Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009176.1 Hibiscus syriacus cultivar Beakdansim tig00112740_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: 348284
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:187912 original size:18 final size:19
Alignment explanation
Indices: 187876--187912 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
187866 TTGAAGACTA
187876 GTGGTTGAAAATGTATAAGT
1 GTGGTTGAAAATG-ATAAGT
187896 GTGGTTGAAAATG-TAAG
1 GTGGTTGAAAATGATAAG
187913 AGTTTCATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (19 bp):
GTGGTTGAAAATGATAAGT
Found at i:188312 original size:20 final size:20
Alignment explanation
Indices: 188287--188325 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
188277 TGAAGACGAC
188287 TGGTTGAAAATGTATAAGTG
1 TGGTTGAAAATGTATAAGTG
188307 TGGTTGAAAATGTATAAGT
1 TGGTTGAAAATGTATAAGT
188326 TTCATGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (20 bp):
TGGTTGAAAATGTATAAGTG
Found at i:194786 original size:13 final size:15
Alignment explanation
Indices: 194741--194781 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
194731 TTTAATTAAT
*
194741 AAAAATAATATTTTTA
1 AAAAAT-ATATTATTA
*
194757 ATAAATATATTATTA
1 AAAAATATATTATTA
194772 AAAAATATAT
1 AAAAATATAT
194782 ATAAACTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAATATATTATTA
Found at i:201680 original size:18 final size:18
Alignment explanation
Indices: 201657--201715 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
201647 CGCAAATTCG
201657 CGTTGCGATTTTCCATTT
1 CGTTGCGATTTTCCATTT
* * *
201675 CGTTGCGATAGTGTACAGTGT
1 CGTTGCGAT--TTTCCA-TTT
201696 CGTTGCGATTTTCCATTT
1 CGTTGCGATTTTCCATTT
201714 CG
1 CG
201716 CGTTGCGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
18 13 0.41
19 4 0.12
20 4 0.12
21 11 0.34
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (18 bp):
CGTTGCGATTTTCCATTT
Found at i:201872 original size:21 final size:21
Alignment explanation
Indices: 201846--201965 Score: 85
Period size: 21 Copynumber: 5.9 Consensus size: 21
201836 TTTTTAATTT
*
201846 ACTGTAGATTATCGCAACGAC
1 ACTGTAGACTATCGCAACGAC
201867 ACTGT--ACTATCGCAACG-C
1 ACTGTAGACTATCGCAACGAC
* **
201885 GA--GATGGAAAATCGCAACGAC
1 -ACTG-TAGACTATCGCAACGAC
201906 ACTGTAGACTATCGCAACG-C
1 ACTGTAGACTATCGCAACGAC
* **
201926 GAAATG--GAAAATCGCAACGAC
1 --ACTGTAGACTATCGCAACGAC
201947 ACTGTAGACTATCGCAACG
1 ACTGTAGACTATCGCAACG
201966 CGATTTTCAA
Statistics
Matches: 75, Mismatches: 12, Indels: 24
0.68 0.11 0.22
Matches are distributed among these distances:
17 1 0.01
18 2 0.03
19 15 0.20
20 23 0.31
21 30 0.40
22 4 0.05
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (21 bp):
ACTGTAGACTATCGCAACGAC
Found at i:201900 original size:20 final size:20
Alignment explanation
Indices: 201875--201944 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
201865 ACACTGTACT
201875 ATCGCAACGCGAGATGGAAA
1 ATCGCAACGCGAGATGGAAA
* **
201895 ATCGCAACGAC-ACTG-TAGACT
1 ATCGCAACG-CGA--GATGGAAA
*
201916 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAGATGGAAA
201936 ATCGCAACG
1 ATCGCAACG
201945 ACACTGTAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
20 23 0.61
21 14 0.37
22 1 0.03
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAGATGGAAA
Found at i:201933 original size:41 final size:41
Alignment explanation
Indices: 201856--201968 Score: 203
Period size: 41 Copynumber: 2.8 Consensus size: 41
201846 ACTGTAGATT
*
201856 ATCGCAACGACACTGT--ACTATCGCAACGCGAGATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
201895 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
201936 ATCGCAACGACACTGTAGACTATCGCAACGCGA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGA
201969 TTTTCAACTA
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
39 16 0.23
41 55 0.77
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.15
Consensus pattern (41 bp):
ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
Found at i:201997 original size:21 final size:21
Alignment explanation
Indices: 201913--201997 Score: 68
Period size: 21 Copynumber: 4.1 Consensus size: 21
201903 GACACTGTAG
*
201913 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * *
201934 A-AATCGCAA--CGACACTGTA
1 ACTATCGCAACGCGA-AATGCA
** *
201953 GACTATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGCA
201975 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
201996 AC
1 AC
201998 GTGAATTTGC
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
18 3 0.06
19 4 0.08
20 8 0.17
21 28 0.58
22 2 0.04
23 3 0.06
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:207875 original size:60 final size:60
Alignment explanation
Indices: 207797--207919 Score: 187
Period size: 60 Copynumber: 2.0 Consensus size: 60
207787 CATTTCGTAT
* * *
207797 TTTTAATAGTCGTGGTACTCAACAAAGCAACATCCTATAGTCG-AGTGATTATTTTGTA-AC
1 TTTTAATAATCGGGGTACTCAACAAAACAACATCCTATAGTCGAAG-GATTA-TTTGTATAC
207857 TTTTAATAATCGGGGTACTCAACAAAACAACATCCTATAGTCGAAGGATTATTTGTATAC
1 TTTTAATAATCGGGGTACTCAACAAAACAACATCCTATAGTCGAAGGATTATTTGTATAC
207917 TTT
1 TTT
207920 ACCCAAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
59 6 0.10
60 50 0.86
61 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (60 bp):
TTTTAATAATCGGGGTACTCAACAAAACAACATCCTATAGTCGAAGGATTATTTGTATAC
Found at i:208451 original size:21 final size:20
Alignment explanation
Indices: 208427--208479 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 20
208417 CAAAAATATT
208427 TATTTTAGATAACGAAATTAA
1 TATTTTAGATAACGAAA-TAA
*
208448 TATTTTCGATAA--AAATAA
1 TATTTTAGATAACGAAATAA
*
208466 TATTTTAAATAACG
1 TATTTTAGATAACG
208480 CTATACTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.48
19 3 0.11
21 11 0.41
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (20 bp):
TATTTTAGATAACGAAATAA
Found at i:209637 original size:19 final size:20
Alignment explanation
Indices: 209598--209649 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
209588 GTTCAATTCA
209598 GGTCAACCTTTAGATTTTTC
1 GGTCAACCTTTAGATTTTTC
*
209618 GGTCATCCTTTAGA-TTTTC
1 GGTCAACCTTTAGATTTTTC
209637 GGATCAACCTTTA
1 GG-TCAACCTTTA
209650 AAATTTTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (20 bp):
GGTCAACCTTTAGATTTTTC
Found at i:226078 original size:21 final size:22
Alignment explanation
Indices: 226036--226078 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
226026 TTTAAACATC
* *
226036 TTAGATTTTATTATTTATTTAA
1 TTAGAATTTATTATTTACTTAA
*
226058 TTAGAATTT-TTATTTGCTTAA
1 TTAGAATTTATTATTTACTTAA
226079 AATTTCGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (22 bp):
TTAGAATTTATTATTTACTTAA
Found at i:232803 original size:31 final size:32
Alignment explanation
Indices: 232759--232822 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
232749 ATAGATGGAC
*
232759 TTATTGCGACTTTT-TTAAAAAAACGCCACTA
1 TTATTACGACTTTTATTAAAAAAACGCCACTA
* * *
232790 TTATTACGGCTTTTATTGAAAAAACGCTACTA
1 TTATTACGACTTTTATTAAAAAAACGCCACTA
232822 T
1 T
232823 AGATGGACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (32 bp):
TTATTACGACTTTTATTAAAAAAACGCCACTA
Found at i:233020 original size:50 final size:50
Alignment explanation
Indices: 232944--233170 Score: 402
Period size: 50 Copynumber: 4.5 Consensus size: 50
232934 ACCTAGCCTG
232944 ATGTCAGCAAGGGTGACTGA-TCGCCCATATAGAGATTGCATGTCATGATA
1 ATGTCAGCAAGGGTGACTGAGT-GCCCATATAGAGATTGCATGTCATGATA
*
232994 ATGTCAGCAAGGGTGACTGAGTGCCCATTTAGAGATTGCATGTCATGATA
1 ATGTCAGCAAGGGTGACTGAGTGCCCATATAGAGATTGCATGTCATGATA
*
233044 ATGTCAGCAAGGGTGACTGAGCGCCCATATAGAGATTGCATGTCATGATA
1 ATGTCAGCAAGGGTGACTGAGTGCCCATATAGAGATTGCATGTCATGATA
233094 ATGTCAGCAAGGGTGACTGAGTGCCCATATAGAGATTGCATGTCATGATA
1 ATGTCAGCAAGGGTGACTGAGTGCCCATATAGAGATTGCATGTCATGATA
**
233144 ATGTCAATAAGGGTGACTGAGTGCCCA
1 ATGTCAGCAAGGGTGACTGAGTGCCCA
233171 ACCAGGTAGG
Statistics
Matches: 170, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
50 169 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (50 bp):
ATGTCAGCAAGGGTGACTGAGTGCCCATATAGAGATTGCATGTCATGATA
Found at i:241382 original size:14 final size:14
Alignment explanation
Indices: 241363--241406 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
241353 CGATAATCTA
241363 TTTGTTTATGTTTG
1 TTTGTTTATGTTTG
**
241377 TTTGTTTATGTTCA
1 TTTGTTTATGTTTG
241391 TTTGTTTATGTTTG
1 TTTGTTTATGTTTG
241405 TT
1 TT
241407 CATGTTCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.09, C:0.02, G:0.18, T:0.70
Consensus pattern (14 bp):
TTTGTTTATGTTTG
Found at i:241403 original size:24 final size:24
Alignment explanation
Indices: 241375--241437 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
241365 TGTTTATGTT
*
241375 TGTTTGTTTATGTTCATTTGTTTA
1 TGTTTGTTTATGTTCATTCGTTTA
*
241399 TGTTTGTTCATGTTCATTCGTTTA
1 TGTTTGTTTATGTTCATTCGTTTA
* *
241423 TATTCGTTTATGTTC
1 TGTTTGTTTATGTTC
241438 TCCAGACCCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.13, C:0.10, G:0.16, T:0.62
Consensus pattern (24 bp):
TGTTTGTTTATGTTCATTCGTTTA
Found at i:241846 original size:2 final size:2
Alignment explanation
Indices: 241839--241871 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
241829 TTTACATGCC
241839 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
241872 CGAGAGTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:266920 original size:31 final size:31
Alignment explanation
Indices: 266885--266973 Score: 101
Period size: 30 Copynumber: 2.9 Consensus size: 31
266875 CATACCTAAC
* *
266885 GTTTACCTTTTGTTTTATTTTAGTACCCGGA-
1 GTTTACCTTTTGTTTCATTTTAGTACCC-CAT
*
266916 GTTTA-CTTTTGTTTCATTTTAATACCCCATT
1 GTTTACCTTTTGTTTCATTTTAGTACCCCA-T
* *
266947 GTTAACTTTTTGTTTCATTTTAGTACC
1 GTTTACCTTTTGTTTCATTTTAGTACC
266974 TAAATTTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 1 0.02
30 20 0.41
31 9 0.18
32 19 0.39
ACGTcount: A:0.18, C:0.17, G:0.11, T:0.54
Consensus pattern (31 bp):
GTTTACCTTTTGTTTCATTTTAGTACCCCAT
Found at i:267302 original size:21 final size:21
Alignment explanation
Indices: 267259--267342 Score: 107
Period size: 21 Copynumber: 4.0 Consensus size: 21
267249 TAATAGTGGA
* *
267259 TTGTTACATAAATAC-AAATAC
1 TTGTTACATTAATACTATA-AC
* **
267280 TTGTTACGTTAATGTTATAAC
1 TTGTTACATTAATACTATAAC
267301 TTGTTACATTAATACTATAAC
1 TTGTTACATTAATACTATAAC
267322 TTGTTACATTAATACTATAAC
1 TTGTTACATTAATACTATAAC
267343 GATCAACAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
21 52 0.96
22 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (21 bp):
TTGTTACATTAATACTATAAC
Found at i:268234 original size:18 final size:18
Alignment explanation
Indices: 268211--268246 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
268201 CAAACCCCGT
268211 GGAAAGCGGCGCGTGTCC
1 GGAAAGCGGCGCGTGTCC
*
268229 GGAAAGTGGCGCGTGTCC
1 GGAAAGCGGCGCGTGTCC
268247 CTATACACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.25, G:0.44, T:0.14
Consensus pattern (18 bp):
GGAAAGCGGCGCGTGTCC
Found at i:268721 original size:4 final size:4
Alignment explanation
Indices: 268712--268749 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
268702 AGTAATTTTG
* *
268712 ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGC ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
268750 TTGGCTTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (4 bp):
ATGT
Found at i:269010 original size:4 final size:4
Alignment explanation
Indices: 269003--269030 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
268993 AAATGTATGT
269003 ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG
269031 CTTAAGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
ATGG
Found at i:269013 original size:99 final size:100
Alignment explanation
Indices: 268823--269030 Score: 296
Period size: 99 Copynumber: 2.1 Consensus size: 100
268813 ATTGGTAGTT
* * *
268823 CCTGGATGGTGTCTACTATGAGAAGAAAGAGCTAGTAGAATTCACCACATGTTTTAATTGCATTG
1 CCTGGATGGTGTCTACTATAAGAAGAAAGAGCTAGTAGAATT--CCACATGTTTGAATTCCATTG
268888 TTTTGAAAATGTATGGATGGATGGATGGAAGGATGGA
64 TTTTGAAAATGTATGGATGGATGGATGGAAGGATGGA
* * * *
268925 CCTGGCTGGTGTTTACTATAAGAAGACAGAGCTAGTAGAATT-CACTTGTTTGAATTCCATTGTT
1 CCTGGATGGTGTCTACTATAAGAAGAAAGAGCTAGTAGAATTCCACATGTTTGAATTCCATTGTT
* *
268989 TTGAAAATGTATGTATGGATGGATGGATGGATGGA
66 TTGAAAATGTATGGATGGATGGATGGAAGGATGGA
269024 --TGGATGG
1 CCTGGATGG
269031 CTTAAGAGAT
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
97 6 0.06
99 52 0.54
102 38 0.40
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (100 bp):
CCTGGATGGTGTCTACTATAAGAAGAAAGAGCTAGTAGAATTCCACATGTTTGAATTCCATTGTT
TTGAAAATGTATGGATGGATGGATGGAAGGATGGA
Found at i:285236 original size:28 final size:28
Alignment explanation
Indices: 285204--285269 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
285194 TTAGTTTTAT
* *
285204 TATATAGTTGGCCCTACCGCCTGATTGA
1 TATATAGTCGGCCATACCGCCTGATTGA
* **
285232 TATATGGTCGGTTATACCGCCTGATTGA
1 TATATAGTCGGCCATACCGCCTGATTGA
*
285260 TATATGGTCG
1 TATATAGTCG
285270 ATCCTGCCAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (28 bp):
TATATAGTCGGCCATACCGCCTGATTGA
Found at i:291356 original size:15 final size:15
Alignment explanation
Indices: 291333--291364 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
291323 TAGAATATTG
291333 TTTTACTTTTGTTTA
1 TTTTACTTTTGTTTA
*
291348 TTTTTCTTTTGTTTA
1 TTTTACTTTTGTTTA
291363 TT
1 TT
291365 ATTGGTGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTTACTTTTGTTTA
Found at i:303731 original size:34 final size:34
Alignment explanation
Indices: 303665--303732 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
303655 GCAAAATATT
*
303665 TTTATATTTTCTTTAAAAAATTAAATTCATAAAA
1 TTTATATTTTCTTTAAAAAATTAAAATCATAAAA
* *
303699 TTTATATTTTTTTTACAAAATTGAAAAT-ATAAAA
1 TTTATATTTTCTTTAAAAAATT-AAAATCATAAAA
303733 AGGTTTAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 26 0.87
35 4 0.13
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (34 bp):
TTTATATTTTCTTTAAAAAATTAAAATCATAAAA
Found at i:304371 original size:72 final size:74
Alignment explanation
Indices: 304254--304399 Score: 278
Period size: 72 Copynumber: 2.0 Consensus size: 74
304244 GACGAATGTG
304254 ATGAATTAGATATGCTATGATGGCAAAAGTTGCCCTTTTATCTTTATATTTAATGGTG-TTTT-T
1 ATGAATTAGATATGCTATGATGGCAAAAGTTGCCCTTTTATCTTTATATTTAATGGTGTTTTTAT
304317 TTTTCGTTT
66 TTTTCGTTT
304326 ATGAATTAGATATGCTATGATGGCAAAAGTTGCCCTTTTATCTTTATATTTAATGGTGTTTTTAT
1 ATGAATTAGATATGCTATGATGGCAAAAGTTGCCCTTTTATCTTTATATTTAATGGTGTTTTTAT
304391 TTTTCGTTT
66 TTTTCGTTT
304400 TCTTAGTTCA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
72 58 0.81
73 4 0.06
74 10 0.14
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.50
Consensus pattern (74 bp):
ATGAATTAGATATGCTATGATGGCAAAAGTTGCCCTTTTATCTTTATATTTAATGGTGTTTTTAT
TTTTCGTTT
Found at i:304486 original size:2 final size:2
Alignment explanation
Indices: 304479--304509 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
304469 GAAAGTTAAT
304479 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
304510 TATGATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:307464 original size:65 final size:64
Alignment explanation
Indices: 307347--307512 Score: 165
Period size: 65 Copynumber: 2.6 Consensus size: 64
307337 TTTCAGGTAA
* * * * * * *
307347 GTGTACCGATGCATAAATCAATGCATCGATGCACCCTTGTTTTAATTGAACATCAAATAGCTTTT
1 GTGTACCGATGCA-CAAGCCATGCATCGATGCACCCATGTATTAATTAAACATCAAATAGATTTT
* *
307412 GTGTACCGATGCACATA-CCATGCATCGATGCACTCCATGTATT-ATTAAAACATCGAATTGATT
1 GTGTACCGATGCACA-AGCCATGCATCGATGCAC-CCATGTATTAATT-AAACATCAAATAGATT
307475 TT
63 TT
* * * *
307477 ATGCACTGATGCACAAGCCATGCATCGATGTACCCA
1 GTGTACCGATGCACAAGCCATGCATCGATGCACCCA
307513 GGCTTTTTCA
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
64 23 0.27
65 62 0.73
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (64 bp):
GTGTACCGATGCACAAGCCATGCATCGATGCACCCATGTATTAATTAAACATCAAATAGATTTT
Found at i:307551 original size:64 final size:64
Alignment explanation
Indices: 307419--307554 Score: 156
Period size: 64 Copynumber: 2.1 Consensus size: 64
307409 TTTGTGTACC
*
307419 GATGCACATACCATGCATCGATGCACTCCATGTATTATTAAAACATCGAATTGATTTTATGCACT
1 GATGCACATACCATGCATCGATGCACTCCAGGTATTATTAAAACATCGAA-TGATTTTATGCACT
*
307484 GATGCACA-AGCCATGCATCGATGTAC-CCAGGCT-TT-TTCAAAACATCGAA-GCATATTTATG
1 GATGCACATA-CCATGCATCGATGCACTCCAGG-TATTATT-AAAACATCGAATG-AT-TTTATG
*
307544 CATT
61 CACT
307548 GATGCAC
1 GATGCAC
307555 CCTCAGTGTA
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
62 1 0.02
63 4 0.06
64 34 0.54
65 24 0.38
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (64 bp):
GATGCACATACCATGCATCGATGCACTCCAGGTATTATTAAAACATCGAATGATTTTATGCACT
Found at i:315230 original size:21 final size:22
Alignment explanation
Indices: 315188--315230 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
315178 CATTTTGAAT
* *
315188 GTTGTTGGATTGTTTTACTTTG
1 GTTGTTGGATTGTTTGAATTTG
315210 GTTGTTGGA-TGTTTGAATTTG
1 GTTGTTGGATTGTTTGAATTTG
315231 TTTAATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.12, C:0.02, G:0.30, T:0.56
Consensus pattern (22 bp):
GTTGTTGGATTGTTTGAATTTG
Found at i:318287 original size:18 final size:18
Alignment explanation
Indices: 318261--318296 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
318251 AATTAGCATG
318261 CACAACCTTGTTCATAAT
1 CACAACCTTGTTCATAAT
* *
318279 CACATCCTTGTTCTTAAT
1 CACAACCTTGTTCATAAT
318297 TCTATCAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.39
Consensus pattern (18 bp):
CACAACCTTGTTCATAAT
Found at i:323063 original size:2 final size:2
Alignment explanation
Indices: 323056--323084 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
323046 AGTTAATTAT
323056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
323085 TAATTATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:324076 original size:16 final size:16
Alignment explanation
Indices: 324051--324081 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
324041 GCATGAGTAA
*
324051 AATTTGGGATATTTTT
1 AATTTAGGATATTTTT
324067 AATTTAGGATATTTT
1 AATTTAGGATATTTT
324082 AGGTAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (16 bp):
AATTTAGGATATTTTT
Found at i:325038 original size:39 final size:39
Alignment explanation
Indices: 324982--325063 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
324972 TAAGACATCC
324982 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
1 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
*
325021 TTCATACAAATATGATGATTAATAATTAAAGTGTTATGG
1 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
325060 TTCA
1 TTCA
325064 ATAGAATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (39 bp):
TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
Found at i:327833 original size:6 final size:6
Alignment explanation
Indices: 327817--327849 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
327807 GAGTCTCAAA
*
327817 ATTTTT A-TTTT ATTTTT ATTTTT AATTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT
327850 ACTTTCGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:332085 original size:12 final size:12
Alignment explanation
Indices: 332068--332095 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
332058 CGAGTCTCAA
332068 ATTTTTTATTTT
1 ATTTTTTATTTT
332080 ATTTTTTATTTT
1 ATTTTTTATTTT
332092 ATTT
1 ATTT
332096 ACTTTCGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
ATTTTTTATTTT
Found at i:332299 original size:14 final size:14
Alignment explanation
Indices: 332280--332314 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
332270 TAAGTTAGGG
332280 TTTAAAGTTTATGA
1 TTTAAAGTTTATGA
332294 TTTAAAGTTTATGA
1 TTTAAAGTTTATGA
332308 TTTAAAG
1 TTTAAAG
332315 GGAATACCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (14 bp):
TTTAAAGTTTATGA
Found at i:333644 original size:39 final size:39
Alignment explanation
Indices: 333590--333710 Score: 206
Period size: 39 Copynumber: 3.1 Consensus size: 39
333580 TAAGACATCC
*
333590 TTCATACAAATAGGATGATTAATAGTTAAAGTGTTATGG
1 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
333629 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
1 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
* * *
333668 TTCATAAAAATAGGATGATTTATAATTAAAGTGTTACGG
1 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
333707 TTCA
1 TTCA
333711 ATAGAATTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (39 bp):
TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
Found at i:337856 original size:25 final size:25
Alignment explanation
Indices: 337822--337875 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
337812 AAGGTAATTG
**
337822 TTTAACTTCATTTATTTAACCATTT
1 TTTAACTTCATAAATTTAACCATTT
* **
337847 TTTAATTTCATAAATTTAATTATTT
1 TTTAACTTCATAAATTTAACCATTT
337872 TTTA
1 TTTA
337876 TTTGTTTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTAACTTCATAAATTTAACCATTT
Found at i:341169 original size:36 final size:37
Alignment explanation
Indices: 341100--341172 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
341090 TCTTTTTTTG
*
341100 GACTTTTAGCTATTAAATTAGATAACATATATGCTAA
1 GACTTTTAACTATTAAATTAGATAACATATATGCTAA
341137 GACTTTTAACTATTAAATTAG-TAACATATATGCTAA
1 GACTTTTAACTATTAAATTAGATAACATATATGCTAA
341173 ATTATGTCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 15 0.43
37 20 0.57
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (37 bp):
GACTTTTAACTATTAAATTAGATAACATATATGCTAA
Done.