Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001327.1 Hibiscus syriacus cultivar Beakdansim tig00002589_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: 69566
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:453 original size:16 final size:16
Alignment explanation
Indices: 432--463 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
422 TAGAACAATA
*
432 ATCATGTGGGGTAGAT
1 ATCATGTGGGATAGAT
448 ATCATGTGGGATAGAT
1 ATCATGTGGGATAGAT
464 TTTTCATTTT
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:0.28, C:0.06, G:0.34, T:0.31
Consensus pattern (16 bp):
ATCATGTGGGATAGAT
Found at i:2428 original size:86 final size:85
Alignment explanation
Indices: 2286--2450 Score: 226
Period size: 86 Copynumber: 1.9 Consensus size: 85
2276 TCCTGAATAT
* * * * *
2286 TTAATTTCAATTAATTAAATAGATTTAATTATTTAAAATAATAAAATCCCTGATATGATTAGGT-
1 TTAAATTCAATTAATTAAATAAATTTAATTATTTAAAATAATAAAAACCCTAATATGACTAGGTA
2350 AACTTGGATATAAAGGATTA
66 AACTTGGATATAAAGGATTA
*
2370 TTAAATTCTAATT-ATTAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAG
1 TTAAATTC-AATTAATTAA-ATAAATTTAATT-ATTTAAAATAATAAAAACCCTAATATGACTAG
*
2434 GTAAACTTGGCTATAAA
63 GTAAACTTGGATATAAA
2451 AGGGTGTATT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
84 12 0.17
85 15 0.21
86 30 0.43
87 13 0.19
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.38
Consensus pattern (85 bp):
TTAAATTCAATTAATTAAATAAATTTAATTATTTAAAATAATAAAAACCCTAATATGACTAGGTA
AACTTGGATATAAAGGATTA
Found at i:9040 original size:19 final size:19
Alignment explanation
Indices: 9007--9043 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
8997 TGAATATTTA
9007 ATTTCAATTAATTAAATAT
1 ATTTCAATTAATTAAATAT
9026 ATTT-AATTAATTTAAATA
1 ATTTCAATTAA-TTAAATA
9044 ATAAATCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTCAATTAATTAAATAT
Found at i:9107 original size:86 final size:89
Alignment explanation
Indices: 9001--9174 Score: 264
Period size: 90 Copynumber: 2.0 Consensus size: 89
8991 TAATCCTGAA
* * * *
9001 TATTTAATTTCAATTAATTAAATAT-ATTTAATTAATTT-AAATAAT-AAATCCATGATATGATT
1 TATTAAATTTCAATTAATTAAATATAATTTAATTAATTTGAAATAATAAAAACCATAATATGACT
9063 AGGGTAACTTGGATATAAAAGGAT
66 AGGGTAACTTGGATATAAAAGGAT
*
9087 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTTCAATTAATTAAATATA-ATTTAATTAATTTGAAATAATAAAAACCATAATATGAC
*
9152 TAGGGTAACTTGGCTATAAAAGG
65 TAGGGTAACTTGGATATAAAAGG
9175 GTGTGTTAGG
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
86 24 0.31
88 13 0.17
89 7 0.09
90 34 0.44
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (89 bp):
TATTAAATTTCAATTAATTAAATATAATTTAATTAATTTGAAATAATAAAAACCATAATATGACT
AGGGTAACTTGGATATAAAAGGAT
Found at i:11732 original size:14 final size:14
Alignment explanation
Indices: 11713--11740 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11703 CATTTTTATC
11713 GTTTTTCCTCCTAA
1 GTTTTTCCTCCTAA
11727 GTTTTTCCTCCTAA
1 GTTTTTCCTCCTAA
11741 AACAAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.07, T:0.50
Consensus pattern (14 bp):
GTTTTTCCTCCTAA
Found at i:12656 original size:165 final size:165
Alignment explanation
Indices: 12379--13816 Score: 1750
Period size: 165 Copynumber: 8.7 Consensus size: 165
12369 TTTTAAAGAA
* * * * * * * *
12379 ATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAAACCTTCGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
*
12444 ACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* *
12509 CCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
131 CCTTCGAGTTCGATTACACTCAGCTTCAAGGGCAC
* * * *
12544 ATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTGGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* * * *
12609 ACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAATCGAGAAGGGCTATTTGCCAAATA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* * *
12674 CCTTCGAGTTTGATTACACTCAAC-TCAAAGGCACC
131 CCTTCGAGTTCGATTACACTCAGCTTCAAGGGCA-C
* * * * * *
12709 AACATTTGA-AGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTTGAC
1 ATCATTT-ACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGAC
* * *
12773 TACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTACCAAAG
65 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
* * *
12838 ACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCAC
130 ACCTTCGAGTTCGATTACACTCAGCTTCAAGGGCAC
* * *
12874 ATCATTTAGAGCATAACTCAAGGCTAGAAGAGTTATCTGTCACC-AAAGTCCTTCGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
** * * *
12938 ACGCTCAGCTATAAGGCACATCATTTTCAACATAGCTTACGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* * *
13003 CCTTCAAGTTCGATTACACTCAACTT-AAAGGCACC
131 CCTTCGAGTTCGATTACACTCAGCTTCAAGGGCA-C
* * * * * * * * *
13038 AACATTTGCAGCATAACTTAAGTCGATAATGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGAT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGAC
*
13102 TATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
65 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
* * *
13167 ACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCAC
130 ACCTTCGAGTTCGATTACACTCAGCTTCAAGGGCAC
*
13203 ATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* * * *
13267 ACACTCAACTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
*
13332 CCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACC
131 CCTTCGAGTTCGATTACACTCAGCTTCAAGGGCA-C
* ** * * * *
13367 AACATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGAC
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGAC
* * *
13431 TACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAAAG
65 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
* *
13496 ACCTTCGAGTTCAATTACACTCAGCTTCGAGGGCAC
130 ACCTTCGAGTTCGATTACACTCAGCTTCAAGGGCAC
* * * * *
13532 ATCATTTACAACATAACTCAATGCTAGAAGGGTTATATGTCATCAAAAAACCTTCGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* * * * *
13597 ATGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAGAA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC---AA
* * * * ** *
13662 AGACCTTTGAGTTCGATTACACTAATCTT-AACGATAT
128 AGACCTTCGAGTTCGATTACACTCAGCTTCAAGGGCAC
* ** * * * * *
13699 ATCATTTGCAATATAACTCAAGGCTAGAAGGGTTGTATGT---TAAAA-ATCGTCGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* * * * *
13760 ACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGAGCTATCT
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT
13817 ATCAACAAAA
Statistics
Matches: 1098, Mismatches: 161, Indels: 30
0.85 0.12 0.02
Matches are distributed among these distances:
163 73 0.07
164 283 0.26
165 656 0.60
166 20 0.02
167 39 0.04
168 27 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (165 bp):
ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
CCTTCGAGTTCGATTACACTCAGCTTCAAGGGCAC
Found at i:13111 original size:329 final size:329
Alignment explanation
Indices: 12381--13816 Score: 2058
Period size: 329 Copynumber: 4.4 Consensus size: 329
12371 TTAAAGAAAT
* * *
12381 CATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAAACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* *
12446 GCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
12511 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGG
131 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGG
* * *
12576 TTATCTGTGACCAAAAGACCTTTGAGTTGGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCA
196 TTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCA
* * * *
12641 TAGCTTAAATCGAGAAGGGCTATTTGCCAAATACCTTCGAGTTTGATTACACTCAACTCAAAGGC
260 TAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGC
12706 ACCAA
325 ACCAA
* *
12711 CATTTGAAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAAGACCTTCGAGTTTGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTA
* *
12775 CGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTACCAAAGAC
65 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* * * *
12840 CCTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTAGAGCATAACTCAAGGCTAGAAGA
130 CCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGG
* * * *
12905 GTTATCTGTCACCAAAGTCCTTCGAGTTCGACTACGCTCAGCTATAAGGCACATCATTTTCAACA
195 GTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCA
* * *
12970 TAGCTTACGTCGAGAAGGGCTATCTGCCAAAGACCTTCAAGTTCGATTACACTCAACTTAAAGGC
260 TAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGC
13035 ACCAA
325 ACCAA
* * * *
13040 CATTTGCAGCATAACTTAAGTCGATAATGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
13105 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * *
13170 CTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGG
131 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGG
* * *
13235 TTATCTGTCACCAAAGACCTTCGAGTTCGACTACACTCAACTCTAAGGCACATCATTTGCAGTAT
196 TTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCAT
*
13300 AGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
261 AGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCA
13365 CCAA
326 CCAA
*
13369 CATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* *
13434 GCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * *
13499 TTCGAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAATGCTAGAAGGG
131 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGG
* * * * * * *
13564 TTATATGTCATCAAAAAACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTGTAGCA
196 TTATCTGTCA-CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCA
* * * *
13629 TAACTTAAGTCGAGAAGGGTTATCTGCCAAGAAAGACCTTTGAGTTCGATTACACT-AATCTTAA
260 TAGCTTAAGTCGAGAAGGGCTATCTGCC---AAAGACCTTCGAGTTCGATTACACTCAA-CTCAA
* ** * *
13693 CGATA-TAT
321 AGGCACCAA
** * * * * * ** * *
13701 CATTTGCAATATAACTCAAGGCTAGAAGGGTTGTATG-TTA--AAA-ATCGTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * * *
13762 GCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGAGCTATCT
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCT
13817 ATCAACAAAA
Statistics
Matches: 994, Mismatches: 105, Indels: 16
0.89 0.09 0.01
Matches are distributed among these distances:
328 63 0.06
329 605 0.61
330 264 0.27
331 1 0.00
332 31 0.03
333 30 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (329 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
CTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGG
TTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCAT
AGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCA
CCAA
Found at i:13415 original size:494 final size:491
Alignment explanation
Indices: 12381--13817 Score: 1816
Period size: 494 Copynumber: 2.9 Consensus size: 491
12371 TTAAAGAAAT
* * *
12381 CATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAAACCTTCGAGTTCGACTAC
1 CATTTG-AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
12446 GCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* *
12511 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGG
130 TTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGTCTAGAAGGG
** * * * *
12576 TTATCTGTGACCAAAAGACCTTTGAGTTGGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCA
195 TTATCTGCAACC-AAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCA
* * * *
12641 TAGCTTAAATCGAGAAGGGCTATTTGCCAAATACCTTCGAGTTTGATTACACTCAAC-TCAAAGG
259 TAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTTCAAAGG
* * * * * *
12705 CACCAACATTTGAAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTT
324 CA-CATCATTT-AAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTC
* *
12770 GACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTACCA
386 GACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCA
* * * *
12835 AAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACAT
451 AAGACCCTCGAGTTCGATTACACTCAGCTTCAAAGGCACAA
* * * * * *
12876 CATTTAGAGCATAACTCAAGGCTAGAAGAGTTATCTGTC-ACCAAAGTCCTTCGAGTTCGACTAC
1 CATTT-GAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
** * * *
12940 GCTCAGCTATAAGGCACATCATTTTCAACATAGCTTACGTCGAGAAGGGCTATCTGCCAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * * * * * * * * * *
13005 TTCAAGTTCGATTACACTCAACTT-AAAGGCACCAACATTTGCAGCATAACTTAAGTCGATAATG
130 TTCGAGTTCGATTACACTCAGCTTCGAGGGCA-CATCATTTACAACATAACTCAAGTCTAGAAGG
*
13069 GTTATCTGCCAACCAAAGACCTTCGAGTTCGATTATGCTCAGCTCCAAGGCACATCATTTGCAGC
194 GTTATCTG-CAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGC
* * * * *
13134 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGG
258 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTTCAAAG
13199 GCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCG
323 GCACATCATTTA-AGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCG
* * * * *
13264 ACTACACTCAACTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
387 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAA
*
13329 AGACCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACCAA
452 AGACCCTCGAGTTCGATTACACTCAGCTTCAAAGGCA-CAA
13369 CATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTG-AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
13434 GCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
*
13499 TTCGAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAA-TGCTAGAAGG
130 TTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGT-CTAGAAGG
* * * * * *
13563 GTTATATGTCATCAAAAAACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTGTAGC
194 GTTATCTG-CAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGC
* * *
13628 ATAACTTAAGTCGAGAAGGGTTATCTGCCAAGAAAGACCTTTGAGTTCGATTACACT-AATCTT-
258 ATAGCTTAAGTCGAGAAGGGCTATCTGCC---AAAGACCTTCGAGTTCGATTACACTCAA-CTTC
* ** * * * * * * *
13691 AACGATATATCATTTGCAA-TATAACTCAAGGCTAGAAGGGTTGTATGTTA--AAA-ATCGTCGA
319 AAAGGCACATCATTT--AAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGA
* * * * *
13752 GTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGAGCTATCT
382 GTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT
13817 A
447 A
13818 TCAACAAAAT
Statistics
Matches: 803, Mismatches: 123, Indels: 34
0.84 0.13 0.04
Matches are distributed among these distances:
492 8 0.01
493 202 0.25
494 481 0.60
495 46 0.06
496 39 0.05
497 26 0.03
498 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (491 bp):
CATTTGAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCT
TCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGTCTAGAAGGGT
TATCTGCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATA
GCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTTCAAAGGCA
CATCATTTAAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGAC
CCTCGAGTTCGATTACACTCAGCTTCAAAGGCACAA
Found at i:17147 original size:26 final size:26
Alignment explanation
Indices: 17110--17176 Score: 107
Period size: 26 Copynumber: 2.5 Consensus size: 26
17100 TAGTAGACAT
17110 CAATATTGAAGAACATAACTGAAAATG
1 CAAT-TTGAAGAACATAACTGAAAATG
* *
17137 CAATTTGAAGAACATAATTGAAATTG
1 CAATTTGAAGAACATAACTGAAAATG
17163 CAATTTGAAGAACA
1 CAATTTGAAGAACA
17177 AAGAGGTATG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 34 0.89
27 4 0.11
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.25
Consensus pattern (26 bp):
CAATTTGAAGAACATAACTGAAAATG
Found at i:21697 original size:24 final size:23
Alignment explanation
Indices: 21666--21724 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 23
21656 AAATGAGTAA
*
21666 AATATATAAAAAAGTAAAAGCAT
1 AATATATAAAAAAGTAAAAGAAT
* *
21689 ATATATATATAAAAGTAAAATAAT
1 A-ATATATAAAAAAGTAAAAGAAT
21713 AATA-ATAAAAAA
1 AATATATAAAAAA
21725 AAGAAAATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 7 0.23
23 4 0.13
24 20 0.65
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (23 bp):
AATATATAAAAAAGTAAAAGAAT
Found at i:21726 original size:24 final size:24
Alignment explanation
Indices: 21667--21732 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
21657 AATGAGTAAA
* **
21667 ATATATAAAAAAGTAAAAGCATAT
1 ATATAAAAAAAAGTAAAATAATAT
* *
21691 ATATATATAAAAGTAAAATAATA-
1 ATATAAAAAAAAGTAAAATAATAT
21714 ATAATAAAAAAAAG-AAAAT
1 AT-ATAAAAAAAAGTAAAAT
21733 CAAAAGTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 7 0.19
24 29 0.81
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (24 bp):
ATATAAAAAAAAGTAAAATAATAT
Found at i:23147 original size:105 final size:105
Alignment explanation
Indices: 22840--23502 Score: 892
Period size: 105 Copynumber: 6.3 Consensus size: 105
22830 CATTGTTCCA
* **
22840 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAA-TTGTTTGTTGACA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-A-TTGGAAAGTTG-TTGTTGACA
* * * *
22903 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
63 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
22946 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T-GAAA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
*
23006 AGCGGTCCCTTCGACGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
23046 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
*
23111 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
23151 AGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTATGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
23216 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * * *
23256 AGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTAACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTG-TTGTTGACAA
23321 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
23363 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAGTTATTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGA-AAGTT-GTTGTTGACAA
* * * * *
23427 TCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
23469 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
23503 CGCGGATGGC
Statistics
Matches: 503, Mismatches: 41, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
100 84 0.17
101 1 0.00
102 7 0.01
103 4 0.01
104 2 0.00
105 193 0.38
106 95 0.19
107 95 0.19
109 22 0.04
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:23398 original size:317 final size:312
Alignment explanation
Indices: 22840--23502 Score: 929
Period size: 317 Copynumber: 2.1 Consensus size: 312
22830 CATTGTTCCA
* *
22840 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCATCCGTTGTGAAGTTGAAATTGGCTATGGAACCGGGAAATTGTTTGTTGACAAC
* * *
22905 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
* * *
22970 TTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGACGTGAAGTTGAACTT
131 TTGAAATTGAATCTGAATGAAATTTTATTAACAACCAGCGGTCCCTTCGACGTGAAGTTGAACTT
*
23035 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTG-GAAAGTT-
196 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTA
*
23098 GTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
260 GTTGTTGACAAGCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* ** *
23151 AGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTAT-GAGATTGGGAAGTTG-TTGTTGACAA
1 AGTCCAATATCATCCGTTGTGAAGTTGAAATTGGCTATGGA-ACCGGGAAATTGTTTGTTGACAA
* * *
23214 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGCTGTGAA
65 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
** *
23279 GTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAG
130 GTTGAAATTGAATCTG-AA-T--G-AAA-T-TTTATTAACAACCAGCGGTCCCTTCGACGTGAAG
23344 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
188 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* * * ** *
23409 GAAGTTATTTGTTGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
253 GAAGTTAGTTGTTGACAAGCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* * *
23469 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCATCCGTTGTGAAGTTGAAAT
23503 CGCGGATGGC
Statistics
Matches: 309, Mismatches: 30, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
310 85 0.28
311 46 0.15
312 1 0.00
314 1 0.00
315 3 0.01
316 1 0.00
317 98 0.32
318 50 0.16
319 3 0.01
321 21 0.07
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (312 bp):
AGTCCAATATCATCCGTTGTGAAGTTGAAATTGGCTATGGAACCGGGAAATTGTTTGTTGACAAC
CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
TTGAAATTGAATCTGAATGAAATTTTATTAACAACCAGCGGTCCCTTCGACGTGAAGTTGAACTT
GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTAG
TTGTTGACAAGCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
Found at i:24227 original size:36 final size:35
Alignment explanation
Indices: 24178--24418 Score: 185
Period size: 36 Copynumber: 6.9 Consensus size: 35
24168 GATTTTGTGT
* *
24178 TTCAAGAGTAACTGTCTCAAGATAGACGAAAATTGA
1 TTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTGA
24214 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTGA
* * * *
24249 GTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGT
1 -TT-CAAGAGAAACTGTCTCAAGAGAGAC-AAAATTGA
* * ** *
24287 TTCAA-AGAAAACATAT-TC---A-A-A-TATTTTGT
1 TTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATTGA
* * * *
24316 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTGA
*
24352 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTGA
*
24387 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTCAAGAGAAACTGTCTCAAGAGAGACAAAA
24419 CTCTTCTAGT
Statistics
Matches: 168, Mismatches: 20, Indels: 34
0.76 0.09 0.15
Matches are distributed among these distances:
28 2 0.01
29 17 0.10
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 12 0.07
36 99 0.59
37 29 0.17
38 3 0.02
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (35 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTGA
Found at i:24440 original size:35 final size:36
Alignment explanation
Indices: 24316--24452 Score: 127
Period size: 36 Copynumber: 3.8 Consensus size: 36
24306 AATATTTTGT
* * * * **
24316 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTAC
* *
24352 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTAC
*
24388 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTAC
* * *
24422 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
24453 TCTTGTTTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
34 5 0.06
35 23 0.26
36 58 0.67
37 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTAC
Found at i:25349 original size:22 final size:22
Alignment explanation
Indices: 25324--25374 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
25314 TTGTGTTTGG
*
25324 TCAAGGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
25346 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
25368 TCAAAGG
1 TCAAAGG
25375 ATTGATGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:26030 original size:34 final size:33
Alignment explanation
Indices: 25983--26068 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 33
25973 TTTTTGTCCC
**
25983 ATTTTTTTATTTTTGTTC-TTTCTTTTTTGTTCTT
1 ATTTTTTCCTTTTTGTTCTTTTC-TTTTT-TTCTT
26017 ATTTTTTCCTTTTTGCTTCTTTTCTTTTTTTCTT
1 ATTTTTTCCTTTTTG-TTCTTTTCTTTTTTTCTT
*
26051 -TTTTTCCCTTTTTGTTCT
1 ATTTTTTCCTTTTTGTTCT
26069 GATTGAATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
32 4 0.09
33 13 0.28
34 18 0.38
35 8 0.17
36 4 0.09
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (33 bp):
ATTTTTTCCTTTTTGTTCTTTTCTTTTTTTCTT
Found at i:26044 original size:21 final size:20
Alignment explanation
Indices: 26001--26068 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 20
25991 ATTTTTGTTC
*
26001 TTTCTTTTTTGTTCTTATTT
1 TTTCCTTTTTGTTCTTATTT
*
26021 TTTCCTTTTTG--C-T-TCT
1 TTTCCTTTTTGTTCTTATTT
26037 TTT-CTTTTT-TTCTT-TTT
1 TTTCCTTTTTGTTCTTATTT
*
26054 TTCCCTTTTTGTTCT
1 TTTCCTTTTTGTTCT
26069 GATTGAATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
15 6 0.15
16 6 0.15
17 6 0.15
18 7 0.18
19 4 0.10
20 10 0.26
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (20 bp):
TTTCCTTTTTGTTCTTATTT
Found at i:26045 original size:16 final size:16
Alignment explanation
Indices: 26020--26068 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
26010 TGTTCTTATT
26020 TTTTCCTTTTTGCTTC
1 TTTTCCTTTTTGCTTC
* * *
26036 TTTTCTTTTTTTCTTT
1 TTTTCCTTTTTGCTTC
26052 TTTTCCCTTTTTG-TTC
1 TTTT-CCTTTTTGCTTC
26068 T
1 T
26069 GATTGAATCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTTCCTTTTTGCTTC
Found at i:26063 original size:10 final size:8
Alignment explanation
Indices: 26018--26056 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
26008 TTTGTTCTTA
*
26018 TTTTTTCC
1 TTTTTTCT
*
26026 TTTTTGCT
1 TTTTTTCT
*
26034 TCTTTTCT
1 TTTTTTCT
26042 TTTTTTCT
1 TTTTTTCT
26050 TTTTTTC
1 TTTTTTC
26057 CCTTTTTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (8 bp):
TTTTTTCT
Found at i:33414 original size:102 final size:101
Alignment explanation
Indices: 33030--33411 Score: 396
Period size: 102 Copynumber: 3.8 Consensus size: 101
33020 TTATGAACTA
* * * *
33030 TTAAGATTATATATTTGAAACCTTTTTAATAAAGAAAAAGTAAGACAAAACAGATTTATATGTAT
1 TTAAG-TTATATATTTGAAACCTTTTTTATTATGAAAATGTAAGACAAAACAGATTTATATGTAT
** * * * * *
33095 AACAATACACATAACACCTTTTTACATTGACAA-TTGT
65 AACAATACAGGTAGCACCTTTTTAAATGGTCAACAT-T
* * * * * *
33132 TTACGTTATATGTTTGAAA-C-TTTTTGTTATGAAAATTTAAGA-AAAATAGATTTACATGTATA
1 TTAAGTTATATATTTGAAACCTTTTTTATTATGAAAATGTAAGACAAAACAGATTTATATGTATA
* *
33194 ACAATAAAGGTAGCATCTTTTTAACATGGTCAACATT
66 ACAATACAGGTAGCACCTTTTTAA-ATGGTCAACATT
** * * * * *
33231 TTAAGTTATATGCTTGATACCTTTTTTATTATGAAAATGCAAGATAAACCAGATTTATATATATA
1 TTAAGTTATATATTTGAAACCTTTTTTATTATGAAAATGTAAGACAAAACAGATTTATATGTATA
* *
33296 ACAATACAGGTAGCGCCTTTTTGAAATGGTCAACCTT
66 ACAATACAGGTAGCACCTTTTT-AAATGGTCAACATT
** *
33333 TTAAGTTATATATTTTTAACTTTTTTTATTATGAAAATGTAAGACAAAACATG-TTTATATGTAT
1 TTAAGTTATATATTTGAAACCTTTTTTATTATGAAAATGTAAGACAAAACA-GATTTATATGTAT
*
33397 AACAATACATGTAGC
65 AACAATACAGGTAGC
33412 GCCACTCACA
Statistics
Matches: 229, Mismatches: 44, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
98 36 0.16
99 39 0.17
100 3 0.01
101 32 0.14
102 116 0.51
103 3 0.01
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.38
Consensus pattern (101 bp):
TTAAGTTATATATTTGAAACCTTTTTTATTATGAAAATGTAAGACAAAACAGATTTATATGTATA
ACAATACAGGTAGCACCTTTTTAAATGGTCAACATT
Found at i:33852 original size:22 final size:24
Alignment explanation
Indices: 33817--33863 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
33807 AATTTAATGT
33817 ATTATGATGTATTATCTT-TTAGG
1 ATTATGATGTATTATCTTATTAGG
* *
33840 ATTA-GATTTATTATTTTATTAGG
1 ATTATGATGTATTATCTTATTAGG
33863 A
1 A
33864 ATTTAACTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (24 bp):
ATTATGATGTATTATCTTATTAGG
Found at i:34374 original size:6 final size:6
Alignment explanation
Indices: 34365--34391 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34355 CAATTCCATT
34365 TTCATA TTCATA TTCATA TTCATA TTC
1 TTCATA TTCATA TTCATA TTCATA TTC
34392 CTTATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCATA
Found at i:44355 original size:20 final size:20
Alignment explanation
Indices: 44330--44367 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
44320 AAGGAATGCA
44330 TAAATATAAATATAATTTTT
1 TAAATATAAATATAATTTTT
*
44350 TAAATATAAATATGATTT
1 TAAATATAAATATAATTT
44368 AATGATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TAAATATAAATATAATTTTT
Found at i:47456 original size:13 final size:13
Alignment explanation
Indices: 47438--47471 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
47428 AAATATGGTC
47438 TTGGAAAGAGGTT
1 TTGGAAAGAGGTT
47451 TTGGAAAGAGGTT
1 TTGGAAAGAGGTT
47464 TTGGAAAG
1 TTGGAAAG
47472 CCATCAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (13 bp):
TTGGAAAGAGGTT
Found at i:52627 original size:7 final size:7
Alignment explanation
Indices: 52611--52825 Score: 414
Period size: 7 Copynumber: 30.7 Consensus size: 7
52601 ATTCTCCAGA
52611 CTTT-TC
1 CTTTCTC
52617 CTTTCTC
1 CTTTCTC
52624 CTTTCTC
1 CTTTCTC
52631 CTTTCTC
1 CTTTCTC
52638 CTTTCTC
1 CTTTCTC
52645 CTTTCTC
1 CTTTCTC
52652 CTTTCTC
1 CTTTCTC
52659 CTTTCTC
1 CTTTCTC
52666 CTTTCTC
1 CTTTCTC
52673 CTTTCTC
1 CTTTCTC
52680 CTTTCTC
1 CTTTCTC
52687 CTTTCTC
1 CTTTCTC
52694 CTTTCTC
1 CTTTCTC
52701 CTTTCTC
1 CTTTCTC
52708 CTTTCTC
1 CTTTCTC
52715 CTTTCTC
1 CTTTCTC
52722 CTTTCTC
1 CTTTCTC
52729 CTTTCTC
1 CTTTCTC
52736 CTTTCTC
1 CTTTCTC
52743 CTTTCTC
1 CTTTCTC
52750 CTTTCTC
1 CTTTCTC
52757 CTTTCTC
1 CTTTCTC
52764 CTTTCTC
1 CTTTCTC
52771 CTTTCTC
1 CTTTCTC
52778 CTTTCTC
1 CTTTCTC
52785 CTTTCTC
1 CTTTCTC
52792 CTTTCTC
1 CTTTCTC
52799 CTTTCTC
1 CTTTCTC
52806 CTTTCTC
1 CTTTCTC
52813 CTTTCTC
1 CTTTCTC
52820 CATTTC
1 C-TTTC
52826 CACGTGTTTC
Statistics
Matches: 207, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
6 4 0.02
7 199 0.96
8 4 0.02
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.57
Consensus pattern (7 bp):
CTTTCTC
Found at i:66156 original size:25 final size:25
Alignment explanation
Indices: 66114--66171 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
66104 AATATTATAT
* * *
66114 TAAAATATTAAATGATATGAGATTA
1 TAAAATTTTAAATGATATAAAATTA
66139 TAAAATTTTAAA-GAATATAAAATTA
1 TAAAATTTTAAATG-ATATAAAATTA
*
66164 AAAAATTT
1 TAAAATTT
66172 GAATAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (25 bp):
TAAAATTTTAAATGATATAAAATTA
Found at i:68531 original size:25 final size:25
Alignment explanation
Indices: 68503--68553 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
68493 CAATTAATAG
68503 ATTAAATGACGTGATATTTTGGTAT
1 ATTAAATGACGTGATATTTTGGTAT
68528 ATTAAATGACGTGATATTTTGGTAT
1 ATTAAATGACGTGATATTTTGGTAT
68553 A
1 A
68554 ATTACACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (25 bp):
ATTAAATGACGTGATATTTTGGTAT
Done.