Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005177.1 Hibiscus syriacus cultivar Beakdansim tig00011683_pilon, 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: 67238
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2537 original size:78 final size:79
Alignment explanation
Indices: 2392--2539 Score: 201
Period size: 78 Copynumber: 1.9 Consensus size: 79
2382 GTTAACGAGT
*
2392 GTCTTGATTAAATGTATTTAAAATAATTTGGTGATCTGATTGACAAAATTTTAAAATTACTGGTC
1 GTCTTGATTAAATGTATTTAAAATAATTTGGTGATCTGATTGACAAAATTTTAAAATTACTAGTC
2457 AAAATAAAAAAGGG
66 AAAATAAAAAAGGG
* * ** * * *
2471 GTCTTGATTGAATGTATTT-AAATAGTTTGGTGA-CTTGATTGATTAACTTTTTAAATTAGTAGT
1 GTCTTGATTAAATGTATTTAAAATAATTTGGTGATC-TGATTGACAAAATTTTAAAATTACTAGT
2534 CAAAAT
65 CAAAAT
2540 GAAAGGAGTC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
77 1 0.02
78 41 0.68
79 18 0.30
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (79 bp):
GTCTTGATTAAATGTATTTAAAATAATTTGGTGATCTGATTGACAAAATTTTAAAATTACTAGTC
AAAATAAAAAAGGG
Found at i:3067 original size:31 final size:31
Alignment explanation
Indices: 3032--3090 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
3022 TTAAAATTTT
3032 AAAAACAT-ATTGAAACAAAAAAATATTCTCA
1 AAAAACATAATT-AAACAAAAAAATATTCTCA
* **
3063 AAAAATATAATTAAATTAAAAAATATTC
1 AAAAACATAATTAAACAAAAAAATATTC
3091 ACTTTGCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (31 bp):
AAAAACATAATTAAACAAAAAAATATTCTCA
Found at i:10035 original size:24 final size:25
Alignment explanation
Indices: 9986--10040 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
9976 GTTTTTTTAT
*
9986 TAAAATTTAATAAAAATATTAAAAA
1 TAAATTTTAATAAAAATATTAAAAA
* *
10011 TAAATTTTAATATAAATATT-TAAA
1 TAAATTTTAATAAAAATATTAAAAA
10035 TAAATT
1 TAAATT
10041 AAAATTACGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TAAATTTTAATAAAAATATTAAAAA
Found at i:31573 original size:6 final size:6
Alignment explanation
Indices: 31562--31622 Score: 104
Period size: 6 Copynumber: 10.2 Consensus size: 6
31552 GACACGTATT
* *
31562 ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
31610 ACCACG ACCACG A
1 ACCACG ACCACG A
31623 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:31630 original size:5 final size:5
Alignment explanation
Indices: 31620--31673 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
31610 ACCACGACCA
* * * *
31620 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAGA
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
31670 CGAG
1 CGAG
31674 ACGGACGGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.17, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:37544 original size:6 final size:6
Alignment explanation
Indices: 37533--37629 Score: 176
Period size: 6 Copynumber: 16.2 Consensus size: 6
37523 GACACGTATT
37533 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* *
37581 ACCACG ACCTCG ACCTCG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
37629 A
1 A
37630 GCCGAGCCGA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:37637 original size:5 final size:5
Alignment explanation
Indices: 37627--37680 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
37617 ACCACGACCA
* * * * * *
37627 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CAAGC CAAGC CGAGA
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
37677 CGAG
1 CGAG
37681 ACGGACGGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.20, C:0.37, G:0.37, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:38596 original size:25 final size:25
Alignment explanation
Indices: 38529--38588 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
38519 AAATATCAAG
38529 TTTCATTAATGGTATTTTGGTGATT
1 TTTCATTAATGGTATTTTGGTGATT
38554 TTTCATTAATGGTATTTTGGTGATT
1 TTTCATTAATGGTATTTTGGTGATT
38579 TTTCATTAAT
1 TTTCATTAAT
38589 TGAATTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.22, C:0.05, G:0.17, T:0.57
Consensus pattern (25 bp):
TTTCATTAATGGTATTTTGGTGATT
Found at i:41006 original size:18 final size:17
Alignment explanation
Indices: 40980--41038 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
40970 ATGTTTACAA
*
40980 TTATTAGATAATTTTCAG
1 TTATCAGAT-ATTTTCAG
40998 TTATCAGATATTTAT-AG
1 TTATCAGATATTT-TCAG
* *
41015 ATATCAGATGTTTTACAG
1 TTATCAGATATTTT-CAG
41033 TTATCA
1 TTATCA
41039 AACACAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 1 0.03
17 17 0.50
18 16 0.47
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.46
Consensus pattern (17 bp):
TTATCAGATATTTTCAG
Found at i:45172 original size:149 final size:147
Alignment explanation
Indices: 44896--45849 Score: 985
Period size: 149 Copynumber: 6.7 Consensus size: 147
44886 TAGATCATTT
* *
44896 TATTTCACCCGGCCTACTCCACACGTTA-AGGCGCTCGGTGTAAGATCAGGTCATCCTGCCTACT
1 TATTTCACCCGGCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
* * * * * * *
44960 CCCCTTTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCCACACATTGAGGCGCTCGA
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACTCTACACGTTGAAGTGCTCGG
* *
45025 CCTGATATTAAAGCACATTC
130 CGTGACATT-AAGCACA-TC
* *
45045 TATTTCACCCGACCTACTCCACACGTTAGGGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
1 TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
* * *
45110 CCCTCTAGAAGCGCTCGGCATGAACTCTGTCAACCCTGCCTACCCTACACGTTGATA-TGCTCGG
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACTCTACACGTTGA-AGTGCTCGG
*
45174 CGTGA-A-T-----C-TGG
130 CGTGACATTAAGCACAT-C
* * * * * *
45185 GA---CACCCTGCCTACTCTACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTATTC
1 TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
* * * * *
45247 CCCTTTGGAAGCGCTCGACATGCACTCTGTCT-CCTCTGCCTACTCTAAACGTTGAAGCGCTCGG
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACC-CTGCCTACTCTACACGTTGAAGTGCTCGG
45311 CGTGACATTAAGGCACATC
130 CGTGACATTAA-GCACATC
* *
45330 TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACTAGGTCATCATGCCTACT
1 -TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
* *
45395 CCCCTCTGGAAGCGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCT-CAACGTTGAAGTGCTCG
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACTCTAC-ACGTTGAAGTGCTCG
**
45459 ATGTGACATTAGAGCACATC
129 GCGTGACATTA-AGCACATC
*
45479 TTGTTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
1 -TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
* * *
45544 CCCCTCTGGAAGCGCTCAGCATGTACTCTGTCTCCCCTGCCTACTCT-CAACGTTGAAGTGCTCG
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACTCTAC-ACGTTGAAGTGCTCG
45608 GCGTG--A-T------AT-
129 GCGTGACATTAAGCACATC
** * * * * *
45617 TATAACACCCTGCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAAGTCATCCTGCCTACTC
1 TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
* * * * *
45682 CCCACTGGAAGCGCTCGGCATGAACTCTGTC-CCCCTTCCAACTCTTA-ACGGTGAAGTGCTCGG
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACTC-TACACGTTGAAGTGCTCGG
* *
45745 CGTGAAAATAAG---A--
130 CGTGACATTAAGCACATC
* * * * * *
45758 -A--T-ACCCTGCCTACCCCATACATTAGAGCGCCCGGCGTAAGATCAGGTCAT-CTGGCCTACT
1 TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCT-GCCTACT
*
45818 CCCCACTGGAAGCGCTCGGCATGAACTCTGTC
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTC
45850 CCCCTTCCAA
Statistics
Matches: 703, Mismatches: 72, Indels: 72
0.83 0.09 0.09
Matches are distributed among these distances:
136 35 0.05
137 277 0.39
138 2 0.00
139 5 0.01
140 2 0.00
141 1 0.00
142 1 0.00
145 1 0.00
146 3 0.00
147 2 0.00
148 1 0.00
149 370 0.53
150 3 0.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (147 bp):
TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACTCTACACGTTGAAGTGCTCGGC
GTGACATTAAGCACATC
Found at i:45240 original size:46 final size:45
Alignment explanation
Indices: 45049--45243 Score: 123
Period size: 46 Copynumber: 4.3 Consensus size: 45
45039 ACATTCTATT
* * *
45049 TCACCC-GACCTACTCCACACGTTAGGGCGCTCGGCGTAAGACCAGG
1 TCACCCTG-CCTACTCTACACGTTAGAGCGCTCGGCGTAA-ATCAGG
* * * * *
45095 TCATCCTGCCTACTC--C-CCTCTAGAAGCGCTCGGCATGAACTC-TG
1 TCACCCTGCCTACTCTACACGT-TAG-AGCGCTCGGCGT-AAATCAGG
* ** * *
45139 TCAACCCTGCCTACCCTACACGTT-GATATGCTCGGCGTGAATCTGGG
1 TC-ACCCTGCCTACTCTACACGTTAGA-GCGCTCGGCGTAAATC-AGG
* *
45186 ACACCCTGCCTACTCTACACGTTAGAGCGCTCGACGTAAGATCAGG
1 TCACCCTGCCTACTCTACACGTTAGAGCGCTCGGCGTAA-ATCAGG
*
45232 TCATCCTGCCTA
1 TCACCCTGCCTA
45244 TTCCCCTTTG
Statistics
Matches: 111, Mismatches: 25, Indels: 26
0.69 0.15 0.16
Matches are distributed among these distances:
43 2 0.02
44 7 0.06
45 26 0.23
46 64 0.58
47 10 0.09
48 2 0.02
ACGTcount: A:0.21, C:0.35, G:0.22, T:0.22
Consensus pattern (45 bp):
TCACCCTGCCTACTCTACACGTTAGAGCGCTCGGCGTAAATCAGG
Found at i:45299 original size:137 final size:137
Alignment explanation
Indices: 45057--45880 Score: 877
Period size: 137 Copynumber: 5.8 Consensus size: 137
45047 TTTCACCCGA
* * *
45057 CCTACTCCACACGTTAGGGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTAGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
** * *
45122 GCTCGGCATGAACTCTGTCAACCCTGCCTACCCTACACGTTGATA-TGCTCGGCGTGA-ATCTGG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGA-AGTGCTCGGCGTGACAT-TGG
*
45185 GACACCCTG
129 AACACCCTG
* * * *
45194 CCTACTCTACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTATTCCCCTTTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * *
45259 GCTCGACATGCACTCTGTCTCCTCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGACATTAAGG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGACATT--GG
*
45324 CACATCTTATTTCACCCGG
129 ---A----A---CACCCTG
*
45343 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGA-CTAGGTCATCATGCCTACTCCCCTCTGGAAG
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGATC-AGGTCATCCTGCCTACTCCCCTCTGGAAG
* * **
45407 CGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGTGCTCGATGTGACATTAGA
65 CGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGACATT-G-
*
45472 GCACATCTTGTTTCACCCGG
128 G-A-A--------CACCCTG
*
45492 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * * **
45557 GCTCAGCATGTACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGTGCTCGGCGTGATATTATAA
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGACATTGGAA
45622 CACCCTG
131 CACCCTG
* * * *
45629 CCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAAGTCATCCTGCCTACTCCCCACTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * * * **
45694 GCTCGGCATGAACTCTGTC-CCCCTTCCAACTCTTAACGGTGAAGTGCTCGGCGTGAAAATAAGA
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTG-ACATTGGA
*
45758 ATACCCTG
130 ACACCCTG
* * * * *
45766 CCTACCCCATACATTAGAGCGCCCGGCGTAAGATCAGGTCAT-CTGGCCTACTCCCCACTGGAAG
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCT-GCCTACTCCCCTCTGGAAG
* * * * *
45830 CGCTCGGCATGAACTCTGTC-CCCCTTCCAACTCTTAATGTTGAAGCGCTCG
65 CGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCG
45881 ACGAAATTCC
Statistics
Matches: 602, Mismatches: 61, Indels: 48
0.85 0.09 0.07
Matches are distributed among these distances:
136 35 0.06
137 305 0.51
138 2 0.00
139 2 0.00
144 1 0.00
145 1 0.00
146 2 0.00
147 2 0.00
148 3 0.00
149 248 0.41
150 1 0.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (137 bp):
CCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGACATTGGAA
CACCCTG
Found at i:45425 original size:286 final size:282
Alignment explanation
Indices: 44901--45880 Score: 1042
Period size: 286 Copynumber: 3.4 Consensus size: 282
44891 CATTTTATTT
*
44901 CACCCGGCCTACTCCACACGTTA-AGGCGCTCGGTGTAAGATCAGGTCATCCTGCCTACTCCCCT
1 CACCCGGCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCT
* * * * * * * * * *
44965 TTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCCACACATTGAGGCGCTCGACCTGA
65 CTGGAAGCGCTCGACATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGA
* * *
45030 TATTAAAGCACATTCTATTTCACCCGACCTACTCCACACGTTAGGGCGCTCGGCGTAAGACCAGG
130 -ATT-AAGCACATT-TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACTAGG
* *
45095 TCATCCTGCCTACTCCCCTCTAGAAGCGCTCGGCATGAACTCTGTCAACCCTGCCTACCCTACAC
192 TCATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTC-CCCCTGCCTACCCTACAC
*
45160 GTTGATA-TGCTCGGCGTGAATCTGGGA
256 GTTGA-AGTGCTCGGCGTGAATCTGGAA
* * * * *
45187 CACCCTGCCTACTCTACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTATTCCCCTT
1 CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
* *
45252 TGGAAGCGCTCGACATGCACTCTGTCTCCTCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGAC
66 TGGAAGCGCTCGACATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGA-
45317 ATTAAGGCACATCTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACTAGGT
130 ATTAA-GCACAT-TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACTAGGT
* * *
45382 CATCATGCCTACTCCCCTCTGGAAGCGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCT-CAAC
193 CATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTC-CCCCTGCCTACCCTAC-AC
**
45446 GTTGAAGTGCTCGATGTGACAT-TAGAGCACA
256 GTTGAAGTGCTCGGCGTGA-ATCT-G-G-A-A
*
45477 TCTTGTTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
1 --------CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTA
* * *
45542 CTCCCCTCTGGAAGCGCTC-AGCATGTACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGTGCT
58 CTCCCCTCTGGAAGCGCTCGA-CATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCT
** * * *
45606 CGGCGTG-A-T------A-TTATAACACCCTGCCTACTCCACACGTTAGAGCGCCCGACGTAAGA
122 CGGCGTGAATTAAGCACATTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGA
* * * *
45662 -TCAAGTCATCCTGCCTACTCCCCACTGGAAGCGCTCGGCATGAACTCTGTCCCCCTTCCAACTC
187 CT-AGGTCATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCCCCCTGCCTAC-C
* * ** *
45726 TTA-ACGGTGAAGTGCTCGGCGTGAAAATAAGAA
250 CTACACGTTGAAGTGCTCGGCGTGAATCT-GGAA
* * * * * * *
45759 TACCCTGCCTACCCCATACATTAGAGCGCCCGGCGTAAGATCAGGTCAT-CTGGCCTACTCCCCA
1 CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCT-GCCTACTCCCCT
* * * * *
45823 CTGGAAGCGCTCGGCATGAACTCTGTC-CCCCTTCCAACTCTTAATGTTGAAGCGCTCG
65 CTGGAAGCGCTCGACATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCG
45881 ACGAAATTCC
Statistics
Matches: 597, Mismatches: 72, Indels: 63
0.82 0.10 0.09
Matches are distributed among these distances:
273 28 0.05
274 77 0.13
282 1 0.00
283 1 0.00
284 2 0.00
285 34 0.06
286 327 0.55
287 5 0.01
288 2 0.00
290 1 0.00
295 1 0.00
296 1 0.00
297 1 0.00
298 116 0.19
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (282 bp):
CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
TGGAAGCGCTCGACATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGAA
TTAAGCACATTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACTAGGTCAT
CCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCCCCCTGCCTACCCTACACGTTGA
AGTGCTCGGCGTGAATCTGGAA
Found at i:45711 original size:435 final size:427
Alignment explanation
Indices: 44895--45882 Score: 1282
Period size: 435 Copynumber: 2.3 Consensus size: 427
44885 CTAGATCATT
*
44895 TTATTTCACCCGGCCTACTCCACACGTTA-AGGCGCTCGGTGTAAGATCAGGTCATCCTGCCTAC
1 TTATTTCACCCGGCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGATCAGGTCAT-CTGCCTAC
* * * * *
44959 TCCCCTTTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTAC-CCCACACATTGAGGCGCTC
64 TCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCA-ACGTTGAAGCGCTC
* *
45023 GACCTGATATTAAAGCACATTCTATTTCACCCGACCTACTCCACACGTTAGGGCGCTCGGCGTAA
128 GACCTGACATTAAAGCACATTCTATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAA
*
45088 GACCAGGTCATCCTGCCTACTCCCCTCTAGAAGCGCTCGGCATGAACTCTGTCAACCCTGCCTAC
193 GACCAGGTCATCCTGCCTACTCCCCTCTAGAAGCGCTCAGCATGAACTCTGTCAACCCTGCCTAC
* * * *
45153 CCTACACGTTGATATGCTCGGCGTGAATCTGGGACACCCTGCCTACTCTACACGTTAGAGCGCTC
258 CCTACACGTTGATATGCTCGGCGTGAATCTAGAACACCCTGCCTACTCCACACGTTAGAGCGCCC
* * ** * *
45218 GACGTAAGATCAGGTCATCCTGCCTATTCCCCTTTGGAAGCGCTCGACATGCACTCTGTCTCCTC
323 GACGTAAGATCAAGTCATCCTGCCTACTCCCCACTGGAAGCGCTCGACATGAACTCTGTC-CCCC
* * * *
45283 TGCCTACTCTAAACGTTGAAGCGCTCGGCGTGACATTAAGGCACA
387 TGCCAACTCTAAACGGTGAAGCGCTCGGCGTGAAAATAA-G---A
45328 TCTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGA-CTAGGTCATCATGCCT
1 --TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATC-AGGTCATC-TGCCT
* *
45392 ACTCCCCTCTGGAAGCGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGTGCT
62 ACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCT
** * * *
45457 CGATGTGACATTAGAGCACA-TCTTGTTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGT
127 CGACCTGACATTAAAGCACATTC-TATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGT
* * **
45521 AAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGCGCTCAGCATGTACTCTGTCTCCCCTGCCT
191 AAGACCAGGTCATCCTGCCTACTCCCCTCTAGAAGCGCTCAGCATGAACTCTGTCAACCCTGCCT
* *
45586 ACTCT-CAACGTTGA-AGTGCTCGGCGTGATAT-TATAACACCCTGCCTACTCCACACGTTAGAG
256 ACCCTAC-ACGTTGATA-TGCTCGGCGTGA-ATCTAGAACACCCTGCCTACTCCACACGTTAGAG
*
45648 CGCCCGACGTAAGATCAAGTCATCCTGCCTACTCCCCACTGGAAGCGCTCGGCATGAACTCTGTC
318 CGCCCGACGTAAGATCAAGTCATCCTGCCTACTCCCCACTGGAAGCGCTCGACATGAACTCTGTC
* * *
45713 CCCCTTCCAACTCTTAACGGTGAAGTGCTCGGCGTGAAAATAAGA
383 CCCCTGCCAACTCTAAACGGTGAAGCGCTCGGCGTGAAAATAAGA
* * * * *
45758 --A--T-ACCCTGCCTACCCCATACATTAGAGCGCCCGGCGTAAGATCAGGTCATCTGGCCTACT
1 TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCT-GCCTACT
* * * * *
45818 CCCCACTGGAAGCGCTCGGCATGAACTCTGTC-CCCCTTCCAACTCTTAATGTTGAAGCGCTCGA
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCTCGA
45882 C
130 C
45883 GAAATTCCTT
Statistics
Matches: 490, Mismatches: 53, Indels: 33
0.85 0.09 0.06
Matches are distributed among these distances:
422 28 0.06
423 79 0.16
424 2 0.00
426 1 0.00
430 1 0.00
433 1 0.00
434 41 0.08
435 331 0.68
436 6 0.01
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (427 bp):
TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCTGCCTACTC
CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCTCGAC
CTGACATTAAAGCACATTCTATTTCACCCGACCTACTCCACACGTTAGAGCGCTCGGCGTAAGAC
CAGGTCATCCTGCCTACTCCCCTCTAGAAGCGCTCAGCATGAACTCTGTCAACCCTGCCTACCCT
ACACGTTGATATGCTCGGCGTGAATCTAGAACACCCTGCCTACTCCACACGTTAGAGCGCCCGAC
GTAAGATCAAGTCATCCTGCCTACTCCCCACTGGAAGCGCTCGACATGAACTCTGTCCCCCTGCC
AACTCTAAACGGTGAAGCGCTCGGCGTGAAAATAAGA
Found at i:46788 original size:32 final size:33
Alignment explanation
Indices: 46717--46788 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
46707 GTTAGACCCT
*
46717 AATATTTTTGGAAAATATAAATTTAACCCTTCA
1 AATATTTTTGGAAAATATAAATTTAAACCTTCA
* * * *
46750 AA-ATTTTT-GAAAATTTTAATTTAAACTTTTA
1 AATATTTTTGGAAAATATAAATTTAAACCTTCA
46781 AATATTTT
1 AATATTTT
46789 AAAGTTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
31 20 0.61
32 11 0.33
33 2 0.06
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (33 bp):
AATATTTTTGGAAAATATAAATTTAAACCTTCA
Found at i:47276 original size:20 final size:21
Alignment explanation
Indices: 47248--47297 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
47238 AACCAACGAA
* *
47248 TTCGTAACACGAA-CTCCAAT
1 TTCGCAACACGAATCGCCAAT
47268 TTCGCAACACGAATTCGCCAAT
1 TTCGCAACACGAA-TCGCCAAT
47290 TTCGCAAC
1 TTCGCAAC
47298 TCAATTACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 12 0.46
22 14 0.54
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.24
Consensus pattern (21 bp):
TTCGCAACACGAATCGCCAAT
Found at i:47477 original size:22 final size:22
Alignment explanation
Indices: 47448--47501 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
47438 CTATATCGGC
*
47448 AATT-GAGTTGCGAAATTGGCG
1 AATTCGAGTTGCGAAATTGGAG
47469 AATTCGAGTTGCGAAATTGGAG
1 AATTCGAGTTGCGAAATTGGAG
*
47491 AATTCAAGTTG
1 AATTCGAGTTG
47502 TGGATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.30
Consensus pattern (22 bp):
AATTCGAGTTGCGAAATTGGAG
Found at i:47591 original size:20 final size:22
Alignment explanation
Indices: 47566--47612 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
47556 TTCGAAATGC
47566 GAATTTGA-AAACT-GAGTTGT
1 GAATTTGAGAAACTCGAGTTGT
* *
47586 GAATTTGAGAAATTCGTGTTGT
1 GAATTTGAGAAACTCGAGTTGT
47608 GAATT
1 GAATT
47613 CCAAATTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 4 0.17
22 11 0.48
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (22 bp):
GAATTTGAGAAACTCGAGTTGT
Found at i:47646 original size:20 final size:21
Alignment explanation
Indices: 47563--47691 Score: 99
Period size: 20 Copynumber: 6.4 Consensus size: 21
47553 GAATTCGAAA
* * *
47563 TGCGAATTTGAAAACT-GAGT
1 TGCGAATTTGGAAATTCGTGT
*
47583 TGTGAATTTGAGAAATTCGTGT
1 TGCGAATTTG-GAAATTCGTGT
* ** *
47605 TGTGAA-TTCCAAATTCGCGT
1 TGCGAATTTGGAAATTCGTGT
*
47625 TGCGAATTTGGAAACT-GTGT
1 TGCGAATTTGGAAATTCGTGT
* * *
47645 TGTGAAATTGG-AGTTCGTGT
1 TGCGAATTTGGAAATTCGTGT
47665 TGCGAATTT-GAAA-TCGTGT
1 TGCGAATTTGGAAATTCGTGT
47684 TGCGAATT
1 TGCGAATT
47692 CGTTGGTTAT
Statistics
Matches: 85, Mismatches: 19, Indels: 11
0.74 0.17 0.10
Matches are distributed among these distances:
19 17 0.20
20 47 0.55
21 12 0.14
22 9 0.11
ACGTcount: A:0.26, C:0.10, G:0.27, T:0.36
Consensus pattern (21 bp):
TGCGAATTTGGAAATTCGTGT
Found at i:57600 original size:18 final size:17
Alignment explanation
Indices: 57572--57614 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
57562 ATATTCGAAT
*
57572 AATTTAATCGAATGTAA
1 AATTTAATCGAATATAA
57589 AATTTGAATCGAATATAA
1 AATTT-AATCGAATATAA
57607 AATCTTAA
1 AAT-TTAA
57615 AATTCATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 16 0.70
19 2 0.09
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (17 bp):
AATTTAATCGAATATAA
Found at i:59364 original size:5 final size:5
Alignment explanation
Indices: 59344--59406 Score: 63
Period size: 5 Copynumber: 12.6 Consensus size: 5
59334 ACATAGATTT
* * * **
59344 AAATA AAACA AAATA ATATA AAATA ACATA AAATA TTATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
**
59394 TTATA AAATA AAA
1 AAATA AAATA AAA
59407 ATATTACTAC
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.25
Consensus pattern (5 bp):
AAATA
Found at i:59374 original size:15 final size:15
Alignment explanation
Indices: 59366--59412 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
59356 ATAATATAAA
*
59366 ATAACATAAAATATT
1 ATAAAATAAAATATT
59381 ATAAAATAAAATATT
1 ATAAAATAAAATATT
59396 ATAAAATAAAAATATT
1 ATAAAAT-AAAATATT
59412 A
1 A
59413 CTACCATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 21 0.70
16 9 0.30
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAAATAAAATATT
Found at i:59406 original size:20 final size:20
Alignment explanation
Indices: 59344--59393 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
59334 ACATAGATTT
*
59344 AAATAAAACAAAATAATATA
1 AAATAAAATAAAATAATATA
* *
59364 AAATAACATAAAATATTATA
1 AAATAAAATAAAATAATATA
59384 AAATAAAATA
1 AAATAAAATA
59394 TTATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (20 bp):
AAATAAAATAAAATAATATA
Found at i:61459 original size:20 final size:20
Alignment explanation
Indices: 61434--61481 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
61424 TGTATAAAAA
* *
61434 ATAATAAAAATATTATTAAT
1 ATAATAAAAATAATAATAAT
*
61454 ATAATAATAATAATAATAAT
1 ATAATAAAAATAATAATAAT
61474 ATAATAAA
1 ATAATAAA
61482 TAATTAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAATAAAAATAATAATAAT
Found at i:61460 original size:3 final size:3
Alignment explanation
Indices: 61433--61485 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
61423 GTGTATAAAA
* * *
61433 AAT AAT AAA AAT ATT ATT AAT -AT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
61479 AAAT AAT
1 -AAT AAT
61486 TAAAACCCGG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:61815 original size:107 final size:107
Alignment explanation
Indices: 61630--61866 Score: 323
Period size: 107 Copynumber: 2.2 Consensus size: 107
61620 GACGACAATG
* * ** ** *
61630 CTCATCCACATTGAAGAGATATGGACGTTTT-TGAAGATGACACTATTCCTTCTCGTTGAGGAAG
1 CTCATCCATATTGAAGAGATTTGGTTGTTTTCAAAAGATGACACTATTCCTTCTCGTTAAGGAAG
*
61694 TCAAGTCAATCCAGAGATAATATGGTGTTGAAGATGACACTA
66 TCAAGTCAATCCAGAGATAACATGGTGTTGAAGATGACACTA
* *
61736 CTCATCTATATTGAAGAGATTTGGTTGTTTTCAAAAGATGACGCTATTCCTTCTCGTTAAGGAAG
1 CTCATCCATATTGAAGAGATTTGGTTGTTTTCAAAAGATGACACTATTCCTTCTCGTTAAGGAAG
** * *
61801 TTGAGTTAATCCAGAGATAACATGGTGTTGAAGATGACACTG
66 TCAAGTCAATCCAGAGATAACATGGTGTTGAAGATGACACTA
* *
61843 CTCATCCATGTTGAAGAGTTTTGG
1 CTCATCCATATTGAAGAGATTTGG
61867 GGCTTTCATA
Statistics
Matches: 113, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
106 26 0.23
107 87 0.77
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (107 bp):
CTCATCCATATTGAAGAGATTTGGTTGTTTTCAAAAGATGACACTATTCCTTCTCGTTAAGGAAG
TCAAGTCAATCCAGAGATAACATGGTGTTGAAGATGACACTA
Found at i:63173 original size:65 final size:65
Alignment explanation
Indices: 63104--63260 Score: 221
Period size: 65 Copynumber: 2.4 Consensus size: 65
63094 GAATAAATTG
* *
63104 AACATCGAATGCATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTC-AGGT-TTTTAT
1 AACATCGAATGCATTTTATGCATCGATGCACA-AGCCATACATCGATGCACTCAAGCTATTTTA-
63166 GAA
64 -AA
*
63169 AACATCGAATGCATTTTATGCATTGATGCACAAGCCATACATCGATGCACTCAAGCTATTTTAAA
1 AACATCGAATGCATTTTATGCATCGATGCACAAGCCATACATCGATGCACTCAAGCTATTTTAAA
**
63234 AACATCGAATGTGTTTTATGCATCGAT
1 AACATCGAATGCATTTTATGCATCGAT
63261 ACACTAAGTG
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
64 1 0.01
65 74 0.89
66 3 0.04
67 5 0.06
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAGCCATACATCGATGCACTCAAGCTATTTTAAA
Done.