Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007846.1 Hibiscus syriacus cultivar Beakdansim tig00110202_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: 846497
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 4 of 4
Found at i:756368 original size:32 final size:30
Alignment explanation
Indices: 756274--756378 Score: 101
Period size: 32 Copynumber: 3.5 Consensus size: 30
756264 TTTAACTAAC
* * *
756274 TTAACGAGCACCAAGTCGAGCAACAATTTTTT
1 TTAACGAGCA-CGAGTCGA-AAACAAATTTTT
* *
756306 TTAATGAGCACGAGT--AAAACAAA--ATT
1 TTAACGAGCACGAGTCGAAAACAAATTTTT
756332 TTAACGAGCAACGAGTCGAATAACAAATTTTT
1 TTAACGAGC-ACGAGTCGAA-AACAAATTTTT
756364 TTAACGAGCACGAGT
1 TTAACGAGCACGAGT
756379 TAAATATTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
26 10 0.17
27 6 0.10
28 5 0.08
29 3 0.05
30 6 0.10
31 10 0.17
32 20 0.33
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (30 bp):
TTAACGAGCACGAGTCGAAAACAAATTTTT
Found at i:758270 original size:15 final size:15
Alignment explanation
Indices: 758246--758276 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
758236 TTAAAGACCA
758246 TACCCAAAGTAAAGC
1 TACCCAAAGTAAAGC
*
758261 TACCCTAAGTAAAGC
1 TACCCAAAGTAAAGC
758276 T
1 T
758277 CAAACTCAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.26, G:0.13, T:0.19
Consensus pattern (15 bp):
TACCCAAAGTAAAGC
Found at i:763482 original size:45 final size:45
Alignment explanation
Indices: 763432--763521 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
763422 AGCAATCCTA
763432 AGTACTCATACTAGTTTTATTGCCTTCTTGCTGCAAAGGTGCTAC
1 AGTACTCATACTAGTTTTATTGCCTTCTTGCTGCAAAGGTGCTAC
*
763477 AGTACTCATACTAGTTTTATTGCCTTCTTGCTGCAAAGTTGCTAC
1 AGTACTCATACTAGTTTTATTGCCTTCTTGCTGCAAAGGTGCTAC
763522 GTTTACCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (45 bp):
AGTACTCATACTAGTTTTATTGCCTTCTTGCTGCAAAGGTGCTAC
Found at i:767484 original size:151 final size:151
Alignment explanation
Indices: 767210--767513 Score: 581
Period size: 151 Copynumber: 2.0 Consensus size: 151
767200 TTGATTCCAT
* *
767210 GTTTTTGAACTCTCTGATGGGTGTACCATCCACAGAGAAGATGATGCGTTGGGTATTCCAGAGGA
1 GTTTTTGAACTCTCTAATAGGTGTACCATCCACAGAGAAGATGATGCGTTGGGTATTCCAGAGGA
*
767275 TGGAGTAAGTATGGAAACCCGTTGTTGGATCAAACCAGAGATAGAACTGTTGTTCTTTATTGCCC
66 TGGAGTAAGTATGGAAACCCATTGTTGGATCAAACCAGAGATAGAACTGTTGTTCTTTATTGCCC
767340 TTTCCTTGGCTGAACAAGTCG
131 TTTCCTTGGCTGAACAAGTCG
767361 GTTTTTGAACTCTCTAATAGGTGTACCATCCACAGAGAAGATGATGCGTTGGGTATTCCAGAGGA
1 GTTTTTGAACTCTCTAATAGGTGTACCATCCACAGAGAAGATGATGCGTTGGGTATTCCAGAGGA
767426 TGGAGTAAGTATGGAAACCCATTGTTGGATCAAACCAGAGATAGAACTGTTGTTCTTTATTGCCC
66 TGGAGTAAGTATGGAAACCCATTGTTGGATCAAACCAGAGATAGAACTGTTGTTCTTTATTGCCC
767491 TTTCCTTGGCTGAACAAGTCG
131 TTTCCTTGGCTGAACAAGTCG
767512 GT
1 GT
767514 GTGAAGAATG
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 150 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (151 bp):
GTTTTTGAACTCTCTAATAGGTGTACCATCCACAGAGAAGATGATGCGTTGGGTATTCCAGAGGA
TGGAGTAAGTATGGAAACCCATTGTTGGATCAAACCAGAGATAGAACTGTTGTTCTTTATTGCCC
TTTCCTTGGCTGAACAAGTCG
Found at i:767938 original size:17 final size:17
Alignment explanation
Indices: 767916--767949 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
767906 AACGAGACAA
767916 CCGACTATAAGAGGCAT
1 CCGACTATAAGAGGCAT
*
767933 CCGACTATATGAGGCAT
1 CCGACTATAAGAGGCAT
767950 AAGCAAGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (17 bp):
CCGACTATAAGAGGCAT
Found at i:768392 original size:24 final size:25
Alignment explanation
Indices: 768349--768396 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
768339 AATCGACTCG
768349 AAGTATTGTACCCGAACCCGACCCA
1 AAGTATTGTACCCGAACCCGACCCA
768374 AAGTATTGTA-CCGAACCCGACCC
1 AAGTATTGTACCCGAACCCGACCC
768397 GATCCCGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.31, C:0.35, G:0.17, T:0.17
Consensus pattern (25 bp):
AAGTATTGTACCCGAACCCGACCCA
Found at i:776800 original size:20 final size:20
Alignment explanation
Indices: 776771--776812 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
776761 ATTCCACCAC
776771 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
776791 ATGCATCTATGTGGTCCTAA
1 ATGCAACTATATGCTCCTAA
776811 AT
1 AT
776813 TTGGTCTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:785756 original size:20 final size:20
Alignment explanation
Indices: 785727--785768 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
785717 ATTCCACCAC
785727 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
785747 ATGCATCTATGTGGTCCTAA
1 ATGCAACTATATGCTCCTAA
785767 AT
1 AT
785769 AAGCTCTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:788726 original size:109 final size:109
Alignment explanation
Indices: 788595--788819 Score: 425
Period size: 109 Copynumber: 2.1 Consensus size: 109
788585 CGTCTTCATA
788595 AGATTAATTTTTTGAATTAAAGTTTCTTTATTCTTCTGTGATGCGTAACATGGAAGAGCCGGTAG
1 AGATTAATTTTTTGAATTAAAGTTTCTTTATTCTTCTGTGATGCGTAACATGGAAGAGCCGGTAG
*
788660 ATTTTGTTTCCAAAATTAGGCCAACCAGGCTTCAATAATTAATT
66 ATTTTGTTTCCAAAACTAGGCCAACCAGGCTTCAATAATTAATT
788704 AGATTAATTTTTTGAATTAAAGTTTCTTTATTCTTCTGTGATGCGTAACATGGAAGAGCCGGTAG
1 AGATTAATTTTTTGAATTAAAGTTTCTTTATTCTTCTGTGATGCGTAACATGGAAGAGCCGGTAG
*
788769 ATTTTGTTTCCAAAACTAGGCCAACCGGGCTTCAATAATTAATT
66 ATTTTGTTTCCAAAACTAGGCCAACCAGGCTTCAATAATTAATT
788813 A-ATTAAT
1 AGATTAAT
788820 GGTATCGCTT
Statistics
Matches: 114, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
108 6 0.05
109 108 0.95
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (109 bp):
AGATTAATTTTTTGAATTAAAGTTTCTTTATTCTTCTGTGATGCGTAACATGGAAGAGCCGGTAG
ATTTTGTTTCCAAAACTAGGCCAACCAGGCTTCAATAATTAATT
Found at i:789635 original size:20 final size:20
Alignment explanation
Indices: 789578--789635 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
789568 CTCTAGAGTT
789578 CTCTAGAATATTT-TAGAAAA
1 CTCTAGAAT-TTTCTAGAAAA
* * *
789598 TTCTA-AACTTATCCAGAAAA
1 CTCTAGAA-TTTTCTAGAAAA
789618 CTCTAGAATTTTCTAGAA
1 CTCTAGAATTTTCTAGAA
789636 TCTCTCCAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
19 4 0.14
20 23 0.79
21 2 0.07
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (20 bp):
CTCTAGAATTTTCTAGAAAA
Found at i:790136 original size:19 final size:19
Alignment explanation
Indices: 790112--790148 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
790102 TATTGGAATA
*
790112 TGCATTCTAGAATATGCAG
1 TGCATTCTAGAACATGCAG
790131 TGCATTCTAGAACATGCA
1 TGCATTCTAGAACATGCA
790149 CTGCTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (19 bp):
TGCATTCTAGAACATGCAG
Found at i:791379 original size:36 final size:36
Alignment explanation
Indices: 791190--791373 Score: 296
Period size: 36 Copynumber: 5.1 Consensus size: 36
791180 GGTGCACAGA
* *
791190 CGATTCAAATCGAACGGAATGAAGCATCGGCACTTT
1 CGATTCAAATCGAACGGAAGGAAGCATCGGCACTTC
*
791226 CGATTCAAATCGAATGGAAGGAAGCATCGGCACTTC
1 CGATTCAAATCGAACGGAAGGAAGCATCGGCACTTC
*
791262 CGATTCAAATCGAACGGAAGGAAGCATCGGCAATTC
1 CGATTCAAATCGAACGGAAGGAAGCATCGGCACTTC
* *
791298 TGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
1 CGATTCAAATCGAACGGAAGGAAGCATCGGCACTTC
* *
791334 CGATTCAAGTCGAACGGAAGGAAGAATCGGCACTTC
1 CGATTCAAATCGAACGGAAGGAAGCATCGGCACTTC
791370 CGAT
1 CGAT
791374 CCAAGTGTTC
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 138 1.00
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (36 bp):
CGATTCAAATCGAACGGAAGGAAGCATCGGCACTTC
Found at i:791460 original size:19 final size:19
Alignment explanation
Indices: 791436--791472 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
791426 TATTGGAATA
*
791436 TGCATTCTAGAATATGCAG
1 TGCATTCTAGAACATGCAG
791455 TGCATTCTAGAACATGCA
1 TGCATTCTAGAACATGCA
791473 CTGCTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (19 bp):
TGCATTCTAGAACATGCAG
Found at i:793664 original size:16 final size:16
Alignment explanation
Indices: 793625--793668 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
793615 CACTAGTTGA
*
793625 TTAAATATTTAATAAAT
1 TTAAATATTT-TTAAAT
*
793642 TT-TATATTTTTAAAT
1 TTAAATATTTTTAAAT
793657 TTAAATATTTTT
1 TTAAATATTTTT
793669 TACAGGAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.30
16 14 0.61
17 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAAATATTTTTAAAT
Found at i:795287 original size:2 final size:2
Alignment explanation
Indices: 795280--795319 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
795270 CCACGTATTA
795280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
795320 TCTAGCTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:800164 original size:17 final size:17
Alignment explanation
Indices: 800142--800192 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
800132 AATTCGTATC
800142 ATTTTTATATAATTAAT
1 ATTTTTATATAATTAAT
* * *
800159 ATTTTTAAATTATTATT
1 ATTTTTATATAATTAAT
800176 ATTTTT-TATAATATAAT
1 ATTTTTATATAAT-TAAT
800193 TGTACTAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTATATAATTAAT
Found at i:800369 original size:28 final size:25
Alignment explanation
Indices: 800306--800362 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
800296 GAAATTACCG
*
800306 TATTTATATTTTATTGAAAACTAAA
1 TATTTATATTTTATTGAAAAATAAA
800331 TATTTATATTTTATTGGAAACAATATAA
1 TATTTATATTTTATT-GAAA-AATA-AA
800359 TATT
1 TATT
800363 ATGATTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 15 0.54
26 4 0.14
27 3 0.11
28 6 0.21
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (25 bp):
TATTTATATTTTATTGAAAAATAAA
Found at i:802603 original size:20 final size:21
Alignment explanation
Indices: 802559--802614 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
802549 CAGTTTCCAA
* *
802559 ATTCGCAACGCGAATATCCAG
1 ATTCGCAACGCGATTATCAAG
*
802580 ATTCGCAACGCGATTGT-AAG
1 ATTCGCAACGCGATTATCAAG
* *
802600 ATTCACAAAGCGATT
1 ATTCGCAACGCGATT
802615 TTGAAAAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (21 bp):
ATTCGCAACGCGATTATCAAG
Found at i:802691 original size:44 final size:41
Alignment explanation
Indices: 802614--802695 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 41
802604 ACAAAGCGAT
* *
802614 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
*
802655 TTTGAAAAACGTGTTGTTGTGATAGTGAAAAAGTGTTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAGTGAAAAAGTGTTGCGA
802696 TAGTGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 9 0.26
43 2 0.06
44 24 0.69
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
Found at i:802705 original size:19 final size:20
Alignment explanation
Indices: 802616--802706 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 20
802606 AAAGCGATTT
802616 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* *
802636 T-TAAAATGTGTTGCGAGAG
1 TGAAAAATGTGTTGCGATAG
*
802655 TTTGAAAAACGTGTTGTTGTGATAG
1 --TGAAAAA--TG-TGTTGCGATAG
802680 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
802699 TGAAAAAT
1 TGAAAAAT
802707 CCAAAATAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 33 0.57
20 2 0.03
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.03
25 9 0.16
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:803018 original size:6 final size:6
Alignment explanation
Indices: 803002--803058 Score: 107
Period size: 6 Copynumber: 9.7 Consensus size: 6
802992 TCCCGTCTCG
803002 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
803049 GGTCGT GGTC
1 GGTCGT GGTC
803059 TGGGGTAGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 46 0.90
ACGTcount: A:0.00, C:0.18, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:809573 original size:21 final size:21
Alignment explanation
Indices: 809547--809587 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
809537 CTAATATTGT
809547 AATGTCAAAATTAGGTGCAAC
1 AATGTCAAAATTAGGTGCAAC
809568 AATGTCAAAATTAGGTGCAA
1 AATGTCAAAATTAGGTGCAA
809588 TAATATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (21 bp):
AATGTCAAAATTAGGTGCAAC
Found at i:814210 original size:21 final size:21
Alignment explanation
Indices: 814184--814224 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
814174 CTAATATTGT
814184 AATGTCAAAATTAGGTGCAAC
1 AATGTCAAAATTAGGTGCAAC
814205 AATGTCAAAATTAGGTGCAA
1 AATGTCAAAATTAGGTGCAA
814225 TAATATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (21 bp):
AATGTCAAAATTAGGTGCAAC
Found at i:818946 original size:20 final size:20
Alignment explanation
Indices: 818921--818963 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
818911 CTTAAACGGG
818921 TCCAATAACTTCATTAATGA
1 TCCAATAACTTCATTAATGA
818941 TCCAATAACTTCATTAATGA
1 TCCAATAACTTCATTAATGA
818961 TCC
1 TCC
818964 CCAACGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (20 bp):
TCCAATAACTTCATTAATGA
Found at i:821827 original size:21 final size:21
Alignment explanation
Indices: 821801--821843 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
821791 TTTCTGGGTT
* *
821801 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
821822 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
821843 A
1 A
821844 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:821904 original size:66 final size:66
Alignment explanation
Indices: 821801--821972 Score: 197
Period size: 66 Copynumber: 2.6 Consensus size: 66
821791 TTTCTGGGTT
* * * *
821801 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCTTCAACGAATATGATTTCCAGAATGC
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGC
821865 -TA
64 TTA
* * *
821867 GAGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATATGAATTCCAGATTGCT
1 -AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCT
821932 TA
65 TA
* *
821934 AGGGGAATCGATA-CCCCAGGGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCA--GGGGGGAACCGATACCCCC
821973 ATGAGAAAAG
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
65 7 0.08
66 49 0.53
67 36 0.39
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (66 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTT
A
Found at i:822310 original size:29 final size:29
Alignment explanation
Indices: 822276--822347 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
822266 CATATTATGA
**
822276 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
822305 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
822334 TACATGACATGAAT
1 TACATGACATGAAT
822348 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:822402 original size:30 final size:31
Alignment explanation
Indices: 822362--822420 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
822352 AGAAAAGTTC
*
822362 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
822393 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
822421 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:822713 original size:22 final size:22
Alignment explanation
Indices: 822639--822705 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
822629 TTATGGACAA
822639 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
822661 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
822683 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
822705 A
1 A
822706 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:828746 original size:21 final size:21
Alignment explanation
Indices: 828720--828762 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
828710 TTTCTGGGTT
* *
828720 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
828741 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
828762 A
1 A
828763 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:828837 original size:67 final size:66
Alignment explanation
Indices: 828742--828891 Score: 212
Period size: 67 Copynumber: 2.3 Consensus size: 66
828732 ACCCATTCAA
* * *
828742 GGGGAACCGATACCCCTTCAACGAATATGATTTCCAGAATGC-TAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTA-AGGGGAATCGATA-CCCCA
828806 GGG
64 GGG
* * *
828809 GGGGAACCGATACCCCCTCATCGTATATGAATTCCAGATTGCTTAAGGGGAATCGATACCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTAAGGGGAATCGATACCCCAGG
828874 G
66 G
*
828875 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
828892 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
66 24 0.32
67 49 0.65
68 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTAAGGGGAATCGATACCCCAGG
G
Found at i:829230 original size:29 final size:29
Alignment explanation
Indices: 829196--829267 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
829186 CATATTATGA
**
829196 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
829225 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
829254 TACATGACATGAAT
1 TACATGACATGAAT
829268 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:829322 original size:30 final size:31
Alignment explanation
Indices: 829282--829340 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
829272 AGAAAAGTTC
*
829282 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
829313 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
829341 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:829634 original size:22 final size:22
Alignment explanation
Indices: 829560--829626 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
829550 TTATGGACAA
829560 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
829582 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
829604 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
829626 A
1 A
829627 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:833387 original size:23 final size:22
Alignment explanation
Indices: 833334--833387 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
833324 GGAACCGATA
*
833334 CCCCTTGAAGAGGATCTGATTC
1 CCCCTTGAAGAGGAACTGATTC
833356 CCCCTTTGAATG-GGAACTGATTC
1 CCCC-TTGAA-GAGGAACTGATTC
833379 CCTCCTTGA
1 CC-CCTTGA
833388 GAGAATCGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.14
23 21 0.75
24 3 0.11
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
CCCCTTGAAGAGGAACTGATTC
Found at i:843891 original size:31 final size:30
Alignment explanation
Indices: 843851--843910 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
843841 ATTTTAATTT
* *
843851 TTTTAATTAAATCCCCTCATATTTTCAAAAG
1 TTTTAATTAAAGCCCCTCA-AATTTCAAAAG
* *
843882 TTTTCATTAAAGCCTCTCAAATTTCAAAA
1 TTTTAATTAAAGCCCCTCAAATTTCAAAA
843911 CTTATAGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (30 bp):
TTTTAATTAAAGCCCCTCAAATTTCAAAAG
Done.