Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_031389
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 104736
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:17807 original size:27 final size:27
Alignment explanation
Indices: 17769--17831 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
17759 CGGGGGCGCA
17769 AAGCCTTCGCCGAAGGCCGAAGAAGAG
1 AAGCCTTCGCCGAAGGCCGAAGAAGAG
17796 AAGCCTTCGCCGAAGGCCGAAGAAGAG
1 AAGCCTTCGCCGAAGGCCGAAGAAGAG
17823 AAGCCTTCG
1 AAGCCTTCG
17832 GCCCTGCCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.32, C:0.27, G:0.32, T:0.10
Consensus pattern (27 bp):
AAGCCTTCGCCGAAGGCCGAAGAAGAG
Left flanking sequence: Indices 17269 -- 17768
GGAACTTTTTTCGTACGTTCTGGATTGCTAACTTCTGTTCATAGTTTTGCTACAGATTCTACACG
AGGAATCTTTTTATGGTTTTTCTTCCTCAACATTACTAGCATATCTTTGATGTTTTTTTTCCAAA
TGAAGCGGCAATCAAGTACTAGGCTAGTTGGTGCATTCTCTGATTTATCATTGAATCAAAGCCTG
AGGGCCCCAAAACCCGTAAACCGGATCTTATGGTATTCGCGGCGAAGTACTCTATTCGTGCACTT
GCGTCAATTTACTCGTTTATCAAAGCTGATGGAGGACGAAGAAGGCCATGACAAACTAATTGGAT
ACAAAGCAAGTAAAATACATAAAGAAAAAAAGCTCTTTTTTTGGGCCAAAGAGAGAAAAAGCTAG
CAACATTTCGAATCCACACGGTGAAACCTTTGGCTTTTCTGTCATTTGTTATGCGAAGGCTCCGC
GCCTTCCAGGAGCTATGGCTACAGAGGTAGCGTACCGGGGGCGCA
Right flanking sequence: Indices 17832 -- 18331
GCCCTGCCAATGAATCATTTTTTTGTTTCAATTTTGAGTTTTTTTATCTTGTATTCTTTTCTTCT
TTAAAGCAAAATCCTAAAAACAAATAGAGCAGATGGTCCAACTACAGAACTTTTTTTTTTTTCTT
ATGTTTATGGTTGTGCTTTGTGGTACGGCAGCACCCATACTATTTCAATGGTTGGTAAGTAGAGA
TGTTCCCACAGGTGCTCCTTTTTCTCATGGTACTATAATACCTATTTTTACCTCTTTATTATTGC
TTCTAGTTCATGTACATTCCAGGGGATTCATACGCTCTATGGAGAAAACAGAAAGGATAGTTTTG
GTAAAAGCAAAACGCATTTTATTACTCAACATAATTGAAAAAAGCTCCCCAAAAACTAGAGCTAA
AAATGCATTTTTTTTCTTTTTTTTTTTTTTTTCGAATTTTTTTATTTTTAAATTTATGGGAGACT
TGTCATATTTAGAATCTTTCTGTAGTGTGCTTTGTTTTTTATTAT
Found at i:18757 original size:19 final size:20
Alignment explanation
Indices: 18715--18757 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18705 GGATGTTGGT
* *
18715 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
18735 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
18754 CATG
1 CATG
18758 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
CATGACTATCGAAAAGTTCA
Left flanking sequence: Indices 18215 -- 18714
GAGCTAAAAATGCATTTTTTTTCTTTTTTTTTTTTTTTTCGAATTTTTTTATTTTTAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTAGTGTGCTTTGTTTTTTATTATTTTGTACATTTTT
TTTATCATTTAAATATAGGCGCGATACGTGGGCAAACGAGGAGCGTAGGCTTGGAATGGAAGAGA
AAAGAAAACCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTGACAGAAAA
AAGAAACAAAGAAATAAAAAGAAAGAAAATTTTTCCTTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAACCAAAATTTTGG
CTTTTTATTCTCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCGAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 18758 -- 19257
GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGCTTATGCGCGACCA
TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCCCAAATTAGTGCAAG
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAATGCCAGGCCGCGGGTAACGCTAGTTGGCAAA
ATGGCGTTAAGCATTCCTAACAATACGGAAAAAGAGGTCGTGATGATATTCATCTACGTTCGTAC
TGTTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGAATAATTCCCATTAAG
TTCCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAA
Found at i:41516 original size:81 final size:81
Alignment explanation
Indices: 41376--41525 Score: 248
Period size: 81 Copynumber: 1.9 Consensus size: 81
41366 AAAATACTCG
* *
41376 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTCCCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
41441 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
41457 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41521 CCAAG
65 CCAAG
41526 TGAGCTTAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
81 62 0.97
82 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 40876 -- 41375
CAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTGGAAATAACATC
AGTATTTCAACAACTTTTTGAGCTCATTTTTCACCCATATAATTCTTTATGTTTTTGTTTGAACA
AGCCAATTTATGCTTCACCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGG
ATAACCACTTAGTAACGAACTTGGGCCCCCACTTTGCCAATTAAGGCCGCAGGCTTTATTAACAG
AACTGGGGCGCGTAGTTTATAGCGAAGCTTTTTTTTTTTAATATTTTGGGAAATCCCCCAAAAAT
ATTTTTTGTTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTTTTTCAATTCAGACATTAAAATACTCG
Right flanking sequence: Indices 41526 -- 42025
TGAGCTTAAGGAAACGAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTCTTTTTGCTAT
TTCATTTTATAGACATCTCCGGCTTATCCCGGCTCGGCTGAATCTGCGGCGTTTTTTCAAATATT
TGAAAAATCTATAGTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTCATTGATTTATACCAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTTGGC
AATGGCAATGACTTTTATACAATATGCAGAATACTCCAAAACCTCTATTTAGAACTAAAAGAAAA
TAATGCTTTTTTAGAAAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAG
TTTTGCCATCTATATAATAGAATATAGTAGAAAATAATAAGTTGGCGAGGAAGTAAAAGTATATA
TATATCTATAGATATATATATATTTTTTTTTTATTCTGTGGATTA
Found at i:63408 original size:14 final size:14
Alignment explanation
Indices: 63389--63416 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
63379 TCTTCGTTTT
63389 TATAAGATATGAAG
1 TATAAGATATGAAG
63403 TATAAGATATGAAG
1 TATAAGATATGAAG
63417 GTATTTTTGT
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:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
TATAAGATATGAAG
Left flanking sequence: Indices 62889 -- 63388
AGAGGCTGTTAAGATAGCTGCTAATGCCATAGGCGCTTTTACTGCGGCGGGGTACTTGGTTGTAC
GTGCACAATTTAAATAGAGCGAATGCATTAGAATTGTAAGAAAAAAGCCTAAAATTGAAAAAGCT
AAAGTTCAATTATAAGGTACTTATTAATGAAGCTAAAAACACGGATCAGCTTTTGGAAGAAATTG
AAGAGCGTTAAATGAAAGAAATTAAGGCTTGTTGGTTGGGTAGTAAAAAAAATGAGTACTGATGA
AGAATGAACAGCCACGTCTAGATGATGCTGTTTAGCGTGTAGTAGAAGCTAAATACAACAAGCTG
CAAGCTAAGGATAAGGGTCTTTGCGCGACAAGATTCGAGATCAGTATGCGGAACAAACGACCATA
AAAGAAAAGCCACGAGTATCATAGGCAGACCTTCAACAGGCACCTAAAAAAAAATTACCACCTAA
ATTATCTATTAAGTACCCTGTCCCAAACGCAAACTTCTTCGTTTT
Right flanking sequence: Indices 63417 -- 63916
GTATTTTTGTTTCTCGAAGAGCCATCGGGAACTTAGGTTCTTTTATTTATCGAGTTTCGCAAGTA
TATCTTTCTTAGGATCTAAATCCTATTAATTTGAACGTAGAGTTGTATGATGCGAAACTATCACT
TACGGGGTGGGTTTAATCTTAGATTTTTTTATTTTCTGGGTTTTTATGGGATTATTATCGCGGGT
TTGTCTATCCTAATGGGCGTCTAACAAAAAAATCGATTTTTTTGTTGGTTGGCCCTTTTGTGGGG
CCTGTTGAAGGGCCGAAGTAGTTCTGAAAAAAACAAGAATATACCAAATGAGTTTGAAAAATACA
TGGCTATTTCCAATTGGTTATTGTGACGCTGCGGAACCTTGGCAATTAGGATTTCAAGACGCAGC
AACACCTATGATGCAAGGAATAATTGAGTGCGCCTAGATATATCATCACGGTTGCAGAGCTCTGC
TCCAACTCTGCCATATCTGCTCGAGCTGGCTATCGCCAGGATGTG
Done.