Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_029355
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: 104624
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:2422 original size:20 final size:20
Alignment explanation
Indices: 2397--2436 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2387 GCAACATATA
2397 TTATATTATATATTGCCGCG
1 TTATATTATATATTGCCGCG
2417 TTATATTATATATTGCCGCG
1 TTATATTATATATTGCCGCG
2437 CCCCTTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (20 bp):
TTATATTATATATTGCCGCG
Left flanking sequence: Indices 1897 -- 2396
AGTCTCTGGATATTGAAGACCAGTTATTTTCCCTATCCAATAGTAGAATCCTGCAAATAAAGCAA
AAACAGCTCCCATAGAAAGAACATAATGGAAATGTGCAACCACATAATAAGTATCATGTAGAGCG
ATGTCCAGCCCAGAATTGGCCAATACTATTCCAGTGAGAGTAGAGTAGGTGCCCTTACTCGCGTG
GGGCCAATTTTGGGTTTCCCTTGCGCTTTTAGTGCACCTCTCTCGTAACCGTACATGATAGTTTT
CCCATCATACGGCTTGCCCGCGCGTTTAATTCTCTCACGACTTGGCACGGGTTTCATAGCCTGTA
CCGACGTGTCGAACGAGGCTGCGGTGCCTCTCCGCTTTCCTTTTTTTCCCTCTGAGTTTATCTTT
TCGATCGAGGAGAGAGAGCCCGAAGAAGTATTTTCCGTGGTCGGCTCTCTCGTGCTCGAGCTTGG
CAAGTGTAGCCAGAGAATAACGCGGCAGCAAGGGCGCAACATATA
Right flanking sequence: Indices 2437 -- 2936
CCCCTTCAACAACTTTCTCAGTTTCATGAGCTTTTAGTCTGGTCATCATCTCGTTTATCTGTGAG
ATGTTCTTGTCGAGTTGGCTCAACTTGCGCTGCTATTGTTGTGTCCTCTTTATTGGTTCGGATTT
GTTGACTAGGCATCTGGTATCGTCCAGTATAGATCTGCCGCGTAGCCTTTTGAAAAGAGGCGTAG
CGGGACCAAGCTTTTTGGTTGGGGTTTTCCAACATACTTGTGTGCTCTTCTTGTCTTGGTTCGGA
CTTCTATAACTGCAGAACACCAGAAAGTCACCTCTGACTTAATTCCGAGTTCCTTTCCCTGGAAA
ATGATGTTGATATATCACTTCTGGAGAAGCCTGCGGCCTCTTGTTTTAATCCGTCCCATTGTAGT
TGTAAGGCGTTTGCTTTTTTTAGTATGATTAGAGTGCGAACACAGCAGCTCCTGATGACGAGTTT
CATTTCATTTGTTAATTGGTAGAACTTATCAACGAACGAATAGTA
Found at i:18160 original size:21 final size:22
Alignment explanation
Indices: 18125--18167 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
18115 CTTTCTGTAG
* *
18125 TGTACTTTGTTTTTTATTATTT
1 TGTACATTGTTTTTTATCATTT
18147 TGTACATT-TTTTTTATCATTT
1 TGTACATTGTTTTTTATCATTT
18168 AAATATAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (22 bp):
TGTACATTGTTTTTTATCATTT
Left flanking sequence: Indices 17625 -- 18124
CCGAAGAAGAGAAGCCTTCGGCCCTGCCAATGAATCATTTTTTTGTTTCAATTTTGAGTTTTTTT
ATCTTGTATTCTTTTCTTCTTTAAAGCAAAATCCTAAAAACAAATAGAGCAGATGGTCCAACTAC
AGAACTTTTTTTTTTTTCTTATGTTTATGGTTGTGCTTTGTGGTACGGCAGCACCCATACTATTT
CAATGGTTGGTAAGTAGAGATGTTCCCACAGGTGCTCCTTTTTCTCATGGTACTATAATACCTAT
TTTTACCTCTTTATTATTGCTTCTAGTTCATGTACATTCCAGGGGATTCATACGCTCTATGGAGA
AAACAGAAAGGATAGTTTTGGTAAAAGCAAAACGCATTTTATTACTCAACATAATTGAAAAAAGC
TCCCCAAAAACTAGAGCTAAAAATGCATTTTTTTTCTTCTTTTTTTTTTTTTCGAATTTTTTTAT
TTTTAAATTTATGGGAGACTTGTCATATTTAGAATCTTTCTGTAG
Right flanking sequence: Indices 18168 -- 18667
AAATATAGGCGCGATACGTGGGCAAACGAGGAGCGTAGGCTTGGAATGGAAGAGAAAAGAAAAGC
GCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTGACAGAAAAAAGAAACAAA
GAAATAAAAAGAAAGAAAACTTTTCCTTTTTATTTCTTTCAAATAAATCCAAAATATTTTTGATT
TATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAACCAAAATTTTGGCTTTTTATTC
TCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGATTTTTTATTG
TTCGCGCCTTACCGAAAAGACTGATGGATGTTGGTCATGACTTTCGAAAAGTTCCCATGACTATG
AAAATTTCACATGGAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGC
CTATGCGCGACCATCTCGTGTTTAAGCTCACGCCATGTGGGCGTG
Found at i:18570 original size:19 final size:20
Alignment explanation
Indices: 18528--18570 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18518 GGATGTTGGT
* *
18528 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
18548 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
18567 CATG
1 CATG
18571 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 18028 -- 18527
GAGCTAAAAATGCATTTTTTTTCTTCTTTTTTTTTTTTTCGAATTTTTTTATTTTTAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTAGTGTACTTTGTTTTTTATTATTTTGTACATTTTT
TTTATCATTTAAATATAGGCGCGATACGTGGGCAAACGAGGAGCGTAGGCTTGGAATGGAAGAGA
AAAGAAAAGCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTGACAGAAAA
AAGAAACAAAGAAATAAAAAGAAAGAAAACTTTTCCTTTTTATTTCTTTCAAATAAATCCAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAGAAAACCAAAATTTTGG
CTTTTTATTCTCTGCTTGCTTTTTTGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCGAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 18571 -- 19070
GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGCCTATGCGCGACCA
TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCTCAAATTAGTGCAAG
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAAAAAAGGCCGCGGGTAACGCTAGTTGGCAAAA
TGGCGTTAAGCATTCCTAACAATACGGAAAAAGAGGTCGTGATGATATTCATCTACGTTCGTACT
GTTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGAATAATTCCCATTAAGT
TCCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAAC
Found at i:41372 original size:81 final size:81
Alignment explanation
Indices: 41237--41386 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
41227 AAAATACTCG
*
41237 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
41302 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
41318 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41382 CCAAG
65 CCAAG
41387 TGAGCTTAAG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
81 63 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 40737 -- 41236
CAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTGGAAATAACATC
AGTATTTCAACAACTTTTTGAGCTCATTTTTCACCCATATAATTCTTTATGTTTTTGTTTGAACA
AGCCAATTTATGCTTCACCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGG
ATAACCACTTAGTAACTAACTTGGGCCCCCACTTTGCCAATTAAGGCCGCAGGCTTTATTAACAG
AACTGGGGCGCGTAGTTTATAGCGAAGCTTTTTTTTTTTAATATTTTGGGAAATCCCCCAAAAAT
ATTTTTTGTTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTTTTTCAATTCAGACATTAAAATACTCG
Right flanking sequence: Indices 41387 -- 41886
TGAGCTTAAGGAAACGAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTCTTTTTGCTAT
TTCATTTTATAGACATCTCCGGCTTATCCCGGCTCGGCTGAATCTGCGGCGTTTTTTCAAATATT
TGAAAAATCTATAGTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTCATTGATTTATACCAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTTGGC
AATGGCAATGACTTTTATACAATATGCAGAATACTCCAAAACCTGTATTTAGAACTAAAAGAAAA
TAATGCTTTTTTATAAAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAG
TTTTGCCATCTATATAATAGAATATAGTAGAAAATAATAAGTTGGCGAGGAAGTAAAAATATATA
TATATATCTATAGATATATATATATTTTTTTTTTATTCTGTGGAT
Found at i:48782 original size:16 final size:17
Alignment explanation
Indices: 48761--48798 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
48751 TAATAAATCG
*
48761 AAAAAG-AGAAAATGAA
1 AAAAAGCAGAAAACGAA
*
48777 AAAAAGCATAAAACGAA
1 AAAAAGCAGAAAACGAA
48794 AAAAA
1 AAAAA
48799 AATTTTTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.05
Consensus pattern (17 bp):
AAAAAGCAGAAAACGAA
Left flanking sequence: Indices 48261 -- 48760
CACATTTCGAAAATTAGCCAAGCAGATAAGTAAACTTCAAAGTGGTTTTGTTTATCATTATGCTT
TTGTAATGTTGATTGGCTTAACCATATTTATTACCATAATAGGTCTGTGGGATTTTATTTCTTTT
TGGGTAGATAATCGATTGTATTTTATTTACATAGTGAGTTTTCTATTTATTCATTTTGAAAACGA
CATTAGCACGAGCTAAAGGGGGCATACTTCCTTATATAATACCATGAAACTTTAAGGGACGCAAT
GATAAGCCAGTGCTACGCCCTTTTTTCGGCTTCGCTGAGAGGGAGGGCTGAGGCCCGACGAAGCC
TAACAAGCAAAAAAAATAGATTTTTTGGAGCCTAAGCTATGCTCTGCGGTCTAGCTACGATAAAT
CGTAAAAAAAAATGGGTCCTCGAATAAAGCACGTTATTGCCTTGGGTCTATGAGGAATCTGAAAA
AGAAGAAGAAAAAAGTAAAGGTTGGAATGATAGAATAATAAATCG
Right flanking sequence: Indices 48799 -- 49298
AATTTTTCGGCTTTTTTTATCCTCCTCGATCGTGACTGAGGCCGTCTGGTCATAATAGCAAGCCC
TAAAGCATTGAACAAAGCGGCAAAAGACGAAGCATGCAATTACATAGTATGCGCGTATAAAAGCT
CATCAAGTTATGCAATTATTGCGGGCTTTATAGAAGTGCAGGGGGTTATGATGATATACCCATAA
GGCCTCTATGGCTGGAAAGCCGAGAAGAAATGTGGACCCGCGGCCTGCGAAGAGAGCTGCGTCCC
CGGGATCTTTTGGAAAAAGAGTAAACATTTATGTTACAATTTTTAGCTCCATTTTATTCCAATCT
CAGTGGTCTTATTCTGTGTCCTTTGTTAGGAAGCATTATTCTTTTTGTTATCCCTAATCCCAGAA
TACGACTGATACAAAGTATTGGTTTGTGCACCTCTTTGATTACTTTTCTATATTCCCTTTTTTTT
TGGATACAATTCGATAATTCTACAGCCAAATTTCAATTCGTGGAA
Found at i:63258 original size:14 final size:14
Alignment explanation
Indices: 63239--63266 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
63229 TCTTCGTTTT
63239 TATAAGATATGAAG
1 TATAAGATATGAAG
63253 TATAAGATATGAAG
1 TATAAGATATGAAG
63267 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 62739 -- 63238
AGAGGCTGTTAAGATAGCTGCTAATGCCATAGGCGCGTTTACTGCGGCGGGGTACTTGGTTGTAC
GTGCACAATTTAAATAGAGCGAATGCATTAGAATTGTAAAAAAAAAGCCTAAAATTGAAAAAGCT
AAAGTTCAATTATAAGGTACTTATTAATGAAGCTAAAAACACGGATCAGCTTTTGGAAGAAATTG
AAGAGCGTTAAATGAAAGAAATTAAGGCTTGTTGGTTGGGTAGTAAAAAAAATGAGTACTGATGA
AGAATGAACAGCCACGTCTAGATGATGCTGTTTAGCGTGTAGTAGAAGCTAAATACAACAAGCTG
CAAGCTAAGGGTAAGGGTCTTCGCGCGACAAGATTCGAGATCAGTATGCGGAACAAACGACCATA
AAAGAAAGGCCACGAGTATCATAGGCAGACCTTCAACAGGCACCTAAAAAAAAATTACCACCTAA
ATTATCTATTAAGTACCCTGTCCCAAACGCAAACTTCTTCGTTTT
Right flanking sequence: Indices 63267 -- 63766
GTATTTTTGTTTCTCGAAGAGCCATCGGGAACTTAGGTTCTTTTATTTATCGAGTTTCGCAAGTA
TATCTTTCTTAGGATCTAAATCCTATTAATTTGAACGTAGAGTTGTATGATGCGAAACTATCACT
TACGGGGTGGGTTTAATCTTAGATTTTTTTATTTTCTGAGTTTTTATGGGATTATTATCGCGGGT
TTGTCTATCCTAATGGGCGTCTAACAAAAAAATCGATTTTTTTGTTGGTTGGCCCTTTTGTGGGG
CCTGTTGAAGGGCCGAAGTAGTTCTGAAAAAAACAAGAATATACCAAATGAGTTTGAAAAATACA
TGGCTATTTCCAATTGGTTATTGTGACGCTGCGGAACCTTGGCAATTAGGATTTCAAGACGCAGC
AACACCTATGATGCAAGGAATAATTGAGTGCGCCTAGATATATCATCACGGTTGCAGAGCTCTGC
TCCAACTCTGCCATATCTGCTCGAGCTGGCTATCGCCAGGATGTG
Found at i:104486 original size:10 final size:10
Alignment explanation
Indices: 104471--104496 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
104461 TCTTCTTATA
104471 AATAATCTTT
1 AATAATCTTT
104481 AATAATCTTT
1 AATAATCTTT
104491 AATAAT
1 AATAAT
104497 GCATAGCTTC
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 103971 -- 104470
TCTATCGGGGGGGGGGGAGTTGTGCATCATAGGTACCTTCTTATTGCTGCGAAGGGCGATATGAA
AATAACCCCCCTATCCAACCTCATTCTGTTGCGCGAAATCCATCATTGGCTAAGCAATTATTTGG
TTATGCCATCTTAGGTTTCGCTTTAACAGAAGCTATTGCTTTGTTTGCCTTAATGATGGCCTTTT
TGATCTTATTTGTTTTTTAATTTTTTGGTGCTGCGATTTTTTGGGAAAAAAACTATATTTTGGCC
GCACCCTATTGGCTTTGCGAATAGGGCTGCGCCCAAAAAATCTAGATTTTTTGGCACCTTAGGGC
CGAACGATTAGTACGTTCGAGCCCTTCACCACTTGCTACCAAAAGCATAAGCGTAAAAAAACTGA
ACTGACAAAGATTTTAACCTTAAAGGCTCATTGGATAAAAAAAGAAGCAGGACAAATATATCTAT
ATATATATTTTTTTTTCTTTTTTAGCTGCTTCACTTCTTCTTATA
Right flanking sequence: Indices 104497 -- 104624
GCATAGCTTCGCGTGCTTTTCGATTGATGATGGGACCGAAGACGAAAGGCGCGAAGCGGCCGCGG
GTCTAGATTCTCGTTTTTTCGGCCGCGCGCCTGCGGCGGCCCTCGGTCGTTGTTAACTTACCA
Done.