Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_026121
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: 104747
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:18726 original size:19 final size:20
Alignment explanation
Indices: 18684--18726 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18674 GGATGTTGGT
* *
18684 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
18704 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
18723 CATG
1 CATG
18727 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 18184 -- 18683
GAGCTAAAAATGCATTTTTTTTCTTTTTTTTTTTTTTTTCGAATTTTTTTATTTTTAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTAGTGTGCTTTGTTTTTTATTATTTTGTACATTTTT
TTTATCATTTAAATATAGGCGCGATACGTGGGCAAACGAGGAGCGTAGGCTTGGAATGGAAGAGA
AAAGAAAACCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTGACAGAAAA
AAGAAACAAAGAAATAAAAAGAAACAAAATTTTTCCTTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAACCAAAATTTTGG
CTTTTTATTCTCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAAA
TTTTTTATTGTTCGCGCCTTACCGAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 18727 -- 19226
GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGCTTATGCGCGACCA
TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCCCAAATTAGTGCAAG
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAATGCCAGGCCGCGGGTAACGCTAGTTGGCAAA
ATGGCGTTAAGCATTCCTAACAATACGGAAAAAGAGGTCGTGATGATATTCATCTACGTTCGTAC
TGTTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGAATAATTCCCATTAAG
TTCCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAA
Found at i:41503 original size:81 final size:81
Alignment explanation
Indices: 41359--41508 Score: 239
Period size: 81 Copynumber: 1.9 Consensus size: 81
41349 AAAATACTCG
* *
41359 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTCCCAGTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCAGTTTCAC
41424 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* * *
41440 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCAGTTTCA
41504 CCAAG
65 CCAAG
41509 TGAGCTTAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
81 61 0.97
82 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCAGTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 40859 -- 41358
CAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTGGAAATAACATC
AGTATTTCAACAACTTTTTGAGCTCATTTTTCACCCATATAATTCTTTATGTTTTTGTTTGAACA
AGCCAATTTATGCTTCACCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGG
ATAACCACTTAGTAACGAACTTGGGCCCCCACTTTGCCAATTAAGGCCGCAGGCTTTATTAACAG
AACTGGGGCGCGTAGTTTATAGCGAAGCTTTTTTTTTTTAATATTTTGGGAAATCCCCCAAAAAT
ATTTTTTGTTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATGGGTGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTTTTTCAATTCAGACATTAAAATACTCG
Right flanking sequence: Indices 41509 -- 42008
TGAGCTTAAGGAAACGAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTCTTTTTGCTAT
TTCATTTTATAGACATCTCCGGCTTATCCCGGCTCGGCTGAATCTGCGGCGTTTTTTCAAATATT
TGAAAAATCTATAGTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTCATTGATTTATACCAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTTGGC
AATGGCAATGACTTTTATACAATATGCAGAATACTCCAAAACCTCTATTTAGAACTAAAAGAAAA
TAATGCTTTTTTAGAAAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAG
TTTTGCCATCTATATAATAGAATATAGTAGAAAATAATAAGTTGGCGAGGAAGTAAAAGTATATA
TATATCTATAGATATATATATACTTTTTTTTTATTCTGTGGATTA
Found at i:63380 original size:14 final size:14
Alignment explanation
Indices: 63361--63388 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
63351 TCTTCGTTTT
63361 TATAAGATATGAAG
1 TATAAGATATGAAG
63375 TATAAGATATGAAG
1 TATAAGATATGAAG
63389 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 62861 -- 63360
TGTAGAGGCTGTTAAGATAGCTGCTAATGCCATAGGCGCTTTTACTGCGGCGGGGTACTTGGTTG
TACGTGCACAATTTAAATAGAGCGAATGCATTAGAATTGTAAGAAAAAAGCCTAAAATTGAAAAA
GCTAAAGTTCAATTATAAGGTACTTATTAATGAAGCTAAAAACACGGATCAGCTTTTGGAAGAAA
TTGAAGAGCGTTAAATGAAAGAAATTAAGGCTTGTTGGTTGGGTAGTAAAAAAAATGAGTACTGA
TGAAGAATGAACAGCCACGTCTAGATGATGCTGTTTAGCGTGTAGTAGAAGCTAAATACAACAAG
CTGCAAGCTAAGAAGGGTCTTTGCGCGACAAGATTCGAGATCAGTATGCGGAACAAACGACCATA
AAAGAAAAGCCACGAGTATCATAGGCAGACCTTCAACAGGCACCTAAAAAAAAATTACCACCTAA
ATTATCTATTAAGTACCCTGTCCCAAACGCAAACTTCTTCGTTTT
Right flanking sequence: Indices 63389 -- 63888
GTATTTTTGTTTCTCGAAGAGCCATCGGGAACTTAGGTTCTTTTATTTATCGAGTTTCGCAAGTA
TATCTTTCTTAGGATCTAAATCCTATTAATTTGAACGTAGAGTTGTATGATGCGAAACTATCACT
TACGGGGTGGGTTTAATCTTAGATTTTTTTATTTTCTGGGTTTTTATGGGATTATTATCGCGGGT
TTGTCTATCCTAATGGGCGTCTAACAAAAAAATCGATTTTTTTGTTGGTTGGCCCTTTTGTGGGG
CCTGTTGAAGGGCCGAAGTAGTTCTGAAAAAAACAAGAATATACCAAATGAGTTTGAAAAATACA
TGGCTATTTCCAATTGGTTATTGTGACGCTGCGGAACCTTGGCAATTAGGATTTCAAGACGCAGC
AACACCTATGATGCAAGGAATAATTGAGTGCGCCTAGATATATCATCACGGTTGCAGAGCTCTGC
TCCAACTCTGCCATATCTGCTCGAGCTGGCTATCGCCAGGATGTG
Found at i:104731 original size:10 final size:10
Alignment explanation
Indices: 104716--104741 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
104706 TCTTCTTATA
104716 AATAATCTTT
1 AATAATCTTT
104726 AATAATCTTT
1 AATAATCTTT
104736 AATAAT
1 AATAAT
104742 GCATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (10 bp):
AATAATCTTT
Left flanking sequence: Indices 104216 -- 104715
TCTATCGGGGGGGGGGGAGTTGTGCATCATAGGTACCTTCTTATTGCTGCGAAGGGCGATATGAA
AATAACCCCCCTATCCAACCTCATTCTGTTGCGCGAAATCCATCATTGGCTAAGCAATTATTTGG
TTATGCCATCTTAGGTTTCGCTTTAACAGAAGCTATTGCTTTGTTTGCCTTAATGATGGCCTTTT
TGATCTTATTTGTTTTTTAATTTTTTGGTGCTGCGATTTTTTGGGAAAAAAACTATATTTTGGCC
GCACCCTATTGGCTTTGCGAATAGGGCTGCGCCCAAAAAATCTAGATTTTTTGGCACCTTAGGGC
CGAACGATTAGTACGTTCGAGCCCTTCACCACTTGCTACCAAAAGCATAAGCGTAAAAAAACTGA
ACTGACAAAGATTTTAACCTTAAAGGCTCATTGGATAAAAAAAGAAGCAGGACAAATATATCTAT
ATATATATTTTTTTTTCTTTTTTAGCTGCTTCACTTCTTCTTATA
Right flanking sequence: Indices 104742 -- 104747
GCATAG
Done.