82 3 0.00
83 199 0.19
84 832 0.79
85 14 0.01
86 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.29, T:0.15
Consensus pattern (84 bp):
GGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
AGGGAAGAAAAGTCTCTAG
Found at i:7878 original size:126 final size:126
Alignment explanation
Indices: 7547--8952 Score: 1150
Period size: 126 Copynumber: 11.2 Consensus size: 126
7537 TAGATGAGGC
* * * * * * * * *
7547 AGTCTTCAAGGTCAAAGCCGACAGGCAGACTGATGGTAGAAAAGTCTCCAGGGTC-AAGATCGAT
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAG-CCGAC
* * * ** * * * * *
7611 AAGCAGGCTAAAGG-T-AGAAAAGTCTCCAGGGTCAAAGCTAACAAGTAGATTAAAGGTAGAAA
65 AGGCAGACT-AAGGATAAG-AAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAAGGGAAGGAA
* * * *** * * *
7673 ATTCACCAAGGTC-CAGCCGATGGGTAGACTGAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGATA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACA
* * * * * *
7737 GGCAAACTAAAGATAAGAAAGTCTCTAAGGTAAAAGCCGACAGGCAGACTAAGGGAAGAAA
66 GGCAGACTAAGGATAAGAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAAGGGAAGGAA
* ** * * *
7798 AGTCTCCAAGGTCAAAGCTGACAATTAGACTAAGGGAAGGAAAGTCCCCAGGATCAAAGCCGACA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACA
* * * * * * * * * *
7863 GGTAGACTGAGGATAACAAAGTCTCCAGGGTC-AAGACCGATAGGCAGGCTAAAGGTAGAAA
66 GGCAGACTAAGGATAAGAAAGTCTCTAGGGTCAAAG-CCGACAGGTAGACTAAGGGAAGGAA
** * * * * * **
7924 AGTCTCCAAGGTCAAAGCTAACAGGCAAACTAAGGGTAGAAAAGTCTCTAAGGTCAAAGCTAACA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACA
* * ** * * * *
7989 GGAAAACTAAGG-GCAGAAAAGTCTCCAAGGTC-CAGCCGAC-GAGTAGACTGAGGGAAGGAA
66 GGCAGACTAAGGATAAG-AAAGTCTCTAGGGTCAAAGCCGACAG-GTAGACTAAGGGAAGGAA
* * *** *
8049 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGTAGGAAAGTCTCCAGGGTCAAAGTTAATA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACA
* * * * * * * **
8114 AGTAGACTAAGGA-AAGGAAAATCTCTAGGGTCAAAGCTGAAAGGAAGAGTAAGGGTTGGAA
66 GGCAGACTAAGGATAA-GAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAAGGGAAGGAA
* * * * *
8175 AGTCTTCAAGGTCAAAGCCGACAGGAAGATTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACA
* * * * * *
8240 GGCAGACTAAGGGA-AGGAAAGTCTCCAAGGTCAAAGCCGATAAGTAGACTAAGGGAAGAAA
66 GGCAGACTAA-GGATAAGAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAAGGGAAGGAA
* * *
8301 AGTCTCTAGGGTCAAAGCCGACAAGCAGACTAAGGAAAGGAAAGTCTCTAGGGTCAAAGCCGACA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACA
* * * * *
8366 GGCAGACTAAGGGTAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAGGCTAAGGGAAAGAA
66 GGCAGACTAAGGATAAGAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAAGGGAAGGAA
* * * * * * * * *
8427 AGTCTCTAGGGTCAAAGCAGACAAGTAGACTAAAGGAAGAAAAGTCTCTAGGGTGAAAGTCGATA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACA
* * * *
8492 GGCAAACTAAGGGA-AGGAAAGTCTCAAGGGTCAAAGTCGACA-GTAGACTAAGGGAAGGAA
66 GGCAGACTAA-GGATAAGAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAAGGGAAGGAA
** * * * * * * *
8552 AGTCTTAAAGGTCGAAGCTGACAGGAAGACTAAGGGAAGGAAAGTCTCCAAGGTCAAAGTCGACA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACA
* * * *
8617 GGCAGACTAAGGGTAGGAAAGTCTCTAGGGTCAAAGCTGACACGTAGACTAAGGGAAGGAA
66 GGCAGACTAAGGATAAGAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAAGGGAAGGAA
* * * * * ** *
8678 AGTCTCCAGGGTCAAAGTCGATAGGTAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGTGGATA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACA
* * *
8743 GGCAGACTTAGG-GAAGAAAAGTCT-TCAGGGTGAAAGCCGACAGGTAGACTAAGGGAAGGAA
66 GGCAGACTAAGGATAAG-AAAGTCTCT-AGGGTCAAAGCCGACAGGTAGACTAAGGGAAGGAA
* * * * * * * ** * *
8804 AGTCTCCAAGGTCAAAGCCGATAAGCAAACTAAGGAAAGGAAAGTTTCCAAGGTTAAAATCAATA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACA
** * * ** * * *
8869 GAAAAACTAAGAGA-AGGAAAGTCTCTAGGGTCAAAATCGATAGGAAGACTAAGGGAAGAAA
66 GGCAGACTAAG-GATAAGAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAAGGGAAGGAA
* * *
8930 AGTCTCTAGGGTGAAAGCCGACA
1 AGTCTCCAAGGTCAAAGCCGACA
8953 GGAAAGTCTT
Statistics
Matches: 1037, Mismatches: 222, Indels: 42
0.80 0.17 0.03
Matches are distributed among these distances:
124 6 0.01
125 293 0.28
126 727 0.70
127 11 0.01
ACGTcount: A:0.39, C:0.17, G:0.29, T:0.15
Consensus pattern (126 bp):
AGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACA
GGCAGACTAAGGATAAGAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAAGGGAAGGAA
Found at i:8956 original size:42 final size:42
Alignment explanation
Indices: 7698--8956 Score: 1095
Period size: 42 Copynumber: 30.0 Consensus size: 42
7688 GCCGATGGGT
* *
7698 AGACTGAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGATAGGCA
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGG-A
* * * * *
7741 A-ACTAA-AGATAAGAAAGTCTCTAAGGTAAAAGCCGACAGGC
1 AGACTAAGGGA-AGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * * * ***
7782 AGACTAAGGGAAGAAAAGTCTCCAAGGTCAAAGCTGACAATT
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * * *
7824 AGACTAAGGGAAGGAAAGTCCCCAGGATCAAAGCCGACAGGT
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* ** * * *
7866 AGACTGA-GGATAACAAAGTCTCCAGGGTC-AAGACCGATAGGC
1 AGACTAAGGGA-AGGAAAGTCTCTAGGGTCAAAG-CCGACAGGA
* * * * * * **
7908 AGGCTAAAGGTAGAAAAGTCTCCAAGGTCAAAGCTAACAGGCA
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGG-A
* * * **
7951 A-ACTAAGGGTAGAAAAGTCTCTAAGGTCAAAGCTAACAGGA
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * * * * * *
7992 AAACTAAGGGCAGAAAAGTCTCCAAGGTC-CAGCCGAC-GAGT
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAG-GA
* * * * *
8033 AGACTGAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGACAAGC
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * *** * * *
8075 AGACTAAGGGTAGGAAAGTCTCCAGGGTCAAAGTTAATAAGT
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * * *
8117 AGACTAAGGAAAGGAAAATCTCTAGGGTCAAAGCTGAAAGGA
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* ** *
8159 AGAGTAAGGGTTGGAAAGTCT-TCAAGGTCAAAGCCGACAGGA
1 AGACTAAGGGAAGGAAAGTCTCT-AGGGTCAAAGCCGACAGGA
* * *
8201 AGATTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAGGC
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * * * *
8243 AGACTAAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGATAAGT
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * *
8285 AGACTAAGGGAAGAAAAGTCTCTAGGGTCAAAGCCGACAAGC
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* *
8327 AGACTAAGGAAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGC
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* *
8369 AGACTAAGGGTAGGAAAGTCTCTAGGGTCAAAGCCGACAGGC
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * * * *
8411 AGGCTAAGGGAAAGAAAGTCTCTAGGGTCAAAGCAGACAAGT
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * * * *
8453 AGACTAAAGGAAGAAAAGTCTCTAGGGTGAAAGTCGATAGGCA
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGG-A
* * *
8496 A-ACTAAGGGAAGGAAAGTCTCAAGGGTCAAAGTCGACA-GT
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * *
8536 AGACTAAGGGAAGGAAAGTCT-TAAAGGTCGAAGCTGACAGGA
1 AGACTAAGGGAAGGAAAGTCTCT-AGGGTCAAAGCCGACAGGA
* * * *
8578 AGACTAAGGGAAGGAAAGTCTCCAAGGTCAAAGTCGACAGGC
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * * *
8620 AGACTAAGGGTAGGAAAGTCTCTAGGGTCAAAGCTGACACGT
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * * *
8662 AGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGTCGATAGGT
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
** * *
8704 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGTGGATAGGC
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * * *
8746 AGACTTAGGGAAGAAAAGTCT-TCAGGGTGAAAGCCGACAGGT
1 AGACTAAGGGAAGGAAAGTCTCT-AGGGTCAAAGCCGACAGGA
* * * *
8788 AGACTAAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGATAAGCA
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGA-CAGGA
* * * * * ** * * *
8831 A-ACTAAGGAAAGGAAAGTTTCCAAGGTTAAAATCAATAGAA
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* * ** *
8872 AAACTAAGAGAAGGAAAGTCTCTAGGGTCAAAATCGATAGGA
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
* *
8914 AGACTAAGGGAAGAAAAGTCTCTAGGGTGAAAGCCGACAGGA
1 AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
8956 A
1 A
8957 AGTCTTTAGA
Statistics
Matches: 1004, Mismatches: 189, Indels: 47
0.81 0.15 0.04
Matches are distributed among these distances:
40 2 0.00
41 80 0.08
42 909 0.91
43 13 0.01
ACGTcount: A:0.40, C:0.16, G:0.30, T:0.15
Consensus pattern (42 bp):
AGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGA
Found at i:14003 original size:20 final size:20
Alignment explanation
Indices: 13978--14016 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13968 TAATTCCCTA
13978 TTTTAA-TCTTTGTGATTTAT
1 TTTTAAGTCTTTGTG-TTTAT
*
13998 TTTTAAGTGTTTGTGTTTA
1 TTTTAAGTCTTTGTGTTTA
14017 CCTTTTATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (20 bp):
TTTTAAGTCTTTGTGTTTAT
Found at i:16769 original size:33 final size:33
Alignment explanation
Indices: 16713--16779 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
16703 TTCAACGATT
*
16713 TGTATCGATACATAAAATGTTGTATCGCTACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
16746 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
16779 T
1 T
16780 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:16841 original size:13 final size:13
Alignment explanation
Indices: 16823--16847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16813 ATTACTCACA
16823 TGTATCGATACAT
1 TGTATCGATACAT
16836 TGTATCGATACA
1 TGTATCGATACA
16848 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:16911 original size:51 final size:52
Alignment explanation
Indices: 16856--16979 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
16846 CACTGATCTT
*
16856 TGTATCGATACATGCAGGCAAATTTG-CCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
16907 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
16959 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
16980 CTTTTCATTA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 26 0.38
52 43 0.62
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Done.