Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000379.1 Hibiscus syriacus cultivar Beakdansim tig00000695_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: 72980
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:7757 original size:44 final size:44
Alignment explanation
Indices: 7708--7831 Score: 162
Period size: 43 Copynumber: 2.8 Consensus size: 44
7698 TTCTCAGTGT
* * * *
7708 TTTTAGGATAGAAACACCGCTAAAGGTCTGGTATATAATGGTGC
1 TTTTAGGATACAAACACTGCTAAAGGTCTGGTATATAACGGCGC
* * *
7752 TTTTAGGATACAAACGCTGCTAAAGGTCT-GTATATAGCGGCGT
1 TTTTAGGATACAAACACTGCTAAAGGTCTGGTATATAACGGCGC
7795 TTTTAGGATACAAACGA-TGCTAAAGGTCTGGTATATA
1 TTTTAGGATACAAAC-ACTGCTAAAGGTCTGGTATATA
7832 GCGACGTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 37 0.53
44 33 0.47
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (44 bp):
TTTTAGGATACAAACACTGCTAAAGGTCTGGTATATAACGGCGC
Found at i:7799 original size:43 final size:44
Alignment explanation
Indices: 7706--7842 Score: 186
Period size: 44 Copynumber: 3.1 Consensus size: 44
7696 ATTTCTCAGT
* * * ** *
7706 GTTTTTAGGATAGAAACACCGCTAAAGGTCTGGTATATAATGGT
1 GTTTTTAGGATACAAACGCTGCTAAAGGTCTGGTATATAGCGGC
*
7750 GCTTTTAGGATACAAACGCTGCTAAAGGTCT-GTATATAGCGGC
1 GTTTTTAGGATACAAACGCTGCTAAAGGTCTGGTATATAGCGGC
* *
7793 GTTTTTAGGATACAAACGATGCTAAAGGTCTGGTATATAGCGAC
1 GTTTTTAGGATACAAACGCTGCTAAAGGTCTGGTATATAGCGGC
7837 GTTTTT
1 GTTTTT
7843 TGTTATAAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
43 38 0.46
44 44 0.54
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (44 bp):
GTTTTTAGGATACAAACGCTGCTAAAGGTCTGGTATATAGCGGC
Found at i:8200 original size:21 final size:21
Alignment explanation
Indices: 8176--8236 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
8166 TCTGCTGATA
* *
8176 TGTTGCTTCTCTCTGTGTTGT
1 TGTTGCTTCTCTCTGTGCTGC
*
8197 TGTTGTTTCTCTCTGTGCTGC
1 TGTTGCTTCTCTCTGTGCTGC
* * *
8218 CGTTGCTTTTCTCTCTGCT
1 TGTTGCTTCTCTCTGTGCT
8237 TTTTCTGCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.00, C:0.25, G:0.21, T:0.54
Consensus pattern (21 bp):
TGTTGCTTCTCTCTGTGCTGC
Found at i:14273 original size:18 final size:17
Alignment explanation
Indices: 14250--14286 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
14240 TATGAAAATG
14250 AAATAAGACAACAATACA
1 AAATAAGACAACAA-ACA
14268 AAATAAGACAACAAACA
1 AAATAAGACAACAAACA
14285 AA
1 AA
14287 CTATACCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.70, C:0.16, G:0.05, T:0.08
Consensus pattern (17 bp):
AAATAAGACAACAAACA
Found at i:14747 original size:2 final size:2
Alignment explanation
Indices: 14742--14767 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14732 TTGTGAGAAA
14742 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
14768 GCATTTCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18330 original size:22 final size:22
Alignment explanation
Indices: 18305--18349 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
18295 TTTTCAAAAG
*
18305 CTATTATTTTCCTATTCGAAAC
1 CTATTATTTTCATATTCGAAAC
*
18327 CTATTATTTTTATATTCGAAAC
1 CTATTATTTTCATATTCGAAAC
18349 C
1 C
18350 GGAAAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (22 bp):
CTATTATTTTCATATTCGAAAC
Found at i:21914 original size:1000 final size:1000
Alignment explanation
Indices: 19975--21961 Score: 3965
Period size: 1000 Copynumber: 2.0 Consensus size: 1000
19965 CTCCACATTG
19975 AGGGCGATTCAGGGGACGATTGGTTGAGAACCAATATTTTCCACACGACTTGCACAGTTGCAGAT
1 AGGGCGATTCAGGGGACGATTGGTTGAGAACCAATATTTTCCACACGACTTGCACAGTTGCAGAT
20040 AAAGTCTGCAAAATGATCATTGACAGCGGCAGTTGTGAGAATGTAGTGTCCGAGGAGGTTGTCCA
66 AAAGTCTGCAAAATGATCATTGACAGCGGCAGTTGTGAGAATGTAGTGTCCGAGGAGGTTGTCCA
20105 GAAATTGCAGTTGAAGACGGACCGTCATCCTAAGCCATACAAGTTGTCATGGCTAAATAAAGACA
131 GAAATTGCAGTTGAAGACGGACCGTCATCCTAAGCCATACAAGTTGTCATGGCTAAATAAAGACA
20170 GTGAGGTAACAGTTGATAGGCGATGCCTGGTGTCTTTTTCAATTGGTAGAAAATATTTTGATAAT
196 GTGAGGTAACAGTTGATAGGCGATGCCTGGTGTCTTTTTCAATTGGTAGAAAATATTTTGATAAT
20235 GCCTGGTGTGATGTTGTGTCTATGGATGCGTGTCATATATTGTTGGGTCGACCTTGGCAGTATGA
261 GCCTGGTGTGATGTTGTGTCTATGGATGCGTGTCATATATTGTTGGGTCGACCTTGGCAGTATGA
20300 TCGCAGTGTCATTCATGATGGACGGAAGAATACATATTCCCTTAGCATCAAGGGAAAAAAGATTG
326 TCGCAGTGTCATTCATGATGGACGGAAGAATACATATTCCCTTAGCATCAAGGGAAAAAAGATTG
20365 TGTTGGCACCCCGGCGGGAAGGACTTACTCCTACCCCAGTAACCCATAATACTAATCTGCTTTCT
391 TGTTGGCACCCCGGCGGGAAGGACTTACTCCTACCCCAGTAACCCATAATACTAATCTGCTTTCT
20430 ATGTCCAGGTTTTTAGATGAGATTGAGCATGGCGACGTGGTCTATGCCTTGCTACCTTGCGAGAA
456 ATGTCCAGGTTTTTAGATGAGATTGAGCATGGCGACGTGGTCTATGCCTTGCTACCTTGCGAGAA
20495 CAATGCAGTAGACGTGGATACAGATTTACCAGTAGAGGTGCAGCGGTTGCTAGCAGAATTCTCTA
521 CAATGCAGTAGACGTGGATACAGATTTACCAGTAGAGGTGCAGCGGTTGCTAGCAGAATTCTCTA
20560 ACTTGATGCCAGAGGATCTTCCTCCTGGACTACCACCTATGAGGGATATTCAGCATCAAATTGAC
586 ACTTGATGCCAGAGGATCTTCCTCCTGGACTACCACCTATGAGGGATATTCAGCATCAAATTGAC
20625 CTTGTTCCTGGGTCAAGTTTGCCAAATCGACCAGCATATCGCCTCAGTCCCAAGGAGGCCGAAGA
651 CTTGTTCCTGGGTCAAGTTTGCCAAATCGACCAGCATATCGCCTCAGTCCCAAGGAGGCCGAAGA
20690 GTTGCAGCGACAGGTGGAAGAGTTGTTGGAGAGGGGCTATATCCGAGAGAGTATGAGCCCATGTG
716 GTTGCAGCGACAGGTGGAAGAGTTGTTGGAGAGGGGCTATATCCGAGAGAGTATGAGCCCATGTG
20755 CAGTCCCTGCTCTGTTAGTGCCAAAGAAAGATGGTTCTTGGCGTATGTGTGTTGACAGCCGAGCG
781 CAGTCCCTGCTCTGTTAGTGCCAAAGAAAGATGGTTCTTGGCGTATGTGTGTTGACAGCCGAGCG
20820 ATCAACAGAATTACAGTGAAGTACCGATTTCCAATTCCCCGTCTAGATGATATGTTGGATCAGCT
846 ATCAACAGAATTACAGTGAAGTACCGATTTCCAATTCCCCGTCTAGATGATATGTTGGATCAGCT
20885 ATCTGGTTCTAAGATCTTCTCAAAAATTGACCTTAAGAGCGGTTACCACCAAATCAGAATAAGGC
911 ATCTGGTTCTAAGATCTTCTCAAAAATTGACCTTAAGAGCGGTTACCACCAAATCAGAATAAGGC
20950 CTGGAGATGAGTCTACTTACCCCCA
976 CTGGAGATGAGTCTACTTACCCCCA
20975 AGGGCGATTCAGGGGACGATTGGTTGAGAACCAATATTTTCCACACGACTTGCACAGTTGCAGAT
1 AGGGCGATTCAGGGGACGATTGGTTGAGAACCAATATTTTCCACACGACTTGCACAGTTGCAGAT
21040 AAAGTCTGCAAAATGATCATTGACAGCGGCAGTTGTGAGAATGTAGTGTCCGAGGAGGTTGTCCA
66 AAAGTCTGCAAAATGATCATTGACAGCGGCAGTTGTGAGAATGTAGTGTCCGAGGAGGTTGTCCA
21105 GAAATTGCAGTTGAAGACGGACCGTCATCCTAAGCCATACAAGTTGTCATGGCTAAATAAAGACA
131 GAAATTGCAGTTGAAGACGGACCGTCATCCTAAGCCATACAAGTTGTCATGGCTAAATAAAGACA
21170 GTGAGGTAACAGTTGATAGGCGATGCCTGGTGTCTTTTTCAATTGGTAGAAAATATTTTGATAAT
196 GTGAGGTAACAGTTGATAGGCGATGCCTGGTGTCTTTTTCAATTGGTAGAAAATATTTTGATAAT
21235 GCCTGGTGTGATGTTGTGTCTATGGATGCGTGTCATATATTGTTGGGTCGACCTTGGCAGTATGA
261 GCCTGGTGTGATGTTGTGTCTATGGATGCGTGTCATATATTGTTGGGTCGACCTTGGCAGTATGA
21300 TCGCAGTGTCATTCATGATGGACGGAAGAATACATATTCCCTTAGCATCAAGGGAAAAAAGATTG
326 TCGCAGTGTCATTCATGATGGACGGAAGAATACATATTCCCTTAGCATCAAGGGAAAAAAGATTG
21365 TGTTGGCACCCCGGCGGGAAGGACTTACTCCTACCCCAGTAACCCATAATACTAATCTGCTTTCT
391 TGTTGGCACCCCGGCGGGAAGGACTTACTCCTACCCCAGTAACCCATAATACTAATCTGCTTTCT
21430 ATGTCCAGGTTTTTAGATGAGATTGAGCATGGCGACGTGGTCTATGCCTTGCTACCTTGCGAGAA
456 ATGTCCAGGTTTTTAGATGAGATTGAGCATGGCGACGTGGTCTATGCCTTGCTACCTTGCGAGAA
21495 CAATGCAGTAGACGTGGATACAGATTTACCAGTAGAGGTGCAGCGGTTGCTAGCAGAATTCTCTA
521 CAATGCAGTAGACGTGGATACAGATTTACCAGTAGAGGTGCAGCGGTTGCTAGCAGAATTCTCTA
21560 ACTTGATGCCAGAGGATCTTCCTCCTGGACTACCACCTATGAGGGATATTCAGCATCAAATTGAC
586 ACTTGATGCCAGAGGATCTTCCTCCTGGACTACCACCTATGAGGGATATTCAGCATCAAATTGAC
21625 CTTGTTCCTGGGTCAAGTTTGCCAAATCGACCAGCATATCGCCTCAGTCCCAAGGAGGCCGAAGA
651 CTTGTTCCTGGGTCAAGTTTGCCAAATCGACCAGCATATCGCCTCAGTCCCAAGGAGGCCGAAGA
21690 GTTGCAGCGACAGGTGGAAGAGTTGTTGGAGAGGGGCTATATCCGAGAGAGTATGAGCCCATGTG
716 GTTGCAGCGACAGGTGGAAGAGTTGTTGGAGAGGGGCTATATCCGAGAGAGTATGAGCCCATGTG
21755 CAGTCCCTGCTCTGTTAGTGCCAAAGAAAGATGGTTCTTGGCGTATGTGTGTTGACAGCCGAGCG
781 CAGTCCCTGCTCTGTTAGTGCCAAAGAAAGATGGTTCTTGGCGTATGTGTGTTGACAGCCGAGCG
*
21820 ATCAACAGAATTACAGTGAAGTACCGGTTTCCAATTCCCCGTCTAGATGATATGTTGGATCAGCT
846 ATCAACAGAATTACAGTGAAGTACCGATTTCCAATTCCCCGTCTAGATGATATGTTGGATCAGCT
21885 ATCTGGTTCTAAGATCTTCTCAAAAATTGACCTTAAGAGCGGTTACCACCAAATCAGAATAAGGC
911 ATCTGGTTCTAAGATCTTCTCAAAAATTGACCTTAAGAGCGGTTACCACCAAATCAGAATAAGGC
21950 CTGGAGATGAGT
976 CTGGAGATGAGT
21962 GGAAGACGGC
Statistics
Matches: 986, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1000 986 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (1000 bp):
AGGGCGATTCAGGGGACGATTGGTTGAGAACCAATATTTTCCACACGACTTGCACAGTTGCAGAT
AAAGTCTGCAAAATGATCATTGACAGCGGCAGTTGTGAGAATGTAGTGTCCGAGGAGGTTGTCCA
GAAATTGCAGTTGAAGACGGACCGTCATCCTAAGCCATACAAGTTGTCATGGCTAAATAAAGACA
GTGAGGTAACAGTTGATAGGCGATGCCTGGTGTCTTTTTCAATTGGTAGAAAATATTTTGATAAT
GCCTGGTGTGATGTTGTGTCTATGGATGCGTGTCATATATTGTTGGGTCGACCTTGGCAGTATGA
TCGCAGTGTCATTCATGATGGACGGAAGAATACATATTCCCTTAGCATCAAGGGAAAAAAGATTG
TGTTGGCACCCCGGCGGGAAGGACTTACTCCTACCCCAGTAACCCATAATACTAATCTGCTTTCT
ATGTCCAGGTTTTTAGATGAGATTGAGCATGGCGACGTGGTCTATGCCTTGCTACCTTGCGAGAA
CAATGCAGTAGACGTGGATACAGATTTACCAGTAGAGGTGCAGCGGTTGCTAGCAGAATTCTCTA
ACTTGATGCCAGAGGATCTTCCTCCTGGACTACCACCTATGAGGGATATTCAGCATCAAATTGAC
CTTGTTCCTGGGTCAAGTTTGCCAAATCGACCAGCATATCGCCTCAGTCCCAAGGAGGCCGAAGA
GTTGCAGCGACAGGTGGAAGAGTTGTTGGAGAGGGGCTATATCCGAGAGAGTATGAGCCCATGTG
CAGTCCCTGCTCTGTTAGTGCCAAAGAAAGATGGTTCTTGGCGTATGTGTGTTGACAGCCGAGCG
ATCAACAGAATTACAGTGAAGTACCGATTTCCAATTCCCCGTCTAGATGATATGTTGGATCAGCT
ATCTGGTTCTAAGATCTTCTCAAAAATTGACCTTAAGAGCGGTTACCACCAAATCAGAATAAGGC
CTGGAGATGAGTCTACTTACCCCCA
Found at i:25160 original size:999 final size:1000
Alignment explanation
Indices: 23223--26208 Score: 5956
Period size: 999 Copynumber: 3.0 Consensus size: 1000
23213 CTCCACATTG
23223 AGGGCGATTCAGGGGACGATTGGTTGAGAACCAATATTTTCCACACGACTTGCACAGTTGCAGAT
1 AGGGCGATTCAGGGGACGATTGGTTGAGAACCAATATTTTCCACACGACTTGCACAGTTGCAGAT
23288 AAAGTCTGCAAAATGATCATTGACAGCGGCAGTTGTGAGAATGTAGTGTCCGAGGAGGTTGTCCA
66 AAAGTCTGCAAAATGATCATTGACAGCGGCAGTTGTGAGAATGTAGTGTCCGAGGAGGTTGTCCA
23353 GAAATTGCAGTTGAAGACGGACCGTCATCCTAAGCCATACAAGTTGTCATGGCTAAATAAAGACA
131 GAAATTGCAGTTGAAGACGGACCGTCATCCTAAGCCATACAAGTTGTCATGGCTAAATAAAGACA
23418 GTGAGGTAACAGTTGATAGGCGATGCCTGGTGTCTTTTTCAATTGGTAGAAAATATTTTGATAAT
196 GTGAGGTAACAGTTGATAGGCGATGCCTGGTGTCTTTTTCAATTGGTAGAAAATATTTTGATAAT
23483 GCCTGGTGTGATGTTGTGTCTATGGATGCGTGTCATATATTGTTGGGTCGACCTTGGCAGTATGA
261 GCCTGGTGTGATGTTGTGTCTATGGATGCGTGTCATATATTGTTGGGTCGACCTTGGCAGTATGA
23548 TCGCAGTGTCATTCATGATGGACGGAAGAATACATATTCCCTTAGCATCAAGGGAAAAAAGATTG
326 TCGCAGTGTCATTCATGATGGACGGAAGAATACATATTCCCTTAGCATCAAGGGAAAAAAGATTG
23613 TGTTGGCACCCCGGCGGGAAGGACTTACTCCTACCCCAGTAACCCATAATACTAATCTGCTTTCT
391 TGTTGGCACCCCGGCGGGAAGGACTTACTCCTACCCCAGTAACCCATAATACTAATCTGCTTTCT
23678 ATGTCCAGGTTTTTAGATGAGATTGAGCATGGCGACGTGGTCTATGCCTTGCTACCTTGCGAGAA
456 ATGTCCAGGTTTTTAGATGAGATTGAGCATGGCGACGTGGTCTATGCCTTGCTACCTTGCGAGAA
23743 CAATGCAGTAGACGTGGATACAGATTTACCAGTAGAGGTGCAGCGGTTGCTAGCAGAATTCTCTA
521 CAATGCAGTAGACGTGGATACAGATTTACCAGTAGAGGTGCAGCGGTTGCTAGCAGAATTCTCTA
23808 ACTTGATGCCAGAGGATCTTCCTCCTGGACTACCACCTATGAGGGATATTCAGCATCAAATTGAC
586 ACTTGATGCCAGAGGATCTTCCTCCTGGACTACCACCTATGAGGGATATTCAGCATCAAATTGAC
23873 CTTGTTCCTGGGTCAAGTTTGCCAAATCGACCAGCATATCGCCTCAGTCCCAAGGAGGCCGAAGA
651 CTTGTTCCTGGGTCAAGTTTGCCAAATCGACCAGCATATCGCCTCAGTCCCAAGGAGGCCGAAGA
23938 GTTGCAGCGACAGGTGGAAGAGTTGTTGGAGAGGGGCTATATCCGAGAGAGTATGAGCCCATGTG
716 GTTGCAGCGACAGGTGGAAGAGTTGTTGGAGAGGGGCTATATCCGAGAGAGTATGAGCCCATGTG
24003 CAGTCCCTGCTCTGTTAGTGCCAAAGAAAGATGGTTCTTGGCGTATGTGTGTTGACAGCCGAGCG
781 CAGTCCCTGCTCTGTTAGTGCCAAAGAAAGATGGTTCTTGGCGTATGTGTGTTGACAGCCGAGCG
24068 ATCAACAGAATTACAGTGAAGTACCGGTTTCCAATTCCCCGTCTAGATGATATGTTGGATCAGCT
846 ATCAACAGAATTACAGTGAAGTACCGGTTTCCAATTCCCCGTCTAGATGATATGTTGGATCAGCT
24133 ATCTGGTTCTAAGATCTTCTCAAAAATTGACCTTAAGAGCGGTTACCACCAAATCAGAATAAGGC
911 ATCTGGTTCTAAGATCTTCTCAAAAATTGACCTTAAGAGCGGTTACCACCAAATCAGAATAAGGC
24198 CTGGAGATGAGTCTACTTACCCCCA
976 CTGGAGATGAGTCTACTTACCCCCA
24223 AGGGCGATTCAGGGGACGATTGGTTGAGAACCAATATTTTCCACACGACTTGCACAGTTGCAGAT
1 AGGGCGATTCAGGGGACGATTGGTTGAGAACCAATATTTTCCACACGACTTGCACAGTTGCAGAT
24288 AAAGTCTGCAAAATGATCATTGACAGCGGCAGTTGTGAGAATGTAGTGTCCGAGGAGGTTGTCCA
66 AAAGTCTGCAAAATGATCATTGACAGCGGCAGTTGTGAGAATGTAGTGTCCGAGGAGGTTGTCCA
24353 GAAATTGCAGTTGAAGACGGACCGTCATCCTAAGCCATACAAGTTGTCATGGCTAAATAAAGACA
131 GAAATTGCAGTTGAAGACGGACCGTCATCCTAAGCCATACAAGTTGTCATGGCTAAATAAAGACA
24418 GTGAGGTAACAGTTGATAGGCGATGCCTGGTGTCTTTTTCAATTGGTAGAAAATA-TTTGATAAT
196 GTGAGGTAACAGTTGATAGGCGATGCCTGGTGTCTTTTTCAATTGGTAGAAAATATTTTGATAAT
24482 GCCTGGTGTGATGTTGTGTCTATGGATGCGTGTCATATATTGTTGGGTCGACCTTGGCAGTATGA
261 GCCTGGTGTGATGTTGTGTCTATGGATGCGTGTCATATATTGTTGGGTCGACCTTGGCAGTATGA
24547 TCGCAGTGTCATTCATGATGGACGGAAGAATACATATTCCCTTAGCATCAAGGGAAAAAAGATTG
326 TCGCAGTGTCATTCATGATGGACGGAAGAATACATATTCCCTTAGCATCAAGGGAAAAAAGATTG
24612 TGTTGGCACCCCGGCGGGAAGGACTTACTCCTACCCCAGTAACCCATAATACTAATCTGCTTTCT
391 TGTTGGCACCCCGGCGGGAAGGACTTACTCCTACCCCAGTAACCCATAATACTAATCTGCTTTCT
24677 ATGTCCAGGTTTTTAGATGAGATTGAGCATGGCGACGTGGTCTATGCCTTGCTACCTTGCGAGAA
456 ATGTCCAGGTTTTTAGATGAGATTGAGCATGGCGACGTGGTCTATGCCTTGCTACCTTGCGAGAA
24742 CAATGCAGTAGACGTGGATACAGATTTACCAGTAGAGGTGCAGCGGTTGCTAGCAGAATTCTCTA
521 CAATGCAGTAGACGTGGATACAGATTTACCAGTAGAGGTGCAGCGGTTGCTAGCAGAATTCTCTA
24807 ACTTGATGCCAGAGGATCTTCCTCCTGGACTACCACCTATGAGGGATATTCAGCATCAAATTGAC
586 ACTTGATGCCAGAGGATCTTCCTCCTGGACTACCACCTATGAGGGATATTCAGCATCAAATTGAC
24872 CTTGTTCCTGGGTCAAGTTTGCCAAATCGACCAGCATATCGCCTCAGTCCCAAGGAGGCCGAAGA
651 CTTGTTCCTGGGTCAAGTTTGCCAAATCGACCAGCATATCGCCTCAGTCCCAAGGAGGCCGAAGA
24937 GTTGCAGCGACAGGTGGAAGAGTTGTTGGAGAGGGGCTATATCCGAGAGAGTATGAGCCCATGTG
716 GTTGCAGCGACAGGTGGAAGAGTTGTTGGAGAGGGGCTATATCCGAGAGAGTATGAGCCCATGTG
25002 CAGTCCCTGCTCTGTTAGTGCCAAAGAAAGATGGTTCTTGGCGTATGTGTGTTGACAGCCGAGCG
781 CAGTCCCTGCTCTGTTAGTGCCAAAGAAAGATGGTTCTTGGCGTATGTGTGTTGACAGCCGAGCG
25067 ATCAACAGAATTACAGTGAAGTACCGGTTTCCAATTCCCCGTCTAGATGATATGTTGGATCAGCT
846 ATCAACAGAATTACAGTGAAGTACCGGTTTCCAATTCCCCGTCTAGATGATATGTTGGATCAGCT
25132 ATCTGGTTCTAAGATCTTCTCAAAAATTGACCTTAAGAGCGGTTACCACCAAATCAGAATAAGGC
911 ATCTGGTTCTAAGATCTTCTCAAAAATTGACCTTAAGAGCGGTTACCACCAAATCAGAATAAGGC
25197 CTGGAGATGAGTCTACTTACCCCCA
976 CTGGAGATGAGTCTACTTACCCCCA
25222 AGGGCGATTCAGGGGACGATTGGTTGAGAACCAATATTTTCCACACGACTTGCACAGTTGCAGAT
1 AGGGCGATTCAGGGGACGATTGGTTGAGAACCAATATTTTCCACACGACTTGCACAGTTGCAGAT
25287 AAAGTCTGCAAAATGATCATTGACAGCGGCAGTTGTGAGAATGTAGTGTCCGAGGAGGTTGTCCA
66 AAAGTCTGCAAAATGATCATTGACAGCGGCAGTTGTGAGAATGTAGTGTCCGAGGAGGTTGTCCA
25352 GAAATTGCAGTTGAAGACGGACCGTCATCCTAAGCCATACAAGTTGTCATGGCTAAATAAAGACA
131 GAAATTGCAGTTGAAGACGGACCGTCATCCTAAGCCATACAAGTTGTCATGGCTAAATAAAGACA
25417 GTGAGGTAACAGTTGATAGGCGATGCCTGGTGTCTTTTTCAATTGGTAGAAAATATTTTGATAAT
196 GTGAGGTAACAGTTGATAGGCGATGCCTGGTGTCTTTTTCAATTGGTAGAAAATATTTTGATAAT
25482 GCCTGGTGTGATGTTGTGTCTATGGATGCGTGTCATATATTGTTGGGTCGACCTTGGCAGTATGA
261 GCCTGGTGTGATGTTGTGTCTATGGATGCGTGTCATATATTGTTGGGTCGACCTTGGCAGTATGA
25547 TCGCAGTGTCATTCATGATGGACGGAAGAATACATATTCCCTTAGCATCAAGGGAAAAAAGATTG
326 TCGCAGTGTCATTCATGATGGACGGAAGAATACATATTCCCTTAGCATCAAGGGAAAAAAGATTG
25612 TGTTGGCACCCCGGCGGGAAGGACTTACTCCTACCCCAGTAACCCATAATACTAATCTGCTTTCT
391 TGTTGGCACCCCGGCGGGAAGGACTTACTCCTACCCCAGTAACCCATAATACTAATCTGCTTTCT
25677 ATGTCCAGGTTTTTAGATGAGATTGAGCATGGCGACGTGGTCTATGCCTTGCTACCTTGCGAGAA
456 ATGTCCAGGTTTTTAGATGAGATTGAGCATGGCGACGTGGTCTATGCCTTGCTACCTTGCGAGAA
25742 CAATGCAGTAGACGTGGATACAGATTTACCAGTAGAGGTGCAGCGGTTGCTAGCAGAATTCTCTA
521 CAATGCAGTAGACGTGGATACAGATTTACCAGTAGAGGTGCAGCGGTTGCTAGCAGAATTCTCTA
25807 ACTTGATGCCAGAGGATCTTCCTCCTGGACTACCACCTATGAGGGATATTCAGCATCAAATTGAC
586 ACTTGATGCCAGAGGATCTTCCTCCTGGACTACCACCTATGAGGGATATTCAGCATCAAATTGAC
25872 CTTGTTCCTGGGTCAAGTTTGCCAAATCGACCAGCATATCGCCTCAGTCCCAAGGAGGCCGAAGA
651 CTTGTTCCTGGGTCAAGTTTGCCAAATCGACCAGCATATCGCCTCAGTCCCAAGGAGGCCGAAGA
25937 GTTGCAGCGACAGGTGGAAGAGTTGTTGGAGAGGGGCTATATCCGAGAGAGTATGAGCCCATGTG
716 GTTGCAGCGACAGGTGGAAGAGTTGTTGGAGAGGGGCTATATCCGAGAGAGTATGAGCCCATGTG
26002 CAGTCCCTGCTCTGTTAGTGCCAAAGAAAGATGGTTCTTGGCGTATGTGTGTTGACAGCCGAGCG
781 CAGTCCCTGCTCTGTTAGTGCCAAAGAAAGATGGTTCTTGGCGTATGTGTGTTGACAGCCGAGCG
26067 ATCAACAGAATTACAGTGAAGTACCGGTTTCCAATTCCCCGTCTAGATGATATGTTGGATCAGCT
846 ATCAACAGAATTACAGTGAAGTACCGGTTTCCAATTCCCCGTCTAGATGATATGTTGGATCAGCT
*
26132 ATCTGATTCTAAGATCTTCTCAAAAATTGACCTTAAGAGCGGTTACCACCAAATCAGAATAAGGC
911 ATCTGGTTCTAAGATCTTCTCAAAAATTGACCTTAAGAGCGGTTACCACCAAATCAGAATAAGGC
26197 CTGGAGATGAGT
976 CTGGAGATGAGT
26209 GGAAGACGGC
Statistics
Matches: 1984, Mismatches: 1, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
999 999 0.50
1000 985 0.50
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (1000 bp):
AGGGCGATTCAGGGGACGATTGGTTGAGAACCAATATTTTCCACACGACTTGCACAGTTGCAGAT
AAAGTCTGCAAAATGATCATTGACAGCGGCAGTTGTGAGAATGTAGTGTCCGAGGAGGTTGTCCA
GAAATTGCAGTTGAAGACGGACCGTCATCCTAAGCCATACAAGTTGTCATGGCTAAATAAAGACA
GTGAGGTAACAGTTGATAGGCGATGCCTGGTGTCTTTTTCAATTGGTAGAAAATATTTTGATAAT
GCCTGGTGTGATGTTGTGTCTATGGATGCGTGTCATATATTGTTGGGTCGACCTTGGCAGTATGA
TCGCAGTGTCATTCATGATGGACGGAAGAATACATATTCCCTTAGCATCAAGGGAAAAAAGATTG
TGTTGGCACCCCGGCGGGAAGGACTTACTCCTACCCCAGTAACCCATAATACTAATCTGCTTTCT
ATGTCCAGGTTTTTAGATGAGATTGAGCATGGCGACGTGGTCTATGCCTTGCTACCTTGCGAGAA
CAATGCAGTAGACGTGGATACAGATTTACCAGTAGAGGTGCAGCGGTTGCTAGCAGAATTCTCTA
ACTTGATGCCAGAGGATCTTCCTCCTGGACTACCACCTATGAGGGATATTCAGCATCAAATTGAC
CTTGTTCCTGGGTCAAGTTTGCCAAATCGACCAGCATATCGCCTCAGTCCCAAGGAGGCCGAAGA
GTTGCAGCGACAGGTGGAAGAGTTGTTGGAGAGGGGCTATATCCGAGAGAGTATGAGCCCATGTG
CAGTCCCTGCTCTGTTAGTGCCAAAGAAAGATGGTTCTTGGCGTATGTGTGTTGACAGCCGAGCG
ATCAACAGAATTACAGTGAAGTACCGGTTTCCAATTCCCCGTCTAGATGATATGTTGGATCAGCT
ATCTGGTTCTAAGATCTTCTCAAAAATTGACCTTAAGAGCGGTTACCACCAAATCAGAATAAGGC
CTGGAGATGAGTCTACTTACCCCCA
Found at i:50375 original size:36 final size:37
Alignment explanation
Indices: 50299--50375 Score: 138
Period size: 36 Copynumber: 2.1 Consensus size: 37
50289 ATTTTCGGGA
*
50299 TTTTGCTATTTTTGGCAAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAAATTCGAATAAAGACGAT
50336 TTTTGCTATTTTTGGC-AAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAAATTCGAATAAAGACGAT
50372 TTTT
1 TTTT
50376 TTGCTATAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 23 0.59
37 16 0.41
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.43
Consensus pattern (37 bp):
TTTTGCTATTTTTGGCAAAAATTCGAATAAAGACGAT
Found at i:53019 original size:2 final size:2
Alignment explanation
Indices: 52854--52999 Score: 292
Period size: 2 Copynumber: 73.0 Consensus size: 2
52844 CAGTCCTTGA
52854 AT 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 AT
52896 AT 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 AT
52938 AT 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 AT
52980 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
53000 TCATGGGTTA
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 144 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53680 original size:25 final size:25
Alignment explanation
Indices: 53652--53710 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
53642 ATTCTATCGT
53652 CAAGTTCAATAATTCCAGAGGCAAC
1 CAAGTTCAATAATTCCAGAGGCAAC
53677 CAAGTTCAATAATTCCAGAGGCAAC
1 CAAGTTCAATAATTCCAGAGGCAAC
53702 CAAGTTCAA
1 CAAGTTCAA
53711 GAGCTTCAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (25 bp):
CAAGTTCAATAATTCCAGAGGCAAC
Found at i:55400 original size:24 final size:24
Alignment explanation
Indices: 55346--55403 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 24
55336 GCCTAAACTA
*
55346 TACATTTTTTGCTAAATAAGTTCC
1 TACATTTTTTTCTAAATAAGTTCC
55370 TAC-TTTTTTTCTAAATAAGTTCC
1 TACATTTTTTTCTAAATAAGTTCC
55393 TACATTTTTTT
1 TACATTTTTTT
55404 GATCCTCAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (24 bp):
TACATTTTTTTCTAAATAAGTTCC
Found at i:63580 original size:18 final size:18
Alignment explanation
Indices: 63547--63581 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
63537 TTTCTCTTCA
* *
63547 TCTTTCCCTTTTTTATTT
1 TCTTTCCCTATCTTATTT
63565 TCTTTCCCTATCTTATT
1 TCTTTCCCTATCTTATT
63582 CTTCAAGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.66
Consensus pattern (18 bp):
TCTTTCCCTATCTTATTT
Found at i:68087 original size:39 final size:39
Alignment explanation
Indices: 68005--68194 Score: 105
Period size: 39 Copynumber: 4.9 Consensus size: 39
67995 GTACACCTAG
* * * * * *
68005 TAAGGGCTTACCCTATGCACAAAGAAGAGAAGCTTGTAC
1 TAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTGTAC
* * **
68044 TAAGGTCTTATCATGTGCACAAAGCAGAGGAGCCTGTTG
1 TAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTGTAC
* * * * *
68083 TAAGGACTTACCCTGAGCACAAAGCTGAGGAGTCTGCGA-
1 TAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTG-TAC
* * * * ** ***
68122 TAAAGACTTGCCCTGAGCACAAAGTTGA-GAGCCTGCGG
1 TAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTGTAC
* * * *
68160 TAAGGACTTACCCTGGGCACAAAGCCGAGAAGCCT
1 TAAGGACTTACCATGTGCACAAAGCAGAGGAGCCT
68195 ACGTGTTGAG
Statistics
Matches: 119, Mismatches: 29, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
38 29 0.24
39 90 0.76
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (39 bp):
TAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTGTAC
Found at i:68168 original size:38 final size:39
Alignment explanation
Indices: 68060--68194 Score: 164
Period size: 39 Copynumber: 3.5 Consensus size: 39
68050 CTTATCATGT
* **
68060 GCACAAAGCAGAGGAGCCTGTTGTAAGGACTTACCCTGA
1 GCACAAAGCTGAGGAGCCTGCGGTAAGGACTTACCCTGA
* * * *
68099 GCACAAAGCTGAGGAGTCTGCGATAAAGACTTGCCCTGA
1 GCACAAAGCTGAGGAGCCTGCGGTAAGGACTTACCCTGA
* *
68138 GCACAAAGTTGA-GAGCCTGCGGTAAGGACTTACCCTGG
1 GCACAAAGCTGAGGAGCCTGCGGTAAGGACTTACCCTGA
* *
68176 GCACAAAGCCGAGAAGCCT
1 GCACAAAGCTGAGGAGCCT
68195 ACGTGTTGAG
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
38 31 0.39
39 48 0.61
ACGTcount: A:0.30, C:0.24, G:0.29, T:0.16
Consensus pattern (39 bp):
GCACAAAGCTGAGGAGCCTGCGGTAAGGACTTACCCTGA
Found at i:69663 original size:23 final size:22
Alignment explanation
Indices: 69632--69675 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
69622 CCAAATATAT
*
69632 TATTAAGTTCAATCATCCAAAG
1 TATTAAGTTCAAACATCCAAAG
*
69654 TATTCAAGTTTAAACATCCAAA
1 TATT-AAGTTCAAACATCCAAA
69676 AAACATATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (22 bp):
TATTAAGTTCAAACATCCAAAG
Found at i:71691 original size:23 final size:22
Alignment explanation
Indices: 71624--71691 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 22
71614 AACGAGTTTG
71624 TCGATGCACATTCAAGGAATGCA
1 TCGATGCACATTCAAGG-ATGCA
* * * *
71647 TCGGTG-TC-TTCATGG-TGTA
1 TCGATGCACATTCAAGGATGCA
71666 TCGATGCACATTCAAGGCATGCA
1 TCGATGCACATTCAAGG-ATGCA
71689 TCG
1 TCG
71692 GTACACTGTC
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
19 8 0.24
20 1 0.03
21 12 0.36
22 1 0.03
23 11 0.33
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (22 bp):
TCGATGCACATTCAAGGATGCA
Done.